Query 041256
Match_columns 244
No_of_seqs 158 out of 1100
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 05:20:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041256.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041256hhsearch_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 2.1E-31 4.6E-36 229.0 17.4 226 8-242 1-227 (342)
2 TIGR02716 C20_methyl_CrtF C-20 99.9 2.6E-27 5.6E-32 206.5 14.8 185 25-234 2-190 (306)
3 PF00891 Methyltransf_2: O-met 99.9 1.5E-27 3.3E-32 201.2 10.3 147 95-243 3-150 (241)
4 PF08100 Dimerisation: Dimeris 99.1 2E-10 4.2E-15 72.8 5.0 51 28-82 1-51 (51)
5 PRK06922 hypothetical protein; 98.1 4.1E-06 9E-11 79.0 6.1 81 153-234 377-460 (677)
6 PF12847 Methyltransf_18: Meth 97.9 7.7E-06 1.7E-10 60.1 2.7 41 194-234 2-43 (112)
7 PRK14103 trans-aconitate 2-met 97.9 4.1E-05 8.8E-10 65.0 7.4 57 182-240 19-76 (255)
8 COG4106 Tam Trans-aconitate me 97.8 6.6E-05 1.4E-09 61.5 6.3 60 181-241 19-80 (257)
9 PRK08287 cobalt-precorrin-6Y C 97.8 3.8E-05 8.1E-10 62.1 4.8 49 185-234 24-73 (187)
10 PRK01683 trans-aconitate 2-met 97.8 6.2E-05 1.4E-09 63.9 6.3 59 181-240 20-80 (258)
11 PF13847 Methyltransf_31: Meth 97.5 9.8E-05 2.1E-09 57.6 3.9 42 193-234 3-46 (152)
12 TIGR03587 Pse_Me-ase pseudamin 97.5 0.00017 3.6E-09 59.4 5.4 49 192-240 42-92 (204)
13 TIGR02469 CbiT precorrin-6Y C5 97.5 0.0002 4.3E-09 53.2 5.3 49 184-233 11-60 (124)
14 TIGR00091 tRNA (guanine-N(7)-) 97.5 0.0002 4.4E-09 58.3 5.1 41 193-233 16-57 (194)
15 PRK00107 gidB 16S rRNA methylt 97.4 0.00038 8.3E-09 56.5 6.0 42 193-234 45-87 (187)
16 PRK15001 SAM-dependent 23S rib 97.4 0.00022 4.7E-09 64.0 4.9 51 183-234 219-270 (378)
17 TIGR02021 BchM-ChlM magnesium 97.3 0.00048 1E-08 57.0 6.0 78 155-234 16-95 (219)
18 PRK04457 spermidine synthase; 97.3 0.00019 4.2E-09 61.3 3.6 43 192-234 65-108 (262)
19 PF08242 Methyltransf_12: Meth 97.3 6.5E-05 1.4E-09 54.0 0.4 37 198-234 1-38 (99)
20 PF09339 HTH_IclR: IclR helix- 97.3 9.9E-05 2.1E-09 47.0 1.2 45 36-89 6-50 (52)
21 PRK00121 trmB tRNA (guanine-N( 97.3 0.00043 9.3E-09 56.8 5.1 49 184-234 33-82 (202)
22 TIGR02752 MenG_heptapren 2-hep 97.3 0.00057 1.2E-08 56.9 5.7 50 183-233 36-87 (231)
23 COG2813 RsmC 16S RNA G1207 met 97.2 0.00051 1.1E-08 59.2 5.2 52 182-234 148-200 (300)
24 TIGR00138 gidB 16S rRNA methyl 97.2 0.00033 7.1E-09 56.5 3.7 40 194-233 43-83 (181)
25 PRK06202 hypothetical protein; 97.2 0.0012 2.6E-08 55.1 7.3 43 192-234 59-106 (232)
26 PRK07402 precorrin-6B methylas 97.2 0.00048 1E-08 56.1 4.7 50 184-234 32-82 (196)
27 PRK14121 tRNA (guanine-N(7)-)- 97.2 0.00072 1.6E-08 60.7 5.7 50 183-233 113-163 (390)
28 PF05175 MTS: Methyltransferas 97.2 0.00025 5.5E-09 56.5 2.4 42 193-234 31-73 (170)
29 smart00346 HTH_ICLR helix_turn 97.1 0.00091 2E-08 47.3 4.5 58 36-104 8-65 (91)
30 TIGR00740 methyltransferase, p 97.1 0.00058 1.3E-08 57.3 3.9 43 192-234 52-97 (239)
31 PRK09489 rsmC 16S ribosomal RN 97.0 0.00087 1.9E-08 59.5 4.9 50 184-234 188-238 (342)
32 COG2242 CobL Precorrin-6B meth 97.0 0.0013 2.8E-08 52.9 5.3 48 186-234 28-76 (187)
33 PRK11207 tellurite resistance 97.0 0.00084 1.8E-08 54.8 4.3 50 182-234 20-70 (197)
34 PRK15451 tRNA cmo(5)U34 methyl 97.0 0.00062 1.3E-08 57.6 3.5 43 192-234 55-100 (247)
35 PRK00274 ksgA 16S ribosomal RN 97.0 0.0016 3.4E-08 56.0 5.7 57 182-241 32-92 (272)
36 PF02390 Methyltransf_4: Putat 97.0 0.0012 2.5E-08 54.0 4.6 47 195-241 19-72 (195)
37 PRK08317 hypothetical protein; 96.9 0.0018 3.8E-08 53.6 5.5 50 184-234 11-62 (241)
38 COG2890 HemK Methylase of poly 96.9 0.00071 1.5E-08 58.4 2.9 39 196-234 113-152 (280)
39 PF13649 Methyltransf_25: Meth 96.9 0.00069 1.5E-08 48.9 2.3 38 197-234 1-42 (101)
40 COG2226 UbiE Methylase involve 96.9 0.0019 4E-08 54.3 5.2 42 193-234 51-93 (238)
41 smart00550 Zalpha Z-DNA-bindin 96.9 0.0025 5.4E-08 42.9 4.8 60 33-102 6-66 (68)
42 smart00650 rADc Ribosomal RNA 96.8 0.0023 5E-08 50.8 5.4 50 182-234 3-53 (169)
43 PRK10258 biotin biosynthesis p 96.8 0.0038 8.2E-08 52.7 6.7 50 182-234 32-82 (251)
44 TIGR03533 L3_gln_methyl protei 96.8 0.0012 2.6E-08 57.1 3.6 42 193-234 121-163 (284)
45 TIGR00477 tehB tellurite resis 96.8 0.0025 5.3E-08 52.0 5.3 49 182-233 20-69 (195)
46 PRK11088 rrmA 23S rRNA methylt 96.8 0.0028 6.2E-08 54.3 5.9 48 193-240 85-137 (272)
47 TIGR03704 PrmC_rel_meth putati 96.8 0.0021 4.5E-08 54.7 4.9 41 194-234 87-128 (251)
48 PRK11036 putative S-adenosyl-L 96.8 0.0026 5.6E-08 54.0 5.6 48 183-234 36-84 (255)
49 TIGR02072 BioC biotin biosynth 96.8 0.0018 3.8E-08 53.7 4.5 42 193-234 34-76 (240)
50 PRK11805 N5-glutamine S-adenos 96.7 0.0012 2.6E-08 57.8 3.2 40 195-234 135-175 (307)
51 TIGR03534 RF_mod_PrmC protein- 96.7 0.0028 6.2E-08 53.2 5.2 42 193-234 87-129 (251)
52 TIGR00080 pimt protein-L-isoas 96.7 0.0042 9.1E-08 51.3 6.0 51 183-234 68-120 (215)
53 COG2264 PrmA Ribosomal protein 96.7 0.0012 2.6E-08 57.1 2.8 63 168-234 140-203 (300)
54 COG1414 IclR Transcriptional r 96.7 0.0024 5.1E-08 54.1 4.4 59 36-105 7-65 (246)
55 PRK00216 ubiE ubiquinone/menaq 96.6 0.0031 6.8E-08 52.3 5.0 51 183-234 42-94 (239)
56 PRK01581 speE spermidine synth 96.6 0.0027 5.8E-08 56.5 4.7 43 192-234 149-192 (374)
57 PTZ00098 phosphoethanolamine N 96.6 0.0031 6.7E-08 53.9 4.8 51 182-234 42-93 (263)
58 PLN02244 tocopherol O-methyltr 96.6 0.0031 6.8E-08 55.9 4.9 41 192-233 117-158 (340)
59 PRK07580 Mg-protoporphyrin IX 96.6 0.0034 7.5E-08 52.0 4.8 41 192-234 62-103 (230)
60 PRK14966 unknown domain/N5-glu 96.6 0.0022 4.7E-08 58.1 3.6 42 193-234 251-293 (423)
61 COG2230 Cfa Cyclopropane fatty 96.5 0.0049 1.1E-07 53.0 5.6 50 182-233 62-112 (283)
62 PRK11188 rrmJ 23S rRNA methylt 96.5 0.0082 1.8E-07 49.5 6.8 45 183-227 41-86 (209)
63 PLN02366 spermidine synthase 96.5 0.0024 5.3E-08 55.8 3.8 42 192-234 90-133 (308)
64 TIGR00536 hemK_fam HemK family 96.5 0.0021 4.6E-08 55.5 3.2 40 195-234 116-156 (284)
65 PRK09328 N5-glutamine S-adenos 96.5 0.0041 8.9E-08 53.1 4.9 44 191-234 106-150 (275)
66 PHA03411 putative methyltransf 96.5 0.0036 7.9E-08 53.6 4.5 47 194-240 65-113 (279)
67 PRK01544 bifunctional N5-gluta 96.5 0.0024 5.2E-08 59.7 3.5 41 194-234 139-180 (506)
68 PRK11569 transcriptional repre 96.4 0.0042 9.1E-08 53.4 4.6 59 36-105 31-89 (274)
69 PRK00811 spermidine synthase; 96.4 0.0028 6E-08 54.8 3.4 43 192-234 75-118 (283)
70 PRK04266 fibrillarin; Provisio 96.4 0.0078 1.7E-07 50.3 5.9 53 188-241 68-125 (226)
71 TIGR01934 MenG_MenH_UbiE ubiqu 96.4 0.0049 1.1E-07 50.5 4.6 51 183-234 30-82 (223)
72 PLN02490 MPBQ/MSBQ methyltrans 96.4 0.0075 1.6E-07 53.4 6.0 42 193-234 113-155 (340)
73 PRK10163 DNA-binding transcrip 96.4 0.0047 1E-07 53.1 4.6 59 36-105 28-86 (271)
74 TIGR02431 pcaR_pcaU beta-ketoa 96.4 0.0043 9.3E-08 52.5 4.3 59 36-107 12-70 (248)
75 PRK05785 hypothetical protein; 96.4 0.004 8.6E-08 52.0 4.0 40 194-234 52-92 (226)
76 PF01978 TrmB: Sugar-specific 96.4 0.0026 5.6E-08 42.6 2.3 56 34-100 9-64 (68)
77 PLN02233 ubiquinone biosynthes 96.4 0.0086 1.9E-07 51.1 6.0 43 191-233 71-115 (261)
78 PRK13942 protein-L-isoaspartat 96.3 0.01 2.2E-07 49.0 6.2 51 183-234 67-119 (212)
79 smart00138 MeTrc Methyltransfe 96.3 0.023 5.1E-07 48.6 8.6 52 182-234 89-150 (264)
80 TIGR00438 rrmJ cell division p 96.3 0.01 2.3E-07 47.8 6.1 44 184-227 23-67 (188)
81 TIGR00755 ksgA dimethyladenosi 96.3 0.0074 1.6E-07 51.2 5.5 49 182-233 19-68 (253)
82 PF13659 Methyltransf_26: Meth 96.3 0.0047 1E-07 45.4 3.7 39 195-234 2-41 (117)
83 PF01209 Ubie_methyltran: ubiE 96.3 0.0036 7.7E-08 52.6 3.4 44 191-234 45-90 (233)
84 PF06325 PrmA: Ribosomal prote 96.3 0.0022 4.8E-08 55.7 2.2 63 168-234 139-202 (295)
85 PRK15090 DNA-binding transcrip 96.3 0.005 1.1E-07 52.4 4.2 58 36-105 17-74 (257)
86 PF13679 Methyltransf_32: Meth 96.3 0.0053 1.2E-07 47.3 4.0 43 191-233 23-70 (141)
87 COG4123 Predicted O-methyltran 96.3 0.0042 9E-08 52.4 3.6 44 191-234 42-86 (248)
88 PLN02336 phosphoethanolamine N 96.3 0.0059 1.3E-07 56.5 5.0 51 182-234 256-307 (475)
89 PRK11705 cyclopropane fatty ac 96.3 0.0065 1.4E-07 54.8 5.0 50 183-234 158-208 (383)
90 PRK14896 ksgA 16S ribosomal RN 96.3 0.0086 1.9E-07 51.0 5.5 50 182-234 19-69 (258)
91 COG0220 Predicted S-adenosylme 96.2 0.0084 1.8E-07 50.1 5.2 38 194-231 49-87 (227)
92 PRK09834 DNA-binding transcrip 96.2 0.0066 1.4E-07 51.8 4.6 61 36-107 14-74 (263)
93 PRK13944 protein-L-isoaspartat 96.2 0.0096 2.1E-07 48.9 5.3 50 184-234 64-115 (205)
94 PF02082 Rrf2: Transcriptional 96.2 0.0098 2.1E-07 41.5 4.6 52 43-103 18-70 (83)
95 PF13489 Methyltransf_23: Meth 96.1 0.018 4E-07 44.5 6.4 39 191-231 20-59 (161)
96 PF02353 CMAS: Mycolic acid cy 96.1 0.0081 1.8E-07 51.7 4.5 49 182-232 52-101 (273)
97 PRK00050 16S rRNA m(4)C1402 me 96.1 0.011 2.5E-07 51.3 5.4 53 181-234 8-62 (296)
98 PRK12335 tellurite resistance 96.1 0.0069 1.5E-07 52.4 4.0 49 183-234 111-160 (287)
99 PRK15068 tRNA mo(5)U34 methylt 96.1 0.012 2.6E-07 51.9 5.5 40 185-226 115-154 (322)
100 TIGR00537 hemK_rel_arch HemK-r 96.1 0.0058 1.3E-07 48.9 3.3 39 194-234 20-59 (179)
101 PRK03612 spermidine synthase; 96.0 0.0091 2E-07 56.0 4.9 42 192-234 296-339 (521)
102 TIGR01444 fkbM_fam methyltrans 96.0 0.0061 1.3E-07 46.6 3.1 39 196-234 1-40 (143)
103 PRK00377 cbiT cobalt-precorrin 96.0 0.011 2.4E-07 48.2 4.7 47 187-234 35-83 (198)
104 TIGR00406 prmA ribosomal prote 96.0 0.0059 1.3E-07 52.9 3.2 41 193-234 159-200 (288)
105 PHA03412 putative methyltransf 95.9 0.0098 2.1E-07 49.9 4.0 47 194-240 50-101 (241)
106 KOG1540 Ubiquinone biosynthesi 95.9 0.021 4.5E-07 48.3 5.9 42 193-234 100-148 (296)
107 PF13412 HTH_24: Winged helix- 95.9 0.011 2.4E-07 36.6 3.3 45 34-88 4-48 (48)
108 PRK00517 prmA ribosomal protei 95.9 0.0069 1.5E-07 51.3 3.1 42 192-234 118-160 (250)
109 PF08241 Methyltransf_11: Meth 95.8 0.0063 1.4E-07 42.5 2.3 36 198-234 1-37 (95)
110 TIGR02081 metW methionine bios 95.8 0.013 2.9E-07 47.5 4.3 40 193-233 13-53 (194)
111 PRK00536 speE spermidine synth 95.7 0.012 2.5E-07 50.3 3.8 41 192-234 71-112 (262)
112 PF13463 HTH_27: Winged helix 95.7 0.02 4.2E-07 38.0 4.1 48 49-103 17-67 (68)
113 TIGR03438 probable methyltrans 95.7 0.011 2.4E-07 51.5 3.6 41 193-233 63-105 (301)
114 PRK14968 putative methyltransf 95.7 0.012 2.7E-07 46.9 3.6 40 192-233 22-62 (188)
115 PLN03075 nicotianamine synthas 95.6 0.017 3.6E-07 50.2 4.4 43 192-234 122-167 (296)
116 TIGR00452 methyltransferase, p 95.6 0.025 5.3E-07 49.7 5.5 40 184-225 113-152 (314)
117 KOG2899 Predicted methyltransf 95.6 0.012 2.6E-07 49.2 3.3 52 183-234 47-100 (288)
118 PLN02336 phosphoethanolamine N 95.6 0.027 5.8E-07 52.2 6.0 49 182-233 27-76 (475)
119 PLN02672 methionine S-methyltr 95.5 0.01 2.3E-07 59.7 3.4 40 195-234 120-160 (1082)
120 PLN02396 hexaprenyldihydroxybe 95.5 0.014 3.1E-07 51.3 3.8 39 194-234 132-171 (322)
121 COG2227 UbiG 2-polyprenyl-3-me 95.5 0.011 2.5E-07 49.3 2.9 39 194-234 60-99 (243)
122 COG3355 Predicted transcriptio 95.5 0.029 6.2E-07 42.3 4.7 46 35-90 29-75 (126)
123 KOG2904 Predicted methyltransf 95.5 0.019 4.1E-07 48.9 4.1 44 191-234 146-190 (328)
124 cd02440 AdoMet_MTases S-adenos 95.4 0.015 3.3E-07 40.4 3.1 37 196-233 1-38 (107)
125 TIGR00417 speE spermidine synt 95.4 0.014 3.1E-07 50.0 3.4 43 192-234 71-114 (270)
126 PF01022 HTH_5: Bacterial regu 95.4 0.013 2.8E-07 36.2 2.2 43 35-88 4-46 (47)
127 TIGR00478 tly hemolysin TlyA f 95.3 0.06 1.3E-06 45.1 6.8 56 182-238 64-121 (228)
128 cd00092 HTH_CRP helix_turn_hel 95.3 0.037 8.1E-07 36.4 4.6 44 49-102 24-67 (67)
129 PRK11727 23S rRNA mA1618 methy 95.3 0.015 3.4E-07 51.1 3.3 42 193-234 114-156 (321)
130 PLN02585 magnesium protoporphy 95.3 0.015 3.2E-07 51.1 3.2 39 194-234 145-184 (315)
131 PRK10141 DNA-binding transcrip 95.3 0.036 7.7E-07 41.5 4.8 68 25-102 8-75 (117)
132 PRK11512 DNA-binding transcrip 95.3 0.11 2.5E-06 39.9 7.8 44 37-90 44-87 (144)
133 PTZ00338 dimethyladenosine tra 95.3 0.039 8.5E-07 48.0 5.6 49 182-233 26-75 (294)
134 COG1959 Predicted transcriptio 95.3 0.036 7.8E-07 43.3 4.9 54 41-103 16-70 (150)
135 PF12840 HTH_20: Helix-turn-he 95.2 0.021 4.5E-07 37.3 3.0 52 28-89 5-56 (61)
136 KOG1271 Methyltransferases [Ge 95.2 0.026 5.7E-07 45.3 3.9 39 193-233 67-108 (227)
137 PRK11873 arsM arsenite S-adeno 95.1 0.027 5.8E-07 48.1 4.1 44 191-234 75-120 (272)
138 PRK13943 protein-L-isoaspartat 95.0 0.044 9.6E-07 48.3 5.2 51 183-234 71-123 (322)
139 COG0421 SpeE Spermidine syntha 95.0 0.025 5.4E-07 48.8 3.6 44 191-234 74-118 (282)
140 TIGR02010 IscR iron-sulfur clu 95.0 0.052 1.1E-06 41.5 5.0 46 49-102 24-69 (135)
141 PRK14967 putative methyltransf 95.0 0.032 6.9E-07 46.3 4.0 43 191-234 34-77 (223)
142 TIGR03840 TMPT_Se_Te thiopurin 94.9 0.053 1.2E-06 44.9 5.2 39 192-232 33-72 (213)
143 smart00419 HTH_CRP helix_turn_ 94.9 0.046 1E-06 33.3 3.8 41 50-101 8-48 (48)
144 PF07021 MetW: Methionine bios 94.8 0.032 6.9E-07 45.2 3.6 33 192-225 12-44 (193)
145 PF13601 HTH_34: Winged helix 94.8 0.029 6.3E-07 39.0 2.9 62 34-105 1-66 (80)
146 PRK10857 DNA-binding transcrip 94.8 0.063 1.4E-06 42.6 5.1 46 49-102 24-69 (164)
147 PLN02823 spermine synthase 94.8 0.03 6.5E-07 49.6 3.6 43 192-234 102-145 (336)
148 PRK13168 rumA 23S rRNA m(5)U19 94.8 0.031 6.8E-07 51.4 3.8 49 183-234 288-337 (443)
149 COG2263 Predicted RNA methylas 94.7 0.026 5.7E-07 45.5 2.9 41 193-234 45-86 (198)
150 smart00418 HTH_ARSR helix_turn 94.7 0.077 1.7E-06 34.1 4.7 42 38-90 2-43 (66)
151 PF07757 AdoMet_MTase: Predict 94.7 0.041 8.9E-07 40.3 3.5 44 179-225 45-88 (112)
152 PF12802 MarR_2: MarR family; 94.7 0.037 7.9E-07 35.9 3.0 48 35-90 7-54 (62)
153 PF08003 Methyltransf_9: Prote 94.7 0.057 1.2E-06 46.9 4.9 40 183-224 106-145 (315)
154 PRK03522 rumB 23S rRNA methylu 94.6 0.056 1.2E-06 47.4 5.0 39 194-234 174-213 (315)
155 PF09012 FeoC: FeoC like trans 94.6 0.044 9.6E-07 36.8 3.4 43 38-90 5-47 (69)
156 PF01047 MarR: MarR family; I 94.6 0.029 6.3E-07 36.1 2.3 45 36-90 6-50 (59)
157 PRK04148 hypothetical protein; 94.5 0.063 1.4E-06 41.1 4.4 48 184-234 8-57 (134)
158 PF03848 TehB: Tellurite resis 94.5 0.09 1.9E-06 42.8 5.4 48 182-232 20-68 (192)
159 TIGR00738 rrf2_super rrf2 fami 94.4 0.07 1.5E-06 40.4 4.5 46 49-102 24-69 (132)
160 PF14947 HTH_45: Winged helix- 94.4 0.043 9.2E-07 37.8 2.9 49 49-108 18-66 (77)
161 PRK06266 transcription initiat 94.3 0.18 3.9E-06 40.5 6.8 44 36-89 25-68 (178)
162 PLN02781 Probable caffeoyl-CoA 94.3 0.084 1.8E-06 44.3 5.0 44 191-234 66-111 (234)
163 PRK00312 pcm protein-L-isoaspa 94.2 0.088 1.9E-06 43.2 5.0 48 184-234 70-118 (212)
164 PRK10901 16S rRNA methyltransf 94.1 0.061 1.3E-06 49.2 4.2 50 184-234 236-286 (427)
165 PTZ00146 fibrillarin; Provisio 94.1 0.11 2.3E-06 45.1 5.4 51 191-241 130-186 (293)
166 PF04703 FaeA: FaeA-like prote 94.1 0.056 1.2E-06 35.6 2.8 45 37-90 4-48 (62)
167 PRK13255 thiopurine S-methyltr 94.1 0.11 2.4E-06 43.1 5.3 39 192-232 36-75 (218)
168 PF05401 NodS: Nodulation prot 94.0 0.043 9.4E-07 44.7 2.7 52 187-241 38-94 (201)
169 KOG1270 Methyltransferases [Co 94.0 0.036 7.7E-07 47.0 2.2 38 195-234 91-129 (282)
170 TIGR02337 HpaR homoprotocatech 94.0 0.14 3E-06 38.0 5.3 65 34-108 29-96 (118)
171 PRK10909 rsmD 16S rRNA m(2)G96 94.0 0.078 1.7E-06 43.4 4.2 40 194-234 54-94 (199)
172 PRK05134 bifunctional 3-demeth 93.9 0.1 2.2E-06 43.4 4.8 39 193-233 48-87 (233)
173 TIGR02702 SufR_cyano iron-sulf 93.9 0.12 2.7E-06 42.3 5.2 62 36-107 4-70 (203)
174 PF07381 DUF1495: Winged helix 93.8 0.11 2.5E-06 36.8 4.1 68 32-107 8-86 (90)
175 smart00347 HTH_MARR helix_turn 93.7 0.1 2.2E-06 36.9 3.9 45 35-89 12-56 (101)
176 PRK14902 16S rRNA methyltransf 93.6 0.089 1.9E-06 48.4 4.3 50 184-234 242-293 (444)
177 PF10294 Methyltransf_16: Puta 93.6 0.098 2.1E-06 41.8 4.0 42 192-233 44-85 (173)
178 PF01135 PCMT: Protein-L-isoas 93.6 0.11 2.4E-06 42.8 4.5 51 183-234 63-115 (209)
179 cd00090 HTH_ARSR Arsenical Res 93.5 0.2 4.4E-06 33.0 5.0 56 36-102 10-65 (78)
180 TIGR02944 suf_reg_Xantho FeS a 93.5 0.11 2.3E-06 39.4 3.9 46 49-102 24-69 (130)
181 PF01564 Spermine_synth: Sperm 93.5 0.06 1.3E-06 45.6 2.7 43 192-234 75-118 (246)
182 TIGR00479 rumA 23S rRNA (uraci 93.4 0.1 2.2E-06 47.8 4.3 47 185-234 285-332 (431)
183 PF08220 HTH_DeoR: DeoR-like h 93.4 0.19 4.2E-06 32.3 4.4 42 38-89 5-46 (57)
184 PF08461 HTH_12: Ribonuclease 93.4 0.13 2.9E-06 34.2 3.7 61 38-105 3-63 (66)
185 PF04967 HTH_10: HTH DNA bindi 93.3 0.12 2.6E-06 32.9 3.3 32 26-63 5-36 (53)
186 KOG3010 Methyltransferase [Gen 93.3 0.085 1.9E-06 44.2 3.3 44 193-238 33-77 (261)
187 COG4976 Predicted methyltransf 93.2 0.083 1.8E-06 44.1 3.0 64 166-232 95-163 (287)
188 TIGR01884 cas_HTH CRISPR locus 93.1 0.18 3.9E-06 41.3 4.9 58 35-103 145-202 (203)
189 TIGR01983 UbiG ubiquinone bios 93.1 0.099 2.1E-06 43.0 3.4 39 193-233 45-84 (224)
190 PF01638 HxlR: HxlR-like helix 93.1 0.12 2.7E-06 36.5 3.5 60 38-108 10-73 (90)
191 PRK01544 bifunctional N5-gluta 93.0 0.11 2.5E-06 48.6 4.1 33 193-225 347-379 (506)
192 PF01728 FtsJ: FtsJ-like methy 93.0 0.14 3E-06 40.9 4.0 47 182-228 10-59 (181)
193 PRK03902 manganese transport t 92.9 0.19 4.1E-06 38.7 4.6 49 49-107 21-69 (142)
194 TIGR00122 birA_repr_reg BirA b 92.8 0.26 5.6E-06 32.9 4.5 56 35-104 2-57 (69)
195 TIGR02085 meth_trns_rumB 23S r 92.7 0.12 2.7E-06 46.4 3.8 39 194-234 234-273 (374)
196 PHA00738 putative HTH transcri 92.7 0.26 5.7E-06 36.0 4.6 60 34-103 13-72 (108)
197 PRK11050 manganese transport r 92.6 0.76 1.6E-05 35.9 7.7 57 38-107 42-98 (152)
198 TIGR00095 RNA methyltransferas 92.4 0.13 2.8E-06 41.8 3.1 40 194-234 50-90 (189)
199 PRK11920 rirA iron-responsive 92.3 0.22 4.7E-06 39.0 4.2 46 49-102 23-68 (153)
200 PRK11014 transcriptional repre 92.2 0.28 6E-06 37.7 4.7 46 49-102 24-69 (141)
201 smart00344 HTH_ASNC helix_turn 92.2 0.21 4.5E-06 36.3 3.8 45 34-88 4-48 (108)
202 smart00420 HTH_DEOR helix_turn 92.2 0.31 6.7E-06 30.0 4.1 42 38-89 5-46 (53)
203 KOG3115 Methyltransferase-like 92.1 0.078 1.7E-06 43.4 1.5 32 194-225 61-92 (249)
204 KOG3420 Predicted RNA methylas 92.1 0.11 2.3E-06 40.4 2.1 48 184-234 40-89 (185)
205 KOG1499 Protein arginine N-met 91.9 0.15 3.3E-06 44.9 3.2 40 194-234 61-100 (346)
206 COG4742 Predicted transcriptio 91.8 0.28 6E-06 41.7 4.5 67 29-110 9-75 (260)
207 PF00398 RrnaAD: Ribosomal RNA 91.6 0.23 4.9E-06 42.4 3.9 58 181-241 19-81 (262)
208 PF06163 DUF977: Bacterial pro 91.4 0.44 9.5E-06 35.8 4.7 49 31-89 10-58 (127)
209 TIGR00563 rsmB ribosomal RNA s 91.3 0.24 5.2E-06 45.3 4.0 50 184-234 230-280 (426)
210 PF06080 DUF938: Protein of un 91.3 0.38 8.2E-06 39.5 4.7 34 192-225 23-57 (204)
211 TIGR01889 Staph_reg_Sar staphy 91.1 0.3 6.4E-06 35.8 3.6 48 35-90 27-76 (109)
212 KOG1541 Predicted protein carb 91.1 0.11 2.3E-06 43.1 1.3 40 193-234 50-90 (270)
213 PF14394 DUF4423: Domain of un 91.0 1.2 2.6E-05 35.6 7.2 64 23-106 22-87 (171)
214 TIGR00373 conserved hypothetic 91.0 0.35 7.5E-06 38.1 4.1 44 36-89 17-60 (158)
215 PRK03573 transcriptional regul 91.0 0.43 9.4E-06 36.6 4.6 44 38-90 36-79 (144)
216 TIGR02143 trmA_only tRNA (urac 91.0 0.3 6.6E-06 43.6 4.2 38 195-234 199-237 (353)
217 smart00345 HTH_GNTR helix_turn 91.0 0.5 1.1E-05 29.9 4.3 34 49-89 18-52 (60)
218 cd07153 Fur_like Ferric uptake 90.9 0.54 1.2E-05 34.5 4.9 51 35-90 3-54 (116)
219 TIGR01177 conserved hypothetic 90.8 0.46 1E-05 41.9 5.2 47 184-233 174-221 (329)
220 COG2518 Pcm Protein-L-isoaspar 90.7 0.49 1.1E-05 38.9 4.8 49 183-234 63-112 (209)
221 PF05148 Methyltransf_8: Hypot 90.6 0.55 1.2E-05 38.7 5.0 66 157-225 32-101 (219)
222 PRK11760 putative 23S rRNA C24 90.5 0.5 1.1E-05 41.9 5.0 48 192-241 210-257 (357)
223 COG2345 Predicted transcriptio 90.3 0.41 8.8E-06 39.7 4.0 59 38-106 16-79 (218)
224 PF08123 DOT1: Histone methyla 90.2 0.53 1.2E-05 38.7 4.7 49 183-232 33-82 (205)
225 PF08279 HTH_11: HTH domain; 89.9 0.66 1.4E-05 29.2 4.0 42 37-87 4-45 (55)
226 PRK05031 tRNA (uracil-5-)-meth 89.8 0.38 8.3E-06 43.1 3.8 38 195-234 208-246 (362)
227 TIGR01610 phage_O_Nterm phage 89.6 0.66 1.4E-05 33.2 4.2 44 49-101 46-89 (95)
228 COG1321 TroR Mn-dependent tran 89.5 0.62 1.3E-05 36.5 4.4 52 49-110 23-74 (154)
229 PRK14165 winged helix-turn-hel 89.4 0.49 1.1E-05 39.3 3.9 53 49-108 20-72 (217)
230 PF01325 Fe_dep_repress: Iron 89.3 0.73 1.6E-05 30.0 3.9 34 49-89 21-54 (60)
231 PF12147 Methyltransf_20: Puta 89.0 0.44 9.5E-06 41.2 3.4 43 192-234 134-179 (311)
232 PHA02943 hypothetical protein; 89.0 0.92 2E-05 35.3 4.8 42 37-89 15-56 (165)
233 PF05185 PRMT5: PRMT5 arginine 88.7 0.86 1.9E-05 42.1 5.3 69 154-229 151-227 (448)
234 PF03291 Pox_MCEL: mRNA cappin 88.6 0.51 1.1E-05 41.8 3.6 61 166-234 38-103 (331)
235 COG0357 GidB Predicted S-adeno 88.5 0.44 9.6E-06 39.5 3.1 32 194-225 68-99 (215)
236 COG4565 CitB Response regulato 88.3 0.69 1.5E-05 38.1 3.9 43 38-89 163-205 (224)
237 PF02527 GidB: rRNA small subu 88.3 0.53 1.1E-05 38.1 3.3 30 196-225 51-80 (184)
238 COG4190 Predicted transcriptio 88.1 0.87 1.9E-05 34.5 4.0 51 29-89 60-110 (144)
239 PF02002 TFIIE_alpha: TFIIE al 88.0 0.49 1.1E-05 34.4 2.7 42 38-89 18-59 (105)
240 COG2512 Predicted membrane-ass 87.9 0.73 1.6E-05 39.3 4.0 48 35-91 197-244 (258)
241 PRK15431 ferrous iron transpor 87.9 1 2.2E-05 31.0 4.0 43 38-90 7-49 (78)
242 smart00529 HTH_DTXR Helix-turn 87.7 0.71 1.5E-05 32.6 3.4 46 53-108 2-47 (96)
243 PF01596 Methyltransf_3: O-met 87.7 0.56 1.2E-05 38.6 3.1 43 192-234 44-88 (205)
244 COG4189 Predicted transcriptio 87.6 1 2.2E-05 37.7 4.5 54 26-89 16-69 (308)
245 TIGR00006 S-adenosyl-methyltra 87.6 1.1 2.4E-05 39.2 5.0 52 182-234 10-62 (305)
246 PRK14901 16S rRNA methyltransf 87.5 0.93 2E-05 41.6 4.8 49 185-234 245-295 (434)
247 PRK14903 16S rRNA methyltransf 87.4 0.82 1.8E-05 42.0 4.4 44 191-234 235-280 (431)
248 PRK11179 DNA-binding transcrip 87.3 0.86 1.9E-05 35.5 3.9 45 34-88 10-54 (153)
249 PF01795 Methyltransf_5: MraW 87.3 0.96 2.1E-05 39.6 4.5 53 181-234 9-62 (310)
250 PRK10870 transcriptional repre 87.1 0.72 1.6E-05 36.9 3.4 62 38-107 60-124 (176)
251 KOG2361 Predicted methyltransf 87.1 0.82 1.8E-05 38.5 3.7 41 194-234 72-115 (264)
252 PRK11169 leucine-responsive tr 86.9 0.78 1.7E-05 36.2 3.5 46 33-88 14-59 (164)
253 COG4262 Predicted spermidine s 86.9 1 2.2E-05 40.3 4.4 41 192-233 288-330 (508)
254 COG5631 Predicted transcriptio 86.9 3.7 8.1E-05 32.3 7.0 76 21-104 64-146 (199)
255 PF09243 Rsm22: Mitochondrial 86.8 1.2 2.6E-05 38.3 4.8 50 183-233 24-75 (274)
256 COG3432 Predicted transcriptio 86.7 0.51 1.1E-05 33.8 2.1 62 38-108 20-82 (95)
257 PF00392 GntR: Bacterial regul 86.6 1 2.2E-05 29.4 3.4 34 49-89 22-56 (64)
258 PF05724 TPMT: Thiopurine S-me 86.5 1.1 2.4E-05 37.1 4.4 40 191-232 35-75 (218)
259 PF01726 LexA_DNA_bind: LexA D 86.5 1 2.2E-05 29.8 3.4 40 42-89 19-58 (65)
260 PF00325 Crp: Bacterial regula 86.3 0.8 1.7E-05 25.9 2.3 31 50-87 2-32 (32)
261 PRK14904 16S rRNA methyltransf 86.1 0.95 2.1E-05 41.7 4.1 44 191-234 248-293 (445)
262 cd07377 WHTH_GntR Winged helix 86.0 2.2 4.8E-05 27.3 4.8 32 51-89 26-57 (66)
263 PRK13256 thiopurine S-methyltr 86.0 0.77 1.7E-05 38.4 3.1 39 192-232 42-81 (226)
264 COG1378 Predicted transcriptio 85.7 1.6 3.5E-05 37.0 4.9 63 35-108 18-80 (247)
265 COG1522 Lrp Transcriptional re 85.7 1.1 2.5E-05 34.4 3.8 46 34-89 9-54 (154)
266 PRK06474 hypothetical protein; 85.6 1.3 2.8E-05 35.6 4.1 71 28-107 6-82 (178)
267 PF07789 DUF1627: Protein of u 85.4 1.4 3E-05 34.1 4.0 46 49-101 5-50 (155)
268 COG0030 KsgA Dimethyladenosine 85.2 2.1 4.5E-05 36.5 5.4 43 181-224 19-61 (259)
269 PRK04172 pheS phenylalanyl-tRN 85.0 1 2.2E-05 42.0 3.8 67 34-111 7-73 (489)
270 PF03141 Methyltransf_29: Puta 84.9 0.83 1.8E-05 42.3 3.0 24 192-215 116-139 (506)
271 TIGR00446 nop2p NOL1/NOP2/sun 84.6 1.5 3.3E-05 37.4 4.4 43 192-234 70-114 (264)
272 PRK04338 N(2),N(2)-dimethylgua 84.6 0.98 2.1E-05 40.8 3.3 40 195-234 59-99 (382)
273 PF12793 SgrR_N: Sugar transpo 84.5 1.4 3E-05 32.8 3.6 40 49-97 18-57 (115)
274 PLN02853 Probable phenylalanyl 84.3 1 2.2E-05 41.8 3.4 68 33-111 3-71 (492)
275 PRK15128 23S rRNA m(5)C1962 me 84.3 0.97 2.1E-05 41.1 3.2 42 192-234 219-261 (396)
276 PF08784 RPA_C: Replication pr 84.3 1.4 3.1E-05 31.7 3.5 48 34-88 48-96 (102)
277 PF02319 E2F_TDP: E2F/DP famil 84.2 0.56 1.2E-05 31.6 1.3 36 49-89 23-61 (71)
278 PLN02476 O-methyltransferase 83.8 1.3 2.8E-05 38.2 3.6 44 191-234 116-161 (278)
279 PRK04214 rbn ribonuclease BN/u 83.4 1.8 3.8E-05 39.5 4.6 43 49-101 309-351 (412)
280 KOG4589 Cell division protein 83.1 2 4.4E-05 34.9 4.2 45 185-229 61-106 (232)
281 TIGR02787 codY_Gpos GTP-sensin 83.0 4.2 9.1E-05 34.2 6.1 63 16-89 168-230 (251)
282 PF03444 HrcA_DNA-bdg: Winged 82.4 3.1 6.8E-05 28.6 4.3 47 49-104 22-69 (78)
283 PRK11783 rlmL 23S rRNA m(2)G24 82.1 1.3 2.7E-05 43.4 3.3 41 193-234 538-579 (702)
284 KOG1500 Protein arginine N-met 81.6 2.2 4.8E-05 37.8 4.2 31 183-214 168-198 (517)
285 PRK05638 threonine synthase; V 81.0 2.1 4.5E-05 39.4 4.1 58 38-106 376-436 (442)
286 COG4122 Predicted O-methyltran 80.8 2 4.2E-05 35.8 3.5 44 191-234 57-102 (219)
287 PRK13509 transcriptional repre 80.7 2.7 5.9E-05 35.6 4.4 43 37-89 9-51 (251)
288 COG1846 MarR Transcriptional r 80.6 2.7 5.8E-05 30.4 3.9 65 33-107 22-89 (126)
289 PF13404 HTH_AsnC-type: AsnC-t 80.4 2.2 4.9E-05 25.6 2.8 27 34-63 4-30 (42)
290 PRK13777 transcriptional regul 80.4 3.8 8.3E-05 33.1 5.0 44 37-90 49-92 (185)
291 PF04072 LCM: Leucine carboxyl 80.2 3.8 8.3E-05 32.8 5.0 42 192-233 77-118 (183)
292 PF10007 DUF2250: Uncharacteri 79.9 2.8 6.2E-05 29.8 3.6 45 35-89 9-53 (92)
293 COG0275 Predicted S-adenosylme 79.7 4.4 9.5E-05 35.3 5.3 52 182-234 13-66 (314)
294 PRK11639 zinc uptake transcrip 79.6 2.8 6.1E-05 33.3 3.9 55 32-90 25-79 (169)
295 PF02796 HTH_7: Helix-turn-hel 79.2 2.4 5.1E-05 25.7 2.7 23 50-79 21-43 (45)
296 COG3413 Predicted DNA binding 79.2 2.6 5.7E-05 34.7 3.8 34 24-63 158-191 (215)
297 PTZ00326 phenylalanyl-tRNA syn 78.8 2.4 5.2E-05 39.5 3.7 69 33-111 6-74 (494)
298 TIGR02147 Fsuc_second hypothet 78.6 4.4 9.5E-05 34.8 5.1 45 50-104 137-183 (271)
299 TIGR02987 met_A_Alw26 type II 78.4 1.5 3.3E-05 41.2 2.4 41 193-233 31-80 (524)
300 PF08221 HTH_9: RNA polymerase 78.4 2.6 5.7E-05 27.6 2.9 42 38-89 18-59 (62)
301 COG1510 Predicted transcriptio 78.1 2.7 5.8E-05 33.4 3.3 36 49-91 40-75 (177)
302 KOG3191 Predicted N6-DNA-methy 78.0 4.2 9.2E-05 32.9 4.4 40 194-233 44-85 (209)
303 PF09929 DUF2161: Uncharacteri 77.5 4.4 9.5E-05 30.1 4.1 51 39-105 65-115 (118)
304 PF04182 B-block_TFIIIC: B-blo 77.3 2.9 6.2E-05 28.4 2.9 48 34-89 3-50 (75)
305 PF13545 HTH_Crp_2: Crp-like h 77.3 2.5 5.5E-05 28.2 2.7 34 49-89 27-60 (76)
306 PF13730 HTH_36: Helix-turn-he 77.3 3.1 6.8E-05 26.0 2.9 29 52-87 27-55 (55)
307 PRK10906 DNA-binding transcrip 77.2 3.5 7.6E-05 35.0 4.0 44 36-89 8-51 (252)
308 PF05732 RepL: Firmicute plasm 76.2 3.8 8.2E-05 32.5 3.7 43 51-103 76-118 (165)
309 COG1349 GlpR Transcriptional r 76.1 4.2 9.1E-05 34.5 4.2 44 36-89 8-51 (253)
310 PRK10411 DNA-binding transcrip 76.1 5.6 0.00012 33.5 5.0 43 37-89 8-50 (240)
311 PF01170 UPF0020: Putative RNA 75.8 4.1 9E-05 32.6 4.0 51 183-234 19-79 (179)
312 PRK00215 LexA repressor; Valid 75.6 5.1 0.00011 32.6 4.5 35 49-90 22-57 (205)
313 PF12324 HTH_15: Helix-turn-he 75.3 3.2 6.9E-05 28.5 2.6 23 38-63 29-51 (77)
314 PF02475 Met_10: Met-10+ like- 74.9 4.1 8.9E-05 33.4 3.7 44 191-234 99-143 (200)
315 PRK10434 srlR DNA-bindng trans 74.8 3.7 8E-05 34.9 3.6 44 36-89 8-51 (256)
316 smart00531 TFIIE Transcription 74.4 4.6 0.0001 31.2 3.8 42 36-87 4-45 (147)
317 KOG3045 Predicted RNA methylas 74.3 6.7 0.00014 33.6 4.8 54 156-209 139-196 (325)
318 COG0293 FtsJ 23S rRNA methylas 74.1 8.6 0.00019 31.6 5.4 52 175-226 27-79 (205)
319 COG3963 Phospholipid N-methylt 73.9 8.9 0.00019 30.7 5.2 33 181-214 37-69 (194)
320 KOG1661 Protein-L-isoaspartate 73.8 2.2 4.7E-05 35.3 1.8 43 192-234 81-126 (237)
321 COG1733 Predicted transcriptio 73.8 6.8 0.00015 29.3 4.4 77 11-107 10-90 (120)
322 PLN02589 caffeoyl-CoA O-methyl 73.6 5.1 0.00011 34.0 4.1 44 191-234 77-122 (247)
323 PF01475 FUR: Ferric uptake re 73.6 2.7 5.8E-05 31.1 2.2 54 33-90 8-61 (120)
324 COG2384 Predicted SAM-dependen 73.4 3.8 8.2E-05 34.0 3.1 31 195-225 18-48 (226)
325 PRK09954 putative kinase; Prov 73.3 6.3 0.00014 35.0 4.9 44 35-88 5-48 (362)
326 TIGR01321 TrpR trp operon repr 73.3 4.5 9.9E-05 28.9 3.1 40 32-82 41-80 (94)
327 KOG2187 tRNA uracil-5-methyltr 73.1 3 6.4E-05 38.9 2.7 49 191-241 381-433 (534)
328 COG1497 Predicted transcriptio 72.9 2.7 5.8E-05 35.3 2.2 85 49-146 24-111 (260)
329 COG1675 TFA1 Transcription ini 72.9 5.5 0.00012 31.9 3.9 45 36-90 21-65 (176)
330 PRK09802 DNA-binding transcrip 72.9 4.6 0.0001 34.6 3.7 45 35-89 19-63 (269)
331 PF00165 HTH_AraC: Bacterial r 72.9 2.8 6E-05 24.8 1.7 28 49-83 7-34 (42)
332 TIGR00498 lexA SOS regulatory 72.2 7.2 0.00016 31.5 4.6 35 49-89 24-58 (199)
333 PF05219 DREV: DREV methyltran 72.1 5 0.00011 34.2 3.6 29 193-221 94-122 (265)
334 PF05206 TRM13: Methyltransfer 72.0 8.7 0.00019 32.8 5.2 36 191-226 16-56 (259)
335 PF05584 Sulfolobus_pRN: Sulfo 71.1 9.4 0.0002 25.8 4.1 43 37-90 9-51 (72)
336 PRK04424 fatty acid biosynthes 70.8 4.1 8.9E-05 32.9 2.8 44 36-89 10-53 (185)
337 PRK09334 30S ribosomal protein 70.3 5 0.00011 28.2 2.8 45 38-89 28-73 (86)
338 KOG2651 rRNA adenine N-6-methy 69.7 5 0.00011 36.2 3.2 44 184-228 144-187 (476)
339 PF08280 HTH_Mga: M protein tr 69.4 5.6 0.00012 25.6 2.7 39 34-82 6-44 (59)
340 PRK11642 exoribonuclease R; Pr 69.3 10 0.00022 37.8 5.7 57 38-102 24-80 (813)
341 PRK10046 dpiA two-component re 68.9 6.9 0.00015 32.1 3.9 44 37-89 166-209 (225)
342 PRK11886 bifunctional biotin-- 68.0 9.6 0.00021 33.3 4.8 56 36-103 7-62 (319)
343 PRK11534 DNA-binding transcrip 67.8 9.1 0.0002 31.4 4.4 34 49-89 29-62 (224)
344 TIGR03338 phnR_burk phosphonat 67.3 8.8 0.00019 31.2 4.2 34 49-89 33-66 (212)
345 PRK01381 Trp operon repressor; 67.1 6.5 0.00014 28.4 2.8 38 33-81 42-79 (99)
346 KOG2940 Predicted methyltransf 66.8 7.4 0.00016 32.8 3.5 48 193-241 72-122 (325)
347 PF03514 GRAS: GRAS domain fam 66.7 7.1 0.00015 35.2 3.7 46 181-227 99-151 (374)
348 PF02384 N6_Mtase: N-6 DNA Met 66.7 9 0.0002 33.2 4.3 42 191-232 44-93 (311)
349 TIGR02404 trehalos_R_Bsub treh 66.6 7.5 0.00016 32.2 3.6 41 52-101 26-66 (233)
350 KOG1709 Guanidinoacetate methy 66.3 15 0.00033 30.7 5.1 43 192-234 100-142 (271)
351 PLN02668 indole-3-acetate carb 66.2 12 0.00026 33.9 5.0 34 193-226 63-111 (386)
352 TIGR02325 C_P_lyase_phnF phosp 66.1 7.6 0.00017 32.1 3.6 42 52-102 34-75 (238)
353 PF13384 HTH_23: Homeodomain-l 66.0 6.2 0.00014 24.0 2.3 39 35-85 7-45 (50)
354 PF14338 Mrr_N: Mrr N-terminal 65.7 37 0.00079 23.8 6.6 65 38-109 25-89 (92)
355 PRK14999 histidine utilization 65.3 7.8 0.00017 32.3 3.5 41 52-101 38-78 (241)
356 PF13518 HTH_28: Helix-turn-he 65.0 10 0.00023 23.0 3.3 29 51-86 13-41 (52)
357 PRK09464 pdhR transcriptional 64.5 11 0.00024 31.6 4.4 44 49-101 32-76 (254)
358 PF05331 DUF742: Protein of un 64.0 9.8 0.00021 28.2 3.4 34 49-89 54-87 (114)
359 cd00006 PTS_IIA_man PTS_IIA, P 63.8 14 0.0003 27.4 4.3 52 183-234 49-102 (122)
360 KOG0820 Ribosomal RNA adenine 63.5 16 0.00035 31.5 5.0 49 181-232 47-96 (315)
361 PRK10421 DNA-binding transcrip 63.5 12 0.00026 31.4 4.4 44 49-101 24-68 (253)
362 PRK09990 DNA-binding transcrip 63.3 12 0.00026 31.3 4.4 43 49-100 29-72 (251)
363 PRK09462 fur ferric uptake reg 62.9 10 0.00022 29.3 3.5 54 34-90 18-71 (148)
364 TIGR02018 his_ut_repres histid 62.7 9.5 0.00021 31.5 3.6 42 52-102 27-68 (230)
365 PF02636 Methyltransf_28: Puta 62.6 9.3 0.0002 32.2 3.5 34 193-226 18-59 (252)
366 PF03297 Ribosomal_S25: S25 ri 62.6 8 0.00017 28.3 2.6 46 37-89 45-91 (105)
367 PRK10225 DNA-binding transcrip 62.6 12 0.00027 31.4 4.3 43 49-100 31-74 (257)
368 COG1189 Predicted rRNA methyla 62.6 19 0.00042 30.3 5.2 32 183-214 69-100 (245)
369 PRK00082 hrcA heat-inducible t 62.5 12 0.00025 33.3 4.2 52 49-109 24-78 (339)
370 COG2519 GCD14 tRNA(1-methylade 62.5 16 0.00034 31.1 4.8 61 173-234 71-137 (256)
371 PRK09775 putative DNA-binding 62.4 12 0.00026 34.6 4.4 53 38-103 5-57 (442)
372 PRK04984 fatty acid metabolism 62.3 13 0.00028 30.8 4.3 44 49-101 29-73 (239)
373 COG0735 Fur Fe2+/Zn2+ uptake r 62.2 8.5 0.00018 29.7 2.9 53 34-90 22-74 (145)
374 PRK09273 hypothetical protein; 61.9 6.7 0.00015 32.3 2.4 43 195-237 64-106 (211)
375 TIGR02812 fadR_gamma fatty aci 61.9 13 0.00029 30.7 4.3 43 49-100 28-71 (235)
376 PF02295 z-alpha: Adenosine de 61.6 10 0.00022 25.1 2.8 60 34-102 5-64 (66)
377 COG1565 Uncharacterized conser 61.5 19 0.00042 32.2 5.3 57 162-225 51-117 (370)
378 PRK09764 DNA-binding transcrip 61.5 11 0.00023 31.5 3.7 43 50-101 28-71 (240)
379 COG3695 Predicted methylated D 61.4 12 0.00025 27.1 3.2 43 35-82 8-50 (103)
380 COG2188 PhnF Transcriptional r 61.1 12 0.00026 31.3 3.9 43 51-102 32-74 (236)
381 PF03428 RP-C: Replication pro 60.9 11 0.00024 30.3 3.4 32 51-89 71-103 (177)
382 TIGR02698 CopY_TcrY copper tra 60.9 17 0.00037 27.4 4.4 46 34-89 5-54 (130)
383 PRK13239 alkylmercury lyase; P 60.7 10 0.00022 31.2 3.3 38 35-82 24-61 (206)
384 PRK11402 DNA-binding transcrip 60.4 11 0.00024 31.3 3.6 43 51-102 34-76 (241)
385 PF09821 AAA_assoc_C: C-termin 60.1 9.9 0.00021 28.4 2.9 46 55-111 2-47 (120)
386 COG5459 Predicted rRNA methyla 60.0 3.4 7.3E-05 36.9 0.4 39 186-225 107-146 (484)
387 TIGR03879 near_KaiC_dom probab 59.6 7.8 0.00017 26.3 2.0 33 49-88 31-63 (73)
388 PRK11414 colanic acid/biofilm 59.6 15 0.00033 30.1 4.2 34 49-89 33-66 (221)
389 PF09824 ArsR: ArsR transcript 59.4 15 0.00033 28.7 3.8 48 28-89 12-59 (160)
390 PRK12423 LexA repressor; Provi 59.1 18 0.00038 29.5 4.5 34 50-89 25-58 (202)
391 PF09681 Phage_rep_org_N: N-te 59.1 19 0.00042 26.9 4.3 48 49-106 52-99 (121)
392 PF03374 ANT: Phage antirepres 58.9 25 0.00055 25.4 4.9 43 35-89 11-53 (111)
393 TIGR00824 EIIA-man PTS system, 58.7 24 0.00052 26.0 4.8 53 183-235 50-104 (116)
394 PF08704 GCD14: tRNA methyltra 58.6 23 0.0005 30.0 5.2 65 168-233 12-82 (247)
395 PHA02701 ORF020 dsRNA-binding 58.6 16 0.00034 29.5 3.9 48 33-89 4-51 (183)
396 PF04760 IF2_N: Translation in 58.4 4.7 0.0001 25.3 0.7 29 50-88 3-32 (54)
397 PRK10079 phosphonate metabolis 57.6 13 0.00029 30.9 3.6 42 52-102 37-78 (241)
398 PF06969 HemN_C: HemN C-termin 57.6 18 0.0004 23.3 3.6 47 49-105 19-65 (66)
399 PF10771 DUF2582: Protein of u 57.5 18 0.0004 23.9 3.5 41 38-88 13-53 (65)
400 COG1725 Predicted transcriptio 57.4 17 0.00037 27.4 3.8 41 51-100 36-76 (125)
401 PHA02591 hypothetical protein; 57.4 17 0.00038 24.9 3.3 31 38-79 51-81 (83)
402 smart00342 HTH_ARAC helix_turn 57.3 47 0.001 21.6 5.8 36 37-82 41-76 (84)
403 TIGR03697 NtcA_cyano global ni 57.0 13 0.00027 29.4 3.2 33 50-89 143-175 (193)
404 PRK03837 transcriptional regul 57.0 19 0.00042 29.7 4.5 42 49-99 35-77 (241)
405 PF06406 StbA: StbA protein; 56.9 26 0.00056 30.7 5.4 63 167-229 246-310 (318)
406 KOG1975 mRNA cap methyltransfe 56.8 11 0.00024 33.3 2.9 58 166-233 99-157 (389)
407 PRK11523 DNA-binding transcrip 56.7 18 0.0004 30.3 4.3 43 49-100 30-73 (253)
408 TIGR00635 ruvB Holliday juncti 56.7 10 0.00023 32.6 2.9 40 49-98 254-294 (305)
409 PF10668 Phage_terminase: Phag 56.6 16 0.00035 23.8 3.0 23 39-63 13-35 (60)
410 PRK10736 hypothetical protein; 56.6 19 0.0004 32.5 4.5 50 37-100 312-361 (374)
411 COG1802 GntR Transcriptional r 56.4 19 0.00041 29.7 4.3 35 48-89 37-71 (230)
412 KOG2793 Putative N2,N2-dimethy 56.4 14 0.00031 31.3 3.5 43 191-234 83-126 (248)
413 COG2186 FadR Transcriptional r 56.1 18 0.00038 30.4 4.1 42 51-101 35-76 (241)
414 PF12692 Methyltransf_17: S-ad 56.0 54 0.0012 25.7 6.3 57 166-225 4-60 (160)
415 PF07091 FmrO: Ribosomal RNA m 55.6 37 0.0008 28.8 5.8 39 193-231 105-144 (251)
416 KOG2165 Anaphase-promoting com 55.4 15 0.00033 35.6 3.8 48 49-103 615-663 (765)
417 PF11312 DUF3115: Protein of u 55.2 16 0.00035 32.0 3.7 39 194-232 87-148 (315)
418 PRK11783 rlmL 23S rRNA m(2)G24 55.1 22 0.00049 34.8 5.2 32 181-213 178-210 (702)
419 PF02502 LacAB_rpiB: Ribose/Ga 54.9 8.5 0.00018 29.6 1.8 40 198-237 60-99 (140)
420 PF11972 HTH_13: HTH DNA bindi 54.6 28 0.00061 22.1 3.8 47 38-100 4-50 (54)
421 cd06445 ATase The DNA repair p 54.5 29 0.00064 23.6 4.3 42 37-86 4-45 (79)
422 PRK11753 DNA-binding transcrip 54.3 15 0.00032 29.5 3.3 33 50-89 168-200 (211)
423 KOG4058 Uncharacterized conser 54.3 12 0.00025 29.4 2.4 48 183-232 63-111 (199)
424 KOG2920 Predicted methyltransf 54.3 11 0.00023 32.6 2.4 33 193-226 116-148 (282)
425 TIGR00589 ogt O-6-methylguanin 54.1 27 0.0006 24.0 4.1 43 35-85 4-46 (80)
426 TIGR00689 rpiB_lacA_lacB sugar 54.0 12 0.00026 29.0 2.5 39 199-237 60-98 (144)
427 COG3682 Predicted transcriptio 53.9 23 0.00051 26.6 3.9 62 34-103 7-68 (123)
428 TIGR00308 TRM1 tRNA(guanine-26 53.6 13 0.00027 33.6 2.9 40 195-234 46-87 (374)
429 PF01418 HTH_6: Helix-turn-hel 53.1 17 0.00036 24.7 2.9 30 49-85 33-62 (77)
430 TIGR01120 rpiB ribose 5-phosph 52.9 13 0.00028 28.8 2.5 39 199-237 61-99 (143)
431 PF09107 SelB-wing_3: Elongati 52.9 31 0.00067 21.5 3.8 40 40-89 3-42 (50)
432 PF14502 HTH_41: Helix-turn-he 52.8 29 0.00063 21.5 3.5 34 50-90 6-39 (48)
433 PF14314 Methyltrans_Mon: Viru 52.7 31 0.00067 33.6 5.5 50 176-227 307-359 (675)
434 PRK11161 fumarate/nitrate redu 52.6 15 0.00034 30.1 3.2 33 50-89 184-216 (235)
435 COG4367 Uncharacterized protei 52.3 16 0.00034 25.7 2.5 26 49-81 22-47 (97)
436 PF03965 Penicillinase_R: Peni 51.2 25 0.00055 25.7 3.8 51 34-90 4-54 (115)
437 PF13936 HTH_38: Helix-turn-he 50.7 23 0.0005 21.2 2.9 24 49-79 19-42 (44)
438 PRK05571 ribose-5-phosphate is 50.7 15 0.00032 28.7 2.5 38 200-237 64-101 (148)
439 PRK13918 CRP/FNR family transc 50.6 18 0.00039 28.8 3.2 33 50-89 149-181 (202)
440 COG1352 CheR Methylase of chem 49.6 58 0.0012 28.0 6.2 42 193-234 96-147 (268)
441 PRK00135 scpB segregation and 49.5 27 0.00058 28.3 4.0 41 36-89 93-133 (188)
442 COG2524 Predicted transcriptio 49.2 24 0.00053 30.1 3.7 48 49-105 24-72 (294)
443 COG0640 ArsR Predicted transcr 49.2 44 0.00095 22.6 4.7 54 27-90 19-72 (110)
444 smart00342 HTH_ARAC helix_turn 48.9 22 0.00047 23.4 3.0 29 50-85 1-29 (84)
445 PF05402 PqqD: Coenzyme PQQ sy 48.5 8.5 0.00019 25.1 0.8 42 38-88 22-68 (68)
446 PRK09391 fixK transcriptional 48.0 20 0.00044 29.5 3.2 33 50-89 179-211 (230)
447 TIGR03329 Phn_aa_oxid putative 47.9 20 0.00044 33.0 3.4 34 195-228 25-60 (460)
448 PF04672 Methyltransf_19: S-ad 47.5 42 0.0009 28.8 5.0 42 193-234 68-113 (267)
449 PF05958 tRNA_U5-meth_tr: tRNA 47.5 11 0.00024 33.6 1.6 48 183-234 188-236 (352)
450 PRK11511 DNA-binding transcrip 47.4 31 0.00068 25.7 3.9 48 49-108 24-71 (127)
451 PRK13626 transcriptional regul 47.2 23 0.00049 33.6 3.7 34 49-89 22-55 (552)
452 PF01358 PARP_regulatory: Poly 47.1 21 0.00046 30.9 3.1 50 192-241 57-110 (294)
453 PF00376 MerR: MerR family reg 46.9 29 0.00062 20.2 2.8 26 52-88 1-26 (38)
454 TIGR03826 YvyF flagellar opero 46.6 28 0.0006 26.7 3.4 26 37-63 34-59 (137)
455 COG0698 RpiB Ribose 5-phosphat 46.5 18 0.0004 28.2 2.5 43 197-239 61-103 (151)
456 TIGR00331 hrcA heat shock gene 46.3 35 0.00077 30.3 4.6 34 49-89 20-55 (337)
457 smart00753 PAM PCI/PINT associ 46.1 54 0.0012 22.3 4.7 48 31-88 8-55 (88)
458 smart00088 PINT motif in prote 46.1 54 0.0012 22.3 4.7 48 31-88 8-55 (88)
459 TIGR01714 phage_rep_org_N phag 45.9 39 0.00084 25.3 4.0 46 49-104 50-95 (119)
460 COG4901 Ribosomal protein S25 45.8 24 0.00052 25.5 2.8 47 36-89 44-91 (107)
461 PF13814 Replic_Relax: Replica 45.7 27 0.00059 27.7 3.5 62 41-109 3-71 (191)
462 PRK10681 DNA-binding transcrip 45.6 29 0.00062 29.3 3.8 41 36-86 10-50 (252)
463 COG3645 Uncharacterized phage- 45.3 24 0.00052 26.9 2.8 43 35-89 34-76 (135)
464 PRK12615 galactose-6-phosphate 44.8 21 0.00045 28.5 2.6 41 199-239 62-102 (171)
465 TIGR02063 RNase_R ribonuclease 44.6 50 0.0011 32.4 5.8 59 38-103 7-65 (709)
466 PF03602 Cons_hypoth95: Conser 44.4 20 0.00044 28.8 2.5 40 194-234 43-83 (183)
467 TIGR01764 excise DNA binding d 44.4 24 0.00051 20.8 2.4 27 51-88 2-28 (49)
468 TIGR03433 padR_acidobact trans 44.4 60 0.0013 23.1 4.8 65 38-108 9-81 (100)
469 COG4567 Response regulator con 44.4 1.1E+02 0.0024 24.1 6.4 65 159-223 15-87 (182)
470 COG3398 Uncharacterized protei 44.0 63 0.0014 27.0 5.3 47 32-88 100-146 (240)
471 PF13542 HTH_Tnp_ISL3: Helix-t 44.0 35 0.00075 20.8 3.1 34 35-80 17-50 (52)
472 TIGR00027 mthyl_TIGR00027 meth 43.2 55 0.0012 27.8 5.2 60 170-232 60-119 (260)
473 PRK10219 DNA-binding transcrip 43.1 30 0.00065 24.7 3.1 50 49-110 20-69 (107)
474 PF04545 Sigma70_r4: Sigma-70, 42.6 24 0.00053 21.4 2.2 25 49-80 19-43 (50)
475 TIGR01119 lacB galactose-6-pho 42.4 23 0.00049 28.3 2.5 38 200-237 63-100 (171)
476 COG0248 GppA Exopolyphosphatas 42.4 21 0.00045 33.5 2.6 24 183-207 120-143 (492)
477 PF00126 HTH_1: Bacterial regu 42.2 36 0.00078 21.6 3.1 54 35-104 3-59 (60)
478 PF01371 Trp_repressor: Trp re 42.2 38 0.00083 23.8 3.3 40 32-82 35-74 (87)
479 PF12242 Eno-Rase_NADH_b: NAD( 41.9 27 0.00059 24.0 2.4 36 191-226 36-75 (78)
480 PHA03103 double-strand RNA-bin 41.9 61 0.0013 26.2 4.8 42 38-89 18-59 (183)
481 PF04539 Sigma70_r3: Sigma-70 41.8 23 0.00049 23.7 2.2 33 49-88 19-51 (78)
482 PF09904 HTH_43: Winged helix- 41.6 23 0.00049 25.1 2.1 43 36-89 11-53 (90)
483 PRK09333 30S ribosomal protein 41.6 65 0.0014 25.1 4.8 55 49-108 66-128 (150)
484 PF12728 HTH_17: Helix-turn-he 41.4 27 0.00059 21.2 2.3 13 51-63 2-14 (51)
485 KOG3851 Sulfide:quinone oxidor 41.4 34 0.00073 30.5 3.5 32 193-224 38-71 (446)
486 PRK13917 plasmid segregation p 41.3 85 0.0018 27.8 6.3 57 171-229 269-325 (344)
487 COG2390 DeoR Transcriptional r 41.2 31 0.00068 30.4 3.4 34 49-89 25-58 (321)
488 PHA01634 hypothetical protein 41.1 21 0.00047 27.2 2.0 22 193-214 28-49 (156)
489 PF13443 HTH_26: Cro/C1-type H 40.9 21 0.00046 22.7 1.8 21 39-63 3-23 (63)
490 KOG2918 Carboxymethyl transfer 40.8 28 0.00062 30.6 3.0 41 191-231 85-127 (335)
491 cd04762 HTH_MerR-trunc Helix-T 40.8 28 0.00061 20.3 2.3 27 51-88 1-27 (49)
492 TIGR02844 spore_III_D sporulat 40.5 38 0.00083 23.4 3.1 23 37-63 10-32 (80)
493 COG3398 Uncharacterized protei 40.2 53 0.0011 27.4 4.3 67 28-104 169-235 (240)
494 smart00421 HTH_LUXR helix_turn 40.1 40 0.00087 20.2 3.0 14 50-63 18-31 (58)
495 PF04157 EAP30: EAP30/Vps36 fa 40.1 23 0.00051 29.3 2.4 33 49-88 189-221 (223)
496 PF00356 LacI: Bacterial regul 40.0 22 0.00048 21.7 1.7 12 52-63 1-12 (46)
497 PTZ00215 ribose 5-phosphate is 40.0 26 0.00057 27.3 2.4 37 200-236 67-103 (151)
498 PRK14096 pgi glucose-6-phospha 39.9 42 0.00091 31.8 4.2 43 36-85 466-508 (528)
499 PRK10402 DNA-binding transcrip 39.8 29 0.00063 28.4 2.9 33 50-89 169-201 (226)
500 cd02190 epsilon_tubulin The tu 39.5 42 0.00092 30.3 4.1 37 182-218 90-131 (379)
No 1
>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]
Probab=99.98 E-value=2.1e-31 Score=228.96 Aligned_cols=226 Identities=47% Similarity=0.832 Sum_probs=199.1
Q ss_pred hhhchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcc
Q 041256 8 EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNAL 87 (244)
Q Consensus 8 ~~~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll 87 (244)
++|.++..+++++++++..+++|++|+||||||+|++.+ + ..|+|..+.. |-+|.+|.. +.|+||.|++.+++
T Consensus 1 ~~e~~~~l~~~~l~~~~~~~~~lk~A~eL~v~d~l~~~~---~--p~~ia~~l~~-~~~~~~p~l-l~r~lr~L~s~~i~ 73 (342)
T KOG3178|consen 1 DEENEASLRAMRLANGFALPMVLKAACELGVFDILANAG---S--PSEIASLLPT-PKNPEAPVL-LDRILRLLVSYSIL 73 (342)
T ss_pred CchhHHHHHHHHHHhhhhhHHHHHHHHHcChHHHHHhCC---C--HHHHHHhccC-CCCCCChhH-HHHHHHHHHHhhhc
Confidence 367788899999999999999999999999999999963 2 7788877764 334555778 99999999999999
Q ss_pred cceeecCCceeecCccccccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHH
Q 041256 88 HCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFND 167 (244)
Q Consensus 88 ~~~~~~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~ 167 (244)
++...... .|++++.++++.++. +..++.+++...+++..++.|.++.++++.+..+|..++|+..|+|...++....
T Consensus 74 k~~~~~~~-~Y~~~~~~~~~l~~~-~~~S~a~~~~~~~~~v~~~~w~~l~dai~eg~~~~~~~~G~~l~~~~~~~~~~~~ 151 (342)
T KOG3178|consen 74 KCRLVGGE-VYSATPVCKYFLKDS-GGGSLAPLVLLNTSKVIMNTWQFLKDAILEGGDAFATAHGMMLGGYGGADERFSK 151 (342)
T ss_pred eeeeecce-eeeccchhhhheecC-CCCchhHHHHHhcccchhhhHHHHHHHHHhcccCCccccchhhhhhcccccccHH
Confidence 96432223 899999999777555 3458889888888888999999999999999999999999889999999998899
Q ss_pred HHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCC-CCceeec
Q 041256 168 VFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY-PGTLFIK 242 (244)
Q Consensus 168 ~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~-~~i~~~~ 242 (244)
.|+++|...+....+.+++.|.+|++..+.||||||.|..+..++.+||+++++.+|+|.|++.++.+ |||+++.
T Consensus 152 ~~~~sm~~l~~~~~~~il~~~~Gf~~v~~avDvGgGiG~v~k~ll~~fp~ik~infdlp~v~~~a~~~~~gV~~v~ 227 (342)
T KOG3178|consen 152 DFNGSMSFLSTLVMKKILEVYTGFKGVNVAVDVGGGIGRVLKNLLSKYPHIKGINFDLPFVLAAAPYLAPGVEHVA 227 (342)
T ss_pred HHHHHHHHHHHHHHHhhhhhhcccccCceEEEcCCcHhHHHHHHHHhCCCCceeecCHHHHHhhhhhhcCCcceec
Confidence 99999999999988899999988999999999999999999999999999999999999999999998 9987653
No 2
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=99.95 E-value=2.6e-27 Score=206.52 Aligned_cols=185 Identities=21% Similarity=0.341 Sum_probs=138.3
Q ss_pred HHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256 25 VLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS 104 (244)
Q Consensus 25 ~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s 104 (244)
...++|++|++|||||+|++ +|+|++|||+++|++ ++. ++|+||+|+++|+|++ . +++|++|+.+
T Consensus 2 ~~~~~l~aa~~Lglfd~L~~----gp~t~~eLA~~~~~~------~~~-~~~lL~~L~~lgll~~---~-~~~y~~t~~~ 66 (306)
T TIGR02716 2 IEFSCMKAAIELDLFSHMAE----GPKDLATLAADTGSV------PPR-LEMLLETLRQMRVINL---E-DGKWSLTEFA 66 (306)
T ss_pred chHHHHHHHHHcCcHHHHhc----CCCCHHHHHHHcCCC------hHH-HHHHHHHHHhCCCeEe---c-CCcEecchhH
Confidence 35789999999999999987 799999999999997 678 9999999999999994 3 4899999999
Q ss_pred cccccCCCCCC---CHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHHHHHHHH-hcchhh
Q 041256 105 AYFVRNNQNGA---SLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGML-SHTSIV 180 (244)
Q Consensus 105 ~~l~~~~~~~~---~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~aM~-~~~~~~ 180 (244)
..+..++ ++. ++.++..+. .......|.+|.+++++ +++|.. .+++....++.. .|...|. ......
T Consensus 67 ~~~l~~~-~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~r~-~~~~~~-----~~~~~~~~~~~~-~~~~~~~~~~~~~~ 137 (306)
T TIGR02716 67 DYMFSPT-PKEPNLHQTPVAKAM-AFLADDFYMGLSQAVRG-QKNFKG-----QVPYPPVTREDN-LYFEEIHRSNAKFA 137 (306)
T ss_pred HhhccCC-ccchhhhcCchHHHH-HHHHHHHHHhHHHHhcC-Cccccc-----ccCCCCCCHHHH-HhHHHHHHhcchhH
Confidence 8555544 222 112333332 11223578999999974 444432 222322233333 3444444 444445
Q ss_pred HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256 181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS 234 (244)
Q Consensus 181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~ 234 (244)
.+.+++.++ +++..+|||||||+|.+++.+++++|+++++++|+|++++.+++
T Consensus 138 ~~~l~~~~~-~~~~~~vlDiG~G~G~~~~~~~~~~p~~~~~~~D~~~~~~~a~~ 190 (306)
T TIGR02716 138 IQLLLEEAK-LDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLPGAIDLVNE 190 (306)
T ss_pred HHHHHHHcC-CCCCCEEEEeCCchhHHHHHHHHHCCCCEEEEEecHHHHHHHHH
Confidence 566778777 88889999999999999999999999999999999999988764
No 3
>PF00891 Methyltransf_2: O-methyltransferase; InterPro: IPR001077 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. This domain includes a range of O-methyltransferases some of which utilise S-adenosyl methionine as substrate []. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. In eukaryotes, DNA methylation has been implicated in the control of several cellular processes, including differentiation, gene regulation, and embryonic development. O-methyltransferases have a common catalytic domain structure, which might be universal among S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases []. Comparative analysis of the predicted amino acid sequences of a number of plant O-methyltransferase cDNA clones show that they share some 32-71% sequence identity, and can be grouped according to the different compounds they utilise as substrates [].; GO: 0008171 O-methyltransferase activity; PDB: 1FPQ_A 1FP1_D 3P9K_B 3P9I_D 3P9C_A 3I53_A 3I5U_A 3I64_A 3I58_A 1ZG3_A ....
Probab=99.95 E-value=1.5e-27 Score=201.16 Aligned_cols=147 Identities=27% Similarity=0.517 Sum_probs=129.9
Q ss_pred CceeecCccccccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHHHHHHHH
Q 041256 95 QRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGML 174 (244)
Q Consensus 95 ~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~aM~ 174 (244)
.++|+||+.|+.|+.++ ++.++..++.+...+..++.|.+|.+++++|+++|+..+|.++|+++.++|+..+.|+.+|+
T Consensus 3 ~~~y~~t~~s~~ll~~~-~~~~~~~~~~~~~~~~~~~~~~~L~~~v~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~~m~ 81 (241)
T PF00891_consen 3 GDRYSLTPLSELLLSDH-SSPSMRGFVLFMISPELYPAWFRLTEAVRTGKPPFEKAFGTPFFEYLEEDPELAKRFNAAMA 81 (241)
T ss_dssp TEEEEE-HHHHGGSTTT-TTTHHHHHHHHHTCHHHHHGGGGHHHHHHHSS-HHHHHHSS-HHHHHHCSHHHHHHHHHHHH
T ss_pred CCEEeChHHHHHHhCCC-CcCcHHHHHHHhcCHHHHHHHHHHHhhhccCCCHHHHhcCCcHHHhhhhChHHHHHHHHHHH
Confidence 48999999999888776 33578888877668889999999999999999999999999999999999999999999999
Q ss_pred hcchhhH-HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCCceeecc
Q 041256 175 SHTSIVM-EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIKF 243 (244)
Q Consensus 175 ~~~~~~~-~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~i~~~~~ 243 (244)
..+.... +.+...++ |++.++|||||||+|.++.+++++||+++++++|+|+|++.+++.++|+++++
T Consensus 82 ~~~~~~~~~~~~~~~d-~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~~~~~~rv~~~~g 150 (241)
T PF00891_consen 82 EYSRLNAFDILLEAFD-FSGFKTVVDVGGGSGHFAIALARAYPNLRATVFDLPEVIEQAKEADRVEFVPG 150 (241)
T ss_dssp HHHHHHHHHHHHHHST-TTTSSEEEEET-TTSHHHHHHHHHSTTSEEEEEE-HHHHCCHHHTTTEEEEES
T ss_pred hhhhcchhhhhhcccc-ccCccEEEeccCcchHHHHHHHHHCCCCcceeeccHhhhhccccccccccccc
Confidence 9998877 77888888 99999999999999999999999999999999999999999988889998875
No 4
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=99.09 E-value=2e-10 Score=72.80 Aligned_cols=51 Identities=49% Similarity=0.821 Sum_probs=42.3
Q ss_pred HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHh
Q 041256 28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLV 82 (244)
Q Consensus 28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~ 82 (244)
++|++|+||||||+|++.| ++++|++||+.++... +|.++.. +.|+||+|+
T Consensus 1 MaLk~aveLgI~dii~~~g-~~~ls~~eia~~l~~~--~p~~~~~-L~RimR~L~ 51 (51)
T PF08100_consen 1 MALKCAVELGIPDIIHNAG-GGPLSLSEIAARLPTS--NPSAPPM-LDRIMRLLV 51 (51)
T ss_dssp HHHHHHHHTTHHHHHHHHT-TS-BEHHHHHHTSTCT---TTHHHH-HHHHHHHHH
T ss_pred CcHHHHHHcCcHHHHHHcC-CCCCCHHHHHHHcCCC--CcchHHH-HHHHHHHhC
Confidence 5899999999999999985 4699999999999832 4555678 999999985
No 5
>PRK06922 hypothetical protein; Provisional
Probab=98.13 E-value=4.1e-06 Score=79.01 Aligned_cols=81 Identities=21% Similarity=0.329 Sum_probs=62.1
Q ss_pred CCchhhccCCchHHHHHHHHHHhcchhh--HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHh
Q 041256 153 MQIYDYLGVDSRFNDVFNNGMLSHTSIV--MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVI 229 (244)
Q Consensus 153 ~~~~e~~~~~~~~~~~f~~aM~~~~~~~--~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi 229 (244)
..+|+++..+++..++|...|....... .......++ +.+..+|||||||.|.++..+++++|+.+++.+|+ |.++
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 4678999988888889988776644332 112233445 66678999999999999999999999999999999 4557
Q ss_pred hhCCC
Q 041256 230 KDAPS 234 (244)
Q Consensus 230 ~~a~~ 234 (244)
+.+++
T Consensus 456 e~Ara 460 (677)
T PRK06922 456 DTLKK 460 (677)
T ss_pred HHHHH
Confidence 76653
No 6
>PF12847 Methyltransf_18: Methyltransferase domain; PDB: 3G2Q_A 3G2O_A 3G2M_B 3G2P_B 3D2L_B 1IM8_B 3NJR_A 3E05_H 3EVZ_A 3HM2_A ....
Probab=97.90 E-value=7.7e-06 Score=60.07 Aligned_cols=41 Identities=20% Similarity=0.355 Sum_probs=37.6
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+|+|||||+|.++..+++++|+.+++.+|. |+.++.+++
T Consensus 2 ~~~vLDlGcG~G~~~~~l~~~~~~~~v~gvD~s~~~~~~a~~ 43 (112)
T PF12847_consen 2 GGRVLDLGCGTGRLSIALARLFPGARVVGVDISPEMLEIARE 43 (112)
T ss_dssp TCEEEEETTTTSHHHHHHHHHHTTSEEEEEESSHHHHHHHHH
T ss_pred CCEEEEEcCcCCHHHHHHHhcCCCCEEEEEeCCHHHHHHHHH
Confidence 36899999999999999999999999999999 888888764
No 7
>PRK14103 trans-aconitate 2-methyltransferase; Provisional
Probab=97.89 E-value=4.1e-05 Score=65.04 Aligned_cols=57 Identities=21% Similarity=0.276 Sum_probs=47.2
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCCCCcee
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSYPGTLF 240 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~~~i~~ 240 (244)
..+++.++ .....+|||||||+|.++..+++++|+.+++.+|+ |..++.+++. ++++
T Consensus 19 ~~ll~~l~-~~~~~~vLDlGcG~G~~~~~l~~~~p~~~v~gvD~s~~~~~~a~~~-~~~~ 76 (255)
T PRK14103 19 YDLLARVG-AERARRVVDLGCGPGNLTRYLARRWPGAVIEALDSSPEMVAAARER-GVDA 76 (255)
T ss_pred HHHHHhCC-CCCCCEEEEEcCCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHhc-CCcE
Confidence 46677776 56779999999999999999999999999999999 8888877652 3443
No 8
>COG4106 Tam Trans-aconitate methyltransferase [General function prediction only]
Probab=97.78 E-value=6.6e-05 Score=61.52 Aligned_cols=60 Identities=22% Similarity=0.432 Sum_probs=51.7
Q ss_pred HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCceee
Q 041256 181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLFI 241 (244)
Q Consensus 181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~~ 241 (244)
...++...+ ......|+|+|||.|....-|++++|+...+.+|- |..++.|++ .|+++|.
T Consensus 19 a~dLla~Vp-~~~~~~v~DLGCGpGnsTelL~~RwP~A~i~GiDsS~~Mla~Aa~rlp~~~f~ 80 (257)
T COG4106 19 ARDLLARVP-LERPRRVVDLGCGPGNSTELLARRWPDAVITGIDSSPAMLAKAAQRLPDATFE 80 (257)
T ss_pred HHHHHhhCC-ccccceeeecCCCCCHHHHHHHHhCCCCeEeeccCCHHHHHHHHHhCCCCcee
Confidence 357777788 78889999999999999999999999999999997 888888875 5776663
No 9
>PRK08287 cobalt-precorrin-6Y C(15)-methyltransferase; Validated
Probab=97.76 E-value=3.8e-05 Score=62.14 Aligned_cols=49 Identities=20% Similarity=0.364 Sum_probs=41.8
Q ss_pred HhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 185 LESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+..++ .....+|+|||||+|.++..+++++|+.+++.+|. |..++.+++
T Consensus 24 ~~~l~-~~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~s~~~~~~a~~ 73 (187)
T PRK08287 24 LSKLE-LHRAKHLIDVGAGTGSVSIEAALQFPSLQVTAIERNPDALRLIKE 73 (187)
T ss_pred HHhcC-CCCCCEEEEECCcCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence 34455 56678999999999999999999999999999999 788887764
No 10
>PRK01683 trans-aconitate 2-methyltransferase; Provisional
Probab=97.76 E-value=6.2e-05 Score=63.87 Aligned_cols=59 Identities=24% Similarity=0.482 Sum_probs=48.6
Q ss_pred HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCcee
Q 041256 181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLF 240 (244)
Q Consensus 181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~ 240 (244)
...++..++ ..+..+|+|||||.|.++..+++++|+.+++.+|+ |..++.+++ .+++++
T Consensus 20 ~~~ll~~~~-~~~~~~vLDiGcG~G~~~~~la~~~~~~~v~gvD~s~~~i~~a~~~~~~~~~ 80 (258)
T PRK01683 20 ARDLLARVP-LENPRYVVDLGCGPGNSTELLVERWPAARITGIDSSPAMLAEARSRLPDCQF 80 (258)
T ss_pred HHHHHhhCC-CcCCCEEEEEcccCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHhCCCCeE
Confidence 346677776 67778999999999999999999999999999999 788887765 345554
No 11
>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=97.52 E-value=9.8e-05 Score=57.57 Aligned_cols=42 Identities=31% Similarity=0.354 Sum_probs=36.8
Q ss_pred CcceEEEecCCccHHHHHHH-HHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMII-SKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~-~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+..+|+|+|||+|.++..++ +.+|..+.+.+|+ |+.++.|++
T Consensus 3 ~~~~iLDlGcG~G~~~~~l~~~~~~~~~i~gvD~s~~~i~~a~~ 46 (152)
T PF13847_consen 3 SNKKILDLGCGTGRLLIQLAKELNPGAKIIGVDISEEMIEYAKK 46 (152)
T ss_dssp TTSEEEEET-TTSHHHHHHHHHSTTTSEEEEEESSHHHHHHHHH
T ss_pred CCCEEEEecCcCcHHHHHHHHhcCCCCEEEEEECcHHHHHHhhc
Confidence 45799999999999999999 5689999999999 889988875
No 12
>TIGR03587 Pse_Me-ase pseudaminic acid biosynthesis-associated methylase. Members of this small clade are methyltransferases of the pfam08241 family and are observed within operons for the biosynthesis of pseudaminic acid, a component of exopolysaccharide and flagellin glycosyl modifications. Notable among these genomes is Pseudomonas fluorescens PfO-1. Possibly one of the two hydroxyl groups of pseudaminic acid, at positions 4 and 8 is converted to a methoxy group by this enzyme
Probab=97.52 E-value=0.00017 Score=59.41 Aligned_cols=49 Identities=14% Similarity=0.405 Sum_probs=41.8
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCcee
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLF 240 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~ 240 (244)
....+|+|||||+|.++..+++..|+.+.+.+|+ |+.++.|++ .+++++
T Consensus 42 ~~~~~VLDiGCG~G~~~~~L~~~~~~~~v~giDiS~~~l~~A~~~~~~~~~ 92 (204)
T TIGR03587 42 PKIASILELGANIGMNLAALKRLLPFKHIYGVEINEYAVEKAKAYLPNINI 92 (204)
T ss_pred CCCCcEEEEecCCCHHHHHHHHhCCCCeEEEEECCHHHHHHHHhhCCCCcE
Confidence 4557899999999999999999999999999998 889998876 455544
No 13
>TIGR02469 CbiT precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit. This model recognizes the CbiT methylase which is responsible, in part (along with CbiE), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiE subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin biosynthesis pathway, is called CobL.
Probab=97.51 E-value=0.0002 Score=53.18 Aligned_cols=49 Identities=16% Similarity=0.175 Sum_probs=40.0
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
+++.++ .....+|+|+|||.|.++..+++++|+.+++.+|. +..++.++
T Consensus 11 ~~~~~~-~~~~~~vldlG~G~G~~~~~l~~~~~~~~v~~vD~s~~~~~~a~ 60 (124)
T TIGR02469 11 TLSKLR-LRPGDVLWDIGAGSGSITIEAARLVPNGRVYAIERNPEALRLIE 60 (124)
T ss_pred HHHHcC-CCCCCEEEEeCCCCCHHHHHHHHHCCCceEEEEcCCHHHHHHHH
Confidence 444555 45557999999999999999999999999999998 66666654
No 14
>TIGR00091 tRNA (guanine-N(7)-)-methyltransferase. In E. coli, this protein flanks the DNA repair protein MutY, also called micA.
Probab=97.45 E-value=0.0002 Score=58.31 Aligned_cols=41 Identities=15% Similarity=0.219 Sum_probs=36.6
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
...++||||||.|.++..+++++|+.+++.+|+ +..++.++
T Consensus 16 ~~~~ilDiGcG~G~~~~~la~~~p~~~v~gvD~~~~~l~~a~ 57 (194)
T TIGR00091 16 KAPLHLEIGCGKGRFLIDMAKQNPDKNFLGIEIHTPIVLAAN 57 (194)
T ss_pred CCceEEEeCCCccHHHHHHHHhCCCCCEEEEEeeHHHHHHHH
Confidence 457999999999999999999999999999999 77776664
No 15
>PRK00107 gidB 16S rRNA methyltransferase GidB; Reviewed
Probab=97.40 E-value=0.00038 Score=56.49 Aligned_cols=42 Identities=21% Similarity=0.159 Sum_probs=37.1
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
...+|+|||||+|..+..+++++|+.+++.+|. |..++.+++
T Consensus 45 ~g~~VLDiGcGtG~~al~la~~~~~~~V~giD~s~~~l~~A~~ 87 (187)
T PRK00107 45 GGERVLDVGSGAGFPGIPLAIARPELKVTLVDSLGKKIAFLRE 87 (187)
T ss_pred CCCeEEEEcCCCCHHHHHHHHHCCCCeEEEEeCcHHHHHHHHH
Confidence 368999999999999999999999999999998 777776654
No 16
>PRK15001 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional
Probab=97.39 E-value=0.00022 Score=64.01 Aligned_cols=51 Identities=20% Similarity=0.271 Sum_probs=41.9
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
-+++.+| .....+|+|+|||+|.++..+++++|+.+++.+|. +..++.+++
T Consensus 219 llL~~lp-~~~~~~VLDLGCGtGvi~i~la~~~P~~~V~~vD~S~~Av~~A~~ 270 (378)
T PRK15001 219 FFMQHLP-ENLEGEIVDLGCGNGVIGLTLLDKNPQAKVVFVDESPMAVASSRL 270 (378)
T ss_pred HHHHhCC-cccCCeEEEEeccccHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence 3455665 33346999999999999999999999999999999 577777764
No 17
>TIGR02021 BchM-ChlM magnesium protoporphyrin O-methyltransferase. This model represents the S-adenosylmethionine-dependent O-methyltransferase responsible for methylation of magnesium protoporphyrin IX. This step is essentiasl for the biosynthesis of both chlorophyll and bacteriochlorophyll. This model encompasses two closely related clades, from cyanobacteria (and plants) where it is called ChlM and other photosynthetic bacteria where it is known as BchM.
Probab=97.33 E-value=0.00048 Score=57.04 Aligned_cols=78 Identities=12% Similarity=0.063 Sum_probs=48.8
Q ss_pred chhhccCCchHHHHHHHHHHhcchhhHHHHHhhcCC-CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256 155 IYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKG-FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA 232 (244)
Q Consensus 155 ~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~-~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a 232 (244)
-|+.+...+.....+...|..........+++.++. ..+..+|+|||||.|.++..+++. +.+.+.+|. |+.++.+
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~vLDiGcG~G~~~~~la~~--~~~v~gvD~s~~~i~~a 93 (219)
T TIGR02021 16 RWARIYGSGDPVSRVRQTVREGRAAMRRKLLDWLPKDPLKGKRVLDAGCGTGLLSIELAKR--GAIVKAVDISEQMVQMA 93 (219)
T ss_pred HHHHhhCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEeCCCCHHHHHHHHC--CCEEEEEECCHHHHHHH
Confidence 344444444444455555533222222334433331 335689999999999999999886 447888898 7888777
Q ss_pred CC
Q 041256 233 PS 234 (244)
Q Consensus 233 ~~ 234 (244)
++
T Consensus 94 ~~ 95 (219)
T TIGR02021 94 RN 95 (219)
T ss_pred HH
Confidence 64
No 18
>PRK04457 spermidine synthase; Provisional
Probab=97.33 E-value=0.00019 Score=61.32 Aligned_cols=43 Identities=21% Similarity=0.356 Sum_probs=39.6
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+.+++|+|||||.|.++..+++.+|+.+++++|+ |+|++.|++
T Consensus 65 ~~~~~vL~IG~G~G~l~~~l~~~~p~~~v~~VEidp~vi~~A~~ 108 (262)
T PRK04457 65 PRPQHILQIGLGGGSLAKFIYTYLPDTRQTAVEINPQVIAVARN 108 (262)
T ss_pred CCCCEEEEECCCHhHHHHHHHHhCCCCeEEEEECCHHHHHHHHH
Confidence 4568899999999999999999999999999999 999998874
No 19
>PF08242 Methyltransf_12: Methyltransferase domain; InterPro: IPR013217 Methyl transfer from the ubiquitous donor S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] Fatty acid synthase (2.3.1.85 from EC), a biosynthetic enzyme catalysing the formation of long-chain fatty acids Glycine N-methyltransferase (2.1.1.20 from EC) which catalyses the SAM-dependent methylation of glycine to form sarcosine and may play a role in regulating the methylation potential of the cell [] Enniatin synthetase, involved in non-ribosomal biosynthesis of cyclohexadepsipeptidase, enniatin [] Histamine N-methyltransferase (2.1.1.8 from EC), a SAM-dependent histamine-inactivating enzyme [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ].; PDB: 2VZ8_A 2VZ9_A.
Probab=97.30 E-value=6.5e-05 Score=54.04 Aligned_cols=37 Identities=24% Similarity=0.522 Sum_probs=31.9
Q ss_pred EEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 198 VDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 198 vDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
||||||+|.++..+++++|..+.+..|. |..++.+++
T Consensus 1 LdiGcG~G~~~~~l~~~~~~~~~~~~D~s~~~l~~a~~ 38 (99)
T PF08242_consen 1 LDIGCGTGRLLRALLEELPDARYTGVDISPSMLERARE 38 (99)
T ss_dssp -EESTTTS-TTTTHHHHC-EEEEEEEESSSSTTSTTCC
T ss_pred CEeCccChHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence 7999999999999999999999999999 888888876
No 20
>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=97.30 E-value=9.9e-05 Score=46.95 Aligned_cols=45 Identities=24% Similarity=0.448 Sum_probs=37.9
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
+.|++.|.+.+ ++.|+.|||+++|++ ..- +.|+|..|+..|++.+
T Consensus 6 l~iL~~l~~~~--~~~t~~eia~~~gl~------~st-v~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 6 LRILEALAESG--GPLTLSEIARALGLP------KST-VHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHHCHHCTB--SCEEHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHcCC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCcCeec
Confidence 45788888875 678999999999996 345 9999999999999995
No 21
>PRK00121 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed
Probab=97.29 E-value=0.00043 Score=56.80 Aligned_cols=49 Identities=18% Similarity=0.173 Sum_probs=40.3
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
|.+.+. ....+|+|||||.|.++..+++.+|+.+.+.+|. |+.++.+++
T Consensus 33 ~~~~~~--~~~~~VLDiGcGtG~~~~~la~~~p~~~v~gVD~s~~~i~~a~~ 82 (202)
T PRK00121 33 WAELFG--NDAPIHLEIGFGKGEFLVEMAKANPDINFIGIEVHEPGVGKALK 82 (202)
T ss_pred HHHHcC--CCCCeEEEEccCCCHHHHHHHHHCCCccEEEEEechHHHHHHHH
Confidence 444444 2558999999999999999999999999999998 777777653
No 22
>TIGR02752 MenG_heptapren 2-heptaprenyl-1,4-naphthoquinone methyltransferase. MenG is a generic term for a methyltransferase that catalyzes the last step in menaquinone biosynthesis; the exact enzymatic activity differs for different MenG because the menaquinone differ in their prenoid side chains in different species. Members of this MenG protein family are 2-heptaprenyl-1,4-naphthoquinone methyltransferase, and are found together in operons with the two subunits of the heptaprenyl diphosphate synthase in Bacillus subtilis and related species.
Probab=97.26 E-value=0.00057 Score=56.91 Aligned_cols=50 Identities=12% Similarity=0.084 Sum_probs=40.3
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~ 233 (244)
.++..++ .....+|||||||+|.++..+++.+ |+.+++.+|+ |..++.++
T Consensus 36 ~~l~~l~-~~~~~~vLDiGcG~G~~~~~la~~~~~~~~v~gvD~s~~~~~~a~ 87 (231)
T TIGR02752 36 DTMKRMN-VQAGTSALDVCCGTADWSIALAEAVGPEGHVIGLDFSENMLSVGR 87 (231)
T ss_pred HHHHhcC-CCCCCEEEEeCCCcCHHHHHHHHHhCCCCEEEEEECCHHHHHHHH
Confidence 3444555 5566899999999999999999986 7789999999 77776665
No 23
>COG2813 RsmC 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]
Probab=97.24 E-value=0.00051 Score=59.24 Aligned_cols=52 Identities=23% Similarity=0.292 Sum_probs=44.2
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+-+++.++ .....+|+|+|||.|.+++.+++.+|+.+.+..|. ...++.+++
T Consensus 148 ~lLl~~l~-~~~~~~vlDlGCG~Gvlg~~la~~~p~~~vtmvDvn~~Av~~ar~ 200 (300)
T COG2813 148 RLLLETLP-PDLGGKVLDLGCGYGVLGLVLAKKSPQAKLTLVDVNARAVESARK 200 (300)
T ss_pred HHHHHhCC-ccCCCcEEEeCCCccHHHHHHHHhCCCCeEEEEecCHHHHHHHHH
Confidence 45677777 44445999999999999999999999999999998 678888875
No 24
>TIGR00138 gidB 16S rRNA methyltransferase GidB. GidB (glucose-inhibited division protein B) appears to be present and in a single copy in nearly all complete eubacterial genomes. It is missing only from some obligate intracellular species of various lineages (Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera, etc.). GidB shows a methytransferase fold in its the crystal structure, and acts as a 7-methylguanosine (m(7)G) methyltransferase, apparently specific to 16S rRNA.
Probab=97.22 E-value=0.00033 Score=56.55 Aligned_cols=40 Identities=20% Similarity=0.186 Sum_probs=34.3
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
..+|+|||||+|.++..++..+|+.+++.+|. |..++.++
T Consensus 43 ~~~vLDiGcGtG~~s~~la~~~~~~~V~~iD~s~~~~~~a~ 83 (181)
T TIGR00138 43 GKKVIDIGSGAGFPGIPLAIARPELKLTLLESNHKKVAFLR 83 (181)
T ss_pred CCeEEEecCCCCccHHHHHHHCCCCeEEEEeCcHHHHHHHH
Confidence 47999999999999999999999999999998 55555543
No 25
>PRK06202 hypothetical protein; Provisional
Probab=97.22 E-value=0.0012 Score=55.12 Aligned_cols=43 Identities=19% Similarity=0.120 Sum_probs=36.4
Q ss_pred CCcceEEEecCCccHHHHHHHHH----CCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISK----YPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~----~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+..+|+|||||.|.++..+++. .|+.+.+.+|+ |..++.+++
T Consensus 59 ~~~~~iLDlGcG~G~~~~~L~~~~~~~g~~~~v~gvD~s~~~l~~a~~ 106 (232)
T PRK06202 59 DRPLTLLDIGCGGGDLAIDLARWARRDGLRLEVTAIDPDPRAVAFARA 106 (232)
T ss_pred CCCcEEEEeccCCCHHHHHHHHHHHhCCCCcEEEEEcCCHHHHHHHHh
Confidence 45689999999999998888763 56789999999 888888875
No 26
>PRK07402 precorrin-6B methylase; Provisional
Probab=97.22 E-value=0.00048 Score=56.10 Aligned_cols=50 Identities=18% Similarity=0.155 Sum_probs=42.0
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
++..++ .....+|+|+|||+|.++..+++..|+.+++.+|+ |..++.+++
T Consensus 32 l~~~l~-~~~~~~VLDiG~G~G~~~~~la~~~~~~~V~~vD~s~~~~~~a~~ 82 (196)
T PRK07402 32 LISQLR-LEPDSVLWDIGAGTGTIPVEAGLLCPKGRVIAIERDEEVVNLIRR 82 (196)
T ss_pred HHHhcC-CCCCCEEEEeCCCCCHHHHHHHHHCCCCEEEEEeCCHHHHHHHHH
Confidence 345555 55668999999999999999999999999999999 888887764
No 27
>PRK14121 tRNA (guanine-N(7)-)-methyltransferase; Provisional
Probab=97.17 E-value=0.00072 Score=60.71 Aligned_cols=50 Identities=20% Similarity=0.208 Sum_probs=39.4
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
.+++.+. -.....+||||||.|.++..+++++|+..++.+|+ +..++.+.
T Consensus 113 ~~~~~~~-~~~~p~vLEIGcGsG~~ll~lA~~~P~~~~iGIEI~~~~i~~a~ 163 (390)
T PRK14121 113 NFLDFIS-KNQEKILIEIGFGSGRHLLYQAKNNPNKLFIGIEIHTPSIEQVL 163 (390)
T ss_pred HHHHHhc-CCCCCeEEEEcCcccHHHHHHHHhCCCCCEEEEECCHHHHHHHH
Confidence 3454554 23457999999999999999999999999999998 55555553
No 28
>PF05175 MTS: Methyltransferase small domain; InterPro: IPR007848 This domain is found in ribosomal RNA small subunit methyltransferase C and in other methyltransferases.; GO: 0008168 methyltransferase activity; PDB: 1WY7_A 1DUS_A 2OZV_A 2PJD_A 1VQ1_A 1NV9_A 1SG9_C 1NV8_A 3Q87_B 3DMF_A ....
Probab=97.15 E-value=0.00025 Score=56.51 Aligned_cols=42 Identities=21% Similarity=0.329 Sum_probs=37.8
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
...+++|+|||+|.++..+++++|+.+++..|. |.+++.+++
T Consensus 31 ~~~~vLDlG~G~G~i~~~la~~~~~~~v~~vDi~~~a~~~a~~ 73 (170)
T PF05175_consen 31 KGGRVLDLGCGSGVISLALAKRGPDAKVTAVDINPDALELAKR 73 (170)
T ss_dssp TTCEEEEETSTTSHHHHHHHHTSTCEEEEEEESBHHHHHHHHH
T ss_pred cCCeEEEecCChHHHHHHHHHhCCCCEEEEEcCCHHHHHHHHH
Confidence 457899999999999999999999999999998 888887764
No 29
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=97.08 E-value=0.00091 Score=47.30 Aligned_cols=58 Identities=21% Similarity=0.336 Sum_probs=46.2
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS 104 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s 104 (244)
+.|++.|.+.+ ++.|+.|||+.+|++ ..- +.|+|+.|...|++.++ ...+.|++++..
T Consensus 8 ~~Il~~l~~~~--~~~t~~~ia~~l~i~------~~t-v~r~l~~L~~~g~l~~~--~~~~~y~l~~~~ 65 (91)
T smart00346 8 LAVLRALAEEP--GGLTLAELAERLGLS------KST-AHRLLNTLQELGYVEQD--GQNGRYRLGPKV 65 (91)
T ss_pred HHHHHHHHhCC--CCcCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCeeec--CCCCceeecHHH
Confidence 56788888753 589999999999996 445 99999999999999963 234678887753
No 30
>TIGR00740 methyltransferase, putative. A simple BLAST search finds all members of this family and weaker hits to a large number of known and predicted methyltransferases. A single iteration with PSI-BLAST, keeping only clear members of the family, leads to a large number of highly significant hits to a set of known and predicted methyltransferases with a large repertoire of different specifities. This model is restricted to a subfamily found so far only in the Proteobacteria, sharing consistent length, full-length homology, and on average better than 35 % identity. It is reasonable to predict equivalent function within this subfamily.
Probab=97.06 E-value=0.00058 Score=57.33 Aligned_cols=43 Identities=16% Similarity=0.167 Sum_probs=37.5
Q ss_pred CCcceEEEecCCccHHHHHHHHH--CCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISK--YPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~--~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
....+|||||||.|.++..++++ +|+.+.+.+|+ |..++.|++
T Consensus 52 ~~~~~iLDlGcG~G~~~~~l~~~~~~p~~~v~gvD~s~~ml~~a~~ 97 (239)
T TIGR00740 52 TPDSNVYDLGCSRGAATLSARRNINQPNVKIIGIDNSQPMVERCRQ 97 (239)
T ss_pred CCCCEEEEecCCCCHHHHHHHHhcCCCCCeEEEEeCCHHHHHHHHH
Confidence 34578999999999999999997 48899999999 888888764
No 31
>PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional
Probab=97.04 E-value=0.00087 Score=59.51 Aligned_cols=50 Identities=20% Similarity=0.332 Sum_probs=40.0
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+++.++ .....+|+|+|||.|.++..+++++|+.+++..|. +..++.+++
T Consensus 188 Ll~~l~-~~~~g~VLDlGCG~G~ls~~la~~~p~~~v~~vDis~~Al~~A~~ 238 (342)
T PRK09489 188 LLSTLT-PHTKGKVLDVGCGAGVLSAVLARHSPKIRLTLSDVSAAALESSRA 238 (342)
T ss_pred HHHhcc-ccCCCeEEEeccCcCHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence 445454 23345899999999999999999999999999998 677777654
No 32
>COG2242 CobL Precorrin-6B methylase 2 [Coenzyme metabolism]
Probab=97.03 E-value=0.0013 Score=52.89 Aligned_cols=48 Identities=15% Similarity=0.073 Sum_probs=40.2
Q ss_pred hhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 186 ESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 186 ~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+. ..+..+++|||||+|.++++++...|..+++.+|. ++.++..++
T Consensus 28 s~L~-~~~g~~l~DIGaGtGsi~iE~a~~~p~~~v~AIe~~~~a~~~~~~ 76 (187)
T COG2242 28 SKLR-PRPGDRLWDIGAGTGSITIEWALAGPSGRVIAIERDEEALELIER 76 (187)
T ss_pred HhhC-CCCCCEEEEeCCCccHHHHHHHHhCCCceEEEEecCHHHHHHHHH
Confidence 3444 56678999999999999999999999999999997 777766653
No 33
>PRK11207 tellurite resistance protein TehB; Provisional
Probab=97.02 E-value=0.00084 Score=54.84 Aligned_cols=50 Identities=24% Similarity=0.309 Sum_probs=39.7
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+.+++.++ .....+|+|+|||.|.++..++++ ..+++.+|+ |..++.+++
T Consensus 20 ~~l~~~l~-~~~~~~vLDiGcG~G~~a~~La~~--g~~V~gvD~S~~~i~~a~~ 70 (197)
T PRK11207 20 SEVLEAVK-VVKPGKTLDLGCGNGRNSLYLAAN--GFDVTAWDKNPMSIANLER 70 (197)
T ss_pred HHHHHhcc-cCCCCcEEEECCCCCHHHHHHHHC--CCEEEEEeCCHHHHHHHHH
Confidence 46666666 455689999999999999999986 468899999 777776653
No 34
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=97.01 E-value=0.00062 Score=57.60 Aligned_cols=43 Identities=21% Similarity=0.225 Sum_probs=37.6
Q ss_pred CCcceEEEecCCccHHHHHHHH--HCCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIIS--KYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~--~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
....+|+|||||+|..+..+++ .+|+.+++.+|. |..++.|++
T Consensus 55 ~~~~~vLDlGcGtG~~~~~l~~~~~~~~~~v~gvD~S~~ml~~A~~ 100 (247)
T PRK15451 55 QPGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDNSPAMIERCRR 100 (247)
T ss_pred CCCCEEEEEcccCCHHHHHHHHhcCCCCCeEEEEeCCHHHHHHHHH
Confidence 3457899999999999999988 479999999998 889988864
No 35
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=96.96 E-value=0.0016 Score=56.01 Aligned_cols=57 Identities=12% Similarity=0.208 Sum_probs=41.9
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCC---CCceee
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSY---PGTLFI 241 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~---~~i~~~ 241 (244)
..+++.++ .....+|+|||||.|.++..++++.+ +++.+|. |..++.+++. ++++++
T Consensus 32 ~~i~~~l~-~~~~~~VLEiG~G~G~lt~~L~~~~~--~v~avE~d~~~~~~~~~~~~~~~v~~i 92 (272)
T PRK00274 32 DKIVDAAG-PQPGDNVLEIGPGLGALTEPLLERAA--KVTAVEIDRDLAPILAETFAEDNLTII 92 (272)
T ss_pred HHHHHhcC-CCCcCeEEEeCCCccHHHHHHHHhCC--cEEEEECCHHHHHHHHHhhccCceEEE
Confidence 34555555 56668999999999999999999987 6777776 7777776542 355543
No 36
>PF02390 Methyltransf_4: Putative methyltransferase ; InterPro: IPR003358 This entry represents tRNA (guanine-N-7) methyltransferase (2.1.1.33 from EC), which catalyses the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. Capping of the pre-mRNA 5' end by addition a monomethylated guanosine cap (m(7)G) is an essential and the earliest modification in the biogenesis of mRNA []. The reaction is catalysed by three enzymes: triphosphatase, guanylyltransferase, and tRNA (guanine-N-7) methyltransferase [, ].; GO: 0008176 tRNA (guanine-N7-)-methyltransferase activity, 0006400 tRNA modification; PDB: 3DXZ_A 3DXY_A 3DXX_A 3CKK_A 3P2I_B 3P2K_D 3P2E_A 3MTE_B 3PB3_B 1YZH_B ....
Probab=96.96 E-value=0.0012 Score=54.01 Aligned_cols=47 Identities=19% Similarity=0.316 Sum_probs=36.6
Q ss_pred ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC------CCCCceee
Q 041256 195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP------SYPGTLFI 241 (244)
Q Consensus 195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~------~~~~i~~~ 241 (244)
..+||||||.|.++.++++++|+...+.+|. +..+..+. .+++|.++
T Consensus 19 ~l~lEIG~G~G~~l~~~A~~~Pd~n~iGiE~~~~~v~~a~~~~~~~~l~Nv~~~ 72 (195)
T PF02390_consen 19 PLILEIGCGKGEFLIELAKRNPDINFIGIEIRKKRVAKALRKAEKRGLKNVRFL 72 (195)
T ss_dssp EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHHTTSSEEEE
T ss_pred CeEEEecCCCCHHHHHHHHHCCCCCEEEEecchHHHHHHHHHHHhhcccceEEE
Confidence 5999999999999999999999999999997 44544442 14566554
No 37
>PRK08317 hypothetical protein; Provisional
Probab=96.91 E-value=0.0018 Score=53.63 Aligned_cols=50 Identities=18% Similarity=0.242 Sum_probs=40.2
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+.+.++ +....+|||||||.|.++..+++.+ |..+.+.+|+ |..++.+++
T Consensus 11 ~~~~~~-~~~~~~vLdiG~G~G~~~~~~a~~~~~~~~v~~~d~~~~~~~~a~~ 62 (241)
T PRK08317 11 TFELLA-VQPGDRVLDVGCGPGNDARELARRVGPEGRVVGIDRSEAMLALAKE 62 (241)
T ss_pred HHHHcC-CCCCCEEEEeCCCCCHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHH
Confidence 445555 6677899999999999999999998 8889999998 565665543
No 38
>COG2890 HemK Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]
Probab=96.88 E-value=0.00071 Score=58.42 Aligned_cols=39 Identities=23% Similarity=0.376 Sum_probs=37.0
Q ss_pred eEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 196 KLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 196 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+|+|||+|+|..++++++++|+.+++..|+ |.+++.|++
T Consensus 113 ~ilDlGTGSG~iai~la~~~~~~~V~a~Dis~~Al~~A~~ 152 (280)
T COG2890 113 RILDLGTGSGAIAIALAKEGPDAEVIAVDISPDALALARE 152 (280)
T ss_pred cEEEecCChHHHHHHHHhhCcCCeEEEEECCHHHHHHHHH
Confidence 899999999999999999999999999999 899988875
No 39
>PF13649 Methyltransf_25: Methyltransferase domain; PDB: 3BXO_B 3GGD_A 3PX2_A 3PX3_A 3PFH_D 3PFG_A 1Y8C_A.
Probab=96.87 E-value=0.00069 Score=48.92 Aligned_cols=38 Identities=24% Similarity=0.503 Sum_probs=30.4
Q ss_pred EEEecCCccHHHHHHHHHC---CCCeEEEccc-hHHhhhCCC
Q 041256 197 LVDVGGGLGITLNMIISKY---PHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 197 vvDVGGG~G~~~~~l~~~~---P~l~~~v~Dl-p~vi~~a~~ 234 (244)
|+|+|||+|..+..+++.+ |+.+.+.+|+ |+.++.+++
T Consensus 1 ILDlgcG~G~~~~~l~~~~~~~~~~~~~gvD~s~~~l~~~~~ 42 (101)
T PF13649_consen 1 ILDLGCGTGRVTRALARRFDAGPSSRVIGVDISPEMLELAKK 42 (101)
T ss_dssp -EEET-TTSHHHHHHHHHS-----SEEEEEES-HHHHHHHHH
T ss_pred CEEeecCCcHHHHHHHHHhhhcccceEEEEECCHHHHHHHHH
Confidence 7999999999999999997 6789999998 777777764
No 40
>COG2226 UbiE Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]
Probab=96.87 E-value=0.0019 Score=54.34 Aligned_cols=42 Identities=17% Similarity=0.170 Sum_probs=38.5
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
...+|+|||||+|-++..+++..+..++++.|. +..++.+++
T Consensus 51 ~g~~vLDva~GTGd~a~~~~k~~g~g~v~~~D~s~~ML~~a~~ 93 (238)
T COG2226 51 PGDKVLDVACGTGDMALLLAKSVGTGEVVGLDISESMLEVARE 93 (238)
T ss_pred CCCEEEEecCCccHHHHHHHHhcCCceEEEEECCHHHHHHHHH
Confidence 568999999999999999999999999999998 788888875
No 41
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=96.85 E-value=0.0025 Score=42.91 Aligned_cols=60 Identities=17% Similarity=0.222 Sum_probs=46.6
Q ss_pred HHhcChhhHHhhcCCCC-CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 33 VVELDVFEIISKAGPGA-KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 33 a~~lgifd~L~~~~~~g-~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
..+-.|+..|.+.| + ++|+.|||+.+|++ ... +.|+|.-|...|++..... .++.|..+.
T Consensus 6 ~~~~~IL~~L~~~g--~~~~ta~eLa~~lgl~------~~~-v~r~L~~L~~~G~V~~~~~-~~~~W~i~~ 66 (68)
T smart00550 6 SLEEKILEFLENSG--DETSTALQLAKNLGLP------KKE-VNRVLYSLEKKGKVCKQGG-TPPLWKLTD 66 (68)
T ss_pred HHHHHHHHHHHHCC--CCCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEecCC-CCCceEeec
Confidence 34567888898874 3 39999999999997 456 9999999999999986321 247787764
No 42
>smart00650 rADc Ribosomal RNA adenine dimethylases.
Probab=96.84 E-value=0.0023 Score=50.81 Aligned_cols=50 Identities=10% Similarity=0.300 Sum_probs=38.9
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+++.++ +....+++|||||.|.++..++++ ..+++.+|. |..++.+++
T Consensus 3 ~~i~~~~~-~~~~~~vLEiG~G~G~lt~~l~~~--~~~v~~vE~~~~~~~~~~~ 53 (169)
T smart00650 3 DKIVRAAN-LRPGDTVLEIGPGKGALTEELLER--AARVTAIEIDPRLAPRLRE 53 (169)
T ss_pred HHHHHhcC-CCCcCEEEEECCCccHHHHHHHhc--CCeEEEEECCHHHHHHHHH
Confidence 34566666 666689999999999999999998 467888887 566666543
No 43
>PRK10258 biotin biosynthesis protein BioC; Provisional
Probab=96.81 E-value=0.0038 Score=52.71 Aligned_cols=50 Identities=18% Similarity=0.251 Sum_probs=38.6
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+++.++ .....+|+|||||+|.++..+.+. ..+++..|+ |..++.+++
T Consensus 32 ~~l~~~l~-~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~~D~s~~~l~~a~~ 82 (251)
T PRK10258 32 DALLAMLP-QRKFTHVLDAGCGPGWMSRYWRER--GSQVTALDLSPPMLAQARQ 82 (251)
T ss_pred HHHHHhcC-ccCCCeEEEeeCCCCHHHHHHHHc--CCeEEEEECCHHHHHHHHh
Confidence 44555555 345689999999999998888764 467899999 888877765
No 44
>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=96.79 E-value=0.0012 Score=57.07 Aligned_cols=42 Identities=21% Similarity=0.269 Sum_probs=38.1
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+..+|+|+|||+|.++..+++++|+.+++.+|. |..++.|++
T Consensus 121 ~~~~vLDlG~GsG~i~~~la~~~~~~~v~avDis~~al~~A~~ 163 (284)
T TIGR03533 121 PVKRILDLCTGSGCIAIACAYAFPEAEVDAVDISPDALAVAEI 163 (284)
T ss_pred CCCEEEEEeCchhHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence 447899999999999999999999999999999 888888764
No 45
>TIGR00477 tehB tellurite resistance protein TehB. Part of a tellurite-reducing operon tehA and tehB
Probab=96.79 E-value=0.0025 Score=51.97 Aligned_cols=49 Identities=22% Similarity=0.149 Sum_probs=38.1
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
..+++.++ .....+|+|||||.|.++..++++ +.+++.+|. |..++.++
T Consensus 20 ~~l~~~~~-~~~~~~vLDiGcG~G~~a~~la~~--g~~V~~iD~s~~~l~~a~ 69 (195)
T TIGR00477 20 SAVREAVK-TVAPCKTLDLGCGQGRNSLYLSLA--GYDVRAWDHNPASIASVL 69 (195)
T ss_pred HHHHHHhc-cCCCCcEEEeCCCCCHHHHHHHHC--CCeEEEEECCHHHHHHHH
Confidence 35556665 445689999999999999999985 568899998 77777654
No 46
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=96.79 E-value=0.0028 Score=54.31 Aligned_cols=48 Identities=29% Similarity=0.497 Sum_probs=38.1
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCC---eEEEccc-hHHhhhCCC-CCCcee
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHI---KGINYDL-PYVIKDAPS-YPGTLF 240 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l---~~~v~Dl-p~vi~~a~~-~~~i~~ 240 (244)
...+|+|||||+|.++..+++.+|.. +++.+|+ |..++.|++ .+++.+
T Consensus 85 ~~~~vLDiGcG~G~~~~~l~~~~~~~~~~~v~giD~s~~~l~~A~~~~~~~~~ 137 (272)
T PRK11088 85 KATALLDIGCGEGYYTHALADALPEITTMQLFGLDISKVAIKYAAKRYPQVTF 137 (272)
T ss_pred CCCeEEEECCcCCHHHHHHHHhcccccCCeEEEECCCHHHHHHHHHhCCCCeE
Confidence 44789999999999999999998864 5799998 777877754 355544
No 47
>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=96.79 E-value=0.0021 Score=54.65 Aligned_cols=41 Identities=20% Similarity=0.184 Sum_probs=37.4
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+++|+|||+|.++..+++++|..+++.+|. |..++.+++
T Consensus 87 ~~~vLDlg~GsG~i~l~la~~~~~~~v~~vDis~~al~~A~~ 128 (251)
T TIGR03704 87 TLVVVDLCCGSGAVGAALAAALDGIELHAADIDPAAVRCARR 128 (251)
T ss_pred CCEEEEecCchHHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence 45899999999999999999999999999999 888888765
No 48
>PRK11036 putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=96.78 E-value=0.0026 Score=53.98 Aligned_cols=48 Identities=25% Similarity=0.311 Sum_probs=37.9
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+++.++ ....+|+|||||.|.++..++++ ..+++.+|+ |+.++.|++
T Consensus 36 ~~l~~l~--~~~~~vLDiGcG~G~~a~~la~~--g~~v~~vD~s~~~l~~a~~ 84 (255)
T PRK11036 36 RLLAELP--PRPLRVLDAGGGEGQTAIKLAEL--GHQVILCDLSAEMIQRAKQ 84 (255)
T ss_pred HHHHhcC--CCCCEEEEeCCCchHHHHHHHHc--CCEEEEEECCHHHHHHHHH
Confidence 3444444 44579999999999999999987 467899999 888888764
No 49
>TIGR02072 BioC biotin biosynthesis protein BioC. This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, is believed to carry out an enzymatic step prior to the formation of pimeloyl-CoA (although attribution of this annotation is not traceable). The enzyme appears related to methyltransferases by homology.
Probab=96.78 E-value=0.0018 Score=53.72 Aligned_cols=42 Identities=19% Similarity=0.423 Sum_probs=35.6
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
...+|||||||.|.++..+++.+|+.+++..|. |..++.+++
T Consensus 34 ~~~~vLDlG~G~G~~~~~l~~~~~~~~~~~~D~~~~~~~~~~~ 76 (240)
T TIGR02072 34 IPASVLDIGCGTGYLTRALLKRFPQAEFIALDISAGMLAQAKT 76 (240)
T ss_pred CCCeEEEECCCccHHHHHHHHhCCCCcEEEEeChHHHHHHHHH
Confidence 347899999999999999999999999999998 566655543
No 50
>PRK11805 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=96.74 E-value=0.0012 Score=57.81 Aligned_cols=40 Identities=18% Similarity=0.238 Sum_probs=37.3
Q ss_pred ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+|+|+|||+|.++..+++++|+.+++.+|+ |..++.|++
T Consensus 135 ~~VLDlG~GsG~iai~la~~~p~~~V~avDis~~al~~A~~ 175 (307)
T PRK11805 135 TRILDLCTGSGCIAIACAYAFPDAEVDAVDISPDALAVAEI 175 (307)
T ss_pred CEEEEEechhhHHHHHHHHHCCCCEEEEEeCCHHHHHHHHH
Confidence 6899999999999999999999999999999 888888865
No 51
>TIGR03534 RF_mod_PrmC protein-(glutamine-N5) methyltransferase, release factor-specific. Members of this protein family are HemK (PrmC), a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. SIMBAL analysis (manuscript in prep.) shows the motif [LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers specificity for the release factors rather than for ribosomal protein L3.
Probab=96.70 E-value=0.0028 Score=53.18 Aligned_cols=42 Identities=19% Similarity=0.299 Sum_probs=37.2
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
...+|+|+|||+|.++..+++.+|+.+++.+|. |..++.+++
T Consensus 87 ~~~~ilDig~G~G~~~~~l~~~~~~~~v~~iD~~~~~~~~a~~ 129 (251)
T TIGR03534 87 GPLRVLDLGTGSGAIALALAKERPDARVTAVDISPEALAVARK 129 (251)
T ss_pred CCCeEEEEeCcHhHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence 346899999999999999999999999999998 777877754
No 52
>TIGR00080 pimt protein-L-isoaspartate(D-aspartate) O-methyltransferase. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt.
Probab=96.69 E-value=0.0042 Score=51.32 Aligned_cols=51 Identities=14% Similarity=0.189 Sum_probs=40.3
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+++.++ .....+|+|||||+|.++..+++..+ +.+++.+|. |+.++.|++
T Consensus 68 ~~~~~l~-~~~~~~VLDiG~GsG~~a~~la~~~~~~g~V~~vD~~~~~~~~A~~ 120 (215)
T TIGR00080 68 MMTELLE-LKPGMKVLEIGTGSGYQAAVLAEIVGRDGLVVSIERIPELAEKAER 120 (215)
T ss_pred HHHHHhC-CCCcCEEEEECCCccHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHH
Confidence 4455555 56678999999999999999999865 567888886 888887764
No 53
>COG2264 PrmA Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]
Probab=96.68 E-value=0.0012 Score=57.11 Aligned_cols=63 Identities=27% Similarity=0.379 Sum_probs=44.3
Q ss_pred HHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 168 VFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 168 ~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.|..+-...+.+.. .+++.+. .+.++++|||||+|.++++.++--.. +++.+|+ |..++.+++
T Consensus 140 AFGTG~HpTT~lcL-~~Le~~~--~~g~~vlDvGcGSGILaIAa~kLGA~-~v~g~DiDp~AV~aa~e 203 (300)
T COG2264 140 AFGTGTHPTTSLCL-EALEKLL--KKGKTVLDVGCGSGILAIAAAKLGAK-KVVGVDIDPQAVEAARE 203 (300)
T ss_pred ccCCCCChhHHHHH-HHHHHhh--cCCCEEEEecCChhHHHHHHHHcCCc-eEEEecCCHHHHHHHHH
Confidence 45444444444433 4455554 47799999999999999998876443 5677787 888888875
No 54
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=96.66 E-value=0.0024 Score=54.13 Aligned_cols=59 Identities=22% Similarity=0.381 Sum_probs=47.5
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA 105 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~ 105 (244)
+.|++.|.+.+ .++++.|||+++|++ ..- +.|+|..|+..||+.+++ ..++|++++..-
T Consensus 7 l~iL~~l~~~~--~~l~l~ela~~~glp------ksT-~~RlL~tL~~~G~v~~d~--~~g~Y~Lg~~~~ 65 (246)
T COG1414 7 LAILDLLAEGP--GGLSLAELAERLGLP------KST-VHRLLQTLVELGYVEQDP--EDGRYRLGPRLL 65 (246)
T ss_pred HHHHHHHHhCC--CCCCHHHHHHHhCcC------HHH-HHHHHHHHHHCCCEEEcC--CCCcEeehHHHH
Confidence 56788888743 457899999999995 345 999999999999999742 257899998753
No 55
>PRK00216 ubiE ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed
Probab=96.64 E-value=0.0031 Score=52.31 Aligned_cols=51 Identities=12% Similarity=0.081 Sum_probs=40.1
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~ 234 (244)
.++..+. .....+|+|||||.|.++..+++.+| +.+++++|+ |..++.+++
T Consensus 42 ~~~~~~~-~~~~~~vldiG~G~G~~~~~l~~~~~~~~~v~~~D~s~~~~~~a~~ 94 (239)
T PRK00216 42 KTIKWLG-VRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFSEGMLAVGRE 94 (239)
T ss_pred HHHHHhC-CCCCCeEEEeCCCCCHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHH
Confidence 3444444 44557999999999999999999998 789999998 666666654
No 56
>PRK01581 speE spermidine synthase; Validated
Probab=96.63 E-value=0.0027 Score=56.54 Aligned_cols=43 Identities=23% Similarity=0.265 Sum_probs=37.1
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.++++|++||||.|..+.++++..|..+.++.|+ |+|++.|++
T Consensus 149 ~~PkrVLIIGgGdG~tlrelLk~~~v~~It~VEIDpeVIelAr~ 192 (374)
T PRK01581 149 IDPKRVLILGGGDGLALREVLKYETVLHVDLVDLDGSMINMARN 192 (374)
T ss_pred CCCCEEEEECCCHHHHHHHHHhcCCCCeEEEEeCCHHHHHHHHh
Confidence 5668999999999999999997656678999998 889998874
No 57
>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional
Probab=96.60 E-value=0.0031 Score=53.92 Aligned_cols=51 Identities=25% Similarity=0.366 Sum_probs=41.1
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+++.++ +....+|||||||.|..+..+++++ +.+++.+|+ |..++.+++
T Consensus 42 ~~~l~~l~-l~~~~~VLDiGcG~G~~a~~la~~~-~~~v~giD~s~~~~~~a~~ 93 (263)
T PTZ00098 42 TKILSDIE-LNENSKVLDIGSGLGGGCKYINEKY-GAHVHGVDICEKMVNIAKL 93 (263)
T ss_pred HHHHHhCC-CCCCCEEEEEcCCCChhhHHHHhhc-CCEEEEEECCHHHHHHHHH
Confidence 45666676 6777899999999999999998876 678999998 666666654
No 58
>PLN02244 tocopherol O-methyltransferase
Probab=96.60 E-value=0.0031 Score=55.91 Aligned_cols=41 Identities=29% Similarity=0.412 Sum_probs=34.5
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
....+|||||||.|.++..+++++ +.+++.+|+ |..++.++
T Consensus 117 ~~~~~VLDiGCG~G~~~~~La~~~-g~~v~gvD~s~~~i~~a~ 158 (340)
T PLN02244 117 KRPKRIVDVGCGIGGSSRYLARKY-GANVKGITLSPVQAARAN 158 (340)
T ss_pred CCCCeEEEecCCCCHHHHHHHHhc-CCEEEEEECCHHHHHHHH
Confidence 456899999999999999999988 778999998 66666554
No 59
>PRK07580 Mg-protoporphyrin IX methyl transferase; Validated
Probab=96.57 E-value=0.0034 Score=52.00 Aligned_cols=41 Identities=20% Similarity=0.311 Sum_probs=33.8
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
....+|+|||||.|.++..++++.+ +++..|+ |..++.+++
T Consensus 62 ~~~~~vLDvGcG~G~~~~~l~~~~~--~v~~~D~s~~~i~~a~~ 103 (230)
T PRK07580 62 LTGLRILDAGCGVGSLSIPLARRGA--KVVASDISPQMVEEARE 103 (230)
T ss_pred CCCCEEEEEeCCCCHHHHHHHHcCC--EEEEEECCHHHHHHHHH
Confidence 4557999999999999999998865 4888898 777777764
No 60
>PRK14966 unknown domain/N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase fusion protein; Provisional
Probab=96.55 E-value=0.0022 Score=58.15 Aligned_cols=42 Identities=19% Similarity=0.245 Sum_probs=38.1
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
...+++|||||+|.++..+++++|+.+++.+|. |..++.+++
T Consensus 251 ~~~rVLDLGcGSG~IaiaLA~~~p~a~VtAVDiS~~ALe~Are 293 (423)
T PRK14966 251 ENGRVWDLGTGSGAVAVTVALERPDAFVRASDISPPALETARK 293 (423)
T ss_pred CCCEEEEEeChhhHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence 346899999999999999999999999999999 888888875
No 61
>COG2230 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]
Probab=96.55 E-value=0.0049 Score=52.96 Aligned_cols=50 Identities=20% Similarity=0.254 Sum_probs=41.9
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
..+.+.+. +++..+|||||||-|.+++-.+++| +.+++.+++ ++-.+.++
T Consensus 62 ~~~~~kl~-L~~G~~lLDiGCGWG~l~~~aA~~y-~v~V~GvTlS~~Q~~~~~ 112 (283)
T COG2230 62 DLILEKLG-LKPGMTLLDIGCGWGGLAIYAAEEY-GVTVVGVTLSEEQLAYAE 112 (283)
T ss_pred HHHHHhcC-CCCCCEEEEeCCChhHHHHHHHHHc-CCEEEEeeCCHHHHHHHH
Confidence 45677777 8899999999999999999999999 999999998 44444443
No 62
>PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional
Probab=96.55 E-value=0.0082 Score=49.51 Aligned_cols=45 Identities=20% Similarity=0.178 Sum_probs=34.1
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccchH
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDLPY 227 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp~ 227 (244)
.+.+.|..+....+|||||||+|.++..++++. |..+++.+|+-+
T Consensus 41 ~~~~~~~~~~~~~~VLDlG~GtG~~t~~l~~~~~~~~~V~aVDi~~ 86 (209)
T PRK11188 41 EIQQSDKLFKPGMTVVDLGAAPGGWSQYAVTQIGDKGRVIACDILP 86 (209)
T ss_pred HHHHHhccCCCCCEEEEEcccCCHHHHHHHHHcCCCceEEEEeccc
Confidence 334444434566799999999999999999987 456888888744
No 63
>PLN02366 spermidine synthase
Probab=96.54 E-value=0.0024 Score=55.83 Aligned_cols=42 Identities=26% Similarity=0.247 Sum_probs=35.2
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~ 234 (244)
++.++|++||||.|..+..+++. |. .+++++|+ |.|++.+++
T Consensus 90 ~~pkrVLiIGgG~G~~~rellk~-~~v~~V~~VEiD~~Vi~~ar~ 133 (308)
T PLN02366 90 PNPKKVLVVGGGDGGVLREIARH-SSVEQIDICEIDKMVIDVSKK 133 (308)
T ss_pred CCCCeEEEEcCCccHHHHHHHhC-CCCCeEEEEECCHHHHHHHHH
Confidence 46789999999999999999865 65 57889998 678888865
No 64
>TIGR00536 hemK_fam HemK family putative methylases. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. Both E. coli and H. influenzae have two members rather than one. The members from the Mycoplasmas have an additional C-terminal domain.
Probab=96.51 E-value=0.0021 Score=55.49 Aligned_cols=40 Identities=23% Similarity=0.405 Sum_probs=36.9
Q ss_pred ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+|+|+|||+|.++..+++.+|+.+++..|. |..++.+++
T Consensus 116 ~~vLDlG~GsG~i~l~la~~~~~~~v~avDis~~al~~a~~ 156 (284)
T TIGR00536 116 LHILDLGTGSGCIALALAYEFPNAEVIAVDISPDALAVAEE 156 (284)
T ss_pred CEEEEEeccHhHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence 6899999999999999999999999999998 888887765
No 65
>PRK09328 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=96.50 E-value=0.0041 Score=53.08 Aligned_cols=44 Identities=18% Similarity=0.310 Sum_probs=37.8
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.....+|+|+|||+|.++..+++.+|..+++..|. |..++.+++
T Consensus 106 ~~~~~~vLDiG~GsG~~~~~la~~~~~~~v~~iDis~~~l~~a~~ 150 (275)
T PRK09328 106 LKEPLRVLDLGTGSGAIALALAKERPDAEVTAVDISPEALAVARR 150 (275)
T ss_pred ccCCCEEEEEcCcHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence 34557899999999999999999999999999998 677776654
No 66
>PHA03411 putative methyltransferase; Provisional
Probab=96.49 E-value=0.0036 Score=53.61 Aligned_cols=47 Identities=17% Similarity=0.260 Sum_probs=39.3
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCcee
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLF 240 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~ 240 (244)
..+|+|+|||.|.++..++++.+..+++.+|+ |..++.+++ .+++++
T Consensus 65 ~grVLDLGcGsGilsl~la~r~~~~~V~gVDisp~al~~Ar~n~~~v~~ 113 (279)
T PHA03411 65 TGKVLDLCAGIGRLSFCMLHRCKPEKIVCVELNPEFARIGKRLLPEAEW 113 (279)
T ss_pred CCeEEEcCCCCCHHHHHHHHhCCCCEEEEEECCHHHHHHHHHhCcCCEE
Confidence 46899999999999999999988889999998 888887765 345554
No 67
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=96.46 E-value=0.0024 Score=59.66 Aligned_cols=41 Identities=22% Similarity=0.330 Sum_probs=37.5
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+|+|||||+|.++..+++++|+.+++.+|+ |.+++.|++
T Consensus 139 ~~~VLDlG~GsG~iai~la~~~p~~~v~avDis~~al~~A~~ 180 (506)
T PRK01544 139 FLNILELGTGSGCIAISLLCELPNANVIATDISLDAIEVAKS 180 (506)
T ss_pred CCEEEEccCchhHHHHHHHHHCCCCeEEEEECCHHHHHHHHH
Confidence 46899999999999999999999999999999 788888765
No 68
>PRK11569 transcriptional repressor IclR; Provisional
Probab=96.43 E-value=0.0042 Score=53.40 Aligned_cols=59 Identities=14% Similarity=0.224 Sum_probs=47.4
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA 105 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~ 105 (244)
+.|.+.|.+.+ ++.|+.|||+.+|++ ..- +.|+|.-|+..||+.++ ...++|++.+...
T Consensus 31 l~IL~~l~~~~--~~~~lseia~~lglp------ksT-v~RlL~tL~~~G~l~~~--~~~~~Y~lG~~l~ 89 (274)
T PRK11569 31 LKLLEWIAESN--GSVALTELAQQAGLP------NST-THRLLTTMQQQGFVRQV--GELGHWAIGAHAF 89 (274)
T ss_pred HHHHHHHHhCC--CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEc--CCCCeEecCHHHH
Confidence 56777887753 689999999999996 345 99999999999999863 2358899987653
No 69
>PRK00811 spermidine synthase; Provisional
Probab=96.43 E-value=0.0028 Score=54.84 Aligned_cols=43 Identities=21% Similarity=0.244 Sum_probs=36.8
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+++++|+|||||.|..+..++++.+.-+++++|+ |.|++.+++
T Consensus 75 ~~p~~VL~iG~G~G~~~~~~l~~~~~~~V~~VEid~~vv~~a~~ 118 (283)
T PRK00811 75 PNPKRVLIIGGGDGGTLREVLKHPSVEKITLVEIDERVVEVCRK 118 (283)
T ss_pred CCCCEEEEEecCchHHHHHHHcCCCCCEEEEEeCCHHHHHHHHH
Confidence 4568999999999999999997655568999998 899988875
No 70
>PRK04266 fibrillarin; Provisional
Probab=96.41 E-value=0.0078 Score=50.31 Aligned_cols=53 Identities=13% Similarity=0.154 Sum_probs=40.0
Q ss_pred cCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHh----hhCCCCCCceee
Q 041256 188 YKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVI----KDAPSYPGTLFI 241 (244)
Q Consensus 188 ~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi----~~a~~~~~i~~~ 241 (244)
++ .....+|+|+|||+|.++..+++..+.-+++.+|+ |+.+ +.+++.++|+++
T Consensus 68 l~-i~~g~~VlD~G~G~G~~~~~la~~v~~g~V~avD~~~~ml~~l~~~a~~~~nv~~i 125 (226)
T PRK04266 68 FP-IKKGSKVLYLGAASGTTVSHVSDIVEEGVVYAVEFAPRPMRELLEVAEERKNIIPI 125 (226)
T ss_pred CC-CCCCCEEEEEccCCCHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHhhhcCCcEEE
Confidence 55 56678999999999999999999998667888998 5433 344444555543
No 71
>TIGR01934 MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis methyltransferases. Note that a number of non-orthologous genes which are members of pfam03737 have been erroneously annotated as MenG methyltransferases.
Probab=96.40 E-value=0.0049 Score=50.54 Aligned_cols=51 Identities=18% Similarity=0.147 Sum_probs=40.0
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~ 234 (244)
.+++... .....+|+|+|||.|.++..+++++|. .+.+.+|. |..++.+++
T Consensus 30 ~~~~~~~-~~~~~~vldiG~G~G~~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~ 82 (223)
T TIGR01934 30 RAVKLIG-VFKGQKVLDVACGTGDLAIELAKSAPDRGKVTGVDFSSEMLEVAKK 82 (223)
T ss_pred HHHHHhc-cCCCCeEEEeCCCCChhHHHHHHhcCCCceEEEEECCHHHHHHHHH
Confidence 3344444 446689999999999999999999998 78999998 666666543
No 72
>PLN02490 MPBQ/MSBQ methyltransferase
Probab=96.39 E-value=0.0075 Score=53.44 Aligned_cols=42 Identities=31% Similarity=0.340 Sum_probs=36.7
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
...+|||||||+|.++..+++++|..+++.+|+ |+.++.+++
T Consensus 113 ~~~~VLDLGcGtG~~~l~La~~~~~~~VtgVD~S~~mL~~A~~ 155 (340)
T PLN02490 113 RNLKVVDVGGGTGFTTLGIVKHVDAKNVTILDQSPHQLAKAKQ 155 (340)
T ss_pred CCCEEEEEecCCcHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence 347999999999999999999999999999998 777777764
No 73
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=96.39 E-value=0.0047 Score=53.05 Aligned_cols=59 Identities=15% Similarity=0.211 Sum_probs=47.3
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA 105 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~ 105 (244)
+.|++.|.+.+ +++|+.|||+.+|++ ..- +.|+|.-|+..||+.++. ..++|+++....
T Consensus 28 l~IL~~~~~~~--~~~tl~eIa~~lglp------kSt-v~RlL~tL~~~G~l~~~~--~~~~Y~lG~~l~ 86 (271)
T PRK10163 28 IAILQYLEKSG--GSSSVSDISLNLDLP------LST-TFRLLKVLQAADFVYQDS--QLGWWHIGLGVF 86 (271)
T ss_pred HHHHHHHHhCC--CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEcC--CCCeEEecHHHH
Confidence 56778887754 579999999999996 445 999999999999998642 357899987643
No 74
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=96.39 E-value=0.0043 Score=52.47 Aligned_cols=59 Identities=25% Similarity=0.363 Sum_probs=47.6
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYF 107 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l 107 (244)
+.|.+.|.+.+ .+.|+.|||+.+|++ ..- +.|+|.-|+..||+.+ + .++|++.+....|
T Consensus 12 l~IL~~l~~~~--~~~~l~eia~~lglp------ksT-~~RlL~tL~~~G~l~~---~-~~~Y~lG~~~~~l 70 (248)
T TIGR02431 12 LAVIEAFGAER--PRLTLTDVAEATGLT------RAA-ARRFLLTLVELGYVTS---D-GRLFWLTPRVLRL 70 (248)
T ss_pred HHHHHHHhcCC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEe---C-CCEEEecHHHHHH
Confidence 56778887653 689999999999995 345 9999999999999994 3 4789998875433
No 75
>PRK05785 hypothetical protein; Provisional
Probab=96.39 E-value=0.004 Score=52.04 Aligned_cols=40 Identities=20% Similarity=0.194 Sum_probs=34.8
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+|+|||||+|.++..+++++ +.+++.+|. |+.++.+++
T Consensus 52 ~~~VLDlGcGtG~~~~~l~~~~-~~~v~gvD~S~~Ml~~a~~ 92 (226)
T PRK05785 52 PKKVLDVAAGKGELSYHFKKVF-KYYVVALDYAENMLKMNLV 92 (226)
T ss_pred CCeEEEEcCCCCHHHHHHHHhc-CCEEEEECCCHHHHHHHHh
Confidence 5799999999999999999988 678999998 777777654
No 76
>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=96.36 E-value=0.0026 Score=42.63 Aligned_cols=56 Identities=16% Similarity=0.201 Sum_probs=42.9
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL 100 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~ 100 (244)
.+..|+..|... |+.|+.|||+.+|++ ... +.+.|+-|...|++.+... .+..|..
T Consensus 9 ~E~~vy~~Ll~~---~~~t~~eIa~~l~i~------~~~-v~~~L~~L~~~GlV~~~~~-~~~~Y~a 64 (68)
T PF01978_consen 9 NEAKVYLALLKN---GPATAEEIAEELGIS------RST-VYRALKSLEEKGLVEREEG-RPKVYRA 64 (68)
T ss_dssp HHHHHHHHHHHH---CHEEHHHHHHHHTSS------HHH-HHHHHHHHHHTTSEEEEEE-CCEEEEE
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEEcC-ceEEEEE
Confidence 345567777654 799999999999996 456 9999999999999997532 2445554
No 77
>PLN02233 ubiquinone biosynthesis methyltransferase
Probab=96.36 E-value=0.0086 Score=51.11 Aligned_cols=43 Identities=16% Similarity=0.123 Sum_probs=36.0
Q ss_pred CCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~ 233 (244)
.....+|+|||||+|.++..+++++ |+.+++.+|. |+.++.|+
T Consensus 71 ~~~~~~VLDlGcGtG~~~~~la~~~~~~~~V~gvD~S~~ml~~A~ 115 (261)
T PLN02233 71 AKMGDRVLDLCCGSGDLAFLLSEKVGSDGKVMGLDFSSEQLAVAA 115 (261)
T ss_pred CCCCCEEEEECCcCCHHHHHHHHHhCCCCEEEEEECCHHHHHHHH
Confidence 4456799999999999999999885 6789999998 77777764
No 78
>PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=96.35 E-value=0.01 Score=49.04 Aligned_cols=51 Identities=16% Similarity=0.224 Sum_probs=40.5
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+++.++ .....+|+|||||+|.++..+++.. ++.+++.+|. |+.++.+++
T Consensus 67 ~~~~~l~-~~~g~~VLdIG~GsG~~t~~la~~~~~~~~V~~vE~~~~~~~~a~~ 119 (212)
T PRK13942 67 IMCELLD-LKEGMKVLEIGTGSGYHAAVVAEIVGKSGKVVTIERIPELAEKAKK 119 (212)
T ss_pred HHHHHcC-CCCcCEEEEECCcccHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHH
Confidence 4455666 6777899999999999998888875 4568888987 788877764
No 79
>smart00138 MeTrc Methyltransferase, chemotaxis proteins. Methylates methyl-accepting chemotaxis proteins to form gamma-glutamyl methyl ester residues.
Probab=96.35 E-value=0.023 Score=48.56 Aligned_cols=52 Identities=13% Similarity=0.215 Sum_probs=38.5
Q ss_pred HHHHhhcCCCCCcceEEEecCCccH----HHHHHHHHCC-----CCeEEEccc-hHHhhhCCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGI----TLNMIISKYP-----HIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~----~~~~l~~~~P-----~l~~~v~Dl-p~vi~~a~~ 234 (244)
+.+++.-+ .....+|+|+|||+|. +++.+++.+| +.+.+..|+ |.+++.|++
T Consensus 89 p~l~~~~~-~~~~~ri~d~GCgtGee~YslA~~l~e~~~~~~~~~~~I~g~Dis~~~L~~Ar~ 150 (264)
T smart00138 89 PLLIASRR-HGRRVRIWSAGCSTGEEPYSLAMLLAETLPKAREPDVKILATDIDLKALEKARA 150 (264)
T ss_pred HHHHHhcC-CCCCEEEEeccccCChHHHHHHHHHHHHhhhcCCCCeEEEEEECCHHHHHHHHc
Confidence 44444333 3455799999999996 5667777765 578899998 888988875
No 80
>TIGR00438 rrmJ cell division protein FtsJ.
Probab=96.34 E-value=0.01 Score=47.85 Aligned_cols=44 Identities=16% Similarity=0.168 Sum_probs=34.7
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccchH
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDLPY 227 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp~ 227 (244)
+.+.+.......+|+|+|||+|.++..+++++ +..+.+.+|+.+
T Consensus 23 ~~~~~~~i~~g~~VLDiG~GtG~~~~~l~~~~~~~~~v~~vDis~ 67 (188)
T TIGR00438 23 LNQKFKLIKPGDTVLDLGAAPGGWSQVAVEQVGGKGRVIAVDLQP 67 (188)
T ss_pred HHHHhcccCCCCEEEEecCCCCHHHHHHHHHhCCCceEEEEeccc
Confidence 44445445667899999999999999999887 667888888844
No 81
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=96.33 E-value=0.0074 Score=51.21 Aligned_cols=49 Identities=14% Similarity=0.287 Sum_probs=37.6
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
..+++..+ +.+..+|+|||||.|.++..++++.+. ++.+|. +..++.++
T Consensus 19 ~~i~~~~~-~~~~~~VLEiG~G~G~lt~~L~~~~~~--v~~iE~d~~~~~~l~ 68 (253)
T TIGR00755 19 QKIVEAAN-VLEGDVVLEIGPGLGALTEPLLKRAKK--VTAIEIDPRLAEILR 68 (253)
T ss_pred HHHHHhcC-CCCcCEEEEeCCCCCHHHHHHHHhCCc--EEEEECCHHHHHHHH
Confidence 45566666 667789999999999999999999976 666665 55555554
No 82
>PF13659 Methyltransf_26: Methyltransferase domain; PDB: 3GJY_A 3LPM_B 2NP6_D 1AQI_B 2ADM_B 2IH2_A 2JG3_A 2IBS_D 2NP7_A 2IBT_A ....
Probab=96.32 E-value=0.0047 Score=45.45 Aligned_cols=39 Identities=21% Similarity=0.292 Sum_probs=34.9
Q ss_pred ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+|+|+|||.|.++..++++. ..+++.+|+ |..++.++.
T Consensus 2 ~~vlD~~~G~G~~~~~~~~~~-~~~~~gvdi~~~~~~~a~~ 41 (117)
T PF13659_consen 2 DRVLDPGCGSGTFLLAALRRG-AARVTGVDIDPEAVELARR 41 (117)
T ss_dssp EEEEEETSTTCHHHHHHHHHC-TCEEEEEESSHHHHHHHHH
T ss_pred CEEEEcCcchHHHHHHHHHHC-CCeEEEEEECHHHHHHHHH
Confidence 589999999999999999999 888999998 888887764
No 83
>PF01209 Ubie_methyltran: ubiE/COQ5 methyltransferase family; InterPro: IPR004033 A number of methyltransferases have been shown to share regions of similarities []. Apart from the ubiquinone/menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the ubiE gene of Escherichia coli), the ubiquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the COQ5 gene of Saccharomyces cerevisiae) and the menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the MENH gene of Bacillus subtilis), this family also includes methyltransferases involved in biotin and sterol biosynthesis and in phosphatidylethanolamine methylation.; GO: 0008168 methyltransferase activity; PDB: 1VL5_C.
Probab=96.32 E-value=0.0036 Score=52.61 Aligned_cols=44 Identities=20% Similarity=0.319 Sum_probs=31.9
Q ss_pred CCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.....+|+|||||+|.++..++++. |+.+++..|. |..++.|++
T Consensus 45 ~~~g~~vLDv~~GtG~~~~~l~~~~~~~~~v~~vD~s~~ML~~a~~ 90 (233)
T PF01209_consen 45 LRPGDRVLDVACGTGDVTRELARRVGPNGKVVGVDISPGMLEVARK 90 (233)
T ss_dssp --S--EEEEET-TTSHHHHHHGGGSS---EEEEEES-HHHHHHHHH
T ss_pred CCCCCEEEEeCCChHHHHHHHHHHCCCccEEEEecCCHHHHHHHHH
Confidence 3456799999999999999999885 6789999998 888888764
No 84
>PF06325 PrmA: Ribosomal protein L11 methyltransferase (PrmA); InterPro: IPR010456 This family consists of several Ribosomal protein L11 methyltransferase sequences. Its genetic determinant is prmA, which forms a bifunctional operon with the downstream panF gene []. The role of L11 methylation in ribosome function is, as yet, unknown. Deletion of the prmA gene in Escherichia coli showed no obvious effect [] except for the production of undermethylated forms of L11 []. Methylation is the most common post-transcriptional modification to ribosomal proteins in all organisms. PrmA is the only bacterial enzyme that catalyses the methylation of a ribosomal protein [].; GO: 0008276 protein methyltransferase activity, 0006479 protein methylation, 0005737 cytoplasm; PDB: 3GRZ_B 1F3L_A 2NXJ_B 3CJT_I 3CJQ_G 2NXE_A 2NXC_A 2ZBP_A 3EGV_A 3CJS_A ....
Probab=96.31 E-value=0.0022 Score=55.67 Aligned_cols=63 Identities=27% Similarity=0.427 Sum_probs=43.6
Q ss_pred HHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 168 VFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 168 ~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.|..+-..++++.. .+++.+. .+..+|+|||||+|.++++.++.... +++.+|. |..++.+++
T Consensus 139 AFGTG~H~TT~lcl-~~l~~~~--~~g~~vLDvG~GSGILaiaA~klGA~-~v~a~DiDp~Av~~a~~ 202 (295)
T PF06325_consen 139 AFGTGHHPTTRLCL-ELLEKYV--KPGKRVLDVGCGSGILAIAAAKLGAK-KVVAIDIDPLAVEAARE 202 (295)
T ss_dssp SS-SSHCHHHHHHH-HHHHHHS--STTSEEEEES-TTSHHHHHHHHTTBS-EEEEEESSCHHHHHHHH
T ss_pred cccCCCCHHHHHHH-HHHHHhc--cCCCEEEEeCCcHHHHHHHHHHcCCC-eEEEecCCHHHHHHHHH
Confidence 45555555555544 3444454 34479999999999999999987553 6888888 888888765
No 85
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=96.30 E-value=0.005 Score=52.38 Aligned_cols=58 Identities=10% Similarity=0.243 Sum_probs=46.3
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA 105 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~ 105 (244)
+.|.+.|.+. ++.|+.|||+.+|++ ..- +.|+|+-|+..||+.++ ...++|++++...
T Consensus 17 l~IL~~l~~~---~~l~l~eia~~lgl~------kst-v~Rll~tL~~~G~l~~~--~~~~~Y~lG~~~~ 74 (257)
T PRK15090 17 FGILQALGEE---REIGITELSQRVMMS------KST-VYRFLQTMKTLGYVAQE--GESEKYSLTLKLF 74 (257)
T ss_pred HHHHHHhhcC---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEc--CCCCcEEecHHHH
Confidence 4567777664 589999999999996 345 99999999999999863 2358899998754
No 86
>PF13679 Methyltransf_32: Methyltransferase domain
Probab=96.30 E-value=0.0053 Score=47.33 Aligned_cols=43 Identities=19% Similarity=0.336 Sum_probs=34.6
Q ss_pred CCCcceEEEecCCccHHHHHHHHH----CCCCeEEEccc-hHHhhhCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISK----YPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~----~P~l~~~v~Dl-p~vi~~a~ 233 (244)
-.+..+|||+|+|.|+++..+... .|+++++.+|. |+.++.+.
T Consensus 23 ~~~~~~vvD~GsG~GyLs~~La~~l~~~~~~~~v~~iD~~~~~~~~a~ 70 (141)
T PF13679_consen 23 SKRCITVVDLGSGKGYLSRALAHLLCNSSPNLRVLGIDCNESLVESAQ 70 (141)
T ss_pred cCCCCEEEEeCCChhHHHHHHHHHHHhcCCCCeEEEEECCcHHHHHHH
Confidence 356799999999999999999982 38899999997 55555553
No 87
>COG4123 Predicted O-methyltransferase [General function prediction only]
Probab=96.30 E-value=0.0042 Score=52.44 Aligned_cols=44 Identities=14% Similarity=0.206 Sum_probs=38.1
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
....++|+|+|+|.|..+..+++++++.+.+.+|+ +...+.|++
T Consensus 42 ~~~~~~IlDlGaG~G~l~L~la~r~~~a~I~~VEiq~~~a~~A~~ 86 (248)
T COG4123 42 VPKKGRILDLGAGNGALGLLLAQRTEKAKIVGVEIQEEAAEMAQR 86 (248)
T ss_pred cccCCeEEEecCCcCHHHHHHhccCCCCcEEEEEeCHHHHHHHHH
Confidence 44579999999999999999999999999999999 666666654
No 88
>PLN02336 phosphoethanolamine N-methyltransferase
Probab=96.29 E-value=0.0059 Score=56.54 Aligned_cols=51 Identities=20% Similarity=0.321 Sum_probs=40.2
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+++.++ ++...+|+|||||.|..+..+++++ +.+++.+|+ |..++.|++
T Consensus 256 e~l~~~~~-~~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvDiS~~~l~~A~~ 307 (475)
T PLN02336 256 KEFVDKLD-LKPGQKVLDVGCGIGGGDFYMAENF-DVHVVGIDLSVNMISFALE 307 (475)
T ss_pred HHHHHhcC-CCCCCEEEEEeccCCHHHHHHHHhc-CCEEEEEECCHHHHHHHHH
Confidence 34555555 5667899999999999999888876 779999999 677776643
No 89
>PRK11705 cyclopropane fatty acyl phospholipid synthase; Provisional
Probab=96.27 E-value=0.0065 Score=54.80 Aligned_cols=50 Identities=14% Similarity=0.200 Sum_probs=40.0
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+++.++ .....+|||||||.|.++..+++++ +.+++.+|+ |+.++.+++
T Consensus 158 ~l~~~l~-l~~g~rVLDIGcG~G~~a~~la~~~-g~~V~giDlS~~~l~~A~~ 208 (383)
T PRK11705 158 LICRKLQ-LKPGMRVLDIGCGWGGLARYAAEHY-GVSVVGVTISAEQQKLAQE 208 (383)
T ss_pred HHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHC-CCEEEEEeCCHHHHHHHHH
Confidence 4555555 6667899999999999999998876 678999998 777777654
No 90
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=96.25 E-value=0.0086 Score=51.00 Aligned_cols=50 Identities=14% Similarity=0.222 Sum_probs=37.8
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+++..+ .....+|+|||||.|.++..++++. .+.+.+|+ +..++.+++
T Consensus 19 ~~iv~~~~-~~~~~~VLEIG~G~G~lt~~L~~~~--~~v~~vEid~~~~~~l~~ 69 (258)
T PRK14896 19 DRIVEYAE-DTDGDPVLEIGPGKGALTDELAKRA--KKVYAIELDPRLAEFLRD 69 (258)
T ss_pred HHHHHhcC-CCCcCeEEEEeCccCHHHHHHHHhC--CEEEEEECCHHHHHHHHH
Confidence 45555555 5566899999999999999999984 46788887 566666543
No 91
>COG0220 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]
Probab=96.24 E-value=0.0084 Score=50.11 Aligned_cols=38 Identities=16% Similarity=0.240 Sum_probs=32.8
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhh
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKD 231 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~ 231 (244)
...+|+||+|.|.++..+++++|+...+.++. ..++..
T Consensus 49 ~pi~lEIGfG~G~~l~~~A~~nP~~nfiGiEi~~~~v~~ 87 (227)
T COG0220 49 APIVLEIGFGMGEFLVEMAKKNPEKNFLGIEIRVPGVAK 87 (227)
T ss_pred CcEEEEECCCCCHHHHHHHHHCCCCCEEEEEEehHHHHH
Confidence 47999999999999999999999999999997 444433
No 92
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=96.22 E-value=0.0066 Score=51.84 Aligned_cols=61 Identities=15% Similarity=0.153 Sum_probs=48.3
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYF 107 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l 107 (244)
+.|++.|.+.+ +++|+.|||+.+|++ ..- +.|+|+.|+..|++.+++ .++.|++++....+
T Consensus 14 l~iL~~l~~~~--~~ls~~eia~~lgl~------kst-v~RlL~tL~~~g~v~~~~--~~~~Y~Lg~~~~~l 74 (263)
T PRK09834 14 LMVLRALNRLD--GGATVGLLAELTGLH------RTT-VRRLLETLQEEGYVRRSA--SDDSFRLTLKVRQL 74 (263)
T ss_pred HHHHHHHHhcC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEec--CCCcEEEcHHHHHH
Confidence 55777787653 569999999999996 345 999999999999999642 35789998876433
No 93
>PRK13944 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=96.19 E-value=0.0096 Score=48.88 Aligned_cols=50 Identities=16% Similarity=0.105 Sum_probs=38.3
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~ 234 (244)
+++.++ .....+|+|||||+|.++..+++..+ .-+++.+|. |+.++.+++
T Consensus 64 ~~~~l~-~~~~~~VLDiG~GsG~~~~~la~~~~~~g~V~~iD~~~~~~~~a~~ 115 (205)
T PRK13944 64 MCELIE-PRPGMKILEVGTGSGYQAAVCAEAIERRGKVYTVEIVKELAIYAAQ 115 (205)
T ss_pred HHHhcC-CCCCCEEEEECcCccHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHH
Confidence 444444 45557999999999999999998875 557888998 777776654
No 94
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=96.19 E-value=0.0098 Score=41.52 Aligned_cols=52 Identities=23% Similarity=0.337 Sum_probs=38.8
Q ss_pred hhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC-CceeecCcc
Q 041256 43 SKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-QRLYSLAPV 103 (244)
Q Consensus 43 ~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~~~y~~t~~ 103 (244)
+..+.+++.|.+|||+.++++ +.. ++++|..|...|+++.. .| .|.|.++.-
T Consensus 18 a~~~~~~~~s~~eiA~~~~i~------~~~-l~kil~~L~~~Gli~s~--~G~~GGy~L~~~ 70 (83)
T PF02082_consen 18 ARHPDGKPVSSKEIAERLGIS------PSY-LRKILQKLKKAGLIESS--RGRGGGYRLARP 70 (83)
T ss_dssp HCTTTSC-BEHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEEE--TSTTSEEEESS-
T ss_pred HhCCCCCCCCHHHHHHHHCcC------HHH-HHHHHHHHhhCCeeEec--CCCCCceeecCC
Confidence 433333569999999999997 678 99999999999999853 23 477888764
No 95
>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=96.13 E-value=0.018 Score=44.46 Aligned_cols=39 Identities=23% Similarity=0.399 Sum_probs=30.7
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhh
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKD 231 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~ 231 (244)
.....+|||||||.|.++..+.+..+ +.+.+|. |..++.
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 8889998 555533
No 96
>PF02353 CMAS: Mycolic acid cyclopropane synthetase; InterPro: IPR003333 This entry represents mycolic acid cyclopropane synthases and related enzymes, including CmaA1, CmaA2 (cyclopropane mycolic acid synthase A1 and A2) and MmaA1-4 (methoxymycolic acid synthase A1-4). All are thought to be S-adenosyl-L-methionine (SAM) utilising methyltransferases []. Mycolic acid cyclopropane synthase or cyclopropane-fatty-acyl-phospholipid synthase (CFA synthase) 2.1.1.79 from EC catalyses the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid -> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid. The major mycolic acid produced by Mycobacterium tuberculosis contains two cis-cyclopropanes in the meromycolate chain. Cyclopropanation may contribute to the structural integrity of the cell wall complex [].; GO: 0008610 lipid biosynthetic process; PDB: 3HA5_A 2FK8_A 3HA7_A 3HA3_A 2FK7_A 1KPG_D 1KP9_B 1KPH_D 3VC2_E 3VC1_D ....
Probab=96.09 E-value=0.0081 Score=51.67 Aligned_cols=49 Identities=16% Similarity=0.181 Sum_probs=34.4
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA 232 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a 232 (244)
..+++..+ .++..+|||||||-|.++..++++| +++++.+.+ ++-.+.+
T Consensus 52 ~~~~~~~~-l~~G~~vLDiGcGwG~~~~~~a~~~-g~~v~gitlS~~Q~~~a 101 (273)
T PF02353_consen 52 DLLCEKLG-LKPGDRVLDIGCGWGGLAIYAAERY-GCHVTGITLSEEQAEYA 101 (273)
T ss_dssp HHHHTTTT---TT-EEEEES-TTSHHHHHHHHHH---EEEEEES-HHHHHHH
T ss_pred HHHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHc-CcEEEEEECCHHHHHHH
Confidence 45677776 7888999999999999999999999 889888887 4434433
No 97
>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional
Probab=96.08 E-value=0.011 Score=51.29 Aligned_cols=53 Identities=21% Similarity=0.183 Sum_probs=44.6
Q ss_pred HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256 181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~ 234 (244)
...+++.+. .....++||+++|.|.++..+++++| +.+++.+|. |++++.+++
T Consensus 8 l~Evl~~L~-~~pg~~vlD~TlG~GGhS~~il~~~~~~g~VigiD~D~~al~~ak~ 62 (296)
T PRK00050 8 LDEVVDALA-IKPDGIYVDGTFGGGGHSRAILERLGPKGRLIAIDRDPDAIAAAKD 62 (296)
T ss_pred HHHHHHhhC-CCCCCEEEEeCcCChHHHHHHHHhCCCCCEEEEEcCCHHHHHHHHH
Confidence 356677665 45557999999999999999999996 789999998 899988875
No 98
>PRK12335 tellurite resistance protein TehB; Provisional
Probab=96.07 E-value=0.0069 Score=52.40 Aligned_cols=49 Identities=18% Similarity=0.198 Sum_probs=36.7
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.++..++ .....+|+|||||.|..+..++++ +.+++.+|. |..++.+++
T Consensus 111 ~~~~~~~-~~~~~~vLDlGcG~G~~~~~la~~--g~~V~avD~s~~ai~~~~~ 160 (287)
T PRK12335 111 EVLEAVQ-TVKPGKALDLGCGQGRNSLYLALL--GFDVTAVDINQQSLENLQE 160 (287)
T ss_pred HHHHHhh-ccCCCCEEEeCCCCCHHHHHHHHC--CCEEEEEECCHHHHHHHHH
Confidence 3444444 334469999999999999999885 578999998 677776643
No 99
>PRK15068 tRNA mo(5)U34 methyltransferase; Provisional
Probab=96.07 E-value=0.012 Score=51.89 Aligned_cols=40 Identities=18% Similarity=0.246 Sum_probs=31.5
Q ss_pred HhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccch
Q 041256 185 LESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLP 226 (244)
Q Consensus 185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 226 (244)
...++.+ ..++|+|||||.|.++..+++..|. +++.+|..
T Consensus 115 ~~~l~~l-~g~~VLDIGCG~G~~~~~la~~g~~-~V~GiD~S 154 (322)
T PRK15068 115 LPHLSPL-KGRTVLDVGCGNGYHMWRMLGAGAK-LVVGIDPS 154 (322)
T ss_pred HHhhCCC-CCCEEEEeccCCcHHHHHHHHcCCC-EEEEEcCC
Confidence 4444323 3489999999999999999999877 48999963
No 100
>TIGR00537 hemK_rel_arch HemK-related putative methylase. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. This model represents an archaeal and eukaryotic protein family that lacks an N-terminal domain found in HemK and its eubacterial homologs. It is found in a single copy in the first six completed archaeal and eukaryotic genomes.
Probab=96.06 E-value=0.0058 Score=48.90 Aligned_cols=39 Identities=18% Similarity=0.394 Sum_probs=33.7
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+|+|+|||+|.++..+.+..+ +++.+|+ |..++.+++
T Consensus 20 ~~~vLdlG~G~G~~~~~l~~~~~--~v~~vD~s~~~~~~a~~ 59 (179)
T TIGR00537 20 PDDVLEIGAGTGLVAIRLKGKGK--CILTTDINPFAVKELRE 59 (179)
T ss_pred CCeEEEeCCChhHHHHHHHhcCC--EEEEEECCHHHHHHHHH
Confidence 36899999999999999999987 7888898 887777664
No 101
>PRK03612 spermidine synthase; Provisional
Probab=96.03 E-value=0.0091 Score=56.04 Aligned_cols=42 Identities=26% Similarity=0.498 Sum_probs=37.0
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~ 234 (244)
++.++|+|||||.|..+.++++ +|. -+++++|+ |++++.+++
T Consensus 296 ~~~~rVL~IG~G~G~~~~~ll~-~~~v~~v~~VEid~~vi~~ar~ 339 (521)
T PRK03612 296 ARPRRVLVLGGGDGLALREVLK-YPDVEQVTLVDLDPAMTELART 339 (521)
T ss_pred CCCCeEEEEcCCccHHHHHHHh-CCCcCeEEEEECCHHHHHHHHh
Confidence 4568999999999999999996 566 68999999 999999876
No 102
>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=96.01 E-value=0.0061 Score=46.60 Aligned_cols=39 Identities=21% Similarity=0.221 Sum_probs=34.2
Q ss_pred eEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 196 KLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 196 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+++|||+|.|.++..+++.+|..+++.+|. |...+.+++
T Consensus 1 ~vlDiGa~~G~~~~~~~~~~~~~~v~~~E~~~~~~~~l~~ 40 (143)
T TIGR01444 1 VVIDVGANIGDTSLYFARKGAEGRVIAFEPLPDAYEILEE 40 (143)
T ss_pred CEEEccCCccHHHHHHHHhCCCCEEEEEecCHHHHHHHHH
Confidence 589999999999999999999999999997 777766553
No 103
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=95.99 E-value=0.011 Score=48.16 Aligned_cols=47 Identities=15% Similarity=0.040 Sum_probs=38.4
Q ss_pred hcCCCCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCCC
Q 041256 187 SYKGFEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 187 ~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.++ .....+|+|+|||+|.++..+++. .|..+++.+|. |..++.+++
T Consensus 35 ~l~-~~~~~~vlDlG~GtG~~s~~~a~~~~~~~~v~avD~~~~~~~~a~~ 83 (198)
T PRK00377 35 KLR-LRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDKDEKAINLTRR 83 (198)
T ss_pred HcC-CCCcCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence 344 566689999999999999999886 46789999999 888876653
No 104
>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=95.98 E-value=0.0059 Score=52.90 Aligned_cols=41 Identities=27% Similarity=0.396 Sum_probs=32.8
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
...+|+|||||+|.++..+++. +.-+++.+|+ |..++.+++
T Consensus 159 ~g~~VLDvGcGsG~lai~aa~~-g~~~V~avDid~~al~~a~~ 200 (288)
T TIGR00406 159 KDKNVIDVGCGSGILSIAALKL-GAAKVVGIDIDPLAVESARK 200 (288)
T ss_pred CCCEEEEeCCChhHHHHHHHHc-CCCeEEEEECCHHHHHHHHH
Confidence 4489999999999999888764 4458899998 677777654
No 105
>PHA03412 putative methyltransferase; Provisional
Probab=95.90 E-value=0.0098 Score=49.90 Aligned_cols=47 Identities=15% Similarity=0.133 Sum_probs=37.6
Q ss_pred cceEEEecCCccHHHHHHHHHC---CCCeEEEccc-hHHhhhCCC-CCCcee
Q 041256 194 VKKLVDVGGGLGITLNMIISKY---PHIKGINYDL-PYVIKDAPS-YPGTLF 240 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~---P~l~~~v~Dl-p~vi~~a~~-~~~i~~ 240 (244)
..+|||+|||+|.++..++++. +..+.+.+|+ |..++.|++ .+++++
T Consensus 50 ~grVLDlG~GSG~Lalala~~~~~~~~~~V~aVEID~~Al~~Ar~n~~~~~~ 101 (241)
T PHA03412 50 SGSVVDLCAGIGGLSFAMVHMMMYAKPREIVCVELNHTYYKLGKRIVPEATW 101 (241)
T ss_pred CCEEEEccChHHHHHHHHHHhcccCCCcEEEEEECCHHHHHHHHhhccCCEE
Confidence 4799999999999999999885 4678899999 788888875 244443
No 106
>KOG1540 consensus Ubiquinone biosynthesis methyltransferase COQ5 [Coenzyme transport and metabolism]
Probab=95.90 E-value=0.021 Score=48.26 Aligned_cols=42 Identities=24% Similarity=0.272 Sum_probs=37.1
Q ss_pred CcceEEEecCCccHHHHHHHHHCCC------CeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPH------IKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~------l~~~v~Dl-p~vi~~a~~ 234 (244)
..-++|||+||+|-++..|+++-++ -+++|.|. |+.++.+++
T Consensus 100 ~~m~~lDvaGGTGDiaFril~~v~s~~~~~~~~V~v~Dinp~mL~vgkq 148 (296)
T KOG1540|consen 100 KGMKVLDVAGGTGDIAFRILRHVKSQFGDRESKVTVLDINPHMLAVGKQ 148 (296)
T ss_pred CCCeEEEecCCcchhHHHHHHhhccccCCCCceEEEEeCCHHHHHHHHH
Confidence 4489999999999999999999988 78999998 888887764
No 107
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=95.89 E-value=0.011 Score=36.57 Aligned_cols=45 Identities=9% Similarity=0.305 Sum_probs=36.5
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
.+..|+..|.+. +++|..|||+.+|++ ... +.+.|+-|...|+++
T Consensus 4 ~~~~Il~~l~~~---~~~t~~ela~~~~is------~~t-v~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLREN---PRITQKELAEKLGIS------RST-VNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHC---TTS-HHHHHHHHTS-------HHH-HHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHhCCC------HHH-HHHHHHHHHHCcCcC
Confidence 355688889886 579999999999997 456 999999999999874
No 108
>PRK00517 prmA ribosomal protein L11 methyltransferase; Reviewed
Probab=95.87 E-value=0.0069 Score=51.30 Aligned_cols=42 Identities=26% Similarity=0.282 Sum_probs=33.6
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
....+|+|||||+|.+++.+++..+. +++.+|. |..++.+++
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 35589999999999999887776554 6888998 778877764
No 109
>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=95.85 E-value=0.0063 Score=42.49 Aligned_cols=36 Identities=17% Similarity=0.267 Sum_probs=30.4
Q ss_pred EEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 198 VDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 198 vDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
||||||.|..+..+.++ |..+.+..|. +..++.+++
T Consensus 1 LdiG~G~G~~~~~l~~~-~~~~v~~~D~~~~~~~~~~~ 37 (95)
T PF08241_consen 1 LDIGCGTGRFAAALAKR-GGASVTGIDISEEMLEQARK 37 (95)
T ss_dssp EEET-TTSHHHHHHHHT-TTCEEEEEES-HHHHHHHHH
T ss_pred CEecCcCCHHHHHHHhc-cCCEEEEEeCCHHHHHHHHh
Confidence 79999999999999999 9999999998 565766654
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=95.79 E-value=0.013 Score=47.49 Aligned_cols=40 Identities=15% Similarity=0.314 Sum_probs=30.3
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
...+|+|||||.|.++..+++. ...+++.+|. |+.++.++
T Consensus 13 ~~~~iLDiGcG~G~~~~~l~~~-~~~~~~giD~s~~~i~~a~ 53 (194)
T TIGR02081 13 PGSRVLDLGCGDGELLALLRDE-KQVRGYGIEIDQDGVLACV 53 (194)
T ss_pred CCCEEEEeCCCCCHHHHHHHhc-cCCcEEEEeCCHHHHHHHH
Confidence 4468999999999999888765 4566788887 55555543
No 111
>PRK00536 speE spermidine synthase; Provisional
Probab=95.72 E-value=0.012 Score=50.31 Aligned_cols=41 Identities=10% Similarity=-0.074 Sum_probs=36.4
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+++|+=||||.|..++++++. |. +++..|+ ++|++.+++
T Consensus 71 ~~pk~VLIiGGGDGg~~REvLkh-~~-~v~mVeID~~Vv~~~k~ 112 (262)
T PRK00536 71 KELKEVLIVDGFDLELAHQLFKY-DT-HVDFVQADEKILDSFIS 112 (262)
T ss_pred CCCCeEEEEcCCchHHHHHHHCc-CC-eeEEEECCHHHHHHHHH
Confidence 56799999999999999999987 55 8999998 889988876
No 112
>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=95.67 E-value=0.02 Score=37.98 Aligned_cols=48 Identities=10% Similarity=0.284 Sum_probs=34.1
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCC---ceeecCcc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ---RLYSLAPV 103 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~---~~y~~t~~ 103 (244)
++.|..+|++.++++ ... +.+.++.|...|++++.....+ ..|++|+.
T Consensus 17 ~~~t~~~l~~~~~~~------~~~-vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~ 67 (68)
T PF13463_consen 17 GPMTQSDLAERLGIS------KST-VSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPA 67 (68)
T ss_dssp S-BEHHHHHHHTT--------HHH-HHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HH
T ss_pred CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCC
Confidence 799999999999997 456 9999999999999975422212 34777764
No 113
>TIGR03438 probable methyltransferase. This model represents a distinct set of uncharacterized proteins found in the bacteria. Analysis by PSI-BLAST shows remote sequence homology to methyltransferases
Probab=95.66 E-value=0.011 Score=51.49 Aligned_cols=41 Identities=15% Similarity=0.293 Sum_probs=34.3
Q ss_pred CcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~ 233 (244)
...+|||+|||+|.....|+++.+ ..+.+.+|+ ++.++.+.
T Consensus 63 ~~~~iLELGcGtG~~t~~Ll~~l~~~~~~~~iDiS~~mL~~a~ 105 (301)
T TIGR03438 63 AGCELVELGSGSSRKTRLLLDALRQPARYVPIDISADALKESA 105 (301)
T ss_pred CCCeEEecCCCcchhHHHHHHhhccCCeEEEEECCHHHHHHHH
Confidence 346899999999999999999998 688999999 55555554
No 114
>PRK14968 putative methyltransferase; Provisional
Probab=95.65 E-value=0.012 Score=46.92 Aligned_cols=40 Identities=25% Similarity=0.448 Sum_probs=33.8
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
.+.++++|+|||.|.++..++++ ..+++.+|+ |++++.++
T Consensus 22 ~~~~~vLd~G~G~G~~~~~l~~~--~~~v~~~D~s~~~~~~a~ 62 (188)
T PRK14968 22 KKGDRVLEVGTGSGIVAIVAAKN--GKKVVGVDINPYAVECAK 62 (188)
T ss_pred cCCCEEEEEccccCHHHHHHHhh--cceEEEEECCHHHHHHHH
Confidence 44578999999999999999998 578899998 77777764
No 115
>PLN03075 nicotianamine synthase; Provisional
Probab=95.61 E-value=0.017 Score=50.18 Aligned_cols=43 Identities=21% Similarity=0.165 Sum_probs=34.1
Q ss_pred CCcceEEEecCCccHH--HHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGIT--LNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~--~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+++|+|||||.|-+ .....+.+|+.+++.+|. |+.++.|++
T Consensus 122 ~~p~~VldIGcGpgpltaiilaa~~~p~~~~~giD~d~~ai~~Ar~ 167 (296)
T PLN03075 122 GVPTKVAFVGSGPLPLTSIVLAKHHLPTTSFHNFDIDPSANDVARR 167 (296)
T ss_pred CCCCEEEEECCCCcHHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHH
Confidence 4779999999998844 333445789999999999 888887764
No 116
>TIGR00452 methyltransferase, putative. Known examples to date are restricted to the proteobacteria.
Probab=95.60 E-value=0.025 Score=49.69 Aligned_cols=40 Identities=20% Similarity=0.246 Sum_probs=31.2
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL 225 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 225 (244)
++..+. ..+.++|+|||||+|.++..++...+. +++.+|.
T Consensus 113 ~l~~l~-~~~g~~VLDvGCG~G~~~~~~~~~g~~-~v~GiDp 152 (314)
T TIGR00452 113 VLPHLS-PLKGRTILDVGCGSGYHMWRMLGHGAK-SLVGIDP 152 (314)
T ss_pred HHHhcC-CCCCCEEEEeccCCcHHHHHHHHcCCC-EEEEEcC
Confidence 344443 234489999999999999999998775 6888996
No 117
>KOG2899 consensus Predicted methyltransferase [General function prediction only]
Probab=95.58 E-value=0.012 Score=49.24 Aligned_cols=52 Identities=19% Similarity=0.287 Sum_probs=43.4
Q ss_pred HHHhhcC-CCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYK-GFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~-~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+..++ +|-..+.++||||+.|.+...+++.|-....+.+|+ |.-|..|++
T Consensus 47 ~rLk~L~~~~f~~~~~LDIGCNsG~lt~~iak~F~~r~iLGvDID~~LI~~Ark 100 (288)
T KOG2899|consen 47 PRLKVLEKDWFEPKQALDIGCNSGFLTLSIAKDFGPRRILGVDIDPVLIQRARK 100 (288)
T ss_pred hhhhhccccccCcceeEeccCCcchhHHHHHHhhccceeeEeeccHHHHHHHHH
Confidence 4444443 366789999999999999999999999999999998 788888865
No 118
>PLN02336 phosphoethanolamine N-methyltransferase
Probab=95.56 E-value=0.027 Score=52.16 Aligned_cols=49 Identities=22% Similarity=0.280 Sum_probs=37.1
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
+.+++.++ .....+|+|||||.|.++..+++.+. +++.+|. |..++.++
T Consensus 27 ~~il~~l~-~~~~~~vLDlGcG~G~~~~~la~~~~--~v~giD~s~~~l~~a~ 76 (475)
T PLN02336 27 PEILSLLP-PYEGKSVLELGAGIGRFTGELAKKAG--QVIALDFIESVIKKNE 76 (475)
T ss_pred hHHHhhcC-ccCCCEEEEeCCCcCHHHHHHHhhCC--EEEEEeCCHHHHHHHH
Confidence 45566665 44557999999999999999999864 5788887 66666554
No 119
>PLN02672 methionine S-methyltransferase
Probab=95.55 E-value=0.01 Score=59.73 Aligned_cols=40 Identities=28% Similarity=0.285 Sum_probs=36.6
Q ss_pred ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+|+|||||+|.+++.+++++|..+++..|+ |..++.|++
T Consensus 120 ~~VLDlG~GSG~Iai~La~~~~~~~v~avDis~~Al~~A~~ 160 (1082)
T PLN02672 120 KTVAELGCGNGWISIAIAEKWLPSKVYGLDINPRAVKVAWI 160 (1082)
T ss_pred CEEEEEecchHHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence 6899999999999999999999999999999 888888753
No 120
>PLN02396 hexaprenyldihydroxybenzoate methyltransferase
Probab=95.53 E-value=0.014 Score=51.33 Aligned_cols=39 Identities=21% Similarity=0.131 Sum_probs=32.3
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+|||||||.|.++..+++ ++.+++.+|. |+.++.|++
T Consensus 132 g~~ILDIGCG~G~~s~~La~--~g~~V~GID~s~~~i~~Ar~ 171 (322)
T PLN02396 132 GLKFIDIGCGGGLLSEPLAR--MGATVTGVDAVDKNVKIARL 171 (322)
T ss_pred CCEEEEeeCCCCHHHHHHHH--cCCEEEEEeCCHHHHHHHHH
Confidence 46899999999999988876 4778999998 777777753
No 121
>COG2227 UbiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme metabolism]
Probab=95.49 E-value=0.011 Score=49.32 Aligned_cols=39 Identities=23% Similarity=0.117 Sum_probs=34.2
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+|||||||-|.++..+++.. .+++..|+ ++-|+.|+.
T Consensus 60 g~~vLDvGCGgG~Lse~mAr~G--a~VtgiD~se~~I~~Ak~ 99 (243)
T COG2227 60 GLRVLDVGCGGGILSEPLARLG--ASVTGIDASEKPIEVAKL 99 (243)
T ss_pred CCeEEEecCCccHhhHHHHHCC--CeeEEecCChHHHHHHHH
Confidence 3899999999999999999997 77888898 788888874
No 122
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=95.46 E-value=0.029 Score=42.32 Aligned_cols=46 Identities=15% Similarity=0.283 Sum_probs=37.5
Q ss_pred hcChhhHHh-hcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 35 ELDVFEIIS-KAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 35 ~lgifd~L~-~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
+..++-+|- .+ +|.|+++||+.++.+ ..- +.|-|+-|...|++.++
T Consensus 29 Dv~v~~~LL~~~---~~~tvdelae~lnr~------rSt-v~rsl~~L~~~GlV~Re 75 (126)
T COG3355 29 DVEVYKALLEEN---GPLTVDELAEILNRS------RST-VYRSLQNLLEAGLVERE 75 (126)
T ss_pred HHHHHHHHHhhc---CCcCHHHHHHHHCcc------HHH-HHHHHHHHHHcCCeeee
Confidence 344666666 43 799999999999996 445 99999999999999974
No 123
>KOG2904 consensus Predicted methyltransferase [General function prediction only]
Probab=95.45 E-value=0.019 Score=48.95 Aligned_cols=44 Identities=20% Similarity=0.270 Sum_probs=37.6
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+.+...++|+|||+|.++..++..-|..+++..|. +.++..|.+
T Consensus 146 ~~~~~~ildlgtGSGaIslsll~~L~~~~v~AiD~S~~Ai~La~e 190 (328)
T KOG2904|consen 146 HSKHTHILDLGTGSGAISLSLLHGLPQCTVTAIDVSKAAIKLAKE 190 (328)
T ss_pred hcccceEEEecCCccHHHHHHHhcCCCceEEEEeccHHHHHHHHH
Confidence 44556899999999999999999999999999998 666666654
No 124
>cd02440 AdoMet_MTases S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
Probab=95.44 E-value=0.015 Score=40.44 Aligned_cols=37 Identities=24% Similarity=0.376 Sum_probs=30.6
Q ss_pred eEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 196 KLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 196 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
+++|+|+|.|.++..+++ .+..+.+.+|+ +..+..++
T Consensus 1 ~ildig~G~G~~~~~~~~-~~~~~~~~~d~~~~~~~~~~ 38 (107)
T cd02440 1 RVLDLGCGTGALALALAS-GPGARVTGVDISPVALELAR 38 (107)
T ss_pred CeEEEcCCccHHHHHHhc-CCCCEEEEEeCCHHHHHHHH
Confidence 589999999999999998 78889999998 45555444
No 125
>TIGR00417 speE spermidine synthase. the SpeE subunit of spermidine synthase catalysesthe reaction (putrescine + S-adenosylmethioninamine = spermidine + 5'-methylthioadenosine) and is involved in polyamine biosynthesis and in the biosynthesis of spermidine from arganine. The region between residues 77 and 120 of the seed alignment is thought to be involved in binding to decarboxylated SAM.
Probab=95.41 E-value=0.014 Score=49.99 Aligned_cols=43 Identities=23% Similarity=0.281 Sum_probs=35.9
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+++++|++||||.|.++..+++..+..+.++.|+ |++++.+++
T Consensus 71 ~~p~~VL~iG~G~G~~~~~ll~~~~~~~v~~veid~~vi~~a~~ 114 (270)
T TIGR00417 71 PNPKHVLVIGGGDGGVLREVLKHKSVEKATLVDIDEKVIELSKK 114 (270)
T ss_pred CCCCEEEEEcCCchHHHHHHHhCCCcceEEEEeCCHHHHHHHHH
Confidence 4567999999999999999998776778888888 788777764
No 126
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=95.39 E-value=0.013 Score=36.22 Aligned_cols=43 Identities=19% Similarity=0.389 Sum_probs=36.6
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
++.|...|.+ ||.++.||++.+|++ ... +.+-|+.|...|+++
T Consensus 4 R~~Il~~L~~----~~~~~~el~~~l~~s------~~~-vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 4 RLRILKLLSE----GPLTVSELAEELGLS------QST-VSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHHTT----SSEEHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHh----CCCchhhHHHhcccc------chH-HHHHHHHHHHCcCee
Confidence 4567778877 799999999999997 456 999999999999986
No 127
>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=95.35 E-value=0.06 Score=45.08 Aligned_cols=56 Identities=16% Similarity=0.119 Sum_probs=38.2
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccch--HHhhhCCCCCCc
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLP--YVIKDAPSYPGT 238 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp--~vi~~a~~~~~i 238 (244)
..+++.++...+.++++|||||+|.++..++++ +--+++.+|.. ......++.++|
T Consensus 64 ~~~l~~~~~~~~~~~vlDiG~gtG~~t~~l~~~-ga~~v~avD~~~~~l~~~l~~~~~v 121 (228)
T TIGR00478 64 KEALEEFNIDVKNKIVLDVGSSTGGFTDCALQK-GAKEVYGVDVGYNQLAEKLRQDERV 121 (228)
T ss_pred HHHHHhcCCCCCCCEEEEcccCCCHHHHHHHHc-CCCEEEEEeCCHHHHHHHHhcCCCe
Confidence 345555541135579999999999999999986 44578889983 344444444444
No 128
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=95.35 E-value=0.037 Score=36.38 Aligned_cols=44 Identities=23% Similarity=0.326 Sum_probs=36.6
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
+++|..+||+.+|++ ... +.|+|+.|...|++.. ...+.|.+++
T Consensus 24 ~~~s~~ela~~~g~s------~~t-v~r~l~~L~~~g~i~~---~~~~~~~l~~ 67 (67)
T cd00092 24 LPLTRQEIADYLGLT------RET-VSRTLKELEEEGLISR---RGRGKYRVNP 67 (67)
T ss_pred CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEe---cCCCeEEeCC
Confidence 689999999999997 456 9999999999999995 2236787764
No 129
>PRK11727 23S rRNA mA1618 methyltransferase; Provisional
Probab=95.33 E-value=0.015 Score=51.05 Aligned_cols=42 Identities=17% Similarity=0.221 Sum_probs=37.1
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
...++||||+|+|.+..-++.+.|+.+++..|+ |..++.|++
T Consensus 114 ~~~~vLDIGtGag~I~~lLa~~~~~~~~~atDId~~Al~~A~~ 156 (321)
T PRK11727 114 ANVRVLDIGVGANCIYPLIGVHEYGWRFVGSDIDPQALASAQA 156 (321)
T ss_pred CCceEEEecCCccHHHHHHHhhCCCCEEEEEeCCHHHHHHHHH
Confidence 458999999999998888899999999999998 888888764
No 130
>PLN02585 magnesium protoporphyrin IX methyltransferase
Probab=95.33 E-value=0.015 Score=51.08 Aligned_cols=39 Identities=15% Similarity=0.109 Sum_probs=32.7
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+|+|||||+|.++..++++ +.+++.+|+ |..++.+++
T Consensus 145 ~~~VLDlGcGtG~~a~~la~~--g~~V~gvD~S~~ml~~A~~ 184 (315)
T PLN02585 145 GVTVCDAGCGTGSLAIPLALE--GAIVSASDISAAMVAEAER 184 (315)
T ss_pred CCEEEEecCCCCHHHHHHHHC--CCEEEEEECCHHHHHHHHH
Confidence 479999999999999999986 568999998 667766654
No 131
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=95.32 E-value=0.036 Score=41.45 Aligned_cols=68 Identities=18% Similarity=0.243 Sum_probs=51.5
Q ss_pred HHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 25 VLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 25 ~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
..+.+|.--.++.|+..|.+. ++.++.||++.++++ +.. +.+-|+.|...|+++...+...-.|++++
T Consensus 8 ~~fkaLadptRl~IL~~L~~~---~~~~v~ela~~l~ls------qst-vS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~ 75 (117)
T PRK10141 8 QLFKILSDETRLGIVLLLRES---GELCVCDLCTALDQS------QPK-ISRHLALLRESGLLLDRKQGKWVHYRLSP 75 (117)
T ss_pred HHHHHhCCHHHHHHHHHHHHc---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCceEEEEEcCEEEEEECc
Confidence 445667777889999999764 589999999999997 445 99999999999999864321122366654
No 132
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=95.29 E-value=0.11 Score=39.95 Aligned_cols=44 Identities=23% Similarity=0.195 Sum_probs=36.6
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
.|+-.|... +++|..+||+.++++ +.. +.++++-|...|++.+.
T Consensus 44 ~vL~~l~~~---~~~t~~eLa~~l~i~------~~t-vsr~l~~Le~~GlI~R~ 87 (144)
T PRK11512 44 KVLCSIRCA---ACITPVELKKVLSVD------LGA-LTRMLDRLVCKGWVERL 87 (144)
T ss_pred HHHHHHHHc---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEec
Confidence 356666654 589999999999997 456 99999999999999964
No 133
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=95.26 E-value=0.039 Score=47.97 Aligned_cols=49 Identities=16% Similarity=0.371 Sum_probs=36.5
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
..+++..+ .....+|+|||||.|.+...++++.. +++.+|+ +..++.++
T Consensus 26 ~~Iv~~~~-~~~~~~VLEIG~G~G~LT~~Ll~~~~--~V~avEiD~~li~~l~ 75 (294)
T PTZ00338 26 DKIVEKAA-IKPTDTVLEIGPGTGNLTEKLLQLAK--KVIAIEIDPRMVAELK 75 (294)
T ss_pred HHHHHhcC-CCCcCEEEEecCchHHHHHHHHHhCC--cEEEEECCHHHHHHHH
Confidence 35555555 56668999999999999999999864 5677776 55665554
No 134
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=95.25 E-value=0.036 Score=43.31 Aligned_cols=54 Identities=22% Similarity=0.276 Sum_probs=42.2
Q ss_pred HHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC-CceeecCcc
Q 041256 41 IISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-QRLYSLAPV 103 (244)
Q Consensus 41 ~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~~~y~~t~~ 103 (244)
.|+..+.+++.|+++||+..+++ +.+ |.++|..|...|+++-. .| .|.|+++.-
T Consensus 16 ~LA~~~~~~~~s~~~IA~~~~is------~~~-L~kil~~L~kaGlV~S~--rG~~GGy~Lar~ 70 (150)
T COG1959 16 YLALLPGGGPVSSAEIAERQGIS------PSY-LEKILSKLRKAGLVKSV--RGKGGGYRLARP 70 (150)
T ss_pred HHHhCCCCCcccHHHHHHHhCcC------HHH-HHHHHHHHHHcCCEEee--cCCCCCccCCCC
Confidence 44544433489999999999997 679 99999999999999853 23 577888663
No 135
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=95.24 E-value=0.021 Score=37.32 Aligned_cols=52 Identities=10% Similarity=0.281 Sum_probs=42.2
Q ss_pred HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.+|.--.++.|++.|... +|.|+.|||+.+|++ +.. +.+-|+.|...|+++.
T Consensus 5 ~aL~~p~R~~Il~~L~~~---~~~t~~ela~~l~~~------~~t-~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 5 KALSDPTRLRILRLLASN---GPMTVSELAEELGIS------QST-VSYHLKKLEEAGLIEV 56 (61)
T ss_dssp HHHTSHHHHHHHHHHHHC---STBEHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEE
T ss_pred HHhCCHHHHHHHHHHhcC---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeEE
Confidence 445555678888889443 699999999999996 456 9999999999999985
No 136
>KOG1271 consensus Methyltransferases [General function prediction only]
Probab=95.20 E-value=0.026 Score=45.34 Aligned_cols=39 Identities=21% Similarity=0.410 Sum_probs=28.4
Q ss_pred CcceEEEecCCccHHHHHHHHH-CCC-CeEEEccc-hHHhhhCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISK-YPH-IKGINYDL-PYVIKDAP 233 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~-~P~-l~~~v~Dl-p~vi~~a~ 233 (244)
...+|||+|||.|+++..|++. ||+ |+| .|- +..++.|+
T Consensus 67 ~A~~VlDLGtGNG~~L~~L~~egf~~~L~G--vDYs~~AV~LA~ 108 (227)
T KOG1271|consen 67 QADRVLDLGTGNGHLLFQLAKEGFQSKLTG--VDYSEKAVELAQ 108 (227)
T ss_pred cccceeeccCCchHHHHHHHHhcCCCCccc--cccCHHHHHHHH
Confidence 3459999999999999999986 555 554 444 55555554
No 137
>PRK11873 arsM arsenite S-adenosylmethyltransferase; Reviewed
Probab=95.08 E-value=0.027 Score=48.13 Aligned_cols=44 Identities=23% Similarity=0.362 Sum_probs=36.1
Q ss_pred CCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.....+|||||||.|..+..+++. .|+.+++.+|+ |..++.+++
T Consensus 75 ~~~g~~VLDiG~G~G~~~~~~a~~~g~~~~v~gvD~s~~~l~~A~~ 120 (272)
T PRK11873 75 LKPGETVLDLGSGGGFDCFLAARRVGPTGKVIGVDMTPEMLAKARA 120 (272)
T ss_pred CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEECCCHHHHHHHHH
Confidence 456689999999999988877776 46678999998 787887764
No 138
>PRK13943 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=95.00 E-value=0.044 Score=48.26 Aligned_cols=51 Identities=12% Similarity=0.177 Sum_probs=38.6
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~ 234 (244)
.+++..+ ..+..+|+|||||+|.++..+++..+. -+++.+|. |+.++.|++
T Consensus 71 ~ll~~L~-i~~g~~VLDIG~GtG~~a~~LA~~~~~~g~VvgVDis~~~l~~Ar~ 123 (322)
T PRK13943 71 LFMEWVG-LDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKR 123 (322)
T ss_pred HHHHhcC-CCCCCEEEEEeCCccHHHHHHHHhcCCCCEEEEEECCHHHHHHHHH
Confidence 3444444 556689999999999999999998874 46788887 777766653
No 139
>COG0421 SpeE Spermidine synthase [Amino acid transport and metabolism]
Probab=95.00 E-value=0.025 Score=48.84 Aligned_cols=44 Identities=27% Similarity=0.389 Sum_probs=39.9
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+.+++|+=||||.|..+.++++..|--+.++.|+ |.|++.+++
T Consensus 74 h~~pk~VLiiGgGdG~tlRevlkh~~ve~i~~VEID~~Vi~~ar~ 118 (282)
T COG0421 74 HPNPKRVLIIGGGDGGTLREVLKHLPVERITMVEIDPAVIELARK 118 (282)
T ss_pred CCCCCeEEEECCCccHHHHHHHhcCCcceEEEEEcCHHHHHHHHH
Confidence 34568999999999999999999999889999999 999999875
No 140
>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=94.99 E-value=0.052 Score=41.50 Aligned_cols=46 Identities=13% Similarity=0.185 Sum_probs=37.3
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
++.|.++||+.++++ +.. ++++|+.|...|++... +...|.|.++.
T Consensus 24 ~~~s~~~ia~~~~ip------~~~-l~kil~~L~~~glv~s~-~G~~Ggy~l~~ 69 (135)
T TIGR02010 24 GPVTLADISERQGIS------LSY-LEQLFAKLRKAGLVKSV-RGPGGGYQLGR 69 (135)
T ss_pred CcCcHHHHHHHHCcC------HHH-HHHHHHHHHHCCceEEE-eCCCCCEeccC
Confidence 589999999999997 678 99999999999999742 22245677755
No 141
>PRK14967 putative methyltransferase; Provisional
Probab=94.96 E-value=0.032 Score=46.34 Aligned_cols=43 Identities=12% Similarity=0.093 Sum_probs=33.3
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.....+|+|+|||+|.++..+++. +..+++.+|+ |..++.+++
T Consensus 34 ~~~~~~vLDlGcG~G~~~~~la~~-~~~~v~~vD~s~~~l~~a~~ 77 (223)
T PRK14967 34 LGPGRRVLDLCTGSGALAVAAAAA-GAGSVTAVDISRRAVRSARL 77 (223)
T ss_pred cCCCCeEEEecCCHHHHHHHHHHc-CCCeEEEEECCHHHHHHHHH
Confidence 444579999999999999998876 3347899998 666765543
No 142
>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=94.92 E-value=0.053 Score=44.88 Aligned_cols=39 Identities=8% Similarity=0.079 Sum_probs=33.1
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA 232 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a 232 (244)
....+++|+|||.|..+..|+++ +.+++.+|+ |..++.+
T Consensus 33 ~~~~rvLd~GCG~G~da~~LA~~--G~~V~gvD~S~~Ai~~~ 72 (213)
T TIGR03840 33 PAGARVFVPLCGKSLDLAWLAEQ--GHRVLGVELSEIAVEQF 72 (213)
T ss_pred CCCCeEEEeCCCchhHHHHHHhC--CCeEEEEeCCHHHHHHH
Confidence 44579999999999999999976 778999999 7777764
No 143
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=94.90 E-value=0.046 Score=33.33 Aligned_cols=41 Identities=17% Similarity=0.180 Sum_probs=34.0
Q ss_pred CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256 50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA 101 (244)
Q Consensus 50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t 101 (244)
+.|..+||+.++++ ... +.+.|+.|...|++.. . .+.|..+
T Consensus 8 ~~s~~~la~~l~~s------~~t-v~~~l~~L~~~g~l~~---~-~~~~~i~ 48 (48)
T smart00419 8 PLTRQEIAELLGLT------RET-VSRTLKRLEKEGLISR---E-GGRIVIL 48 (48)
T ss_pred ccCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE---e-CCEEEEC
Confidence 78999999999997 456 9999999999999984 3 3667643
No 144
>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=94.84 E-value=0.032 Score=45.23 Aligned_cols=33 Identities=21% Similarity=0.432 Sum_probs=27.0
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL 225 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 225 (244)
+...+|+|+|||.|.++..|.+. -++++..+|+
T Consensus 12 ~pgsrVLDLGCGdG~LL~~L~~~-k~v~g~GvEi 44 (193)
T PF07021_consen 12 EPGSRVLDLGCGDGELLAYLKDE-KQVDGYGVEI 44 (193)
T ss_pred CCCCEEEecCCCchHHHHHHHHh-cCCeEEEEec
Confidence 34589999999999999777775 5888877776
No 145
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=94.81 E-value=0.029 Score=38.97 Aligned_cols=62 Identities=18% Similarity=0.233 Sum_probs=45.2
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc----eeecCcccc
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR----LYSLAPVSA 105 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~----~y~~t~~s~ 105 (244)
++++|...|... +..+..+|.+.+|++ ... +.+-|+.|...|+++...+...+ .|++|+.++
T Consensus 1 vRl~Il~~L~~~---~~~~f~~L~~~l~lt------~g~-Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr 66 (80)
T PF13601_consen 1 VRLAILALLYAN---EEATFSELKEELGLT------DGN-LSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGR 66 (80)
T ss_dssp HHHHHHHHHHHH---SEEEHHHHHHHTT--------HHH-HHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHH
T ss_pred CHHHHHHHHhhc---CCCCHHHHHHHhCcC------HHH-HHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHH
Confidence 467788888875 589999999999997 456 99999999999999865332111 377777664
No 146
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=94.80 E-value=0.063 Score=42.61 Aligned_cols=46 Identities=13% Similarity=0.165 Sum_probs=37.6
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
++.|+++||+.++++ +.. +.++|+.|...|++... ....|.|.+..
T Consensus 24 ~~vs~~eIA~~~~ip------~~~-l~kIl~~L~~aGLv~s~-rG~~GGy~Lar 69 (164)
T PRK10857 24 GPVPLADISERQGIS------LSY-LEQLFSRLRKNGLVSSV-RGPGGGYLLGK 69 (164)
T ss_pred CcCcHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEeC-CCCCCCeeccC
Confidence 589999999999997 678 99999999999999842 12246687754
No 147
>PLN02823 spermine synthase
Probab=94.78 E-value=0.03 Score=49.62 Aligned_cols=43 Identities=21% Similarity=0.234 Sum_probs=37.9
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.++++|+-||||.|..+..+++..+..+.+++|+ |.|++.+++
T Consensus 102 ~~pk~VLiiGgG~G~~~re~l~~~~~~~v~~VEiD~~vv~lar~ 145 (336)
T PLN02823 102 PNPKTVFIMGGGEGSTAREVLRHKTVEKVVMCDIDQEVVDFCRK 145 (336)
T ss_pred CCCCEEEEECCCchHHHHHHHhCCCCCeEEEEECCHHHHHHHHH
Confidence 3568999999999999999998777778999998 999999875
No 148
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=94.76 E-value=0.031 Score=51.40 Aligned_cols=49 Identities=14% Similarity=0.112 Sum_probs=37.7
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+++.++ ..+..+|+|+|||+|.++..+++.. .+++.+|. |+.++.|++
T Consensus 288 ~vl~~l~-~~~~~~VLDlgcGtG~~sl~la~~~--~~V~gvD~s~~al~~A~~ 337 (443)
T PRK13168 288 RALEWLD-PQPGDRVLDLFCGLGNFTLPLARQA--AEVVGVEGVEAMVERARE 337 (443)
T ss_pred HHHHHhc-CCCCCEEEEEeccCCHHHHHHHHhC--CEEEEEeCCHHHHHHHHH
Confidence 3344444 3455799999999999999999886 47888998 788887764
No 149
>COG2263 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=94.74 E-value=0.026 Score=45.52 Aligned_cols=41 Identities=22% Similarity=0.255 Sum_probs=33.5
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..++|+|+|||+|.++++.+-..|. +++.+|. |+.++.+++
T Consensus 45 ~g~~V~DlG~GTG~La~ga~~lGa~-~V~~vdiD~~a~ei~r~ 86 (198)
T COG2263 45 EGKTVLDLGAGTGILAIGAALLGAS-RVLAVDIDPEALEIARA 86 (198)
T ss_pred CCCEEEEcCCCcCHHHHHHHhcCCc-EEEEEecCHHHHHHHHH
Confidence 3488999999999999998887766 5666676 888888875
No 150
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=94.71 E-value=0.077 Score=34.06 Aligned_cols=42 Identities=14% Similarity=0.326 Sum_probs=34.2
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
|+..|.. ++.|..+|++.++++ ... +.+.|+.|...|++...
T Consensus 2 il~~l~~----~~~~~~~i~~~l~is------~~~-v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 2 ILKLLAE----GELCVCELAEILGLS------QST-VSHHLKKLREAGLVESR 43 (66)
T ss_pred HHHHhhc----CCccHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeeee
Confidence 4455552 689999999999997 345 99999999999999853
No 151
>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=94.71 E-value=0.041 Score=40.28 Aligned_cols=44 Identities=23% Similarity=0.357 Sum_probs=30.4
Q ss_pred hhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256 179 IVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL 225 (244)
Q Consensus 179 ~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 225 (244)
+.+.-|.+.+. -.....+||||||+|.+.--|.+. +.+|..+|.
T Consensus 45 yLi~LW~~~~~-~~~~~~FVDlGCGNGLLV~IL~~E--Gy~G~GiD~ 88 (112)
T PF07757_consen 45 YLIELWRDMYG-EQKFQGFVDLGCGNGLLVYILNSE--GYPGWGIDA 88 (112)
T ss_pred HHHHHHhcccC-CCCCCceEEccCCchHHHHHHHhC--CCCcccccc
Confidence 33445555555 356789999999999988777665 445666663
No 152
>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=94.67 E-value=0.037 Score=35.93 Aligned_cols=48 Identities=10% Similarity=0.272 Sum_probs=37.1
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
+..++-.|...+. .++|..|||+.++++ +.. +.++++.|...|++++.
T Consensus 7 q~~vL~~l~~~~~-~~~t~~~la~~l~~~------~~~-vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 7 QFRVLMALARHPG-EELTQSELAERLGIS------KST-VSRIVKRLEKKGLVERE 54 (62)
T ss_dssp HHHHHHHHHHSTT-SGEEHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHCCC-CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEe
Confidence 3445666777531 128999999999997 566 99999999999999964
No 153
>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=94.66 E-value=0.057 Score=46.88 Aligned_cols=40 Identities=18% Similarity=0.286 Sum_probs=29.7
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEcc
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYD 224 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D 224 (244)
.+...++.+++ ++|+|||||+|.++...+++.|.. ++.+|
T Consensus 106 rl~p~l~~L~g-k~VLDIGC~nGY~~frM~~~GA~~-ViGiD 145 (315)
T PF08003_consen 106 RLLPHLPDLKG-KRVLDIGCNNGYYSFRMLGRGAKS-VIGID 145 (315)
T ss_pred HHHhhhCCcCC-CEEEEecCCCcHHHHHHhhcCCCE-EEEEC
Confidence 34444432444 899999999999999999997763 56666
No 154
>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed
Probab=94.64 E-value=0.056 Score=47.38 Aligned_cols=39 Identities=13% Similarity=0.019 Sum_probs=33.2
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+|+|+|||.|.++..++++ ..+++.+|. |..++.|++
T Consensus 174 ~~~VLDl~cG~G~~sl~la~~--~~~V~gvD~s~~av~~A~~ 213 (315)
T PRK03522 174 PRSMWDLFCGVGGFGLHCATP--GMQLTGIEISAEAIACAKQ 213 (315)
T ss_pred CCEEEEccCCCCHHHHHHHhc--CCEEEEEeCCHHHHHHHHH
Confidence 479999999999999999984 467899998 888887764
No 155
>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=94.63 E-value=0.044 Score=36.77 Aligned_cols=43 Identities=12% Similarity=0.288 Sum_probs=35.2
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
|-+.|.+. +..|..|||..++++ ++. +..+|..|+..|.+.+.
T Consensus 5 i~~~l~~~---~~~S~~eLa~~~~~s------~~~-ve~mL~~l~~kG~I~~~ 47 (69)
T PF09012_consen 5 IRDYLRER---GRVSLAELAREFGIS------PEA-VEAMLEQLIRKGYIRKV 47 (69)
T ss_dssp HHHHHHHS----SEEHHHHHHHTT--------HHH-HHHHHHHHHCCTSCEEE
T ss_pred HHHHHHHc---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCcEEEe
Confidence 56778775 689999999999997 677 99999999999999963
No 156
>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=94.57 E-value=0.029 Score=36.13 Aligned_cols=45 Identities=9% Similarity=0.310 Sum_probs=36.4
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
+.+...|.+. +++|..+||+.++++ ... +.++++-|...||+++.
T Consensus 6 ~~iL~~l~~~---~~~~~~~la~~~~~~------~~~-~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 6 FRILRILYEN---GGITQSELAEKLGIS------RST-VTRIIKRLEKKGLIERE 50 (59)
T ss_dssp HHHHHHHHHH---SSEEHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHc---CCCCHHHHHHHHCCC------hhH-HHHHHHHHHHCCCEEec
Confidence 3445556665 589999999999997 456 99999999999999964
No 157
>PRK04148 hypothetical protein; Provisional
Probab=94.54 E-value=0.063 Score=41.06 Aligned_cols=48 Identities=21% Similarity=0.302 Sum_probs=34.3
Q ss_pred HHhhcCCCCCcceEEEecCCccH-HHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGI-TLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~-~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+.+.++ -.+..+++|||+|.|. ++..|.+. +..++..|. |..++.+++
T Consensus 8 l~~~~~-~~~~~kileIG~GfG~~vA~~L~~~--G~~ViaIDi~~~aV~~a~~ 57 (134)
T PRK04148 8 IAENYE-KGKNKKIVELGIGFYFKVAKKLKES--GFDVIVIDINEKAVEKAKK 57 (134)
T ss_pred HHHhcc-cccCCEEEEEEecCCHHHHHHHHHC--CCEEEEEECCHHHHHHHHH
Confidence 445555 2345789999999996 77777754 568899998 777776643
No 158
>PF03848 TehB: Tellurite resistance protein TehB; InterPro: IPR015985 Tellurite resistance protein TehB is part of a tellurite-reducing operon tehA and tehB. When present in high copy number, TehB is responsible for potassium tellurite resistance, probably by increasing the reduction rate of tellurite to metallic tellurium within the bacterium. TehB is a cytoplasmic protein which possesses three conserved motifs (I, II, and III) found in S-adenosyl-L-methionine (SAM)-dependent non-nucleic acid methyltransferases []. Conformational changes in TehB are observed upon binding of both tellurite and SAM, suggesting that TehB utilises a methyltransferase activity in the detoxification of tellurite. This entry represents the methyltransferase domain found in all TehB proteins.; PDB: 2KW5_A 3MER_B 3M70_A 2I6G_A 4DQ0_D 2XVA_B 2XVM_A.
Probab=94.46 E-value=0.09 Score=42.81 Aligned_cols=48 Identities=23% Similarity=0.318 Sum_probs=35.1
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA 232 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a 232 (244)
..+++.++ .-+..++||+|||.|..+.-|+++ +..++.+|. +..++.+
T Consensus 20 s~v~~a~~-~~~~g~~LDlgcG~GRNalyLA~~--G~~VtAvD~s~~al~~l 68 (192)
T PF03848_consen 20 SEVLEAVP-LLKPGKALDLGCGEGRNALYLASQ--GFDVTAVDISPVALEKL 68 (192)
T ss_dssp HHHHHHCT-TS-SSEEEEES-TTSHHHHHHHHT--T-EEEEEESSHHHHHHH
T ss_pred HHHHHHHh-hcCCCcEEEcCCCCcHHHHHHHHC--CCeEEEEECCHHHHHHH
Confidence 35666777 556789999999999999999998 667888887 4455443
No 159
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=94.44 E-value=0.07 Score=40.37 Aligned_cols=46 Identities=24% Similarity=0.275 Sum_probs=36.3
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
++.|.++||+.++++ +.. ++++|+.|...|++.... ...|.|.++.
T Consensus 24 ~~~s~~eia~~~~i~------~~~-v~~il~~L~~~gli~~~~-g~~ggy~l~~ 69 (132)
T TIGR00738 24 GPVSVKEIAERQGIS------RSY-LEKILRTLRRAGLVESVR-GPGGGYRLAR 69 (132)
T ss_pred CcCcHHHHHHHHCcC------HHH-HHHHHHHHHHCCcEEecc-CCCCCccCCC
Confidence 589999999999996 567 999999999999998421 1235577654
No 160
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=94.37 E-value=0.043 Score=37.77 Aligned_cols=49 Identities=18% Similarity=0.205 Sum_probs=37.6
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV 108 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~ 108 (244)
++.+..+|+..++++ ... +.+.|+.|...|++.. +++.|.+|+.+..+.
T Consensus 18 ~~~~~t~i~~~~~L~------~~~-~~~yL~~L~~~gLI~~----~~~~Y~lTekG~~~l 66 (77)
T PF14947_consen 18 GGAKKTEIMYKANLN------YST-LKKYLKELEEKGLIKK----KDGKYRLTEKGKEFL 66 (77)
T ss_dssp T-B-HHHHHTTST--------HHH-HHHHHHHHHHTTSEEE----ETTEEEE-HHHHHHH
T ss_pred CCCCHHHHHHHhCcC------HHH-HHHHHHHHHHCcCeeC----CCCEEEECccHHHHH
Confidence 689999999999996 556 9999999999999973 368999999886443
No 161
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=94.32 E-value=0.18 Score=40.53 Aligned_cols=44 Identities=18% Similarity=0.266 Sum_probs=38.6
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
..|+++|... |++|.++||+.+|++ ... ++++|..|...|++..
T Consensus 25 ~~Vl~~L~~~---g~~tdeeLA~~Lgi~------~~~-VRk~L~~L~e~gLv~~ 68 (178)
T PRK06266 25 FEVLKALIKK---GEVTDEEIAEQTGIK------LNT-VRKILYKLYDARLADY 68 (178)
T ss_pred hHHHHHHHHc---CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeEE
Confidence 3488889886 699999999999997 456 9999999999999984
No 162
>PLN02781 Probable caffeoyl-CoA O-methyltransferase
Probab=94.25 E-value=0.084 Score=44.31 Aligned_cols=44 Identities=14% Similarity=0.091 Sum_probs=37.0
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+.++|+|||+|.|..+..+++..| +-+++.+|. |+.++.|++
T Consensus 66 ~~~~~~vLEiGt~~G~s~l~la~~~~~~g~v~tiD~d~~~~~~A~~ 111 (234)
T PLN02781 66 IMNAKNTLEIGVFTGYSLLTTALALPEDGRITAIDIDKEAYEVGLE 111 (234)
T ss_pred HhCCCEEEEecCcccHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence 45678999999999999999998865 678999998 777777764
No 163
>PRK00312 pcm protein-L-isoaspartate O-methyltransferase; Reviewed
Probab=94.25 E-value=0.088 Score=43.22 Aligned_cols=48 Identities=10% Similarity=0.189 Sum_probs=34.5
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+++.++ .....+|+|||||+|.++..+++... +.+.+|. |..++.+++
T Consensus 70 l~~~l~-~~~~~~VLeiG~GsG~~t~~la~~~~--~v~~vd~~~~~~~~a~~ 118 (212)
T PRK00312 70 MTELLE-LKPGDRVLEIGTGSGYQAAVLAHLVR--RVFSVERIKTLQWEAKR 118 (212)
T ss_pred HHHhcC-CCCCCEEEEECCCccHHHHHHHHHhC--EEEEEeCCHHHHHHHHH
Confidence 344444 56668999999999999887777654 5667776 676666643
No 164
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=94.14 E-value=0.061 Score=49.25 Aligned_cols=50 Identities=10% Similarity=0.131 Sum_probs=40.2
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
++..++ .....+|+|+|||.|..+..+++..++.+++.+|. |..++.+++
T Consensus 236 ~~~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~~~~v~a~D~s~~~l~~~~~ 286 (427)
T PRK10901 236 AATLLA-PQNGERVLDACAAPGGKTAHILELAPQAQVVALDIDAQRLERVRE 286 (427)
T ss_pred HHHHcC-CCCCCEEEEeCCCCChHHHHHHHHcCCCEEEEEeCCHHHHHHHHH
Confidence 334444 45568999999999999999999998888999998 777766653
No 165
>PTZ00146 fibrillarin; Provisional
Probab=94.14 E-value=0.11 Score=45.14 Aligned_cols=51 Identities=16% Similarity=0.169 Sum_probs=38.2
Q ss_pred CCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccchH-----HhhhCCCCCCceee
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDLPY-----VIKDAPSYPGTLFI 241 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp~-----vi~~a~~~~~i~~~ 241 (244)
+....+|||+|||+|.++..+++.. |.=+++.+|..+ .++.+++.++|.++
T Consensus 130 IkpG~~VLDLGaG~G~~t~~lAdiVG~~G~VyAVD~s~r~~~dLl~~ak~r~NI~~I 186 (293)
T PTZ00146 130 IKPGSKVLYLGAASGTTVSHVSDLVGPEGVVYAVEFSHRSGRDLTNMAKKRPNIVPI 186 (293)
T ss_pred cCCCCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEECcHHHHHHHHHHhhhcCCCEEE
Confidence 4566899999999999999999987 345788888743 55666555666554
No 166
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=94.10 E-value=0.056 Score=35.61 Aligned_cols=45 Identities=20% Similarity=0.191 Sum_probs=35.0
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
.|.+.|.+.. +|.|..|||+.+|++ ... .+++|..|...|.+...
T Consensus 4 ~Il~~i~~~~--~p~~T~eiA~~~gls------~~~-aR~yL~~Le~eG~V~~~ 48 (62)
T PF04703_consen 4 KILEYIKEQN--GPLKTREIADALGLS------IYQ-ARYYLEKLEKEGKVERS 48 (62)
T ss_dssp CHHHHHHHHT--S-EEHHHHHHHHTS-------HHH-HHHHHHHHHHCTSEEEE
T ss_pred HHHHHHHHcC--CCCCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCEEEe
Confidence 3566666632 799999999999997 445 99999999999999853
No 167
>PRK13255 thiopurine S-methyltransferase; Reviewed
Probab=94.08 E-value=0.11 Score=43.14 Aligned_cols=39 Identities=5% Similarity=0.058 Sum_probs=32.8
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA 232 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a 232 (244)
....+|+|+|||.|..+..|+++ +.+++.+|+ |..++.+
T Consensus 36 ~~~~rvL~~gCG~G~da~~LA~~--G~~V~avD~s~~Ai~~~ 75 (218)
T PRK13255 36 PAGSRVLVPLCGKSLDMLWLAEQ--GHEVLGVELSELAVEQF 75 (218)
T ss_pred CCCCeEEEeCCCChHhHHHHHhC--CCeEEEEccCHHHHHHH
Confidence 44579999999999999999875 778999999 6767754
No 168
>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=94.04 E-value=0.043 Score=44.66 Aligned_cols=52 Identities=15% Similarity=0.355 Sum_probs=40.1
Q ss_pred hcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC----CCCceee
Q 041256 187 SYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS----YPGTLFI 241 (244)
Q Consensus 187 ~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~----~~~i~~~ 241 (244)
.+| -....++++||||.|.+...|+.++- +.++.|. |..++.|++ .++|+++
T Consensus 38 aLp-~~ry~~alEvGCs~G~lT~~LA~rCd--~LlavDis~~Al~~Ar~Rl~~~~~V~~~ 94 (201)
T PF05401_consen 38 ALP-RRRYRRALEVGCSIGVLTERLAPRCD--RLLAVDISPRALARARERLAGLPHVEWI 94 (201)
T ss_dssp HHT-TSSEEEEEEE--TTSHHHHHHGGGEE--EEEEEES-HHHHHHHHHHTTT-SSEEEE
T ss_pred hcC-ccccceeEecCCCccHHHHHHHHhhC--ceEEEeCCHHHHHHHHHhcCCCCCeEEE
Confidence 456 56778999999999999999999963 5788898 899999875 4677765
No 169
>KOG1270 consensus Methyltransferases [Coenzyme transport and metabolism]
Probab=93.99 E-value=0.036 Score=47.01 Aligned_cols=38 Identities=21% Similarity=0.201 Sum_probs=32.5
Q ss_pred ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+|||||||.|.++.-|++.. ..++..|. +..|+.|++
T Consensus 91 ~~ilDvGCGgGLLSepLArlg--a~V~GID~s~~~V~vA~~ 129 (282)
T KOG1270|consen 91 MKILDVGCGGGLLSEPLARLG--AQVTGIDASDDMVEVANE 129 (282)
T ss_pred ceEEEeccCccccchhhHhhC--CeeEeecccHHHHHHHHH
Confidence 679999999999999999986 55777888 788888875
No 170
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=93.99 E-value=0.14 Score=37.98 Aligned_cols=65 Identities=12% Similarity=0.175 Sum_probs=47.1
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccccc
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYFV 108 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l~ 108 (244)
.+..++..|... +++|..+||+.++++ ... +.++++-|...|++++.+...+. .+.+|+.+..+.
T Consensus 29 ~q~~iL~~l~~~---~~~t~~ela~~~~~~------~~t-vs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~ 96 (118)
T TIGR02337 29 QQWRILRILAEQ---GSMEFTQLANQACIL------RPS-LTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALY 96 (118)
T ss_pred HHHHHHHHHHHc---CCcCHHHHHHHhCCC------chh-HHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHH
Confidence 344477777765 689999999999997 345 99999999999999963211122 477777665443
No 171
>PRK10909 rsmD 16S rRNA m(2)G966-methyltransferase; Provisional
Probab=93.98 E-value=0.078 Score=43.43 Aligned_cols=40 Identities=15% Similarity=0.110 Sum_probs=32.0
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+++|+|||+|.++.+.+.+.. .+++.+|. |.+++.+++
T Consensus 54 ~~~vLDl~~GsG~l~l~~lsr~a-~~V~~vE~~~~a~~~a~~ 94 (199)
T PRK10909 54 DARCLDCFAGSGALGLEALSRYA-AGATLLEMDRAVAQQLIK 94 (199)
T ss_pred CCEEEEcCCCccHHHHHHHHcCC-CEEEEEECCHHHHHHHHH
Confidence 46899999999999998776654 57888887 777777654
No 172
>PRK05134 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional
Probab=93.94 E-value=0.1 Score=43.42 Aligned_cols=39 Identities=26% Similarity=0.199 Sum_probs=30.4
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
...+|+|||||.|.++..+.+. ..+++..|. |..++.++
T Consensus 48 ~~~~vLdiG~G~G~~~~~l~~~--~~~v~~iD~s~~~~~~a~ 87 (233)
T PRK05134 48 FGKRVLDVGCGGGILSESMARL--GADVTGIDASEENIEVAR 87 (233)
T ss_pred CCCeEEEeCCCCCHHHHHHHHc--CCeEEEEcCCHHHHHHHH
Confidence 4578999999999999988876 456888887 55555554
No 173
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=93.91 E-value=0.12 Score=42.28 Aligned_cols=62 Identities=16% Similarity=0.231 Sum_probs=45.6
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceee-cCCce----eecCcccccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFV-DGQRL----YSLAPVSAYF 107 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~-~~~~~----y~~t~~s~~l 107 (244)
..|+..|... ++.|..+||+.++++ +.. +.+.|+.|...|++++... .+.|+ |++|+.+..+
T Consensus 4 ~~IL~~L~~~---~~~t~~eLA~~lgis------~~t-V~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~ 70 (203)
T TIGR02702 4 EDILSYLLKQ---GQATAAALAEALAIS------PQA-VRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQ 70 (203)
T ss_pred HHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhh
Confidence 3467777765 689999999999997 456 9999999999999986311 11222 6777766533
No 174
>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=93.79 E-value=0.11 Score=36.81 Aligned_cols=68 Identities=19% Similarity=0.176 Sum_probs=48.1
Q ss_pred HHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHH----------HHhhCCcc-cceeecCCceeec
Q 041256 32 AVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLR----------LLVSYNAL-HCSFVDGQRLYSL 100 (244)
Q Consensus 32 ~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr----------~L~~~gll-~~~~~~~~~~y~~ 100 (244)
.=++..|+..|.+..+ .+.++.|||..++++ +.. +.--|+ .|+.+|++ .+....+...|++
T Consensus 8 S~~R~~vl~~L~~~yp-~~~~~~eIar~v~~~------~sn-V~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~g~k~Y~l 79 (90)
T PF07381_consen 8 SKVRKKVLEYLCSIYP-EPAYPSEIARSVGSD------YSN-VLGALRGDGKRYNKEDSLVGLGLVEEEEEKGGFKYYRL 79 (90)
T ss_pred HHHHHHHHHHHHHcCC-CcCCHHHHHHHHCCC------HHH-HHHHHhcCCCCcCcchhHHHcCCeeEeeecCCeeEEEe
Confidence 5567788999998843 589999999999997 333 444443 58899999 4322233457999
Q ss_pred Ccccccc
Q 041256 101 APVSAYF 107 (244)
Q Consensus 101 t~~s~~l 107 (244)
|+.+..+
T Consensus 80 T~~G~~~ 86 (90)
T PF07381_consen 80 TEKGKRI 86 (90)
T ss_pred ChhhhhH
Confidence 8876543
No 175
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=93.73 E-value=0.1 Score=36.92 Aligned_cols=45 Identities=22% Similarity=0.339 Sum_probs=38.0
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
++.|+..|... ++.|..+||+.++++ ... +.+.++-|...|++..
T Consensus 12 ~~~il~~l~~~---~~~~~~~la~~~~~s------~~~-i~~~l~~L~~~g~v~~ 56 (101)
T smart00347 12 QFLVLRILYEE---GPLSVSELAKRLGVS------PST-VTRVLDRLEKKGLIRR 56 (101)
T ss_pred HHHHHHHHHHc---CCcCHHHHHHHHCCC------chh-HHHHHHHHHHCCCeEe
Confidence 55677788765 579999999999997 445 9999999999999985
No 176
>PRK14902 16S rRNA methyltransferase B; Provisional
Probab=93.60 E-value=0.089 Score=48.39 Aligned_cols=50 Identities=14% Similarity=0.030 Sum_probs=39.7
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+...++ ..+..+|+|+|||.|..+..+++.. |..+++.+|+ +..++.+++
T Consensus 242 v~~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~~~~~v~avDi~~~~l~~~~~ 293 (444)
T PRK14902 242 VAPALD-PKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEE 293 (444)
T ss_pred HHHHhC-CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHH
Confidence 334444 4556899999999999999999986 6789999999 777776654
No 177
>PF10294 Methyltransf_16: Putative methyltransferase; InterPro: IPR019410 There are a number of unidentified genes that have a high probability of coding for methyltransferases. They make up approximately 0.6-1.6% of the genes in the yeast, human, mouse, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, and Escherichia coli genomes []. This entry represents putative nicotinamide N-methyltransferases involved in rDNA silencing and in lifespan determination. ; PDB: 3BZB_A.
Probab=93.59 E-value=0.098 Score=41.76 Aligned_cols=42 Identities=14% Similarity=0.158 Sum_probs=32.3
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAP 233 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~ 233 (244)
...++|+++|+|.|..++.+++.++..++++-|.|++++..+
T Consensus 44 ~~~~~VLELGaG~Gl~gi~~a~~~~~~~Vv~TD~~~~l~~l~ 85 (173)
T PF10294_consen 44 FRGKRVLELGAGTGLPGIAAAKLFGAARVVLTDYNEVLELLR 85 (173)
T ss_dssp TTTSEEEETT-TTSHHHHHHHHT-T-SEEEEEE-S-HHHHHH
T ss_pred cCCceEEEECCccchhHHHHHhccCCceEEEeccchhhHHHH
Confidence 456899999999999999999998888899999988877654
No 178
>PF01135 PCMT: Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT); InterPro: IPR000682 Protein-L-isoaspartate(D-aspartate) O-methyltransferase (2.1.1.77 from EC) (PCMT) [] (which is also known as L-isoaspartyl protein carboxyl methyltransferase) is an enzyme that catalyses the transfer of a methyl group from S-adenosylmethionine to the free carboxyl groups of D-aspartyl or L-isoaspartyl residues in a variety of peptides and proteins. The enzyme does not act on normal L-aspartyl residues L-isoaspartyl and D-aspartyl are the products of the spontaneous deamidation and/or isomerisation of normal L-aspartyl and L-asparaginyl residues in proteins. PCMT plays a role in the repair and/or degradation of these damaged proteins; the enzymatic methyl esterification of the abnormal residues can lead to their conversion to normal L-aspartyl residues. The SAM domain is present in most of these proteins.; GO: 0004719 protein-L-isoaspartate (D-aspartate) O-methyltransferase activity, 0006464 protein modification process; PDB: 3LBF_A 1DL5_B 1JG3_B 1JG2_A 1JG1_A 1JG4_A 2YXE_A 2PBF_B 1VBF_C 1R18_A ....
Probab=93.59 E-value=0.11 Score=42.84 Aligned_cols=51 Identities=16% Similarity=0.346 Sum_probs=37.2
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+++.++ .....+|+|||+|+|+++.-++... +.-+++.+|. |..++.|++
T Consensus 63 ~~l~~L~-l~pg~~VLeIGtGsGY~aAlla~lvg~~g~Vv~vE~~~~l~~~A~~ 115 (209)
T PF01135_consen 63 RMLEALD-LKPGDRVLEIGTGSGYQAALLAHLVGPVGRVVSVERDPELAERARR 115 (209)
T ss_dssp HHHHHTT-C-TT-EEEEES-TTSHHHHHHHHHHSTTEEEEEEESBHHHHHHHHH
T ss_pred HHHHHHh-cCCCCEEEEecCCCcHHHHHHHHhcCccceEEEECccHHHHHHHHH
Confidence 4566676 7778999999999999999888864 4445677775 888888765
No 179
>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=93.49 E-value=0.2 Score=33.03 Aligned_cols=56 Identities=20% Similarity=0.334 Sum_probs=40.2
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
..|+..+.. ++.+..||++.++++ ... +.+.|+.|...|++..........|+.++
T Consensus 10 ~~il~~l~~----~~~~~~ei~~~~~i~------~~~-i~~~l~~L~~~g~i~~~~~~~~~~~~~~~ 65 (78)
T cd00090 10 LRILRLLLE----GPLTVSELAERLGLS------QST-VSRHLKKLEEAGLVESRREGRRVYYSLTD 65 (78)
T ss_pred HHHHHHHHH----CCcCHHHHHHHHCcC------HhH-HHHHHHHHHHCCCeEEEEeccEEEEEeCC
Confidence 345666666 349999999999996 445 99999999999999853211124455554
No 180
>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=93.47 E-value=0.11 Score=39.36 Aligned_cols=46 Identities=26% Similarity=0.269 Sum_probs=36.4
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
++.|+.|||+.++++ +.. +.++|+.|...|++.... ...+.|.+..
T Consensus 24 ~~~s~~eia~~l~is------~~~-v~~~l~~L~~~Gli~~~~-g~~ggy~l~~ 69 (130)
T TIGR02944 24 QPYSAAEIAEQTGLN------APT-VSKILKQLSLAGIVTSKR-GVEGGYTLAR 69 (130)
T ss_pred CCccHHHHHHHHCcC------HHH-HHHHHHHHHHCCcEEecC-CCCCChhhcC
Confidence 689999999999997 567 999999999999997421 1235677644
No 181
>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=93.47 E-value=0.06 Score=45.58 Aligned_cols=43 Identities=23% Similarity=0.302 Sum_probs=36.2
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+++++|+=||||.|..+.++++..|-.+.+++|+ |.|++.+++
T Consensus 75 ~~p~~VLiiGgG~G~~~~ell~~~~~~~i~~VEiD~~Vv~~a~~ 118 (246)
T PF01564_consen 75 PNPKRVLIIGGGDGGTARELLKHPPVESITVVEIDPEVVELARK 118 (246)
T ss_dssp SST-EEEEEESTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHH
T ss_pred CCcCceEEEcCCChhhhhhhhhcCCcceEEEEecChHHHHHHHH
Confidence 4679999999999999999997777778999999 999998864
No 182
>TIGR00479 rumA 23S rRNA (uracil-5-)-methyltransferase RumA. This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA.
Probab=93.39 E-value=0.1 Score=47.81 Aligned_cols=47 Identities=17% Similarity=0.249 Sum_probs=37.0
Q ss_pred HhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 185 LESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+... ..+..+|+|+|||.|.++..+++... +++.+|. |..++.|++
T Consensus 285 ~~~l~-~~~~~~vLDl~cG~G~~sl~la~~~~--~V~~vE~~~~av~~a~~ 332 (431)
T TIGR00479 285 LEALE-LQGEELVVDAYCGVGTFTLPLAKQAK--SVVGIEVVPESVEKAQQ 332 (431)
T ss_pred HHHhc-cCCCCEEEEcCCCcCHHHHHHHHhCC--EEEEEEcCHHHHHHHHH
Confidence 33334 45567999999999999999998753 6788888 888888775
No 183
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=93.38 E-value=0.19 Score=32.33 Aligned_cols=42 Identities=19% Similarity=0.331 Sum_probs=36.5
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
|.+.|.+. +..|++|||+.++++ +.- ++|=|..|...|++.+
T Consensus 5 Il~~l~~~---~~~s~~ela~~~~VS------~~T-iRRDl~~L~~~g~i~r 46 (57)
T PF08220_consen 5 ILELLKEK---GKVSVKELAEEFGVS------EMT-IRRDLNKLEKQGLIKR 46 (57)
T ss_pred HHHHHHHc---CCEEHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence 56778775 699999999999997 445 9999999999999985
No 184
>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=93.36 E-value=0.13 Score=34.24 Aligned_cols=61 Identities=11% Similarity=0.196 Sum_probs=43.7
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA 105 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~ 105 (244)
|.+.|.+.+ +|++..+|++.++..+.+-. ++. ++|.|++|...|++.+ .+.+.+.+|+.+.
T Consensus 3 IL~~L~~~~--~P~g~~~l~~~L~~~g~~~s-e~a-vRrrLr~me~~Glt~~---~g~~G~~iT~~G~ 63 (66)
T PF08461_consen 3 ILRILAESD--KPLGRKQLAEELKLRGEELS-EEA-VRRRLRAMERDGLTRK---VGRQGRIITEKGL 63 (66)
T ss_pred HHHHHHHcC--CCCCHHHHHHHHHhcChhhh-HHH-HHHHHHHHHHCCCccc---cCCcccccCHHHH
Confidence 567788775 79999999999976522221 356 9999999999997774 3334456776543
No 185
>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=93.34 E-value=0.12 Score=32.87 Aligned_cols=32 Identities=16% Similarity=0.459 Sum_probs=28.1
Q ss_pred HHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCC
Q 041256 26 LPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLK 63 (244)
Q Consensus 26 ~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~ 63 (244)
+-.+|.+|+++|-||.=. ..|..|||+.+|++
T Consensus 5 Q~e~L~~A~~~GYfd~PR------~~tl~elA~~lgis 36 (53)
T PF04967_consen 5 QREILKAAYELGYFDVPR------RITLEELAEELGIS 36 (53)
T ss_pred HHHHHHHHHHcCCCCCCC------cCCHHHHHHHhCCC
Confidence 457899999999999753 58999999999997
No 186
>KOG3010 consensus Methyltransferase [General function prediction only]
Probab=93.31 E-value=0.085 Score=44.21 Aligned_cols=44 Identities=27% Similarity=0.273 Sum_probs=33.9
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCCCCc
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSYPGT 238 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~~~i 238 (244)
..+.++|||||+|..++.++..|-+ +|..|. +..++.+++.+++
T Consensus 33 ~h~~a~DvG~G~Gqa~~~iae~~k~--VIatD~s~~mL~~a~k~~~~ 77 (261)
T KOG3010|consen 33 GHRLAWDVGTGNGQAARGIAEHYKE--VIATDVSEAMLKVAKKHPPV 77 (261)
T ss_pred CcceEEEeccCCCcchHHHHHhhhh--heeecCCHHHHHHhhcCCCc
Confidence 4469999999999888888888766 566787 7778888775443
No 187
>COG4976 Predicted methyltransferase (contains TPR repeat) [General function prediction only]
Probab=93.19 E-value=0.083 Score=44.07 Aligned_cols=64 Identities=14% Similarity=0.346 Sum_probs=41.4
Q ss_pred HHHHHHHHHhcchhhHHH----HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256 166 NDVFNNGMLSHTSIVMEK----VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA 232 (244)
Q Consensus 166 ~~~f~~aM~~~~~~~~~~----~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a 232 (244)
+++|.+.....-.+..|. .+...+ ...+++|+|+|||+|..+.+|...--.++| +|+ ...++.|
T Consensus 95 Ae~Fd~~LVdkL~Y~vP~~l~emI~~~~-~g~F~~~lDLGCGTGL~G~~lR~~a~~ltG--vDiS~nMl~kA 163 (287)
T COG4976 95 AERFDHILVDKLGYSVPELLAEMIGKAD-LGPFRRMLDLGCGTGLTGEALRDMADRLTG--VDISENMLAKA 163 (287)
T ss_pred HHHHHHHHHHHhcCccHHHHHHHHHhcc-CCccceeeecccCcCcccHhHHHHHhhccC--CchhHHHHHHH
Confidence 457777665544333333 333444 445899999999999999998887666555 566 3344444
No 188
>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=93.12 E-value=0.18 Score=41.33 Aligned_cols=58 Identities=24% Similarity=0.290 Sum_probs=45.1
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV 103 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~ 103 (244)
++.+...|.+. ++.+..+||+.++++ +.. +.|.|..|...|++.+... ....|.+|+.
T Consensus 145 ~~~IL~~l~~~---g~~s~~eia~~l~is------~st-v~r~L~~Le~~GlI~r~~~-r~~~~~lT~~ 202 (203)
T TIGR01884 145 ELKVLEVLKAE---GEKSVKNIAKKLGKS------LST-ISRHLRELEKKGLVEQKGR-KGKRYSLTKL 202 (203)
T ss_pred HHHHHHHHHHc---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEEcC-CccEEEeCCC
Confidence 44567777764 579999999999997 455 9999999999999996421 3456888765
No 189
>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=93.09 E-value=0.099 Score=43.03 Aligned_cols=39 Identities=21% Similarity=0.130 Sum_probs=30.7
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
...+|+|+|||.|.++..+++..+ +++..|+ |..++.++
T Consensus 45 ~~~~vLdlG~G~G~~~~~l~~~~~--~v~~iD~s~~~~~~a~ 84 (224)
T TIGR01983 45 FGLRVLDVGCGGGLLSEPLARLGA--NVTGIDASEENIEVAK 84 (224)
T ss_pred CCCeEEEECCCCCHHHHHHHhcCC--eEEEEeCCHHHHHHHH
Confidence 357999999999999999988765 4888888 55666554
No 190
>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=93.09 E-value=0.12 Score=36.49 Aligned_cols=60 Identities=12% Similarity=0.185 Sum_probs=42.9
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCcccceeecCC---ceeecCccccccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ---RLYSLAPVSAYFV 108 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~---~~y~~t~~s~~l~ 108 (244)
|...|.. |+....||.+.+ +++ +.. |.+-|+.|...|++++...... -.|++|+.+..|.
T Consensus 10 IL~~l~~----g~~rf~el~~~l~~is------~~~-L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~ 73 (90)
T PF01638_consen 10 ILRALFQ----GPMRFSELQRRLPGIS------PKV-LSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL 73 (90)
T ss_dssp HHHHHTT----SSEEHHHHHHHSTTS-------HHH-HHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred HHHHHHh----CCCcHHHHHHhcchhH------HHH-HHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence 4455655 699999999999 786 556 9999999999999986422111 2488888776554
No 191
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=93.05 E-value=0.11 Score=48.59 Aligned_cols=33 Identities=18% Similarity=0.238 Sum_probs=31.1
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL 225 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 225 (244)
+...+||||||.|.++..+++++|+...+.+|.
T Consensus 347 ~~p~~lEIG~G~G~~~~~~A~~~p~~~~iGiE~ 379 (506)
T PRK01544 347 KRKVFLEIGFGMGEHFINQAKMNPDALFIGVEV 379 (506)
T ss_pred CCceEEEECCCchHHHHHHHHhCCCCCEEEEEe
Confidence 468999999999999999999999999999997
No 192
>PF01728 FtsJ: FtsJ-like methyltransferase; InterPro: IPR002877 RrmJ (FtsJ) is a well conserved heat shock protein present in prokaryotes, archaea, and eukaryotes. RrmJ is responsible for methylating 23 S rRNA at position U2552 in the aminoacyl (A)1-site of the ribosome []. U2552 is one of the five universally conserved A-loop residues and has been shown to be methylated at the ribose 2'-OH group in the majority of organisms investigated so far. This suggests that this modification plays an important role in the A-loop function. RrmJ recognises its methylation target only when the 23 S rRNA is present in 50 S ribosomal subunits. This suggests that the RrmJ-mediated methylation must occur late in the maturation process of the ribosome. This is in contrast to other known 23 S rRNA modifications that occur in earlier maturation steps. The 1.5 A crystal structure of RrmJ in complex with its cofactor S-adenosylmethionine revealed that RrmJ has a methyltransferase fold. The active site of RrmJ appears to be formed by a catalytic triad consisting of two lysine residues and the negatively charged aspartate residue. Another highly conserved glutamate residue that is present in the active site of RrmJ appears to play only a minor role in the methyltransfer reaction in vivo []. ; GO: 0003676 nucleic acid binding, 0008168 methyltransferase activity, 0032259 methylation; PDB: 3GCZ_A 2PLW_A 2NYU_A 2OXT_C 3EMD_A 3ELY_A 3ELW_A 3ELU_A 3ELD_A 3EMB_A ....
Probab=92.96 E-value=0.14 Score=40.93 Aligned_cols=47 Identities=19% Similarity=0.251 Sum_probs=36.7
Q ss_pred HHHHhhcCCCC--CcceEEEecCCccHHHHHHHHHC-CCCeEEEccchHH
Q 041256 182 EKVLESYKGFE--HVKKLVDVGGGLGITLNMIISKY-PHIKGINYDLPYV 228 (244)
Q Consensus 182 ~~~~~~~~~~~--~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp~v 228 (244)
.++.+.|+.++ +..++||+|++.|.++..++++. +..+++.+|+...
T Consensus 10 ~ei~~~~~~~~~~~~~~vlDlG~aPGGws~~~~~~~~~~~~v~avDl~~~ 59 (181)
T PF01728_consen 10 YEIDEKFKIFKPGKGFTVLDLGAAPGGWSQVLLQRGGPAGRVVAVDLGPM 59 (181)
T ss_dssp HHHHHTTSSS-TTTTEEEEEET-TTSHHHHHHHTSTTTEEEEEEEESSST
T ss_pred HHHHHHCCCCCcccccEEEEcCCcccceeeeeeecccccceEEEEecccc
Confidence 45666666333 45999999999999999999998 7888999998654
No 193
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=92.94 E-value=0.19 Score=38.65 Aligned_cols=49 Identities=14% Similarity=0.175 Sum_probs=40.4
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYF 107 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l 107 (244)
++.++.+||+.++++ +.. +.+.++.|...|++.+. ..+.|++|+.+..+
T Consensus 21 ~~~~~~ela~~l~vs------~~s-vs~~l~~L~~~Gli~~~---~~~~i~LT~~G~~~ 69 (142)
T PRK03902 21 GYARVSDIAEALSVH------PSS-VTKMVQKLDKDEYLIYE---KYRGLVLTPKGKKI 69 (142)
T ss_pred CCcCHHHHHHHhCCC------hhH-HHHHHHHHHHCCCEEEe---cCceEEECHHHHHH
Confidence 689999999999997 445 99999999999999852 24668998887644
No 194
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=92.75 E-value=0.26 Score=32.85 Aligned_cols=56 Identities=11% Similarity=0.221 Sum_probs=41.8
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS 104 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s 104 (244)
++.++..|.+ ++.|..+||+.+|++ ... +.+-++.|...|+.... . ...|...+..
T Consensus 2 ~~~il~~L~~----~~~~~~eLa~~l~vS------~~t-v~~~l~~L~~~g~~i~~--~-~~g~~l~~~~ 57 (69)
T TIGR00122 2 PLRLLALLAD----NPFSGEKLGEALGMS------RTA-VNKHIQTLREWGVDVLT--V-GKGYRLPPPI 57 (69)
T ss_pred hHHHHHHHHc----CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeEEe--c-CCceEecCcc
Confidence 3456777876 588999999999997 445 99999999999996532 2 3456665543
No 195
>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=92.75 E-value=0.12 Score=46.43 Aligned_cols=39 Identities=15% Similarity=0.037 Sum_probs=32.4
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+|+|+|||+|.++..++.. ..+++.+|. |..++.+++
T Consensus 234 ~~~vLDL~cG~G~~~l~la~~--~~~v~~vE~~~~av~~a~~ 273 (374)
T TIGR02085 234 VTQMWDLFCGVGGFGLHCAGP--DTQLTGIEIESEAIACAQQ 273 (374)
T ss_pred CCEEEEccCCccHHHHHHhhc--CCeEEEEECCHHHHHHHHH
Confidence 368999999999999999854 467888997 888887764
No 196
>PHA00738 putative HTH transcription regulator
Probab=92.66 E-value=0.26 Score=36.00 Aligned_cols=60 Identities=15% Similarity=0.115 Sum_probs=44.7
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV 103 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~ 103 (244)
.++.|++.|.+. ++.++.+|++.++++ ... +-+-|+.|...|++....+...-.|++++-
T Consensus 13 tRr~IL~lL~~~---e~~~V~eLae~l~lS------Qpt-VS~HLKvLreAGLV~srK~Gr~vyY~Ln~~ 72 (108)
T PHA00738 13 LRRKILELIAEN---YILSASLISHTLLLS------YTT-VLRHLKILNEQGYIELYKEGRTLYAKIREN 72 (108)
T ss_pred HHHHHHHHHHHc---CCccHHHHHHhhCCC------HHH-HHHHHHHHHHCCceEEEEECCEEEEEECCC
Confidence 467788889873 479999999999997 345 999999999999999643211224555553
No 197
>PRK11050 manganese transport regulator MntR; Provisional
Probab=92.62 E-value=0.76 Score=35.85 Aligned_cols=57 Identities=14% Similarity=0.243 Sum_probs=43.5
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYF 107 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l 107 (244)
|...+... ++.+..+||+.++++ ... +.+.++.|...|++... . ...+.+|+.+..+
T Consensus 42 I~~~l~~~---~~~t~~eLA~~l~is------~st-Vsr~l~~Le~~GlI~r~--~-~~~v~LT~~G~~l 98 (152)
T PRK11050 42 IADLIAEV---GEARQVDIAARLGVS------QPT-VAKMLKRLARDGLVEMR--P-YRGVFLTPEGEKL 98 (152)
T ss_pred HHHHHHhc---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEEe--c-CCceEECchHHHH
Confidence 55566653 689999999999997 456 99999999999999852 2 3457777766544
No 198
>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=92.39 E-value=0.13 Score=41.77 Aligned_cols=40 Identities=15% Similarity=0.036 Sum_probs=32.9
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+++|++||+|.++.+++.+... +++.+|. +.+++.+++
T Consensus 50 g~~vLDLfaGsG~lglea~srga~-~v~~vE~~~~a~~~~~~ 90 (189)
T TIGR00095 50 GAHLLDVFAGSGLLGEEALSRGAK-VAFLEEDDRKANQTLKE 90 (189)
T ss_pred CCEEEEecCCCcHHHHHHHhCCCC-EEEEEeCCHHHHHHHHH
Confidence 378999999999999999999774 6788887 677766653
No 199
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=92.30 E-value=0.22 Score=39.02 Aligned_cols=46 Identities=15% Similarity=0.095 Sum_probs=37.6
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
++.|..+||+..+++ +.+ |.++|..|...|++.-.. ...|.|+++.
T Consensus 23 ~~~s~~eIA~~~~is------~~~-L~kIl~~L~~aGlv~S~r-G~~GGy~La~ 68 (153)
T PRK11920 23 KLSRIPEIARAYGVS------ELF-LFKILQPLVEAGLVETVR-GRNGGVRLGR 68 (153)
T ss_pred CcCcHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEeec-CCCCCeeecC
Confidence 578999999999997 678 999999999999998532 2246788755
No 200
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=92.23 E-value=0.28 Score=37.72 Aligned_cols=46 Identities=9% Similarity=0.052 Sum_probs=36.4
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
.+.+..+||+..|++ +.. ++++|+.|...|++...+ ...|.|.+..
T Consensus 24 ~~~s~~~ia~~~~is------~~~-vrk~l~~L~~~Glv~s~~-G~~GG~~l~~ 69 (141)
T PRK11014 24 RMTSISEVTEVYGVS------RNH-MVKIINQLSRAGYVTAVR-GKNGGIRLGK 69 (141)
T ss_pred CccCHHHHHHHHCcC------HHH-HHHHHHHHHhCCEEEEec-CCCCCeeecC
Confidence 478999999999997 567 999999999999998532 1135677653
No 201
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=92.21 E-value=0.21 Score=36.30 Aligned_cols=45 Identities=18% Similarity=0.376 Sum_probs=39.0
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
.+..|+..|.+. ++.|..+||+.+|++ +.. +.+.++.|...|++.
T Consensus 4 ~D~~il~~L~~~---~~~~~~~la~~l~~s------~~t-v~~~l~~L~~~g~i~ 48 (108)
T smart00344 4 IDRKILEELQKD---ARISLAELAKKVGLS------PST-VHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHHh---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCee
Confidence 456788888875 689999999999997 556 999999999999998
No 202
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=92.18 E-value=0.31 Score=29.98 Aligned_cols=42 Identities=21% Similarity=0.337 Sum_probs=35.0
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
+++.|.+. ++.|..+|++.++++ +.. +.+.|..|...|++.+
T Consensus 5 il~~l~~~---~~~s~~~l~~~l~~s------~~t-v~~~l~~L~~~g~i~~ 46 (53)
T smart00420 5 ILELLAQQ---GKVSVEELAELLGVS------EMT-IRRDLNKLEEQGLLTR 46 (53)
T ss_pred HHHHHHHc---CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE
Confidence 45666654 579999999999997 455 9999999999999985
No 203
>KOG3115 consensus Methyltransferase-like protein [General function prediction only]
Probab=92.10 E-value=0.078 Score=43.36 Aligned_cols=32 Identities=22% Similarity=0.419 Sum_probs=28.1
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL 225 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 225 (244)
-..++|||||-|.+++.|...||+--.+..++
T Consensus 61 kvefaDIGCGyGGLlv~Lsp~fPdtLiLGmEI 92 (249)
T KOG3115|consen 61 KVEFADIGCGYGGLLMKLAPKFPDTLILGMEI 92 (249)
T ss_pred cceEEeeccCccchhhhccccCccceeeeehh
Confidence 47799999999999999999999977766665
No 204
>KOG3420 consensus Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=92.06 E-value=0.11 Score=40.39 Aligned_cols=48 Identities=27% Similarity=0.449 Sum_probs=36.0
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCe-EEEccc-hHHhhhCCC
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIK-GINYDL-PYVIKDAPS 234 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dl-p~vi~~a~~ 234 (244)
+-+-|.+++ .+++.|+|||.|.++ +.-.+|..+ ++.+|+ |+.++.+.+
T Consensus 40 Ih~TygdiE-gkkl~DLgcgcGmLs--~a~sm~~~e~vlGfDIdpeALEIf~r 89 (185)
T KOG3420|consen 40 IHNTYGDIE-GKKLKDLGCGCGMLS--IAFSMPKNESVLGFDIDPEALEIFTR 89 (185)
T ss_pred HHhhhcccc-CcchhhhcCchhhhH--HHhhcCCCceEEeeecCHHHHHHHhh
Confidence 334454344 389999999999999 556777765 688998 888888765
No 205
>KOG1499 consensus Protein arginine N-methyltransferase PRMT1 and related enzymes [Posttranslational modification, protein turnover, chaperones; Transcription; Signal transduction mechanisms]
Probab=91.90 E-value=0.15 Score=44.88 Aligned_cols=40 Identities=23% Similarity=0.145 Sum_probs=33.6
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~ 234 (244)
.++|+|||||+|.+++-.+++. .-++..+|-.++++.|.+
T Consensus 61 dK~VlDVGcGtGILS~F~akAG-A~~V~aVe~S~ia~~a~~ 100 (346)
T KOG1499|consen 61 DKTVLDVGCGTGILSMFAAKAG-ARKVYAVEASSIADFARK 100 (346)
T ss_pred CCEEEEcCCCccHHHHHHHHhC-cceEEEEechHHHHHHHH
Confidence 4899999999999999988887 667888888877776654
No 206
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=91.84 E-value=0.28 Score=41.75 Aligned_cols=67 Identities=12% Similarity=0.219 Sum_probs=55.6
Q ss_pred HHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256 29 VMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV 108 (244)
Q Consensus 29 ~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~ 108 (244)
.+...-+.+|+=.|.+ ||+|.+||-..++++ +.. +..=++-|...|++.+ . ++.|++|..+..++
T Consensus 9 if~SekRk~lLllL~e----gPkti~EI~~~l~vs------~~a-i~pqiKkL~~~~LV~~---~-~~~Y~LS~~G~iiv 73 (260)
T COG4742 9 LFLSEKRKDLLLLLKE----GPKTIEEIKNELNVS------SSA-ILPQIKKLKDKGLVVQ---E-GDRYSLSSLGKIIV 73 (260)
T ss_pred HHccHHHHHHHHHHHh----CCCCHHHHHHHhCCC------cHH-HHHHHHHHhhCCCEEe---c-CCEEEecchHHHHH
Confidence 3445567788888888 799999999999997 456 8888899999999995 3 59999999999877
Q ss_pred cC
Q 041256 109 RN 110 (244)
Q Consensus 109 ~~ 110 (244)
..
T Consensus 74 ~k 75 (260)
T COG4742 74 EK 75 (260)
T ss_pred HH
Confidence 55
No 207
>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=91.60 E-value=0.23 Score=42.38 Aligned_cols=58 Identities=16% Similarity=0.346 Sum_probs=41.8
Q ss_pred HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC----CCCceee
Q 041256 181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS----YPGTLFI 241 (244)
Q Consensus 181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~----~~~i~~~ 241 (244)
...+++..+ ..+...|+|||.|.|.+...|++.. -+.+++|. |.-++..++ .++++++
T Consensus 19 ~~~Iv~~~~-~~~~~~VlEiGpG~G~lT~~L~~~~--~~v~~vE~d~~~~~~L~~~~~~~~~~~vi 81 (262)
T PF00398_consen 19 ADKIVDALD-LSEGDTVLEIGPGPGALTRELLKRG--KRVIAVEIDPDLAKHLKERFASNPNVEVI 81 (262)
T ss_dssp HHHHHHHHT-CGTTSEEEEESSTTSCCHHHHHHHS--SEEEEEESSHHHHHHHHHHCTTCSSEEEE
T ss_pred HHHHHHhcC-CCCCCEEEEeCCCCccchhhHhccc--CcceeecCcHhHHHHHHHHhhhcccceee
Confidence 456777776 6778999999999999999999998 55666665 554444432 3455544
No 208
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=91.43 E-value=0.44 Score=35.80 Aligned_cols=49 Identities=18% Similarity=0.337 Sum_probs=41.0
Q ss_pred HHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 31 QAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 31 ~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
+..+...|.+.+.++ |.+|..+++..+|++ -.. +.+.++.|++.|-|..
T Consensus 10 r~eLk~rIvElVRe~---GRiTi~ql~~~TGas------R~T-vk~~lreLVa~G~l~~ 58 (127)
T PF06163_consen 10 REELKARIVELVREH---GRITIKQLVAKTGAS------RNT-VKRYLRELVARGDLYR 58 (127)
T ss_pred HHHHHHHHHHHHHHc---CCccHHHHHHHHCCC------HHH-HHHHHHHHHHcCCeEe
Confidence 345667788888887 799999999999996 234 9999999999998884
No 209
>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=91.34 E-value=0.24 Score=45.32 Aligned_cols=50 Identities=14% Similarity=0.139 Sum_probs=39.7
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+...++ .....+|+|+|+|.|..+..+++..|+.+.+..|. ++.++.+++
T Consensus 230 ~~~~L~-~~~g~~VLDlcag~G~kt~~la~~~~~~~v~a~D~~~~~l~~~~~ 280 (426)
T TIGR00563 230 VATWLA-PQNEETILDACAAPGGKTTHILELAPQAQVVALDIHEHRLKRVYE 280 (426)
T ss_pred HHHHhC-CCCCCeEEEeCCCccHHHHHHHHHcCCCeEEEEeCCHHHHHHHHH
Confidence 344455 45568999999999999999999998778899998 777766653
No 210
>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=91.31 E-value=0.38 Score=39.49 Aligned_cols=34 Identities=15% Similarity=0.267 Sum_probs=27.9
Q ss_pred CCcc-eEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256 192 EHVK-KLVDVGGGLGITLNMIISKYPHIKGINYDL 225 (244)
Q Consensus 192 ~~~~-~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 225 (244)
.... +|+.||.|+|..+..+++++|+++--==|.
T Consensus 23 ~~~~~~vLEiaSGtGqHa~~FA~~lP~l~WqPSD~ 57 (204)
T PF06080_consen 23 PDSGTRVLEIASGTGQHAVYFAQALPHLTWQPSDP 57 (204)
T ss_pred CccCceEEEEcCCccHHHHHHHHHCCCCEEcCCCC
Confidence 4444 599999999999999999999998644454
No 211
>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=91.07 E-value=0.3 Score=35.79 Aligned_cols=48 Identities=23% Similarity=0.350 Sum_probs=37.0
Q ss_pred hcChhhHHh--hcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 35 ELDVFEIIS--KAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 35 ~lgifd~L~--~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
++.++..|. ... ++++|..+||+.++++ ... +.++++.|...|++.+.
T Consensus 27 q~~vL~~l~~~~~~-~~~~t~~eL~~~l~~~------~st-vs~~i~~Le~kg~I~r~ 76 (109)
T TIGR01889 27 ELLILYYLGKLENN-EGKLTLKEIIKEILIK------QSA-LVKIIKKLSKKGYLSKE 76 (109)
T ss_pred HHHHHHHHHhhhcc-CCcCcHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEecc
Confidence 344555555 211 1689999999999997 456 99999999999999964
No 212
>KOG1541 consensus Predicted protein carboxyl methylase [General function prediction only]
Probab=91.06 E-value=0.11 Score=43.15 Aligned_cols=40 Identities=20% Similarity=0.386 Sum_probs=32.1
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
....|+|||||+|..+..+... +...+.+|. |..++.|.+
T Consensus 50 ~~~~iLDIGCGsGLSg~vL~~~--Gh~wiGvDiSpsML~~a~~ 90 (270)
T KOG1541|consen 50 KSGLILDIGCGSGLSGSVLSDS--GHQWIGVDISPSMLEQAVE 90 (270)
T ss_pred CCcEEEEeccCCCcchheeccC--CceEEeecCCHHHHHHHHH
Confidence 5799999999999988776554 467789998 888887763
No 213
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=91.03 E-value=1.2 Score=35.57 Aligned_cols=64 Identities=14% Similarity=0.120 Sum_probs=47.5
Q ss_pred hhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhC--CCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256 23 AIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI--PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL 100 (244)
Q Consensus 23 g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~--~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~ 100 (244)
..|...+++..+.+.= +.-++++||+++ +++ +.. ++.-|..|..+|++++ .++|.|..
T Consensus 22 ~~W~~~~ir~l~~l~~----------~~~d~~~iak~l~p~is------~~e-v~~sL~~L~~~gli~k---~~~g~y~~ 81 (171)
T PF14394_consen 22 SSWYHPAIRELLPLMP----------FAPDPEWIAKRLRPKIS------AEE-VRDSLEFLEKLGLIKK---DGDGKYVQ 81 (171)
T ss_pred hhhHHHHHHHHhhcCC----------CCCCHHHHHHHhcCCCC------HHH-HHHHHHHHHHCCCeEE---CCCCcEEE
Confidence 5566666665544321 233899999999 886 556 9999999999999995 45689999
Q ss_pred Cccccc
Q 041256 101 APVSAY 106 (244)
Q Consensus 101 t~~s~~ 106 (244)
|..+-.
T Consensus 82 t~~~l~ 87 (171)
T PF14394_consen 82 TDKSLT 87 (171)
T ss_pred ecceee
Confidence 876544
No 214
>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=91.01 E-value=0.35 Score=38.13 Aligned_cols=44 Identities=14% Similarity=0.074 Sum_probs=37.5
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
..|+++|... +.+|-+|||+.+|++ ... ++++|..|...|++..
T Consensus 17 v~Vl~aL~~~---~~~tdEeLa~~Lgi~------~~~-VRk~L~~L~e~~Lv~~ 60 (158)
T TIGR00373 17 GLVLFSLGIK---GEFTDEEISLELGIK------LNE-VRKALYALYDAGLADY 60 (158)
T ss_pred HHHHHHHhcc---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCcee
Confidence 3478888765 689999999999997 455 9999999999999964
No 215
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=91.00 E-value=0.43 Score=36.58 Aligned_cols=44 Identities=16% Similarity=0.145 Sum_probs=35.3
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
++..|...+ ++.|..+||+.++++ +.. +.++++-|...|++++.
T Consensus 36 vL~~l~~~~--~~~t~~eLa~~l~~~------~~t-vt~~v~~Le~~GlV~r~ 79 (144)
T PRK03573 36 TLHNIHQLP--PEQSQIQLAKAIGIE------QPS-LVRTLDQLEEKGLISRQ 79 (144)
T ss_pred HHHHHHHcC--CCCCHHHHHHHhCCC------hhh-HHHHHHHHHHCCCEeee
Confidence 455665532 468999999999997 445 99999999999999964
No 216
>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=90.98 E-value=0.3 Score=43.57 Aligned_cols=38 Identities=11% Similarity=0.134 Sum_probs=32.2
Q ss_pred ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+++|++||+|.++..+.+... +++.+|. ++.++.+++
T Consensus 199 ~~vlDl~~G~G~~sl~la~~~~--~v~~vE~~~~av~~a~~ 237 (353)
T TIGR02143 199 GDLLELYCGNGNFSLALAQNFR--RVLATEIAKPSVNAAQY 237 (353)
T ss_pred CcEEEEeccccHHHHHHHHhCC--EEEEEECCHHHHHHHHH
Confidence 4699999999999999998874 7888887 788887765
No 217
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=90.97 E-value=0.5 Score=29.85 Aligned_cols=34 Identities=24% Similarity=0.245 Sum_probs=29.5
Q ss_pred CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
..+ |..+||+.++++ ... +++.|+.|...|++..
T Consensus 18 ~~l~s~~~la~~~~vs------~~t-v~~~l~~L~~~g~i~~ 52 (60)
T smart00345 18 DKLPSERELAAQLGVS------RTT-VREALSRLEAEGLVQR 52 (60)
T ss_pred CcCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE
Confidence 345 899999999997 456 9999999999999985
No 218
>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=90.94 E-value=0.54 Score=34.53 Aligned_cols=51 Identities=24% Similarity=0.365 Sum_probs=37.5
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCc-chhccHHHHHHHHhhCCcccce
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPE-AAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~-~~~~~l~rlLr~L~~~gll~~~ 90 (244)
+.-|++.|.+.+ ++.|++||.+.+.-. .|. ...- ++|.|+.|+..|++.+.
T Consensus 3 R~~Il~~l~~~~--~~~sa~ei~~~l~~~--~~~i~~~T-VYR~L~~L~~~Gli~~~ 54 (116)
T cd07153 3 RLAILEVLLESD--GHLTAEEIYERLRKK--GPSISLAT-VYRTLELLEEAGLVREI 54 (116)
T ss_pred HHHHHHHHHhCC--CCCCHHHHHHHHHhc--CCCCCHHH-HHHHHHHHHhCCCEEEE
Confidence 345788888754 689999999998432 111 0233 99999999999999864
No 219
>TIGR01177 conserved hypothetical protein TIGR01177. This family is found exclusively in the Archaea.
Probab=90.77 E-value=0.46 Score=41.86 Aligned_cols=47 Identities=17% Similarity=0.036 Sum_probs=34.8
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~ 233 (244)
++.... +....+|+|+|||+|.++.+.+. ...+.+..|. |..+..++
T Consensus 174 ~~~l~~-~~~g~~vLDp~cGtG~~lieaa~--~~~~v~g~Di~~~~~~~a~ 221 (329)
T TIGR01177 174 MVNLAR-VTEGDRVLDPFCGTGGFLIEAGL--MGAKVIGCDIDWKMVAGAR 221 (329)
T ss_pred HHHHhC-CCCcCEEEECCCCCCHHHHHHHH--hCCeEEEEcCCHHHHHHHH
Confidence 333334 66668999999999999988655 3667888898 77776654
No 220
>COG2518 Pcm Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=90.66 E-value=0.49 Score=38.93 Aligned_cols=49 Identities=10% Similarity=0.259 Sum_probs=38.0
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+++.+. .+...+|++||+|+|..+.-+.+--- +++-+|+ ++.++.|++
T Consensus 63 ~m~~~L~-~~~g~~VLEIGtGsGY~aAvla~l~~--~V~siEr~~~L~~~A~~ 112 (209)
T COG2518 63 RMLQLLE-LKPGDRVLEIGTGSGYQAAVLARLVG--RVVSIERIEELAEQARR 112 (209)
T ss_pred HHHHHhC-CCCCCeEEEECCCchHHHHHHHHHhC--eEEEEEEcHHHHHHHHH
Confidence 4456666 77889999999999999888777655 6777776 777777764
No 221
>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=90.56 E-value=0.55 Score=38.71 Aligned_cols=66 Identities=15% Similarity=0.191 Sum_probs=34.8
Q ss_pred hhccCCchHHHHHHH----HHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256 157 DYLGVDSRFNDVFNN----GMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL 225 (244)
Q Consensus 157 e~~~~~~~~~~~f~~----aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 225 (244)
+.+.++|+....++. .+..|-......+++.+...++...|.|.|||.+.++.++.+ ..++.-|||
T Consensus 32 ~lf~~dP~~F~~YH~Gfr~Qv~~WP~nPvd~iI~~l~~~~~~~viaD~GCGdA~la~~~~~---~~~V~SfDL 101 (219)
T PF05148_consen 32 KLFQEDPELFDIYHEGFRQQVKKWPVNPVDVIIEWLKKRPKSLVIADFGCGDAKLAKAVPN---KHKVHSFDL 101 (219)
T ss_dssp HHHHH-HHHHHHHHHHHHHHHCTSSS-HHHHHHHHHCTS-TTS-EEEES-TT-HHHHH--S------EEEEES
T ss_pred HHHHhCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHhcCCCEEEEECCCchHHHHHhccc---CceEEEeec
Confidence 344556665554444 444444445566777665334557999999999999976642 246677776
No 222
>PRK11760 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional
Probab=90.52 E-value=0.5 Score=41.89 Aligned_cols=48 Identities=10% Similarity=-0.006 Sum_probs=37.7
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCCceee
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFI 241 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~i~~~ 241 (244)
....++||||++.|.+...++++ +.+++.+|.-..-+.....++|+++
T Consensus 210 ~~g~~vlDLGAsPGGWT~~L~~r--G~~V~AVD~g~l~~~L~~~~~V~h~ 257 (357)
T PRK11760 210 APGMRAVDLGAAPGGWTYQLVRR--GMFVTAVDNGPMAQSLMDTGQVEHL 257 (357)
T ss_pred CCCCEEEEeCCCCcHHHHHHHHc--CCEEEEEechhcCHhhhCCCCEEEE
Confidence 45689999999999999999998 5689999976665555555666554
No 223
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=90.25 E-value=0.41 Score=39.68 Aligned_cols=59 Identities=19% Similarity=0.318 Sum_probs=44.9
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC-----CceeecCccccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-----QRLYSLAPVSAY 106 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-----~~~y~~t~~s~~ 106 (244)
|...|.+. +|.|+.|||+++|++ +.. ++|-|..|++.|+++.....+ .-.|++|..+..
T Consensus 16 il~lL~~~---g~~sa~elA~~Lgis------~~a-vR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~ 79 (218)
T COG2345 16 ILELLKKS---GPVSADELAEELGIS------PMA-VRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE 79 (218)
T ss_pred HHHHHhcc---CCccHHHHHHHhCCC------HHH-HHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchh
Confidence 44556655 799999999999997 567 999999999999998532211 124888888764
No 224
>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=90.18 E-value=0.53 Score=38.72 Aligned_cols=49 Identities=18% Similarity=0.282 Sum_probs=32.2
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA 232 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a 232 (244)
.+++.+. +....+++|||+|.|....+.+-.++--+++.+++ |...+.|
T Consensus 33 ~il~~~~-l~~~dvF~DlGSG~G~~v~~aal~~~~~~~~GIEi~~~~~~~a 82 (205)
T PF08123_consen 33 KILDELN-LTPDDVFYDLGSGVGNVVFQAALQTGCKKSVGIEILPELHDLA 82 (205)
T ss_dssp HHHHHTT---TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE-SHHHHHHH
T ss_pred HHHHHhC-CCCCCEEEECCCCCCHHHHHHHHHcCCcEEEEEEechHHHHHH
Confidence 4555565 66678999999999999998888887666888887 5555444
No 225
>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=89.92 E-value=0.66 Score=29.21 Aligned_cols=42 Identities=7% Similarity=0.283 Sum_probs=32.1
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcc
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNAL 87 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll 87 (244)
.|+..|.+.+ +++|.++||+.++++ ..- +.+-+..|...|+.
T Consensus 4 ~il~~L~~~~--~~it~~eLa~~l~vS------~rT-i~~~i~~L~~~~~~ 45 (55)
T PF08279_consen 4 QILKLLLESK--EPITAKELAEELGVS------RRT-IRRDIKELREWGIP 45 (55)
T ss_dssp HHHHHHHHTT--TSBEHHHHHHHCTS-------HHH-HHHHHHHHHHTT-E
T ss_pred HHHHHHHHcC--CCcCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCe
Confidence 3566675443 579999999999997 445 99999999999933
No 226
>PRK05031 tRNA (uracil-5-)-methyltransferase; Validated
Probab=89.76 E-value=0.38 Score=43.06 Aligned_cols=38 Identities=11% Similarity=0.127 Sum_probs=31.8
Q ss_pred ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+++|++||+|.++..+.+... +++.+|. +..++.+++
T Consensus 208 ~~vLDl~~G~G~~sl~la~~~~--~v~~vE~~~~ai~~a~~ 246 (362)
T PRK05031 208 GDLLELYCGNGNFTLALARNFR--RVLATEISKPSVAAAQY 246 (362)
T ss_pred CeEEEEeccccHHHHHHHhhCC--EEEEEECCHHHHHHHHH
Confidence 4699999999999999998875 6788887 777777764
No 227
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=89.60 E-value=0.66 Score=33.16 Aligned_cols=44 Identities=7% Similarity=0.105 Sum_probs=36.4
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA 101 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t 101 (244)
.++|-.|||+.+|++ ..- +.|.|..|...|++... .+-+.|+.|
T Consensus 46 ~~is~~eLa~~~g~s------r~t-Vsr~L~~Le~~GlI~r~--~~~~~~~~n 89 (95)
T TIGR01610 46 DRVTATVIAELTGLS------RTH-VSDAIKSLARRRIIFRQ--GMMGIVGVN 89 (95)
T ss_pred CccCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeeee--cCCceeecC
Confidence 589999999999997 445 99999999999999962 234777776
No 228
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=89.55 E-value=0.62 Score=36.54 Aligned_cols=52 Identities=8% Similarity=0.072 Sum_probs=43.1
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccccC
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRN 110 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~~ 110 (244)
++....+||+.++++ |.- +...++-|...|++++. . .+.+.+|+.+...+..
T Consensus 23 ~~~~~~diA~~L~Vs------p~s-Vt~ml~rL~~~GlV~~~--~-y~gi~LT~~G~~~a~~ 74 (154)
T COG1321 23 GFARTKDIAERLKVS------PPS-VTEMLKRLERLGLVEYE--P-YGGVTLTEKGREKAKE 74 (154)
T ss_pred CcccHHHHHHHhCCC------cHH-HHHHHHHHHHCCCeEEe--c-CCCeEEChhhHHHHHH
Confidence 799999999999997 445 88999999999999973 3 4779999987755544
No 229
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=89.45 E-value=0.49 Score=39.26 Aligned_cols=53 Identities=15% Similarity=0.187 Sum_probs=41.3
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV 108 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~ 108 (244)
..+|..+||+.++++ +.. +.|.|+.|...|++++........+++|+.+..+.
T Consensus 20 ~~IS~~eLA~~L~iS------~~T-vsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll 72 (217)
T PRK14165 20 VKISSSEFANHTGTS------SKT-AARILKQLEDEGYITRTIVPRGQLITITEKGLDVL 72 (217)
T ss_pred CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHH
Confidence 469999999999997 456 99999999999999864322245678888776443
No 230
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=89.27 E-value=0.73 Score=30.02 Aligned_cols=34 Identities=9% Similarity=0.236 Sum_probs=30.2
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
++.+..+||+.++++ +.- +...++-|...|+++.
T Consensus 21 ~~v~~~~iA~~L~vs------~~t-vt~ml~~L~~~GlV~~ 54 (60)
T PF01325_consen 21 GPVRTKDIAERLGVS------PPT-VTEMLKRLAEKGLVEY 54 (60)
T ss_dssp SSBBHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEE
T ss_pred CCccHHHHHHHHCCC------hHH-HHHHHHHHHHCCCEEe
Confidence 799999999999997 445 8999999999999996
No 231
>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=89.03 E-value=0.44 Score=41.20 Aligned_cols=43 Identities=16% Similarity=0.243 Sum_probs=36.2
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCC--CeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPH--IKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~--l~~~v~Dl-p~vi~~a~~ 234 (244)
....+||||.||+|.+...+++.+|. ..+.+.|. |.-|+..++
T Consensus 134 g~pvrIlDIAaG~GRYvlDal~~~~~~~~~i~LrDys~~Nv~~g~~ 179 (311)
T PF12147_consen 134 GRPVRILDIAAGHGRYVLDALEKHPERPDSILLRDYSPINVEKGRA 179 (311)
T ss_pred CCceEEEEeccCCcHHHHHHHHhCCCCCceEEEEeCCHHHHHHHHH
Confidence 36799999999999999999999998 67788887 666666653
No 232
>PHA02943 hypothetical protein; Provisional
Probab=88.98 E-value=0.92 Score=35.28 Aligned_cols=42 Identities=10% Similarity=0.157 Sum_probs=34.8
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.|.+.|.. |..|..|||+++|++ -.. .+-.|..|...|.+.+
T Consensus 15 eILE~Lk~----G~~TtseIAkaLGlS------~~q-a~~~LyvLErEG~Vkr 56 (165)
T PHA02943 15 KTLRLLAD----GCKTTSRIANKLGVS------HSM-ARNALYQLAKEGMVLK 56 (165)
T ss_pred HHHHHHhc----CCccHHHHHHHHCCC------HHH-HHHHHHHHHHcCceEE
Confidence 45666733 789999999999997 345 8899999999999995
No 233
>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=88.68 E-value=0.86 Score=42.08 Aligned_cols=69 Identities=17% Similarity=0.231 Sum_probs=43.1
Q ss_pred CchhhccCCchHHHHHHHHHHhcchhhHHHHHhhcCCC---CCcceEEEecCCccHHHHHHHHHC----CCCeEEEccc-
Q 041256 154 QIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGF---EHVKKLVDVGGGLGITLNMIISKY----PHIKGINYDL- 225 (244)
Q Consensus 154 ~~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~~---~~~~~vvDVGGG~G~~~~~l~~~~----P~l~~~v~Dl- 225 (244)
.-||.+++|+..-+.+.+|+.. .+.+....- .+.+.|+|||+|+|-++...+++. -..++..++-
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 3578888899877888887632 223222211 135889999999999987776654 4567777765
Q ss_pred hHHh
Q 041256 226 PYVI 229 (244)
Q Consensus 226 p~vi 229 (244)
|..+
T Consensus 224 ~~A~ 227 (448)
T PF05185_consen 224 PNAV 227 (448)
T ss_dssp THHH
T ss_pred HhHH
Confidence 4443
No 234
>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=88.56 E-value=0.51 Score=41.79 Aligned_cols=61 Identities=20% Similarity=0.161 Sum_probs=39.1
Q ss_pred HHHHHHHHHhcchhhHHHHHhhcC----CCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 166 NDVFNNGMLSHTSIVMEKVLESYK----GFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 166 ~~~f~~aM~~~~~~~~~~~~~~~~----~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+.|+.++.+ .++..|- .-....+|+|+|||.|..+....++.+. ..+..|+ ++.|+.|++
T Consensus 38 lR~fNNwvKs-------~LI~~~~~~~~~~~~~~~VLDl~CGkGGDL~Kw~~~~i~-~~vg~Dis~~si~ea~~ 103 (331)
T PF03291_consen 38 LRNFNNWVKS-------VLIQKYAKKVKQNRPGLTVLDLCCGKGGDLQKWQKAKIK-HYVGIDISEESIEEARE 103 (331)
T ss_dssp HHHHHHHHHH-------HHHHHHCHCCCCTTTT-EEEEET-TTTTTHHHHHHTT-S-EEEEEES-HHHHHHHHH
T ss_pred HHHHhHHHHH-------HHHHHHHHhhhccCCCCeEEEecCCCchhHHHHHhcCCC-EEEEEeCCHHHHHHHHH
Confidence 5788888865 2333331 0115689999999999999888887332 3577888 666666643
No 235
>COG0357 GidB Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]
Probab=88.54 E-value=0.44 Score=39.46 Aligned_cols=32 Identities=22% Similarity=0.423 Sum_probs=29.8
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL 225 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 225 (244)
..+++|||-|.|.=++=++=.+|+++.+++|-
T Consensus 68 ~~~~~DIGSGaGfPGipLAI~~p~~~vtLles 99 (215)
T COG0357 68 AKRVLDIGSGAGFPGIPLAIAFPDLKVTLLES 99 (215)
T ss_pred CCEEEEeCCCCCCchhhHHHhccCCcEEEEcc
Confidence 68999999999999998889999999999994
No 236
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=88.31 E-value=0.69 Score=38.13 Aligned_cols=43 Identities=23% Similarity=0.330 Sum_probs=34.2
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
|.+.|... +.+.|++|||+++|++ -.- .+|.|.+|++.|++.-
T Consensus 163 i~~~~~~~--~~~~Taeela~~~giS------RvT-aRRYLeyl~~~~~l~a 205 (224)
T COG4565 163 VREALKEP--DQELTAEELAQALGIS------RVT-ARRYLEYLVSNGILEA 205 (224)
T ss_pred HHHHHhCc--CCccCHHHHHHHhCcc------HHH-HHHHHHHHHhcCeeeE
Confidence 45556522 2689999999999996 233 8999999999999984
No 237
>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=88.30 E-value=0.53 Score=38.07 Aligned_cols=30 Identities=20% Similarity=0.313 Sum_probs=27.5
Q ss_pred eEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256 196 KLVDVGGGLGITLNMIISKYPHIKGINYDL 225 (244)
Q Consensus 196 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 225 (244)
+++|||.|.|.=++-++=.+|+++++++|-
T Consensus 51 ~~lDiGSGaGfPGipLaI~~p~~~~~LvEs 80 (184)
T PF02527_consen 51 KVLDIGSGAGFPGIPLAIARPDLQVTLVES 80 (184)
T ss_dssp EEEEETSTTTTTHHHHHHH-TTSEEEEEES
T ss_pred eEEecCCCCCChhHHHHHhCCCCcEEEEeC
Confidence 799999999999999999999999999994
No 238
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=88.10 E-value=0.87 Score=34.50 Aligned_cols=51 Identities=16% Similarity=0.264 Sum_probs=42.3
Q ss_pred HHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 29 VMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 29 ~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.+.+=-.+.+...|+.. +|.|..|||+.+|-+ +.. +.|-|+.|.-.|++.-
T Consensus 60 ~vLsp~nleLl~~Ia~~---~P~Si~ElAe~vgRd------v~n-vhr~Ls~l~~~GlI~f 110 (144)
T COG4190 60 RVLSPRNLELLELIAQE---EPASINELAELVGRD------VKN-VHRTLSTLADLGLIFF 110 (144)
T ss_pred HHhChhHHHHHHHHHhc---CcccHHHHHHHhCcc------hHH-HHHHHHHHHhcCeEEE
Confidence 33344457788889886 699999999999986 566 9999999999999986
No 239
>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=87.98 E-value=0.49 Score=34.35 Aligned_cols=42 Identities=12% Similarity=0.282 Sum_probs=31.7
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
|++.|... |.++-++||+.++++ +.- ++++|..|...||+..
T Consensus 18 Il~~L~~~---~~l~de~la~~~~l~------~~~-vRkiL~~L~~~~lv~~ 59 (105)
T PF02002_consen 18 ILDALLRK---GELTDEDLAKKLGLK------PKE-VRKILYKLYEDGLVSY 59 (105)
T ss_dssp HHHHHHHH-----B-HHHHHHTT-S-------HHH-HHHHHHHHHHHSS-EE
T ss_pred HHHHHHHc---CCcCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCeEE
Confidence 68888865 689999999999997 456 9999999999999975
No 240
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=87.90 E-value=0.73 Score=39.30 Aligned_cols=48 Identities=21% Similarity=0.391 Sum_probs=40.9
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccccee
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSF 91 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~ 91 (244)
+..+.++|.+.| |-++-+||.+++|.+ ..- +.|+|+-|...|++++.+
T Consensus 197 e~~il~~i~~~G--Gri~Q~eL~r~lgls------ktT-vsR~L~~LEk~GlIe~~K 244 (258)
T COG2512 197 EKEILDLIRERG--GRITQAELRRALGLS------KTT-VSRILRRLEKRGLIEKEK 244 (258)
T ss_pred HHHHHHHHHHhC--CEEeHHHHHHhhCCC------hHH-HHHHHHHHHhCCceEEEE
Confidence 456888898876 779999999999996 334 999999999999999753
No 241
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=87.88 E-value=1 Score=30.97 Aligned_cols=43 Identities=16% Similarity=0.244 Sum_probs=37.3
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
|=|.|... |..++.+||..++++ +.. ++.+|..++..|-+++.
T Consensus 7 lRd~l~~~---gr~s~~~Ls~~~~~p------~~~-VeaMLe~l~~kGkverv 49 (78)
T PRK15431 7 VRDLLALR---GRMEAAQISQTLNTP------QPM-INAMLQQLESMGKAVRI 49 (78)
T ss_pred HHHHHHHc---CcccHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEee
Confidence 44778876 689999999999997 678 99999999999999963
No 242
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=87.74 E-value=0.71 Score=32.61 Aligned_cols=46 Identities=13% Similarity=0.197 Sum_probs=35.9
Q ss_pred HHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256 53 VAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV 108 (244)
Q Consensus 53 ~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~ 108 (244)
+.+||+.++++ +.. +.+.++.|...|++.. ..+..|.+|+.+..+.
T Consensus 2 ~~ela~~l~is------~st-vs~~l~~L~~~glI~r---~~~~~~~lT~~g~~~~ 47 (96)
T smart00529 2 TSEIAERLNVS------PPT-VTQMLKKLEKDGLVEY---EPYRGITLTEKGRRLA 47 (96)
T ss_pred HHHHHHHhCCC------hHH-HHHHHHHHHHCCCEEE---cCCCceEechhHHHHH
Confidence 46899999997 455 9999999999999996 2235688888765443
No 243
>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=87.66 E-value=0.56 Score=38.59 Aligned_cols=43 Identities=16% Similarity=0.196 Sum_probs=35.9
Q ss_pred CCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~ 234 (244)
.++++||+||.+.|.-+..+++..| +.+.+.+|. |+-.+.|++
T Consensus 44 ~~~k~vLEIGt~~GySal~la~~l~~~g~i~tiE~~~~~~~~A~~ 88 (205)
T PF01596_consen 44 TRPKRVLEIGTFTGYSALWLAEALPEDGKITTIEIDPERAEIARE 88 (205)
T ss_dssp HT-SEEEEESTTTSHHHHHHHHTSTTTSEEEEEESSHHHHHHHHH
T ss_pred cCCceEEEeccccccHHHHHHHhhcccceEEEecCcHHHHHHHHH
Confidence 4679999999999999999999987 588998988 767776654
No 244
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=87.62 E-value=1 Score=37.67 Aligned_cols=54 Identities=13% Similarity=0.317 Sum_probs=46.5
Q ss_pred HHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 26 LPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 26 ~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
..++|...+++.|.+.|+.. +|+.+.|||+++|++ ..- +..=+..|...|++.-
T Consensus 16 v~kalaS~vRv~Il~lL~~k---~plNvneiAe~lgLp------qst-~s~~ik~Le~aGlirT 69 (308)
T COG4189 16 VLKALASKVRVAILQLLHRK---GPLNVNEIAEALGLP------QST-MSANIKVLEKAGLIRT 69 (308)
T ss_pred HHHHHHHHHHHHHHHHHHHh---CCCCHHHHHHHhCCc------hhh-hhhhHHHHHhcCceee
Confidence 45788899999999999986 699999999999996 334 7788999999999974
No 245
>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=87.61 E-value=1.1 Score=39.19 Aligned_cols=52 Identities=21% Similarity=0.215 Sum_probs=43.9
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+++.+. ......+||.=.|.|..+.+++++.|+.+.+.+|. |.+++.+++
T Consensus 10 ~Evl~~L~-~~~ggiyVD~TlG~GGHS~~iL~~l~~g~vigiD~D~~Al~~ak~ 62 (305)
T TIGR00006 10 DEVVEGLN-IKPDGIYIDCTLGFGGHSKAILEQLGTGRLIGIDRDPQAIAFAKE 62 (305)
T ss_pred HHHHHhcC-cCCCCEEEEeCCCChHHHHHHHHhCCCCEEEEEcCCHHHHHHHHH
Confidence 46666665 45567999999999999999999998889999998 888888765
No 246
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=87.52 E-value=0.93 Score=41.61 Aligned_cols=49 Identities=10% Similarity=-0.067 Sum_probs=37.3
Q ss_pred HhhcCCCCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256 185 LESYKGFEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~ 234 (244)
...++ .....+|+|+|+|.|..+..+++..+ .-+.+.+|. ++-++.+++
T Consensus 245 ~~~l~-~~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~~~~rl~~~~~ 295 (434)
T PRK14901 245 APLLD-PQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQE 295 (434)
T ss_pred HHHhC-CCCcCEEEEeCCCCchhHHHHHHHhCCCceEEEEcCCHHHHHHHHH
Confidence 33444 45568999999999999999999864 468899998 666666653
No 247
>PRK14903 16S rRNA methyltransferase B; Provisional
Probab=87.39 E-value=0.82 Score=41.98 Aligned_cols=44 Identities=16% Similarity=0.064 Sum_probs=35.8
Q ss_pred CCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.....+|+|+|+|.|..+..+++.. +.-+++.+|+ +.-++.+++
T Consensus 235 ~~~g~~VLD~cagpGgkt~~la~~~~~~g~V~a~Dis~~rl~~~~~ 280 (431)
T PRK14903 235 LEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEK 280 (431)
T ss_pred CCCCCEEEEeCCCccHHHHHHHHHcCCCCEEEEEECCHHHHHHHHH
Confidence 4556799999999999999999876 5678999998 676766653
No 248
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=87.35 E-value=0.86 Score=35.49 Aligned_cols=45 Identities=11% Similarity=0.216 Sum_probs=39.4
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
.+..|.+.|... +..|..+||+++|++ +.. +.+=++-|...|++.
T Consensus 10 ~D~~Il~~Lq~d---~R~s~~eiA~~lglS------~~t-V~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 10 LDRGILEALMEN---ARTPYAELAKQFGVS------PGT-IHVRVEKMKQAGIIT 54 (153)
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCee
Confidence 567788999885 689999999999997 455 889999999999997
No 249
>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=87.32 E-value=0.96 Score=39.59 Aligned_cols=53 Identities=26% Similarity=0.262 Sum_probs=40.8
Q ss_pred HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
...+++.+. ......+||.==|.|..+.++++++|+.+.+.+|. |.+++.+++
T Consensus 9 l~Evl~~L~-~~~~g~~vD~T~G~GGHS~aiL~~~~~~~li~~DrD~~a~~~a~~ 62 (310)
T PF01795_consen 9 LKEVLEALN-PKPGGIYVDCTFGGGGHSKAILEKLPNGRLIGIDRDPEALERAKE 62 (310)
T ss_dssp HHHHHHHHT---TT-EEEETT-TTSHHHHHHHHT-TT-EEEEEES-HHHHHHHHC
T ss_pred HHHHHHhhC-cCCCceEEeecCCcHHHHHHHHHhCCCCeEEEecCCHHHHHHHHH
Confidence 356677776 56678999999999999999999999999999999 999987765
No 250
>PRK10870 transcriptional repressor MprA; Provisional
Probab=87.14 E-value=0.72 Score=36.91 Aligned_cols=62 Identities=11% Similarity=0.090 Sum_probs=42.4
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF 107 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l 107 (244)
+.-.|...+ ++++|..|||+.++++ ... +.|++.-|...|++++.....+. ...+|+.+..+
T Consensus 60 iL~~L~~~~-~~~it~~eLa~~l~l~------~~t-vsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~ 124 (176)
T PRK10870 60 ALITLESQE-NHSIQPSELSCALGSS------RTN-ATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEF 124 (176)
T ss_pred HHHHHhcCC-CCCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHH
Confidence 455554321 2579999999999997 445 99999999999999974322222 34555555433
No 251
>KOG2361 consensus Predicted methyltransferase [General function prediction only]
Probab=87.06 E-value=0.82 Score=38.49 Aligned_cols=41 Identities=24% Similarity=0.448 Sum_probs=36.7
Q ss_pred cceEEEecCCccHHHHHHHHHCCC--CeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPH--IKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~--l~~~v~Dl-p~vi~~a~~ 234 (244)
..+|+.||||.|...--+++.+|+ ++....|- |..|+..++
T Consensus 72 ~~~ilEvGCGvGNtvfPll~~~~n~~l~v~acDfsp~Ai~~vk~ 115 (264)
T KOG2361|consen 72 AETILEVGCGVGNTVFPLLKTSPNNRLKVYACDFSPRAIELVKK 115 (264)
T ss_pred hhhheeeccCCCcccchhhhcCCCCCeEEEEcCCChHHHHHHHh
Confidence 348999999999999999999999 99999997 888888775
No 252
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=86.94 E-value=0.78 Score=36.21 Aligned_cols=46 Identities=13% Similarity=0.213 Sum_probs=40.0
Q ss_pred HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
.++..|..+|.+. +.+|..+||+++|++ +.. +.+=++-|...|++.
T Consensus 14 ~~D~~IL~~Lq~d---~R~s~~eiA~~lglS------~~t-v~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 14 RIDRNILNELQKD---GRISNVELSKRVGLS------PTP-CLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHhccC---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeE
Confidence 3677899999885 799999999999997 455 889999999999997
No 253
>COG4262 Predicted spermidine synthase with an N-terminal membrane domain [General function prediction only]
Probab=86.92 E-value=1 Score=40.33 Aligned_cols=41 Identities=32% Similarity=0.550 Sum_probs=35.0
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAP 233 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~ 233 (244)
.+.++++-+|||.|.-+.+++ +||+ -+.+..|| |.+|+.++
T Consensus 288 ~~a~~vLvlGGGDGLAlRell-kyP~~~qI~lVdLDP~miela~ 330 (508)
T COG4262 288 RGARSVLVLGGGDGLALRELL-KYPQVEQITLVDLDPRMIELAS 330 (508)
T ss_pred cccceEEEEcCCchHHHHHHH-hCCCcceEEEEecCHHHHHHhh
Confidence 457899999999999998876 5885 56788898 99999987
No 254
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=86.88 E-value=3.7 Score=32.27 Aligned_cols=76 Identities=17% Similarity=0.158 Sum_probs=53.9
Q ss_pred HhhhHHHHHHHHHHhcC-------hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeec
Q 041256 21 ASAIVLPAVMQAVVELD-------VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVD 93 (244)
Q Consensus 21 ~~g~~~~~~L~~a~~lg-------ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~ 93 (244)
.++.|...|+.++.+.+ |..++.-.+ .|+++++|+..++.+ | ... +..-||-|...|+++.....
T Consensus 64 Af~rW~vrCmAaag~~~ls~~e~l~lH~irhrd--R~K~laDic~~ln~e--D---th~-itYslrKL~k~gLit~t~~g 135 (199)
T COG5631 64 AFGRWQVRCMAAAGEFSLSGPENLLLHIIRHRD--RPKSLADICQMLNRE--D---THN-ITYSLRKLLKGGLITRTGSG 135 (199)
T ss_pred HHHHHHHHHHHHhcCCCCcchHHHHHHHHhhcC--chhhHHHHHHHhccc--c---chh-HHHHHHHHHhccceecCCCC
Confidence 55788888998887766 344554443 699999999999997 3 235 78889999999999942111
Q ss_pred CCceeecCccc
Q 041256 94 GQRLYSLAPVS 104 (244)
Q Consensus 94 ~~~~y~~t~~s 104 (244)
..-+|..|+.+
T Consensus 136 kevTy~vTa~G 146 (199)
T COG5631 136 KEVTYEVTALG 146 (199)
T ss_pred ceEEEEEecch
Confidence 12347776654
No 255
>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=86.80 E-value=1.2 Score=38.32 Aligned_cols=50 Identities=22% Similarity=0.348 Sum_probs=35.9
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCe-EEEccc-hHHhhhCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIK-GINYDL-PYVIKDAP 233 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dl-p~vi~~a~ 233 (244)
.+....|+| .+++|+|+|+|.|..+-++...+|++. .+.+|. +...+.++
T Consensus 24 El~~r~p~f-~P~~vLD~GsGpGta~wAa~~~~~~~~~~~~vd~s~~~~~l~~ 75 (274)
T PF09243_consen 24 ELRKRLPDF-RPRSVLDFGSGPGTALWAAREVWPSLKEYTCVDRSPEMLELAK 75 (274)
T ss_pred HHHHhCcCC-CCceEEEecCChHHHHHHHHHHhcCceeeeeecCCHHHHHHHH
Confidence 334344533 457999999999999999999999764 578887 55555443
No 256
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=86.71 E-value=0.51 Score=33.77 Aligned_cols=62 Identities=15% Similarity=0.287 Sum_probs=44.4
Q ss_pred hhhHHh-hcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256 38 VFEIIS-KAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV 108 (244)
Q Consensus 38 ifd~L~-~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~ 108 (244)
+||+|. ..+ +++...-|.-.++++ -.. ...+++.|+..|++..........|.+|+.+..|.
T Consensus 20 i~dIL~~~~~--~~~~~Tri~y~aNln------y~~-~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fl 82 (95)
T COG3432 20 IFDILKAISE--GGIGITRIIYGANLN------YKR-AQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFL 82 (95)
T ss_pred HHHHHHHhcC--CCCCceeeeeecCcC------HHH-HHHHHHHHHhCCCEEeccCCccceEEEChhHHHHH
Confidence 567776 222 688888899999986 456 89999999999966642111112699999887554
No 257
>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=86.57 E-value=1 Score=29.45 Aligned_cols=34 Identities=18% Similarity=0.220 Sum_probs=28.2
Q ss_pred CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
..+ |..+||+..+++ ..- +++.|+.|...|++..
T Consensus 22 ~~lps~~~la~~~~vs------r~t-vr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 22 DRLPSERELAERYGVS------RTT-VREALRRLEAEGLIER 56 (64)
T ss_dssp SBE--HHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEE
T ss_pred CEeCCHHHHHHHhccC------CcH-HHHHHHHHHHCCcEEE
Confidence 467 999999999996 345 9999999999999986
No 258
>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=86.52 E-value=1.1 Score=37.13 Aligned_cols=40 Identities=20% Similarity=0.300 Sum_probs=34.6
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA 232 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a 232 (244)
.....+|++.|||.|+.+..|+++ +.+++.+|+ |..|+.+
T Consensus 35 ~~~~~rvLvPgCG~g~D~~~La~~--G~~VvGvDls~~Ai~~~ 75 (218)
T PF05724_consen 35 LKPGGRVLVPGCGKGYDMLWLAEQ--GHDVVGVDLSPTAIEQA 75 (218)
T ss_dssp TSTSEEEEETTTTTSCHHHHHHHT--TEEEEEEES-HHHHHHH
T ss_pred CCCCCeEEEeCCCChHHHHHHHHC--CCeEEEEecCHHHHHHH
Confidence 455679999999999999999987 578999999 7788776
No 259
>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=86.50 E-value=1 Score=29.83 Aligned_cols=40 Identities=25% Similarity=0.321 Sum_probs=30.1
Q ss_pred HhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 42 ISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 42 L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
+.+.| -|-|+.|||+.+|+. . +.. +.+.|+.|...|++.+
T Consensus 19 ~~~~G--~~Pt~rEIa~~~g~~---S--~~t-v~~~L~~Le~kG~I~r 58 (65)
T PF01726_consen 19 IEENG--YPPTVREIAEALGLK---S--TST-VQRHLKALERKGYIRR 58 (65)
T ss_dssp HHHHS--S---HHHHHHHHTSS---S--HHH-HHHHHHHHHHTTSEEE
T ss_pred HHHcC--CCCCHHHHHHHhCCC---C--hHH-HHHHHHHHHHCcCccC
Confidence 34444 477999999999995 2 445 9999999999999995
No 260
>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=86.27 E-value=0.8 Score=25.87 Aligned_cols=31 Identities=16% Similarity=0.295 Sum_probs=24.2
Q ss_pred CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcc
Q 041256 50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNAL 87 (244)
Q Consensus 50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll 87 (244)
|+|-+|||..+|+. .+- +.|+|..|...|++
T Consensus 2 ~mtr~diA~~lG~t------~ET-VSR~l~~l~~~glI 32 (32)
T PF00325_consen 2 PMTRQDIADYLGLT------RET-VSRILKKLERQGLI 32 (32)
T ss_dssp E--HHHHHHHHTS-------HHH-HHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHhCCc------HHH-HHHHHHHHHHcCCC
Confidence 57889999999997 455 99999999988874
No 261
>PRK14904 16S rRNA methyltransferase B; Provisional
Probab=86.08 E-value=0.95 Score=41.68 Aligned_cols=44 Identities=11% Similarity=0.040 Sum_probs=34.5
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~ 234 (244)
.....+|+|+|||.|..+..+++..+ .-+++.+|+ +..++.+++
T Consensus 248 ~~~g~~VLDlgaG~G~kt~~la~~~~~~~~V~avD~s~~~l~~~~~ 293 (445)
T PRK14904 248 PQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRS 293 (445)
T ss_pred CCCCCEEEEECCCCCHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH
Confidence 34457999999999999998888764 457899998 777766654
No 262
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=85.99 E-value=2.2 Score=27.34 Aligned_cols=32 Identities=16% Similarity=0.166 Sum_probs=28.1
Q ss_pred CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 51 LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 51 ~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.|..+||+.++++ ... +.+.|..|...|+++.
T Consensus 26 ~~~~~la~~~~is------~~~-v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 26 PSERELAEELGVS------RTT-VREALRELEAEGLVER 57 (66)
T ss_pred CCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEe
Confidence 3599999999997 456 9999999999999984
No 263
>PRK13256 thiopurine S-methyltransferase; Reviewed
Probab=85.96 E-value=0.77 Score=38.37 Aligned_cols=39 Identities=18% Similarity=0.145 Sum_probs=33.1
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA 232 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a 232 (244)
....+|++.|||.|..+..|+++ +.+++.+|+ |..|+.+
T Consensus 42 ~~~~rvLvPgCGkg~D~~~LA~~--G~~V~GvDlS~~Ai~~~ 81 (226)
T PRK13256 42 NDSSVCLIPMCGCSIDMLFFLSK--GVKVIGIELSEKAVLSF 81 (226)
T ss_pred CCCCeEEEeCCCChHHHHHHHhC--CCcEEEEecCHHHHHHH
Confidence 34579999999999999999886 667999999 7777775
No 264
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=85.68 E-value=1.6 Score=37.00 Aligned_cols=63 Identities=16% Similarity=0.146 Sum_probs=47.3
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV 108 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~ 108 (244)
|..++-+|-.. |+.|+.|||+..|++ + .. ++.+|+-|...|++... ...+..|+.-+....+.
T Consensus 18 Ea~vY~aLl~~---g~~tA~eis~~sgvP----~--~k-vY~vl~sLe~kG~v~~~-~g~P~~y~av~p~~~i~ 80 (247)
T COG1378 18 EAKVYLALLCL---GEATAKEISEASGVP----R--PK-VYDVLRSLEKKGLVEVI-EGRPKKYRAVPPEELIE 80 (247)
T ss_pred HHHHHHHHHHh---CCccHHHHHHHcCCC----c--hh-HHHHHHHHHHCCCEEee-CCCCceEEeCCHHHHHH
Confidence 34456666665 699999999999995 3 35 99999999999999853 23467888877655443
No 265
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=85.68 E-value=1.1 Score=34.43 Aligned_cols=46 Identities=15% Similarity=0.331 Sum_probs=39.5
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
++..|.+.|.+. ++.+..+||+++|++ +.. +.+-++-|...|++..
T Consensus 9 ~D~~IL~~L~~d---~r~~~~eia~~lglS------~~~-v~~Ri~~L~~~GiI~~ 54 (154)
T COG1522 9 IDRRILRLLQED---ARISNAELAERVGLS------PST-VLRRIKRLEEEGVIKG 54 (154)
T ss_pred HHHHHHHHHHHh---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCceee
Confidence 466788889885 689999999999997 455 8999999999999983
No 266
>PRK06474 hypothetical protein; Provisional
Probab=85.59 E-value=1.3 Score=35.60 Aligned_cols=71 Identities=18% Similarity=0.302 Sum_probs=50.9
Q ss_pred HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCcccceeec--C---CceeecC
Q 041256 28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVD--G---QRLYSLA 101 (244)
Q Consensus 28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~--~---~~~y~~t 101 (244)
.+|.--.++.|++.|...+ ++.|+.+|++.+ +++ ..- +.|-|+.|...|++...... + ...|+.+
T Consensus 6 ~~La~p~R~~Il~~L~~~~--~~~ta~el~~~l~~is------~aT-vYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~ 76 (178)
T PRK06474 6 EILMHPVRMKICQVLMRNK--EGLTPLELVKILKDVP------QAT-LYRHLQTMVDSGILHVVKEKKVRSVSEKYYAIN 76 (178)
T ss_pred HhhCCHHHHHHHHHHHhCC--CCCCHHHHHHHhcCCC------HHH-HHHHHHHHHHCCCEEEeecccccCceeEEEEec
Confidence 4556667888999998753 359999999999 564 234 89999999999999964221 1 1247777
Q ss_pred cccccc
Q 041256 102 PVSAYF 107 (244)
Q Consensus 102 ~~s~~l 107 (244)
+.+..+
T Consensus 77 ~~~~~~ 82 (178)
T PRK06474 77 EEDAKI 82 (178)
T ss_pred cceeee
Confidence 765443
No 267
>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=85.40 E-value=1.4 Score=34.06 Aligned_cols=46 Identities=11% Similarity=0.192 Sum_probs=35.5
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA 101 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t 101 (244)
|++|.+|||.+.|++ .+. +.--|-++++.|-+.+....+.=+|..+
T Consensus 5 Ga~T~eELA~~FGvt------tRk-vaStLa~~ta~Grl~Rv~q~gkfRy~iP 50 (155)
T PF07789_consen 5 GAKTAEELAGKFGVT------TRK-VASTLAMVTATGRLIRVNQNGKFRYCIP 50 (155)
T ss_pred CcccHHHHHHHhCcc------hhh-hHHHHHHHHhcceeEEecCCCceEEeCC
Confidence 899999999999997 556 8889999999999886432222345553
No 268
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=85.21 E-value=2.1 Score=36.54 Aligned_cols=43 Identities=19% Similarity=0.475 Sum_probs=35.3
Q ss_pred HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEcc
Q 041256 181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYD 224 (244)
Q Consensus 181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D 224 (244)
...+++..+ ......|+.||.|.|.+...|+++...+.++=.|
T Consensus 19 ~~kIv~~a~-~~~~d~VlEIGpG~GaLT~~Ll~~~~~v~aiEiD 61 (259)
T COG0030 19 IDKIVEAAN-ISPGDNVLEIGPGLGALTEPLLERAARVTAIEID 61 (259)
T ss_pred HHHHHHhcC-CCCCCeEEEECCCCCHHHHHHHhhcCeEEEEEeC
Confidence 456777666 5557899999999999999999999887776666
No 269
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=85.00 E-value=1 Score=42.04 Aligned_cols=67 Identities=12% Similarity=0.182 Sum_probs=51.4
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccccCC
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNN 111 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~~~ 111 (244)
.+..+...|... ++.|..+||+.++++ +.. +.+.++-|.+.|+++...+ ....|.+|+.++.+....
T Consensus 7 ~e~~vL~~L~~~---~~~s~~eLA~~l~l~------~~t-Vt~~i~~Le~kGlV~~~~~-~~~~i~LTeeG~~~~~~g 73 (489)
T PRK04172 7 NEKKVLKALKEL---KEATLEELAEKLGLP------PEA-VMRAAEWLEEKGLVKVEER-VEEVYVLTEEGKKYAEEG 73 (489)
T ss_pred HHHHHHHHHHhC---CCCCHHHHHHHhCcC------HHH-HHHHHHHHHhCCCEEEEee-eEEEEEECHHHHHHHHhc
Confidence 344556667664 589999999999997 456 9999999999999996432 236799999998665544
No 270
>PF03141 Methyltransf_29: Putative S-adenosyl-L-methionine-dependent methyltransferase; InterPro: IPR004159 Members of this family of hypothetical plant proteins are putative methyltransferases. ; GO: 0008168 methyltransferase activity
Probab=84.90 E-value=0.83 Score=42.33 Aligned_cols=24 Identities=17% Similarity=0.336 Sum_probs=21.7
Q ss_pred CCcceEEEecCCccHHHHHHHHHC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKY 215 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~ 215 (244)
...++++|||||.|.++..++++.
T Consensus 116 g~iR~~LDvGcG~aSF~a~l~~r~ 139 (506)
T PF03141_consen 116 GGIRTALDVGCGVASFGAYLLERN 139 (506)
T ss_pred CceEEEEeccceeehhHHHHhhCC
Confidence 357999999999999999999985
No 271
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=84.62 E-value=1.5 Score=37.35 Aligned_cols=43 Identities=9% Similarity=0.033 Sum_probs=34.3
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~ 234 (244)
....+|+|+|+|.|..+..+++..++ -+++..|. +..++.+++
T Consensus 70 ~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~~~~~l~~~~~ 114 (264)
T TIGR00446 70 DPPERVLDMAAAPGGKTTQISALMKNEGAIVANEFSKSRTKVLIA 114 (264)
T ss_pred CCcCEEEEECCCchHHHHHHHHHcCCCCEEEEEcCCHHHHHHHHH
Confidence 45578999999999999999988754 57888998 666666553
No 272
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=84.56 E-value=0.98 Score=40.82 Aligned_cols=40 Identities=15% Similarity=0.013 Sum_probs=35.2
Q ss_pred ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+|+|+++|+|.+++.++.+.+-.+++..|. |..++.+++
T Consensus 59 ~~vLDl~aGsG~~~l~~a~~~~~~~V~a~Din~~Av~~a~~ 99 (382)
T PRK04338 59 ESVLDALSASGIRGIRYALETGVEKVTLNDINPDAVELIKK 99 (382)
T ss_pred CEEEECCCcccHHHHHHHHHCCCCEEEEEeCCHHHHHHHHH
Confidence 5899999999999999999888667899998 888888764
No 273
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=84.48 E-value=1.4 Score=32.78 Aligned_cols=40 Identities=8% Similarity=0.097 Sum_probs=33.6
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCce
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRL 97 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~ 97 (244)
.++|++|||+.+.++ ++. ++.+|+-|...|+++-. ++.|+
T Consensus 18 ~~vtl~elA~~l~cS------~Rn-~r~lLkkm~~~gWi~W~--pg~GR 57 (115)
T PF12793_consen 18 VEVTLDELAELLFCS------RRN-ARTLLKKMQEEGWITWQ--PGRGR 57 (115)
T ss_pred cceeHHHHHHHhCCC------HHH-HHHHHHHHHHCCCeeee--CCCCC
Confidence 578999999999998 567 99999999999999963 34454
No 274
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=84.34 E-value=1 Score=41.79 Aligned_cols=68 Identities=10% Similarity=0.161 Sum_probs=53.9
Q ss_pred HHhcChhhHHhhcCCCCC-CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccccCC
Q 041256 33 VVELDVFEIISKAGPGAK-LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNN 111 (244)
Q Consensus 33 a~~lgifd~L~~~~~~g~-~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~~~ 111 (244)
+++..|...|.+. ++ .+..+||+.+|++ .+. +.+.+..|.+.|+++...+ ....|.+|+.++.++..+
T Consensus 3 ~~e~~iL~~l~~~---~~~~~~~~la~~~g~~------~~~-v~~~~~~L~~kg~v~~~~~-~~~~~~LT~eG~~~l~~G 71 (492)
T PLN02853 3 MAEEALLGALSNN---EEISDSGQFAASHGLD------HNE-VVGVIKSLHGFRYVDAQDI-KRETWVLTEEGKKYAAEG 71 (492)
T ss_pred hHHHHHHHHHHhc---CCCCCHHHHHHHcCCC------HHH-HHHHHHHHHhCCCEEEEEE-EEEEEEECHHHHHHHHcC
Confidence 4567788888874 44 7999999999997 456 9999999999999986533 357899999998555544
No 275
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=84.26 E-value=0.97 Score=41.05 Aligned_cols=42 Identities=10% Similarity=-0.071 Sum_probs=32.8
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+.++|+|+|||+|.++...+.. ...+++.+|+ |..++.+++
T Consensus 219 ~~g~rVLDlfsgtG~~~l~aa~~-ga~~V~~VD~s~~al~~a~~ 261 (396)
T PRK15128 219 VENKRVLNCFSYTGGFAVSALMG-GCSQVVSVDTSQEALDIARQ 261 (396)
T ss_pred cCCCeEEEeccCCCHHHHHHHhC-CCCEEEEEECCHHHHHHHHH
Confidence 34589999999999998876643 3457899998 788877765
No 276
>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=84.25 E-value=1.4 Score=31.70 Aligned_cols=48 Identities=17% Similarity=0.281 Sum_probs=36.4
Q ss_pred HhcChhhHHhh-cCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 34 VELDVFEIISK-AGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 34 ~~lgifd~L~~-~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
+.-.|++.|.. ...+.++++.+|+++++++ +.. ++..|+.|+..|++-
T Consensus 48 ~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~------~~~-v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 48 LQDKVLNFIKQQPNSEEGVHVDEIAQQLGMS------ENE-VRKALDFLSNEGHIY 96 (102)
T ss_dssp HHHHHHHHHHC----TTTEEHHHHHHHSTS-------HHH-HHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHhcCCCCCcccHHHHHHHhCcC------HHH-HHHHHHHHHhCCeEe
Confidence 45557777776 2123579999999999996 456 999999999999886
No 277
>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=84.17 E-value=0.56 Score=31.65 Aligned_cols=36 Identities=17% Similarity=0.290 Sum_probs=30.4
Q ss_pred CCCCHHHHHHhC---CCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 49 AKLSVAEIVAQI---PLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 49 g~~t~~eLA~~~---~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
+.+++.++|+.+ +.. +. .++ ++-++.+|.++|++++
T Consensus 23 ~~i~l~~ia~~l~~~~~k--~~--~RR-lYDI~NVLealgli~K 61 (71)
T PF02319_consen 23 KSISLNEIADKLISENVK--TQ--RRR-LYDIINVLEALGLIEK 61 (71)
T ss_dssp TEEEHHHHHHHCHHHCCH--HH--CHH-HHHHHHHHHHCTSEEE
T ss_pred CcccHHHHHHHHcccccc--cc--cch-hhHHHHHHHHhCceee
Confidence 689999999999 872 11 456 9999999999999995
No 278
>PLN02476 O-methyltransferase
Probab=83.79 E-value=1.3 Score=38.22 Aligned_cols=44 Identities=11% Similarity=0.046 Sum_probs=36.5
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~ 234 (244)
..++++||+||.+.|..++.+++..| +-+.+-+|. |+..+.|++
T Consensus 116 ~~~ak~VLEIGT~tGySal~lA~al~~~G~V~TiE~d~e~~~~Ar~ 161 (278)
T PLN02476 116 ILGAERCIEVGVYTGYSSLAVALVLPESGCLVACERDSNSLEVAKR 161 (278)
T ss_pred hcCCCeEEEecCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence 45789999999999999999999876 567788888 666777754
No 279
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=83.43 E-value=1.8 Score=39.53 Aligned_cols=43 Identities=26% Similarity=0.235 Sum_probs=35.6
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA 101 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t 101 (244)
.|.|.++|++.++++ ++. ++++|+.|...|++.+ .+++.|.+.
T Consensus 309 ~~~t~~~La~~l~~~------~~~-v~~iL~~L~~agLI~~---~~~g~~~l~ 351 (412)
T PRK04214 309 KALDVDEIRRLEPMG------YDE-LGELLCELARIGLLRR---GERGQWVLA 351 (412)
T ss_pred CCCCHHHHHHHhCCC------HHH-HHHHHHHHHhCCCeEe---cCCCceEec
Confidence 689999999999996 567 9999999999999984 344556553
No 280
>KOG4589 consensus Cell division protein FtsJ [Cell cycle control, cell division, chromosome partitioning]
Probab=83.06 E-value=2 Score=34.87 Aligned_cols=45 Identities=16% Similarity=0.228 Sum_probs=35.1
Q ss_pred HhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccchHHh
Q 041256 185 LESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDLPYVI 229 (244)
Q Consensus 185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp~vi 229 (244)
-+.|..+....+|+|+|+-.|..+.-..++. |+-.+...||-++.
T Consensus 61 ndKy~~l~p~~~VlD~G~APGsWsQVavqr~~p~g~v~gVDllh~~ 106 (232)
T KOG4589|consen 61 NDKYRFLRPEDTVLDCGAAPGSWSQVAVQRVNPNGMVLGVDLLHIE 106 (232)
T ss_pred hhhccccCCCCEEEEccCCCChHHHHHHHhhCCCceEEEEeeeecc
Confidence 3445545667999999999999998877776 99888888985544
No 281
>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=83.00 E-value=4.2 Score=34.22 Aligned_cols=63 Identities=19% Similarity=0.272 Sum_probs=45.2
Q ss_pred HHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 16 YAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 16 ~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.+.+++.+.....=|.+.- .|++.|... +|-++..+||+++|++ ... +++-+|.|.+.|+++-
T Consensus 168 a~Vq~Ai~tLSySEleAv~--~IL~~L~~~--egrlse~eLAerlGVS------Rs~-ireAlrkLE~aGvIe~ 230 (251)
T TIGR02787 168 AAVQMAINTLSYSELEAVE--HIFEELDGN--EGLLVASKIADRVGIT------RSV-IVNALRKLESAGVIES 230 (251)
T ss_pred HHHHHHHHhccHhHHHHHH--HHHHHhccc--cccccHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEe
Confidence 4444544544444343322 478888762 2689999999999997 456 9999999999999984
No 282
>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=82.36 E-value=3.1 Score=28.61 Aligned_cols=47 Identities=6% Similarity=-0.024 Sum_probs=37.2
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC-CceeecCccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-QRLYSLAPVS 104 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~~~y~~t~~s 104 (244)
.|+...+||+.++.+ +.- ++-.|..|..+||++.. ++ .+.|..|..+
T Consensus 22 ~PVgSk~ia~~l~~s------~aT-IRN~M~~Le~lGlve~~--p~~s~GriPT~~a 69 (78)
T PF03444_consen 22 EPVGSKTIAEELGRS------PAT-IRNEMADLEELGLVESQ--PHPSGGRIPTDKA 69 (78)
T ss_pred CCcCHHHHHHHHCCC------hHH-HHHHHHHHHHCCCccCC--CCCCCCCCcCHHH
Confidence 699999999999997 445 99999999999999841 22 3557777665
No 283
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=82.14 E-value=1.3 Score=43.37 Aligned_cols=41 Identities=10% Similarity=-0.059 Sum_probs=34.1
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+.++|+|+|||+|.++..+++. ..-+++.+|+ +..++.+++
T Consensus 538 ~g~rVLDlf~gtG~~sl~aa~~-Ga~~V~~vD~s~~al~~a~~ 579 (702)
T PRK11783 538 KGKDFLNLFAYTGTASVHAALG-GAKSTTTVDMSNTYLEWAER 579 (702)
T ss_pred CCCeEEEcCCCCCHHHHHHHHC-CCCEEEEEeCCHHHHHHHHH
Confidence 4589999999999999999986 3336899998 888888775
No 284
>KOG1500 consensus Protein arginine N-methyltransferase CARM1 [Posttranslational modification, protein turnover, chaperones; Transcription]
Probab=81.62 E-value=2.2 Score=37.77 Aligned_cols=31 Identities=32% Similarity=0.502 Sum_probs=21.6
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHH
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISK 214 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 214 (244)
.+++.-.+|++ +.|||||+|+|.++.-.+++
T Consensus 168 Ail~N~sDF~~-kiVlDVGaGSGILS~FAaqA 198 (517)
T KOG1500|consen 168 AILENHSDFQD-KIVLDVGAGSGILSFFAAQA 198 (517)
T ss_pred HHHhcccccCC-cEEEEecCCccHHHHHHHHh
Confidence 44443322555 89999999999988765554
No 285
>PRK05638 threonine synthase; Validated
Probab=80.95 E-value=2.1 Score=39.43 Aligned_cols=58 Identities=17% Similarity=0.256 Sum_probs=42.0
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCC--CCCCCCcchhccHHHHHHHHhhCCcccceeecC-CceeecCccccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIP--LKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-QRLYSLAPVSAY 106 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~--~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~~~y~~t~~s~~ 106 (244)
|+..|.+ ++.+.-||++.++ ++ ... +.+.|+.|...|+++...+.+ .-.|++|+.+..
T Consensus 376 IL~~L~~----~~~~~~el~~~l~~~~s------~~~-v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~ 436 (442)
T PRK05638 376 ILKILSE----REMYGYEIWKALGKPLK------YQA-VYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRR 436 (442)
T ss_pred HHHHHhh----CCccHHHHHHHHcccCC------cch-HHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHH
Confidence 5555654 6899999999998 54 345 999999999999997421122 234888887753
No 286
>COG4122 Predicted O-methyltransferase [General function prediction only]
Probab=80.80 E-value=2 Score=35.77 Aligned_cols=44 Identities=11% Similarity=0.154 Sum_probs=38.9
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+++++++.||.+.|.-++.++..-| +-+.+-+|+ |+-++.|++
T Consensus 57 ~~~~k~iLEiGT~~GySal~mA~~l~~~g~l~tiE~~~e~~~~A~~ 102 (219)
T COG4122 57 LSGPKRILEIGTAIGYSALWMALALPDDGRLTTIERDEERAEIARE 102 (219)
T ss_pred hcCCceEEEeecccCHHHHHHHhhCCCCCeEEEEeCCHHHHHHHHH
Confidence 56889999999999999999999999 778888998 777777765
No 287
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=80.74 E-value=2.7 Score=35.59 Aligned_cols=43 Identities=14% Similarity=0.251 Sum_probs=37.4
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.|.+.|.+. +..++.|||+.+|++ +.- ++|-|+.|...|++.+
T Consensus 9 ~Il~~l~~~---~~~~~~ela~~l~vS------~~T-irRdL~~Le~~g~i~r 51 (251)
T PRK13509 9 ILLELLAQL---GFVTVEKVIERLGIS------PAT-ARRDINKLDESGKLKK 51 (251)
T ss_pred HHHHHHHHc---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence 477888875 689999999999997 445 9999999999999985
No 288
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=80.56 E-value=2.7 Score=30.44 Aligned_cols=65 Identities=17% Similarity=0.203 Sum_probs=44.5
Q ss_pred HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256 33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF 107 (244)
Q Consensus 33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l 107 (244)
-.+..+...|... ++.+..+||+.++++ ... +.++++-|...|++.+.....+. .+.+|+.+..+
T Consensus 22 ~~q~~~L~~l~~~---~~~~~~~la~~l~i~------~~~-vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~ 89 (126)
T COG1846 22 PPQYQVLLALYEA---GGITVKELAERLGLD------RST-VTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGREL 89 (126)
T ss_pred HHHHHHHHHHHHh---CCCcHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeeecCCccccceeeEEECccHHHH
Confidence 3455566677775 344449999999997 456 99999999999999964222122 35666665533
No 289
>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=80.42 E-value=2.2 Score=25.56 Aligned_cols=27 Identities=15% Similarity=0.409 Sum_probs=20.8
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCC
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLK 63 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~ 63 (244)
++..|.+.|.+. +..+.++||+.+|++
T Consensus 4 ~D~~Il~~Lq~d---~r~s~~~la~~lglS 30 (42)
T PF13404_consen 4 LDRKILRLLQED---GRRSYAELAEELGLS 30 (42)
T ss_dssp HHHHHHHHHHH----TTS-HHHHHHHHTS-
T ss_pred HHHHHHHHHHHc---CCccHHHHHHHHCcC
Confidence 456688889885 689999999999997
No 290
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=80.41 E-value=3.8 Score=33.13 Aligned_cols=44 Identities=16% Similarity=0.040 Sum_probs=35.9
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
.+.-.|... +++|..+||+.++++ ..- +.++++-|...|++.+.
T Consensus 49 ~iL~~L~~~---~~itq~eLa~~l~l~------~sT-vtr~l~rLE~kGlI~R~ 92 (185)
T PRK13777 49 HILWIAYHL---KGASISEIAKFGVMH------VST-AFNFSKKLEERGYLTFS 92 (185)
T ss_pred HHHHHHHhC---CCcCHHHHHHHHCCC------Hhh-HHHHHHHHHHCCCEEec
Confidence 455666664 589999999999986 345 89999999999999964
No 291
>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=80.23 E-value=3.8 Score=32.76 Aligned_cols=42 Identities=21% Similarity=0.290 Sum_probs=33.0
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAP 233 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~ 233 (244)
++...||-+|+|-=.....+...+++++.+=+|+|+|++.-+
T Consensus 77 ~~~~qvV~LGaGlDTr~~Rl~~~~~~~~~~evD~p~v~~~K~ 118 (183)
T PF04072_consen 77 PGARQVVNLGAGLDTRAYRLDNPAGGVRWFEVDLPEVIALKR 118 (183)
T ss_dssp TTESEEEEET-TT--HHHHHHHTTTTEEEEEEE-HHHHHHHH
T ss_pred CCCcEEEEcCCCCCchHHHhhccccceEEEEeCCHHHHHHHH
Confidence 345699999999999999999999999999999999987643
No 292
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=79.86 E-value=2.8 Score=29.83 Aligned_cols=45 Identities=16% Similarity=0.211 Sum_probs=38.7
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.+.|..+|.+. ||=.+.-||..++++ .+. +...++-|..+|++++
T Consensus 9 ~~~IL~hl~~~---~~Dy~k~ia~~l~~~------~~~-v~~~l~~Le~~GLler 53 (92)
T PF10007_consen 9 DLKILQHLKKA---GPDYAKSIARRLKIP------LEE-VREALEKLEEMGLLER 53 (92)
T ss_pred HHHHHHHHHHH---CCCcHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeEE
Confidence 45677888887 588999999999997 566 9999999999999996
No 293
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=79.71 E-value=4.4 Score=35.32 Aligned_cols=52 Identities=25% Similarity=0.206 Sum_probs=44.8
Q ss_pred HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCe-EEEccc-hHHhhhCCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIK-GINYDL-PYVIKDAPS 234 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dl-p~vi~~a~~ 234 (244)
..+++.+. .......||.==|.|..+.+|++++|++. .+.+|. |++++.|++
T Consensus 13 ~E~i~~L~-~~~~giyiD~TlG~GGHS~~iL~~l~~~~~li~~DrD~~Ai~~a~~ 66 (314)
T COG0275 13 NEVVELLA-PKPDGIYIDGTLGAGGHSRAILEKLPDLGRLIGIDRDPQAIAIAKE 66 (314)
T ss_pred HHHHHhcc-cCCCcEEEEecCCCcHhHHHHHHhCCCCCeEEEEcCCHHHHHHHHH
Confidence 45666666 55669999999999999999999999887 899998 999999986
No 294
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=79.58 E-value=2.8 Score=33.28 Aligned_cols=55 Identities=20% Similarity=0.301 Sum_probs=39.8
Q ss_pred HHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 32 AVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 32 ~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
+--+.-|++.|.+.+ +++|+++|.+.+.-. .|.....+++|.|+.|+..|++.+-
T Consensus 25 T~qR~~IL~~l~~~~--~hlSa~eI~~~L~~~--~~~is~aTVYRtL~~L~e~Glv~~~ 79 (169)
T PRK11639 25 TPQRLEVLRLMSLQP--GAISAYDLLDLLREA--EPQAKPPTVYRALDFLLEQGFVHKV 79 (169)
T ss_pred CHHHHHHHHHHHhcC--CCCCHHHHHHHHHhh--CCCCCcchHHHHHHHHHHCCCEEEE
Confidence 334566888888764 699999999988643 1110123399999999999999853
No 295
>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=79.18 E-value=2.4 Score=25.70 Aligned_cols=23 Identities=30% Similarity=0.400 Sum_probs=15.4
Q ss_pred CCCHHHHHHhCCCCCCCCcchhccHHHHHH
Q 041256 50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLR 79 (244)
Q Consensus 50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr 79 (244)
+.|+.+||+.+|++ ..- ++|+|+
T Consensus 21 G~si~~IA~~~gvs------r~T-vyR~l~ 43 (45)
T PF02796_consen 21 GMSIAEIAKQFGVS------RST-VYRYLN 43 (45)
T ss_dssp T--HHHHHHHTTS-------HHH-HHHHHC
T ss_pred CCCHHHHHHHHCcC------HHH-HHHHHh
Confidence 49999999999996 333 777764
No 296
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=79.16 E-value=2.6 Score=34.71 Aligned_cols=34 Identities=9% Similarity=0.238 Sum_probs=29.7
Q ss_pred hHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCC
Q 041256 24 IVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLK 63 (244)
Q Consensus 24 ~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~ 63 (244)
..+-.+|+.|.++|-||.=. ..+..|||+.+|++
T Consensus 158 drQ~~vL~~A~~~GYFd~PR------~~~l~dLA~~lGIS 191 (215)
T COG3413 158 DRQLEVLRLAYKMGYFDYPR------RVSLKDLAKELGIS 191 (215)
T ss_pred HHHHHHHHHHHHcCCCCCCc------cCCHHHHHHHhCCC
Confidence 35668999999999999763 58999999999998
No 297
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=78.80 E-value=2.4 Score=39.51 Aligned_cols=69 Identities=9% Similarity=0.184 Sum_probs=53.3
Q ss_pred HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccccCC
Q 041256 33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNN 111 (244)
Q Consensus 33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~~~ 111 (244)
..+..|...|.+.. +..+..+||+.+|++ .+. +.+.+..|.+.|+++.+.+. ...|.+|+.++.++.++
T Consensus 6 ~~e~~iL~~l~~~~--~~~~~~~la~~~~~~------~~~-v~~~~~~L~~kg~v~~~~~~-~~~~~LT~eG~~~~~~G 74 (494)
T PTZ00326 6 LEENTILSKLESEN--EIVNSLALAESLNID------HQK-VVGAIKSLESANYITTEMKK-SNTWTLTEEGEDYLKNG 74 (494)
T ss_pred HHHHHHHHHHHhcC--CCCCHHHHHHHcCCC------HHH-HHHHHHHHHhCCCEEEEEEE-EEEEEECHHHHHHHHcC
Confidence 34556777787622 478999999999997 456 99999999999999865433 57899999998555554
No 298
>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=78.59 E-value=4.4 Score=34.84 Aligned_cols=45 Identities=13% Similarity=0.160 Sum_probs=36.9
Q ss_pred CCCHHHHHHhCC--CCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256 50 KLSVAEIVAQIP--LKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS 104 (244)
Q Consensus 50 ~~t~~eLA~~~~--~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s 104 (244)
..++++||+.++ ++ ... ++.-|..|...|++++ .++|.|..|..+
T Consensus 137 ~~~~~~ia~~l~p~is------~~e-v~~sL~~L~~~glikk---~~~g~y~~t~~~ 183 (271)
T TIGR02147 137 ADDPEELAKRCFPKIS------AEQ-VKESLDLLERLGLIKK---NEDGFYKQTDKA 183 (271)
T ss_pred CCCHHHHHHHhCCCCC------HHH-HHHHHHHHHHCCCeeE---CCCCcEEeecce
Confidence 447899999998 54 445 8899999999999995 467889998764
No 299
>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=78.43 E-value=1.5 Score=41.19 Aligned_cols=41 Identities=20% Similarity=0.231 Sum_probs=31.8
Q ss_pred CcceEEEecCCccHHHHHHHHHCCC--------CeEEEccc-hHHhhhCC
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPH--------IKGINYDL-PYVIKDAP 233 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~--------l~~~v~Dl-p~vi~~a~ 233 (244)
...+|+|.|||+|.++.+++++.+. +....+|. |.+++.++
T Consensus 31 ~~~~ilDP~cGsG~fl~~~~~~~~~~~~~~~~~~~i~g~DId~~a~~~a~ 80 (524)
T TIGR02987 31 TKTKIIDPCCGDGRLIAALLKKNEEINYFKEVELNIYFADIDKTLLKRAK 80 (524)
T ss_pred cceEEEeCCCCccHHHHHHHHHHHhcCCcccceeeeeeechhHHHHHHHH
Confidence 4579999999999999999988763 45677887 66655543
No 300
>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=78.42 E-value=2.6 Score=27.55 Aligned_cols=42 Identities=24% Similarity=0.373 Sum_probs=33.1
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
|++.|-.. |+.|+.+|++.++++ ++. ++.-|-.|...|++..
T Consensus 18 V~~~Ll~~---G~ltl~~i~~~t~l~------~~~-Vk~~L~~LiQh~~v~y 59 (62)
T PF08221_consen 18 VGEVLLSR---GRLTLREIVRRTGLS------PKQ-VKKALVVLIQHNLVQY 59 (62)
T ss_dssp HHHHHHHC----SEEHHHHHHHHT--------HHH-HHHHHHHHHHTTSEEE
T ss_pred HHHHHHHc---CCcCHHHHHHHhCCC------HHH-HHHHHHHHHHcCCeee
Confidence 56677765 699999999999997 566 9999999999998874
No 301
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=78.06 E-value=2.7 Score=33.42 Aligned_cols=36 Identities=19% Similarity=0.310 Sum_probs=31.4
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccccee
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSF 91 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~ 91 (244)
+|+|+.||++++|.+ -.. +-.-|+-|...|++.+..
T Consensus 40 ~Pmtl~Ei~E~lg~S------ks~-vS~~lkkL~~~~lV~~~~ 75 (177)
T COG1510 40 KPLTLDEIAEALGMS------KSN-VSMGLKKLQDWNLVKKVF 75 (177)
T ss_pred CCccHHHHHHHHCCC------cch-HHHHHHHHHhcchHHhhh
Confidence 799999999999997 345 889999999999999643
No 302
>KOG3191 consensus Predicted N6-DNA-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=77.99 E-value=4.2 Score=32.88 Aligned_cols=40 Identities=18% Similarity=0.343 Sum_probs=32.1
Q ss_pred cceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~ 233 (244)
...+++||||+|..+..+.+.. |+.....-|+ |+.++...
T Consensus 44 ~~i~lEIG~GSGvvstfL~~~i~~~~~~latDiNp~A~~~Tl 85 (209)
T KOG3191|consen 44 PEICLEIGCGSGVVSTFLASVIGPQALYLATDINPEALEATL 85 (209)
T ss_pred ceeEEEecCCcchHHHHHHHhcCCCceEEEecCCHHHHHHHH
Confidence 6889999999999998888754 7777778888 77776643
No 303
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=77.55 E-value=4.4 Score=30.15 Aligned_cols=51 Identities=14% Similarity=0.187 Sum_probs=38.1
Q ss_pred hhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256 39 FEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA 105 (244)
Q Consensus 39 fd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~ 105 (244)
..+|.+. ||.+..+|++.++.+ . ..++|+. --.|+|++ .+-|.|.+|+.++
T Consensus 65 A~~L~~~---Gp~~~~~l~~~~~~~--------~-A~~IL~~-N~YGWFeR---v~rGvY~LT~~G~ 115 (118)
T PF09929_consen 65 AAALAEH---GPSRPADLRKATGVP--------K-ATSILRD-NHYGWFER---VERGVYALTPAGR 115 (118)
T ss_pred HHHHHHc---CCCCHHHHHHhcCCC--------h-HHHHHHh-Ccccceee---eccceEecCcchh
Confidence 3567765 799999999999984 2 4455543 34689995 4569999999875
No 304
>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=77.34 E-value=2.9 Score=28.42 Aligned_cols=48 Identities=8% Similarity=0.110 Sum_probs=39.1
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
++..+.+.++.... .+++..+|++.+|.| ++. +...++.|...|++.+
T Consensus 3 ~~~~~Le~I~rsR~-~Gi~q~~L~~~~~~D------~r~-i~~~~k~L~~~gLI~k 50 (75)
T PF04182_consen 3 IQYCLLERIARSRY-NGITQSDLSKLLGID------PRS-IFYRLKKLEKKGLIVK 50 (75)
T ss_pred hHHHHHHHHHhcCC-CCEehhHHHHHhCCC------chH-HHHHHHHHHHCCCEEE
Confidence 34556777777654 478999999999997 456 9999999999999995
No 305
>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=77.33 E-value=2.5 Score=28.25 Aligned_cols=34 Identities=18% Similarity=0.276 Sum_probs=30.5
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
-++|-++||..+|++ ... +.|+|+.|...|++..
T Consensus 27 ~~lt~~~iA~~~g~s------r~t-v~r~l~~l~~~g~I~~ 60 (76)
T PF13545_consen 27 LPLTQEEIADMLGVS------RET-VSRILKRLKDEGIIEV 60 (76)
T ss_dssp EESSHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEE
T ss_pred ecCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE
Confidence 378999999999997 456 9999999999999984
No 306
>PF13730 HTH_36: Helix-turn-helix domain
Probab=77.25 E-value=3.1 Score=26.01 Aligned_cols=29 Identities=10% Similarity=0.205 Sum_probs=25.7
Q ss_pred CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcc
Q 041256 52 SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNAL 87 (244)
Q Consensus 52 t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll 87 (244)
|.+.||+.+|++ .+- +.+.++.|...|++
T Consensus 27 S~~~la~~~g~s------~~T-v~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVS------RRT-VQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcC------HHH-HHHHHHHHHHCcCC
Confidence 899999999997 445 99999999999985
No 307
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=77.19 E-value=3.5 Score=34.98 Aligned_cols=44 Identities=18% Similarity=0.276 Sum_probs=37.6
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
..|.+.|.+. +.+++.|||+.++++ +.- ++|-|..|...|++.+
T Consensus 8 ~~Il~~l~~~---~~~~~~ela~~l~vS------~~T-iRRdL~~Le~~g~l~r 51 (252)
T PRK10906 8 DAIIELVKQQ---GYVSTEELVEHFSVS------PQT-IRRDLNDLAEQNKILR 51 (252)
T ss_pred HHHHHHHHHc---CCEeHHHHHHHhCCC------HHH-HHHHHHHHHHCCCEEE
Confidence 3467788775 689999999999997 444 9999999999999985
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=76.23 E-value=3.8 Score=32.50 Aligned_cols=43 Identities=16% Similarity=0.254 Sum_probs=36.7
Q ss_pred CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256 51 LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV 103 (244)
Q Consensus 51 ~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~ 103 (244)
.|..+||+.+|++ ..- +.|.+..|...+++.+ ...|.|..||.
T Consensus 76 ~t~~~ia~~l~iS------~~T-v~r~ik~L~e~~iI~k---~~~G~Y~iNP~ 118 (165)
T PF05732_consen 76 ATQKEIAEKLGIS------KPT-VSRAIKELEEKNIIKK---IRNGAYMINPN 118 (165)
T ss_pred eeHHHHHHHhCCC------HHH-HHHHHHHHHhCCcEEE---ccCCeEEECcH
Confidence 5899999999997 344 9999999999999995 34688999885
No 309
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=76.12 E-value=4.2 Score=34.51 Aligned_cols=44 Identities=20% Similarity=0.271 Sum_probs=38.4
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
..|.+.|.+. |.++++|||+.++++ +.- ++|=|+.|...|++.+
T Consensus 8 ~~Il~~l~~~---g~v~v~eLa~~~~VS------~~T-IRRDL~~Le~~g~l~R 51 (253)
T COG1349 8 QKILELLKEK---GKVSVEELAELFGVS------EMT-IRRDLNELEEQGLLLR 51 (253)
T ss_pred HHHHHHHHHc---CcEEHHHHHHHhCCC------HHH-HHHhHHHHHHCCcEEE
Confidence 3477888886 699999999999997 444 9999999999999995
No 310
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=76.10 E-value=5.6 Score=33.46 Aligned_cols=43 Identities=12% Similarity=0.238 Sum_probs=36.9
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.|.+.|.+. +..+.+|||+.++++ +.- ++|-|..|...|++.+
T Consensus 8 ~Il~~l~~~---~~~~~~eLa~~l~VS------~~T-iRRdL~~L~~~~~l~r 50 (240)
T PRK10411 8 AIVDLLLNH---TSLTTEALAEQLNVS------KET-IRRDLNELQTQGKILR 50 (240)
T ss_pred HHHHHHHHc---CCCcHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence 467788775 689999999999997 455 9999999999999984
No 311
>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=75.84 E-value=4.1 Score=32.55 Aligned_cols=51 Identities=20% Similarity=0.147 Sum_probs=36.2
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCe---------EEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIK---------GINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~---------~~v~Dl-p~vi~~a~~ 234 (244)
.++.... |.+...|+|-=||+|.++++.+...++.. .+..|. +..++.+++
T Consensus 19 ~ll~la~-~~~~~~vlDP~CGsGtiliEaa~~~~~~~~~~~~~~~~~~g~Di~~~~v~~a~~ 79 (179)
T PF01170_consen 19 ALLNLAG-WRPGDVVLDPFCGSGTILIEAALMGANIPPLNDINELKIIGSDIDPKAVRGARE 79 (179)
T ss_dssp HHHHHTT---TTS-EEETT-TTSHHHHHHHHHHTTTSTTTH-CH--EEEEESSHHHHHHHHH
T ss_pred HHHHHhC-CCCCCEEeecCCCCCHHHHHHHHHhhCcccccccccccEEecCCCHHHHHHHHH
Confidence 3344444 67778999999999999999888777776 788887 777777654
No 312
>PRK00215 LexA repressor; Validated
Probab=75.56 E-value=5.1 Score=32.61 Aligned_cols=35 Identities=17% Similarity=0.130 Sum_probs=30.7
Q ss_pred CCCCHHHHHHhCCC-CCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 49 AKLSVAEIVAQIPL-KDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 49 g~~t~~eLA~~~~~-~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
.+.|..|||+.+|+ + ..- +.|+|+.|...|++++.
T Consensus 22 ~~~s~~ela~~~~~~~------~~t-v~~~l~~L~~~g~i~~~ 57 (205)
T PRK00215 22 YPPSRREIADALGLRS------PSA-VHEHLKALERKGFIRRD 57 (205)
T ss_pred CCCCHHHHHHHhCCCC------hHH-HHHHHHHHHHCCCEEeC
Confidence 57899999999999 6 345 99999999999999863
No 313
>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=75.25 E-value=3.2 Score=28.49 Aligned_cols=23 Identities=13% Similarity=0.395 Sum_probs=16.6
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCC
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLK 63 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~ 63 (244)
++..|++. .|.|.++||.++|++
T Consensus 29 LLr~LA~G---~PVt~~~LA~a~g~~ 51 (77)
T PF12324_consen 29 LLRLLAKG---QPVTVEQLAAALGWP 51 (77)
T ss_dssp HHHHHTTT---S-B-HHHHHHHHT--
T ss_pred HHHHHHcC---CCcCHHHHHHHHCCC
Confidence 67788873 799999999999996
No 314
>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=74.91 E-value=4.1 Score=33.37 Aligned_cols=44 Identities=16% Similarity=0.097 Sum_probs=34.1
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.....+|+|.-||.|.++..+++..+..+++..|+ |..++..++
T Consensus 99 v~~~e~VlD~faGIG~f~l~~ak~~~~~~V~A~d~Np~a~~~L~~ 143 (200)
T PF02475_consen 99 VKPGEVVLDMFAGIGPFSLPIAKHGKAKRVYAVDLNPDAVEYLKE 143 (200)
T ss_dssp --TT-EEEETT-TTTTTHHHHHHHT-SSEEEEEES-HHHHHHHHH
T ss_pred CCcceEEEEccCCccHHHHHHhhhcCccEEEEecCCHHHHHHHHH
Confidence 34568999999999999999999888888999999 788776653
No 315
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=74.83 E-value=3.7 Score=34.88 Aligned_cols=44 Identities=18% Similarity=0.228 Sum_probs=38.0
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
..|.+.|.+. +.+++.|||+.++++ +.- ++|=|+.|...|++.+
T Consensus 8 ~~Il~~L~~~---~~v~v~eLa~~l~VS------~~T-IRRDL~~Le~~g~l~r 51 (256)
T PRK10434 8 AAILEYLQKQ---GKTSVEELAQYFDTT------GTT-IRKDLVILEHAGTVIR 51 (256)
T ss_pred HHHHHHHHHc---CCEEHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE
Confidence 4577888886 689999999999997 445 9999999999999985
No 316
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.36 E-value=4.6 Score=31.24 Aligned_cols=42 Identities=14% Similarity=0.292 Sum_probs=34.5
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNAL 87 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll 87 (244)
.-|+|+|-.. +.+|-++||+.+|++ ... ++++|..|...+++
T Consensus 4 ~~v~d~L~~~---~~~~dedLa~~l~i~------~n~-vRkiL~~L~ed~~~ 45 (147)
T smart00531 4 FLVLDALMRN---GCVTEEDLAELLGIK------QKQ-LRKILYLLYDEKLI 45 (147)
T ss_pred EeehHHHHhc---CCcCHHHHHHHhCCC------HHH-HHHHHHHHHhhhcc
Confidence 3478888775 689999999999997 456 99999999995544
No 317
>KOG3045 consensus Predicted RNA methylase involved in rRNA processing [RNA processing and modification]
Probab=74.25 E-value=6.7 Score=33.61 Aligned_cols=54 Identities=17% Similarity=0.262 Sum_probs=34.4
Q ss_pred hhhccCCchHHHHHHHHHHhc----chhhHHHHHhhcCCCCCcceEEEecCCccHHHH
Q 041256 156 YDYLGVDSRFNDVFNNGMLSH----TSIVMEKVLESYKGFEHVKKLVDVGGGLGITLN 209 (244)
Q Consensus 156 ~e~~~~~~~~~~~f~~aM~~~----~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~ 209 (244)
++.+.+||...+.|+++-+.. -......|++.+..-++...|-|+|||.+.++.
T Consensus 139 ~~lfkedp~afdlYH~gfr~QV~kWP~nPld~ii~~ik~r~~~~vIaD~GCGEakiA~ 196 (325)
T KOG3045|consen 139 FDLFKEDPTAFDLYHAGFRSQVKKWPENPLDVIIRKIKRRPKNIVIADFGCGEAKIAS 196 (325)
T ss_pred HHHHhcCcHHHHHHHHHHHHHHHhCCCChHHHHHHHHHhCcCceEEEecccchhhhhh
Confidence 334556777666666655442 222344566655434566889999999999886
No 318
>COG0293 FtsJ 23S rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=74.11 E-value=8.6 Score=31.62 Aligned_cols=52 Identities=21% Similarity=0.169 Sum_probs=38.4
Q ss_pred hcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccch
Q 041256 175 SHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDLP 226 (244)
Q Consensus 175 ~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp 226 (244)
+.+.+-...+.+.|..+++...|+|+|...|..+.-+.++-. .-+.+.+|+-
T Consensus 27 SRAa~KL~el~~k~~i~~~~~~ViDLGAAPGgWsQva~~~~~~~~~ivavDi~ 79 (205)
T COG0293 27 SRAAYKLLELNEKFKLFKPGMVVVDLGAAPGGWSQVAAKKLGAGGKIVAVDIL 79 (205)
T ss_pred chHHHHHHHHHHhcCeecCCCEEEEcCCCCCcHHHHHHHHhCCCCcEEEEECc
Confidence 333443456677776678889999999999999998777654 4567888863
No 319
>COG3963 Phospholipid N-methyltransferase [Lipid metabolism]
Probab=73.86 E-value=8.9 Score=30.66 Aligned_cols=33 Identities=21% Similarity=0.344 Sum_probs=27.4
Q ss_pred HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHH
Q 041256 181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISK 214 (244)
Q Consensus 181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 214 (244)
++......+ |++..-|+.+|.|+|.+..+++++
T Consensus 37 A~~M~s~I~-pesglpVlElGPGTGV~TkaIL~~ 69 (194)
T COG3963 37 ARKMASVID-PESGLPVLELGPGTGVITKAILSR 69 (194)
T ss_pred HHHHHhccC-cccCCeeEEEcCCccHhHHHHHhc
Confidence 445556667 888889999999999999999885
No 320
>KOG1661 consensus Protein-L-isoaspartate(D-aspartate) O-methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=73.82 E-value=2.2 Score=35.29 Aligned_cols=43 Identities=14% Similarity=0.139 Sum_probs=31.9
Q ss_pred CCcceEEEecCCccHHHHHHHHH--CCCCeEEEccc-hHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISK--YPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~--~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
...-+.||||+|+|.+...+..- -|....+..|+ |++++.+++
T Consensus 81 ~pG~s~LdvGsGSGYLt~~~~~mvg~~g~~~~GIEh~~eLVe~Sk~ 126 (237)
T KOG1661|consen 81 QPGASFLDVGSGSGYLTACFARMVGATGGNVHGIEHIPELVEYSKK 126 (237)
T ss_pred ccCcceeecCCCccHHHHHHHHHhcCCCccccchhhhHHHHHHHHH
Confidence 44578999999999988877643 34444466776 999988765
No 321
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=73.79 E-value=6.8 Score=29.30 Aligned_cols=77 Identities=14% Similarity=0.126 Sum_probs=53.2
Q ss_pred chhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCC-CCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 11 TNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIP-LKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 11 ~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~-~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.-..+...+++-+-|....|+... . |+.-..||-..++ ++ +.- |.+-|+.|...|++.+
T Consensus 10 ~c~~~~~l~~ig~kW~~lIl~~L~---------~----g~~RF~eL~r~i~~Is------~k~-Ls~~Lk~Le~~Glv~R 69 (120)
T COG1733 10 PCPVEEALEVIGGKWTLLILRDLF---------D----GPKRFNELRRSIGGIS------PKM-LSRRLKELEEDGLVER 69 (120)
T ss_pred CCCHHHHHHHHcCccHHHHHHHHh---------c----CCCcHHHHHHHccccC------HHH-HHHHHHHHHHCCCEEe
Confidence 345667777777777777665533 2 4788889998888 76 456 9999999999999996
Q ss_pred eeecC---CceeecCcccccc
Q 041256 90 SFVDG---QRLYSLAPVSAYF 107 (244)
Q Consensus 90 ~~~~~---~~~y~~t~~s~~l 107 (244)
..-.. .-.|++|+.++-|
T Consensus 70 ~~~~~~PprveY~LT~~G~~L 90 (120)
T COG1733 70 VVYPEEPPRVEYRLTEKGRDL 90 (120)
T ss_pred eecCCCCceeEEEEhhhHHHH
Confidence 31110 1247777765543
No 322
>PLN02589 caffeoyl-CoA O-methyltransferase
Probab=73.64 E-value=5.1 Score=33.96 Aligned_cols=44 Identities=16% Similarity=0.107 Sum_probs=35.8
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+++++|+||.+.|.-+..+++..| +-+.+-+|. |+..+.|++
T Consensus 77 ~~~ak~iLEiGT~~GySal~la~al~~~g~v~tiE~~~~~~~~Ar~ 122 (247)
T PLN02589 77 LINAKNTMEIGVYTGYSLLATALALPEDGKILAMDINRENYELGLP 122 (247)
T ss_pred HhCCCEEEEEeChhhHHHHHHHhhCCCCCEEEEEeCCHHHHHHHHH
Confidence 35678999999999999999998864 678888887 666666654
No 323
>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=73.62 E-value=2.7 Score=31.11 Aligned_cols=54 Identities=22% Similarity=0.320 Sum_probs=39.5
Q ss_pred HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
.-+.-|++.|.+.+ ++.|++||-+.+.-. ++.-...+++|-|+.|...|++.+.
T Consensus 8 ~~R~~Il~~l~~~~--~~~ta~ei~~~l~~~--~~~is~~TVYR~L~~L~e~Gli~~~ 61 (120)
T PF01475_consen 8 PQRLAILELLKESP--EHLTAEEIYDKLRKK--GPRISLATVYRTLDLLEEAGLIRKI 61 (120)
T ss_dssp HHHHHHHHHHHHHS--SSEEHHHHHHHHHHT--TTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHcCC--CCCCHHHHHHHhhhc--cCCcCHHHHHHHHHHHHHCCeEEEE
Confidence 34566888888875 699999999988633 1211112399999999999999864
No 324
>COG2384 Predicted SAM-dependent methyltransferase [General function prediction only]
Probab=73.40 E-value=3.8 Score=34.05 Aligned_cols=31 Identities=10% Similarity=0.278 Sum_probs=28.8
Q ss_pred ceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256 195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL 225 (244)
Q Consensus 195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 225 (244)
..+.||||-|+.+.+.+++.+|..+++.-|.
T Consensus 18 ~~iaDIGsDHAYLp~~Lv~~~~~~~~va~eV 48 (226)
T COG2384 18 ARIADIGSDHAYLPIYLVKNNPASTAVAGEV 48 (226)
T ss_pred CceeeccCchhHhHHHHHhcCCcceEEEeec
Confidence 4499999999999999999999999998886
No 325
>PRK09954 putative kinase; Provisional
Probab=73.31 E-value=6.3 Score=35.01 Aligned_cols=44 Identities=11% Similarity=0.229 Sum_probs=37.3
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
+..|...|.+. +.+|..|||+.++++ ... +.+.|+.|...|++.
T Consensus 5 ~~~il~~l~~~---~~~s~~~la~~l~~s------~~~-v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 5 EKEILAILRRN---PLIQQNEIADILQIS------RSR-VAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHHC---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCcC
Confidence 34577888875 689999999999997 455 999999999999986
No 326
>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=73.26 E-value=4.5 Score=28.89 Aligned_cols=40 Identities=15% Similarity=0.158 Sum_probs=31.3
Q ss_pred HHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHh
Q 041256 32 AVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLV 82 (244)
Q Consensus 32 ~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~ 82 (244)
.+.+.+|+..|-+ +++|-.|||+.+|++ ... +.|.=+.|-
T Consensus 41 l~~R~~i~~~Ll~----~~~tQrEIa~~lGiS------~at-IsR~sn~lk 80 (94)
T TIGR01321 41 LGDRIRIVNELLN----GNMSQREIASKLGVS------IAT-ITRGSNNLK 80 (94)
T ss_pred HHHHHHHHHHHHh----CCCCHHHHHHHhCCC------hhh-hhHHHhhcc
Confidence 4568999998877 689999999999997 344 666665553
No 327
>KOG2187 consensus tRNA uracil-5-methyltransferase and related tRNA-modifying enzymes [Translation, ribosomal structure and biogenesis]
Probab=73.06 E-value=3 Score=38.87 Aligned_cols=49 Identities=22% Similarity=0.226 Sum_probs=36.7
Q ss_pred CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC---CCCceee
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS---YPGTLFI 241 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~---~~~i~~~ 241 (244)
.+.-+.++||-||+|.++.++++..-. ++.+++ |+.++.|+. .+||+.-
T Consensus 381 l~~~k~llDv~CGTG~iglala~~~~~--ViGvEi~~~aV~dA~~nA~~NgisNa 433 (534)
T KOG2187|consen 381 LPADKTLLDVCCGTGTIGLALARGVKR--VIGVEISPDAVEDAEKNAQINGISNA 433 (534)
T ss_pred CCCCcEEEEEeecCCceehhhhccccc--eeeeecChhhcchhhhcchhcCccce
Confidence 455599999999999999999887655 554544 999999875 3555543
No 328
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=72.91 E-value=2.7 Score=35.29 Aligned_cols=85 Identities=15% Similarity=0.286 Sum_probs=56.0
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc-ccccCCCCCCCHHHHHHHh-cC
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA-YFVRNNQNGASLSPYMALC-LD 126 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~-~l~~~~~~~~~~~~~~~~~-~~ 126 (244)
.-....|||+++|+. ++. +-.-++-|+..|++.+ .+-++|..|..+. ++...- ..++.|.... ..
T Consensus 24 p~v~q~eIA~~lgiT------~Qa-VsehiK~Lv~eG~i~~---~gR~~Y~iTkkG~e~l~~~~---~dlr~f~~ev~~~ 90 (260)
T COG1497 24 PRVKQKEIAKKLGIT------LQA-VSEHIKELVKEGLIEK---EGRGEYEITKKGAEWLLEQL---SDLRRFSEEVELV 90 (260)
T ss_pred CCCCHHHHHHHcCCC------HHH-HHHHHHHHHhccceee---cCCeeEEEehhHHHHHHHHH---HHHHHHHHHHHHH
Confidence 358999999999998 778 9999999999999995 3457899999986 443322 2455555433 11
Q ss_pred hhhhhhccchHH-HHhcCCch
Q 041256 127 KVCLDGWFGLKK-QLLEGGIA 146 (244)
Q Consensus 127 ~~~~~~~~~l~~-~l~~g~~~ 146 (244)
-.+...|..+.+ -++.|.+.
T Consensus 91 l~~~~vw~AIA~edI~~Gd~V 111 (260)
T COG1497 91 LDYVMVWTAIAKEDIKEGDTV 111 (260)
T ss_pred HhhHHHHHHhhHhhhccCCEE
Confidence 112235554433 24445443
No 329
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=72.89 E-value=5.5 Score=31.92 Aligned_cols=45 Identities=16% Similarity=0.225 Sum_probs=37.6
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
.-|+++|.+. |-.|=++||..+|+. ..- ++|+|..|...|++...
T Consensus 21 ~~v~~~l~~k---ge~tDeela~~l~i~------~~~-vrriL~~L~e~~li~~~ 65 (176)
T COG1675 21 VLVVDALLEK---GELTDEELAELLGIK------KNE-VRRILYALYEDGLISYR 65 (176)
T ss_pred hHHHHHHHhc---CCcChHHHHHHhCcc------HHH-HHHHHHHHHhCCceEEE
Confidence 3477888874 469999999999996 445 99999999999999853
No 330
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=72.87 E-value=4.6 Score=34.58 Aligned_cols=45 Identities=9% Similarity=0.124 Sum_probs=38.5
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
...|.+.|.+. +..|+.|||+.++++ +.- ++|=|..|...|++.+
T Consensus 19 ~~~Il~~L~~~---~~vtv~eLa~~l~VS------~~T-IRRDL~~Le~~G~l~r 63 (269)
T PRK09802 19 REQIIQRLRQQ---GSVQVNDLSALYGVS------TVT-IRNDLAFLEKQGIAVR 63 (269)
T ss_pred HHHHHHHHHHc---CCEeHHHHHHHHCCC------HHH-HHHHHHHHHhCCCeEE
Confidence 44578888886 589999999999997 444 9999999999999995
No 331
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=72.87 E-value=2.8 Score=24.78 Aligned_cols=28 Identities=18% Similarity=0.357 Sum_probs=20.3
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhh
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVS 83 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~ 83 (244)
.+.|+++||..+|.+ +.. +.|+.+....
T Consensus 7 ~~~~l~~iA~~~g~S------~~~-f~r~Fk~~~g 34 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFS------PSY-FSRLFKKETG 34 (42)
T ss_dssp SS--HHHHHHHHTS-------HHH-HHHHHHHHTS
T ss_pred CCCCHHHHHHHHCCC------HHH-HHHHHHHHHC
Confidence 479999999999997 677 8888876543
No 332
>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=72.20 E-value=7.2 Score=31.55 Aligned_cols=35 Identities=17% Similarity=0.194 Sum_probs=29.5
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
-+.|..|||+.+|++ . +.- +.+.|+.|...|++..
T Consensus 24 ~~~~~~ela~~~~~~---s--~~t-v~~~l~~L~~~g~i~~ 58 (199)
T TIGR00498 24 YPPSIREIARAVGLR---S--PSA-AEEHLKALERKGYIER 58 (199)
T ss_pred CCCcHHHHHHHhCCC---C--hHH-HHHHHHHHHHCCCEec
Confidence 468999999999994 2 234 8999999999999995
No 333
>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=72.13 E-value=5 Score=34.24 Aligned_cols=29 Identities=21% Similarity=0.357 Sum_probs=25.1
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEE
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGI 221 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~ 221 (244)
+..+++|||.|.|.....++..|.++.+|
T Consensus 94 ~~~~lLDlGAGdG~VT~~l~~~f~~v~aT 122 (265)
T PF05219_consen 94 KDKSLLDLGAGDGEVTERLAPLFKEVYAT 122 (265)
T ss_pred cCCceEEecCCCcHHHHHHHhhcceEEee
Confidence 45889999999999999999999886554
No 334
>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=72.00 E-value=8.7 Score=32.79 Aligned_cols=36 Identities=14% Similarity=0.162 Sum_probs=31.5
Q ss_pred CCCcceEEEecCCccHHHHHHHHHC-----CCCeEEEccch
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKY-----PHIKGINYDLP 226 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~-----P~l~~~v~Dlp 226 (244)
+.....+|+.|+|.|.++..+.... +..+.+++|+-
T Consensus 16 l~~~~~~vEfGaGrg~LS~~v~~~~~~~~~~~~~~~lIDR~ 56 (259)
T PF05206_consen 16 LNPDSCFVEFGAGRGELSRWVAQALQEDKPSNSRFVLIDRA 56 (259)
T ss_pred CCCCCEEEEECCCchHHHHHHHHHhhhcccCCccEEEEecC
Confidence 5667899999999999999999998 56788999984
No 335
>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=71.11 E-value=9.4 Score=25.85 Aligned_cols=43 Identities=16% Similarity=0.161 Sum_probs=35.4
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
.|...|+. +..|.+||-+.+|++ ..- +-..|.-|...|++.+.
T Consensus 9 ~IL~~ls~----~c~TLeeL~ekTgi~------k~~-LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 9 KILIILSK----RCCTLEELEEKTGIS------KNT-LLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHHh----ccCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeeee
Confidence 35556666 589999999999996 345 88999999999999964
No 336
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=70.83 E-value=4.1 Score=32.86 Aligned_cols=44 Identities=9% Similarity=-0.023 Sum_probs=37.5
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
..|.+.|.+. +..++.+||+.++++ +.- ++|=|+.|...|++.+
T Consensus 10 ~~Il~~l~~~---~~~~~~~La~~~~vS------~~T-iRRDl~~L~~~g~~~r 53 (185)
T PRK04424 10 KALQELIEEN---PFITDEELAEKFGVS------IQT-IRLDRMELGIPELRER 53 (185)
T ss_pred HHHHHHHHHC---CCEEHHHHHHHHCcC------HHH-HHHHHHHHhcchHHHH
Confidence 3467788876 689999999999997 445 9999999999999984
No 337
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=70.29 E-value=5 Score=28.17 Aligned_cols=45 Identities=16% Similarity=0.209 Sum_probs=34.7
Q ss_pred hhhHHhhc-CCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 38 VFEIISKA-GPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 38 ifd~L~~~-~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.+|.|.+. +.-.-+|+..||+++++. -.. .++.||.|...|++..
T Consensus 28 t~dkl~kEV~~~K~ITps~lserlkI~------~Sl-Ar~~Lr~L~~kG~Ik~ 73 (86)
T PRK09334 28 LLKRVAKEVKKEKIVTPYTLASKYGIK------ISV-AKKVLRELEKRGVLVL 73 (86)
T ss_pred HHHHHHHHhccCcEEcHHHHHHHhcch------HHH-HHHHHHHHHHCCCEEE
Confidence 55555532 212458999999999996 567 8999999999999974
No 338
>KOG2651 consensus rRNA adenine N-6-methyltransferase [RNA processing and modification]
Probab=69.68 E-value=5 Score=36.15 Aligned_cols=44 Identities=20% Similarity=0.305 Sum_probs=30.7
Q ss_pred HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHH
Q 041256 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYV 228 (244)
Q Consensus 184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~v 228 (244)
++.....|.+..++||||.|.|+++.-+.-.| ++.+..+|-.++
T Consensus 144 lvSsi~~f~gi~~vvD~GaG~G~LSr~lSl~y-~lsV~aIegsq~ 187 (476)
T KOG2651|consen 144 LVSSISDFTGIDQVVDVGAGQGHLSRFLSLGY-GLSVKAIEGSQR 187 (476)
T ss_pred HHHHHHhhcCCCeeEEcCCCchHHHHHHhhcc-CceEEEeccchH
Confidence 33333337788999999999999987665555 566666665443
No 339
>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=69.43 E-value=5.6 Score=25.56 Aligned_cols=39 Identities=13% Similarity=0.290 Sum_probs=28.8
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHh
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLV 82 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~ 82 (244)
-++.+++.|-+. +.+|+.+||+.++++ ++- ++.-+..|-
T Consensus 6 rq~~Ll~~L~~~---~~~~~~ela~~l~~S------~rt-i~~~i~~L~ 44 (59)
T PF08280_consen 6 RQLKLLELLLKN---KWITLKELAKKLNIS------ERT-IKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHH---TSBBHHHHHHHCTS-------HHH-HHHHHHHHH
T ss_pred HHHHHHHHHHcC---CCCcHHHHHHHHCCC------HHH-HHHHHHHHH
Confidence 356678888774 699999999999997 444 666666664
No 340
>PRK11642 exoribonuclease R; Provisional
Probab=69.25 E-value=10 Score=37.77 Aligned_cols=57 Identities=21% Similarity=0.309 Sum_probs=42.0
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
|.+.|.+.+ +|++..+|++.++++ ....... |.+.|+.|...|.+.+ ...+.|.+..
T Consensus 24 Il~~l~~~~--~~~~~~~L~~~l~l~--~~~~~~~-l~~~L~~L~~~g~l~~---~~~~~~~~~~ 80 (813)
T PRK11642 24 ILEHLTKRE--KPASREELAVELNIE--GEEQLEA-LRRRLRAMERDGQLVF---TRRQCYALPE 80 (813)
T ss_pred HHHHHHhcC--CCCCHHHHHHHhCCC--ChHHHHH-HHHHHHHHHHCCCEEE---cCCceEecCC
Confidence 666776543 799999999999996 2111245 9999999999999984 3346676653
No 341
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=68.86 E-value=6.9 Score=32.06 Aligned_cols=44 Identities=11% Similarity=0.221 Sum_probs=34.8
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.|.+.+.+.. .+.|.+|||++++++ +.- +++.+.+|+..|++..
T Consensus 166 ~Vl~~~~~g~--~g~s~~eIa~~l~iS------~~T-v~~~~~~~~~~~~~~~ 209 (225)
T PRK10046 166 AVRKLFKEPG--VQHTAETVAQALTIS------RTT-ARRYLEYCASRHLIIA 209 (225)
T ss_pred HHHHHHHcCC--CCcCHHHHHHHhCcc------HHH-HHHHHHHHHhCCeEEE
Confidence 3566666511 268999999999997 444 9999999999999984
No 342
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=67.99 E-value=9.6 Score=33.35 Aligned_cols=56 Identities=18% Similarity=0.244 Sum_probs=40.7
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV 103 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~ 103 (244)
..|.+.|.+. .+.+..+||+++|++ ... +.+.++.|...|+..+. ..+ ..|.+.+.
T Consensus 7 ~~il~~L~~~---~~~s~~~LA~~lgvs------r~t-V~~~l~~L~~~G~~i~~-~~~-~Gy~L~~~ 62 (319)
T PRK11886 7 LQLLSLLADG---DFHSGEQLGEELGIS------RAA-IWKHIQTLEEWGLDIFS-VKG-KGYRLAEP 62 (319)
T ss_pred HHHHHHHHcC---CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCceEE-ecC-CeEEecCc
Confidence 3566677663 579999999999997 456 99999999999995432 122 35776544
No 343
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=67.76 E-value=9.1 Score=31.44 Aligned_cols=34 Identities=21% Similarity=0.255 Sum_probs=29.9
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
..++..+||+.+|++ -.- ++.-|+.|...|+++.
T Consensus 29 ~~L~e~eLae~lgVS------Rtp-VREAL~~L~~eGlv~~ 62 (224)
T PRK11534 29 EKLRMSLLTSRYALG------VGP-LREALSQLVAERLVTV 62 (224)
T ss_pred CcCCHHHHHHHHCCC------hHH-HHHHHHHHHHCCCEEE
Confidence 578999999999997 234 9999999999999985
No 344
>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=67.31 E-value=8.8 Score=31.16 Aligned_cols=34 Identities=21% Similarity=0.280 Sum_probs=30.0
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
..++-.+||+.+|++ ..- ++.-|+.|...|+++.
T Consensus 33 ~~L~e~~La~~lgVS------Rtp-VReAL~~L~~eGlv~~ 66 (212)
T TIGR03338 33 AKLNESDIAARLGVS------RGP-VREAFRALEEAGLVRN 66 (212)
T ss_pred CEecHHHHHHHhCCC------hHH-HHHHHHHHHHCCCEEE
Confidence 578999999999997 334 9999999999999985
No 345
>PRK01381 Trp operon repressor; Provisional
Probab=67.08 E-value=6.5 Score=28.37 Aligned_cols=38 Identities=21% Similarity=0.234 Sum_probs=29.8
Q ss_pred HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHH
Q 041256 33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLL 81 (244)
Q Consensus 33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L 81 (244)
+.+++|+..|.+ |.+|-.|||+.+|++ ... +.|.=+.|
T Consensus 42 ~~R~~I~~~L~~----g~~sQREIa~~lGvS------iaT-ITRgsn~L 79 (99)
T PRK01381 42 GTRVRIVEELLR----GELSQREIKQELGVG------IAT-ITRGSNSL 79 (99)
T ss_pred HHHHHHHHHHHc----CCcCHHHHHHHhCCc------eee-ehhhHHHh
Confidence 468899999987 789999999999997 233 55555554
No 346
>KOG2940 consensus Predicted methyltransferase [General function prediction only]
Probab=66.81 E-value=7.4 Score=32.76 Aligned_cols=48 Identities=21% Similarity=0.115 Sum_probs=33.9
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC--CCCceee
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS--YPGTLFI 241 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~--~~~i~~~ 241 (244)
..++..|||||.|++...+..+. =-+.|..|. -..++.++. .|+|+..
T Consensus 72 ~fp~a~diGcs~G~v~rhl~~e~-vekli~~DtS~~M~~s~~~~qdp~i~~~ 122 (325)
T KOG2940|consen 72 SFPTAFDIGCSLGAVKRHLRGEG-VEKLIMMDTSYDMIKSCRDAQDPSIETS 122 (325)
T ss_pred hCcceeecccchhhhhHHHHhcc-hhheeeeecchHHHHHhhccCCCceEEE
Confidence 56799999999999999998887 224566676 344555543 4676643
No 347
>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=66.74 E-value=7.1 Score=35.16 Aligned_cols=46 Identities=22% Similarity=0.443 Sum_probs=35.6
Q ss_pred HHHHHhhcCCCCCcceEEEecCCccH----HHHHHHHHC---CCCeEEEccchH
Q 041256 181 MEKVLESYKGFEHVKKLVDVGGGLGI----TLNMIISKY---PHIKGINYDLPY 227 (244)
Q Consensus 181 ~~~~~~~~~~~~~~~~vvDVGGG~G~----~~~~l~~~~---P~l~~~v~Dlp~ 227 (244)
.+.|++++. -.+..+|||+|-|.|. +..+|+++. |.+|.|.++.|.
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 357788887 4677999999999998 555555553 889999999854
No 348
>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=66.73 E-value=9 Score=33.18 Aligned_cols=42 Identities=17% Similarity=0.126 Sum_probs=31.7
Q ss_pred CCCcceEEEecCCccHHHHHHHHH-------CCCCeEEEccc-hHHhhhC
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISK-------YPHIKGINYDL-PYVIKDA 232 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~-------~P~l~~~v~Dl-p~vi~~a 232 (244)
.....+|+|-.||+|.++.++.+. .+..+...+|. |..+..+
T Consensus 44 ~~~~~~VlDPacGsG~fL~~~~~~i~~~~~~~~~~~i~G~ei~~~~~~la 93 (311)
T PF02384_consen 44 PKKGDSVLDPACGSGGFLVAAMEYIKEKRNKIKEINIYGIEIDPEAVALA 93 (311)
T ss_dssp T-TTEEEEETT-TTSHHHHHHHHHHHTCHHHHCCEEEEEEES-HHHHHHH
T ss_pred ccccceeechhhhHHHHHHHHHHhhcccccccccceeEeecCcHHHHHHH
Confidence 355578999999999999998874 57888888988 5555544
No 349
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=66.58 E-value=7.5 Score=32.22 Aligned_cols=41 Identities=22% Similarity=0.257 Sum_probs=34.7
Q ss_pred CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256 52 SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA 101 (244)
Q Consensus 52 t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t 101 (244)
|-.|||+..|++ +.++++-|+.|+..|++.+ +.|.|+|-..
T Consensus 26 sE~eLa~~~gVS-------R~TVR~Al~~L~~eGli~r--~~G~GTfV~~ 66 (233)
T TIGR02404 26 SEHELMDQYGAS-------RETVRKALNLLTEAGYIQK--IQGKGSIVLN 66 (233)
T ss_pred CHHHHHHHHCCC-------HHHHHHHHHHHHHCCCEEE--eCCceEEEec
Confidence 788999999996 4449999999999999997 4577888753
No 350
>KOG1709 consensus Guanidinoacetate methyltransferase and related proteins [Amino acid transport and metabolism]
Probab=66.29 E-value=15 Score=30.67 Aligned_cols=43 Identities=26% Similarity=0.286 Sum_probs=39.5
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS 234 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~ 234 (244)
.+..+|+.||=|-|.....+.++.|+.+.|+---|.|.+.-+.
T Consensus 100 tkggrvLnVGFGMgIidT~iQe~~p~~H~IiE~hp~V~krmr~ 142 (271)
T KOG1709|consen 100 TKGGRVLNVGFGMGIIDTFIQEAPPDEHWIIEAHPDVLKRMRD 142 (271)
T ss_pred hCCceEEEeccchHHHHHHHhhcCCcceEEEecCHHHHHHHHh
Confidence 6679999999999999999999999999999999999988764
No 351
>PLN02668 indole-3-acetate carboxyl methyltransferase
Probab=66.17 E-value=12 Score=33.92 Aligned_cols=34 Identities=24% Similarity=0.264 Sum_probs=24.4
Q ss_pred CcceEEEecCCccHHHH--------HHHHH-------CCCCeEEEccch
Q 041256 193 HVKKLVDVGGGLGITLN--------MIISK-------YPHIKGINYDLP 226 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~--------~l~~~-------~P~l~~~v~Dlp 226 (244)
+.-+|+|+|||+|..+. ++.++ -|++++..=|||
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 46789999999996543 23333 357788888988
No 352
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=66.13 E-value=7.6 Score=32.13 Aligned_cols=42 Identities=17% Similarity=0.270 Sum_probs=35.1
Q ss_pred CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 52 SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 52 t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
|-.|||+..|++ +.++++-|..|+..|++.. +.|.|+|-..+
T Consensus 34 sE~eLa~~~~VS-------R~TvR~Al~~L~~eGli~r--~~G~GtfV~~~ 75 (238)
T TIGR02325 34 AEMQLAERFGVN-------RHTVRRAIAALVERGLLRA--EQGRGTFVAAR 75 (238)
T ss_pred CHHHHHHHHCCC-------HHHHHHHHHHHHHCCCEEE--ecCCEEEECCC
Confidence 888999999996 4459999999999999997 45678887543
No 353
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=65.99 E-value=6.2 Score=24.02 Aligned_cols=39 Identities=10% Similarity=0.226 Sum_probs=21.5
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCC
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYN 85 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~g 85 (244)
++.+...+.+ +.|..+||+.+|++ ..- +.++++.-...|
T Consensus 7 R~~ii~l~~~-----G~s~~~ia~~lgvs------~~T-v~~w~kr~~~~G 45 (50)
T PF13384_consen 7 RAQIIRLLRE-----GWSIREIAKRLGVS------RST-VYRWIKRYREEG 45 (50)
T ss_dssp ---HHHHHHH-----T--HHHHHHHHTS-------HHH-HHHHHT------
T ss_pred HHHHHHHHHC-----CCCHHHHHHHHCcC------HHH-HHHHHHHccccc
Confidence 4455566655 68999999999997 455 899988766555
No 354
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=65.72 E-value=37 Score=23.77 Aligned_cols=65 Identities=9% Similarity=0.105 Sum_probs=40.0
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccccccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVR 109 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~ 109 (244)
|.+.+.+. -.+|.+|....+.-.++.+.-... +.=-+.+|...|+++. +..|.|++|+.++.+..
T Consensus 25 i~~~v~~~---~~ls~e~~~~~~~sg~~~~~~~~r-i~Wa~~~L~~aGli~~---~~rG~~~iT~~G~~~l~ 89 (92)
T PF14338_consen 25 IYERVAER---FGLSDEERNERLPSGQGYSRFKNR-IRWARSYLKKAGLIER---PKRGIWRITEKGRKALA 89 (92)
T ss_pred HHHHHHHH---hCCCHHHHHHHcccCCcchhHHHh-HHHHHHHHHHCCCccC---CCCCceEECHhHHHHHh
Confidence 55555554 356666666654311011121223 5556789999999984 45689999999975443
No 355
>PRK14999 histidine utilization repressor; Provisional
Probab=65.29 E-value=7.8 Score=32.33 Aligned_cols=41 Identities=34% Similarity=0.376 Sum_probs=34.5
Q ss_pred CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256 52 SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA 101 (244)
Q Consensus 52 t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t 101 (244)
|-.+||+..|++ +.++++-|+.|+..|++.+ +.|.|+|-..
T Consensus 38 sE~eLa~~~gVS-------R~TVR~Al~~L~~eGli~r--~~GkGTfV~~ 78 (241)
T PRK14999 38 SEAELVAQYGFS-------RMTINRALRELTDEGWLVR--LQGVGTFVAE 78 (241)
T ss_pred CHHHHHHHHCCC-------HHHHHHHHHHHHHCCCEEE--ecCcEEEECC
Confidence 889999999996 3449999999999999997 4567888654
No 356
>PF13518 HTH_28: Helix-turn-helix domain
Probab=65.00 E-value=10 Score=23.01 Aligned_cols=29 Identities=17% Similarity=0.133 Sum_probs=25.0
Q ss_pred CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCc
Q 041256 51 LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNA 86 (244)
Q Consensus 51 ~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gl 86 (244)
.|+.++|+..|++ ... +.+|++..-..|+
T Consensus 13 ~s~~~~a~~~gis------~~t-v~~w~~~y~~~G~ 41 (52)
T PF13518_consen 13 ESVREIAREFGIS------RST-VYRWIKRYREGGI 41 (52)
T ss_pred CCHHHHHHHHCCC------HhH-HHHHHHHHHhcCH
Confidence 4999999999997 455 9999999988775
No 357
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=64.53 E-value=11 Score=31.59 Aligned_cols=44 Identities=18% Similarity=0.204 Sum_probs=34.4
Q ss_pred CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256 49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA 101 (244)
Q Consensus 49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t 101 (244)
..+ +-.+||+.+|++ -.- ++.-|+.|.+.|+++. ..+.|.|-..
T Consensus 32 ~~LpsE~eLa~~lgVS------Rtp-VREAL~~L~~eGlv~~--~~~~G~~V~~ 76 (254)
T PRK09464 32 EKLPPERELAKQFDVS------RPS-LREAIQRLEAKGLLLR--RQGGGTFVQS 76 (254)
T ss_pred CcCCCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCEEE--ecCceeEEec
Confidence 456 889999999997 334 9999999999999986 3445665544
No 358
>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=63.95 E-value=9.8 Score=28.23 Aligned_cols=34 Identities=26% Similarity=0.303 Sum_probs=29.5
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.|.|++|||..++++ ... ++-++--|...|++.-
T Consensus 54 ~~~SVAEiAA~L~lP------lgV-vrVLvsDL~~~G~v~v 87 (114)
T PF05331_consen 54 RPLSVAEIAARLGLP------LGV-VRVLVSDLADAGLVRV 87 (114)
T ss_pred CCccHHHHHHhhCCC------chh-hhhhHHHHHhCCCEEE
Confidence 489999999999996 456 8889999999999983
No 359
>cd00006 PTS_IIA_man PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. IIA subunits receive phosphoryl groups from HPr and transfer them to IIB subunits, which in turn phosphorylate the substrate.
Probab=63.80 E-value=14 Score=27.40 Aligned_cols=52 Identities=21% Similarity=0.284 Sum_probs=35.7
Q ss_pred HHHhhcCCCCCcceEEEe-cCCccHHHHHHHHHCCCCeE-EEccchHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDV-GGGLGITLNMIISKYPHIKG-INYDLPYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDV-GGG~G~~~~~l~~~~P~l~~-~v~Dlp~vi~~a~~ 234 (244)
.+++.++.-++.-.++|+ ||..-..+..+...++++.. +..++|-+++.+..
T Consensus 49 ~~i~~~~~~~~viil~Dl~GGSp~n~~~~~~~~~~~~~visG~nlpmlle~~~~ 102 (122)
T cd00006 49 AALAELDSGEGVLILTDLFGGSPNNAAARLSMEHPPVEVIAGVNLPMLLEAARA 102 (122)
T ss_pred HHHHHhCCCCcEEEEEeCCCCCHHHHHHHHHhcCCCEEEEEccCHHHHHHHHHc
Confidence 334445523567889999 55554466667777788764 88999999987654
No 360
>KOG0820 consensus Ribosomal RNA adenine dimethylase [RNA processing and modification]
Probab=63.53 E-value=16 Score=31.55 Aligned_cols=49 Identities=12% Similarity=0.335 Sum_probs=36.3
Q ss_pred HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256 181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA 232 (244)
Q Consensus 181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a 232 (244)
...+++.-+ ....-+|+.||.|+|.+...++++--. ++.+++ |..++..
T Consensus 47 ~~~I~~ka~-~k~tD~VLEvGPGTGnLT~~lLe~~kk--VvA~E~Dprmvael 96 (315)
T KOG0820|consen 47 IDQIVEKAD-LKPTDVVLEVGPGTGNLTVKLLEAGKK--VVAVEIDPRMVAEL 96 (315)
T ss_pred HHHHHhccC-CCCCCEEEEeCCCCCHHHHHHHHhcCe--EEEEecCcHHHHHH
Confidence 356677666 777899999999999999999998554 555554 5544443
No 361
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=63.51 E-value=12 Score=31.43 Aligned_cols=44 Identities=23% Similarity=0.200 Sum_probs=33.9
Q ss_pred CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256 49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA 101 (244)
Q Consensus 49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t 101 (244)
..+ +-.+||+.+|++ -.- ++.-|+.|...|+++. ..+.|.|-..
T Consensus 24 ~~LpsE~eLae~~gVS------Rtp-VREAL~~Le~~GlV~~--~~~~G~~V~~ 68 (253)
T PRK10421 24 MKLPAERQLAMQLGVS------RNS-LREALAKLVSEGVLLS--RRGGGTFIRW 68 (253)
T ss_pred CcCCCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCEEE--eCCCeEEEec
Confidence 457 688999999997 334 9999999999999985 3445655443
No 362
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=63.30 E-value=12 Score=31.28 Aligned_cols=43 Identities=14% Similarity=0.227 Sum_probs=33.5
Q ss_pred CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256 49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL 100 (244)
Q Consensus 49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~ 100 (244)
..+ +-.+||+.+|++ -.- ++.-|+.|...|+++. ..+.|.|-.
T Consensus 29 ~~LPsE~eLa~~~gVS------Rtp-VREAL~~L~~eGlV~~--~~~~G~~V~ 72 (251)
T PRK09990 29 QALPSERRLCEKLGFS------RSA-LREGLTVLRGRGIIET--AQGRGSFVA 72 (251)
T ss_pred CcCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE--eCCCeeEEe
Confidence 568 789999999997 234 9999999999999986 334455443
No 363
>PRK09462 fur ferric uptake regulator; Provisional
Probab=62.93 E-value=10 Score=29.26 Aligned_cols=54 Identities=15% Similarity=0.210 Sum_probs=37.8
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
-+.-|++.|.... +++.|++||-+.+.-. +|.-...+++|.|+.|+..|++.+-
T Consensus 18 qR~~Il~~l~~~~-~~h~sa~eI~~~l~~~--~~~i~~aTVYR~L~~L~e~Gli~~~ 71 (148)
T PRK09462 18 PRLKILEVLQEPD-NHHVSAEDLYKRLIDM--GEEIGLATVYRVLNQFDDAGIVTRH 71 (148)
T ss_pred HHHHHHHHHHhCC-CCCCCHHHHHHHHHhh--CCCCCHHHHHHHHHHHHHCCCEEEE
Confidence 4556888887632 1589999999888543 1210112399999999999999853
No 364
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=62.73 E-value=9.5 Score=31.54 Aligned_cols=42 Identities=33% Similarity=0.378 Sum_probs=34.8
Q ss_pred CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 52 SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 52 t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
|-.+||+..|++ +.++++-|..|+..|++.+ +.|.|+|-..+
T Consensus 27 sE~eLa~~~~VS-------R~TVR~Al~~L~~eGli~r--~~G~GtfV~~~ 68 (230)
T TIGR02018 27 SEHELVAQYGCS-------RMTVNRALRELTDAGLLER--RQGVGTFVAEP 68 (230)
T ss_pred CHHHHHHHHCCC-------HHHHHHHHHHHHHCCCEEE--ecCCEEEEccC
Confidence 888999999996 4449999999999999997 45678886543
No 365
>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=62.57 E-value=9.3 Score=32.20 Aligned_cols=34 Identities=15% Similarity=0.286 Sum_probs=24.5
Q ss_pred CcceEEEecCCccHHHHHHHHHCCC--------CeEEEccch
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPH--------IKGINYDLP 226 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~--------l~~~v~Dlp 226 (244)
..-+||++|+|.|.++..+++..-. ++.++++..
T Consensus 18 ~~~~ivE~GaG~G~La~diL~~l~~~~p~~~~~~~y~ivE~S 59 (252)
T PF02636_consen 18 EPLRIVEIGAGRGTLARDILRYLRKFSPEVYKRLRYHIVEIS 59 (252)
T ss_dssp S-EEEEEES-TTSHHHHHHHHHHCCTTHHHHTTCEEEEE-TT
T ss_pred cCcEEEEECCCchHHHHHHHHHHHHhChhhhhcceEEEEcCC
Confidence 3589999999999999998885433 467777764
No 366
>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=62.57 E-value=8 Score=28.26 Aligned_cols=46 Identities=13% Similarity=0.253 Sum_probs=35.0
Q ss_pred ChhhHHhhcCC-CCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 37 DVFEIISKAGP-GAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 37 gifd~L~~~~~-~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
..||.|..+-+ -.-+|+..||+++++. -.. .+++||.|...|++..
T Consensus 45 ~~~~kl~kEV~~~K~ITp~~lserlkI~------~Sl-Ar~~Lr~L~~kG~Ik~ 91 (105)
T PF03297_consen 45 ETYDKLLKEVPKMKLITPSVLSERLKIN------GSL-ARKALRELESKGLIKP 91 (105)
T ss_dssp HHHHHHHHHCTTSSCECHHHHHHHHCCS------CHH-HHHHHHHHHHCCSSEE
T ss_pred HHHHHHHHHhccCcEeeHHHHHHhHhhH------HHH-HHHHHHHHHHCCCEEE
Confidence 35566654311 1348999999999996 567 8999999999999975
No 367
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=62.56 E-value=12 Score=31.39 Aligned_cols=43 Identities=19% Similarity=0.308 Sum_probs=33.4
Q ss_pred CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256 49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL 100 (244)
Q Consensus 49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~ 100 (244)
..+ |-.+||+.+|++ -.- ++.-|+.|.+.|+++. ..+.|.|-.
T Consensus 31 ~~LpsE~eLa~~~gVS------Rtp-VREAL~~L~~eGlV~~--~~~~G~~V~ 74 (257)
T PRK10225 31 ERLPPEREIAEMLDVT------RTV-VREALIMLEIKGLVEV--RRGAGIYVL 74 (257)
T ss_pred CcCcCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCEEE--ecCCEEEEe
Confidence 567 688999999997 234 9999999999999985 334455543
No 368
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=62.56 E-value=19 Score=30.33 Aligned_cols=32 Identities=22% Similarity=0.353 Sum_probs=25.4
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHH
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISK 214 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 214 (244)
..++.|+...+.+.++|||.++|.|.--++++
T Consensus 69 ~ale~F~l~~k~kv~LDiGsSTGGFTd~lLq~ 100 (245)
T COG1189 69 KALEEFELDVKGKVVLDIGSSTGGFTDVLLQR 100 (245)
T ss_pred HHHHhcCcCCCCCEEEEecCCCccHHHHHHHc
Confidence 45666662236799999999999999998887
No 369
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=62.48 E-value=12 Score=33.34 Aligned_cols=52 Identities=12% Similarity=0.102 Sum_probs=39.1
Q ss_pred CCCCHHHHHHh--CCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc-ccccc
Q 041256 49 AKLSVAEIVAQ--IPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS-AYFVR 109 (244)
Q Consensus 49 g~~t~~eLA~~--~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s-~~l~~ 109 (244)
+|.+..+||+. ++++ +.- +++-|..|...|++.+. .+...+-+|..+ +++++
T Consensus 24 ~pv~s~~l~~~~~l~~S------~aT-IR~dm~~Le~~G~l~~~--h~sagrIPT~kGYR~YVd 78 (339)
T PRK00082 24 EPVGSKTLSKRYGLGVS------SAT-IRNDMADLEELGLLEKP--HTSSGRIPTDKGYRYFVD 78 (339)
T ss_pred CCcCHHHHHHHhCCCCC------hHH-HHHHHHHHHhCCCcCCC--cCCCCCCcCHHHHHHHHH
Confidence 79999999977 8886 444 99999999999999963 223345677766 45553
No 370
>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]
Probab=62.47 E-value=16 Score=31.07 Aligned_cols=61 Identities=16% Similarity=0.232 Sum_probs=45.1
Q ss_pred HHhcchhh----HHHHHhhcCCCCCcceEEEecCCccHHHHHHHH-HCCCCeEEEccc-hHHhhhCCC
Q 041256 173 MLSHTSIV----MEKVLESYKGFEHVKKLVDVGGGLGITLNMIIS-KYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 173 M~~~~~~~----~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~-~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
|...++.. +.-|+.... .+...+|+|.|-|+|.++..|++ -.|.=+.+.+|. ++-.+.|.+
T Consensus 71 ~~R~tQiIyPKD~~~I~~~~g-i~pg~rVlEAGtGSG~lt~~La~~vg~~G~v~tyE~r~d~~k~A~~ 137 (256)
T COG2519 71 MKRRTQIIYPKDAGYIVARLG-ISPGSRVLEAGTGSGALTAYLARAVGPEGHVTTYEIREDFAKTARE 137 (256)
T ss_pred CcCCCceecCCCHHHHHHHcC-CCCCCEEEEcccCchHHHHHHHHhhCCCceEEEEEecHHHHHHHHH
Confidence 55555533 233555555 77889999999999999999997 678888888886 666666653
No 371
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=62.45 E-value=12 Score=34.60 Aligned_cols=53 Identities=23% Similarity=0.231 Sum_probs=36.0
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV 103 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~ 103 (244)
|-..|.. ||.|+.||++.+|++ -.. +-|.|+.| .|+|..-++...-+|++...
T Consensus 5 ~~~~L~~----g~~~~~eL~~~l~~s------q~~-~s~~L~~L--~~~V~~~~~gr~~~Y~l~~~ 57 (442)
T PRK09775 5 LTTLLLQ----GPLSAAELAARLGVS------QAT-LSRLLAAL--GDQVVRFGKARATRYALLRP 57 (442)
T ss_pred HHHHHhc----CCCCHHHHHHHhCCC------HHH-HHHHHHHh--hcceeEeccCceEEEEeccc
Confidence 4456665 799999999999997 234 88888888 78887432211234666544
No 372
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=62.34 E-value=13 Score=30.84 Aligned_cols=44 Identities=20% Similarity=0.144 Sum_probs=34.4
Q ss_pred CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256 49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA 101 (244)
Q Consensus 49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t 101 (244)
..+ |-.+||+.+|++ -.- ++.-|+.|...|+++. ..+.|.|-.+
T Consensus 29 ~~LPsE~eLae~~gVS------Rt~-VReAL~~L~~eGlv~~--~~g~G~~V~~ 73 (239)
T PRK04984 29 SILPAERELSELIGVT------RTT-LREVLQRLARDGWLTI--QHGKPTKVNN 73 (239)
T ss_pred CcCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE--eCCCeeEeCC
Confidence 467 788999999996 234 9999999999999996 3455666543
No 373
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=62.19 E-value=8.5 Score=29.72 Aligned_cols=53 Identities=26% Similarity=0.371 Sum_probs=38.7
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
-++.|++.|.+.+ ++.|+++|=..+.-. .|+..-.+++|.|+.|...|++.+-
T Consensus 22 qR~~vl~~L~~~~--~~~sAeei~~~l~~~--~p~islaTVYr~L~~l~e~Glv~~~ 74 (145)
T COG0735 22 QRLAVLELLLEAD--GHLSAEELYEELREE--GPGISLATVYRTLKLLEEAGLVHRL 74 (145)
T ss_pred HHHHHHHHHHhcC--CCCCHHHHHHHHHHh--CCCCCHhHHHHHHHHHHHCCCEEEE
Confidence 3566889998875 679999988877632 2221112399999999999999853
No 374
>PRK09273 hypothetical protein; Provisional
Probab=61.90 E-value=6.7 Score=32.31 Aligned_cols=43 Identities=14% Similarity=0.054 Sum_probs=33.7
Q ss_pred ceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCC
Q 041256 195 KKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237 (244)
Q Consensus 195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~ 237 (244)
....=++||+|.=..-.+.++|++++.+.--|.....++++.+
T Consensus 64 ~d~GIliCGTGiG~siAANK~pGIraalc~d~~sA~lar~hNn 106 (211)
T PRK09273 64 VDFVVTGCGTGQGAMLALNSFPGVVCGYCIDPTDAYLFAQINN 106 (211)
T ss_pred CCEEEEEcCcHHHHHHHHhcCCCeEEEEeCCHHHHHHHHHhcC
Confidence 4456688999999999999999999866555777777776543
No 375
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=61.87 E-value=13 Score=30.71 Aligned_cols=43 Identities=21% Similarity=0.150 Sum_probs=33.4
Q ss_pred CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256 49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL 100 (244)
Q Consensus 49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~ 100 (244)
..+ |-.+||+.+|++ -.- ++.-|+.|...|+++. ..+.|.|-.
T Consensus 28 ~~LpsE~~La~~lgVS------Rtp-VREAL~~Le~eGlV~~--~~~~G~~V~ 71 (235)
T TIGR02812 28 SILPAERELSELIGVT------RTT-LREVLQRLARDGWLTI--QHGKPTKVN 71 (235)
T ss_pred CcCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE--eCCCccEec
Confidence 567 789999999997 234 9999999999999986 334454443
No 376
>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=61.57 E-value=10 Score=25.14 Aligned_cols=60 Identities=18% Similarity=0.242 Sum_probs=38.5
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
.+-.|.+.|.+.| +.++..+|...|+. =| ... +.+.|.-|...|.+.++. ..+-.|+++.
T Consensus 5 ~ee~Il~~L~~~g---~~~a~~ia~~~~L~--~~--kk~-VN~~LY~L~k~g~v~k~~-~~PP~W~l~~ 64 (66)
T PF02295_consen 5 LEEKILDFLKELG---GSTATAIAKALGLS--VP--KKE-VNRVLYRLEKQGKVCKEG-GTPPKWSLTE 64 (66)
T ss_dssp HHHHHHHHHHHHT---SSEEEHHHHHHHHT--S---HHH-HHHHHHHHHHTTSEEEEC-SSSTEEEE-H
T ss_pred HHHHHHHHHHhcC---CccHHHHHHHhCcc--hh--HHH-HHHHHHHHHHCCCEeeCC-CCCCceEecc
Confidence 4556788888874 55555555555542 01 234 999999999999998642 2256677654
No 377
>COG1565 Uncharacterized conserved protein [Function unknown]
Probab=61.54 E-value=19 Score=32.23 Aligned_cols=57 Identities=19% Similarity=0.347 Sum_probs=38.5
Q ss_pred CchHHHHHHHHHHhcchhhHHHHHhhcCC--CCCcceEEEecCCccHHHHHHHHH----CC----CCeEEEccc
Q 041256 162 DSRFNDVFNNGMLSHTSIVMEKVLESYKG--FEHVKKLVDVGGGLGITLNMIISK----YP----HIKGINYDL 225 (244)
Q Consensus 162 ~~~~~~~f~~aM~~~~~~~~~~~~~~~~~--~~~~~~vvDVGGG~G~~~~~l~~~----~P----~l~~~v~Dl 225 (244)
-|+..+.|.+..+. .+++.+.. -.....+|.+|.|+|.++.-+++. +| .++..+++.
T Consensus 51 Apels~lFGella~-------~~~~~wq~~g~p~~~~lvEiGaG~G~l~~DiL~~l~~L~P~~~~~~~~~iiE~ 117 (370)
T COG1565 51 APELSQLFGELLAE-------QFLQLWQELGRPAPLKLVEIGAGRGTLASDILRTLRRLYPELYEALSYYIIEP 117 (370)
T ss_pred chhHHHHHHHHHHH-------HHHHHHHHhcCCCCceEEEeCCCcChHHHHHHHHHHHhCHHHHhcceEEEEec
Confidence 57888888877654 33333221 344578999999999988887764 45 355666665
No 378
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=61.46 E-value=11 Score=31.52 Aligned_cols=43 Identities=21% Similarity=0.361 Sum_probs=35.1
Q ss_pred CC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256 50 KL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA 101 (244)
Q Consensus 50 ~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t 101 (244)
.+ |-.+||+..|++ +.++++-|..|+..|++.+ +.+.|+|-..
T Consensus 28 ~LPsE~eL~~~~~VS-------R~TvR~Al~~L~~eGli~r--~~G~GtfV~~ 71 (240)
T PRK09764 28 ALPTESALQTEFGVS-------RVTVRQALRQLVEQQILES--IQGSGTYVKE 71 (240)
T ss_pred cCCCHHHHHHHHCCC-------HHHHHHHHHHHHHCCCEEE--ecCceeEEcc
Confidence 45 789999999996 4449999999999999997 4567887643
No 379
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=61.38 E-value=12 Score=27.14 Aligned_cols=43 Identities=21% Similarity=0.308 Sum_probs=31.6
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHh
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLV 82 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~ 82 (244)
.-.|++.+...+.+.=.|+-+||+..|.+ +.++. +.++|..|.
T Consensus 8 ~~~v~~vv~~IP~GkV~TYGdIA~laG~p----~~ARq-VG~il~~l~ 50 (103)
T COG3695 8 TQRVLDVVAAIPEGKVSTYGDIAKLAGLP----RAARQ-VGRILKHLP 50 (103)
T ss_pred HHHHHHHHHhCCCCceeeHHHHHHHhCCC----hhHHH-HHHHHhhCC
Confidence 34567777777655668999999999993 43566 888887763
No 380
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=61.11 E-value=12 Score=31.27 Aligned_cols=43 Identities=23% Similarity=0.298 Sum_probs=36.7
Q ss_pred CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 51 LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 51 ~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
-|-.|||+..|++ +.++++-|+.|+..|++.+ +.|.|+|-..+
T Consensus 32 PsE~eLa~~f~VS-------R~TvRkAL~~L~~eGli~r--~~G~GtfV~~~ 74 (236)
T COG2188 32 PSERELAEQFGVS-------RMTVRKALDELVEEGLIVR--RQGKGTFVASP 74 (236)
T ss_pred CCHHHHHHHHCCc-------HHHHHHHHHHHHHCCcEEE--EecCeeEEcCc
Confidence 3778999999996 4459999999999999997 45789988877
No 381
>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=60.92 E-value=11 Score=30.26 Aligned_cols=32 Identities=22% Similarity=0.209 Sum_probs=28.6
Q ss_pred CCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 51 LSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 51 ~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.|-++|++.+ |++ +.- ++|.++.|+..|++..
T Consensus 71 pSN~~La~r~~G~s------~~t-lrR~l~~LveaGLI~r 103 (177)
T PF03428_consen 71 PSNAQLAERLNGMS------ERT-LRRHLARLVEAGLIVR 103 (177)
T ss_pred cCHHHHHHHHcCCC------HHH-HHHHHHHHHHCCCeee
Confidence 4789999999 997 556 9999999999999986
No 382
>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=60.88 E-value=17 Score=27.44 Aligned_cols=46 Identities=15% Similarity=0.276 Sum_probs=34.0
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhC----CCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQI----PLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~----~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.|+.|...|=+. ++.|+.||.+.+ +++ ..- +..+|+-|...|++..
T Consensus 5 ~E~~VM~vlW~~---~~~t~~eI~~~l~~~~~~~------~tT-v~T~L~rL~~KG~v~~ 54 (130)
T TIGR02698 5 AEWEVMRVVWTL---GETTSRDIIRILAEKKDWS------DST-IKTLLGRLVDKGCLTT 54 (130)
T ss_pred HHHHHHHHHHcC---CCCCHHHHHHHHhhccCCc------HHH-HHHHHHHHHHCCceee
Confidence 355566666554 689999977765 443 233 8999999999999985
No 383
>PRK13239 alkylmercury lyase; Provisional
Probab=60.66 E-value=10 Score=31.18 Aligned_cols=38 Identities=18% Similarity=0.355 Sum_probs=27.8
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHh
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLV 82 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~ 82 (244)
-.-|+..|++ | .|.|.++||+.+|++ .+. +++.|+.|.
T Consensus 24 ~~~llr~la~-G--~pvt~~~lA~~~~~~------~~~-v~~~L~~l~ 61 (206)
T PRK13239 24 LVPLLRLLAK-G--RPVSVTTLAAALGWP------VEE-VEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHc-C--CCCCHHHHHHHhCCC------HHH-HHHHHHhCC
Confidence 3446777885 3 799999999999996 445 666666654
No 384
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=60.43 E-value=11 Score=31.33 Aligned_cols=43 Identities=16% Similarity=0.224 Sum_probs=35.2
Q ss_pred CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 51 LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 51 ~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
-|-.|||+..|++ +.++++-|..|+..|++.+ +.|.|+|-..+
T Consensus 34 PsE~eLa~~~~VS-------R~TvR~Al~~L~~eGli~r--~~G~GTfV~~~ 76 (241)
T PRK11402 34 PTENELCTQYNVS-------RITIRKAISDLVADGVLIR--WQGKGTFVQSQ 76 (241)
T ss_pred cCHHHHHHHHCCC-------HHHHHHHHHHHHHCCCEEE--ecCceeEECCC
Confidence 4788999999996 4559999999999999997 45678886443
No 385
>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=60.06 E-value=9.9 Score=28.45 Aligned_cols=46 Identities=11% Similarity=0.151 Sum_probs=37.7
Q ss_pred HHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccccCC
Q 041256 55 EIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNN 111 (244)
Q Consensus 55 eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~~~ 111 (244)
+||+.++.+ -+- |--++.++..+||++. .+|-..+|+.++.++..+
T Consensus 2 ~La~~l~~e------iDd-L~p~~eAaelLgf~~~----~~Gdi~LT~~G~~f~~a~ 47 (120)
T PF09821_consen 2 QLADELHLE------IDD-LLPIVEAAELLGFAEV----EEGDIRLTPLGRRFAEAD 47 (120)
T ss_pred chHHHhCCc------HHH-HHHHHHHHHHcCCeee----cCCcEEeccchHHHHHCC
Confidence 478888886 455 8899999999999994 357789999999887665
No 386
>COG5459 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=60.04 E-value=3.4 Score=36.89 Aligned_cols=39 Identities=23% Similarity=0.459 Sum_probs=30.6
Q ss_pred hhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeE-EEccc
Q 041256 186 ESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKG-INYDL 225 (244)
Q Consensus 186 ~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~-~v~Dl 225 (244)
...|+|+ +++|+|||-|.|.-+-++-.-+|+++. ++++.
T Consensus 107 ~~~~dfa-pqsiLDvG~GPgtgl~A~n~i~Pdl~sa~ile~ 146 (484)
T COG5459 107 KRVPDFA-PQSILDVGAGPGTGLWALNDIWPDLKSAVILEA 146 (484)
T ss_pred HhCCCcC-cchhhccCCCCchhhhhhcccCCCchhhhhhcc
Confidence 3344344 477999999999999999999999984 66665
No 387
>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=59.57 E-value=7.8 Score=26.34 Aligned_cols=33 Identities=15% Similarity=0.100 Sum_probs=27.7
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
...|.+|||+.+|++ +.. +...++.+...|.+.
T Consensus 31 eGlS~kEIAe~LGIS------~~T-Vk~~l~~~~~~~~~~ 63 (73)
T TIGR03879 31 AGKTASEIAEELGRT------EQT-VRNHLKGETKAGGLV 63 (73)
T ss_pred cCCCHHHHHHHHCcC------HHH-HHHHHhcCcccchHH
Confidence 378999999999997 556 889998888888765
No 388
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=59.57 E-value=15 Score=30.07 Aligned_cols=34 Identities=29% Similarity=0.344 Sum_probs=29.6
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
..++..+||+.+|++ -.- ++.-|+.|...|+++.
T Consensus 33 ~~L~e~~La~~lgVS------Rtp-VREAL~~L~~eGLV~~ 66 (221)
T PRK11414 33 ARLITKNLAEQLGMS------ITP-VREALLRLVSVNALSV 66 (221)
T ss_pred CccCHHHHHHHHCCC------chh-HHHHHHHHHHCCCEEe
Confidence 578899999999997 234 9999999999999985
No 389
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=59.36 E-value=15 Score=28.74 Aligned_cols=48 Identities=15% Similarity=0.176 Sum_probs=39.5
Q ss_pred HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
++......-.||+.|.+ +.+|..||.+..|-+ ..+-|.+|-..|+++.
T Consensus 12 ~~f~s~~~kkV~~~Ls~----~W~T~~El~e~~G~d----------~~~~L~~LkK~gLiE~ 59 (160)
T PF09824_consen 12 QTFNSEVYKKVYDELSK----GWMTEEELEEKYGKD----------VRESLLILKKGGLIES 59 (160)
T ss_pred HHhCCHHHHHHHHHHHh----ccCCHHHHHHHHCcC----------HHHHHHHHHHcCchhh
Confidence 44455566789999998 799999999999975 5678888999999983
No 390
>PRK12423 LexA repressor; Provisional
Probab=59.13 E-value=18 Score=29.51 Aligned_cols=34 Identities=15% Similarity=0.199 Sum_probs=28.5
Q ss_pred CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
+-|..|||+.+|+. . ... ++..|+.|...|+++.
T Consensus 25 ~Ps~~eia~~~g~~---s--~~~-v~~~l~~L~~~G~l~~ 58 (202)
T PRK12423 25 PPSLAEIAQAFGFA---S--RSV-ARKHVQALAEAGLIEV 58 (202)
T ss_pred CCCHHHHHHHhCCC---C--hHH-HHHHHHHHHHCCCEEe
Confidence 56999999999952 1 345 8899999999999995
No 391
>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=59.12 E-value=19 Score=26.93 Aligned_cols=48 Identities=4% Similarity=0.037 Sum_probs=38.9
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAY 106 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~ 106 (244)
-|.|.++||..++-+ .+- ++.-|.++...|+++. .+++.|..+....+
T Consensus 52 ipy~~e~LA~~~~~~------~~~-V~~AL~~f~k~glIe~---~ed~~i~i~~~~~~ 99 (121)
T PF09681_consen 52 IPYTAEMLALEFDRP------VDT-VRLALAVFQKLGLIEI---DEDGVIYIPNWEKH 99 (121)
T ss_pred CCCcHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE---ecCCeEEeecHHHH
Confidence 699999999999986 556 9999999999999995 44677777665443
No 392
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=58.88 E-value=25 Score=25.37 Aligned_cols=43 Identities=7% Similarity=0.162 Sum_probs=32.5
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
+-..+|.+.... +.+|+.++|+.+|+. +. ++.+.|...|++.+
T Consensus 11 Ka~~~d~~~~~~--~~~ti~~~AK~L~i~------~~----~l~~~Lr~~g~l~~ 53 (111)
T PF03374_consen 11 KAEFYDAFVDSD--GLYTIREAAKLLGIG------RN----KLFQWLREKGWLYR 53 (111)
T ss_pred hhHHHHHHHcCC--CCccHHHHHHHhCCC------HH----HHHHHHHhCCceEE
Confidence 345678887764 789999999999996 33 45666666899984
No 393
>TIGR00824 EIIA-man PTS system, mannose/fructose/sorbose family, IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIA components.
Probab=58.70 E-value=24 Score=25.98 Aligned_cols=53 Identities=26% Similarity=0.318 Sum_probs=36.5
Q ss_pred HHHhhcCCCCCcceEEEecCCccH-HHHHHHHHCCCCeE-EEccchHHhhhCCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGI-TLNMIISKYPHIKG-INYDLPYVIKDAPSY 235 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~-~~~~l~~~~P~l~~-~v~Dlp~vi~~a~~~ 235 (244)
.+++.++.=++.-.+.|+=||+=. .+..+..++|+++. ...+||-+++.+..+
T Consensus 50 ~~i~~~~~~~~vivltDl~GGSp~n~a~~~~~~~~~~~vIsG~NLpmlle~~~~~ 104 (116)
T TIGR00824 50 AALADLDTEEEVLFLVDIFGGSPYNAAARIIVDKPHMDVIAGVNLPLLLETLMAR 104 (116)
T ss_pred HHHHhcCCCCCEEEEEeCCCCCHHHHHHHHHhhcCCEEEEEecCHHHHHHHHHhc
Confidence 334444422456788999666655 55557778899985 889999999886543
No 394
>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=58.60 E-value=23 Score=29.98 Aligned_cols=65 Identities=14% Similarity=0.237 Sum_probs=40.2
Q ss_pred HHHHHHHhcchhh----HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCC
Q 041256 168 VFNNGMLSHTSIV----MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAP 233 (244)
Q Consensus 168 ~f~~aM~~~~~~~----~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~ 233 (244)
.|...|...++.. +.-|+...+ .....+||+.|-|+|.++..|++. .|+=+..-+|. ++-.+.|+
T Consensus 12 ~~~~~l~rrtQIiYpkD~~~I~~~l~-i~pG~~VlEaGtGSG~lt~~l~r~v~p~G~v~t~E~~~~~~~~A~ 82 (247)
T PF08704_consen 12 LWTLSLPRRTQIIYPKDISYILMRLD-IRPGSRVLEAGTGSGSLTHALARAVGPTGHVYTYEFREDRAEKAR 82 (247)
T ss_dssp HHHHTS-SSS----HHHHHHHHHHTT---TT-EEEEE--TTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHH
T ss_pred HHHHhccCCcceeeCchHHHHHHHcC-CCCCCEEEEecCCcHHHHHHHHHHhCCCeEEEccccCHHHHHHHH
Confidence 4555555555533 223555566 777899999999999999999975 58888888886 55555554
No 395
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=58.57 E-value=16 Score=29.47 Aligned_cols=48 Identities=21% Similarity=0.368 Sum_probs=39.0
Q ss_pred HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
-++..|.|.|...| ...|+-+||+++|++ ..- +.|-|.-|...|.|..
T Consensus 4 ~~~~~i~~~l~~~~--~~~~a~~i~k~l~i~------k~~-vNr~LY~L~~~~~v~~ 51 (183)
T PHA02701 4 DCASLILTLLSSSG--DKLPAKRIAKELGIS------KHE-ANRCLYRLLESDAVSC 51 (183)
T ss_pred hHHHHHHHHHHhcC--CCCcHHHHHHHhCcc------HHH-HHHHHHHHhhcCcEec
Confidence 35677899999874 269999999999996 345 8899999999998864
No 396
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=58.44 E-value=4.7 Score=25.34 Aligned_cols=29 Identities=14% Similarity=0.351 Sum_probs=20.9
Q ss_pred CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhh-CCccc
Q 041256 50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVS-YNALH 88 (244)
Q Consensus 50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~-~gll~ 88 (244)
++++.|||+.+|++ ...+++.|.. .|+..
T Consensus 3 ~i~V~elAk~l~v~----------~~~ii~~l~~~~Gi~~ 32 (54)
T PF04760_consen 3 KIRVSELAKELGVP----------SKEIIKKLFKELGIMV 32 (54)
T ss_dssp EE-TTHHHHHHSSS----------HHHHHHHH-HHHTS--
T ss_pred ceEHHHHHHHHCcC----------HHHHHHHHHHhCCcCc
Confidence 68999999999996 4568888844 88884
No 397
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=57.64 E-value=13 Score=30.93 Aligned_cols=42 Identities=19% Similarity=0.226 Sum_probs=34.7
Q ss_pred CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256 52 SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP 102 (244)
Q Consensus 52 t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~ 102 (244)
|-.+||+..|++ +.++++-|+.|+..|++.. +.|.|+|-..+
T Consensus 37 sE~eLa~~~~VS-------R~TVR~Al~~L~~eGli~r--~~G~GtfV~~~ 78 (241)
T PRK10079 37 AEQQLAARYEVN-------RHTLRRAIDQLVEKGWVQR--RQGVGVLVLMR 78 (241)
T ss_pred CHHHHHHHHCCC-------HHHHHHHHHHHHHCCCEEE--ecCCEEEEecC
Confidence 778999999996 4459999999999999997 45678886543
No 398
>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=57.60 E-value=18 Score=23.34 Aligned_cols=47 Identities=15% Similarity=0.134 Sum_probs=34.2
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA 105 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~ 105 (244)
.+++.+++.++.|.+ . ... ....+..+...|+++. . ++++++|+.+.
T Consensus 19 ~Gi~~~~~~~~~g~~---~--~~~-~~~~l~~l~~~Gll~~---~-~~~l~lT~~G~ 65 (66)
T PF06969_consen 19 EGIDLSEFEQRFGID---F--AEE-FQKELEELQEDGLLEI---D-GGRLRLTEKGR 65 (66)
T ss_dssp SEEEHHHHHHHTT-----T--HHH--HHHHHHHHHTTSEEE-----SSEEEE-TTTG
T ss_pred CCcCHHHHHHHHCcC---H--HHH-HHHHHHHHHHCCCEEE---e-CCEEEECcccC
Confidence 478999999999975 2 234 6788999999999994 3 58899998764
No 399
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=57.54 E-value=18 Score=23.92 Aligned_cols=41 Identities=17% Similarity=0.269 Sum_probs=28.3
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
|++.|.+. ++.|+.+|++.++++ ... +..-+--|+..|=+.
T Consensus 13 Vw~~L~~~---~~~s~~el~k~~~l~------~~~-~~~AiGWLarE~KI~ 53 (65)
T PF10771_consen 13 VWQLLNEN---GEWSVSELKKATGLS------DKE-VYLAIGWLARENKIE 53 (65)
T ss_dssp HHHHHCCS---SSEEHHHHHHHCT-S------CHH-HHHHHHHHHCTTSEE
T ss_pred HHHHHhhC---CCcCHHHHHHHhCcC------HHH-HHHHHHHHhccCcee
Confidence 77888875 799999999999996 223 555555555555433
No 400
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=57.44 E-value=17 Score=27.40 Aligned_cols=41 Identities=17% Similarity=0.274 Sum_probs=32.5
Q ss_pred CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256 51 LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL 100 (244)
Q Consensus 51 ~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~ 100 (244)
-|+.+||..++++ | .- +.|-.+.|...||+.. ..+.|.|-.
T Consensus 36 PSvRelA~~~~VN---p---nT-v~raY~eLE~eG~i~t--~rg~G~fV~ 76 (125)
T COG1725 36 PSVRELAKDLGVN---P---NT-VQRAYQELEREGIVET--KRGKGTFVT 76 (125)
T ss_pred CcHHHHHHHhCCC---H---HH-HHHHHHHHHHCCCEEE--ecCeeEEEc
Confidence 5999999999996 4 44 9999999999999985 234566544
No 401
>PHA02591 hypothetical protein; Provisional
Probab=57.37 E-value=17 Score=24.93 Aligned_cols=31 Identities=16% Similarity=0.285 Sum_probs=23.5
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHH
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLR 79 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr 79 (244)
+...|.+ .+.|.++||+.+|++ ... +++.|+
T Consensus 51 vA~eL~e----qGlSqeqIA~~LGVs------qet-VrKYL~ 81 (83)
T PHA02591 51 VTHELAR----KGFTVEKIASLLGVS------VRK-VRRYLE 81 (83)
T ss_pred HHHHHHH----cCCCHHHHHHHhCCC------HHH-HHHHHh
Confidence 5567777 479999999999997 344 666665
No 402
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=57.28 E-value=47 Score=21.65 Aligned_cols=36 Identities=19% Similarity=0.385 Sum_probs=25.6
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHh
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLV 82 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~ 82 (244)
.+.+.|.. +++++.+||..+|.. + +.. +.|..+...
T Consensus 41 ~a~~~l~~----~~~~~~~ia~~~g~~--s---~~~-f~r~Fk~~~ 76 (84)
T smart00342 41 RARRLLRD----TDLSVTEIALRVGFS--S---QSY-FSRAFKKLF 76 (84)
T ss_pred HHHHHHHc----CCCCHHHHHHHhCCC--C---hHH-HHHHHHHHH
Confidence 35666765 479999999999993 1 456 777766543
No 403
>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=57.04 E-value=13 Score=29.44 Aligned_cols=33 Identities=21% Similarity=0.197 Sum_probs=29.9
Q ss_pred CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
|+|-+|||..+|++ ... +.|+|+.|...|++..
T Consensus 143 ~~t~~~iA~~lG~t------ret-vsR~l~~l~~~g~I~~ 175 (193)
T TIGR03697 143 RLSHQAIAEAIGST------RVT-ITRLLGDLRKKKLISI 175 (193)
T ss_pred CCCHHHHHHHhCCc------HHH-HHHHHHHHHHCCCEEe
Confidence 68999999999997 456 9999999999999984
No 404
>PRK03837 transcriptional regulator NanR; Provisional
Probab=56.96 E-value=19 Score=29.74 Aligned_cols=42 Identities=21% Similarity=0.246 Sum_probs=33.0
Q ss_pred CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceee
Q 041256 49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYS 99 (244)
Q Consensus 49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~ 99 (244)
..+ +..+||+.+|++ -.- ++.-|+.|...|+++.. .+.|.|-
T Consensus 35 ~~Lp~E~~Lae~~gVS------Rt~-VREAL~~L~~eGlv~~~--~~~G~~V 77 (241)
T PRK03837 35 DQLPSERELMAFFGVG------RPA-VREALQALKRKGLVQIS--HGERARV 77 (241)
T ss_pred CCCCCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCEEEe--cCCceeE
Confidence 467 899999999997 334 99999999999999963 3445443
No 405
>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=56.93 E-value=26 Score=30.68 Aligned_cols=63 Identities=17% Similarity=0.311 Sum_probs=41.2
Q ss_pred HHHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCC--CCeEEEccchHHh
Q 041256 167 DVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYP--HIKGINYDLPYVI 229 (244)
Q Consensus 167 ~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P--~l~~~v~Dlp~vi 229 (244)
....+.+..........+.+.+..+.+..+|+=+|||.-.+..++.+.+| +-++++.|-|+..
T Consensus 246 ~~v~~~i~~~~~~l~~~i~~~~~~~~~~~~I~~vGGGA~ll~~~Ik~~~~~~~~~i~i~~~pqfA 310 (318)
T PF06406_consen 246 DDVSEVIEEAVEELINRILRELGDFSDIDRIFFVGGGAILLKDAIKEAFPVPNERIVIVDDPQFA 310 (318)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTS-S-SEEEEESTTHHHHHHHHHHHHT--GGGEE--SSGGGH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhccCCeEEEECCcHHHHHHHHHHhhCCCCCcEEECCCchhh
Confidence 34444444444333445555544467778899999999999999999987 5678888888754
No 406
>KOG1975 consensus mRNA cap methyltransferase [RNA processing and modification]
Probab=56.84 E-value=11 Score=33.34 Aligned_cols=58 Identities=26% Similarity=0.234 Sum_probs=40.0
Q ss_pred HHHHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHH-hhhCC
Q 041256 166 NDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYV-IKDAP 233 (244)
Q Consensus 166 ~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~v-i~~a~ 233 (244)
.++||.||.+ .++..|- +....++|+|||-|..++..-++--+ ..+..|..+| |++|+
T Consensus 99 lRnfNNwIKs-------~LI~~y~--~~~~~~~~LgCGKGGDLlKw~kAgI~-~~igiDIAevSI~qa~ 157 (389)
T KOG1975|consen 99 LRNFNNWIKS-------VLINLYT--KRGDDVLDLGCGKGGDLLKWDKAGIG-EYIGIDIAEVSINQAR 157 (389)
T ss_pred hhhhhHHHHH-------HHHHHHh--ccccccceeccCCcccHhHhhhhccc-ceEeeehhhccHHHHH
Confidence 5788888864 4566663 56678899999999998887765222 2477787544 55554
No 407
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=56.70 E-value=18 Score=30.28 Aligned_cols=43 Identities=12% Similarity=0.136 Sum_probs=33.1
Q ss_pred CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256 49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL 100 (244)
Q Consensus 49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~ 100 (244)
..+ |-.+||+.+|++ -.- ++.-|+.|...|+++. ..+.|.|-.
T Consensus 30 ~~LpsE~eLae~~gVS------Rtp-VREAL~~L~~eGlV~~--~~~~G~~V~ 73 (253)
T PRK11523 30 DKLPAERFIADEKNVS------RTV-VREAIIMLEVEGYVEV--RKGSGIHVV 73 (253)
T ss_pred CCCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE--ecCCeeEEe
Confidence 567 578999999996 234 9999999999999985 344455443
No 408
>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=56.68 E-value=10 Score=32.58 Aligned_cols=40 Identities=13% Similarity=0.171 Sum_probs=32.7
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHH-HHhhCCcccceeecCCcee
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLR-LLVSYNALHCSFVDGQRLY 98 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr-~L~~~gll~~~~~~~~~~y 98 (244)
++.+++++|+.+|.+ +.. +.++++ .|+..|++.. ++.|++
T Consensus 254 ~~~~~~~ia~~lg~~------~~~-~~~~~e~~Li~~~li~~---~~~g~~ 294 (305)
T TIGR00635 254 GPVGLKTLAAALGED------ADT-IEDVYEPYLLQIGFLQR---TPRGRI 294 (305)
T ss_pred CcccHHHHHHHhCCC------cch-HHHhhhHHHHHcCCccc---CCchhh
Confidence 689999999999997 455 899999 7999999983 444543
No 409
>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=56.60 E-value=16 Score=23.82 Aligned_cols=23 Identities=22% Similarity=0.524 Sum_probs=17.4
Q ss_pred hhHHhhcCCCCCCCHHHHHHhCCCC
Q 041256 39 FEIISKAGPGAKLSVAEIVAQIPLK 63 (244)
Q Consensus 39 fd~L~~~~~~g~~t~~eLA~~~~~~ 63 (244)
|+.-.+.+ |.++..+||+.+|++
T Consensus 13 ~e~y~~~~--g~i~lkdIA~~Lgvs 35 (60)
T PF10668_consen 13 FEIYKESN--GKIKLKDIAEKLGVS 35 (60)
T ss_pred HHHHHHhC--CCccHHHHHHHHCCC
Confidence 33444443 789999999999997
No 410
>PRK10736 hypothetical protein; Provisional
Probab=56.59 E-value=19 Score=32.54 Aligned_cols=50 Identities=8% Similarity=-0.035 Sum_probs=39.0
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL 100 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~ 100 (244)
.|++.|.. .|.++++|+.++|++ ... +..+|-.|.-.|++.+ ...+.|+.
T Consensus 312 ~v~~~l~~----~~~~iD~L~~~~~l~------~~~-v~~~L~~LEl~G~v~~---~~g~~~~~ 361 (374)
T PRK10736 312 ELLANVGD----EVTPVDVVAERAGQP------VPE-VVTQLLELELAGWIAA---VPGGYVRL 361 (374)
T ss_pred HHHHhcCC----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHhCCcEEE---cCCcEEEE
Confidence 46666654 589999999999997 556 8889999999999995 33456655
No 411
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=56.45 E-value=19 Score=29.70 Aligned_cols=35 Identities=20% Similarity=0.304 Sum_probs=30.9
Q ss_pred CCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 48 GAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 48 ~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
+..++..+||+.+|++ ..- ++.-|..|...|+++.
T Consensus 37 G~~l~e~~La~~~gvS------rtP-VReAL~rL~~eGlv~~ 71 (230)
T COG1802 37 GERLSEEELAEELGVS------RTP-VREALRRLEAEGLVEI 71 (230)
T ss_pred CCCccHHHHHHHhCCC------Ccc-HHHHHHHHHHCCCeEe
Confidence 3689999999999997 334 9999999999999996
No 412
>KOG2793 consensus Putative N2,N2-dimethylguanosine tRNA methyltransferase [RNA processing and modification]
Probab=56.38 E-value=14 Score=31.28 Aligned_cols=43 Identities=19% Similarity=0.380 Sum_probs=33.2
Q ss_pred CC-CcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256 191 FE-HVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS 234 (244)
Q Consensus 191 ~~-~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~ 234 (244)
|. ....+|.+|+|.| +...++......+++.-|+|.+++.-+.
T Consensus 83 ~~~~~~~vlELGsGtg-lvG~~aa~~~~~~v~ltD~~~~~~~L~~ 126 (248)
T KOG2793|consen 83 FKTKYINVLELGSGTG-LVGILAALLLGAEVVLTDLPKVVENLKF 126 (248)
T ss_pred ccccceeEEEecCCcc-HHHHHHHHHhcceeccCCchhhHHHHHH
Confidence 44 5678999999999 4445555667888999999988877653
No 413
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=56.05 E-value=18 Score=30.42 Aligned_cols=42 Identities=12% Similarity=0.183 Sum_probs=34.7
Q ss_pred CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256 51 LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA 101 (244)
Q Consensus 51 ~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t 101 (244)
-+-.|||+..|++ | .. ++.-|+.|.+.|+++. +.|.|.|-.+
T Consensus 35 P~EreLae~fgVS----R--~~-vREAl~~L~a~Glve~--r~G~Gt~V~~ 76 (241)
T COG2186 35 PSERELAERFGVS----R--TV-VREALKRLEAKGLVEI--RQGSGTFVRP 76 (241)
T ss_pred CCHHHHHHHHCCC----c--HH-HHHHHHHHHHCCCeee--cCCCceEecC
Confidence 3678999999996 2 34 9999999999999996 4677888865
No 414
>PF12692 Methyltransf_17: S-adenosyl-L-methionine methyltransferase; PDB: 3IHT_B.
Probab=56.02 E-value=54 Score=25.66 Aligned_cols=57 Identities=18% Similarity=0.260 Sum_probs=35.8
Q ss_pred HHHHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256 166 NDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL 225 (244)
Q Consensus 166 ~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 225 (244)
...|-+-|.+..... ........+. ..-|+++|=|+|-.=-.+.+.+|+-+..|||+
T Consensus 4 LDsfi~RmtaQR~~L-~~a~~~v~~~--~G~VlElGLGNGRTydHLRe~~p~R~I~vfDR 60 (160)
T PF12692_consen 4 LDSFIRRMTAQRDCL-NWAAAQVAGL--PGPVLELGLGNGRTYDHLREIFPDRRIYVFDR 60 (160)
T ss_dssp HHHHHHHHHHHHHHH-HHHHHHTTT----S-EEEE--TTSHHHHHHHHH--SS-EEEEES
T ss_pred HHHHHHHHHHHHHHH-HHHHHHhcCC--CCceEEeccCCCccHHHHHHhCCCCeEEEEee
Confidence 456767776644432 2334444422 26899999999999999999999999999997
No 415
>PF07091 FmrO: Ribosomal RNA methyltransferase (FmrO); PDB: 3LCU_A 3LCV_B 3FRH_A 3FRI_A 3B89_A 3FZG_A.
Probab=55.63 E-value=37 Score=28.83 Aligned_cols=39 Identities=21% Similarity=0.301 Sum_probs=29.3
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhh
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKD 231 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~ 231 (244)
.+.+|+|||||.-=++.=.....|+.+.+..|+ ...++.
T Consensus 105 ~p~sVlDigCGlNPlalp~~~~~~~a~Y~a~DID~~~ve~ 144 (251)
T PF07091_consen 105 PPDSVLDIGCGLNPLALPWMPEAPGATYIAYDIDSQLVEF 144 (251)
T ss_dssp --SEEEEET-TTCHHHHHTTTSSTT-EEEEEESBHHHHHH
T ss_pred CCchhhhhhccCCceehhhcccCCCcEEEEEeCCHHHHHH
Confidence 479999999999999988888999999999998 444433
No 416
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=55.42 E-value=15 Score=35.56 Aligned_cols=48 Identities=10% Similarity=0.173 Sum_probs=38.1
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceee-cCCceeecCcc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFV-DGQRLYSLAPV 103 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~-~~~~~y~~t~~ 103 (244)
..-|.++||+.+|++ +.. ++|-|......|++.+++- .+++.|+.++.
T Consensus 615 ~twt~eelse~l~ip------~~~-lrrrL~fWi~~GvL~e~~~~s~tgt~T~iEs 663 (765)
T KOG2165|consen 615 NTWTLEELSESLGIP------VPA-LRRRLSFWIQKGVLREEPIISDTGTLTVIES 663 (765)
T ss_pred ccccHHHHHHHhCCC------HHH-HHHHHHHHHHcCeeecCCCCCCCceeeeccc
Confidence 478999999999996 567 9999999999999995210 01477887774
No 417
>PF11312 DUF3115: Protein of unknown function (DUF3115); InterPro: IPR021463 This eukaryotic family of proteins has no known function.
Probab=55.24 E-value=16 Score=32.02 Aligned_cols=39 Identities=21% Similarity=0.419 Sum_probs=27.8
Q ss_pred cceEEEecCCccHHHHHHHHHC--------------------CCCeEEEccc---hHHhhhC
Q 041256 194 VKKLVDVGGGLGITLNMIISKY--------------------PHIKGINYDL---PYVIKDA 232 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~--------------------P~l~~~v~Dl---p~vi~~a 232 (244)
..+||-||||.|.=..+++..+ |.+..+++|. ..|+...
T Consensus 87 ~~~VlCIGGGAGAElVAlAa~~~~~~~~~~s~~~~~~~~~~~~~l~itlvDiAdWs~VV~~L 148 (315)
T PF11312_consen 87 SLRVLCIGGGAGAELVALAAAFRTRSSEFLSKSPSGVSLSSPPSLSITLVDIADWSSVVDRL 148 (315)
T ss_pred CceEEEECCChHHHHHHHHHHHhhcccccCCcccccccccCCCcceEEEEEecChHHHHHHH
Confidence 4799999999998666665554 3367788876 4666553
No 418
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=55.12 E-value=22 Score=34.81 Aligned_cols=32 Identities=19% Similarity=0.112 Sum_probs=24.0
Q ss_pred HHHHHhhcCCC-CCcceEEEecCCccHHHHHHHH
Q 041256 181 MEKVLESYKGF-EHVKKLVDVGGGLGITLNMIIS 213 (244)
Q Consensus 181 ~~~~~~~~~~~-~~~~~vvDVGGG~G~~~~~l~~ 213 (244)
+..++.... | .....++|-.||+|.++++.+.
T Consensus 178 Aaa~l~~a~-w~~~~~~l~DP~CGSGTilIEAa~ 210 (702)
T PRK11783 178 AAAILLRSG-WPQEGTPLLDPMCGSGTLLIEAAM 210 (702)
T ss_pred HHHHHHHcC-CCCCCCeEEccCCCccHHHHHHHH
Confidence 344554444 7 4468999999999999998766
No 419
>PF02502 LacAB_rpiB: Ribose/Galactose Isomerase; InterPro: IPR003500 This entry represents the sugar isomerase enzymes ribose 5-phosphate isomerase B (rpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB). Galactose-6-phosphate isomerase (5.3.1.26 from EC) is a heteromultimeric protein consisting of subunits LacA and LacB, and catalyses the conversion of D-galactose 6-phosphate to D-tagatose and 6-phosphate in the tagatose 6-phosphate pathway of lactose catabolism []. Galactose-6-phosphate isomerase is induced by galactose or lactose. This entry represents the LacB subunit. Ribose 5-phosphate isomerase (5.3.1.6 from EC) forms a homodimer and catalyses the interconversion of D-ribose 5-phosphate and D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway. This reaction permits the synthesis of ribose from other sugars, as well as the recycling of sugars from nucleotide breakdown. Two unrelated enzymes can catalyse this reaction: RpiA (found in most organisms) and RpiB (found in some bacteria and eukaryotes). RpiB is also involved in metabolism of the rare sugar, allose, in addition to ribose sugars. The structures of RpiA and RpiB are distinct, RpiB having a Rossmann-type alpha/beta/alpha sandwich topology [].; GO: 0005975 carbohydrate metabolic process; PDB: 3HEE_A 3HE8_A 3PH3_B 3PH4_B 3ONO_A 4EM8_B 3S5P_B 1O1X_A 2BES_D 2VVP_D ....
Probab=54.89 E-value=8.5 Score=29.64 Aligned_cols=40 Identities=25% Similarity=0.241 Sum_probs=28.5
Q ss_pred EEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCC
Q 041256 198 VDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237 (244)
Q Consensus 198 vDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~ 237 (244)
-=+.||+|.=..-.+.++|++++.+.--|.....++++.+
T Consensus 60 GIliCgtGiG~~iaANK~~GIrAa~~~d~~~A~~ar~hNd 99 (140)
T PF02502_consen 60 GILICGTGIGMSIAANKVPGIRAALCSDPYSAKMAREHND 99 (140)
T ss_dssp EEEEESSSHHHHHHHHTSTT--EEE-SSHHHHHHHHHTT-
T ss_pred EEEEcCCChhhhhHhhcCCCEEEEeeCCHHHHHHHHHhcC
Confidence 3456788888888899999999977777888888876543
No 420
>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=54.56 E-value=28 Score=22.14 Aligned_cols=47 Identities=9% Similarity=0.222 Sum_probs=32.3
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL 100 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~ 100 (244)
+.|.|-..| =.|+.-+++.++++ +.. ..++++- +|+ .+ -++.++|+.
T Consensus 4 Lidll~~~P---~Vsa~mva~~L~vT------~~~-A~~li~e---Lg~-rE--iTGr~R~Ra 50 (54)
T PF11972_consen 4 LIDLLLSRP---LVSAPMVAKELGVT------PQA-AQRLIAE---LGL-RE--ITGRGRYRA 50 (54)
T ss_pred HHHHHHhCc---cccHHHHHHHhCCC------HHH-HHHHHHH---hhc-ee--ecCCcccch
Confidence 567777642 47999999999997 455 6666655 466 32 366778864
No 421
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=54.51 E-value=29 Score=23.61 Aligned_cols=42 Identities=14% Similarity=0.060 Sum_probs=29.1
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCc
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNA 86 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gl 86 (244)
.|++.+...+.+.-.|+.+||+.+|.+ .. .+.+-.+|..+.+
T Consensus 4 ~V~~~v~~IP~G~v~TYg~iA~~~g~p-------~~-~R~Vg~al~~np~ 45 (79)
T cd06445 4 RVWEALRQIPYGEVTTYGQIAKLAGTP-------KA-ARAVGSALARNPI 45 (79)
T ss_pred HHHHHHhcCCCCCcCcHHHHHHHHCCC-------Cc-HHHHHHHHHhCCC
Confidence 466777777666779999999999983 23 4555555555554
No 422
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=54.32 E-value=15 Score=29.51 Aligned_cols=33 Identities=24% Similarity=0.341 Sum_probs=29.8
Q ss_pred CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
++|-.+||+.+|++ +.. +.|+|+.|...|++..
T Consensus 168 ~~t~~~lA~~lG~t------r~t-vsR~l~~l~~~gii~~ 200 (211)
T PRK11753 168 KITRQEIGRIVGCS------REM-VGRVLKMLEDQGLISA 200 (211)
T ss_pred CCCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCEEe
Confidence 78999999999997 456 9999999999999984
No 423
>KOG4058 consensus Uncharacterized conserved protein [Function unknown]
Probab=54.31 E-value=12 Score=29.39 Aligned_cols=48 Identities=23% Similarity=0.278 Sum_probs=32.9
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA 232 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a 232 (244)
.++...+ -....++||+|.|.|.+..+.++.. -.+.+.++| |..+..+
T Consensus 63 nVLSll~-~n~~GklvDlGSGDGRiVlaaar~g-~~~a~GvELNpwLVays 111 (199)
T KOG4058|consen 63 NVLSLLR-GNPKGKLVDLGSGDGRIVLAAARCG-LRPAVGVELNPWLVAYS 111 (199)
T ss_pred HHHHHcc-CCCCCcEEeccCCCceeehhhhhhC-CCcCCceeccHHHHHHH
Confidence 4455454 2445899999999999888877765 445677777 5555443
No 424
>KOG2920 consensus Predicted methyltransferase [General function prediction only]
Probab=54.31 E-value=11 Score=32.61 Aligned_cols=33 Identities=15% Similarity=0.161 Sum_probs=25.3
Q ss_pred CcceEEEecCCccHHHHHHHHHCCCCeEEEccch
Q 041256 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDLP 226 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 226 (244)
..++|+|+|||.|.-.+-...+.- .++..||..
T Consensus 116 ~~k~vLELgCg~~Lp~i~~~~~~~-~~~~fqD~n 148 (282)
T KOG2920|consen 116 SGKRVLELGCGAALPGIFAFVKGA-VSVHFQDFN 148 (282)
T ss_pred cCceeEecCCcccccchhhhhhcc-ceeeeEecc
Confidence 459999999999998777666543 666777764
No 425
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=54.11 E-value=27 Score=24.02 Aligned_cols=43 Identities=14% Similarity=0.050 Sum_probs=30.5
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCC
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYN 85 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~g 85 (244)
...|++.|.+.+.+.-.|+.+||+.+|.+ .. .+.+-.+|..+-
T Consensus 4 ~~~V~~~l~~IP~G~v~TYg~iA~~~g~p-------~~-~RaVg~al~~np 46 (80)
T TIGR00589 4 QQRVWQALRTIPYGETKSYGQLAARIGNP-------KA-VRAVGGANGRNP 46 (80)
T ss_pred HHHHHHHHhCCCCCCcCCHHHHHHHhCCC-------Ch-HHHHHHHHHhCC
Confidence 45678888888766789999999999973 23 445555555543
No 426
>TIGR00689 rpiB_lacA_lacB sugar-phosphate isomerases, RpiB/LacA/LacB family. Proteins of known function in this family act as sugar (pentose and/or hexose)-phosphate isomerases, including the LacA and LacB subunits of galactose-6-phosphate isomerases from Gram-positive bacteria and RpiB. RpiB is the second ribose phosphate isomerase of E. coli. It lacks homology to RpiA, its inducer is unknown (but is not ribose), and it can be replaced by the homologous galactose-6-phosphate isomerase of Streptococcus mutans, all of which suggests that the ribose phosphate isomerase activity of RpiB is a secondary function. On the other hand, there appear to be a significant number of species which contain rpiB, lack rpiA and seem to require rpi activity in order to copplete the pentose phosphate pathway.
Probab=53.98 E-value=12 Score=29.02 Aligned_cols=39 Identities=18% Similarity=0.129 Sum_probs=30.6
Q ss_pred EecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCC
Q 041256 199 DVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237 (244)
Q Consensus 199 DVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~ 237 (244)
=+.||+|.=..-.+.++|++++.+.--|.....++++.+
T Consensus 60 IliCGtGiG~siaANK~~GIraa~~~d~~~A~~ar~hNn 98 (144)
T TIGR00689 60 ILICGTGIGMSIAANKFKGIRAALCVDEYTAALARQHND 98 (144)
T ss_pred EEEcCCcHHHHHHHhcCCCeEEEEECCHHHHHHHHHhcC
Confidence 356888888888899999999866666888888776543
No 427
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=53.89 E-value=23 Score=26.60 Aligned_cols=62 Identities=23% Similarity=0.366 Sum_probs=43.9
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV 103 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~ 103 (244)
.|..|.++|=.. ||.|+.||-+.+..+ .+.. ..- +.-+|+-|+--|++... .+++.|.-+|+
T Consensus 7 aE~eVM~ilW~~---~~~t~~eI~~~l~~~-~ews-~sT-V~TLl~RL~KKg~l~~~--kdgr~~~y~pL 68 (123)
T COG3682 7 AEWEVMEILWSR---GPATVREIIEELPAD-REWS-YST-VKTLLNRLVKKGLLTRK--KDGRAFRYSPL 68 (123)
T ss_pred HHHHHHHHHHHc---CCccHHHHHHHHhhc-cccc-HHH-HHHHHHHHHhccchhhh--hcCCeeeeecc
Confidence 455667777665 699999988887754 1111 223 88999999999999974 33467777664
No 428
>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=53.57 E-value=13 Score=33.62 Aligned_cols=40 Identities=13% Similarity=0.169 Sum_probs=34.1
Q ss_pred ceEEEecCCccHHHHHHHHHCCCC-eEEEccc-hHHhhhCCC
Q 041256 195 KKLVDVGGGLGITLNMIISKYPHI-KGINYDL-PYVIKDAPS 234 (244)
Q Consensus 195 ~~vvDVGGG~G~~~~~l~~~~P~l-~~~v~Dl-p~vi~~a~~ 234 (244)
-+|+|.-+|+|..++..+++.++. +++..|+ |..++.+++
T Consensus 46 ~~vLD~faGsG~rgir~a~e~~ga~~Vv~nD~n~~Av~~i~~ 87 (374)
T TIGR00308 46 INIADALSASGIRAIRYAHEIEGVREVFANDINPKAVESIKN 87 (374)
T ss_pred CEEEECCCchhHHHHHHHhhCCCCCEEEEEeCCHHHHHHHHH
Confidence 589999999999999999997765 4677888 888888765
No 429
>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=53.08 E-value=17 Score=24.66 Aligned_cols=30 Identities=17% Similarity=0.188 Sum_probs=19.0
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCC
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYN 85 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~g 85 (244)
...|..|||+.++++ +.- +-|+.+.|--.|
T Consensus 33 ~~~si~elA~~~~vS------~st-i~Rf~kkLG~~g 62 (77)
T PF01418_consen 33 AFMSISELAEKAGVS------PST-IVRFCKKLGFSG 62 (77)
T ss_dssp CT--HHHHHHHCTS-------HHH-HHHHHHHCTTTC
T ss_pred HHccHHHHHHHcCCC------HHH-HHHHHHHhCCCC
Confidence 368999999999997 445 666666654333
No 430
>TIGR01120 rpiB ribose 5-phosphate isomerase B. Involved in the non-oxidative branch of the pentose phospate pathway.
Probab=52.90 E-value=13 Score=28.80 Aligned_cols=39 Identities=18% Similarity=0.253 Sum_probs=30.4
Q ss_pred EecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCC
Q 041256 199 DVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237 (244)
Q Consensus 199 DVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~ 237 (244)
=+.||+|.=..-.+.++|++++.+.--|.....++++.+
T Consensus 61 IliCGtGiG~siaANK~~GIraa~~~d~~~A~~ar~hNn 99 (143)
T TIGR01120 61 ILICGTGIGMSIAANKFAGIRAALCSEPYMAQMSRLHND 99 (143)
T ss_pred EEEcCCcHHHHHHHhcCCCeEEEEECCHHHHHHHHHhcC
Confidence 356888888888899999999876666877777776543
No 431
>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=52.87 E-value=31 Score=21.49 Aligned_cols=40 Identities=20% Similarity=0.203 Sum_probs=32.9
Q ss_pred hHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 40 EIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 40 d~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
+++.+. +++|++++=+.+|++ -.+ .-.+|.++-..|+..+
T Consensus 3 ~~~~~~---~~itv~~~rd~lg~s------RK~-ai~lLE~lD~~g~T~R 42 (50)
T PF09107_consen 3 ELLQKN---GEITVAEFRDLLGLS------RKY-AIPLLEYLDREGITRR 42 (50)
T ss_dssp HHHHTT---SSBEHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEE
T ss_pred HHHhcC---CcCcHHHHHHHHCcc------HHH-HHHHHHHHhccCCEEE
Confidence 455554 799999999999996 346 8899999999999985
No 432
>PF14502 HTH_41: Helix-turn-helix domain
Probab=52.76 E-value=29 Score=21.50 Aligned_cols=34 Identities=12% Similarity=0.236 Sum_probs=28.7
Q ss_pred CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
=.|+.|++++++++ .-- ++.-|..|...|.+..+
T Consensus 6 i~tI~e~~~~~~vs------~Gt-iQ~Alk~Le~~gaI~Le 39 (48)
T PF14502_consen 6 IPTISEYSEKFGVS------RGT-IQNALKFLEENGAIKLE 39 (48)
T ss_pred cCCHHHHHHHhCcc------hhH-HHHHHHHHHHCCcEEee
Confidence 46999999999996 334 99999999999988863
No 433
>PF14314 Methyltrans_Mon: Virus-capping methyltransferase
Probab=52.69 E-value=31 Score=33.60 Aligned_cols=50 Identities=14% Similarity=0.218 Sum_probs=37.1
Q ss_pred cchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeE---EEccchH
Q 041256 176 HTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKG---INYDLPY 227 (244)
Q Consensus 176 ~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~---~v~Dlp~ 227 (244)
.+.+-.+.++..+. . ..+-.+-+|=|+|.+...+++.||..++ .++|+..
T Consensus 307 GAHYKlRsIL~~~~-i-~~~d~l~~GDGSGGita~lLR~~p~sr~iFNSLL~~~~ 359 (675)
T PF14314_consen 307 GAHYKLRSILKNLN-I-KYRDALCGGDGSGGITACLLRMNPTSRGIFNSLLELDG 359 (675)
T ss_pred cchhhHHHHHHhcC-C-CcceeEEEecCchHHHHHHHHhCcccceeeeccccccC
Confidence 34455677887765 2 3356688899999999999999999998 5566533
No 434
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=52.59 E-value=15 Score=30.09 Aligned_cols=33 Identities=15% Similarity=0.217 Sum_probs=29.9
Q ss_pred CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
|+|-++||..+|++ ... +.|+|..|...|++..
T Consensus 184 ~lt~~~iA~~lG~s------r~t-vsR~l~~l~~~g~I~~ 216 (235)
T PRK11161 184 TMTRGDIGNYLGLT------VET-ISRLLGRFQKSGMLAV 216 (235)
T ss_pred cccHHHHHHHhCCc------HHH-HHHHHHHHHHCCCEEe
Confidence 68999999999997 456 9999999999999994
No 435
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.26 E-value=16 Score=25.74 Aligned_cols=26 Identities=23% Similarity=0.383 Sum_probs=21.5
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHH
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLL 81 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L 81 (244)
.++|.++||++++++ +.. +.++|.+-
T Consensus 22 ~~LS~~~iA~~Ln~t------~~~-lekil~~t 47 (97)
T COG4367 22 CPLSDEEIATALNWT------EVK-LEKILQVT 47 (97)
T ss_pred ccccHHHHHHHhCCC------HHH-HHHHHHHh
Confidence 489999999999997 566 88888543
No 436
>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=51.22 E-value=25 Score=25.69 Aligned_cols=51 Identities=25% Similarity=0.353 Sum_probs=37.2
Q ss_pred HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
.|+.|.+.|=+. ++.|+.||.+.+.-+ .+. ...- +.-+|+-|+.-|++...
T Consensus 4 ~E~~IM~~lW~~---~~~t~~eI~~~l~~~-~~~-~~sT-v~t~L~rL~~Kg~l~~~ 54 (115)
T PF03965_consen 4 LELEIMEILWES---GEATVREIHEALPEE-RSW-AYST-VQTLLNRLVEKGFLTRE 54 (115)
T ss_dssp HHHHHHHHHHHH---SSEEHHHHHHHHCTT-SS---HHH-HHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHhC---CCCCHHHHHHHHHhc-ccc-chhH-HHHHHHHHHhCCceeEe
Confidence 455667777776 579999999998653 112 1233 89999999999999974
No 437
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=50.66 E-value=23 Score=21.19 Aligned_cols=24 Identities=21% Similarity=0.360 Sum_probs=14.4
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHH
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLR 79 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr 79 (244)
.+.|..+||+.+|.+ +.- +.+.|+
T Consensus 19 ~G~s~~~IA~~lg~s------~sT-V~relk 42 (44)
T PF13936_consen 19 QGMSIREIAKRLGRS------RST-VSRELK 42 (44)
T ss_dssp S---HHHHHHHTT--------HHH-HHHHHH
T ss_pred cCCCHHHHHHHHCcC------cHH-HHHHHh
Confidence 369999999999997 444 666654
No 438
>PRK05571 ribose-5-phosphate isomerase B; Provisional
Probab=50.65 E-value=15 Score=28.65 Aligned_cols=38 Identities=18% Similarity=0.148 Sum_probs=30.0
Q ss_pred ecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCC
Q 041256 200 VGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237 (244)
Q Consensus 200 VGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~ 237 (244)
+-||+|.=..-.+.++|++++.+.--|.....++++.+
T Consensus 64 liCGtGiG~siaANK~~GIRAA~~~d~~~A~~ar~hNn 101 (148)
T PRK05571 64 LICGTGIGMSIAANKVKGIRAALCHDTYSAHLAREHNN 101 (148)
T ss_pred EEcCCcHHHHHHHhcCCCeEEEEECCHHHHHHHHHhcC
Confidence 45778887778899999999977766888888877543
No 439
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=50.64 E-value=18 Score=28.81 Aligned_cols=33 Identities=12% Similarity=0.101 Sum_probs=29.8
Q ss_pred CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
++|-++||..+|++ ++. +.|+|..|...|++..
T Consensus 149 ~~t~~~iA~~lG~t------ret-vsR~l~~l~~~g~I~~ 181 (202)
T PRK13918 149 YATHDELAAAVGSV------RET-VTKVIGELSREGYIRS 181 (202)
T ss_pred cCCHHHHHHHhCcc------HHH-HHHHHHHHHHCCCEEc
Confidence 68999999999997 456 9999999999999994
No 440
>COG1352 CheR Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]
Probab=49.62 E-value=58 Score=27.98 Aligned_cols=42 Identities=12% Similarity=0.164 Sum_probs=33.8
Q ss_pred CcceEEEecCCccH----HHHHHHHHCCC-----CeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGI----TLNMIISKYPH-----IKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~----~~~~l~~~~P~-----l~~~v~Dl-p~vi~~a~~ 234 (244)
+.-+|--.||++|. +++.+.+..|. .+.+.-|+ ..+++.|++
T Consensus 96 ~~irIWSaaCStGEEpYSiAm~l~e~~~~~~~~~~~I~AtDId~~~L~~A~~ 147 (268)
T COG1352 96 RPIRIWSAACSTGEEPYSLAMLLLEALGKLAGFRVKILATDIDLSVLEKARA 147 (268)
T ss_pred CceEEEecCcCCCccHHHHHHHHHHHhccccCCceEEEEEECCHHHHHHHhc
Confidence 57899999999997 66667778864 66777788 889988875
No 441
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=49.54 E-value=27 Score=28.33 Aligned_cols=41 Identities=22% Similarity=0.254 Sum_probs=34.0
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
|.+...++-. +|+|-.+|++..|++ ...+++.|...|++.+
T Consensus 93 LEtLaiIay~---qPiTr~eI~~irGv~----------~~~ii~~L~~~gLI~e 133 (188)
T PRK00135 93 LEVLAIIAYK---QPITRIEIDEIRGVN----------SDGALQTLLAKGLIKE 133 (188)
T ss_pred HHHHHHHHHc---CCcCHHHHHHHHCCC----------HHHHHHHHHHCCCeEE
Confidence 4456677765 799999999999996 4579999999999984
No 442
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=49.21 E-value=24 Score=30.13 Aligned_cols=48 Identities=10% Similarity=0.109 Sum_probs=39.3
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC-CceeecCcccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-QRLYSLAPVSA 105 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~~~y~~t~~s~ 105 (244)
+++.-+|||+.++-+ |.. ++-.|..|-++|+++-. +| .|.|..|..+-
T Consensus 24 r~IKgeeIA~~l~rn------pGT-VRNqmq~LkaLgLVegv--pGPkGGY~PT~kAY 72 (294)
T COG2524 24 RPIKGEEIAEVLNRN------PGT-VRNQMQSLKALGLVEGV--PGPKGGYKPTSKAY 72 (294)
T ss_pred CCcchHHHHHHHccC------cch-HHHHHHHHHhcCccccc--cCCCCCccccHHHH
Confidence 799999999999986 445 89999999999999953 34 47799887763
No 443
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=49.18 E-value=44 Score=22.61 Aligned_cols=54 Identities=13% Similarity=0.315 Sum_probs=42.2
Q ss_pred HHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256 27 PAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS 90 (244)
Q Consensus 27 ~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~ 90 (244)
..+|....++.++..|.+. .+.++.+|+..++.+ ... +.+-|..|...|++...
T Consensus 19 ~~~l~~~~r~~il~~l~~~---~~~~~~~l~~~~~~~------~~~-v~~hL~~L~~~glv~~~ 72 (110)
T COG0640 19 LKALADPTRLEILSLLAEG---GELTVGELAEALGLS------QST-VSHHLKVLREAGLVELR 72 (110)
T ss_pred HHHhCCHHHHHHHHHHHhc---CCccHHHHHHHHCCC------hhH-HHHHHHHHHHCCCeEEE
Confidence 3455555777888888773 378999999999886 345 88999999999999963
No 444
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=48.86 E-value=22 Score=23.37 Aligned_cols=29 Identities=10% Similarity=0.287 Sum_probs=22.3
Q ss_pred CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCC
Q 041256 50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYN 85 (244)
Q Consensus 50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~g 85 (244)
+.|+++||+.+|++ +.. +.++++......
T Consensus 1 ~~~~~~la~~~~~s------~~~-l~~~f~~~~~~s 29 (84)
T smart00342 1 PLTLEDLAEALGMS------PRH-LQRLFKKETGTT 29 (84)
T ss_pred CCCHHHHHHHhCCC------HHH-HHHHHHHHhCcC
Confidence 47899999999997 566 888877664443
No 445
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=48.49 E-value=8.5 Score=25.11 Aligned_cols=42 Identities=24% Similarity=0.408 Sum_probs=22.6
Q ss_pred hhhHHhhcCCCCCCCHHHHHHh----CCCCCCCCc-chhccHHHHHHHHhhCCccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQ----IPLKDNNPE-AAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~----~~~~~~~~~-~~~~~l~rlLr~L~~~gll~ 88 (244)
|++.+ + |+.|+++|++. .+.+ +. .... +..+|..|...|+++
T Consensus 22 Iw~~~-~----g~~t~~ei~~~l~~~y~~~---~~~~~~d-v~~fl~~L~~~glIe 68 (68)
T PF05402_consen 22 IWELL-D----GPRTVEEIVDALAEEYDVD---PEEAEED-VEEFLEQLREKGLIE 68 (68)
T ss_dssp HHHH-------SSS-HHHHHHHHHHHTT-----HHHHHHH-HHHHHHHHHHTT---
T ss_pred HHHHc-c----CCCCHHHHHHHHHHHcCCC---HHHHHHH-HHHHHHHHHHCcCcC
Confidence 45555 2 57888876654 4443 32 1223 889999999999874
No 446
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=47.99 E-value=20 Score=29.55 Aligned_cols=33 Identities=18% Similarity=0.205 Sum_probs=29.6
Q ss_pred CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
++|-.+||..+|++ +.. +.|+|+.|...|++..
T Consensus 179 ~lt~~~IA~~lGis------ret-lsR~L~~L~~~GlI~~ 211 (230)
T PRK09391 179 PMSRRDIADYLGLT------IET-VSRALSQLQDRGLIGL 211 (230)
T ss_pred cCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCcEEe
Confidence 67899999999997 456 9999999999999984
No 447
>TIGR03329 Phn_aa_oxid putative aminophosphonate oxidoreductase. This clade of sequences are members of the pfam01266 family of FAD-dependent oxidoreductases. Characterized proteins within this family include glycerol-3-phosphate dehydrogenase (1.1.99.5), sarcosine oxidase beta subunit (1.5.3.1) and a number of deaminating amino acid oxidases (1.4.-.-). These genes have been consistently observed in a genomic context including genes for the import and catabolism of 2-aminoethylphosphonate (AEP). If the substrate of this oxidoreductase is AEP itself, then it is probably acting in the manner of a deaminating oxidase, resulting in the same product (phosphonoacetaldehyde) as the transaminase PhnW (TIGR02326), but releasing ammonia instead of coupling to pyruvate:alanine. Alternatively, it is reasonable to suppose that the various ABC cassette transporters which are also associated with these loci allow the import of phosphonates closely related to AEP which may not be substrates for PhnW.
Probab=47.91 E-value=20 Score=32.97 Aligned_cols=34 Identities=24% Similarity=0.380 Sum_probs=26.9
Q ss_pred ceEEEecCC-ccHHHH-HHHHHCCCCeEEEccchHH
Q 041256 195 KKLVDVGGG-LGITLN-MIISKYPHIKGINYDLPYV 228 (244)
Q Consensus 195 ~~vvDVGGG-~G~~~~-~l~~~~P~l~~~v~Dlp~v 228 (244)
.-|+=|||| .|.... .|+++.|+.+++|+|--.+
T Consensus 25 ~DVvIIGgGi~Gls~A~~La~~~~G~~V~vlE~~~~ 60 (460)
T TIGR03329 25 ADVCIVGGGFTGLWTAIMIKQQRPALDVLVLEADLC 60 (460)
T ss_pred eCEEEECCCHHHHHHHHHHHHhCCCCeEEEEeCCcc
Confidence 469999999 677555 5777789999999997544
No 448
>PF04672 Methyltransf_19: S-adenosyl methyltransferase; InterPro: IPR006764 This is a family of uncharacterised proteins.; PDB: 3GIW_A 3GO4_A 2QE6_A.
Probab=47.54 E-value=42 Score=28.83 Aligned_cols=42 Identities=21% Similarity=0.395 Sum_probs=25.7
Q ss_pred CcceEEEecCCccH---HHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 193 HVKKLVDVGGGLGI---TLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 193 ~~~~vvDVGGG~G~---~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
+++.+||||+|.=. .---..+..|+.+++=.|. |-|++.++.
T Consensus 68 GIrQFLDlGsGlPT~~nvHevAq~~~P~aRVVYVD~DPvv~ah~ra 113 (267)
T PF04672_consen 68 GIRQFLDLGSGLPTAGNVHEVAQRVAPDARVVYVDNDPVVLAHARA 113 (267)
T ss_dssp ---EEEEET--S--SS-HHHHHHHH-TT-EEEEEESSHHHHHCCHH
T ss_pred CcceEEEcccCCCCCCCHhHHHHhhCCCceEEEECCCchHHHHHHh
Confidence 78999999999653 3333355689999988887 899988875
No 449
>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=47.46 E-value=11 Score=33.60 Aligned_cols=48 Identities=19% Similarity=0.220 Sum_probs=33.4
Q ss_pred HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
.+.+..+ .++. .|+|+=||.|.++..+++..-. ++.+|. ++.++.|++
T Consensus 188 ~~~~~l~-~~~~-~vlDlycG~G~fsl~la~~~~~--V~gvE~~~~av~~A~~ 236 (352)
T PF05958_consen 188 QALEWLD-LSKG-DVLDLYCGVGTFSLPLAKKAKK--VIGVEIVEEAVEDARE 236 (352)
T ss_dssp HHHHHCT-T-TT-EEEEES-TTTCCHHHHHCCSSE--EEEEES-HHHHHHHHH
T ss_pred HHHHHhh-cCCC-cEEEEeecCCHHHHHHHhhCCe--EEEeeCCHHHHHHHHH
Confidence 3444444 3333 7999999999999999998865 454565 777777764
No 450
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=47.38 E-value=31 Score=25.71 Aligned_cols=48 Identities=10% Similarity=0.099 Sum_probs=34.8
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV 108 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~ 108 (244)
.+.|+++||+.+|++ +.. +.|+++......+-.. -..+++......|.
T Consensus 24 ~~~sl~~lA~~~g~S------~~~-l~r~Fk~~~G~s~~~~-----l~~~Rl~~A~~~L~ 71 (127)
T PRK11511 24 SPLSLEKVSERSGYS------KWH-LQRMFKKETGHSLGQY-----IRSRKMTEIAQKLK 71 (127)
T ss_pred CCCCHHHHHHHHCcC------HHH-HHHHHHHHHCcCHHHH-----HHHHHHHHHHHHHH
Confidence 479999999999997 667 9999998877776663 13345544445444
No 451
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=47.16 E-value=23 Score=33.56 Aligned_cols=34 Identities=9% Similarity=0.119 Sum_probs=31.0
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
...|+.|||+.+.++ ++. ++.+|+.|...|+++=
T Consensus 22 ~~~~l~~la~~l~cs------~R~-~~~~l~~~~~~gwl~w 55 (552)
T PRK13626 22 QETTLNELAELLNCS------RRH-MRTLLNTMQQRGWLTW 55 (552)
T ss_pred ceeeHHHHHHHhcCC------hhH-HHHHHHHHHHCCCeee
Confidence 578999999999998 567 9999999999999985
No 452
>PF01358 PARP_regulatory: Poly A polymerase regulatory subunit; InterPro: IPR000176 This family contains viral proteins that are bifunctional, acting as both an mRNA cap-specific RNA 2'-O-methyltransferase, which methylates the ribose 2' OH group of the first transcribed nucleotide, thereby producing a 2'-o-methylpurine cap and a poly(A) polymerase processivity factor which binds to Poly(A) but has no catalytic activity. The structure of this protein is known [].; GO: 0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity, 0006370 mRNA capping, 0006397 mRNA processing; PDB: 4DCG_A 1B42_A 3ERC_A 1AV6_A 2VP3_A 1JTF_A 1JTE_A 1VP3_A 3ER9_A 1P39_A ....
Probab=47.07 E-value=21 Score=30.94 Aligned_cols=50 Identities=14% Similarity=0.230 Sum_probs=34.4
Q ss_pred CCcceEEEecCCccHHHHHHHHHCCCCe----EEEccchHHhhhCCCCCCceee
Q 041256 192 EHVKKLVDVGGGLGITLNMIISKYPHIK----GINYDLPYVIKDAPSYPGTLFI 241 (244)
Q Consensus 192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~----~~v~Dlp~vi~~a~~~~~i~~~ 241 (244)
.+..+||=+|.+.|....-|.+.||+++ .+++|--.-+...++.+.|+++
T Consensus 57 ~~~~~VVYiGsApG~Hi~~L~~lf~~~~~~i~wvLiDp~~f~~~l~~l~~v~l~ 110 (294)
T PF01358_consen 57 DGPVTVVYIGSAPGTHIPFLFDLFPDLKVPIKWVLIDPRPFCISLEELSNVTLI 110 (294)
T ss_dssp TT-EEEEEES-SS-HHHHHHHHHHHHTT--EEEEEEESS---GGGTT-TTEEEE
T ss_pred CCceEEEEecCCCcchHHHHHHHHHhcCCceEEEEECCcchhhhhcccCcEEee
Confidence 4568999999999999999999999976 8999964444445555556654
No 453
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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 is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=46.86 E-value=29 Score=20.18 Aligned_cols=26 Identities=19% Similarity=0.296 Sum_probs=20.1
Q ss_pred CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 52 SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 52 t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
|..|+|+.+|++ .+-||+....|++.
T Consensus 1 ti~e~A~~~gvs-----------~~tlR~ye~~Gll~ 26 (38)
T PF00376_consen 1 TIGEVAKLLGVS-----------PRTLRYYEREGLLP 26 (38)
T ss_dssp EHHHHHHHHTS------------HHHHHHHHHTTSS-
T ss_pred CHHHHHHHHCCC-----------HHHHHHHHHCCCCC
Confidence 467999999995 25788888999994
No 454
>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=46.64 E-value=28 Score=26.74 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=19.2
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCC
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLK 63 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~ 63 (244)
.|-+.|.+.+ +...|+.+|++.+|++
T Consensus 34 kV~~yLr~~p-~~~ati~eV~e~tgVs 59 (137)
T TIGR03826 34 KVYKFLRKHE-NRQATVSEIVEETGVS 59 (137)
T ss_pred HHHHHHHHCC-CCCCCHHHHHHHHCcC
Confidence 3556677653 2348999999999997
No 455
>COG0698 RpiB Ribose 5-phosphate isomerase RpiB [Carbohydrate transport and metabolism]
Probab=46.53 E-value=18 Score=28.16 Aligned_cols=43 Identities=23% Similarity=0.152 Sum_probs=32.5
Q ss_pred EEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCCce
Q 041256 197 LVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTL 239 (244)
Q Consensus 197 vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~i~ 239 (244)
..=+.||+|.=..-.+.++|++++.+.--|.....++++.+.+
T Consensus 61 ~GIliCGTGiG~~iaANKv~GiraAl~~D~~sA~~ar~hNnaN 103 (151)
T COG0698 61 LGILICGTGIGMSIAANKVPGIRAALVSDPTSAKLAREHNNAN 103 (151)
T ss_pred eeEEEecCChhHHHHhhccCCeEEEEecCHHHHHHHHhcCCCc
Confidence 4446788888888889999999986665588888887765433
No 456
>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=46.32 E-value=35 Score=30.26 Aligned_cols=34 Identities=9% Similarity=0.133 Sum_probs=30.5
Q ss_pred CCCCHHHHHHh--CCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 49 AKLSVAEIVAQ--IPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 49 g~~t~~eLA~~--~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
+|.+..+|++. ++++ +.- ++|-|..|...|++.+
T Consensus 20 ~pv~s~~l~~~~~~~vS------~aT-iR~d~~~Le~~G~l~~ 55 (337)
T TIGR00331 20 QPVGSKTLLEKYNLGLS------SAT-IRNDMADLEDLGFIEK 55 (337)
T ss_pred CCcCHHHHHhhcCCCCC------hHH-HHHHHHHHHHCCCccC
Confidence 79999999999 8886 344 9999999999999986
No 457
>smart00753 PAM PCI/PINT associated module.
Probab=46.15 E-value=54 Score=22.30 Aligned_cols=48 Identities=4% Similarity=0.217 Sum_probs=35.8
Q ss_pred HHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 31 QAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 31 ~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
....+..++...... ..++.++||+.++++ .+. +.+++.-+...|.+.
T Consensus 8 ~~~~~~~l~~l~~~y---~~i~~~~i~~~~~l~------~~~-vE~~i~~~i~~~~l~ 55 (88)
T smart00753 8 RKIRLTNLLQLSEPY---SSISLSDLAKLLGLS------VPE-VEKLVSKAIRDGEIS 55 (88)
T ss_pred HHHHHHHHHHHhHHh---ceeeHHHHHHHhCcC------HHH-HHHHHHHHHHCCCeE
Confidence 334444455555443 579999999999997 345 899999999999887
No 458
>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=46.15 E-value=54 Score=22.30 Aligned_cols=48 Identities=4% Similarity=0.217 Sum_probs=35.8
Q ss_pred HHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 31 QAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 31 ~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
....+..++...... ..++.++||+.++++ .+. +.+++.-+...|.+.
T Consensus 8 ~~~~~~~l~~l~~~y---~~i~~~~i~~~~~l~------~~~-vE~~i~~~i~~~~l~ 55 (88)
T smart00088 8 RKIRLTNLLQLSEPY---SSISLSDLAKLLGLS------VPE-VEKLVSKAIRDGEIS 55 (88)
T ss_pred HHHHHHHHHHHhHHh---ceeeHHHHHHHhCcC------HHH-HHHHHHHHHHCCCeE
Confidence 334444455555443 579999999999997 345 899999999999887
No 459
>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=45.85 E-value=39 Score=25.27 Aligned_cols=46 Identities=11% Similarity=0.014 Sum_probs=37.3
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS 104 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s 104 (244)
-|-|.+.||..++-+ ..- ++.-|..+..+|+++. .++|.|..+...
T Consensus 50 ipy~~e~LA~~~~~~------~~~-V~~Al~~f~k~glIe~---~d~g~i~i~~~~ 95 (119)
T TIGR01714 50 APYNAEMLATMFNRN------VGD-IRITLQTLESLGLIEK---KNNGDIFLENWE 95 (119)
T ss_pred CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE---ecCCcEEehhHH
Confidence 699999999999985 455 9999999999999995 345767776644
No 460
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=45.77 E-value=24 Score=25.54 Aligned_cols=47 Identities=13% Similarity=0.151 Sum_probs=35.3
Q ss_pred cChhhHHhhc-CCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 36 LDVFEIISKA-GPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 36 lgifd~L~~~-~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
-.+++.+.+. +...-+|+-.||.+.|+. -.. .+++||.|...|++..
T Consensus 44 ee~~~ki~KEV~~~r~VTpy~la~r~gI~------~Sv-Ar~vLR~LeeeGvv~l 91 (107)
T COG4901 44 EELLDKIRKEVPRERVVTPYVLASRYGIN------GSV-ARIVLRHLEEEGVVQL 91 (107)
T ss_pred HHHHHHHHHhcccceeecHHHHHHHhccc------hHH-HHHHHHHHHhCCceee
Confidence 3456665543 111358999999999996 556 8899999999999884
No 461
>PF13814 Replic_Relax: Replication-relaxation
Probab=45.73 E-value=27 Score=27.67 Aligned_cols=62 Identities=15% Similarity=0.173 Sum_probs=44.2
Q ss_pred HHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeec-------CCceeecCcccccccc
Q 041256 41 IISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVD-------GQRLYSLAPVSAYFVR 109 (244)
Q Consensus 41 ~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~-------~~~~y~~t~~s~~l~~ 109 (244)
.|.+. +.+|..+|+.....+ .+.+.. +.+.|+-|...|++...... .+..|.+|+.+..++.
T Consensus 3 ~L~~~---r~lt~~Qi~~l~~~~---~~~~~~-~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~ 71 (191)
T PF13814_consen 3 LLARH---RFLTTDQIARLLFPS---SKSERT-ARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLLA 71 (191)
T ss_pred hHHHh---cCcCHHHHHHHHcCC---CcchHH-HHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHHH
Confidence 34454 589999999999886 211235 99999999999999864321 2357899999864443
No 462
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=45.61 E-value=29 Score=29.33 Aligned_cols=41 Identities=12% Similarity=0.173 Sum_probs=33.3
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNA 86 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gl 86 (244)
..|.+.|.+. |..++.|||+.++++ +.- ++|=|+.|...+.
T Consensus 10 ~~I~~~l~~~---~~v~v~eLa~~~~VS------~~T-IRRDL~~Le~~~~ 50 (252)
T PRK10681 10 GQLLQALKRS---DKLHLKDAAALLGVS------EMT-IRRDLNAHSAPVV 50 (252)
T ss_pred HHHHHHHHHc---CCCcHHHHHHHhCCC------HHH-HHHHHHHhhcCeE
Confidence 3467888886 689999999999997 444 9999999986543
No 463
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=45.26 E-value=24 Score=26.91 Aligned_cols=43 Identities=12% Similarity=0.186 Sum_probs=32.9
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
+-.-+|.+.+.. |.+++.|+|+.+++. +. |+.+-|...|++..
T Consensus 34 Kv~f~D~v~~~~--gli~~re~AK~lkig------e~----~l~~~L~e~~~l~~ 76 (135)
T COG3645 34 KVEFADAVVEAS--GLILFRELAKLLKIG------EN----RLFAWLRENKYLIK 76 (135)
T ss_pred chHHHHHHhcCc--cceeHHHHHHHHccC------HH----HHHHHHHHCCEEEE
Confidence 445689998875 889999999999996 33 45555667788884
No 464
>PRK12615 galactose-6-phosphate isomerase subunit LacB; Reviewed
Probab=44.75 E-value=21 Score=28.51 Aligned_cols=41 Identities=17% Similarity=0.029 Sum_probs=31.2
Q ss_pred EecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCCce
Q 041256 199 DVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTL 239 (244)
Q Consensus 199 DVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~i~ 239 (244)
=+.||+|.=..-.+.++|++++.+.--|.....++++.+.+
T Consensus 62 IliCGTGiG~siaANK~~GIRAA~~~d~~~A~~ar~hNnaN 102 (171)
T PRK12615 62 VCICGTGVGINNAVNKVPGIRSALVRDMTTALYAKEELNAN 102 (171)
T ss_pred EEEcCCcHHHHHHHhcCCCeEEEEeCCHHHHHHHHHhcCCc
Confidence 35678888778889999999986665588888887755433
No 465
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=44.64 E-value=50 Score=32.42 Aligned_cols=59 Identities=22% Similarity=0.374 Sum_probs=41.4
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV 103 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~ 103 (244)
|.+.|.+.. +.|++..+|++.++++ ....... +.+.|+.|...|.+.+ ...+.|.....
T Consensus 7 il~~l~~~~-~~~~~~~~l~~~l~~~--~~~~~~~-l~~~l~~l~~~g~l~~---~~~~~~~~~~~ 65 (709)
T TIGR02063 7 ILEFLKSKK-GKPISLKELAKAFHLK--GADEKKA-LRKRLRALEDDGLVKK---NRRGLYALPES 65 (709)
T ss_pred HHHHHHhCC-CCCCCHHHHHHHhCCC--ChHHHHH-HHHHHHHHHHCCCEEE---cCCceEecCCC
Confidence 566666421 2689999999999996 2111345 9999999999999984 33466655443
No 466
>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=44.42 E-value=20 Score=28.76 Aligned_cols=40 Identities=15% Similarity=0.030 Sum_probs=29.0
Q ss_pred cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS 234 (244)
Q Consensus 194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~ 234 (244)
..+++|+=+|+|.++.+.+.+.-. +++.+|. +..+...++
T Consensus 43 g~~vLDLFaGSGalGlEALSRGA~-~v~fVE~~~~a~~~i~~ 83 (183)
T PF03602_consen 43 GARVLDLFAGSGALGLEALSRGAK-SVVFVEKNRKAIKIIKK 83 (183)
T ss_dssp T-EEEETT-TTSHHHHHHHHTT-S-EEEEEES-HHHHHHHHH
T ss_pred CCeEEEcCCccCccHHHHHhcCCC-eEEEEECCHHHHHHHHH
Confidence 489999999999999999988643 5677777 666665543
No 467
>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=44.41 E-value=24 Score=20.76 Aligned_cols=27 Identities=19% Similarity=0.260 Sum_probs=18.6
Q ss_pred CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 51 LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 51 ~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
+|.+|+|+.+|++ ... +.++ +..|.+.
T Consensus 2 lt~~e~a~~lgis------~~t-i~~~----~~~g~i~ 28 (49)
T TIGR01764 2 LTVEEAAEYLGVS------KDT-VYRL----IHEGELP 28 (49)
T ss_pred CCHHHHHHHHCCC------HHH-HHHH----HHcCCCC
Confidence 5899999999996 333 4444 4556555
No 468
>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=44.41 E-value=60 Score=23.08 Aligned_cols=65 Identities=15% Similarity=0.169 Sum_probs=39.4
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCC-C--CCCcchhccHHHHHHHHhhCCcccceeecC-----CceeecCccccccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLK-D--NNPEAAAMTLDRVLRLLVSYNALHCSFVDG-----QRLYSLAPVSAYFV 108 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~-~--~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-----~~~y~~t~~s~~l~ 108 (244)
|.-.|.+ +|.+--||.+.++-. . -+.. +.. +.++|+-|...|+++...+.. .-.|++|+.++.+.
T Consensus 9 iL~~L~~----~~~~GYei~~~l~~~~~~~~~i~-~gt-lY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l 81 (100)
T TIGR03433 9 ILKTLSL----GPLHGYGIAQRIQQISEDVLQVE-EGS-LYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQL 81 (100)
T ss_pred HHHHHhc----CCCCHHHHHHHHHHHcCCccccC-CCc-HHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHH
Confidence 4445554 578888888775211 0 0011 334 999999999999998631111 13488887766433
No 469
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=44.37 E-value=1.1e+02 Score=24.14 Aligned_cols=65 Identities=17% Similarity=0.283 Sum_probs=0.0
Q ss_pred ccCCchHHHHHHHHHHhcchhh-----HHHHHhhcCCCCCcceEEE--ecCCccH-HHHHHHHHCCCCeEEEc
Q 041256 159 LGVDSRFNDVFNNGMLSHTSIV-----MEKVLESYKGFEHVKKLVD--VGGGLGI-TLNMIISKYPHIKGINY 223 (244)
Q Consensus 159 ~~~~~~~~~~f~~aM~~~~~~~-----~~~~~~~~~~~~~~~~vvD--VGGG~G~-~~~~l~~~~P~l~~~v~ 223 (244)
+..|+-+.+...++|......+ ...-+.........--||| +|+|+|. ...++.++.|+.+.+++
T Consensus 15 vdDD~~f~~~LaRa~e~RGf~v~~a~~~~eal~~art~~PayAvvDlkL~~gsGL~~i~~lr~~~~d~rivvL 87 (182)
T COG4567 15 VDDDTPFLRTLARAMERRGFAVVTAESVEEALAAARTAPPAYAVVDLKLGDGSGLAVIEALRERRADMRIVVL 87 (182)
T ss_pred ecCChHHHHHHHHHHhccCceeEeeccHHHHHHHHhcCCCceEEEEeeecCCCchHHHHHHHhcCCcceEEEE
No 470
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=44.04 E-value=63 Score=26.98 Aligned_cols=47 Identities=19% Similarity=0.268 Sum_probs=38.4
Q ss_pred HHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 32 AVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 32 ~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
.-.+.+++..+... ++.++.|+++.++++ -.- ++-.||.|.+.++++
T Consensus 100 ns~R~~Iy~~i~~n---PG~~lsEl~~nl~i~------R~T-lRyhlriLe~~~li~ 146 (240)
T COG3398 100 NSKRDGIYNYIKPN---PGFSLSELRANLYIN------RST-LRYHLRILESNPLIE 146 (240)
T ss_pred hhhHHHHHHHhccC---CCccHHHHHHhcCCC------hHH-HHHHHHHHHhCcchh
Confidence 33456788888876 589999999999995 234 889999999999998
No 471
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=44.04 E-value=35 Score=20.75 Aligned_cols=34 Identities=9% Similarity=0.273 Sum_probs=24.8
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHH
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRL 80 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~ 80 (244)
+.-|...+.+ ..|..++|+.+|++ ..- +.|+++.
T Consensus 17 ~~~i~~~~~~-----~~s~~~vA~~~~vs------~~T-V~ri~~~ 50 (52)
T PF13542_consen 17 EQYILKLLRE-----SRSFKDVARELGVS------WST-VRRIFDR 50 (52)
T ss_pred HHHHHHHHhh-----cCCHHHHHHHHCCC------HHH-HHHHHHh
Confidence 3345666654 37999999999997 445 7887764
No 472
>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=43.22 E-value=55 Score=27.81 Aligned_cols=60 Identities=15% Similarity=0.143 Sum_probs=37.7
Q ss_pred HHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhC
Q 041256 170 NNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDA 232 (244)
Q Consensus 170 ~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a 232 (244)
...+...+.+. ..++..+- -.+...||.+|+|-=.-...+-.. ++++..=+|+|+|++.=
T Consensus 60 ~~~~~~Rtr~~-D~~i~~~~-~~g~~qvV~LGaGlDTr~~Rl~~~-~~~~~~EvD~P~v~~~K 119 (260)
T TIGR00027 60 ADFIAVRTRFF-DDFLLAAV-AAGIRQVVILGAGLDTRAYRLPWP-DGTRVFEVDQPAVLAFK 119 (260)
T ss_pred HHHHHHHHHHH-HHHHHHHH-hcCCcEEEEeCCccccHHHhcCCC-CCCeEEECCChHHHHHH
Confidence 33444444443 33343332 135678999999987777666321 25788888999998753
No 473
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=43.05 E-value=30 Score=24.68 Aligned_cols=50 Identities=12% Similarity=0.080 Sum_probs=34.0
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccccC
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRN 110 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~~ 110 (244)
.+.|+++||+.++++ +.. +.|+.+......+-+. -..++.......|..+
T Consensus 20 ~~~~~~~lA~~~~~S------~~~-l~r~f~~~~g~s~~~~-----i~~~Rl~~a~~~L~~~ 69 (107)
T PRK10219 20 QPLNIDVVAKKSGYS------KWY-LQRMFRTVTHQTLGDY-----IRQRRLLLAAVELRTT 69 (107)
T ss_pred CCCCHHHHHHHHCCC------HHH-HHHHHHHHHCcCHHHH-----HHHHHHHHHHHHHHcc
Confidence 479999999999997 567 8888888766665553 1224444444455443
No 474
>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=42.64 E-value=24 Score=21.40 Aligned_cols=25 Identities=20% Similarity=0.444 Sum_probs=18.2
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHH
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRL 80 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~ 80 (244)
.+.|.+|||+.+|++ ... +.++.+-
T Consensus 19 ~~~t~~eIa~~lg~s------~~~-V~~~~~~ 43 (50)
T PF04545_consen 19 EGLTLEEIAERLGIS------RST-VRRILKR 43 (50)
T ss_dssp ST-SHHHHHHHHTSC------HHH-HHHHHHH
T ss_pred CCCCHHHHHHHHCCc------HHH-HHHHHHH
Confidence 479999999999997 444 6666543
No 475
>TIGR01119 lacB galactose-6-phosphate isomerase, LacB subunit. This family contains four members from low GC gram-positive bacteria. Galactose-6-phosphate isomerase is involved in lactose catabolism by the tagatose-6-phosphate pathway.
Probab=42.42 E-value=23 Score=28.30 Aligned_cols=38 Identities=16% Similarity=0.061 Sum_probs=29.5
Q ss_pred ecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCC
Q 041256 200 VGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237 (244)
Q Consensus 200 VGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~ 237 (244)
+-||+|.-..-.++++|++++.+.--|.....++++.+
T Consensus 63 liCGTGiG~siaANKv~GIRAAl~~d~~sA~~ar~hNn 100 (171)
T TIGR01119 63 CICGTGVGINNAVNKVPGVRSALVRDMTSALYAKEELN 100 (171)
T ss_pred EEcCCcHHHHHHHhcCCCeEEEEeCCHHHHHHHHHhcC
Confidence 45788887778899999999866655888888876543
No 476
>COG0248 GppA Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]
Probab=42.37 E-value=21 Score=33.46 Aligned_cols=24 Identities=21% Similarity=0.252 Sum_probs=18.2
Q ss_pred HHHhhcCCCCCcceEEEecCCccHH
Q 041256 183 KVLESYKGFEHVKKLVDVGGGLGIT 207 (244)
Q Consensus 183 ~~~~~~~~~~~~~~vvDVGGG~G~~ 207 (244)
.+...++ +.+...++|||||+=.+
T Consensus 120 Gv~~~~~-~~~~~lv~DIGGGStEl 143 (492)
T COG0248 120 GVASTLP-RKGDGLVIDIGGGSTEL 143 (492)
T ss_pred HHHhcCC-CCCCEEEEEecCCeEEE
Confidence 5566677 57779999999997543
No 477
>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=42.21 E-value=36 Score=21.60 Aligned_cols=54 Identities=13% Similarity=0.211 Sum_probs=37.3
Q ss_pred hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhh---CCcccceeecCCceeecCccc
Q 041256 35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVS---YNALHCSFVDGQRLYSLAPVS 104 (244)
Q Consensus 35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~---~gll~~~~~~~~~~y~~t~~s 104 (244)
++.+|..+.+. .++..-|+.++++ +.. +.+-++.|.. .-+|.+ . .+.+.+|+.+
T Consensus 3 ~l~~f~~v~~~-----gs~~~AA~~l~is------~~~-vs~~i~~LE~~lg~~Lf~r---~-~~~~~lT~~G 59 (60)
T PF00126_consen 3 QLRYFLAVAET-----GSISAAAEELGIS------QSA-VSRQIKQLEEELGVPLFER---S-GRGLRLTEAG 59 (60)
T ss_dssp HHHHHHHHHHH-----SSHHHHHHHCTSS------HHH-HHHHHHHHHHHHTS-SEEE---C-SSSEEE-HHH
T ss_pred HHHHHHHHHHh-----CCHHHHHHHhhcc------chH-HHHHHHHHHHHhCCeEEEE---C-CCCeeEChhh
Confidence 45678888874 4899999999997 445 7777777765 457774 3 3558888764
No 478
>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=42.18 E-value=38 Score=23.78 Aligned_cols=40 Identities=23% Similarity=0.173 Sum_probs=28.8
Q ss_pred HHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHh
Q 041256 32 AVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLV 82 (244)
Q Consensus 32 ~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~ 82 (244)
.+-++.|+..|-. ++.|..|||+.+|++ ..- +.|.=|.|-
T Consensus 35 l~~R~~va~~lL~----~g~syreIa~~tgvS------~aT-ItRvsr~Lk 74 (87)
T PF01371_consen 35 LAQRWQVAKELLD----EGKSYREIAEETGVS------IAT-ITRVSRCLK 74 (87)
T ss_dssp HHHHHHHHHHHHH----TTSSHHHHHHHHTST------HHH-HHHHHHHHH
T ss_pred HHHHHHHHHHHHH----CCCCHHHHHHHhCCC------HHH-HHHHHHHHH
Confidence 3467889983434 479999999999997 333 666666653
No 479
>PF12242 Eno-Rase_NADH_b: NAD(P)H binding domain of trans-2-enoyl-CoA reductase; PDB: 3ZU5_A 3ZU3_A 3ZU4_A 3ZU2_A 3S8M_A.
Probab=41.92 E-value=27 Score=23.97 Aligned_cols=36 Identities=19% Similarity=0.439 Sum_probs=20.7
Q ss_pred CCCcceEEEecCCccH-HHHHHHHHCC-CCe--EEEccch
Q 041256 191 FEHVKKLVDVGGGLGI-TLNMIISKYP-HIK--GINYDLP 226 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~-~~~~l~~~~P-~l~--~~v~Dlp 226 (244)
.+++++||-||+++|. ++.++..+|- +.. ++-||.|
T Consensus 36 ~~GpK~VLViGaStGyGLAsRIa~aFg~gA~TiGV~fEk~ 75 (78)
T PF12242_consen 36 INGPKKVLVIGASTGYGLASRIAAAFGAGADTIGVSFEKP 75 (78)
T ss_dssp -TS-SEEEEES-SSHHHHHHHHHHHHCC--EEEEEE----
T ss_pred CCCCceEEEEecCCcccHHHHHHHHhcCCCCEEEEeeccC
Confidence 5678999999999999 6667877762 222 3566654
No 480
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=41.87 E-value=61 Score=26.18 Aligned_cols=42 Identities=12% Similarity=0.178 Sum_probs=33.4
Q ss_pred hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
+.+-|.. ++..|+.+||+++|++ ..- +.|.|.-|...|.+..
T Consensus 18 ~~~~l~~---~~~~~a~~i~~~l~~~------k~~-vNr~LY~l~~~~~v~~ 59 (183)
T PHA03103 18 EVKNLGL---GEGITAIEISRKLNIE------KSE-VNKQLYKLQREGMVYM 59 (183)
T ss_pred HHHHhcc---CCCccHHHHHHHhCCC------HHH-HHHHHHHHHhcCceec
Confidence 3445544 3789999999999996 345 8899999999999975
No 481
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=41.77 E-value=23 Score=23.69 Aligned_cols=33 Identities=12% Similarity=0.127 Sum_probs=22.8
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
..-|.+|||+.+|++ +.. +..+|......--+.
T Consensus 19 r~Pt~eEiA~~lgis------~~~-v~~~l~~~~~~~Sl~ 51 (78)
T PF04539_consen 19 REPTDEEIAEELGIS------VEE-VRELLQASRRPVSLD 51 (78)
T ss_dssp S--BHHHHHHHHTS-------HHH-HHHHHHHHSCCEESS
T ss_pred CCCCHHHHHHHHccc------HHH-HHHHHHhCCCCeEEe
Confidence 467999999999997 556 888888765544444
No 482
>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=41.59 E-value=23 Score=25.09 Aligned_cols=43 Identities=12% Similarity=0.130 Sum_probs=28.0
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
|=|.-.+.. +..++..|-+.+|++ +++++..+.+|..+|+-.+
T Consensus 11 lyla~li~~----~~~nvp~L~~~TGmP-------rRT~Qd~i~aL~~~~I~~~ 53 (90)
T PF09904_consen 11 LYLAYLIDS----GERNVPALMEATGMP-------RRTIQDTIKALPELGIECE 53 (90)
T ss_dssp HHHHHHHHH----S-B-HHHHHHHH----------HHHHHHHHHGGGGGT-EEE
T ss_pred HHHHHHHhc----CCccHHHHHHHhCCC-------HhHHHHHHHHhhcCCeEEE
Confidence 334445555 355999999999994 4449999999999998763
No 483
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=41.59 E-value=65 Score=25.13 Aligned_cols=55 Identities=7% Similarity=0.152 Sum_probs=37.2
Q ss_pred CCCCHHHHHHhCCCCC------CCCc--chhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256 49 AKLSVAEIVAQIPLKD------NNPE--AAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV 108 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~------~~~~--~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~ 108 (244)
+|+.+..|++..|..+ ++-. .-.. ++..|+.|..+|+++.+ ..|+ .+|+.++-+.
T Consensus 66 gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~i-iR~~LqqLE~~glVek~---~~GR-~lT~~G~~~L 128 (150)
T PRK09333 66 GPVGVERLRTAYGGRKNRGVRPEHFVKGSGSI-IRKILQQLEKAGLVEKT---KKGR-VITPKGRSLL 128 (150)
T ss_pred CCccHHHHHHHHCCCcCCCCCCCccccCccHH-HHHHHHHHHHCCCeeeC---CCCC-EeCHHHHHHH
Confidence 7999999999999841 1110 0123 89999999999999953 2344 4666555333
No 484
>PF12728 HTH_17: Helix-turn-helix domain
Probab=41.42 E-value=27 Score=21.20 Aligned_cols=13 Identities=23% Similarity=0.358 Sum_probs=11.8
Q ss_pred CCHHHHHHhCCCC
Q 041256 51 LSVAEIVAQIPLK 63 (244)
Q Consensus 51 ~t~~eLA~~~~~~ 63 (244)
+|++|+|+.+|++
T Consensus 2 lt~~e~a~~l~is 14 (51)
T PF12728_consen 2 LTVKEAAELLGIS 14 (51)
T ss_pred CCHHHHHHHHCcC
Confidence 5899999999996
No 485
>KOG3851 consensus Sulfide:quinone oxidoreductase/flavo-binding protein [Energy production and conversion]
Probab=41.36 E-value=34 Score=30.48 Aligned_cols=32 Identities=22% Similarity=0.030 Sum_probs=24.7
Q ss_pred CcceEEEecCCccHHHHH--HHHHCCCCeEEEcc
Q 041256 193 HVKKLVDVGGGLGITLNM--IISKYPHIKGINYD 224 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~--l~~~~P~l~~~v~D 224 (244)
..-.|+-||||+|.++++ +.++.|.=+..++|
T Consensus 38 ~h~kvLVvGGGsgGi~~A~k~~rkl~~g~vgIve 71 (446)
T KOG3851|consen 38 KHFKVLVVGGGSGGIGMAAKFYRKLGSGSVGIVE 71 (446)
T ss_pred cceEEEEEcCCcchhHHHHHHHhhcCCCceEEec
Confidence 446789999999986554 88899987766655
No 486
>PRK13917 plasmid segregation protein ParM; Provisional
Probab=41.32 E-value=85 Score=27.83 Aligned_cols=57 Identities=16% Similarity=0.169 Sum_probs=37.5
Q ss_pred HHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHh
Q 041256 171 NGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVI 229 (244)
Q Consensus 171 ~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi 229 (244)
+............+...++.+.+..+|+=+|||.-.+-..|.+.||+. .+.|-|+-.
T Consensus 269 ~~~~~~~~~i~~~i~~~~~~~~~~d~IiL~GGGA~ll~~~lk~~f~~~--~~~~~p~~A 325 (344)
T PRK13917 269 KEQDSVIDEVMSGFEIAVGNINSFDRVIVTGGGANIFFDSLSHWYSDV--EKADESQFA 325 (344)
T ss_pred HHHHHHHHHHHHHHHHHhcccCCCCEEEEECCcHHHHHHHHHHHcCCe--EEcCChHHH
Confidence 333333333334444444435667889999999999888899999975 666766543
No 487
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=41.23 E-value=31 Score=30.44 Aligned_cols=34 Identities=18% Similarity=0.235 Sum_probs=30.3
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
.++|=.|||+++|++ ... +.|+|..+...|+++.
T Consensus 25 ~gltQ~eIA~~LgiS------R~~-v~rlL~~Ar~~GiV~I 58 (321)
T COG2390 25 EGLTQSEIAERLGIS------RAT-VSRLLAKAREEGIVKI 58 (321)
T ss_pred cCCCHHHHHHHhCCC------HHH-HHHHHHHHHHCCeEEE
Confidence 489999999999997 345 9999999999999985
No 488
>PHA01634 hypothetical protein
Probab=41.09 E-value=21 Score=27.22 Aligned_cols=22 Identities=14% Similarity=0.184 Sum_probs=19.0
Q ss_pred CcceEEEecCCccHHHHHHHHH
Q 041256 193 HVKKLVDVGGGLGITLNMIISK 214 (244)
Q Consensus 193 ~~~~vvDVGGG~G~~~~~l~~~ 214 (244)
..++|+|||++.|.-++-++-+
T Consensus 28 k~KtV~dIGA~iGdSaiYF~l~ 49 (156)
T PHA01634 28 YQRTIQIVGADCGSSALYFLLR 49 (156)
T ss_pred cCCEEEEecCCccchhhHHhhc
Confidence 3499999999999999888765
No 489
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=40.89 E-value=21 Score=22.69 Aligned_cols=21 Identities=5% Similarity=0.252 Sum_probs=13.2
Q ss_pred hhHHhhcCCCCCCCHHHHHHhCCCC
Q 041256 39 FEIISKAGPGAKLSVAEIVAQIPLK 63 (244)
Q Consensus 39 fd~L~~~~~~g~~t~~eLA~~~~~~ 63 (244)
-..+.+ ..+|..+||+.+|++
T Consensus 3 ~~~m~~----~~it~~~La~~~gis 23 (63)
T PF13443_consen 3 KELMAE----RGITQKDLARKTGIS 23 (63)
T ss_dssp HHHHHH----TT--HHHHHHHHT--
T ss_pred HHHHHH----cCCCHHHHHHHHCcC
Confidence 345666 468999999999996
No 490
>KOG2918 consensus Carboxymethyl transferase [Posttranslational modification, protein turnover, chaperones]
Probab=40.81 E-value=28 Score=30.55 Aligned_cols=41 Identities=24% Similarity=0.400 Sum_probs=37.0
Q ss_pred CCCcceEEEecCCccHHHHHHHHHC--CCCeEEEccchHHhhh
Q 041256 191 FEHVKKLVDVGGGLGITLNMIISKY--PHIKGINYDLPYVIKD 231 (244)
Q Consensus 191 ~~~~~~vvDVGGG~G~~~~~l~~~~--P~l~~~v~Dlp~vi~~ 231 (244)
+++...||-+|||.-.....++..+ +.++.+=+|-|++++.
T Consensus 85 ~~~~~qivnLGcG~D~l~frL~s~~~~~~~~fievDfp~~~~r 127 (335)
T KOG2918|consen 85 TDGKKQIVNLGAGFDTLYFRLLSSGELDRVKFIEVDFPEVVER 127 (335)
T ss_pred cCCceEEEEcCCCccchhhhhhccCCCCcceEEEecCcHHHHH
Confidence 4567899999999999999999998 8899999999999875
No 491
>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=40.76 E-value=28 Score=20.27 Aligned_cols=27 Identities=22% Similarity=0.267 Sum_probs=18.2
Q ss_pred CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 51 LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 51 ~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
.|..|+|+.+|++ +.- +.++ +..|.+.
T Consensus 1 ~s~~e~a~~lgvs------~~t-l~~~----~~~g~~~ 27 (49)
T cd04762 1 LTTKEAAELLGVS------PST-LRRW----VKEGKLK 27 (49)
T ss_pred CCHHHHHHHHCcC------HHH-HHHH----HHcCCCC
Confidence 4789999999996 333 4444 4457664
No 492
>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=40.50 E-value=38 Score=23.39 Aligned_cols=23 Identities=17% Similarity=0.215 Sum_probs=18.9
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHhCCCC
Q 041256 37 DVFEIISKAGPGAKLSVAEIVAQIPLK 63 (244)
Q Consensus 37 gifd~L~~~~~~g~~t~~eLA~~~~~~ 63 (244)
-|.+.|.+ +..|+.+||+..|++
T Consensus 10 ~I~e~l~~----~~~ti~dvA~~~gvS 32 (80)
T TIGR02844 10 EIGKYIVE----TKATVRETAKVFGVS 32 (80)
T ss_pred HHHHHHHH----CCCCHHHHHHHhCCC
Confidence 35677777 488999999999997
No 493
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=40.18 E-value=53 Score=27.42 Aligned_cols=67 Identities=13% Similarity=0.089 Sum_probs=48.0
Q ss_pred HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256 28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS 104 (244)
Q Consensus 28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s 104 (244)
..|+-...-.+++.|.+. +..|.-+||..+|++ ..- +.--|..|...|++.++.+...-.|+.||.-
T Consensus 169 ~~Lkn~~~k~I~~eiq~~---~~~t~~~ia~~l~ls------~aT-V~~~lk~l~~~Gii~~~~~Gr~iiy~in~s~ 235 (240)
T COG3398 169 LSLKNETSKAIIYEIQEN---KCNTNLLIAYELNLS------VAT-VAYHLKKLEELGIIPEDREGRSIIYSINPSI 235 (240)
T ss_pred HHhhchhHHHHHHHHhcC---CcchHHHHHHHcCcc------HHH-HHHHHHHHHHcCCCcccccCceEEEEeCHHH
Confidence 344555556788888874 579999999999997 334 7788999999999996432112247777643
No 494
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=40.10 E-value=40 Score=20.25 Aligned_cols=14 Identities=21% Similarity=0.361 Sum_probs=13.0
Q ss_pred CCCHHHHHHhCCCC
Q 041256 50 KLSVAEIVAQIPLK 63 (244)
Q Consensus 50 ~~t~~eLA~~~~~~ 63 (244)
+.+..+||+.++++
T Consensus 18 g~s~~eia~~l~is 31 (58)
T smart00421 18 GLTNKEIAERLGIS 31 (58)
T ss_pred CCCHHHHHHHHCCC
Confidence 58999999999997
No 495
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=40.10 E-value=23 Score=29.29 Aligned_cols=33 Identities=12% Similarity=0.143 Sum_probs=29.1
Q ss_pred CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256 49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH 88 (244)
Q Consensus 49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~ 88 (244)
|..|+.+|++.++++ ... ....|+.+...|++.
T Consensus 189 g~vt~~~l~~~~~ws------~~~-a~~~L~~~~~~G~l~ 221 (223)
T PF04157_consen 189 GGVTASELAEKLGWS------VER-AKEALEELEREGLLW 221 (223)
T ss_dssp SEEEHHHHHHHHTB-------HHH-HHHHHHHHHHTTSEE
T ss_pred CCCCHHHHHHHhCCC------HHH-HHHHHHHHHhCCCEe
Confidence 799999999999997 567 889999999999886
No 496
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=40.03 E-value=22 Score=21.66 Aligned_cols=12 Identities=8% Similarity=0.324 Sum_probs=8.4
Q ss_pred CHHHHHHhCCCC
Q 041256 52 SVAEIVAQIPLK 63 (244)
Q Consensus 52 t~~eLA~~~~~~ 63 (244)
|..|||+.+|++
T Consensus 1 Ti~dIA~~agvS 12 (46)
T PF00356_consen 1 TIKDIAREAGVS 12 (46)
T ss_dssp CHHHHHHHHTSS
T ss_pred CHHHHHHHHCcC
Confidence 566777777775
No 497
>PTZ00215 ribose 5-phosphate isomerase; Provisional
Probab=39.97 E-value=26 Score=27.33 Aligned_cols=37 Identities=16% Similarity=0.144 Sum_probs=29.0
Q ss_pred ecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCC
Q 041256 200 VGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYP 236 (244)
Q Consensus 200 VGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~ 236 (244)
+-||+|.-..-.+.++|++++.+.--|.....++++.
T Consensus 67 liCGtGiG~siaANK~~GIRAa~~~d~~~A~~ar~hN 103 (151)
T PTZ00215 67 LVCGSGIGISIAANKVKGIRCALCHDHYTARMSRQHN 103 (151)
T ss_pred EEcCCcHHHHHHHhcCCCeEEEEECCHHHHHHHHHhc
Confidence 4578888778889999999997766677777777654
No 498
>PRK14096 pgi glucose-6-phosphate isomerase; Provisional
Probab=39.88 E-value=42 Score=31.78 Aligned_cols=43 Identities=28% Similarity=0.431 Sum_probs=32.5
Q ss_pred cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCC
Q 041256 36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYN 85 (244)
Q Consensus 36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~g 85 (244)
-.|-..|.+.+ ++.|+++||+++|.+ +. .+. +..+||.|++.+
T Consensus 466 ~~~~~~~~~~~--~~~~~~~~~~~~~~~--~~--~~~-~~~i~~~~~~n~ 508 (528)
T PRK14096 466 KKVEELLKEDG--GELSIEEIAAALGAP--EQ--VET-IYKILRHLAANN 508 (528)
T ss_pred HHHHHHHhccC--CCCCHHHHHHHcCCC--cc--HHH-HHHHHHHHhcCC
Confidence 44556665544 789999999999984 22 456 999999999963
No 499
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=39.81 E-value=29 Score=28.44 Aligned_cols=33 Identities=12% Similarity=0.009 Sum_probs=29.3
Q ss_pred CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256 50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89 (244)
Q Consensus 50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~ 89 (244)
+.|-++||+.+|++ .+. +.|.|..|...|+++.
T Consensus 169 ~~t~~~lA~~lG~s------ret-vsR~L~~L~~~G~I~~ 201 (226)
T PRK10402 169 HEKHTQAAEYLGVS------YRH-LLYVLAQFIQDGYLKK 201 (226)
T ss_pred cchHHHHHHHHCCc------HHH-HHHHHHHHHHCCCEEe
Confidence 56889999999997 456 9999999999999994
No 500
>cd02190 epsilon_tubulin The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The epsilon-tubulins which are widespread but not ubiquitous among eukaryotes play a role in basal body/centriole morphogenesis.
Probab=39.53 E-value=42 Score=30.27 Aligned_cols=37 Identities=24% Similarity=0.551 Sum_probs=28.0
Q ss_pred HHHHhhcCCCCCcceEEEecCCcc-----HHHHHHHHHCCCC
Q 041256 182 EKVLESYKGFEHVKKLVDVGGGLG-----ITLNMIISKYPHI 218 (244)
Q Consensus 182 ~~~~~~~~~~~~~~~vvDVGGG~G-----~~~~~l~~~~P~l 218 (244)
+..++.+|.+.++..+-.+|||+| .++..+...||..
T Consensus 90 r~~~E~cd~l~gf~i~~sl~GGTGSG~gs~l~e~l~~~y~~~ 131 (379)
T cd02190 90 RKAAEKCDSLQSFFILHSLGGGTGSGLGTYVLELLADEFPEV 131 (379)
T ss_pred HHHHhhCcCcceEEEEeecCCCcchhHHHHHHHHHHHhcCcc
Confidence 455677776788899999999998 3555566788875
Done!