Query 036971
Match_columns 221
No_of_seqs 122 out of 1073
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 07:15:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036971.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036971hhsearch_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 6.2E-25 1.4E-29 186.6 16.6 200 14-221 2-202 (342)
2 TIGR02716 C20_methyl_CrtF C-20 99.9 7.3E-24 1.6E-28 181.7 13.0 169 30-221 2-174 (306)
3 PF00891 Methyltransf_2: O-met 99.9 4E-21 8.6E-26 159.4 10.8 123 98-221 2-125 (241)
4 PF08100 Dimerisation: Dimeris 99.1 1.5E-10 3.3E-15 72.5 5.2 50 33-85 1-51 (51)
5 PF09339 HTH_IclR: IclR helix- 97.4 5.8E-05 1.3E-09 47.4 0.9 46 41-93 6-51 (52)
6 PRK06922 hypothetical protein; 97.3 0.00049 1.1E-08 64.4 6.3 64 156-220 377-442 (677)
7 smart00346 HTH_ICLR helix_turn 97.2 0.00054 1.2E-08 47.7 4.4 58 41-108 8-65 (91)
8 smart00550 Zalpha Z-DNA-bindin 97.0 0.0017 3.7E-08 43.1 5.1 60 38-106 6-66 (68)
9 COG1414 IclR Transcriptional r 97.0 0.00099 2.2E-08 55.6 4.3 59 41-109 7-65 (246)
10 TIGR02431 pcaR_pcaU beta-ketoa 96.8 0.0013 2.9E-08 54.7 4.0 58 41-110 12-69 (248)
11 PRK11569 transcriptional repre 96.8 0.0016 3.4E-08 55.2 4.4 59 41-109 31-89 (274)
12 PRK10163 DNA-binding transcrip 96.8 0.0017 3.7E-08 54.8 4.5 59 41-109 28-86 (271)
13 PF02082 Rrf2: Transcriptional 96.8 0.0015 3.3E-08 45.1 3.3 55 47-108 17-71 (83)
14 PRK15090 DNA-binding transcrip 96.7 0.002 4.4E-08 53.9 4.3 58 41-109 17-74 (257)
15 PRK09834 DNA-binding transcrip 96.7 0.0025 5.4E-08 53.6 4.7 61 41-111 14-74 (263)
16 PF12840 HTH_20: Helix-turn-he 96.5 0.0024 5.1E-08 41.4 2.5 54 32-93 4-57 (61)
17 PF01978 TrmB: Sugar-specific 96.3 0.0022 4.7E-08 42.4 1.7 46 40-93 10-55 (68)
18 TIGR02469 CbiT precorrin-6Y C5 96.3 0.0096 2.1E-07 43.2 5.3 33 187-220 11-43 (124)
19 TIGR02021 BchM-ChlM magnesium 96.3 0.011 2.4E-07 48.0 6.1 61 158-218 16-77 (219)
20 PF01022 HTH_5: Bacterial regu 96.3 0.0028 6.1E-08 38.8 1.9 44 40-92 4-47 (47)
21 COG2813 RsmC 16S RNA G1207 met 96.1 0.0079 1.7E-07 51.3 4.6 35 185-220 148-182 (300)
22 PRK10857 DNA-binding transcrip 96.1 0.011 2.4E-07 46.2 5.0 47 54-107 24-70 (164)
23 PF13412 HTH_24: Winged helix- 96.1 0.0065 1.4E-07 37.2 2.9 45 39-91 4-48 (48)
24 COG1959 Predicted transcriptio 96.0 0.012 2.6E-07 45.4 4.7 56 46-108 16-71 (150)
25 PF09012 FeoC: FeoC like trans 96.0 0.0076 1.7E-07 40.0 3.1 43 43-93 5-47 (69)
26 PF04703 FaeA: FaeA-like prote 96.0 0.0098 2.1E-07 38.8 3.4 45 42-93 4-48 (62)
27 PRK10141 DNA-binding transcrip 95.9 0.014 3E-07 43.1 4.3 56 30-93 8-63 (117)
28 PF14947 HTH_45: Winged helix- 95.9 0.0059 1.3E-07 41.6 2.2 56 43-112 11-66 (77)
29 TIGR02010 IscR iron-sulfur clu 95.9 0.016 3.4E-07 43.8 4.7 46 54-106 24-69 (135)
30 smart00419 HTH_CRP helix_turn_ 95.9 0.012 2.7E-07 35.5 3.4 40 55-104 8-47 (48)
31 PRK15001 SAM-dependent 23S rib 95.8 0.013 2.8E-07 51.9 4.6 35 185-220 218-252 (378)
32 cd00092 HTH_CRP helix_turn_hel 95.7 0.016 3.6E-07 37.6 3.8 44 54-106 24-67 (67)
33 PRK00274 ksgA 16S ribosomal RN 95.7 0.018 3.9E-07 48.7 4.8 35 185-220 32-66 (272)
34 COG3355 Predicted transcriptio 95.7 0.02 4.3E-07 42.7 4.4 47 40-94 29-76 (126)
35 PF13463 HTH_27: Winged helix 95.6 0.017 3.6E-07 37.8 3.5 49 54-107 17-67 (68)
36 TIGR00738 rrf2_super rrf2 fami 95.5 0.023 4.9E-07 42.4 4.4 46 54-106 24-69 (132)
37 PRK00107 gidB 16S rRNA methylt 95.4 0.031 6.7E-07 44.7 5.1 25 196-220 45-69 (187)
38 COG2345 Predicted transcriptio 95.2 0.036 7.8E-07 45.2 4.9 63 42-112 15-81 (218)
39 smart00347 HTH_MARR helix_turn 95.2 0.032 6.9E-07 38.9 4.1 65 40-112 12-78 (101)
40 PRK14121 tRNA (guanine-N(7)-)- 95.1 0.03 6.5E-07 49.7 4.6 33 187-220 114-146 (390)
41 PRK03902 manganese transport t 95.1 0.039 8.4E-07 41.9 4.6 50 54-112 21-70 (142)
42 TIGR02944 suf_reg_Xantho FeS a 95.1 0.03 6.6E-07 41.8 3.9 46 54-106 24-69 (130)
43 PRK00121 trmB tRNA (guanine-N( 95.0 0.032 7E-07 44.9 4.1 32 187-220 33-64 (202)
44 TIGR02702 SufR_cyano iron-sulf 95.0 0.046 9.9E-07 44.1 4.9 65 40-112 3-71 (203)
45 PF07381 DUF1495: Winged helix 94.9 0.049 1.1E-06 38.2 4.2 69 37-112 8-87 (90)
46 TIGR02752 MenG_heptapren 2-hep 94.9 0.04 8.6E-07 45.0 4.4 32 186-218 36-67 (231)
47 COG2230 Cfa Cyclopropane fatty 94.9 0.053 1.1E-06 46.1 5.1 34 184-218 61-94 (283)
48 PRK15068 tRNA mo(5)U34 methylt 94.8 0.039 8.4E-07 47.9 4.4 24 197-220 123-146 (322)
49 PRK07402 precorrin-6B methylas 94.8 0.068 1.5E-06 42.6 5.4 33 187-220 32-64 (196)
50 PRK10258 biotin biosynthesis p 94.7 0.082 1.8E-06 43.8 5.9 34 183-217 30-63 (251)
51 PRK09489 rsmC 16S ribosomal RN 94.7 0.049 1.1E-06 47.7 4.6 33 187-220 188-220 (342)
52 TIGR02337 HpaR homoprotocatech 94.6 0.12 2.7E-06 37.7 6.0 68 39-114 29-98 (118)
53 PF02353 CMAS: Mycolic acid cy 94.6 0.04 8.7E-07 46.7 3.8 34 184-218 51-84 (273)
54 PRK07580 Mg-protoporphyrin IX 94.6 0.069 1.5E-06 43.4 5.1 26 194-219 61-86 (230)
55 PF08461 HTH_12: Ribonuclease 94.5 0.058 1.2E-06 35.6 3.7 60 43-109 3-63 (66)
56 PF13601 HTH_34: Winged helix 94.5 0.029 6.2E-07 38.5 2.3 64 39-110 1-67 (80)
57 TIGR03587 Pse_Me-ase pseudamin 94.5 0.047 1E-06 44.1 3.9 25 196-220 43-67 (204)
58 smart00420 HTH_DEOR helix_turn 94.5 0.084 1.8E-06 32.2 4.2 43 43-93 5-47 (53)
59 PRK06202 hypothetical protein; 94.4 0.084 1.8E-06 43.3 5.3 23 195-217 59-81 (232)
60 PHA00738 putative HTH transcri 94.4 0.079 1.7E-06 38.3 4.4 48 38-93 12-59 (108)
61 PRK06266 transcription initiat 94.4 0.12 2.6E-06 41.0 5.8 45 41-93 25-69 (178)
62 KOG3115 Methyltransferase-like 94.4 0.018 3.8E-07 46.5 1.0 24 197-220 61-84 (249)
63 PRK11036 putative S-adenosyl-L 94.3 0.076 1.6E-06 44.2 4.9 31 186-218 36-66 (255)
64 TIGR00122 birA_repr_reg BirA b 94.3 0.075 1.6E-06 35.1 3.9 55 40-107 2-56 (69)
65 PRK11050 manganese transport r 94.3 0.078 1.7E-06 40.9 4.5 59 42-112 41-99 (152)
66 TIGR00138 gidB 16S rRNA methyl 94.3 0.035 7.6E-07 44.0 2.6 24 197-220 43-66 (181)
67 PF12802 MarR_2: MarR family; 94.3 0.04 8.6E-07 35.2 2.4 49 40-94 7-55 (62)
68 COG4742 Predicted transcriptio 94.2 0.081 1.8E-06 44.3 4.7 67 34-114 9-75 (260)
69 PF08220 HTH_DeoR: DeoR-like h 94.2 0.1 2.3E-06 33.2 4.2 44 42-93 4-47 (57)
70 TIGR00452 methyltransferase, p 94.2 0.091 2E-06 45.4 5.1 33 187-220 113-145 (314)
71 PRK11920 rirA iron-responsive 94.1 0.07 1.5E-06 41.2 4.0 47 54-107 23-69 (153)
72 PRK11188 rrmJ 23S rRNA methylt 94.1 0.11 2.4E-06 42.1 5.4 32 187-218 42-73 (209)
73 PF01047 MarR: MarR family; I 94.0 0.036 7.9E-07 35.2 1.8 47 40-94 5-51 (59)
74 PRK11088 rrmA 23S rRNA methylt 94.0 0.16 3.5E-06 42.8 6.2 25 196-220 85-109 (272)
75 TIGR00080 pimt protein-L-isoas 93.9 0.11 2.5E-06 42.0 5.1 33 186-219 68-100 (215)
76 smart00418 HTH_ARSR helix_turn 93.9 0.13 2.8E-06 32.5 4.4 42 43-93 2-43 (66)
77 COG1321 TroR Mn-dependent tran 93.9 0.12 2.5E-06 40.1 4.8 51 54-113 23-73 (154)
78 PTZ00098 phosphoethanolamine N 93.8 0.093 2E-06 44.1 4.5 33 185-218 42-74 (263)
79 TIGR03438 probable methyltrans 93.8 0.097 2.1E-06 44.9 4.6 60 155-219 27-86 (301)
80 TIGR01884 cas_HTH CRISPR locus 93.8 0.12 2.5E-06 41.8 4.8 58 40-107 145-202 (203)
81 COG2264 PrmA Ribosomal protein 93.8 0.056 1.2E-06 46.3 3.0 43 171-216 140-182 (300)
82 PLN02336 phosphoethanolamine N 93.6 0.083 1.8E-06 48.1 4.1 35 184-219 26-60 (475)
83 COG4976 Predicted methyltransf 93.6 0.078 1.7E-06 43.7 3.4 47 168-215 94-144 (287)
84 smart00344 HTH_ASNC helix_turn 93.6 0.1 2.2E-06 37.4 3.7 47 39-93 4-50 (108)
85 COG0220 Predicted S-adenosylme 93.6 0.11 2.3E-06 42.9 4.3 24 198-221 50-73 (227)
86 cd00090 HTH_ARSR Arsenical Res 93.5 0.15 3.3E-06 33.1 4.3 57 40-106 9-65 (78)
87 PF08003 Methyltransf_9: Prote 93.5 0.097 2.1E-06 44.9 3.9 33 187-220 107-139 (315)
88 PLN02244 tocopherol O-methyltr 93.4 0.14 3.1E-06 44.7 5.0 24 195-218 117-140 (340)
89 PF07757 AdoMet_MTase: Predict 93.4 0.24 5.2E-06 35.9 5.2 36 179-215 42-77 (112)
90 cd07153 Fur_like Ferric uptake 93.3 0.18 4E-06 36.5 4.8 64 40-105 3-66 (116)
91 PF06163 DUF977: Bacterial pro 93.3 0.17 3.8E-06 37.5 4.5 50 36-93 10-59 (127)
92 PRK00216 ubiE ubiquinone/menaq 93.2 0.16 3.5E-06 41.2 4.9 33 186-219 42-74 (239)
93 PRK11705 cyclopropane fatty ac 93.2 0.18 3.8E-06 44.9 5.4 33 185-218 157-189 (383)
94 PRK13944 protein-L-isoaspartat 93.2 0.18 3.9E-06 40.6 5.1 33 186-219 63-95 (205)
95 TIGR01934 MenG_MenH_UbiE ubiqu 93.2 0.18 3.8E-06 40.5 5.0 33 187-220 31-63 (223)
96 TIGR00740 methyltransferase, p 93.1 0.096 2.1E-06 43.1 3.3 23 196-218 53-75 (239)
97 PHA02943 hypothetical protein; 93.1 0.43 9.3E-06 36.7 6.5 105 42-177 15-119 (165)
98 PRK15431 ferrous iron transpor 93.0 0.18 3.8E-06 34.3 3.9 43 43-93 7-49 (78)
99 COG4190 Predicted transcriptio 93.0 0.2 4.2E-06 37.5 4.4 53 33-93 59-111 (144)
100 PRK15451 tRNA cmo(5)U34 methyl 93.0 0.1 2.2E-06 43.3 3.4 25 196-220 56-82 (247)
101 KOG2899 Predicted methyltransf 93.0 0.089 1.9E-06 43.7 2.9 34 185-218 46-80 (288)
102 PF01638 HxlR: HxlR-like helix 93.0 0.07 1.5E-06 37.2 2.0 61 43-112 10-73 (90)
103 PF04967 HTH_10: HTH DNA bindi 92.9 0.11 2.4E-06 32.7 2.6 43 30-83 4-46 (53)
104 PF01726 LexA_DNA_bind: LexA D 92.8 0.13 2.9E-06 33.7 3.1 42 46-93 18-59 (65)
105 smart00529 HTH_DTXR Helix-turn 92.8 0.12 2.7E-06 36.1 3.1 46 58-112 2-47 (96)
106 TIGR03534 RF_mod_PrmC protein- 92.7 0.21 4.5E-06 41.1 4.8 24 197-220 88-111 (251)
107 PTZ00338 dimethyladenosine tra 92.6 0.19 4.1E-06 43.1 4.6 34 185-219 26-59 (294)
108 PRK11014 transcriptional repre 92.5 0.22 4.8E-06 37.7 4.4 46 54-106 24-69 (141)
109 TIGR03704 PrmC_rel_meth putati 92.5 0.25 5.4E-06 41.2 5.0 24 197-220 87-110 (251)
110 PRK09328 N5-glutamine S-adenos 92.4 0.23 5.1E-06 41.5 4.8 27 194-220 106-132 (275)
111 smart00345 HTH_GNTR helix_turn 92.4 0.27 5.8E-06 30.7 4.0 35 54-93 18-53 (60)
112 COG2226 UbiE Methylase involve 92.4 0.29 6.4E-06 40.6 5.2 24 196-219 51-74 (238)
113 PF05185 PRMT5: PRMT5 arginine 92.3 0.23 5E-06 45.1 5.0 57 157-217 151-207 (448)
114 PF06325 PrmA: Ribosomal prote 92.3 0.16 3.5E-06 43.5 3.8 42 172-216 140-181 (295)
115 COG2890 HemK Methylase of poly 92.3 0.2 4.2E-06 42.7 4.3 22 199-220 113-134 (280)
116 PF13679 Methyltransf_32: Meth 92.3 0.1 2.2E-06 39.5 2.2 24 194-217 23-46 (141)
117 PRK04266 fibrillarin; Provisio 92.2 0.18 3.8E-06 41.6 3.7 29 190-219 67-95 (226)
118 TIGR00373 conserved hypothetic 92.2 0.22 4.8E-06 38.7 4.1 45 41-93 17-61 (158)
119 PLN02233 ubiquinone biosynthes 92.2 0.4 8.6E-06 40.2 5.9 25 194-218 71-95 (261)
120 PF14394 DUF4423: Domain of un 92.1 0.27 6E-06 38.7 4.6 65 27-110 21-87 (171)
121 cd07377 WHTH_GntR Winged helix 92.1 0.32 7E-06 31.0 4.2 33 56-93 26-58 (66)
122 PF04182 B-block_TFIIIC: B-blo 92.1 0.22 4.7E-06 33.6 3.5 49 39-93 3-51 (75)
123 TIGR03533 L3_gln_methyl protei 92.0 0.15 3.3E-06 43.3 3.3 24 197-220 122-145 (284)
124 PRK05785 hypothetical protein; 92.0 0.15 3.3E-06 41.8 3.1 22 197-218 52-73 (226)
125 PF10007 DUF2250: Uncharacteri 92.0 0.26 5.7E-06 34.7 3.8 47 39-93 8-54 (92)
126 COG2227 UbiG 2-polyprenyl-3-me 91.8 0.12 2.7E-06 42.7 2.3 21 197-217 60-80 (243)
127 PRK13942 protein-L-isoaspartat 91.7 0.34 7.4E-06 39.3 4.9 32 186-218 67-98 (212)
128 COG4189 Predicted transcriptio 91.7 0.33 7.2E-06 40.0 4.7 55 32-94 17-71 (308)
129 PF05148 Methyltransf_8: Hypot 91.7 0.25 5.5E-06 40.2 4.0 58 159-216 31-92 (219)
130 PRK04457 spermidine synthase; 91.6 0.19 4.1E-06 42.2 3.4 25 196-220 66-90 (262)
131 smart00138 MeTrc Methyltransfe 91.6 0.52 1.1E-05 39.6 6.0 34 185-219 89-126 (264)
132 KOG1271 Methyltransferases [Ge 91.5 0.26 5.7E-06 39.3 3.8 21 197-217 68-88 (227)
133 PLN02336 phosphoethanolamine N 91.5 0.27 5.7E-06 44.8 4.5 34 184-218 255-288 (475)
134 TIGR02147 Fsuc_second hypothet 91.4 0.83 1.8E-05 38.7 7.0 47 55-110 137-185 (271)
135 PF01325 Fe_dep_repress: Iron 91.3 0.25 5.5E-06 31.8 3.0 35 54-93 21-55 (60)
136 PRK03573 transcriptional regul 91.3 0.45 9.9E-06 35.9 4.9 63 43-112 36-100 (144)
137 PRK12335 tellurite resistance 91.3 0.24 5.2E-06 42.1 3.7 21 197-217 121-141 (287)
138 COG3432 Predicted transcriptio 91.2 0.14 3E-06 36.2 1.8 60 43-113 20-83 (95)
139 PRK11805 N5-glutamine S-adenos 91.2 0.17 3.8E-06 43.5 2.8 23 198-220 135-157 (307)
140 PF08279 HTH_11: HTH domain; 91.1 0.48 1E-05 29.5 4.1 44 42-92 4-47 (55)
141 COG4123 Predicted O-methyltran 91.1 0.25 5.4E-06 41.2 3.5 27 194-220 42-68 (248)
142 PLN02490 MPBQ/MSBQ methyltrans 90.9 0.45 9.7E-06 41.6 5.1 33 187-220 104-137 (340)
143 PRK14966 unknown domain/N5-glu 90.8 0.37 8E-06 43.3 4.5 25 196-220 251-275 (423)
144 TIGR00478 tly hemolysin TlyA f 90.8 0.5 1.1E-05 39.0 5.0 33 185-217 64-96 (228)
145 TIGR00536 hemK_fam HemK family 90.7 0.21 4.5E-06 42.4 2.8 23 198-220 116-138 (284)
146 PRK00517 prmA ribosomal protei 90.5 0.31 6.7E-06 40.6 3.6 24 196-219 119-142 (250)
147 TIGR00406 prmA ribosomal prote 90.4 0.34 7.5E-06 41.2 3.9 29 187-217 152-180 (288)
148 PRK00377 cbiT cobalt-precorrin 90.4 0.39 8.5E-06 38.3 4.0 30 188-218 33-62 (198)
149 TIGR01610 phage_O_Nterm phage 90.2 0.47 1E-05 33.5 3.9 44 54-105 46-89 (95)
150 PRK01544 bifunctional N5-gluta 89.9 0.3 6.5E-06 45.0 3.3 26 196-221 347-372 (506)
151 PF01209 Ubie_methyltran: ubiE 89.9 0.31 6.7E-06 40.3 3.1 25 194-218 45-69 (233)
152 PF08784 RPA_C: Replication pr 89.8 0.28 6E-06 35.0 2.4 51 38-93 47-98 (102)
153 PRK01544 bifunctional N5-gluta 89.7 0.32 6.9E-06 44.9 3.3 24 197-220 139-162 (506)
154 PRK06474 hypothetical protein; 89.6 0.58 1.3E-05 37.1 4.3 72 33-111 6-82 (178)
155 PRK13943 protein-L-isoaspartat 89.6 0.61 1.3E-05 40.5 4.8 32 187-219 72-103 (322)
156 PRK11512 DNA-binding transcrip 89.5 0.61 1.3E-05 35.3 4.3 63 41-112 43-108 (144)
157 PF02002 TFIIE_alpha: TFIIE al 89.4 0.3 6.5E-06 35.0 2.3 43 43-93 18-60 (105)
158 PRK11179 DNA-binding transcrip 89.3 0.53 1.2E-05 36.1 3.8 47 39-93 10-56 (153)
159 KOG1499 Protein arginine N-met 89.2 0.61 1.3E-05 40.6 4.5 22 197-218 61-82 (346)
160 PLN02396 hexaprenyldihydroxybe 89.2 0.32 6.9E-06 42.2 2.8 21 197-217 132-152 (322)
161 PRK13168 rumA 23S rRNA m(5)U19 89.2 0.41 9E-06 43.3 3.6 33 185-218 287-319 (443)
162 KOG1270 Methyltransferases [Co 89.2 0.2 4.3E-06 42.0 1.4 20 198-217 91-110 (282)
163 PRK04214 rbn ribonuclease BN/u 89.1 0.54 1.2E-05 42.2 4.3 43 54-105 309-351 (412)
164 COG2512 Predicted membrane-ass 89.0 0.5 1.1E-05 39.7 3.7 48 40-94 197-244 (258)
165 PRK00312 pcm protein-L-isoaspa 89.0 0.7 1.5E-05 37.2 4.5 30 187-217 70-99 (212)
166 PRK11169 leucine-responsive tr 89.0 0.48 1E-05 36.9 3.4 47 38-92 14-60 (164)
167 PF03444 HrcA_DNA-bdg: Winged 88.9 0.85 1.9E-05 31.0 4.1 63 33-109 8-70 (78)
168 PLN02366 spermidine synthase 88.9 0.42 9.1E-06 41.3 3.2 25 195-220 90-114 (308)
169 PRK14967 putative methyltransf 88.7 0.51 1.1E-05 38.4 3.5 29 188-217 29-57 (223)
170 PRK05134 bifunctional 3-demeth 88.6 0.81 1.8E-05 37.3 4.7 22 196-217 48-69 (233)
171 PF07789 DUF1627: Protein of u 88.1 0.89 1.9E-05 34.7 4.1 35 54-93 5-39 (155)
172 TIGR00498 lexA SOS regulatory 87.8 1 2.2E-05 36.0 4.7 40 54-103 24-64 (199)
173 COG1522 Lrp Transcriptional re 87.8 0.82 1.8E-05 34.7 4.0 48 38-93 8-55 (154)
174 PRK04172 pheS phenylalanyl-tRN 87.7 0.6 1.3E-05 42.9 3.7 68 39-116 7-75 (489)
175 COG1378 Predicted transcriptio 87.6 1.3 2.8E-05 37.0 5.3 56 44-109 22-77 (247)
176 TIGR01889 Staph_reg_Sar staphy 87.5 0.83 1.8E-05 32.9 3.6 66 40-112 27-97 (109)
177 KOG1541 Predicted protein carb 87.2 0.34 7.4E-06 39.8 1.6 27 187-214 40-68 (270)
178 PLN02585 magnesium protoporphy 86.9 0.56 1.2E-05 40.6 2.8 21 197-217 145-165 (315)
179 PRK00811 spermidine synthase; 86.8 0.58 1.2E-05 39.8 2.9 23 195-217 75-97 (283)
180 PRK10870 transcriptional repre 86.7 0.86 1.9E-05 35.9 3.6 66 42-113 59-126 (176)
181 PHA03412 putative methyltransf 86.4 0.5 1.1E-05 39.2 2.2 23 197-219 50-72 (241)
182 PRK14165 winged helix-turn-hel 86.3 0.9 1.9E-05 37.2 3.6 53 54-112 20-72 (217)
183 PRK05638 threonine synthase; V 86.3 1.1 2.4E-05 40.6 4.5 61 43-112 376-438 (442)
184 COG4565 CitB Response regulato 86.2 0.94 2E-05 36.9 3.5 44 43-93 163-206 (224)
185 PF08123 DOT1: Histone methyla 86.1 0.93 2E-05 36.8 3.6 32 186-218 33-64 (205)
186 KOG1500 Protein arginine N-met 86.0 1.5 3.2E-05 38.4 4.8 23 190-214 173-195 (517)
187 PF00325 Crp: Bacterial regula 86.0 0.49 1.1E-05 26.5 1.3 31 55-90 2-32 (32)
188 KOG2904 Predicted methyltransf 85.7 1.2 2.7E-05 37.7 4.1 27 194-220 146-172 (328)
189 PHA03411 putative methyltransf 85.7 0.76 1.6E-05 39.0 2.9 23 197-219 65-87 (279)
190 PLN02853 Probable phenylalanyl 85.6 0.86 1.9E-05 41.7 3.5 71 37-116 2-73 (492)
191 PF08221 HTH_9: RNA polymerase 85.6 0.77 1.7E-05 29.7 2.3 43 43-93 18-60 (62)
192 PF01135 PCMT: Protein-L-isoas 85.5 1.5 3.3E-05 35.6 4.5 31 185-216 62-92 (209)
193 PRK10901 16S rRNA methyltransf 85.3 1 2.3E-05 40.5 3.9 32 187-219 236-267 (427)
194 PRK11873 arsM arsenite S-adeno 85.3 0.89 1.9E-05 38.1 3.2 25 194-218 75-99 (272)
195 PRK13255 thiopurine S-methyltr 84.8 1.6 3.4E-05 35.7 4.3 23 195-217 36-58 (218)
196 PF03141 Methyltransf_29: Puta 84.3 0.84 1.8E-05 41.7 2.8 23 195-217 116-138 (506)
197 PRK13509 transcriptional repre 84.1 1.7 3.8E-05 36.2 4.4 45 41-93 8-52 (251)
198 PF13404 HTH_AsnC-type: AsnC-t 84.1 1 2.2E-05 26.8 2.2 29 39-71 4-32 (42)
199 PLN03075 nicotianamine synthas 83.9 1.5 3.4E-05 37.5 4.1 25 196-220 123-149 (296)
200 PF00392 GntR: Bacterial regul 83.5 1.2 2.5E-05 28.8 2.5 35 54-93 22-57 (64)
201 TIGR00479 rumA 23S rRNA (uraci 83.5 1.2 2.7E-05 40.0 3.5 25 194-218 290-314 (431)
202 TIGR01983 UbiG ubiquinone bios 83.4 1.1 2.5E-05 36.0 3.0 23 197-219 46-68 (224)
203 PF01475 FUR: Ferric uptake re 83.3 1.3 2.8E-05 32.4 3.0 68 37-106 7-74 (120)
204 COG1733 Predicted transcriptio 83.3 3.6 7.8E-05 30.4 5.3 77 18-112 12-91 (120)
205 PRK01581 speE spermidine synth 83.1 1.1 2.3E-05 39.7 2.9 24 195-218 149-172 (374)
206 PLN02672 methionine S-methyltr 82.7 1 2.2E-05 45.2 2.9 23 198-220 120-142 (1082)
207 PF12324 HTH_15: Helix-turn-he 82.6 2.2 4.8E-05 28.9 3.6 40 43-93 29-68 (77)
208 COG1497 Predicted transcriptio 82.4 1.2 2.7E-05 36.8 2.8 85 54-149 24-111 (260)
209 PF05584 Sulfolobus_pRN: Sulfo 82.3 2.7 6E-05 28.1 3.9 44 41-93 8-51 (72)
210 COG2263 Predicted RNA methylas 82.2 1.1 2.4E-05 35.9 2.4 20 197-216 46-65 (198)
211 COG5631 Predicted transcriptio 82.1 10 0.00022 29.5 7.5 78 25-109 63-147 (199)
212 PTZ00326 phenylalanyl-tRNA syn 82.0 1.8 3.8E-05 39.8 3.9 69 39-116 7-76 (494)
213 PF13545 HTH_Crp_2: Crp-like h 81.9 1.6 3.4E-05 28.9 2.8 34 55-93 28-61 (76)
214 TIGR01177 conserved hypothetic 81.9 2.3 5E-05 36.9 4.5 30 186-216 173-202 (329)
215 PRK11727 23S rRNA mA1618 methy 81.7 1.6 3.4E-05 38.0 3.3 25 196-220 114-138 (321)
216 PTZ00146 fibrillarin; Provisio 81.7 1.4 3.1E-05 37.7 3.0 25 194-218 130-154 (293)
217 PF05732 RepL: Firmicute plasm 81.4 1.9 4E-05 33.8 3.4 45 56-109 76-120 (165)
218 PRK11886 bifunctional biotin-- 80.9 2.7 5.8E-05 36.3 4.5 56 41-107 7-62 (319)
219 KOG1540 Ubiquinone biosynthesi 80.8 4 8.7E-05 34.4 5.2 23 197-219 101-123 (296)
220 PF00165 HTH_AraC: Bacterial r 80.5 0.92 2E-05 26.6 1.1 28 54-86 7-34 (42)
221 TIGR00417 speE spermidine synt 80.2 1.7 3.6E-05 36.6 3.0 24 195-218 71-94 (270)
222 PRK14902 16S rRNA methyltransf 80.2 2.1 4.6E-05 38.7 3.8 31 187-218 242-272 (444)
223 PRK03612 spermidine synthase; 80.2 1.7 3.7E-05 40.2 3.3 24 195-219 296-319 (521)
224 TIGR02085 meth_trns_rumB 23S r 80.1 1.8 4E-05 38.3 3.3 21 197-217 234-254 (374)
225 PRK03522 rumB 23S rRNA methylu 80.0 1.8 4E-05 37.2 3.2 22 197-218 174-195 (315)
226 PRK11642 exoribonuclease R; Pr 80.0 3.9 8.4E-05 40.1 5.7 58 42-106 23-80 (813)
227 TIGR02787 codY_Gpos GTP-sensin 79.9 11 0.00023 31.4 7.4 66 19-93 166-231 (251)
228 PLN02781 Probable caffeoyl-CoA 79.7 3.1 6.7E-05 34.3 4.4 24 196-219 68-91 (234)
229 PF09929 DUF2161: Uncharacteri 79.6 4.3 9.3E-05 29.8 4.5 56 33-109 60-115 (118)
230 PRK10411 DNA-binding transcrip 79.2 3.6 7.7E-05 34.1 4.6 45 41-93 7-51 (240)
231 COG2518 Pcm Protein-L-isoaspar 79.0 3.5 7.7E-05 33.5 4.3 30 186-216 63-92 (209)
232 COG3413 Predicted DNA binding 79.0 1.9 4.1E-05 35.0 2.8 37 28-71 157-193 (215)
233 PRK09802 DNA-binding transcrip 79.0 2.7 5.9E-05 35.4 3.9 46 40-93 19-64 (269)
234 PRK10906 DNA-binding transcrip 78.7 2.7 5.9E-05 35.1 3.8 45 41-93 8-52 (252)
235 PRK09462 fur ferric uptake reg 78.2 4.9 0.00011 30.6 4.8 55 38-93 17-71 (148)
236 PRK10909 rsmD 16S rRNA m(2)G96 78.2 3.8 8.2E-05 33.0 4.3 21 197-217 54-74 (199)
237 PF13730 HTH_36: Helix-turn-he 78.1 1.8 4E-05 26.7 2.0 30 56-90 26-55 (55)
238 PRK09334 30S ribosomal protein 77.9 3.1 6.8E-05 28.9 3.2 35 54-93 40-74 (86)
239 PRK11639 zinc uptake transcrip 77.4 4.6 9.9E-05 31.6 4.5 55 37-93 25-79 (169)
240 PRK00215 LexA repressor; Valid 77.0 5.5 0.00012 31.9 5.0 36 54-93 22-57 (205)
241 COG2524 Predicted transcriptio 76.8 5.1 0.00011 33.7 4.7 49 54-109 24-72 (294)
242 TIGR00563 rsmB ribosomal RNA s 76.5 2.8 6.1E-05 37.7 3.4 32 187-219 230-261 (426)
243 PF02796 HTH_7: Helix-turn-hel 76.0 2.8 6.1E-05 25.1 2.3 22 55-81 21-42 (45)
244 COG3963 Phospholipid N-methylt 75.8 5.2 0.00011 31.6 4.3 37 180-217 33-69 (194)
245 smart00531 TFIIE Transcription 75.7 3.1 6.6E-05 31.8 3.0 43 42-92 5-49 (147)
246 COG1510 Predicted transcriptio 75.6 2.7 5.7E-05 33.1 2.6 36 54-94 40-75 (177)
247 PRK10046 dpiA two-component re 75.5 4 8.7E-05 32.9 3.9 45 42-93 166-210 (225)
248 PF02319 E2F_TDP: E2F/DP famil 75.2 1.5 3.3E-05 29.1 1.1 36 54-93 23-62 (71)
249 PF03297 Ribosomal_S25: S25 ri 75.1 4.2 9.1E-05 29.3 3.4 36 54-94 58-93 (105)
250 COG0293 FtsJ 23S rRNA methylas 75.1 6.7 0.00015 31.8 4.9 39 180-218 29-67 (205)
251 PF13518 HTH_28: Helix-turn-he 75.1 4.2 9.1E-05 24.5 3.0 29 56-89 13-41 (52)
252 COG0735 Fur Fe2+/Zn2+ uptake r 75.1 6.1 0.00013 30.1 4.5 67 39-107 22-88 (145)
253 COG1846 MarR Transcriptional r 74.9 4.3 9.4E-05 28.8 3.6 70 37-114 21-92 (126)
254 KOG2361 Predicted methyltransf 74.7 3.6 7.7E-05 34.3 3.3 23 198-220 73-95 (264)
255 PRK10434 srlR DNA-bindng trans 74.5 3.8 8.3E-05 34.2 3.6 45 41-93 8-52 (256)
256 PF06969 HemN_C: HemN C-termin 74.4 5.9 0.00013 25.4 3.7 47 54-109 19-65 (66)
257 TIGR02143 trmA_only tRNA (urac 74.3 3.5 7.5E-05 36.2 3.4 22 198-219 199-220 (353)
258 PRK10736 hypothetical protein; 74.1 4.1 9E-05 36.1 3.8 51 42-105 312-362 (374)
259 TIGR00095 RNA methyltransferas 74.1 3.5 7.7E-05 32.8 3.1 23 197-219 50-72 (189)
260 PRK11534 DNA-binding transcrip 73.9 6.1 0.00013 32.0 4.5 35 54-93 29-63 (224)
261 PRK14901 16S rRNA methyltransf 73.6 4.1 8.9E-05 36.8 3.8 31 188-219 245-275 (434)
262 TIGR02698 CopY_TcrY copper tra 73.1 7.9 0.00017 28.9 4.6 47 39-93 5-55 (130)
263 COG1725 Predicted transcriptio 73.0 5.2 0.00011 29.8 3.5 42 55-104 35-76 (125)
264 COG1675 TFA1 Transcription ini 73.0 4.8 0.0001 31.8 3.5 45 41-93 21-65 (176)
265 COG1349 GlpR Transcriptional r 72.5 5 0.00011 33.5 3.8 45 41-93 8-52 (253)
266 PF13384 HTH_23: Homeodomain-l 72.3 2.3 5E-05 25.7 1.3 39 40-88 7-45 (50)
267 PF03374 ANT: Phage antirepres 72.0 8.2 0.00018 27.6 4.4 44 40-93 11-54 (111)
268 PF00126 HTH_1: Bacterial regu 71.9 5.1 0.00011 25.4 2.9 54 40-108 3-59 (60)
269 PRK13777 transcriptional regul 71.8 6.6 0.00014 31.3 4.1 62 42-112 49-113 (185)
270 TIGR00446 nop2p NOL1/NOP2/sun 71.7 5.4 0.00012 33.4 3.8 25 195-219 70-94 (264)
271 PRK14904 16S rRNA methyltransf 71.6 4.9 0.00011 36.4 3.8 25 194-218 248-272 (445)
272 PF05219 DREV: DREV methyltran 71.5 5 0.00011 33.7 3.5 24 197-220 95-118 (265)
273 PF14338 Mrr_N: Mrr N-terminal 71.3 12 0.00026 25.9 5.0 35 78-116 58-92 (92)
274 PF12147 Methyltransf_20: Puta 71.1 4.3 9.4E-05 34.8 3.1 26 195-220 134-159 (311)
275 TIGR03338 phnR_burk phosphonat 70.9 7 0.00015 31.2 4.2 35 54-93 33-67 (212)
276 PF09821 AAA_assoc_C: C-termin 70.4 4.3 9.3E-05 30.0 2.6 46 60-115 2-47 (120)
277 COG1565 Uncharacterized conser 70.2 12 0.00026 33.1 5.6 50 164-218 50-99 (370)
278 KOG4589 Cell division protein 70.0 8.4 0.00018 31.0 4.3 30 189-218 62-91 (232)
279 COG1802 GntR Transcriptional r 69.9 9.2 0.0002 31.1 4.8 46 54-108 38-83 (230)
280 TIGR01321 TrpR trp operon repr 69.6 6.7 0.00015 27.7 3.3 41 36-85 40-80 (94)
281 COG4901 Ribosomal protein S25 69.6 6.3 0.00014 28.2 3.1 49 40-93 43-92 (107)
282 PRK05031 tRNA (uracil-5-)-meth 69.5 4.7 0.0001 35.5 3.1 22 198-219 208-229 (362)
283 PRK14903 16S rRNA methyltransf 69.4 5.9 0.00013 35.8 3.8 48 170-218 212-259 (431)
284 TIGR00635 ruvB Holliday juncti 69.2 4.7 0.0001 34.2 3.0 35 54-93 254-289 (305)
285 PF12793 SgrR_N: Sugar transpo 69.1 5.1 0.00011 29.4 2.7 35 54-93 18-52 (115)
286 PRK11414 colanic acid/biofilm 69.0 9.6 0.00021 30.8 4.7 35 54-93 33-67 (221)
287 PF09681 Phage_rep_org_N: N-te 68.2 8.5 0.00018 28.5 3.8 49 54-111 52-100 (121)
288 PRK12423 LexA repressor; Provi 68.2 9.8 0.00021 30.5 4.5 35 55-93 25-59 (202)
289 PF05401 NodS: Nodulation prot 68.0 4.3 9.3E-05 32.8 2.3 28 190-218 38-65 (201)
290 PF05331 DUF742: Protein of un 67.8 8.3 0.00018 28.3 3.6 34 55-93 55-88 (114)
291 PRK09954 putative kinase; Prov 67.4 5.9 0.00013 34.6 3.3 44 40-91 5-48 (362)
292 COG3682 Predicted transcriptio 67.1 9.8 0.00021 28.2 3.9 63 38-107 6-68 (123)
293 PF07091 FmrO: Ribosomal RNA m 67.1 3.8 8.1E-05 34.3 1.9 17 196-212 105-121 (251)
294 PHA02591 hypothetical protein; 67.0 7.1 0.00015 26.5 2.8 32 43-83 51-82 (83)
295 PRK00536 speE spermidine synth 66.9 5.1 0.00011 33.8 2.6 23 195-217 71-93 (262)
296 PRK11753 DNA-binding transcrip 66.7 7.2 0.00016 30.9 3.5 34 55-93 168-201 (211)
297 KOG3045 Predicted RNA methylas 66.6 7.4 0.00016 32.9 3.5 54 159-212 139-196 (325)
298 PF10771 DUF2582: Protein of u 66.6 9.9 0.00021 24.9 3.4 43 43-93 13-55 (65)
299 TIGR03879 near_KaiC_dom probab 66.6 3.7 8E-05 27.6 1.4 33 55-92 32-64 (73)
300 PHA02701 ORF020 dsRNA-binding 66.6 11 0.00023 30.0 4.2 48 39-93 5-52 (183)
301 PF10294 Methyltransf_16: Puta 66.5 5.5 0.00012 31.1 2.6 22 196-217 45-66 (173)
302 KOG0820 Ribosomal RNA adenine 65.8 12 0.00026 31.9 4.5 34 184-218 47-80 (315)
303 KOG3420 Predicted RNA methylas 65.7 6.7 0.00015 30.3 2.8 27 187-214 40-66 (185)
304 PF00538 Linker_histone: linke 65.5 14 0.0003 24.7 4.1 51 54-105 20-76 (77)
305 PF10668 Phage_terminase: Phag 65.3 6.9 0.00015 25.2 2.4 30 44-80 13-42 (60)
306 KOG2165 Anaphase-promoting com 64.9 6.7 0.00015 37.3 3.2 48 54-106 615-662 (765)
307 PRK11161 fumarate/nitrate redu 64.5 7 0.00015 31.6 3.0 34 55-93 184-217 (235)
308 PF08280 HTH_Mga: M protein tr 64.5 6.7 0.00014 24.9 2.3 38 40-85 7-44 (59)
309 PRK04424 fatty acid biosynthes 64.3 4.1 8.9E-05 32.4 1.5 45 41-93 10-54 (185)
310 TIGR03697 NtcA_cyano global ni 64.2 8.8 0.00019 29.8 3.5 34 55-93 143-176 (193)
311 PLN02668 indole-3-acetate carb 63.9 18 0.00039 32.3 5.6 19 196-214 63-81 (386)
312 PRK01381 Trp operon repressor; 63.9 9.5 0.00021 27.2 3.1 30 37-71 41-70 (99)
313 PF02295 z-alpha: Adenosine de 63.7 7.6 0.00017 25.4 2.5 58 39-106 5-64 (66)
314 COG0421 SpeE Spermidine syntha 63.3 7.7 0.00017 33.1 3.1 26 194-219 74-99 (282)
315 PRK00135 scpB segregation and 63.0 15 0.00033 29.3 4.6 42 41-93 93-134 (188)
316 COG5459 Predicted rRNA methyla 62.8 6.9 0.00015 34.6 2.7 32 189-221 107-138 (484)
317 PF02527 GidB: rRNA small subu 62.5 15 0.00033 29.1 4.5 23 199-221 51-73 (184)
318 PRK09391 fixK transcriptional 61.2 10 0.00023 30.8 3.5 34 55-93 179-212 (230)
319 PF09904 HTH_43: Winged helix- 61.1 8 0.00017 27.0 2.3 40 44-92 14-53 (90)
320 PRK13918 CRP/FNR family transc 60.6 12 0.00026 29.4 3.6 34 55-93 149-182 (202)
321 PRK13239 alkylmercury lyase; P 60.5 24 0.00051 28.7 5.3 37 41-85 25-61 (206)
322 PF01596 Methyltransf_3: O-met 60.5 10 0.00022 30.6 3.2 25 196-220 45-69 (205)
323 TIGR02063 RNase_R ribonuclease 60.1 23 0.00049 34.2 6.0 59 42-106 6-64 (709)
324 PRK09464 pdhR transcriptional 59.2 13 0.00029 30.6 3.8 44 54-105 32-76 (254)
325 PF05402 PqqD: Coenzyme PQQ sy 59.0 8.2 0.00018 24.8 2.1 43 43-91 22-68 (68)
326 TIGR03826 YvyF flagellar opero 58.9 11 0.00023 28.6 2.9 35 42-82 34-68 (137)
327 PLN02823 spermine synthase 58.8 9.7 0.00021 33.3 3.0 24 196-219 103-126 (336)
328 PRK10225 DNA-binding transcrip 58.8 13 0.00029 30.7 3.8 43 54-104 31-74 (257)
329 COG1654 BirA Biotin operon rep 58.3 18 0.0004 24.6 3.7 50 54-111 18-67 (79)
330 COG0357 GidB Predicted S-adeno 58.2 17 0.00036 29.8 4.1 25 197-221 68-92 (215)
331 COG3398 Uncharacterized protei 58.1 13 0.00028 30.5 3.4 67 33-108 169-235 (240)
332 PF03965 Penicillinase_R: Peni 58.0 16 0.00034 26.4 3.6 51 39-93 4-54 (115)
333 TIGR01714 phage_rep_org_N phag 57.9 19 0.0004 26.6 3.9 48 54-110 50-97 (119)
334 PRK09775 putative DNA-binding 57.7 16 0.00035 33.2 4.3 40 43-93 5-44 (442)
335 KOG2651 rRNA adenine N-6-methy 57.3 12 0.00027 33.3 3.3 24 194-217 151-174 (476)
336 PF02186 TFIIE_beta: TFIIE bet 57.2 46 0.001 21.7 5.3 40 45-93 12-51 (65)
337 PF11312 DUF3115: Protein of u 57.0 31 0.00067 29.9 5.7 21 198-218 88-108 (315)
338 TIGR02812 fadR_gamma fatty aci 56.9 16 0.00034 29.7 3.9 35 54-93 28-63 (235)
339 COG3398 Uncharacterized protei 56.8 20 0.00044 29.4 4.3 51 35-93 98-148 (240)
340 PF03428 RP-C: Replication pro 56.8 12 0.00027 29.5 3.0 56 31-93 45-104 (177)
341 PF13542 HTH_Tnp_ISL3: Helix-t 56.6 15 0.00033 22.1 2.9 35 40-84 17-51 (52)
342 PF13936 HTH_38: Helix-turn-he 56.6 11 0.00025 22.3 2.2 23 55-82 20-42 (44)
343 PRK00080 ruvB Holliday junctio 56.0 11 0.00023 32.6 2.8 35 54-93 275-310 (328)
344 COG2390 DeoR Transcriptional r 55.9 12 0.00025 32.6 3.0 34 55-93 26-59 (321)
345 cd02190 epsilon_tubulin The tu 55.8 14 0.00031 32.7 3.7 36 185-220 90-130 (379)
346 PF04492 Phage_rep_O: Bacterio 55.7 16 0.00034 26.1 3.1 35 54-93 53-87 (100)
347 COG0640 ArsR Predicted transcr 55.3 28 0.0006 23.2 4.5 53 33-93 20-72 (110)
348 PRK10421 DNA-binding transcrip 55.3 17 0.00036 30.0 3.8 44 54-105 24-68 (253)
349 KOG2940 Predicted methyltransf 55.2 26 0.00056 29.3 4.7 21 197-217 73-93 (325)
350 PRK09990 DNA-binding transcrip 55.2 19 0.00041 29.6 4.1 35 54-93 29-64 (251)
351 smart00342 HTH_ARAC helix_turn 55.1 12 0.00025 24.4 2.4 29 55-88 1-29 (84)
352 PF03291 Pox_MCEL: mRNA cappin 55.1 10 0.00022 33.0 2.6 46 169-217 38-83 (331)
353 KOG3191 Predicted N6-DNA-methy 55.1 11 0.00025 30.1 2.5 21 197-217 44-64 (209)
354 PF02981 FokI_N: Restriction e 55.0 9.7 0.00021 28.9 2.0 38 73-113 105-142 (145)
355 smart00088 PINT motif in prote 54.9 33 0.00071 23.1 4.7 51 35-93 7-57 (88)
356 smart00753 PAM PCI/PINT associ 54.9 33 0.00071 23.1 4.7 51 35-93 7-57 (88)
357 PF13814 Replic_Relax: Replica 54.9 21 0.00046 27.8 4.2 63 46-113 3-71 (191)
358 PF11994 DUF3489: Protein of u 54.4 44 0.00094 22.4 4.9 43 43-93 15-59 (72)
359 PF06971 Put_DNA-bind_N: Putat 54.0 8.1 0.00018 23.9 1.3 37 37-79 11-47 (50)
360 cd00073 H15 linker histone 1 a 54.0 36 0.00078 23.4 4.7 53 54-106 22-77 (88)
361 PRK10402 DNA-binding transcrip 53.7 16 0.00034 29.6 3.3 34 55-93 169-202 (226)
362 PRK00082 hrcA heat-inducible t 53.4 18 0.00039 31.6 3.8 52 46-108 19-72 (339)
363 PRK04984 fatty acid metabolism 53.3 19 0.00042 29.3 3.8 43 54-104 29-72 (239)
364 PF04157 EAP30: EAP30/Vps36 fa 53.3 16 0.00035 29.8 3.4 35 54-93 189-223 (223)
365 smart00421 HTH_LUXR helix_turn 53.0 17 0.00036 21.7 2.7 24 55-83 18-41 (58)
366 PF13443 HTH_26: Cro/C1-type H 52.9 7.7 0.00017 24.5 1.1 31 43-82 2-32 (63)
367 PRK11511 DNA-binding transcrip 52.9 18 0.00039 26.6 3.3 34 54-92 24-57 (127)
368 PRK11760 putative 23S rRNA C24 52.7 14 0.00031 32.4 3.0 23 195-217 210-232 (357)
369 PF05491 RuvB_C: Holliday junc 52.6 20 0.00043 24.3 3.1 49 40-93 10-59 (76)
370 PRK03837 transcriptional regul 52.6 22 0.00047 29.0 4.0 35 54-93 35-70 (241)
371 PLN03238 probable histone acet 52.5 32 0.0007 29.4 5.0 47 28-93 207-253 (290)
372 PF11972 HTH_13: HTH DNA bindi 52.2 28 0.0006 21.9 3.4 47 43-104 4-50 (54)
373 PRK11523 DNA-binding transcrip 51.6 21 0.00046 29.4 3.8 35 54-93 30-65 (253)
374 cd06170 LuxR_C_like C-terminal 51.2 19 0.0004 21.6 2.7 24 55-83 15-38 (57)
375 COG3695 Predicted methylated D 51.2 19 0.00041 25.7 2.9 41 41-86 9-51 (103)
376 TIGR02844 spore_III_D sporulat 50.4 17 0.00036 24.9 2.5 31 42-81 10-40 (80)
377 PF09107 SelB-wing_3: Elongati 50.0 27 0.00058 21.5 3.1 41 45-93 3-43 (50)
378 PF04760 IF2_N: Translation in 49.5 6.6 0.00014 24.3 0.4 30 55-92 3-33 (54)
379 PF09106 SelB-wing_2: Elongati 49.5 23 0.00051 22.3 3.0 35 54-93 16-53 (59)
380 COG0758 Smf Predicted Rossmann 49.4 25 0.00054 31.0 4.0 35 54-93 308-342 (350)
381 PLN02476 O-methyltransferase 49.4 19 0.00041 30.7 3.2 26 194-219 116-141 (278)
382 PF05344 DUF746: Domain of Unk 49.3 18 0.0004 23.6 2.4 27 54-85 12-38 (65)
383 PF04539 Sigma70_r3: Sigma-70 48.9 10 0.00022 25.1 1.3 34 54-92 19-52 (78)
384 PRK11783 rlmL 23S rRNA m(2)G24 48.9 26 0.00056 33.8 4.4 35 182-217 176-211 (702)
385 TIGR01764 excise DNA binding d 48.8 14 0.0003 21.5 1.8 22 56-82 2-23 (49)
386 TIGR00331 hrcA heat shock gene 48.5 23 0.0005 31.0 3.7 50 33-94 6-57 (337)
387 PRK10219 DNA-binding transcrip 48.4 15 0.00034 25.8 2.2 34 54-92 20-53 (107)
388 cd04762 HTH_MerR-trunc Helix-T 48.3 14 0.0003 21.4 1.7 23 56-83 1-23 (49)
389 PF05724 TPMT: Thiopurine S-me 48.2 22 0.00048 29.0 3.4 24 194-217 35-58 (218)
390 PRK15418 transcriptional regul 48.0 19 0.00042 31.1 3.1 34 55-93 29-62 (318)
391 cd02188 gamma_tubulin Gamma-tu 48.0 23 0.00049 32.1 3.7 36 185-220 121-161 (431)
392 PF07848 PaaX: PaaX-like prote 47.6 18 0.00039 23.9 2.3 48 54-107 19-69 (70)
393 PRK03601 transcriptional regul 47.3 24 0.00053 29.2 3.6 59 40-113 5-66 (275)
394 PF01418 HTH_6: Helix-turn-hel 47.0 18 0.00039 24.2 2.2 31 54-89 33-63 (77)
395 TIGR00637 ModE_repress ModE mo 46.9 27 0.00058 24.7 3.2 63 40-112 6-71 (99)
396 cd00286 Tubulin_FtsZ Tubulin/F 46.8 27 0.00059 30.1 3.9 36 185-220 80-120 (328)
397 PF13551 HTH_29: Winged helix- 46.8 19 0.0004 25.3 2.4 28 57-89 14-41 (112)
398 TIGR03433 padR_acidobact trans 46.7 54 0.0012 23.0 4.8 62 43-113 9-82 (100)
399 smart00342 HTH_ARAC helix_turn 46.7 76 0.0016 20.3 6.6 36 42-85 41-76 (84)
400 PF09824 ArsR: ArsR transcript 46.1 29 0.00064 26.8 3.5 49 33-93 12-60 (160)
401 PF08281 Sigma70_r4_2: Sigma-7 46.1 23 0.00049 21.5 2.5 24 54-82 25-48 (54)
402 PLN00104 MYST -like histone ac 46.0 42 0.00091 30.6 5.0 47 28-93 358-404 (450)
403 PRK10430 DNA-binding transcrip 45.9 23 0.00049 28.7 3.1 35 54-93 177-211 (239)
404 PRK10094 DNA-binding transcrip 45.9 21 0.00046 30.2 3.1 58 40-112 6-66 (308)
405 cd06445 ATase The DNA repair p 45.5 51 0.0011 22.1 4.3 42 42-89 4-45 (79)
406 PF00196 GerE: Bacterial regul 45.4 13 0.00028 23.2 1.2 27 39-71 7-33 (58)
407 PRK15128 23S rRNA m(5)C1962 me 45.3 19 0.0004 32.3 2.7 21 196-216 220-240 (396)
408 PF14557 AphA_like: Putative A 45.2 44 0.00096 26.2 4.3 65 36-109 9-83 (175)
409 PRK08208 coproporphyrinogen II 45.0 37 0.00081 30.6 4.6 58 43-113 352-409 (430)
410 PRK04338 N(2),N(2)-dimethylgua 44.9 15 0.00032 32.7 2.0 22 198-219 59-80 (382)
411 PRK11783 rlmL 23S rRNA m(2)G24 44.5 19 0.0004 34.8 2.7 21 197-217 539-559 (702)
412 PF12728 HTH_17: Helix-turn-he 44.5 17 0.00038 21.8 1.7 22 56-82 2-23 (51)
413 COG5340 Predicted transcriptio 44.2 17 0.00036 30.0 1.9 46 54-108 29-74 (269)
414 COG0248 GppA Exopolyphosphatas 44.1 22 0.00047 32.9 2.9 23 185-208 119-141 (492)
415 PF08704 GCD14: tRNA methyltra 44.1 36 0.00079 28.4 4.1 31 186-217 31-61 (247)
416 COG2186 FadR Transcriptional r 43.8 35 0.00076 28.2 3.9 41 57-105 36-76 (241)
417 cd04761 HTH_MerR-SF Helix-Turn 43.5 18 0.00038 21.3 1.6 27 56-91 1-27 (49)
418 PF09959 DUF2193: Uncharacteri 43.4 74 0.0016 28.6 5.9 81 132-212 67-152 (499)
419 cd06059 Tubulin The tubulin su 43.4 34 0.00074 30.3 4.1 37 184-220 79-120 (382)
420 PHA03103 double-strand RNA-bin 43.2 31 0.00067 27.5 3.3 53 43-105 18-70 (183)
421 PF08672 APC2: Anaphase promot 42.8 28 0.0006 22.3 2.5 25 75-104 36-60 (60)
422 TIGR00589 ogt O-6-methylguanin 42.8 62 0.0013 21.9 4.4 42 40-87 4-45 (80)
423 TIGR03439 methyl_EasF probable 42.5 49 0.0011 28.8 4.7 59 155-218 40-98 (319)
424 PRK14999 histidine utilization 42.4 34 0.00074 28.0 3.7 43 55-105 35-78 (241)
425 PF01564 Spermine_synth: Sperm 41.8 20 0.00044 29.7 2.2 23 196-218 76-98 (246)
426 PRK13256 thiopurine S-methyltr 41.7 38 0.00081 27.9 3.8 22 196-217 43-64 (226)
427 PF14881 Tubulin_3: Tubulin do 41.3 31 0.00068 27.3 3.1 34 184-217 64-97 (180)
428 PRK10512 selenocysteinyl-tRNA- 40.7 48 0.001 31.5 4.8 35 54-93 505-539 (614)
429 PF01853 MOZ_SAS: MOZ/SAS fami 40.6 32 0.00069 27.5 3.0 31 55-93 150-180 (188)
430 cd06171 Sigma70_r4 Sigma70, re 40.5 33 0.00072 19.8 2.6 33 42-83 17-49 (55)
431 TIGR02404 trehalos_R_Bsub treh 40.5 32 0.0007 27.9 3.2 41 57-105 26-66 (233)
432 COG3645 Uncharacterized phage- 40.3 29 0.00062 26.2 2.6 45 39-93 33-77 (135)
433 TIGR00475 selB selenocysteine- 40.3 44 0.00095 31.5 4.4 42 54-104 487-528 (581)
434 TIGR03339 phn_lysR aminoethylp 40.2 43 0.00094 27.3 4.0 57 41-112 2-61 (279)
435 COG1386 scpB Chromosome segreg 40.0 69 0.0015 25.5 4.9 58 41-109 95-155 (184)
436 PRK09906 DNA-binding transcrip 39.9 40 0.00087 28.0 3.8 59 40-113 5-66 (296)
437 PTZ00387 epsilon tubulin; Prov 39.9 35 0.00075 31.3 3.6 36 185-220 122-162 (465)
438 PLN03239 histone acetyltransfe 39.8 1.1E+02 0.0025 26.9 6.5 50 28-93 265-314 (351)
439 PRK10837 putative DNA-binding 39.6 44 0.00095 27.6 4.0 58 40-112 7-67 (290)
440 PF04545 Sigma70_r4: Sigma-70, 39.6 23 0.0005 21.2 1.7 25 54-83 19-43 (50)
441 TIGR02531 yecD_yerC TrpR-relat 39.5 30 0.00066 24.0 2.5 33 41-83 41-73 (88)
442 PRK09764 DNA-binding transcrip 39.4 43 0.00094 27.4 3.8 44 54-105 27-71 (240)
443 TIGR02424 TF_pcaQ pca operon t 39.1 35 0.00076 28.4 3.4 58 40-112 7-67 (300)
444 PF07638 Sigma70_ECF: ECF sigm 39.1 31 0.00067 27.1 2.8 35 41-84 141-175 (185)
445 PF02384 N6_Mtase: N-6 DNA Met 39.0 41 0.0009 28.5 3.8 24 194-217 44-67 (311)
446 KOG0822 Protein kinase inhibit 39.0 63 0.0014 30.3 5.0 53 158-217 334-388 (649)
447 COG2519 GCD14 tRNA(1-methylade 38.9 51 0.0011 27.7 4.1 31 186-217 85-115 (256)
448 PF00356 LacI: Bacterial regul 38.8 17 0.00036 22.0 0.9 11 57-67 1-11 (46)
449 PF05158 RNA_pol_Rpc34: RNA po 38.4 33 0.00072 29.9 3.1 46 43-94 89-134 (327)
450 PF01381 HTH_3: Helix-turn-hel 38.3 21 0.00046 21.6 1.4 24 54-82 8-31 (55)
451 PF12298 Bot1p: Eukaryotic mit 38.1 36 0.00077 26.8 3.0 42 35-85 17-58 (172)
452 TIGR02325 C_P_lyase_phnF phosp 38.1 37 0.0008 27.5 3.2 42 57-106 34-75 (238)
453 PRK11242 DNA-binding transcrip 38.0 43 0.00093 27.7 3.7 58 40-112 5-65 (296)
454 PRK11074 putative DNA-binding 37.9 36 0.00078 28.5 3.2 58 40-112 6-66 (300)
455 cd06060 misato Human Misato sh 37.8 34 0.00075 31.6 3.2 34 184-217 141-174 (493)
456 PRK14096 pgi glucose-6-phospha 37.6 52 0.0011 30.7 4.4 42 41-87 466-507 (528)
457 PF10078 DUF2316: Uncharacteri 37.3 46 0.001 23.2 3.1 32 43-83 15-46 (89)
458 COG5023 Tubulin [Cytoskeleton] 37.1 66 0.0014 28.7 4.6 46 170-220 111-161 (443)
459 TIGR02018 his_ut_repres histid 37.0 39 0.00084 27.4 3.2 45 54-106 23-68 (230)
460 PRK10341 DNA-binding transcrip 36.7 43 0.00092 28.3 3.5 59 39-112 10-71 (312)
461 PRK11062 nhaR transcriptional 36.7 43 0.00094 28.0 3.5 58 40-112 8-68 (296)
462 KOG4300 Predicted methyltransf 36.3 66 0.0014 26.5 4.2 15 196-210 76-90 (252)
463 PRK09791 putative DNA-binding 36.2 47 0.001 27.7 3.7 58 40-112 9-69 (302)
464 PRK15121 right oriC-binding tr 36.2 48 0.0011 27.9 3.7 34 54-92 20-53 (289)
465 PF07120 DUF1376: Protein of u 36.1 46 0.00099 22.9 3.0 44 54-108 37-82 (88)
466 PRK11233 nitrogen assimilation 35.9 49 0.0011 27.8 3.7 58 40-112 5-65 (305)
467 PF08721 Tn7_Tnp_TnsA_C: TnsA 35.7 76 0.0016 20.6 4.0 43 42-92 31-77 (79)
468 PRK10681 DNA-binding transcrip 35.4 49 0.0011 27.5 3.6 40 41-88 10-49 (252)
469 PRK05660 HemN family oxidoredu 35.3 45 0.00098 29.5 3.5 49 55-113 321-369 (378)
470 PF14502 HTH_41: Helix-turn-he 35.2 77 0.0017 19.4 3.4 35 54-93 5-39 (48)
471 COG4367 Uncharacterized protei 35.1 53 0.0011 22.9 3.0 32 44-84 16-47 (97)
472 KOG3987 Uncharacterized conser 35.0 32 0.00069 28.3 2.2 23 194-216 109-132 (288)
473 PHA00542 putative Cro-like pro 34.9 38 0.00082 22.9 2.4 24 54-82 30-53 (82)
474 PF09202 Rio2_N: Rio2, N-termi 34.8 32 0.00069 23.6 1.9 48 55-109 24-71 (82)
475 PRK13626 transcriptional regul 34.6 34 0.00074 31.8 2.8 36 54-94 22-57 (552)
476 PF01371 Trp_repressor: Trp re 34.4 43 0.00092 23.3 2.5 39 36-84 34-73 (87)
477 COG2188 PhnF Transcriptional r 34.4 47 0.001 27.2 3.3 43 56-106 32-74 (236)
478 COG1189 Predicted rRNA methyla 34.3 59 0.0013 27.1 3.8 32 186-217 69-100 (245)
479 PRK09986 DNA-binding transcrip 34.1 53 0.0012 27.1 3.7 59 39-112 10-71 (294)
480 KOG1975 mRNA cap methyltransfe 34.0 38 0.00083 29.7 2.7 38 169-215 99-136 (389)
481 PF14493 HTH_40: Helix-turn-he 34.0 59 0.0013 22.3 3.3 30 55-89 13-42 (91)
482 CHL00180 rbcR LysR transcripti 33.7 52 0.0011 27.6 3.6 57 40-111 9-68 (305)
483 COG4519 Uncharacterized protei 33.6 1E+02 0.0022 21.1 4.1 35 54-93 21-55 (95)
484 smart00422 HTH_MERR helix_turn 33.3 30 0.00066 22.0 1.6 28 56-92 1-28 (70)
485 cd07977 TFIIE_beta_winged_heli 33.1 1.2E+02 0.0025 20.3 4.5 37 45-86 16-53 (75)
486 cd02187 beta_tubulin The tubul 33.1 49 0.0011 29.9 3.4 36 185-220 120-160 (425)
487 PRK04217 hypothetical protein; 33.1 53 0.0012 23.8 3.0 32 42-82 49-80 (110)
488 cd02189 delta_tubulin The tubu 32.9 55 0.0012 29.8 3.7 36 185-220 117-157 (446)
489 PRK13558 bacterio-opsin activa 32.9 39 0.00084 32.0 2.9 45 28-83 609-653 (665)
490 PRK15201 fimbriae regulatory p 32.7 45 0.00098 26.6 2.7 28 38-71 136-163 (198)
491 KOG4058 Uncharacterized conser 32.6 57 0.0012 25.4 3.2 30 186-216 63-92 (199)
492 PF09079 Cdc6_C: CDC6, C termi 32.6 70 0.0015 21.5 3.5 36 57-94 24-59 (85)
493 PF01710 HTH_Tnp_IS630: Transp 32.6 58 0.0012 23.7 3.2 39 44-93 63-101 (119)
494 COG4754 Uncharacterized conser 32.5 1E+02 0.0022 23.7 4.4 65 41-116 15-79 (157)
495 PRK15411 rcsA colanic acid cap 32.5 48 0.001 26.5 3.0 29 37-71 139-167 (207)
496 COG2344 AT-rich DNA-binding pr 32.4 49 0.0011 26.7 2.9 41 41-87 19-59 (211)
497 PRK05472 redox-sensing transcr 32.3 69 0.0015 25.7 3.9 47 36-88 14-60 (213)
498 PF10141 ssDNA-exonuc_C: Singl 32.0 55 0.0012 26.1 3.2 41 57-107 118-158 (195)
499 TIGR02036 dsdC D-serine deamin 31.8 50 0.0011 27.7 3.2 59 39-112 11-72 (302)
500 KOG1661 Protein-L-isoaspartate 31.6 40 0.00087 27.7 2.3 21 195-215 81-101 (237)
No 1
>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]
Probab=99.93 E-value=6.2e-25 Score=186.59 Aligned_cols=200 Identities=45% Similarity=0.712 Sum_probs=174.5
Q ss_pred hhHHHHHHHHHHHhhhHHHHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCC-CCCcchhhhHHHHHHHHhcCCceee
Q 036971 14 EEEEVYSHAMVLGSAIVLPAVFQAVVNLDVLDIINKAGPGAELSASEIASQIPT-KNPEGAAKMLDRVLGLLVSFNILCC 92 (221)
Q Consensus 14 ~~~~~~~~l~~~~~g~~~~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~-~~~~~~~~~l~rlLr~L~~~gll~~ 92 (221)
++.++..+++++++++..+++|.+|++|||||+|++++ + +.|||..+.. .++. ++..+.|+||.|++.+++..
T Consensus 2 ~e~~~~l~~~~l~~~~~~~~~lk~A~eL~v~d~l~~~~---~--p~~ia~~l~~~~~~~-~p~ll~r~lr~L~s~~i~k~ 75 (342)
T KOG3178|consen 2 EENEASLRAMRLANGFALPMVLKAACELGVFDILANAG---S--PSEIASLLPTPKNPE-APVLLDRILRLLVSYSILKC 75 (342)
T ss_pred chhHHHHHHHHHHhhhhhHHHHHHHHHcChHHHHHhCC---C--HHHHHHhccCCCCCC-ChhHHHHHHHHHHHhhhcee
Confidence 56677899999999999999999999999999999964 2 7777777762 1444 56699999999999999998
Q ss_pred eccCCCCcceeccccccccccCCCCCChHHHHHHhcCccchhhhhhhHHHHhcCCchhHhhhCCchhhhhccCchHHHHH
Q 036971 93 SFSTHGVRLYSLAPVAKYYVSDQNGVSMRPYMNLSLDKVMMPGWFQLKDQILEGELSYNKALGMDFYDYLGTDSRFNEVF 172 (221)
Q Consensus 93 ~~~~~~~~~y~lt~~s~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~f~~~~g~~~~~~l~~~p~~~~~F 172 (221)
.... .. .|+++++++++..++.+.++++++...+++..++.|..|.++++.++.+|..++|...|+|...++.....|
T Consensus 76 ~~~~-~~-~Y~~~~~~~~~l~~~~~~S~a~~~~~~~~~v~~~~w~~l~dai~eg~~~~~~~~G~~l~~~~~~~~~~~~~~ 153 (342)
T KOG3178|consen 76 RLVG-GE-VYSATPVCKYFLKDSGGGSLAPLVLLNTSKVIMNTWQFLKDAILEGGDAFATAHGMMLGGYGGADERFSKDF 153 (342)
T ss_pred eeec-ce-eeeccchhhhheecCCCCchhHHHHHhcccchhhhHHHHHHHHHhcccCCccccchhhhhhcccccccHHHH
Confidence 7321 12 899999999877544345899999888888899999999999999999999999988999999999999999
Q ss_pred HHHHhhhhHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCCC
Q 036971 173 NNGMIGQTSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHNFQIPSY 221 (221)
Q Consensus 173 ~~aM~~~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l 221 (221)
+++|...+....+.+++.|.+|++...+||||||.|..+..++..||++
T Consensus 154 ~~sm~~l~~~~~~~il~~~~Gf~~v~~avDvGgGiG~v~k~ll~~fp~i 202 (342)
T KOG3178|consen 154 NGSMSFLSTLVMKKILEVYTGFKGVNVAVDVGGGIGRVLKNLLSKYPHI 202 (342)
T ss_pred HHHHHHHHHHHHHhhhhhhcccccCceEEEcCCcHhHHHHHHHHhCCCC
Confidence 9999999998888889999889999999999999999999999999975
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=99.91 E-value=7.3e-24 Score=181.74 Aligned_cols=169 Identities=17% Similarity=0.289 Sum_probs=125.4
Q ss_pred HHHHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc
Q 036971 30 VLPAVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK 109 (221)
Q Consensus 30 ~~~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~ 109 (221)
+...+|++|++|||||+|++ +|.|++|||+++|+ +++ .++|+||+|+++|+|++. +++|+||+.++
T Consensus 2 ~~~~~l~aa~~Lglfd~L~~----gp~t~~eLA~~~~~-~~~----~~~~lL~~L~~lgll~~~-----~~~y~~t~~~~ 67 (306)
T TIGR02716 2 IEFSCMKAAIELDLFSHMAE----GPKDLATLAADTGS-VPP----RLEMLLETLRQMRVINLE-----DGKWSLTEFAD 67 (306)
T ss_pred chHHHHHHHHHcCcHHHHhc----CCCCHHHHHHHcCC-ChH----HHHHHHHHHHhCCCeEec-----CCcEecchhHH
Confidence 35789999999999999998 69999999999999 998 999999999999999985 78999999998
Q ss_pred ccccCCCCC---ChHHHHHHhcCccchhhhhhhHHHHhcCCchhHhhhCCchhhhhccCchHHHHHHHHHh-hhhHHHHH
Q 036971 110 YYVSDQNGV---SMRPYMNLSLDKVMMPGWFQLKDQILEGELSYNKALGMDFYDYLGTDSRFNEVFNNGMI-GQTSFVIN 185 (221)
Q Consensus 110 ~L~~~~~~~---~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~f~~~~g~~~~~~l~~~p~~~~~F~~aM~-~~~~~~~~ 185 (221)
.+..++++. ++.+++.+.. ......|.+|.+++| ++++|... +++....++.. .|...|. .......+
T Consensus 68 ~~l~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~r-~~~~~~~~-----~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 139 (306)
T TIGR02716 68 YMFSPTPKEPNLHQTPVAKAMA-FLADDFYMGLSQAVR-GQKNFKGQ-----VPYPPVTREDN-LYFEEIHRSNAKFAIQ 139 (306)
T ss_pred hhccCCccchhhhcCchHHHHH-HHHHHHHHhHHHHhc-CCcccccc-----cCCCCCCHHHH-HhHHHHHHhcchhHHH
Confidence 665543311 1123443331 123356899999998 45555332 22222223332 3444444 43444556
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCCC
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNFQIPSY 221 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l 221 (221)
.+++.++ +++..+|||||||+|.++.++++++|++
T Consensus 140 ~l~~~~~-~~~~~~vlDiG~G~G~~~~~~~~~~p~~ 174 (306)
T TIGR02716 140 LLLEEAK-LDGVKKMIDVGGGIGDISAAMLKHFPEL 174 (306)
T ss_pred HHHHHcC-CCCCCEEEEeCCchhHHHHHHHHHCCCC
Confidence 6788888 8888999999999999999999999974
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=99.85 E-value=4e-21 Score=159.40 Aligned_cols=123 Identities=28% Similarity=0.568 Sum_probs=107.8
Q ss_pred CCcceeccccccccccCCCCCChHHHHHHhcCccchhhhhhhHHHHhcCCchhHhhhCCchhhhhccCchHHHHHHHHHh
Q 036971 98 GVRLYSLAPVAKYYVSDQNGVSMRPYMNLSLDKVMMPGWFQLKDQILEGELSYNKALGMDFYDYLGTDSRFNEVFNNGMI 177 (221)
Q Consensus 98 ~~~~y~lt~~s~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~f~~~~g~~~~~~l~~~p~~~~~F~~aM~ 177 (221)
++++|+||++|+.|+.+++..++..++.+...+..++.|.+|.+++++|+++|+..+|.++|+|+.++|+..+.|+++|.
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 58999999999988766542367888877666778999999999999999999999998999999999999999999999
Q ss_pred hhhHHHH-HHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCCC
Q 036971 178 GQTSFVI-NKIVESYKGFQNITRLVDVGGGLGITLSDHNFQIPSY 221 (221)
Q Consensus 178 ~~~~~~~-~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l 221 (221)
..+.... +.+++.++ |++.++|||||||.|+++.+++++||+|
T Consensus 82 ~~~~~~~~~~~~~~~d-~~~~~~vvDvGGG~G~~~~~l~~~~P~l 125 (241)
T PF00891_consen 82 EYSRLNAFDILLEAFD-FSGFKTVVDVGGGSGHFAIALARAYPNL 125 (241)
T ss_dssp HHHHHHHHHHHHHHST-TTTSSEEEEET-TTSHHHHHHHHHSTTS
T ss_pred hhhhcchhhhhhcccc-ccCccEEEeccCcchHHHHHHHHHCCCC
Confidence 9988877 78889999 9999999999999999999999999986
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=99.11 E-value=1.5e-10 Score=72.55 Aligned_cols=50 Identities=50% Similarity=0.816 Sum_probs=43.0
Q ss_pred HHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCC-CCCCcchhhhHHHHHHHHh
Q 036971 33 AVFQAVVNLDVLDIINKAGPGAELSASEIASQIP-TKNPEGAAKMLDRVLGLLV 85 (221)
Q Consensus 33 ~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g-~~~~~~~~~~l~rlLr~L~ 85 (221)
.+|++|++|||||+|++.| |+++|++||+.++. . +|. ++..|.|+||+|+
T Consensus 1 MaLk~aveLgI~dii~~~g-~~~ls~~eia~~l~~~-~p~-~~~~L~RimR~L~ 51 (51)
T PF08100_consen 1 MALKCAVELGIPDIIHNAG-GGPLSLSEIAARLPTS-NPS-APPMLDRIMRLLV 51 (51)
T ss_dssp HHHHHHHHTTHHHHHHHHT-TS-BEHHHHHHTSTCT--TT-HHHHHHHHHHHHH
T ss_pred CcHHHHHHcCcHHHHHHcC-CCCCCHHHHHHHcCCC-Ccc-hHHHHHHHHHHhC
Confidence 4799999999999999996 47999999999999 6 665 7779999999985
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=97.39 E-value=5.8e-05 Score=47.44 Aligned_cols=46 Identities=26% Similarity=0.357 Sum_probs=40.3
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+.|++.|.+.+ +++|+.|||+++|+ +.. -+.|+|..|+..|+++++
T Consensus 6 l~iL~~l~~~~--~~~t~~eia~~~gl-~~s----tv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESG--GPLTLSEIARALGL-PKS----TVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHHCHHCTB--SCEEHHHHHHHHTS--HH----HHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHHcCC--CCCCHHHHHHHHCc-CHH----HHHHHHHHHHHCcCeecC
Confidence 45788899876 67899999999999 776 899999999999999985
No 6
>PRK06922 hypothetical protein; Provisional
Probab=97.32 E-value=0.00049 Score=64.40 Aligned_cols=64 Identities=17% Similarity=0.248 Sum_probs=47.7
Q ss_pred CchhhhhccCchHHHHHHHHHhhhhHHH--HHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 156 MDFYDYLGTDSRFNEVFNNGMIGQTSFV--INKIVESYKGFQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 156 ~~~~~~l~~~p~~~~~F~~aM~~~~~~~--~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
..+|+++..+++..++|.+.|....... .......++ |....+|||||||.|.++..+++.+|+
T Consensus 377 ~~~fd~fg~r~D~~dRf~~~~~yle~m~~~~~~k~~i~d-~~~g~rVLDIGCGTG~ls~~LA~~~P~ 442 (677)
T PRK06922 377 VLLFDFFGLRKDAYDRFHNEEVYLEHMNSSADDKRIILD-YIKGDTIVDVGAGGGVMLDMIEEETED 442 (677)
T ss_pred hHHHHHhccChhhHhHHHhHHHHHHhccccHHHHHHHhh-hcCCCEEEEeCCCCCHHHHHHHHhCCC
Confidence 4689999999989888988776543321 111233455 556789999999999999999999886
No 7
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=97.22 E-value=0.00054 Score=47.75 Aligned_cols=58 Identities=21% Similarity=0.255 Sum_probs=48.3
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccc
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVA 108 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s 108 (221)
+.|++.|...+ +++|+.|||+.+|+ +.. .+.|.|+.|...|++.+.. ..+.|++++..
T Consensus 8 ~~Il~~l~~~~--~~~t~~~ia~~l~i-~~~----tv~r~l~~L~~~g~l~~~~---~~~~y~l~~~~ 65 (91)
T smart00346 8 LAVLRALAEEP--GGLTLAELAERLGL-SKS----TAHRLLNTLQELGYVEQDG---QNGRYRLGPKV 65 (91)
T ss_pred HHHHHHHHhCC--CCcCHHHHHHHhCC-CHH----HHHHHHHHHHHCCCeeecC---CCCceeecHHH
Confidence 56788888863 48999999999999 887 9999999999999999862 36678887743
No 8
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=97.02 E-value=0.0017 Score=43.13 Aligned_cols=60 Identities=18% Similarity=0.271 Sum_probs=48.9
Q ss_pred HHhhChhhHHHhcCCCC-CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 38 VVNLDVLDIINKAGPGA-ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 38 av~lglfd~L~~~g~~~-~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
.++-.|.+.|.+.| + ++|+.|||+.+|+ +.. .++|+|.-|...|+|+.... .++.|+.+.
T Consensus 6 ~~~~~IL~~L~~~g--~~~~ta~eLa~~lgl-~~~----~v~r~L~~L~~~G~V~~~~~--~~~~W~i~~ 66 (68)
T smart00550 6 SLEEKILEFLENSG--DETSTALQLAKNLGL-PKK----EVNRVLYSLEKKGKVCKQGG--TPPLWKLTD 66 (68)
T ss_pred HHHHHHHHHHHHCC--CCCcCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEecCC--CCCceEeec
Confidence 35567888999985 3 3999999999999 887 99999999999999998621 247787764
No 9
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=96.96 E-value=0.00099 Score=55.56 Aligned_cols=59 Identities=24% Similarity=0.315 Sum_probs=49.4
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK 109 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~ 109 (221)
+.|.+.|...+ .++++.|||+++|+ +.. -+.|+|..|+..|+++++. ++++|++++-..
T Consensus 7 l~iL~~l~~~~--~~l~l~ela~~~gl-pks----T~~RlL~tL~~~G~v~~d~---~~g~Y~Lg~~~~ 65 (246)
T COG1414 7 LAILDLLAEGP--GGLSLAELAERLGL-PKS----TVHRLLQTLVELGYVEQDP---EDGRYRLGPRLL 65 (246)
T ss_pred HHHHHHHHhCC--CCCCHHHHHHHhCc-CHH----HHHHHHHHHHHCCCEEEcC---CCCcEeehHHHH
Confidence 56788888843 45779999999999 887 9999999999999999982 357899998643
No 10
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=96.82 E-value=0.0013 Score=54.71 Aligned_cols=58 Identities=21% Similarity=0.279 Sum_probs=49.5
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccccc
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKY 110 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~ 110 (221)
+.|.+.|.... +++++.|||+.+|+ +.. -+.|+|.-|+..|+++++ ++.|++++....
T Consensus 12 l~IL~~l~~~~--~~~~l~eia~~lgl-pks----T~~RlL~tL~~~G~l~~~-----~~~Y~lG~~~~~ 69 (248)
T TIGR02431 12 LAVIEAFGAER--PRLTLTDVAEATGL-TRA----AARRFLLTLVELGYVTSD-----GRLFWLTPRVLR 69 (248)
T ss_pred HHHHHHHhcCC--CCCCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEeC-----CCEEEecHHHHH
Confidence 56788888754 68999999999999 877 899999999999999984 688999986543
No 11
>PRK11569 transcriptional repressor IclR; Provisional
Probab=96.82 E-value=0.0016 Score=55.19 Aligned_cols=59 Identities=15% Similarity=0.170 Sum_probs=49.5
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK 109 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~ 109 (221)
+.|.+.|.+.. +++++.|||+.+|+ +.. -+.|+|..|+..|+++++. +.++|++.+...
T Consensus 31 l~IL~~l~~~~--~~~~lseia~~lgl-pks----Tv~RlL~tL~~~G~l~~~~---~~~~Y~lG~~l~ 89 (274)
T PRK11569 31 LKLLEWIAESN--GSVALTELAQQAGL-PNS----TTHRLLTTMQQQGFVRQVG---ELGHWAIGAHAF 89 (274)
T ss_pred HHHHHHHHhCC--CCcCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEEcC---CCCeEecCHHHH
Confidence 45777787754 68999999999999 877 8999999999999999862 468999987643
No 12
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=96.79 E-value=0.0017 Score=54.84 Aligned_cols=59 Identities=15% Similarity=0.200 Sum_probs=49.7
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK 109 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~ 109 (221)
+.|++.|.+.+ +++++.|||+.+|+ +.. -+.|+|..|+..|++.++. ..+.|++++-..
T Consensus 28 l~IL~~~~~~~--~~~tl~eIa~~lgl-pkS----tv~RlL~tL~~~G~l~~~~---~~~~Y~lG~~l~ 86 (271)
T PRK10163 28 IAILQYLEKSG--GSSSVSDISLNLDL-PLS----TTFRLLKVLQAADFVYQDS---QLGWWHIGLGVF 86 (271)
T ss_pred HHHHHHHHhCC--CCcCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEEcC---CCCeEEecHHHH
Confidence 55778888764 57999999999999 877 9999999999999999862 467899987543
No 13
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=96.77 E-value=0.0015 Score=45.06 Aligned_cols=55 Identities=24% Similarity=0.286 Sum_probs=41.6
Q ss_pred HHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccc
Q 036971 47 INKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVA 108 (221)
Q Consensus 47 L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s 108 (221)
|+..+.++++|.++||+.+++ ++. .+++++..|...|+++... |..|.|.++.-.
T Consensus 17 la~~~~~~~~s~~eiA~~~~i-~~~----~l~kil~~L~~~Gli~s~~--G~~GGy~L~~~~ 71 (83)
T PF02082_consen 17 LARHPDGKPVSSKEIAERLGI-SPS----YLRKILQKLKKAGLIESSR--GRGGGYRLARPP 71 (83)
T ss_dssp HHCTTTSC-BEHHHHHHHHTS--HH----HHHHHHHHHHHTTSEEEET--STTSEEEESS-C
T ss_pred HHhCCCCCCCCHHHHHHHHCc-CHH----HHHHHHHHHhhCCeeEecC--CCCCceeecCCH
Confidence 344433356999999999999 888 9999999999999998764 246778877543
No 14
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=96.71 E-value=0.002 Score=53.91 Aligned_cols=58 Identities=14% Similarity=0.215 Sum_probs=48.4
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK 109 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~ 109 (221)
+.|.+.|... +++|+.|||+.+|+ +.. -+.|+|+.|+..|+++++. +.+.|++++...
T Consensus 17 l~IL~~l~~~---~~l~l~eia~~lgl-~ks----tv~Rll~tL~~~G~l~~~~---~~~~Y~lG~~~~ 74 (257)
T PRK15090 17 FGILQALGEE---REIGITELSQRVMM-SKS----TVYRFLQTMKTLGYVAQEG---ESEKYSLTLKLF 74 (257)
T ss_pred HHHHHHhhcC---CCCCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEEcC---CCCcEEecHHHH
Confidence 4566777764 48999999999999 887 9999999999999999862 468899998654
No 15
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=96.69 E-value=0.0025 Score=53.61 Aligned_cols=61 Identities=16% Similarity=0.114 Sum_probs=50.6
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccccc
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYY 111 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L 111 (221)
+.|++.|...+ +++++.|||+.+|+ +.. -+.|+|..|...|+++++. +++.|++++....|
T Consensus 14 l~iL~~l~~~~--~~ls~~eia~~lgl-~ks----tv~RlL~tL~~~g~v~~~~---~~~~Y~Lg~~~~~l 74 (263)
T PRK09834 14 LMVLRALNRLD--GGATVGLLAELTGL-HRT----TVRRLLETLQEEGYVRRSA---SDDSFRLTLKVRQL 74 (263)
T ss_pred HHHHHHHHhcC--CCCCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEEec---CCCcEEEcHHHHHH
Confidence 55777887754 46999999999999 887 9999999999999999872 46789999865544
No 16
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=96.48 E-value=0.0024 Score=41.37 Aligned_cols=54 Identities=13% Similarity=0.203 Sum_probs=44.8
Q ss_pred HHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 32 PAVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 32 ~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+.+|.--.++.|+..|... +++|+.+||+.+|+ ++. .+.+-|+.|...|+++..
T Consensus 4 ~~aL~~p~R~~Il~~L~~~---~~~t~~ela~~l~~-~~~----t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 4 FKALSDPTRLRILRLLASN---GPMTVSELAEELGI-SQS----TVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp HHHHTSHHHHHHHHHHHHC---STBEHHHHHHHHTS--HH----HHHHHHHHHHHTTSEEEE
T ss_pred HHHhCCHHHHHHHHHHhcC---CCCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCeEEe
Confidence 3455556778888889554 59999999999999 777 899999999999999986
No 17
>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=96.31 E-value=0.0022 Score=42.42 Aligned_cols=46 Identities=20% Similarity=0.148 Sum_probs=39.4
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+..++..|-.. +++|+++||+.+|+ +.. .+.+.|+.|...|++++.
T Consensus 10 E~~vy~~Ll~~---~~~t~~eIa~~l~i-~~~----~v~~~L~~L~~~GlV~~~ 55 (68)
T PF01978_consen 10 EAKVYLALLKN---GPATAEEIAEELGI-SRS----TVYRALKSLEEKGLVERE 55 (68)
T ss_dssp HHHHHHHHHHH---CHEEHHHHHHHHTS-SHH----HHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHc---CCCCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEEE
Confidence 44556666554 59999999999999 877 999999999999999997
No 18
>TIGR02469 CbiT precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit. This model recognizes the CbiT methylase which is responsible, in part (along with CbiE), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiE subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin biosynthesis pathway, is called CobL.
Probab=96.30 E-value=0.0096 Score=43.23 Aligned_cols=33 Identities=18% Similarity=0.311 Sum_probs=26.9
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
+++.++ .....+|+|||||.|.++..+++.+|+
T Consensus 11 ~~~~~~-~~~~~~vldlG~G~G~~~~~l~~~~~~ 43 (124)
T TIGR02469 11 TLSKLR-LRPGDVLWDIGAGSGSITIEAARLVPN 43 (124)
T ss_pred HHHHcC-CCCCCEEEEeCCCCCHHHHHHHHHCCC
Confidence 455555 555579999999999999999999875
No 19
>TIGR02021 BchM-ChlM magnesium protoporphyrin O-methyltransferase. This model represents the S-adenosylmethionine-dependent O-methyltransferase responsible for methylation of magnesium protoporphyrin IX. This step is essentiasl for the biosynthesis of both chlorophyll and bacteriochlorophyll. This model encompasses two closely related clades, from cyanobacteria (and plants) where it is called ChlM and other photosynthetic bacteria where it is known as BchM.
Probab=96.28 E-value=0.011 Score=48.03 Aligned_cols=61 Identities=10% Similarity=0.017 Sum_probs=36.6
Q ss_pred hhhhhccCchHHHHHHHHHhhhhHHHHHHHHHhcCC-CCCCCeEEEecCCccHHHHHHHhhC
Q 036971 158 FYDYLGTDSRFNEVFNNGMIGQTSFVINKIVESYKG-FQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 158 ~~~~l~~~p~~~~~F~~aM~~~~~~~~~~~l~~~~~-~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
.|+.+...+.....+...|..........+++..+. .....+|+|||||.|.++..+++..
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~vLDiGcG~G~~~~~la~~~ 77 (219)
T TIGR02021 16 RWARIYGSGDPVSRVRQTVREGRAAMRRKLLDWLPKDPLKGKRVLDAGCGTGLLSIELAKRG 77 (219)
T ss_pred HHHHhhCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEeCCCCHHHHHHHHCC
Confidence 455555555555566666643222222333333321 2346899999999999999988754
No 20
>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=96.27 E-value=0.0028 Score=38.78 Aligned_cols=44 Identities=18% Similarity=0.295 Sum_probs=38.3
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceee
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCC 92 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~ 92 (221)
++.|...|.+ ++.++.||++.+|+ ++. .+.+-|+.|...|+++.
T Consensus 4 R~~Il~~L~~----~~~~~~el~~~l~~-s~~----~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 4 RLRILKLLSE----GPLTVSELAEELGL-SQS----TVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHHTT----SSEEHHHHHHHHTS--HH----HHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHh----CCCchhhHHHhccc-cch----HHHHHHHHHHHCcCeeC
Confidence 5667788888 69999999999999 776 99999999999999874
No 21
>COG2813 RsmC 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]
Probab=96.14 E-value=0.0079 Score=51.29 Aligned_cols=35 Identities=17% Similarity=0.200 Sum_probs=29.3
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
+.+++.++ .....+|+|+|||.|.+++.+++.+|+
T Consensus 148 ~lLl~~l~-~~~~~~vlDlGCG~Gvlg~~la~~~p~ 182 (300)
T COG2813 148 RLLLETLP-PDLGGKVLDLGCGYGVLGLVLAKKSPQ 182 (300)
T ss_pred HHHHHhCC-ccCCCcEEEeCCCccHHHHHHHHhCCC
Confidence 45677888 444459999999999999999999995
No 22
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=96.10 E-value=0.011 Score=46.22 Aligned_cols=47 Identities=11% Similarity=0.082 Sum_probs=40.3
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPV 107 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~ 107 (221)
+++|+++||+.+++ +++ .+.++|..|...||+.... |.+|.|.+..-
T Consensus 24 ~~vs~~eIA~~~~i-p~~----~l~kIl~~L~~aGLv~s~r--G~~GGy~Lar~ 70 (164)
T PRK10857 24 GPVPLADISERQGI-SLS----YLEQLFSRLRKNGLVSSVR--GPGGGYLLGKD 70 (164)
T ss_pred CcCcHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEeCC--CCCCCeeccCC
Confidence 58999999999999 888 9999999999999999753 25677887643
No 23
>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=96.09 E-value=0.0065 Score=37.18 Aligned_cols=45 Identities=13% Similarity=0.280 Sum_probs=37.9
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCcee
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILC 91 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~ 91 (221)
.+..|+..|.+. +.+|..|||+.+|+ +.. .+.+.++-|...|+++
T Consensus 4 ~~~~Il~~l~~~---~~~t~~ela~~~~i-s~~----tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLREN---PRITQKELAEKLGI-SRS----TVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHC---TTS-HHHHHHHHTS--HH----HHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHhCC-CHH----HHHHHHHHHHHCcCcC
Confidence 456788899997 47999999999999 777 9999999999999875
No 24
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=96.03 E-value=0.012 Score=45.38 Aligned_cols=56 Identities=21% Similarity=0.224 Sum_probs=45.7
Q ss_pred HHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccc
Q 036971 46 IINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVA 108 (221)
Q Consensus 46 ~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s 108 (221)
.|+..+++++.|+++||+..++ +|. .|.++|..|...||++-.+ |..|.|+++.-.
T Consensus 16 ~LA~~~~~~~~s~~~IA~~~~i-s~~----~L~kil~~L~kaGlV~S~r--G~~GGy~Lar~~ 71 (150)
T COG1959 16 YLALLPGGGPVSSAEIAERQGI-SPS----YLEKILSKLRKAGLVKSVR--GKGGGYRLARPP 71 (150)
T ss_pred HHHhCCCCCcccHHHHHHHhCc-CHH----HHHHHHHHHHHcCCEEeec--CCCCCccCCCCh
Confidence 4555543348999999999999 988 9999999999999999875 357888887543
No 25
>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=96.00 E-value=0.0076 Score=40.03 Aligned_cols=43 Identities=19% Similarity=0.320 Sum_probs=37.1
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
|-++|.+. +.+|..|||..+++ ++. .++.+|..|+..|.+++.
T Consensus 5 i~~~l~~~---~~~S~~eLa~~~~~-s~~----~ve~mL~~l~~kG~I~~~ 47 (69)
T PF09012_consen 5 IRDYLRER---GRVSLAELAREFGI-SPE----AVEAMLEQLIRKGYIRKV 47 (69)
T ss_dssp HHHHHHHS----SEEHHHHHHHTT---HH----HHHHHHHHHHCCTSCEEE
T ss_pred HHHHHHHc---CCcCHHHHHHHHCc-CHH----HHHHHHHHHHHCCcEEEe
Confidence 56788887 58999999999999 888 999999999999999987
No 26
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=95.96 E-value=0.0098 Score=38.76 Aligned_cols=45 Identities=20% Similarity=0.129 Sum_probs=37.5
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.|.+.|.... +|++..|||+++|+ +.. ..+++|..|...|.+++.
T Consensus 4 ~Il~~i~~~~--~p~~T~eiA~~~gl-s~~----~aR~yL~~Le~eG~V~~~ 48 (62)
T PF04703_consen 4 KILEYIKEQN--GPLKTREIADALGL-SIY----QARYYLEKLEKEGKVERS 48 (62)
T ss_dssp CHHHHHHHHT--S-EEHHHHHHHHTS--HH----HHHHHHHHHHHCTSEEEE
T ss_pred HHHHHHHHcC--CCCCHHHHHHHhCC-CHH----HHHHHHHHHHHCCCEEEe
Confidence 5677777733 69999999999999 877 899999999999999986
No 27
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=95.89 E-value=0.014 Score=43.11 Aligned_cols=56 Identities=16% Similarity=0.285 Sum_probs=48.5
Q ss_pred HHHHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 30 VLPAVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 30 ~~~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
-.+.+|.--+++.|+..|... ++.++.||++.+++ .+. .+.+-|+.|...|++...
T Consensus 8 ~~fkaLadptRl~IL~~L~~~---~~~~v~ela~~l~l-sqs----tvS~HL~~L~~AGLV~~~ 63 (117)
T PRK10141 8 QLFKILSDETRLGIVLLLRES---GELCVCDLCTALDQ-SQP----KISRHLALLRESGLLLDR 63 (117)
T ss_pred HHHHHhCCHHHHHHHHHHHHc---CCcCHHHHHHHHCc-CHH----HHHHHHHHHHHCCceEEE
Confidence 345677777889999999875 48999999999999 776 999999999999999987
No 28
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=95.88 E-value=0.0059 Score=41.55 Aligned_cols=56 Identities=21% Similarity=0.230 Sum_probs=42.6
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccccccc
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
|...+.. ++.+..+|+..+++ +.. .+.+.|..|...|++.. .++.|.+|+.+..+.
T Consensus 11 IL~~l~~----~~~~~t~i~~~~~L-~~~----~~~~yL~~L~~~gLI~~-----~~~~Y~lTekG~~~l 66 (77)
T PF14947_consen 11 ILKILSK----GGAKKTEIMYKANL-NYS----TLKKYLKELEEKGLIKK-----KDGKYRLTEKGKEFL 66 (77)
T ss_dssp HHHHH-T----T-B-HHHHHTTST---HH----HHHHHHHHHHHTTSEEE-----ETTEEEE-HHHHHHH
T ss_pred HHHHHHc----CCCCHHHHHHHhCc-CHH----HHHHHHHHHHHCcCeeC-----CCCEEEECccHHHHH
Confidence 4445543 58999999999999 887 99999999999999977 499999999987654
No 29
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=95.87 E-value=0.016 Score=43.78 Aligned_cols=46 Identities=11% Similarity=0.114 Sum_probs=39.1
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
++.|.++||+.+++ ++. .++++|+.|...|++.... |..|.|.++.
T Consensus 24 ~~~s~~~ia~~~~i-p~~----~l~kil~~L~~~glv~s~~--G~~Ggy~l~~ 69 (135)
T TIGR02010 24 GPVTLADISERQGI-SLS----YLEQLFAKLRKAGLVKSVR--GPGGGYQLGR 69 (135)
T ss_pred CcCcHHHHHHHHCc-CHH----HHHHHHHHHHHCCceEEEe--CCCCCEeccC
Confidence 58999999999999 888 9999999999999998653 2456677765
No 30
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=95.86 E-value=0.012 Score=35.47 Aligned_cols=40 Identities=20% Similarity=0.172 Sum_probs=35.4
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceec
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSL 104 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~l 104 (221)
+++..+||+.+++ +.. .+.+.|+.|...|+++.. .+.|..
T Consensus 8 ~~s~~~la~~l~~-s~~----tv~~~l~~L~~~g~l~~~-----~~~~~i 47 (48)
T smart00419 8 PLTRQEIAELLGL-TRE----TVSRTLKRLEKEGLISRE-----GGRIVI 47 (48)
T ss_pred ccCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEe-----CCEEEE
Confidence 6899999999999 777 999999999999999985 566654
No 31
>PRK15001 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional
Probab=95.81 E-value=0.013 Score=51.91 Aligned_cols=35 Identities=17% Similarity=0.112 Sum_probs=28.2
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
..+++.+| .....+|+|||||.|.++..+++++|+
T Consensus 218 rllL~~lp-~~~~~~VLDLGCGtGvi~i~la~~~P~ 252 (378)
T PRK15001 218 RFFMQHLP-ENLEGEIVDLGCGNGVIGLTLLDKNPQ 252 (378)
T ss_pred HHHHHhCC-cccCCeEEEEeccccHHHHHHHHhCCC
Confidence 34566776 333469999999999999999999996
No 32
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=95.72 E-value=0.016 Score=37.60 Aligned_cols=44 Identities=25% Similarity=0.320 Sum_probs=38.6
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
.++|..+||+.+|+ ++. .+.++|+.|...|++... ..+.|.+++
T Consensus 24 ~~~s~~ela~~~g~-s~~----tv~r~l~~L~~~g~i~~~----~~~~~~l~~ 67 (67)
T cd00092 24 LPLTRQEIADYLGL-TRE----TVSRTLKELEEEGLISRR----GRGKYRVNP 67 (67)
T ss_pred CCcCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEec----CCCeEEeCC
Confidence 58999999999999 877 999999999999999986 337787764
No 33
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=95.69 E-value=0.018 Score=48.70 Aligned_cols=35 Identities=23% Similarity=0.260 Sum_probs=28.3
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
..+++.++ .....+|+|||||.|.++..++++.++
T Consensus 32 ~~i~~~l~-~~~~~~VLEiG~G~G~lt~~L~~~~~~ 66 (272)
T PRK00274 32 DKIVDAAG-PQPGDNVLEIGPGLGALTEPLLERAAK 66 (272)
T ss_pred HHHHHhcC-CCCcCeEEEeCCCccHHHHHHHHhCCc
Confidence 44566666 666689999999999999999998764
No 34
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=95.68 E-value=0.02 Score=42.66 Aligned_cols=47 Identities=15% Similarity=0.201 Sum_probs=38.5
Q ss_pred hhChhhHHH-hcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeec
Q 036971 40 NLDVLDIIN-KAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSF 94 (221)
Q Consensus 40 ~lglfd~L~-~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~ 94 (221)
+..++-+|- .+ +|.|+++||+.++. +.. -+.|-|+-|...|++.+.+
T Consensus 29 Dv~v~~~LL~~~---~~~tvdelae~lnr-~rS----tv~rsl~~L~~~GlV~Rek 76 (126)
T COG3355 29 DVEVYKALLEEN---GPLTVDELAEILNR-SRS----TVYRSLQNLLEAGLVEREK 76 (126)
T ss_pred HHHHHHHHHhhc---CCcCHHHHHHHHCc-cHH----HHHHHHHHHHHcCCeeeee
Confidence 344444444 44 69999999999999 776 8999999999999999974
No 35
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=95.60 E-value=0.017 Score=37.76 Aligned_cols=49 Identities=14% Similarity=0.280 Sum_probs=35.8
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccC--CCCcceecccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFST--HGVRLYSLAPV 107 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~--~~~~~y~lt~~ 107 (221)
++++..+||+.+++ +.. .+.+.++.|...|++++.... .....|++|+.
T Consensus 17 ~~~t~~~l~~~~~~-~~~----~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~ 67 (68)
T PF13463_consen 17 GPMTQSDLAERLGI-SKS----TVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPA 67 (68)
T ss_dssp S-BEHHHHHHHTT---HH----HHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HH
T ss_pred CCcCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCC
Confidence 69999999999999 877 899999999999999876321 11235888764
No 36
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=95.52 E-value=0.023 Score=42.42 Aligned_cols=46 Identities=22% Similarity=0.182 Sum_probs=38.1
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
++.+.++||+.+++ ++. .++++|+.|...|++.... |..|.|.++.
T Consensus 24 ~~~s~~eia~~~~i-~~~----~v~~il~~L~~~gli~~~~--g~~ggy~l~~ 69 (132)
T TIGR00738 24 GPVSVKEIAERQGI-SRS----YLEKILRTLRRAGLVESVR--GPGGGYRLAR 69 (132)
T ss_pred CcCcHHHHHHHHCc-CHH----HHHHHHHHHHHCCcEEecc--CCCCCccCCC
Confidence 48999999999999 888 9999999999999998742 1345666654
No 37
>PRK00107 gidB 16S rRNA methyltransferase GidB; Reviewed
Probab=95.42 E-value=0.031 Score=44.67 Aligned_cols=25 Identities=28% Similarity=0.393 Sum_probs=22.2
Q ss_pred CCCeEEEecCCccHHHHHHHhhCCC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
...+|+|||||+|..+..+++.+|+
T Consensus 45 ~g~~VLDiGcGtG~~al~la~~~~~ 69 (187)
T PRK00107 45 GGERVLDVGSGAGFPGIPLAIARPE 69 (187)
T ss_pred CCCeEEEEcCCCCHHHHHHHHHCCC
Confidence 3679999999999999999988875
No 38
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=95.21 E-value=0.036 Score=45.23 Aligned_cols=63 Identities=22% Similarity=0.361 Sum_probs=49.4
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCC----Ccceeccccccccc
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHG----VRLYSLAPVAKYYV 112 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~----~~~y~lt~~s~~L~ 112 (221)
.|...|.+. +|+|+.|||+++|+ ++. .+++-|..|.+.|+++.....++ .-.|++|..++...
T Consensus 15 ~il~lL~~~---g~~sa~elA~~Lgi-s~~----avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~~f 81 (218)
T COG2345 15 RILELLKKS---GPVSADELAEELGI-SPM----AVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGREQF 81 (218)
T ss_pred HHHHHHhcc---CCccHHHHHHHhCC-CHH----HHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchhhc
Confidence 355677776 59999999999999 888 99999999999999997632111 22599999877544
No 39
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=95.19 E-value=0.032 Score=38.94 Aligned_cols=65 Identities=26% Similarity=0.293 Sum_probs=47.5
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccC--CCCcceeccccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFST--HGVRLYSLAPVAKYYV 112 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~--~~~~~y~lt~~s~~L~ 112 (221)
++.|+..|... ++++..+||+.+++ ++. .+.+.++-|...|++...... .....|.+|+.+..+.
T Consensus 12 ~~~il~~l~~~---~~~~~~~la~~~~~-s~~----~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~ 78 (101)
T smart00347 12 QFLVLRILYEE---GPLSVSELAKRLGV-SPS----TVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELI 78 (101)
T ss_pred HHHHHHHHHHc---CCcCHHHHHHHHCC-Cch----hHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHH
Confidence 55677788776 47999999999999 877 899999999999999976210 0012455565555443
No 40
>PRK14121 tRNA (guanine-N(7)-)-methyltransferase; Provisional
Probab=95.15 E-value=0.03 Score=49.72 Aligned_cols=33 Identities=18% Similarity=0.214 Sum_probs=26.4
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
+++.+. -.....+||||||.|.++..+++.+|+
T Consensus 114 ~~~~~~-~~~~p~vLEIGcGsG~~ll~lA~~~P~ 146 (390)
T PRK14121 114 FLDFIS-KNQEKILIEIGFGSGRHLLYQAKNNPN 146 (390)
T ss_pred HHHHhc-CCCCCeEEEEcCcccHHHHHHHHhCCC
Confidence 444444 234568999999999999999999996
No 41
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=95.13 E-value=0.039 Score=41.93 Aligned_cols=50 Identities=20% Similarity=0.189 Sum_probs=43.4
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccccccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
++.++.+||+.+++ ++. .+.+.++.|...|++... ..+.|.+|+.+..+.
T Consensus 21 ~~~~~~ela~~l~v-s~~----svs~~l~~L~~~Gli~~~----~~~~i~LT~~G~~~a 70 (142)
T PRK03902 21 GYARVSDIAEALSV-HPS----SVTKMVQKLDKDEYLIYE----KYRGLVLTPKGKKIG 70 (142)
T ss_pred CCcCHHHHHHHhCC-Chh----HHHHHHHHHHHCCCEEEe----cCceEEECHHHHHHH
Confidence 58999999999999 777 999999999999999975 467799999886543
No 42
>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=95.11 E-value=0.03 Score=41.79 Aligned_cols=46 Identities=28% Similarity=0.226 Sum_probs=37.8
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
++.++.+||+++++ ++. .+.++|+.|...|++.... +..+.|.+..
T Consensus 24 ~~~s~~eia~~l~i-s~~----~v~~~l~~L~~~Gli~~~~--g~~ggy~l~~ 69 (130)
T TIGR02944 24 QPYSAAEIAEQTGL-NAP----TVSKILKQLSLAGIVTSKR--GVEGGYTLAR 69 (130)
T ss_pred CCccHHHHHHHHCc-CHH----HHHHHHHHHHHCCcEEecC--CCCCChhhcC
Confidence 58999999999999 887 9999999999999998642 1345666644
No 43
>PRK00121 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed
Probab=95.01 E-value=0.032 Score=44.93 Aligned_cols=32 Identities=19% Similarity=0.236 Sum_probs=26.1
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
|.+.|.. ...+|+|||||.|..+..+++.+|+
T Consensus 33 ~~~~~~~--~~~~VLDiGcGtG~~~~~la~~~p~ 64 (202)
T PRK00121 33 WAELFGN--DAPIHLEIGFGKGEFLVEMAKANPD 64 (202)
T ss_pred HHHHcCC--CCCeEEEEccCCCHHHHHHHHHCCC
Confidence 4555552 4579999999999999999998885
No 44
>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=94.97 E-value=0.046 Score=44.13 Aligned_cols=65 Identities=18% Similarity=0.278 Sum_probs=49.3
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCc----ceeccccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVR----LYSLAPVAKYYV 112 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~----~y~lt~~s~~L~ 112 (221)
+..|+..|... +++|..+||+.+++ ++. .+.+.|+.|...|+++........| .|.+|+.+..+.
T Consensus 3 r~~IL~~L~~~---~~~t~~eLA~~lgi-s~~----tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~ 71 (203)
T TIGR02702 3 KEDILSYLLKQ---GQATAAALAEALAI-SPQ----AVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQF 71 (203)
T ss_pred HHHHHHHHHHc---CCCCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhc
Confidence 34577778776 48999999999999 887 9999999999999998762100122 378887776554
No 45
>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=94.92 E-value=0.049 Score=38.21 Aligned_cols=69 Identities=22% Similarity=0.230 Sum_probs=51.2
Q ss_pred HHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHH----------HHHhcCCce-eeeccCCCCcceecc
Q 036971 37 AVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVL----------GLLVSFNIL-CCSFSTHGVRLYSLA 105 (221)
Q Consensus 37 ~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlL----------r~L~~~gll-~~~~~~~~~~~y~lt 105 (221)
.=++..|+..|...-+ .+.++.|||..++. ++. .+.-.| +.|+.+|++ ++... ++.-.|++|
T Consensus 8 S~~R~~vl~~L~~~yp-~~~~~~eIar~v~~-~~s----nV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~-~g~k~Y~lT 80 (90)
T PF07381_consen 8 SKVRKKVLEYLCSIYP-EPAYPSEIARSVGS-DYS----NVLGALRGDGKRYNKEDSLVGLGLVEEEEEK-GGFKYYRLT 80 (90)
T ss_pred HHHHHHHHHHHHHcCC-CcCCHHHHHHHHCC-CHH----HHHHHHhcCCCCcCcchhHHHcCCeeEeeec-CCeeEEEeC
Confidence 5577889999999833 58999999999999 887 666666 468999999 44321 123479999
Q ss_pred ccccccc
Q 036971 106 PVAKYYV 112 (221)
Q Consensus 106 ~~s~~L~ 112 (221)
+.+..++
T Consensus 81 ~~G~~~~ 87 (90)
T PF07381_consen 81 EKGKRIA 87 (90)
T ss_pred hhhhhHH
Confidence 8776443
No 46
>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=94.87 E-value=0.04 Score=44.98 Aligned_cols=32 Identities=16% Similarity=-0.006 Sum_probs=26.0
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
.+++.++ .....+|||||||.|.++..+++.+
T Consensus 36 ~~l~~l~-~~~~~~vLDiGcG~G~~~~~la~~~ 67 (231)
T TIGR02752 36 DTMKRMN-VQAGTSALDVCCGTADWSIALAEAV 67 (231)
T ss_pred HHHHhcC-CCCCCEEEEeCCCcCHHHHHHHHHh
Confidence 3555566 5666899999999999999999876
No 47
>COG2230 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]
Probab=94.87 E-value=0.053 Score=46.07 Aligned_cols=34 Identities=21% Similarity=0.234 Sum_probs=30.3
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 184 INKIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 184 ~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
...+++.+. +++..+|||||||-|.+++-.++.|
T Consensus 61 ~~~~~~kl~-L~~G~~lLDiGCGWG~l~~~aA~~y 94 (283)
T COG2230 61 LDLILEKLG-LKPGMTLLDIGCGWGGLAIYAAEEY 94 (283)
T ss_pred HHHHHHhcC-CCCCCEEEEeCCChhHHHHHHHHHc
Confidence 456788888 8899999999999999999999887
No 48
>PRK15068 tRNA mo(5)U34 methyltransferase; Provisional
Probab=94.84 E-value=0.039 Score=47.89 Aligned_cols=24 Identities=21% Similarity=0.085 Sum_probs=21.4
Q ss_pred CCeEEEecCCccHHHHHHHhhCCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
.++|+|||||.|.++..+++..|.
T Consensus 123 g~~VLDIGCG~G~~~~~la~~g~~ 146 (322)
T PRK15068 123 GRTVLDVGCGNGYHMWRMLGAGAK 146 (322)
T ss_pred CCEEEEeccCCcHHHHHHHHcCCC
Confidence 489999999999999999988764
No 49
>PRK07402 precorrin-6B methylase; Provisional
Probab=94.75 E-value=0.068 Score=42.64 Aligned_cols=33 Identities=18% Similarity=0.410 Sum_probs=26.4
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
+++.++ .....+|+|||||+|.++..+++..|+
T Consensus 32 l~~~l~-~~~~~~VLDiG~G~G~~~~~la~~~~~ 64 (196)
T PRK07402 32 LISQLR-LEPDSVLWDIGAGTGTIPVEAGLLCPK 64 (196)
T ss_pred HHHhcC-CCCCCEEEEeCCCCCHHHHHHHHHCCC
Confidence 455555 556689999999999999999887764
No 50
>PRK10258 biotin biosynthesis protein BioC; Provisional
Probab=94.71 E-value=0.082 Score=43.79 Aligned_cols=34 Identities=15% Similarity=0.197 Sum_probs=25.1
Q ss_pred HHHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhh
Q 036971 183 VINKIVESYKGFQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 183 ~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
.+..+++.++ .....+|+|||||+|.++..+.+.
T Consensus 30 ~a~~l~~~l~-~~~~~~vLDiGcG~G~~~~~l~~~ 63 (251)
T PRK10258 30 SADALLAMLP-QRKFTHVLDAGCGPGWMSRYWRER 63 (251)
T ss_pred HHHHHHHhcC-ccCCCeEEEeeCCCCHHHHHHHHc
Confidence 3445566666 445679999999999998887654
No 51
>PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional
Probab=94.68 E-value=0.049 Score=47.68 Aligned_cols=33 Identities=18% Similarity=0.322 Sum_probs=25.7
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
+++.++ -....+|+|+|||.|.++..+++.+|+
T Consensus 188 Ll~~l~-~~~~g~VLDlGCG~G~ls~~la~~~p~ 220 (342)
T PRK09489 188 LLSTLT-PHTKGKVLDVGCGAGVLSAVLARHSPK 220 (342)
T ss_pred HHHhcc-ccCCCeEEEeccCcCHHHHHHHHhCCC
Confidence 445555 222458999999999999999999985
No 52
>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=94.61 E-value=0.12 Score=37.69 Aligned_cols=68 Identities=15% Similarity=0.152 Sum_probs=51.5
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCC--CcceeccccccccccC
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHG--VRLYSLAPVAKYYVSD 114 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~--~~~y~lt~~s~~L~~~ 114 (221)
.+..|+..|... +++|..+||+.+++ +.. .+.++++-|...|++.......+ .-.+.+|+.+..+...
T Consensus 29 ~q~~iL~~l~~~---~~~t~~ela~~~~~-~~~----tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~ 98 (118)
T TIGR02337 29 QQWRILRILAEQ---GSMEFTQLANQACI-LRP----SLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYAS 98 (118)
T ss_pred HHHHHHHHHHHc---CCcCHHHHHHHhCC-Cch----hHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence 344467777776 58999999999999 887 99999999999999998632101 1258888888766543
No 53
>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=94.58 E-value=0.04 Score=46.67 Aligned_cols=34 Identities=18% Similarity=0.235 Sum_probs=25.5
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 184 INKIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 184 ~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
...+++..+ .++..+|||||||-|.++..++++|
T Consensus 51 ~~~~~~~~~-l~~G~~vLDiGcGwG~~~~~~a~~~ 84 (273)
T PF02353_consen 51 LDLLCEKLG-LKPGDRVLDIGCGWGGLAIYAAERY 84 (273)
T ss_dssp HHHHHTTTT---TT-EEEEES-TTSHHHHHHHHHH
T ss_pred HHHHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHc
Confidence 345677777 8888999999999999999999875
No 54
>PRK07580 Mg-protoporphyrin IX methyl transferase; Validated
Probab=94.58 E-value=0.069 Score=43.38 Aligned_cols=26 Identities=19% Similarity=0.086 Sum_probs=21.3
Q ss_pred CCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
.....+|+|||||.|.++..+++..+
T Consensus 61 ~~~~~~vLDvGcG~G~~~~~l~~~~~ 86 (230)
T PRK07580 61 DLTGLRILDAGCGVGSLSIPLARRGA 86 (230)
T ss_pred CCCCCEEEEEeCCCCHHHHHHHHcCC
Confidence 34457999999999999999887654
No 55
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=94.54 E-value=0.058 Score=35.58 Aligned_cols=60 Identities=13% Similarity=0.134 Sum_probs=44.5
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCc-chhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPE-GAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK 109 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~-~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~ 109 (221)
|.+.|.+.+ +|++..+|++.++. ... .....++|.|++|-..|++++. ....+.+|+.+.
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--KPLGRKQLAEELKL-RGEELSEEAVRRRLRAMERDGLTRKV----GRQGRIITEKGL 63 (66)
T ss_pred HHHHHHHcC--CCCCHHHHHHHHHh-cChhhhHHHHHHHHHHHHHCCCcccc----CCcccccCHHHH
Confidence 567888877 79999999999976 322 1124899999999999988875 344556666543
No 56
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=94.52 E-value=0.029 Score=38.49 Aligned_cols=64 Identities=19% Similarity=0.173 Sum_probs=47.9
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccC-CC--Ccceeccccccc
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFST-HG--VRLYSLAPVAKY 110 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~-~~--~~~y~lt~~s~~ 110 (221)
++++|...|... +.++..+|.+.+|+ +.. .|.+.|..|...|+++....- +. .-.|++|+.++.
T Consensus 1 vRl~Il~~L~~~---~~~~f~~L~~~l~l-t~g----~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~ 67 (80)
T PF13601_consen 1 VRLAILALLYAN---EEATFSELKEELGL-TDG----NLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGRE 67 (80)
T ss_dssp HHHHHHHHHHHH---SEEEHHHHHHHTT---HH----HHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHH
T ss_pred CHHHHHHHHhhc---CCCCHHHHHHHhCc-CHH----HHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHH
Confidence 567888888886 48999999999999 776 999999999999999986431 11 113777777764
No 57
>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=94.49 E-value=0.047 Score=44.14 Aligned_cols=25 Identities=20% Similarity=0.543 Sum_probs=21.7
Q ss_pred CCCeEEEecCCccHHHHHHHhhCCC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
...+|+|||||+|..+..+++..|+
T Consensus 43 ~~~~VLDiGCG~G~~~~~L~~~~~~ 67 (204)
T TIGR03587 43 KIASILELGANIGMNLAALKRLLPF 67 (204)
T ss_pred CCCcEEEEecCCCHHHHHHHHhCCC
Confidence 4578999999999999999887664
No 58
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=94.46 E-value=0.084 Score=32.20 Aligned_cols=43 Identities=19% Similarity=0.301 Sum_probs=37.3
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
|++.|.+. ++.+..+|++.+++ ++. .+.+.|..|...|++.+.
T Consensus 5 il~~l~~~---~~~s~~~l~~~l~~-s~~----tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 5 ILELLAQQ---GKVSVEELAELLGV-SEM----TIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HHHHHHHc---CCcCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEe
Confidence 55666665 47999999999999 887 999999999999999986
No 59
>PRK06202 hypothetical protein; Provisional
Probab=94.43 E-value=0.084 Score=43.27 Aligned_cols=23 Identities=26% Similarity=0.185 Sum_probs=19.3
Q ss_pred CCCCeEEEecCCccHHHHHHHhh
Q 036971 195 QNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
.+..+|+|||||.|.++..+++.
T Consensus 59 ~~~~~iLDlGcG~G~~~~~L~~~ 81 (232)
T PRK06202 59 DRPLTLLDIGCGGGDLAIDLARW 81 (232)
T ss_pred CCCcEEEEeccCCCHHHHHHHHH
Confidence 45679999999999998888753
No 60
>PHA00738 putative HTH transcription regulator
Probab=94.41 E-value=0.079 Score=38.27 Aligned_cols=48 Identities=21% Similarity=0.187 Sum_probs=42.3
Q ss_pred HHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 38 VVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 38 av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
-.++.|++.|... +++++.+|++.+++ ... .+.+-|+.|...||+...
T Consensus 12 ptRr~IL~lL~~~---e~~~V~eLae~l~l-SQp----tVS~HLKvLreAGLV~sr 59 (108)
T PHA00738 12 ILRRKILELIAEN---YILSASLISHTLLL-SYT----TVLRHLKILNEQGYIELY 59 (108)
T ss_pred HHHHHHHHHHHHc---CCccHHHHHHhhCC-CHH----HHHHHHHHHHHCCceEEE
Confidence 3577889999884 37999999999999 666 999999999999999987
No 61
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=94.38 E-value=0.12 Score=40.98 Aligned_cols=45 Identities=22% Similarity=0.264 Sum_probs=40.1
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..|+++|... |++|.++||..+|+ ... .++++|..|...||+...
T Consensus 25 ~~Vl~~L~~~---g~~tdeeLA~~Lgi-~~~----~VRk~L~~L~e~gLv~~~ 69 (178)
T PRK06266 25 FEVLKALIKK---GEVTDEEIAEQTGI-KLN----TVRKILYKLYDARLADYK 69 (178)
T ss_pred hHHHHHHHHc---CCcCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCeEEe
Confidence 3478888887 48999999999999 887 999999999999999954
No 62
>KOG3115 consensus Methyltransferase-like protein [General function prediction only]
Probab=94.36 E-value=0.018 Score=46.51 Aligned_cols=24 Identities=25% Similarity=0.389 Sum_probs=22.1
Q ss_pred CCeEEEecCCccHHHHHHHhhCCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
...++|||||.|.++.+|.-.||+
T Consensus 61 kvefaDIGCGyGGLlv~Lsp~fPd 84 (249)
T KOG3115|consen 61 KVEFADIGCGYGGLLMKLAPKFPD 84 (249)
T ss_pred cceEEeeccCccchhhhccccCcc
Confidence 367999999999999999999996
No 63
>PRK11036 putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=94.32 E-value=0.076 Score=44.24 Aligned_cols=31 Identities=23% Similarity=0.278 Sum_probs=23.5
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
.+++.++ ....+|+|||||.|.++..+++..
T Consensus 36 ~~l~~l~--~~~~~vLDiGcG~G~~a~~la~~g 66 (255)
T PRK11036 36 RLLAELP--PRPLRVLDAGGGEGQTAIKLAELG 66 (255)
T ss_pred HHHHhcC--CCCCEEEEeCCCchHHHHHHHHcC
Confidence 3444544 345799999999999999998764
No 64
>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=94.31 E-value=0.075 Score=35.06 Aligned_cols=55 Identities=13% Similarity=0.259 Sum_probs=43.4
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPV 107 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~ 107 (221)
++.|+..|.+ ++.+..+||+.+++ ... .+++-++.|...|+.... .+..|.+.+.
T Consensus 2 ~~~il~~L~~----~~~~~~eLa~~l~v-S~~----tv~~~l~~L~~~g~~i~~----~~~g~~l~~~ 56 (69)
T TIGR00122 2 PLRLLALLAD----NPFSGEKLGEALGM-SRT----AVNKHIQTLREWGVDVLT----VGKGYRLPPP 56 (69)
T ss_pred hHHHHHHHHc----CCcCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCeEEe----cCCceEecCc
Confidence 4567788887 58999999999999 777 899999999999997665 3445555443
No 65
>PRK11050 manganese transport regulator MntR; Provisional
Probab=94.31 E-value=0.078 Score=40.88 Aligned_cols=59 Identities=17% Similarity=0.199 Sum_probs=47.1
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccccccc
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
-|..++... ++.+..+||+.+++ ++. .+.+.++.|...|++... ....+.+|+.+..+.
T Consensus 41 ~I~~~l~~~---~~~t~~eLA~~l~i-s~s----tVsr~l~~Le~~GlI~r~----~~~~v~LT~~G~~l~ 99 (152)
T PRK11050 41 LIADLIAEV---GEARQVDIAARLGV-SQP----TVAKMLKRLARDGLVEMR----PYRGVFLTPEGEKLA 99 (152)
T ss_pred HHHHHHHhc---CCCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEe----cCCceEECchHHHHH
Confidence 355577664 58999999999999 887 999999999999999885 345677777666543
No 66
>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=94.28 E-value=0.035 Score=44.03 Aligned_cols=24 Identities=21% Similarity=0.393 Sum_probs=21.3
Q ss_pred CCeEEEecCCccHHHHHHHhhCCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
..+|+|||||+|..+..+++.+|+
T Consensus 43 ~~~vLDiGcGtG~~s~~la~~~~~ 66 (181)
T TIGR00138 43 GKKVIDIGSGAGFPGIPLAIARPE 66 (181)
T ss_pred CCeEEEecCCCCccHHHHHHHCCC
Confidence 579999999999999999888775
No 67
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=94.27 E-value=0.04 Score=35.25 Aligned_cols=49 Identities=18% Similarity=0.230 Sum_probs=39.0
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeec
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSF 94 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~ 94 (221)
+..|+-.|...++ ..+|..+||+.+++ ++. .+.++++.|...|++++..
T Consensus 7 q~~vL~~l~~~~~-~~~t~~~la~~l~~-~~~----~vs~~v~~L~~~Glv~r~~ 55 (62)
T PF12802_consen 7 QFRVLMALARHPG-EELTQSELAERLGI-SKS----TVSRIVKRLEKKGLVERER 55 (62)
T ss_dssp HHHHHHHHHHSTT-SGEEHHHHHHHHTS--HH----HHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHCCC-CCcCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEEeC
Confidence 3445666777641 12899999999999 877 9999999999999999973
No 68
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=94.22 E-value=0.081 Score=44.33 Aligned_cols=67 Identities=16% Similarity=0.223 Sum_probs=58.9
Q ss_pred HHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccccccc
Q 036971 34 VFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYVS 113 (221)
Q Consensus 34 aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~~ 113 (221)
.+...-+.+|+=.|.+ ||.|.+||-..+++ ++. .+..=++-|...|++.++ ++.|++|..+..++.
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-SSS----AILPQIKKLKDKGLVVQE-----GDRYSLSSLGKIIVE 74 (260)
T ss_pred HHccHHHHHHHHHHHh----CCCCHHHHHHHhCC-CcH----HHHHHHHHHhhCCCEEec-----CCEEEecchHHHHHH
Confidence 4455677888889999 69999999999999 887 899999999999999995 999999999988775
Q ss_pred C
Q 036971 114 D 114 (221)
Q Consensus 114 ~ 114 (221)
.
T Consensus 75 k 75 (260)
T COG4742 75 K 75 (260)
T ss_pred H
Confidence 4
No 69
>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=94.18 E-value=0.1 Score=33.18 Aligned_cols=44 Identities=16% Similarity=0.308 Sum_probs=39.6
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.|.+.|.+. +.+|+++||+.+++ .+. -++|=|..|...|++.+.
T Consensus 4 ~Il~~l~~~---~~~s~~ela~~~~V-S~~----TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 4 QILELLKEK---GKVSVKELAEEFGV-SEM----TIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHc---CCEEHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEEE
Confidence 367788887 59999999999999 887 899999999999999997
No 70
>TIGR00452 methyltransferase, putative. Known examples to date are restricted to the proteobacteria.
Probab=94.17 E-value=0.091 Score=45.44 Aligned_cols=33 Identities=15% Similarity=0.093 Sum_probs=24.4
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
++..+. ....++|+|||||.|.++..+++..++
T Consensus 113 ~l~~l~-~~~g~~VLDvGCG~G~~~~~~~~~g~~ 145 (314)
T TIGR00452 113 VLPHLS-PLKGRTILDVGCGSGYHMWRMLGHGAK 145 (314)
T ss_pred HHHhcC-CCCCCEEEEeccCCcHHHHHHHHcCCC
Confidence 444444 233489999999999999998887663
No 71
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=94.13 E-value=0.07 Score=41.20 Aligned_cols=47 Identities=17% Similarity=0.000 Sum_probs=40.7
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPV 107 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~ 107 (221)
.++++++||+..++ ++. .|+++|..|...|+++-.+ |..|.|+++.-
T Consensus 23 ~~~s~~eIA~~~~i-s~~----~L~kIl~~L~~aGlv~S~r--G~~GGy~La~~ 69 (153)
T PRK11920 23 KLSRIPEIARAYGV-SEL----FLFKILQPLVEAGLVETVR--GRNGGVRLGRP 69 (153)
T ss_pred CcCcHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEeec--CCCCCeeecCC
Confidence 47899999999999 888 9999999999999999875 35678887753
No 72
>PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional
Probab=94.13 E-value=0.11 Score=42.08 Aligned_cols=32 Identities=31% Similarity=0.180 Sum_probs=24.4
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
+.+.|..+....+|||||||+|.++..+++..
T Consensus 42 ~~~~~~~~~~~~~VLDlG~GtG~~t~~l~~~~ 73 (209)
T PRK11188 42 IQQSDKLFKPGMTVVDLGAAPGGWSQYAVTQI 73 (209)
T ss_pred HHHHhccCCCCCEEEEEcccCCHHHHHHHHHc
Confidence 34445424556799999999999999988875
No 73
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=93.98 E-value=0.036 Score=35.18 Aligned_cols=47 Identities=15% Similarity=0.271 Sum_probs=39.0
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeec
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSF 94 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~ 94 (221)
++.+...|.+. ++++..+||+.+++ ++. .+.++++.|...|++++..
T Consensus 5 q~~iL~~l~~~---~~~~~~~la~~~~~-~~~----~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 5 QFRILRILYEN---GGITQSELAEKLGI-SRS----TVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHHH---SSEEHHHHHHHHTS--HH----HHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHc---CCCCHHHHHHHHCC-Chh----HHHHHHHHHHHCCCEEecc
Confidence 34455567777 48999999999999 877 9999999999999999863
No 74
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=93.95 E-value=0.16 Score=42.77 Aligned_cols=25 Identities=28% Similarity=0.399 Sum_probs=21.5
Q ss_pred CCCeEEEecCCccHHHHHHHhhCCC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
...+|+|||||.|.++..+++.+|+
T Consensus 85 ~~~~vLDiGcG~G~~~~~l~~~~~~ 109 (272)
T PRK11088 85 KATALLDIGCGEGYYTHALADALPE 109 (272)
T ss_pred CCCeEEEECCcCCHHHHHHHHhccc
Confidence 3468999999999999999988763
No 75
>TIGR00080 pimt protein-L-isoaspartate(D-aspartate) O-methyltransferase. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt.
Probab=93.94 E-value=0.11 Score=42.04 Aligned_cols=33 Identities=12% Similarity=0.202 Sum_probs=26.4
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
.+++.++ .....+|+|||||+|.++..+++..+
T Consensus 68 ~~~~~l~-~~~~~~VLDiG~GsG~~a~~la~~~~ 100 (215)
T TIGR00080 68 MMTELLE-LKPGMKVLEIGTGSGYQAAVLAEIVG 100 (215)
T ss_pred HHHHHhC-CCCcCEEEEECCCccHHHHHHHHHhC
Confidence 4455555 56678999999999999999988764
No 76
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=93.91 E-value=0.13 Score=32.46 Aligned_cols=42 Identities=17% Similarity=0.266 Sum_probs=36.2
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
|+..|.. ++.|..+|++.+++ ++. .+.+.|+.|...|++...
T Consensus 2 il~~l~~----~~~~~~~i~~~l~i-s~~----~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 2 ILKLLAE----GELCVCELAEILGL-SQS----TVSHHLKKLREAGLVESR 43 (66)
T ss_pred HHHHhhc----CCccHHHHHHHHCC-CHH----HHHHHHHHHHHCCCeeee
Confidence 4555653 58999999999999 887 899999999999999975
No 77
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=93.90 E-value=0.12 Score=40.08 Aligned_cols=51 Identities=12% Similarity=0.126 Sum_probs=45.9
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccccccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYVS 113 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~~ 113 (221)
+++...+||+.+++ .|. .+...++-|...|+++.. ..+.+.+|+.+..+..
T Consensus 23 ~~~~~~diA~~L~V-sp~----sVt~ml~rL~~~GlV~~~----~y~gi~LT~~G~~~a~ 73 (154)
T COG1321 23 GFARTKDIAERLKV-SPP----SVTEMLKRLERLGLVEYE----PYGGVTLTEKGREKAK 73 (154)
T ss_pred CcccHHHHHHHhCC-CcH----HHHHHHHHHHHCCCeEEe----cCCCeEEChhhHHHHH
Confidence 69999999999999 887 899999999999999998 6889999998875553
No 78
>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional
Probab=93.84 E-value=0.093 Score=44.11 Aligned_cols=33 Identities=24% Similarity=0.405 Sum_probs=27.0
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
..+++.++ .....+|||||||.|..+..+++.+
T Consensus 42 ~~~l~~l~-l~~~~~VLDiGcG~G~~a~~la~~~ 74 (263)
T PTZ00098 42 TKILSDIE-LNENSKVLDIGSGLGGGCKYINEKY 74 (263)
T ss_pred HHHHHhCC-CCCCCEEEEEcCCCChhhHHHHhhc
Confidence 45677777 7777899999999999998887654
No 79
>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=93.82 E-value=0.097 Score=44.89 Aligned_cols=60 Identities=10% Similarity=0.060 Sum_probs=36.1
Q ss_pred CCchhhhhccCchHHHHHHHHHhhhhHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 155 GMDFYDYLGTDSRFNEVFNNGMIGQTSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 155 g~~~~~~l~~~p~~~~~F~~aM~~~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
|..+|+-+...|++-. +..-+.- -...++.+++..+ ...+|||+|||+|.....|+++.|
T Consensus 27 G~~lf~~i~~~peYy~-tr~E~~i-l~~~~~~ia~~~~---~~~~iLELGcGtG~~t~~Ll~~l~ 86 (301)
T TIGR03438 27 GSELFEQICELPEYYP-TRTEAAI-LERHADEIAAATG---AGCELVELGSGSSRKTRLLLDALR 86 (301)
T ss_pred HHHHHHHHHCCCcccc-HHHHHHH-HHHHHHHHHHhhC---CCCeEEecCCCcchhHHHHHHhhc
Confidence 4566666666665542 1111111 1122334454443 346899999999999999998865
No 80
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=93.80 E-value=0.12 Score=41.78 Aligned_cols=58 Identities=22% Similarity=0.265 Sum_probs=46.2
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPV 107 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~ 107 (221)
+..|...|.+. ++++..+||+.+++ ++. .+.+.|..|...|++.+... ....|.+|+.
T Consensus 145 ~~~IL~~l~~~---g~~s~~eia~~l~i-s~s----tv~r~L~~Le~~GlI~r~~~--r~~~~~lT~~ 202 (203)
T TIGR01884 145 ELKVLEVLKAE---GEKSVKNIAKKLGK-SLS----TISRHLRELEKKGLVEQKGR--KGKRYSLTKL 202 (203)
T ss_pred HHHHHHHHHHc---CCcCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEEEcC--CccEEEeCCC
Confidence 44567777775 47999999999999 877 89999999999999999721 2456777764
No 81
>COG2264 PrmA Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]
Probab=93.78 E-value=0.056 Score=46.30 Aligned_cols=43 Identities=26% Similarity=0.302 Sum_probs=29.5
Q ss_pred HHHHHHhhhhHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHHh
Q 036971 171 VFNNGMIGQTSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHNF 216 (221)
Q Consensus 171 ~F~~aM~~~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~ 216 (221)
.|-..--..+++.. .+++.+. . +.++++|||||+|.++++.++
T Consensus 140 AFGTG~HpTT~lcL-~~Le~~~-~-~g~~vlDvGcGSGILaIAa~k 182 (300)
T COG2264 140 AFGTGTHPTTSLCL-EALEKLL-K-KGKTVLDVGCGSGILAIAAAK 182 (300)
T ss_pred ccCCCCChhHHHHH-HHHHHhh-c-CCCEEEEecCChhHHHHHHHH
Confidence 35444334445554 3566665 3 568999999999999988765
No 82
>PLN02336 phosphoethanolamine N-methyltransferase
Probab=93.62 E-value=0.083 Score=48.08 Aligned_cols=35 Identities=11% Similarity=0.135 Sum_probs=27.2
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 184 INKIVESYKGFQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 184 ~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
.+.+++.++ .....+|||||||.|.++..+++.+.
T Consensus 26 ~~~il~~l~-~~~~~~vLDlGcG~G~~~~~la~~~~ 60 (475)
T PLN02336 26 RPEILSLLP-PYEGKSVLELGAGIGRFTGELAKKAG 60 (475)
T ss_pred hhHHHhhcC-ccCCCEEEEeCCCcCHHHHHHHhhCC
Confidence 345666666 44567999999999999999988754
No 83
>COG4976 Predicted methyltransferase (contains TPR repeat) [General function prediction only]
Probab=93.60 E-value=0.078 Score=43.70 Aligned_cols=47 Identities=17% Similarity=0.443 Sum_probs=31.0
Q ss_pred HHHHHHHHHhhhhHHH----HHHHHHhcCCCCCCCeEEEecCCccHHHHHHH
Q 036971 168 FNEVFNNGMIGQTSFV----INKIVESYKGFQNITRLVDVGGGLGITLSDHN 215 (221)
Q Consensus 168 ~~~~F~~aM~~~~~~~----~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~ 215 (221)
+.++|.+.....-... ...++...+ ...+++++|+|||+|..+.+|.
T Consensus 94 ~Ae~Fd~~LVdkL~Y~vP~~l~emI~~~~-~g~F~~~lDLGCGTGL~G~~lR 144 (287)
T COG4976 94 YAERFDHILVDKLGYSVPELLAEMIGKAD-LGPFRRMLDLGCGTGLTGEALR 144 (287)
T ss_pred HHHHHHHHHHHHhcCccHHHHHHHHHhcc-CCccceeeecccCcCcccHhHH
Confidence 4566777665432222 233444555 5558999999999999987764
No 84
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=93.56 E-value=0.1 Score=37.43 Aligned_cols=47 Identities=17% Similarity=0.289 Sum_probs=41.5
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.+..|...|... +++|..+||+.+|+ ++. .+.+.++.|...|++...
T Consensus 4 ~D~~il~~L~~~---~~~~~~~la~~l~~-s~~----tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKD---ARISLAELAKKVGL-SPS----TVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHh---CCCCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCeece
Confidence 467788899887 48999999999999 887 999999999999999853
No 85
>COG0220 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]
Probab=93.55 E-value=0.11 Score=42.87 Aligned_cols=24 Identities=21% Similarity=0.346 Sum_probs=22.5
Q ss_pred CeEEEecCCccHHHHHHHhhCCCC
Q 036971 198 TRLVDVGGGLGITLSDHNFQIPSY 221 (221)
Q Consensus 198 ~~vvDVGGG~G~~~~~l~~~~P~l 221 (221)
..+|+||||.|.++.++++++|+.
T Consensus 50 pi~lEIGfG~G~~l~~~A~~nP~~ 73 (227)
T COG0220 50 PIVLEIGFGMGEFLVEMAKKNPEK 73 (227)
T ss_pred cEEEEECCCCCHHHHHHHHHCCCC
Confidence 589999999999999999999974
No 86
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=93.51 E-value=0.15 Score=33.10 Aligned_cols=57 Identities=21% Similarity=0.268 Sum_probs=42.5
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
+..|...+... +.+..+|++.+++ +.. .+.+.|+.|...|++...... ....|+.++
T Consensus 9 ~~~il~~l~~~----~~~~~ei~~~~~i-~~~----~i~~~l~~L~~~g~i~~~~~~-~~~~~~~~~ 65 (78)
T cd00090 9 RLRILRLLLEG----PLTVSELAERLGL-SQS----TVSRHLKKLEEAGLVESRREG-RRVYYSLTD 65 (78)
T ss_pred HHHHHHHHHHC----CcCHHHHHHHHCc-CHh----HHHHHHHHHHHCCCeEEEEec-cEEEEEeCC
Confidence 34466667763 5999999999999 877 899999999999999986210 124455554
No 87
>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=93.46 E-value=0.097 Score=44.87 Aligned_cols=33 Identities=12% Similarity=0.125 Sum_probs=25.1
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
+...++.+.+ ++|+|||||.|-++.+++++-|.
T Consensus 107 l~p~l~~L~g-k~VLDIGC~nGY~~frM~~~GA~ 139 (315)
T PF08003_consen 107 LLPHLPDLKG-KRVLDIGCNNGYYSFRMLGRGAK 139 (315)
T ss_pred HHhhhCCcCC-CEEEEecCCCcHHHHHHhhcCCC
Confidence 3344432544 89999999999999999887764
No 88
>PLN02244 tocopherol O-methyltransferase
Probab=93.39 E-value=0.14 Score=44.68 Aligned_cols=24 Identities=29% Similarity=0.365 Sum_probs=21.0
Q ss_pred CCCCeEEEecCCccHHHHHHHhhC
Q 036971 195 QNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
....+|||||||.|..+..+++.+
T Consensus 117 ~~~~~VLDiGCG~G~~~~~La~~~ 140 (340)
T PLN02244 117 KRPKRIVDVGCGIGGSSRYLARKY 140 (340)
T ss_pred CCCCeEEEecCCCCHHHHHHHHhc
Confidence 456799999999999999998875
No 89
>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=93.38 E-value=0.24 Score=35.91 Aligned_cols=36 Identities=25% Similarity=0.367 Sum_probs=24.6
Q ss_pred hhHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHH
Q 036971 179 QTSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHN 215 (221)
Q Consensus 179 ~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~ 215 (221)
.+...+..|-+.+. -.....+||||||.|.+..-|.
T Consensus 42 IAAyLi~LW~~~~~-~~~~~~FVDlGCGNGLLV~IL~ 77 (112)
T PF07757_consen 42 IAAYLIELWRDMYG-EQKFQGFVDLGCGNGLLVYILN 77 (112)
T ss_pred HHHHHHHHHhcccC-CCCCCceEEccCCchHHHHHHH
Confidence 33444555666665 3456789999999999875554
No 90
>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=93.34 E-value=0.18 Score=36.54 Aligned_cols=64 Identities=23% Similarity=0.309 Sum_probs=43.6
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLA 105 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt 105 (221)
+.-|++.|...+ ++.|++||.+.+.-..+..+..-+.|.|+.|+..|++.+....+....|..+
T Consensus 3 R~~Il~~l~~~~--~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~~ 66 (116)
T cd07153 3 RLAILEVLLESD--GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELN 66 (116)
T ss_pred HHHHHHHHHhCC--CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEeC
Confidence 455788888764 6899999999984211111223789999999999999987422112346543
No 91
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=93.26 E-value=0.17 Score=37.47 Aligned_cols=50 Identities=10% Similarity=0.231 Sum_probs=44.1
Q ss_pred HHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 36 QAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 36 ~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+..+...|.+.+.++ |.+|..|++..+|+ +-. .+.++++.|++.|-|...
T Consensus 10 r~eLk~rIvElVRe~---GRiTi~ql~~~TGa-sR~----Tvk~~lreLVa~G~l~~~ 59 (127)
T PF06163_consen 10 REELKARIVELVREH---GRITIKQLVAKTGA-SRN----TVKRYLRELVARGDLYRH 59 (127)
T ss_pred HHHHHHHHHHHHHHc---CCccHHHHHHHHCC-CHH----HHHHHHHHHHHcCCeEeC
Confidence 345667788899998 59999999999999 887 899999999999999985
No 92
>PRK00216 ubiE ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed
Probab=93.25 E-value=0.16 Score=41.20 Aligned_cols=33 Identities=12% Similarity=0.096 Sum_probs=25.9
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
.+++.+. .....+|+|||||.|.++..+++.+|
T Consensus 42 ~~~~~~~-~~~~~~vldiG~G~G~~~~~l~~~~~ 74 (239)
T PRK00216 42 KTIKWLG-VRPGDKVLDLACGTGDLAIALAKAVG 74 (239)
T ss_pred HHHHHhC-CCCCCeEEEeCCCCCHHHHHHHHHcC
Confidence 3444555 44457999999999999999998886
No 93
>PRK11705 cyclopropane fatty acyl phospholipid synthase; Provisional
Probab=93.22 E-value=0.18 Score=44.87 Aligned_cols=33 Identities=18% Similarity=0.227 Sum_probs=26.8
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
..+++.++ .....+|||||||.|.++..+++.+
T Consensus 157 ~~l~~~l~-l~~g~rVLDIGcG~G~~a~~la~~~ 189 (383)
T PRK11705 157 DLICRKLQ-LKPGMRVLDIGCGWGGLARYAAEHY 189 (383)
T ss_pred HHHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHC
Confidence 34566666 6667899999999999999988765
No 94
>PRK13944 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=93.22 E-value=0.18 Score=40.63 Aligned_cols=33 Identities=18% Similarity=0.193 Sum_probs=24.9
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
.+++.++ .....+|+|||||+|..+..+++..+
T Consensus 63 ~~~~~l~-~~~~~~VLDiG~GsG~~~~~la~~~~ 95 (205)
T PRK13944 63 MMCELIE-PRPGMKILEVGTGSGYQAAVCAEAIE 95 (205)
T ss_pred HHHHhcC-CCCCCEEEEECcCccHHHHHHHHhcC
Confidence 3455555 45567999999999999988887653
No 95
>TIGR01934 MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis methyltransferases. Note that a number of non-orthologous genes which are members of pfam03737 have been erroneously annotated as MenG methyltransferases.
Probab=93.22 E-value=0.18 Score=40.48 Aligned_cols=33 Identities=18% Similarity=0.155 Sum_probs=26.3
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
+++... .....+|+|||||.|.++..+++.+|+
T Consensus 31 ~~~~~~-~~~~~~vldiG~G~G~~~~~~~~~~~~ 63 (223)
T TIGR01934 31 AVKLIG-VFKGQKVLDVACGTGDLAIELAKSAPD 63 (223)
T ss_pred HHHHhc-cCCCCeEEEeCCCCChhHHHHHHhcCC
Confidence 444444 445689999999999999999998874
No 96
>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=93.11 E-value=0.096 Score=43.13 Aligned_cols=23 Identities=17% Similarity=0.170 Sum_probs=20.3
Q ss_pred CCCeEEEecCCccHHHHHHHhhC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
...+|||||||.|..+..+++.+
T Consensus 53 ~~~~iLDlGcG~G~~~~~l~~~~ 75 (239)
T TIGR00740 53 PDSNVYDLGCSRGAATLSARRNI 75 (239)
T ss_pred CCCEEEEecCCCCHHHHHHHHhc
Confidence 45789999999999999999874
No 97
>PHA02943 hypothetical protein; Provisional
Probab=93.10 E-value=0.43 Score=36.66 Aligned_cols=105 Identities=11% Similarity=0.166 Sum_probs=68.7
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccccccccCCCCCChH
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYVSDQNGVSMR 121 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~~~~~~~~~~ 121 (221)
.|.+.|.. |+.|..|||+++|+ +-. .++-.|..|...|.+.++ .- ...+-+.+.+. -..
T Consensus 15 eILE~Lk~----G~~TtseIAkaLGl-S~~----qa~~~LyvLErEG~VkrV----~~-----G~~tyw~l~~d---ay~ 73 (165)
T PHA02943 15 KTLRLLAD----GCKTTSRIANKLGV-SHS----MARNALYQLAKEGMVLKV----EI-----GRAAIWCLDED---AYT 73 (165)
T ss_pred HHHHHHhc----CCccHHHHHHHHCC-CHH----HHHHHHHHHHHcCceEEE----ee-----cceEEEEEChH---HHH
Confidence 46677733 68999999999999 776 899999999999999997 22 22333444332 122
Q ss_pred HHHHHhcCccchhhhhhhHHHHhcCCchhHhhhCCchhhhhccCchHHHHHHHHHh
Q 036971 122 PYMNLSLDKVMMPGWFQLKDQILEGELSYNKALGMDFYDYLGTDSRFNEVFNNGMI 177 (221)
Q Consensus 122 ~~~~~~~~~~~~~~~~~L~~~l~~g~~~f~~~~g~~~~~~l~~~p~~~~~F~~aM~ 177 (221)
+.+. ++ +..|-..+++.+-.|- .-..++.-++++++..+.|.+...
T Consensus 74 ~~v~----~~----~Relwrlv~s~~~kfi--~p~~l~~li~kd~~a~~~~ak~v~ 119 (165)
T PHA02943 74 NLVF----EI----KRELWRLVCNSRLKFI--TPSRLLRLIAKDTEAHNIFAKYVP 119 (165)
T ss_pred HHHH----HH----HHHHHHHHHhcccccc--ChHHHHHHHHhCHHHHHHHHHhcC
Confidence 2221 11 2333456666543332 224677888889888888887664
No 98
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=93.02 E-value=0.18 Score=34.32 Aligned_cols=43 Identities=21% Similarity=0.284 Sum_probs=39.3
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
|=|+|+.+ |.+++.+||..+++ ++. .++.+|..++.+|-+++.
T Consensus 7 lRd~l~~~---gr~s~~~Ls~~~~~-p~~----~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 7 VRDLLALR---GRMEAAQISQTLNT-PQP----MINAMLQQLESMGKAVRI 49 (78)
T ss_pred HHHHHHHc---CcccHHHHHHHHCc-CHH----HHHHHHHHHHHCCCeEee
Confidence 45788888 59999999999999 887 999999999999999987
No 99
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=93.01 E-value=0.2 Score=37.51 Aligned_cols=53 Identities=21% Similarity=0.335 Sum_probs=45.3
Q ss_pred HHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 33 AVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 33 ~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..+.+=-.+.|.+.|+.. +|.|+.|+|+.+|- ++. .+.|-|+-|...|++...
T Consensus 59 a~vLsp~nleLl~~Ia~~---~P~Si~ElAe~vgR-dv~----nvhr~Ls~l~~~GlI~fe 111 (144)
T COG4190 59 ARVLSPRNLELLELIAQE---EPASINELAELVGR-DVK----NVHRTLSTLADLGLIFFE 111 (144)
T ss_pred HHHhChhHHHHHHHHHhc---CcccHHHHHHHhCc-chH----HHHHHHHHHHhcCeEEEe
Confidence 334444557788899987 59999999999999 887 999999999999999987
No 100
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=92.98 E-value=0.1 Score=43.31 Aligned_cols=25 Identities=20% Similarity=0.163 Sum_probs=20.8
Q ss_pred CCCeEEEecCCccHHHHHHHhh--CCC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQ--IPS 220 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~--~P~ 220 (221)
...+|+|||||+|..+..+++. +|+
T Consensus 56 ~~~~vLDlGcGtG~~~~~l~~~~~~~~ 82 (247)
T PRK15451 56 PGTQVYDLGCSLGAATLSVRRNIHHDN 82 (247)
T ss_pred CCCEEEEEcccCCHHHHHHHHhcCCCC
Confidence 4578999999999999998884 454
No 101
>KOG2899 consensus Predicted methyltransferase [General function prediction only]
Probab=92.97 E-value=0.089 Score=43.69 Aligned_cols=34 Identities=9% Similarity=0.130 Sum_probs=27.5
Q ss_pred HHHHHhcCC-CCCCCeEEEecCCccHHHHHHHhhC
Q 036971 185 NKIVESYKG-FQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 185 ~~~l~~~~~-~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
+.+++.++. |-..+.++||||+.|.+...+++.|
T Consensus 46 D~rLk~L~~~~f~~~~~LDIGCNsG~lt~~iak~F 80 (288)
T KOG2899|consen 46 DPRLKVLEKDWFEPKQALDIGCNSGFLTLSIAKDF 80 (288)
T ss_pred ChhhhhccccccCcceeEeccCCcchhHHHHHHhh
Confidence 445666553 6667899999999999999999877
No 102
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=92.96 E-value=0.07 Score=37.25 Aligned_cols=61 Identities=18% Similarity=0.203 Sum_probs=45.5
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhC-CCCCCcchhhhHHHHHHHHhcCCceeeeccCCCC--cceeccccccccc
Q 036971 43 VLDIINKAGPGAELSASEIASQI-PTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGV--RLYSLAPVAKYYV 112 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~-g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~--~~y~lt~~s~~L~ 112 (221)
|...|.. |+....||.+.+ ++ ++. .|.+-|+.|...|++.+....+.+ -.|++|+.+..|.
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-SPK----VLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL 73 (90)
T ss_dssp HHHHHTT----SSEEHHHHHHHSTTS--HH----HHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred HHHHHHh----CCCcHHHHHHhcchh-HHH----HHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence 3445555 599999999999 88 777 899999999999999986321111 2599999888776
No 103
>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=92.88 E-value=0.11 Score=32.68 Aligned_cols=43 Identities=14% Similarity=0.244 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHH
Q 036971 30 VLPAVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGL 83 (221)
Q Consensus 30 ~~~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~ 83 (221)
.+-.+|.+|+++|-||.=. .+|+.|||+.+|+ .+. .+...||-
T Consensus 4 ~Q~e~L~~A~~~GYfd~PR------~~tl~elA~~lgi-s~s----t~~~~LRr 46 (53)
T PF04967_consen 4 RQREILKAAYELGYFDVPR------RITLEELAEELGI-SKS----TVSEHLRR 46 (53)
T ss_pred HHHHHHHHHHHcCCCCCCC------cCCHHHHHHHhCC-CHH----HHHHHHHH
Confidence 3456899999999998633 5999999999999 665 55555543
No 104
>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=92.84 E-value=0.13 Score=33.74 Aligned_cols=42 Identities=21% Similarity=0.209 Sum_probs=33.1
Q ss_pred HHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 46 IINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 46 ~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.+.+.| -|-|+.|||+.+|++.+. .+.+.|+.|...|++...
T Consensus 18 ~~~~~G--~~Pt~rEIa~~~g~~S~~----tv~~~L~~Le~kG~I~r~ 59 (65)
T PF01726_consen 18 YIEENG--YPPTVREIAEALGLKSTS----TVQRHLKALERKGYIRRD 59 (65)
T ss_dssp HHHHHS--S---HHHHHHHHTSSSHH----HHHHHHHHHHHTTSEEEG
T ss_pred HHHHcC--CCCCHHHHHHHhCCCChH----HHHHHHHHHHHCcCccCC
Confidence 566666 578999999999993255 899999999999999986
No 105
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=92.77 E-value=0.12 Score=36.05 Aligned_cols=46 Identities=20% Similarity=0.228 Sum_probs=39.1
Q ss_pred HHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccccccc
Q 036971 58 ASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 58 ~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
+.+||+.+++ ++. .+.+.++.|...|++... .+..|.+|+.+..+.
T Consensus 2 ~~ela~~l~i-s~s----tvs~~l~~L~~~glI~r~----~~~~~~lT~~g~~~~ 47 (96)
T smart00529 2 TSEIAERLNV-SPP----TVTQMLKKLEKDGLVEYE----PYRGITLTEKGRRLA 47 (96)
T ss_pred HHHHHHHhCC-ChH----HHHHHHHHHHHCCCEEEc----CCCceEechhHHHHH
Confidence 5689999999 887 999999999999999997 345788888776554
No 106
>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=92.67 E-value=0.21 Score=41.07 Aligned_cols=24 Identities=25% Similarity=0.340 Sum_probs=21.8
Q ss_pred CCeEEEecCCccHHHHHHHhhCCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
..+|+|+|||.|.++..+++.+|+
T Consensus 88 ~~~ilDig~G~G~~~~~l~~~~~~ 111 (251)
T TIGR03534 88 PLRVLDLGTGSGAIALALAKERPD 111 (251)
T ss_pred CCeEEEEeCcHhHHHHHHHHHCCC
Confidence 468999999999999999998875
No 107
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=92.65 E-value=0.19 Score=43.08 Aligned_cols=34 Identities=21% Similarity=0.255 Sum_probs=26.6
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
..+++..+ .....+|+|||||.|.+...+++...
T Consensus 26 ~~Iv~~~~-~~~~~~VLEIG~G~G~LT~~Ll~~~~ 59 (294)
T PTZ00338 26 DKIVEKAA-IKPTDTVLEIGPGTGNLTEKLLQLAK 59 (294)
T ss_pred HHHHHhcC-CCCcCEEEEecCchHHHHHHHHHhCC
Confidence 34566565 55667999999999999999987654
No 108
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=92.51 E-value=0.22 Score=37.73 Aligned_cols=46 Identities=11% Similarity=0.023 Sum_probs=39.1
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
...+.++||+..|+ ++. .++++|+.|...|+++-.+. .+|.|.+..
T Consensus 24 ~~~s~~~ia~~~~i-s~~----~vrk~l~~L~~~Glv~s~~G--~~GG~~l~~ 69 (141)
T PRK11014 24 RMTSISEVTEVYGV-SRN----HMVKIINQLSRAGYVTAVRG--KNGGIRLGK 69 (141)
T ss_pred CccCHHHHHHHHCc-CHH----HHHHHHHHHHhCCEEEEecC--CCCCeeecC
Confidence 57899999999999 888 99999999999999998742 356777764
No 109
>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=92.47 E-value=0.25 Score=41.24 Aligned_cols=24 Identities=17% Similarity=0.118 Sum_probs=21.4
Q ss_pred CCeEEEecCCccHHHHHHHhhCCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
..+++|+|||+|.++..+++.+|.
T Consensus 87 ~~~vLDlg~GsG~i~l~la~~~~~ 110 (251)
T TIGR03704 87 TLVVVDLCCGSGAVGAALAAALDG 110 (251)
T ss_pred CCEEEEecCchHHHHHHHHHhCCC
Confidence 458999999999999999988874
No 110
>PRK09328 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=92.41 E-value=0.23 Score=41.48 Aligned_cols=27 Identities=22% Similarity=0.357 Sum_probs=23.0
Q ss_pred CCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
.....+|+|||||+|..+..+++.+|+
T Consensus 106 ~~~~~~vLDiG~GsG~~~~~la~~~~~ 132 (275)
T PRK09328 106 LKEPLRVLDLGTGSGAIALALAKERPD 132 (275)
T ss_pred ccCCCEEEEEcCcHHHHHHHHHHHCCC
Confidence 344578999999999999999998874
No 111
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=92.36 E-value=0.27 Score=30.73 Aligned_cols=35 Identities=20% Similarity=0.227 Sum_probs=31.6
Q ss_pred CCC-CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AEL-SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~-t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..+ |..+||+.+++ +.. .+++.|..|...|++...
T Consensus 18 ~~l~s~~~la~~~~v-s~~----tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 18 DKLPSERELAAQLGV-SRT----TVREALSRLEAEGLVQRR 53 (60)
T ss_pred CcCcCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEe
Confidence 356 89999999999 877 999999999999999876
No 112
>COG2226 UbiE Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]
Probab=92.36 E-value=0.29 Score=40.60 Aligned_cols=24 Identities=17% Similarity=0.057 Sum_probs=21.8
Q ss_pred CCCeEEEecCCccHHHHHHHhhCC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
...+|+|||||+|-++..+++..+
T Consensus 51 ~g~~vLDva~GTGd~a~~~~k~~g 74 (238)
T COG2226 51 PGDKVLDVACGTGDMALLLAKSVG 74 (238)
T ss_pred CCCEEEEecCCccHHHHHHHHhcC
Confidence 468999999999999999999875
No 113
>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=92.32 E-value=0.23 Score=45.06 Aligned_cols=57 Identities=14% Similarity=0.113 Sum_probs=35.5
Q ss_pred chhhhhccCchHHHHHHHHHhhhhHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhh
Q 036971 157 DFYDYLGTDSRFNEVFNNGMIGQTSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 157 ~~~~~l~~~p~~~~~F~~aM~~~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
..|+.+++||.+-+.|.+|+.. ......+.-..-...+.|+|||+|+|.++...+++
T Consensus 151 ~tYe~fE~D~vKY~~Ye~AI~~----al~D~~~~~~~~~~~~vVldVGAGrGpL~~~al~A 207 (448)
T PF05185_consen 151 QTYEVFEKDPVKYDQYERAIEE----ALKDRVRKNSYSSKDKVVLDVGAGRGPLSMFALQA 207 (448)
T ss_dssp HHHHHHCC-HHHHHHHHHHHHH----HHHHHHTTS-SEETT-EEEEES-TTSHHHHHHHHT
T ss_pred ccHhhHhcCHHHHHHHHHHHHH----HHHhhhhhccccccceEEEEeCCCccHHHHHHHHH
Confidence 4688899999999999998742 11122222210012578999999999998776654
No 114
>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=92.32 E-value=0.16 Score=43.49 Aligned_cols=42 Identities=29% Similarity=0.406 Sum_probs=26.3
Q ss_pred HHHHHhhhhHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHHh
Q 036971 172 FNNGMIGQTSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHNF 216 (221)
Q Consensus 172 F~~aM~~~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~ 216 (221)
|-..--..+++... +++.+. .+ ..+|+|||||+|.++++-++
T Consensus 140 FGTG~H~TT~lcl~-~l~~~~-~~-g~~vLDvG~GSGILaiaA~k 181 (295)
T PF06325_consen 140 FGTGHHPTTRLCLE-LLEKYV-KP-GKRVLDVGCGSGILAIAAAK 181 (295)
T ss_dssp S-SSHCHHHHHHHH-HHHHHS-ST-TSEEEEES-TTSHHHHHHHH
T ss_pred ccCCCCHHHHHHHH-HHHHhc-cC-CCEEEEeCCcHHHHHHHHHH
Confidence 44443344555554 455554 43 47999999999999987665
No 115
>COG2890 HemK Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]
Probab=92.31 E-value=0.2 Score=42.66 Aligned_cols=22 Identities=27% Similarity=0.418 Sum_probs=21.1
Q ss_pred eEEEecCCccHHHHHHHhhCCC
Q 036971 199 RLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 199 ~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
+|+|||+|+|..+..++.++|+
T Consensus 113 ~ilDlGTGSG~iai~la~~~~~ 134 (280)
T COG2890 113 RILDLGTGSGAIAIALAKEGPD 134 (280)
T ss_pred cEEEecCChHHHHHHHHhhCcC
Confidence 8999999999999999999995
No 116
>PF13679 Methyltransf_32: Methyltransferase domain
Probab=92.26 E-value=0.1 Score=39.51 Aligned_cols=24 Identities=21% Similarity=0.257 Sum_probs=20.8
Q ss_pred CCCCCeEEEecCCccHHHHHHHhh
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
-.+..+|||+|+|.|.++..++..
T Consensus 23 ~~~~~~vvD~GsG~GyLs~~La~~ 46 (141)
T PF13679_consen 23 SKRCITVVDLGSGKGYLSRALAHL 46 (141)
T ss_pred cCCCCEEEEeCCChhHHHHHHHHH
Confidence 345789999999999999999883
No 117
>PRK04266 fibrillarin; Provisional
Probab=92.22 E-value=0.18 Score=41.57 Aligned_cols=29 Identities=14% Similarity=0.283 Sum_probs=24.4
Q ss_pred hcCCCCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 190 SYKGFQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 190 ~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
.++ .....+|+|+|||+|.++..+++..|
T Consensus 67 ~l~-i~~g~~VlD~G~G~G~~~~~la~~v~ 95 (226)
T PRK04266 67 NFP-IKKGSKVLYLGAASGTTVSHVSDIVE 95 (226)
T ss_pred hCC-CCCCCEEEEEccCCCHHHHHHHHhcC
Confidence 355 66678999999999999999988765
No 118
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=92.18 E-value=0.22 Score=38.70 Aligned_cols=45 Identities=16% Similarity=0.075 Sum_probs=39.0
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..|+++|... +.+|-+|||+.+|+ +.+ -++++|..|...||+...
T Consensus 17 v~Vl~aL~~~---~~~tdEeLa~~Lgi-~~~----~VRk~L~~L~e~~Lv~~~ 61 (158)
T TIGR00373 17 GLVLFSLGIK---GEFTDEEISLELGI-KLN----EVRKALYALYDAGLADYK 61 (158)
T ss_pred HHHHHHHhcc---CCCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCceee
Confidence 3467788765 58999999999999 888 999999999999999754
No 119
>PLN02233 ubiquinone biosynthesis methyltransferase
Probab=92.16 E-value=0.4 Score=40.22 Aligned_cols=25 Identities=16% Similarity=0.016 Sum_probs=21.2
Q ss_pred CCCCCeEEEecCCccHHHHHHHhhC
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
.....+|+|||||+|.++..+++.+
T Consensus 71 ~~~~~~VLDlGcGtG~~~~~la~~~ 95 (261)
T PLN02233 71 AKMGDRVLDLCCGSGDLAFLLSEKV 95 (261)
T ss_pred CCCCCEEEEECCcCCHHHHHHHHHh
Confidence 4456799999999999999888875
No 120
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=92.10 E-value=0.27 Score=38.67 Aligned_cols=65 Identities=12% Similarity=0.083 Sum_probs=51.4
Q ss_pred hhhHHHHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhC--CCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceec
Q 036971 27 SAIVLPAVFQAVVNLDVLDIINKAGPGAELSASEIASQI--PTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSL 104 (221)
Q Consensus 27 ~g~~~~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~--g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~l 104 (221)
+..|...+++..+.+. . +.-++.+||+++ ++ ... -++.-|+.|..+|+++++ ++|.|..
T Consensus 21 ~~~W~~~~ir~l~~l~------~----~~~d~~~iak~l~p~i-s~~----ev~~sL~~L~~~gli~k~----~~g~y~~ 81 (171)
T PF14394_consen 21 YSSWYHPAIRELLPLM------P----FAPDPEWIAKRLRPKI-SAE----EVRDSLEFLEKLGLIKKD----GDGKYVQ 81 (171)
T ss_pred HhhhHHHHHHHHhhcC------C----CCCCHHHHHHHhcCCC-CHH----HHHHHHHHHHHCCCeEEC----CCCcEEE
Confidence 3567777777755532 1 244999999999 88 776 899999999999999998 6789999
Q ss_pred cccccc
Q 036971 105 APVAKY 110 (221)
Q Consensus 105 t~~s~~ 110 (221)
|..+-.
T Consensus 82 t~~~l~ 87 (171)
T PF14394_consen 82 TDKSLT 87 (171)
T ss_pred ecceee
Confidence 986655
No 121
>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=92.09 E-value=0.32 Score=31.00 Aligned_cols=33 Identities=15% Similarity=0.123 Sum_probs=29.9
Q ss_pred CCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 56 LSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 56 ~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.+..+||+.+++ +.. .+++.|..|...|++...
T Consensus 26 ~~~~~la~~~~i-s~~----~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 26 PSERELAEELGV-SRT----TVREALRELEAEGLVERR 58 (66)
T ss_pred CCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEec
Confidence 459999999999 877 999999999999999875
No 122
>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=92.08 E-value=0.22 Score=33.57 Aligned_cols=49 Identities=12% Similarity=0.188 Sum_probs=43.3
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.+..+++.|+.+.. .+++..+|++.++. |++ .+...++.|...|++.+.
T Consensus 3 ~~~~~Le~I~rsR~-~Gi~q~~L~~~~~~-D~r----~i~~~~k~L~~~gLI~k~ 51 (75)
T PF04182_consen 3 IQYCLLERIARSRY-NGITQSDLSKLLGI-DPR----SIFYRLKKLEKKGLIVKQ 51 (75)
T ss_pred hHHHHHHHHHhcCC-CCEehhHHHHHhCC-Cch----HHHHHHHHHHHCCCEEEE
Confidence 45667888888765 57999999999999 999 999999999999999986
No 123
>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=92.05 E-value=0.15 Score=43.34 Aligned_cols=24 Identities=21% Similarity=0.475 Sum_probs=21.9
Q ss_pred CCeEEEecCCccHHHHHHHhhCCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
..+|+|+|||+|.++..+++.+|+
T Consensus 122 ~~~vLDlG~GsG~i~~~la~~~~~ 145 (284)
T TIGR03533 122 VKRILDLCTGSGCIAIACAYAFPE 145 (284)
T ss_pred CCEEEEEeCchhHHHHHHHHHCCC
Confidence 468999999999999999999885
No 124
>PRK05785 hypothetical protein; Provisional
Probab=91.96 E-value=0.15 Score=41.84 Aligned_cols=22 Identities=18% Similarity=0.203 Sum_probs=19.7
Q ss_pred CCeEEEecCCccHHHHHHHhhC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
..+|+|||||+|.++..+++.+
T Consensus 52 ~~~VLDlGcGtG~~~~~l~~~~ 73 (226)
T PRK05785 52 PKKVLDVAAGKGELSYHFKKVF 73 (226)
T ss_pred CCeEEEEcCCCCHHHHHHHHhc
Confidence 5799999999999999998874
No 125
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=91.95 E-value=0.26 Score=34.70 Aligned_cols=47 Identities=23% Similarity=0.257 Sum_probs=42.0
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.++.|..+|... +|-.+.-||..+++ +.. .+.+.|+-|..+|++++.
T Consensus 8 l~~~IL~hl~~~---~~Dy~k~ia~~l~~-~~~----~v~~~l~~Le~~GLler~ 54 (92)
T PF10007_consen 8 LDLKILQHLKKA---GPDYAKSIARRLKI-PLE----EVREALEKLEEMGLLERV 54 (92)
T ss_pred hHHHHHHHHHHH---CCCcHHHHHHHHCC-CHH----HHHHHHHHHHHCCCeEEe
Confidence 356688889998 48899999999999 887 999999999999999998
No 126
>COG2227 UbiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme metabolism]
Probab=91.77 E-value=0.12 Score=42.70 Aligned_cols=21 Identities=33% Similarity=0.273 Sum_probs=18.7
Q ss_pred CCeEEEecCCccHHHHHHHhh
Q 036971 197 ITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~ 217 (221)
..+|+|||||-|.++..+++.
T Consensus 60 g~~vLDvGCGgG~Lse~mAr~ 80 (243)
T COG2227 60 GLRVLDVGCGGGILSEPLARL 80 (243)
T ss_pred CCeEEEecCCccHhhHHHHHC
Confidence 478999999999999998875
No 127
>PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=91.73 E-value=0.34 Score=39.27 Aligned_cols=32 Identities=13% Similarity=0.225 Sum_probs=25.4
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
.+++.++ .....+|+|||||+|..+..+++..
T Consensus 67 ~~~~~l~-~~~g~~VLdIG~GsG~~t~~la~~~ 98 (212)
T PRK13942 67 IMCELLD-LKEGMKVLEIGTGSGYHAAVVAEIV 98 (212)
T ss_pred HHHHHcC-CCCcCEEEEECCcccHHHHHHHHhc
Confidence 4555666 6677899999999999998877654
No 128
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=91.72 E-value=0.33 Score=39.95 Aligned_cols=55 Identities=13% Similarity=0.247 Sum_probs=48.5
Q ss_pred HHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeec
Q 036971 32 PAVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSF 94 (221)
Q Consensus 32 ~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~ 94 (221)
-+||...++..|.+.|+.. +|+.+.|||+++|+ +.. -+..-+..|...|+++-.+
T Consensus 17 ~kalaS~vRv~Il~lL~~k---~plNvneiAe~lgL-pqs----t~s~~ik~Le~aGlirT~t 71 (308)
T COG4189 17 LKALASKVRVAILQLLHRK---GPLNVNEIAEALGL-PQS----TMSANIKVLEKAGLIRTET 71 (308)
T ss_pred HHHHHHHHHHHHHHHHHHh---CCCCHHHHHHHhCC-chh----hhhhhHHHHHhcCceeeee
Confidence 4678889999999999998 59999999999999 776 7888899999999998754
No 129
>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=91.68 E-value=0.25 Score=40.16 Aligned_cols=58 Identities=12% Similarity=0.104 Sum_probs=31.1
Q ss_pred hhhhccCchHHHHHHH----HHhhhhHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHHh
Q 036971 159 YDYLGTDSRFNEVFNN----GMIGQTSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHNF 216 (221)
Q Consensus 159 ~~~l~~~p~~~~~F~~----aM~~~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~ 216 (221)
++.+.++|+.-+.|+. .+..|-..+.+.+++.+..-+....|.|.|||.+.++.++..
T Consensus 31 ~~lf~~dP~~F~~YH~Gfr~Qv~~WP~nPvd~iI~~l~~~~~~~viaD~GCGdA~la~~~~~ 92 (219)
T PF05148_consen 31 LKLFQEDPELFDIYHEGFRQQVKKWPVNPVDVIIEWLKKRPKSLVIADFGCGDAKLAKAVPN 92 (219)
T ss_dssp HHHHHH-HHHHHHHHHHHHHHHCTSSS-HHHHHHHHHCTS-TTS-EEEES-TT-HHHHH--S
T ss_pred HHHHHhCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHhcCCCEEEEECCCchHHHHHhccc
Confidence 4455667766554444 444444445555555554233457999999999999987754
No 130
>PRK04457 spermidine synthase; Provisional
Probab=91.58 E-value=0.19 Score=42.25 Aligned_cols=25 Identities=16% Similarity=0.170 Sum_probs=22.8
Q ss_pred CCCeEEEecCCccHHHHHHHhhCCC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
..++|+|||||.|.++..+++.+|+
T Consensus 66 ~~~~vL~IG~G~G~l~~~l~~~~p~ 90 (262)
T PRK04457 66 RPQHILQIGLGGGSLAKFIYTYLPD 90 (262)
T ss_pred CCCEEEEECCCHhHHHHHHHHhCCC
Confidence 4679999999999999999999986
No 131
>smart00138 MeTrc Methyltransferase, chemotaxis proteins. Methylates methyl-accepting chemotaxis proteins to form gamma-glutamyl methyl ester residues.
Probab=91.58 E-value=0.52 Score=39.63 Aligned_cols=34 Identities=15% Similarity=0.123 Sum_probs=22.2
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccH----HHHHHHhhCC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGI----TLSDHNFQIP 219 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~----~~~~l~~~~P 219 (221)
|.+++.-+ .....+|+|+|||+|. +++.+++.+|
T Consensus 89 p~l~~~~~-~~~~~ri~d~GCgtGee~YslA~~l~e~~~ 126 (264)
T smart00138 89 PLLIASRR-HGRRVRIWSAGCSTGEEPYSLAMLLAETLP 126 (264)
T ss_pred HHHHHhcC-CCCCEEEEeccccCChHHHHHHHHHHHHhh
Confidence 44444333 3345799999999996 5566666654
No 132
>KOG1271 consensus Methyltransferases [General function prediction only]
Probab=91.54 E-value=0.26 Score=39.28 Aligned_cols=21 Identities=29% Similarity=0.390 Sum_probs=18.3
Q ss_pred CCeEEEecCCccHHHHHHHhh
Q 036971 197 ITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~ 217 (221)
..+|||+|||.|+++..|++.
T Consensus 68 A~~VlDLGtGNG~~L~~L~~e 88 (227)
T KOG1271|consen 68 ADRVLDLGTGNGHLLFQLAKE 88 (227)
T ss_pred ccceeeccCCchHHHHHHHHh
Confidence 349999999999999999764
No 133
>PLN02336 phosphoethanolamine N-methyltransferase
Probab=91.54 E-value=0.27 Score=44.79 Aligned_cols=34 Identities=18% Similarity=0.229 Sum_probs=26.5
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 184 INKIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 184 ~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
...+++.++ .+...+|||||||.|..+..+++.+
T Consensus 255 te~l~~~~~-~~~~~~vLDiGcG~G~~~~~la~~~ 288 (475)
T PLN02336 255 TKEFVDKLD-LKPGQKVLDVGCGIGGGDFYMAENF 288 (475)
T ss_pred HHHHHHhcC-CCCCCEEEEEeccCCHHHHHHHHhc
Confidence 344666666 6667899999999999998887754
No 134
>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=91.42 E-value=0.83 Score=38.68 Aligned_cols=47 Identities=17% Similarity=0.153 Sum_probs=39.4
Q ss_pred CCCHHHHHhhCC--CCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccccc
Q 036971 55 ELSASEIASQIP--TKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKY 110 (221)
Q Consensus 55 ~~t~~eLA~~~g--~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~ 110 (221)
..++++||+.++ + ... -++..|+.|..+||++++ ++|.|..|..+-.
T Consensus 137 ~~~~~~ia~~l~p~i-s~~----ev~~sL~~L~~~glikk~----~~g~y~~t~~~l~ 185 (271)
T TIGR02147 137 ADDPEELAKRCFPKI-SAE----QVKESLDLLERLGLIKKN----EDGFYKQTDKAVS 185 (271)
T ss_pred CCCHHHHHHHhCCCC-CHH----HHHHHHHHHHHCCCeeEC----CCCcEEeecceee
Confidence 458999999998 4 444 789999999999999997 6889999987544
No 135
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=91.30 E-value=0.25 Score=31.81 Aligned_cols=35 Identities=14% Similarity=0.277 Sum_probs=32.1
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++++..+||+.+++ .+. .+...++-|...|+++..
T Consensus 21 ~~v~~~~iA~~L~v-s~~----tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 21 GPVRTKDIAERLGV-SPP----TVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp SSBBHHHHHHHHTS--HH----HHHHHHHHHHHTTSEEEE
T ss_pred CCccHHHHHHHHCC-ChH----HHHHHHHHHHHCCCEEec
Confidence 69999999999999 776 899999999999999986
No 136
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=91.30 E-value=0.45 Score=35.89 Aligned_cols=63 Identities=19% Similarity=0.167 Sum_probs=45.7
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCC--Ccceeccccccccc
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHG--VRLYSLAPVAKYYV 112 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~--~~~y~lt~~s~~L~ 112 (221)
+...|...+ ++.|..+||+.+++ ++. .+.++++-|...|++++.....+ .-...+|+.++.+.
T Consensus 36 vL~~l~~~~--~~~t~~eLa~~l~~-~~~----tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~ 100 (144)
T PRK03573 36 TLHNIHQLP--PEQSQIQLAKAIGI-EQP----SLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLI 100 (144)
T ss_pred HHHHHHHcC--CCCCHHHHHHHhCC-Chh----hHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHH
Confidence 455665543 36899999999999 887 99999999999999998732101 12366666666554
No 137
>PRK12335 tellurite resistance protein TehB; Provisional
Probab=91.25 E-value=0.24 Score=42.07 Aligned_cols=21 Identities=19% Similarity=0.186 Sum_probs=18.4
Q ss_pred CCeEEEecCCccHHHHHHHhh
Q 036971 197 ITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~ 217 (221)
..+|+|||||.|..+..+++.
T Consensus 121 ~~~vLDlGcG~G~~~~~la~~ 141 (287)
T PRK12335 121 PGKALDLGCGQGRNSLYLALL 141 (287)
T ss_pred CCCEEEeCCCCCHHHHHHHHC
Confidence 469999999999999888764
No 138
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=91.24 E-value=0.14 Score=36.20 Aligned_cols=60 Identities=15% Similarity=0.268 Sum_probs=47.6
Q ss_pred hhhHHH-hcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCc---ceecccccccccc
Q 036971 43 VLDIIN-KAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVR---LYSLAPVAKYYVS 113 (221)
Q Consensus 43 lfd~L~-~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~---~y~lt~~s~~L~~ 113 (221)
+||+|. ..+ +++..--|.-.+++ +-+ ..+.+++.|+..|++... .++ .|.+|+.+.-+..
T Consensus 20 i~dIL~~~~~--~~~~~Tri~y~aNl-ny~----~~~~yi~~L~~~Gli~~~----~~~~~~~y~lT~KG~~fle 83 (95)
T COG3432 20 IFDILKAISE--GGIGITRIIYGANL-NYK----RAQKYIEMLVEKGLIIKQ----DNGRRKVYELTEKGKRFLE 83 (95)
T ss_pred HHHHHHHhcC--CCCCceeeeeecCc-CHH----HHHHHHHHHHhCCCEEec----cCCccceEEEChhHHHHHH
Confidence 456666 322 68888999999999 888 999999999999977776 333 6999999987654
No 139
>PRK11805 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=91.20 E-value=0.17 Score=43.53 Aligned_cols=23 Identities=26% Similarity=0.489 Sum_probs=21.5
Q ss_pred CeEEEecCCccHHHHHHHhhCCC
Q 036971 198 TRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 198 ~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
.+|+|+|||+|.++..+++.+|+
T Consensus 135 ~~VLDlG~GsG~iai~la~~~p~ 157 (307)
T PRK11805 135 TRILDLCTGSGCIAIACAYAFPD 157 (307)
T ss_pred CEEEEEechhhHHHHHHHHHCCC
Confidence 68999999999999999999885
No 140
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=91.13 E-value=0.48 Score=29.48 Aligned_cols=44 Identities=16% Similarity=0.284 Sum_probs=34.0
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceee
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCC 92 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~ 92 (221)
.|...|.+.. +++|.++||+.+++ +.+ -+++-+..|...++.-.
T Consensus 4 ~il~~L~~~~--~~it~~eLa~~l~v-S~r----Ti~~~i~~L~~~~~~I~ 47 (55)
T PF08279_consen 4 QILKLLLESK--EPITAKELAEELGV-SRR----TIRRDIKELREWGIPIE 47 (55)
T ss_dssp HHHHHHHHTT--TSBEHHHHHHHCTS--HH----HHHHHHHHHHHTT-EEE
T ss_pred HHHHHHHHcC--CCcCHHHHHHHhCC-CHH----HHHHHHHHHHHCCCeEE
Confidence 4566775543 57999999999999 887 99999999999994333
No 141
>COG4123 Predicted O-methyltransferase [General function prediction only]
Probab=91.10 E-value=0.25 Score=41.21 Aligned_cols=27 Identities=19% Similarity=0.171 Sum_probs=23.6
Q ss_pred CCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
.....+|+|+|+|.|..+..+++++|+
T Consensus 42 ~~~~~~IlDlGaG~G~l~L~la~r~~~ 68 (248)
T COG4123 42 VPKKGRILDLGAGNGALGLLLAQRTEK 68 (248)
T ss_pred cccCCeEEEecCCcCHHHHHHhccCCC
Confidence 344789999999999999999999774
No 142
>PLN02490 MPBQ/MSBQ methyltransferase
Probab=90.89 E-value=0.45 Score=41.64 Aligned_cols=33 Identities=27% Similarity=0.405 Sum_probs=24.8
Q ss_pred HHHhcCCCC-CCCeEEEecCCccHHHHHHHhhCCC
Q 036971 187 IVESYKGFQ-NITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 187 ~l~~~~~~~-~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
+++... +. ...+|||||||+|.++..+++.+|.
T Consensus 104 ~l~~~~-l~~~~~~VLDLGcGtG~~~l~La~~~~~ 137 (340)
T PLN02490 104 ALEPAD-LSDRNLKVVDVGGGTGFTTLGIVKHVDA 137 (340)
T ss_pred HHhhcc-cCCCCCEEEEEecCCcHHHHHHHHHCCC
Confidence 444444 42 3469999999999999999887763
No 143
>PRK14966 unknown domain/N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase fusion protein; Provisional
Probab=90.78 E-value=0.37 Score=43.30 Aligned_cols=25 Identities=24% Similarity=0.376 Sum_probs=21.9
Q ss_pred CCCeEEEecCCccHHHHHHHhhCCC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
...+|+|||||+|.++..+++.+|+
T Consensus 251 ~~~rVLDLGcGSG~IaiaLA~~~p~ 275 (423)
T PRK14966 251 ENGRVWDLGTGSGAVAVTVALERPD 275 (423)
T ss_pred CCCEEEEEeChhhHHHHHHHHhCCC
Confidence 3468999999999999999988875
No 144
>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=90.76 E-value=0.5 Score=38.98 Aligned_cols=33 Identities=15% Similarity=0.070 Sum_probs=24.3
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccHHHHHHHhh
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
..+++.++..-...+++|||||+|.++..+++.
T Consensus 64 ~~~l~~~~~~~~~~~vlDiG~gtG~~t~~l~~~ 96 (228)
T TIGR00478 64 KEALEEFNIDVKNKIVLDVGSSTGGFTDCALQK 96 (228)
T ss_pred HHHHHhcCCCCCCCEEEEcccCCCHHHHHHHHc
Confidence 345666651124478999999999999988875
No 145
>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=90.73 E-value=0.21 Score=42.40 Aligned_cols=23 Identities=22% Similarity=0.520 Sum_probs=21.3
Q ss_pred CeEEEecCCccHHHHHHHhhCCC
Q 036971 198 TRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 198 ~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
.+|+|||||+|.++..++..+|+
T Consensus 116 ~~vLDlG~GsG~i~l~la~~~~~ 138 (284)
T TIGR00536 116 LHILDLGTGSGCIALALAYEFPN 138 (284)
T ss_pred CEEEEEeccHhHHHHHHHHHCCC
Confidence 68999999999999999999885
No 146
>PRK00517 prmA ribosomal protein L11 methyltransferase; Reviewed
Probab=90.55 E-value=0.31 Score=40.56 Aligned_cols=24 Identities=25% Similarity=0.156 Sum_probs=19.5
Q ss_pred CCCeEEEecCCccHHHHHHHhhCC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
...+|+|||||+|..+..+++..+
T Consensus 119 ~~~~VLDiGcGsG~l~i~~~~~g~ 142 (250)
T PRK00517 119 PGKTVLDVGCGSGILAIAAAKLGA 142 (250)
T ss_pred CCCEEEEeCCcHHHHHHHHHHcCC
Confidence 457999999999999888776543
No 147
>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=90.41 E-value=0.34 Score=41.21 Aligned_cols=29 Identities=24% Similarity=0.260 Sum_probs=21.6
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhh
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
++..+. . ...+|+|||||+|.++..+++.
T Consensus 152 ~l~~~~-~-~g~~VLDvGcGsG~lai~aa~~ 180 (288)
T TIGR00406 152 WLEDLD-L-KDKNVIDVGCGSGILSIAALKL 180 (288)
T ss_pred HHHhhc-C-CCCEEEEeCCChhHHHHHHHHc
Confidence 344444 3 3489999999999999887764
No 148
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=90.40 E-value=0.39 Score=38.35 Aligned_cols=30 Identities=13% Similarity=0.379 Sum_probs=23.7
Q ss_pred HHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 188 VESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 188 l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
+...+ .....+|+|+|||+|.++..+++..
T Consensus 33 l~~l~-~~~~~~vlDlG~GtG~~s~~~a~~~ 62 (198)
T PRK00377 33 LSKLR-LRKGDMILDIGCGTGSVTVEASLLV 62 (198)
T ss_pred HHHcC-CCCcCEEEEeCCcCCHHHHHHHHHh
Confidence 34455 5566899999999999999987754
No 149
>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=90.23 E-value=0.47 Score=33.46 Aligned_cols=44 Identities=11% Similarity=0.061 Sum_probs=37.3
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLA 105 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt 105 (221)
.++|..|||+.+|+ ++. .+.|.|..|...|++.... .-+.|..+
T Consensus 46 ~~is~~eLa~~~g~-sr~----tVsr~L~~Le~~GlI~r~~---~~~~~~~n 89 (95)
T TIGR01610 46 DRVTATVIAELTGL-SRT----HVSDAIKSLARRRIIFRQG---MMGIVGVN 89 (95)
T ss_pred CccCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCeeeec---CCceeecC
Confidence 48999999999999 887 9999999999999999862 23666655
No 150
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=89.93 E-value=0.3 Score=45.03 Aligned_cols=26 Identities=15% Similarity=0.291 Sum_probs=23.6
Q ss_pred CCCeEEEecCCccHHHHHHHhhCCCC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQIPSY 221 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~P~l 221 (221)
+...+||||||.|.++.++++++|+.
T Consensus 347 ~~p~~lEIG~G~G~~~~~~A~~~p~~ 372 (506)
T PRK01544 347 KRKVFLEIGFGMGEHFINQAKMNPDA 372 (506)
T ss_pred CCceEEEECCCchHHHHHHHHhCCCC
Confidence 35799999999999999999999973
No 151
>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=89.93 E-value=0.31 Score=40.30 Aligned_cols=25 Identities=20% Similarity=0.288 Sum_probs=18.1
Q ss_pred CCCCCeEEEecCCccHHHHHHHhhC
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
.....+|+|||||+|.++..++++.
T Consensus 45 ~~~g~~vLDv~~GtG~~~~~l~~~~ 69 (233)
T PF01209_consen 45 LRPGDRVLDVACGTGDVTRELARRV 69 (233)
T ss_dssp --S--EEEEET-TTSHHHHHHGGGS
T ss_pred CCCCCEEEEeCCChHHHHHHHHHHC
Confidence 3446799999999999999998875
No 152
>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=89.83 E-value=0.28 Score=34.98 Aligned_cols=51 Identities=18% Similarity=0.270 Sum_probs=38.8
Q ss_pred HHhhChhhHHHh-cCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 38 VVNLDVLDIINK-AGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 38 av~lglfd~L~~-~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.+.-.|++.|.. ...+.++++++|++++++ +.. .++..|+.|+..|++--.
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~-~~~----~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQLGM-SEN----EVRKALDFLSNEGHIYST 98 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHSTS--HH----HHHHHHHHHHHTTSEEES
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHhCc-CHH----HHHHHHHHHHhCCeEecc
Confidence 345567777776 222257999999999999 887 999999999999998764
No 153
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=89.66 E-value=0.32 Score=44.90 Aligned_cols=24 Identities=17% Similarity=0.401 Sum_probs=21.7
Q ss_pred CCeEEEecCCccHHHHHHHhhCCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
..+|+|||||+|.++..+++.+|+
T Consensus 139 ~~~VLDlG~GsG~iai~la~~~p~ 162 (506)
T PRK01544 139 FLNILELGTGSGCIAISLLCELPN 162 (506)
T ss_pred CCEEEEccCchhHHHHHHHHHCCC
Confidence 468999999999999999998885
No 154
>PRK06474 hypothetical protein; Provisional
Probab=89.65 E-value=0.58 Score=37.05 Aligned_cols=72 Identities=14% Similarity=0.193 Sum_probs=53.0
Q ss_pred HHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhC-CCCCCcchhhhHHHHHHHHhcCCceeeeccC----CCCcceecccc
Q 036971 33 AVFQAVVNLDVLDIINKAGPGAELSASEIASQI-PTKNPEGAAKMLDRVLGLLVSFNILCCSFST----HGVRLYSLAPV 107 (221)
Q Consensus 33 ~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~-g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~----~~~~~y~lt~~ 107 (221)
.+|.--.++.|++.|...+ .++|+.+|++.+ ++ +.. -+.|.|+.|...|+++..... +..-.|+.++.
T Consensus 6 ~~La~p~R~~Il~~L~~~~--~~~ta~el~~~l~~i-s~a----TvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~ 78 (178)
T PRK06474 6 EILMHPVRMKICQVLMRNK--EGLTPLELVKILKDV-PQA----TLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEE 78 (178)
T ss_pred HhhCCHHHHHHHHHHHhCC--CCCCHHHHHHHhcCC-CHH----HHHHHHHHHHHCCCEEEeecccccCceeEEEEeccc
Confidence 4566677888999998864 359999999999 56 554 799999999999999986321 01134777776
Q ss_pred cccc
Q 036971 108 AKYY 111 (221)
Q Consensus 108 s~~L 111 (221)
...+
T Consensus 79 ~~~~ 82 (178)
T PRK06474 79 DAKI 82 (178)
T ss_pred eeee
Confidence 5443
No 155
>PRK13943 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=89.56 E-value=0.61 Score=40.49 Aligned_cols=32 Identities=19% Similarity=0.332 Sum_probs=25.4
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
+++..+ .....+|+|||||+|.++..+++.++
T Consensus 72 ll~~L~-i~~g~~VLDIG~GtG~~a~~LA~~~~ 103 (322)
T PRK13943 72 FMEWVG-LDKGMRVLEIGGGTGYNAAVMSRVVG 103 (322)
T ss_pred HHHhcC-CCCCCEEEEEeCCccHHHHHHHHhcC
Confidence 445555 55568999999999999999988765
No 156
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=89.54 E-value=0.61 Score=35.26 Aligned_cols=63 Identities=21% Similarity=0.154 Sum_probs=46.6
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCc---ceeccccccccc
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVR---LYSLAPVAKYYV 112 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~---~y~lt~~s~~L~ 112 (221)
..|+-.|... +++|..+||+.+++ ++. .+.++++-|...|++.+.... .+. ...+|+.++.+.
T Consensus 43 ~~vL~~l~~~---~~~t~~eLa~~l~i-~~~----tvsr~l~~Le~~GlI~R~~~~-~DrR~~~l~LT~~G~~~~ 108 (144)
T PRK11512 43 FKVLCSIRCA---ACITPVELKKVLSV-DLG----ALTRMLDRLVCKGWVERLPNP-NDKRGVLVKLTTSGAAIC 108 (144)
T ss_pred HHHHHHHHHc---CCCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEeccCc-ccCCeeEeEEChhHHHHH
Confidence 3456666654 58999999999999 887 999999999999999986321 111 256666666544
No 157
>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=89.37 E-value=0.3 Score=35.00 Aligned_cols=43 Identities=19% Similarity=0.372 Sum_probs=33.3
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
|++.|... +.++-++||+.+++ ++. -++++|..|...||+...
T Consensus 18 Il~~L~~~---~~l~de~la~~~~l-~~~----~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 18 ILDALLRK---GELTDEDLAKKLGL-KPK----EVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp HHHHHHHH-----B-HHHHHHTT-S--HH----HHHHHHHHHHHHSS-EEE
T ss_pred HHHHHHHc---CCcCHHHHHHHhCC-CHH----HHHHHHHHHHHCCCeEEE
Confidence 57788865 58999999999999 888 999999999999999765
No 158
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=89.32 E-value=0.53 Score=36.14 Aligned_cols=47 Identities=15% Similarity=0.247 Sum_probs=42.1
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.+..|.+.|..+ +..+..+||+++|+ .+. .+++=++-|...|++...
T Consensus 10 ~D~~Il~~Lq~d---~R~s~~eiA~~lgl-S~~----tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 10 LDRGILEALMEN---ARTPYAELAKQFGV-SPG----TIHVRVEKMKQAGIITGT 56 (153)
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCeeeE
Confidence 677899999997 59999999999999 887 899999999999999853
No 159
>KOG1499 consensus Protein arginine N-methyltransferase PRMT1 and related enzymes [Posttranslational modification, protein turnover, chaperones; Transcription; Signal transduction mechanisms]
Probab=89.24 E-value=0.61 Score=40.62 Aligned_cols=22 Identities=27% Similarity=0.152 Sum_probs=18.5
Q ss_pred CCeEEEecCCccHHHHHHHhhC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
.++|+|||||+|.+++--+++-
T Consensus 61 dK~VlDVGcGtGILS~F~akAG 82 (346)
T KOG1499|consen 61 DKTVLDVGCGTGILSMFAAKAG 82 (346)
T ss_pred CCEEEEcCCCccHHHHHHHHhC
Confidence 4899999999999988766653
No 160
>PLN02396 hexaprenyldihydroxybenzoate methyltransferase
Probab=89.23 E-value=0.32 Score=42.23 Aligned_cols=21 Identities=19% Similarity=0.251 Sum_probs=18.0
Q ss_pred CCeEEEecCCccHHHHHHHhh
Q 036971 197 ITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~ 217 (221)
..+|||||||.|.++..+++.
T Consensus 132 g~~ILDIGCG~G~~s~~La~~ 152 (322)
T PLN02396 132 GLKFIDIGCGGGLLSEPLARM 152 (322)
T ss_pred CCEEEEeeCCCCHHHHHHHHc
Confidence 468999999999999888763
No 161
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=89.21 E-value=0.41 Score=43.30 Aligned_cols=33 Identities=24% Similarity=0.102 Sum_probs=24.3
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
..+++.++ .....+|+|+|||+|.++..+++..
T Consensus 287 ~~vl~~l~-~~~~~~VLDlgcGtG~~sl~la~~~ 319 (443)
T PRK13168 287 ARALEWLD-PQPGDRVLDLFCGLGNFTLPLARQA 319 (443)
T ss_pred HHHHHHhc-CCCCCEEEEEeccCCHHHHHHHHhC
Confidence 33444444 3445799999999999999998764
No 162
>KOG1270 consensus Methyltransferases [Coenzyme transport and metabolism]
Probab=89.19 E-value=0.2 Score=42.05 Aligned_cols=20 Identities=25% Similarity=0.336 Sum_probs=18.0
Q ss_pred CeEEEecCCccHHHHHHHhh
Q 036971 198 TRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 198 ~~vvDVGGG~G~~~~~l~~~ 217 (221)
.+|+|||||.|.++..|++-
T Consensus 91 ~~ilDvGCGgGLLSepLArl 110 (282)
T KOG1270|consen 91 MKILDVGCGGGLLSEPLARL 110 (282)
T ss_pred ceEEEeccCccccchhhHhh
Confidence 67999999999999988874
No 163
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=89.11 E-value=0.54 Score=42.20 Aligned_cols=43 Identities=23% Similarity=0.234 Sum_probs=37.2
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLA 105 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt 105 (221)
.+.|.++|++.+++ +++ .++++|+.|...|++.+. +++.|.+.
T Consensus 309 ~~~t~~~La~~l~~-~~~----~v~~iL~~L~~agLI~~~----~~g~~~l~ 351 (412)
T PRK04214 309 KALDVDEIRRLEPM-GYD----ELGELLCELARIGLLRRG----ERGQWVLA 351 (412)
T ss_pred CCCCHHHHHHHhCC-CHH----HHHHHHHHHHhCCCeEec----CCCceEec
Confidence 68999999999999 888 999999999999999975 45556544
No 164
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=89.00 E-value=0.5 Score=39.74 Aligned_cols=48 Identities=17% Similarity=0.318 Sum_probs=43.0
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeec
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSF 94 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~ 94 (221)
+..+.++|.+.| |.++-+||.+++|+ +.. -+.|+|+-|..+|++++.+
T Consensus 197 e~~il~~i~~~G--Gri~Q~eL~r~lgl-skt----TvsR~L~~LEk~GlIe~~K 244 (258)
T COG2512 197 EKEILDLIRERG--GRITQAELRRALGL-SKT----TVSRILRRLEKRGLIEKEK 244 (258)
T ss_pred HHHHHHHHHHhC--CEEeHHHHHHhhCC-ChH----HHHHHHHHHHhCCceEEEE
Confidence 345788999987 78999999999999 777 8999999999999999975
No 165
>PRK00312 pcm protein-L-isoaspartate O-methyltransferase; Reviewed
Probab=88.98 E-value=0.7 Score=37.22 Aligned_cols=30 Identities=17% Similarity=0.295 Sum_probs=22.4
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhh
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
++...+ .....+|+|||||+|..+..+++.
T Consensus 70 l~~~l~-~~~~~~VLeiG~GsG~~t~~la~~ 99 (212)
T PRK00312 70 MTELLE-LKPGDRVLEIGTGSGYQAAVLAHL 99 (212)
T ss_pred HHHhcC-CCCCCEEEEECCCccHHHHHHHHH
Confidence 344455 556689999999999988766654
No 166
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=88.97 E-value=0.48 Score=36.85 Aligned_cols=47 Identities=13% Similarity=0.192 Sum_probs=42.4
Q ss_pred HHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceee
Q 036971 38 VVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCC 92 (221)
Q Consensus 38 av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~ 92 (221)
.++..|..+|.++ +.+|..+||+++|+ .+. .+.+=++-|...|+++.
T Consensus 14 ~~D~~IL~~Lq~d---~R~s~~eiA~~lgl-S~~----tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 14 RIDRNILNELQKD---GRISNVELSKRVGL-SPT----PCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHhccC---CCCCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCeEE
Confidence 4688899999998 59999999999999 887 89999999999999985
No 167
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=88.95 E-value=0.85 Score=31.02 Aligned_cols=63 Identities=14% Similarity=0.158 Sum_probs=46.6
Q ss_pred HHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc
Q 036971 33 AVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK 109 (221)
Q Consensus 33 ~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~ 109 (221)
..|.+.|+ +++... .|+...+||+.++. ++. -++-.|..|..+||++... |..+.|..|..+.
T Consensus 8 ~IL~alV~----~Y~~~~---~PVgSk~ia~~l~~-s~a----TIRN~M~~Le~lGlve~~p--~~s~GriPT~~aY 70 (78)
T PF03444_consen 8 EILKALVE----LYIETG---EPVGSKTIAEELGR-SPA----TIRNEMADLEELGLVESQP--HPSGGRIPTDKAY 70 (78)
T ss_pred HHHHHHHH----HHHhcC---CCcCHHHHHHHHCC-ChH----HHHHHHHHHHHCCCccCCC--CCCCCCCcCHHHH
Confidence 34555555 244443 69999999999999 887 8999999999999998531 1356677776554
No 168
>PLN02366 spermidine synthase
Probab=88.86 E-value=0.42 Score=41.25 Aligned_cols=25 Identities=32% Similarity=0.407 Sum_probs=21.2
Q ss_pred CCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 195 QNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
++.++|++||||.|..+.++++. |+
T Consensus 90 ~~pkrVLiIGgG~G~~~rellk~-~~ 114 (308)
T PLN02366 90 PNPKKVLVVGGGDGGVLREIARH-SS 114 (308)
T ss_pred CCCCeEEEEcCCccHHHHHHHhC-CC
Confidence 45789999999999999999865 53
No 169
>PRK14967 putative methyltransferase; Provisional
Probab=88.69 E-value=0.51 Score=38.42 Aligned_cols=29 Identities=14% Similarity=0.107 Sum_probs=22.0
Q ss_pred HHhcCCCCCCCeEEEecCCccHHHHHHHhh
Q 036971 188 VESYKGFQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 188 l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
+.... .....+|+|+|||.|.++..+++.
T Consensus 29 l~~~~-~~~~~~vLDlGcG~G~~~~~la~~ 57 (223)
T PRK14967 29 LAAEG-LGPGRRVLDLCTGSGALAVAAAAA 57 (223)
T ss_pred HHhcc-cCCCCeEEEecCCHHHHHHHHHHc
Confidence 33444 444579999999999999888764
No 170
>PRK05134 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional
Probab=88.60 E-value=0.81 Score=37.27 Aligned_cols=22 Identities=32% Similarity=0.262 Sum_probs=18.5
Q ss_pred CCCeEEEecCCccHHHHHHHhh
Q 036971 196 NITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
...+|+|||||.|.++..+++.
T Consensus 48 ~~~~vLdiG~G~G~~~~~l~~~ 69 (233)
T PRK05134 48 FGKRVLDVGCGGGILSESMARL 69 (233)
T ss_pred CCCeEEEeCCCCCHHHHHHHHc
Confidence 3578999999999998888764
No 171
>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=88.08 E-value=0.89 Score=34.69 Aligned_cols=35 Identities=14% Similarity=0.185 Sum_probs=33.1
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
|++|++|||.+.|+ ..+ .+---|-.+++.|-+.+.
T Consensus 5 Ga~T~eELA~~FGv-ttR----kvaStLa~~ta~Grl~Rv 39 (155)
T PF07789_consen 5 GAKTAEELAGKFGV-TTR----KVASTLAMVTATGRLIRV 39 (155)
T ss_pred CcccHHHHHHHhCc-chh----hhHHHHHHHHhcceeEEe
Confidence 69999999999999 888 999999999999999997
No 172
>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=87.82 E-value=1 Score=35.98 Aligned_cols=40 Identities=18% Similarity=0.029 Sum_probs=34.8
Q ss_pred CCCCHHHHHhhCCCCC-CcchhhhHHHHHHHHhcCCceeeeccCCCCccee
Q 036971 54 AELSASEIASQIPTKN-PEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYS 103 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~-~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~ 103 (221)
-+.|..|||+.+|+ + +. .+.+.|+.|...|++... ++.|+
T Consensus 24 ~~~~~~ela~~~~~-~s~~----tv~~~l~~L~~~g~i~~~-----~~~~~ 64 (199)
T TIGR00498 24 YPPSIREIARAVGL-RSPS----AAEEHLKALERKGYIERD-----PGKPR 64 (199)
T ss_pred CCCcHHHHHHHhCC-CChH----HHHHHHHHHHHCCCEecC-----CCCCC
Confidence 46889999999999 7 66 899999999999999995 56654
No 173
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=87.75 E-value=0.82 Score=34.70 Aligned_cols=48 Identities=17% Similarity=0.275 Sum_probs=42.8
Q ss_pred HHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 38 VVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 38 av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..+..|.+.|.+. +..+..+||+++|+ ++. .+.+-++-|...|++...
T Consensus 8 ~~D~~IL~~L~~d---~r~~~~eia~~lgl-S~~----~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 8 DIDRRILRLLQED---ARISNAELAERVGL-SPS----TVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred HHHHHHHHHHHHh---CCCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCceeeE
Confidence 3567788999997 58999999999999 887 899999999999999976
No 174
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=87.73 E-value=0.6 Score=42.87 Aligned_cols=68 Identities=19% Similarity=0.207 Sum_probs=53.3
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccccccc-CCC
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYVS-DQN 116 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~~-~~~ 116 (221)
.+..|...|... ++++..+||+.+++ ++. .+.++++.|.+.|+++.... ....|.+|+.++.++. ..|
T Consensus 7 ~e~~vL~~L~~~---~~~s~~eLA~~l~l-~~~----tVt~~i~~Le~kGlV~~~~~--~~~~i~LTeeG~~~~~~g~p 75 (489)
T PRK04172 7 NEKKVLKALKEL---KEATLEELAEKLGL-PPE----AVMRAAEWLEEKGLVKVEER--VEEVYVLTEEGKKYAEEGLP 75 (489)
T ss_pred HHHHHHHHHHhC---CCCCHHHHHHHhCc-CHH----HHHHHHHHHHhCCCEEEEee--eEEEEEECHHHHHHHHhcCH
Confidence 344556667665 48999999999999 887 99999999999999998621 2457999999986654 444
No 175
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=87.56 E-value=1.3 Score=36.96 Aligned_cols=56 Identities=16% Similarity=0.048 Sum_probs=45.0
Q ss_pred hhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc
Q 036971 44 LDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK 109 (221)
Q Consensus 44 fd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~ 109 (221)
.-+|-.. |++|+.|||+.+|+ +.. .+..+|+.|...|+++... |.+..|+.-+...
T Consensus 22 Y~aLl~~---g~~tA~eis~~sgv-P~~----kvY~vl~sLe~kG~v~~~~--g~P~~y~av~p~~ 77 (247)
T COG1378 22 YLALLCL---GEATAKEISEASGV-PRP----KVYDVLRSLEKKGLVEVIE--GRPKKYRAVPPEE 77 (247)
T ss_pred HHHHHHh---CCccHHHHHHHcCC-Cch----hHHHHHHHHHHCCCEEeeC--CCCceEEeCCHHH
Confidence 3444444 59999999999999 777 9999999999999999863 2567788776554
No 176
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=87.48 E-value=0.83 Score=32.92 Aligned_cols=66 Identities=17% Similarity=0.174 Sum_probs=46.0
Q ss_pred hhChhhHHH--hcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCc---ceeccccccccc
Q 036971 40 NLDVLDIIN--KAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVR---LYSLAPVAKYYV 112 (221)
Q Consensus 40 ~lglfd~L~--~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~---~y~lt~~s~~L~ 112 (221)
++.++..|. ... +++++..+||..+++ ++. .+.++++.|...|++.+.... .+. .+.+|+.+..+.
T Consensus 27 q~~vL~~l~~~~~~-~~~~t~~eL~~~l~~-~~s----tvs~~i~~Le~kg~I~r~~~~-~D~R~~~i~lT~~G~~~~ 97 (109)
T TIGR01889 27 ELLILYYLGKLENN-EGKLTLKEIIKEILI-KQS----ALVKIIKKLSKKGYLSKERSE-DDERKVIISINKEQRSKI 97 (109)
T ss_pred HHHHHHHHHhhhcc-CCcCcHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEeccCCc-ccCCeEEEEECHHHHHHH
Confidence 344555555 211 158999999999999 887 999999999999999986321 122 255666665443
No 177
>KOG1541 consensus Predicted protein carboxyl methylase [General function prediction only]
Probab=87.21 E-value=0.34 Score=39.79 Aligned_cols=27 Identities=22% Similarity=0.305 Sum_probs=19.4
Q ss_pred HHHhcCCCCC--CCeEEEecCCccHHHHHH
Q 036971 187 IVESYKGFQN--ITRLVDVGGGLGITLSDH 214 (221)
Q Consensus 187 ~l~~~~~~~~--~~~vvDVGGG~G~~~~~l 214 (221)
.++.++ +++ ...|+|||||+|.-+..+
T Consensus 40 aLELLa-lp~~~~~~iLDIGCGsGLSg~vL 68 (270)
T KOG1541|consen 40 ALELLA-LPGPKSGLILDIGCGSGLSGSVL 68 (270)
T ss_pred HHHHhh-CCCCCCcEEEEeccCCCcchhee
Confidence 344444 544 689999999999876554
No 178
>PLN02585 magnesium protoporphyrin IX methyltransferase
Probab=86.87 E-value=0.56 Score=40.62 Aligned_cols=21 Identities=19% Similarity=0.210 Sum_probs=18.6
Q ss_pred CCeEEEecCCccHHHHHHHhh
Q 036971 197 ITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~ 217 (221)
..+|+|||||+|.++..+++.
T Consensus 145 ~~~VLDlGcGtG~~a~~la~~ 165 (315)
T PLN02585 145 GVTVCDAGCGTGSLAIPLALE 165 (315)
T ss_pred CCEEEEecCCCCHHHHHHHHC
Confidence 469999999999999988865
No 179
>PRK00811 spermidine synthase; Provisional
Probab=86.84 E-value=0.58 Score=39.79 Aligned_cols=23 Identities=35% Similarity=0.414 Sum_probs=20.2
Q ss_pred CCCCeEEEecCCccHHHHHHHhh
Q 036971 195 QNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
++.++|+|||||.|..+.++++.
T Consensus 75 ~~p~~VL~iG~G~G~~~~~~l~~ 97 (283)
T PRK00811 75 PNPKRVLIIGGGDGGTLREVLKH 97 (283)
T ss_pred CCCCEEEEEecCchHHHHHHHcC
Confidence 34689999999999999999875
No 180
>PRK10870 transcriptional repressor MprA; Provisional
Probab=86.66 E-value=0.86 Score=35.93 Aligned_cols=66 Identities=11% Similarity=0.070 Sum_probs=47.3
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCC--Ccceecccccccccc
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHG--VRLYSLAPVAKYYVS 113 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~--~~~y~lt~~s~~L~~ 113 (221)
.+.-.|...+ ++++|..+||+.+++ ++. .+.+++.-|...|++++.....+ .-...+|+.++.+..
T Consensus 59 ~iL~~L~~~~-~~~it~~eLa~~l~l-~~~----tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~ 126 (176)
T PRK10870 59 MALITLESQE-NHSIQPSELSCALGS-SRT----NATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLR 126 (176)
T ss_pred HHHHHHhcCC-CCCcCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHH
Confidence 3455555422 157999999999999 887 99999999999999998632101 124677777776554
No 181
>PHA03412 putative methyltransferase; Provisional
Probab=86.37 E-value=0.5 Score=39.21 Aligned_cols=23 Identities=17% Similarity=0.112 Sum_probs=20.0
Q ss_pred CCeEEEecCCccHHHHHHHhhCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
..+|||+|||+|.++..++++.+
T Consensus 50 ~grVLDlG~GSG~Lalala~~~~ 72 (241)
T PHA03412 50 SGSVVDLCAGIGGLSFAMVHMMM 72 (241)
T ss_pred CCEEEEccChHHHHHHHHHHhcc
Confidence 46999999999999999987653
No 182
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=86.35 E-value=0.9 Score=37.19 Aligned_cols=53 Identities=17% Similarity=0.179 Sum_probs=42.6
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccccccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
..+|..+||+.+++ ++. .+.|.|+.|...|++++.... ....+.+|+.+..+.
T Consensus 20 ~~IS~~eLA~~L~i-S~~----Tvsr~Lk~LEe~GlI~R~~~~-r~~~v~LTekG~~ll 72 (217)
T PRK14165 20 VKISSSEFANHTGT-SSK----TAARILKQLEDEGYITRTIVP-RGQLITITEKGLDVL 72 (217)
T ss_pred CCcCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEEEEcC-CceEEEECHHHHHHH
Confidence 46999999999999 887 999999999999999986311 245677777776544
No 183
>PRK05638 threonine synthase; Validated
Probab=86.30 E-value=1.1 Score=40.58 Aligned_cols=61 Identities=13% Similarity=0.201 Sum_probs=45.6
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCC--CCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccccccc
Q 036971 43 VLDIINKAGPGAELSASEIASQIP--TKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g--~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
|+..|.+ ++++.-||++.++ + .+. .+.+.|+.|...|+++.....+..-.|++|+.++.+.
T Consensus 376 IL~~L~~----~~~~~~el~~~l~~~~-s~~----~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l 438 (442)
T PRK05638 376 ILKILSE----REMYGYEIWKALGKPL-KYQ----AVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLL 438 (442)
T ss_pred HHHHHhh----CCccHHHHHHHHcccC-Ccc----hHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHH
Confidence 5667776 5899999999998 6 666 8999999999999998632111223488888776543
No 184
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=86.15 E-value=0.94 Score=36.89 Aligned_cols=44 Identities=30% Similarity=0.339 Sum_probs=36.4
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
|.+.|...+ .+.|.+|+|+++|+ ..- -.+|.|.+|++.|+++..
T Consensus 163 i~~~~~~~~--~~~Taeela~~~gi-SRv----TaRRYLeyl~~~~~l~a~ 206 (224)
T COG4565 163 VREALKEPD--QELTAEELAQALGI-SRV----TARRYLEYLVSNGILEAE 206 (224)
T ss_pred HHHHHhCcC--CccCHHHHHHHhCc-cHH----HHHHHHHHHHhcCeeeEE
Confidence 445666332 69999999999999 665 789999999999999875
No 185
>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=86.14 E-value=0.93 Score=36.76 Aligned_cols=32 Identities=22% Similarity=0.392 Sum_probs=21.7
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
.+++.+. ......++|||+|.|....+.+-.+
T Consensus 33 ~il~~~~-l~~~dvF~DlGSG~G~~v~~aal~~ 64 (205)
T PF08123_consen 33 KILDELN-LTPDDVFYDLGSGVGNVVFQAALQT 64 (205)
T ss_dssp HHHHHTT---TT-EEEEES-TTSHHHHHHHHHH
T ss_pred HHHHHhC-CCCCCEEEECCCCCCHHHHHHHHHc
Confidence 4566677 7777899999999999987766443
No 186
>KOG1500 consensus Protein arginine N-methyltransferase CARM1 [Posttranslational modification, protein turnover, chaperones; Transcription]
Probab=85.97 E-value=1.5 Score=38.36 Aligned_cols=23 Identities=35% Similarity=0.442 Sum_probs=17.6
Q ss_pred hcCCCCCCCeEEEecCCccHHHHHH
Q 036971 190 SYKGFQNITRLVDVGGGLGITLSDH 214 (221)
Q Consensus 190 ~~~~~~~~~~vvDVGGG~G~~~~~l 214 (221)
.-| |++ +.|||||+|+|.++.=-
T Consensus 173 ~sD-F~~-kiVlDVGaGSGILS~FA 195 (517)
T KOG1500|consen 173 HSD-FQD-KIVLDVGAGSGILSFFA 195 (517)
T ss_pred ccc-cCC-cEEEEecCCccHHHHHH
Confidence 344 665 88999999999987533
No 187
>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=85.96 E-value=0.49 Score=26.47 Aligned_cols=31 Identities=19% Similarity=0.324 Sum_probs=24.8
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCce
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNIL 90 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll 90 (221)
++|-.|||..+|+ .++ -+.|+|..|...|++
T Consensus 2 ~mtr~diA~~lG~-t~E----TVSR~l~~l~~~glI 32 (32)
T PF00325_consen 2 PMTRQDIADYLGL-TRE----TVSRILKKLERQGLI 32 (32)
T ss_dssp E--HHHHHHHHTS--HH----HHHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHhCC-cHH----HHHHHHHHHHHcCCC
Confidence 5788999999999 777 899999999888864
No 188
>KOG2904 consensus Predicted methyltransferase [General function prediction only]
Probab=85.73 E-value=1.2 Score=37.74 Aligned_cols=27 Identities=22% Similarity=0.359 Sum_probs=22.7
Q ss_pred CCCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
+.....++|+|||+|..+..++...|+
T Consensus 146 ~~~~~~ildlgtGSGaIslsll~~L~~ 172 (328)
T KOG2904|consen 146 HSKHTHILDLGTGSGAISLSLLHGLPQ 172 (328)
T ss_pred hcccceEEEecCCccHHHHHHHhcCCC
Confidence 444568999999999999999987774
No 189
>PHA03411 putative methyltransferase; Provisional
Probab=85.67 E-value=0.76 Score=39.03 Aligned_cols=23 Identities=13% Similarity=0.135 Sum_probs=19.9
Q ss_pred CCeEEEecCCccHHHHHHHhhCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
..+|+|+|||.|.++..+++..+
T Consensus 65 ~grVLDLGcGsGilsl~la~r~~ 87 (279)
T PHA03411 65 TGKVLDLCAGIGRLSFCMLHRCK 87 (279)
T ss_pred CCeEEEcCCCCCHHHHHHHHhCC
Confidence 46899999999999998887664
No 190
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=85.65 E-value=0.86 Score=41.69 Aligned_cols=71 Identities=13% Similarity=0.106 Sum_probs=56.6
Q ss_pred HHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccccc-ccCC
Q 036971 37 AVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYY-VSDQ 115 (221)
Q Consensus 37 ~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L-~~~~ 115 (221)
++.+..|...|...+ ...+.++||+.+|+ ++. .+.+.+..|.+.|+++-... ....|.+|+.++.+ ..+.
T Consensus 2 ~~~e~~iL~~l~~~~--~~~~~~~la~~~g~-~~~----~v~~~~~~L~~kg~v~~~~~--~~~~~~LT~eG~~~l~~G~ 72 (492)
T PLN02853 2 AMAEEALLGALSNNE--EISDSGQFAASHGL-DHN----EVVGVIKSLHGFRYVDAQDI--KRETWVLTEEGKKYAAEGS 72 (492)
T ss_pred chHHHHHHHHHHhcC--CCCCHHHHHHHcCC-CHH----HHHHHHHHHHhCCCEEEEEE--EEEEEEECHHHHHHHHcCC
Confidence 345677888888753 13899999999999 887 99999999999999987632 36789999999855 4566
Q ss_pred C
Q 036971 116 N 116 (221)
Q Consensus 116 ~ 116 (221)
|
T Consensus 73 P 73 (492)
T PLN02853 73 P 73 (492)
T ss_pred H
Confidence 5
No 191
>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=85.56 E-value=0.77 Score=29.75 Aligned_cols=43 Identities=19% Similarity=0.318 Sum_probs=34.7
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
|++.|-.. |..|+.+|.+.+++ +++ .++.-|-.|...|++...
T Consensus 18 V~~~Ll~~---G~ltl~~i~~~t~l-~~~----~Vk~~L~~LiQh~~v~y~ 60 (62)
T PF08221_consen 18 VGEVLLSR---GRLTLREIVRRTGL-SPK----QVKKALVVLIQHNLVQYF 60 (62)
T ss_dssp HHHHHHHC----SEEHHHHHHHHT---HH----HHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHc---CCcCHHHHHHHhCC-CHH----HHHHHHHHHHHcCCeeee
Confidence 45566666 59999999999999 887 999999999999999864
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=85.52 E-value=1.5 Score=35.63 Aligned_cols=31 Identities=16% Similarity=0.363 Sum_probs=22.6
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccHHHHHHHh
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGITLSDHNF 216 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~ 216 (221)
..+++.++ .....+|+|||+|+|..+.-+++
T Consensus 62 a~~l~~L~-l~pg~~VLeIGtGsGY~aAlla~ 92 (209)
T PF01135_consen 62 ARMLEALD-LKPGDRVLEIGTGSGYQAALLAH 92 (209)
T ss_dssp HHHHHHTT-C-TT-EEEEES-TTSHHHHHHHH
T ss_pred HHHHHHHh-cCCCCEEEEecCCCcHHHHHHHH
Confidence 34667777 77788999999999999877764
No 193
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=85.30 E-value=1 Score=40.53 Aligned_cols=32 Identities=19% Similarity=0.035 Sum_probs=25.1
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
++..++ .....+|+|+|||+|..+..+++..|
T Consensus 236 ~~~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~ 267 (427)
T PRK10901 236 AATLLA-PQNGERVLDACAAPGGKTAHILELAP 267 (427)
T ss_pred HHHHcC-CCCCCEEEEeCCCCChHHHHHHHHcC
Confidence 344455 44567999999999999999998876
No 194
>PRK11873 arsM arsenite S-adenosylmethyltransferase; Reviewed
Probab=85.29 E-value=0.89 Score=38.07 Aligned_cols=25 Identities=16% Similarity=0.224 Sum_probs=20.0
Q ss_pred CCCCCeEEEecCCccHHHHHHHhhC
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
.....+|||||||.|..+..+++.+
T Consensus 75 ~~~g~~VLDiG~G~G~~~~~~a~~~ 99 (272)
T PRK11873 75 LKPGETVLDLGSGGGFDCFLAARRV 99 (272)
T ss_pred CCCCCEEEEeCCCCCHHHHHHHHHh
Confidence 4556899999999999887776653
No 195
>PRK13255 thiopurine S-methyltransferase; Reviewed
Probab=84.79 E-value=1.6 Score=35.72 Aligned_cols=23 Identities=13% Similarity=-0.091 Sum_probs=19.4
Q ss_pred CCCCeEEEecCCccHHHHHHHhh
Q 036971 195 QNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
....+|+|+|||.|..+..|+++
T Consensus 36 ~~~~rvL~~gCG~G~da~~LA~~ 58 (218)
T PRK13255 36 PAGSRVLVPLCGKSLDMLWLAEQ 58 (218)
T ss_pred CCCCeEEEeCCCChHhHHHHHhC
Confidence 34579999999999999988764
No 196
>PF03141 Methyltransf_29: Putative S-adenosyl-L-methionine-dependent methyltransferase; InterPro: IPR004159 Members of this family of hypothetical plant proteins are putative methyltransferases. ; GO: 0008168 methyltransferase activity
Probab=84.34 E-value=0.84 Score=41.70 Aligned_cols=23 Identities=22% Similarity=0.115 Sum_probs=20.1
Q ss_pred CCCCeEEEecCCccHHHHHHHhh
Q 036971 195 QNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
...++++|||||.|.++..++++
T Consensus 116 g~iR~~LDvGcG~aSF~a~l~~r 138 (506)
T PF03141_consen 116 GGIRTALDVGCGVASFGAYLLER 138 (506)
T ss_pred CceEEEEeccceeehhHHHHhhC
Confidence 45789999999999999988765
No 197
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=84.12 E-value=1.7 Score=36.20 Aligned_cols=45 Identities=11% Similarity=0.137 Sum_probs=40.1
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..|.+.|.+. +.+++.|||+.+++ .+. -++|-|+.|...|++.+.
T Consensus 8 ~~Il~~l~~~---~~~~~~ela~~l~v-S~~----TirRdL~~Le~~g~i~r~ 52 (251)
T PRK13509 8 QILLELLAQL---GFVTVEKVIERLGI-SPA----TARRDINKLDESGKLKKV 52 (251)
T ss_pred HHHHHHHHHc---CCcCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEEe
Confidence 3477888887 58999999999999 777 899999999999999987
No 198
>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=84.11 E-value=1 Score=26.81 Aligned_cols=29 Identities=14% Similarity=0.315 Sum_probs=22.5
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCc
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPE 71 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~ 71 (221)
++..|.+.|.+. +..+..+||+.+|+ .+.
T Consensus 4 ~D~~Il~~Lq~d---~r~s~~~la~~lgl-S~~ 32 (42)
T PF13404_consen 4 LDRKILRLLQED---GRRSYAELAEELGL-SES 32 (42)
T ss_dssp HHHHHHHHHHH----TTS-HHHHHHHHTS--HH
T ss_pred HHHHHHHHHHHc---CCccHHHHHHHHCc-CHH
Confidence 567788899997 59999999999999 665
No 199
>PLN03075 nicotianamine synthase; Provisional
Probab=83.87 E-value=1.5 Score=37.54 Aligned_cols=25 Identities=20% Similarity=0.202 Sum_probs=17.7
Q ss_pred CCCeEEEecCCccHH--HHHHHhhCCC
Q 036971 196 NITRLVDVGGGLGIT--LSDHNFQIPS 220 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~--~~~l~~~~P~ 220 (221)
..++|+|||||.|-+ +...++.+|+
T Consensus 123 ~p~~VldIGcGpgpltaiilaa~~~p~ 149 (296)
T PLN03075 123 VPTKVAFVGSGPLPLTSIVLAKHHLPT 149 (296)
T ss_pred CCCEEEEECCCCcHHHHHHHHHhcCCC
Confidence 578999999998844 3334445664
No 200
>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=83.51 E-value=1.2 Score=28.78 Aligned_cols=35 Identities=17% Similarity=0.157 Sum_probs=30.5
Q ss_pred CCC-CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AEL-SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~-t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..+ +..+||+..++ +.. .+++.|+.|...|++...
T Consensus 22 ~~lps~~~la~~~~v-sr~----tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 22 DRLPSERELAERYGV-SRT----TVREALRRLEAEGLIERR 57 (64)
T ss_dssp SBE--HHHHHHHHTS--HH----HHHHHHHHHHHTTSEEEE
T ss_pred CEeCCHHHHHHHhcc-CCc----HHHHHHHHHHHCCcEEEE
Confidence 467 99999999999 777 899999999999999986
No 201
>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=83.48 E-value=1.2 Score=40.00 Aligned_cols=25 Identities=24% Similarity=0.117 Sum_probs=21.1
Q ss_pred CCCCCeEEEecCCccHHHHHHHhhC
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
..+..+|+|+|||.|.++..+++..
T Consensus 290 ~~~~~~vLDl~cG~G~~sl~la~~~ 314 (431)
T TIGR00479 290 LQGEELVVDAYCGVGTFTLPLAKQA 314 (431)
T ss_pred cCCCCEEEEcCCCcCHHHHHHHHhC
Confidence 4455799999999999999988754
No 202
>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=83.36 E-value=1.1 Score=36.02 Aligned_cols=23 Identities=26% Similarity=0.172 Sum_probs=19.3
Q ss_pred CCeEEEecCCccHHHHHHHhhCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
..+|+|||||.|.++..+++..+
T Consensus 46 ~~~vLdlG~G~G~~~~~l~~~~~ 68 (224)
T TIGR01983 46 GLRVLDVGCGGGLLSEPLARLGA 68 (224)
T ss_pred CCeEEEECCCCCHHHHHHHhcCC
Confidence 56899999999999988876543
No 203
>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=83.31 E-value=1.3 Score=32.37 Aligned_cols=68 Identities=22% Similarity=0.302 Sum_probs=47.1
Q ss_pred HHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 37 AVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 37 ~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
+..+.-|++.|.+.+ ++.|+++|-+.+.-..+..+..-+.|.|+.|...|++.+....++...|....
T Consensus 7 T~~R~~Il~~l~~~~--~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~~ 74 (120)
T PF01475_consen 7 TPQRLAILELLKESP--EHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHHHHS--SSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS
T ss_pred CHHHHHHHHHHHcCC--CCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEeecC
Confidence 345666888999876 69999999998853123323335899999999999999974321233565554
No 204
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=83.27 E-value=3.6 Score=30.38 Aligned_cols=77 Identities=14% Similarity=0.094 Sum_probs=56.1
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCC-CCCCcchhhhHHHHHHHHhcCCceeeeccC
Q 036971 18 VYSHAMVLGSAIVLPAVFQAVVNLDVLDIINKAGPGAELSASEIASQIP-TKNPEGAAKMLDRVLGLLVSFNILCCSFST 96 (221)
Q Consensus 18 ~~~~l~~~~~g~~~~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g-~~~~~~~~~~l~rlLr~L~~~gll~~~~~~ 96 (221)
+....++++.+=|..-.|+... . |+.-..||-..++ + .++ .|.+-|+.|...|++.+..-.
T Consensus 12 ~~~~~l~~ig~kW~~lIl~~L~---------~----g~~RF~eL~r~i~~I-s~k----~Ls~~Lk~Le~~Glv~R~~~~ 73 (120)
T COG1733 12 PVEEALEVIGGKWTLLILRDLF---------D----GPKRFNELRRSIGGI-SPK----MLSRRLKELEEDGLVERVVYP 73 (120)
T ss_pred CHHHHHHHHcCccHHHHHHHHh---------c----CCCcHHHHHHHcccc-CHH----HHHHHHHHHHHCCCEEeeecC
Confidence 3555666666666666665533 3 4899999999998 8 887 999999999999999987210
Q ss_pred --CCCcceeccccccccc
Q 036971 97 --HGVRLYSLAPVAKYYV 112 (221)
Q Consensus 97 --~~~~~y~lt~~s~~L~ 112 (221)
...-.|++|+.++.|.
T Consensus 74 ~~PprveY~LT~~G~~L~ 91 (120)
T COG1733 74 EEPPRVEYRLTEKGRDLL 91 (120)
T ss_pred CCCceeEEEEhhhHHHHH
Confidence 0123588888877665
No 205
>PRK01581 speE spermidine synthase; Validated
Probab=83.12 E-value=1.1 Score=39.66 Aligned_cols=24 Identities=25% Similarity=0.331 Sum_probs=20.4
Q ss_pred CCCCeEEEecCCccHHHHHHHhhC
Q 036971 195 QNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
.+.++|++||||.|..+.++++..
T Consensus 149 ~~PkrVLIIGgGdG~tlrelLk~~ 172 (374)
T PRK01581 149 IDPKRVLILGGGDGLALREVLKYE 172 (374)
T ss_pred CCCCEEEEECCCHHHHHHHHHhcC
Confidence 357899999999999999988743
No 206
>PLN02672 methionine S-methyltransferase
Probab=82.71 E-value=1 Score=45.19 Aligned_cols=23 Identities=13% Similarity=0.088 Sum_probs=21.4
Q ss_pred CeEEEecCCccHHHHHHHhhCCC
Q 036971 198 TRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 198 ~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
.+|+|||||+|..+..+++.+|+
T Consensus 120 ~~VLDlG~GSG~Iai~La~~~~~ 142 (1082)
T PLN02672 120 KTVAELGCGNGWISIAIAEKWLP 142 (1082)
T ss_pred CEEEEEecchHHHHHHHHHHCCC
Confidence 58999999999999999999884
No 207
>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=82.64 E-value=2.2 Score=28.92 Aligned_cols=40 Identities=13% Similarity=0.182 Sum_probs=24.3
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
|+..|+.. .|+|+.+||.++|. +. .++-.+|..+-=.+.+
T Consensus 29 LLr~LA~G---~PVt~~~LA~a~g~-~~-------e~v~~~L~~~p~tEyD 68 (77)
T PF12324_consen 29 LLRLLAKG---QPVTVEQLAAALGW-PV-------EEVRAALAAMPDTEYD 68 (77)
T ss_dssp HHHHHTTT---S-B-HHHHHHHHT---H-------HHHHHHHHH-TTSEEE
T ss_pred HHHHHHcC---CCcCHHHHHHHHCC-CH-------HHHHHHHHhCCCceEc
Confidence 56688884 79999999999999 44 4444455444445555
No 208
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=82.44 E-value=1.2 Score=36.79 Aligned_cols=85 Identities=15% Similarity=0.236 Sum_probs=59.0
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc-ccccCCCCCChHHHHHHh-cCcc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK-YYVSDQNGVSMRPYMNLS-LDKV 131 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~-~L~~~~~~~~~~~~~~~~-~~~~ 131 (221)
+.+...|||+.+|+ -+. .+...++-|+..|++++. +.+.|..|.-+. +|...- ..++.+.... ..-.
T Consensus 24 p~v~q~eIA~~lgi-T~Q----aVsehiK~Lv~eG~i~~~----gR~~Y~iTkkG~e~l~~~~--~dlr~f~~ev~~~l~ 92 (260)
T COG1497 24 PRVKQKEIAKKLGI-TLQ----AVSEHIKELVKEGLIEKE----GRGEYEITKKGAEWLLEQL--SDLRRFSEEVELVLD 92 (260)
T ss_pred CCCCHHHHHHHcCC-CHH----HHHHHHHHHHhccceeec----CCeeEEEehhHHHHHHHHH--HHHHHHHHHHHHHHh
Confidence 47999999999999 887 999999999999999996 678999999876 444322 1355454433 1111
Q ss_pred chhhhhhhHH-HHhcCCch
Q 036971 132 MMPGWFQLKD-QILEGELS 149 (221)
Q Consensus 132 ~~~~~~~L~~-~l~~g~~~ 149 (221)
+...|..+++ -++.|+..
T Consensus 93 ~~~vw~AIA~edI~~Gd~V 111 (260)
T COG1497 93 YVMVWTAIAKEDIKEGDTV 111 (260)
T ss_pred hHHHHHHhhHhhhccCCEE
Confidence 2345666654 35656543
No 209
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=82.26 E-value=2.7 Score=28.09 Aligned_cols=44 Identities=18% Similarity=0.128 Sum_probs=38.2
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..|...++. +..|.++|-+.+|+ +.. .|-..|--|...|++.+.
T Consensus 8 ~~IL~~ls~----~c~TLeeL~ekTgi-~k~----~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 8 QKILIILSK----RCCTLEELEEKTGI-SKN----TLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHHHh----ccCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCeeee
Confidence 345566777 59999999999999 887 899999999999999985
No 210
>COG2263 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=82.18 E-value=1.1 Score=35.86 Aligned_cols=20 Identities=25% Similarity=0.421 Sum_probs=16.9
Q ss_pred CCeEEEecCCccHHHHHHHh
Q 036971 197 ITRLVDVGGGLGITLSDHNF 216 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~ 216 (221)
.++|+|+|||+|.++...+-
T Consensus 46 g~~V~DlG~GTG~La~ga~~ 65 (198)
T COG2263 46 GKTVLDLGAGTGILAIGAAL 65 (198)
T ss_pred CCEEEEcCCCcCHHHHHHHh
Confidence 37899999999999887653
No 211
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=82.10 E-value=10 Score=29.52 Aligned_cols=78 Identities=13% Similarity=0.103 Sum_probs=58.2
Q ss_pred HHhhhHHHHHHHHHHhhC-------hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCC
Q 036971 25 LGSAIVLPAVFQAVVNLD-------VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTH 97 (221)
Q Consensus 25 ~~~g~~~~~aL~~av~lg-------lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~ 97 (221)
.+++.|...|+.+|...+ |..++.-.+ .+.++.+|+..++.+| +..+..-||-|...|++..... +
T Consensus 63 ~Af~rW~vrCmAaag~~~ls~~e~l~lH~irhrd--R~K~laDic~~ln~eD----th~itYslrKL~k~gLit~t~~-g 135 (199)
T COG5631 63 EAFGRWQVRCMAAAGEFSLSGPENLLLHIIRHRD--RPKSLADICQMLNRED----THNITYSLRKLLKGGLITRTGS-G 135 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcchHHHHHHHHhhcC--chhhHHHHHHHhcccc----chhHHHHHHHHHhccceecCCC-C
Confidence 345778888888887766 355666665 7999999999998833 3488999999999999998631 1
Q ss_pred CCcceecccccc
Q 036971 98 GVRLYSLAPVAK 109 (221)
Q Consensus 98 ~~~~y~lt~~s~ 109 (221)
..-+|.-|+.+.
T Consensus 136 kevTy~vTa~G~ 147 (199)
T COG5631 136 KEVTYEVTALGH 147 (199)
T ss_pred ceEEEEEecchH
Confidence 234688777764
No 212
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=81.99 E-value=1.8 Score=39.81 Aligned_cols=69 Identities=10% Similarity=0.144 Sum_probs=54.8
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccccc-ccCCC
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYY-VSDQN 116 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L-~~~~~ 116 (221)
.+..|...|.+.+ +..+.++||+.+|+ ++. .+.+.+..|.+.|+++-... ....|.+|+-++.+ ..+.|
T Consensus 7 ~e~~iL~~l~~~~--~~~~~~~la~~~~~-~~~----~v~~~~~~L~~kg~v~~~~~--~~~~~~LT~eG~~~~~~G~P 76 (494)
T PTZ00326 7 EENTILSKLESEN--EIVNSLALAESLNI-DHQ----KVVGAIKSLESANYITTEMK--KSNTWTLTEEGEDYLKNGSP 76 (494)
T ss_pred HHHHHHHHHHhcC--CCCCHHHHHHHcCC-CHH----HHHHHHHHHHhCCCEEEEEE--EEEEEEECHHHHHHHHcCCH
Confidence 4556677777632 47999999999999 887 99999999999999987632 36789999999854 45565
No 213
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=81.91 E-value=1.6 Score=28.86 Aligned_cols=34 Identities=26% Similarity=0.322 Sum_probs=31.9
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++|-++||..+|+ ... .+.|+|+.|...|+++..
T Consensus 28 ~lt~~~iA~~~g~-sr~----tv~r~l~~l~~~g~I~~~ 61 (76)
T PF13545_consen 28 PLTQEEIADMLGV-SRE----TVSRILKRLKDEGIIEVK 61 (76)
T ss_dssp ESSHHHHHHHHTS-CHH----HHHHHHHHHHHTTSEEEE
T ss_pred cCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEc
Confidence 6899999999999 887 899999999999999985
No 214
>TIGR01177 conserved hypothetical protein TIGR01177. This family is found exclusively in the Archaea.
Probab=81.89 E-value=2.3 Score=36.86 Aligned_cols=30 Identities=20% Similarity=0.191 Sum_probs=22.6
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHh
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNF 216 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~ 216 (221)
.++.... +....+|+|+|||+|.++.+.+.
T Consensus 173 ~~~~l~~-~~~g~~vLDp~cGtG~~lieaa~ 202 (329)
T TIGR01177 173 AMVNLAR-VTEGDRVLDPFCGTGGFLIEAGL 202 (329)
T ss_pred HHHHHhC-CCCcCEEEECCCCCCHHHHHHHH
Confidence 3444445 66678999999999999887654
No 215
>PRK11727 23S rRNA mA1618 methyltransferase; Provisional
Probab=81.70 E-value=1.6 Score=37.97 Aligned_cols=25 Identities=16% Similarity=0.147 Sum_probs=20.0
Q ss_pred CCCeEEEecCCccHHHHHHHhhCCC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
...++||||+|.|....-++.+.|+
T Consensus 114 ~~~~vLDIGtGag~I~~lLa~~~~~ 138 (321)
T PRK11727 114 ANVRVLDIGVGANCIYPLIGVHEYG 138 (321)
T ss_pred CCceEEEecCCccHHHHHHHhhCCC
Confidence 4579999999999887777776664
No 216
>PTZ00146 fibrillarin; Provisional
Probab=81.70 E-value=1.4 Score=37.72 Aligned_cols=25 Identities=16% Similarity=0.244 Sum_probs=21.4
Q ss_pred CCCCCeEEEecCCccHHHHHHHhhC
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
+....+|||+|||+|.++..++...
T Consensus 130 IkpG~~VLDLGaG~G~~t~~lAdiV 154 (293)
T PTZ00146 130 IKPGSKVLYLGAASGTTVSHVSDLV 154 (293)
T ss_pred cCCCCEEEEeCCcCCHHHHHHHHHh
Confidence 5566799999999999999988764
No 217
>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=81.41 E-value=1.9 Score=33.79 Aligned_cols=45 Identities=20% Similarity=0.174 Sum_probs=39.4
Q ss_pred CCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc
Q 036971 56 LSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK 109 (221)
Q Consensus 56 ~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~ 109 (221)
+|.++||+.+++ ... -+.|.+..|...+++.+. ..|.|..+|--.
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-SKP----TVSRAIKELEEKNIIKKI----RNGAYMINPNFF 120 (165)
T ss_pred eeHHHHHHHhCC-CHH----HHHHHHHHHHhCCcEEEc----cCCeEEECcHHh
Confidence 789999999999 776 899999999999999997 578888888543
No 218
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=80.86 E-value=2.7 Score=36.28 Aligned_cols=56 Identities=14% Similarity=0.186 Sum_probs=42.8
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccc
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPV 107 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~ 107 (221)
..|.+.|.+. ...+..+||+++++ ... .+.+.++.|...|++.... .+..|.+.+-
T Consensus 7 ~~il~~L~~~---~~~s~~~LA~~lgv-sr~----tV~~~l~~L~~~G~~i~~~---~~~Gy~L~~~ 62 (319)
T PRK11886 7 LQLLSLLADG---DFHSGEQLGEELGI-SRA----AIWKHIQTLEEWGLDIFSV---KGKGYRLAEP 62 (319)
T ss_pred HHHHHHHHcC---CCcCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCceEEe---cCCeEEecCc
Confidence 4566777764 58999999999999 887 9999999999999955431 2345776544
No 219
>KOG1540 consensus Ubiquinone biosynthesis methyltransferase COQ5 [Coenzyme transport and metabolism]
Probab=80.76 E-value=4 Score=34.39 Aligned_cols=23 Identities=22% Similarity=0.218 Sum_probs=20.1
Q ss_pred CCeEEEecCCccHHHHHHHhhCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
.-++|||+||+|-.+..|++.-+
T Consensus 101 ~m~~lDvaGGTGDiaFril~~v~ 123 (296)
T KOG1540|consen 101 GMKVLDVAGGTGDIAFRILRHVK 123 (296)
T ss_pred CCeEEEecCCcchhHHHHHHhhc
Confidence 47999999999999999988654
No 220
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=80.48 E-value=0.92 Score=26.59 Aligned_cols=28 Identities=21% Similarity=0.321 Sum_probs=21.1
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVS 86 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~ 86 (221)
.+.++++||..+|+ ++. .+.|+.+....
T Consensus 7 ~~~~l~~iA~~~g~-S~~----~f~r~Fk~~~g 34 (42)
T PF00165_consen 7 QKLTLEDIAEQAGF-SPS----YFSRLFKKETG 34 (42)
T ss_dssp SS--HHHHHHHHTS--HH----HHHHHHHHHTS
T ss_pred CCCCHHHHHHHHCC-CHH----HHHHHHHHHHC
Confidence 37999999999999 887 99998876544
No 221
>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=80.23 E-value=1.7 Score=36.60 Aligned_cols=24 Identities=25% Similarity=0.289 Sum_probs=20.1
Q ss_pred CCCCeEEEecCCccHHHHHHHhhC
Q 036971 195 QNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
++.++|++||||.|..+.++++..
T Consensus 71 ~~p~~VL~iG~G~G~~~~~ll~~~ 94 (270)
T TIGR00417 71 PNPKHVLVIGGGDGGVLREVLKHK 94 (270)
T ss_pred CCCCEEEEEcCCchHHHHHHHhCC
Confidence 345799999999999999887654
No 222
>PRK14902 16S rRNA methyltransferase B; Provisional
Probab=80.23 E-value=2.1 Score=38.72 Aligned_cols=31 Identities=6% Similarity=0.007 Sum_probs=24.1
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
+...++ .....+|+|+|||+|..+..+++..
T Consensus 242 v~~~l~-~~~g~~VLDlgaG~G~~t~~la~~~ 272 (444)
T PRK14902 242 VAPALD-PKGGDTVLDACAAPGGKTTHIAELL 272 (444)
T ss_pred HHHHhC-CCCCCEEEEeCCCCCHHHHHHHHHh
Confidence 334444 4556799999999999999998875
No 223
>PRK03612 spermidine synthase; Provisional
Probab=80.16 E-value=1.7 Score=40.23 Aligned_cols=24 Identities=29% Similarity=0.492 Sum_probs=20.6
Q ss_pred CCCCeEEEecCCccHHHHHHHhhCC
Q 036971 195 QNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
++.++|+|||||.|..+.++++ +|
T Consensus 296 ~~~~rVL~IG~G~G~~~~~ll~-~~ 319 (521)
T PRK03612 296 ARPRRVLVLGGGDGLALREVLK-YP 319 (521)
T ss_pred CCCCeEEEEcCCccHHHHHHHh-CC
Confidence 3568999999999999999986 44
No 224
>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=80.08 E-value=1.8 Score=38.28 Aligned_cols=21 Identities=19% Similarity=0.031 Sum_probs=18.3
Q ss_pred CCeEEEecCCccHHHHHHHhh
Q 036971 197 ITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~ 217 (221)
..+|+|++||.|.++..++..
T Consensus 234 ~~~vLDL~cG~G~~~l~la~~ 254 (374)
T TIGR02085 234 VTQMWDLFCGVGGFGLHCAGP 254 (374)
T ss_pred CCEEEEccCCccHHHHHHhhc
Confidence 368999999999999988754
No 225
>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed
Probab=80.03 E-value=1.8 Score=37.23 Aligned_cols=22 Identities=14% Similarity=-0.145 Sum_probs=19.2
Q ss_pred CCeEEEecCCccHHHHHHHhhC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
..+|+|+|||.|.++..+++..
T Consensus 174 ~~~VLDl~cG~G~~sl~la~~~ 195 (315)
T PRK03522 174 PRSMWDLFCGVGGFGLHCATPG 195 (315)
T ss_pred CCEEEEccCCCCHHHHHHHhcC
Confidence 4799999999999999988743
No 226
>PRK11642 exoribonuclease R; Provisional
Probab=80.01 E-value=3.9 Score=40.06 Aligned_cols=58 Identities=21% Similarity=0.216 Sum_probs=44.2
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
.|.+.|...+ .+++..+|++.+++ +.......|.+.|+.|...|.+.+. ..+.|.+..
T Consensus 23 ~Il~~l~~~~--~~~~~~~L~~~l~l-~~~~~~~~l~~~L~~L~~~g~l~~~----~~~~~~~~~ 80 (813)
T PRK11642 23 FILEHLTKRE--KPASREELAVELNI-EGEEQLEALRRRLRAMERDGQLVFT----RRQCYALPE 80 (813)
T ss_pred HHHHHHHhcC--CCCCHHHHHHHhCC-CChHHHHHHHHHHHHHHHCCCEEEc----CCceEecCC
Confidence 3666776644 69999999999999 6532334699999999999999986 466676553
No 227
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=79.93 E-value=11 Score=31.43 Aligned_cols=66 Identities=17% Similarity=0.177 Sum_probs=47.1
Q ss_pred HHHHHHHHhhhHHHHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 19 YSHAMVLGSAIVLPAVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 19 ~~~l~~~~~g~~~~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
-..+.+++.+.....=|.+. -.|++.|.... +-++..+||+++|+ .+. .+++-++.|.+.|+++-.
T Consensus 166 kka~Vq~Ai~tLSySEleAv--~~IL~~L~~~e--grlse~eLAerlGV-SRs----~ireAlrkLE~aGvIe~r 231 (251)
T TIGR02787 166 KKAAVQMAINTLSYSELEAV--EHIFEELDGNE--GLLVASKIADRVGI-TRS----VIVNALRKLESAGVIESR 231 (251)
T ss_pred HHHHHHHHHHhccHhHHHHH--HHHHHHhcccc--ccccHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEec
Confidence 33444454444333323322 24777887732 58999999999999 887 899999999999999986
No 228
>PLN02781 Probable caffeoyl-CoA O-methyltransferase
Probab=79.65 E-value=3.1 Score=34.28 Aligned_cols=24 Identities=21% Similarity=0.382 Sum_probs=21.0
Q ss_pred CCCeEEEecCCccHHHHHHHhhCC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
+.++|+|||+|.|.-+..+++..|
T Consensus 68 ~~~~vLEiGt~~G~s~l~la~~~~ 91 (234)
T PLN02781 68 NAKNTLEIGVFTGYSLLTTALALP 91 (234)
T ss_pred CCCEEEEecCcccHHHHHHHHhCC
Confidence 478999999999999888888765
No 229
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=79.58 E-value=4.3 Score=29.83 Aligned_cols=56 Identities=7% Similarity=0.160 Sum_probs=41.8
Q ss_pred HHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc
Q 036971 33 AVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK 109 (221)
Q Consensus 33 ~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~ 109 (221)
.||++|. +|.+. ||.+..+|++.++. +. ..++|+ ---.|.|++. +.|.|.+|+.++
T Consensus 60 ~Al~~A~------~L~~~---Gp~~~~~l~~~~~~-~~------A~~IL~-~N~YGWFeRv----~rGvY~LT~~G~ 115 (118)
T PF09929_consen 60 DALRCAA------ALAEH---GPSRPADLRKATGV-PK------ATSILR-DNHYGWFERV----ERGVYALTPAGR 115 (118)
T ss_pred HHHHHHH------HHHHc---CCCCHHHHHHhcCC-Ch------HHHHHH-hCcccceeee----ccceEecCcchh
Confidence 4555554 67876 59999999999988 42 344443 2457899998 799999999875
No 230
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=79.24 E-value=3.6 Score=34.13 Aligned_cols=45 Identities=18% Similarity=0.271 Sum_probs=39.5
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..|.+.|.+. +.++++|||+.+++ .+. -++|-|..|...|++.+.
T Consensus 7 ~~Il~~l~~~---~~~~~~eLa~~l~V-S~~----TiRRdL~~L~~~~~l~r~ 51 (240)
T PRK10411 7 QAIVDLLLNH---TSLTTEALAEQLNV-SKE----TIRRDLNELQTQGKILRN 51 (240)
T ss_pred HHHHHHHHHc---CCCcHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEEe
Confidence 3477788886 59999999999999 887 899999999999999886
No 231
>COG2518 Pcm Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=79.02 E-value=3.5 Score=33.51 Aligned_cols=30 Identities=13% Similarity=0.307 Sum_probs=23.9
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHh
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNF 216 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~ 216 (221)
.++.... .+...+|++||+|+|-.+.-+++
T Consensus 63 ~m~~~L~-~~~g~~VLEIGtGsGY~aAvla~ 92 (209)
T COG2518 63 RMLQLLE-LKPGDRVLEIGTGSGYQAAVLAR 92 (209)
T ss_pred HHHHHhC-CCCCCeEEEECCCchHHHHHHHH
Confidence 4566666 77789999999999998876654
No 232
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=79.00 E-value=1.9 Score=35.02 Aligned_cols=37 Identities=11% Similarity=0.146 Sum_probs=30.8
Q ss_pred hhHHHHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCc
Q 036971 28 AIVLPAVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPE 71 (221)
Q Consensus 28 g~~~~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~ 71 (221)
-..+-.+|+.|.++|-||.=. .+++.|||+.+|+ .+.
T Consensus 157 TdrQ~~vL~~A~~~GYFd~PR------~~~l~dLA~~lGI-Sks 193 (215)
T COG3413 157 TDRQLEVLRLAYKMGYFDYPR------RVSLKDLAKELGI-SKS 193 (215)
T ss_pred CHHHHHHHHHHHHcCCCCCCc------cCCHHHHHHHhCC-CHH
Confidence 345678999999999999643 5999999999999 554
No 233
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=78.99 E-value=2.7 Score=35.44 Aligned_cols=46 Identities=7% Similarity=0.156 Sum_probs=40.8
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
...|.+.|.+. +.+++.|||+.+++ .+. -++|=|..|...|++.+.
T Consensus 19 ~~~Il~~L~~~---~~vtv~eLa~~l~V-S~~----TIRRDL~~Le~~G~l~r~ 64 (269)
T PRK09802 19 REQIIQRLRQQ---GSVQVNDLSALYGV-STV----TIRNDLAFLEKQGIAVRA 64 (269)
T ss_pred HHHHHHHHHHc---CCEeHHHHHHHHCC-CHH----HHHHHHHHHHhCCCeEEE
Confidence 34577889887 48999999999999 777 899999999999999997
No 234
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=78.73 E-value=2.7 Score=35.06 Aligned_cols=45 Identities=16% Similarity=0.304 Sum_probs=40.1
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..|.+.|.+. +.+++.|||+.+++ .+. -++|-|..|...|++.+.
T Consensus 8 ~~Il~~l~~~---~~~~~~ela~~l~v-S~~----TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 8 DAIIELVKQQ---GYVSTEELVEHFSV-SPQ----TIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHc---CCEeHHHHHHHhCC-CHH----HHHHHHHHHHHCCCEEEe
Confidence 4577888886 58999999999999 776 899999999999999987
No 235
>PRK09462 fur ferric uptake regulator; Provisional
Probab=78.20 E-value=4.9 Score=30.56 Aligned_cols=55 Identities=16% Similarity=0.242 Sum_probs=40.0
Q ss_pred HHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 38 VVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 38 av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
--+.-|++.|..... ++.|++||-+.+.-..+..+..-+.|.|+.|+..|++.+.
T Consensus 17 ~qR~~Il~~l~~~~~-~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~ 71 (148)
T PRK09462 17 LPRLKILEVLQEPDN-HHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRH 71 (148)
T ss_pred HHHHHHHHHHHhCCC-CCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEE
Confidence 345667888876411 5999999998884312322334789999999999999986
No 236
>PRK10909 rsmD 16S rRNA m(2)G966-methyltransferase; Provisional
Probab=78.18 E-value=3.8 Score=33.02 Aligned_cols=21 Identities=19% Similarity=0.033 Sum_probs=17.3
Q ss_pred CCeEEEecCCccHHHHHHHhh
Q 036971 197 ITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~ 217 (221)
..+++|+|||+|.++.+.+.+
T Consensus 54 ~~~vLDl~~GsG~l~l~~lsr 74 (199)
T PRK10909 54 DARCLDCFAGSGALGLEALSR 74 (199)
T ss_pred CCEEEEcCCCccHHHHHHHHc
Confidence 468999999999999875443
No 237
>PF13730 HTH_36: Helix-turn-helix domain
Probab=78.08 E-value=1.8 Score=26.73 Aligned_cols=30 Identities=13% Similarity=0.206 Sum_probs=27.1
Q ss_pred CCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCce
Q 036971 56 LSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNIL 90 (221)
Q Consensus 56 ~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll 90 (221)
-|.+.||+.+|+ ..+ -+.+.+..|...|++
T Consensus 26 pS~~~la~~~g~-s~~----Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 26 PSQETLAKDLGV-SRR----TVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHHCc-CHH----HHHHHHHHHHHCcCC
Confidence 389999999999 877 899999999999875
No 238
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=77.94 E-value=3.1 Score=28.87 Aligned_cols=35 Identities=17% Similarity=0.128 Sum_probs=32.0
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.-+|+..||+++++ +-. ..+++||.|...|++...
T Consensus 40 K~ITps~lserlkI-~~S----lAr~~Lr~L~~kG~Ik~V 74 (86)
T PRK09334 40 KIVTPYTLASKYGI-KIS----VAKKVLRELEKRGVLVLY 74 (86)
T ss_pred cEEcHHHHHHHhcc-hHH----HHHHHHHHHHHCCCEEEE
Confidence 45999999999999 776 899999999999999886
No 239
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=77.36 E-value=4.6 Score=31.60 Aligned_cols=55 Identities=16% Similarity=0.275 Sum_probs=40.7
Q ss_pred HHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 37 AVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 37 ~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+--+.-|++.|...+ ++.|+++|.+.+.-..+..+..-+.|.|+.|+..|++.+.
T Consensus 25 T~qR~~IL~~l~~~~--~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~ 79 (169)
T PRK11639 25 TPQRLEVLRLMSLQP--GAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKV 79 (169)
T ss_pred CHHHHHHHHHHHhcC--CCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEE
Confidence 344566778888764 6999999998885312222223689999999999999997
No 240
>PRK00215 LexA repressor; Validated
Probab=77.01 E-value=5.5 Score=31.88 Aligned_cols=36 Identities=19% Similarity=0.173 Sum_probs=31.3
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.+.|..|||+++|+++.. .+.|+|..|...|++++.
T Consensus 22 ~~~s~~ela~~~~~~~~~----tv~~~l~~L~~~g~i~~~ 57 (205)
T PRK00215 22 YPPSRREIADALGLRSPS----AVHEHLKALERKGFIRRD 57 (205)
T ss_pred CCCCHHHHHHHhCCCChH----HHHHHHHHHHHCCCEEeC
Confidence 578999999999982233 899999999999999986
No 241
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=76.80 E-value=5.1 Score=33.68 Aligned_cols=49 Identities=16% Similarity=0.129 Sum_probs=42.6
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK 109 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~ 109 (221)
+++--+|||..++. ||- -++-.|..|-++||++-.. |..|.|..|..+.
T Consensus 24 r~IKgeeIA~~l~r-npG----TVRNqmq~LkaLgLVegvp--GPkGGY~PT~kAY 72 (294)
T COG2524 24 RPIKGEEIAEVLNR-NPG----TVRNQMQSLKALGLVEGVP--GPKGGYKPTSKAY 72 (294)
T ss_pred CCcchHHHHHHHcc-Ccc----hHHHHHHHHHhcCcccccc--CCCCCccccHHHH
Confidence 69999999999999 998 9999999999999999864 3567888886543
No 242
>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=76.48 E-value=2.8 Score=37.73 Aligned_cols=32 Identities=16% Similarity=0.045 Sum_probs=24.7
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
++..++ .....+|+|+|||.|..+..+++..|
T Consensus 230 ~~~~L~-~~~g~~VLDlcag~G~kt~~la~~~~ 261 (426)
T TIGR00563 230 VATWLA-PQNEETILDACAAPGGKTTHILELAP 261 (426)
T ss_pred HHHHhC-CCCCCeEEEeCCCccHHHHHHHHHcC
Confidence 344455 44557999999999999999988765
No 243
>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=76.04 E-value=2.8 Score=25.06 Aligned_cols=22 Identities=32% Similarity=0.348 Sum_probs=15.3
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHH
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVL 81 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlL 81 (221)
+.|+.+||+.+|+ ... -+.|+|
T Consensus 21 G~si~~IA~~~gv-sr~----TvyR~l 42 (45)
T PF02796_consen 21 GMSIAEIAKQFGV-SRS----TVYRYL 42 (45)
T ss_dssp T--HHHHHHHTTS--HH----HHHHHH
T ss_pred CCCHHHHHHHHCc-CHH----HHHHHH
Confidence 4999999999999 655 666665
No 244
>COG3963 Phospholipid N-methyltransferase [Lipid metabolism]
Probab=75.75 E-value=5.2 Score=31.57 Aligned_cols=37 Identities=14% Similarity=0.204 Sum_probs=30.3
Q ss_pred hHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhh
Q 036971 180 TSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 180 ~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
|...++.+....+ |++..-|+.+|.|+|.+..+|+++
T Consensus 33 Ss~lA~~M~s~I~-pesglpVlElGPGTGV~TkaIL~~ 69 (194)
T COG3963 33 SSILARKMASVID-PESGLPVLELGPGTGVITKAILSR 69 (194)
T ss_pred cHHHHHHHHhccC-cccCCeeEEEcCCccHhHHHHHhc
Confidence 3344566777888 888889999999999999998764
No 245
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=75.72 E-value=3.1 Score=31.80 Aligned_cols=43 Identities=19% Similarity=0.252 Sum_probs=35.9
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhc--CCceee
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVS--FNILCC 92 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~--~gll~~ 92 (221)
-|+++|-.. +.+|-++||+.+|+ +.+ .++++|..|.. +.+...
T Consensus 5 ~v~d~L~~~---~~~~dedLa~~l~i-~~n----~vRkiL~~L~ed~~~~~~~ 49 (147)
T smart00531 5 LVLDALMRN---GCVTEEDLAELLGI-KQK----QLRKILYLLYDEKLIKIDY 49 (147)
T ss_pred eehHHHHhc---CCcCHHHHHHHhCC-CHH----HHHHHHHHHHhhhcchhhe
Confidence 467878776 58999999999999 888 99999999999 554544
No 246
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=75.62 E-value=2.7 Score=33.06 Aligned_cols=36 Identities=22% Similarity=0.245 Sum_probs=33.1
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeec
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSF 94 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~ 94 (221)
+|+|++||++++|+ .-. .+.--++-|...|++.+..
T Consensus 40 ~Pmtl~Ei~E~lg~-Sks----~vS~~lkkL~~~~lV~~~~ 75 (177)
T COG1510 40 KPLTLDEIAEALGM-SKS----NVSMGLKKLQDWNLVKKVF 75 (177)
T ss_pred CCccHHHHHHHHCC-Ccc----hHHHHHHHHHhcchHHhhh
Confidence 69999999999999 776 8999999999999999873
No 247
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=75.54 E-value=4 Score=32.91 Aligned_cols=45 Identities=16% Similarity=0.256 Sum_probs=37.6
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.|...+.+.. .+.|.+|||+++++ .+. -+++.+..|+..|++..+
T Consensus 166 ~Vl~~~~~g~--~g~s~~eIa~~l~i-S~~----Tv~~~~~~~~~~~~~~~~ 210 (225)
T PRK10046 166 AVRKLFKEPG--VQHTAETVAQALTI-SRT----TARRYLEYCASRHLIIAE 210 (225)
T ss_pred HHHHHHHcCC--CCcCHHHHHHHhCc-cHH----HHHHHHHHHHhCCeEEEE
Confidence 4566777621 25899999999999 887 899999999999999985
No 248
>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=75.24 E-value=1.5 Score=29.11 Aligned_cols=36 Identities=19% Similarity=0.323 Sum_probs=30.9
Q ss_pred CCCCHHHHHhhC---CCC-CCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQI---PTK-NPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~---g~~-~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+.+++.++|+.+ +.+ ..+ .+..++..|.++|++++.
T Consensus 23 ~~i~l~~ia~~l~~~~~k~~~R----RlYDI~NVLealgli~K~ 62 (71)
T PF02319_consen 23 KSISLNEIADKLISENVKTQRR----RLYDIINVLEALGLIEKQ 62 (71)
T ss_dssp TEEEHHHHHHHCHHHCCHHHCH----HHHHHHHHHHHCTSEEEE
T ss_pred CcccHHHHHHHHcccccccccc----hhhHHHHHHHHhCceeec
Confidence 589999999999 662 234 899999999999999996
No 249
>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=75.14 E-value=4.2 Score=29.34 Aligned_cols=36 Identities=14% Similarity=0.122 Sum_probs=32.6
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeec
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSF 94 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~ 94 (221)
.-+|+..||+++++ +-. ..+++||.|..-|++....
T Consensus 58 K~ITp~~lserlkI-~~S----lAr~~Lr~L~~kG~Ik~V~ 93 (105)
T PF03297_consen 58 KLITPSVLSERLKI-NGS----LARKALRELESKGLIKPVS 93 (105)
T ss_dssp SCECHHHHHHHHCC-SCH----HHHHHHHHHHHCCSSEEEE
T ss_pred cEeeHHHHHHhHhh-HHH----HHHHHHHHHHHCCCEEEEe
Confidence 35999999999999 887 8999999999999999873
No 250
>COG0293 FtsJ 23S rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=75.14 E-value=6.7 Score=31.80 Aligned_cols=39 Identities=18% Similarity=0.220 Sum_probs=29.6
Q ss_pred hHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 180 TSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 180 ~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
+..-...+.+.|.-|++..+|+|+|...|.++.-..+..
T Consensus 29 Aa~KL~el~~k~~i~~~~~~ViDLGAAPGgWsQva~~~~ 67 (205)
T COG0293 29 AAYKLLELNEKFKLFKPGMVVVDLGAAPGGWSQVAAKKL 67 (205)
T ss_pred HHHHHHHHHHhcCeecCCCEEEEcCCCCCcHHHHHHHHh
Confidence 333444566777657888999999999999998777654
No 251
>PF13518 HTH_28: Helix-turn-helix domain
Probab=75.13 E-value=4.2 Score=24.53 Aligned_cols=29 Identities=21% Similarity=0.085 Sum_probs=25.8
Q ss_pred CCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCc
Q 036971 56 LSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNI 89 (221)
Q Consensus 56 ~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gl 89 (221)
.|+.++|+.+|+ ++. .+.+|++..-..|+
T Consensus 13 ~s~~~~a~~~gi-s~~----tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 13 ESVREIAREFGI-SRS----TVYRWIKRYREGGI 41 (52)
T ss_pred CCHHHHHHHHCC-CHh----HHHHHHHHHHhcCH
Confidence 499999999999 887 99999998888775
No 252
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=75.09 E-value=6.1 Score=30.10 Aligned_cols=67 Identities=24% Similarity=0.269 Sum_probs=46.7
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccc
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPV 107 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~ 107 (221)
-++.|++.|.+++ ++.|+++|=..+.-..|+....-+.|.|+.|...|++.+....++.-+|.++.-
T Consensus 22 qR~~vl~~L~~~~--~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y~~~~~ 88 (145)
T COG0735 22 QRLAVLELLLEAD--GHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRYELNSE 88 (145)
T ss_pred HHHHHHHHHHhcC--CCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEEecCCC
Confidence 4566889999876 679999998887632343334478999999999999999732111223555544
No 253
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=74.89 E-value=4.3 Score=28.81 Aligned_cols=70 Identities=16% Similarity=0.189 Sum_probs=50.1
Q ss_pred HHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCC--CcceeccccccccccC
Q 036971 37 AVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHG--VRLYSLAPVAKYYVSD 114 (221)
Q Consensus 37 ~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~--~~~y~lt~~s~~L~~~ 114 (221)
...+..+...|...+ +.+..+||+.+++ ++. .+.++++-|...|++++.....+ .-.+.+|+.++.+...
T Consensus 21 t~~q~~~L~~l~~~~---~~~~~~la~~l~i-~~~----~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~ 92 (126)
T COG1846 21 TPPQYQVLLALYEAG---GITVKELAERLGL-DRS----TVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQ 92 (126)
T ss_pred CHHHHHHHHHHHHhC---CCcHHHHHHHHCC-CHH----HHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHH
Confidence 334555666777753 4444999999999 887 99999999999999999742101 1247777777765543
No 254
>KOG2361 consensus Predicted methyltransferase [General function prediction only]
Probab=74.72 E-value=3.6 Score=34.32 Aligned_cols=23 Identities=26% Similarity=0.385 Sum_probs=21.2
Q ss_pred CeEEEecCCccHHHHHHHhhCCC
Q 036971 198 TRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 198 ~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
.+|+.||||.|...--|++..|+
T Consensus 73 ~~ilEvGCGvGNtvfPll~~~~n 95 (264)
T KOG2361|consen 73 ETILEVGCGVGNTVFPLLKTSPN 95 (264)
T ss_pred hhheeeccCCCcccchhhhcCCC
Confidence 38999999999999999999887
No 255
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=74.51 E-value=3.8 Score=34.24 Aligned_cols=45 Identities=18% Similarity=0.228 Sum_probs=40.4
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..|.+.|.+. +.+++.|||+.+++ .+. -++|=|..|...|++.+.
T Consensus 8 ~~Il~~L~~~---~~v~v~eLa~~l~V-S~~----TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 8 AAILEYLQKQ---GKTSVEELAQYFDT-TGT----TIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHc---CCEEHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEE
Confidence 4578899987 58999999999999 776 899999999999999997
No 256
>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=74.41 E-value=5.9 Score=25.42 Aligned_cols=47 Identities=13% Similarity=0.080 Sum_probs=35.7
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK 109 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~ 109 (221)
.+++.+++.++.|. +.. +.....+..+...|+++.+ ++++++|+.+.
T Consensus 19 ~Gi~~~~~~~~~g~-~~~---~~~~~~l~~l~~~Gll~~~-----~~~l~lT~~G~ 65 (66)
T PF06969_consen 19 EGIDLSEFEQRFGI-DFA---EEFQKELEELQEDGLLEID-----GGRLRLTEKGR 65 (66)
T ss_dssp SEEEHHHHHHHTT---TH---HH-HHHHHHHHHTTSEEE------SSEEEE-TTTG
T ss_pred CCcCHHHHHHHHCc-CHH---HHHHHHHHHHHHCCCEEEe-----CCEEEECcccC
Confidence 37999999999998 654 2558889999999999995 89999998764
No 257
>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=74.32 E-value=3.5 Score=36.24 Aligned_cols=22 Identities=14% Similarity=-0.003 Sum_probs=19.0
Q ss_pred CeEEEecCCccHHHHHHHhhCC
Q 036971 198 TRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 198 ~~vvDVGGG~G~~~~~l~~~~P 219 (221)
.+++|++||.|.++..+++.+.
T Consensus 199 ~~vlDl~~G~G~~sl~la~~~~ 220 (353)
T TIGR02143 199 GDLLELYCGNGNFSLALAQNFR 220 (353)
T ss_pred CcEEEEeccccHHHHHHHHhCC
Confidence 3699999999999999887653
No 258
>PRK10736 hypothetical protein; Provisional
Probab=74.15 E-value=4.1 Score=36.13 Aligned_cols=51 Identities=10% Similarity=-0.035 Sum_probs=41.8
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecc
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLA 105 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt 105 (221)
.|++.|.. .++++++|+..+|+ +.. .+..+|-.|.-.|++.+. .++.|+.-
T Consensus 312 ~v~~~l~~----~~~~iD~L~~~~~l-~~~----~v~~~L~~LEl~G~v~~~----~g~~~~~~ 362 (374)
T PRK10736 312 ELLANVGD----EVTPVDVVAERAGQ-PVP----EVVTQLLELELAGWIAAV----PGGYVRLR 362 (374)
T ss_pred HHHHhcCC----CCCCHHHHHHHHCc-CHH----HHHHHHHHHHhCCcEEEc----CCcEEEEe
Confidence 46666665 48999999999999 887 899999999999999997 45656553
No 259
>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=74.14 E-value=3.5 Score=32.78 Aligned_cols=23 Identities=22% Similarity=0.114 Sum_probs=19.9
Q ss_pred CCeEEEecCCccHHHHHHHhhCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
..+++|++||+|.++.+.+.+..
T Consensus 50 g~~vLDLfaGsG~lglea~srga 72 (189)
T TIGR00095 50 GAHLLDVFAGSGLLGEEALSRGA 72 (189)
T ss_pred CCEEEEecCCCcHHHHHHHhCCC
Confidence 47899999999999999987643
No 260
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=73.85 E-value=6.1 Score=31.98 Aligned_cols=35 Identities=20% Similarity=0.188 Sum_probs=32.4
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..++..+||+.+|+ ... .++.-|+.|...|+|+..
T Consensus 29 ~~L~e~eLae~lgV-SRt----pVREAL~~L~~eGlv~~~ 63 (224)
T PRK11534 29 EKLRMSLLTSRYAL-GVG----PLREALSQLVAERLVTVV 63 (224)
T ss_pred CcCCHHHHHHHHCC-ChH----HHHHHHHHHHHCCCEEEe
Confidence 57899999999999 777 899999999999999986
No 261
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=73.56 E-value=4.1 Score=36.76 Aligned_cols=31 Identities=10% Similarity=-0.092 Sum_probs=23.6
Q ss_pred HHhcCCCCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 188 VESYKGFQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 188 l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
...++ .....+|+|+|||.|..+..+++..+
T Consensus 245 ~~~l~-~~~g~~VLDl~ag~G~kt~~la~~~~ 275 (434)
T PRK14901 245 APLLD-PQPGEVILDACAAPGGKTTHIAELMG 275 (434)
T ss_pred HHHhC-CCCcCEEEEeCCCCchhHHHHHHHhC
Confidence 33444 44557999999999999999887653
No 262
>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=73.13 E-value=7.9 Score=28.89 Aligned_cols=47 Identities=17% Similarity=0.273 Sum_probs=37.1
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhC----CCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQI----PTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~----g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.++.|...|-.. ++.|+.+|.+.+ ++ ... -+..+|+-|...|++...
T Consensus 5 ~E~~VM~vlW~~---~~~t~~eI~~~l~~~~~~-~~t----Tv~T~L~rL~~KG~v~~~ 55 (130)
T TIGR02698 5 AEWEVMRVVWTL---GETTSRDIIRILAEKKDW-SDS----TIKTLLGRLVDKGCLTTE 55 (130)
T ss_pred HHHHHHHHHHcC---CCCCHHHHHHHHhhccCC-cHH----HHHHHHHHHHHCCceeee
Confidence 456677777776 489999977665 55 555 789999999999999976
No 263
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=73.05 E-value=5.2 Score=29.83 Aligned_cols=42 Identities=21% Similarity=0.211 Sum_probs=35.8
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceec
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSL 104 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~l 104 (221)
=-|+.+||..+++ ||. -+.|..+-|...|++.-.. +.|+|-.
T Consensus 35 LPSvRelA~~~~V-Npn----Tv~raY~eLE~eG~i~t~r---g~G~fV~ 76 (125)
T COG1725 35 LPSVRELAKDLGV-NPN----TVQRAYQELEREGIVETKR---GKGTFVT 76 (125)
T ss_pred CCcHHHHHHHhCC-CHH----HHHHHHHHHHHCCCEEEec---CeeEEEc
Confidence 4689999999999 998 8999999999999999873 3555544
No 264
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=72.97 E-value=4.8 Score=31.81 Aligned_cols=45 Identities=20% Similarity=0.270 Sum_probs=39.2
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..|++.|.+. |.+|=++||..+|+ ... -++|+|..|...|++...
T Consensus 21 ~~v~~~l~~k---ge~tDeela~~l~i-~~~----~vrriL~~L~e~~li~~~ 65 (176)
T COG1675 21 VLVVDALLEK---GELTDEELAELLGI-KKN----EVRRILYALYEDGLISYR 65 (176)
T ss_pred hHHHHHHHhc---CCcChHHHHHHhCc-cHH----HHHHHHHHHHhCCceEEE
Confidence 3467788885 37999999999999 887 899999999999999965
No 265
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=72.48 E-value=5 Score=33.53 Aligned_cols=45 Identities=18% Similarity=0.258 Sum_probs=40.7
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
-.|.++|.+. |.++++|||+.+++ .+. =++|=|+.|...|++.+.
T Consensus 8 ~~Il~~l~~~---g~v~v~eLa~~~~V-S~~----TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 8 QKILELLKEK---GKVSVEELAELFGV-SEM----TIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHHc---CcEEHHHHHHHhCC-CHH----HHHHhHHHHHHCCcEEEE
Confidence 3478899997 59999999999999 776 899999999999999997
No 266
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=72.30 E-value=2.3 Score=25.67 Aligned_cols=39 Identities=13% Similarity=0.174 Sum_probs=22.6
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCC
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFN 88 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~g 88 (221)
+..+...+.+ +.|..+||+.+|+ ++. -+.+|++.-...|
T Consensus 7 R~~ii~l~~~-----G~s~~~ia~~lgv-s~~----Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 7 RAQIIRLLRE-----GWSIREIAKRLGV-SRS----TVYRWIKRYREEG 45 (50)
T ss_dssp ---HHHHHHH-----T--HHHHHHHHTS--HH----HHHHHHT------
T ss_pred HHHHHHHHHC-----CCCHHHHHHHHCc-CHH----HHHHHHHHccccc
Confidence 4455566666 6999999999999 887 8999987765555
No 267
>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=71.99 E-value=8.2 Score=27.60 Aligned_cols=44 Identities=14% Similarity=0.087 Sum_probs=33.4
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+-..+|.+...+ +.+++.++|+.+|+ .++ .| .+.|...|++...
T Consensus 11 Ka~~~d~~~~~~--~~~ti~~~AK~L~i-~~~----~l---~~~Lr~~g~l~~~ 54 (111)
T PF03374_consen 11 KAEFYDAFVDSD--GLYTIREAAKLLGI-GRN----KL---FQWLREKGWLYRR 54 (111)
T ss_pred hhHHHHHHHcCC--CCccHHHHHHHhCC-CHH----HH---HHHHHhCCceEEC
Confidence 345677888765 78999999999999 654 44 4555569999984
No 268
>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=71.89 E-value=5.1 Score=25.37 Aligned_cols=54 Identities=17% Similarity=0.116 Sum_probs=39.9
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceeccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVA 108 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s 108 (221)
++.+|..+.+ .-++..-|+.+++ .+. .+.+-++.|. ..-||++. .+.+.+|+.+
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 QLRYFLAVAE-----TGSISAAAEELGI-SQS----AVSRQIKQLEEELGVPLFERS-----GRGLRLTEAG 59 (60)
T ss_dssp HHHHHHHHHH-----HSSHHHHHHHCTS-SHH----HHHHHHHHHHHHHTS-SEEEC-----SSSEEE-HHH
T ss_pred HHHHHHHHHH-----hCCHHHHHHHhhc-cch----HHHHHHHHHHHHhCCeEEEEC-----CCCeeEChhh
Confidence 4567888888 4599999999999 776 7877777665 47788885 5568888764
No 269
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=71.79 E-value=6.6 Score=31.30 Aligned_cols=62 Identities=18% Similarity=-0.015 Sum_probs=46.5
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCc---ceeccccccccc
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVR---LYSLAPVAKYYV 112 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~---~y~lt~~s~~L~ 112 (221)
.|.-.|... +++|..+||+.+.+ +.. .+.++++-|...|++.+.... .+. ...+|+.++.+.
T Consensus 49 ~iL~~L~~~---~~itq~eLa~~l~l-~~s----Tvtr~l~rLE~kGlI~R~~~~-~DrR~~~I~LTekG~~l~ 113 (185)
T PRK13777 49 HILWIAYHL---KGASISEIAKFGVM-HVS----TAFNFSKKLEERGYLTFSKKE-DDKRNTYIELTEKGEELL 113 (185)
T ss_pred HHHHHHHhC---CCcCHHHHHHHHCC-CHh----hHHHHHHHHHHCCCEEecCCC-CCCCeeEEEECHHHHHHH
Confidence 456667765 48999999999999 876 899999999999999986321 122 356666666554
No 270
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=71.67 E-value=5.4 Score=33.41 Aligned_cols=25 Identities=12% Similarity=0.150 Sum_probs=20.7
Q ss_pred CCCCeEEEecCCccHHHHHHHhhCC
Q 036971 195 QNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
....+|+|+|+|.|..+..+++..+
T Consensus 70 ~~g~~VLDl~ag~G~kt~~la~~~~ 94 (264)
T TIGR00446 70 DPPERVLDMAAAPGGKTTQISALMK 94 (264)
T ss_pred CCcCEEEEECCCchHHHHHHHHHcC
Confidence 3457899999999999998887653
No 271
>PRK14904 16S rRNA methyltransferase B; Provisional
Probab=71.65 E-value=4.9 Score=36.41 Aligned_cols=25 Identities=12% Similarity=-0.076 Sum_probs=19.8
Q ss_pred CCCCCeEEEecCCccHHHHHHHhhC
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
.....+|+|+|||.|..+..+++..
T Consensus 248 ~~~g~~VLDlgaG~G~kt~~la~~~ 272 (445)
T PRK14904 248 PQPGSTVLDLCAAPGGKSTFMAELM 272 (445)
T ss_pred CCCCCEEEEECCCCCHHHHHHHHHh
Confidence 3345799999999999888777654
No 272
>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=71.49 E-value=5 Score=33.75 Aligned_cols=24 Identities=21% Similarity=0.191 Sum_probs=20.7
Q ss_pred CCeEEEecCCccHHHHHHHhhCCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
..+++|||.|.|.....++.-|.+
T Consensus 95 ~~~lLDlGAGdG~VT~~l~~~f~~ 118 (265)
T PF05219_consen 95 DKSLLDLGAGDGEVTERLAPLFKE 118 (265)
T ss_pred CCceEEecCCCcHHHHHHHhhcce
Confidence 478999999999999999877654
No 273
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=71.31 E-value=12 Score=25.92 Aligned_cols=35 Identities=3% Similarity=0.062 Sum_probs=27.5
Q ss_pred HHHHHHHhcCCceeeeccCCCCcceeccccccccccCCC
Q 036971 78 DRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYVSDQN 116 (221)
Q Consensus 78 ~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~~~~~ 116 (221)
.=-+..|...|+++.. ..|.|++|+.++.+...+|
T Consensus 58 ~Wa~~~L~~aGli~~~----~rG~~~iT~~G~~~l~~~p 92 (92)
T PF14338_consen 58 RWARSYLKKAGLIERP----KRGIWRITEKGRKALAEHP 92 (92)
T ss_pred HHHHHHHHHCCCccCC----CCCceEECHhHHHHHhhCc
Confidence 3345788999999987 6889999999987665443
No 274
>PF12147 Methyltransf_20: Putative methyltransferase; InterPro: IPR022744 This C-terminal region is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with PF00561 from PFAM. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins. This domain belongs to the S-adenosyl-L-methionine-dependent methyltransferases superfamily.
Probab=71.10 E-value=4.3 Score=34.77 Aligned_cols=26 Identities=23% Similarity=0.330 Sum_probs=23.5
Q ss_pred CCCCeEEEecCCccHHHHHHHhhCCC
Q 036971 195 QNITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
....+||||.||+|-+....++.+|.
T Consensus 134 g~pvrIlDIAaG~GRYvlDal~~~~~ 159 (311)
T PF12147_consen 134 GRPVRILDIAAGHGRYVLDALEKHPE 159 (311)
T ss_pred CCceEEEEeccCCcHHHHHHHHhCCC
Confidence 35689999999999999999999996
No 275
>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=70.92 E-value=7 Score=31.23 Aligned_cols=35 Identities=17% Similarity=0.225 Sum_probs=32.5
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..++-.+||+.+|+ ... .++.-|+.|...|+|+..
T Consensus 33 ~~L~e~~La~~lgV-SRt----pVReAL~~L~~eGlv~~~ 67 (212)
T TIGR03338 33 AKLNESDIAARLGV-SRG----PVREAFRALEEAGLVRNE 67 (212)
T ss_pred CEecHHHHHHHhCC-ChH----HHHHHHHHHHHCCCEEEe
Confidence 57899999999999 777 899999999999999986
No 276
>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=70.39 E-value=4.3 Score=30.01 Aligned_cols=46 Identities=9% Similarity=0.127 Sum_probs=40.3
Q ss_pred HHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccccccccCC
Q 036971 60 EIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYVSDQ 115 (221)
Q Consensus 60 eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~~~~ 115 (221)
+||+.+++ +-+ -|-.+++++..+||++.. +|-..+|+.++.++...
T Consensus 2 ~La~~l~~-eiD----dL~p~~eAaelLgf~~~~-----~Gdi~LT~~G~~f~~a~ 47 (120)
T PF09821_consen 2 QLADELHL-EID----DLLPIVEAAELLGFAEVE-----EGDIRLTPLGRRFAEAD 47 (120)
T ss_pred chHHHhCC-cHH----HHHHHHHHHHHcCCeeec-----CCcEEeccchHHHHHCC
Confidence 57888988 776 899999999999999995 89999999999887654
No 277
>COG1565 Uncharacterized conserved protein [Function unknown]
Probab=70.20 E-value=12 Score=33.09 Aligned_cols=50 Identities=20% Similarity=0.234 Sum_probs=34.4
Q ss_pred cCchHHHHHHHHHhhhhHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 164 TDSRFNEVFNNGMIGQTSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 164 ~~p~~~~~F~~aM~~~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
..|+..+.|-...+.+.... ..... -+..-.||.||.|+|.++..+++..
T Consensus 50 TApels~lFGella~~~~~~----wq~~g-~p~~~~lvEiGaG~G~l~~DiL~~l 99 (370)
T COG1565 50 TAPELSQLFGELLAEQFLQL----WQELG-RPAPLKLVEIGAGRGTLASDILRTL 99 (370)
T ss_pred echhHHHHHHHHHHHHHHHH----HHHhc-CCCCceEEEeCCCcChHHHHHHHHH
Confidence 46888888888876543321 22222 2345689999999999998887653
No 278
>KOG4589 consensus Cell division protein FtsJ [Cell cycle control, cell division, chromosome partitioning]
Probab=70.05 E-value=8.4 Score=31.03 Aligned_cols=30 Identities=13% Similarity=0.190 Sum_probs=22.8
Q ss_pred HhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 189 ESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 189 ~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
+.|..+....+|+|+|+..|.++.-..++.
T Consensus 62 dKy~~l~p~~~VlD~G~APGsWsQVavqr~ 91 (232)
T KOG4589|consen 62 DKYRFLRPEDTVLDCGAAPGSWSQVAVQRV 91 (232)
T ss_pred hhccccCCCCEEEEccCCCChHHHHHHHhh
Confidence 445535667899999999999997666654
No 279
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=69.90 E-value=9.2 Score=31.12 Aligned_cols=46 Identities=20% Similarity=0.187 Sum_probs=38.1
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVA 108 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s 108 (221)
..++-.+||+.+|+ +.. .++.-|.-|.+.|+++.. ....+.-++++
T Consensus 38 ~~l~e~~La~~~gv-Srt----PVReAL~rL~~eGlv~~~----p~rG~~V~~~~ 83 (230)
T COG1802 38 ERLSEEELAEELGV-SRT----PVREALRRLEAEGLVEIE----PNRGAFVAPLS 83 (230)
T ss_pred CCccHHHHHHHhCC-CCc----cHHHHHHHHHHCCCeEec----CCCCCeeCCCC
Confidence 68999999999999 887 899999999999999997 33344444444
No 280
>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=69.63 E-value=6.7 Score=27.70 Aligned_cols=41 Identities=17% Similarity=0.178 Sum_probs=31.7
Q ss_pred HHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh
Q 036971 36 QAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV 85 (221)
Q Consensus 36 ~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~ 85 (221)
..+.+.+|+..|-. +++|-.|||+.+|+ ... .+.|+=+.|.
T Consensus 40 ~l~~R~~i~~~Ll~----~~~tQrEIa~~lGi-S~a----tIsR~sn~lk 80 (94)
T TIGR01321 40 DLGDRIRIVNELLN----GNMSQREIASKLGV-SIA----TITRGSNNLK 80 (94)
T ss_pred HHHHHHHHHHHHHh----CCCCHHHHHHHhCC-Chh----hhhHHHhhcc
Confidence 35678899998887 58999999999999 655 6666555544
No 281
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=69.57 E-value=6.3 Score=28.18 Aligned_cols=49 Identities=20% Similarity=0.136 Sum_probs=37.3
Q ss_pred hhChhhHHHhcC-CCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 40 NLDVLDIINKAG-PGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 40 ~lglfd~L~~~g-~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+-.+++.+.+.= -..-+|+-.||.+.|+ +-. ..+++||.|...|++...
T Consensus 43 dee~~~ki~KEV~~~r~VTpy~la~r~gI-~~S----vAr~vLR~LeeeGvv~lv 92 (107)
T COG4901 43 DEELLDKIRKEVPRERVVTPYVLASRYGI-NGS----VARIVLRHLEEEGVVQLV 92 (107)
T ss_pred cHHHHHHHHHhcccceeecHHHHHHHhcc-chH----HHHHHHHHHHhCCceeee
Confidence 334555554421 0035999999999999 876 889999999999999987
No 282
>PRK05031 tRNA (uracil-5-)-methyltransferase; Validated
Probab=69.54 E-value=4.7 Score=35.51 Aligned_cols=22 Identities=14% Similarity=-0.000 Sum_probs=19.3
Q ss_pred CeEEEecCCccHHHHHHHhhCC
Q 036971 198 TRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 198 ~~vvDVGGG~G~~~~~l~~~~P 219 (221)
.+++|++||.|.++..+++.+.
T Consensus 208 ~~vLDl~~G~G~~sl~la~~~~ 229 (362)
T PRK05031 208 GDLLELYCGNGNFTLALARNFR 229 (362)
T ss_pred CeEEEEeccccHHHHHHHhhCC
Confidence 4699999999999999988764
No 283
>PRK14903 16S rRNA methyltransferase B; Provisional
Probab=69.44 E-value=5.9 Score=35.78 Aligned_cols=48 Identities=10% Similarity=0.050 Sum_probs=29.1
Q ss_pred HHHHHHHhhhhHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 170 EVFNNGMIGQTSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 170 ~~F~~aM~~~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
..|..............+....+ .....+|+|+|+|+|..+..+++..
T Consensus 212 ~~~~~G~~~~Qd~~s~~~~~~l~-~~~g~~VLD~cagpGgkt~~la~~~ 259 (431)
T PRK14903 212 RVIKDGLATVQGESSQIVPLLME-LEPGLRVLDTCAAPGGKTTAIAELM 259 (431)
T ss_pred hHHHCCeEEEECHHHHHHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHc
Confidence 34555443332222222333344 4456799999999999998888764
No 284
>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=69.20 E-value=4.7 Score=34.20 Aligned_cols=35 Identities=11% Similarity=0.286 Sum_probs=32.1
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHH-HHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLG-LLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr-~L~~~gll~~~ 93 (221)
++.++++||+.+|. ++. .+.++++ .|+..|++...
T Consensus 254 ~~~~~~~ia~~lg~-~~~----~~~~~~e~~Li~~~li~~~ 289 (305)
T TIGR00635 254 GPVGLKTLAAALGE-DAD----TIEDVYEPYLLQIGFLQRT 289 (305)
T ss_pred CcccHHHHHHHhCC-Ccc----hHHHhhhHHHHHcCCcccC
Confidence 58999999999999 888 9999999 79999999865
No 285
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=69.05 E-value=5.1 Score=29.36 Aligned_cols=35 Identities=11% Similarity=0.088 Sum_probs=32.8
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.++|++|||+.+.. .++ .++.+|+-+...|.+.-.
T Consensus 18 ~~vtl~elA~~l~c-S~R----n~r~lLkkm~~~gWi~W~ 52 (115)
T PF12793_consen 18 VEVTLDELAELLFC-SRR----NARTLLKKMQEEGWITWQ 52 (115)
T ss_pred cceeHHHHHHHhCC-CHH----HHHHHHHHHHHCCCeeee
Confidence 46899999999999 888 999999999999999986
No 286
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=68.98 E-value=9.6 Score=30.76 Aligned_cols=35 Identities=29% Similarity=0.272 Sum_probs=32.3
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..++..+||+.+|+ ... .++.-|+.|...|+|+..
T Consensus 33 ~~L~e~~La~~lgV-SRt----pVREAL~~L~~eGLV~~~ 67 (221)
T PRK11414 33 ARLITKNLAEQLGM-SIT----PVREALLRLVSVNALSVA 67 (221)
T ss_pred CccCHHHHHHHHCC-Cch----hHHHHHHHHHHCCCEEec
Confidence 57899999999999 777 899999999999999976
No 287
>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=68.22 E-value=8.5 Score=28.49 Aligned_cols=49 Identities=8% Similarity=0.065 Sum_probs=42.0
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYY 111 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L 111 (221)
-|.|.++||..++- +.. -++.-|..+..+|+++.. +++.|..+......
T Consensus 52 ipy~~e~LA~~~~~-~~~----~V~~AL~~f~k~glIe~~----ed~~i~i~~~~~~~ 100 (121)
T PF09681_consen 52 IPYTAEMLALEFDR-PVD----TVRLALAVFQKLGLIEID----EDGVIYIPNWEKHQ 100 (121)
T ss_pred CCCcHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEe----cCCeEEeecHHHHh
Confidence 59999999999998 777 999999999999999997 67888777655443
No 288
>PRK12423 LexA repressor; Provisional
Probab=68.21 E-value=9.8 Score=30.53 Aligned_cols=35 Identities=14% Similarity=0.104 Sum_probs=30.3
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+-|..|||+++|+..+. .+++.|+.|...|+++..
T Consensus 25 ~Ps~~eia~~~g~~s~~----~v~~~l~~L~~~G~l~~~ 59 (202)
T PRK12423 25 PPSLAEIAQAFGFASRS----VARKHVQALAEAGLIEVV 59 (202)
T ss_pred CCCHHHHHHHhCCCChH----HHHHHHHHHHHCCCEEec
Confidence 56999999999962444 789999999999999986
No 289
>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=68.02 E-value=4.3 Score=32.77 Aligned_cols=28 Identities=14% Similarity=0.226 Sum_probs=20.5
Q ss_pred hcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 190 SYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 190 ~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
.+| -....+++|||||.|.+...|+.++
T Consensus 38 aLp-~~ry~~alEvGCs~G~lT~~LA~rC 65 (201)
T PF05401_consen 38 ALP-RRRYRRALEVGCSIGVLTERLAPRC 65 (201)
T ss_dssp HHT-TSSEEEEEEE--TTSHHHHHHGGGE
T ss_pred hcC-ccccceeEecCCCccHHHHHHHHhh
Confidence 355 4456799999999999999998764
No 290
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=67.81 E-value=8.3 Score=28.26 Aligned_cols=34 Identities=18% Similarity=0.212 Sum_probs=31.4
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+.|+.|||..+++ +.. .++-++--|...|++.-.
T Consensus 55 ~~SVAEiAA~L~l-Plg----VvrVLvsDL~~~G~v~v~ 88 (114)
T PF05331_consen 55 PLSVAEIAARLGL-PLG----VVRVLVSDLADAGLVRVR 88 (114)
T ss_pred CccHHHHHHhhCC-Cch----hhhhhHHHHHhCCCEEEe
Confidence 8999999999999 887 889999999999999975
No 291
>PRK09954 putative kinase; Provisional
Probab=67.39 E-value=5.9 Score=34.57 Aligned_cols=44 Identities=14% Similarity=0.172 Sum_probs=38.6
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCcee
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILC 91 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~ 91 (221)
+..|.+.|.++ +.+|..+||+.+++ ... .+++.|+-|...|++.
T Consensus 5 ~~~il~~l~~~---~~~s~~~la~~l~~-s~~----~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 5 EKEILAILRRN---PLIQQNEIADILQI-SRS----RVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHHC---CCCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCcC
Confidence 44578888887 58999999999999 777 8999999999999885
No 292
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=67.11 E-value=9.8 Score=28.25 Aligned_cols=63 Identities=19% Similarity=0.325 Sum_probs=47.5
Q ss_pred HHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccc
Q 036971 38 VVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPV 107 (221)
Q Consensus 38 av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~ 107 (221)
+.|..|.++|-.. ++.|+.||-+.+.- +.+-...-+.-+|+-|+-.|++...+ +++.|.-+|+
T Consensus 6 ~aE~eVM~ilW~~---~~~t~~eI~~~l~~-~~ews~sTV~TLl~RL~KKg~l~~~k---dgr~~~y~pL 68 (123)
T COG3682 6 AAEWEVMEILWSR---GPATVREIIEELPA-DREWSYSTVKTLLNRLVKKGLLTRKK---DGRAFRYSPL 68 (123)
T ss_pred HHHHHHHHHHHHc---CCccHHHHHHHHhh-cccccHHHHHHHHHHHHhccchhhhh---cCCeeeeecc
Confidence 3566677888887 59999999988876 53322235889999999999999874 5667777764
No 293
>PF07091 FmrO: Ribosomal RNA methyltransferase (FmrO); PDB: 3LCU_A 3LCV_B 3FRH_A 3FRI_A 3B89_A 3FZG_A.
Probab=67.09 E-value=3.8 Score=34.28 Aligned_cols=17 Identities=24% Similarity=0.317 Sum_probs=11.2
Q ss_pred CCCeEEEecCCccHHHH
Q 036971 196 NITRLVDVGGGLGITLS 212 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~ 212 (221)
...+|+|||||---++.
T Consensus 105 ~p~sVlDigCGlNPlal 121 (251)
T PF07091_consen 105 PPDSVLDIGCGLNPLAL 121 (251)
T ss_dssp --SEEEEET-TTCHHHH
T ss_pred CCchhhhhhccCCceeh
Confidence 37899999999765554
No 294
>PHA02591 hypothetical protein; Provisional
Probab=66.98 E-value=7.1 Score=26.49 Aligned_cols=32 Identities=19% Similarity=0.224 Sum_probs=25.4
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHH
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGL 83 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~ 83 (221)
+...|.+. +.|.++||+.+|+ +.+ .+++.|+.
T Consensus 51 vA~eL~eq----GlSqeqIA~~LGV-sqe----tVrKYL~~ 82 (83)
T PHA02591 51 VTHELARK----GFTVEKIASLLGV-SVR----KVRRYLES 82 (83)
T ss_pred HHHHHHHc----CCCHHHHHHHhCC-CHH----HHHHHHhc
Confidence 44567774 7999999999999 776 88887763
No 295
>PRK00536 speE spermidine synthase; Provisional
Probab=66.87 E-value=5.1 Score=33.78 Aligned_cols=23 Identities=9% Similarity=-0.178 Sum_probs=20.9
Q ss_pred CCCCeEEEecCCccHHHHHHHhh
Q 036971 195 QNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
+.+++|+=||||.|..++++++.
T Consensus 71 ~~pk~VLIiGGGDGg~~REvLkh 93 (262)
T PRK00536 71 KELKEVLIVDGFDLELAHQLFKY 93 (262)
T ss_pred CCCCeEEEEcCCchHHHHHHHCc
Confidence 46799999999999999999975
No 296
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=66.69 E-value=7.2 Score=30.85 Aligned_cols=34 Identities=24% Similarity=0.414 Sum_probs=31.8
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++|-.+||+.+|+ .+. .+.|+|..|...|++...
T Consensus 168 ~~t~~~lA~~lG~-tr~----tvsR~l~~l~~~gii~~~ 201 (211)
T PRK11753 168 KITRQEIGRIVGC-SRE----MVGRVLKMLEDQGLISAH 201 (211)
T ss_pred CCCHHHHHHHhCC-CHH----HHHHHHHHHHHCCCEEec
Confidence 6889999999999 887 999999999999999985
No 297
>KOG3045 consensus Predicted RNA methylase involved in rRNA processing [RNA processing and modification]
Probab=66.64 E-value=7.4 Score=32.94 Aligned_cols=54 Identities=17% Similarity=0.241 Sum_probs=33.4
Q ss_pred hhhhccCchHHHHHHHHHhh----hhHHHHHHHHHhcCCCCCCCeEEEecCCccHHHH
Q 036971 159 YDYLGTDSRFNEVFNNGMIG----QTSFVINKIVESYKGFQNITRLVDVGGGLGITLS 212 (221)
Q Consensus 159 ~~~l~~~p~~~~~F~~aM~~----~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~ 212 (221)
+..+.++|...+.|+..... |-....+.+++.+..-+....|.|+|||.+.++.
T Consensus 139 ~~lfkedp~afdlYH~gfr~QV~kWP~nPld~ii~~ik~r~~~~vIaD~GCGEakiA~ 196 (325)
T KOG3045|consen 139 FDLFKEDPTAFDLYHAGFRSQVKKWPENPLDVIIRKIKRRPKNIVIADFGCGEAKIAS 196 (325)
T ss_pred HHHHhcCcHHHHHHHHHHHHHHHhCCCChHHHHHHHHHhCcCceEEEecccchhhhhh
Confidence 44566788777666665543 2222344455444422356789999999998774
No 298
>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=66.60 E-value=9.9 Score=24.91 Aligned_cols=43 Identities=21% Similarity=0.235 Sum_probs=34.1
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
|+++|.+. ++.|+.+|++.+++ +.. -+..-+.-|+..+=+...
T Consensus 13 Vw~~L~~~---~~~s~~el~k~~~l-~~~----~~~~AiGWLarE~KI~~~ 55 (65)
T PF10771_consen 13 VWQLLNEN---GEWSVSELKKATGL-SDK----EVYLAIGWLARENKIEFE 55 (65)
T ss_dssp HHHHHCCS---SSEEHHHHHHHCT--SCH----HHHHHHHHHHCTTSEEEE
T ss_pred HHHHHhhC---CCcCHHHHHHHhCc-CHH----HHHHHHHHHhccCceeEE
Confidence 78889987 59999999999999 777 777777777777666554
No 299
>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=66.55 E-value=3.7 Score=27.58 Aligned_cols=33 Identities=21% Similarity=0.079 Sum_probs=28.0
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCC 92 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~ 92 (221)
.+|..|||+.+|+ ++. .+...+..+...|.+.+
T Consensus 32 GlS~kEIAe~LGI-S~~----TVk~~l~~~~~~~~~~~ 64 (73)
T TIGR03879 32 GKTASEIAEELGR-TEQ----TVRNHLKGETKAGGLVK 64 (73)
T ss_pred CCCHHHHHHHHCc-CHH----HHHHHHhcCcccchHHH
Confidence 7999999999999 887 89998888777776643
No 300
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=66.55 E-value=11 Score=29.99 Aligned_cols=48 Identities=21% Similarity=0.365 Sum_probs=40.8
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++..|.|.|...| ...|+-+||+++|+ +-. -+.|-|--|-..+.|...
T Consensus 5 ~~~~i~~~l~~~~--~~~~a~~i~k~l~i-~k~----~vNr~LY~L~~~~~v~~~ 52 (183)
T PHA02701 5 CASLILTLLSSSG--DKLPAKRIAKELGI-SKH----EANRCLYRLLESDAVSCE 52 (183)
T ss_pred HHHHHHHHHHhcC--CCCcHHHHHHHhCc-cHH----HHHHHHHHHhhcCcEecC
Confidence 4667899999985 36999999999999 776 788999889888988765
No 301
>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=66.51 E-value=5.5 Score=31.14 Aligned_cols=22 Identities=18% Similarity=0.276 Sum_probs=18.4
Q ss_pred CCCeEEEecCCccHHHHHHHhh
Q 036971 196 NITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
..++|+++|+|.|..++.+++.
T Consensus 45 ~~~~VLELGaG~Gl~gi~~a~~ 66 (173)
T PF10294_consen 45 RGKRVLELGAGTGLPGIAAAKL 66 (173)
T ss_dssp TTSEEEETT-TTSHHHHHHHHT
T ss_pred CCceEEEECCccchhHHHHHhc
Confidence 3589999999999999988876
No 302
>KOG0820 consensus Ribosomal RNA adenine dimethylase [RNA processing and modification]
Probab=65.77 E-value=12 Score=31.94 Aligned_cols=34 Identities=24% Similarity=0.240 Sum_probs=27.5
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 184 INKIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 184 ~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
++.++..-+ ......|+.||+|+|.+...++++-
T Consensus 47 ~~~I~~ka~-~k~tD~VLEvGPGTGnLT~~lLe~~ 80 (315)
T KOG0820|consen 47 IDQIVEKAD-LKPTDVVLEVGPGTGNLTVKLLEAG 80 (315)
T ss_pred HHHHHhccC-CCCCCEEEEeCCCCCHHHHHHHHhc
Confidence 345666666 7777899999999999999988763
No 303
>KOG3420 consensus Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=65.65 E-value=6.7 Score=30.29 Aligned_cols=27 Identities=26% Similarity=0.484 Sum_probs=19.2
Q ss_pred HHHhcCCCCCCCeEEEecCCccHHHHHH
Q 036971 187 IVESYKGFQNITRLVDVGGGLGITLSDH 214 (221)
Q Consensus 187 ~l~~~~~~~~~~~vvDVGGG~G~~~~~l 214 (221)
+-..|..+++ +++.|+|||.|.++.++
T Consensus 40 Ih~TygdiEg-kkl~DLgcgcGmLs~a~ 66 (185)
T KOG3420|consen 40 IHNTYGDIEG-KKLKDLGCGCGMLSIAF 66 (185)
T ss_pred HHhhhccccC-cchhhhcCchhhhHHHh
Confidence 3345554444 78999999999998443
No 304
>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=65.49 E-value=14 Score=24.75 Aligned_cols=51 Identities=22% Similarity=0.112 Sum_probs=35.6
Q ss_pred CCCCHHHHHhhCC------CCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecc
Q 036971 54 AELSASEIASQIP------TKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLA 105 (221)
Q Consensus 54 ~~~t~~eLA~~~g------~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt 105 (221)
.+.|...|.+.+. . ++..-...|.+-|+.++..|.|.++...|..|.|+++
T Consensus 20 ~GsS~~aI~kyI~~~y~~~~-~~~~~~~~l~~aLk~~v~~G~l~~~kg~G~sgsfkl~ 76 (77)
T PF00538_consen 20 KGSSLQAIKKYIKAKYKVDL-NPANFKSRLKRALKRGVEKGKLVQVKGKGASGSFKLS 76 (77)
T ss_dssp SSEEHHHHHHHHHHHSSCCC-CHTTHHHHHHHHHHHHHHCTSEEECSCSTTSSEEEES
T ss_pred CCCCHHHHHHHHHHhcCcCC-ChHHHHHHHHHHHHHHHHCCcEEeecccCCccceecC
Confidence 5788888876553 2 2210123588999999999999998544456889876
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=65.29 E-value=6.9 Score=25.22 Aligned_cols=30 Identities=10% Similarity=0.330 Sum_probs=21.5
Q ss_pred hhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHH
Q 036971 44 LDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRV 80 (221)
Q Consensus 44 fd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rl 80 (221)
|++--+.+ |.++..+||+.+|+ ++. -+++|
T Consensus 13 ~e~y~~~~--g~i~lkdIA~~Lgv-s~~----tIr~W 42 (60)
T PF10668_consen 13 FEIYKESN--GKIKLKDIAEKLGV-SES----TIRKW 42 (60)
T ss_pred HHHHHHhC--CCccHHHHHHHHCC-CHH----HHHHH
Confidence 33334443 68999999999999 775 66554
No 306
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=64.85 E-value=6.7 Score=37.31 Aligned_cols=48 Identities=10% Similarity=0.086 Sum_probs=39.1
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
..-|.++||+.+|+ ++. .|+|.|......|++.+..-..+.++|+.++
T Consensus 615 ~twt~eelse~l~i-p~~----~lrrrL~fWi~~GvL~e~~~~s~tgt~T~iE 662 (765)
T KOG2165|consen 615 NTWTLEELSESLGI-PVP----ALRRRLSFWIQKGVLREEPIISDTGTLTVIE 662 (765)
T ss_pred ccccHHHHHHHhCC-CHH----HHHHHHHHHHHcCeeecCCCCCCCceeeecc
Confidence 47999999999999 887 9999999999999999962111247777776
No 307
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=64.53 E-value=7 Score=31.63 Aligned_cols=34 Identities=18% Similarity=0.349 Sum_probs=31.8
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++|-++||..+|+ .+. .+.|+|..|...|+++..
T Consensus 184 ~lt~~~iA~~lG~-sr~----tvsR~l~~l~~~g~I~~~ 217 (235)
T PRK11161 184 TMTRGDIGNYLGL-TVE----TISRLLGRFQKSGMLAVK 217 (235)
T ss_pred cccHHHHHHHhCC-cHH----HHHHHHHHHHHCCCEEec
Confidence 6899999999999 777 999999999999999985
No 308
>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=64.49 E-value=6.7 Score=24.87 Aligned_cols=38 Identities=16% Similarity=0.287 Sum_probs=29.2
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV 85 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~ 85 (221)
++.|.+.|-+. +.+++++||+.+++ ..+ -++.-+..|-
T Consensus 7 q~~Ll~~L~~~---~~~~~~ela~~l~~-S~r----ti~~~i~~L~ 44 (59)
T PF08280_consen 7 QLKLLELLLKN---KWITLKELAKKLNI-SER----TIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHH---TSBBHHHHHHHCTS--HH----HHHHHHHHHH
T ss_pred HHHHHHHHHcC---CCCcHHHHHHHHCC-CHH----HHHHHHHHHH
Confidence 56678888775 59999999999999 776 6777666554
No 309
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=64.27 E-value=4.1 Score=32.36 Aligned_cols=45 Identities=9% Similarity=-0.016 Sum_probs=39.4
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..|.+.|.+. +.+++.+||+.+++ .+. -++|=|+.|...|++.+.
T Consensus 10 ~~Il~~l~~~---~~~~~~~La~~~~v-S~~----TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 10 KALQELIEEN---PFITDEELAEKFGV-SIQ----TIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHHC---CCEEHHHHHHHHCc-CHH----HHHHHHHHHhcchHHHHH
Confidence 3467788887 58999999999999 776 899999999999999875
No 310
>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=64.17 E-value=8.8 Score=29.83 Aligned_cols=34 Identities=26% Similarity=0.328 Sum_probs=31.9
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++|-+|||..+|+ .+. .+.|+|..|...|++...
T Consensus 143 ~~t~~~iA~~lG~-tre----tvsR~l~~l~~~g~I~~~ 176 (193)
T TIGR03697 143 RLSHQAIAEAIGS-TRV----TITRLLGDLRKKKLISIH 176 (193)
T ss_pred CCCHHHHHHHhCC-cHH----HHHHHHHHHHHCCCEEec
Confidence 6899999999999 887 999999999999999985
No 311
>PLN02668 indole-3-acetate carboxyl methyltransferase
Probab=63.95 E-value=18 Score=32.30 Aligned_cols=19 Identities=21% Similarity=0.087 Sum_probs=14.5
Q ss_pred CCCeEEEecCCccHHHHHH
Q 036971 196 NITRLVDVGGGLGITLSDH 214 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l 214 (221)
..-+|+|+|||+|..+..+
T Consensus 63 ~~~~iaDlGcs~G~ntl~~ 81 (386)
T PLN02668 63 VPFTAVDLGCSSGSNTIHI 81 (386)
T ss_pred cceeEEEecCCCCccHHHH
Confidence 3568999999999765433
No 312
>PRK01381 Trp operon repressor; Provisional
Probab=63.93 E-value=9.5 Score=27.19 Aligned_cols=30 Identities=17% Similarity=0.254 Sum_probs=25.8
Q ss_pred HHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCc
Q 036971 37 AVVNLDVLDIINKAGPGAELSASEIASQIPTKNPE 71 (221)
Q Consensus 37 ~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~ 71 (221)
.+.+++|+..|-. |.+|-.|||+.+|+ ...
T Consensus 41 l~~R~~I~~~L~~----g~~sQREIa~~lGv-Sia 70 (99)
T PRK01381 41 LGTRVRIVEELLR----GELSQREIKQELGV-GIA 70 (99)
T ss_pred HHHHHHHHHHHHc----CCcCHHHHHHHhCC-cee
Confidence 4578999999998 68999999999999 554
No 313
>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=63.71 E-value=7.6 Score=25.44 Aligned_cols=58 Identities=22% Similarity=0.288 Sum_probs=42.3
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCC--CcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKN--PEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~--~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
.+-.|.+.|...| +.++-.||...|+ . .. -+.++|..|...|.+.+... .+-.|+++.
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---GSTATAIAKALGL-SVPKK----EVNRVLYRLEKQGKVCKEGG--TPPKWSLTE 64 (66)
T ss_dssp HHHHHHHHHHHHT---SSEEEHHHHHHHH-TS-HH----HHHHHHHHHHHTTSEEEECS--SSTEEEE-H
T ss_pred HHHHHHHHHHhcC---CccHHHHHHHhCc-chhHH----HHHHHHHHHHHCCCEeeCCC--CCCceEecc
Confidence 4567888999984 6677777776666 4 34 79999999999999998621 356677654
No 314
>COG0421 SpeE Spermidine synthase [Amino acid transport and metabolism]
Probab=63.29 E-value=7.7 Score=33.06 Aligned_cols=26 Identities=35% Similarity=0.498 Sum_probs=22.4
Q ss_pred CCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
.++.++|+=||||.|..++++++..|
T Consensus 74 h~~pk~VLiiGgGdG~tlRevlkh~~ 99 (282)
T COG0421 74 HPNPKRVLIIGGGDGGTLREVLKHLP 99 (282)
T ss_pred CCCCCeEEEECCCccHHHHHHHhcCC
Confidence 45568999999999999999998764
No 315
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=62.98 E-value=15 Score=29.32 Aligned_cols=42 Identities=26% Similarity=0.254 Sum_probs=35.2
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+.+...|+-. +|+|..+|++..|+ + ...+++-|...|++.+.
T Consensus 93 LEtLaiIay~---qPiTr~eI~~irGv-~-------~~~ii~~L~~~gLI~e~ 134 (188)
T PRK00135 93 LEVLAIIAYK---QPITRIEIDEIRGV-N-------SDGALQTLLAKGLIKEV 134 (188)
T ss_pred HHHHHHHHHc---CCcCHHHHHHHHCC-C-------HHHHHHHHHHCCCeEEc
Confidence 3456778877 69999999999999 4 37889999999999874
No 316
>COG5459 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=62.84 E-value=6.9 Score=34.58 Aligned_cols=32 Identities=28% Similarity=0.379 Sum_probs=25.3
Q ss_pred HhcCCCCCCCeEEEecCCccHHHHHHHhhCCCC
Q 036971 189 ESYKGFQNITRLVDVGGGLGITLSDHNFQIPSY 221 (221)
Q Consensus 189 ~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l 221 (221)
...|+|+. ++|+|||-|.|+-+-++..-+|+|
T Consensus 107 ~~~~dfap-qsiLDvG~GPgtgl~A~n~i~Pdl 138 (484)
T COG5459 107 KRVPDFAP-QSILDVGAGPGTGLWALNDIWPDL 138 (484)
T ss_pred HhCCCcCc-chhhccCCCCchhhhhhcccCCCc
Confidence 33454544 679999999999999998888875
No 317
>PF02527 GidB: rRNA small subunit methyltransferase G; InterPro: IPR003682 This entry represents a rRNA small subunit methyltransferase G. Previously identified as a glucose-inhibited division protein B that appears to be present and in a single copy in all complete eubacterial genomes so far sequenced. Specifically methylates the N7 position of a guanosine in 16S rRNA [, , ].; GO: 0008649 rRNA methyltransferase activity, 0006364 rRNA processing, 0005737 cytoplasm; PDB: 1XDZ_A 3G88_A 3G8A_B 3G89_B 3G8B_B 1JSX_A.
Probab=62.51 E-value=15 Score=29.14 Aligned_cols=23 Identities=22% Similarity=0.459 Sum_probs=20.0
Q ss_pred eEEEecCCccHHHHHHHhhCCCC
Q 036971 199 RLVDVGGGLGITLSDHNFQIPSY 221 (221)
Q Consensus 199 ~vvDVGGG~G~~~~~l~~~~P~l 221 (221)
+++|||.|-|.=++-++=.+|++
T Consensus 51 ~~lDiGSGaGfPGipLaI~~p~~ 73 (184)
T PF02527_consen 51 KVLDIGSGAGFPGIPLAIARPDL 73 (184)
T ss_dssp EEEEETSTTTTTHHHHHHH-TTS
T ss_pred eEEecCCCCCChhHHHHHhCCCC
Confidence 79999999999999998888874
No 318
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=61.20 E-value=10 Score=30.78 Aligned_cols=34 Identities=24% Similarity=0.264 Sum_probs=31.4
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++|-++||..+|+ .+. .+.|+|..|...|+++..
T Consensus 179 ~lt~~~IA~~lGi-sre----tlsR~L~~L~~~GlI~~~ 212 (230)
T PRK09391 179 PMSRRDIADYLGL-TIE----TVSRALSQLQDRGLIGLS 212 (230)
T ss_pred cCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCcEEec
Confidence 5789999999999 887 999999999999999874
No 319
>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=61.07 E-value=8 Score=27.02 Aligned_cols=40 Identities=13% Similarity=0.203 Sum_probs=28.1
Q ss_pred hhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceee
Q 036971 44 LDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCC 92 (221)
Q Consensus 44 fd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~ 92 (221)
.-++.. +..++..|-+.+|+ +.+ -+++.+.+|..+|+..+
T Consensus 14 a~li~~----~~~nvp~L~~~TGm-PrR----T~Qd~i~aL~~~~I~~~ 53 (90)
T PF09904_consen 14 AYLIDS----GERNVPALMEATGM-PRR----TIQDTIKALPELGIECE 53 (90)
T ss_dssp HHHHHH----S-B-HHHHHHHH----HH----HHHHHHHGGGGGT-EEE
T ss_pred HHHHhc----CCccHHHHHHHhCC-CHh----HHHHHHHHhhcCCeEEE
Confidence 334555 34599999999999 887 89999999999999877
No 320
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=60.57 E-value=12 Score=29.40 Aligned_cols=34 Identities=18% Similarity=0.238 Sum_probs=31.5
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++|-++||..+|+ .+. .+.|+|.-|...|++...
T Consensus 149 ~~t~~~iA~~lG~-tre----tvsR~l~~l~~~g~I~~~ 182 (202)
T PRK13918 149 YATHDELAAAVGS-VRE----TVTKVIGELSREGYIRSG 182 (202)
T ss_pred cCCHHHHHHHhCc-cHH----HHHHHHHHHHHCCCEEcC
Confidence 5899999999999 887 999999999999999963
No 321
>PRK13239 alkylmercury lyase; Provisional
Probab=60.49 E-value=24 Score=28.70 Aligned_cols=37 Identities=19% Similarity=0.299 Sum_probs=28.0
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV 85 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~ 85 (221)
.-|+..|++. .|.|+.+||+.+|. +.+ .++..|+.+.
T Consensus 25 ~~llr~la~G---~pvt~~~lA~~~~~-~~~----~v~~~L~~l~ 61 (206)
T PRK13239 25 VPLLRLLAKG---RPVSVTTLAAALGW-PVE----EVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHcC---CCCCHHHHHHHhCC-CHH----HHHHHHHhCC
Confidence 3456678853 79999999999999 665 6776666654
No 322
>PF01596 Methyltransf_3: O-methyltransferase; InterPro: IPR002935 Members of this family are O-methyltransferases. The family includes also bacterial O-methyltransferases that may be involved in antibiotic production [].; GO: 0008171 O-methyltransferase activity; PDB: 1SUI_C 1SUS_D 3CBG_A 2GPY_B 3TR6_A 2AVD_A 3DUL_B 3DUW_B 2ZTH_A 1VID_A ....
Probab=60.47 E-value=10 Score=30.65 Aligned_cols=25 Identities=16% Similarity=0.190 Sum_probs=22.0
Q ss_pred CCCeEEEecCCccHHHHHHHhhCCC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQIPS 220 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~P~ 220 (221)
+.++||+||++.|.-+..+++..|+
T Consensus 45 ~~k~vLEIGt~~GySal~la~~l~~ 69 (205)
T PF01596_consen 45 RPKRVLEIGTFTGYSALWLAEALPE 69 (205)
T ss_dssp T-SEEEEESTTTSHHHHHHHHTSTT
T ss_pred CCceEEEeccccccHHHHHHHhhcc
Confidence 3789999999999999999998874
No 323
>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=60.07 E-value=23 Score=34.22 Aligned_cols=59 Identities=20% Similarity=0.254 Sum_probs=43.2
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
.|.+.|.+.. +.|++..+|++.+++ +...+...+.+.|+.|...|.+.+. ..+.|.+..
T Consensus 6 ~il~~l~~~~-~~~~~~~~l~~~l~~-~~~~~~~~l~~~l~~l~~~g~l~~~----~~~~~~~~~ 64 (709)
T TIGR02063 6 LILEFLKSKK-GKPISLKELAKAFHL-KGADEKKALRKRLRALEDDGLVKKN----RRGLYALPE 64 (709)
T ss_pred HHHHHHHhCC-CCCCCHHHHHHHhCC-CChHHHHHHHHHHHHHHHCCCEEEc----CCceEecCC
Confidence 3666776521 168999999999999 6522334699999999999999876 456665543
No 324
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=59.17 E-value=13 Score=30.58 Aligned_cols=44 Identities=18% Similarity=0.187 Sum_probs=36.0
Q ss_pred CCC-CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecc
Q 036971 54 AEL-SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLA 105 (221)
Q Consensus 54 ~~~-t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt 105 (221)
..+ +-.+||+.+|+ ... .++.-|+.|.+.|+++... ..|.|-..
T Consensus 32 ~~LpsE~eLa~~lgV-SRt----pVREAL~~L~~eGlv~~~~---~~G~~V~~ 76 (254)
T PRK09464 32 EKLPPERELAKQFDV-SRP----SLREAIQRLEAKGLLLRRQ---GGGTFVQS 76 (254)
T ss_pred CcCCCHHHHHHHhCC-CHH----HHHHHHHHHHHCCCEEEec---CceeEEec
Confidence 467 78999999999 776 8999999999999999763 35555544
No 325
>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=58.98 E-value=8.2 Score=24.83 Aligned_cols=43 Identities=16% Similarity=0.332 Sum_probs=23.7
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhC----CCCCCcchhhhHHHHHHHHhcCCcee
Q 036971 43 VLDIINKAGPGAELSASEIASQI----PTKNPEGAAKMLDRVLGLLVSFNILC 91 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~----g~~~~~~~~~~l~rlLr~L~~~gll~ 91 (221)
||+.+ + ++.|+++|++.+ +. ++..-..-+..+|..|...|+++
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 56667 3 478888877544 56 55422335678888888888874
No 326
>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=58.92 E-value=11 Score=28.60 Aligned_cols=35 Identities=14% Similarity=0.282 Sum_probs=25.6
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHH
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLG 82 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr 82 (221)
.|-+.|.++. +...|+.+|++++|+ ++. .+.+|+|
T Consensus 34 kV~~yLr~~p-~~~ati~eV~e~tgV-s~~----~I~~~Ir 68 (137)
T TIGR03826 34 KVYKFLRKHE-NRQATVSEIVEETGV-SEK----LILKFIR 68 (137)
T ss_pred HHHHHHHHCC-CCCCCHHHHHHHHCc-CHH----HHHHHHH
Confidence 4567788763 123899999999999 776 6666665
No 327
>PLN02823 spermine synthase
Probab=58.84 E-value=9.7 Score=33.29 Aligned_cols=24 Identities=25% Similarity=0.243 Sum_probs=20.7
Q ss_pred CCCeEEEecCCccHHHHHHHhhCC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
+.++|+-||||.|..+.++++..|
T Consensus 103 ~pk~VLiiGgG~G~~~re~l~~~~ 126 (336)
T PLN02823 103 NPKTVFIMGGGEGSTAREVLRHKT 126 (336)
T ss_pred CCCEEEEECCCchHHHHHHHhCCC
Confidence 568999999999999999987543
No 328
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=58.78 E-value=13 Score=30.68 Aligned_cols=43 Identities=21% Similarity=0.282 Sum_probs=35.0
Q ss_pred CCC-CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceec
Q 036971 54 AEL-SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSL 104 (221)
Q Consensus 54 ~~~-t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~l 104 (221)
..+ +-.+||+.+|+ ... .++.-|+.|.+.|+++... ..|.|-.
T Consensus 31 ~~LpsE~eLa~~~gV-SRt----pVREAL~~L~~eGlV~~~~---~~G~~V~ 74 (257)
T PRK10225 31 ERLPPEREIAEMLDV-TRT----VVREALIMLEIKGLVEVRR---GAGIYVL 74 (257)
T ss_pred CcCcCHHHHHHHhCC-CHH----HHHHHHHHHHHCCCEEEec---CCEEEEe
Confidence 577 68899999999 776 8999999999999999763 3444443
No 329
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=58.27 E-value=18 Score=24.60 Aligned_cols=50 Identities=12% Similarity=0.059 Sum_probs=39.9
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYY 111 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L 111 (221)
.+.|-++||+.+|+ ... .+...++.|...|+=.+.. ....|++......+
T Consensus 18 ~~~SGe~La~~Lgi-SRt----aVwK~Iq~Lr~~G~~I~s~---~~kGY~L~~~~~ll 67 (79)
T COG1654 18 NFVSGEKLAEELGI-SRT----AVWKHIQQLREEGVDIESV---RGKGYLLPQLPDLL 67 (79)
T ss_pred CcccHHHHHHHHCc-cHH----HHHHHHHHHHHhCCceEec---CCCceeccCccccC
Confidence 58999999999999 777 9999999999999988762 23367776655433
No 330
>COG0357 GidB Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]
Probab=58.18 E-value=17 Score=29.76 Aligned_cols=25 Identities=24% Similarity=0.485 Sum_probs=21.3
Q ss_pred CCeEEEecCCccHHHHHHHhhCCCC
Q 036971 197 ITRLVDVGGGLGITLSDHNFQIPSY 221 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~~P~l 221 (221)
..+++|||-|.|.=+.-++=.+|++
T Consensus 68 ~~~~~DIGSGaGfPGipLAI~~p~~ 92 (215)
T COG0357 68 AKRVLDIGSGAGFPGIPLAIAFPDL 92 (215)
T ss_pred CCEEEEeCCCCCCchhhHHHhccCC
Confidence 5899999999999888887777764
No 331
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=58.10 E-value=13 Score=30.51 Aligned_cols=67 Identities=13% Similarity=0.079 Sum_probs=51.7
Q ss_pred HHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccc
Q 036971 33 AVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVA 108 (221)
Q Consensus 33 ~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s 108 (221)
..|+-...-.|++.|.++ ++.|.-+||..+++ +.. -+.--+..|...|++.++.. |..-.|+.||.-
T Consensus 169 ~~Lkn~~~k~I~~eiq~~---~~~t~~~ia~~l~l-s~a----TV~~~lk~l~~~Gii~~~~~-Gr~iiy~in~s~ 235 (240)
T COG3398 169 LSLKNETSKAIIYEIQEN---KCNTNLLIAYELNL-SVA----TVAYHLKKLEELGIIPEDRE-GRSIIYSINPSI 235 (240)
T ss_pred HHhhchhHHHHHHHHhcC---CcchHHHHHHHcCc-cHH----HHHHHHHHHHHcCCCccccc-CceEEEEeCHHH
Confidence 455666667899999996 47999999999999 776 78888999999999999731 122347766643
No 332
>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=57.97 E-value=16 Score=26.41 Aligned_cols=51 Identities=24% Similarity=0.397 Sum_probs=39.8
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.++.|.+.|-+.| ++|+.||.+.+.- +..-...-+.-+|+-|+..|++...
T Consensus 4 ~E~~IM~~lW~~~---~~t~~eI~~~l~~-~~~~~~sTv~t~L~rL~~Kg~l~~~ 54 (115)
T PF03965_consen 4 LELEIMEILWESG---EATVREIHEALPE-ERSWAYSTVQTLLNRLVEKGFLTRE 54 (115)
T ss_dssp HHHHHHHHHHHHS---SEEHHHHHHHHCT-TSS--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHhCC---CCCHHHHHHHHHh-ccccchhHHHHHHHHHHhCCceeEe
Confidence 4666778888884 7999999999876 4221233689999999999999997
No 333
>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=57.86 E-value=19 Score=26.63 Aligned_cols=48 Identities=19% Similarity=0.050 Sum_probs=40.4
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKY 110 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~ 110 (221)
-|.+.+.||..++- +.. -++.-|..+..+|+++.. ++|.|..+.....
T Consensus 50 ipy~~e~LA~~~~~-~~~----~V~~Al~~f~k~glIe~~----d~g~i~i~~~~~~ 97 (119)
T TIGR01714 50 APYNAEMLATMFNR-NVG----DIRITLQTLESLGLIEKK----NNGDIFLENWEKH 97 (119)
T ss_pred CCCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEe----cCCcEEehhHHHH
Confidence 58999999999998 777 899999999999999997 5677776665443
No 334
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=57.71 E-value=16 Score=33.21 Aligned_cols=40 Identities=23% Similarity=0.311 Sum_probs=32.9
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
|-..|.. |+.|+.|||+.+|+ ... .+.+.|+.| .|+|...
T Consensus 5 ~~~~L~~----g~~~~~eL~~~l~~-sq~----~~s~~L~~L--~~~V~~~ 44 (442)
T PRK09775 5 LTTLLLQ----GPLSAAELAARLGV-SQA----TLSRLLAAL--GDQVVRF 44 (442)
T ss_pred HHHHHhc----CCCCHHHHHHHhCC-CHH----HHHHHHHHh--hcceeEe
Confidence 4456666 69999999999999 665 899999999 7887765
No 335
>KOG2651 consensus rRNA adenine N-6-methyltransferase [RNA processing and modification]
Probab=57.34 E-value=12 Score=33.33 Aligned_cols=24 Identities=33% Similarity=0.481 Sum_probs=20.0
Q ss_pred CCCCCeEEEecCCccHHHHHHHhh
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
|-++..+||||-|.|+++.-+.-.
T Consensus 151 f~gi~~vvD~GaG~G~LSr~lSl~ 174 (476)
T KOG2651|consen 151 FTGIDQVVDVGAGQGHLSRFLSLG 174 (476)
T ss_pred hcCCCeeEEcCCCchHHHHHHhhc
Confidence 667899999999999998766443
No 336
>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=57.16 E-value=46 Score=21.68 Aligned_cols=40 Identities=18% Similarity=0.167 Sum_probs=25.1
Q ss_pred hHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 45 DIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 45 d~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++|.+.+ .|+|++||...+.+ +.. +.+..+|+ ...=++.+
T Consensus 12 eymK~r~--~Plt~~eI~d~l~~-d~~---~~~~~~Lk---~npKI~~d 51 (65)
T PF02186_consen 12 EYMKKRD--HPLTLEEILDYLSL-DIG---KKLKQWLK---NNPKIEYD 51 (65)
T ss_dssp HHHHHH---S-B-HHHHHHHHTS-SS----HHHHHHHH---H-TTEEEE
T ss_pred HHHHhcC--CCcCHHHHHHHHcC-CCC---HHHHHHHH---cCCCEEEe
Confidence 3777776 79999999999998 765 24556665 55555554
No 337
>PF11312 DUF3115: Protein of unknown function (DUF3115); InterPro: IPR021463 This eukaryotic family of proteins has no known function.
Probab=57.05 E-value=31 Score=29.90 Aligned_cols=21 Identities=29% Similarity=0.480 Sum_probs=17.9
Q ss_pred CeEEEecCCccHHHHHHHhhC
Q 036971 198 TRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 198 ~~vvDVGGG~G~~~~~l~~~~ 218 (221)
.+||.||||.|.=+.+|+..+
T Consensus 88 ~~VlCIGGGAGAElVAlAa~~ 108 (315)
T PF11312_consen 88 LRVLCIGGGAGAELVALAAAF 108 (315)
T ss_pred ceEEEECCChHHHHHHHHHHH
Confidence 699999999998888877655
No 338
>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=56.92 E-value=16 Score=29.74 Aligned_cols=35 Identities=23% Similarity=0.189 Sum_probs=31.9
Q ss_pred CCC-CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AEL-SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~-t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..+ +-.+||+.+|+ ... .++.-|+.|...|+++..
T Consensus 28 ~~LpsE~~La~~lgV-SRt----pVREAL~~Le~eGlV~~~ 63 (235)
T TIGR02812 28 SILPAERELSELIGV-TRT----TLREVLQRLARDGWLTIQ 63 (235)
T ss_pred CcCcCHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEEe
Confidence 578 78999999999 776 899999999999999986
No 339
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=56.85 E-value=20 Score=29.40 Aligned_cols=51 Identities=20% Similarity=0.202 Sum_probs=44.3
Q ss_pred HHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 35 FQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 35 L~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+..-.+.+|++.+..+ ++.++.|+.+.+++ +.. -++-.||.|.+.++++-.
T Consensus 98 ~~ns~R~~Iy~~i~~n---PG~~lsEl~~nl~i-~R~----TlRyhlriLe~~~li~a~ 148 (240)
T COG3398 98 FLNSKRDGIYNYIKPN---PGFSLSELRANLYI-NRS----TLRYHLRILESNPLIEAG 148 (240)
T ss_pred HhhhhHHHHHHHhccC---CCccHHHHHHhcCC-ChH----HHHHHHHHHHhCcchhhh
Confidence 4445677899999998 48999999999999 776 899999999999999865
No 340
>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=56.79 E-value=12 Score=29.55 Aligned_cols=56 Identities=20% Similarity=0.213 Sum_probs=40.3
Q ss_pred HHHHHHHHHhhChhhHHHhcCCCCC---CCHHHHHhhC-CCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 31 LPAVFQAVVNLDVLDIINKAGPGAE---LSASEIASQI-PTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 31 ~~~aL~~av~lglfd~L~~~g~~~~---~t~~eLA~~~-g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.-.+|.+.+.+==.+-+...+ .| .|-.+|++.+ |+ .+. -++|.++.|+..||+...
T Consensus 45 ~l~vL~aLls~~~~~d~~~~~--~piVfpSN~~La~r~~G~-s~~----tlrR~l~~LveaGLI~rr 104 (177)
T PF03428_consen 45 ALAVLDALLSFTPPDDWEPGR--RPIVFPSNAQLAERLNGM-SER----TLRRHLARLVEAGLIVRR 104 (177)
T ss_pred HHHHHHHHHHhCCcccccCCC--CceeecCHHHHHHHHcCC-CHH----HHHHHHHHHHHCCCeeec
Confidence 334555555544444443321 23 5779999999 99 888 999999999999999985
No 341
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=56.58 E-value=15 Score=22.13 Aligned_cols=35 Identities=11% Similarity=0.238 Sum_probs=26.5
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHH
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLL 84 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L 84 (221)
+.-|...+.+ ..|..+||+.+|+ +.. -+.|+++..
T Consensus 17 ~~~i~~~~~~-----~~s~~~vA~~~~v-s~~----TV~ri~~~~ 51 (52)
T PF13542_consen 17 EQYILKLLRE-----SRSFKDVARELGV-SWS----TVRRIFDRY 51 (52)
T ss_pred HHHHHHHHhh-----cCCHHHHHHHHCC-CHH----HHHHHHHhh
Confidence 3345556665 4799999999999 877 888887653
No 342
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=56.57 E-value=11 Score=22.28 Aligned_cols=23 Identities=26% Similarity=0.341 Sum_probs=15.0
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHH
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLG 82 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr 82 (221)
+.|..+||+.+|. ++. -+.+.|+
T Consensus 20 G~s~~~IA~~lg~-s~s----TV~relk 42 (44)
T PF13936_consen 20 GMSIREIAKRLGR-SRS----TVSRELK 42 (44)
T ss_dssp ---HHHHHHHTT---HH----HHHHHHH
T ss_pred CCCHHHHHHHHCc-CcH----HHHHHHh
Confidence 6999999999999 776 7777664
No 343
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=56.03 E-value=11 Score=32.61 Aligned_cols=35 Identities=9% Similarity=0.233 Sum_probs=32.5
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHH-HHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLG-LLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr-~L~~~gll~~~ 93 (221)
++.+++.||+.+|. ++. .+..+++ .|+..|+++..
T Consensus 275 ~~~~~~~~a~~lg~-~~~----~~~~~~e~~Li~~~li~~~ 310 (328)
T PRK00080 275 GPVGLDTLAAALGE-ERD----TIEDVYEPYLIQQGFIQRT 310 (328)
T ss_pred CceeHHHHHHHHCC-Ccc----hHHHHhhHHHHHcCCcccC
Confidence 69999999999999 888 8999999 99999999865
No 344
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=55.90 E-value=12 Score=32.65 Aligned_cols=34 Identities=26% Similarity=0.268 Sum_probs=31.9
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++|-.|||+++|+ ... .+.|+|..+...|+|+-.
T Consensus 26 gltQ~eIA~~Lgi-SR~----~v~rlL~~Ar~~GiV~I~ 59 (321)
T COG2390 26 GLTQSEIAERLGI-SRA----TVSRLLAKAREEGIVKIS 59 (321)
T ss_pred CCCHHHHHHHhCC-CHH----HHHHHHHHHHHCCeEEEE
Confidence 7999999999999 777 899999999999999975
No 345
>cd02190 epsilon_tubulin The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The epsilon-tubulins which are widespread but not ubiquitous among eukaryotes play a role in basal body/centriole morphogenesis.
Probab=55.76 E-value=14 Score=32.74 Aligned_cols=36 Identities=28% Similarity=0.386 Sum_probs=27.6
Q ss_pred HHHHHhcCCCCCCCeEEEecCCcc-----HHHHHHHhhCCC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLG-----ITLSDHNFQIPS 220 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G-----~~~~~l~~~~P~ 220 (221)
+..++.+|.+.++..+..+|||+| .++..+...||+
T Consensus 90 r~~~E~cd~l~gf~i~~sl~GGTGSG~gs~l~e~l~~~y~~ 130 (379)
T cd02190 90 RKAAEKCDSLQSFFILHSLGGGTGSGLGTYVLELLADEFPE 130 (379)
T ss_pred HHHHhhCcCcceEEEEeecCCCcchhHHHHHHHHHHHhcCc
Confidence 445677887788899999999998 445666777775
No 346
>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=55.71 E-value=16 Score=26.13 Aligned_cols=35 Identities=17% Similarity=0.250 Sum_probs=32.3
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..+|..++++.+|+ ++. .+.+.+..|+.++++..+
T Consensus 53 d~Is~sq~~e~tg~-~~~----~V~~al~~Li~~~vI~~~ 87 (100)
T PF04492_consen 53 DRISNSQIAEMTGL-SRD----HVSKALNELIRRGVIIRD 87 (100)
T ss_pred ceeeHHHHHHHHCc-CHH----HHHHHHHHHHHCCCEEeC
Confidence 36999999999999 888 999999999999999875
No 347
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=55.33 E-value=28 Score=23.25 Aligned_cols=53 Identities=15% Similarity=0.290 Sum_probs=43.7
Q ss_pred HHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 33 AVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 33 ~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.++....+..+...|.+. .+.++.+|+..+++ ... .+.+-|..|...|++...
T Consensus 20 ~~l~~~~r~~il~~l~~~---~~~~~~~l~~~~~~-~~~----~v~~hL~~L~~~glv~~~ 72 (110)
T COG0640 20 KALADPTRLEILSLLAEG---GELTVGELAEALGL-SQS----TVSHHLKVLREAGLVELR 72 (110)
T ss_pred HHhCCHHHHHHHHHHHhc---CCccHHHHHHHHCC-Chh----HHHHHHHHHHHCCCeEEE
Confidence 344455777778888873 27899999999999 777 899999999999999986
No 348
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=55.32 E-value=17 Score=30.03 Aligned_cols=44 Identities=23% Similarity=0.212 Sum_probs=35.3
Q ss_pred CCC-CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecc
Q 036971 54 AEL-SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLA 105 (221)
Q Consensus 54 ~~~-t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt 105 (221)
..+ +-.+||+.+|+ ... .++.-|+.|.+.|+++... ..|.|-..
T Consensus 24 ~~LpsE~eLae~~gV-SRt----pVREAL~~Le~~GlV~~~~---~~G~~V~~ 68 (253)
T PRK10421 24 MKLPAERQLAMQLGV-SRN----SLREALAKLVSEGVLLSRR---GGGTFIRW 68 (253)
T ss_pred CcCCCHHHHHHHhCC-CHH----HHHHHHHHHHHCCCEEEeC---CCeEEEec
Confidence 567 67899999999 776 8999999999999999762 34555443
No 349
>KOG2940 consensus Predicted methyltransferase [General function prediction only]
Probab=55.22 E-value=26 Score=29.29 Aligned_cols=21 Identities=19% Similarity=0.246 Sum_probs=17.8
Q ss_pred CCeEEEecCCccHHHHHHHhh
Q 036971 197 ITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~ 217 (221)
...+.|||||.|+....+...
T Consensus 73 fp~a~diGcs~G~v~rhl~~e 93 (325)
T KOG2940|consen 73 FPTAFDIGCSLGAVKRHLRGE 93 (325)
T ss_pred CcceeecccchhhhhHHHHhc
Confidence 468999999999999888654
No 350
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=55.16 E-value=19 Score=29.62 Aligned_cols=35 Identities=17% Similarity=0.185 Sum_probs=31.9
Q ss_pred CCC-CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AEL-SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~-t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..+ +-.+||+.+|+ ... .++.-|+.|...|+|+..
T Consensus 29 ~~LPsE~eLa~~~gV-SRt----pVREAL~~L~~eGlV~~~ 64 (251)
T PRK09990 29 QALPSERRLCEKLGF-SRS----ALREGLTVLRGRGIIETA 64 (251)
T ss_pred CcCcCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEe
Confidence 578 78899999999 776 899999999999999986
No 351
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=55.13 E-value=12 Score=24.37 Aligned_cols=29 Identities=17% Similarity=0.303 Sum_probs=23.3
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCC
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFN 88 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~g 88 (221)
+.|+++||+.+|+ ++. .+.++++......
T Consensus 1 ~~~~~~la~~~~~-s~~----~l~~~f~~~~~~s 29 (84)
T smart00342 1 PLTLEDLAEALGM-SPR----HLQRLFKKETGTT 29 (84)
T ss_pred CCCHHHHHHHhCC-CHH----HHHHHHHHHhCcC
Confidence 4789999999999 887 8888887665443
No 352
>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=55.08 E-value=10 Score=33.05 Aligned_cols=46 Identities=22% Similarity=0.154 Sum_probs=25.1
Q ss_pred HHHHHHHHhhhhHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhh
Q 036971 169 NEVFNNGMIGQTSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 169 ~~~F~~aM~~~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
.+.|+..+... .+...++....=....+|+|+|||.|..+.--.+.
T Consensus 38 lR~fNNwvKs~---LI~~~~~~~~~~~~~~~VLDl~CGkGGDL~Kw~~~ 83 (331)
T PF03291_consen 38 LRNFNNWVKSV---LIQKYAKKVKQNRPGLTVLDLCCGKGGDLQKWQKA 83 (331)
T ss_dssp HHHHHHHHHHH---HHHHHCHCCCCTTTT-EEEEET-TTTTTHHHHHHT
T ss_pred HHHHhHHHHHH---HHHHHHHhhhccCCCCeEEEecCCCchhHHHHHhc
Confidence 45677765532 12222222210114579999999999988765544
No 353
>KOG3191 consensus Predicted N6-DNA-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=55.07 E-value=11 Score=30.11 Aligned_cols=21 Identities=14% Similarity=0.132 Sum_probs=18.0
Q ss_pred CCeEEEecCCccHHHHHHHhh
Q 036971 197 ITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~ 217 (221)
...+++||||+|..+..+++.
T Consensus 44 ~~i~lEIG~GSGvvstfL~~~ 64 (209)
T KOG3191|consen 44 PEICLEIGCGSGVVSTFLASV 64 (209)
T ss_pred ceeEEEecCCcchHHHHHHHh
Confidence 578999999999998887654
No 354
>PF02981 FokI_N: Restriction endonuclease FokI, recognition domain; InterPro: IPR004234 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Thie entry represents the type IIS restriction endonuclease FokI (3.1.21.4 from EC), which is a member of an unusual class of bipartite restriction enzymes that recognise a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence []. FokI contains amino- and carboxy-terminal domains corresponding to the DNA-recognition and cleavage functions (IPR004233 from INTERPRO), respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP []. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1FOK_A 2FOK_B.
Probab=54.95 E-value=9.7 Score=28.94 Aligned_cols=38 Identities=24% Similarity=0.248 Sum_probs=30.0
Q ss_pred hhhhHHHHHHHHhcCCceeeeccCCCCcceecccccccccc
Q 036971 73 AAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYVS 113 (221)
Q Consensus 73 ~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~~ 113 (221)
+.+.-.-+||-.+++||++.+. +.++|+.|.+++.+++
T Consensus 105 ddW~Ad~flrwAvslgfl~~~~---~~Dtf~IT~lG~~~~~ 142 (145)
T PF02981_consen 105 DDWTADGFLRWAVSLGFLDYDR---ETDTFSITELGKKYVK 142 (145)
T ss_dssp -HHHHHHHHHHHHHTTSEEEET---TTTEEEE-HHHHHHHH
T ss_pred cCCCccceeeeeeeeCceeecc---CCCEEEeehhHHHHhh
Confidence 3445577899999999999985 6899999999987654
No 355
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=54.90 E-value=33 Score=23.09 Aligned_cols=51 Identities=8% Similarity=0.139 Sum_probs=38.8
Q ss_pred HHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 35 FQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 35 L~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.....+..++.....- ..++.++||+.+++ +.+ -+++++.-++..|.+.-.
T Consensus 7 ~~~~~~~~l~~l~~~y---~~i~~~~i~~~~~l-~~~----~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00088 7 QRKIRLTNLLQLSEPY---SSISLSDLAKLLGL-SVP----EVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HHHHHHHHHHHHhHHh---ceeeHHHHHHHhCc-CHH----HHHHHHHHHHHCCCeEEE
Confidence 3344455555555554 58999999999999 776 799999999999988753
No 356
>smart00753 PAM PCI/PINT associated module.
Probab=54.90 E-value=33 Score=23.09 Aligned_cols=51 Identities=8% Similarity=0.139 Sum_probs=38.8
Q ss_pred HHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 35 FQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 35 L~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.....+..++.....- ..++.++||+.+++ +.+ -+++++.-++..|.+.-.
T Consensus 7 ~~~~~~~~l~~l~~~y---~~i~~~~i~~~~~l-~~~----~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00753 7 QRKIRLTNLLQLSEPY---SSISLSDLAKLLGL-SVP----EVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HHHHHHHHHHHHhHHh---ceeeHHHHHHHhCc-CHH----HHHHHHHHHHHCCCeEEE
Confidence 3344455555555554 58999999999999 776 799999999999988753
No 357
>PF13814 Replic_Relax: Replication-relaxation
Probab=54.88 E-value=21 Score=27.82 Aligned_cols=63 Identities=14% Similarity=0.193 Sum_probs=46.6
Q ss_pred HHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccC------CCCcceecccccccccc
Q 036971 46 IINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFST------HGVRLYSLAPVAKYYVS 113 (221)
Q Consensus 46 ~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~------~~~~~y~lt~~s~~L~~ 113 (221)
.|.+. +.+|.++|+..... +.. ..+.+++.|+-|...|++...... ..+-.|.+|+.+..++.
T Consensus 3 ~L~~~---r~lt~~Qi~~l~~~-~~~-~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~ 71 (191)
T PF13814_consen 3 LLARH---RFLTTDQIARLLFP-SSK-SERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLLA 71 (191)
T ss_pred hHHHh---cCcCHHHHHHHHcC-CCc-chHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHHH
Confidence 45555 58999999999988 553 123699999999999999987321 12357999999875543
No 358
>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=54.41 E-value=44 Score=22.38 Aligned_cols=43 Identities=14% Similarity=0.240 Sum_probs=30.3
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHH--hcCCceeee
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLL--VSFNILCCS 93 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L--~~~gll~~~ 93 (221)
|.+.|..- ++.|+++|++++|. .+- -++-.|-.+ -..||-...
T Consensus 15 li~mL~rp---~GATi~ei~~atGW-q~H----TvRgalsg~~kKklGl~i~s 59 (72)
T PF11994_consen 15 LIAMLRRP---EGATIAEICEATGW-QPH----TVRGALSGLLKKKLGLTITS 59 (72)
T ss_pred HHHHHcCC---CCCCHHHHHHhhCC-chh----hHHHHHHHHHHHhcCcEEEe
Confidence 45566664 47999999999999 886 666666655 445655443
No 359
>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=54.00 E-value=8.1 Score=23.89 Aligned_cols=37 Identities=19% Similarity=0.369 Sum_probs=25.5
Q ss_pred HHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHH
Q 036971 37 AVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDR 79 (221)
Q Consensus 37 ~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~r 79 (221)
...-+.+++.|...|. .-++..+||+.+|+ ++. .+++
T Consensus 11 L~~Y~r~L~~l~~~G~-~~vSS~~La~~~gi-~~~----qVRK 47 (50)
T PF06971_consen 11 LPLYLRYLEQLKEEGV-ERVSSQELAEALGI-TPA----QVRK 47 (50)
T ss_dssp HHHHHHHHHHHHHTT--SEE-HHHHHHHHTS--HH----HHHH
T ss_pred HHHHHHHHHHHHHcCC-eeECHHHHHHHHCC-CHH----Hhcc
Confidence 4445667778888765 37999999999999 876 5554
No 360
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=54.00 E-value=36 Score=23.40 Aligned_cols=53 Identities=23% Similarity=0.123 Sum_probs=35.2
Q ss_pred CCCCHHHHHhhCCCC---CCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 54 AELSASEIASQIPTK---NPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~---~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
.+.|...|.+.+.-. +...-..++.+-|.-++..|.|.+....|..|.|++++
T Consensus 22 ~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v~~G~l~~~kG~g~~gsfkl~~ 77 (88)
T cd00073 22 KGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGTGASGSFKLSK 77 (88)
T ss_pred CCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHHHCCCeEeecCCCCccceEeCC
Confidence 578888888776531 10101235778899999999999984222248888874
No 361
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=53.65 E-value=16 Score=29.58 Aligned_cols=34 Identities=18% Similarity=0.041 Sum_probs=31.4
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+.|-.+||+.+|+ .++ .+.|+|.-|...|+++..
T Consensus 169 ~~t~~~lA~~lG~-sre----tvsR~L~~L~~~G~I~~~ 202 (226)
T PRK10402 169 HEKHTQAAEYLGV-SYR----HLLYVLAQFIQDGYLKKS 202 (226)
T ss_pred cchHHHHHHHHCC-cHH----HHHHHHHHHHHCCCEEee
Confidence 4688999999999 887 999999999999999985
No 362
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=53.35 E-value=18 Score=31.63 Aligned_cols=52 Identities=6% Similarity=0.035 Sum_probs=40.5
Q ss_pred HHHhcCCCCCCCHHHHHhh--CCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccc
Q 036971 46 IINKAGPGAELSASEIASQ--IPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVA 108 (221)
Q Consensus 46 ~L~~~g~~~~~t~~eLA~~--~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s 108 (221)
++... +|++.++||+. +++ .+. -+++-|..|...|++.+.. .....-.|..+
T Consensus 19 yi~~~---~pv~s~~l~~~~~l~~-S~a----TIR~dm~~Le~~G~l~~~h---~sagrIPT~kG 72 (339)
T PRK00082 19 YIATG---EPVGSKTLSKRYGLGV-SSA----TIRNDMADLEELGLLEKPH---TSSGRIPTDKG 72 (339)
T ss_pred HHhcC---CCcCHHHHHHHhCCCC-ChH----HHHHHHHHHHhCCCcCCCc---CCCCCCcCHHH
Confidence 55554 69999999977 888 676 8999999999999999973 44445555555
No 363
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=53.32 E-value=19 Score=29.30 Aligned_cols=43 Identities=21% Similarity=0.127 Sum_probs=35.5
Q ss_pred CCC-CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceec
Q 036971 54 AEL-SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSL 104 (221)
Q Consensus 54 ~~~-t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~l 104 (221)
..+ |-.+||+.+|+ .-. .++.-|+.|...|+++... ..|.|-.
T Consensus 29 ~~LPsE~eLae~~gV-SRt----~VReAL~~L~~eGlv~~~~---g~G~~V~ 72 (239)
T PRK04984 29 SILPAERELSELIGV-TRT----TLREVLQRLARDGWLTIQH---GKPTKVN 72 (239)
T ss_pred CcCCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEeC---CCeeEeC
Confidence 467 68899999999 776 8999999999999999863 3555554
No 364
>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=53.31 E-value=16 Score=29.77 Aligned_cols=35 Identities=23% Similarity=0.188 Sum_probs=30.9
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+.+|+.+|++.+++ ++. .....|+.+...|++..+
T Consensus 189 g~vt~~~l~~~~~w-s~~----~a~~~L~~~~~~G~l~~D 223 (223)
T PF04157_consen 189 GGVTASELAEKLGW-SVE----RAKEALEELEREGLLWRD 223 (223)
T ss_dssp SEEEHHHHHHHHTB--HH----HHHHHHHHHHHTTSEEEE
T ss_pred CCCCHHHHHHHhCC-CHH----HHHHHHHHHHhCCCEeeC
Confidence 69999999999999 777 899999999999999863
No 365
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=52.97 E-value=17 Score=21.74 Aligned_cols=24 Identities=21% Similarity=0.270 Sum_probs=19.0
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHH
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGL 83 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~ 83 (221)
+.+..+||+.+++ .+. .+.+.+..
T Consensus 18 g~s~~eia~~l~i-s~~----tv~~~~~~ 41 (58)
T smart00421 18 GLTNKEIAERLGI-SEK----TVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHCC-CHH----HHHHHHHH
Confidence 6899999999999 776 66655543
No 366
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=52.95 E-value=7.7 Score=24.47 Aligned_cols=31 Identities=13% Similarity=0.368 Sum_probs=20.1
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHH
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLG 82 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr 82 (221)
|-+.+.+ ..+|..+||+.+|+ ++. .+.+++.
T Consensus 2 L~~~m~~----~~it~~~La~~~gi-s~~----tl~~~~~ 32 (63)
T PF13443_consen 2 LKELMAE----RGITQKDLARKTGI-SRS----TLSRILN 32 (63)
T ss_dssp HHHHHHH----TT--HHHHHHHHT---HH----HHHHHHT
T ss_pred HHHHHHH----cCCCHHHHHHHHCc-CHH----HHHHHHh
Confidence 4567777 46899999999999 665 6766654
No 367
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=52.89 E-value=18 Score=26.61 Aligned_cols=34 Identities=12% Similarity=0.063 Sum_probs=28.7
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCC 92 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~ 92 (221)
.+.++++||+.+|+ +++ .+.|+++....+.+-+.
T Consensus 24 ~~~sl~~lA~~~g~-S~~----~l~r~Fk~~~G~s~~~~ 57 (127)
T PRK11511 24 SPLSLEKVSERSGY-SKW----HLQRMFKKETGHSLGQY 57 (127)
T ss_pred CCCCHHHHHHHHCc-CHH----HHHHHHHHHHCcCHHHH
Confidence 37999999999999 888 99999988777666554
No 368
>PRK11760 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional
Probab=52.72 E-value=14 Score=32.45 Aligned_cols=23 Identities=22% Similarity=0.046 Sum_probs=19.9
Q ss_pred CCCCeEEEecCCccHHHHHHHhh
Q 036971 195 QNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
....++||||+++|.++..++++
T Consensus 210 ~~g~~vlDLGAsPGGWT~~L~~r 232 (357)
T PRK11760 210 APGMRAVDLGAAPGGWTYQLVRR 232 (357)
T ss_pred CCCCEEEEeCCCCcHHHHHHHHc
Confidence 45689999999999999988765
No 369
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=52.64 E-value=20 Score=24.28 Aligned_cols=49 Identities=12% Similarity=0.251 Sum_probs=33.4
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHH-HHHhcCCceeee
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVL-GLLVSFNILCCS 93 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlL-r~L~~~gll~~~ 93 (221)
+..+...|.+.=.|||+.++.||..++. ++. -+..+. -+|...|++.+.
T Consensus 10 D~~yL~~l~~~f~ggPvGl~tlA~~l~e-d~~----Tie~v~EPyLiq~G~I~RT 59 (76)
T PF05491_consen 10 DRRYLKTLIENFKGGPVGLDTLAAALGE-DKE----TIEDVIEPYLIQIGFIQRT 59 (76)
T ss_dssp HHHHHHHHHHCSTTS-B-HHHHHHHTTS--HH----HHHHTTHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHcCCCCeeHHHHHHHHCC-CHh----HHHHHhhHHHHHhhhHhhC
Confidence 3445566666312289999999999999 776 666544 478999999997
No 370
>PRK03837 transcriptional regulator NanR; Provisional
Probab=52.61 E-value=22 Score=28.96 Aligned_cols=35 Identities=17% Similarity=0.151 Sum_probs=31.9
Q ss_pred CCC-CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AEL-SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~-t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..+ +-.+||+.+|+ ... .++.-|+.|...|+++..
T Consensus 35 ~~Lp~E~~Lae~~gV-SRt----~VREAL~~L~~eGlv~~~ 70 (241)
T PRK03837 35 DQLPSERELMAFFGV-GRP----AVREALQALKRKGLVQIS 70 (241)
T ss_pred CCCCCHHHHHHHhCC-CHH----HHHHHHHHHHHCCCEEEe
Confidence 468 88999999999 776 899999999999999986
No 371
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=52.45 E-value=32 Score=29.35 Aligned_cols=47 Identities=9% Similarity=0.147 Sum_probs=35.7
Q ss_pred hhHHHHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 28 AIVLPAVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 28 g~~~~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++|....+... ...+ ..+|+++|++.+++ ....++..|..+|++...
T Consensus 207 ~YW~~~il~~L---------~~~~--~~isi~~is~~T~i--------~~~Dii~tL~~l~~l~~~ 253 (290)
T PLN03238 207 SYWTRVLLEQL---------RDVK--GDVSIKDLSLATGI--------RGEDIVSTLQSLNLIKYW 253 (290)
T ss_pred HHHHHHHHHHH---------HhcC--CCccHHHHHHHhCC--------CHHHHHHHHHHCCcEEEE
Confidence 56665555554 2322 58999999999999 567789999999999875
No 372
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=52.18 E-value=28 Score=21.94 Aligned_cols=47 Identities=17% Similarity=0.298 Sum_probs=32.4
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceec
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSL 104 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~l 104 (221)
+.|.+-.. .-+|+.-+|+.+++ .+. ...++++- +|+ .|-+ +.++|+.
T Consensus 4 Lidll~~~---P~Vsa~mva~~L~v-T~~----~A~~li~e---Lg~-rEiT---Gr~R~Ra 50 (54)
T PF11972_consen 4 LIDLLLSR---PLVSAPMVAKELGV-TPQ----AAQRLIAE---LGL-REIT---GRGRYRA 50 (54)
T ss_pred HHHHHHhC---ccccHHHHHHHhCC-CHH----HHHHHHHH---hhc-eeec---CCcccch
Confidence 55667664 25899999999999 776 77777654 455 4432 4667763
No 373
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=51.61 E-value=21 Score=29.42 Aligned_cols=35 Identities=11% Similarity=0.075 Sum_probs=31.3
Q ss_pred CCC-CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AEL-SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~-t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
..+ +-.+||+.+|+ ... .++.-|+.|...|+++..
T Consensus 30 ~~LpsE~eLae~~gV-SRt----pVREAL~~L~~eGlV~~~ 65 (253)
T PRK11523 30 DKLPAERFIADEKNV-SRT----VVREAIIMLEVEGYVEVR 65 (253)
T ss_pred CCCCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEe
Confidence 577 47899999999 776 899999999999999976
No 374
>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=51.22 E-value=19 Score=21.62 Aligned_cols=24 Identities=17% Similarity=0.123 Sum_probs=19.1
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHH
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGL 83 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~ 83 (221)
+.+..+||+.+++ ++. .+.+.++.
T Consensus 15 ~~s~~eia~~l~~-s~~----tv~~~~~~ 38 (57)
T cd06170 15 GKTNKEIADILGI-SEK----TVKTHLRN 38 (57)
T ss_pred CCCHHHHHHHHCC-CHH----HHHHHHHH
Confidence 6899999999999 776 66665544
No 375
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=51.21 E-value=19 Score=25.73 Aligned_cols=41 Identities=22% Similarity=0.250 Sum_probs=30.2
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCC--CcchhhhHHHHHHHHhc
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKN--PEGAAKMLDRVLGLLVS 86 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~--~~~~~~~l~rlLr~L~~ 86 (221)
..|++.+....+|.-.|.-|||+-.|+ + ++ .+.++|..|..
T Consensus 9 ~~v~~vv~~IP~GkV~TYGdIA~laG~-p~~AR----qVG~il~~l~~ 51 (103)
T COG3695 9 QRVLDVVAAIPEGKVSTYGDIAKLAGL-PRAAR----QVGRILKHLPE 51 (103)
T ss_pred HHHHHHHHhCCCCceeeHHHHHHHhCC-ChhHH----HHHHHHhhCCC
Confidence 345666666655577999999999999 6 44 78888876654
No 376
>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=50.44 E-value=17 Score=24.85 Aligned_cols=31 Identities=10% Similarity=0.127 Sum_probs=24.2
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHH
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVL 81 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlL 81 (221)
.|.++|.+ | ..|+.+||+..|+ ... -+.|.|
T Consensus 10 ~I~e~l~~-~---~~ti~dvA~~~gv-S~~----TVsr~L 40 (80)
T TIGR02844 10 EIGKYIVE-T---KATVRETAKVFGV-SKS----TVHKDV 40 (80)
T ss_pred HHHHHHHH-C---CCCHHHHHHHhCC-CHH----HHHHHh
Confidence 46678888 4 8999999999999 665 666644
No 377
>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=49.98 E-value=27 Score=21.53 Aligned_cols=41 Identities=15% Similarity=0.157 Sum_probs=35.5
Q ss_pred hHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 45 DIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 45 d~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
+++.+. +.+|+.++=+.+|+ .-+ .+--+|.++-..|+....
T Consensus 3 ~~~~~~---~~itv~~~rd~lg~-sRK----~ai~lLE~lD~~g~T~R~ 43 (50)
T PF09107_consen 3 ELLQKN---GEITVAEFRDLLGL-SRK----YAIPLLEYLDREGITRRV 43 (50)
T ss_dssp HHHHTT---SSBEHHHHHHHHTS--HH----HHHHHHHHHHHTTSEEEE
T ss_pred HHHhcC---CcCcHHHHHHHHCc-cHH----HHHHHHHHHhccCCEEEe
Confidence 456665 59999999999999 777 899999999999999987
No 378
>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=49.49 E-value=6.6 Score=24.31 Aligned_cols=30 Identities=17% Similarity=0.325 Sum_probs=20.3
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhc-CCceee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVS-FNILCC 92 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~-~gll~~ 92 (221)
++++.|||+.+|+ + ...+++.|.. +|+...
T Consensus 3 ~i~V~elAk~l~v-~-------~~~ii~~l~~~~Gi~~~ 33 (54)
T PF04760_consen 3 KIRVSELAKELGV-P-------SKEIIKKLFKELGIMVK 33 (54)
T ss_dssp EE-TTHHHHHHSS-S-------HHHHHHHH-HHHTS---
T ss_pred ceEHHHHHHHHCc-C-------HHHHHHHHHHhCCcCcC
Confidence 6899999999999 4 4677777744 787743
No 379
>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=49.47 E-value=23 Score=22.27 Aligned_cols=35 Identities=20% Similarity=0.332 Sum_probs=28.9
Q ss_pred CCCCHHHHHhhC---CCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQI---PTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~---g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.+++-++|-+++ ++ +++ ....+|+.|+..|.+..+
T Consensus 16 ~G~~keeLrsrl~~~~l-~~k----~~~~ll~~l~~~g~l~~~ 53 (59)
T PF09106_consen 16 PGMPKEELRSRLFKPRL-PPK----LFNALLEALVAEGRLKVE 53 (59)
T ss_dssp S-EEHHHHHHHCST-TS--HC----CHHHHHHHHHHTTSEEEE
T ss_pred cCcCHHHHHHHHhhccC-CHH----HHHHHHHHHHHCCCeeeE
Confidence 358889999888 66 666 999999999999999985
No 380
>COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]
Probab=49.38 E-value=25 Score=31.00 Aligned_cols=35 Identities=11% Similarity=-0.220 Sum_probs=32.0
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.|+++++|++.+|+ ... .+..+|-.|.-.|.+...
T Consensus 308 ~~~~~d~l~~~~~~-~~~----~~~~~L~~lel~G~i~~~ 342 (350)
T COG0758 308 EPKEIDRLASCTGL-TIA----QVLAWLLELELEGKVKRL 342 (350)
T ss_pred CCccHHHHHHHhCC-CHH----HHHHHHHHHHhcCcEEee
Confidence 59999999999999 776 888999999999999986
No 381
>PLN02476 O-methyltransferase
Probab=49.37 E-value=19 Score=30.67 Aligned_cols=26 Identities=19% Similarity=0.268 Sum_probs=22.5
Q ss_pred CCCCCeEEEecCCccHHHHHHHhhCC
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~~P 219 (221)
..+.++||+||.+.|..+..+++..|
T Consensus 116 ~~~ak~VLEIGT~tGySal~lA~al~ 141 (278)
T PLN02476 116 ILGAERCIEVGVYTGYSSLAVALVLP 141 (278)
T ss_pred hcCCCeEEEecCCCCHHHHHHHHhCC
Confidence 34579999999999999999998766
No 382
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=49.28 E-value=18 Score=23.63 Aligned_cols=27 Identities=19% Similarity=0.400 Sum_probs=22.4
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLV 85 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~ 85 (221)
.++++.|.|+.+|+ ++. .+.++++...
T Consensus 12 ~~~s~~~Aa~~lG~-~~~----~v~~wv~~fR 38 (65)
T PF05344_consen 12 QQISVAQAADRLGT-DPG----TVRRWVRMFR 38 (65)
T ss_pred ccccHHHHHHHHCc-CHH----HHHHHHHHHH
Confidence 48999999999999 887 7877776543
No 383
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=48.93 E-value=10 Score=25.10 Aligned_cols=34 Identities=21% Similarity=0.081 Sum_probs=24.9
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCC 92 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~ 92 (221)
..-|.+|||+.+|+ ++. .+..++......-.+..
T Consensus 19 r~Pt~eEiA~~lgi-s~~----~v~~~l~~~~~~~Sl~~ 52 (78)
T PF04539_consen 19 REPTDEEIAEELGI-SVE----EVRELLQASRRPVSLDL 52 (78)
T ss_dssp S--BHHHHHHHHTS--HH----HHHHHHHHHSCCEESSH
T ss_pred CCCCHHHHHHHHcc-cHH----HHHHHHHhCCCCeEEee
Confidence 47899999999999 887 89999887666554444
No 384
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=48.85 E-value=26 Score=33.83 Aligned_cols=35 Identities=23% Similarity=0.174 Sum_probs=26.8
Q ss_pred HHHHHHHHhcCCC-CCCCeEEEecCCccHHHHHHHhh
Q 036971 182 FVINKIVESYKGF-QNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 182 ~~~~~~l~~~~~~-~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
..+..++.... | .+...++|-.||+|+++++-+..
T Consensus 176 tlAaa~l~~a~-w~~~~~~l~DP~CGSGTilIEAa~~ 211 (702)
T PRK11783 176 NLAAAILLRSG-WPQEGTPLLDPMCGSGTLLIEAAMM 211 (702)
T ss_pred HHHHHHHHHcC-CCCCCCeEEccCCCccHHHHHHHHH
Confidence 44556666666 7 45679999999999999887653
No 385
>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=48.82 E-value=14 Score=21.52 Aligned_cols=22 Identities=18% Similarity=0.304 Sum_probs=17.7
Q ss_pred CCHHHHHhhCCCCCCcchhhhHHHHHH
Q 036971 56 LSASEIASQIPTKNPEGAAKMLDRVLG 82 (221)
Q Consensus 56 ~t~~eLA~~~g~~~~~~~~~~l~rlLr 82 (221)
+|++|+|+.+|+ ++. .+.++++
T Consensus 2 lt~~e~a~~lgi-s~~----ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGV-SKD----TVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCC-CHH----HHHHHHH
Confidence 588999999999 776 6777654
No 386
>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=48.55 E-value=23 Score=30.97 Aligned_cols=50 Identities=8% Similarity=0.218 Sum_probs=39.9
Q ss_pred HHHHHHHhhChhhHHHhcCCCCCCCHHHHHhh--CCCCCCcchhhhHHHHHHHHhcCCceeeec
Q 036971 33 AVFQAVVNLDVLDIINKAGPGAELSASEIASQ--IPTKNPEGAAKMLDRVLGLLVSFNILCCSF 94 (221)
Q Consensus 33 ~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~--~g~~~~~~~~~~l~rlLr~L~~~gll~~~~ 94 (221)
..|.+.|+ +++... +|++..+|++. +++ .+. -++|-|..|...|++.+..
T Consensus 6 ~il~aIV~----~~l~~~---~pv~s~~l~~~~~~~v-S~a----TiR~d~~~Le~~G~l~~~h 57 (337)
T TIGR00331 6 KILKAIVE----EYIKTG---QPVGSKTLLEKYNLGL-SSA----TIRNDMADLEDLGFIEKPH 57 (337)
T ss_pred HHHHHHHH----HHHhcC---CCcCHHHHHhhcCCCC-ChH----HHHHHHHHHHHCCCccCCC
Confidence 34445554 466665 69999999999 888 665 7899999999999999973
No 387
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=48.40 E-value=15 Score=25.84 Aligned_cols=34 Identities=12% Similarity=0.048 Sum_probs=27.1
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCC 92 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~ 92 (221)
.+.++++||+.+++ +++ .|.|+++....+.+-+.
T Consensus 20 ~~~~~~~lA~~~~~-S~~----~l~r~f~~~~g~s~~~~ 53 (107)
T PRK10219 20 QPLNIDVVAKKSGY-SKW----YLQRMFRTVTHQTLGDY 53 (107)
T ss_pred CCCCHHHHHHHHCC-CHH----HHHHHHHHHHCcCHHHH
Confidence 37999999999999 888 89998887655544443
No 388
>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=48.27 E-value=14 Score=21.39 Aligned_cols=23 Identities=26% Similarity=0.335 Sum_probs=18.4
Q ss_pred CCHHHHHhhCCCCCCcchhhhHHHHHHH
Q 036971 56 LSASEIASQIPTKNPEGAAKMLDRVLGL 83 (221)
Q Consensus 56 ~t~~eLA~~~g~~~~~~~~~~l~rlLr~ 83 (221)
+|..|+|+.+|+ ++. .+.++.+.
T Consensus 1 ~s~~e~a~~lgv-s~~----tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGV-SPS----TLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCc-CHH----HHHHHHHc
Confidence 478999999999 776 77777664
No 389
>PF05724 TPMT: Thiopurine S-methyltransferase (TPMT); InterPro: IPR008854 This family consists of thiopurine S-methyltransferase proteins from both eukaryotes and prokaryotes. Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that catalyses S-methylation of aromatic and heterocyclic sulphydryl compounds, including anticancer and immunosuppressive thiopurines [].; GO: 0008119 thiopurine S-methyltransferase activity, 0008152 metabolic process, 0005737 cytoplasm; PDB: 1PJZ_A 2H11_A 2BZG_A 3LCC_A 3BGD_A 2GB4_A 3BGI_B.
Probab=48.23 E-value=22 Score=28.97 Aligned_cols=24 Identities=21% Similarity=0.109 Sum_probs=19.8
Q ss_pred CCCCCeEEEecCCccHHHHHHHhh
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
.....+|++.|||.|..+..|+++
T Consensus 35 ~~~~~rvLvPgCG~g~D~~~La~~ 58 (218)
T PF05724_consen 35 LKPGGRVLVPGCGKGYDMLWLAEQ 58 (218)
T ss_dssp TSTSEEEEETTTTTSCHHHHHHHT
T ss_pred CCCCCeEEEeCCCChHHHHHHHHC
Confidence 344579999999999999988764
No 390
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=48.01 E-value=19 Score=31.13 Aligned_cols=34 Identities=21% Similarity=0.177 Sum_probs=31.3
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.+|-+|||+++|+ ... .+.|+|......|+|+-.
T Consensus 29 g~tQ~eIA~~lgi-SR~----~VsRlL~~Ar~~GiV~I~ 62 (318)
T PRK15418 29 GLTQSEIGERLGL-TRL----KVSRLLEKGRQSGIIRVQ 62 (318)
T ss_pred CCCHHHHHHHhCC-CHH----HHHHHHHHHHHcCcEEEE
Confidence 7999999999999 666 899999999999999865
No 391
>cd02188 gamma_tubulin Gamma-tubulin is a ubiquitous phylogenetically conserved member of tubulin superfamily. Gamma is a low abundance protein present within the cells in both various types of microtubule-organizing centers and cytoplasmic protein complexes. Gamma-tubulin recruits the alpha/beta-tubulin dimers that form the minus ends of microtubules and is thought to be involved in microtubule nucleation and capping.
Probab=48.01 E-value=23 Score=32.12 Aligned_cols=36 Identities=17% Similarity=0.318 Sum_probs=27.4
Q ss_pred HHHHHhcCCCCCCCeEEEecCCcc-----HHHHHHHhhCCC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLG-----ITLSDHNFQIPS 220 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G-----~~~~~l~~~~P~ 220 (221)
+..++.+|.+.++..+-.+|||+| .++..|...||+
T Consensus 121 r~~~E~cd~l~gf~i~~SlgGGTGSG~gs~l~e~L~d~y~~ 161 (431)
T cd02188 121 DREADGSDSLEGFVLCHSIAGGTGSGMGSYLLERLNDRYPK 161 (431)
T ss_pred HHHHhcCCCcceeEEEecCCCCcchhHHHHHHHHHHhHcCc
Confidence 345667887888999999999998 345667777774
No 392
>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=47.60 E-value=18 Score=23.95 Aligned_cols=48 Identities=13% Similarity=0.061 Sum_probs=31.2
Q ss_pred CCCCHHHHH---hhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccc
Q 036971 54 AELSASEIA---SQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPV 107 (221)
Q Consensus 54 ~~~t~~eLA---~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~ 107 (221)
+++.+.+|. +..|+ ++. .++--|-=|+..|+++.... |..-.|++|+-
T Consensus 19 ~~i~~~~Li~ll~~~Gv-~e~----avR~alsRl~~~G~L~~~r~-Gr~~~Y~Lt~~ 69 (70)
T PF07848_consen 19 GWIWVASLIRLLAAFGV-SES----AVRTALSRLVRRGWLESERR-GRRSYYRLTER 69 (70)
T ss_dssp S-EEHHHHHHHHCCTT---HH----HHHHHHHHHHHTTSEEEECC-CTEEEEEE-HH
T ss_pred CceeHHHHHHHHHHcCC-ChH----HHHHHHHHHHHcCceeeeec-CccceEeeCCC
Confidence 566666555 55677 776 89999999999999999731 11226888863
No 393
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=47.26 E-value=24 Score=29.22 Aligned_cols=59 Identities=8% Similarity=0.041 Sum_probs=47.1
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceecccccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYVS 113 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~~ 113 (221)
++..|..+.+ .-+...-|+++++ .+. .+.+-++.|. ...||++. +..+++|+.++.|.+
T Consensus 5 ~l~~f~~v~~-----~gs~s~AA~~L~i-sqp----avS~~I~~LE~~lG~~LF~R~-----~r~~~lT~~G~~l~~ 66 (275)
T PRK03601 5 LLKTFLEVSR-----TRHFGRAAESLYL-TQS----AVSFRIRQLENQLGVNLFTRH-----RNNIRLTAAGERLLP 66 (275)
T ss_pred HHHHHHHHHH-----cCCHHHHHHHhCC-ChH----HHHHHHHHHHHHhCCceEEEC-----CCceEECHhHHHHHH
Confidence 4678888998 5789999999999 766 7777776665 47888885 788999999886653
No 394
>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=46.99 E-value=18 Score=24.17 Aligned_cols=31 Identities=26% Similarity=0.191 Sum_probs=20.4
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNI 89 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gl 89 (221)
...|+.+||+.+++ .+. .+-|+.+.|--.|+
T Consensus 33 ~~~si~elA~~~~v-S~s----ti~Rf~kkLG~~gf 63 (77)
T PF01418_consen 33 AFMSISELAEKAGV-SPS----TIVRFCKKLGFSGF 63 (77)
T ss_dssp CT--HHHHHHHCTS--HH----HHHHHHHHCTTTCH
T ss_pred HHccHHHHHHHcCC-CHH----HHHHHHHHhCCCCH
Confidence 36999999999999 665 67777666544443
No 395
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=46.87 E-value=27 Score=24.71 Aligned_cols=63 Identities=11% Similarity=-0.008 Sum_probs=45.3
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceeccccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
++.+|..+.+ .-++..-|+.+++ .+. .+.+-++.|. ..-+|++.+....++.+.+|+.+..|.
T Consensus 6 ~l~~~~av~~-----~gSis~AA~~L~i-S~s----tvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~ 71 (99)
T TIGR00637 6 RVALLKAIAR-----MGSISQAAKDAGI-SYK----SAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLI 71 (99)
T ss_pred HHHHHHHHHH-----hCCHHHHHHHHCC-CHH----HHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHH
Confidence 4668888888 5789999999999 776 7776666655 466788752100145789999888765
No 396
>cd00286 Tubulin_FtsZ Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis. FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts.
Probab=46.76 E-value=27 Score=30.10 Aligned_cols=36 Identities=22% Similarity=0.274 Sum_probs=26.7
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccH-----HHHHHHhhCCC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGI-----TLSDHNFQIPS 220 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~-----~~~~l~~~~P~ 220 (221)
+..++.+|.+..+..+.++|||+|. ++..+...||+
T Consensus 80 r~~~E~cD~~~gf~i~~slgGGTGsG~~~~i~e~l~d~y~~ 120 (328)
T cd00286 80 RKEAEECDSLQGFFITHSLGGGTGSGLGPVLAERLKDEYPK 120 (328)
T ss_pred HHHHHhCCCccceEEEeecCCCccccHHHHHHHHHHHHcCc
Confidence 4456778867788999999998883 45666666763
No 397
>PF13551 HTH_29: Winged helix-turn helix
Probab=46.76 E-value=19 Score=25.26 Aligned_cols=28 Identities=21% Similarity=0.153 Sum_probs=25.7
Q ss_pred CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCc
Q 036971 57 SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNI 89 (221)
Q Consensus 57 t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gl 89 (221)
|+.++|+.+|+ +++ -+.++++.....|+
T Consensus 14 ~~~~ia~~lg~-s~~----Tv~r~~~~~~~~G~ 41 (112)
T PF13551_consen 14 TIAEIARRLGI-SRR----TVYRWLKRYREGGI 41 (112)
T ss_pred cHHHHHHHHCc-CHH----HHHHHHHHHHcccH
Confidence 79999999999 888 99999999998883
No 398
>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=46.67 E-value=54 Score=22.99 Aligned_cols=62 Identities=16% Similarity=0.244 Sum_probs=43.0
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhC--------CCCCCcchhhhHHHHHHHHhcCCceeeeccCCC----Ccceeccccccc
Q 036971 43 VLDIINKAGPGAELSASEIASQI--------PTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHG----VRLYSLAPVAKY 110 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~--------g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~----~~~y~lt~~s~~ 110 (221)
|.-.|.+ +|.+--||.+.+ .+ ++. .+.++|+-|...|++......++ .-.|++|+.++.
T Consensus 9 iL~~L~~----~~~~GYei~~~l~~~~~~~~~i-~~g----tlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~ 79 (100)
T TIGR03433 9 ILKTLSL----GPLHGYGIAQRIQQISEDVLQV-EEG----SLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRK 79 (100)
T ss_pred HHHHHhc----CCCCHHHHHHHHHHHcCCcccc-CCC----cHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHH
Confidence 3445555 588888888775 45 555 89999999999999998411001 235889888886
Q ss_pred ccc
Q 036971 111 YVS 113 (221)
Q Consensus 111 L~~ 113 (221)
+..
T Consensus 80 ~l~ 82 (100)
T TIGR03433 80 QLA 82 (100)
T ss_pred HHH
Confidence 553
No 399
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=46.65 E-value=76 Score=20.27 Aligned_cols=36 Identities=19% Similarity=0.321 Sum_probs=26.6
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV 85 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~ 85 (221)
.+.+.|.. .+.++++||..+|..++. .+.|..+...
T Consensus 41 ~a~~~l~~----~~~~~~~ia~~~g~~s~~----~f~r~Fk~~~ 76 (84)
T smart00342 41 RARRLLRD----TDLSVTEIALRVGFSSQS----YFSRAFKKLF 76 (84)
T ss_pred HHHHHHHc----CCCCHHHHHHHhCCCChH----HHHHHHHHHH
Confidence 35677776 479999999999994444 7777776544
No 400
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=46.12 E-value=29 Score=26.84 Aligned_cols=49 Identities=16% Similarity=0.220 Sum_probs=40.5
Q ss_pred HHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 33 AVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 33 ~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++....+.-.||+.|.+ +-+|.+||.+..|- + ..+-|..|-..|+++..
T Consensus 12 ~~f~s~~~kkV~~~Ls~----~W~T~~El~e~~G~-d-------~~~~L~~LkK~gLiE~q 60 (160)
T PF09824_consen 12 QTFNSEVYKKVYDELSK----GWMTEEELEEKYGK-D-------VRESLLILKKGGLIESQ 60 (160)
T ss_pred HHhCCHHHHHHHHHHHh----ccCCHHHHHHHHCc-C-------HHHHHHHHHHcCchhhc
Confidence 44455677889999999 69999999999998 3 37778889999999864
No 401
>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=46.09 E-value=23 Score=21.51 Aligned_cols=24 Identities=25% Similarity=0.277 Sum_probs=15.7
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHH
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLG 82 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr 82 (221)
...|.+|||+.+|+ ++. .+...+.
T Consensus 25 ~g~s~~eIa~~l~~-s~~----~v~~~l~ 48 (54)
T PF08281_consen 25 QGMSYAEIAEILGI-SES----TVKRRLR 48 (54)
T ss_dssp S---HHHHHHHCTS--HH----HHHHHHH
T ss_pred HCcCHHHHHHHHCc-CHH----HHHHHHH
Confidence 37999999999999 776 6665553
No 402
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=45.96 E-value=42 Score=30.56 Aligned_cols=47 Identities=13% Similarity=0.213 Sum_probs=36.9
Q ss_pred hhHHHHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 28 AIVLPAVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 28 g~~~~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++|....+.... +.. +.+|+++|++.+++ ....++..|..+|++...
T Consensus 358 ~YW~~~i~~~L~---------~~~--~~~si~~is~~T~i--------~~~Dii~tL~~l~~l~~~ 404 (450)
T PLN00104 358 GYWTRVLLEILK---------KHK--GNISIKELSDMTAI--------KAEDIVSTLQSLNLIQYR 404 (450)
T ss_pred HHHHHHHHHHHH---------hcC--CCccHHHHHHHhCC--------CHHHHHHHHHHCCCEEec
Confidence 666666665542 322 48999999999999 668899999999999975
No 403
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=45.90 E-value=23 Score=28.71 Aligned_cols=35 Identities=29% Similarity=0.294 Sum_probs=31.6
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.+.|.++||+.+++ .+. -++..+..|+..|++.+.
T Consensus 177 ~g~s~~eIA~~l~i-S~~----Tv~~~~~~~~~~~~~~~~ 211 (239)
T PRK10430 177 YEFSTDELANAVNI-SRV----SCRKYLIWLVNCHILFTS 211 (239)
T ss_pred CCcCHHHHHHHhCc-hHH----HHHHHHHHHHhCCEEEEE
Confidence 36899999999999 887 899999999999999654
No 404
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=45.86 E-value=21 Score=30.18 Aligned_cols=58 Identities=14% Similarity=0.159 Sum_probs=46.5
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhc---CCceeeeccCCCCcceeccccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVS---FNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~---~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
.+.+|..+.+ ..+...-|+++++ .+. .+.+-++.|.. .-||++. +..+.+|+.+..|.
T Consensus 6 ~L~~f~~v~e-----~gs~s~AA~~L~i-SQp----avS~~I~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~ 66 (308)
T PRK10094 6 TLRTFIAVAE-----TGSFSKAAERLCK-TTA----TISYRIKLLEENTGVALFFRT-----TRSVTLTAAGEHLL 66 (308)
T ss_pred HHHHHHHHHH-----hCCHHHHHHHhcC-CHH----HHHHHHHHHHHHhCCEEEeeC-----CCceeECHhHHHHH
Confidence 4678888998 5699999999999 665 88887777764 6788885 77899999987664
No 405
>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=45.55 E-value=51 Score=22.09 Aligned_cols=42 Identities=19% Similarity=0.090 Sum_probs=28.4
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCc
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNI 89 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gl 89 (221)
.|++.+..-..|.-.|..+||+.+|. +. ..+.+-.+|....+
T Consensus 4 ~V~~~v~~IP~G~v~TYg~iA~~~g~-p~-----~~R~Vg~al~~np~ 45 (79)
T cd06445 4 RVWEALRQIPYGEVTTYGQIAKLAGT-PK-----AARAVGSALARNPI 45 (79)
T ss_pred HHHHHHhcCCCCCcCcHHHHHHHHCC-CC-----cHHHHHHHHHhCCC
Confidence 35566666555578999999999999 63 45555555555444
No 406
>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=45.37 E-value=13 Score=23.22 Aligned_cols=27 Identities=26% Similarity=0.465 Sum_probs=21.5
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCc
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPE 71 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~ 71 (221)
-|..|+..+.. +.+..+||+.+++ .+.
T Consensus 7 ~E~~vl~~l~~-----G~~~~eIA~~l~i-s~~ 33 (58)
T PF00196_consen 7 RELEVLRLLAQ-----GMSNKEIAEELGI-SEK 33 (58)
T ss_dssp HHHHHHHHHHT-----TS-HHHHHHHHTS-HHH
T ss_pred HHHHHHHHHHh-----cCCcchhHHhcCc-chh
Confidence 45667788887 7999999999999 765
No 407
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=45.27 E-value=19 Score=32.26 Aligned_cols=21 Identities=10% Similarity=-0.083 Sum_probs=17.2
Q ss_pred CCCeEEEecCCccHHHHHHHh
Q 036971 196 NITRLVDVGGGLGITLSDHNF 216 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~ 216 (221)
..++|+|+|||+|.++.+.+.
T Consensus 220 ~g~rVLDlfsgtG~~~l~aa~ 240 (396)
T PRK15128 220 ENKRVLNCFSYTGGFAVSALM 240 (396)
T ss_pred CCCeEEEeccCCCHHHHHHHh
Confidence 357999999999999876543
No 408
>PF14557 AphA_like: Putative AphA-like transcriptional regulator
Probab=45.19 E-value=44 Score=26.23 Aligned_cols=65 Identities=15% Similarity=0.221 Sum_probs=49.5
Q ss_pred HHHHhhChhhHHHhcCCCCCCCHHHHHhhCC--------CCCCcchhhhHHHHHHHHhcCCceeeeccC--CCCcceecc
Q 036971 36 QAVVNLDVLDIINKAGPGAELSASEIASQIP--------TKNPEGAAKMLDRVLGLLVSFNILCCSFST--HGVRLYSLA 105 (221)
Q Consensus 36 ~~av~lglfd~L~~~g~~~~~t~~eLA~~~g--------~~~~~~~~~~l~rlLr~L~~~gll~~~~~~--~~~~~y~lt 105 (221)
+-++++++.-.|+. +|.+.+++|+.+. - ... .+.--++.|.-.|+++....+ ++.-.|..|
T Consensus 9 re~v~L~vLG~la~----~p~~~~~va~~vrh~~sr~~gp-s~~----Ll~~sie~Lr~eGlve~~~g~g~e~~a~l~iT 79 (175)
T PF14557_consen 9 REAVRLCVLGTLAR----GPRRYEEVAGAVRHFASRIWGP-SLD----LLGTSIELLREEGLVEAVDGEGMEDNALLAIT 79 (175)
T ss_pred HHHHHHHHHHHHhc----CCcCHHHHHHHHHHhccccccC-chh----hhhhHHHHHHhcCCcccccccCCCccceeeeC
Confidence 56788888888998 6999999998873 3 334 888999999999999987322 123468888
Q ss_pred cccc
Q 036971 106 PVAK 109 (221)
Q Consensus 106 ~~s~ 109 (221)
+-++
T Consensus 80 ~~Gr 83 (175)
T PF14557_consen 80 DAGR 83 (175)
T ss_pred cchH
Confidence 7764
No 409
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=44.96 E-value=37 Score=30.57 Aligned_cols=58 Identities=14% Similarity=0.063 Sum_probs=45.8
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccccccc
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYVS 113 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~~ 113 (221)
++-.|... .++..+++.+..|. ++. .....++.|...|++..+ ++++++|+.++.+.+
T Consensus 352 ~~~~Lr~~---~gl~~~~~~~~~g~-~~~----~~~~~l~~l~~~gll~~~-----~~~l~lT~~G~~~~d 409 (430)
T PRK08208 352 IIKSLLQA---QGLDLADYRQRFGS-DPL----RDFPELELLIDRGWLEQN-----GGRLRLTEEGLALSD 409 (430)
T ss_pred HHHHHHHh---CCcCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEE-----CCEEEECcchhhHHH
Confidence 33345443 37999999999999 776 567789999999999985 889999998877663
No 410
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=44.85 E-value=15 Score=32.73 Aligned_cols=22 Identities=14% Similarity=0.084 Sum_probs=19.4
Q ss_pred CeEEEecCCccHHHHHHHhhCC
Q 036971 198 TRLVDVGGGLGITLSDHNFQIP 219 (221)
Q Consensus 198 ~~vvDVGGG~G~~~~~l~~~~P 219 (221)
.+|+|++||.|.++..++...+
T Consensus 59 ~~vLDl~aGsG~~~l~~a~~~~ 80 (382)
T PRK04338 59 ESVLDALSASGIRGIRYALETG 80 (382)
T ss_pred CEEEECCCcccHHHHHHHHHCC
Confidence 5899999999999999987654
No 411
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=44.50 E-value=19 Score=34.81 Aligned_cols=21 Identities=5% Similarity=-0.047 Sum_probs=18.8
Q ss_pred CCeEEEecCCccHHHHHHHhh
Q 036971 197 ITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 197 ~~~vvDVGGG~G~~~~~l~~~ 217 (221)
.++|+|+|||+|.++..+++.
T Consensus 539 g~rVLDlf~gtG~~sl~aa~~ 559 (702)
T PRK11783 539 GKDFLNLFAYTGTASVHAALG 559 (702)
T ss_pred CCeEEEcCCCCCHHHHHHHHC
Confidence 579999999999999998864
No 412
>PF12728 HTH_17: Helix-turn-helix domain
Probab=44.47 E-value=17 Score=21.83 Aligned_cols=22 Identities=18% Similarity=0.193 Sum_probs=18.1
Q ss_pred CCHHHHHhhCCCCCCcchhhhHHHHHH
Q 036971 56 LSASEIASQIPTKNPEGAAKMLDRVLG 82 (221)
Q Consensus 56 ~t~~eLA~~~g~~~~~~~~~~l~rlLr 82 (221)
+|++|+|+.+|+ ++. .+.++++
T Consensus 2 lt~~e~a~~l~i-s~~----tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGI-SRS----TVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCc-CHH----HHHHHHH
Confidence 589999999999 776 7777764
No 413
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=44.15 E-value=17 Score=30.04 Aligned_cols=46 Identities=15% Similarity=0.174 Sum_probs=40.6
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccc
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVA 108 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s 108 (221)
+-+|++|+|+..++ +|. .++.++--|...|.+++. ..|.|.--++-
T Consensus 29 kiiTirdvae~~ev-~~n----~lr~lasrLekkG~LeRi----~rG~YlI~~lp 74 (269)
T COG5340 29 KIITIRDVAETLEV-APN----TLRELASRLEKKGWLERI----LRGRYLIIPLP 74 (269)
T ss_pred ceEEeHHhhhhccC-CHH----HHHHHHhhhhhcchhhhh----cCccEEEeecC
Confidence 47999999999999 888 899999999999999998 68888877653
No 414
>COG0248 GppA Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]
Probab=44.11 E-value=22 Score=32.88 Aligned_cols=23 Identities=17% Similarity=0.307 Sum_probs=17.9
Q ss_pred HHHHHhcCCCCCCCeEEEecCCcc
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLG 208 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G 208 (221)
-.+...++ +.+...++|||||+=
T Consensus 119 lGv~~~~~-~~~~~lv~DIGGGSt 141 (492)
T COG0248 119 LGVASTLP-RKGDGLVIDIGGGST 141 (492)
T ss_pred HHHHhcCC-CCCCEEEEEecCCeE
Confidence 35667777 667789999999974
No 415
>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=44.09 E-value=36 Score=28.38 Aligned_cols=31 Identities=16% Similarity=0.193 Sum_probs=21.3
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHhh
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
.++-..+ .....+||+.|-|+|.++..|++.
T Consensus 31 ~I~~~l~-i~pG~~VlEaGtGSG~lt~~l~r~ 61 (247)
T PF08704_consen 31 YILMRLD-IRPGSRVLEAGTGSGSLTHALARA 61 (247)
T ss_dssp HHHHHTT---TT-EEEEE--TTSHHHHHHHHH
T ss_pred HHHHHcC-CCCCCEEEEecCCcHHHHHHHHHH
Confidence 4555666 666799999999999999999875
No 416
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=43.75 E-value=35 Score=28.17 Aligned_cols=41 Identities=15% Similarity=0.161 Sum_probs=35.5
Q ss_pred CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecc
Q 036971 57 SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLA 105 (221)
Q Consensus 57 t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt 105 (221)
+-.+||+.+|+ .-. .++.-|+.|.+.|+++-.+ +.|+|-.+
T Consensus 36 ~EreLae~fgV-SR~----~vREAl~~L~a~Glve~r~---G~Gt~V~~ 76 (241)
T COG2186 36 SERELAERFGV-SRT----VVREALKRLEAKGLVEIRQ---GSGTFVRP 76 (241)
T ss_pred CHHHHHHHHCC-CcH----HHHHHHHHHHHCCCeeecC---CCceEecC
Confidence 46899999999 776 8999999999999999874 57788765
No 417
>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=43.45 E-value=18 Score=21.32 Aligned_cols=27 Identities=19% Similarity=0.265 Sum_probs=19.8
Q ss_pred CCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCcee
Q 036971 56 LSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILC 91 (221)
Q Consensus 56 ~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~ 91 (221)
+|+.|+|+.+|+ ++. .++++ ...|++.
T Consensus 1 ~~~~e~a~~~gv-~~~----tlr~~----~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTGV-SPS----TLRYY----ERIGLLS 27 (49)
T ss_pred CcHHHHHHHHCc-CHH----HHHHH----HHCCCCC
Confidence 478999999999 765 55554 5666665
No 418
>PF09959 DUF2193: Uncharacterized protein conserved in archaea (DUF2193); InterPro: IPR018694 This family of various hypothetical archaeal proteins has no known function
Probab=43.43 E-value=74 Score=28.56 Aligned_cols=81 Identities=17% Similarity=0.158 Sum_probs=53.7
Q ss_pred chhhhhhhHHHHhcCCchhHhhhC-Cchhhhhc-cCchHHH---HHHHHHhhhhHHHHHHHHHhcCCCCCCCeEEEecCC
Q 036971 132 MMPGWFQLKDQILEGELSYNKALG-MDFYDYLG-TDSRFNE---VFNNGMIGQTSFVINKIVESYKGFQNITRLVDVGGG 206 (221)
Q Consensus 132 ~~~~~~~L~~~l~~g~~~f~~~~g-~~~~~~l~-~~p~~~~---~F~~aM~~~~~~~~~~~l~~~~~~~~~~~vvDVGGG 206 (221)
.+.....|.+.+|....||-.-|. ....|.|. ++|.+.+ .|.++.............+.|.+|=++..|||-.=-
T Consensus 67 HyeiL~~LT~tvrPeDDPFVEhyQTP~ilEILy~eD~~F~ks~~kfi~~I~~sealIg~E~~RrygGFYGpTcVvDFAli 146 (499)
T PF09959_consen 67 HYEILKSLTDTVRPEDDPFVEHYQTPAILEILYEEDPAFRKSVEKFIEAIGKSEALIGKESARRYGGFYGPTCVVDFALI 146 (499)
T ss_pred HHHHHHHHhcccCCCCCchHhhccccHHHHHHHhcCHHHHHHHHHHHHHHhhhHHHhhHHHHHHhcCccCCceeeeeeec
Confidence 355677888888888888755443 45566555 4666654 444444444445556678889888889999997766
Q ss_pred ccHHHH
Q 036971 207 LGITLS 212 (221)
Q Consensus 207 ~G~~~~ 212 (221)
.|..+.
T Consensus 147 PGSTsN 152 (499)
T PF09959_consen 147 PGSTSN 152 (499)
T ss_pred CCchHH
Confidence 665543
No 419
>cd06059 Tubulin The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly. The delta- and epsilon-tubulins are widespread but unlike the alpha, beta, and gamma-tubulins they are not ubiquitous among eukaryotes. The alpha/beta-tubulin heterodimer is the structural subunit of microtubules. The alpha- and beta-tubulins share 40% amino-acid sequence identity, exist in several isotype forms, and undergo a variety of posttranslational modifications. The structures of alpha- and beta-tubulin are basically identical: each monomer is formed by a core of two beta-sheets surrounded by alpha-helices. The monomer structure is very compact, but can be divided into three regions based on function: the amino-termi
Probab=43.40 E-value=34 Score=30.30 Aligned_cols=37 Identities=30% Similarity=0.374 Sum_probs=25.8
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCccHH-----HHHHHhhCCC
Q 036971 184 INKIVESYKGFQNITRLVDVGGGLGIT-----LSDHNFQIPS 220 (221)
Q Consensus 184 ~~~~l~~~~~~~~~~~vvDVGGG~G~~-----~~~l~~~~P~ 220 (221)
++..++.+|.+.++..+.++|||+|.= +..+...||+
T Consensus 79 ir~~~E~cD~l~gf~i~~sl~GGTGSG~gs~l~e~l~d~y~~ 120 (382)
T cd06059 79 IRKQVEKCDSLQGFQITHSLGGGTGSGLGSLLLELLSDEYPK 120 (382)
T ss_pred HHHHHHhCCCcCceEEEEecCCCcchhHHHHHHHHHHHhcCc
Confidence 345678888778889999999998722 2334455653
No 420
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=43.19 E-value=31 Score=27.49 Aligned_cols=53 Identities=13% Similarity=0.085 Sum_probs=40.2
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecc
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLA 105 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt 105 (221)
+.+.|..+ +..|+.+||+++|+ +-. -+.|.|--|-..|.|..... .+.+|..+
T Consensus 18 ~~~~l~~~---~~~~a~~i~~~l~~-~k~----~vNr~LY~l~~~~~v~~~~~--~pp~w~~~ 70 (183)
T PHA03103 18 EVKNLGLG---EGITAIEISRKLNI-EKS----EVNKQLYKLQREGMVYMSDS--NPPKWFKT 70 (183)
T ss_pred HHHHhccC---CCccHHHHHHHhCC-CHH----HHHHHHHHHHhcCceecCCC--CCCCcccc
Confidence 44566664 59999999999999 776 79999999999999987621 24454443
No 421
>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=42.82 E-value=28 Score=22.34 Aligned_cols=25 Identities=36% Similarity=0.384 Sum_probs=20.6
Q ss_pred hhHHHHHHHHhcCCceeeeccCCCCcceec
Q 036971 75 KMLDRVLGLLVSFNILCCSFSTHGVRLYSL 104 (221)
Q Consensus 75 ~~l~rlLr~L~~~gll~~~~~~~~~~~y~l 104 (221)
+-|+.+|..++..|.++.+ +|.|++
T Consensus 36 ~eL~~fL~~lv~e~~L~~~-----~G~YkL 60 (60)
T PF08672_consen 36 EELQEFLDRLVEEGKLECS-----GGSYKL 60 (60)
T ss_dssp HHHHHHHHHHHHTTSEE-------TTEEEE
T ss_pred HHHHHHHHHHHHCCcEEec-----CCEEeC
Confidence 3799999999999999995 888875
No 422
>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=42.82 E-value=62 Score=21.94 Aligned_cols=42 Identities=17% Similarity=0.082 Sum_probs=29.4
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcC
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSF 87 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~ 87 (221)
...|++.|.+-..|.-.|..+||+.+|. +. ..+.+-.+|...
T Consensus 4 ~~~V~~~l~~IP~G~v~TYg~iA~~~g~-p~-----~~RaVg~al~~n 45 (80)
T TIGR00589 4 QQRVWQALRTIPYGETKSYGQLAARIGN-PK-----AVRAVGGANGRN 45 (80)
T ss_pred HHHHHHHHhCCCCCCcCCHHHHHHHhCC-CC-----hHHHHHHHHHhC
Confidence 3457777777766678999999999997 43 445555555544
No 423
>TIGR03439 methyl_EasF probable methyltransferase domain, EasF family. This model represents an uncharacterized domain of about 300 amino acids with homology to S-adenosylmethionine-dependent methyltransferases. Proteins with this domain are exclusively fungal. A few, such as EasF from Neotyphodium lolii, are associated with the biosynthesis of ergot alkaloids, a class of fungal secondary metabolites. EasF may, in fact, be the AdoMet:dimethylallyltryptophan N-methyltransferase, the enzyme that follows tryptophan dimethylallyltransferase (DMATS) in ergot alkaloid biosynthesis. Several other members of this family, including mug158 (meiotically up-regulated gene 158 protein) from Schizosaccharomyces pombe, contain an additional uncharacterized domain DUF323 (pfam03781).
Probab=42.52 E-value=49 Score=28.75 Aligned_cols=59 Identities=14% Similarity=0.111 Sum_probs=33.8
Q ss_pred CCchhhhhccCchHHHHHHHHHhhhhHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhhC
Q 036971 155 GMDFYDYLGTDSRFNEVFNNGMIGQTSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 155 g~~~~~~l~~~p~~~~~F~~aM~~~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
|..+|+-+-..|++-- .+.-+.-. +..++.+++.++ ....|||+|||.|.=..-|+++.
T Consensus 40 Gs~LFe~It~lpEYYp-tr~E~~iL-~~~~~~Ia~~i~---~~~~lIELGsG~~~Kt~~LL~aL 98 (319)
T TIGR03439 40 GLKLFEEITYSPEYYL-TNDEIEIL-KKHSSDIAASIP---SGSMLVELGSGNLRKVGILLEAL 98 (319)
T ss_pred HHHHHHHHHcCCccCC-hHHHHHHH-HHHHHHHHHhcC---CCCEEEEECCCchHHHHHHHHHH
Confidence 5667776666665531 11111111 122345666655 34589999999998766665543
No 424
>PRK14999 histidine utilization repressor; Provisional
Probab=42.42 E-value=34 Score=27.95 Aligned_cols=43 Identities=21% Similarity=0.208 Sum_probs=36.5
Q ss_pred CC-CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecc
Q 036971 55 EL-SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLA 105 (221)
Q Consensus 55 ~~-t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt 105 (221)
.+ |-.+||+..|+ .-. -+++-|+.|+..|++...+ +.|+|-..
T Consensus 35 ~LPsE~eLa~~~gV-SR~----TVR~Al~~L~~eGli~r~~---GkGTfV~~ 78 (241)
T PRK14999 35 RIPSEAELVAQYGF-SRM----TINRALRELTDEGWLVRLQ---GVGTFVAE 78 (241)
T ss_pred cCCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEec---CcEEEECC
Confidence 45 78999999999 766 7999999999999999974 57777654
No 425
>PF01564 Spermine_synth: Spermine/spermidine synthase; InterPro: IPR001045 Synonym(s): Spermidine aminopropyltransferase A group of polyamine biosynthetic enzymes involved in the fifth (last) step in the biosynthesis of spermidine from arginine and methionine which includes; spermidine synthase (2.5.1.16 from EC), spermine synthase (2.5.1.22 from EC) and putrescine N-methyltransferase (2.1.1.53 from EC) []. The Thermotoga maritima spermidine synthase monomer consists of two domains: an N-terminal domain composed of six beta-strands, and a Rossmann-like C- terminal domain []. The larger C-terminal catalytic core domain consists of a seven-stranded beta-sheet flanked by nine alpha helices. This domain resembles a topology observed in a number of nucleotide and dinucleotide-binding enzymes, and in S-adenosyl-L-methionine (AdoMet)- dependent methyltransferase (MTases) [].; GO: 0003824 catalytic activity; PDB: 2E5W_C 2ZSU_E 2O0L_B 2O05_B 2O06_B 2O07_B 3RW9_B 2PWP_A 2HTE_B 3RIE_B ....
Probab=41.81 E-value=20 Score=29.73 Aligned_cols=23 Identities=30% Similarity=0.306 Sum_probs=19.4
Q ss_pred CCCeEEEecCCccHHHHHHHhhC
Q 036971 196 NITRLVDVGGGLGITLSDHNFQI 218 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~~ 218 (221)
+.++|+=||||.|..+.++++..
T Consensus 76 ~p~~VLiiGgG~G~~~~ell~~~ 98 (246)
T PF01564_consen 76 NPKRVLIIGGGDGGTARELLKHP 98 (246)
T ss_dssp ST-EEEEEESTTSHHHHHHTTST
T ss_pred CcCceEEEcCCChhhhhhhhhcC
Confidence 57899999999999999998654
No 426
>PRK13256 thiopurine S-methyltransferase; Reviewed
Probab=41.68 E-value=38 Score=27.90 Aligned_cols=22 Identities=9% Similarity=-0.142 Sum_probs=18.8
Q ss_pred CCCeEEEecCCccHHHHHHHhh
Q 036971 196 NITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
...+|++.|||.|..+.-|+++
T Consensus 43 ~~~rvLvPgCGkg~D~~~LA~~ 64 (226)
T PRK13256 43 DSSVCLIPMCGCSIDMLFFLSK 64 (226)
T ss_pred CCCeEEEeCCCChHHHHHHHhC
Confidence 4479999999999999888764
No 427
>PF14881 Tubulin_3: Tubulin domain
Probab=41.34 E-value=31 Score=27.26 Aligned_cols=34 Identities=24% Similarity=0.226 Sum_probs=28.6
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhh
Q 036971 184 INKIVESYKGFQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 184 ~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
...+++.||.+.+++.++|+-+|-|.++..+++.
T Consensus 64 lR~f~EECD~lQGfQ~~~d~d~gwgGfas~~Le~ 97 (180)
T PF14881_consen 64 LRFFLEECDSLQGFQVLTDVDDGWGGFASSLLEH 97 (180)
T ss_pred HHHHHHHcccccceEEEecCCCchHhHHHHHHHH
Confidence 3567889998899999999999999998777654
No 428
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=40.70 E-value=48 Score=31.51 Aligned_cols=35 Identities=11% Similarity=0.114 Sum_probs=32.1
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.|-++.||++.+++ ++. ....+|+.|+..|.+.+.
T Consensus 505 ~p~~~~~~~~~l~~-~~~----~~~~~l~~l~~~g~lv~l 539 (614)
T PRK10512 505 EPWWVRDLAKETGT-DEQ----AMRLTLRQAAQQGIITAI 539 (614)
T ss_pred CCCCHHHHHHHhCC-CHH----HHHHHHHHHHHCCCEEEe
Confidence 48999999999999 887 899999999999988886
No 429
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=40.56 E-value=32 Score=27.54 Aligned_cols=31 Identities=13% Similarity=0.230 Sum_probs=25.6
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.+|+++|++++++ ....++..|..++++...
T Consensus 150 ~isi~~is~~Tgi--------~~~DIi~tL~~l~~l~~~ 180 (188)
T PF01853_consen 150 SISIKDISQETGI--------RPEDIISTLQQLGMLKYY 180 (188)
T ss_dssp -EEHHHHHHHH-B--------THHHHHHHHHHTT-EEEE
T ss_pred eEEHHHHHHHHCC--------CHHHHHHHHHHCCCEEEE
Confidence 5999999999999 567889999999999986
No 430
>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=40.54 E-value=33 Score=19.85 Aligned_cols=33 Identities=21% Similarity=0.148 Sum_probs=23.7
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHH
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGL 83 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~ 83 (221)
.+|..+.. ...+..+||+.+|+ +.. .+.+++..
T Consensus 17 ~~~~~~~~----~~~~~~~ia~~~~~-s~~----~i~~~~~~ 49 (55)
T cd06171 17 EVILLRFG----EGLSYEEIAEILGI-SRS----TVRQRLHR 49 (55)
T ss_pred HHHHHHHh----cCCCHHHHHHHHCc-CHH----HHHHHHHH
Confidence 34445543 26899999999999 776 77766654
No 431
>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=40.46 E-value=32 Score=27.89 Aligned_cols=41 Identities=22% Similarity=0.193 Sum_probs=35.4
Q ss_pred CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecc
Q 036971 57 SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLA 105 (221)
Q Consensus 57 t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt 105 (221)
|-.|||+..|+ .-. -+++-|+.|+..|++.+.+ +.|+|-..
T Consensus 26 sE~eLa~~~gV-SR~----TVR~Al~~L~~eGli~r~~---G~GTfV~~ 66 (233)
T TIGR02404 26 SEHELMDQYGA-SRE----TVRKALNLLTEAGYIQKIQ---GKGSIVLN 66 (233)
T ss_pred CHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEeC---CceEEEec
Confidence 67899999999 666 7999999999999999985 57888643
No 432
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=40.29 E-value=29 Score=26.17 Aligned_cols=45 Identities=16% Similarity=0.181 Sum_probs=33.6
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
-+-..+|.+.++. |-+++.|+|+.+++ -++ |+.+.|...+++...
T Consensus 33 PKv~f~D~v~~~~--gli~~re~AK~lki-ge~-------~l~~~L~e~~~l~~~ 77 (135)
T COG3645 33 PKVEFADAVVEAS--GLILFRELAKLLKI-GEN-------RLFAWLRENKYLIKR 77 (135)
T ss_pred cchHHHHHHhcCc--cceeHHHHHHHHcc-CHH-------HHHHHHHHCCEEEEc
Confidence 3445688888876 67999999999999 554 445555678888775
No 433
>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=40.29 E-value=44 Score=31.53 Aligned_cols=42 Identities=5% Similarity=-0.183 Sum_probs=35.9
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceec
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSL 104 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~l 104 (221)
.|-.+.|+++.+++ ++. .++.+|+.|+..|.+.+- .++.|-+
T Consensus 487 ~~~~~~~~~~~~~~-~~~----~~~~~l~~l~~~g~~~~~----~~~~~~~ 528 (581)
T TIGR00475 487 KGAWVREFAEEVNG-DEK----VMLKRVRKAGHRGGETLI----VKDRLLK 528 (581)
T ss_pred CCCCHHHHHhhhCC-CHH----HHHHHHHHHHhCCCEEEE----eCCeEHH
Confidence 48999999999999 887 899999999999988876 4666555
No 434
>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=40.20 E-value=43 Score=27.30 Aligned_cols=57 Identities=11% Similarity=0.106 Sum_probs=45.6
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceeccccccccc
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
+..|..+.+ .-+...-|+++++ .+. .+.+-+..|. ..-||++. +...++|+.+..|.
T Consensus 2 l~~f~~v~~-----~gs~~~AA~~L~i-sqs----avS~~i~~LE~~lg~~Lf~R~-----~~~~~lT~~G~~l~ 61 (279)
T TIGR03339 2 LKAFHAVAR-----CGSFTRAAERLGL-SQP----TVTDQVRKLEERYGVELFHRN-----GRRLELTDAGHRLL 61 (279)
T ss_pred chhhHHHHh-----cCCHHHHHHHhcC-Cch----HHHHHHHHHHHHhCCccEEEc-----CCeEEEChhHHHHH
Confidence 567888998 4699999999999 776 7877777666 46888885 77899999887654
No 435
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=39.99 E-value=69 Score=25.50 Aligned_cols=58 Identities=19% Similarity=0.151 Sum_probs=42.0
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccC---CCCcceecccccc
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFST---HGVRLYSLAPVAK 109 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~---~~~~~y~lt~~s~ 109 (221)
+.+.-+|+=. +|+|-.+|-+.-|. ...++++.|...|++++.... |.+-.|..|+...
T Consensus 95 lEtLAiIAY~---QPiTR~eI~~iRGv--------~~~~~i~~L~e~glI~~~g~~~~~Grp~ly~tT~~Fl 155 (184)
T COG1386 95 LETLAIIAYK---QPVTRSEIEEIRGV--------AVSQVISTLLERGLIREVGRRDTPGRPYLYGTTEKFL 155 (184)
T ss_pred HHHHHHHHHc---CCccHHHHHHHhCc--------cHHHHHHHHHHCCCeEecCCCCCCCCceeeeccHHHH
Confidence 3455566666 69999999999999 456699999999999997321 2234566666543
No 436
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=39.92 E-value=40 Score=28.00 Aligned_cols=59 Identities=17% Similarity=0.243 Sum_probs=46.8
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceecccccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYVS 113 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~~ 113 (221)
.|.+|-.+.+ .-++..-|+.+++ .+. .+.|-++.|. ..-||++. +....+|+.+..|.+
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 HLRYFVAVAE-----ELNFTKAAEKLHT-AQP----SLSQQIKDLENCVGVPLLVRD-----KRKVALTAAGEVFLQ 66 (296)
T ss_pred HHHHHHHHHh-----hCCHHHHHHHhCC-CCc----HHHHHHHHHHHHhCCeeeeeC-----CCcceEcHhHHHHHH
Confidence 4677888888 4699999999999 776 7877777766 47888885 778999998876653
No 437
>PTZ00387 epsilon tubulin; Provisional
Probab=39.89 E-value=35 Score=31.31 Aligned_cols=36 Identities=25% Similarity=0.397 Sum_probs=26.3
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccH-----HHHHHHhhCCC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGI-----TLSDHNFQIPS 220 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~-----~~~~l~~~~P~ 220 (221)
+..++.+|.+.++..+-.+|||+|. ++..+...||+
T Consensus 122 r~~~E~cD~l~gf~i~~slgGGTGSGlgs~lle~l~d~y~~ 162 (465)
T PTZ00387 122 RRQVEQCDSLQSFFLMHSLGGGTGSGLGTRILGMLEDEFPH 162 (465)
T ss_pred HHHHHhccCcceEEEEeecCCCcchhHHHHHHHHHHHhccc
Confidence 4567788877888999999999982 34455566664
No 438
>PLN03239 histone acetyltransferase; Provisional
Probab=39.77 E-value=1.1e+02 Score=26.88 Aligned_cols=50 Identities=20% Similarity=0.228 Sum_probs=37.4
Q ss_pred hhHHHHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 28 AIVLPAVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 28 g~~~~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
++|....+....+. .+.+..+|+++|++.+|+ ....++..|..+|++...
T Consensus 265 ~YW~~~il~~L~~~--------~~~~~~~si~dis~~Tgi--------~~~DIi~tL~~l~~l~~~ 314 (351)
T PLN03239 265 PYWGSTIVDFLLNH--------SGNDSSLSIMDIAKKTSI--------MAEDIVFALNQLGILKFI 314 (351)
T ss_pred HHHHHHHHHHHHhc--------cCCCCCccHHHHHHHhCC--------CHHHHHHHHHHCCcEEEE
Confidence 66776666654432 111136999999999999 668899999999999875
No 439
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=39.58 E-value=44 Score=27.59 Aligned_cols=58 Identities=10% Similarity=0.088 Sum_probs=45.3
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceeccccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
.+..|-.+.+ ..++..-|+++++ .+. .+.+-++.|. ..-||++. +..+.+|+.+..|.
T Consensus 7 ~L~~f~~v~e-----~~s~t~AA~~L~i-sqp----avS~~I~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~ 67 (290)
T PRK10837 7 QLEVFAEVLK-----SGSTTQASVMLAL-SQS----AVSAALTDLEGQLGVQLFDRV-----GKRLVVNEHGRLLY 67 (290)
T ss_pred HHHHHHHHHH-----cCCHHHHHHHhCC-Ccc----HHHHHHHHHHHHhCCccEeec-----CCeEEECHhHHHHH
Confidence 4667888888 4699999999999 666 7777666665 47889885 77799999987655
No 440
>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=39.58 E-value=23 Score=21.23 Aligned_cols=25 Identities=24% Similarity=0.343 Sum_probs=18.9
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHH
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGL 83 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~ 83 (221)
.+.|..|||+.+|+ +.. .++++.+-
T Consensus 19 ~~~t~~eIa~~lg~-s~~----~V~~~~~~ 43 (50)
T PF04545_consen 19 EGLTLEEIAERLGI-SRS----TVRRILKR 43 (50)
T ss_dssp ST-SHHHHHHHHTS-CHH----HHHHHHHH
T ss_pred CCCCHHHHHHHHCC-cHH----HHHHHHHH
Confidence 47999999999999 776 67666543
No 441
>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=39.49 E-value=30 Score=24.02 Aligned_cols=33 Identities=18% Similarity=0.293 Sum_probs=26.3
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHH
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGL 83 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~ 83 (221)
..|+..+.. +.|..+||+.+|+ +.. -+.|+.+.
T Consensus 41 ~~I~~ll~~-----G~S~~eIA~~LgI-Srs----TIyRi~R~ 73 (88)
T TIGR02531 41 LQVAKMLKQ-----GKTYSDIEAETGA-STA----TISRVKRC 73 (88)
T ss_pred HHHHHHHHC-----CCCHHHHHHHHCc-CHH----HHHHHHHh
Confidence 556677776 6899999999999 776 78887764
No 442
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=39.40 E-value=43 Score=27.36 Aligned_cols=44 Identities=20% Similarity=0.222 Sum_probs=36.5
Q ss_pred CCC-CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecc
Q 036971 54 AEL-SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLA 105 (221)
Q Consensus 54 ~~~-t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt 105 (221)
..+ |-.+||+..|+ .-. -+++-|+.|+..|++...+ +.|+|-..
T Consensus 27 ~~LPsE~eL~~~~~V-SR~----TvR~Al~~L~~eGli~r~~---G~GtfV~~ 71 (240)
T PRK09764 27 DALPTESALQTEFGV-SRV----TVRQALRQLVEQQILESIQ---GSGTYVKE 71 (240)
T ss_pred CcCCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEec---CceeEEcc
Confidence 356 67999999999 766 7999999999999999874 56777643
No 443
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=39.10 E-value=35 Score=28.41 Aligned_cols=58 Identities=12% Similarity=0.135 Sum_probs=45.4
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceeccccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
.+.+|-.+.+ ..|...-|+++++ .+. .+.+-++.|. ..-||++. +..+.+|+.+..|.
T Consensus 7 ~l~~f~~v~~-----~gS~s~AA~~L~i-sq~----avS~~I~~LE~~lg~~LF~R~-----~~~~~lT~~G~~l~ 67 (300)
T TIGR02424 7 HLQCFVEVAR-----QGSVKRAAEALHI-TQP----AVSKTLRELEEILGTPLFERD-----RRGIRLTRYGELFL 67 (300)
T ss_pred HHHHHHHHHH-----hCCHHHHHHHhCC-ChH----HHHHHHHHHHHHhCCeEEEEc-----CCCccccHhHHHHH
Confidence 4567888888 5699999999999 776 7877777665 47888885 77789999886554
No 444
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=39.08 E-value=31 Score=27.07 Aligned_cols=35 Identities=23% Similarity=0.206 Sum_probs=25.8
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHH
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLL 84 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L 84 (221)
..+++...- .+.|.+|||+.+|+ .++ .+.|-|+.+
T Consensus 141 ~~~v~l~~~----~Gls~~EIA~~lgi-S~~----tV~r~l~~a 175 (185)
T PF07638_consen 141 RRVVELRFF----EGLSVEEIAERLGI-SER----TVRRRLRRA 175 (185)
T ss_pred HHHHHHHHH----CCCCHHHHHHHHCc-CHH----HHHHHHHHH
Confidence 345555554 37999999999999 887 777766654
No 445
>PF02384 N6_Mtase: N-6 DNA Methylase; InterPro: IPR003356 This domain is fpound in N-6 adenine-specific DNA methylase (2.1.1.72 from EC) from Type I and Type IC restriction systems. These enzymes are responsible for the methylation of specific DNA sequences in order to prevent the host from digesting its own genome via its restriction enzymes. These methylases have the same sequence specificity as their corresponding restriction enzymes. The type I restriction and modification system is composed of three polypeptides R, M and S. The M and S subunits together form a methyltransferase that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. In the presence of the R subunit, the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence. When the target site is unmodified, the DNA is cut. When the target site is hemimethylated, the complex acts as a maintenance methyltransferase, modifying the DNA so that both strands become methylated.; GO: 0003677 DNA binding, 0008170 N-methyltransferase activity, 0006306 DNA methylation; PDB: 2F8L_A 2Y7C_C 2Y7H_C 2AR0_B 3KHK_A 3LKD_A 2OKC_B.
Probab=38.97 E-value=41 Score=28.51 Aligned_cols=24 Identities=17% Similarity=-0.035 Sum_probs=18.1
Q ss_pred CCCCCeEEEecCCccHHHHHHHhh
Q 036971 194 FQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 194 ~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
-....+|+|-.||+|.++.++.+.
T Consensus 44 ~~~~~~VlDPacGsG~fL~~~~~~ 67 (311)
T PF02384_consen 44 PKKGDSVLDPACGSGGFLVAAMEY 67 (311)
T ss_dssp T-TTEEEEETT-TTSHHHHHHHHH
T ss_pred ccccceeechhhhHHHHHHHHHHh
Confidence 334568999999999999888763
No 446
>KOG0822 consensus Protein kinase inhibitor [Cell cycle control, cell division, chromosome partitioning]
Probab=38.96 E-value=63 Score=30.28 Aligned_cols=53 Identities=11% Similarity=0.222 Sum_probs=36.7
Q ss_pred hhhhhccCchHHHHHHHHHhhhhHHHHHHHHHhcCCCC--CCCeEEEecCCccHHHHHHHhh
Q 036971 158 FYDYLGTDSRFNEVFNNGMIGQTSFVINKIVESYKGFQ--NITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 158 ~~~~l~~~p~~~~~F~~aM~~~~~~~~~~~l~~~~~~~--~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
.|+.++++|-.-+.|++|.- ..+++..+.-+ ....|.=+|||+|-+..+..++
T Consensus 334 TYetFEkD~VKY~~Yq~Ai~-------~AL~Drvpd~~a~~~tVimvlGaGRGPLv~~~lka 388 (649)
T KOG0822|consen 334 TYETFEKDPVKYDQYQQAIL-------KALLDRVPDESAKTTTVIMVLGAGRGPLVDASLKA 388 (649)
T ss_pred hhhhhhccchHHHHHHHHHH-------HHHHhhCcccccCceEEEEEecCCCccHHHHHHHH
Confidence 57777888877777777753 24455555212 2568889999999998777654
No 447
>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]
Probab=38.93 E-value=51 Score=27.67 Aligned_cols=31 Identities=19% Similarity=0.199 Sum_probs=25.4
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHhh
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
.++.... .+...+|+|.|-|+|.++..|++.
T Consensus 85 ~I~~~~g-i~pg~rVlEAGtGSG~lt~~La~~ 115 (256)
T COG2519 85 YIVARLG-ISPGSRVLEAGTGSGALTAYLARA 115 (256)
T ss_pred HHHHHcC-CCCCCEEEEcccCchHHHHHHHHh
Confidence 4555666 667899999999999999999864
No 448
>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=38.78 E-value=17 Score=21.98 Aligned_cols=11 Identities=18% Similarity=0.274 Sum_probs=7.1
Q ss_pred CHHHHHhhCCC
Q 036971 57 SASEIASQIPT 67 (221)
Q Consensus 57 t~~eLA~~~g~ 67 (221)
|+.|||+.+|+
T Consensus 1 Ti~dIA~~agv 11 (46)
T PF00356_consen 1 TIKDIAREAGV 11 (46)
T ss_dssp CHHHHHHHHTS
T ss_pred CHHHHHHHHCc
Confidence 45666666666
No 449
>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=38.36 E-value=33 Score=29.87 Aligned_cols=46 Identities=20% Similarity=0.265 Sum_probs=36.0
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeec
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSF 94 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~ 94 (221)
|+++|..+|. .++-..+|-.++++ +.. .+.+.|+.|.+.+++...+
T Consensus 89 vy~~I~~ag~-~GIw~~~i~~~t~l-~~~----~~~k~lk~Le~k~lIK~vk 134 (327)
T PF05158_consen 89 VYQLIEEAGN-KGIWTKDIKKKTNL-HQT----QLTKILKSLESKKLIKSVK 134 (327)
T ss_dssp HHHHHHHHTT-T-EEHHHHHHHCT---HH----HHHHHHHHHHHTTSEEEE-
T ss_pred HHHHHHHhCC-CCCcHHHHHHHcCC-CHH----HHHHHHHHHHhCCCEEEec
Confidence 4666777654 57889999999999 887 9999999999999999974
No 450
>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=38.30 E-value=21 Score=21.62 Aligned_cols=24 Identities=21% Similarity=0.339 Sum_probs=17.7
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHH
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLG 82 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr 82 (221)
..+|..|+|+.+|+ ++. .+.+++.
T Consensus 8 ~gls~~~la~~~gi-s~~----~i~~~~~ 31 (55)
T PF01381_consen 8 KGLSQKELAEKLGI-SRS----TISRIEN 31 (55)
T ss_dssp TTS-HHHHHHHHTS--HH----HHHHHHT
T ss_pred cCCCHHHHHHHhCC-Ccc----hhHHHhc
Confidence 47999999999999 776 7777654
No 451
>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=38.13 E-value=36 Score=26.83 Aligned_cols=42 Identities=7% Similarity=0.132 Sum_probs=32.2
Q ss_pred HHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh
Q 036971 35 FQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV 85 (221)
Q Consensus 35 L~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~ 85 (221)
|.--++..|++.+.. .+.|+.+||+..|+ +.. .+..++|.-.
T Consensus 17 lse~~r~~Iy~~~~~----~~~sv~~vS~~ygi-~~~----RV~AIvrLke 58 (172)
T PF12298_consen 17 LSEELREQIYEDVMQ----DGKSVREVSQKYGI-KIQ----RVEAIVRLKE 58 (172)
T ss_pred CCHHHHHHHHHHHHh----CCCCHHHHHHHhCC-CHH----HHHHHHHHHH
Confidence 334456678888888 47899999999999 776 7877777644
No 452
>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=38.09 E-value=37 Score=27.51 Aligned_cols=42 Identities=19% Similarity=0.264 Sum_probs=35.6
Q ss_pred CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 57 SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 57 t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
|-.|||+..|+ .-. -+++-|+.|+..|++...+ +.|+|-...
T Consensus 34 sE~eLa~~~~V-SR~----TvR~Al~~L~~eGli~r~~---G~GtfV~~~ 75 (238)
T TIGR02325 34 AEMQLAERFGV-NRH----TVRRAIAALVERGLLRAEQ---GRGTFVAAR 75 (238)
T ss_pred CHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEec---CCEEEECCC
Confidence 67799999999 665 7999999999999999984 577887543
No 453
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=38.03 E-value=43 Score=27.72 Aligned_cols=58 Identities=12% Similarity=0.150 Sum_probs=45.2
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceeccccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
++.+|..+.+ ..++..-|+++++ .+. .+.+-+..|. ..-||.+. ...+.+|+.+..|.
T Consensus 5 ~L~~f~~v~~-----~gs~s~AA~~L~i-sqs----avS~~i~~LE~~lg~~Lf~R~-----~~~~~lT~~G~~l~ 65 (296)
T PRK11242 5 HIRYFLAVAE-----HGNFTRAAEALHV-SQP----TLSQQIRQLEESLGVQLFDRS-----GRTVRLTDAGEVYL 65 (296)
T ss_pred HHHHHHHHHH-----hCCHHHHHHHcCC-Cch----HHHHHHHHHHHHhCCeeEeEc-----CCceeechhHHHHH
Confidence 4678888888 4689999999999 776 7877777666 46788884 77788888876554
No 454
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=37.94 E-value=36 Score=28.50 Aligned_cols=58 Identities=21% Similarity=0.321 Sum_probs=46.9
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceeccccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
++.+|..+.+ ..+...-|+++++ .+. .+.+-+..|. ..-||.+. +..+.+|+.+..|.
T Consensus 6 ~L~~f~~v~e-----~~s~s~AA~~L~i-sQp----avS~~I~~LE~~lg~~LF~R~-----~r~~~lT~~G~~l~ 66 (300)
T PRK11074 6 SLEVVDAVAR-----TGSFSAAAQELHR-VPS----AVSYTVRQLEEWLAVPLFERR-----HRDVELTPAGEWFV 66 (300)
T ss_pred HHHHHHHHHH-----hCCHHHHHHHhCC-CHH----HHHHHHHHHHHHhCCeeEEeC-----CCCceECccHHHHH
Confidence 4678999998 5689999999999 666 8888777776 47788885 77799999987665
No 455
>cd06060 misato Human Misato shows similarity with Tubulin/FtsZ family of GTPases and is localized to the the outer membrane of mitochondria. It has a role in mitochondrial fusion and in mitochondrial distribution and morphology. Mutations in its Drosophila homolog (misato) lead to irregular chromosome segregation during mitosis. Deletion of the budding yeast homolog DML1 is lethal and unregulate expression of DML1 leads to mitochondrial dispersion and abnormalities in cell morphology. The Misato/DML1 protein family is conserved from yeast to human, but its exact function is still unknown.
Probab=37.77 E-value=34 Score=31.59 Aligned_cols=34 Identities=18% Similarity=0.103 Sum_probs=28.5
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCccHHHHHHHhh
Q 036971 184 INKIVESYKGFQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 184 ~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
++..++.+|.+.++..+.|++||.|.++..+++.
T Consensus 141 IR~~vEeCD~LQGFqi~~sl~gG~sG~gs~lLE~ 174 (493)
T cd06060 141 LRFYVEECDYLQGFQVLCDLHDGFSGVGAKCLEH 174 (493)
T ss_pred HHHHHHhCcccccEEEEEecCCcccchHHHHHHH
Confidence 3556788998899999999999999998877664
No 456
>PRK14096 pgi glucose-6-phosphate isomerase; Provisional
Probab=37.58 E-value=52 Score=30.70 Aligned_cols=42 Identities=24% Similarity=0.367 Sum_probs=33.2
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcC
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSF 87 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~ 87 (221)
-.|-..|...+ ++.|+++||+++|. +. +.+.+..+||.|++.
T Consensus 466 ~~~~~~~~~~~--~~~~~~~~~~~~~~-~~--~~~~~~~i~~~~~~n 507 (528)
T PRK14096 466 KKVEELLKEDG--GELSIEEIAAALGA-PE--QVETIYKILRHLAAN 507 (528)
T ss_pred HHHHHHHhccC--CCCCHHHHHHHcCC-Cc--cHHHHHHHHHHHhcC
Confidence 44566775655 68999999999998 44 355899999999986
No 457
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=37.30 E-value=46 Score=23.22 Aligned_cols=32 Identities=34% Similarity=0.490 Sum_probs=25.0
Q ss_pred hhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHH
Q 036971 43 VLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGL 83 (221)
Q Consensus 43 lfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~ 83 (221)
+=+.+... .+|.++||+.+++ ++. .+.++|..
T Consensus 15 Lq~nf~~~----~ls~~~ia~dL~~-s~~----~le~vL~l 46 (89)
T PF10078_consen 15 LQANFELS----GLSLEQIAADLGT-SPE----HLEQVLNL 46 (89)
T ss_pred HHHHHHHc----CCCHHHHHHHhCC-CHH----HHHHHHcC
Confidence 34566664 6999999999999 887 88887753
No 458
>COG5023 Tubulin [Cytoskeleton]
Probab=37.13 E-value=66 Score=28.70 Aligned_cols=46 Identities=26% Similarity=0.406 Sum_probs=33.2
Q ss_pred HHHHHHHhhhhHHHHHHHHHhcCCCCCCCeEEEecCCccH-----HHHHHHhhCCC
Q 036971 170 EVFNNGMIGQTSFVINKIVESYKGFQNITRLVDVGGGLGI-----TLSDHNFQIPS 220 (221)
Q Consensus 170 ~~F~~aM~~~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~-----~~~~l~~~~P~ 220 (221)
++++..|.- ++...+.+|.++++..+=-+|||+|. ++.+|+..||+
T Consensus 111 e~~ddvmd~-----IrreAd~cD~LqGF~l~HS~gGGTGSG~GslLLerl~~eypk 161 (443)
T COG5023 111 EIIDDVMDM-----IRREADGCDGLQGFLLLHSLGGGTGSGLGSLLLERLREEYPK 161 (443)
T ss_pred HHHHHHHHH-----HHHHhhcCccccceeeeeeccCcCcccHHHHHHHHHHHhcch
Confidence 345555543 34456678888888888899999985 46778888885
No 459
>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=37.02 E-value=39 Score=27.37 Aligned_cols=45 Identities=22% Similarity=0.282 Sum_probs=37.0
Q ss_pred CCC-CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 54 AEL-SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 54 ~~~-t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
..+ |-.+||+..|+ .-. -+++-|..|+..|++...+ +.|+|-..+
T Consensus 23 ~~LPsE~eLa~~~~V-SR~----TVR~Al~~L~~eGli~r~~---G~GtfV~~~ 68 (230)
T TIGR02018 23 HRIPSEHELVAQYGC-SRM----TVNRALRELTDAGLLERRQ---GVGTFVAEP 68 (230)
T ss_pred CcCcCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEec---CCEEEEccC
Confidence 345 77899999999 766 7999999999999999984 577776543
No 460
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=36.73 E-value=43 Score=28.28 Aligned_cols=59 Identities=10% Similarity=0.167 Sum_probs=46.4
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceeccccccccc
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
-.+.+|..+.+ ..|...-|+++++ .+. .+.+-++.|. ..-||++. +....+|+.+..|.
T Consensus 10 ~~L~~F~av~e-----~gs~s~AA~~L~i-SQp----avS~~I~~LE~~lg~~LF~R~-----~r~~~lT~~G~~l~ 71 (312)
T PRK10341 10 QHLVVFQEVIR-----SGSIGSAAKELGL-TQP----AVSKIINDIEDYFGVELIVRK-----NTGVTLTPAGQVLL 71 (312)
T ss_pred HHHHHHHHHHH-----cCCHHHHHHHhCC-ChH----HHHHHHHHHHHHhCCeEEEEc-----CCCceEChhHHHHH
Confidence 45778888998 6799999999999 666 7877777666 46788885 77889998886554
No 461
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=36.72 E-value=43 Score=27.99 Aligned_cols=58 Identities=14% Similarity=0.056 Sum_probs=45.4
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceeccccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
.+.+|-.+.+ ..++..-|+++++ .+. .+.+-++.|. ..-||.+. ...+.+|+.++.|.
T Consensus 8 ~L~~F~~v~e-----~gs~s~AA~~L~i-sqp----avS~~I~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~ 68 (296)
T PRK11062 8 HLYYFWMVCK-----EGSVVGAAEALFL-TPQ----TITGQIKALEERLQGKLFKRK-----GRGLEPTELGELVF 68 (296)
T ss_pred HHHHHHHHHh-----cCCHHHHHHHhCC-ChH----HHHHHHHHHHHHcCccceeec-----CCceeECHhHHHHH
Confidence 5778888888 5789999999999 666 7776666665 47788885 77899999887554
No 462
>KOG4300 consensus Predicted methyltransferase [General function prediction only]
Probab=36.34 E-value=66 Score=26.51 Aligned_cols=15 Identities=27% Similarity=0.508 Sum_probs=12.1
Q ss_pred CCCeEEEecCCccHH
Q 036971 196 NITRLVDVGGGLGIT 210 (221)
Q Consensus 196 ~~~~vvDVGGG~G~~ 210 (221)
....|+.||||+|..
T Consensus 76 ~K~~vLEvgcGtG~N 90 (252)
T KOG4300|consen 76 GKGDVLEVGCGTGAN 90 (252)
T ss_pred CccceEEecccCCCC
Confidence 345789999999974
No 463
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=36.20 E-value=47 Score=27.74 Aligned_cols=58 Identities=7% Similarity=0.095 Sum_probs=45.2
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceeccccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
.+.+|..+.+ .-+...-|+++++ .+. .+.+-++.|. ..-||++. +..+.+|+.+..|.
T Consensus 9 ~L~~f~~v~~-----~gs~s~AA~~L~i-sQ~----avS~~i~~LE~~lG~~LF~R~-----~r~~~lT~~G~~l~ 69 (302)
T PRK09791 9 QIRAFVEVAR-----QGSIRGASRMLNM-SQP----ALTKSIQELEEGLAAQLFFRR-----SKGVTLTDAGESFY 69 (302)
T ss_pred HHHHHHHHHH-----cCCHHHHHHHhCC-ChH----HHHHHHHHHHHHhCCeEEEEc-----CCCceECccHHHHH
Confidence 5678888888 4599999999999 666 7776666665 57888885 77789999887654
No 464
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=36.16 E-value=48 Score=27.88 Aligned_cols=34 Identities=18% Similarity=0.136 Sum_probs=29.0
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCC 92 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~ 92 (221)
.+.++++||+.+|+ ++. .+.|+++......+-+.
T Consensus 20 ~~~~l~~lA~~~~~-S~~----~l~r~F~~~~g~s~~~y 53 (289)
T PRK15121 20 QPLSLDNVAAKAGY-SKW----HLQRMFKDVTGHAIGAY 53 (289)
T ss_pred CCCCHHHHHHHHCc-CHH----HHHHHHHHHHCcCHHHH
Confidence 38999999999999 888 99999988877666554
No 465
>PF07120 DUF1376: Protein of unknown function (DUF1376); InterPro: IPR010781 This entry is represented by Bacteriophage PBC5 (Sinorhizobium phage PBC5), Orf49. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical bacterial proteins of around 95 residues in length. The function of this family is unknown.
Probab=36.12 E-value=46 Score=22.88 Aligned_cols=44 Identities=9% Similarity=0.009 Sum_probs=33.1
Q ss_pred CCCCHHH--HHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccc
Q 036971 54 AELSASE--IASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVA 108 (221)
Q Consensus 54 ~~~t~~e--LA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s 108 (221)
+|+.-++ ||..+|. ..+ .-.+.+..+...++ .. .+|.|.+...-
T Consensus 37 ~plp~d~~~Lar~~~~-s~~----~~~~a~~~ll~~f~-~~-----~dg~~~~~r~e 82 (88)
T PF07120_consen 37 GPLPDDDKRLARICGC-STK----EWRKALDFLLREFF-RL-----EDGRWWNKRCE 82 (88)
T ss_pred CCCCCCHHHHHHHHCc-CHH----HHHHHHHHHHHhCC-CC-----CCCCEehHHHH
Confidence 6877544 9999999 766 67888888888888 43 47888776543
No 466
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=35.93 E-value=49 Score=27.81 Aligned_cols=58 Identities=16% Similarity=0.061 Sum_probs=45.1
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceeccccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
++..|-.+.+ ..+...-|+.+++ .+. .+.+-++.|. ..-||++. +..+.+|+.++.|.
T Consensus 5 ~L~~F~~v~~-----~~S~s~AA~~L~i-sQ~----avS~~I~~LE~~lg~~LF~R~-----~r~v~lT~~G~~l~ 65 (305)
T PRK11233 5 RLKYFVKIVD-----IGSLTQAAEVLHI-AQP----ALSQQVATLEGELNQQLLIRT-----KRGVTPTEAGKILY 65 (305)
T ss_pred HHHHHHHHHH-----cCCHHHHHHHhCC-Cch----HHHHHHHHHHHHhCCceEEeC-----CCCceECHhHHHHH
Confidence 4667888888 5699999999999 776 7777766665 57888885 67888998886544
No 467
>PF08721 Tn7_Tnp_TnsA_C: TnsA endonuclease C terminal; InterPro: IPR014832 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The C-terminal domain of TnsA binds DNA. ; PDB: 1F1Z_B 1T0F_B.
Probab=35.66 E-value=76 Score=20.64 Aligned_cols=43 Identities=12% Similarity=0.208 Sum_probs=32.5
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhC----CCCCCcchhhhHHHHHHHHhcCCceee
Q 036971 42 DVLDIINKAGPGAELSASEIASQI----PTKNPEGAAKMLDRVLGLLVSFNILCC 92 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~----g~~~~~~~~~~l~rlLr~L~~~gll~~ 92 (221)
.+...|.+. +..|+.+|.+.+ ++ ++. ..-.++++|++.+.+.-
T Consensus 31 ~i~~~l~~~---~~~tl~~l~~~~d~~~~l-~~g----~~L~~l~~LiA~k~i~~ 77 (79)
T PF08721_consen 31 LILARLRKN---PTMTLRDLCKELDKDYEL-EPG----TALPLLRHLIATKRIKV 77 (79)
T ss_dssp HHHHHHHHT---TTSBHHHHHHHHHHHCT---TT----HHHHHHHHHHHTTSEE-
T ss_pred HHHHHHHHc---CCCCHHHHHHHHHHhcCC-CcC----ChHHHHHHHHhCChhcc
Confidence 367788887 479999999877 78 776 77889999999887764
No 468
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=35.37 E-value=49 Score=27.45 Aligned_cols=40 Identities=13% Similarity=0.135 Sum_probs=33.6
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCC
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFN 88 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~g 88 (221)
..|.+.|.+. +.+++.+||+.+++ .+. -+||=|+.|...+
T Consensus 10 ~~I~~~l~~~---~~v~v~eLa~~~~V-S~~----TIRRDL~~Le~~~ 49 (252)
T PRK10681 10 GQLLQALKRS---DKLHLKDAAALLGV-SEM----TIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHHc---CCCcHHHHHHHhCC-CHH----HHHHHHHHhhcCe
Confidence 4578899987 58999999999999 776 7899999888544
No 469
>PRK05660 HemN family oxidoreductase; Provisional
Probab=35.33 E-value=45 Score=29.47 Aligned_cols=49 Identities=6% Similarity=0.114 Sum_probs=40.9
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccccccc
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYVS 113 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~~ 113 (221)
+++..++.+..|. +.. .....++.|...|++..+ ++++++|+.+..+.+
T Consensus 321 G~~~~~~~~~~g~-~~~----~~~~~l~~l~~~gl~~~~-----~~~~~lt~~G~~~~d 369 (378)
T PRK05660 321 AAPRADFEAYTGL-PES----VIRPQLDEALAQGYLTET-----ADHWQITEHGKLFLN 369 (378)
T ss_pred CCCHHHHHHHHCC-CHH----HHHHHHHHHHHCCCEEEe-----CCEEEECcchhHHHH
Confidence 6889999999998 765 566788999999999985 789999998876653
No 470
>PF14502 HTH_41: Helix-turn-helix domain
Probab=35.21 E-value=77 Score=19.42 Aligned_cols=35 Identities=11% Similarity=0.074 Sum_probs=30.7
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
.=.|++|+++++++ ..- -++.-|..|...|.+.-.
T Consensus 5 Ri~tI~e~~~~~~v-s~G----tiQ~Alk~Le~~gaI~Le 39 (48)
T PF14502_consen 5 RIPTISEYSEKFGV-SRG----TIQNALKFLEENGAIKLE 39 (48)
T ss_pred ccCCHHHHHHHhCc-chh----HHHHHHHHHHHCCcEEee
Confidence 35789999999999 766 899999999999998876
No 471
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.09 E-value=53 Score=22.91 Aligned_cols=32 Identities=22% Similarity=0.248 Sum_probs=24.7
Q ss_pred hhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHH
Q 036971 44 LDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLL 84 (221)
Q Consensus 44 fd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L 84 (221)
-..+.. .++|.++||+++++ .+. .++++|..-
T Consensus 16 qan~el----~~LS~~~iA~~Ln~-t~~----~lekil~~t 47 (97)
T COG4367 16 QANFEL----CPLSDEEIATALNW-TEV----KLEKILQVT 47 (97)
T ss_pred HHhhhh----ccccHHHHHHHhCC-CHH----HHHHHHHHh
Confidence 344555 58999999999999 777 888887543
No 472
>KOG3987 consensus Uncharacterized conserved protein DREV/CGI-81 [Function unknown]
Probab=34.98 E-value=32 Score=28.31 Aligned_cols=23 Identities=22% Similarity=0.247 Sum_probs=18.1
Q ss_pred CC-CCCeEEEecCCccHHHHHHHh
Q 036971 194 FQ-NITRLVDVGGGLGITLSDHNF 216 (221)
Q Consensus 194 ~~-~~~~vvDVGGG~G~~~~~l~~ 216 (221)
|. ...+++|+|.|.|.....++-
T Consensus 109 w~~~~~~lLDlGAGdGeit~~m~p 132 (288)
T KOG3987|consen 109 WGQEPVTLLDLGAGDGEITLRMAP 132 (288)
T ss_pred cCCCCeeEEeccCCCcchhhhhcc
Confidence 64 368999999999998766543
No 473
>PHA00542 putative Cro-like protein
Probab=34.95 E-value=38 Score=22.95 Aligned_cols=24 Identities=21% Similarity=0.246 Sum_probs=18.5
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHH
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLG 82 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr 82 (221)
..+|..+||+.+|+ ... .+.+++.
T Consensus 30 ~glTq~elA~~lgI-s~~----tIsr~e~ 53 (82)
T PHA00542 30 AGWSQEQIADATDV-SQP----TICRIYS 53 (82)
T ss_pred CCCCHHHHHHHHCc-CHH----HHHHHHc
Confidence 47999999999999 665 6666553
No 474
>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=34.84 E-value=32 Score=23.56 Aligned_cols=48 Identities=13% Similarity=0.043 Sum_probs=36.2
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccccc
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAK 109 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~ 109 (221)
-+..+.|++..++ ++. .+...|.-|...+++..... .-+.|++|-.+-
T Consensus 24 ~VP~~~I~~~s~l-~~~----~~~~~L~~L~~~kLv~~~~~--~Y~GYrLT~~GY 71 (82)
T PF09202_consen 24 WVPLELIEKISGL-SEG----EVEKRLKRLVKLKLVSRRNK--PYDGYRLTFLGY 71 (82)
T ss_dssp SEEHHHHHHHHT---HH----HHHHHHHHHHHTTSEEEE-S--SS-EEEE-HHHH
T ss_pred cCCHHHHHHHhCc-CHH----HHHHHHHHHHhcCCccccCC--CcceEEEeecch
Confidence 6889999999999 776 89999999999999999621 236788887664
No 475
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=34.55 E-value=34 Score=31.83 Aligned_cols=36 Identities=14% Similarity=0.147 Sum_probs=33.4
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeec
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSF 94 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~ 94 (221)
..+|++|||+.+.. .++ .++.+|+.+...|.++=..
T Consensus 22 ~~~~l~~la~~l~c-s~R----~~~~~l~~~~~~gwl~w~~ 57 (552)
T PRK13626 22 QETTLNELAELLNC-SRR----HMRTLLNTMQQRGWLTWQA 57 (552)
T ss_pred ceeeHHHHHHHhcC-Chh----HHHHHHHHHHHCCCeeeec
Confidence 57999999999999 898 9999999999999999763
No 476
>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=34.43 E-value=43 Score=23.26 Aligned_cols=39 Identities=21% Similarity=0.207 Sum_probs=28.3
Q ss_pred HHHHhhChhh-HHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHH
Q 036971 36 QAVVNLDVLD-IINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLL 84 (221)
Q Consensus 36 ~~av~lglfd-~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L 84 (221)
..+-++.|+. .|.. ..|..+||+.+|+ ..- -+.|+=|.|
T Consensus 34 ~l~~R~~va~~lL~~-----g~syreIa~~tgv-S~a----TItRvsr~L 73 (87)
T PF01371_consen 34 ALAQRWQVAKELLDE-----GKSYREIAEETGV-SIA----TITRVSRCL 73 (87)
T ss_dssp HHHHHHHHHHHHHHT-----TSSHHHHHHHHTS-THH----HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHC-----CCCHHHHHHHhCC-CHH----HHHHHHHHH
Confidence 3566788998 6665 7999999999999 543 455554444
No 477
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=34.35 E-value=47 Score=27.24 Aligned_cols=43 Identities=21% Similarity=0.255 Sum_probs=37.2
Q ss_pred CCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccc
Q 036971 56 LSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAP 106 (221)
Q Consensus 56 ~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~ 106 (221)
=|=.+||+..|+ ... -+++-|+.|+..|++.+.+ +.|+|-..+
T Consensus 32 PsE~eLa~~f~V-SR~----TvRkAL~~L~~eGli~r~~---G~GtfV~~~ 74 (236)
T COG2188 32 PSERELAEQFGV-SRM----TVRKALDELVEEGLIVRRQ---GKGTFVASP 74 (236)
T ss_pred CCHHHHHHHHCC-cHH----HHHHHHHHHHHCCcEEEEe---cCeeEEcCc
Confidence 355799999999 766 7999999999999999985 688888887
No 478
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=34.35 E-value=59 Score=27.10 Aligned_cols=32 Identities=16% Similarity=0.065 Sum_probs=24.0
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHhh
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNFQ 217 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 217 (221)
..++.|+-....+.++|||.++|.|..-+++.
T Consensus 69 ~ale~F~l~~k~kv~LDiGsSTGGFTd~lLq~ 100 (245)
T COG1189 69 KALEEFELDVKGKVVLDIGSSTGGFTDVLLQR 100 (245)
T ss_pred HHHHhcCcCCCCCEEEEecCCCccHHHHHHHc
Confidence 45677772234689999999999998777654
No 479
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=34.07 E-value=53 Score=27.13 Aligned_cols=59 Identities=15% Similarity=0.091 Sum_probs=45.9
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceeccccccccc
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
-.+.+|..+.+ ..++..-|+.+++ .+. .+.+-++.|. ...||++. +..+.+|+.++.|.
T Consensus 10 ~~l~~f~~v~~-----~gs~t~AA~~L~i-tq~----avS~~i~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~ 71 (294)
T PRK09986 10 KLLRYFLAVAE-----ELHFGRAAARLNI-SQP----PLSIHIKELEDQLGTPLFIRH-----SRSVVLTHAGKILM 71 (294)
T ss_pred HHHHHHHHHHH-----hcCHHHHHHHhCC-CCC----HHHHHHHHHHHHhCCeeEeeC-----CCceeECHhHHHHH
Confidence 35678888888 4689999999999 776 7777776666 57888885 77799999886544
No 480
>KOG1975 consensus mRNA cap methyltransferase [RNA processing and modification]
Probab=33.98 E-value=38 Score=29.68 Aligned_cols=38 Identities=24% Similarity=0.349 Sum_probs=24.5
Q ss_pred HHHHHHHHhhhhHHHHHHHHHhcCCCCCCCeEEEecCCccHHHHHHH
Q 036971 169 NEVFNNGMIGQTSFVINKIVESYKGFQNITRLVDVGGGLGITLSDHN 215 (221)
Q Consensus 169 ~~~F~~aM~~~~~~~~~~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~ 215 (221)
.+.||++|.+ .++..|- +....++|+|||-|..++..-
T Consensus 99 lRnfNNwIKs-------~LI~~y~--~~~~~~~~LgCGKGGDLlKw~ 136 (389)
T KOG1975|consen 99 LRNFNNWIKS-------VLINLYT--KRGDDVLDLGCGKGGDLLKWD 136 (389)
T ss_pred hhhhhHHHHH-------HHHHHHh--ccccccceeccCCcccHhHhh
Confidence 4456666653 2334442 345688999999999886543
No 481
>PF14493 HTH_40: Helix-turn-helix domain
Probab=33.97 E-value=59 Score=22.30 Aligned_cols=30 Identities=23% Similarity=0.097 Sum_probs=21.1
Q ss_pred CCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCc
Q 036971 55 ELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNI 89 (221)
Q Consensus 55 ~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gl 89 (221)
++|+++||+.-++ .+. -+...|-.++..|.
T Consensus 13 G~si~eIA~~R~L-~~s----TI~~HL~~~~~~g~ 42 (91)
T PF14493_consen 13 GLSIEEIAKIRGL-KES----TIYGHLAELIESGE 42 (91)
T ss_pred CCCHHHHHHHcCC-CHH----HHHHHHHHHHHhCC
Confidence 6999999999999 664 55554444444444
No 482
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=33.69 E-value=52 Score=27.61 Aligned_cols=57 Identities=18% Similarity=0.121 Sum_probs=45.1
Q ss_pred hhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceecccccccc
Q 036971 40 NLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYY 111 (221)
Q Consensus 40 ~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L 111 (221)
.+.+|..+.+ .-+...-|+++++ .+. .+.+-++.|. ..-||++. +..+.+|+.+..|
T Consensus 9 ~L~~f~~v~e-----~gs~s~AA~~L~i-sqp----avS~~i~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l 68 (305)
T CHL00180 9 QLRILKAIAT-----EGSFKKAAESLYI-SQP----AVSLQIKNLEKQLNIPLFDRS-----KNKASLTEAGELL 68 (305)
T ss_pred HHHHHHHHHH-----cCCHHHHHHHhcC-CCh----HHHHHHHHHHHHhCCEEEEec-----CCCceECHhHHHH
Confidence 4678888988 4689999999999 776 8888777776 46788885 6678888887655
No 483
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.65 E-value=1e+02 Score=21.15 Aligned_cols=35 Identities=11% Similarity=0.058 Sum_probs=31.1
Q ss_pred CCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 54 AELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 54 ~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
...++.+|-+++|. +.+ -++.++.+|-.+|++.+-
T Consensus 21 e~~nVP~lm~~TGw-PRR----T~QDvikAlpglgi~l~F 55 (95)
T COG4519 21 ETANVPELMAATGW-PRR----TAQDVIKALPGLGIVLEF 55 (95)
T ss_pred ccCChHHHHHHcCC-chh----HHHHHHHhCcCCCeEEEe
Confidence 47899999999999 887 899999999999998764
No 484
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=33.33 E-value=30 Score=22.03 Aligned_cols=28 Identities=14% Similarity=0.052 Sum_probs=21.4
Q ss_pred CCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceee
Q 036971 56 LSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCC 92 (221)
Q Consensus 56 ~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~ 92 (221)
.|+.|+|+.+|+ ++. .++++.+ .|++..
T Consensus 1 ~s~~eva~~~gv-s~~----tlr~~~~----~gli~~ 28 (70)
T smart00422 1 YTIGEVAKLAGV-SVR----TLRYYER----IGLLPP 28 (70)
T ss_pred CCHHHHHHHHCc-CHH----HHHHHHH----CCCCCC
Confidence 478999999999 776 7776654 777753
No 485
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=33.14 E-value=1.2e+02 Score=20.35 Aligned_cols=37 Identities=19% Similarity=0.128 Sum_probs=26.4
Q ss_pred hHHHhcCCCCCCCHHHHHhhCC-CCCCcchhhhHHHHHHHHhc
Q 036971 45 DIINKAGPGAELSASEIASQIP-TKNPEGAAKMLDRVLGLLVS 86 (221)
Q Consensus 45 d~L~~~g~~~~~t~~eLA~~~g-~~~~~~~~~~l~rlLr~L~~ 86 (221)
++|.+.+. .|+|++||...++ + +.. +.+..||+...-
T Consensus 16 ~ymK~r~~-~Plt~~EIl~~ls~~-d~~---~~~~~~L~~~~~ 53 (75)
T cd07977 16 DYMKKRHQ-HPLTLDEILDYLSLL-DIG---PKLKEWLKSEAL 53 (75)
T ss_pred HHHHhcCC-CCccHHHHHHHHhcc-Ccc---HHHHHHHHhhhh
Confidence 47887642 4999999999999 7 665 256677774433
No 486
>cd02187 beta_tubulin The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly. The delta- and epsilon-tubulins are widespread but unlike the alpha, beta, and gamma-tubulins they are not ubiquitous among eukaryotes. The alpha/beta-tubulin heterodimer is the structural subunit of microtubules. The alpha- and beta-tubulins share 40% amino-acid sequence identity, exist in several isotype forms, and undergo a variety of posttranslational modifications. The structures of alpha- and beta-tubulin are basically identical: each monomer is formed by a core of two beta-sheets surrounded by alpha-helices. The monomer structure is very compact, but can be divided into three regions based on function: the amino-
Probab=33.11 E-value=49 Score=29.90 Aligned_cols=36 Identities=28% Similarity=0.359 Sum_probs=26.1
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccHH-----HHHHHhhCCC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGIT-----LSDHNFQIPS 220 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~~-----~~~l~~~~P~ 220 (221)
+..++.+|.+.++..+-.+|||+|.= +..|...||+
T Consensus 120 r~~~E~cD~l~gf~~~~sl~GGTGSG~gs~l~e~l~d~y~~ 160 (425)
T cd02187 120 RKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPD 160 (425)
T ss_pred HHhhccCCCcceEEEEeecCCCccccHHHHHHHHHHHhcCC
Confidence 34566788778889999999999832 3456667775
No 487
>PRK04217 hypothetical protein; Provisional
Probab=33.11 E-value=53 Score=23.83 Aligned_cols=32 Identities=16% Similarity=0.272 Sum_probs=22.7
Q ss_pred ChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHH
Q 036971 42 DVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLG 82 (221)
Q Consensus 42 glfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr 82 (221)
.++..+.. ..+|.+|||+.+|+ +.. .+.+.+.
T Consensus 49 eai~l~~~----eGlS~~EIAk~LGI-S~s----TV~r~L~ 80 (110)
T PRK04217 49 EALRLVDY----EGLTQEEAGKRMGV-SRG----TVWRALT 80 (110)
T ss_pred HHHHHHHH----cCCCHHHHHHHHCc-CHH----HHHHHHH
Confidence 45555555 37999999999999 775 5555443
No 488
>cd02189 delta_tubulin The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly. The delta- and epsilon-tubulins are widespread but unlike the alpha, beta, and gamma-tubulins they are not ubiquitous among eukaryotes. Delta-tubulin plays an essential role in forming the triplet microtubules of centrioles and basal bodies.
Probab=32.93 E-value=55 Score=29.78 Aligned_cols=36 Identities=25% Similarity=0.318 Sum_probs=26.4
Q ss_pred HHHHHhcCCCCCCCeEEEecCCccH-----HHHHHHhhCCC
Q 036971 185 NKIVESYKGFQNITRLVDVGGGLGI-----TLSDHNFQIPS 220 (221)
Q Consensus 185 ~~~l~~~~~~~~~~~vvDVGGG~G~-----~~~~l~~~~P~ 220 (221)
+..++.+|.+.++..+-.+|||+|. ++..|...||+
T Consensus 117 r~~~E~cd~~~gf~~~~sl~GGtGSG~gs~l~e~l~d~y~~ 157 (446)
T cd02189 117 RKEVEKCDSFEGFLVLHSLAGGTGSGLGSRVTELLRDEYPE 157 (446)
T ss_pred HHHHHhCCCccceEEEecCCCCcchHHHHHHHHHHHHhcCc
Confidence 3457788878889999999999983 34455666664
No 489
>PRK13558 bacterio-opsin activator; Provisional
Probab=32.91 E-value=39 Score=31.96 Aligned_cols=45 Identities=9% Similarity=0.048 Sum_probs=35.1
Q ss_pred hhHHHHHHHHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHH
Q 036971 28 AIVLPAVFQAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGL 83 (221)
Q Consensus 28 g~~~~~aL~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~ 83 (221)
-..+-.+|.+|.+.|-|+.=. ..|.+|||+.+|+ .+. .+...||.
T Consensus 609 t~~q~e~l~~a~~~gyf~~pr------~~~~~e~a~~l~i-s~~----t~~~~lr~ 653 (665)
T PRK13558 609 TDRQLTALQKAYVSGYFEWPR------RVEGEELAESMGI-SRS----TFHQHLRA 653 (665)
T ss_pred CHHHHHHHHHHHHcCCCCCCc------cCCHHHHHHHhCC-CHH----HHHHHHHH
Confidence 445667999999999998633 5999999999999 665 55555554
No 490
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=32.74 E-value=45 Score=26.60 Aligned_cols=28 Identities=25% Similarity=0.313 Sum_probs=23.8
Q ss_pred HHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCc
Q 036971 38 VVNLDVLDIINKAGPGAELSASEIASQIPTKNPE 71 (221)
Q Consensus 38 av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~ 71 (221)
--|..|+..+.+ +.|..|||+.+++ .++
T Consensus 136 pRErEVLrLLAq-----GkTnKEIAe~L~I-S~r 163 (198)
T PRK15201 136 VTERHLLKLIAS-----GYHLSETAALLSL-SEE 163 (198)
T ss_pred HHHHHHHHHHHC-----CCCHHHHHHHhCC-CHH
Confidence 356778889988 7999999999999 775
No 491
>KOG4058 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.65 E-value=57 Score=25.37 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=20.4
Q ss_pred HHHHhcCCCCCCCeEEEecCCccHHHHHHHh
Q 036971 186 KIVESYKGFQNITRLVDVGGGLGITLSDHNF 216 (221)
Q Consensus 186 ~~l~~~~~~~~~~~vvDVGGG~G~~~~~l~~ 216 (221)
.++...+ -....++||+|.|.|-...+.++
T Consensus 63 nVLSll~-~n~~GklvDlGSGDGRiVlaaar 92 (199)
T KOG4058|consen 63 NVLSLLR-GNPKGKLVDLGSGDGRIVLAAAR 92 (199)
T ss_pred HHHHHcc-CCCCCcEEeccCCCceeehhhhh
Confidence 3454444 23457999999999987665544
No 492
>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=32.59 E-value=70 Score=21.47 Aligned_cols=36 Identities=11% Similarity=0.168 Sum_probs=26.6
Q ss_pred CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeec
Q 036971 57 SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSF 94 (221)
Q Consensus 57 t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~ 94 (221)
...+|++..|. +|. ..+.+..+|.-|..+|+++...
T Consensus 24 ~Y~~lc~~~~~-~pl-s~~r~~~~l~eL~~~gli~~~~ 59 (85)
T PF09079_consen 24 VYEELCESLGV-DPL-SYRRFSDYLSELEMLGLIESER 59 (85)
T ss_dssp HHHHHHHHTTS------HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHcCC-CCC-CHHHHHHHHHHHHhCCCeEEEe
Confidence 45778999999 887 5567888899999999999863
No 493
>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=32.56 E-value=58 Score=23.68 Aligned_cols=39 Identities=13% Similarity=0.260 Sum_probs=28.2
Q ss_pred hhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeee
Q 036971 44 LDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCS 93 (221)
Q Consensus 44 fd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~ 93 (221)
-+.+.+. ..+|..|||+.+|+ ++ ..+-++|-.+|+..+.
T Consensus 63 ~~~v~~~---pd~tl~Ela~~l~V-s~-------~ti~~~Lkrlg~t~KK 101 (119)
T PF01710_consen 63 KALVEEN---PDATLRELAERLGV-SP-------STIWRALKRLGITRKK 101 (119)
T ss_pred HHHHHHC---CCcCHHHHHHHcCC-CH-------HHHHHHHHHcCchhcc
Confidence 3444554 47999999999999 54 4555677788887774
No 494
>COG4754 Uncharacterized conserved protein [Function unknown]
Probab=32.52 E-value=1e+02 Score=23.71 Aligned_cols=65 Identities=11% Similarity=0.120 Sum_probs=52.5
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceeccccccccccCCC
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPVAKYYVSDQN 116 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~s~~L~~~~~ 116 (221)
.||.+.+... =+|...+--|++.+++ +-+ -|-.+...+..+||+.-. .|-..+|+.++.+++..+
T Consensus 15 ~GLL~~l~n~-fnGraDl~~L~~e~~v-did----DL~piv~ta~~Lglv~~e-----~GDiilT~~Gk~~v~~~~ 79 (157)
T COG4754 15 VGLLYVLNNI-FNGRADLPYLEKEMEV-DID----DLMPIVETASLLGLVTAE-----SGDIILTDEGKEYVESPI 79 (157)
T ss_pred HHHHHHHHHH-hCCcccchhHHHHhCC-Chh----hHHHHHHHHHhcCceecc-----CCCEEEehhhHHHHhCCh
Confidence 4566666662 1168999999999999 777 889999999999999984 888899999998876543
No 495
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=32.50 E-value=48 Score=26.53 Aligned_cols=29 Identities=10% Similarity=0.139 Sum_probs=24.4
Q ss_pred HHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCc
Q 036971 37 AVVNLDVLDIINKAGPGAELSASEIASQIPTKNPE 71 (221)
Q Consensus 37 ~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~ 71 (221)
.--|..|+..+.+ +.|..|||+++++ .++
T Consensus 139 T~RE~eVL~lla~-----G~snkeIA~~L~i-S~~ 167 (207)
T PRK15411 139 SRTESSMLRMWMA-----GQGTIQISDQMNI-KAK 167 (207)
T ss_pred CHHHHHHHHHHHc-----CCCHHHHHHHcCC-CHH
Confidence 4456778888887 7999999999999 775
No 496
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=32.40 E-value=49 Score=26.67 Aligned_cols=41 Identities=15% Similarity=0.333 Sum_probs=30.5
Q ss_pred hChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcC
Q 036971 41 LDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSF 87 (221)
Q Consensus 41 lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~ 87 (221)
-.+++.|...+. ..++.+|||+++|+ ++. .++|=+-+.-.+
T Consensus 19 yR~le~l~a~~v-~rvsS~els~~~~v-dsa----tIRrDfSYFG~l 59 (211)
T COG2344 19 YRVLERLHASGV-ERVSSKELSEALGV-DSA----TIRRDFSYFGEL 59 (211)
T ss_pred HHHHHHHHHcCC-ceecHHHHHHHhCC-CHH----HHhhhhHHHHhc
Confidence 456788888775 37999999999999 886 777755544443
No 497
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=32.34 E-value=69 Score=25.73 Aligned_cols=47 Identities=15% Similarity=0.279 Sum_probs=35.8
Q ss_pred HHHHhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHhcCC
Q 036971 36 QAVVNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLVSFN 88 (221)
Q Consensus 36 ~~av~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~g 88 (221)
+.-....|.+.|.+.|. ..+++++||+.+|+ ++. -++|=|..+...|
T Consensus 14 r~~~~~~il~~l~~~~~-~~vs~~~L~~~~~v-~~~----tirrDl~~l~~~G 60 (213)
T PRK05472 14 RLPLYYRYLKELKEEGV-ERVSSKELAEALGV-DSA----QIRKDLSYFGEFG 60 (213)
T ss_pred HhHHHHHHHHHHHHcCC-cEEeHHHHHHHhCc-CHH----HHHHHHHHHHhcC
Confidence 34556677888888631 17999999999999 886 8888888885554
No 498
>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=32.01 E-value=55 Score=26.09 Aligned_cols=41 Identities=17% Similarity=0.296 Sum_probs=35.3
Q ss_pred CHHHHHhhCCCCCCcchhhhHHHHHHHHhcCCceeeeccCCCCcceecccc
Q 036971 57 SASEIASQIPTKNPEGAAKMLDRVLGLLVSFNILCCSFSTHGVRLYSLAPV 107 (221)
Q Consensus 57 t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~y~lt~~ 107 (221)
...+||+.+|+ +++ .+.-++++.-.+|||... +|....++-
T Consensus 118 ~~~~La~~l~i-~~~----~l~fml~VF~EL~FVti~-----~g~i~~~~~ 158 (195)
T PF10141_consen 118 QLQALAKYLGI-SPD----TLKFMLKVFFELGFVTIE-----DGVISLNPN 158 (195)
T ss_pred HHHHHHHHHCc-CHH----HHHHHHHHHHHcCcEEEe-----CCEEEeCCC
Confidence 35899999999 888 999999999999999985 777776653
No 499
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=31.80 E-value=50 Score=27.72 Aligned_cols=59 Identities=15% Similarity=0.213 Sum_probs=46.8
Q ss_pred HhhChhhHHHhcCCCCCCCHHHHHhhCCCCCCcchhhhHHHHHHHHh---cCCceeeeccCCCCcceeccccccccc
Q 036971 39 VNLDVLDIINKAGPGAELSASEIASQIPTKNPEGAAKMLDRVLGLLV---SFNILCCSFSTHGVRLYSLAPVAKYYV 112 (221)
Q Consensus 39 v~lglfd~L~~~g~~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~---~~gll~~~~~~~~~~~y~lt~~s~~L~ 112 (221)
-.+.+|-.+.+ .-++..-|+.+++ ... .+.+-++.|. ...||++. +..+.+|+.+..|.
T Consensus 11 ~~L~~F~~va~-----~gs~s~AA~~L~i-sQp----avS~~I~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~ 72 (302)
T TIGR02036 11 SKMHTFEVAAR-----HQSFSLAAEELSL-TPS----AISHRINQLEEELGIQLFVRS-----HRKVELTHEGKRIY 72 (302)
T ss_pred HHHHHHHHHHH-----hCCHHHHHHHHCC-CHH----HHHHHHHHHHHHhCCceEEEC-----CCceeECHhHHHHH
Confidence 35677888888 5789999999999 665 7877777766 47888885 88999999987655
No 500
>KOG1661 consensus Protein-L-isoaspartate(D-aspartate) O-methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=31.62 E-value=40 Score=27.69 Aligned_cols=21 Identities=29% Similarity=0.349 Sum_probs=17.1
Q ss_pred CCCCeEEEecCCccHHHHHHH
Q 036971 195 QNITRLVDVGGGLGITLSDHN 215 (221)
Q Consensus 195 ~~~~~vvDVGGG~G~~~~~l~ 215 (221)
....+.||||+|+|-+...++
T Consensus 81 ~pG~s~LdvGsGSGYLt~~~~ 101 (237)
T KOG1661|consen 81 QPGASFLDVGSGSGYLTACFA 101 (237)
T ss_pred ccCcceeecCCCccHHHHHHH
Confidence 345789999999999887665
Done!