Query 036188
Match_columns 210
No_of_seqs 119 out of 1085
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 10:17:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036188.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036188hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3178 Hydroxyindole-O-methyl 99.9 1.3E-23 2.8E-28 176.2 15.5 191 10-210 4-197 (342)
2 TIGR02716 C20_methyl_CrtF C-20 99.9 2.1E-23 4.5E-28 176.5 12.7 165 24-210 2-169 (306)
3 PF00891 Methyltransf_2: O-met 99.8 3E-19 6.5E-24 146.2 10.0 118 92-210 2-120 (241)
4 PF08100 Dimerisation: Dimeris 99.2 1.8E-11 3.9E-16 75.8 3.9 51 27-78 1-51 (51)
5 PF09339 HTH_IclR: IclR helix- 97.7 2.2E-05 4.8E-10 48.8 2.0 46 35-86 6-51 (52)
6 smart00346 HTH_ICLR helix_turn 97.5 0.00015 3.3E-09 49.9 4.5 58 34-101 7-64 (91)
7 smart00550 Zalpha Z-DNA-bindin 97.3 0.00056 1.2E-08 44.9 5.2 60 32-100 6-66 (68)
8 COG1414 IclR Transcriptional r 97.2 0.0004 8.7E-09 57.2 4.5 60 35-104 7-66 (246)
9 PF02082 Rrf2: Transcriptional 97.1 0.0007 1.5E-08 46.1 4.2 55 41-102 17-71 (83)
10 PF12840 HTH_20: Helix-turn-he 97.1 0.00067 1.4E-08 43.4 3.4 54 26-86 4-57 (61)
11 TIGR02431 pcaR_pcaU beta-ketoa 97.1 0.00067 1.5E-08 55.7 4.2 59 35-105 12-70 (248)
12 PRK11569 transcriptional repre 97.0 0.00083 1.8E-08 56.1 4.6 59 35-103 31-89 (274)
13 PRK10163 DNA-binding transcrip 97.0 0.00086 1.9E-08 55.9 4.7 60 35-104 28-87 (271)
14 PF01022 HTH_5: Bacterial regu 97.0 0.00076 1.6E-08 40.9 2.9 44 34-85 4-47 (47)
15 PRK09834 DNA-binding transcrip 97.0 0.0012 2.7E-08 54.7 5.0 61 35-105 14-74 (263)
16 PF13412 HTH_24: Winged helix- 96.9 0.0015 3.4E-08 39.5 3.8 45 33-84 4-48 (48)
17 PRK15090 DNA-binding transcrip 96.9 0.0012 2.7E-08 54.5 4.5 60 35-105 17-76 (257)
18 PRK10857 DNA-binding transcrip 96.7 0.0037 8.1E-08 48.3 5.4 61 27-100 9-69 (164)
19 PF04703 FaeA: FaeA-like prote 96.7 0.0039 8.4E-08 40.1 4.4 45 36-86 4-48 (62)
20 cd00092 HTH_CRP helix_turn_hel 96.7 0.0035 7.6E-08 40.3 4.2 44 48-100 24-67 (67)
21 PRK10141 DNA-binding transcrip 96.6 0.0038 8.3E-08 45.5 4.7 65 24-100 8-75 (117)
22 smart00419 HTH_CRP helix_turn_ 96.6 0.0037 8E-08 37.4 3.9 40 49-98 8-47 (48)
23 PF01978 TrmB: Sugar-specific 96.6 0.0019 4E-08 42.2 2.5 47 33-86 9-55 (68)
24 PRK06922 hypothetical protein; 96.5 0.0046 9.9E-08 57.3 5.4 59 150-209 377-437 (677)
25 COG1959 Predicted transcriptio 96.4 0.0063 1.4E-07 46.3 4.9 55 40-101 16-70 (150)
26 TIGR02010 IscR iron-sulfur clu 96.4 0.0067 1.5E-07 45.2 5.0 46 48-100 24-69 (135)
27 PF09012 FeoC: FeoC like trans 96.3 0.0048 1E-07 40.5 3.4 44 37-87 5-48 (69)
28 PF14947 HTH_45: Winged helix- 96.3 0.0036 7.8E-08 42.1 2.8 49 48-106 18-66 (77)
29 TIGR00738 rrf2_super rrf2 fami 96.2 0.0092 2E-07 44.0 4.8 46 48-100 24-69 (132)
30 PF13463 HTH_27: Winged helix 96.2 0.0069 1.5E-07 39.2 3.6 50 48-101 17-67 (68)
31 PF12802 MarR_2: MarR family; 96.0 0.0082 1.8E-07 38.1 3.2 48 34-86 7-54 (62)
32 TIGR02021 BchM-ChlM magnesium 96.0 0.017 3.6E-07 46.3 5.7 58 152-209 16-74 (219)
33 TIGR02944 suf_reg_Xantho FeS a 96.0 0.011 2.3E-07 43.7 4.2 46 48-100 24-69 (130)
34 smart00347 HTH_MARR helix_turn 96.0 0.014 3.1E-07 40.2 4.6 46 34-86 12-57 (101)
35 PRK11920 rirA iron-responsive 95.8 0.021 4.6E-07 43.5 5.1 61 27-101 9-69 (153)
36 smart00420 HTH_DEOR helix_turn 95.7 0.026 5.7E-07 34.1 4.6 43 37-86 5-47 (53)
37 PRK03902 manganese transport t 95.7 0.019 4.1E-07 43.1 4.6 50 48-106 21-70 (142)
38 PF08220 HTH_DeoR: DeoR-like h 95.7 0.026 5.6E-07 35.6 4.4 44 36-86 4-47 (57)
39 PF01047 MarR: MarR family; I 95.6 0.013 2.8E-07 36.8 3.0 46 34-86 5-50 (59)
40 PHA00738 putative HTH transcri 95.6 0.024 5.3E-07 40.4 4.6 47 33-86 13-59 (108)
41 TIGR00122 birA_repr_reg BirA b 95.6 0.024 5.3E-07 36.9 4.3 56 34-102 2-57 (69)
42 COG4742 Predicted transcriptio 95.6 0.018 4E-07 47.5 4.4 67 28-108 9-75 (260)
43 PRK11014 transcriptional repre 95.6 0.028 6E-07 42.2 5.0 61 27-100 9-69 (141)
44 PF13601 HTH_34: Winged helix 95.5 0.012 2.5E-07 39.9 2.4 64 33-103 1-66 (80)
45 PF08461 HTH_12: Ribonuclease 95.4 0.027 6E-07 36.6 4.0 60 37-103 3-63 (66)
46 TIGR02702 SufR_cyano iron-sulf 95.4 0.035 7.7E-07 44.2 5.3 65 35-107 4-72 (203)
47 TIGR02337 HpaR homoprotocatech 95.4 0.036 7.9E-07 40.0 4.9 66 34-106 30-96 (118)
48 PRK06266 transcription initiat 95.3 0.06 1.3E-06 42.2 6.2 45 35-86 25-69 (178)
49 PRK11050 manganese transport r 95.2 0.034 7.3E-07 42.4 4.5 57 37-105 42-98 (152)
50 smart00418 HTH_ARSR helix_turn 95.2 0.052 1.1E-06 33.9 4.7 42 37-86 2-43 (66)
51 PF01726 LexA_DNA_bind: LexA D 95.1 0.044 9.5E-07 35.6 4.1 42 40-86 18-59 (65)
52 TIGR01884 cas_HTH CRISPR locus 95.0 0.049 1.1E-06 43.4 5.0 58 34-101 145-202 (203)
53 COG3355 Predicted transcriptio 94.9 0.061 1.3E-06 39.6 4.9 47 34-87 29-76 (126)
54 cd00090 HTH_ARSR Arsenical Res 94.7 0.075 1.6E-06 34.2 4.7 45 34-86 9-53 (78)
55 smart00344 HTH_ASNC helix_turn 94.7 0.051 1.1E-06 38.5 4.0 46 33-85 4-49 (108)
56 PF08279 HTH_11: HTH domain; 94.7 0.052 1.1E-06 33.6 3.6 42 36-83 4-45 (55)
57 COG1321 TroR Mn-dependent tran 94.6 0.069 1.5E-06 40.8 4.7 50 48-106 23-72 (154)
58 PF06163 DUF977: Bacterial pro 94.6 0.084 1.8E-06 38.6 4.8 50 30-86 10-59 (127)
59 smart00345 HTH_GNTR helix_turn 94.5 0.085 1.9E-06 32.7 4.4 35 48-86 18-53 (60)
60 COG4190 Predicted transcriptio 94.3 0.098 2.1E-06 38.6 4.7 53 27-86 59-111 (144)
61 PF01638 HxlR: HxlR-like helix 94.2 0.03 6.5E-07 38.7 1.9 62 37-106 10-73 (90)
62 COG2264 PrmA Ribosomal protein 94.2 0.037 8E-07 46.8 2.7 43 165-210 140-182 (300)
63 PRK10258 biotin biosynthesis p 94.2 0.092 2E-06 42.9 5.1 32 177-209 30-61 (251)
64 PF07381 DUF1495: Winged helix 94.2 0.096 2.1E-06 36.3 4.2 68 31-105 8-86 (90)
65 COG2345 Predicted transcriptio 94.1 0.07 1.5E-06 43.0 3.9 64 37-107 16-82 (218)
66 TIGR00373 conserved hypothetic 94.0 0.1 2.2E-06 40.0 4.6 45 35-86 17-61 (158)
67 COG4189 Predicted transcriptio 93.9 0.11 2.5E-06 42.1 4.8 55 25-86 16-70 (308)
68 smart00529 HTH_DTXR Helix-turn 93.9 0.079 1.7E-06 36.6 3.5 46 52-106 2-47 (96)
69 PRK06474 hypothetical protein; 93.9 0.14 3E-06 40.1 5.3 73 27-105 6-82 (178)
70 cd07377 WHTH_GntR Winged helix 93.9 0.17 3.7E-06 31.9 4.9 33 50-86 26-58 (66)
71 PF04967 HTH_10: HTH DNA bindi 93.8 0.1 2.3E-06 32.4 3.6 43 25-77 5-47 (53)
72 cd07153 Fur_like Ferric uptake 93.8 0.12 2.6E-06 37.1 4.5 63 34-99 3-66 (116)
73 PF00325 Crp: Bacterial regula 93.8 0.067 1.4E-06 29.6 2.4 31 49-83 2-32 (32)
74 PRK06202 hypothetical protein; 93.8 0.1 2.3E-06 42.1 4.5 21 189-209 59-79 (232)
75 PRK15431 ferrous iron transpor 93.7 0.13 2.8E-06 34.5 4.0 43 37-86 7-49 (78)
76 PF07757 AdoMet_MTase: Predict 93.6 0.16 3.5E-06 36.3 4.6 35 173-208 42-76 (112)
77 COG2230 Cfa Cyclopropane fatty 93.4 0.1 2.3E-06 43.7 4.0 31 178-209 61-91 (283)
78 PF14394 DUF4423: Domain of un 93.3 0.17 3.6E-06 39.4 4.8 64 22-104 22-87 (171)
79 PRK00274 ksgA 16S ribosomal RN 93.3 0.099 2.1E-06 43.6 3.7 30 179-209 32-61 (272)
80 PRK07580 Mg-protoporphyrin IX 93.3 0.15 3.2E-06 40.9 4.6 22 188-209 61-82 (230)
81 PF04182 B-block_TFIIIC: B-blo 93.1 0.14 3E-06 34.1 3.6 49 33-86 3-51 (75)
82 TIGR01610 phage_O_Nterm phage 93.1 0.17 3.8E-06 35.3 4.2 44 48-99 46-89 (95)
83 PF01325 Fe_dep_repress: Iron 93.1 0.18 3.9E-06 32.1 3.9 35 48-86 21-55 (60)
84 PHA02943 hypothetical protein; 93.0 0.19 4.2E-06 38.0 4.5 105 36-171 15-119 (165)
85 TIGR02752 MenG_heptapren 2-hep 93.0 0.1 2.2E-06 42.0 3.3 29 180-209 36-64 (231)
86 PF02353 CMAS: Mycolic acid cy 92.9 0.099 2.1E-06 43.7 3.1 30 179-209 52-81 (273)
87 PRK15068 tRNA mo(5)U34 methylt 92.8 0.11 2.4E-06 44.4 3.4 27 182-209 115-141 (322)
88 PRK11188 rrmJ 23S rRNA methylt 92.7 0.15 3.3E-06 40.8 3.8 29 181-209 42-70 (209)
89 PF06325 PrmA: Ribosomal prote 92.6 0.085 1.8E-06 44.6 2.4 42 165-209 139-180 (295)
90 PRK11512 DNA-binding transcrip 92.6 0.24 5.2E-06 37.1 4.6 44 36-86 44-87 (144)
91 PRK04214 rbn ribonuclease BN/u 92.5 0.17 3.8E-06 44.7 4.3 43 48-99 309-351 (412)
92 PF00392 GntR: Bacterial regul 92.4 0.2 4.3E-06 32.0 3.5 35 48-86 22-57 (64)
93 PRK11036 putative S-adenosyl-L 92.2 0.17 3.6E-06 41.6 3.6 28 180-209 36-63 (255)
94 PF02002 TFIIE_alpha: TFIIE al 92.0 0.15 3.2E-06 36.2 2.7 43 37-86 18-60 (105)
95 TIGR00080 pimt protein-L-isoas 91.9 0.2 4.4E-06 40.1 3.7 29 180-209 68-96 (215)
96 COG2813 RsmC 16S RNA G1207 met 91.9 0.17 3.7E-06 42.7 3.3 31 179-210 148-178 (300)
97 COG4976 Predicted methyltransf 91.9 0.22 4.8E-06 40.6 3.8 46 162-208 94-143 (287)
98 PRK03573 transcriptional regul 91.9 0.34 7.5E-06 36.1 4.7 44 37-86 36-79 (144)
99 PRK11179 DNA-binding transcrip 91.8 0.27 5.9E-06 37.3 4.1 47 33-86 10-56 (153)
100 TIGR00452 methyltransferase, p 91.8 0.23 4.9E-06 42.4 4.0 29 180-209 112-140 (314)
101 PF08784 RPA_C: Replication pr 91.8 0.16 3.4E-06 35.8 2.6 51 32-86 47-98 (102)
102 PTZ00098 phosphoethanolamine N 91.6 0.22 4.7E-06 41.3 3.7 30 179-209 42-71 (263)
103 PF05148 Methyltransf_8: Hypot 91.5 0.39 8.4E-06 38.6 4.8 72 130-208 15-90 (219)
104 PRK11169 leucine-responsive tr 91.5 0.26 5.6E-06 37.9 3.8 47 32-85 14-60 (164)
105 PRK15001 SAM-dependent 23S rib 91.4 0.2 4.3E-06 43.9 3.3 29 180-209 219-247 (378)
106 TIGR01889 Staph_reg_Sar staphy 91.4 0.31 6.7E-06 34.7 3.9 66 34-104 27-95 (109)
107 COG1733 Predicted transcriptio 91.3 0.77 1.7E-05 33.5 5.8 86 4-106 4-91 (120)
108 PRK07402 precorrin-6B methylas 91.3 0.22 4.7E-06 39.2 3.2 28 181-209 32-59 (196)
109 COG3432 Predicted transcriptio 91.2 0.1 2.2E-06 36.5 1.1 62 37-106 20-82 (95)
110 PF13545 HTH_Crp_2: Crp-like h 91.1 0.27 5.8E-06 32.3 3.1 35 48-86 27-61 (76)
111 PRK13944 protein-L-isoaspartat 91.1 0.29 6.2E-06 38.9 3.8 29 180-209 63-91 (205)
112 PRK00107 gidB 16S rRNA methylt 91.1 0.36 7.8E-06 38.0 4.3 21 189-209 44-64 (187)
113 PLN02244 tocopherol O-methyltr 91.1 0.27 5.8E-06 42.4 3.8 21 189-209 117-137 (340)
114 PF07789 DUF1627: Protein of u 91.0 0.41 8.9E-06 36.0 4.2 35 48-86 5-39 (155)
115 PRK14165 winged helix-turn-hel 91.0 0.37 8.1E-06 38.9 4.3 53 48-106 20-72 (217)
116 PF10007 DUF2250: Uncharacteri 90.8 0.48 1E-05 33.0 4.2 46 34-86 9-54 (92)
117 TIGR00498 lexA SOS regulatory 90.8 0.46 1E-05 37.5 4.7 48 33-86 7-59 (199)
118 COG1522 Lrp Transcriptional re 90.7 0.42 9.1E-06 35.9 4.2 47 33-86 9-55 (154)
119 PRK11705 cyclopropane fatty ac 90.6 0.35 7.6E-06 42.4 4.2 30 179-209 157-186 (383)
120 KOG1271 Methyltransferases [Ge 90.6 0.27 5.9E-06 38.7 3.0 21 190-210 67-87 (227)
121 PRK13942 protein-L-isoaspartat 90.5 0.33 7.1E-06 38.9 3.7 30 179-209 66-95 (212)
122 PRK12335 tellurite resistance 90.5 0.24 5.3E-06 41.5 3.0 28 181-209 112-139 (287)
123 TIGR03587 Pse_Me-ase pseudamin 90.4 0.23 4.9E-06 39.7 2.6 21 189-209 42-62 (204)
124 PRK00121 trmB tRNA (guanine-N( 90.3 0.27 5.9E-06 39.0 3.0 28 180-209 32-59 (202)
125 PF03444 HrcA_DNA-bdg: Winged 90.2 0.65 1.4E-05 31.2 4.2 48 48-102 22-69 (78)
126 PRK11639 zinc uptake transcrip 90.0 0.86 1.9E-05 35.3 5.5 79 1-87 1-80 (169)
127 COG2512 Predicted membrane-ass 89.8 0.42 9.1E-06 39.7 3.8 47 34-86 197-243 (258)
128 TIGR02147 Fsuc_second hypothet 89.6 0.63 1.4E-05 38.9 4.7 47 49-104 137-185 (271)
129 PF09929 DUF2161: Uncharacteri 89.6 0.75 1.6E-05 33.3 4.5 52 37-103 64-115 (118)
130 PRK13509 transcriptional repre 89.6 0.68 1.5E-05 38.1 4.9 45 35-86 8-52 (251)
131 TIGR00740 methyltransferase, p 89.6 0.24 5.2E-06 40.2 2.2 21 189-209 52-72 (239)
132 COG1378 Predicted transcriptio 89.5 0.84 1.8E-05 37.6 5.3 59 37-105 21-79 (247)
133 PF05732 RepL: Firmicute plasm 89.4 0.47 1E-05 36.7 3.5 45 50-103 76-120 (165)
134 COG4565 CitB Response regulato 89.3 0.5 1.1E-05 37.9 3.7 44 37-86 163-206 (224)
135 PRK11088 rrmA 23S rRNA methylt 89.3 0.46 9.9E-06 39.5 3.7 20 190-209 85-104 (272)
136 COG2227 UbiG 2-polyprenyl-3-me 89.3 0.22 4.9E-06 40.7 1.8 19 191-209 60-78 (243)
137 PLN02336 phosphoethanolamine N 89.2 0.37 8E-06 43.3 3.3 30 179-209 256-285 (475)
138 PF12793 SgrR_N: Sugar transpo 89.2 0.54 1.2E-05 34.1 3.5 35 48-86 18-52 (115)
139 TIGR00406 prmA ribosomal prote 89.1 0.47 1E-05 39.9 3.7 27 181-209 152-178 (288)
140 KOG1541 Predicted protein carb 89.0 0.22 4.7E-06 40.4 1.5 29 179-208 38-68 (270)
141 PF00165 HTH_AraC: Bacterial r 88.9 0.42 9.1E-06 27.7 2.3 29 48-80 7-35 (42)
142 PRK04172 pheS phenylalanyl-tRN 88.9 0.44 9.5E-06 43.2 3.6 66 33-108 7-72 (489)
143 TIGR00138 gidB 16S rRNA methyl 88.8 0.27 5.8E-06 38.5 1.8 19 191-209 43-61 (181)
144 PRK05785 hypothetical protein; 88.6 0.29 6.2E-06 39.6 2.0 19 191-209 52-70 (226)
145 PRK05638 threonine synthase; V 88.5 0.63 1.4E-05 41.6 4.2 60 37-105 376-437 (442)
146 PRK09489 rsmC 16S ribosomal RN 88.4 0.5 1.1E-05 40.8 3.5 28 181-209 188-215 (342)
147 KOG2899 Predicted methyltransf 88.4 0.33 7E-06 39.9 2.1 31 180-210 47-78 (288)
148 PRK15451 tRNA cmo(5)U34 methyl 88.3 0.34 7.5E-06 39.6 2.2 21 189-209 55-75 (247)
149 PLN02233 ubiquinone biosynthes 88.2 0.84 1.8E-05 37.8 4.5 22 188-209 71-92 (261)
150 smart00138 MeTrc Methyltransfe 88.2 2.6 5.7E-05 34.9 7.5 24 179-203 89-112 (264)
151 PF08003 Methyltransf_9: Prote 88.2 0.37 8E-06 40.9 2.4 29 180-209 106-134 (315)
152 PF13404 HTH_AsnC-type: AsnC-t 88.2 0.8 1.7E-05 26.9 3.2 37 33-76 4-40 (42)
153 COG1497 Predicted transcriptio 88.2 0.77 1.7E-05 37.5 4.1 94 36-142 14-110 (260)
154 PF13730 HTH_36: Helix-turn-he 88.1 0.55 1.2E-05 28.8 2.6 30 50-83 26-55 (55)
155 PRK00216 ubiE ubiquinone/menaq 88.1 0.56 1.2E-05 37.5 3.4 29 180-209 42-70 (239)
156 COG5631 Predicted transcriptio 88.0 1.9 4.1E-05 33.1 5.8 77 20-103 64-147 (199)
157 PF02796 HTH_7: Helix-turn-hel 87.8 0.44 9.4E-06 28.3 1.9 30 37-75 14-43 (45)
158 TIGR03438 probable methyltrans 87.8 0.68 1.5E-05 39.1 3.8 20 190-209 63-82 (301)
159 TIGR00478 tly hemolysin TlyA f 87.7 0.85 1.8E-05 37.1 4.2 30 179-209 64-94 (228)
160 PRK04266 fibrillarin; Provisio 87.6 0.67 1.5E-05 37.6 3.6 25 184-209 67-91 (226)
161 PRK00377 cbiT cobalt-precorrin 87.6 0.55 1.2E-05 37.0 3.0 27 182-209 33-59 (198)
162 TIGR03534 RF_mod_PrmC protein- 87.6 0.64 1.4E-05 37.6 3.4 20 190-209 87-106 (251)
163 PRK00517 prmA ribosomal protei 87.4 0.39 8.4E-06 39.4 2.0 21 189-209 118-138 (250)
164 COG2226 UbiE Methylase involve 87.4 0.63 1.4E-05 38.1 3.2 21 190-210 51-71 (238)
165 PRK05134 bifunctional 3-demeth 87.0 0.94 2E-05 36.4 4.1 20 190-209 48-67 (233)
166 PRK00312 pcm protein-L-isoaspa 87.0 0.84 1.8E-05 36.2 3.7 28 180-208 69-96 (212)
167 PLN02396 hexaprenyldihydroxybe 86.9 0.43 9.4E-06 40.9 2.2 20 190-209 131-150 (322)
168 PRK14121 tRNA (guanine-N(7)-)- 86.9 0.72 1.6E-05 40.6 3.5 29 180-209 113-141 (390)
169 PRK10411 DNA-binding transcrip 86.9 1.2 2.6E-05 36.4 4.7 46 34-86 6-51 (240)
170 PF13384 HTH_23: Homeodomain-l 86.8 0.63 1.4E-05 27.9 2.3 40 34-82 7-46 (50)
171 PRK09328 N5-glutamine S-adenos 86.8 0.74 1.6E-05 37.9 3.5 22 188-209 106-127 (275)
172 PRK00215 LexA repressor; Valid 86.3 1.4 3E-05 34.9 4.7 36 48-86 22-57 (205)
173 PLN02585 magnesium protoporphy 86.2 0.52 1.1E-05 40.3 2.2 20 190-209 144-163 (315)
174 COG2890 HemK Methylase of poly 86.1 0.78 1.7E-05 38.5 3.2 18 193-210 113-130 (280)
175 PRK10906 DNA-binding transcrip 86.1 1.1 2.4E-05 37.0 4.1 46 34-86 7-52 (252)
176 PRK09802 DNA-binding transcrip 86.0 1.2 2.6E-05 37.1 4.3 47 33-86 18-64 (269)
177 TIGR03704 PrmC_rel_meth putati 86.0 0.92 2E-05 37.4 3.6 20 190-209 86-105 (251)
178 COG4123 Predicted O-methyltran 85.9 0.82 1.8E-05 37.7 3.2 30 181-210 35-64 (248)
179 PRK11886 bifunctional biotin-- 85.9 1.5 3.2E-05 37.3 4.9 57 35-102 7-63 (319)
180 PRK10434 srlR DNA-bindng trans 85.7 1.1 2.4E-05 37.1 3.9 46 34-86 7-52 (256)
181 PF12324 HTH_15: Helix-turn-he 85.7 0.89 1.9E-05 30.4 2.7 35 37-78 29-63 (77)
182 PF05584 Sulfolobus_pRN: Sulfo 85.7 2.1 4.5E-05 28.3 4.4 42 37-86 10-51 (72)
183 PRK10870 transcriptional repre 85.6 1.1 2.5E-05 34.8 3.7 55 48-106 70-125 (176)
184 PF01209 Ubie_methyltran: ubiE 85.4 0.7 1.5E-05 37.7 2.6 22 188-209 45-66 (233)
185 PF08221 HTH_9: RNA polymerase 85.4 1.2 2.5E-05 28.5 3.1 43 37-86 18-60 (62)
186 COG1846 MarR Transcriptional r 85.1 1.5 3.2E-05 30.9 4.0 68 32-106 22-90 (126)
187 PF02319 E2F_TDP: E2F/DP famil 85.1 0.38 8.2E-06 31.7 0.7 37 48-86 23-62 (71)
188 PRK00811 spermidine synthase; 85.0 0.7 1.5E-05 38.7 2.5 22 189-210 75-96 (283)
189 PF01475 FUR: Ferric uptake re 84.8 1.2 2.6E-05 32.1 3.3 66 32-100 8-74 (120)
190 PRK10046 dpiA two-component re 84.6 1.5 3.2E-05 35.0 4.1 45 36-86 166-210 (225)
191 PLN02366 spermidine synthase 84.5 0.73 1.6E-05 39.2 2.4 23 188-210 89-111 (308)
192 PF01135 PCMT: Protein-L-isoas 84.5 1.2 2.5E-05 35.8 3.4 30 179-209 62-91 (209)
193 PLN02853 Probable phenylalanyl 84.3 1.1 2.3E-05 40.6 3.4 69 32-110 3-73 (492)
194 PRK13943 protein-L-isoaspartat 84.0 1.2 2.7E-05 38.1 3.5 29 180-209 71-99 (322)
195 PHA02701 ORF020 dsRNA-binding 83.9 1.8 3.8E-05 33.9 4.0 48 33-86 5-52 (183)
196 COG1349 GlpR Transcriptional r 83.9 1.6 3.5E-05 36.0 4.1 45 35-86 8-52 (253)
197 PF05185 PRMT5: PRMT5 arginine 83.8 1.8 4E-05 38.8 4.7 52 150-208 150-204 (448)
198 PF13518 HTH_28: Helix-turn-he 83.7 1.8 3.8E-05 25.9 3.3 29 50-82 13-41 (52)
199 PRK13168 rumA 23S rRNA m(5)U19 83.6 0.7 1.5E-05 41.3 2.0 29 180-209 288-316 (443)
200 PRK11534 DNA-binding transcrip 83.5 2.2 4.9E-05 34.1 4.7 37 46-86 27-63 (224)
201 KOG1270 Methyltransferases [Co 83.4 0.56 1.2E-05 38.9 1.1 18 192-209 91-108 (282)
202 COG2263 Predicted RNA methylas 83.2 0.94 2E-05 35.8 2.3 20 190-209 45-64 (198)
203 KOG3115 Methyltransferase-like 82.9 0.72 1.6E-05 37.0 1.5 20 190-209 60-79 (249)
204 TIGR03533 L3_gln_methyl protei 82.8 0.8 1.7E-05 38.4 1.9 20 190-209 121-140 (284)
205 TIGR02787 codY_Gpos GTP-sensin 82.7 2.4 5.2E-05 34.8 4.5 45 36-86 187-231 (251)
206 COG3413 Predicted DNA binding 82.7 1.7 3.7E-05 34.8 3.7 45 23-77 158-202 (215)
207 COG1802 GntR Transcriptional r 82.6 2.8 6.1E-05 33.7 5.0 37 46-86 36-72 (230)
208 smart00531 TFIIE Transcription 82.5 1.6 3.6E-05 32.9 3.3 41 36-83 5-45 (147)
209 PF03141 Methyltransf_29: Puta 82.5 0.99 2.1E-05 40.7 2.4 22 189-210 116-137 (506)
210 TIGR00536 hemK_fam HemK family 82.3 1.4 3E-05 36.9 3.2 18 192-209 116-133 (284)
211 PRK13777 transcriptional regul 82.1 2.5 5.5E-05 33.2 4.4 63 37-106 50-113 (185)
212 PF08123 DOT1: Histone methyla 82.1 2.3 5E-05 34.0 4.2 28 180-208 33-60 (205)
213 PRK09775 putative DNA-binding 81.8 2.4 5.2E-05 38.0 4.6 40 37-86 5-44 (442)
214 PTZ00326 phenylalanyl-tRNA syn 81.8 1.8 3.9E-05 39.2 3.8 70 32-110 6-76 (494)
215 PF09904 HTH_43: Winged helix- 81.7 2.2 4.7E-05 29.4 3.3 59 34-100 10-70 (90)
216 COG1510 Predicted transcriptio 81.7 1.4 3.1E-05 34.1 2.7 35 48-86 40-74 (177)
217 KOG2904 Predicted methyltransf 81.6 1.7 3.7E-05 36.5 3.3 23 188-210 146-168 (328)
218 PF02295 z-alpha: Adenosine de 81.4 2.7 5.9E-05 27.2 3.6 60 33-100 5-64 (66)
219 PHA02591 hypothetical protein; 81.3 1.8 3.9E-05 28.9 2.7 31 37-75 51-81 (83)
220 TIGR03338 phnR_burk phosphonat 81.2 2.7 5.9E-05 33.2 4.4 36 47-86 32-67 (212)
221 PLN02490 MPBQ/MSBQ methyltrans 81.2 2 4.3E-05 37.2 3.8 28 181-209 104-132 (340)
222 COG2518 Pcm Protein-L-isoaspar 80.9 2 4.3E-05 34.5 3.4 30 179-209 62-91 (209)
223 COG1675 TFA1 Transcription ini 80.9 2.5 5.3E-05 33.0 3.8 45 35-86 21-65 (176)
224 PRK12423 LexA repressor; Provi 80.9 3.1 6.7E-05 33.0 4.6 35 49-86 25-59 (202)
225 TIGR01321 TrpR trp operon repr 80.7 2.4 5.2E-05 29.6 3.4 40 31-78 41-80 (94)
226 PRK11642 exoribonuclease R; Pr 80.4 2.7 5.9E-05 40.6 4.7 57 37-100 24-80 (813)
227 PRK10909 rsmD 16S rRNA m(2)G96 80.2 1.8 3.8E-05 34.5 2.9 19 190-208 53-71 (199)
228 PRK11805 N5-glutamine S-adenos 79.9 1 2.2E-05 38.3 1.5 18 192-209 135-152 (307)
229 PRK09334 30S ribosomal protein 79.9 2.4 5.2E-05 29.1 3.1 46 37-86 28-74 (86)
230 PRK11414 colanic acid/biofilm 79.9 3.8 8.2E-05 32.7 4.8 37 46-86 31-67 (221)
231 PRK03522 rumB 23S rRNA methylu 79.8 2 4.2E-05 36.6 3.3 19 191-209 174-192 (315)
232 PRK11753 DNA-binding transcrip 79.8 2.5 5.4E-05 33.1 3.7 34 49-86 168-201 (211)
233 KOG1540 Ubiquinone biosynthesi 79.4 3.8 8.1E-05 34.1 4.6 43 165-210 75-120 (296)
234 PRK04424 fatty acid biosynthes 79.3 1.4 3E-05 34.6 2.0 46 34-86 9-54 (185)
235 PRK11873 arsM arsenite S-adeno 79.2 1.5 3.2E-05 36.3 2.3 21 188-208 75-95 (272)
236 COG4519 Uncharacterized protei 79.2 5.3 0.00012 26.9 4.4 35 48-86 21-55 (95)
237 PF09681 Phage_rep_org_N: N-te 79.0 3.7 8.1E-05 30.0 4.1 49 48-105 52-100 (121)
238 TIGR03697 NtcA_cyano global ni 78.9 2.9 6.3E-05 32.2 3.8 34 49-86 143-176 (193)
239 PRK09464 pdhR transcriptional 78.9 3.2 6.9E-05 33.9 4.2 46 47-100 31-77 (254)
240 PF13936 HTH_38: Helix-turn-he 78.9 1.8 3.9E-05 25.5 2.0 24 48-75 19-42 (44)
241 TIGR00635 ruvB Holliday juncti 78.8 2.1 4.5E-05 35.9 3.1 35 48-86 254-289 (305)
242 PRK04457 spermidine synthase; 78.8 1.5 3.2E-05 36.4 2.2 21 189-209 65-85 (262)
243 PRK10225 DNA-binding transcrip 78.6 3.2 6.9E-05 34.0 4.1 46 46-99 29-75 (257)
244 COG1725 Predicted transcriptio 78.6 3.2 7E-05 30.5 3.6 43 49-99 35-77 (125)
245 TIGR01983 UbiG ubiquinone bios 78.5 1.6 3.4E-05 34.7 2.2 20 190-209 45-64 (224)
246 PF05331 DUF742: Protein of un 78.4 3.2 7E-05 30.0 3.6 35 48-86 54-88 (114)
247 PRK01544 bifunctional N5-gluta 78.4 1.3 2.7E-05 40.4 1.8 19 191-209 139-157 (506)
248 PHA03412 putative methyltransf 78.3 1.1 2.5E-05 36.6 1.3 19 191-209 50-68 (241)
249 PRK14966 unknown domain/N5-glu 78.3 1.5 3.2E-05 39.0 2.1 20 190-209 251-270 (423)
250 TIGR02812 fadR_gamma fatty aci 78.3 3.5 7.7E-05 33.2 4.3 46 46-99 26-72 (235)
251 PRK01581 speE spermidine synth 78.3 1.6 3.4E-05 38.1 2.3 73 127-210 90-170 (374)
252 PRK09954 putative kinase; Prov 78.2 2.7 5.9E-05 36.2 3.8 44 34-84 5-48 (362)
253 PF08280 HTH_Mga: M protein tr 78.1 2.4 5.2E-05 26.6 2.5 39 33-78 6-44 (59)
254 PRK09990 DNA-binding transcrip 77.9 4 8.6E-05 33.3 4.4 46 46-99 27-73 (251)
255 PRK11161 fumarate/nitrate redu 77.8 2.4 5.2E-05 34.0 3.1 34 49-86 184-217 (235)
256 PRK01381 Trp operon repressor; 77.8 3.3 7.2E-05 29.1 3.3 53 16-78 28-80 (99)
257 KOG1499 Protein arginine N-met 77.8 1.6 3.4E-05 37.7 2.0 18 190-207 60-77 (346)
258 PRK10736 hypothetical protein; 77.7 3.4 7.3E-05 36.2 4.1 43 36-86 312-354 (374)
259 PTZ00146 fibrillarin; Provisio 77.7 1.6 3.4E-05 37.0 2.0 22 188-209 130-151 (293)
260 TIGR00417 speE spermidine synt 77.6 1.9 4E-05 35.9 2.4 21 189-209 71-91 (270)
261 TIGR01177 conserved hypothetic 77.4 3 6.6E-05 35.6 3.8 27 181-208 174-200 (329)
262 COG0735 Fur Fe2+/Zn2+ uptake r 77.1 4.6 9.9E-05 30.4 4.2 66 34-102 23-89 (145)
263 TIGR02698 CopY_TcrY copper tra 76.9 5.6 0.00012 29.3 4.6 47 33-86 5-55 (130)
264 COG3695 Predicted methylated D 76.7 3.2 7E-05 29.2 3.0 48 34-83 8-55 (103)
265 PRK10421 DNA-binding transcrip 76.6 4.4 9.6E-05 33.1 4.4 46 46-99 22-68 (253)
266 PRK04984 fatty acid metabolism 76.5 4.2 9.1E-05 32.8 4.2 45 47-99 28-73 (239)
267 PF11994 DUF3489: Protein of u 76.4 9.6 0.00021 25.2 5.0 41 37-84 15-57 (72)
268 PRK10901 16S rRNA methyltransf 76.4 1.9 4.1E-05 38.3 2.3 49 27-79 72-124 (427)
269 PRK09462 fur ferric uptake reg 76.3 5.3 0.00011 30.0 4.4 54 33-87 18-72 (148)
270 TIGR00095 RNA methyltransferas 76.3 2.1 4.5E-05 33.7 2.3 20 191-210 50-69 (189)
271 TIGR03879 near_KaiC_dom probab 76.2 2 4.4E-05 28.5 1.8 33 48-84 31-63 (73)
272 TIGR00479 rumA 23S rRNA (uraci 76.0 2.2 4.8E-05 37.8 2.6 22 188-209 290-311 (431)
273 PRK14902 16S rRNA methyltransf 75.6 2 4.4E-05 38.3 2.3 51 27-81 74-129 (444)
274 PRK09391 fixK transcriptional 75.6 3.9 8.5E-05 32.9 3.8 34 49-86 179-212 (230)
275 PF03297 Ribosomal_S25: S25 ri 75.5 3.9 8.4E-05 29.1 3.2 46 37-86 46-92 (105)
276 PF06969 HemN_C: HemN C-termin 75.3 5.2 0.00011 25.3 3.6 46 48-103 19-65 (66)
277 PRK03837 transcriptional regul 74.9 5.7 0.00012 32.0 4.6 45 47-99 34-79 (241)
278 COG0293 FtsJ 23S rRNA methylas 74.8 4.5 9.8E-05 32.4 3.8 43 167-209 22-64 (205)
279 PRK11523 DNA-binding transcrip 74.4 5.1 0.00011 32.7 4.2 46 47-100 29-75 (253)
280 PRK13239 alkylmercury lyase; P 73.8 3.6 7.7E-05 33.0 3.0 41 33-80 23-63 (206)
281 PRK03612 spermidine synthase; 73.8 2.6 5.6E-05 38.6 2.5 22 189-210 296-317 (521)
282 PHA03411 putative methyltransf 73.7 2.1 4.6E-05 35.9 1.8 19 191-209 65-83 (279)
283 PF11972 HTH_13: HTH DNA bindi 73.7 7.3 0.00016 24.2 3.7 46 37-97 4-49 (54)
284 PF03374 ANT: Phage antirepres 73.7 7.2 0.00016 27.5 4.4 44 34-86 11-54 (111)
285 PF13443 HTH_26: Cro/C1-type H 73.6 2.5 5.3E-05 26.5 1.7 31 37-75 2-32 (63)
286 TIGR02085 meth_trns_rumB 23S r 73.5 2.5 5.5E-05 36.9 2.3 19 191-209 234-252 (374)
287 PLN02781 Probable caffeoyl-CoA 73.1 4.9 0.00011 32.7 3.8 22 188-209 66-87 (234)
288 TIGR03826 YvyF flagellar opero 73.1 4.6 9.9E-05 30.2 3.2 35 36-75 34-68 (137)
289 PRK13918 CRP/FNR family transc 72.8 4.2 9.2E-05 31.6 3.3 34 49-86 149-182 (202)
290 PF04539 Sigma70_r3: Sigma-70 72.7 3.3 7.1E-05 27.2 2.2 34 48-85 19-52 (78)
291 smart00421 HTH_LUXR helix_turn 72.4 5.4 0.00012 23.7 3.1 25 49-77 18-42 (58)
292 COG3398 Uncharacterized protei 72.4 4.3 9.3E-05 32.8 3.1 63 27-101 169-234 (240)
293 KOG2165 Anaphase-promoting com 71.8 4.9 0.00011 37.8 3.7 48 48-100 615-662 (765)
294 PF03428 RP-C: Replication pro 71.8 5.3 0.00012 31.2 3.5 55 26-86 46-104 (177)
295 PRK11511 DNA-binding transcrip 71.6 6.4 0.00014 28.7 3.8 43 38-85 15-57 (127)
296 PF09821 AAA_assoc_C: C-termin 71.2 3.4 7.4E-05 30.2 2.2 46 54-109 2-47 (120)
297 KOG1500 Protein arginine N-met 71.1 7.5 0.00016 33.7 4.5 18 188-206 176-193 (517)
298 COG1654 BirA Biotin operon rep 71.1 9.8 0.00021 25.6 4.2 50 48-105 18-67 (79)
299 COG4901 Ribosomal protein S25 70.9 4.7 0.0001 28.4 2.7 48 35-86 44-92 (107)
300 cd06170 LuxR_C_like C-terminal 70.9 6.5 0.00014 23.5 3.2 34 35-77 6-39 (57)
301 PF08222 HTH_CodY: CodY helix- 70.8 6 0.00013 24.9 2.8 35 48-86 3-37 (61)
302 PF00126 HTH_1: Bacterial regu 70.7 5.8 0.00013 24.8 3.0 54 34-102 3-59 (60)
303 PRK14999 histidine utilization 70.6 8 0.00017 31.3 4.5 45 48-100 34-79 (241)
304 PF09107 SelB-wing_3: Elongati 70.6 11 0.00024 23.0 4.0 41 39-86 3-43 (50)
305 PF10668 Phage_terminase: Phag 70.5 5.8 0.00012 25.3 2.8 22 48-73 21-42 (60)
306 PRK10402 DNA-binding transcrip 70.5 5.7 0.00012 31.8 3.6 34 49-86 169-202 (226)
307 smart00342 HTH_ARAC helix_turn 70.1 5.1 0.00011 25.8 2.7 29 49-81 1-29 (84)
308 PF00196 GerE: Bacterial regul 69.9 4.3 9.4E-05 25.1 2.2 35 33-76 7-41 (58)
309 PRK10219 DNA-binding transcrip 69.8 5.5 0.00012 27.9 3.0 33 48-84 20-52 (107)
310 KOG2651 rRNA adenine N-6-methy 69.7 4.3 9.3E-05 35.7 2.8 29 180-208 143-171 (476)
311 PF04157 EAP30: EAP30/Vps36 fa 69.6 5 0.00011 32.4 3.0 45 35-85 177-222 (223)
312 TIGR02018 his_ut_repres histid 69.6 8.3 0.00018 31.0 4.4 45 48-100 23-68 (230)
313 COG3398 Uncharacterized protei 69.5 14 0.00031 29.9 5.5 52 28-86 97-148 (240)
314 TIGR03433 padR_acidobact trans 68.8 16 0.00036 25.3 5.2 62 37-106 9-81 (100)
315 TIGR01714 phage_rep_org_N phag 68.4 10 0.00023 27.6 4.2 48 48-104 50-97 (119)
316 COG4367 Uncharacterized protei 68.2 5.3 0.00012 27.4 2.4 26 48-77 22-47 (97)
317 PF10771 DUF2582: Protein of u 68.1 6.1 0.00013 25.6 2.6 41 37-84 13-53 (65)
318 PRK00135 scpB segregation and 68.1 9.2 0.0002 30.2 4.2 42 35-86 93-134 (188)
319 PRK00536 speE spermidine synth 67.8 4.7 0.0001 33.5 2.6 23 188-210 70-92 (262)
320 COG3963 Phospholipid N-methylt 67.8 7.7 0.00017 30.3 3.5 33 177-210 36-68 (194)
321 COG0220 Predicted S-adenosylme 67.6 3.7 8.1E-05 33.4 1.9 20 191-210 49-68 (227)
322 COG2186 FadR Transcriptional r 67.6 8.5 0.00018 31.4 4.1 41 51-99 36-76 (241)
323 smart00342 HTH_ARAC helix_turn 67.5 29 0.00064 22.1 6.3 37 36-79 41-77 (84)
324 smart00088 PINT motif in prote 67.4 16 0.00034 24.4 4.8 52 28-86 6-57 (88)
325 smart00753 PAM PCI/PINT associ 67.4 16 0.00034 24.4 4.8 52 28-86 6-57 (88)
326 PRK09764 DNA-binding transcrip 67.3 10 0.00022 30.7 4.5 45 48-100 27-72 (240)
327 TIGR01764 excise DNA binding d 67.3 5.4 0.00012 23.1 2.2 22 50-75 2-23 (49)
328 cd04762 HTH_MerR-trunc Helix-T 67.1 5.5 0.00012 22.9 2.2 23 50-76 1-23 (49)
329 PF13814 Replic_Relax: Replica 67.0 8.7 0.00019 29.7 3.9 60 40-106 3-70 (191)
330 PF14338 Mrr_N: Mrr N-terminal 66.7 16 0.00034 25.0 4.7 30 73-107 60-89 (92)
331 PF04545 Sigma70_r4: Sigma-70, 66.5 6.2 0.00014 23.5 2.4 26 48-77 19-44 (50)
332 COG2524 Predicted transcriptio 66.4 14 0.0003 30.8 4.9 52 48-106 24-76 (294)
333 PF09824 ArsR: ArsR transcript 66.4 9 0.0002 29.2 3.6 48 27-85 12-59 (160)
334 KOG0820 Ribosomal RNA adenine 66.4 8.5 0.00018 32.4 3.7 32 178-210 47-78 (315)
335 PRK03601 transcriptional regul 66.3 7.2 0.00016 32.0 3.5 59 34-107 5-66 (275)
336 PF02787 CPSase_L_D3: Carbamoy 66.1 6.3 0.00014 28.8 2.7 40 37-85 16-55 (123)
337 PRK13626 transcriptional regul 66.1 6.9 0.00015 36.0 3.6 36 48-87 22-57 (552)
338 COG2390 DeoR Transcriptional r 66.1 6.6 0.00014 33.7 3.2 35 48-86 25-59 (321)
339 PF13542 HTH_Tnp_ISL3: Helix-t 65.9 10 0.00022 22.7 3.2 34 35-77 18-51 (52)
340 TIGR00563 rsmB ribosomal RNA s 65.7 4.1 9E-05 36.2 2.0 30 179-209 228-257 (426)
341 KOG4589 Cell division protein 65.7 8.4 0.00018 30.6 3.4 26 183-208 62-87 (232)
342 PHA03103 double-strand RNA-bin 65.7 10 0.00022 29.8 3.9 43 37-86 18-60 (183)
343 PRK10430 DNA-binding transcrip 65.3 8.8 0.00019 30.8 3.7 35 48-86 177-211 (239)
344 PRK00082 hrcA heat-inducible t 65.2 9.5 0.00021 32.9 4.1 47 48-102 24-72 (339)
345 TIGR02404 trehalos_R_Bsub treh 65.1 9.5 0.00021 30.7 3.9 41 51-99 26-66 (233)
346 COG0640 ArsR Predicted transcr 65.1 16 0.00035 24.2 4.6 53 27-86 20-72 (110)
347 TIGR02844 spore_III_D sporulat 64.9 8 0.00017 26.1 2.8 32 35-74 9-40 (80)
348 PF10294 Methyltransf_16: Puta 64.9 4 8.7E-05 31.5 1.6 22 188-209 43-64 (173)
349 PLN02672 methionine S-methyltr 64.8 3.7 8.1E-05 40.8 1.6 19 191-209 119-137 (1082)
350 KOG3045 Predicted RNA methylas 64.3 11 0.00025 31.5 4.1 55 152-206 138-196 (325)
351 TIGR02297 HpaA 4-hydroxyphenyl 64.3 7.7 0.00017 32.0 3.3 68 38-119 192-259 (287)
352 PF03551 PadR: Transcriptional 64.3 7.5 0.00016 25.4 2.6 61 39-103 3-70 (75)
353 PF01371 Trp_repressor: Trp re 64.2 11 0.00025 25.8 3.5 39 31-78 35-74 (87)
354 PF14557 AphA_like: Putative A 64.1 16 0.00035 28.3 4.6 70 29-103 8-83 (175)
355 TIGR02325 C_P_lyase_phnF phosp 63.8 11 0.00023 30.3 3.9 45 48-100 30-75 (238)
356 PF05344 DUF746: Domain of Unk 63.8 10 0.00022 24.5 3.0 28 48-79 12-39 (65)
357 PRK00080 ruvB Holliday junctio 63.3 7.6 0.00016 33.1 3.1 35 48-86 275-310 (328)
358 PF13551 HTH_29: Winged helix- 63.2 8.5 0.00019 26.7 2.9 30 49-82 11-41 (112)
359 TIGR00589 ogt O-6-methylguanin 63.1 11 0.00023 25.4 3.2 41 34-76 4-44 (80)
360 PRK14901 16S rRNA methyltransf 63.0 5.1 0.00011 35.7 2.1 29 180-209 243-271 (434)
361 TIGR02531 yecD_yerC TrpR-relat 62.8 15 0.00033 25.2 4.0 35 35-78 41-75 (88)
362 COG2188 PhnF Transcriptional r 62.6 11 0.00025 30.5 3.9 42 51-100 33-74 (236)
363 PF04492 Phage_rep_O: Bacterio 62.4 9.8 0.00021 26.8 3.0 35 48-86 53-87 (100)
364 PF00356 LacI: Bacterial regul 62.1 6 0.00013 23.6 1.6 11 51-61 1-11 (46)
365 PF01381 HTH_3: Helix-turn-hel 62.1 8.4 0.00018 23.2 2.4 24 48-75 8-31 (55)
366 PRK15418 transcriptional regul 62.0 9.2 0.0002 32.7 3.4 35 48-86 28-62 (318)
367 cd04761 HTH_MerR-SF Helix-Turn 61.9 7.7 0.00017 22.7 2.1 27 50-84 1-27 (49)
368 PF12728 HTH_17: Helix-turn-he 61.6 7.8 0.00017 23.1 2.2 22 50-75 2-23 (51)
369 cd06445 ATase The DNA repair p 61.4 23 0.00049 23.6 4.6 42 36-82 4-45 (79)
370 COG5340 Predicted transcriptio 61.4 9.2 0.0002 31.1 3.0 46 48-102 29-74 (269)
371 PRK14903 16S rRNA methyltransf 61.3 6 0.00013 35.3 2.2 44 165-209 213-256 (431)
372 PRK14904 16S rRNA methyltransf 61.1 6.5 0.00014 35.1 2.4 51 27-80 74-128 (445)
373 cd06171 Sigma70_r4 Sigma70, re 61.0 12 0.00026 21.6 3.0 34 36-77 17-50 (55)
374 PRK11402 DNA-binding transcrip 60.6 13 0.00029 30.0 4.0 43 50-100 34-76 (241)
375 TIGR00331 hrcA heat shock gene 60.4 12 0.00027 32.2 3.9 41 40-87 15-57 (337)
376 TIGR00446 nop2p NOL1/NOP2/sun 60.2 7.3 0.00016 32.2 2.4 22 188-209 69-90 (264)
377 PRK10681 DNA-binding transcrip 59.8 13 0.00029 30.5 3.8 41 34-81 9-49 (252)
378 TIGR02143 trmA_only tRNA (urac 59.7 11 0.00024 32.7 3.5 18 192-209 199-216 (353)
379 PF07638 Sigma70_ECF: ECF sigm 59.4 11 0.00025 29.2 3.3 36 35-78 141-176 (185)
380 PF04218 CENP-B_N: CENP-B N-te 59.1 13 0.00028 22.8 2.8 34 33-75 11-44 (53)
381 PF05401 NodS: Nodulation prot 59.1 8.7 0.00019 30.6 2.5 25 184-209 38-62 (201)
382 PF09106 SelB-wing_2: Elongati 58.9 16 0.00034 22.8 3.2 35 48-86 16-53 (59)
383 PLN03075 nicotianamine synthas 58.6 11 0.00024 31.9 3.3 22 182-204 116-137 (296)
384 PF01418 HTH_6: Helix-turn-hel 58.2 9.8 0.00021 25.1 2.3 31 48-82 33-63 (77)
385 PRK11727 23S rRNA mA1618 methy 57.9 7.6 0.00017 33.3 2.2 19 190-208 114-132 (321)
386 PRK04217 hypothetical protein; 57.9 14 0.00031 26.5 3.2 35 34-76 47-81 (110)
387 PF08281 Sigma70_r4_2: Sigma-7 57.9 12 0.00026 22.5 2.6 25 48-76 25-49 (54)
388 PHA00542 putative Cro-like pro 57.8 13 0.00027 25.0 2.8 24 48-75 30-53 (82)
389 PF01035 DNA_binding_1: 6-O-me 57.6 9.5 0.00021 25.9 2.2 40 35-76 5-44 (85)
390 TIGR02063 RNase_R ribonuclease 57.6 16 0.00035 34.8 4.5 58 37-100 7-64 (709)
391 PF05219 DREV: DREV methyltran 57.1 11 0.00023 31.5 2.8 20 190-209 94-113 (265)
392 PF06971 Put_DNA-bind_N: Putat 57.0 7.4 0.00016 23.8 1.4 33 35-72 15-47 (50)
393 PF05158 RNA_pol_Rpc34: RNA po 57.0 12 0.00027 32.1 3.3 45 37-86 89-133 (327)
394 PF13744 HTH_37: Helix-turn-he 56.8 17 0.00037 24.1 3.4 30 37-74 23-52 (80)
395 COG3645 Uncharacterized phage- 56.8 12 0.00027 27.8 2.8 45 33-86 33-77 (135)
396 PRK15201 fimbriae regulatory p 56.7 13 0.00028 29.2 3.0 43 31-82 135-178 (198)
397 PRK13558 bacterio-opsin activa 56.6 11 0.00023 35.3 3.1 46 22-77 609-654 (665)
398 PF03965 Penicillinase_R: Peni 56.0 15 0.00033 26.2 3.2 51 33-86 4-54 (115)
399 COG0421 SpeE Spermidine syntha 55.8 10 0.00022 32.0 2.5 23 188-210 74-96 (282)
400 COG3682 Predicted transcriptio 55.7 22 0.00047 26.1 3.9 61 33-100 7-67 (123)
401 PRK14096 pgi glucose-6-phospha 55.5 18 0.00038 33.3 4.2 43 35-81 466-508 (528)
402 PF00376 MerR: MerR family reg 55.2 7.5 0.00016 22.1 1.2 26 51-84 1-26 (38)
403 COG4883 Uncharacterized protei 55.1 64 0.0014 27.7 7.1 75 127-201 69-148 (500)
404 PF10078 DUF2316: Uncharacteri 54.9 16 0.00035 25.2 2.9 31 38-76 16-46 (89)
405 COG1565 Uncharacterized conser 54.5 26 0.00056 30.6 4.8 46 159-209 51-96 (370)
406 PF07574 SMC_Nse1: Nse1 non-SM 54.4 7.8 0.00017 30.7 1.6 42 52-102 155-196 (200)
407 PRK13750 replication protein; 54.0 34 0.00074 28.3 5.1 38 49-86 91-133 (285)
408 PRK10079 phosphonate metabolis 53.7 19 0.00042 29.1 3.8 42 51-100 37-78 (241)
409 PRK15121 right oriC-binding tr 53.6 22 0.00047 29.6 4.2 59 48-119 20-78 (289)
410 COG1339 Transcriptional regula 53.6 18 0.00038 28.9 3.3 34 49-86 19-52 (214)
411 PF03291 Pox_MCEL: mRNA cappin 53.5 13 0.00028 32.0 2.9 41 163-206 38-78 (331)
412 PLN02668 indole-3-acetate carb 53.3 25 0.00055 31.0 4.7 19 190-208 63-81 (386)
413 PLN02823 spermine synthase 53.2 11 0.00024 32.5 2.4 22 189-210 102-123 (336)
414 PF07848 PaaX: PaaX-like prote 53.2 9 0.00019 25.1 1.4 45 48-101 19-69 (70)
415 PRK15411 rcsA colanic acid cap 53.1 15 0.00032 29.1 3.0 36 30-74 138-173 (207)
416 PF12298 Bot1p: Eukaryotic mit 53.1 17 0.00038 28.2 3.3 44 32-83 20-63 (172)
417 smart00422 HTH_MERR helix_turn 53.0 12 0.00027 23.6 2.2 27 50-84 1-27 (70)
418 PF14502 HTH_41: Helix-turn-he 52.9 39 0.00085 20.4 4.0 35 48-86 5-39 (48)
419 PF10141 ssDNA-exonuc_C: Singl 52.8 20 0.00042 28.3 3.6 41 51-101 118-158 (195)
420 TIGR03474 incFII_RepA incFII f 52.5 37 0.00081 27.8 5.1 39 49-87 83-126 (275)
421 PRK01544 bifunctional N5-gluta 52.1 10 0.00022 34.6 2.1 20 190-209 347-366 (506)
422 PF02186 TFIIE_beta: TFIIE bet 51.8 55 0.0012 21.1 4.9 41 38-86 11-51 (65)
423 PRK08208 coproporphyrinogen II 51.2 26 0.00056 31.2 4.5 50 48-107 360-409 (430)
424 PF02387 IncFII_repA: IncFII R 50.8 16 0.00035 30.7 3.0 38 49-86 95-138 (281)
425 PRK10512 selenocysteinyl-tRNA- 50.6 29 0.00062 32.6 4.9 35 48-86 505-539 (614)
426 COG2378 Predicted transcriptio 50.6 22 0.00049 30.2 3.9 59 35-102 11-69 (311)
427 TIGR02277 PaaX_trns_reg phenyl 50.5 21 0.00047 29.9 3.7 50 48-103 16-68 (280)
428 PLN03238 probable histone acet 50.1 41 0.0009 28.4 5.2 32 48-86 222-253 (290)
429 PRK05031 tRNA (uracil-5-)-meth 50.1 10 0.00023 32.9 1.8 18 192-209 208-225 (362)
430 PRK09413 IS2 repressor TnpA; R 50.1 24 0.00051 25.5 3.4 31 48-82 28-58 (121)
431 PF13411 MerR_1: MerR HTH fami 49.7 10 0.00023 24.0 1.4 27 51-85 2-28 (69)
432 PF00538 Linker_histone: linke 49.3 36 0.00079 22.3 4.0 51 48-99 20-76 (77)
433 KOG3191 Predicted N6-DNA-methy 49.3 13 0.00028 29.4 2.0 19 191-209 44-62 (209)
434 COG0758 Smf Predicted Rossmann 49.1 29 0.00062 30.2 4.3 35 48-86 308-342 (350)
435 PRK11482 putative DNA-binding 49.0 21 0.00045 30.1 3.4 59 33-106 32-93 (317)
436 TIGR00475 selB selenocysteine- 48.3 24 0.00052 32.8 4.0 42 48-98 487-528 (581)
437 TIGR03339 phn_lysR aminoethylp 48.1 26 0.00055 28.3 3.8 58 35-107 2-62 (279)
438 PF04433 SWIRM: SWIRM domain; 48.0 44 0.00096 22.4 4.4 54 26-84 31-85 (86)
439 PRK05472 redox-sensing transcr 47.9 33 0.00071 27.3 4.3 45 30-81 14-60 (213)
440 smart00351 PAX Paired Box doma 47.8 26 0.00056 25.5 3.4 44 33-85 22-65 (125)
441 PF01710 HTH_Tnp_IS630: Transp 47.6 25 0.00054 25.3 3.2 39 38-86 63-101 (119)
442 PF08535 KorB: KorB domain; I 47.6 11 0.00025 25.8 1.4 27 48-78 2-28 (93)
443 TIGR03070 couple_hipB transcri 47.2 16 0.00034 21.9 1.9 23 48-74 14-36 (58)
444 PF07037 DUF1323: Putative tra 46.9 16 0.00035 26.6 2.1 30 50-86 1-30 (122)
445 PRK05660 HemN family oxidoredu 46.9 23 0.00049 31.0 3.4 50 48-107 320-369 (378)
446 PF13022 HTH_Tnp_1_2: Helix-tu 46.8 16 0.00034 27.4 2.1 31 39-75 26-56 (142)
447 PF09114 MotA_activ: Transcrip 46.8 38 0.00082 23.4 3.7 57 36-105 20-78 (96)
448 COG1693 Repressor of nif and g 46.7 24 0.00053 29.8 3.3 62 35-103 9-71 (325)
449 TIGR03882 cyclo_dehyd_2 bacter 46.5 23 0.00051 27.9 3.2 37 48-86 41-77 (193)
450 TIGR00180 parB_part ParB-like 46.4 22 0.00048 27.7 3.0 27 48-78 119-145 (187)
451 PRK09392 ftrB transcriptional 46.3 21 0.00046 28.5 2.9 30 49-82 173-202 (236)
452 PF07091 FmrO: Ribosomal RNA m 46.1 15 0.00033 30.3 2.1 16 190-205 105-120 (251)
453 TIGR02607 antidote_HigA addict 45.9 23 0.0005 22.9 2.6 23 48-74 17-39 (78)
454 PRK15340 transcriptional regul 45.7 49 0.0011 26.7 4.9 46 35-85 112-157 (216)
455 cd04764 HTH_MlrA-like_sg1 Heli 45.6 19 0.00042 22.7 2.2 23 50-76 1-23 (67)
456 PF04760 IF2_N: Translation in 45.6 8.8 0.00019 23.4 0.5 29 48-83 2-31 (54)
457 PRK10216 DNA-binding transcrip 45.4 25 0.00055 29.4 3.4 57 34-105 12-71 (319)
458 KOG2578 Transcription factor E 45.4 11 0.00023 32.0 1.0 34 49-86 44-77 (388)
459 PRK10130 transcriptional regul 45.2 28 0.0006 30.2 3.7 57 39-107 247-303 (350)
460 cd04780 HTH_MerR-like_sg5 Heli 45.2 26 0.00056 24.2 2.9 29 50-86 1-29 (95)
461 PRK13890 conjugal transfer pro 45.2 20 0.00043 26.0 2.3 30 37-74 10-39 (120)
462 PRK10837 putative DNA-binding 45.0 30 0.00064 28.3 3.7 59 34-107 7-68 (290)
463 PF09940 DUF2172: Domain of un 45.0 14 0.00031 32.3 1.8 44 35-84 343-386 (386)
464 PRK13503 transcriptional activ 44.8 31 0.00068 28.1 3.8 44 37-85 176-219 (278)
465 PRK09906 DNA-binding transcrip 44.5 28 0.00061 28.6 3.5 59 34-107 5-66 (296)
466 PF13413 HTH_25: Helix-turn-he 44.5 17 0.00037 23.1 1.7 21 48-72 9-29 (62)
467 smart00530 HTH_XRE Helix-turn- 44.2 31 0.00067 19.4 2.8 23 48-74 9-31 (56)
468 PRK09791 putative DNA-binding 44.1 33 0.00071 28.3 3.9 60 33-107 8-70 (302)
469 PRK10094 DNA-binding transcrip 43.9 25 0.00054 29.4 3.1 59 34-107 6-67 (308)
470 KOG4058 Uncharacterized conser 43.9 24 0.00053 27.0 2.7 28 179-207 62-89 (199)
471 PF08704 GCD14: tRNA methyltra 43.8 30 0.00066 28.5 3.5 29 180-209 31-59 (247)
472 COG4465 CodY Pleiotropic trans 43.6 40 0.00086 27.4 3.9 44 37-86 194-237 (261)
473 KOG3420 Predicted RNA methylas 43.6 19 0.00042 27.5 2.1 28 180-208 39-66 (185)
474 PRK15128 23S rRNA m(5)C1962 me 43.5 17 0.00037 32.1 2.1 20 189-208 219-238 (396)
475 PRK15466 carboxysome structura 43.5 33 0.00071 26.4 3.4 42 48-99 123-164 (166)
476 PRK08558 adenine phosphoribosy 43.4 24 0.00053 28.8 2.9 39 31-75 7-45 (238)
477 PRK10572 DNA-binding transcrip 43.4 33 0.00072 28.3 3.8 44 37-85 188-231 (290)
478 PF08672 APC2: Anaphase promot 43.3 20 0.00043 22.7 1.8 44 49-98 11-60 (60)
479 PRK13824 replication initiatio 43.2 29 0.00062 30.8 3.5 34 50-87 83-117 (404)
480 PRK00118 putative DNA-binding 43.0 24 0.00051 25.1 2.4 24 48-75 32-55 (104)
481 PF13560 HTH_31: Helix-turn-he 42.8 19 0.00042 22.5 1.8 23 48-74 13-35 (64)
482 cd04763 HTH_MlrA-like Helix-Tu 42.8 23 0.00049 22.5 2.1 28 50-84 1-28 (68)
483 COG2865 Predicted transcriptio 42.6 26 0.00056 31.7 3.1 43 37-86 407-449 (467)
484 PF06056 Terminase_5: Putative 42.5 30 0.00065 21.7 2.6 24 48-75 12-35 (58)
485 PF05402 PqqD: Coenzyme PQQ sy 42.4 35 0.00077 21.4 3.1 39 37-84 22-68 (68)
486 PF09959 DUF2193: Uncharacteri 42.3 98 0.0021 27.5 6.4 79 127-205 68-151 (499)
487 PRK13719 conjugal transfer tra 42.1 29 0.00062 28.1 3.0 48 29-85 143-191 (217)
488 PLN00104 MYST -like histone ac 42.0 58 0.0012 29.3 5.1 47 22-86 358-404 (450)
489 cd00131 PAX Paired Box domain 41.9 17 0.00038 26.6 1.7 48 29-85 18-65 (128)
490 PRK11783 rlmL 23S rRNA m(2)G24 41.9 18 0.0004 34.4 2.2 21 190-210 538-558 (702)
491 cd01104 HTH_MlrA-CarA Helix-Tu 41.8 24 0.00052 22.2 2.2 22 50-75 1-22 (68)
492 PF00440 TetR_N: Bacterial reg 41.6 26 0.00056 20.5 2.1 21 48-72 15-35 (47)
493 TIGR03337 phnR transcriptional 41.5 39 0.00085 26.8 3.8 42 51-100 27-68 (231)
494 PRK09685 DNA-binding transcrip 41.5 22 0.00049 29.5 2.5 36 36-76 201-237 (302)
495 PF09202 Rio2_N: Rio2, N-termi 41.4 39 0.00085 22.8 3.2 47 49-102 24-70 (82)
496 smart00354 HTH_LACI helix_turn 41.3 20 0.00044 23.1 1.7 19 51-73 2-20 (70)
497 PF09079 Cdc6_C: CDC6, C termi 41.3 32 0.00069 22.9 2.8 35 51-86 24-58 (85)
498 TIGR00721 tfx DNA-binding prot 41.2 32 0.00069 25.7 3.0 34 33-75 10-43 (137)
499 PF10678 DUF2492: Protein of u 41.1 1.1E+02 0.0024 20.5 5.4 42 48-99 18-72 (78)
500 COG0248 GppA Exopolyphosphatas 41.1 25 0.00054 32.1 2.8 22 180-202 120-141 (492)
No 1
>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]
Probab=99.91 E-value=1.3e-23 Score=176.20 Aligned_cols=191 Identities=46% Similarity=0.792 Sum_probs=169.1
Q ss_pred chHHHHHHHHHhhchHHHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcC-CCCCCcccHHHHHHHHhcccceeeecc
Q 036188 10 DQSFAYADQLATGVVLPMAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLT-KNKDAPMMLDRILRLLASYSVVECSLD 88 (210)
Q Consensus 10 ~~~~~~l~~~~~~~~~~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~-~~~~~~~~l~rlLr~L~~~gl~~~~~~ 88 (210)
.++..++++++.++..++++.+|+||||||+|+.++ + ..|||..+-. +++.+|..++|+||.|++.+++++..
T Consensus 4 ~~~~l~~~~l~~~~~~~~~lk~A~eL~v~d~l~~~~---~--p~~ia~~l~~~~~~~~p~ll~r~lr~L~s~~i~k~~~- 77 (342)
T KOG3178|consen 4 NEASLRAMRLANGFALPMVLKAACELGVFDILANAG---S--PSEIASLLPTPKNPEAPVLLDRILRLLVSYSILKCRL- 77 (342)
T ss_pred hHHHHHHHHHHhhhhhHHHHHHHHHcChHHHHHhCC---C--HHHHHHhccCCCCCCChhHHHHHHHHHHHhhhceeee-
Confidence 456678999999999999999999999999999964 2 8888888773 46668999999999999999999873
Q ss_pred CCCccc--ceeccccccccccCCCCCChHHHHHHhcChhHHHHHhhHHHHHhcCCchhhhhhCCchhHhhccCchHHHHH
Q 036188 89 ASGARR--LYSLNSVSKYYVPNKDGVLLGPLIQIIQDKVILESWSQLKDAILEGGIPFNRAHGVHIFEYAGLNPRFNKHF 166 (210)
Q Consensus 89 ~~~~~~--~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~f~~~~g~~~fe~l~~~p~~~~~f 166 (210)
.+ .|.++|.++++.++....++.+++...+.+..++.|.++.++++.+..+|..++|...|+|...++.....|
T Consensus 78 ----~~~~~Y~~~~~~~~~l~~~~~~S~a~~~~~~~~~v~~~~w~~l~dai~eg~~~~~~~~G~~l~~~~~~~~~~~~~~ 153 (342)
T KOG3178|consen 78 ----VGGEVYSATPVCKYFLKDSGGGSLAPLVLLNTSKVIMNTWQFLKDAILEGGDAFATAHGMMLGGYGGADERFSKDF 153 (342)
T ss_pred ----ecceeeeccchhhhheecCCCCchhHHHHHhcccchhhhHHHHHHHHHhcccCCccccchhhhhhcccccccHHHH
Confidence 33 899999999776444346899999888888899999999999999999999999988999999999999999
Q ss_pred HHHHhhhhhhhHHHHHHhCCCCCCCCeEEEecCCccHHHHhhhC
Q 036188 167 NAAMYNYTSLVMSNILESYKGFDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 167 ~~~M~~~~~~~~~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
+++|...+....+.+++.|.+|++...+||||||.|..+..+++
T Consensus 154 ~~sm~~l~~~~~~~il~~~~Gf~~v~~avDvGgGiG~v~k~ll~ 197 (342)
T KOG3178|consen 154 NGSMSFLSTLVMKKILEVYTGFKGVNVAVDVGGGIGRVLKNLLS 197 (342)
T ss_pred HHHHHHHHHHHHHhhhhhhcccccCceEEEcCCcHhHHHHHHHH
Confidence 99999999998889999998899999999999999999988763
No 2
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=99.90 E-value=2.1e-23 Score=176.54 Aligned_cols=165 Identities=20% Similarity=0.301 Sum_probs=120.7
Q ss_pred hHHHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccc
Q 036188 24 VLPMAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSK 103 (210)
Q Consensus 24 ~~~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~ 103 (210)
+..++|++|++|||||.|++ +|.|++|||+++++ +++.++||||+|+++|++++. +++|++|+.+.
T Consensus 2 ~~~~~l~aa~~Lglfd~L~~----gp~t~~eLA~~~~~----~~~~~~~lL~~L~~lgll~~~------~~~y~~t~~~~ 67 (306)
T TIGR02716 2 IEFSCMKAAIELDLFSHMAE----GPKDLATLAADTGS----VPPRLEMLLETLRQMRVINLE------DGKWSLTEFAD 67 (306)
T ss_pred chHHHHHHHHHcCcHHHHhc----CCCCHHHHHHHcCC----ChHHHHHHHHHHHhCCCeEec------CCcEecchhHH
Confidence 45789999999999999987 69999999999999 999999999999999999986 68999999998
Q ss_pred ccccCCCCC---ChHHHHHHhcChhHHHHHhhHHHHHhcCCchhhhhhCCchhHhhccCchHHHHHHHHHhhhhhhhHHH
Q 036188 104 YYVPNKDGV---LLGPLIQIIQDKVILESWSQLKDAILEGGIPFNRAHGVHIFEYAGLNPRFNKHFNAAMYNYTSLVMSN 180 (210)
Q Consensus 104 ~l~~~~~~~---~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~f~~~~g~~~fe~l~~~p~~~~~f~~~M~~~~~~~~~~ 180 (210)
.+..++++. ++.++..+.. ......|.+|+++++ ++++|... +++....++....|...+........+.
T Consensus 68 ~~l~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~r-~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 (306)
T TIGR02716 68 YMFSPTPKEPNLHQTPVAKAMA-FLADDFYMGLSQAVR-GQKNFKGQ-----VPYPPVTREDNLYFEEIHRSNAKFAIQL 140 (306)
T ss_pred hhccCCccchhhhcCchHHHHH-HHHHHHHHhHHHHhc-CCcccccc-----cCCCCCCHHHHHhHHHHHHhcchhHHHH
Confidence 655444321 1223443331 123357999999997 44455432 2232233333334444433444444566
Q ss_pred HHHhCCCCCCCCeEEEecCCccHHHHhhhC
Q 036188 181 ILESYKGFDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 181 ~l~~~~~~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
+++.++ +++..+|||||||+|.+++.+++
T Consensus 141 l~~~~~-~~~~~~vlDiG~G~G~~~~~~~~ 169 (306)
T TIGR02716 141 LLEEAK-LDGVKKMIDVGGGIGDISAAMLK 169 (306)
T ss_pred HHHHcC-CCCCCEEEEeCCchhHHHHHHHH
Confidence 777777 99999999999999999998863
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=99.80 E-value=3e-19 Score=146.18 Aligned_cols=118 Identities=30% Similarity=0.545 Sum_probs=102.1
Q ss_pred cccceeccccccccccCCCCCChHHHHHHhcChhHHHHHhhHHHHHhcCCchhhhhhCCchhHhhccCchHHHHHHHHHh
Q 036188 92 ARRLYSLNSVSKYYVPNKDGVLLGPLIQIIQDKVILESWSQLKDAILEGGIPFNRAHGVHIFEYAGLNPRFNKHFNAAMY 171 (210)
Q Consensus 92 ~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~f~~~~g~~~fe~l~~~p~~~~~f~~~M~ 171 (210)
+++.|+||+.|+.|+.+++..++..++.++..+..++.|.+|++++++|+++|+.++|.++|+|+.++|+..+.|+.+|.
T Consensus 2 ~~~~y~~t~~s~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~v~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~~m~ 81 (241)
T PF00891_consen 2 EGDRYSLTPLSELLLSDHSSPSMRGFVLFMISPELYPAWFRLTEAVRTGKPPFEKAFGTPFFEYLEEDPELAKRFNAAMA 81 (241)
T ss_dssp STEEEEE-HHHHGGSTTTTTTHHHHHHHHHTCHHHHHGGGGHHHHHHHSS-HHHHHHSS-HHHHHHCSHHHHHHHHHHHH
T ss_pred CCCEEeChHHHHHHhCCCCcCcHHHHHHHhcCHHHHHHHHHHHhhhccCCCHHHHhcCCcHHHhhhhChHHHHHHHHHHH
Confidence 37899999999987766643467888877667888999999999999999999999999999999999999999999999
Q ss_pred hhhhhhH-HHHHHhCCCCCCCCeEEEecCCccHHHHhhhC
Q 036188 172 NYTSLVM-SNILESYKGFDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 172 ~~~~~~~-~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
..+.... +.++..++ |++.++|||||||+|++++++++
T Consensus 82 ~~~~~~~~~~~~~~~d-~~~~~~vvDvGGG~G~~~~~l~~ 120 (241)
T PF00891_consen 82 EYSRLNAFDILLEAFD-FSGFKTVVDVGGGSGHFAIALAR 120 (241)
T ss_dssp HHHHHHHHHHHHHHST-TTTSSEEEEET-TTSHHHHHHHH
T ss_pred hhhhcchhhhhhcccc-ccCccEEEeccCcchHHHHHHHH
Confidence 9998887 78888898 99999999999999999999873
No 4
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=99.20 E-value=1.8e-11 Score=75.80 Aligned_cols=51 Identities=57% Similarity=0.801 Sum_probs=43.3
Q ss_pred HHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHh
Q 036188 27 MAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLA 78 (210)
Q Consensus 27 ~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~ 78 (210)
++|++|++|||||.|+..| |+++|++||+.++...+|.++..|+|+||+|+
T Consensus 1 MaLk~aveLgI~dii~~~g-~~~ls~~eia~~l~~~~p~~~~~L~RimR~L~ 51 (51)
T PF08100_consen 1 MALKCAVELGIPDIIHNAG-GGPLSLSEIAARLPTSNPSAPPMLDRIMRLLV 51 (51)
T ss_dssp HHHHHHHHTTHHHHHHHHT-TS-BEHHHHHHTSTCT-TTHHHHHHHHHHHHH
T ss_pred CcHHHHHHcCcHHHHHHcC-CCCCCHHHHHHHcCCCCcchHHHHHHHHHHhC
Confidence 5899999999999999986 47999999999999436667889999999985
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=97.70 E-value=2.2e-05 Score=48.76 Aligned_cols=46 Identities=33% Similarity=0.390 Sum_probs=40.6
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+.|.+.|.+.+ +++|+.|||+++|+ +..-+.|+|..|+..|++.++
T Consensus 6 l~iL~~l~~~~--~~~t~~eia~~~gl----~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESG--GPLTLSEIARALGL----PKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHHCHHCTB--SCEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHHcCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCcCeecC
Confidence 45788888875 67899999999999 999999999999999999875
No 6
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=97.53 E-value=0.00015 Score=49.92 Aligned_cols=58 Identities=21% Similarity=0.245 Sum_probs=48.6
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSV 101 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~ 101 (210)
-+.|.+.|.+.+ ++.|+.|||+++++ +...+.|+|+.|...|++.+.. ..+.|.+++.
T Consensus 7 ~~~Il~~l~~~~--~~~t~~~ia~~l~i----~~~tv~r~l~~L~~~g~l~~~~----~~~~y~l~~~ 64 (91)
T smart00346 7 GLAVLRALAEEP--GGLTLAELAERLGL----SKSTAHRLLNTLQELGYVEQDG----QNGRYRLGPK 64 (91)
T ss_pred HHHHHHHHHhCC--CCcCHHHHHHHhCC----CHHHHHHHHHHHHHCCCeeecC----CCCceeecHH
Confidence 356788888753 58999999999999 9999999999999999998752 3567888764
No 7
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=97.34 E-value=0.00056 Score=44.93 Aligned_cols=60 Identities=25% Similarity=0.279 Sum_probs=48.7
Q ss_pred HHhhChhhHHhhcCCCC-CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 32 VYELGIFEILDKAGPGT-KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 32 a~~lglfd~L~~~g~~~-~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
..+-.|.++|.+.| + ++|+.|||+++|+ +...++|+|.-|...|+++... ..++.|..+.
T Consensus 6 ~~~~~IL~~L~~~g--~~~~ta~eLa~~lgl----~~~~v~r~L~~L~~~G~V~~~~---~~~~~W~i~~ 66 (68)
T smart00550 6 SLEEKILEFLENSG--DETSTALQLAKNLGL----PKKEVNRVLYSLEKKGKVCKQG---GTPPLWKLTD 66 (68)
T ss_pred HHHHHHHHHHHHCC--CCCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEecC---CCCCceEeec
Confidence 34567888898875 3 3999999999999 9999999999999999998752 1246777664
No 8
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=97.24 E-value=0.0004 Score=57.15 Aligned_cols=60 Identities=23% Similarity=0.276 Sum_probs=50.8
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccc
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKY 104 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~ 104 (210)
+.|.++|++.+ .++++.|||+++|+ ++.-+.|+|..|+..|+++++. ..++|.+++....
T Consensus 7 l~iL~~l~~~~--~~l~l~ela~~~gl----pksT~~RlL~tL~~~G~v~~d~----~~g~Y~Lg~~~~~ 66 (246)
T COG1414 7 LAILDLLAEGP--GGLSLAELAERLGL----PKSTVHRLLQTLVELGYVEQDP----EDGRYRLGPRLLE 66 (246)
T ss_pred HHHHHHHHhCC--CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCCCEEEcC----CCCcEeehHHHHH
Confidence 56788898843 45779999999999 9999999999999999999983 3578999986543
No 9
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=97.15 E-value=0.0007 Score=46.14 Aligned_cols=55 Identities=29% Similarity=0.395 Sum_probs=41.1
Q ss_pred HhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccc
Q 036188 41 LDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVS 102 (210)
Q Consensus 41 L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s 102 (210)
|+..+.+++.|.+|||+++++ ++..+++++..|...|+++... +..|.|.++.-.
T Consensus 17 la~~~~~~~~s~~eiA~~~~i----~~~~l~kil~~L~~~Gli~s~~---G~~GGy~L~~~~ 71 (83)
T PF02082_consen 17 LARHPDGKPVSSKEIAERLGI----SPSYLRKILQKLKKAGLIESSR---GRGGGYRLARPP 71 (83)
T ss_dssp HHCTTTSC-BEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEET---STTSEEEESS-C
T ss_pred HHhCCCCCCCCHHHHHHHHCc----CHHHHHHHHHHHhhCCeeEecC---CCCCceeecCCH
Confidence 344332256999999999999 9999999999999999998763 235778877643
No 10
>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=97.08 E-value=0.00067 Score=43.43 Aligned_cols=54 Identities=19% Similarity=0.241 Sum_probs=45.3
Q ss_pred HHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 26 PMAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 26 ~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+.+|.--.++.|+..|... +|+|+.|||+.+|+ ++..+.+-|+.|...|+++..
T Consensus 4 ~~aL~~p~R~~Il~~L~~~---~~~t~~ela~~l~~----~~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 4 FKALSDPTRLRILRLLASN---GPMTVSELAEELGI----SQSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp HHHHTSHHHHHHHHHHHHC---STBEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHhCCHHHHHHHHHHhcC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEe
Confidence 3455556778888889543 69999999999999 999999999999999999876
No 11
>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=97.07 E-value=0.00067 Score=55.73 Aligned_cols=59 Identities=20% Similarity=0.237 Sum_probs=50.4
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccccc
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYY 105 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l 105 (210)
+.|.+.|+..+ .++|+.|||+++|+ +..-+.|+|..|+..|+++++ .+.|.+.+....|
T Consensus 12 l~IL~~l~~~~--~~~~l~eia~~lgl----pksT~~RlL~tL~~~G~l~~~------~~~Y~lG~~~~~l 70 (248)
T TIGR02431 12 LAVIEAFGAER--PRLTLTDVAEATGL----TRAAARRFLLTLVELGYVTSD------GRLFWLTPRVLRL 70 (248)
T ss_pred HHHHHHHhcCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeC------CCEEEecHHHHHH
Confidence 56788887654 68999999999999 999999999999999999875 5789999865433
No 12
>PRK11569 transcriptional repressor IclR; Provisional
Probab=97.05 E-value=0.00083 Score=56.11 Aligned_cols=59 Identities=12% Similarity=0.142 Sum_probs=50.4
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccc
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSK 103 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~ 103 (210)
+.|.+.|++.+ +++|+.|||+++|+ +..-+.|+|..|+..|++.++. ..++|.+.+...
T Consensus 31 l~IL~~l~~~~--~~~~lseia~~lgl----pksTv~RlL~tL~~~G~l~~~~----~~~~Y~lG~~l~ 89 (274)
T PRK11569 31 LKLLEWIAESN--GSVALTELAQQAGL----PNSTTHRLLTTMQQQGFVRQVG----ELGHWAIGAHAF 89 (274)
T ss_pred HHHHHHHHhCC--CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEcC----CCCeEecCHHHH
Confidence 56778887754 68999999999999 9999999999999999998762 468899987654
No 13
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=97.04 E-value=0.00086 Score=55.92 Aligned_cols=60 Identities=22% Similarity=0.199 Sum_probs=50.8
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccc
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKY 104 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~ 104 (210)
+.|.+.|++.+ +++|+.|||+++|+ +..-+.|+|..|+..|++.++. ..++|.+++....
T Consensus 28 l~IL~~~~~~~--~~~tl~eIa~~lgl----pkStv~RlL~tL~~~G~l~~~~----~~~~Y~lG~~l~~ 87 (271)
T PRK10163 28 IAILQYLEKSG--GSSSVSDISLNLDL----PLSTTFRLLKVLQAADFVYQDS----QLGWWHIGLGVFN 87 (271)
T ss_pred HHHHHHHHhCC--CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEcC----CCCeEEecHHHHH
Confidence 66788888764 58999999999999 9999999999999999998862 4678999875443
No 14
>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=96.99 E-value=0.00076 Score=40.86 Aligned_cols=44 Identities=25% Similarity=0.343 Sum_probs=38.8
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
++.|...|.+ +|.++.|||+.+++ ++..+.+-|+.|...|++++
T Consensus 4 R~~Il~~L~~----~~~~~~el~~~l~~----s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 4 RLRILKLLSE----GPLTVSELAEELGL----SQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHHTT----SSEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHh----CCCchhhHHHhccc----cchHHHHHHHHHHHCcCeeC
Confidence 5667778887 69999999999999 99999999999999999863
No 15
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=96.97 E-value=0.0012 Score=54.73 Aligned_cols=61 Identities=15% Similarity=0.115 Sum_probs=51.3
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccccc
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYY 105 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l 105 (210)
+.|.+.|...+ +++|+.|||+++|+ +..-+.|+|..|+..|+++++. ..+.|.+++....|
T Consensus 14 l~iL~~l~~~~--~~ls~~eia~~lgl----~kstv~RlL~tL~~~g~v~~~~----~~~~Y~Lg~~~~~l 74 (263)
T PRK09834 14 LMVLRALNRLD--GGATVGLLAELTGL----HRTTVRRLLETLQEEGYVRRSA----SDDSFRLTLKVRQL 74 (263)
T ss_pred HHHHHHHHhcC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEec----CCCcEEEcHHHHHH
Confidence 56777887654 57999999999999 9999999999999999999863 46789999865544
No 16
>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=96.92 E-value=0.0015 Score=39.51 Aligned_cols=45 Identities=18% Similarity=0.331 Sum_probs=38.4
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhccccee
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVE 84 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~ 84 (210)
.+..|+..|.++ +++|..|||+.+|+ +...+.+.++-|...|+++
T Consensus 4 ~~~~Il~~l~~~---~~~t~~ela~~~~i----s~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLREN---PRITQKELAEKLGI----SRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHC---TTS-HHHHHHHHTS-----HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHhCC----CHHHHHHHHHHHHHCcCcC
Confidence 456788899986 47999999999999 9999999999999999974
No 17
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=96.91 E-value=0.0012 Score=54.46 Aligned_cols=60 Identities=15% Similarity=0.256 Sum_probs=49.7
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccccc
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYY 105 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l 105 (210)
+.|.+.|.+. +++|+.|||+++|+ +..-+.|+|+.|+..|++.++. ..+.|.+.+....|
T Consensus 17 l~IL~~l~~~---~~l~l~eia~~lgl----~kstv~Rll~tL~~~G~l~~~~----~~~~Y~lG~~~~~l 76 (257)
T PRK15090 17 FGILQALGEE---REIGITELSQRVMM----SKSTVYRFLQTMKTLGYVAQEG----ESEKYSLTLKLFEL 76 (257)
T ss_pred HHHHHHhhcC---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEcC----CCCcEEecHHHHHH
Confidence 4566777664 58999999999999 9999999999999999999862 46889999865433
No 18
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=96.71 E-value=0.0037 Score=48.29 Aligned_cols=61 Identities=18% Similarity=0.272 Sum_probs=45.9
Q ss_pred HHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 27 MAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 27 ~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
.||++.+.+. .... +++.|+++||+++++ ++++++++|..|...|++.... +..|.|.+..
T Consensus 9 yAl~~l~~lA----~~~~--~~~vs~~eIA~~~~i----p~~~l~kIl~~L~~aGLv~s~r---G~~GGy~Lar 69 (164)
T PRK10857 9 YAVTAMLDVA----LNSE--AGPVPLADISERQGI----SLSYLEQLFSRLRKNGLVSSVR---GPGGGYLLGK 69 (164)
T ss_pred HHHHHHHHHH----hCCC--CCcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeCC---CCCCCeeccC
Confidence 4555555554 1121 258999999999999 9999999999999999999652 1456777654
No 19
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=96.68 E-value=0.0039 Score=40.13 Aligned_cols=45 Identities=24% Similarity=0.186 Sum_probs=37.9
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.|.++|.+.. +|.+..|||+.+|+ +...++++|..|...|.+.+.
T Consensus 4 ~Il~~i~~~~--~p~~T~eiA~~~gl----s~~~aR~yL~~Le~eG~V~~~ 48 (62)
T PF04703_consen 4 KILEYIKEQN--GPLKTREIADALGL----SIYQARYYLEKLEKEGKVERS 48 (62)
T ss_dssp CHHHHHHHHT--S-EEHHHHHHHHTS-----HHHHHHHHHHHHHCTSEEEE
T ss_pred HHHHHHHHcC--CCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 4677777733 69999999999999 999999999999999999875
No 20
>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=96.65 E-value=0.0035 Score=40.35 Aligned_cols=44 Identities=23% Similarity=0.277 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
.++|..|||+.+|+ ++..+.|.|+.|...|++... ..+.|.++|
T Consensus 24 ~~~s~~ela~~~g~----s~~tv~r~l~~L~~~g~i~~~-----~~~~~~l~~ 67 (67)
T cd00092 24 LPLTRQEIADYLGL----TRETVSRTLKELEEEGLISRR-----GRGKYRVNP 67 (67)
T ss_pred CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec-----CCCeEEeCC
Confidence 58999999999999 999999999999999999986 347787764
No 21
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=96.63 E-value=0.0038 Score=45.46 Aligned_cols=65 Identities=22% Similarity=0.258 Sum_probs=53.7
Q ss_pred hHHHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccc---eeccc
Q 036188 24 VLPMAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRL---YSLNS 100 (210)
Q Consensus 24 ~~~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~---y~~t~ 100 (210)
..+.+|.--.++.|+..|... ++.++.||++.+++ .+..+.+-|+.|...|+++.. ..|+ |++++
T Consensus 8 ~~fkaLadptRl~IL~~L~~~---~~~~v~ela~~l~l----sqstvS~HL~~L~~AGLV~~~-----r~Gr~~~Y~l~~ 75 (117)
T PRK10141 8 QLFKILSDETRLGIVLLLRES---GELCVCDLCTALDQ----SQPKISRHLALLRESGLLLDR-----KQGKWVHYRLSP 75 (117)
T ss_pred HHHHHhCCHHHHHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCceEEE-----EEcCEEEEEECc
Confidence 345677777889999999764 58999999999999 999999999999999999866 3554 66544
No 22
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=96.61 E-value=0.0037 Score=37.42 Aligned_cols=40 Identities=18% Similarity=0.169 Sum_probs=36.1
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceec
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSL 98 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~ 98 (210)
++|..|||+.+++ ++..+.+.|+.|...|++... .+.|..
T Consensus 8 ~~s~~~la~~l~~----s~~tv~~~l~~L~~~g~l~~~------~~~~~i 47 (48)
T smart00419 8 PLTRQEIAELLGL----TRETVSRTLKRLEKEGLISRE------GGRIVI 47 (48)
T ss_pred ccCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe------CCEEEE
Confidence 7899999999999 999999999999999999876 466654
No 23
>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=96.58 E-value=0.0019 Score=42.22 Aligned_cols=47 Identities=26% Similarity=0.239 Sum_probs=40.4
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.+..|+..|-.. ++.|+.|||+.+|+ +...+.+.|+-|...|++++.
T Consensus 9 ~E~~vy~~Ll~~---~~~t~~eIa~~l~i----~~~~v~~~L~~L~~~GlV~~~ 55 (68)
T PF01978_consen 9 NEAKVYLALLKN---GPATAEEIAEELGI----SRSTVYRALKSLEEKGLVERE 55 (68)
T ss_dssp HHHHHHHHHHHH---CHEEHHHHHHHHTS----SHHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEE
Confidence 344566666544 69999999999999 999999999999999999987
No 24
>PRK06922 hypothetical protein; Provisional
Probab=96.50 E-value=0.0046 Score=57.30 Aligned_cols=59 Identities=22% Similarity=0.310 Sum_probs=42.9
Q ss_pred CchhHhhccCchHHHHHHHHHhhhhhhh--HHHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 150 VHIFEYAGLNPRFNKHFNAAMYNYTSLV--MSNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 150 ~~~fe~l~~~p~~~~~f~~~M~~~~~~~--~~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+|+++..+++..++|...|....... .......++ +.+..+|||||||.|.++..++
T Consensus 377 ~~~fd~fg~r~D~~dRf~~~~~yle~m~~~~~~k~~i~d-~~~g~rVLDIGCGTG~ls~~LA 437 (677)
T PRK06922 377 VLLFDFFGLRKDAYDRFHNEEVYLEHMNSSADDKRIILD-YIKGDTIVDVGAGGGVMLDMIE 437 (677)
T ss_pred hHHHHHhccChhhHhHHHhHHHHHHhccccHHHHHHHhh-hcCCCEEEEeCCCCCHHHHHHH
Confidence 5789999999998888888776543331 112233455 6678899999999999887664
No 25
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=96.41 E-value=0.0063 Score=46.31 Aligned_cols=55 Identities=25% Similarity=0.292 Sum_probs=44.0
Q ss_pred HHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccc
Q 036188 40 ILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSV 101 (210)
Q Consensus 40 ~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~ 101 (210)
.|+..+.+++.|+++||+..++ +|.+|+++|..|...|+++... +..|.|.++.-
T Consensus 16 ~LA~~~~~~~~s~~~IA~~~~i----s~~~L~kil~~L~kaGlV~S~r---G~~GGy~Lar~ 70 (150)
T COG1959 16 YLALLPGGGPVSSAEIAERQGI----SPSYLEKILSKLRKAGLVKSVR---GKGGGYRLARP 70 (150)
T ss_pred HHHhCCCCCcccHHHHHHHhCc----CHHHHHHHHHHHHHcCCEEeec---CCCCCccCCCC
Confidence 3554432248999999999999 9999999999999999998763 23678887753
No 26
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=96.41 E-value=0.0067 Score=45.20 Aligned_cols=46 Identities=17% Similarity=0.229 Sum_probs=38.9
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
++.|+++||+++++ ++..++++|+.|...|++.... +..|.|.++.
T Consensus 24 ~~~s~~~ia~~~~i----p~~~l~kil~~L~~~glv~s~~---G~~Ggy~l~~ 69 (135)
T TIGR02010 24 GPVTLADISERQGI----SLSYLEQLFAKLRKAGLVKSVR---GPGGGYQLGR 69 (135)
T ss_pred CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCceEEEe---CCCCCEeccC
Confidence 58999999999999 9999999999999999998642 1356677664
No 27
>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=96.34 E-value=0.0048 Score=40.48 Aligned_cols=44 Identities=16% Similarity=0.227 Sum_probs=37.4
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeec
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSL 87 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~ 87 (210)
|-++|.+. +.+|..|||.++++ ++..++.+|..|+..|.+.+..
T Consensus 5 i~~~l~~~---~~~S~~eLa~~~~~----s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 5 IRDYLRER---GRVSLAELAREFGI----SPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHHHHHS----SEEHHHHHHHTT------HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEEec
Confidence 56778775 59999999999999 9999999999999999999873
No 28
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=96.32 E-value=0.0036 Score=42.09 Aligned_cols=49 Identities=14% Similarity=0.162 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYV 106 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~ 106 (210)
++.+..+|+..+++ +...+.+.|..|...|+++.. .+.|.+|+.+.-+.
T Consensus 18 ~~~~~t~i~~~~~L----~~~~~~~yL~~L~~~gLI~~~------~~~Y~lTekG~~~l 66 (77)
T PF14947_consen 18 GGAKKTEIMYKANL----NYSTLKKYLKELEEKGLIKKK------DGKYRLTEKGKEFL 66 (77)
T ss_dssp T-B-HHHHHTTST------HHHHHHHHHHHHHTTSEEEE------TTEEEE-HHHHHHH
T ss_pred CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCcCeeCC------CCEEEECccHHHHH
Confidence 69999999999999 999999999999999999764 89999999987544
No 29
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=96.22 E-value=0.0092 Score=44.01 Aligned_cols=46 Identities=28% Similarity=0.325 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
++.|.++||+.+++ ++..++++|+.|...|++.... +..|.|.++.
T Consensus 24 ~~~s~~eia~~~~i----~~~~v~~il~~L~~~gli~~~~---g~~ggy~l~~ 69 (132)
T TIGR00738 24 GPVSVKEIAERQGI----SRSYLEKILRTLRRAGLVESVR---GPGGGYRLAR 69 (132)
T ss_pred CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEecc---CCCCCccCCC
Confidence 48999999999999 9999999999999999998642 1245666644
No 30
>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=96.20 E-value=0.0069 Score=39.15 Aligned_cols=50 Identities=24% Similarity=0.342 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccC-CCcccceecccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDA-SGARRLYSLNSV 101 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~-~~~~~~y~~t~~ 101 (210)
++++..+||+.+++ +...+.+.++-|...|++++..+. ......|++|+.
T Consensus 17 ~~~t~~~l~~~~~~----~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~ 67 (68)
T PF13463_consen 17 GPMTQSDLAERLGI----SKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPA 67 (68)
T ss_dssp S-BEHHHHHHHTT------HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HH
T ss_pred CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCC
Confidence 69999999999999 999999999999999999766321 112245888875
No 31
>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=96.02 E-value=0.0082 Score=38.05 Aligned_cols=48 Identities=21% Similarity=0.317 Sum_probs=38.9
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+..|.-.|...++ .++|+.|||+.+++ ++..+.++++.|...|++++.
T Consensus 7 q~~vL~~l~~~~~-~~~t~~~la~~l~~----~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 7 QFRVLMALARHPG-EELTQSELAERLGI----SKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp HHHHHHHHHHSTT-SGEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHCCC-CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence 4455666777541 12899999999999 999999999999999999976
No 32
>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=95.99 E-value=0.017 Score=46.34 Aligned_cols=58 Identities=9% Similarity=-0.010 Sum_probs=35.0
Q ss_pred hhHhhccCchHHHHHHHHHhhhhhhhHHHHHHhCCC-CCCCCeEEEecCCccHHHHhhh
Q 036188 152 IFEYAGLNPRFNKHFNAAMYNYTSLVMSNILESYKG-FDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 152 ~fe~l~~~p~~~~~f~~~M~~~~~~~~~~~l~~~~~-~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.|+.+...+.....+...|..........+++..+. .....+|+|||||.|.++..++
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~vLDiGcG~G~~~~~la 74 (219)
T TIGR02021 16 RWARIYGSGDPVSRVRQTVREGRAAMRRKLLDWLPKDPLKGKRVLDAGCGTGLLSIELA 74 (219)
T ss_pred HHHHhhCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEeCCCCHHHHHHH
Confidence 345555545555556665543333333444443331 3457899999999999988775
No 33
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=95.99 E-value=0.011 Score=43.66 Aligned_cols=46 Identities=26% Similarity=0.299 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
++.|+.|||+++++ ++..+.++|+.|...|++.... +..|.|.+..
T Consensus 24 ~~~s~~eia~~l~i----s~~~v~~~l~~L~~~Gli~~~~---g~~ggy~l~~ 69 (130)
T TIGR02944 24 QPYSAAEIAEQTGL----NAPTVSKILKQLSLAGIVTSKR---GVEGGYTLAR 69 (130)
T ss_pred CCccHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEecC---CCCCChhhcC
Confidence 68999999999999 9999999999999999997641 1245676644
No 34
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=95.96 E-value=0.014 Score=40.21 Aligned_cols=46 Identities=24% Similarity=0.348 Sum_probs=40.8
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
++.|+..|... ++.|..+||+.+++ ++..+.+.++-|...|++++.
T Consensus 12 ~~~il~~l~~~---~~~~~~~la~~~~~----s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 12 QFLVLRILYEE---GPLSVSELAKRLGV----SPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHHHc---CCcCHHHHHHHHCC----CchhHHHHHHHHHHCCCeEec
Confidence 56677788775 47999999999999 999999999999999999875
No 35
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=95.76 E-value=0.021 Score=43.55 Aligned_cols=61 Identities=21% Similarity=0.188 Sum_probs=46.4
Q ss_pred HHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccc
Q 036188 27 MAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSV 101 (210)
Q Consensus 27 ~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~ 101 (210)
.|+++.+.+- ..+ +++.|+++||++.++ ++.+|+++|..|...|+++... +..|.|.++.-
T Consensus 9 YAlr~L~~LA------~~~-~~~~s~~eIA~~~~i----s~~~L~kIl~~L~~aGlv~S~r---G~~GGy~La~~ 69 (153)
T PRK11920 9 YAIRMLMYCA------AND-GKLSRIPEIARAYGV----SELFLFKILQPLVEAGLVETVR---GRNGGVRLGRP 69 (153)
T ss_pred HHHHHHHHHH------hCC-CCcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeec---CCCCCeeecCC
Confidence 4666665443 221 257899999999999 9999999999999999998763 23577877643
No 36
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=95.74 E-value=0.026 Score=34.09 Aligned_cols=43 Identities=26% Similarity=0.333 Sum_probs=38.0
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|.+.|.+. ++.|+.+|++.+++ ++..+.+.|..|...|++.+.
T Consensus 5 il~~l~~~---~~~s~~~l~~~l~~----s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 5 ILELLAQQ---GKVSVEELAELLGV----SEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HHHHHHHc---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 55666664 47999999999999 999999999999999999876
No 37
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=95.71 E-value=0.019 Score=43.11 Aligned_cols=50 Identities=20% Similarity=0.131 Sum_probs=43.9
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYV 106 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~ 106 (210)
++.++.+||+.+++ ++..+.+.++.|...|++... ..+.|.+|+.++.+.
T Consensus 21 ~~~~~~ela~~l~v----s~~svs~~l~~L~~~Gli~~~-----~~~~i~LT~~G~~~a 70 (142)
T PRK03902 21 GYARVSDIAEALSV----HPSSVTKMVQKLDKDEYLIYE-----KYRGLVLTPKGKKIG 70 (142)
T ss_pred CCcCHHHHHHHhCC----ChhHHHHHHHHHHHCCCEEEe-----cCceEEECHHHHHHH
Confidence 68999999999999 999999999999999999865 357799998886543
No 38
>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=95.69 E-value=0.026 Score=35.59 Aligned_cols=44 Identities=23% Similarity=0.367 Sum_probs=40.1
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.|.++|.+. +.+|++|||+.+++ ++.-++|=|..|...|++.+.
T Consensus 4 ~Il~~l~~~---~~~s~~ela~~~~V----S~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 4 QILELLKEK---GKVSVKELAEEFGV----SEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHc---CCEEHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEE
Confidence 367778776 59999999999999 999999999999999999987
No 39
>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=95.64 E-value=0.013 Score=36.81 Aligned_cols=46 Identities=22% Similarity=0.354 Sum_probs=38.7
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
++.+...|.+. +++|..+||+.+++ ++..+.++++-|...|++++.
T Consensus 5 q~~iL~~l~~~---~~~~~~~la~~~~~----~~~~~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 5 QFRILRILYEN---GGITQSELAEKLGI----SRSTVTRIIKRLEKKGLIERE 50 (59)
T ss_dssp HHHHHHHHHHH---SSEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHc---CCCCHHHHHHHHCC----ChhHHHHHHHHHHHCCCEEec
Confidence 34455567676 48999999999999 999999999999999999876
No 40
>PHA00738 putative HTH transcription regulator
Probab=95.64 E-value=0.024 Score=40.35 Aligned_cols=47 Identities=28% Similarity=0.272 Sum_probs=42.4
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.++.|++.|... ++.++.||++.+++ ....+.+-|+.|...|+++..
T Consensus 13 tRr~IL~lL~~~---e~~~V~eLae~l~l----SQptVS~HLKvLreAGLV~sr 59 (108)
T PHA00738 13 LRRKILELIAEN---YILSASLISHTLLL----SYTTVLRHLKILNEQGYIELY 59 (108)
T ss_pred HHHHHHHHHHHc---CCccHHHHHHhhCC----CHHHHHHHHHHHHHCCceEEE
Confidence 567889999873 37999999999999 999999999999999999876
No 41
>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=95.61 E-value=0.024 Score=36.95 Aligned_cols=56 Identities=14% Similarity=0.238 Sum_probs=44.1
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVS 102 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s 102 (210)
++.|...|.+ ++.|.++||+++++ ....+.+-++.|...|+.... ....|...+..
T Consensus 2 ~~~il~~L~~----~~~~~~eLa~~l~v----S~~tv~~~l~~L~~~g~~i~~-----~~~g~~l~~~~ 57 (69)
T TIGR00122 2 PLRLLALLAD----NPFSGEKLGEALGM----SRTAVNKHIQTLREWGVDVLT-----VGKGYRLPPPI 57 (69)
T ss_pred hHHHHHHHHc----CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEe-----cCCceEecCcc
Confidence 4557777876 68899999999999 999999999999999997654 23455554433
No 42
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=95.59 E-value=0.018 Score=47.51 Aligned_cols=67 Identities=16% Similarity=0.169 Sum_probs=59.6
Q ss_pred HHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccccccc
Q 036188 28 AIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYVP 107 (210)
Q Consensus 28 al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~~ 107 (210)
.+...-+.+|.=+|.+ ||.|.+||-..+++ ++..+..-++-|...|++.+. ++.|++|..++.++.
T Consensus 9 if~SekRk~lLllL~e----gPkti~EI~~~l~v----s~~ai~pqiKkL~~~~LV~~~------~~~Y~LS~~G~iiv~ 74 (260)
T COG4742 9 LFLSEKRKDLLLLLKE----GPKTIEEIKNELNV----SSSAILPQIKKLKDKGLVVQE------GDRYSLSSLGKIIVE 74 (260)
T ss_pred HHccHHHHHHHHHHHh----CCCCHHHHHHHhCC----CcHHHHHHHHHHhhCCCEEec------CCEEEecchHHHHHH
Confidence 4455667888888888 79999999999999 999999999999999999996 899999999998875
Q ss_pred C
Q 036188 108 N 108 (210)
Q Consensus 108 ~ 108 (210)
.
T Consensus 75 k 75 (260)
T COG4742 75 K 75 (260)
T ss_pred H
Confidence 4
No 43
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=95.55 E-value=0.028 Score=42.16 Aligned_cols=61 Identities=15% Similarity=0.130 Sum_probs=45.5
Q ss_pred HHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 27 MAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 27 ~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
.|+++.+.++. ..+|.+.|..+||+++++ ++..++++|+.|...|+++... +..|.|.+..
T Consensus 9 YAl~~~i~la~------~~~g~~~s~~~ia~~~~i----s~~~vrk~l~~L~~~Glv~s~~---G~~GG~~l~~ 69 (141)
T PRK11014 9 YGLRALIYMAS------LPEGRMTSISEVTEVYGV----SRNHMVKIINQLSRAGYVTAVR---GKNGGIRLGK 69 (141)
T ss_pred HHHHHHHHHhc------CCCCCccCHHHHHHHHCc----CHHHHHHHHHHHHhCCEEEEec---CCCCCeeecC
Confidence 35555555443 122257899999999999 9999999999999999998763 1245677653
No 44
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=95.46 E-value=0.012 Score=39.94 Aligned_cols=64 Identities=23% Similarity=0.296 Sum_probs=46.9
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCc--ccceecccccc
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGA--RRLYSLNSVSK 103 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~--~~~y~~t~~s~ 103 (210)
+++.|...|... +.++..+|.+.+++ +...+.+-|+.|...|+++......+. .-.|++|+.++
T Consensus 1 vRl~Il~~L~~~---~~~~f~~L~~~l~l----t~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr 66 (80)
T PF13601_consen 1 VRLAILALLYAN---EEATFSELKEELGL----TDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGR 66 (80)
T ss_dssp HHHHHHHHHHHH---SEEEHHHHHHHTT------HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHH
T ss_pred CHHHHHHHHhhc---CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHH
Confidence 467888888886 59999999999999 999999999999999999865311001 12377777665
No 45
>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=95.44 E-value=0.027 Score=36.65 Aligned_cols=60 Identities=17% Similarity=0.197 Sum_probs=44.7
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCC-CCcccHHHHHHHHhcccceeeeccCCCcccceecccccc
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNK-DAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSK 103 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~-~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~ 103 (210)
|.++|.+.+ +|++..+|++.+..+.- +.++.++|.|++|...|++.+. ..+.+.+|+.+.
T Consensus 3 IL~~L~~~~--~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~-----g~~G~~iT~~G~ 63 (66)
T PF08461_consen 3 ILRILAESD--KPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKV-----GRQGRIITEKGL 63 (66)
T ss_pred HHHHHHHcC--CCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCcccc-----CCcccccCHHHH
Confidence 567788876 89999999999964100 1358899999999999977765 455567777653
No 46
>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=95.37 E-value=0.035 Score=44.20 Aligned_cols=65 Identities=22% Similarity=0.267 Sum_probs=49.8
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCccc----ceecccccccccc
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARR----LYSLNSVSKYYVP 107 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~----~y~~t~~s~~l~~ 107 (210)
..|...|... ++.|+.|||+.+++ ++..+.+.|+.|...|++++..... +.| .|.+|+.+..+..
T Consensus 4 ~~IL~~L~~~---~~~t~~eLA~~lgi----s~~tV~~~L~~Le~~GlV~r~~~~~-~~gRp~~~y~LT~~G~~~~~ 72 (203)
T TIGR02702 4 EDILSYLLKQ---GQATAAALAEALAI----SPQAVRRHLKDLETEGLIEYEAVVQ-GMGRPQYHYQLSRQGREQFP 72 (203)
T ss_pred HHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEeeccc-CCCCCceEEEECcchhhhcc
Confidence 4567777665 58999999999999 9999999999999999998752100 122 3788888875443
No 47
>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=95.36 E-value=0.036 Score=40.04 Aligned_cols=66 Identities=20% Similarity=0.154 Sum_probs=49.4
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCC-Ccccceeccccccccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDAS-GARRLYSLNSVSKYYV 106 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~-~~~~~y~~t~~s~~l~ 106 (210)
+..|+..|... ++.|..|||+.+++ ++..+.++++-|...|++++..+.. ...-.+.+|+.++.+.
T Consensus 30 q~~iL~~l~~~---~~~t~~ela~~~~~----~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~ 96 (118)
T TIGR02337 30 QWRILRILAEQ---GSMEFTQLANQACI----LRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALY 96 (118)
T ss_pred HHHHHHHHHHc---CCcCHHHHHHHhCC----CchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHH
Confidence 34466667665 58999999999999 9999999999999999999753110 0122477777776544
No 48
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=95.28 E-value=0.06 Score=42.15 Aligned_cols=45 Identities=18% Similarity=0.190 Sum_probs=40.0
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
..|++.|... +++|.+|||+.+|+ ....++++|..|...|++...
T Consensus 25 ~~Vl~~L~~~---g~~tdeeLA~~Lgi----~~~~VRk~L~~L~e~gLv~~~ 69 (178)
T PRK06266 25 FEVLKALIKK---GEVTDEEIAEQTGI----KLNTVRKILYKLYDARLADYK 69 (178)
T ss_pred hHHHHHHHHc---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEe
Confidence 3478888775 59999999999999 999999999999999999843
No 49
>PRK11050 manganese transport regulator MntR; Provisional
Probab=95.22 E-value=0.034 Score=42.35 Aligned_cols=57 Identities=23% Similarity=0.242 Sum_probs=46.1
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccccc
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYY 105 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l 105 (210)
|..++... ++.+..|||+.+++ ++..+.+.++.|...|++... ....+.+|+.+..+
T Consensus 42 I~~~l~~~---~~~t~~eLA~~l~i----s~stVsr~l~~Le~~GlI~r~-----~~~~v~LT~~G~~l 98 (152)
T PRK11050 42 IADLIAEV---GEARQVDIAARLGV----SQPTVAKMLKRLARDGLVEMR-----PYRGVFLTPEGEKL 98 (152)
T ss_pred HHHHHHhc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe-----cCCceEECchHHHH
Confidence 55566653 58999999999999 999999999999999999876 34567777766544
No 50
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=95.15 E-value=0.052 Score=33.92 Aligned_cols=42 Identities=21% Similarity=0.305 Sum_probs=36.6
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|+..|.. ++.|..+|++.+++ ++..+.+.++.|...|++...
T Consensus 2 il~~l~~----~~~~~~~i~~~l~i----s~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 2 ILKLLAE----GELCVCELAEILGL----SQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred HHHHhhc----CCccHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeee
Confidence 4455653 68999999999999 999999999999999999865
No 51
>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=95.06 E-value=0.044 Score=35.59 Aligned_cols=42 Identities=19% Similarity=0.256 Sum_probs=33.3
Q ss_pred HHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 40 ILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 40 ~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
++.+.| -|-|+.|||+.+|++ ++..+.+.|+.|...|++.+.
T Consensus 18 ~~~~~G--~~Pt~rEIa~~~g~~---S~~tv~~~L~~Le~kG~I~r~ 59 (65)
T PF01726_consen 18 YIEENG--YPPTVREIAEALGLK---STSTVQRHLKALERKGYIRRD 59 (65)
T ss_dssp HHHHHS--S---HHHHHHHHTSS---SHHHHHHHHHHHHHTTSEEEG
T ss_pred HHHHcC--CCCCHHHHHHHhCCC---ChHHHHHHHHHHHHCcCccCC
Confidence 344555 577999999999993 499999999999999999986
No 52
>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=94.98 E-value=0.049 Score=43.38 Aligned_cols=58 Identities=29% Similarity=0.349 Sum_probs=46.6
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSV 101 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~ 101 (210)
++.|...|.+. ++.+..|||+.+++ ++..+.|.+..|...|++++... ....|.+|+.
T Consensus 145 ~~~IL~~l~~~---g~~s~~eia~~l~i----s~stv~r~L~~Le~~GlI~r~~~---r~~~~~lT~~ 202 (203)
T TIGR01884 145 ELKVLEVLKAE---GEKSVKNIAKKLGK----SLSTISRHLRELEKKGLVEQKGR---KGKRYSLTKL 202 (203)
T ss_pred HHHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEcC---CccEEEeCCC
Confidence 45567777765 48999999999999 99999999999999999998720 2345777764
No 53
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=94.90 E-value=0.061 Score=39.55 Aligned_cols=47 Identities=19% Similarity=0.235 Sum_probs=39.0
Q ss_pred hhChhhHHh-hcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeec
Q 036188 34 ELGIFEILD-KAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSL 87 (210)
Q Consensus 34 ~lglfd~L~-~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~ 87 (210)
+..++-+|- .+ +|.|++|||+.++. +..-+.|-|+-|...|++.+..
T Consensus 29 Dv~v~~~LL~~~---~~~tvdelae~lnr----~rStv~rsl~~L~~~GlV~Rek 76 (126)
T COG3355 29 DVEVYKALLEEN---GPLTVDELAEILNR----SRSTVYRSLQNLLEAGLVEREK 76 (126)
T ss_pred HHHHHHHHHhhc---CCcCHHHHHHHHCc----cHHHHHHHHHHHHHcCCeeeee
Confidence 344444444 44 69999999999999 9999999999999999998763
No 54
>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=94.75 E-value=0.075 Score=34.22 Aligned_cols=45 Identities=27% Similarity=0.350 Sum_probs=38.2
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+..|...+.. ++.+..||++.+++ +...+.+.++.|...|++...
T Consensus 9 ~~~il~~l~~----~~~~~~ei~~~~~i----~~~~i~~~l~~L~~~g~i~~~ 53 (78)
T cd00090 9 RLRILRLLLE----GPLTVSELAERLGL----SQSTVSRHLKKLEEAGLVESR 53 (78)
T ss_pred HHHHHHHHHH----CCcCHHHHHHHHCc----CHhHHHHHHHHHHHCCCeEEE
Confidence 3445666666 35999999999999 999999999999999999875
No 55
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=94.69 E-value=0.051 Score=38.51 Aligned_cols=46 Identities=20% Similarity=0.316 Sum_probs=41.5
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
.+..|...|.++ +++|..+||+++|+ ++..+.+.++.|...|++..
T Consensus 4 ~D~~il~~L~~~---~~~~~~~la~~l~~----s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKD---ARISLAELAKKVGL----SPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHh---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeec
Confidence 467788888886 58999999999999 99999999999999999984
No 56
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=94.68 E-value=0.052 Score=33.57 Aligned_cols=42 Identities=17% Similarity=0.310 Sum_probs=33.9
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccce
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVV 83 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~ 83 (210)
.|...|.+++ +++|+++||+.+++ +.+-+.+-+..|...|+.
T Consensus 4 ~il~~L~~~~--~~it~~eLa~~l~v----S~rTi~~~i~~L~~~~~~ 45 (55)
T PF08279_consen 4 QILKLLLESK--EPITAKELAEELGV----SRRTIRRDIKELREWGIP 45 (55)
T ss_dssp HHHHHHHHTT--TSBEHHHHHHHCTS-----HHHHHHHHHHHHHTT-E
T ss_pred HHHHHHHHcC--CCcCHHHHHHHhCC----CHHHHHHHHHHHHHCCCe
Confidence 4566675443 57999999999999 999999999999999943
No 57
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=94.58 E-value=0.069 Score=40.80 Aligned_cols=50 Identities=20% Similarity=0.209 Sum_probs=45.9
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYV 106 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~ 106 (210)
+++...+||+.+++ .|.-+...++-|...|+++.. ..+.+.+|+.++-..
T Consensus 23 ~~~~~~diA~~L~V----sp~sVt~ml~rL~~~GlV~~~-----~y~gi~LT~~G~~~a 72 (154)
T COG1321 23 GFARTKDIAERLKV----SPPSVTEMLKRLERLGLVEYE-----PYGGVTLTEKGREKA 72 (154)
T ss_pred CcccHHHHHHHhCC----CcHHHHHHHHHHHHCCCeEEe-----cCCCeEEChhhHHHH
Confidence 69999999999999 999999999999999999997 588999999887554
No 58
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=94.57 E-value=0.084 Score=38.64 Aligned_cols=50 Identities=14% Similarity=0.175 Sum_probs=45.0
Q ss_pred HHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 30 QAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 30 ~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+..+...|.+++.++ |.+|+.|++..+|+ +-..+.++++.|++.|-+-..
T Consensus 10 r~eLk~rIvElVRe~---GRiTi~ql~~~TGa----sR~Tvk~~lreLVa~G~l~~~ 59 (127)
T PF06163_consen 10 REELKARIVELVREH---GRITIKQLVAKTGA----SRNTVKRYLRELVARGDLYRH 59 (127)
T ss_pred HHHHHHHHHHHHHHc---CCccHHHHHHHHCC----CHHHHHHHHHHHHHcCCeEeC
Confidence 455778899999987 59999999999999 999999999999999988876
No 59
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=94.54 E-value=0.085 Score=32.67 Aligned_cols=35 Identities=29% Similarity=0.295 Sum_probs=32.4
Q ss_pred CCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
..+ |..|||+.+++ +...+++.++.|...|++...
T Consensus 18 ~~l~s~~~la~~~~v----s~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 18 DKLPSERELAAQLGV----SRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred CcCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 456 89999999999 999999999999999999876
No 60
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=94.34 E-value=0.098 Score=38.60 Aligned_cols=53 Identities=15% Similarity=0.201 Sum_probs=45.9
Q ss_pred HHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 27 MAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 27 ~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
..+.+=-.+.|.+.|++. +|.|+.|+|+.+|- +...+.|=|+.|.-.|++...
T Consensus 59 a~vLsp~nleLl~~Ia~~---~P~Si~ElAe~vgR----dv~nvhr~Ls~l~~~GlI~fe 111 (144)
T COG4190 59 ARVLSPRNLELLELIAQE---EPASINELAELVGR----DVKNVHRTLSTLADLGLIFFE 111 (144)
T ss_pred HHHhChhHHHHHHHHHhc---CcccHHHHHHHhCc----chHHHHHHHHHHHhcCeEEEe
Confidence 344444567788999886 69999999999999 999999999999999999865
No 61
>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=94.24 E-value=0.03 Score=38.65 Aligned_cols=62 Identities=24% Similarity=0.270 Sum_probs=45.7
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHh-cCCCCCCcccHHHHHHHHhcccceeeeccCCC-cccceeccccccccc
Q 036188 37 IFEILDKAGPGTKLSASDIAAQL-LTKNKDAPMMLDRILRLLASYSVVECSLDASG-ARRLYSLNSVSKYYV 106 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~-~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~-~~~~y~~t~~s~~l~ 106 (210)
|...|.. ++....||.+.+ ++ ++..|.+-|+.|...|++++...... ..-.|++|+.++.|.
T Consensus 10 IL~~l~~----g~~rf~el~~~l~~i----s~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~ 73 (90)
T PF01638_consen 10 ILRALFQ----GPMRFSELQRRLPGI----SPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL 73 (90)
T ss_dssp HHHHHTT----SSEEHHHHHHHSTTS-----HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred HHHHHHh----CCCcHHHHHHhcchh----HHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence 3444555 699999999999 89 99999999999999999988632110 112488888887665
No 62
>COG2264 PrmA Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]
Probab=94.23 E-value=0.037 Score=46.77 Aligned_cols=43 Identities=28% Similarity=0.323 Sum_probs=28.9
Q ss_pred HHHHHHhhhhhhhHHHHHHhCCCCCCCCeEEEecCCccHHHHhhhC
Q 036188 165 HFNAAMYNYTSLVMSNILESYKGFDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 165 ~f~~~M~~~~~~~~~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
.|-.+-...+.... .+++.+. .+..+++|+|||+|.++++.++
T Consensus 140 AFGTG~HpTT~lcL-~~Le~~~--~~g~~vlDvGcGSGILaIAa~k 182 (300)
T COG2264 140 AFGTGTHPTTSLCL-EALEKLL--KKGKTVLDVGCGSGILAIAAAK 182 (300)
T ss_pred ccCCCCChhHHHHH-HHHHHhh--cCCCEEEEecCChhHHHHHHHH
Confidence 34433333333333 4566665 5889999999999999998753
No 63
>PRK10258 biotin biosynthesis protein BioC; Provisional
Probab=94.22 E-value=0.092 Score=42.90 Aligned_cols=32 Identities=13% Similarity=0.140 Sum_probs=23.5
Q ss_pred hHHHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 177 VMSNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 177 ~~~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.+..+++.++ -....+|+|||||+|.++..+.
T Consensus 30 ~a~~l~~~l~-~~~~~~vLDiGcG~G~~~~~l~ 61 (251)
T PRK10258 30 SADALLAMLP-QRKFTHVLDAGCGPGWMSRYWR 61 (251)
T ss_pred HHHHHHHhcC-ccCCCeEEEeeCCCCHHHHHHH
Confidence 3445566665 4567899999999999877653
No 64
>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=94.17 E-value=0.096 Score=36.27 Aligned_cols=68 Identities=21% Similarity=0.154 Sum_probs=50.9
Q ss_pred HHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHH----------HHHhcccce-eeeccCCCcccceecc
Q 036188 31 AVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRIL----------RLLASYSVV-ECSLDASGARRLYSLN 99 (210)
Q Consensus 31 ~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlL----------r~L~~~gl~-~~~~~~~~~~~~y~~t 99 (210)
.=++..|+..|...-| .+.++.|||+.+++ ++..+.--| +-|+.+|++ ++... ++.-.|++|
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 SKVRKKVLEYLCSIYP-EPAYPSEIARSVGS----DYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEK--GGFKYYRLT 80 (90)
T ss_pred HHHHHHHHHHHHHcCC-CcCCHHHHHHHHCC----CHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeec--CCeeEEEeC
Confidence 4567789999998732 79999999999999 999887777 458999999 43311 123369998
Q ss_pred cccccc
Q 036188 100 SVSKYY 105 (210)
Q Consensus 100 ~~s~~l 105 (210)
+.+..+
T Consensus 81 ~~G~~~ 86 (90)
T PF07381_consen 81 EKGKRI 86 (90)
T ss_pred hhhhhH
Confidence 877543
No 65
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=94.05 E-value=0.07 Score=43.01 Aligned_cols=64 Identities=31% Similarity=0.474 Sum_probs=48.7
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCC--Cc-ccceecccccccccc
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDAS--GA-RRLYSLNSVSKYYVP 107 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~--~~-~~~y~~t~~s~~l~~ 107 (210)
|...|.+. +|+|+.|||+++|+ ++..++|-|..|.+.|++......+ +. .-.|++|..+.-...
T Consensus 16 il~lL~~~---g~~sa~elA~~Lgi----s~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~~f~ 82 (218)
T COG2345 16 ILELLKKS---GPVSADELAEELGI----SPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGREQFP 82 (218)
T ss_pred HHHHHhcc---CCccHHHHHHHhCC----CHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchhhcc
Confidence 45567665 69999999999999 9999999999999999997552111 01 123999998775443
No 66
>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=94.00 E-value=0.1 Score=40.00 Aligned_cols=45 Identities=11% Similarity=0.041 Sum_probs=38.9
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
..|+++|-.. +.+|-+|||+.+|+ +..-++++|..|...||+...
T Consensus 17 v~Vl~aL~~~---~~~tdEeLa~~Lgi----~~~~VRk~L~~L~e~~Lv~~~ 61 (158)
T TIGR00373 17 GLVLFSLGIK---GEFTDEEISLELGI----KLNEVRKALYALYDAGLADYK 61 (158)
T ss_pred HHHHHHHhcc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCceee
Confidence 3467777754 58999999999999 999999999999999999643
No 67
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=93.94 E-value=0.11 Score=42.09 Aligned_cols=55 Identities=15% Similarity=0.276 Sum_probs=49.4
Q ss_pred HHHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 25 LPMAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 25 ~~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.-+||...+++.|...|++. +|+.+.|||+++|+ +..-+..=+..|...|+++-.
T Consensus 16 v~kalaS~vRv~Il~lL~~k---~plNvneiAe~lgL----pqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 16 VLKALASKVRVAILQLLHRK---GPLNVNEIAEALGL----PQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHHHHHHh---CCCCHHHHHHHhCC----chhhhhhhHHHHHhcCceeee
Confidence 34688899999999999997 59999999999999 999999999999999999743
No 68
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=93.91 E-value=0.079 Score=36.61 Aligned_cols=46 Identities=24% Similarity=0.325 Sum_probs=38.7
Q ss_pred HHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccccc
Q 036188 52 ASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYV 106 (210)
Q Consensus 52 ~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~ 106 (210)
+.+||+.+++ ++..+.+.++.|...|++.+. ....|.+|+.+..+.
T Consensus 2 ~~ela~~l~i----s~stvs~~l~~L~~~glI~r~-----~~~~~~lT~~g~~~~ 47 (96)
T smart00529 2 TSEIAERLNV----SPPTVTQMLKKLEKDGLVEYE-----PYRGITLTEKGRRLA 47 (96)
T ss_pred HHHHHHHhCC----ChHHHHHHHHHHHHCCCEEEc-----CCCceEechhHHHHH
Confidence 4689999999 999999999999999999987 345677777766543
No 69
>PRK06474 hypothetical protein; Provisional
Probab=93.90 E-value=0.14 Score=40.06 Aligned_cols=73 Identities=14% Similarity=0.188 Sum_probs=55.0
Q ss_pred HHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHh-cCCCCCCcccHHHHHHHHhcccceeeeccC---CCcccceeccccc
Q 036188 27 MAIQAVYELGIFEILDKAGPGTKLSASDIAAQL-LTKNKDAPMMLDRILRLLASYSVVECSLDA---SGARRLYSLNSVS 102 (210)
Q Consensus 27 ~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~-~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~---~~~~~~y~~t~~s 102 (210)
.+|..-.++.|++.|...+ .++|+.||++.+ ++ +..-+.|-|+.|...|+++..... +...-.|+.++.+
T Consensus 6 ~~La~p~R~~Il~~L~~~~--~~~ta~el~~~l~~i----s~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~~ 79 (178)
T PRK06474 6 EILMHPVRMKICQVLMRNK--EGLTPLELVKILKDV----PQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEED 79 (178)
T ss_pred HhhCCHHHHHHHHHHHhCC--CCCCHHHHHHHhcCC----CHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccce
Confidence 4566677888999998754 359999999999 57 888899999999999999976311 1122358788766
Q ss_pred ccc
Q 036188 103 KYY 105 (210)
Q Consensus 103 ~~l 105 (210)
..+
T Consensus 80 ~~~ 82 (178)
T PRK06474 80 AKI 82 (178)
T ss_pred eee
Confidence 544
No 70
>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=93.86 E-value=0.17 Score=31.92 Aligned_cols=33 Identities=24% Similarity=0.245 Sum_probs=30.6
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.|..+||+.+++ +...+.+.+..|...|+++..
T Consensus 26 ~~~~~la~~~~i----s~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 26 PSERELAEELGV----SRTTVREALRELEAEGLVERR 58 (66)
T ss_pred CCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec
Confidence 459999999999 999999999999999999865
No 71
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=93.85 E-value=0.1 Score=32.40 Aligned_cols=43 Identities=23% Similarity=0.404 Sum_probs=35.2
Q ss_pred HHHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHH
Q 036188 25 LPMAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLL 77 (210)
Q Consensus 25 ~~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L 77 (210)
+-.+|.+|+++|-||.= ...|..|||+.+|+ .+..+..-||-.
T Consensus 5 Q~e~L~~A~~~GYfd~P------R~~tl~elA~~lgi----s~st~~~~LRra 47 (53)
T PF04967_consen 5 QREILKAAYELGYFDVP------RRITLEELAEELGI----SKSTVSEHLRRA 47 (53)
T ss_pred HHHHHHHHHHcCCCCCC------CcCCHHHHHHHhCC----CHHHHHHHHHHH
Confidence 45689999999999742 47899999999999 888777777654
No 72
>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=93.84 E-value=0.12 Score=37.08 Aligned_cols=63 Identities=27% Similarity=0.302 Sum_probs=45.0
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCC-CCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTK-NKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~-~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
+..|++.|.+.+ ++.|++||.+++.-. ++++..-+.|.|+.|+..|++.+....+ +...|..+
T Consensus 3 R~~Il~~l~~~~--~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~-~~~~y~~~ 66 (116)
T cd07153 3 RLAILEVLLESD--GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGD-GKARYELN 66 (116)
T ss_pred HHHHHHHHHhCC--CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCC-CceEEEeC
Confidence 345788887754 699999999999421 1128889999999999999999874211 12356553
No 73
>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=93.82 E-value=0.067 Score=29.63 Aligned_cols=31 Identities=26% Similarity=0.333 Sum_probs=26.1
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccce
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVV 83 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~ 83 (210)
|+|-+|||..+|+ .++-+.|+|..|...|++
T Consensus 2 ~mtr~diA~~lG~----t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 2 PMTRQDIADYLGL----TRETVSRILKKLERQGLI 32 (32)
T ss_dssp E--HHHHHHHHTS-----HHHHHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHhCC----cHHHHHHHHHHHHHcCCC
Confidence 6789999999999 999999999999998875
No 74
>PRK06202 hypothetical protein; Provisional
Probab=93.75 E-value=0.1 Score=42.14 Aligned_cols=21 Identities=24% Similarity=0.270 Sum_probs=17.6
Q ss_pred CCCCeEEEecCCccHHHHhhh
Q 036188 189 DNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.+..+|+|||||.|.++..|+
T Consensus 59 ~~~~~iLDlGcG~G~~~~~L~ 79 (232)
T PRK06202 59 DRPLTLLDIGCGGGDLAIDLA 79 (232)
T ss_pred CCCcEEEEeccCCCHHHHHHH
Confidence 466899999999999877664
No 75
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=93.67 E-value=0.13 Score=34.54 Aligned_cols=43 Identities=21% Similarity=0.277 Sum_probs=39.6
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|=|+|+.. |.+++.+||.+++. ++..++-.|..++.+|-+++.
T Consensus 7 lRd~l~~~---gr~s~~~Ls~~~~~----p~~~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 7 VRDLLALR---GRMEAAQISQTLNT----PQPMINAMLQQLESMGKAVRI 49 (78)
T ss_pred HHHHHHHc---CcccHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEee
Confidence 45788886 59999999999999 999999999999999999987
No 76
>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=93.60 E-value=0.16 Score=36.30 Aligned_cols=35 Identities=14% Similarity=0.277 Sum_probs=23.7
Q ss_pred hhhhhHHHHHHhCCCCCCCCeEEEecCCccHHHHhh
Q 036188 173 YTSLVMSNILESYKGFDNIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 173 ~~~~~~~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l 208 (210)
.+...+.-|-..|. -.....+||||||.|.+.--|
T Consensus 42 IAAyLi~LW~~~~~-~~~~~~FVDlGCGNGLLV~IL 76 (112)
T PF07757_consen 42 IAAYLIELWRDMYG-EQKFQGFVDLGCGNGLLVYIL 76 (112)
T ss_pred HHHHHHHHHhcccC-CCCCCceEEccCCchHHHHHH
Confidence 34444455555655 356789999999999876443
No 77
>COG2230 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]
Probab=93.44 E-value=0.1 Score=43.71 Aligned_cols=31 Identities=23% Similarity=0.228 Sum_probs=26.5
Q ss_pred HHHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 178 MSNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 178 ~~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.+.+++.+. +++..+|||||||-|.+++..+
T Consensus 61 ~~~~~~kl~-L~~G~~lLDiGCGWG~l~~~aA 91 (283)
T COG2230 61 LDLILEKLG-LKPGMTLLDIGCGWGGLAIYAA 91 (283)
T ss_pred HHHHHHhcC-CCCCCEEEEeCCChhHHHHHHH
Confidence 356678887 9999999999999999998765
No 78
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=93.35 E-value=0.17 Score=39.37 Aligned_cols=64 Identities=16% Similarity=0.067 Sum_probs=50.2
Q ss_pred hchHHHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHh--cCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 22 GVVLPMAIQAVYELGIFEILDKAGPGTKLSASDIAAQL--LTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 22 ~~~~~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~--~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
..|...+++..+.+. + +..+..+||++| ++ ...-++.-|..|..+|+++++ ++|.|..|
T Consensus 22 ~~W~~~~ir~l~~l~--------~--~~~d~~~iak~l~p~i----s~~ev~~sL~~L~~~gli~k~-----~~g~y~~t 82 (171)
T PF14394_consen 22 SSWYHPAIRELLPLM--------P--FAPDPEWIAKRLRPKI----SAEEVRDSLEFLEKLGLIKKD-----GDGKYVQT 82 (171)
T ss_pred hhhHHHHHHHHhhcC--------C--CCCCHHHHHHHhcCCC----CHHHHHHHHHHHHHCCCeEEC-----CCCcEEEe
Confidence 445555666544332 1 233899999999 99 999999999999999999998 67899999
Q ss_pred ccccc
Q 036188 100 SVSKY 104 (210)
Q Consensus 100 ~~s~~ 104 (210)
..+-.
T Consensus 83 ~~~l~ 87 (171)
T PF14394_consen 83 DKSLT 87 (171)
T ss_pred cceee
Confidence 87655
No 79
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=93.31 E-value=0.099 Score=43.59 Aligned_cols=30 Identities=13% Similarity=0.300 Sum_probs=23.9
Q ss_pred HHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 179 SNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 179 ~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+++.++ .....+|+|||||.|.++..++
T Consensus 32 ~~i~~~l~-~~~~~~VLEiG~G~G~lt~~L~ 61 (272)
T PRK00274 32 DKIVDAAG-PQPGDNVLEIGPGLGALTEPLL 61 (272)
T ss_pred HHHHHhcC-CCCcCeEEEeCCCccHHHHHHH
Confidence 45566665 6677899999999999998875
No 80
>PRK07580 Mg-protoporphyrin IX methyl transferase; Validated
Probab=93.26 E-value=0.15 Score=40.89 Aligned_cols=22 Identities=14% Similarity=0.110 Sum_probs=18.5
Q ss_pred CCCCCeEEEecCCccHHHHhhh
Q 036188 188 FDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.....+|||||||.|.++..++
T Consensus 61 ~~~~~~vLDvGcG~G~~~~~l~ 82 (230)
T PRK07580 61 DLTGLRILDAGCGVGSLSIPLA 82 (230)
T ss_pred CCCCCEEEEEeCCCCHHHHHHH
Confidence 4456799999999999988775
No 81
>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=93.15 E-value=0.14 Score=34.09 Aligned_cols=49 Identities=14% Similarity=0.167 Sum_probs=42.1
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.+..+.+.|+.+.. .+.+..||++.++. |++.+...++.|...|++.+.
T Consensus 3 ~~~~~Le~I~rsR~-~Gi~q~~L~~~~~~----D~r~i~~~~k~L~~~gLI~k~ 51 (75)
T PF04182_consen 3 IQYCLLERIARSRY-NGITQSDLSKLLGI----DPRSIFYRLKKLEKKGLIVKQ 51 (75)
T ss_pred hHHHHHHHHHhcCC-CCEehhHHHHHhCC----CchHHHHHHHHHHHCCCEEEE
Confidence 45567777877542 68899999999999 999999999999999999986
No 82
>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=93.10 E-value=0.17 Score=35.26 Aligned_cols=44 Identities=14% Similarity=0.094 Sum_probs=38.1
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
.++|..|||+.+|+ ++..+.|.|..|...|++.... ..+.|..|
T Consensus 46 ~~is~~eLa~~~g~----sr~tVsr~L~~Le~~GlI~r~~----~~~~~~~n 89 (95)
T TIGR01610 46 DRVTATVIAELTGL----SRTHVSDAIKSLARRRIIFRQG----MMGIVGVN 89 (95)
T ss_pred CccCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeeeec----CCceeecC
Confidence 48999999999999 9999999999999999999762 34666665
No 83
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=93.09 E-value=0.18 Score=32.09 Aligned_cols=35 Identities=29% Similarity=0.393 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
++.+..+||+.+++ .+.-+...++-|...|+++..
T Consensus 21 ~~v~~~~iA~~L~v----s~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 21 GPVRTKDIAERLGV----SPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp SSBBHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred CCccHHHHHHHHCC----ChHHHHHHHHHHHHCCCEEec
Confidence 79999999999999 999999999999999999875
No 84
>PHA02943 hypothetical protein; Provisional
Probab=93.05 E-value=0.19 Score=38.01 Aligned_cols=105 Identities=14% Similarity=0.142 Sum_probs=65.0
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccccccCCCCCChH
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYVPNKDGVLLG 115 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~~~~~~~~~~ 115 (210)
.|.+.|.. |+.|..|||+++|+ +-..++-.|..|...|.+.+. .-|.. +-..+.+.. + .
T Consensus 15 eILE~Lk~----G~~TtseIAkaLGl----S~~qa~~~LyvLErEG~VkrV-----~~G~~-----tyw~l~~da--y-~ 73 (165)
T PHA02943 15 KTLRLLAD----GCKTTSRIANKLGV----SHSMARNALYQLAKEGMVLKV-----EIGRA-----AIWCLDEDA--Y-T 73 (165)
T ss_pred HHHHHHhc----CCccHHHHHHHHCC----CHHHHHHHHHHHHHcCceEEE-----eecce-----EEEEEChHH--H-H
Confidence 46677733 68999999999999 999999999999999999987 33321 112222221 2 2
Q ss_pred HHHHHhcChhHHHHHhhHHHHHhcCCchhhhhhCCchhHhhccCchHHHHHHHHHh
Q 036188 116 PLIQIIQDKVILESWSQLKDAILEGGIPFNRAHGVHIFEYAGLNPRFNKHFNAAMY 171 (210)
Q Consensus 116 ~~~~~~~~~~~~~~~~~L~~~l~~g~~~f~~~~g~~~fe~l~~~p~~~~~f~~~M~ 171 (210)
..+. ..+...|.- +++.+--| .....++.-+.+|++..+.|....-
T Consensus 74 ~~v~----~~~Relwrl----v~s~~~kf--i~p~~l~~li~kd~~a~~~~ak~v~ 119 (165)
T PHA02943 74 NLVF----EIKRELWRL----VCNSRLKF--ITPSRLLRLIAKDTEAHNIFAKYVP 119 (165)
T ss_pred HHHH----HHHHHHHHH----HHhccccc--cChHHHHHHHHhCHHHHHHHHHhcC
Confidence 2211 112223433 33222111 1224567778888988888877654
No 85
>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=93.03 E-value=0.1 Score=42.00 Aligned_cols=29 Identities=10% Similarity=0.028 Sum_probs=22.6
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.++...+ .....+|||||||+|.++..++
T Consensus 36 ~~l~~l~-~~~~~~vLDiGcG~G~~~~~la 64 (231)
T TIGR02752 36 DTMKRMN-VQAGTSALDVCCGTADWSIALA 64 (231)
T ss_pred HHHHhcC-CCCCCEEEEeCCCcCHHHHHHH
Confidence 4455555 6667899999999999987764
No 86
>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=92.85 E-value=0.099 Score=43.72 Aligned_cols=30 Identities=13% Similarity=0.143 Sum_probs=22.3
Q ss_pred HHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 179 SNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 179 ~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+++... .+...+|||||||-|.+++.++
T Consensus 52 ~~~~~~~~-l~~G~~vLDiGcGwG~~~~~~a 81 (273)
T PF02353_consen 52 DLLCEKLG-LKPGDRVLDIGCGWGGLAIYAA 81 (273)
T ss_dssp HHHHTTTT---TT-EEEEES-TTSHHHHHHH
T ss_pred HHHHHHhC-CCCCCEEEEeCCCccHHHHHHH
Confidence 46677777 8889999999999999998875
No 87
>PRK15068 tRNA mo(5)U34 methyltransferase; Provisional
Probab=92.79 E-value=0.11 Score=44.42 Aligned_cols=27 Identities=19% Similarity=0.278 Sum_probs=20.2
Q ss_pred HHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 182 LESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 182 l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
+..++.. ..++|+|||||.|.++..++
T Consensus 115 ~~~l~~l-~g~~VLDIGCG~G~~~~~la 141 (322)
T PRK15068 115 LPHLSPL-KGRTVLDVGCGNGYHMWRML 141 (322)
T ss_pred HHhhCCC-CCCEEEEeccCCcHHHHHHH
Confidence 4454413 35899999999999988775
No 88
>PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional
Probab=92.66 E-value=0.15 Score=40.79 Aligned_cols=29 Identities=31% Similarity=0.209 Sum_probs=21.1
Q ss_pred HHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 181 ILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 181 ~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
+...|..+....+|||||||+|.++..++
T Consensus 42 ~~~~~~~~~~~~~VLDlG~GtG~~t~~l~ 70 (209)
T PRK11188 42 IQQSDKLFKPGMTVVDLGAAPGGWSQYAV 70 (209)
T ss_pred HHHHhccCCCCCEEEEEcccCCHHHHHHH
Confidence 34444424567799999999999887664
No 89
>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=92.64 E-value=0.085 Score=44.64 Aligned_cols=42 Identities=29% Similarity=0.397 Sum_probs=26.4
Q ss_pred HHHHHHhhhhhhhHHHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 165 HFNAAMYNYTSLVMSNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 165 ~f~~~M~~~~~~~~~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.|-.+-...++... .+++.+. ....+|+|||||+|.++++-+
T Consensus 139 AFGTG~H~TT~lcl-~~l~~~~--~~g~~vLDvG~GSGILaiaA~ 180 (295)
T PF06325_consen 139 AFGTGHHPTTRLCL-ELLEKYV--KPGKRVLDVGCGSGILAIAAA 180 (295)
T ss_dssp SS-SSHCHHHHHHH-HHHHHHS--STTSEEEEES-TTSHHHHHHH
T ss_pred cccCCCCHHHHHHH-HHHHHhc--cCCCEEEEeCCcHHHHHHHHH
Confidence 35544444455444 4456665 344799999999999998754
No 90
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=92.55 E-value=0.24 Score=37.06 Aligned_cols=44 Identities=18% Similarity=0.126 Sum_probs=38.2
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.|.-.|... +++|..|||+.+++ ++..+.++++-|...|++.+.
T Consensus 44 ~vL~~l~~~---~~~t~~eLa~~l~i----~~~tvsr~l~~Le~~GlI~R~ 87 (144)
T PRK11512 44 KVLCSIRCA---ACITPVELKKVLSV----DLGALTRMLDRLVCKGWVERL 87 (144)
T ss_pred HHHHHHHHc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec
Confidence 345556554 58999999999999 999999999999999999976
No 91
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=92.50 E-value=0.17 Score=44.73 Aligned_cols=43 Identities=19% Similarity=0.147 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
+|.|.+||++++++ +++.++++++.|...|++.+. ++|.|.+.
T Consensus 309 ~~~t~~~La~~l~~----~~~~v~~iL~~L~~agLI~~~-----~~g~~~l~ 351 (412)
T PRK04214 309 KALDVDEIRRLEPM----GYDELGELLCELARIGLLRRG-----ERGQWVLA 351 (412)
T ss_pred CCCCHHHHHHHhCC----CHHHHHHHHHHHHhCCCeEec-----CCCceEec
Confidence 69999999999999 999999999999999999976 45656443
No 92
>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=92.45 E-value=0.2 Score=32.03 Aligned_cols=35 Identities=20% Similarity=0.280 Sum_probs=31.1
Q ss_pred CCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
..+ |..+||++.++ +...+++-|+.|...|+++..
T Consensus 22 ~~lps~~~la~~~~v----sr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 22 DRLPSERELAERYGV----SRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp SBE--HHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred CEeCCHHHHHHHhcc----CCcHHHHHHHHHHHCCcEEEE
Confidence 578 99999999999 999999999999999999876
No 93
>PRK11036 putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=92.17 E-value=0.17 Score=41.61 Aligned_cols=28 Identities=21% Similarity=0.356 Sum_probs=21.8
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.+++.++ ++..+|+|||||.|.++..++
T Consensus 36 ~~l~~l~--~~~~~vLDiGcG~G~~a~~la 63 (255)
T PRK11036 36 RLLAELP--PRPLRVLDAGGGEGQTAIKLA 63 (255)
T ss_pred HHHHhcC--CCCCEEEEeCCCchHHHHHHH
Confidence 4455554 456799999999999998875
No 94
>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=92.05 E-value=0.15 Score=36.17 Aligned_cols=43 Identities=26% Similarity=0.322 Sum_probs=33.3
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|++.|... +.++-+|||+.+++ ++.-++++|..|...||+...
T Consensus 18 Il~~L~~~---~~l~de~la~~~~l----~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 18 ILDALLRK---GELTDEDLAKKLGL----KPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp HHHHHHHH-----B-HHHHHHTT-S-----HHHHHHHHHHHHHHSS-EEE
T ss_pred HHHHHHHc---CCcCHHHHHHHhCC----CHHHHHHHHHHHHHCCCeEEE
Confidence 67888765 58999999999999 999999999999999999654
No 95
>TIGR00080 pimt protein-L-isoaspartate(D-aspartate) O-methyltransferase. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt.
Probab=91.94 E-value=0.2 Score=40.05 Aligned_cols=29 Identities=10% Similarity=0.228 Sum_probs=23.0
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.+++.++ .....+|+|||||+|.++..++
T Consensus 68 ~~~~~l~-~~~~~~VLDiG~GsG~~a~~la 96 (215)
T TIGR00080 68 MMTELLE-LKPGMKVLEIGTGSGYQAAVLA 96 (215)
T ss_pred HHHHHhC-CCCcCEEEEECCCccHHHHHHH
Confidence 4455555 6677899999999999998765
No 96
>COG2813 RsmC 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]
Probab=91.88 E-value=0.17 Score=42.73 Aligned_cols=31 Identities=23% Similarity=0.252 Sum_probs=23.8
Q ss_pred HHHHHhCCCCCCCCeEEEecCCccHHHHhhhC
Q 036188 179 SNILESYKGFDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 179 ~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
+-+++.++ .....+|+|+|||.|.+++.+++
T Consensus 148 ~lLl~~l~-~~~~~~vlDlGCG~Gvlg~~la~ 178 (300)
T COG2813 148 RLLLETLP-PDLGGKVLDLGCGYGVLGLVLAK 178 (300)
T ss_pred HHHHHhCC-ccCCCcEEEeCCCccHHHHHHHH
Confidence 35567777 44344999999999999998764
No 97
>COG4976 Predicted methyltransferase (contains TPR repeat) [General function prediction only]
Probab=91.88 E-value=0.22 Score=40.61 Aligned_cols=46 Identities=13% Similarity=0.398 Sum_probs=28.5
Q ss_pred HHHHHHHHHhhhhhhhHHHH----HHhCCCCCCCCeEEEecCCccHHHHhh
Q 036188 162 FNKHFNAAMYNYTSLVMSNI----LESYKGFDNIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 162 ~~~~f~~~M~~~~~~~~~~~----l~~~~~~~~~~~vvDiGGg~G~~~~~l 208 (210)
++..|....-.--....+.. +...+ ...+++++|+|||+|..+.+|
T Consensus 94 ~Ae~Fd~~LVdkL~Y~vP~~l~emI~~~~-~g~F~~~lDLGCGTGL~G~~l 143 (287)
T COG4976 94 YAERFDHILVDKLGYSVPELLAEMIGKAD-LGPFRRMLDLGCGTGLTGEAL 143 (287)
T ss_pred HHHHHHHHHHHHhcCccHHHHHHHHHhcc-CCccceeeecccCcCcccHhH
Confidence 34567666543222222332 33344 445899999999999988765
No 98
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=91.86 E-value=0.34 Score=36.08 Aligned_cols=44 Identities=14% Similarity=0.101 Sum_probs=37.2
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+...|...+ ++.|..|||+.+++ ++..+.+++.-|...|++++.
T Consensus 36 vL~~l~~~~--~~~t~~eLa~~l~~----~~~tvt~~v~~Le~~GlV~r~ 79 (144)
T PRK03573 36 TLHNIHQLP--PEQSQIQLAKAIGI----EQPSLVRTLDQLEEKGLISRQ 79 (144)
T ss_pred HHHHHHHcC--CCCCHHHHHHHhCC----ChhhHHHHHHHHHHCCCEeee
Confidence 344555443 46899999999999 999999999999999999986
No 99
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=91.79 E-value=0.27 Score=37.28 Aligned_cols=47 Identities=15% Similarity=0.263 Sum_probs=42.6
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.+..|.+.|.++ +..|..+||+++|+ ++..+.+=++-|...|++...
T Consensus 10 ~D~~Il~~Lq~d---~R~s~~eiA~~lgl----S~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 10 LDRGILEALMEN---ARTPYAELAKQFGV----SPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeeeE
Confidence 577889999886 59999999999999 999999999999999999743
No 100
>TIGR00452 methyltransferase, putative. Known examples to date are restricted to the proteobacteria.
Probab=91.78 E-value=0.23 Score=42.44 Aligned_cols=29 Identities=17% Similarity=0.226 Sum_probs=21.1
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.++..+. ....++|+|||||+|.++..++
T Consensus 112 ~~l~~l~-~~~g~~VLDvGCG~G~~~~~~~ 140 (314)
T TIGR00452 112 RVLPHLS-PLKGRTILDVGCGSGYHMWRML 140 (314)
T ss_pred HHHHhcC-CCCCCEEEEeccCCcHHHHHHH
Confidence 3455544 3445899999999999887664
No 101
>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=91.75 E-value=0.16 Score=35.79 Aligned_cols=51 Identities=12% Similarity=0.183 Sum_probs=39.5
Q ss_pred HHhhChhhHHhh-cCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 32 VYELGIFEILDK-AGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 32 a~~lglfd~L~~-~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
-++-.|+++|.. ...+.++++.+|++++++ +...++..++.|+..|++=..
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~----~~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQLGM----SENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHSTS-----HHHHHHHHHHHHHTTSEEES
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHhCc----CHHHHHHHHHHHHhCCeEecc
Confidence 345567888876 222368999999999999 999999999999999988543
No 102
>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional
Probab=91.57 E-value=0.22 Score=41.30 Aligned_cols=30 Identities=23% Similarity=0.475 Sum_probs=24.3
Q ss_pred HHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 179 SNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 179 ~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+++.+. .....+|||||||.|..+..++
T Consensus 42 ~~~l~~l~-l~~~~~VLDiGcG~G~~a~~la 71 (263)
T PTZ00098 42 TKILSDIE-LNENSKVLDIGSGLGGGCKYIN 71 (263)
T ss_pred HHHHHhCC-CCCCCEEEEEcCCCChhhHHHH
Confidence 45677776 7788899999999999877664
No 103
>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=91.52 E-value=0.39 Score=38.59 Aligned_cols=72 Identities=13% Similarity=0.138 Sum_probs=37.7
Q ss_pred HhhHHHHHhcCCchhhhhhCCchhHhhccCchHHH----HHHHHHhhhhhhhHHHHHHhCCCCCCCCeEEEecCCccHHH
Q 036188 130 WSQLKDAILEGGIPFNRAHGVHIFEYAGLNPRFNK----HFNAAMYNYTSLVMSNILESYKGFDNIKQLVDVGGSLGVTL 205 (210)
Q Consensus 130 ~~~L~~~l~~g~~~f~~~~g~~~fe~l~~~p~~~~----~f~~~M~~~~~~~~~~~l~~~~~~~~~~~vvDiGGg~G~~~ 205 (210)
++.|-|.+-+..+ .+-++.+.++|+.-. .|.+.+..+...+.+.+++.+..-++...|.|.|||.+.++
T Consensus 15 FR~lNE~LYT~~s-------~~A~~lf~~dP~~F~~YH~Gfr~Qv~~WP~nPvd~iI~~l~~~~~~~viaD~GCGdA~la 87 (219)
T PF05148_consen 15 FRWLNEQLYTTSS-------EEALKLFQEDPELFDIYHEGFRQQVKKWPVNPVDVIIEWLKKRPKSLVIADFGCGDAKLA 87 (219)
T ss_dssp HHHHHHHHHHS-H-------HHHHHHHHH-HHHHHHHHHHHHHHHCTSSS-HHHHHHHHHCTS-TTS-EEEES-TT-HHH
T ss_pred hHHHHHhHhcCCH-------HHHHHHHHhCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHhcCCCEEEEECCCchHHHH
Confidence 4455565544332 222455566776544 44444444444556666665542345679999999999999
Q ss_pred Hhh
Q 036188 206 QAI 208 (210)
Q Consensus 206 ~~l 208 (210)
.++
T Consensus 88 ~~~ 90 (219)
T PF05148_consen 88 KAV 90 (219)
T ss_dssp HH-
T ss_pred Hhc
Confidence 765
No 104
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=91.50 E-value=0.26 Score=37.86 Aligned_cols=47 Identities=15% Similarity=0.195 Sum_probs=42.9
Q ss_pred HHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 32 VYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 32 a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
.++..|...|.++ +.+|..|||+++|+ ++..+.+=++-|...|++..
T Consensus 14 ~~D~~IL~~Lq~d---~R~s~~eiA~~lgl----S~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 14 RIDRNILNELQKD---GRISNVELSKRVGL----SPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHhccC---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEE
Confidence 3678899999886 59999999999999 99999999999999999974
No 105
>PRK15001 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional
Probab=91.41 E-value=0.2 Score=43.92 Aligned_cols=29 Identities=17% Similarity=0.174 Sum_probs=21.9
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
-+++.++ .....+|+|+|||+|.+++.++
T Consensus 219 llL~~lp-~~~~~~VLDLGCGtGvi~i~la 247 (378)
T PRK15001 219 FFMQHLP-ENLEGEIVDLGCGNGVIGLTLL 247 (378)
T ss_pred HHHHhCC-cccCCeEEEEeccccHHHHHHH
Confidence 4456666 3334699999999999998875
No 106
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=91.40 E-value=0.31 Score=34.72 Aligned_cols=66 Identities=20% Similarity=0.248 Sum_probs=45.3
Q ss_pred hhChhhHHh--hcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCC-Ccccceeccccccc
Q 036188 34 ELGIFEILD--KAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDAS-GARRLYSLNSVSKY 104 (210)
Q Consensus 34 ~lglfd~L~--~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~-~~~~~y~~t~~s~~ 104 (210)
++.+...|. .+. +++.|..+||+.+++ ++..+.++++.|...|++.+..+.. ...-.+.+|+.+..
T Consensus 27 q~~vL~~l~~~~~~-~~~~t~~eL~~~l~~----~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~ 95 (109)
T TIGR01889 27 ELLILYYLGKLENN-EGKLTLKEIIKEILI----KQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRS 95 (109)
T ss_pred HHHHHHHHHhhhcc-CCcCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHH
Confidence 344555555 221 158999999999999 9999999999999999999753110 01122556665543
No 107
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=91.26 E-value=0.77 Score=33.53 Aligned_cols=86 Identities=17% Similarity=0.118 Sum_probs=61.0
Q ss_pred ccchhcchHHHHHHHHHhhchHHHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhc-CCCCCCcccHHHHHHHHhcccc
Q 036188 4 IVDGERDQSFAYADQLATGVVLPMAIQAVYELGIFEILDKAGPGTKLSASDIAAQLL-TKNKDAPMMLDRILRLLASYSV 82 (210)
Q Consensus 4 ~~~~~~~~~~~~l~~~~~~~~~~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~-~~~~~~~~~l~rlLr~L~~~gl 82 (210)
..+....-+.....+++.+-|..-.|+. |.. |+.-..||-..++ + .+..|.+=|+.|...|+
T Consensus 4 ~~~~~~~c~~~~~l~~ig~kW~~lIl~~---------L~~----g~~RF~eL~r~i~~I----s~k~Ls~~Lk~Le~~Gl 66 (120)
T COG1733 4 EDLEEPPCPVEEALEVIGGKWTLLILRD---------LFD----GPKRFNELRRSIGGI----SPKMLSRRLKELEEDGL 66 (120)
T ss_pred cccCCCCCCHHHHHHHHcCccHHHHHHH---------Hhc----CCCcHHHHHHHcccc----CHHHHHHHHHHHHHCCC
Confidence 3333334456677777777777666655 333 4889999999998 8 99999999999999999
Q ss_pred eeeeccCCC-cccceeccccccccc
Q 036188 83 VECSLDASG-ARRLYSLNSVSKYYV 106 (210)
Q Consensus 83 ~~~~~~~~~-~~~~y~~t~~s~~l~ 106 (210)
+++...... ..-.|++|+.++-|.
T Consensus 67 v~R~~~~~~PprveY~LT~~G~~L~ 91 (120)
T COG1733 67 VERVVYPEEPPRVEYRLTEKGRDLL 91 (120)
T ss_pred EEeeecCCCCceeEEEEhhhHHHHH
Confidence 998731110 123488887776554
No 108
>PRK07402 precorrin-6B methylase; Provisional
Probab=91.25 E-value=0.22 Score=39.21 Aligned_cols=28 Identities=14% Similarity=0.275 Sum_probs=21.6
Q ss_pred HHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 181 ILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 181 ~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
++..++ .....+|+|||||+|.++..++
T Consensus 32 l~~~l~-~~~~~~VLDiG~G~G~~~~~la 59 (196)
T PRK07402 32 LISQLR-LEPDSVLWDIGAGTGTIPVEAG 59 (196)
T ss_pred HHHhcC-CCCCCEEEEeCCCCCHHHHHHH
Confidence 345554 5667899999999999988764
No 109
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=91.20 E-value=0.1 Score=36.47 Aligned_cols=62 Identities=18% Similarity=0.278 Sum_probs=47.4
Q ss_pred hhhHHh-hcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccccc
Q 036188 37 IFEILD-KAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYV 106 (210)
Q Consensus 37 lfd~L~-~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~ 106 (210)
+||+|. .++ ++...--|.-.+++ +-+...++++.|+..|++...+ ++....|.+|+.+.-|.
T Consensus 20 i~dIL~~~~~--~~~~~Tri~y~aNl----ny~~~~~yi~~L~~~Gli~~~~--~~~~~~y~lT~KG~~fl 82 (95)
T COG3432 20 IFDILKAISE--GGIGITRIIYGANL----NYKRAQKYIEMLVEKGLIIKQD--NGRRKVYELTEKGKRFL 82 (95)
T ss_pred HHHHHHHhcC--CCCCceeeeeecCc----CHHHHHHHHHHHHhCCCEEecc--CCccceEEEChhHHHHH
Confidence 467776 333 67888889999999 9999999999999999777662 01122699999987654
No 110
>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=91.13 E-value=0.27 Score=32.29 Aligned_cols=35 Identities=26% Similarity=0.342 Sum_probs=33.0
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
-+.|-++||..+|+ ....+.|+|+.|...|++...
T Consensus 27 ~~lt~~~iA~~~g~----sr~tv~r~l~~l~~~g~I~~~ 61 (76)
T PF13545_consen 27 LPLTQEEIADMLGV----SRETVSRILKRLKDEGIIEVK 61 (76)
T ss_dssp EESSHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEE
T ss_pred ecCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEc
Confidence 37899999999999 999999999999999999976
No 111
>PRK13944 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=91.12 E-value=0.29 Score=38.95 Aligned_cols=29 Identities=14% Similarity=0.112 Sum_probs=21.4
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.+++.+. .....+|+|||||+|..+..++
T Consensus 63 ~~~~~l~-~~~~~~VLDiG~GsG~~~~~la 91 (205)
T PRK13944 63 MMCELIE-PRPGMKILEVGTGSGYQAAVCA 91 (205)
T ss_pred HHHHhcC-CCCCCEEEEECcCccHHHHHHH
Confidence 3445554 5566899999999999886654
No 112
>PRK00107 gidB 16S rRNA methyltransferase GidB; Reviewed
Probab=91.07 E-value=0.36 Score=38.02 Aligned_cols=21 Identities=19% Similarity=0.319 Sum_probs=17.4
Q ss_pred CCCCeEEEecCCccHHHHhhh
Q 036188 189 DNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l~ 209 (210)
+...+|+|||||+|..+..++
T Consensus 44 ~~g~~VLDiGcGtG~~al~la 64 (187)
T PRK00107 44 PGGERVLDVGSGAGFPGIPLA 64 (187)
T ss_pred CCCCeEEEEcCCCCHHHHHHH
Confidence 346899999999999888664
No 113
>PLN02244 tocopherol O-methyltransferase
Probab=91.06 E-value=0.27 Score=42.38 Aligned_cols=21 Identities=29% Similarity=0.484 Sum_probs=18.0
Q ss_pred CCCCeEEEecCCccHHHHhhh
Q 036188 189 DNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l~ 209 (210)
....+|||||||.|.++..++
T Consensus 117 ~~~~~VLDiGCG~G~~~~~La 137 (340)
T PLN02244 117 KRPKRIVDVGCGIGGSSRYLA 137 (340)
T ss_pred CCCCeEEEecCCCCHHHHHHH
Confidence 567899999999999988765
No 114
>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=91.02 E-value=0.41 Score=36.04 Aligned_cols=35 Identities=9% Similarity=0.082 Sum_probs=33.6
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|++|++|||.+.|+ ..|.+..-|-++++.|-+.+.
T Consensus 5 Ga~T~eELA~~FGv----ttRkvaStLa~~ta~Grl~Rv 39 (155)
T PF07789_consen 5 GAKTAEELAGKFGV----TTRKVASTLAMVTATGRLIRV 39 (155)
T ss_pred CcccHHHHHHHhCc----chhhhHHHHHHHHhcceeEEe
Confidence 69999999999999 999999999999999999887
No 115
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=90.98 E-value=0.37 Score=38.91 Aligned_cols=53 Identities=19% Similarity=0.212 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYV 106 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~ 106 (210)
..+|..|||+.+++ ++..+.|.++.|...|++++.... ....+.+|+.++.+.
T Consensus 20 ~~IS~~eLA~~L~i----S~~Tvsr~Lk~LEe~GlI~R~~~~--r~~~v~LTekG~~ll 72 (217)
T PRK14165 20 VKISSSEFANHTGT----SSKTAARILKQLEDEGYITRTIVP--RGQLITITEKGLDVL 72 (217)
T ss_pred CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEEcC--CceEEEECHHHHHHH
Confidence 46899999999999 999999999999999999886311 244577777766443
No 116
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=90.84 E-value=0.48 Score=32.96 Aligned_cols=46 Identities=26% Similarity=0.226 Sum_probs=41.3
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
++.|..+|... +|=.+.-||..+++ +...+.++++-|..+|++++.
T Consensus 9 ~~~IL~hl~~~---~~Dy~k~ia~~l~~----~~~~v~~~l~~Le~~GLler~ 54 (92)
T PF10007_consen 9 DLKILQHLKKA---GPDYAKSIARRLKI----PLEEVREALEKLEEMGLLERV 54 (92)
T ss_pred HHHHHHHHHHH---CCCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEe
Confidence 45677788887 48888999999999 999999999999999999998
No 117
>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=90.77 E-value=0.46 Score=37.50 Aligned_cols=48 Identities=17% Similarity=0.240 Sum_probs=38.8
Q ss_pred HhhChhhHHhh----cCCCCCCCHHHHHHHhcCCCCCC-cccHHHHHHHHhcccceeee
Q 036188 33 YELGIFEILDK----AGPGTKLSASDIAAQLLTKNKDA-PMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 33 ~~lglfd~L~~----~g~~~~~t~~eLA~~~~~~~~~~-~~~l~rlLr~L~~~gl~~~~ 86 (210)
.+..|++.|.+ .+ -+.|+.|||+++++ + +..+.+.|+.|...|+++..
T Consensus 7 ~q~~iL~~l~~~~~~~~--~~~~~~ela~~~~~----~s~~tv~~~l~~L~~~g~i~~~ 59 (199)
T TIGR00498 7 RQQEVLDLIRAHIESTG--YPPSIREIARAVGL----RSPSAAEEHLKALERKGYIERD 59 (199)
T ss_pred HHHHHHHHHHHHHHhcC--CCCcHHHHHHHhCC----CChHHHHHHHHHHHHCCCEecC
Confidence 34445555553 22 57899999999999 8 89999999999999999986
No 118
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=90.72 E-value=0.42 Score=35.86 Aligned_cols=47 Identities=17% Similarity=0.315 Sum_probs=42.5
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
++..|...|.++ ++.|..+||+++|+ ++..+.+-++-|...|++...
T Consensus 9 ~D~~IL~~L~~d---~r~~~~eia~~lgl----S~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 9 IDRRILRLLQED---ARISNAELAERVGL----SPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred HHHHHHHHHHHh---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCceeeE
Confidence 567788889886 58999999999999 999999999999999999865
No 119
>PRK11705 cyclopropane fatty acyl phospholipid synthase; Provisional
Probab=90.58 E-value=0.35 Score=42.42 Aligned_cols=30 Identities=13% Similarity=0.166 Sum_probs=23.8
Q ss_pred HHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 179 SNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 179 ~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+++.++ .+...+|||||||.|.++..++
T Consensus 157 ~~l~~~l~-l~~g~rVLDIGcG~G~~a~~la 186 (383)
T PRK11705 157 DLICRKLQ-LKPGMRVLDIGCGWGGLARYAA 186 (383)
T ss_pred HHHHHHhC-CCCCCEEEEeCCCccHHHHHHH
Confidence 34556665 6777899999999999998765
No 120
>KOG1271 consensus Methyltransferases [General function prediction only]
Probab=90.57 E-value=0.27 Score=38.71 Aligned_cols=21 Identities=19% Similarity=0.365 Sum_probs=18.0
Q ss_pred CCCeEEEecCCccHHHHhhhC
Q 036188 190 NIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~~ 210 (210)
+..+|||+|||.|+++.+|++
T Consensus 67 ~A~~VlDLGtGNG~~L~~L~~ 87 (227)
T KOG1271|consen 67 QADRVLDLGTGNGHLLFQLAK 87 (227)
T ss_pred cccceeeccCCchHHHHHHHH
Confidence 445999999999999998864
No 121
>PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=90.53 E-value=0.33 Score=38.87 Aligned_cols=30 Identities=10% Similarity=0.236 Sum_probs=23.3
Q ss_pred HHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 179 SNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 179 ~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+++.++ .+...+|+|||||+|.++..++
T Consensus 66 ~~~~~~l~-~~~g~~VLdIG~GsG~~t~~la 95 (212)
T PRK13942 66 AIMCELLD-LKEGMKVLEIGTGSGYHAAVVA 95 (212)
T ss_pred HHHHHHcC-CCCcCEEEEECCcccHHHHHHH
Confidence 34556666 7778899999999999986653
No 122
>PRK12335 tellurite resistance protein TehB; Provisional
Probab=90.48 E-value=0.24 Score=41.49 Aligned_cols=28 Identities=18% Similarity=0.226 Sum_probs=20.2
Q ss_pred HHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 181 ILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 181 ~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
++..++ .....+|||||||.|..+..++
T Consensus 112 ~~~~~~-~~~~~~vLDlGcG~G~~~~~la 139 (287)
T PRK12335 112 VLEAVQ-TVKPGKALDLGCGQGRNSLYLA 139 (287)
T ss_pred HHHHhh-ccCCCCEEEeCCCCCHHHHHHH
Confidence 344333 3345699999999999988775
No 123
>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=90.44 E-value=0.23 Score=39.66 Aligned_cols=21 Identities=24% Similarity=0.661 Sum_probs=17.7
Q ss_pred CCCCeEEEecCCccHHHHhhh
Q 036188 189 DNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l~ 209 (210)
....+|||||||+|..+..+.
T Consensus 42 ~~~~~VLDiGCG~G~~~~~L~ 62 (204)
T TIGR03587 42 PKIASILELGANIGMNLAALK 62 (204)
T ss_pred CCCCcEEEEecCCCHHHHHHH
Confidence 456789999999999988764
No 124
>PRK00121 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed
Probab=90.29 E-value=0.27 Score=39.01 Aligned_cols=28 Identities=14% Similarity=0.232 Sum_probs=21.4
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.|.+.++ ....+|||||||.|.++..++
T Consensus 32 ~~~~~~~--~~~~~VLDiGcGtG~~~~~la 59 (202)
T PRK00121 32 DWAELFG--NDAPIHLEIGFGKGEFLVEMA 59 (202)
T ss_pred CHHHHcC--CCCCeEEEEccCCCHHHHHHH
Confidence 4455555 256899999999999988775
No 125
>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=90.16 E-value=0.65 Score=31.19 Aligned_cols=48 Identities=15% Similarity=0.107 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVS 102 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s 102 (210)
.|+...+||++++. ++--++-.|..|..+||++... ...+.|..|..+
T Consensus 22 ~PVgSk~ia~~l~~----s~aTIRN~M~~Le~lGlve~~p---~~s~GriPT~~a 69 (78)
T PF03444_consen 22 EPVGSKTIAEELGR----SPATIRNEMADLEELGLVESQP---HPSGGRIPTDKA 69 (78)
T ss_pred CCcCHHHHHHHHCC----ChHHHHHHHHHHHHCCCccCCC---CCCCCCCcCHHH
Confidence 69999999999999 9999999999999999998421 024667766655
No 126
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=90.00 E-value=0.86 Score=35.26 Aligned_cols=79 Identities=16% Similarity=0.095 Sum_probs=53.2
Q ss_pred CCcccchhcchHHHHHHHHHhhchHHHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCC-CCCCcccHHHHHHHHhc
Q 036188 1 MDSIVDGERDQSFAYADQLATGVVLPMAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTK-NKDAPMMLDRILRLLAS 79 (210)
Q Consensus 1 ~~~~~~~~~~~~~~~l~~~~~~~~~~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~-~~~~~~~l~rlLr~L~~ 79 (210)
|+.+.++++.+....+.+-. |.. .+--+.-|++.|...+ ++.|++||.+++.-. ++++..-+.|.|+.|+.
T Consensus 1 ~~~~~~~~~~~~~~~~L~~~-GlR-----~T~qR~~IL~~l~~~~--~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e 72 (169)
T PRK11639 1 MEKTTTQELLAQAEKLCAQR-NVR-----LTPQRLEVLRLMSLQP--GAISAYDLLDLLREAEPQAKPPTVYRALDFLLE 72 (169)
T ss_pred CCCccHHHHHHHHHHHHHHc-CCC-----CCHHHHHHHHHHHhcC--CCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHH
Confidence 66666666666554443322 111 1234455777777654 699999999998641 22367789999999999
Q ss_pred ccceeeec
Q 036188 80 YSVVECSL 87 (210)
Q Consensus 80 ~gl~~~~~ 87 (210)
.|++.+..
T Consensus 73 ~Glv~~~~ 80 (169)
T PRK11639 73 QGFVHKVE 80 (169)
T ss_pred CCCEEEEe
Confidence 99999873
No 127
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=89.84 E-value=0.42 Score=39.66 Aligned_cols=47 Identities=21% Similarity=0.402 Sum_probs=42.1
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+..+.++|.+.| |..+=+||.+++|+ +..-+.|.|+-|..+|++++.
T Consensus 197 e~~il~~i~~~G--Gri~Q~eL~r~lgl----sktTvsR~L~~LEk~GlIe~~ 243 (258)
T COG2512 197 EKEILDLIRERG--GRITQAELRRALGL----SKTTVSRILRRLEKRGLIEKE 243 (258)
T ss_pred HHHHHHHHHHhC--CEEeHHHHHHhhCC----ChHHHHHHHHHHHhCCceEEE
Confidence 345788888876 78999999999999 999999999999999999876
No 128
>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=89.63 E-value=0.63 Score=38.91 Aligned_cols=47 Identities=11% Similarity=0.177 Sum_probs=41.2
Q ss_pred CCCHHHHHHHhc--CCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccc
Q 036188 49 KLSASDIAAQLL--TKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKY 104 (210)
Q Consensus 49 ~~t~~eLA~~~~--~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~ 104 (210)
..++++||++|+ + ...-++.-|..|..+||++++ ++|.|..|..+..
T Consensus 137 ~~~~~~ia~~l~p~i----s~~ev~~sL~~L~~~glikk~-----~~g~y~~t~~~l~ 185 (271)
T TIGR02147 137 ADDPEELAKRCFPKI----SAEQVKESLDLLERLGLIKKN-----EDGFYKQTDKAVS 185 (271)
T ss_pred CCCHHHHHHHhCCCC----CHHHHHHHHHHHHHCCCeeEC-----CCCcEEeecceee
Confidence 447889999999 6 889999999999999999998 6899999987544
No 129
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=89.63 E-value=0.75 Score=33.34 Aligned_cols=52 Identities=19% Similarity=0.208 Sum_probs=40.2
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccc
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSK 103 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~ 103 (210)
+..+|.+. ||.+..+|++.++. + ...++|+. --.|+|++. +.|.|.+|+.++
T Consensus 64 ~A~~L~~~---Gp~~~~~l~~~~~~----~--~A~~IL~~-N~YGWFeRv-----~rGvY~LT~~G~ 115 (118)
T PF09929_consen 64 CAAALAEH---GPSRPADLRKATGV----P--KATSILRD-NHYGWFERV-----ERGVYALTPAGR 115 (118)
T ss_pred HHHHHHHc---CCCCHHHHHHhcCC----C--hHHHHHHh-Ccccceeee-----ccceEecCcchh
Confidence 34568876 69999999999998 4 34445543 457899998 799999999875
No 130
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=89.57 E-value=0.68 Score=38.15 Aligned_cols=45 Identities=13% Similarity=0.145 Sum_probs=40.9
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
..|.+.|.+. +..+++|||+.+++ .+.-++|-|+.|...|++.+.
T Consensus 8 ~~Il~~l~~~---~~~~~~ela~~l~v----S~~TirRdL~~Le~~g~i~r~ 52 (251)
T PRK13509 8 QILLELLAQL---GFVTVEKVIERLGI----SPATARRDINKLDESGKLKKV 52 (251)
T ss_pred HHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence 4478888885 58999999999999 999999999999999999886
No 131
>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=89.57 E-value=0.24 Score=40.21 Aligned_cols=21 Identities=19% Similarity=0.199 Sum_probs=17.6
Q ss_pred CCCCeEEEecCCccHHHHhhh
Q 036188 189 DNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l~ 209 (210)
....+|||||||.|..+..++
T Consensus 52 ~~~~~iLDlGcG~G~~~~~l~ 72 (239)
T TIGR00740 52 TPDSNVYDLGCSRGAATLSAR 72 (239)
T ss_pred CCCCEEEEecCCCCHHHHHHH
Confidence 456799999999999987664
No 132
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=89.48 E-value=0.84 Score=37.63 Aligned_cols=59 Identities=17% Similarity=0.140 Sum_probs=46.7
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccccc
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYY 105 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l 105 (210)
+.-.|-.. |++|+.|||+.+|+ +...+..+|+-|...|+++... +.+-.|+.-+-..++
T Consensus 21 vY~aLl~~---g~~tA~eis~~sgv----P~~kvY~vl~sLe~kG~v~~~~---g~P~~y~av~p~~~i 79 (247)
T COG1378 21 VYLALLCL---GEATAKEISEASGV----PRPKVYDVLRSLEKKGLVEVIE---GRPKKYRAVPPEELI 79 (247)
T ss_pred HHHHHHHh---CCccHHHHHHHcCC----CchhHHHHHHHHHHCCCEEeeC---CCCceEEeCCHHHHH
Confidence 44445444 69999999999999 9999999999999999999762 246778776655544
No 133
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=89.42 E-value=0.47 Score=36.67 Aligned_cols=45 Identities=16% Similarity=0.184 Sum_probs=40.7
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccc
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSK 103 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~ 103 (210)
.|..+||+.+++ +..-+.|.+..|...+++.+. ..|.|..||.-.
T Consensus 76 ~t~~~ia~~l~i----S~~Tv~r~ik~L~e~~iI~k~-----~~G~Y~iNP~~~ 120 (165)
T PF05732_consen 76 ATQKEIAEKLGI----SKPTVSRAIKELEEKNIIKKI-----RNGAYMINPNFF 120 (165)
T ss_pred eeHHHHHHHhCC----CHHHHHHHHHHHHhCCcEEEc-----cCCeEEECcHHh
Confidence 688999999999 999999999999999999987 578999998643
No 134
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=89.33 E-value=0.5 Score=37.94 Aligned_cols=44 Identities=25% Similarity=0.359 Sum_probs=36.9
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|.+.|... +.+.|++|+|+++|+ +.--.+|.|.+|++.|+++..
T Consensus 163 i~~~~~~~--~~~~Taeela~~~gi----SRvTaRRYLeyl~~~~~l~a~ 206 (224)
T COG4565 163 VREALKEP--DQELTAEELAQALGI----SRVTARRYLEYLVSNGILEAE 206 (224)
T ss_pred HHHHHhCc--CCccCHHHHHHHhCc----cHHHHHHHHHHHHhcCeeeEE
Confidence 44555532 269999999999999 999999999999999999865
No 135
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=89.31 E-value=0.46 Score=39.46 Aligned_cols=20 Identities=25% Similarity=0.418 Sum_probs=16.9
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
...+|||||||+|.++..++
T Consensus 85 ~~~~vLDiGcG~G~~~~~l~ 104 (272)
T PRK11088 85 KATALLDIGCGEGYYTHALA 104 (272)
T ss_pred CCCeEEEECCcCCHHHHHHH
Confidence 45789999999999988764
No 136
>COG2227 UbiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme metabolism]
Probab=89.31 E-value=0.22 Score=40.66 Aligned_cols=19 Identities=21% Similarity=0.333 Sum_probs=17.0
Q ss_pred CCeEEEecCCccHHHHhhh
Q 036188 191 IKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 191 ~~~vvDiGGg~G~~~~~l~ 209 (210)
..+|||||||-|.++..++
T Consensus 60 g~~vLDvGCGgG~Lse~mA 78 (243)
T COG2227 60 GLRVLDVGCGGGILSEPLA 78 (243)
T ss_pred CCeEEEecCCccHhhHHHH
Confidence 5799999999999998775
No 137
>PLN02336 phosphoethanolamine N-methyltransferase
Probab=89.22 E-value=0.37 Score=43.26 Aligned_cols=30 Identities=13% Similarity=0.260 Sum_probs=22.9
Q ss_pred HHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 179 SNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 179 ~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+++.++ .+...+|||||||.|..++.++
T Consensus 256 e~l~~~~~-~~~~~~vLDiGcG~G~~~~~la 285 (475)
T PLN02336 256 KEFVDKLD-LKPGQKVLDVGCGIGGGDFYMA 285 (475)
T ss_pred HHHHHhcC-CCCCCEEEEEeccCCHHHHHHH
Confidence 34556665 6677899999999998877664
No 138
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=89.18 E-value=0.54 Score=34.09 Aligned_cols=35 Identities=9% Similarity=0.171 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.+.|++|||+.+.+ .++.++.+|+-|...|.++-.
T Consensus 18 ~~vtl~elA~~l~c----S~Rn~r~lLkkm~~~gWi~W~ 52 (115)
T PF12793_consen 18 VEVTLDELAELLFC----SRRNARTLLKKMQEEGWITWQ 52 (115)
T ss_pred cceeHHHHHHHhCC----CHHHHHHHHHHHHHCCCeeee
Confidence 46899999999999 999999999999999999976
No 139
>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=89.11 E-value=0.47 Score=39.86 Aligned_cols=27 Identities=30% Similarity=0.375 Sum_probs=20.3
Q ss_pred HHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 181 ILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 181 ~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
+++.+. . ...+|+|||||+|.+++.++
T Consensus 152 ~l~~~~-~-~g~~VLDvGcGsG~lai~aa 178 (288)
T TIGR00406 152 WLEDLD-L-KDKNVIDVGCGSGILSIAAL 178 (288)
T ss_pred HHHhhc-C-CCCEEEEeCCChhHHHHHHH
Confidence 355554 3 45899999999999987764
No 140
>KOG1541 consensus Predicted protein carboxyl methylase [General function prediction only]
Probab=89.02 E-value=0.22 Score=40.41 Aligned_cols=29 Identities=17% Similarity=0.299 Sum_probs=20.6
Q ss_pred HHHHHhCCCCCC--CCeEEEecCCccHHHHhh
Q 036188 179 SNILESYKGFDN--IKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 179 ~~~l~~~~~~~~--~~~vvDiGGg~G~~~~~l 208 (210)
..-++..+ +++ ...|+|||||+|.-+..|
T Consensus 38 eRaLELLa-lp~~~~~~iLDIGCGsGLSg~vL 68 (270)
T KOG1541|consen 38 ERALELLA-LPGPKSGLILDIGCGSGLSGSVL 68 (270)
T ss_pred HHHHHHhh-CCCCCCcEEEEeccCCCcchhee
Confidence 34455544 554 889999999999876554
No 141
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=88.91 E-value=0.42 Score=27.75 Aligned_cols=29 Identities=28% Similarity=0.362 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASY 80 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~ 80 (210)
.+.+++|||..+|+ ++..+.|+.+....+
T Consensus 7 ~~~~l~~iA~~~g~----S~~~f~r~Fk~~~g~ 35 (42)
T PF00165_consen 7 QKLTLEDIAEQAGF----SPSYFSRLFKKETGM 35 (42)
T ss_dssp SS--HHHHHHHHTS-----HHHHHHHHHHHTSS
T ss_pred CCCCHHHHHHHHCC----CHHHHHHHHHHHHCc
Confidence 48999999999999 999999998876543
No 142
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=88.91 E-value=0.44 Score=43.19 Aligned_cols=66 Identities=18% Similarity=0.263 Sum_probs=52.2
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccccccC
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYVPN 108 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~~~ 108 (210)
.+..|...|... ++.|..+||+++++ ++..+.+.++-|.+.|+++.... ....|.+|+.++.+..+
T Consensus 7 ~e~~vL~~L~~~---~~~s~~eLA~~l~l----~~~tVt~~i~~Le~kGlV~~~~~---~~~~i~LTeeG~~~~~~ 72 (489)
T PRK04172 7 NEKKVLKALKEL---KEATLEELAEKLGL----PPEAVMRAAEWLEEKGLVKVEER---VEEVYVLTEEGKKYAEE 72 (489)
T ss_pred HHHHHHHHHHhC---CCCCHHHHHHHhCc----CHHHHHHHHHHHHhCCCEEEEee---eEEEEEECHHHHHHHHh
Confidence 344555666654 58999999999999 99999999999999999987620 24579999999865543
No 143
>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=88.77 E-value=0.27 Score=38.46 Aligned_cols=19 Identities=21% Similarity=0.410 Sum_probs=16.1
Q ss_pred CCeEEEecCCccHHHHhhh
Q 036188 191 IKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 191 ~~~vvDiGGg~G~~~~~l~ 209 (210)
..+|+|||||+|.++..++
T Consensus 43 ~~~vLDiGcGtG~~s~~la 61 (181)
T TIGR00138 43 GKKVIDIGSGAGFPGIPLA 61 (181)
T ss_pred CCeEEEecCCCCccHHHHH
Confidence 5799999999999877653
No 144
>PRK05785 hypothetical protein; Provisional
Probab=88.64 E-value=0.29 Score=39.65 Aligned_cols=19 Identities=21% Similarity=0.230 Sum_probs=16.7
Q ss_pred CCeEEEecCCccHHHHhhh
Q 036188 191 IKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 191 ~~~vvDiGGg~G~~~~~l~ 209 (210)
..+|+|||||+|.++..+.
T Consensus 52 ~~~VLDlGcGtG~~~~~l~ 70 (226)
T PRK05785 52 PKKVLDVAAGKGELSYHFK 70 (226)
T ss_pred CCeEEEEcCCCCHHHHHHH
Confidence 6799999999999988764
No 145
>PRK05638 threonine synthase; Validated
Probab=88.51 E-value=0.63 Score=41.59 Aligned_cols=60 Identities=18% Similarity=0.254 Sum_probs=44.9
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhc--CCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccccc
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLL--TKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYY 105 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~--~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l 105 (210)
|...|.+ ++++..||+++++ + .+..+.+.|+.|...|+++..... +..-.|++|+.++.+
T Consensus 376 IL~~L~~----~~~~~~el~~~l~~~~----s~~~v~~hL~~Le~~GLV~~~~~~-g~~~~Y~Lt~~g~~~ 437 (442)
T PRK05638 376 ILKILSE----REMYGYEIWKALGKPL----KYQAVYQHIKELEELGLIEEAYRK-GRRVYYKLTEKGRRL 437 (442)
T ss_pred HHHHHhh----CCccHHHHHHHHcccC----CcchHHHHHHHHHHCCCEEEeecC-CCcEEEEECcHHHHH
Confidence 4555655 6899999999998 7 899999999999999999753100 112348888877643
No 146
>PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional
Probab=88.43 E-value=0.5 Score=40.81 Aligned_cols=28 Identities=21% Similarity=0.351 Sum_probs=20.2
Q ss_pred HHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 181 ILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 181 ~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
+++.++ -....+|+|+|||.|.+++.++
T Consensus 188 Ll~~l~-~~~~g~VLDlGCG~G~ls~~la 215 (342)
T PRK09489 188 LLSTLT-PHTKGKVLDVGCGAGVLSAVLA 215 (342)
T ss_pred HHHhcc-ccCCCeEEEeccCcCHHHHHHH
Confidence 344444 2334589999999999998775
No 147
>KOG2899 consensus Predicted methyltransferase [General function prediction only]
Probab=88.37 E-value=0.33 Score=39.93 Aligned_cols=31 Identities=23% Similarity=0.277 Sum_probs=24.1
Q ss_pred HHHHhCC-CCCCCCeEEEecCCccHHHHhhhC
Q 036188 180 NILESYK-GFDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 180 ~~l~~~~-~~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
..+..++ .|-....++||||+.|.+.+.|+|
T Consensus 47 ~rLk~L~~~~f~~~~~LDIGCNsG~lt~~iak 78 (288)
T KOG2899|consen 47 PRLKVLEKDWFEPKQALDIGCNSGFLTLSIAK 78 (288)
T ss_pred hhhhhccccccCcceeEeccCCcchhHHHHHH
Confidence 4444443 277889999999999999998864
No 148
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=88.26 E-value=0.34 Score=39.63 Aligned_cols=21 Identities=29% Similarity=0.393 Sum_probs=17.4
Q ss_pred CCCCeEEEecCCccHHHHhhh
Q 036188 189 DNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l~ 209 (210)
....+|+|||||+|..+..++
T Consensus 55 ~~~~~vLDlGcGtG~~~~~l~ 75 (247)
T PRK15451 55 QPGTQVYDLGCSLGAATLSVR 75 (247)
T ss_pred CCCCEEEEEcccCCHHHHHHH
Confidence 456799999999999887654
No 149
>PLN02233 ubiquinone biosynthesis methyltransferase
Probab=88.22 E-value=0.84 Score=37.76 Aligned_cols=22 Identities=9% Similarity=-0.003 Sum_probs=17.9
Q ss_pred CCCCCeEEEecCCccHHHHhhh
Q 036188 188 FDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.....+|+|||||+|.++..++
T Consensus 71 ~~~~~~VLDlGcGtG~~~~~la 92 (261)
T PLN02233 71 AKMGDRVLDLCCGSGDLAFLLS 92 (261)
T ss_pred CCCCCEEEEECCcCCHHHHHHH
Confidence 4557899999999999877654
No 150
>smart00138 MeTrc Methyltransferase, chemotaxis proteins. Methylates methyl-accepting chemotaxis proteins to form gamma-glutamyl methyl ester residues.
Probab=88.20 E-value=2.6 Score=34.94 Aligned_cols=24 Identities=17% Similarity=0.207 Sum_probs=16.6
Q ss_pred HHHHHhCCCCCCCCeEEEecCCccH
Q 036188 179 SNILESYKGFDNIKQLVDVGGSLGV 203 (210)
Q Consensus 179 ~~~l~~~~~~~~~~~vvDiGGg~G~ 203 (210)
+.+++.-+ ..+..+|+|+|||+|.
T Consensus 89 p~l~~~~~-~~~~~ri~d~GCgtGe 112 (264)
T smart00138 89 PLLIASRR-HGRRVRIWSAGCSTGE 112 (264)
T ss_pred HHHHHhcC-CCCCEEEEeccccCCh
Confidence 34444333 4456799999999996
No 151
>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=88.20 E-value=0.37 Score=40.86 Aligned_cols=29 Identities=17% Similarity=0.258 Sum_probs=20.9
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.+...++++ ..++|+|||||.|.++.+++
T Consensus 106 rl~p~l~~L-~gk~VLDIGC~nGY~~frM~ 134 (315)
T PF08003_consen 106 RLLPHLPDL-KGKRVLDIGCNNGYYSFRML 134 (315)
T ss_pred HHHhhhCCc-CCCEEEEecCCCcHHHHHHh
Confidence 344454324 35799999999999987764
No 152
>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=88.17 E-value=0.8 Score=26.87 Aligned_cols=37 Identities=19% Similarity=0.276 Sum_probs=26.6
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHH
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRL 76 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~ 76 (210)
++..|...|.++ +..|..+||+++|+ ++..+.+=++.
T Consensus 4 ~D~~Il~~Lq~d---~r~s~~~la~~lgl----S~~~v~~Ri~r 40 (42)
T PF13404_consen 4 LDRKILRLLQED---GRRSYAELAEELGL----SESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHH----TTS-HHHHHHHHTS-----HHHHHHHHHH
T ss_pred HHHHHHHHHHHc---CCccHHHHHHHHCc----CHHHHHHHHHH
Confidence 456788888886 59999999999999 88766554443
No 153
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=88.16 E-value=0.77 Score=37.51 Aligned_cols=94 Identities=14% Similarity=0.214 Sum_probs=62.3
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccc-ccccCCCCCCh
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSK-YYVPNKDGVLL 114 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~-~l~~~~~~~~~ 114 (210)
.|.-.|.... ....-.|||+++|+ .+..+...++-|+..|++++. +.++|..|..+. .+...-. .+
T Consensus 14 qIL~ei~~~q--p~v~q~eIA~~lgi----T~QaVsehiK~Lv~eG~i~~~-----gR~~Y~iTkkG~e~l~~~~~--dl 80 (260)
T COG1497 14 QILSEIAVRQ--PRVKQKEIAKKLGI----TLQAVSEHIKELVKEGLIEKE-----GRGEYEITKKGAEWLLEQLS--DL 80 (260)
T ss_pred HHHHHHHHhC--CCCCHHHHHHHcCC----CHHHHHHHHHHHHhccceeec-----CCeeEEEehhHHHHHHHHHH--HH
Confidence 3344444432 36889999999999 999999999999999999997 678999999886 4443221 24
Q ss_pred HHHHHHhcC-hhHHHHHhhHHHH-HhcCCc
Q 036188 115 GPLIQIIQD-KVILESWSQLKDA-ILEGGI 142 (210)
Q Consensus 115 ~~~~~~~~~-~~~~~~~~~L~~~-l~~g~~ 142 (210)
+.++..... -.+...|..+++. ++.|..
T Consensus 81 r~f~~ev~~~l~~~~vw~AIA~edI~~Gd~ 110 (260)
T COG1497 81 RRFSEEVELVLDYVMVWTAIAKEDIKEGDT 110 (260)
T ss_pred HHHHHHHHHHHhhHHHHHHhhHhhhccCCE
Confidence 444433211 1123467666543 555544
No 154
>PF13730 HTH_36: Helix-turn-helix domain
Probab=88.09 E-value=0.55 Score=28.82 Aligned_cols=30 Identities=17% Similarity=0.222 Sum_probs=28.0
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHHHHhcccce
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILRLLASYSVV 83 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~ 83 (210)
-|.+.||+.+|+ ..+-+.|.++.|...|++
T Consensus 26 pS~~~la~~~g~----s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 26 PSQETLAKDLGV----SRRTVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHHCc----CHHHHHHHHHHHHHCcCC
Confidence 389999999999 999999999999999975
No 155
>PRK00216 ubiE ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed
Probab=88.08 E-value=0.56 Score=37.45 Aligned_cols=29 Identities=10% Similarity=0.106 Sum_probs=21.4
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.++..+. .....+|+|||||.|.++..++
T Consensus 42 ~~~~~~~-~~~~~~vldiG~G~G~~~~~l~ 70 (239)
T PRK00216 42 KTIKWLG-VRPGDKVLDLACGTGDLAIALA 70 (239)
T ss_pred HHHHHhC-CCCCCeEEEeCCCCCHHHHHHH
Confidence 3444444 4456899999999999988764
No 156
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=87.99 E-value=1.9 Score=33.11 Aligned_cols=77 Identities=18% Similarity=0.197 Sum_probs=55.9
Q ss_pred HhhchHHHHHHHHHhhCh-------hhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCc
Q 036188 20 ATGVVLPMAIQAVYELGI-------FEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGA 92 (210)
Q Consensus 20 ~~~~~~~~al~~a~~lgl-------fd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~ 92 (210)
.++.|...|+.+|.+.++ .-++...+ .|.++.||+..++.. |-..+..-||-|...|+++... + +.
T Consensus 64 Af~rW~vrCmAaag~~~ls~~e~l~lH~irhrd--R~K~laDic~~ln~e---Dth~itYslrKL~k~gLit~t~-~-gk 136 (199)
T COG5631 64 AFGRWQVRCMAAAGEFSLSGPENLLLHIIRHRD--RPKSLADICQMLNRE---DTHNITYSLRKLLKGGLITRTG-S-GK 136 (199)
T ss_pred HHHHHHHHHHHHhcCCCCcchHHHHHHHHhhcC--chhhHHHHHHHhccc---cchhHHHHHHHHHhccceecCC-C-Cc
Confidence 456778888888887664 23333333 799999999999993 6668888999999999999762 1 12
Q ss_pred ccceecccccc
Q 036188 93 RRLYSLNSVSK 103 (210)
Q Consensus 93 ~~~y~~t~~s~ 103 (210)
+-.|..|+.+.
T Consensus 137 evTy~vTa~G~ 147 (199)
T COG5631 137 EVTYEVTALGH 147 (199)
T ss_pred eEEEEEecchH
Confidence 23477777654
No 157
>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=87.84 E-value=0.44 Score=28.31 Aligned_cols=30 Identities=27% Similarity=0.298 Sum_probs=20.8
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
+..++.+ +.|+.+||+.+|+ ...-+.|+++
T Consensus 14 i~~l~~~-----G~si~~IA~~~gv----sr~TvyR~l~ 43 (45)
T PF02796_consen 14 IKELYAE-----GMSIAEIAKQFGV----SRSTVYRYLN 43 (45)
T ss_dssp HHHHHHT-----T--HHHHHHHTTS-----HHHHHHHHC
T ss_pred HHHHHHC-----CCCHHHHHHHHCc----CHHHHHHHHh
Confidence 3444554 5999999999999 8888888764
No 158
>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=87.75 E-value=0.68 Score=39.14 Aligned_cols=20 Identities=15% Similarity=0.174 Sum_probs=16.8
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
...+|||+|||+|.....|+
T Consensus 63 ~~~~iLELGcGtG~~t~~Ll 82 (301)
T TIGR03438 63 AGCELVELGSGSSRKTRLLL 82 (301)
T ss_pred CCCeEEecCCCcchhHHHHH
Confidence 34689999999999887765
No 159
>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=87.71 E-value=0.85 Score=37.13 Aligned_cols=30 Identities=27% Similarity=0.335 Sum_probs=22.7
Q ss_pred HHHHHhCCCC-CCCCeEEEecCCccHHHHhhh
Q 036188 179 SNILESYKGF-DNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 179 ~~~l~~~~~~-~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+++.++ . -...+++|||||+|.++..++
T Consensus 64 ~~~l~~~~-~~~~~~~vlDiG~gtG~~t~~l~ 94 (228)
T TIGR00478 64 KEALEEFN-IDVKNKIVLDVGSSTGGFTDCAL 94 (228)
T ss_pred HHHHHhcC-CCCCCCEEEEcccCCCHHHHHHH
Confidence 45566665 3 356799999999999988775
No 160
>PRK04266 fibrillarin; Provisional
Probab=87.62 E-value=0.67 Score=37.61 Aligned_cols=25 Identities=12% Similarity=0.380 Sum_probs=20.7
Q ss_pred hCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 184 SYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 184 ~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.++ .....+|+|+|||+|.++..++
T Consensus 67 ~l~-i~~g~~VlD~G~G~G~~~~~la 91 (226)
T PRK04266 67 NFP-IKKGSKVLYLGAASGTTVSHVS 91 (226)
T ss_pred hCC-CCCCCEEEEEccCCCHHHHHHH
Confidence 355 6777899999999999988765
No 161
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=87.59 E-value=0.55 Score=37.02 Aligned_cols=27 Identities=15% Similarity=0.299 Sum_probs=21.1
Q ss_pred HHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 182 LESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 182 l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
+...+ .....+|+|+|+|+|.++..++
T Consensus 33 l~~l~-~~~~~~vlDlG~GtG~~s~~~a 59 (198)
T PRK00377 33 LSKLR-LRKGDMILDIGCGTGSVTVEAS 59 (198)
T ss_pred HHHcC-CCCcCEEEEeCCcCCHHHHHHH
Confidence 34445 6677899999999999988754
No 162
>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=87.58 E-value=0.64 Score=37.63 Aligned_cols=20 Identities=20% Similarity=0.338 Sum_probs=17.2
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
+..+|+|+|||+|.++..++
T Consensus 87 ~~~~ilDig~G~G~~~~~l~ 106 (251)
T TIGR03534 87 GPLRVLDLGTGSGAIALALA 106 (251)
T ss_pred CCCeEEEEeCcHhHHHHHHH
Confidence 45689999999999988775
No 163
>PRK00517 prmA ribosomal protein L11 methyltransferase; Reviewed
Probab=87.37 E-value=0.39 Score=39.43 Aligned_cols=21 Identities=29% Similarity=0.254 Sum_probs=17.6
Q ss_pred CCCCeEEEecCCccHHHHhhh
Q 036188 189 DNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l~ 209 (210)
....+|+|||||+|.+++.+.
T Consensus 118 ~~~~~VLDiGcGsG~l~i~~~ 138 (250)
T PRK00517 118 LPGKTVLDVGCGSGILAIAAA 138 (250)
T ss_pred CCCCEEEEeCCcHHHHHHHHH
Confidence 456899999999999887654
No 164
>COG2226 UbiE Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]
Probab=87.36 E-value=0.63 Score=38.15 Aligned_cols=21 Identities=14% Similarity=0.137 Sum_probs=18.6
Q ss_pred CCCeEEEecCCccHHHHhhhC
Q 036188 190 NIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~~ 210 (210)
...+|||||||+|.++..+.+
T Consensus 51 ~g~~vLDva~GTGd~a~~~~k 71 (238)
T COG2226 51 PGDKVLDVACGTGDMALLLAK 71 (238)
T ss_pred CCCEEEEecCCccHHHHHHHH
Confidence 578999999999999998763
No 165
>PRK05134 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional
Probab=87.01 E-value=0.94 Score=36.40 Aligned_cols=20 Identities=25% Similarity=0.361 Sum_probs=16.9
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
...+|||||||.|.++..++
T Consensus 48 ~~~~vLdiG~G~G~~~~~l~ 67 (233)
T PRK05134 48 FGKRVLDVGCGGGILSESMA 67 (233)
T ss_pred CCCeEEEeCCCCCHHHHHHH
Confidence 56789999999999887664
No 166
>PRK00312 pcm protein-L-isoaspartate O-methyltransferase; Reviewed
Probab=86.96 E-value=0.84 Score=36.25 Aligned_cols=28 Identities=11% Similarity=0.281 Sum_probs=21.1
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l 208 (210)
.++..+. .....+|+|||||+|..+..+
T Consensus 69 ~l~~~l~-~~~~~~VLeiG~GsG~~t~~l 96 (212)
T PRK00312 69 RMTELLE-LKPGDRVLEIGTGSGYQAAVL 96 (212)
T ss_pred HHHHhcC-CCCCCEEEEECCCccHHHHHH
Confidence 4445555 667789999999999987644
No 167
>PLN02396 hexaprenyldihydroxybenzoate methyltransferase
Probab=86.94 E-value=0.43 Score=40.87 Aligned_cols=20 Identities=15% Similarity=0.330 Sum_probs=16.9
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
...+|||||||.|.++..++
T Consensus 131 ~g~~ILDIGCG~G~~s~~La 150 (322)
T PLN02396 131 EGLKFIDIGCGGGLLSEPLA 150 (322)
T ss_pred CCCEEEEeeCCCCHHHHHHH
Confidence 44689999999999988764
No 168
>PRK14121 tRNA (guanine-N(7)-)-methyltransferase; Provisional
Probab=86.86 E-value=0.72 Score=40.57 Aligned_cols=29 Identities=24% Similarity=0.256 Sum_probs=21.5
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.+++.+. -.....+||||||.|.++..++
T Consensus 113 ~~~~~~~-~~~~p~vLEIGcGsG~~ll~lA 141 (390)
T PRK14121 113 NFLDFIS-KNQEKILIEIGFGSGRHLLYQA 141 (390)
T ss_pred HHHHHhc-CCCCCeEEEEcCcccHHHHHHH
Confidence 3444443 3456799999999999998876
No 169
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=86.86 E-value=1.2 Score=36.43 Aligned_cols=46 Identities=22% Similarity=0.232 Sum_probs=40.6
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+..|.+.|.+. +..+++|||+.+++ +++-++|-|..|...|++.+.
T Consensus 6 ~~~Il~~l~~~---~~~~~~eLa~~l~V----S~~TiRRdL~~L~~~~~l~r~ 51 (240)
T PRK10411 6 QQAIVDLLLNH---TSLTTEALAEQLNV----SKETIRRDLNELQTQGKILRN 51 (240)
T ss_pred HHHHHHHHHHc---CCCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence 34577888775 59999999999999 999999999999999999876
No 170
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=86.81 E-value=0.63 Score=27.91 Aligned_cols=40 Identities=18% Similarity=0.194 Sum_probs=23.5
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSV 82 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl 82 (210)
+..+...+.+ +.|..+||+.+|+ ++.-+.++++--...|+
T Consensus 7 R~~ii~l~~~-----G~s~~~ia~~lgv----s~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 7 RAQIIRLLRE-----GWSIREIAKRLGV----SRSTVYRWIKRYREEGL 46 (50)
T ss_dssp ---HHHHHHH-----T--HHHHHHHHTS-----HHHHHHHHT-------
T ss_pred HHHHHHHHHC-----CCCHHHHHHHHCc----CHHHHHHHHHHcccccc
Confidence 3455555655 7899999999999 99999999988776664
No 171
>PRK09328 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=86.81 E-value=0.74 Score=37.92 Aligned_cols=22 Identities=18% Similarity=0.353 Sum_probs=18.4
Q ss_pred CCCCCeEEEecCCccHHHHhhh
Q 036188 188 FDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+..+|+|+|||+|.++..++
T Consensus 106 ~~~~~~vLDiG~GsG~~~~~la 127 (275)
T PRK09328 106 LKEPLRVLDLGTGSGAIALALA 127 (275)
T ss_pred ccCCCEEEEEcCcHHHHHHHHH
Confidence 4456799999999999988775
No 172
>PRK00215 LexA repressor; Validated
Probab=86.32 E-value=1.4 Score=34.93 Aligned_cols=36 Identities=19% Similarity=0.212 Sum_probs=32.9
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.+.|..|||+++|++ +...+.|+|+.|...|++++.
T Consensus 22 ~~~s~~ela~~~~~~---~~~tv~~~l~~L~~~g~i~~~ 57 (205)
T PRK00215 22 YPPSRREIADALGLR---SPSAVHEHLKALERKGFIRRD 57 (205)
T ss_pred CCCCHHHHHHHhCCC---ChHHHHHHHHHHHHCCCEEeC
Confidence 588999999999984 678999999999999999886
No 173
>PLN02585 magnesium protoporphyrin IX methyltransferase
Probab=86.15 E-value=0.52 Score=40.26 Aligned_cols=20 Identities=15% Similarity=0.147 Sum_probs=17.3
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
...+|||||||+|.+++.++
T Consensus 144 ~~~~VLDlGcGtG~~a~~la 163 (315)
T PLN02585 144 AGVTVCDAGCGTGSLAIPLA 163 (315)
T ss_pred CCCEEEEecCCCCHHHHHHH
Confidence 35799999999999988775
No 174
>COG2890 HemK Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]
Probab=86.07 E-value=0.78 Score=38.50 Aligned_cols=18 Identities=22% Similarity=0.470 Sum_probs=16.5
Q ss_pred eEEEecCCccHHHHhhhC
Q 036188 193 QLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 193 ~vvDiGGg~G~~~~~l~~ 210 (210)
+|+|||+|+|..++++++
T Consensus 113 ~ilDlGTGSG~iai~la~ 130 (280)
T COG2890 113 RILDLGTGSGAIAIALAK 130 (280)
T ss_pred cEEEecCChHHHHHHHHh
Confidence 899999999999998864
No 175
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=86.06 E-value=1.1 Score=36.96 Aligned_cols=46 Identities=17% Similarity=0.241 Sum_probs=41.3
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+..|.+.|.+. +.+++.|||+.+++ ++.-++|-|..|...|++.+.
T Consensus 7 ~~~Il~~l~~~---~~~~~~ela~~l~v----S~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 7 HDAIIELVKQQ---GYVSTEELVEHFSV----SPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHc---CCEeHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 44577888875 58999999999999 999999999999999999887
No 176
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=85.99 E-value=1.2 Score=37.14 Aligned_cols=47 Identities=13% Similarity=0.149 Sum_probs=42.4
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
....|.+.|.+. +.+++.|||+.+++ +++-++|=|..|...|++.+.
T Consensus 18 R~~~Il~~L~~~---~~vtv~eLa~~l~V----S~~TIRRDL~~Le~~G~l~r~ 64 (269)
T PRK09802 18 RREQIIQRLRQQ---GSVQVNDLSALYGV----STVTIRNDLAFLEKQGIAVRA 64 (269)
T ss_pred HHHHHHHHHHHc---CCEeHHHHHHHHCC----CHHHHHHHHHHHHhCCCeEEE
Confidence 445688889886 48999999999999 999999999999999999987
No 177
>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=85.97 E-value=0.92 Score=37.36 Aligned_cols=20 Identities=20% Similarity=0.170 Sum_probs=16.9
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
+..+++|+|||+|.++..++
T Consensus 86 ~~~~vLDlg~GsG~i~l~la 105 (251)
T TIGR03704 86 GTLVVVDLCCGSGAVGAALA 105 (251)
T ss_pred CCCEEEEecCchHHHHHHHH
Confidence 34589999999999998765
No 178
>COG4123 Predicted O-methyltransferase [General function prediction only]
Probab=85.92 E-value=0.82 Score=37.67 Aligned_cols=30 Identities=13% Similarity=0.298 Sum_probs=22.4
Q ss_pred HHHhCCCCCCCCeEEEecCCccHHHHhhhC
Q 036188 181 ILESYKGFDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 181 ~l~~~~~~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
++..+.......+|+|+|+|.|.++..+++
T Consensus 35 LL~~~~~~~~~~~IlDlGaG~G~l~L~la~ 64 (248)
T COG4123 35 LLAAFAPVPKKGRILDLGAGNGALGLLLAQ 64 (248)
T ss_pred HHHhhcccccCCeEEEecCCcCHHHHHHhc
Confidence 344443244589999999999999988764
No 179
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=85.85 E-value=1.5 Score=37.35 Aligned_cols=57 Identities=14% Similarity=0.181 Sum_probs=43.3
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccc
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVS 102 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s 102 (210)
..|.+.|.+. .+.+.++||+++++ +...+.+.++.|...|++.... ....|.+.+..
T Consensus 7 ~~il~~L~~~---~~~s~~~LA~~lgv----sr~tV~~~l~~L~~~G~~i~~~----~~~Gy~L~~~~ 63 (319)
T PRK11886 7 LQLLSLLADG---DFHSGEQLGEELGI----SRAAIWKHIQTLEEWGLDIFSV----KGKGYRLAEPL 63 (319)
T ss_pred HHHHHHHHcC---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCceEEe----cCCeEEecCcc
Confidence 4566777663 58999999999999 9999999999999999944331 22357765443
No 180
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=85.69 E-value=1.1 Score=37.05 Aligned_cols=46 Identities=24% Similarity=0.245 Sum_probs=41.8
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+..|.+.|.+. +.+++.|||+.+++ ++.-++|=|+.|...|++.+.
T Consensus 7 ~~~Il~~L~~~---~~v~v~eLa~~l~V----S~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 7 QAAILEYLQKQ---GKTSVEELAQYFDT----TGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHHc---CCEEHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEE
Confidence 45578889886 58999999999999 999999999999999999887
No 181
>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=85.67 E-value=0.89 Score=30.44 Aligned_cols=35 Identities=20% Similarity=0.276 Sum_probs=24.8
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHh
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLA 78 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~ 78 (210)
|+..|+. | +|.|+++||+++|+ +.+.++..|..+-
T Consensus 29 LLr~LA~-G--~PVt~~~LA~a~g~----~~e~v~~~L~~~p 63 (77)
T PF12324_consen 29 LLRLLAK-G--QPVTVEQLAAALGW----PVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHTT-T--S-B-HHHHHHHHT------HHHHHHHHHH-T
T ss_pred HHHHHHc-C--CCcCHHHHHHHHCC----CHHHHHHHHHhCC
Confidence 6778887 3 79999999999999 8888777777664
No 182
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=85.66 E-value=2.1 Score=28.28 Aligned_cols=42 Identities=21% Similarity=0.169 Sum_probs=37.4
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|...|+. +..|.+||-+.||+ +...+-..|.-|...|++.+.
T Consensus 10 IL~~ls~----~c~TLeeL~ekTgi----~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 10 ILIILSK----RCCTLEELEEKTGI----SKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHh----ccCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeee
Confidence 4556666 59999999999999 999999999999999999875
No 183
>PRK10870 transcriptional repressor MprA; Provisional
Probab=85.59 E-value=1.1 Score=34.77 Aligned_cols=55 Identities=13% Similarity=0.106 Sum_probs=41.7
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCC-Ccccceeccccccccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDAS-GARRLYSLNSVSKYYV 106 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~-~~~~~y~~t~~s~~l~ 106 (210)
+++|..|||+.+++ ++..+.+++.-|...|++++..... ...-...+|+.++.+.
T Consensus 70 ~~it~~eLa~~l~l----~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~ 125 (176)
T PRK10870 70 HSIQPSELSCALGS----SRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFL 125 (176)
T ss_pred CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence 57999999999999 9999999999999999999763110 0112366666666444
No 184
>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=85.42 E-value=0.7 Score=37.69 Aligned_cols=22 Identities=14% Similarity=0.228 Sum_probs=15.3
Q ss_pred CCCCCeEEEecCCccHHHHhhh
Q 036188 188 FDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.....+|+|||||+|.++..++
T Consensus 45 ~~~g~~vLDv~~GtG~~~~~l~ 66 (233)
T PF01209_consen 45 LRPGDRVLDVACGTGDVTRELA 66 (233)
T ss_dssp --S--EEEEET-TTSHHHHHHG
T ss_pred CCCCCEEEEeCCChHHHHHHHH
Confidence 4556799999999999998775
No 185
>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=85.38 E-value=1.2 Score=28.53 Aligned_cols=43 Identities=19% Similarity=0.238 Sum_probs=35.1
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|++.|-.. |+.|+.+|.+.+++ +++.++.-|-.|.-.|++...
T Consensus 18 V~~~Ll~~---G~ltl~~i~~~t~l----~~~~Vk~~L~~LiQh~~v~y~ 60 (62)
T PF08221_consen 18 VGEVLLSR---GRLTLREIVRRTGL----SPKQVKKALVVLIQHNLVQYF 60 (62)
T ss_dssp HHHHHHHC----SEEHHHHHHHHT------HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHc---CCcCHHHHHHHhCC----CHHHHHHHHHHHHHcCCeeee
Confidence 56667665 59999999999999 999999999999999998754
No 186
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=85.14 E-value=1.5 Score=30.93 Aligned_cols=68 Identities=18% Similarity=0.218 Sum_probs=47.7
Q ss_pred HHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCC-Ccccceeccccccccc
Q 036188 32 VYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDAS-GARRLYSLNSVSKYYV 106 (210)
Q Consensus 32 a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~-~~~~~y~~t~~s~~l~ 106 (210)
..+..+...|...+ +.+..+||+++++ ++..+.++++-|...|++.+..+.. ...-.+.+|+.++-+.
T Consensus 22 ~~q~~~L~~l~~~~---~~~~~~la~~l~i----~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~ 90 (126)
T COG1846 22 PPQYQVLLALYEAG---GITVKELAERLGL----DRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELL 90 (126)
T ss_pred HHHHHHHHHHHHhC---CCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHH
Confidence 34555666677653 4444999999999 9999999999999999998764211 0122467777666443
No 187
>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=85.09 E-value=0.38 Score=31.67 Aligned_cols=37 Identities=24% Similarity=0.327 Sum_probs=32.0
Q ss_pred CCCCHHHHHHHh---cCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQL---LTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~---~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+.+++.++|+++ +.+ ...|++.-++..|.++|++++.
T Consensus 23 ~~i~l~~ia~~l~~~~~k--~~~RRlYDI~NVLealgli~K~ 62 (71)
T PF02319_consen 23 KSISLNEIADKLISENVK--TQRRRLYDIINVLEALGLIEKQ 62 (71)
T ss_dssp TEEEHHHHHHHCHHHCCH--HHCHHHHHHHHHHHHCTSEEEE
T ss_pred CcccHHHHHHHHcccccc--cccchhhHHHHHHHHhCceeec
Confidence 689999999999 551 0678999999999999999986
No 188
>PRK00811 spermidine synthase; Provisional
Probab=85.03 E-value=0.7 Score=38.75 Aligned_cols=22 Identities=32% Similarity=0.469 Sum_probs=19.1
Q ss_pred CCCCeEEEecCCccHHHHhhhC
Q 036188 189 DNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
++.++|+|||||.|..+.++++
T Consensus 75 ~~p~~VL~iG~G~G~~~~~~l~ 96 (283)
T PRK00811 75 PNPKRVLIIGGGDGGTLREVLK 96 (283)
T ss_pred CCCCEEEEEecCchHHHHHHHc
Confidence 4678999999999999988764
No 189
>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=84.81 E-value=1.2 Score=32.12 Aligned_cols=66 Identities=23% Similarity=0.274 Sum_probs=47.0
Q ss_pred HHhhChhhHHhhcCCCCCCCHHHHHHHhcCC-CCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 32 VYELGIFEILDKAGPGTKLSASDIAAQLLTK-NKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 32 a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~-~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
.-+.-|++.|.+.+ ++.|++||-+.+.-+ +.++..-+.|-|+.|...|++.+.... .+...|..+.
T Consensus 8 ~~R~~Il~~l~~~~--~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~-~~~~~Y~~~~ 74 (120)
T PF01475_consen 8 PQRLAILELLKESP--EHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG-DGESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHHHS--SSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET-TSEEEEEESS
T ss_pred HHHHHHHHHHHcCC--CCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC-CCcceEeecC
Confidence 34566888998876 699999999999641 122556799999999999999987422 1234566654
No 190
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=84.58 E-value=1.5 Score=35.00 Aligned_cols=45 Identities=18% Similarity=0.267 Sum_probs=38.0
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.|.+.+++.. .+.|.+|||+++++ .++-+++.+.+|+.+|++...
T Consensus 166 ~Vl~~~~~g~--~g~s~~eIa~~l~i----S~~Tv~~~~~~~~~~~~~~~~ 210 (225)
T PRK10046 166 AVRKLFKEPG--VQHTAETVAQALTI----SRTTARRYLEYCASRHLIIAE 210 (225)
T ss_pred HHHHHHHcCC--CCcCHHHHHHHhCc----cHHHHHHHHHHHHhCCeEEEE
Confidence 4566676521 26899999999999 999999999999999999876
No 191
>PLN02366 spermidine synthase
Probab=84.54 E-value=0.73 Score=39.24 Aligned_cols=23 Identities=35% Similarity=0.481 Sum_probs=19.7
Q ss_pred CCCCCeEEEecCCccHHHHhhhC
Q 036188 188 FDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
.++.++||+||||.|..+.++++
T Consensus 89 ~~~pkrVLiIGgG~G~~~rellk 111 (308)
T PLN02366 89 IPNPKKVLVVGGGDGGVLREIAR 111 (308)
T ss_pred CCCCCeEEEEcCCccHHHHHHHh
Confidence 35688999999999999988864
No 192
>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=84.51 E-value=1.2 Score=35.79 Aligned_cols=30 Identities=13% Similarity=0.354 Sum_probs=21.7
Q ss_pred HHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 179 SNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 179 ~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+++.++ .+...+|+|||+|+|..+.-++
T Consensus 62 a~~l~~L~-l~pg~~VLeIGtGsGY~aAlla 91 (209)
T PF01135_consen 62 ARMLEALD-LKPGDRVLEIGTGSGYQAALLA 91 (209)
T ss_dssp HHHHHHTT-C-TT-EEEEES-TTSHHHHHHH
T ss_pred HHHHHHHh-cCCCCEEEEecCCCcHHHHHHH
Confidence 35567776 8888999999999999987664
No 193
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=84.32 E-value=1.1 Score=40.55 Aligned_cols=69 Identities=13% Similarity=0.107 Sum_probs=55.0
Q ss_pred HHhhChhhHHhhcCCCCC-CCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccc-cccCC
Q 036188 32 VYELGIFEILDKAGPGTK-LSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKY-YVPNK 109 (210)
Q Consensus 32 a~~lglfd~L~~~g~~~~-~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~-l~~~~ 109 (210)
+.+..|...|... ++ .+..+||+.+|+ ++..+.+.+..|.+.|+++-.. .....|.+|+.++. +..+.
T Consensus 3 ~~e~~iL~~l~~~---~~~~~~~~la~~~g~----~~~~v~~~~~~L~~kg~v~~~~---~~~~~~~LT~eG~~~l~~G~ 72 (492)
T PLN02853 3 MAEEALLGALSNN---EEISDSGQFAASHGL----DHNEVVGVIKSLHGFRYVDAQD---IKRETWVLTEEGKKYAAEGS 72 (492)
T ss_pred hHHHHHHHHHHhc---CCCCCHHHHHHHcCC----CHHHHHHHHHHHHhCCCEEEEE---EEEEEEEECHHHHHHHHcCC
Confidence 4567778888774 34 899999999999 9999999999999999987432 13678999999984 55555
Q ss_pred C
Q 036188 110 D 110 (210)
Q Consensus 110 ~ 110 (210)
|
T Consensus 73 P 73 (492)
T PLN02853 73 P 73 (492)
T ss_pred H
Confidence 4
No 194
>PRK13943 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=83.97 E-value=1.2 Score=38.11 Aligned_cols=29 Identities=17% Similarity=0.374 Sum_probs=22.1
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.+++..+ .+...+|+|||||+|.++..++
T Consensus 71 ~ll~~L~-i~~g~~VLDIG~GtG~~a~~LA 99 (322)
T PRK13943 71 LFMEWVG-LDKGMRVLEIGGGTGYNAAVMS 99 (322)
T ss_pred HHHHhcC-CCCCCEEEEEeCCccHHHHHHH
Confidence 3445554 6667899999999999987765
No 195
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=83.93 E-value=1.8 Score=33.93 Aligned_cols=48 Identities=29% Similarity=0.344 Sum_probs=41.8
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.+..|.|+|...| .+.|+-+||+++|+ +..-+.|-|--|...|.|...
T Consensus 5 ~~~~i~~~l~~~~--~~~~a~~i~k~l~i----~k~~vNr~LY~L~~~~~v~~~ 52 (183)
T PHA02701 5 CASLILTLLSSSG--DKLPAKRIAKELGI----SKHEANRCLYRLLESDAVSCE 52 (183)
T ss_pred HHHHHHHHHHhcC--CCCcHHHHHHHhCc----cHHHHHHHHHHHhhcCcEecC
Confidence 5677999999875 36999999999999 999999999999999988654
No 196
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=83.91 E-value=1.6 Score=35.98 Aligned_cols=45 Identities=22% Similarity=0.261 Sum_probs=41.6
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
-.|.++|.+. |.++++|||+.+++ .+.-++|=|+.|...|++.+.
T Consensus 8 ~~Il~~l~~~---g~v~v~eLa~~~~V----S~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 8 QKILELLKEK---GKVSVEELAELFGV----SEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHHc---CcEEHHHHHHHhCC----CHHHHHHhHHHHHHCCcEEEE
Confidence 4578889886 59999999999999 999999999999999999997
No 197
>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=83.83 E-value=1.8 Score=38.79 Aligned_cols=52 Identities=15% Similarity=0.188 Sum_probs=32.2
Q ss_pred CchhHhhccCchHHHHHHHHHhhhhhhhHHHHHHhCCCC---CCCCeEEEecCCccHHHHhh
Q 036188 150 VHIFEYAGLNPRFNKHFNAAMYNYTSLVMSNILESYKGF---DNIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 150 ~~~fe~l~~~p~~~~~f~~~M~~~~~~~~~~~l~~~~~~---~~~~~vvDiGGg~G~~~~~l 208 (210)
..-||.+++||..=+.|.+++.. .+.+....- .+...|+|||+|+|-++...
T Consensus 150 s~tYe~fE~D~vKY~~Ye~AI~~-------al~D~~~~~~~~~~~~vVldVGAGrGpL~~~a 204 (448)
T PF05185_consen 150 SQTYEVFEKDPVKYDQYERAIEE-------ALKDRVRKNSYSSKDKVVLDVGAGRGPLSMFA 204 (448)
T ss_dssp HHHHHHHCC-HHHHHHHHHHHHH-------HHHHHHTTS-SEETT-EEEEES-TTSHHHHHH
T ss_pred cccHhhHhcCHHHHHHHHHHHHH-------HHHhhhhhccccccceEEEEeCCCccHHHHHH
Confidence 35688899999887778877642 222222101 14678999999999997543
No 198
>PF13518 HTH_28: Helix-turn-helix domain
Probab=83.67 E-value=1.8 Score=25.92 Aligned_cols=29 Identities=14% Similarity=0.106 Sum_probs=26.8
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHHHHhcccc
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILRLLASYSV 82 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl 82 (210)
.|+.++|+++|+ ++..+.+|++.....|+
T Consensus 13 ~s~~~~a~~~gi----s~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 13 ESVREIAREFGI----SRSTVYRWIKRYREGGI 41 (52)
T ss_pred CCHHHHHHHHCC----CHhHHHHHHHHHHhcCH
Confidence 499999999999 99999999999988875
No 199
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=83.58 E-value=0.7 Score=41.27 Aligned_cols=29 Identities=17% Similarity=0.098 Sum_probs=21.7
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.+++.++ .....+|+|+|||+|.+++.++
T Consensus 288 ~vl~~l~-~~~~~~VLDlgcGtG~~sl~la 316 (443)
T PRK13168 288 RALEWLD-PQPGDRVLDLFCGLGNFTLPLA 316 (443)
T ss_pred HHHHHhc-CCCCCEEEEEeccCCHHHHHHH
Confidence 4444444 4456799999999999998875
No 200
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=83.48 E-value=2.2 Score=34.09 Aligned_cols=37 Identities=22% Similarity=0.185 Sum_probs=34.1
Q ss_pred CCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 46 PGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 46 ~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
||..++..+||+++|+ +...++.-|+.|...|+++..
T Consensus 27 pG~~L~e~eLae~lgV----SRtpVREAL~~L~~eGlv~~~ 63 (224)
T PRK11534 27 PDEKLRMSLLTSRYAL----GVGPLREALSQLVAERLVTVV 63 (224)
T ss_pred CCCcCCHHHHHHHHCC----ChHHHHHHHHHHHHCCCEEEe
Confidence 3468899999999999 999999999999999999876
No 201
>KOG1270 consensus Methyltransferases [Coenzyme transport and metabolism]
Probab=83.44 E-value=0.56 Score=38.94 Aligned_cols=18 Identities=22% Similarity=0.442 Sum_probs=15.9
Q ss_pred CeEEEecCCccHHHHhhh
Q 036188 192 KQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 192 ~~vvDiGGg~G~~~~~l~ 209 (210)
.+|||||||.|.+++-|+
T Consensus 91 ~~ilDvGCGgGLLSepLA 108 (282)
T KOG1270|consen 91 MKILDVGCGGGLLSEPLA 108 (282)
T ss_pred ceEEEeccCccccchhhH
Confidence 679999999999988765
No 202
>COG2263 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=83.22 E-value=0.94 Score=35.82 Aligned_cols=20 Identities=20% Similarity=0.360 Sum_probs=17.1
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
+.++|+|+|||+|.++++.+
T Consensus 45 ~g~~V~DlG~GTG~La~ga~ 64 (198)
T COG2263 45 EGKTVLDLGAGTGILAIGAA 64 (198)
T ss_pred CCCEEEEcCCCcCHHHHHHH
Confidence 56789999999999998753
No 203
>KOG3115 consensus Methyltransferase-like protein [General function prediction only]
Probab=82.91 E-value=0.72 Score=36.98 Aligned_cols=20 Identities=20% Similarity=0.361 Sum_probs=16.7
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
.-..++|||||-|-+++.|.
T Consensus 60 ~kvefaDIGCGyGGLlv~Ls 79 (249)
T KOG3115|consen 60 KKVEFADIGCGYGGLLMKLA 79 (249)
T ss_pred ccceEEeeccCccchhhhcc
Confidence 34789999999999988764
No 204
>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=82.80 E-value=0.8 Score=38.44 Aligned_cols=20 Identities=20% Similarity=0.302 Sum_probs=17.3
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
+..+|+|+|||+|.+++.++
T Consensus 121 ~~~~vLDlG~GsG~i~~~la 140 (284)
T TIGR03533 121 PVKRILDLCTGSGCIAIACA 140 (284)
T ss_pred CCCEEEEEeCchhHHHHHHH
Confidence 45689999999999998875
No 205
>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=82.72 E-value=2.4 Score=34.78 Aligned_cols=45 Identities=36% Similarity=0.347 Sum_probs=39.4
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.|++.|.... +-++..+||+++|+ .+..+++=+|.|...|+++..
T Consensus 187 ~IL~~L~~~e--grlse~eLAerlGV----SRs~ireAlrkLE~aGvIe~r 231 (251)
T TIGR02787 187 HIFEELDGNE--GLLVASKIADRVGI----TRSVIVNALRKLESAGVIESR 231 (251)
T ss_pred HHHHHhcccc--ccccHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec
Confidence 3677776632 68999999999999 999999999999999999876
No 206
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=82.71 E-value=1.7 Score=34.82 Aligned_cols=45 Identities=22% Similarity=0.290 Sum_probs=35.7
Q ss_pred chHHHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHH
Q 036188 23 VVLPMAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLL 77 (210)
Q Consensus 23 ~~~~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L 77 (210)
..+-.+|+.|.++|-||.= ...+..|||+.+|+ .+..+...||-.
T Consensus 158 drQ~~vL~~A~~~GYFd~P------R~~~l~dLA~~lGI----Skst~~ehLRrA 202 (215)
T COG3413 158 DRQLEVLRLAYKMGYFDYP------RRVSLKDLAKELGI----SKSTLSEHLRRA 202 (215)
T ss_pred HHHHHHHHHHHHcCCCCCC------ccCCHHHHHHHhCC----CHHHHHHHHHHH
Confidence 3466799999999999752 47899999999999 777666666543
No 207
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=82.57 E-value=2.8 Score=33.74 Aligned_cols=37 Identities=30% Similarity=0.433 Sum_probs=34.8
Q ss_pred CCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 46 PGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 46 ~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
||.+++-.+||+++|+ +...++.-|.-|...|+++..
T Consensus 36 pG~~l~e~~La~~~gv----SrtPVReAL~rL~~eGlv~~~ 72 (230)
T COG1802 36 PGERLSEEELAEELGV----SRTPVREALRRLEAEGLVEIE 72 (230)
T ss_pred CCCCccHHHHHHHhCC----CCccHHHHHHHHHHCCCeEec
Confidence 4579999999999999 999999999999999999976
No 208
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=82.46 E-value=1.6 Score=32.87 Aligned_cols=41 Identities=22% Similarity=0.254 Sum_probs=35.1
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccce
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVV 83 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~ 83 (210)
-|+|.|-.. +.+|-+|||+.+|+ +...++++|..|..-+++
T Consensus 5 ~v~d~L~~~---~~~~dedLa~~l~i----~~n~vRkiL~~L~ed~~~ 45 (147)
T smart00531 5 LVLDALMRN---GCVTEEDLAELLGI----KQKQLRKILYLLYDEKLI 45 (147)
T ss_pred eehHHHHhc---CCcCHHHHHHHhCC----CHHHHHHHHHHHHhhhcc
Confidence 467777765 58999999999999 999999999999994443
No 209
>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=82.45 E-value=0.99 Score=40.74 Aligned_cols=22 Identities=18% Similarity=0.223 Sum_probs=19.2
Q ss_pred CCCCeEEEecCCccHHHHhhhC
Q 036188 189 DNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
...++++|||||.|.++..+++
T Consensus 116 g~iR~~LDvGcG~aSF~a~l~~ 137 (506)
T PF03141_consen 116 GGIRTALDVGCGVASFGAYLLE 137 (506)
T ss_pred CceEEEEeccceeehhHHHHhh
Confidence 4679999999999999998764
No 210
>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=82.35 E-value=1.4 Score=36.90 Aligned_cols=18 Identities=22% Similarity=0.427 Sum_probs=16.3
Q ss_pred CeEEEecCCccHHHHhhh
Q 036188 192 KQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 192 ~~vvDiGGg~G~~~~~l~ 209 (210)
.+|+|+|||+|.++..++
T Consensus 116 ~~vLDlG~GsG~i~l~la 133 (284)
T TIGR00536 116 LHILDLGTGSGCIALALA 133 (284)
T ss_pred CEEEEEeccHhHHHHHHH
Confidence 689999999999988875
No 211
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=82.12 E-value=2.5 Score=33.23 Aligned_cols=63 Identities=14% Similarity=0.004 Sum_probs=44.7
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCC-Ccccceeccccccccc
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDAS-GARRLYSLNSVSKYYV 106 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~-~~~~~y~~t~~s~~l~ 106 (210)
|.-.|... +++|..+||+.+++ ++..+.+++.-|...|++.+..... ...-...+|+.++.+.
T Consensus 50 iL~~L~~~---~~itq~eLa~~l~l----~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~ 113 (185)
T PRK13777 50 ILWIAYHL---KGASISEIAKFGVM----HVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELL 113 (185)
T ss_pred HHHHHHhC---CCcCHHHHHHHHCC----CHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence 45556554 58999999999999 9999999999999999999752110 0112255666655443
No 212
>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=82.05 E-value=2.3 Score=34.00 Aligned_cols=28 Identities=18% Similarity=0.335 Sum_probs=19.1
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l 208 (210)
.+++.+. ......++|||+|.|....+.
T Consensus 33 ~il~~~~-l~~~dvF~DlGSG~G~~v~~a 60 (205)
T PF08123_consen 33 KILDELN-LTPDDVFYDLGSGVGNVVFQA 60 (205)
T ss_dssp HHHHHTT---TT-EEEEES-TTSHHHHHH
T ss_pred HHHHHhC-CCCCCEEEECCCCCCHHHHHH
Confidence 5566666 777889999999999987654
No 213
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=81.84 E-value=2.4 Score=37.99 Aligned_cols=40 Identities=30% Similarity=0.281 Sum_probs=34.2
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|-..|.+ +|.|+.||++.+++ +...+.|.|+.| .|+|...
T Consensus 5 ~~~~L~~----g~~~~~eL~~~l~~----sq~~~s~~L~~L--~~~V~~~ 44 (442)
T PRK09775 5 LTTLLLQ----GPLSAAELAARLGV----SQATLSRLLAAL--GDQVVRF 44 (442)
T ss_pred HHHHHhc----CCCCHHHHHHHhCC----CHHHHHHHHHHh--hcceeEe
Confidence 4456666 79999999999999 999999999999 8887654
No 214
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=81.82 E-value=1.8 Score=39.23 Aligned_cols=70 Identities=13% Similarity=0.160 Sum_probs=54.4
Q ss_pred HHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccc-ccccCCC
Q 036188 32 VYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSK-YYVPNKD 110 (210)
Q Consensus 32 a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~-~l~~~~~ 110 (210)
..+..|...|...+ +..+..+||+.+|+ +...+.+.+.-|.+.|+++-.. .....|.+|+.++ ++..+.|
T Consensus 6 ~~e~~iL~~l~~~~--~~~~~~~la~~~~~----~~~~v~~~~~~L~~kg~v~~~~---~~~~~~~LT~eG~~~~~~G~P 76 (494)
T PTZ00326 6 LEENTILSKLESEN--EIVNSLALAESLNI----DHQKVVGAIKSLESANYITTEM---KKSNTWTLTEEGEDYLKNGSP 76 (494)
T ss_pred HHHHHHHHHHHhcC--CCCCHHHHHHHcCC----CHHHHHHHHHHHHhCCCEEEEE---EEEEEEEECHHHHHHHHcCCH
Confidence 34556777777632 47999999999999 9999999999999999997442 1367899999998 4555554
No 215
>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=81.71 E-value=2.2 Score=29.44 Aligned_cols=59 Identities=7% Similarity=0.103 Sum_probs=35.5
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCC--Ccccceeccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDAS--GARRLYSLNS 100 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~--~~~~~y~~t~ 100 (210)
+|=|.-++.. +..++..|-+.||+ +.+-+...+.+|..+|+..+-.-+| ...|.|+++.
T Consensus 10 rlyla~li~~----~~~nvp~L~~~TGm----PrRT~Qd~i~aL~~~~I~~~Fvq~G~R~~~GyY~i~~ 70 (90)
T PF09904_consen 10 RLYLAYLIDS----GERNVPALMEATGM----PRRTIQDTIKALPELGIECEFVQDGERNNAGYYRISD 70 (90)
T ss_dssp HHHHHHHHHH----S-B-HHHHHHHH-------HHHHHHHHHGGGGGT-EEEEE--TTS-S--EEEEEE
T ss_pred HHHHHHHHhc----CCccHHHHHHHhCC----CHhHHHHHHHHhhcCCeEEEEEecCccCCCCcEEeee
Confidence 3444455666 35599999999999 9999999999999999876521111 1356676653
No 216
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=81.71 E-value=1.4 Score=34.12 Aligned_cols=35 Identities=20% Similarity=0.209 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+|+|++||+++||. +...+..-|+-|...+++.+.
T Consensus 40 ~Pmtl~Ei~E~lg~----Sks~vS~~lkkL~~~~lV~~~ 74 (177)
T COG1510 40 KPLTLDEIAEALGM----SKSNVSMGLKKLQDWNLVKKV 74 (177)
T ss_pred CCccHHHHHHHHCC----CcchHHHHHHHHHhcchHHhh
Confidence 79999999999999 999999999999999999865
No 217
>KOG2904 consensus Predicted methyltransferase [General function prediction only]
Probab=81.58 E-value=1.7 Score=36.48 Aligned_cols=23 Identities=13% Similarity=0.290 Sum_probs=19.3
Q ss_pred CCCCCeEEEecCCccHHHHhhhC
Q 036188 188 FDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
+.+...++|+|||+|.++..+++
T Consensus 146 ~~~~~~ildlgtGSGaIslsll~ 168 (328)
T KOG2904|consen 146 HSKHTHILDLGTGSGAISLSLLH 168 (328)
T ss_pred hcccceEEEecCCccHHHHHHHh
Confidence 45667999999999999988763
No 218
>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=81.39 E-value=2.7 Score=27.22 Aligned_cols=60 Identities=25% Similarity=0.227 Sum_probs=40.4
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
.+-.|.++|...| +.++-.||...|+. .+..-+.+.|.-|...|.+.+.. +.+-.|.+++
T Consensus 5 ~ee~Il~~L~~~g---~~~a~~ia~~~~L~--~~kk~VN~~LY~L~k~g~v~k~~---~~PP~W~l~~ 64 (66)
T PF02295_consen 5 LEEKILDFLKELG---GSTATAIAKALGLS--VPKKEVNRVLYRLEKQGKVCKEG---GTPPKWSLTE 64 (66)
T ss_dssp HHHHHHHHHHHHT---SSEEEHHHHHHHHT--S-HHHHHHHHHHHHHTTSEEEEC---SSSTEEEE-H
T ss_pred HHHHHHHHHHhcC---CccHHHHHHHhCcc--hhHHHHHHHHHHHHHCCCEeeCC---CCCCceEecc
Confidence 4566888998874 55555566655550 05789999999999999998762 1355565543
No 219
>PHA02591 hypothetical protein; Provisional
Probab=81.25 E-value=1.8 Score=28.95 Aligned_cols=31 Identities=19% Similarity=0.216 Sum_probs=26.3
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
+...|.+ .+.|.++||+.+|+ +.+.+++.++
T Consensus 51 vA~eL~e----qGlSqeqIA~~LGV----sqetVrKYL~ 81 (83)
T PHA02591 51 VTHELAR----KGFTVEKIASLLGV----SVRKVRRYLE 81 (83)
T ss_pred HHHHHHH----cCCCHHHHHHHhCC----CHHHHHHHHh
Confidence 4556777 59999999999999 9999988876
No 220
>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=81.23 E-value=2.7 Score=33.22 Aligned_cols=36 Identities=33% Similarity=0.366 Sum_probs=33.6
Q ss_pred CCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 47 GTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 47 ~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|..++-.+||+.+|+ +...++.-|+.|...|+++..
T Consensus 32 G~~L~e~~La~~lgV----SRtpVReAL~~L~~eGlv~~~ 67 (212)
T TIGR03338 32 GAKLNESDIAARLGV----SRGPVREAFRALEEAGLVRNE 67 (212)
T ss_pred CCEecHHHHHHHhCC----ChHHHHHHHHHHHHCCCEEEe
Confidence 468899999999999 999999999999999999876
No 221
>PLN02490 MPBQ/MSBQ methyltransferase
Probab=81.19 E-value=2 Score=37.17 Aligned_cols=28 Identities=36% Similarity=0.493 Sum_probs=20.2
Q ss_pred HHHhCCCCC-CCCeEEEecCCccHHHHhhh
Q 036188 181 ILESYKGFD-NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 181 ~l~~~~~~~-~~~~vvDiGGg~G~~~~~l~ 209 (210)
+++... +. ...+|||||||+|.++..++
T Consensus 104 ~l~~~~-l~~~~~~VLDLGcGtG~~~l~La 132 (340)
T PLN02490 104 ALEPAD-LSDRNLKVVDVGGGTGFTTLGIV 132 (340)
T ss_pred HHhhcc-cCCCCCEEEEEecCCcHHHHHHH
Confidence 344444 43 45799999999999887664
No 222
>COG2518 Pcm Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=80.95 E-value=2 Score=34.49 Aligned_cols=30 Identities=10% Similarity=0.319 Sum_probs=24.2
Q ss_pred HHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 179 SNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 179 ~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+++... .+...+|++||+|+|..+.-++
T Consensus 62 A~m~~~L~-~~~g~~VLEIGtGsGY~aAvla 91 (209)
T COG2518 62 ARMLQLLE-LKPGDRVLEIGTGSGYQAAVLA 91 (209)
T ss_pred HHHHHHhC-CCCCCeEEEECCCchHHHHHHH
Confidence 35566666 7888999999999999887664
No 223
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=80.89 E-value=2.5 Score=33.04 Aligned_cols=45 Identities=18% Similarity=0.180 Sum_probs=38.8
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
..|++.|.+. |-+|-+|||..+|+ ...-++|+|..|...|++...
T Consensus 21 ~~v~~~l~~k---ge~tDeela~~l~i----~~~~vrriL~~L~e~~li~~~ 65 (176)
T COG1675 21 VLVVDALLEK---GELTDEELAELLGI----KKNEVRRILYALYEDGLISYR 65 (176)
T ss_pred hHHHHHHHhc---CCcChHHHHHHhCc----cHHHHHHHHHHHHhCCceEEE
Confidence 3467777774 37999999999999 999999999999999999844
No 224
>PRK12423 LexA repressor; Provisional
Probab=80.88 E-value=3.1 Score=33.04 Aligned_cols=35 Identities=17% Similarity=0.161 Sum_probs=31.0
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+-|..|||+++|++ .+..+++.|+.|...|+++..
T Consensus 25 ~Ps~~eia~~~g~~---s~~~v~~~l~~L~~~G~l~~~ 59 (202)
T PRK12423 25 PPSLAEIAQAFGFA---SRSVARKHVQALAEAGLIEVV 59 (202)
T ss_pred CCCHHHHHHHhCCC---ChHHHHHHHHHHHHCCCEEec
Confidence 56999999999952 677899999999999999976
No 225
>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=80.70 E-value=2.4 Score=29.55 Aligned_cols=40 Identities=20% Similarity=0.107 Sum_probs=33.7
Q ss_pred HHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHh
Q 036188 31 AVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLA 78 (210)
Q Consensus 31 ~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~ 78 (210)
.+.+.+|+..|-+ +++|-.|||+++|+ ....+.|.=+.|.
T Consensus 41 l~~R~~i~~~Ll~----~~~tQrEIa~~lGi----S~atIsR~sn~lk 80 (94)
T TIGR01321 41 LGDRIRIVNELLN----GNMSQREIASKLGV----SIATITRGSNNLK 80 (94)
T ss_pred HHHHHHHHHHHHh----CCCCHHHHHHHhCC----ChhhhhHHHhhcc
Confidence 4567899998877 69999999999999 8888888776665
No 226
>PRK11642 exoribonuclease R; Provisional
Probab=80.37 E-value=2.7 Score=40.59 Aligned_cols=57 Identities=25% Similarity=0.310 Sum_probs=42.3
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
|.++|...+ +|++..+|++++++....+...|.+.|+.|...|.+.+. ..+.|.+..
T Consensus 24 Il~~l~~~~--~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~-----~~~~~~~~~ 80 (813)
T PRK11642 24 ILEHLTKRE--KPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFT-----RRQCYALPE 80 (813)
T ss_pred HHHHHHhcC--CCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEc-----CCceEecCC
Confidence 667776544 799999999999992111234699999999999999876 456665553
No 227
>PRK10909 rsmD 16S rRNA m(2)G966-methyltransferase; Provisional
Probab=80.18 E-value=1.8 Score=34.48 Aligned_cols=19 Identities=11% Similarity=-0.132 Sum_probs=16.2
Q ss_pred CCCeEEEecCCccHHHHhh
Q 036188 190 NIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l 208 (210)
...+++|+|+|+|.++++.
T Consensus 53 ~~~~vLDl~~GsG~l~l~~ 71 (199)
T PRK10909 53 VDARCLDCFAGSGALGLEA 71 (199)
T ss_pred CCCEEEEcCCCccHHHHHH
Confidence 3569999999999999864
No 228
>PRK11805 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=79.91 E-value=1 Score=38.33 Aligned_cols=18 Identities=17% Similarity=0.237 Sum_probs=16.3
Q ss_pred CeEEEecCCccHHHHhhh
Q 036188 192 KQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 192 ~~vvDiGGg~G~~~~~l~ 209 (210)
.+|+|+|||+|.+++.++
T Consensus 135 ~~VLDlG~GsG~iai~la 152 (307)
T PRK11805 135 TRILDLCTGSGCIAIACA 152 (307)
T ss_pred CEEEEEechhhHHHHHHH
Confidence 689999999999998875
No 229
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=79.87 E-value=2.4 Score=29.06 Aligned_cols=46 Identities=13% Similarity=0.140 Sum_probs=36.7
Q ss_pred hhhHHhhc-CCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKA-GPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~-g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.+|-|... +.-.-+|...||+++++ .-...++.||.|...|++...
T Consensus 28 t~dkl~kEV~~~K~ITps~lserlkI----~~SlAr~~Lr~L~~kG~Ik~V 74 (86)
T PRK09334 28 LLKRVAKEVKKEKIVTPYTLASKYGI----KISVAKKVLRELEKRGVLVLY 74 (86)
T ss_pred HHHHHHHHhccCcEEcHHHHHHHhcc----hHHHHHHHHHHHHHCCCEEEE
Confidence 45555432 11145899999999999 999999999999999999765
No 230
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=79.86 E-value=3.8 Score=32.71 Aligned_cols=37 Identities=24% Similarity=0.317 Sum_probs=34.0
Q ss_pred CCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 46 PGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 46 ~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
||..++..+||+++|+ +...++.-|+.|...|+++..
T Consensus 31 pG~~L~e~~La~~lgV----SRtpVREAL~~L~~eGLV~~~ 67 (221)
T PRK11414 31 PGARLITKNLAEQLGM----SITPVREALLRLVSVNALSVA 67 (221)
T ss_pred CCCccCHHHHHHHHCC----CchhHHHHHHHHHHCCCEEec
Confidence 3468899999999999 999999999999999999875
No 231
>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed
Probab=79.84 E-value=2 Score=36.58 Aligned_cols=19 Identities=11% Similarity=-0.071 Sum_probs=17.1
Q ss_pred CCeEEEecCCccHHHHhhh
Q 036188 191 IKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 191 ~~~vvDiGGg~G~~~~~l~ 209 (210)
..+|+|+|||.|.++..++
T Consensus 174 ~~~VLDl~cG~G~~sl~la 192 (315)
T PRK03522 174 PRSMWDLFCGVGGFGLHCA 192 (315)
T ss_pred CCEEEEccCCCCHHHHHHH
Confidence 4799999999999998876
No 232
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=79.75 E-value=2.5 Score=33.12 Aligned_cols=34 Identities=18% Similarity=0.384 Sum_probs=32.2
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+.|-.+||+.+|+ .++.+.|+|+.|...|++...
T Consensus 168 ~~t~~~lA~~lG~----tr~tvsR~l~~l~~~gii~~~ 201 (211)
T PRK11753 168 KITRQEIGRIVGC----SREMVGRVLKMLEDQGLISAH 201 (211)
T ss_pred CCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEec
Confidence 7889999999999 999999999999999999875
No 233
>KOG1540 consensus Ubiquinone biosynthesis methyltransferase COQ5 [Coenzyme transport and metabolism]
Probab=79.38 E-value=3.8 Score=34.12 Aligned_cols=43 Identities=19% Similarity=0.062 Sum_probs=27.0
Q ss_pred HHHHHHhhhhhhhHHHHHHhCCC---CCCCCeEEEecCCccHHHHhhhC
Q 036188 165 HFNAAMYNYTSLVMSNILESYKG---FDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 165 ~f~~~M~~~~~~~~~~~l~~~~~---~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
..|++|...... -|-+.+.+ -...-++|||+||+|-++..|++
T Consensus 75 ~mND~mSlGiHR---lWKd~~v~~L~p~~~m~~lDvaGGTGDiaFril~ 120 (296)
T KOG1540|consen 75 IMNDAMSLGIHR---LWKDMFVSKLGPGKGMKVLDVAGGTGDIAFRILR 120 (296)
T ss_pred HHHHHhhcchhH---HHHHHhhhccCCCCCCeEEEecCCcchhHHHHHH
Confidence 556666644332 22222221 23458999999999999988763
No 234
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=79.25 E-value=1.4 Score=34.65 Aligned_cols=46 Identities=9% Similarity=0.053 Sum_probs=40.7
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+..|.+.|.+. +.++++|||+.+++ ++.-++|=|+.|...|++.+.
T Consensus 9 ~~~Il~~l~~~---~~~~~~~La~~~~v----S~~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 9 QKALQELIEEN---PFITDEELAEKFGV----SIQTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHHHC---CCEEHHHHHHHHCc----CHHHHHHHHHHHhcchHHHHH
Confidence 34577888886 58999999999999 999999999999999999864
No 235
>PRK11873 arsM arsenite S-adenosylmethyltransferase; Reviewed
Probab=79.23 E-value=1.5 Score=36.26 Aligned_cols=21 Identities=14% Similarity=0.192 Sum_probs=17.1
Q ss_pred CCCCCeEEEecCCccHHHHhh
Q 036188 188 FDNIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l 208 (210)
.....+|||||||.|..+..+
T Consensus 75 ~~~g~~VLDiG~G~G~~~~~~ 95 (272)
T PRK11873 75 LKPGETVLDLGSGGGFDCFLA 95 (272)
T ss_pred CCCCCEEEEeCCCCCHHHHHH
Confidence 566789999999999876543
No 236
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.15 E-value=5.3 Score=26.91 Aligned_cols=35 Identities=9% Similarity=0.049 Sum_probs=32.1
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
...++.+|.+++|+ +.+-+..++.+|-.+|+..+-
T Consensus 21 e~~nVP~lm~~TGw----PRRT~QDvikAlpglgi~l~F 55 (95)
T COG4519 21 ETANVPELMAATGW----PRRTAQDVIKALPGLGIVLEF 55 (95)
T ss_pred ccCChHHHHHHcCC----chhHHHHHHHhCcCCCeEEEe
Confidence 47899999999999 999999999999999988654
No 237
>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=79.01 E-value=3.7 Score=29.99 Aligned_cols=49 Identities=10% Similarity=0.069 Sum_probs=42.9
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYY 105 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l 105 (210)
-|.|.++||..++- +...++.-|.++...|+++.. ++|.|..+....+.
T Consensus 52 ipy~~e~LA~~~~~----~~~~V~~AL~~f~k~glIe~~-----ed~~i~i~~~~~~~ 100 (121)
T PF09681_consen 52 IPYTAEMLALEFDR----PVDTVRLALAVFQKLGLIEID-----EDGVIYIPNWEKHQ 100 (121)
T ss_pred CCCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe-----cCCeEEeecHHHHh
Confidence 59999999999999 999999999999999999987 57878777655544
No 238
>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=78.89 E-value=2.9 Score=32.20 Aligned_cols=34 Identities=21% Similarity=0.290 Sum_probs=32.4
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|+|-+|||..+|+ .+..+.|.|+.|...|+++..
T Consensus 143 ~~t~~~iA~~lG~----tretvsR~l~~l~~~g~I~~~ 176 (193)
T TIGR03697 143 RLSHQAIAEAIGS----TRVTITRLLGDLRKKKLISIH 176 (193)
T ss_pred CCCHHHHHHHhCC----cHHHHHHHHHHHHHCCCEEec
Confidence 6899999999999 999999999999999999875
No 239
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=78.88 E-value=3.2 Score=33.90 Aligned_cols=46 Identities=17% Similarity=0.197 Sum_probs=38.3
Q ss_pred CCCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 47 GTKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 47 ~~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
|..+ |-.+||+++|+ +...++.-|+.|...|+++... +.|.|....
T Consensus 31 G~~LpsE~eLa~~lgV----SRtpVREAL~~L~~eGlv~~~~----~~G~~V~~~ 77 (254)
T PRK09464 31 GEKLPPERELAKQFDV----SRPSLREAIQRLEAKGLLLRRQ----GGGTFVQSS 77 (254)
T ss_pred CCcCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEec----CceeEEecC
Confidence 3577 88999999999 9999999999999999998663 456666553
No 240
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=78.86 E-value=1.8 Score=25.50 Aligned_cols=24 Identities=25% Similarity=0.303 Sum_probs=16.7
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
.+.|..+||+.+|. ++.-+.+.++
T Consensus 19 ~G~s~~~IA~~lg~----s~sTV~relk 42 (44)
T PF13936_consen 19 QGMSIREIAKRLGR----SRSTVSRELK 42 (44)
T ss_dssp S---HHHHHHHTT------HHHHHHHHH
T ss_pred cCCCHHHHHHHHCc----CcHHHHHHHh
Confidence 37999999999999 9998888775
No 241
>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=78.83 E-value=2.1 Score=35.90 Aligned_cols=35 Identities=11% Similarity=0.164 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHH-HHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILR-LLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr-~L~~~gl~~~~ 86 (210)
++.+++++|+.+|. ++..+.++++ .|...|++...
T Consensus 254 ~~~~~~~ia~~lg~----~~~~~~~~~e~~Li~~~li~~~ 289 (305)
T TIGR00635 254 GPVGLKTLAAALGE----DADTIEDVYEPYLLQIGFLQRT 289 (305)
T ss_pred CcccHHHHHHHhCC----CcchHHHhhhHHHHHcCCcccC
Confidence 68999999999999 9999999999 79999999765
No 242
>PRK04457 spermidine synthase; Provisional
Probab=78.82 E-value=1.5 Score=36.39 Aligned_cols=21 Identities=14% Similarity=0.175 Sum_probs=17.8
Q ss_pred CCCCeEEEecCCccHHHHhhh
Q 036188 189 DNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l~ 209 (210)
++.++|+|||||.|.++..++
T Consensus 65 ~~~~~vL~IG~G~G~l~~~l~ 85 (262)
T PRK04457 65 PRPQHILQIGLGGGSLAKFIY 85 (262)
T ss_pred CCCCEEEEECCCHhHHHHHHH
Confidence 456799999999999988764
No 243
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=78.57 E-value=3.2 Score=33.97 Aligned_cols=46 Identities=26% Similarity=0.413 Sum_probs=38.0
Q ss_pred CCCCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 46 PGTKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 46 ~~~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
||..+ |-.+||+++|+ +...++.-|+.|...|+++... +.|.|...
T Consensus 29 pG~~LpsE~eLa~~~gV----SRtpVREAL~~L~~eGlV~~~~----~~G~~V~~ 75 (257)
T PRK10225 29 PGERLPPEREIAEMLDV----TRTVVREALIMLEIKGLVEVRR----GAGIYVLD 75 (257)
T ss_pred CCCcCcCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEec----CCEEEEeC
Confidence 34678 68899999999 9999999999999999998663 45555544
No 244
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=78.56 E-value=3.2 Score=30.53 Aligned_cols=43 Identities=19% Similarity=0.227 Sum_probs=36.2
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
=-|+.|||..+++ +|.-+.|-.+.|...|++.... +.|.|-..
T Consensus 35 LPSvRelA~~~~V----NpnTv~raY~eLE~eG~i~t~r----g~G~fV~~ 77 (125)
T COG1725 35 LPSVRELAKDLGV----NPNTVQRAYQELEREGIVETKR----GKGTFVTE 77 (125)
T ss_pred CCcHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEec----CeeEEEcC
Confidence 3589999999999 9999999999999999998763 45655543
No 245
>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=78.49 E-value=1.6 Score=34.70 Aligned_cols=20 Identities=20% Similarity=0.243 Sum_probs=16.9
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
+..+|+|||||.|.++..++
T Consensus 45 ~~~~vLdlG~G~G~~~~~l~ 64 (224)
T TIGR01983 45 FGLRVLDVGCGGGLLSEPLA 64 (224)
T ss_pred CCCeEEEECCCCCHHHHHHH
Confidence 46799999999999887664
No 246
>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=78.39 E-value=3.2 Score=30.00 Aligned_cols=35 Identities=26% Similarity=0.234 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.+.|+.|||..+++ +...++-++--|...|++.-.
T Consensus 54 ~~~SVAEiAA~L~l----PlgVvrVLvsDL~~~G~v~v~ 88 (114)
T PF05331_consen 54 RPLSVAEIAARLGL----PLGVVRVLVSDLADAGLVRVR 88 (114)
T ss_pred CCccHHHHHHhhCC----CchhhhhhHHHHHhCCCEEEe
Confidence 49999999999999 999999999999999999865
No 247
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=78.39 E-value=1.3 Score=40.45 Aligned_cols=19 Identities=11% Similarity=0.317 Sum_probs=16.7
Q ss_pred CCeEEEecCCccHHHHhhh
Q 036188 191 IKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 191 ~~~vvDiGGg~G~~~~~l~ 209 (210)
..+|+|||||+|.+++.++
T Consensus 139 ~~~VLDlG~GsG~iai~la 157 (506)
T PRK01544 139 FLNILELGTGSGCIAISLL 157 (506)
T ss_pred CCEEEEccCchhHHHHHHH
Confidence 4689999999999998775
No 248
>PHA03412 putative methyltransferase; Provisional
Probab=78.33 E-value=1.1 Score=36.65 Aligned_cols=19 Identities=21% Similarity=0.228 Sum_probs=16.7
Q ss_pred CCeEEEecCCccHHHHhhh
Q 036188 191 IKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 191 ~~~vvDiGGg~G~~~~~l~ 209 (210)
..+|||+|+|+|.++..++
T Consensus 50 ~grVLDlG~GSG~Lalala 68 (241)
T PHA03412 50 SGSVVDLCAGIGGLSFAMV 68 (241)
T ss_pred CCEEEEccChHHHHHHHHH
Confidence 5699999999999998764
No 249
>PRK14966 unknown domain/N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase fusion protein; Provisional
Probab=78.31 E-value=1.5 Score=39.04 Aligned_cols=20 Identities=15% Similarity=0.273 Sum_probs=16.8
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
...+|+|||||+|.+++.++
T Consensus 251 ~~~rVLDLGcGSG~IaiaLA 270 (423)
T PRK14966 251 ENGRVWDLGTGSGAVAVTVA 270 (423)
T ss_pred CCCEEEEEeChhhHHHHHHH
Confidence 34589999999999988765
No 250
>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=78.30 E-value=3.5 Score=33.19 Aligned_cols=46 Identities=17% Similarity=0.217 Sum_probs=38.0
Q ss_pred CCCCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 46 PGTKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 46 ~~~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
||..+ |-.+||+++|+ +...++.-|+.|...|+++... +.|.|...
T Consensus 26 pG~~LpsE~~La~~lgV----SRtpVREAL~~Le~eGlV~~~~----~~G~~V~~ 72 (235)
T TIGR02812 26 PGSILPAERELSELIGV----TRTTLREVLQRLARDGWLTIQH----GKPTKVNN 72 (235)
T ss_pred CCCcCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEeC----CCccEecC
Confidence 34678 89999999999 9999999999999999998763 34555543
No 251
>PRK01581 speE spermidine synthase; Validated
Probab=78.26 E-value=1.6 Score=38.13 Aligned_cols=73 Identities=12% Similarity=0.178 Sum_probs=40.8
Q ss_pred HHHHhhHHHHHhcCCchhhhhhC--CchhHhhccCchH------HHHHHHHHhhhhhhhHHHHHHhCCCCCCCCeEEEec
Q 036188 127 LESWSQLKDAILEGGIPFNRAHG--VHIFEYAGLNPRF------NKHFNAAMYNYTSLVMSNILESYKGFDNIKQLVDVG 198 (210)
Q Consensus 127 ~~~~~~L~~~l~~g~~~f~~~~g--~~~fe~l~~~p~~------~~~f~~~M~~~~~~~~~~~l~~~~~~~~~~~vvDiG 198 (210)
...|....+.+..++++||...- ..-| .+-.|... .-.|++.|.. +.+.. ..+.++||+||
T Consensus 90 ~~~~~~~~~vl~~~~S~yQ~I~I~et~~~-~L~LDG~~Q~se~DE~iYHE~Lvh------p~m~~----h~~PkrVLIIG 158 (374)
T PRK01581 90 KEIQAGEHTNLFAEKSNYQNINLLQVSDI-RLYLDKQLQFSSVDEQIYHEALVH------PIMSK----VIDPKRVLILG 158 (374)
T ss_pred HHHhhcccCEEEecCCCCceEEEEEcCCE-EEEECCeeccccccHHHHHHHHHH------HHHHh----CCCCCEEEEEC
Confidence 34677777777778888876321 1111 12222111 1134444431 11111 35678999999
Q ss_pred CCccHHHHhhhC
Q 036188 199 GSLGVTLQAITT 210 (210)
Q Consensus 199 Gg~G~~~~~l~~ 210 (210)
||.|..+.++++
T Consensus 159 gGdG~tlrelLk 170 (374)
T PRK01581 159 GGDGLALREVLK 170 (374)
T ss_pred CCHHHHHHHHHh
Confidence 999999888763
No 252
>PRK09954 putative kinase; Provisional
Probab=78.23 E-value=2.7 Score=36.21 Aligned_cols=44 Identities=18% Similarity=0.182 Sum_probs=39.1
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhccccee
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVE 84 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~ 84 (210)
+..|...|.++ +++|..|||+++++ ....+.+.++-|...|++.
T Consensus 5 ~~~il~~l~~~---~~~s~~~la~~l~~----s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 5 EKEILAILRRN---PLIQQNEIADILQI----SRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHHC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCcC
Confidence 34577888886 59999999999999 9999999999999999985
No 253
>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=78.09 E-value=2.4 Score=26.62 Aligned_cols=39 Identities=18% Similarity=0.243 Sum_probs=32.3
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHh
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLA 78 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~ 78 (210)
-++.|.++|-.. +..|+.|||+.+++ .++-++.-+..|.
T Consensus 6 rq~~Ll~~L~~~---~~~~~~ela~~l~~----S~rti~~~i~~L~ 44 (59)
T PF08280_consen 6 RQLKLLELLLKN---KWITLKELAKKLNI----SERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHH---TSBBHHHHHHHCTS-----HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcC---CCCcHHHHHHHHCC----CHHHHHHHHHHHH
Confidence 456788888774 69999999999999 9999988888776
No 254
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=77.85 E-value=4 Score=33.26 Aligned_cols=46 Identities=20% Similarity=0.234 Sum_probs=38.0
Q ss_pred CCCCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 46 PGTKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 46 ~~~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
||..+ +-.+||+.+|+ +...++.-|+.|...|+++... +.|.|-.+
T Consensus 27 pG~~LPsE~eLa~~~gV----SRtpVREAL~~L~~eGlV~~~~----~~G~~V~~ 73 (251)
T PRK09990 27 VGQALPSERRLCEKLGF----SRSALREGLTVLRGRGIIETAQ----GRGSFVAR 73 (251)
T ss_pred CCCcCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEeC----CCeeEEec
Confidence 34688 88999999999 9999999999999999998763 34555544
No 255
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=77.84 E-value=2.4 Score=33.99 Aligned_cols=34 Identities=15% Similarity=0.212 Sum_probs=32.4
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|+|-++||..+|+ .+..+.|+|+.|...|++...
T Consensus 184 ~lt~~~iA~~lG~----sr~tvsR~l~~l~~~g~I~~~ 217 (235)
T PRK11161 184 TMTRGDIGNYLGL----TVETISRLLGRFQKSGMLAVK 217 (235)
T ss_pred cccHHHHHHHhCC----cHHHHHHHHHHHHHCCCEEec
Confidence 6899999999999 999999999999999999986
No 256
>PRK01381 Trp operon repressor; Provisional
Probab=77.80 E-value=3.3 Score=29.12 Aligned_cols=53 Identities=21% Similarity=0.017 Sum_probs=37.0
Q ss_pred HHHHHhhchHHHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHh
Q 036188 16 ADQLATGVVLPMAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLA 78 (210)
Q Consensus 16 l~~~~~~~~~~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~ 78 (210)
++..+.-+-+-.+ .+.+++|+..|.+ |++|--|||+.+|+ ....+.|.=+.|-
T Consensus 28 ~l~~llTp~Er~a--l~~R~~I~~~L~~----g~~sQREIa~~lGv----SiaTITRgsn~Lk 80 (99)
T PRK01381 28 LLTLLLTPDEREA--LGTRVRIVEELLR----GELSQREIKQELGV----GIATITRGSNSLK 80 (99)
T ss_pred HHHHhCCHHHHHH--HHHHHHHHHHHHc----CCcCHHHHHHHhCC----ceeeehhhHHHhc
Confidence 3333344444333 3568899999988 68999999999999 7666666555553
No 257
>KOG1499 consensus Protein arginine N-methyltransferase PRMT1 and related enzymes [Posttranslational modification, protein turnover, chaperones; Transcription; Signal transduction mechanisms]
Probab=77.75 E-value=1.6 Score=37.65 Aligned_cols=18 Identities=28% Similarity=0.346 Sum_probs=15.6
Q ss_pred CCCeEEEecCCccHHHHh
Q 036188 190 NIKQLVDVGGSLGVTLQA 207 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~ 207 (210)
+.+.|+|||||+|.+++-
T Consensus 60 ~dK~VlDVGcGtGILS~F 77 (346)
T KOG1499|consen 60 KDKTVLDVGCGTGILSMF 77 (346)
T ss_pred CCCEEEEcCCCccHHHHH
Confidence 568999999999998764
No 258
>PRK10736 hypothetical protein; Provisional
Probab=77.74 E-value=3.4 Score=36.20 Aligned_cols=43 Identities=7% Similarity=-0.075 Sum_probs=38.3
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.|.+.|.. .|.++++|+.++++ +...+..+|-.|.-.|++++.
T Consensus 312 ~v~~~l~~----~~~~iD~L~~~~~l----~~~~v~~~L~~LEl~G~v~~~ 354 (374)
T PRK10736 312 ELLANVGD----EVTPVDVVAERAGQ----PVPEVVTQLLELELAGWIAAV 354 (374)
T ss_pred HHHHhcCC----CCCCHHHHHHHHCc----CHHHHHHHHHHHHhCCcEEEc
Confidence 46666654 58999999999999 999999999999999999987
No 259
>PTZ00146 fibrillarin; Provisional
Probab=77.71 E-value=1.6 Score=36.96 Aligned_cols=22 Identities=14% Similarity=0.324 Sum_probs=19.0
Q ss_pred CCCCCeEEEecCCccHHHHhhh
Q 036188 188 FDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
++...+|||+|||+|.++..++
T Consensus 130 IkpG~~VLDLGaG~G~~t~~lA 151 (293)
T PTZ00146 130 IKPGSKVLYLGAASGTTVSHVS 151 (293)
T ss_pred cCCCCEEEEeCCcCCHHHHHHH
Confidence 6677899999999999888765
No 260
>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=77.56 E-value=1.9 Score=35.86 Aligned_cols=21 Identities=29% Similarity=0.460 Sum_probs=17.9
Q ss_pred CCCCeEEEecCCccHHHHhhh
Q 036188 189 DNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l~ 209 (210)
++.++|++||||.|.++..++
T Consensus 71 ~~p~~VL~iG~G~G~~~~~ll 91 (270)
T TIGR00417 71 PNPKHVLVIGGGDGGVLREVL 91 (270)
T ss_pred CCCCEEEEEcCCchHHHHHHH
Confidence 456799999999999988775
No 261
>TIGR01177 conserved hypothetical protein TIGR01177. This family is found exclusively in the Archaea.
Probab=77.42 E-value=3 Score=35.61 Aligned_cols=27 Identities=11% Similarity=0.038 Sum_probs=20.8
Q ss_pred HHHhCCCCCCCCeEEEecCCccHHHHhh
Q 036188 181 ILESYKGFDNIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 181 ~l~~~~~~~~~~~vvDiGGg~G~~~~~l 208 (210)
++.... +....+|+|+|||+|.++++.
T Consensus 174 ~~~l~~-~~~g~~vLDp~cGtG~~liea 200 (329)
T TIGR01177 174 MVNLAR-VTEGDRVLDPFCGTGGFLIEA 200 (329)
T ss_pred HHHHhC-CCCcCEEEECCCCCCHHHHHH
Confidence 344444 677789999999999998765
No 262
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=77.06 E-value=4.6 Score=30.40 Aligned_cols=66 Identities=26% Similarity=0.272 Sum_probs=47.3
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcC-CCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLT-KNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVS 102 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~-~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s 102 (210)
++.|+++|.+++ ++.|+++|=.++.- -|++.+.-+.|.|+.|...|++.+....+ +.-+|.++...
T Consensus 23 R~~vl~~L~~~~--~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~-~~~~y~~~~~~ 89 (145)
T COG0735 23 RLAVLELLLEAD--GHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEG-GKTRYELNSEP 89 (145)
T ss_pred HHHHHHHHHhcC--CCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC-CEEEEecCCCC
Confidence 456788998875 67999999888863 13337778999999999999999874211 12336555543
No 263
>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=76.86 E-value=5.6 Score=29.31 Aligned_cols=47 Identities=13% Similarity=0.116 Sum_probs=36.6
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHh----cCCCCCCcccHHHHHHHHhcccceeee
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQL----LTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~----~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.|+.|...|=.. ++.|+.||.+.+ ++ ...-+..+|+-|...|++...
T Consensus 5 ~E~~VM~vlW~~---~~~t~~eI~~~l~~~~~~----~~tTv~T~L~rL~~KG~v~~~ 55 (130)
T TIGR02698 5 AEWEVMRVVWTL---GETTSRDIIRILAEKKDW----SDSTIKTLLGRLVDKGCLTTE 55 (130)
T ss_pred HHHHHHHHHHcC---CCCCHHHHHHHHhhccCC----cHHHHHHHHHHHHHCCceeee
Confidence 345555556444 589999977776 67 888999999999999999875
No 264
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=76.69 E-value=3.2 Score=29.23 Aligned_cols=48 Identities=21% Similarity=0.191 Sum_probs=35.8
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccce
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVV 83 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~ 83 (210)
.-.|++.++..+.|.-.|..|||+-.|. |-.+|.+.++|..|..--.+
T Consensus 8 ~~~v~~vv~~IP~GkV~TYGdIA~laG~--p~~ARqVG~il~~l~~~s~l 55 (103)
T COG3695 8 TQRVLDVVAAIPEGKVSTYGDIAKLAGL--PRAARQVGRILKHLPEGSDL 55 (103)
T ss_pred HHHHHHHHHhCCCCceeeHHHHHHHhCC--ChhHHHHHHHHhhCCCCCCC
Confidence 3457777777766678999999999999 11388999999887654433
No 265
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=76.58 E-value=4.4 Score=33.08 Aligned_cols=46 Identities=24% Similarity=0.162 Sum_probs=37.8
Q ss_pred CCCCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 46 PGTKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 46 ~~~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
||..+ +-.|||+++|+ +...++.-|+.|...|+++... +.|.|...
T Consensus 22 pG~~LpsE~eLae~~gV----SRtpVREAL~~Le~~GlV~~~~----~~G~~V~~ 68 (253)
T PRK10421 22 AGMKLPAERQLAMQLGV----SRNSLREALAKLVSEGVLLSRR----GGGTFIRW 68 (253)
T ss_pred CCCcCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEeC----CCeEEEec
Confidence 34677 68899999999 9999999999999999998653 45666554
No 266
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=76.47 E-value=4.2 Score=32.82 Aligned_cols=45 Identities=16% Similarity=0.166 Sum_probs=38.1
Q ss_pred CCCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 47 GTKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 47 ~~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
|..+ |-.+||+++|+ +...++.-|+.|...|+++... +.|.|-.+
T Consensus 28 G~~LPsE~eLae~~gV----SRt~VReAL~~L~~eGlv~~~~----g~G~~V~~ 73 (239)
T PRK04984 28 GSILPAERELSELIGV----TRTTLREVLQRLARDGWLTIQH----GKPTKVNN 73 (239)
T ss_pred CCcCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEeC----CCeeEeCC
Confidence 3678 78899999999 9999999999999999998763 45666654
No 267
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=76.41 E-value=9.6 Score=25.18 Aligned_cols=41 Identities=12% Similarity=0.148 Sum_probs=30.2
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHH--hccccee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLL--ASYSVVE 84 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L--~~~gl~~ 84 (210)
|.+.|... ++.|++||++++|+ .+.-++-.|--+ -..|+--
T Consensus 15 li~mL~rp---~GATi~ei~~atGW----q~HTvRgalsg~~kKklGl~i 57 (72)
T PF11994_consen 15 LIAMLRRP---EGATIAEICEATGW----QPHTVRGALSGLLKKKLGLTI 57 (72)
T ss_pred HHHHHcCC---CCCCHHHHHHhhCC----chhhHHHHHHHHHHHhcCcEE
Confidence 55667653 58999999999999 888776666655 4556543
No 268
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=76.39 E-value=1.9 Score=38.34 Aligned_cols=49 Identities=16% Similarity=0.264 Sum_probs=30.8
Q ss_pred HHHHHHHhhChhhHHhhc-CCCCCCCH---HHHHHHhcCCCCCCcccHHHHHHHHhc
Q 036188 27 MAIQAVYELGIFEILDKA-GPGTKLSA---SDIAAQLLTKNKDAPMMLDRILRLLAS 79 (210)
Q Consensus 27 ~al~~a~~lglfd~L~~~-g~~~~~t~---~eLA~~~~~~~~~~~~~l~rlLr~L~~ 79 (210)
..+++..++++++++... + ....+ -+||++.+- +-....+..+||.+..
T Consensus 72 ~~~r~iLrla~yell~~~iP--~~a~vneaVelak~~~~--~~~~~fVNaVLr~i~~ 124 (427)
T PRK10901 72 RIVHALLLVGLYQLLYTRIP--AHAAVDETVEAAKALKR--PWAKGLVNAVLRRFQR 124 (427)
T ss_pred HHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHhcCC--ccchhhHHHHHHHhhh
Confidence 357788889999988742 2 23333 367766554 1144578888888765
No 269
>PRK09462 fur ferric uptake regulator; Provisional
Probab=76.31 E-value=5.3 Score=29.96 Aligned_cols=54 Identities=20% Similarity=0.277 Sum_probs=40.5
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCC-CCCCcccHHHHHHHHhcccceeeec
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTK-NKDAPMMLDRILRLLASYSVVECSL 87 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~-~~~~~~~l~rlLr~L~~~gl~~~~~ 87 (210)
-+.-|++.|.... +++.|++||-+++.-. +.++..-+.|.|+.|+..|++.+..
T Consensus 18 qR~~Il~~l~~~~-~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 18 PRLKILEVLQEPD-NHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHHHHhCC-CCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 3455788887531 1599999999988531 2236778999999999999998763
No 270
>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=76.26 E-value=2.1 Score=33.65 Aligned_cols=20 Identities=20% Similarity=0.129 Sum_probs=17.5
Q ss_pred CCeEEEecCCccHHHHhhhC
Q 036188 191 IKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 191 ~~~vvDiGGg~G~~~~~l~~ 210 (210)
..+++|++||+|.+++++++
T Consensus 50 g~~vLDLfaGsG~lglea~s 69 (189)
T TIGR00095 50 GAHLLDVFAGSGLLGEEALS 69 (189)
T ss_pred CCEEEEecCCCcHHHHHHHh
Confidence 56899999999999998763
No 271
>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=76.25 E-value=2 Score=28.48 Aligned_cols=33 Identities=18% Similarity=0.071 Sum_probs=29.2
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhccccee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVE 84 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~ 84 (210)
..+|..|||+.+|+ ++..++..++.+...|.+.
T Consensus 31 eGlS~kEIAe~LGI----S~~TVk~~l~~~~~~~~~~ 63 (73)
T TIGR03879 31 AGKTASEIAEELGR----TEQTVRNHLKGETKAGGLV 63 (73)
T ss_pred cCCCHHHHHHHHCc----CHHHHHHHHhcCcccchHH
Confidence 48999999999999 9999999999888777654
No 272
>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=76.03 E-value=2.2 Score=37.85 Aligned_cols=22 Identities=14% Similarity=0.178 Sum_probs=19.0
Q ss_pred CCCCCeEEEecCCccHHHHhhh
Q 036188 188 FDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+..+|+|+|||.|.++..++
T Consensus 290 ~~~~~~vLDl~cG~G~~sl~la 311 (431)
T TIGR00479 290 LQGEELVVDAYCGVGTFTLPLA 311 (431)
T ss_pred cCCCCEEEEcCCCcCHHHHHHH
Confidence 5566799999999999998875
No 273
>PRK14902 16S rRNA methyltransferase B; Provisional
Probab=75.61 E-value=2 Score=38.32 Aligned_cols=51 Identities=12% Similarity=0.194 Sum_probs=32.8
Q ss_pred HHHHHHHhhChhhHHhhcCCCCC--CCH---HHHHHHhcCCCCCCcccHHHHHHHHhccc
Q 036188 27 MAIQAVYELGIFEILDKAGPGTK--LSA---SDIAAQLLTKNKDAPMMLDRILRLLASYS 81 (210)
Q Consensus 27 ~al~~a~~lglfd~L~~~g~~~~--~t~---~eLA~~~~~~~~~~~~~l~rlLr~L~~~g 81 (210)
..++.+.++++++++-..+ -| ..+ =+||++.+- +-....+..+||-+...+
T Consensus 74 ~~~r~iLrla~~el~~~~~--~p~~~~ineav~lak~~~~--~~~~~fVNaVL~~i~~~~ 129 (444)
T PRK14902 74 PWVRNLLRMSLYQLLYLDK--VPDHAAVNEAVEIAKKRGH--KGIAKFVNGVLRNILREG 129 (444)
T ss_pred HHHHHHHHHHHHHHHhccC--CCCceeHHHHHHHHHHhCC--CchhHHHHHHHHHHhhcc
Confidence 3457788899998876421 13 222 378877654 013568999999887653
No 274
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=75.57 E-value=3.9 Score=32.87 Aligned_cols=34 Identities=26% Similarity=0.222 Sum_probs=31.9
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
++|-++||..+|+ .+..+.|+|+.|...|+++..
T Consensus 179 ~lt~~~IA~~lGi----sretlsR~L~~L~~~GlI~~~ 212 (230)
T PRK09391 179 PMSRRDIADYLGL----TIETVSRALSQLQDRGLIGLS 212 (230)
T ss_pred cCCHHHHHHHHCC----CHHHHHHHHHHHHHCCcEEec
Confidence 6788999999999 999999999999999999864
No 275
>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=75.54 E-value=3.9 Score=29.14 Aligned_cols=46 Identities=20% Similarity=0.237 Sum_probs=36.6
Q ss_pred hhhHHhhcCCC-CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPG-TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~-~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.+|-|...-+. .-+|...||+++++ .-...+++||.|...|++...
T Consensus 46 ~~~kl~kEV~~~K~ITp~~lserlkI----~~SlAr~~Lr~L~~kG~Ik~V 92 (105)
T PF03297_consen 46 TYDKLLKEVPKMKLITPSVLSERLKI----NGSLARKALRELESKGLIKPV 92 (105)
T ss_dssp HHHHHHHHCTTSSCECHHHHHHHHCC----SCHHHHHHHHHHHHCCSSEEE
T ss_pred HHHHHHHHhccCcEeeHHHHHHhHhh----HHHHHHHHHHHHHHCCCEEEE
Confidence 45555432111 35899999999999 999999999999999999866
No 276
>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=75.32 E-value=5.2 Score=25.32 Aligned_cols=46 Identities=11% Similarity=0.094 Sum_probs=34.8
Q ss_pred CCCCHHHHHHHhcCCCCCCcc-cHHHHHHHHhcccceeeeccCCCcccceecccccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPM-MLDRILRLLASYSVVECSLDASGARRLYSLNSVSK 103 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~-~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~ 103 (210)
.+++.+++.++.|. +.. .....+.-+...|+++.+ ++++++|+.+.
T Consensus 19 ~Gi~~~~~~~~~g~----~~~~~~~~~l~~l~~~Gll~~~------~~~l~lT~~G~ 65 (66)
T PF06969_consen 19 EGIDLSEFEQRFGI----DFAEEFQKELEELQEDGLLEID------GGRLRLTEKGR 65 (66)
T ss_dssp SEEEHHHHHHHTT------THHH-HHHHHHHHHTTSEEE-------SSEEEE-TTTG
T ss_pred CCcCHHHHHHHHCc----CHHHHHHHHHHHHHHCCCEEEe------CCEEEECcccC
Confidence 48899999999998 643 347778899999999986 79999998765
No 277
>PRK03837 transcriptional regulator NanR; Provisional
Probab=74.90 E-value=5.7 Score=32.01 Aligned_cols=45 Identities=20% Similarity=0.193 Sum_probs=37.5
Q ss_pred CCCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 47 GTKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 47 ~~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
|..+ +-.+||+++|+ +...++.-|+.|...|+++... +.|.|-..
T Consensus 34 G~~Lp~E~~Lae~~gV----SRt~VREAL~~L~~eGlv~~~~----~~G~~V~~ 79 (241)
T PRK03837 34 GDQLPSERELMAFFGV----GRPAVREALQALKRKGLVQISH----GERARVSR 79 (241)
T ss_pred CCCCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEec----CCceeEec
Confidence 3678 89999999999 9999999999999999998763 34555443
No 278
>COG0293 FtsJ 23S rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=74.78 E-value=4.5 Score=32.39 Aligned_cols=43 Identities=19% Similarity=0.192 Sum_probs=30.7
Q ss_pred HHHHhhhhhhhHHHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 167 NAAMYNYTSLVMSNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 167 ~~~M~~~~~~~~~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.+..++.+..-...+.+.|.-|++...|+|+|..+|.+++.+.
T Consensus 22 ~~gyRSRAa~KL~el~~k~~i~~~~~~ViDLGAAPGgWsQva~ 64 (205)
T COG0293 22 KEGYRSRAAYKLLELNEKFKLFKPGMVVVDLGAAPGGWSQVAA 64 (205)
T ss_pred hccccchHHHHHHHHHHhcCeecCCCEEEEcCCCCCcHHHHHH
Confidence 3334444455455667777547899999999999999987653
No 279
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=74.44 E-value=5.1 Score=32.73 Aligned_cols=46 Identities=17% Similarity=0.185 Sum_probs=37.7
Q ss_pred CCCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 47 GTKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 47 ~~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
|..+ |-.+||+.+|+ +...++.-|+.|...|+++... +.|.|-...
T Consensus 29 G~~LpsE~eLae~~gV----SRtpVREAL~~L~~eGlV~~~~----~~G~~V~~~ 75 (253)
T PRK11523 29 GDKLPAERFIADEKNV----SRTVVREAIIMLEVEGYVEVRK----GSGIHVVSN 75 (253)
T ss_pred CCCCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEec----CCeeEEecC
Confidence 4678 57899999999 9999999999999999998663 456555443
No 280
>PRK13239 alkylmercury lyase; Provisional
Probab=73.85 E-value=3.6 Score=32.98 Aligned_cols=41 Identities=20% Similarity=0.275 Sum_probs=32.8
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcc
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASY 80 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~ 80 (210)
+-.-|+..|++ | +|.|+++||+.+|. +.+.+++.|+.+...
T Consensus 23 ~~~~llr~la~-G--~pvt~~~lA~~~~~----~~~~v~~~L~~l~~~ 63 (206)
T PRK13239 23 LLVPLLRLLAK-G--RPVSVTTLAAALGW----PVEEVEAVLEAMPDT 63 (206)
T ss_pred HHHHHHHHHHc-C--CCCCHHHHHHHhCC----CHHHHHHHHHhCCCe
Confidence 34456777885 3 79999999999999 999988888887543
No 281
>PRK03612 spermidine synthase; Provisional
Probab=73.82 E-value=2.6 Score=38.59 Aligned_cols=22 Identities=18% Similarity=0.457 Sum_probs=18.9
Q ss_pred CCCCeEEEecCCccHHHHhhhC
Q 036188 189 DNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
++.++|+|||||.|..+.++++
T Consensus 296 ~~~~rVL~IG~G~G~~~~~ll~ 317 (521)
T PRK03612 296 ARPRRVLVLGGGDGLALREVLK 317 (521)
T ss_pred CCCCeEEEEcCCccHHHHHHHh
Confidence 4678999999999999988764
No 282
>PHA03411 putative methyltransferase; Provisional
Probab=73.75 E-value=2.1 Score=35.90 Aligned_cols=19 Identities=11% Similarity=0.211 Sum_probs=16.0
Q ss_pred CCeEEEecCCccHHHHhhh
Q 036188 191 IKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 191 ~~~vvDiGGg~G~~~~~l~ 209 (210)
..+|+|+|||.|.++..++
T Consensus 65 ~grVLDLGcGsGilsl~la 83 (279)
T PHA03411 65 TGKVLDLCAGIGRLSFCML 83 (279)
T ss_pred CCeEEEcCCCCCHHHHHHH
Confidence 4689999999999887653
No 283
>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=73.72 E-value=7.3 Score=24.22 Aligned_cols=46 Identities=22% Similarity=0.281 Sum_probs=33.0
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCccccee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYS 97 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~ 97 (210)
+.|.+-..+ -.|+.-+|+++++ .+....++++-| |+ .|.+ +.++|+
T Consensus 4 Lidll~~~P---~Vsa~mva~~L~v----T~~~A~~li~eL---g~-rEiT----Gr~R~R 49 (54)
T PF11972_consen 4 LIDLLLSRP---LVSAPMVAKELGV----TPQAAQRLIAEL---GL-REIT----GRGRYR 49 (54)
T ss_pred HHHHHHhCc---cccHHHHHHHhCC----CHHHHHHHHHHh---hc-eeec----CCcccc
Confidence 566676642 5899999999999 999998887554 44 4442 456664
No 284
>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=73.67 E-value=7.2 Score=27.53 Aligned_cols=44 Identities=11% Similarity=0.026 Sum_probs=33.4
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+...+|.+..+. +.+|+.|+|+.+|+ .+..|.++|| ..|++-+.
T Consensus 11 Ka~~~d~~~~~~--~~~ti~~~AK~L~i----~~~~l~~~Lr---~~g~l~~~ 54 (111)
T PF03374_consen 11 KAEFYDAFVDSD--GLYTIREAAKLLGI----GRNKLFQWLR---EKGWLYRR 54 (111)
T ss_pred hhHHHHHHHcCC--CCccHHHHHHHhCC----CHHHHHHHHH---hCCceEEC
Confidence 345577776654 78999999999999 8776655555 58988873
No 285
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=73.64 E-value=2.5 Score=26.52 Aligned_cols=31 Identities=23% Similarity=0.353 Sum_probs=21.3
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
|-+.+.+ ..+|..+||+.+|+ ++..+.+++.
T Consensus 2 L~~~m~~----~~it~~~La~~~gi----s~~tl~~~~~ 32 (63)
T PF13443_consen 2 LKELMAE----RGITQKDLARKTGI----SRSTLSRILN 32 (63)
T ss_dssp HHHHHHH----TT--HHHHHHHHT------HHHHHHHHT
T ss_pred HHHHHHH----cCCCHHHHHHHHCc----CHHHHHHHHh
Confidence 3456677 58899999999999 8888877765
No 286
>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=73.50 E-value=2.5 Score=36.88 Aligned_cols=19 Identities=16% Similarity=0.027 Sum_probs=16.7
Q ss_pred CCeEEEecCCccHHHHhhh
Q 036188 191 IKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 191 ~~~vvDiGGg~G~~~~~l~ 209 (210)
..+|+|++||.|.++..++
T Consensus 234 ~~~vLDL~cG~G~~~l~la 252 (374)
T TIGR02085 234 VTQMWDLFCGVGGFGLHCA 252 (374)
T ss_pred CCEEEEccCCccHHHHHHh
Confidence 4689999999999998775
No 287
>PLN02781 Probable caffeoyl-CoA O-methyltransferase
Probab=73.09 E-value=4.9 Score=32.68 Aligned_cols=22 Identities=23% Similarity=0.311 Sum_probs=17.7
Q ss_pred CCCCCeEEEecCCccHHHHhhh
Q 036188 188 FDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+.++|||||+|.|.-+..++
T Consensus 66 ~~~~~~vLEiGt~~G~s~l~la 87 (234)
T PLN02781 66 IMNAKNTLEIGVFTGYSLLTTA 87 (234)
T ss_pred HhCCCEEEEecCcccHHHHHHH
Confidence 4568899999999998766554
No 288
>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=73.06 E-value=4.6 Score=30.23 Aligned_cols=35 Identities=14% Similarity=0.322 Sum_probs=27.1
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
.|-++|.+++ +...|+.||++.||+ ++..+.+|+|
T Consensus 34 kV~~yLr~~p-~~~ati~eV~e~tgV----s~~~I~~~Ir 68 (137)
T TIGR03826 34 KVYKFLRKHE-NRQATVSEIVEETGV----SEKLILKFIR 68 (137)
T ss_pred HHHHHHHHCC-CCCCCHHHHHHHHCc----CHHHHHHHHH
Confidence 3566777753 234899999999999 9988877775
No 289
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=72.80 E-value=4.2 Score=31.60 Aligned_cols=34 Identities=9% Similarity=0.155 Sum_probs=32.0
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
++|-++||..+|+ .+..+.|+|+-|...|++...
T Consensus 149 ~~t~~~iA~~lG~----tretvsR~l~~l~~~g~I~~~ 182 (202)
T PRK13918 149 YATHDELAAAVGS----VRETVTKVIGELSREGYIRSG 182 (202)
T ss_pred cCCHHHHHHHhCc----cHHHHHHHHHHHHHCCCEEcC
Confidence 6899999999999 999999999999999999864
No 290
>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=72.71 E-value=3.3 Score=27.21 Aligned_cols=34 Identities=12% Similarity=0.092 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
..-|.+|||+.+|+ ++..+..++......-.+..
T Consensus 19 r~Pt~eEiA~~lgi----s~~~v~~~l~~~~~~~Sl~~ 52 (78)
T PF04539_consen 19 REPTDEEIAEELGI----SVEEVRELLQASRRPVSLDL 52 (78)
T ss_dssp S--BHHHHHHHHTS-----HHHHHHHHHHHSCCEESSH
T ss_pred CCCCHHHHHHHHcc----cHHHHHHHHHhCCCCeEEee
Confidence 57799999999999 99999999998766554443
No 291
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=72.39 E-value=5.4 Score=23.74 Aligned_cols=25 Identities=20% Similarity=0.214 Sum_probs=21.5
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHH
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLL 77 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L 77 (210)
+.|..|||+.+++ ++..+++.++.+
T Consensus 18 g~s~~eia~~l~i----s~~tv~~~~~~~ 42 (58)
T smart00421 18 GLTNKEIAERLGI----SEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHCC----CHHHHHHHHHHH
Confidence 7899999999999 998888777654
No 292
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=72.38 E-value=4.3 Score=32.84 Aligned_cols=63 Identities=14% Similarity=0.121 Sum_probs=51.5
Q ss_pred HHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccc---eecccc
Q 036188 27 MAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRL---YSLNSV 101 (210)
Q Consensus 27 ~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~---y~~t~~ 101 (210)
..|.-...-.|++.|-++ ++.|.-+||.++++ +..-+.--+..|...|++.++ ..|+ |+.||.
T Consensus 169 ~~Lkn~~~k~I~~eiq~~---~~~t~~~ia~~l~l----s~aTV~~~lk~l~~~Gii~~~-----~~Gr~iiy~in~s 234 (240)
T COG3398 169 LSLKNETSKAIIYEIQEN---KCNTNLLIAYELNL----SVATVAYHLKKLEELGIIPED-----REGRSIIYSINPS 234 (240)
T ss_pred HHhhchhHHHHHHHHhcC---CcchHHHHHHHcCc----cHHHHHHHHHHHHHcCCCccc-----ccCceEEEEeCHH
Confidence 455566667889999875 57999999999999 999999999999999999987 3443 666654
No 293
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=71.79 E-value=4.9 Score=37.76 Aligned_cols=48 Identities=10% Similarity=0.034 Sum_probs=41.2
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
..-|.+|||+.+|+ ++..++|.|......|++.+..+. .++|.|+.++
T Consensus 615 ~twt~eelse~l~i----p~~~lrrrL~fWi~~GvL~e~~~~-s~tgt~T~iE 662 (765)
T KOG2165|consen 615 NTWTLEELSESLGI----PVPALRRRLSFWIQKGVLREEPII-SDTGTLTVIE 662 (765)
T ss_pred ccccHHHHHHHhCC----CHHHHHHHHHHHHHcCeeecCCCC-CCCceeeecc
Confidence 57999999999999 999999999999999999987322 1368888887
No 294
>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=71.78 E-value=5.3 Score=31.21 Aligned_cols=55 Identities=15% Similarity=0.092 Sum_probs=39.7
Q ss_pred HHHHHHHHhhChhhHHhhcCCCCC---CCHHHHHHHh-cCCCCCCcccHHHHHHHHhcccceeee
Q 036188 26 PMAIQAVYELGIFEILDKAGPGTK---LSASDIAAQL-LTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 26 ~~al~~a~~lglfd~L~~~g~~~~---~t~~eLA~~~-~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
..+|.+.+.+-=.+-+...+ .| .|-.+||..+ |+ +++-++|.++.|+..|++...
T Consensus 46 l~vL~aLls~~~~~d~~~~~--~piVfpSN~~La~r~~G~----s~~tlrR~l~~LveaGLI~rr 104 (177)
T PF03428_consen 46 LAVLDALLSFTPPDDWEPGR--RPIVFPSNAQLAERLNGM----SERTLRRHLARLVEAGLIVRR 104 (177)
T ss_pred HHHHHHHHHhCCcccccCCC--CceeecCHHHHHHHHcCC----CHHHHHHHHHHHHHCCCeeec
Confidence 33444444444344443321 23 5778999999 99 999999999999999999886
No 295
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=71.64 E-value=6.4 Score=28.71 Aligned_cols=43 Identities=12% Similarity=0.142 Sum_probs=33.2
Q ss_pred hhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 38 FEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 38 fd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
.+.|..+- ..+.|+++||+.+|+ +++.+.|+++....+.+-+.
T Consensus 15 ~~~I~~~~-~~~~sl~~lA~~~g~----S~~~l~r~Fk~~~G~s~~~~ 57 (127)
T PRK11511 15 LDWIEDNL-ESPLSLEKVSERSGY----SKWHLQRMFKKETGHSLGQY 57 (127)
T ss_pred HHHHHHhc-CCCCCHHHHHHHHCc----CHHHHHHHHHHHHCcCHHHH
Confidence 44454432 148999999999999 99999999998877766654
No 296
>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=71.19 E-value=3.4 Score=30.15 Aligned_cols=46 Identities=13% Similarity=0.091 Sum_probs=41.3
Q ss_pred HHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccccccCC
Q 036188 54 DIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYVPNK 109 (210)
Q Consensus 54 eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~~~~ 109 (210)
+||+.++. +-+-|-.++.++..+||++.. +|-..+|+.++-++..+
T Consensus 2 ~La~~l~~----eiDdL~p~~eAaelLgf~~~~------~Gdi~LT~~G~~f~~a~ 47 (120)
T PF09821_consen 2 QLADELHL----EIDDLLPIVEAAELLGFAEVE------EGDIRLTPLGRRFAEAD 47 (120)
T ss_pred chHHHhCC----cHHHHHHHHHHHHHcCCeeec------CCcEEeccchHHHHHCC
Confidence 58999999 999999999999999999986 79999999999877544
No 297
>KOG1500 consensus Protein arginine N-methyltransferase CARM1 [Posttranslational modification, protein turnover, chaperones; Transcription]
Probab=71.12 E-value=7.5 Score=33.72 Aligned_cols=18 Identities=33% Similarity=0.486 Sum_probs=14.7
Q ss_pred CCCCCeEEEecCCccHHHH
Q 036188 188 FDNIKQLVDVGGSLGVTLQ 206 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~ 206 (210)
|+ .+.|||||+|+|.++.
T Consensus 176 F~-~kiVlDVGaGSGILS~ 193 (517)
T KOG1500|consen 176 FQ-DKIVLDVGAGSGILSF 193 (517)
T ss_pred cC-CcEEEEecCCccHHHH
Confidence 54 4689999999998864
No 298
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=71.09 E-value=9.8 Score=25.61 Aligned_cols=50 Identities=16% Similarity=0.106 Sum_probs=40.6
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYY 105 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l 105 (210)
.+.|=++||+++|+ ....+...+..|...|+=.+.. ....|.+......+
T Consensus 18 ~~~SGe~La~~Lgi----SRtaVwK~Iq~Lr~~G~~I~s~----~~kGY~L~~~~~ll 67 (79)
T COG1654 18 NFVSGEKLAEELGI----SRTAVWKHIQQLREEGVDIESV----RGKGYLLPQLPDLL 67 (79)
T ss_pred CcccHHHHHHHHCc----cHHHHHHHHHHHHHhCCceEec----CCCceeccCccccC
Confidence 58999999999999 9999999999999999877662 23367777655444
No 299
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=70.93 E-value=4.7 Score=28.43 Aligned_cols=48 Identities=15% Similarity=0.114 Sum_probs=37.9
Q ss_pred hChhhHHhhc-CCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 35 LGIFEILDKA-GPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 35 lglfd~L~~~-g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
-.+++.+... +.-.-+|...||.+.|+ +-...+++||.|...|++...
T Consensus 44 ee~~~ki~KEV~~~r~VTpy~la~r~gI----~~SvAr~vLR~LeeeGvv~lv 92 (107)
T COG4901 44 EELLDKIRKEVPRERVVTPYVLASRYGI----NGSVARIVLRHLEEEGVVQLV 92 (107)
T ss_pred HHHHHHHHHhcccceeecHHHHHHHhcc----chHHHHHHHHHHHhCCceeee
Confidence 3456665442 21246899999999999 999999999999999999765
No 300
>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=70.88 E-value=6.5 Score=23.46 Aligned_cols=34 Identities=18% Similarity=0.210 Sum_probs=25.6
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHH
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLL 77 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L 77 (210)
..++..+.. +.|..+||+.+++ +++.+++.++.+
T Consensus 6 ~~i~~~~~~-----~~s~~eia~~l~~----s~~tv~~~~~~~ 39 (57)
T cd06170 6 REVLRLLAE-----GKTNKEIADILGI----SEKTVKTHLRNI 39 (57)
T ss_pred HHHHHHHHc-----CCCHHHHHHHHCC----CHHHHHHHHHHH
Confidence 345555433 7899999999999 998888777654
No 301
>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=70.84 E-value=6 Score=24.91 Aligned_cols=35 Identities=31% Similarity=0.329 Sum_probs=29.0
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+-++++.||++.|+ -...+-.-||-|.+.|+++..
T Consensus 3 g~lvas~iAd~~Gi----TRSvIVNALRKleSaGvIesr 37 (61)
T PF08222_consen 3 GRLVASKIADRVGI----TRSVIVNALRKLESAGVIESR 37 (61)
T ss_dssp EEE-HHHHHHHHT------HHHHHHHHHHHHHTTSEEEE
T ss_pred ceehHHHHHHHhCc----cHHHHHHHHHHHHhcCceeec
Confidence 45789999999999 899999999999999999865
No 302
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=70.75 E-value=5.8 Score=24.76 Aligned_cols=54 Identities=22% Similarity=0.206 Sum_probs=41.3
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhc---ccceeeeccCCCcccceeccccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLAS---YSVVECSLDASGARRLYSLNSVS 102 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~---~gl~~~~~~~~~~~~~y~~t~~s 102 (210)
++.+|..+.+. .|+..-|+.+++ ++..+.+-++.|.. .-+|.+. .+.+.+|+.+
T Consensus 3 ~l~~f~~v~~~-----gs~~~AA~~l~i----s~~~vs~~i~~LE~~lg~~Lf~r~------~~~~~lT~~G 59 (60)
T PF00126_consen 3 QLRYFLAVAET-----GSISAAAEELGI----SQSAVSRQIKQLEEELGVPLFERS------GRGLRLTEAG 59 (60)
T ss_dssp HHHHHHHHHHH-----SSHHHHHHHCTS----SHHHHHHHHHHHHHHHTS-SEEEC------SSSEEE-HHH
T ss_pred HHHHHHHHHHh-----CCHHHHHHHhhc----cchHHHHHHHHHHHHhCCeEEEEC------CCCeeEChhh
Confidence 46678888884 399999999999 99999998887754 4588875 4568888765
No 303
>PRK14999 histidine utilization repressor; Provisional
Probab=70.63 E-value=8 Score=31.34 Aligned_cols=45 Identities=18% Similarity=0.196 Sum_probs=38.8
Q ss_pred CCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 48 TKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 48 ~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
..+ |-.|||++.|+ +..-+++-|..|+..|++.+.. +.|.|-..+
T Consensus 34 ~~LPsE~eLa~~~gV----SR~TVR~Al~~L~~eGli~r~~----GkGTfV~~~ 79 (241)
T PRK14999 34 DRIPSEAELVAQYGF----SRMTINRALRELTDEGWLVRLQ----GVGTFVAEP 79 (241)
T ss_pred CcCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEec----CcEEEECCC
Confidence 455 78999999999 9999999999999999999875 678887543
No 304
>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=70.63 E-value=11 Score=22.96 Aligned_cols=41 Identities=15% Similarity=0.170 Sum_probs=35.8
Q ss_pred hHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 39 EILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 39 d~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+++.++ +++|++++-+.+|+ +-.++--+|.++-..|+..+.
T Consensus 3 ~~~~~~---~~itv~~~rd~lg~----sRK~ai~lLE~lD~~g~T~R~ 43 (50)
T PF09107_consen 3 ELLQKN---GEITVAEFRDLLGL----SRKYAIPLLEYLDREGITRRV 43 (50)
T ss_dssp HHHHTT---SSBEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHhcC---CcCcHHHHHHHHCc----cHHHHHHHHHHHhccCCEEEe
Confidence 456554 69999999999999 999999999999999999887
No 305
>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=70.51 E-value=5.8 Score=25.26 Aligned_cols=22 Identities=23% Similarity=0.276 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRI 73 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rl 73 (210)
|.++..|||+++|+ ++.-++++
T Consensus 21 g~i~lkdIA~~Lgv----s~~tIr~W 42 (60)
T PF10668_consen 21 GKIKLKDIAEKLGV----SESTIRKW 42 (60)
T ss_pred CCccHHHHHHHHCC----CHHHHHHH
Confidence 79999999999999 88877765
No 306
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=70.50 E-value=5.7 Score=31.76 Aligned_cols=34 Identities=15% Similarity=-0.023 Sum_probs=31.9
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+.|-+|||+.+|+ .++.+.|.|.-|...|+++..
T Consensus 169 ~~t~~~lA~~lG~----sretvsR~L~~L~~~G~I~~~ 202 (226)
T PRK10402 169 HEKHTQAAEYLGV----SYRHLLYVLAQFIQDGYLKKS 202 (226)
T ss_pred cchHHHHHHHHCC----cHHHHHHHHHHHHHCCCEEee
Confidence 5688999999999 999999999999999999875
No 307
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=70.06 E-value=5.1 Score=25.84 Aligned_cols=29 Identities=24% Similarity=0.359 Sum_probs=24.2
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhccc
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYS 81 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~g 81 (210)
+.|+++||+.+|+ +++.+.++++......
T Consensus 1 ~~~~~~la~~~~~----s~~~l~~~f~~~~~~s 29 (84)
T smart00342 1 PLTLEDLAEALGM----SPRHLQRLFKKETGTT 29 (84)
T ss_pred CCCHHHHHHHhCC----CHHHHHHHHHHHhCcC
Confidence 4689999999999 9999999988765443
No 308
>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=69.88 E-value=4.3 Score=25.11 Aligned_cols=35 Identities=23% Similarity=0.295 Sum_probs=27.0
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHH
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRL 76 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~ 76 (210)
.|..|+..+.. +.|..|||+.+++ .+.-+...++.
T Consensus 7 ~E~~vl~~l~~-----G~~~~eIA~~l~i----s~~tV~~~~~~ 41 (58)
T PF00196_consen 7 RELEVLRLLAQ-----GMSNKEIAEELGI----SEKTVKSHRRR 41 (58)
T ss_dssp HHHHHHHHHHT-----TS-HHHHHHHHTS----HHHHHHHHHHH
T ss_pred HHHHHHHHHHh-----cCCcchhHHhcCc----chhhHHHHHHH
Confidence 46677888876 8999999999999 88876665543
No 309
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=69.80 E-value=5.5 Score=27.86 Aligned_cols=33 Identities=15% Similarity=0.197 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhccccee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVE 84 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~ 84 (210)
.+.|+++||+++++ +++.+.|+.+....+.+-+
T Consensus 20 ~~~~~~~lA~~~~~----S~~~l~r~f~~~~g~s~~~ 52 (107)
T PRK10219 20 QPLNIDVVAKKSGY----SKWYLQRMFRTVTHQTLGD 52 (107)
T ss_pred CCCCHHHHHHHHCC----CHHHHHHHHHHHHCcCHHH
Confidence 58999999999999 9999999998876555444
No 310
>KOG2651 consensus rRNA adenine N-6-methyltransferase [RNA processing and modification]
Probab=69.74 E-value=4.3 Score=35.68 Aligned_cols=29 Identities=31% Similarity=0.511 Sum_probs=22.4
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l 208 (210)
+++....+|-+..++||||-|.|+++.-+
T Consensus 143 elvSsi~~f~gi~~vvD~GaG~G~LSr~l 171 (476)
T KOG2651|consen 143 ELVSSISDFTGIDQVVDVGAGQGHLSRFL 171 (476)
T ss_pred HHHHHHHhhcCCCeeEEcCCCchHHHHHH
Confidence 44554434888999999999999998644
No 311
>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=69.59 E-value=5 Score=32.39 Aligned_cols=45 Identities=20% Similarity=0.181 Sum_probs=35.7
Q ss_pred hChhhHH-hhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 35 LGIFEIL-DKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 35 lglfd~L-~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
..|.+.+ ...+ +++|+.+|++.+++ ++......|..+...|++..
T Consensus 177 ~~il~~~~~~~~--g~vt~~~l~~~~~w----s~~~a~~~L~~~~~~G~l~~ 222 (223)
T PF04157_consen 177 SRILELAEEENG--GGVTASELAEKLGW----SVERAKEALEELEREGLLWR 222 (223)
T ss_dssp HHHHHHH--TTT--SEEEHHHHHHHHTB-----HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHhhcC--CCCCHHHHHHHhCC----CHHHHHHHHHHHHhCCCEee
Confidence 3445555 3333 79999999999999 99999999999999999875
No 312
>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=69.57 E-value=8.3 Score=30.95 Aligned_cols=45 Identities=20% Similarity=0.280 Sum_probs=38.9
Q ss_pred CCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 48 TKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 48 ~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
..+ |-.|||++.|+ +..-+++-|..|+..|++.+.. +.|.|...+
T Consensus 23 ~~LPsE~eLa~~~~V----SR~TVR~Al~~L~~eGli~r~~----G~GtfV~~~ 68 (230)
T TIGR02018 23 HRIPSEHELVAQYGC----SRMTVNRALRELTDAGLLERRQ----GVGTFVAEP 68 (230)
T ss_pred CcCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEec----CCEEEEccC
Confidence 455 78899999999 9999999999999999999875 678887554
No 313
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=69.52 E-value=14 Score=29.90 Aligned_cols=52 Identities=23% Similarity=0.305 Sum_probs=44.9
Q ss_pred HHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 28 AIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 28 al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
++..-.+.+|+..+..+| +.++.|+++-+++ +...++-.+|.|.+.++++-.
T Consensus 97 v~~ns~R~~Iy~~i~~nP---G~~lsEl~~nl~i----~R~TlRyhlriLe~~~li~a~ 148 (240)
T COG3398 97 VFLNSKRDGIYNYIKPNP---GFSLSELRANLYI----NRSTLRYHLRILESNPLIEAG 148 (240)
T ss_pred hHhhhhHHHHHHHhccCC---CccHHHHHHhcCC----ChHHHHHHHHHHHhCcchhhh
Confidence 444556678899998874 8999999999999 999999999999999999754
No 314
>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=68.82 E-value=16 Score=25.34 Aligned_cols=62 Identities=16% Similarity=0.201 Sum_probs=42.7
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHh--------cCCCCCCcccHHHHHHHHhcccceeeecc-C--CCcccceecccccccc
Q 036188 37 IFEILDKAGPGTKLSASDIAAQL--------LTKNKDAPMMLDRILRLLASYSVVECSLD-A--SGARRLYSLNSVSKYY 105 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~--------~~~~~~~~~~l~rlLr~L~~~gl~~~~~~-~--~~~~~~y~~t~~s~~l 105 (210)
|.-.|.. +|.+--||++.+ .+ ++..+.+.|+-|...|+++.... + +...-.|++|+.++.+
T Consensus 9 iL~~L~~----~~~~GYei~~~l~~~~~~~~~i----~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~ 80 (100)
T TIGR03433 9 ILKTLSL----GPLHGYGIAQRIQQISEDVLQV----EEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQ 80 (100)
T ss_pred HHHHHhc----CCCCHHHHHHHHHHHcCCcccc----CCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHH
Confidence 3344555 588888888875 45 88899999999999999987310 1 0112348888877644
Q ss_pred c
Q 036188 106 V 106 (210)
Q Consensus 106 ~ 106 (210)
.
T Consensus 81 l 81 (100)
T TIGR03433 81 L 81 (100)
T ss_pred H
Confidence 3
No 315
>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=68.39 E-value=10 Score=27.59 Aligned_cols=48 Identities=17% Similarity=0.054 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKY 104 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~ 104 (210)
-|-+++.||..++- +..-++.-|..+...|+++.. ++|.|..+.....
T Consensus 50 ipy~~e~LA~~~~~----~~~~V~~Al~~f~k~glIe~~-----d~g~i~i~~~~~~ 97 (119)
T TIGR01714 50 APYNAEMLATMFNR----NVGDIRITLQTLESLGLIEKK-----NNGDIFLENWEKH 97 (119)
T ss_pred CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe-----cCCcEEehhHHHH
Confidence 59999999999999 999999999999999999987 4566766655443
No 316
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.17 E-value=5.3 Score=27.39 Aligned_cols=26 Identities=31% Similarity=0.408 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLL 77 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L 77 (210)
.++|.++||+++++ .+..++++|.+-
T Consensus 22 ~~LS~~~iA~~Ln~----t~~~lekil~~t 47 (97)
T COG4367 22 CPLSDEEIATALNW----TEVKLEKILQVT 47 (97)
T ss_pred ccccHHHHHHHhCC----CHHHHHHHHHHh
Confidence 59999999999999 999999988654
No 317
>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=68.13 E-value=6.1 Score=25.57 Aligned_cols=41 Identities=15% Similarity=0.191 Sum_probs=32.2
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhccccee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVE 84 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~ 84 (210)
|..+|.+. ++.|+.+|++.+++ +..-+..=+.-|...+=+.
T Consensus 13 Vw~~L~~~---~~~s~~el~k~~~l----~~~~~~~AiGWLarE~KI~ 53 (65)
T PF10771_consen 13 VWQLLNEN---GEWSVSELKKATGL----SDKEVYLAIGWLARENKIE 53 (65)
T ss_dssp HHHHHCCS---SSEEHHHHHHHCT-----SCHHHHHHHHHHHCTTSEE
T ss_pred HHHHHhhC---CCcCHHHHHHHhCc----CHHHHHHHHHHHhccCcee
Confidence 67788875 69999999999999 8888877777777776443
No 318
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=68.07 E-value=9.2 Score=30.18 Aligned_cols=42 Identities=14% Similarity=0.184 Sum_probs=35.5
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+.+...|+-. +|+|..||++..|+ ++ ..+++.|...|++.+.
T Consensus 93 LEtLaiIay~---qPiTr~eI~~irGv----~~---~~ii~~L~~~gLI~e~ 134 (188)
T PRK00135 93 LEVLAIIAYK---QPITRIEIDEIRGV----NS---DGALQTLLAKGLIKEV 134 (188)
T ss_pred HHHHHHHHHc---CCcCHHHHHHHHCC----CH---HHHHHHHHHCCCeEEc
Confidence 4456667775 69999999999999 76 7899999999999874
No 319
>PRK00536 speE spermidine synthase; Provisional
Probab=67.82 E-value=4.7 Score=33.53 Aligned_cols=23 Identities=13% Similarity=0.029 Sum_probs=20.5
Q ss_pred CCCCCeEEEecCCccHHHHhhhC
Q 036188 188 FDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
-+++++||=||||.|..++++++
T Consensus 70 h~~pk~VLIiGGGDGg~~REvLk 92 (262)
T PRK00536 70 KKELKEVLIVDGFDLELAHQLFK 92 (262)
T ss_pred CCCCCeEEEEcCCchHHHHHHHC
Confidence 35789999999999999999985
No 320
>COG3963 Phospholipid N-methyltransferase [Lipid metabolism]
Probab=67.77 E-value=7.7 Score=30.28 Aligned_cols=33 Identities=15% Similarity=0.238 Sum_probs=27.5
Q ss_pred hHHHHHHhCCCCCCCCeEEEecCCccHHHHhhhC
Q 036188 177 VMSNILESYKGFDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 177 ~~~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
.+...++..+ |+...-|+.+|-|+|.+..+|++
T Consensus 36 lA~~M~s~I~-pesglpVlElGPGTGV~TkaIL~ 68 (194)
T COG3963 36 LARKMASVID-PESGLPVLELGPGTGVITKAILS 68 (194)
T ss_pred HHHHHHhccC-cccCCeeEEEcCCccHhHHHHHh
Confidence 3455566777 99999999999999999999874
No 321
>COG0220 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]
Probab=67.59 E-value=3.7 Score=33.38 Aligned_cols=20 Identities=15% Similarity=0.316 Sum_probs=17.3
Q ss_pred CCeEEEecCCccHHHHhhhC
Q 036188 191 IKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 191 ~~~vvDiGGg~G~~~~~l~~ 210 (210)
.+.+|+||+|.|.+..++++
T Consensus 49 ~pi~lEIGfG~G~~l~~~A~ 68 (227)
T COG0220 49 APIVLEIGFGMGEFLVEMAK 68 (227)
T ss_pred CcEEEEECCCCCHHHHHHHH
Confidence 46999999999999988763
No 322
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=67.55 E-value=8.5 Score=31.42 Aligned_cols=41 Identities=15% Similarity=0.198 Sum_probs=36.1
Q ss_pred CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 51 SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 51 t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
+-.|||+++|+ +...++.-|+.|.+.|+++... +.|.|..+
T Consensus 36 ~EreLae~fgV----SR~~vREAl~~L~a~Glve~r~----G~Gt~V~~ 76 (241)
T COG2186 36 SERELAERFGV----SRTVVREALKRLEAKGLVEIRQ----GSGTFVRP 76 (241)
T ss_pred CHHHHHHHHCC----CcHHHHHHHHHHHHCCCeeecC----CCceEecC
Confidence 45799999999 9999999999999999998764 67888865
No 323
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=67.45 E-value=29 Score=22.06 Aligned_cols=37 Identities=22% Similarity=0.257 Sum_probs=28.5
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhc
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLAS 79 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~ 79 (210)
.+.+.|.. .+.++++||..+|.. ++..+.|..+....
T Consensus 41 ~a~~~l~~----~~~~~~~ia~~~g~~---s~~~f~r~Fk~~~g 77 (84)
T smart00342 41 RARRLLRD----TDLSVTEIALRVGFS---SQSYFSRAFKKLFG 77 (84)
T ss_pred HHHHHHHc----CCCCHHHHHHHhCCC---ChHHHHHHHHHHHC
Confidence 35667766 479999999999995 77888888765543
No 324
>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=67.44 E-value=16 Score=24.39 Aligned_cols=52 Identities=10% Similarity=0.119 Sum_probs=40.9
Q ss_pred HHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 28 AIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 28 al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
......+..|+.+...- ..++.++||+.+++ +.+.+++++.-+...|.+.-.
T Consensus 6 l~~~~~~~~l~~l~~~y---~~i~~~~i~~~~~l----~~~~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00088 6 LQRKIRLTNLLQLSEPY---SSISLSDLAKLLGL----SVPEVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HHHHHHHHHHHHHhHHh---ceeeHHHHHHHhCc----CHHHHHHHHHHHHHCCCeEEE
Confidence 34455556666666553 58999999999999 888999999999999988643
No 325
>smart00753 PAM PCI/PINT associated module.
Probab=67.44 E-value=16 Score=24.39 Aligned_cols=52 Identities=10% Similarity=0.119 Sum_probs=40.9
Q ss_pred HHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 28 AIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 28 al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
......+..|+.+...- ..++.++||+.+++ +.+.+++++.-+...|.+.-.
T Consensus 6 l~~~~~~~~l~~l~~~y---~~i~~~~i~~~~~l----~~~~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00753 6 LQRKIRLTNLLQLSEPY---SSISLSDLAKLLGL----SVPEVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HHHHHHHHHHHHHhHHh---ceeeHHHHHHHhCc----CHHHHHHHHHHHHHCCCeEEE
Confidence 34455556666666553 58999999999999 888999999999999988643
No 326
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=67.34 E-value=10 Score=30.68 Aligned_cols=45 Identities=16% Similarity=0.237 Sum_probs=38.6
Q ss_pred CCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 48 TKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 48 ~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
..+ |-.|||++.|+ +..-+++-|..|+..|++.+.. +.|.|....
T Consensus 27 ~~LPsE~eL~~~~~V----SR~TvR~Al~~L~~eGli~r~~----G~GtfV~~~ 72 (240)
T PRK09764 27 DALPTESALQTEFGV----SRVTVRQALRQLVEQQILESIQ----GSGTYVKEE 72 (240)
T ss_pred CcCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEec----CceeEEccc
Confidence 456 77899999999 9999999999999999999875 578887543
No 327
>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=67.29 E-value=5.4 Score=23.09 Aligned_cols=22 Identities=18% Similarity=0.226 Sum_probs=19.2
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
+|++|+|+.+|+ ++..+.++++
T Consensus 2 lt~~e~a~~lgi----s~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGV----SKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCC----CHHHHHHHHH
Confidence 589999999999 9998888764
No 328
>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=67.13 E-value=5.5 Score=22.92 Aligned_cols=23 Identities=26% Similarity=0.342 Sum_probs=19.7
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHHH
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILRL 76 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr~ 76 (210)
.|..|+|+.+|+ ++..+.++.+.
T Consensus 1 ~s~~e~a~~lgv----s~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGV----SPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCc----CHHHHHHHHHc
Confidence 478999999999 99988888764
No 329
>PF13814 Replic_Relax: Replication-relaxation
Probab=67.00 E-value=8.7 Score=29.70 Aligned_cols=60 Identities=18% Similarity=0.234 Sum_probs=45.9
Q ss_pred HHhhcCCCCCCCHHHHHHHhcCCCCCCcc---cHHHHHHHHhcccceeeeccC-----CCcccceeccccccccc
Q 036188 40 ILDKAGPGTKLSASDIAAQLLTKNKDAPM---MLDRILRLLASYSVVECSLDA-----SGARRLYSLNSVSKYYV 106 (210)
Q Consensus 40 ~L~~~g~~~~~t~~eLA~~~~~~~~~~~~---~l~rlLr~L~~~gl~~~~~~~-----~~~~~~y~~t~~s~~l~ 106 (210)
.|.+. +.+|..+|+..... +.. .+.+.|+-|...|++...... +..+-.|.+|+.+.-++
T Consensus 3 ~L~~~---r~lt~~Qi~~l~~~----~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l 70 (191)
T PF13814_consen 3 LLARH---RFLTTDQIARLLFP----SSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLL 70 (191)
T ss_pred hHHHh---cCcCHHHHHHHHcC----CCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHH
Confidence 45555 58999999999999 665 899999999999999876321 12345799999986443
No 330
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=66.70 E-value=16 Score=24.99 Aligned_cols=30 Identities=10% Similarity=0.203 Sum_probs=24.6
Q ss_pred HHHHHhcccceeeeccCCCcccceecccccccccc
Q 036188 73 ILRLLASYSVVECSLDASGARRLYSLNSVSKYYVP 107 (210)
Q Consensus 73 lLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~~ 107 (210)
-+-+|...|+++.. ..|.|++|+.++.+..
T Consensus 60 a~~~L~~aGli~~~-----~rG~~~iT~~G~~~l~ 89 (92)
T PF14338_consen 60 ARSYLKKAGLIERP-----KRGIWRITEKGRKALA 89 (92)
T ss_pred HHHHHHHCCCccCC-----CCCceEECHhHHHHHh
Confidence 45788999999987 6899999999985443
No 331
>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=66.52 E-value=6.2 Score=23.52 Aligned_cols=26 Identities=27% Similarity=0.317 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLL 77 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L 77 (210)
.+.|.+|||+.+|+ +...++++.+-.
T Consensus 19 ~~~t~~eIa~~lg~----s~~~V~~~~~~a 44 (50)
T PF04545_consen 19 EGLTLEEIAERLGI----SRSTVRRILKRA 44 (50)
T ss_dssp ST-SHHHHHHHHTS----CHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCC----cHHHHHHHHHHH
Confidence 58999999999999 999988887643
No 332
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=66.40 E-value=14 Score=30.79 Aligned_cols=52 Identities=19% Similarity=0.226 Sum_probs=43.5
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccc-cccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVS-KYYV 106 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s-~~l~ 106 (210)
+++--+|||+.++. +|-.++-.|-.|.++||++-.. +-.|.|..|..+ +.|.
T Consensus 24 r~IKgeeIA~~l~r----npGTVRNqmq~LkaLgLVegvp---GPkGGY~PT~kAYe~L~ 76 (294)
T COG2524 24 RPIKGEEIAEVLNR----NPGTVRNQMQSLKALGLVEGVP---GPKGGYKPTSKAYEALS 76 (294)
T ss_pred CCcchHHHHHHHcc----CcchHHHHHHHHHhcCcccccc---CCCCCccccHHHHHHhc
Confidence 68889999999999 9999999999999999998763 246789888755 3443
No 333
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=66.38 E-value=9 Score=29.25 Aligned_cols=48 Identities=10% Similarity=0.151 Sum_probs=41.2
Q ss_pred HHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 27 MAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 27 ~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
++......-.||+.|.. +-+|.+||.+..|- +. .+-|.+|-..|+++.
T Consensus 12 ~~f~s~~~kkV~~~Ls~----~W~T~~El~e~~G~----d~---~~~L~~LkK~gLiE~ 59 (160)
T PF09824_consen 12 QTFNSEVYKKVYDELSK----GWMTEEELEEKYGK----DV---RESLLILKKGGLIES 59 (160)
T ss_pred HHhCCHHHHHHHHHHHh----ccCCHHHHHHHHCc----CH---HHHHHHHHHcCchhh
Confidence 44555667789999998 79999999999999 76 788999999999984
No 334
>KOG0820 consensus Ribosomal RNA adenine dimethylase [RNA processing and modification]
Probab=66.36 E-value=8.5 Score=32.38 Aligned_cols=32 Identities=16% Similarity=0.279 Sum_probs=26.0
Q ss_pred HHHHHHhCCCCCCCCeEEEecCCccHHHHhhhC
Q 036188 178 MSNILESYKGFDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 178 ~~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
+..+++..+ ......|+.||+|+|.+...+++
T Consensus 47 ~~~I~~ka~-~k~tD~VLEvGPGTGnLT~~lLe 78 (315)
T KOG0820|consen 47 IDQIVEKAD-LKPTDVVLEVGPGTGNLTVKLLE 78 (315)
T ss_pred HHHHHhccC-CCCCCEEEEeCCCCCHHHHHHHH
Confidence 345666666 77889999999999999988764
No 335
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=66.27 E-value=7.2 Score=32.01 Aligned_cols=59 Identities=15% Similarity=0.154 Sum_probs=49.3
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhc---ccceeeeccCCCcccceecccccccccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLAS---YSVVECSLDASGARRLYSLNSVSKYYVP 107 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~---~gl~~~~~~~~~~~~~y~~t~~s~~l~~ 107 (210)
++.+|..+.+ ..|...-|+++++ .+..+.+-++.|.. .-||.+. ...+.+|+.++.|..
T Consensus 5 ~l~~f~~v~~-----~gs~s~AA~~L~i----sqpavS~~I~~LE~~lG~~LF~R~------~r~~~lT~~G~~l~~ 66 (275)
T PRK03601 5 LLKTFLEVSR-----TRHFGRAAESLYL----TQSAVSFRIRQLENQLGVNLFTRH------RNNIRLTAAGERLLP 66 (275)
T ss_pred HHHHHHHHHH-----cCCHHHHHHHhCC----ChHHHHHHHHHHHHHhCCceEEEC------CCceEECHhHHHHHH
Confidence 4678889988 4499999999999 99999998888866 4589986 678999999987764
No 336
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=66.09 E-value=6.3 Score=28.85 Aligned_cols=40 Identities=20% Similarity=0.246 Sum_probs=26.8
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
|+++|.. +.|+++|.+.|++ ||-.|.++-+......-+..
T Consensus 16 i~eAlrr-----G~sveeI~e~T~I----D~wFL~~i~~Iv~~e~~L~~ 55 (123)
T PF02787_consen 16 IAEALRR-----GYSVEEIHELTKI----DPWFLEQIKNIVDMEKELKE 55 (123)
T ss_dssp HHHHHHT-----TB-HHHHHHHH-------HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHc-----CCCHHHHHHHHCc----cHHHHHHHHHHHHHHHHHHH
Confidence 3455544 7899999999999 99999998877665555543
No 337
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=66.07 E-value=6.9 Score=35.96 Aligned_cols=36 Identities=8% Similarity=0.110 Sum_probs=33.6
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeec
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSL 87 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~ 87 (210)
...|++|||+.+.+ .+|.++.+|+.|...|.++-..
T Consensus 22 ~~~~l~~la~~l~c----s~R~~~~~l~~~~~~gwl~w~~ 57 (552)
T PRK13626 22 QETTLNELAELLNC----SRRHMRTLLNTMQQRGWLTWQA 57 (552)
T ss_pred ceeeHHHHHHHhcC----ChhHHHHHHHHHHHCCCeeeec
Confidence 47899999999999 9999999999999999999763
No 338
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=66.06 E-value=6.6 Score=33.70 Aligned_cols=35 Identities=26% Similarity=0.295 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.++|=+|||+++|+ ....+.|+|..+...|+++-.
T Consensus 25 ~gltQ~eIA~~Lgi----SR~~v~rlL~~Ar~~GiV~I~ 59 (321)
T COG2390 25 EGLTQSEIAERLGI----SRATVSRLLAKAREEGIVKIS 59 (321)
T ss_pred cCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCeEEEE
Confidence 38999999999999 999999999999999999854
No 339
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=65.87 E-value=10 Score=22.68 Aligned_cols=34 Identities=24% Similarity=0.216 Sum_probs=26.5
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHH
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLL 77 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L 77 (210)
.-|...+.. ..|..++|+.+|+ +..-+.|+++..
T Consensus 18 ~~i~~~~~~-----~~s~~~vA~~~~v----s~~TV~ri~~~~ 51 (52)
T PF13542_consen 18 QYILKLLRE-----SRSFKDVARELGV----SWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHhh-----cCCHHHHHHHHCC----CHHHHHHHHHhh
Confidence 345555554 4799999999999 999999998753
No 340
>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=65.74 E-value=4.1 Score=36.15 Aligned_cols=30 Identities=13% Similarity=0.056 Sum_probs=21.6
Q ss_pred HHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 179 SNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 179 ~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..++..++ .....+|+|+|+|+|..+..++
T Consensus 228 ~~~~~~L~-~~~g~~VLDlcag~G~kt~~la 257 (426)
T TIGR00563 228 QWVATWLA-PQNEETILDACAAPGGKTTHIL 257 (426)
T ss_pred HHHHHHhC-CCCCCeEEEeCCCccHHHHHHH
Confidence 34444455 5566899999999998877654
No 341
>KOG4589 consensus Cell division protein FtsJ [Cell cycle control, cell division, chromosome partitioning]
Probab=65.72 E-value=8.4 Score=30.65 Aligned_cols=26 Identities=19% Similarity=0.295 Sum_probs=19.8
Q ss_pred HhCCCCCCCCeEEEecCCccHHHHhh
Q 036188 183 ESYKGFDNIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 183 ~~~~~~~~~~~vvDiGGg~G~~~~~l 208 (210)
+.|.-+....+|+|||+.+|.++...
T Consensus 62 dKy~~l~p~~~VlD~G~APGsWsQVa 87 (232)
T KOG4589|consen 62 DKYRFLRPEDTVLDCGAAPGSWSQVA 87 (232)
T ss_pred hhccccCCCCEEEEccCCCChHHHHH
Confidence 34542567799999999999998754
No 342
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=65.65 E-value=10 Score=29.76 Aligned_cols=43 Identities=19% Similarity=0.133 Sum_probs=36.9
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+.+.|... +..|+.+||+++|+ +..-+.|.|--|...|.+...
T Consensus 18 ~~~~l~~~---~~~~a~~i~~~l~~----~k~~vNr~LY~l~~~~~v~~~ 60 (183)
T PHA03103 18 EVKNLGLG---EGITAIEISRKLNI----EKSEVNKQLYKLQREGMVYMS 60 (183)
T ss_pred HHHHhccC---CCccHHHHHHHhCC----CHHHHHHHHHHHHhcCceecC
Confidence 45566653 69999999999999 999999999999999998765
No 343
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=65.28 E-value=8.8 Score=30.78 Aligned_cols=35 Identities=14% Similarity=0.180 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.+.|.++||+++++ .+.-++..++.|+..|++.+.
T Consensus 177 ~g~s~~eIA~~l~i----S~~Tv~~~~~~~~~~~~~~~~ 211 (239)
T PRK10430 177 YEFSTDELANAVNI----SRVSCRKYLIWLVNCHILFTS 211 (239)
T ss_pred CCcCHHHHHHHhCc----hHHHHHHHHHHHHhCCEEEEE
Confidence 48899999999999 999999999999999999654
No 344
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=65.19 E-value=9.5 Score=32.94 Aligned_cols=47 Identities=6% Similarity=0.015 Sum_probs=38.0
Q ss_pred CCCCHHHHHHH--hcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccc
Q 036188 48 TKLSASDIAAQ--LLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVS 102 (210)
Q Consensus 48 ~~~t~~eLA~~--~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s 102 (210)
+|.+..+||+. +++ ++.-+++-|..|...|++++.. ....+-.|..+
T Consensus 24 ~pv~s~~l~~~~~l~~----S~aTIR~dm~~Le~~G~l~~~h----~sagrIPT~kG 72 (339)
T PRK00082 24 EPVGSKTLSKRYGLGV----SSATIRNDMADLEELGLLEKPH----TSSGRIPTDKG 72 (339)
T ss_pred CCcCHHHHHHHhCCCC----ChHHHHHHHHHHHhCCCcCCCc----CCCCCCcCHHH
Confidence 79999999977 888 9999999999999999999763 23334455444
No 345
>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=65.06 E-value=9.5 Score=30.66 Aligned_cols=41 Identities=17% Similarity=0.176 Sum_probs=36.8
Q ss_pred CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 51 SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 51 t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
|-.|||++.|+ +..-+++-|+.|+..|++.+.. +.|.|-..
T Consensus 26 sE~eLa~~~gV----SR~TVR~Al~~L~~eGli~r~~----G~GTfV~~ 66 (233)
T TIGR02404 26 SEHELMDQYGA----SRETVRKALNLLTEAGYIQKIQ----GKGSIVLN 66 (233)
T ss_pred CHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEeC----CceEEEec
Confidence 67899999999 9999999999999999999885 67888754
No 346
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=65.06 E-value=16 Score=24.18 Aligned_cols=53 Identities=21% Similarity=0.295 Sum_probs=44.9
Q ss_pred HHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 27 MAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 27 ~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.++....++.|...|.+. .+.++.+|+..++. +...+.+-|..|...|+++..
T Consensus 20 ~~l~~~~r~~il~~l~~~---~~~~~~~l~~~~~~----~~~~v~~hL~~L~~~glv~~~ 72 (110)
T COG0640 20 KALADPTRLEILSLLAEG---GELTVGELAEALGL----SQSTVSHHLKVLREAGLVELR 72 (110)
T ss_pred HHhCCHHHHHHHHHHHhc---CCccHHHHHHHHCC----ChhHHHHHHHHHHHCCCeEEE
Confidence 355555778888888773 27899999999999 999999999999999999875
No 347
>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=64.89 E-value=8 Score=26.09 Aligned_cols=32 Identities=13% Similarity=0.080 Sum_probs=26.2
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHH
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRIL 74 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlL 74 (210)
..|.+.|.. | ..|+.|||+.+|+ ...-+.|.|
T Consensus 9 ~~I~e~l~~-~---~~ti~dvA~~~gv----S~~TVsr~L 40 (80)
T TIGR02844 9 LEIGKYIVE-T---KATVRETAKVFGV----SKSTVHKDV 40 (80)
T ss_pred HHHHHHHHH-C---CCCHHHHHHHhCC----CHHHHHHHh
Confidence 346677877 4 8999999999999 888888755
No 348
>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=64.89 E-value=4 Score=31.49 Aligned_cols=22 Identities=18% Similarity=0.255 Sum_probs=17.3
Q ss_pred CCCCCeEEEecCCccHHHHhhh
Q 036188 188 FDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
..+.++|+++|+|.|..++.++
T Consensus 43 ~~~~~~VLELGaG~Gl~gi~~a 64 (173)
T PF10294_consen 43 LFRGKRVLELGAGTGLPGIAAA 64 (173)
T ss_dssp GTTTSEEEETT-TTSHHHHHHH
T ss_pred hcCCceEEEECCccchhHHHHH
Confidence 3467899999999999888764
No 349
>PLN02672 methionine S-methyltransferase
Probab=64.79 E-value=3.7 Score=40.81 Aligned_cols=19 Identities=26% Similarity=0.251 Sum_probs=16.8
Q ss_pred CCeEEEecCCccHHHHhhh
Q 036188 191 IKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 191 ~~~vvDiGGg~G~~~~~l~ 209 (210)
..+|+|||||+|.+++.++
T Consensus 119 ~~~VLDlG~GSG~Iai~La 137 (1082)
T PLN02672 119 DKTVAELGCGNGWISIAIA 137 (1082)
T ss_pred CCEEEEEecchHHHHHHHH
Confidence 3589999999999999875
No 350
>KOG3045 consensus Predicted RNA methylase involved in rRNA processing [RNA processing and modification]
Probab=64.32 E-value=11 Score=31.46 Aligned_cols=55 Identities=13% Similarity=0.138 Sum_probs=33.8
Q ss_pred hhHhhccCchHHHHHHHHHh----hhhhhhHHHHHHhCCCCCCCCeEEEecCCccHHHH
Q 036188 152 IFEYAGLNPRFNKHFNAAMY----NYTSLVMSNILESYKGFDNIKQLVDVGGSLGVTLQ 206 (210)
Q Consensus 152 ~fe~l~~~p~~~~~f~~~M~----~~~~~~~~~~l~~~~~~~~~~~vvDiGGg~G~~~~ 206 (210)
-+..+.+||+.-+.|+++.+ .+-......|++.+..-++...|-|+|||.+.++.
T Consensus 138 A~~lfkedp~afdlYH~gfr~QV~kWP~nPld~ii~~ik~r~~~~vIaD~GCGEakiA~ 196 (325)
T KOG3045|consen 138 AFDLFKEDPTAFDLYHAGFRSQVKKWPENPLDVIIRKIKRRPKNIVIADFGCGEAKIAS 196 (325)
T ss_pred HHHHHhcCcHHHHHHHHHHHHHHHhCCCChHHHHHHHHHhCcCceEEEecccchhhhhh
Confidence 34555677776555555443 23233345555554323467889999999998874
No 351
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=64.31 E-value=7.7 Score=32.00 Aligned_cols=68 Identities=10% Similarity=0.057 Sum_probs=44.2
Q ss_pred hhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccccccCCCCCChHHH
Q 036188 38 FEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYVPNKDGVLLGPL 117 (210)
Q Consensus 38 fd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~~~~~~~~~~~~ 117 (210)
.+.|.++. ..+.|+++||+++++ +++.+.|+.+-...+.+...- ..+++..+-..|...+ .++..+
T Consensus 192 ~~~I~~~~-~~~~sl~~lA~~~~~----S~~~l~r~Fk~~~G~t~~~yi-------~~~Rl~~A~~lL~~t~--~sI~eI 257 (287)
T TIGR02297 192 NFLIEENY-KQHLRLPEYADRLGI----SESRLNDICRRFSALSPKRLI-------IERVMQEARRLLLFTQ--HSINQI 257 (287)
T ss_pred HHHHHHhh-ccCCCHHHHHHHHCC----CHHHHHHHHHHHhCCCHHHHH-------HHHHHHHHHHHHHcCC--CCHHHH
Confidence 34555432 258999999999999 999999999988776655432 3345555444454332 245555
Q ss_pred HH
Q 036188 118 IQ 119 (210)
Q Consensus 118 ~~ 119 (210)
..
T Consensus 258 A~ 259 (287)
T TIGR02297 258 AY 259 (287)
T ss_pred HH
Confidence 43
No 352
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=64.27 E-value=7.5 Score=25.40 Aligned_cols=61 Identities=18% Similarity=0.298 Sum_probs=40.4
Q ss_pred hHHhhcCCCCCCCHHHHHHHhcCC----CCCCcccHHHHHHHHhcccceeeeccC---CCcccceecccccc
Q 036188 39 EILDKAGPGTKLSASDIAAQLLTK----NKDAPMMLDRILRLLASYSVVECSLDA---SGARRLYSLNSVSK 103 (210)
Q Consensus 39 d~L~~~g~~~~~t~~eLA~~~~~~----~~~~~~~l~rlLr~L~~~gl~~~~~~~---~~~~~~y~~t~~s~ 103 (210)
-.|.. +|++--||.+.+.-. -.+++..+...|+-|...|+++..... +-..-.|++|+.++
T Consensus 3 ~~L~~----~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~ 70 (75)
T PF03551_consen 3 GLLSE----GPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGR 70 (75)
T ss_dssp HHHHH----S-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHH
T ss_pred hhhcc----CCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHH
Confidence 34555 588888888876530 022677899999999999999866311 00122488888775
No 353
>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=64.18 E-value=11 Score=25.78 Aligned_cols=39 Identities=21% Similarity=0.214 Sum_probs=31.9
Q ss_pred HHHhhChhh-HHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHh
Q 036188 31 AVYELGIFE-ILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLA 78 (210)
Q Consensus 31 ~a~~lglfd-~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~ 78 (210)
.+-++.|+. .|.+ +.|..|||+.+|+ +.--+.|.=|.|.
T Consensus 35 l~~R~~va~~lL~~-----g~syreIa~~tgv----S~aTItRvsr~Lk 74 (87)
T PF01371_consen 35 LAQRWQVAKELLDE-----GKSYREIAEETGV----SIATITRVSRCLK 74 (87)
T ss_dssp HHHHHHHHHHHHHT-----TSSHHHHHHHHTS----THHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHC-----CCCHHHHHHHhCC----CHHHHHHHHHHHH
Confidence 456788998 6765 8999999999999 8888888777765
No 354
>PF14557 AphA_like: Putative AphA-like transcriptional regulator
Probab=64.07 E-value=16 Score=28.26 Aligned_cols=70 Identities=13% Similarity=0.160 Sum_probs=50.8
Q ss_pred HHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcC-----CCCCCcccHHHHHHHHhcccceeeeccCC-Ccccceeccccc
Q 036188 29 IQAVYELGIFEILDKAGPGTKLSASDIAAQLLT-----KNKDAPMMLDRILRLLASYSVVECSLDAS-GARRLYSLNSVS 102 (210)
Q Consensus 29 l~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~-----~~~~~~~~l~rlLr~L~~~gl~~~~~~~~-~~~~~y~~t~~s 102 (210)
-+-++++++.-.|++ +|.+++++|+.+.- --| ....+.--+..|...|+++-.++.+ +..-.|..|+.+
T Consensus 8 pre~v~L~vLG~la~----~p~~~~~va~~vrh~~sr~~gp-s~~Ll~~sie~Lr~eGlve~~~g~g~e~~a~l~iT~~G 82 (175)
T PF14557_consen 8 PREAVRLCVLGTLAR----GPRRYEEVAGAVRHFASRIWGP-SLDLLGTSIELLREEGLVEAVDGEGMEDNALLAITDAG 82 (175)
T ss_pred HHHHHHHHHHHHHhc----CCcCHHHHHHHHHHhccccccC-chhhhhhHHHHHHhcCCcccccccCCCccceeeeCcch
Confidence 345777888778888 79999999998742 001 6778999999999999999763222 123458888766
Q ss_pred c
Q 036188 103 K 103 (210)
Q Consensus 103 ~ 103 (210)
+
T Consensus 83 r 83 (175)
T PF14557_consen 83 R 83 (175)
T ss_pred H
Confidence 4
No 355
>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=63.83 E-value=11 Score=30.34 Aligned_cols=45 Identities=11% Similarity=0.161 Sum_probs=38.6
Q ss_pred CCC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 48 TKL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 48 ~~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
..+ |-.|||++.|+ +..-+++-|..|+..|++.+.. +.|.|-..+
T Consensus 30 ~~LPsE~eLa~~~~V----SR~TvR~Al~~L~~eGli~r~~----G~GtfV~~~ 75 (238)
T TIGR02325 30 DYLPAEMQLAERFGV----NRHTVRRAIAALVERGLLRAEQ----GRGTFVAAR 75 (238)
T ss_pred CcCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEec----CCEEEECCC
Confidence 344 77899999999 9999999999999999999875 678888644
No 356
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=63.79 E-value=10 Score=24.49 Aligned_cols=28 Identities=25% Similarity=0.382 Sum_probs=24.8
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLAS 79 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~ 79 (210)
.++|+.|.|+.+|+ ++..+.++++....
T Consensus 12 ~~~s~~~Aa~~lG~----~~~~v~~wv~~fR~ 39 (65)
T PF05344_consen 12 QQISVAQAADRLGT----DPGTVRRWVRMFRQ 39 (65)
T ss_pred ccccHHHHHHHHCc----CHHHHHHHHHHHHH
Confidence 49999999999999 99999999887653
No 357
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=63.32 E-value=7.6 Score=33.08 Aligned_cols=35 Identities=11% Similarity=0.166 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHH-HHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILR-LLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr-~L~~~gl~~~~ 86 (210)
++.+++.||+.+|. ++..+..+++ .|...|++.+.
T Consensus 275 ~~~~~~~~a~~lg~----~~~~~~~~~e~~Li~~~li~~~ 310 (328)
T PRK00080 275 GPVGLDTLAAALGE----ERDTIEDVYEPYLIQQGFIQRT 310 (328)
T ss_pred CceeHHHHHHHHCC----CcchHHHHhhHHHHHcCCcccC
Confidence 79999999999999 9999999999 99999999865
No 358
>PF13551 HTH_29: Winged helix-turn helix
Probab=63.15 E-value=8.5 Score=26.71 Aligned_cols=30 Identities=17% Similarity=0.168 Sum_probs=27.4
Q ss_pred CC-CHHHHHHHhcCCCCCCcccHHHHHHHHhcccc
Q 036188 49 KL-SASDIAAQLLTKNKDAPMMLDRILRLLASYSV 82 (210)
Q Consensus 49 ~~-t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl 82 (210)
+. |+.++|+.+|+ +++-+.++++.....|+
T Consensus 11 g~~~~~~ia~~lg~----s~~Tv~r~~~~~~~~G~ 41 (112)
T PF13551_consen 11 GVSTIAEIARRLGI----SRRTVYRWLKRYREGGI 41 (112)
T ss_pred CCCcHHHHHHHHCc----CHHHHHHHHHHHHcccH
Confidence 44 69999999999 99999999999999883
No 359
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=63.10 E-value=11 Score=25.43 Aligned_cols=41 Identities=17% Similarity=0.110 Sum_probs=28.0
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHH
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRL 76 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~ 76 (210)
...|++.|.+.+.|.-.|..+||+.+|. +. .++.+.+.|+.
T Consensus 4 ~~~V~~~l~~IP~G~v~TYg~iA~~~g~-p~-~~RaVg~al~~ 44 (80)
T TIGR00589 4 QQRVWQALRTIPYGETKSYGQLAARIGN-PK-AVRAVGGANGR 44 (80)
T ss_pred HHHHHHHHhCCCCCCcCCHHHHHHHhCC-CC-hHHHHHHHHHh
Confidence 4457778877766788999999999997 10 33444444433
No 360
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=62.97 E-value=5.1 Score=35.69 Aligned_cols=29 Identities=10% Similarity=0.012 Sum_probs=21.0
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.+...++ .....+|+|+|+|+|..+..++
T Consensus 243 l~~~~l~-~~~g~~VLDl~ag~G~kt~~la 271 (434)
T PRK14901 243 LVAPLLD-PQPGEVILDACAAPGGKTTHIA 271 (434)
T ss_pred HHHHHhC-CCCcCEEEEeCCCCchhHHHHH
Confidence 3334444 5566899999999999887664
No 361
>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=62.84 E-value=15 Score=25.19 Aligned_cols=35 Identities=26% Similarity=0.338 Sum_probs=28.6
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHh
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLA 78 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~ 78 (210)
..|+..+.. +.|..+||+.+|+ +..-+.|+.|.+.
T Consensus 41 ~~I~~ll~~-----G~S~~eIA~~LgI----SrsTIyRi~R~~n 75 (88)
T TIGR02531 41 LQVAKMLKQ-----GKTYSDIEAETGA----STATISRVKRCLN 75 (88)
T ss_pred HHHHHHHHC-----CCCHHHHHHHHCc----CHHHHHHHHHhcc
Confidence 566777765 6899999999999 9999999876533
No 362
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=62.65 E-value=11 Score=30.52 Aligned_cols=42 Identities=14% Similarity=0.196 Sum_probs=38.3
Q ss_pred CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 51 SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 51 t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
|-.|||++.++ +..-+++=|+.|+..|++.+.. +.|.|-..+
T Consensus 33 sE~eLa~~f~V----SR~TvRkAL~~L~~eGli~r~~----G~GtfV~~~ 74 (236)
T COG2188 33 SERELAEQFGV----SRMTVRKALDELVEEGLIVRRQ----GKGTFVASP 74 (236)
T ss_pred CHHHHHHHHCC----cHHHHHHHHHHHHHCCcEEEEe----cCeeEEcCc
Confidence 55699999999 9999999999999999999875 688999887
No 363
>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=62.43 E-value=9.8 Score=26.80 Aligned_cols=35 Identities=20% Similarity=0.137 Sum_probs=32.6
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.-+|.+++++.+|+ ++..+.+-+..|..+|++...
T Consensus 53 d~Is~sq~~e~tg~----~~~~V~~al~~Li~~~vI~~~ 87 (100)
T PF04492_consen 53 DRISNSQIAEMTGL----SRDHVSKALNELIRRGVIIRD 87 (100)
T ss_pred ceeeHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeC
Confidence 36899999999999 999999999999999999775
No 364
>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=62.11 E-value=6 Score=23.64 Aligned_cols=11 Identities=27% Similarity=0.226 Sum_probs=7.6
Q ss_pred CHHHHHHHhcC
Q 036188 51 SASDIAAQLLT 61 (210)
Q Consensus 51 t~~eLA~~~~~ 61 (210)
|+.|||+.+|+
T Consensus 1 Ti~dIA~~agv 11 (46)
T PF00356_consen 1 TIKDIAREAGV 11 (46)
T ss_dssp CHHHHHHHHTS
T ss_pred CHHHHHHHHCc
Confidence 46677777776
No 365
>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=62.06 E-value=8.4 Score=23.17 Aligned_cols=24 Identities=25% Similarity=0.296 Sum_probs=19.1
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
..+|..|+|+++|+ ++..+.++.+
T Consensus 8 ~gls~~~la~~~gi----s~~~i~~~~~ 31 (55)
T PF01381_consen 8 KGLSQKELAEKLGI----SRSTISRIEN 31 (55)
T ss_dssp TTS-HHHHHHHHTS-----HHHHHHHHT
T ss_pred cCCCHHHHHHHhCC----CcchhHHHhc
Confidence 58999999999999 8888887764
No 366
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=62.03 E-value=9.2 Score=32.68 Aligned_cols=35 Identities=17% Similarity=0.260 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
..+|=+|||+++|+ +...+.|+|......|+++-.
T Consensus 28 ~g~tQ~eIA~~lgi----SR~~VsRlL~~Ar~~GiV~I~ 62 (318)
T PRK15418 28 DGLTQSEIGERLGL----TRLKVSRLLEKGRQSGIIRVQ 62 (318)
T ss_pred cCCCHHHHHHHhCC----CHHHHHHHHHHHHHcCcEEEE
Confidence 38899999999999 999999999999999999743
No 367
>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=61.91 E-value=7.7 Score=22.66 Aligned_cols=27 Identities=11% Similarity=0.156 Sum_probs=21.1
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHHHHhccccee
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVE 84 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~ 84 (210)
+|+.|+|+.+|+ +++.++++ ...|++.
T Consensus 1 ~~~~e~a~~~gv----~~~tlr~~----~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTGV----SPSTLRYY----ERIGLLS 27 (49)
T ss_pred CcHHHHHHHHCc----CHHHHHHH----HHCCCCC
Confidence 478999999999 88876655 5667665
No 368
>PF12728 HTH_17: Helix-turn-helix domain
Probab=61.62 E-value=7.8 Score=23.11 Aligned_cols=22 Identities=23% Similarity=0.229 Sum_probs=19.4
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
+|++|+|+.+|+ ++..+.++++
T Consensus 2 lt~~e~a~~l~i----s~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGI----SRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCc----CHHHHHHHHH
Confidence 589999999999 9998888875
No 369
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=61.43 E-value=23 Score=23.55 Aligned_cols=42 Identities=19% Similarity=0.124 Sum_probs=28.0
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccc
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSV 82 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl 82 (210)
.|.+.+.+.+.|.-.|..+||+.+|. + ...+.+-.+|..+.+
T Consensus 4 ~V~~~v~~IP~G~v~TYg~iA~~~g~----p-~~~R~Vg~al~~np~ 45 (79)
T cd06445 4 RVWEALRQIPYGEVTTYGQIAKLAGT----P-KAARAVGSALARNPI 45 (79)
T ss_pred HHHHHHhcCCCCCcCcHHHHHHHHCC----C-CcHHHHHHHHHhCCC
Confidence 35666666666678999999999999 4 344444444444443
No 370
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=61.42 E-value=9.2 Score=31.08 Aligned_cols=46 Identities=22% Similarity=0.241 Sum_probs=41.7
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVS 102 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s 102 (210)
+-+|+.|+|+..++ +|..++.++--|...|++++. ..|.|-..++-
T Consensus 29 kiiTirdvae~~ev----~~n~lr~lasrLekkG~LeRi-----~rG~YlI~~lp 74 (269)
T COG5340 29 KIITIRDVAETLEV----APNTLRELASRLEKKGWLERI-----LRGRYLIIPLP 74 (269)
T ss_pred ceEEeHHhhhhccC----CHHHHHHHHhhhhhcchhhhh-----cCccEEEeecC
Confidence 47999999999999 999999999999999999998 68999877653
No 371
>PRK14903 16S rRNA methyltransferase B; Provisional
Probab=61.34 E-value=6 Score=35.29 Aligned_cols=44 Identities=9% Similarity=0.024 Sum_probs=26.4
Q ss_pred HHHHHHhhhhhhhHHHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 165 HFNAAMYNYTSLVMSNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 165 ~f~~~M~~~~~~~~~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.|..+....+......+....+ .....+|+|+|+|+|..+..++
T Consensus 213 ~~~~G~~~~Qd~~s~~~~~~l~-~~~g~~VLD~cagpGgkt~~la 256 (431)
T PRK14903 213 VIKDGLATVQGESSQIVPLLME-LEPGLRVLDTCAAPGGKTTAIA 256 (431)
T ss_pred HHHCCeEEEECHHHHHHHHHhC-CCCCCEEEEeCCCccHHHHHHH
Confidence 4554444333333333333344 5567799999999998776554
No 372
>PRK14904 16S rRNA methyltransferase B; Provisional
Probab=61.08 E-value=6.5 Score=35.15 Aligned_cols=51 Identities=14% Similarity=0.308 Sum_probs=31.5
Q ss_pred HHHHHHHhhChhhHHhhcC-CCCCCCH---HHHHHHhcCCCCCCcccHHHHHHHHhcc
Q 036188 27 MAIQAVYELGIFEILDKAG-PGTKLSA---SDIAAQLLTKNKDAPMMLDRILRLLASY 80 (210)
Q Consensus 27 ~al~~a~~lglfd~L~~~g-~~~~~t~---~eLA~~~~~~~~~~~~~l~rlLr~L~~~ 80 (210)
..++++.++++++++-... | ....+ -+||++.+- +.....+.-+||-+...
T Consensus 74 ~~~r~iLrla~~ell~~~~~p-~~a~vneaVelak~~~~--~~~~~fVNgVLr~i~~~ 128 (445)
T PRK14904 74 PVLKNILRLGVYQLLFLDRVP-RWAAVNECVKLARKYKG--EHMAKLVNGVLRNISPE 128 (445)
T ss_pred HHHHHHHHHHHHHHHhCCCCC-CeeeHHHHHHHHHHhCC--CccccchHHHHHHHHHh
Confidence 4677788888888886421 0 12333 367776644 11456788888877663
No 373
>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=61.02 E-value=12 Score=21.59 Aligned_cols=34 Identities=18% Similarity=0.048 Sum_probs=25.8
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHH
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLL 77 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L 77 (210)
.++..+.. ...|..+||+.+|+ ++..+.+++.-.
T Consensus 17 ~~~~~~~~----~~~~~~~ia~~~~~----s~~~i~~~~~~~ 50 (55)
T cd06171 17 EVILLRFG----EGLSYEEIAEILGI----SRSTVRQRLHRA 50 (55)
T ss_pred HHHHHHHh----cCCCHHHHHHHHCc----CHHHHHHHHHHH
Confidence 34544543 37899999999999 999888887653
No 374
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=60.57 E-value=13 Score=29.98 Aligned_cols=43 Identities=7% Similarity=0.112 Sum_probs=37.4
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
=|-.|||+..|+ +..-+++-|..|+..|++.+.. +.|.|-..+
T Consensus 34 PsE~eLa~~~~V----SR~TvR~Al~~L~~eGli~r~~----G~GTfV~~~ 76 (241)
T PRK11402 34 PTENELCTQYNV----SRITIRKAISDLVADGVLIRWQ----GKGTFVQSQ 76 (241)
T ss_pred cCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEec----CceeEECCC
Confidence 366899999999 9999999999999999999885 678887544
No 375
>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=60.37 E-value=12 Score=32.19 Aligned_cols=41 Identities=7% Similarity=0.101 Sum_probs=36.3
Q ss_pred HHhhcCCCCCCCHHHHHHH--hcCCCCCCcccHHHHHHHHhcccceeeec
Q 036188 40 ILDKAGPGTKLSASDIAAQ--LLTKNKDAPMMLDRILRLLASYSVVECSL 87 (210)
Q Consensus 40 ~L~~~g~~~~~t~~eLA~~--~~~~~~~~~~~l~rlLr~L~~~gl~~~~~ 87 (210)
++... +|.+..+|++. +++ .+.-++|-|..|...|++.+..
T Consensus 15 ~l~~~---~pv~s~~l~~~~~~~v----S~aTiR~d~~~Le~~G~l~~~h 57 (337)
T TIGR00331 15 YIKTG---QPVGSKTLLEKYNLGL----SSATIRNDMADLEDLGFIEKPH 57 (337)
T ss_pred HHhcC---CCcCHHHHHhhcCCCC----ChHHHHHHHHHHHHCCCccCCC
Confidence 45553 79999999999 999 9999999999999999998863
No 376
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=60.16 E-value=7.3 Score=32.20 Aligned_cols=22 Identities=18% Similarity=0.262 Sum_probs=17.9
Q ss_pred CCCCCeEEEecCCccHHHHhhh
Q 036188 188 FDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
-....+|+|+|+|+|..+..++
T Consensus 69 ~~~g~~VLDl~ag~G~kt~~la 90 (264)
T TIGR00446 69 PDPPERVLDMAAAPGGKTTQIS 90 (264)
T ss_pred CCCcCEEEEECCCchHHHHHHH
Confidence 3456789999999999887654
No 377
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=59.79 E-value=13 Score=30.49 Aligned_cols=41 Identities=24% Similarity=0.209 Sum_probs=35.8
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYS 81 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~g 81 (210)
+..|.+.|.+. +.+++.|||+.+++ .+.-++|=|+.|...+
T Consensus 9 ~~~I~~~l~~~---~~v~v~eLa~~~~V----S~~TIRRDL~~Le~~~ 49 (252)
T PRK10681 9 IGQLLQALKRS---DKLHLKDAAALLGV----SEMTIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHHHc---CCCcHHHHHHHhCC----CHHHHHHHHHHhhcCe
Confidence 45578889886 59999999999999 9999999999999654
No 378
>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=59.72 E-value=11 Score=32.68 Aligned_cols=18 Identities=17% Similarity=0.110 Sum_probs=15.7
Q ss_pred CeEEEecCCccHHHHhhh
Q 036188 192 KQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 192 ~~vvDiGGg~G~~~~~l~ 209 (210)
.+++|++||+|.+++.+.
T Consensus 199 ~~vlDl~~G~G~~sl~la 216 (353)
T TIGR02143 199 GDLLELYCGNGNFSLALA 216 (353)
T ss_pred CcEEEEeccccHHHHHHH
Confidence 369999999999998765
No 379
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=59.41 E-value=11 Score=29.17 Aligned_cols=36 Identities=25% Similarity=0.170 Sum_probs=28.1
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHh
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLA 78 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~ 78 (210)
..++...-- .+.|.+|||+.+|+ +++.++|-++.+.
T Consensus 141 ~~~v~l~~~----~Gls~~EIA~~lgi----S~~tV~r~l~~aR 176 (185)
T PF07638_consen 141 RRVVELRFF----EGLSVEEIAERLGI----SERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHH----CCCCHHHHHHHHCc----CHHHHHHHHHHHH
Confidence 334555444 48999999999999 9999998887664
No 380
>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=59.09 E-value=13 Score=22.80 Aligned_cols=34 Identities=26% Similarity=0.353 Sum_probs=23.8
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
-++.|...+.. |+ +..+||...|+ ...-+..++.
T Consensus 11 eK~~iI~~~e~----g~-s~~~ia~~fgv----~~sTv~~I~K 44 (53)
T PF04218_consen 11 EKLEIIKRLEE----GE-SKRDIAREFGV----SRSTVSTILK 44 (53)
T ss_dssp HHHHHHHHHHC----TT--HHHHHHHHT------CCHHHHHHH
T ss_pred HHHHHHHHHHc----CC-CHHHHHHHhCC----CHHHHHHHHH
Confidence 34566677765 34 99999999999 9998888875
No 381
>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=59.06 E-value=8.7 Score=30.63 Aligned_cols=25 Identities=20% Similarity=0.388 Sum_probs=18.5
Q ss_pred hCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 184 SYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 184 ~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.+| -....+++|||||.|.+...|+
T Consensus 38 aLp-~~ry~~alEvGCs~G~lT~~LA 62 (201)
T PF05401_consen 38 ALP-RRRYRRALEVGCSIGVLTERLA 62 (201)
T ss_dssp HHT-TSSEEEEEEE--TTSHHHHHHG
T ss_pred hcC-ccccceeEecCCCccHHHHHHH
Confidence 344 4567899999999999998875
No 382
>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=58.89 E-value=16 Score=22.81 Aligned_cols=35 Identities=11% Similarity=0.316 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHh---cCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQL---LTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~---~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.+++-++|..++ ++ ++.....+|..|+..|.+...
T Consensus 16 ~G~~keeLrsrl~~~~l----~~k~~~~ll~~l~~~g~l~~~ 53 (59)
T PF09106_consen 16 PGMPKEELRSRLFKPRL----PPKLFNALLEALVAEGRLKVE 53 (59)
T ss_dssp S-EEHHHHHHHCST-TS-----HCCHHHHHHHHHHTTSEEEE
T ss_pred cCcCHHHHHHHHhhccC----CHHHHHHHHHHHHHCCCeeeE
Confidence 478899999888 67 999999999999999999876
No 383
>PLN03075 nicotianamine synthase; Provisional
Probab=58.57 E-value=11 Score=31.90 Aligned_cols=22 Identities=14% Similarity=-0.108 Sum_probs=15.9
Q ss_pred HHhCCCCCCCCeEEEecCCccHH
Q 036188 182 LESYKGFDNIKQLVDVGGSLGVT 204 (210)
Q Consensus 182 l~~~~~~~~~~~vvDiGGg~G~~ 204 (210)
+..+. ..+.++|+|||||+|-+
T Consensus 116 L~~~~-~~~p~~VldIGcGpgpl 137 (296)
T PLN03075 116 LSQHV-NGVPTKVAFVGSGPLPL 137 (296)
T ss_pred HHHhh-cCCCCEEEEECCCCcHH
Confidence 44443 34789999999998833
No 384
>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=58.23 E-value=9.8 Score=25.14 Aligned_cols=31 Identities=19% Similarity=0.208 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSV 82 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl 82 (210)
...|+.|||+.+++ .+.-+-|+.+.|--.|+
T Consensus 33 ~~~si~elA~~~~v----S~sti~Rf~kkLG~~gf 63 (77)
T PF01418_consen 33 AFMSISELAEKAGV----SPSTIVRFCKKLGFSGF 63 (77)
T ss_dssp CT--HHHHHHHCTS-----HHHHHHHHHHCTTTCH
T ss_pred HHccHHHHHHHcCC----CHHHHHHHHHHhCCCCH
Confidence 36899999999999 99988887776644443
No 385
>PRK11727 23S rRNA mA1618 methyltransferase; Provisional
Probab=57.93 E-value=7.6 Score=33.30 Aligned_cols=19 Identities=16% Similarity=0.230 Sum_probs=14.7
Q ss_pred CCCeEEEecCCccHHHHhh
Q 036188 190 NIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l 208 (210)
...++||||+|+|.+..-+
T Consensus 114 ~~~~vLDIGtGag~I~~lL 132 (321)
T PRK11727 114 ANVRVLDIGVGANCIYPLI 132 (321)
T ss_pred CCceEEEecCCccHHHHHH
Confidence 5689999999998665433
No 386
>PRK04217 hypothetical protein; Provisional
Probab=57.87 E-value=14 Score=26.51 Aligned_cols=35 Identities=14% Similarity=0.174 Sum_probs=26.7
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHH
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRL 76 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~ 76 (210)
+..++..+.. ..+|.+|||+.+|+ +...+.+.++.
T Consensus 47 ereai~l~~~----eGlS~~EIAk~LGI----S~sTV~r~L~R 81 (110)
T PRK04217 47 EFEALRLVDY----EGLTQEEAGKRMGV----SRGTVWRALTS 81 (110)
T ss_pred HHHHHHHHHH----cCCCHHHHHHHHCc----CHHHHHHHHHH
Confidence 3455656655 48899999999999 98888777653
No 387
>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=57.86 E-value=12 Score=22.50 Aligned_cols=25 Identities=28% Similarity=0.251 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRL 76 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~ 76 (210)
.+.|..|||+.+|+ ++..++..+.-
T Consensus 25 ~g~s~~eIa~~l~~----s~~~v~~~l~r 49 (54)
T PF08281_consen 25 QGMSYAEIAEILGI----SESTVKRRLRR 49 (54)
T ss_dssp S---HHHHHHHCTS-----HHHHHHHHHH
T ss_pred HCcCHHHHHHHHCc----CHHHHHHHHHH
Confidence 58999999999999 99988877653
No 388
>PHA00542 putative Cro-like protein
Probab=57.83 E-value=13 Score=25.02 Aligned_cols=24 Identities=21% Similarity=0.120 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
.++|..+||+.+|+ .+..+.++.+
T Consensus 30 ~glTq~elA~~lgI----s~~tIsr~e~ 53 (82)
T PHA00542 30 AGWSQEQIADATDV----SQPTICRIYS 53 (82)
T ss_pred CCCCHHHHHHHHCc----CHHHHHHHHc
Confidence 58999999999999 8887777654
No 389
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=57.64 E-value=9.5 Score=25.86 Aligned_cols=40 Identities=18% Similarity=0.134 Sum_probs=25.5
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHH
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRL 76 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~ 76 (210)
..|.+.+.+.+.|.-.|..|||+.+|. +..++.+...|+.
T Consensus 5 ~~V~~~v~~IP~G~v~TYg~iA~~~g~--p~~ar~Vg~al~~ 44 (85)
T PF01035_consen 5 RRVWEAVRQIPYGKVTTYGEIARLLGR--PKAARAVGSALAR 44 (85)
T ss_dssp HHHHHHHTTS-TT-BEEHHHHHHHTT---TTCHHHHHHHHHT
T ss_pred HHHHHHHHcCCCCceEeHHHHHHHHhh--cccHHHHHHHhcc
Confidence 345666666666678999999999994 1166666555544
No 390
>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=57.56 E-value=16 Score=34.79 Aligned_cols=58 Identities=29% Similarity=0.417 Sum_probs=40.8
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
|.+.|.+.. +.|++..+|++++++....+...+.+.|+.|...|.+.+. ..+.|....
T Consensus 7 il~~l~~~~-~~~~~~~~l~~~l~~~~~~~~~~l~~~l~~l~~~g~l~~~-----~~~~~~~~~ 64 (709)
T TIGR02063 7 ILEFLKSKK-GKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKN-----RRGLYALPE 64 (709)
T ss_pred HHHHHHhCC-CCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEc-----CCceEecCC
Confidence 566666421 2699999999999992111234699999999999999875 345554443
No 391
>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=57.10 E-value=11 Score=31.47 Aligned_cols=20 Identities=25% Similarity=0.403 Sum_probs=16.8
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
+..+++|||-|.|.....+.
T Consensus 94 ~~~~lLDlGAGdG~VT~~l~ 113 (265)
T PF05219_consen 94 KDKSLLDLGAGDGEVTERLA 113 (265)
T ss_pred cCCceEEecCCCcHHHHHHH
Confidence 46789999999999887664
No 392
>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=57.04 E-value=7.4 Score=23.76 Aligned_cols=33 Identities=24% Similarity=0.423 Sum_probs=21.8
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHH
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDR 72 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~r 72 (210)
+.+.+.|.+.|. .-+|..+||+.+|+ ++..+++
T Consensus 15 ~r~L~~l~~~G~-~~vSS~~La~~~gi----~~~qVRK 47 (50)
T PF06971_consen 15 LRYLEQLKEEGV-ERVSSQELAEALGI----TPAQVRK 47 (50)
T ss_dssp HHHHHHHHHTT--SEE-HHHHHHHHTS-----HHHHHH
T ss_pred HHHHHHHHHcCC-eeECHHHHHHHHCC----CHHHhcc
Confidence 344555665432 36899999999999 8887765
No 393
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=56.96 E-value=12 Score=32.14 Aligned_cols=45 Identities=20% Similarity=0.400 Sum_probs=36.9
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|+++|.++| +.++-..+|..++++ +...+.+.|+.|...+++.+.
T Consensus 89 vy~~I~~ag-~~GIw~~~i~~~t~l----~~~~~~k~lk~Le~k~lIK~v 133 (327)
T PF05158_consen 89 VYQLIEEAG-NKGIWTKDIKKKTNL----HQTQLTKILKSLESKKLIKSV 133 (327)
T ss_dssp HHHHHHHHT-TT-EEHHHHHHHCT------HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHhC-CCCCcHHHHHHHcCC----CHHHHHHHHHHHHhCCCEEEe
Confidence 566777766 378999999999999 999999999999999999875
No 394
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=56.77 E-value=17 Score=24.13 Aligned_cols=30 Identities=20% Similarity=0.293 Sum_probs=20.9
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHH
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRIL 74 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlL 74 (210)
|-+.+.+ ...|-.|+|+.+|+ ++..+.+++
T Consensus 23 i~~~~~~----~~ltQ~e~A~~lgi----sq~~vS~l~ 52 (80)
T PF13744_consen 23 IRELREE----RGLTQAELAERLGI----SQPRVSRLE 52 (80)
T ss_dssp HHHHHHC----CT--HHHHHHHHTS-----HHHHHHHH
T ss_pred HHHHHHH----cCCCHHHHHHHHCC----ChhHHHHHH
Confidence 6666766 68999999999999 666665555
No 395
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=56.75 E-value=12 Score=27.76 Aligned_cols=45 Identities=11% Similarity=-0.032 Sum_probs=34.1
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
-+-.-+|.+.++. +-+++.|+|+.+++ -+..+..|| ...|++.+.
T Consensus 33 PKv~f~D~v~~~~--gli~~re~AK~lki----ge~~l~~~L---~e~~~l~~~ 77 (135)
T COG3645 33 PKVEFADAVVEAS--GLILFRELAKLLKI----GENRLFAWL---RENKYLIKR 77 (135)
T ss_pred cchHHHHHHhcCc--cceeHHHHHHHHcc----CHHHHHHHH---HHCCEEEEc
Confidence 3455688888765 67999999999999 787666555 467777765
No 396
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=56.71 E-value=13 Score=29.23 Aligned_cols=43 Identities=16% Similarity=0.195 Sum_probs=31.9
Q ss_pred HHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHH-HHHhcccc
Q 036188 31 AVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRIL-RLLASYSV 82 (210)
Q Consensus 31 ~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlL-r~L~~~gl 82 (210)
+-.|..|+..+++ +.|..|||+++++ +++-++..+ +.+..+|+
T Consensus 135 SpRErEVLrLLAq-----GkTnKEIAe~L~I----S~rTVkth~srImkKLgV 178 (198)
T PRK15201 135 SVTERHLLKLIAS-----GYHLSETAALLSL----SEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CHHHHHHHHHHHC-----CCCHHHHHHHhCC----CHHHHHHHHHHHHHHhCC
Confidence 4567889999987 8999999999999 888665544 33334443
No 397
>PRK13558 bacterio-opsin activator; Provisional
Probab=56.63 E-value=11 Score=35.26 Aligned_cols=46 Identities=20% Similarity=0.235 Sum_probs=36.9
Q ss_pred hchHHHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHH
Q 036188 22 GVVLPMAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLL 77 (210)
Q Consensus 22 ~~~~~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L 77 (210)
-..+-.+|.+|++.|-|+. + ...|.+|||+++|+ .+.-+...||..
T Consensus 609 t~~q~e~l~~a~~~gyf~~-p-----r~~~~~e~a~~l~i----s~~t~~~~lr~a 654 (665)
T PRK13558 609 TDRQLTALQKAYVSGYFEW-P-----RRVEGEELAESMGI----SRSTFHQHLRAA 654 (665)
T ss_pred CHHHHHHHHHHHHcCCCCC-C-----ccCCHHHHHHHhCC----CHHHHHHHHHHH
Confidence 3445569999999999963 2 47899999999999 888777777654
No 398
>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=56.05 E-value=15 Score=26.15 Aligned_cols=51 Identities=22% Similarity=0.212 Sum_probs=38.1
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.|+.|-+.|=+. +++|+.||.+.+.-.....+.-+..+|+-|+..|+++..
T Consensus 4 ~E~~IM~~lW~~---~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~ 54 (115)
T PF03965_consen 4 LELEIMEILWES---GEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTRE 54 (115)
T ss_dssp HHHHHHHHHHHH---SSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHhC---CCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEe
Confidence 345566666565 479999999999761111477899999999999999987
No 399
>COG0421 SpeE Spermidine synthase [Amino acid transport and metabolism]
Probab=55.79 E-value=10 Score=31.95 Aligned_cols=23 Identities=30% Similarity=0.447 Sum_probs=19.8
Q ss_pred CCCCCeEEEecCCccHHHHhhhC
Q 036188 188 FDNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 188 ~~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
.++.++||=||||.|.++.++++
T Consensus 74 h~~pk~VLiiGgGdG~tlRevlk 96 (282)
T COG0421 74 HPNPKRVLIIGGGDGGTLREVLK 96 (282)
T ss_pred CCCCCeEEEECCCccHHHHHHHh
Confidence 45668999999999999999874
No 400
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=55.74 E-value=22 Score=26.09 Aligned_cols=61 Identities=15% Similarity=0.160 Sum_probs=40.9
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
.|..|-++|=.. +|.|+.||-+.+.......+.-+.-||+-|+..|++.... .++.|.-+|
T Consensus 7 aE~eVM~ilW~~---~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~k----dgr~~~y~p 67 (123)
T COG3682 7 AEWEVMEILWSR---GPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKK----DGRAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHc---CCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhh----cCCeeeeec
Confidence 344455555444 6999998888776511115667999999999999998762 234455444
No 401
>PRK14096 pgi glucose-6-phosphate isomerase; Provisional
Probab=55.47 E-value=18 Score=33.32 Aligned_cols=43 Identities=33% Similarity=0.386 Sum_probs=34.2
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhccc
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYS 81 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~g 81 (210)
-.|-..|...+ ++.|+++||+++|. +.+.+.+..+||+|++.+
T Consensus 466 ~~~~~~~~~~~--~~~~~~~~~~~~~~--~~~~~~~~~i~~~~~~n~ 508 (528)
T PRK14096 466 KKVEELLKEDG--GELSIEEIAAALGA--PEQVETIYKILRHLAANN 508 (528)
T ss_pred HHHHHHHhccC--CCCCHHHHHHHcCC--CccHHHHHHHHHHHhcCC
Confidence 44666775554 79999999999998 336678999999999873
No 402
>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=55.25 E-value=7.5 Score=22.14 Aligned_cols=26 Identities=19% Similarity=0.291 Sum_probs=18.9
Q ss_pred CHHHHHHHhcCCCCCCcccHHHHHHHHhccccee
Q 036188 51 SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVE 84 (210)
Q Consensus 51 t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~ 84 (210)
|+.|+|+.+|+ +++. ||+-...|++.
T Consensus 1 ti~e~A~~~gv----s~~t----lR~ye~~Gll~ 26 (38)
T PF00376_consen 1 TIGEVAKLLGV----SPRT----LRYYEREGLLP 26 (38)
T ss_dssp EHHHHHHHHTS-----HHH----HHHHHHTTSS-
T ss_pred CHHHHHHHHCC----CHHH----HHHHHHCCCCC
Confidence 57899999999 7775 55666678883
No 403
>COG4883 Uncharacterized protein conserved in archaea [Function unknown]
Probab=55.11 E-value=64 Score=27.70 Aligned_cols=75 Identities=21% Similarity=0.232 Sum_probs=47.5
Q ss_pred HHHHhhHHHHHhcCCchhhhhhC-CchhHhhc-cCchHHHHHHHHHhh---hhhhhHHHHHHhCCCCCCCCeEEEecCCc
Q 036188 127 LESWSQLKDAILEGGIPFNRAHG-VHIFEYAG-LNPRFNKHFNAAMYN---YTSLVMSNILESYKGFDNIKQLVDVGGSL 201 (210)
Q Consensus 127 ~~~~~~L~~~l~~g~~~f~~~~g-~~~fe~l~-~~p~~~~~f~~~M~~---~~~~~~~~~l~~~~~~~~~~~vvDiGGg~ 201 (210)
+.....|++.+|-...||-.-+. ..+.|.+. +||++.+...++... .........++.|.+|-++..|||..==.
T Consensus 69 yeil~sltdtvrpeddpfvehyqtp~ileilyeed~~f~ksv~kfie~ieksealigke~irryggfygptcvvdfal~p 148 (500)
T COG4883 69 YEILTSLTDTVRPEDDPFVEHYQTPPILEILYEEDPAFHKSVMKFIEEIEKSEALIGKESIRRYGGFYGPTCVVDFALVP 148 (500)
T ss_pred HHHHHhhhcccCCCCCchhhhccCchHHHHHHhcCHHHHHHHHHHHHHHhHHHhhhhHHHHHHhcCccCCceEEEEEecC
Confidence 45667788888776677755444 45666654 577765544433333 33334456678887798999999965333
No 404
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=54.89 E-value=16 Score=25.21 Aligned_cols=31 Identities=35% Similarity=0.437 Sum_probs=25.2
Q ss_pred hhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHH
Q 036188 38 FEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRL 76 (210)
Q Consensus 38 fd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~ 76 (210)
=+.+.. .++|.++||+.+++ ++..+.++|.+
T Consensus 16 q~nf~~----~~ls~~~ia~dL~~----s~~~le~vL~l 46 (89)
T PF10078_consen 16 QANFEL----SGLSLEQIAADLGT----SPEHLEQVLNL 46 (89)
T ss_pred HHHHHH----cCCCHHHHHHHhCC----CHHHHHHHHcC
Confidence 344555 48999999999999 99999888854
No 405
>COG1565 Uncharacterized conserved protein [Function unknown]
Probab=54.50 E-value=26 Score=30.64 Aligned_cols=46 Identities=17% Similarity=0.242 Sum_probs=31.1
Q ss_pred CchHHHHHHHHHhhhhhhhHHHHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 159 NPRFNKHFNAAMYNYTSLVMSNILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 159 ~p~~~~~f~~~M~~~~~~~~~~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
-|+..+.|-+..+.. ..+.|-+ .. -.....||.||.|+|+++.-++
T Consensus 51 Apels~lFGella~~---~~~~wq~-~g-~p~~~~lvEiGaG~G~l~~DiL 96 (370)
T COG1565 51 APELSQLFGELLAEQ---FLQLWQE-LG-RPAPLKLVEIGAGRGTLASDIL 96 (370)
T ss_pred chhHHHHHHHHHHHH---HHHHHHH-hc-CCCCceEEEeCCCcChHHHHHH
Confidence 488888888776532 2223222 22 3456789999999999998765
No 406
>PF07574 SMC_Nse1: Nse1 non-SMC component of SMC5-6 complex; InterPro: IPR011513 Saccharomyces cerevisiae Nse1 (Q07913 from SWISSPROT) forms part of a complex with SMC5-SMC6. This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism [, ]. It is conserved in eukaryotes from yeast to human.; PDB: 3NW0_A.
Probab=54.36 E-value=7.8 Score=30.73 Aligned_cols=42 Identities=17% Similarity=0.140 Sum_probs=25.4
Q ss_pred HHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccc
Q 036188 52 ASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVS 102 (210)
Q Consensus 52 ~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s 102 (210)
..+.++..++ .....+.+|.-|+..|+|.+. ..|.|.+++.+
T Consensus 155 ~~~~~~~~~L----~~~eae~lL~~lv~~gWl~~s-----~~G~y~L~~Ra 196 (200)
T PF07574_consen 155 STQLAQDKGL----SKSEAESLLDRLVEDGWLYRS-----REGFYSLGPRA 196 (200)
T ss_dssp ----------------HHHHHHHHHHHHTTSE-EE-----ETTEEEE-HHH
T ss_pred cccccccccc----hHHHHHHHHHHHHHCCCceeC-----CCCEEEEChHH
Confidence 3455566666 788899999999999999877 68999999865
No 407
>PRK13750 replication protein; Provisional
Probab=54.01 E-value=34 Score=28.27 Aligned_cols=38 Identities=18% Similarity=0.154 Sum_probs=28.3
Q ss_pred CCCHHHHHHHhcCCC-----CCCcccHHHHHHHHhcccceeee
Q 036188 49 KLSASDIAAQLLTKN-----KDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~-----~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
..|+++||..||+.- +..=....|++..|..+|++...
T Consensus 91 ~aSIeqLadeCGLST~S~aGnkSITRASR~I~fLEpmGfI~ce 133 (285)
T PRK13750 91 QCSITTLAIECGLATESAAGKLSITRATRALTFLAELGLITYQ 133 (285)
T ss_pred HHHHHHHHHHhCCcccCcCCCcchHHHHHHHHHHHhcCceeee
Confidence 469999999999810 00223567888999999999865
No 408
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=53.71 E-value=19 Score=29.08 Aligned_cols=42 Identities=17% Similarity=0.120 Sum_probs=37.0
Q ss_pred CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 51 SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 51 t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
|-.+||++.|+ +..-+++=|..|+..|++.+.. +.|.|-..+
T Consensus 37 sE~eLa~~~~V----SR~TVR~Al~~L~~eGli~r~~----G~GtfV~~~ 78 (241)
T PRK10079 37 AEQQLAARYEV----NRHTLRRAIDQLVEKGWVQRRQ----GVGVLVLMR 78 (241)
T ss_pred CHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEec----CCEEEEecC
Confidence 66799999999 9999999999999999999875 678887544
No 409
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=53.62 E-value=22 Score=29.63 Aligned_cols=59 Identities=14% Similarity=0.076 Sum_probs=41.7
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccccccccCCCCCChHHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYVPNKDGVLLGPLIQ 119 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~~~~~~~~~~~~~~ 119 (210)
.+.|+++||+.+++ +++.+.|+.+......+-+.. ...++..+...|.... .++..+..
T Consensus 20 ~~~~l~~lA~~~~~----S~~~l~r~F~~~~g~s~~~yi-------~~~Rl~~A~~~L~~~~--~~i~~iA~ 78 (289)
T PRK15121 20 QPLSLDNVAAKAGY----SKWHLQRMFKDVTGHAIGAYI-------RARRLSKAAVALRLTS--RPILDIAL 78 (289)
T ss_pred CCCCHHHHHHHHCc----CHHHHHHHHHHHHCcCHHHHH-------HHHHHHHHHHHHHcCC--CCHHHHHH
Confidence 48999999999999 999999999998887766543 4455555555554322 24544443
No 410
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=53.56 E-value=18 Score=28.85 Aligned_cols=34 Identities=21% Similarity=0.263 Sum_probs=32.3
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.+|.++||++++. ++....|+|..|...|++++.
T Consensus 19 ~~t~~ela~~l~~----S~qta~R~l~~le~~~~I~R~ 52 (214)
T COG1339 19 KVTSSELAKRLGV----SSQTAARKLKELEDEGYITRT 52 (214)
T ss_pred cccHHHHHHHhCc----CcHHHHHHHHhhccCCcEEEE
Confidence 5899999999999 999999999999999999976
No 411
>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=53.54 E-value=13 Score=32.04 Aligned_cols=41 Identities=17% Similarity=0.135 Sum_probs=21.8
Q ss_pred HHHHHHHHhhhhhhhHHHHHHhCCCCCCCCeEEEecCCccHHHH
Q 036188 163 NKHFNAAMYNYTSLVMSNILESYKGFDNIKQLVDVGGSLGVTLQ 206 (210)
Q Consensus 163 ~~~f~~~M~~~~~~~~~~~l~~~~~~~~~~~vvDiGGg~G~~~~ 206 (210)
.+.||-++.+. .+...+.....=....+|||+|||.|..+.
T Consensus 38 lR~fNNwvKs~---LI~~~~~~~~~~~~~~~VLDl~CGkGGDL~ 78 (331)
T PF03291_consen 38 LRNFNNWVKSV---LIQKYAKKVKQNRPGLTVLDLCCGKGGDLQ 78 (331)
T ss_dssp HHHHHHHHHHH---HHHHHCHCCCCTTTT-EEEEET-TTTTTHH
T ss_pred HHHHhHHHHHH---HHHHHHHhhhccCCCCeEEEecCCCchhHH
Confidence 55677666532 222222222101167899999999997654
No 412
>PLN02668 indole-3-acetate carboxyl methyltransferase
Probab=53.28 E-value=25 Score=30.96 Aligned_cols=19 Identities=32% Similarity=0.202 Sum_probs=15.5
Q ss_pred CCCeEEEecCCccHHHHhh
Q 036188 190 NIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l 208 (210)
+.-.|+|+|||+|..+..+
T Consensus 63 ~~~~iaDlGcs~G~ntl~~ 81 (386)
T PLN02668 63 VPFTAVDLGCSSGSNTIHI 81 (386)
T ss_pred cceeEEEecCCCCccHHHH
Confidence 4678999999999776654
No 413
>PLN02823 spermine synthase
Probab=53.21 E-value=11 Score=32.50 Aligned_cols=22 Identities=27% Similarity=0.368 Sum_probs=18.8
Q ss_pred CCCCeEEEecCCccHHHHhhhC
Q 036188 189 DNIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l~~ 210 (210)
.+.++|+-||||.|..+.++++
T Consensus 102 ~~pk~VLiiGgG~G~~~re~l~ 123 (336)
T PLN02823 102 PNPKTVFIMGGGEGSTAREVLR 123 (336)
T ss_pred CCCCEEEEECCCchHHHHHHHh
Confidence 4678999999999999988764
No 414
>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=53.17 E-value=9 Score=25.10 Aligned_cols=45 Identities=13% Similarity=0.113 Sum_probs=32.5
Q ss_pred CCCCHHHHHH---HhcCCCCCCcccHHHHHHHHhcccceeeeccCCCccc---ceecccc
Q 036188 48 TKLSASDIAA---QLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARR---LYSLNSV 101 (210)
Q Consensus 48 ~~~t~~eLA~---~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~---~y~~t~~ 101 (210)
+++++.+|.+ .+|+ ++..++--|-=|+..|+++.. ..| .|++|+.
T Consensus 19 ~~i~~~~Li~ll~~~Gv----~e~avR~alsRl~~~G~L~~~-----r~Gr~~~Y~Lt~~ 69 (70)
T PF07848_consen 19 GWIWVASLIRLLAAFGV----SESAVRTALSRLVRRGWLESE-----RRGRRSYYRLTER 69 (70)
T ss_dssp S-EEHHHHHHHHCCTT------HHHHHHHHHHHHHTTSEEEE-----CCCTEEEEEE-HH
T ss_pred CceeHHHHHHHHHHcCC----ChHHHHHHHHHHHHcCceeee-----ecCccceEeeCCC
Confidence 6777776555 5678 999999999999999999987 345 5888864
No 415
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=53.11 E-value=15 Score=29.13 Aligned_cols=36 Identities=8% Similarity=0.008 Sum_probs=28.7
Q ss_pred HHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHH
Q 036188 30 QAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRIL 74 (210)
Q Consensus 30 ~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlL 74 (210)
.+-.|..|+..+.+ +.|..|||+++++ .++-++..+
T Consensus 138 LT~RE~eVL~lla~-----G~snkeIA~~L~i----S~~TVk~h~ 173 (207)
T PRK15411 138 LSRTESSMLRMWMA-----GQGTIQISDQMNI----KAKTVSSHK 173 (207)
T ss_pred CCHHHHHHHHHHHc-----CCCHHHHHHHcCC----CHHHHHHHH
Confidence 45567778888887 8999999999999 888665444
No 416
>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=53.07 E-value=17 Score=28.21 Aligned_cols=44 Identities=14% Similarity=0.060 Sum_probs=34.9
Q ss_pred HHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccce
Q 036188 32 VYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVV 83 (210)
Q Consensus 32 a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~ 83 (210)
-.+-.|++.+.. .+.|+.+||++.|+ +.+++..++|+-.-.+=.
T Consensus 20 ~~r~~Iy~~~~~----~~~sv~~vS~~ygi----~~~RV~AIvrLkeiE~~~ 63 (172)
T PF12298_consen 20 ELREQIYEDVMQ----DGKSVREVSQKYGI----KIQRVEAIVRLKEIEKRW 63 (172)
T ss_pred HHHHHHHHHHHh----CCCCHHHHHHHhCC----CHHHHHHHHHHHHHHHHH
Confidence 345567777777 57899999999999 999999999987654433
No 417
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=53.03 E-value=12 Score=23.60 Aligned_cols=27 Identities=11% Similarity=0.059 Sum_probs=22.2
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHHHHhccccee
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVE 84 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~ 84 (210)
.|+.|+|+.+|+ +++.++++.+ .|++.
T Consensus 1 ~s~~eva~~~gv----s~~tlr~~~~----~gli~ 27 (70)
T smart00422 1 YTIGEVAKLAGV----SVRTLRYYER----IGLLP 27 (70)
T ss_pred CCHHHHHHHHCc----CHHHHHHHHH----CCCCC
Confidence 478999999999 9998877754 77775
No 418
>PF14502 HTH_41: Helix-turn-helix domain
Probab=52.95 E-value=39 Score=20.45 Aligned_cols=35 Identities=9% Similarity=0.143 Sum_probs=31.5
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.-.|++|+++++++ ..-.+..-|..|...|-+.-.
T Consensus 5 Ri~tI~e~~~~~~v----s~GtiQ~Alk~Le~~gaI~Le 39 (48)
T PF14502_consen 5 RIPTISEYSEKFGV----SRGTIQNALKFLEENGAIKLE 39 (48)
T ss_pred ccCCHHHHHHHhCc----chhHHHHHHHHHHHCCcEEee
Confidence 45799999999999 999999999999999988754
No 419
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain; InterPro: IPR018779 This entry represents a domain found at the C terminus of a set of single-stranded DNA-specific exonucleases, including RecJ. Its function has not, as yet, been determined.
Probab=52.80 E-value=20 Score=28.32 Aligned_cols=41 Identities=22% Similarity=0.239 Sum_probs=36.0
Q ss_pred CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccc
Q 036188 51 SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSV 101 (210)
Q Consensus 51 t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~ 101 (210)
...+||+.+|+ +++.+.-++++.-.+|||+.. +|....++.
T Consensus 118 ~~~~La~~l~i----~~~~l~fml~VF~EL~FVti~------~g~i~~~~~ 158 (195)
T PF10141_consen 118 QLQALAKYLGI----SPDTLKFMLKVFFELGFVTIE------DGVISLNPN 158 (195)
T ss_pred HHHHHHHHHCc----CHHHHHHHHHHHHHcCcEEEe------CCEEEeCCC
Confidence 35799999999 999999999999999999986 787777654
No 420
>TIGR03474 incFII_RepA incFII family plasmid replication initiator RepA. Members of this protein are the plasmid replication initiator RepA of incFII (plasmid incompatibility group F-II) plasmids. R1 and R100 are plasmids in this group. Immediately upstream of repA is found tap, a leader peptide of about 24 amino acids, often not assigned as a gene in annotated plasmid sequences. Note that other, non-homologous plasmid replication proteins share the gene symbol (repA) and similar names (plasmid replication protein RepA).
Probab=52.50 E-value=37 Score=27.85 Aligned_cols=39 Identities=13% Similarity=0.120 Sum_probs=28.5
Q ss_pred CCCHHHHHHHhcCCC-----CCCcccHHHHHHHHhcccceeeec
Q 036188 49 KLSASDIAAQLLTKN-----KDAPMMLDRILRLLASYSVVECSL 87 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~-----~~~~~~l~rlLr~L~~~gl~~~~~ 87 (210)
..|+++||..||+.- +..=....|++..|..+|++....
T Consensus 83 ~aSIeqLadeCGLST~S~aGnkSITRASR~I~fLEpmGfI~cek 126 (275)
T TIGR03474 83 QRSITNLAIECGLATESKSGNLSITRATRALTFLSELGLITYQT 126 (275)
T ss_pred HHHHHHHHHHhCCcccCcCCCchhHHHHHHHHHHHhcCceeeee
Confidence 469999999999810 002235678888999999998653
No 421
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=52.15 E-value=10 Score=34.65 Aligned_cols=20 Identities=15% Similarity=0.288 Sum_probs=17.8
Q ss_pred CCCeEEEecCCccHHHHhhh
Q 036188 190 NIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~ 209 (210)
+...+||||||.|.++.+++
T Consensus 347 ~~p~~lEIG~G~G~~~~~~A 366 (506)
T PRK01544 347 KRKVFLEIGFGMGEHFINQA 366 (506)
T ss_pred CCceEEEECCCchHHHHHHH
Confidence 57899999999999998876
No 422
>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=51.76 E-value=55 Score=21.05 Aligned_cols=41 Identities=17% Similarity=0.178 Sum_probs=23.7
Q ss_pred hhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 38 FEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 38 fd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.++|-+.+ .|+|++||...|.+ +... .++..|...-=+..+
T Consensus 11 VeymK~r~--~Plt~~eI~d~l~~----d~~~--~~~~~Lk~npKI~~d 51 (65)
T PF02186_consen 11 VEYMKKRD--HPLTLEEILDYLSL----DIGK--KLKQWLKNNPKIEYD 51 (65)
T ss_dssp HHHHHHH---S-B-HHHHHHHHTS----SS-H--HHHHHHHH-TTEEEE
T ss_pred HHHHHhcC--CCcCHHHHHHHHcC----CCCH--HHHHHHHcCCCEEEe
Confidence 45666654 79999999999998 6542 344444455555544
No 423
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=51.23 E-value=26 Score=31.20 Aligned_cols=50 Identities=16% Similarity=0.057 Sum_probs=43.2
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccccccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYVP 107 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~~ 107 (210)
.++..+++.++.|. +.......++.|...|+++.+ ++++.+|+.++.+.+
T Consensus 360 ~gl~~~~~~~~~g~----~~~~~~~~l~~l~~~gll~~~------~~~l~lT~~G~~~~d 409 (430)
T PRK08208 360 QGLDLADYRQRFGS----DPLRDFPELELLIDRGWLEQN------GGRLRLTEEGLALSD 409 (430)
T ss_pred CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEE------CCEEEECcchhhHHH
Confidence 48899999999999 776677789999999999986 788999999888764
No 424
>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=50.84 E-value=16 Score=30.70 Aligned_cols=38 Identities=13% Similarity=0.296 Sum_probs=27.5
Q ss_pred CCCHHHHHHHhcCCC-----CCCcccHHHHH-HHHhcccceeee
Q 036188 49 KLSASDIAAQLLTKN-----KDAPMMLDRIL-RLLASYSVVECS 86 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~-----~~~~~~l~rlL-r~L~~~gl~~~~ 86 (210)
.+|+++||..||+.. +....++.|++ ++|..+|+++..
T Consensus 95 ~~sie~LA~ecGLst~s~~Gn~sitRasR~i~e~le~~Gli~~~ 138 (281)
T PF02387_consen 95 QASIEQLADECGLSTKSAAGNKSITRASRLISEFLEPLGLITCE 138 (281)
T ss_pred eecHHHHHHHhCCcccCCCCCeeHHHHHHHHHHHHHhcCCeeee
Confidence 689999999999711 11233577777 668899999764
No 425
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=50.61 E-value=29 Score=32.59 Aligned_cols=35 Identities=17% Similarity=0.120 Sum_probs=32.6
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.|-++.||++.+++ ++...+.+|+.|+..|.+.+.
T Consensus 505 ~p~~~~~~~~~l~~----~~~~~~~~l~~l~~~g~lv~l 539 (614)
T PRK10512 505 EPWWVRDLAKETGT----DEQAMRLTLRQAAQQGIITAI 539 (614)
T ss_pred CCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 48899999999999 999999999999999988876
No 426
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=50.60 E-value=22 Score=30.22 Aligned_cols=59 Identities=20% Similarity=0.187 Sum_probs=43.9
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccc
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVS 102 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s 102 (210)
+.|..+|... ...|+.+||+.+++ +.+-+.|=++.|...|+-.+.. .+..+.|.+-+--
T Consensus 11 ~~ii~~L~~~---~~vta~~lA~~~~V----S~RTi~RDi~~L~~~gvPI~~e--~G~~~gy~~~~~~ 69 (311)
T COG2378 11 LQIIQILRAK---ETVTAAELADEFEV----SVRTIYRDIATLRAAGVPIEGE--RGKGGGYRLRPGF 69 (311)
T ss_pred HHHHHHHHhC---ccchHHHHHHhcCC----CHHHHHHHHHHHHHCCCCeEee--cCCCccEEEccCC
Confidence 3455566554 35899999999999 9999999999999999986652 0123567766643
No 427
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator 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.
Probab=50.53 E-value=21 Score=29.88 Aligned_cols=50 Identities=16% Similarity=0.219 Sum_probs=38.7
Q ss_pred CCCCHHHHH---HHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccc
Q 036188 48 TKLSASDIA---AQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSK 103 (210)
Q Consensus 48 ~~~t~~eLA---~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~ 103 (210)
+.+++.+|. +.+|+ ++..++-.|.-|+..|+++.... +....|++|+.++
T Consensus 16 g~i~~~~Li~l~~~~gi----~~~~vr~al~RL~~~G~l~~~~~--grr~~Y~LT~~g~ 68 (280)
T TIGR02277 16 GAIWLGSLIEFLAGLGI----NERLVRTAVSRLVAQGWLQSERK--GRRSFYSLTDKGR 68 (280)
T ss_pred CceeHHHHHHHHHhcCC----CcchHHHHHHHHHHCCCEEeeec--CCCCEEEECHHHH
Confidence 677777555 56678 99999999999999999987520 1236799999876
No 428
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=50.14 E-value=41 Score=28.36 Aligned_cols=32 Identities=16% Similarity=0.133 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
..+|+++|++.|++ .++ -++..|..+|++...
T Consensus 222 ~~isi~~is~~T~i----~~~---Dii~tL~~l~~l~~~ 253 (290)
T PLN03238 222 GDVSIKDLSLATGI----RGE---DIVSTLQSLNLIKYW 253 (290)
T ss_pred CCccHHHHHHHhCC----CHH---HHHHHHHHCCcEEEE
Confidence 58999999999999 444 488899999999765
No 429
>PRK05031 tRNA (uracil-5-)-methyltransferase; Validated
Probab=50.09 E-value=10 Score=32.90 Aligned_cols=18 Identities=17% Similarity=0.124 Sum_probs=15.9
Q ss_pred CeEEEecCCccHHHHhhh
Q 036188 192 KQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 192 ~~vvDiGGg~G~~~~~l~ 209 (210)
.+++|++||+|.+++.+.
T Consensus 208 ~~vLDl~~G~G~~sl~la 225 (362)
T PRK05031 208 GDLLELYCGNGNFTLALA 225 (362)
T ss_pred CeEEEEeccccHHHHHHH
Confidence 479999999999998775
No 430
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=50.09 E-value=24 Score=25.48 Aligned_cols=31 Identities=19% Similarity=-0.023 Sum_probs=27.5
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSV 82 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl 82 (210)
.+.|+.+||+..|+ ++..+.+|.+.....|.
T Consensus 28 ~g~sv~evA~e~gI----s~~tl~~W~r~y~~~~~ 58 (121)
T PRK09413 28 PGMTVSLVARQHGV----AASQLFLWRKQYQEGSL 58 (121)
T ss_pred CCCCHHHHHHHHCc----CHHHHHHHHHHHhhccc
Confidence 48899999999999 99999999999876554
No 431
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=49.70 E-value=10 Score=23.98 Aligned_cols=27 Identities=15% Similarity=0.116 Sum_probs=20.6
Q ss_pred CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 51 SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 51 t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
|+.|+|+.+|+ +++.|+.+. ..|++..
T Consensus 2 ti~eva~~~gv----s~~tlr~y~----~~gll~~ 28 (69)
T PF13411_consen 2 TIKEVAKLLGV----SPSTLRYYE----REGLLPP 28 (69)
T ss_dssp EHHHHHHHTTT----THHHHHHHH----HTTSSTT
T ss_pred cHHHHHHHHCc----CHHHHHHHH----HhcCccc
Confidence 68999999999 888776664 4666543
No 432
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=49.34 E-value=36 Score=22.35 Aligned_cols=51 Identities=22% Similarity=0.140 Sum_probs=34.7
Q ss_pred CCCCHHHHHHHhcCCCC--CCc----ccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 48 TKLSASDIAAQLLTKNK--DAP----MMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~--~~~----~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
.+.|...|.+-+.-+.+ .++ ..+.+-|+.++..|.|.+..+. +..|.|.++
T Consensus 20 ~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg~-G~sgsfkl~ 76 (77)
T PF00538_consen 20 KGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVKGK-GASGSFKLS 76 (77)
T ss_dssp SSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECSCS-TTSSEEEES
T ss_pred CCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeeccc-CCccceecC
Confidence 57899998886643221 133 3588889999999999987311 124778765
No 433
>KOG3191 consensus Predicted N6-DNA-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=49.29 E-value=13 Score=29.45 Aligned_cols=19 Identities=16% Similarity=0.260 Sum_probs=16.4
Q ss_pred CCeEEEecCCccHHHHhhh
Q 036188 191 IKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 191 ~~~vvDiGGg~G~~~~~l~ 209 (210)
...+++||||+|..+..|.
T Consensus 44 ~~i~lEIG~GSGvvstfL~ 62 (209)
T KOG3191|consen 44 PEICLEIGCGSGVVSTFLA 62 (209)
T ss_pred ceeEEEecCCcchHHHHHH
Confidence 7789999999999887664
No 434
>COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]
Probab=49.12 E-value=29 Score=30.22 Aligned_cols=35 Identities=11% Similarity=-0.163 Sum_probs=33.5
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.|.++.+|+..+|+ ....+...|-.|.-.|.+.+.
T Consensus 308 ~~~~~d~l~~~~~~----~~~~~~~~L~~lel~G~i~~~ 342 (350)
T COG0758 308 EPKEIDRLASCTGL----TIAQVLAWLLELELEGKVKRL 342 (350)
T ss_pred CCccHHHHHHHhCC----CHHHHHHHHHHHHhcCcEEee
Confidence 69999999999999 999999999999999999987
No 435
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=49.00 E-value=21 Score=30.08 Aligned_cols=59 Identities=14% Similarity=0.049 Sum_probs=46.8
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhc---ccceeeeccCCCcccceeccccccccc
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLAS---YSVVECSLDASGARRLYSLNSVSKYYV 106 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~---~gl~~~~~~~~~~~~~y~~t~~s~~l~ 106 (210)
-.+..|..+.+ ..|...-|+++++ .+..+.+-++.|.. .-||++. .....+|+.++.|.
T Consensus 32 ~~L~~f~av~e-----~gs~s~AA~~L~i----sQpavS~~I~~LE~~lG~~LF~R~------~r~v~lT~~G~~l~ 93 (317)
T PRK11482 32 NLLTIFEAVYV-----HKGIVNAAKILNL----TPSAISQSIQKLRVIFPDPLFIRK------GQGVTPTAYATHLH 93 (317)
T ss_pred hHHHHHHHHHH-----cCCHHHHHHHhCC----ChHHHHHHHHHHHHHhCCcceEec------CCCccCCHHHHHHH
Confidence 34667888888 4499999999999 99999998888865 4588886 57788888877543
No 436
>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=48.28 E-value=24 Score=32.81 Aligned_cols=42 Identities=5% Similarity=-0.092 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceec
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSL 98 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~ 98 (210)
.|-++.|+++.++. ++..+.++++.|...|.+.+. .++.|-+
T Consensus 487 ~~~~~~~~~~~~~~----~~~~~~~~l~~l~~~g~~~~~-----~~~~~~~ 528 (581)
T TIGR00475 487 KGAWVREFAEEVNG----DEKVMLKRVRKAGHRGGETLI-----VKDRLLK 528 (581)
T ss_pred CCCCHHHHHhhhCC----CHHHHHHHHHHHHhCCCEEEE-----eCCeEHH
Confidence 48899999999999 999999999999999988776 4677766
No 437
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=48.13 E-value=26 Score=28.32 Aligned_cols=58 Identities=17% Similarity=0.192 Sum_probs=47.8
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhc---ccceeeeccCCCcccceecccccccccc
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLAS---YSVVECSLDASGARRLYSLNSVSKYYVP 107 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~---~gl~~~~~~~~~~~~~y~~t~~s~~l~~ 107 (210)
+..|..+.+. .|+..-|+++++ .+..+.+-++-|.. .-||.+. .....+|+.++.|..
T Consensus 2 l~~f~~v~~~-----gs~~~AA~~L~i----sqsavS~~i~~LE~~lg~~Lf~R~------~~~~~lT~~G~~l~~ 62 (279)
T TIGR03339 2 LKAFHAVARC-----GSFTRAAERLGL----SQPTVTDQVRKLEERYGVELFHRN------GRRLELTDAGHRLLP 62 (279)
T ss_pred chhhHHHHhc-----CCHHHHHHHhcC----CchHHHHHHHHHHHHhCCccEEEc------CCeEEEChhHHHHHH
Confidence 5678889884 499999999999 99999988887765 4688886 678999999987653
No 438
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=47.97 E-value=44 Score=22.37 Aligned_cols=54 Identities=13% Similarity=0.114 Sum_probs=42.5
Q ss_pred HHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhc-CCCCCCcccHHHHHHHHhccccee
Q 036188 26 PMAIQAVYELGIFEILDKAGPGTKLSASDIAAQLL-TKNKDAPMMLDRILRLLASYSVVE 84 (210)
Q Consensus 26 ~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~-~~~~~~~~~l~rlLr~L~~~gl~~ 84 (210)
....+..++-.|......++ ++.+|..+.-+.+. . |...+.|+.++|...|++.
T Consensus 31 ~p~~Yl~iRn~il~~w~~n~-~~~lt~~~~~~~i~~~----d~~~~~ri~~FL~~~G~IN 85 (86)
T PF04433_consen 31 TPEQYLKIRNTILAEWRKNP-NKYLTKTDARKLIKGI----DVNKIRRIYDFLERWGLIN 85 (86)
T ss_dssp HHHHHHHHHHHHHHHHHHHT-TS---HHHHHHHTTSS----SHHHHHHHHHHHHHTTSSS
T ss_pred ChHHHHHHHHHHHHHHHHCC-CCcccHHHHHHHcccc----CHHHHHHHHHHHHHcCccC
Confidence 56688888888888865543 37899999999888 8 9999999999999999874
No 439
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=47.90 E-value=33 Score=27.27 Aligned_cols=45 Identities=11% Similarity=0.196 Sum_probs=36.6
Q ss_pred HHHHhhChhhHHhhcCCCC--CCCHHHHHHHhcCCCCCCcccHHHHHHHHhccc
Q 036188 30 QAVYELGIFEILDKAGPGT--KLSASDIAAQLLTKNKDAPMMLDRILRLLASYS 81 (210)
Q Consensus 30 ~~a~~lglfd~L~~~g~~~--~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~g 81 (210)
+.-....|.+.|.+. + .+|..|||+.+|+ ++.-++|=|..+...|
T Consensus 14 r~~~~~~il~~l~~~---~~~~vs~~~L~~~~~v----~~~tirrDl~~l~~~G 60 (213)
T PRK05472 14 RLPLYYRYLKELKEE---GVERVSSKELAEALGV----DSAQIRKDLSYFGEFG 60 (213)
T ss_pred HhHHHHHHHHHHHHc---CCcEEeHHHHHHHhCc----CHHHHHHHHHHHHhcC
Confidence 445566788888875 5 7899999999999 9998899888886555
No 440
>smart00351 PAX Paired Box domain.
Probab=47.79 E-value=26 Score=25.50 Aligned_cols=44 Identities=18% Similarity=0.174 Sum_probs=35.1
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
.+..|..+..+ +.|..+||+++|+ ++.-+.+|++-....|.+..
T Consensus 22 ~R~riv~~~~~-----G~s~~~iA~~~gv----s~~tV~kwi~r~~~~G~~~p 65 (125)
T smart00351 22 ERQRIVELAQN-----GVRPCDISRQLCV----SHGCVSKILGRYYETGSIRP 65 (125)
T ss_pred HHHHHHHHHHc-----CCCHHHHHHHHCc----CHHHHHHHHHHHHHcCCcCC
Confidence 34455555443 7799999999999 99999999999888887764
No 441
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=47.61 E-value=25 Score=25.29 Aligned_cols=39 Identities=13% Similarity=0.222 Sum_probs=27.5
Q ss_pred hhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 38 FEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 38 fd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
-..+.+. ..+|..|||+.+|+ ++..+. ++|-.+|+--+.
T Consensus 63 ~~~v~~~---pd~tl~Ela~~l~V----s~~ti~---~~Lkrlg~t~KK 101 (119)
T PF01710_consen 63 KALVEEN---PDATLRELAERLGV----SPSTIW---RALKRLGITRKK 101 (119)
T ss_pred HHHHHHC---CCcCHHHHHHHcCC----CHHHHH---HHHHHcCchhcc
Confidence 3344443 47999999999999 877655 555566776654
No 442
>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=47.61 E-value=11 Score=25.77 Aligned_cols=27 Identities=22% Similarity=0.208 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHh
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLA 78 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~ 78 (210)
.+.|-.|||+++|. ++..+.+.|+++.
T Consensus 2 ~G~tq~eIA~~lGk----s~s~Vs~~l~Ll~ 28 (93)
T PF08535_consen 2 FGWTQEEIAKRLGK----SRSWVSNHLALLD 28 (93)
T ss_dssp TT--HHHHHHHTT------HHHHHHHHGGGS
T ss_pred CCCCHHHHHHHHCC----CHHHHHHHHHHHc
Confidence 37899999999999 9999999988763
No 443
>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=47.23 E-value=16 Score=21.87 Aligned_cols=23 Identities=13% Similarity=0.104 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRIL 74 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlL 74 (210)
..+|.+++|+++|+ ++..+.++.
T Consensus 14 ~gltq~~lA~~~gv----s~~~vs~~e 36 (58)
T TIGR03070 14 LGLTQADLADLAGV----GLRFIRDVE 36 (58)
T ss_pred cCCCHHHHHHHhCC----CHHHHHHHH
Confidence 48899999999999 888777765
No 444
>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=46.95 E-value=16 Score=26.57 Aligned_cols=30 Identities=10% Similarity=0.083 Sum_probs=24.8
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+|.+|||..+|. ...-+.||.| ..|.-++.
T Consensus 1 MT~eELA~~tG~----srQTINrWvR---kegW~T~p 30 (122)
T PF07037_consen 1 MTPEELAELTGY----SRQTINRWVR---KEGWKTEP 30 (122)
T ss_pred CCHHHHHHHhCc----cHHHHHHHHH---hcCceecc
Confidence 588999999999 9999999987 45666654
No 445
>PRK05660 HemN family oxidoreductase; Provisional
Probab=46.93 E-value=23 Score=30.98 Aligned_cols=50 Identities=8% Similarity=0.058 Sum_probs=42.1
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccccccc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYVP 107 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~~ 107 (210)
.+++.+++.++.|. +.......++.|...|+++.+ ++++.+|+.+..+.+
T Consensus 320 ~G~~~~~~~~~~g~----~~~~~~~~l~~l~~~gl~~~~------~~~~~lt~~G~~~~d 369 (378)
T PRK05660 320 EAAPRADFEAYTGL----PESVIRPQLDEALAQGYLTET------ADHWQITEHGKLFLN 369 (378)
T ss_pred cCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe------CCEEEECcchhHHHH
Confidence 37888999999999 766667789999999999986 679999998887763
No 446
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=46.84 E-value=16 Score=27.43 Aligned_cols=31 Identities=19% Similarity=0.303 Sum_probs=20.3
Q ss_pred hHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 39 EILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 39 d~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
+++..++ +..|-++||+.+|+ ++.-|.||..
T Consensus 26 e~~~~~~--~r~T~~eiAee~Gi----s~~tLYrWr~ 56 (142)
T PF13022_consen 26 ELMPENG--ERRTQAEIAEEVGI----SRSTLYRWRQ 56 (142)
T ss_dssp HHS--------S-HHHHHHHHTS-----HHHHHHHHH
T ss_pred HHhhhcc--ccchHHHHHHHhCC----CHHHHHHHHh
Confidence 4555544 58999999999999 9999999974
No 447
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=46.83 E-value=38 Score=23.39 Aligned_cols=57 Identities=14% Similarity=0.144 Sum_probs=40.6
Q ss_pred ChhhHHhhcCCCCCCCHHHHHHHh--cCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccccc
Q 036188 36 GIFEILDKAGPGTKLSASDIAAQL--LTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYY 105 (210)
Q Consensus 36 glfd~L~~~g~~~~~t~~eLA~~~--~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l 105 (210)
+|+=.+.+. .-.|++++++.+ .. ....+.+=...|...|++++. ++| |-.|..+.-+
T Consensus 20 ~ilI~v~Kk---~Fit~~ev~e~l~~~~----~~~~V~SNIGvLIKkglIEKS-----GDG-lv~T~~g~~I 78 (96)
T PF09114_consen 20 NILIQVAKK---NFITASEVREALATEM----NKASVNSNIGVLIKKGLIEKS-----GDG-LVITEEGMDI 78 (96)
T ss_dssp HHHHHHHHS---TTB-HHHHHH-T-TTS-----HHHHHHHHHHHHHTTSEEEE-----TTE-EEE-HHHHHH
T ss_pred HHHHHHHHH---ccCCHHHHHHHHHHHh----hhhHHHHhHHHHHHcCccccc-----CCc-eEEechHHHH
Confidence 345566664 367999999987 56 667888889999999999998 455 8888777644
No 448
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=46.74 E-value=24 Score=29.76 Aligned_cols=62 Identities=16% Similarity=0.114 Sum_probs=45.8
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCC-CCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccc
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTK-NKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSK 103 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~-~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~ 103 (210)
..|.+.|++++ .|+.+..||..+.-+ -++.+|.++.-|+.|-..||..+. +...=.+|+.+.
T Consensus 9 ieIl~il~esd--~plgak~Ia~el~kRGy~igeRavRYhlk~lderglt~kv-----gyagr~iTe~Gl 71 (325)
T COG1693 9 IEILRILAESD--EPLGAKIIALELRKRGYNIGERAVRYHLKKLDERGLTRKV-----GYAGREITEKGL 71 (325)
T ss_pred HHHHHHHHhcC--CccchHHHHHHHHhcccchhHHHHHHHHHHHhhccchhhc-----cccceeehHhhH
Confidence 34778899986 799999999987410 012889999999999999999987 344444555554
No 449
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=46.55 E-value=23 Score=27.86 Aligned_cols=37 Identities=14% Similarity=0.004 Sum_probs=31.0
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
|..|++||.+++.- ..++..+..+|+.|...|++++.
T Consensus 41 G~rt~~eI~~~l~~--~~p~~~v~~~L~~L~~~G~l~~~ 77 (193)
T TIGR03882 41 GRRTLDEIIAALAG--RFPAEEVLYALDRLERRGYLVED 77 (193)
T ss_pred CCCCHHHHHHHhhc--cCCHHHHHHHHHHHHHCCCEecc
Confidence 69999999888865 01577899999999999999975
No 450
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=46.38 E-value=22 Score=27.71 Aligned_cols=27 Identities=22% Similarity=0.397 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHh
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLA 78 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~ 78 (210)
.+.|.++||+++|. ++..+.+.|+++.
T Consensus 119 ~g~s~~~iA~~lg~----s~~~V~r~l~l~~ 145 (187)
T TIGR00180 119 FSMTQEDLAKKIGK----SRAHITNLLRLLK 145 (187)
T ss_pred hCCCHHHHHHHHCc----CHHHHHHHHHHHc
Confidence 47899999999999 9999999998864
No 451
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=46.27 E-value=21 Score=28.47 Aligned_cols=30 Identities=30% Similarity=0.252 Sum_probs=27.9
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccc
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSV 82 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl 82 (210)
+.|-++||..+|+ .++.+.|+++.|...|+
T Consensus 173 ~~t~~~iA~~lG~----tretvsR~l~~L~~~gl 202 (236)
T PRK09392 173 PYEKRVLASYLGM----TPENLSRAFAALASHGV 202 (236)
T ss_pred eCCHHHHHHHhCC----ChhHHHHHHHHHHhCCe
Confidence 5667899999999 99999999999999996
No 452
>PF07091 FmrO: Ribosomal RNA methyltransferase (FmrO); PDB: 3LCU_A 3LCV_B 3FRH_A 3FRI_A 3B89_A 3FZG_A.
Probab=46.14 E-value=15 Score=30.32 Aligned_cols=16 Identities=19% Similarity=0.287 Sum_probs=10.5
Q ss_pred CCCeEEEecCCccHHH
Q 036188 190 NIKQLVDVGGSLGVTL 205 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~ 205 (210)
...+|+|||||---++
T Consensus 105 ~p~sVlDigCGlNPla 120 (251)
T PF07091_consen 105 PPDSVLDIGCGLNPLA 120 (251)
T ss_dssp --SEEEEET-TTCHHH
T ss_pred CCchhhhhhccCCcee
Confidence 4899999999975544
No 453
>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=45.87 E-value=23 Score=22.91 Aligned_cols=23 Identities=30% Similarity=0.290 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRIL 74 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlL 74 (210)
..+|..++|+++|+ +...+.+++
T Consensus 17 ~~~t~~~lA~~~gi----s~~tis~~~ 39 (78)
T TIGR02607 17 LGLSIRALAKALGV----SRSTLSRIV 39 (78)
T ss_pred cCCCHHHHHHHhCC----CHHHHHHHH
Confidence 58899999999999 888777764
No 454
>PRK15340 transcriptional regulator InvF; Provisional
Probab=45.66 E-value=49 Score=26.73 Aligned_cols=46 Identities=4% Similarity=-0.119 Sum_probs=36.3
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
.+|...|..... .+.++++||+.+|+ +++.++|+.+-......-..
T Consensus 112 y~l~~~Ll~~~~-~~~sleeLA~~~gv----S~r~f~RlFk~~~G~tpk~y 157 (216)
T PRK15340 112 YWLVGYLLAQST-SGNTMRMLGEDYGV----SYTHFRRLCSRALGGKAKSE 157 (216)
T ss_pred HHHHHHHHhCcc-CCCCHHHHHHHHCc----CHHHHHHHHHHHHCcCHHHH
Confidence 356666655332 68899999999999 99999999999888876543
No 455
>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=45.64 E-value=19 Score=22.70 Aligned_cols=23 Identities=9% Similarity=0.115 Sum_probs=19.0
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHHH
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILRL 76 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr~ 76 (210)
.|+.|+|+.+|+ +++.++.+-+.
T Consensus 1 ~~i~evA~~~gv----s~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGV----KPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCc----CHHHHHHHHHh
Confidence 378999999999 99988877553
No 456
>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=45.62 E-value=8.8 Score=23.42 Aligned_cols=29 Identities=21% Similarity=0.355 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhc-ccce
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLAS-YSVV 83 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~-~gl~ 83 (210)
.++++.|||+.+|+ ++. .+++.|.. .|+.
T Consensus 2 ~~i~V~elAk~l~v----~~~---~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 2 EKIRVSELAKELGV----PSK---EIIKKLFKELGIM 31 (54)
T ss_dssp -EE-TTHHHHHHSS----SHH---HHHHHH-HHHTS-
T ss_pred CceEHHHHHHHHCc----CHH---HHHHHHHHhCCcC
Confidence 37899999999999 655 56777744 7877
No 457
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=45.38 E-value=25 Score=29.40 Aligned_cols=57 Identities=14% Similarity=0.070 Sum_probs=45.2
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhc---ccceeeeccCCCcccceecccccccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLAS---YSVVECSLDASGARRLYSLNSVSKYY 105 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~---~gl~~~~~~~~~~~~~y~~t~~s~~l 105 (210)
++.+|..+.+. .|+..-|+++++ .+..+.+-++.|.. .-||.+. .....+|+.++.+
T Consensus 12 ~L~~f~av~e~-----gs~t~AA~~L~i----SQpavS~~I~~LE~~lg~~LF~R~------~r~~~lT~~G~~l 71 (319)
T PRK10216 12 LLLCLQLLMQE-----RSVTKAAKRMNV----TPSAVSKSLAKLRAWFDDPLFVNT------PLGLSPTPLMVSM 71 (319)
T ss_pred HHHHHHHHHHh-----CCHHHHHHHhCC----CHHHHHHHHHHHHHHhCCceEEec------CCCcccCHHHHHH
Confidence 46678888884 499999999999 99999998888865 4488886 5668888877644
No 458
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=45.37 E-value=11 Score=32.05 Aligned_cols=34 Identities=21% Similarity=0.164 Sum_probs=31.6
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
-...++.|.++|+ ..|++..+...|.+.|++.+.
T Consensus 44 lvgLddaA~KlgV----ErRRIYDiVNvlEsig~var~ 77 (388)
T KOG2578|consen 44 LVGLDDAARKLGV----ERRRIYDIVNVLESIGAVARR 77 (388)
T ss_pred eechhhHHHhcCc----hHHHHHHHHHHHHHHHHHHhc
Confidence 4678999999999 999999999999999999876
No 459
>PRK10130 transcriptional regulator EutR; Provisional
Probab=45.24 E-value=28 Score=30.20 Aligned_cols=57 Identities=14% Similarity=0.149 Sum_probs=40.7
Q ss_pred hHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecccccccccc
Q 036188 39 EILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVSKYYVP 107 (210)
Q Consensus 39 d~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s~~l~~ 107 (210)
++|.++- +.++|+++||+++++ +++.|.|..+-...+.....- ..++++..-+.|..
T Consensus 247 ~~i~~~~-~~~ltv~~lA~~~gv----S~r~L~r~Fk~~~G~sp~~yl-------r~~RL~~ar~lL~~ 303 (350)
T PRK10130 247 EYVLENM-SEPVTVLDLCNQLHV----SRRTLQNAFHAILGIGPNAWL-------KRIRLNAVRRELIS 303 (350)
T ss_pred HHHHhhh-cCCCCHHHHHHHHCC----CHHHHHHHHHHHHCcCHHHHH-------HHHHHHHHHHHHhc
Confidence 4554431 258999999999999 999999999887777666543 34556655555543
No 460
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=45.21 E-value=26 Score=24.23 Aligned_cols=29 Identities=3% Similarity=0.067 Sum_probs=22.7
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
+++.|+|+.+|+ .++. +|+-...|++...
T Consensus 1 m~I~eva~~~gv----s~~t----lR~Ye~~GLl~p~ 29 (95)
T cd04780 1 MRMSELSKRSGV----SVAT----IKYYLREGLLPEG 29 (95)
T ss_pred CCHHHHHHHHCc----CHHH----HHHHHHCCCCCCC
Confidence 478999999999 7764 5666669998753
No 461
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=45.17 E-value=20 Score=26.03 Aligned_cols=30 Identities=10% Similarity=0.319 Sum_probs=23.2
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHH
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRIL 74 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlL 74 (210)
|-..+.+ .++|.+|||+++|+ ++..+.++.
T Consensus 10 l~~ll~~----~Glsq~eLA~~~Gi----s~~~is~iE 39 (120)
T PRK13890 10 VLRLLDE----RHMTKKELSERSGV----SISFLSDLT 39 (120)
T ss_pred HHHHHHH----cCCCHHHHHHHHCc----CHHHHHHHH
Confidence 4556666 58999999999999 777766654
No 462
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=44.98 E-value=30 Score=28.26 Aligned_cols=59 Identities=15% Similarity=0.179 Sum_probs=48.3
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhc---ccceeeeccCCCcccceecccccccccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLAS---YSVVECSLDASGARRLYSLNSVSKYYVP 107 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~---~gl~~~~~~~~~~~~~y~~t~~s~~l~~ 107 (210)
.+.+|-.+.+ ..|+..-|+++++ .+..+.+-++.|.. .-||++. ...+.+|+.++.|.+
T Consensus 7 ~L~~f~~v~e-----~~s~t~AA~~L~i----sqpavS~~I~~LE~~lg~~Lf~R~------~r~~~lT~~G~~l~~ 68 (290)
T PRK10837 7 QLEVFAEVLK-----SGSTTQASVMLAL----SQSAVSAALTDLEGQLGVQLFDRV------GKRLVVNEHGRLLYP 68 (290)
T ss_pred HHHHHHHHHH-----cCCHHHHHHHhCC----CccHHHHHHHHHHHHhCCccEeec------CCeEEECHhHHHHHH
Confidence 4677888888 4499999999999 89988888887765 5689886 677999999987753
No 463
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=44.95 E-value=14 Score=32.33 Aligned_cols=44 Identities=20% Similarity=0.162 Sum_probs=34.2
Q ss_pred hChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhccccee
Q 036188 35 LGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVE 84 (210)
Q Consensus 35 lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~ 84 (210)
.-+.+.|.-++ |..|+-|||+++|+ +-..+...++.|...|+++
T Consensus 343 ~~~l~~L~~~D--G~~slldIA~~~~~----~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 343 MAMLWVLNYSD--GKNSLLDIAERIGL----PFDELADAARKLLEAGLLK 386 (386)
T ss_dssp HHHHHHHHH-E--EEEEHHHHHHHHT------HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHhcc--CCCcHHHHHHHHCc----CHHHHHHHHHHHHHcCCCC
Confidence 33667776654 79999999999999 9999999999999999874
No 464
>PRK13503 transcriptional activator RhaS; Provisional
Probab=44.80 E-value=31 Score=28.11 Aligned_cols=44 Identities=14% Similarity=0.133 Sum_probs=33.6
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
+.+.|.++- ..+.|+++||+++++ +++.+.|+.+.....-+.+.
T Consensus 176 ~~~~I~~~~-~~~~tl~~lA~~~~l----S~~~l~r~Fk~~~G~S~~~y 219 (278)
T PRK13503 176 LLAWLEDHF-AEEVNWEALADQFSL----SLRTLHRQLKQQTGLTPQRY 219 (278)
T ss_pred HHHHHHHhh-cCCCCHHHHHHHHCC----CHHHHHHHHHHHhCcCHHHH
Confidence 455555532 158999999999999 99999999987776665554
No 465
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=44.52 E-value=28 Score=28.58 Aligned_cols=59 Identities=19% Similarity=0.275 Sum_probs=48.8
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhc---ccceeeeccCCCcccceecccccccccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLAS---YSVVECSLDASGARRLYSLNSVSKYYVP 107 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~---~gl~~~~~~~~~~~~~y~~t~~s~~l~~ 107 (210)
.|.+|-.+.+. .|+..-|+++++ .+..+.|-++-|.. .-+|.+. .....+|+.++.|.+
T Consensus 5 ~L~~f~~v~~~-----gs~s~AA~~L~i----sQ~avSr~i~~LE~~lg~~Lf~R~------~~~~~lT~~G~~l~~ 66 (296)
T PRK09906 5 HLRYFVAVAEE-----LNFTKAAEKLHT----AQPSLSQQIKDLENCVGVPLLVRD------KRKVALTAAGEVFLQ 66 (296)
T ss_pred HHHHHHHHHhh-----CCHHHHHHHhCC----CCcHHHHHHHHHHHHhCCeeeeeC------CCcceEcHhHHHHHH
Confidence 46788889884 499999999999 99999998888764 4688886 678999999987764
No 466
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=44.48 E-value=17 Score=23.06 Aligned_cols=21 Identities=24% Similarity=0.254 Sum_probs=14.0
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDR 72 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~r 72 (210)
.++|++|+|..+++ .+..+..
T Consensus 9 ~glsl~~va~~t~I----~~~~l~a 29 (62)
T PF13413_consen 9 KGLSLEDVAEETKI----SVSYLEA 29 (62)
T ss_dssp TT--HHHHHHHCS------HHHHHH
T ss_pred cCCCHHHHHHHhCC----CHHHHHH
Confidence 58999999999999 8776544
No 467
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=44.25 E-value=31 Score=19.36 Aligned_cols=23 Identities=26% Similarity=0.322 Sum_probs=18.2
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRIL 74 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlL 74 (210)
..+|..++|+.+++ ++..+.++.
T Consensus 9 ~~~s~~~la~~~~i----~~~~i~~~~ 31 (56)
T smart00530 9 KGLTQEELAEKLGV----SRSTLSRIE 31 (56)
T ss_pred cCCCHHHHHHHhCC----CHHHHHHHH
Confidence 47899999999999 777766543
No 468
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=44.15 E-value=33 Score=28.35 Aligned_cols=60 Identities=10% Similarity=0.074 Sum_probs=48.5
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHh---cccceeeeccCCCcccceecccccccccc
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLA---SYSVVECSLDASGARRLYSLNSVSKYYVP 107 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~---~~gl~~~~~~~~~~~~~y~~t~~s~~l~~ 107 (210)
-.+.+|..+.+. .|...-|+++++ .+..+.+-++.|. ..-||.+. ...+.+|+.++.|..
T Consensus 8 ~~L~~f~~v~~~-----gs~s~AA~~L~i----sQ~avS~~i~~LE~~lG~~LF~R~------~r~~~lT~~G~~l~~ 70 (302)
T PRK09791 8 HQIRAFVEVARQ-----GSIRGASRMLNM----SQPALTKSIQELEEGLAAQLFFRR------SKGVTLTDAGESFYQ 70 (302)
T ss_pred HHHHHHHHHHHc-----CCHHHHHHHhCC----ChHHHHHHHHHHHHHhCCeEEEEc------CCCceECccHHHHHH
Confidence 357788889884 499999999999 8988888887776 45688886 677999999987653
No 469
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=43.92 E-value=25 Score=29.40 Aligned_cols=59 Identities=17% Similarity=0.183 Sum_probs=48.9
Q ss_pred hhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhc---ccceeeeccCCCcccceecccccccccc
Q 036188 34 ELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLAS---YSVVECSLDASGARRLYSLNSVSKYYVP 107 (210)
Q Consensus 34 ~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~---~gl~~~~~~~~~~~~~y~~t~~s~~l~~ 107 (210)
.|.+|..+.+ ..|+..-|+++++ ....+.|-++.|.. .-||.+. ...+.+|+.++.|.+
T Consensus 6 ~L~~f~~v~e-----~gs~s~AA~~L~i----SQpavS~~I~~LE~~lg~~Lf~R~------~r~~~lT~~G~~l~~ 67 (308)
T PRK10094 6 TLRTFIAVAE-----TGSFSKAAERLCK----TTATISYRIKLLEENTGVALFFRT------TRSVTLTAAGEHLLS 67 (308)
T ss_pred HHHHHHHHHH-----hCCHHHHHHHhcC----CHHHHHHHHHHHHHHhCCEEEeeC------CCceeECHhHHHHHH
Confidence 5678999988 4599999999999 99999998887764 4588886 677999999987753
No 470
>KOG4058 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.88 E-value=24 Score=27.01 Aligned_cols=28 Identities=29% Similarity=0.361 Sum_probs=19.8
Q ss_pred HHHHHhCCCCCCCCeEEEecCCccHHHHh
Q 036188 179 SNILESYKGFDNIKQLVDVGGSLGVTLQA 207 (210)
Q Consensus 179 ~~~l~~~~~~~~~~~vvDiGGg~G~~~~~ 207 (210)
+.+++..+ -....++||+|.|.|....+
T Consensus 62 ~nVLSll~-~n~~GklvDlGSGDGRiVla 89 (199)
T KOG4058|consen 62 ENVLSLLR-GNPKGKLVDLGSGDGRIVLA 89 (199)
T ss_pred HHHHHHcc-CCCCCcEEeccCCCceeehh
Confidence 45566655 33457999999999986544
No 471
>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=43.83 E-value=30 Score=28.49 Aligned_cols=29 Identities=17% Similarity=0.255 Sum_probs=19.5
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAIT 209 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l~ 209 (210)
.|+...+ .....+||+.|-|+|.++..|+
T Consensus 31 ~I~~~l~-i~pG~~VlEaGtGSG~lt~~l~ 59 (247)
T PF08704_consen 31 YILMRLD-IRPGSRVLEAGTGSGSLTHALA 59 (247)
T ss_dssp HHHHHTT---TT-EEEEE--TTSHHHHHHH
T ss_pred HHHHHcC-CCCCCEEEEecCCcHHHHHHHH
Confidence 4455665 7778999999999999998875
No 472
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=43.61 E-value=40 Score=27.36 Aligned_cols=44 Identities=36% Similarity=0.365 Sum_probs=37.5
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
||+.|..+. |-+.++-||.+.|+ ....+---||-|.+.|+++..
T Consensus 194 I~eELdG~E--G~lvASkiADrvGI----TRSVIVNALRKlESAGvIeSR 237 (261)
T COG4465 194 IFEELDGNE--GLLVASKIADRVGI----TRSVIVNALRKLESAGVIESR 237 (261)
T ss_pred HHHhcCCcc--ceeeehhhhhhhCc----hHHHHHHHHHHhhhcCceeec
Confidence 677776543 78999999999999 888888899999999999865
No 473
>KOG3420 consensus Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=43.55 E-value=19 Score=27.49 Aligned_cols=28 Identities=29% Similarity=0.388 Sum_probs=19.8
Q ss_pred HHHHhCCCCCCCCeEEEecCCccHHHHhh
Q 036188 180 NILESYKGFDNIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G~~~~~l 208 (210)
.+-..|.++ ..++|.|+|||-|.+.++.
T Consensus 39 ~Ih~Tygdi-Egkkl~DLgcgcGmLs~a~ 66 (185)
T KOG3420|consen 39 TIHNTYGDI-EGKKLKDLGCGCGMLSIAF 66 (185)
T ss_pred HHHhhhccc-cCcchhhhcCchhhhHHHh
Confidence 334455523 4678999999999998654
No 474
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=43.52 E-value=17 Score=32.10 Aligned_cols=20 Identities=10% Similarity=-0.057 Sum_probs=16.6
Q ss_pred CCCCeEEEecCCccHHHHhh
Q 036188 189 DNIKQLVDVGGSLGVTLQAI 208 (210)
Q Consensus 189 ~~~~~vvDiGGg~G~~~~~l 208 (210)
.+.++|+|+|+|+|.++++.
T Consensus 219 ~~g~rVLDlfsgtG~~~l~a 238 (396)
T PRK15128 219 VENKRVLNCFSYTGGFAVSA 238 (396)
T ss_pred cCCCeEEEeccCCCHHHHHH
Confidence 34679999999999988764
No 475
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=43.49 E-value=33 Score=26.43 Aligned_cols=42 Identities=19% Similarity=0.148 Sum_probs=36.3
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
.++|+.|+|.+.++ +.+..+.-|..|-+.|-+.+. .-+|++-
T Consensus 123 ~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~------~~~~~~~ 164 (166)
T PRK15466 123 QGMTAGEVAAHFGW----PLEKARNALEQLFSAGTLRKR------SSRYRLK 164 (166)
T ss_pred ccccHHHHHHHhCC----cHHHHHHHHHHHHhccchhhc------ccccccc
Confidence 59999999999999 999999999999999998875 5666653
No 476
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=43.43 E-value=24 Score=28.81 Aligned_cols=39 Identities=10% Similarity=0.155 Sum_probs=29.9
Q ss_pred HHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 31 AVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 31 ~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
...++.+.+.|...- .-.|.+||++.||+ ++..|+|..+
T Consensus 7 ~~~~~~~v~~lr~lk--~~~ty~el~~~~g~----p~~~l~RYv~ 45 (238)
T PRK08558 7 VRLQLRAVRVLRSLK--KTYTYEELSSITGL----PESVLNRYVN 45 (238)
T ss_pred HHHHHHHHHHHHHHh--cccCHHHHHHHHCC----CHHHHHHHHc
Confidence 445666677776643 46899999999999 8888887764
No 477
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=43.38 E-value=33 Score=28.30 Aligned_cols=44 Identities=14% Similarity=0.234 Sum_probs=34.5
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
+.+.|..+- ..+.|+++||+++++ +++.+.|+.+--....+.+.
T Consensus 188 ~~~~i~~~~-~~~isl~~lA~~~~l----S~~~l~r~Fk~~~G~tp~~~ 231 (290)
T PRK10572 188 ACQYISDHL-ASEFDIESVAQHVCL----SPSRLAHLFRQQLGISVLRW 231 (290)
T ss_pred HHHHHHhcc-cCCCCHHHHHHHHCC----CHHHHHHHHHHHHCcCHHHH
Confidence 445564432 268999999999999 99999999998877766654
No 478
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=43.25 E-value=20 Score=22.74 Aligned_cols=44 Identities=25% Similarity=0.228 Sum_probs=28.2
Q ss_pred CCCHHHHHHHhcCC------CCCCcccHHHHHHHHhcccceeeeccCCCcccceec
Q 036188 49 KLSASDIAAQLLTK------NKDAPMMLDRILRLLASYSVVECSLDASGARRLYSL 98 (210)
Q Consensus 49 ~~t~~eLA~~~~~~------~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~ 98 (210)
+++++.|..-++.. -+++.+-|+.+|.-++..|.++.. .|.|++
T Consensus 11 sl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~------~G~YkL 60 (60)
T PF08672_consen 11 SLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLECS------GGSYKL 60 (60)
T ss_dssp SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE--------TTEEEE
T ss_pred CCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEec------CCEEeC
Confidence 45555555544321 122677899999999999999986 788874
No 479
>PRK13824 replication initiation protein RepC; Provisional
Probab=43.22 E-value=29 Score=30.82 Aligned_cols=34 Identities=18% Similarity=0.059 Sum_probs=30.6
Q ss_pred CCHHHHHHHh-cCCCCCCcccHHHHHHHHhcccceeeec
Q 036188 50 LSASDIAAQL-LTKNKDAPMMLDRILRLLASYSVVECSL 87 (210)
Q Consensus 50 ~t~~eLA~~~-~~~~~~~~~~l~rlLr~L~~~gl~~~~~ 87 (210)
.|-.+|+.++ |+ .++.|+|.++.|+..||+...+
T Consensus 83 pSN~~La~r~~Gm----s~~tlrRhla~LveaGLI~rrD 117 (404)
T PRK13824 83 PSNAQLSLRAHGM----AGATLRRHLAALVEAGLIIRRD 117 (404)
T ss_pred hhHHHHHHHHcCC----CHHHHHHHHHHHHHCCCeEeec
Confidence 5678999985 99 9999999999999999998763
No 480
>PRK00118 putative DNA-binding protein; Validated
Probab=42.95 E-value=24 Score=25.08 Aligned_cols=24 Identities=13% Similarity=0.163 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
...|..|||+.+|+ ++..+.+.+.
T Consensus 32 eg~S~~EIAe~lGI----S~~TV~r~L~ 55 (104)
T PRK00118 32 DDYSLGEIAEEFNV----SRQAVYDNIK 55 (104)
T ss_pred cCCCHHHHHHHHCc----CHHHHHHHHH
Confidence 48999999999999 8888877764
No 481
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=42.85 E-value=19 Score=22.50 Aligned_cols=23 Identities=26% Similarity=0.300 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRIL 74 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlL 74 (210)
.++|..++|+++|+ ++..+.++.
T Consensus 13 ~gls~~~lA~~~g~----s~s~v~~iE 35 (64)
T PF13560_consen 13 AGLSQAQLADRLGV----SQSTVSRIE 35 (64)
T ss_dssp HTS-HHHHHHHHTS-----HHHHHHHH
T ss_pred cCCCHHHHHHHHCc----CHHHHHHHH
Confidence 47899999999999 888877764
No 482
>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=42.76 E-value=23 Score=22.49 Aligned_cols=28 Identities=14% Similarity=0.221 Sum_probs=20.7
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHHHHhccccee
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVE 84 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~ 84 (210)
.++.|+|+.+|+ ++..++.+-+. .|++.
T Consensus 1 ~~i~e~A~~~gV----s~~tlr~ye~~---~gl~~ 28 (68)
T cd04763 1 YTIGEVALLTGI----KPHVLRAWERE---FGLLK 28 (68)
T ss_pred CCHHHHHHHHCc----CHHHHHHHHHh---cCCCC
Confidence 378999999999 99887766432 26653
No 483
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=42.59 E-value=26 Score=31.70 Aligned_cols=43 Identities=16% Similarity=0.251 Sum_probs=38.5
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
++.++.++ +++|..+|++.+++ +.+..+|.+..|...|++...
T Consensus 407 il~~~~en---~~~T~~~L~~~l~i----s~~~i~r~i~~Lv~~g~~~~~ 449 (467)
T COG2865 407 ILELIKEN---GKVTARELREILGI----SSETIRRRIANLVKRGLLKQL 449 (467)
T ss_pred HHHHHhhc---cccCHHHHHHHhCc----chhhHHHHHHHHhcccHHHHh
Confidence 56667775 59999999999999 999999999999999999875
No 484
>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=42.51 E-value=30 Score=21.67 Aligned_cols=24 Identities=17% Similarity=0.032 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
.+.++.|||+.+|+ +++-+..+.+
T Consensus 12 ~G~~~~eIA~~Lg~----~~~TV~~W~~ 35 (58)
T PF06056_consen 12 QGWSIKEIAEELGV----PRSTVYSWKD 35 (58)
T ss_pred cCCCHHHHHHHHCC----ChHHHHHHHH
Confidence 48899999999999 8887777654
No 485
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=42.42 E-value=35 Score=21.45 Aligned_cols=39 Identities=23% Similarity=0.378 Sum_probs=22.3
Q ss_pred hhhHHhhcCCCCCCCHHHHHHHh----cCCCCCCcc----cHHHHHHHHhccccee
Q 036188 37 IFEILDKAGPGTKLSASDIAAQL----LTKNKDAPM----MLDRILRLLASYSVVE 84 (210)
Q Consensus 37 lfd~L~~~g~~~~~t~~eLA~~~----~~~~~~~~~----~l~rlLr~L~~~gl~~ 84 (210)
|++.+ . ++.|+++|++.+ +. ++. .+..+|..|...|+++
T Consensus 22 Iw~~~-~----g~~t~~ei~~~l~~~y~~----~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 22 IWELL-D----GPRTVEEIVDALAEEYDV----DPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp HHHH-------SSS-HHHHHHHHHHHTT------HHHHHHHHHHHHHHHHHTT---
T ss_pred HHHHc-c----CCCCHHHHHHHHHHHcCC----CHHHHHHHHHHHHHHHHHCcCcC
Confidence 45556 2 588998877755 45 554 4677888888888864
No 486
>PF09959 DUF2193: Uncharacterized protein conserved in archaea (DUF2193); InterPro: IPR018694 This family of various hypothetical archaeal proteins has no known function
Probab=42.32 E-value=98 Score=27.48 Aligned_cols=79 Identities=23% Similarity=0.225 Sum_probs=51.8
Q ss_pred HHHHhhHHHHHhcCCchhhhhhC-CchhHhhc-cCchHHHHHHHHHhh---hhhhhHHHHHHhCCCCCCCCeEEEecCCc
Q 036188 127 LESWSQLKDAILEGGIPFNRAHG-VHIFEYAG-LNPRFNKHFNAAMYN---YTSLVMSNILESYKGFDNIKQLVDVGGSL 201 (210)
Q Consensus 127 ~~~~~~L~~~l~~g~~~f~~~~g-~~~fe~l~-~~p~~~~~f~~~M~~---~~~~~~~~~l~~~~~~~~~~~vvDiGGg~ 201 (210)
+.....|++.+|-...||-+-+. ....|.|. +||.+.+...+.+.. .......+.++.|.+|=++..|||-.=-.
T Consensus 68 yeiL~~LT~tvrPeDDPFVEhyQTP~ilEILy~eD~~F~ks~~kfi~~I~~sealIg~E~~RrygGFYGpTcVvDFAliP 147 (499)
T PF09959_consen 68 YEILKSLTDTVRPEDDPFVEHYQTPAILEILYEEDPAFRKSVEKFIEAIGKSEALIGKESARRYGGFYGPTCVVDFALIP 147 (499)
T ss_pred HHHHHHHhcccCCCCCchHhhccccHHHHHHHhcCHHHHHHHHHHHHHHhhhHHHhhHHHHHHhcCccCCceeeeeeecC
Confidence 45667788888776778755444 45666654 577776644444443 33344556678888899999999976555
Q ss_pred cHHH
Q 036188 202 GVTL 205 (210)
Q Consensus 202 G~~~ 205 (210)
|..+
T Consensus 148 GSTs 151 (499)
T PF09959_consen 148 GSTS 151 (499)
T ss_pred CchH
Confidence 5443
No 487
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=42.14 E-value=29 Score=28.09 Aligned_cols=48 Identities=15% Similarity=0.119 Sum_probs=35.4
Q ss_pred HHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHH-HHHhcccceee
Q 036188 29 IQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRIL-RLLASYSVVEC 85 (210)
Q Consensus 29 l~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlL-r~L~~~gl~~~ 85 (210)
-.+..|..|+..+++ ++|..|||+++++ .++-++..+ +.+..+|+-.+
T Consensus 143 ~LS~RE~eVL~Lia~-----G~SnkEIA~~L~I----S~~TVk~hvs~I~~KLgv~sR 191 (217)
T PRK13719 143 KVTKYQNDVFILYSF-----GFSHEYIAQLLNI----TVGSSKNKISEILKFFGISSR 191 (217)
T ss_pred CCCHHHHHHHHHHHC-----CCCHHHHHHHhCC----CHHHHHHHHHHHHHHhCCCCH
Confidence 345677889999987 8999999999999 888665443 45555555433
No 488
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=42.03 E-value=58 Score=29.34 Aligned_cols=47 Identities=13% Similarity=0.243 Sum_probs=34.7
Q ss_pred hchHHHHHHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 22 GVVLPMAIQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 22 ~~~~~~al~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
.||....+... .+.. +.+|+.+|++.|++ .+ .-++..|..+|++...
T Consensus 358 ~YW~~~i~~~L---------~~~~--~~~si~~is~~T~i----~~---~Dii~tL~~l~~l~~~ 404 (450)
T PLN00104 358 GYWTRVLLEIL---------KKHK--GNISIKELSDMTAI----KA---EDIVSTLQSLNLIQYR 404 (450)
T ss_pred HHHHHHHHHHH---------HhcC--CCccHHHHHHHhCC----CH---HHHHHHHHHCCCEEec
Confidence 56665555553 2332 58999999999999 44 4689999999999865
No 489
>cd00131 PAX Paired Box domain
Probab=41.94 E-value=17 Score=26.61 Aligned_cols=48 Identities=17% Similarity=0.189 Sum_probs=37.1
Q ss_pred HHHHHhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceee
Q 036188 29 IQAVYELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVEC 85 (210)
Q Consensus 29 l~~a~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~ 85 (210)
+..-.+..|..+..+ +.|..+||+++++ ....+.+|+.-....|=+..
T Consensus 18 lS~d~R~rIv~~~~~-----G~s~~~iA~~~~V----s~~tV~r~i~r~~e~G~v~p 65 (128)
T cd00131 18 LPDSIRQRIVELAQS-----GIRPCDISRQLRV----SHGCVSKILNRYYETGSIRP 65 (128)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCc----CHHHHHHHHHHHHHcCCcCC
Confidence 333445566655543 7899999999999 99999999999888886643
No 490
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=41.85 E-value=18 Score=34.39 Aligned_cols=21 Identities=10% Similarity=0.028 Sum_probs=0.0
Q ss_pred CCCeEEEecCCccHHHHhhhC
Q 036188 190 NIKQLVDVGGSLGVTLQAITT 210 (210)
Q Consensus 190 ~~~~vvDiGGg~G~~~~~l~~ 210 (210)
+.++|+|+|||+|.+++.+++
T Consensus 538 ~g~rVLDlf~gtG~~sl~aa~ 558 (702)
T PRK11783 538 KGKDFLNLFAYTGTASVHAAL 558 (702)
T ss_pred CCCeEEEcCCCCCHHHHHHHH
No 491
>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=41.78 E-value=24 Score=22.16 Aligned_cols=22 Identities=18% Similarity=0.104 Sum_probs=19.1
Q ss_pred CCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 50 LSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 50 ~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
.|+.|+|+.+|+ +++.++++-+
T Consensus 1 ~s~~eva~~~gv----s~~tlr~w~~ 22 (68)
T cd01104 1 YTIGAVARLTGV----SPDTLRAWER 22 (68)
T ss_pred CCHHHHHHHHCc----CHHHHHHHHH
Confidence 378999999999 9999888764
No 492
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=41.61 E-value=26 Score=20.51 Aligned_cols=21 Identities=24% Similarity=0.135 Sum_probs=17.7
Q ss_pred CCCCHHHHHHHhcCCCCCCcccHHH
Q 036188 48 TKLSASDIAAQLLTKNKDAPMMLDR 72 (210)
Q Consensus 48 ~~~t~~eLA~~~~~~~~~~~~~l~r 72 (210)
...|+.+||+++|+ ++..+.+
T Consensus 15 ~~~s~~~Ia~~~gv----s~~~~y~ 35 (47)
T PF00440_consen 15 EAVSIRDIARRAGV----SKGSFYR 35 (47)
T ss_dssp TTSSHHHHHHHHTS----CHHHHHH
T ss_pred HhCCHHHHHHHHcc----chhhHHH
Confidence 58999999999999 7776654
No 493
>TIGR03337 phnR transcriptional regulator protein. 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 Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=41.53 E-value=39 Score=26.84 Aligned_cols=42 Identities=14% Similarity=0.181 Sum_probs=36.0
Q ss_pred CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccc
Q 036188 51 SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNS 100 (210)
Q Consensus 51 t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~ 100 (210)
|-.|||+++|+ +..-+++=|+.|...|++.+.. +.|.|-..+
T Consensus 27 sE~eLa~~~~V----sr~Tvr~Al~~L~~eGli~~~~----g~Gt~V~~~ 68 (231)
T TIGR03337 27 SERDLGERFNT----TRVTIREALQQLEAEGLIYRED----RRGWFVSPP 68 (231)
T ss_pred CHHHHHHHHCC----CHHHHHHHHHHHHHCCeEEEeC----CCEEEECCc
Confidence 67899999999 9889999999999999999874 567776543
No 494
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=41.51 E-value=22 Score=29.46 Aligned_cols=36 Identities=19% Similarity=0.202 Sum_probs=27.0
Q ss_pred ChhhHHhhcCCCCC-CCHHHHHHHhcCCCCCCcccHHHHHHH
Q 036188 36 GIFEILDKAGPGTK-LSASDIAAQLLTKNKDAPMMLDRILRL 76 (210)
Q Consensus 36 glfd~L~~~g~~~~-~t~~eLA~~~~~~~~~~~~~l~rlLr~ 76 (210)
.+.++|.++=. .| +|+++||+++|+ +++.|.|+.+-
T Consensus 201 ~~~~~I~~~l~-~~~ls~~~lA~~~gi----S~r~L~r~Fk~ 237 (302)
T PRK09685 201 KVVALIDQSIQ-EEILRPEWIAGELGI----SVRSLYRLFAE 237 (302)
T ss_pred HHHHHHHHhcC-CCCCCHHHHHHHHCC----CHHHHHHHHHH
Confidence 34455555311 35 899999999999 99999998864
No 495
>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=41.37 E-value=39 Score=22.81 Aligned_cols=47 Identities=13% Similarity=0.006 Sum_probs=35.1
Q ss_pred CCCHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeeeccCCCcccceeccccc
Q 036188 49 KLSASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECSLDASGARRLYSLNSVS 102 (210)
Q Consensus 49 ~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t~~s 102 (210)
-...+.|++.+++ ++..+...|.-|...+++.... ..-..|++|-.+
T Consensus 24 ~VP~~~I~~~s~l----~~~~~~~~L~~L~~~kLv~~~~---~~Y~GYrLT~~G 70 (82)
T PF09202_consen 24 WVPLELIEKISGL----SEGEVEKRLKRLVKLKLVSRRN---KPYDGYRLTFLG 70 (82)
T ss_dssp SEEHHHHHHHHT------HHHHHHHHHHHHHTTSEEEE----SSS-EEEE-HHH
T ss_pred cCCHHHHHHHhCc----CHHHHHHHHHHHHhcCCccccC---CCcceEEEeecc
Confidence 5778999999999 9999999999999999999862 123557777654
No 496
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=41.27 E-value=20 Score=23.07 Aligned_cols=19 Identities=16% Similarity=0.221 Sum_probs=11.0
Q ss_pred CHHHHHHHhcCCCCCCcccHHHH
Q 036188 51 SASDIAAQLLTKNKDAPMMLDRI 73 (210)
Q Consensus 51 t~~eLA~~~~~~~~~~~~~l~rl 73 (210)
|..|||+++|+ ...-+.|+
T Consensus 2 t~~~iA~~~gv----S~~TVSr~ 20 (70)
T smart00354 2 TIKDVARLAGV----SKATVSRV 20 (70)
T ss_pred CHHHHHHHHCC----CHHHHHHH
Confidence 55677777776 54444443
No 497
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=41.26 E-value=32 Score=22.91 Aligned_cols=35 Identities=11% Similarity=0.091 Sum_probs=26.2
Q ss_pred CHHHHHHHhcCCCCCCcccHHHHHHHHhcccceeee
Q 036188 51 SASDIAAQLLTKNKDAPMMLDRILRLLASYSVVECS 86 (210)
Q Consensus 51 t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gl~~~~ 86 (210)
...+|++..|+ +|...+.+..++.-|..+|+++..
T Consensus 24 ~Y~~lc~~~~~-~pls~~r~~~~l~eL~~~gli~~~ 58 (85)
T PF09079_consen 24 VYEELCESLGV-DPLSYRRFSDYLSELEMLGLIESE 58 (85)
T ss_dssp HHHHHHHHTTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHcCC-CCCCHHHHHHHHHHHHhCCCeEEE
Confidence 45788999999 566777888889999999999765
No 498
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=41.23 E-value=32 Score=25.71 Aligned_cols=34 Identities=24% Similarity=0.353 Sum_probs=25.4
Q ss_pred HhhChhhHHhhcCCCCCCCHHHHHHHhcCCCCCCcccHHHHHH
Q 036188 33 YELGIFEILDKAGPGTKLSASDIAAQLLTKNKDAPMMLDRILR 75 (210)
Q Consensus 33 ~~lglfd~L~~~g~~~~~t~~eLA~~~~~~~~~~~~~l~rlLr 75 (210)
.+..++.+.. .+.|.+|||+.+|+ ++..+.++.+
T Consensus 10 ~qr~VL~Lr~-----~GlTq~EIAe~Lgi----S~stV~~~e~ 43 (137)
T TIGR00721 10 RQIKVLELRE-----KGLSQKEIAKELKT----TRANVSAIEK 43 (137)
T ss_pred HHHHHHHHHH-----cCCCHHHHHHHHCc----CHHHHHHHHH
Confidence 3445565543 48999999999999 8888876553
No 499
>PF10678 DUF2492: Protein of unknown function (DUF2492); InterPro: IPR019620 This entry describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulphatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulphur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulphatase/maturase systems.
Probab=41.09 E-value=1.1e+02 Score=20.54 Aligned_cols=42 Identities=10% Similarity=0.142 Sum_probs=31.9
Q ss_pred CCCCHHHH----HHHhcCCCCCCcc---------cHHHHHHHHhcccceeeeccCCCcccceecc
Q 036188 48 TKLSASDI----AAQLLTKNKDAPM---------MLDRILRLLASYSVVECSLDASGARRLYSLN 99 (210)
Q Consensus 48 ~~~t~~eL----A~~~~~~~~~~~~---------~l~rlLr~L~~~gl~~~~~~~~~~~~~y~~t 99 (210)
.|.|.++| .++.|. +.+ -+..|+..|...|=|.+. ++.|..+
T Consensus 18 ~~~t~~~L~~ai~~~FG~----~arFhTCSae~m~a~eLv~FL~~rgKfi~~------~~g~t~~ 72 (78)
T PF10678_consen 18 NPYTKEELKAAIIEKFGE----DARFHTCSAEGMTADELVDFLEERGKFIPS------DDGFTVN 72 (78)
T ss_pred CCcCHHHHHHHHHHHhCC----CceEEecCCCCCCHHHHHHHHHHcCCEeec------CCCEEEc
Confidence 69999888 666676 554 388999999999988875 5555544
No 500
>COG0248 GppA Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]
Probab=41.06 E-value=25 Score=32.06 Aligned_cols=22 Identities=14% Similarity=0.270 Sum_probs=17.2
Q ss_pred HHHHhCCCCCCCCeEEEecCCcc
Q 036188 180 NILESYKGFDNIKQLVDVGGSLG 202 (210)
Q Consensus 180 ~~l~~~~~~~~~~~vvDiGGg~G 202 (210)
.+...++ +.+...++|||||+=
T Consensus 120 Gv~~~~~-~~~~~lv~DIGGGSt 141 (492)
T COG0248 120 GVASTLP-RKGDGLVIDIGGGST 141 (492)
T ss_pred HHHhcCC-CCCCEEEEEecCCeE
Confidence 4466677 678889999999974
Done!