Query 039903
Match_columns 233
No_of_seqs 137 out of 1160
Neff 8.8
Searched_HMMs 46136
Date Fri Mar 29 03:11:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039903.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039903hhsearch_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 1.7E-34 3.6E-39 243.1 15.3 226 1-233 11-243 (342)
2 TIGR02716 C20_methyl_CrtF C-20 100.0 7.5E-33 1.6E-37 236.9 18.0 205 8-233 2-222 (306)
3 PF00891 Methyltransf_2: O-met 100.0 4.6E-33 9.9E-38 230.5 11.5 158 75-233 2-165 (241)
4 PF08100 Dimerisation: Dimeris 99.2 5.9E-11 1.3E-15 73.6 5.0 51 11-62 1-51 (51)
5 PF12847 Methyltransf_18: Meth 98.9 5.4E-09 1.2E-13 75.8 6.5 64 169-232 2-76 (112)
6 PRK06922 hypothetical protein; 98.7 3.6E-08 7.7E-13 90.9 8.5 104 128-232 377-493 (677)
7 PRK08287 cobalt-precorrin-6Y C 98.7 5.3E-08 1.2E-12 77.4 7.0 71 161-232 25-103 (187)
8 PRK14103 trans-aconitate 2-met 98.5 3.4E-07 7.3E-12 76.4 8.4 74 157-232 19-95 (255)
9 PF13847 Methyltransf_31: Meth 98.5 2E-07 4.3E-12 71.6 6.4 65 168-232 3-79 (152)
10 COG4106 Tam Trans-aconitate me 98.5 2.5E-07 5.5E-12 73.9 6.7 81 149-231 13-97 (257)
11 TIGR03587 Pse_Me-ase pseudamin 98.5 4.1E-07 8.9E-12 73.5 8.0 67 166-232 41-111 (204)
12 PRK01683 trans-aconitate 2-met 98.5 1.2E-06 2.6E-11 73.1 10.0 76 156-232 20-99 (258)
13 PF05175 MTS: Methyltransferas 98.5 3.2E-07 7E-12 71.9 6.1 66 167-232 30-104 (170)
14 TIGR02752 MenG_heptapren 2-hep 98.5 5.9E-07 1.3E-11 73.6 7.8 74 158-232 36-120 (231)
15 PRK04457 spermidine synthase; 98.4 3.7E-07 8E-12 76.6 5.9 66 167-232 65-142 (262)
16 PRK15451 tRNA cmo(5)U34 methyl 98.4 5.3E-07 1.2E-11 74.9 6.0 66 167-232 55-131 (247)
17 TIGR03533 L3_gln_methyl protei 98.4 6.3E-07 1.4E-11 76.0 6.5 65 168-232 121-195 (284)
18 TIGR00740 methyltransferase, p 98.4 7.1E-07 1.5E-11 73.7 6.6 66 167-232 52-128 (239)
19 PRK11805 N5-glutamine S-adenos 98.4 5.4E-07 1.2E-11 77.2 5.8 63 170-232 135-207 (307)
20 PRK15001 SAM-dependent 23S rib 98.4 1E-06 2.2E-11 77.4 7.0 73 159-232 220-304 (378)
21 COG2226 UbiE Methylase involve 98.3 1.8E-06 3.8E-11 71.0 7.6 65 168-232 51-125 (238)
22 PTZ00098 phosphoethanolamine N 98.3 2.3E-06 4.9E-11 71.8 7.8 74 157-232 42-123 (263)
23 COG2890 HemK Methylase of poly 98.3 9.1E-07 2E-11 74.9 5.4 62 171-232 113-182 (280)
24 COG2242 CobL Precorrin-6B meth 98.3 2.4E-06 5.1E-11 67.2 7.2 71 161-232 28-108 (187)
25 TIGR00536 hemK_fam HemK family 98.3 2.2E-06 4.8E-11 72.7 7.5 63 170-232 116-188 (284)
26 PLN02244 tocopherol O-methyltr 98.3 2.6E-06 5.6E-11 74.2 8.0 65 167-232 117-192 (340)
27 TIGR02469 CbiT precorrin-6Y C5 98.3 4.2E-06 9E-11 61.3 7.8 73 159-232 11-94 (124)
28 PRK00107 gidB 16S rRNA methylt 98.3 3.5E-06 7.7E-11 67.1 7.3 66 167-232 44-118 (187)
29 PRK11207 tellurite resistance 98.2 3.7E-06 7.9E-11 67.5 7.0 73 157-232 20-101 (197)
30 TIGR03534 RF_mod_PrmC protein- 98.2 3.6E-06 7.9E-11 69.6 7.2 65 168-232 87-160 (251)
31 smart00828 PKS_MT Methyltransf 98.2 2.8E-06 6E-11 69.3 6.4 62 170-231 1-72 (224)
32 TIGR00091 tRNA (guanine-N(7)-) 98.2 1.9E-06 4.2E-11 69.0 5.2 65 168-232 16-93 (194)
33 TIGR00138 gidB 16S rRNA methyl 98.2 2.5E-06 5.4E-11 67.6 5.6 64 169-232 43-115 (181)
34 PF13649 Methyltransf_25: Meth 98.2 2E-06 4.3E-11 61.3 4.2 61 172-232 1-73 (101)
35 PRK14966 unknown domain/N5-glu 98.2 4.8E-06 1E-10 73.6 7.3 65 168-232 251-325 (423)
36 TIGR02021 BchM-ChlM magnesium 98.2 8.9E-06 1.9E-10 66.2 8.5 100 131-232 17-125 (219)
37 PLN02336 phosphoethanolamine N 98.2 6.2E-06 1.3E-10 74.9 8.0 74 157-232 256-338 (475)
38 PRK01544 bifunctional N5-gluta 98.2 3.3E-06 7.1E-11 77.2 6.0 64 169-232 139-212 (506)
39 PF01209 Ubie_methyltran: ubiE 98.2 3.8E-06 8.2E-11 69.2 5.8 67 166-232 45-122 (233)
40 COG2813 RsmC 16S RNA G1207 met 98.1 8.5E-06 1.8E-10 68.7 7.6 74 158-232 149-230 (300)
41 PLN02233 ubiquinone biosynthes 98.1 1E-05 2.2E-10 67.9 8.0 67 166-232 71-151 (261)
42 PRK10258 biotin biosynthesis p 98.1 1.8E-05 3.8E-10 65.8 9.3 74 156-232 31-109 (251)
43 PRK11088 rrmA 23S rRNA methylt 98.1 1E-05 2.2E-10 68.2 7.8 64 168-231 85-156 (272)
44 PRK08317 hypothetical protein; 98.1 1.2E-05 2.5E-10 65.7 8.0 73 159-232 11-93 (241)
45 PRK00121 trmB tRNA (guanine-N( 98.1 5.6E-06 1.2E-10 66.7 6.0 65 168-232 40-117 (202)
46 PF08242 Methyltransf_12: Meth 98.1 9.5E-07 2.1E-11 62.6 1.3 60 173-232 1-72 (99)
47 PRK13942 protein-L-isoaspartat 98.1 1.4E-05 3E-10 64.9 8.3 74 158-232 67-151 (212)
48 TIGR02072 BioC biotin biosynth 98.1 7.3E-06 1.6E-10 67.0 6.6 64 169-232 35-104 (240)
49 TIGR00080 pimt protein-L-isoas 98.1 1.3E-05 2.8E-10 65.2 8.0 74 158-232 68-152 (215)
50 PRK09328 N5-glutamine S-adenos 98.1 1E-05 2.2E-10 68.0 7.6 67 166-232 106-181 (275)
51 PRK07402 precorrin-6B methylas 98.1 9.9E-06 2.2E-10 64.9 7.1 63 159-222 32-101 (196)
52 smart00650 rADc Ribosomal RNA 98.1 1.1E-05 2.4E-10 63.0 7.3 72 157-231 3-82 (169)
53 PRK14121 tRNA (guanine-N(7)-)- 98.1 8.8E-06 1.9E-10 71.4 7.3 73 159-232 114-198 (390)
54 PRK00216 ubiE ubiquinone/menaq 98.1 1.6E-05 3.5E-10 65.0 8.5 74 158-232 42-127 (239)
55 PF08241 Methyltransf_11: Meth 98.1 8E-06 1.7E-10 56.7 5.6 59 173-232 1-66 (95)
56 TIGR03704 PrmC_rel_meth putati 98.1 1.1E-05 2.4E-10 67.3 7.3 64 169-232 87-159 (251)
57 PRK09489 rsmC 16S ribosomal RN 98.1 1.3E-05 2.9E-10 69.7 7.9 73 159-232 188-267 (342)
58 PRK13944 protein-L-isoaspartat 98.1 1.8E-05 3.8E-10 64.0 8.0 73 159-232 64-148 (205)
59 PRK11036 putative S-adenosyl-L 98.1 1.2E-05 2.7E-10 67.0 7.1 71 158-232 36-118 (255)
60 TIGR01934 MenG_MenH_UbiE ubiqu 98.1 1.6E-05 3.5E-10 64.4 7.6 74 158-232 30-112 (223)
61 PLN02490 MPBQ/MSBQ methyltrans 98.0 1.8E-05 3.9E-10 68.6 7.7 65 168-232 113-184 (340)
62 PLN03075 nicotianamine synthas 98.0 1.9E-05 4E-10 67.0 7.4 66 167-232 122-201 (296)
63 smart00138 MeTrc Methyltransfe 98.0 8.4E-05 1.8E-09 62.4 11.3 66 167-232 98-209 (264)
64 PRK06202 hypothetical protein; 98.0 4E-05 8.7E-10 62.9 9.3 66 167-232 59-135 (232)
65 PF13659 Methyltransf_26: Meth 98.0 7.4E-06 1.6E-10 59.6 4.4 62 170-232 2-76 (117)
66 COG4123 Predicted O-methyltran 98.0 1E-05 2.2E-10 66.8 5.4 74 159-232 35-121 (248)
67 PRK14896 ksgA 16S ribosomal RN 98.0 2.2E-05 4.7E-10 65.7 7.4 72 157-231 19-96 (258)
68 PRK00274 ksgA 16S ribosomal RN 98.0 2.1E-05 4.5E-10 66.4 7.1 66 157-225 32-102 (272)
69 PHA03411 putative methyltransf 98.0 2.1E-05 4.6E-10 65.9 6.7 64 169-232 65-132 (279)
70 PLN02366 spermidine synthase 98.0 1.6E-05 3.4E-10 68.2 6.1 65 167-232 90-171 (308)
71 KOG1540 Ubiquinone biosynthesi 97.9 6.7E-05 1.4E-09 61.7 8.6 64 169-232 101-183 (296)
72 TIGR00537 hemK_rel_arch HemK-r 97.9 3.7E-05 8E-10 60.6 6.6 63 168-232 19-88 (179)
73 PRK07580 Mg-protoporphyrin IX 97.9 4.7E-05 1E-09 62.1 7.2 63 167-232 62-133 (230)
74 PRK00811 spermidine synthase; 97.9 2.4E-05 5.3E-10 66.3 5.3 66 167-232 75-156 (283)
75 PRK05785 hypothetical protein; 97.8 3.8E-05 8.2E-10 63.0 6.2 62 168-232 51-116 (226)
76 PRK11188 rrmJ 23S rRNA methylt 97.8 0.0001 2.2E-09 59.7 8.3 60 159-222 42-102 (209)
77 TIGR00477 tehB tellurite resis 97.8 9.6E-05 2.1E-09 59.2 7.9 73 157-232 20-100 (195)
78 TIGR00755 ksgA dimethyladenosi 97.8 6.3E-05 1.4E-09 62.7 7.1 69 157-228 19-93 (253)
79 PRK11873 arsM arsenite S-adeno 97.8 5.3E-05 1.1E-09 63.7 6.5 67 166-232 75-152 (272)
80 PHA03412 putative methyltransf 97.8 5.8E-05 1.3E-09 61.9 6.3 64 169-232 50-120 (241)
81 PF05401 NodS: Nodulation prot 97.8 4.1E-05 8.9E-10 60.8 5.1 68 162-232 38-112 (201)
82 PRK01581 speE spermidine synth 97.7 6E-05 1.3E-09 65.6 6.0 67 166-232 148-232 (374)
83 PRK15068 tRNA mo(5)U34 methylt 97.7 0.00012 2.7E-09 63.2 7.9 71 160-232 115-195 (322)
84 COG2230 Cfa Cyclopropane fatty 97.7 0.0001 2.2E-09 62.0 7.1 64 157-222 62-133 (283)
85 PRK00377 cbiT cobalt-precorrin 97.7 0.00012 2.5E-09 58.8 7.2 71 161-232 34-117 (198)
86 PRK14967 putative methyltransf 97.7 8.8E-05 1.9E-09 60.6 6.4 66 166-232 34-107 (223)
87 PRK00312 pcm protein-L-isoaspa 97.7 0.00017 3.7E-09 58.4 8.0 71 159-232 70-150 (212)
88 PF02353 CMAS: Mycolic acid cy 97.7 7.8E-05 1.7E-09 62.9 6.1 73 157-231 52-132 (273)
89 PLN02672 methionine S-methyltr 97.7 5.1E-05 1.1E-09 74.4 5.5 62 170-231 120-208 (1082)
90 PRK14968 putative methyltransf 97.7 0.00011 2.4E-09 57.9 6.5 64 167-232 22-96 (188)
91 PRK00050 16S rRNA m(4)C1402 me 97.7 0.00012 2.6E-09 62.3 6.6 76 156-232 8-96 (296)
92 PRK12335 tellurite resistance 97.6 0.00015 3.3E-09 61.5 6.9 72 158-232 111-190 (287)
93 PF09339 HTH_IclR: IclR helix- 97.6 2.8E-05 6E-10 48.6 1.7 46 19-70 6-51 (52)
94 PLN02396 hexaprenyldihydroxybe 97.6 8.1E-05 1.8E-09 64.2 5.2 62 169-232 132-204 (322)
95 PRK13943 protein-L-isoaspartat 97.6 0.00021 4.6E-09 61.6 7.7 73 159-232 72-155 (322)
96 PTZ00338 dimethyladenosine tra 97.6 0.0002 4.4E-09 61.0 7.4 72 157-231 26-106 (294)
97 PRK03612 spermidine synthase; 97.6 0.00012 2.6E-09 67.3 6.3 65 167-232 296-379 (521)
98 PRK04266 fibrillarin; Provisio 97.6 0.0003 6.5E-09 57.7 8.0 68 163-231 68-146 (226)
99 TIGR00438 rrmJ cell division p 97.6 0.00031 6.6E-09 55.8 7.8 58 161-222 25-83 (188)
100 PF02390 Methyltransf_4: Putat 97.6 0.00011 2.4E-09 58.9 5.1 53 170-222 19-78 (195)
101 PLN02336 phosphoethanolamine N 97.6 0.00023 5E-09 64.7 7.8 74 156-232 26-109 (475)
102 PLN02781 Probable caffeoyl-CoA 97.6 0.00022 4.9E-09 58.8 6.9 67 166-232 66-150 (234)
103 smart00346 HTH_ICLR helix_turn 97.6 0.00022 4.9E-09 49.5 5.9 60 18-86 7-66 (91)
104 TIGR03438 probable methyltrans 97.5 0.00011 2.5E-09 62.8 4.8 55 168-222 63-126 (301)
105 PRK04148 hypothetical protein; 97.5 0.00045 9.7E-09 51.8 7.0 69 159-231 8-82 (134)
106 PF07021 MetW: Methionine bios 97.5 0.0002 4.3E-09 56.7 5.4 64 167-232 12-81 (193)
107 PF01135 PCMT: Protein-L-isoas 97.5 0.00022 4.7E-09 57.8 5.7 75 157-232 62-147 (209)
108 cd02440 AdoMet_MTases S-adenos 97.5 0.00033 7.1E-09 48.4 5.9 61 171-232 1-72 (107)
109 TIGR03840 TMPT_Se_Te thiopurin 97.5 0.00057 1.2E-08 55.6 7.6 54 167-222 33-105 (213)
110 TIGR02081 metW methionine bios 97.4 0.00049 1.1E-08 54.9 7.2 64 167-232 12-81 (194)
111 KOG2904 Predicted methyltransf 97.4 0.00041 8.9E-09 57.7 6.6 60 166-225 146-217 (328)
112 PRK13168 rumA 23S rRNA m(5)U19 97.4 0.00017 3.7E-09 65.0 4.6 72 158-232 288-373 (443)
113 PRK10909 rsmD 16S rRNA m(2)G96 97.4 0.0003 6.5E-09 56.6 5.2 63 169-232 54-127 (199)
114 COG0421 SpeE Spermidine syntha 97.4 0.00033 7.1E-09 59.2 5.7 66 167-232 75-155 (282)
115 PLN02823 spermine synthase 97.4 0.0003 6.6E-09 61.0 5.6 66 167-232 102-182 (336)
116 PRK11705 cyclopropane fatty ac 97.4 0.00062 1.3E-08 60.2 7.6 71 158-231 158-233 (383)
117 TIGR00452 methyltransferase, p 97.4 0.00083 1.8E-08 57.8 8.1 72 159-232 113-194 (314)
118 COG1414 IclR Transcriptional r 97.4 0.00038 8.2E-09 57.9 5.8 61 19-88 7-67 (246)
119 PF03848 TehB: Tellurite resis 97.4 0.00062 1.3E-08 54.3 6.7 72 157-231 20-99 (192)
120 TIGR00417 speE spermidine synt 97.4 0.00032 7E-09 59.1 5.3 66 167-232 71-151 (270)
121 TIGR00406 prmA ribosomal prote 97.4 0.00034 7.4E-09 59.5 5.5 64 168-232 159-231 (288)
122 smart00550 Zalpha Z-DNA-bindin 97.3 0.00061 1.3E-08 45.0 5.4 60 16-83 6-66 (68)
123 COG2263 Predicted RNA methylas 97.3 0.00063 1.4E-08 53.7 6.1 63 169-232 46-114 (198)
124 PRK03522 rumB 23S rRNA methylu 97.3 0.00051 1.1E-08 59.2 6.2 62 169-232 174-246 (315)
125 PF06325 PrmA: Ribosomal prote 97.3 0.00028 6E-09 60.1 4.4 82 143-231 139-230 (295)
126 PRK14902 16S rRNA methyltransf 97.3 0.00058 1.3E-08 61.6 6.4 71 161-232 244-326 (444)
127 PRK11569 transcriptional repre 97.2 0.00064 1.4E-08 57.4 5.8 62 18-88 30-91 (274)
128 PF09445 Methyltransf_15: RNA 97.2 0.00023 4.9E-09 55.2 2.7 62 170-233 1-76 (163)
129 PRK10163 DNA-binding transcrip 97.2 0.00077 1.7E-08 56.8 5.9 62 18-88 27-88 (271)
130 COG2264 PrmA Ribosomal protein 97.2 0.00073 1.6E-08 57.4 5.6 43 167-210 161-204 (300)
131 COG2518 Pcm Protein-L-isoaspar 97.2 0.002 4.3E-08 51.9 7.6 72 158-232 63-144 (209)
132 PRK11727 23S rRNA mA1618 methy 97.2 0.00072 1.6E-08 58.2 5.4 64 168-231 114-194 (321)
133 KOG1271 Methyltransferases [Ge 97.2 0.001 2.2E-08 52.2 5.6 64 168-231 67-141 (227)
134 PLN02585 magnesium protoporphy 97.2 0.00092 2E-08 57.6 5.9 61 169-232 145-218 (315)
135 TIGR02431 pcaR_pcaU beta-ketoa 97.2 0.00082 1.8E-08 55.8 5.5 59 19-88 12-70 (248)
136 PRK13255 thiopurine S-methyltr 97.1 0.0018 4E-08 52.8 7.4 64 166-231 35-121 (218)
137 PRK00536 speE spermidine synth 97.1 0.001 2.2E-08 55.7 5.9 62 167-232 71-145 (262)
138 PRK09834 DNA-binding transcrip 97.1 0.0011 2.3E-08 55.7 6.1 64 18-90 13-76 (263)
139 KOG2899 Predicted methyltransf 97.1 0.00063 1.4E-08 55.6 4.4 54 157-210 46-101 (288)
140 PRK15090 DNA-binding transcrip 97.1 0.00093 2E-08 55.8 5.6 60 19-88 17-76 (257)
141 TIGR01177 conserved hypothetic 97.1 0.0016 3.5E-08 56.4 7.1 71 159-232 174-254 (329)
142 PRK00517 prmA ribosomal protei 97.1 0.00061 1.3E-08 56.7 4.1 42 167-209 118-160 (250)
143 PTZ00146 fibrillarin; Provisio 97.1 0.0023 5.1E-08 54.2 7.5 67 166-232 130-208 (293)
144 PF14947 HTH_45: Winged helix- 97.1 0.0014 3.1E-08 44.3 5.2 50 32-90 18-67 (77)
145 PF02082 Rrf2: Transcriptional 97.1 0.0008 1.7E-08 46.2 3.8 55 23-83 15-69 (83)
146 PF05185 PRMT5: PRMT5 arginine 97.0 0.0019 4.2E-08 58.2 6.9 96 129-231 151-263 (448)
147 KOG1499 Protein arginine N-met 97.0 0.001 2.2E-08 57.1 4.9 62 169-231 61-132 (346)
148 PF08123 DOT1: Histone methyla 97.0 0.0012 2.5E-08 53.4 5.0 74 158-232 33-128 (205)
149 PRK10901 16S rRNA methyltransf 97.0 0.002 4.3E-08 57.9 6.8 73 159-232 236-319 (427)
150 KOG1500 Protein arginine N-met 97.0 0.0019 4.1E-08 55.3 6.2 64 166-231 176-248 (517)
151 TIGR02085 meth_trns_rumB 23S r 97.0 0.00081 1.8E-08 59.3 4.0 62 169-232 234-306 (374)
152 PF13489 Methyltransf_23: Meth 97.0 0.0036 7.9E-08 47.6 7.2 39 166-206 20-59 (161)
153 KOG0820 Ribosomal RNA adenine 97.0 0.0028 6E-08 52.8 6.7 73 156-231 47-128 (315)
154 COG0220 Predicted S-adenosylme 96.9 0.0014 3.1E-08 53.7 4.8 53 170-222 50-109 (227)
155 PF01564 Spermine_synth: Sperm 96.9 0.0011 2.3E-08 55.2 4.1 66 167-232 75-156 (246)
156 PF01596 Methyltransf_3: O-met 96.9 0.0015 3.2E-08 52.8 4.8 67 166-232 43-127 (205)
157 PF13679 Methyltransf_32: Meth 96.9 0.0015 3.3E-08 49.5 4.5 57 166-222 23-93 (141)
158 PF12840 HTH_20: Helix-turn-he 96.9 0.0011 2.3E-08 42.7 3.1 54 10-70 4-57 (61)
159 TIGR00479 rumA 23S rRNA (uraci 96.9 0.0011 2.3E-08 59.7 4.1 65 166-232 290-368 (431)
160 PLN02476 O-methyltransferase 96.9 0.0035 7.6E-08 52.9 6.8 67 166-232 116-200 (278)
161 PF13463 HTH_27: Winged helix 96.9 0.0027 5.9E-08 41.4 5.0 58 21-85 8-68 (68)
162 PF01978 TrmB: Sugar-specific 96.9 0.00095 2E-08 43.9 2.7 48 17-71 9-56 (68)
163 TIGR01444 fkbM_fam methyltrans 96.8 0.0018 4E-08 48.7 4.5 52 171-222 1-59 (143)
164 PF01022 HTH_5: Bacterial regu 96.8 0.0011 2.4E-08 40.3 2.6 44 18-69 4-47 (47)
165 PRK05134 bifunctional 3-demeth 96.7 0.005 1.1E-07 50.4 6.8 63 168-232 48-120 (233)
166 KOG3420 Predicted RNA methylas 96.7 0.0018 3.9E-08 49.0 3.6 68 162-232 43-120 (185)
167 PF13412 HTH_24: Winged helix- 96.7 0.0027 5.9E-08 38.6 3.9 45 17-68 4-48 (48)
168 PRK10141 DNA-binding transcrip 96.6 0.0038 8.3E-08 45.8 4.8 68 8-83 8-75 (117)
169 PF04816 DUF633: Family of unk 96.6 0.0027 5.9E-08 51.3 4.2 61 172-232 1-72 (205)
170 PRK14904 16S rRNA methyltransf 96.6 0.0053 1.1E-07 55.5 6.5 67 166-232 248-324 (445)
171 PF00398 RrnaAD: Ribosomal RNA 96.6 0.0047 1E-07 51.8 5.6 68 156-226 19-92 (262)
172 COG2227 UbiG 2-polyprenyl-3-me 96.6 0.002 4.3E-08 52.7 3.2 40 169-210 60-100 (243)
173 cd00092 HTH_CRP helix_turn_hel 96.6 0.0048 1E-07 40.0 4.5 44 32-83 24-67 (67)
174 TIGR01983 UbiG ubiquinone bios 96.6 0.0048 1E-07 50.0 5.5 63 168-232 45-118 (224)
175 PF13601 HTH_34: Winged helix 96.6 0.004 8.7E-08 42.5 4.1 66 17-89 1-69 (80)
176 smart00347 HTH_MARR helix_turn 96.5 0.0072 1.6E-07 42.3 5.4 68 17-91 11-80 (101)
177 PF05724 TPMT: Thiopurine S-me 96.5 0.0054 1.2E-07 50.0 5.3 55 166-222 35-108 (218)
178 KOG1541 Predicted protein carb 96.5 0.0023 5E-08 51.7 3.0 61 168-231 50-117 (270)
179 PRK11783 rlmL 23S rRNA m(2)G24 96.5 0.004 8.7E-08 59.4 5.0 64 168-232 538-614 (702)
180 TIGR00095 RNA methyltransferas 96.5 0.0028 6.1E-08 50.5 3.3 53 169-222 50-110 (189)
181 PRK15128 23S rRNA m(5)C1962 me 96.4 0.0041 8.8E-08 55.3 4.6 65 167-232 219-299 (396)
182 smart00419 HTH_CRP helix_turn_ 96.4 0.006 1.3E-07 36.7 4.0 41 33-82 8-48 (48)
183 COG4262 Predicted spermidine s 96.4 0.0084 1.8E-07 52.0 6.1 55 167-222 288-357 (508)
184 PRK10857 DNA-binding transcrip 96.4 0.0082 1.8E-07 46.7 5.5 62 10-83 8-69 (164)
185 PRK03902 manganese transport t 96.4 0.011 2.5E-07 44.7 6.1 50 32-89 21-70 (142)
186 PF09012 FeoC: FeoC like trans 96.4 0.0056 1.2E-07 40.4 3.9 44 21-71 5-48 (69)
187 PRK11760 putative 23S rRNA C24 96.3 0.013 2.8E-07 50.7 6.9 63 167-231 210-275 (357)
188 PF01170 UPF0020: Putative RNA 96.3 0.0093 2E-07 47.1 5.7 74 157-231 18-111 (179)
189 PF01795 Methyltransf_5: MraW 96.3 0.011 2.5E-07 50.5 6.6 66 156-222 9-80 (310)
190 PRK01544 bifunctional N5-gluta 96.3 0.0061 1.3E-07 55.9 5.2 64 168-231 347-422 (506)
191 COG1959 Predicted transcriptio 96.3 0.0087 1.9E-07 45.9 5.3 57 22-84 14-70 (150)
192 PRK13256 thiopurine S-methyltr 96.3 0.02 4.3E-07 46.9 7.6 54 167-222 42-114 (226)
193 TIGR02010 IscR iron-sulfur clu 96.3 0.0094 2E-07 44.8 5.4 46 32-83 24-69 (135)
194 COG2519 GCD14 tRNA(1-methylade 96.3 0.022 4.8E-07 47.1 7.9 84 148-232 71-169 (256)
195 PRK14901 16S rRNA methyltransf 96.3 0.0089 1.9E-07 53.8 6.1 71 161-232 246-331 (434)
196 KOG1270 Methyltransferases [Co 96.3 0.0037 8.1E-08 51.8 3.2 60 170-231 91-163 (282)
197 TIGR02337 HpaR homoprotocatech 96.3 0.014 3.1E-07 42.6 6.0 67 18-91 30-98 (118)
198 TIGR00563 rsmB ribosomal RNA s 96.3 0.0081 1.7E-07 54.0 5.5 73 159-232 230-315 (426)
199 TIGR02143 trmA_only tRNA (urac 96.2 0.0071 1.5E-07 53.0 5.0 51 170-222 199-256 (353)
200 COG3355 Predicted transcriptio 96.2 0.013 2.7E-07 43.3 5.3 46 20-72 31-77 (126)
201 PF07381 DUF1495: Winged helix 96.2 0.014 3.1E-07 40.5 5.2 69 15-89 8-87 (90)
202 COG0030 KsgA Dimethyladenosine 96.2 0.022 4.9E-07 47.5 7.2 68 156-226 19-92 (259)
203 TIGR00738 rrf2_super rrf2 fami 96.1 0.012 2.6E-07 43.8 5.1 47 32-84 24-70 (132)
204 TIGR00478 tly hemolysin TlyA f 96.1 0.021 4.5E-07 46.9 6.9 55 158-214 65-122 (228)
205 PF08461 HTH_12: Ribonuclease 96.1 0.014 3E-07 38.3 4.7 61 21-87 3-64 (66)
206 PRK14903 16S rRNA methyltransf 96.1 0.014 3E-07 52.6 6.0 67 166-232 235-313 (431)
207 TIGR00006 S-adenosyl-methyltra 96.1 0.019 4.1E-07 49.2 6.5 66 156-222 9-80 (305)
208 TIGR02702 SufR_cyano iron-sulf 96.1 0.016 3.4E-07 46.7 5.8 67 18-91 3-73 (203)
209 COG1321 TroR Mn-dependent tran 96.0 0.021 4.5E-07 44.0 5.9 52 32-91 23-74 (154)
210 PRK11050 manganese transport r 95.9 0.024 5.2E-07 43.5 6.0 59 21-90 42-100 (152)
211 PF04703 FaeA: FaeA-like prote 95.9 0.014 3E-07 37.7 3.8 45 20-70 4-48 (62)
212 PF12147 Methyltransf_20: Puta 95.9 0.025 5.5E-07 47.7 6.3 56 167-222 134-199 (311)
213 PRK05031 tRNA (uracil-5-)-meth 95.9 0.0087 1.9E-07 52.6 3.8 51 170-222 208-265 (362)
214 PF08003 Methyltransf_9: Prote 95.9 0.013 2.8E-07 49.9 4.6 39 159-199 107-145 (315)
215 PLN02589 caffeoyl-CoA O-methyl 95.8 0.0099 2.1E-07 49.4 3.7 67 166-232 77-162 (247)
216 PF08220 HTH_DeoR: DeoR-like h 95.7 0.024 5.2E-07 35.9 4.5 44 20-70 4-47 (57)
217 COG4976 Predicted methyltransf 95.7 0.011 2.4E-07 48.2 3.5 67 141-210 95-166 (287)
218 COG4742 Predicted transcriptio 95.7 0.027 5.9E-07 46.9 5.9 67 12-91 9-75 (260)
219 PF05148 Methyltransf_8: Hypot 95.7 0.041 8.9E-07 44.3 6.6 107 108-232 15-128 (219)
220 PF12802 MarR_2: MarR family; 95.7 0.016 3.5E-07 36.9 3.7 49 18-71 7-55 (62)
221 TIGR00446 nop2p NOL1/NOP2/sun 95.7 0.025 5.4E-07 47.5 5.6 66 167-232 70-146 (264)
222 COG3432 Predicted transcriptio 95.7 0.015 3.3E-07 40.7 3.5 64 21-91 20-84 (95)
223 PF01638 HxlR: HxlR-like helix 95.6 0.02 4.4E-07 39.8 4.2 62 21-90 10-74 (90)
224 PHA00738 putative HTH transcri 95.6 0.028 6.1E-07 40.2 4.9 61 16-84 12-72 (108)
225 PF10294 Methyltransf_16: Puta 95.6 0.014 3E-07 45.8 3.7 57 166-222 43-108 (173)
226 smart00420 HTH_DEOR helix_turn 95.6 0.033 7.1E-07 34.0 4.7 44 20-70 4-47 (53)
227 TIGR02944 suf_reg_Xantho FeS a 95.6 0.022 4.8E-07 42.4 4.5 46 32-83 24-69 (130)
228 cd00090 HTH_ARSR Arsenical Res 95.6 0.031 6.7E-07 36.5 4.8 57 18-83 9-65 (78)
229 cd07153 Fur_like Ferric uptake 95.5 0.035 7.6E-07 40.3 5.3 63 18-82 3-66 (116)
230 COG4122 Predicted O-methyltran 95.5 0.02 4.4E-07 46.6 4.2 67 166-232 57-138 (219)
231 PF01728 FtsJ: FtsJ-like methy 95.5 0.012 2.5E-07 46.3 2.8 60 158-221 11-73 (181)
232 smart00418 HTH_ARSR helix_turn 95.5 0.054 1.2E-06 34.2 5.5 54 21-83 2-55 (66)
233 TIGR01884 cas_HTH CRISPR locus 95.3 0.031 6.8E-07 45.0 5.0 59 18-85 145-203 (203)
234 PF01047 MarR: MarR family; I 95.3 0.018 3.8E-07 36.5 2.8 48 18-72 5-52 (59)
235 COG2345 Predicted transcriptio 95.3 0.04 8.7E-07 44.7 5.3 64 20-90 15-82 (218)
236 PRK04338 N(2),N(2)-dimethylgua 95.2 0.031 6.7E-07 49.5 4.9 63 170-232 59-131 (382)
237 KOG3115 Methyltransferase-like 95.2 0.0095 2.1E-07 47.6 1.3 33 169-201 61-93 (249)
238 TIGR00122 birA_repr_reg BirA b 95.1 0.037 8E-07 36.3 4.0 55 18-84 2-56 (69)
239 PF02475 Met_10: Met-10+ like- 95.1 0.037 8E-07 44.5 4.6 67 166-232 99-175 (200)
240 smart00529 HTH_DTXR Helix-turn 95.1 0.047 1E-06 38.1 4.6 47 36-90 2-48 (96)
241 PRK11920 rirA iron-responsive 95.0 0.041 9E-07 42.3 4.6 46 32-83 23-68 (153)
242 PF04967 HTH_10: HTH DNA bindi 95.0 0.026 5.7E-07 35.2 2.8 43 9-61 5-47 (53)
243 PRK11512 DNA-binding transcrip 95.0 0.062 1.4E-06 40.6 5.4 65 20-91 44-110 (144)
244 PF08704 GCD14: tRNA methyltra 95.0 0.085 1.8E-06 43.9 6.5 88 144-232 13-119 (247)
245 PRK03573 transcriptional regul 94.8 0.1 2.2E-06 39.3 6.2 65 21-91 36-102 (144)
246 PF08279 HTH_11: HTH domain; 94.8 0.081 1.8E-06 32.9 4.7 41 19-65 3-43 (55)
247 PF07757 AdoMet_MTase: Predict 94.8 0.035 7.5E-07 39.8 3.2 32 167-200 57-88 (112)
248 COG0293 FtsJ 23S rRNA methylas 94.7 0.11 2.3E-06 41.9 6.2 63 156-222 33-96 (205)
249 COG0275 Predicted S-adenosylme 94.7 0.092 2E-06 44.6 6.1 66 156-222 12-84 (314)
250 PF10007 DUF2250: Uncharacteri 94.7 0.12 2.6E-06 36.1 5.7 47 17-70 8-54 (92)
251 smart00344 HTH_ASNC helix_turn 94.5 0.069 1.5E-06 38.2 4.4 46 17-69 4-49 (108)
252 TIGR01889 Staph_reg_Sar staphy 94.5 0.1 2.2E-06 37.6 5.3 68 18-90 27-98 (109)
253 PRK15431 ferrous iron transpor 94.4 0.095 2.1E-06 35.3 4.5 43 21-70 7-49 (78)
254 cd07377 WHTH_GntR Winged helix 94.4 0.11 2.5E-06 33.1 4.9 40 34-81 26-65 (66)
255 KOG1661 Protein-L-isoaspartate 94.4 0.11 2.4E-06 41.9 5.5 66 166-231 80-167 (237)
256 PRK11783 rlmL 23S rRNA m(2)G24 94.4 0.13 2.8E-06 49.3 7.0 76 156-232 178-309 (702)
257 KOG3010 Methyltransferase [Gen 94.3 0.047 1E-06 44.8 3.4 43 168-212 33-76 (261)
258 PRK14165 winged helix-turn-hel 94.1 0.12 2.7E-06 42.0 5.5 55 32-91 20-74 (217)
259 KOG2361 Predicted methyltransf 94.1 0.048 1E-06 44.8 3.1 64 169-232 72-150 (264)
260 KOG2730 Methylase [General fun 94.1 0.032 7E-07 45.2 2.0 53 168-222 94-154 (263)
261 COG4076 Predicted RNA methylas 94.1 0.12 2.5E-06 41.1 5.0 60 170-231 34-101 (252)
262 PF06080 DUF938: Protein of un 94.0 0.065 1.4E-06 43.1 3.7 37 166-202 22-59 (204)
263 COG2384 Predicted SAM-dependen 94.0 0.11 2.3E-06 42.2 4.8 64 169-232 17-91 (226)
264 PRK11014 transcriptional repre 94.0 0.13 2.8E-06 38.9 5.1 46 32-83 24-69 (141)
265 smart00345 HTH_GNTR helix_turn 93.9 0.17 3.6E-06 31.6 4.9 34 33-70 19-53 (60)
266 KOG3191 Predicted N6-DNA-methy 93.8 0.14 3.1E-06 40.3 5.0 64 169-232 44-116 (209)
267 PF07091 FmrO: Ribosomal RNA m 93.7 0.19 4.2E-06 41.6 5.9 88 145-232 76-177 (251)
268 PF01726 LexA_DNA_bind: LexA D 93.7 0.13 2.9E-06 33.4 4.1 48 18-70 8-59 (65)
269 PRK04172 pheS phenylalanyl-tRN 93.7 0.12 2.6E-06 47.4 5.2 67 17-92 7-73 (489)
270 PF06163 DUF977: Bacterial pro 93.6 0.21 4.5E-06 36.8 5.3 53 11-70 7-59 (127)
271 PF01739 CheR: CheR methyltran 93.6 0.37 8E-06 38.6 7.4 66 168-233 31-143 (196)
272 COG4189 Predicted transcriptio 93.5 0.17 3.6E-06 41.3 5.1 57 7-70 14-70 (308)
273 PRK06266 transcription initiat 93.4 0.25 5.4E-06 39.0 5.9 45 19-70 25-69 (178)
274 COG4190 Predicted transcriptio 93.4 0.21 4.6E-06 37.0 5.1 55 9-70 57-111 (144)
275 PHA02943 hypothetical protein; 93.4 0.24 5.2E-06 37.7 5.5 55 20-83 15-69 (165)
276 PF01325 Fe_dep_repress: Iron 93.4 0.14 3.1E-06 32.7 3.8 35 32-70 21-55 (60)
277 PRK06474 hypothetical protein; 93.3 0.17 3.7E-06 39.9 4.9 71 10-86 5-80 (178)
278 PRK05638 threonine synthase; V 93.1 0.19 4.2E-06 45.3 5.5 66 17-90 372-439 (442)
279 PF14394 DUF4423: Domain of un 92.8 0.25 5.5E-06 38.7 5.1 47 33-87 39-87 (171)
280 TIGR00373 conserved hypothetic 92.6 0.21 4.5E-06 38.6 4.4 45 19-70 17-61 (158)
281 TIGR01610 phage_O_Nterm phage 92.5 0.26 5.6E-06 34.6 4.4 44 32-82 46-89 (95)
282 PLN02853 Probable phenylalanyl 92.4 0.28 6E-06 44.6 5.5 69 15-92 2-71 (492)
283 COG3963 Phospholipid N-methylt 92.4 0.36 7.9E-06 37.6 5.3 67 155-222 36-105 (194)
284 PRK10870 transcriptional repre 92.3 0.3 6.6E-06 38.4 5.1 56 32-91 70-127 (176)
285 PF00325 Crp: Bacterial regula 92.3 0.15 3.2E-06 28.3 2.3 31 33-67 2-32 (32)
286 KOG3045 Predicted RNA methylas 92.1 0.55 1.2E-05 39.2 6.3 88 131-231 139-233 (325)
287 COG1352 CheR Methylase of chem 91.8 1.4 3.1E-05 37.0 8.8 66 168-233 96-209 (268)
288 COG1846 MarR Transcriptional r 91.7 0.46 1E-05 34.1 5.1 69 17-92 23-93 (126)
289 PF07789 DUF1627: Protein of u 91.5 0.35 7.7E-06 36.5 4.3 36 32-71 5-40 (155)
290 PF02527 GidB: rRNA small subu 91.5 0.23 5E-06 39.4 3.5 62 171-232 51-121 (184)
291 PRK11179 DNA-binding transcrip 91.4 0.38 8.3E-06 36.8 4.6 47 16-69 9-55 (153)
292 COG0357 GidB Predicted S-adeno 91.4 0.2 4.4E-06 40.7 3.1 53 169-221 68-127 (215)
293 PF03444 HrcA_DNA-bdg: Winged 91.1 0.95 2.1E-05 30.5 5.6 53 32-90 22-74 (78)
294 PF01475 FUR: Ferric uptake re 91.0 0.31 6.7E-06 35.6 3.6 67 15-83 7-74 (120)
295 PF04182 B-block_TFIIIC: B-blo 91.0 0.36 7.8E-06 32.3 3.6 49 17-70 3-51 (75)
296 PRK11169 leucine-responsive tr 90.9 0.38 8.2E-06 37.3 4.2 48 15-69 13-60 (164)
297 COG1522 Lrp Transcriptional re 90.8 0.46 1E-05 36.0 4.6 48 16-70 8-55 (154)
298 PTZ00326 phenylalanyl-tRNA syn 90.7 0.62 1.3E-05 42.5 5.9 69 16-92 6-74 (494)
299 COG5459 Predicted rRNA methyla 90.6 0.33 7.1E-06 42.2 3.8 68 164-232 110-188 (484)
300 COG1378 Predicted transcriptio 90.5 0.72 1.6E-05 38.4 5.8 61 19-88 19-79 (247)
301 PRK13509 transcriptional repre 90.5 0.53 1.1E-05 39.2 5.0 47 17-70 6-52 (251)
302 PF02002 TFIIE_alpha: TFIIE al 90.5 0.33 7.2E-06 34.6 3.3 44 20-70 17-60 (105)
303 PRK13777 transcriptional regul 90.3 0.86 1.9E-05 36.2 5.8 65 20-91 49-115 (185)
304 PF04672 Methyltransf_19: S-ad 90.2 0.85 1.8E-05 38.3 5.8 56 168-223 68-133 (267)
305 COG1733 Predicted transcriptio 90.1 1 2.3E-05 33.1 5.7 55 32-90 35-92 (120)
306 COG2512 Predicted membrane-ass 90.1 0.43 9.3E-06 39.9 4.0 48 18-71 197-244 (258)
307 PF04072 LCM: Leucine carboxyl 90.0 0.61 1.3E-05 36.7 4.7 56 167-222 77-141 (183)
308 PF05732 RepL: Firmicute plasm 89.8 0.47 1E-05 37.0 3.8 43 34-84 76-118 (165)
309 PRK04214 rbn ribonuclease BN/u 89.8 0.53 1.2E-05 42.2 4.7 43 32-82 309-351 (412)
310 COG2521 Predicted archaeal met 89.7 0.49 1.1E-05 38.9 3.9 64 167-231 133-210 (287)
311 PF12793 SgrR_N: Sugar transpo 89.7 0.57 1.2E-05 34.2 4.0 36 32-71 18-53 (115)
312 PF13545 HTH_Crp_2: Crp-like h 89.7 0.57 1.2E-05 30.9 3.8 42 33-83 28-69 (76)
313 KOG4589 Cell division protein 89.7 0.57 1.2E-05 37.2 4.2 44 161-204 62-106 (232)
314 PRK10611 chemotaxis methyltran 89.6 6.6 0.00014 33.4 10.9 64 169-232 116-229 (287)
315 TIGR00498 lexA SOS regulatory 89.2 0.89 1.9E-05 36.3 5.2 49 16-70 6-59 (199)
316 PF03602 Cons_hypoth95: Conser 89.0 0.33 7.2E-06 38.4 2.6 64 168-232 42-120 (183)
317 PRK10411 DNA-binding transcrip 89.0 0.87 1.9E-05 37.7 5.1 47 17-70 5-51 (240)
318 PF08784 RPA_C: Replication pr 88.9 0.54 1.2E-05 33.3 3.4 51 16-70 47-98 (102)
319 TIGR02147 Fsuc_second hypothet 88.8 0.87 1.9E-05 38.4 5.0 46 32-85 136-183 (271)
320 PF09243 Rsm22: Mitochondrial 88.7 0.91 2E-05 38.3 5.1 49 159-208 25-75 (274)
321 PF00126 HTH_1: Bacterial regu 88.4 1.5 3.3E-05 27.7 4.9 55 18-86 3-60 (60)
322 PF03291 Pox_MCEL: mRNA cappin 88.3 1.1 2.4E-05 38.9 5.5 78 141-222 38-132 (331)
323 PF08221 HTH_9: RNA polymerase 88.3 0.67 1.5E-05 29.8 3.2 44 20-70 17-60 (62)
324 COG4565 CitB Response regulato 88.1 0.89 1.9E-05 36.8 4.4 44 21-70 163-206 (224)
325 PRK10906 DNA-binding transcrip 88.1 0.87 1.9E-05 38.0 4.6 47 17-70 6-52 (252)
326 PF03141 Methyltransf_29: Puta 88.0 0.43 9.3E-06 43.3 2.8 24 167-190 116-139 (506)
327 PF00392 GntR: Bacterial regul 87.8 0.8 1.7E-05 29.4 3.3 35 32-70 22-57 (64)
328 PRK09802 DNA-binding transcrip 87.7 0.96 2.1E-05 38.1 4.7 48 16-70 17-64 (269)
329 COG5631 Predicted transcriptio 87.5 1.3 2.9E-05 34.1 4.7 78 4-87 64-148 (199)
330 PF09821 AAA_assoc_C: C-termin 87.5 0.95 2.1E-05 33.3 3.9 46 38-92 2-47 (120)
331 PF13730 HTH_36: Helix-turn-he 87.3 0.75 1.6E-05 28.4 2.9 29 35-67 27-55 (55)
332 PF13404 HTH_AsnC-type: AsnC-t 87.2 0.99 2.1E-05 26.6 3.2 37 17-60 4-40 (42)
333 PF02796 HTH_7: Helix-turn-hel 87.2 0.75 1.6E-05 27.4 2.7 23 33-59 21-43 (45)
334 PF02384 N6_Mtase: N-6 DNA Met 87.1 1.4 3.1E-05 37.5 5.5 67 166-232 44-131 (311)
335 TIGR00308 TRM1 tRNA(guanine-26 86.9 0.95 2.1E-05 40.0 4.3 63 170-232 46-120 (374)
336 PF02319 E2F_TDP: E2F/DP famil 86.8 0.2 4.3E-06 33.2 -0.0 37 32-70 23-62 (71)
337 PF14338 Mrr_N: Mrr N-terminal 86.8 4.6 0.0001 27.9 7.0 32 57-92 60-91 (92)
338 PRK09462 fur ferric uptake reg 86.7 1.8 3.9E-05 32.8 5.3 66 16-82 17-83 (148)
339 COG0735 Fur Fe2+/Zn2+ uptake r 86.7 1.3 2.9E-05 33.6 4.5 65 18-84 23-88 (145)
340 TIGR02987 met_A_Alw26 type II 86.5 0.69 1.5E-05 42.7 3.4 55 168-222 31-100 (524)
341 PF05958 tRNA_U5-meth_tr: tRNA 86.4 0.65 1.4E-05 40.7 3.0 47 171-219 199-252 (352)
342 COG3413 Predicted DNA binding 86.2 0.68 1.5E-05 37.5 2.8 43 8-60 159-201 (215)
343 KOG2187 tRNA uracil-5-methyltr 86.2 0.74 1.6E-05 41.9 3.3 55 166-222 381-445 (534)
344 PF09929 DUF2161: Uncharacteri 85.9 1.8 4E-05 31.5 4.6 59 9-87 58-116 (118)
345 PF05584 Sulfolobus_pRN: Sulfo 85.8 2.2 4.7E-05 28.3 4.5 44 19-70 8-51 (72)
346 PRK11639 zinc uptake transcrip 85.6 1.8 3.9E-05 33.7 4.9 53 17-71 27-80 (169)
347 COG1349 GlpR Transcriptional r 85.4 1.4 2.9E-05 36.8 4.3 53 18-81 7-59 (253)
348 PRK10742 putative methyltransf 85.3 2.4 5.3E-05 35.2 5.7 73 157-232 76-170 (250)
349 PRK10434 srlR DNA-bindng trans 85.1 1.4 3E-05 36.8 4.3 47 17-70 6-52 (256)
350 PF01861 DUF43: Protein of unk 85.0 1.6 3.6E-05 36.0 4.5 70 159-231 37-117 (243)
351 KOG1975 mRNA cap methyltransfe 84.9 1.6 3.4E-05 37.8 4.4 71 141-222 99-183 (389)
352 PRK11886 bifunctional biotin-- 84.7 1.8 3.9E-05 37.3 4.9 57 18-84 6-62 (319)
353 COG0116 Predicted N6-adenine-s 84.6 3.1 6.6E-05 36.8 6.3 75 157-232 181-305 (381)
354 PF13384 HTH_23: Homeodomain-l 84.6 0.96 2.1E-05 27.3 2.4 40 17-65 6-45 (50)
355 COG1497 Predicted transcriptio 83.8 3.7 8E-05 33.8 6.0 49 33-89 25-73 (260)
356 TIGR01321 TrpR trp operon repr 83.4 1.8 3.9E-05 30.3 3.5 40 15-62 41-80 (94)
357 PF13518 HTH_28: Helix-turn-he 83.4 2.2 4.9E-05 25.6 3.7 29 34-66 13-41 (52)
358 COG2265 TrmA SAM-dependent met 83.3 1.1 2.3E-05 40.5 3.0 65 166-232 291-368 (432)
359 PF09681 Phage_rep_org_N: N-te 83.3 2.7 5.9E-05 30.9 4.7 49 32-88 52-100 (121)
360 KOG0822 Protein kinase inhibit 83.0 5.2 0.00011 36.9 7.1 94 130-230 334-443 (649)
361 KOG1709 Guanidinoacetate methy 83.0 5.4 0.00012 32.6 6.5 61 166-226 99-167 (271)
362 PRK10046 dpiA two-component re 82.8 2.3 5.1E-05 34.3 4.6 45 20-70 166-210 (225)
363 KOG1562 Spermidine synthase [A 82.8 0.81 1.8E-05 38.9 1.9 66 166-232 119-201 (337)
364 TIGR02698 CopY_TcrY copper tra 81.9 3.2 7E-05 30.9 4.7 51 17-70 5-55 (130)
365 PRK11642 exoribonuclease R; Pr 81.6 2.8 6E-05 41.0 5.3 58 20-83 23-80 (813)
366 PF13814 Replic_Relax: Replica 81.4 3.9 8.5E-05 32.0 5.4 61 24-91 3-72 (191)
367 PF08280 HTH_Mga: M protein tr 81.1 2.4 5.2E-05 26.8 3.3 39 17-62 6-44 (59)
368 PF10668 Phage_terminase: Phag 81.0 2.5 5.5E-05 27.0 3.3 30 22-57 13-42 (60)
369 PF06969 HemN_C: HemN C-termin 81.0 3.1 6.6E-05 26.6 3.8 46 32-86 19-65 (66)
370 PRK04424 fatty acid biosynthes 80.9 1.4 3.1E-05 34.9 2.6 47 17-70 8-54 (185)
371 KOG2651 rRNA adenine N-6-methy 80.9 2.8 6.1E-05 37.0 4.5 46 158-204 143-188 (476)
372 COG1092 Predicted SAM-dependen 80.6 1.7 3.6E-05 38.7 3.2 65 167-232 216-296 (393)
373 COG1568 Predicted methyltransf 80.6 7.6 0.00017 32.9 6.8 166 34-226 35-216 (354)
374 PF12324 HTH_15: Helix-turn-he 80.5 1.7 3.6E-05 29.2 2.4 36 21-63 29-64 (77)
375 PRK11161 fumarate/nitrate redu 80.1 3.2 6.9E-05 33.7 4.5 42 33-83 184-225 (235)
376 PRK09775 putative DNA-binding 79.8 3.1 6.6E-05 37.7 4.6 53 21-84 5-57 (442)
377 PRK01381 Trp operon repressor; 79.7 2.5 5.4E-05 29.9 3.2 40 15-62 41-80 (99)
378 PF00165 HTH_AraC: Bacterial r 79.7 1.3 2.8E-05 25.7 1.5 28 32-63 7-34 (42)
379 TIGR02787 codY_Gpos GTP-sensin 79.6 4 8.6E-05 33.7 4.8 45 20-70 187-231 (251)
380 PRK12423 LexA repressor; Provi 79.6 2.9 6.4E-05 33.5 4.1 48 18-70 8-59 (202)
381 PF04989 CmcI: Cephalosporin h 79.5 3.1 6.6E-05 33.6 4.1 55 168-222 32-96 (206)
382 PF02981 FokI_N: Restriction e 79.2 2.5 5.5E-05 31.8 3.2 36 53-91 108-143 (145)
383 TIGR03433 padR_acidobact trans 79.0 8.5 0.00018 27.1 5.9 67 21-91 9-83 (100)
384 PF03428 RP-C: Replication pro 78.6 3.3 7.1E-05 32.6 4.0 33 35-71 72-105 (177)
385 PF05206 TRM13: Methyltransfer 78.6 3.7 8E-05 34.4 4.5 37 166-202 16-57 (259)
386 PF05491 RuvB_C: Holliday junc 78.5 5.7 0.00012 26.6 4.5 59 18-87 10-71 (76)
387 PRK10094 DNA-binding transcrip 78.4 4.5 9.8E-05 34.4 5.1 60 17-90 5-67 (308)
388 PRK11753 DNA-binding transcrip 78.2 3.7 8.1E-05 32.5 4.3 34 33-70 168-201 (211)
389 PRK09391 fixK transcriptional 78.2 4 8.7E-05 33.2 4.6 43 33-83 179-221 (230)
390 COG1510 Predicted transcriptio 78.0 2.4 5.2E-05 33.0 2.9 36 32-71 40-75 (177)
391 COG2520 Predicted methyltransf 78.0 2.9 6.3E-05 36.4 3.8 64 168-232 188-262 (341)
392 PF05219 DREV: DREV methyltran 77.9 2.4 5.1E-05 35.5 3.1 27 168-194 94-120 (265)
393 TIGR03697 NtcA_cyano global ni 77.9 4.3 9.3E-05 31.6 4.5 34 33-70 143-176 (193)
394 PF03059 NAS: Nicotianamine sy 77.7 3.9 8.5E-05 34.6 4.4 65 168-232 120-198 (276)
395 PF11972 HTH_13: HTH DNA bindi 77.6 6.4 0.00014 24.5 4.2 46 21-80 4-49 (54)
396 KOG4058 Uncharacterized conser 77.4 2.6 5.6E-05 32.3 2.9 66 158-225 63-137 (199)
397 TIGR03439 methyl_EasF probable 77.1 5.7 0.00012 34.3 5.3 63 157-222 68-143 (319)
398 COG3682 Predicted transcriptio 77.1 4.7 0.0001 29.7 4.1 62 16-83 6-67 (123)
399 PRK13918 CRP/FNR family transc 76.9 4.6 9.9E-05 31.8 4.5 43 33-84 149-191 (202)
400 smart00531 TFIIE Transcription 76.9 4 8.6E-05 31.0 3.9 43 20-69 5-49 (147)
401 COG3897 Predicted methyltransf 76.5 9.2 0.0002 30.7 5.9 65 166-232 77-148 (218)
402 TIGR00637 ModE_repress ModE mo 76.3 10 0.00022 26.8 5.6 65 17-90 5-72 (99)
403 PF05331 DUF742: Protein of un 76.2 4.3 9.3E-05 29.6 3.7 35 32-70 54-88 (114)
404 COG4754 Uncharacterized conser 76.1 7.5 0.00016 29.4 5.0 66 18-93 14-79 (157)
405 PLN02668 indole-3-acetate carb 75.9 4.8 0.0001 35.8 4.6 34 168-201 63-111 (386)
406 PF07848 PaaX: PaaX-like prote 75.9 4.5 9.7E-05 26.7 3.4 49 32-85 19-70 (70)
407 PHA02701 ORF020 dsRNA-binding 75.9 5.4 0.00012 31.5 4.4 49 16-70 4-52 (183)
408 TIGR03879 near_KaiC_dom probab 75.8 2.8 6E-05 27.9 2.4 34 32-69 31-64 (73)
409 PF04445 SAM_MT: Putative SAM- 75.7 5.4 0.00012 32.9 4.6 73 157-232 63-157 (234)
410 PRK00135 scpB segregation and 75.7 8.4 0.00018 30.7 5.5 42 19-70 93-134 (188)
411 COG1675 TFA1 Transcription ini 75.6 5.4 0.00012 31.4 4.3 44 20-70 22-65 (176)
412 PF12692 Methyltransf_17: S-ad 75.6 6.4 0.00014 30.1 4.5 79 142-223 5-83 (160)
413 PF05971 Methyltransf_10: Prot 75.6 4.7 0.0001 34.5 4.4 56 168-224 102-171 (299)
414 PRK03601 transcriptional regul 75.6 7.3 0.00016 32.4 5.6 60 18-91 5-67 (275)
415 TIGR00635 ruvB Holliday juncti 75.3 4.4 9.6E-05 34.3 4.2 46 32-86 254-300 (305)
416 PRK09954 putative kinase; Prov 75.3 4.4 9.5E-05 35.4 4.3 44 18-68 5-48 (362)
417 TIGR01714 phage_rep_org_N phag 74.9 8.4 0.00018 28.3 5.0 47 32-86 50-96 (119)
418 PF03374 ANT: Phage antirepres 74.5 8.5 0.00018 27.4 5.0 42 20-70 13-54 (111)
419 smart00753 PAM PCI/PINT associ 74.3 11 0.00024 25.4 5.4 52 12-70 6-57 (88)
420 smart00088 PINT motif in prote 74.3 11 0.00024 25.4 5.4 52 12-70 6-57 (88)
421 COG1088 RfbB dTDP-D-glucose 4, 73.6 7.6 0.00017 33.3 5.0 48 175-222 5-62 (340)
422 TIGR03339 phn_lysR aminoethylp 73.5 8.3 0.00018 31.7 5.4 59 19-91 2-63 (279)
423 PF09904 HTH_43: Winged helix- 73.5 4.7 0.0001 27.9 3.1 57 18-82 10-69 (90)
424 PRK00215 LexA repressor; Valid 73.4 9.6 0.00021 30.4 5.5 36 32-70 22-57 (205)
425 COG1725 Predicted transcriptio 73.2 6.5 0.00014 29.1 4.0 39 34-79 36-74 (125)
426 PF03551 PadR: Transcriptional 73.0 4.3 9.3E-05 26.8 2.9 57 32-88 8-72 (75)
427 PF03514 GRAS: GRAS domain fam 72.8 4 8.6E-05 36.1 3.4 46 156-202 99-151 (374)
428 KOG2915 tRNA(1-methyladenosine 72.7 21 0.00045 30.3 7.3 88 144-232 78-183 (314)
429 PF13936 HTH_38: Helix-turn-he 72.7 6.2 0.00013 23.3 3.2 23 33-59 20-42 (44)
430 PRK11534 DNA-binding transcrip 72.5 6.9 0.00015 31.6 4.6 46 32-85 29-74 (224)
431 PRK10402 DNA-binding transcrip 72.3 5.9 0.00013 32.1 4.1 41 33-82 169-209 (226)
432 PF03965 Penicillinase_R: Peni 72.0 5.7 0.00012 28.6 3.6 52 17-71 4-55 (115)
433 COG2524 Predicted transcriptio 71.9 11 0.00024 31.5 5.5 52 32-89 24-75 (294)
434 PRK09334 30S ribosomal protein 71.7 5.3 0.00012 27.5 3.0 46 21-70 28-74 (86)
435 COG1339 Transcriptional regula 71.6 11 0.00024 30.2 5.2 54 33-91 19-72 (214)
436 PHA02591 hypothetical protein; 71.5 6.3 0.00014 26.5 3.2 33 20-60 50-82 (83)
437 PRK10736 hypothetical protein; 71.3 7.3 0.00016 34.5 4.6 51 20-82 312-362 (374)
438 PF04492 Phage_rep_O: Bacterio 71.2 7.4 0.00016 27.6 3.8 51 16-70 32-87 (100)
439 KOG4300 Predicted methyltransf 71.2 7.2 0.00016 31.7 4.1 63 168-231 76-150 (252)
440 PRK09906 DNA-binding transcrip 70.7 9.4 0.0002 31.9 5.1 61 17-91 4-67 (296)
441 COG4367 Uncharacterized protei 70.5 5.2 0.00011 27.5 2.7 26 32-61 22-47 (97)
442 PF13578 Methyltransf_24: Meth 70.4 3.4 7.4E-05 29.0 2.0 60 173-232 1-75 (106)
443 TIGR02424 TF_pcaQ pca operon t 70.3 9.7 0.00021 31.9 5.2 60 18-91 7-69 (300)
444 PF11994 DUF3489: Protein of u 69.7 17 0.00038 24.1 5.0 54 21-81 15-71 (72)
445 PRK10837 putative DNA-binding 69.7 11 0.00025 31.2 5.4 61 17-91 6-69 (290)
446 PRK11062 nhaR transcriptional 69.5 12 0.00025 31.5 5.4 61 17-91 7-70 (296)
447 PRK09791 putative DNA-binding 69.0 9.9 0.00021 31.9 4.9 61 17-91 8-71 (302)
448 KOG1331 Predicted methyltransf 68.9 7.2 0.00016 33.1 3.9 56 167-226 44-101 (293)
449 TIGR03418 chol_sulf_TF putativ 68.7 8 0.00017 32.2 4.3 59 18-90 5-66 (291)
450 TIGR03338 phnR_burk phosphonat 68.6 10 0.00022 30.3 4.7 46 32-85 33-78 (212)
451 PRK13239 alkylmercury lyase; P 68.5 6.7 0.00015 31.6 3.5 41 17-64 23-63 (206)
452 PRK11242 DNA-binding transcrip 68.3 12 0.00025 31.2 5.2 60 18-91 5-67 (296)
453 smart00421 HTH_LUXR helix_turn 68.2 9.2 0.0002 22.9 3.5 25 33-61 18-42 (58)
454 KOG2165 Anaphase-promoting com 68.1 8.3 0.00018 36.6 4.4 48 32-83 615-662 (765)
455 TIGR00027 mthyl_TIGR00027 meth 68.1 10 0.00022 31.8 4.6 54 167-222 80-143 (260)
456 PF02636 Methyltransf_28: Puta 67.8 6 0.00013 32.8 3.3 35 169-203 19-61 (252)
457 COG2390 DeoR Transcriptional r 67.8 7 0.00015 33.8 3.7 35 32-70 25-59 (321)
458 TIGR03826 YvyF flagellar opero 67.7 8.5 0.00018 29.0 3.7 35 20-59 34-68 (137)
459 PRK14997 LysR family transcrip 67.5 12 0.00025 31.4 5.1 61 17-91 5-68 (301)
460 PRK10341 DNA-binding transcrip 66.9 12 0.00027 31.6 5.1 63 14-90 7-72 (312)
461 PF13542 HTH_Tnp_ISL3: Helix-t 66.8 11 0.00024 22.6 3.6 35 18-61 17-51 (52)
462 PF02295 z-alpha: Adenosine de 66.7 11 0.00023 24.6 3.6 49 17-70 5-53 (66)
463 CHL00180 rbcR LysR transcripti 66.7 12 0.00026 31.5 5.0 59 17-89 8-69 (305)
464 COG0640 ArsR Predicted transcr 66.4 14 0.00031 24.8 4.6 54 11-71 20-73 (110)
465 PF01371 Trp_repressor: Trp re 66.3 9.1 0.0002 26.4 3.3 39 15-62 35-74 (87)
466 PRK15121 right oriC-binding tr 66.1 12 0.00025 31.7 4.8 60 21-91 10-69 (289)
467 TIGR02719 repress_PhaQ poly-be 66.0 46 0.001 25.1 7.4 80 8-91 16-101 (138)
468 PF11312 DUF3115: Protein of u 66.0 8.5 0.00019 33.1 3.8 37 169-205 87-146 (315)
469 PRK15092 DNA-binding transcrip 65.9 14 0.00031 31.4 5.3 61 17-91 14-77 (310)
470 COG5340 Predicted transcriptio 65.9 7.2 0.00016 31.9 3.1 45 32-84 29-73 (269)
471 cd06170 LuxR_C_like C-terminal 65.7 11 0.00024 22.6 3.5 25 33-61 15-39 (57)
472 PF07574 SMC_Nse1: Nse1 non-SM 65.6 5.6 0.00012 31.8 2.6 33 50-86 165-197 (200)
473 PRK00082 hrcA heat-inducible t 65.5 17 0.00038 31.6 5.8 48 32-86 24-73 (339)
474 TIGR02531 yecD_yerC TrpR-relat 65.5 9.2 0.0002 26.4 3.3 35 19-62 41-75 (88)
475 smart00342 HTH_ARAC helix_turn 65.5 9 0.00019 24.9 3.3 30 33-66 1-30 (84)
476 PRK11233 nitrogen assimilation 65.4 16 0.00034 30.9 5.4 60 18-91 5-67 (305)
477 TIGR02844 spore_III_D sporulat 65.3 9.9 0.00021 25.8 3.3 32 19-58 9-40 (80)
478 COG3398 Uncharacterized protei 65.2 16 0.00035 29.8 5.0 68 12-87 170-237 (240)
479 cd04762 HTH_MerR-trunc Helix-T 65.1 7.2 0.00016 22.6 2.5 23 34-60 1-23 (49)
480 PF03297 Ribosomal_S25: S25 ri 65.0 10 0.00022 27.1 3.5 47 21-71 46-93 (105)
481 TIGR01764 excise DNA binding d 65.0 7.6 0.00016 22.6 2.5 22 34-59 2-23 (49)
482 TIGR02036 dsdC D-serine deamin 64.8 16 0.00034 30.9 5.3 61 17-91 11-74 (302)
483 PRK11414 colanic acid/biofilm 64.8 12 0.00026 30.1 4.4 35 32-70 33-67 (221)
484 PF09107 SelB-wing_3: Elongati 64.7 16 0.00035 22.3 3.9 41 23-70 3-43 (50)
485 PF00196 GerE: Bacterial regul 64.4 8.1 0.00017 24.0 2.7 37 16-61 6-42 (58)
486 PF01418 HTH_6: Helix-turn-hel 64.2 11 0.00023 25.1 3.4 44 19-66 19-63 (77)
487 PRK11074 putative DNA-binding 64.1 14 0.0003 31.1 4.9 60 18-91 6-68 (300)
488 COG3695 Predicted methylated D 63.9 11 0.00025 26.6 3.5 47 17-65 7-53 (103)
489 PF13443 HTH_26: Cro/C1-type H 63.8 5.5 0.00012 25.1 1.8 31 21-59 2-32 (63)
490 PF05891 Methyltransf_PK: AdoM 63.5 12 0.00026 30.4 4.1 41 168-209 55-96 (218)
491 TIGR00331 hrcA heat shock gene 63.3 13 0.00029 32.3 4.7 42 23-71 14-57 (337)
492 PF13551 HTH_29: Winged helix- 63.2 10 0.00022 26.6 3.4 27 35-65 14-40 (112)
493 PRK11511 DNA-binding transcrip 63.1 15 0.00032 27.0 4.3 60 21-91 14-73 (127)
494 PRK13626 transcriptional regul 63.1 9.4 0.0002 35.5 3.9 37 32-72 22-58 (552)
495 PF04545 Sigma70_r4: Sigma-70, 62.8 9.7 0.00021 22.8 2.7 26 32-61 19-44 (50)
496 PRK10430 DNA-binding transcrip 62.7 14 0.0003 29.9 4.5 35 32-70 177-211 (239)
497 COG3398 Uncharacterized protei 62.6 18 0.00038 29.6 4.8 51 13-70 98-148 (240)
498 COG1802 GntR Transcriptional r 62.3 13 0.00029 30.1 4.3 47 32-86 38-84 (230)
499 PF12728 HTH_17: Helix-turn-he 62.2 8.8 0.00019 23.0 2.5 23 34-60 2-24 (51)
500 PF06406 StbA: StbA protein; 62.0 25 0.00054 30.3 6.1 62 142-203 246-309 (318)
No 1
>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]
Probab=100.00 E-value=1.7e-34 Score=243.10 Aligned_cols=226 Identities=42% Similarity=0.706 Sum_probs=201.2
Q ss_pred CcccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCC-CCCCChhhHHHHHHHHhcCCceeeeccCCCCCce
Q 039903 1 MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPS-SNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLY 79 (233)
Q Consensus 1 ~~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~-~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y 79 (233)
+++++++..+++|.+|+|||+||+|++.+ + ..|||..+.. .+|.++..++|+||.|++.++++...-. .+ .|
T Consensus 11 ~~l~~~~~~~~~lk~A~eL~v~d~l~~~~---~--p~~ia~~l~~~~~~~~p~ll~r~lr~L~s~~i~k~~~~~-~~-~Y 83 (342)
T KOG3178|consen 11 MRLANGFALPMVLKAACELGVFDILANAG---S--PSEIASLLPTPKNPEAPVLLDRILRLLVSYSILKCRLVG-GE-VY 83 (342)
T ss_pred HHHHhhhhhHHHHHHHHHcChHHHHHhCC---C--HHHHHHhccCCCCCCChhHHHHHHHHHHHhhhceeeeec-ce-ee
Confidence 36788999999999999999999999963 2 8888888885 3567899999999999999999986321 12 89
Q ss_pred eccHhhhHhhcCCCCCCccchhccccC-----chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchh
Q 039903 80 GLAHVAKYFVLNRDGVSLCPSRPWLET-----KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSI 154 (233)
Q Consensus 80 ~lt~~s~~l~~~~~~~~~~~~~~~~~~-----~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~ 154 (233)
+++|.++.+..+....|+.+++....+ .|..|.++++.++.+|..++|+..|+|...++.....|+++|...+..
T Consensus 84 ~~~~~~~~~l~~~~~~S~a~~~~~~~~~v~~~~w~~l~dai~eg~~~~~~~~G~~l~~~~~~~~~~~~~~~~sm~~l~~~ 163 (342)
T KOG3178|consen 84 SATPVCKYFLKDSGGGSLAPLVLLNTSKVIMNTWQFLKDAILEGGDAFATAHGMMLGGYGGADERFSKDFNGSMSFLSTL 163 (342)
T ss_pred eccchhhhheecCCCCchhHHHHHhcccchhhhHHHHHHHHHhcccCCccccchhhhhhcccccccHHHHHHHHHHHHHH
Confidence 999999998855444578888776543 899999999999999999999888999999998889999999999999
Q ss_pred cHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-CCceEEecCcCCCCCCCCEEEeC
Q 039903 155 VTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-SGVKHIGGIMLERIPKGDAILIK 233 (233)
Q Consensus 155 ~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-~ri~~~~gD~f~~~P~~D~~~lk 233 (233)
..+.+++.|.+|++..++||||||.|..+..++.+||+++++.+|+|.+++.+... +.|+++.||+|+..|++|+|+||
T Consensus 164 ~~~~il~~~~Gf~~v~~avDvGgGiG~v~k~ll~~fp~ik~infdlp~v~~~a~~~~~gV~~v~gdmfq~~P~~daI~mk 243 (342)
T KOG3178|consen 164 VMKKILEVYTGFKGVNVAVDVGGGIGRVLKNLLSKYPHIKGINFDLPFVLAAAPYLAPGVEHVAGDMFQDTPKGDAIWMK 243 (342)
T ss_pred HHHhhhhhhcccccCceEEEcCCcHhHHHHHHHHhCCCCceeecCHHHHHhhhhhhcCCcceecccccccCCCcCeEEEE
Confidence 88888999888999999999999999999999999999999999999999999888 88999999999999999999986
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=100.00 E-value=7.5e-33 Score=236.88 Aligned_cols=205 Identities=20% Similarity=0.298 Sum_probs=159.7
Q ss_pred hHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhH
Q 039903 8 VLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKY 87 (233)
Q Consensus 8 ~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~ 87 (233)
+.+++|++|++|||||.|.+ +|.|++|||+++++ +++.++||||+|+++|+|++. +++|+||+.++.
T Consensus 2 ~~~~~l~aa~~Lglfd~L~~----gp~t~~eLA~~~~~----~~~~~~~lL~~L~~lgll~~~-----~~~y~~t~~~~~ 68 (306)
T TIGR02716 2 IEFSCMKAAIELDLFSHMAE----GPKDLATLAADTGS----VPPRLEMLLETLRQMRVINLE-----DGKWSLTEFADY 68 (306)
T ss_pred chHHHHHHHHHcCcHHHHhc----CCCCHHHHHHHcCC----ChHHHHHHHHHHHhCCCeEec-----CCcEecchhHHh
Confidence 46789999999999999987 69999999999999 999999999999999999984 689999999998
Q ss_pred hhcCCCCC---Cccchhcccc----CchhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHH-hcchhcHHHH
Q 039903 88 FVLNRDGV---SLCPSRPWLE----TKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAML-NHTSIVTNRI 159 (233)
Q Consensus 88 l~~~~~~~---~~~~~~~~~~----~~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~-~~~~~~~~~~ 159 (233)
++.+++.. ++.++..+.. ..|.+|+++++ ++++|... +++....++.. .|...|. .......+.+
T Consensus 69 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~r-~~~~~~~~-----~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l 141 (306)
T TIGR02716 69 MFSPTPKEPNLHQTPVAKAMAFLADDFYMGLSQAVR-GQKNFKGQ-----VPYPPVTREDN-LYFEEIHRSNAKFAIQLL 141 (306)
T ss_pred hccCCccchhhhcCchHHHHHHHHHHHHHhHHHHhc-CCcccccc-----cCCCCCCHHHH-HhHHHHHHhcchhHHHHH
Confidence 77655421 1223333221 26899999997 44444332 22222333333 3444554 3333445667
Q ss_pred HHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCC-CCCCCCEEE
Q 039903 160 IDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLE-RIPKGDAIL 231 (233)
Q Consensus 160 ~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~-~~P~~D~~~ 231 (233)
++.++ +++..+|+|||||+|.+++.+++++|+++++++|+|++++.++++ +||+++.+|+|+ ++|.+|+|+
T Consensus 142 ~~~~~-~~~~~~vlDiG~G~G~~~~~~~~~~p~~~~~~~D~~~~~~~a~~~~~~~gl~~rv~~~~~d~~~~~~~~~D~v~ 220 (306)
T TIGR02716 142 LEEAK-LDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLPGAIDLVNENAAEKGVADRMRGIAVDIYKESYPEADAVL 220 (306)
T ss_pred HHHcC-CCCCCEEEEeCCchhHHHHHHHHHCCCCEEEEEecHHHHHHHHHHHHhCCccceEEEEecCccCCCCCCCCEEE
Confidence 77777 888899999999999999999999999999999999999887642 689999999997 778789998
Q ss_pred eC
Q 039903 232 IK 233 (233)
Q Consensus 232 lk 233 (233)
++
T Consensus 221 ~~ 222 (306)
T TIGR02716 221 FC 222 (306)
T ss_pred eE
Confidence 63
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=100.00 E-value=4.6e-33 Score=230.54 Aligned_cols=158 Identities=24% Similarity=0.438 Sum_probs=138.3
Q ss_pred CCCceeccHhhhHhhcCCCCCCccchhccccC-----chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHH
Q 039903 75 DQRLYGLAHVAKYFVLNRDGVSLCPSRPWLET-----KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAML 149 (233)
Q Consensus 75 ~~~~y~lt~~s~~l~~~~~~~~~~~~~~~~~~-----~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~ 149 (233)
++++|+||+.|+.|+.+++..++..++.+... .|.+|++++++|+++|+..+|.++|+|+.++|+..+.|+++|.
T Consensus 2 ~~~~y~~t~~s~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~v~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~~m~ 81 (241)
T PF00891_consen 2 EGDRYSLTPLSELLLSDHSSPSMRGFVLFMISPELYPAWFRLTEAVRTGKPPFEKAFGTPFFEYLEEDPELAKRFNAAMA 81 (241)
T ss_dssp STEEEEE-HHHHGGSTTTTTTHHHHHHHHHTCHHHHHGGGGHHHHHHHSS-HHHHHHSS-HHHHHHCSHHHHHHHHHHHH
T ss_pred CCCEEeChHHHHHHhCCCCcCcHHHHHHHhcCHHHHHHHHHHHhhhccCCCHHHHhcCCcHHHhhhhChHHHHHHHHHHH
Confidence 57999999999999888763356666655332 8999999999999999999998899999999999999999999
Q ss_pred hcchhcH-HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCCCCCCCC
Q 039903 150 NHTSIVT-NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGD 228 (233)
Q Consensus 150 ~~~~~~~-~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~~~P~~D 228 (233)
..+.... +.+++.++ |++.++|||||||+|.++.+++++||+++++++|+|+|++.+++.+||++++||||+++|++|
T Consensus 82 ~~~~~~~~~~~~~~~d-~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~~~~~~rv~~~~gd~f~~~P~~D 160 (241)
T PF00891_consen 82 EYSRLNAFDILLEAFD-FSGFKTVVDVGGGSGHFAIALARAYPNLRATVFDLPEVIEQAKEADRVEFVPGDFFDPLPVAD 160 (241)
T ss_dssp HHHHHHHHHHHHHHST-TTTSSEEEEET-TTSHHHHHHHHHSTTSEEEEEE-HHHHCCHHHTTTEEEEES-TTTCCSSES
T ss_pred hhhhcchhhhhhcccc-ccCccEEEeccCcchHHHHHHHHHCCCCcceeeccHhhhhccccccccccccccHHhhhcccc
Confidence 9998887 77888888 999999999999999999999999999999999999999998888999999999999999999
Q ss_pred EEEeC
Q 039903 229 AILIK 233 (233)
Q Consensus 229 ~~~lk 233 (233)
+|+||
T Consensus 161 ~~~l~ 165 (241)
T PF00891_consen 161 VYLLR 165 (241)
T ss_dssp EEEEE
T ss_pred ceeee
Confidence 99985
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=99.16 E-value=5.9e-11 Score=73.63 Aligned_cols=51 Identities=55% Similarity=0.813 Sum_probs=43.4
Q ss_pred HHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHh
Q 039903 11 AAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLV 62 (233)
Q Consensus 11 ~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~ 62 (233)
++|++|++|||||+|+..| ++++|++||++++...+|.++..++|+||+|+
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 5899999999999999985 36999999999999446667889999999986
No 5
>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=98.87 E-value=5.4e-09 Score=75.77 Aligned_cols=64 Identities=13% Similarity=0.227 Sum_probs=53.3
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCc-CC-CCCCC-CEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIM-LE-RIPKG-DAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~-f~-~~P~~-D~~~l 232 (233)
..+|+|||||+|.++..+++++|..+++.+|. |+.++.++++ +||+++.+|+ +. ..+.. |++++
T Consensus 2 ~~~vLDlGcG~G~~~~~l~~~~~~~~v~gvD~s~~~~~~a~~~~~~~~~~~~i~~~~~d~~~~~~~~~~~D~v~~ 76 (112)
T PF12847_consen 2 GGRVLDLGCGTGRLSIALARLFPGARVVGVDISPEMLEIARERAAEEGLSDRITFVQGDAEFDPDFLEPFDLVIC 76 (112)
T ss_dssp TCEEEEETTTTSHHHHHHHHHHTTSEEEEEESSHHHHHHHHHHHHHTTTTTTEEEEESCCHGGTTTSSCEEEEEE
T ss_pred CCEEEEEcCcCCHHHHHHHhcCCCCEEEEEeCCHHHHHHHHHHHHhcCCCCCeEEEECccccCcccCCCCCEEEE
Confidence 36899999999999999999999999999998 5677766542 7999999999 44 34444 98875
No 6
>PRK06922 hypothetical protein; Provisional
Probab=98.74 E-value=3.6e-08 Score=90.88 Aligned_cols=104 Identities=18% Similarity=0.205 Sum_probs=77.7
Q ss_pred CccccccccCchHHHHHHHHHHhcchhc--HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HH
Q 039903 128 TGFYEYAGNDFRFNGVFNKAMLNHTSIV--TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VI 204 (233)
Q Consensus 128 ~~~~~~~~~~~~~~~~f~~am~~~~~~~--~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~ 204 (233)
..+|+++..+++..++|.+.|....... .......++ +.+..+|+|||||+|.++..+++++|+.+++++|+++ ++
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 4578899888888888887776643332 111223344 6667899999999999999999999999999999975 57
Q ss_pred hhccCC-----CCceEEecCcCC-C--CCCC--CEEEe
Q 039903 205 QDSSSY-----SGVKHIGGIMLE-R--IPKG--DAILI 232 (233)
Q Consensus 205 ~~a~~~-----~ri~~~~gD~f~-~--~P~~--D~~~l 232 (233)
+.+++. .+++++.+|..+ + +|.+ |+|+.
T Consensus 456 e~Ararl~~~g~~ie~I~gDa~dLp~~fedeSFDvVVs 493 (677)
T PRK06922 456 DTLKKKKQNEGRSWNVIKGDAINLSSSFEKESVDTIVY 493 (677)
T ss_pred HHHHHHhhhcCCCeEEEEcchHhCccccCCCCEEEEEE
Confidence 766542 468888999876 3 5543 99875
No 7
>PRK08287 cobalt-precorrin-6Y C(15)-methyltransferase; Validated
Probab=98.68 E-value=5.3e-08 Score=77.45 Aligned_cols=71 Identities=20% Similarity=0.285 Sum_probs=57.6
Q ss_pred HhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCCC-CEEEe
Q 039903 161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPKG-DAILI 232 (233)
Q Consensus 161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~~-D~~~l 232 (233)
..++ .....+++|||||+|.++..+++++|+.+++.+|. |+.++.++++ ++|+++.+|...+++.. |++++
T Consensus 25 ~~l~-~~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~s~~~~~~a~~n~~~~~~~~i~~~~~d~~~~~~~~~D~v~~ 103 (187)
T PRK08287 25 SKLE-LHRAKHLIDVGAGTGSVSIEAALQFPSLQVTAIERNPDALRLIKENRQRFGCGNIDIIPGEAPIELPGKADAIFI 103 (187)
T ss_pred HhcC-CCCCCEEEEECCcCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHhCCCCeEEEecCchhhcCcCCCEEEE
Confidence 4444 56678999999999999999999999999999999 5677776542 57999999986656553 98875
No 8
>PRK14103 trans-aconitate 2-methyltransferase; Provisional
Probab=98.55 E-value=3.4e-07 Score=76.43 Aligned_cols=74 Identities=18% Similarity=0.263 Sum_probs=60.5
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCCCCCC--CCEEEe
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLERIPK--GDAILI 232 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~~~P~--~D~~~l 232 (233)
..+++.++ .....+|||||||+|.++..+++++|+.+++.+|+ |..++.+++ .+++++.+|+.+..|. .|+|+.
T Consensus 19 ~~ll~~l~-~~~~~~vLDlGcG~G~~~~~l~~~~p~~~v~gvD~s~~~~~~a~~-~~~~~~~~d~~~~~~~~~fD~v~~ 95 (255)
T PRK14103 19 YDLLARVG-AERARRVVDLGCGPGNLTRYLARRWPGAVIEALDSSPEMVAAARE-RGVDARTGDVRDWKPKPDTDVVVS 95 (255)
T ss_pred HHHHHhCC-CCCCCEEEEEcCCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHh-cCCcEEEcChhhCCCCCCceEEEE
Confidence 45667666 66678999999999999999999999999999999 568887776 4799999998763333 399875
No 9
>PF13847 Methyltransf_31: Methyltransferase domain; PDB: 3T0I_B 3SVZ_B 3SXJ_A 3F4K_A 3GU3_B 2GH1_A 1R8Y_E 1R8X_B 2B3T_A 1T43_A ....
Probab=98.54 E-value=2e-07 Score=71.56 Aligned_cols=65 Identities=18% Similarity=0.263 Sum_probs=53.1
Q ss_pred CcceEEEecCCccHHHHHHH-HHcCCCcEEEeec-hHHHhhccC------CCCceEEecCcCC-C--CCC-CCEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIII-SNYLHIKGVNFDL-SHVIQDSSS------YSGVKHIGGIMLE-R--IPK-GDAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~-~~~P~l~~~v~Dl-p~v~~~a~~------~~ri~~~~gD~f~-~--~P~-~D~~~l 232 (233)
+..+|+|+|||+|.++..++ +.+|..+++.+|+ |+.++.|++ .++++|+.+|+++ + ++. .|+++.
T Consensus 3 ~~~~iLDlGcG~G~~~~~l~~~~~~~~~i~gvD~s~~~i~~a~~~~~~~~~~ni~~~~~d~~~l~~~~~~~~D~I~~ 79 (152)
T PF13847_consen 3 SNKKILDLGCGTGRLLIQLAKELNPGAKIIGVDISEEMIEYAKKRAKELGLDNIEFIQGDIEDLPQELEEKFDIIIS 79 (152)
T ss_dssp TTSEEEEET-TTSHHHHHHHHHSTTTSEEEEEESSHHHHHHHHHHHHHTTSTTEEEEESBTTCGCGCSSTTEEEEEE
T ss_pred CCCEEEEecCcCcHHHHHHHHhcCCCCEEEEEECcHHHHHHhhcccccccccccceEEeehhccccccCCCeeEEEE
Confidence 45789999999999999999 5689999999998 568887765 2689999999999 4 333 398875
No 10
>COG4106 Tam Trans-aconitate methyltransferase [General function prediction only]
Probab=98.53 E-value=2.5e-07 Score=73.91 Aligned_cols=81 Identities=12% Similarity=0.217 Sum_probs=66.5
Q ss_pred HhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCCCCCC
Q 039903 149 LNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLERIPK 226 (233)
Q Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~~~P~ 226 (233)
...+++ +..++...+ ......|+|+|||.|.....|+++||....+.+|- |+.++.|+.. +.++|..+|.-+-.|+
T Consensus 13 ~eRtRP-a~dLla~Vp-~~~~~~v~DLGCGpGnsTelL~~RwP~A~i~GiDsS~~Mla~Aa~rlp~~~f~~aDl~~w~p~ 90 (257)
T COG4106 13 DERTRP-ARDLLARVP-LERPRRVVDLGCGPGNSTELLARRWPDAVITGIDSSPAMLAKAAQRLPDATFEEADLRTWKPE 90 (257)
T ss_pred HhccCc-HHHHHhhCC-ccccceeeecCCCCCHHHHHHHHhCCCCeEeeccCCHHHHHHHHHhCCCCceecccHhhcCCC
Confidence 444444 456777777 78889999999999999999999999999999997 6788887664 8999999999986564
Q ss_pred --CCEEE
Q 039903 227 --GDAIL 231 (233)
Q Consensus 227 --~D~~~ 231 (233)
.|+++
T Consensus 91 ~~~dllf 97 (257)
T COG4106 91 QPTDLLF 97 (257)
T ss_pred Cccchhh
Confidence 37654
No 11
>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=98.52 E-value=4.1e-07 Score=73.47 Aligned_cols=67 Identities=13% Similarity=0.372 Sum_probs=56.9
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCCCCCCC--CEEEe
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLERIPKG--DAILI 232 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~~~P~~--D~~~l 232 (233)
..+..+|+|||||+|.++..+++..|..+++.+|+ |+.++.|++. +++++..+|+++++|.+ |+++.
T Consensus 41 ~~~~~~VLDiGCG~G~~~~~L~~~~~~~~v~giDiS~~~l~~A~~~~~~~~~~~~d~~~~~~~~sfD~V~~ 111 (204)
T TIGR03587 41 LPKIASILELGANIGMNLAALKRLLPFKHIYGVEINEYAVEKAKAYLPNINIIQGSLFDPFKDNFFDLVLT 111 (204)
T ss_pred cCCCCcEEEEecCCCHHHHHHHHhCCCCeEEEEECCHHHHHHHHhhCCCCcEEEeeccCCCCCCCEEEEEE
Confidence 34567899999999999999999989999999998 4688888763 77899999999877653 98875
No 12
>PRK01683 trans-aconitate 2-methyltransferase; Provisional
Probab=98.48 E-value=1.2e-06 Score=73.11 Aligned_cols=76 Identities=14% Similarity=0.288 Sum_probs=61.6
Q ss_pred HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCCCCCC--CCEEE
Q 039903 156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLERIPK--GDAIL 231 (233)
Q Consensus 156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~~~P~--~D~~~ 231 (233)
...++..++ .++..+|+|||||+|.++..+++++|..+++.+|+ |..++.+++. ++++++.+|+.+..|. .|+++
T Consensus 20 ~~~ll~~~~-~~~~~~vLDiGcG~G~~~~~la~~~~~~~v~gvD~s~~~i~~a~~~~~~~~~~~~d~~~~~~~~~fD~v~ 98 (258)
T PRK01683 20 ARDLLARVP-LENPRYVVDLGCGPGNSTELLVERWPAARITGIDSSPAMLAEARSRLPDCQFVEADIASWQPPQALDLIF 98 (258)
T ss_pred HHHHHhhCC-CcCCCEEEEEcccCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHhCCCCeEEECchhccCCCCCccEEE
Confidence 345667666 67778999999999999999999999999999999 5578777664 7899999999763333 38886
Q ss_pred e
Q 039903 232 I 232 (233)
Q Consensus 232 l 232 (233)
.
T Consensus 99 ~ 99 (258)
T PRK01683 99 A 99 (258)
T ss_pred E
Confidence 4
No 13
>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=98.47 E-value=3.2e-07 Score=71.92 Aligned_cols=66 Identities=18% Similarity=0.258 Sum_probs=55.4
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCCCCCC-C-CEEEe
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLERIPK-G-DAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~~~P~-~-D~~~l 232 (233)
....+++|+|||+|..+..+++++|+.+++.+|.. .+++.++++ +.|+++.+|+++.++. . |+|+.
T Consensus 30 ~~~~~vLDlG~G~G~i~~~la~~~~~~~v~~vDi~~~a~~~a~~n~~~n~~~~v~~~~~d~~~~~~~~~fD~Iv~ 104 (170)
T PF05175_consen 30 HKGGRVLDLGCGSGVISLALAKRGPDAKVTAVDINPDALELAKRNAERNGLENVEVVQSDLFEALPDGKFDLIVS 104 (170)
T ss_dssp HTTCEEEEETSTTSHHHHHHHHTSTCEEEEEEESBHHHHHHHHHHHHHTTCTTEEEEESSTTTTCCTTCEEEEEE
T ss_pred ccCCeEEEecCChHHHHHHHHHhCCCCEEEEEcCCHHHHHHHHHHHHhcCccccccccccccccccccceeEEEE
Confidence 35678999999999999999999999999999984 577777653 3499999999998774 3 99875
No 14
>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=98.47 E-value=5.9e-07 Score=73.63 Aligned_cols=74 Identities=12% Similarity=0.129 Sum_probs=58.3
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccC------CCCceEEecCcCC-CCCCC-
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSS------YSGVKHIGGIMLE-RIPKG- 227 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~------~~ri~~~~gD~f~-~~P~~- 227 (233)
.++..++ .....+|||||||+|.++..+++.+ |+.+++.+|+ |+.++.+++ .++++++.+|+.+ ++|.+
T Consensus 36 ~~l~~l~-~~~~~~vLDiGcG~G~~~~~la~~~~~~~~v~gvD~s~~~~~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~~ 114 (231)
T TIGR02752 36 DTMKRMN-VQAGTSALDVCCGTADWSIALAEAVGPEGHVIGLDFSENMLSVGRQKVKDAGLHNVELVHGNAMELPFDDNS 114 (231)
T ss_pred HHHHhcC-CCCCCEEEEeCCCcCHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHhcCCCceEEEEechhcCCCCCCC
Confidence 3445555 5666899999999999999999986 6789999999 567666553 2689999999988 66653
Q ss_pred -CEEEe
Q 039903 228 -DAILI 232 (233)
Q Consensus 228 -D~~~l 232 (233)
|++++
T Consensus 115 fD~V~~ 120 (231)
T TIGR02752 115 FDYVTI 120 (231)
T ss_pred ccEEEE
Confidence 98875
No 15
>PRK04457 spermidine synthase; Provisional
Probab=98.44 E-value=3.7e-07 Score=76.56 Aligned_cols=66 Identities=17% Similarity=0.209 Sum_probs=56.0
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC---CCCCC-CEEEe
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE---RIPKG-DAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~---~~P~~-D~~~l 232 (233)
++.++++|||||.|.++..+++.+|+.+++++|+ |++++.++++ +|++++.+|..+ ..|.. |+|++
T Consensus 65 ~~~~~vL~IG~G~G~l~~~l~~~~p~~~v~~VEidp~vi~~A~~~f~~~~~~~rv~v~~~Da~~~l~~~~~~yD~I~~ 142 (262)
T PRK04457 65 PRPQHILQIGLGGGSLAKFIYTYLPDTRQTAVEINPQVIAVARNHFELPENGERFEVIEADGAEYIAVHRHSTDVILV 142 (262)
T ss_pred CCCCEEEEECCCHhHHHHHHHHhCCCCeEEEEECCHHHHHHHHHHcCCCCCCCceEEEECCHHHHHHhCCCCCCEEEE
Confidence 4567899999999999999999999999999999 7898887652 689999999875 34544 99875
No 16
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=98.40 E-value=5.3e-07 Score=74.93 Aligned_cols=66 Identities=18% Similarity=0.224 Sum_probs=54.7
Q ss_pred cCcceEEEecCCccHHHHHHHH--HcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCCCEEEe
Q 039903 167 EQIKQLVDVGGGLGVNVNIIIS--NYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKGDAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~--~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~D~~~l 232 (233)
.+..+|+|||||+|..+..+++ .+|+.+++.+|. |+.++.|+++ .+|+++.+|+.+ ++|..|++++
T Consensus 55 ~~~~~vLDlGcGtG~~~~~l~~~~~~~~~~v~gvD~S~~ml~~A~~~~~~~~~~~~v~~~~~d~~~~~~~~~D~vv~ 131 (247)
T PRK15451 55 QPGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDNSPAMIERCRRHIDAYKAPTPVDVIEGDIRDIAIENASMVVL 131 (247)
T ss_pred CCCCEEEEEcccCCHHHHHHHHhcCCCCCeEEEEeCCHHHHHHHHHHHHhcCCCCCeEEEeCChhhCCCCCCCEEeh
Confidence 4557899999999999999988 469999999998 6788877652 489999999987 6666688764
No 17
>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=98.40 E-value=6.3e-07 Score=76.04 Aligned_cols=65 Identities=15% Similarity=0.209 Sum_probs=55.4
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC-C-CEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK-G-DAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~-~-D~~~l 232 (233)
+..+++|+|||+|.++..+++++|+.+++.+|+ +.+++.|+++ ++|+++.+|+++++|. . |+++.
T Consensus 121 ~~~~vLDlG~GsG~i~~~la~~~~~~~v~avDis~~al~~A~~n~~~~~~~~~i~~~~~D~~~~~~~~~fD~Iv~ 195 (284)
T TIGR03533 121 PVKRILDLCTGSGCIAIACAYAFPEAEVDAVDISPDALAVAEINIERHGLEDRVTLIQSDLFAALPGRKYDLIVS 195 (284)
T ss_pred CCCEEEEEeCchhHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEECchhhccCCCCccEEEE
Confidence 346899999999999999999999999999999 5677777653 5799999999987765 3 98874
No 18
>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=98.39 E-value=7.1e-07 Score=73.71 Aligned_cols=66 Identities=12% Similarity=0.142 Sum_probs=54.5
Q ss_pred cCcceEEEecCCccHHHHHHHHH--cCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCCCEEEe
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISN--YLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKGDAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~--~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~D~~~l 232 (233)
....+|||||||+|.++..++++ +|+.+++.+|+ |++++.|++. .+|+++.+|+.+ ++|..|+++.
T Consensus 52 ~~~~~iLDlGcG~G~~~~~l~~~~~~p~~~v~gvD~s~~ml~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~d~v~~ 128 (239)
T TIGR00740 52 TPDSNVYDLGCSRGAATLSARRNINQPNVKIIGIDNSQPMVERCRQHIAAYHSEIPVEILCNDIRHVEIKNASMVIL 128 (239)
T ss_pred CCCCEEEEecCCCCHHHHHHHHhcCCCCCeEEEEeCCHHHHHHHHHHHHhcCCCCCeEEEECChhhCCCCCCCEEee
Confidence 45578999999999999999997 48899999999 6788777542 479999999998 6776787653
No 19
>PRK11805 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=98.38 E-value=5.4e-07 Score=77.23 Aligned_cols=63 Identities=14% Similarity=0.169 Sum_probs=54.7
Q ss_pred ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC--CCEEEe
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK--GDAILI 232 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~--~D~~~l 232 (233)
.+++|+|||+|.++..+++++|+.+++.+|+ |.+++.|+++ +||+++.+|+++.+|. .|+++.
T Consensus 135 ~~VLDlG~GsG~iai~la~~~p~~~V~avDis~~al~~A~~n~~~~~l~~~i~~~~~D~~~~l~~~~fDlIvs 207 (307)
T PRK11805 135 TRILDLCTGSGCIAIACAYAFPDAEVDAVDISPDALAVAEINIERHGLEDRVTLIESDLFAALPGRRYDLIVS 207 (307)
T ss_pred CEEEEEechhhHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHHHHHhCCCCcEEEEECchhhhCCCCCccEEEE
Confidence 6899999999999999999999999999999 6688777653 5799999999987765 399874
No 20
>PRK15001 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional
Probab=98.36 E-value=1e-06 Score=77.42 Aligned_cols=73 Identities=19% Similarity=0.162 Sum_probs=57.7
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC---------CCceEEecCcCCCCCC-C
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY---------SGVKHIGGIMLERIPK-G 227 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~---------~ri~~~~gD~f~~~P~-~ 227 (233)
+++.++ .....+|+|+|||+|.+++.+++++|..+++.+|.. .+++.++++ ++++++.+|.++.++. .
T Consensus 220 lL~~lp-~~~~~~VLDLGCGtGvi~i~la~~~P~~~V~~vD~S~~Av~~A~~N~~~n~~~~~~~v~~~~~D~l~~~~~~~ 298 (378)
T PRK15001 220 FMQHLP-ENLEGEIVDLGCGNGVIGLTLLDKNPQAKVVFVDESPMAVASSRLNVETNMPEALDRCEFMINNALSGVEPFR 298 (378)
T ss_pred HHHhCC-cccCCeEEEEeccccHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCcccCceEEEEEccccccCCCCC
Confidence 455555 333368999999999999999999999999999996 467766542 3789999999986654 3
Q ss_pred -CEEEe
Q 039903 228 -DAILI 232 (233)
Q Consensus 228 -D~~~l 232 (233)
|+|+.
T Consensus 299 fDlIls 304 (378)
T PRK15001 299 FNAVLC 304 (378)
T ss_pred EEEEEE
Confidence 98875
No 21
>COG2226 UbiE Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]
Probab=98.34 E-value=1.8e-06 Score=71.04 Aligned_cols=65 Identities=20% Similarity=0.253 Sum_probs=57.1
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCC-CCCCC--CEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-RIPKG--DAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~~P~~--D~~~l 232 (233)
...++||||||+|-++..+++..+..+++++|.. ..++.|++. ..|+|+.+|..+ |+|.. |+|.+
T Consensus 51 ~g~~vLDva~GTGd~a~~~~k~~g~g~v~~~D~s~~ML~~a~~k~~~~~~~~i~fv~~dAe~LPf~D~sFD~vt~ 125 (238)
T COG2226 51 PGDKVLDVACGTGDMALLLAKSVGTGEVVGLDISESMLEVAREKLKKKGVQNVEFVVGDAENLPFPDNSFDAVTI 125 (238)
T ss_pred CCCEEEEecCCccHHHHHHHHhcCCceEEEEECCHHHHHHHHHHhhccCccceEEEEechhhCCCCCCccCEEEe
Confidence 5689999999999999999999999999999985 588888763 239999999999 99984 99876
No 22
>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional
Probab=98.31 E-value=2.3e-06 Score=71.85 Aligned_cols=74 Identities=18% Similarity=0.358 Sum_probs=59.0
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC----CCCceEEecCcCC-CCCCC--C
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS----YSGVKHIGGIMLE-RIPKG--D 228 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~~ri~~~~gD~f~-~~P~~--D 228 (233)
..++..++ ..+..+|||||||+|..+..+++.+ ..+++.+|+. ..++.+++ .++|+++.+|+.+ ++|.+ |
T Consensus 42 ~~~l~~l~-l~~~~~VLDiGcG~G~~a~~la~~~-~~~v~giD~s~~~~~~a~~~~~~~~~i~~~~~D~~~~~~~~~~FD 119 (263)
T PTZ00098 42 TKILSDIE-LNENSKVLDIGSGLGGGCKYINEKY-GAHVHGVDICEKMVNIAKLRNSDKNKIEFEANDILKKDFPENTFD 119 (263)
T ss_pred HHHHHhCC-CCCCCEEEEEcCCCChhhHHHHhhc-CCEEEEEECCHHHHHHHHHHcCcCCceEEEECCcccCCCCCCCeE
Confidence 45666666 7777899999999999999998875 6789999984 56666654 2689999999997 78764 9
Q ss_pred EEEe
Q 039903 229 AILI 232 (233)
Q Consensus 229 ~~~l 232 (233)
+++.
T Consensus 120 ~V~s 123 (263)
T PTZ00098 120 MIYS 123 (263)
T ss_pred EEEE
Confidence 9874
No 23
>COG2890 HemK Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]
Probab=98.31 E-value=9.1e-07 Score=74.86 Aligned_cols=62 Identities=15% Similarity=0.204 Sum_probs=53.4
Q ss_pred eEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCCC-CEEEe
Q 039903 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPKG-DAILI 232 (233)
Q Consensus 171 ~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~~-D~~~l 232 (233)
+++|||+|+|..++++++++|+.+++..|+ |++++.|+.+ .|+.++.+|+|++++.. |+++.
T Consensus 113 ~ilDlGTGSG~iai~la~~~~~~~V~a~Dis~~Al~~A~~Na~~~~l~~~~~~~~dlf~~~~~~fDlIVs 182 (280)
T COG2890 113 RILDLGTGSGAIAIALAKEGPDAEVIAVDISPDALALARENAERNGLVRVLVVQSDLFEPLRGKFDLIVS 182 (280)
T ss_pred cEEEecCChHHHHHHHHhhCcCCeEEEEECCHHHHHHHHHHHHHcCCccEEEEeeecccccCCceeEEEe
Confidence 799999999999999999999999999998 5688877654 56777777999988764 98874
No 24
>COG2242 CobL Precorrin-6B methylase 2 [Coenzyme metabolism]
Probab=98.31 E-value=2.4e-06 Score=67.16 Aligned_cols=71 Identities=17% Similarity=0.156 Sum_probs=58.0
Q ss_pred HhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCC---CCCCCEE
Q 039903 161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLER---IPKGDAI 230 (233)
Q Consensus 161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~---~P~~D~~ 230 (233)
..+. ..+..+++|||||+|..+++++..+|+.|++.+|. ++.++..+.+ ++++.+.||.-+. .|..|.+
T Consensus 28 s~L~-~~~g~~l~DIGaGtGsi~iE~a~~~p~~~v~AIe~~~~a~~~~~~N~~~fg~~n~~vv~g~Ap~~L~~~~~~dai 106 (187)
T COG2242 28 SKLR-PRPGDRLWDIGAGTGSITIEWALAGPSGRVIAIERDEEALELIERNAARFGVDNLEVVEGDAPEALPDLPSPDAI 106 (187)
T ss_pred HhhC-CCCCCEEEEeCCCccHHHHHHHHhCCCceEEEEecCHHHHHHHHHHHHHhCCCcEEEEeccchHhhcCCCCCCEE
Confidence 4454 66778999999999999999999999999999997 4566655543 8999999998874 4445998
Q ss_pred Ee
Q 039903 231 LI 232 (233)
Q Consensus 231 ~l 232 (233)
++
T Consensus 107 FI 108 (187)
T COG2242 107 FI 108 (187)
T ss_pred EE
Confidence 86
No 25
>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=98.30 E-value=2.2e-06 Score=72.71 Aligned_cols=63 Identities=16% Similarity=0.286 Sum_probs=54.1
Q ss_pred ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC-C-CEEEe
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK-G-DAILI 232 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~-~-D~~~l 232 (233)
.+++|+|||+|.++..+++.+|+.+++.+|+ +..++.++++ +||+++.+|+++++|. . |+++.
T Consensus 116 ~~vLDlG~GsG~i~l~la~~~~~~~v~avDis~~al~~a~~n~~~~~~~~~v~~~~~d~~~~~~~~~fDlIvs 188 (284)
T TIGR00536 116 LHILDLGTGSGCIALALAYEFPNAEVIAVDISPDALAVAEENAEKNQLEHRVEFIQSNLFEPLAGQKIDIIVS 188 (284)
T ss_pred CEEEEEeccHhHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEECchhccCcCCCccEEEE
Confidence 6899999999999999999999999999998 5577777653 4699999999997765 3 88874
No 26
>PLN02244 tocopherol O-methyltransferase
Probab=98.30 E-value=2.6e-06 Score=74.16 Aligned_cols=65 Identities=22% Similarity=0.284 Sum_probs=52.7
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCC-CCCCC--CEEEe
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLE-RIPKG--DAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~-~~P~~--D~~~l 232 (233)
+...+|||||||.|.++..+++++ ..+++.+|+. ..++.+++. ++|+++.+|+.+ ++|.+ |+|+.
T Consensus 117 ~~~~~VLDiGCG~G~~~~~La~~~-g~~v~gvD~s~~~i~~a~~~~~~~g~~~~v~~~~~D~~~~~~~~~~FD~V~s 192 (340)
T PLN02244 117 KRPKRIVDVGCGIGGSSRYLARKY-GANVKGITLSPVQAARANALAAAQGLSDKVSFQVADALNQPFEDGQFDLVWS 192 (340)
T ss_pred CCCCeEEEecCCCCHHHHHHHHhc-CCEEEEEECCHHHHHHHHHHHHhcCCCCceEEEEcCcccCCCCCCCccEEEE
Confidence 456899999999999999999988 7789999985 455555431 589999999988 77764 98874
No 27
>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=98.28 E-value=4.2e-06 Score=61.34 Aligned_cols=73 Identities=14% Similarity=0.089 Sum_probs=54.7
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC------CCCceEEecCcCC---CCCC-C
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS------YSGVKHIGGIMLE---RIPK-G 227 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~------~~ri~~~~gD~f~---~~P~-~ 227 (233)
+++.+. .....+++|+|||.|.++..+++++|+.+++.+|.. ..++.++. .++++++.+|... ..+. .
T Consensus 11 ~~~~~~-~~~~~~vldlG~G~G~~~~~l~~~~~~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (124)
T TIGR02469 11 TLSKLR-LRPGDVLWDIGAGSGSITIEAARLVPNGRVYAIERNPEALRLIERNARRFGVSNIVIVEGDAPEALEDSLPEP 89 (124)
T ss_pred HHHHcC-CCCCCEEEEeCCCCCHHHHHHHHHCCCceEEEEcCCHHHHHHHHHHHHHhCCCceEEEeccccccChhhcCCC
Confidence 344444 455579999999999999999999999999999984 46665543 2678999898764 2233 3
Q ss_pred CEEEe
Q 039903 228 DAILI 232 (233)
Q Consensus 228 D~~~l 232 (233)
|++++
T Consensus 90 D~v~~ 94 (124)
T TIGR02469 90 DRVFI 94 (124)
T ss_pred CEEEE
Confidence 88875
No 28
>PRK00107 gidB 16S rRNA methyltransferase GidB; Reviewed
Probab=98.25 E-value=3.5e-06 Score=67.08 Aligned_cols=66 Identities=18% Similarity=0.090 Sum_probs=53.0
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCC-CCEEEe
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPK-GDAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~-~D~~~l 232 (233)
+...+++|||||+|..+..+++++|..+++.+|. ++.++.++++ ++|+++.+|..+ +.+. .|+++.
T Consensus 44 ~~g~~VLDiGcGtG~~al~la~~~~~~~V~giD~s~~~l~~A~~~~~~~~l~~i~~~~~d~~~~~~~~~fDlV~~ 118 (187)
T PRK00107 44 PGGERVLDVGSGAGFPGIPLAIARPELKVTLVDSLGKKIAFLREVAAELGLKNVTVVHGRAEEFGQEEKFDVVTS 118 (187)
T ss_pred CCCCeEEEEcCCCCHHHHHHHHHCCCCeEEEEeCcHHHHHHHHHHHHHcCCCCEEEEeccHhhCCCCCCccEEEE
Confidence 3468999999999999999999999999999998 4567666542 469999999877 3332 398875
No 29
>PRK11207 tellurite resistance protein TehB; Provisional
Probab=98.23 E-value=3.7e-06 Score=67.53 Aligned_cols=73 Identities=16% Similarity=0.184 Sum_probs=55.7
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCC-
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKG- 227 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~- 227 (233)
+.+++.++ .....++||+|||.|.++..++++ ..+++.+|+ |..++.+++. .+|+++..|+.+ +++..
T Consensus 20 ~~l~~~l~-~~~~~~vLDiGcG~G~~a~~La~~--g~~V~gvD~S~~~i~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~f 96 (197)
T PRK11207 20 SEVLEAVK-VVKPGKTLDLGCGNGRNSLYLAAN--GFDVTAWDKNPMSIANLERIKAAENLDNLHTAVVDLNNLTFDGEY 96 (197)
T ss_pred HHHHHhcc-cCCCCcEEEECCCCCHHHHHHHHC--CCEEEEEeCCHHHHHHHHHHHHHcCCCcceEEecChhhCCcCCCc
Confidence 45666666 555689999999999999999986 468999999 5566666542 458899999987 55554
Q ss_pred CEEEe
Q 039903 228 DAILI 232 (233)
Q Consensus 228 D~~~l 232 (233)
|+|+.
T Consensus 97 D~I~~ 101 (197)
T PRK11207 97 DFILS 101 (197)
T ss_pred CEEEE
Confidence 98863
No 30
>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=98.23 E-value=3.6e-06 Score=69.65 Aligned_cols=65 Identities=15% Similarity=0.204 Sum_probs=54.0
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC--CCEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK--GDAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~--~D~~~l 232 (233)
+..+++|+|||+|.++..+++.+|+.+++.+|. +..++.++.+ ++++++.+|++++++. .|+++.
T Consensus 87 ~~~~ilDig~G~G~~~~~l~~~~~~~~v~~iD~~~~~~~~a~~~~~~~~~~~~~~~~~d~~~~~~~~~fD~Vi~ 160 (251)
T TIGR03534 87 GPLRVLDLGTGSGAIALALAKERPDARVTAVDISPEALAVARKNAARLGLDNVTFLQSDWFEPLPGGKFDLIVS 160 (251)
T ss_pred CCCeEEEEeCcHhHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCCCeEEEEECchhccCcCCceeEEEE
Confidence 346899999999999999999999999999997 5577766542 5799999999987654 388864
No 31
>smart00828 PKS_MT Methyltransferase in polyketide synthase (PKS) enzymes.
Probab=98.23 E-value=2.8e-06 Score=69.32 Aligned_cols=62 Identities=15% Similarity=0.243 Sum_probs=50.6
Q ss_pred ceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC-------CCCceEEecCcCC-CCCCC-CEEE
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS-------YSGVKHIGGIMLE-RIPKG-DAIL 231 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~-------~~ri~~~~gD~f~-~~P~~-D~~~ 231 (233)
++|||||||.|.++..+++.+|+.+++.+|+. +.++.+++ .++|+++.+|+.+ +.|.. |+++
T Consensus 1 ~~vLDiGcG~G~~~~~la~~~~~~~v~gid~s~~~~~~a~~~~~~~gl~~~i~~~~~d~~~~~~~~~fD~I~ 72 (224)
T smart00828 1 KRVLDFGCGYGSDLIDLAERHPHLQLHGYTISPEQAEVGRERIRALGLQGRIRIFYRDSAKDPFPDTYDLVF 72 (224)
T ss_pred CeEEEECCCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHhcCCCcceEEEecccccCCCCCCCCEee
Confidence 47999999999999999999999999999985 45555544 2689999999987 55554 8876
No 32
>TIGR00091 tRNA (guanine-N(7)-)-methyltransferase. In E. coli, this protein flanks the DNA repair protein MutY, also called micA.
Probab=98.22 E-value=1.9e-06 Score=68.96 Aligned_cols=65 Identities=11% Similarity=0.221 Sum_probs=51.9
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-C---CCCC--CEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-R---IPKG--DAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~---~P~~--D~~~l 232 (233)
...+++|||||+|.++..+++++|+.+++.+|+ +..++.+.+. ++|+++.+|+.+ . +|.+ |.+++
T Consensus 16 ~~~~ilDiGcG~G~~~~~la~~~p~~~v~gvD~~~~~l~~a~~~~~~~~l~ni~~i~~d~~~~~~~~~~~~~~d~v~~ 93 (194)
T TIGR00091 16 KAPLHLEIGCGKGRFLIDMAKQNPDKNFLGIEIHTPIVLAANNKANKLGLKNLHVLCGDANELLDKFFPDGSLSKVFL 93 (194)
T ss_pred CCceEEEeCCCccHHHHHHHHhCCCCCEEEEEeeHHHHHHHHHHHHHhCCCCEEEEccCHHHHHHhhCCCCceeEEEE
Confidence 457899999999999999999999999999998 4566665432 689999999975 1 4442 77654
No 33
>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=98.21 E-value=2.5e-06 Score=67.64 Aligned_cols=64 Identities=17% Similarity=0.171 Sum_probs=50.4
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC------CCCceEEecCcCC-CCCC-CCEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS------YSGVKHIGGIMLE-RIPK-GDAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~------~~ri~~~~gD~f~-~~P~-~D~~~l 232 (233)
..+++|||||+|.++..++..+|+.+++.+|..+ .++.+++ .++|+++.+|+.+ +... .|+|+.
T Consensus 43 ~~~vLDiGcGtG~~s~~la~~~~~~~V~~iD~s~~~~~~a~~~~~~~~~~~i~~i~~d~~~~~~~~~fD~I~s 115 (181)
T TIGR00138 43 GKKVIDIGSGAGFPGIPLAIARPELKLTLLESNHKKVAFLREVKAELGLNNVEIVNGRAEDFQHEEQFDVITS 115 (181)
T ss_pred CCeEEEecCCCCccHHHHHHHCCCCeEEEEeCcHHHHHHHHHHHHHhCCCCeEEEecchhhccccCCccEEEe
Confidence 5799999999999999999999999999999864 5544432 2579999999977 3222 398874
No 34
>PF13649 Methyltransf_25: Methyltransferase domain; PDB: 3BXO_B 3GGD_A 3PX2_A 3PX3_A 3PFH_D 3PFG_A 1Y8C_A.
Probab=98.19 E-value=2e-06 Score=61.33 Aligned_cols=61 Identities=13% Similarity=0.261 Sum_probs=46.5
Q ss_pred EEEecCCccHHHHHHHHHc---CCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-CCCC--CCEEEe
Q 039903 172 LVDVGGGLGVNVNIIISNY---LHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-RIPK--GDAILI 232 (233)
Q Consensus 172 vvDvGGG~G~~~~~l~~~~---P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~~P~--~D~~~l 232 (233)
|+|+|||+|..+..+++.+ |..+.+.+|+. +.++.+++. .+++++..|+.+ +++. .|+|+.
T Consensus 1 ILDlgcG~G~~~~~l~~~~~~~~~~~~~gvD~s~~~l~~~~~~~~~~~~~~~~~~~D~~~l~~~~~~~D~v~~ 73 (101)
T PF13649_consen 1 ILDLGCGTGRVTRALARRFDAGPSSRVIGVDISPEMLELAKKRFSEDGPKVRFVQADARDLPFSDGKFDLVVC 73 (101)
T ss_dssp -EEET-TTSHHHHHHHHHS-----SEEEEEES-HHHHHHHHHHSHHTTTTSEEEESCTTCHHHHSSSEEEEEE
T ss_pred CEEeecCCcHHHHHHHHHhhhcccceEEEEECCHHHHHHHHHhchhcCCceEEEECCHhHCcccCCCeeEEEE
Confidence 6999999999999999997 66899999984 577776653 489999999987 5444 388875
No 35
>PRK14966 unknown domain/N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase fusion protein; Provisional
Probab=98.19 E-value=4.8e-06 Score=73.63 Aligned_cols=65 Identities=15% Similarity=0.194 Sum_probs=54.2
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCCC-CCC---CCEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLER-IPK---GDAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~~-~P~---~D~~~l 232 (233)
+..+++|||||+|.++..+++++|+.+++.+|+ |++++.++++ .+|+++.+|+++. .|. -|+++.
T Consensus 251 ~~~rVLDLGcGSG~IaiaLA~~~p~a~VtAVDiS~~ALe~AreNa~~~g~rV~fi~gDl~e~~l~~~~~FDLIVS 325 (423)
T PRK14966 251 ENGRVWDLGTGSGAVAVTVALERPDAFVRASDISPPALETARKNAADLGARVEFAHGSWFDTDMPSEGKWDIIVS 325 (423)
T ss_pred CCCEEEEEeChhhHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCcEEEEEcchhccccccCCCccEEEE
Confidence 346899999999999999999999999999999 6688877653 4799999999973 442 288875
No 36
>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=98.19 E-value=8.9e-06 Score=66.22 Aligned_cols=100 Identities=11% Similarity=0.051 Sum_probs=64.5
Q ss_pred ccccccCchHHHHHHHHHHhcchhcHHHHHHhccc-ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhcc
Q 039903 131 YEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKG-FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSS 208 (233)
Q Consensus 131 ~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~-~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~ 208 (233)
|+.+..++.....+...|..........+++.+.. ..+..+++|||||+|.++..+++. ..+++.+|. |+.++.|+
T Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~vLDiGcG~G~~~~~la~~--~~~v~gvD~s~~~i~~a~ 94 (219)
T TIGR02021 17 WARIYGSGDPVSRVRQTVREGRAAMRRKLLDWLPKDPLKGKRVLDAGCGTGLLSIELAKR--GAIVKAVDISEQMVQMAR 94 (219)
T ss_pred HHHhhCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEeCCCCHHHHHHHHC--CCEEEEEECCHHHHHHHH
Confidence 44444444444455555533333333444444331 334689999999999999999886 447899998 55777765
Q ss_pred CC-------CCceEEecCcCCCCCCCCEEEe
Q 039903 209 SY-------SGVKHIGGIMLERIPKGDAILI 232 (233)
Q Consensus 209 ~~-------~ri~~~~gD~f~~~P~~D~~~l 232 (233)
+. +++++..+|+.+....-|+++.
T Consensus 95 ~~~~~~~~~~~i~~~~~d~~~~~~~fD~ii~ 125 (219)
T TIGR02021 95 NRAQGRDVAGNVEFEVNDLLSLCGEFDIVVC 125 (219)
T ss_pred HHHHhcCCCCceEEEECChhhCCCCcCEEEE
Confidence 42 4899999998763233488764
No 37
>PLN02336 phosphoethanolamine N-methyltransferase
Probab=98.17 E-value=6.2e-06 Score=74.89 Aligned_cols=74 Identities=22% Similarity=0.313 Sum_probs=58.0
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-CCCCC--
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-RIPKG-- 227 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~~P~~-- 227 (233)
..+++.+. .++..+|+|||||+|..+..+++++ +.+++.+|+. +.++.|+++ .+|+++.+|+++ ++|.+
T Consensus 256 e~l~~~~~-~~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvDiS~~~l~~A~~~~~~~~~~v~~~~~d~~~~~~~~~~f 333 (475)
T PLN02336 256 KEFVDKLD-LKPGQKVLDVGCGIGGGDFYMAENF-DVHVVGIDLSVNMISFALERAIGRKCSVEFEVADCTKKTYPDNSF 333 (475)
T ss_pred HHHHHhcC-CCCCCEEEEEeccCCHHHHHHHHhc-CCEEEEEECCHHHHHHHHHHhhcCCCceEEEEcCcccCCCCCCCE
Confidence 34555555 5667899999999999999998876 7799999995 567666542 589999999998 67763
Q ss_pred CEEEe
Q 039903 228 DAILI 232 (233)
Q Consensus 228 D~~~l 232 (233)
|+|+.
T Consensus 334 D~I~s 338 (475)
T PLN02336 334 DVIYS 338 (475)
T ss_pred EEEEE
Confidence 98874
No 38
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=98.16 E-value=3.3e-06 Score=77.20 Aligned_cols=64 Identities=19% Similarity=0.243 Sum_probs=54.5
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC--CCEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK--GDAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~--~D~~~l 232 (233)
..+|+|||||+|.+++.+++++|+.+++.+|+ |.+++.|+++ ++|+++.+|+++.++. -|+++.
T Consensus 139 ~~~VLDlG~GsG~iai~la~~~p~~~v~avDis~~al~~A~~N~~~~~l~~~v~~~~~D~~~~~~~~~fDlIvs 212 (506)
T PRK01544 139 FLNILELGTGSGCIAISLLCELPNANVIATDISLDAIEVAKSNAIKYEVTDRIQIIHSNWFENIEKQKFDFIVS 212 (506)
T ss_pred CCEEEEccCchhHHHHHHHHHCCCCeEEEEECCHHHHHHHHHHHHHcCCccceeeeecchhhhCcCCCccEEEE
Confidence 46899999999999999999999999999999 5677777653 5899999999987664 388874
No 39
>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=98.16 E-value=3.8e-06 Score=69.24 Aligned_cols=67 Identities=16% Similarity=0.238 Sum_probs=47.3
Q ss_pred ccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCC--CEEEe
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKG--DAILI 232 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~--D~~~l 232 (233)
.....+|+|||||+|.++..++++. |+.+++++|. ++.++.|++. .+|+++.+|..+ |+|.. |++++
T Consensus 45 ~~~g~~vLDv~~GtG~~~~~l~~~~~~~~~v~~vD~s~~ML~~a~~k~~~~~~~~i~~v~~da~~lp~~d~sfD~v~~ 122 (233)
T PF01209_consen 45 LRPGDRVLDVACGTGDVTRELARRVGPNGKVVGVDISPGMLEVARKKLKREGLQNIEFVQGDAEDLPFPDNSFDAVTC 122 (233)
T ss_dssp --S--EEEEET-TTSHHHHHHGGGSS---EEEEEES-HHHHHHHHHHHHHTT--SEEEEE-BTTB--S-TT-EEEEEE
T ss_pred CCCCCEEEEeCCChHHHHHHHHHHCCCccEEEEecCCHHHHHHHHHHHHhhCCCCeeEEEcCHHHhcCCCCceeEEEH
Confidence 4556799999999999999999875 6789999998 4588877652 589999999999 89874 98875
No 40
>COG2813 RsmC 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]
Probab=98.14 E-value=8.5e-06 Score=68.71 Aligned_cols=74 Identities=14% Similarity=0.183 Sum_probs=58.6
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC------CCceEEecCcCCCCCCC-CE
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY------SGVKHIGGIMLERIPKG-DA 229 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~------~ri~~~~gD~f~~~P~~-D~ 229 (233)
-+++.++ .....+|+|+|||.|.+++.+++.+|+.+.+.+|... +++.++++ ++..+...|.+++...- |+
T Consensus 149 lLl~~l~-~~~~~~vlDlGCG~Gvlg~~la~~~p~~~vtmvDvn~~Av~~ar~Nl~~N~~~~~~v~~s~~~~~v~~kfd~ 227 (300)
T COG2813 149 LLLETLP-PDLGGKVLDLGCGYGVLGLVLAKKSPQAKLTLVDVNARAVESARKNLAANGVENTEVWASNLYEPVEGKFDL 227 (300)
T ss_pred HHHHhCC-ccCCCcEEEeCCCccHHHHHHHHhCCCCeEEEEecCHHHHHHHHHhHHHcCCCccEEEEecccccccccccE
Confidence 4667777 4444599999999999999999999999999999864 88888775 33367788999876653 87
Q ss_pred EEe
Q 039903 230 ILI 232 (233)
Q Consensus 230 ~~l 232 (233)
|+.
T Consensus 228 Iis 230 (300)
T COG2813 228 IIS 230 (300)
T ss_pred EEe
Confidence 764
No 41
>PLN02233 ubiquinone biosynthesis methyltransferase
Probab=98.14 E-value=1e-05 Score=67.85 Aligned_cols=67 Identities=19% Similarity=0.229 Sum_probs=54.2
Q ss_pred ccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeech-HHHhhccC---------CCCceEEecCcCC-CCCCC--CEEE
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLS-HVIQDSSS---------YSGVKHIGGIMLE-RIPKG--DAIL 231 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp-~v~~~a~~---------~~ri~~~~gD~f~-~~P~~--D~~~ 231 (233)
..+..+|+|||||+|.++..+++++ |+.+++.+|.. +.++.|++ .++|+++.+|+.+ |+|.+ |+++
T Consensus 71 ~~~~~~VLDlGcGtG~~~~~la~~~~~~~~V~gvD~S~~ml~~A~~r~~~~~~~~~~~i~~~~~d~~~lp~~~~sfD~V~ 150 (261)
T PLN02233 71 AKMGDRVLDLCCGSGDLAFLLSEKVGSDGKVMGLDFSSEQLAVAASRQELKAKSCYKNIEWIEGDATDLPFDDCYFDAIT 150 (261)
T ss_pred CCCCCEEEEECCcCCHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHhhhhhhccCCCeEEEEcccccCCCCCCCEeEEE
Confidence 4556799999999999999999885 67899999984 57776643 2589999999988 78763 9887
Q ss_pred e
Q 039903 232 I 232 (233)
Q Consensus 232 l 232 (233)
+
T Consensus 151 ~ 151 (261)
T PLN02233 151 M 151 (261)
T ss_pred E
Confidence 5
No 42
>PRK10258 biotin biosynthesis protein BioC; Provisional
Probab=98.13 E-value=1.8e-05 Score=65.80 Aligned_cols=74 Identities=11% Similarity=0.155 Sum_probs=55.5
Q ss_pred HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCC-CCCCC--CEE
Q 039903 156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLE-RIPKG--DAI 230 (233)
Q Consensus 156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~-~~P~~--D~~ 230 (233)
+..+++.++ .....+|+|||||+|.++..+.+. ..+++.+|+ |..++.++.. ..+.++.+|+.+ ++|.. |++
T Consensus 31 a~~l~~~l~-~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~~D~s~~~l~~a~~~~~~~~~~~~d~~~~~~~~~~fD~V 107 (251)
T PRK10258 31 ADALLAMLP-QRKFTHVLDAGCGPGWMSRYWRER--GSQVTALDLSPPMLAQARQKDAADHYLAGDIESLPLATATFDLA 107 (251)
T ss_pred HHHHHHhcC-ccCCCeEEEeeCCCCHHHHHHHHc--CCeEEEEECCHHHHHHHHhhCCCCCEEEcCcccCcCCCCcEEEE
Confidence 344555555 345689999999999999888774 467999999 6688877764 456788999977 66653 888
Q ss_pred Ee
Q 039903 231 LI 232 (233)
Q Consensus 231 ~l 232 (233)
+.
T Consensus 108 ~s 109 (251)
T PRK10258 108 WS 109 (251)
T ss_pred EE
Confidence 63
No 43
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=98.12 E-value=1e-05 Score=68.21 Aligned_cols=64 Identities=19% Similarity=0.251 Sum_probs=52.6
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCC---cEEEeec-hHHHhhccCC-CCceEEecCcCC-CCCCC--CEEE
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHI---KGVNFDL-SHVIQDSSSY-SGVKHIGGIMLE-RIPKG--DAIL 231 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l---~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~-~~P~~--D~~~ 231 (233)
+..+|+|||||+|.++..+++.+|.. +++.+|+ +..++.|++. +++++..+|..+ +++.+ |+|+
T Consensus 85 ~~~~vLDiGcG~G~~~~~l~~~~~~~~~~~v~giD~s~~~l~~A~~~~~~~~~~~~d~~~lp~~~~sfD~I~ 156 (272)
T PRK11088 85 KATALLDIGCGEGYYTHALADALPEITTMQLFGLDISKVAIKYAAKRYPQVTFCVASSHRLPFADQSLDAII 156 (272)
T ss_pred CCCeEEEECCcCCHHHHHHHHhcccccCCeEEEECCCHHHHHHHHHhCCCCeEEEeecccCCCcCCceeEEE
Confidence 44789999999999999999998864 6799998 4577777654 789999999988 77763 8876
No 44
>PRK08317 hypothetical protein; Provisional
Probab=98.12 E-value=1.2e-05 Score=65.73 Aligned_cols=73 Identities=19% Similarity=0.233 Sum_probs=57.1
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-CCCCC--C
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-RIPKG--D 228 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~~P~~--D 228 (233)
+++.++ .....+|||||||.|.++..+++.+ |..+++.+|+. ..++.+++. ++++++.+|+.+ +++.+ |
T Consensus 11 ~~~~~~-~~~~~~vLdiG~G~G~~~~~~a~~~~~~~~v~~~d~~~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~~~~D 89 (241)
T PRK08317 11 TFELLA-VQPGDRVLDVGCGPGNDARELARRVGPEGRVVGIDRSEAMLALAKERAAGLGPNVEFVRGDADGLPFPDGSFD 89 (241)
T ss_pred HHHHcC-CCCCCEEEEeCCCCCHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHHHhhCCCCceEEEecccccCCCCCCCce
Confidence 445555 6677899999999999999999998 78899999985 455555442 679999999887 66653 8
Q ss_pred EEEe
Q 039903 229 AILI 232 (233)
Q Consensus 229 ~~~l 232 (233)
+++.
T Consensus 90 ~v~~ 93 (241)
T PRK08317 90 AVRS 93 (241)
T ss_pred EEEE
Confidence 8775
No 45
>PRK00121 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed
Probab=98.12 E-value=5.6e-06 Score=66.74 Aligned_cols=65 Identities=15% Similarity=0.241 Sum_probs=51.7
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCC--C--CCCC--CEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE--R--IPKG--DAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~--~--~P~~--D~~~l 232 (233)
...+|+|||||+|.++..+++.+|+.+++.+|.. +.++.+++. ++|+++.+|+.+ + ++.+ |++++
T Consensus 40 ~~~~VLDiGcGtG~~~~~la~~~p~~~v~gVD~s~~~i~~a~~~~~~~~~~~v~~~~~d~~~~l~~~~~~~~~D~V~~ 117 (202)
T PRK00121 40 DAPIHLEIGFGKGEFLVEMAKANPDINFIGIEVHEPGVGKALKKIEEEGLTNLRLLCGDAVEVLLDMFPDGSLDRIYL 117 (202)
T ss_pred CCCeEEEEccCCCHHHHHHHHHCCCccEEEEEechHHHHHHHHHHHHcCCCCEEEEecCHHHHHHHHcCccccceEEE
Confidence 4578999999999999999999999999999984 567666532 689999999933 3 4443 77764
No 46
>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=98.12 E-value=9.5e-07 Score=62.63 Aligned_cols=60 Identities=12% Similarity=0.244 Sum_probs=40.2
Q ss_pred EEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---------CCceEEecCcCCCCCC-C-CEEEe
Q 039903 173 VDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---------SGVKHIGGIMLERIPK-G-DAILI 232 (233)
Q Consensus 173 vDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---------~ri~~~~gD~f~~~P~-~-D~~~l 232 (233)
||||||+|.++..+++++|..+.+.+|. |..++.+++. .++++...|.++..+. . |+|++
T Consensus 1 LdiGcG~G~~~~~l~~~~~~~~~~~~D~s~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fD~V~~ 72 (99)
T PF08242_consen 1 LDIGCGTGRLLRALLEELPDARYTGVDISPSMLERARERLAELGNDNFERLRFDVLDLFDYDPPESFDLVVA 72 (99)
T ss_dssp -EESTTTS-TTTTHHHHC-EEEEEEEESSSSTTSTTCCCHHHCT---EEEEE--SSS---CCC----SEEEE
T ss_pred CEeCccChHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHhhhcCCcceeEEEeecCChhhcccccccceehh
Confidence 7999999999999999999999999998 4578777664 2456666666664443 3 98875
No 47
>PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=98.12 E-value=1.4e-05 Score=64.91 Aligned_cols=74 Identities=14% Similarity=0.172 Sum_probs=56.8
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC-CC-
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP-KG- 227 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P-~~- 227 (233)
.+++.++ ..+..+++|||||+|.++..+++.. ++.+++.+|. |+.++.++++ ++|+++.+|.++..| .+
T Consensus 67 ~~~~~l~-~~~g~~VLdIG~GsG~~t~~la~~~~~~~~V~~vE~~~~~~~~a~~~l~~~g~~~v~~~~gd~~~~~~~~~~ 145 (212)
T PRK13942 67 IMCELLD-LKEGMKVLEIGTGSGYHAAVVAEIVGKSGKVVTIERIPELAEKAKKTLKKLGYDNVEVIVGDGTLGYEENAP 145 (212)
T ss_pred HHHHHcC-CCCcCEEEEECCcccHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHHHHHHcCCCCeEEEECCcccCCCcCCC
Confidence 4455555 6777899999999999999988875 4568899997 5577766552 589999999988443 33
Q ss_pred -CEEEe
Q 039903 228 -DAILI 232 (233)
Q Consensus 228 -D~~~l 232 (233)
|+|++
T Consensus 146 fD~I~~ 151 (212)
T PRK13942 146 YDRIYV 151 (212)
T ss_pred cCEEEE
Confidence 99875
No 48
>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=98.11 E-value=7.3e-06 Score=67.03 Aligned_cols=64 Identities=17% Similarity=0.325 Sum_probs=52.6
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--CCceEEecCcCC-CCCCC--CEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--SGVKHIGGIMLE-RIPKG--DAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--~ri~~~~gD~f~-~~P~~--D~~~l 232 (233)
..+|||||||+|.++..+++.+|+.+++.+|.. ..++.++.. ++++++.+|+.+ ++|.. |+++.
T Consensus 35 ~~~vLDlG~G~G~~~~~l~~~~~~~~~~~~D~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~fD~vi~ 104 (240)
T TIGR02072 35 PASVLDIGCGTGYLTRALLKRFPQAEFIALDISAGMLAQAKTKLSENVQFICGDAEKLPLEDSSFDLIVS 104 (240)
T ss_pred CCeEEEECCCccHHHHHHHHhCCCCcEEEEeChHHHHHHHHHhcCCCCeEEecchhhCCCCCCceeEEEE
Confidence 478999999999999999999999999999985 455555543 589999999987 65553 98874
No 49
>TIGR00080 pimt protein-L-isoaspartate(D-aspartate) O-methyltransferase. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt.
Probab=98.11 E-value=1.3e-05 Score=65.19 Aligned_cols=74 Identities=12% Similarity=0.112 Sum_probs=56.8
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC---
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK--- 226 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~--- 226 (233)
.+++.++ .+...+++|||||+|.++..+++..+ +.+++.+|. |+.++.|+++ ++|+++.+|..+..+.
T Consensus 68 ~~~~~l~-~~~~~~VLDiG~GsG~~a~~la~~~~~~g~V~~vD~~~~~~~~A~~~~~~~g~~~v~~~~~d~~~~~~~~~~ 146 (215)
T TIGR00080 68 MMTELLE-LKPGMKVLEIGTGSGYQAAVLAEIVGRDGLVVSIERIPELAEKAERRLRKLGLDNVIVIVGDGTQGWEPLAP 146 (215)
T ss_pred HHHHHhC-CCCcCEEEEECCCccHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHHCCCCCeEEEECCcccCCcccCC
Confidence 4445555 56678999999999999999999865 567899997 5677776542 6799999999874432
Q ss_pred CCEEEe
Q 039903 227 GDAILI 232 (233)
Q Consensus 227 ~D~~~l 232 (233)
-|++++
T Consensus 147 fD~Ii~ 152 (215)
T TIGR00080 147 YDRIYV 152 (215)
T ss_pred CCEEEE
Confidence 398875
No 50
>PRK09328 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=98.11 E-value=1e-05 Score=68.03 Aligned_cols=67 Identities=18% Similarity=0.260 Sum_probs=54.8
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCCCCCC--CCEEEe
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLERIPK--GDAILI 232 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~~~P~--~D~~~l 232 (233)
..+..+++|+|||+|.++..+++.+|..+++.+|.. ..++.++++ .+++++.+|++++++. .|+++.
T Consensus 106 ~~~~~~vLDiG~GsG~~~~~la~~~~~~~v~~iDis~~~l~~a~~n~~~~~~~~i~~~~~d~~~~~~~~~fD~Iv~ 181 (275)
T PRK09328 106 LKEPLRVLDLGTGSGAIALALAKERPDAEVTAVDISPEALAVARRNAKHGLGARVEFLQGDWFEPLPGGRFDLIVS 181 (275)
T ss_pred ccCCCEEEEEcCcHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHhCCCCcEEEEEccccCcCCCCceeEEEE
Confidence 345578999999999999999999999999999985 466666542 5899999999987663 388864
No 51
>PRK07402 precorrin-6B methylase; Provisional
Probab=98.11 E-value=9.9e-06 Score=64.86 Aligned_cols=63 Identities=19% Similarity=0.137 Sum_probs=51.4
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE 222 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~ 222 (233)
+++.++ .....+|+|+|||+|.++..+++..|..+++.+|+ |+.++.++++ ++|+++.+|..+
T Consensus 32 l~~~l~-~~~~~~VLDiG~G~G~~~~~la~~~~~~~V~~vD~s~~~~~~a~~n~~~~~~~~v~~~~~d~~~ 101 (196)
T PRK07402 32 LISQLR-LEPDSVLWDIGAGTGTIPVEAGLLCPKGRVIAIERDEEVVNLIRRNCDRFGVKNVEVIEGSAPE 101 (196)
T ss_pred HHHhcC-CCCCCEEEEeCCCCCHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHHHHHhCCCCeEEEECchHH
Confidence 445554 55668999999999999999999999999999998 6677776542 579999998865
No 52
>smart00650 rADc Ribosomal RNA adenine dimethylases.
Probab=98.11 E-value=1.1e-05 Score=63.04 Aligned_cols=72 Identities=13% Similarity=0.283 Sum_probs=55.4
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC----CCceEEecCcCC-CCCCC--C
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY----SGVKHIGGIMLE-RIPKG--D 228 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~----~ri~~~~gD~f~-~~P~~--D 228 (233)
..+++.++ ..+..+++|||||.|.++..++++ ..+++.+|+.. .++.++++ ++++++.+|+++ +.+.. |
T Consensus 3 ~~i~~~~~-~~~~~~vLEiG~G~G~lt~~l~~~--~~~v~~vE~~~~~~~~~~~~~~~~~~v~ii~~D~~~~~~~~~~~d 79 (169)
T smart00650 3 DKIVRAAN-LRPGDTVLEIGPGKGALTEELLER--AARVTAIEIDPRLAPRLREKFAAADNLTVIHGDALKFDLPKLQPY 79 (169)
T ss_pred HHHHHhcC-CCCcCEEEEECCCccHHHHHHHhc--CCeEEEEECCHHHHHHHHHHhccCCCEEEEECchhcCCccccCCC
Confidence 34556665 666789999999999999999998 46789999864 66655442 689999999998 66652 7
Q ss_pred EEE
Q 039903 229 AIL 231 (233)
Q Consensus 229 ~~~ 231 (233)
.++
T Consensus 80 ~vi 82 (169)
T smart00650 80 KVV 82 (169)
T ss_pred EEE
Confidence 665
No 53
>PRK14121 tRNA (guanine-N(7)-)-methyltransferase; Provisional
Probab=98.11 E-value=8.8e-06 Score=71.44 Aligned_cols=73 Identities=18% Similarity=0.192 Sum_probs=54.4
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC------CCCceEEecCcC---CCCCCC-
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS------YSGVKHIGGIML---ERIPKG- 227 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~------~~ri~~~~gD~f---~~~P~~- 227 (233)
+++.+. -.....+||||||+|.++..+++++|+..++++|+. ..++.+.. .++|.++.+|.. +.+|.+
T Consensus 114 ~~~~~~-~~~~p~vLEIGcGsG~~ll~lA~~~P~~~~iGIEI~~~~i~~a~~ka~~~gL~NV~~i~~DA~~ll~~~~~~s 192 (390)
T PRK14121 114 FLDFIS-KNQEKILIEIGFGSGRHLLYQAKNNPNKLFIGIEIHTPSIEQVLKQIELLNLKNLLIINYDARLLLELLPSNS 192 (390)
T ss_pred HHHHhc-CCCCCeEEEEcCcccHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCCcEEEEECCHHHhhhhCCCCc
Confidence 444443 233468999999999999999999999999999984 45554432 268999999974 356654
Q ss_pred -CEEEe
Q 039903 228 -DAILI 232 (233)
Q Consensus 228 -D~~~l 232 (233)
|.+++
T Consensus 193 ~D~I~l 198 (390)
T PRK14121 193 VEKIFV 198 (390)
T ss_pred eeEEEE
Confidence 77764
No 54
>PRK00216 ubiE ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed
Probab=98.10 E-value=1.6e-05 Score=65.04 Aligned_cols=74 Identities=18% Similarity=0.180 Sum_probs=56.5
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCC-CCCCC
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLE-RIPKG 227 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~-~~P~~ 227 (233)
.+++.+. ..+..+|+|||||.|.++..+++.+| +.+++++|+. ..++.+++. .+++++.+|+.+ +.+.+
T Consensus 42 ~~~~~~~-~~~~~~vldiG~G~G~~~~~l~~~~~~~~~v~~~D~s~~~~~~a~~~~~~~~~~~~~~~~~~d~~~~~~~~~ 120 (239)
T PRK00216 42 KTIKWLG-VRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFSEGMLAVGREKLRDLGLSGNVEFVQGDAEALPFPDN 120 (239)
T ss_pred HHHHHhC-CCCCCeEEEeCCCCCHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHhhcccccccCeEEEecccccCCCCCC
Confidence 3444444 44557999999999999999999998 7899999984 466665542 579999999987 55443
Q ss_pred --CEEEe
Q 039903 228 --DAILI 232 (233)
Q Consensus 228 --D~~~l 232 (233)
|+|++
T Consensus 121 ~~D~I~~ 127 (239)
T PRK00216 121 SFDAVTI 127 (239)
T ss_pred CccEEEE
Confidence 88864
No 55
>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=98.09 E-value=8e-06 Score=56.67 Aligned_cols=59 Identities=19% Similarity=0.317 Sum_probs=47.2
Q ss_pred EEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC---CCceEEecCcCC-CCCCC--CEEEe
Q 039903 173 VDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY---SGVKHIGGIMLE-RIPKG--DAILI 232 (233)
Q Consensus 173 vDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~---~ri~~~~gD~f~-~~P~~--D~~~l 232 (233)
||||||.|..+..++++ |..+++.+|..+ .++.+++. .+++++.+|+.+ ++|.. |+++.
T Consensus 1 LdiG~G~G~~~~~l~~~-~~~~v~~~D~~~~~~~~~~~~~~~~~~~~~~~d~~~l~~~~~sfD~v~~ 66 (95)
T PF08241_consen 1 LDIGCGTGRFAAALAKR-GGASVTGIDISEEMLEQARKRLKNEGVSFRQGDAEDLPFPDNSFDVVFS 66 (95)
T ss_dssp EEET-TTSHHHHHHHHT-TTCEEEEEES-HHHHHHHHHHTTTSTEEEEESBTTSSSS-TT-EEEEEE
T ss_pred CEecCcCCHHHHHHHhc-cCCEEEEEeCCHHHHHHHHhcccccCchheeehHHhCcccccccccccc
Confidence 79999999999999999 999999999854 57766652 567899999998 88874 88874
No 56
>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=98.09 E-value=1.1e-05 Score=67.28 Aligned_cols=64 Identities=16% Similarity=0.145 Sum_probs=52.9
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---CCceEEecCcCCCCC----C-CCEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---SGVKHIGGIMLERIP----K-GDAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---~ri~~~~gD~f~~~P----~-~D~~~l 232 (233)
..+++|+|||+|.++..+++++|..+++.+|. |.+++.++++ .+++++.+|+++.++ . -|+++.
T Consensus 87 ~~~vLDlg~GsG~i~l~la~~~~~~~v~~vDis~~al~~A~~N~~~~~~~~~~~D~~~~l~~~~~~~fDlVv~ 159 (251)
T TIGR03704 87 TLVVVDLCCGSGAVGAALAAALDGIELHAADIDPAAVRCARRNLADAGGTVHEGDLYDALPTALRGRVDILAA 159 (251)
T ss_pred CCEEEEecCchHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCEEEEeechhhcchhcCCCEeEEEE
Confidence 45899999999999999999999999999998 6788877764 347899999987554 2 288774
No 57
>PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional
Probab=98.08 E-value=1.3e-05 Score=69.66 Aligned_cols=73 Identities=18% Similarity=0.216 Sum_probs=55.1
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCCCCCCC-CEEE
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLERIPKG-DAIL 231 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~~~P~~-D~~~ 231 (233)
+++.++ -....+|+|+|||.|.++..+++++|+.+++.+|.. .+++.++.+ -..+++.+|.++..+.. |+|+
T Consensus 188 Ll~~l~-~~~~g~VLDlGCG~G~ls~~la~~~p~~~v~~vDis~~Al~~A~~nl~~n~l~~~~~~~D~~~~~~~~fDlIv 266 (342)
T PRK09489 188 LLSTLT-PHTKGKVLDVGCGAGVLSAVLARHSPKIRLTLSDVSAAALESSRATLAANGLEGEVFASNVFSDIKGRFDMII 266 (342)
T ss_pred HHHhcc-ccCCCeEEEeccCcCHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCCCEEEEcccccccCCCccEEE
Confidence 344444 223358999999999999999999999999999985 477766542 24567889998865554 9887
Q ss_pred e
Q 039903 232 I 232 (233)
Q Consensus 232 l 232 (233)
.
T Consensus 267 s 267 (342)
T PRK09489 267 S 267 (342)
T ss_pred E
Confidence 4
No 58
>PRK13944 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=98.07 E-value=1.8e-05 Score=63.98 Aligned_cols=73 Identities=15% Similarity=0.125 Sum_probs=54.4
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCCC---
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIPK--- 226 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P~--- 226 (233)
+++.++ .....+++|||||+|.++..+++..+ .-+++.+|.. +.++.++++ ++++++.+|+.+.+|.
T Consensus 64 ~~~~l~-~~~~~~VLDiG~GsG~~~~~la~~~~~~g~V~~iD~~~~~~~~a~~~l~~~~~~~~v~~~~~d~~~~~~~~~~ 142 (205)
T PRK13944 64 MCELIE-PRPGMKILEVGTGSGYQAAVCAEAIERRGKVYTVEIVKELAIYAAQNIERLGYWGVVEVYHGDGKRGLEKHAP 142 (205)
T ss_pred HHHhcC-CCCCCEEEEECcCccHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHHHHHHcCCCCcEEEEECCcccCCccCCC
Confidence 444444 45567999999999999999998865 5678999984 566666542 4699999999885543
Q ss_pred CCEEEe
Q 039903 227 GDAILI 232 (233)
Q Consensus 227 ~D~~~l 232 (233)
.|++++
T Consensus 143 fD~Ii~ 148 (205)
T PRK13944 143 FDAIIV 148 (205)
T ss_pred ccEEEE
Confidence 298875
No 59
>PRK11036 putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=98.06 E-value=1.2e-05 Score=67.02 Aligned_cols=71 Identities=20% Similarity=0.253 Sum_probs=53.3
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC--CCCC-
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE--RIPK- 226 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~--~~P~- 226 (233)
.+++.++ ++..+|+|||||+|.++..+++. ..+++.+|+ |+.++.|++. ++++++.+|+.+ +++.
T Consensus 36 ~~l~~l~--~~~~~vLDiGcG~G~~a~~la~~--g~~v~~vD~s~~~l~~a~~~~~~~g~~~~v~~~~~d~~~l~~~~~~ 111 (255)
T PRK11036 36 RLLAELP--PRPLRVLDAGGGEGQTAIKLAEL--GHQVILCDLSAEMIQRAKQAAEAKGVSDNMQFIHCAAQDIAQHLET 111 (255)
T ss_pred HHHHhcC--CCCCEEEEeCCCchHHHHHHHHc--CCEEEEEECCHHHHHHHHHHHHhcCCccceEEEEcCHHHHhhhcCC
Confidence 3444443 44579999999999999999987 467899998 5677777642 579999999976 3443
Q ss_pred -CCEEEe
Q 039903 227 -GDAILI 232 (233)
Q Consensus 227 -~D~~~l 232 (233)
.|++++
T Consensus 112 ~fD~V~~ 118 (255)
T PRK11036 112 PVDLILF 118 (255)
T ss_pred CCCEEEe
Confidence 398875
No 60
>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=98.06 E-value=1.6e-05 Score=64.37 Aligned_cols=74 Identities=16% Similarity=0.129 Sum_probs=57.0
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHcCC-CcEEEeec-hHHHhhccCC----CCceEEecCcCC-CCCCC--C
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDL-SHVIQDSSSY----SGVKHIGGIMLE-RIPKG--D 228 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~v~~~a~~~----~ri~~~~gD~f~-~~P~~--D 228 (233)
.+++... ..+..+|+|+|||.|.++..+++++|. .+++++|. |..++.+++. ++++++.+|+.+ +++.+ |
T Consensus 30 ~~~~~~~-~~~~~~vldiG~G~G~~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~~~~i~~~~~d~~~~~~~~~~~D 108 (223)
T TIGR01934 30 RAVKLIG-VFKGQKVLDVACGTGDLAIELAKSAPDRGKVTGVDFSSEMLEVAKKKSELPLNIEFIQADAEALPFEDNSFD 108 (223)
T ss_pred HHHHHhc-cCCCCeEEEeCCCCChhHHHHHHhcCCCceEEEEECCHHHHHHHHHHhccCCCceEEecchhcCCCCCCcEE
Confidence 3444444 446689999999999999999999997 88999998 4566666542 579999999998 55543 8
Q ss_pred EEEe
Q 039903 229 AILI 232 (233)
Q Consensus 229 ~~~l 232 (233)
++++
T Consensus 109 ~i~~ 112 (223)
T TIGR01934 109 AVTI 112 (223)
T ss_pred EEEE
Confidence 8764
No 61
>PLN02490 MPBQ/MSBQ methyltransferase
Probab=98.03 E-value=1.8e-05 Score=68.64 Aligned_cols=65 Identities=23% Similarity=0.278 Sum_probs=54.1
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---CCceEEecCcCC-CCCCC--CEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---SGVKHIGGIMLE-RIPKG--DAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---~ri~~~~gD~f~-~~P~~--D~~~l 232 (233)
...+|||||||+|.++..+++.+|..+++++|+ ++.++.+++. .+++++.+|+.+ +++.+ |+|+.
T Consensus 113 ~~~~VLDLGcGtG~~~l~La~~~~~~~VtgVD~S~~mL~~A~~k~~~~~i~~i~gD~e~lp~~~~sFDvVIs 184 (340)
T PLN02490 113 RNLKVVDVGGGTGFTTLGIVKHVDAKNVTILDQSPHQLAKAKQKEPLKECKIIEGDAEDLPFPTDYADRYVS 184 (340)
T ss_pred CCCEEEEEecCCcHHHHHHHHHCCCCEEEEEECCHHHHHHHHHhhhccCCeEEeccHHhCCCCCCceeEEEE
Confidence 346899999999999999999999899999998 5567777653 579999999987 67653 98874
No 62
>PLN03075 nicotianamine synthase; Provisional
Probab=98.02 E-value=1.9e-05 Score=67.00 Aligned_cols=66 Identities=12% Similarity=0.081 Sum_probs=50.5
Q ss_pred cCcceEEEecCCccHH--HHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEEecCcCCCCC--CC-CEEEe
Q 039903 167 EQIKQLVDVGGGLGVN--VNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHIGGIMLERIP--KG-DAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~--~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~gD~f~~~P--~~-D~~~l 232 (233)
.+.++|+|||||.|-+ ...+++.+|+.+++.+|.. +.++.|++. +||+|+.+|..+..+ .. |+|++
T Consensus 122 ~~p~~VldIGcGpgpltaiilaa~~~p~~~~~giD~d~~ai~~Ar~~~~~~~gL~~rV~F~~~Da~~~~~~l~~FDlVF~ 201 (296)
T PLN03075 122 GVPTKVAFVGSGPLPLTSIVLAKHHLPTTSFHNFDIDPSANDVARRLVSSDPDLSKRMFFHTADVMDVTESLKEYDVVFL 201 (296)
T ss_pred CCCCEEEEECCCCcHHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHHHhhhccCccCCcEEEECchhhcccccCCcCEEEE
Confidence 4779999999998854 3334457899999999984 577666542 689999999998433 23 99986
No 63
>smart00138 MeTrc Methyltransferase, chemotaxis proteins. Methylates methyl-accepting chemotaxis proteins to form gamma-glutamyl methyl ester residues.
Probab=98.02 E-value=8.4e-05 Score=62.42 Aligned_cols=66 Identities=15% Similarity=0.215 Sum_probs=50.4
Q ss_pred cCcceEEEecCCccH----HHHHHHHHcC-----CCcEEEeech-HHHhhccCC--------------------------
Q 039903 167 EQIKQLVDVGGGLGV----NVNIIISNYL-----HIKGVNFDLS-HVIQDSSSY-------------------------- 210 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~----~~~~l~~~~P-----~l~~~v~Dlp-~v~~~a~~~-------------------------- 210 (233)
.+..+|+|+|||+|. +++.+++.+| +.+++..|+. ++++.|++.
T Consensus 98 ~~~~ri~d~GCgtGee~YslA~~l~e~~~~~~~~~~~I~g~Dis~~~L~~Ar~~~y~~~~~~~~~~~~~~~yf~~~~~~~ 177 (264)
T smart00138 98 GRRVRIWSAGCSTGEEPYSLAMLLAETLPKAREPDVKILATDIDLKALEKARAGIYPERELEDLPKALLARYFSRVEDKY 177 (264)
T ss_pred CCCEEEEeccccCChHHHHHHHHHHHHhhhcCCCCeEEEEEECCHHHHHHHHcCCCCHHHHhcCCHHHHhhhEEeCCCeE
Confidence 445799999999996 5666777765 5789999985 578877652
Q ss_pred -------CCceEEecCcCC-CCCCC--CEEEe
Q 039903 211 -------SGVKHIGGIMLE-RIPKG--DAILI 232 (233)
Q Consensus 211 -------~ri~~~~gD~f~-~~P~~--D~~~l 232 (233)
++|+|..+|+.+ +.|.+ |+|+.
T Consensus 178 ~v~~~ir~~V~F~~~dl~~~~~~~~~fD~I~c 209 (264)
T smart00138 178 RVKPELKERVRFAKHNLLAESPPLGDFDLIFC 209 (264)
T ss_pred EEChHHhCcCEEeeccCCCCCCccCCCCEEEe
Confidence 379999999999 44443 99875
No 64
>PRK06202 hypothetical protein; Provisional
Probab=98.02 E-value=4e-05 Score=62.95 Aligned_cols=66 Identities=17% Similarity=0.107 Sum_probs=47.3
Q ss_pred cCcceEEEecCCccHHHHHHHHH----cCCCcEEEeec-hHHHhhccCC---CCceEEecCcCC-CCCC--CCEEEe
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISN----YLHIKGVNFDL-SHVIQDSSSY---SGVKHIGGIMLE-RIPK--GDAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~----~P~l~~~v~Dl-p~v~~~a~~~---~ri~~~~gD~f~-~~P~--~D~~~l 232 (233)
.+..+|+|||||+|.++..|++. .|+.+++.+|+ |+.++.+++. .++++..+|.-. +.+. .|+++.
T Consensus 59 ~~~~~iLDlGcG~G~~~~~L~~~~~~~g~~~~v~gvD~s~~~l~~a~~~~~~~~~~~~~~~~~~l~~~~~~fD~V~~ 135 (232)
T PRK06202 59 DRPLTLLDIGCGGGDLAIDLARWARRDGLRLEVTAIDPDPRAVAFARANPRRPGVTFRQAVSDELVAEGERFDVVTS 135 (232)
T ss_pred CCCcEEEEeccCCCHHHHHHHHHHHhCCCCcEEEEEcCCHHHHHHHHhccccCCCeEEEEecccccccCCCccEEEE
Confidence 45689999999999998888764 46789999998 5688877654 456665554322 2233 388875
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=98.01 E-value=7.4e-06 Score=59.62 Aligned_cols=62 Identities=19% Similarity=0.296 Sum_probs=51.2
Q ss_pred ceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCC-C--CCCC--CEEEe
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLE-R--IPKG--DAILI 232 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~-~--~P~~--D~~~l 232 (233)
.+|+|+|||+|.++..+++.. ..+++.+|+. ..++.++.+ +|++++.+|+++ . ++.. |+|+.
T Consensus 2 ~~vlD~~~G~G~~~~~~~~~~-~~~~~gvdi~~~~~~~a~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~D~Iv~ 76 (117)
T PF13659_consen 2 DRVLDPGCGSGTFLLAALRRG-AARVTGVDIDPEAVELARRNLPRNGLDDRVEVIVGDARDLPEPLPDGKFDLIVT 76 (117)
T ss_dssp EEEEEETSTTCHHHHHHHHHC-TCEEEEEESSHHHHHHHHHHCHHCTTTTTEEEEESHHHHHHHTCTTT-EEEEEE
T ss_pred CEEEEcCcchHHHHHHHHHHC-CCeEEEEEECHHHHHHHHHHHHHccCCceEEEEECchhhchhhccCceeEEEEE
Confidence 579999999999999999998 8899999984 566766542 689999999997 3 5543 88875
No 66
>COG4123 Predicted O-methyltransferase [General function prediction only]
Probab=98.00 E-value=1e-05 Score=66.78 Aligned_cols=74 Identities=14% Similarity=0.180 Sum_probs=57.5
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC-------CCceEEecCcCC---CCCCC
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY-------SGVKHIGGIMLE---RIPKG 227 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~-------~ri~~~~gD~f~---~~P~~ 227 (233)
++..+.......+|+|+|+|.|..+..+++++++.+++.+|+.+ .++.|+++ +||+++..|+-+ ..+.+
T Consensus 35 LL~~~~~~~~~~~IlDlGaG~G~l~L~la~r~~~a~I~~VEiq~~~a~~A~~nv~ln~l~~ri~v~~~Di~~~~~~~~~~ 114 (248)
T COG4123 35 LLAAFAPVPKKGRILDLGAGNGALGLLLAQRTEKAKIVGVEIQEEAAEMAQRNVALNPLEERIQVIEADIKEFLKALVFA 114 (248)
T ss_pred HHHhhcccccCCeEEEecCCcCHHHHHHhccCCCCcEEEEEeCHHHHHHHHHHHHhCcchhceeEehhhHHHhhhccccc
Confidence 33443313447999999999999999999999999999999964 66677653 899999999987 23333
Q ss_pred --CEEEe
Q 039903 228 --DAILI 232 (233)
Q Consensus 228 --D~~~l 232 (233)
|+|+.
T Consensus 115 ~fD~Ii~ 121 (248)
T COG4123 115 SFDLIIC 121 (248)
T ss_pred ccCEEEe
Confidence 78764
No 67
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=98.00 E-value=2.2e-05 Score=65.74 Aligned_cols=72 Identities=17% Similarity=0.267 Sum_probs=54.8
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC----CCCceEEecCcCC-CCCCCCEE
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS----YSGVKHIGGIMLE-RIPKGDAI 230 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~~ri~~~~gD~f~-~~P~~D~~ 230 (233)
..+++.++ ..+..+++|||||.|.++..++++. .+++++|+. ..++.+++ .++|+++.+|+++ ++|..|.+
T Consensus 19 ~~iv~~~~-~~~~~~VLEIG~G~G~lt~~L~~~~--~~v~~vEid~~~~~~l~~~~~~~~~v~ii~~D~~~~~~~~~d~V 95 (258)
T PRK14896 19 DRIVEYAE-DTDGDPVLEIGPGKGALTDELAKRA--KKVYAIELDPRLAEFLRDDEIAAGNVEIIEGDALKVDLPEFNKV 95 (258)
T ss_pred HHHHHhcC-CCCcCeEEEEeCccCHHHHHHHHhC--CEEEEEECCHHHHHHHHHHhccCCCEEEEEeccccCCchhceEE
Confidence 44555555 5566899999999999999999984 478999986 45655543 3689999999998 66665665
Q ss_pred E
Q 039903 231 L 231 (233)
Q Consensus 231 ~ 231 (233)
+
T Consensus 96 v 96 (258)
T PRK14896 96 V 96 (258)
T ss_pred E
Confidence 4
No 68
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=97.98 E-value=2.1e-05 Score=66.37 Aligned_cols=66 Identities=15% Similarity=0.286 Sum_probs=51.7
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC---CCceEEecCcCC-CCC
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY---SGVKHIGGIMLE-RIP 225 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~---~ri~~~~gD~f~-~~P 225 (233)
..+++.++ .....+|+|||||+|.++..++++.+ +++.+|.. ..++.+++. ++++++.+|+.+ +++
T Consensus 32 ~~i~~~l~-~~~~~~VLEiG~G~G~lt~~L~~~~~--~v~avE~d~~~~~~~~~~~~~~~v~~i~~D~~~~~~~ 102 (272)
T PRK00274 32 DKIVDAAG-PQPGDNVLEIGPGLGALTEPLLERAA--KVTAVEIDRDLAPILAETFAEDNLTIIEGDALKVDLS 102 (272)
T ss_pred HHHHHhcC-CCCcCeEEEeCCCccHHHHHHHHhCC--cEEEEECCHHHHHHHHHhhccCceEEEEChhhcCCHH
Confidence 34555555 66668999999999999999999987 78889884 466666543 689999999987 544
No 69
>PHA03411 putative methyltransferase; Provisional
Probab=97.97 E-value=2.1e-05 Score=65.86 Aligned_cols=64 Identities=14% Similarity=0.124 Sum_probs=53.1
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCCCC-CC-CCEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLERI-PK-GDAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~~~-P~-~D~~~l 232 (233)
..+|+|+|||+|.++..++++.+..+++.+|+ |..++.++++ ++++++.+|+++.. +. -|+|+.
T Consensus 65 ~grVLDLGcGsGilsl~la~r~~~~~V~gVDisp~al~~Ar~n~~~v~~v~~D~~e~~~~~kFDlIIs 132 (279)
T PHA03411 65 TGKVLDLCAGIGRLSFCMLHRCKPEKIVCVELNPEFARIGKRLLPEAEWITSDVFEFESNEKFDVVIS 132 (279)
T ss_pred CCeEEEcCCCCCHHHHHHHHhCCCCEEEEEECCHHHHHHHHHhCcCCEEEECchhhhcccCCCcEEEE
Confidence 46899999999999999999988889999998 4577777764 78999999999843 33 388875
No 70
>PLN02366 spermidine synthase
Probab=97.96 E-value=1.6e-05 Score=68.20 Aligned_cols=65 Identities=26% Similarity=0.288 Sum_probs=51.6
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCC-CcEEEeechH-HHhhccCC----------CCceEEecCcCC---CCCC-C-CE
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDLSH-VIQDSSSY----------SGVKHIGGIMLE---RIPK-G-DA 229 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dlp~-v~~~a~~~----------~ri~~~~gD~f~---~~P~-~-D~ 229 (233)
++.++||+||||.|..+.++++. |. .+++++|+.+ |++.++++ +|++++.+|.++ ..|. . |+
T Consensus 90 ~~pkrVLiIGgG~G~~~rellk~-~~v~~V~~VEiD~~Vi~~ar~~f~~~~~~~~dpRv~vi~~Da~~~l~~~~~~~yDv 168 (308)
T PLN02366 90 PNPKKVLVVGGGDGGVLREIARH-SSVEQIDICEIDKMVIDVSKKFFPDLAVGFDDPRVNLHIGDGVEFLKNAPEGTYDA 168 (308)
T ss_pred CCCCeEEEEcCCccHHHHHHHhC-CCCCeEEEEECCHHHHHHHHHhhhhhccccCCCceEEEEChHHHHHhhccCCCCCE
Confidence 56789999999999999999865 65 5789999865 78877652 699999999764 4444 3 99
Q ss_pred EEe
Q 039903 230 ILI 232 (233)
Q Consensus 230 ~~l 232 (233)
|++
T Consensus 169 Ii~ 171 (308)
T PLN02366 169 IIV 171 (308)
T ss_pred EEE
Confidence 875
No 71
>KOG1540 consensus Ubiquinone biosynthesis methyltransferase COQ5 [Coenzyme transport and metabolism]
Probab=97.92 E-value=6.7e-05 Score=61.67 Aligned_cols=64 Identities=23% Similarity=0.262 Sum_probs=54.9
Q ss_pred cceEEEecCCccHHHHHHHHHcCC------CcEEEeec-hHHHhhccCC---------CCceEEecCcCC-CCCCC--CE
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLH------IKGVNFDL-SHVIQDSSSY---------SGVKHIGGIMLE-RIPKG--DA 229 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~------l~~~v~Dl-p~v~~~a~~~---------~ri~~~~gD~f~-~~P~~--D~ 229 (233)
.-++|||+||+|..+-.+++.-+. -+++++|+ |+.++.+++. .|+.++.+|.-+ |+|.. |.
T Consensus 101 ~m~~lDvaGGTGDiaFril~~v~s~~~~~~~~V~v~Dinp~mL~vgkqRa~~~~l~~~~~~~w~~~dAE~LpFdd~s~D~ 180 (296)
T KOG1540|consen 101 GMKVLDVAGGTGDIAFRILRHVKSQFGDRESKVTVLDINPHMLAVGKQRAKKRPLKASSRVEWVEGDAEDLPFDDDSFDA 180 (296)
T ss_pred CCeEEEecCCcchhHHHHHHhhccccCCCCceEEEEeCCHHHHHHHHHHHhhcCCCcCCceEEEeCCcccCCCCCCccee
Confidence 378999999999999999999888 78999998 6777766542 469999999999 99984 99
Q ss_pred EEe
Q 039903 230 ILI 232 (233)
Q Consensus 230 ~~l 232 (233)
|.+
T Consensus 181 yTi 183 (296)
T KOG1540|consen 181 YTI 183 (296)
T ss_pred EEE
Confidence 986
No 72
>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=97.89 E-value=3.7e-05 Score=60.61 Aligned_cols=63 Identities=13% Similarity=0.207 Sum_probs=49.8
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCCCCCC-CCEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLERIPK-GDAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~~~P~-~D~~~l 232 (233)
+..+++|+|||+|.++..+++..+ +++.+|+ |..++.++.+ -+++++.+|+++..+. .|+++.
T Consensus 19 ~~~~vLdlG~G~G~~~~~l~~~~~--~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~fD~Vi~ 88 (179)
T TIGR00537 19 KPDDVLEIGAGTGLVAIRLKGKGK--CILTTDINPFAVKELRENAKLNNVGLDVVMTDLFKGVRGKFDVILF 88 (179)
T ss_pred CCCeEEEeCCChhHHHHHHHhcCC--EEEEEECCHHHHHHHHHHHHHcCCceEEEEcccccccCCcccEEEE
Confidence 346899999999999999999887 7999998 5677766553 3688899999884443 488874
No 73
>PRK07580 Mg-protoporphyrin IX methyl transferase; Validated
Probab=97.87 E-value=4.7e-05 Score=62.15 Aligned_cols=63 Identities=17% Similarity=0.196 Sum_probs=47.4
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC-CCEEEe
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK-GDAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~-~D~~~l 232 (233)
.+..+|+|||||+|.++..++++.+ +++.+|+ +..++.+++. ++|+++.+| ++..+. -|+++.
T Consensus 62 ~~~~~vLDvGcG~G~~~~~l~~~~~--~v~~~D~s~~~i~~a~~~~~~~~~~~~i~~~~~d-~~~~~~~fD~v~~ 133 (230)
T PRK07580 62 LTGLRILDAGCGVGSLSIPLARRGA--KVVASDISPQMVEEARERAPEAGLAGNITFEVGD-LESLLGRFDTVVC 133 (230)
T ss_pred CCCCEEEEEeCCCCHHHHHHHHcCC--EEEEEECCHHHHHHHHHHHHhcCCccCcEEEEcC-chhccCCcCEEEE
Confidence 4557999999999999999998765 4999998 4577766542 489999999 443233 387763
No 74
>PRK00811 spermidine synthase; Provisional
Probab=97.85 E-value=2.4e-05 Score=66.32 Aligned_cols=66 Identities=17% Similarity=0.236 Sum_probs=52.0
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC-----------CCCceEEecCcCCCC--CC-C-CEE
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS-----------YSGVKHIGGIMLERI--PK-G-DAI 230 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~-----------~~ri~~~~gD~f~~~--P~-~-D~~ 230 (233)
++.++|+|||||.|..+..+++..+..+++++|+ |.+++.+++ .+||+++.+|.++-+ +. . |+|
T Consensus 75 ~~p~~VL~iG~G~G~~~~~~l~~~~~~~V~~VEid~~vv~~a~~~~~~~~~~~~~d~rv~v~~~Da~~~l~~~~~~yDvI 154 (283)
T PRK00811 75 PNPKRVLIIGGGDGGTLREVLKHPSVEKITLVEIDERVVEVCRKYLPEIAGGAYDDPRVELVIGDGIKFVAETENSFDVI 154 (283)
T ss_pred CCCCEEEEEecCchHHHHHHHcCCCCCEEEEEeCCHHHHHHHHHHhHHhccccccCCceEEEECchHHHHhhCCCcccEE
Confidence 4568999999999999999997645568999998 457777764 268999999988722 33 3 998
Q ss_pred Ee
Q 039903 231 LI 232 (233)
Q Consensus 231 ~l 232 (233)
++
T Consensus 155 i~ 156 (283)
T PRK00811 155 IV 156 (283)
T ss_pred EE
Confidence 75
No 75
>PRK05785 hypothetical protein; Provisional
Probab=97.85 E-value=3.8e-05 Score=63.04 Aligned_cols=62 Identities=15% Similarity=0.180 Sum_probs=50.1
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCC-CCCCC--CEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLE-RIPKG--DAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~-~~P~~--D~~~l 232 (233)
...+|+|||||+|.++..+++++ +.+++.+|. ++.++.|++. ..++.+|+.+ |+|.. |+++.
T Consensus 51 ~~~~VLDlGcGtG~~~~~l~~~~-~~~v~gvD~S~~Ml~~a~~~--~~~~~~d~~~lp~~d~sfD~v~~ 116 (226)
T PRK05785 51 RPKKVLDVAAGKGELSYHFKKVF-KYYVVALDYAENMLKMNLVA--DDKVVGSFEALPFRDKSFDVVMS 116 (226)
T ss_pred CCCeEEEEcCCCCHHHHHHHHhc-CCEEEEECCCHHHHHHHHhc--cceEEechhhCCCCCCCEEEEEe
Confidence 35799999999999999999987 678999998 5688877653 3567888887 77764 98874
No 76
>PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional
Probab=97.82 E-value=0.0001 Score=59.75 Aligned_cols=60 Identities=20% Similarity=0.234 Sum_probs=46.2
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeechHHHhhccCCCCceEEecCcCC
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE 222 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~ 222 (233)
+.+.+..+++..+|||||||+|.++..++++. |..+++.+|+.+. ...++|+++.+|+.+
T Consensus 42 ~~~~~~~~~~~~~VLDlG~GtG~~t~~l~~~~~~~~~V~aVDi~~~----~~~~~v~~i~~D~~~ 102 (209)
T PRK11188 42 IQQSDKLFKPGMTVVDLGAAPGGWSQYAVTQIGDKGRVIACDILPM----DPIVGVDFLQGDFRD 102 (209)
T ss_pred HHHHhccCCCCCEEEEEcccCCHHHHHHHHHcCCCceEEEEecccc----cCCCCcEEEecCCCC
Confidence 33444424566799999999999999999987 4578999998662 223579999999987
No 77
>TIGR00477 tehB tellurite resistance protein TehB. Part of a tellurite-reducing operon tehA and tehB
Probab=97.81 E-value=9.6e-05 Score=59.20 Aligned_cols=73 Identities=14% Similarity=0.074 Sum_probs=51.6
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-CCCCC-C
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-RIPKG-D 228 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~~P~~-D 228 (233)
..+++.++ .....+++|||||+|.++..++++ ..+++.+|+. ..++.+++. -++++..+|+.. +++.. |
T Consensus 20 ~~l~~~~~-~~~~~~vLDiGcG~G~~a~~la~~--g~~V~~iD~s~~~l~~a~~~~~~~~~~v~~~~~d~~~~~~~~~fD 96 (195)
T TIGR00477 20 SAVREAVK-TVAPCKTLDLGCGQGRNSLYLSLA--GYDVRAWDHNPASIASVLDMKARENLPLRTDAYDINAAALNEDYD 96 (195)
T ss_pred HHHHHHhc-cCCCCcEEEeCCCCCHHHHHHHHC--CCeEEEEECCHHHHHHHHHHHHHhCCCceeEeccchhccccCCCC
Confidence 34555555 445679999999999999999986 5689999984 466655431 247777888765 44443 8
Q ss_pred EEEe
Q 039903 229 AILI 232 (233)
Q Consensus 229 ~~~l 232 (233)
+++.
T Consensus 97 ~I~~ 100 (195)
T TIGR00477 97 FIFS 100 (195)
T ss_pred EEEE
Confidence 8763
No 78
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=97.81 E-value=6.3e-05 Score=62.72 Aligned_cols=69 Identities=14% Similarity=0.305 Sum_probs=52.7
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC----CCCceEEecCcCC-CCCCCC
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS----YSGVKHIGGIMLE-RIPKGD 228 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~~ri~~~~gD~f~-~~P~~D 228 (233)
..+++.++ ..+..+|+|||||.|.++..++++.+. ++.+|.. ..++.++. .++++++.+|+.+ +++..|
T Consensus 19 ~~i~~~~~-~~~~~~VLEiG~G~G~lt~~L~~~~~~--v~~iE~d~~~~~~l~~~~~~~~~v~v~~~D~~~~~~~~~d 93 (253)
T TIGR00755 19 QKIVEAAN-VLEGDVVLEIGPGLGALTEPLLKRAKK--VTAIEIDPRLAEILRKLLSLYERLEVIEGDALKVDLPDFP 93 (253)
T ss_pred HHHHHhcC-CCCcCEEEEeCCCCCHHHHHHHHhCCc--EEEEECCHHHHHHHHHHhCcCCcEEEEECchhcCChhHcC
Confidence 45556665 667789999999999999999999875 8888874 45555543 3689999999998 665434
No 79
>PRK11873 arsM arsenite S-adenosylmethyltransferase; Reviewed
Probab=97.80 E-value=5.3e-05 Score=63.75 Aligned_cols=67 Identities=15% Similarity=0.243 Sum_probs=53.2
Q ss_pred ccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCC--CEEEe
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKG--DAILI 232 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~--D~~~l 232 (233)
.....+|||||||+|..+..+++. .|+.+++.+|+ |..++.++++ ++++++.+|+.+ ++|.+ |+++.
T Consensus 75 ~~~g~~VLDiG~G~G~~~~~~a~~~g~~~~v~gvD~s~~~l~~A~~~~~~~g~~~v~~~~~d~~~l~~~~~~fD~Vi~ 152 (272)
T PRK11873 75 LKPGETVLDLGSGGGFDCFLAARRVGPTGKVIGVDMTPEMLAKARANARKAGYTNVEFRLGEIEALPVADNSVDVIIS 152 (272)
T ss_pred CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEECCCHHHHHHHHHHHHHcCCCCEEEEEcchhhCCCCCCceeEEEE
Confidence 556689999999999988877776 46678999998 5677777652 689999999887 67653 88863
No 80
>PHA03412 putative methyltransferase; Provisional
Probab=97.79 E-value=5.8e-05 Score=61.89 Aligned_cols=64 Identities=14% Similarity=0.074 Sum_probs=52.0
Q ss_pred cceEEEecCCccHHHHHHHHHc---CCCcEEEeech-HHHhhccCC-CCceEEecCcCC-CCCC-CCEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNY---LHIKGVNFDLS-HVIQDSSSY-SGVKHIGGIMLE-RIPK-GDAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~---P~l~~~v~Dlp-~v~~~a~~~-~ri~~~~gD~f~-~~P~-~D~~~l 232 (233)
..+|||+|||+|.++..++++. +..+++.+|+. .+++.|+.+ .++.++.+|++. +++. -|+|+.
T Consensus 50 ~grVLDlG~GSG~Lalala~~~~~~~~~~V~aVEID~~Al~~Ar~n~~~~~~~~~D~~~~~~~~~FDlIIs 120 (241)
T PHA03412 50 SGSVVDLCAGIGGLSFAMVHMMMYAKPREIVCVELNHTYYKLGKRIVPEATWINADALTTEFDTLFDMAIS 120 (241)
T ss_pred CCEEEEccChHHHHHHHHHHhcccCCCcEEEEEECCHHHHHHHHhhccCCEEEEcchhcccccCCccEEEE
Confidence 4699999999999999999875 46789999995 477778765 789999999987 4443 398874
No 81
>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=97.78 E-value=4.1e-05 Score=60.80 Aligned_cols=68 Identities=18% Similarity=0.289 Sum_probs=52.0
Q ss_pred hcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----CCCceEEecCcCCCCCCC--CEEEe
Q 039903 162 SSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----YSGVKHIGGIMLERIPKG--DAILI 232 (233)
Q Consensus 162 ~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----~~ri~~~~gD~f~~~P~~--D~~~l 232 (233)
.++ -..+.++++||||.|.++..|+.++- +.++.|. |.+++.|++ .++|+++..|+-+..|.+ |+|++
T Consensus 38 aLp-~~ry~~alEvGCs~G~lT~~LA~rCd--~LlavDis~~Al~~Ar~Rl~~~~~V~~~~~dvp~~~P~~~FDLIV~ 112 (201)
T PF05401_consen 38 ALP-RRRYRRALEVGCSIGVLTERLAPRCD--RLLAVDISPRALARARERLAGLPHVEWIQADVPEFWPEGRFDLIVL 112 (201)
T ss_dssp HHT-TSSEEEEEEE--TTSHHHHHHGGGEE--EEEEEES-HHHHHHHHHHTTT-SSEEEEES-TTT---SS-EEEEEE
T ss_pred hcC-ccccceeEecCCCccHHHHHHHHhhC--ceEEEeCCHHHHHHHHHhcCCCCCeEEEECcCCCCCCCCCeeEEEE
Confidence 456 56778999999999999999999973 5899998 668888865 378999999998888875 99986
No 82
>PRK01581 speE spermidine synthase; Validated
Probab=97.75 E-value=6e-05 Score=65.58 Aligned_cols=67 Identities=19% Similarity=0.163 Sum_probs=52.8
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC-------------CCCceEEecCcCCCC---CCC-
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS-------------YSGVKHIGGIMLERI---PKG- 227 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~-------------~~ri~~~~gD~f~~~---P~~- 227 (233)
..+.++|++||||.|..+.++++..|..+++++|+. ++++.|++ .+|++++.+|.++-+ +..
T Consensus 148 h~~PkrVLIIGgGdG~tlrelLk~~~v~~It~VEIDpeVIelAr~~~~L~~~~~~~~~DpRV~vvi~Da~~fL~~~~~~Y 227 (374)
T PRK01581 148 VIDPKRVLILGGGDGLALREVLKYETVLHVDLVDLDGSMINMARNVPELVSLNKSAFFDNRVNVHVCDAKEFLSSPSSLY 227 (374)
T ss_pred CCCCCEEEEECCCHHHHHHHHHhcCCCCeEEEEeCCHHHHHHHHhccccchhccccCCCCceEEEECcHHHHHHhcCCCc
Confidence 356789999999999999999986556789999984 57887774 279999999999732 223
Q ss_pred CEEEe
Q 039903 228 DAILI 232 (233)
Q Consensus 228 D~~~l 232 (233)
|+|++
T Consensus 228 DVIIv 232 (374)
T PRK01581 228 DVIII 232 (374)
T ss_pred cEEEE
Confidence 88875
No 83
>PRK15068 tRNA mo(5)U34 methyltransferase; Provisional
Probab=97.74 E-value=0.00012 Score=63.19 Aligned_cols=71 Identities=14% Similarity=0.119 Sum_probs=50.8
Q ss_pred HHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhcc-------CCCCceEEecCcCC-CCCCC-CE
Q 039903 160 IDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSS-------SYSGVKHIGGIMLE-RIPKG-DA 229 (233)
Q Consensus 160 ~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~-------~~~ri~~~~gD~f~-~~P~~-D~ 229 (233)
+..++.++ .++|+|||||+|.++..+++..|. +++++|... .+..++ ...+|+++.+|+.+ +.+.. |+
T Consensus 115 ~~~l~~l~-g~~VLDIGCG~G~~~~~la~~g~~-~V~GiD~S~~~l~q~~a~~~~~~~~~~i~~~~~d~e~lp~~~~FD~ 192 (322)
T PRK15068 115 LPHLSPLK-GRTVLDVGCGNGYHMWRMLGAGAK-LVVGIDPSQLFLCQFEAVRKLLGNDQRAHLLPLGIEQLPALKAFDT 192 (322)
T ss_pred HHhhCCCC-CCEEEEeccCCcHHHHHHHHcCCC-EEEEEcCCHHHHHHHHHHHHhcCCCCCeEEEeCCHHHCCCcCCcCE
Confidence 34443233 479999999999999999999877 499999654 222211 12589999999877 55554 98
Q ss_pred EEe
Q 039903 230 ILI 232 (233)
Q Consensus 230 ~~l 232 (233)
|+.
T Consensus 193 V~s 195 (322)
T PRK15068 193 VFS 195 (322)
T ss_pred EEE
Confidence 874
No 84
>COG2230 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]
Probab=97.74 E-value=0.0001 Score=61.99 Aligned_cols=64 Identities=17% Similarity=0.158 Sum_probs=52.3
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC-------CCCceEEecCcCC
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS-------YSGVKHIGGIMLE 222 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~-------~~ri~~~~gD~f~ 222 (233)
..+++.+. +++..+|||||||-|.+++..+++| +.+++.+++.+ ..+.+++ .++|++...|+-+
T Consensus 62 ~~~~~kl~-L~~G~~lLDiGCGWG~l~~~aA~~y-~v~V~GvTlS~~Q~~~~~~r~~~~gl~~~v~v~l~d~rd 133 (283)
T COG2230 62 DLILEKLG-LKPGMTLLDIGCGWGGLAIYAAEEY-GVTVVGVTLSEEQLAYAEKRIAARGLEDNVEVRLQDYRD 133 (283)
T ss_pred HHHHHhcC-CCCCCEEEEeCCChhHHHHHHHHHc-CCEEEEeeCCHHHHHHHHHHHHHcCCCcccEEEeccccc
Confidence 45677777 8999999999999999999999999 99999999853 4444443 1578888888765
No 85
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=97.73 E-value=0.00012 Score=58.78 Aligned_cols=71 Identities=20% Similarity=0.124 Sum_probs=53.7
Q ss_pred HhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC---CCC-C
Q 039903 161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER---IPK-G 227 (233)
Q Consensus 161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~---~P~-~ 227 (233)
..++ .....+++|+|||+|.++..+++.. |..+++.+|+ |+.++.++++ ++++++.+|+.+. .+. .
T Consensus 34 ~~l~-~~~~~~vlDlG~GtG~~s~~~a~~~~~~~~v~avD~~~~~~~~a~~n~~~~g~~~~v~~~~~d~~~~l~~~~~~~ 112 (198)
T PRK00377 34 SKLR-LRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDKDEKAINLTRRNAEKFGVLNNIVLIKGEAPEILFTINEKF 112 (198)
T ss_pred HHcC-CCCcCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHhCCCCCeEEEEechhhhHhhcCCCC
Confidence 3344 5666899999999999999998864 6789999998 6677766432 5789999999762 222 4
Q ss_pred CEEEe
Q 039903 228 DAILI 232 (233)
Q Consensus 228 D~~~l 232 (233)
|++++
T Consensus 113 D~V~~ 117 (198)
T PRK00377 113 DRIFI 117 (198)
T ss_pred CEEEE
Confidence 88875
No 86
>PRK14967 putative methyltransferase; Provisional
Probab=97.71 E-value=8.8e-05 Score=60.62 Aligned_cols=66 Identities=12% Similarity=0.081 Sum_probs=50.4
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCCCCCC-C-CEEEe
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLERIPK-G-DAILI 232 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~~~P~-~-D~~~l 232 (233)
.....+++|+|||+|.++..+++. +..+++.+|+. ..++.++++ -+++++.+|+++.++. . |+|+.
T Consensus 34 ~~~~~~vLDlGcG~G~~~~~la~~-~~~~v~~vD~s~~~l~~a~~n~~~~~~~~~~~~~d~~~~~~~~~fD~Vi~ 107 (223)
T PRK14967 34 LGPGRRVLDLCTGSGALAVAAAAA-GAGSVTAVDISRRAVRSARLNALLAGVDVDVRRGDWARAVEFRPFDVVVS 107 (223)
T ss_pred cCCCCeEEEecCCHHHHHHHHHHc-CCCeEEEEECCHHHHHHHHHHHHHhCCeeEEEECchhhhccCCCeeEEEE
Confidence 455579999999999999998876 44588999985 466655542 3588899999886664 3 98875
No 87
>PRK00312 pcm protein-L-isoaspartate O-methyltransferase; Reviewed
Probab=97.71 E-value=0.00017 Score=58.37 Aligned_cols=71 Identities=13% Similarity=0.208 Sum_probs=52.3
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC-C--C
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK-G--D 228 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~-~--D 228 (233)
++..++ ..+..+|+|||||+|.++..+++... +++.+|. |+.++.++++ .+|+++.+|+++.+|. + |
T Consensus 70 l~~~l~-~~~~~~VLeiG~GsG~~t~~la~~~~--~v~~vd~~~~~~~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~~fD 146 (212)
T PRK00312 70 MTELLE-LKPGDRVLEIGTGSGYQAAVLAHLVR--RVFSVERIKTLQWEAKRRLKQLGLHNVSVRHGDGWKGWPAYAPFD 146 (212)
T ss_pred HHHhcC-CCCCCEEEEECCCccHHHHHHHHHhC--EEEEEeCCHHHHHHHHHHHHHCCCCceEEEECCcccCCCcCCCcC
Confidence 344444 56678999999999999988887754 6788887 4566666542 5699999999886553 2 9
Q ss_pred EEEe
Q 039903 229 AILI 232 (233)
Q Consensus 229 ~~~l 232 (233)
++++
T Consensus 147 ~I~~ 150 (212)
T PRK00312 147 RILV 150 (212)
T ss_pred EEEE
Confidence 8875
No 88
>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=97.71 E-value=7.8e-05 Score=62.88 Aligned_cols=73 Identities=15% Similarity=0.082 Sum_probs=47.6
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC-------CCCceEEecCcCCCCCCCC
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS-------YSGVKHIGGIMLERIPKGD 228 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~-------~~ri~~~~gD~f~~~P~~D 228 (233)
..+++.++ .+...+|||||||-|.+++.++++| +++++.+.+.+ -.+.+++ .++|++...|+.+--+.-|
T Consensus 52 ~~~~~~~~-l~~G~~vLDiGcGwG~~~~~~a~~~-g~~v~gitlS~~Q~~~a~~~~~~~gl~~~v~v~~~D~~~~~~~fD 129 (273)
T PF02353_consen 52 DLLCEKLG-LKPGDRVLDIGCGWGGLAIYAAERY-GCHVTGITLSEEQAEYARERIREAGLEDRVEVRLQDYRDLPGKFD 129 (273)
T ss_dssp HHHHTTTT---TT-EEEEES-TTSHHHHHHHHHH---EEEEEES-HHHHHHHHHHHHCSTSSSTEEEEES-GGG---S-S
T ss_pred HHHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHc-CcEEEEEECCHHHHHHHHHHHHhcCCCCceEEEEeeccccCCCCC
Confidence 45667776 7888999999999999999999999 88999999854 4444432 2789999999876222236
Q ss_pred EEE
Q 039903 229 AIL 231 (233)
Q Consensus 229 ~~~ 231 (233)
.|+
T Consensus 130 ~Iv 132 (273)
T PF02353_consen 130 RIV 132 (273)
T ss_dssp EEE
T ss_pred EEE
Confidence 654
No 89
>PLN02672 methionine S-methyltransferase
Probab=97.70 E-value=5.1e-05 Score=74.39 Aligned_cols=62 Identities=19% Similarity=0.202 Sum_probs=51.0
Q ss_pred ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----------------------CCceEEecCcCCCCCC
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----------------------SGVKHIGGIMLERIPK 226 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----------------------~ri~~~~gD~f~~~P~ 226 (233)
.+|+|||||+|..++.+++++|+.+++.+|+ |.+++.|+++ +||+++.+|+++.++.
T Consensus 120 ~~VLDlG~GSG~Iai~La~~~~~~~v~avDis~~Al~~A~~Na~~n~l~~~~~~~~~~~~~~l~~rV~f~~sDl~~~~~~ 199 (1082)
T PLN02672 120 KTVAELGCGNGWISIAIAEKWLPSKVYGLDINPRAVKVAWINLYLNALDDDGLPVYDGEGKTLLDRVEFYESDLLGYCRD 199 (1082)
T ss_pred CEEEEEecchHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCcccccccccccccccccccEEEEECchhhhccc
Confidence 5899999999999999999999999999998 4577666321 4799999999986642
Q ss_pred ----CCEEE
Q 039903 227 ----GDAIL 231 (233)
Q Consensus 227 ----~D~~~ 231 (233)
-|+|+
T Consensus 200 ~~~~fDlIV 208 (1082)
T PLN02672 200 NNIELDRIV 208 (1082)
T ss_pred cCCceEEEE
Confidence 27765
No 90
>PRK14968 putative methyltransferase; Provisional
Probab=97.69 E-value=0.00011 Score=57.86 Aligned_cols=64 Identities=22% Similarity=0.295 Sum_probs=50.3
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CC-ceEEecCcCCCCCC--CCEEEe
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SG-VKHIGGIMLERIPK--GDAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~r-i~~~~gD~f~~~P~--~D~~~l 232 (233)
.+..+++|+|||+|.++..++++ ..+++.+|+ |++++.++++ ++ +.++.+|++++++. .|+++.
T Consensus 22 ~~~~~vLd~G~G~G~~~~~l~~~--~~~v~~~D~s~~~~~~a~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~d~vi~ 96 (188)
T PRK14968 22 KKGDRVLEVGTGSGIVAIVAAKN--GKKVVGVDINPYAVECAKCNAKLNNIRNNGVEVIRSDLFEPFRGDKFDVILF 96 (188)
T ss_pred cCCCEEEEEccccCHHHHHHHhh--cceEEEEECCHHHHHHHHHHHHHcCCCCcceEEEeccccccccccCceEEEE
Confidence 45578999999999999999998 578999998 4577766432 23 89999999987665 388764
No 91
>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional
Probab=97.67 E-value=0.00012 Score=62.32 Aligned_cols=76 Identities=16% Similarity=0.161 Sum_probs=59.0
Q ss_pred HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC----CCceEEecCcCC---CCCC
Q 039903 156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY----SGVKHIGGIMLE---RIPK 226 (233)
Q Consensus 156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~----~ri~~~~gD~f~---~~P~ 226 (233)
..++++.+. -....++||++||.|.++..++++.| +.+++.+|. |++++.+++. +||+++.+||-+ ..+.
T Consensus 8 l~Evl~~L~-~~pg~~vlD~TlG~GGhS~~il~~~~~~g~VigiD~D~~al~~ak~~L~~~~ri~~i~~~f~~l~~~l~~ 86 (296)
T PRK00050 8 LDEVVDALA-IKPDGIYVDGTFGGGGHSRAILERLGPKGRLIAIDRDPDAIAAAKDRLKPFGRFTLVHGNFSNLKEVLAE 86 (296)
T ss_pred HHHHHHhhC-CCCCCEEEEeCcCChHHHHHHHHhCCCCCEEEEEcCCHHHHHHHHHhhccCCcEEEEeCCHHHHHHHHHc
Confidence 456667665 44557999999999999999999996 789999998 5677777652 589999999986 1322
Q ss_pred ----CCEEEe
Q 039903 227 ----GDAILI 232 (233)
Q Consensus 227 ----~D~~~l 232 (233)
-|.+++
T Consensus 87 ~~~~vDgIl~ 96 (296)
T PRK00050 87 GLGKVDGILL 96 (296)
T ss_pred CCCccCEEEE
Confidence 377765
No 92
>PRK12335 tellurite resistance protein TehB; Provisional
Probab=97.63 E-value=0.00015 Score=61.55 Aligned_cols=72 Identities=14% Similarity=0.150 Sum_probs=52.2
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-CCCCC-CE
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-RIPKG-DA 229 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~~P~~-D~ 229 (233)
.++..++ ..+..++||||||+|.++..++++ ..+++.+|.. .+++.+++. -++++..+|+.. .++.. |+
T Consensus 111 ~~~~~~~-~~~~~~vLDlGcG~G~~~~~la~~--g~~V~avD~s~~ai~~~~~~~~~~~l~v~~~~~D~~~~~~~~~fD~ 187 (287)
T PRK12335 111 EVLEAVQ-TVKPGKALDLGCGQGRNSLYLALL--GFDVTAVDINQQSLENLQEIAEKENLNIRTGLYDINSASIQEEYDF 187 (287)
T ss_pred HHHHHhh-ccCCCCEEEeCCCCCHHHHHHHHC--CCEEEEEECCHHHHHHHHHHHHHcCCceEEEEechhcccccCCccE
Confidence 4445444 344569999999999999999885 5789999985 566655432 368888889877 44443 98
Q ss_pred EEe
Q 039903 230 ILI 232 (233)
Q Consensus 230 ~~l 232 (233)
++.
T Consensus 188 I~~ 190 (287)
T PRK12335 188 ILS 190 (287)
T ss_pred EEE
Confidence 864
No 93
>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=97.63 E-value=2.8e-05 Score=48.58 Aligned_cols=46 Identities=24% Similarity=0.386 Sum_probs=40.4
Q ss_pred hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
+.|++.|...+ ++.|+.|||+++|+ +...+.|+|..|+..|+++++
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 45788888875 57899999999999 999999999999999999984
No 94
>PLN02396 hexaprenyldihydroxybenzoate methyltransferase
Probab=97.63 E-value=8.1e-05 Score=64.20 Aligned_cols=62 Identities=15% Similarity=0.091 Sum_probs=47.8
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCC-CCCC--CCEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLE-RIPK--GDAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~-~~P~--~D~~~l 232 (233)
..+|||||||.|.++..+++ ++.+++.+|.. +.++.|+.+ .+|+++.+|+-+ +.+. .|+++.
T Consensus 132 g~~ILDIGCG~G~~s~~La~--~g~~V~GID~s~~~i~~Ar~~~~~~~~~~~i~~~~~dae~l~~~~~~FD~Vi~ 204 (322)
T PLN02396 132 GLKFIDIGCGGGLLSEPLAR--MGATVTGVDAVDKNVKIARLHADMDPVTSTIEYLCTTAEKLADEGRKFDAVLS 204 (322)
T ss_pred CCEEEEeeCCCCHHHHHHHH--cCCEEEEEeCCHHHHHHHHHHHHhcCcccceeEEecCHHHhhhccCCCCEEEE
Confidence 36899999999999998886 46789999984 577766532 479999999865 4444 298874
No 95
>PRK13943 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=97.63 E-value=0.00021 Score=61.62 Aligned_cols=73 Identities=16% Similarity=0.259 Sum_probs=54.0
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCC-CcEEEeech-HHHhhccC------CCCceEEecCcCCCCCC---C
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDLS-HVIQDSSS------YSGVKHIGGIMLERIPK---G 227 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dlp-~v~~~a~~------~~ri~~~~gD~f~~~P~---~ 227 (233)
+++.++ .++..+|+|||||+|.++..+++..+. -+++.+|.. +.++.|++ .++|+++.+|..+..+. .
T Consensus 72 ll~~L~-i~~g~~VLDIG~GtG~~a~~LA~~~~~~g~VvgVDis~~~l~~Ar~~l~~~g~~nV~~i~gD~~~~~~~~~~f 150 (322)
T PRK13943 72 FMEWVG-LDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKRNVRRLGIENVIFVCGDGYYGVPEFAPY 150 (322)
T ss_pred HHHhcC-CCCCCEEEEEeCCccHHHHHHHHhcCCCCEEEEEECCHHHHHHHHHHHHHcCCCcEEEEeCChhhcccccCCc
Confidence 344444 556689999999999999999998874 468889974 56665554 26799999998874442 3
Q ss_pred CEEEe
Q 039903 228 DAILI 232 (233)
Q Consensus 228 D~~~l 232 (233)
|++++
T Consensus 151 D~Ii~ 155 (322)
T PRK13943 151 DVIFV 155 (322)
T ss_pred cEEEE
Confidence 88875
No 96
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=97.62 E-value=0.0002 Score=61.02 Aligned_cols=72 Identities=15% Similarity=0.321 Sum_probs=53.5
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC-------CCCceEEecCcCC-CCCCC
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS-------YSGVKHIGGIMLE-RIPKG 227 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~-------~~ri~~~~gD~f~-~~P~~ 227 (233)
..+++... .....+|+|||||.|.++..++++.. +++.+|+. ..++.+++ .++++++.+|+.+ ..|..
T Consensus 26 ~~Iv~~~~-~~~~~~VLEIG~G~G~LT~~Ll~~~~--~V~avEiD~~li~~l~~~~~~~~~~~~v~ii~~Dal~~~~~~~ 102 (294)
T PTZ00338 26 DKIVEKAA-IKPTDTVLEIGPGTGNLTEKLLQLAK--KVIAIEIDPRMVAELKKRFQNSPLASKLEVIEGDALKTEFPYF 102 (294)
T ss_pred HHHHHhcC-CCCcCEEEEecCchHHHHHHHHHhCC--cEEEEECCHHHHHHHHHHHHhcCCCCcEEEEECCHhhhccccc
Confidence 34555555 56668999999999999999999854 58888885 35555443 3689999999998 56555
Q ss_pred CEEE
Q 039903 228 DAIL 231 (233)
Q Consensus 228 D~~~ 231 (233)
|.++
T Consensus 103 d~Vv 106 (294)
T PTZ00338 103 DVCV 106 (294)
T ss_pred CEEE
Confidence 7654
No 97
>PRK03612 spermidine synthase; Provisional
Probab=97.61 E-value=0.00012 Score=67.28 Aligned_cols=65 Identities=15% Similarity=0.332 Sum_probs=52.9
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCC-CcEEEeec-hHHHhhccCC-------------CCceEEecCcCC---CCCCC-
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDL-SHVIQDSSSY-------------SGVKHIGGIMLE---RIPKG- 227 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~v~~~a~~~-------------~ri~~~~gD~f~---~~P~~- 227 (233)
++.++|+|||||+|..+.++++ +|. -+++++|+ |++++.++++ +|++++.+|.++ ..+..
T Consensus 296 ~~~~rVL~IG~G~G~~~~~ll~-~~~v~~v~~VEid~~vi~~ar~~~~l~~~~~~~~~dprv~vi~~Da~~~l~~~~~~f 374 (521)
T PRK03612 296 ARPRRVLVLGGGDGLALREVLK-YPDVEQVTLVDLDPAMTELARTSPALRALNGGALDDPRVTVVNDDAFNWLRKLAEKF 374 (521)
T ss_pred CCCCeEEEEcCCccHHHHHHHh-CCCcCeEEEEECCHHHHHHHHhCCcchhhhccccCCCceEEEEChHHHHHHhCCCCC
Confidence 4568999999999999999997 576 78999999 6788887761 689999999887 23444
Q ss_pred CEEEe
Q 039903 228 DAILI 232 (233)
Q Consensus 228 D~~~l 232 (233)
|+|++
T Consensus 375 DvIi~ 379 (521)
T PRK03612 375 DVIIV 379 (521)
T ss_pred CEEEE
Confidence 99875
No 98
>PRK04266 fibrillarin; Provisional
Probab=97.61 E-value=0.0003 Score=57.71 Aligned_cols=68 Identities=9% Similarity=0.047 Sum_probs=51.8
Q ss_pred cccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHh----hccCCCCceEEecCcCCC-----CCCC-CEEE
Q 039903 163 SKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQ----DSSSYSGVKHIGGIMLER-----IPKG-DAIL 231 (233)
Q Consensus 163 ~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~----~a~~~~ri~~~~gD~f~~-----~P~~-D~~~ 231 (233)
++ .++..+|+|+|||+|.++..+++..+.-+++.+|+. +.++ .+++.++|.++.+|..++ ++.. |+++
T Consensus 68 l~-i~~g~~VlD~G~G~G~~~~~la~~v~~g~V~avD~~~~ml~~l~~~a~~~~nv~~i~~D~~~~~~~~~l~~~~D~i~ 146 (226)
T PRK04266 68 FP-IKKGSKVLYLGAASGTTVSHVSDIVEEGVVYAVEFAPRPMRELLEVAEERKNIIPILADARKPERYAHVVEKVDVIY 146 (226)
T ss_pred CC-CCCCCEEEEEccCCCHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHhhhcCCcEEEECCCCCcchhhhccccCCEEE
Confidence 44 667789999999999999999999986688999984 3443 444447899999998753 2333 8876
No 99
>TIGR00438 rrmJ cell division protein FtsJ.
Probab=97.60 E-value=0.00031 Score=55.83 Aligned_cols=58 Identities=16% Similarity=0.170 Sum_probs=45.8
Q ss_pred HhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeechHHHhhccCCCCceEEecCcCC
Q 039903 161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE 222 (233)
Q Consensus 161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~ 222 (233)
+.+....+..+|+|+|||+|.++..+++++ +..+++.+|+.+.. ..++++++.+|+.+
T Consensus 25 ~~~~~i~~g~~VLDiG~GtG~~~~~l~~~~~~~~~v~~vDis~~~----~~~~i~~~~~d~~~ 83 (188)
T TIGR00438 25 QKFKLIKPGDTVLDLGAAPGGWSQVAVEQVGGKGRVIAVDLQPMK----PIENVDFIRGDFTD 83 (188)
T ss_pred HHhcccCCCCEEEEecCCCCHHHHHHHHHhCCCceEEEEeccccc----cCCCceEEEeeCCC
Confidence 334434667899999999999999999887 66789999997643 23678999999876
No 100
>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=97.59 E-value=0.00011 Score=58.89 Aligned_cols=53 Identities=13% Similarity=0.230 Sum_probs=42.1
Q ss_pred ceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC------CCCceEEecCcCC
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS------YSGVKHIGGIMLE 222 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~------~~ri~~~~gD~f~ 222 (233)
..+||||||.|.++.++++++|+..++++|+- ..+..+.. .+++.++.+|...
T Consensus 19 ~l~lEIG~G~G~~l~~~A~~~Pd~n~iGiE~~~~~v~~a~~~~~~~~l~Nv~~~~~da~~ 78 (195)
T PF02390_consen 19 PLILEIGCGKGEFLIELAKRNPDINFIGIEIRKKRVAKALRKAEKRGLKNVRFLRGDARE 78 (195)
T ss_dssp EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHHTTSSEEEEES-CTT
T ss_pred CeEEEecCCCCHHHHHHHHHCCCCCEEEEecchHHHHHHHHHHHhhcccceEEEEccHHH
Confidence 49999999999999999999999999999974 34444432 3899999999876
No 101
>PLN02336 phosphoethanolamine N-methyltransferase
Probab=97.59 E-value=0.00023 Score=64.68 Aligned_cols=74 Identities=22% Similarity=0.310 Sum_probs=54.4
Q ss_pred HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC----CCCceEEecCcCC---CCCCC
Q 039903 156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS----YSGVKHIGGIMLE---RIPKG 227 (233)
Q Consensus 156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~~ri~~~~gD~f~---~~P~~ 227 (233)
.+.+++.++ ..+..+++|||||+|.++..+++.+. +++.+|.. +.++.+.. .++++++.+|+.+ ++|..
T Consensus 26 ~~~il~~l~-~~~~~~vLDlGcG~G~~~~~la~~~~--~v~giD~s~~~l~~a~~~~~~~~~i~~~~~d~~~~~~~~~~~ 102 (475)
T PLN02336 26 RPEILSLLP-PYEGKSVLELGAGIGRFTGELAKKAG--QVIALDFIESVIKKNESINGHYKNVKFMCADVTSPDLNISDG 102 (475)
T ss_pred hhHHHhhcC-ccCCCEEEEeCCCcCHHHHHHHhhCC--EEEEEeCCHHHHHHHHHHhccCCceEEEEecccccccCCCCC
Confidence 345566655 44557999999999999999999864 68999974 56665542 2689999999964 45543
Q ss_pred --CEEEe
Q 039903 228 --DAILI 232 (233)
Q Consensus 228 --D~~~l 232 (233)
|+|+.
T Consensus 103 ~fD~I~~ 109 (475)
T PLN02336 103 SVDLIFS 109 (475)
T ss_pred CEEEEeh
Confidence 88874
No 102
>PLN02781 Probable caffeoyl-CoA O-methyltransferase
Probab=97.58 E-value=0.00022 Score=58.78 Aligned_cols=67 Identities=12% Similarity=0.108 Sum_probs=53.0
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCC-------C--C
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIP-------K--G 227 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P-------~--~ 227 (233)
..+.++++|||+|+|.-+..+++..| +.+++.+|.. +.++.|+++ ++|+++.||..+.+| . -
T Consensus 66 ~~~~~~vLEiGt~~G~s~l~la~~~~~~g~v~tiD~d~~~~~~A~~n~~~~gl~~~i~~~~gda~~~L~~l~~~~~~~~f 145 (234)
T PLN02781 66 IMNAKNTLEIGVFTGYSLLTTALALPEDGRITAIDIDKEAYEVGLEFIKKAGVDHKINFIQSDALSALDQLLNNDPKPEF 145 (234)
T ss_pred HhCCCEEEEecCcccHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEEccHHHHHHHHHhCCCCCCC
Confidence 45678999999999999999998865 7899999985 566666653 689999999987321 2 3
Q ss_pred CEEEe
Q 039903 228 DAILI 232 (233)
Q Consensus 228 D~~~l 232 (233)
|++++
T Consensus 146 D~Vfi 150 (234)
T PLN02781 146 DFAFV 150 (234)
T ss_pred CEEEE
Confidence 88875
No 103
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=97.57 E-value=0.00022 Score=49.55 Aligned_cols=60 Identities=17% Similarity=0.212 Sum_probs=50.4
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhh
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAK 86 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~ 86 (233)
-+.|++.|...+ ++.|..|||+.+++ +...+.|+|+.|+..|++.+.. .++.|++++...
T Consensus 7 ~~~Il~~l~~~~--~~~t~~~ia~~l~i----~~~tv~r~l~~L~~~g~l~~~~---~~~~y~l~~~~~ 66 (91)
T smart00346 7 GLAVLRALAEEP--GGLTLAELAERLGL----SKSTAHRLLNTLQELGYVEQDG---QNGRYRLGPKVL 66 (91)
T ss_pred HHHHHHHHHhCC--CCcCHHHHHHHhCC----CHHHHHHHHHHHHHCCCeeecC---CCCceeecHHHH
Confidence 456888888763 48999999999999 9999999999999999999852 357899887543
No 104
>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=97.54 E-value=0.00011 Score=62.81 Aligned_cols=55 Identities=18% Similarity=0.274 Sum_probs=44.4
Q ss_pred CcceEEEecCCccHHHHHHHHHcC-CCcEEEeechH-HHhhccCC-----C--CceEEecCcCC
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLSH-VIQDSSSY-----S--GVKHIGGIMLE 222 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp~-v~~~a~~~-----~--ri~~~~gD~f~ 222 (233)
...+|||+|||+|..+..|+++.+ ..+++.+|+.+ .++.+.+. + +|.++.+||++
T Consensus 63 ~~~~iLELGcGtG~~t~~Ll~~l~~~~~~~~iDiS~~mL~~a~~~l~~~~p~~~v~~i~gD~~~ 126 (301)
T TIGR03438 63 AGCELVELGSGSSRKTRLLLDALRQPARYVPIDISADALKESAAALAADYPQLEVHGICADFTQ 126 (301)
T ss_pred CCCeEEecCCCcchhHHHHHHhhccCCeEEEEECCHHHHHHHHHHHHhhCCCceEEEEEEcccc
Confidence 446899999999999999999988 68999999965 55555432 3 46778999987
No 105
>PRK04148 hypothetical protein; Provisional
Probab=97.51 E-value=0.00045 Score=51.80 Aligned_cols=69 Identities=12% Similarity=0.195 Sum_probs=50.0
Q ss_pred HHHhcccccCcceEEEecCCccH-HHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCCCCCC----CCEEE
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGV-NVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLERIPK----GDAIL 231 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~-~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~~~P~----~D~~~ 231 (233)
+.+.++ -.+..+++|||+|.|. ++..|.+. +..++.+|. |..++.+++ ..++++.+|.|++-+. +|++.
T Consensus 8 l~~~~~-~~~~~kileIG~GfG~~vA~~L~~~--G~~ViaIDi~~~aV~~a~~-~~~~~v~dDlf~p~~~~y~~a~liy 82 (134)
T PRK04148 8 IAENYE-KGKNKKIVELGIGFYFKVAKKLKES--GFDVIVIDINEKAVEKAKK-LGLNAFVDDLFNPNLEIYKNAKLIY 82 (134)
T ss_pred HHHhcc-cccCCEEEEEEecCCHHHHHHHHHC--CCEEEEEECCHHHHHHHHH-hCCeEEECcCCCCCHHHHhcCCEEE
Confidence 444444 2234789999999996 77777765 568999998 457777765 3689999999996554 37653
No 106
>PF07021 MetW: Methionine biosynthesis protein MetW; InterPro: IPR010743 This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins. Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalysed by the products of the metXW genes and is equivalent to the first step in enterobacteria, Gram-positive bacteria and fungi, except that in these microorganisms the reaction is catalysed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In P. putida, as in Gram-positive bacteria and certain fungi, the second and third steps are a direct sulphydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells [].
Probab=97.51 E-value=0.0002 Score=56.75 Aligned_cols=64 Identities=20% Similarity=0.371 Sum_probs=48.8
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHH-HhhccCCCCceEEecCcCC---CCCCC--CEEEe
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHV-IQDSSSYSGVKHIGGIMLE---RIPKG--DAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v-~~~a~~~~ri~~~~gD~f~---~~P~~--D~~~l 232 (233)
+...+|+|+|||.|.++..|.+. .++++..+|+.+. +..+-+ ..++.+.+|.-+ .+|.. |.++|
T Consensus 12 ~pgsrVLDLGCGdG~LL~~L~~~-k~v~g~GvEid~~~v~~cv~-rGv~Viq~Dld~gL~~f~d~sFD~VIl 81 (193)
T PF07021_consen 12 EPGSRVLDLGCGDGELLAYLKDE-KQVDGYGVEIDPDNVAACVA-RGVSVIQGDLDEGLADFPDQSFDYVIL 81 (193)
T ss_pred CCCCEEEecCCCchHHHHHHHHh-cCCeEEEEecCHHHHHHHHH-cCCCEEECCHHHhHhhCCCCCccEEeh
Confidence 44589999999999999888875 6999999998543 333322 478899999887 46653 98886
No 107
>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=97.50 E-value=0.00022 Score=57.80 Aligned_cols=75 Identities=15% Similarity=0.263 Sum_probs=54.0
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC-C
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK-G 227 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~-~ 227 (233)
..+++.++ .+...+++|||+|+|.++..+++-.- .-+++.+|. |+.++.|+++ .+|+++.||-....|. +
T Consensus 62 a~~l~~L~-l~pg~~VLeIGtGsGY~aAlla~lvg~~g~Vv~vE~~~~l~~~A~~~l~~~~~~nv~~~~gdg~~g~~~~a 140 (209)
T PF01135_consen 62 ARMLEALD-LKPGDRVLEIGTGSGYQAALLAHLVGPVGRVVSVERDPELAERARRNLARLGIDNVEVVVGDGSEGWPEEA 140 (209)
T ss_dssp HHHHHHTT-C-TT-EEEEES-TTSHHHHHHHHHHSTTEEEEEEESBHHHHHHHHHHHHHHTTHSEEEEES-GGGTTGGG-
T ss_pred HHHHHHHh-cCCCCEEEEecCCCcHHHHHHHHhcCccceEEEECccHHHHHHHHHHHHHhccCceeEEEcchhhccccCC
Confidence 34566666 77889999999999999999988754 445777786 5677777653 5899999999987765 4
Q ss_pred --CEEEe
Q 039903 228 --DAILI 232 (233)
Q Consensus 228 --D~~~l 232 (233)
|.|++
T Consensus 141 pfD~I~v 147 (209)
T PF01135_consen 141 PFDRIIV 147 (209)
T ss_dssp SEEEEEE
T ss_pred CcCEEEE
Confidence 88875
No 108
>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=97.49 E-value=0.00033 Score=48.44 Aligned_cols=61 Identities=20% Similarity=0.173 Sum_probs=47.6
Q ss_pred eEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhcc------CCCCceEEecCcCCCC---CC-CCEEEe
Q 039903 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSS------SYSGVKHIGGIMLERI---PK-GDAILI 232 (233)
Q Consensus 171 ~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~------~~~ri~~~~gD~f~~~---P~-~D~~~l 232 (233)
+++|+|||.|.++..+++ .+..+++.+|+.+ .+..++ ...+++++.+|+.+.. +. .|+++.
T Consensus 1 ~ildig~G~G~~~~~~~~-~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~i~~ 72 (107)
T cd02440 1 RVLDLGCGTGALALALAS-GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPEADESFDVIIS 72 (107)
T ss_pred CeEEEcCCccHHHHHHhc-CCCCEEEEEeCCHHHHHHHHHHHhcccccceEEEEcChhhhccccCCceEEEEE
Confidence 589999999999999999 7888999999864 555444 1268999999999843 23 388875
No 109
>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=97.45 E-value=0.00057 Score=55.57 Aligned_cols=54 Identities=7% Similarity=0.083 Sum_probs=43.4
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC------------------CCCceEEecCcCC
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS------------------YSGVKHIGGIMLE 222 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~------------------~~ri~~~~gD~f~ 222 (233)
....+++|+|||.|..+..|+++ ..+++.+|+.+ .++.+.. ..+|+++.+|+|+
T Consensus 33 ~~~~rvLd~GCG~G~da~~LA~~--G~~V~gvD~S~~Ai~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~D~~~ 105 (213)
T TIGR03840 33 PAGARVFVPLCGKSLDLAWLAEQ--GHRVLGVELSEIAVEQFFAENGLTPTVTQQGEFTRYRAGNIEIFCGDFFA 105 (213)
T ss_pred CCCCeEEEeCCCchhHHHHHHhC--CCeEEEEeCCHHHHHHHHHHcCCCcceeccccceeeecCceEEEEccCCC
Confidence 34579999999999999999986 77899999954 5665311 2479999999998
No 110
>TIGR02081 metW methionine biosynthesis protein MetW. This protein is found alongside MetX, of the enzyme that acylates homoserine as a first step toward methionine biosynthesis, in many species. It appears to act in methionine biosynthesis but is not fully characterized.
Probab=97.45 E-value=0.00049 Score=54.91 Aligned_cols=64 Identities=19% Similarity=0.361 Sum_probs=47.9
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCCCCceEEecCcCC---CCCC--CCEEEe
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSYSGVKHIGGIMLE---RIPK--GDAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~~ri~~~~gD~f~---~~P~--~D~~~l 232 (233)
+...+++|||||+|.++..+++. ...+++.+|.. +.++.++. .+++++.+|+.+ +++. .|++++
T Consensus 12 ~~~~~iLDiGcG~G~~~~~l~~~-~~~~~~giD~s~~~i~~a~~-~~~~~~~~d~~~~l~~~~~~sfD~Vi~ 81 (194)
T TIGR02081 12 PPGSRVLDLGCGDGELLALLRDE-KQVRGYGIEIDQDGVLACVA-RGVNVIQGDLDEGLEAFPDKSFDYVIL 81 (194)
T ss_pred CCCCEEEEeCCCCCHHHHHHHhc-cCCcEEEEeCCHHHHHHHHH-cCCeEEEEEhhhcccccCCCCcCEEEE
Confidence 34468999999999999988875 45678899984 46666654 468899999875 2443 398875
No 111
>KOG2904 consensus Predicted methyltransferase [General function prediction only]
Probab=97.44 E-value=0.00041 Score=57.67 Aligned_cols=60 Identities=15% Similarity=0.219 Sum_probs=48.1
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC-------CCceEE----ecCcCCCCC
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY-------SGVKHI----GGIMLERIP 225 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~-------~ri~~~----~gD~f~~~P 225 (233)
+.....++|+|||+|..+..+++.-|..+++..|... ++..|.++ +||..+ .+|.+.+.|
T Consensus 146 ~~~~~~ildlgtGSGaIslsll~~L~~~~v~AiD~S~~Ai~La~eN~qr~~l~g~i~v~~~~me~d~~~~~~ 217 (328)
T KOG2904|consen 146 HSKHTHILDLGTGSGAISLSLLHGLPQCTVTAIDVSKAAIKLAKENAQRLKLSGRIEVIHNIMESDASDEHP 217 (328)
T ss_pred hcccceEEEecCCccHHHHHHHhcCCCceEEEEeccHHHHHHHHHHHHHHhhcCceEEEecccccccccccc
Confidence 4455689999999999999999999999999999865 56666554 777776 677777544
No 112
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=97.42 E-value=0.00017 Score=65.01 Aligned_cols=72 Identities=14% Similarity=0.113 Sum_probs=53.2
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCCCC-----C
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLERI-----P 225 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~~~-----P 225 (233)
.+++.+. ..+..+++|+|||+|.++..+++.. .+++.+|.. +.++.|+++ ++++++.+|+.+.+ +
T Consensus 288 ~vl~~l~-~~~~~~VLDlgcGtG~~sl~la~~~--~~V~gvD~s~~al~~A~~n~~~~~~~~v~~~~~d~~~~l~~~~~~ 364 (443)
T PRK13168 288 RALEWLD-PQPGDRVLDLFCGLGNFTLPLARQA--AEVVGVEGVEAMVERARENARRNGLDNVTFYHANLEEDFTDQPWA 364 (443)
T ss_pred HHHHHhc-CCCCCEEEEEeccCCHHHHHHHHhC--CEEEEEeCCHHHHHHHHHHHHHcCCCceEEEEeChHHhhhhhhhh
Confidence 3444443 3455799999999999999999886 578999984 577777653 57999999997532 2
Q ss_pred C--CCEEEe
Q 039903 226 K--GDAILI 232 (233)
Q Consensus 226 ~--~D~~~l 232 (233)
. .|++++
T Consensus 365 ~~~fD~Vi~ 373 (443)
T PRK13168 365 LGGFDKVLL 373 (443)
T ss_pred cCCCCEEEE
Confidence 2 388875
No 113
>PRK10909 rsmD 16S rRNA m(2)G966-methyltransferase; Provisional
Probab=97.39 E-value=0.0003 Score=56.57 Aligned_cols=63 Identities=13% Similarity=0.127 Sum_probs=47.9
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC--C--CCEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP--K--GDAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P--~--~D~~~l 232 (233)
..+++|+|||+|.++.+++.+.. .+++.+|. |++++.++++ .+++++.+|+++.++ . .|++++
T Consensus 54 ~~~vLDl~~GsG~l~l~~lsr~a-~~V~~vE~~~~a~~~a~~Nl~~~~~~~v~~~~~D~~~~l~~~~~~fDlV~~ 127 (199)
T PRK10909 54 DARCLDCFAGSGALGLEALSRYA-AGATLLEMDRAVAQQLIKNLATLKAGNARVVNTNALSFLAQPGTPHNVVFV 127 (199)
T ss_pred CCEEEEcCCCccHHHHHHHHcCC-CEEEEEECCHHHHHHHHHHHHHhCCCcEEEEEchHHHHHhhcCCCceEEEE
Confidence 46899999999999998666654 58899997 4566666553 579999999987432 2 388875
No 114
>COG0421 SpeE Spermidine synthase [Amino acid transport and metabolism]
Probab=97.39 E-value=0.00033 Score=59.24 Aligned_cols=66 Identities=20% Similarity=0.243 Sum_probs=55.8
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----------CCceEEecCcCC---CCCC-CCEEE
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----------SGVKHIGGIMLE---RIPK-GDAIL 231 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----------~ri~~~~gD~f~---~~P~-~D~~~ 231 (233)
+++++||=||||.|..++++++..|.-+.+++|+ |.|++.+++. +|++.+.+|-++ ..+. .|+|+
T Consensus 75 ~~pk~VLiiGgGdG~tlRevlkh~~ve~i~~VEID~~Vi~~ar~~l~~~~~~~~dpRv~i~i~Dg~~~v~~~~~~fDvIi 154 (282)
T COG0421 75 PNPKRVLIIGGGDGGTLREVLKHLPVERITMVEIDPAVIELARKYLPEPSGGADDPRVEIIIDDGVEFLRDCEEKFDVII 154 (282)
T ss_pred CCCCeEEEECCCccHHHHHHHhcCCcceEEEEEcCHHHHHHHHHhccCcccccCCCceEEEeccHHHHHHhCCCcCCEEE
Confidence 4557999999999999999999988889999999 5688888762 799999999887 3444 49988
Q ss_pred e
Q 039903 232 I 232 (233)
Q Consensus 232 l 232 (233)
+
T Consensus 155 ~ 155 (282)
T COG0421 155 V 155 (282)
T ss_pred E
Confidence 5
No 115
>PLN02823 spermine synthase
Probab=97.39 E-value=0.0003 Score=61.00 Aligned_cols=66 Identities=18% Similarity=0.165 Sum_probs=53.2
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----------CCceEEecCcCCCC---CCC-CEEE
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----------SGVKHIGGIMLERI---PKG-DAIL 231 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----------~ri~~~~gD~f~~~---P~~-D~~~ 231 (233)
.+.++++-||||.|..++.+++..+.-+++++|+ |.|++.++++ +|++++.+|.++-+ +.. |+|+
T Consensus 102 ~~pk~VLiiGgG~G~~~re~l~~~~~~~v~~VEiD~~vv~lar~~~~~~~~~~~dprv~v~~~Da~~~L~~~~~~yDvIi 181 (336)
T PLN02823 102 PNPKTVFIMGGGEGSTAREVLRHKTVEKVVMCDIDQEVVDFCRKHLTVNREAFCDKRLELIINDARAELEKRDEKFDVII 181 (336)
T ss_pred CCCCEEEEECCCchHHHHHHHhCCCCCeEEEEECCHHHHHHHHHhcccccccccCCceEEEEChhHHHHhhCCCCccEEE
Confidence 4568999999999999999998766778999998 5688887652 69999999998732 233 8887
Q ss_pred e
Q 039903 232 I 232 (233)
Q Consensus 232 l 232 (233)
+
T Consensus 182 ~ 182 (336)
T PLN02823 182 G 182 (336)
T ss_pred e
Confidence 5
No 116
>PRK11705 cyclopropane fatty acyl phospholipid synthase; Provisional
Probab=97.38 E-value=0.00062 Score=60.23 Aligned_cols=71 Identities=14% Similarity=0.079 Sum_probs=52.0
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---CCceEEecCcCCCCCC-CCEEE
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---SGVKHIGGIMLERIPK-GDAIL 231 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---~ri~~~~gD~f~~~P~-~D~~~ 231 (233)
.+++.++ .+...+|||||||.|.++..+++++ +.+++.+|+ |+.++.+++. ..|++..+|+.+. +. -|+++
T Consensus 158 ~l~~~l~-l~~g~rVLDIGcG~G~~a~~la~~~-g~~V~giDlS~~~l~~A~~~~~~l~v~~~~~D~~~l-~~~fD~Iv 233 (383)
T PRK11705 158 LICRKLQ-LKPGMRVLDIGCGWGGLARYAAEHY-GVSVVGVTISAEQQKLAQERCAGLPVEIRLQDYRDL-NGQFDRIV 233 (383)
T ss_pred HHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHC-CCEEEEEeCCHHHHHHHHHHhccCeEEEEECchhhc-CCCCCEEE
Confidence 3445555 6667899999999999999999876 678999998 4577766543 2478888887542 33 37765
No 117
>TIGR00452 methyltransferase, putative. Known examples to date are restricted to the proteobacteria.
Probab=97.38 E-value=0.00083 Score=57.78 Aligned_cols=72 Identities=11% Similarity=0.037 Sum_probs=48.6
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhc---c----CCCCceEEecCcCC-CCCCC-C
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDS---S----SYSGVKHIGGIMLE-RIPKG-D 228 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a---~----~~~ri~~~~gD~f~-~~P~~-D 228 (233)
++..+. ..+.++|+|||||+|.++..++...++ +++.+|... .+..+ + ...++.+..+|+-+ +.+.. |
T Consensus 113 ~l~~l~-~~~g~~VLDvGCG~G~~~~~~~~~g~~-~v~GiDpS~~ml~q~~~~~~~~~~~~~v~~~~~~ie~lp~~~~FD 190 (314)
T TIGR00452 113 VLPHLS-PLKGRTILDVGCGSGYHMWRMLGHGAK-SLVGIDPTVLFLCQFEAVRKLLDNDKRAILEPLGIEQLHELYAFD 190 (314)
T ss_pred HHHhcC-CCCCCEEEEeccCCcHHHHHHHHcCCC-EEEEEcCCHHHHHHHHHHHHHhccCCCeEEEECCHHHCCCCCCcC
Confidence 344443 233489999999999999999988775 689999744 33322 1 12578888888755 32233 8
Q ss_pred EEEe
Q 039903 229 AILI 232 (233)
Q Consensus 229 ~~~l 232 (233)
+|+.
T Consensus 191 ~V~s 194 (314)
T TIGR00452 191 TVFS 194 (314)
T ss_pred EEEE
Confidence 8864
No 118
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=97.38 E-value=0.00038 Score=57.87 Aligned_cols=61 Identities=18% Similarity=0.293 Sum_probs=51.1
Q ss_pred hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903 19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF 88 (233)
Q Consensus 19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l 88 (233)
+.|++.|...+ .+.++.|||+++|+ +...+.|+|..|+..|+++++. ++++|++++....|
T Consensus 7 l~iL~~l~~~~--~~l~l~ela~~~gl----pksT~~RlL~tL~~~G~v~~d~---~~g~Y~Lg~~~~~l 67 (246)
T COG1414 7 LAILDLLAEGP--GGLSLAELAERLGL----PKSTVHRLLQTLVELGYVEQDP---EDGRYRLGPRLLEL 67 (246)
T ss_pred HHHHHHHHhCC--CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCCCEEEcC---CCCcEeehHHHHHH
Confidence 56888888853 45779999999999 9999999999999999999973 35789999865443
No 119
>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=97.37 E-value=0.00062 Score=54.30 Aligned_cols=72 Identities=15% Similarity=0.239 Sum_probs=50.2
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC-----CCCceEEecCcCC-CCCCC-C
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS-----YSGVKHIGGIMLE-RIPKG-D 228 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~-----~~ri~~~~gD~f~-~~P~~-D 228 (233)
+.+++..+ .-+..++||+|||.|..+.-|+++ +..++.+|... .++.+.. .-.|+....|+.+ .+|.. |
T Consensus 20 s~v~~a~~-~~~~g~~LDlgcG~GRNalyLA~~--G~~VtAvD~s~~al~~l~~~a~~~~l~i~~~~~Dl~~~~~~~~yD 96 (192)
T PF03848_consen 20 SEVLEAVP-LLKPGKALDLGCGEGRNALYLASQ--GFDVTAVDISPVALEKLQRLAEEEGLDIRTRVADLNDFDFPEEYD 96 (192)
T ss_dssp HHHHHHCT-TS-SSEEEEES-TTSHHHHHHHHT--T-EEEEEESSHHHHHHHHHHHHHTT-TEEEEE-BGCCBS-TTTEE
T ss_pred HHHHHHHh-hcCCCcEEEcCCCCcHHHHHHHHC--CCeEEEEECCHHHHHHHHHHHhhcCceeEEEEecchhccccCCcC
Confidence 45666666 556789999999999999999998 77799999864 4443322 2348899999988 66655 8
Q ss_pred EEE
Q 039903 229 AIL 231 (233)
Q Consensus 229 ~~~ 231 (233)
+|+
T Consensus 97 ~I~ 99 (192)
T PF03848_consen 97 FIV 99 (192)
T ss_dssp EEE
T ss_pred EEE
Confidence 875
No 120
>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=97.36 E-value=0.00032 Score=59.05 Aligned_cols=66 Identities=20% Similarity=0.235 Sum_probs=50.7
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC----------CCceEEecCcCC--C-CCCC-CEEE
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY----------SGVKHIGGIMLE--R-IPKG-DAIL 231 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~----------~ri~~~~gD~f~--~-~P~~-D~~~ 231 (233)
++.++|++||||.|..+..+++..+..+++++|+. .+++.++++ +|++++.+|.++ . .+.. |+|+
T Consensus 71 ~~p~~VL~iG~G~G~~~~~ll~~~~~~~v~~veid~~vi~~a~~~~~~~~~~~~~~~v~i~~~D~~~~l~~~~~~yDvIi 150 (270)
T TIGR00417 71 PNPKHVLVIGGGDGGVLREVLKHKSVEKATLVDIDEKVIELSKKFLPSLAGSYDDPRVDLQIDDGFKFLADTENTFDVII 150 (270)
T ss_pred CCCCEEEEEcCCchHHHHHHHhCCCcceEEEEeCCHHHHHHHHHHhHhhcccccCCceEEEECchHHHHHhCCCCccEEE
Confidence 45679999999999999999987667789999985 576766542 689999999876 2 2333 8887
Q ss_pred e
Q 039903 232 I 232 (233)
Q Consensus 232 l 232 (233)
+
T Consensus 151 ~ 151 (270)
T TIGR00417 151 V 151 (270)
T ss_pred E
Confidence 5
No 121
>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=97.36 E-value=0.00034 Score=59.48 Aligned_cols=64 Identities=19% Similarity=0.196 Sum_probs=45.0
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCCC-CCEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIPK-GDAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P~-~D~~~l 232 (233)
+..+|+|||||+|.+++.+++. +.-+++.+|+. ..++.++++ +++.+..+|.....+. .|+++.
T Consensus 159 ~g~~VLDvGcGsG~lai~aa~~-g~~~V~avDid~~al~~a~~n~~~n~~~~~~~~~~~~~~~~~~~~fDlVva 231 (288)
T TIGR00406 159 KDKNVIDVGCGSGILSIAALKL-GAAKVVGIDIDPLAVESARKNAELNQVSDRLQVKLIYLEQPIEGKADVIVA 231 (288)
T ss_pred CCCEEEEeCCChhHHHHHHHHc-CCCeEEEEECCHHHHHHHHHHHHHcCCCcceEEEecccccccCCCceEEEE
Confidence 4489999999999999888764 45689999985 466666553 4667666664332233 388864
No 122
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=97.34 E-value=0.00061 Score=45.00 Aligned_cols=60 Identities=17% Similarity=0.260 Sum_probs=49.2
Q ss_pred HHhhChhHHHHhcCCCC-CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 16 ASELGVFEIIAKAGPTA-KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 16 a~~lglfd~L~~~~~~~-~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
..+-.|++.|...| + ++|+.|||+++|+ +...++|+|..|...|+++.... ....|+++.
T Consensus 6 ~~~~~IL~~L~~~g--~~~~ta~eLa~~lgl----~~~~v~r~L~~L~~~G~V~~~~~--~~~~W~i~~ 66 (68)
T smart00550 6 SLEEKILEFLENSG--DETSTALQLAKNLGL----PKKEVNRVLYSLEKKGKVCKQGG--TPPLWKLTD 66 (68)
T ss_pred HHHHHHHHHHHHCC--CCCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEecCC--CCCceEeec
Confidence 45667899999985 2 3999999999999 99999999999999999998531 136777654
No 123
>COG2263 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.32 E-value=0.00063 Score=53.65 Aligned_cols=63 Identities=14% Similarity=0.148 Sum_probs=47.6
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCCCCCCCCEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLERIPKGDAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~~~P~~D~~~l 232 (233)
.++|+|+|||+|.+++..+-..|+ +++.+|+ |+.++.++++ .+|+|+..|.-+--+.-|.++|
T Consensus 46 g~~V~DlG~GTG~La~ga~~lGa~-~V~~vdiD~~a~ei~r~N~~~l~g~v~f~~~dv~~~~~~~dtvim 114 (198)
T COG2263 46 GKTVLDLGAGTGILAIGAALLGAS-RVLAVDIDPEALEIARANAEELLGDVEFVVADVSDFRGKFDTVIM 114 (198)
T ss_pred CCEEEEcCCCcCHHHHHHHhcCCc-EEEEEecCHHHHHHHHHHHHhhCCceEEEEcchhhcCCccceEEE
Confidence 378999999999999998876654 6777787 6688877765 6899999998763333355554
No 124
>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed
Probab=97.32 E-value=0.00051 Score=59.17 Aligned_cols=62 Identities=11% Similarity=0.046 Sum_probs=48.4
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCC---CCC-CCEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLER---IPK-GDAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~---~P~-~D~~~l 232 (233)
..+|+|+|||+|.++..+++. ..+++.+|. ++.++.|+++ ++|+++.+|+.+- ... .|++++
T Consensus 174 ~~~VLDl~cG~G~~sl~la~~--~~~V~gvD~s~~av~~A~~n~~~~~l~~v~~~~~D~~~~~~~~~~~~D~Vv~ 246 (315)
T PRK03522 174 PRSMWDLFCGVGGFGLHCATP--GMQLTGIEISAEAIACAKQSAAELGLTNVQFQALDSTQFATAQGEVPDLVLV 246 (315)
T ss_pred CCEEEEccCCCCHHHHHHHhc--CCEEEEEeCCHHHHHHHHHHHHHcCCCceEEEEcCHHHHHHhcCCCCeEEEE
Confidence 478999999999999999984 467999998 5577776543 5799999999762 222 388875
No 125
>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=97.32 E-value=0.00028 Score=60.08 Aligned_cols=82 Identities=16% Similarity=0.186 Sum_probs=50.9
Q ss_pred HHHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCce
Q 039903 143 VFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVK 214 (233)
Q Consensus 143 ~f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~ 214 (233)
.|-.+-+.++++.... ++.+. .+..+|+|||||+|.++++.++... -+++.+|. |.+++.|+++ +++.
T Consensus 139 AFGTG~H~TT~lcl~~-l~~~~--~~g~~vLDvG~GSGILaiaA~klGA-~~v~a~DiDp~Av~~a~~N~~~N~~~~~~~ 214 (295)
T PF06325_consen 139 AFGTGHHPTTRLCLEL-LEKYV--KPGKRVLDVGCGSGILAIAAAKLGA-KKVVAIDIDPLAVEAARENAELNGVEDRIE 214 (295)
T ss_dssp SS-SSHCHHHHHHHHH-HHHHS--STTSEEEEES-TTSHHHHHHHHTTB-SEEEEEESSCHHHHHHHHHHHHTT-TTCEE
T ss_pred cccCCCCHHHHHHHHH-HHHhc--cCCCEEEEeCCcHHHHHHHHHHcCC-CeEEEecCCHHHHHHHHHHHHHcCCCeeEE
Confidence 3555555555554333 34443 3447999999999999999888644 47899998 4567777664 5565
Q ss_pred EEecCcCCCCCC--CCEEE
Q 039903 215 HIGGIMLERIPK--GDAIL 231 (233)
Q Consensus 215 ~~~gD~f~~~P~--~D~~~ 231 (233)
.. .....+. .|+|+
T Consensus 215 v~---~~~~~~~~~~dlvv 230 (295)
T PF06325_consen 215 VS---LSEDLVEGKFDLVV 230 (295)
T ss_dssp ES---CTSCTCCS-EEEEE
T ss_pred EE---EecccccccCCEEE
Confidence 42 1223333 38876
No 126
>PRK14902 16S rRNA methyltransferase B; Provisional
Probab=97.28 E-value=0.00058 Score=61.63 Aligned_cols=71 Identities=14% Similarity=0.054 Sum_probs=54.3
Q ss_pred HhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC------CCceEEecCcCCC---CCC-CC
Q 039903 161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLER---IPK-GD 228 (233)
Q Consensus 161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~---~P~-~D 228 (233)
..++ ..+..+|+|+|||+|..+..+++.. |..+++.+|+ +..++.++++ ++|+++.+|+.+. ++. .|
T Consensus 244 ~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~~~~~v~avDi~~~~l~~~~~n~~~~g~~~v~~~~~D~~~~~~~~~~~fD 322 (444)
T PRK14902 244 PALD-PKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDARKVHEKFAEKFD 322 (444)
T ss_pred HHhC-CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHHcCCCeEEEEeCCcccccchhcccCC
Confidence 3444 4556899999999999999999986 6789999999 5566666542 4699999999762 343 39
Q ss_pred EEEe
Q 039903 229 AILI 232 (233)
Q Consensus 229 ~~~l 232 (233)
+|++
T Consensus 323 ~Vl~ 326 (444)
T PRK14902 323 KILV 326 (444)
T ss_pred EEEE
Confidence 8875
No 127
>PRK11569 transcriptional repressor IclR; Provisional
Probab=97.24 E-value=0.00064 Score=57.38 Aligned_cols=62 Identities=18% Similarity=0.231 Sum_probs=51.7
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF 88 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l 88 (233)
=+.|++.|.+.+ ++.|+.|||+.+|+ +..-+.|+|..|+..|+++++. ..++|++.+....|
T Consensus 30 al~IL~~l~~~~--~~~~lseia~~lgl----pksTv~RlL~tL~~~G~l~~~~---~~~~Y~lG~~l~~L 91 (274)
T PRK11569 30 GLKLLEWIAESN--GSVALTELAQQAGL----PNSTTHRLLTTMQQQGFVRQVG---ELGHWAIGAHAFIV 91 (274)
T ss_pred HHHHHHHHHhCC--CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEcC---CCCeEecCHHHHHH
Confidence 356788888754 58999999999999 9999999999999999999863 46899998765443
No 128
>PF09445 Methyltransf_15: RNA cap guanine-N2 methyltransferase; InterPro: IPR019012 RNA cap guanine-N2 methyltransferases such as Schizosaccharomyces pombe (Fission yeast) trimethylguanosine synthase (Tgs1) and Giardia lamblia (Giardia intestinalis) Tgs2, catalyse the methylation step(s) for the conversion of the 7-monomethylguanosine (m(7)G) caps of snRNAs and snoRNAs to a 2,2,7-trimethylguanosine (m(2,2,7)G) cap structure [, , ]. Trimethylguanosine synthase is specific for guanine, and N7 methylation must precede N2 methylation. This enzyme is required for pre-mRNA splicing, pre-rRNA processing and small ribosomal subunit synthesis. As such, this enzyme plays a role in transcriptional regulation. ; GO: 0008168 methyltransferase activity, 0001510 RNA methylation, 0009452 RNA capping; PDB: 3EGI_B 3GDH_A.
Probab=97.23 E-value=0.00023 Score=55.25 Aligned_cols=62 Identities=16% Similarity=0.266 Sum_probs=44.8
Q ss_pred ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC---CC--C-CCEEEeC
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER---IP--K-GDAILIK 233 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~---~P--~-~D~~~lk 233 (233)
.+|+|+-||.|..++++++.+++ ++.+|+ |.-++.++.+ +||.++.||+++- +. . .|++++.
T Consensus 1 ~~vlD~fcG~GGNtIqFA~~~~~--Viaidid~~~~~~a~hNa~vYGv~~~I~~i~gD~~~~~~~~~~~~~~D~vFlS 76 (163)
T PF09445_consen 1 TTVLDAFCGVGGNTIQFARTFDR--VIAIDIDPERLECAKHNAEVYGVADNIDFICGDFFELLKRLKSNKIFDVVFLS 76 (163)
T ss_dssp SEEEETT-TTSHHHHHHHHTT-E--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHGGGB------SEEEE-
T ss_pred CEEEEeccCcCHHHHHHHHhCCe--EEEEECCHHHHHHHHHHHHHcCCCCcEEEEeCCHHHHHhhccccccccEEEEC
Confidence 47999999999999999999776 777787 4566666653 6999999999983 22 2 3888873
No 129
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=97.20 E-value=0.00077 Score=56.83 Aligned_cols=62 Identities=13% Similarity=0.180 Sum_probs=52.0
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF 88 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l 88 (233)
=+.|++.|...+ ++.|+.|||+.+|+ +...+.|+|..|+..|+|.++. ..+.|++++....|
T Consensus 27 ~l~IL~~~~~~~--~~~tl~eIa~~lgl----pkStv~RlL~tL~~~G~l~~~~---~~~~Y~lG~~l~~L 88 (271)
T PRK10163 27 GIAILQYLEKSG--GSSSVSDISLNLDL----PLSTTFRLLKVLQAADFVYQDS---QLGWWHIGLGVFNV 88 (271)
T ss_pred HHHHHHHHHhCC--CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEcC---CCCeEEecHHHHHH
Confidence 356888888764 57999999999999 9999999999999999999863 46889998765443
No 130
>COG2264 PrmA Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]
Probab=97.20 E-value=0.00073 Score=57.37 Aligned_cols=43 Identities=21% Similarity=0.224 Sum_probs=34.8
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY 210 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~ 210 (233)
.+..+++|||||+|.++++.++- -..+++.+|+.+ +++.|+++
T Consensus 161 ~~g~~vlDvGcGSGILaIAa~kL-GA~~v~g~DiDp~AV~aa~eN 204 (300)
T COG2264 161 KKGKTVLDVGCGSGILAIAAAKL-GAKKVVGVDIDPQAVEAAREN 204 (300)
T ss_pred cCCCEEEEecCChhHHHHHHHHc-CCceEEEecCCHHHHHHHHHH
Confidence 46799999999999999998885 455689999854 67777664
No 131
>COG2518 Pcm Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=97.17 E-value=0.002 Score=51.87 Aligned_cols=72 Identities=14% Similarity=0.252 Sum_probs=56.7
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCCCCCC-C--
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLERIPK-G-- 227 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~~~P~-~-- 227 (233)
.+++.+. .+...+||+||+|+|..+.-+++--- +++-+|+- +..+.|+++ .+|.++.||=.+-+|. +
T Consensus 63 ~m~~~L~-~~~g~~VLEIGtGsGY~aAvla~l~~--~V~siEr~~~L~~~A~~~L~~lg~~nV~v~~gDG~~G~~~~aPy 139 (209)
T COG2518 63 RMLQLLE-LKPGDRVLEIGTGSGYQAAVLARLVG--RVVSIERIEELAEQARRNLETLGYENVTVRHGDGSKGWPEEAPY 139 (209)
T ss_pred HHHHHhC-CCCCCeEEEECCCchHHHHHHHHHhC--eEEEEEEcHHHHHHHHHHHHHcCCCceEEEECCcccCCCCCCCc
Confidence 4556666 78889999999999999988888755 77778874 456667653 6799999999998887 5
Q ss_pred CEEEe
Q 039903 228 DAILI 232 (233)
Q Consensus 228 D~~~l 232 (233)
|.|++
T Consensus 140 D~I~V 144 (209)
T COG2518 140 DRIIV 144 (209)
T ss_pred CEEEE
Confidence 98875
No 132
>PRK11727 23S rRNA mA1618 methyltransferase; Provisional
Probab=97.17 E-value=0.00072 Score=58.24 Aligned_cols=64 Identities=16% Similarity=0.191 Sum_probs=47.7
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEEe----cCcCCCC--CCC--CEE
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHIG----GIMLERI--PKG--DAI 230 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~----gD~f~~~--P~~--D~~ 230 (233)
...++||||||+|.....++.+.|+.+++..|+. .+++.|+++ +||++.. .++|+.+ |.. |++
T Consensus 114 ~~~~vLDIGtGag~I~~lLa~~~~~~~~~atDId~~Al~~A~~Nv~~Np~l~~~I~~~~~~~~~~i~~~i~~~~~~fDli 193 (321)
T PRK11727 114 ANVRVLDIGVGANCIYPLIGVHEYGWRFVGSDIDPQALASAQAIISANPGLNGAIRLRLQKDSKAIFKGIIHKNERFDAT 193 (321)
T ss_pred CCceEEEecCCccHHHHHHHhhCCCCEEEEEeCCHHHHHHHHHHHHhccCCcCcEEEEEccchhhhhhcccccCCceEEE
Confidence 3578999999999998888999999999999984 577777642 4777753 4566532 332 877
Q ss_pred E
Q 039903 231 L 231 (233)
Q Consensus 231 ~ 231 (233)
+
T Consensus 194 v 194 (321)
T PRK11727 194 L 194 (321)
T ss_pred E
Confidence 6
No 133
>KOG1271 consensus Methyltransferases [General function prediction only]
Probab=97.16 E-value=0.001 Score=52.19 Aligned_cols=64 Identities=16% Similarity=0.243 Sum_probs=45.9
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC------C-CCceEEecCcCCC--CCCC-CEEE
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS------Y-SGVKHIGGIMLER--IPKG-DAIL 231 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~------~-~ri~~~~gD~f~~--~P~~-D~~~ 231 (233)
+..+|||+|||.|+++..|++.--.-+.+..|.. .+++.|+. . +.|+|...|+++| .+.. |+|+
T Consensus 67 ~A~~VlDLGtGNG~~L~~L~~egf~~~L~GvDYs~~AV~LA~niAe~~~~~n~I~f~q~DI~~~~~~~~qfdlvl 141 (227)
T KOG1271|consen 67 QADRVLDLGTGNGHLLFQLAKEGFQSKLTGVDYSEKAVELAQNIAERDGFSNEIRFQQLDITDPDFLSGQFDLVL 141 (227)
T ss_pred cccceeeccCCchHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHhcCCCcceeEEEeeccCCcccccceeEEe
Confidence 3459999999999999999987444345677764 35555542 2 4499999999984 3333 7776
No 134
>PLN02585 magnesium protoporphyrin IX methyltransferase
Probab=97.15 E-value=0.00092 Score=57.55 Aligned_cols=61 Identities=13% Similarity=0.039 Sum_probs=45.6
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC-----------CCceEEecCcCCCCCC-CCEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY-----------SGVKHIGGIMLERIPK-GDAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~-----------~ri~~~~gD~f~~~P~-~D~~~l 232 (233)
..+|||||||+|.++..++++ ..+++.+|+.+ .++.++++ .+++|..+|+.+ ++. -|+|+.
T Consensus 145 ~~~VLDlGcGtG~~a~~la~~--g~~V~gvD~S~~ml~~A~~~~~~~~~~~~~~~~~~f~~~Dl~~-l~~~fD~Vv~ 218 (315)
T PLN02585 145 GVTVCDAGCGTGSLAIPLALE--GAIVSASDISAAMVAEAERRAKEALAALPPEVLPKFEANDLES-LSGKYDTVTC 218 (315)
T ss_pred CCEEEEecCCCCHHHHHHHHC--CCEEEEEECCHHHHHHHHHHHHhcccccccccceEEEEcchhh-cCCCcCEEEE
Confidence 479999999999999999986 56899999854 66666542 357888888753 233 387763
No 135
>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=97.15 E-value=0.00082 Score=55.81 Aligned_cols=59 Identities=19% Similarity=0.223 Sum_probs=50.6
Q ss_pred hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903 19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF 88 (233)
Q Consensus 19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l 88 (233)
+.|.+.|...+ .+.|+.|||+.+|+ +...+.|+|..|+..|+++++ ++.|++.+.-..|
T Consensus 12 l~IL~~l~~~~--~~~~l~eia~~lgl----pksT~~RlL~tL~~~G~l~~~-----~~~Y~lG~~~~~l 70 (248)
T TIGR02431 12 LAVIEAFGAER--PRLTLTDVAEATGL----TRAAARRFLLTLVELGYVTSD-----GRLFWLTPRVLRL 70 (248)
T ss_pred HHHHHHHhcCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeC-----CCEEEecHHHHHH
Confidence 56788887654 58999999999999 999999999999999999984 6889999865444
No 136
>PRK13255 thiopurine S-methyltransferase; Reviewed
Probab=97.15 E-value=0.0018 Score=52.79 Aligned_cols=64 Identities=9% Similarity=0.089 Sum_probs=47.8
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC------------------CCCceEEecCcCCCCCC
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS------------------YSGVKHIGGIMLERIPK 226 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~------------------~~ri~~~~gD~f~~~P~ 226 (233)
..+..+++|+|||.|..+..|+++ ..+++.+|+.+ .++.+.. ..+|++..+|+|+..|.
T Consensus 35 ~~~~~rvL~~gCG~G~da~~LA~~--G~~V~avD~s~~Ai~~~~~~~~l~~~~~~~~~~~~~~~~~v~~~~~D~~~l~~~ 112 (218)
T PRK13255 35 LPAGSRVLVPLCGKSLDMLWLAEQ--GHEVLGVELSELAVEQFFAENGLTPQTRQSGEFEHYQAGEITIYCGDFFALTAA 112 (218)
T ss_pred CCCCCeEEEeCCCChHhHHHHHhC--CCeEEEEccCHHHHHHHHHHcCCCccccccccccccccCceEEEECcccCCCcc
Confidence 344579999999999999999985 77899999864 5554311 15799999999984332
Q ss_pred --C--CEEE
Q 039903 227 --G--DAIL 231 (233)
Q Consensus 227 --~--D~~~ 231 (233)
+ |+++
T Consensus 113 ~~~~fd~v~ 121 (218)
T PRK13255 113 DLADVDAVY 121 (218)
T ss_pred cCCCeeEEE
Confidence 2 6665
No 137
>PRK00536 speE spermidine synthase; Provisional
Probab=97.14 E-value=0.001 Score=55.71 Aligned_cols=62 Identities=15% Similarity=0.109 Sum_probs=48.7
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC----------CCceEEecCcCCCCC-CC-CEEEe
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY----------SGVKHIGGIMLERIP-KG-DAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~----------~ri~~~~gD~f~~~P-~~-D~~~l 232 (233)
+++++||=||||.|..++++++. |. +++.+|+. .|++.++++ +|++.+. ++.+.. .- |+|++
T Consensus 71 ~~pk~VLIiGGGDGg~~REvLkh-~~-~v~mVeID~~Vv~~~k~~lP~~~~~~~DpRv~l~~--~~~~~~~~~fDVIIv 145 (262)
T PRK00536 71 KELKEVLIVDGFDLELAHQLFKY-DT-HVDFVQADEKILDSFISFFPHFHEVKNNKNFTHAK--QLLDLDIKKYDLIIC 145 (262)
T ss_pred CCCCeEEEEcCCchHHHHHHHCc-CC-eeEEEECCHHHHHHHHHHCHHHHHhhcCCCEEEee--hhhhccCCcCCEEEE
Confidence 56799999999999999999995 66 99999995 588888762 7999886 344323 33 88875
No 138
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=97.13 E-value=0.0011 Score=55.70 Aligned_cols=64 Identities=13% Similarity=0.123 Sum_probs=53.2
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL 90 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~ 90 (233)
-+.|++.|...+ ++.|+.|||+.+++ +...+.|+|+.|+..|+++++. +.+.|++++....|..
T Consensus 13 al~iL~~l~~~~--~~ls~~eia~~lgl----~kstv~RlL~tL~~~g~v~~~~---~~~~Y~Lg~~~~~l~~ 76 (263)
T PRK09834 13 GLMVLRALNRLD--GGATVGLLAELTGL----HRTTVRRLLETLQEEGYVRRSA---SDDSFRLTLKVRQLSE 76 (263)
T ss_pred HHHHHHHHHhcC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEec---CCCcEEEcHHHHHHHH
Confidence 356788887754 46999999999999 9999999999999999999863 3678999987665543
No 139
>KOG2899 consensus Predicted methyltransferase [General function prediction only]
Probab=97.12 E-value=0.00063 Score=55.63 Aligned_cols=54 Identities=17% Similarity=0.199 Sum_probs=45.0
Q ss_pred HHHHHhcc-cccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC
Q 039903 157 NRIIDSSK-GFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY 210 (233)
Q Consensus 157 ~~~~~~~~-~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~ 210 (233)
+..++.++ +|-....+|||||++|.++..+++.|-....+.+|+.+ -|+.|+++
T Consensus 46 D~rLk~L~~~~f~~~~~LDIGCNsG~lt~~iak~F~~r~iLGvDID~~LI~~Ark~ 101 (288)
T KOG2899|consen 46 DPRLKVLEKDWFEPKQALDIGCNSGFLTLSIAKDFGPRRILGVDIDPVLIQRARKE 101 (288)
T ss_pred ChhhhhccccccCcceeEeccCCcchhHHHHHHhhccceeeEeeccHHHHHHHHHh
Confidence 45566665 36777999999999999999999999999999999966 56778764
No 140
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=97.12 E-value=0.00093 Score=55.83 Aligned_cols=60 Identities=13% Similarity=0.234 Sum_probs=50.4
Q ss_pred hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903 19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF 88 (233)
Q Consensus 19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l 88 (233)
+.|.+.|... ++.|+.|||+.+|+ +...+.|+|+.|+..|+++++. +++.|++.+....|
T Consensus 17 l~IL~~l~~~---~~l~l~eia~~lgl----~kstv~Rll~tL~~~G~l~~~~---~~~~Y~lG~~~~~l 76 (257)
T PRK15090 17 FGILQALGEE---REIGITELSQRVMM----SKSTVYRFLQTMKTLGYVAQEG---ESEKYSLTLKLFEL 76 (257)
T ss_pred HHHHHHhhcC---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEcC---CCCcEEecHHHHHH
Confidence 4577777764 48999999999999 9999999999999999999863 46889999765444
No 141
>TIGR01177 conserved hypothetical protein TIGR01177. This family is found exclusively in the Archaea.
Probab=97.10 E-value=0.0016 Score=56.40 Aligned_cols=71 Identities=13% Similarity=0.050 Sum_probs=52.2
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCC--CC
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPK--GD 228 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~--~D 228 (233)
++.... ++...+++|+|||+|.++++.+.. ..+++..|+ +..++.++.+ +.+.++.+|+.+ +++. .|
T Consensus 174 ~~~l~~-~~~g~~vLDp~cGtG~~lieaa~~--~~~v~g~Di~~~~~~~a~~nl~~~g~~~i~~~~~D~~~l~~~~~~~D 250 (329)
T TIGR01177 174 MVNLAR-VTEGDRVLDPFCGTGGFLIEAGLM--GAKVIGCDIDWKMVAGARINLEHYGIEDFFVKRGDATKLPLSSESVD 250 (329)
T ss_pred HHHHhC-CCCcCEEEECCCCCCHHHHHHHHh--CCeEEEEcCCHHHHHHHHHHHHHhCCCCCeEEecchhcCCcccCCCC
Confidence 333334 666789999999999999887653 677899998 4567665543 458899999998 6654 38
Q ss_pred EEEe
Q 039903 229 AILI 232 (233)
Q Consensus 229 ~~~l 232 (233)
+++.
T Consensus 251 ~Iv~ 254 (329)
T TIGR01177 251 AIAT 254 (329)
T ss_pred EEEE
Confidence 8875
No 142
>PRK00517 prmA ribosomal protein L11 methyltransferase; Reviewed
Probab=97.08 E-value=0.00061 Score=56.70 Aligned_cols=42 Identities=19% Similarity=0.216 Sum_probs=33.0
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS 209 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~ 209 (233)
....+++|||||+|.+++.+++..+. +++.+|+. ..++.+++
T Consensus 118 ~~~~~VLDiGcGsG~l~i~~~~~g~~-~v~giDis~~~l~~A~~ 160 (250)
T PRK00517 118 LPGKTVLDVGCGSGILAIAAAKLGAK-KVLAVDIDPQAVEAARE 160 (250)
T ss_pred CCCCEEEEeCCcHHHHHHHHHHcCCC-eEEEEECCHHHHHHHHH
Confidence 45689999999999999987775544 68999984 56776665
No 143
>PTZ00146 fibrillarin; Provisional
Probab=97.08 E-value=0.0023 Score=54.22 Aligned_cols=67 Identities=13% Similarity=0.058 Sum_probs=51.0
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeechH-----HHhhccCCCCceEEecCcCCCC------CCCCEEEe
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLSH-----VIQDSSSYSGVKHIGGIMLERI------PKGDAILI 232 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp~-----v~~~a~~~~ri~~~~gD~f~~~------P~~D~~~l 232 (233)
++...+|||+|||+|.++..+++... .=+++.+|+.+ .++.++..++|.++.+|...+. +..|++++
T Consensus 130 IkpG~~VLDLGaG~G~~t~~lAdiVG~~G~VyAVD~s~r~~~dLl~~ak~r~NI~~I~~Da~~p~~y~~~~~~vDvV~~ 208 (293)
T PTZ00146 130 IKPGSKVLYLGAASGTTVSHVSDLVGPEGVVYAVEFSHRSGRDLTNMAKKRPNIVPIIEDARYPQKYRMLVPMVDVIFA 208 (293)
T ss_pred cCCCCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEECcHHHHHHHHHHhhhcCCCEEEECCccChhhhhcccCCCCEEEE
Confidence 45668999999999999999999863 55788889764 4555555578999999987542 22498875
No 144
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=97.08 E-value=0.0014 Score=44.32 Aligned_cols=50 Identities=18% Similarity=0.193 Sum_probs=41.2
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL 90 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~ 90 (233)
++.+..+|+..+++ +...+.+.|+.|...|+++. .++.|.+|+.|..++.
T Consensus 18 ~~~~~t~i~~~~~L----~~~~~~~yL~~L~~~gLI~~-----~~~~Y~lTekG~~~l~ 67 (77)
T PF14947_consen 18 GGAKKTEIMYKANL----NYSTLKKYLKELEEKGLIKK-----KDGKYRLTEKGKEFLE 67 (77)
T ss_dssp T-B-HHHHHTTST------HHHHHHHHHHHHHTTSEEE-----ETTEEEE-HHHHHHHH
T ss_pred CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCcCeeC-----CCCEEEECccHHHHHH
Confidence 68999999999999 99999999999999999977 4899999999987653
No 145
>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=97.05 E-value=0.0008 Score=46.20 Aligned_cols=55 Identities=22% Similarity=0.265 Sum_probs=42.4
Q ss_pred HHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 23 EIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 23 d~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
-.|+..+.+++.|..|||+.+++ ++..++++++.|...|+++.... .+|.|.++.
T Consensus 15 ~~la~~~~~~~~s~~eiA~~~~i----~~~~l~kil~~L~~~Gli~s~~G--~~GGy~L~~ 69 (83)
T PF02082_consen 15 LYLARHPDGKPVSSKEIAERLGI----SPSYLRKILQKLKKAGLIESSRG--RGGGYRLAR 69 (83)
T ss_dssp HHHHCTTTSC-BEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEETS--TTSEEEESS
T ss_pred HHHHhCCCCCCCCHHHHHHHHCc----CHHHHHHHHHHHhhCCeeEecCC--CCCceeecC
Confidence 33454433346999999999999 99999999999999999987642 468888875
No 146
>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=97.02 E-value=0.0019 Score=58.18 Aligned_cols=96 Identities=21% Similarity=0.207 Sum_probs=61.1
Q ss_pred ccccccccCchHHHHHHHHHHhcchhcHHHHHHhcccc---cCcceEEEecCCccHHHHHHHHH----cCCCcEEEeech
Q 039903 129 GFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGF---EQIKQLVDVGGGLGVNVNIIISN----YLHIKGVNFDLS 201 (233)
Q Consensus 129 ~~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~~---~~~~~vvDvGGG~G~~~~~l~~~----~P~l~~~v~Dlp 201 (233)
..||.+++|+..-+.+.+|+.. .+.+....- .+...|+|||+|+|-++...+++ .-..++..++-.
T Consensus 151 ~tYe~fE~D~vKY~~Ye~AI~~-------al~D~~~~~~~~~~~~vVldVGAGrGpL~~~al~A~~~~~~a~~VyAVEkn 223 (448)
T PF05185_consen 151 QTYEVFEKDPVKYDQYERAIEE-------ALKDRVRKNSYSSKDKVVLDVGAGRGPLSMFALQAGARAGGAVKVYAVEKN 223 (448)
T ss_dssp HHHHHHCC-HHHHHHHHHHHHH-------HHHHHHTTS-SEETT-EEEEES-TTSHHHHHHHHTTHHHCCESEEEEEESS
T ss_pred ccHhhHhcCHHHHHHHHHHHHH-------HHHhhhhhccccccceEEEEeCCCccHHHHHHHHHHHHhCCCeEEEEEcCC
Confidence 3577788888877778877642 222221111 13578999999999998666554 346788888864
Q ss_pred H-HHhhc----cCC---CCceEEecCcCC-CCCC-CCEEE
Q 039903 202 H-VIQDS----SSY---SGVKHIGGIMLE-RIPK-GDAIL 231 (233)
Q Consensus 202 ~-v~~~a----~~~---~ri~~~~gD~f~-~~P~-~D~~~ 231 (233)
+ ++... +.+ ++|+++.+|+-+ +.|+ +|+++
T Consensus 224 ~~A~~~l~~~v~~n~w~~~V~vi~~d~r~v~lpekvDIIV 263 (448)
T PF05185_consen 224 PNAVVTLQKRVNANGWGDKVTVIHGDMREVELPEKVDIIV 263 (448)
T ss_dssp THHHHHHHHHHHHTTTTTTEEEEES-TTTSCHSS-EEEEE
T ss_pred HhHHHHHHHHHHhcCCCCeEEEEeCcccCCCCCCceeEEE
Confidence 3 33221 222 899999999999 8887 59875
No 147
>KOG1499 consensus Protein arginine N-methyltransferase PRMT1 and related enzymes [Posttranslational modification, protein turnover, chaperones; Transcription; Signal transduction mechanisms]
Probab=97.01 E-value=0.001 Score=57.13 Aligned_cols=62 Identities=21% Similarity=0.227 Sum_probs=51.0
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccC----C---CCceEEecCcCC-CCCC-C-CEEE
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSS----Y---SGVKHIGGIMLE-RIPK-G-DAIL 231 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~----~---~ri~~~~gD~f~-~~P~-~-D~~~ 231 (233)
.++|+|||||+|.+++-.+++. ..++..+|-.++++.|.+ + +.|+++.|..-+ ++|. . |+++
T Consensus 61 dK~VlDVGcGtGILS~F~akAG-A~~V~aVe~S~ia~~a~~iv~~N~~~~ii~vi~gkvEdi~LP~eKVDiIv 132 (346)
T KOG1499|consen 61 DKTVLDVGCGTGILSMFAAKAG-ARKVYAVEASSIADFARKIVKDNGLEDVITVIKGKVEDIELPVEKVDIIV 132 (346)
T ss_pred CCEEEEcCCCccHHHHHHHHhC-cceEEEEechHHHHHHHHHHHhcCccceEEEeecceEEEecCccceeEEe
Confidence 4899999999999999999887 678899998887777654 2 679999998888 8883 4 8764
No 148
>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=97.01 E-value=0.0012 Score=53.38 Aligned_cols=74 Identities=19% Similarity=0.253 Sum_probs=46.4
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC---------------CCCceEEecCcC
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS---------------YSGVKHIGGIML 221 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~---------------~~ri~~~~gD~f 221 (233)
.+++.+. .....+++|||+|.|....+.+-.++--+++++++- ...+.|.. ..+|++..|||+
T Consensus 33 ~il~~~~-l~~~dvF~DlGSG~G~~v~~aal~~~~~~~~GIEi~~~~~~~a~~~~~~~~~~~~~~g~~~~~v~l~~gdfl 111 (205)
T PF08123_consen 33 KILDELN-LTPDDVFYDLGSGVGNVVFQAALQTGCKKSVGIEILPELHDLAEELLEELKKRMKHYGKRPGKVELIHGDFL 111 (205)
T ss_dssp HHHHHTT---TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE-SHHHHHHHHHHHHHHHHHHHHCTB---EEEEECS-TT
T ss_pred HHHHHhC-CCCCCEEEECCCCCCHHHHHHHHHcCCcEEEEEEechHHHHHHHHHHHHHHHHHHHhhcccccceeeccCcc
Confidence 4555555 666789999999999999888887776669999874 34433322 157899999999
Q ss_pred C-C-----CCCCCEEEe
Q 039903 222 E-R-----IPKGDAILI 232 (233)
Q Consensus 222 ~-~-----~P~~D~~~l 232 (233)
+ + +..||++++
T Consensus 112 ~~~~~~~~~s~AdvVf~ 128 (205)
T PF08123_consen 112 DPDFVKDIWSDADVVFV 128 (205)
T ss_dssp THHHHHHHGHC-SEEEE
T ss_pred ccHhHhhhhcCCCEEEE
Confidence 7 3 244798876
No 149
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=97.00 E-value=0.002 Score=57.90 Aligned_cols=73 Identities=14% Similarity=0.064 Sum_probs=54.4
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCCC---CCC--C
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLER---IPK--G 227 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~~---~P~--~ 227 (233)
++..++ .....+|+|+|||+|..+..+++..++.+++.+|+ ++.++.++++ -+++++.+|..+. .+. .
T Consensus 236 ~~~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~~~~v~a~D~s~~~l~~~~~n~~~~g~~~~~~~~D~~~~~~~~~~~~f 314 (427)
T PRK10901 236 AATLLA-PQNGERVLDACAAPGGKTAHILELAPQAQVVALDIDAQRLERVRENLQRLGLKATVIVGDARDPAQWWDGQPF 314 (427)
T ss_pred HHHHcC-CCCCCEEEEeCCCCChHHHHHHHHcCCCEEEEEeCCHHHHHHHHHHHHHcCCCeEEEEcCcccchhhcccCCC
Confidence 333444 45568999999999999999999998888999998 4566666543 2478899999862 222 3
Q ss_pred CEEEe
Q 039903 228 DAILI 232 (233)
Q Consensus 228 D~~~l 232 (233)
|.|++
T Consensus 315 D~Vl~ 319 (427)
T PRK10901 315 DRILL 319 (427)
T ss_pred CEEEE
Confidence 88874
No 150
>KOG1500 consensus Protein arginine N-methyltransferase CARM1 [Posttranslational modification, protein turnover, chaperones; Transcription]
Probab=96.99 E-value=0.0019 Score=55.33 Aligned_cols=64 Identities=23% Similarity=0.346 Sum_probs=50.7
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCC-CCCCC-CEEE
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLE-RIPKG-DAIL 231 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~-~~P~~-D~~~ 231 (233)
|++ +.|||||+|+|.++.-.+++- .-++-.++-.+..+.|++. +||+.++|-.-+ ++|+. |+++
T Consensus 176 F~~-kiVlDVGaGSGILS~FAaqAG-A~~vYAvEAS~MAqyA~~Lv~~N~~~~rItVI~GKiEdieLPEk~DviI 248 (517)
T KOG1500|consen 176 FQD-KIVLDVGAGSGILSFFAAQAG-AKKVYAVEASEMAQYARKLVASNNLADRITVIPGKIEDIELPEKVDVII 248 (517)
T ss_pred cCC-cEEEEecCCccHHHHHHHHhC-cceEEEEehhHHHHHHHHHHhcCCccceEEEccCccccccCchhccEEE
Confidence 655 789999999999987776653 3456677777777777652 899999999998 99984 9875
No 151
>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=96.96 E-value=0.00081 Score=59.34 Aligned_cols=62 Identities=11% Similarity=0.050 Sum_probs=47.7
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC---C-CCEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP---K-GDAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P---~-~D~~~l 232 (233)
..+++|+|||+|.++..++.+ ..+++.+|. |+.++.|+++ ++++++.+|+.+..+ . .|++++
T Consensus 234 ~~~vLDL~cG~G~~~l~la~~--~~~v~~vE~~~~av~~a~~N~~~~~~~~~~~~~~d~~~~~~~~~~~~D~vi~ 306 (374)
T TIGR02085 234 VTQMWDLFCGVGGFGLHCAGP--DTQLTGIEIESEAIACAQQSAQMLGLDNLSFAALDSAKFATAQMSAPELVLV 306 (374)
T ss_pred CCEEEEccCCccHHHHHHhhc--CCeEEEEECCHHHHHHHHHHHHHcCCCcEEEEECCHHHHHHhcCCCCCEEEE
Confidence 468999999999999999964 467899997 5577766653 579999999976222 2 388875
No 152
>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=96.96 E-value=0.0036 Score=47.62 Aligned_cols=39 Identities=21% Similarity=0.373 Sum_probs=31.2
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhh
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQD 206 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~ 206 (233)
.....+|||||||.|.++..+++..+ +++.+|..+ .++.
T Consensus 20 ~~~~~~vLDiGcG~G~~~~~l~~~~~--~~~g~D~~~~~~~~ 59 (161)
T PF13489_consen 20 LKPGKRVLDIGCGTGSFLRALAKRGF--EVTGVDISPQMIEK 59 (161)
T ss_dssp TTTTSEEEEESSTTSHHHHHHHHTTS--EEEEEESSHHHHHH
T ss_pred cCCCCEEEEEcCCCCHHHHHHHHhCC--EEEEEECCHHHHhh
Confidence 35668999999999999999966644 899999854 5544
No 153
>KOG0820 consensus Ribosomal RNA adenine dimethylase [RNA processing and modification]
Probab=96.96 E-value=0.0028 Score=52.80 Aligned_cols=73 Identities=15% Similarity=0.336 Sum_probs=54.6
Q ss_pred HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----C---CCceEEecCcCC-CCCC
Q 039903 156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----Y---SGVKHIGGIMLE-RIPK 226 (233)
Q Consensus 156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----~---~ri~~~~gD~f~-~~P~ 226 (233)
+..++..-+ .+....|+.||.|+|.+...++++ .-+++.+++ |..++...+ . ...+.+.|||++ ++|-
T Consensus 47 ~~~I~~ka~-~k~tD~VLEvGPGTGnLT~~lLe~--~kkVvA~E~Dprmvael~krv~gtp~~~kLqV~~gD~lK~d~P~ 123 (315)
T KOG0820|consen 47 IDQIVEKAD-LKPTDVVLEVGPGTGNLTVKLLEA--GKKVVAVEIDPRMVAELEKRVQGTPKSGKLQVLHGDFLKTDLPR 123 (315)
T ss_pred HHHHHhccC-CCCCCEEEEeCCCCCHHHHHHHHh--cCeEEEEecCcHHHHHHHHHhcCCCccceeeEEecccccCCCcc
Confidence 345666656 778899999999999999999998 445777776 455544332 2 579999999999 8887
Q ss_pred CCEEE
Q 039903 227 GDAIL 231 (233)
Q Consensus 227 ~D~~~ 231 (233)
-|.++
T Consensus 124 fd~cV 128 (315)
T KOG0820|consen 124 FDGCV 128 (315)
T ss_pred cceee
Confidence 65543
No 154
>COG0220 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]
Probab=96.92 E-value=0.0014 Score=53.67 Aligned_cols=53 Identities=9% Similarity=0.172 Sum_probs=42.0
Q ss_pred ceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC----C--CCceEEecCcCC
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS----Y--SGVKHIGGIMLE 222 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~--~ri~~~~gD~f~ 222 (233)
..+|+||||.|.+...+++++|+.-++++|.- .++..+.. . ++|..+.+|.-+
T Consensus 50 pi~lEIGfG~G~~l~~~A~~nP~~nfiGiEi~~~~v~~~l~k~~~~~l~Nlri~~~DA~~ 109 (227)
T COG0220 50 PIVLEIGFGMGEFLVEMAKKNPEKNFLGIEIRVPGVAKALKKIKELGLKNLRLLCGDAVE 109 (227)
T ss_pred cEEEEECCCCCHHHHHHHHHCCCCCEEEEEEehHHHHHHHHHHHHcCCCcEEEEcCCHHH
Confidence 68999999999999999999999999999973 34433322 1 478888887665
No 155
>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=96.91 E-value=0.0011 Score=55.18 Aligned_cols=66 Identities=18% Similarity=0.242 Sum_probs=51.3
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----------CCceEEecCcCC---CCCC-C-CEE
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----------SGVKHIGGIMLE---RIPK-G-DAI 230 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----------~ri~~~~gD~f~---~~P~-~-D~~ 230 (233)
++.++||=||||.|..+.++++..|-.+++++|+ |.|++.+++. +|++.+.+|-+. ..+. . |+|
T Consensus 75 ~~p~~VLiiGgG~G~~~~ell~~~~~~~i~~VEiD~~Vv~~a~~~f~~~~~~~~d~r~~i~~~Dg~~~l~~~~~~~yDvI 154 (246)
T PF01564_consen 75 PNPKRVLIIGGGDGGTARELLKHPPVESITVVEIDPEVVELARKYFPEFSEGLDDPRVRIIIGDGRKFLKETQEEKYDVI 154 (246)
T ss_dssp SST-EEEEEESTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHTHHHHTTGGSTTEEEEESTHHHHHHTSSST-EEEE
T ss_pred CCcCceEEEcCCChhhhhhhhhcCCcceEEEEecChHHHHHHHHhchhhccccCCCceEEEEhhhHHHHHhccCCcccEE
Confidence 5689999999999999999998666778999999 5588877652 699999999875 4455 4 877
Q ss_pred Ee
Q 039903 231 LI 232 (233)
Q Consensus 231 ~l 232 (233)
++
T Consensus 155 i~ 156 (246)
T PF01564_consen 155 IV 156 (246)
T ss_dssp EE
T ss_pred EE
Confidence 64
No 156
>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=96.91 E-value=0.0015 Score=52.78 Aligned_cols=67 Identities=18% Similarity=0.275 Sum_probs=51.8
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCC-------CC--
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIP-------KG-- 227 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P-------~~-- 227 (233)
..+.+++|+||++.|.-+..+++..| +.+++-+|.. +-.+.|+++ +||+++.||..+.+| .+
T Consensus 43 ~~~~k~vLEIGt~~GySal~la~~l~~~g~i~tiE~~~~~~~~A~~~~~~ag~~~~I~~~~gda~~~l~~l~~~~~~~~f 122 (205)
T PF01596_consen 43 LTRPKRVLEIGTFTGYSALWLAEALPEDGKITTIEIDPERAEIARENFRKAGLDDRIEVIEGDALEVLPELANDGEEGQF 122 (205)
T ss_dssp HHT-SEEEEESTTTSHHHHHHHHTSTTTSEEEEEESSHHHHHHHHHHHHHTTGGGGEEEEES-HHHHHHHHHHTTTTTSE
T ss_pred hcCCceEEEeccccccHHHHHHHhhcccceEEEecCcHHHHHHHHHHHHhcCCCCcEEEEEeccHhhHHHHHhccCCCce
Confidence 46789999999999999999999987 5899999984 466666542 799999999986332 12
Q ss_pred CEEEe
Q 039903 228 DAILI 232 (233)
Q Consensus 228 D~~~l 232 (233)
|++++
T Consensus 123 D~VFi 127 (205)
T PF01596_consen 123 DFVFI 127 (205)
T ss_dssp EEEEE
T ss_pred eEEEE
Confidence 88876
No 157
>PF13679 Methyltransf_32: Methyltransferase domain
Probab=96.90 E-value=0.0015 Score=49.47 Aligned_cols=57 Identities=14% Similarity=0.255 Sum_probs=42.1
Q ss_pred ccCcceEEEecCCccHHHHHHHHH----cCCCcEEEeech-HHHhhccCC---------CCceEEecCcCC
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISN----YLHIKGVNFDLS-HVIQDSSSY---------SGVKHIGGIMLE 222 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~----~P~l~~~v~Dlp-~v~~~a~~~---------~ri~~~~gD~f~ 222 (233)
-.+..+|||+|||.|+++..++.. .|+++++.+|.. +.++.+.+. .++++..+++..
T Consensus 23 ~~~~~~vvD~GsG~GyLs~~La~~l~~~~~~~~v~~iD~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~ 93 (141)
T PF13679_consen 23 SKRCITVVDLGSGKGYLSRALAHLLCNSSPNLRVLGIDCNESLVESAQKRAQKLGSDLEKRLSFIQGDIAD 93 (141)
T ss_pred cCCCCEEEEeCCChhHHHHHHHHHHHhcCCCCeEEEEECCcHHHHHHHHHHHHhcchhhccchhhccchhh
Confidence 366789999999999999999992 288999999974 344444331 456777766654
No 158
>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=96.90 E-value=0.0011 Score=42.75 Aligned_cols=54 Identities=13% Similarity=0.246 Sum_probs=46.8
Q ss_pred HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
..+|..-.++.|++.|... +|.|+.|||+.+++ ++..+.+-|+.|...|+++..
T Consensus 4 ~~aL~~p~R~~Il~~L~~~---~~~t~~ela~~l~~----~~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 4 FKALSDPTRLRILRLLASN---GPMTVSELAEELGI----SQSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp HHHHTSHHHHHHHHHHHHC---STBEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHhCCHHHHHHHHHHhcC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEe
Confidence 4566667889999999554 69999999999999 999999999999999999986
No 159
>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=96.88 E-value=0.0011 Score=59.67 Aligned_cols=65 Identities=15% Similarity=0.284 Sum_probs=50.3
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC-----C--CCEEE
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP-----K--GDAIL 231 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P-----~--~D~~~ 231 (233)
..+..+++|+|||+|.++..+++... +++.+|. ++.++.|+++ ++|+++.+|+.+.+| . .|+++
T Consensus 290 ~~~~~~vLDl~cG~G~~sl~la~~~~--~V~~vE~~~~av~~a~~n~~~~~~~nv~~~~~d~~~~l~~~~~~~~~~D~vi 367 (431)
T TIGR00479 290 LQGEELVVDAYCGVGTFTLPLAKQAK--SVVGIEVVPESVEKAQQNAELNGIANVEFLAGTLETVLPKQPWAGQIPDVLL 367 (431)
T ss_pred cCCCCEEEEcCCCcCHHHHHHHHhCC--EEEEEEcCHHHHHHHHHHHHHhCCCceEEEeCCHHHHHHHHHhcCCCCCEEE
Confidence 45567999999999999999998753 6899998 5678777653 689999999865221 1 38887
Q ss_pred e
Q 039903 232 I 232 (233)
Q Consensus 232 l 232 (233)
+
T Consensus 368 ~ 368 (431)
T TIGR00479 368 L 368 (431)
T ss_pred E
Confidence 5
No 160
>PLN02476 O-methyltransferase
Probab=96.87 E-value=0.0035 Score=52.92 Aligned_cols=67 Identities=13% Similarity=0.111 Sum_probs=53.2
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCC--------CC-
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIP--------KG- 227 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P--------~~- 227 (233)
..+.+++|+||.+.|..+..+++..| +-+++-+|.. +..+.|+++ ++|+++.||..+.+| ..
T Consensus 116 ~~~ak~VLEIGT~tGySal~lA~al~~~G~V~TiE~d~e~~~~Ar~n~~~aGl~~~I~li~GdA~e~L~~l~~~~~~~~F 195 (278)
T PLN02476 116 ILGAERCIEVGVYTGYSSLAVALVLPESGCLVACERDSNSLEVAKRYYELAGVSHKVNVKHGLAAESLKSMIQNGEGSSY 195 (278)
T ss_pred hcCCCeEEEecCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEEcCHHHHHHHHHhcccCCCC
Confidence 56789999999999999999999876 6678889985 466666553 699999999987332 23
Q ss_pred CEEEe
Q 039903 228 DAILI 232 (233)
Q Consensus 228 D~~~l 232 (233)
|++++
T Consensus 196 D~VFI 200 (278)
T PLN02476 196 DFAFV 200 (278)
T ss_pred CEEEE
Confidence 88876
No 161
>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=96.86 E-value=0.0027 Score=41.42 Aligned_cols=58 Identities=14% Similarity=0.273 Sum_probs=41.5
Q ss_pred hhHHHH-hcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhh
Q 039903 21 VFEIIA-KAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVA 85 (233)
Q Consensus 21 lfd~L~-~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s 85 (233)
|...|. .. ++.+..+||+.+++ +...+.+.++.|...|++++..+.. ....|++|+.|
T Consensus 8 vL~~l~~~~---~~~t~~~l~~~~~~----~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 8 VLRALAHSD---GPMTQSDLAERLGI----SKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHHHT--T---S-BEHHHHHHHTT------HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHHHccC---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 444555 32 69999999999999 9999999999999999998765431 22468888865
No 162
>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=96.85 E-value=0.00095 Score=43.93 Aligned_cols=48 Identities=21% Similarity=0.236 Sum_probs=41.8
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS 71 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~ 71 (233)
.+..++..|... ++.|..|||+.+++ +...+.+.|+.|...|++++..
T Consensus 9 ~E~~vy~~Ll~~---~~~t~~eIa~~l~i----~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 9 NEAKVYLALLKN---GPATAEEIAEELGI----SRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHHH---CHEEHHHHHHHHTS----SHHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEc
Confidence 355677777655 69999999999999 9999999999999999999874
No 163
>TIGR01444 fkbM_fam methyltransferase, FkbM family. Members of this family are characterized by two well-conserved short regions separated by a variable in both sequence and length. The first of the two regions is found in a large number of proteins outside this subfamily, a number of which have been characterized as methyltransferases. One member of the present family, FkbM, was shown to be required for a specific methylation in the biosynthesis of the immunosuppressant FK506 in Streptomyces strain MA6548.
Probab=96.82 E-value=0.0018 Score=48.66 Aligned_cols=52 Identities=12% Similarity=0.135 Sum_probs=39.4
Q ss_pred eEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC
Q 039903 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE 222 (233)
Q Consensus 171 ~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~ 222 (233)
+++|||||.|.++..+++.+|+.+++.+|. |...+.++++ ++++++...+..
T Consensus 1 ~vlDiGa~~G~~~~~~~~~~~~~~v~~~E~~~~~~~~l~~~~~~n~~~~v~~~~~al~~ 59 (143)
T TIGR01444 1 VVIDVGANIGDTSLYFARKGAEGRVIAFEPLPDAYEILEENVKLNNLPNVVLLNAAVGD 59 (143)
T ss_pred CEEEccCCccHHHHHHHHhCCCCEEEEEecCHHHHHHHHHHHHHcCCCcEEEEEeeeeC
Confidence 589999999999999999999999999996 4555544331 346666555543
No 164
>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=96.82 E-value=0.0011 Score=40.31 Aligned_cols=44 Identities=11% Similarity=0.277 Sum_probs=39.2
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC 69 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~ 69 (233)
++.|...|.+ +|.++.|||+.+++ +...+.+-|+.|...|++++
T Consensus 4 R~~Il~~L~~----~~~~~~el~~~l~~----s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 4 RLRILKLLSE----GPLTVSELAEELGL----SQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHHTT----SSEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHh----CCCchhhHHHhccc----cchHHHHHHHHHHHCcCeeC
Confidence 5678888888 69999999999999 99999999999999999874
No 165
>PRK05134 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional
Probab=96.74 E-value=0.005 Score=50.39 Aligned_cols=63 Identities=17% Similarity=0.062 Sum_probs=45.1
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-C-CC-CC-CEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-R-IP-KG-DAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~-~P-~~-D~~~l 232 (233)
+..+|+|||||.|.++..+++. ..+++..|.. ..++.++++ .+++++.+|+.+ + .+ .. |++++
T Consensus 48 ~~~~vLdiG~G~G~~~~~l~~~--~~~v~~iD~s~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~fD~Ii~ 120 (233)
T PRK05134 48 FGKRVLDVGCGGGILSESMARL--GADVTGIDASEENIEVARLHALESGLKIDYRQTTAEELAAEHPGQFDVVTC 120 (233)
T ss_pred CCCeEEEeCCCCCHHHHHHHHc--CCeEEEEcCCHHHHHHHHHHHHHcCCceEEEecCHHHhhhhcCCCccEEEE
Confidence 4578999999999999988886 4578999985 455555432 357888888765 2 22 23 88864
No 166
>KOG3420 consensus Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=96.74 E-value=0.0018 Score=48.99 Aligned_cols=68 Identities=22% Similarity=0.283 Sum_probs=49.0
Q ss_pred hcccccCcceEEEecCCccHHHHHHHHHcCCCc-EEEeec-hHHHhhccCC-----CCceEEecCcCCCCCCC---CEEE
Q 039903 162 SSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIK-GVNFDL-SHVIQDSSSY-----SGVKHIGGIMLERIPKG---DAIL 231 (233)
Q Consensus 162 ~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~-~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~~~P~~---D~~~ 231 (233)
-|.++++ +++.|+|||.|.++ ++-.+|..+ ++++|+ |++++..+.+ -+|.+..+|+.++.|.+ |..+
T Consensus 43 TygdiEg-kkl~DLgcgcGmLs--~a~sm~~~e~vlGfDIdpeALEIf~rNaeEfEvqidlLqcdildle~~~g~fDtav 119 (185)
T KOG3420|consen 43 TYGDIEG-KKLKDLGCGCGMLS--IAFSMPKNESVLGFDIDPEALEIFTRNAEEFEVQIDLLQCDILDLELKGGIFDTAV 119 (185)
T ss_pred hhccccC-cchhhhcCchhhhH--HHhhcCCCceEEeeecCHHHHHHHhhchHHhhhhhheeeeeccchhccCCeEeeEE
Confidence 3443444 78999999999999 445566665 789998 6688877665 36788889988866652 5554
Q ss_pred e
Q 039903 232 I 232 (233)
Q Consensus 232 l 232 (233)
+
T Consensus 120 i 120 (185)
T KOG3420|consen 120 I 120 (185)
T ss_pred e
Confidence 3
No 167
>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=96.72 E-value=0.0027 Score=38.63 Aligned_cols=45 Identities=13% Similarity=0.304 Sum_probs=38.7
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCcee
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLR 68 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~ 68 (233)
.+..|+..|.+.| ++|..|||+.+|+ +...+.+.++-|...|+++
T Consensus 4 ~~~~Il~~l~~~~---~~t~~ela~~~~i----s~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLRENP---RITQKELAEKLGI----SRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHCT---TS-HHHHHHHHTS-----HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHcC---CCCHHHHHHHhCC----CHHHHHHHHHHHHHCcCcC
Confidence 4667889999974 7999999999999 9999999999999999874
No 168
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=96.64 E-value=0.0038 Score=45.75 Aligned_cols=68 Identities=16% Similarity=0.280 Sum_probs=55.9
Q ss_pred hHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 8 VLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 8 ~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
..+.+|.--.++.|+..|... ++.++.|||+.+++ ++..+.+-|+.|...|+++....+ ..-.|++++
T Consensus 8 ~~fkaLadptRl~IL~~L~~~---~~~~v~ela~~l~l----sqstvS~HL~~L~~AGLV~~~r~G-r~~~Y~l~~ 75 (117)
T PRK10141 8 QLFKILSDETRLGIVLLLRES---GELCVCDLCTALDQ----SQPKISRHLALLRESGLLLDRKQG-KWVHYRLSP 75 (117)
T ss_pred HHHHHhCCHHHHHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCceEEEEEc-CEEEEEECc
Confidence 456777788899999999874 48999999999999 999999999999999999976421 233477765
No 169
>PF04816 DUF633: Family of unknown function (DUF633) ; InterPro: IPR006901 This is a family of uncharacterised bacterial proteins.; GO: 0016429 tRNA (adenine-N1-)-methyltransferase activity; PDB: 3LEC_A 3KU1_G 3KR9_A 3GNL_B.
Probab=96.62 E-value=0.0027 Score=51.26 Aligned_cols=61 Identities=20% Similarity=0.221 Sum_probs=46.3
Q ss_pred EEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC---CCEEEe
Q 039903 172 LVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK---GDAILI 232 (233)
Q Consensus 172 vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~---~D~~~l 232 (233)
|.||||-||.+.+.|+++...-+++..|+ |.-++.|+++ ++|++.-||=|+.++. .|++++
T Consensus 1 vaDIGtDHgyLpi~L~~~~~~~~~ia~DI~~gpL~~A~~~i~~~~l~~~i~~rlgdGL~~l~~~e~~d~ivI 72 (205)
T PF04816_consen 1 VADIGTDHGYLPIYLLKNGKAPKAIAVDINPGPLEKAKENIAKYGLEDRIEVRLGDGLEVLKPGEDVDTIVI 72 (205)
T ss_dssp EEEET-STTHHHHHHHHTTSEEEEEEEESSHHHHHHHHHHHHHTT-TTTEEEEE-SGGGG--GGG---EEEE
T ss_pred CceeccchhHHHHHHHhcCCCCEEEEEeCCHHHHHHHHHHHHHcCCcccEEEEECCcccccCCCCCCCEEEE
Confidence 68999999999999999999999999998 4466666542 7999999999987765 367664
No 170
>PRK14904 16S rRNA methyltransferase B; Provisional
Probab=96.60 E-value=0.0053 Score=55.47 Aligned_cols=67 Identities=16% Similarity=0.113 Sum_probs=50.3
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC------CCceEEecCcCCCCCC--CCEEEe
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLERIPK--GDAILI 232 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~~~P~--~D~~~l 232 (233)
.....+|+|+|||+|..+..+++..+ .-+++.+|+. +.++.++++ ++|+++.+|..+..|. .|+|++
T Consensus 248 ~~~g~~VLDlgaG~G~kt~~la~~~~~~~~V~avD~s~~~l~~~~~~~~~~g~~~v~~~~~Da~~~~~~~~fD~Vl~ 324 (445)
T PRK14904 248 PQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRSHASALGITIIETIEGDARSFSPEEQPDAILL 324 (445)
T ss_pred CCCCCEEEEECCCCCHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHHHHHhCCCeEEEEeCcccccccCCCCCEEEE
Confidence 34457999999999999999888754 4589999985 466655542 5789999999873343 398875
No 171
>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=96.58 E-value=0.0047 Score=51.80 Aligned_cols=68 Identities=13% Similarity=0.300 Sum_probs=51.5
Q ss_pred HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC----CCCceEEecCcCC-CCCC
Q 039903 156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS----YSGVKHIGGIMLE-RIPK 226 (233)
Q Consensus 156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~----~~ri~~~~gD~f~-~~P~ 226 (233)
+..+++.++ ..+...|+|||.|.|.++..|++.. -+.+++|..+ -++..++ .++++.+.+|+++ ..+.
T Consensus 19 ~~~Iv~~~~-~~~~~~VlEiGpG~G~lT~~L~~~~--~~v~~vE~d~~~~~~L~~~~~~~~~~~vi~~D~l~~~~~~ 92 (262)
T PF00398_consen 19 ADKIVDALD-LSEGDTVLEIGPGPGALTRELLKRG--KRVIAVEIDPDLAKHLKERFASNPNVEVINGDFLKWDLYD 92 (262)
T ss_dssp HHHHHHHHT-CGTTSEEEEESSTTSCCHHHHHHHS--SEEEEEESSHHHHHHHHHHCTTCSSEEEEES-TTTSCGGG
T ss_pred HHHHHHhcC-CCCCCEEEEeCCCCccchhhHhccc--CcceeecCcHhHHHHHHHHhhhcccceeeecchhccccHH
Confidence 355666666 6778999999999999999999998 6688888753 4443333 4899999999998 5544
No 172
>COG2227 UbiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme metabolism]
Probab=96.57 E-value=0.002 Score=52.75 Aligned_cols=40 Identities=20% Similarity=0.117 Sum_probs=34.4
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY 210 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~ 210 (233)
..+|||||||.|.++..+++.. .+++..|+. +.|+.|+.+
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 3789999999999999999986 789999985 478888754
No 173
>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=96.56 E-value=0.0048 Score=40.03 Aligned_cols=44 Identities=16% Similarity=0.187 Sum_probs=39.2
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
.+.|..|||+.+++ +...+.++|+.|...|+++.. ..+.|.++|
T Consensus 24 ~~~s~~ela~~~g~----s~~tv~r~l~~L~~~g~i~~~----~~~~~~l~~ 67 (67)
T cd00092 24 LPLTRQEIADYLGL----TRETVSRTLKELEEEGLISRR----GRGKYRVNP 67 (67)
T ss_pred CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec----CCCeEEeCC
Confidence 58999999999999 999999999999999999985 337787764
No 174
>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=96.56 E-value=0.0048 Score=50.04 Aligned_cols=63 Identities=16% Similarity=0.019 Sum_probs=45.8
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCC-CC--CC-CCEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-RI--PK-GDAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~~--P~-~D~~~l 232 (233)
+..+|+|+|||+|.++..+++..+ +++..|+. ..++.+++. .++++..+|+.+ +. |. .|++++
T Consensus 45 ~~~~vLdlG~G~G~~~~~l~~~~~--~v~~iD~s~~~~~~a~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~D~i~~ 118 (224)
T TIGR01983 45 FGLRVLDVGCGGGLLSEPLARLGA--NVTGIDASEENIEVAKLHAKKDPLLKIEYRCTSVEDLAEKGAKSFDVVTC 118 (224)
T ss_pred CCCeEEEECCCCCHHHHHHHhcCC--eEEEEeCCHHHHHHHHHHHHHcCCCceEEEeCCHHHhhcCCCCCccEEEe
Confidence 357899999999999999988755 48899985 466655442 258888888765 22 23 388864
No 175
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=96.55 E-value=0.004 Score=42.45 Aligned_cols=66 Identities=11% Similarity=0.154 Sum_probs=51.2
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC---CCCceeccHhhhHhh
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD---DQRLYGLAHVAKYFV 89 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~---~~~~y~lt~~s~~l~ 89 (233)
++++|...|... +..+..+|.+.+++ +...+.+.|+.|...|+++....-. ....|++|+.|+...
T Consensus 1 vRl~Il~~L~~~---~~~~f~~L~~~l~l----t~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~ 69 (80)
T PF13601_consen 1 VRLAILALLYAN---EEATFSELKEELGL----TDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAF 69 (80)
T ss_dssp HHHHHHHHHHHH---SEEEHHHHHHHTT------HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHH
T ss_pred CHHHHHHHHhhc---CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHH
Confidence 578899999986 58999999999999 9999999999999999999764321 112589999987544
No 176
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=96.50 E-value=0.0072 Score=42.25 Aligned_cols=68 Identities=16% Similarity=0.274 Sum_probs=53.2
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~ 91 (233)
.++.|+..|... ++.|..+||+.+++ +...+.+.++-|+..|++++....+ ....|.+|+.+..+...
T Consensus 11 ~~~~il~~l~~~---~~~~~~~la~~~~~----s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~ 80 (101)
T smart00347 11 TQFLVLRILYEE---GPLSVSELAKRLGV----SPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEE 80 (101)
T ss_pred HHHHHHHHHHHc---CCcCHHHHHHHHCC----CchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence 356788888876 47999999999999 9999999999999999999763210 12367888888766543
No 177
>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=96.49 E-value=0.0054 Score=50.03 Aligned_cols=55 Identities=18% Similarity=0.202 Sum_probs=42.8
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhcc--C----------------CCCceEEecCcCC
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSS--S----------------YSGVKHIGGIMLE 222 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~--~----------------~~ri~~~~gD~f~ 222 (233)
.....++++.|||.|.-+..|+++ ..+++++|+.+ +++.+. . .++|++..||||+
T Consensus 35 ~~~~~rvLvPgCG~g~D~~~La~~--G~~VvGvDls~~Ai~~~~~e~~~~~~~~~~~~~~~~~~~~i~~~~gDfF~ 108 (218)
T PF05724_consen 35 LKPGGRVLVPGCGKGYDMLWLAEQ--GHDVVGVDLSPTAIEQAFEENNLEPTVTSVGGFKRYQAGRITIYCGDFFE 108 (218)
T ss_dssp TSTSEEEEETTTTTSCHHHHHHHT--TEEEEEEES-HHHHHHHHHHCTTEEECTTCTTEEEETTSSEEEEES-TTT
T ss_pred CCCCCeEEEeCCCChHHHHHHHHC--CCeEEEEecCHHHHHHHHHHhccCCCcccccceeeecCCceEEEEccccc
Confidence 355579999999999999999997 56899999965 666551 1 0478999999998
No 178
>KOG1541 consensus Predicted protein carboxyl methylase [General function prediction only]
Probab=96.48 E-value=0.0023 Score=51.73 Aligned_cols=61 Identities=16% Similarity=0.310 Sum_probs=44.1
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCc--eEEecCcCC--CCCCC--CEEE
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGV--KHIGGIMLE--RIPKG--DAIL 231 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri--~~~~gD~f~--~~P~~--D~~~ 231 (233)
...-|||||||+|..+..+... ....+.+|+ |+.++.|.+ ..+ .++-+|+=+ |+++| |.++
T Consensus 50 ~~~~iLDIGCGsGLSg~vL~~~--Gh~wiGvDiSpsML~~a~~-~e~egdlil~DMG~GlpfrpGtFDg~I 117 (270)
T KOG1541|consen 50 KSGLILDIGCGSGLSGSVLSDS--GHQWIGVDISPSMLEQAVE-RELEGDLILCDMGEGLPFRPGTFDGVI 117 (270)
T ss_pred CCcEEEEeccCCCcchheeccC--CceEEeecCCHHHHHHHHH-hhhhcCeeeeecCCCCCCCCCccceEE
Confidence 3789999999999888777664 567899998 678888875 223 356677777 44455 6554
No 179
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=96.46 E-value=0.004 Score=59.40 Aligned_cols=64 Identities=14% Similarity=0.038 Sum_probs=49.9
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEEecCcCCC---CCCC-CEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHIGGIMLER---IPKG-DAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~gD~f~~---~P~~-D~~~l 232 (233)
+.++|+|+|||+|.++..+++. ...+++.+|+. ..++.++++ ++++++.+|.++. .+.. |+|++
T Consensus 538 ~g~rVLDlf~gtG~~sl~aa~~-Ga~~V~~vD~s~~al~~a~~N~~~ng~~~~~v~~i~~D~~~~l~~~~~~fDlIil 614 (702)
T PRK11783 538 KGKDFLNLFAYTGTASVHAALG-GAKSTTTVDMSNTYLEWAERNFALNGLSGRQHRLIQADCLAWLKEAREQFDLIFI 614 (702)
T ss_pred CCCeEEEcCCCCCHHHHHHHHC-CCCEEEEEeCCHHHHHHHHHHHHHhCCCccceEEEEccHHHHHHHcCCCcCEEEE
Confidence 4579999999999999999986 34469999985 577777653 4899999999873 2333 98876
No 180
>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=96.45 E-value=0.0028 Score=50.53 Aligned_cols=53 Identities=15% Similarity=0.013 Sum_probs=42.9
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCC
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLE 222 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~ 222 (233)
..+++|++||+|.++.+++.+... +++.+|.. .+++.++++ ++++++.+|.++
T Consensus 50 g~~vLDLfaGsG~lglea~srga~-~v~~vE~~~~a~~~~~~N~~~~~~~~~~~~~~~D~~~ 110 (189)
T TIGR00095 50 GAHLLDVFAGSGLLGEEALSRGAK-VAFLEEDDRKANQTLKENLALLKSGEQAEVVRNSALR 110 (189)
T ss_pred CCEEEEecCCCcHHHHHHHhCCCC-EEEEEeCCHHHHHHHHHHHHHhCCcccEEEEehhHHH
Confidence 478999999999999999999764 78888985 466555442 478999999976
No 181
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=96.44 E-value=0.0041 Score=55.28 Aligned_cols=65 Identities=12% Similarity=0.049 Sum_probs=48.5
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEEecCcCCCC------CC-CCEE
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHIGGIMLERI------PK-GDAI 230 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~gD~f~~~------P~-~D~~ 230 (233)
.+.++|+|+|||+|.++.+.+.. ...+++.+|+. ..++.++++ ++++++.+|.|+.+ .. .|+|
T Consensus 219 ~~g~rVLDlfsgtG~~~l~aa~~-ga~~V~~VD~s~~al~~a~~N~~~Ngl~~~~v~~i~~D~~~~l~~~~~~~~~fDlV 297 (396)
T PRK15128 219 VENKRVLNCFSYTGGFAVSALMG-GCSQVVSVDTSQEALDIARQNVELNKLDLSKAEFVRDDVFKLLRTYRDRGEKFDVI 297 (396)
T ss_pred cCCCeEEEeccCCCHHHHHHHhC-CCCEEEEEECCHHHHHHHHHHHHHcCCCCCcEEEEEccHHHHHHHHHhcCCCCCEE
Confidence 44589999999999998876653 45589999985 467666553 37999999999732 11 3998
Q ss_pred Ee
Q 039903 231 LI 232 (233)
Q Consensus 231 ~l 232 (233)
++
T Consensus 298 il 299 (396)
T PRK15128 298 VM 299 (396)
T ss_pred EE
Confidence 86
No 182
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=96.43 E-value=0.006 Score=36.73 Aligned_cols=41 Identities=15% Similarity=0.121 Sum_probs=36.6
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA 82 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt 82 (233)
+.|..|||+.+++ +...+.+.|+.|...|+++.. .+.|.++
T Consensus 8 ~~s~~~la~~l~~----s~~tv~~~l~~L~~~g~l~~~-----~~~~~i~ 48 (48)
T smart00419 8 PLTRQEIAELLGL----TRETVSRTLKRLEKEGLISRE-----GGRIVIL 48 (48)
T ss_pred ccCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe-----CCEEEEC
Confidence 7899999999999 999999999999999999985 5677653
No 183
>COG4262 Predicted spermidine synthase with an N-terminal membrane domain [General function prediction only]
Probab=96.41 E-value=0.0084 Score=52.03 Aligned_cols=55 Identities=18% Similarity=0.297 Sum_probs=46.5
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCC-CcEEEeec-hHHHhhccCC-------------CCceEEecCcCC
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDL-SHVIQDSSSY-------------SGVKHIGGIMLE 222 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~v~~~a~~~-------------~ri~~~~gD~f~ 222 (233)
++..+++-+|||.|..++++++ ||. -+++.+|+ |.+++.++++ +|++.+.-|.|+
T Consensus 288 ~~a~~vLvlGGGDGLAlRellk-yP~~~qI~lVdLDP~miela~~~~vlr~~N~~sf~dpRv~Vv~dDAf~ 357 (508)
T COG4262 288 RGARSVLVLGGGDGLALRELLK-YPQVEQITLVDLDPRMIELASHATVLRALNQGSFSDPRVTVVNDDAFQ 357 (508)
T ss_pred cccceEEEEcCCchHHHHHHHh-CCCcceEEEEecCHHHHHHhhhhhHhhhhccCCccCCeeEEEeccHHH
Confidence 4568999999999999999987 895 46888898 7799988742 799999999997
No 184
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=96.38 E-value=0.0082 Score=46.73 Aligned_cols=62 Identities=11% Similarity=0.177 Sum_probs=47.0
Q ss_pred HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
-.+|++.+.+. ....+ ++.|.++||+++++ ++..+.++|+.|...|++..... .+|.|.+..
T Consensus 8 ~yAl~~l~~lA----~~~~~--~~vs~~eIA~~~~i----p~~~l~kIl~~L~~aGLv~s~rG--~~GGy~Lar 69 (164)
T PRK10857 8 RYAVTAMLDVA----LNSEA--GPVPLADISERQGI----SLSYLEQLFSRLRKNGLVSSVRG--PGGGYLLGK 69 (164)
T ss_pred HHHHHHHHHHH----hCCCC--CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeCCC--CCCCeeccC
Confidence 34555555554 12212 58999999999999 99999999999999999997432 467788764
No 185
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=96.37 E-value=0.011 Score=44.69 Aligned_cols=50 Identities=14% Similarity=0.080 Sum_probs=44.8
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhh
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFV 89 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~ 89 (233)
++.+..+||+.+++ ++..+.+.++.|...|++.+. ....|.+|+.|..+.
T Consensus 21 ~~~~~~ela~~l~v----s~~svs~~l~~L~~~Gli~~~----~~~~i~LT~~G~~~a 70 (142)
T PRK03902 21 GYARVSDIAEALSV----HPSSVTKMVQKLDKDEYLIYE----KYRGLVLTPKGKKIG 70 (142)
T ss_pred CCcCHHHHHHHhCC----ChhHHHHHHHHHHHCCCEEEe----cCceEEECHHHHHHH
Confidence 68899999999999 999999999999999999975 467899999997654
No 186
>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=96.37 E-value=0.0056 Score=40.44 Aligned_cols=44 Identities=14% Similarity=0.295 Sum_probs=37.6
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS 71 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~ 71 (233)
|-++|.+. +.+|..|||..+++ ++..++.+|+.|+..|.+++..
T Consensus 5 i~~~l~~~---~~~S~~eLa~~~~~----s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 5 IRDYLRER---GRVSLAELAREFGI----SPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHHHHHS----SEEHHHHHHHTT------HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEEec
Confidence 56778886 58999999999999 9999999999999999999874
No 187
>PRK11760 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional
Probab=96.34 E-value=0.013 Score=50.74 Aligned_cols=63 Identities=16% Similarity=0.135 Sum_probs=50.5
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCCCCC-C-C-CEEE
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIP-K-G-DAIL 231 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~~~P-~-~-D~~~ 231 (233)
....++||||++.|.++..++++ +.+++.+|...........+||+++.+|-|...| . . |.++
T Consensus 210 ~~g~~vlDLGAsPGGWT~~L~~r--G~~V~AVD~g~l~~~L~~~~~V~h~~~d~fr~~p~~~~vDwvV 275 (357)
T PRK11760 210 APGMRAVDLGAAPGGWTYQLVRR--GMFVTAVDNGPMAQSLMDTGQVEHLRADGFKFRPPRKNVDWLV 275 (357)
T ss_pred CCCCEEEEeCCCCcHHHHHHHHc--CCEEEEEechhcCHhhhCCCCEEEEeccCcccCCCCCCCCEEE
Confidence 45689999999999999999998 5589999976655555667999999999998555 2 2 6654
No 188
>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=96.34 E-value=0.0093 Score=47.10 Aligned_cols=74 Identities=16% Similarity=0.160 Sum_probs=52.0
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCc---------EEEeec-hHHHhhccCC-------CCceEEecC
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIK---------GVNFDL-SHVIQDSSSY-------SGVKHIGGI 219 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~---------~~v~Dl-p~v~~~a~~~-------~ri~~~~gD 219 (233)
..++.... |++...++|-=||+|.++++.+...++.. ++..|. +..++.++.+ +.|.+...|
T Consensus 18 ~~ll~la~-~~~~~~vlDP~CGsGtiliEaa~~~~~~~~~~~~~~~~~~g~Di~~~~v~~a~~N~~~ag~~~~i~~~~~D 96 (179)
T PF01170_consen 18 AALLNLAG-WRPGDVVLDPFCGSGTILIEAALMGANIPPLNDINELKIIGSDIDPKAVRGARENLKAAGVEDYIDFIQWD 96 (179)
T ss_dssp HHHHHHTT---TTS-EEETT-TTSHHHHHHHHHHTTTSTTTH-CH--EEEEESSHHHHHHHHHHHHHTT-CGGEEEEE--
T ss_pred HHHHHHhC-CCCCCEEeecCCCCCHHHHHHHHHhhCcccccccccccEEecCCCHHHHHHHHHHHHhcccCCceEEEecc
Confidence 34445444 77778999999999999999888888877 889998 4577766653 568999999
Q ss_pred cCC-CCCCC--CEEE
Q 039903 220 MLE-RIPKG--DAIL 231 (233)
Q Consensus 220 ~f~-~~P~~--D~~~ 231 (233)
+++ +++.+ |.++
T Consensus 97 ~~~l~~~~~~~d~Iv 111 (179)
T PF01170_consen 97 ARELPLPDGSVDAIV 111 (179)
T ss_dssp GGGGGGTTSBSCEEE
T ss_pred hhhcccccCCCCEEE
Confidence 998 75543 8776
No 189
>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=96.34 E-value=0.011 Score=50.48 Aligned_cols=66 Identities=12% Similarity=0.113 Sum_probs=49.7
Q ss_pred HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC
Q 039903 156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE 222 (233)
Q Consensus 156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~ 222 (233)
..++++.+. -.....+||+==|.|.++.++++++|+.+.+.+|. |.+++.+++. +|+.++.++|-+
T Consensus 9 l~Evl~~L~-~~~~g~~vD~T~G~GGHS~aiL~~~~~~~li~~DrD~~a~~~a~~~l~~~~~r~~~~~~~F~~ 80 (310)
T PF01795_consen 9 LKEVLEALN-PKPGGIYVDCTFGGGGHSKAILEKLPNGRLIGIDRDPEALERAKERLKKFDDRFIFIHGNFSN 80 (310)
T ss_dssp HHHHHHHHT---TT-EEEETT-TTSHHHHHHHHT-TT-EEEEEES-HHHHHHHHCCTCCCCTTEEEEES-GGG
T ss_pred HHHHHHhhC-cCCCceEEeecCCcHHHHHHHHHhCCCCeEEEecCCHHHHHHHHHHHhhccceEEEEeccHHH
Confidence 456777766 56678999999999999999999999999999998 5688777653 799999999865
No 190
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=96.33 E-value=0.0061 Score=55.93 Aligned_cols=64 Identities=13% Similarity=0.112 Sum_probs=45.8
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeech--HHHhhccC-----CCCceEEecCcC---CCCCCC--CEEE
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS--HVIQDSSS-----YSGVKHIGGIML---ERIPKG--DAIL 231 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp--~v~~~a~~-----~~ri~~~~gD~f---~~~P~~--D~~~ 231 (233)
+...+||||||.|.++..+++++|+..++++|.- .+....+. ..++.++.+|+- .-+|.+ |.++
T Consensus 347 ~~p~~lEIG~G~G~~~~~~A~~~p~~~~iGiE~~~~~~~~~~~~~~~~~l~N~~~~~~~~~~~~~~~~~~sv~~i~ 422 (506)
T PRK01544 347 KRKVFLEIGFGMGEHFINQAKMNPDALFIGVEVYLNGVANVLKLAGEQNITNFLLFPNNLDLILNDLPNNSLDGIY 422 (506)
T ss_pred CCceEEEECCCchHHHHHHHHhCCCCCEEEEEeeHHHHHHHHHHHHHcCCCeEEEEcCCHHHHHHhcCcccccEEE
Confidence 3588999999999999999999999999999974 23322221 256777777763 245653 4443
No 191
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=96.33 E-value=0.0087 Score=45.89 Aligned_cols=57 Identities=21% Similarity=0.224 Sum_probs=46.1
Q ss_pred hHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903 22 FEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV 84 (233)
Q Consensus 22 fd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~ 84 (233)
.-.|+..+.+++.|+++||+..++ ++.+|.++|..|...|+++-.+. .+|.|+|..-
T Consensus 14 L~~LA~~~~~~~~s~~~IA~~~~i----s~~~L~kil~~L~kaGlV~S~rG--~~GGy~Lar~ 70 (150)
T COG1959 14 LLYLALLPGGGPVSSAEIAERQGI----SPSYLEKILSKLRKAGLVKSVRG--KGGGYRLARP 70 (150)
T ss_pred HHHHHhCCCCCcccHHHHHHHhCc----CHHHHHHHHHHHHHcCCEEeecC--CCCCccCCCC
Confidence 344555443348899999999999 99999999999999999998753 4788988753
No 192
>PRK13256 thiopurine S-methyltransferase; Reviewed
Probab=96.32 E-value=0.02 Score=46.95 Aligned_cols=54 Identities=11% Similarity=0.100 Sum_probs=43.7
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC------------------CCCceEEecCcCC
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS------------------YSGVKHIGGIMLE 222 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~------------------~~ri~~~~gD~f~ 222 (233)
.+..+|++.|||.|..+.-|++. ..+++.+|+.+ .++.+.+ ..+|++..+|||+
T Consensus 42 ~~~~rvLvPgCGkg~D~~~LA~~--G~~V~GvDlS~~Ai~~~~~e~~~~~~~~~~~~~~~~~~~~i~~~~gD~f~ 114 (226)
T PRK13256 42 NDSSVCLIPMCGCSIDMLFFLSK--GVKVIGIELSEKAVLSFFSQNTINYEVIHGNDYKLYKGDDIEIYVADIFN 114 (226)
T ss_pred CCCCeEEEeCCCChHHHHHHHhC--CCcEEEEecCHHHHHHHHHHcCCCcceecccccceeccCceEEEEccCcC
Confidence 34579999999999999999997 66799999965 5655311 1589999999998
No 193
>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=96.32 E-value=0.0094 Score=44.81 Aligned_cols=46 Identities=11% Similarity=0.213 Sum_probs=39.7
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
++.|.+|||+.+++ ++..++++|+.|...|+++.... .+|.|.++.
T Consensus 24 ~~~s~~~ia~~~~i----p~~~l~kil~~L~~~glv~s~~G--~~Ggy~l~~ 69 (135)
T TIGR02010 24 GPVTLADISERQGI----SLSYLEQLFAKLRKAGLVKSVRG--PGGGYQLGR 69 (135)
T ss_pred CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCceEEEeC--CCCCEeccC
Confidence 48999999999999 99999999999999999986432 456788765
No 194
>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]
Probab=96.31 E-value=0.022 Score=47.07 Aligned_cols=84 Identities=14% Similarity=0.166 Sum_probs=64.4
Q ss_pred HHhcchhc----HHHHHHhcccccCcceEEEecCCccHHHHHHHH-HcCCCcEEEeec-hHHHhhccCC-------CCce
Q 039903 148 MLNHTSIV----TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIIS-NYLHIKGVNFDL-SHVIQDSSSY-------SGVK 214 (233)
Q Consensus 148 m~~~~~~~----~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~-~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~ 214 (233)
|...++.. +..++.... .+...+|+|.|-|+|.++..|+. -.|.=+.+.+|. ++-.+.|+++ ++|+
T Consensus 71 ~~R~tQiIyPKD~~~I~~~~g-i~pg~rVlEAGtGSG~lt~~La~~vg~~G~v~tyE~r~d~~k~A~~Nl~~~~l~d~v~ 149 (256)
T COG2519 71 MKRRTQIIYPKDAGYIVARLG-ISPGSRVLEAGTGSGALTAYLARAVGPEGHVTTYEIREDFAKTARENLSEFGLGDRVT 149 (256)
T ss_pred CcCCCceecCCCHHHHHHHcC-CCCCCEEEEcccCchHHHHHHHHhhCCCceEEEEEecHHHHHHHHHHHHHhccccceE
Confidence 55555543 344555555 78889999999999999999997 578888999986 5677777664 6799
Q ss_pred EEecCcCC-CCCCC-CEEEe
Q 039903 215 HIGGIMLE-RIPKG-DAILI 232 (233)
Q Consensus 215 ~~~gD~f~-~~P~~-D~~~l 232 (233)
+..+|..+ ..+.- |+++|
T Consensus 150 ~~~~Dv~~~~~~~~vDav~L 169 (256)
T COG2519 150 LKLGDVREGIDEEDVDAVFL 169 (256)
T ss_pred EEeccccccccccccCEEEE
Confidence 99999998 44443 88876
No 195
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=96.30 E-value=0.0089 Score=53.84 Aligned_cols=71 Identities=11% Similarity=-0.036 Sum_probs=52.0
Q ss_pred HhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC------CCceEEecCcCC-C----CCC-
Q 039903 161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-R----IPK- 226 (233)
Q Consensus 161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~----~P~- 226 (233)
..++ .....+|+|+|||.|..+..+++..+ .-+++.+|. ++.++.++++ ++|+++.+|..+ + .+.
T Consensus 246 ~~l~-~~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~~~~rl~~~~~n~~r~g~~~v~~~~~D~~~~~~~~~~~~~ 324 (434)
T PRK14901 246 PLLD-PQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGLKSIKILAADSRNLLELKPQWRG 324 (434)
T ss_pred HHhC-CCCcCEEEEeCCCCchhHHHHHHHhCCCceEEEEcCCHHHHHHHHHHHHHcCCCeEEEEeCChhhcccccccccc
Confidence 3344 44568999999999999999999854 568999998 4466655442 569999999876 2 222
Q ss_pred -CCEEEe
Q 039903 227 -GDAILI 232 (233)
Q Consensus 227 -~D~~~l 232 (233)
.|.|++
T Consensus 325 ~fD~Vl~ 331 (434)
T PRK14901 325 YFDRILL 331 (434)
T ss_pred cCCEEEE
Confidence 398875
No 196
>KOG1270 consensus Methyltransferases [Coenzyme transport and metabolism]
Probab=96.29 E-value=0.0037 Score=51.78 Aligned_cols=60 Identities=17% Similarity=0.123 Sum_probs=42.8
Q ss_pred ceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--------C----CceEEecCcCCCCCCCCEEE
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------S----GVKHIGGIMLERIPKGDAIL 231 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~----ri~~~~gD~f~~~P~~D~~~ 231 (233)
.+|||||||.|.++..|++.. .+++..|.- ..++.|+++ . |+++...|.-.-.+.-|+++
T Consensus 91 ~~ilDvGCGgGLLSepLArlg--a~V~GID~s~~~V~vA~~h~~~dP~~~~~~~y~l~~~~~~~E~~~~~fDaVv 163 (282)
T KOG1270|consen 91 MKILDVGCGGGLLSEPLARLG--AQVTGIDASDDMVEVANEHKKMDPVLEGAIAYRLEYEDTDVEGLTGKFDAVV 163 (282)
T ss_pred ceEEEeccCccccchhhHhhC--CeeEeecccHHHHHHHHHhhhcCchhccccceeeehhhcchhhcccccceee
Confidence 679999999999999999985 668899984 577777663 2 46665555444333346554
No 197
>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=96.27 E-value=0.014 Score=42.57 Aligned_cols=67 Identities=15% Similarity=0.156 Sum_probs=53.9
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~ 91 (233)
+..|+..|... ++.|..|||+.+++ +...+.++++-|...|++++..... ..-.+.+|+.|..+...
T Consensus 30 q~~iL~~l~~~---~~~t~~ela~~~~~----~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~ 98 (118)
T TIGR02337 30 QWRILRILAEQ---GSMEFTQLANQACI----LRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYAS 98 (118)
T ss_pred HHHHHHHHHHc---CCcCHHHHHHHhCC----CchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence 33477777776 58999999999999 9999999999999999999864321 12378999999887755
No 198
>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=96.26 E-value=0.0081 Score=53.96 Aligned_cols=73 Identities=14% Similarity=0.093 Sum_probs=51.5
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------C-CceEEecCcCCC-C--CC-
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------S-GVKHIGGIMLER-I--PK- 226 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~-ri~~~~gD~f~~-~--P~- 226 (233)
++..++ .....+|+|+|||.|..+..+++..|..+++.+|. ++.++.++++ + ++.++.+|..+. . +.
T Consensus 230 ~~~~L~-~~~g~~VLDlcag~G~kt~~la~~~~~~~v~a~D~~~~~l~~~~~n~~r~g~~~~v~~~~~d~~~~~~~~~~~ 308 (426)
T TIGR00563 230 VATWLA-PQNEETILDACAAPGGKTTHILELAPQAQVVALDIHEHRLKRVYENLKRLGLTIKAETKDGDGRGPSQWAENE 308 (426)
T ss_pred HHHHhC-CCCCCeEEEeCCCccHHHHHHHHHcCCCeEEEEeCCHHHHHHHHHHHHHcCCCeEEEEecccccccccccccc
Confidence 334444 45568999999999999999999988788999998 4566655542 2 344477887652 2 22
Q ss_pred -CCEEEe
Q 039903 227 -GDAILI 232 (233)
Q Consensus 227 -~D~~~l 232 (233)
.|.|++
T Consensus 309 ~fD~Vll 315 (426)
T TIGR00563 309 QFDRILL 315 (426)
T ss_pred ccCEEEE
Confidence 388875
No 199
>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=96.25 E-value=0.0071 Score=52.99 Aligned_cols=51 Identities=14% Similarity=0.121 Sum_probs=42.6
Q ss_pred ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE 222 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~ 222 (233)
.+++|++||+|.++..+++... +++.+|. ++.++.++++ ++++++.+|..+
T Consensus 199 ~~vlDl~~G~G~~sl~la~~~~--~v~~vE~~~~av~~a~~n~~~~~~~~v~~~~~d~~~ 256 (353)
T TIGR02143 199 GDLLELYCGNGNFSLALAQNFR--RVLATEIAKPSVNAAQYNIAANNIDNVQIIRMSAEE 256 (353)
T ss_pred CcEEEEeccccHHHHHHHHhCC--EEEEEECCHHHHHHHHHHHHHcCCCcEEEEEcCHHH
Confidence 4699999999999999998874 7999997 5577777653 579999999876
No 200
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=96.20 E-value=0.013 Score=43.34 Aligned_cols=46 Identities=13% Similarity=0.217 Sum_probs=39.7
Q ss_pred ChhHHHH-hcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeecc
Q 039903 20 GVFEIIA-KAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSA 72 (233)
Q Consensus 20 glfd~L~-~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~ 72 (233)
.++.+|- .+ +|.|+++||+.++. +...++|-|+-|...|++.+...
T Consensus 31 ~v~~~LL~~~---~~~tvdelae~lnr----~rStv~rsl~~L~~~GlV~Rek~ 77 (126)
T COG3355 31 EVYKALLEEN---GPLTVDELAEILNR----SRSTVYRSLQNLLEAGLVEREKV 77 (126)
T ss_pred HHHHHHHhhc---CCcCHHHHHHHHCc----cHHHHHHHHHHHHHcCCeeeeee
Confidence 4566665 44 69999999999999 99999999999999999998643
No 201
>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=96.18 E-value=0.014 Score=40.53 Aligned_cols=69 Identities=22% Similarity=0.185 Sum_probs=54.2
Q ss_pred HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHH----------HhcCCce-eeeccCCCCCceeccH
Q 039903 15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL----------LVTHRVL-RCTSAGDDQRLYGLAH 83 (233)
Q Consensus 15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~----------L~~~gll-~~~~~~~~~~~y~lt~ 83 (233)
.=++..|+..|....| .+.++.|||..+++ ++..+.--|+. |+.+|++ ++.... +...|++|+
T Consensus 8 S~~R~~vl~~L~~~yp-~~~~~~eIar~v~~----~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~-g~k~Y~lT~ 81 (90)
T PF07381_consen 8 SKVRKKVLEYLCSIYP-EPAYPSEIARSVGS----DYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEKG-GFKYYRLTE 81 (90)
T ss_pred HHHHHHHHHHHHHcCC-CcCCHHHHHHHHCC----CHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeecC-CeeEEEeCh
Confidence 5567889999999833 58999999999999 99888777764 8999999 443222 356899999
Q ss_pred hhhHhh
Q 039903 84 VAKYFV 89 (233)
Q Consensus 84 ~s~~l~ 89 (233)
.+..++
T Consensus 82 ~G~~~~ 87 (90)
T PF07381_consen 82 KGKRIA 87 (90)
T ss_pred hhhhHH
Confidence 887654
No 202
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=96.16 E-value=0.022 Score=47.47 Aligned_cols=68 Identities=15% Similarity=0.374 Sum_probs=50.1
Q ss_pred HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhcc----CCCCceEEecCcCC-CCCC
Q 039903 156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSS----SYSGVKHIGGIMLE-RIPK 226 (233)
Q Consensus 156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~----~~~ri~~~~gD~f~-~~P~ 226 (233)
...+++..+ -.....|+.||.|.|.+...|+++... ++.+++.. -++..+ ..++++.+.||+.+ .+|.
T Consensus 19 ~~kIv~~a~-~~~~d~VlEIGpG~GaLT~~Ll~~~~~--v~aiEiD~~l~~~L~~~~~~~~n~~vi~~DaLk~d~~~ 92 (259)
T COG0030 19 IDKIVEAAN-ISPGDNVLEIGPGLGALTEPLLERAAR--VTAIEIDRRLAEVLKERFAPYDNLTVINGDALKFDFPS 92 (259)
T ss_pred HHHHHHhcC-CCCCCeEEEECCCCCHHHHHHHhhcCe--EEEEEeCHHHHHHHHHhcccccceEEEeCchhcCcchh
Confidence 456666665 455789999999999999999999777 55555433 222222 24899999999998 7774
No 203
>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=96.15 E-value=0.012 Score=43.82 Aligned_cols=47 Identities=26% Similarity=0.286 Sum_probs=39.5
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV 84 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~ 84 (233)
++.|.++||+.+++ ++..++++|+.|...|++..... ..+.|.++..
T Consensus 24 ~~~s~~eia~~~~i----~~~~v~~il~~L~~~gli~~~~g--~~ggy~l~~~ 70 (132)
T TIGR00738 24 GPVSVKEIAERQGI----SRSYLEKILRTLRRAGLVESVRG--PGGGYRLARP 70 (132)
T ss_pred CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEeccC--CCCCccCCCC
Confidence 48999999999999 99999999999999999987421 3457877643
No 204
>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=96.14 E-value=0.021 Score=46.92 Aligned_cols=55 Identities=15% Similarity=0.134 Sum_probs=38.8
Q ss_pred HHHHhcccc-cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHh-hccCCCCce
Q 039903 158 RIIDSSKGF-EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQ-DSSSYSGVK 214 (233)
Q Consensus 158 ~~~~~~~~~-~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~-~a~~~~ri~ 214 (233)
.+++.++ . .+..+++|||||+|.++..++++ +.-+++.+|... .+. ..+.++||.
T Consensus 65 ~~l~~~~-~~~~~~~vlDiG~gtG~~t~~l~~~-ga~~v~avD~~~~~l~~~l~~~~~v~ 122 (228)
T TIGR00478 65 EALEEFN-IDVKNKIVLDVGSSTGGFTDCALQK-GAKEVYGVDVGYNQLAEKLRQDERVK 122 (228)
T ss_pred HHHHhcC-CCCCCCEEEEcccCCCHHHHHHHHc-CCCEEEEEeCCHHHHHHHHhcCCCee
Confidence 4445544 2 24578999999999999999986 556799999865 443 345555644
No 205
>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=96.13 E-value=0.014 Score=38.27 Aligned_cols=61 Identities=11% Similarity=0.140 Sum_probs=48.0
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCC-CCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhH
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKY 87 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~-~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~ 87 (233)
|++.|.+.+ +|++..+|++.++.. ...+++.++|.|+.|-..|++.+. ..+.+.+|+.+..
T Consensus 3 IL~~L~~~~--~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~----g~~G~~iT~~G~~ 64 (66)
T PF08461_consen 3 ILRILAESD--KPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKV----GRQGRIITEKGLD 64 (66)
T ss_pred HHHHHHHcC--CCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCcccc----CCcccccCHHHHh
Confidence 567888875 799999999999762 122578999999999999988775 4566678887754
No 206
>PRK14903 16S rRNA methyltransferase B; Provisional
Probab=96.07 E-value=0.014 Score=52.58 Aligned_cols=67 Identities=19% Similarity=0.060 Sum_probs=50.5
Q ss_pred ccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeech-HHHhhccCC------CCceEEecCcCC-C-C-CC-CCEEEe
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-R-I-PK-GDAILI 232 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~-~-P~-~D~~~l 232 (233)
.....+|+|+|||.|..+..+++.. +.-+++.+|+. +.++.++++ ++|+++.+|..+ + . +. -|.|++
T Consensus 235 ~~~g~~VLD~cagpGgkt~~la~~~~~~g~V~a~Dis~~rl~~~~~n~~r~g~~~v~~~~~Da~~l~~~~~~~fD~Vl~ 313 (431)
T PRK14903 235 LEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHAKRLKLSSIEIKIADAERLTEYVQDTFDRILV 313 (431)
T ss_pred CCCCCEEEEeCCCccHHHHHHHHHcCCCCEEEEEECCHHHHHHHHHHHHHcCCCeEEEEECchhhhhhhhhccCCEEEE
Confidence 4556799999999999999999886 56789999984 466655542 468899999875 2 2 22 388875
No 207
>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=96.06 E-value=0.019 Score=49.15 Aligned_cols=66 Identities=12% Similarity=0.122 Sum_probs=53.5
Q ss_pred HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC
Q 039903 156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE 222 (233)
Q Consensus 156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~ 222 (233)
..++++.+. -.....+||+=.|.|..+.+++++.|+.+++.+|. |.+++.+++. +|++++.++|-+
T Consensus 9 l~Evl~~L~-~~~ggiyVD~TlG~GGHS~~iL~~l~~g~vigiD~D~~Al~~ak~~L~~~~~R~~~i~~nF~~ 80 (305)
T TIGR00006 9 LDEVVEGLN-IKPDGIYIDCTLGFGGHSKAILEQLGTGRLIGIDRDPQAIAFAKERLSDFEGRVVLIHDNFAN 80 (305)
T ss_pred HHHHHHhcC-cCCCCEEEEeCCCChHHHHHHHHhCCCCEEEEEcCCHHHHHHHHHHHhhcCCcEEEEeCCHHH
Confidence 356666665 45567999999999999999999998889999998 5577777552 589999999885
No 208
>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=96.05 E-value=0.016 Score=46.70 Aligned_cols=67 Identities=15% Similarity=0.198 Sum_probs=51.8
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeecc-C--C-CCCceeccHhhhHhhcC
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSA-G--D-DQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~-~--~-~~~~y~lt~~s~~l~~~ 91 (233)
+..|+..|... ++.|..|||+.+++ ++..+.+.|+.|...|++++... . + ..-.|.+|+.+..+...
T Consensus 3 r~~IL~~L~~~---~~~t~~eLA~~lgi----s~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~~~ 73 (203)
T TIGR02702 3 KEDILSYLLKQ---GQATAAALAEALAI----SPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQFPQ 73 (203)
T ss_pred HHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhccc
Confidence 34577788766 58999999999999 99999999999999999987521 1 0 12237888888766543
No 209
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=95.99 E-value=0.021 Score=43.98 Aligned_cols=52 Identities=10% Similarity=0.041 Sum_probs=47.4
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
+++...+||+.+++ ++..+..+++-|...|+++.. ..+.+.+|+.|......
T Consensus 23 ~~~~~~diA~~L~V----sp~sVt~ml~rL~~~GlV~~~----~y~gi~LT~~G~~~a~~ 74 (154)
T COG1321 23 GFARTKDIAERLKV----SPPSVTEMLKRLERLGLVEYE----PYGGVTLTEKGREKAKE 74 (154)
T ss_pred CcccHHHHHHHhCC----CcHHHHHHHHHHHHCCCeEEe----cCCCeEEChhhHHHHHH
Confidence 69999999999999 999999999999999999997 68899999998866544
No 210
>PRK11050 manganese transport regulator MntR; Provisional
Probab=95.93 E-value=0.024 Score=43.54 Aligned_cols=59 Identities=17% Similarity=0.229 Sum_probs=49.1
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL 90 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~ 90 (233)
|..++... ++.+..|||+.+++ +...+.++++.|...|++.+. ....+.+|+.|..+..
T Consensus 42 I~~~l~~~---~~~t~~eLA~~l~i----s~stVsr~l~~Le~~GlI~r~----~~~~v~LT~~G~~l~~ 100 (152)
T PRK11050 42 IADLIAEV---GEARQVDIAARLGV----SQPTVAKMLKRLARDGLVEMR----PYRGVFLTPEGEKLAQ 100 (152)
T ss_pred HHHHHHhc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe----cCCceEECchHHHHHH
Confidence 44455553 58999999999999 999999999999999999986 4567889998887654
No 211
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=95.90 E-value=0.014 Score=37.69 Aligned_cols=45 Identities=16% Similarity=0.149 Sum_probs=38.0
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.|.+.|.... +|.+..|||+.+++ +....+++|..|...|.+++.
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 5677777732 69999999999999 999999999999999999975
No 212
>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=95.89 E-value=0.025 Score=47.74 Aligned_cols=56 Identities=13% Similarity=0.105 Sum_probs=46.0
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCC--CcEEEeech-HHHhhccCC------CC-ceEEecCcCC
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLH--IKGVNFDLS-HVIQDSSSY------SG-VKHIGGIMLE 222 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~--l~~~v~Dlp-~v~~~a~~~------~r-i~~~~gD~f~ 222 (233)
....+||||.||+|-+....++.+|. .++.+.|.. ..++.+++. .. ++|..+|.|+
T Consensus 134 g~pvrIlDIAaG~GRYvlDal~~~~~~~~~i~LrDys~~Nv~~g~~li~~~gL~~i~~f~~~dAfd 199 (311)
T PF12147_consen 134 GRPVRILDIAAGHGRYVLDALEKHPERPDSILLRDYSPINVEKGRALIAERGLEDIARFEQGDAFD 199 (311)
T ss_pred CCceEEEEeccCCcHHHHHHHHhCCCCCceEEEEeCCHHHHHHHHHHHHHcCCccceEEEecCCCC
Confidence 35689999999999999999999998 778888974 466666542 44 5999999997
No 213
>PRK05031 tRNA (uracil-5-)-methyltransferase; Validated
Probab=95.87 E-value=0.0087 Score=52.60 Aligned_cols=51 Identities=14% Similarity=0.119 Sum_probs=42.2
Q ss_pred ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE 222 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~ 222 (233)
.+++|++||+|.++..+++... +++.+|. ++.++.++++ ++++++.+|.++
T Consensus 208 ~~vLDl~~G~G~~sl~la~~~~--~v~~vE~~~~ai~~a~~N~~~~~~~~v~~~~~d~~~ 265 (362)
T PRK05031 208 GDLLELYCGNGNFTLALARNFR--RVLATEISKPSVAAAQYNIAANGIDNVQIIRMSAEE 265 (362)
T ss_pred CeEEEEeccccHHHHHHHhhCC--EEEEEECCHHHHHHHHHHHHHhCCCcEEEEECCHHH
Confidence 4799999999999999998864 6899997 4577766653 589999999876
No 214
>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=95.87 E-value=0.013 Score=49.86 Aligned_cols=39 Identities=13% Similarity=0.236 Sum_probs=30.2
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEee
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFD 199 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~D 199 (233)
+...++++++ ++|+|||||+|.++-.++++.|. .++++|
T Consensus 107 l~p~l~~L~g-k~VLDIGC~nGY~~frM~~~GA~-~ViGiD 145 (315)
T PF08003_consen 107 LLPHLPDLKG-KRVLDIGCNNGYYSFRMLGRGAK-SVIGID 145 (315)
T ss_pred HHhhhCCcCC-CEEEEecCCCcHHHHHHhhcCCC-EEEEEC
Confidence 3344432544 79999999999999999999776 378888
No 215
>PLN02589 caffeoyl-CoA O-methyltransferase
Probab=95.81 E-value=0.0099 Score=49.41 Aligned_cols=67 Identities=13% Similarity=0.100 Sum_probs=52.7
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCC---------CC
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIP---------KG 227 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P---------~~ 227 (233)
..+.+++|+||.+.|.-+..+++..| +-+++-+|.. +..+.|+++ ++|+++.||..+.+| ..
T Consensus 77 ~~~ak~iLEiGT~~GySal~la~al~~~g~v~tiE~~~~~~~~Ar~~~~~ag~~~~I~~~~G~a~e~L~~l~~~~~~~~~ 156 (247)
T PLN02589 77 LINAKNTMEIGVYTGYSLLATALALPEDGKILAMDINRENYELGLPVIQKAGVAHKIDFREGPALPVLDQMIEDGKYHGT 156 (247)
T ss_pred HhCCCEEEEEeChhhHHHHHHHhhCCCCCEEEEEeCCHHHHHHHHHHHHHCCCCCceEEEeccHHHHHHHHHhccccCCc
Confidence 45678999999999999999999865 7789999984 456666542 799999999887432 23
Q ss_pred -CEEEe
Q 039903 228 -DAILI 232 (233)
Q Consensus 228 -D~~~l 232 (233)
|++++
T Consensus 157 fD~iFi 162 (247)
T PLN02589 157 FDFIFV 162 (247)
T ss_pred ccEEEe
Confidence 88876
No 216
>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=95.75 E-value=0.024 Score=35.91 Aligned_cols=44 Identities=20% Similarity=0.367 Sum_probs=40.5
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.|.+.|.+. +..|+.|||+.+++ ++.-++|=|..|...|++.+.
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 467888886 59999999999999 999999999999999999997
No 217
>COG4976 Predicted methyltransferase (contains TPR repeat) [General function prediction only]
Probab=95.74 E-value=0.011 Score=48.21 Aligned_cols=67 Identities=10% Similarity=0.268 Sum_probs=45.7
Q ss_pred HHHHHHHHHhcchhcHHHHH----HhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC
Q 039903 141 NGVFNKAMLNHTSIVTNRII----DSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY 210 (233)
Q Consensus 141 ~~~f~~am~~~~~~~~~~~~----~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~ 210 (233)
.++|.+.....-....|..+ ...+ ...+++++|+|||+|....+|...--+ .+.+|+.+ .++.|.+.
T Consensus 95 Ae~Fd~~LVdkL~Y~vP~~l~emI~~~~-~g~F~~~lDLGCGTGL~G~~lR~~a~~--ltGvDiS~nMl~kA~eK 166 (287)
T COG4976 95 AERFDHILVDKLGYSVPELLAEMIGKAD-LGPFRRMLDLGCGTGLTGEALRDMADR--LTGVDISENMLAKAHEK 166 (287)
T ss_pred HHHHHHHHHHHhcCccHHHHHHHHHhcc-CCccceeeecccCcCcccHhHHHHHhh--ccCCchhHHHHHHHHhc
Confidence 45677776665444444433 3333 334899999999999999888877444 67789875 67777653
No 218
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=95.73 E-value=0.027 Score=46.87 Aligned_cols=67 Identities=10% Similarity=0.163 Sum_probs=59.8
Q ss_pred HHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 12 AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 12 ~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
.+...-|.+|+=.|.+ ||.|.+||-..+++ ++..+..=++-|...|++.+ +++.|++|++|..++..
T Consensus 9 if~SekRk~lLllL~e----gPkti~EI~~~l~v----s~~ai~pqiKkL~~~~LV~~-----~~~~Y~LS~~G~iiv~k 75 (260)
T COG4742 9 LFLSEKRKDLLLLLKE----GPKTIEEIKNELNV----SSSAILPQIKKLKDKGLVVQ-----EGDRYSLSSLGKIIVEK 75 (260)
T ss_pred HHccHHHHHHHHHHHh----CCCCHHHHHHHhCC----CcHHHHHHHHHHhhCCCEEe-----cCCEEEecchHHHHHHH
Confidence 4455668889999998 79999999999999 99999999999999999999 48999999999988755
No 219
>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=95.71 E-value=0.041 Score=44.34 Aligned_cols=107 Identities=11% Similarity=0.051 Sum_probs=55.2
Q ss_pred hhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHH----HHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHH
Q 039903 108 PYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFN----KAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNV 183 (233)
Q Consensus 108 ~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~----~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~ 183 (233)
+..|.|.|-+..+ ..-++.+.++|+.-..++ +.+..|.......+++.+...++...|.|.|||.+.++
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 FRWLNEQLYTTSS-------EEALKLFQEDPELFDIYHEGFRQQVKKWPVNPVDVIIEWLKKRPKSLVIADFGCGDAKLA 87 (219)
T ss_dssp HHHHHHHHHHS-H-------HHHHHHHHH-HHHHHHHHHHHHHHHCTSSS-HHHHHHHHHCTS-TTS-EEEES-TT-HHH
T ss_pred hHHHHHhHhcCCH-------HHHHHHHHhCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHhcCCCEEEEECCCchHHHH
Confidence 4455565554432 122344556777655444 44444444445566666552344579999999999999
Q ss_pred HHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCC-CCCCC--CEEEe
Q 039903 184 NIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE-RIPKG--DAILI 232 (233)
Q Consensus 184 ~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~-~~P~~--D~~~l 232 (233)
.++.+ ..++--|||-.. +++ .+++|+-+ |++.+ |++++
T Consensus 88 ~~~~~---~~~V~SfDLva~------n~~--Vtacdia~vPL~~~svDv~Vf 128 (219)
T PF05148_consen 88 KAVPN---KHKVHSFDLVAP------NPR--VTACDIANVPLEDESVDVAVF 128 (219)
T ss_dssp HH--S------EEEEESS-S------STT--EEES-TTS-S--TT-EEEEEE
T ss_pred Hhccc---CceEEEeeccCC------CCC--EEEecCccCcCCCCceeEEEE
Confidence 66542 356777887432 244 45799976 77764 88764
No 220
>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=95.70 E-value=0.016 Score=36.92 Aligned_cols=49 Identities=14% Similarity=0.266 Sum_probs=39.8
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS 71 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~ 71 (233)
+..|+-.|...++ .+.|..|||+.+++ ++..+.++++.|...|++++..
T Consensus 7 q~~vL~~l~~~~~-~~~t~~~la~~l~~----~~~~vs~~v~~L~~~Glv~r~~ 55 (62)
T PF12802_consen 7 QFRVLMALARHPG-EELTQSELAERLGI----SKSTVSRIVKRLEKKGLVERER 55 (62)
T ss_dssp HHHHHHHHHHSTT-SGEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHCCC-CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEeC
Confidence 4556667777641 12899999999999 9999999999999999999874
No 221
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=95.67 E-value=0.025 Score=47.46 Aligned_cols=66 Identities=18% Similarity=0.033 Sum_probs=48.4
Q ss_pred cCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC------CCceEEecCcCC-CC--CCCCEEEe
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-RI--PKGDAILI 232 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~~--P~~D~~~l 232 (233)
....+|+|+|+|.|..+..+++... .-+++.+|+. ..++.++++ .+|+++.+|... +. +..|.|++
T Consensus 70 ~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~~~~~l~~~~~n~~~~g~~~v~~~~~D~~~~~~~~~~fD~Vl~ 146 (264)
T TIGR00446 70 DPPERVLDMAAAPGGKTTQISALMKNEGAIVANEFSKSRTKVLIANINRCGVLNVAVTNFDGRVFGAAVPKFDAILL 146 (264)
T ss_pred CCcCEEEEECCCchHHHHHHHHHcCCCCEEEEEcCCHHHHHHHHHHHHHcCCCcEEEecCCHHHhhhhccCCCEEEE
Confidence 4557899999999999999998875 3578999984 456555432 568888888654 22 23488875
No 222
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=95.66 E-value=0.015 Score=40.72 Aligned_cols=64 Identities=16% Similarity=0.267 Sum_probs=49.8
Q ss_pred hhHHHH-hcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 21 VFEIIA-KAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 21 lfd~L~-~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
+||+|. ..+ ++....-|+-.+++ +.+..+.+++.|+..|++.... ++....|.+|+.|..|...
T Consensus 20 i~dIL~~~~~--~~~~~Tri~y~aNl----ny~~~~~yi~~L~~~Gli~~~~-~~~~~~y~lT~KG~~fle~ 84 (95)
T COG3432 20 IFDILKAISE--GGIGITRIIYGANL----NYKRAQKYIEMLVEKGLIIKQD-NGRRKVYELTEKGKRFLEK 84 (95)
T ss_pred HHHHHHHhcC--CCCCceeeeeecCc----CHHHHHHHHHHHHhCCCEEecc-CCccceEEEChhHHHHHHH
Confidence 577777 222 68888899999999 9999999999999999766652 1112379999999988654
No 223
>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=95.64 E-value=0.02 Score=39.82 Aligned_cols=62 Identities=11% Similarity=0.166 Sum_probs=47.9
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL 90 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~ 90 (233)
|...|.. |+....||.+.+ ++ ++..|.+=|+.|...|++++..... ..-.|++|+.|..|..
T Consensus 10 IL~~l~~----g~~rf~el~~~l~~i----s~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~~ 74 (90)
T PF01638_consen 10 ILRALFQ----GPMRFSELQRRLPGI----SPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELLP 74 (90)
T ss_dssp HHHHHTT----SSEEHHHHHHHSTTS-----HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHHH
T ss_pred HHHHHHh----CCCcHHHHHHhcchh----HHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHHH
Confidence 4455665 699999999999 89 9999999999999999999864321 1135999999988763
No 224
>PHA00738 putative HTH transcription regulator
Probab=95.64 E-value=0.028 Score=40.19 Aligned_cols=61 Identities=16% Similarity=0.139 Sum_probs=49.9
Q ss_pred HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903 16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV 84 (233)
Q Consensus 16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~ 84 (233)
-.++.|++.|... ++.++.||++.+++ +...+.+-|+.|...|+++....+ ..-.|++++.
T Consensus 12 ptRr~IL~lL~~~---e~~~V~eLae~l~l----SQptVS~HLKvLreAGLV~srK~G-r~vyY~Ln~~ 72 (108)
T PHA00738 12 ILRRKILELIAEN---YILSASLISHTLLL----SYTTVLRHLKILNEQGYIELYKEG-RTLYAKIREN 72 (108)
T ss_pred HHHHHHHHHHHHc---CCccHHHHHHhhCC----CHHHHHHHHHHHHHCCceEEEEEC-CEEEEEECCC
Confidence 4678899999884 37999999999999 999999999999999999987432 3345666653
No 225
>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=95.63 E-value=0.014 Score=45.82 Aligned_cols=57 Identities=14% Similarity=0.032 Sum_probs=38.4
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC---------CCceEEecCcCC
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY---------SGVKHIGGIMLE 222 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~---------~ri~~~~gD~f~ 222 (233)
..+..+|+++|+|.|..++.+++.++..++++-|.+++++..+.+ .+|++.+.|+-+
T Consensus 43 ~~~~~~VLELGaG~Gl~gi~~a~~~~~~~Vv~TD~~~~l~~l~~Ni~~N~~~~~~~v~v~~L~Wg~ 108 (173)
T PF10294_consen 43 LFRGKRVLELGAGTGLPGIAAAKLFGAARVVLTDYNEVLELLRRNIELNGSLLDGRVSVRPLDWGD 108 (173)
T ss_dssp GTTTSEEEETT-TTSHHHHHHHHT-T-SEEEEEE-S-HHHHHHHHHHTT--------EEEE--TTS
T ss_pred hcCCceEEEECCccchhHHHHHhccCCceEEEeccchhhHHHHHHHHhccccccccccCcEEEecC
Confidence 345589999999999999999998888889999999877655432 679999999876
No 226
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=95.60 E-value=0.033 Score=33.96 Aligned_cols=44 Identities=23% Similarity=0.342 Sum_probs=38.7
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.|++.|... ++.+..+|++.+++ +...+.+.|+.|...|++.+.
T Consensus 4 ~il~~l~~~---~~~s~~~l~~~l~~----s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 4 QILELLAQQ---GKVSVEELAELLGV----SEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HHHHHHHHc---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 356667665 47999999999999 999999999999999999986
No 227
>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=95.59 E-value=0.022 Score=42.37 Aligned_cols=46 Identities=28% Similarity=0.274 Sum_probs=38.3
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
++.|..|||+++++ ++..+.++|+.|...|++..... .++.|.+..
T Consensus 24 ~~~s~~eia~~l~i----s~~~v~~~l~~L~~~Gli~~~~g--~~ggy~l~~ 69 (130)
T TIGR02944 24 QPYSAAEIAEQTGL----NAPTVSKILKQLSLAGIVTSKRG--VEGGYTLAR 69 (130)
T ss_pred CCccHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEecCC--CCCChhhcC
Confidence 58999999999999 99999999999999999986421 345676643
No 228
>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=95.58 E-value=0.031 Score=36.49 Aligned_cols=57 Identities=16% Similarity=0.345 Sum_probs=45.4
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
+..|+..+.. ++.+..||++.+++ +...+.+.|+.|...|++...... ....|++|+
T Consensus 9 ~~~il~~l~~----~~~~~~ei~~~~~i----~~~~i~~~l~~L~~~g~i~~~~~~-~~~~~~~~~ 65 (78)
T cd00090 9 RLRILRLLLE----GPLTVSELAERLGL----SQSTVSRHLKKLEEAGLVESRREG-RRVYYSLTD 65 (78)
T ss_pred HHHHHHHHHH----CCcCHHHHHHHHCc----CHhHHHHHHHHHHHCCCeEEEEec-cEEEEEeCC
Confidence 4456677776 35999999999999 999999999999999999975322 236777775
No 229
>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=95.52 E-value=0.035 Score=40.27 Aligned_cols=63 Identities=22% Similarity=0.361 Sum_probs=46.4
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCC-CCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA 82 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~-~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt 82 (233)
+.-|++.|...+ ++.|+.||.+++.-. ++.+..-++|.|+.|+..|++.+...+++...|.++
T Consensus 3 R~~Il~~l~~~~--~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~~ 66 (116)
T cd07153 3 RLAILEVLLESD--GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELN 66 (116)
T ss_pred HHHHHHHHHhCC--CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEeC
Confidence 456888888764 689999999998421 122888999999999999999987543222456543
No 230
>COG4122 Predicted O-methyltransferase [General function prediction only]
Probab=95.48 E-value=0.02 Score=46.61 Aligned_cols=67 Identities=10% Similarity=0.172 Sum_probs=54.0
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEe-cCcCCC---C-CCC-CEE
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIG-GIMLER---I-PKG-DAI 230 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~-gD~f~~---~-P~~-D~~ 230 (233)
.++.++++.||.+.|.-++.++..-| +-+.+-+|+. +-++.|+++ ++|+.+. ||..+. . ... |++
T Consensus 57 ~~~~k~iLEiGT~~GySal~mA~~l~~~g~l~tiE~~~e~~~~A~~n~~~ag~~~~i~~~~~gdal~~l~~~~~~~fDli 136 (219)
T COG4122 57 LSGPKRILEIGTAIGYSALWMALALPDDGRLTTIERDEERAEIARENLAEAGVDDRIELLLGGDALDVLSRLLDGSFDLV 136 (219)
T ss_pred hcCCceEEEeecccCHHHHHHHhhCCCCCeEEEEeCCHHHHHHHHHHHHHcCCcceEEEEecCcHHHHHHhccCCCccEE
Confidence 56889999999999999999999999 8888999985 567777764 6788888 588762 2 222 998
Q ss_pred Ee
Q 039903 231 LI 232 (233)
Q Consensus 231 ~l 232 (233)
|+
T Consensus 137 FI 138 (219)
T COG4122 137 FI 138 (219)
T ss_pred EE
Confidence 86
No 231
>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=95.47 E-value=0.012 Score=46.31 Aligned_cols=60 Identities=20% Similarity=0.188 Sum_probs=41.3
Q ss_pred HHHHhccccc--CcceEEEecCCccHHHHHHHHHc-CCCcEEEeechHHHhhccCCCCceEEecCcC
Q 039903 158 RIIDSSKGFE--QIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLSHVIQDSSSYSGVKHIGGIML 221 (233)
Q Consensus 158 ~~~~~~~~~~--~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f 221 (233)
++.+.++-++ +..++||+|++.|.++..++++. +..+++.+|+...- ....+.++.+|++
T Consensus 11 ei~~~~~~~~~~~~~~vlDlG~aPGGws~~~~~~~~~~~~v~avDl~~~~----~~~~~~~i~~d~~ 73 (181)
T PF01728_consen 11 EIDEKFKIFKPGKGFTVLDLGAAPGGWSQVLLQRGGPAGRVVAVDLGPMD----PLQNVSFIQGDIT 73 (181)
T ss_dssp HHHHTTSSS-TTTTEEEEEET-TTSHHHHHHHTSTTTEEEEEEEESSSTG----S-TTEEBTTGGGE
T ss_pred HHHHHCCCCCcccccEEEEcCCcccceeeeeeecccccceEEEEeccccc----cccceeeeecccc
Confidence 4555555233 45999999999999999999998 78889999987651 1134444455554
No 232
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=95.46 E-value=0.054 Score=34.19 Aligned_cols=54 Identities=15% Similarity=0.337 Sum_probs=42.4
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
|+..|.. ++.|..+|++.+++ +...+.+.|+.|...|++...... ....|.+|.
T Consensus 2 il~~l~~----~~~~~~~i~~~l~i----s~~~v~~~l~~L~~~g~i~~~~~~-~~~~~~~~~ 55 (66)
T smart00418 2 ILKLLAE----GELCVCELAEILGL----SQSTVSHHLKKLREAGLVESRREG-KRVYYSLTD 55 (66)
T ss_pred HHHHhhc----CCccHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeeeecC-CEEEEEEch
Confidence 4555653 58999999999999 999999999999999999975321 235666665
No 233
>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=95.35 E-value=0.031 Score=44.95 Aligned_cols=59 Identities=22% Similarity=0.338 Sum_probs=48.5
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA 85 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s 85 (233)
+..|...|... ++.+..|||+.+++ ++..+.|.|+.|...|++++... ....|.+|+.|
T Consensus 145 ~~~IL~~l~~~---g~~s~~eia~~l~i----s~stv~r~L~~Le~~GlI~r~~~--r~~~~~lT~~G 203 (203)
T TIGR01884 145 ELKVLEVLKAE---GEKSVKNIAKKLGK----SLSTISRHLRELEKKGLVEQKGR--KGKRYSLTKLG 203 (203)
T ss_pred HHHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEcC--CccEEEeCCCC
Confidence 45677888775 48899999999999 99999999999999999998631 24668887653
No 234
>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=95.32 E-value=0.018 Score=36.47 Aligned_cols=48 Identities=15% Similarity=0.306 Sum_probs=40.7
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeecc
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSA 72 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~ 72 (233)
+..+...|.+. ++.+..|||+.+++ +...+.++++-|...|++++...
T Consensus 5 q~~iL~~l~~~---~~~~~~~la~~~~~----~~~~~t~~i~~L~~~g~I~r~~~ 52 (59)
T PF01047_consen 5 QFRILRILYEN---GGITQSELAEKLGI----SRSTVTRIIKRLEKKGLIERERD 52 (59)
T ss_dssp HHHHHHHHHHH---SSEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHHc---CCCCHHHHHHHHCC----ChhHHHHHHHHHHHCCCEEeccC
Confidence 45566677777 48999999999999 99999999999999999998653
No 235
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=95.28 E-value=0.04 Score=44.70 Aligned_cols=64 Identities=19% Similarity=0.283 Sum_probs=50.4
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC----CCCceeccHhhhHhhc
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD----DQRLYGLAHVAKYFVL 90 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~----~~~~y~lt~~s~~l~~ 90 (233)
.|...|.+. +|+|+.|||+++|+ ++..++|-|..|++.|+++.....+ ..-.|++|..+.....
T Consensus 15 ~il~lL~~~---g~~sa~elA~~Lgi----s~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~~f~ 82 (218)
T COG2345 15 RILELLKKS---GPVSADELAEELGI----SPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGREQFP 82 (218)
T ss_pred HHHHHHhcc---CCccHHHHHHHhCC----CHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchhhcc
Confidence 456667766 69999999999999 9999999999999999998653221 2347888887766443
No 236
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=95.22 E-value=0.031 Score=49.49 Aligned_cols=63 Identities=13% Similarity=-0.050 Sum_probs=48.6
Q ss_pred ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC---CCCEEEe
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP---KGDAILI 232 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P---~~D~~~l 232 (233)
.+++|++||+|.+++.++.+.+..+++..|. |..++.++++ +.+++..+|..+-++ ..|++.+
T Consensus 59 ~~vLDl~aGsG~~~l~~a~~~~~~~V~a~Din~~Av~~a~~N~~~N~~~~~~v~~~Da~~~l~~~~~fD~V~l 131 (382)
T PRK04338 59 ESVLDALSASGIRGIRYALETGVEKVTLNDINPDAVELIKKNLELNGLENEKVFNKDANALLHEERKFDVVDI 131 (382)
T ss_pred CEEEECCCcccHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHHHHHhCCCceEEEhhhHHHHHhhcCCCCEEEE
Confidence 5899999999999999999888668999998 5577777653 456788888765222 2488765
No 237
>KOG3115 consensus Methyltransferase-like protein [General function prediction only]
Probab=95.16 E-value=0.0095 Score=47.62 Aligned_cols=33 Identities=12% Similarity=0.255 Sum_probs=29.8
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeech
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS 201 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp 201 (233)
-..++|||||.|.+++.|...||+--..++++-
T Consensus 61 kvefaDIGCGyGGLlv~Lsp~fPdtLiLGmEIR 93 (249)
T KOG3115|consen 61 KVEFADIGCGYGGLLMKLAPKFPDTLILGMEIR 93 (249)
T ss_pred cceEEeeccCccchhhhccccCccceeeeehhh
Confidence 367999999999999999999999888888864
No 238
>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=95.15 E-value=0.037 Score=36.34 Aligned_cols=55 Identities=15% Similarity=0.173 Sum_probs=44.2
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV 84 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~ 84 (233)
++.|+..|.+ ++.+..+||+.+++ +...+.+-++.|...|+.... .+..|.+.+.
T Consensus 2 ~~~il~~L~~----~~~~~~eLa~~l~v----S~~tv~~~l~~L~~~g~~i~~----~~~g~~l~~~ 56 (69)
T TIGR00122 2 PLRLLALLAD----NPFSGEKLGEALGM----SRTAVNKHIQTLREWGVDVLT----VGKGYRLPPP 56 (69)
T ss_pred hHHHHHHHHc----CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEe----cCCceEecCc
Confidence 3567778887 58899999999999 999999999999999996654 3455666543
No 239
>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=95.10 E-value=0.037 Score=44.51 Aligned_cols=67 Identities=16% Similarity=0.170 Sum_probs=47.2
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC--CCEEEe
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK--GDAILI 232 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~--~D~~~l 232 (233)
.....+|+|.-||.|.|+..+++..+..++...|+ |.+++..+++ ++|..+.+|..+-.+. +|-++|
T Consensus 99 v~~~e~VlD~faGIG~f~l~~ak~~~~~~V~A~d~Np~a~~~L~~Ni~lNkv~~~i~~~~~D~~~~~~~~~~drvim 175 (200)
T PF02475_consen 99 VKPGEVVLDMFAGIGPFSLPIAKHGKAKRVYAVDLNPDAVEYLKENIRLNKVENRIEVINGDAREFLPEGKFDRVIM 175 (200)
T ss_dssp --TT-EEEETT-TTTTTHHHHHHHT-SSEEEEEES-HHHHHHHHHHHHHTT-TTTEEEEES-GGG---TT-EEEEEE
T ss_pred CCcceEEEEccCCccHHHHHHhhhcCccEEEEecCCHHHHHHHHHHHHHcCCCCeEEEEcCCHHHhcCccccCEEEE
Confidence 35568999999999999999999888888999999 5666655442 7899999999874433 377765
No 240
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=95.08 E-value=0.047 Score=38.12 Aligned_cols=47 Identities=15% Similarity=0.194 Sum_probs=41.6
Q ss_pred HHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903 36 AVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL 90 (233)
Q Consensus 36 ~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~ 90 (233)
..+||+.+++ +...+.+.++.|...|++.+. .+..|.+|+.+..+..
T Consensus 2 ~~ela~~l~i----s~stvs~~l~~L~~~glI~r~----~~~~~~lT~~g~~~~~ 48 (96)
T smart00529 2 TSEIAERLNV----SPPTVTQMLKKLEKDGLVEYE----PYRGITLTEKGRRLAR 48 (96)
T ss_pred HHHHHHHhCC----ChHHHHHHHHHHHHCCCEEEc----CCCceEechhHHHHHH
Confidence 4689999999 999999999999999999997 4568999998887753
No 241
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=95.03 E-value=0.041 Score=42.29 Aligned_cols=46 Identities=20% Similarity=0.151 Sum_probs=40.8
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
++.|..+||+..++ ++.+|+++|..|...|+++-.+. .+|.|+++.
T Consensus 23 ~~~s~~eIA~~~~i----s~~~L~kIl~~L~~aGlv~S~rG--~~GGy~La~ 68 (153)
T PRK11920 23 KLSRIPEIARAYGV----SELFLFKILQPLVEAGLVETVRG--RNGGVRLGR 68 (153)
T ss_pred CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeecC--CCCCeeecC
Confidence 47899999999999 99999999999999999998753 568898875
No 242
>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=95.03 E-value=0.026 Score=35.19 Aligned_cols=43 Identities=26% Similarity=0.362 Sum_probs=35.3
Q ss_pred HHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHH
Q 039903 9 LPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLL 61 (233)
Q Consensus 9 ~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L 61 (233)
.-.+|.+|+++|-||.=. ..|+.|||+.+|+ ++..+...||-.
T Consensus 5 Q~e~L~~A~~~GYfd~PR------~~tl~elA~~lgi----s~st~~~~LRra 47 (53)
T PF04967_consen 5 QREILKAAYELGYFDVPR------RITLEELAEELGI----SKSTVSEHLRRA 47 (53)
T ss_pred HHHHHHHHHHcCCCCCCC------cCCHHHHHHHhCC----CHHHHHHHHHHH
Confidence 457899999999999754 5899999999999 887777666643
No 243
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=95.00 E-value=0.062 Score=40.65 Aligned_cols=65 Identities=22% Similarity=0.139 Sum_probs=50.4
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~ 91 (233)
.|+-.|... ++.|..|||+.+++ ++..+.++++-|...|++++..... ..-...+|+.|..+...
T Consensus 44 ~vL~~l~~~---~~~t~~eLa~~l~i----~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~ 110 (144)
T PRK11512 44 KVLCSIRCA---ACITPVELKKVLSV----DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ 110 (144)
T ss_pred HHHHHHHHc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence 345566554 58999999999999 9999999999999999999864421 12345778888876644
No 244
>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=94.97 E-value=0.085 Score=43.86 Aligned_cols=88 Identities=11% Similarity=0.138 Sum_probs=55.5
Q ss_pred HHHHHHhcchhc----HHHHHHhcccccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccCC-------
Q 039903 144 FNKAMLNHTSIV----TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSSY------- 210 (233)
Q Consensus 144 f~~am~~~~~~~----~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~~------- 210 (233)
|...|...++.. +..++-.++ .....+|++.|-|+|.++..|++. .|+=++.-+|. ++-++.|+++
T Consensus 13 ~~~~l~rrtQIiYpkD~~~I~~~l~-i~pG~~VlEaGtGSG~lt~~l~r~v~p~G~v~t~E~~~~~~~~A~~n~~~~gl~ 91 (247)
T PF08704_consen 13 WTLSLPRRTQIIYPKDISYILMRLD-IRPGSRVLEAGTGSGSLTHALARAVGPTGHVYTYEFREDRAEKARKNFERHGLD 91 (247)
T ss_dssp HHHTS-SSS----HHHHHHHHHHTT---TT-EEEEE--TTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTTCC
T ss_pred HHHhccCCcceeeCchHHHHHHHcC-CCCCCEEEEecCCcHHHHHHHHHHhCCCeEEEccccCHHHHHHHHHHHHHcCCC
Confidence 444444444432 344556666 778899999999999999999975 68888888887 4456666553
Q ss_pred CCceEEecCcCC-CCC----C-CCEEEe
Q 039903 211 SGVKHIGGIMLE-RIP----K-GDAILI 232 (233)
Q Consensus 211 ~ri~~~~gD~f~-~~P----~-~D~~~l 232 (233)
++|++..+|.-+ .++ . .|+++|
T Consensus 92 ~~v~~~~~Dv~~~g~~~~~~~~~DavfL 119 (247)
T PF08704_consen 92 DNVTVHHRDVCEEGFDEELESDFDAVFL 119 (247)
T ss_dssp TTEEEEES-GGCG--STT-TTSEEEEEE
T ss_pred CCceeEecceecccccccccCcccEEEE
Confidence 689999999975 343 2 398886
No 245
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=94.82 E-value=0.1 Score=39.34 Aligned_cols=65 Identities=14% Similarity=0.147 Sum_probs=50.0
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~ 91 (233)
++..|...+ ++.|..|||+.+++ +...+.++++-|...|++++...+. ..-...+|+.|..+...
T Consensus 36 vL~~l~~~~--~~~t~~eLa~~l~~----~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~ 102 (144)
T PRK03573 36 TLHNIHQLP--PEQSQIQLAKAIGI----EQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISE 102 (144)
T ss_pred HHHHHHHcC--CCCCHHHHHHHhCC----ChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHH
Confidence 445555433 36899999999999 9999999999999999999875421 12356788988877654
No 246
>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=94.80 E-value=0.081 Score=32.88 Aligned_cols=41 Identities=15% Similarity=0.239 Sum_probs=34.2
Q ss_pred hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCC
Q 039903 19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHR 65 (233)
Q Consensus 19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~g 65 (233)
..|...|.... +++|..+||+.+++ +.+-+++-+..|...|
T Consensus 3 ~~il~~L~~~~--~~it~~eLa~~l~v----S~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESK--EPITAKELAEELGV----SRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTT--TSBEHHHHHHHCTS-----HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcC--CCcCHHHHHHHhCC----CHHHHHHHHHHHHHCC
Confidence 34667775543 57999999999999 9999999999999999
No 247
>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=94.76 E-value=0.035 Score=39.84 Aligned_cols=32 Identities=31% Similarity=0.475 Sum_probs=24.9
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL 200 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl 200 (233)
.....+||||||+|.+.--|.+. ..+|..+|.
T Consensus 57 ~~~~~FVDlGCGNGLLV~IL~~E--Gy~G~GiD~ 88 (112)
T PF07757_consen 57 QKFQGFVDLGCGNGLLVYILNSE--GYPGWGIDA 88 (112)
T ss_pred CCCCceEEccCCchHHHHHHHhC--CCCcccccc
Confidence 35678999999999987777665 555777774
No 248
>COG0293 FtsJ 23S rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=94.71 E-value=0.11 Score=41.91 Aligned_cols=63 Identities=19% Similarity=0.137 Sum_probs=48.5
Q ss_pred HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeechHHHhhccCCCCceEEecCcCC
Q 039903 156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE 222 (233)
Q Consensus 156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~ 222 (233)
..++.+.+.-|++..+|+|+|.-.|.++..+++.-. ..+++.+|+-+.-. .+.|.++.+||+.
T Consensus 33 L~el~~k~~i~~~~~~ViDLGAAPGgWsQva~~~~~~~~~ivavDi~p~~~----~~~V~~iq~d~~~ 96 (205)
T COG0293 33 LLELNEKFKLFKPGMVVVDLGAAPGGWSQVAAKKLGAGGKIVAVDILPMKP----IPGVIFLQGDITD 96 (205)
T ss_pred HHHHHHhcCeecCCCEEEEcCCCCCcHHHHHHHHhCCCCcEEEEECccccc----CCCceEEeeeccC
Confidence 345666665468889999999999999998887754 46689999765432 2458999999996
No 249
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=94.71 E-value=0.092 Score=44.59 Aligned_cols=66 Identities=14% Similarity=0.125 Sum_probs=54.3
Q ss_pred HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCc-EEEeec-hHHHhhccCC-----CCceEEecCcCC
Q 039903 156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIK-GVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE 222 (233)
Q Consensus 156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~-~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~ 222 (233)
..++++.+. .......||+-=|.|.++.++++++|+.. .+.+|. |.+++.|++. +|++++.++|-+
T Consensus 12 l~E~i~~L~-~~~~giyiD~TlG~GGHS~~iL~~l~~~~~li~~DrD~~Ai~~a~~~l~~~~~r~~~v~~~F~~ 84 (314)
T COG0275 12 LNEVVELLA-PKPDGIYIDGTLGAGGHSRAILEKLPDLGRLIGIDRDPQAIAIAKERLKEFDGRVTLVHGNFAN 84 (314)
T ss_pred HHHHHHhcc-cCCCcEEEEecCCCcHhHHHHHHhCCCCCeEEEEcCCHHHHHHHHHHhhccCCcEEEEeCcHHH
Confidence 345666665 55668999999999999999999999887 899998 5688888763 699999998764
No 250
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=94.70 E-value=0.12 Score=36.13 Aligned_cols=47 Identities=19% Similarity=0.152 Sum_probs=41.9
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
..+.|...|... ||-...-||..+++ +...+...|+-|..+|++++.
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 356678888887 47888999999999 999999999999999999997
No 251
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=94.53 E-value=0.069 Score=38.17 Aligned_cols=46 Identities=20% Similarity=0.274 Sum_probs=41.8
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC 69 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~ 69 (233)
.+..|+..|... ++.|..+||+.+|+ ++..+.+.++.|...|++.+
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 467788899886 58999999999999 99999999999999999985
No 252
>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=94.52 E-value=0.1 Score=37.58 Aligned_cols=68 Identities=16% Similarity=0.211 Sum_probs=50.3
Q ss_pred hhChhHHHH--hcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCC--CCceeccHhhhHhhc
Q 039903 18 ELGVFEIIA--KAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDD--QRLYGLAHVAKYFVL 90 (233)
Q Consensus 18 ~lglfd~L~--~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~--~~~y~lt~~s~~l~~ 90 (233)
+..++..|. ... .++.|..+||..+++ +...+.++++.|...|++.+...+.+ .-.+.+|+.+..+..
T Consensus 27 q~~vL~~l~~~~~~-~~~~t~~eL~~~l~~----~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~ 98 (109)
T TIGR01889 27 ELLILYYLGKLENN-EGKLTLKEIIKEILI----KQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIE 98 (109)
T ss_pred HHHHHHHHHhhhcc-CCcCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHH
Confidence 344566665 221 158999999999999 99999999999999999998654311 124568888876653
No 253
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=94.43 E-value=0.095 Score=35.29 Aligned_cols=43 Identities=16% Similarity=0.262 Sum_probs=39.6
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
|=|+|... |..++.|||..++. ++..++-+|..++.+|-+++.
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 45778887 58999999999999 999999999999999999987
No 254
>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=94.40 E-value=0.11 Score=33.06 Aligned_cols=40 Identities=18% Similarity=0.104 Sum_probs=33.7
Q ss_pred CCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903 34 ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL 81 (233)
Q Consensus 34 ~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l 81 (233)
.|..+||..+++ +...+.+.+..|...|+++.. .+..|.+
T Consensus 26 ~~~~~la~~~~i----s~~~v~~~l~~L~~~G~i~~~----~~~~~~l 65 (66)
T cd07377 26 PSERELAEELGV----SRTTVREALRELEAEGLVERR----PGRGTFV 65 (66)
T ss_pred CCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec----CCCeEEe
Confidence 359999999999 999999999999999999875 3445544
No 255
>KOG1661 consensus Protein-L-isoaspartate(D-aspartate) O-methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=94.37 E-value=0.11 Score=41.90 Aligned_cols=66 Identities=15% Similarity=0.113 Sum_probs=45.9
Q ss_pred ccCcceEEEecCCccHHHHHHHHH--cCCCcEEEeec-hHHHhhccCC----------------CCceEEecCcCCCCCC
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISN--YLHIKGVNFDL-SHVIQDSSSY----------------SGVKHIGGIMLERIPK 226 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~--~P~l~~~v~Dl-p~v~~~a~~~----------------~ri~~~~gD~f~~~P~ 226 (233)
+....++||||+|+|.++..++.- -|....+.+|+ |++++.+.++ .++.++.||=.+-.|.
T Consensus 80 L~pG~s~LdvGsGSGYLt~~~~~mvg~~g~~~~GIEh~~eLVe~Sk~nl~k~i~~~e~~~~~~~~~l~ivvGDgr~g~~e 159 (237)
T KOG1661|consen 80 LQPGASFLDVGSGSGYLTACFARMVGATGGNVHGIEHIPELVEYSKKNLDKDITTSESSSKLKRGELSIVVGDGRKGYAE 159 (237)
T ss_pred hccCcceeecCCCccHHHHHHHHHhcCCCccccchhhhHHHHHHHHHHHHhhccCchhhhhhccCceEEEeCCccccCCc
Confidence 456678999999999987766632 23332356664 7888877653 5789999999884443
Q ss_pred -C--CEEE
Q 039903 227 -G--DAIL 231 (233)
Q Consensus 227 -~--D~~~ 231 (233)
+ |.|.
T Consensus 160 ~a~YDaIh 167 (237)
T KOG1661|consen 160 QAPYDAIH 167 (237)
T ss_pred cCCcceEE
Confidence 3 7765
No 256
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=94.36 E-value=0.13 Score=49.27 Aligned_cols=76 Identities=17% Similarity=0.108 Sum_probs=53.5
Q ss_pred HHHHHHhcccc-cCcceEEEecCCccHHHHHHHHH------------c------------------------------CC
Q 039903 156 TNRIIDSSKGF-EQIKQLVDVGGGLGVNVNIIISN------------Y------------------------------LH 192 (233)
Q Consensus 156 ~~~~~~~~~~~-~~~~~vvDvGGG~G~~~~~l~~~------------~------------------------------P~ 192 (233)
+..++.... | ++...++|-.||+|.++++.+.. | +.
T Consensus 178 Aaa~l~~a~-w~~~~~~l~DP~CGSGTilIEAa~~~~~~~pg~~r~~f~f~~~~~~~~~~w~~~~~~a~~~~~~~~~~~~ 256 (702)
T PRK11783 178 AAAILLRSG-WPQEGTPLLDPMCGSGTLLIEAAMMAADIAPGLHRERWGFSGWLGHDEALWQELLEEAQERARAGLAELP 256 (702)
T ss_pred HHHHHHHcC-CCCCCCeEEccCCCccHHHHHHHHHHhcCCCCccccccccccCCCCCHHHHHHHHHHHHHHHhhcccccC
Confidence 344554434 7 45689999999999999887652 1 12
Q ss_pred CcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCC----CCEEEe
Q 039903 193 IKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPK----GDAILI 232 (233)
Q Consensus 193 l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~----~D~~~l 232 (233)
.+++.+|+ |.+++.|+.+ ++|++..+|+++ +.|. .|+++.
T Consensus 257 ~~i~G~Did~~av~~A~~N~~~~g~~~~i~~~~~D~~~~~~~~~~~~~d~Ivt 309 (702)
T PRK11783 257 SKFYGSDIDPRVIQAARKNARRAGVAELITFEVKDVADLKNPLPKGPTGLVIS 309 (702)
T ss_pred ceEEEEECCHHHHHHHHHHHHHcCCCcceEEEeCChhhcccccccCCCCEEEE
Confidence 36889998 5688877764 579999999987 4432 377753
No 257
>KOG3010 consensus Methyltransferase [General function prediction only]
Probab=94.29 E-value=0.047 Score=44.84 Aligned_cols=43 Identities=21% Similarity=0.225 Sum_probs=33.7
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCCCC
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSYSG 212 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~~r 212 (233)
..+.++|||||+|..++.+++.|-+ ++..|.. ..++.+++.++
T Consensus 33 ~h~~a~DvG~G~Gqa~~~iae~~k~--VIatD~s~~mL~~a~k~~~ 76 (261)
T KOG3010|consen 33 GHRLAWDVGTGNGQAARGIAEHYKE--VIATDVSEAMLKVAKKHPP 76 (261)
T ss_pred CcceEEEeccCCCcchHHHHHhhhh--heeecCCHHHHHHhhcCCC
Confidence 3459999999999778888887665 7888985 47888887633
No 258
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=94.12 E-value=0.12 Score=41.99 Aligned_cols=55 Identities=22% Similarity=0.213 Sum_probs=46.8
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
..+|..|||+.+++ +...+.|+|+.|...|++++.... .+..+.+|+.+..+...
T Consensus 20 ~~IS~~eLA~~L~i----S~~Tvsr~Lk~LEe~GlI~R~~~~-r~~~v~LTekG~~ll~~ 74 (217)
T PRK14165 20 VKISSSEFANHTGT----SSKTAARILKQLEDEGYITRTIVP-RGQLITITEKGLDVLYN 74 (217)
T ss_pred CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEEcC-CceEEEECHHHHHHHHH
Confidence 46899999999999 999999999999999999986433 46789999999866533
No 259
>KOG2361 consensus Predicted methyltransferase [General function prediction only]
Probab=94.11 E-value=0.048 Score=44.78 Aligned_cols=64 Identities=20% Similarity=0.247 Sum_probs=49.2
Q ss_pred cceEEEecCCccHHHHHHHHHcCC--CcEEEeec-hHHHhhccCC-----CCceEEecCcCC-----CCCCC--CEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLH--IKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE-----RIPKG--DAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~--l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~-----~~P~~--D~~~l 232 (233)
..+++.||||.|...--+++.+|+ ++...+|. |.+++..+++ .|+.....|+-. +.+++ |++.|
T Consensus 72 ~~~ilEvGCGvGNtvfPll~~~~n~~l~v~acDfsp~Ai~~vk~~~~~~e~~~~afv~Dlt~~~~~~~~~~~svD~it~ 150 (264)
T KOG2361|consen 72 AETILEVGCGVGNTVFPLLKTSPNNRLKVYACDFSPRAIELVKKSSGYDESRVEAFVWDLTSPSLKEPPEEGSVDIITL 150 (264)
T ss_pred hhhheeeccCCCcccchhhhcCCCCCeEEEEcCCChHHHHHHHhccccchhhhcccceeccchhccCCCCcCccceEEE
Confidence 348999999999999999999998 88899997 6688877664 467766777765 23334 77654
No 260
>KOG2730 consensus Methylase [General function prediction only]
Probab=94.09 E-value=0.032 Score=45.19 Aligned_cols=53 Identities=19% Similarity=0.158 Sum_probs=44.8
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE 222 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~ 222 (233)
....++|.=||-|...++++.++|. ++.+|+ |.-|..|+.+ +||+|+.|||++
T Consensus 94 ~~~~iidaf~g~gGntiqfa~~~~~--VisIdiDPikIa~AkhNaeiYGI~~rItFI~GD~ld 154 (263)
T KOG2730|consen 94 NAEVIVDAFCGVGGNTIQFALQGPY--VIAIDIDPVKIACARHNAEVYGVPDRITFICGDFLD 154 (263)
T ss_pred CcchhhhhhhcCCchHHHHHHhCCe--EEEEeccHHHHHHHhccceeecCCceeEEEechHHH
Confidence 5678999999999999999999998 566666 5567777765 799999999997
No 261
>COG4076 Predicted RNA methylase [General function prediction only]
Probab=94.07 E-value=0.12 Score=41.10 Aligned_cols=60 Identities=10% Similarity=0.179 Sum_probs=47.3
Q ss_pred ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCCCEEE
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKGDAIL 231 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~D~~~ 231 (233)
.++.|+|.|+|.++.-.+++ .-|++.+++ |...+.|.++ .+++.+.||..+ .+-.||+++
T Consensus 34 d~~~DLGaGsGiLs~~Aa~~--A~rViAiE~dPk~a~~a~eN~~v~g~~n~evv~gDA~~y~fe~ADvvi 101 (252)
T COG4076 34 DTFADLGAGSGILSVVAAHA--AERVIAIEKDPKRARLAEENLHVPGDVNWEVVVGDARDYDFENADVVI 101 (252)
T ss_pred hceeeccCCcchHHHHHHhh--hceEEEEecCcHHHHHhhhcCCCCCCcceEEEecccccccccccceeH
Confidence 57899999999998877776 556777776 5566667664 689999999999 785578874
No 262
>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=94.04 E-value=0.065 Score=43.09 Aligned_cols=37 Identities=11% Similarity=0.190 Sum_probs=30.2
Q ss_pred ccCcc-eEEEecCCccHHHHHHHHHcCCCcEEEeechH
Q 039903 166 FEQIK-QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH 202 (233)
Q Consensus 166 ~~~~~-~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~ 202 (233)
+.... +||.||+|+|..+..+++++|+++.-==|.+.
T Consensus 22 l~~~~~~vLEiaSGtGqHa~~FA~~lP~l~WqPSD~~~ 59 (204)
T PF06080_consen 22 LPDSGTRVLEIASGTGQHAVYFAQALPHLTWQPSDPDD 59 (204)
T ss_pred hCccCceEEEEcCCccHHHHHHHHHCCCCEEcCCCCCh
Confidence 44445 49999999999999999999999875556544
No 263
>COG2384 Predicted SAM-dependent methyltransferase [General function prediction only]
Probab=93.98 E-value=0.11 Score=42.17 Aligned_cols=64 Identities=14% Similarity=0.131 Sum_probs=48.7
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhc----cCC---CCceEEecCcCCCCC-C-C-CEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDS----SSY---SGVKHIGGIMLERIP-K-G-DAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a----~~~---~ri~~~~gD~f~~~P-~-~-D~~~l 232 (233)
...+.||||-|+.+.+.+++.+|..+++.-|. |.-++.| +++ +||+..-||=|.++- . . |++++
T Consensus 17 ~~~iaDIGsDHAYLp~~Lv~~~~~~~~va~eV~~gpl~~a~~~v~~~~l~~~i~vr~~dgl~~l~~~d~~d~ivI 91 (226)
T COG2384 17 GARIADIGSDHAYLPIYLVKNNPASTAVAGEVVPGPLESAIRNVKKNNLSERIDVRLGDGLAVLELEDEIDVIVI 91 (226)
T ss_pred CCceeeccCchhHhHHHHHhcCCcceEEEeecccCHHHHHHHHHHhcCCcceEEEeccCCccccCccCCcCEEEE
Confidence 34499999999999999999999999999997 3333333 332 899999999988543 3 2 66653
No 264
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=93.97 E-value=0.13 Score=38.87 Aligned_cols=46 Identities=11% Similarity=0.056 Sum_probs=39.2
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
.+.+..+||+.+++ +...++++|+.|...|+++.... .+|.|.++.
T Consensus 24 ~~~s~~~ia~~~~i----s~~~vrk~l~~L~~~Glv~s~~G--~~GG~~l~~ 69 (141)
T PRK11014 24 RMTSISEVTEVYGV----SRNHMVKIINQLSRAGYVTAVRG--KNGGIRLGK 69 (141)
T ss_pred CccCHHHHHHHHCc----CHHHHHHHHHHHHhCCEEEEecC--CCCCeeecC
Confidence 47899999999999 99999999999999999998642 346787764
No 265
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=93.94 E-value=0.17 Score=31.58 Aligned_cols=34 Identities=24% Similarity=0.273 Sum_probs=31.8
Q ss_pred CC-CHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 33 KI-SAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 33 ~~-t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.+ |..|||+.+++ +...+++.++.|...|+++..
T Consensus 19 ~l~s~~~la~~~~v----s~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 19 KLPSERELAAQLGV----SRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred cCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 45 89999999999 999999999999999999876
No 266
>KOG3191 consensus Predicted N6-DNA-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=93.79 E-value=0.14 Score=40.35 Aligned_cols=64 Identities=13% Similarity=0.193 Sum_probs=46.5
Q ss_pred cceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccC----C-CCceEEecCcCCCCC-CC-CEEEe
Q 039903 169 IKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSS----Y-SGVKHIGGIMLERIP-KG-DAILI 232 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~----~-~ri~~~~gD~f~~~P-~~-D~~~l 232 (233)
..-.++||||+|..+..+++. -|......-|+ |++++...+ + -++..+..|++..+- .. |+.++
T Consensus 44 ~~i~lEIG~GSGvvstfL~~~i~~~~~~latDiNp~A~~~Tl~TA~~n~~~~~~V~tdl~~~l~~~~VDvLvf 116 (209)
T KOG3191|consen 44 PEICLEIGCGSGVVSTFLASVIGPQALYLATDINPEALEATLETARCNRVHIDVVRTDLLSGLRNESVDVLVF 116 (209)
T ss_pred ceeEEEecCCcchHHHHHHHhcCCCceEEEecCCHHHHHHHHHHHHhcCCccceeehhHHhhhccCCccEEEE
Confidence 688999999999998888775 36777888898 555554332 2 457788889998433 33 87765
No 267
>PF07091 FmrO: Ribosomal RNA methyltransferase (FmrO); PDB: 3LCU_A 3LCV_B 3FRH_A 3FRI_A 3B89_A 3FZG_A.
Probab=93.70 E-value=0.19 Score=41.59 Aligned_cols=88 Identities=15% Similarity=0.155 Sum_probs=55.8
Q ss_pred HHHHHhcchhc--HHHHHHhccc-c---cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC-----CCC
Q 039903 145 NKAMLNHTSIV--TNRIIDSSKG-F---EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS-----YSG 212 (233)
Q Consensus 145 ~~am~~~~~~~--~~~~~~~~~~-~---~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~-----~~r 212 (233)
.++|..+.+.. .+.+-+.|+. | ..+.+|+|||||--=++.-.....|+...+..|+.. .++.... ..+
T Consensus 76 r~lL~~HaST~ERl~~Ld~fY~~if~~~~~p~sVlDigCGlNPlalp~~~~~~~a~Y~a~DID~~~ve~l~~~l~~l~~~ 155 (251)
T PF07091_consen 76 RRLLAGHASTRERLPNLDEFYDEIFGRIPPPDSVLDIGCGLNPLALPWMPEAPGATYIAYDIDSQLVEFLNAFLAVLGVP 155 (251)
T ss_dssp HHHHHTSHHHHCCGGGHHHHHHHHCCCS---SEEEEET-TTCHHHHHTTTSSTT-EEEEEESBHHHHHHHHHHHHHTT-C
T ss_pred HHHHhhccchhhhhhhHHHHHHHHHhcCCCCchhhhhhccCCceehhhcccCCCcEEEEEeCCHHHHHHHHHHHHhhCCC
Confidence 34666555431 2233333331 3 337899999999999999888999999999999975 4443332 267
Q ss_pred ceEEecCcCCCCCC--CCEEEe
Q 039903 213 VKHIGGIMLERIPK--GDAILI 232 (233)
Q Consensus 213 i~~~~gD~f~~~P~--~D~~~l 232 (233)
.+....|.+...|. +|+.+|
T Consensus 156 ~~~~v~Dl~~~~~~~~~DlaLl 177 (251)
T PF07091_consen 156 HDARVRDLLSDPPKEPADLALL 177 (251)
T ss_dssp EEEEEE-TTTSHTTSEESEEEE
T ss_pred cceeEeeeeccCCCCCcchhhH
Confidence 88888899997665 488765
No 268
>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=93.68 E-value=0.13 Score=33.44 Aligned_cols=48 Identities=23% Similarity=0.275 Sum_probs=36.0
Q ss_pred hhChhHHHHh----cCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 18 ELGVFEIIAK----AGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 18 ~lglfd~L~~----~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
+..|++.|.+ .| -|-|+.|||+.+|++ ++..+.+.|+.|...|++++.
T Consensus 8 Q~~vL~~I~~~~~~~G--~~Pt~rEIa~~~g~~---S~~tv~~~L~~Le~kG~I~r~ 59 (65)
T PF01726_consen 8 QKEVLEFIREYIEENG--YPPTVREIAEALGLK---STSTVQRHLKALERKGYIRRD 59 (65)
T ss_dssp HHHHHHHHHHHHHHHS--S---HHHHHHHHTSS---SHHHHHHHHHHHHHTTSEEEG
T ss_pred HHHHHHHHHHHHHHcC--CCCCHHHHHHHhCCC---ChHHHHHHHHHHHHCcCccCC
Confidence 4445555544 45 467999999999992 499999999999999999985
No 269
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=93.67 E-value=0.12 Score=47.35 Aligned_cols=67 Identities=13% Similarity=0.183 Sum_probs=55.4
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCC
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNR 92 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~ 92 (233)
.+..|...|... ++.|..+||+.+++ ++..+.++++.|.+.|+++.... ....|.+|+.|+.++.+.
T Consensus 7 ~e~~vL~~L~~~---~~~s~~eLA~~l~l----~~~tVt~~i~~Le~kGlV~~~~~--~~~~i~LTeeG~~~~~~g 73 (489)
T PRK04172 7 NEKKVLKALKEL---KEATLEELAEKLGL----PPEAVMRAAEWLEEKGLVKVEER--VEEVYVLTEEGKKYAEEG 73 (489)
T ss_pred HHHHHHHHHHhC---CCCCHHHHHHHhCc----CHHHHHHHHHHHHhCCCEEEEee--eEEEEEECHHHHHHHHhc
Confidence 455667777765 58999999999999 99999999999999999998632 246799999999877653
No 270
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=93.64 E-value=0.21 Score=36.78 Aligned_cols=53 Identities=17% Similarity=0.235 Sum_probs=46.9
Q ss_pred HHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 11 AAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 11 ~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
+-=+..+...|.+...++ |.+|..|++..+|+ +-..+.+.++.|++.|-|-..
T Consensus 7 ~eer~eLk~rIvElVRe~---GRiTi~ql~~~TGa----sR~Tvk~~lreLVa~G~l~~~ 59 (127)
T PF06163_consen 7 PEEREELKARIVELVREH---GRITIKQLVAKTGA----SRNTVKRYLRELVARGDLYRH 59 (127)
T ss_pred HHHHHHHHHHHHHHHHHc---CCccHHHHHHHHCC----CHHHHHHHHHHHHHcCCeEeC
Confidence 334556778899999998 69999999999999 999999999999999999985
No 271
>PF01739 CheR: CheR methyltransferase, SAM binding domain; InterPro: IPR022642 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 []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region []. CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the C-terminal SAM-binding domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF03705 from PFAM. ; PDB: 1AF7_A 1BC5_A.
Probab=93.63 E-value=0.37 Score=38.62 Aligned_cols=66 Identities=17% Similarity=0.220 Sum_probs=38.8
Q ss_pred CcceEEEecCCccH--HHHH--HHHHc---C--CCcEEEeech-HHHhhccCC---------------------------
Q 039903 168 QIKQLVDVGGGLGV--NVNI--IISNY---L--HIKGVNFDLS-HVIQDSSSY--------------------------- 210 (233)
Q Consensus 168 ~~~~vvDvGGG~G~--~~~~--l~~~~---P--~l~~~v~Dlp-~v~~~a~~~--------------------------- 210 (233)
+.-+|...||++|. ++++ +.+.. . ++++..-|+. .+++.|++-
T Consensus 31 ~~lrIWSagCStGeE~YSlAmll~e~~~~~~~~~~~I~atDi~~~~L~~Ar~G~Y~~~~~~~~~~~~~~ryf~~~~~~~~ 110 (196)
T PF01739_consen 31 RPLRIWSAGCSTGEEPYSLAMLLLELLPGALGWDFRILATDISPSALEKARAGIYPERSLRGLPPAYLRRYFTERDGGGY 110 (196)
T ss_dssp S-EEEEETT-TTTHHHHHHHHHHHHHH-S-TT-SEEEEEEES-HHHHHHHHHTEEEGGGGTTS-HHHHHHHEEEE-CCCT
T ss_pred CCeEEEECCCCCChhHHHHHHHHHHHhcccCCCceEEEEEECCHHHHHHHHhCCCCHHHHhhhHHHHHHHhccccCCCce
Confidence 56789999999996 4444 44422 2 3567778985 588877641
Q ss_pred -------CCceEEecCcCC-CCCCC--CEEEeC
Q 039903 211 -------SGVKHIGGIMLE-RIPKG--DAILIK 233 (233)
Q Consensus 211 -------~ri~~~~gD~f~-~~P~~--D~~~lk 233 (233)
.+|+|..+|.++ +.|.+ |+|+.|
T Consensus 111 ~v~~~lr~~V~F~~~NL~~~~~~~~~fD~I~CR 143 (196)
T PF01739_consen 111 RVKPELRKMVRFRRHNLLDPDPPFGRFDLIFCR 143 (196)
T ss_dssp TE-HHHHTTEEEEE--TT-S------EEEEEE-
T ss_pred eEChHHcCceEEEecccCCCCcccCCccEEEec
Confidence 589999999999 33333 999754
No 272
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=93.49 E-value=0.17 Score=41.34 Aligned_cols=57 Identities=11% Similarity=0.268 Sum_probs=51.2
Q ss_pred chHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 7 IVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 7 ~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
+=.-++|...++..|.+.|+.. +|+.+.|||+++++ +..-+..-+..|...|+++-.
T Consensus 14 ~dv~kalaS~vRv~Il~lL~~k---~plNvneiAe~lgL----pqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 14 LDVLKALASKVRVAILQLLHRK---GPLNVNEIAEALGL----PQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred chHHHHHHHHHHHHHHHHHHHh---CCCCHHHHHHHhCC----chhhhhhhHHHHHhcCceeee
Confidence 3456799999999999999997 59999999999999 899999999999999999853
No 273
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=93.42 E-value=0.25 Score=39.00 Aligned_cols=45 Identities=22% Similarity=0.262 Sum_probs=40.7
Q ss_pred hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
..|+++|... |++|.+|||..+|+ +...++++|..|...|++...
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 3489998886 59999999999999 999999999999999999953
No 274
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=93.41 E-value=0.21 Score=37.00 Aligned_cols=55 Identities=20% Similarity=0.184 Sum_probs=47.5
Q ss_pred HHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 9 LPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 9 ~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
....+.+=-.+.|...|++. +|.|..|+|+..|- +...+.|=|+.|...|++...
T Consensus 57 ~la~vLsp~nleLl~~Ia~~---~P~Si~ElAe~vgR----dv~nvhr~Ls~l~~~GlI~fe 111 (144)
T COG4190 57 DLARVLSPRNLELLELIAQE---EPASINELAELVGR----DVKNVHRTLSTLADLGLIFFE 111 (144)
T ss_pred HHHHHhChhHHHHHHHHHhc---CcccHHHHHHHhCc----chHHHHHHHHHHHhcCeEEEe
Confidence 33444455577899999987 69999999999999 999999999999999999985
No 275
>PHA02943 hypothetical protein; Provisional
Probab=93.39 E-value=0.24 Score=37.67 Aligned_cols=55 Identities=15% Similarity=0.201 Sum_probs=43.5
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
.|.+.|.. |+.|..|||+++|+ +-..++-.|..|...|.+.+.+-+ ....|.+.+
T Consensus 15 eILE~Lk~----G~~TtseIAkaLGl----S~~qa~~~LyvLErEG~VkrV~~G-~~tyw~l~~ 69 (165)
T PHA02943 15 KTLRLLAD----GCKTTSRIANKLGV----SHSMARNALYQLAKEGMVLKVEIG-RAAIWCLDE 69 (165)
T ss_pred HHHHHHhc----CCccHHHHHHHHCC----CHHHHHHHHHHHHHcCceEEEeec-ceEEEEECh
Confidence 46677733 69999999999999 999999999999999999997432 233455554
No 276
>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=93.38 E-value=0.14 Score=32.72 Aligned_cols=35 Identities=11% Similarity=0.265 Sum_probs=32.6
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
++++..+||+.+++ ++..+...++-|...|+++..
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 69999999999999 999999999999999999985
No 277
>PRK06474 hypothetical protein; Provisional
Probab=93.29 E-value=0.17 Score=39.91 Aligned_cols=71 Identities=10% Similarity=0.250 Sum_probs=55.1
Q ss_pred HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccC----CCCCceeccHh
Q 039903 10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAG----DDQRLYGLAHV 84 (233)
Q Consensus 10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~----~~~~~y~lt~~ 84 (233)
..+|.--.++.|++.|...+ .+.|+.||++.+ ++ +...++|.|+.|...|++++.... +....|++++.
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 45677778999999998864 359999999999 67 888999999999999999986421 01235777765
Q ss_pred hh
Q 039903 85 AK 86 (233)
Q Consensus 85 s~ 86 (233)
+.
T Consensus 79 ~~ 80 (178)
T PRK06474 79 DA 80 (178)
T ss_pred ee
Confidence 43
No 278
>PRK05638 threonine synthase; Validated
Probab=93.08 E-value=0.19 Score=45.35 Aligned_cols=66 Identities=11% Similarity=0.156 Sum_probs=53.0
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCC--CCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMP--SSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL 90 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~--~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~ 90 (233)
.++.|+..|.+ ++.+..||++.++ + +...+++.|+.|...|+++.....+..-.|++|+.+..++.
T Consensus 372 ~r~~IL~~L~~----~~~~~~el~~~l~~~~----s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~ 439 (442)
T PRK05638 372 TKLEILKILSE----REMYGYEIWKALGKPL----KYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLE 439 (442)
T ss_pred hHHHHHHHHhh----CCccHHHHHHHHcccC----CcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHH
Confidence 46778888987 5899999999998 7 88999999999999999986321112346999999887653
No 279
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=92.78 E-value=0.25 Score=38.67 Aligned_cols=47 Identities=13% Similarity=0.044 Sum_probs=41.6
Q ss_pred CCCHHHHHHhC--CCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhH
Q 039903 33 KISAVEIAAQM--PSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKY 87 (233)
Q Consensus 33 ~~t~~elA~~~--~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~ 87 (233)
..+..+||+++ ++ +..-++.-|+.|..+|+++++ ++|.|..|..+-.
T Consensus 39 ~~d~~~iak~l~p~i----s~~ev~~sL~~L~~~gli~k~----~~g~y~~t~~~l~ 87 (171)
T PF14394_consen 39 APDPEWIAKRLRPKI----SAEEVRDSLEFLEKLGLIKKD----GDGKYVQTDKSLT 87 (171)
T ss_pred CCCHHHHHHHhcCCC----CHHHHHHHHHHHHHCCCeEEC----CCCcEEEecceee
Confidence 34999999999 99 999999999999999999998 6789998876544
No 280
>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=92.63 E-value=0.21 Score=38.62 Aligned_cols=45 Identities=11% Similarity=0.017 Sum_probs=39.7
Q ss_pred hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
..|+++|... +.+|-+|||+.+|+ +...++++|..|...|++...
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 3478888765 58999999999999 999999999999999999653
No 281
>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=92.49 E-value=0.26 Score=34.63 Aligned_cols=44 Identities=14% Similarity=0.204 Sum_probs=38.1
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA 82 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt 82 (233)
.++|-.|||+.+++ +...+.|.|+.|...|++.+.. +-+.|..|
T Consensus 46 ~~is~~eLa~~~g~----sr~tVsr~L~~Le~~GlI~r~~---~~~~~~~n 89 (95)
T TIGR01610 46 DRVTATVIAELTGL----SRTHVSDAIKSLARRRIIFRQG---MMGIVGVN 89 (95)
T ss_pred CccCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeeeec---CCceeecC
Confidence 48999999999999 9999999999999999999752 23677665
No 282
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=92.40 E-value=0.28 Score=44.63 Aligned_cols=69 Identities=12% Similarity=0.132 Sum_probs=57.7
Q ss_pred HHHhhChhHHHHhcCCCCC-CCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCC
Q 039903 15 AASELGVFEIIAKAGPTAK-ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNR 92 (233)
Q Consensus 15 ~a~~lglfd~L~~~~~~~~-~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~ 92 (233)
++.+..|...|... ++ .+..+||+.+|+ +...+.+.+..|.+.|+++.... ....|.+|+.|+..+.+.
T Consensus 2 ~~~e~~iL~~l~~~---~~~~~~~~la~~~g~----~~~~v~~~~~~L~~kg~v~~~~~--~~~~~~LT~eG~~~l~~G 71 (492)
T PLN02853 2 AMAEEALLGALSNN---EEISDSGQFAASHGL----DHNEVVGVIKSLHGFRYVDAQDI--KRETWVLTEEGKKYAAEG 71 (492)
T ss_pred chHHHHHHHHHHhc---CCCCCHHHHHHHcCC----CHHHHHHHHHHHHhCCCEEEEEE--EEEEEEECHHHHHHHHcC
Confidence 35677788888875 34 799999999999 99999999999999999986543 468999999999877654
No 283
>COG3963 Phospholipid N-methyltransferase [Lipid metabolism]
Probab=92.36 E-value=0.36 Score=37.60 Aligned_cols=67 Identities=18% Similarity=0.272 Sum_probs=50.0
Q ss_pred cHHHHHHhcccccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhh-ccCCCCceEEecCcCC
Q 039903 155 VTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQD-SSSYSGVKHIGGIMLE 222 (233)
Q Consensus 155 ~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~-a~~~~ri~~~~gD~f~ 222 (233)
.+..+....+ +++..-|+.+|-|+|.+..+++++ .+.-..+..+. |+-... -+..+.++++.||.|.
T Consensus 36 lA~~M~s~I~-pesglpVlElGPGTGV~TkaIL~~gv~~~~L~~iE~~~dF~~~L~~~~p~~~ii~gda~~ 105 (194)
T COG3963 36 LARKMASVID-PESGLPVLELGPGTGVITKAILSRGVRPESLTAIEYSPDFVCHLNQLYPGVNIINGDAFD 105 (194)
T ss_pred HHHHHHhccC-cccCCeeEEEcCCccHhHHHHHhcCCCccceEEEEeCHHHHHHHHHhCCCccccccchhh
Confidence 3556666777 888889999999999999998886 44455566654 554444 3446889999999986
No 284
>PRK10870 transcriptional repressor MprA; Provisional
Probab=92.32 E-value=0.3 Score=38.35 Aligned_cols=56 Identities=14% Similarity=0.124 Sum_probs=46.3
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~ 91 (233)
++.|..|||+.+++ +...+.++++-|...|++++...+. ..-...+|+.|..+...
T Consensus 70 ~~it~~eLa~~l~l----~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~ 127 (176)
T PRK10870 70 HSIQPSELSCALGS----SRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLRE 127 (176)
T ss_pred CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence 57899999999999 9999999999999999999865431 11356789999887755
No 285
>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=92.27 E-value=0.15 Score=28.26 Aligned_cols=31 Identities=19% Similarity=0.295 Sum_probs=25.7
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCce
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVL 67 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll 67 (233)
|+|-.|||..+|+ ..+-+.|+|..|...|++
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 5788999999999 999999999999988874
No 286
>KOG3045 consensus Predicted RNA methylase involved in rRNA processing [RNA processing and modification]
Probab=92.07 E-value=0.55 Score=39.23 Aligned_cols=88 Identities=18% Similarity=0.149 Sum_probs=50.9
Q ss_pred ccccccCchHHHHHHHHHHh----cchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhh
Q 039903 131 YEYAGNDFRFNGVFNKAMLN----HTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQD 206 (233)
Q Consensus 131 ~~~~~~~~~~~~~f~~am~~----~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~ 206 (233)
++.+..||..-+.|++.... |-......+++.+..-++-..|-|+|||.+-++. .. .-++.-|||-.+
T Consensus 139 ~~lfkedp~afdlYH~gfr~QV~kWP~nPld~ii~~ik~r~~~~vIaD~GCGEakiA~---~~--~~kV~SfDL~a~--- 210 (325)
T KOG3045|consen 139 FDLFKEDPTAFDLYHAGFRSQVKKWPENPLDVIIRKIKRRPKNIVIADFGCGEAKIAS---SE--RHKVHSFDLVAV--- 210 (325)
T ss_pred HHHHhcCcHHHHHHHHHHHHHHHhCCCChHHHHHHHHHhCcCceEEEecccchhhhhh---cc--ccceeeeeeecC---
Confidence 34455677766666555443 3333344555555423456789999999998776 11 223566676432
Q ss_pred ccCCCCceEEecCcCC-CCCC--CCEEE
Q 039903 207 SSSYSGVKHIGGIMLE-RIPK--GDAIL 231 (233)
Q Consensus 207 a~~~~ri~~~~gD~f~-~~P~--~D~~~ 231 (233)
++ ..+++|+-+ |++. .|+.+
T Consensus 211 ---~~--~V~~cDm~~vPl~d~svDvaV 233 (325)
T KOG3045|consen 211 ---NE--RVIACDMRNVPLEDESVDVAV 233 (325)
T ss_pred ---CC--ceeeccccCCcCccCcccEEE
Confidence 13 345788887 6654 26654
No 287
>COG1352 CheR Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]
Probab=91.84 E-value=1.4 Score=37.04 Aligned_cols=66 Identities=12% Similarity=0.143 Sum_probs=49.7
Q ss_pred CcceEEEecCCccH----HHHHHHHHcC-----CCcEEEeech-HHHhhccCC---------------------------
Q 039903 168 QIKQLVDVGGGLGV----NVNIIISNYL-----HIKGVNFDLS-HVIQDSSSY--------------------------- 210 (233)
Q Consensus 168 ~~~~vvDvGGG~G~----~~~~l~~~~P-----~l~~~v~Dlp-~v~~~a~~~--------------------------- 210 (233)
+.-+|--.||++|. +++.+.+.+| .++++.-|+. .+++.|+.-
T Consensus 96 ~~irIWSaaCStGEEpYSiAm~l~e~~~~~~~~~~~I~AtDId~~~L~~A~~G~Y~~~~~~~~~~~~~~~ryF~~~~~~~ 175 (268)
T COG1352 96 RPIRIWSAACSTGEEPYSLAMLLLEALGKLAGFRVKILATDIDLSVLEKARAGIYPSRELLRGLPPELLRRYFERGGDGS 175 (268)
T ss_pred CceEEEecCcCCCccHHHHHHHHHHHhccccCCceEEEEEECCHHHHHHHhcCCCChhHhhccCCHHHHhhhEeecCCCc
Confidence 46789999999995 5666778887 4677888986 478777540
Q ss_pred --------CCceEEecCcCCC--CCCC-CEEEeC
Q 039903 211 --------SGVKHIGGIMLER--IPKG-DAILIK 233 (233)
Q Consensus 211 --------~ri~~~~gD~f~~--~P~~-D~~~lk 233 (233)
..|.|..+|.+++ .+.. |+|+-|
T Consensus 176 y~v~~~ir~~V~F~~~NLl~~~~~~~~fD~IfCR 209 (268)
T COG1352 176 YRVKEELRKMVRFRRHNLLDDSPFLGKFDLIFCR 209 (268)
T ss_pred EEEChHHhcccEEeecCCCCCccccCCCCEEEEc
Confidence 3699999999984 4444 999864
No 288
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=91.67 E-value=0.46 Score=34.06 Aligned_cols=69 Identities=16% Similarity=0.213 Sum_probs=52.3
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcCC
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLNR 92 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~~ 92 (233)
.+..+...|...+ +.+..+||+.+++ +...+.++++-|...|++++..... ..-.+.+|+.|..+....
T Consensus 23 ~q~~~L~~l~~~~---~~~~~~la~~l~i----~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~ 93 (126)
T COG1846 23 PQYQVLLALYEAG---GITVKELAERLGL----DRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQL 93 (126)
T ss_pred HHHHHHHHHHHhC---CCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHh
Confidence 4455666777753 3443999999999 9999999999999999999875431 123678899888776554
No 289
>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=91.54 E-value=0.35 Score=36.52 Aligned_cols=36 Identities=14% Similarity=0.131 Sum_probs=34.3
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS 71 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~ 71 (233)
|++|++|||.+.|+ +.+.+-.-|.++++.|-|.+..
T Consensus 5 Ga~T~eELA~~FGv----ttRkvaStLa~~ta~Grl~Rv~ 40 (155)
T PF07789_consen 5 GAKTAEELAGKFGV----TTRKVASTLAMVTATGRLIRVN 40 (155)
T ss_pred CcccHHHHHHHhCc----chhhhHHHHHHHHhcceeEEec
Confidence 79999999999999 9999999999999999999874
No 290
>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=91.46 E-value=0.23 Score=39.39 Aligned_cols=62 Identities=16% Similarity=0.220 Sum_probs=42.5
Q ss_pred eEEEecCCccHHHHHHHHHcCCCcEEEeech----HHHhhccC---CCCceEEecCcCC-CCCCC-CEEEe
Q 039903 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLS----HVIQDSSS---YSGVKHIGGIMLE-RIPKG-DAILI 232 (233)
Q Consensus 171 ~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp----~v~~~a~~---~~ri~~~~gD~f~-~~P~~-D~~~l 232 (233)
+++|||.|.|.=++-++=.+|+++++++|-- ..++.+.. .++|+.+.+..-+ ..+.. |+++.
T Consensus 51 ~~lDiGSGaGfPGipLaI~~p~~~~~LvEs~~KK~~FL~~~~~~L~L~nv~v~~~R~E~~~~~~~fd~v~a 121 (184)
T PF02527_consen 51 KVLDIGSGAGFPGIPLAIARPDLQVTLVESVGKKVAFLKEVVRELGLSNVEVINGRAEEPEYRESFDVVTA 121 (184)
T ss_dssp EEEEETSTTTTTHHHHHHH-TTSEEEEEESSHHHHHHHHHHHHHHT-SSEEEEES-HHHTTTTT-EEEEEE
T ss_pred eEEecCCCCCChhHHHHHhCCCCcEEEEeCCchHHHHHHHHHHHhCCCCEEEEEeeecccccCCCccEEEe
Confidence 7999999999999999999999999999953 22333222 2678887777666 23332 77664
No 291
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=91.42 E-value=0.38 Score=36.79 Aligned_cols=47 Identities=13% Similarity=0.200 Sum_probs=42.9
Q ss_pred HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee
Q 039903 16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC 69 (233)
Q Consensus 16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~ 69 (233)
..+..|.+.|..+ +..|..+||+++|+ ++..+.+=++-|...|++..
T Consensus 9 ~~D~~Il~~Lq~d---~R~s~~eiA~~lgl----S~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 9 NLDRGILEALMEN---ARTPYAELAKQFGV----SPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeee
Confidence 3577899999987 58999999999999 99999999999999999985
No 292
>COG0357 GidB Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]
Probab=91.40 E-value=0.2 Score=40.70 Aligned_cols=53 Identities=15% Similarity=0.247 Sum_probs=38.7
Q ss_pred cceEEEecCCccHHHHHHHHHcCCCcEEEeech----HHHhhccC---CCCceEEecCcC
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS----HVIQDSSS---YSGVKHIGGIML 221 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp----~v~~~a~~---~~ri~~~~gD~f 221 (233)
..+++|||.|.|.=++-++=.+|+++++++|-- .-++.+.. .++++++.+..=
T Consensus 68 ~~~~~DIGSGaGfPGipLAI~~p~~~vtLles~~Kk~~FL~~~~~eL~L~nv~i~~~RaE 127 (215)
T COG0357 68 AKRVLDIGSGAGFPGIPLAIAFPDLKVTLLESLGKKIAFLREVKKELGLENVEIVHGRAE 127 (215)
T ss_pred CCEEEEeCCCCCCchhhHHHhccCCcEEEEccCchHHHHHHHHHHHhCCCCeEEehhhHh
Confidence 589999999999999999889999999999943 22333322 255666655443
No 293
>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=91.12 E-value=0.95 Score=30.51 Aligned_cols=53 Identities=8% Similarity=-0.041 Sum_probs=42.8
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL 90 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~ 90 (233)
.|+...+||+.++. ++--++..|..|..+|+++.... ..+.|..|..+-.+..
T Consensus 22 ~PVgSk~ia~~l~~----s~aTIRN~M~~Le~lGlve~~p~--~s~GriPT~~aYr~~~ 74 (78)
T PF03444_consen 22 EPVGSKTIAEELGR----SPATIRNEMADLEELGLVESQPH--PSGGRIPTDKAYRALN 74 (78)
T ss_pred CCcCHHHHHHHHCC----ChHHHHHHHHHHHHCCCccCCCC--CCCCCCcCHHHHHHHc
Confidence 59999999999999 99999999999999999985211 2466778877765443
No 294
>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=91.03 E-value=0.31 Score=35.57 Aligned_cols=67 Identities=21% Similarity=0.334 Sum_probs=49.1
Q ss_pred HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCC-CCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~-~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
+.-+.-|++.|.+.+ ++.|+.||-+.+.-. ++.+..-++|-|+.|...|++.+...+++...|....
T Consensus 7 T~~R~~Il~~l~~~~--~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~~ 74 (120)
T PF01475_consen 7 TPQRLAILELLKESP--EHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHHHHS--SSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS
T ss_pred CHHHHHHHHHHHcCC--CCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEeecC
Confidence 445677899999976 699999999988531 1227778999999999999999975432334565544
No 295
>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=90.96 E-value=0.36 Score=32.28 Aligned_cols=49 Identities=12% Similarity=0.089 Sum_probs=42.7
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.+..+++.|+.++. .+.+..||++.++. |++.+...++.|...|++.+.
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 45567788888653 47899999999999 999999999999999999985
No 296
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=90.86 E-value=0.38 Score=37.30 Aligned_cols=48 Identities=15% Similarity=0.185 Sum_probs=43.5
Q ss_pred HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee
Q 039903 15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC 69 (233)
Q Consensus 15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~ 69 (233)
-..+..|..+|..+ +.+|..|||+++|+ ++..+.+=++-|...|+++.
T Consensus 13 D~~D~~IL~~Lq~d---~R~s~~eiA~~lgl----S~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 13 DRIDRNILNELQKD---GRISNVELSKRVGL----SPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHHhccC---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEE
Confidence 34678899999987 59999999999999 99999999999999999985
No 297
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=90.80 E-value=0.46 Score=36.01 Aligned_cols=48 Identities=17% Similarity=0.266 Sum_probs=43.3
Q ss_pred HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
..+..|.+.|... ++.+..+||+++|+ ++..+.+-++-|...|++...
T Consensus 8 ~~D~~IL~~L~~d---~r~~~~eia~~lgl----S~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 8 DIDRRILRLLQED---ARISNAELAERVGL----SPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred HHHHHHHHHHHHh---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCceeeE
Confidence 3567788999987 58999999999999 999999999999999999875
No 298
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=90.69 E-value=0.62 Score=42.53 Aligned_cols=69 Identities=7% Similarity=0.129 Sum_probs=57.1
Q ss_pred HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCC
Q 039903 16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNR 92 (233)
Q Consensus 16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~ 92 (233)
..+..|...|...+ +..+..+||+.+++ +...+.+.+..|.+.|+++.... ....|.+|+.|+..+.+.
T Consensus 6 ~~e~~iL~~l~~~~--~~~~~~~la~~~~~----~~~~v~~~~~~L~~kg~v~~~~~--~~~~~~LT~eG~~~~~~G 74 (494)
T PTZ00326 6 LEENTILSKLESEN--EIVNSLALAESLNI----DHQKVVGAIKSLESANYITTEMK--KSNTWTLTEEGEDYLKNG 74 (494)
T ss_pred HHHHHHHHHHHhcC--CCCCHHHHHHHcCC----CHHHHHHHHHHHHhCCCEEEEEE--EEEEEEECHHHHHHHHcC
Confidence 45667788888722 47899999999999 99999999999999999986543 468999999999877654
No 299
>COG5459 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=90.64 E-value=0.33 Score=42.23 Aligned_cols=68 Identities=19% Similarity=0.272 Sum_probs=44.2
Q ss_pred ccccCcceEEEecCCccHHHHHHHHHcCCCcE-EEeechH----HHhhccCC---CCceEEecCcCC---CCCCCCEEEe
Q 039903 164 KGFEQIKQLVDVGGGLGVNVNIIISNYLHIKG-VNFDLSH----VIQDSSSY---SGVKHIGGIMLE---RIPKGDAILI 232 (233)
Q Consensus 164 ~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~-~v~Dlp~----v~~~a~~~---~ri~~~~gD~f~---~~P~~D~~~l 232 (233)
++|+ .++|+|||-|.|.-+.++-.-+|+++- ++++... |+....++ .+-..-..|+-. ++|.+|.|.+
T Consensus 110 ~dfa-pqsiLDvG~GPgtgl~A~n~i~Pdl~sa~ile~sp~lrkV~~tl~~nv~t~~td~r~s~vt~dRl~lp~ad~ytl 188 (484)
T COG5459 110 PDFA-PQSILDVGAGPGTGLWALNDIWPDLKSAVILEASPALRKVGDTLAENVSTEKTDWRASDVTEDRLSLPAADLYTL 188 (484)
T ss_pred CCcC-cchhhccCCCCchhhhhhcccCCCchhhhhhccCHHHHHHHHHHHhhcccccCCCCCCccchhccCCCccceeeh
Confidence 3344 367999999999999999999999984 6666543 33322222 222333445543 6777888865
No 300
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=90.54 E-value=0.72 Score=38.36 Aligned_cols=61 Identities=13% Similarity=0.132 Sum_probs=48.2
Q ss_pred hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903 19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF 88 (233)
Q Consensus 19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l 88 (233)
-.+.-+|-.. |+.|+.|||+.+|+ +...++.+|+.|...|+++.... ....|+.-+-...+
T Consensus 19 a~vY~aLl~~---g~~tA~eis~~sgv----P~~kvY~vl~sLe~kG~v~~~~g--~P~~y~av~p~~~i 79 (247)
T COG1378 19 AKVYLALLCL---GEATAKEISEASGV----PRPKVYDVLRSLEKKGLVEVIEG--RPKKYRAVPPEELI 79 (247)
T ss_pred HHHHHHHHHh---CCccHHHHHHHcCC----CchhHHHHHHHHHHCCCEEeeCC--CCceEEeCCHHHHH
Confidence 3455555555 69999999999999 99999999999999999998632 56788776655443
No 301
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=90.53 E-value=0.53 Score=39.21 Aligned_cols=47 Identities=11% Similarity=0.126 Sum_probs=42.4
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.+..|.+.|.+. +..+..|||+.+++ ++.-++|-|+.|...|++.+.
T Consensus 6 R~~~Il~~l~~~---~~~~~~ela~~l~v----S~~TirRdL~~Le~~g~i~r~ 52 (251)
T PRK13509 6 RHQILLELLAQL---GFVTVEKVIERLGI----SPATARRDINKLDESGKLKKV 52 (251)
T ss_pred HHHHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence 345688889887 58999999999999 999999999999999999987
No 302
>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=90.46 E-value=0.33 Score=34.60 Aligned_cols=44 Identities=9% Similarity=0.238 Sum_probs=34.3
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
-|++.|... |.++-+|||+.+++ +..-++++|..|...|++...
T Consensus 17 ~Il~~L~~~---~~l~de~la~~~~l----~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 17 RILDALLRK---GELTDEDLAKKLGL----KPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp HHHHHHHHH-----B-HHHHHHTT-S-----HHHHHHHHHHHHHHSS-EEE
T ss_pred HHHHHHHHc---CCcCHHHHHHHhCC----CHHHHHHHHHHHHHCCCeEEE
Confidence 378888866 58999999999999 999999999999999999764
No 303
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=90.30 E-value=0.86 Score=36.18 Aligned_cols=65 Identities=15% Similarity=0.045 Sum_probs=50.9
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~ 91 (233)
.+.-.|... ++.|..+||+.+.+ +...+.++++-|...|++.+...++ ..-...+|+.|+.+...
T Consensus 49 ~iL~~L~~~---~~itq~eLa~~l~l----~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~ 115 (185)
T PRK13777 49 HILWIAYHL---KGASISEIAKFGVM----HVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLE 115 (185)
T ss_pred HHHHHHHhC---CCcCHHHHHHHHCC----CHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence 456666665 48999999999999 9899999999999999999864321 22345789999887654
No 304
>PF04672 Methyltransf_19: S-adenosyl methyltransferase; InterPro: IPR006764 This is a family of uncharacterised proteins.; PDB: 3GIW_A 3GO4_A 2QE6_A.
Probab=90.16 E-value=0.85 Score=38.29 Aligned_cols=56 Identities=16% Similarity=0.175 Sum_probs=32.9
Q ss_pred CcceEEEecCCcc---HHHHHHHHHcCCCcEEEeech-HHHhhccC----CCC--ceEEecCcCCC
Q 039903 168 QIKQLVDVGGGLG---VNVNIIISNYLHIKGVNFDLS-HVIQDSSS----YSG--VKHIGGIMLER 223 (233)
Q Consensus 168 ~~~~vvDvGGG~G---~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~~r--i~~~~gD~f~~ 223 (233)
++..+||||+|.- ..-....+..|+.+++=.|.. -|+.+++. +++ ..++.+|+.++
T Consensus 68 GIrQFLDlGsGlPT~~nvHevAq~~~P~aRVVYVD~DPvv~ah~ralL~~~~~g~t~~v~aD~r~p 133 (267)
T PF04672_consen 68 GIRQFLDLGSGLPTAGNVHEVAQRVAPDARVVYVDNDPVVLAHARALLADNPRGRTAYVQADLRDP 133 (267)
T ss_dssp ---EEEEET--S--SS-HHHHHHHH-TT-EEEEEESSHHHHHCCHHHHTT-TTSEEEEEE--TT-H
T ss_pred CcceEEEcccCCCCCCCHhHHHHhhCCCceEEEECCCchHHHHHHhhhcCCCCccEEEEeCCCCCH
Confidence 7899999999975 333334556999999999984 57787765 245 89999999873
No 305
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=90.11 E-value=1 Score=33.05 Aligned_cols=55 Identities=15% Similarity=0.132 Sum_probs=45.8
Q ss_pred CCCCHHHHHHhCC-CCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903 32 AKISAVEIAAQMP-SSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL 90 (233)
Q Consensus 32 ~~~t~~elA~~~~-~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~ 90 (233)
|+.-..||-..++ + ++.-|.+=|+.|...|++++..-+. ..-.|++|+.+..|..
T Consensus 35 g~~RF~eL~r~i~~I----s~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~~ 92 (120)
T COG1733 35 GPKRFNELRRSIGGI----SPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLLP 92 (120)
T ss_pred CCCcHHHHHHHcccc----CHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHHH
Confidence 5899999999999 9 9999999999999999999864321 1347999999887763
No 306
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=90.08 E-value=0.43 Score=39.94 Aligned_cols=48 Identities=21% Similarity=0.391 Sum_probs=43.8
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS 71 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~ 71 (233)
+..+.++|...| |..+-+||.+++|+ +...+.|+|+-|..+|++++..
T Consensus 197 e~~il~~i~~~G--Gri~Q~eL~r~lgl----sktTvsR~L~~LEk~GlIe~~K 244 (258)
T COG2512 197 EKEILDLIRERG--GRITQAELRRALGL----SKTTVSRILRRLEKRGLIEKEK 244 (258)
T ss_pred HHHHHHHHHHhC--CEEeHHHHHHhhCC----ChHHHHHHHHHHHhCCceEEEE
Confidence 456889999987 78999999999999 9999999999999999999864
No 307
>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=89.99 E-value=0.61 Score=36.74 Aligned_cols=56 Identities=16% Similarity=0.213 Sum_probs=41.1
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC---------CCceEEecCcCC
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY---------SGVKHIGGIMLE 222 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~---------~ri~~~~gD~f~ 222 (233)
++...||-+|||-=.....+...+++++..=+|+|+|++.-++. .++++++.|+.+
T Consensus 77 ~~~~qvV~LGaGlDTr~~Rl~~~~~~~~~~evD~p~v~~~K~~~l~~~~~~~~~~~~~v~~Dl~~ 141 (183)
T PF04072_consen 77 PGARQVVNLGAGLDTRAYRLDNPAGGVRWFEVDLPEVIALKRRLLPESGARPPANYRYVPADLRD 141 (183)
T ss_dssp TTESEEEEET-TT--HHHHHHHTTTTEEEEEEE-HHHHHHHHHHHHHTHHHHHEESSEEES-TTS
T ss_pred CCCcEEEEcCCCCCchHHHhhccccceEEEEeCCHHHHHHHHHHHHhCcccCCcceeEEeccccc
Confidence 45669999999999999999998889999999999988754331 236789999986
No 308
>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=89.83 E-value=0.47 Score=36.96 Aligned_cols=43 Identities=14% Similarity=0.209 Sum_probs=39.6
Q ss_pred CCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903 34 ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV 84 (233)
Q Consensus 34 ~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~ 84 (233)
.|..+||+.+++ +..-+.|.+..|...+++.+. ..+.|.++|.
T Consensus 76 ~t~~~ia~~l~i----S~~Tv~r~ik~L~e~~iI~k~----~~G~Y~iNP~ 118 (165)
T PF05732_consen 76 ATQKEIAEKLGI----SKPTVSRAIKELEEKNIIKKI----RNGAYMINPN 118 (165)
T ss_pred eeHHHHHHHhCC----CHHHHHHHHHHHHhCCcEEEc----cCCeEEECcH
Confidence 488999999999 999999999999999999997 5789999984
No 309
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=89.77 E-value=0.53 Score=42.15 Aligned_cols=43 Identities=23% Similarity=0.197 Sum_probs=38.1
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA 82 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt 82 (233)
.|.|.+||++.+++ +++.++++|+.|...|++.+. +++.|.+.
T Consensus 309 ~~~t~~~La~~l~~----~~~~v~~iL~~L~~agLI~~~----~~g~~~l~ 351 (412)
T PRK04214 309 KALDVDEIRRLEPM----GYDELGELLCELARIGLLRRG----ERGQWVLA 351 (412)
T ss_pred CCCCHHHHHHHhCC----CHHHHHHHHHHHHhCCCeEec----CCCceEec
Confidence 58999999999999 999999999999999999975 45667554
No 310
>COG2521 Predicted archaeal methyltransferase [General function prediction only]
Probab=89.73 E-value=0.49 Score=38.95 Aligned_cols=64 Identities=20% Similarity=0.165 Sum_probs=48.9
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcE-EEeechHHHhhccCC--------CCceEEecCcCC---CCCCC--CEEE
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKG-VNFDLSHVIQDSSSY--------SGVKHIGGIMLE---RIPKG--DAIL 231 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~-~v~Dlp~v~~~a~~~--------~ri~~~~gD~f~---~~P~~--D~~~ 231 (233)
++..+|+|..+|-|..+++.+++-. +++ ++---|.|++.|.-+ .+|+.+-||.++ .++.. |+++
T Consensus 133 ~~G~rVLDtC~GLGYtAi~a~~rGA-~~VitvEkdp~VLeLa~lNPwSr~l~~~~i~iilGD~~e~V~~~~D~sfDaIi 210 (287)
T COG2521 133 KRGERVLDTCTGLGYTAIEALERGA-IHVITVEKDPNVLELAKLNPWSRELFEIAIKIILGDAYEVVKDFDDESFDAII 210 (287)
T ss_pred ccCCEeeeeccCccHHHHHHHHcCC-cEEEEEeeCCCeEEeeccCCCCccccccccEEecccHHHHHhcCCccccceEe
Confidence 5678999999999999999999854 244 343348899988765 478999999997 45542 7765
No 311
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=89.72 E-value=0.57 Score=34.19 Aligned_cols=36 Identities=8% Similarity=0.096 Sum_probs=33.8
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS 71 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~ 71 (233)
.++|++|||+.+.+ +++.++.+|+-|...|.++...
T Consensus 18 ~~vtl~elA~~l~c----S~Rn~r~lLkkm~~~gWi~W~p 53 (115)
T PF12793_consen 18 VEVTLDELAELLFC----SRRNARTLLKKMQEEGWITWQP 53 (115)
T ss_pred cceeHHHHHHHhCC----CHHHHHHHHHHHHHCCCeeeeC
Confidence 47899999999999 9999999999999999999863
No 312
>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=89.70 E-value=0.57 Score=30.94 Aligned_cols=42 Identities=17% Similarity=0.218 Sum_probs=37.1
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
+.|-++||..+|+ +...+.|+|+.|...|+++.. .+.+....
T Consensus 28 ~lt~~~iA~~~g~----sr~tv~r~l~~l~~~g~I~~~-----~~~i~I~d 69 (76)
T PF13545_consen 28 PLTQEEIADMLGV----SRETVSRILKRLKDEGIIEVK-----RGKIIILD 69 (76)
T ss_dssp ESSHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEE-----TTEEEESS
T ss_pred cCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEc-----CCEEEECC
Confidence 7899999999999 999999999999999999985 56665543
No 313
>KOG4589 consensus Cell division protein FtsJ [Cell cycle control, cell division, chromosome partitioning]
Probab=89.69 E-value=0.57 Score=37.23 Aligned_cols=44 Identities=16% Similarity=0.195 Sum_probs=34.9
Q ss_pred HhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeechHHH
Q 039903 161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLSHVI 204 (233)
Q Consensus 161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp~v~ 204 (233)
+.|.-++...+|+|||+-.|.++.-..++. |+-.+..+|+-++.
T Consensus 62 dKy~~l~p~~~VlD~G~APGsWsQVavqr~~p~g~v~gVDllh~~ 106 (232)
T KOG4589|consen 62 DKYRFLRPEDTVLDCGAAPGSWSQVAVQRVNPNGMVLGVDLLHIE 106 (232)
T ss_pred hhccccCCCCEEEEccCCCChHHHHHHHhhCCCceEEEEeeeecc
Confidence 344424667999999999999998888875 99888999986544
No 314
>PRK10611 chemotaxis methyltransferase CheR; Provisional
Probab=89.56 E-value=6.6 Score=33.42 Aligned_cols=64 Identities=16% Similarity=0.073 Sum_probs=44.9
Q ss_pred cceEEEecCCccH--HH--HHHHHHcC----CCcEEEeech-HHHhhccCC-----------------------------
Q 039903 169 IKQLVDVGGGLGV--NV--NIIISNYL----HIKGVNFDLS-HVIQDSSSY----------------------------- 210 (233)
Q Consensus 169 ~~~vvDvGGG~G~--~~--~~l~~~~P----~l~~~v~Dlp-~v~~~a~~~----------------------------- 210 (233)
.-+|...||++|. ++ +.+.+..+ +++++.-|+. .+++.|++-
T Consensus 116 ~irIWSAgCStGEEpYSlAmll~e~~~~~~~~~~I~atDIs~~aL~~Ar~G~Y~~~~~r~~p~~~~~ryF~~~~~~~~~~ 195 (287)
T PRK10611 116 EYRVWSAAASTGEEPYSIAMTLADTLGTAPGRWKVFASDIDTEVLEKARSGIYRQEELKTLSPQQLQRYFMRGTGPHEGL 195 (287)
T ss_pred CEEEEEccccCCHHHHHHHHHHHHhhcccCCCcEEEEEECCHHHHHHHHhCCCCHHHHhcCCHHHHHHHcccccCCCCce
Confidence 3689999999996 44 44555443 4678888985 477766430
Q ss_pred --------CCceEEecCcCC-CCC-C-C-CEEEe
Q 039903 211 --------SGVKHIGGIMLE-RIP-K-G-DAILI 232 (233)
Q Consensus 211 --------~ri~~~~gD~f~-~~P-~-~-D~~~l 232 (233)
.+|+|..+|.++ +.| . . |+|+.
T Consensus 196 ~~v~~~lr~~V~F~~~NL~~~~~~~~~~fD~I~c 229 (287)
T PRK10611 196 VRVRQELANYVDFQQLNLLAKQWAVPGPFDAIFC 229 (287)
T ss_pred EEEChHHHccCEEEcccCCCCCCccCCCcceeeH
Confidence 468999999998 555 2 3 99874
No 315
>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=89.20 E-value=0.89 Score=36.26 Aligned_cols=49 Identities=20% Similarity=0.185 Sum_probs=39.8
Q ss_pred HHhhChhHHHHhc----CCCCCCCHHHHHHhCCCCCCCC-hhhHHHHHHHHhcCCceeee
Q 039903 16 ASELGVFEIIAKA----GPTAKISAVEIAAQMPSSNPNA-AVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 16 a~~lglfd~L~~~----~~~~~~t~~elA~~~~~~~~~~-~~~l~rlL~~L~~~gll~~~ 70 (233)
..+..|++.|.+. + -+.|..|||+.+++ + ...+.+.|+.|...|++++.
T Consensus 6 ~~q~~iL~~l~~~~~~~~--~~~~~~ela~~~~~----~s~~tv~~~l~~L~~~g~i~~~ 59 (199)
T TIGR00498 6 ARQQEVLDLIRAHIESTG--YPPSIREIARAVGL----RSPSAAEEHLKALERKGYIERD 59 (199)
T ss_pred HHHHHHHHHHHHHHHhcC--CCCcHHHHHHHhCC----CChHHHHHHHHHHHHCCCEecC
Confidence 3455666666642 2 36889999999999 8 89999999999999999985
No 316
>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=89.04 E-value=0.33 Score=38.41 Aligned_cols=64 Identities=16% Similarity=0.108 Sum_probs=44.5
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCCCC------CCC-CEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERI------PKG-DAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~------P~~-D~~~l 232 (233)
...++||+=+|+|.++.+.+.+.- -+++.+|.. .++...+++ ++++.+.+|.+..+ ... |+|++
T Consensus 42 ~g~~vLDLFaGSGalGlEALSRGA-~~v~fVE~~~~a~~~i~~N~~~l~~~~~~~v~~~d~~~~l~~~~~~~~~fDiIfl 120 (183)
T PF03602_consen 42 EGARVLDLFAGSGALGLEALSRGA-KSVVFVEKNRKAIKIIKKNLEKLGLEDKIRVIKGDAFKFLLKLAKKGEKFDIIFL 120 (183)
T ss_dssp TT-EEEETT-TTSHHHHHHHHTT--SEEEEEES-HHHHHHHHHHHHHHT-GGGEEEEESSHHHHHHHHHHCTS-EEEEEE
T ss_pred CCCeEEEcCCccCccHHHHHhcCC-CeEEEEECCHHHHHHHHHHHHHhCCCcceeeeccCHHHHHHhhcccCCCceEEEE
Confidence 347899999999999999998853 368888874 466655543 57899999987522 233 98886
No 317
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=88.97 E-value=0.87 Score=37.67 Aligned_cols=47 Identities=13% Similarity=0.205 Sum_probs=41.8
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.+..|.+.|.+. +..+..|||+.+++ +++-++|-|..|...|.+.+.
T Consensus 5 R~~~Il~~l~~~---~~~~~~eLa~~l~V----S~~TiRRdL~~L~~~~~l~r~ 51 (240)
T PRK10411 5 RQQAIVDLLLNH---TSLTTEALAEQLNV----SKETIRRDLNELQTQGKILRN 51 (240)
T ss_pred HHHHHHHHHHHc---CCCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence 345688888886 59999999999999 999999999999999999876
No 318
>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=88.92 E-value=0.54 Score=33.28 Aligned_cols=51 Identities=18% Similarity=0.195 Sum_probs=40.2
Q ss_pred HHhhChhHHHHhc-CCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 16 ASELGVFEIIAKA-GPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 16 a~~lglfd~L~~~-~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.++-.|++.|... ..+.++++.+|++++++ ++..++..|+.|+..|++=.+
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~----~~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQLGM----SENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHSTS-----HHHHHHHHHHHHHTTSEEES
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHhCc----CHHHHHHHHHHHHhCCeEecc
Confidence 3456788888872 22358999999999999 999999999999999988654
No 319
>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=88.78 E-value=0.87 Score=38.40 Aligned_cols=46 Identities=17% Similarity=0.150 Sum_probs=40.0
Q ss_pred CCCCHHHHHHhCC--CCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903 32 AKISAVEIAAQMP--SSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA 85 (233)
Q Consensus 32 ~~~t~~elA~~~~--~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s 85 (233)
+..+..+||+.++ + +..-++.-|+.|..+|+++++ ++|.|..|..+
T Consensus 136 ~~~~~~~ia~~l~p~i----s~~ev~~sL~~L~~~glikk~----~~g~y~~t~~~ 183 (271)
T TIGR02147 136 FADDPEELAKRCFPKI----SAEQVKESLDLLERLGLIKKN----EDGFYKQTDKA 183 (271)
T ss_pred CCCCHHHHHHHhCCCC----CHHHHHHHHHHHHHCCCeeEC----CCCcEEeecce
Confidence 3447889999998 6 899999999999999999997 67889988764
No 320
>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=88.69 E-value=0.91 Score=38.31 Aligned_cols=49 Identities=16% Similarity=0.243 Sum_probs=35.0
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCc-EEEeech-HHHhhcc
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIK-GVNFDLS-HVIQDSS 208 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~-~~v~Dlp-~v~~~a~ 208 (233)
+....++| .+.+|||+|+|.|.-+-+..+.+|+++ .+.+|.. ..++.++
T Consensus 25 l~~r~p~f-~P~~vLD~GsGpGta~wAa~~~~~~~~~~~~vd~s~~~~~l~~ 75 (274)
T PF09243_consen 25 LRKRLPDF-RPRSVLDFGSGPGTALWAAREVWPSLKEYTCVDRSPEMLELAK 75 (274)
T ss_pred HHHhCcCC-CCceEEEecCChHHHHHHHHHHhcCceeeeeecCCHHHHHHHH
Confidence 33333433 347999999999999999999999654 6788975 3555443
No 321
>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=88.42 E-value=1.5 Score=27.70 Aligned_cols=55 Identities=16% Similarity=0.176 Sum_probs=43.6
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhh
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAK 86 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~ 86 (233)
++.+|..+.+. .+...-|+.+++ ++..+.+-++.|.. .-+|++. ++.+.+|+.|+
T Consensus 3 ~l~~f~~v~~~-----gs~~~AA~~l~i----s~~~vs~~i~~LE~~lg~~Lf~r~-----~~~~~lT~~G~ 60 (60)
T PF00126_consen 3 QLRYFLAVAET-----GSISAAAEELGI----SQSAVSRQIKQLEEELGVPLFERS-----GRGLRLTEAGE 60 (60)
T ss_dssp HHHHHHHHHHH-----SSHHHHHHHCTS----SHHHHHHHHHHHHHHHTS-SEEEC-----SSSEEE-HHHH
T ss_pred HHHHHHHHHHh-----CCHHHHHHHhhc----cchHHHHHHHHHHHHhCCeEEEEC-----CCCeeEChhhC
Confidence 46678888884 499999999999 99999999888766 6788884 56799998774
No 322
>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=88.33 E-value=1.1 Score=38.89 Aligned_cols=78 Identities=14% Similarity=0.084 Sum_probs=45.9
Q ss_pred HHHHHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC---------
Q 039903 141 NGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------- 210 (233)
Q Consensus 141 ~~~f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------- 210 (233)
.+.|+.++...- +...+.....-.+..+|||+|||.|.-+....++.+ -+.+.+|+. +.|+.|++.
T Consensus 38 lR~fNNwvKs~L---I~~~~~~~~~~~~~~~VLDl~CGkGGDL~Kw~~~~i-~~~vg~Dis~~si~ea~~Ry~~~~~~~~ 113 (331)
T PF03291_consen 38 LRNFNNWVKSVL---IQKYAKKVKQNRPGLTVLDLCCGKGGDLQKWQKAKI-KHYVGIDISEESIEEARERYKQLKKRNN 113 (331)
T ss_dssp HHHHHHHHHHHH---HHHHCHCCCCTTTT-EEEEET-TTTTTHHHHHHTT--SEEEEEES-HHHHHHHHHHHHHHHTSTT
T ss_pred HHHHhHHHHHHH---HHHHHHhhhccCCCCeEEEecCCCchhHHHHHhcCC-CEEEEEeCCHHHHHHHHHHHHHhccccc
Confidence 456777666422 222222211011568999999999999888887632 246889986 467766541
Q ss_pred ---C----CceEEecCcCC
Q 039903 211 ---S----GVKHIGGIMLE 222 (233)
Q Consensus 211 ---~----ri~~~~gD~f~ 222 (233)
. ...|+.+|-|.
T Consensus 114 ~~~~~~~f~a~f~~~D~f~ 132 (331)
T PF03291_consen 114 SKQYRFDFIAEFIAADCFS 132 (331)
T ss_dssp -HTSEECCEEEEEESTTCC
T ss_pred cccccccchhheecccccc
Confidence 1 35678888885
No 323
>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=88.32 E-value=0.67 Score=29.79 Aligned_cols=44 Identities=16% Similarity=0.274 Sum_probs=36.6
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.|++.|-.. |+.|+.+|++.+++ +.+.++.-|-.|...|++...
T Consensus 17 ~V~~~Ll~~---G~ltl~~i~~~t~l----~~~~Vk~~L~~LiQh~~v~y~ 60 (62)
T PF08221_consen 17 KVGEVLLSR---GRLTLREIVRRTGL----SPKQVKKALVVLIQHNLVQYF 60 (62)
T ss_dssp HHHHHHHHC----SEEHHHHHHHHT------HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHc---CCcCHHHHHHHhCC----CHHHHHHHHHHHHHcCCeeee
Confidence 467777776 69999999999999 999999999999999999864
No 324
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=88.08 E-value=0.89 Score=36.77 Aligned_cols=44 Identities=25% Similarity=0.363 Sum_probs=37.2
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
|.+.|... +.+.|++|+|+++|+ +.--.+|-|.+|++.|+++..
T Consensus 163 i~~~~~~~--~~~~Taeela~~~gi----SRvTaRRYLeyl~~~~~l~a~ 206 (224)
T COG4565 163 VREALKEP--DQELTAEELAQALGI----SRVTARRYLEYLVSNGILEAE 206 (224)
T ss_pred HHHHHhCc--CCccCHHHHHHHhCc----cHHHHHHHHHHHHhcCeeeEE
Confidence 45566632 259999999999999 999999999999999999864
No 325
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=88.06 E-value=0.87 Score=37.95 Aligned_cols=47 Identities=13% Similarity=0.195 Sum_probs=42.5
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.+..|.+.|.+. +.+++.|||+.+++ ++.-++|-|+.|...|++.+.
T Consensus 6 R~~~Il~~l~~~---~~~~~~ela~~l~v----S~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 6 RHDAIIELVKQQ---GYVSTEELVEHFSV----SPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHHc---CCEeHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 455688889886 58999999999999 999999999999999999987
No 326
>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=88.02 E-value=0.43 Score=43.34 Aligned_cols=24 Identities=21% Similarity=0.327 Sum_probs=21.7
Q ss_pred cCcceEEEecCCccHHHHHHHHHc
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNY 190 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~ 190 (233)
..+++++|||||.|.|+..|++++
T Consensus 116 g~iR~~LDvGcG~aSF~a~l~~r~ 139 (506)
T PF03141_consen 116 GGIRTALDVGCGVASFGAYLLERN 139 (506)
T ss_pred CceEEEEeccceeehhHHHHhhCC
Confidence 457999999999999999999984
No 327
>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=87.77 E-value=0.8 Score=29.36 Aligned_cols=35 Identities=17% Similarity=0.241 Sum_probs=30.8
Q ss_pred CCC-CHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 32 AKI-SAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 32 ~~~-t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
..+ |..+||+.+++ +..-+++-|+.|...|+++..
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 89999999999 999999999999999999986
No 328
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=87.71 E-value=0.96 Score=38.08 Aligned_cols=48 Identities=8% Similarity=0.136 Sum_probs=43.5
Q ss_pred HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
-....|.+.|... +..++.|||+.+++ +++-++|=|..|...|++.+.
T Consensus 17 eR~~~Il~~L~~~---~~vtv~eLa~~l~V----S~~TIRRDL~~Le~~G~l~r~ 64 (269)
T PRK09802 17 ERREQIIQRLRQQ---GSVQVNDLSALYGV----STVTIRNDLAFLEKQGIAVRA 64 (269)
T ss_pred HHHHHHHHHHHHc---CCEeHHHHHHHHCC----CHHHHHHHHHHHHhCCCeEEE
Confidence 3556789999987 58999999999999 999999999999999999997
No 329
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=87.51 E-value=1.3 Score=34.07 Aligned_cols=78 Identities=19% Similarity=0.238 Sum_probs=56.8
Q ss_pred cccchHHHHHHHHHhhCh-------hHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCC
Q 039903 4 AMSIVLPAAMQAASELGV-------FEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQ 76 (233)
Q Consensus 4 ~~~~~~s~~L~~a~~lgl-------fd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~ 76 (233)
+++.|.-.|+.+|.+.++ .-++...+ .|+++.||+..++.+ +...+.--||-|...|+++....+ .+
T Consensus 64 Af~rW~vrCmAaag~~~ls~~e~l~lH~irhrd--R~K~laDic~~ln~e---Dth~itYslrKL~k~gLit~t~~g-ke 137 (199)
T COG5631 64 AFGRWQVRCMAAAGEFSLSGPENLLLHIIRHRD--RPKSLADICQMLNRE---DTHNITYSLRKLLKGGLITRTGSG-KE 137 (199)
T ss_pred HHHHHHHHHHHHhcCCCCcchHHHHHHHHhhcC--chhhHHHHHHHhccc---cchhHHHHHHHHHhccceecCCCC-ce
Confidence 356677777777766542 23333333 599999999999994 566778889999999999987443 34
Q ss_pred CceeccHhhhH
Q 039903 77 RLYGLAHVAKY 87 (233)
Q Consensus 77 ~~y~lt~~s~~ 87 (233)
-+|..|+.+..
T Consensus 138 vTy~vTa~G~~ 148 (199)
T COG5631 138 VTYEVTALGHR 148 (199)
T ss_pred EEEEEecchHH
Confidence 68999988754
No 330
>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=87.49 E-value=0.95 Score=33.28 Aligned_cols=46 Identities=11% Similarity=0.021 Sum_probs=41.9
Q ss_pred HHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCC
Q 039903 38 EIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNR 92 (233)
Q Consensus 38 elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~ 92 (233)
+||+.+++ +-+-|--+++++..+|+++.. +|-..+|+.|+.++...
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 58999999 999999999999999999994 78899999999998664
No 331
>PF13730 HTH_36: Helix-turn-helix domain
Probab=87.32 E-value=0.75 Score=28.38 Aligned_cols=29 Identities=14% Similarity=0.224 Sum_probs=27.5
Q ss_pred CHHHHHHhCCCCCCCChhhHHHHHHHHhcCCce
Q 039903 35 SAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVL 67 (233)
Q Consensus 35 t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll 67 (233)
|.+.||+.+|+ +.+.+.+.++.|...|++
T Consensus 27 S~~~la~~~g~----s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGV----SRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCc----CHHHHHHHHHHHHHCcCC
Confidence 88999999999 999999999999999975
No 332
>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=87.21 E-value=0.99 Score=26.56 Aligned_cols=37 Identities=14% Similarity=0.256 Sum_probs=26.8
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHH
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~ 60 (233)
++..|.+.|... +..|..+||+.+|+ ++..+.+=++.
T Consensus 4 ~D~~Il~~Lq~d---~r~s~~~la~~lgl----S~~~v~~Ri~r 40 (42)
T PF13404_consen 4 LDRKILRLLQED---GRRSYAELAEELGL----SESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHH----TTS-HHHHHHHHTS-----HHHHHHHHHH
T ss_pred HHHHHHHHHHHc---CCccHHHHHHHHCc----CHHHHHHHHHH
Confidence 456788889887 58999999999999 88776554443
No 333
>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=87.17 E-value=0.75 Score=27.40 Aligned_cols=23 Identities=30% Similarity=0.297 Sum_probs=17.9
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHH
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILR 59 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~ 59 (233)
+.|..+||+.+|+ +..-++|+|+
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 9999998874
No 334
>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=87.05 E-value=1.4 Score=37.54 Aligned_cols=67 Identities=16% Similarity=0.110 Sum_probs=44.3
Q ss_pred ccCcceEEEecCCccHHHHHHHHH-------cCCCcEEEeechH-HHhhccCC--------CCceEEecCcCC-C-CC--
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISN-------YLHIKGVNFDLSH-VIQDSSSY--------SGVKHIGGIMLE-R-IP-- 225 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~-------~P~l~~~v~Dlp~-v~~~a~~~--------~ri~~~~gD~f~-~-~P-- 225 (233)
-....+|+|-.||+|.++.++.+. .+..+..++|..+ ++..+..+ .......+|.|. + ..
T Consensus 44 ~~~~~~VlDPacGsG~fL~~~~~~i~~~~~~~~~~~i~G~ei~~~~~~la~~nl~l~~~~~~~~~i~~~d~l~~~~~~~~ 123 (311)
T PF02384_consen 44 PKKGDSVLDPACGSGGFLVAAMEYIKEKRNKIKEINIYGIEIDPEAVALAKLNLLLHGIDNSNINIIQGDSLENDKFIKN 123 (311)
T ss_dssp T-TTEEEEETT-TTSHHHHHHHHHHHTCHHHHCCEEEEEEES-HHHHHHHHHHHHHTTHHCBGCEEEES-TTTSHSCTST
T ss_pred ccccceeechhhhHHHHHHHHHHhhcccccccccceeEeecCcHHHHHHHHhhhhhhccccccccccccccccccccccc
Confidence 345578999999999999998874 5888899999854 55544321 334678899987 2 32
Q ss_pred C-CCEEEe
Q 039903 226 K-GDAILI 232 (233)
Q Consensus 226 ~-~D~~~l 232 (233)
. .|+++.
T Consensus 124 ~~~D~ii~ 131 (311)
T PF02384_consen 124 QKFDVIIG 131 (311)
T ss_dssp --EEEEEE
T ss_pred cccccccC
Confidence 2 287764
No 335
>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=86.90 E-value=0.95 Score=40.02 Aligned_cols=63 Identities=8% Similarity=0.036 Sum_probs=46.8
Q ss_pred ceEEEecCCccHHHHHHHHHcCCC-cEEEeec-hHHHhhccCC------CCceEEecCcCCCCC---C-CCEEEe
Q 039903 170 KQLVDVGGGLGVNVNIIISNYLHI-KGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP---K-GDAILI 232 (233)
Q Consensus 170 ~~vvDvGGG~G~~~~~l~~~~P~l-~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P---~-~D~~~l 232 (233)
-+++|.-+|+|..+++.+++-++. +++..|+ |++++.++++ ..++++.+|.+.-+. . .|+|.+
T Consensus 46 ~~vLD~faGsG~rgir~a~e~~ga~~Vv~nD~n~~Av~~i~~N~~~N~~~~~~v~~~Da~~~l~~~~~~fDvIdl 120 (374)
T TIGR00308 46 INIADALSASGIRAIRYAHEIEGVREVFANDINPKAVESIKNNVEYNSVENIEVPNEDAANVLRYRNRKFHVIDI 120 (374)
T ss_pred CEEEECCCchhHHHHHHHhhCCCCCEEEEEeCCHHHHHHHHHHHHHhCCCcEEEEchhHHHHHHHhCCCCCEEEe
Confidence 479999999999999999987654 5788898 5677766553 357788888886222 2 387765
No 336
>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=86.81 E-value=0.2 Score=33.24 Aligned_cols=37 Identities=22% Similarity=0.198 Sum_probs=31.9
Q ss_pred CCCCHHHHHHhC---CCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 32 AKISAVEIAAQM---PSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 32 ~~~t~~elA~~~---~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
+.+++.++|+.+ +. ....++++-++.+|.++|++++.
T Consensus 23 ~~i~l~~ia~~l~~~~~--k~~~RRlYDI~NVLealgli~K~ 62 (71)
T PF02319_consen 23 KSISLNEIADKLISENV--KTQRRRLYDIINVLEALGLIEKQ 62 (71)
T ss_dssp TEEEHHHHHHHCHHHCC--HHHCHHHHHHHHHHHHCTSEEEE
T ss_pred CcccHHHHHHHHccccc--ccccchhhHHHHHHHHhCceeec
Confidence 689999999999 64 11578999999999999999996
No 337
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=86.78 E-value=4.6 Score=27.92 Aligned_cols=32 Identities=3% Similarity=0.108 Sum_probs=27.4
Q ss_pred HHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCC
Q 039903 57 ILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNR 92 (233)
Q Consensus 57 lL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~ 92 (233)
-+..|...|+++++ ..|.|++|+.|+.++..+
T Consensus 60 a~~~L~~aGli~~~----~rG~~~iT~~G~~~l~~~ 91 (92)
T PF14338_consen 60 ARSYLKKAGLIERP----KRGIWRITEKGRKALAEH 91 (92)
T ss_pred HHHHHHHCCCccCC----CCCceEECHhHHHHHhhC
Confidence 36889999999997 689999999999877654
No 338
>PRK09462 fur ferric uptake regulator; Provisional
Probab=86.69 E-value=1.8 Score=32.84 Aligned_cols=66 Identities=11% Similarity=0.222 Sum_probs=46.7
Q ss_pred HHhhChhHHHHhcCCCCCCCHHHHHHhCCCC-CCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903 16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA 82 (233)
Q Consensus 16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~-~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt 82 (233)
.-+.-|++.|.... .++.|+.||-+.+.-. ++.+..-++|.|+.|+..|++.+...+++..+|.++
T Consensus 17 ~qR~~Il~~l~~~~-~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~~~ 83 (148)
T PRK09462 17 LPRLKILEVLQEPD-NHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFELT 83 (148)
T ss_pred HHHHHHHHHHHhCC-CCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEEeC
Confidence 34566899998631 1589999999888531 233788899999999999999986432123456543
No 339
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=86.66 E-value=1.3 Score=33.58 Aligned_cols=65 Identities=20% Similarity=0.262 Sum_probs=49.0
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCC-CCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPS-SNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV 84 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~-~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~ 84 (233)
|+.|+++|.+++ ++.|+++|=.++.- .++++..-++|-|+.|...|++++...+++..+|.++..
T Consensus 23 R~~vl~~L~~~~--~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y~~~~~ 88 (145)
T COG0735 23 RLAVLELLLEAD--GHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRYELNSE 88 (145)
T ss_pred HHHHHHHHHhcC--CCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEEecCCC
Confidence 567999999875 67999999888774 245588899999999999999998754322234655443
No 340
>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=86.48 E-value=0.69 Score=42.72 Aligned_cols=55 Identities=11% Similarity=0.141 Sum_probs=39.3
Q ss_pred CcceEEEecCCccHHHHHHHHHcCC--------CcEEEeechH-HHhhccCC----C--CceEEecCcCC
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLH--------IKGVNFDLSH-VIQDSSSY----S--GVKHIGGIMLE 222 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~--------l~~~v~Dlp~-v~~~a~~~----~--ri~~~~gD~f~ 222 (233)
...+|+|.|||+|.++.+++++.+. +....+|+.+ ++..++.+ . .++...+|++.
T Consensus 31 ~~~~ilDP~cGsG~fl~~~~~~~~~~~~~~~~~~~i~g~DId~~a~~~a~~~l~~~~~~~~~i~~~d~l~ 100 (524)
T TIGR02987 31 TKTKIIDPCCGDGRLIAALLKKNEEINYFKEVELNIYFADIDKTLLKRAKKLLGEFALLEINVINFNSLS 100 (524)
T ss_pred cceEEEeCCCCccHHHHHHHHHHHhcCCcccceeeeeeechhHHHHHHHHHHHhhcCCCCceeeeccccc
Confidence 4568999999999999999988763 4568888854 55555432 2 45666666664
No 341
>PF05958 tRNA_U5-meth_tr: tRNA (Uracil-5-)-methyltransferase; InterPro: IPR010280 This family consists of (uracil-5-)-methyltransferases 2.1.1.35 from EC from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalysed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity []. This protein family also contains the 23SrRNA methyltransferases, first proposed to be RNA methyltransferases by homology to the TrmA family. The member from Escherichia 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 [].; GO: 0008173 RNA methyltransferase activity, 0006396 RNA processing; PDB: 2VS1_A 2JJQ_A 2BH2_A 1UWV_A 3BT7_B.
Probab=86.43 E-value=0.65 Score=40.67 Aligned_cols=47 Identities=15% Similarity=0.260 Sum_probs=35.0
Q ss_pred eEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecC
Q 039903 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGI 219 (233)
Q Consensus 171 ~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD 219 (233)
.++|+=||.|.++..+++..-+ ++.+|. ++.++.|+.+ ++++|+.++
T Consensus 199 ~vlDlycG~G~fsl~la~~~~~--V~gvE~~~~av~~A~~Na~~N~i~n~~f~~~~ 252 (352)
T PF05958_consen 199 DVLDLYCGVGTFSLPLAKKAKK--VIGVEIVEEAVEDARENAKLNGIDNVEFIRGD 252 (352)
T ss_dssp EEEEES-TTTCCHHHHHCCSSE--EEEEES-HHHHHHHHHHHHHTT--SEEEEE--
T ss_pred cEEEEeecCCHHHHHHHhhCCe--EEEeeCCHHHHHHHHHHHHHcCCCcceEEEee
Confidence 7999999999999999998754 777776 5677777653 688988654
No 342
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=86.19 E-value=0.68 Score=37.54 Aligned_cols=43 Identities=19% Similarity=0.274 Sum_probs=34.2
Q ss_pred hHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHH
Q 039903 8 VLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60 (233)
Q Consensus 8 ~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~ 60 (233)
..-.+|+.|.++|-||.=. ..++.|||+.+|+ ++..+...||-
T Consensus 159 rQ~~vL~~A~~~GYFd~PR------~~~l~dLA~~lGI----Skst~~ehLRr 201 (215)
T COG3413 159 RQLEVLRLAYKMGYFDYPR------RVSLKDLAKELGI----SKSTLSEHLRR 201 (215)
T ss_pred HHHHHHHHHHHcCCCCCCc------cCCHHHHHHHhCC----CHHHHHHHHHH
Confidence 3557999999999999764 5899999999999 66655555543
No 343
>KOG2187 consensus tRNA uracil-5-methyltransferase and related tRNA-modifying enzymes [Translation, ribosomal structure and biogenesis]
Probab=86.19 E-value=0.74 Score=41.94 Aligned_cols=55 Identities=18% Similarity=0.250 Sum_probs=42.7
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEec---CcCC
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGG---IMLE 222 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~g---D~f~ 222 (233)
.+..+.++||-||+|.++.++++..- +++.+++ |+.++.|+.+ .+.+|+.| |.|.
T Consensus 381 l~~~k~llDv~CGTG~iglala~~~~--~ViGvEi~~~aV~dA~~nA~~NgisNa~Fi~gqaE~~~~ 445 (534)
T KOG2187|consen 381 LPADKTLLDVCCGTGTIGLALARGVK--RVIGVEISPDAVEDAEKNAQINGISNATFIVGQAEDLFP 445 (534)
T ss_pred CCCCcEEEEEeecCCceehhhhcccc--ceeeeecChhhcchhhhcchhcCccceeeeecchhhccc
Confidence 45558999999999999999998644 4666654 7888888764 67899988 5554
No 344
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=85.92 E-value=1.8 Score=31.50 Aligned_cols=59 Identities=14% Similarity=0.155 Sum_probs=43.0
Q ss_pred HHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhH
Q 039903 9 LPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKY 87 (233)
Q Consensus 9 ~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~ 87 (233)
.-+||++| ..|.+. ||.+..+|++.+++ + ...+||+. --.|+|++. +-|.|.||+.++.
T Consensus 58 RQ~Al~~A------~~L~~~---Gp~~~~~l~~~~~~----~--~A~~IL~~-N~YGWFeRv----~rGvY~LT~~G~~ 116 (118)
T PF09929_consen 58 RQDALRCA------AALAEH---GPSRPADLRKATGV----P--KATSILRD-NHYGWFERV----ERGVYALTPAGRA 116 (118)
T ss_pred HHHHHHHH------HHHHHc---CCCCHHHHHHhcCC----C--hHHHHHHh-Ccccceeee----ccceEecCcchhh
Confidence 34566655 467766 69999999999998 3 33344432 347999998 7999999998763
No 345
>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=85.83 E-value=2.2 Score=28.32 Aligned_cols=44 Identities=14% Similarity=0.104 Sum_probs=38.7
Q ss_pred hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
..|...++. ++.|++||-+.+|+ +...+-..|.-|...|++.+.
T Consensus 8 ~~IL~~ls~----~c~TLeeL~ekTgi----~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 8 QKILIILSK----RCCTLEELEEKTGI----SKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHHHh----ccCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeee
Confidence 345666776 59999999999999 999999999999999999984
No 346
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=85.56 E-value=1.8 Score=33.73 Aligned_cols=53 Identities=15% Similarity=0.227 Sum_probs=42.6
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCC-CCCChhhHHHHHHHHhcCCceeeec
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILRLLVTHRVLRCTS 71 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~-~~~~~~~l~rlL~~L~~~gll~~~~ 71 (233)
-++-|++.|...+ ++.|++||.+.+.-. ++.+..-++|.|+.|+..|++.+..
T Consensus 27 qR~~IL~~l~~~~--~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~ 80 (169)
T PRK11639 27 QRLEVLRLMSLQP--GAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVE 80 (169)
T ss_pred HHHHHHHHHHhcC--CCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEe
Confidence 3556889988764 699999999998642 2337778999999999999999973
No 347
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=85.45 E-value=1.4 Score=36.83 Aligned_cols=53 Identities=17% Similarity=0.164 Sum_probs=46.1
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL 81 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l 81 (233)
+..|.++|.+. |.++++|||+.+++ ++.-++|=|+.|...|++.+. -+|....
T Consensus 7 ~~~Il~~l~~~---g~v~v~eLa~~~~V----S~~TIRRDL~~Le~~g~l~R~----hGGa~~~ 59 (253)
T COG1349 7 HQKILELLKEK---GKVSVEELAELFGV----SEMTIRRDLNELEEQGLLLRV----HGGAVLP 59 (253)
T ss_pred HHHHHHHHHHc---CcEEHHHHHHHhCC----CHHHHHHhHHHHHHCCcEEEE----eCCEecC
Confidence 45688999997 59999999999999 999999999999999999997 4555543
No 348
>PRK10742 putative methyltransferase; Provisional
Probab=85.26 E-value=2.4 Score=35.21 Aligned_cols=73 Identities=14% Similarity=0.180 Sum_probs=52.1
Q ss_pred HHHHHhcccccCcc--eEEEecCCccHHHHHHHHHcCCCcEEEeechHHHh--------hcc------C--CCCceEEec
Q 039903 157 NRIIDSSKGFEQIK--QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQ--------DSS------S--YSGVKHIGG 218 (233)
Q Consensus 157 ~~~~~~~~~~~~~~--~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~--------~a~------~--~~ri~~~~g 218 (233)
+.+++... .++.. +|+|+=+|.|..+..++.+ ..+++.+|...++. .+. . ..||+.+.+
T Consensus 76 ~~l~kAvg-lk~g~~p~VLD~TAGlG~Da~~las~--G~~V~~vEr~p~vaalL~dgL~ra~~~~~~~~~~~~ri~l~~~ 152 (250)
T PRK10742 76 EAVAKAVG-IKGDYLPDVVDATAGLGRDAFVLASV--GCRVRMLERNPVVAALLDDGLARGYADAEIGGWLQERLQLIHA 152 (250)
T ss_pred cHHHHHhC-CCCCCCCEEEECCCCccHHHHHHHHc--CCEEEEEECCHHHHHHHHHHHHHhhhccccchhhhceEEEEeC
Confidence 45666665 55544 9999999999999999998 66699999864432 221 0 047999999
Q ss_pred CcCC---CCCCC-CEEEe
Q 039903 219 IMLE---RIPKG-DAILI 232 (233)
Q Consensus 219 D~f~---~~P~~-D~~~l 232 (233)
|..+ ..+.. |+|+|
T Consensus 153 da~~~L~~~~~~fDVVYl 170 (250)
T PRK10742 153 SSLTALTDITPRPQVVYL 170 (250)
T ss_pred cHHHHHhhCCCCCcEEEE
Confidence 9887 23443 99886
No 349
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=85.15 E-value=1.4 Score=36.79 Aligned_cols=47 Identities=19% Similarity=0.240 Sum_probs=42.9
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.+..|.+.|.+. +.+++.|||+.+++ ++.-++|=|+.|...|++.+.
T Consensus 6 R~~~Il~~L~~~---~~v~v~eLa~~l~V----S~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 6 RQAAILEYLQKQ---GKTSVEELAQYFDT----TGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHHHc---CCEEHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEE
Confidence 455688999987 58999999999999 999999999999999999987
No 350
>PF01861 DUF43: Protein of unknown function DUF43; InterPro: IPR002723 This family of prokaryotic proteins have not been characterised. All the members are 350-400 amino acids long.; PDB: 2QM3_A.
Probab=85.00 E-value=1.6 Score=35.98 Aligned_cols=70 Identities=11% Similarity=0.181 Sum_probs=37.2
Q ss_pred HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC----C-CCceEEecCcCCCCCC---C--
Q 039903 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS----Y-SGVKHIGGIMLERIPK---G-- 227 (233)
Q Consensus 159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~----~-~ri~~~~gD~f~~~P~---~-- 227 (233)
+.+..+ +.+ ++|+=|| -+=..|++++-.++..+++|+|+.+ .++..++ . -.|+.+.+|+.+++|. +
T Consensus 37 ~~~~gd-L~g-k~il~lG-DDDLtSlA~al~~~~~~I~VvDiDeRll~fI~~~a~~~gl~i~~~~~DlR~~LP~~~~~~f 113 (243)
T PF01861_consen 37 MAERGD-LEG-KRILFLG-DDDLTSLALALTGLPKRITVVDIDERLLDFINRVAEEEGLPIEAVHYDLRDPLPEELRGKF 113 (243)
T ss_dssp HHHTT--STT--EEEEES--TT-HHHHHHHHT--SEEEEE-S-HHHHHHHHHHHHHHT--EEEE---TTS---TTTSS-B
T ss_pred HHhcCc-ccC-CEEEEEc-CCcHHHHHHHhhCCCCeEEEEEcCHHHHHHHHHHHHHcCCceEEEEecccccCCHHHhcCC
Confidence 334433 443 7788888 4455677777778888999999975 5544332 1 2499999999999996 3
Q ss_pred CEEE
Q 039903 228 DAIL 231 (233)
Q Consensus 228 D~~~ 231 (233)
|+++
T Consensus 114 D~f~ 117 (243)
T PF01861_consen 114 DVFF 117 (243)
T ss_dssp SEEE
T ss_pred CEEE
Confidence 8876
No 351
>KOG1975 consensus mRNA cap methyltransferase [RNA processing and modification]
Probab=84.86 E-value=1.6 Score=37.75 Aligned_cols=71 Identities=15% Similarity=0.186 Sum_probs=50.6
Q ss_pred HHHHHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCC-cEEEeechH-HHhhccCC--------
Q 039903 141 NGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHI-KGVNFDLSH-VIQDSSSY-------- 210 (233)
Q Consensus 141 ~~~f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l-~~~v~Dlp~-v~~~a~~~-------- 210 (233)
.++||.+|.+ .++..|- +....++|+|||-|.-++..-++ .+ ..+..|+.+ .|+++++.
T Consensus 99 lRnfNNwIKs-------~LI~~y~--~~~~~~~~LgCGKGGDLlKw~kA--gI~~~igiDIAevSI~qa~~RYrdm~~r~ 167 (389)
T KOG1975|consen 99 LRNFNNWIKS-------VLINLYT--KRGDDVLDLGCGKGGDLLKWDKA--GIGEYIGIDIAEVSINQARKRYRDMKNRF 167 (389)
T ss_pred hhhhhHHHHH-------HHHHHHh--ccccccceeccCCcccHhHhhhh--cccceEeeehhhccHHHHHHHHHHHHhhh
Confidence 3567766653 4555543 66788999999999998887765 33 368899987 57878762
Q ss_pred C----CceEEecCcCC
Q 039903 211 S----GVKHIGGIMLE 222 (233)
Q Consensus 211 ~----ri~~~~gD~f~ 222 (233)
+ .+.|+.+|=|.
T Consensus 168 ~~~~f~a~f~~~Dc~~ 183 (389)
T KOG1975|consen 168 KKFIFTAVFIAADCFK 183 (389)
T ss_pred hcccceeEEEEeccch
Confidence 2 36788888875
No 352
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=84.71 E-value=1.8 Score=37.26 Aligned_cols=57 Identities=12% Similarity=0.125 Sum_probs=43.8
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV 84 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~ 84 (233)
...|.+.|.+. .+.+..+||+++++ +...+.+.++.|...|++-+.. .+..|.+.+.
T Consensus 6 ~~~il~~L~~~---~~~s~~~LA~~lgv----sr~tV~~~l~~L~~~G~~i~~~---~~~Gy~L~~~ 62 (319)
T PRK11886 6 MLQLLSLLADG---DFHSGEQLGEELGI----SRAAIWKHIQTLEEWGLDIFSV---KGKGYRLAEP 62 (319)
T ss_pred HHHHHHHHHcC---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCceEEe---cCCeEEecCc
Confidence 34567777764 47899999999999 9999999999999999944331 2346876543
No 353
>COG0116 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]
Probab=84.63 E-value=3.1 Score=36.79 Aligned_cols=75 Identities=13% Similarity=0.109 Sum_probs=55.1
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCc---------------------------------------EEE
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIK---------------------------------------GVN 197 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~---------------------------------------~~v 197 (233)
..++..- +|.....++|==||+|.++++.+...+++- .+.
T Consensus 181 aAil~la-gw~~~~pl~DPmCGSGTi~IEAAl~~~niAPg~~R~~~f~~w~~~~~~lw~~~~~ea~~~a~~~~~~~~~~G 259 (381)
T COG0116 181 AAILLLA-GWKPDEPLLDPMCGSGTILIEAALIAANIAPGLNRRFGFEFWDWFDKDLWDKLREEAEERARRGKELPIIYG 259 (381)
T ss_pred HHHHHHc-CCCCCCccccCCCCccHHHHHHHHhccccCCccccccchhhhhhccHHHHHHHHHHHHHHHhhcCccceEEE
Confidence 3444433 387778999999999999999888876422 568
Q ss_pred eec-hHHHhhccCC-------CCceEEecCcCC-CCC-CC-CEEEe
Q 039903 198 FDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIP-KG-DAILI 232 (233)
Q Consensus 198 ~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P-~~-D~~~l 232 (233)
.|+ |.+++.|+.+ +.|+|..+|+-. +-| .. |+++.
T Consensus 260 ~Did~r~i~~Ak~NA~~AGv~d~I~f~~~d~~~l~~~~~~~gvvI~ 305 (381)
T COG0116 260 SDIDPRHIEGAKANARAAGVGDLIEFKQADATDLKEPLEEYGVVIS 305 (381)
T ss_pred ecCCHHHHHHHHHHHHhcCCCceEEEEEcchhhCCCCCCcCCEEEe
Confidence 898 4588877765 789999999887 444 33 77653
No 354
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=84.63 E-value=0.96 Score=27.26 Aligned_cols=40 Identities=13% Similarity=0.151 Sum_probs=23.6
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCC
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHR 65 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~g 65 (233)
.++.+...+.+ +.|..+||+.+|+ +..-+.+|++--...|
T Consensus 6 ~R~~ii~l~~~-----G~s~~~ia~~lgv----s~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 6 RRAQIIRLLRE-----GWSIREIAKRLGV----SRSTVYRWIKRYREEG 45 (50)
T ss_dssp ----HHHHHHH-----T--HHHHHHHHTS-----HHHHHHHHT------
T ss_pred HHHHHHHHHHC-----CCCHHHHHHHHCc----CHHHHHHHHHHccccc
Confidence 34556666666 6899999999999 9999999997765555
No 355
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=83.84 E-value=3.7 Score=33.84 Aligned_cols=49 Identities=12% Similarity=0.232 Sum_probs=43.9
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhh
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFV 89 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~ 89 (233)
.....|||+++|+ .+..+..-++-|+.-|++++. +-+.|..|..+...+
T Consensus 25 ~v~q~eIA~~lgi----T~QaVsehiK~Lv~eG~i~~~----gR~~Y~iTkkG~e~l 73 (260)
T COG1497 25 RVKQKEIAKKLGI----TLQAVSEHIKELVKEGLIEKE----GRGEYEITKKGAEWL 73 (260)
T ss_pred CCCHHHHHHHcCC----CHHHHHHHHHHHHhccceeec----CCeeEEEehhHHHHH
Confidence 6788999999999 999999999999999999995 567999999987533
No 356
>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=83.44 E-value=1.8 Score=30.33 Aligned_cols=40 Identities=15% Similarity=0.191 Sum_probs=33.8
Q ss_pred HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHh
Q 039903 15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLV 62 (233)
Q Consensus 15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~ 62 (233)
.+.+.||+..|-. ++.|-.|||+.+|+ +...+.|+=+.|.
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 4568899998877 58999999999999 8888888777665
No 357
>PF13518 HTH_28: Helix-turn-helix domain
Probab=83.41 E-value=2.2 Score=25.65 Aligned_cols=29 Identities=17% Similarity=0.113 Sum_probs=26.4
Q ss_pred CCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCc
Q 039903 34 ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRV 66 (233)
Q Consensus 34 ~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gl 66 (233)
.|..++|+.+|+ +...+.+|++..-..|+
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 99999999998888775
No 358
>COG2265 TrmA SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=83.33 E-value=1.1 Score=40.52 Aligned_cols=65 Identities=14% Similarity=0.147 Sum_probs=48.3
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC--C-CC--C-CCEEEe
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE--R-IP--K-GDAILI 232 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~--~-~P--~-~D~~~l 232 (233)
..+..+++|.=||.|.|+..++++ --+++..|+ |+.++.|+++ ++++|+.+|..+ + +. . .|++++
T Consensus 291 ~~~~~~vlDlYCGvG~f~l~lA~~--~~~V~gvEi~~~aV~~A~~NA~~n~i~N~~f~~~~ae~~~~~~~~~~~~d~Vvv 368 (432)
T COG2265 291 LAGGERVLDLYCGVGTFGLPLAKR--VKKVHGVEISPEAVEAAQENAAANGIDNVEFIAGDAEEFTPAWWEGYKPDVVVV 368 (432)
T ss_pred hcCCCEEEEeccCCChhhhhhccc--CCEEEEEecCHHHHHHHHHHHHHcCCCcEEEEeCCHHHHhhhccccCCCCEEEE
Confidence 345679999999999999999965 445777776 6677776653 679999999887 2 22 2 388775
No 359
>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=83.29 E-value=2.7 Score=30.92 Aligned_cols=49 Identities=8% Similarity=0.045 Sum_probs=42.9
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF 88 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l 88 (233)
-|.|.++||..++- +.+.++.-|.++...|+++.. +++.|.++.....-
T Consensus 52 ipy~~e~LA~~~~~----~~~~V~~AL~~f~k~glIe~~----ed~~i~i~~~~~~~ 100 (121)
T PF09681_consen 52 IPYTAEMLALEFDR----PVDTVRLALAVFQKLGLIEID----EDGVIYIPNWEKHQ 100 (121)
T ss_pred CCCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe----cCCeEEeecHHHHh
Confidence 49999999999999 999999999999999999997 68888777655443
No 360
>KOG0822 consensus Protein kinase inhibitor [Cell cycle control, cell division, chromosome partitioning]
Probab=82.98 E-value=5.2 Score=36.87 Aligned_cols=94 Identities=19% Similarity=0.210 Sum_probs=56.6
Q ss_pred cccccccCchHHHHHHHHHHhcchhcHHHHHHhccccc--CcceEEEecCCccHHHHHHHHH----cCCCcEEEeec-hH
Q 039903 130 FYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFE--QIKQLVDVGGGLGVNVNIIISN----YLHIKGVNFDL-SH 202 (233)
Q Consensus 130 ~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~~~--~~~~vvDvGGG~G~~~~~l~~~----~P~l~~~v~Dl-p~ 202 (233)
.|+.+++||-.=..+.+|.- ..+++..++-+ ....+.-+|||.|-+..+..++ +-+++..+++- |.
T Consensus 334 TYetFEkD~VKY~~Yq~Ai~-------~AL~Drvpd~~a~~~tVimvlGaGRGPLv~~~lkaa~~~~RkVklyavEKNPN 406 (649)
T KOG0822|consen 334 TYETFEKDPVKYDQYQQAIL-------KALLDRVPDESAKTTTVIMVLGAGRGPLVDASLKAAEETDRKVKLYAVEKNPN 406 (649)
T ss_pred hhhhhhccchHHHHHHHHHH-------HHHHhhCcccccCceEEEEEecCCCccHHHHHHHHHHHhcCceEEEEEecCcc
Confidence 35666677755555555433 23444333222 2677888999999876655443 44566666664 55
Q ss_pred HHhhccC------CCCceEEecCcCC-CCC-C-CCEE
Q 039903 203 VIQDSSS------YSGVKHIGGIMLE-RIP-K-GDAI 230 (233)
Q Consensus 203 v~~~a~~------~~ri~~~~gD~f~-~~P-~-~D~~ 230 (233)
++-.... ..||+.+.+||.+ .-| . +|++
T Consensus 407 AivtL~~~n~~~W~~~Vtii~~DMR~w~ap~eq~DI~ 443 (649)
T KOG0822|consen 407 AIVTLQNRNFECWDNRVTIISSDMRKWNAPREQADII 443 (649)
T ss_pred hhhhhhhhchhhhcCeeEEEeccccccCCchhhccch
Confidence 4433322 1789999999999 544 2 5765
No 361
>KOG1709 consensus Guanidinoacetate methyltransferase and related proteins [Amino acid transport and metabolism]
Probab=82.96 E-value=5.4 Score=32.59 Aligned_cols=61 Identities=15% Similarity=0.166 Sum_probs=49.6
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-----CCceEEecCcC---CCCCC
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-----SGVKHIGGIML---ERIPK 226 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-----~ri~~~~gD~f---~~~P~ 226 (233)
+.+..+|+.||=|-|.....+-++.|..+.++---|+|.+.-+.. ++|....|-+= ..+|.
T Consensus 99 ~tkggrvLnVGFGMgIidT~iQe~~p~~H~IiE~hp~V~krmr~~gw~ek~nViil~g~WeDvl~~L~d 167 (271)
T KOG1709|consen 99 STKGGRVLNVGFGMGIIDTFIQEAPPDEHWIIEAHPDVLKRMRDWGWREKENVIILEGRWEDVLNTLPD 167 (271)
T ss_pred hhCCceEEEeccchHHHHHHHhhcCCcceEEEecCHHHHHHHHhcccccccceEEEecchHhhhccccc
Confidence 467799999999999999999999999999999999999887763 56766666433 34554
No 362
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=82.84 E-value=2.3 Score=34.29 Aligned_cols=45 Identities=13% Similarity=0.236 Sum_probs=37.2
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.|.+.+.+.- ++.|..|||+++++ ++.-+++-+..|+..|++...
T Consensus 166 ~Vl~~~~~g~--~g~s~~eIa~~l~i----S~~Tv~~~~~~~~~~~~~~~~ 210 (225)
T PRK10046 166 AVRKLFKEPG--VQHTAETVAQALTI----SRTTARRYLEYCASRHLIIAE 210 (225)
T ss_pred HHHHHHHcCC--CCcCHHHHHHHhCc----cHHHHHHHHHHHHhCCeEEEE
Confidence 3556665510 15899999999999 999999999999999999974
No 363
>KOG1562 consensus Spermidine synthase [Amino acid transport and metabolism]
Probab=82.80 E-value=0.81 Score=38.91 Aligned_cols=66 Identities=24% Similarity=0.344 Sum_probs=49.7
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCc-EEEeechH-HHhhccCC----------CCceEEecCcCC---CCCCC--C
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIK-GVNFDLSH-VIQDSSSY----------SGVKHIGGIMLE---RIPKG--D 228 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~-~~v~Dlp~-v~~~a~~~----------~ri~~~~gD~f~---~~P~~--D 228 (233)
..+++.++-||||.|.+.+..++. +.+. ..++|..+ |++..+++ +||..+.||=|. -.+.. |
T Consensus 119 ~~npkkvlVVgggDggvlrevikH-~~ve~i~~~eiD~~Vie~sk~y~p~la~gy~~~~v~l~iGDG~~fl~~~~~~~~d 197 (337)
T KOG1562|consen 119 HPNPKKVLVVGGGDGGVLREVIKH-KSVENILLCEIDENVIESSKQYLPTLACGYEGKKVKLLIGDGFLFLEDLKENPFD 197 (337)
T ss_pred CCCCCeEEEEecCCccceeeeecc-ccccceeeehhhHHHHHHHHHHhHHHhcccCCCceEEEeccHHHHHHHhccCCce
Confidence 356789999999999999999886 7765 56778765 66655542 799999999775 34443 8
Q ss_pred EEEe
Q 039903 229 AILI 232 (233)
Q Consensus 229 ~~~l 232 (233)
+++.
T Consensus 198 Vii~ 201 (337)
T KOG1562|consen 198 VIIT 201 (337)
T ss_pred EEEE
Confidence 7764
No 364
>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=81.92 E-value=3.2 Score=30.86 Aligned_cols=51 Identities=14% Similarity=0.206 Sum_probs=38.5
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.|+.|.+.|=.. ++.|+.||.+.++-..+.+..-+..+|+-|...|++++.
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 466677777665 589999977776311111888999999999999999975
No 365
>PRK11642 exoribonuclease R; Provisional
Probab=81.58 E-value=2.8 Score=40.99 Aligned_cols=58 Identities=22% Similarity=0.244 Sum_probs=44.3
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
.|.+.|...+ +|++..+|++++++.+..+...+.+.|+.|...|.+.+. ..+.|.+..
T Consensus 23 ~Il~~l~~~~--~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~----~~~~~~~~~ 80 (813)
T PRK11642 23 FILEHLTKRE--KPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFT----RRQCYALPE 80 (813)
T ss_pred HHHHHHHhcC--CCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEc----CCceEecCC
Confidence 4677776643 699999999999993222345699999999999999986 466776653
No 366
>PF13814 Replic_Relax: Replication-relaxation
Probab=81.39 E-value=3.9 Score=32.04 Aligned_cols=61 Identities=13% Similarity=0.146 Sum_probs=48.0
Q ss_pred HHHhcCCCCCCCHHHHHHhCCCCCCCChh---hHHHHHHHHhcCCceeeeccC------CCCCceeccHhhhHhhcC
Q 039903 24 IIAKAGPTAKISAVEIAAQMPSSNPNAAV---MLDRILRLLVTHRVLRCTSAG------DDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 24 ~L~~~~~~~~~t~~elA~~~~~~~~~~~~---~l~rlL~~L~~~gll~~~~~~------~~~~~y~lt~~s~~l~~~ 91 (233)
.|... +.+|..||+..... +.. .+++.|+-|...|++...... ...-.|.+|+.|..++.+
T Consensus 3 ~L~~~---r~lt~~Qi~~l~~~----~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~~ 72 (191)
T PF13814_consen 3 LLARH---RFLTTDQIARLLFP----SSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLLAD 72 (191)
T ss_pred hHHHh---cCcCHHHHHHHHcC----CCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHHHh
Confidence 34554 48999999999998 554 899999999999999987431 134689999999877653
No 367
>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=81.07 E-value=2.4 Score=26.77 Aligned_cols=39 Identities=18% Similarity=0.243 Sum_probs=32.8
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHh
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLV 62 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~ 62 (233)
.++.|++.|-+. +..|+.|||+.+++ +++-++.-+..|-
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 467788888875 58999999999999 9999988888776
No 368
>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=81.05 E-value=2.5 Score=26.98 Aligned_cols=30 Identities=23% Similarity=0.388 Sum_probs=23.7
Q ss_pred hHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHH
Q 039903 22 FEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRI 57 (233)
Q Consensus 22 fd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rl 57 (233)
|++-.+++ |.+++.|||+++|+ ++.-+++|
T Consensus 13 ~e~y~~~~--g~i~lkdIA~~Lgv----s~~tIr~W 42 (60)
T PF10668_consen 13 FEIYKESN--GKIKLKDIAEKLGV----SESTIRKW 42 (60)
T ss_pred HHHHHHhC--CCccHHHHHHHHCC----CHHHHHHH
Confidence 44444444 79999999999999 88888776
No 369
>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=81.00 E-value=3.1 Score=26.65 Aligned_cols=46 Identities=13% Similarity=0.086 Sum_probs=35.0
Q ss_pred CCCCHHHHHHhCCCCCCCCh-hhHHHHHHHHhcCCceeeeccCCCCCceeccHhhh
Q 039903 32 AKISAVEIAAQMPSSNPNAA-VMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAK 86 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~-~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~ 86 (233)
.+++.+++.++.|. +. ......++.+...|+++.+ ++++++|+.|.
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 37899999999998 53 3447789999999999994 89999999775
No 370
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=80.93 E-value=1.4 Score=34.90 Aligned_cols=47 Identities=13% Similarity=0.035 Sum_probs=42.4
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.+..|.+.|... +.+++.|||+.+++ ++.-++|=|+.|...|++.+.
T Consensus 8 R~~~Il~~l~~~---~~~~~~~La~~~~v----S~~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 8 RQKALQELIEEN---PFITDEELAEKFGV----SIQTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHHHHC---CCEEHHHHHHHHCc----CHHHHHHHHHHHhcchHHHHH
Confidence 445678888887 58999999999999 999999999999999999986
No 371
>KOG2651 consensus rRNA adenine N-6-methyltransferase [RNA processing and modification]
Probab=80.91 E-value=2.8 Score=36.98 Aligned_cols=46 Identities=26% Similarity=0.397 Sum_probs=34.7
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHH
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVI 204 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~ 204 (233)
+++..+-+|.++.++||||.|.|+++.-+.=.| ++++..+|-..+.
T Consensus 143 elvSsi~~f~gi~~vvD~GaG~G~LSr~lSl~y-~lsV~aIegsq~~ 188 (476)
T KOG2651|consen 143 ELVSSISDFTGIDQVVDVGAGQGHLSRFLSLGY-GLSVKAIEGSQRL 188 (476)
T ss_pred HHHHHHHhhcCCCeeEEcCCCchHHHHHHhhcc-CceEEEeccchHH
Confidence 445544448899999999999999988776654 6778888866543
No 372
>COG1092 Predicted SAM-dependent methyltransferases [General function prediction only]
Probab=80.64 E-value=1.7 Score=38.70 Aligned_cols=65 Identities=15% Similarity=0.120 Sum_probs=51.0
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC--------CCceEEecCcCCCC----CCC---CEE
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY--------SGVKHIGGIMLERI----PKG---DAI 230 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~--------~ri~~~~gD~f~~~----P~~---D~~ 230 (233)
.+.++|||+=|=+|.++...+..- .-++|.+|+.. +++.|+++ ++++++.+|.|+-+ ..+ |+|
T Consensus 216 ~~GkrvLNlFsYTGgfSv~Aa~gG-A~~vt~VD~S~~al~~a~~N~~LNg~~~~~~~~i~~Dvf~~l~~~~~~g~~fDlI 294 (393)
T COG1092 216 AAGKRVLNLFSYTGGFSVHAALGG-ASEVTSVDLSKRALEWARENAELNGLDGDRHRFIVGDVFKWLRKAERRGEKFDLI 294 (393)
T ss_pred ccCCeEEEecccCcHHHHHHHhcC-CCceEEEeccHHHHHHHHHHHHhcCCCccceeeehhhHHHHHHHHHhcCCcccEE
Confidence 347899999999999999988862 23789999975 78877764 67999999999732 323 888
Q ss_pred Ee
Q 039903 231 LI 232 (233)
Q Consensus 231 ~l 232 (233)
+|
T Consensus 295 il 296 (393)
T COG1092 295 IL 296 (393)
T ss_pred EE
Confidence 86
No 373
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=80.63 E-value=7.6 Score=32.94 Aligned_cols=166 Identities=11% Similarity=0.102 Sum_probs=94.4
Q ss_pred CCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCCCCCCccchhcc----ccC---
Q 039903 34 ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPW----LET--- 106 (233)
Q Consensus 34 ~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~~~~~~~~~~~~----~~~--- 106 (233)
-+.-.|+....+ +.+.+..+++.|...|++..+ ++...+|..|..|+..- .+..--.+ +..
T Consensus 35 ~d~wkIvd~s~~----plp~v~~i~~~l~~egiv~~~-----~g~v~~TekG~E~~e~~---gi~~~~~~~C~~CeGrgi 102 (354)
T COG1568 35 NDFWKIVDYSDL----PLPLVASILEILEDEGIVKIE-----EGGVELTEKGEELAEEL---GIKKKYDYTCECCEGRGI 102 (354)
T ss_pred cchHhhhhhccC----CchHHHHHHHHHHhcCcEEEe-----cCcEeehhhhHHHHHHh---CCCccccccccCcCCccc
Confidence 388899999999 899999999999999999996 55599999999888642 12211111 110
Q ss_pred chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchhcHHHHHHhcc--cccCcceEEEecCCccHHHH
Q 039903 107 KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSK--GFEQIKQLVDVGGGLGVNVN 184 (233)
Q Consensus 107 ~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~--~~~~~~~vvDvGGG~G~~~~ 184 (233)
......|.++ .|-++....|+-...++++-...-.. ...++=.+. ++.+ +.++-|| -.-..++
T Consensus 103 ~l~~f~dll~------------kf~eiaK~RP~p~~~yDQgfvTpEtt-v~Rv~lm~~RGDL~g-K~I~vvG-DDDLtsi 167 (354)
T COG1568 103 SLQAFKDLLE------------KFREIAKDRPEPLHQYDQGFVTPETT-VSRVALMYSRGDLEG-KEIFVVG-DDDLTSI 167 (354)
T ss_pred cchhHHHHHH------------HHHHHHhcCCCcchhcccccccccce-eeeeeeeccccCcCC-CeEEEEc-CchhhHH
Confidence 1111222211 11122222333222222211110000 000000111 1222 5677787 6666677
Q ss_pred HHHHHcCCCcEEEeechH-HHhh----ccC--CCCceEEecCcCCCCCC
Q 039903 185 IIISNYLHIKGVNFDLSH-VIQD----SSS--YSGVKHIGGIMLERIPK 226 (233)
Q Consensus 185 ~l~~~~P~l~~~v~Dlp~-v~~~----a~~--~~ri~~~~gD~f~~~P~ 226 (233)
+++-.+---++.|+|+.+ .+.- |++ .++|+.+..|..+|+|+
T Consensus 168 a~aLt~mpk~iaVvDIDERli~fi~k~aee~g~~~ie~~~~Dlr~plpe 216 (354)
T COG1568 168 ALALTGMPKRIAVVDIDERLIKFIEKVAEELGYNNIEAFVFDLRNPLPE 216 (354)
T ss_pred HHHhcCCCceEEEEechHHHHHHHHHHHHHhCccchhheeehhcccChH
Confidence 766655555789999876 3332 233 26799999999999996
No 374
>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=80.47 E-value=1.7 Score=29.23 Aligned_cols=36 Identities=17% Similarity=0.287 Sum_probs=25.0
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT 63 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~ 63 (233)
|+..|+. | .|+|.++||+++|. +.+.+...|..+..
T Consensus 29 LLr~LA~-G--~PVt~~~LA~a~g~----~~e~v~~~L~~~p~ 64 (77)
T PF12324_consen 29 LLRLLAK-G--QPVTVEQLAAALGW----PVEEVRAALAAMPD 64 (77)
T ss_dssp HHHHHTT-T--S-B-HHHHHHHHT------HHHHHHHHHH-TT
T ss_pred HHHHHHc-C--CCcCHHHHHHHHCC----CHHHHHHHHHhCCC
Confidence 6777887 4 69999999999999 88887777776653
No 375
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=80.07 E-value=3.2 Score=33.65 Aligned_cols=42 Identities=10% Similarity=0.182 Sum_probs=37.0
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
|+|-++||..+|+ +...+.|+|+.|...|+++.. .+.+....
T Consensus 184 ~lt~~~iA~~lG~----sr~tvsR~l~~l~~~g~I~~~-----~~~i~i~d 225 (235)
T PRK11161 184 TMTRGDIGNYLGL----TVETISRLLGRFQKSGMLAVK-----GKYITIEN 225 (235)
T ss_pred cccHHHHHHHhCC----cHHHHHHHHHHHHHCCCEEec-----CCEEEEcC
Confidence 6899999999999 999999999999999999985 56666654
No 376
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=79.81 E-value=3.1 Score=37.71 Aligned_cols=53 Identities=21% Similarity=0.278 Sum_probs=40.9
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV 84 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~ 84 (233)
|-..|.+ ||.|+.|||+.+++ +...+.+.|+.| .|+|.....+ ..-+|+++..
T Consensus 5 ~~~~L~~----g~~~~~eL~~~l~~----sq~~~s~~L~~L--~~~V~~~~~g-r~~~Y~l~~~ 57 (442)
T PRK09775 5 LTTLLLQ----GPLSAAELAARLGV----SQATLSRLLAAL--GDQVVRFGKA-RATRYALLRP 57 (442)
T ss_pred HHHHHhc----CCCCHHHHHHHhCC----CHHHHHHHHHHh--hcceeEeccC-ceEEEEeccc
Confidence 4456665 79999999999999 999999999999 8888765332 3346666643
No 377
>PRK01381 Trp operon repressor; Provisional
Probab=79.75 E-value=2.5 Score=29.89 Aligned_cols=40 Identities=15% Similarity=0.205 Sum_probs=31.7
Q ss_pred HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHh
Q 039903 15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLV 62 (233)
Q Consensus 15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~ 62 (233)
.+.+++|+..|.. |+.|-.|||+.+|+ +-..+.|.-+.|-
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 3568899999988 68999999999999 6666666555543
No 378
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=79.71 E-value=1.3 Score=25.75 Aligned_cols=28 Identities=18% Similarity=0.237 Sum_probs=21.6
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVT 63 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~ 63 (233)
.+.|+.|||..+|+ ++..+.|+.+....
T Consensus 7 ~~~~l~~iA~~~g~----S~~~f~r~Fk~~~g 34 (42)
T PF00165_consen 7 QKLTLEDIAEQAGF----SPSYFSRLFKKETG 34 (42)
T ss_dssp SS--HHHHHHHHTS-----HHHHHHHHHHHTS
T ss_pred CCCCHHHHHHHHCC----CHHHHHHHHHHHHC
Confidence 47999999999999 99999999876543
No 379
>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=79.62 E-value=4 Score=33.73 Aligned_cols=45 Identities=20% Similarity=0.254 Sum_probs=39.2
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.|++.|... +|-++..+||+++|+ +...+++=++.|.+.|+++..
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 477777662 258999999999999 999999999999999999986
No 380
>PRK12423 LexA repressor; Provisional
Probab=79.58 E-value=2.9 Score=33.49 Aligned_cols=48 Identities=17% Similarity=0.241 Sum_probs=37.0
Q ss_pred hhChhHHHHh----cCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 18 ELGVFEIIAK----AGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 18 ~lglfd~L~~----~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
+..|++.|.+ .| -+-|..|||+.+|+. +...++..|+.|...|+++..
T Consensus 8 q~~il~~l~~~i~~~g--~~Ps~~eia~~~g~~---s~~~v~~~l~~L~~~G~l~~~ 59 (202)
T PRK12423 8 RAAILAFIRERIAQAG--QPPSLAEIAQAFGFA---SRSVARKHVQALAEAGLIEVV 59 (202)
T ss_pred HHHHHHHHHHHHHHcC--CCCCHHHHHHHhCCC---ChHHHHHHHHHHHHCCCEEec
Confidence 4455665554 22 256999999999941 677889999999999999986
No 381
>PF04989 CmcI: Cephalosporin hydroxylase; InterPro: IPR007072 This entry contains Rhamnosyl O-methyltransferase which catalyses the O-methylation of the hydroxyl group located on C-2 of the first rhamnosyl residue linked to the phenolic group of glycosylated phenolphthiocerol dimycocerosates (PGL) and p-hydroxybenzoic acid derivatives (p-HBAD) []. Members of this family are about 220 amino acids long. It also includes the CmcI protein O85726 from SWISSPROT, which is presumed to represent the cephalosporin-7--hydroxylase []. However this has not been experimentally verified.; GO: 0008168 methyltransferase activity, 0008610 lipid biosynthetic process; PDB: 2BR4_B 2BR3_E 2BR5_E 2BM8_J 2BM9_E.
Probab=79.45 E-value=3.1 Score=33.61 Aligned_cols=55 Identities=11% Similarity=0.119 Sum_probs=31.1
Q ss_pred CcceEEEecCCccHH---HHHHHHHc-CCCcEEEeech--HHHhhccCC----CCceEEecCcCC
Q 039903 168 QIKQLVDVGGGLGVN---VNIIISNY-LHIKGVNFDLS--HVIQDSSSY----SGVKHIGGIMLE 222 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~---~~~l~~~~-P~l~~~v~Dlp--~v~~~a~~~----~ri~~~~gD~f~ 222 (233)
++.+|+.+|--+|.- ...+++.. ++.+++.+|+. ..-..+.+. +||+++.||--+
T Consensus 32 kPd~IIE~Gi~~GGSli~~A~ml~~~~~~~~VigiDIdir~~~~~a~e~hp~~~rI~~i~Gds~d 96 (206)
T PF04989_consen 32 KPDLIIETGIAHGGSLIFWASMLELLGGKGKVIGIDIDIRPHNRKAIESHPMSPRITFIQGDSID 96 (206)
T ss_dssp --SEEEEE--TTSHHHHHHHHHHHHTT---EEEEEES-GTT--S-GGGG----TTEEEEES-SSS
T ss_pred CCCeEEEEecCCCchHHHHHHHHHHhCCCceEEEEeCCcchhchHHHhhccccCceEEEECCCCC
Confidence 468999999766654 44556666 88899999982 222222222 899999999875
No 382
>PF02981 FokI_N: Restriction endonuclease FokI, recognition domain; InterPro: IPR004234 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Thie entry represents the type IIS restriction endonuclease FokI (3.1.21.4 from EC), which is a member of an unusual class of bipartite restriction enzymes that recognise a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence []. FokI contains amino- and carboxy-terminal domains corresponding to the DNA-recognition and cleavage functions (IPR004233 from INTERPRO), respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP []. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1FOK_A 2FOK_B.
Probab=79.23 E-value=2.5 Score=31.79 Aligned_cols=36 Identities=19% Similarity=0.334 Sum_probs=30.1
Q ss_pred hHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 53 MLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 53 ~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
.-.-.||..+++||++.+. +.++|.+|.+|+.+...
T Consensus 108 ~Ad~flrwAvslgfl~~~~---~~Dtf~IT~lG~~~~~~ 143 (145)
T PF02981_consen 108 TADGFLRWAVSLGFLDYDR---ETDTFSITELGKKYVKS 143 (145)
T ss_dssp HHHHHHHHHHHTTSEEEET---TTTEEEE-HHHHHHHHS
T ss_pred CccceeeeeeeeCceeecc---CCCEEEeehhHHHHhhc
Confidence 4567899999999999987 68999999999988753
No 383
>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=79.01 E-value=8.5 Score=27.06 Aligned_cols=67 Identities=10% Similarity=0.124 Sum_probs=46.4
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCC----CCCChhhHHHHHHHHhcCCceeeec--c-CC-CCCceeccHhhhHhhcC
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSS----NPNAAVMLDRILRLLVTHRVLRCTS--A-GD-DQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~----~~~~~~~l~rlL~~L~~~gll~~~~--~-~~-~~~~y~lt~~s~~l~~~ 91 (233)
|.-.|.. +|.+--||++.++-. -+.++..+.++|+-|...|+++... . ++ ....|++|+.|+.+...
T Consensus 9 iL~~L~~----~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~ 83 (100)
T TIGR03433 9 ILKTLSL----GPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAA 83 (100)
T ss_pred HHHHHhc----CCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHH
Confidence 4445554 578888888875220 0228889999999999999999731 1 11 22579999999876644
No 384
>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=78.63 E-value=3.3 Score=32.62 Aligned_cols=33 Identities=21% Similarity=0.227 Sum_probs=30.7
Q ss_pred CHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903 35 SAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTS 71 (233)
Q Consensus 35 t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~ 71 (233)
|-.+||..+ |+ +++.++|.++.|+..|++...+
T Consensus 72 SN~~La~r~~G~----s~~tlrR~l~~LveaGLI~rrD 105 (177)
T PF03428_consen 72 SNAQLAERLNGM----SERTLRRHLARLVEAGLIVRRD 105 (177)
T ss_pred CHHHHHHHHcCC----CHHHHHHHHHHHHHCCCeeecc
Confidence 668999999 99 9999999999999999999853
No 385
>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=78.62 E-value=3.7 Score=34.41 Aligned_cols=37 Identities=16% Similarity=0.158 Sum_probs=32.2
Q ss_pred ccCcceEEEecCCccHHHHHHHHHc-----CCCcEEEeechH
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNY-----LHIKGVNFDLSH 202 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~-----P~l~~~v~Dlp~ 202 (233)
+.+...+|+.|+|.|.++..+.+.. +..+++++|+..
T Consensus 16 l~~~~~~vEfGaGrg~LS~~v~~~~~~~~~~~~~~~lIDR~~ 57 (259)
T PF05206_consen 16 LNPDSCFVEFGAGRGELSRWVAQALQEDKPSNSRFVLIDRAS 57 (259)
T ss_pred CCCCCEEEEECCCchHHHHHHHHHhhhcccCCccEEEEecCc
Confidence 5667899999999999999999998 667899999853
No 386
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=78.54 E-value=5.7 Score=26.64 Aligned_cols=59 Identities=10% Similarity=0.130 Sum_probs=41.8
Q ss_pred hhChhHHHHhc--CCCCCCCHHHHHHhCCCCCCCChhhHHHHH-HHHhcCCceeeeccCCCCCceeccHhhhH
Q 039903 18 ELGVFEIIAKA--GPTAKISAVEIAAQMPSSNPNAAVMLDRIL-RLLVTHRVLRCTSAGDDQRLYGLAHVAKY 87 (233)
Q Consensus 18 ~lglfd~L~~~--~~~~~~t~~elA~~~~~~~~~~~~~l~rlL-~~L~~~gll~~~~~~~~~~~y~lt~~s~~ 87 (233)
+..+.+.|.+. | ||..++-||..++. +.+-+..+. -+|...|++.++ ..|+ .+|+.+..
T Consensus 10 D~~yL~~l~~~f~g--gPvGl~tlA~~l~e----d~~Tie~v~EPyLiq~G~I~RT----~rGR-~~T~~a~~ 71 (76)
T PF05491_consen 10 DRRYLKTLIENFKG--GPVGLDTLAAALGE----DKETIEDVIEPYLIQIGFIQRT----PRGR-VATPKAYE 71 (76)
T ss_dssp HHHHHHHHHHCSTT--S-B-HHHHHHHTTS-----HHHHHHTTHHHHHHTTSEEEE----TTEE-EE-HHHHH
T ss_pred HHHHHHHHHHHcCC--CCeeHHHHHHHHCC----CHhHHHHHhhHHHHHhhhHhhC----ccHH-HhHHHHHH
Confidence 33456666663 4 79999999999999 888888666 689999999998 5666 56666543
No 387
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=78.39 E-value=4.5 Score=34.35 Aligned_cols=60 Identities=17% Similarity=0.152 Sum_probs=50.1
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhc
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVL 90 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~ 90 (233)
-+|.+|..+.+ ..+...-|+++++ ++..+.+-++.|.. .-+|++. +..+.+|+.|+.|..
T Consensus 5 ~~L~~f~~v~e-----~gs~s~AA~~L~i----SQpavS~~I~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~~ 67 (308)
T PRK10094 5 ETLRTFIAVAE-----TGSFSKAAERLCK----TTATISYRIKLLEENTGVALFFRT-----TRSVTLTAAGEHLLS 67 (308)
T ss_pred HHHHHHHHHHH-----hCCHHHHHHHhcC----CHHHHHHHHHHHHHHhCCEEEeeC-----CCceeECHhHHHHHH
Confidence 35778999998 4599999999999 99999999888876 6788884 778999999977653
No 388
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=78.21 E-value=3.7 Score=32.53 Aligned_cols=34 Identities=24% Similarity=0.406 Sum_probs=32.3
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
++|-.+||+.+|+ +...+.|+|+.|...|++...
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 7888999999999 999999999999999999984
No 389
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=78.15 E-value=4 Score=33.19 Aligned_cols=43 Identities=19% Similarity=0.197 Sum_probs=36.4
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
+.|-.+||..+|+ +...+.|+|+.|...|+++.. ..+++....
T Consensus 179 ~lt~~~IA~~lGi----sretlsR~L~~L~~~GlI~~~----~~~~i~I~D 221 (230)
T PRK09391 179 PMSRRDIADYLGL----TIETVSRALSQLQDRGLIGLS----GARQIELRN 221 (230)
T ss_pred cCCHHHHHHHHCC----CHHHHHHHHHHHHHCCcEEec----CCceEEEcC
Confidence 6788999999999 999999999999999999874 235666543
No 390
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=78.04 E-value=2.4 Score=33.03 Aligned_cols=36 Identities=14% Similarity=0.092 Sum_probs=33.9
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS 71 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~ 71 (233)
+|+|+.||++++|. +...+..-|+-|...|++.+.-
T Consensus 40 ~Pmtl~Ei~E~lg~----Sks~vS~~lkkL~~~~lV~~~~ 75 (177)
T COG1510 40 KPLTLDEIAEALGM----SKSNVSMGLKKLQDWNLVKKVF 75 (177)
T ss_pred CCccHHHHHHHHCC----CcchHHHHHHHHHhcchHHhhh
Confidence 79999999999999 9999999999999999999864
No 391
>COG2520 Predicted methyltransferase [General function prediction only]
Probab=78.01 E-value=2.9 Score=36.44 Aligned_cols=64 Identities=19% Similarity=0.120 Sum_probs=50.3
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC--C-CCCCEEEe
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER--I-PKGDAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~--~-P~~D~~~l 232 (233)
...+|||.=.|-|.|++.++++-.- +++..|+ |.+++..+++ ++|+.+.||-.+- . +.+|-++|
T Consensus 188 ~GE~V~DmFAGVGpfsi~~Ak~g~~-~V~A~diNP~A~~~L~eNi~LN~v~~~v~~i~gD~rev~~~~~~aDrIim 262 (341)
T COG2520 188 EGETVLDMFAGVGPFSIPIAKKGRP-KVYAIDINPDAVEYLKENIRLNKVEGRVEPILGDAREVAPELGVADRIIM 262 (341)
T ss_pred CCCEEEEccCCcccchhhhhhcCCc-eEEEEecCHHHHHHHHHHHHhcCccceeeEEeccHHHhhhccccCCEEEe
Confidence 3689999999999999999986433 3899998 6677766553 6799999999983 3 44788876
No 392
>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=77.95 E-value=2.4 Score=35.50 Aligned_cols=27 Identities=22% Similarity=0.346 Sum_probs=23.6
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCc
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIK 194 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~ 194 (233)
+..+++|||.|.|.....++..|.++.
T Consensus 94 ~~~~lLDlGAGdG~VT~~l~~~f~~v~ 120 (265)
T PF05219_consen 94 KDKSLLDLGAGDGEVTERLAPLFKEVY 120 (265)
T ss_pred cCCceEEecCCCcHHHHHHHhhcceEE
Confidence 457899999999999999999888843
No 393
>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=77.90 E-value=4.3 Score=31.61 Aligned_cols=34 Identities=24% Similarity=0.346 Sum_probs=32.5
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
|.|-+|||..+|+ +...+.|+|+.|...|+++..
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 999999999999999999985
No 394
>PF03059 NAS: Nicotianamine synthase protein; InterPro: IPR004298 Nicotianamine synthase 2.5.1.43 from EC catalyzes the trimerization of S-adenosylmethionine to yield one molecule of nicotianamine. Nicotianamine has an important role in plant iron uptake mechanisms. Plants adopt two strategies (termed I and II) of iron acquisition. Strategy I is adopted by all higher plants except graminaceous plants, which adopt strategy II [, ]. In strategy I plants, the role of nicotianamine is not fully determined: possible roles include the formation of more stable complexes with ferrous than with ferric ion, which might serve as a sensor of the physiological status of iron within a plant, or which might be involved in the transport of iron []. In strategy II (graminaceous) plants, nicotianamine is the key intermediate (and nicotianamine synthase the key enzyme) in the synthesis of the mugineic family (the only known family in plants) of phytosiderophores. Phytosiderophores are iron chelators whose secretion by the roots is greatly increased in instances of iron deficiency []. The 3D structures of five example NAS from Methanothermobacter thermautotrophicus reveal the monomer to consist of a five-helical bundle N-terminal domain on top of a classic Rossmann fold C-terminal domain. The N-terminal domain is unique to the NAS family, whereas the C-terminal domain is homologous to the class I family of SAM-dependent methyltransferases. An active site is created at the interface of the two domains, at the rim of a large cavity that corresponds to the nucleotide binding site such as is found in other proteins adopting a Rossmann fold [].; GO: 0030410 nicotianamine synthase activity, 0030418 nicotianamine biosynthetic process; PDB: 3O31_B 3FPH_A 3FPJ_A 3FPE_B 3FPF_B 3FPG_B.
Probab=77.73 E-value=3.9 Score=34.57 Aligned_cols=65 Identities=11% Similarity=0.131 Sum_probs=37.9
Q ss_pred CcceEEEecCCcc-HHHHHHHHHc-CCCcEEEeec-hHHHhhccC--------CCCceEEecCcCC-CCC--CCCEEEe
Q 039903 168 QIKQLVDVGGGLG-VNVNIIISNY-LHIKGVNFDL-SHVIQDSSS--------YSGVKHIGGIMLE-RIP--KGDAILI 232 (233)
Q Consensus 168 ~~~~vvDvGGG~G-~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~--------~~ri~~~~gD~f~-~~P--~~D~~~l 232 (233)
.+++|+=||+|.= .-++-+++++ ++.+++++|+ |++++.+++ ..|++|+.+|..+ +.. .-|+|++
T Consensus 120 ~p~rVaFIGSGPLPlT~i~la~~~~~~~~v~~iD~d~~A~~~a~~lv~~~~~L~~~m~f~~~d~~~~~~dl~~~DvV~l 198 (276)
T PF03059_consen 120 PPSRVAFIGSGPLPLTSIVLAKQHGPGARVHNIDIDPEANELARRLVASDLGLSKRMSFITADVLDVTYDLKEYDVVFL 198 (276)
T ss_dssp ---EEEEE---SS-HHHHHHH--HTT--EEEEEESSHHHHHHHHHHHH---HH-SSEEEEES-GGGG-GG----SEEEE
T ss_pred ccceEEEEcCCCcchHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHhhcccccCCeEEEecchhccccccccCCEEEE
Confidence 3469999999965 4566666655 6888999998 557776654 1689999999986 332 2388876
No 395
>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=77.63 E-value=6.4 Score=24.53 Aligned_cols=46 Identities=15% Similarity=0.230 Sum_probs=33.8
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCcee
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYG 80 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~ 80 (233)
+.|.+-..| =.|...+|+.+++ ++....++++-| |+-+-+ +-++|+
T Consensus 4 Lidll~~~P---~Vsa~mva~~L~v----T~~~A~~li~eL---g~rEiT----Gr~R~R 49 (54)
T PF11972_consen 4 LIDLLLSRP---LVSAPMVAKELGV----TPQAAQRLIAEL---GLREIT----GRGRYR 49 (54)
T ss_pred HHHHHHhCc---cccHHHHHHHhCC----CHHHHHHHHHHh---hceeec----CCcccc
Confidence 567777754 5699999999999 999999988655 442222 466775
No 396
>KOG4058 consensus Uncharacterized conserved protein [Function unknown]
Probab=77.38 E-value=2.6 Score=32.28 Aligned_cols=66 Identities=15% Similarity=0.111 Sum_probs=43.9
Q ss_pred HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC-------CCceEEecCcCC-CCC
Q 039903 158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY-------SGVKHIGGIMLE-RIP 225 (233)
Q Consensus 158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~-------~ri~~~~gD~f~-~~P 225 (233)
.++..++ -.+-.+++|+|.|.|....+.++.. -.+.+..++.+ -+..++-+ .+.+|+--|.|+ .+-
T Consensus 63 nVLSll~-~n~~GklvDlGSGDGRiVlaaar~g-~~~a~GvELNpwLVaysrl~a~R~g~~k~trf~RkdlwK~dl~ 137 (199)
T KOG4058|consen 63 NVLSLLR-GNPKGKLVDLGSGDGRIVLAAARCG-LRPAVGVELNPWLVAYSRLHAWRAGCAKSTRFRRKDLWKVDLR 137 (199)
T ss_pred HHHHHcc-CCCCCcEEeccCCCceeehhhhhhC-CCcCCceeccHHHHHHHHHHHHHHhcccchhhhhhhhhhcccc
Confidence 4455544 2445899999999999888777754 45678888865 34333321 567777778776 443
No 397
>TIGR03439 methyl_EasF probable methyltransferase domain, EasF family. This model represents an uncharacterized domain of about 300 amino acids with homology to S-adenosylmethionine-dependent methyltransferases. Proteins with this domain are exclusively fungal. A few, such as EasF from Neotyphodium lolii, are associated with the biosynthesis of ergot alkaloids, a class of fungal secondary metabolites. EasF may, in fact, be the AdoMet:dimethylallyltryptophan N-methyltransferase, the enzyme that follows tryptophan dimethylallyltransferase (DMATS) in ergot alkaloid biosynthesis. Several other members of this family, including mug158 (meiotically up-regulated gene 158 protein) from Schizosaccharomyces pombe, contain an additional uncharacterized domain DUF323 (pfam03781).
Probab=77.07 E-value=5.7 Score=34.34 Aligned_cols=63 Identities=22% Similarity=0.281 Sum_probs=42.2
Q ss_pred HHHHHhcccccCcceEEEecCCccHHHHHHHHHc----CCCcEEEeechH-HHhhccC------CCCceE--EecCcCC
Q 039903 157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY----LHIKGVNFDLSH-VIQDSSS------YSGVKH--IGGIMLE 222 (233)
Q Consensus 157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~----P~l~~~v~Dlp~-v~~~a~~------~~ri~~--~~gD~f~ 222 (233)
..+++.++ ...++||+|||+|.=...|+++. ...+.+-+|+.. .++.+.. .+.|++ +.|||.+
T Consensus 68 ~~Ia~~i~---~~~~lIELGsG~~~Kt~~LL~aL~~~~~~~~Y~plDIS~~~L~~a~~~L~~~~~p~l~v~~l~gdy~~ 143 (319)
T TIGR03439 68 SDIAASIP---SGSMLVELGSGNLRKVGILLEALERQKKSVDYYALDVSRSELQRTLAELPLGNFSHVRCAGLLGTYDD 143 (319)
T ss_pred HHHHHhcC---CCCEEEEECCCchHHHHHHHHHHHhcCCCceEEEEECCHHHHHHHHHhhhhccCCCeEEEEEEecHHH
Confidence 34555533 44589999999998666655554 356789999874 5554432 255655 7899976
No 398
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=77.05 E-value=4.7 Score=29.69 Aligned_cols=62 Identities=23% Similarity=0.317 Sum_probs=47.1
Q ss_pred HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
+.|.-|.++|=.. ||.|+.||-+.+...+...+.-+.-+|+-|+..|++.... +++.|.-+|
T Consensus 6 ~aE~eVM~ilW~~---~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~k---dgr~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSR---GPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKK---DGRAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHc---CCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhh---cCCeeeeec
Confidence 4566778888777 6999998888777622226778899999999999999875 456676555
No 399
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=76.95 E-value=4.6 Score=31.81 Aligned_cols=43 Identities=16% Similarity=0.149 Sum_probs=36.9
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV 84 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~ 84 (233)
+.|-++||..+|+ ....+.|+|+-|...|+++. +.+.......
T Consensus 149 ~~t~~~iA~~lG~----tretvsR~l~~l~~~g~I~~-----~~~~i~I~d~ 191 (202)
T PRK13918 149 YATHDELAAAVGS----VRETVTKVIGELSREGYIRS-----GYGKIQLLDL 191 (202)
T ss_pred cCCHHHHHHHhCc----cHHHHHHHHHHHHHCCCEEc-----CCCEEEEECH
Confidence 6899999999999 99999999999999999997 3566655433
No 400
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=76.91 E-value=4 Score=31.02 Aligned_cols=43 Identities=16% Similarity=0.201 Sum_probs=36.1
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc--CCceee
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT--HRVLRC 69 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~--~gll~~ 69 (233)
-|+|+|-.. +.+|-++||+.+|+ +...++++|..|.. +++...
T Consensus 5 ~v~d~L~~~---~~~~dedLa~~l~i----~~n~vRkiL~~L~ed~~~~~~~ 49 (147)
T smart00531 5 LVLDALMRN---GCVTEEDLAELLGI----KQKQLRKILYLLYDEKLIKIDY 49 (147)
T ss_pred eehHHHHhc---CCcCHHHHHHHhCC----CHHHHHHHHHHHHhhhcchhhe
Confidence 467877776 58999999999999 99999999999999 444443
No 401
>COG3897 Predicted methyltransferase [General function prediction only]
Probab=76.53 E-value=9.2 Score=30.75 Aligned_cols=65 Identities=17% Similarity=0.129 Sum_probs=42.3
Q ss_pred ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC-----CCceEEecCcCCCCCC-CCEEEe
Q 039903 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY-----SGVKHIGGIMLERIPK-GDAILI 232 (233)
Q Consensus 166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~-----~ri~~~~gD~f~~~P~-~D~~~l 232 (233)
+=..++|+|.|.|+|..+++-++.-- ...+.-|.+. .++.++-+ -.|.++.-|..- .|. .|++++
T Consensus 77 tVrgkrVLd~gagsgLvaIAaa~aGA-~~v~a~d~~P~~~~ai~lNa~angv~i~~~~~d~~g-~~~~~Dl~La 148 (218)
T COG3897 77 TVRGKRVLDLGAGSGLVAIAAARAGA-AEVVAADIDPWLEQAIRLNAAANGVSILFTHADLIG-SPPAFDLLLA 148 (218)
T ss_pred ccccceeeecccccChHHHHHHHhhh-HHHHhcCCChHHHHHhhcchhhccceeEEeeccccC-CCcceeEEEe
Confidence 44569999999999999888777632 2344445543 33333322 357787778777 444 488875
No 402
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=76.34 E-value=10 Score=26.78 Aligned_cols=65 Identities=11% Similarity=0.071 Sum_probs=49.2
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhc
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVL 90 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~ 90 (233)
-++.+|..+.+. -|...-|+.+++ ++..+.+-++.|.. .-+|++...+..++.+.+|+.+..|..
T Consensus 5 ~~l~~~~av~~~-----gSis~AA~~L~i----S~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~~ 72 (99)
T TIGR00637 5 RRVALLKAIARM-----GSISQAAKDAGI----SYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLIQ 72 (99)
T ss_pred HHHHHHHHHHHh-----CCHHHHHHHHCC----CHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHHH
Confidence 356788899884 588999999999 99999888877766 556777521001458999999998873
No 403
>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=76.20 E-value=4.3 Score=29.55 Aligned_cols=35 Identities=20% Similarity=0.237 Sum_probs=32.5
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.+.|++|||+.+++ +..-++.|+.-|...|++...
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 38999999999999 898999999999999999975
No 404
>COG4754 Uncharacterized conserved protein [Function unknown]
Probab=76.15 E-value=7.5 Score=29.45 Aligned_cols=66 Identities=11% Similarity=0.039 Sum_probs=55.6
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCCC
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRD 93 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~~ 93 (233)
=.||.+.+... -+|...+..|++..++ +-+-|--++..+..+|+++- +.|-..+|+.++.++....
T Consensus 14 l~GLL~~l~n~-fnGraDl~~L~~e~~v----didDL~piv~ta~~Lglv~~-----e~GDiilT~~Gk~~v~~~~ 79 (157)
T COG4754 14 LVGLLYVLNNI-FNGRADLPYLEKEMEV----DIDDLMPIVETASLLGLVTA-----ESGDIILTDEGKEYVESPI 79 (157)
T ss_pred HHHHHHHHHHH-hCCcccchhHHHHhCC----ChhhHHHHHHHHHhcCceec-----cCCCEEEehhhHHHHhCCh
Confidence 34677777763 2268999999999999 99999999999999999998 5778999999999887643
No 405
>PLN02668 indole-3-acetate carboxyl methyltransferase
Probab=75.95 E-value=4.8 Score=35.77 Aligned_cols=34 Identities=24% Similarity=0.203 Sum_probs=24.2
Q ss_pred CcceEEEecCCccHHHH--------HHHHHc-------CCCcEEEeech
Q 039903 168 QIKQLVDVGGGLGVNVN--------IIISNY-------LHIKGVNFDLS 201 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~--------~l~~~~-------P~l~~~v~Dlp 201 (233)
+.-+|+|+|||+|.++. ++.+++ |.+++..=|+|
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 45689999999996542 333333 56777777998
No 406
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=75.92 E-value=4.5 Score=26.68 Aligned_cols=49 Identities=18% Similarity=0.215 Sum_probs=33.9
Q ss_pred CCCCH---HHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903 32 AKISA---VEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA 85 (233)
Q Consensus 32 ~~~t~---~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s 85 (233)
++++. -++.+..|+ ++..++.=|.=|+..|+|+....+ ....|++|+.+
T Consensus 19 ~~i~~~~Li~ll~~~Gv----~e~avR~alsRl~~~G~L~~~r~G-r~~~Y~Lt~~g 70 (70)
T PF07848_consen 19 GWIWVASLIRLLAAFGV----SESAVRTALSRLVRRGWLESERRG-RRSYYRLTERG 70 (70)
T ss_dssp S-EEHHHHHHHHCCTT------HHHHHHHHHHHHHTTSEEEECCC-TEEEEEE-HHH
T ss_pred CceeHHHHHHHHHHcCC----ChHHHHHHHHHHHHcCceeeeecC-ccceEeeCCCC
Confidence 45544 466778889 999999999999999999987321 23379998753
No 407
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=75.87 E-value=5.4 Score=31.46 Aligned_cols=49 Identities=18% Similarity=0.319 Sum_probs=41.9
Q ss_pred HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
-++..|.|.|...| ...|+-+||+++|+ +...+.|-|--|...|.|...
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 35677999999874 26999999999999 899999999999998888764
No 408
>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=75.83 E-value=2.8 Score=27.94 Aligned_cols=34 Identities=21% Similarity=0.067 Sum_probs=29.9
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC 69 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~ 69 (233)
...|..|||+.+++ ++..+..+++.+...|.+.+
T Consensus 31 eGlS~kEIAe~LGI----S~~TVk~~l~~~~~~~~~~~ 64 (73)
T TIGR03879 31 AGKTASEIAEELGR----TEQTVRNHLKGETKAGGLVK 64 (73)
T ss_pred cCCCHHHHHHHHCc----CHHHHHHHHhcCcccchHHH
Confidence 37999999999999 99999999998888877654
No 409
>PF04445 SAM_MT: Putative SAM-dependent methyltransferase; InterPro: IPR007536 This family of proteins is functionally uncharacterised.; PDB: 2PGX_A 2OYR_A 2R6Z_A 2PKW_A.
Probab=75.74 E-value=5.4 Score=32.86 Aligned_cols=73 Identities=22% Similarity=0.263 Sum_probs=44.8
Q ss_pred HHHHHhcccccCc--ceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhcc--------CC--------CCceEEec
Q 039903 157 NRIIDSSKGFEQI--KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSS--------SY--------SGVKHIGG 218 (233)
Q Consensus 157 ~~~~~~~~~~~~~--~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~--------~~--------~ri~~~~g 218 (233)
+.++++.. .++. .+|+|+=.|-|.-+.-++.. ..+++.++...++...- .. .||+.+.+
T Consensus 63 ~~l~kA~G-lk~~~~~~VLDaTaGLG~Da~vlA~~--G~~V~~lErspvia~Ll~dGL~r~~~~~~~~~~~~~ri~l~~~ 139 (234)
T PF04445_consen 63 DPLAKAVG-LKPGMRPSVLDATAGLGRDAFVLASL--GCKVTGLERSPVIAALLKDGLKRAQQDPELLAEAMRRIQLIHG 139 (234)
T ss_dssp SHHHHHTT--BTTB---EEETT-TTSHHHHHHHHH--T--EEEEE--HHHHHHHHHHHHHHHHSTTTHHHHHHHEEEEES
T ss_pred cHHHHHhC-CCCCCCCEEEECCCcchHHHHHHHcc--CCeEEEEECCHHHHHHHHHHHHHHHhCcHhHHHHHhCCEEEcC
Confidence 45666664 4443 49999999999988888754 66899999876654221 11 48999999
Q ss_pred CcCC--CCCC--CCEEEe
Q 039903 219 IMLE--RIPK--GDAILI 232 (233)
Q Consensus 219 D~f~--~~P~--~D~~~l 232 (233)
|..+ ..|. -|+|.|
T Consensus 140 d~~~~L~~~~~s~DVVY~ 157 (234)
T PF04445_consen 140 DALEYLRQPDNSFDVVYF 157 (234)
T ss_dssp -CCCHCCCHSS--SEEEE
T ss_pred CHHHHHhhcCCCCCEEEE
Confidence 9988 3443 398876
No 410
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=75.68 E-value=8.4 Score=30.66 Aligned_cols=42 Identities=26% Similarity=0.343 Sum_probs=35.7
Q ss_pred hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
|.+..+|+.. +|+|..||++..|+ +. ..+++.|...|++.+.
T Consensus 93 LEtLaiIay~---qPiTr~eI~~irGv----~~---~~ii~~L~~~gLI~e~ 134 (188)
T PRK00135 93 LEVLAIIAYK---QPITRIEIDEIRGV----NS---DGALQTLLAKGLIKEV 134 (188)
T ss_pred HHHHHHHHHc---CCcCHHHHHHHHCC----CH---HHHHHHHHHCCCeEEc
Confidence 4467777776 69999999999999 65 7899999999999863
No 411
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=75.64 E-value=5.4 Score=31.36 Aligned_cols=44 Identities=16% Similarity=0.198 Sum_probs=38.8
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
-|++.|.+. |-.|=+|||..+|+ ...-++|+|..|...|++...
T Consensus 22 ~v~~~l~~k---ge~tDeela~~l~i----~~~~vrriL~~L~e~~li~~~ 65 (176)
T COG1675 22 LVVDALLEK---GELTDEELAELLGI----KKNEVRRILYALYEDGLISYR 65 (176)
T ss_pred HHHHHHHhc---CCcChHHHHHHhCc----cHHHHHHHHHHHHhCCceEEE
Confidence 467777774 47999999999999 999999999999999999954
No 412
>PF12692 Methyltransf_17: S-adenosyl-L-methionine methyltransferase; PDB: 3IHT_B.
Probab=75.63 E-value=6.4 Score=30.11 Aligned_cols=79 Identities=18% Similarity=0.166 Sum_probs=40.5
Q ss_pred HHHHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcC
Q 039903 142 GVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIML 221 (233)
Q Consensus 142 ~~f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f 221 (233)
+.|.+-|.+..... ..+.....+. ..-|+++|=|+|-.=-.|.+.+|+-++.|||+.-.+.-...-+.=.++-||+.
T Consensus 5 Dsfi~RmtaQR~~L-~~a~~~v~~~--~G~VlElGLGNGRTydHLRe~~p~R~I~vfDR~l~~hp~~~P~~~~~ilGdi~ 81 (160)
T PF12692_consen 5 DSFIRRMTAQRDCL-NWAAAQVAGL--PGPVLELGLGNGRTYDHLREIFPDRRIYVFDRALACHPSSTPPEEDLILGDIR 81 (160)
T ss_dssp HHHHHHHHHHHHHH-HHHHHHTTT----S-EEEE--TTSHHHHHHHHH--SS-EEEEESS--S-GGG---GGGEEES-HH
T ss_pred HHHHHHHHHHHHHH-HHHHHHhcCC--CCceEEeccCCCccHHHHHHhCCCCeEEEEeeecccCCCCCCchHheeeccHH
Confidence 34555555433221 2233333312 26799999999999999999999999999998543332222233355666666
Q ss_pred CC
Q 039903 222 ER 223 (233)
Q Consensus 222 ~~ 223 (233)
+.
T Consensus 82 ~t 83 (160)
T PF12692_consen 82 ET 83 (160)
T ss_dssp HH
T ss_pred HH
Confidence 53
No 413
>PF05971 Methyltransf_10: Protein of unknown function (DUF890); InterPro: IPR010286 This family consists of several conserved hypothetical proteins from both eukaryotes and prokaryotes. The function of members of this family are unknown but are predicted to be SAM-dependent methyltransferases.; GO: 0008168 methyltransferase activity; PDB: 2H00_A.
Probab=75.63 E-value=4.7 Score=34.50 Aligned_cols=56 Identities=14% Similarity=0.146 Sum_probs=34.5
Q ss_pred CcceEEEecCCccH-HHHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEE----ecCcCCCC
Q 039903 168 QIKQLVDVGGGLGV-NVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHI----GGIMLERI 224 (233)
Q Consensus 168 ~~~~vvDvGGG~G~-~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~----~gD~f~~~ 224 (233)
...+.+|||.|.-. |...-++.| +.+++.-|+. ..++.|+++ +||+.+ ..++|..+
T Consensus 102 ~~v~glDIGTGAscIYpLLg~~~~-~W~fvaTdID~~sl~~A~~nv~~N~~L~~~I~l~~~~~~~~i~~~i 171 (299)
T PF05971_consen 102 EKVRGLDIGTGASCIYPLLGAKLY-GWSFVATDIDPKSLESARENVERNPNLESRIELRKQKNPDNIFDGI 171 (299)
T ss_dssp ---EEEEES-TTTTHHHHHHHHHH---EEEEEES-HHHHHHHHHHHHHT-T-TTTEEEEE--ST-SSTTTS
T ss_pred cceEeecCCccHHHHHHHHhhhhc-CCeEEEecCCHHHHHHHHHHHHhccccccceEEEEcCCccccchhh
Confidence 35789999999885 455555555 8999999985 477777652 678876 33567643
No 414
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=75.62 E-value=7.3 Score=32.39 Aligned_cols=60 Identities=10% Similarity=0.030 Sum_probs=50.3
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
++..|..+.+. .+...-|+++++ ++..+.+-++.|.. .-+|++. ...+.+|+.|+.|...
T Consensus 5 ~l~~f~~v~~~-----gs~s~AA~~L~i----sqpavS~~I~~LE~~lG~~LF~R~-----~r~~~lT~~G~~l~~~ 67 (275)
T PRK03601 5 LLKTFLEVSRT-----RHFGRAAESLYL----TQSAVSFRIRQLENQLGVNLFTRH-----RNNIRLTAAGERLLPY 67 (275)
T ss_pred HHHHHHHHHHc-----CCHHHHHHHhCC----ChHHHHHHHHHHHHHhCCceEEEC-----CCceEECHhHHHHHHH
Confidence 57789999984 588899999999 89999888888776 7789985 6889999999877644
No 415
>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=75.30 E-value=4.4 Score=34.31 Aligned_cols=46 Identities=15% Similarity=0.174 Sum_probs=38.0
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHH-HHhcCCceeeeccCCCCCceeccHhhh
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILR-LLVTHRVLRCTSAGDDQRLYGLAHVAK 86 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~-~L~~~gll~~~~~~~~~~~y~lt~~s~ 86 (233)
++.++.+||+.+|. ++..+.++++ .|+..|++..+ +.|++ .|..+.
T Consensus 254 ~~~~~~~ia~~lg~----~~~~~~~~~e~~Li~~~li~~~----~~g~~-~~~~~~ 300 (305)
T TIGR00635 254 GPVGLKTLAAALGE----DADTIEDVYEPYLLQIGFLQRT----PRGRI-ATELAY 300 (305)
T ss_pred CcccHHHHHHHhCC----CcchHHHhhhHHHHHcCCcccC----Cchhh-hhHHHH
Confidence 58999999999999 9999999999 79999999875 45555 454444
No 416
>PRK09954 putative kinase; Provisional
Probab=75.26 E-value=4.4 Score=35.37 Aligned_cols=44 Identities=16% Similarity=0.192 Sum_probs=39.5
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCcee
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLR 68 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~ 68 (233)
+..|.+.|.++ +.+|..|||+.+++ +...+.+.++-|...|++.
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 44688888887 48999999999999 9999999999999999985
No 417
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=74.92 E-value=8.4 Score=28.25 Aligned_cols=47 Identities=15% Similarity=0.029 Sum_probs=41.1
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhh
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAK 86 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~ 86 (233)
-|.+.++||..++- +..-++.-|..+...|+++.. +++.|.++....
T Consensus 50 ipy~~e~LA~~~~~----~~~~V~~Al~~f~k~glIe~~----d~g~i~i~~~~~ 96 (119)
T TIGR01714 50 APYNAEMLATMFNR----NVGDIRITLQTLESLGLIEKK----NNGDIFLENWEK 96 (119)
T ss_pred CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe----cCCcEEehhHHH
Confidence 48999999999999 999999999999999999997 567787766443
No 418
>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=74.54 E-value=8.5 Score=27.41 Aligned_cols=42 Identities=14% Similarity=0.074 Sum_probs=33.1
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
..+|.+..+. +..|+.|+|+.+++ .+..+..+|+ ..|++-+.
T Consensus 13 ~~~d~~~~~~--~~~ti~~~AK~L~i----~~~~l~~~Lr---~~g~l~~~ 54 (111)
T PF03374_consen 13 EFYDAFVDSD--GLYTIREAAKLLGI----GRNKLFQWLR---EKGWLYRR 54 (111)
T ss_pred HHHHHHHcCC--CCccHHHHHHHhCC----CHHHHHHHHH---hCCceEEC
Confidence 4567777654 78999999999999 8777666665 49999884
No 419
>smart00753 PAM PCI/PINT associated module.
Probab=74.34 E-value=11 Score=25.37 Aligned_cols=52 Identities=6% Similarity=0.114 Sum_probs=41.4
Q ss_pred HHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 12 AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 12 ~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
......+..++...... ..++.++||+.+++ +.+.+++++.-+...|.+.-.
T Consensus 6 l~~~~~~~~l~~l~~~y---~~i~~~~i~~~~~l----~~~~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00753 6 LQRKIRLTNLLQLSEPY---SSISLSDLAKLLGL----SVPEVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HHHHHHHHHHHHHhHHh---ceeeHHHHHHHhCc----CHHHHHHHHHHHHHCCCeEEE
Confidence 44455566666666654 58999999999999 888999999999999988743
No 420
>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=74.34 E-value=11 Score=25.37 Aligned_cols=52 Identities=6% Similarity=0.114 Sum_probs=41.4
Q ss_pred HHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 12 AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 12 ~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
......+..++...... ..++.++||+.+++ +.+.+++++.-+...|.+.-.
T Consensus 6 l~~~~~~~~l~~l~~~y---~~i~~~~i~~~~~l----~~~~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00088 6 LQRKIRLTNLLQLSEPY---SSISLSDLAKLLGL----SVPEVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HHHHHHHHHHHHHhHHh---ceeeHHHHHHHhCc----CHHHHHHHHHHHHHCCCeEEE
Confidence 44455566666666654 58999999999999 888999999999999988743
No 421
>COG1088 RfbB dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]
Probab=73.65 E-value=7.6 Score=33.29 Aligned_cols=48 Identities=23% Similarity=0.290 Sum_probs=35.6
Q ss_pred ecCCccHH----HHHHHHHcCCCcEEEeec------hHHHhhccCCCCceEEecCcCC
Q 039903 175 VGGGLGVN----VNIIISNYLHIKGVNFDL------SHVIQDSSSYSGVKHIGGIMLE 222 (233)
Q Consensus 175 vGGG~G~~----~~~l~~~~P~l~~~v~Dl------p~v~~~a~~~~ri~~~~gD~f~ 222 (233)
|-||.|+. ...+++++|+.+++++|- ++.+......+|++|+.||.-+
T Consensus 5 VTGGaGFIGsnfvr~~~~~~~d~~v~~~DkLTYAgn~~~l~~~~~~~~~~fv~~DI~D 62 (340)
T COG1088 5 VTGGAGFIGSNFVRYILNKHPDDHVVNLDKLTYAGNLENLADVEDSPRYRFVQGDICD 62 (340)
T ss_pred EecCcchHHHHHHHHHHhcCCCceEEEEecccccCCHHHHHhhhcCCCceEEeccccC
Confidence 45788875 456677899999999994 3444444445899999999875
No 422
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=73.51 E-value=8.3 Score=31.69 Aligned_cols=59 Identities=15% Similarity=0.147 Sum_probs=49.0
Q ss_pred hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
|..|..+.+. .|...-|+++++ ++..+.+-++.|.. .-+|++. +....+|+.|..|...
T Consensus 2 l~~f~~v~~~-----gs~~~AA~~L~i----sqsavS~~i~~LE~~lg~~Lf~R~-----~~~~~lT~~G~~l~~~ 63 (279)
T TIGR03339 2 LKAFHAVARC-----GSFTRAAERLGL----SQPTVTDQVRKLEERYGVELFHRN-----GRRLELTDAGHRLLPI 63 (279)
T ss_pred chhhHHHHhc-----CCHHHHHHHhcC----CchHHHHHHHHHHHHhCCccEEEc-----CCeEEEChhHHHHHHH
Confidence 6778999984 589999999999 89999888888776 6788884 7789999999776543
No 423
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=73.50 E-value=4.7 Score=27.92 Aligned_cols=57 Identities=7% Similarity=0.047 Sum_probs=35.0
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC---CCCceecc
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD---DQRLYGLA 82 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~---~~~~y~lt 82 (233)
+|=|.-++.. +..++..|.+.+|. +.+-++..+.+|..+|+-.+-.-++ ..|.|+++
T Consensus 10 rlyla~li~~----~~~nvp~L~~~TGm----PrRT~Qd~i~aL~~~~I~~~Fvq~G~R~~~GyY~i~ 69 (90)
T PF09904_consen 10 RLYLAYLIDS----GERNVPALMEATGM----PRRTIQDTIKALPELGIECEFVQDGERNNAGYYRIS 69 (90)
T ss_dssp HHHHHHHHHH----S-B-HHHHHHHH-------HHHHHHHHHGGGGGT-EEEEE--TTS-S--EEEEE
T ss_pred HHHHHHHHhc----CCccHHHHHHHhCC----CHhHHHHHHHHhhcCCeEEEEEecCccCCCCcEEee
Confidence 4445555665 45599999999999 9999999999999999977621111 34566654
No 424
>PRK00215 LexA repressor; Validated
Probab=73.38 E-value=9.6 Score=30.41 Aligned_cols=36 Identities=19% Similarity=0.142 Sum_probs=31.8
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.+.|..|||+.+++. +...+.|+|+.|...|++++.
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 478999999999972 467899999999999999986
No 425
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=73.22 E-value=6.5 Score=29.12 Aligned_cols=39 Identities=13% Similarity=0.174 Sum_probs=34.6
Q ss_pred CCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCce
Q 039903 34 ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLY 79 (233)
Q Consensus 34 ~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y 79 (233)
-|+.|+|..+++ ++.-+.|-.+-|...|++.... +.|.|
T Consensus 36 PSvRelA~~~~V----NpnTv~raY~eLE~eG~i~t~r---g~G~f 74 (125)
T COG1725 36 PSVRELAKDLGV----NPNTVQRAYQELEREGIVETKR---GKGTF 74 (125)
T ss_pred CcHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEec---CeeEE
Confidence 388999999999 9999999999999999999874 45666
No 426
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=72.97 E-value=4.3 Score=26.79 Aligned_cols=57 Identities=11% Similarity=0.144 Sum_probs=39.9
Q ss_pred CCCCHHHHHHhCCCC--C--CCChhhHHHHHHHHhcCCceeeeccCC----CCCceeccHhhhHh
Q 039903 32 AKISAVEIAAQMPSS--N--PNAAVMLDRILRLLVTHRVLRCTSAGD----DQRLYGLAHVAKYF 88 (233)
Q Consensus 32 ~~~t~~elA~~~~~~--~--~~~~~~l~rlL~~L~~~gll~~~~~~~----~~~~y~lt~~s~~l 88 (233)
+|.+--||.+.+.-. . +.++..++..|+-|...|+++...... ....|++|+.|+..
T Consensus 8 ~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~ 72 (75)
T PF03551_consen 8 GPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREE 72 (75)
T ss_dssp S-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHH
T ss_pred CCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHH
Confidence 477777777665531 0 227889999999999999999764320 12469999998753
No 427
>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=72.79 E-value=4 Score=36.12 Aligned_cols=46 Identities=17% Similarity=0.282 Sum_probs=36.2
Q ss_pred HHHHHHhcccccCcceEEEecCCccH----HHHHHHHHc---CCCcEEEeechH
Q 039903 156 TNRIIDSSKGFEQIKQLVDVGGGLGV----NVNIIISNY---LHIKGVNFDLSH 202 (233)
Q Consensus 156 ~~~~~~~~~~~~~~~~vvDvGGG~G~----~~~~l~~~~---P~l~~~v~Dlp~ 202 (233)
.+.|++.+. -++..+|||+|-|.|. +..+|+++. |++|+|.++.|.
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 456788877 4567899999999996 566777764 889999999853
No 428
>KOG2915 consensus tRNA(1-methyladenosine) methyltransferase, subunit GCD14 [Translation, ribosomal structure and biogenesis]
Probab=72.69 E-value=21 Score=30.31 Aligned_cols=88 Identities=14% Similarity=0.142 Sum_probs=61.3
Q ss_pred HHHHHHhcchhc----HHHHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeechHHH-hhc----cCC---
Q 039903 144 FNKAMLNHTSIV----TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLSHVI-QDS----SSY--- 210 (233)
Q Consensus 144 f~~am~~~~~~~----~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp~v~-~~a----~~~--- 210 (233)
+..+|...++.. +.-++..++ -....+|+.-|-|+|.++-+|+++- |.=+..-||.-+.. +.| +++
T Consensus 78 WTl~LphRTQI~Yt~Dia~I~~~L~-i~PGsvV~EsGTGSGSlShaiaraV~ptGhl~tfefH~~Ra~ka~eeFr~hgi~ 156 (314)
T KOG2915|consen 78 WTLALPHRTQILYTPDIAMILSMLE-IRPGSVVLESGTGSGSLSHAIARAVAPTGHLYTFEFHETRAEKALEEFREHGIG 156 (314)
T ss_pred hhhhccCcceEEecccHHHHHHHhc-CCCCCEEEecCCCcchHHHHHHHhhCcCcceEEEEecHHHHHHHHHHHHHhCCC
Confidence 555666555432 455666666 6778999999999999999999985 66677777764322 222 222
Q ss_pred CCceEEecCcCC-CCCC----CCEEEe
Q 039903 211 SGVKHIGGIMLE-RIPK----GDAILI 232 (233)
Q Consensus 211 ~ri~~~~gD~f~-~~P~----~D~~~l 232 (233)
+.+++..-|.-. .++. +|+++|
T Consensus 157 ~~vt~~hrDVc~~GF~~ks~~aDaVFL 183 (314)
T KOG2915|consen 157 DNVTVTHRDVCGSGFLIKSLKADAVFL 183 (314)
T ss_pred cceEEEEeecccCCccccccccceEEE
Confidence 678888888887 4553 588886
No 429
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=72.68 E-value=6.2 Score=23.27 Aligned_cols=23 Identities=26% Similarity=0.332 Sum_probs=16.4
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHH
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILR 59 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~ 59 (233)
+.|..+||+.+|. ++.-+.+.|+
T Consensus 20 G~s~~~IA~~lg~----s~sTV~relk 42 (44)
T PF13936_consen 20 GMSIREIAKRLGR----SRSTVSRELK 42 (44)
T ss_dssp ---HHHHHHHTT------HHHHHHHHH
T ss_pred CCCHHHHHHHHCc----CcHHHHHHHh
Confidence 6999999999999 9999988775
No 430
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=72.51 E-value=6.9 Score=31.59 Aligned_cols=46 Identities=20% Similarity=0.283 Sum_probs=37.8
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA 85 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s 85 (233)
..++..+||+.+|+ +-..++.-|+.|...|+|+.. .+..+...+.+
T Consensus 29 ~~L~e~eLae~lgV----SRtpVREAL~~L~~eGlv~~~----~~~G~~V~~~~ 74 (224)
T PRK11534 29 EKLRMSLLTSRYAL----GVGPLREALSQLVAERLVTVV----NQKGYRVASMS 74 (224)
T ss_pred CcCCHHHHHHHHCC----ChHHHHHHHHHHHHCCCEEEe----CCCceEeCCCC
Confidence 57889999999999 999999999999999999976 34445555443
No 431
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=72.33 E-value=5.9 Score=32.07 Aligned_cols=41 Identities=15% Similarity=0.117 Sum_probs=36.0
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA 82 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt 82 (233)
+.|-.|||+.+|+ +.+.+.|.|.-|...|+++.. .+.+...
T Consensus 169 ~~t~~~lA~~lG~----sretvsR~L~~L~~~G~I~~~-----~~~i~I~ 209 (226)
T PRK10402 169 HEKHTQAAEYLGV----SYRHLLYVLAQFIQDGYLKKS-----KRGYLIK 209 (226)
T ss_pred cchHHHHHHHHCC----cHHHHHHHHHHHHHCCCEEee-----CCEEEEe
Confidence 5688999999999 999999999999999999984 5566654
No 432
>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=72.00 E-value=5.7 Score=28.63 Aligned_cols=52 Identities=23% Similarity=0.310 Sum_probs=41.9
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS 71 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~ 71 (233)
.|+.|.+.|=+. ++.|+.||.+.+.-..+....-+.-+|+-|+..|+++...
T Consensus 4 ~E~~IM~~lW~~---~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~ 55 (115)
T PF03965_consen 4 LELEIMEILWES---GEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREK 55 (115)
T ss_dssp HHHHHHHHHHHH---SSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHhC---CCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEee
Confidence 567788888887 4799999999988632335788999999999999999874
No 433
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=71.88 E-value=11 Score=31.53 Aligned_cols=52 Identities=13% Similarity=0.056 Sum_probs=45.0
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhh
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFV 89 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~ 89 (233)
+++.-+|||..++- +|-.++-.|..|-++|+++-... ..|.|..|..+...+
T Consensus 24 r~IKgeeIA~~l~r----npGTVRNqmq~LkaLgLVegvpG--PkGGY~PT~kAYe~L 75 (294)
T COG2524 24 RPIKGEEIAEVLNR----NPGTVRNQMQSLKALGLVEGVPG--PKGGYKPTSKAYEAL 75 (294)
T ss_pred CCcchHHHHHHHcc----CcchHHHHHHHHHhcCccccccC--CCCCccccHHHHHHh
Confidence 68999999999999 99999999999999999997643 578899987765443
No 434
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=71.66 E-value=5.3 Score=27.49 Aligned_cols=46 Identities=17% Similarity=0.213 Sum_probs=37.4
Q ss_pred hhHHHHhc-CCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 21 VFEIIAKA-GPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 21 lfd~L~~~-~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.+|.|... +...-+|...||+++++ .-...++.||.|...|++...
T Consensus 28 t~dkl~kEV~~~K~ITps~lserlkI----~~SlAr~~Lr~L~~kG~Ik~V 74 (86)
T PRK09334 28 LLKRVAKEVKKEKIVTPYTLASKYGI----KISVAKKVLRELEKRGVLVLY 74 (86)
T ss_pred HHHHHHHHhccCcEEcHHHHHHHhcc----hHHHHHHHHHHHHHCCCEEEE
Confidence 45555543 32356899999999999 999999999999999999765
No 435
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=71.63 E-value=11 Score=30.16 Aligned_cols=54 Identities=15% Similarity=0.183 Sum_probs=44.6
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
.+|..++|+.++. +.....|+|..|...|++++.... ++.....|+.+..++.+
T Consensus 19 ~~t~~ela~~l~~----S~qta~R~l~~le~~~~I~R~~~~-~Gq~i~iTekG~~~L~~ 72 (214)
T COG1339 19 KVTSSELAKRLGV----SSQTAARKLKELEDEGYITRTISK-RGQLITITEKGIDLLYK 72 (214)
T ss_pred cccHHHHHHHhCc----CcHHHHHHHHhhccCCcEEEEecC-CCcEEEehHhHHHHHHH
Confidence 5899999999999 999999999999999999976432 35667788888766644
No 436
>PHA02591 hypothetical protein; Provisional
Probab=71.55 E-value=6.3 Score=26.48 Aligned_cols=33 Identities=18% Similarity=0.197 Sum_probs=26.9
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHH
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~ 60 (233)
.+...|.+. +.|.++||+.+|+ +.+.+++.++.
T Consensus 50 ~vA~eL~eq----GlSqeqIA~~LGV----sqetVrKYL~~ 82 (83)
T PHA02591 50 SVTHELARK----GFTVEKIASLLGV----SVRKVRRYLES 82 (83)
T ss_pred HHHHHHHHc----CCCHHHHHHHhCC----CHHHHHHHHhc
Confidence 355567774 7999999999999 99999888763
No 437
>PRK10736 hypothetical protein; Provisional
Probab=71.33 E-value=7.3 Score=34.48 Aligned_cols=51 Identities=8% Similarity=-0.045 Sum_probs=42.2
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA 82 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt 82 (233)
.|++.|.. .|.+.+||+.++++ +...+..+|-.|.-.|++++. .++.|+.-
T Consensus 312 ~v~~~l~~----~~~~iD~L~~~~~l----~~~~v~~~L~~LEl~G~v~~~----~g~~~~~~ 362 (374)
T PRK10736 312 ELLANVGD----EVTPVDVVAERAGQ----PVPEVVTQLLELELAGWIAAV----PGGYVRLR 362 (374)
T ss_pred HHHHhcCC----CCCCHHHHHHHHCc----CHHHHHHHHHHHHhCCcEEEc----CCcEEEEe
Confidence 45566654 48999999999999 999999999999999999997 45666553
No 438
>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=71.22 E-value=7.4 Score=27.59 Aligned_cols=51 Identities=20% Similarity=0.247 Sum_probs=40.2
Q ss_pred HHhhChhHHHHhc--C---CCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 16 ASELGVFEIIAKA--G---PTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 16 a~~lglfd~L~~~--~---~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
..+++|+.++... | +..-+|..++|+.+++ +...+.+-+..|+.+|++.+.
T Consensus 32 ~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~----~~~~V~~al~~Li~~~vI~~~ 87 (100)
T PF04492_consen 32 GRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGL----SRDHVSKALNELIRRGVIIRD 87 (100)
T ss_pred HHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeC
Confidence 4455666665542 1 1236899999999999 999999999999999999874
No 439
>KOG4300 consensus Predicted methyltransferase [General function prediction only]
Probab=71.22 E-value=7.2 Score=31.70 Aligned_cols=63 Identities=14% Similarity=0.130 Sum_probs=36.4
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhc----cC--CCCce-EEecCcCC-C-CCCC--CEEE
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDS----SS--YSGVK-HIGGIMLE-R-IPKG--DAIL 231 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a----~~--~~ri~-~~~gD~f~-~-~P~~--D~~~ 231 (233)
.-..++.||||+|..-.-. .--|..++|.+|-.+ .-+.+ ++ ...+. |+.++--+ + ++.+ |+|+
T Consensus 76 ~K~~vLEvgcGtG~Nfkfy-~~~p~~svt~lDpn~~mee~~~ks~~E~k~~~~~~fvva~ge~l~~l~d~s~DtVV 150 (252)
T KOG4300|consen 76 GKGDVLEVGCGTGANFKFY-PWKPINSVTCLDPNEKMEEIADKSAAEKKPLQVERFVVADGENLPQLADGSYDTVV 150 (252)
T ss_pred CccceEEecccCCCCcccc-cCCCCceEEEeCCcHHHHHHHHHHHhhccCcceEEEEeechhcCcccccCCeeeEE
Confidence 3467899999999764211 112456689999643 22222 22 25566 66666555 3 4444 7664
No 440
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=70.70 E-value=9.4 Score=31.87 Aligned_cols=61 Identities=18% Similarity=0.249 Sum_probs=50.2
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
-.|.+|-.+.+. .|...-|+++++ ++..+.|-++.|.. .-+|++. +..+.+|+.|..|...
T Consensus 4 ~~L~~f~~v~~~-----gs~s~AA~~L~i----sQ~avSr~i~~LE~~lg~~Lf~R~-----~~~~~lT~~G~~l~~~ 67 (296)
T PRK09906 4 RHLRYFVAVAEE-----LNFTKAAEKLHT----AQPSLSQQIKDLENCVGVPLLVRD-----KRKVALTAAGEVFLQD 67 (296)
T ss_pred HHHHHHHHHHhh-----CCHHHHHHHhCC----CCcHHHHHHHHHHHHhCCeeeeeC-----CCcceEcHhHHHHHHH
Confidence 357788899984 599999999999 88899888887776 6789884 7889999999877644
No 441
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.49 E-value=5.2 Score=27.50 Aligned_cols=26 Identities=31% Similarity=0.433 Sum_probs=23.5
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHH
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLL 61 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L 61 (233)
.++|.++||++++. .+..++++|.+-
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 999999998764
No 442
>PF13578 Methyltransf_24: Methyltransferase domain; PDB: 3SSO_A 3SSN_C 3SSM_D.
Probab=70.44 E-value=3.4 Score=29.00 Aligned_cols=60 Identities=20% Similarity=0.138 Sum_probs=18.7
Q ss_pred EEecCCccHHHHHHHHHcCCC---cEEEeechH----HHhhccC---CCCceEEecCcCCC---CC-CC-CEEEe
Q 039903 173 VDVGGGLGVNVNIIISNYLHI---KGVNFDLSH----VIQDSSS---YSGVKHIGGIMLER---IP-KG-DAILI 232 (233)
Q Consensus 173 vDvGGG~G~~~~~l~~~~P~l---~~~v~Dlp~----v~~~a~~---~~ri~~~~gD~f~~---~P-~~-D~~~l 232 (233)
|+||...|..+..+++..+.. +++.+|... +-+..++ .++++++.+|+.+- ++ .. |++++
T Consensus 1 lEiG~~~G~st~~l~~~~~~~~~~~~~~vD~~~~~~~~~~~~~~~~~~~~~~~~~g~s~~~l~~~~~~~~dli~i 75 (106)
T PF13578_consen 1 LEIGTYSGYSTLWLASALRDNGRGKLYSVDPFPGDEQAQEIIKKAGLSDRVEFIQGDSPDFLPSLPDGPIDLIFI 75 (106)
T ss_dssp --------------------------EEEESS------------GGG-BTEEEEES-THHHHHHHHH--EEEEEE
T ss_pred CccccccccccccccccccccccCCEEEEECCCcccccchhhhhcCCCCeEEEEEcCcHHHHHHcCCCCEEEEEE
Confidence 578999999988888877655 578888755 2222222 27899999999763 33 22 76654
No 443
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=70.34 E-value=9.7 Score=31.87 Aligned_cols=60 Identities=18% Similarity=0.203 Sum_probs=49.6
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
.+.+|..+.+. .|...-|+++++ ++..+.+-++.|.. .-+|++. ...+.+|+.|..|...
T Consensus 7 ~l~~f~~v~~~-----gS~s~AA~~L~i----sq~avS~~I~~LE~~lg~~LF~R~-----~~~~~lT~~G~~l~~~ 69 (300)
T TIGR02424 7 HLQCFVEVARQ-----GSVKRAAEALHI----TQPAVSKTLRELEEILGTPLFERD-----RRGIRLTRYGELFLRH 69 (300)
T ss_pred HHHHHHHHHHh-----CCHHHHHHHhCC----ChHHHHHHHHHHHHHhCCeEEEEc-----CCCccccHhHHHHHHH
Confidence 56788888884 599999999999 89999988888876 7788885 6779999999776643
No 444
>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=69.69 E-value=17 Score=24.07 Aligned_cols=54 Identities=13% Similarity=0.122 Sum_probs=35.9
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHH--hcCCceeeeccCC-CCCceec
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLL--VTHRVLRCTSAGD-DQRLYGL 81 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L--~~~gll~~~~~~~-~~~~y~l 81 (233)
|.+.|... ++.|++||++++|. .+.-++-.|--+ -.+|+--..+..+ +..+|++
T Consensus 15 li~mL~rp---~GATi~ei~~atGW----q~HTvRgalsg~~kKklGl~i~s~k~~g~~r~YrI 71 (72)
T PF11994_consen 15 LIAMLRRP---EGATIAEICEATGW----QPHTVRGALSGLLKKKLGLTITSEKVDGGGRRYRI 71 (72)
T ss_pred HHHHHcCC---CCCCHHHHHHhhCC----chhhHHHHHHHHHHHhcCcEEEeeecCCCeeeEee
Confidence 45556553 58999999999999 888887777766 4456654433221 2456654
No 445
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=69.68 E-value=11 Score=31.18 Aligned_cols=61 Identities=11% Similarity=0.105 Sum_probs=49.2
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
-.|..|..+.+. .+...-|+++++ ++..+.+-++.|.. .-+|++. ...+++|+.|+.|...
T Consensus 6 ~~L~~f~~v~e~-----~s~t~AA~~L~i----sqpavS~~I~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~~~ 69 (290)
T PRK10837 6 RQLEVFAEVLKS-----GSTTQASVMLAL----SQSAVSAALTDLEGQLGVQLFDRV-----GKRLVVNEHGRLLYPR 69 (290)
T ss_pred HHHHHHHHHHHc-----CCHHHHHHHhCC----CccHHHHHHHHHHHHhCCccEeec-----CCeEEECHhHHHHHHH
Confidence 356788888884 589999999999 88888888777766 6889884 6789999999776543
No 446
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=69.54 E-value=12 Score=31.52 Aligned_cols=61 Identities=13% Similarity=0.112 Sum_probs=50.0
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
-+|.+|-.+.+ ..+...-|+++++ ++..+.|-++.|.. .-+|++. ...+.+|+.|+.|...
T Consensus 7 ~~L~~F~~v~e-----~gs~s~AA~~L~i----sqpavS~~I~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~~~ 70 (296)
T PRK11062 7 NHLYYFWMVCK-----EGSVVGAAEALFL----TPQTITGQIKALEERLQGKLFKRK-----GRGLEPTELGELVFRY 70 (296)
T ss_pred HHHHHHHHHHh-----cCCHHHHHHHhCC----ChHHHHHHHHHHHHHcCccceeec-----CCceeECHhHHHHHHH
Confidence 46788999998 4588899999999 88888888877776 6788884 7789999999766543
No 447
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=69.02 E-value=9.9 Score=31.94 Aligned_cols=61 Identities=11% Similarity=0.109 Sum_probs=50.0
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
-.|.+|..+.+. .+...-|+++++ ++..+.+-++.|.. .-+|++. .....+|+.|+.|.+.
T Consensus 8 ~~L~~f~~v~~~-----gs~s~AA~~L~i----sQ~avS~~i~~LE~~lG~~LF~R~-----~r~~~lT~~G~~l~~~ 71 (302)
T PRK09791 8 HQIRAFVEVARQ-----GSIRGASRMLNM----SQPALTKSIQELEEGLAAQLFFRR-----SKGVTLTDAGESFYQH 71 (302)
T ss_pred HHHHHHHHHHHc-----CCHHHHHHHhCC----ChHHHHHHHHHHHHHhCCeEEEEc-----CCCceECccHHHHHHH
Confidence 467889999984 499999999999 88888888877765 7788884 6779999999876643
No 448
>KOG1331 consensus Predicted methyltransferase [General function prediction only]
Probab=68.94 E-value=7.2 Score=33.07 Aligned_cols=56 Identities=16% Similarity=0.085 Sum_probs=40.4
Q ss_pred cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCCCCceEEecCcCC-CCCC
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSYSGVKHIGGIMLE-RIPK 226 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~~ri~~~~gD~f~-~~P~ 226 (233)
+....++|+|||.|.+.. -+|.+..+..|+-. .+..++..+.......|..+ |.+.
T Consensus 44 ~~gsv~~d~gCGngky~~----~~p~~~~ig~D~c~~l~~~ak~~~~~~~~~ad~l~~p~~~ 101 (293)
T KOG1331|consen 44 PTGSVGLDVGCGNGKYLG----VNPLCLIIGCDLCTGLLGGAKRSGGDNVCRADALKLPFRE 101 (293)
T ss_pred CCcceeeecccCCcccCc----CCCcceeeecchhhhhccccccCCCceeehhhhhcCCCCC
Confidence 446889999999998753 35999999999986 44555543333566788887 6554
No 449
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=68.67 E-value=8 Score=32.21 Aligned_cols=59 Identities=19% Similarity=0.165 Sum_probs=49.5
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhc
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVL 90 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~ 90 (233)
.|.+|..+.+. .|...-|+++++ ++..+.+-+..|.. .-+|++. ...+.+|+.|+.|..
T Consensus 5 ~L~~f~~v~~~-----gs~s~AA~~L~i----tqpavS~~Ik~LE~~lg~~LF~R~-----~r~~~lT~~G~~l~~ 66 (291)
T TIGR03418 5 ALRVFESAARL-----ASFTAAARELGS----TQPAVSQQVKRLEEELGTPLFERG-----HRGIELTEDGQRLFE 66 (291)
T ss_pred HHHHHHHHHHh-----CCHHHHHHHhCC----CHHHHHHHHHHHHHHhCcHHhhcC-----CCceeEcHhHHHHHH
Confidence 57789999984 599999999999 99999998888876 6788884 678999999987654
No 450
>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=68.64 E-value=10 Score=30.28 Aligned_cols=46 Identities=20% Similarity=0.223 Sum_probs=37.8
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA 85 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s 85 (233)
..++-.+||+.+|+ +...++.-|+.|...|+|+.. .+..+..++.+
T Consensus 33 ~~L~e~~La~~lgV----SRtpVReAL~~L~~eGlv~~~----~~~G~~V~~~~ 78 (212)
T TIGR03338 33 AKLNESDIAARLGV----SRGPVREAFRALEEAGLVRNE----KNRGVFVREIS 78 (212)
T ss_pred CEecHHHHHHHhCC----ChHHHHHHHHHHHHCCCEEEe----cCCCeEEecCC
Confidence 57888999999999 999999999999999999976 34445454443
No 451
>PRK13239 alkylmercury lyase; Provisional
Probab=68.49 E-value=6.7 Score=31.65 Aligned_cols=41 Identities=17% Similarity=0.279 Sum_probs=33.6
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcC
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTH 64 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~ 64 (233)
+..-|+..|++ | .|.|.++||+.+|. +.+.++..|+.|...
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 44557888885 4 69999999999999 999999888887544
No 452
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=68.28 E-value=12 Score=31.23 Aligned_cols=60 Identities=13% Similarity=0.164 Sum_probs=49.2
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
+|.+|..+.+. .|...-|+++++ ++..+.+-+.-|.. .-+|.+. +..+.+|+.|+.|...
T Consensus 5 ~L~~f~~v~~~-----gs~s~AA~~L~i----sqsavS~~i~~LE~~lg~~Lf~R~-----~~~~~lT~~G~~l~~~ 67 (296)
T PRK11242 5 HIRYFLAVAEH-----GNFTRAAEALHV----SQPTLSQQIRQLEESLGVQLFDRS-----GRTVRLTDAGEVYLRY 67 (296)
T ss_pred HHHHHHHHHHh-----CCHHHHHHHcCC----CchHHHHHHHHHHHHhCCeeEeEc-----CCceeechhHHHHHHH
Confidence 57788999984 588899999999 88899888888776 6788884 7889999999766543
No 453
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=68.19 E-value=9.2 Score=22.87 Aligned_cols=25 Identities=16% Similarity=0.194 Sum_probs=21.5
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHH
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLL 61 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L 61 (233)
+.+..|||+.+++ +...+++.++-+
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 6899999999999 898888877654
No 454
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=68.14 E-value=8.3 Score=36.56 Aligned_cols=48 Identities=17% Similarity=0.158 Sum_probs=39.8
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH 83 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~ 83 (233)
..-|.+|+|+.+|+ +...++|.|......|++.+.....+.++|..++
T Consensus 615 ~twt~eelse~l~i----p~~~lrrrL~fWi~~GvL~e~~~~s~tgt~T~iE 662 (765)
T KOG2165|consen 615 NTWTLEELSESLGI----PVPALRRRLSFWIQKGVLREEPIISDTGTLTVIE 662 (765)
T ss_pred ccccHHHHHHHhCC----CHHHHHHHHHHHHHcCeeecCCCCCCCceeeecc
Confidence 47899999999999 9999999999999999999962111247777776
No 455
>TIGR00027 mthyl_TIGR00027 methyltransferase, putative, TIGR00027 family. This model represents a set of probable methyltransferases, about 300 amino acids long, with essentially full length homology. Members share an N-terminal region described by Pfam model pfam02409. Included are a paralogous family of 12 proteins in Mycobacterium tuberculosis, plus close homologs in related species, a family of 8 in the archaeon Methanosarcina acetivorans, and small numbers of members in other species, including plants.
Probab=68.08 E-value=10 Score=31.78 Aligned_cols=54 Identities=15% Similarity=0.163 Sum_probs=40.0
Q ss_pred cCcceEEEecCCccHHHHHHHHHcC-CCcEEEeechHHHhhccC---------CCCceEEecCcCC
Q 039903 167 EQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLSHVIQDSSS---------YSGVKHIGGIMLE 222 (233)
Q Consensus 167 ~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp~v~~~a~~---------~~ri~~~~gD~f~ 222 (233)
++...||.+|||-=.-.-.+ .+| ++++.=+|+|+|++.=++ .+++.+++.|+++
T Consensus 80 ~g~~qvV~LGaGlDTr~~Rl--~~~~~~~~~EvD~P~v~~~K~~~l~~~~~~~~~~~~~v~~Dl~~ 143 (260)
T TIGR00027 80 AGIRQVVILGAGLDTRAYRL--PWPDGTRVFEVDQPAVLAFKEKVLAELGAEPPAHRRAVPVDLRQ 143 (260)
T ss_pred cCCcEEEEeCCccccHHHhc--CCCCCCeEEECCChHHHHHHHHHHHHcCCCCCCceEEeccCchh
Confidence 45678999999987766666 344 588888899998863221 2689999999873
No 456
>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=67.83 E-value=6 Score=32.76 Aligned_cols=35 Identities=17% Similarity=0.253 Sum_probs=25.3
Q ss_pred cceEEEecCCccHHHHHHHHHcCC--------CcEEEeechHH
Q 039903 169 IKQLVDVGGGLGVNVNIIISNYLH--------IKGVNFDLSHV 203 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~P~--------l~~~v~Dlp~v 203 (233)
.-+||++|+|+|.++.-+++..-. ++.+++|..+.
T Consensus 19 ~~~ivE~GaG~G~La~diL~~l~~~~p~~~~~~~y~ivE~Sp~ 61 (252)
T PF02636_consen 19 PLRIVEIGAGRGTLARDILRYLRKFSPEVYKRLRYHIVEISPY 61 (252)
T ss_dssp -EEEEEES-TTSHHHHHHHHHHCCTTHHHHTTCEEEEE-TTCC
T ss_pred CcEEEEECCCchHHHHHHHHHHHHhChhhhhcceEEEEcCCHH
Confidence 479999999999999888775443 57888887543
No 457
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=67.75 E-value=7 Score=33.85 Aligned_cols=35 Identities=14% Similarity=0.269 Sum_probs=33.2
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.++|-.|||+++|+ +...+.|+|..+...|+++-.
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 38999999999999 999999999999999999976
No 458
>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=67.69 E-value=8.5 Score=28.99 Aligned_cols=35 Identities=14% Similarity=0.316 Sum_probs=26.7
Q ss_pred ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHH
Q 039903 20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILR 59 (233)
Q Consensus 20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~ 59 (233)
.|-+.|.+.+ ...+|+.|||+.+|+ ++..+.+|++
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 3556677653 124899999999999 9999888875
No 459
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=67.51 E-value=12 Score=31.42 Aligned_cols=61 Identities=15% Similarity=0.232 Sum_probs=50.2
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
-+|.+|..+.+ ..|...-|+++++ ++..+.+-++.|.. .-+|++. +....+|+.|+.|...
T Consensus 5 ~~L~~f~~va~-----~gs~s~AA~~L~i----sQpavS~~I~~LE~~lG~~LF~R~-----~r~~~lT~~G~~l~~~ 68 (301)
T PRK14997 5 NDFAWFVHVVE-----EGGFAAAGRALDE----PKSKLSRRIAQLEERLGVRLIQRT-----TRQFNVTEVGQTFYEH 68 (301)
T ss_pred HHHHHHHHHHH-----cCCHHHHHHHhCC----CHHHHHHHHHHHHHHhCCEeeeec-----cCcceEcHhHHHHHHH
Confidence 46788999998 4589999999999 88899888888776 6778884 7789999999776644
No 460
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=66.88 E-value=12 Score=31.60 Aligned_cols=63 Identities=11% Similarity=0.095 Sum_probs=51.7
Q ss_pred HHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhc
Q 039903 14 QAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVL 90 (233)
Q Consensus 14 ~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~ 90 (233)
...-+|.+|..+.+ ..|...-|+++++ ++..+.+-++.|.. .-+|++. +....+|+.|..|..
T Consensus 7 ~~~~~L~~F~av~e-----~gs~s~AA~~L~i----SQpavS~~I~~LE~~lg~~LF~R~-----~r~~~lT~~G~~l~~ 72 (312)
T PRK10341 7 PKTQHLVVFQEVIR-----SGSIGSAAKELGL----TQPAVSKIINDIEDYFGVELIVRK-----NTGVTLTPAGQVLLS 72 (312)
T ss_pred ccHHHHHHHHHHHH-----cCCHHHHHHHhCC----ChHHHHHHHHHHHHHhCCeEEEEc-----CCCceEChhHHHHHH
Confidence 34567889999998 4689999999999 88899888887776 6788884 788999999977664
No 461
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=66.82 E-value=11 Score=22.61 Aligned_cols=35 Identities=14% Similarity=0.207 Sum_probs=27.6
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHH
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLL 61 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L 61 (233)
+.-|...+.. ..|..+||+.+|+ +..-+.|+++-.
T Consensus 17 ~~~i~~~~~~-----~~s~~~vA~~~~v----s~~TV~ri~~~~ 51 (52)
T PF13542_consen 17 EQYILKLLRE-----SRSFKDVARELGV----SWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHHhh-----cCCHHHHHHHHCC----CHHHHHHHHHhh
Confidence 3345666665 4799999999999 999999998753
No 462
>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=66.73 E-value=11 Score=24.56 Aligned_cols=49 Identities=18% Similarity=0.184 Sum_probs=35.8
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.+-.|.+.|...| +.++..||...++. .+..-+.+.|..|...|.+.+.
T Consensus 5 ~ee~Il~~L~~~g---~~~a~~ia~~~~L~--~~kk~VN~~LY~L~k~g~v~k~ 53 (66)
T PF02295_consen 5 LEEKILDFLKELG---GSTATAIAKALGLS--VPKKEVNRVLYRLEKQGKVCKE 53 (66)
T ss_dssp HHHHHHHHHHHHT---SSEEEHHHHHHHHT--S-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHhcC---CccHHHHHHHhCcc--hhHHHHHHHHHHHHHCCCEeeC
Confidence 4567889999884 55555555555540 0578999999999999999985
No 463
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=66.72 E-value=12 Score=31.50 Aligned_cols=59 Identities=12% Similarity=0.122 Sum_probs=49.1
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhh
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFV 89 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~ 89 (233)
-.|.+|..+.+. .+...-|+++++ ++..+.+-++.|.. .-+|++. ...+.+|+.|+.|.
T Consensus 8 ~~L~~f~~v~e~-----gs~s~AA~~L~i----sqpavS~~i~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~ 69 (305)
T CHL00180 8 DQLRILKAIATE-----GSFKKAAESLYI----SQPAVSLQIKNLEKQLNIPLFDRS-----KNKASLTEAGELLL 69 (305)
T ss_pred HHHHHHHHHHHc-----CCHHHHHHHhcC----CChHHHHHHHHHHHHhCCEEEEec-----CCCceECHhHHHHH
Confidence 357889999984 589999999999 88899888888876 6788884 67799999998773
No 464
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=66.38 E-value=14 Score=24.80 Aligned_cols=54 Identities=13% Similarity=0.285 Sum_probs=46.0
Q ss_pred HHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903 11 AAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS 71 (233)
Q Consensus 11 ~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~ 71 (233)
.+|....++.+...|.+. .+.++.+|+..++. +...+.+-|..|...|+++...
T Consensus 20 ~~l~~~~r~~il~~l~~~---~~~~~~~l~~~~~~----~~~~v~~hL~~L~~~glv~~~~ 73 (110)
T COG0640 20 KALADPTRLEILSLLAEG---GELTVGELAEALGL----SQSTVSHHLKVLREAGLVELRR 73 (110)
T ss_pred HHhCCHHHHHHHHHHHhc---CCccHHHHHHHHCC----ChhHHHHHHHHHHHCCCeEEEe
Confidence 355555678888999883 27889999999999 9999999999999999999863
No 465
>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=66.28 E-value=9.1 Score=26.42 Aligned_cols=39 Identities=23% Similarity=0.224 Sum_probs=31.7
Q ss_pred HHHhhChhH-HHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHh
Q 039903 15 AASELGVFE-IIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLV 62 (233)
Q Consensus 15 ~a~~lglfd-~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~ 62 (233)
.+-++.|+. .|.. +.|..|||+.+|+ +..-+.|.=|.|-
T Consensus 35 l~~R~~va~~lL~~-----g~syreIa~~tgv----S~aTItRvsr~Lk 74 (87)
T PF01371_consen 35 LAQRWQVAKELLDE-----GKSYREIAEETGV----SIATITRVSRCLK 74 (87)
T ss_dssp HHHHHHHHHHHHHT-----TSSHHHHHHHHTS----THHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHC-----CCCHHHHHHHhCC----CHHHHHHHHHHHH
Confidence 456788998 5554 7999999999999 8888888777764
No 466
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=66.14 E-value=12 Score=31.66 Aligned_cols=60 Identities=17% Similarity=0.136 Sum_probs=45.8
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
+.+.|.+.. ..+.|+++||+.+++ +++.+.|+.+..+...+-+.. ...++......|...
T Consensus 10 ~~~~i~~~~-~~~~~l~~lA~~~~~----S~~~l~r~F~~~~g~s~~~yi------~~~Rl~~A~~~L~~~ 69 (289)
T PRK15121 10 LLIWLEGHL-DQPLSLDNVAAKAGY----SKWHLQRMFKDVTGHAIGAYI------RARRLSKAAVALRLT 69 (289)
T ss_pred HHHHHHhcc-cCCCCHHHHHHHHCc----CHHHHHHHHHHHHCcCHHHHH------HHHHHHHHHHHHHcC
Confidence 344455431 248999999999999 999999999999888877763 557777777777643
No 467
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=66.02 E-value=46 Score=25.06 Aligned_cols=80 Identities=10% Similarity=0.090 Sum_probs=54.6
Q ss_pred hHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCC--CCCChhhHHHHHHHHhcCCceeeeccCCC----CCceec
Q 039903 8 VLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSS--NPNAAVMLDRILRLLVTHRVLRCTSAGDD----QRLYGL 81 (233)
Q Consensus 8 ~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~--~~~~~~~l~rlL~~L~~~gll~~~~~~~~----~~~y~l 81 (233)
+.++...-.+++=|...|.+ +|..--+|.+.+.-- -+.++..++++|+-|...|+++......+ -..|++
T Consensus 16 ~~~ql~kg~l~~~IL~~L~~----~p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~L 91 (138)
T TIGR02719 16 QINGAPKNFLVPFLLLCLKD----WNLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSL 91 (138)
T ss_pred HHHHHHHHHHHHHHHHHHcc----CCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEE
Confidence 34566777777778888877 466666666554320 12378899999999999999986321101 245999
Q ss_pred cHhhhHhhcC
Q 039903 82 AHVAKYFVLN 91 (233)
Q Consensus 82 t~~s~~l~~~ 91 (233)
|+.|+..+..
T Consensus 92 Te~Gr~~L~~ 101 (138)
T TIGR02719 92 TDAGEQYLSM 101 (138)
T ss_pred CHHHHHHHHH
Confidence 9999876544
No 468
>PF11312 DUF3115: Protein of unknown function (DUF3115); InterPro: IPR021463 This eukaryotic family of proteins has no known function.
Probab=65.99 E-value=8.5 Score=33.08 Aligned_cols=37 Identities=16% Similarity=0.387 Sum_probs=27.4
Q ss_pred cceEEEecCCccHHHHHHHHHc--------------------CCCcEEEeech---HHHh
Q 039903 169 IKQLVDVGGGLGVNVNIIISNY--------------------LHIKGVNFDLS---HVIQ 205 (233)
Q Consensus 169 ~~~vvDvGGG~G~~~~~l~~~~--------------------P~l~~~v~Dlp---~v~~ 205 (233)
..+||-||||.|.=..+++..+ |.+..+++|+. .|+.
T Consensus 87 ~~~VlCIGGGAGAElVAlAa~~~~~~~~~~s~~~~~~~~~~~~~l~itlvDiAdWs~VV~ 146 (315)
T PF11312_consen 87 SLRVLCIGGGAGAELVALAAAFRTRSSEFLSKSPSGVSLSSPPSLSITLVDIADWSSVVD 146 (315)
T ss_pred CceEEEECCChHHHHHHHHHHHhhcccccCCcccccccccCCCcceEEEEEecChHHHHH
Confidence 3699999999998666666555 34788999975 4554
No 469
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=65.95 E-value=14 Score=31.44 Aligned_cols=61 Identities=13% Similarity=0.035 Sum_probs=50.2
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
-+|.+|..+.+ ..+...-|+++++ ++..+.+-++.|.. .-+|++. ...+.+|+.|+.|...
T Consensus 14 ~~L~~F~~v~e-----~gs~s~AA~~L~i----SQpavS~~I~~LE~~lG~~LF~R~-----~~~~~LT~~G~~l~~~ 77 (310)
T PRK15092 14 DLLRTFVAVAD-----LNTFAAAAAAVCR----TQSAVSQQMQRLEQLVGKELFARH-----GRNKLLTEHGIQLLGY 77 (310)
T ss_pred HHHHHHHHHHH-----cCCHHHHHHHhCC----ChHHHHHHHHHHHHHhCcceEEEC-----CCCceECHhHHHHHHH
Confidence 45778999998 5688999999999 89999888888776 7788884 6778999999877544
No 470
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=65.88 E-value=7.2 Score=31.87 Aligned_cols=45 Identities=16% Similarity=0.107 Sum_probs=40.8
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV 84 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~ 84 (233)
+=+|..|+|+..++ ++..++.++--|...|++++. ..|.|...++
T Consensus 29 kiiTirdvae~~ev----~~n~lr~lasrLekkG~LeRi----~rG~YlI~~l 73 (269)
T COG5340 29 KIITIRDVAETLEV----APNTLRELASRLEKKGWLERI----LRGRYLIIPL 73 (269)
T ss_pred ceEEeHHhhhhccC----CHHHHHHHHhhhhhcchhhhh----cCccEEEeec
Confidence 46799999999999 999999999999999999998 7899987764
No 471
>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=65.73 E-value=11 Score=22.56 Aligned_cols=25 Identities=20% Similarity=0.145 Sum_probs=21.6
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHH
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLL 61 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L 61 (233)
+.|..|||+.+++ ++..+++.++.+
T Consensus 15 ~~s~~eia~~l~~----s~~tv~~~~~~~ 39 (57)
T cd06170 15 GKTNKEIADILGI----SEKTVKTHLRNI 39 (57)
T ss_pred CCCHHHHHHHHCC----CHHHHHHHHHHH
Confidence 6899999999999 898888877654
No 472
>PF07574 SMC_Nse1: Nse1 non-SMC component of SMC5-6 complex; InterPro: IPR011513 Saccharomyces cerevisiae Nse1 (Q07913 from SWISSPROT) forms part of a complex with SMC5-SMC6. This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism [, ]. It is conserved in eukaryotes from yeast to human.; PDB: 3NW0_A.
Probab=65.57 E-value=5.6 Score=31.84 Aligned_cols=33 Identities=21% Similarity=0.216 Sum_probs=25.8
Q ss_pred ChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhh
Q 039903 50 AAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAK 86 (233)
Q Consensus 50 ~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~ 86 (233)
.....+.+|.-|+..|+|.+. .+|.|.+++.+-
T Consensus 165 ~~~eae~lL~~lv~~gWl~~s----~~G~y~L~~Ral 197 (200)
T PF07574_consen 165 SKSEAESLLDRLVEDGWLYRS----REGFYSLGPRAL 197 (200)
T ss_dssp --HHHHHHHHHHHHTTSE-EE----ETTEEEE-HHHH
T ss_pred hHHHHHHHHHHHHHCCCceeC----CCCEEEEChHHH
Confidence 567899999999999999887 689999998764
No 473
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=65.51 E-value=17 Score=31.64 Aligned_cols=48 Identities=4% Similarity=-0.039 Sum_probs=39.3
Q ss_pred CCCCHHHHHHh--CCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhh
Q 039903 32 AKISAVEIAAQ--MPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAK 86 (233)
Q Consensus 32 ~~~t~~elA~~--~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~ 86 (233)
+|++..+||+. +++ ++.-+++-|..|...|++++... ....-.|..|-
T Consensus 24 ~pv~s~~l~~~~~l~~----S~aTIR~dm~~Le~~G~l~~~h~---sagrIPT~kGY 73 (339)
T PRK00082 24 EPVGSKTLSKRYGLGV----SSATIRNDMADLEELGLLEKPHT---SSGRIPTDKGY 73 (339)
T ss_pred CCcCHHHHHHHhCCCC----ChHHHHHHHHHHHhCCCcCCCcC---CCCCCcCHHHH
Confidence 69999999977 999 99999999999999999998753 23334566664
No 474
>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=65.49 E-value=9.2 Score=26.43 Aligned_cols=35 Identities=20% Similarity=0.303 Sum_probs=27.9
Q ss_pred hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHh
Q 039903 19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLV 62 (233)
Q Consensus 19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~ 62 (233)
..|+..+.. +.|..+||+.+++ +..-+.|+.+.+.
T Consensus 41 ~~I~~ll~~-----G~S~~eIA~~LgI----SrsTIyRi~R~~n 75 (88)
T TIGR02531 41 LQVAKMLKQ-----GKTYSDIEAETGA----STATISRVKRCLN 75 (88)
T ss_pred HHHHHHHHC-----CCCHHHHHHHHCc----CHHHHHHHHHhcc
Confidence 345666654 6899999999999 9999999887543
No 475
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=65.46 E-value=9 Score=24.90 Aligned_cols=30 Identities=10% Similarity=0.169 Sum_probs=25.2
Q ss_pred CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCc
Q 039903 33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRV 66 (233)
Q Consensus 33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gl 66 (233)
+.|+++||+.+++ ++..+.++++......+
T Consensus 1 ~~~~~~la~~~~~----s~~~l~~~f~~~~~~s~ 30 (84)
T smart00342 1 PLTLEDLAEALGM----SPRHLQRLFKKETGTTP 30 (84)
T ss_pred CCCHHHHHHHhCC----CHHHHHHHHHHHhCcCH
Confidence 4689999999999 99999999987755444
No 476
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=65.40 E-value=16 Score=30.88 Aligned_cols=60 Identities=20% Similarity=0.109 Sum_probs=49.0
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
+|..|-.+.+ ..|...-|+++++ ++..+.+-++.|.. .-+|++. ...+.+|+.|+.|...
T Consensus 5 ~L~~F~~v~~-----~~S~s~AA~~L~i----sQ~avS~~I~~LE~~lg~~LF~R~-----~r~v~lT~~G~~l~~~ 67 (305)
T PRK11233 5 RLKYFVKIVD-----IGSLTQAAEVLHI----AQPALSQQVATLEGELNQQLLIRT-----KRGVTPTEAGKILYTH 67 (305)
T ss_pred HHHHHHHHHH-----cCCHHHHHHHhCC----CchHHHHHHHHHHHHhCCceEEeC-----CCCceECHhHHHHHHH
Confidence 5678889988 4599999999999 88899888877766 7788884 6789999999665533
No 477
>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=65.32 E-value=9.9 Score=25.79 Aligned_cols=32 Identities=16% Similarity=0.130 Sum_probs=26.6
Q ss_pred hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHH
Q 039903 19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRIL 58 (233)
Q Consensus 19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL 58 (233)
.-|.++|.. | ..|..+||+.+|+ +..-+.|.|
T Consensus 9 ~~I~e~l~~-~---~~ti~dvA~~~gv----S~~TVsr~L 40 (80)
T TIGR02844 9 LEIGKYIVE-T---KATVRETAKVFGV----SKSTVHKDV 40 (80)
T ss_pred HHHHHHHHH-C---CCCHHHHHHHhCC----CHHHHHHHh
Confidence 457778887 4 8999999999999 888888855
No 478
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=65.23 E-value=16 Score=29.79 Aligned_cols=68 Identities=10% Similarity=0.130 Sum_probs=52.9
Q ss_pred HHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhH
Q 039903 12 AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKY 87 (233)
Q Consensus 12 ~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~ 87 (233)
.|.-...-.|++.|.++ ++.|.-+||.++++ +..-+.--+..|...|++.+++.+ ..-.|+.||.-..
T Consensus 170 ~Lkn~~~k~I~~eiq~~---~~~t~~~ia~~l~l----s~aTV~~~lk~l~~~Gii~~~~~G-r~iiy~in~s~~~ 237 (240)
T COG3398 170 SLKNETSKAIIYEIQEN---KCNTNLLIAYELNL----SVATVAYHLKKLEELGIIPEDREG-RSIIYSINPSIEK 237 (240)
T ss_pred HhhchhHHHHHHHHhcC---CcchHHHHHHHcCc----cHHHHHHHHHHHHHcCCCcccccC-ceEEEEeCHHHHh
Confidence 44445556789999886 47999999999999 999999999999999999997432 2346777775443
No 479
>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=65.13 E-value=7.2 Score=22.58 Aligned_cols=23 Identities=17% Similarity=0.221 Sum_probs=20.1
Q ss_pred CCHHHHHHhCCCCCCCChhhHHHHHHH
Q 039903 34 ISAVEIAAQMPSSNPNAAVMLDRILRL 60 (233)
Q Consensus 34 ~t~~elA~~~~~~~~~~~~~l~rlL~~ 60 (233)
.|..|+|+.+++ ++..+.+|.+.
T Consensus 1 ~s~~e~a~~lgv----s~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGV----SPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCc----CHHHHHHHHHc
Confidence 478999999999 99999988774
No 480
>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=65.04 E-value=10 Score=27.14 Aligned_cols=47 Identities=13% Similarity=0.227 Sum_probs=37.9
Q ss_pred hhHHHHhc-CCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903 21 VFEIIAKA-GPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS 71 (233)
Q Consensus 21 lfd~L~~~-~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~ 71 (233)
.+|.|..+ +...-+|...||+++++ .-...+++|+.|...|++....
T Consensus 46 ~~~kl~kEV~~~K~ITp~~lserlkI----~~SlAr~~Lr~L~~kG~Ik~V~ 93 (105)
T PF03297_consen 46 TYDKLLKEVPKMKLITPSVLSERLKI----NGSLARKALRELESKGLIKPVS 93 (105)
T ss_dssp HHHHHHHHCTTSSCECHHHHHHHHCC----SCHHHHHHHHHHHHCCSSEEEE
T ss_pred HHHHHHHHhccCcEeeHHHHHHhHhh----HHHHHHHHHHHHHHCCCEEEEe
Confidence 45555443 22346899999999999 9999999999999999998763
No 481
>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=64.96 E-value=7.6 Score=22.62 Aligned_cols=22 Identities=14% Similarity=0.203 Sum_probs=19.6
Q ss_pred CCHHHHHHhCCCCCCCChhhHHHHHH
Q 039903 34 ISAVEIAAQMPSSNPNAAVMLDRILR 59 (233)
Q Consensus 34 ~t~~elA~~~~~~~~~~~~~l~rlL~ 59 (233)
+|..|+|+.+|+ +...+.++++
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 9999988875
No 482
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=64.81 E-value=16 Score=30.85 Aligned_cols=61 Identities=18% Similarity=0.202 Sum_probs=50.7
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
-+|.+|-.+.+. .|...-|+.+++ ++..+.+-++.|.. .-+|++. +..+.+|+.|+.|...
T Consensus 11 ~~L~~F~~va~~-----gs~s~AA~~L~i----sQpavS~~I~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~~~ 74 (302)
T TIGR02036 11 SKMHTFEVAARH-----QSFSLAAEELSL----TPSAISHRINQLEEELGIQLFVRS-----HRKVELTHEGKRIYWA 74 (302)
T ss_pred HHHHHHHHHHHh-----CCHHHHHHHHCC----CHHHHHHHHHHHHHHhCCceEEEC-----CCceeECHhHHHHHHH
Confidence 467788899984 588888999999 99999998888876 6788884 7889999999776644
No 483
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=64.76 E-value=12 Score=30.13 Aligned_cols=35 Identities=20% Similarity=0.229 Sum_probs=32.6
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
..++..+||+.+|+ +-..++.-|+.|...|+|+..
T Consensus 33 ~~L~e~~La~~lgV----SRtpVREAL~~L~~eGLV~~~ 67 (221)
T PRK11414 33 ARLITKNLAEQLGM----SITPVREALLRLVSVNALSVA 67 (221)
T ss_pred CccCHHHHHHHHCC----CchhHHHHHHHHHHCCCEEec
Confidence 57788999999999 999999999999999999976
No 484
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=64.74 E-value=16 Score=22.33 Aligned_cols=41 Identities=17% Similarity=0.205 Sum_probs=35.8
Q ss_pred HHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 23 EIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 23 d~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
+++.+. +++|++++=+.+|+ +-...--+|+++=..|+..+.
T Consensus 3 ~~~~~~---~~itv~~~rd~lg~----sRK~ai~lLE~lD~~g~T~R~ 43 (50)
T PF09107_consen 3 ELLQKN---GEITVAEFRDLLGL----SRKYAIPLLEYLDREGITRRV 43 (50)
T ss_dssp HHHHTT---SSBEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHhcC---CcCcHHHHHHHHCc----cHHHHHHHHHHHhccCCEEEe
Confidence 456554 69999999999999 999999999999999999986
No 485
>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=64.42 E-value=8.1 Score=24.01 Aligned_cols=37 Identities=24% Similarity=0.329 Sum_probs=28.4
Q ss_pred HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHH
Q 039903 16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLL 61 (233)
Q Consensus 16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L 61 (233)
-.|..|+..+.. +.+..|||+.+++ ++..+...++.+
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 356778888887 7999999999999 888776665443
No 486
>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=64.24 E-value=11 Score=25.14 Aligned_cols=44 Identities=16% Similarity=0.089 Sum_probs=28.0
Q ss_pred hChhHHHHhcC-CCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCc
Q 039903 19 LGVFEIIAKAG-PTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRV 66 (233)
Q Consensus 19 lglfd~L~~~~-~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gl 66 (233)
-.|.+.|-+.+ .-...|..|||+.+++ ++..+.|+.+.|--.|+
T Consensus 19 ~~Ia~yil~~~~~~~~~si~elA~~~~v----S~sti~Rf~kkLG~~gf 63 (77)
T PF01418_consen 19 KKIADYILENPDEIAFMSISELAEKAGV----SPSTIVRFCKKLGFSGF 63 (77)
T ss_dssp HHHHHHHHH-HHHHCT--HHHHHHHCTS-----HHHHHHHHHHCTTTCH
T ss_pred HHHHHHHHhCHHHHHHccHHHHHHHcCC----CHHHHHHHHHHhCCCCH
Confidence 34555554431 0136899999999999 99999998887755554
No 487
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=64.14 E-value=14 Score=31.09 Aligned_cols=60 Identities=18% Similarity=0.222 Sum_probs=50.0
Q ss_pred hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
+|.+|..+.+. .+...-|+++++ ++..+.+-++.|.. .-+|.+. +..+.+|+.|..|...
T Consensus 6 ~L~~f~~v~e~-----~s~s~AA~~L~i----sQpavS~~I~~LE~~lg~~LF~R~-----~r~~~lT~~G~~l~~~ 68 (300)
T PRK11074 6 SLEVVDAVART-----GSFSAAAQELHR----VPSAVSYTVRQLEEWLAVPLFERR-----HRDVELTPAGEWFVKE 68 (300)
T ss_pred HHHHHHHHHHh-----CCHHHHHHHhCC----CHHHHHHHHHHHHHHhCCeeEEeC-----CCCceECccHHHHHHH
Confidence 57789999984 588999999999 99999999888876 6788884 7779999999776543
No 488
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=63.92 E-value=11 Score=26.63 Aligned_cols=47 Identities=23% Similarity=0.195 Sum_probs=34.6
Q ss_pred HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCC
Q 039903 17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHR 65 (233)
Q Consensus 17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~g 65 (233)
..-.|++.+...|...-.|.-|||+-.|. |-.++-+.++|+.|..--
T Consensus 7 f~~~v~~vv~~IP~GkV~TYGdIA~laG~--p~~ARqVG~il~~l~~~s 53 (103)
T COG3695 7 FTQRVLDVVAAIPEGKVSTYGDIAKLAGL--PRAARQVGRILKHLPEGS 53 (103)
T ss_pred HHHHHHHHHHhCCCCceeeHHHHHHHhCC--ChhHHHHHHHHhhCCCCC
Confidence 34567888888765457799999999999 112888899888765533
No 489
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=63.83 E-value=5.5 Score=25.06 Aligned_cols=31 Identities=26% Similarity=0.368 Sum_probs=21.6
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHH
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILR 59 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~ 59 (233)
|-+.+.+ ..+|..+||+.+|+ ++..+.++++
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 3456666 47899999999999 8988888875
No 490
>PF05891 Methyltransf_PK: AdoMet dependent proline di-methyltransferase; InterPro: IPR008576 This family consists of several eukaryotic proteins of unknown function that are S-adenosyl-L-methionine-dependent methyltransferase-like.; GO: 0008168 methyltransferase activity; PDB: 1XTP_A 2EX4_B.
Probab=63.47 E-value=12 Score=30.44 Aligned_cols=41 Identities=10% Similarity=0.207 Sum_probs=26.9
Q ss_pred CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC
Q 039903 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS 209 (233)
Q Consensus 168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~ 209 (233)
+..+.+|+|+|.|-.+..++-.+- -++.++|- +.-++.|++
T Consensus 55 ~~~~alDcGAGIGRVTk~lLl~~f-~~VDlVEp~~~Fl~~a~~ 96 (218)
T PF05891_consen 55 KFNRALDCGAGIGRVTKGLLLPVF-DEVDLVEPVEKFLEQAKE 96 (218)
T ss_dssp --SEEEEET-TTTHHHHHTCCCC--SEEEEEES-HHHHHHHHH
T ss_pred CcceEEecccccchhHHHHHHHhc-CEeEEeccCHHHHHHHHH
Confidence 468999999999999998766431 23566664 456666663
No 491
>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=63.34 E-value=13 Score=32.31 Aligned_cols=42 Identities=7% Similarity=0.080 Sum_probs=37.1
Q ss_pred HHHHhcCCCCCCCHHHHHHh--CCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903 23 EIIAKAGPTAKISAVEIAAQ--MPSSNPNAAVMLDRILRLLVTHRVLRCTS 71 (233)
Q Consensus 23 d~L~~~~~~~~~t~~elA~~--~~~~~~~~~~~l~rlL~~L~~~gll~~~~ 71 (233)
+++... +|.+..+|++. +++ ++.-++|-|..|...|++.+..
T Consensus 14 ~~l~~~---~pv~s~~l~~~~~~~v----S~aTiR~d~~~Le~~G~l~~~h 57 (337)
T TIGR00331 14 EYIKTG---QPVGSKTLLEKYNLGL----SSATIRNDMADLEDLGFIEKPH 57 (337)
T ss_pred HHHhcC---CCcCHHHHHhhcCCCC----ChHHHHHHHHHHHHCCCccCCC
Confidence 355554 69999999999 999 9999999999999999999974
No 492
>PF13551 HTH_29: Winged helix-turn helix
Probab=63.23 E-value=10 Score=26.60 Aligned_cols=27 Identities=19% Similarity=0.137 Sum_probs=25.8
Q ss_pred CHHHHHHhCCCCCCCChhhHHHHHHHHhcCC
Q 039903 35 SAVEIAAQMPSSNPNAAVMLDRILRLLVTHR 65 (233)
Q Consensus 35 t~~elA~~~~~~~~~~~~~l~rlL~~L~~~g 65 (233)
|..+||+.+|+ +.+-+++|++....-|
T Consensus 14 ~~~~ia~~lg~----s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGI----SRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCc----CHHHHHHHHHHHHccc
Confidence 79999999999 9999999999998888
No 493
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=63.06 E-value=15 Score=27.01 Aligned_cols=60 Identities=12% Similarity=0.158 Sum_probs=44.4
Q ss_pred hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903 21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN 91 (233)
Q Consensus 21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~ 91 (233)
+.+.|.+.. ..+.|+++||+.+++ +++.+.|+++.-..+.+-+.. ..+++......|...
T Consensus 14 ~~~~I~~~~-~~~~sl~~lA~~~g~----S~~~l~r~Fk~~~G~s~~~~l------~~~Rl~~A~~~L~~t 73 (127)
T PRK11511 14 ILDWIEDNL-ESPLSLEKVSERSGY----SKWHLQRMFKKETGHSLGQYI------RSRKMTEIAQKLKES 73 (127)
T ss_pred HHHHHHHhc-CCCCCHHHHHHHHCc----CHHHHHHHHHHHHCcCHHHHH------HHHHHHHHHHHHHcC
Confidence 445555542 247999999999999 999999999998888777763 446666666666543
No 494
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=63.06 E-value=9.4 Score=35.52 Aligned_cols=37 Identities=11% Similarity=0.139 Sum_probs=34.4
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeecc
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSA 72 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~ 72 (233)
...|+.|||+.+.+ ++|.++.+|+.|...|.++....
T Consensus 22 ~~~~l~~la~~l~c----s~R~~~~~l~~~~~~gwl~w~~~ 58 (552)
T PRK13626 22 QETTLNELAELLNC----SRRHMRTLLNTMQQRGWLTWQAE 58 (552)
T ss_pred ceeeHHHHHHHhcC----ChhHHHHHHHHHHHCCCeeeecC
Confidence 57899999999999 99999999999999999998653
No 495
>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=62.83 E-value=9.7 Score=22.80 Aligned_cols=26 Identities=23% Similarity=0.302 Sum_probs=21.6
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHH
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLL 61 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L 61 (233)
.+.|..|||+.+|+ +...+.++.+-.
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 999998887543
No 496
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=62.66 E-value=14 Score=29.94 Aligned_cols=35 Identities=23% Similarity=0.219 Sum_probs=32.2
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
.+.|..|||+++++ ++.-++..++.|+..|++.+.
T Consensus 177 ~g~s~~eIA~~l~i----S~~Tv~~~~~~~~~~~~~~~~ 211 (239)
T PRK10430 177 YEFSTDELANAVNI----SRVSCRKYLIWLVNCHILFTS 211 (239)
T ss_pred CCcCHHHHHHHhCc----hHHHHHHHHHHHHhCCEEEEE
Confidence 37899999999999 999999999999999999664
No 497
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=62.59 E-value=18 Score=29.58 Aligned_cols=51 Identities=18% Similarity=0.244 Sum_probs=43.9
Q ss_pred HHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903 13 MQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT 70 (233)
Q Consensus 13 L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~ 70 (233)
+..-.+.+|++.+..+| +.++.|+++.+++ +-..++-.+|.|.+.++++-.
T Consensus 98 ~~ns~R~~Iy~~i~~nP---G~~lsEl~~nl~i----~R~TlRyhlriLe~~~li~a~ 148 (240)
T COG3398 98 FLNSKRDGIYNYIKPNP---GFSLSELRANLYI----NRSTLRYHLRILESNPLIEAG 148 (240)
T ss_pred HhhhhHHHHHHHhccCC---CccHHHHHHhcCC----ChHHHHHHHHHHHhCcchhhh
Confidence 34445778999999985 8999999999999 888999999999999999864
No 498
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=62.32 E-value=13 Score=30.12 Aligned_cols=47 Identities=17% Similarity=0.171 Sum_probs=40.2
Q ss_pred CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhh
Q 039903 32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAK 86 (233)
Q Consensus 32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~ 86 (233)
.+++-.+||+.+|+ +.-.++.-|.-|+..|+++.. .+..+..++.+.
T Consensus 38 ~~l~e~~La~~~gv----SrtPVReAL~rL~~eGlv~~~----p~rG~~V~~~~~ 84 (230)
T COG1802 38 ERLSEEELAEELGV----SRTPVREALRRLEAEGLVEIE----PNRGAFVAPLSL 84 (230)
T ss_pred CCccHHHHHHHhCC----CCccHHHHHHHHHHCCCeEec----CCCCCeeCCCCH
Confidence 68999999999999 999999999999999999997 455565665554
No 499
>PF12728 HTH_17: Helix-turn-helix domain
Probab=62.24 E-value=8.8 Score=23.03 Aligned_cols=23 Identities=17% Similarity=0.182 Sum_probs=20.2
Q ss_pred CCHHHHHHhCCCCCCCChhhHHHHHHH
Q 039903 34 ISAVEIAAQMPSSNPNAAVMLDRILRL 60 (233)
Q Consensus 34 ~t~~elA~~~~~~~~~~~~~l~rlL~~ 60 (233)
+|++|+|+.+++ +...+++|++.
T Consensus 2 lt~~e~a~~l~i----s~~tv~~~~~~ 24 (51)
T PF12728_consen 2 LTVKEAAELLGI----SRSTVYRWIRQ 24 (51)
T ss_pred CCHHHHHHHHCc----CHHHHHHHHHc
Confidence 588999999999 99999988853
No 500
>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=62.05 E-value=25 Score=30.25 Aligned_cols=62 Identities=19% Similarity=0.233 Sum_probs=40.6
Q ss_pred HHHHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcC--CCcEEEeechHH
Q 039903 142 GVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL--HIKGVNFDLSHV 203 (233)
Q Consensus 142 ~~f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P--~l~~~v~Dlp~v 203 (233)
....+.+..........+.+.+..++...+|+=+|||.-.+..++.+.+| +-++++.|-|+.
T Consensus 246 ~~v~~~i~~~~~~l~~~i~~~~~~~~~~~~I~~vGGGA~ll~~~Ik~~~~~~~~~i~i~~~pqf 309 (318)
T PF06406_consen 246 DDVSEVIEEAVEELINRILRELGDFSDIDRIFFVGGGAILLKDAIKEAFPVPNERIVIVDDPQF 309 (318)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTS-S-SEEEEESTTHHHHHHHHHHHHT--GGGEE--SSGGG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhccCCeEEEECCcHHHHHHHHHHhhCCCCCcEEECCCchh
Confidence 33444444444444445555544477788899999999999999999988 567888888863
Done!