Query 040620
Match_columns 214
No_of_seqs 106 out of 1133
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 10:08:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040620.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040620hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02716 C20_methyl_CrtF C-20 99.9 2.5E-24 5.4E-29 185.7 12.0 165 28-214 2-183 (306)
2 KOG3178 Hydroxyindole-O-methyl 99.9 1.1E-22 2.3E-27 174.9 14.6 188 12-213 2-210 (342)
3 PF00891 Methyltransf_2: O-met 99.8 2.5E-18 5.3E-23 143.5 8.1 112 96-214 3-134 (241)
4 PF08100 Dimerisation: Dimeris 98.9 4.7E-10 1E-14 71.3 2.0 49 31-79 1-51 (51)
5 PF09339 HTH_IclR: IclR helix- 97.8 6.2E-06 1.4E-10 52.5 1.0 47 39-88 6-52 (52)
6 PRK14103 trans-aconitate 2-met 97.7 0.00011 2.4E-09 61.7 6.5 43 168-212 19-61 (255)
7 COG4106 Tam Trans-aconitate me 97.5 0.00012 2.7E-09 60.0 4.8 44 167-212 19-62 (257)
8 PRK08287 cobalt-precorrin-6Y C 97.5 0.00017 3.6E-09 57.8 5.4 35 178-212 29-63 (187)
9 TIGR02469 CbiT precorrin-6Y C5 97.5 0.00029 6.3E-09 51.7 6.0 41 170-212 11-51 (124)
10 smart00346 HTH_ICLR helix_turn 97.4 0.00014 3E-09 51.2 3.1 57 39-104 8-64 (91)
11 PRK01683 trans-aconitate 2-met 97.4 0.00032 6.8E-09 58.9 5.6 44 167-212 20-63 (258)
12 COG2813 RsmC 16S RNA G1207 met 97.3 0.00038 8.2E-09 59.8 5.4 43 168-212 148-190 (300)
13 PRK15001 SAM-dependent 23S rib 97.3 0.00046 9.9E-09 61.6 5.5 42 170-213 220-261 (378)
14 COG1414 IclR Transcriptional r 97.3 0.00022 4.7E-09 60.0 3.1 57 39-104 7-63 (246)
15 smart00550 Zalpha Z-DNA-bindin 97.2 0.00053 1.1E-08 46.1 3.7 60 37-104 7-67 (68)
16 PRK06922 hypothetical protein; 97.2 0.0008 1.7E-08 63.6 6.1 36 178-213 416-451 (677)
17 PRK11569 transcriptional repre 97.2 0.00035 7.5E-09 59.6 3.4 57 39-104 31-87 (274)
18 PRK00107 gidB 16S rRNA methylt 97.1 0.00063 1.4E-08 54.9 4.5 32 181-212 46-77 (187)
19 PRK10163 DNA-binding transcrip 97.1 0.00043 9.3E-09 58.9 3.6 57 39-104 28-84 (271)
20 PF05175 MTS: Methyltransferas 97.1 0.00059 1.3E-08 53.9 3.8 33 180-212 31-63 (170)
21 PRK15090 DNA-binding transcrip 97.0 0.00051 1.1E-08 57.9 3.4 56 39-104 17-72 (257)
22 TIGR02752 MenG_heptapren 2-hep 97.0 0.0012 2.5E-08 54.4 5.4 43 169-213 36-79 (231)
23 TIGR02431 pcaR_pcaU beta-ketoa 97.0 0.00051 1.1E-08 57.6 3.2 55 39-104 12-66 (248)
24 TIGR00138 gidB 16S rRNA methyl 97.0 0.00067 1.4E-08 54.4 3.7 33 181-213 43-75 (181)
25 COG2230 Cfa Cyclopropane fatty 97.0 0.0016 3.5E-08 55.7 6.1 43 167-212 61-103 (283)
26 PRK14121 tRNA (guanine-N(7)-)- 97.0 0.0013 2.7E-08 58.9 5.3 33 180-212 122-154 (390)
27 PRK07402 precorrin-6B methylas 97.0 0.0017 3.7E-08 52.3 5.5 41 170-212 32-72 (196)
28 TIGR03587 Pse_Me-ase pseudamin 96.9 0.0013 2.8E-08 53.7 4.6 34 179-212 42-75 (204)
29 PRK00121 trmB tRNA (guanine-N( 96.9 0.0011 2.4E-08 53.9 4.1 33 180-212 40-72 (202)
30 PRK09834 DNA-binding transcrip 96.9 0.00085 1.8E-08 56.8 3.4 57 39-104 14-70 (263)
31 PRK09489 rsmC 16S ribosomal RN 96.9 0.0018 4E-08 57.0 5.5 33 181-213 197-229 (342)
32 TIGR02072 BioC biotin biosynth 96.9 0.0026 5.7E-08 51.9 6.1 34 180-213 34-67 (240)
33 TIGR00740 methyltransferase, p 96.9 0.0014 3.1E-08 54.4 4.4 33 180-212 53-87 (239)
34 PF12840 HTH_20: Helix-turn-he 96.8 0.00073 1.6E-08 44.3 1.5 54 31-88 5-58 (61)
35 PRK15451 tRNA cmo(5)U34 methyl 96.7 0.0018 3.8E-08 54.3 4.1 33 180-212 56-90 (247)
36 PF13412 HTH_24: Winged helix- 96.7 0.0011 2.3E-08 41.2 2.0 44 38-85 5-48 (48)
37 PRK11207 tellurite resistance 96.7 0.0028 6E-08 51.3 5.0 41 168-212 20-60 (197)
38 cd00092 HTH_CRP helix_turn_hel 96.7 0.0083 1.8E-07 39.4 6.3 44 50-103 24-67 (67)
39 PRK15068 tRNA mo(5)U34 methylt 96.6 0.0028 6E-08 55.4 4.8 32 180-212 122-153 (322)
40 PF02353 CMAS: Mycolic acid cy 96.6 0.0031 6.7E-08 53.9 4.9 42 168-212 52-93 (273)
41 PRK00274 ksgA 16S ribosomal RN 96.6 0.0038 8.2E-08 53.1 5.4 41 168-212 32-72 (272)
42 TIGR03533 L3_gln_methyl protei 96.6 0.0027 5.8E-08 54.5 4.4 33 180-212 121-153 (284)
43 PRK04457 spermidine synthase; 96.6 0.003 6.5E-08 53.6 4.4 33 180-212 66-98 (262)
44 PF01978 TrmB: Sugar-specific 96.6 0.00053 1.2E-08 45.9 -0.2 47 38-88 10-56 (68)
45 COG2890 HemK Methylase of poly 96.5 0.0025 5.4E-08 54.7 3.8 30 183-212 113-142 (280)
46 PF13489 Methyltransf_23: Meth 96.5 0.0044 9.5E-08 47.4 4.9 33 178-212 20-52 (161)
47 TIGR03534 RF_mod_PrmC protein- 96.5 0.0031 6.8E-08 52.3 4.3 33 180-212 87-119 (251)
48 PRK06202 hypothetical protein; 96.5 0.0079 1.7E-07 49.7 6.6 34 179-212 59-96 (232)
49 TIGR00477 tehB tellurite resis 96.5 0.0042 9.2E-08 50.1 4.9 41 169-213 21-61 (195)
50 PRK00216 ubiE ubiquinone/menaq 96.5 0.0057 1.2E-07 50.1 5.7 42 170-213 43-85 (239)
51 PRK11805 N5-glutamine S-adenos 96.5 0.0029 6.3E-08 54.9 4.0 31 182-212 135-165 (307)
52 PRK09328 N5-glutamine S-adenos 96.5 0.0057 1.2E-07 51.6 5.8 34 179-212 107-140 (275)
53 PRK14966 unknown domain/N5-glu 96.5 0.0045 9.7E-08 55.8 5.2 33 180-212 251-283 (423)
54 PF01022 HTH_5: Bacterial regu 96.5 0.0013 2.9E-08 40.7 1.3 44 38-86 4-47 (47)
55 TIGR00536 hemK_fam HemK family 96.5 0.0055 1.2E-07 52.5 5.5 31 182-212 116-146 (284)
56 COG2242 CobL Precorrin-6B meth 96.4 0.0056 1.2E-07 49.2 5.0 35 178-212 32-66 (187)
57 TIGR03704 PrmC_rel_meth putati 96.4 0.0073 1.6E-07 50.9 5.9 32 181-212 87-118 (251)
58 PLN02244 tocopherol O-methyltr 96.4 0.0072 1.6E-07 53.1 6.1 33 179-212 117-149 (340)
59 PRK10258 biotin biosynthesis p 96.4 0.0088 1.9E-07 49.9 6.3 43 166-212 30-72 (251)
60 PF13463 HTH_27: Winged helix 96.4 0.0019 4.1E-08 42.7 1.7 58 43-104 10-67 (68)
61 TIGR00452 methyltransferase, p 96.3 0.0073 1.6E-07 52.6 5.6 33 179-212 120-152 (314)
62 TIGR02021 BchM-ChlM magnesium 96.3 0.014 3E-07 47.8 6.9 31 180-212 55-85 (219)
63 PRK05785 hypothetical protein; 96.3 0.0059 1.3E-07 50.6 4.8 31 181-212 52-82 (226)
64 PF02082 Rrf2: Transcriptional 96.3 0.0047 1E-07 43.0 3.5 47 50-104 24-70 (83)
65 smart00419 HTH_CRP helix_turn_ 96.3 0.007 1.5E-07 37.0 3.9 36 50-88 7-42 (48)
66 PTZ00098 phosphoethanolamine N 96.3 0.0076 1.6E-07 51.0 5.3 44 167-213 41-84 (263)
67 COG2226 UbiE Methylase involve 96.3 0.0055 1.2E-07 51.3 4.3 33 180-212 51-83 (238)
68 COG4123 Predicted O-methyltran 96.3 0.0043 9.2E-08 52.2 3.6 43 170-213 35-77 (248)
69 PRK01544 bifunctional N5-gluta 96.2 0.0051 1.1E-07 57.0 4.2 32 181-212 139-170 (506)
70 TIGR00438 rrmJ cell division p 96.2 0.01 2.2E-07 47.4 5.4 35 178-212 30-65 (188)
71 PF13679 Methyltransf_32: Meth 96.2 0.0064 1.4E-07 46.5 4.0 35 178-212 23-61 (141)
72 TIGR01934 MenG_MenH_UbiE ubiqu 96.2 0.0097 2.1E-07 48.1 5.2 34 179-212 38-72 (223)
73 PRK10857 DNA-binding transcrip 96.2 0.011 2.4E-07 46.7 5.3 47 50-104 24-70 (164)
74 PRK10141 DNA-binding transcrip 96.1 0.0059 1.3E-07 45.6 3.4 56 29-88 9-64 (117)
75 PRK11705 cyclopropane fatty ac 96.1 0.013 2.9E-07 52.3 6.2 40 170-212 159-198 (383)
76 PRK07580 Mg-protoporphyrin IX 96.1 0.017 3.8E-07 47.1 6.3 32 179-212 62-93 (230)
77 PF09012 FeoC: FeoC like trans 96.1 0.0029 6.3E-08 42.5 1.4 44 41-88 5-48 (69)
78 PLN02336 phosphoethanolamine N 96.1 0.01 2.2E-07 54.2 5.3 43 168-213 256-298 (475)
79 PRK11188 rrmJ 23S rRNA methylt 96.0 0.0095 2.1E-07 48.8 4.4 34 179-212 50-84 (209)
80 COG0220 Predicted S-adenosylme 96.0 0.0075 1.6E-07 50.2 3.7 31 182-212 50-80 (227)
81 PRK11088 rrmA 23S rRNA methylt 96.0 0.009 1.9E-07 50.7 4.2 33 180-212 85-120 (272)
82 TIGR00755 ksgA dimethyladenosi 96.0 0.014 2.9E-07 49.1 5.3 41 168-212 19-59 (253)
83 PLN02233 ubiquinone biosynthes 96.0 0.01 2.2E-07 50.2 4.5 34 179-212 72-106 (261)
84 TIGR02337 HpaR homoprotocatech 95.9 0.015 3.2E-07 43.0 4.7 67 38-113 30-96 (118)
85 TIGR00080 pimt protein-L-isoas 95.9 0.017 3.7E-07 47.2 5.5 42 169-212 68-110 (215)
86 PRK14896 ksgA 16S ribosomal RN 95.9 0.017 3.8E-07 48.7 5.6 42 167-212 18-59 (258)
87 PRK13944 protein-L-isoaspartat 95.9 0.022 4.7E-07 46.3 5.9 35 178-212 70-105 (205)
88 KOG2899 Predicted methyltransf 95.9 0.01 2.2E-07 49.8 3.9 46 168-213 46-91 (288)
89 PF04703 FaeA: FaeA-like prote 95.9 0.0056 1.2E-07 40.5 2.0 46 40-88 4-49 (62)
90 smart00347 HTH_MARR helix_turn 95.9 0.0086 1.9E-07 42.1 3.1 62 38-104 12-73 (101)
91 PRK11036 putative S-adenosyl-L 95.8 0.016 3.5E-07 48.6 5.1 31 180-212 44-74 (255)
92 PF08220 HTH_DeoR: DeoR-like h 95.8 0.014 3E-07 37.8 3.6 44 41-88 5-48 (57)
93 PRK04266 fibrillarin; Provisio 95.8 0.02 4.4E-07 47.5 5.5 35 178-212 70-104 (226)
94 PRK12335 tellurite resistance 95.8 0.016 3.4E-07 49.7 4.9 31 180-212 120-150 (287)
95 TIGR03438 probable methyltrans 95.7 0.016 3.6E-07 50.0 4.9 34 180-213 63-97 (301)
96 PLN03075 nicotianamine synthas 95.7 0.018 3.9E-07 49.7 5.0 33 180-212 123-157 (296)
97 TIGR02010 IscR iron-sulfur clu 95.7 0.024 5.3E-07 43.1 5.1 47 50-104 24-70 (135)
98 PRK00517 prmA ribosomal protei 95.7 0.014 3E-07 49.0 4.1 32 180-212 119-150 (250)
99 PRK00377 cbiT cobalt-precorrin 95.7 0.021 4.6E-07 46.0 5.0 35 178-212 38-73 (198)
100 PF08003 Methyltransf_9: Prote 95.6 0.017 3.7E-07 49.9 4.4 32 179-211 114-145 (315)
101 PRK13942 protein-L-isoaspartat 95.6 0.033 7.1E-07 45.6 5.9 42 169-212 67-109 (212)
102 PLN02490 MPBQ/MSBQ methyltrans 95.5 0.018 3.8E-07 50.8 4.4 33 180-212 113-145 (340)
103 PF12802 MarR_2: MarR family; 95.5 0.0066 1.4E-07 39.3 1.3 46 39-88 8-55 (62)
104 COG2345 Predicted transcriptio 95.5 0.027 5.9E-07 46.4 5.1 72 41-121 16-89 (218)
105 smart00420 HTH_DEOR helix_turn 95.5 0.019 4E-07 35.5 3.2 44 41-88 5-48 (53)
106 PRK03902 manganese transport t 95.5 0.019 4E-07 44.0 3.8 54 44-112 16-69 (142)
107 COG3355 Predicted transcriptio 95.4 0.021 4.7E-07 43.0 3.9 43 43-89 35-77 (126)
108 PF01209 Ubie_methyltran: ubiE 95.4 0.014 3.1E-07 48.6 3.2 34 179-212 46-80 (233)
109 PHA03411 putative methyltransf 95.4 0.021 4.6E-07 48.8 4.3 32 181-212 65-96 (279)
110 TIGR00738 rrf2_super rrf2 fami 95.3 0.023 5E-07 42.7 3.9 47 50-104 24-70 (132)
111 COG2227 UbiG 2-polyprenyl-3-me 95.3 0.018 3.9E-07 48.0 3.5 32 180-213 59-90 (243)
112 TIGR00122 birA_repr_reg BirA b 95.3 0.021 4.6E-07 38.1 3.2 54 39-104 3-56 (69)
113 PLN02396 hexaprenyldihydroxybe 95.3 0.023 4.9E-07 49.8 4.1 31 180-212 131-161 (322)
114 smart00138 MeTrc Methyltransfe 95.2 0.097 2.1E-06 44.4 7.8 33 180-212 99-140 (264)
115 PF01047 MarR: MarR family; I 95.2 0.0072 1.6E-07 38.9 0.7 45 40-88 7-51 (59)
116 PLN02672 methionine S-methyltr 95.2 0.022 4.8E-07 57.0 4.2 32 181-212 119-150 (1082)
117 TIGR02702 SufR_cyano iron-sulf 95.1 0.044 9.5E-07 44.6 5.1 67 40-114 5-72 (203)
118 COG1321 TroR Mn-dependent tran 95.1 0.029 6.2E-07 43.9 3.8 50 49-112 22-71 (154)
119 PRK06266 transcription initiat 95.1 0.039 8.6E-07 44.2 4.7 45 40-88 26-70 (178)
120 PF08279 HTH_11: HTH domain; 95.1 0.026 5.7E-07 35.7 3.0 44 41-87 5-48 (55)
121 PF06325 PrmA: Ribosomal prote 95.0 0.031 6.8E-07 48.3 4.3 53 155-212 140-192 (295)
122 PLN02336 phosphoethanolamine N 95.0 0.041 8.8E-07 50.3 5.4 41 168-212 27-67 (475)
123 TIGR00406 prmA ribosomal prote 95.0 0.037 8E-07 47.5 4.7 33 180-213 159-191 (288)
124 PLN02366 spermidine synthase 95.0 0.027 5.9E-07 48.9 3.8 34 179-213 90-124 (308)
125 PF03848 TehB: Tellurite resis 95.0 0.045 9.7E-07 44.4 4.8 41 168-212 20-60 (192)
126 PF14947 HTH_45: Winged helix- 94.9 0.0084 1.8E-07 41.2 0.4 56 41-113 11-66 (77)
127 PRK00811 spermidine synthase; 94.9 0.029 6.4E-07 48.0 3.8 33 180-212 76-108 (283)
128 PRK01544 bifunctional N5-gluta 94.9 0.03 6.5E-07 51.9 4.1 33 180-212 347-379 (506)
129 PF07757 AdoMet_MTase: Predict 94.9 0.044 9.5E-07 40.2 4.0 32 179-212 57-88 (112)
130 smart00344 HTH_ASNC helix_turn 94.9 0.023 5E-07 41.1 2.6 46 37-86 4-49 (108)
131 PRK03573 transcriptional regul 94.8 0.076 1.6E-06 40.5 5.6 65 41-113 36-100 (144)
132 PRK11727 23S rRNA mA1618 methy 94.8 0.036 7.9E-07 48.4 4.2 33 180-212 114-146 (321)
133 PRK14967 putative methyltransf 94.8 0.048 1E-06 44.8 4.8 35 178-213 34-68 (223)
134 TIGR01884 cas_HTH CRISPR locus 94.8 0.039 8.4E-07 44.9 4.1 58 38-104 145-202 (203)
135 PF01325 Fe_dep_repress: Iron 94.8 0.028 6E-07 36.8 2.7 37 49-88 20-56 (60)
136 PRK11050 manganese transport r 94.8 0.031 6.8E-07 43.5 3.4 58 41-113 42-99 (152)
137 smart00418 HTH_ARSR helix_turn 94.8 0.057 1.2E-06 34.4 4.2 43 41-88 2-44 (66)
138 PLN02585 magnesium protoporphy 94.8 0.033 7.1E-07 48.6 3.8 32 180-213 144-175 (315)
139 PRK10901 16S rRNA methyltransf 94.8 0.044 9.6E-07 49.7 4.7 35 178-212 242-276 (427)
140 KOG3115 Methyltransferase-like 94.7 0.014 3.1E-07 47.6 1.3 32 181-212 61-92 (249)
141 PRK11873 arsM arsenite S-adeno 94.7 0.052 1.1E-06 45.8 4.7 35 178-212 75-110 (272)
142 COG2264 PrmA Ribosomal protein 94.6 0.04 8.7E-07 47.6 3.9 54 154-212 140-193 (300)
143 TIGR02944 suf_reg_Xantho FeS a 94.6 0.041 8.9E-07 41.4 3.6 47 50-104 24-70 (130)
144 PHA00738 putative HTH transcri 94.6 0.042 9E-07 40.2 3.4 60 37-104 13-72 (108)
145 COG1959 Predicted transcriptio 94.6 0.039 8.4E-07 42.9 3.4 47 50-104 24-70 (150)
146 TIGR00478 tly hemolysin TlyA f 94.6 0.088 1.9E-06 43.8 5.7 42 169-212 65-106 (228)
147 PF08461 HTH_12: Ribonuclease 94.6 0.029 6.2E-07 37.5 2.3 48 41-88 3-52 (66)
148 PF01726 LexA_DNA_bind: LexA D 94.5 0.027 5.8E-07 37.6 2.0 41 45-88 19-60 (65)
149 PHA03412 putative methyltransf 94.5 0.045 9.8E-07 45.8 3.7 32 181-212 50-84 (241)
150 KOG1270 Methyltransferases [Co 94.4 0.044 9.5E-07 46.4 3.5 30 181-212 90-119 (282)
151 PF04967 HTH_10: HTH DNA bindi 94.4 0.066 1.4E-06 34.2 3.6 42 30-78 6-47 (53)
152 TIGR03840 TMPT_Se_Te thiopurin 94.4 0.08 1.7E-06 43.5 5.0 31 180-212 34-64 (213)
153 KOG2904 Predicted methyltransf 94.3 0.05 1.1E-06 46.4 3.6 33 180-212 148-180 (328)
154 PF13601 HTH_34: Winged helix 94.3 0.0087 1.9E-07 41.5 -0.8 64 37-104 1-64 (80)
155 TIGR00373 conserved hypothetic 94.3 0.047 1E-06 42.8 3.3 44 40-87 18-61 (158)
156 PRK14902 16S rRNA methyltransf 94.3 0.062 1.3E-06 48.9 4.5 35 178-212 248-283 (444)
157 PF05148 Methyltransf_8: Hypot 94.2 0.14 2.9E-06 42.2 5.9 64 145-212 38-101 (219)
158 PTZ00338 dimethyladenosine tra 94.2 0.1 2.3E-06 45.0 5.5 41 168-212 26-66 (294)
159 PRK11512 DNA-binding transcrip 94.1 0.054 1.2E-06 41.4 3.3 65 40-113 44-108 (144)
160 PF06163 DUF977: Bacterial pro 94.1 0.058 1.3E-06 40.5 3.2 51 34-88 10-60 (127)
161 cd07377 WHTH_GntR Winged helix 94.0 0.15 3.3E-06 32.8 5.0 34 52-88 26-59 (66)
162 PRK05134 bifunctional 3-demeth 94.0 0.12 2.6E-06 42.5 5.4 32 180-213 48-79 (233)
163 PRK13168 rumA 23S rRNA m(5)U19 94.0 0.062 1.3E-06 48.9 4.0 32 179-212 296-327 (443)
164 COG4190 Predicted transcriptio 94.0 0.063 1.4E-06 40.6 3.2 47 38-88 66-112 (144)
165 PRK13943 protein-L-isoaspartat 93.9 0.13 2.8E-06 45.0 5.7 35 178-212 78-113 (322)
166 PRK11014 transcriptional repre 93.9 0.077 1.7E-06 40.6 3.8 61 32-104 10-70 (141)
167 cd00090 HTH_ARSR Arsenical Res 93.9 0.084 1.8E-06 34.6 3.6 44 40-88 11-54 (78)
168 PF10294 Methyltransf_16: Puta 93.8 0.14 3E-06 40.6 5.2 37 178-214 43-79 (173)
169 smart00345 HTH_GNTR helix_turn 93.8 0.14 3.1E-06 32.3 4.4 36 50-88 18-54 (60)
170 PRK01581 speE spermidine synth 93.8 0.082 1.8E-06 47.0 4.1 35 179-213 149-183 (374)
171 PRK00312 pcm protein-L-isoaspa 93.7 0.15 3.2E-06 41.5 5.3 33 178-212 76-108 (212)
172 COG4742 Predicted transcriptio 93.7 0.069 1.5E-06 45.2 3.3 64 33-113 10-73 (260)
173 PRK04148 hypothetical protein; 93.6 0.15 3.3E-06 38.9 4.8 40 169-212 7-47 (134)
174 PRK11920 rirA iron-responsive 93.6 0.11 2.4E-06 40.5 4.1 47 50-104 23-69 (153)
175 TIGR00563 rsmB ribosomal RNA s 93.5 0.11 2.4E-06 47.1 4.6 35 178-212 236-270 (426)
176 KOG1540 Ubiquinone biosynthesi 93.5 0.08 1.7E-06 44.8 3.4 34 180-213 100-139 (296)
177 PRK13255 thiopurine S-methyltr 93.4 0.15 3.3E-06 42.0 5.0 32 179-212 36-67 (218)
178 TIGR01889 Staph_reg_Sar staphy 93.4 0.067 1.5E-06 39.1 2.6 37 50-89 42-78 (109)
179 cd07153 Fur_like Ferric uptake 93.4 0.086 1.9E-06 38.6 3.1 59 39-103 4-67 (116)
180 PRK06474 hypothetical protein; 93.3 0.13 2.8E-06 41.2 4.3 71 31-104 6-78 (178)
181 TIGR00417 speE spermidine synt 93.2 0.11 2.4E-06 44.1 4.0 34 180-213 72-105 (270)
182 PF00325 Crp: Bacterial regula 93.2 0.077 1.7E-06 30.2 2.0 31 51-84 2-32 (32)
183 TIGR01983 UbiG ubiquinone bios 93.0 0.11 2.3E-06 42.3 3.4 32 180-213 45-76 (224)
184 PRK15431 ferrous iron transpor 93.0 0.15 3.3E-06 35.1 3.6 44 41-88 7-50 (78)
185 PRK03522 rumB 23S rRNA methylu 92.9 0.14 3.1E-06 44.4 4.3 30 181-212 174-203 (315)
186 smart00529 HTH_DTXR Helix-turn 92.5 0.14 3.1E-06 36.0 3.2 46 54-113 2-47 (96)
187 PF02002 TFIIE_alpha: TFIIE al 92.5 0.052 1.1E-06 39.4 0.9 44 41-88 18-61 (105)
188 PF01638 HxlR: HxlR-like helix 92.3 0.051 1.1E-06 38.3 0.6 62 42-113 11-73 (90)
189 COG4189 Predicted transcriptio 92.2 0.19 4.1E-06 41.9 3.8 55 29-87 16-70 (308)
190 TIGR01610 phage_O_Nterm phage 92.2 0.29 6.3E-06 34.9 4.4 44 50-102 46-89 (95)
191 PF07381 DUF1495: Winged helix 92.0 0.18 3.9E-06 35.8 3.1 63 35-104 8-82 (90)
192 TIGR02085 meth_trns_rumB 23S r 92.0 0.19 4.2E-06 44.7 4.1 31 180-212 233-263 (374)
193 PRK11169 leucine-responsive tr 91.9 0.15 3.2E-06 40.1 2.9 47 36-86 14-60 (164)
194 KOG1271 Methyltransferases [Ge 91.9 0.23 4.9E-06 40.1 3.9 22 181-202 68-89 (227)
195 PF02319 E2F_TDP: E2F/DP famil 91.9 0.15 3.3E-06 34.4 2.5 36 50-88 23-63 (71)
196 PF07789 DUF1627: Protein of u 91.8 0.32 6.8E-06 37.6 4.4 36 50-88 5-40 (155)
197 PRK03612 spermidine synthase; 91.8 0.2 4.3E-06 46.7 4.0 33 179-212 296-329 (521)
198 PRK10909 rsmD 16S rRNA m(2)G96 91.8 0.31 6.6E-06 39.7 4.6 32 180-212 53-84 (199)
199 PF02527 GidB: rRNA small subu 91.7 0.35 7.5E-06 38.9 4.9 30 183-212 51-80 (184)
200 COG4565 CitB Response regulato 91.5 0.18 4E-06 41.4 3.1 42 43-87 165-206 (224)
201 PRK10870 transcriptional repre 91.5 0.43 9.4E-06 37.9 5.2 65 41-113 60-125 (176)
202 PRK11179 DNA-binding transcrip 91.5 0.17 3.7E-06 39.2 2.8 46 37-86 10-55 (153)
203 PF08221 HTH_9: RNA polymerase 91.3 0.13 2.7E-06 33.9 1.6 43 41-87 18-60 (62)
204 PF14394 DUF4423: Domain of un 91.2 0.62 1.3E-05 37.0 5.7 61 26-104 22-84 (171)
205 PRK04214 rbn ribonuclease BN/u 91.1 0.29 6.3E-06 44.2 4.3 46 49-104 308-353 (412)
206 COG1522 Lrp Transcriptional re 91.1 0.2 4.2E-06 38.4 2.8 48 37-88 9-56 (154)
207 COG0357 GidB Predicted S-adeno 91.1 0.21 4.5E-06 41.3 3.0 32 181-212 68-99 (215)
208 PLN02781 Probable caffeoyl-CoA 91.0 0.32 6.9E-06 40.5 4.2 36 178-213 66-102 (234)
209 TIGR00479 rumA 23S rRNA (uraci 91.0 0.34 7.3E-06 43.9 4.5 33 178-212 290-322 (431)
210 PF00398 RrnaAD: Ribosomal RNA 90.9 0.32 7E-06 41.0 4.2 43 166-212 18-60 (262)
211 PF09243 Rsm22: Mitochondrial 90.9 0.48 1E-05 40.4 5.2 33 180-212 33-66 (274)
212 TIGR00095 RNA methyltransferas 90.8 0.32 7E-06 39.1 3.8 32 180-212 49-80 (189)
213 PF13545 HTH_Crp_2: Crp-like h 90.2 0.39 8.6E-06 32.1 3.3 36 50-88 27-62 (76)
214 PF08784 RPA_C: Replication pr 90.0 0.16 3.6E-06 36.5 1.4 47 38-87 49-98 (102)
215 PF08123 DOT1: Histone methyla 89.9 0.53 1.1E-05 38.5 4.4 43 168-212 32-74 (205)
216 COG1378 Predicted transcriptio 89.9 0.51 1.1E-05 39.7 4.4 47 50-104 29-75 (247)
217 PF01135 PCMT: Protein-L-isoas 89.8 0.75 1.6E-05 37.7 5.3 41 169-211 63-104 (209)
218 PTZ00146 fibrillarin; Provisio 89.8 0.47 1E-05 41.0 4.2 35 178-212 130-165 (293)
219 TIGR01177 conserved hypothetic 89.7 0.64 1.4E-05 40.6 5.1 33 178-212 180-212 (329)
220 PRK14903 16S rRNA methyltransf 89.7 0.52 1.1E-05 42.9 4.7 35 178-212 235-270 (431)
221 PRK13509 transcriptional repre 89.7 0.41 8.8E-06 40.3 3.7 45 40-88 9-53 (251)
222 KOG1499 Protein arginine N-met 89.6 0.41 8.8E-06 42.1 3.7 32 179-211 59-90 (346)
223 COG4976 Predicted methyltransf 89.6 0.44 9.6E-06 39.9 3.7 26 180-205 125-150 (287)
224 PRK04172 pheS phenylalanyl-tRN 89.4 0.22 4.7E-06 46.1 2.0 63 38-113 8-70 (489)
225 PRK14165 winged helix-turn-hel 89.3 0.51 1.1E-05 39.0 3.9 58 44-113 15-72 (217)
226 PLN02823 spermine synthase 89.3 0.51 1.1E-05 41.6 4.1 33 180-212 103-135 (336)
227 PRK00215 LexA repressor; Valid 89.2 0.48 1E-05 38.3 3.7 38 48-88 20-58 (205)
228 PF13730 HTH_36: Helix-turn-he 89.2 0.38 8.3E-06 30.2 2.5 29 53-84 27-55 (55)
229 PF04182 B-block_TFIIIC: B-blo 89.1 0.36 7.7E-06 32.9 2.4 49 37-88 3-52 (75)
230 PF13404 HTH_AsnC-type: AsnC-t 89.1 0.2 4.3E-06 30.3 1.0 36 37-76 4-39 (42)
231 KOG1541 Predicted protein carb 89.1 0.21 4.6E-06 41.5 1.5 31 180-212 50-80 (270)
232 PRK14901 16S rRNA methyltransf 89.0 0.6 1.3E-05 42.4 4.5 35 178-212 250-285 (434)
233 PRK00536 speE spermidine synth 89.0 0.44 9.6E-06 40.5 3.4 32 179-212 71-102 (262)
234 TIGR00498 lexA SOS regulatory 89.0 0.52 1.1E-05 38.0 3.7 37 49-88 23-60 (199)
235 PF03444 HrcA_DNA-bdg: Winged 88.9 0.76 1.7E-05 31.7 3.9 35 49-86 21-55 (78)
236 TIGR02787 codY_Gpos GTP-sensin 88.9 0.48 1E-05 39.7 3.4 46 40-88 187-232 (251)
237 TIGR02143 trmA_only tRNA (urac 88.8 0.71 1.5E-05 40.8 4.7 29 182-212 199-227 (353)
238 PF00392 GntR: Bacterial regul 88.7 0.54 1.2E-05 30.7 3.0 36 50-88 22-58 (64)
239 COG1497 Predicted transcriptio 88.5 0.47 1E-05 39.7 3.1 90 40-143 14-108 (260)
240 TIGR00446 nop2p NOL1/NOP2/sun 88.4 0.86 1.9E-05 38.5 4.8 34 179-212 70-104 (264)
241 COG0030 KsgA Dimethyladenosine 88.4 1.1 2.3E-05 38.1 5.3 43 167-211 19-61 (259)
242 COG1846 MarR Transcriptional r 88.4 0.44 9.5E-06 34.3 2.7 69 36-113 22-90 (126)
243 COG0421 SpeE Spermidine syntha 88.1 0.64 1.4E-05 40.0 3.9 34 179-212 75-108 (282)
244 PRK10906 DNA-binding transcrip 88.1 0.4 8.7E-06 40.4 2.6 45 40-88 9-53 (252)
245 KOG3010 Methyltransferase [Gen 88.0 0.38 8.2E-06 40.4 2.3 27 179-205 32-58 (261)
246 PHA02943 hypothetical protein; 87.8 0.73 1.6E-05 35.9 3.6 44 40-88 15-58 (165)
247 KOG3420 Predicted RNA methylas 87.7 0.39 8.5E-06 37.4 2.1 32 180-213 48-80 (185)
248 PRK14904 16S rRNA methyltransf 87.6 0.87 1.9E-05 41.5 4.6 34 179-212 249-283 (445)
249 PRK09802 DNA-binding transcrip 87.6 0.46 9.9E-06 40.4 2.7 45 40-88 21-65 (269)
250 PRK11886 bifunctional biotin-- 87.4 0.62 1.3E-05 40.5 3.5 56 39-104 7-62 (319)
251 COG1349 GlpR Transcriptional r 87.3 0.59 1.3E-05 39.4 3.2 54 40-104 9-62 (253)
252 PF02796 HTH_7: Helix-turn-hel 87.3 0.23 5E-06 30.3 0.5 23 51-76 21-43 (45)
253 PRK10046 dpiA two-component re 87.1 0.62 1.3E-05 37.9 3.1 45 40-87 166-210 (225)
254 PF01596 Methyltransf_3: O-met 87.1 0.93 2E-05 37.0 4.1 34 179-212 44-78 (205)
255 PF10007 DUF2250: Uncharacteri 87.0 0.61 1.3E-05 33.2 2.6 46 39-88 10-55 (92)
256 PF05732 RepL: Firmicute plasm 86.8 0.8 1.7E-05 36.2 3.5 43 52-104 76-118 (165)
257 PRK13777 transcriptional regul 86.8 0.66 1.4E-05 37.4 3.0 65 40-113 49-113 (185)
258 COG3432 Predicted transcriptio 86.7 0.2 4.3E-06 35.9 -0.0 62 41-113 20-82 (95)
259 PRK10434 srlR DNA-bindng trans 86.7 0.53 1.1E-05 39.7 2.5 45 40-88 9-53 (256)
260 COG2512 Predicted membrane-ass 86.6 0.51 1.1E-05 40.0 2.4 47 39-88 198-244 (258)
261 PRK10411 DNA-binding transcrip 86.5 0.91 2E-05 38.0 3.8 45 40-88 8-52 (240)
262 PRK05031 tRNA (uracil-5-)-meth 86.5 0.99 2.1E-05 40.0 4.3 29 182-212 208-236 (362)
263 COG1510 Predicted transcriptio 86.4 0.74 1.6E-05 36.5 3.0 44 42-88 32-75 (177)
264 COG2518 Pcm Protein-L-isoaspar 86.2 1.7 3.6E-05 35.8 5.1 33 169-203 63-95 (209)
265 COG1733 Predicted transcriptio 86.0 2.7 5.7E-05 31.4 5.7 81 14-113 10-91 (120)
266 KOG3045 Predicted RNA methylas 85.9 1.6 3.4E-05 37.3 4.9 55 141-196 142-196 (325)
267 PF12793 SgrR_N: Sugar transpo 85.7 1.1 2.3E-05 33.3 3.5 36 50-88 18-53 (115)
268 PF05401 NodS: Nodulation prot 85.6 1.1 2.4E-05 36.5 3.7 33 178-212 41-73 (201)
269 PRK11639 zinc uptake transcrip 85.2 1.6 3.4E-05 34.5 4.4 48 38-88 28-80 (169)
270 PF13518 HTH_28: Helix-turn-he 85.2 0.79 1.7E-05 28.2 2.2 29 52-83 13-41 (52)
271 smart00531 TFIIE Transcription 84.9 0.9 2E-05 35.1 2.9 41 40-84 5-45 (147)
272 COG2263 Predicted RNA methylas 84.9 0.82 1.8E-05 37.0 2.7 34 178-212 43-76 (198)
273 TIGR02147 Fsuc_second hypothet 84.6 1.3 2.7E-05 37.9 3.9 45 50-104 136-182 (271)
274 PF03141 Methyltransf_29: Puta 84.6 0.55 1.2E-05 43.3 1.7 23 179-201 116-138 (506)
275 PRK12423 LexA repressor; Provi 83.7 1.4 3.1E-05 35.7 3.7 36 50-88 24-60 (202)
276 PF13384 HTH_23: Homeodomain-l 83.1 0.57 1.2E-05 28.8 0.9 38 40-83 9-46 (50)
277 PF01564 Spermine_synth: Sperm 83.1 1.1 2.3E-05 37.7 2.8 33 180-212 76-108 (246)
278 COG3413 Predicted DNA binding 83.1 1.5 3.2E-05 35.9 3.6 42 29-77 160-201 (215)
279 PF00165 HTH_AraC: Bacterial r 82.9 0.69 1.5E-05 27.5 1.2 27 50-79 7-33 (42)
280 PLN02853 Probable phenylalanyl 82.5 0.83 1.8E-05 42.2 2.0 65 36-113 3-68 (492)
281 PF05584 Sulfolobus_pRN: Sulfo 82.3 2 4.3E-05 29.1 3.3 42 41-87 10-51 (72)
282 COG1675 TFA1 Transcription ini 82.2 1.4 3E-05 35.3 2.9 45 40-88 22-66 (176)
283 PLN02476 O-methyltransferase 81.8 2 4.4E-05 36.8 4.0 36 178-213 116-152 (278)
284 KOG2361 Predicted methyltransf 81.7 0.74 1.6E-05 38.7 1.3 30 182-211 73-104 (264)
285 PRK05638 threonine synthase; V 81.6 1.4 3E-05 40.2 3.2 60 41-112 376-437 (442)
286 TIGR03879 near_KaiC_dom probab 81.4 0.66 1.4E-05 31.6 0.7 34 50-86 31-64 (73)
287 PF03428 RP-C: Replication pro 81.3 2 4.4E-05 34.3 3.6 57 29-88 45-105 (177)
288 COG1654 BirA Biotin operon rep 81.1 3 6.6E-05 28.8 4.0 52 42-104 12-63 (79)
289 PRK10736 hypothetical protein; 81.0 2 4.2E-05 38.5 3.8 50 40-101 312-361 (374)
290 PRK15128 23S rRNA m(5)C1962 me 80.9 2 4.2E-05 38.8 3.8 32 180-212 220-251 (396)
291 PTZ00326 phenylalanyl-tRNA syn 80.8 1 2.2E-05 41.7 1.9 66 36-113 6-71 (494)
292 PRK11760 putative 23S rRNA C24 80.8 2.2 4.7E-05 37.8 3.9 33 178-212 209-241 (357)
293 PRK11753 DNA-binding transcrip 80.7 2.1 4.6E-05 34.1 3.7 35 51-88 168-202 (211)
294 COG4122 Predicted O-methyltran 80.5 2.5 5.5E-05 35.0 4.0 36 178-213 57-93 (219)
295 TIGR01321 TrpR trp operon repr 80.5 1.3 2.8E-05 31.7 2.0 41 34-79 40-80 (94)
296 PRK09954 putative kinase; Prov 80.4 1.3 2.8E-05 39.0 2.4 43 39-85 6-48 (362)
297 PRK04424 fatty acid biosynthes 80.4 0.66 1.4E-05 37.2 0.6 44 40-87 11-54 (185)
298 PF01475 FUR: Ferric uptake re 80.3 0.89 1.9E-05 33.5 1.2 61 37-103 9-74 (120)
299 PF08280 HTH_Mga: M protein tr 80.0 0.61 1.3E-05 30.1 0.2 38 38-79 7-44 (59)
300 PRK04338 N(2),N(2)-dimethylgua 79.9 2.2 4.9E-05 38.2 3.8 32 181-212 58-89 (382)
301 TIGR03697 NtcA_cyano global ni 79.6 2.7 5.9E-05 33.0 3.9 36 50-88 142-177 (193)
302 PF03374 ANT: Phage antirepres 79.6 3.6 7.8E-05 29.8 4.2 42 40-87 13-54 (111)
303 PRK11534 DNA-binding transcrip 79.5 3.7 7.9E-05 33.5 4.7 37 49-88 28-64 (224)
304 PHA02591 hypothetical protein; 79.4 1.3 2.9E-05 30.4 1.7 32 41-77 51-82 (83)
305 PF12324 HTH_15: Helix-turn-he 79.4 2.5 5.5E-05 29.0 3.1 41 41-88 29-69 (77)
306 PF09929 DUF2161: Uncharacteri 79.1 2.4 5.2E-05 31.5 3.1 48 43-104 66-113 (118)
307 COG3963 Phospholipid N-methylt 78.8 3 6.5E-05 33.3 3.7 35 165-201 35-69 (194)
308 PRK11783 rlmL 23S rRNA m(2)G24 78.5 2.4 5.3E-05 41.0 3.9 32 180-212 538-569 (702)
309 PHA02701 ORF020 dsRNA-binding 78.3 2.2 4.8E-05 34.2 2.9 48 38-88 6-53 (183)
310 COG1802 GntR Transcriptional r 78.0 4.8 0.0001 33.0 5.0 37 49-88 37-73 (230)
311 PRK00135 scpB segregation and 77.8 3.1 6.8E-05 33.6 3.7 43 39-88 93-135 (188)
312 TIGR03338 phnR_burk phosphonat 77.7 3.9 8.4E-05 32.9 4.3 37 49-88 32-68 (212)
313 PRK09462 fur ferric uptake reg 77.7 3.1 6.8E-05 31.9 3.6 59 38-102 19-83 (148)
314 PRK11642 exoribonuclease R; Pr 77.0 4.3 9.3E-05 40.0 5.1 57 41-104 24-81 (813)
315 PRK11161 fumarate/nitrate redu 76.9 3.3 7.1E-05 33.8 3.7 36 50-88 183-218 (235)
316 KOG4589 Cell division protein 76.9 3.8 8.1E-05 33.4 3.9 35 178-212 67-102 (232)
317 PF07037 DUF1323: Putative tra 76.9 1.7 3.6E-05 32.4 1.7 31 52-88 1-31 (122)
318 cd04762 HTH_MerR-trunc Helix-T 76.8 2 4.3E-05 25.5 1.8 22 52-76 1-22 (49)
319 TIGR02698 CopY_TcrY copper tra 76.6 3.4 7.3E-05 31.2 3.4 47 38-88 6-56 (130)
320 PF12147 Methyltransf_20: Puta 76.5 3.4 7.4E-05 35.7 3.8 33 180-212 135-169 (311)
321 PRK13256 thiopurine S-methyltr 76.3 5.7 0.00012 33.0 4.9 32 180-213 43-74 (226)
322 PRK11414 colanic acid/biofilm 76.2 5.7 0.00012 32.3 5.0 37 49-88 32-68 (221)
323 PF04760 IF2_N: Translation in 76.1 0.93 2E-05 28.6 0.2 32 50-87 2-34 (54)
324 TIGR01764 excise DNA binding d 75.9 2.2 4.7E-05 25.5 1.8 22 52-76 2-23 (49)
325 PF02475 Met_10: Met-10+ like- 75.6 3 6.6E-05 33.9 3.1 34 179-212 100-133 (200)
326 PF05724 TPMT: Thiopurine S-me 75.5 3.3 7.1E-05 34.1 3.3 33 178-212 35-67 (218)
327 PF10668 Phage_terminase: Phag 75.4 2.1 4.5E-05 28.0 1.7 23 49-74 20-42 (60)
328 PRK13918 CRP/FNR family transc 75.3 4.3 9.4E-05 32.1 3.9 35 50-87 148-182 (202)
329 PRK09391 fixK transcriptional 75.3 4.1 8.8E-05 33.4 3.9 36 50-88 178-213 (230)
330 PRK01381 Trp operon repressor; 75.2 2.5 5.4E-05 30.5 2.2 40 34-78 40-79 (99)
331 PF05331 DUF742: Protein of un 75.1 4.3 9.3E-05 30.1 3.5 37 50-89 54-90 (114)
332 PRK09775 putative DNA-binding 74.8 3.2 6.9E-05 38.0 3.4 53 41-104 5-57 (442)
333 COG0735 Fur Fe2+/Zn2+ uptake r 74.2 3.1 6.7E-05 32.0 2.7 64 38-104 23-88 (145)
334 KOG0820 Ribosomal RNA adenine 74.2 6.5 0.00014 33.8 4.8 35 167-203 47-81 (315)
335 PF05219 DREV: DREV methyltran 73.8 4.6 9.9E-05 34.3 3.8 29 180-208 94-122 (265)
336 TIGR00635 ruvB Holliday juncti 73.6 3 6.5E-05 35.5 2.8 37 49-88 253-290 (305)
337 TIGR02987 met_A_Alw26 type II 72.4 2.7 6E-05 39.0 2.4 25 180-204 31-55 (524)
338 PRK10430 DNA-binding transcrip 72.4 4.8 0.00011 32.9 3.7 36 50-88 177-212 (239)
339 PF12728 HTH_17: Helix-turn-he 72.0 3 6.4E-05 25.6 1.8 22 52-76 2-23 (51)
340 PF09681 Phage_rep_org_N: N-te 72.0 7.9 0.00017 29.0 4.4 45 50-104 52-96 (121)
341 COG5459 Predicted rRNA methyla 72.0 1.4 3E-05 39.2 0.3 31 181-211 114-145 (484)
342 cd04761 HTH_MerR-SF Helix-Turn 71.5 3.1 6.7E-05 25.0 1.8 27 52-85 1-27 (49)
343 PRK09464 pdhR transcriptional 70.9 6.5 0.00014 32.7 4.1 36 50-88 32-68 (254)
344 COG5631 Predicted transcriptio 70.6 34 0.00074 27.1 7.6 76 23-104 63-145 (199)
345 PRK11511 DNA-binding transcrip 70.5 3.4 7.3E-05 30.9 2.1 35 50-87 24-58 (127)
346 PF13936 HTH_38: Helix-turn-he 70.5 2.4 5.2E-05 25.6 1.1 24 50-76 19-42 (44)
347 COG1725 Predicted transcriptio 70.4 7.2 0.00016 29.4 3.8 45 50-103 34-78 (125)
348 PRK09990 DNA-binding transcrip 70.3 6.9 0.00015 32.4 4.2 37 49-88 28-65 (251)
349 TIGR03826 YvyF flagellar opero 70.1 3.1 6.8E-05 31.8 1.9 33 41-76 35-68 (137)
350 COG2390 DeoR Transcriptional r 70.1 4.7 0.0001 35.3 3.2 36 50-88 25-60 (321)
351 PF04492 Phage_rep_O: Bacterio 69.6 5.8 0.00013 28.6 3.1 36 50-88 53-88 (100)
352 smart00342 HTH_ARAC helix_turn 69.4 4.4 9.5E-05 26.7 2.3 27 51-80 1-27 (84)
353 PRK10402 DNA-binding transcrip 69.4 6.6 0.00014 32.0 3.8 36 50-88 168-203 (226)
354 PF11312 DUF3115: Protein of u 69.2 6.9 0.00015 34.1 4.0 22 181-202 87-108 (315)
355 TIGR00331 hrcA heat shock gene 69.1 5.8 0.00013 34.9 3.6 42 43-88 14-57 (337)
356 PRK10225 DNA-binding transcrip 69.0 7.3 0.00016 32.4 4.1 37 49-88 30-67 (257)
357 PRK09334 30S ribosomal protein 68.9 5.2 0.00011 28.1 2.6 41 44-88 35-75 (86)
358 PF02384 N6_Mtase: N-6 DNA Met 68.8 6.6 0.00014 33.6 3.8 34 179-212 45-85 (311)
359 KOG2165 Anaphase-promoting com 68.7 6.6 0.00014 37.7 4.0 49 50-104 615-663 (765)
360 PF09107 SelB-wing_3: Elongati 68.7 6.3 0.00014 24.7 2.7 42 43-88 3-44 (50)
361 PF13551 HTH_29: Winged helix- 68.4 4.3 9.4E-05 28.8 2.3 28 53-83 14-41 (112)
362 PF10771 DUF2582: Protein of u 68.0 4.4 9.4E-05 26.9 2.0 41 41-85 13-53 (65)
363 PF09904 HTH_43: Winged helix- 67.9 2.3 5E-05 30.1 0.6 54 43-104 15-71 (90)
364 smart00421 HTH_LUXR helix_turn 67.9 4.4 9.5E-05 24.7 1.9 26 50-78 17-42 (58)
365 TIGR02812 fadR_gamma fatty aci 67.8 8.2 0.00018 31.6 4.1 36 50-88 28-64 (235)
366 COG2519 GCD14 tRNA(1-methylade 67.7 14 0.00031 31.3 5.4 54 157-212 69-127 (256)
367 PF06969 HemN_C: HemN C-termin 67.7 7.8 0.00017 25.1 3.2 45 50-104 19-63 (66)
368 PRK10681 DNA-binding transcrip 66.7 4.2 9.1E-05 34.1 2.1 39 40-82 11-49 (252)
369 PRK10421 DNA-binding transcrip 66.7 8.9 0.00019 31.9 4.1 36 50-88 24-60 (253)
370 smart00342 HTH_ARAC helix_turn 66.6 15 0.00032 24.0 4.6 34 41-79 42-76 (84)
371 PF02295 z-alpha: Adenosine de 66.6 0.88 1.9E-05 30.3 -1.6 48 37-88 5-54 (66)
372 PLN02589 caffeoyl-CoA O-methyl 66.2 8.7 0.00019 32.3 3.9 36 178-213 77-113 (247)
373 PRK04984 fatty acid metabolism 66.1 9.4 0.0002 31.3 4.1 36 50-88 29-65 (239)
374 PF13443 HTH_26: Cro/C1-type H 65.9 2.2 4.8E-05 27.3 0.3 29 43-76 4-32 (63)
375 PF05185 PRMT5: PRMT5 arginine 65.8 4.7 0.0001 37.0 2.4 23 180-202 186-208 (448)
376 PF11972 HTH_13: HTH DNA bindi 65.7 6.2 0.00013 25.2 2.2 47 41-101 4-50 (54)
377 PRK13239 alkylmercury lyase; P 65.6 4.2 9E-05 33.3 1.8 43 39-88 25-67 (206)
378 PF04545 Sigma70_r4: Sigma-70, 65.5 4.8 0.0001 24.6 1.7 25 50-77 19-43 (50)
379 PLN02668 indole-3-acetate carb 65.4 12 0.00026 33.7 4.8 35 180-214 63-112 (386)
380 PRK10219 DNA-binding transcrip 65.1 6 0.00013 28.2 2.4 33 50-85 20-52 (107)
381 PRK03837 transcriptional regul 65.0 11 0.00023 31.0 4.2 37 49-88 34-71 (241)
382 PHA03103 double-strand RNA-bin 64.9 7.9 0.00017 31.1 3.3 44 41-88 18-61 (183)
383 PF04539 Sigma70_r3: Sigma-70 64.9 4.6 0.0001 27.1 1.7 29 50-81 19-47 (78)
384 PF13022 HTH_Tnp_1_2: Helix-tu 64.8 3.9 8.5E-05 31.4 1.4 30 43-75 26-55 (142)
385 PF00356 LacI: Bacterial regul 64.6 3.6 7.8E-05 25.3 1.0 20 53-75 1-20 (46)
386 PF03514 GRAS: GRAS domain fam 64.4 8 0.00017 34.5 3.6 44 168-213 100-150 (374)
387 PRK11523 DNA-binding transcrip 64.2 11 0.00023 31.4 4.2 37 49-88 29-66 (253)
388 cd06170 LuxR_C_like C-terminal 63.9 5.9 0.00013 24.2 2.0 26 50-78 14-39 (57)
389 PF03297 Ribosomal_S25: S25 ri 63.7 9.8 0.00021 27.8 3.3 36 50-88 58-93 (105)
390 PF01170 UPF0020: Putative RNA 63.4 16 0.00034 29.0 4.8 43 168-212 18-69 (179)
391 KOG1500 Protein arginine N-met 63.4 6.3 0.00014 35.0 2.6 21 181-201 178-198 (517)
392 PF07091 FmrO: Ribosomal RNA m 63.2 5.6 0.00012 33.6 2.2 34 179-212 104-137 (251)
393 COG0293 FtsJ 23S rRNA methylas 62.5 19 0.00041 29.5 5.1 46 167-213 33-79 (205)
394 PF13542 HTH_Tnp_ISL3: Helix-t 61.9 5.5 0.00012 24.4 1.5 32 40-77 19-50 (52)
395 PF08281 Sigma70_r4_2: Sigma-7 61.8 5.5 0.00012 24.6 1.5 24 50-76 25-48 (54)
396 PF01418 HTH_6: Helix-turn-hel 61.7 3.8 8.3E-05 27.8 0.8 30 50-82 33-62 (77)
397 PF06056 Terminase_5: Putative 61.7 8.4 0.00018 24.9 2.4 25 50-77 12-36 (58)
398 PF01381 HTH_3: Helix-turn-hel 61.6 4.3 9.2E-05 25.1 1.0 24 50-76 8-31 (55)
399 PRK15418 transcriptional regul 61.5 9.4 0.0002 33.3 3.4 35 50-87 28-62 (318)
400 smart00422 HTH_MERR helix_turn 61.5 6.1 0.00013 25.7 1.8 28 52-86 1-28 (70)
401 KOG2651 rRNA adenine N-6-methy 61.3 8.8 0.00019 34.6 3.2 31 178-209 151-181 (476)
402 PRK13824 replication initiatio 61.0 10 0.00022 34.3 3.7 66 29-101 57-126 (404)
403 COG4901 Ribosomal protein S25 60.2 11 0.00023 27.4 2.8 42 43-88 52-93 (107)
404 TIGR02844 spore_III_D sporulat 60.1 5.6 0.00012 27.5 1.4 30 41-75 11-40 (80)
405 PF13814 Replic_Relax: Replica 59.5 11 0.00025 29.6 3.4 65 44-113 3-70 (191)
406 KOG3191 Predicted N6-DNA-methy 59.5 8.7 0.00019 31.1 2.6 32 181-212 44-76 (209)
407 COG0640 ArsR Predicted transcr 59.3 13 0.00029 25.0 3.4 54 31-88 20-73 (110)
408 PLN03238 probable histone acet 59.2 32 0.00069 29.7 6.1 49 25-88 206-254 (290)
409 TIGR01714 phage_rep_org_N phag 59.0 18 0.00039 27.0 4.1 49 45-104 46-94 (119)
410 PF04157 EAP30: EAP30/Vps36 fa 59.0 5.6 0.00012 32.7 1.5 44 41-87 179-223 (223)
411 PF06971 Put_DNA-bind_N: Putat 58.8 2.1 4.5E-05 26.9 -0.9 31 41-74 17-48 (50)
412 PF08704 GCD14: tRNA methyltra 58.7 26 0.00056 29.5 5.4 43 168-212 30-73 (247)
413 PRK00082 hrcA heat-inducible t 58.7 12 0.00025 33.0 3.5 40 44-87 19-60 (339)
414 PF05344 DUF746: Domain of Unk 58.6 13 0.00027 24.7 2.8 29 50-81 12-40 (65)
415 PF03965 Penicillinase_R: Peni 58.6 4.9 0.00011 29.3 1.0 50 38-88 5-55 (115)
416 PRK05472 redox-sensing transcr 58.6 9.2 0.0002 31.1 2.7 44 35-82 15-60 (213)
417 PF07638 Sigma70_ECF: ECF sigm 58.5 8.4 0.00018 30.5 2.4 27 50-79 150-176 (185)
418 PF13411 MerR_1: MerR HTH fami 58.5 4.8 0.0001 26.2 0.8 27 52-85 1-27 (69)
419 PF00196 GerE: Bacterial regul 58.1 4.6 9.9E-05 25.6 0.7 36 37-78 7-42 (58)
420 COG2186 FadR Transcriptional r 58.1 16 0.00035 30.4 4.1 41 53-102 36-76 (241)
421 TIGR02531 yecD_yerC TrpR-relat 57.9 7.5 0.00016 27.4 1.8 33 39-77 41-73 (88)
422 PF03291 Pox_MCEL: mRNA cappin 57.7 10 0.00022 33.3 3.0 32 180-212 62-93 (331)
423 PLN03239 histone acetyltransfe 57.7 39 0.00085 30.0 6.5 52 25-88 264-315 (351)
424 COG2378 Predicted transcriptio 57.6 9.3 0.0002 33.2 2.7 56 41-104 13-68 (311)
425 KOG1661 Protein-L-isoaspartate 57.5 10 0.00022 31.5 2.7 23 178-200 80-102 (237)
426 PF01371 Trp_repressor: Trp re 57.2 7.6 0.00016 27.3 1.7 40 34-79 34-74 (87)
427 smart00753 PAM PCI/PINT associ 57.2 14 0.00031 25.1 3.2 47 37-87 11-57 (88)
428 smart00088 PINT motif in prote 57.2 14 0.00031 25.1 3.2 47 37-87 11-57 (88)
429 COG0758 Smf Predicted Rossmann 56.8 14 0.00031 32.7 3.7 45 39-88 299-343 (350)
430 TIGR03433 padR_acidobact trans 56.8 23 0.00049 25.2 4.2 64 41-113 9-81 (100)
431 COG4977 Transcriptional regula 56.6 6.5 0.00014 34.6 1.5 38 43-83 227-265 (328)
432 COG0500 SmtA SAM-dependent met 56.5 17 0.00036 25.5 3.6 28 184-212 52-80 (257)
433 COG3682 Predicted transcriptio 56.2 11 0.00023 28.4 2.4 61 37-104 7-68 (123)
434 PRK00080 ruvB Holliday junctio 56.0 12 0.00027 32.3 3.3 37 49-88 274-311 (328)
435 PF09106 SelB-wing_2: Elongati 56.0 17 0.00038 23.1 3.2 36 50-88 16-54 (59)
436 cd07977 TFIIE_beta_winged_heli 55.9 24 0.00053 24.0 4.0 37 42-80 15-53 (75)
437 PRK09413 IS2 repressor TnpA; R 55.8 9.4 0.0002 28.2 2.1 31 50-83 28-58 (121)
438 PRK13626 transcriptional regul 55.8 11 0.00023 35.3 3.0 37 50-89 22-58 (552)
439 cd06171 Sigma70_r4 Sigma70, re 55.3 13 0.00029 21.9 2.5 26 50-78 25-50 (55)
440 PF01853 MOZ_SAS: MOZ/SAS fami 54.9 27 0.00059 28.2 4.7 51 25-88 131-181 (188)
441 TIGR03739 PRTRC_D PRTRC system 54.7 43 0.00093 28.9 6.4 45 168-213 262-306 (320)
442 PF08222 HTH_CodY: CodY helix- 54.4 13 0.00029 24.1 2.3 36 50-88 3-38 (61)
443 PRK15121 right oriC-binding tr 53.8 9.9 0.00021 32.3 2.2 35 50-87 20-54 (289)
444 TIGR03070 couple_hipB transcri 53.7 9.3 0.0002 23.4 1.6 23 50-75 14-36 (58)
445 PF09821 AAA_assoc_C: C-termin 53.7 11 0.00024 28.1 2.2 43 56-113 2-44 (120)
446 COG3645 Uncharacterized phage- 53.5 11 0.00024 28.7 2.1 43 40-88 36-78 (135)
447 cd04764 HTH_MlrA-like_sg1 Heli 53.4 10 0.00022 24.6 1.8 22 52-76 1-22 (67)
448 PHA00542 putative Cro-like pro 53.1 8.2 0.00018 26.6 1.3 24 50-76 30-53 (82)
449 COG4367 Uncharacterized protei 52.7 12 0.00025 26.5 2.0 26 50-78 22-47 (97)
450 PF04218 CENP-B_N: CENP-B N-te 52.6 13 0.00028 23.4 2.1 34 37-76 11-44 (53)
451 PRK08558 adenine phosphoribosy 52.5 7 0.00015 32.7 1.1 38 35-75 7-44 (238)
452 PF07848 PaaX: PaaX-like prote 52.4 14 0.0003 24.8 2.3 54 43-103 12-68 (70)
453 cd01104 HTH_MlrA-CarA Helix-Tu 52.4 11 0.00023 24.4 1.8 22 52-76 1-22 (68)
454 KOG4300 Predicted methyltransf 52.4 31 0.00066 28.7 4.7 55 154-211 52-106 (252)
455 COG2524 Predicted transcriptio 51.6 23 0.0005 30.2 4.0 49 48-104 22-70 (294)
456 PF00376 MerR: MerR family reg 51.2 6.7 0.00015 23.0 0.6 26 53-85 1-26 (38)
457 cd04763 HTH_MlrA-like Helix-Tu 50.7 12 0.00025 24.4 1.8 28 52-85 1-28 (68)
458 PHA01634 hypothetical protein 50.6 19 0.00041 27.6 3.0 26 181-208 29-54 (156)
459 TIGR02063 RNase_R ribonuclease 50.4 20 0.00044 34.8 4.0 57 41-104 7-65 (709)
460 TIGR02404 trehalos_R_Bsub treh 50.0 22 0.00048 29.0 3.7 40 53-101 26-65 (233)
461 PHA01976 helix-turn-helix prot 49.9 12 0.00025 24.2 1.6 22 50-74 14-35 (67)
462 TIGR02325 C_P_lyase_phnF phosp 49.1 23 0.0005 28.9 3.7 41 53-102 34-74 (238)
463 PRK11302 DNA-binding transcrip 49.0 7.1 0.00015 32.9 0.6 42 40-84 20-64 (284)
464 PRK09392 ftrB transcriptional 49.0 18 0.0004 29.3 3.1 30 51-83 173-202 (236)
465 PRK15411 rcsA colanic acid cap 48.9 13 0.00029 30.0 2.2 35 35-75 139-173 (207)
466 PF02387 IncFII_repA: IncFII R 48.8 18 0.0004 31.1 3.1 39 50-88 94-139 (281)
467 COG2963 Transposase and inacti 48.7 17 0.00037 26.3 2.6 35 50-87 23-58 (116)
468 COG5340 Predicted transcriptio 48.6 7.1 0.00015 32.5 0.5 45 50-104 29-73 (269)
469 PLN00104 MYST -like histone ac 48.4 23 0.00049 32.5 3.7 49 25-88 357-405 (450)
470 TIGR03439 methyl_EasF probable 48.3 37 0.0008 29.7 4.9 41 168-212 68-112 (319)
471 PRK14999 histidine utilization 48.1 24 0.00052 29.0 3.7 60 31-103 19-79 (241)
472 PF02186 TFIIE_beta: TFIIE bet 47.8 31 0.00067 22.8 3.4 41 43-88 12-52 (65)
473 PRK09764 DNA-binding transcrip 47.8 30 0.00065 28.5 4.2 59 31-102 12-71 (240)
474 PF10078 DUF2316: Uncharacteri 47.7 11 0.00024 26.6 1.3 25 50-77 22-46 (89)
475 PF12242 Eno-Rase_NADH_b: NAD( 47.7 28 0.00061 23.9 3.2 36 178-213 36-75 (78)
476 PF14502 HTH_41: Helix-turn-he 47.6 42 0.00091 20.9 3.7 36 50-88 5-40 (48)
477 PRK15201 fimbriae regulatory p 47.2 14 0.00031 29.7 2.0 33 37-75 137-169 (198)
478 smart00351 PAX Paired Box doma 47.2 17 0.00036 27.1 2.3 45 37-87 22-66 (125)
479 PRK04217 hypothetical protein; 47.1 17 0.00037 26.7 2.3 31 41-76 50-80 (110)
480 PRK00118 putative DNA-binding 47.1 15 0.00033 26.7 2.0 24 50-76 32-55 (104)
481 PRK15466 carboxysome structura 46.9 16 0.00034 28.8 2.2 43 50-103 123-165 (166)
482 COG1565 Uncharacterized conser 46.9 29 0.00063 31.0 4.1 23 179-201 76-98 (370)
483 PF09202 Rio2_N: Rio2, N-termi 46.7 40 0.00086 23.3 4.0 47 50-104 23-69 (82)
484 PRK11557 putative DNA-binding 46.6 9.3 0.0002 32.2 0.9 32 50-84 29-60 (278)
485 PRK13558 bacterio-opsin activa 46.5 22 0.00048 33.7 3.6 43 29-78 612-654 (665)
486 PF04072 LCM: Leucine carboxyl 46.5 30 0.00064 27.3 3.8 36 179-214 77-112 (183)
487 PF12298 Bot1p: Eukaryotic mit 46.5 13 0.00028 29.6 1.7 39 36-79 20-58 (172)
488 TIGR02607 antidote_HigA addict 46.1 16 0.00034 24.3 1.8 23 50-75 17-39 (78)
489 PF08535 KorB: KorB domain; I 46.1 8.6 0.00019 27.0 0.5 26 50-78 2-27 (93)
490 PRK15340 transcriptional regul 45.8 20 0.00043 29.6 2.7 33 50-85 124-156 (216)
491 TIGR00475 selB selenocysteine- 45.8 26 0.00057 33.2 3.9 36 50-88 487-522 (581)
492 PF12692 Methyltransf_17: S-ad 45.7 32 0.0007 26.9 3.7 33 181-213 29-61 (160)
493 smart00354 HTH_LACI helix_turn 45.7 13 0.00028 24.6 1.4 20 53-75 2-21 (70)
494 TIGR02018 his_ut_repres histid 45.5 28 0.00061 28.4 3.6 41 53-102 27-67 (230)
495 COG4262 Predicted spermidine s 45.5 26 0.00055 31.7 3.5 34 179-213 288-322 (508)
496 COG5625 Predicted transcriptio 45.4 9.1 0.0002 27.7 0.6 62 39-104 24-85 (113)
497 PRK14096 pgi glucose-6-phospha 45.3 17 0.00036 34.1 2.5 43 39-82 466-508 (528)
498 PF00888 Cullin: Cullin family 45.2 6.9 0.00015 36.5 -0.1 40 44-87 528-567 (588)
499 KOG4058 Uncharacterized conser 44.8 21 0.00045 28.1 2.5 33 168-202 62-94 (199)
500 COG1386 scpB Chromosome segreg 44.7 36 0.00078 27.3 4.0 58 39-104 95-153 (184)
No 1
>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=99.91 E-value=2.5e-24 Score=185.74 Aligned_cols=165 Identities=18% Similarity=0.286 Sum_probs=127.3
Q ss_pred hHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcc
Q 040620 28 MKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDF 107 (214)
Q Consensus 28 ~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~ 107 (214)
+...+|++|+++||||+|++ +|.|++|||+++|+++ +.++||||+|+++|+++++ +++|++|+.
T Consensus 2 ~~~~~l~aa~~Lglfd~L~~--gp~t~~eLA~~~~~~~---~~~~~lL~~L~~lgll~~~--------~~~y~~t~~--- 65 (306)
T TIGR02716 2 IEFSCMKAAIELDLFSHMAE--GPKDLATLAADTGSVP---PRLEMLLETLRQMRVINLE--------DGKWSLTEF--- 65 (306)
T ss_pred chHHHHHHHHHcCcHHHHhc--CCCCHHHHHHHcCCCh---HHHHHHHHHHHhCCCeEec--------CCcEecchh---
Confidence 46789999999999999987 8999999999999999 9999999999999999987 489999999
Q ss_pred cccccc-c--cc----hHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHH---------HHHHHHHhhhh-hhhhHHHH
Q 040620 108 FSRISL-Q--LQ----GSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTA---------DGIFYEAMITD-FELIASVL 170 (214)
Q Consensus 108 ~s~~l~-~--~~----~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~---------~g~f~~am~~~-~~~~~~~~ 170 (214)
++.++ + +. +..+...+.. .....|.++.+++|++. +|... ...|...|... .....+.+
T Consensus 66 -~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~r~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 141 (306)
T TIGR02716 66 -ADYMFSPTPKEPNLHQTPVAKAMAF-LADDFYMGLSQAVRGQK--NFKGQVPYPPVTREDNLYFEEIHRSNAKFAIQLL 141 (306)
T ss_pred -HHhhccCCccchhhhcCchHHHHHH-HHHHHHHhHHHHhcCCc--ccccccCCCCCCHHHHHhHHHHHHhcchhHHHHH
Confidence 88776 2 21 1123322211 23356899999998532 23211 11455555433 33445556
Q ss_pred HhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCCC
Q 040620 171 IEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL 214 (214)
Q Consensus 171 l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~ 214 (214)
++..+ +++..+|||||||+|.+++.+++++|+++++++|+|+
T Consensus 142 ~~~~~--~~~~~~vlDiG~G~G~~~~~~~~~~p~~~~~~~D~~~ 183 (306)
T TIGR02716 142 LEEAK--LDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLPG 183 (306)
T ss_pred HHHcC--CCCCCEEEEeCCchhHHHHHHHHHCCCCEEEEEecHH
Confidence 77766 7788999999999999999999999999999999873
No 2
>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]
Probab=99.89 E-value=1.1e-22 Score=174.91 Aligned_cols=188 Identities=22% Similarity=0.282 Sum_probs=160.9
Q ss_pred hhhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcC--CCCCCcccHHHHHHHHHhCCceeeecC
Q 040620 12 EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALN--VHPNKTRCTQILVCLLAHSGFFVQQKD 89 (214)
Q Consensus 12 ~~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g--~~~~~~~~l~rlLr~L~~~g~l~~~~~ 89 (214)
+..++..+++++++++..+++|++|+||||||+|+++ ++ +.|||..+. ..|+.+..+.|+||.|++.+++++...
T Consensus 2 ~e~~~~l~~~~l~~~~~~~~~lk~A~eL~v~d~l~~~-~~--p~~ia~~l~~~~~~~~p~ll~r~lr~L~s~~i~k~~~~ 78 (342)
T KOG3178|consen 2 EENEASLRAMRLANGFALPMVLKAACELGVFDILANA-GS--PSEIASLLPTPKNPEAPVLLDRILRLLVSYSILKCRLV 78 (342)
T ss_pred chhHHHHHHHHHHhhhhhHHHHHHHHHcChHHHHHhC-CC--HHHHHHhccCCCCCCChhHHHHHHHHHHHhhhceeeee
Confidence 4567788999999999999999999999999999986 33 788888776 333344899999999999999998862
Q ss_pred CCCCCccceeeCCCCCcccccccc----ccchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH------------
Q 040620 90 GKNEQEEESILLPPHLDFFSRISL----QLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG------------ 153 (214)
Q Consensus 90 ~~~~~~~~~y~~t~~~~~~s~~l~----~~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g------------ 153 (214)
. . + .|++++. ++.++ ..++.+++........++.|.++.++++.++ .+|..++|
T Consensus 79 ~---~-~-~Y~~~~~----~~~~l~~~~~~S~a~~~~~~~~~v~~~~w~~l~dai~eg~-~~~~~~~G~~l~~~~~~~~~ 148 (342)
T KOG3178|consen 79 G---G-E-VYSATPV----CKYFLKDSGGGSLAPLVLLNTSKVIMNTWQFLKDAILEGG-DAFATAHGMMLGGYGGADER 148 (342)
T ss_pred c---c-e-eeeccch----hhhheecCCCCchhHHHHHhcccchhhhHHHHHHHHHhcc-cCCccccchhhhhhcccccc
Confidence 0 1 2 8999999 99987 2678888888888889999999999999876 35555554
Q ss_pred ---HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 154 ---IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 154 ---~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
.|+++|...++...+.+++.+. +|++..++||||||.|..+..++.+||+++++.||+|
T Consensus 149 ~~~~~~~sm~~l~~~~~~~il~~~~-Gf~~v~~avDvGgGiG~v~k~ll~~fp~ik~infdlp 210 (342)
T KOG3178|consen 149 FSKDFNGSMSFLSTLVMKKILEVYT-GFKGVNVAVDVGGGIGRVLKNLLSKYPHIKGINFDLP 210 (342)
T ss_pred cHHHHHHHHHHHHHHHHHhhhhhhc-ccccCceEEEcCCcHhHHHHHHHHhCCCCceeecCHH
Confidence 7899998888888888889887 5899999999999999999999999999999999998
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=99.75 E-value=2.5e-18 Score=143.50 Aligned_cols=112 Identities=29% Similarity=0.416 Sum_probs=93.8
Q ss_pred cceeeCCCCCcccccccc-c---cchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH---------------HHH
Q 040620 96 EESILLPPHLDFFSRISL-Q---LQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFY 156 (214)
Q Consensus 96 ~~~y~~t~~~~~~s~~l~-~---~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g---------------~f~ 156 (214)
+++|++|+. |+.|+ + .++..++.++.....+..|.+|.+++++|+ ++|...+| .|+
T Consensus 3 ~~~y~~t~~----s~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~v~~g~-~~~~~~~g~~~~~~~~~~~~~~~~f~ 77 (241)
T PF00891_consen 3 GDRYSLTPL----SELLLSDHSSPSMRGFVLFMISPELYPAWFRLTEAVRTGK-PPFEKAFGTPFFEYLEEDPELAKRFN 77 (241)
T ss_dssp TEEEEE-HH----HHGGSTTTTTTHHHHHHHHHTCHHHHHGGGGHHHHHHHSS--HHHHHHSS-HHHHHHCSHHHHHHHH
T ss_pred CCEEeChHH----HHHHhCCCCcCcHHHHHHHhcCHHHHHHHHHHHhhhccCC-CHHHHhcCCcHHHhhhhChHHHHHHH
Confidence 689999999 99988 3 357777777677788999999999999987 66666544 789
Q ss_pred HHhhhhhhhhH-HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCCC
Q 040620 157 EAMITDFELIA-SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL 214 (214)
Q Consensus 157 ~am~~~~~~~~-~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~ 214 (214)
++|...+.... ..++..++ +++.++|||||||+|.++.+++++||+++++++|+|+
T Consensus 78 ~~m~~~~~~~~~~~~~~~~d--~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~ 134 (241)
T PF00891_consen 78 AAMAEYSRLNAFDILLEAFD--FSGFKTVVDVGGGSGHFAIALARAYPNLRATVFDLPE 134 (241)
T ss_dssp HHHHHHHHHHHHHHHHHHST--TTTSSEEEEET-TTSHHHHHHHHHSTTSEEEEEE-HH
T ss_pred HHHHhhhhcchhhhhhcccc--ccCccEEEeccCcchHHHHHHHHHCCCCcceeeccHh
Confidence 99998888776 77888888 8888999999999999999999999999999999984
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=98.92 E-value=4.7e-10 Score=71.35 Aligned_cols=49 Identities=37% Similarity=0.640 Sum_probs=42.3
Q ss_pred HHHHHHHhcCcchhhhcCC-CCCCHHHHHHHcC-CCCCCcccHHHHHHHHH
Q 040620 31 LSLKRAIQLRIPDIINNSG-QPMTLTQIIVALN-VHPNKTRCTQILVCLLA 79 (214)
Q Consensus 31 ~~L~~a~~lglfd~L~~~~-~p~t~~eLA~~~g-~~~~~~~~l~rlLr~L~ 79 (214)
.+|++|+||||||+|+.+| +|+|..||+.++. .+|.+...|+|+||+|+
T Consensus 1 MaLk~aveLgI~dii~~~g~~~ls~~eia~~l~~~~p~~~~~L~RimR~L~ 51 (51)
T PF08100_consen 1 MALKCAVELGIPDIIHNAGGGPLSLSEIAARLPTSNPSAPPMLDRIMRLLV 51 (51)
T ss_dssp HHHHHHHHTTHHHHHHHHTTS-BEHHHHHHTSTCT-TTHHHHHHHHHHHHH
T ss_pred CcHHHHHHcCcHHHHHHcCCCCCCHHHHHHHcCCCCcchHHHHHHHHHHhC
Confidence 4799999999999999986 7999999999999 77756679999999986
No 5
>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=97.83 E-value=6.2e-06 Score=52.52 Aligned_cols=47 Identities=30% Similarity=0.485 Sum_probs=41.5
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+.|+++|...++++|+.|||+++|++. ..++|+|..|+..|++.+++
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~---stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPK---STVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCcCeecCc
Confidence 457888888878899999999999999 99999999999999999873
No 6
>PRK14103 trans-aconitate 2-methyltransferase; Provisional
Probab=97.67 E-value=0.00011 Score=61.72 Aligned_cols=43 Identities=19% Similarity=0.382 Sum_probs=37.3
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+++.++ .....+|||||||+|.++..+++++|+.+++++|+
T Consensus 19 ~~ll~~l~--~~~~~~vLDlGcG~G~~~~~l~~~~p~~~v~gvD~ 61 (255)
T PRK14103 19 YDLLARVG--AERARRVVDLGCGPGNLTRYLARRWPGAVIEALDS 61 (255)
T ss_pred HHHHHhCC--CCCCCEEEEEcCCCCHHHHHHHHHCCCCEEEEEEC
Confidence 45666665 55678999999999999999999999999999997
No 7
>COG4106 Tam Trans-aconitate methyltransferase [General function prediction only]
Probab=97.54 E-value=0.00012 Score=59.99 Aligned_cols=44 Identities=23% Similarity=0.326 Sum_probs=39.2
Q ss_pred HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+-.++..++ ......|+|+|||+|.....|++++|...++++|-
T Consensus 19 a~dLla~Vp--~~~~~~v~DLGCGpGnsTelL~~RwP~A~i~GiDs 62 (257)
T COG4106 19 ARDLLARVP--LERPRRVVDLGCGPGNSTELLARRWPDAVITGIDS 62 (257)
T ss_pred HHHHHhhCC--ccccceeeecCCCCCHHHHHHHHhCCCCeEeeccC
Confidence 355777787 77889999999999999999999999999999984
No 8
>PRK08287 cobalt-precorrin-6Y C(15)-methyltransferase; Validated
Probab=97.53 E-value=0.00017 Score=57.77 Aligned_cols=35 Identities=31% Similarity=0.466 Sum_probs=32.3
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+..+|||||||+|.+++.+++++|+.+++.+|.
T Consensus 29 ~~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~ 63 (187)
T PRK08287 29 LHRAKHLIDVGAGTGSVSIEAALQFPSLQVTAIER 63 (187)
T ss_pred CCCCCEEEEECCcCCHHHHHHHHHCCCCEEEEEEC
Confidence 45678999999999999999999999999999997
No 9
>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=97.50 E-value=0.00029 Score=51.67 Aligned_cols=41 Identities=15% Similarity=0.246 Sum_probs=34.1
Q ss_pred HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+++.++ .....+++|+|||.|.++..+++++|+.+++.+|.
T Consensus 11 ~~~~~~--~~~~~~vldlG~G~G~~~~~l~~~~~~~~v~~vD~ 51 (124)
T TIGR02469 11 TLSKLR--LRPGDVLWDIGAGSGSITIEAARLVPNGRVYAIER 51 (124)
T ss_pred HHHHcC--CCCCCEEEEeCCCCCHHHHHHHHHCCCceEEEEcC
Confidence 344444 34456999999999999999999999999999996
No 10
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=97.41 E-value=0.00014 Score=51.17 Aligned_cols=57 Identities=18% Similarity=0.255 Sum_probs=48.5
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+.|++.|...++++|+.|||+.+|+++ ..++|.|+.|...|++...+. ++.|.+++.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~---~tv~r~l~~L~~~g~l~~~~~------~~~y~l~~~ 64 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSK---STAHRLLNTLQELGYVEQDGQ------NGRYRLGPK 64 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCeeecCC------CCceeecHH
Confidence 456777876546899999999999999 999999999999999998742 567888776
No 11
>PRK01683 trans-aconitate 2-methyltransferase; Provisional
Probab=97.39 E-value=0.00032 Score=58.86 Aligned_cols=44 Identities=18% Similarity=0.299 Sum_probs=37.8
Q ss_pred HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...++..++ ..+..+|+|||||.|.++..+++++|+.+++.+|.
T Consensus 20 ~~~ll~~~~--~~~~~~vLDiGcG~G~~~~~la~~~~~~~v~gvD~ 63 (258)
T PRK01683 20 ARDLLARVP--LENPRYVVDLGCGPGNSTELLVERWPAARITGIDS 63 (258)
T ss_pred HHHHHhhCC--CcCCCEEEEEcccCCHHHHHHHHHCCCCEEEEEEC
Confidence 345666665 56678999999999999999999999999999997
No 12
>COG2813 RsmC 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]
Probab=97.33 E-value=0.00038 Score=59.81 Aligned_cols=43 Identities=21% Similarity=0.296 Sum_probs=36.1
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.-+++.++ .....+|+|+|||.|.+++.+++.+|+.+++.+|.
T Consensus 148 ~lLl~~l~--~~~~~~vlDlGCG~Gvlg~~la~~~p~~~vtmvDv 190 (300)
T COG2813 148 RLLLETLP--PDLGGKVLDLGCGYGVLGLVLAKKSPQAKLTLVDV 190 (300)
T ss_pred HHHHHhCC--ccCCCcEEEeCCCccHHHHHHHHhCCCCeEEEEec
Confidence 44667777 33344999999999999999999999999999885
No 13
>PRK15001 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional
Probab=97.27 E-value=0.00046 Score=61.55 Aligned_cols=42 Identities=14% Similarity=0.237 Sum_probs=34.7
Q ss_pred HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
+++.++ .....+|+|+|||+|..++.+++++|+.+++.+|..
T Consensus 220 lL~~lp--~~~~~~VLDLGCGtGvi~i~la~~~P~~~V~~vD~S 261 (378)
T PRK15001 220 FMQHLP--ENLEGEIVDLGCGNGVIGLTLLDKNPQAKVVFVDES 261 (378)
T ss_pred HHHhCC--cccCCeEEEEeccccHHHHHHHHhCCCCEEEEEECC
Confidence 455555 222369999999999999999999999999999974
No 14
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=97.25 E-value=0.00022 Score=60.00 Aligned_cols=57 Identities=19% Similarity=0.320 Sum_probs=49.9
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+.|+++|...+.++++.|||+++|+++ ..++|+|..|+..|++.+++. +++|.+++.
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpk---sT~~RlL~tL~~~G~v~~d~~------~g~Y~Lg~~ 63 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPK---STVHRLLQTLVELGYVEQDPE------DGRYRLGPR 63 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCH---HHHHHHHHHHHHCCCEEEcCC------CCcEeehHH
Confidence 457888887545577999999999999 999999999999999999974 578999988
No 15
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=97.17 E-value=0.00053 Score=46.15 Aligned_cols=60 Identities=18% Similarity=0.219 Sum_probs=48.4
Q ss_pred HhcCcchhhhcCCC-CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 37 IQLRIPDIINNSGQ-PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 37 ~~lglfd~L~~~~~-p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
.+-.|+..|..+|+ ++|+.|||+.+|++. ..++|.|..|...|+++..+.. +..|.++..
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~---~~v~r~L~~L~~~G~V~~~~~~-----~~~W~i~~~ 67 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPK---KEVNRVLYSLEKKGKVCKQGGT-----PPLWKLTDK 67 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecCCC-----CCceEeecC
Confidence 44567788888744 399999999999999 9999999999999999986520 367777653
No 16
>PRK06922 hypothetical protein; Provisional
Probab=97.16 E-value=0.0008 Score=63.55 Aligned_cols=36 Identities=22% Similarity=0.208 Sum_probs=32.8
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
+.+..+|||||||+|.++..+++.+|+.+++++|+.
T Consensus 416 ~~~g~rVLDIGCGTG~ls~~LA~~~P~~kVtGIDIS 451 (677)
T PRK06922 416 YIKGDTIVDVGAGGGVMLDMIEEETEDKRIYGIDIS 451 (677)
T ss_pred hcCCCEEEEeCCCCCHHHHHHHHhCCCCEEEEEECC
Confidence 345689999999999999999999999999999985
No 17
>PRK11569 transcriptional repressor IclR; Provisional
Probab=97.16 E-value=0.00035 Score=59.56 Aligned_cols=57 Identities=19% Similarity=0.283 Sum_probs=49.9
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+.|+++|.+.+.|+|+.|||+++|+++ ..++|+|..|+..||+.+++. .++|++.+.
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpk---sTv~RlL~tL~~~G~l~~~~~------~~~Y~lG~~ 87 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPN---STTHRLLTTMQQQGFVRQVGE------LGHWAIGAH 87 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEcCC------CCeEecCHH
Confidence 457777776557899999999999999 999999999999999998753 689999877
No 18
>PRK00107 gidB 16S rRNA methyltransferase GidB; Reviewed
Probab=97.13 E-value=0.00063 Score=54.89 Aligned_cols=32 Identities=28% Similarity=0.378 Sum_probs=30.4
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+|+|||||+|..+..+++++|+.+++.+|.
T Consensus 46 g~~VLDiGcGtG~~al~la~~~~~~~V~giD~ 77 (187)
T PRK00107 46 GERVLDVGSGAGFPGIPLAIARPELKVTLVDS 77 (187)
T ss_pred CCeEEEEcCCCCHHHHHHHHHCCCCeEEEEeC
Confidence 68999999999999999999999999999986
No 19
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=97.12 E-value=0.00043 Score=58.92 Aligned_cols=57 Identities=18% Similarity=0.193 Sum_probs=50.2
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+.|++.|..+++++|+.|||+++|+++ ..+.|+|..|+..|++.+++. .++|.+++.
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpk---Stv~RlL~tL~~~G~l~~~~~------~~~Y~lG~~ 84 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPL---STTFRLLKVLQAADFVYQDSQ------LGWWHIGLG 84 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEcCC------CCeEEecHH
Confidence 567788877657899999999999999 999999999999999998753 688999887
No 20
>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=97.07 E-value=0.00059 Score=53.93 Aligned_cols=33 Identities=27% Similarity=0.369 Sum_probs=30.7
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...+++|+|||+|..++.+++++|+.+++..|.
T Consensus 31 ~~~~vLDlG~G~G~i~~~la~~~~~~~v~~vDi 63 (170)
T PF05175_consen 31 KGGRVLDLGCGSGVISLALAKRGPDAKVTAVDI 63 (170)
T ss_dssp TTCEEEEETSTTSHHHHHHHHTSTCEEEEEEES
T ss_pred cCCeEEEecCChHHHHHHHHHhCCCCEEEEEcC
Confidence 467999999999999999999999999998886
No 21
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=97.05 E-value=0.00051 Score=57.89 Aligned_cols=56 Identities=11% Similarity=0.195 Sum_probs=49.1
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+.|++.|... +++|+.|||+++|+++ ..++|+|+.|+..|++.+++. .++|.+.+.
T Consensus 17 l~IL~~l~~~-~~l~l~eia~~lgl~k---stv~Rll~tL~~~G~l~~~~~------~~~Y~lG~~ 72 (257)
T PRK15090 17 FGILQALGEE-REIGITELSQRVMMSK---STVYRFLQTMKTLGYVAQEGE------SEKYSLTLK 72 (257)
T ss_pred HHHHHHhhcC-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEcCC------CCcEEecHH
Confidence 4566777765 6899999999999999 999999999999999998753 589999988
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=97.04 E-value=0.0012 Score=54.38 Aligned_cols=43 Identities=19% Similarity=0.169 Sum_probs=34.7
Q ss_pred HHHhhcccccCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecCC
Q 040620 169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFACH 213 (214)
Q Consensus 169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp 213 (214)
.++..++ .....+|||||||+|.++..+++.+ |+.+++++|+-
T Consensus 36 ~~l~~l~--~~~~~~vLDiGcG~G~~~~~la~~~~~~~~v~gvD~s 79 (231)
T TIGR02752 36 DTMKRMN--VQAGTSALDVCCGTADWSIALAEAVGPEGHVIGLDFS 79 (231)
T ss_pred HHHHhcC--CCCCCEEEEeCCCcCHHHHHHHHHhCCCCEEEEEECC
Confidence 3445444 5556899999999999999999986 67899999973
No 23
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=97.03 E-value=0.00051 Score=57.56 Aligned_cols=55 Identities=16% Similarity=0.282 Sum_probs=49.0
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+.|++.|...+.|+|+.|||+++|+++ ..++|+|..|+..|++.++ +++|.+.+.
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpk---sT~~RlL~tL~~~G~l~~~--------~~~Y~lG~~ 66 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTR---AAARRFLLTLVELGYVTSD--------GRLFWLTPR 66 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEeC--------CCEEEecHH
Confidence 567788876558899999999999999 9999999999999999875 478999988
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=97.03 E-value=0.00067 Score=54.38 Aligned_cols=33 Identities=27% Similarity=0.419 Sum_probs=30.5
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
..+|+|||||+|..+..++..+|+.+++.+|.-
T Consensus 43 ~~~vLDiGcGtG~~s~~la~~~~~~~V~~iD~s 75 (181)
T TIGR00138 43 GKKVIDIGSGAGFPGIPLAIARPELKLTLLESN 75 (181)
T ss_pred CCeEEEecCCCCccHHHHHHHCCCCeEEEEeCc
Confidence 679999999999999999999999999999863
No 25
>COG2230 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]
Probab=97.02 E-value=0.0016 Score=55.71 Aligned_cols=43 Identities=19% Similarity=0.214 Sum_probs=37.5
Q ss_pred HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.+.+++.+. +.+..+|||||||-|.+++-.+++| +.+++.+++
T Consensus 61 ~~~~~~kl~--L~~G~~lLDiGCGWG~l~~~aA~~y-~v~V~GvTl 103 (283)
T COG2230 61 LDLILEKLG--LKPGMTLLDIGCGWGGLAIYAAEEY-GVTVVGVTL 103 (283)
T ss_pred HHHHHHhcC--CCCCCEEEEeCCChhHHHHHHHHHc-CCEEEEeeC
Confidence 355667666 8889999999999999999999999 999998876
No 26
>PRK14121 tRNA (guanine-N(7)-)-methyltransferase; Provisional
Probab=96.97 E-value=0.0013 Score=58.86 Aligned_cols=33 Identities=18% Similarity=0.130 Sum_probs=30.7
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
....+||||||+|.++..+++++|+..++++|+
T Consensus 122 ~~p~vLEIGcGsG~~ll~lA~~~P~~~~iGIEI 154 (390)
T PRK14121 122 QEKILIEIGFGSGRHLLYQAKNNPNKLFIGIEI 154 (390)
T ss_pred CCCeEEEEcCcccHHHHHHHHhCCCCCEEEEEC
Confidence 456999999999999999999999999999986
No 27
>PRK07402 precorrin-6B methylase; Provisional
Probab=96.96 E-value=0.0017 Score=52.34 Aligned_cols=41 Identities=22% Similarity=0.272 Sum_probs=34.1
Q ss_pred HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
++..++ .....+|+|+|||+|.++..+++..|..+++.+|+
T Consensus 32 l~~~l~--~~~~~~VLDiG~G~G~~~~~la~~~~~~~V~~vD~ 72 (196)
T PRK07402 32 LISQLR--LEPDSVLWDIGAGTGTIPVEAGLLCPKGRVIAIER 72 (196)
T ss_pred HHHhcC--CCCCCEEEEeCCCCCHHHHHHHHHCCCCEEEEEeC
Confidence 344444 44567999999999999999999999999999997
No 28
>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=96.92 E-value=0.0013 Score=53.72 Aligned_cols=34 Identities=12% Similarity=0.213 Sum_probs=30.9
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.+..+|||||||+|..+..+++..|..+++.+|+
T Consensus 42 ~~~~~VLDiGCG~G~~~~~L~~~~~~~~v~giDi 75 (204)
T TIGR03587 42 PKIASILELGANIGMNLAALKRLLPFKHIYGVEI 75 (204)
T ss_pred CCCCcEEEEecCCCHHHHHHHHhCCCCeEEEEEC
Confidence 3567999999999999999999999999999986
No 29
>PRK00121 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed
Probab=96.90 E-value=0.0011 Score=53.88 Aligned_cols=33 Identities=18% Similarity=0.217 Sum_probs=30.6
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+..+|+|||||+|.++..+++.+|+.+++.+|.
T Consensus 40 ~~~~VLDiGcGtG~~~~~la~~~p~~~v~gVD~ 72 (202)
T PRK00121 40 DAPIHLEIGFGKGEFLVEMAKANPDINFIGIEV 72 (202)
T ss_pred CCCeEEEEccCCCHHHHHHHHHCCCccEEEEEe
Confidence 467999999999999999999999999999986
No 30
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=96.89 E-value=0.00085 Score=56.79 Aligned_cols=57 Identities=16% Similarity=0.205 Sum_probs=49.5
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+.|++.|...++++|..|||+++|+++ ..+.|+|+.|...|++.+++. +++|.+++.
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~k---stv~RlL~tL~~~g~v~~~~~------~~~Y~Lg~~ 70 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHR---TTVRRLLETLQEEGYVRRSAS------DDSFRLTLK 70 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEecC------CCcEEEcHH
Confidence 456777776546799999999999999 999999999999999998863 578999887
No 31
>PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional
Probab=96.88 E-value=0.0018 Score=57.01 Aligned_cols=33 Identities=21% Similarity=0.351 Sum_probs=30.2
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
..+|+|+|||.|.+++.+++++|+.+++..|.-
T Consensus 197 ~g~VLDlGCG~G~ls~~la~~~p~~~v~~vDis 229 (342)
T PRK09489 197 KGKVLDVGCGAGVLSAVLARHSPKIRLTLSDVS 229 (342)
T ss_pred CCeEEEeccCcCHHHHHHHHhCCCCEEEEEECC
Confidence 458999999999999999999999999999863
No 32
>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=96.87 E-value=0.0026 Score=51.95 Aligned_cols=34 Identities=24% Similarity=0.440 Sum_probs=30.6
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
...+|||||||.|.++..+++..|+.++++.|..
T Consensus 34 ~~~~vLDlG~G~G~~~~~l~~~~~~~~~~~~D~~ 67 (240)
T TIGR02072 34 IPASVLDIGCGTGYLTRALLKRFPQAEFIALDIS 67 (240)
T ss_pred CCCeEEEECCCccHHHHHHHHhCCCCcEEEEeCh
Confidence 3478999999999999999999999999998863
No 33
>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=96.85 E-value=0.0014 Score=54.36 Aligned_cols=33 Identities=18% Similarity=0.162 Sum_probs=29.8
Q ss_pred CCCcEEeecCCchHHHHHHHHH--CCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATA--FPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~--~P~l~~~v~Dl 212 (214)
+..+|||||||+|..+..++++ +|+.+++++|+
T Consensus 53 ~~~~iLDlGcG~G~~~~~l~~~~~~p~~~v~gvD~ 87 (239)
T TIGR00740 53 PDSNVYDLGCSRGAATLSARRNINQPNVKIIGIDN 87 (239)
T ss_pred CCCEEEEecCCCCHHHHHHHHhcCCCCCeEEEEeC
Confidence 4578999999999999999997 48999999997
No 34
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=96.75 E-value=0.00073 Score=44.26 Aligned_cols=54 Identities=19% Similarity=0.351 Sum_probs=44.6
Q ss_pred HHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 31 LSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 31 ~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.+|.--.++.|+..|... +|+|+.|||+.+|+++ ..+.+-|+.|...|++....
T Consensus 5 ~aL~~p~R~~Il~~L~~~-~~~t~~ela~~l~~~~---~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 5 KALSDPTRLRILRLLASN-GPMTVSELAEELGISQ---STVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHTSHHHHHHHHHHHHC-STBEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEEE
T ss_pred HHhCCHHHHHHHHHHhcC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeEEec
Confidence 344445667788888444 8999999999999999 99999999999999999875
No 35
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=96.72 E-value=0.0018 Score=54.27 Aligned_cols=33 Identities=15% Similarity=0.159 Sum_probs=29.7
Q ss_pred CCCcEEeecCCchHHHHHHHH--HCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIAT--AFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~--~~P~l~~~v~Dl 212 (214)
+..+|+|||||+|..+..+++ .+|+.+++.+|.
T Consensus 56 ~~~~vLDlGcGtG~~~~~l~~~~~~~~~~v~gvD~ 90 (247)
T PRK15451 56 PGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDN 90 (247)
T ss_pred CCCEEEEEcccCCHHHHHHHHhcCCCCCeEEEEeC
Confidence 457899999999999999998 479999999996
No 36
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=96.72 E-value=0.0011 Score=41.22 Aligned_cols=44 Identities=14% Similarity=0.215 Sum_probs=37.4
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCcee
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFV 85 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~ 85 (214)
+..|+..|.++ +++|..|||+++|++. ..+++.++-|...|+++
T Consensus 5 ~~~Il~~l~~~-~~~t~~ela~~~~is~---~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLREN-PRITQKELAEKLGISR---STVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHC-TTS-HHHHHHHHTS-H---HHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHc-CCCCHHHHHHHhCCCH---HHHHHHHHHHHHCcCcC
Confidence 45677888887 7799999999999999 99999999999999874
No 37
>PRK11207 tellurite resistance protein TehB; Provisional
Probab=96.71 E-value=0.0028 Score=51.29 Aligned_cols=41 Identities=17% Similarity=0.178 Sum_probs=33.0
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+.+++.++ .....+|||+|||.|..+..++++ ..+++.+|+
T Consensus 20 ~~l~~~l~--~~~~~~vLDiGcG~G~~a~~La~~--g~~V~gvD~ 60 (197)
T PRK11207 20 SEVLEAVK--VVKPGKTLDLGCGNGRNSLYLAAN--GFDVTAWDK 60 (197)
T ss_pred HHHHHhcc--cCCCCcEEEECCCCCHHHHHHHHC--CCEEEEEeC
Confidence 45556555 445689999999999999999986 568999987
No 38
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=96.66 E-value=0.0083 Score=39.36 Aligned_cols=44 Identities=16% Similarity=0.206 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP 103 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~ 103 (214)
.++|..+||+.+|+++ ..+.+.++.|...|++.... .+.|.++|
T Consensus 24 ~~~s~~ela~~~g~s~---~tv~r~l~~L~~~g~i~~~~-------~~~~~l~~ 67 (67)
T cd00092 24 LPLTRQEIADYLGLTR---ETVSRTLKELEEEGLISRRG-------RGKYRVNP 67 (67)
T ss_pred CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecC-------CCeEEeCC
Confidence 7899999999999999 99999999999999999875 37787764
No 39
>PRK15068 tRNA mo(5)U34 methyltransferase; Provisional
Probab=96.64 E-value=0.0028 Score=55.37 Aligned_cols=32 Identities=16% Similarity=0.059 Sum_probs=28.2
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..++|+|||||+|.++..+++..|. +++++|.
T Consensus 122 ~g~~VLDIGCG~G~~~~~la~~g~~-~V~GiD~ 153 (322)
T PRK15068 122 KGRTVLDVGCGNGYHMWRMLGAGAK-LVVGIDP 153 (322)
T ss_pred CCCEEEEeccCCcHHHHHHHHcCCC-EEEEEcC
Confidence 4589999999999999999999877 4888884
No 40
>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=96.63 E-value=0.0031 Score=53.86 Aligned_cols=42 Identities=21% Similarity=0.219 Sum_probs=30.7
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+++..+ ..+..+|||||||-|.+++.++++| +.+++++.+
T Consensus 52 ~~~~~~~~--l~~G~~vLDiGcGwG~~~~~~a~~~-g~~v~gitl 93 (273)
T PF02353_consen 52 DLLCEKLG--LKPGDRVLDIGCGWGGLAIYAAERY-GCHVTGITL 93 (273)
T ss_dssp HHHHTTTT----TT-EEEEES-TTSHHHHHHHHHH---EEEEEES
T ss_pred HHHHHHhC--CCCCCEEEEeCCCccHHHHHHHHHc-CcEEEEEEC
Confidence 45666665 7778899999999999999999999 889888765
No 41
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=96.61 E-value=0.0038 Score=53.14 Aligned_cols=41 Identities=10% Similarity=0.262 Sum_probs=32.6
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+++.++ .....+|+|||||+|.++..++++.+ +++.+|.
T Consensus 32 ~~i~~~l~--~~~~~~VLEiG~G~G~lt~~L~~~~~--~v~avE~ 72 (272)
T PRK00274 32 DKIVDAAG--PQPGDNVLEIGPGLGALTEPLLERAA--KVTAVEI 72 (272)
T ss_pred HHHHHhcC--CCCcCeEEEeCCCccHHHHHHHHhCC--cEEEEEC
Confidence 44555554 45567999999999999999999987 7777775
No 42
>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=96.60 E-value=0.0027 Score=54.48 Aligned_cols=33 Identities=27% Similarity=0.436 Sum_probs=30.6
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+..+|+|+|||+|.+++.+++++|+.+++.+|+
T Consensus 121 ~~~~vLDlG~GsG~i~~~la~~~~~~~v~avDi 153 (284)
T TIGR03533 121 PVKRILDLCTGSGCIAIACAYAFPEAEVDAVDI 153 (284)
T ss_pred CCCEEEEEeCchhHHHHHHHHHCCCCEEEEEEC
Confidence 356899999999999999999999999999997
No 43
>PRK04457 spermidine synthase; Provisional
Probab=96.56 E-value=0.003 Score=53.58 Aligned_cols=33 Identities=27% Similarity=0.422 Sum_probs=31.1
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+.++|+|||||.|.++..+++.+|+.+++++|+
T Consensus 66 ~~~~vL~IG~G~G~l~~~l~~~~p~~~v~~VEi 98 (262)
T PRK04457 66 RPQHILQIGLGGGSLAKFIYTYLPDTRQTAVEI 98 (262)
T ss_pred CCCEEEEECCCHhHHHHHHHHhCCCCeEEEEEC
Confidence 467999999999999999999999999999998
No 44
>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=96.56 E-value=0.00053 Score=45.86 Aligned_cols=47 Identities=13% Similarity=0.165 Sum_probs=39.9
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+..++..|-.+ +++|+++||+.+|++. ..+++.|+.|...|++....
T Consensus 10 E~~vy~~Ll~~-~~~t~~eIa~~l~i~~---~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 10 EAKVYLALLKN-GPATAEEIAEELGISR---STVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHH-CHEEHHHHHHHHTSSH---HHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEc
Confidence 34455555444 8999999999999999 99999999999999999885
No 45
>COG2890 HemK Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]
Probab=96.55 E-value=0.0025 Score=54.65 Aligned_cols=30 Identities=27% Similarity=0.469 Sum_probs=29.0
Q ss_pred cEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 183 PLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 183 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+|+|||+|+|..+++++++.|+++++..|+
T Consensus 113 ~ilDlGTGSG~iai~la~~~~~~~V~a~Di 142 (280)
T COG2890 113 RILDLGTGSGAIAIALAKEGPDAEVIAVDI 142 (280)
T ss_pred cEEEecCChHHHHHHHHhhCcCCeEEEEEC
Confidence 799999999999999999999999999986
No 46
>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=96.54 E-value=0.0044 Score=47.38 Aligned_cols=33 Identities=30% Similarity=0.271 Sum_probs=27.5
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.....+|||||||.|.++..+.+..+ +++++|.
T Consensus 20 ~~~~~~vLDiGcG~G~~~~~l~~~~~--~~~g~D~ 52 (161)
T PF13489_consen 20 LKPGKRVLDIGCGTGSFLRALAKRGF--EVTGVDI 52 (161)
T ss_dssp TTTTSEEEEESSTTSHHHHHHHHTTS--EEEEEES
T ss_pred cCCCCEEEEEcCCCCHHHHHHHHhCC--EEEEEEC
Confidence 34678999999999999999977644 8888885
No 47
>TIGR03534 RF_mod_PrmC protein-(glutamine-N5) methyltransferase, release factor-specific. Members of this protein family are HemK (PrmC), a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. SIMBAL analysis (manuscript in prep.) shows the motif [LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers specificity for the release factors rather than for ribosomal protein L3.
Probab=96.54 E-value=0.0031 Score=52.25 Aligned_cols=33 Identities=30% Similarity=0.507 Sum_probs=30.3
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...+|+|+|||+|.++..+++.+|+.+++++|.
T Consensus 87 ~~~~ilDig~G~G~~~~~l~~~~~~~~v~~iD~ 119 (251)
T TIGR03534 87 GPLRVLDLGTGSGAIALALAKERPDARVTAVDI 119 (251)
T ss_pred CCCeEEEEeCcHhHHHHHHHHHCCCCEEEEEEC
Confidence 346899999999999999999999999999986
No 48
>PRK06202 hypothetical protein; Provisional
Probab=96.52 E-value=0.0079 Score=49.66 Aligned_cols=34 Identities=21% Similarity=0.154 Sum_probs=28.7
Q ss_pred CCCCcEEeecCCchHHHHHHHHH----CCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATA----FPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~----~P~l~~~v~Dl 212 (214)
.+..+|+|||||+|.++..|++. .|+.+++++|+
T Consensus 59 ~~~~~iLDlGcG~G~~~~~L~~~~~~~g~~~~v~gvD~ 96 (232)
T PRK06202 59 DRPLTLLDIGCGGGDLAIDLARWARRDGLRLEVTAIDP 96 (232)
T ss_pred CCCcEEEEeccCCCHHHHHHHHHHHhCCCCcEEEEEcC
Confidence 45679999999999999988864 46789999997
No 49
>TIGR00477 tehB tellurite resistance protein TehB. Part of a tellurite-reducing operon tehA and tehB
Probab=96.52 E-value=0.0042 Score=50.14 Aligned_cols=41 Identities=12% Similarity=0.148 Sum_probs=31.9
Q ss_pred HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
.+++.++ .....+|+|||||.|..+..++++ ..+++.+|+-
T Consensus 21 ~l~~~~~--~~~~~~vLDiGcG~G~~a~~la~~--g~~V~~iD~s 61 (195)
T TIGR00477 21 AVREAVK--TVAPCKTLDLGCGQGRNSLYLSLA--GYDVRAWDHN 61 (195)
T ss_pred HHHHHhc--cCCCCcEEEeCCCCCHHHHHHHHC--CCeEEEEECC
Confidence 3445444 334679999999999999999985 5789999873
No 50
>PRK00216 ubiE ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed
Probab=96.52 E-value=0.0057 Score=50.05 Aligned_cols=42 Identities=19% Similarity=0.162 Sum_probs=33.9
Q ss_pred HHhhcccccCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620 170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH 213 (214)
Q Consensus 170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp 213 (214)
++..+. ..+..+|+|||||.|.++..+++..| +.+++++|+.
T Consensus 43 ~~~~~~--~~~~~~vldiG~G~G~~~~~l~~~~~~~~~v~~~D~s 85 (239)
T PRK00216 43 TIKWLG--VRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFS 85 (239)
T ss_pred HHHHhC--CCCCCeEEEeCCCCCHHHHHHHHHcCCCCeEEEEeCC
Confidence 344443 33457999999999999999999998 7899999973
No 51
>PRK11805 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=96.51 E-value=0.0029 Score=54.93 Aligned_cols=31 Identities=29% Similarity=0.451 Sum_probs=29.7
Q ss_pred CcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 182 KPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 182 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.+|+|+|||+|.+++.+++.+|+.+++.+|+
T Consensus 135 ~~VLDlG~GsG~iai~la~~~p~~~V~avDi 165 (307)
T PRK11805 135 TRILDLCTGSGCIAIACAYAFPDAEVDAVDI 165 (307)
T ss_pred CEEEEEechhhHHHHHHHHHCCCCEEEEEeC
Confidence 6899999999999999999999999999997
No 52
>PRK09328 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=96.51 E-value=0.0057 Score=51.58 Aligned_cols=34 Identities=29% Similarity=0.436 Sum_probs=31.1
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.+..+|+|+|||+|..+..+++..|+.+++..|.
T Consensus 107 ~~~~~vLDiG~GsG~~~~~la~~~~~~~v~~iDi 140 (275)
T PRK09328 107 KEPLRVLDLGTGSGAIALALAKERPDAEVTAVDI 140 (275)
T ss_pred cCCCEEEEEcCcHHHHHHHHHHHCCCCEEEEEEC
Confidence 3467899999999999999999999999999986
No 53
>PRK14966 unknown domain/N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase fusion protein; Provisional
Probab=96.49 E-value=0.0045 Score=55.84 Aligned_cols=33 Identities=21% Similarity=0.238 Sum_probs=30.5
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+..+++|+|||+|.+++.+++++|+.+++.+|+
T Consensus 251 ~~~rVLDLGcGSG~IaiaLA~~~p~a~VtAVDi 283 (423)
T PRK14966 251 ENGRVWDLGTGSGAVAVTVALERPDAFVRASDI 283 (423)
T ss_pred CCCEEEEEeChhhHHHHHHHHhCCCCEEEEEEC
Confidence 446899999999999999999999999999997
No 54
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=96.49 E-value=0.0013 Score=40.74 Aligned_cols=44 Identities=18% Similarity=0.366 Sum_probs=38.1
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ 86 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~ 86 (214)
++.|...|.+ +|.++.|||+.+|+++ ..+.+-|+.|...|++..
T Consensus 4 R~~Il~~L~~--~~~~~~el~~~l~~s~---~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 4 RLRILKLLSE--GPLTVSELAEELGLSQ---STVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHHTT--SSEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHh--CCCchhhHHHhccccc---hHHHHHHHHHHHCcCeeC
Confidence 3456777887 8999999999999999 999999999999999863
No 55
>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=96.48 E-value=0.0055 Score=52.45 Aligned_cols=31 Identities=26% Similarity=0.502 Sum_probs=29.6
Q ss_pred CcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 182 KPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 182 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.+|+|+|||+|.+++.+++.+|+.+++.+|+
T Consensus 116 ~~vLDlG~GsG~i~l~la~~~~~~~v~avDi 146 (284)
T TIGR00536 116 LHILDLGTGSGCIALALAYEFPNAEVIAVDI 146 (284)
T ss_pred CEEEEEeccHhHHHHHHHHHCCCCEEEEEEC
Confidence 6899999999999999999999999999986
No 56
>COG2242 CobL Precorrin-6B methylase 2 [Coenzyme metabolism]
Probab=96.44 E-value=0.0056 Score=49.20 Aligned_cols=35 Identities=23% Similarity=0.280 Sum_probs=32.2
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+...++|||||+|..++..+...|+.+++-+|.
T Consensus 32 ~~~g~~l~DIGaGtGsi~iE~a~~~p~~~v~AIe~ 66 (187)
T COG2242 32 PRPGDRLWDIGAGTGSITIEWALAGPSGRVIAIER 66 (187)
T ss_pred CCCCCEEEEeCCCccHHHHHHHHhCCCceEEEEec
Confidence 55678999999999999999999999999998885
No 57
>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=96.43 E-value=0.0073 Score=50.86 Aligned_cols=32 Identities=19% Similarity=0.213 Sum_probs=29.7
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+++|+|||+|.++..+++..|..+++.+|+
T Consensus 87 ~~~vLDlg~GsG~i~l~la~~~~~~~v~~vDi 118 (251)
T TIGR03704 87 TLVVVDLCCGSGAVGAALAAALDGIELHAADI 118 (251)
T ss_pred CCEEEEecCchHHHHHHHHHhCCCCEEEEEEC
Confidence 45899999999999999999999999999986
No 58
>PLN02244 tocopherol O-methyltransferase
Probab=96.42 E-value=0.0072 Score=53.12 Aligned_cols=33 Identities=27% Similarity=0.372 Sum_probs=29.4
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
....+|||||||.|.++..+++++ +.+++++|+
T Consensus 117 ~~~~~VLDiGCG~G~~~~~La~~~-g~~v~gvD~ 149 (340)
T PLN02244 117 KRPKRIVDVGCGIGGSSRYLARKY-GANVKGITL 149 (340)
T ss_pred CCCCeEEEecCCCCHHHHHHHHhc-CCEEEEEEC
Confidence 456799999999999999999988 778999886
No 59
>PRK10258 biotin biosynthesis protein BioC; Provisional
Probab=96.42 E-value=0.0088 Score=49.90 Aligned_cols=43 Identities=19% Similarity=0.255 Sum_probs=32.4
Q ss_pred hHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 166 IASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 166 ~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.+..+++.++ .....+|||+|||+|.++..+.+. ..+++.+|+
T Consensus 30 ~a~~l~~~l~--~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~~D~ 72 (251)
T PRK10258 30 SADALLAMLP--QRKFTHVLDAGCGPGWMSRYWRER--GSQVTALDL 72 (251)
T ss_pred HHHHHHHhcC--ccCCCeEEEeeCCCCHHHHHHHHc--CCeEEEEEC
Confidence 4455566555 335679999999999999988764 567888886
No 60
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=96.39 E-value=0.0019 Score=42.75 Aligned_cols=58 Identities=17% Similarity=0.337 Sum_probs=39.7
Q ss_pred hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
..|...+++++..+||+.+++++ ..+.+.++.|...|++.+....+|.- ...|.+|+.
T Consensus 10 ~~l~~~~~~~t~~~l~~~~~~~~---~~vs~~i~~L~~~glv~~~~~~~d~R-~~~~~LT~~ 67 (68)
T PF13463_consen 10 RALAHSDGPMTQSDLAERLGISK---STVSRIIKKLEEKGLVEKERDPHDKR-SKRYRLTPA 67 (68)
T ss_dssp HHHT--TS-BEHHHHHHHTT--H---HHHHHHHHHHHHTTSEEEEEESSCTT-SEEEEE-HH
T ss_pred HHHHccCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEecCCCCcCC-eeEEEeCCC
Confidence 34442238999999999999999 99999999999999998765422222 245777753
No 61
>TIGR00452 methyltransferase, putative. Known examples to date are restricted to the proteobacteria.
Probab=96.35 E-value=0.0073 Score=52.63 Aligned_cols=33 Identities=12% Similarity=0.031 Sum_probs=28.1
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...++|+|||||+|.++..+++..++ +++++|.
T Consensus 120 ~~g~~VLDvGCG~G~~~~~~~~~g~~-~v~GiDp 152 (314)
T TIGR00452 120 LKGRTILDVGCGSGYHMWRMLGHGAK-SLVGIDP 152 (314)
T ss_pred CCCCEEEEeccCCcHHHHHHHHcCCC-EEEEEcC
Confidence 44689999999999999999998775 6888884
No 62
>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=96.33 E-value=0.014 Score=47.76 Aligned_cols=31 Identities=19% Similarity=0.235 Sum_probs=26.7
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+..+++|||||.|.++..+++. +.+++++|.
T Consensus 55 ~~~~vLDiGcG~G~~~~~la~~--~~~v~gvD~ 85 (219)
T TIGR02021 55 KGKRVLDAGCGTGLLSIELAKR--GAIVKAVDI 85 (219)
T ss_pred CCCEEEEEeCCCCHHHHHHHHC--CCEEEEEEC
Confidence 4689999999999999999886 457888886
No 63
>PRK05785 hypothetical protein; Provisional
Probab=96.33 E-value=0.0059 Score=50.56 Aligned_cols=31 Identities=16% Similarity=0.291 Sum_probs=28.0
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+|||||||+|.++..+++++ +.+++++|.
T Consensus 52 ~~~VLDlGcGtG~~~~~l~~~~-~~~v~gvD~ 82 (226)
T PRK05785 52 PKKVLDVAAGKGELSYHFKKVF-KYYVVALDY 82 (226)
T ss_pred CCeEEEEcCCCCHHHHHHHHhc-CCEEEEECC
Confidence 5799999999999999999988 678999886
No 64
>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=96.31 E-value=0.0047 Score=42.99 Aligned_cols=47 Identities=15% Similarity=0.292 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+++|.++||+++++++ ..+++++..|...|++..... . .+.|.++..
T Consensus 24 ~~~s~~eiA~~~~i~~---~~l~kil~~L~~~Gli~s~~G----~-~GGy~L~~~ 70 (83)
T PF02082_consen 24 KPVSSKEIAERLGISP---SYLRKILQKLKKAGLIESSRG----R-GGGYRLARP 70 (83)
T ss_dssp C-BEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEETS----T-TSEEEESS-
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHHHHhhCCeeEecCC----C-CCceeecCC
Confidence 5699999999999999 999999999999999986642 1 477888776
No 65
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=96.30 E-value=0.007 Score=36.98 Aligned_cols=36 Identities=17% Similarity=0.230 Sum_probs=33.3
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
-|+|..+||+.+++++ ..+.+.|+.|...|++....
T Consensus 7 ~~~s~~~la~~l~~s~---~tv~~~l~~L~~~g~l~~~~ 42 (48)
T smart00419 7 LPLTRQEIAELLGLTR---ETVSRTLKRLEKEGLISREG 42 (48)
T ss_pred eccCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEeC
Confidence 4789999999999999 99999999999999998763
No 66
>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional
Probab=96.30 E-value=0.0076 Score=51.04 Aligned_cols=44 Identities=11% Similarity=0.222 Sum_probs=35.1
Q ss_pred HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
...+++.++ ..+..+|||||||.|..+..+++.+ ..+++.+|+-
T Consensus 41 ~~~~l~~l~--l~~~~~VLDiGcG~G~~a~~la~~~-~~~v~giD~s 84 (263)
T PTZ00098 41 TTKILSDIE--LNENSKVLDIGSGLGGGCKYINEKY-GAHVHGVDIC 84 (263)
T ss_pred HHHHHHhCC--CCCCCEEEEEcCCCChhhHHHHhhc-CCEEEEEECC
Confidence 355666665 6677899999999999999998875 6789988863
No 67
>COG2226 UbiE Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]
Probab=96.28 E-value=0.0055 Score=51.30 Aligned_cols=33 Identities=21% Similarity=0.196 Sum_probs=31.1
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...+|||||||+|-++..+++..++.++++.|.
T Consensus 51 ~g~~vLDva~GTGd~a~~~~k~~g~g~v~~~D~ 83 (238)
T COG2226 51 PGDKVLDVACGTGDMALLLAKSVGTGEVVGLDI 83 (238)
T ss_pred CCCEEEEecCCccHHHHHHHHhcCCceEEEEEC
Confidence 478999999999999999999999999999996
No 68
>COG4123 Predicted O-methyltransferase [General function prediction only]
Probab=96.28 E-value=0.0043 Score=52.18 Aligned_cols=43 Identities=14% Similarity=0.196 Sum_probs=35.4
Q ss_pred HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
++..|. ..+..++|+|+|+|.|..++.++++.|+.+++.+|+-
T Consensus 35 LL~~~~-~~~~~~~IlDlGaG~G~l~L~la~r~~~a~I~~VEiq 77 (248)
T COG4123 35 LLAAFA-PVPKKGRILDLGAGNGALGLLLAQRTEKAKIVGVEIQ 77 (248)
T ss_pred HHHhhc-ccccCCeEEEecCCcCHHHHHHhccCCCCcEEEEEeC
Confidence 455543 1344889999999999999999999999999998874
No 69
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=96.22 E-value=0.0051 Score=56.98 Aligned_cols=32 Identities=13% Similarity=0.370 Sum_probs=30.1
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+|+|||||+|.+++.+++.+|+.+++.+|+
T Consensus 139 ~~~VLDlG~GsG~iai~la~~~p~~~v~avDi 170 (506)
T PRK01544 139 FLNILELGTGSGCIAISLLCELPNANVIATDI 170 (506)
T ss_pred CCEEEEccCchhHHHHHHHHHCCCCeEEEEEC
Confidence 46899999999999999999999999999997
No 70
>TIGR00438 rrmJ cell division protein FtsJ.
Probab=96.21 E-value=0.01 Score=47.44 Aligned_cols=35 Identities=11% Similarity=0.183 Sum_probs=30.0
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl 212 (214)
..+..+|||+|||+|.++..+++++ +..+++.+|+
T Consensus 30 i~~g~~VLDiG~GtG~~~~~l~~~~~~~~~v~~vDi 65 (188)
T TIGR00438 30 IKPGDTVLDLGAAPGGWSQVAVEQVGGKGRVIAVDL 65 (188)
T ss_pred cCCCCEEEEecCCCCHHHHHHHHHhCCCceEEEEec
Confidence 3567899999999999999999887 6678888886
No 71
>PF13679 Methyltransf_32: Methyltransferase domain
Probab=96.19 E-value=0.0064 Score=46.52 Aligned_cols=35 Identities=31% Similarity=0.529 Sum_probs=30.0
Q ss_pred cCCCCcEEeecCCchHHHHHHHHH----CCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATA----FPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~----~P~l~~~v~Dl 212 (214)
..+..+|||+|||.|+++..|+.. .|+++++.+|.
T Consensus 23 ~~~~~~vvD~GsG~GyLs~~La~~l~~~~~~~~v~~iD~ 61 (141)
T PF13679_consen 23 SKRCITVVDLGSGKGYLSRALAHLLCNSSPNLRVLGIDC 61 (141)
T ss_pred cCCCCEEEEeCCChhHHHHHHHHHHHhcCCCCeEEEEEC
Confidence 356789999999999999999992 38889999885
No 72
>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=96.18 E-value=0.0097 Score=48.13 Aligned_cols=34 Identities=29% Similarity=0.308 Sum_probs=30.6
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl 212 (214)
.+..+|+|+|||.|..+..+++.+|+ .+++++|.
T Consensus 38 ~~~~~vldiG~G~G~~~~~~~~~~~~~~~~~~iD~ 72 (223)
T TIGR01934 38 FKGQKVLDVACGTGDLAIELAKSAPDRGKVTGVDF 72 (223)
T ss_pred CCCCeEEEeCCCCChhHHHHHHhcCCCceEEEEEC
Confidence 35689999999999999999999998 78999886
No 73
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=96.18 E-value=0.011 Score=46.66 Aligned_cols=47 Identities=17% Similarity=0.221 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+|+|+++||+++++++ +.|.++|..|...|++..... . .+.|.+..-
T Consensus 24 ~~vs~~eIA~~~~ip~---~~l~kIl~~L~~aGLv~s~rG----~-~GGy~Lar~ 70 (164)
T PRK10857 24 GPVPLADISERQGISL---SYLEQLFSRLRKNGLVSSVRG----P-GGGYLLGKD 70 (164)
T ss_pred CcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEeCCC----C-CCCeeccCC
Confidence 6899999999999999 999999999999999997531 1 567888776
No 74
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=96.13 E-value=0.0059 Score=45.57 Aligned_cols=56 Identities=20% Similarity=0.236 Sum_probs=48.5
Q ss_pred HHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 29 KSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 29 ~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.+.+|.--.++.|+..|.+. +++++.|||+.+++++ ..+.+-|+.|...|++....
T Consensus 9 ~fkaLadptRl~IL~~L~~~-~~~~v~ela~~l~lsq---stvS~HL~~L~~AGLV~~~r 64 (117)
T PRK10141 9 LFKILSDETRLGIVLLLRES-GELCVCDLCTALDQSQ---PKISRHLALLRESGLLLDRK 64 (117)
T ss_pred HHHHhCCHHHHHHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCceEEEE
Confidence 45566667778888888754 7899999999999999 99999999999999998776
No 75
>PRK11705 cyclopropane fatty acyl phospholipid synthase; Provisional
Probab=96.12 E-value=0.013 Score=52.33 Aligned_cols=40 Identities=18% Similarity=0.194 Sum_probs=31.8
Q ss_pred HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+++.++ ..+..+|||||||.|.++..+++.+ +.+++.+|+
T Consensus 159 l~~~l~--l~~g~rVLDIGcG~G~~a~~la~~~-g~~V~giDl 198 (383)
T PRK11705 159 ICRKLQ--LKPGMRVLDIGCGWGGLARYAAEHY-GVSVVGVTI 198 (383)
T ss_pred HHHHhC--CCCCCEEEEeCCCccHHHHHHHHHC-CCEEEEEeC
Confidence 344444 4566799999999999999999876 678998886
No 76
>PRK07580 Mg-protoporphyrin IX methyl transferase; Validated
Probab=96.09 E-value=0.017 Score=47.14 Aligned_cols=32 Identities=16% Similarity=0.130 Sum_probs=26.7
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.+..+|||||||+|.++..+++..+ ++++.|+
T Consensus 62 ~~~~~vLDvGcG~G~~~~~l~~~~~--~v~~~D~ 93 (230)
T PRK07580 62 LTGLRILDAGCGVGSLSIPLARRGA--KVVASDI 93 (230)
T ss_pred CCCCEEEEEeCCCCHHHHHHHHcCC--EEEEEEC
Confidence 4467999999999999999998754 4787775
No 77
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=96.09 E-value=0.0029 Score=42.54 Aligned_cols=44 Identities=14% Similarity=0.366 Sum_probs=37.2
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|-+.|.+. +.+|..|||.+++++| ..+..+|+.|+..|.+.+..
T Consensus 5 i~~~l~~~-~~~S~~eLa~~~~~s~---~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 5 IRDYLRER-GRVSLAELAREFGISP---EAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHHHHHS--SEEHHHHHHHTT--H---HHHHHHHHHHHCCTSCEEEE
T ss_pred HHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEEec
Confidence 45677776 8999999999999999 99999999999999999875
No 78
>PLN02336 phosphoethanolamine N-methyltransferase
Probab=96.07 E-value=0.01 Score=54.25 Aligned_cols=43 Identities=19% Similarity=0.220 Sum_probs=34.1
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
..+++.++ ..+..+|||||||+|..+..+++.+ +.+++.+|+-
T Consensus 256 e~l~~~~~--~~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvDiS 298 (475)
T PLN02336 256 KEFVDKLD--LKPGQKVLDVGCGIGGGDFYMAENF-DVHVVGIDLS 298 (475)
T ss_pred HHHHHhcC--CCCCCEEEEEeccCCHHHHHHHHhc-CCEEEEEECC
Confidence 34555554 4556799999999999999999876 7799999973
No 79
>PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional
Probab=96.02 E-value=0.0095 Score=48.77 Aligned_cols=34 Identities=18% Similarity=0.219 Sum_probs=28.9
Q ss_pred CCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl 212 (214)
.+..+|||||||+|.++..++++. |.-+++.+|+
T Consensus 50 ~~~~~VLDlG~GtG~~t~~l~~~~~~~~~V~aVDi 84 (209)
T PRK11188 50 KPGMTVVDLGAAPGGWSQYAVTQIGDKGRVIACDI 84 (209)
T ss_pred CCCCEEEEEcccCCHHHHHHHHHcCCCceEEEEec
Confidence 456799999999999999999987 4568888886
No 80
>COG0220 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]
Probab=95.99 E-value=0.0075 Score=50.17 Aligned_cols=31 Identities=13% Similarity=0.212 Sum_probs=29.1
Q ss_pred CcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 182 KPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 182 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+|+||||.|.+...+|+++|+..++++++
T Consensus 50 pi~lEIGfG~G~~l~~~A~~nP~~nfiGiEi 80 (227)
T COG0220 50 PIVLEIGFGMGEFLVEMAKKNPEKNFLGIEI 80 (227)
T ss_pred cEEEEECCCCCHHHHHHHHHCCCCCEEEEEE
Confidence 5899999999999999999999999998875
No 81
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=95.98 E-value=0.009 Score=50.70 Aligned_cols=33 Identities=24% Similarity=0.396 Sum_probs=28.2
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCC---eEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDT---KCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l---~~~v~Dl 212 (214)
...+|||||||+|.++..+++.+|.. +++++|+
T Consensus 85 ~~~~vLDiGcG~G~~~~~l~~~~~~~~~~~v~giD~ 120 (272)
T PRK11088 85 KATALLDIGCGEGYYTHALADALPEITTMQLFGLDI 120 (272)
T ss_pred CCCeEEEECCcCCHHHHHHHHhcccccCCeEEEECC
Confidence 34689999999999999999998864 5788886
No 82
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=95.97 E-value=0.014 Score=49.10 Aligned_cols=41 Identities=12% Similarity=0.233 Sum_probs=32.3
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+++..+ ..+..+|+|||||.|.++..++++.+. ++.+|.
T Consensus 19 ~~i~~~~~--~~~~~~VLEiG~G~G~lt~~L~~~~~~--v~~iE~ 59 (253)
T TIGR00755 19 QKIVEAAN--VLEGDVVLEIGPGLGALTEPLLKRAKK--VTAIEI 59 (253)
T ss_pred HHHHHhcC--CCCcCEEEEeCCCCCHHHHHHHHhCCc--EEEEEC
Confidence 45556555 556789999999999999999999875 666654
No 83
>PLN02233 ubiquinone biosynthesis methyltransferase
Probab=95.97 E-value=0.01 Score=50.20 Aligned_cols=34 Identities=18% Similarity=0.178 Sum_probs=29.6
Q ss_pred CCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl 212 (214)
.+..+|+|||||+|.++..+++++ |+.+++.+|.
T Consensus 72 ~~~~~VLDlGcGtG~~~~~la~~~~~~~~V~gvD~ 106 (261)
T PLN02233 72 KMGDRVLDLCCGSGDLAFLLSEKVGSDGKVMGLDF 106 (261)
T ss_pred CCCCEEEEECCcCCHHHHHHHHHhCCCCEEEEEEC
Confidence 446799999999999999999885 6789999986
No 84
>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=95.92 E-value=0.015 Score=42.98 Aligned_cols=67 Identities=19% Similarity=0.264 Sum_probs=51.3
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
+..|+..|..+ +++|..+||+.+++++ ..+.+.++-|...|++......+|.- .-.+.+|+. ++.+.
T Consensus 30 q~~iL~~l~~~-~~~t~~ela~~~~~~~---~tvs~~l~~Le~~GlI~r~~~~~D~R-~~~v~LT~~----G~~~~ 96 (118)
T TIGR02337 30 QWRILRILAEQ-GSMEFTQLANQACILR---PSLTGILARLERDGLVTRLKASNDQR-RVYISLTPK----GQALY 96 (118)
T ss_pred HHHHHHHHHHc-CCcCHHHHHHHhCCCc---hhHHHHHHHHHHCCCEEeccCCCCCC-eeEEEECHh----HHHHH
Confidence 34466777766 7899999999999999 89999999999999999865211111 235888888 66654
No 85
>TIGR00080 pimt protein-L-isoaspartate(D-aspartate) O-methyltransferase. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt.
Probab=95.91 E-value=0.017 Score=47.23 Aligned_cols=42 Identities=17% Similarity=0.164 Sum_probs=32.0
Q ss_pred HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620 169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC 212 (214)
Q Consensus 169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl 212 (214)
.+++.++ .....+|+|||||+|.++..+++..+ +.+++.+|+
T Consensus 68 ~~~~~l~--~~~~~~VLDiG~GsG~~a~~la~~~~~~g~V~~vD~ 110 (215)
T TIGR00080 68 MMTELLE--LKPGMKVLEIGTGSGYQAAVLAEIVGRDGLVVSIER 110 (215)
T ss_pred HHHHHhC--CCCcCEEEEECCCccHHHHHHHHHhCCCCEEEEEeC
Confidence 3444444 45678999999999999999999875 456777774
No 86
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=95.89 E-value=0.017 Score=48.68 Aligned_cols=42 Identities=14% Similarity=0.317 Sum_probs=32.5
Q ss_pred HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...+++..+ ..+..+|+|||||.|.++..++++. .+++++|+
T Consensus 18 ~~~iv~~~~--~~~~~~VLEIG~G~G~lt~~L~~~~--~~v~~vEi 59 (258)
T PRK14896 18 VDRIVEYAE--DTDGDPVLEIGPGKGALTDELAKRA--KKVYAIEL 59 (258)
T ss_pred HHHHHHhcC--CCCcCeEEEEeCccCHHHHHHHHhC--CEEEEEEC
Confidence 345555554 5567899999999999999999984 46777775
No 87
>PRK13944 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=95.88 E-value=0.022 Score=46.34 Aligned_cols=35 Identities=20% Similarity=0.209 Sum_probs=28.7
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl 212 (214)
..+..+|+|||||+|..+..+++..+ ..+++.+|.
T Consensus 70 ~~~~~~VLDiG~GsG~~~~~la~~~~~~g~V~~iD~ 105 (205)
T PRK13944 70 PRPGMKILEVGTGSGYQAAVCAEAIERRGKVYTVEI 105 (205)
T ss_pred CCCCCEEEEECcCccHHHHHHHHhcCCCCEEEEEeC
Confidence 34557999999999999999998875 557888875
No 88
>KOG2899 consensus Predicted methyltransferase [General function prediction only]
Probab=95.87 E-value=0.01 Score=49.75 Aligned_cols=46 Identities=15% Similarity=0.129 Sum_probs=38.3
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
...++.++..+-..+.+|||||++|.+++.|++.|-...++++|+-
T Consensus 46 D~rLk~L~~~~f~~~~~LDIGCNsG~lt~~iak~F~~r~iLGvDID 91 (288)
T KOG2899|consen 46 DPRLKVLEKDWFEPKQALDIGCNSGFLTLSIAKDFGPRRILGVDID 91 (288)
T ss_pred ChhhhhccccccCcceeEeccCCcchhHHHHHHhhccceeeEeecc
Confidence 4456666544556889999999999999999999999999999873
No 89
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=95.87 E-value=0.0056 Score=40.45 Aligned_cols=46 Identities=17% Similarity=0.218 Sum_probs=37.1
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.|.+.|....+|++..|||+.+|++. ..++++|..|...|.+...+
T Consensus 4 ~Il~~i~~~~~p~~T~eiA~~~gls~---~~aR~yL~~Le~eG~V~~~~ 49 (62)
T PF04703_consen 4 KILEYIKEQNGPLKTREIADALGLSI---YQARYYLEKLEKEGKVERSP 49 (62)
T ss_dssp CHHHHHHHHTS-EEHHHHHHHHTS-H---HHHHHHHHHHHHCTSEEEES
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEec
Confidence 34555665228999999999999998 99999999999999998765
No 90
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=95.87 E-value=0.0086 Score=42.15 Aligned_cols=62 Identities=15% Similarity=0.283 Sum_probs=47.1
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
++.|+..|... +++|..+||+.+++++ ..+.+.++.|...|++.......+.. ...|.+|+.
T Consensus 12 ~~~il~~l~~~-~~~~~~~la~~~~~s~---~~i~~~l~~L~~~g~v~~~~~~~~~r-~~~~~lT~~ 73 (101)
T smart00347 12 QFLVLRILYEE-GPLSVSELAKRLGVSP---STVTRVLDRLEKKGLIRRLPSPEDRR-SVLVSLTEE 73 (101)
T ss_pred HHHHHHHHHHc-CCcCHHHHHHHHCCCc---hhHHHHHHHHHHCCCeEecCCCCCCC-eEEEEECHh
Confidence 34566677665 6799999999999999 99999999999999998765211111 235777777
No 91
>PRK11036 putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=95.82 E-value=0.016 Score=48.56 Aligned_cols=31 Identities=19% Similarity=0.270 Sum_probs=27.1
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...+|+|||||.|.++..+++. ..+++++|+
T Consensus 44 ~~~~vLDiGcG~G~~a~~la~~--g~~v~~vD~ 74 (255)
T PRK11036 44 RPLRVLDAGGGEGQTAIKLAEL--GHQVILCDL 74 (255)
T ss_pred CCCEEEEeCCCchHHHHHHHHc--CCEEEEEEC
Confidence 4579999999999999999987 567888886
No 92
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=95.80 E-value=0.014 Score=37.77 Aligned_cols=44 Identities=9% Similarity=0.207 Sum_probs=40.1
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|.++|... +.+|+++||+.+++++ .-++|-|..|...|++...-
T Consensus 5 Il~~l~~~-~~~s~~ela~~~~VS~---~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 5 ILELLKEK-GKVSVKELAEEFGVSE---MTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHc-CCEEHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEc
Confidence 56777776 8999999999999999 99999999999999998875
No 93
>PRK04266 fibrillarin; Provisional
Probab=95.79 E-value=0.02 Score=47.48 Aligned_cols=35 Identities=11% Similarity=0.152 Sum_probs=30.6
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+..+|+|+|||+|.++..+++..|.-+++.+|+
T Consensus 70 i~~g~~VlD~G~G~G~~~~~la~~v~~g~V~avD~ 104 (226)
T PRK04266 70 IKKGSKVLYLGAASGTTVSHVSDIVEEGVVYAVEF 104 (226)
T ss_pred CCCCCEEEEEccCCCHHHHHHHHhcCCCeEEEEEC
Confidence 55678999999999999999999998667888886
No 94
>PRK12335 tellurite resistance protein TehB; Provisional
Probab=95.76 E-value=0.016 Score=49.67 Aligned_cols=31 Identities=16% Similarity=0.113 Sum_probs=27.1
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...+|||||||+|..+..+++. ..+++.+|.
T Consensus 120 ~~~~vLDlGcG~G~~~~~la~~--g~~V~avD~ 150 (287)
T PRK12335 120 KPGKALDLGCGQGRNSLYLALL--GFDVTAVDI 150 (287)
T ss_pred CCCCEEEeCCCCCHHHHHHHHC--CCEEEEEEC
Confidence 4569999999999999999885 578999886
No 95
>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=95.72 E-value=0.016 Score=49.97 Aligned_cols=34 Identities=15% Similarity=0.211 Sum_probs=30.1
Q ss_pred CCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH 213 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp 213 (214)
...+|||+|||+|..+..|+++.+ ..+++.+|+-
T Consensus 63 ~~~~iLELGcGtG~~t~~Ll~~l~~~~~~~~iDiS 97 (301)
T TIGR03438 63 AGCELVELGSGSSRKTRLLLDALRQPARYVPIDIS 97 (301)
T ss_pred CCCeEEecCCCcchhHHHHHHhhccCCeEEEEECC
Confidence 457899999999999999999988 6889999974
No 96
>PLN03075 nicotianamine synthase; Provisional
Probab=95.71 E-value=0.018 Score=49.75 Aligned_cols=33 Identities=18% Similarity=0.074 Sum_probs=27.6
Q ss_pred CCCcEEeecCCch--HHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTG--TMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G--~~~~~l~~~~P~l~~~v~Dl 212 (214)
+.++|+|||||+| +....+++.+|+.+++++|.
T Consensus 123 ~p~~VldIGcGpgpltaiilaa~~~p~~~~~giD~ 157 (296)
T PLN03075 123 VPTKVAFVGSGPLPLTSIVLAKHHLPTTSFHNFDI 157 (296)
T ss_pred CCCEEEEECCCCcHHHHHHHHHhcCCCCEEEEEeC
Confidence 6799999999998 44555557899999999996
No 97
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=95.68 E-value=0.024 Score=43.09 Aligned_cols=47 Identities=17% Similarity=0.186 Sum_probs=40.2
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+++|+++||+++++++ ..++++|+.|...|++..... . .|.|.++.-
T Consensus 24 ~~~s~~~ia~~~~ip~---~~l~kil~~L~~~glv~s~~G----~-~Ggy~l~~~ 70 (135)
T TIGR02010 24 GPVTLADISERQGISL---SYLEQLFAKLRKAGLVKSVRG----P-GGGYQLGRP 70 (135)
T ss_pred CcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCceEEEeC----C-CCCEeccCC
Confidence 6899999999999999 999999999999999986431 1 466887776
No 98
>PRK00517 prmA ribosomal protein L11 methyltransferase; Reviewed
Probab=95.66 E-value=0.014 Score=48.98 Aligned_cols=32 Identities=28% Similarity=0.247 Sum_probs=26.3
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...+|+|||||+|.+++.+++..+. +++.+|+
T Consensus 119 ~~~~VLDiGcGsG~l~i~~~~~g~~-~v~giDi 150 (250)
T PRK00517 119 PGKTVLDVGCGSGILAIAAAKLGAK-KVLAVDI 150 (250)
T ss_pred CCCEEEEeCCcHHHHHHHHHHcCCC-eEEEEEC
Confidence 5689999999999999987776543 6888886
No 99
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=95.65 E-value=0.021 Score=46.04 Aligned_cols=35 Identities=14% Similarity=0.155 Sum_probs=30.1
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl 212 (214)
.....+++|+|||+|.++..+++.. |..+++.+|+
T Consensus 38 ~~~~~~vlDlG~GtG~~s~~~a~~~~~~~~v~avD~ 73 (198)
T PRK00377 38 LRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDK 73 (198)
T ss_pred CCCcCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEEC
Confidence 4566899999999999999998874 6778999986
No 100
>PF08003 Methyltransf_9: Protein of unknown function (DUF1698); InterPro: IPR010017 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. This entry represents a set of bacterial AdoMet-dependent tRNA (mo5U34)-methyltransferases. These enzymes catalyse the conversion of 5-hydroxyuridine (ho5U) to 5-methoxyuridine (mo5U) at the wobble position (34) of tRNA []. The 5-methoxyuridine is subsequently converted to uridine-5-oxyacetic acid, a modified nucleoside that is apparently necessary for the efficient decoding of G-ending Pro, Ala, and Val codons in these organisms [].; GO: 0016300 tRNA (uracil) methyltransferase activity, 0002098 tRNA wobble uridine modification
Probab=95.60 E-value=0.017 Score=49.91 Aligned_cols=32 Identities=13% Similarity=0.079 Sum_probs=26.2
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEec
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFA 211 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D 211 (214)
...++|+|||||+|.++..++++-|.. ++++|
T Consensus 114 L~gk~VLDIGC~nGY~~frM~~~GA~~-ViGiD 145 (315)
T PF08003_consen 114 LKGKRVLDIGCNNGYYSFRMLGRGAKS-VIGID 145 (315)
T ss_pred cCCCEEEEecCCCcHHHHHHhhcCCCE-EEEEC
Confidence 357899999999999999999995543 56665
No 101
>PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=95.59 E-value=0.033 Score=45.61 Aligned_cols=42 Identities=17% Similarity=0.213 Sum_probs=32.7
Q ss_pred HHHhhcccccCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620 169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC 212 (214)
Q Consensus 169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl 212 (214)
.+++..+ ..+..+|||||||+|..+..+++.. ++.+++.+|.
T Consensus 67 ~~~~~l~--~~~g~~VLdIG~GsG~~t~~la~~~~~~~~V~~vE~ 109 (212)
T PRK13942 67 IMCELLD--LKEGMKVLEIGTGSGYHAAVVAEIVGKSGKVVTIER 109 (212)
T ss_pred HHHHHcC--CCCcCEEEEECCcccHHHHHHHHhcCCCCEEEEEeC
Confidence 3455555 5567899999999999999998875 4568888875
No 102
>PLN02490 MPBQ/MSBQ methyltransferase
Probab=95.55 E-value=0.018 Score=50.77 Aligned_cols=33 Identities=27% Similarity=0.342 Sum_probs=30.0
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...+|||||||+|.++..+++.+|..+++++|+
T Consensus 113 ~~~~VLDLGcGtG~~~l~La~~~~~~~VtgVD~ 145 (340)
T PLN02490 113 RNLKVVDVGGGTGFTTLGIVKHVDAKNVTILDQ 145 (340)
T ss_pred CCCEEEEEecCCcHHHHHHHHHCCCCEEEEEEC
Confidence 356999999999999999999999999999986
No 103
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=95.53 E-value=0.0066 Score=39.34 Aligned_cols=46 Identities=13% Similarity=0.243 Sum_probs=37.9
Q ss_pred cCcchhhhcCCCC--CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 39 LRIPDIINNSGQP--MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 39 lglfd~L~~~~~p--~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
..|+-.|... ++ +|..|||+.+++++ ..+.++++.|...|+++...
T Consensus 8 ~~vL~~l~~~-~~~~~t~~~la~~l~~~~---~~vs~~v~~L~~~Glv~r~~ 55 (62)
T PF12802_consen 8 FRVLMALARH-PGEELTQSELAERLGISK---STVSRIVKRLEKKGLVERER 55 (62)
T ss_dssp HHHHHHHHHS-TTSGEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHC-CCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEeC
Confidence 3445556665 34 89999999999999 99999999999999999876
No 104
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=95.51 E-value=0.027 Score=46.41 Aligned_cols=72 Identities=13% Similarity=0.212 Sum_probs=54.0
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCC--CccceeeCCCCCccccccccccchH
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNE--QEEESILLPPHLDFFSRISLQLQGS 118 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~--~~~~~y~~t~~~~~~s~~l~~~~~~ 118 (214)
|.-.|..+ +|+|+.|||+++|+++ ..+++-|..|...|++.....+ .+ --...|++|.. +...++..+.
T Consensus 16 il~lL~~~-g~~sa~elA~~Lgis~---~avR~HL~~Le~~Glv~~~~~~-~g~GRP~~~y~Lt~~----g~~~f~~~y~ 86 (218)
T COG2345 16 ILELLKKS-GPVSADELAEELGISP---MAVRRHLDDLEAEGLVEVERQQ-GGRGRPAKLYRLTEK----GREQFPKRYG 86 (218)
T ss_pred HHHHHhcc-CCccHHHHHHHhCCCH---HHHHHHHHHHHhCcceeeeecc-CCCCCCceeeeeccc----chhhcchhhH
Confidence 44556655 9999999999999999 9999999999999999865321 11 01356999999 8876655544
Q ss_pred HHH
Q 040620 119 TIL 121 (214)
Q Consensus 119 ~~~ 121 (214)
.+.
T Consensus 87 ~l~ 89 (218)
T COG2345 87 ELA 89 (218)
T ss_pred HHH
Confidence 443
No 105
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=95.47 E-value=0.019 Score=35.54 Aligned_cols=44 Identities=11% Similarity=0.210 Sum_probs=37.9
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|++.|..+ ++++..+||+.+++++ ..+++.|..|...|++....
T Consensus 5 il~~l~~~-~~~s~~~l~~~l~~s~---~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 5 ILELLAQQ-GKVSVEELAELLGVSE---MTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEee
Confidence 44555555 6799999999999999 99999999999999998764
No 106
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=95.46 E-value=0.019 Score=44.04 Aligned_cols=54 Identities=22% Similarity=0.400 Sum_probs=46.1
Q ss_pred hhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCccccccc
Q 040620 44 IINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRIS 112 (214)
Q Consensus 44 ~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l 112 (214)
++... ++.++.+||+.+++++ ..+.+.++.|...|++.+.. ...|.+|+. ++.+
T Consensus 16 l~~~~-~~~~~~ela~~l~vs~---~svs~~l~~L~~~Gli~~~~-------~~~i~LT~~----G~~~ 69 (142)
T PRK03902 16 LIEEK-GYARVSDIAEALSVHP---SSVTKMVQKLDKDEYLIYEK-------YRGLVLTPK----GKKI 69 (142)
T ss_pred HHhcC-CCcCHHHHHHHhCCCh---hHHHHHHHHHHHCCCEEEec-------CceEEECHH----HHHH
Confidence 34444 8899999999999999 99999999999999999765 478999999 6655
No 107
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=95.44 E-value=0.021 Score=42.99 Aligned_cols=43 Identities=16% Similarity=0.246 Sum_probs=37.7
Q ss_pred hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecC
Q 040620 43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKD 89 (214)
Q Consensus 43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~ 89 (214)
.+|..+ +|+|+++||+.++.+. ..++|-|+-|...|++.....
T Consensus 35 ~LL~~~-~~~tvdelae~lnr~r---Stv~rsl~~L~~~GlV~Rek~ 77 (126)
T COG3355 35 ALLEEN-GPLTVDELAEILNRSR---STVYRSLQNLLEAGLVEREKV 77 (126)
T ss_pred HHHhhc-CCcCHHHHHHHHCccH---HHHHHHHHHHHHcCCeeeeee
Confidence 445344 9999999999999998 999999999999999998763
No 108
>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=95.41 E-value=0.014 Score=48.64 Aligned_cols=34 Identities=24% Similarity=0.342 Sum_probs=24.7
Q ss_pred CCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl 212 (214)
....+|||||||+|.++..++++. |+.++++.|.
T Consensus 46 ~~g~~vLDv~~GtG~~~~~l~~~~~~~~~v~~vD~ 80 (233)
T PF01209_consen 46 RPGDRVLDVACGTGDVTRELARRVGPNGKVVGVDI 80 (233)
T ss_dssp -S--EEEEET-TTSHHHHHHGGGSS---EEEEEES
T ss_pred CCCCEEEEeCCChHHHHHHHHHHCCCccEEEEecC
Confidence 446799999999999999999875 6789999986
No 109
>PHA03411 putative methyltransferase; Provisional
Probab=95.40 E-value=0.021 Score=48.77 Aligned_cols=32 Identities=9% Similarity=0.126 Sum_probs=29.3
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+|+|+|||+|.++..++++.+..+++.+|+
T Consensus 65 ~grVLDLGcGsGilsl~la~r~~~~~V~gVDi 96 (279)
T PHA03411 65 TGKVLDLCAGIGRLSFCMLHRCKPEKIVCVEL 96 (279)
T ss_pred CCeEEEcCCCCCHHHHHHHHhCCCCEEEEEEC
Confidence 46999999999999999999988889999986
No 110
>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=95.33 E-value=0.023 Score=42.68 Aligned_cols=47 Identities=11% Similarity=0.179 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+|+|.++||+.+++++ ..++++++.|...|++..... . .+.|.++.-
T Consensus 24 ~~~s~~eia~~~~i~~---~~v~~il~~L~~~gli~~~~g----~-~ggy~l~~~ 70 (132)
T TIGR00738 24 GPVSVKEIAERQGISR---SYLEKILRTLRRAGLVESVRG----P-GGGYRLARP 70 (132)
T ss_pred CcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEeccC----C-CCCccCCCC
Confidence 5999999999999999 999999999999999986521 1 457887766
No 111
>COG2227 UbiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme metabolism]
Probab=95.32 E-value=0.018 Score=48.04 Aligned_cols=32 Identities=19% Similarity=0.231 Sum_probs=28.1
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
...+|||||||-|.++..+++. +.+++..|+-
T Consensus 59 ~g~~vLDvGCGgG~Lse~mAr~--Ga~VtgiD~s 90 (243)
T COG2227 59 PGLRVLDVGCGGGILSEPLARL--GASVTGIDAS 90 (243)
T ss_pred CCCeEEEecCCccHhhHHHHHC--CCeeEEecCC
Confidence 4679999999999999999999 4888888863
No 112
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=95.28 E-value=0.021 Score=38.11 Aligned_cols=54 Identities=20% Similarity=0.271 Sum_probs=44.0
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+.|+..|.+ ++.+..+||+++|++. ..+++.++.|...|+..... ...|.+.+.
T Consensus 3 ~~il~~L~~--~~~~~~eLa~~l~vS~---~tv~~~l~~L~~~g~~i~~~-------~~g~~l~~~ 56 (69)
T TIGR00122 3 LRLLALLAD--NPFSGEKLGEALGMSR---TAVNKHIQTLREWGVDVLTV-------GKGYRLPPP 56 (69)
T ss_pred HHHHHHHHc--CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeEEec-------CCceEecCc
Confidence 456677886 7899999999999999 99999999999999976554 355666555
No 113
>PLN02396 hexaprenyldihydroxybenzoate methyltransferase
Probab=95.26 E-value=0.023 Score=49.75 Aligned_cols=31 Identities=16% Similarity=0.235 Sum_probs=26.5
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...+|||||||.|.++..+++ ++.+++++|.
T Consensus 131 ~g~~ILDIGCG~G~~s~~La~--~g~~V~GID~ 161 (322)
T PLN02396 131 EGLKFIDIGCGGGLLSEPLAR--MGATVTGVDA 161 (322)
T ss_pred CCCEEEEeeCCCCHHHHHHHH--cCCEEEEEeC
Confidence 346899999999999998886 4778999885
No 114
>smart00138 MeTrc Methyltransferase, chemotaxis proteins. Methylates methyl-accepting chemotaxis proteins to form gamma-glutamyl methyl ester residues.
Probab=95.22 E-value=0.097 Score=44.38 Aligned_cols=33 Identities=27% Similarity=0.309 Sum_probs=26.4
Q ss_pred CCCcEEeecCCchH----HHHHHHHHCC-----CCeEEEecC
Q 040620 180 GLKPLVDVGGSTGT----MARAIATAFP-----DTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~----~~~~l~~~~P-----~l~~~v~Dl 212 (214)
+..+|+|+|||+|. +++.+++..| +.+++..|+
T Consensus 99 ~~~ri~d~GCgtGee~YslA~~l~e~~~~~~~~~~~I~g~Di 140 (264)
T smart00138 99 RRVRIWSAGCSTGEEPYSLAMLLAETLPKAREPDVKILATDI 140 (264)
T ss_pred CCEEEEeccccCChHHHHHHHHHHHHhhhcCCCCeEEEEEEC
Confidence 45699999999996 6777888766 467888886
No 115
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=95.20 E-value=0.0072 Score=38.89 Aligned_cols=45 Identities=16% Similarity=0.294 Sum_probs=37.9
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.+...|..+ ++++..+||+.+++++ ..+.++++.|...|++....
T Consensus 7 ~iL~~l~~~-~~~~~~~la~~~~~~~---~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 7 RILRILYEN-GGITQSELAEKLGISR---STVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHH-SSEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHc-CCCCHHHHHHHHCCCh---hHHHHHHHHHHHCCCEEecc
Confidence 344455565 7899999999999999 99999999999999999765
No 116
>PLN02672 methionine S-methyltransferase
Probab=95.17 E-value=0.022 Score=57.04 Aligned_cols=32 Identities=22% Similarity=0.257 Sum_probs=30.0
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+|+|||||+|..++.+++++|+.+++..|+
T Consensus 119 ~~~VLDlG~GSG~Iai~La~~~~~~~v~avDi 150 (1082)
T PLN02672 119 DKTVAELGCGNGWISIAIAEKWLPSKVYGLDI 150 (1082)
T ss_pred CCEEEEEecchHHHHHHHHHHCCCCEEEEEEC
Confidence 46899999999999999999999999999986
No 117
>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=95.09 E-value=0.044 Score=44.58 Aligned_cols=67 Identities=13% Similarity=0.114 Sum_probs=50.3
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecC-CCCCCccceeeCCCCCccccccccc
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKD-GKNEQEEESILLPPHLDFFSRISLQ 114 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~-~~~~~~~~~y~~t~~~~~~s~~l~~ 114 (214)
.|+..|... +++|..+||+.+|+++ ..+++.|+.|...|++..... ...|--...|.+|+. ++.+++
T Consensus 5 ~IL~~L~~~-~~~t~~eLA~~lgis~---~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~----G~~~~~ 72 (203)
T TIGR02702 5 DILSYLLKQ-GQATAAALAEALAISP---QAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQ----GREQFP 72 (203)
T ss_pred HHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcc----hhhhcc
Confidence 456666655 7899999999999999 999999999999999987631 001111234889988 777653
No 118
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=95.08 E-value=0.029 Score=43.90 Aligned_cols=50 Identities=16% Similarity=0.131 Sum_probs=46.0
Q ss_pred CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCccccccc
Q 040620 49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRIS 112 (214)
Q Consensus 49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l 112 (214)
++++...+||+.++++| ..+..+++-|...|++.+.+ .+.+.+|+. ++..
T Consensus 22 ~~~~~~~diA~~L~Vsp---~sVt~ml~rL~~~GlV~~~~-------y~gi~LT~~----G~~~ 71 (154)
T COG1321 22 KGFARTKDIAERLKVSP---PSVTEMLKRLERLGLVEYEP-------YGGVTLTEK----GREK 71 (154)
T ss_pred cCcccHHHHHHHhCCCc---HHHHHHHHHHHHCCCeEEec-------CCCeEEChh----hHHH
Confidence 38999999999999999 99999999999999999987 689999999 6655
No 119
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=95.07 E-value=0.039 Score=44.16 Aligned_cols=45 Identities=7% Similarity=0.050 Sum_probs=40.6
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.|+++|..+ |++|.++||..+|++. ..++++|..|...|++....
T Consensus 26 ~Vl~~L~~~-g~~tdeeLA~~Lgi~~---~~VRk~L~~L~e~gLv~~~r 70 (178)
T PRK06266 26 EVLKALIKK-GEVTDEEIAEQTGIKL---NTVRKILYKLYDARLADYKR 70 (178)
T ss_pred HHHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeEEee
Confidence 377888876 8999999999999999 99999999999999999654
No 120
>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=95.06 E-value=0.026 Score=35.74 Aligned_cols=44 Identities=20% Similarity=0.259 Sum_probs=34.5
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
|+..|..+++++|.++||+.++++. +.+++-+..|...|+..+.
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~---rTi~~~i~~L~~~~~~I~~ 48 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSR---RTIRRDIKELREWGIPIES 48 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-H---HHHHHHHHHHHHTT-EEEE
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCeEEe
Confidence 4556644447899999999999999 9999999999999944444
No 121
>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=95.05 E-value=0.031 Score=48.28 Aligned_cols=53 Identities=25% Similarity=0.213 Sum_probs=34.6
Q ss_pred HHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 155 FYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 155 f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
|..+-...+++..+. +..+. .+.++|+|||||+|.++++-++.-. -+++.+|.
T Consensus 140 FGTG~H~TT~lcl~~-l~~~~---~~g~~vLDvG~GSGILaiaA~klGA-~~v~a~Di 192 (295)
T PF06325_consen 140 FGTGHHPTTRLCLEL-LEKYV---KPGKRVLDVGCGSGILAIAAAKLGA-KKVVAIDI 192 (295)
T ss_dssp S-SSHCHHHHHHHHH-HHHHS---STTSEEEEES-TTSHHHHHHHHTTB-SEEEEEES
T ss_pred ccCCCCHHHHHHHHH-HHHhc---cCCCEEEEeCCcHHHHHHHHHHcCC-CeEEEecC
Confidence 334444555555443 34443 3457999999999999999888733 35777776
No 122
>PLN02336 phosphoethanolamine N-methyltransferase
Probab=95.04 E-value=0.041 Score=50.33 Aligned_cols=41 Identities=10% Similarity=0.165 Sum_probs=31.3
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+++.++ ..+..++||||||+|.++..+++.+. +++.+|.
T Consensus 27 ~~il~~l~--~~~~~~vLDlGcG~G~~~~~la~~~~--~v~giD~ 67 (475)
T PLN02336 27 PEILSLLP--PYEGKSVLELGAGIGRFTGELAKKAG--QVIALDF 67 (475)
T ss_pred hHHHhhcC--ccCCCEEEEeCCCcCHHHHHHHhhCC--EEEEEeC
Confidence 44555555 34467999999999999999999854 6777775
No 123
>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=95.00 E-value=0.037 Score=47.48 Aligned_cols=33 Identities=21% Similarity=0.225 Sum_probs=26.9
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
+..+|+|||||+|.+++.+++. +..+++.+|+-
T Consensus 159 ~g~~VLDvGcGsG~lai~aa~~-g~~~V~avDid 191 (288)
T TIGR00406 159 KDKNVIDVGCGSGILSIAALKL-GAAKVVGIDID 191 (288)
T ss_pred CCCEEEEeCCChhHHHHHHHHc-CCCeEEEEECC
Confidence 3589999999999999988764 45688888863
No 124
>PLN02366 spermidine synthase
Probab=94.99 E-value=0.027 Score=48.93 Aligned_cols=34 Identities=24% Similarity=0.360 Sum_probs=28.4
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecCC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFACH 213 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dlp 213 (214)
++.++||+||||.|..+..+++. |. .+++++|+.
T Consensus 90 ~~pkrVLiIGgG~G~~~rellk~-~~v~~V~~VEiD 124 (308)
T PLN02366 90 PNPKKVLVVGGGDGGVLREIARH-SSVEQIDICEID 124 (308)
T ss_pred CCCCeEEEEcCCccHHHHHHHhC-CCCCeEEEEECC
Confidence 35789999999999999999865 65 578888864
No 125
>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=94.98 E-value=0.045 Score=44.39 Aligned_cols=41 Identities=20% Similarity=0.152 Sum_probs=31.2
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+.+++.++ ..+..++||+|||.|.-+.-|+++ +..++.+|.
T Consensus 20 s~v~~a~~--~~~~g~~LDlgcG~GRNalyLA~~--G~~VtAvD~ 60 (192)
T PF03848_consen 20 SEVLEAVP--LLKPGKALDLGCGEGRNALYLASQ--GFDVTAVDI 60 (192)
T ss_dssp HHHHHHCT--TS-SSEEEEES-TTSHHHHHHHHT--T-EEEEEES
T ss_pred HHHHHHHh--hcCCCcEEEcCCCCcHHHHHHHHC--CCeEEEEEC
Confidence 44556665 456789999999999999999998 888888885
No 126
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=94.93 E-value=0.0084 Score=41.24 Aligned_cols=56 Identities=16% Similarity=0.186 Sum_probs=42.3
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
|...+.. ++.+..+|+..++++. ..+.++|..|...|++... .+.|.+|+. +..++
T Consensus 11 IL~~l~~--~~~~~t~i~~~~~L~~---~~~~~yL~~L~~~gLI~~~--------~~~Y~lTek----G~~~l 66 (77)
T PF14947_consen 11 ILKILSK--GGAKKTEIMYKANLNY---STLKKYLKELEEKGLIKKK--------DGKYRLTEK----GKEFL 66 (77)
T ss_dssp HHHHH-T--T-B-HHHHHTTST--H---HHHHHHHHHHHHTTSEEEE--------TTEEEE-HH----HHHHH
T ss_pred HHHHHHc--CCCCHHHHHHHhCcCH---HHHHHHHHHHHHCcCeeCC--------CCEEEECcc----HHHHH
Confidence 3344443 8999999999999999 9999999999999999775 589999999 76654
No 127
>PRK00811 spermidine synthase; Provisional
Probab=94.92 E-value=0.029 Score=48.04 Aligned_cols=33 Identities=21% Similarity=0.259 Sum_probs=28.4
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+.++|||||||.|..+..++++.+..+++++|+
T Consensus 76 ~p~~VL~iG~G~G~~~~~~l~~~~~~~V~~VEi 108 (283)
T PRK00811 76 NPKRVLIIGGGDGGTLREVLKHPSVEKITLVEI 108 (283)
T ss_pred CCCEEEEEecCchHHHHHHHcCCCCCEEEEEeC
Confidence 568999999999999999997655668998886
No 128
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=94.89 E-value=0.03 Score=51.92 Aligned_cols=33 Identities=18% Similarity=0.124 Sum_probs=30.6
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+...+||||||.|.+...+++++|+..++++|.
T Consensus 347 ~~p~~lEIG~G~G~~~~~~A~~~p~~~~iGiE~ 379 (506)
T PRK01544 347 KRKVFLEIGFGMGEHFINQAKMNPDALFIGVEV 379 (506)
T ss_pred CCceEEEECCCchHHHHHHHHhCCCCCEEEEEe
Confidence 467999999999999999999999999999885
No 129
>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=94.88 E-value=0.044 Score=40.22 Aligned_cols=32 Identities=13% Similarity=0.203 Sum_probs=23.6
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.....+||||||.|.+.--|.+. .-++.++|.
T Consensus 57 ~~~~~FVDlGCGNGLLV~IL~~E--Gy~G~GiD~ 88 (112)
T PF07757_consen 57 QKFQGFVDLGCGNGLLVYILNSE--GYPGWGIDA 88 (112)
T ss_pred CCCCceEEccCCchHHHHHHHhC--CCCcccccc
Confidence 35679999999999988777665 445555553
No 130
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=94.85 E-value=0.023 Score=41.12 Aligned_cols=46 Identities=15% Similarity=0.262 Sum_probs=41.0
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ 86 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~ 86 (214)
.+..|+.+|..+ +++|..+||+++|+++ ..+++.++.|...|++..
T Consensus 4 ~D~~il~~L~~~-~~~~~~~la~~l~~s~---~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKD-ARISLAELAKKVGLSP---STVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHh-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeec
Confidence 356677888886 7899999999999999 999999999999999983
No 131
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=94.85 E-value=0.076 Score=40.49 Aligned_cols=65 Identities=12% Similarity=0.113 Sum_probs=46.8
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
++..|...++++|..+||+.+++++ ..+.++++-|...|+++.....+|.- .-.+.+|+. ++.+.
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~~~---~tvt~~v~~Le~~GlV~r~~~~~DrR-~~~l~LT~~----G~~~~ 100 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGIEQ---PSLVRTLDQLEEKGLISRQTCASDRR-AKRIKLTEK----AEPLI 100 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCh---hhHHHHHHHHHHCCCEeeecCCCCcC-eeeeEEChH----HHHHH
Confidence 3455554335689999999999999 99999999999999999875321111 234667777 55553
No 132
>PRK11727 23S rRNA mA1618 methyltransferase; Provisional
Probab=94.84 E-value=0.036 Score=48.43 Aligned_cols=33 Identities=9% Similarity=-0.034 Sum_probs=29.8
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...++||||||+|.....++.+.|+++++..|+
T Consensus 114 ~~~~vLDIGtGag~I~~lLa~~~~~~~~~atDI 146 (321)
T PRK11727 114 ANVRVLDIGVGANCIYPLIGVHEYGWRFVGSDI 146 (321)
T ss_pred CCceEEEecCCccHHHHHHHhhCCCCEEEEEeC
Confidence 357999999999999999999999999999986
No 133
>PRK14967 putative methyltransferase; Provisional
Probab=94.83 E-value=0.048 Score=44.80 Aligned_cols=35 Identities=20% Similarity=0.165 Sum_probs=28.3
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
.....+|+|+|||+|.++..+++. +..+++.+|+-
T Consensus 34 ~~~~~~vLDlGcG~G~~~~~la~~-~~~~v~~vD~s 68 (223)
T PRK14967 34 LGPGRRVLDLCTGSGALAVAAAAA-GAGSVTAVDIS 68 (223)
T ss_pred cCCCCeEEEecCCHHHHHHHHHHc-CCCeEEEEECC
Confidence 344579999999999999999876 44588888863
No 134
>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=94.82 E-value=0.039 Score=44.88 Aligned_cols=58 Identities=12% Similarity=0.143 Sum_probs=47.7
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+..|+..|..+ ++++..+||+.+++++ ..+++.|..|...|++...+.. ...|.+|+.
T Consensus 145 ~~~IL~~l~~~-g~~s~~eia~~l~is~---stv~r~L~~Le~~GlI~r~~~r-----~~~~~lT~~ 202 (203)
T TIGR01884 145 ELKVLEVLKAE-GEKSVKNIAKKLGKSL---STISRHLRELEKKGLVEQKGRK-----GKRYSLTKL 202 (203)
T ss_pred HHHHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEcCC-----ccEEEeCCC
Confidence 34566677765 6899999999999999 9999999999999999988511 467888875
No 135
>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=94.82 E-value=0.028 Score=36.80 Aligned_cols=37 Identities=24% Similarity=0.351 Sum_probs=34.1
Q ss_pred CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+++++..+||+.++++| ..+...++-|...|++...+
T Consensus 20 ~~~v~~~~iA~~L~vs~---~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 20 GGPVRTKDIAERLGVSP---PTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp TSSBBHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEET
T ss_pred CCCccHHHHHHHHCCCh---HHHHHHHHHHHHCCCEEecC
Confidence 48999999999999999 99999999999999999885
No 136
>PRK11050 manganese transport regulator MntR; Provisional
Probab=94.80 E-value=0.031 Score=43.45 Aligned_cols=58 Identities=19% Similarity=0.250 Sum_probs=48.1
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
|..++... ++++..+||+.+++++ ..+.++++.|...|++.... ...+.+|+. +..+.
T Consensus 42 I~~~l~~~-~~~t~~eLA~~l~is~---stVsr~l~~Le~~GlI~r~~-------~~~v~LT~~----G~~l~ 99 (152)
T PRK11050 42 IADLIAEV-GEARQVDIAARLGVSQ---PTVAKMLKRLARDGLVEMRP-------YRGVFLTPE----GEKLA 99 (152)
T ss_pred HHHHHHhc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEec-------CCceEECch----HHHHH
Confidence 55566654 7899999999999999 99999999999999998765 467888888 66553
No 137
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=94.79 E-value=0.057 Score=34.36 Aligned_cols=43 Identities=9% Similarity=0.201 Sum_probs=36.9
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|+..|.. ++.|..+|++.+++++ ..+++.++.|...|++....
T Consensus 2 il~~l~~--~~~~~~~i~~~l~is~---~~v~~~l~~L~~~g~i~~~~ 44 (66)
T smart00418 2 ILKLLAE--GELCVCELAEILGLSQ---STVSHHLKKLREAGLVESRR 44 (66)
T ss_pred HHHHhhc--CCccHHHHHHHHCCCH---HHHHHHHHHHHHCCCeeeee
Confidence 3445553 7899999999999999 99999999999999998654
No 138
>PLN02585 magnesium protoporphyrin IX methyltransferase
Probab=94.78 E-value=0.033 Score=48.60 Aligned_cols=32 Identities=19% Similarity=0.205 Sum_probs=27.4
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
+..+|||||||+|.++..++++ +.+++.+|+-
T Consensus 144 ~~~~VLDlGcGtG~~a~~la~~--g~~V~gvD~S 175 (315)
T PLN02585 144 AGVTVCDAGCGTGSLAIPLALE--GAIVSASDIS 175 (315)
T ss_pred CCCEEEEecCCCCHHHHHHHHC--CCEEEEEECC
Confidence 3579999999999999999986 5788988863
No 139
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=94.76 E-value=0.044 Score=49.66 Aligned_cols=35 Identities=11% Similarity=0.193 Sum_probs=31.0
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.....+|+|+|||+|..+..+++..|+.+++.+|+
T Consensus 242 ~~~g~~VLDlgaG~G~~t~~la~~~~~~~v~a~D~ 276 (427)
T PRK10901 242 PQNGERVLDACAAPGGKTAHILELAPQAQVVALDI 276 (427)
T ss_pred CCCCCEEEEeCCCCChHHHHHHHHcCCCEEEEEeC
Confidence 34567999999999999999999998888998886
No 140
>KOG3115 consensus Methyltransferase-like protein [General function prediction only]
Probab=94.73 E-value=0.014 Score=47.60 Aligned_cols=32 Identities=25% Similarity=0.346 Sum_probs=28.5
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
-..++|||||-|.+.+.|+..||+.-+.++++
T Consensus 61 kvefaDIGCGyGGLlv~Lsp~fPdtLiLGmEI 92 (249)
T KOG3115|consen 61 KVEFADIGCGYGGLLMKLAPKFPDTLILGMEI 92 (249)
T ss_pred cceEEeeccCccchhhhccccCccceeeeehh
Confidence 36899999999999999999999998877654
No 141
>PRK11873 arsM arsenite S-adenosylmethyltransferase; Reviewed
Probab=94.66 E-value=0.052 Score=45.82 Aligned_cols=35 Identities=20% Similarity=0.153 Sum_probs=29.0
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl 212 (214)
.....+|||||||.|..+..+++.. |+.+++.+|+
T Consensus 75 ~~~g~~VLDiG~G~G~~~~~~a~~~g~~~~v~gvD~ 110 (272)
T PRK11873 75 LKPGETVLDLGSGGGFDCFLAARRVGPTGKVIGVDM 110 (272)
T ss_pred CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEECC
Confidence 4467899999999999988777764 6678999986
No 142
>COG2264 PrmA Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]
Probab=94.64 E-value=0.04 Score=47.61 Aligned_cols=54 Identities=24% Similarity=0.161 Sum_probs=35.7
Q ss_pred HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 154 IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 154 ~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.|..+-...+.+..+ +++.+. .+.++++|||||+|.++++.++--. .+++.+|+
T Consensus 140 AFGTG~HpTT~lcL~-~Le~~~---~~g~~vlDvGcGSGILaIAa~kLGA-~~v~g~Di 193 (300)
T COG2264 140 AFGTGTHPTTSLCLE-ALEKLL---KKGKTVLDVGCGSGILAIAAAKLGA-KKVVGVDI 193 (300)
T ss_pred ccCCCCChhHHHHHH-HHHHhh---cCCCEEEEecCChhHHHHHHHHcCC-ceEEEecC
Confidence 343444444455443 445554 3688999999999999999888622 24666665
No 143
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=94.63 E-value=0.041 Score=41.40 Aligned_cols=47 Identities=15% Similarity=0.228 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+++|+.|||+++++++ ..++++|+.|...|++..... . .+.|.+...
T Consensus 24 ~~~s~~eia~~l~is~---~~v~~~l~~L~~~Gli~~~~g----~-~ggy~l~~~ 70 (130)
T TIGR02944 24 QPYSAAEIAEQTGLNA---PTVSKILKQLSLAGIVTSKRG----V-EGGYTLARA 70 (130)
T ss_pred CCccHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEecCC----C-CCChhhcCC
Confidence 7899999999999999 999999999999999976421 0 356776655
No 144
>PHA00738 putative HTH transcription regulator
Probab=94.61 E-value=0.042 Score=40.20 Aligned_cols=60 Identities=12% Similarity=0.141 Sum_probs=48.3
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
.++.|+..|... +++++.+|++.++++. ..+.+-|+.|...|++..... |. ...|++++.
T Consensus 13 tRr~IL~lL~~~-e~~~V~eLae~l~lSQ---ptVS~HLKvLreAGLV~srK~---Gr-~vyY~Ln~~ 72 (108)
T PHA00738 13 LRRKILELIAEN-YILSASLISHTLLLSY---TTVLRHLKILNEQGYIELYKE---GR-TLYAKIREN 72 (108)
T ss_pred HHHHHHHHHHHc-CCccHHHHHHhhCCCH---HHHHHHHHHHHHCCceEEEEE---CC-EEEEEECCC
Confidence 456678888873 5799999999999999 999999999999999998762 11 244777776
No 145
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=94.58 E-value=0.039 Score=42.92 Aligned_cols=47 Identities=13% Similarity=0.220 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
++.|+++||++.+++| .+|.+++..|...|++.-.... .|-|.+..-
T Consensus 24 ~~~s~~~IA~~~~is~---~~L~kil~~L~kaGlV~S~rG~-----~GGy~Lar~ 70 (150)
T COG1959 24 GPVSSAEIAERQGISP---SYLEKILSKLRKAGLVKSVRGK-----GGGYRLARP 70 (150)
T ss_pred CcccHHHHHHHhCcCH---HHHHHHHHHHHHcCCEEeecCC-----CCCccCCCC
Confidence 4899999999999999 9999999999999999866421 577888777
No 146
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=94.57 E-value=0.088 Score=43.80 Aligned_cols=42 Identities=21% Similarity=0.196 Sum_probs=30.8
Q ss_pred HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.+++.++- ....++++|||||+|.++..++++ +-.+++.+|.
T Consensus 65 ~~l~~~~~-~~~~~~vlDiG~gtG~~t~~l~~~-ga~~v~avD~ 106 (228)
T TIGR00478 65 EALEEFNI-DVKNKIVLDVGSSTGGFTDCALQK-GAKEVYGVDV 106 (228)
T ss_pred HHHHhcCC-CCCCCEEEEcccCCCHHHHHHHHc-CCCEEEEEeC
Confidence 34454431 124679999999999999999986 5557888885
No 147
>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=94.56 E-value=0.029 Score=37.48 Aligned_cols=48 Identities=15% Similarity=0.235 Sum_probs=38.1
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCC--cccHHHHHHHHHhCCceeeec
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNK--TRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~--~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|+++|.+.++|++..+|++.++....+ ++.+++.|+.|-..|++....
T Consensus 3 IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~g 52 (66)
T PF08461_consen 3 ILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKVG 52 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccccC
Confidence 456777777999999999998753322 288999999999999777654
No 148
>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=94.52 E-value=0.027 Score=37.55 Aligned_cols=41 Identities=24% Similarity=0.374 Sum_probs=33.0
Q ss_pred hhcCCCCCCHHHHHHHcCCC-CCCcccHHHHHHHHHhCCceeeec
Q 040620 45 INNSGQPMTLTQIIVALNVH-PNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 45 L~~~~~p~t~~eLA~~~g~~-~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+.++|-|-|+.|||+.+|+. + ..+++.|+.|...|++...+
T Consensus 19 ~~~~G~~Pt~rEIa~~~g~~S~---~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 19 IEENGYPPTVREIAEALGLKST---STVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp HHHHSS---HHHHHHHHTSSSH---HHHHHHHHHHHHTTSEEEGC
T ss_pred HHHcCCCCCHHHHHHHhCCCCh---HHHHHHHHHHHHCcCccCCC
Confidence 34455677999999999996 7 89999999999999999875
No 149
>PHA03412 putative methyltransferase; Provisional
Probab=94.46 E-value=0.045 Score=45.80 Aligned_cols=32 Identities=13% Similarity=0.171 Sum_probs=27.8
Q ss_pred CCcEEeecCCchHHHHHHHHHC---CCCeEEEecC
Q 040620 181 LKPLVDVGGSTGTMARAIATAF---PDTKCTVFAC 212 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~---P~l~~~v~Dl 212 (214)
..+|||+|||+|.++..++++. ++.+++.+|+
T Consensus 50 ~grVLDlG~GSG~Lalala~~~~~~~~~~V~aVEI 84 (241)
T PHA03412 50 SGSVVDLCAGIGGLSFAMVHMMMYAKPREIVCVEL 84 (241)
T ss_pred CCEEEEccChHHHHHHHHHHhcccCCCcEEEEEEC
Confidence 5799999999999999999985 4668888886
No 150
>KOG1270 consensus Methyltransferases [Coenzyme transport and metabolism]
Probab=94.40 E-value=0.044 Score=46.39 Aligned_cols=30 Identities=20% Similarity=0.296 Sum_probs=25.6
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.++|||||||.|.++..|++. ...++..|.
T Consensus 90 g~~ilDvGCGgGLLSepLArl--ga~V~GID~ 119 (282)
T KOG1270|consen 90 GMKILDVGCGGGLLSEPLARL--GAQVTGIDA 119 (282)
T ss_pred CceEEEeccCccccchhhHhh--CCeeEeecc
Confidence 367999999999999999998 467777775
No 151
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=94.39 E-value=0.066 Score=34.18 Aligned_cols=42 Identities=19% Similarity=0.135 Sum_probs=34.5
Q ss_pred HHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHH
Q 040620 30 SLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLL 78 (214)
Q Consensus 30 ~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L 78 (214)
-.+|.+|++.|-||.=. ..|.+|||+.+|+++ ..+...||-.
T Consensus 6 ~e~L~~A~~~GYfd~PR----~~tl~elA~~lgis~---st~~~~LRra 47 (53)
T PF04967_consen 6 REILKAAYELGYFDVPR----RITLEELAEELGISK---STVSEHLRRA 47 (53)
T ss_pred HHHHHHHHHcCCCCCCC----cCCHHHHHHHhCCCH---HHHHHHHHHH
Confidence 46899999999998644 489999999999998 7776666643
No 152
>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=94.35 E-value=0.08 Score=43.51 Aligned_cols=31 Identities=3% Similarity=-0.231 Sum_probs=27.9
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...+++|+|||.|..++.|+++ ..++|.+|+
T Consensus 34 ~~~rvLd~GCG~G~da~~LA~~--G~~V~gvD~ 64 (213)
T TIGR03840 34 AGARVFVPLCGKSLDLAWLAEQ--GHRVLGVEL 64 (213)
T ss_pred CCCeEEEeCCCchhHHHHHHhC--CCeEEEEeC
Confidence 4579999999999999999986 888999986
No 153
>KOG2904 consensus Predicted methyltransferase [General function prediction only]
Probab=94.28 E-value=0.05 Score=46.43 Aligned_cols=33 Identities=15% Similarity=0.399 Sum_probs=29.9
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
....++|+|||+|..+..++..-|+.+++-.|+
T Consensus 148 ~~~~ildlgtGSGaIslsll~~L~~~~v~AiD~ 180 (328)
T KOG2904|consen 148 KHTHILDLGTGSGAISLSLLHGLPQCTVTAIDV 180 (328)
T ss_pred ccceEEEecCCccHHHHHHHhcCCCceEEEEec
Confidence 345899999999999999999999999998886
No 154
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=94.27 E-value=0.0087 Score=41.53 Aligned_cols=64 Identities=13% Similarity=0.173 Sum_probs=45.6
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
++++|..+|... +.+++.+|.+.+|++. -.+.+-|..|...|++.....-.+..-.-.|++|+.
T Consensus 1 vRl~Il~~L~~~-~~~~f~~L~~~l~lt~---g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~ 64 (80)
T PF13601_consen 1 VRLAILALLYAN-EEATFSELKEELGLTD---GNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDK 64 (80)
T ss_dssp HHHHHHHHHHHH-SEEEHHHHHHHTT--H---HHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HH
T ss_pred CHHHHHHHHhhc-CCCCHHHHHHHhCcCH---HHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHH
Confidence 456777788876 7899999999999999 999999999999999997753111100123666666
No 155
>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=94.26 E-value=0.047 Score=42.85 Aligned_cols=44 Identities=11% Similarity=0.039 Sum_probs=38.9
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
.|+++|..+ +.+|-++||+.+|++. ..++++|..|...|++.+.
T Consensus 18 ~Vl~aL~~~-~~~tdEeLa~~Lgi~~---~~VRk~L~~L~e~~Lv~~~ 61 (158)
T TIGR00373 18 LVLFSLGIK-GEFTDEEISLELGIKL---NEVRKALYALYDAGLADYK 61 (158)
T ss_pred HHHHHHhcc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCceee
Confidence 366777765 7999999999999999 9999999999999999754
No 156
>PRK14902 16S rRNA methyltransferase B; Provisional
Probab=94.26 E-value=0.062 Score=48.90 Aligned_cols=35 Identities=20% Similarity=0.261 Sum_probs=30.4
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl 212 (214)
..+..+|+|+|||+|..+..+++.. |+.+++.+|+
T Consensus 248 ~~~g~~VLDlgaG~G~~t~~la~~~~~~~~v~avDi 283 (444)
T PRK14902 248 PKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDI 283 (444)
T ss_pred CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEEeC
Confidence 3456799999999999999999987 7788999987
No 157
>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=94.22 E-value=0.14 Score=42.17 Aligned_cols=64 Identities=19% Similarity=0.136 Sum_probs=37.4
Q ss_pred CChhhHHHHHHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 145 QTLFGTADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 145 ~~~f~~~~g~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
|..|+..|.-|.+.+..+.......+++.+. ..++...|.|.|||.+.++.++.+. .++--|||
T Consensus 38 P~~F~~YH~Gfr~Qv~~WP~nPvd~iI~~l~-~~~~~~viaD~GCGdA~la~~~~~~---~~V~SfDL 101 (219)
T PF05148_consen 38 PELFDIYHEGFRQQVKKWPVNPVDVIIEWLK-KRPKSLVIADFGCGDAKLAKAVPNK---HKVHSFDL 101 (219)
T ss_dssp HHHHHHHHHHHHHHHCTSSS-HHHHHHHHHC-TS-TTS-EEEES-TT-HHHHH--S------EEEEES
T ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHHH-hcCCCEEEEECCCchHHHHHhcccC---ceEEEeec
Confidence 4567766656888888777666666666554 2344579999999999999765422 34555554
No 158
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=94.19 E-value=0.1 Score=45.01 Aligned_cols=41 Identities=15% Similarity=0.294 Sum_probs=30.8
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+++..+ .....+|+|||||.|.++..+++... +++.+|+
T Consensus 26 ~~Iv~~~~--~~~~~~VLEIG~G~G~LT~~Ll~~~~--~V~avEi 66 (294)
T PTZ00338 26 DKIVEKAA--IKPTDTVLEIGPGTGNLTEKLLQLAK--KVIAIEI 66 (294)
T ss_pred HHHHHhcC--CCCcCEEEEecCchHHHHHHHHHhCC--cEEEEEC
Confidence 44555554 45567999999999999999999854 5666664
No 159
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=94.14 E-value=0.054 Score=41.44 Aligned_cols=65 Identities=11% Similarity=0.087 Sum_probs=47.9
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
.|+-.|... +++|..+||+.+++++ ..+.++++-|...|++......+|.- .-.+.+|+. ++.+.
T Consensus 44 ~vL~~l~~~-~~~t~~eLa~~l~i~~---~tvsr~l~~Le~~GlI~R~~~~~DrR-~~~l~LT~~----G~~~~ 108 (144)
T PRK11512 44 KVLCSIRCA-ACITPVELKKVLSVDL---GALTRMLDRLVCKGWVERLPNPNDKR-GVLVKLTTS----GAAIC 108 (144)
T ss_pred HHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEeccCcccCC-eeEeEEChh----HHHHH
Confidence 345566654 7899999999999999 99999999999999999775321111 223566777 55543
No 160
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=94.07 E-value=0.058 Score=40.50 Aligned_cols=51 Identities=12% Similarity=0.253 Sum_probs=46.1
Q ss_pred HHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 34 KRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 34 ~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+..++..|.+.+.++ |.+|..|++..+|++. ..+.++++-|++.|-+...+
T Consensus 10 r~eLk~rIvElVRe~-GRiTi~ql~~~TGasR---~Tvk~~lreLVa~G~l~~~G 60 (127)
T PF06163_consen 10 REELKARIVELVREH-GRITIKQLVAKTGASR---NTVKRYLRELVARGDLYRHG 60 (127)
T ss_pred HHHHHHHHHHHHHHc-CCccHHHHHHHHCCCH---HHHHHHHHHHHHcCCeEeCC
Confidence 456677888999998 9999999999999998 89999999999999999885
No 161
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=94.04 E-value=0.15 Score=32.81 Aligned_cols=34 Identities=12% Similarity=0.109 Sum_probs=30.9
Q ss_pred CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 52 MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 52 ~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.|..+||+.+++++ ..+++.+..|...|++....
T Consensus 26 ~~~~~la~~~~is~---~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 26 PSERELAEELGVSR---TTVREALRELEAEGLVERRP 59 (66)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecC
Confidence 35999999999999 99999999999999998664
No 162
>PRK05134 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional
Probab=94.02 E-value=0.12 Score=42.46 Aligned_cols=32 Identities=22% Similarity=0.258 Sum_probs=26.5
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
+..+|||||||.|.++..+++. ..++++.|..
T Consensus 48 ~~~~vLdiG~G~G~~~~~l~~~--~~~v~~iD~s 79 (233)
T PRK05134 48 FGKRVLDVGCGGGILSESMARL--GADVTGIDAS 79 (233)
T ss_pred CCCeEEEeCCCCCHHHHHHHHc--CCeEEEEcCC
Confidence 4678999999999999999886 4678888763
No 163
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=94.02 E-value=0.062 Score=48.91 Aligned_cols=32 Identities=9% Similarity=0.040 Sum_probs=26.9
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.+..+|+|+|||+|.+++.+++.. .+++.+|.
T Consensus 296 ~~~~~VLDlgcGtG~~sl~la~~~--~~V~gvD~ 327 (443)
T PRK13168 296 QPGDRVLDLFCGLGNFTLPLARQA--AEVVGVEG 327 (443)
T ss_pred CCCCEEEEEeccCCHHHHHHHHhC--CEEEEEeC
Confidence 345799999999999999999986 57777775
No 164
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=93.95 E-value=0.063 Score=40.63 Aligned_cols=47 Identities=13% Similarity=0.301 Sum_probs=42.1
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.+.|...|+.. +|.|+.|+|+.+|-+. ..|.|-|+.|+..|++.-..
T Consensus 66 nleLl~~Ia~~-~P~Si~ElAe~vgRdv---~nvhr~Ls~l~~~GlI~fe~ 112 (144)
T COG4190 66 NLELLELIAQE-EPASINELAELVGRDV---KNVHRTLSTLADLGLIFFEE 112 (144)
T ss_pred HHHHHHHHHhc-CcccHHHHHHHhCcch---HHHHHHHHHHHhcCeEEEec
Confidence 35567788887 9999999999999999 99999999999999998775
No 165
>PRK13943 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=93.93 E-value=0.13 Score=45.03 Aligned_cols=35 Identities=14% Similarity=0.198 Sum_probs=28.9
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl 212 (214)
..+..+|||||||+|.++..+++..+. -+++.+|.
T Consensus 78 i~~g~~VLDIG~GtG~~a~~LA~~~~~~g~VvgVDi 113 (322)
T PRK13943 78 LDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEY 113 (322)
T ss_pred CCCCCEEEEEeCCccHHHHHHHHhcCCCCEEEEEEC
Confidence 445679999999999999999998875 46777775
No 166
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=93.93 E-value=0.077 Score=40.59 Aligned_cols=61 Identities=13% Similarity=0.251 Sum_probs=45.3
Q ss_pred HHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 32 SLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 32 ~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+++..+.++. +.. |.+++.++||++.|+++ ..++++++.|...|++.-.... .+.|.+...
T Consensus 10 Al~~~i~la~---~~~-g~~~s~~~ia~~~~is~---~~vrk~l~~L~~~Glv~s~~G~-----~GG~~l~~~ 70 (141)
T PRK11014 10 GLRALIYMAS---LPE-GRMTSISEVTEVYGVSR---NHMVKIINQLSRAGYVTAVRGK-----NGGIRLGKP 70 (141)
T ss_pred HHHHHHHHhc---CCC-CCccCHHHHHHHHCcCH---HHHHHHHHHHHhCCEEEEecCC-----CCCeeecCC
Confidence 4555554443 222 26789999999999999 9999999999999999877521 356766655
No 167
>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=93.90 E-value=0.084 Score=34.58 Aligned_cols=44 Identities=16% Similarity=0.309 Sum_probs=37.0
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.|+..+.. ++++..+||+.++++. ..+++.++.|...|++....
T Consensus 11 ~il~~l~~--~~~~~~ei~~~~~i~~---~~i~~~l~~L~~~g~i~~~~ 54 (78)
T cd00090 11 RILRLLLE--GPLTVSELAERLGLSQ---STVSRHLKKLEEAGLVESRR 54 (78)
T ss_pred HHHHHHHH--CCcCHHHHHHHHCcCH---hHHHHHHHHHHHCCCeEEEE
Confidence 34555555 3499999999999998 99999999999999999764
No 168
>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=93.81 E-value=0.14 Score=40.59 Aligned_cols=37 Identities=19% Similarity=0.174 Sum_probs=28.7
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCCC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL 214 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~ 214 (214)
....++|+++|+|.|..++.+++..+..++++-|.|+
T Consensus 43 ~~~~~~VLELGaG~Gl~gi~~a~~~~~~~Vv~TD~~~ 79 (173)
T PF10294_consen 43 LFRGKRVLELGAGTGLPGIAAAKLFGAARVVLTDYNE 79 (173)
T ss_dssp GTTTSEEEETT-TTSHHHHHHHHT-T-SEEEEEE-S-
T ss_pred hcCCceEEEECCccchhHHHHHhccCCceEEEeccch
Confidence 4457899999999999999999998888999998874
No 169
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=93.81 E-value=0.14 Score=32.32 Aligned_cols=36 Identities=11% Similarity=0.201 Sum_probs=32.7
Q ss_pred CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
..+ |..+||+.+++++ ..+++.+..|...|++....
T Consensus 18 ~~l~s~~~la~~~~vs~---~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 18 DKLPSERELAAQLGVSR---TTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred CcCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEec
Confidence 456 8999999999999 99999999999999998764
No 170
>PRK01581 speE spermidine synthase; Validated
Probab=93.76 E-value=0.082 Score=47.00 Aligned_cols=35 Identities=14% Similarity=0.137 Sum_probs=29.3
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
.++++||+||||.|..+..+++..|..+++++|+-
T Consensus 149 ~~PkrVLIIGgGdG~tlrelLk~~~v~~It~VEID 183 (374)
T PRK01581 149 IDPKRVLILGGGDGLALREVLKYETVLHVDLVDLD 183 (374)
T ss_pred CCCCEEEEECCCHHHHHHHHHhcCCCCeEEEEeCC
Confidence 45789999999999999999986556789988863
No 171
>PRK00312 pcm protein-L-isoaspartate O-methyltransferase; Reviewed
Probab=93.70 E-value=0.15 Score=41.46 Aligned_cols=33 Identities=15% Similarity=0.178 Sum_probs=25.7
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+..+|+|||||+|..+..+++... +++.+|.
T Consensus 76 ~~~~~~VLeiG~GsG~~t~~la~~~~--~v~~vd~ 108 (212)
T PRK00312 76 LKPGDRVLEIGTGSGYQAAVLAHLVR--RVFSVER 108 (212)
T ss_pred CCCCCEEEEECCCccHHHHHHHHHhC--EEEEEeC
Confidence 45568999999999999988777753 5666664
No 172
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=93.65 E-value=0.069 Score=45.18 Aligned_cols=64 Identities=19% Similarity=0.238 Sum_probs=57.2
Q ss_pred HHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCccccccc
Q 040620 33 LKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRIS 112 (214)
Q Consensus 33 L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l 112 (214)
+...-+.+|+-.|.+ ||.|.+||-..+++++ ..+..=+.-|...|++.++ ++.|++|+. ++..
T Consensus 10 f~SekRk~lLllL~e--gPkti~EI~~~l~vs~---~ai~pqiKkL~~~~LV~~~--------~~~Y~LS~~----G~ii 72 (260)
T COG4742 10 FLSEKRKDLLLLLKE--GPKTIEEIKNELNVSS---SAILPQIKKLKDKGLVVQE--------GDRYSLSSL----GKII 72 (260)
T ss_pred HccHHHHHHHHHHHh--CCCCHHHHHHHhCCCc---HHHHHHHHHHhhCCCEEec--------CCEEEecch----HHHH
Confidence 345566777888887 9999999999999999 9999999999999999999 489999999 9988
Q ss_pred c
Q 040620 113 L 113 (214)
Q Consensus 113 ~ 113 (214)
+
T Consensus 73 v 73 (260)
T COG4742 73 V 73 (260)
T ss_pred H
Confidence 7
No 173
>PRK04148 hypothetical protein; Provisional
Probab=93.58 E-value=0.15 Score=38.93 Aligned_cols=40 Identities=15% Similarity=0.178 Sum_probs=28.8
Q ss_pred HHHhhcccccCCCCcEEeecCCchH-HHHHHHHHCCCCeEEEecC
Q 040620 169 VLIEDCNEVSKGLKPLVDVGGSTGT-MARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 169 ~~l~~~~~~~~~~~~vvDVGGG~G~-~~~~l~~~~P~l~~~v~Dl 212 (214)
.+.+.++ -.+..+++|||+|.|. ++..|.+. +..++..|.
T Consensus 7 ~l~~~~~--~~~~~kileIG~GfG~~vA~~L~~~--G~~ViaIDi 47 (134)
T PRK04148 7 FIAENYE--KGKNKKIVELGIGFYFKVAKKLKES--GFDVIVIDI 47 (134)
T ss_pred HHHHhcc--cccCCEEEEEEecCCHHHHHHHHHC--CCEEEEEEC
Confidence 3445454 2234789999999996 88888765 678888885
No 174
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=93.55 E-value=0.11 Score=40.47 Aligned_cols=47 Identities=13% Similarity=0.104 Sum_probs=40.5
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+++|+++||++.++++ .+|.+++..|...|++.-.... .|-|.++.-
T Consensus 23 ~~~s~~eIA~~~~is~---~~L~kIl~~L~~aGlv~S~rG~-----~GGy~La~~ 69 (153)
T PRK11920 23 KLSRIPEIARAYGVSE---LFLFKILQPLVEAGLVETVRGR-----NGGVRLGRP 69 (153)
T ss_pred CcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEeecCC-----CCCeeecCC
Confidence 6789999999999999 9999999999999999866521 467777776
No 175
>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB. The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles.
Probab=93.46 E-value=0.11 Score=47.08 Aligned_cols=35 Identities=11% Similarity=0.231 Sum_probs=30.7
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.....+|+|+|||+|..+..+++..|+.+++.+|.
T Consensus 236 ~~~g~~VLDlcag~G~kt~~la~~~~~~~v~a~D~ 270 (426)
T TIGR00563 236 PQNEETILDACAAPGGKTTHILELAPQAQVVALDI 270 (426)
T ss_pred CCCCCeEEEeCCCccHHHHHHHHHcCCCeEEEEeC
Confidence 34567999999999999999999998788888886
No 176
>KOG1540 consensus Ubiquinone biosynthesis methyltransferase COQ5 [Coenzyme transport and metabolism]
Probab=93.46 E-value=0.08 Score=44.77 Aligned_cols=34 Identities=29% Similarity=0.355 Sum_probs=30.6
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCC------CeEEEecCC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPD------TKCTVFACH 213 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~------l~~~v~Dlp 213 (214)
..-++|||+||+|-.+..|+++-++ .+++|.|+-
T Consensus 100 ~~m~~lDvaGGTGDiaFril~~v~s~~~~~~~~V~v~Din 139 (296)
T KOG1540|consen 100 KGMKVLDVAGGTGDIAFRILRHVKSQFGDRESKVTVLDIN 139 (296)
T ss_pred CCCeEEEecCCcchhHHHHHHhhccccCCCCceEEEEeCC
Confidence 3479999999999999999999999 789999974
No 177
>PRK13255 thiopurine S-methyltransferase; Reviewed
Probab=93.44 E-value=0.15 Score=42.02 Aligned_cols=32 Identities=3% Similarity=-0.234 Sum_probs=28.1
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
....+|+|+|||.|..+..|+++ ..+++.+|+
T Consensus 36 ~~~~rvL~~gCG~G~da~~LA~~--G~~V~avD~ 67 (218)
T PRK13255 36 PAGSRVLVPLCGKSLDMLWLAEQ--GHEVLGVEL 67 (218)
T ss_pred CCCCeEEEeCCCChHhHHHHHhC--CCeEEEEcc
Confidence 34579999999999999999985 888999986
No 178
>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=93.40 E-value=0.067 Score=39.06 Aligned_cols=37 Identities=16% Similarity=0.365 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKD 89 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~ 89 (214)
+++|..+||+.+++++ ..+.++++.|...|++.....
T Consensus 42 ~~~t~~eL~~~l~~~~---stvs~~i~~Le~kg~I~r~~~ 78 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQ---SALVKIIKKLSKKGYLSKERS 78 (109)
T ss_pred CcCcHHHHHHHHCCCH---HHHHHHHHHHHHCCCEeccCC
Confidence 7899999999999999 999999999999999997653
No 179
>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=93.36 E-value=0.086 Score=38.58 Aligned_cols=59 Identities=17% Similarity=0.183 Sum_probs=44.4
Q ss_pred cCcchhhhcCCCCCCHHHHHHHc-----CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620 39 LRIPDIINNSGQPMTLTQIIVAL-----NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP 103 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~-----g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~ 103 (214)
..|++.|...++++|++||.+++ +++. ..+.|.|+.|+..|++.+... ++. ..+|..+.
T Consensus 4 ~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~---~TVYR~L~~L~~~Gli~~~~~--~~~-~~~y~~~~ 67 (116)
T cd07153 4 LAILEVLLESDGHLTAEEIYERLRKKGPSISL---ATVYRTLELLEEAGLVREIEL--GDG-KARYELNT 67 (116)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCH---HHHHHHHHHHHhCCCEEEEEe--CCC-ceEEEeCC
Confidence 34677777655899999999998 4666 899999999999999998753 111 35676543
No 180
>PRK06474 hypothetical protein; Provisional
Probab=93.34 E-value=0.13 Score=41.16 Aligned_cols=71 Identities=14% Similarity=0.188 Sum_probs=53.4
Q ss_pred HHHHHHHhcCcchhhhcCCCCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCC-CCCccceeeCCCC
Q 040620 31 LSLKRAIQLRIPDIINNSGQPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGK-NEQEEESILLPPH 104 (214)
Q Consensus 31 ~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~-~~~~~~~y~~t~~ 104 (214)
.+|.--.++.|++.|...++++|+.+|++.+ +++. ..+.|.|+.|...|++....... .+..+..|+.++.
T Consensus 6 ~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~---aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~ 78 (178)
T PRK06474 6 EILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQ---ATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEE 78 (178)
T ss_pred HhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCH---HHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccc
Confidence 4555566778888888764459999999999 6777 78999999999999999865321 1111356888887
No 181
>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=93.23 E-value=0.11 Score=44.08 Aligned_cols=34 Identities=21% Similarity=0.302 Sum_probs=28.6
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
+.++|++||||.|..+..+++..|..++++.|+-
T Consensus 72 ~p~~VL~iG~G~G~~~~~ll~~~~~~~v~~veid 105 (270)
T TIGR00417 72 NPKHVLVIGGGDGGVLREVLKHKSVEKATLVDID 105 (270)
T ss_pred CCCEEEEEcCCchHHHHHHHhCCCcceEEEEeCC
Confidence 4579999999999999999987666778888763
No 182
>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=93.19 E-value=0.077 Score=30.23 Aligned_cols=31 Identities=23% Similarity=0.303 Sum_probs=25.7
Q ss_pred CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCce
Q 040620 51 PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFF 84 (214)
Q Consensus 51 p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l 84 (214)
|+|-+|||+.+|+.+ .-+.|+|..|...|++
T Consensus 2 ~mtr~diA~~lG~t~---ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 2 PMTRQDIADYLGLTR---ETVSRILKKLERQGLI 32 (32)
T ss_dssp E--HHHHHHHHTS-H---HHHHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHhCCcH---HHHHHHHHHHHHcCCC
Confidence 589999999999999 9999999999988874
No 183
>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=93.00 E-value=0.11 Score=42.35 Aligned_cols=32 Identities=19% Similarity=0.135 Sum_probs=26.1
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
...+|+|+|||+|.++..+++..+ ++++.|+.
T Consensus 45 ~~~~vLdlG~G~G~~~~~l~~~~~--~v~~iD~s 76 (224)
T TIGR01983 45 FGLRVLDVGCGGGLLSEPLARLGA--NVTGIDAS 76 (224)
T ss_pred CCCeEEEECCCCCHHHHHHHhcCC--eEEEEeCC
Confidence 467999999999999999988754 47777753
No 184
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=92.98 E-value=0.15 Score=35.11 Aligned_cols=44 Identities=20% Similarity=0.208 Sum_probs=40.0
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|=|+|+.+ |-+++.+||.++++++ ..++.+|..++..|-+++..
T Consensus 7 lRd~l~~~-gr~s~~~Ls~~~~~p~---~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 7 VRDLLALR-GRMEAAQISQTLNTPQ---PMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHHc-CcccHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEeec
Confidence 34778887 8999999999999999 99999999999999999875
No 185
>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed
Probab=92.89 E-value=0.14 Score=44.39 Aligned_cols=30 Identities=17% Similarity=0.091 Sum_probs=26.0
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+|+|+|||+|.++..+++. ..+++.+|.
T Consensus 174 ~~~VLDl~cG~G~~sl~la~~--~~~V~gvD~ 203 (315)
T PRK03522 174 PRSMWDLFCGVGGFGLHCATP--GMQLTGIEI 203 (315)
T ss_pred CCEEEEccCCCCHHHHHHHhc--CCEEEEEeC
Confidence 579999999999999999984 467888875
No 186
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=92.54 E-value=0.14 Score=36.03 Aligned_cols=46 Identities=22% Similarity=0.243 Sum_probs=40.2
Q ss_pred HHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 54 LTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 54 ~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
+.+||+.+++++ ..+.+.++.|...|++...+ ...|.+|+. +..+.
T Consensus 2 ~~ela~~l~is~---stvs~~l~~L~~~glI~r~~-------~~~~~lT~~----g~~~~ 47 (96)
T smart00529 2 TSEIAERLNVSP---PTVTQMLKKLEKDGLVEYEP-------YRGITLTEK----GRRLA 47 (96)
T ss_pred HHHHHHHhCCCh---HHHHHHHHHHHHCCCEEEcC-------CCceEechh----HHHHH
Confidence 579999999999 99999999999999999986 468999998 65553
No 187
>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=92.52 E-value=0.052 Score=39.37 Aligned_cols=44 Identities=16% Similarity=0.264 Sum_probs=33.7
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|++.|... +.++-++||+.+|+++ ..++++|..|...|++....
T Consensus 18 Il~~L~~~-~~l~de~la~~~~l~~---~~vRkiL~~L~~~~lv~~~~ 61 (105)
T PF02002_consen 18 ILDALLRK-GELTDEDLAKKLGLKP---KEVRKILYKLYEDGLVSYRR 61 (105)
T ss_dssp HHHHHHHH---B-HHHHHHTT-S-H---HHHHHHHHHHHHHSS-EEEE
T ss_pred HHHHHHHc-CCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCeEEEE
Confidence 56777765 7899999999999999 99999999999999997664
No 188
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=92.31 E-value=0.051 Score=38.31 Aligned_cols=62 Identities=13% Similarity=0.162 Sum_probs=45.6
Q ss_pred chhhhcCCCCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 42 PDIINNSGQPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 42 fd~L~~~~~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
...|.. ++....||.+.+ ++++ +.|.+-|+.|...|++.......... .-.|.+|+. ++.|.
T Consensus 11 L~~l~~--g~~rf~el~~~l~~is~---~~L~~~L~~L~~~GLv~r~~~~~~p~-~v~Y~LT~~----G~~l~ 73 (90)
T PF01638_consen 11 LRALFQ--GPMRFSELQRRLPGISP---KVLSQRLKELEEAGLVERRVYPEVPP-RVEYSLTEK----GKELL 73 (90)
T ss_dssp HHHHTT--SSEEHHHHHHHSTTS-H---HHHHHHHHHHHHTTSEEEEEESSSSS-EEEEEE-HH----HHHHH
T ss_pred HHHHHh--CCCcHHHHHHhcchhHH---HHHHHHHHHHHHcchhhcccccCCCC-CCccCCCcC----HHHHH
Confidence 334555 899999999999 8999 99999999999999998764210000 235999998 77764
No 189
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=92.17 E-value=0.19 Score=41.90 Aligned_cols=55 Identities=15% Similarity=0.295 Sum_probs=49.3
Q ss_pred HHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 29 KSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 29 ~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
..++|...++..|..+|+.. +|+.+.|||+++|++. ..+..-+..|...|+++..
T Consensus 16 v~kalaS~vRv~Il~lL~~k-~plNvneiAe~lgLpq---st~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 16 VLKALASKVRVAILQLLHRK-GPLNVNEIAEALGLPQ---STMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHHHHHHh-CCCCHHHHHHHhCCch---hhhhhhHHHHHhcCceeee
Confidence 35678888999999999997 8999999999999998 8888899999999999754
No 190
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=92.16 E-value=0.29 Score=34.92 Aligned_cols=44 Identities=14% Similarity=-0.007 Sum_probs=38.6
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLP 102 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t 102 (214)
.++|..|||+.+|+++ ..+.|.|..|...|++..... .+.|..|
T Consensus 46 ~~is~~eLa~~~g~sr---~tVsr~L~~Le~~GlI~r~~~------~~~~~~n 89 (95)
T TIGR01610 46 DRVTATVIAELTGLSR---THVSDAIKSLARRRIIFRQGM------MGIVGVN 89 (95)
T ss_pred CccCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeeeecC------CceeecC
Confidence 7899999999999999 999999999999999997642 3667666
No 191
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=92.03 E-value=0.18 Score=35.79 Aligned_cols=63 Identities=8% Similarity=0.057 Sum_probs=47.6
Q ss_pred HHHhcCcchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHH----------HHHHhCCce-eeecCCCCCCccceeeCC
Q 040620 35 RAIQLRIPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILV----------CLLAHSGFF-VQQKDGKNEQEEESILLP 102 (214)
Q Consensus 35 ~a~~lglfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlL----------r~L~~~g~l-~~~~~~~~~~~~~~y~~t 102 (214)
.-++..|+..|.+. +.+.++.|||..+++++ ..+.--| +.|+.+|++ .+... ++ ...|++|
T Consensus 8 S~~R~~vl~~L~~~yp~~~~~~eIar~v~~~~---snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~--~g--~k~Y~lT 80 (90)
T PF07381_consen 8 SKVRKKVLEYLCSIYPEPAYPSEIARSVGSDY---SNVLGALRGDGKRYNKEDSLVGLGLVEEEEEK--GG--FKYYRLT 80 (90)
T ss_pred HHHHHHHHHHHHHcCCCcCCHHHHHHHHCCCH---HHHHHHHhcCCCCcCcchhHHHcCCeeEeeec--CC--eeEEEeC
Confidence 44566677788776 68899999999999999 7776666 459999999 33321 12 4579999
Q ss_pred CC
Q 040620 103 PH 104 (214)
Q Consensus 103 ~~ 104 (214)
+.
T Consensus 81 ~~ 82 (90)
T PF07381_consen 81 EK 82 (90)
T ss_pred hh
Confidence 88
No 192
>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=92.02 E-value=0.19 Score=44.72 Aligned_cols=31 Identities=19% Similarity=0.125 Sum_probs=25.6
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...+|+|+|||+|.+++.++.. ..+++.+|.
T Consensus 233 ~~~~vLDL~cG~G~~~l~la~~--~~~v~~vE~ 263 (374)
T TIGR02085 233 PVTQMWDLFCGVGGFGLHCAGP--DTQLTGIEI 263 (374)
T ss_pred CCCEEEEccCCccHHHHHHhhc--CCeEEEEEC
Confidence 3478999999999999999964 467888775
No 193
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=91.92 E-value=0.15 Score=40.05 Aligned_cols=47 Identities=15% Similarity=0.178 Sum_probs=42.8
Q ss_pred HHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620 36 AIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ 86 (214)
Q Consensus 36 a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~ 86 (214)
.++..|..+|..+ +.+|..+||+++|+++ ..+++=++-|...|++..
T Consensus 14 ~~D~~IL~~Lq~d-~R~s~~eiA~~lglS~---~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 14 RIDRNILNELQKD-GRISNVELSKRVGLSP---TPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHhccC-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEE
Confidence 3677889999987 8999999999999999 999999999999999973
No 194
>KOG1271 consensus Methyltransferases [General function prediction only]
Probab=91.91 E-value=0.23 Score=40.13 Aligned_cols=22 Identities=18% Similarity=0.297 Sum_probs=19.3
Q ss_pred CCcEEeecCCchHHHHHHHHHC
Q 040620 181 LKPLVDVGGSTGTMARAIATAF 202 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~ 202 (214)
..+|||+|||.|+++..|++.-
T Consensus 68 A~~VlDLGtGNG~~L~~L~~eg 89 (227)
T KOG1271|consen 68 ADRVLDLGTGNGHLLFQLAKEG 89 (227)
T ss_pred ccceeeccCCchHHHHHHHHhc
Confidence 3499999999999999999863
No 195
>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=91.85 E-value=0.15 Score=34.43 Aligned_cols=36 Identities=25% Similarity=0.355 Sum_probs=33.9
Q ss_pred CCCCHHHHHHHc---CC--CCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVAL---NV--HPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~---g~--~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+.+++.++|+.+ ++ .. |+++.++..|.+.|++.+..
T Consensus 23 ~~i~l~~ia~~l~~~~~k~~~---RRlYDI~NVLealgli~K~~ 63 (71)
T PF02319_consen 23 KSISLNEIADKLISENVKTQR---RRLYDIINVLEALGLIEKQS 63 (71)
T ss_dssp TEEEHHHHHHHCHHHCCHHHC---HHHHHHHHHHHHCTSEEEEE
T ss_pred CcccHHHHHHHHccccccccc---chhhHHHHHHHHhCceeecC
Confidence 789999999999 98 88 99999999999999999965
No 196
>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=91.85 E-value=0.32 Score=37.58 Aligned_cols=36 Identities=11% Similarity=0.194 Sum_probs=34.5
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|++|.+|||-+.|++. |.+.--|..+.+.|-+....
T Consensus 5 Ga~T~eELA~~FGvtt---RkvaStLa~~ta~Grl~Rv~ 40 (155)
T PF07789_consen 5 GAKTAEELAGKFGVTT---RKVASTLAMVTATGRLIRVN 40 (155)
T ss_pred CcccHHHHHHHhCcch---hhhHHHHHHHHhcceeEEec
Confidence 8999999999999999 99999999999999999875
No 197
>PRK03612 spermidine synthase; Provisional
Probab=91.82 E-value=0.2 Score=46.71 Aligned_cols=33 Identities=21% Similarity=0.463 Sum_probs=28.5
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl 212 (214)
++.++|+|||||.|..+..+++ +|. .+++++|+
T Consensus 296 ~~~~rVL~IG~G~G~~~~~ll~-~~~v~~v~~VEi 329 (521)
T PRK03612 296 ARPRRVLVLGGGDGLALREVLK-YPDVEQVTLVDL 329 (521)
T ss_pred CCCCeEEEEcCCccHHHHHHHh-CCCcCeEEEEEC
Confidence 3568999999999999999996 576 78999886
No 198
>PRK10909 rsmD 16S rRNA m(2)G966-methyltransferase; Provisional
Probab=91.76 E-value=0.31 Score=39.68 Aligned_cols=32 Identities=9% Similarity=0.123 Sum_probs=25.1
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...+++|+|||+|.+++..+.+.. .+++.+|.
T Consensus 53 ~~~~vLDl~~GsG~l~l~~lsr~a-~~V~~vE~ 84 (199)
T PRK10909 53 VDARCLDCFAGSGALGLEALSRYA-AGATLLEM 84 (199)
T ss_pred CCCEEEEcCCCccHHHHHHHHcCC-CEEEEEEC
Confidence 346999999999999997666654 57777764
No 199
>PF02527 GidB: rRNA small subunit methyltransferase G; InterPro: IPR003682 This entry represents a rRNA small subunit methyltransferase G. Previously identified as a glucose-inhibited division protein B that appears to be present and in a single copy in all complete eubacterial genomes so far sequenced. Specifically methylates the N7 position of a guanosine in 16S rRNA [, , ].; GO: 0008649 rRNA methyltransferase activity, 0006364 rRNA processing, 0005737 cytoplasm; PDB: 1XDZ_A 3G88_A 3G8A_B 3G89_B 3G8B_B 1JSX_A.
Probab=91.73 E-value=0.35 Score=38.92 Aligned_cols=30 Identities=27% Similarity=0.445 Sum_probs=27.2
Q ss_pred cEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 183 PLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 183 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+++|||.|-|.=++.++=.+|+++++.+|-
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 799999999999999999999999999873
No 200
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=91.54 E-value=0.18 Score=41.38 Aligned_cols=42 Identities=14% Similarity=0.272 Sum_probs=35.7
Q ss_pred hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
+.|...+.+.|.+|+|+++|++. ...+|.|.+|++.|++...
T Consensus 165 ~~~~~~~~~~Taeela~~~giSR---vTaRRYLeyl~~~~~l~a~ 206 (224)
T COG4565 165 EALKEPDQELTAEELAQALGISR---VTARRYLEYLVSNGILEAE 206 (224)
T ss_pred HHHhCcCCccCHHHHHHHhCccH---HHHHHHHHHHHhcCeeeEE
Confidence 44442238999999999999998 8999999999999999854
No 201
>PRK10870 transcriptional repressor MprA; Provisional
Probab=91.53 E-value=0.43 Score=37.94 Aligned_cols=65 Identities=9% Similarity=0.124 Sum_probs=47.4
Q ss_pred cchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 41 IPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 41 lfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
++-.|... ++++|..+||+.+++++ ..+.+++.-|...|++......+|.- .-.+.+|+. ++.++
T Consensus 60 iL~~L~~~~~~~it~~eLa~~l~l~~---~tvsr~v~rLe~kGlV~R~~~~~DrR-~~~v~LT~~----G~~~~ 125 (176)
T PRK10870 60 ALITLESQENHSIQPSELSCALGSSR---TNATRIADELEKRGWIERRESDNDRR-CLHLQLTEK----GHEFL 125 (176)
T ss_pred HHHHHhcCCCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecCCCCCCC-eeEEEECHH----HHHHH
Confidence 44455432 26799999999999999 99999999999999999875321111 134667777 66654
No 202
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=91.50 E-value=0.17 Score=39.24 Aligned_cols=46 Identities=11% Similarity=0.227 Sum_probs=42.0
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ 86 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~ 86 (214)
++..|.++|..+ +..|..+||+++|+++ ..+++=++-|...|++..
T Consensus 10 ~D~~Il~~Lq~d-~R~s~~eiA~~lglS~---~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 10 LDRGILEALMEN-ARTPYAELAKQFGVSP---GTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeee
Confidence 566788899987 8999999999999999 999999999999999974
No 203
>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=91.31 E-value=0.13 Score=33.88 Aligned_cols=43 Identities=12% Similarity=0.254 Sum_probs=34.7
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
|++.|-.. |+.|..+|++.+++++ +.++.-|-.|...+++.+.
T Consensus 18 V~~~Ll~~-G~ltl~~i~~~t~l~~---~~Vk~~L~~LiQh~~v~y~ 60 (62)
T PF08221_consen 18 VGEVLLSR-GRLTLREIVRRTGLSP---KQVKKALVVLIQHNLVQYF 60 (62)
T ss_dssp HHHHHHHC--SEEHHHHHHHHT--H---HHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHc-CCcCHHHHHHHhCCCH---HHHHHHHHHHHHcCCeeee
Confidence 44555555 8999999999999999 9999999999999999875
No 204
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=91.17 E-value=0.62 Score=37.01 Aligned_cols=61 Identities=8% Similarity=0.076 Sum_probs=49.1
Q ss_pred HHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHc--CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620 26 NYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL--NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP 103 (214)
Q Consensus 26 g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~--g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~ 103 (214)
.-|...+++..+.+ .+ +.-++++||+++ +++. ..++.-|..|...|++..++ ++.|..|.
T Consensus 22 ~~W~~~~ir~l~~l-----~~---~~~d~~~iak~l~p~is~---~ev~~sL~~L~~~gli~k~~-------~g~y~~t~ 83 (171)
T PF14394_consen 22 SSWYHPAIRELLPL-----MP---FAPDPEWIAKRLRPKISA---EEVRDSLEFLEKLGLIKKDG-------DGKYVQTD 83 (171)
T ss_pred hhhHHHHHHHHhhc-----CC---CCCCHHHHHHHhcCCCCH---HHHHHHHHHHHHCCCeEECC-------CCcEEEec
Confidence 45666666665432 22 334999999999 9999 99999999999999999997 67999998
Q ss_pred C
Q 040620 104 H 104 (214)
Q Consensus 104 ~ 104 (214)
.
T Consensus 84 ~ 84 (171)
T PF14394_consen 84 K 84 (171)
T ss_pred c
Confidence 7
No 205
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=91.14 E-value=0.29 Score=44.21 Aligned_cols=46 Identities=17% Similarity=0.232 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+.|.|.++|++++++++ +.++++++.|...|++.+.+ ++.|.+..-
T Consensus 308 g~~~t~~~La~~l~~~~---~~v~~iL~~L~~agLI~~~~-------~g~~~l~rd 353 (412)
T PRK04214 308 GKALDVDEIRRLEPMGY---DELGELLCELARIGLLRRGE-------RGQWVLARD 353 (412)
T ss_pred CCCCCHHHHHHHhCCCH---HHHHHHHHHHHhCCCeEecC-------CCceEecCC
Confidence 48999999999999999 99999999999999999764 466776655
No 206
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=91.10 E-value=0.2 Score=38.43 Aligned_cols=48 Identities=13% Similarity=0.202 Sum_probs=42.7
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
++..|...|..+ ++.|..+||+++|+++ ..+.+-++-|...|++..-.
T Consensus 9 ~D~~IL~~L~~d-~r~~~~eia~~lglS~---~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 9 IDRRILRLLQED-ARISNAELAERVGLSP---STVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred HHHHHHHHHHHh-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCceeeEE
Confidence 456678888887 8899999999999999 99999999999999998653
No 207
>COG0357 GidB Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]
Probab=91.08 E-value=0.21 Score=41.25 Aligned_cols=32 Identities=34% Similarity=0.579 Sum_probs=29.9
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+++|||.|.|.=++-++=.+|+++++++|-
T Consensus 68 ~~~~~DIGSGaGfPGipLAI~~p~~~vtLles 99 (215)
T COG0357 68 AKRVLDIGSGAGFPGIPLAIAFPDLKVTLLES 99 (215)
T ss_pred CCEEEEeCCCCCCchhhHHHhccCCcEEEEcc
Confidence 58999999999999999999999999999883
No 208
>PLN02781 Probable caffeoyl-CoA O-methyltransferase
Probab=91.03 E-value=0.32 Score=40.46 Aligned_cols=36 Identities=25% Similarity=0.265 Sum_probs=30.3
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH 213 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp 213 (214)
..+.+++||||+|.|..++.+++..| +.+++.+|..
T Consensus 66 ~~~~~~vLEiGt~~G~s~l~la~~~~~~g~v~tiD~d 102 (234)
T PLN02781 66 IMNAKNTLEIGVFTGYSLLTTALALPEDGRITAIDID 102 (234)
T ss_pred HhCCCEEEEecCcccHHHHHHHHhCCCCCEEEEEECC
Confidence 34578999999999999999999866 6788888864
No 209
>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=90.95 E-value=0.34 Score=43.89 Aligned_cols=33 Identities=18% Similarity=0.170 Sum_probs=26.8
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+..+|+|+|||+|.++..+++.. .+++.+|.
T Consensus 290 ~~~~~~vLDl~cG~G~~sl~la~~~--~~V~~vE~ 322 (431)
T TIGR00479 290 LQGEELVVDAYCGVGTFTLPLAKQA--KSVVGIEV 322 (431)
T ss_pred cCCCCEEEEcCCCcCHHHHHHHHhC--CEEEEEEc
Confidence 3455799999999999999999875 36777775
No 210
>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=90.94 E-value=0.32 Score=41.03 Aligned_cols=43 Identities=12% Similarity=0.273 Sum_probs=33.1
Q ss_pred hHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 166 IASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 166 ~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.+..+++..+ .....+|+|||+|.|.++..|++.. -+++++|.
T Consensus 18 ~~~~Iv~~~~--~~~~~~VlEiGpG~G~lT~~L~~~~--~~v~~vE~ 60 (262)
T PF00398_consen 18 IADKIVDALD--LSEGDTVLEIGPGPGALTRELLKRG--KRVIAVEI 60 (262)
T ss_dssp HHHHHHHHHT--CGTTSEEEEESSTTSCCHHHHHHHS--SEEEEEES
T ss_pred HHHHHHHhcC--CCCCCEEEEeCCCCccchhhHhccc--CcceeecC
Confidence 3455666665 5577899999999999999999997 55665553
No 211
>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=90.86 E-value=0.48 Score=40.39 Aligned_cols=33 Identities=24% Similarity=0.360 Sum_probs=28.1
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCe-EEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTK-CTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dl 212 (214)
.+++|||+|+|+|..+-+..+.+|++. ++++|.
T Consensus 33 ~P~~vLD~GsGpGta~wAa~~~~~~~~~~~~vd~ 66 (274)
T PF09243_consen 33 RPRSVLDFGSGPGTALWAAREVWPSLKEYTCVDR 66 (274)
T ss_pred CCceEEEecCChHHHHHHHHHHhcCceeeeeecC
Confidence 367999999999999999999999664 777774
No 212
>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=90.78 E-value=0.32 Score=39.09 Aligned_cols=32 Identities=13% Similarity=-0.008 Sum_probs=26.9
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
...+++|++||+|.++++++++... +++.+|.
T Consensus 49 ~g~~vLDLfaGsG~lglea~srga~-~v~~vE~ 80 (189)
T TIGR00095 49 QGAHLLDVFAGSGLLGEEALSRGAK-VAFLEED 80 (189)
T ss_pred CCCEEEEecCCCcHHHHHHHhCCCC-EEEEEeC
Confidence 3578999999999999999999764 6777775
No 213
>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=90.17 E-value=0.39 Score=32.12 Aligned_cols=36 Identities=19% Similarity=0.266 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
-++|-++||+.+|+++ ..+.++|+.|...|++....
T Consensus 27 ~~lt~~~iA~~~g~sr---~tv~r~l~~l~~~g~I~~~~ 62 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSR---ETVSRILKRLKDEGIIEVKR 62 (76)
T ss_dssp EESSHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEET
T ss_pred ecCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEcC
Confidence 5799999999999999 99999999999999999774
No 214
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=90.04 E-value=0.16 Score=36.47 Aligned_cols=47 Identities=15% Similarity=0.237 Sum_probs=36.6
Q ss_pred hcCcchhhhc---CCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 38 QLRIPDIINN---SGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 38 ~lglfd~L~~---~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
+-.|++.|.. ...++++++|+++++++. ..++..|+.|...|++=..
T Consensus 49 ~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~---~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 49 QDKVLNFIKQQPNSEEGVHVDEIAQQLGMSE---NEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp HHHHHHHHHC----TTTEEHHHHHHHSTS-H---HHHHHHHHHHHHTTSEEES
T ss_pred HHHHHHHHHhcCCCCCcccHHHHHHHhCcCH---HHHHHHHHHHHhCCeEecc
Confidence 3445555555 127899999999999998 9999999999999987543
No 215
>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=89.92 E-value=0.53 Score=38.52 Aligned_cols=43 Identities=16% Similarity=0.143 Sum_probs=27.3
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+++.+. ......++|+|+|.|....+.+-.++=-+++++++
T Consensus 32 ~~il~~~~--l~~~dvF~DlGSG~G~~v~~aal~~~~~~~~GIEi 74 (205)
T PF08123_consen 32 SKILDELN--LTPDDVFYDLGSGVGNVVFQAALQTGCKKSVGIEI 74 (205)
T ss_dssp HHHHHHTT----TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE-
T ss_pred HHHHHHhC--CCCCCEEEECCCCCCHHHHHHHHHcCCcEEEEEEe
Confidence 34455554 55678999999999999998887776555777664
No 216
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=89.86 E-value=0.51 Score=39.75 Aligned_cols=47 Identities=15% Similarity=0.043 Sum_probs=41.4
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
|+.|+.|||+.+|++. .++..+|+.|...|++...+. . +..|+.-+-
T Consensus 29 g~~tA~eis~~sgvP~---~kvY~vl~sLe~kG~v~~~~g----~-P~~y~av~p 75 (247)
T COG1378 29 GEATAKEISEASGVPR---PKVYDVLRSLEKKGLVEVIEG----R-PKKYRAVPP 75 (247)
T ss_pred CCccHHHHHHHcCCCc---hhHHHHHHHHHHCCCEEeeCC----C-CceEEeCCH
Confidence 8999999999999999 999999999999999998742 1 577877776
No 217
>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=89.83 E-value=0.75 Score=37.70 Aligned_cols=41 Identities=15% Similarity=0.192 Sum_probs=27.6
Q ss_pred HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEec
Q 040620 169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFA 211 (214)
Q Consensus 169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~D 211 (214)
.+++..+ ..+..+|+|||+|+|..+..+++..- .-+++.+|
T Consensus 63 ~~l~~L~--l~pg~~VLeIGtGsGY~aAlla~lvg~~g~Vv~vE 104 (209)
T PF01135_consen 63 RMLEALD--LKPGDRVLEIGTGSGYQAALLAHLVGPVGRVVSVE 104 (209)
T ss_dssp HHHHHTT--C-TT-EEEEES-TTSHHHHHHHHHHSTTEEEEEEE
T ss_pred HHHHHHh--cCCCCEEEEecCCCcHHHHHHHHhcCccceEEEEC
Confidence 3455555 66778999999999999999988743 33455554
No 218
>PTZ00146 fibrillarin; Provisional
Probab=89.79 E-value=0.47 Score=40.96 Aligned_cols=35 Identities=11% Similarity=0.133 Sum_probs=28.1
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl 212 (214)
+....+|||+|||+|.++..+++... .=+++.+|.
T Consensus 130 IkpG~~VLDLGaG~G~~t~~lAdiVG~~G~VyAVD~ 165 (293)
T PTZ00146 130 IKPGSKVLYLGAASGTTVSHVSDLVGPEGVVYAVEF 165 (293)
T ss_pred cCCCCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEEC
Confidence 45667999999999999999999874 446777664
No 219
>TIGR01177 conserved hypothetical protein TIGR01177. This family is found exclusively in the Archaea.
Probab=89.74 E-value=0.64 Score=40.57 Aligned_cols=33 Identities=12% Similarity=-0.051 Sum_probs=26.5
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+.+..+|+|+|||+|.++++.+.. ..+++..|+
T Consensus 180 ~~~g~~vLDp~cGtG~~lieaa~~--~~~v~g~Di 212 (329)
T TIGR01177 180 VTEGDRVLDPFCGTGGFLIEAGLM--GAKVIGCDI 212 (329)
T ss_pred CCCcCEEEECCCCCCHHHHHHHHh--CCeEEEEcC
Confidence 445679999999999999886653 677888886
No 220
>PRK14903 16S rRNA methyltransferase B; Provisional
Probab=89.72 E-value=0.52 Score=42.86 Aligned_cols=35 Identities=17% Similarity=0.101 Sum_probs=29.4
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl 212 (214)
..+..+|+|+|||+|..+..+++.. +..+++.+|+
T Consensus 235 ~~~g~~VLD~cagpGgkt~~la~~~~~~g~V~a~Di 270 (431)
T PRK14903 235 LEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDI 270 (431)
T ss_pred CCCCCEEEEeCCCccHHHHHHHHHcCCCCEEEEEEC
Confidence 3456799999999999999999986 5668888886
No 221
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=89.72 E-value=0.41 Score=40.29 Aligned_cols=45 Identities=16% Similarity=0.247 Sum_probs=40.5
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.|.+.|.+. +.+++.|||+.+|+++ ..++|.|+.|...|++...-
T Consensus 9 ~Il~~l~~~-~~~~~~ela~~l~vS~---~TirRdL~~Le~~g~i~r~~ 53 (251)
T PRK13509 9 ILLELLAQL-GFVTVEKVIERLGISP---ATARRDINKLDESGKLKKVR 53 (251)
T ss_pred HHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEec
Confidence 367788876 8999999999999999 99999999999999998765
No 222
>KOG1499 consensus Protein arginine N-methyltransferase PRMT1 and related enzymes [Posttranslational modification, protein turnover, chaperones; Transcription; Signal transduction mechanisms]
Probab=89.62 E-value=0.41 Score=42.12 Aligned_cols=32 Identities=28% Similarity=0.209 Sum_probs=24.5
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEec
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFA 211 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D 211 (214)
-..++|+|||||+|-+++-.+++- .-++..+|
T Consensus 59 f~dK~VlDVGcGtGILS~F~akAG-A~~V~aVe 90 (346)
T KOG1499|consen 59 FKDKTVLDVGCGTGILSMFAAKAG-ARKVYAVE 90 (346)
T ss_pred cCCCEEEEcCCCccHHHHHHHHhC-cceEEEEe
Confidence 357899999999999999988886 33444443
No 223
>COG4976 Predicted methyltransferase (contains TPR repeat) [General function prediction only]
Probab=89.58 E-value=0.44 Score=39.86 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=21.2
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDT 205 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l 205 (214)
..++++|+|||+|..+.+|-..--.+
T Consensus 125 ~F~~~lDLGCGTGL~G~~lR~~a~~l 150 (287)
T COG4976 125 PFRRMLDLGCGTGLTGEALRDMADRL 150 (287)
T ss_pred ccceeeecccCcCcccHhHHHHHhhc
Confidence 37899999999999999887764433
No 224
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=89.42 E-value=0.22 Score=46.09 Aligned_cols=63 Identities=14% Similarity=0.199 Sum_probs=51.7
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
+..|...|... +++|..+||+++++++ ..+.++++.|.+.|++...... ...|.+|+. ++.++
T Consensus 8 e~~vL~~L~~~-~~~s~~eLA~~l~l~~---~tVt~~i~~Le~kGlV~~~~~~-----~~~i~LTee----G~~~~ 70 (489)
T PRK04172 8 EKKVLKALKEL-KEATLEELAEKLGLPP---EAVMRAAEWLEEKGLVKVEERV-----EEVYVLTEE----GKKYA 70 (489)
T ss_pred HHHHHHHHHhC-CCCCHHHHHHHhCcCH---HHHHHHHHHHHhCCCEEEEeee-----EEEEEECHH----HHHHH
Confidence 34455666665 7899999999999999 9999999999999999976421 357999999 88876
No 225
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=89.29 E-value=0.51 Score=38.98 Aligned_cols=58 Identities=10% Similarity=0.163 Sum_probs=46.7
Q ss_pred hhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 44 IINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 44 ~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
.+.+. ..+|..+||+.+++++ ..+.|.|+.|...|++..... .. ...+.+|+. ++.++
T Consensus 15 ~l~~~-~~IS~~eLA~~L~iS~---~Tvsr~Lk~LEe~GlI~R~~~---~r-~~~v~LTek----G~~ll 72 (217)
T PRK14165 15 AVNNT-VKISSSEFANHTGTSS---KTAARILKQLEDEGYITRTIV---PR-GQLITITEK----GLDVL 72 (217)
T ss_pred ccCCC-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEEc---CC-ceEEEECHH----HHHHH
Confidence 45543 5699999999999999 999999999999999987642 01 467888888 77665
No 226
>PLN02823 spermine synthase
Probab=89.25 E-value=0.51 Score=41.57 Aligned_cols=33 Identities=21% Similarity=0.269 Sum_probs=29.2
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+.++||.||||.|..++.+++..|..+++++|+
T Consensus 103 ~pk~VLiiGgG~G~~~re~l~~~~~~~v~~VEi 135 (336)
T PLN02823 103 NPKTVFIMGGGEGSTAREVLRHKTVEKVVMCDI 135 (336)
T ss_pred CCCEEEEECCCchHHHHHHHhCCCCCeEEEEEC
Confidence 568999999999999999998777778998886
No 227
>PRK00215 LexA repressor; Validated
Probab=89.20 E-value=0.48 Score=38.34 Aligned_cols=38 Identities=24% Similarity=0.374 Sum_probs=34.7
Q ss_pred CCCCCCHHHHHHHcCC-CCCCcccHHHHHHHHHhCCceeeec
Q 040620 48 SGQPMTLTQIIVALNV-HPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 48 ~~~p~t~~eLA~~~g~-~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
++.+.|..|||+++|+ ++ ..+.++|..|...|++....
T Consensus 20 ~~~~~s~~ela~~~~~~~~---~tv~~~l~~L~~~g~i~~~~ 58 (205)
T PRK00215 20 TGYPPSRREIADALGLRSP---SAVHEHLKALERKGFIRRDP 58 (205)
T ss_pred hCCCCCHHHHHHHhCCCCh---HHHHHHHHHHHHCCCEEeCC
Confidence 3468899999999999 88 89999999999999998875
No 228
>PF13730 HTH_36: Helix-turn-helix domain
Probab=89.20 E-value=0.38 Score=30.24 Aligned_cols=29 Identities=21% Similarity=0.248 Sum_probs=27.6
Q ss_pred CHHHHHHHcCCCCCCcccHHHHHHHHHhCCce
Q 040620 53 TLTQIIVALNVHPNKTRCTQILVCLLAHSGFF 84 (214)
Q Consensus 53 t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l 84 (214)
|.+.||+.+|+++ +.+++.+..|...|++
T Consensus 27 S~~~la~~~g~s~---~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSR---RTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCH---HHHHHHHHHHHHCcCC
Confidence 8999999999999 9999999999999985
No 229
>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=89.14 E-value=0.36 Score=32.88 Aligned_cols=49 Identities=24% Similarity=0.298 Sum_probs=41.2
Q ss_pred HhcCcchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 37 IQLRIPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 37 ~~lglfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
++..+++.++.+ ..+++..+|++.+|.|+ +.+...+..|...|++....
T Consensus 3 ~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~---r~i~~~~k~L~~~gLI~k~~ 52 (75)
T PF04182_consen 3 IQYCLLERIARSRYNGITQSDLSKLLGIDP---RSIFYRLKKLEKKGLIVKQS 52 (75)
T ss_pred hHHHHHHHHHhcCCCCEehhHHHHHhCCCc---hHHHHHHHHHHHCCCEEEEE
Confidence 344556666654 27899999999999999 99999999999999999875
No 230
>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=89.10 E-value=0.2 Score=30.28 Aligned_cols=36 Identities=6% Similarity=0.152 Sum_probs=25.3
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
++..|...|..+ +..|..+||+++|+++ ..+.+=++
T Consensus 4 ~D~~Il~~Lq~d-~r~s~~~la~~lglS~---~~v~~Ri~ 39 (42)
T PF13404_consen 4 LDRKILRLLQED-GRRSYAELAEELGLSE---STVRRRIR 39 (42)
T ss_dssp HHHHHHHHHHH--TTS-HHHHHHHHTS-H---HHHHHHHH
T ss_pred HHHHHHHHHHHc-CCccHHHHHHHHCcCH---HHHHHHHH
Confidence 445677888887 8999999999999998 65554433
No 231
>KOG1541 consensus Predicted protein carboxyl methylase [General function prediction only]
Probab=89.06 E-value=0.21 Score=41.45 Aligned_cols=31 Identities=10% Similarity=0.182 Sum_probs=23.7
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
....|||||||+|..+..|... ....+++|+
T Consensus 50 ~~~~iLDIGCGsGLSg~vL~~~--Gh~wiGvDi 80 (270)
T KOG1541|consen 50 KSGLILDIGCGSGLSGSVLSDS--GHQWIGVDI 80 (270)
T ss_pred CCcEEEEeccCCCcchheeccC--CceEEeecC
Confidence 3789999999999988776654 455666665
No 232
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=89.04 E-value=0.6 Score=42.43 Aligned_cols=35 Identities=11% Similarity=0.072 Sum_probs=29.0
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl 212 (214)
..+..+|+|+|||+|..+..+++..+ .-+++.+|+
T Consensus 250 ~~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~ 285 (434)
T PRK14901 250 PQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDR 285 (434)
T ss_pred CCCcCEEEEeCCCCchhHHHHHHHhCCCceEEEEcC
Confidence 34467999999999999999999864 457888886
No 233
>PRK00536 speE spermidine synthase; Provisional
Probab=89.01 E-value=0.44 Score=40.49 Aligned_cols=32 Identities=19% Similarity=0.170 Sum_probs=28.0
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+++++||=||||.|..++++++. |. +++..|+
T Consensus 71 ~~pk~VLIiGGGDGg~~REvLkh-~~-~v~mVeI 102 (262)
T PRK00536 71 KELKEVLIVDGFDLELAHQLFKY-DT-HVDFVQA 102 (262)
T ss_pred CCCCeEEEEcCCchHHHHHHHCc-CC-eeEEEEC
Confidence 46799999999999999999987 55 8888876
No 234
>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=88.96 E-value=0.52 Score=37.96 Aligned_cols=37 Identities=19% Similarity=0.405 Sum_probs=33.9
Q ss_pred CCCCCHHHHHHHcCCC-CCCcccHHHHHHHHHhCCceeeec
Q 040620 49 GQPMTLTQIIVALNVH-PNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 49 ~~p~t~~eLA~~~g~~-~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+-|.|..|||+.+|++ + ..+++.|+.|...|++...+
T Consensus 23 ~~~~~~~ela~~~~~~s~---~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 23 GYPPSIREIARAVGLRSP---SAAEEHLKALERKGYIERDP 60 (199)
T ss_pred CCCCcHHHHHHHhCCCCh---HHHHHHHHHHHHCCCEecCC
Confidence 3578999999999998 8 89999999999999999874
No 235
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=88.91 E-value=0.76 Score=31.68 Aligned_cols=35 Identities=20% Similarity=0.260 Sum_probs=33.0
Q ss_pred CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620 49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ 86 (214)
Q Consensus 49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~ 86 (214)
+.|+...+||+.++++| -.++..+..|..+|++..
T Consensus 21 ~~PVgSk~ia~~l~~s~---aTIRN~M~~Le~lGlve~ 55 (78)
T PF03444_consen 21 GEPVGSKTIAEELGRSP---ATIRNEMADLEELGLVES 55 (78)
T ss_pred CCCcCHHHHHHHHCCCh---HHHHHHHHHHHHCCCccC
Confidence 48999999999999999 999999999999999984
No 236
>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=88.87 E-value=0.48 Score=39.70 Aligned_cols=46 Identities=9% Similarity=0.112 Sum_probs=41.1
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.|++.|..+++-++..+||+++|+++ ..+++-++.|.+.|++...+
T Consensus 187 ~IL~~L~~~egrlse~eLAerlGVSR---s~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 187 HIFEELDGNEGLLVASKIADRVGITR---SVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHHHhccccccccHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecc
Confidence 57888887438899999999999999 99999999999999999774
No 237
>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=88.79 E-value=0.71 Score=40.84 Aligned_cols=29 Identities=17% Similarity=0.261 Sum_probs=24.6
Q ss_pred CcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 182 KPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 182 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.+++|++||+|.+++.+++... +++.+|.
T Consensus 199 ~~vlDl~~G~G~~sl~la~~~~--~v~~vE~ 227 (353)
T TIGR02143 199 GDLLELYCGNGNFSLALAQNFR--RVLATEI 227 (353)
T ss_pred CcEEEEeccccHHHHHHHHhCC--EEEEEEC
Confidence 4699999999999999999874 6777764
No 238
>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=88.65 E-value=0.54 Score=30.70 Aligned_cols=36 Identities=8% Similarity=0.123 Sum_probs=31.5
Q ss_pred CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
..+ |..+||++.+++. .-+++-++.|...|++...+
T Consensus 22 ~~lps~~~la~~~~vsr---~tvr~al~~L~~~g~i~~~~ 58 (64)
T PF00392_consen 22 DRLPSERELAERYGVSR---TTVREALRRLEAEGLIERRP 58 (64)
T ss_dssp SBE--HHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEET
T ss_pred CEeCCHHHHHHHhccCC---cHHHHHHHHHHHCCcEEEEC
Confidence 567 9999999999999 99999999999999999875
No 239
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=88.49 E-value=0.47 Score=39.67 Aligned_cols=90 Identities=8% Similarity=0.028 Sum_probs=62.0
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc---ccc
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL---QLQ 116 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~---~~~ 116 (214)
.|...|...-+-....|||+++|+.+ +.+...+.-|+..|++.+.+ .++|..|.. +..++ -..
T Consensus 14 qIL~ei~~~qp~v~q~eIA~~lgiT~---QaVsehiK~Lv~eG~i~~~g-------R~~Y~iTkk----G~e~l~~~~~d 79 (260)
T COG1497 14 QILSEIAVRQPRVKQKEIAKKLGITL---QAVSEHIKELVKEGLIEKEG-------RGEYEITKK----GAEWLLEQLSD 79 (260)
T ss_pred HHHHHHHHhCCCCCHHHHHHHcCCCH---HHHHHHHHHHHhccceeecC-------CeeEEEehh----HHHHHHHHHHH
Confidence 34444443325589999999999999 99999999999999999976 579999999 87766 134
Q ss_pred hHHHHHHhhc-cchhhhhHhHH-HhhcCC
Q 040620 117 GSTILLLIAD-ATFTTSFHFLS-TWLQND 143 (214)
Q Consensus 117 ~~~~~~~~~~-~~~~~~~~~l~-~~lr~~ 143 (214)
++.|...... ..+...|..+. +-++.|
T Consensus 80 lr~f~~ev~~~l~~~~vw~AIA~edI~~G 108 (260)
T COG1497 80 LRRFSEEVELVLDYVMVWTAIAKEDIKEG 108 (260)
T ss_pred HHHHHHHHHHHHhhHHHHHHhhHhhhccC
Confidence 4444433311 12335566654 334544
No 240
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=88.43 E-value=0.86 Score=38.53 Aligned_cols=34 Identities=9% Similarity=0.145 Sum_probs=28.1
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl 212 (214)
....+|+|+|||+|..+..+++..++ -+++.+|+
T Consensus 70 ~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~ 104 (264)
T TIGR00446 70 DPPERVLDMAAAPGGKTTQISALMKNEGAIVANEF 104 (264)
T ss_pred CCcCEEEEECCCchHHHHHHHHHcCCCCEEEEEcC
Confidence 34678999999999999999998764 46787775
No 241
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=88.39 E-value=1.1 Score=38.13 Aligned_cols=43 Identities=9% Similarity=0.200 Sum_probs=32.8
Q ss_pred HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEec
Q 040620 167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFA 211 (214)
Q Consensus 167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D 211 (214)
.+.+++..+ ......|++||+|.|.+...|+++-....++=.|
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 455666655 4457899999999999999999997775555444
No 242
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=88.38 E-value=0.44 Score=34.34 Aligned_cols=69 Identities=14% Similarity=0.189 Sum_probs=49.7
Q ss_pred HHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 36 AIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 36 a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
..+..+...|... ++.+..+||+++++++ ..+.++++-|...|++.......|.= .-.+.+|+. ++.+.
T Consensus 22 ~~q~~~L~~l~~~-~~~~~~~la~~l~i~~---~~vt~~l~~Le~~glv~r~~~~~DrR-~~~l~lT~~----G~~~~ 90 (126)
T COG1846 22 PPQYQVLLALYEA-GGITVKELAERLGLDR---STVTRLLKRLEDKGLIERLRDPEDRR-AVLVRLTEK----GRELL 90 (126)
T ss_pred HHHHHHHHHHHHh-CCCcHHHHHHHHCCCH---HHHHHHHHHHHHCCCeeecCCccccc-eeeEEECcc----HHHHH
Confidence 3445566666665 4555599999999999 99999999999999999876321110 235777777 66654
No 243
>COG0421 SpeE Spermidine synthase [Amino acid transport and metabolism]
Probab=88.14 E-value=0.64 Score=39.95 Aligned_cols=34 Identities=21% Similarity=0.366 Sum_probs=30.7
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
++.++||=||||.|..++.+++..|--++++.|+
T Consensus 75 ~~pk~VLiiGgGdG~tlRevlkh~~ve~i~~VEI 108 (282)
T COG0421 75 PNPKRVLIIGGGDGGTLREVLKHLPVERITMVEI 108 (282)
T ss_pred CCCCeEEEECCCccHHHHHHHhcCCcceEEEEEc
Confidence 3457999999999999999999999889999886
No 244
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=88.08 E-value=0.4 Score=40.37 Aligned_cols=45 Identities=11% Similarity=0.217 Sum_probs=40.3
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.|.++|.+. +.+++.|||+.+++++ .-++|-|..|...|++...-
T Consensus 9 ~Il~~l~~~-~~~~~~ela~~l~vS~---~TiRRdL~~Le~~g~l~r~~ 53 (252)
T PRK10906 9 AIIELVKQQ-GYVSTEELVEHFSVSP---QTIRRDLNDLAEQNKILRHH 53 (252)
T ss_pred HHHHHHHHc-CCEeHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEec
Confidence 466788776 8899999999999999 99999999999999998764
No 245
>KOG3010 consensus Methyltransferase [General function prediction only]
Probab=87.99 E-value=0.38 Score=40.36 Aligned_cols=27 Identities=33% Similarity=0.534 Sum_probs=22.2
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDT 205 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l 205 (214)
.+.+.++|||||+|..++.+++.|.+.
T Consensus 32 ~~h~~a~DvG~G~Gqa~~~iae~~k~V 58 (261)
T KOG3010|consen 32 EGHRLAWDVGTGNGQAARGIAEHYKEV 58 (261)
T ss_pred CCcceEEEeccCCCcchHHHHHhhhhh
Confidence 355699999999998888888887654
No 246
>PHA02943 hypothetical protein; Provisional
Probab=87.80 E-value=0.73 Score=35.87 Aligned_cols=44 Identities=16% Similarity=0.214 Sum_probs=38.4
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.|.+.|.. |+.|..|||+++|++- ..++-.|..|...|.+.+..
T Consensus 15 eILE~Lk~--G~~TtseIAkaLGlS~---~qa~~~LyvLErEG~VkrV~ 58 (165)
T PHA02943 15 KTLRLLAD--GCKTTSRIANKLGVSH---SMARNALYQLAKEGMVLKVE 58 (165)
T ss_pred HHHHHHhc--CCccHHHHHHHHCCCH---HHHHHHHHHHHHcCceEEEe
Confidence 35566643 8899999999999998 89999999999999999875
No 247
>KOG3420 consensus Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=87.74 E-value=0.39 Score=37.39 Aligned_cols=32 Identities=28% Similarity=0.404 Sum_probs=25.8
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCe-EEEecCC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTK-CTVFACH 213 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dlp 213 (214)
..+++.|+|||.|-++ ++-.+|..+ +++||+-
T Consensus 48 Egkkl~DLgcgcGmLs--~a~sm~~~e~vlGfDId 80 (185)
T KOG3420|consen 48 EGKKLKDLGCGCGMLS--IAFSMPKNESVLGFDID 80 (185)
T ss_pred cCcchhhhcCchhhhH--HHhhcCCCceEEeeecC
Confidence 3689999999999998 555667775 8888873
No 248
>PRK14904 16S rRNA methyltransferase B; Provisional
Probab=87.60 E-value=0.87 Score=41.51 Aligned_cols=34 Identities=12% Similarity=0.124 Sum_probs=27.8
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl 212 (214)
....+|+|+|||+|..+..+++..+ ..+++.+|+
T Consensus 249 ~~g~~VLDlgaG~G~kt~~la~~~~~~~~V~avD~ 283 (445)
T PRK14904 249 QPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDR 283 (445)
T ss_pred CCCCEEEEECCCCCHHHHHHHHHhCCCcEEEEEEC
Confidence 3457999999999999999988764 457888886
No 249
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=87.58 E-value=0.46 Score=40.43 Aligned_cols=45 Identities=11% Similarity=0.163 Sum_probs=40.1
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.|.++|... +.+++.|||+.+++++ +-++|-|..|...|++...-
T Consensus 21 ~Il~~L~~~-~~vtv~eLa~~l~VS~---~TIRRDL~~Le~~G~l~r~~ 65 (269)
T PRK09802 21 QIIQRLRQQ-GSVQVNDLSALYGVST---VTIRNDLAFLEKQGIAVRAY 65 (269)
T ss_pred HHHHHHHHc-CCEeHHHHHHHHCCCH---HHHHHHHHHHHhCCCeEEEe
Confidence 356777776 7899999999999999 99999999999999999875
No 250
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=87.40 E-value=0.62 Score=40.45 Aligned_cols=56 Identities=11% Similarity=0.062 Sum_probs=44.2
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
..|.+.|.++ .+++.++||+++|+++ ..+++.++.|...|++.+... ...|.+.+.
T Consensus 7 ~~il~~L~~~-~~~s~~~LA~~lgvsr---~tV~~~l~~L~~~G~~i~~~~------~~Gy~L~~~ 62 (319)
T PRK11886 7 LQLLSLLADG-DFHSGEQLGEELGISR---AAIWKHIQTLEEWGLDIFSVK------GKGYRLAEP 62 (319)
T ss_pred HHHHHHHHcC-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCceEEec------CCeEEecCc
Confidence 3466677764 7899999999999999 999999999999999554431 346776555
No 251
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=87.35 E-value=0.59 Score=39.41 Aligned_cols=54 Identities=9% Similarity=0.217 Sum_probs=45.7
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
.|.++|.++ |-++++|||+.+++++ .-+||=|+.|...|++...- ++....+..
T Consensus 9 ~Il~~l~~~-g~v~v~eLa~~~~VS~---~TIRRDL~~Le~~g~l~R~h-------GGa~~~~~~ 62 (253)
T COG1349 9 KILELLKEK-GKVSVEELAELFGVSE---MTIRRDLNELEEQGLLLRVH-------GGAVLPDSE 62 (253)
T ss_pred HHHHHHHHc-CcEEHHHHHHHhCCCH---HHHHHhHHHHHHCCcEEEEe-------CCEecCCCc
Confidence 367888887 8999999999999999 99999999999999999965 455554444
No 252
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=87.29 E-value=0.23 Score=30.29 Aligned_cols=23 Identities=13% Similarity=0.154 Sum_probs=17.1
Q ss_pred CCCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 51 PMTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 51 p~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
++|+.+||+.+|++. ..+.|+|+
T Consensus 21 G~si~~IA~~~gvsr---~TvyR~l~ 43 (45)
T PF02796_consen 21 GMSIAEIAKQFGVSR---STVYRYLN 43 (45)
T ss_dssp T--HHHHHHHTTS-H---HHHHHHHC
T ss_pred CCCHHHHHHHHCcCH---HHHHHHHh
Confidence 399999999999998 88888763
No 253
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=87.11 E-value=0.62 Score=37.95 Aligned_cols=45 Identities=11% Similarity=0.202 Sum_probs=37.7
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
.|+.++.+...+.|.+|||+++++++ +-+++.+..|+..|++...
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~---~Tv~~~~~~~~~~~~~~~~ 210 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISR---TTARRYLEYCASRHLIIAE 210 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccH---HHHHHHHHHHHhCCeEEEE
Confidence 35566665112689999999999999 9999999999999999876
No 254
>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=87.06 E-value=0.93 Score=37.05 Aligned_cols=34 Identities=32% Similarity=0.382 Sum_probs=29.1
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl 212 (214)
.+.++||+||++.|..++.+++..| +.+++.+|.
T Consensus 44 ~~~k~vLEIGt~~GySal~la~~l~~~g~i~tiE~ 78 (205)
T PF01596_consen 44 TRPKRVLEIGTFTGYSALWLAEALPEDGKITTIEI 78 (205)
T ss_dssp HT-SEEEEESTTTSHHHHHHHHTSTTTSEEEEEES
T ss_pred cCCceEEEeccccccHHHHHHHhhcccceEEEecC
Confidence 3578999999999999999999988 578888775
No 255
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=86.96 E-value=0.61 Score=33.25 Aligned_cols=46 Identities=15% Similarity=0.169 Sum_probs=40.8
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+.|..+|... +|=.+.-||..++++. ..+.+.|+.|..+|++++..
T Consensus 10 ~~IL~hl~~~-~~Dy~k~ia~~l~~~~---~~v~~~l~~Le~~GLler~~ 55 (92)
T PF10007_consen 10 LKILQHLKKA-GPDYAKSIARRLKIPL---EEVREALEKLEEMGLLERVE 55 (92)
T ss_pred HHHHHHHHHH-CCCcHHHHHHHHCCCH---HHHHHHHHHHHHCCCeEEec
Confidence 4466677776 8899999999999999 99999999999999999886
No 256
>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=86.80 E-value=0.8 Score=36.17 Aligned_cols=43 Identities=12% Similarity=0.186 Sum_probs=40.3
Q ss_pred CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 52 MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 52 ~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+|..+||+.+|++. ..+.|.+..|...+++.... .+.|..+|.
T Consensus 76 ~t~~~ia~~l~iS~---~Tv~r~ik~L~e~~iI~k~~-------~G~Y~iNP~ 118 (165)
T PF05732_consen 76 ATQKEIAEKLGISK---PTVSRAIKELEEKNIIKKIR-------NGAYMINPN 118 (165)
T ss_pred eeHHHHHHHhCCCH---HHHHHHHHHHHhCCcEEEcc-------CCeEEECcH
Confidence 68999999999999 99999999999999999886 689999998
No 257
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=86.77 E-value=0.66 Score=37.36 Aligned_cols=65 Identities=15% Similarity=0.114 Sum_probs=47.7
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
.+...|..+ +++|..+||+.+++++ ..+.++++-|...|++.......|-- .-...+|+. ++.+.
T Consensus 49 ~iL~~L~~~-~~itq~eLa~~l~l~~---sTvtr~l~rLE~kGlI~R~~~~~DrR-~~~I~LTek----G~~l~ 113 (185)
T PRK13777 49 HILWIAYHL-KGASISEIAKFGVMHV---STAFNFSKKLEERGYLTFSKKEDDKR-NTYIELTEK----GEELL 113 (185)
T ss_pred HHHHHHHhC-CCcCHHHHHHHHCCCH---hhHHHHHHHHHHCCCEEecCCCCCCC-eeEEEECHH----HHHHH
Confidence 355666665 7899999999999998 88999999999999999764211110 223666777 66554
No 258
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=86.71 E-value=0.2 Score=35.90 Aligned_cols=62 Identities=23% Similarity=0.320 Sum_probs=47.3
Q ss_pred cchhhh-cCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 41 IPDIIN-NSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 41 lfd~L~-~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
+||+|. .+++++...-|.-.++++- +..+++++.|+..|++..... +. ...|.+|+. +..|+
T Consensus 20 i~dIL~~~~~~~~~~Tri~y~aNlny---~~~~~yi~~L~~~Gli~~~~~---~~-~~~y~lT~K----G~~fl 82 (95)
T COG3432 20 IFDILKAISEGGIGITRIIYGANLNY---KRAQKYIEMLVEKGLIIKQDN---GR-RKVYELTEK----GKRFL 82 (95)
T ss_pred HHHHHHHhcCCCCCceeeeeecCcCH---HHHHHHHHHHHhCCCEEeccC---Cc-cceEEEChh----HHHHH
Confidence 345555 2338899999999999998 999999999999996665541 11 236999999 87774
No 259
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=86.65 E-value=0.53 Score=39.72 Aligned_cols=45 Identities=9% Similarity=0.207 Sum_probs=40.5
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.|.+.|... +.+++.|||+.+++++ .-+||=|..|...|++...-
T Consensus 9 ~Il~~L~~~-~~v~v~eLa~~l~VS~---~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 9 AILEYLQKQ-GKTSVEELAQYFDTTG---TTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHc-CCEEHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEEE
Confidence 467888887 8899999999999999 99999999999999998764
No 260
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=86.59 E-value=0.51 Score=40.02 Aligned_cols=47 Identities=21% Similarity=0.320 Sum_probs=42.5
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
..+.++|.++||-++-+||.+++|.+. ..+.|+|+-|...|+++..+
T Consensus 198 ~~il~~i~~~GGri~Q~eL~r~lglsk---tTvsR~L~~LEk~GlIe~~K 244 (258)
T COG2512 198 KEILDLIRERGGRITQAELRRALGLSK---TTVSRILRRLEKRGLIEKEK 244 (258)
T ss_pred HHHHHHHHHhCCEEeHHHHHHhhCCCh---HHHHHHHHHHHhCCceEEEE
Confidence 446788888878899999999999999 99999999999999999876
No 261
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=86.45 E-value=0.91 Score=37.95 Aligned_cols=45 Identities=20% Similarity=0.232 Sum_probs=39.7
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.|.+.|.++ +.++++|||+.+++++ +.++|.|..|...|.+....
T Consensus 8 ~Il~~l~~~-~~~~~~eLa~~l~VS~---~TiRRdL~~L~~~~~l~r~~ 52 (240)
T PRK10411 8 AIVDLLLNH-TSLTTEALAEQLNVSK---ETIRRDLNELQTQGKILRNH 52 (240)
T ss_pred HHHHHHHHc-CCCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEec
Confidence 366777776 8999999999999999 99999999999999998754
No 262
>PRK05031 tRNA (uracil-5-)-methyltransferase; Validated
Probab=86.45 E-value=0.99 Score=40.05 Aligned_cols=29 Identities=17% Similarity=0.253 Sum_probs=24.5
Q ss_pred CcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 182 KPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 182 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.+++|++||+|.+++.+++... +++.+|.
T Consensus 208 ~~vLDl~~G~G~~sl~la~~~~--~v~~vE~ 236 (362)
T PRK05031 208 GDLLELYCGNGNFTLALARNFR--RVLATEI 236 (362)
T ss_pred CeEEEEeccccHHHHHHHhhCC--EEEEEEC
Confidence 4799999999999999999865 6777664
No 263
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=86.40 E-value=0.74 Score=36.53 Aligned_cols=44 Identities=20% Similarity=0.162 Sum_probs=37.0
Q ss_pred chhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 42 PDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 42 fd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+-+|=-+.+|+|++||++.+|++. ..+..-++-|-..+++.+.-
T Consensus 32 Ygilyls~~Pmtl~Ei~E~lg~Sk---s~vS~~lkkL~~~~lV~~~~ 75 (177)
T COG1510 32 YGILYLSRKPLTLDEIAEALGMSK---SNVSMGLKKLQDWNLVKKVF 75 (177)
T ss_pred hhhheecCCCccHHHHHHHHCCCc---chHHHHHHHHHhcchHHhhh
Confidence 333333349999999999999999 99999999999999998754
No 264
>COG2518 Pcm Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=86.17 E-value=1.7 Score=35.75 Aligned_cols=33 Identities=15% Similarity=0.205 Sum_probs=26.0
Q ss_pred HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCC
Q 040620 169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFP 203 (214)
Q Consensus 169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P 203 (214)
.+++... .....+||+||+|+|..+.-|++.--
T Consensus 63 ~m~~~L~--~~~g~~VLEIGtGsGY~aAvla~l~~ 95 (209)
T COG2518 63 RMLQLLE--LKPGDRVLEIGTGSGYQAAVLARLVG 95 (209)
T ss_pred HHHHHhC--CCCCCeEEEECCCchHHHHHHHHHhC
Confidence 3455555 66789999999999999998887643
No 265
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=85.96 E-value=2.7 Score=31.40 Aligned_cols=81 Identities=11% Similarity=0.080 Sum_probs=62.7
Q ss_pred hhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcC-CCCCCcccHHHHHHHHHhCCceeeecCCCC
Q 040620 14 FQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALN-VHPNKTRCTQILVCLLAHSGFFVQQKDGKN 92 (214)
Q Consensus 14 ~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g-~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~ 92 (214)
.-+....++++.+-|...+|+... . |+....||-..++ +++ +-|.+-|+.|...|++....-.+-
T Consensus 10 ~c~~~~~l~~ig~kW~~lIl~~L~---------~--g~~RF~eL~r~i~~Is~---k~Ls~~Lk~Le~~Glv~R~~~~~~ 75 (120)
T COG1733 10 PCPVEEALEVIGGKWTLLILRDLF---------D--GPKRFNELRRSIGGISP---KMLSRRLKELEEDGLVERVVYPEE 75 (120)
T ss_pred CCCHHHHHHHHcCccHHHHHHHHh---------c--CCCcHHHHHHHccccCH---HHHHHHHHHHHHCCCEEeeecCCC
Confidence 345667788888888888877653 2 7899999999998 999 999999999999999997652100
Q ss_pred CCccceeeCCCCCcccccccc
Q 040620 93 EQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 93 ~~~~~~y~~t~~~~~~s~~l~ 113 (214)
-. .-.|++|+. ++.|.
T Consensus 76 Pp-rveY~LT~~----G~~L~ 91 (120)
T COG1733 76 PP-RVEYRLTEK----GRDLL 91 (120)
T ss_pred Cc-eeEEEEhhh----HHHHH
Confidence 01 356999999 77765
No 266
>KOG3045 consensus Predicted RNA methylase involved in rRNA processing [RNA processing and modification]
Probab=85.91 E-value=1.6 Score=37.27 Aligned_cols=55 Identities=18% Similarity=0.110 Sum_probs=35.7
Q ss_pred cCCCCChhhHHHHHHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHH
Q 040620 141 QNDDQTLFGTADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMAR 196 (214)
Q Consensus 141 r~~~~~~f~~~~g~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~ 196 (214)
..++|+.|+..|.-|..-...+.......++..+. .-++...|.|+|||.+-++.
T Consensus 142 fkedp~afdlYH~gfr~QV~kWP~nPld~ii~~ik-~r~~~~vIaD~GCGEakiA~ 196 (325)
T KOG3045|consen 142 FKEDPTAFDLYHAGFRSQVKKWPENPLDVIIRKIK-RRPKNIVIADFGCGEAKIAS 196 (325)
T ss_pred HhcCcHHHHHHHHHHHHHHHhCCCChHHHHHHHHH-hCcCceEEEecccchhhhhh
Confidence 33455667766655666555665555555655443 23456799999999998875
No 267
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=85.74 E-value=1.1 Score=33.27 Aligned_cols=36 Identities=19% Similarity=0.239 Sum_probs=34.3
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.++|++|||+.+.+++ |.++.+|+-+...|.++-.+
T Consensus 18 ~~vtl~elA~~l~cS~---Rn~r~lLkkm~~~gWi~W~p 53 (115)
T PF12793_consen 18 VEVTLDELAELLFCSR---RNARTLLKKMQEEGWITWQP 53 (115)
T ss_pred cceeHHHHHHHhCCCH---HHHHHHHHHHHHCCCeeeeC
Confidence 5789999999999999 99999999999999999886
No 268
>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=85.56 E-value=1.1 Score=36.49 Aligned_cols=33 Identities=15% Similarity=0.290 Sum_probs=24.0
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
-..+.+++|||||.|.+...|+.+. -+.++.|.
T Consensus 41 ~~ry~~alEvGCs~G~lT~~LA~rC--d~LlavDi 73 (201)
T PF05401_consen 41 RRRYRRALEVGCSIGVLTERLAPRC--DRLLAVDI 73 (201)
T ss_dssp TSSEEEEEEE--TTSHHHHHHGGGE--EEEEEEES
T ss_pred ccccceeEecCCCccHHHHHHHHhh--CceEEEeC
Confidence 4556899999999999999998875 34566654
No 269
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=85.21 E-value=1.6 Score=34.54 Aligned_cols=48 Identities=13% Similarity=0.235 Sum_probs=38.9
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHcC-----CCCCCcccHHHHHHHHHhCCceeeec
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVALN-----VHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~g-----~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+.-|+++|...++++|+++|.+++. ++. ..++|.|+.|+..|++.+..
T Consensus 28 R~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~---aTVYRtL~~L~e~Glv~~~~ 80 (169)
T PRK11639 28 RLEVLRLMSLQPGAISAYDLLDLLREAEPQAKP---PTVYRALDFLLEQGFVHKVE 80 (169)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCc---chHHHHHHHHHHCCCEEEEe
Confidence 3446777766558999999998884 344 78999999999999999875
No 270
>PF13518 HTH_28: Helix-turn-helix domain
Probab=85.20 E-value=0.79 Score=28.18 Aligned_cols=29 Identities=7% Similarity=0.103 Sum_probs=26.7
Q ss_pred CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCc
Q 040620 52 MTLTQIIVALNVHPNKTRCTQILVCLLAHSGF 83 (214)
Q Consensus 52 ~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~ 83 (214)
.|..++|+.+|+++ ..+.+|++.....|+
T Consensus 13 ~s~~~~a~~~gis~---~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 13 ESVREIAREFGISR---STVYRWIKRYREGGI 41 (52)
T ss_pred CCHHHHHHHHCCCH---hHHHHHHHHHHhcCH
Confidence 49999999999999 999999999988875
No 271
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=84.90 E-value=0.9 Score=35.05 Aligned_cols=41 Identities=12% Similarity=0.164 Sum_probs=35.4
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCce
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFF 84 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l 84 (214)
-|+++|-.+ +.+|-++||+.+|++. ..++++|..|...++.
T Consensus 5 ~v~d~L~~~-~~~~dedLa~~l~i~~---n~vRkiL~~L~ed~~~ 45 (147)
T smart00531 5 LVLDALMRN-GCVTEEDLAELLGIKQ---KQLRKILYLLYDEKLI 45 (147)
T ss_pred eehHHHHhc-CCcCHHHHHHHhCCCH---HHHHHHHHHHHhhhcc
Confidence 467777766 7899999999999999 9999999999995554
No 272
>COG2263 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=84.88 E-value=0.82 Score=37.00 Aligned_cols=34 Identities=21% Similarity=0.206 Sum_probs=25.0
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
....++|+|+|||+|.+++..+-.-|. +++.+|+
T Consensus 43 ~l~g~~V~DlG~GTG~La~ga~~lGa~-~V~~vdi 76 (198)
T COG2263 43 DLEGKTVLDLGAGTGILAIGAALLGAS-RVLAVDI 76 (198)
T ss_pred CcCCCEEEEcCCCcCHHHHHHHhcCCc-EEEEEec
Confidence 345679999999999999988776443 4555553
No 273
>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=84.63 E-value=1.3 Score=37.93 Aligned_cols=45 Identities=7% Similarity=-0.011 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHcC--CCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALN--VHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g--~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+..++++||++++ ++. ..++.-|+.|...|++..++ ++.|..|..
T Consensus 136 ~~~~~~~ia~~l~p~is~---~ev~~sL~~L~~~glikk~~-------~g~y~~t~~ 182 (271)
T TIGR02147 136 FADDPEELAKRCFPKISA---EQVKESLDLLERLGLIKKNE-------DGFYKQTDK 182 (271)
T ss_pred CCCCHHHHHHHhCCCCCH---HHHHHHHHHHHHCCCeeECC-------CCcEEeecc
Confidence 4457999999998 777 88999999999999999987 689999887
No 274
>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=84.57 E-value=0.55 Score=43.28 Aligned_cols=23 Identities=17% Similarity=0.393 Sum_probs=20.9
Q ss_pred CCCCcEEeecCCchHHHHHHHHH
Q 040620 179 KGLKPLVDVGGSTGTMARAIATA 201 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~ 201 (214)
...+++||||||.|+|+..|+++
T Consensus 116 g~iR~~LDvGcG~aSF~a~l~~r 138 (506)
T PF03141_consen 116 GGIRTALDVGCGVASFGAYLLER 138 (506)
T ss_pred CceEEEEeccceeehhHHHHhhC
Confidence 45789999999999999999987
No 275
>PRK12423 LexA repressor; Provisional
Probab=83.69 E-value=1.4 Score=35.72 Aligned_cols=36 Identities=25% Similarity=0.288 Sum_probs=32.0
Q ss_pred CCCCHHHHHHHcCC-CCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNV-HPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~-~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
-+-|..|||+++|+ ++ ..+++.|+.|...|++...+
T Consensus 24 ~~Ps~~eia~~~g~~s~---~~v~~~l~~L~~~G~l~~~~ 60 (202)
T PRK12423 24 QPPSLAEIAQAFGFASR---SVARKHVQALAEAGLIEVVP 60 (202)
T ss_pred CCCCHHHHHHHhCCCCh---HHHHHHHHHHHHCCCEEecC
Confidence 35699999999995 76 78899999999999999875
No 276
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=83.14 E-value=0.57 Score=28.79 Aligned_cols=38 Identities=13% Similarity=0.197 Sum_probs=22.2
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCc
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGF 83 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~ 83 (214)
.+...+. .+.|..+||+.+|+++ ..+++|++.....|+
T Consensus 9 ~ii~l~~---~G~s~~~ia~~lgvs~---~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 9 QIIRLLR---EGWSIREIAKRLGVSR---STVYRWIKRYREEGL 46 (50)
T ss_dssp -HHHHHH---HT--HHHHHHHHTS-H---HHHHHHHT-------
T ss_pred HHHHHHH---CCCCHHHHHHHHCcCH---HHHHHHHHHcccccc
Confidence 3444444 3689999999999999 999999887666553
No 277
>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=83.12 E-value=1.1 Score=37.66 Aligned_cols=33 Identities=27% Similarity=0.350 Sum_probs=27.7
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+.++||=||||.|..+..+++..|-.+++++|+
T Consensus 76 ~p~~VLiiGgG~G~~~~ell~~~~~~~i~~VEi 108 (246)
T PF01564_consen 76 NPKRVLIIGGGDGGTARELLKHPPVESITVVEI 108 (246)
T ss_dssp ST-EEEEEESTTSHHHHHHTTSTT-SEEEEEES
T ss_pred CcCceEEEcCCChhhhhhhhhcCCcceEEEEec
Confidence 579999999999999999997776778998886
No 278
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=83.08 E-value=1.5 Score=35.88 Aligned_cols=42 Identities=12% Similarity=0.062 Sum_probs=34.3
Q ss_pred HHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHH
Q 040620 29 KSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCL 77 (214)
Q Consensus 29 ~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~ 77 (214)
.-.+|+.|++.|-||.=. ..+..+||+.+|+++ ..+...||-
T Consensus 160 Q~~vL~~A~~~GYFd~PR----~~~l~dLA~~lGISk---st~~ehLRr 201 (215)
T COG3413 160 QLEVLRLAYKMGYFDYPR----RVSLKDLAKELGISK---STLSEHLRR 201 (215)
T ss_pred HHHHHHHHHHcCCCCCCc----cCCHHHHHHHhCCCH---HHHHHHHHH
Confidence 567899999999999744 489999999999988 666555554
No 279
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=82.91 E-value=0.69 Score=27.46 Aligned_cols=27 Identities=22% Similarity=0.149 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLA 79 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~ 79 (214)
.+.++++||+.+|+++ ..+.|..+...
T Consensus 7 ~~~~l~~iA~~~g~S~---~~f~r~Fk~~~ 33 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSP---SYFSRLFKKET 33 (42)
T ss_dssp SS--HHHHHHHHTS-H---HHHHHHHHHHT
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHHHHHH
Confidence 5799999999999998 99988877554
No 280
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=82.47 E-value=0.83 Score=42.16 Aligned_cols=65 Identities=9% Similarity=0.015 Sum_probs=53.9
Q ss_pred HHhcCcchhhhcCCCC-CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 36 AIQLRIPDIINNSGQP-MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 36 a~~lglfd~L~~~~~p-~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
+++..|...|... ++ .+.++||+.+|+++ ..+.+.+..|.+.|++...... ...|.+|+. ++..+
T Consensus 3 ~~e~~iL~~l~~~-~~~~~~~~la~~~g~~~---~~v~~~~~~L~~kg~v~~~~~~-----~~~~~LT~e----G~~~l 68 (492)
T PLN02853 3 MAEEALLGALSNN-EEISDSGQFAASHGLDH---NEVVGVIKSLHGFRYVDAQDIK-----RETWVLTEE----GKKYA 68 (492)
T ss_pred hHHHHHHHHHHhc-CCCCCHHHHHHHcCCCH---HHHHHHHHHHHhCCCEEEEEEE-----EEEEEECHH----HHHHH
Confidence 4566677788875 54 89999999999999 9999999999999999865431 578999999 88876
No 281
>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=82.27 E-value=2 Score=29.14 Aligned_cols=42 Identities=17% Similarity=0.219 Sum_probs=37.1
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
|...++. +..|.+||-+++|++. ..|-..|.-|+..|++...
T Consensus 10 IL~~ls~--~c~TLeeL~ekTgi~k---~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 10 ILIILSK--RCCTLEELEEKTGISK---NTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHh--ccCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeeee
Confidence 4556666 6899999999999999 8999999999999999876
No 282
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=82.24 E-value=1.4 Score=35.25 Aligned_cols=45 Identities=13% Similarity=0.189 Sum_probs=39.4
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.|++.|... |-+|-++||..+|+.. .-++++|..|...|++....
T Consensus 22 ~v~~~l~~k-ge~tDeela~~l~i~~---~~vrriL~~L~e~~li~~~k 66 (176)
T COG1675 22 LVVDALLEK-GELTDEELAELLGIKK---NEVRRILYALYEDGLISYRK 66 (176)
T ss_pred HHHHHHHhc-CCcChHHHHHHhCccH---HHHHHHHHHHHhCCceEEEe
Confidence 466777774 5699999999999999 99999999999999999664
No 283
>PLN02476 O-methyltransferase
Probab=81.80 E-value=2 Score=36.79 Aligned_cols=36 Identities=22% Similarity=0.229 Sum_probs=30.0
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH 213 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp 213 (214)
..+.+++|+||.+.|..++.+++.-| +-+++-+|..
T Consensus 116 ~~~ak~VLEIGT~tGySal~lA~al~~~G~V~TiE~d 152 (278)
T PLN02476 116 ILGAERCIEVGVYTGYSSLAVALVLPESGCLVACERD 152 (278)
T ss_pred hcCCCeEEEecCCCCHHHHHHHHhCCCCCEEEEEECC
Confidence 44689999999999999999999876 5577777764
No 284
>KOG2361 consensus Predicted methyltransferase [General function prediction only]
Probab=81.72 E-value=0.74 Score=38.67 Aligned_cols=30 Identities=17% Similarity=0.324 Sum_probs=25.7
Q ss_pred CcEEeecCCchHHHHHHHHHCCC--CeEEEec
Q 040620 182 KPLVDVGGSTGTMARAIATAFPD--TKCTVFA 211 (214)
Q Consensus 182 ~~vvDVGGG~G~~~~~l~~~~P~--l~~~v~D 211 (214)
.+|+.||||.|....-|++.+|+ +++...|
T Consensus 73 ~~ilEvGCGvGNtvfPll~~~~n~~l~v~acD 104 (264)
T KOG2361|consen 73 ETILEVGCGVGNTVFPLLKTSPNNRLKVYACD 104 (264)
T ss_pred hhheeeccCCCcccchhhhcCCCCCeEEEEcC
Confidence 38999999999999999999999 5555554
No 285
>PRK05638 threonine synthase; Validated
Probab=81.65 E-value=1.4 Score=40.17 Aligned_cols=60 Identities=17% Similarity=0.110 Sum_probs=45.1
Q ss_pred cchhhhcCCCCCCHHHHHHHcC--CCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCccccccc
Q 040620 41 IPDIINNSGQPMTLTQIIVALN--VHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRIS 112 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g--~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l 112 (214)
|+.+|.+ ++++.-||++.++ +++ ..+++.|+.|...|+++.... .+. ...|++|+. ++.+
T Consensus 376 IL~~L~~--~~~~~~el~~~l~~~~s~---~~v~~hL~~Le~~GLV~~~~~--~g~-~~~Y~Lt~~----g~~~ 437 (442)
T PRK05638 376 ILKILSE--REMYGYEIWKALGKPLKY---QAVYQHIKELEELGLIEEAYR--KGR-RVYYKLTEK----GRRL 437 (442)
T ss_pred HHHHHhh--CCccHHHHHHHHcccCCc---chHHHHHHHHHHCCCEEEeec--CCC-cEEEEECcH----HHHH
Confidence 4555554 6899999999998 777 899999999999999975311 011 345889988 6554
No 286
>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=81.37 E-value=0.66 Score=31.62 Aligned_cols=34 Identities=15% Similarity=0.046 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ 86 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~ 86 (214)
..+|..|||+.+|+++ ..++.++..+...|.+..
T Consensus 31 eGlS~kEIAe~LGIS~---~TVk~~l~~~~~~~~~~~ 64 (73)
T TIGR03879 31 AGKTASEIAEELGRTE---QTVRNHLKGETKAGGLVK 64 (73)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHhcCcccchHHH
Confidence 5799999999999999 999999998888877654
No 287
>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=81.29 E-value=2 Score=34.31 Aligned_cols=57 Identities=18% Similarity=0.247 Sum_probs=41.4
Q ss_pred HHHHHHHHHhcCcchhhhcCCCC---CCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 29 KSLSLKRAIQLRIPDIINNSGQP---MTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 29 ~~~~L~~a~~lglfd~L~~~~~p---~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
...+|.+.+.+-=-+-+...+.| .|-.+||+.+ |+++ +.++|.++.|+..|++...+
T Consensus 45 ~l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~~G~s~---~tlrR~l~~LveaGLI~rrD 105 (177)
T PF03428_consen 45 ALAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERLNGMSE---RTLRRHLARLVEAGLIVRRD 105 (177)
T ss_pred HHHHHHHHHHhCCcccccCCCCceeecCHHHHHHHHcCCCH---HHHHHHHHHHHHCCCeeecc
Confidence 33445555544444444432233 5779999999 9999 99999999999999999865
No 288
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=81.06 E-value=3 Score=28.81 Aligned_cols=52 Identities=12% Similarity=0.125 Sum_probs=43.3
Q ss_pred chhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 42 PDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 42 fd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+..+.. .++|=++||+++|++. ..+..-++.|...|+=.+... ..-|++...
T Consensus 12 l~~~~~--~~~SGe~La~~LgiSR---taVwK~Iq~Lr~~G~~I~s~~------~kGY~L~~~ 63 (79)
T COG1654 12 LLLLTG--NFVSGEKLAEELGISR---TAVWKHIQQLREEGVDIESVR------GKGYLLPQL 63 (79)
T ss_pred HHHcCC--CcccHHHHHHHHCccH---HHHHHHHHHHHHhCCceEecC------CCceeccCc
Confidence 344443 7999999999999999 999999999999999888763 347888777
No 289
>PRK10736 hypothetical protein; Provisional
Probab=80.99 E-value=2 Score=38.48 Aligned_cols=50 Identities=6% Similarity=0.011 Sum_probs=43.0
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeC
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILL 101 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~ 101 (214)
.|++.|.. .|+++++|+.++|++. ..+...|-.|.-.|++.+.+ ++.|+.
T Consensus 312 ~v~~~l~~--~~~~iD~L~~~~~l~~---~~v~~~L~~LEl~G~v~~~~-------g~~~~~ 361 (374)
T PRK10736 312 ELLANVGD--EVTPVDVVAERAGQPV---PEVVTQLLELELAGWIAAVP-------GGYVRL 361 (374)
T ss_pred HHHHhcCC--CCCCHHHHHHHHCcCH---HHHHHHHHHHHhCCcEEEcC-------CcEEEE
Confidence 46677765 7899999999999999 99999999999999999987 566654
No 290
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=80.91 E-value=2 Score=38.75 Aligned_cols=32 Identities=13% Similarity=0.035 Sum_probs=25.4
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+.++|||+|||+|.+++..+.. +..+++.+|+
T Consensus 220 ~g~rVLDlfsgtG~~~l~aa~~-ga~~V~~VD~ 251 (396)
T PRK15128 220 ENKRVLNCFSYTGGFAVSALMG-GCSQVVSVDT 251 (396)
T ss_pred CCCeEEEeccCCCHHHHHHHhC-CCCEEEEEEC
Confidence 4689999999999998876643 4457888886
No 291
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=80.85 E-value=1 Score=41.71 Aligned_cols=66 Identities=9% Similarity=0.064 Sum_probs=53.6
Q ss_pred HHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 36 AIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 36 a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
..+..|+..|...++..+.++||+.+|+++ ..+.+.+..|.+.|+++..... ...|.+|+. ++..+
T Consensus 6 ~~e~~iL~~l~~~~~~~~~~~la~~~~~~~---~~v~~~~~~L~~kg~v~~~~~~-----~~~~~LT~e----G~~~~ 71 (494)
T PTZ00326 6 LEENTILSKLESENEIVNSLALAESLNIDH---QKVVGAIKSLESANYITTEMKK-----SNTWTLTEE----GEDYL 71 (494)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHcCCCH---HHHHHHHHHHHhCCCEEEEEEE-----EEEEEECHH----HHHHH
Confidence 345556677776326799999999999999 9999999999999999865431 578999999 88877
No 292
>PRK11760 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional
Probab=80.76 E-value=2.2 Score=37.82 Aligned_cols=33 Identities=15% Similarity=0.085 Sum_probs=28.6
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+....++||||+++|.++..++++ +.+++.+|.
T Consensus 209 ~~~g~~vlDLGAsPGGWT~~L~~r--G~~V~AVD~ 241 (357)
T PRK11760 209 LAPGMRAVDLGAAPGGWTYQLVRR--GMFVTAVDN 241 (357)
T ss_pred cCCCCEEEEeCCCCcHHHHHHHHc--CCEEEEEec
Confidence 345789999999999999999998 668888884
No 293
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=80.68 E-value=2.1 Score=34.12 Aligned_cols=35 Identities=11% Similarity=0.140 Sum_probs=33.0
Q ss_pred CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 51 PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 51 p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
++|-++||+.+|+++ ..+.|+|..|...|++....
T Consensus 168 ~~t~~~lA~~lG~tr---~tvsR~l~~l~~~gii~~~~ 202 (211)
T PRK11753 168 KITRQEIGRIVGCSR---EMVGRVLKMLEDQGLISAHG 202 (211)
T ss_pred CCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEecC
Confidence 789999999999999 99999999999999998774
No 294
>COG4122 Predicted O-methyltransferase [General function prediction only]
Probab=80.51 E-value=2.5 Score=34.95 Aligned_cols=36 Identities=28% Similarity=0.399 Sum_probs=32.3
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH 213 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp 213 (214)
.++.+++++||.+.|..++.++..-| +-+.|-+|+.
T Consensus 57 ~~~~k~iLEiGT~~GySal~mA~~l~~~g~l~tiE~~ 93 (219)
T COG4122 57 LSGPKRILEIGTAIGYSALWMALALPDDGRLTTIERD 93 (219)
T ss_pred hcCCceEEEeecccCHHHHHHHhhCCCCCeEEEEeCC
Confidence 45789999999999999999999999 8888888864
No 295
>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=80.45 E-value=1.3 Score=31.73 Aligned_cols=41 Identities=20% Similarity=0.077 Sum_probs=33.4
Q ss_pred HHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHH
Q 040620 34 KRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLA 79 (214)
Q Consensus 34 ~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~ 79 (214)
..+.+.+|+..|-. +++|-.|||+++|++. ..+.|+=+.|-
T Consensus 40 ~l~~R~~i~~~Ll~--~~~tQrEIa~~lGiS~---atIsR~sn~lk 80 (94)
T TIGR01321 40 DLGDRIRIVNELLN--GNMSQREIASKLGVSI---ATITRGSNNLK 80 (94)
T ss_pred HHHHHHHHHHHHHh--CCCCHHHHHHHhCCCh---hhhhHHHhhcc
Confidence 45667889988776 7899999999999998 88888765554
No 296
>PRK09954 putative kinase; Provisional
Probab=80.40 E-value=1.3 Score=38.99 Aligned_cols=43 Identities=14% Similarity=0.114 Sum_probs=38.6
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCcee
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFV 85 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~ 85 (214)
..|+..|.++ +++|..|||+.+++++ ..+++.++-|...|++.
T Consensus 6 ~~il~~l~~~-~~~s~~~la~~l~~s~---~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 6 KEILAILRRN-PLIQQNEIADILQISR---SRVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCcC
Confidence 3477788887 7999999999999999 99999999999999984
No 297
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=80.36 E-value=0.66 Score=37.23 Aligned_cols=44 Identities=9% Similarity=0.070 Sum_probs=39.3
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
.|.++|..+ +.+++++||+.+++++ .-++|=|+.|...|.+...
T Consensus 11 ~Il~~l~~~-~~~~~~~La~~~~vS~---~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 11 ALQELIEEN-PFITDEELAEKFGVSI---QTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHC-CCEEHHHHHHHHCcCH---HHHHHHHHHHhcchHHHHH
Confidence 356777776 8999999999999999 9999999999999999865
No 298
>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=80.29 E-value=0.89 Score=33.46 Aligned_cols=61 Identities=20% Similarity=0.247 Sum_probs=44.3
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcC-----CCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALN-----VHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP 103 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g-----~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~ 103 (214)
-+.-|++.|.+.+++.|++||-+.+. ++. ..+.|.|+.|...|++.+.... +. ..+|....
T Consensus 9 ~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~---~TVYR~L~~L~e~Gli~~~~~~--~~-~~~Y~~~~ 74 (120)
T PF01475_consen 9 QRLAILELLKESPEHLTAEEIYDKLRKKGPRISL---ATVYRTLDLLEEAGLIRKIEFG--DG-ESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--H---HHHHHHHHHHHHTTSEEEEEET--TS-EEEEEESS
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCH---HHHHHHHHHHHHCCeEEEEEcC--CC-cceEeecC
Confidence 34456777877667999999999884 333 5799999999999999987531 11 35677654
No 299
>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=80.04 E-value=0.61 Score=30.13 Aligned_cols=38 Identities=21% Similarity=0.307 Sum_probs=29.9
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHH
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLA 79 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~ 79 (214)
++.|+++|-++ +.+|+++||+.+++++ +.++..+..|-
T Consensus 7 q~~Ll~~L~~~-~~~~~~ela~~l~~S~---rti~~~i~~L~ 44 (59)
T PF08280_consen 7 QLKLLELLLKN-KWITLKELAKKLNISE---RTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHH-TSBBHHHHHHHCTS-H---HHHHHHHHHHH
T ss_pred HHHHHHHHHcC-CCCcHHHHHHHHCCCH---HHHHHHHHHHH
Confidence 34566777664 8999999999999999 88888877765
No 300
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=79.88 E-value=2.2 Score=38.18 Aligned_cols=32 Identities=16% Similarity=0.052 Sum_probs=27.8
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
..+++|++||+|.+++.+++..+-.+++..|.
T Consensus 58 ~~~vLDl~aGsG~~~l~~a~~~~~~~V~a~Di 89 (382)
T PRK04338 58 RESVLDALSASGIRGIRYALETGVEKVTLNDI 89 (382)
T ss_pred CCEEEECCCcccHHHHHHHHHCCCCEEEEEeC
Confidence 35899999999999999999888667888875
No 301
>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=79.62 E-value=2.7 Score=32.95 Aligned_cols=36 Identities=14% Similarity=0.060 Sum_probs=33.7
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
-|+|-+|||+.+|+++ ..+.|.|..|...|++....
T Consensus 142 ~~~t~~~iA~~lG~tr---etvsR~l~~l~~~g~I~~~~ 177 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTR---VTITRLLGDLRKKKLISIHK 177 (193)
T ss_pred CCCCHHHHHHHhCCcH---HHHHHHHHHHHHCCCEEecC
Confidence 4789999999999999 99999999999999998874
No 302
>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=79.57 E-value=3.6 Score=29.77 Aligned_cols=42 Identities=14% Similarity=0.149 Sum_probs=32.7
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
..+|.+.++++.+|+.++|+.+|+.+ +.|.+| |...|++...
T Consensus 13 ~~~d~~~~~~~~~ti~~~AK~L~i~~---~~l~~~---Lr~~g~l~~~ 54 (111)
T PF03374_consen 13 EFYDAFVDSDGLYTIREAAKLLGIGR---NKLFQW---LREKGWLYRR 54 (111)
T ss_pred HHHHHHHcCCCCccHHHHHHHhCCCH---HHHHHH---HHhCCceEEC
Confidence 34566666668999999999999999 555555 6669999985
No 303
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=79.52 E-value=3.7 Score=33.47 Aligned_cols=37 Identities=3% Similarity=0.005 Sum_probs=34.2
Q ss_pred CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|..++..+||+.+|++. .-++.-|+.|.+.|+++..+
T Consensus 28 G~~L~e~eLae~lgVSR---tpVREAL~~L~~eGlv~~~~ 64 (224)
T PRK11534 28 DEKLRMSLLTSRYALGV---GPLREALSQLVAERLVTVVN 64 (224)
T ss_pred CCcCCHHHHHHHHCCCh---HHHHHHHHHHHHCCCEEEeC
Confidence 36789999999999999 89999999999999999876
No 304
>PHA02591 hypothetical protein; Provisional
Probab=79.44 E-value=1.3 Score=30.42 Aligned_cols=32 Identities=16% Similarity=0.162 Sum_probs=26.2
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHH
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCL 77 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~ 77 (214)
+...|.+ .++|.++||+.+|++. ..++++++.
T Consensus 51 vA~eL~e--qGlSqeqIA~~LGVsq---etVrKYL~~ 82 (83)
T PHA02591 51 VTHELAR--KGFTVEKIASLLGVSV---RKVRRYLES 82 (83)
T ss_pred HHHHHHH--cCCCHHHHHHHhCCCH---HHHHHHHhc
Confidence 4455666 6899999999999998 888888763
No 305
>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=79.40 E-value=2.5 Score=29.03 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=26.3
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|+..|+. |.|+|+++||.++|.+. ..+...|..+ -=.++++
T Consensus 29 LLr~LA~-G~PVt~~~LA~a~g~~~---e~v~~~L~~~---p~tEyD~ 69 (77)
T PF12324_consen 29 LLRLLAK-GQPVTVEQLAAALGWPV---EEVRAALAAM---PDTEYDD 69 (77)
T ss_dssp HHHHHTT-TS-B-HHHHHHHHT--H---HHHHHHHHH----TTSEEET
T ss_pred HHHHHHc-CCCcCHHHHHHHHCCCH---HHHHHHHHhC---CCceEcC
Confidence 6778887 59999999999999987 6665555444 3355554
No 306
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=79.14 E-value=2.4 Score=31.54 Aligned_cols=48 Identities=17% Similarity=0.233 Sum_probs=37.6
Q ss_pred hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
.+|.++ ||.+..+|++.++++. ..++|+ --.-|.|+..+ .+.|.+|+.
T Consensus 66 ~~L~~~-Gp~~~~~l~~~~~~~~-----A~~IL~-~N~YGWFeRv~-------rGvY~LT~~ 113 (118)
T PF09929_consen 66 AALAEH-GPSRPADLRKATGVPK-----ATSILR-DNHYGWFERVE-------RGVYALTPA 113 (118)
T ss_pred HHHHHc-CCCCHHHHHHhcCCCh-----HHHHHH-hCcccceeeec-------cceEecCcc
Confidence 578866 9999999999999953 233332 35678999997 799999998
No 307
>COG3963 Phospholipid N-methyltransferase [Lipid metabolism]
Probab=78.81 E-value=3 Score=33.29 Aligned_cols=35 Identities=20% Similarity=0.421 Sum_probs=28.9
Q ss_pred hhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHH
Q 040620 165 LIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATA 201 (214)
Q Consensus 165 ~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 201 (214)
..+...+...+ ++...-|+++|.|+|.+..+|+++
T Consensus 35 ~lA~~M~s~I~--pesglpVlElGPGTGV~TkaIL~~ 69 (194)
T COG3963 35 ILARKMASVID--PESGLPVLELGPGTGVITKAILSR 69 (194)
T ss_pred HHHHHHHhccC--cccCCeeEEEcCCccHhHHHHHhc
Confidence 34566777777 777889999999999999998874
No 308
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=78.52 E-value=2.4 Score=40.98 Aligned_cols=32 Identities=19% Similarity=0.079 Sum_probs=26.7
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+.++|||+|||+|.+++.+++. ...+++.+|+
T Consensus 538 ~g~rVLDlf~gtG~~sl~aa~~-Ga~~V~~vD~ 569 (702)
T PRK11783 538 KGKDFLNLFAYTGTASVHAALG-GAKSTTTVDM 569 (702)
T ss_pred CCCeEEEcCCCCCHHHHHHHHC-CCCEEEEEeC
Confidence 4689999999999999999986 3346888886
No 309
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=78.30 E-value=2.2 Score=34.20 Aligned_cols=48 Identities=15% Similarity=0.151 Sum_probs=41.4
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+..|.|.|..+|...|+-+||+++|++. ..++|-|--|-..|.+...+
T Consensus 6 ~~~i~~~l~~~~~~~~a~~i~k~l~i~k---~~vNr~LY~L~~~~~v~~~~ 53 (183)
T PHA02701 6 ASLILTLLSSSGDKLPAKRIAKELGISK---HEANRCLYRLLESDAVSCED 53 (183)
T ss_pred HHHHHHHHHhcCCCCcHHHHHHHhCccH---HHHHHHHHHHhhcCcEecCC
Confidence 4568899998854699999999999998 89999999999999986653
No 310
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=78.03 E-value=4.8 Score=32.97 Aligned_cols=37 Identities=14% Similarity=0.168 Sum_probs=35.1
Q ss_pred CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|.+++-.+||+.+|++. .-++.-|.-|++.|+++..+
T Consensus 37 G~~l~e~~La~~~gvSr---tPVReAL~rL~~eGlv~~~p 73 (230)
T COG1802 37 GERLSEEELAEELGVSR---TPVREALRRLEAEGLVEIEP 73 (230)
T ss_pred CCCccHHHHHHHhCCCC---ccHHHHHHHHHHCCCeEecC
Confidence 48899999999999999 89999999999999999986
No 311
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=77.76 E-value=3.1 Score=33.55 Aligned_cols=43 Identities=23% Similarity=0.224 Sum_probs=37.0
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+.+..+++-+ +|+|..+|++..|+++ ..+++.|...|++.+.+
T Consensus 93 LEtLaiIay~-qPiTr~eI~~irGv~~------~~ii~~L~~~gLI~e~g 135 (188)
T PRK00135 93 LEVLAIIAYK-QPITRIEIDEIRGVNS------DGALQTLLAKGLIKEVG 135 (188)
T ss_pred HHHHHHHHHc-CCcCHHHHHHHHCCCH------HHHHHHHHHCCCeEEcC
Confidence 4456777777 9999999999999987 78899999999998754
No 312
>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=77.74 E-value=3.9 Score=32.95 Aligned_cols=37 Identities=19% Similarity=0.237 Sum_probs=34.2
Q ss_pred CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|..++-.+||+.+|++. .-++.-|+.|...|+++..+
T Consensus 32 G~~L~e~~La~~lgVSR---tpVReAL~~L~~eGlv~~~~ 68 (212)
T TIGR03338 32 GAKLNESDIAARLGVSR---GPVREAFRALEEAGLVRNEK 68 (212)
T ss_pred CCEecHHHHHHHhCCCh---HHHHHHHHHHHHCCCEEEec
Confidence 37789999999999999 89999999999999999876
No 313
>PRK09462 fur ferric uptake regulator; Provisional
Probab=77.69 E-value=3.1 Score=31.87 Aligned_cols=59 Identities=8% Similarity=0.174 Sum_probs=42.5
Q ss_pred hcCcchhhhcC-CCCCCHHHHHHHcC-----CCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCC
Q 040620 38 QLRIPDIINNS-GQPMTLTQIIVALN-----VHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLP 102 (214)
Q Consensus 38 ~lglfd~L~~~-~~p~t~~eLA~~~g-----~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t 102 (214)
+.-|++.|... ++++|++||-+++. ++. .-++|.|+.|+..|++.+.... ++ ..+|..+
T Consensus 19 R~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~---aTVYR~L~~L~e~Gli~~~~~~-~~--~~~y~~~ 83 (148)
T PRK09462 19 RLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGL---ATVYRVLNQFDDAGIVTRHNFE-GG--KSVFELT 83 (148)
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCH---HHHHHHHHHHHHCCCEEEEEcC-CC--cEEEEeC
Confidence 34467777753 36999999998873 345 7899999999999999876421 11 3467654
No 314
>PRK11642 exoribonuclease R; Provisional
Probab=77.00 E-value=4.3 Score=40.02 Aligned_cols=57 Identities=16% Similarity=0.299 Sum_probs=43.3
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCC-cccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNK-TRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~-~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
|.+.|...+.|++..+|+++++++... ...|++.|+.|...|.+.... .+.|.+...
T Consensus 24 Il~~l~~~~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~~-------~~~~~~~~~ 81 (813)
T PRK11642 24 ILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTR-------RQCYALPER 81 (813)
T ss_pred HHHHHHhcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcC-------CceEecCCc
Confidence 556666544899999999999996411 245999999999999998765 466766544
No 315
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=76.95 E-value=3.3 Score=33.77 Aligned_cols=36 Identities=19% Similarity=0.137 Sum_probs=33.6
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
-|+|-++||+.+|+++ ..+.|+|..|...|++....
T Consensus 183 ~~lt~~~iA~~lG~sr---~tvsR~l~~l~~~g~I~~~~ 218 (235)
T PRK11161 183 LTMTRGDIGNYLGLTV---ETISRLLGRFQKSGMLAVKG 218 (235)
T ss_pred ccccHHHHHHHhCCcH---HHHHHHHHHHHHCCCEEecC
Confidence 3789999999999999 99999999999999999884
No 316
>KOG4589 consensus Cell division protein FtsJ [Cell cycle control, cell division, chromosome partitioning]
Probab=76.93 E-value=3.8 Score=33.39 Aligned_cols=35 Identities=11% Similarity=0.221 Sum_probs=29.7
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl 212 (214)
+.+..+|+|+|+-+|..++-..++- |+-.+.++|+
T Consensus 67 l~p~~~VlD~G~APGsWsQVavqr~~p~g~v~gVDl 102 (232)
T KOG4589|consen 67 LRPEDTVLDCGAAPGSWSQVAVQRVNPNGMVLGVDL 102 (232)
T ss_pred cCCCCEEEEccCCCChHHHHHHHhhCCCceEEEEee
Confidence 4457899999999999999766665 9999998887
No 317
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=76.91 E-value=1.7 Score=32.41 Aligned_cols=31 Identities=16% Similarity=0.147 Sum_probs=25.7
Q ss_pred CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 52 MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 52 ~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
||.+|||+.+|+.. .-+++|+| ..|.-++..
T Consensus 1 MT~eELA~~tG~sr---QTINrWvR---kegW~T~p~ 31 (122)
T PF07037_consen 1 MTPEELAELTGYSR---QTINRWVR---KEGWKTEPK 31 (122)
T ss_pred CCHHHHHHHhCccH---HHHHHHHH---hcCceeccC
Confidence 68999999999998 99999976 456666554
No 318
>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=76.78 E-value=2 Score=25.50 Aligned_cols=22 Identities=23% Similarity=0.203 Sum_probs=18.6
Q ss_pred CCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 52 MTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 52 ~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
+|..|+|+.+|+++ ..+++|.+
T Consensus 1 ~s~~e~a~~lgvs~---~tl~~~~~ 22 (49)
T cd04762 1 LTTKEAAELLGVSP---STLRRWVK 22 (49)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHH
Confidence 47899999999998 77777765
No 319
>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=76.59 E-value=3.4 Score=31.20 Aligned_cols=47 Identities=17% Similarity=0.202 Sum_probs=36.3
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHc----CCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVAL----NVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~----g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|+.|+.+|=.. ++.|+.+|.+.+ +.+. ..+..+|+-|...|++....
T Consensus 6 E~~VM~vlW~~-~~~t~~eI~~~l~~~~~~~~---tTv~T~L~rL~~KG~v~~~k 56 (130)
T TIGR02698 6 EWEVMRVVWTL-GETTSRDIIRILAEKKDWSD---STIKTLLGRLVDKGCLTTEK 56 (130)
T ss_pred HHHHHHHHHcC-CCCCHHHHHHHHhhccCCcH---HHHHHHHHHHHHCCceeeec
Confidence 44455556444 789999977765 5666 88999999999999998765
No 320
>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=76.53 E-value=3.4 Score=35.75 Aligned_cols=33 Identities=9% Similarity=0.150 Sum_probs=28.9
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCC--CeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPD--TKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~--l~~~v~Dl 212 (214)
...+||||.||+|.+....++.+|. .++.+.|.
T Consensus 135 ~pvrIlDIAaG~GRYvlDal~~~~~~~~~i~LrDy 169 (311)
T PF12147_consen 135 RPVRILDIAAGHGRYVLDALEKHPERPDSILLRDY 169 (311)
T ss_pred CceEEEEeccCCcHHHHHHHHhCCCCCceEEEEeC
Confidence 4679999999999999999999998 66777764
No 321
>PRK13256 thiopurine S-methyltransferase; Reviewed
Probab=76.28 E-value=5.7 Score=33.02 Aligned_cols=32 Identities=3% Similarity=-0.240 Sum_probs=28.3
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
+..+|++.|||.|.-+.-|+++ +.+++++|+-
T Consensus 43 ~~~rvLvPgCGkg~D~~~LA~~--G~~V~GvDlS 74 (226)
T PRK13256 43 DSSVCLIPMCGCSIDMLFFLSK--GVKVIGIELS 74 (226)
T ss_pred CCCeEEEeCCCChHHHHHHHhC--CCcEEEEecC
Confidence 4579999999999999999997 7889999873
No 322
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=76.21 E-value=5.7 Score=32.27 Aligned_cols=37 Identities=8% Similarity=0.024 Sum_probs=34.0
Q ss_pred CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|..++..+||+.+|++. .-++.-|+.|...|+++..+
T Consensus 32 G~~L~e~~La~~lgVSR---tpVREAL~~L~~eGLV~~~~ 68 (221)
T PRK11414 32 GARLITKNLAEQLGMSI---TPVREALLRLVSVNALSVAP 68 (221)
T ss_pred CCccCHHHHHHHHCCCc---hhHHHHHHHHHHCCCEEecC
Confidence 37788999999999999 89999999999999999775
No 323
>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=76.06 E-value=0.93 Score=28.60 Aligned_cols=32 Identities=16% Similarity=0.315 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHh-CCceeee
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAH-SGFFVQQ 87 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~-~g~l~~~ 87 (214)
.++++.|||+.+|+++ ..+++.|.. .|+....
T Consensus 2 ~~i~V~elAk~l~v~~------~~ii~~l~~~~Gi~~~~ 34 (54)
T PF04760_consen 2 EKIRVSELAKELGVPS------KEIIKKLFKELGIMVKS 34 (54)
T ss_dssp -EE-TTHHHHHHSSSH------HHHHHHH-HHHTS---S
T ss_pred CceEHHHHHHHHCcCH------HHHHHHHHHhCCcCcCC
Confidence 4689999999999998 788888955 8988433
No 324
>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=75.92 E-value=2.2 Score=25.48 Aligned_cols=22 Identities=18% Similarity=0.167 Sum_probs=18.5
Q ss_pred CCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 52 MTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 52 ~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
+|++|+|+.+|+++ ..+++|++
T Consensus 2 lt~~e~a~~lgis~---~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSK---DTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHH
Confidence 68999999999998 77777753
No 325
>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=75.64 E-value=3 Score=33.93 Aligned_cols=34 Identities=15% Similarity=0.081 Sum_probs=27.1
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.+..+|+|+-||.|.+++.+++..+..+++..|+
T Consensus 100 ~~~e~VlD~faGIG~f~l~~ak~~~~~~V~A~d~ 133 (200)
T PF02475_consen 100 KPGEVVLDMFAGIGPFSLPIAKHGKAKRVYAVDL 133 (200)
T ss_dssp -TT-EEEETT-TTTTTHHHHHHHT-SSEEEEEES
T ss_pred CcceEEEEccCCccHHHHHHhhhcCccEEEEecC
Confidence 3578999999999999999999888888888886
No 326
>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=75.47 E-value=3.3 Score=34.13 Aligned_cols=33 Identities=12% Similarity=-0.073 Sum_probs=28.8
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
.....++++.|||.|.-+..|+++ +.+++++|+
T Consensus 35 ~~~~~rvLvPgCG~g~D~~~La~~--G~~VvGvDl 67 (218)
T PF05724_consen 35 LKPGGRVLVPGCGKGYDMLWLAEQ--GHDVVGVDL 67 (218)
T ss_dssp TSTSEEEEETTTTTSCHHHHHHHT--TEEEEEEES
T ss_pred CCCCCeEEEeCCCChHHHHHHHHC--CCeEEEEec
Confidence 344579999999999999999997 789999987
No 327
>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=75.39 E-value=2.1 Score=28.04 Aligned_cols=23 Identities=17% Similarity=0.173 Sum_probs=20.7
Q ss_pred CCCCCHHHHHHHcCCCCCCcccHHHH
Q 040620 49 GQPMTLTQIIVALNVHPNKTRCTQIL 74 (214)
Q Consensus 49 ~~p~t~~eLA~~~g~~~~~~~~l~rl 74 (214)
+|.++..+||+++|+++ ..+++|
T Consensus 20 ~g~i~lkdIA~~Lgvs~---~tIr~W 42 (60)
T PF10668_consen 20 NGKIKLKDIAEKLGVSE---STIRKW 42 (60)
T ss_pred CCCccHHHHHHHHCCCH---HHHHHH
Confidence 48999999999999998 888877
No 328
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=75.27 E-value=4.3 Score=32.12 Aligned_cols=35 Identities=11% Similarity=0.127 Sum_probs=32.8
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
-|+|-++||+-+|+.+ ..+.|.|.-|...|++...
T Consensus 148 ~~~t~~~iA~~lG~tr---etvsR~l~~l~~~g~I~~~ 182 (202)
T PRK13918 148 IYATHDELAAAVGSVR---ETVTKVIGELSREGYIRSG 182 (202)
T ss_pred ecCCHHHHHHHhCccH---HHHHHHHHHHHHCCCEEcC
Confidence 4689999999999999 9999999999999999865
No 329
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=75.25 E-value=4.1 Score=33.41 Aligned_cols=36 Identities=17% Similarity=0.153 Sum_probs=33.0
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
-++|-++||+.+|+++ ..+.|+|..|...|++....
T Consensus 178 i~lt~~~IA~~lGisr---etlsR~L~~L~~~GlI~~~~ 213 (230)
T PRK09391 178 LPMSRRDIADYLGLTI---ETVSRALSQLQDRGLIGLSG 213 (230)
T ss_pred ecCCHHHHHHHHCCCH---HHHHHHHHHHHHCCcEEecC
Confidence 4689999999999999 99999999999999998763
No 330
>PRK01381 Trp operon repressor; Provisional
Probab=75.20 E-value=2.5 Score=30.52 Aligned_cols=40 Identities=15% Similarity=0.045 Sum_probs=32.0
Q ss_pred HHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHH
Q 040620 34 KRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLL 78 (214)
Q Consensus 34 ~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L 78 (214)
..+.+++|+..|-. |.+|-.|||+.+|++. ..+.|.-+.|
T Consensus 40 al~~R~~I~~~L~~--g~~sQREIa~~lGvSi---aTITRgsn~L 79 (99)
T PRK01381 40 ALGTRVRIVEELLR--GELSQREIKQELGVGI---ATITRGSNSL 79 (99)
T ss_pred HHHHHHHHHHHHHc--CCcCHHHHHHHhCCce---eeehhhHHHh
Confidence 34667889999887 8899999999999987 6666655444
No 331
>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=75.07 E-value=4.3 Score=30.08 Aligned_cols=37 Identities=22% Similarity=0.394 Sum_probs=34.1
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKD 89 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~ 89 (214)
.|.|+.|||..++++- --++-++.-|+..|++....+
T Consensus 54 ~~~SVAEiAA~L~lPl---gVvrVLvsDL~~~G~v~v~~p 90 (114)
T PF05331_consen 54 RPLSVAEIAARLGLPL---GVVRVLVSDLADAGLVRVRAP 90 (114)
T ss_pred CCccHHHHHHhhCCCc---hhhhhhHHHHHhCCCEEEeCC
Confidence 6999999999999998 889999999999999998763
No 332
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=74.76 E-value=3.2 Score=37.98 Aligned_cols=53 Identities=13% Similarity=0.192 Sum_probs=40.5
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
|-.+|.+ ||.|+.|||+.+|++. ..+.+.|+.| .|+|...+. +. .-+|++...
T Consensus 5 ~~~~L~~--g~~~~~eL~~~l~~sq---~~~s~~L~~L--~~~V~~~~~---gr-~~~Y~l~~~ 57 (442)
T PRK09775 5 LTTLLLQ--GPLSAAELAARLGVSQ---ATLSRLLAAL--GDQVVRFGK---AR-ATRYALLRP 57 (442)
T ss_pred HHHHHhc--CCCCHHHHHHHhCCCH---HHHHHHHHHh--hcceeEecc---Cc-eEEEEeccc
Confidence 3456665 8999999999999998 8999999999 888887652 11 234666554
No 333
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=74.23 E-value=3.1 Score=32.01 Aligned_cols=64 Identities=9% Similarity=0.092 Sum_probs=45.5
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHcCC--CCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVALNV--HPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~g~--~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+..|+++|.+++++.|+++|=+.+.- ++.+...++|.|+.|...|++.+... .++ ..+|.++..
T Consensus 23 R~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~--~~~-~~~y~~~~~ 88 (145)
T COG0735 23 RLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEF--EGG-KTRYELNSE 88 (145)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEe--CCC-EEEEecCCC
Confidence 34578888877688999999887752 22222789999999999999998763 111 234666655
No 334
>KOG0820 consensus Ribosomal RNA adenine dimethylase [RNA processing and modification]
Probab=74.18 E-value=6.5 Score=33.81 Aligned_cols=35 Identities=20% Similarity=0.302 Sum_probs=28.0
Q ss_pred HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCC
Q 040620 167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFP 203 (214)
Q Consensus 167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P 203 (214)
...+++.-+ .....+|++||+|+|.+...|+++-.
T Consensus 47 ~~~I~~ka~--~k~tD~VLEvGPGTGnLT~~lLe~~k 81 (315)
T KOG0820|consen 47 IDQIVEKAD--LKPTDVVLEVGPGTGNLTVKLLEAGK 81 (315)
T ss_pred HHHHHhccC--CCCCCEEEEeCCCCCHHHHHHHHhcC
Confidence 355556555 66788999999999999999999843
No 335
>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=73.80 E-value=4.6 Score=34.34 Aligned_cols=29 Identities=28% Similarity=0.471 Sum_probs=25.2
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEE
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCT 208 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~ 208 (214)
+..+++|||.|.|.....++..|.+..+|
T Consensus 94 ~~~~lLDlGAGdG~VT~~l~~~f~~v~aT 122 (265)
T PF05219_consen 94 KDKSLLDLGAGDGEVTERLAPLFKEVYAT 122 (265)
T ss_pred cCCceEEecCCCcHHHHHHHhhcceEEee
Confidence 45799999999999999999999886554
No 336
>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=73.64 E-value=3 Score=35.55 Aligned_cols=37 Identities=22% Similarity=0.334 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHcCCCCCCcccHHHHHH-HHHhCCceeeec
Q 040620 49 GQPMTLTQIIVALNVHPNKTRCTQILVC-LLAHSGFFVQQK 88 (214)
Q Consensus 49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr-~L~~~g~l~~~~ 88 (214)
+++.+++++|+.+|.++ ..+.++++ .|+..|++..++
T Consensus 253 ~~~~~~~~ia~~lg~~~---~~~~~~~e~~Li~~~li~~~~ 290 (305)
T TIGR00635 253 GGPVGLKTLAAALGEDA---DTIEDVYEPYLLQIGFLQRTP 290 (305)
T ss_pred CCcccHHHHHHHhCCCc---chHHHhhhHHHHHcCCcccCC
Confidence 37899999999999999 99999999 799999997554
No 337
>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=72.44 E-value=2.7 Score=39.03 Aligned_cols=25 Identities=12% Similarity=0.163 Sum_probs=22.0
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPD 204 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~ 204 (214)
...+|+|.+||+|.++.+++++.+.
T Consensus 31 ~~~~ilDP~cGsG~fl~~~~~~~~~ 55 (524)
T TIGR02987 31 TKTKIIDPCCGDGRLIAALLKKNEE 55 (524)
T ss_pred cceEEEeCCCCccHHHHHHHHHHHh
Confidence 4569999999999999999998864
No 338
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=72.40 E-value=4.8 Score=32.89 Aligned_cols=36 Identities=8% Similarity=0.125 Sum_probs=33.1
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.++|.++||+++++++ ..++..+..|+..|++.+..
T Consensus 177 ~g~s~~eIA~~l~iS~---~Tv~~~~~~~~~~~~~~~~~ 212 (239)
T PRK10430 177 YEFSTDELANAVNISR---VSCRKYLIWLVNCHILFTSI 212 (239)
T ss_pred CCcCHHHHHHHhCchH---HHHHHHHHHHHhCCEEEEEe
Confidence 6789999999999999 99999999999999996653
No 339
>PF12728 HTH_17: Helix-turn-helix domain
Probab=72.04 E-value=3 Score=25.65 Aligned_cols=22 Identities=9% Similarity=0.093 Sum_probs=18.9
Q ss_pred CCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 52 MTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 52 ~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
+|++|+|+.+|+++ ..+++|++
T Consensus 2 lt~~e~a~~l~is~---~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISR---STVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHH
Confidence 68999999999998 77877764
No 340
>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=72.03 E-value=7.9 Score=28.96 Aligned_cols=45 Identities=11% Similarity=0.276 Sum_probs=40.5
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
.|.|.++||..++.+. ..++.-|..+...|+++..+ ++.|..+..
T Consensus 52 ipy~~e~LA~~~~~~~---~~V~~AL~~f~k~glIe~~e-------d~~i~i~~~ 96 (121)
T PF09681_consen 52 IPYTAEMLALEFDRPV---DTVRLALAVFQKLGLIEIDE-------DGVIYIPNW 96 (121)
T ss_pred CCCcHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEec-------CCeEEeecH
Confidence 7999999999999998 99999999999999999986 577777665
No 341
>COG5459 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=71.96 E-value=1.4 Score=39.17 Aligned_cols=31 Identities=29% Similarity=0.541 Sum_probs=26.5
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCe-EEEec
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTK-CTVFA 211 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~D 211 (214)
.++|||||-|+|..+.++-.-+|+++ +++++
T Consensus 114 pqsiLDvG~GPgtgl~A~n~i~Pdl~sa~ile 145 (484)
T COG5459 114 PQSILDVGAGPGTGLWALNDIWPDLKSAVILE 145 (484)
T ss_pred cchhhccCCCCchhhhhhcccCCCchhhhhhc
Confidence 56899999999999999999999997 44443
No 342
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=71.47 E-value=3.1 Score=25.04 Aligned_cols=27 Identities=15% Similarity=0.272 Sum_probs=21.4
Q ss_pred CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCcee
Q 040620 52 MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFV 85 (214)
Q Consensus 52 ~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~ 85 (214)
+|+.|+|+.+|+++ +.++.| ...|++.
T Consensus 1 ~~~~e~a~~~gv~~---~tlr~~----~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTGVSP---STLRYY----ERIGLLS 27 (49)
T ss_pred CcHHHHHHHHCcCH---HHHHHH----HHCCCCC
Confidence 47899999999997 666555 6777776
No 343
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=70.86 E-value=6.5 Score=32.66 Aligned_cols=36 Identities=8% Similarity=0.219 Sum_probs=33.1
Q ss_pred CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
..+ +-.+||+.+|++. .-++.-|+.|.+.|+++..+
T Consensus 32 ~~LpsE~eLa~~lgVSR---tpVREAL~~L~~eGlv~~~~ 68 (254)
T PRK09464 32 EKLPPERELAKQFDVSR---PSLREAIQRLEAKGLLLRRQ 68 (254)
T ss_pred CcCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEec
Confidence 567 7899999999998 89999999999999999775
No 344
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=70.61 E-value=34 Score=27.07 Aligned_cols=76 Identities=16% Similarity=0.194 Sum_probs=57.7
Q ss_pred HHHHHhHHHHHHHHHhcCc-------chhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCc
Q 040620 23 YTYNYMKSLSLKRAIQLRI-------PDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQE 95 (214)
Q Consensus 23 ~~~g~~~~~~L~~a~~lgl-------fd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~ 95 (214)
..++-|--.|+.+|.+.++ ..++...+.|.++.+|++.++++. .-.+.=-||-|...|+++..+. +-
T Consensus 63 ~Af~rW~vrCmAaag~~~ls~~e~l~lH~irhrdR~K~laDic~~ln~eD--th~itYslrKL~k~gLit~t~~---gk- 136 (199)
T COG5631 63 EAFGRWQVRCMAAAGEFSLSGPENLLLHIIRHRDRPKSLADICQMLNRED--THNITYSLRKLLKGGLITRTGS---GK- 136 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcchHHHHHHHHhhcCchhhHHHHHHHhcccc--chhHHHHHHHHHhccceecCCC---Cc-
Confidence 3557888899999988773 445555568999999999999965 2355666899999999998762 22
Q ss_pred cceeeCCCC
Q 040620 96 EESILLPPH 104 (214)
Q Consensus 96 ~~~y~~t~~ 104 (214)
+-.|..|+.
T Consensus 137 evTy~vTa~ 145 (199)
T COG5631 137 EVTYEVTAL 145 (199)
T ss_pred eEEEEEecc
Confidence 357888888
No 345
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=70.49 E-value=3.4 Score=30.85 Aligned_cols=35 Identities=9% Similarity=-0.044 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
.+.|+++||+.+|+++ +.+.|+.+......+-...
T Consensus 24 ~~~sl~~lA~~~g~S~---~~l~r~Fk~~~G~s~~~~l 58 (127)
T PRK11511 24 SPLSLEKVSERSGYSK---WHLQRMFKKETGHSLGQYI 58 (127)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHHHHHCcCHHHHH
Confidence 6799999999999999 9999998776665555543
No 346
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=70.45 E-value=2.4 Score=25.61 Aligned_cols=24 Identities=17% Similarity=0.095 Sum_probs=16.2
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
.++|..+||+.+|.++ ..+.+.|+
T Consensus 19 ~G~s~~~IA~~lg~s~---sTV~relk 42 (44)
T PF13936_consen 19 QGMSIREIAKRLGRSR---STVSRELK 42 (44)
T ss_dssp S---HHHHHHHTT--H---HHHHHHHH
T ss_pred cCCCHHHHHHHHCcCc---HHHHHHHh
Confidence 5699999999999998 88877764
No 347
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=70.43 E-value=7.2 Score=29.38 Aligned_cols=45 Identities=13% Similarity=0.208 Sum_probs=37.5
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP 103 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~ 103 (214)
.=-|+.|+|..+|++| .-++|-.+-|...||+..... .+.|-...
T Consensus 34 kLPSvRelA~~~~VNp---nTv~raY~eLE~eG~i~t~rg------~G~fV~~~ 78 (125)
T COG1725 34 KLPSVRELAKDLGVNP---NTVQRAYQELEREGIVETKRG------KGTFVTED 78 (125)
T ss_pred CCCcHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEecC------eeEEEcCC
Confidence 3358999999999999 999999999999999987753 46665544
No 348
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=70.26 E-value=6.9 Score=32.43 Aligned_cols=37 Identities=14% Similarity=0.196 Sum_probs=33.8
Q ss_pred CCCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 49 GQPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 49 ~~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|..+ +-.+||+.+|++. .-++.-|+.|...|++...+
T Consensus 28 G~~LPsE~eLa~~~gVSR---tpVREAL~~L~~eGlV~~~~ 65 (251)
T PRK09990 28 GQALPSERRLCEKLGFSR---SALREGLTVLRGRGIIETAQ 65 (251)
T ss_pred CCcCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEeC
Confidence 4678 7889999999998 89999999999999999876
No 349
>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=70.13 E-value=3.1 Score=31.84 Aligned_cols=33 Identities=9% Similarity=0.197 Sum_probs=25.0
Q ss_pred cchhhhcCC-CCCCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 41 IPDIINNSG-QPMTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 41 lfd~L~~~~-~p~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
|-+.|.+++ .+.|+.+||+.||+++ ..+.+|+|
T Consensus 35 V~~yLr~~p~~~ati~eV~e~tgVs~---~~I~~~Ir 68 (137)
T TIGR03826 35 VYKFLRKHENRQATVSEIVEETGVSE---KLILKFIR 68 (137)
T ss_pred HHHHHHHCCCCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 445666652 2379999999999999 78877765
No 350
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=70.13 E-value=4.7 Score=35.34 Aligned_cols=36 Identities=14% Similarity=0.150 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.++|=.|||+++|++. ..++|+|......|+++-.-
T Consensus 25 ~gltQ~eIA~~LgiSR---~~v~rlL~~Ar~~GiV~I~i 60 (321)
T COG2390 25 EGLTQSEIAERLGISR---ATVSRLLAKAREEGIVKISI 60 (321)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCeEEEEe
Confidence 6899999999999999 99999999999999998653
No 351
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=69.58 E-value=5.8 Score=28.65 Aligned_cols=36 Identities=11% Similarity=0.130 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.-+|..++|+.+|+++ +.+.+-+..|+..|++..++
T Consensus 53 d~Is~sq~~e~tg~~~---~~V~~al~~Li~~~vI~~~g 88 (100)
T PF04492_consen 53 DRISNSQIAEMTGLSR---DHVSKALNELIRRGVIIRDG 88 (100)
T ss_pred ceeeHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEeCC
Confidence 5699999999999999 99999999999999998774
No 352
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=69.39 E-value=4.4 Score=26.69 Aligned_cols=27 Identities=33% Similarity=0.391 Sum_probs=22.5
Q ss_pred CCCHHHHHHHcCCCCCCcccHHHHHHHHHh
Q 040620 51 PMTLTQIIVALNVHPNKTRCTQILVCLLAH 80 (214)
Q Consensus 51 p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~ 80 (214)
+.|+++||+.+|+++ +.+.++++....
T Consensus 1 ~~~~~~la~~~~~s~---~~l~~~f~~~~~ 27 (84)
T smart00342 1 PLTLEDLAEALGMSP---RHLQRLFKKETG 27 (84)
T ss_pred CCCHHHHHHHhCCCH---HHHHHHHHHHhC
Confidence 479999999999999 888888775543
No 353
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=69.36 E-value=6.6 Score=31.99 Aligned_cols=36 Identities=19% Similarity=0.182 Sum_probs=33.0
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
-+.|-++||+.+|+++ +.|.|.|.-|...|++....
T Consensus 168 ~~~t~~~lA~~lG~sr---etvsR~L~~L~~~G~I~~~~ 203 (226)
T PRK10402 168 YHEKHTQAAEYLGVSY---RHLLYVLAQFIQDGYLKKSK 203 (226)
T ss_pred ccchHHHHHHHHCCcH---HHHHHHHHHHHHCCCEEeeC
Confidence 3568899999999999 99999999999999999874
No 354
>PF11312 DUF3115: Protein of unknown function (DUF3115); InterPro: IPR021463 This eukaryotic family of proteins has no known function.
Probab=69.25 E-value=6.9 Score=34.14 Aligned_cols=22 Identities=32% Similarity=0.489 Sum_probs=18.2
Q ss_pred CCcEEeecCCchHHHHHHHHHC
Q 040620 181 LKPLVDVGGSTGTMARAIATAF 202 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~ 202 (214)
..+||.||||.|.=..+++..+
T Consensus 87 ~~~VlCIGGGAGAElVAlAa~~ 108 (315)
T PF11312_consen 87 SLRVLCIGGGAGAELVALAAAF 108 (315)
T ss_pred CceEEEECCChHHHHHHHHHHH
Confidence 4699999999998777777666
No 355
>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=69.14 E-value=5.8 Score=34.93 Aligned_cols=42 Identities=17% Similarity=0.273 Sum_probs=36.8
Q ss_pred hhhhcCCCCCCHHHHHHH--cCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 43 DIINNSGQPMTLTQIIVA--LNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 43 d~L~~~~~p~t~~eLA~~--~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+++... +|+++++||+. +++++ .-+|+-|..|...|++.+.-
T Consensus 14 ~~l~~~-~pv~s~~l~~~~~~~vS~---aTiR~d~~~Le~~G~l~~~h 57 (337)
T TIGR00331 14 EYIKTG-QPVGSKTLLEKYNLGLSS---ATIRNDMADLEDLGFIEKPH 57 (337)
T ss_pred HHHhcC-CCcCHHHHHhhcCCCCCh---HHHHHHHHHHHHCCCccCCC
Confidence 355554 99999999999 99999 99999999999999998753
No 356
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=68.97 E-value=7.3 Score=32.42 Aligned_cols=37 Identities=16% Similarity=0.275 Sum_probs=33.3
Q ss_pred CCCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 49 GQPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 49 ~~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|..+ |-.+||+.+|++. .-++.-|+.|.+.|++...+
T Consensus 30 G~~LpsE~eLa~~~gVSR---tpVREAL~~L~~eGlV~~~~ 67 (257)
T PRK10225 30 GERLPPEREIAEMLDVTR---TVVREALIMLEIKGLVEVRR 67 (257)
T ss_pred CCcCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEec
Confidence 3677 6889999999998 89999999999999999775
No 357
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=68.94 E-value=5.2 Score=28.11 Aligned_cols=41 Identities=10% Similarity=0.122 Sum_probs=34.7
Q ss_pred hhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 44 IINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 44 ~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.++.. .-+|+..||+++++.- ...++.||.|...|++....
T Consensus 35 EV~~~-K~ITps~lserlkI~~---SlAr~~Lr~L~~kG~Ik~V~ 75 (86)
T PRK09334 35 EVKKE-KIVTPYTLASKYGIKI---SVAKKVLRELEKRGVLVLYS 75 (86)
T ss_pred HhccC-cEEcHHHHHHHhcchH---HHHHHHHHHHHHCCCEEEEe
Confidence 34443 6799999999999988 89999999999999997653
No 358
>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=68.83 E-value=6.6 Score=33.64 Aligned_cols=34 Identities=12% Similarity=0.051 Sum_probs=26.8
Q ss_pred CCCCcEEeecCCchHHHHHHHHH-------CCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATA-------FPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~-------~P~l~~~v~Dl 212 (214)
....+|+|-.||+|.++.++.+. .+..++.++|.
T Consensus 45 ~~~~~VlDPacGsG~fL~~~~~~i~~~~~~~~~~~i~G~ei 85 (311)
T PF02384_consen 45 KKGDSVLDPACGSGGFLVAAMEYIKEKRNKIKEINIYGIEI 85 (311)
T ss_dssp -TTEEEEETT-TTSHHHHHHHHHHHTCHHHHCCEEEEEEES
T ss_pred cccceeechhhhHHHHHHHHHHhhcccccccccceeEeecC
Confidence 34568999999999999998874 57888888875
No 359
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=68.73 E-value=6.6 Score=37.70 Aligned_cols=49 Identities=8% Similarity=0.101 Sum_probs=40.5
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
...|.++||+.+|+++ ..|+|-|......|++++.+.. .+ ++.|...+.
T Consensus 615 ~twt~eelse~l~ip~---~~lrrrL~fWi~~GvL~e~~~~--s~-tgt~T~iEs 663 (765)
T KOG2165|consen 615 NTWTLEELSESLGIPV---PALRRRLSFWIQKGVLREEPII--SD-TGTLTVIES 663 (765)
T ss_pred ccccHHHHHHHhCCCH---HHHHHHHHHHHHcCeeecCCCC--CC-Cceeeeccc
Confidence 5699999999999999 9999999999999999998632 11 456666554
No 360
>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=68.65 E-value=6.3 Score=24.69 Aligned_cols=42 Identities=12% Similarity=0.207 Sum_probs=36.7
Q ss_pred hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+++..+ +++|+.++-+.+|++. .++-.+|.++=..|+....+
T Consensus 3 ~~~~~~-~~itv~~~rd~lg~sR---K~ai~lLE~lD~~g~T~R~g 44 (50)
T PF09107_consen 3 ELLQKN-GEITVAEFRDLLGLSR---KYAIPLLEYLDREGITRRVG 44 (50)
T ss_dssp HHHHTT-SSBEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEET
T ss_pred HHHhcC-CcCcHHHHHHHHCccH---HHHHHHHHHHhccCCEEEeC
Confidence 455555 8999999999999998 99999999999999999886
No 361
>PF13551 HTH_29: Winged helix-turn helix
Probab=68.37 E-value=4.3 Score=28.82 Aligned_cols=28 Identities=18% Similarity=0.223 Sum_probs=26.5
Q ss_pred CHHHHHHHcCCCCCCcccHHHHHHHHHhCCc
Q 040620 53 TLTQIIVALNVHPNKTRCTQILVCLLAHSGF 83 (214)
Q Consensus 53 t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~ 83 (214)
|+.++|+.+|+++ +.+++|++.....|+
T Consensus 14 ~~~~ia~~lg~s~---~Tv~r~~~~~~~~G~ 41 (112)
T PF13551_consen 14 TIAEIARRLGISR---RTVYRWLKRYREGGI 41 (112)
T ss_pred cHHHHHHHHCcCH---HHHHHHHHHHHcccH
Confidence 7999999999999 999999999999994
No 362
>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=68.02 E-value=4.4 Score=26.94 Aligned_cols=41 Identities=10% Similarity=0.156 Sum_probs=30.2
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCcee
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFV 85 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~ 85 (214)
|.++|.+. +++|+.+|++.++++. ..+..-+.-|+.-+=+.
T Consensus 13 Vw~~L~~~-~~~s~~el~k~~~l~~---~~~~~AiGWLarE~KI~ 53 (65)
T PF10771_consen 13 VWQLLNEN-GEWSVSELKKATGLSD---KEVYLAIGWLARENKIE 53 (65)
T ss_dssp HHHHHCCS-SSEEHHHHHHHCT-SC---HHHHHHHHHHHCTTSEE
T ss_pred HHHHHhhC-CCcCHHHHHHHhCcCH---HHHHHHHHHHhccCcee
Confidence 67888886 8999999999999988 66655555555554443
No 363
>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=67.88 E-value=2.3 Score=30.09 Aligned_cols=54 Identities=13% Similarity=0.132 Sum_probs=32.7
Q ss_pred hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee---ecCCCCCCccceeeCCCC
Q 040620 43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ---QKDGKNEQEEESILLPPH 104 (214)
Q Consensus 43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~---~~~~~~~~~~~~y~~t~~ 104 (214)
-+++. +..++..|-+.||++. |.++..+.+|..+|+-++ ++..++ .|.|+++.=
T Consensus 15 ~li~~--~~~nvp~L~~~TGmPr---RT~Qd~i~aL~~~~I~~~Fvq~G~R~~---~GyY~i~~W 71 (90)
T PF09904_consen 15 YLIDS--GERNVPALMEATGMPR---RTIQDTIKALPELGIECEFVQDGERNN---AGYYRISDW 71 (90)
T ss_dssp HHHHH--S-B-HHHHHHHH---H---HHHHHHHHGGGGGT-EEEEE--TTS-S-----EEEEEE-
T ss_pred HHHhc--CCccHHHHHHHhCCCH---hHHHHHHHHhhcCCeEEEEEecCccCC---CCcEEeeec
Confidence 34555 4449999999999999 999999999999999876 221111 456766544
No 364
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=67.88 E-value=4.4 Score=24.68 Aligned_cols=26 Identities=12% Similarity=0.189 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLL 78 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L 78 (214)
.+++..+||+.+++++ ..+++.++.+
T Consensus 17 ~g~s~~eia~~l~is~---~tv~~~~~~~ 42 (58)
T smart00421 17 EGLTNKEIAERLGISE---KTVKTHLSNI 42 (58)
T ss_pred cCCCHHHHHHHHCCCH---HHHHHHHHHH
Confidence 4589999999999998 7777776654
No 365
>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=67.81 E-value=8.2 Score=31.64 Aligned_cols=36 Identities=14% Similarity=0.186 Sum_probs=33.2
Q ss_pred CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
..+ |-.+||+.+|++. .-++.-|+.|...|+++..+
T Consensus 28 ~~LpsE~~La~~lgVSR---tpVREAL~~Le~eGlV~~~~ 64 (235)
T TIGR02812 28 SILPAERELSELIGVTR---TTLREVLQRLARDGWLTIQH 64 (235)
T ss_pred CcCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEeC
Confidence 668 7899999999998 89999999999999999775
No 366
>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]
Probab=67.70 E-value=14 Score=31.25 Aligned_cols=54 Identities=15% Similarity=0.260 Sum_probs=38.5
Q ss_pred HHhhhhhhhh----HHHHHhhcccccCCCCcEEeecCCchHHHHHHHH-HCCCCeEEEecC
Q 040620 157 EAMITDFELI----ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIAT-AFPDTKCTVFAC 212 (214)
Q Consensus 157 ~am~~~~~~~----~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~-~~P~l~~~v~Dl 212 (214)
..|...++.. +..++.... .....+|+|.|-|+|.++..|+. -.|.=+++.+|.
T Consensus 69 ~~~~R~tQiIyPKD~~~I~~~~g--i~pg~rVlEAGtGSG~lt~~La~~vg~~G~v~tyE~ 127 (256)
T COG2519 69 LSMKRRTQIIYPKDAGYIVARLG--ISPGSRVLEAGTGSGALTAYLARAVGPEGHVTTYEI 127 (256)
T ss_pred HhCcCCCceecCCCHHHHHHHcC--CCCCCEEEEcccCchHHHHHHHHhhCCCceEEEEEe
Confidence 3465544331 334444444 66789999999999999999997 667778887774
No 367
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=67.66 E-value=7.8 Score=25.05 Aligned_cols=45 Identities=11% Similarity=0.099 Sum_probs=34.0
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
.+++.+++.++.|.+- .......+..+...|+++.+ ++++++|+.
T Consensus 19 ~Gi~~~~~~~~~g~~~--~~~~~~~l~~l~~~Gll~~~--------~~~l~lT~~ 63 (66)
T PF06969_consen 19 EGIDLSEFEQRFGIDF--AEEFQKELEELQEDGLLEID--------GGRLRLTEK 63 (66)
T ss_dssp SEEEHHHHHHHTT--T--HHH-HHHHHHHHHTTSEEE---------SSEEEE-TT
T ss_pred CCcCHHHHHHHHCcCH--HHHHHHHHHHHHHCCCEEEe--------CCEEEECcc
Confidence 5789999999999875 13447789999999999998 489999987
No 368
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=66.74 E-value=4.2 Score=34.14 Aligned_cols=39 Identities=10% Similarity=0.062 Sum_probs=34.2
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCC
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSG 82 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g 82 (214)
.|.++|... +.+++.+||+.+++++ .-+||=|+.|...+
T Consensus 11 ~I~~~l~~~-~~v~v~eLa~~~~VS~---~TIRRDL~~Le~~~ 49 (252)
T PRK10681 11 QLLQALKRS-DKLHLKDAAALLGVSE---MTIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHc-CCCcHHHHHHHhCCCH---HHHHHHHHHhhcCe
Confidence 367788887 8999999999999999 99999999998654
No 369
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=66.65 E-value=8.9 Score=31.87 Aligned_cols=36 Identities=14% Similarity=0.256 Sum_probs=32.6
Q ss_pred CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
..+ +-.+||+++|++. .-++.-|+.|.+.|++...+
T Consensus 24 ~~LpsE~eLae~~gVSR---tpVREAL~~Le~~GlV~~~~ 60 (253)
T PRK10421 24 MKLPAERQLAMQLGVSR---NSLREALAKLVSEGVLLSRR 60 (253)
T ss_pred CcCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEeC
Confidence 567 6789999999998 89999999999999998765
No 370
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=66.58 E-value=15 Score=23.98 Aligned_cols=34 Identities=9% Similarity=0.126 Sum_probs=27.0
Q ss_pred cchhhhcCCCCCCHHHHHHHcCC-CCCCcccHHHHHHHHH
Q 040620 41 IPDIINNSGQPMTLTQIIVALNV-HPNKTRCTQILVCLLA 79 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~-~~~~~~~l~rlLr~L~ 79 (214)
+.+.|.. +++++++||..+|+ ++ ..+.+..+...
T Consensus 42 a~~~l~~--~~~~~~~ia~~~g~~s~---~~f~r~Fk~~~ 76 (84)
T smart00342 42 ARRLLRD--TDLSVTEIALRVGFSSQ---SYFSRAFKKLF 76 (84)
T ss_pred HHHHHHc--CCCCHHHHHHHhCCCCh---HHHHHHHHHHH
Confidence 5667765 57999999999999 88 88888765543
No 371
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=66.57 E-value=0.88 Score=30.30 Aligned_cols=48 Identities=21% Similarity=0.231 Sum_probs=35.3
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcC--CCCCCcccHHHHHHHHHhCCceeeec
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALN--VHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g--~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.+-.|.+.|... ++.++..||...| ++. ..+++.|..|...|.+...+
T Consensus 5 ~ee~Il~~L~~~-g~~~a~~ia~~~~L~~~k---k~VN~~LY~L~k~g~v~k~~ 54 (66)
T PF02295_consen 5 LEEKILDFLKEL-GGSTATAIAKALGLSVPK---KEVNRVLYRLEKQGKVCKEG 54 (66)
T ss_dssp HHHHHHHHHHHH-TSSEEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEEC
T ss_pred HHHHHHHHHHhc-CCccHHHHHHHhCcchhH---HHHHHHHHHHHHCCCEeeCC
Confidence 345577778876 4666666666555 446 89999999999999999874
No 372
>PLN02589 caffeoyl-CoA O-methyltransferase
Probab=66.21 E-value=8.7 Score=32.32 Aligned_cols=36 Identities=28% Similarity=0.261 Sum_probs=30.1
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH 213 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp 213 (214)
..+.+++|+||.+.|..++.+++..| +.+++-+|..
T Consensus 77 ~~~ak~iLEiGT~~GySal~la~al~~~g~v~tiE~~ 113 (247)
T PLN02589 77 LINAKNTMEIGVYTGYSLLATALALPEDGKILAMDIN 113 (247)
T ss_pred HhCCCEEEEEeChhhHHHHHHHhhCCCCCEEEEEeCC
Confidence 34578999999999999999999875 6788888764
No 373
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=66.10 E-value=9.4 Score=31.33 Aligned_cols=36 Identities=14% Similarity=0.186 Sum_probs=32.9
Q ss_pred CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
..+ |-.+||+++|++. .-+++-|+.|...|++...+
T Consensus 29 ~~LPsE~eLae~~gVSR---t~VReAL~~L~~eGlv~~~~ 65 (239)
T PRK04984 29 SILPAERELSELIGVTR---TTLREVLQRLARDGWLTIQH 65 (239)
T ss_pred CcCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEeC
Confidence 567 6889999999998 89999999999999999775
No 374
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=65.92 E-value=2.2 Score=27.33 Aligned_cols=29 Identities=3% Similarity=0.142 Sum_probs=20.0
Q ss_pred hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
.++.+ ..+|..+||+.+|+++ ..+.+++.
T Consensus 4 ~~m~~--~~it~~~La~~~gis~---~tl~~~~~ 32 (63)
T PF13443_consen 4 ELMAE--RGITQKDLARKTGISR---STLSRILN 32 (63)
T ss_dssp HHHHH--TT--HHHHHHHHT--H---HHHHHHHT
T ss_pred HHHHH--cCCCHHHHHHHHCcCH---HHHHHHHh
Confidence 45666 6789999999999998 88888764
No 375
>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=65.85 E-value=4.7 Score=36.98 Aligned_cols=23 Identities=26% Similarity=0.250 Sum_probs=17.0
Q ss_pred CCCcEEeecCCchHHHHHHHHHC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAF 202 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~ 202 (214)
+.+.|+|||+|+|-++...+++.
T Consensus 186 ~~~vVldVGAGrGpL~~~al~A~ 208 (448)
T PF05185_consen 186 KDKVVLDVGAGRGPLSMFALQAG 208 (448)
T ss_dssp TT-EEEEES-TTSHHHHHHHHTT
T ss_pred cceEEEEeCCCccHHHHHHHHHH
Confidence 35789999999999987766653
No 376
>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=65.69 E-value=6.2 Score=25.23 Aligned_cols=47 Identities=15% Similarity=0.236 Sum_probs=32.4
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeC
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILL 101 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~ 101 (214)
+.|.+-+. .-+|+..+|+.+|+++ +...++++ .+|. .|-.. .++|+.
T Consensus 4 Lidll~~~-P~Vsa~mva~~L~vT~---~~A~~li~---eLg~-rEiTG------r~R~Ra 50 (54)
T PF11972_consen 4 LIDLLLSR-PLVSAPMVAKELGVTP---QAAQRLIA---ELGL-REITG------RGRYRA 50 (54)
T ss_pred HHHHHHhC-ccccHHHHHHHhCCCH---HHHHHHHH---Hhhc-eeecC------Ccccch
Confidence 45666663 4489999999999999 88877764 4555 44332 467764
No 377
>PRK13239 alkylmercury lyase; Provisional
Probab=65.56 E-value=4.2 Score=33.35 Aligned_cols=43 Identities=12% Similarity=0.191 Sum_probs=32.3
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.-|+..|++ |.|.|+++||+.+|.+. ..+++.|+.+ .-...++
T Consensus 25 ~~llr~la~-G~pvt~~~lA~~~~~~~---~~v~~~L~~l---~~~~~d~ 67 (206)
T PRK13239 25 VPLLRLLAK-GRPVSVTTLAAALGWPV---EEVEAVLEAM---PDTEYDE 67 (206)
T ss_pred HHHHHHHHc-CCCCCHHHHHHHhCCCH---HHHHHHHHhC---CCeEECC
Confidence 345677885 69999999999999998 7777776665 4445554
No 378
>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=65.53 E-value=4.8 Score=24.63 Aligned_cols=25 Identities=16% Similarity=0.216 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCL 77 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~ 77 (214)
.++|.+|||+.+|++. ..++++.+-
T Consensus 19 ~~~t~~eIa~~lg~s~---~~V~~~~~~ 43 (50)
T PF04545_consen 19 EGLTLEEIAERLGISR---STVRRILKR 43 (50)
T ss_dssp ST-SHHHHHHHHTSCH---HHHHHHHHH
T ss_pred CCCCHHHHHHHHCCcH---HHHHHHHHH
Confidence 6799999999999998 888777654
No 379
>PLN02668 indole-3-acetate carboxyl methyltransferase
Probab=65.38 E-value=12 Score=33.71 Aligned_cols=35 Identities=17% Similarity=0.094 Sum_probs=24.7
Q ss_pred CCCcEEeecCCchHHHHH--------HHHH-------CCCCeEEEecCCC
Q 040620 180 GLKPLVDVGGSTGTMARA--------IATA-------FPDTKCTVFACHL 214 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~--------l~~~-------~P~l~~~v~Dlp~ 214 (214)
+.-+|+|+|||+|..+.. +.++ -|.+++..=|+|.
T Consensus 63 ~~~~iaDlGcs~G~ntl~~vs~iI~~i~~~~~~~~~~~pe~qv~~nDLP~ 112 (386)
T PLN02668 63 VPFTAVDLGCSSGSNTIHIIDVIVKHMSKRYESAGLDPPEFSAFFSDLPS 112 (386)
T ss_pred cceeEEEecCCCCccHHHHHHHHHHHHHHHhhhcCCCCCcceEEecCCCC
Confidence 356899999999965542 3333 3567888888884
No 380
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=65.08 E-value=6 Score=28.25 Aligned_cols=33 Identities=12% Similarity=0.095 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCcee
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFV 85 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~ 85 (214)
.++|+++||+.+++++ +.+.|+.+......+-.
T Consensus 20 ~~~~~~~lA~~~~~S~---~~l~r~f~~~~g~s~~~ 52 (107)
T PRK10219 20 QPLNIDVVAKKSGYSK---WYLQRMFRTVTHQTLGD 52 (107)
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHHHHHHCcCHHH
Confidence 6799999999999999 99999877665444443
No 381
>PRK03837 transcriptional regulator NanR; Provisional
Probab=64.98 E-value=11 Score=30.95 Aligned_cols=37 Identities=11% Similarity=0.206 Sum_probs=33.6
Q ss_pred CCCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 49 GQPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 49 ~~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|..+ +-.+||+++|++. .-++.-|+.|...|+++..+
T Consensus 34 G~~Lp~E~~Lae~~gVSR---t~VREAL~~L~~eGlv~~~~ 71 (241)
T PRK03837 34 GDQLPSERELMAFFGVGR---PAVREALQALKRKGLVQISH 71 (241)
T ss_pred CCCCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEec
Confidence 3567 8899999999998 89999999999999999875
No 382
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=64.94 E-value=7.9 Score=31.13 Aligned_cols=44 Identities=14% Similarity=0.107 Sum_probs=37.9
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+.+-|..+ +..|+.+||.++|++. ..++|.|--|...|.+...+
T Consensus 18 ~~~~l~~~-~~~~a~~i~~~l~~~k---~~vNr~LY~l~~~~~v~~~~ 61 (183)
T PHA03103 18 EVKNLGLG-EGITAIEISRKLNIEK---SEVNKQLYKLQREGMVYMSD 61 (183)
T ss_pred HHHHhccC-CCccHHHHHHHhCCCH---HHHHHHHHHHHhcCceecCC
Confidence 34556664 8999999999999998 89999999999999998764
No 383
>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=64.93 E-value=4.6 Score=27.08 Aligned_cols=29 Identities=14% Similarity=0.028 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHS 81 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~ 81 (214)
..-|.+|||+.+|+++ ..++.++......
T Consensus 19 r~Pt~eEiA~~lgis~---~~v~~~l~~~~~~ 47 (78)
T PF04539_consen 19 REPTDEEIAEELGISV---EEVRELLQASRRP 47 (78)
T ss_dssp S--BHHHHHHHHTS-H---HHHHHHHHHHSCC
T ss_pred CCCCHHHHHHHHcccH---HHHHHHHHhCCCC
Confidence 5679999999999999 9999998865443
No 384
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=64.75 E-value=3.9 Score=31.38 Aligned_cols=30 Identities=10% Similarity=0.163 Sum_probs=19.9
Q ss_pred hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHH
Q 040620 43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILV 75 (214)
Q Consensus 43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlL 75 (214)
+++..+++-.|-++||+.+|+++ ..|++|.
T Consensus 26 e~~~~~~~r~T~~eiAee~Gis~---~tLYrWr 55 (142)
T PF13022_consen 26 ELMPENGERRTQAEIAEEVGISR---STLYRWR 55 (142)
T ss_dssp HHS------S-HHHHHHHHTS-H---HHHHHHH
T ss_pred HHhhhccccchHHHHHHHhCCCH---HHHHHHH
Confidence 55665557799999999999999 9999995
No 385
>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=64.64 E-value=3.6 Score=25.28 Aligned_cols=20 Identities=15% Similarity=0.169 Sum_probs=14.4
Q ss_pred CHHHHHHHcCCCCCCcccHHHHH
Q 040620 53 TLTQIIVALNVHPNKTRCTQILV 75 (214)
Q Consensus 53 t~~eLA~~~g~~~~~~~~l~rlL 75 (214)
|+.+||+.+|+++ .-+.|.|
T Consensus 1 Ti~dIA~~agvS~---~TVSr~l 20 (46)
T PF00356_consen 1 TIKDIAREAGVSK---STVSRVL 20 (46)
T ss_dssp CHHHHHHHHTSSH---HHHHHHH
T ss_pred CHHHHHHHHCcCH---HHHHHHH
Confidence 6788888888876 5555544
No 386
>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=64.39 E-value=8 Score=34.52 Aligned_cols=44 Identities=18% Similarity=0.271 Sum_probs=34.1
Q ss_pred HHHHhhcccccCCCCcEEeecCCchH----HHHHHHHHC---CCCeEEEecCC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGT----MARAIATAF---PDTKCTVFACH 213 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~----~~~~l~~~~---P~l~~~v~Dlp 213 (214)
+.|++.+. -...-.|||+|-|.|. +..+|+++. |.+|+|+++.|
T Consensus 100 qaIleA~~--g~~~vHIID~~i~~G~QW~~LiqaLa~R~~gpp~LrIT~i~~~ 150 (374)
T PF03514_consen 100 QAILEAFE--GERRVHIIDFGIGFGVQWPSLIQALASRPGGPPSLRITGIGPP 150 (374)
T ss_pred HHHHHHhc--cCcceEEEeccCCcchHHHHHHHHHhcCCCCCCeEEEEeccCC
Confidence 55777776 3456799999999987 566777664 88999999986
No 387
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=64.21 E-value=11 Score=31.38 Aligned_cols=37 Identities=19% Similarity=0.241 Sum_probs=33.0
Q ss_pred CCCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 49 GQPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 49 ~~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|..+ +-.+||+.+|++. .-++.-|+.|...|+++..+
T Consensus 29 G~~LpsE~eLae~~gVSR---tpVREAL~~L~~eGlV~~~~ 66 (253)
T PRK11523 29 GDKLPAERFIADEKNVSR---TVVREAIIMLEVEGYVEVRK 66 (253)
T ss_pred CCCCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEec
Confidence 3677 4789999999998 89999999999999998775
No 388
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=63.90 E-value=5.9 Score=24.19 Aligned_cols=26 Identities=12% Similarity=0.091 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLL 78 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L 78 (214)
.++|..+||+.+++++ +.+++.++.+
T Consensus 14 ~~~s~~eia~~l~~s~---~tv~~~~~~~ 39 (57)
T cd06170 14 EGKTNKEIADILGISE---KTVKTHLRNI 39 (57)
T ss_pred cCCCHHHHHHHHCCCH---HHHHHHHHHH
Confidence 4689999999999998 8777776653
No 389
>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=63.68 E-value=9.8 Score=27.77 Aligned_cols=36 Identities=11% Similarity=0.113 Sum_probs=33.0
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.-+|+..||+++++.- ...++.||.|...|++....
T Consensus 58 K~ITp~~lserlkI~~---SlAr~~Lr~L~~kG~Ik~V~ 93 (105)
T PF03297_consen 58 KLITPSVLSERLKING---SLARKALRELESKGLIKPVS 93 (105)
T ss_dssp SCECHHHHHHHHCCSC---HHHHHHHHHHHHCCSSEEEE
T ss_pred cEeeHHHHHHhHhhHH---HHHHHHHHHHHHCCCEEEEe
Confidence 5699999999999998 89999999999999998764
No 390
>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=63.40 E-value=16 Score=28.96 Aligned_cols=43 Identities=12% Similarity=-0.047 Sum_probs=29.1
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCe---------EEEecC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTK---------CTVFAC 212 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~---------~~v~Dl 212 (214)
..++.... +.+...|+|-=||+|+++++-+...++.. +++.|.
T Consensus 18 ~~ll~la~--~~~~~~vlDP~CGsGtiliEaa~~~~~~~~~~~~~~~~~~g~Di 69 (179)
T PF01170_consen 18 AALLNLAG--WRPGDVVLDPFCGSGTILIEAALMGANIPPLNDINELKIIGSDI 69 (179)
T ss_dssp HHHHHHTT----TTS-EEETT-TTSHHHHHHHHHHTTTSTTTH-CH--EEEEES
T ss_pred HHHHHHhC--CCCCCEEeecCCCCCHHHHHHHHHhhCcccccccccccEEecCC
Confidence 33444444 45667999999999999998888777766 666664
No 391
>KOG1500 consensus Protein arginine N-methyltransferase CARM1 [Posttranslational modification, protein turnover, chaperones; Transcription]
Probab=63.40 E-value=6.3 Score=34.99 Aligned_cols=21 Identities=33% Similarity=0.409 Sum_probs=17.2
Q ss_pred CCcEEeecCCchHHHHHHHHH
Q 040620 181 LKPLVDVGGSTGTMARAIATA 201 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~ 201 (214)
.+-|||||+|+|.++.--+++
T Consensus 178 ~kiVlDVGaGSGILS~FAaqA 198 (517)
T KOG1500|consen 178 DKIVLDVGAGSGILSFFAAQA 198 (517)
T ss_pred CcEEEEecCCccHHHHHHHHh
Confidence 578999999999988755554
No 392
>PF07091 FmrO: Ribosomal RNA methyltransferase (FmrO); PDB: 3LCU_A 3LCV_B 3FRH_A 3FRI_A 3B89_A 3FZG_A.
Probab=63.16 E-value=5.6 Score=33.58 Aligned_cols=34 Identities=12% Similarity=0.215 Sum_probs=25.9
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
....+|+|||||-=-++.-.....|++..+..|+
T Consensus 104 ~~p~sVlDigCGlNPlalp~~~~~~~a~Y~a~DI 137 (251)
T PF07091_consen 104 PPPDSVLDIGCGLNPLALPWMPEAPGATYIAYDI 137 (251)
T ss_dssp ---SEEEEET-TTCHHHHHTTTSSTT-EEEEEES
T ss_pred CCCchhhhhhccCCceehhhcccCCCcEEEEEeC
Confidence 3478999999999888888888888889888886
No 393
>COG0293 FtsJ 23S rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=62.47 E-value=19 Score=29.51 Aligned_cols=46 Identities=20% Similarity=0.144 Sum_probs=34.6
Q ss_pred HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecCC
Q 040620 167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFACH 213 (214)
Q Consensus 167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dlp 213 (214)
...+.+.+. -+.+...|+|+|.-+|..++-++++-.. .+++.+|+-
T Consensus 33 L~el~~k~~-i~~~~~~ViDLGAAPGgWsQva~~~~~~~~~ivavDi~ 79 (205)
T COG0293 33 LLELNEKFK-LFKPGMVVVDLGAAPGGWSQVAAKKLGAGGKIVAVDIL 79 (205)
T ss_pred HHHHHHhcC-eecCCCEEEEcCCCCCcHHHHHHHHhCCCCcEEEEECc
Confidence 345566663 4677899999999999999988776554 457777763
No 394
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=61.92 E-value=5.5 Score=24.44 Aligned_cols=32 Identities=9% Similarity=0.098 Sum_probs=25.4
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHH
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCL 77 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~ 77 (214)
-|...+.. ..|..+||+.+|++. ..+.|+++.
T Consensus 19 ~i~~~~~~---~~s~~~vA~~~~vs~---~TV~ri~~~ 50 (52)
T PF13542_consen 19 YILKLLRE---SRSFKDVARELGVSW---STVRRIFDR 50 (52)
T ss_pred HHHHHHhh---cCCHHHHHHHHCCCH---HHHHHHHHh
Confidence 34555664 379999999999999 888888764
No 395
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=61.81 E-value=5.5 Score=24.64 Aligned_cols=24 Identities=17% Similarity=0.173 Sum_probs=17.1
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
.++|.+|||+.+|+++ ..++.++.
T Consensus 25 ~g~s~~eIa~~l~~s~---~~v~~~l~ 48 (54)
T PF08281_consen 25 QGMSYAEIAEILGISE---STVKRRLR 48 (54)
T ss_dssp S---HHHHHHHCTS-H---HHHHHHHH
T ss_pred HCcCHHHHHHHHCcCH---HHHHHHHH
Confidence 5799999999999998 87777664
No 396
>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=61.69 E-value=3.8 Score=27.78 Aligned_cols=30 Identities=20% Similarity=0.253 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSG 82 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g 82 (214)
..+|+.+||+.+++++ ..+.|+++.|--.|
T Consensus 33 ~~~si~elA~~~~vS~---sti~Rf~kkLG~~g 62 (77)
T PF01418_consen 33 AFMSISELAEKAGVSP---STIVRFCKKLGFSG 62 (77)
T ss_dssp CT--HHHHHHHCTS-H---HHHHHHHHHCTTTC
T ss_pred HHccHHHHHHHcCCCH---HHHHHHHHHhCCCC
Confidence 4689999999999999 66666655543333
No 397
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=61.67 E-value=8.4 Score=24.86 Aligned_cols=25 Identities=16% Similarity=0.020 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCL 77 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~ 77 (214)
.+.++.+||+.+|+++ +.++.|.+.
T Consensus 12 ~G~~~~eIA~~Lg~~~---~TV~~W~~r 36 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPR---STVYSWKDR 36 (58)
T ss_pred cCCCHHHHHHHHCCCh---HHHHHHHHh
Confidence 4689999999999998 889888643
No 398
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=61.62 E-value=4.3 Score=25.12 Aligned_cols=24 Identities=4% Similarity=0.087 Sum_probs=19.1
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
..+|..|+|+++|+++ ..+.++.+
T Consensus 8 ~gls~~~la~~~gis~---~~i~~~~~ 31 (55)
T PF01381_consen 8 KGLSQKELAEKLGISR---STISRIEN 31 (55)
T ss_dssp TTS-HHHHHHHHTS-H---HHHHHHHT
T ss_pred cCCCHHHHHHHhCCCc---chhHHHhc
Confidence 5799999999999999 88888854
No 399
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=61.51 E-value=9.4 Score=33.29 Aligned_cols=35 Identities=20% Similarity=0.078 Sum_probs=32.5
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
..+|=+|||+++|++. ..+.|+|......|+++-.
T Consensus 28 ~g~tQ~eIA~~lgiSR---~~VsRlL~~Ar~~GiV~I~ 62 (318)
T PRK15418 28 DGLTQSEIGERLGLTR---LKVSRLLEKGRQSGIIRVQ 62 (318)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHHHHHHHcCcEEEE
Confidence 5799999999999998 8999999999999999854
No 400
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=61.49 E-value=6.1 Score=25.68 Aligned_cols=28 Identities=14% Similarity=0.179 Sum_probs=22.5
Q ss_pred CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620 52 MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ 86 (214)
Q Consensus 52 ~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~ 86 (214)
+|+.|+|+.+|+++ +.++.|. ..|++..
T Consensus 1 ~s~~eva~~~gvs~---~tlr~~~----~~gli~~ 28 (70)
T smart00422 1 YTIGEVAKLAGVSV---RTLRYYE----RIGLLPP 28 (70)
T ss_pred CCHHHHHHHHCcCH---HHHHHHH----HCCCCCC
Confidence 47899999999998 7777774 4888763
No 401
>KOG2651 consensus rRNA adenine N-6-methyltransferase [RNA processing and modification]
Probab=61.33 E-value=8.8 Score=34.56 Aligned_cols=31 Identities=23% Similarity=0.514 Sum_probs=23.9
Q ss_pred cCCCCcEEeecCCchHHHHHHHHHCCCCeEEE
Q 040620 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTV 209 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v 209 (214)
|-+..++||||.|.|+++.-+.=.| ++.+..
T Consensus 151 f~gi~~vvD~GaG~G~LSr~lSl~y-~lsV~a 181 (476)
T KOG2651|consen 151 FTGIDQVVDVGAGQGHLSRFLSLGY-GLSVKA 181 (476)
T ss_pred hcCCCeeEEcCCCchHHHHHHhhcc-CceEEE
Confidence 6688999999999999998776555 344433
No 402
>PRK13824 replication initiation protein RepC; Provisional
Probab=60.98 E-value=10 Score=34.27 Aligned_cols=66 Identities=6% Similarity=0.054 Sum_probs=45.3
Q ss_pred HHHHHHHHHhcCcchhhhcCCC---CCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeC
Q 040620 29 KSLSLKRAIQLRIPDIINNSGQ---PMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILL 101 (214)
Q Consensus 29 ~~~~L~~a~~lglfd~L~~~~~---p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~ 101 (214)
...+|.+.+.+-=-+.+..... -.|-.+|+.++ |+++ +.|+|.|+.|+..|++...+. + | ..+|..
T Consensus 57 ~l~vL~aLlsf~p~~~~~~~~~~IVfpSN~~La~r~~Gms~---~tlrRhla~LveaGLI~rrDS--p-N-GKRyar 126 (404)
T PRK13824 57 ALAVLNALLSFYPETELSEEAGLVVFPSNAQLSLRAHGMAG---ATLRRHLAALVEAGLIIRRDS--P-N-GKRYAR 126 (404)
T ss_pred HHHHHHHHHhhCCcccccCCCCceechhHHHHHHHHcCCCH---HHHHHHHHHHHHCCCeEeecC--C-C-Ccccce
Confidence 3445555555533344543212 25779999985 9999 999999999999999998753 1 1 456754
No 403
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=60.20 E-value=11 Score=27.42 Aligned_cols=42 Identities=10% Similarity=0.116 Sum_probs=35.3
Q ss_pred hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+.++.. .-+|+-.||++.|++- ...+++||.|...|++....
T Consensus 52 KEV~~~-r~VTpy~la~r~gI~~---SvAr~vLR~LeeeGvv~lvs 93 (107)
T COG4901 52 KEVPRE-RVVTPYVLASRYGING---SVARIVLRHLEEEGVVQLVS 93 (107)
T ss_pred Hhcccc-eeecHHHHHHHhccch---HHHHHHHHHHHhCCceeeec
Confidence 334433 6799999999999988 88899999999999998765
No 404
>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=60.12 E-value=5.6 Score=27.54 Aligned_cols=30 Identities=17% Similarity=0.104 Sum_probs=24.5
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHH
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILV 75 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlL 75 (214)
|.++|.. +.+|+.+||+.+|++. ..++|.|
T Consensus 11 I~e~l~~--~~~ti~dvA~~~gvS~---~TVsr~L 40 (80)
T TIGR02844 11 IGKYIVE--TKATVRETAKVFGVSK---STVHKDV 40 (80)
T ss_pred HHHHHHH--CCCCHHHHHHHhCCCH---HHHHHHh
Confidence 4566776 7889999999999998 7777754
No 405
>PF13814 Replic_Relax: Replication-relaxation
Probab=59.54 E-value=11 Score=29.57 Aligned_cols=65 Identities=15% Similarity=0.134 Sum_probs=45.5
Q ss_pred hhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCC---CCCCccceeeCCCCCcccccccc
Q 040620 44 IINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDG---KNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 44 ~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~---~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
.|... ..+|.+||++....+....+.+++.|+-|...|++...... ..+..+..|.+|+. +..++
T Consensus 3 ~L~~~-r~lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~----G~~~l 70 (191)
T PF13814_consen 3 LLARH-RFLTTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPA----GARLL 70 (191)
T ss_pred hHHHh-cCcCHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHH----HHHHH
Confidence 45555 78999999999999872113799999999999999876531 00001356777777 65554
No 406
>KOG3191 consensus Predicted N6-DNA-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=59.47 E-value=8.7 Score=31.13 Aligned_cols=32 Identities=13% Similarity=0.264 Sum_probs=23.9
Q ss_pred CCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620 181 LKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC 212 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl 212 (214)
..-.++||||+|..+..|++.. |+.....-|+
T Consensus 44 ~~i~lEIG~GSGvvstfL~~~i~~~~~~latDi 76 (209)
T KOG3191|consen 44 PEICLEIGCGSGVVSTFLASVIGPQALYLATDI 76 (209)
T ss_pred ceeEEEecCCcchHHHHHHHhcCCCceEEEecC
Confidence 5789999999999998887753 5555555444
No 407
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=59.26 E-value=13 Score=25.01 Aligned_cols=54 Identities=15% Similarity=0.259 Sum_probs=44.7
Q ss_pred HHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 31 LSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 31 ~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.++....+..++..|... .+.++.+|+..++++. ..+.+-|..|...|++....
T Consensus 20 ~~l~~~~r~~il~~l~~~-~~~~~~~l~~~~~~~~---~~v~~hL~~L~~~glv~~~~ 73 (110)
T COG0640 20 KALADPTRLEILSLLAEG-GELTVGELAEALGLSQ---STVSHHLKVLREAGLVELRR 73 (110)
T ss_pred HHhCCHHHHHHHHHHHhc-CCccHHHHHHHHCCCh---hHHHHHHHHHHHCCCeEEEe
Confidence 344445667777777763 4789999999999999 99999999999999999865
No 408
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=59.22 E-value=32 Score=29.69 Aligned_cols=49 Identities=12% Similarity=0.165 Sum_probs=39.0
Q ss_pred HHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 25 YNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 25 ~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.+||....+....+ .+..+|+++|+++|++.+ ..++..|-.+|++....
T Consensus 206 ~~YW~~~il~~L~~---------~~~~isi~~is~~T~i~~------~Dii~tL~~l~~l~~~~ 254 (290)
T PLN03238 206 RSYWTRVLLEQLRD---------VKGDVSIKDLSLATGIRG------EDIVSTLQSLNLIKYWK 254 (290)
T ss_pred HHHHHHHHHHHHHh---------cCCCccHHHHHHHhCCCH------HHHHHHHHHCCcEEEEC
Confidence 37887777666632 226899999999999988 67899999999998765
No 409
>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=59.01 E-value=18 Score=26.99 Aligned_cols=49 Identities=16% Similarity=0.236 Sum_probs=41.7
Q ss_pred hhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 45 INNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 45 L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+..+ -|.|.+.||..++.+. ..++.-|..+..+|+++..+ ++.|..+..
T Consensus 46 ~~~~-ipy~~e~LA~~~~~~~---~~V~~Al~~f~k~glIe~~d-------~g~i~i~~~ 94 (119)
T TIGR01714 46 LNEL-APYNAEMLATMFNRNV---GDIRITLQTLESLGLIEKKN-------NGDIFLENW 94 (119)
T ss_pred EcCC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEec-------CCcEEehhH
Confidence 3444 8999999999999998 99999999999999999886 466666665
No 410
>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=58.96 E-value=5.6 Score=32.73 Aligned_cols=44 Identities=14% Similarity=0.201 Sum_probs=35.0
Q ss_pred cchhh-hcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 41 IPDII-NNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 41 lfd~L-~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
|.+.+ ...++++|..+||+.+|.++ ......|+.+...|++..+
T Consensus 179 il~~~~~~~~g~vt~~~l~~~~~ws~---~~a~~~L~~~~~~G~l~~D 223 (223)
T PF04157_consen 179 ILELAEEENGGGVTASELAEKLGWSV---ERAKEALEELEREGLLWRD 223 (223)
T ss_dssp HHHHH--TTTSEEEHHHHHHHHTB-H---HHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHhhcCCCCCHHHHHHHhCCCH---HHHHHHHHHHHhCCCEeeC
Confidence 34444 33348999999999999999 9999999999999998754
No 411
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=58.76 E-value=2.1 Score=26.95 Aligned_cols=31 Identities=13% Similarity=0.242 Sum_probs=20.7
Q ss_pred cchhhhcCC-CCCCHHHHHHHcCCCCCCcccHHHH
Q 040620 41 IPDIINNSG-QPMTLTQIIVALNVHPNKTRCTQIL 74 (214)
Q Consensus 41 lfd~L~~~~-~p~t~~eLA~~~g~~~~~~~~l~rl 74 (214)
++..|...| .-++..+||+.+|++| ..+++=
T Consensus 17 ~L~~l~~~G~~~vSS~~La~~~gi~~---~qVRKD 48 (50)
T PF06971_consen 17 YLEQLKEEGVERVSSQELAEALGITP---AQVRKD 48 (50)
T ss_dssp HHHHHHHTT-SEE-HHHHHHHHTS-H---HHHHHH
T ss_pred HHHHHHHcCCeeECHHHHHHHHCCCH---HHhccc
Confidence 344555543 5689999999999998 777653
No 412
>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=58.68 E-value=26 Score=29.53 Aligned_cols=43 Identities=14% Similarity=0.288 Sum_probs=29.1
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHH-HCCCCeEEEecC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIAT-AFPDTKCTVFAC 212 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~-~~P~l~~~v~Dl 212 (214)
..++...+ .....+||+-|-|+|.++..|++ -.|+=++.-+|.
T Consensus 30 ~~I~~~l~--i~pG~~VlEaGtGSG~lt~~l~r~v~p~G~v~t~E~ 73 (247)
T PF08704_consen 30 SYILMRLD--IRPGSRVLEAGTGSGSLTHALARAVGPTGHVYTYEF 73 (247)
T ss_dssp HHHHHHTT----TT-EEEEE--TTSHHHHHHHHHHTTTSEEEEEES
T ss_pred HHHHHHcC--CCCCCEEEEecCCcHHHHHHHHHHhCCCeEEEcccc
Confidence 33455555 66689999999999999999996 457777777764
No 413
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=58.68 E-value=12 Score=33.04 Aligned_cols=40 Identities=15% Similarity=0.184 Sum_probs=35.0
Q ss_pred hhhcCCCCCCHHHHHHH--cCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 44 IINNSGQPMTLTQIIVA--LNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 44 ~L~~~~~p~t~~eLA~~--~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
++... +|++..+||+. +++++ .-+|+-|..|...|++.+.
T Consensus 19 yi~~~-~pv~s~~l~~~~~l~~S~---aTIR~dm~~Le~~G~l~~~ 60 (339)
T PRK00082 19 YIATG-EPVGSKTLSKRYGLGVSS---ATIRNDMADLEELGLLEKP 60 (339)
T ss_pred HHhcC-CCcCHHHHHHHhCCCCCh---HHHHHHHHHHHhCCCcCCC
Confidence 34443 99999999977 89999 9999999999999999965
No 414
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=58.64 E-value=13 Score=24.74 Aligned_cols=29 Identities=17% Similarity=0.221 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHS 81 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~ 81 (214)
-++|+.|.|+.+|+++ ..+.+|++.....
T Consensus 12 ~~~s~~~Aa~~lG~~~---~~v~~wv~~fR~w 40 (65)
T PF05344_consen 12 QQISVAQAADRLGTDP---GTVRRWVRMFRQW 40 (65)
T ss_pred ccccHHHHHHHHCcCH---HHHHHHHHHHHHH
Confidence 6899999999999999 9999998876543
No 415
>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=58.64 E-value=4.9 Score=29.35 Aligned_cols=50 Identities=28% Similarity=0.325 Sum_probs=37.6
Q ss_pred hcCcchhhhcCCCCCCHHHHHHHcCCC-CCCcccHHHHHHHHHhCCceeeec
Q 040620 38 QLRIPDIINNSGQPMTLTQIIVALNVH-PNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 38 ~lglfd~L~~~~~p~t~~eLA~~~g~~-~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|..|.++|=+. +++|+.||.+.+.-+ .-....+..+|+-|+..|++....
T Consensus 5 E~~IM~~lW~~-~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~ 55 (115)
T PF03965_consen 5 ELEIMEILWES-GEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREK 55 (115)
T ss_dssp HHHHHHHHHHH-SSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHhC-CCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEee
Confidence 44455555555 679999999998754 112278899999999999999886
No 416
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=58.58 E-value=9.2 Score=31.08 Aligned_cols=44 Identities=11% Similarity=0.122 Sum_probs=36.0
Q ss_pred HHHhcCcchhhhcCCC--CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCC
Q 040620 35 RAIQLRIPDIINNSGQ--PMTLTQIIVALNVHPNKTRCTQILVCLLAHSG 82 (214)
Q Consensus 35 ~a~~lglfd~L~~~~~--p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g 82 (214)
.-....|.+.|... + .+|+++||+.+|+++ ..++|=|..+...|
T Consensus 15 ~~~~~~il~~l~~~-~~~~vs~~~L~~~~~v~~---~tirrDl~~l~~~G 60 (213)
T PRK05472 15 LPLYYRYLKELKEE-GVERVSSKELAEALGVDS---AQIRKDLSYFGEFG 60 (213)
T ss_pred hHHHHHHHHHHHHc-CCcEEeHHHHHHHhCcCH---HHHHHHHHHHHhcC
Confidence 34445677788876 6 899999999999999 89999999886666
No 417
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=58.50 E-value=8.4 Score=30.54 Aligned_cols=27 Identities=11% Similarity=0.150 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLA 79 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~ 79 (214)
.++|.+|||+.+|+++ +.++|-++..-
T Consensus 150 ~Gls~~EIA~~lgiS~---~tV~r~l~~aR 176 (185)
T PF07638_consen 150 EGLSVEEIAERLGISE---RTVRRRLRRAR 176 (185)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHHHHH
Confidence 5799999999999999 88888776553
No 418
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=58.45 E-value=4.8 Score=26.19 Aligned_cols=27 Identities=19% Similarity=0.370 Sum_probs=20.3
Q ss_pred CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCcee
Q 040620 52 MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFV 85 (214)
Q Consensus 52 ~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~ 85 (214)
+|+.|+|+.+|+++ +.|+.| ...|++.
T Consensus 1 yti~eva~~~gvs~---~tlr~y----~~~gll~ 27 (69)
T PF13411_consen 1 YTIKEVAKLLGVSP---STLRYY----EREGLLP 27 (69)
T ss_dssp EEHHHHHHHTTTTH---HHHHHH----HHTTSST
T ss_pred CcHHHHHHHHCcCH---HHHHHH----HHhcCcc
Confidence 37899999999997 666666 5566644
No 419
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=58.15 E-value=4.6 Score=25.60 Aligned_cols=36 Identities=14% Similarity=0.184 Sum_probs=26.1
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHH
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLL 78 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L 78 (214)
-|..|+..+. .+.+..|||+.+++++ ..++..++.+
T Consensus 7 ~E~~vl~~l~---~G~~~~eIA~~l~is~---~tV~~~~~~i 42 (58)
T PF00196_consen 7 RELEVLRLLA---QGMSNKEIAEELGISE---KTVKSHRRRI 42 (58)
T ss_dssp HHHHHHHHHH---TTS-HHHHHHHHTSHH---HHHHHHHHHH
T ss_pred HHHHHHHHHH---hcCCcchhHHhcCcch---hhHHHHHHHH
Confidence 3555677777 5799999999999998 7766555443
No 420
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=58.15 E-value=16 Score=30.42 Aligned_cols=41 Identities=10% Similarity=0.156 Sum_probs=35.5
Q ss_pred CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCC
Q 040620 53 TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLP 102 (214)
Q Consensus 53 t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t 102 (214)
+-.+||+++|++. ..++.-|+.|.+.|++.-... .|.|=.+
T Consensus 36 ~EreLae~fgVSR---~~vREAl~~L~a~Glve~r~G------~Gt~V~~ 76 (241)
T COG2186 36 SERELAERFGVSR---TVVREALKRLEAKGLVEIRQG------SGTFVRP 76 (241)
T ss_pred CHHHHHHHHCCCc---HHHHHHHHHHHHCCCeeecCC------CceEecC
Confidence 6789999999999 899999999999999997753 5677654
No 421
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=57.93 E-value=7.5 Score=27.40 Aligned_cols=33 Identities=12% Similarity=0.134 Sum_probs=26.7
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHH
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCL 77 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~ 77 (214)
..|+..+. .++|..+||+.+|++. ..+.|+.+.
T Consensus 41 ~~I~~ll~---~G~S~~eIA~~LgISr---sTIyRi~R~ 73 (88)
T TIGR02531 41 LQVAKMLK---QGKTYSDIEAETGAST---ATISRVKRC 73 (88)
T ss_pred HHHHHHHH---CCCCHHHHHHHHCcCH---HHHHHHHHh
Confidence 45666667 4589999999999998 888887764
No 422
>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=57.72 E-value=10 Score=33.32 Aligned_cols=32 Identities=9% Similarity=-0.092 Sum_probs=22.7
Q ss_pred CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC 212 (214)
Q Consensus 180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 212 (214)
+..+|||+|||.|.-+..-.+.. =-+.++.|+
T Consensus 62 ~~~~VLDl~CGkGGDL~Kw~~~~-i~~~vg~Di 93 (331)
T PF03291_consen 62 PGLTVLDLCCGKGGDLQKWQKAK-IKHYVGIDI 93 (331)
T ss_dssp TT-EEEEET-TTTTTHHHHHHTT--SEEEEEES
T ss_pred CCCeEEEecCCCchhHHHHHhcC-CCEEEEEeC
Confidence 56899999999999888887762 224677775
No 423
>PLN03239 histone acetyltransferase; Provisional
Probab=57.67 E-value=39 Score=29.95 Aligned_cols=52 Identities=13% Similarity=0.163 Sum_probs=40.9
Q ss_pred HHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 25 YNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 25 ~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.+||...++....+. ... +..+|+++||+.||+.+ ..++..|-.+|++....
T Consensus 264 ~~YW~~~il~~L~~~-----~~~-~~~~si~dis~~Tgi~~------~DIi~tL~~l~~l~~~~ 315 (351)
T PLN03239 264 IPYWGSTIVDFLLNH-----SGN-DSSLSIMDIAKKTSIMA------EDIVFALNQLGILKFIN 315 (351)
T ss_pred HHHHHHHHHHHHHhc-----cCC-CCCccHHHHHHHhCCCH------HHHHHHHHHCCcEEEEC
Confidence 478888888776543 121 14699999999999988 77899999999998774
No 424
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=57.62 E-value=9.3 Score=33.22 Aligned_cols=56 Identities=16% Similarity=0.208 Sum_probs=42.5
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
|..+|... ..+|+++||+.++++. |.+.|=++.|...|+-.+... |. .+.|.+-+.
T Consensus 13 ii~~L~~~-~~vta~~lA~~~~VS~---RTi~RDi~~L~~~gvPI~~e~---G~-~~gy~~~~~ 68 (311)
T COG2378 13 IIQILRAK-ETVTAAELADEFEVSV---RTIYRDIATLRAAGVPIEGER---GK-GGGYRLRPG 68 (311)
T ss_pred HHHHHHhC-ccchHHHHHHhcCCCH---HHHHHHHHHHHHCCCCeEeec---CC-CccEEEccC
Confidence 44455654 4499999999999999 999999999999999977653 11 245555555
No 425
>KOG1661 consensus Protein-L-isoaspartate(D-aspartate) O-methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=57.50 E-value=10 Score=31.47 Aligned_cols=23 Identities=22% Similarity=0.369 Sum_probs=19.0
Q ss_pred cCCCCcEEeecCCchHHHHHHHH
Q 040620 178 SKGLKPLVDVGGSTGTMARAIAT 200 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~~~~~l~~ 200 (214)
+....++||||+|+|.++..++.
T Consensus 80 L~pG~s~LdvGsGSGYLt~~~~~ 102 (237)
T KOG1661|consen 80 LQPGASFLDVGSGSGYLTACFAR 102 (237)
T ss_pred hccCcceeecCCCccHHHHHHHH
Confidence 45677999999999998887764
No 426
>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=57.23 E-value=7.6 Score=27.33 Aligned_cols=40 Identities=10% Similarity=0.096 Sum_probs=30.8
Q ss_pred HHHHhcCcch-hhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHH
Q 040620 34 KRAIQLRIPD-IINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLA 79 (214)
Q Consensus 34 ~~a~~lglfd-~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~ 79 (214)
..+-++.|+. .|. +++|..|||+.+|++. ..+.|.=|.|-
T Consensus 34 ~l~~R~~va~~lL~---~g~syreIa~~tgvS~---aTItRvsr~Lk 74 (87)
T PF01371_consen 34 ALAQRWQVAKELLD---EGKSYREIAEETGVSI---ATITRVSRCLK 74 (87)
T ss_dssp HHHHHHHHHHHHHH---TTSSHHHHHHHHTSTH---HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH---CCCCHHHHHHHhCCCH---HHHHHHHHHHH
Confidence 3455677888 777 6799999999999998 66666666554
No 427
>smart00753 PAM PCI/PINT associated module.
Probab=57.20 E-value=14 Score=25.12 Aligned_cols=47 Identities=11% Similarity=0.101 Sum_probs=36.7
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
.+..++...... ..++.++||+.++++. ..+.+++.-+...|.+.-.
T Consensus 11 ~~~~l~~l~~~y-~~i~~~~i~~~~~l~~---~~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00753 11 RLTNLLQLSEPY-SSISLSDLAKLLGLSV---PEVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HHHHHHHHhHHh-ceeeHHHHHHHhCcCH---HHHHHHHHHHHHCCCeEEE
Confidence 333444444443 7899999999999998 7899999999999988643
No 428
>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=57.20 E-value=14 Score=25.12 Aligned_cols=47 Identities=11% Similarity=0.101 Sum_probs=36.7
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
.+..++...... ..++.++||+.++++. ..+.+++.-+...|.+.-.
T Consensus 11 ~~~~l~~l~~~y-~~i~~~~i~~~~~l~~---~~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00088 11 RLTNLLQLSEPY-SSISLSDLAKLLGLSV---PEVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HHHHHHHHhHHh-ceeeHHHHHHHhCcCH---HHHHHHHHHHHHCCCeEEE
Confidence 333444444443 7899999999999998 7899999999999988643
No 429
>COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]
Probab=56.81 E-value=14 Score=32.74 Aligned_cols=45 Identities=9% Similarity=0.091 Sum_probs=38.8
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
..+.+.+.. .|++++.||+.+|++. ..+..+|-.|.-.|.+...+
T Consensus 299 ~~~~~~~~~--~~~~~d~l~~~~~~~~---~~~~~~L~~lel~G~i~~~~ 343 (350)
T COG0758 299 LALLANLGD--EPKEIDRLASCTGLTI---AQVLAWLLELELEGKVKRLG 343 (350)
T ss_pred HHHHHHhcC--CCccHHHHHHHhCCCH---HHHHHHHHHHHhcCcEEeeC
Confidence 334455555 8999999999999999 99999999999999999886
No 430
>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=56.79 E-value=23 Score=25.19 Aligned_cols=64 Identities=16% Similarity=0.157 Sum_probs=44.9
Q ss_pred cchhhhcCCCCCCHHHHHHHc--------CCCCCCcccHHHHHHHHHhCCceeeecCC-CCCCccceeeCCCCCcccccc
Q 040620 41 IPDIINNSGQPMTLTQIIVAL--------NVHPNKTRCTQILVCLLAHSGFFVQQKDG-KNEQEEESILLPPHLDFFSRI 111 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~--------g~~~~~~~~l~rlLr~L~~~g~l~~~~~~-~~~~~~~~y~~t~~~~~~s~~ 111 (214)
|+.+|.. +|++--||++.+ .+++ -.+...|+-|...|++...... .++.-...|.+|+. ++.
T Consensus 9 iL~~L~~--~~~~GYei~~~l~~~~~~~~~i~~---gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~----Gr~ 79 (100)
T TIGR03433 9 ILKTLSL--GPLHGYGIAQRIQQISEDVLQVEE---GSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAA----GRK 79 (100)
T ss_pred HHHHHhc--CCCCHHHHHHHHHHHcCCccccCC---CcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHH----HHH
Confidence 3445554 788888888874 4666 8999999999999999974211 11111356999999 777
Q ss_pred cc
Q 040620 112 SL 113 (214)
Q Consensus 112 l~ 113 (214)
++
T Consensus 80 ~l 81 (100)
T TIGR03433 80 QL 81 (100)
T ss_pred HH
Confidence 64
No 431
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=56.62 E-value=6.5 Score=34.58 Aligned_cols=38 Identities=11% Similarity=0.156 Sum_probs=28.5
Q ss_pred hhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCc
Q 040620 43 DIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGF 83 (214)
Q Consensus 43 d~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~ 83 (214)
+.+..+ +.|+|+++||+..++++ |.+.|+-+.-.....
T Consensus 227 ~~me~nle~plsl~~LA~~~~~S~---R~leRlF~~~lG~sP 265 (328)
T COG4977 227 ELMEANLEEPLSLEELADRAGLSR---RQLERLFRAELGVSP 265 (328)
T ss_pred HHHHHhhcCCcCHHHHHHHhCCCH---HHHHHHHHHHhCCCH
Confidence 444443 38999999999999999 999888665544433
No 432
>COG0500 SmtA SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]
Probab=56.55 E-value=17 Score=25.50 Aligned_cols=28 Identities=21% Similarity=0.234 Sum_probs=18.6
Q ss_pred EEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620 184 LVDVGGSTGTMARAIATAFPD-TKCTVFAC 212 (214)
Q Consensus 184 vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl 212 (214)
++|+|||.|... .+.+..+. ..++.+|.
T Consensus 52 ~ld~~~g~g~~~-~~~~~~~~~~~~~~~d~ 80 (257)
T COG0500 52 VLDIGCGTGRLA-LLARLGGRGAYVVGVDL 80 (257)
T ss_pred eEEecCCcCHHH-HHHHhCCCCceEEEEeC
Confidence 999999999977 44444443 35555554
No 433
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=56.25 E-value=11 Score=28.38 Aligned_cols=61 Identities=20% Similarity=0.337 Sum_probs=46.3
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcCCCCC-CcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALNVHPN-KTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~-~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
.|..|.++|=.. +|.|+.||-+.+.-+++ ...-+.-+|+-|+..|++..... +++|.-+|+
T Consensus 7 aE~eVM~ilW~~-~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kd------gr~~~y~pL 68 (123)
T COG3682 7 AEWEVMEILWSR-GPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKD------GRAFRYSPL 68 (123)
T ss_pred HHHHHHHHHHHc-CCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhc------CCeeeeecc
Confidence 344556666666 89999999888875420 11578999999999999998874 678888888
No 434
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=56.01 E-value=12 Score=32.35 Aligned_cols=37 Identities=22% Similarity=0.335 Sum_probs=33.8
Q ss_pred CCCCCHHHHHHHcCCCCCCcccHHHHHH-HHHhCCceeeec
Q 040620 49 GQPMTLTQIIVALNVHPNKTRCTQILVC-LLAHSGFFVQQK 88 (214)
Q Consensus 49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr-~L~~~g~l~~~~ 88 (214)
++|.+++.||+.+|.++ ..+...++ .|+..|++...+
T Consensus 274 ~~~~~~~~~a~~lg~~~---~~~~~~~e~~Li~~~li~~~~ 311 (328)
T PRK00080 274 GGPVGLDTLAAALGEER---DTIEDVYEPYLIQQGFIQRTP 311 (328)
T ss_pred CCceeHHHHHHHHCCCc---chHHHHhhHHHHHcCCcccCC
Confidence 48999999999999999 99999999 999999997664
No 435
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 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 2". 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: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=56.00 E-value=17 Score=23.14 Aligned_cols=36 Identities=17% Similarity=0.190 Sum_probs=30.9
Q ss_pred CCCCHHHHHHHc---CCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVAL---NVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~---g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.+++-++|-+++ ++++ +....+|+.|+..|.+..++
T Consensus 16 ~G~~keeLrsrl~~~~l~~---k~~~~ll~~l~~~g~l~~~g 54 (59)
T PF09106_consen 16 PGMPKEELRSRLFKPRLPP---KLFNALLEALVAEGRLKVEG 54 (59)
T ss_dssp S-EEHHHHHHHCST-TS-H---CCHHHHHHHHHHTTSEEEES
T ss_pred cCcCHHHHHHHHhhccCCH---HHHHHHHHHHHHCCCeeeEC
Confidence 568999999988 6787 99999999999999999884
No 436
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=55.95 E-value=24 Score=23.96 Aligned_cols=37 Identities=19% Similarity=0.158 Sum_probs=26.3
Q ss_pred chhhhcCC-CCCCHHHHHHHcC-CCCCCcccHHHHHHHHHh
Q 040620 42 PDIINNSG-QPMTLTQIIVALN-VHPNKTRCTQILVCLLAH 80 (214)
Q Consensus 42 fd~L~~~~-~p~t~~eLA~~~g-~~~~~~~~l~rlLr~L~~ 80 (214)
.++|...+ .|+|++||...++ ++. -..+.+||+...-
T Consensus 15 V~ymK~r~~~Plt~~EIl~~ls~~d~--~~~~~~~L~~~~~ 53 (75)
T cd07977 15 VDYMKKRHQHPLTLDEILDYLSLLDI--GPKLKEWLKSEAL 53 (75)
T ss_pred HHHHHhcCCCCccHHHHHHHHhccCc--cHHHHHHHHhhhh
Confidence 36777777 8999999999999 766 1344566664333
No 437
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=55.81 E-value=9.4 Score=28.22 Aligned_cols=31 Identities=10% Similarity=0.007 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCc
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGF 83 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~ 83 (214)
++.|+.+||+..|+++ ..+++|.+..-..|.
T Consensus 28 ~g~sv~evA~e~gIs~---~tl~~W~r~y~~~~~ 58 (121)
T PRK09413 28 PGMTVSLVARQHGVAA---SQLFLWRKQYQEGSL 58 (121)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHHHHhhccc
Confidence 6789999999999999 999999998865554
No 438
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=55.77 E-value=11 Score=35.31 Aligned_cols=37 Identities=24% Similarity=0.365 Sum_probs=34.4
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKD 89 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~ 89 (214)
..+|++|||+.+.+++ |.++.+|+.|...|.++-.+.
T Consensus 22 ~~~~l~~la~~l~cs~---R~~~~~l~~~~~~gwl~w~~~ 58 (552)
T PRK13626 22 QETTLNELAELLNCSR---RHMRTLLNTMQQRGWLTWQAE 58 (552)
T ss_pred ceeeHHHHHHHhcCCh---hHHHHHHHHHHHCCCeeeecC
Confidence 5689999999999999 999999999999999997763
No 439
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=55.27 E-value=13 Score=21.89 Aligned_cols=26 Identities=8% Similarity=0.088 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLL 78 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L 78 (214)
..++..+||+.+|+++ ..+.+++...
T Consensus 25 ~~~~~~~ia~~~~~s~---~~i~~~~~~~ 50 (55)
T cd06171 25 EGLSYEEIAEILGISR---STVRQRLHRA 50 (55)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 4589999999999998 8888887653
No 440
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=54.88 E-value=27 Score=28.20 Aligned_cols=51 Identities=14% Similarity=0.365 Sum_probs=37.9
Q ss_pred HHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 25 YNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 25 ~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.+||...++....+.. .. ..+|+++|+++||+.+ ..++..|-.+|++....
T Consensus 131 ~sYW~~~i~~~L~~~~-----~~--~~isi~~is~~Tgi~~------~DIi~tL~~l~~l~~~~ 181 (188)
T PF01853_consen 131 RSYWRRVILEYLLEFK-----GK--KSISIKDISQETGIRP------EDIISTLQQLGMLKYYK 181 (188)
T ss_dssp HHHHHHHHHHHHHHTS-----SE----EEHHHHHHHH-BTH------HHHHHHHHHTT-EEEET
T ss_pred HHHHHHHHHHHHHhcC-----CC--CeEEHHHHHHHHCCCH------HHHHHHHHHCCCEEEEC
Confidence 3788888777765442 11 3699999999999998 78899999999999885
No 441
>TIGR03739 PRTRC_D PRTRC system protein D. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated PRTRC system protein D. The gray zone, between trusted and noise, includes proteins found in the same genomes as other proteins of the PRTRC systems, but not in the same contiguous gene region.
Probab=54.73 E-value=43 Score=28.95 Aligned_cols=45 Identities=20% Similarity=0.316 Sum_probs=32.8
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
..+...+. ...+..+|+=+|||.-.+...+.++||+.++.+.|=|
T Consensus 262 ~~i~~~~~-~~~~~~~Iil~GGGa~ll~~~l~~~f~~~~i~~~~dp 306 (320)
T TIGR03739 262 STMMTWIG-APESIQNIVLVGGGAFLFKKAVKAAFPKHRIVEVDEP 306 (320)
T ss_pred HHHHHhcc-cCCcccEEEEeCCcHHHHHHHHHHHCCCCeeEecCCc
Confidence 34444442 2334678998999999998899999999887766655
No 442
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=54.42 E-value=13 Score=24.07 Aligned_cols=36 Identities=8% Similarity=0.097 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
|-++...||++.|+.. .-.-.-||-|.+.|++....
T Consensus 3 g~lvas~iAd~~GiTR---SvIVNALRKleSaGvIesrS 38 (61)
T PF08222_consen 3 GRLVASKIADRVGITR---SVIVNALRKLESAGVIESRS 38 (61)
T ss_dssp EEE-HHHHHHHHT--H---HHHHHHHHHHHHTTSEEEEE
T ss_pred ceehHHHHHHHhCccH---HHHHHHHHHHHhcCceeecc
Confidence 4578899999999987 77888899999999999664
No 443
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=53.81 E-value=9.9 Score=32.31 Aligned_cols=35 Identities=11% Similarity=0.044 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
.++|+++||+.+|+++ +.+.|+.+......+-...
T Consensus 20 ~~~~l~~lA~~~~~S~---~~l~r~F~~~~g~s~~~yi 54 (289)
T PRK15121 20 QPLSLDNVAAKAGYSK---WHLQRMFKDVTGHAIGAYI 54 (289)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHHHHHCcCHHHHH
Confidence 6899999999999999 9999998888777666655
No 444
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=53.69 E-value=9.3 Score=23.43 Aligned_cols=23 Identities=13% Similarity=-0.002 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILV 75 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlL 75 (214)
..+|.+++|+++|+++ ..+.+|.
T Consensus 14 ~gltq~~lA~~~gvs~---~~vs~~e 36 (58)
T TIGR03070 14 LGLTQADLADLAGVGL---RFIRDVE 36 (58)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHH
Confidence 5789999999999998 8888874
No 445
>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=53.68 E-value=11 Score=28.07 Aligned_cols=43 Identities=23% Similarity=0.138 Sum_probs=39.8
Q ss_pred HHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620 56 QIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL 113 (214)
Q Consensus 56 eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~ 113 (214)
+||+.++++- +-|--+++++.-+||+... +|...+|+. ++.++
T Consensus 2 ~La~~l~~ei---DdL~p~~eAaelLgf~~~~--------~Gdi~LT~~----G~~f~ 44 (120)
T PF09821_consen 2 QLADELHLEI---DDLLPIVEAAELLGFAEVE--------EGDIRLTPL----GRRFA 44 (120)
T ss_pred chHHHhCCcH---HHHHHHHHHHHHcCCeeec--------CCcEEeccc----hHHHH
Confidence 5889999988 9999999999999999998 589999999 99998
No 446
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=53.47 E-value=11 Score=28.74 Aligned_cols=43 Identities=7% Similarity=0.186 Sum_probs=33.5
Q ss_pred CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
..+|.+.+..|.+++.|+|+.+++-+ +.|.+| |...|++-..+
T Consensus 36 ~f~D~v~~~~gli~~re~AK~lkige---~~l~~~---L~e~~~l~~~~ 78 (135)
T COG3645 36 EFADAVVEASGLILFRELAKLLKIGE---NRLFAW---LRENKYLIKRG 78 (135)
T ss_pred HHHHHHhcCccceeHHHHHHHHccCH---HHHHHH---HHHCCEEEEcc
Confidence 34677776658899999999999988 666666 66788888773
No 447
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=53.39 E-value=10 Score=24.61 Aligned_cols=22 Identities=14% Similarity=0.232 Sum_probs=18.2
Q ss_pred CCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 52 MTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 52 ~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
+++.|+|+.+|+++ +.++.|-+
T Consensus 1 ~~i~evA~~~gvs~---~tlR~~~~ 22 (67)
T cd04764 1 YTIKEVSEIIGVKP---HTLRYYEK 22 (67)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHH
Confidence 47899999999998 77777744
No 448
>PHA00542 putative Cro-like protein
Probab=53.11 E-value=8.2 Score=26.58 Aligned_cols=24 Identities=17% Similarity=0.021 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
.++|..+||+.+|+++ ..+.+|.+
T Consensus 30 ~glTq~elA~~lgIs~---~tIsr~e~ 53 (82)
T PHA00542 30 AGWSQEQIADATDVSQ---PTICRIYS 53 (82)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHc
Confidence 6799999999999998 78887753
No 449
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.70 E-value=12 Score=26.47 Aligned_cols=26 Identities=19% Similarity=0.173 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLL 78 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L 78 (214)
.++|.++||.+++..+ ..+.++|..-
T Consensus 22 ~~LS~~~iA~~Ln~t~---~~lekil~~t 47 (97)
T COG4367 22 CPLSDEEIATALNWTE---VKLEKILQVT 47 (97)
T ss_pred ccccHHHHHHHhCCCH---HHHHHHHHHh
Confidence 6899999999999999 8888887543
No 450
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=52.56 E-value=13 Score=23.35 Aligned_cols=34 Identities=12% Similarity=0.125 Sum_probs=23.8
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
-++.|...+.. |+ +..+||+..|++. ..++.|+.
T Consensus 11 eK~~iI~~~e~--g~-s~~~ia~~fgv~~---sTv~~I~K 44 (53)
T PF04218_consen 11 EKLEIIKRLEE--GE-SKRDIAREFGVSR---STVSTILK 44 (53)
T ss_dssp HHHHHHHHHHC--TT--HHHHHHHHT--C---CHHHHHHH
T ss_pred HHHHHHHHHHc--CC-CHHHHHHHhCCCH---HHHHHHHH
Confidence 34556677775 55 9999999999998 88888864
No 451
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=52.50 E-value=7 Score=32.68 Aligned_cols=38 Identities=13% Similarity=0.149 Sum_probs=27.9
Q ss_pred HHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHH
Q 040620 35 RAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILV 75 (214)
Q Consensus 35 ~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlL 75 (214)
+..++++.++|..-..-.|++||++.+|+++ ..|.|..
T Consensus 7 ~~~~~~~v~~lr~lk~~~ty~el~~~~g~p~---~~l~RYv 44 (238)
T PRK08558 7 VRLQLRAVRVLRSLKKTYTYEELSSITGLPE---SVLNRYV 44 (238)
T ss_pred HHHHHHHHHHHHHHhcccCHHHHHHHHCCCH---HHHHHHH
Confidence 3455555666665446689999999999998 7776664
No 452
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=52.42 E-value=14 Score=24.84 Aligned_cols=54 Identities=13% Similarity=0.223 Sum_probs=36.1
Q ss_pred hhhhcCCCCCCHHHHHHH---cCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620 43 DIINNSGQPMTLTQIIVA---LNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP 103 (214)
Q Consensus 43 d~L~~~~~p~t~~eLA~~---~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~ 103 (214)
|++...++++++.+|.+. .|+++ ..++.-|-=|+..|+++.... +. .-.|++|+
T Consensus 12 dy~~~~g~~i~~~~Li~ll~~~Gv~e---~avR~alsRl~~~G~L~~~r~---Gr-~~~Y~Lt~ 68 (70)
T PF07848_consen 12 DYLRPRGGWIWVASLIRLLAAFGVSE---SAVRTALSRLVRRGWLESERR---GR-RSYYRLTE 68 (70)
T ss_dssp HHCCTTTS-EEHHHHHHHHCCTT--H---HHHHHHHHHHHHTTSEEEECC---CT-EEEEEE-H
T ss_pred HHhccCCCceeHHHHHHHHHHcCCCh---HHHHHHHHHHHHcCceeeeec---Cc-cceEeeCC
Confidence 344555577888877764 56788 999999999999999998862 11 23588775
No 453
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=52.42 E-value=11 Score=24.40 Aligned_cols=22 Identities=14% Similarity=0.102 Sum_probs=19.0
Q ss_pred CCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 52 MTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 52 ~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
.|+.|+|+.+|+++ +.+++|..
T Consensus 1 ~s~~eva~~~gvs~---~tlr~w~~ 22 (68)
T cd01104 1 YTIGAVARLTGVSP---DTLRAWER 22 (68)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHH
Confidence 47899999999999 88888864
No 454
>KOG4300 consensus Predicted methyltransferase [General function prediction only]
Probab=52.41 E-value=31 Score=28.71 Aligned_cols=55 Identities=18% Similarity=0.103 Sum_probs=30.6
Q ss_pred HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEec
Q 040620 154 IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFA 211 (214)
Q Consensus 154 ~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D 211 (214)
.|++-|.++-+-.++.+- .+- ..++-..||.||||+|.--. ...--|..++|.+|
T Consensus 52 ~yne~~~~ykrelFs~i~-~~~-gk~~K~~vLEvgcGtG~Nfk-fy~~~p~~svt~lD 106 (252)
T KOG4300|consen 52 IYNEIADSYKRELFSGIY-YFL-GKSGKGDVLEVGCGTGANFK-FYPWKPINSVTCLD 106 (252)
T ss_pred HHHHHHHHHHHHHHhhhH-HHh-cccCccceEEecccCCCCcc-cccCCCCceEEEeC
Confidence 677788777444333322 111 12334578999999997431 22222455677766
No 455
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=51.60 E-value=23 Score=30.22 Aligned_cols=49 Identities=14% Similarity=0.116 Sum_probs=41.6
Q ss_pred CCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 48 SGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 48 ~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
.+.++-.+|||+.++.+| -.+|..+..|-++|++.-.+ |+ .|-|..|..
T Consensus 22 ~~r~IKgeeIA~~l~rnp---GTVRNqmq~LkaLgLVegvp----GP-kGGY~PT~k 70 (294)
T COG2524 22 KKRPIKGEEIAEVLNRNP---GTVRNQMQSLKALGLVEGVP----GP-KGGYKPTSK 70 (294)
T ss_pred cCCCcchHHHHHHHccCc---chHHHHHHHHHhcCcccccc----CC-CCCccccHH
Confidence 347999999999999999 99999999999999998654 22 577887765
No 456
>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=51.25 E-value=6.7 Score=22.95 Aligned_cols=26 Identities=23% Similarity=0.425 Sum_probs=18.7
Q ss_pred CHHHHHHHcCCCCCCcccHHHHHHHHHhCCcee
Q 040620 53 TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFV 85 (214)
Q Consensus 53 t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~ 85 (214)
|+.|+|+.+|+++ + .||.-...|++.
T Consensus 1 ti~e~A~~~gvs~---~----tlR~ye~~Gll~ 26 (38)
T PF00376_consen 1 TIGEVAKLLGVSP---R----TLRYYEREGLLP 26 (38)
T ss_dssp EHHHHHHHHTS-H---H----HHHHHHHTTSS-
T ss_pred CHHHHHHHHCCCH---H----HHHHHHHCCCCC
Confidence 5789999999996 4 456667778884
No 457
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=50.75 E-value=12 Score=24.43 Aligned_cols=28 Identities=11% Similarity=0.210 Sum_probs=20.6
Q ss_pred CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCcee
Q 040620 52 MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFV 85 (214)
Q Consensus 52 ~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~ 85 (214)
.++.|+|+.+|+++ ..++.|-+. .|++.
T Consensus 1 ~~i~e~A~~~gVs~---~tlr~ye~~---~gl~~ 28 (68)
T cd04763 1 YTIGEVALLTGIKP---HVLRAWERE---FGLLK 28 (68)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHHh---cCCCC
Confidence 37899999999998 777766332 26663
No 458
>PHA01634 hypothetical protein
Probab=50.61 E-value=19 Score=27.59 Aligned_cols=26 Identities=15% Similarity=0.153 Sum_probs=20.3
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEE
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCT 208 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~ 208 (214)
.++|+|||++.|..++-++-+ +++.+
T Consensus 29 ~KtV~dIGA~iGdSaiYF~l~--GAK~V 54 (156)
T PHA01634 29 QRTIQIVGADCGSSALYFLLR--GASFV 54 (156)
T ss_pred CCEEEEecCCccchhhHHhhc--CccEE
Confidence 589999999999998877655 44433
No 459
>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=50.39 E-value=20 Score=34.75 Aligned_cols=57 Identities=16% Similarity=0.375 Sum_probs=42.5
Q ss_pred cchhhhc-CCCCCCHHHHHHHcCCCCC-CcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 41 IPDIINN-SGQPMTLTQIIVALNVHPN-KTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 41 lfd~L~~-~~~p~t~~eLA~~~g~~~~-~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
|.+.|.. .+.|++..+|+++++++.. ....+.+.|+.|...|.+.... .+.|.....
T Consensus 7 il~~l~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~~l~~l~~~g~l~~~~-------~~~~~~~~~ 65 (709)
T TIGR02063 7 ILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNR-------RGLYALPES 65 (709)
T ss_pred HHHHHHhCCCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcC-------CceEecCCC
Confidence 5555653 2489999999999999641 2246999999999999998765 466665554
No 460
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=49.98 E-value=22 Score=29.02 Aligned_cols=40 Identities=15% Similarity=0.291 Sum_probs=35.1
Q ss_pred CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeC
Q 040620 53 TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILL 101 (214)
Q Consensus 53 t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~ 101 (214)
|-.|||+..|++. --+++-|+.|+..|++..... .|.|=.
T Consensus 26 sE~eLa~~~gVSR---~TVR~Al~~L~~eGli~r~~G------~GTfV~ 65 (233)
T TIGR02404 26 SEHELMDQYGASR---ETVRKALNLLTEAGYIQKIQG------KGSIVL 65 (233)
T ss_pred CHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEeCC------ceEEEe
Confidence 7899999999998 899999999999999998763 567754
No 461
>PHA01976 helix-turn-helix protein
Probab=49.91 E-value=12 Score=24.16 Aligned_cols=22 Identities=5% Similarity=-0.034 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQIL 74 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rl 74 (214)
..+|.+++|+++|+++ ..+.+|
T Consensus 14 ~glt~~~lA~~~gvs~---~~v~~~ 35 (67)
T PHA01976 14 RAWSAPELSRRAGVRH---SLIYDF 35 (67)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHH
Confidence 5799999999999998 888887
No 462
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=49.09 E-value=23 Score=28.87 Aligned_cols=41 Identities=10% Similarity=0.204 Sum_probs=35.3
Q ss_pred CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCC
Q 040620 53 TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLP 102 (214)
Q Consensus 53 t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t 102 (214)
|-.|||+..|++. --+++-|+.|+..|++..... .|.|-..
T Consensus 34 sE~eLa~~~~VSR---~TvR~Al~~L~~eGli~r~~G------~GtfV~~ 74 (238)
T TIGR02325 34 AEMQLAERFGVNR---HTVRRAIAALVERGLLRAEQG------RGTFVAA 74 (238)
T ss_pred CHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEecC------CEEEECC
Confidence 7789999999998 899999999999999998753 5667643
No 463
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=49.04 E-value=7.1 Score=32.90 Aligned_cols=42 Identities=17% Similarity=0.212 Sum_probs=29.6
Q ss_pred CcchhhhcCC---CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCce
Q 040620 40 RIPDIINNSG---QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFF 84 (214)
Q Consensus 40 glfd~L~~~~---~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l 84 (214)
.|.+.+-++. .-+|+.+||+++++++ ..+.|+++.|--.||-
T Consensus 20 ~Ia~yil~n~~~v~~~si~~lA~~~~vS~---aTv~Rf~kklG~~gf~ 64 (284)
T PRK11302 20 KVAEVILASPQTAIHSSIATLAKMANVSE---PTVNRFCRSLDTKGFP 64 (284)
T ss_pred HHHHHHHhCHHHHHhcCHHHHHHHhCCCH---HHHHHHHHHcCCCCHH
Confidence 3444444432 3489999999999999 7777777776666664
No 464
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=49.02 E-value=18 Score=29.35 Aligned_cols=30 Identities=20% Similarity=0.242 Sum_probs=28.1
Q ss_pred CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCc
Q 040620 51 PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGF 83 (214)
Q Consensus 51 p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~ 83 (214)
|+|-++||+.+|+++ +.+.|+|+.|...|+
T Consensus 173 ~~t~~~iA~~lG~tr---etvsR~l~~L~~~gl 202 (236)
T PRK09392 173 PYEKRVLASYLGMTP---ENLSRAFAALASHGV 202 (236)
T ss_pred eCCHHHHHHHhCCCh---hHHHHHHHHHHhCCe
Confidence 677899999999999 999999999999996
No 465
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=48.92 E-value=13 Score=29.99 Aligned_cols=35 Identities=9% Similarity=0.003 Sum_probs=26.0
Q ss_pred HHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHH
Q 040620 35 RAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILV 75 (214)
Q Consensus 35 ~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlL 75 (214)
+--|..|+.++. .+.|..|||+++++++ +.++..+
T Consensus 139 T~RE~eVL~lla---~G~snkeIA~~L~iS~---~TVk~h~ 173 (207)
T PRK15411 139 SRTESSMLRMWM---AGQGTIQISDQMNIKA---KTVSSHK 173 (207)
T ss_pred CHHHHHHHHHHH---cCCCHHHHHHHcCCCH---HHHHHHH
Confidence 344556777777 5799999999999998 6554443
No 466
>PF02387 IncFII_repA: IncFII RepA protein family; InterPro: IPR003446 These proteins are plasmid encoded and essential for plasmid replication, they are also involved in copy control functions [].; GO: 0006276 plasmid maintenance
Probab=48.81 E-value=18 Score=31.06 Aligned_cols=39 Identities=13% Similarity=0.169 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHcCCCCCC------cccHHHHH-HHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNK------TRCTQILV-CLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~------~~~l~rlL-r~L~~~g~l~~~~ 88 (214)
-.+++++||..||+++.+ +.++.|++ +.|..+|++++..
T Consensus 94 V~~sie~LA~ecGLst~s~~Gn~sitRasR~i~e~le~~Gli~~~~ 139 (281)
T PF02387_consen 94 VQASIEQLADECGLSTKSAAGNKSITRASRLISEFLEPLGLITCEK 139 (281)
T ss_pred eeecHHHHHHHhCCcccCCCCCeeHHHHHHHHHHHHHhcCCeeeee
Confidence 679999999999985411 23456666 5578899998754
No 467
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=48.74 E-value=17 Score=26.32 Aligned_cols=35 Identities=9% Similarity=0.008 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHcCC-CCCCcccHHHHHHHHHhCCceeee
Q 040620 50 QPMTLTQIIVALNV-HPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 50 ~p~t~~eLA~~~g~-~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
+..|+.+||.+.|+ ++ ..+++|.+.+...+.....
T Consensus 23 ~g~sv~~vAr~~gv~~~---~~l~~W~~~~~~~~~~~~~ 58 (116)
T COG2963 23 GGDTVSEVAREFGIVSA---TQLYKWRIQLQKGGGLAFS 58 (116)
T ss_pred cCccHHHHHHHhCCCCh---HHHHHHHHHHHHccccccc
Confidence 56699999999996 99 9999999998887765544
No 468
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=48.64 E-value=7.1 Score=32.50 Aligned_cols=45 Identities=20% Similarity=0.327 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
+-+|++|+|+..+++| ..++.++.-|...|++.... .|+|...++
T Consensus 29 kiiTirdvae~~ev~~---n~lr~lasrLekkG~LeRi~-------rG~YlI~~l 73 (269)
T COG5340 29 KIITIRDVAETLEVAP---NTLRELASRLEKKGWLERIL-------RGRYLIIPL 73 (269)
T ss_pred ceEEeHHhhhhccCCH---HHHHHHHhhhhhcchhhhhc-------CccEEEeec
Confidence 7799999999999999 99999999999999999987 688887777
No 469
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=48.42 E-value=23 Score=32.54 Aligned_cols=49 Identities=10% Similarity=0.141 Sum_probs=40.0
Q ss_pred HHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 25 YNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 25 ~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.+||...++....+ ..+.+|+++|++.|++.+ ..++..|-.+|++.+..
T Consensus 357 ~~YW~~~i~~~L~~---------~~~~~si~~is~~T~i~~------~Dii~tL~~l~~l~~~k 405 (450)
T PLN00104 357 RGYWTRVLLEILKK---------HKGNISIKELSDMTAIKA------EDIVSTLQSLNLIQYRK 405 (450)
T ss_pred HHHHHHHHHHHHHh---------cCCCccHHHHHHHhCCCH------HHHHHHHHHCCCEEecC
Confidence 47888877777532 226899999999999988 78899999999999875
No 470
>TIGR03439 methyl_EasF probable methyltransferase domain, EasF family. This model represents an uncharacterized domain of about 300 amino acids with homology to S-adenosylmethionine-dependent methyltransferases. Proteins with this domain are exclusively fungal. A few, such as EasF from Neotyphodium lolii, are associated with the biosynthesis of ergot alkaloids, a class of fungal secondary metabolites. EasF may, in fact, be the AdoMet:dimethylallyltryptophan N-methyltransferase, the enzyme that follows tryptophan dimethylallyltransferase (DMATS) in ergot alkaloid biosynthesis. Several other members of this family, including mug158 (meiotically up-regulated gene 158 protein) from Schizosaccharomyces pombe, contain an additional uncharacterized domain DUF323 (pfam03781).
Probab=48.32 E-value=37 Score=29.71 Aligned_cols=41 Identities=12% Similarity=0.095 Sum_probs=27.7
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCC----CCeEEEecC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFP----DTKCTVFAC 212 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P----~l~~~v~Dl 212 (214)
..++..++ ....|||+|||+|.=...|+++.. ..+++-+|+
T Consensus 68 ~~Ia~~i~----~~~~lIELGsG~~~Kt~~LL~aL~~~~~~~~Y~plDI 112 (319)
T TIGR03439 68 SDIAASIP----SGSMLVELGSGNLRKVGILLEALERQKKSVDYYALDV 112 (319)
T ss_pred HHHHHhcC----CCCEEEEECCCchHHHHHHHHHHHhcCCCceEEEEEC
Confidence 34445443 445899999999997776666553 456777775
No 471
>PRK14999 histidine utilization repressor; Provisional
Probab=48.14 E-value=24 Score=29.05 Aligned_cols=60 Identities=8% Similarity=0.145 Sum_probs=43.2
Q ss_pred HHHHHHHhcCcchhhhcCCCCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620 31 LSLKRAIQLRIPDIINNSGQPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP 103 (214)
Q Consensus 31 ~~L~~a~~lglfd~L~~~~~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~ 103 (214)
..|...|+.|.+ .. |..+ |-.+||+..|++. .-+++-|+.|+..|++..... .|.|=..+
T Consensus 19 ~~i~~~I~~g~~---~~-G~~LPsE~eLa~~~gVSR---~TVR~Al~~L~~eGli~r~~G------kGTfV~~~ 79 (241)
T PRK14999 19 QDICKKIAGGVW---QP-HDRIPSEAELVAQYGFSR---MTINRALRELTDEGWLVRLQG------VGTFVAEP 79 (241)
T ss_pred HHHHHHHHcCCC---CC-CCcCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEecC------cEEEECCC
Confidence 344445555543 21 1334 8899999999998 899999999999999997753 56775443
No 472
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=47.83 E-value=31 Score=22.80 Aligned_cols=41 Identities=12% Similarity=0.182 Sum_probs=23.6
Q ss_pred hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
+.|.+.+.|+|++||.+.+.++. ...+..||+ ...=+..++
T Consensus 12 eymK~r~~Plt~~eI~d~l~~d~--~~~~~~~Lk---~npKI~~d~ 52 (65)
T PF02186_consen 12 EYMKKRDHPLTLEEILDYLSLDI--GKKLKQWLK---NNPKIEYDP 52 (65)
T ss_dssp HHHHHH-S-B-HHHHHHHHTSSS---HHHHHHHH---H-TTEEEE-
T ss_pred HHHHhcCCCcCHHHHHHHHcCCC--CHHHHHHHH---cCCCEEEec
Confidence 34444459999999999999875 124445554 666666664
No 473
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=47.81 E-value=30 Score=28.50 Aligned_cols=59 Identities=8% Similarity=0.071 Sum_probs=42.8
Q ss_pred HHHHHHHhcCcchhhhcCCCCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCC
Q 040620 31 LSLKRAIQLRIPDIINNSGQPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLP 102 (214)
Q Consensus 31 ~~L~~a~~lglfd~L~~~~~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t 102 (214)
..|...|..|-+ .. |..+ |-.+||+..|++. .-+++-|+.|+..|++..... .|.|-..
T Consensus 12 ~~L~~~I~~g~~---~~-G~~LPsE~eL~~~~~VSR---~TvR~Al~~L~~eGli~r~~G------~GtfV~~ 71 (240)
T PRK09764 12 DRIREQIARGEL---KP-GDALPTESALQTEFGVSR---VTVRQALRQLVEQQILESIQG------SGTYVKE 71 (240)
T ss_pred HHHHHHHHcCCC---CC-CCcCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEecC------ceeEEcc
Confidence 344455555544 22 2345 7799999999998 899999999999999997653 4666543
No 474
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=47.69 E-value=11 Score=26.61 Aligned_cols=25 Identities=24% Similarity=0.371 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCL 77 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~ 77 (214)
.++|.++||+.+++++ ..|.++|..
T Consensus 22 ~~ls~~~ia~dL~~s~---~~le~vL~l 46 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSP---EHLEQVLNL 46 (89)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHHcC
Confidence 5799999999999999 888887654
No 475
>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=47.66 E-value=28 Score=23.94 Aligned_cols=36 Identities=33% Similarity=0.451 Sum_probs=19.3
Q ss_pred cCCCCcEEeecCCchH-HHHHHHHHC-CCCe--EEEecCC
Q 040620 178 SKGLKPLVDVGGSTGT-MARAIATAF-PDTK--CTVFACH 213 (214)
Q Consensus 178 ~~~~~~vvDVGGG~G~-~~~~l~~~~-P~l~--~~v~Dlp 213 (214)
..+++++|=||+++|. ++.+++.+| -+.. ++-||.|
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 4677999999999998 444677665 1222 4555554
No 476
>PF14502 HTH_41: Helix-turn-helix domain
Probab=47.59 E-value=42 Score=20.87 Aligned_cols=36 Identities=14% Similarity=0.110 Sum_probs=31.8
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.-.|++|++++++++. -.++.-|..|...|.+.-..
T Consensus 5 Ri~tI~e~~~~~~vs~---GtiQ~Alk~Le~~gaI~Le~ 40 (48)
T PF14502_consen 5 RIPTISEYSEKFGVSR---GTIQNALKFLEENGAIKLES 40 (48)
T ss_pred ccCCHHHHHHHhCcch---hHHHHHHHHHHHCCcEEeee
Confidence 3469999999999998 88999999999999998765
No 477
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=47.19 E-value=14 Score=29.69 Aligned_cols=33 Identities=15% Similarity=0.184 Sum_probs=25.4
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHH
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILV 75 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlL 75 (214)
-|..|+..++ .++|..|||+++++++ +.++..+
T Consensus 137 RErEVLrLLA---qGkTnKEIAe~L~IS~---rTVkth~ 169 (198)
T PRK15201 137 TERHLLKLIA---SGYHLSETAALLSLSE---EQTKSLR 169 (198)
T ss_pred HHHHHHHHHH---CCCCHHHHHHHhCCCH---HHHHHHH
Confidence 4556777777 5799999999999998 6665443
No 478
>smart00351 PAX Paired Box domain.
Probab=47.17 E-value=17 Score=27.12 Aligned_cols=45 Identities=16% Similarity=0.170 Sum_probs=35.6
Q ss_pred HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
.+..|..+.. ++.+..+||+++|+++ ..+.+|++-....|.+...
T Consensus 22 ~R~riv~~~~---~G~s~~~iA~~~gvs~---~tV~kwi~r~~~~G~~~pk 66 (125)
T smart00351 22 ERQRIVELAQ---NGVRPCDISRQLCVSH---GCVSKILGRYYETGSIRPG 66 (125)
T ss_pred HHHHHHHHHH---cCCCHHHHHHHHCcCH---HHHHHHHHHHHHcCCcCCc
Confidence 3344454544 4679999999999999 9999999999998887654
No 479
>PRK04217 hypothetical protein; Provisional
Probab=47.10 E-value=17 Score=26.70 Aligned_cols=31 Identities=6% Similarity=0.004 Sum_probs=22.7
Q ss_pred cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
++..+.. ..+|.+|||+.+|+++ ..+++.+.
T Consensus 50 ai~l~~~--eGlS~~EIAk~LGIS~---sTV~r~L~ 80 (110)
T PRK04217 50 ALRLVDY--EGLTQEEAGKRMGVSR---GTVWRALT 80 (110)
T ss_pred HHHHHHH--cCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 3444443 5789999999999998 76666654
No 480
>PRK00118 putative DNA-binding protein; Validated
Probab=47.05 E-value=15 Score=26.66 Aligned_cols=24 Identities=17% Similarity=0.131 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVC 76 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr 76 (214)
..+|..|||+.+|+++ ..+.+++.
T Consensus 32 eg~S~~EIAe~lGIS~---~TV~r~L~ 55 (104)
T PRK00118 32 DDYSLGEIAEEFNVSR---QAVYDNIK 55 (104)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 5799999999999998 77766653
No 481
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=46.94 E-value=16 Score=28.83 Aligned_cols=43 Identities=16% Similarity=0.129 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP 103 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~ 103 (214)
.++|..|+|.+.+.+- +.-+.-|..|.+.|-+.+.. .+|++.+
T Consensus 123 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~--------~~~~~~~ 165 (166)
T PRK15466 123 QGMTAGEVAAHFGWPL---EKARNALEQLFSAGTLRKRS--------SRYRLKP 165 (166)
T ss_pred ccccHHHHHHHhCCcH---HHHHHHHHHHHhccchhhcc--------ccccccC
Confidence 7899999999999988 88899999999999999985 6887753
No 482
>COG1565 Uncharacterized conserved protein [Function unknown]
Probab=46.92 E-value=29 Score=30.96 Aligned_cols=23 Identities=30% Similarity=0.471 Sum_probs=18.7
Q ss_pred CCCCcEEeecCCchHHHHHHHHH
Q 040620 179 KGLKPLVDVGGSTGTMARAIATA 201 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~ 201 (214)
+....+|.+|.|+|+++.-+++.
T Consensus 76 p~~~~lvEiGaG~G~l~~DiL~~ 98 (370)
T COG1565 76 PAPLKLVEIGAGRGTLASDILRT 98 (370)
T ss_pred CCCceEEEeCCCcChHHHHHHHH
Confidence 34578999999999998877654
No 483
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=46.72 E-value=40 Score=23.35 Aligned_cols=47 Identities=9% Similarity=-0.066 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
.-++.+.|++.+|+++ ..+...|.-|...+++...... -+-|++|-.
T Consensus 23 E~VP~~~I~~~s~l~~---~~~~~~L~~L~~~kLv~~~~~~-----Y~GYrLT~~ 69 (82)
T PF09202_consen 23 EWVPLELIEKISGLSE---GEVEKRLKRLVKLKLVSRRNKP-----YDGYRLTFL 69 (82)
T ss_dssp SSEEHHHHHHHHT--H---HHHHHHHHHHHHTTSEEEE-SS-----S-EEEE-HH
T ss_pred ccCCHHHHHHHhCcCH---HHHHHHHHHHHhcCCccccCCC-----cceEEEeec
Confidence 7789999999999998 8999999999999999986310 245776654
No 484
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=46.58 E-value=9.3 Score=32.18 Aligned_cols=32 Identities=16% Similarity=0.142 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCce
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFF 84 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l 84 (214)
.-+|+.|||+++++++ ..+.|+++.|--.||-
T Consensus 29 ~~~si~elA~~~~vS~---aTv~Rf~kklG~~Gf~ 60 (278)
T PRK11557 29 RHLSSQQLANEAGVSQ---SSVVKFAQKLGYKGFP 60 (278)
T ss_pred HhcCHHHHHHHhCCCH---HHHHHHHHHcCCCCHH
Confidence 3489999999999999 7777777776666653
No 485
>PRK13558 bacterio-opsin activator; Provisional
Probab=46.48 E-value=22 Score=33.69 Aligned_cols=43 Identities=5% Similarity=-0.040 Sum_probs=35.2
Q ss_pred HHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHH
Q 040620 29 KSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLL 78 (214)
Q Consensus 29 ~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L 78 (214)
.-.+|.+|++.|.|+.=. ..|.+|||+++|+++ ..+...||..
T Consensus 612 q~e~l~~a~~~gyf~~pr----~~~~~e~a~~l~is~---~t~~~~lr~a 654 (665)
T PRK13558 612 QLTALQKAYVSGYFEWPR----RVEGEELAESMGISR---STFHQHLRAA 654 (665)
T ss_pred HHHHHHHHHHcCCCCCCc----cCCHHHHHHHhCCCH---HHHHHHHHHH
Confidence 456899999999998644 479999999999998 7777766643
No 486
>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=46.46 E-value=30 Score=27.32 Aligned_cols=36 Identities=14% Similarity=0.142 Sum_probs=28.2
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCCC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL 214 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~ 214 (214)
++...||-+|||-=+....+...+|+.++.-+|+|+
T Consensus 77 ~~~~qvV~LGaGlDTr~~Rl~~~~~~~~~~evD~p~ 112 (183)
T PF04072_consen 77 PGARQVVNLGAGLDTRAYRLDNPAGGVRWFEVDLPE 112 (183)
T ss_dssp TTESEEEEET-TT--HHHHHHHTTTTEEEEEEE-HH
T ss_pred CCCcEEEEcCCCCCchHHHhhccccceEEEEeCCHH
Confidence 356699999999999999999999999999999873
No 487
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=46.45 E-value=13 Score=29.59 Aligned_cols=39 Identities=8% Similarity=0.123 Sum_probs=31.2
Q ss_pred HHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHH
Q 040620 36 AIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLA 79 (214)
Q Consensus 36 a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~ 79 (214)
-++..|++.+.. ++.|+.+||++.|++. +++..++|+-.
T Consensus 20 ~~r~~Iy~~~~~--~~~sv~~vS~~ygi~~---~RV~AIvrLke 58 (172)
T PF12298_consen 20 ELREQIYEDVMQ--DGKSVREVSQKYGIKI---QRVEAIVRLKE 58 (172)
T ss_pred HHHHHHHHHHHh--CCCCHHHHHHHhCCCH---HHHHHHHHHHH
Confidence 344556777776 6789999999999998 99988888654
No 488
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=46.09 E-value=16 Score=24.28 Aligned_cols=23 Identities=17% Similarity=0.218 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILV 75 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlL 75 (214)
..+|.+++|+++|+++ ..+.+|+
T Consensus 17 ~~~t~~~lA~~~gis~---~tis~~~ 39 (78)
T TIGR02607 17 LGLSIRALAKALGVSR---STLSRIV 39 (78)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHH
Confidence 6789999999999998 7777774
No 489
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=46.05 E-value=8.6 Score=26.99 Aligned_cols=26 Identities=19% Similarity=0.059 Sum_probs=18.4
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHH
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLL 78 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L 78 (214)
.+.|-+|||+++|-++ ..+.+.|+++
T Consensus 2 ~G~tq~eIA~~lGks~---s~Vs~~l~Ll 27 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSR---SWVSNHLALL 27 (93)
T ss_dssp TT--HHHHHHHTT--H---HHHHHHHGGG
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHHHHH
Confidence 4689999999999998 8888887755
No 490
>PRK15340 transcriptional regulator InvF; Provisional
Probab=45.85 E-value=20 Score=29.64 Aligned_cols=33 Identities=9% Similarity=-0.166 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCcee
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFV 85 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~ 85 (214)
.+.++++||+.+|+++ ++++|+.+-......-.
T Consensus 124 ~~~sleeLA~~~gvS~---r~f~RlFk~~~G~tpk~ 156 (216)
T PRK15340 124 SGNTMRMLGEDYGVSY---THFRRLCSRALGGKAKS 156 (216)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHHHHHCcCHHH
Confidence 6789999999999999 99999988776666543
No 491
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=45.84 E-value=26 Score=33.18 Aligned_cols=36 Identities=11% Similarity=-0.069 Sum_probs=33.3
Q ss_pred CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620 50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK 88 (214)
Q Consensus 50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~ 88 (214)
.|.++.|+++.+++++ ..++++++.|+..|.+.+-.
T Consensus 487 ~~~~~~~~~~~~~~~~---~~~~~~l~~l~~~g~~~~~~ 522 (581)
T TIGR00475 487 KGAWVREFAEEVNGDE---KVMLKRVRKAGHRGGETLIV 522 (581)
T ss_pred CCCCHHHHHhhhCCCH---HHHHHHHHHHHhCCCEEEEe
Confidence 6889999999999998 99999999999999888775
No 492
>PF12692 Methyltransf_17: S-adenosyl-L-methionine methyltransferase; PDB: 3IHT_B.
Probab=45.74 E-value=32 Score=26.85 Aligned_cols=33 Identities=24% Similarity=0.457 Sum_probs=24.4
Q ss_pred CCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620 181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFACH 213 (214)
Q Consensus 181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp 213 (214)
..-|+|+|=|.|-.=-.|.+.+|+=++.|||+.
T Consensus 29 ~G~VlElGLGNGRTydHLRe~~p~R~I~vfDR~ 61 (160)
T PF12692_consen 29 PGPVLELGLGNGRTYDHLREIFPDRRIYVFDRA 61 (160)
T ss_dssp -S-EEEE--TTSHHHHHHHHH--SS-EEEEESS
T ss_pred CCceEEeccCCCccHHHHHHhCCCCeEEEEeee
Confidence 378999999999999999999999999999973
No 493
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=45.67 E-value=13 Score=24.57 Aligned_cols=20 Identities=10% Similarity=0.127 Sum_probs=13.4
Q ss_pred CHHHHHHHcCCCCCCcccHHHHH
Q 040620 53 TLTQIIVALNVHPNKTRCTQILV 75 (214)
Q Consensus 53 t~~eLA~~~g~~~~~~~~l~rlL 75 (214)
|..|||+++|++. ..+.++|
T Consensus 2 t~~~iA~~~gvS~---~TVSr~l 21 (70)
T smart00354 2 TIKDVARLAGVSK---ATVSRVL 21 (70)
T ss_pred CHHHHHHHHCCCH---HHHHHHH
Confidence 6678888888876 5554443
No 494
>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=45.50 E-value=28 Score=28.38 Aligned_cols=41 Identities=5% Similarity=0.134 Sum_probs=35.3
Q ss_pred CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCC
Q 040620 53 TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLP 102 (214)
Q Consensus 53 t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t 102 (214)
|-.+||+..|++. --+++-|..|+..|++..... .|.|=..
T Consensus 27 sE~eLa~~~~VSR---~TVR~Al~~L~~eGli~r~~G------~GtfV~~ 67 (230)
T TIGR02018 27 SEHELVAQYGCSR---MTVNRALRELTDAGLLERRQG------VGTFVAE 67 (230)
T ss_pred CHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEecC------CEEEEcc
Confidence 7889999999998 899999999999999998763 4666543
No 495
>COG4262 Predicted spermidine synthase with an N-terminal membrane domain [General function prediction only]
Probab=45.46 E-value=26 Score=31.66 Aligned_cols=34 Identities=21% Similarity=0.531 Sum_probs=27.8
Q ss_pred CCCCcEEeecCCchHHHHHHHHHCCCC-eEEEecCC
Q 040620 179 KGLKPLVDVGGSTGTMARAIATAFPDT-KCTVFACH 213 (214)
Q Consensus 179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l-~~~v~Dlp 213 (214)
.+.++++-+|||.|..++++.+ ||+. +++..|+-
T Consensus 288 ~~a~~vLvlGGGDGLAlRellk-yP~~~qI~lVdLD 322 (508)
T COG4262 288 RGARSVLVLGGGDGLALRELLK-YPQVEQITLVDLD 322 (508)
T ss_pred cccceEEEEcCCchHHHHHHHh-CCCcceEEEEecC
Confidence 4678999999999999999875 6855 58888874
No 496
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=45.37 E-value=9.1 Score=27.72 Aligned_cols=62 Identities=19% Similarity=0.279 Sum_probs=43.7
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH 104 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~ 104 (214)
..|+.+|-.-++++.+.||+..++++. +.++.-+-.|...|++...-.++.+. +-.|+.++-
T Consensus 24 I~IY~lLve~~~~mri~ei~rEl~is~---rtvr~~v~~l~rrGll~relvqkgWv-GYiya~~~P 85 (113)
T COG5625 24 IRIYSLLVEKGRGMRIREIQRELGISE---RTVRAAVAVLLRRGLLARELVQKGWV-GYIYATTPP 85 (113)
T ss_pred hhhhhHHHHhcCCchHHHHHHHHhHHH---HHHHHHHHHHHHhhHHHHHHHhccce-eeEecCCCC
Confidence 456677766656799999999999988 88888888888888887544333343 334444444
No 497
>PRK14096 pgi glucose-6-phosphate isomerase; Provisional
Probab=45.33 E-value=17 Score=34.14 Aligned_cols=43 Identities=14% Similarity=0.315 Sum_probs=34.0
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCC
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSG 82 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g 82 (214)
-.|-..|...+++.|+++||+++|.+. ....+..+||+|++.+
T Consensus 466 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~~~n~ 508 (528)
T PRK14096 466 KKVEELLKEDGGELSIEEIAAALGAPE-QVETIYKILRHLAANN 508 (528)
T ss_pred HHHHHHHhccCCCCCHHHHHHHcCCCc-cHHHHHHHHHHHhcCC
Confidence 445667766668999999999999944 2378999999999873
No 498
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=45.24 E-value=6.9 Score=36.50 Aligned_cols=40 Identities=13% Similarity=0.183 Sum_probs=31.9
Q ss_pred hhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620 44 IINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ 87 (214)
Q Consensus 44 ~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~ 87 (214)
++.+. ..+|++||++++|+++ ..+.+.|..|+..+++...
T Consensus 528 ~Fn~~-~~~t~~ei~~~~~~~~---~~l~~~L~~l~~~~~l~~~ 567 (588)
T PF00888_consen 528 LFNDN-DSLTVEEISEKTGISE---EELKRALKSLVKSKILILL 567 (588)
T ss_dssp GGGSS-SEEEHHHHHHHC---H---HHHHHHHHCCCTTTTCSEE
T ss_pred HHccC-CCccHHHHHHHHCcCH---HHHHHHHHHHHhCCcceee
Confidence 34444 7899999999999999 9999999999999999854
No 499
>KOG4058 consensus Uncharacterized conserved protein [Function unknown]
Probab=44.85 E-value=21 Score=28.07 Aligned_cols=33 Identities=21% Similarity=0.210 Sum_probs=23.1
Q ss_pred HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHC
Q 040620 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF 202 (214)
Q Consensus 168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 202 (214)
+.+++-.+ -.+..+++|+|.|.|....+.++.-
T Consensus 62 ~nVLSll~--~n~~GklvDlGSGDGRiVlaaar~g 94 (199)
T KOG4058|consen 62 ENVLSLLR--GNPKGKLVDLGSGDGRIVLAAARCG 94 (199)
T ss_pred HHHHHHcc--CCCCCcEEeccCCCceeehhhhhhC
Confidence 34444443 2334799999999999888877763
No 500
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=44.73 E-value=36 Score=27.35 Aligned_cols=58 Identities=17% Similarity=0.114 Sum_probs=44.0
Q ss_pred cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCC-CCCCccceeeCCCC
Q 040620 39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDG-KNEQEEESILLPPH 104 (214)
Q Consensus 39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~-~~~~~~~~y~~t~~ 104 (214)
+.+..+++=+ .|+|..+|.+--|++. .++++.|...|++++.+.. ++|. +-.|..|+.
T Consensus 95 lEtLAiIAY~-QPiTR~eI~~iRGv~~------~~~i~~L~e~glI~~~g~~~~~Gr-p~ly~tT~~ 153 (184)
T COG1386 95 LETLAIIAYK-QPVTRSEIEEIRGVAV------SQVISTLLERGLIREVGRRDTPGR-PYLYGTTEK 153 (184)
T ss_pred HHHHHHHHHc-CCccHHHHHHHhCccH------HHHHHHHHHCCCeEecCCCCCCCC-ceeeeccHH
Confidence 4456677766 8999999999999987 6689999999999988632 1222 345776666
Done!