Query 023574
Match_columns 280
No_of_seqs 73 out of 75
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 05:04:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023574.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023574hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00550 Zalpha Z-DNA-bindin 94.8 0.071 1.5E-06 39.9 5.1 45 80-124 4-49 (68)
2 PRK13239 alkylmercury lyase; P 94.7 0.068 1.5E-06 48.8 5.7 53 81-139 21-73 (206)
3 PF12324 HTH_15: Helix-turn-he 93.6 0.12 2.6E-06 41.0 4.4 52 81-138 23-74 (77)
4 PF09339 HTH_IclR: IclR helix- 93.5 0.11 2.3E-06 36.5 3.5 40 85-124 6-45 (52)
5 PRK06266 transcription initiat 92.8 0.79 1.7E-05 40.6 8.8 84 81-167 21-107 (178)
6 smart00346 HTH_ICLR helix_turn 92.5 1.1 2.5E-05 33.4 8.1 77 85-164 8-88 (91)
7 TIGR00373 conserved hypothetic 92.5 1.1 2.3E-05 38.9 9.0 79 86-167 18-99 (158)
8 COG3355 Predicted transcriptio 92.2 1.5 3.3E-05 37.5 9.4 86 85-172 30-118 (126)
9 PF13412 HTH_24: Winged helix- 91.7 0.52 1.1E-05 32.2 5.0 42 82-124 3-44 (48)
10 PF12840 HTH_20: Helix-turn-he 91.3 0.59 1.3E-05 33.6 5.3 53 80-135 8-60 (61)
11 PF04703 FaeA: FaeA-like prote 90.7 0.4 8.6E-06 36.2 4.0 53 85-139 3-57 (62)
12 PF06163 DUF977: Bacterial pro 90.6 0.53 1.1E-05 40.5 5.1 51 81-134 11-61 (127)
13 KOG3341 RNA polymerase II tran 90.2 0.83 1.8E-05 42.9 6.4 83 68-151 159-244 (249)
14 PF08220 HTH_DeoR: DeoR-like h 88.9 1.2 2.5E-05 32.2 5.1 41 84-125 2-42 (57)
15 cd00090 HTH_ARSR Arsenical Res 88.8 3.7 7.9E-05 28.1 7.4 60 79-142 4-64 (78)
16 smart00420 HTH_DEOR helix_turn 88.4 2 4.3E-05 28.4 5.7 45 84-131 2-46 (53)
17 smart00418 HTH_ARSR helix_turn 88.4 1.6 3.4E-05 29.3 5.2 49 87-139 2-50 (66)
18 PF08279 HTH_11: HTH domain; 88.2 2.2 4.8E-05 29.6 6.0 42 84-125 2-43 (55)
19 TIGR02844 spore_III_D sporulat 87.6 0.81 1.8E-05 36.1 3.8 34 83-118 7-40 (80)
20 PF08784 RPA_C: Replication pr 87.3 1.5 3.3E-05 34.4 5.3 44 81-124 46-92 (102)
21 PF09743 DUF2042: Uncharacteri 86.9 1.6 3.4E-05 41.2 6.1 57 80-138 53-109 (272)
22 PRK15466 carboxysome structura 85.7 1.8 3.9E-05 38.8 5.4 41 84-124 111-151 (166)
23 PF08221 HTH_9: RNA polymerase 85.5 2.3 5E-05 31.5 5.1 39 85-124 16-54 (62)
24 PF01978 TrmB: Sugar-specific 85.1 3.5 7.6E-05 29.9 5.9 53 84-139 10-62 (68)
25 PF04539 Sigma70_r3: Sigma-70 82.9 1.9 4.1E-05 31.9 3.7 53 83-135 6-58 (78)
26 PF01726 LexA_DNA_bind: LexA D 82.4 2.8 6E-05 31.5 4.5 45 84-130 12-57 (65)
27 smart00753 PAM PCI/PINT associ 82.2 6.2 0.00014 29.6 6.4 68 79-146 6-73 (88)
28 smart00088 PINT motif in prote 82.2 6.2 0.00014 29.6 6.4 68 79-146 6-73 (88)
29 PF12802 MarR_2: MarR family; 82.1 4 8.6E-05 28.5 5.0 42 84-125 7-49 (62)
30 cd07377 WHTH_GntR Winged helix 77.8 5.4 0.00012 27.5 4.5 49 81-131 4-57 (66)
31 PF06969 HemN_C: HemN C-termin 77.8 6.8 0.00015 28.1 5.1 53 83-136 7-65 (66)
32 COG2512 Predicted membrane-ass 77.5 4.6 9.9E-05 38.0 5.2 46 78-124 192-237 (258)
33 PRK10141 DNA-binding transcrip 77.1 28 0.0006 29.1 9.2 60 79-141 13-72 (117)
34 PRK10434 srlR DNA-bindng trans 76.8 16 0.00034 33.5 8.4 43 81-124 4-46 (256)
35 PF13404 HTH_AsnC-type: AsnC-t 76.8 6.6 0.00014 27.2 4.6 39 82-121 3-41 (42)
36 PRK09802 DNA-binding transcrip 76.8 7.6 0.00016 36.0 6.4 53 80-135 15-67 (269)
37 PF14257 DUF4349: Domain of un 76.7 9.4 0.0002 34.7 6.9 79 85-174 149-234 (262)
38 TIGR02702 SufR_cyano iron-sulf 76.3 4.9 0.00011 35.3 4.8 41 83-124 2-42 (203)
39 cd07153 Fur_like Ferric uptake 75.9 12 0.00026 29.4 6.5 59 83-141 2-65 (116)
40 cd00092 HTH_CRP helix_turn_hel 75.2 18 0.00039 25.3 6.7 38 96-135 24-61 (67)
41 PRK04424 fatty acid biosynthes 75.0 5.7 0.00012 34.9 4.9 42 82-124 7-48 (185)
42 smart00344 HTH_ASNC helix_turn 73.9 7.5 0.00016 30.1 4.8 41 83-124 4-44 (108)
43 smart00347 HTH_MARR helix_turn 73.5 33 0.00072 25.1 9.3 48 84-134 12-59 (101)
44 PF01022 HTH_5: Bacterial regu 72.7 8.1 0.00018 26.5 4.2 41 82-124 2-42 (47)
45 PHA02943 hypothetical protein; 72.3 26 0.00057 31.5 8.3 79 82-169 8-87 (165)
46 PRK12423 LexA repressor; Provi 71.8 12 0.00026 33.1 6.1 52 82-135 6-62 (202)
47 COG1675 TFA1 Transcription ini 71.7 25 0.00054 31.7 8.1 82 85-169 21-105 (176)
48 smart00345 HTH_GNTR helix_turn 71.0 4.7 0.0001 27.3 2.7 38 94-133 16-54 (60)
49 PF02002 TFIIE_alpha: TFIIE al 70.2 16 0.00035 28.8 6.0 79 85-166 16-97 (105)
50 PRK00135 scpB segregation and 69.0 14 0.0003 33.2 5.9 59 82-141 4-66 (188)
51 PF10717 ODV-E18: Occlusion-de 67.0 9.7 0.00021 31.0 4.1 26 171-196 18-43 (85)
52 PRK10681 DNA-binding transcrip 66.5 31 0.00068 31.5 7.9 43 81-124 6-48 (252)
53 PF04405 ScdA_N: Domain of Unk 66.4 6.2 0.00013 29.2 2.7 38 84-121 12-55 (56)
54 COG1349 GlpR Transcriptional r 66.2 12 0.00027 34.3 5.2 57 80-137 3-65 (253)
55 COG2345 Predicted transcriptio 65.7 13 0.00027 34.6 5.2 50 75-125 4-53 (218)
56 PF00392 GntR: Bacterial regul 64.5 7.4 0.00016 28.1 2.8 40 85-124 7-51 (64)
57 PRK13509 transcriptional repre 63.6 14 0.00029 33.8 5.0 43 81-124 4-46 (251)
58 TIGR02431 pcaR_pcaU beta-ketoa 62.7 11 0.00024 33.7 4.2 44 86-131 13-56 (248)
59 PF04157 EAP30: EAP30/Vps36 fa 62.5 14 0.00031 33.1 4.8 43 82-124 174-217 (223)
60 PRK10906 DNA-binding transcrip 61.8 17 0.00037 33.4 5.3 99 82-186 5-110 (252)
61 smart00531 TFIIE Transcription 61.7 58 0.0013 27.6 8.1 78 87-167 6-89 (147)
62 PF03965 Penicillinase_R: Peni 61.0 38 0.00082 27.1 6.6 80 82-168 3-86 (115)
63 PF01035 DNA_binding_1: 6-O-me 60.9 14 0.0003 28.8 3.9 57 82-138 2-64 (85)
64 PRK11569 transcriptional repre 60.3 14 0.0003 33.9 4.4 47 85-133 31-77 (274)
65 PF00356 LacI: Bacterial regul 60.2 7.8 0.00017 27.5 2.2 21 99-119 1-21 (46)
66 TIGR00589 ogt O-6-methylguanin 60.0 11 0.00023 29.5 3.1 57 82-138 2-64 (80)
67 PF00356 LacI: Bacterial regul 59.6 7.9 0.00017 27.4 2.1 22 77-98 24-45 (46)
68 PRK10163 DNA-binding transcrip 58.6 16 0.00034 33.5 4.5 48 85-134 28-75 (271)
69 PRK10411 DNA-binding transcrip 58.2 93 0.002 28.4 9.3 47 82-131 4-50 (240)
70 PF06224 HTH_42: Winged helix 58.0 29 0.00062 32.0 6.1 61 83-145 168-230 (327)
71 smart00419 HTH_CRP helix_turn_ 58.0 13 0.00029 24.3 2.9 35 96-132 7-41 (48)
72 PF03640 Lipoprotein_15: Secre 57.3 9.7 0.00021 27.2 2.3 22 124-145 6-27 (48)
73 PRK09834 DNA-binding transcrip 56.3 18 0.00039 32.9 4.4 46 86-133 15-60 (263)
74 PF13463 HTH_27: Winged helix 56.0 24 0.00051 24.9 4.2 50 84-133 5-54 (68)
75 PF01047 MarR: MarR family; I 55.6 32 0.00069 23.8 4.7 41 84-125 5-45 (59)
76 PF09105 SelB-wing_1: Elongati 55.4 34 0.00075 25.8 5.0 45 85-129 5-49 (61)
77 TIGR00498 lexA SOS regulatory 54.9 25 0.00054 30.4 4.9 43 82-124 6-53 (199)
78 PF11625 DUF3253: Protein of u 54.5 34 0.00073 27.6 5.2 65 81-149 6-77 (83)
79 COG1414 IclR Transcriptional r 53.2 22 0.00048 32.5 4.5 48 85-134 7-54 (246)
80 PRK05472 redox-sensing transcr 53.1 28 0.00061 30.7 5.0 40 82-121 16-56 (213)
81 COG1609 PurR Transcriptional r 52.8 46 0.001 31.3 6.7 59 78-136 26-98 (333)
82 PF08006 DUF1700: Protein of u 52.8 1.5E+02 0.0033 25.5 9.3 35 78-112 16-55 (181)
83 PF01325 Fe_dep_repress: Iron 52.6 37 0.00081 24.9 4.8 32 93-124 18-49 (60)
84 PTZ00326 phenylalanyl-tRNA syn 52.5 69 0.0015 33.1 8.3 71 81-153 5-75 (494)
85 PF10771 DUF2582: Protein of u 52.2 30 0.00065 26.5 4.4 52 86-140 12-63 (65)
86 PRK11014 transcriptional repre 51.9 22 0.00048 29.5 4.0 43 82-124 10-52 (141)
87 PRK09480 slmA division inhibit 51.4 17 0.00036 30.1 3.2 32 81-112 9-45 (194)
88 PRK10014 DNA-binding transcrip 51.4 12 0.00026 33.6 2.5 25 95-119 4-28 (342)
89 cd06445 ATase The DNA repair p 50.9 29 0.00064 26.5 4.2 55 84-138 2-62 (79)
90 COG2846 Regulator of cell morp 50.5 14 0.0003 34.5 2.8 32 94-125 31-62 (221)
91 PLN02853 Probable phenylalanyl 50.5 78 0.0017 32.8 8.3 69 82-152 3-71 (492)
92 PRK11179 DNA-binding transcrip 50.5 37 0.00079 28.6 5.1 42 83-125 10-51 (153)
93 PF05331 DUF742: Protein of un 50.4 25 0.00055 29.5 4.0 43 88-134 46-90 (114)
94 PF10717 ODV-E18: Occlusion-de 50.2 23 0.00051 28.8 3.6 28 177-204 27-54 (85)
95 PF07106 TBPIP: Tat binding pr 49.7 55 0.0012 28.0 6.1 57 83-141 2-60 (169)
96 COG3695 Predicted methylated D 49.6 31 0.00068 28.9 4.4 58 81-138 5-68 (103)
97 PF09012 FeoC: FeoC like trans 49.5 30 0.00066 25.5 4.0 36 89-124 6-41 (69)
98 PLN03238 probable histone acet 49.1 23 0.0005 34.3 4.1 53 84-141 210-262 (290)
99 PF14947 HTH_45: Winged helix- 48.9 33 0.00072 26.0 4.2 48 86-135 10-62 (77)
100 PLN03083 E3 UFM1-protein ligas 48.6 34 0.00073 37.4 5.6 56 80-138 58-113 (803)
101 PRK10286 O-6-alkylguanine-DNA: 48.2 29 0.00062 31.0 4.3 74 81-159 87-166 (171)
102 PRK10992 iron-sulfur cluster r 48.1 19 0.00042 32.8 3.3 42 85-126 16-63 (220)
103 PF01475 FUR: Ferric uptake re 48.0 87 0.0019 24.9 6.7 62 82-143 8-74 (120)
104 PF05158 RNA_pol_Rpc34: RNA po 47.4 78 0.0017 30.7 7.4 60 81-141 8-70 (327)
105 PF15581 Imm35: Immunity prote 46.6 35 0.00076 28.2 4.2 33 107-139 44-77 (93)
106 PF10025 DUF2267: Uncharacteri 46.3 13 0.00029 30.5 1.8 80 100-179 6-100 (125)
107 PRK15090 DNA-binding transcrip 45.8 29 0.00062 31.3 4.0 45 86-133 18-62 (257)
108 PF01853 MOZ_SAS: MOZ/SAS fami 45.6 30 0.00065 31.6 4.0 39 84-122 135-175 (188)
109 TIGR02787 codY_Gpos GTP-sensin 44.7 31 0.00067 32.9 4.1 45 87-133 188-232 (251)
110 PF01316 Arg_repressor: Argini 44.1 78 0.0017 24.4 5.6 46 83-144 21-67 (70)
111 PF15145 DUF4577: Domain of un 43.5 9.5 0.00021 32.8 0.5 34 171-204 61-94 (128)
112 PF10975 DUF2802: Protein of u 43.4 19 0.00042 27.6 2.1 29 88-116 35-63 (70)
113 PHA02701 ORF020 dsRNA-binding 43.4 43 0.00094 30.5 4.7 90 82-171 4-127 (183)
114 PF03297 Ribosomal_S25: S25 ri 43.0 71 0.0015 26.6 5.5 59 81-140 44-102 (105)
115 PRK09492 treR trehalose repres 42.8 17 0.00038 32.2 2.1 24 96-119 3-26 (315)
116 PRK07598 RNA polymerase sigma 42.7 1.2E+02 0.0026 30.6 8.1 87 92-178 273-364 (415)
117 PHA03093 EEV glycoprotein; Pro 42.7 44 0.00096 30.6 4.6 30 164-194 30-59 (185)
118 TIGR02944 suf_reg_Xantho FeS a 42.4 49 0.0011 26.8 4.5 44 86-131 13-57 (130)
119 PRK05441 murQ N-acetylmuramic 41.6 32 0.0007 32.5 3.8 43 84-130 250-292 (299)
120 PRK09334 30S ribosomal protein 41.5 88 0.0019 25.4 5.7 60 79-140 24-84 (86)
121 PRK09526 lacI lac repressor; R 41.4 20 0.00044 32.2 2.3 48 96-143 4-72 (342)
122 PRK14987 gluconate operon tran 40.4 20 0.00043 32.3 2.1 24 95-118 3-26 (331)
123 KOG3970 Predicted E3 ubiquitin 40.3 64 0.0014 31.1 5.4 44 150-196 220-271 (299)
124 COG1321 TroR Mn-dependent tran 40.0 56 0.0012 28.3 4.7 46 91-136 18-69 (154)
125 PRK11169 leucine-responsive tr 39.0 58 0.0013 27.7 4.6 42 83-125 15-56 (164)
126 TIGR01884 cas_HTH CRISPR locus 39.0 1.3E+02 0.0028 26.4 6.9 48 83-133 144-191 (203)
127 smart00874 B5 tRNA synthetase 38.8 48 0.001 24.1 3.6 51 97-149 5-55 (71)
128 TIGR02405 trehalos_R_Ecol treh 38.6 23 0.0005 31.7 2.2 23 97-119 1-23 (311)
129 PHA01815 hypothetical protein 38.5 1.2E+02 0.0026 22.6 5.5 25 158-182 12-36 (55)
130 PRK11050 manganese transport r 38.2 2.5E+02 0.0054 23.8 8.9 46 85-133 40-85 (152)
131 PF04967 HTH_10: HTH DNA bindi 38.1 86 0.0019 23.0 4.7 37 84-120 5-46 (53)
132 PRK06474 hypothetical protein; 37.8 74 0.0016 27.9 5.2 56 77-134 6-62 (178)
133 TIGR03826 YvyF flagellar opero 37.5 63 0.0014 28.0 4.6 53 83-141 31-84 (137)
134 PF02295 z-alpha: Adenosine de 37.3 46 0.001 25.1 3.3 43 82-125 4-48 (66)
135 TIGR01610 phage_O_Nterm phage 37.0 97 0.0021 24.3 5.3 31 94-124 44-74 (95)
136 TIGR00738 rrf2_super rrf2 fami 36.7 67 0.0015 25.7 4.4 38 87-124 13-52 (132)
137 PRK10344 DNA-binding transcrip 36.6 56 0.0012 27.0 3.9 33 84-118 10-42 (92)
138 COG1386 scpB Chromosome segreg 36.6 1E+02 0.0022 27.8 5.9 55 81-135 7-65 (184)
139 PRK11041 DNA-binding transcrip 36.5 1.3E+02 0.0027 26.6 6.5 55 77-131 2-70 (309)
140 PRK11552 putative DNA-binding 36.5 32 0.00068 30.4 2.7 32 82-113 13-48 (225)
141 TIGR02698 CopY_TcrY copper tra 36.4 2.5E+02 0.0055 23.4 8.4 77 82-165 4-84 (130)
142 TIGR00274 N-acetylmuramic acid 36.3 52 0.0011 31.2 4.2 43 84-130 245-287 (291)
143 PLN02343 allene oxide cyclase 35.9 12 0.00027 34.9 0.1 13 249-261 125-137 (229)
144 PRK15008 HTH-type transcriptio 35.8 38 0.00083 29.2 3.1 32 82-113 18-54 (212)
145 PF00165 HTH_AraC: Bacterial r 35.7 35 0.00075 22.6 2.2 26 94-119 5-30 (42)
146 PRK10703 DNA-binding transcrip 35.5 26 0.00057 31.5 2.1 46 98-143 2-68 (341)
147 PRK09526 lacI lac repressor; R 35.5 1.3E+02 0.0027 27.2 6.4 56 77-132 30-99 (342)
148 PRK11161 fumarate/nitrate redu 35.4 64 0.0014 27.9 4.4 51 81-133 154-218 (235)
149 PRK14996 TetR family transcrip 34.7 33 0.0007 28.8 2.4 29 84-112 10-43 (192)
150 PRK04172 pheS phenylalanyl-tRN 34.2 2.2E+02 0.0047 28.8 8.5 65 83-150 7-71 (489)
151 PF02796 HTH_7: Helix-turn-hel 34.0 33 0.00072 23.5 2.0 32 87-118 11-42 (45)
152 PRK14987 gluconate operon tran 33.7 1.6E+02 0.0035 26.4 6.9 57 77-133 30-100 (331)
153 PRK07122 RNA polymerase sigma 33.6 1.9E+02 0.0041 26.6 7.3 44 78-121 117-167 (264)
154 COG0640 ArsR Predicted transcr 33.4 1.7E+02 0.0037 20.5 6.2 58 80-140 23-80 (110)
155 PF13542 HTH_Tnp_ISL3: Helix-t 33.4 76 0.0016 21.5 3.7 37 81-120 14-50 (52)
156 TIGR01481 ccpA catabolite cont 33.3 30 0.00066 30.9 2.1 46 98-143 2-68 (329)
157 PF13545 HTH_Crp_2: Crp-like h 33.1 74 0.0016 22.9 3.8 28 97-124 28-55 (76)
158 PF11772 EpuA: DNA-directed RN 32.9 19 0.00042 26.1 0.6 19 258-276 22-40 (47)
159 PF05055 DUF677: Protein of un 32.6 1.3E+02 0.0029 29.5 6.5 51 141-191 144-205 (336)
160 PHA02673 ORF109 EEV glycoprote 32.3 85 0.0018 28.3 4.7 27 166-193 29-55 (161)
161 PF13693 HTH_35: Winged helix- 32.2 49 0.0011 26.2 2.9 33 84-118 4-36 (78)
162 PRK00441 argR arginine repress 32.2 1.7E+02 0.0036 25.4 6.4 56 84-145 6-67 (149)
163 COG1522 Lrp Transcriptional re 32.0 1.1E+02 0.0024 24.9 5.0 51 82-133 8-61 (154)
164 TIGR02393 RpoD_Cterm RNA polym 31.9 2.4E+02 0.0053 25.1 7.6 28 92-119 98-125 (238)
165 PF02082 Rrf2: Transcriptional 31.7 1E+02 0.0022 23.3 4.5 44 87-132 13-58 (83)
166 PRK10014 DNA-binding transcrip 31.5 1.8E+02 0.0039 26.1 6.8 54 77-130 31-98 (342)
167 cd00569 HTH_Hin_like Helix-tur 31.5 99 0.0022 17.2 3.5 34 79-115 6-39 (42)
168 PF07245 Phlebovirus_G2: Phleb 31.4 43 0.00092 34.6 3.0 16 134-149 421-436 (507)
169 PF04079 DUF387: Putative tran 31.3 1.1E+02 0.0023 26.8 5.1 49 91-141 7-58 (159)
170 PRK09975 DNA-binding transcrip 31.3 52 0.0011 27.8 3.1 31 83-113 12-47 (213)
171 TIGR00122 birA_repr_reg BirA b 31.2 1.5E+02 0.0032 21.5 5.1 36 86-123 4-39 (69)
172 PF14451 Ub-Mut7C: Mut7-C ubiq 30.8 58 0.0012 25.7 3.0 48 93-143 28-76 (81)
173 PF07070 Spo0M: SpoOM protein; 30.6 58 0.0013 30.1 3.5 48 56-103 109-156 (218)
174 cd00131 PAX Paired Box domain 30.3 1.2E+02 0.0027 25.2 5.1 44 77-123 16-59 (128)
175 PRK10727 DNA-binding transcrip 30.3 35 0.00076 31.0 2.0 46 98-143 2-68 (343)
176 COG4565 CitB Response regulato 30.3 1.3E+02 0.0028 28.4 5.7 69 73-141 145-219 (224)
177 PRK10339 DNA-binding transcrip 30.1 29 0.00063 31.2 1.5 22 98-119 2-23 (327)
178 PRK09210 RNA polymerase sigma 30.1 2.4E+02 0.0052 27.4 7.7 29 91-119 226-254 (367)
179 PHA00738 putative HTH transcri 30.0 2.2E+02 0.0047 24.1 6.4 58 81-141 11-68 (108)
180 KOG2587 RNA polymerase III (C) 30.0 1.8E+02 0.0039 30.7 7.2 88 85-172 22-114 (551)
181 PF04545 Sigma70_r4: Sigma-70, 30.0 1.8E+02 0.0039 19.7 5.2 40 77-119 3-42 (50)
182 PRK10401 DNA-binding transcrip 29.8 38 0.00082 30.8 2.2 21 98-118 2-22 (346)
183 TIGR03613 RutR pyrimidine util 29.8 45 0.00098 28.0 2.5 32 82-113 8-44 (202)
184 PF14394 DUF4423: Domain of un 29.4 96 0.0021 27.2 4.5 55 79-133 21-83 (171)
185 PLN00104 MYST -like histone ac 29.4 71 0.0015 32.8 4.1 39 84-122 361-399 (450)
186 PF08100 Dimerisation: Dimeris 29.3 84 0.0018 22.8 3.5 27 82-108 6-33 (51)
187 PRK05949 RNA polymerase sigma 29.1 2.3E+02 0.005 27.2 7.4 29 91-119 188-216 (327)
188 TIGR02417 fruct_sucro_rep D-fr 28.9 2E+02 0.0043 25.8 6.5 56 78-133 28-97 (327)
189 PF09743 DUF2042: Uncharacteri 28.8 74 0.0016 30.2 3.9 44 95-140 128-171 (272)
190 TIGR02997 Sig70-cyanoRpoD RNA 28.8 2.9E+02 0.0062 25.7 7.8 30 92-121 172-201 (298)
191 PRK12570 N-acetylmuramic acid- 28.5 65 0.0014 30.6 3.6 42 85-130 247-288 (296)
192 smart00421 HTH_LUXR helix_turn 28.4 1.2E+02 0.0026 19.7 3.9 45 78-126 3-47 (58)
193 PRK07405 RNA polymerase sigma 28.3 2.4E+02 0.0051 26.8 7.3 31 91-121 178-208 (317)
194 PF01399 PCI: PCI domain; Int 28.3 1.9E+02 0.004 21.5 5.4 58 76-133 39-96 (105)
195 PRK10423 transcriptional repre 28.3 2.2E+02 0.0048 25.3 6.7 56 77-132 23-92 (327)
196 smart00351 PAX Paired Box doma 28.2 1.6E+02 0.0035 24.2 5.5 48 73-123 12-59 (125)
197 COG1802 GntR Transcriptional r 28.1 41 0.0009 29.6 2.0 59 81-141 23-82 (230)
198 PRK06811 RNA polymerase factor 27.8 81 0.0018 26.7 3.7 58 77-138 130-189 (189)
199 PF06971 Put_DNA-bind_N: Putat 27.8 1E+02 0.0023 22.4 3.7 33 86-118 16-49 (50)
200 PF08280 HTH_Mga: M protein tr 27.6 1.3E+02 0.0027 21.7 4.2 42 84-126 7-48 (59)
201 PRK11303 DNA-binding transcrip 27.6 1.9E+02 0.0042 25.8 6.2 55 78-132 29-97 (328)
202 PHA01976 helix-turn-helix prot 27.5 1E+02 0.0023 21.7 3.7 32 81-114 1-32 (67)
203 KOG0860 Synaptobrevin/VAMP-lik 27.4 1.8E+02 0.0038 25.0 5.6 33 152-192 79-111 (116)
204 TIGR03697 NtcA_cyano global ni 27.3 1.8E+02 0.0039 24.0 5.6 50 81-132 113-176 (193)
205 PRK09954 putative kinase; Prov 27.3 1.2E+02 0.0025 28.6 4.9 50 83-133 4-56 (362)
206 PRK10402 DNA-binding transcrip 27.1 1.7E+02 0.0036 25.6 5.6 49 81-131 149-201 (226)
207 PF00325 Crp: Bacterial regula 27.0 83 0.0018 21.1 2.9 27 98-124 3-29 (32)
208 PF10668 Phage_terminase: Phag 26.8 1.1E+02 0.0023 23.3 3.8 33 83-115 8-40 (60)
209 TIGR02337 HpaR homoprotocatech 26.7 1.2E+02 0.0025 24.0 4.2 45 85-132 31-75 (118)
210 PF09753 Use1: Membrane fusion 26.7 1.3E+02 0.0028 27.5 5.1 16 152-167 212-227 (251)
211 PF13730 HTH_36: Helix-turn-he 26.6 81 0.0018 21.6 2.9 26 99-124 27-52 (55)
212 PF12263 DUF3611: Protein of u 26.6 1.2E+02 0.0025 27.5 4.6 38 159-196 4-41 (183)
213 PRK11753 DNA-binding transcrip 26.5 1.4E+02 0.0031 25.1 4.9 46 80-125 138-196 (211)
214 PRK10668 DNA-binding transcrip 26.4 71 0.0015 27.1 3.1 28 86-113 19-47 (215)
215 COG0735 Fur Fe2+/Zn2+ uptake r 26.3 3.1E+02 0.0067 23.3 6.9 64 81-144 20-88 (145)
216 PF07790 DUF1628: Protein of u 26.3 1.3E+02 0.0028 22.7 4.2 21 177-197 7-27 (80)
217 PRK11303 DNA-binding transcrip 26.1 49 0.0011 29.6 2.2 22 98-119 1-22 (328)
218 PRK00215 LexA repressor; Valid 26.1 1.2E+02 0.0027 26.2 4.6 58 84-143 6-69 (205)
219 PF09756 DDRGK: DDRGK domain; 26.1 1.3E+02 0.0027 27.4 4.8 64 83-149 100-165 (188)
220 PRK13276 cell wall biosynthesi 26.0 1.2E+02 0.0027 28.2 4.8 39 85-123 16-61 (224)
221 PRK09492 treR trehalose repres 25.8 2.5E+02 0.0053 25.0 6.5 23 77-99 29-51 (315)
222 PF13182 DUF4007: Protein of u 25.8 1.8E+02 0.0039 27.5 5.9 65 77-142 196-273 (286)
223 PRK10703 DNA-binding transcrip 25.4 1.5E+02 0.0033 26.6 5.2 57 77-133 26-96 (341)
224 PRK11414 colanic acid/biofilm 25.1 4.6E+02 0.0099 22.8 8.1 50 93-146 30-80 (221)
225 TIGR03652 FeS_repair_RIC iron- 25.1 79 0.0017 28.3 3.3 41 85-125 9-55 (216)
226 PRK10820 DNA-binding transcrip 25.1 1.5E+02 0.0031 30.2 5.5 72 67-141 32-106 (520)
227 PLN03239 histone acetyltransfe 25.0 97 0.0021 31.0 4.1 59 84-147 268-329 (351)
228 PF11268 DUF3071: Protein of u 25.0 85 0.0018 28.1 3.4 33 82-116 56-88 (170)
229 TIGR03384 betaine_BetI transcr 24.8 55 0.0012 26.8 2.1 27 87-113 17-44 (189)
230 TIGR02010 IscR iron-sulfur clu 24.5 1.4E+02 0.0031 24.6 4.5 29 96-124 24-52 (135)
231 TIGR01481 ccpA catabolite cont 24.5 62 0.0014 28.9 2.5 56 77-132 26-95 (329)
232 smart00354 HTH_LACI helix_turn 24.4 62 0.0013 23.9 2.1 21 98-118 1-21 (70)
233 PF05379 Peptidase_C23: Carlav 24.1 72 0.0016 25.5 2.5 57 85-141 19-80 (89)
234 PRK10617 cytochrome c-type pro 24.1 1.5E+02 0.0032 27.2 4.9 21 253-273 109-129 (200)
235 PRK03837 transcriptional regul 24.0 1.5E+02 0.0033 25.9 4.8 63 79-144 14-81 (241)
236 PRK07921 RNA polymerase sigma 23.8 3.6E+02 0.0078 26.0 7.6 42 78-119 163-211 (324)
237 PRK15435 bifunctional DNA-bind 23.7 74 0.0016 30.9 3.0 75 81-160 269-349 (353)
238 cd02106 Band_7 The band 7 doma 23.6 1.5E+02 0.0033 22.0 4.2 69 80-150 50-118 (121)
239 TIGR02405 trehalos_R_Ecol treh 23.5 3.1E+02 0.0068 24.5 6.8 56 77-132 26-95 (311)
240 PRK03573 transcriptional regul 23.5 1.5E+02 0.0032 24.1 4.4 40 85-124 34-73 (144)
241 PRK03887 methylated-DNA--prote 23.3 83 0.0018 28.6 3.0 56 81-136 91-151 (175)
242 PRK04984 fatty acid metabolism 23.1 1.6E+02 0.0034 25.9 4.8 55 82-138 11-71 (239)
243 PF09681 Phage_rep_org_N: N-te 23.1 2.6E+02 0.0056 23.6 5.8 40 98-139 54-93 (121)
244 PRK08392 hypothetical protein; 22.9 82 0.0018 27.8 2.9 35 67-101 146-180 (215)
245 PF13384 HTH_23: Homeodomain-l 22.9 1.1E+02 0.0024 20.5 3.0 40 80-122 3-42 (50)
246 PRK11202 DNA-binding transcrip 22.9 79 0.0017 27.2 2.8 31 81-111 10-46 (203)
247 TIGR02417 fruct_sucro_rep D-fr 22.7 62 0.0014 29.0 2.2 20 99-118 1-20 (327)
248 PRK03902 manganese transport t 22.4 4.4E+02 0.0096 21.7 8.7 38 91-130 16-53 (142)
249 PF13443 HTH_26: Cro/C1-type H 22.4 1.4E+02 0.003 20.9 3.5 28 87-116 2-29 (63)
250 PRK10727 DNA-binding transcrip 22.3 73 0.0016 28.9 2.6 56 77-132 26-95 (343)
251 TIGR02161 napC_nirT periplasmi 22.3 1.4E+02 0.0031 26.8 4.3 23 253-275 100-122 (185)
252 PF00802 Glycoprotein_G: Pneum 22.2 29 0.00064 33.2 0.0 16 161-176 3-18 (263)
253 PRK09391 fixK transcriptional 22.2 2E+02 0.0043 25.3 5.2 44 81-124 153-206 (230)
254 COG0350 Ada Methylated DNA-pro 22.0 1.7E+02 0.0038 25.6 4.7 73 81-160 87-167 (168)
255 PF00376 MerR: MerR family reg 21.9 67 0.0014 21.7 1.7 16 99-114 1-16 (38)
256 PRK12702 mannosyl-3-phosphogly 21.8 1.2E+02 0.0026 29.6 4.1 28 97-124 123-150 (302)
257 PRK11534 DNA-binding transcrip 21.7 90 0.002 27.2 2.9 40 94-135 27-67 (224)
258 PF12298 Bot1p: Eukaryotic mit 21.6 1.8E+02 0.0039 26.0 4.8 43 79-124 17-59 (172)
259 smart00342 HTH_ARAC helix_turn 21.5 1.8E+02 0.004 20.1 4.0 35 85-119 37-73 (84)
260 KOG3830 Uncharacterized conser 21.4 96 0.0021 32.4 3.4 41 77-117 283-323 (542)
261 TIGR03338 phnR_burk phosphonat 21.3 93 0.002 26.7 2.9 57 83-141 20-77 (212)
262 PRK10339 DNA-binding transcrip 21.1 74 0.0016 28.7 2.3 23 78-100 29-51 (327)
263 PF13038 DUF3899: Domain of un 21.1 99 0.0021 23.9 2.7 32 163-194 58-89 (92)
264 PRK08215 sporulation sigma fac 20.9 3E+02 0.0066 24.8 6.2 44 78-121 113-163 (258)
265 PF13744 HTH_37: Helix-turn-he 20.9 2.8E+02 0.0061 20.9 5.2 38 95-132 29-78 (80)
266 cd07977 TFIIE_beta_winged_heli 20.9 2.5E+02 0.0054 21.7 4.9 34 85-118 12-47 (75)
267 PF13518 HTH_28: Helix-turn-he 20.9 2.4E+02 0.0053 18.6 4.4 36 85-123 3-38 (52)
268 TIGR02161 napC_nirT periplasmi 20.9 49 0.0011 29.7 1.1 12 174-185 14-25 (185)
269 cd06171 Sigma70_r4 Sigma70, re 20.7 2.3E+02 0.005 17.8 4.1 26 96-121 25-50 (55)
270 PRK10513 sugar phosphate phosp 20.6 3.8E+02 0.0082 23.6 6.7 59 78-142 20-78 (270)
271 COG1497 Predicted transcriptio 20.3 2.1E+02 0.0046 27.6 5.2 42 83-124 11-52 (260)
272 PF14493 HTH_40: Helix-turn-he 20.3 1.5E+02 0.0032 22.9 3.6 80 89-175 5-88 (91)
273 PF02186 TFIIE_beta: TFIIE bet 20.3 3.1E+02 0.0067 20.8 5.2 53 83-139 6-59 (65)
274 COG1308 EGD2 Transcription fac 20.2 87 0.0019 27.0 2.4 23 98-120 83-108 (122)
275 PF11548 Receptor_IA-2: Protei 20.1 39 0.00085 27.7 0.3 27 92-118 52-78 (91)
No 1
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=94.80 E-value=0.071 Score=39.87 Aligned_cols=45 Identities=16% Similarity=0.266 Sum_probs=41.1
Q ss_pred CchHHHHHHHHHHHcCC-ceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 80 PADVRNRAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 80 ~~~~~~~im~Ave~lg~-RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
+..++.+|++++.+.|. .+|+.|+|.+.|++...+.+.|..|..+
T Consensus 4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 4 QDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK 49 (68)
T ss_pred chHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 44677899999999988 6999999999999999999999999876
No 2
>PRK13239 alkylmercury lyase; Provisional
Probab=94.68 E-value=0.068 Score=48.82 Aligned_cols=53 Identities=19% Similarity=0.297 Sum_probs=46.2
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEE
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY 139 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlY 139 (280)
..+.-.|++.+. .|.-+|+.|+|+.+|.+.+++++.|.+|. ..+.+++|+||-
T Consensus 21 ~~~~~~llr~la-~G~pvt~~~lA~~~~~~~~~v~~~L~~l~-----~~~~d~~g~iv~ 73 (206)
T PRK13239 21 ATLLVPLLRLLA-KGRPVSVTTLAAALGWPVEEVEAVLEAMP-----DTEYDEDGRIIG 73 (206)
T ss_pred hHHHHHHHHHHH-cCCCCCHHHHHHHhCCCHHHHHHHHHhCC-----CeEECCCCCEEe
Confidence 457778899988 99999999999999999999999999985 347888999974
No 3
>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=93.63 E-value=0.12 Score=41.00 Aligned_cols=52 Identities=23% Similarity=0.321 Sum_probs=37.4
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEE
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL 138 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIl 138 (280)
+.+-..+++.+.+ |.-||+.++|+.+|.++++++++|.+.. ..|-+++|.||
T Consensus 23 ~~L~r~LLr~LA~-G~PVt~~~LA~a~g~~~e~v~~~L~~~p-----~tEyD~~GrIV 74 (77)
T PF12324_consen 23 AWLLRPLLRLLAK-GQPVTVEQLAAALGWPVEEVRAALAAMP-----DTEYDDQGRIV 74 (77)
T ss_dssp HHHHHHHHHHHTT-TS-B-HHHHHHHHT--HHHHHHHHHH-T-----TSEEETTSEEE
T ss_pred HHHHHHHHHHHHc-CCCcCHHHHHHHHCCCHHHHHHHHHhCC-----CceEcCCCCee
Confidence 3344456666666 9999999999999999999999988775 47778888886
No 4
>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=93.46 E-value=0.11 Score=36.52 Aligned_cols=40 Identities=23% Similarity=0.398 Sum_probs=35.8
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
-+|++++.+.+...|+.|+|.++|++...+.+-|..|...
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3689999999999999999999999999999999999865
No 5
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=92.82 E-value=0.79 Score=40.59 Aligned_cols=84 Identities=19% Similarity=0.164 Sum_probs=59.6
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc--C-CceEeccCCcEEEEcCcchHHHHhhhhHHHh
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--D-GFLEVSDEGDVLYVFPNNYRAKLAAKSFRLK 157 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~--~-GhLqVsesGEIlYvFP~~fRs~l~~Ks~r~r 157 (280)
.+..-+|++++.+.| .+|..|+|...|++.+++++.|..|..+. . -..+..+.|-+.|.+=-+...+. ...+.+
T Consensus 21 ~~~~~~Vl~~L~~~g-~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~--d~ik~~ 97 (178)
T PRK06266 21 DEEGFEVLKALIKKG-EVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLP--EIIKKK 97 (178)
T ss_pred CccHhHHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHH--HHHHHH
Confidence 445578999999888 69999999999999999999999999994 2 22333357999998754445433 333444
Q ss_pred HHHHHHHhhh
Q 023574 158 VEPVIDKAKA 167 (280)
Q Consensus 158 l~~~~~k~w~ 167 (280)
+....+++..
T Consensus 98 ~~~~~~klk~ 107 (178)
T PRK06266 98 KMEELKKLKE 107 (178)
T ss_pred HHHHHHHHHH
Confidence 4444444433
No 6
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=92.46 E-value=1.1 Score=33.43 Aligned_cols=77 Identities=21% Similarity=0.379 Sum_probs=51.6
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc-CcchH---HHHhhhhHHHhHHH
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF-PNNYR---AKLAAKSFRLKVEP 160 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvF-P~~fR---s~l~~Ks~r~rl~~ 160 (280)
.+|++.+.+.++.+|+.|+|...|++...+.+-|..|.+. |-|+-..++. .|.. |+.++ ..+.+..+.....+
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~--g~l~~~~~~~-~y~l~~~~~~~~~~~~~~~~l~~~~~~ 84 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQEL--GYVEQDGQNG-RYRLGPKVLELGQSYLSSLDLREVAKP 84 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC--CCeeecCCCC-ceeecHHHHHHHHHHHhcCCHHHHHHH
Confidence 4678888887678999999999999999999999999764 7777654333 3554 22222 22333344444555
Q ss_pred HHHH
Q 023574 161 VIDK 164 (280)
Q Consensus 161 ~~~k 164 (280)
..+.
T Consensus 85 ~l~~ 88 (91)
T smart00346 85 VLEE 88 (91)
T ss_pred HHHH
Confidence 5444
No 7
>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=92.45 E-value=1.1 Score=38.86 Aligned_cols=79 Identities=24% Similarity=0.256 Sum_probs=59.2
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCC---ceEeccCCcEEEEcCcchHHHHhhhhHHHhHHHHH
Q 023574 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG---FLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVI 162 (280)
Q Consensus 86 ~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~G---hLqVsesGEIlYvFP~~fRs~l~~Ks~r~rl~~~~ 162 (280)
.+++|+-..| -+|-.|+|...|++++++++.|..|..+.=. +.+-.++|-+.|.+=-|+..+. ...+.++....
T Consensus 18 ~Vl~aL~~~~-~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i~--d~Ik~~~~~~~ 94 (158)
T TIGR00373 18 LVLFSLGIKG-EFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKAL--DVLKRKLEETA 94 (158)
T ss_pred HHHHHHhccC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHH--HHHHHHHHHHH
Confidence 5677877666 6999999999999999999999999999532 5556667999999745777765 44444555555
Q ss_pred HHhhh
Q 023574 163 DKAKA 167 (280)
Q Consensus 163 ~k~w~ 167 (280)
+++..
T Consensus 95 ~~lk~ 99 (158)
T TIGR00373 95 KKLRE 99 (158)
T ss_pred HHHHH
Confidence 55443
No 8
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=92.21 E-value=1.5 Score=37.53 Aligned_cols=86 Identities=19% Similarity=0.157 Sum_probs=66.5
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc-CCceEec-cCCcEEEEc-CcchHHHHhhhhHHHhHHHH
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT-DGFLEVS-DEGDVLYVF-PNNYRAKLAAKSFRLKVEPV 161 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~-~GhLqVs-esGEIlYvF-P~~fRs~l~~Ks~r~rl~~~ 161 (280)
-.++.++-+.++..|+-|+|..-+++...|+++|+.|.... ==.-+++ +.|---|.+ |.++-.+ .+-....+++|
T Consensus 30 v~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~--k~~i~~~l~~w 107 (126)
T COG3355 30 VEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEI--KKKILKDLDEW 107 (126)
T ss_pred HHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHH--HHHHHHHHHHH
Confidence 45666666688999999999999999999999999999874 1222344 679999999 8888763 35567778888
Q ss_pred HHHhhhhhhhH
Q 023574 162 IDKAKAAAEYS 172 (280)
Q Consensus 162 ~~k~w~v~~yl 172 (280)
.+++...+..+
T Consensus 108 ~~~~~~~i~~~ 118 (126)
T COG3355 108 YDKMKQLIEEF 118 (126)
T ss_pred HHHHHHHHHHH
Confidence 88887766543
No 9
>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=91.71 E-value=0.52 Score=32.18 Aligned_cols=42 Identities=19% Similarity=0.382 Sum_probs=34.7
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
+.+.+|++++.+ +++.|+.|+|...|++...+.+.|..|..+
T Consensus 3 ~~~~~Il~~l~~-~~~~t~~ela~~~~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 3 ETQRKILNYLRE-NPRITQKELAEKLGISRSTVNRYLKKLEEK 44 (48)
T ss_dssp HHHHHHHHHHHH-CTTS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHH-cCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 356789999999 455999999999999999999999998765
No 10
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=91.33 E-value=0.59 Score=33.58 Aligned_cols=53 Identities=26% Similarity=0.439 Sum_probs=44.6
Q ss_pred CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC
Q 023574 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (280)
Q Consensus 80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesG 135 (280)
....|-+|++.+ ..+...|++++|...|++...+..-|..|.. .|-+++.++|
T Consensus 8 ~~p~R~~Il~~L-~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~--aGli~~~~~g 60 (61)
T PF12840_consen 8 SDPTRLRILRLL-ASNGPMTVSELAEELGISQSTVSYHLKKLEE--AGLIEVEREG 60 (61)
T ss_dssp TSHHHHHHHHHH-HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEEEET
T ss_pred CCHHHHHHHHHH-hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCeEEeccC
Confidence 346788899999 7788899999999999999999999999977 5677777766
No 11
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=90.74 E-value=0.4 Score=36.20 Aligned_cols=53 Identities=23% Similarity=0.394 Sum_probs=40.9
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc--CCcEEE
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD--EGDVLY 139 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse--sGEIlY 139 (280)
++|++.+++.+.-+|..|||...|++..+|+.=|..|..+ |.++-++ .|-..|
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~e--G~V~~~~~~rG~~~~ 57 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKE--GKVERSPVRRGKSTY 57 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHC--TSEEEES-SSSSS-E
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEecCCCCccee
Confidence 6789999998888999999999999999999999999876 4555544 355443
No 12
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=90.64 E-value=0.53 Score=40.53 Aligned_cols=51 Identities=25% Similarity=0.377 Sum_probs=42.2
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses 134 (280)
+++..+|++.|++. +|+|++|++..+|++.+.+++-|..|++ .|+|..+..
T Consensus 11 ~eLk~rIvElVRe~-GRiTi~ql~~~TGasR~Tvk~~lreLVa--~G~l~~~G~ 61 (127)
T PF06163_consen 11 EELKARIVELVREH-GRITIKQLVAKTGASRNTVKRYLRELVA--RGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHc-CCccHHHHHHHHCCCHHHHHHHHHHHHH--cCCeEeCCC
Confidence 56667888888765 5899999999999999999999999886 577777554
No 13
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=90.22 E-value=0.83 Score=42.93 Aligned_cols=83 Identities=17% Similarity=0.306 Sum_probs=69.3
Q ss_pred cCCCcccccCCCCchHH---HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcc
Q 023574 68 VGPGRIVESDKLPADVR---NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (280)
Q Consensus 68 ~~~~~~v~~~~l~~~~~---~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~ 144 (280)
++.||.----++|-+++ ..|+++++.+|| ||+.-+-+.-|-.-.-|.++|..|..+.=+-+.-...+|-.|-||.+
T Consensus 159 ~~iggK~~vrSVP~ELn~Dht~ILela~~~gy-vt~s~l~~~l~We~~Ra~qaLe~lv~egL~WiD~q~g~e~~YW~ps~ 237 (249)
T KOG3341|consen 159 IKIGGKKLVRSVPTELNMDHTVILELAEILGY-VTISLLKANLGWERSRAIQALEHLVKEGLAWIDLQAGDEAAYWFPSL 237 (249)
T ss_pred EEecCEEeeecCcchhcccHHHHHHHHHhcCc-eeHHHHHHhccchHHHHHHHHHHHHhccceeeeccCCcceeeechhh
Confidence 44556655566676665 579999999999 99999988889999999999999999998888888889999999999
Q ss_pred hHHHHhh
Q 023574 145 YRAKLAA 151 (280)
Q Consensus 145 fRs~l~~ 151 (280)
|-.....
T Consensus 238 ~~~~~~q 244 (249)
T KOG3341|consen 238 FTDQYAQ 244 (249)
T ss_pred hhHHHhh
Confidence 9775543
No 14
>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=88.92 E-value=1.2 Score=32.22 Aligned_cols=41 Identities=12% Similarity=0.282 Sum_probs=36.5
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~ 125 (280)
+..|++.+++. +.+|+.|+|..-|.|...+++.|..|+...
T Consensus 2 ~~~Il~~l~~~-~~~s~~ela~~~~VS~~TiRRDl~~L~~~g 42 (57)
T PF08220_consen 2 QQQILELLKEK-GKVSVKELAEEFGVSEMTIRRDLNKLEKQG 42 (57)
T ss_pred HHHHHHHHHHc-CCEEHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 46789999876 689999999999999999999999998763
No 15
>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=88.78 E-value=3.7 Score=28.11 Aligned_cols=60 Identities=25% Similarity=0.424 Sum_probs=46.2
Q ss_pred CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC-cEEEEcC
Q 023574 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG-DVLYVFP 142 (280)
Q Consensus 79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesG-EIlYvFP 142 (280)
+..+.+..++.++.+.+ ++..|+|...|++...+.+.|..|.+. |.+....++ ...|.+.
T Consensus 4 ~~~~~~~~il~~l~~~~--~~~~ei~~~~~i~~~~i~~~l~~L~~~--g~i~~~~~~~~~~~~~~ 64 (78)
T cd00090 4 LSDPTRLRILRLLLEGP--LTVSELAERLGLSQSTVSRHLKKLEEA--GLVESRREGRRVYYSLT 64 (78)
T ss_pred ccChHHHHHHHHHHHCC--cCHHHHHHHHCcCHhHHHHHHHHHHHC--CCeEEEEeccEEEEEeC
Confidence 34456678888888765 999999999999999999999999765 566665543 4556554
No 16
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=88.39 E-value=2 Score=28.40 Aligned_cols=45 Identities=16% Similarity=0.338 Sum_probs=37.1
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqV 131 (280)
+..+++.+.+.+ .+|+.|++..-|++...+.+.|..|..+ |.++-
T Consensus 2 ~~~il~~l~~~~-~~s~~~l~~~l~~s~~tv~~~l~~L~~~--g~i~~ 46 (53)
T smart00420 2 QQQILELLAQQG-KVSVEELAELLGVSEMTIRRDLNKLEEQ--GLLTR 46 (53)
T ss_pred HHHHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEE
Confidence 356788888765 5999999999999999999999999876 44543
No 17
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=88.39 E-value=1.6 Score=29.32 Aligned_cols=49 Identities=20% Similarity=0.391 Sum_probs=38.4
Q ss_pred HHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEE
Q 023574 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY 139 (280)
Q Consensus 87 im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlY 139 (280)
|+..+. ....|+.|++...|++...+.+.|..|.++ |-++....|.-.|
T Consensus 2 il~~l~--~~~~~~~~i~~~l~is~~~v~~~l~~L~~~--g~i~~~~~~~~~~ 50 (66)
T smart00418 2 ILKLLA--EGELCVCELAEILGLSQSTVSHHLKKLREA--GLVESRREGKRVY 50 (66)
T ss_pred HHHHhh--cCCccHHHHHHHHCCCHHHHHHHHHHHHHC--CCeeeeecCCEEE
Confidence 566666 667899999999999999999999999975 5666555444433
No 18
>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=88.17 E-value=2.2 Score=29.60 Aligned_cols=42 Identities=10% Similarity=0.193 Sum_probs=34.3
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~ 125 (280)
+.+|++.+.+.+..+|..++|.+-|+|...+++.|..|-+..
T Consensus 2 ~~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 2 QKQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 357888896666669999999999999999999999994443
No 19
>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=87.62 E-value=0.81 Score=36.14 Aligned_cols=34 Identities=12% Similarity=0.081 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHH
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL 118 (280)
-+..|++.+.+ +.+|+.|||..+|++.+.+.+.|
T Consensus 7 R~~~I~e~l~~--~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 7 RVLEIGKYIVE--TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHHH--CCCCHHHHHHHhCCCHHHHHHHh
Confidence 45678999999 99999999999999999998876
No 20
>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=87.27 E-value=1.5 Score=34.37 Aligned_cols=44 Identities=20% Similarity=0.459 Sum_probs=37.6
Q ss_pred chHHHHHHHHHHH---cCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 81 ADVRNRAMDAVDA---CNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 81 ~~~~~~im~Ave~---lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
..++.+|+++++. ..-.+.+.+|+.+-|++.++++++|..|..+
T Consensus 46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~e 92 (102)
T PF08784_consen 46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNE 92 (102)
T ss_dssp -HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhC
Confidence 4578899999998 5667999999999999999999999999876
No 21
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=86.94 E-value=1.6 Score=41.17 Aligned_cols=57 Identities=18% Similarity=0.367 Sum_probs=48.9
Q ss_pred CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEE
Q 023574 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL 138 (280)
Q Consensus 80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIl 138 (280)
|..++..|.+.+...|+|+++.|++..-++.++..|+.+..++.+-. +++.. .||++
T Consensus 53 ~~~L~~EI~~el~~~gGRv~~~dL~~~LnVd~~~ie~~~~~i~~~~~-~~~l~-~geli 109 (272)
T PF09743_consen 53 PEQLEKEIKDELYVHGGRVNLVDLAQALNVDLDHIERRAQEIVKSDK-SLQLV-QGELI 109 (272)
T ss_pred HHHHHHHHHHHHHHcCCceEHHHHHHhcCcCHHHHHHHHHHHHhCCC-cEEEE-CCEEc
Confidence 45677889999999999999999999999999999999999998876 55543 68873
No 22
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=85.68 E-value=1.8 Score=38.79 Aligned_cols=41 Identities=24% Similarity=0.404 Sum_probs=36.9
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
.+.++.-+-...+..|.|+||+.-|.+|++++.+|..|-++
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 151 (166)
T PRK15466 111 ADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSA 151 (166)
T ss_pred HHHHHHHHHHHHccccHHHHHHHhCCcHHHHHHHHHHHHhc
Confidence 46677778888999999999999999999999999999876
No 23
>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=85.51 E-value=2.3 Score=31.51 Aligned_cols=39 Identities=21% Similarity=0.360 Sum_probs=31.1
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
.+|.+.+-+.| +.|+.+++..++++.++++++|..|.+.
T Consensus 16 ~~V~~~Ll~~G-~ltl~~i~~~t~l~~~~Vk~~L~~LiQh 54 (62)
T PF08221_consen 16 AKVGEVLLSRG-RLTLREIVRRTGLSPKQVKKALVVLIQH 54 (62)
T ss_dssp HHHHHHHHHC--SEEHHHHHHHHT--HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHcC-CcCHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence 46677776665 9999999999999999999999999764
No 24
>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=85.05 E-value=3.5 Score=29.93 Aligned_cols=53 Identities=21% Similarity=0.312 Sum_probs=41.4
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEE
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY 139 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlY 139 (280)
..++..++- ..+..|+.|||..+|++...+.+.|..|... |-++..+...-+|
T Consensus 10 E~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~--GlV~~~~~~~~~Y 62 (68)
T PF01978_consen 10 EAKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK--GLVEREEGRPKVY 62 (68)
T ss_dssp HHHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT--TSEEEEEECCEEE
T ss_pred HHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEcCceEEE
Confidence 345666666 5678999999999999999999999999876 6667666443333
No 25
>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=82.89 E-value=1.9 Score=31.86 Aligned_cols=53 Identities=23% Similarity=0.245 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesG 135 (280)
++....+.-.++|...|..+||...|+++++.++.|.....-..=++.+..++
T Consensus 6 i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~ 58 (78)
T PF04539_consen 6 IERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDED 58 (78)
T ss_dssp HHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSS
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCC
Confidence 34445555668899999999999999999999888876544334444555443
No 26
>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=82.39 E-value=2.8 Score=31.54 Aligned_cols=45 Identities=22% Similarity=0.361 Sum_probs=34.3
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCC-HHHHHHHHHHHHhhcCCceE
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLK-LNEAQKALQALAADTDGFLE 130 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~-L~~Ae~aL~aLAsD~~GhLq 130 (280)
-.-|.+.+++.|+-.|+.|+|..-|++ .+.+++-|.+|..+ |.|+
T Consensus 12 L~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~k--G~I~ 57 (65)
T PF01726_consen 12 LEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERK--GYIR 57 (65)
T ss_dssp HHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHT--TSEE
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC--cCcc
Confidence 344566678899999999999999997 99999999999865 4444
No 27
>smart00753 PAM PCI/PINT associated module.
Probab=82.19 E-value=6.2 Score=29.55 Aligned_cols=68 Identities=15% Similarity=0.178 Sum_probs=49.2
Q ss_pred CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchH
Q 023574 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYR 146 (280)
Q Consensus 79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fR 146 (280)
|-...+.+.+..+-+.-..+|..++|...+++.+++|..|..+..+..=+-.++....+++.--..-|
T Consensus 6 l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00753 6 LQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred HHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 33455666666666677889999999999999999999999888885333345666566666544444
No 28
>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=82.19 E-value=6.2 Score=29.55 Aligned_cols=68 Identities=15% Similarity=0.178 Sum_probs=49.2
Q ss_pred CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchH
Q 023574 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYR 146 (280)
Q Consensus 79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fR 146 (280)
|-...+.+.+..+-+.-..+|..++|...+++.+++|..|..+..+..=+-.++....+++.--..-|
T Consensus 6 l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00088 6 LQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred HHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 33455666666666677889999999999999999999999888885333345666566666544444
No 29
>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=82.13 E-value=4 Score=28.48 Aligned_cols=42 Identities=14% Similarity=0.240 Sum_probs=35.9
Q ss_pred HHHHHHHHHHcCCc-eehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574 84 RNRAMDAVDACNRR-VTIGDVAGKAGLKLNEAQKALQALAADT 125 (280)
Q Consensus 84 ~~~im~Ave~lg~R-vTvGDVAa~aGL~L~~Ae~aL~aLAsD~ 125 (280)
+-+++.++...++. +|+.|+|...|++...+.+.+..|..+.
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~G 49 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKG 49 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 45678888888887 9999999999999999999999988763
No 30
>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=77.83 E-value=5.4 Score=27.52 Aligned_cols=49 Identities=20% Similarity=0.361 Sum_probs=35.5
Q ss_pred chHHHHHHHHHHHc----CCc-eehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023574 81 ADVRNRAMDAVDAC----NRR-VTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (280)
Q Consensus 81 ~~~~~~im~Ave~l----g~R-vTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqV 131 (280)
.++...+.+.+... |.. .|+.|+|...|++...+.++|..|+.. |-|+.
T Consensus 4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~--G~i~~ 57 (66)
T cd07377 4 EQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAE--GLVER 57 (66)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEe
Confidence 34556666665543 222 459999999999999999999999884 34543
No 31
>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=77.77 E-value=6.8 Score=28.11 Aligned_cols=53 Identities=25% Similarity=0.479 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHH-HHHHHHHHhh-----cCCceEeccCCc
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEA-QKALQALAAD-----TDGFLEVSDEGD 136 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~A-e~aL~aLAsD-----~~GhLqVsesGE 136 (280)
.++.+|..+.. ..++.+.++..+.|.++.+. .+.|..+.++ .+++|.+|+.|-
T Consensus 7 ~~e~i~~~LR~-~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~~~~~l~lT~~G~ 65 (66)
T PF06969_consen 7 LREYIMLGLRC-NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLLEIDGGRLRLTEKGR 65 (66)
T ss_dssp HHHHHHHHHHH-HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE-SSEEEE-TTTG
T ss_pred HHHHHHHHHHh-HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEEeCCEEEECcccC
Confidence 45667777755 67899999999999987766 7778888886 488888888873
No 32
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=77.48 E-value=4.6 Score=37.97 Aligned_cols=46 Identities=20% Similarity=0.328 Sum_probs=39.7
Q ss_pred CCCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 78 ~l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
.|+.+ ...++++++..|+|+|+.|+..+.|+|...+=+.|..|...
T Consensus 192 ~L~~~-e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~ 237 (258)
T COG2512 192 DLNED-EKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKR 237 (258)
T ss_pred CCCHH-HHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhC
Confidence 34433 35789999999999999999999999999999999998764
No 33
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=77.12 E-value=28 Score=29.12 Aligned_cols=60 Identities=13% Similarity=0.139 Sum_probs=47.0
Q ss_pred CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 023574 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (280)
Q Consensus 79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvF 141 (280)
|....|-+|+..+... +..|++|+|...|++...+-+-|..|.. -|-+....+|.-+|..
T Consensus 13 LadptRl~IL~~L~~~-~~~~v~ela~~l~lsqstvS~HL~~L~~--AGLV~~~r~Gr~~~Y~ 72 (117)
T PRK10141 13 LSDETRLGIVLLLRES-GELCVCDLCTALDQSQPKISRHLALLRE--SGLLLDRKQGKWVHYR 72 (117)
T ss_pred hCCHHHHHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCceEEEEEcCEEEEE
Confidence 5567788999988654 4699999999999999999998888864 4667777777655544
No 34
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=76.84 E-value=16 Score=33.54 Aligned_cols=43 Identities=9% Similarity=0.102 Sum_probs=37.9
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
.+-+.+|++.+++.| ++|+.|+|..-|+|...+++.|..|+..
T Consensus 4 ~eR~~~Il~~L~~~~-~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 4 RQRQAAILEYLQKQG-KTSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred HHHHHHHHHHHHHcC-CEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 456778888888855 6999999999999999999999999876
No 35
>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=76.81 E-value=6.6 Score=27.17 Aligned_cols=39 Identities=13% Similarity=0.313 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHH
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aL 121 (280)
++..+|++++.+. +|.+..++|...|++-.++.+-+..|
T Consensus 3 ~~D~~Il~~Lq~d-~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 3 ELDRKILRLLQED-GRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHHH--TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHc-CCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 3557888888776 88999999999999999999888765
No 36
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=76.78 E-value=7.6 Score=35.97 Aligned_cols=53 Identities=15% Similarity=0.250 Sum_probs=43.1
Q ss_pred CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC
Q 023574 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (280)
Q Consensus 80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesG 135 (280)
..+-+.+|++.+++.+. +|+.|+|..-|+|...+++.|..|.+. |-++-..-|
T Consensus 15 ~~eR~~~Il~~L~~~~~-vtv~eLa~~l~VS~~TIRRDL~~Le~~--G~l~r~~GG 67 (269)
T PRK09802 15 TSERREQIIQRLRQQGS-VQVNDLSALYGVSTVTIRNDLAFLEKQ--GIAVRAYGG 67 (269)
T ss_pred HHHHHHHHHHHHHHcCC-EeHHHHHHHHCCCHHHHHHHHHHHHhC--CCeEEEeCC
Confidence 35677888999998776 999999999999999999999999664 555544434
No 37
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=76.71 E-value=9.4 Score=34.73 Aligned_cols=79 Identities=11% Similarity=0.146 Sum_probs=40.3
Q ss_pred HHHHHHHHHcCCceehhhhhhhcC------CCHHHHHHHHHHHHhhc-CCceEeccCCcEEEEcCcchHHHHhhhhHHHh
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAG------LKLNEAQKALQALAADT-DGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLK 157 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aG------L~L~~Ae~aL~aLAsD~-~GhLqVsesGEIlYvFP~~fRs~l~~Ks~r~r 157 (280)
.|+.+.+++-+ |+.|+..-.. -.+++.+..+..|.... -.++.++=...- ..-. .+.++-.+
T Consensus 149 ~rl~~ll~ka~---~~~d~l~ie~~L~~v~~eIe~~~~~~~~l~~~v~~sti~i~l~~~~------~~~~--~~~~~~~~ 217 (262)
T PF14257_consen 149 ERLLELLEKAK---TVEDLLEIERELSRVRSEIEQLEGQLKYLDDRVDYSTITISLYEPE------SIKP--ESPSFGSR 217 (262)
T ss_pred HHHHHHHHhcC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhceEEEEEEEEecC------CCCC--CCCCcchH
Confidence 34444555444 8888876444 14455555555666663 455444322110 0000 33455556
Q ss_pred HHHHHHHhhhhhhhHhh
Q 023574 158 VEPVIDKAKAAAEYSIR 174 (280)
Q Consensus 158 l~~~~~k~w~v~~yliR 174 (280)
+...+...|..+..++.
T Consensus 218 ~~~al~~~~~~~~~~~~ 234 (262)
T PF14257_consen 218 FRDALKNGWNALVSFLS 234 (262)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 66666677777665554
No 38
>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=76.32 E-value=4.9 Score=35.30 Aligned_cols=41 Identities=10% Similarity=0.182 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
.+.+|+..+.+.|. .|+.|+|...|++...+.+.|..|.++
T Consensus 2 tr~~IL~~L~~~~~-~t~~eLA~~lgis~~tV~~~L~~Le~~ 42 (203)
T TIGR02702 2 TKEDILSYLLKQGQ-ATAAALAEALAISPQAVRRHLKDLETE 42 (203)
T ss_pred HHHHHHHHHHHcCC-CCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 57899999998876 999999999999999999999999876
No 39
>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=75.91 E-value=12 Score=29.35 Aligned_cols=59 Identities=12% Similarity=0.129 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~a-----GL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvF 141 (280)
.|..|++++.+.+.-+|+.||..+. ++++..+=+.|..|+...=-+=-..++|...|..
T Consensus 2 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~ 65 (116)
T cd07153 2 QRLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYEL 65 (116)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEe
Confidence 4788999999998899999999876 6899999999999998754333333346677764
No 40
>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=75.19 E-value=18 Score=25.26 Aligned_cols=38 Identities=21% Similarity=0.391 Sum_probs=32.6
Q ss_pred CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC
Q 023574 96 RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (280)
Q Consensus 96 ~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesG 135 (280)
..+|..|+|...|++...+.+.|..|..+ |-|+....|
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~--g~i~~~~~~ 61 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEE--GLISRRGRG 61 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEecCCC
Confidence 57999999999999999999999999886 677766544
No 41
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=74.99 E-value=5.7 Score=34.94 Aligned_cols=42 Identities=14% Similarity=0.202 Sum_probs=37.0
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
+-+.+|++.+.+ .+.+|+.|+|..-|.|...+++.|..|+.+
T Consensus 7 ~R~~~Il~~l~~-~~~~~~~~La~~~~vS~~TiRRDl~~L~~~ 48 (185)
T PRK04424 7 ERQKALQELIEE-NPFITDEELAEKFGVSIQTIRLDRMELGIP 48 (185)
T ss_pred HHHHHHHHHHHH-CCCEEHHHHHHHHCcCHHHHHHHHHHHhcc
Confidence 566778888888 556999999999999999999999999876
No 42
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=73.86 E-value=7.5 Score=30.13 Aligned_cols=41 Identities=15% Similarity=0.414 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
...+|+.++.+. ++.|..|+|.+.|++...+.+.|..|.++
T Consensus 4 ~D~~il~~L~~~-~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 4 IDRKILEELQKD-ARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred HHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 557889999886 58999999999999999999999999987
No 43
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=73.46 E-value=33 Score=25.11 Aligned_cols=48 Identities=10% Similarity=0.232 Sum_probs=40.4
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses 134 (280)
.-.|+..+...+ ..|+.|+|...+++...+.+.|..|..+ |-++..++
T Consensus 12 ~~~il~~l~~~~-~~~~~~la~~~~~s~~~i~~~l~~L~~~--g~v~~~~~ 59 (101)
T smart00347 12 QFLVLRILYEEG-PLSVSELAKRLGVSPSTVTRVLDRLEKK--GLIRRLPS 59 (101)
T ss_pred HHHHHHHHHHcC-CcCHHHHHHHHCCCchhHHHHHHHHHHC--CCeEecCC
Confidence 567788888766 6999999999999999999999999986 66766554
No 44
>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=72.73 E-value=8.1 Score=26.52 Aligned_cols=41 Identities=20% Similarity=0.323 Sum_probs=34.9
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
..|-+|+.++.+ +..|+.|+|...|++...+.+-|..|-..
T Consensus 2 ~~R~~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL~~L~~~ 42 (47)
T PF01022_consen 2 PTRLRILKLLSE--GPLTVSELAEELGLSQSTVSHHLKKLREA 42 (47)
T ss_dssp HHHHHHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHh--CCCchhhHHHhccccchHHHHHHHHHHHC
Confidence 357889999999 66999999999999999999999888653
No 45
>PHA02943 hypothetical protein; Provisional
Probab=72.34 E-value=26 Score=31.52 Aligned_cols=79 Identities=19% Similarity=0.187 Sum_probs=55.0
Q ss_pred hHHHHHHHHHHH-cCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHhhhhHHHhHHH
Q 023574 82 DVRNRAMDAVDA-CNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEP 160 (280)
Q Consensus 82 ~~~~~im~Ave~-lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fRs~l~~Ks~r~rl~~ 160 (280)
.+.+|+.+.+|- ..+-.|..+||-..|+|-.+|+-.|..|..+ |-++--+-|-..|.+=.+ . .+... ...
T Consensus 8 ~v~~R~~eILE~Lk~G~~TtseIAkaLGlS~~qa~~~LyvLErE--G~VkrV~~G~~tyw~l~~-d-----ay~~~-v~~ 78 (165)
T PHA02943 8 TVHTRMIKTLRLLADGCKTTSRIANKLGVSHSMARNALYQLAKE--GMVLKVEIGRAAIWCLDE-D-----AYTNL-VFE 78 (165)
T ss_pred HHHHHHHHHHHHHhcCCccHHHHHHHHCCCHHHHHHHHHHHHHc--CceEEEeecceEEEEECh-H-----HHHHH-HHH
Confidence 455666666666 5566779999999999999999999998775 455555689888888444 1 12222 556
Q ss_pred HHHHhhhhh
Q 023574 161 VIDKAKAAA 169 (280)
Q Consensus 161 ~~~k~w~v~ 169 (280)
+.+.+|+.+
T Consensus 79 ~~Relwrlv 87 (165)
T PHA02943 79 IKRELWRLV 87 (165)
T ss_pred HHHHHHHHH
Confidence 666666543
No 46
>PRK12423 LexA repressor; Provisional
Probab=71.78 E-value=12 Score=33.09 Aligned_cols=52 Identities=23% Similarity=0.357 Sum_probs=40.4
Q ss_pred hHHHHHHH----HHHHcCCceehhhhhhhcCC-CHHHHHHHHHHHHhhcCCceEeccCC
Q 023574 82 DVRNRAMD----AVDACNRRVTIGDVAGKAGL-KLNEAQKALQALAADTDGFLEVSDEG 135 (280)
Q Consensus 82 ~~~~~im~----Ave~lg~RvTvGDVAa~aGL-~L~~Ae~aL~aLAsD~~GhLqVsesG 135 (280)
..|.++++ .+++.|+.-|+.|+|.+-|+ +...+++.|.+|+.. |.|+++..+
T Consensus 6 ~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~--G~l~~~~~~ 62 (202)
T PRK12423 6 PKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEA--GLIEVVPNQ 62 (202)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC--CCEEecCCC
Confidence 34555555 45556778899999999995 899999999999875 677777664
No 47
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=71.65 E-value=25 Score=31.71 Aligned_cols=82 Identities=24% Similarity=0.236 Sum_probs=61.3
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc--CCceEecc-CCcEEEEcCcchHHHHhhhhHHHhHHHH
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DGFLEVSD-EGDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~--~GhLqVse-sGEIlYvFP~~fRs~l~~Ks~r~rl~~~ 161 (280)
-.+.+++...| -+|=-++|...|+.++++++.|.+|-.+- ..+=+.++ +|...|..=-+++.++ -..+.+....
T Consensus 21 ~~v~~~l~~kg-e~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~~~~~~~y~w~~~~~~v~--~~l~~~~~~~ 97 (176)
T COG1675 21 VLVVDALLEKG-ELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDEESGWEEYTWYINYEKVL--EVLKGKKRKI 97 (176)
T ss_pred hHHHHHHHhcC-CcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCCCcEEEEEEechHHHH--HHHHHHHHHH
Confidence 46788898888 99999999999999999999999998884 44555555 5999998877777765 3344444445
Q ss_pred HHHhhhhh
Q 023574 162 IDKAKAAA 169 (280)
Q Consensus 162 ~~k~w~v~ 169 (280)
++++...+
T Consensus 98 le~Lk~~l 105 (176)
T COG1675 98 LEKLKRKL 105 (176)
T ss_pred HHHHHHHH
Confidence 55544444
No 48
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=70.98 E-value=4.7 Score=27.27 Aligned_cols=38 Identities=18% Similarity=0.359 Sum_probs=31.5
Q ss_pred cCCce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 023574 94 CNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (280)
Q Consensus 94 lg~Rv-TvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse 133 (280)
.|.++ |..|+|..-|++...++++|..|..+ |-|+...
T Consensus 16 ~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~--g~i~~~~ 54 (60)
T smart00345 16 PGDKLPSERELAAQLGVSRTTVREALSRLEAE--GLVQRRP 54 (60)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEec
Confidence 35677 89999999999999999999999986 4565443
No 49
>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=70.23 E-value=16 Score=28.77 Aligned_cols=79 Identities=25% Similarity=0.261 Sum_probs=40.6
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC---CcEEEEcCcchHHHHhhhhHHHhHHHH
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE---GDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses---GEIlYvFP~~fRs~l~~Ks~r~rl~~~ 161 (280)
-.||+++-+.| .+|=.|+|..+|++..++++.|..|..+.=-+.+-..+ |-..|.+=-|++.+. ...+.++...
T Consensus 16 ~~Il~~L~~~~-~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~i~~~~~~--~~ik~r~~~~ 92 (105)
T PF02002_consen 16 VRILDALLRKG-ELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWYIDYDQII--DVIKYRIYKM 92 (105)
T ss_dssp HHHHHHHHHH---B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE-THHHH-------------
T ss_pred HHHHHHHHHcC-CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEEEcHHHHH--HHHHHHHHHH
Confidence 46899998765 58999999999999999999999999986554443332 555566655666543 3344455555
Q ss_pred HHHhh
Q 023574 162 IDKAK 166 (280)
Q Consensus 162 ~~k~w 166 (280)
.+++.
T Consensus 93 ~~~l~ 97 (105)
T PF02002_consen 93 REKLK 97 (105)
T ss_dssp -----
T ss_pred HHHHH
Confidence 54443
No 50
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=68.96 E-value=14 Score=33.24 Aligned_cols=59 Identities=17% Similarity=0.206 Sum_probs=44.7
Q ss_pred hHHHHHHHHHHHcCC-ceehhhhhhhcCCCHHHHHHHHHHHHhhcC---CceEeccCCcEEEEc
Q 023574 82 DVRNRAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKALQALAADTD---GFLEVSDEGDVLYVF 141 (280)
Q Consensus 82 ~~~~~im~Ave~lg~-RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~---GhLqVsesGEIlYvF 141 (280)
.....|.-++=-.|- .+|+.++|...|++.++++++|..|..++. .-+++.+.|+- |.|
T Consensus 4 ~~~~~iEA~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~-y~l 66 (188)
T PRK00135 4 NYKSIIEALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDV-YKL 66 (188)
T ss_pred cHHHHHHHHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCE-EEE
Confidence 334444444445565 499999999999999999999999999974 34888887665 666
No 51
>PF10717 ODV-E18: Occlusion-derived virus envelope protein ODV-E18; InterPro: IPR019655 Baculovirus occlusion-derived virus (ODV) derives its envelope from an intranuclear membrane source. Occlusion-derived viral envelope proteins that are detected in viral-induced intranuclear microvesicles, but not detected in the plasma membrane, cytoplasmic membranes, or the nuclear envelope. This entry represents ODV-E18 protein which is encoded by baculovirus late genes with transcription initiating from a TAAG motif. ODV-E18 exists as a dimer in the ODV envelope, which contains a hydrophobic domain that putatively acts as a target or retention signal for intranuclear microvesicles []. ; GO: 0019031 viral envelope
Probab=67.00 E-value=9.7 Score=30.96 Aligned_cols=26 Identities=19% Similarity=0.171 Sum_probs=12.4
Q ss_pred hHhhHHHHHHHHHHHHHHHHHHHHHH
Q 023574 171 YSIRVLFGTALIASIVIVFTAIIAIL 196 (280)
Q Consensus 171 yliRisFGi~LIaSivLv~~aIiail 196 (280)
|+-++.=.+++.+=|+||.+++++++
T Consensus 18 ~~~~l~pn~lMtILivLVIIiLlIml 43 (85)
T PF10717_consen 18 NLNGLNPNTLMTILIVLVIIILLIML 43 (85)
T ss_pred cccccChhHHHHHHHHHHHHHHHHHH
Confidence 33444444444444455555555555
No 52
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=66.47 E-value=31 Score=31.46 Aligned_cols=43 Identities=16% Similarity=0.262 Sum_probs=36.9
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
.+-+.+|++.+++.| ++|+.|+|..-|.|...+++.|..|...
T Consensus 6 ~eR~~~I~~~l~~~~-~v~v~eLa~~~~VS~~TIRRDL~~Le~~ 48 (252)
T PRK10681 6 DERIGQLLQALKRSD-KLHLKDAAALLGVSEMTIRRDLNAHSAP 48 (252)
T ss_pred HHHHHHHHHHHHHcC-CCcHHHHHHHhCCCHHHHHHHHHHhhcC
Confidence 356677888888855 5999999999999999999999998853
No 53
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=66.44 E-value=6.2 Score=29.15 Aligned_cols=38 Identities=21% Similarity=0.287 Sum_probs=32.0
Q ss_pred HHHHHHHHHHc------CCceehhhhhhhcCCCHHHHHHHHHHH
Q 023574 84 RNRAMDAVDAC------NRRVTIGDVAGKAGLKLNEAQKALQAL 121 (280)
Q Consensus 84 ~~~im~Ave~l------g~RvTvGDVAa~aGL~L~~Ae~aL~aL 121 (280)
.++..+.+++. |+..|+.+++.+.|+++++.-++|.+|
T Consensus 12 ~p~~a~vf~~~gIDfCCgG~~~L~eA~~~~~ld~~~vl~~L~~l 55 (56)
T PF04405_consen 12 DPRAARVFRKYGIDFCCGGNRSLEEACEEKGLDPEEVLEELNAL 55 (56)
T ss_pred ChHHHHHHHHcCCcccCCCCchHHHHHHHcCCCHHHHHHHHHHc
Confidence 45666777774 678999999999999999999999875
No 54
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=66.16 E-value=12 Score=34.25 Aligned_cols=57 Identities=12% Similarity=0.267 Sum_probs=46.1
Q ss_pred CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh------cCCceEeccCCcE
Q 023574 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD------TDGFLEVSDEGDV 137 (280)
Q Consensus 80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD------~~GhLqVsesGEI 137 (280)
+.+-+.+|++.|++ .+.+++.|+|..-|.|...+++.|..|+.. +||-.-.+...+.
T Consensus 3 ~~eR~~~Il~~l~~-~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~hGGa~~~~~~~~~ 65 (253)
T COG1349 3 KEERHQKILELLKE-KGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVHGGAVLPDSESEY 65 (253)
T ss_pred hHHHHHHHHHHHHH-cCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEeCCEecCCCcccc
Confidence 44567788998888 568999999999999999999999999987 4666655555444
No 55
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=65.74 E-value=13 Score=34.57 Aligned_cols=50 Identities=16% Similarity=0.281 Sum_probs=44.1
Q ss_pred ccCCCCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574 75 ESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (280)
Q Consensus 75 ~~~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~ 125 (280)
++.+.++..+.+|+..+.+.|+ +|++|+|.+-|++...|++-|..|.++.
T Consensus 4 ~~~~~~~~tr~~il~lL~~~g~-~sa~elA~~Lgis~~avR~HL~~Le~~G 53 (218)
T COG2345 4 MLADPSGSTRERILELLKKSGP-VSADELAEELGISPMAVRRHLDDLEAEG 53 (218)
T ss_pred cccCCCccHHHHHHHHHhccCC-ccHHHHHHHhCCCHHHHHHHHHHHHhCc
Confidence 4567788899999988887765 7999999999999999999999999875
No 56
>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=64.55 E-value=7.4 Score=28.06 Aligned_cols=40 Identities=20% Similarity=0.319 Sum_probs=30.6
Q ss_pred HHHHHHHHH----cCCce-ehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 85 NRAMDAVDA----CNRRV-TIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 85 ~~im~Ave~----lg~Rv-TvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
..|.+.+.. .|.++ |..++|..-|++...++++|..|+++
T Consensus 7 ~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~ 51 (64)
T PF00392_consen 7 DQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAE 51 (64)
T ss_dssp HHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHC
Confidence 344444444 56778 99999999999999999999999986
No 57
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=63.64 E-value=14 Score=33.85 Aligned_cols=43 Identities=16% Similarity=0.233 Sum_probs=37.8
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
.+-+.+|++.+++ .+.+|+.|+|..-|++...+++.|..|.+.
T Consensus 4 ~~R~~~Il~~l~~-~~~~~~~ela~~l~vS~~TirRdL~~Le~~ 46 (251)
T PRK13509 4 AQRHQILLELLAQ-LGFVTVEKVIERLGISPATARRDINKLDES 46 (251)
T ss_pred HHHHHHHHHHHHH-cCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3566788888886 688999999999999999999999999764
No 58
>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=62.66 E-value=11 Score=33.67 Aligned_cols=44 Identities=30% Similarity=0.416 Sum_probs=36.5
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023574 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (280)
Q Consensus 86 ~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqV 131 (280)
+|++++.+.+..+|+.|+|...|++...+-+=|..|.+. |.|+=
T Consensus 13 ~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~--G~l~~ 56 (248)
T TIGR02431 13 AVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVEL--GYVTS 56 (248)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEe
Confidence 467777777788999999999999999999999998765 45653
No 59
>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=62.49 E-value=14 Score=33.11 Aligned_cols=43 Identities=23% Similarity=0.386 Sum_probs=36.5
Q ss_pred hHHHHHHHHH-HHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 82 DVRNRAMDAV-DACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 82 ~~~~~im~Av-e~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
....+|++.+ +..++.+|+.+++...|.+..-|+..|..+..+
T Consensus 174 ~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~ 217 (223)
T PF04157_consen 174 KDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELERE 217 (223)
T ss_dssp HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhC
Confidence 6678889998 888999999999999999999999999886544
No 60
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=61.79 E-value=17 Score=33.36 Aligned_cols=99 Identities=13% Similarity=0.119 Sum_probs=59.3
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh------cCCceEeccCCcEEEEcCcchHHHHhhhhHH
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD------TDGFLEVSDEGDVLYVFPNNYRAKLAAKSFR 155 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD------~~GhLqVsesGEIlYvFP~~fRs~l~~Ks~r 155 (280)
+-+.+|++.+++. +.+|+.|+|..-++|...+++.|..|..+ +||-......-+ . |-..|.. .+..-|
T Consensus 5 ~R~~~Il~~l~~~-~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~~GGa~~~~~~~~--~--~~~~r~~-~~~~~K 78 (252)
T PRK10906 5 QRHDAIIELVKQQ-GYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRHHGGAALPSSSVN--T--PWHDRKA-TQTEEK 78 (252)
T ss_pred HHHHHHHHHHHHc-CCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCEEecCCCCC--C--CHHHHhh-hcHHHH
Confidence 5677889999665 47999999999999999999999999985 244432211111 1 2122332 222233
Q ss_pred Hh-HHHHHHHhhhhhhhHhhHHHHHHHHHHHH
Q 023574 156 LK-VEPVIDKAKAAAEYSIRVLFGTALIASIV 186 (280)
Q Consensus 156 ~r-l~~~~~k~w~v~~yliRisFGi~LIaSiv 186 (280)
.+ .+...+.+...-..++=.+--+..++..+
T Consensus 79 ~~IA~~Aa~~I~~g~tIflD~GtT~~~la~~L 110 (252)
T PRK10906 79 ERIARKVASQIPNGATLFIDIGTTPEAVAHAL 110 (252)
T ss_pred HHHHHHHHhhCCCCCEEEEcCcHHHHHHHHHh
Confidence 33 44444555544445555555555555544
No 61
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=61.70 E-value=58 Score=27.60 Aligned_cols=78 Identities=22% Similarity=0.178 Sum_probs=52.6
Q ss_pred HHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcC--C--ceEecc-CC-cEEEEcCcchHHHHhhhhHHHhHHH
Q 023574 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTD--G--FLEVSD-EG-DVLYVFPNNYRAKLAAKSFRLKVEP 160 (280)
Q Consensus 87 im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~--G--hLqVse-sG-EIlYvFP~~fRs~l~~Ks~r~rl~~ 160 (280)
|++++-+.| -+|-.|+|...|++++++++.|..|-.|-- . .-+-++ +| -..|.|==|++.+. -..+.++..
T Consensus 6 v~d~L~~~~-~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~--~vik~r~~~ 82 (147)
T smart00531 6 VLDALMRNG-CVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLL--DVVKYKLDK 82 (147)
T ss_pred ehHHHHhcC-CcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHH--HHHHHHHHH
Confidence 577777765 799999999999999999999999998632 2 222333 35 47777655666654 334445555
Q ss_pred HHHHhhh
Q 023574 161 VIDKAKA 167 (280)
Q Consensus 161 ~~~k~w~ 167 (280)
..+++..
T Consensus 83 ~~~~L~~ 89 (147)
T smart00531 83 MRKRLED 89 (147)
T ss_pred HHHHHHH
Confidence 5555443
No 62
>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=60.99 E-value=38 Score=27.14 Aligned_cols=80 Identities=16% Similarity=0.214 Sum_probs=55.1
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhcC----CCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHhhhhHHHh
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKAG----LKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLK 157 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~aG----L~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fRs~l~~Ks~r~r 157 (280)
+....||+.+=+.|. +|+.||...-. ++.+.++.-|..|.. -|.|++...|---+..|.-=+. .+.+..
T Consensus 3 ~~E~~IM~~lW~~~~-~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~--Kg~l~~~~~gr~~~Y~p~is~~----e~~~~~ 75 (115)
T PF03965_consen 3 DLELEIMEILWESGE-ATVREIHEALPEERSWAYSTVQTLLNRLVE--KGFLTREKIGRAYVYSPLISRE----EYLAQE 75 (115)
T ss_dssp HHHHHHHHHHHHHSS-EEHHHHHHHHCTTSS--HHHHHHHHHHHHH--TTSEEEEEETTCEEEEESSSHH----HHHHHH
T ss_pred HHHHHHHHHHHhCCC-CCHHHHHHHHHhccccchhHHHHHHHHHHh--CCceeEeecCCceEEEeCCcHH----HHHHHH
Confidence 456789999999999 99999987544 567777777777776 6899999988754444433333 445555
Q ss_pred HHHHHHHhhhh
Q 023574 158 VEPVIDKAKAA 168 (280)
Q Consensus 158 l~~~~~k~w~v 168 (280)
++.+.+++..+
T Consensus 76 ~~~~l~~~~~g 86 (115)
T PF03965_consen 76 LRQFLDRLFDG 86 (115)
T ss_dssp HHHHHHHHSTT
T ss_pred HHHHHHHHhCC
Confidence 66666665443
No 63
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=60.91 E-value=14 Score=28.81 Aligned_cols=57 Identities=19% Similarity=0.207 Sum_probs=45.0
Q ss_pred hHHHHHHHHHHHcC--CceehhhhhhhcC--CCHHHHHHHHHH--HHhhcCCceEeccCCcEE
Q 023574 82 DVRNRAMDAVDACN--RRVTIGDVAGKAG--LKLNEAQKALQA--LAADTDGFLEVSDEGDVL 138 (280)
Q Consensus 82 ~~~~~im~Ave~lg--~RvTvGDVAa~aG--L~L~~Ae~aL~a--LAsD~~GhLqVsesGEIl 138 (280)
+.+.++.+++.+.. .-+|-||||...| -....+-.+|.. +.....+|==|+.+|.+-
T Consensus 2 ~f~~~V~~~v~~IP~G~v~TYg~iA~~~g~p~~ar~Vg~al~~np~~~~iP~HRVv~~~G~l~ 64 (85)
T PF01035_consen 2 PFQRRVWEAVRQIPYGKVTTYGEIARLLGRPKAARAVGSALARNPIPIIIPCHRVVNSDGSLG 64 (85)
T ss_dssp HHHHHHHHHHTTS-TT-BEEHHHHHHHTT-TTCHHHHHHHHHTSSCTTTSGGGGEEBTTSBEC
T ss_pred hHHHHHHHHHHcCCCCceEeHHHHHHHHhhcccHHHHHHHhccccccCCCCeEEEECCCCCcC
Confidence 46778888888864 6688999999999 667777777766 556679999999999983
No 64
>PRK11569 transcriptional repressor IclR; Provisional
Probab=60.29 E-value=14 Score=33.87 Aligned_cols=47 Identities=19% Similarity=0.383 Sum_probs=39.1
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse 133 (280)
-+|++++.+.+..+|+.|+|...|++...+-+=|..|... |-|+-++
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~--G~l~~~~ 77 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQ--GFVRQVG 77 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEcC
Confidence 4578888888888999999999999999999998888764 6676544
No 65
>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=60.16 E-value=7.8 Score=27.46 Aligned_cols=21 Identities=33% Similarity=0.528 Sum_probs=18.7
Q ss_pred ehhhhhhhcCCCHHHHHHHHH
Q 023574 99 TIGDVAGKAGLKLNEAQKALQ 119 (280)
Q Consensus 99 TvGDVAa~aGL~L~~Ae~aL~ 119 (280)
|+.|||..+|++...+-++|.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 789999999999999987773
No 66
>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=60.03 E-value=11 Score=29.52 Aligned_cols=57 Identities=14% Similarity=0.123 Sum_probs=42.4
Q ss_pred hHHHHHHHHHHHc--CCceehhhhhhhcCCCH--HHHHHHHHHH--HhhcCCceEeccCCcEE
Q 023574 82 DVRNRAMDAVDAC--NRRVTIGDVAGKAGLKL--NEAQKALQAL--AADTDGFLEVSDEGDVL 138 (280)
Q Consensus 82 ~~~~~im~Ave~l--g~RvTvGDVAa~aGL~L--~~Ae~aL~aL--AsD~~GhLqVsesGEIl 138 (280)
+.+.++.+++++. |..+|-||||...|.+- ..+-.+|... .-...+|==|+.+|+|-
T Consensus 2 ~f~~~V~~~l~~IP~G~v~TYg~iA~~~g~p~~~RaVg~al~~np~~~~iPcHRVv~s~G~l~ 64 (80)
T TIGR00589 2 PFQQRVWQALRTIPYGETKSYGQLAARIGNPKAVRAVGGANGRNPLAILVPCHRVIGKNGSLT 64 (80)
T ss_pred hHHHHHHHHHhCCCCCCcCCHHHHHHHhCCCChHHHHHHHHHhCCCCCCCCCceeECCCCCCC
Confidence 4678899999987 77788999999999643 4444444332 33478999999999984
No 67
>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=59.58 E-value=7.9 Score=27.42 Aligned_cols=22 Identities=18% Similarity=0.412 Sum_probs=19.4
Q ss_pred CCCCchHHHHHHHHHHHcCCce
Q 023574 77 DKLPADVRNRAMDAVDACNRRV 98 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~Rv 98 (280)
+++..+.+++|+++++++||+.
T Consensus 24 ~~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 24 PRVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp SSSTHHHHHHHHHHHHHHTB-S
T ss_pred CCCCHHHHHHHHHHHHHHCCCC
Confidence 6889999999999999999973
No 68
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=58.57 E-value=16 Score=33.54 Aligned_cols=48 Identities=15% Similarity=0.248 Sum_probs=40.1
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses 134 (280)
-+|++++.+.+...|+.|+|...|++...+-+=|..|.+. |.|+-+++
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~--G~l~~~~~ 75 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAA--DFVYQDSQ 75 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEcCC
Confidence 4678888888888999999999999999999988888765 66765554
No 69
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=58.20 E-value=93 Score=28.37 Aligned_cols=47 Identities=13% Similarity=0.157 Sum_probs=39.6
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqV 131 (280)
+-+.+|++.+++.+ .+|+.|+|..-|++...+++.|..|... |.|+-
T Consensus 4 ~R~~~Il~~l~~~~-~~~~~eLa~~l~VS~~TiRRdL~~L~~~--~~l~r 50 (240)
T PRK10411 4 ARQQAIVDLLLNHT-SLTTEALAEQLNVSKETIRRDLNELQTQ--GKILR 50 (240)
T ss_pred HHHHHHHHHHHHcC-CCcHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEE
Confidence 44677899998755 8999999999999999999999999873 56654
No 70
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=58.00 E-value=29 Score=32.03 Aligned_cols=61 Identities=28% Similarity=0.398 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC-CcE-EEEcCcch
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-GDV-LYVFPNNY 145 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses-GEI-lYvFP~~f 145 (280)
...-+.+.+...| -+|+.|+|--+|++..+++++|..|.++ +.=.+|+-+ |.- .|.-|.+-
T Consensus 168 ~~~Lv~Ryl~~~G-Pat~~d~a~w~gl~~~~~r~~l~~l~~~-~~L~~v~~~~G~~~~~~~~~~~ 230 (327)
T PF06224_consen 168 LAELVRRYLRAYG-PATLADFAWWSGLPKTQARRALAQLVEE-GELVEVEVEGGKEPLYDLPEDL 230 (327)
T ss_pred HHHHHHHHHHHcC-CccHHHHHHHhccCHHHHHHHHHhhccC-CcEEEEEEcCcceeEEechhhh
Confidence 3444556666666 7999999999999999999998877652 333556655 776 88888765
No 71
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=57.99 E-value=13 Score=24.28 Aligned_cols=35 Identities=20% Similarity=0.342 Sum_probs=29.2
Q ss_pred CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEec
Q 023574 96 RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (280)
Q Consensus 96 ~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVs 132 (280)
..+|+.|+|...|++...+.+.|..|.++ |-|+..
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~~--g~l~~~ 41 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEKE--GLISRE 41 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEe
Confidence 46789999999999999999999999884 455543
No 72
>PF03640 Lipoprotein_15: Secreted repeat of unknown function; InterPro: IPR005297 This repeat is found in tandem in a set of lipoproteins. The alignment contains a Y-X4-D motif.
Probab=57.34 E-value=9.7 Score=27.25 Aligned_cols=22 Identities=32% Similarity=0.543 Sum_probs=18.9
Q ss_pred hcCCceEeccCCcEEEEcCcch
Q 023574 124 DTDGFLEVSDEGDVLYVFPNNY 145 (280)
Q Consensus 124 D~~GhLqVsesGEIlYvFP~~f 145 (280)
...|..+|+.+|-.||.|.+|=
T Consensus 6 ~~dG~~~~~~~G~~LY~f~~D~ 27 (48)
T PF03640_consen 6 RADGTIQVDYNGMPLYYFDKDS 27 (48)
T ss_pred eCCCCEEECCCCCEEEEECCCC
Confidence 3469999999999999997764
No 73
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=56.32 E-value=18 Score=32.86 Aligned_cols=46 Identities=22% Similarity=0.398 Sum_probs=37.2
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 023574 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (280)
Q Consensus 86 ~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse 133 (280)
+|++++...+..+|+.|+|.+.|++...+-+-|..|... |-|+-++
T Consensus 15 ~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~--g~v~~~~ 60 (263)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEE--GYVRRSA 60 (263)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEec
Confidence 456677666777999999999999999999999998764 5665543
No 74
>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=56.01 E-value=24 Score=24.87 Aligned_cols=50 Identities=14% Similarity=0.159 Sum_probs=35.3
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse 133 (280)
+-.+|..+...+...|+.|||...|++...+-+.|..|....==.-+.++
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~ 54 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDP 54 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEES
T ss_pred HHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCC
Confidence 34577888888899999999999999999999999999887333333333
No 75
>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=55.56 E-value=32 Score=23.82 Aligned_cols=41 Identities=15% Similarity=0.242 Sum_probs=34.6
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~ 125 (280)
+=.+|..+.+.++ .|+.|+|...+++...+-+.+..|..+.
T Consensus 5 q~~iL~~l~~~~~-~~~~~la~~~~~~~~~~t~~i~~L~~~g 45 (59)
T PF01047_consen 5 QFRILRILYENGG-ITQSELAEKLGISRSTVTRIIKRLEKKG 45 (59)
T ss_dssp HHHHHHHHHHHSS-EEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHcCC-CCHHHHHHHHCCChhHHHHHHHHHHHCC
Confidence 4467888998888 9999999999999999989888887763
No 76
>PF09105 SelB-wing_1: Elongation factor SelB, winged helix ; InterPro: IPR015189 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 1". 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 []. ; PDB: 2V9V_A 1LVA_A 2PLY_A.
Probab=55.44 E-value=34 Score=25.77 Aligned_cols=45 Identities=24% Similarity=0.281 Sum_probs=33.5
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCce
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFL 129 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhL 129 (280)
+-+-+.+........-.+.|.++.|++++.++-|+..|+...-.|
T Consensus 5 kilaqiiqehregldwqeaatraslsleetrkllqsmaaagqvtl 49 (61)
T PF09105_consen 5 KILAQIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQVTL 49 (61)
T ss_dssp HHHHHHHHC-TT-EEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHccCcHHHHHHHhhccHHHHHHHHHHHHhcCceEE
Confidence 444667778888888999999999999999999999998765443
No 77
>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=54.86 E-value=25 Score=30.43 Aligned_cols=43 Identities=23% Similarity=0.365 Sum_probs=36.4
Q ss_pred hHHHHHHHHHHH----cCCceehhhhhhhcCCC-HHHHHHHHHHHHhh
Q 023574 82 DVRNRAMDAVDA----CNRRVTIGDVAGKAGLK-LNEAQKALQALAAD 124 (280)
Q Consensus 82 ~~~~~im~Ave~----lg~RvTvGDVAa~aGL~-L~~Ae~aL~aLAsD 124 (280)
+.+.+|++.+.+ .+...|+.|+|...|++ ...+.+.|..|..+
T Consensus 6 ~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~ 53 (199)
T TIGR00498 6 ARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERK 53 (199)
T ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 456677777763 57779999999999998 99999999999987
No 78
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=54.51 E-value=34 Score=27.57 Aligned_cols=65 Identities=23% Similarity=0.364 Sum_probs=43.3
Q ss_pred chHHHHHHHHHHHcCCceeh--hhhhhhcCCC-----HHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHH
Q 023574 81 ADVRNRAMDAVDACNRRVTI--GDVAGKAGLK-----LNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKL 149 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTv--GDVAa~aGL~-----L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fRs~l 149 (280)
..+...|++.+.+.+..-|+ .|||-.-+-+ +++++++-..|+. .|.++++..|++| =|.+||...
T Consensus 6 ~~l~~~Il~ll~~R~~~ktiCPSevARal~~~~WR~lm~~vR~~A~~L~~--~G~i~I~qkG~~V--dp~~~rGpi 77 (83)
T PF11625_consen 6 ARLEAAILALLAARGPGKTICPSEVARALGPDDWRDLMPPVRAAARRLAR--AGRIEITQKGKPV--DPETFRGPI 77 (83)
T ss_dssp HHHHHHHHHHHHHS-TT--B-HHHHHHHH-TTS-GGGHHHHHHHHHHHHH--TTSEEEEETTEE----TTT--S--
T ss_pred HHHHHHHHHHHHhcCCCCccCHHHHHHHHCchhhHHHHHHHHHHHHHHHH--CCcEEEEECCEec--CcccCcCCe
Confidence 45678889999999888887 7999877644 5666666666665 5899999999987 677777654
No 79
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=53.21 E-value=22 Score=32.47 Aligned_cols=48 Identities=21% Similarity=0.353 Sum_probs=38.8
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses 134 (280)
-+|++++.+.+..+|+.|+|.++|++...+-+-|..|... |-++-+++
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~--G~v~~d~~ 54 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVEL--GYVEQDPE 54 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHC--CCEEEcCC
Confidence 3578888886666899999999999999999999888764 55655553
No 80
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=53.08 E-value=28 Score=30.70 Aligned_cols=40 Identities=18% Similarity=0.258 Sum_probs=36.2
Q ss_pred hHHHHHHHHHHHcC-CceehhhhhhhcCCCHHHHHHHHHHH
Q 023574 82 DVRNRAMDAVDACN-RRVTIGDVAGKAGLKLNEAQKALQAL 121 (280)
Q Consensus 82 ~~~~~im~Ave~lg-~RvTvGDVAa~aGL~L~~Ae~aL~aL 121 (280)
....+|++.+.+.| .++++.|+|..+|++-.++++.|..|
T Consensus 16 ~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l 56 (213)
T PRK05472 16 PLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYF 56 (213)
T ss_pred HHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHH
Confidence 44678899999987 79999999999999999999999999
No 81
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=52.78 E-value=46 Score=31.29 Aligned_cols=59 Identities=15% Similarity=0.195 Sum_probs=45.2
Q ss_pred CCCchHHHHHHHHHHHcCCceehhhhhhhcC--------------CCHHHHHHHHHHHHhhcCCceEeccCCc
Q 023574 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAG--------------LKLNEAQKALQALAADTDGFLEVSDEGD 136 (280)
Q Consensus 78 ~l~~~~~~~im~Ave~lg~RvTvGDVAa~aG--------------L~L~~Ae~aL~aLAsD~~GhLqVsesGE 136 (280)
++..+.++||++++|++||+....--+.+++ .--.+.-+++...+.+.|=++-+....+
T Consensus 26 ~Vs~eTr~kV~~a~~elgY~pN~~Ar~L~~~~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~ 98 (333)
T COG1609 26 YVSEETREKVLAAIKELGYRPNAVARSLRTGRTKTIGLVVPDITNPFFAEILKGIEEAAREAGYSLLLANTDD 98 (333)
T ss_pred CCCHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEECCCC
Confidence 7899999999999999999977665555554 2345666778888888888877766554
No 82
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=52.77 E-value=1.5e+02 Score=25.50 Aligned_cols=35 Identities=14% Similarity=0.287 Sum_probs=20.7
Q ss_pred CCCchHHHHHHHHHHHc-----CCceehhhhhhhcCCCHH
Q 023574 78 KLPADVRNRAMDAVDAC-----NRRVTIGDVAGKAGLKLN 112 (280)
Q Consensus 78 ~l~~~~~~~im~Ave~l-----g~RvTvGDVAa~aGL~L~ 112 (280)
+||.+.++.+++..++. -..-|-.||.++=|=|.+
T Consensus 16 ~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~ 55 (181)
T PF08006_consen 16 KLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKE 55 (181)
T ss_pred cCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHH
Confidence 68888888888766543 122344555555553333
No 83
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=52.59 E-value=37 Score=24.91 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=28.7
Q ss_pred HcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 93 ~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
+.+..++..|||..-|++...|-+.|..|+.+
T Consensus 18 ~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~ 49 (60)
T PF01325_consen 18 EEGGPVRTKDIAERLGVSPPTVTEMLKRLAEK 49 (60)
T ss_dssp HCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCccHHHHHHHHCCChHHHHHHHHHHHHC
Confidence 47899999999999999999999999999875
No 84
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=52.48 E-value=69 Score=33.14 Aligned_cols=71 Identities=11% Similarity=0.129 Sum_probs=60.8
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHhhhh
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKS 153 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fRs~l~~Ks 153 (280)
+....+|++++++.+...+..++|...|++.+++.+++..|+++ |-++|.+.=...|+-...=+..+++-+
T Consensus 5 ~~~e~~iL~~l~~~~~~~~~~~la~~~~~~~~~v~~~~~~L~~k--g~v~~~~~~~~~~~LT~eG~~~~~~G~ 75 (494)
T PTZ00326 5 ELEENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESA--NYITTEMKKSNTWTLTEEGEDYLKNGS 75 (494)
T ss_pred hHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhC--CCEEEEEEEEEEEEECHHHHHHHHcCC
Confidence 56778999999996666999999999999999999999999997 688998888888998777777776633
No 85
>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=52.22 E-value=30 Score=26.47 Aligned_cols=52 Identities=21% Similarity=0.337 Sum_probs=42.9
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEE
Q 023574 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (280)
Q Consensus 86 ~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYv 140 (280)
.|-+++.. .+..|+.+++..+|++-.++..||==||.+ +.+++.++++.+|+
T Consensus 12 ~Vw~~L~~-~~~~s~~el~k~~~l~~~~~~~AiGWLarE--~KI~~~~~~~~~~v 63 (65)
T PF10771_consen 12 KVWQLLNE-NGEWSVSELKKATGLSDKEVYLAIGWLARE--NKIEFEEKNGELYV 63 (65)
T ss_dssp HHHHHHCC-SSSEEHHHHHHHCT-SCHHHHHHHHHHHCT--TSEEEEEETTEEEE
T ss_pred HHHHHHhh-CCCcCHHHHHHHhCcCHHHHHHHHHHHhcc--CceeEEeeCCEEEE
Confidence 45677777 678999999999999999999999888875 67888888777776
No 86
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=51.94 E-value=22 Score=29.48 Aligned_cols=43 Identities=21% Similarity=0.190 Sum_probs=35.2
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
+++..|+.+...-|..+++.++|.+.|+|..-++++|..|..+
T Consensus 10 Al~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 10 GLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 4555566665556678899999999999999999999999875
No 87
>PRK09480 slmA division inhibitor protein; Provisional
Probab=51.45 E-value=17 Score=30.11 Aligned_cols=32 Identities=19% Similarity=0.415 Sum_probs=24.0
Q ss_pred chHHHHHHHHH----H-HcCCceehhhhhhhcCCCHH
Q 023574 81 ADVRNRAMDAV----D-ACNRRVTIGDVAGKAGLKLN 112 (280)
Q Consensus 81 ~~~~~~im~Av----e-~lg~RvTvGDVAa~aGL~L~ 112 (280)
.+.+++|++|. . +.|..+|+.|||.++|++..
T Consensus 9 ~~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~g 45 (194)
T PRK09480 9 GERREQILQALAQMLESPPGERITTAKLAARVGVSEA 45 (194)
T ss_pred hhHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHh
Confidence 45667777773 2 33689999999999998753
No 88
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=51.38 E-value=12 Score=33.64 Aligned_cols=25 Identities=32% Similarity=0.468 Sum_probs=22.4
Q ss_pred CCceehhhhhhhcCCCHHHHHHHHH
Q 023574 95 NRRVTIGDVAGKAGLKLNEAQKALQ 119 (280)
Q Consensus 95 g~RvTvGDVAa~aGL~L~~Ae~aL~ 119 (280)
..++|+.|||..+|+|...+-++|.
T Consensus 4 ~~~~Ti~dIA~~agVS~~TVSr~Ln 28 (342)
T PRK10014 4 AKKITIHDVALAAGVSVSTVSLVLS 28 (342)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHHHC
Confidence 4579999999999999999988884
No 89
>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=50.90 E-value=29 Score=26.45 Aligned_cols=55 Identities=20% Similarity=0.175 Sum_probs=42.8
Q ss_pred HHHHHHHHHH--cCCceehhhhhhhcCC--CHHHHHHHHHHHHh--hcCCceEeccCCcEE
Q 023574 84 RNRAMDAVDA--CNRRVTIGDVAGKAGL--KLNEAQKALQALAA--DTDGFLEVSDEGDVL 138 (280)
Q Consensus 84 ~~~im~Ave~--lg~RvTvGDVAa~aGL--~L~~Ae~aL~aLAs--D~~GhLqVsesGEIl 138 (280)
+.++.+++++ .|.-+|-||||...|. ....+-.+|.+.-. +..+|==|+.+|.+.
T Consensus 2 ~~~V~~~v~~IP~G~v~TYg~iA~~~g~p~~~R~Vg~al~~np~~~~vP~HRVv~~~g~~~ 62 (79)
T cd06445 2 QRRVWEALRQIPYGEVTTYGQIAKLAGTPKAARAVGSALARNPIPILIPCHRVVRSDGGLG 62 (79)
T ss_pred HHHHHHHHhcCCCCCcCcHHHHHHHHCCCCcHHHHHHHHHhCCCCCCCCceeEECCCCCcC
Confidence 3566777776 5677899999999999 57777777766544 579998899988876
No 90
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=50.51 E-value=14 Score=34.53 Aligned_cols=32 Identities=31% Similarity=0.606 Sum_probs=30.1
Q ss_pred cCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574 94 CNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (280)
Q Consensus 94 lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~ 125 (280)
+|+.+|+.+.|.+.|+.+++-++.|.+|....
T Consensus 31 CGG~~~L~~Aa~~k~l~~~~i~a~L~~l~~~~ 62 (221)
T COG2846 31 CGGKVTLERAAAEKGLDIDEIEARLNALQQEP 62 (221)
T ss_pred cCChHHHHHHHHHcCCCHHHHHHHHHHHHhcc
Confidence 79999999999999999999999999998764
No 91
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=50.48 E-value=78 Score=32.83 Aligned_cols=69 Identities=16% Similarity=0.199 Sum_probs=59.5
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHhhh
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAK 152 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fRs~l~~K 152 (280)
+...+|+++++..+...+..++|...|++.+++.+++..|+++ |-++|.+.=+..|+-...=+..+++-
T Consensus 3 ~~e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k--g~v~~~~~~~~~~~LT~eG~~~l~~G 71 (492)
T PLN02853 3 MAEEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGF--RYVDAQDIKRETWVLTEEGKKYAAEG 71 (492)
T ss_pred hHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhC--CCEEEEEEEEEEEEECHHHHHHHHcC
Confidence 5678999999998767899999999999999999999999998 68888888888888877767766653
No 92
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=50.47 E-value=37 Score=28.56 Aligned_cols=42 Identities=10% Similarity=0.180 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~ 125 (280)
...+|++++.+. +|.+..++|.+.|++...+++-+..|-++.
T Consensus 10 ~D~~Il~~Lq~d-~R~s~~eiA~~lglS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 10 LDRGILEALMEN-ARTPYAELAKQFGVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 667788888765 899999999999999999999999998773
No 93
>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=50.38 E-value=25 Score=29.54 Aligned_cols=43 Identities=23% Similarity=0.545 Sum_probs=33.5
Q ss_pred HHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh--cCCceEeccC
Q 023574 88 MDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD--TDGFLEVSDE 134 (280)
Q Consensus 88 m~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD--~~GhLqVses 134 (280)
-+.++-|....+|+|||+..+|++..+ +.|++| ..|+++|...
T Consensus 46 ~~Il~lC~~~~SVAEiAA~L~lPlgVv----rVLvsDL~~~G~v~v~~p 90 (114)
T PF05331_consen 46 RAILELCRRPLSVAEIAARLGLPLGVV----RVLVSDLADAGLVRVRAP 90 (114)
T ss_pred HHHHHHHCCCccHHHHHHhhCCCchhh----hhhHHHHHhCCCEEEeCC
Confidence 344455555999999999999999988 456666 4899999775
No 94
>PF10717 ODV-E18: Occlusion-derived virus envelope protein ODV-E18; InterPro: IPR019655 Baculovirus occlusion-derived virus (ODV) derives its envelope from an intranuclear membrane source. Occlusion-derived viral envelope proteins that are detected in viral-induced intranuclear microvesicles, but not detected in the plasma membrane, cytoplasmic membranes, or the nuclear envelope. This entry represents ODV-E18 protein which is encoded by baculovirus late genes with transcription initiating from a TAAG motif. ODV-E18 exists as a dimer in the ODV envelope, which contains a hydrophobic domain that putatively acts as a target or retention signal for intranuclear microvesicles []. ; GO: 0019031 viral envelope
Probab=50.20 E-value=23 Score=28.81 Aligned_cols=28 Identities=21% Similarity=0.331 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCC
Q 023574 177 FGTALIASIVIVFTAIIAILSSKSDDDD 204 (280)
Q Consensus 177 FGi~LIaSivLv~~aIiailss~s~~D~ 204 (280)
++++||+=++|+.+.+.+..||.+++++
T Consensus 27 lMtILivLVIIiLlImlfqsSS~~~~s~ 54 (85)
T PF10717_consen 27 LMTILIVLVIIILLIMLFQSSSNGNSSS 54 (85)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCCCCC
Confidence 6889999999999999999988765554
No 95
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=49.71 E-value=55 Score=28.03 Aligned_cols=57 Identities=19% Similarity=0.271 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhc--CCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKA--GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~a--GL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvF 141 (280)
....|.+.+++.+.-.++.||..-- +++...++++|..|+.+ |.|.+-.-|--.+.|
T Consensus 2 Ae~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~--g~i~~K~~GKqkiY~ 60 (169)
T PF07106_consen 2 AEDAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEE--GKIVEKEYGKQKIYF 60 (169)
T ss_pred hHHHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhC--CCeeeeeecceEEEe
Confidence 3567899999999999999998844 69999999999999987 777777777655444
No 96
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=49.64 E-value=31 Score=28.95 Aligned_cols=58 Identities=26% Similarity=0.365 Sum_probs=46.0
Q ss_pred chHHHHHHHHHHHc--CCceehhhhhhhcCCC--HHHHHHHHHHHHhh--cCCceEeccCCcEE
Q 023574 81 ADVRNRAMDAVDAC--NRRVTIGDVAGKAGLK--LNEAQKALQALAAD--TDGFLEVSDEGDVL 138 (280)
Q Consensus 81 ~~~~~~im~Ave~l--g~RvTvGDVAa~aGL~--L~~Ae~aL~aLAsD--~~GhLqVsesGEIl 138 (280)
.+..+++.+.|.+. |+-.|-||||.-+|++ .-++-+.|..|-.+ ..-|=-|+..|.|-
T Consensus 5 def~~~v~~vv~~IP~GkV~TYGdIA~laG~p~~ARqVG~il~~l~~~s~lPWhRVvns~G~is 68 (103)
T COG3695 5 DEFTQRVLDVVAAIPEGKVSTYGDIAKLAGLPRAARQVGRILKHLPEGSDLPWHRVVNSDGRIS 68 (103)
T ss_pred hHHHHHHHHHHHhCCCCceeeHHHHHHHhCCChhHHHHHHHHhhCCCCCCCChhheecCCCccc
Confidence 35677888888774 7789999999999999 77887778766555 47888888888883
No 97
>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=49.47 E-value=30 Score=25.46 Aligned_cols=36 Identities=17% Similarity=0.234 Sum_probs=27.0
Q ss_pred HHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 89 DAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 89 ~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
+..-+.++++|+.|+|..-+++.+.++.-|..|...
T Consensus 6 ~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~k 41 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRK 41 (69)
T ss_dssp HHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCC
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 344456789999999999999999998888777654
No 98
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=49.11 E-value=23 Score=34.34 Aligned_cols=53 Identities=17% Similarity=0.251 Sum_probs=40.5
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvF 141 (280)
+..|++++.+.+..+|+.|++..||+..+|+-.+|..| +.|.+-..+-+|++=
T Consensus 210 ~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l-----~~l~~~~g~~~i~~~ 262 (290)
T PLN03238 210 TRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL-----NLIKYWKGQHVIHVD 262 (290)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC-----CcEEEECCcEEEEeC
Confidence 46788888888899999999999999999997777654 555554444444443
No 99
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=48.89 E-value=33 Score=25.99 Aligned_cols=48 Identities=19% Similarity=0.311 Sum_probs=31.2
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc-----CCceEeccCC
Q 023574 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT-----DGFLEVSDEG 135 (280)
Q Consensus 86 ~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~-----~GhLqVsesG 135 (280)
.|++.+. .+..+..+++..++|+-..+++-|..|.... ++...+|+.|
T Consensus 10 ~IL~~l~--~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~~~~~Y~lTekG 62 (77)
T PF14947_consen 10 DILKILS--KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKKKDGKYRLTEKG 62 (77)
T ss_dssp HHHHHH---TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEEETTEEEE-HHH
T ss_pred HHHHHHH--cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeCCCCEEEECccH
Confidence 3444444 7788889999999999999999999998763 4444444444
No 100
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=48.61 E-value=34 Score=37.42 Aligned_cols=56 Identities=21% Similarity=0.349 Sum_probs=45.2
Q ss_pred CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEE
Q 023574 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL 138 (280)
Q Consensus 80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIl 138 (280)
|..++..|++-+. .|+|+.+-|++..-++.++-.|+.+..++.+- .++.. ..|||+
T Consensus 58 ~~qL~~EI~~El~-~gGRvnlvdLa~~LnVD~~hiEr~~~~iv~~d-~~~~l-~~GeLi 113 (803)
T PLN03083 58 QDQLRNEIEAEIK-KLGRVSLVDLADTIGVDLYHVERQAQQVVSDD-PGLML-VQGEII 113 (803)
T ss_pred HHHHHHHHHHHHH-hCCCeeHHHHhhhcCCCHHHHHHHHHHHhcCC-CceEE-ecCEec
Confidence 4456777888885 58999999999999999999999999998885 44443 567874
No 101
>PRK10286 O-6-alkylguanine-DNA:cysteine-protein methyltransferase; Provisional
Probab=48.19 E-value=29 Score=30.99 Aligned_cols=74 Identities=12% Similarity=0.195 Sum_probs=52.7
Q ss_pred chHHHHHHHHHHHc--CCceehhhhhhhcCCC--HHHHHHHH--HHHHhhcCCceEeccCCcEEEEcCcchHHHHhhhhH
Q 023574 81 ADVRNRAMDAVDAC--NRRVTIGDVAGKAGLK--LNEAQKAL--QALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSF 154 (280)
Q Consensus 81 ~~~~~~im~Ave~l--g~RvTvGDVAa~aGL~--L~~Ae~aL--~aLAsD~~GhLqVsesGEIlYvFP~~fRs~l~~Ks~ 154 (280)
.+.+.++.+++.+. |.-.|-||+|...|-+ ...+-.++ +.+.-...||==|..+|.+- +|+.-+..|.+
T Consensus 87 t~fq~~V~~~l~~IP~G~~~tYg~iA~~~g~p~aaRaVG~A~~~Np~~i~iPCHRVv~~~G~l~-----gy~gG~~~K~~ 161 (171)
T PRK10286 87 TPFQREVWQTLRTIPCGQVMHYGQLAEQLGRPGAARAVGAANGSNPISIVVPCHRVIGRNGTMT-----GYAGGVQRKEW 161 (171)
T ss_pred CHHHHHHHHHHHcCCCCCcEeHHHHHHHhCCCChHHHHHHHHHhCCCCCccCCceEECCCCCcC-----CCCCcHHHHHH
Confidence 46799999999998 7778889999999974 34444444 22344468999999999984 34444455666
Q ss_pred HHhHH
Q 023574 155 RLKVE 159 (280)
Q Consensus 155 r~rl~ 159 (280)
.+.+|
T Consensus 162 LL~~E 166 (171)
T PRK10286 162 LLRHE 166 (171)
T ss_pred HHHHc
Confidence 65554
No 102
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=48.14 E-value=19 Score=32.76 Aligned_cols=42 Identities=21% Similarity=0.334 Sum_probs=34.6
Q ss_pred HHHHHHHHH------cCCceehhhhhhhcCCCHHHHHHHHHHHHhhcC
Q 023574 85 NRAMDAVDA------CNRRVTIGDVAGKAGLKLNEAQKALQALAADTD 126 (280)
Q Consensus 85 ~~im~Ave~------lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~ 126 (280)
++..+.+++ +|+..|+++++.+.|++.++.-++|.+++.+..
T Consensus 16 p~~~~vf~~~~idfCcgG~~~l~ea~~~~~i~~~~~~~~l~~~~~~~~ 63 (220)
T PRK10992 16 PRATALFREYDLDFCCGGKQTLARAAARKNLDIDVIEARLAALQEQPI 63 (220)
T ss_pred ccHHHHHHHcCCcccCCCCchHHHHHHHcCCCHHHHHHHHHHHHhccc
Confidence 344455565 578999999999999999999999999986653
No 103
>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=47.96 E-value=87 Score=24.89 Aligned_cols=62 Identities=13% Similarity=0.127 Sum_probs=46.2
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCc
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~a-----GL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~ 143 (280)
..|..|++++.+.+.-+|+.||.... .+++..+=+.|..|....=-+=-..++|...|.+-.
T Consensus 8 ~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~~ 74 (120)
T PF01475_consen 8 PQRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEeecC
Confidence 46788999999999999999987743 588889999999998875333333446788887743
No 104
>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=47.35 E-value=78 Score=30.71 Aligned_cols=60 Identities=18% Similarity=0.227 Sum_probs=48.3
Q ss_pred chHHHHHHHHHHHc--CCceehhhhhhh-cCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 023574 81 ADVRNRAMDAVDAC--NRRVTIGDVAGK-AGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (280)
Q Consensus 81 ~~~~~~im~Ave~l--g~RvTvGDVAa~-aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvF 141 (280)
.++.++|++.+.+. +..+|..|+... .++++.+...+|+.|.++.--.|-. ..|.++|..
T Consensus 8 ~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~-~~~~l~~~~ 70 (327)
T PF05158_consen 8 SELEKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLK-KGGGLSYKA 70 (327)
T ss_dssp HHHHHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE--SSSEEEEE
T ss_pred HHHHHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEE-cCCEEEEEE
Confidence 35788999999998 999999999998 7899999999999999987666655 557799987
No 105
>PF15581 Imm35: Immunity protein 35
Probab=46.64 E-value=35 Score=28.18 Aligned_cols=33 Identities=27% Similarity=0.483 Sum_probs=30.2
Q ss_pred cCCCHHHHHHHHHHHHhh-cCCceEeccCCcEEE
Q 023574 107 AGLKLNEAQKALQALAAD-TDGFLEVSDEGDVLY 139 (280)
Q Consensus 107 aGL~L~~Ae~aL~aLAsD-~~GhLqVsesGEIlY 139 (280)
-||+-.|+++-|.+.|+. .++..+|-.+|++|.
T Consensus 44 RGl~~~qV~~kl~ava~~~~~~~~vvKkE~~~Iw 77 (93)
T PF15581_consen 44 RGLPEEQVLYKLEAVAAKGPEAKIVVKKEGNIIW 77 (93)
T ss_pred cCCCHHHHHHHHHHHHhcCCCcceEEEecCCeEE
Confidence 599999999999999998 599999999999886
No 106
>PF10025 DUF2267: Uncharacterized conserved protein (DUF2267); InterPro: IPR018727 This entry contains proteins that have no known function. ; PDB: 2YSK_A.
Probab=46.33 E-value=13 Score=30.48 Aligned_cols=80 Identities=23% Similarity=0.312 Sum_probs=56.9
Q ss_pred hhhhhhhcCC-CHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHhh------hhHHHhHHHHHHHhhh-----
Q 023574 100 IGDVAGKAGL-KLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAA------KSFRLKVEPVIDKAKA----- 167 (280)
Q Consensus 100 vGDVAa~aGL-~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fRs~l~~------Ks~r~rl~~~~~k~w~----- 167 (280)
+.+|+..+|+ +.++|++++.+...--+-+|.+.+.-++.=..|.-.|..+.. ..-+..+++|+..+..
T Consensus 6 l~~V~~~~~l~~~~~A~~a~~avL~~L~~rL~~~ea~~La~qLP~~l~~~l~~gw~~~~~~~~~~~~eF~~rVa~~~~~~ 85 (125)
T PF10025_consen 6 LDEVRERAGLPDREEAYRATRAVLHTLRERLPPEEAADLAAQLPMELRGILYEGWRPSEGPGRFDLDEFLARVAERLGGA 85 (125)
T ss_dssp HHHHHHHHT---HHHHHHHHHHHHHHHHTTS-HHHHHHHHTTS-HHHHHHHHTT--TTS-----SHHHHHHHHHHTSEET
T ss_pred HHHHHHHhCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHhCCHHHHHHHHhcccCCCCCCCCCHHHHHHHHHHHccCC
Confidence 5688999999 899999999999988899999999888888889999999953 1222557777777766
Q ss_pred ---hhhhHhhHHHHH
Q 023574 168 ---AAEYSIRVLFGT 179 (280)
Q Consensus 168 ---v~~yliRisFGi 179 (280)
-..+++|..|.+
T Consensus 86 ~~~~a~~~~~aV~~~ 100 (125)
T PF10025_consen 86 DEDDAERLARAVFAA 100 (125)
T ss_dssp TEE-HHHHHHHHHHH
T ss_pred CcccHHHHHHHHHHH
Confidence 455666665554
No 107
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=45.78 E-value=29 Score=31.32 Aligned_cols=45 Identities=13% Similarity=0.269 Sum_probs=35.3
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 023574 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (280)
Q Consensus 86 ~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse 133 (280)
+|++++.+. ..+|+.|+|...|++...+-+=|..|... |-|+-++
T Consensus 18 ~IL~~l~~~-~~l~l~eia~~lgl~kstv~Rll~tL~~~--G~l~~~~ 62 (257)
T PRK15090 18 GILQALGEE-REIGITELSQRVMMSKSTVYRFLQTMKTL--GYVAQEG 62 (257)
T ss_pred HHHHHhhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEcC
Confidence 456666654 46999999999999999999999888765 5575543
No 108
>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=45.56 E-value=30 Score=31.58 Aligned_cols=39 Identities=18% Similarity=0.382 Sum_probs=33.6
Q ss_pred HHHHHHHHHHcCCc--eehhhhhhhcCCCHHHHHHHHHHHH
Q 023574 84 RNRAMDAVDACNRR--VTIGDVAGKAGLKLNEAQKALQALA 122 (280)
Q Consensus 84 ~~~im~Ave~lg~R--vTvGDVAa~aGL~L~~Ae~aL~aLA 122 (280)
+..|++++.+.... +|+.|++.+||+..+++-.+|..|-
T Consensus 135 ~~~i~~~L~~~~~~~~isi~~is~~Tgi~~~DIi~tL~~l~ 175 (188)
T PF01853_consen 135 RRVILEYLLEFKGKKSISIKDISQETGIRPEDIISTLQQLG 175 (188)
T ss_dssp HHHHHHHHHHTSSE--EEHHHHHHHH-BTHHHHHHHHHHTT
T ss_pred HHHHHHHHHhcCCCCeEEHHHHHHHHCCCHHHHHHHHHHCC
Confidence 46789999998885 9999999999999999999887764
No 109
>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=44.74 E-value=31 Score=32.93 Aligned_cols=45 Identities=18% Similarity=0.344 Sum_probs=36.2
Q ss_pred HHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 023574 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (280)
Q Consensus 87 im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse 133 (280)
|++.+.+..+|++-.++|.+-|++.....+++..|.+. |-+++..
T Consensus 188 IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~a--GvIe~r~ 232 (251)
T TIGR02787 188 IFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESA--GVIESRS 232 (251)
T ss_pred HHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEecc
Confidence 44444444579999999999999999999999999875 6666666
No 110
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=44.14 E-value=78 Score=24.41 Aligned_cols=46 Identities=22% Similarity=0.455 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEec-cCCcEEEEcCcc
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS-DEGDVLYVFPNN 144 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVs-esGEIlYvFP~~ 144 (280)
-++.+++.+++.|..+|.+-|+ +.|..| |-..|. ++|.-+|..|.+
T Consensus 21 sQ~eL~~~L~~~Gi~vTQaTiS-----------RDLkeL-----~~vKv~~~~g~~~Y~l~~~ 67 (70)
T PF01316_consen 21 SQEELVELLEEEGIEVTQATIS-----------RDLKEL-----GAVKVPDGNGKYRYVLPEE 67 (70)
T ss_dssp SHHHHHHHHHHTT-T--HHHHH-----------HHHHHH-----T-EEEECTTSSEEEE-TTS
T ss_pred CHHHHHHHHHHcCCCcchhHHH-----------HHHHHc-----CcEEeeCCCCCEEEEecCc
Confidence 3577888888888888776553 344444 445666 689999999875
No 111
>PF15145 DUF4577: Domain of unknown function (DUF4577)
Probab=43.48 E-value=9.5 Score=32.81 Aligned_cols=34 Identities=26% Similarity=0.230 Sum_probs=25.7
Q ss_pred hHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Q 023574 171 YSIRVLFGTALIASIVIVFTAIIAILSSKSDDDD 204 (280)
Q Consensus 171 yliRisFGi~LIaSivLv~~aIiailss~s~~D~ 204 (280)
-++=|.+-++|++|.+||...|+.|+.-.+.=|+
T Consensus 61 ~lffvglii~LivSLaLVsFvIFLiiQTgnkMdd 94 (128)
T PF15145_consen 61 SLFFVGLIIVLIVSLALVSFVIFLIIQTGNKMDD 94 (128)
T ss_pred eehHHHHHHHHHHHHHHHHHHHHheeeccchHHH
Confidence 3555788899999999999999988755444333
No 112
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=43.43 E-value=19 Score=27.63 Aligned_cols=29 Identities=17% Similarity=0.318 Sum_probs=24.1
Q ss_pred HHHHHHcCCceehhhhhhhcCCCHHHHHH
Q 023574 88 MDAVDACNRRVTIGDVAGKAGLKLNEAQK 116 (280)
Q Consensus 88 m~Ave~lg~RvTvGDVAa~aGL~L~~Ae~ 116 (280)
-+|++-...++++.||+..+||+..||+-
T Consensus 35 ~~A~klv~~Ga~~~el~~~CgL~~aEAeL 63 (70)
T PF10975_consen 35 SQAIKLVRQGASVEELMEECGLSRAEAEL 63 (70)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHH
Confidence 45666667789999999999999999953
No 113
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=43.39 E-value=43 Score=30.54 Aligned_cols=90 Identities=18% Similarity=0.288 Sum_probs=62.5
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc-----CCc-----eEe--c--------cCC------
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT-----DGF-----LEV--S--------DEG------ 135 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~-----~Gh-----LqV--s--------esG------ 135 (280)
+-..+|++.+.+.|-++|.-+||.+-|++..++.+.|-.|-... .++ ++- + ++.
T Consensus 4 ~~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~~~~pP~W~~~~~~~~~~~~~~~~~~~~~~~~ 83 (183)
T PHA02701 4 DCASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLESDAVSCEDGCPPLWSVECEPDEKKEEGSGSDTEPMETE 83 (183)
T ss_pred hHHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEecCCCCCCccccccCCCCCcccccccccCccccc
Confidence 44578999999999779999999999999999999998776531 111 000 0 001
Q ss_pred ---cEEE-----EcCcchHHHHhhhhHHHhHHHHHHHhhhhhhh
Q 023574 136 ---DVLY-----VFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEY 171 (280)
Q Consensus 136 ---EIlY-----vFP~~fRs~l~~Ks~r~rl~~~~~k~w~v~~y 171 (280)
+=+| +-|..+=-.+..+..+-+||||.++-+....|
T Consensus 84 ~~~~~~f~~~~d~~~~~~i~~~k~~DpKS~LQE~~Q~~~~~l~Y 127 (183)
T PHA02701 84 AGCDTLFGGDIDVLTVSAVMRLKTLNPVSAVNEFCMRTHRPLEF 127 (183)
T ss_pred ccccccccCccccccHHHhhcCCCCCccHHHHHHHHhcCCCCeE
Confidence 1122 34555555566677888999999887665544
No 114
>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=42.98 E-value=71 Score=26.58 Aligned_cols=59 Identities=14% Similarity=0.124 Sum_probs=41.6
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEE
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYv 140 (280)
.+.-+++++-|-+. .-+|+.-||.+-+++...|+++|..|++..-=.+=+-..+-.||.
T Consensus 44 ~~~~~kl~kEV~~~-K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~k~~~~~IYt 102 (105)
T PF03297_consen 44 KETYDKLLKEVPKM-KLITPSVLSERLKINGSLARKALRELESKGLIKPVSKHHRQRIYT 102 (105)
T ss_dssp CHHHHHHHHHCTTS-SCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEEECCTTCEEEE
T ss_pred HHHHHHHHHHhccC-cEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEEeccCCeEEEe
Confidence 33444444444443 559999999999999999999999999875444444445667774
No 115
>PRK09492 treR trehalose repressor; Provisional
Probab=42.83 E-value=17 Score=32.22 Aligned_cols=24 Identities=25% Similarity=0.448 Sum_probs=21.0
Q ss_pred CceehhhhhhhcCCCHHHHHHHHH
Q 023574 96 RRVTIGDVAGKAGLKLNEAQKALQ 119 (280)
Q Consensus 96 ~RvTvGDVAa~aGL~L~~Ae~aL~ 119 (280)
.++|+.|||..+|+|...+-++|.
T Consensus 3 ~~~ti~dIA~~agVS~~TVSrvLn 26 (315)
T PRK09492 3 NKLTIKDIARLSGVGKSTVSRVLN 26 (315)
T ss_pred CCCcHHHHHHHhCCCHHHHhHHhC
Confidence 468999999999999998888874
No 116
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=42.74 E-value=1.2e+02 Score=30.57 Aligned_cols=87 Identities=17% Similarity=0.202 Sum_probs=52.2
Q ss_pred HHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCc-----EEEEcCcchHHHHhhhhHHHhHHHHHHHhh
Q 023574 92 DACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-----VLYVFPNNYRAKLAAKSFRLKVEPVIDKAK 166 (280)
Q Consensus 92 e~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGE-----IlYvFP~~fRs~l~~Ks~r~rl~~~~~k~w 166 (280)
.++|...|+.+||...|+++++.++.|.....-..-+..|.+++| ++-.-..+--..+.....+..|+.++..+-
T Consensus 273 ~~lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~~~pee~~~~~~l~~~L~~~L~~L~ 352 (415)
T PRK07598 273 QEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDDISPEEMLMRESLQRDLQHLLADLT 352 (415)
T ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHHHccCCcccccccCCCccccHHHhccCCCCCHHHHHHHHHHHHHHHHHHHhCC
Confidence 457888999999999999999998877653322233334433333 221111112222333445556777777766
Q ss_pred hhhhhHhhHHHH
Q 023574 167 AAAEYSIRVLFG 178 (280)
Q Consensus 167 ~v~~yliRisFG 178 (280)
.--.-+++..||
T Consensus 353 ~reR~VI~LRyg 364 (415)
T PRK07598 353 SRERDVIRMRFG 364 (415)
T ss_pred HHHHHHHHHHHh
Confidence 666666666665
No 117
>PHA03093 EEV glycoprotein; Provisional
Probab=42.67 E-value=44 Score=30.63 Aligned_cols=30 Identities=13% Similarity=0.241 Sum_probs=22.1
Q ss_pred HhhhhhhhHhhHHHHHHHHHHHHHHHHHHHH
Q 023574 164 KAKAAAEYSIRVLFGTALIASIVIVFTAIIA 194 (280)
Q Consensus 164 k~w~v~~yliRisFGi~LIaSivLv~~aIia 194 (280)
|..+.+...|||+..|.+| |.+++.++++.
T Consensus 30 kk~r~i~i~~RisiiiSIl-sL~~i~~~LAl 59 (185)
T PHA03093 30 KKVKCIGICIRISIIISIL-SLIAITATLAL 59 (185)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 6667788899999999888 55555555543
No 118
>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=42.41 E-value=49 Score=26.78 Aligned_cols=44 Identities=16% Similarity=0.312 Sum_probs=34.1
Q ss_pred HHHHHHHHc-CCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023574 86 RAMDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (280)
Q Consensus 86 ~im~Ave~l-g~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqV 131 (280)
++|..+-+. +.++|+.|+|.+.|++...+++-|..|... |-++.
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~--Gli~~ 57 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLA--GIVTS 57 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHC--CcEEe
Confidence 344455443 568999999999999999999999999874 44544
No 119
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=41.57 E-value=32 Score=32.52 Aligned_cols=43 Identities=33% Similarity=0.415 Sum_probs=35.8
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLq 130 (280)
.+...+++++.+|.|-++=+...+|++.++|++.|. +++|||+
T Consensus 250 ~~~a~~~l~~~~~~vk~a~~~~~~~~~~~~a~~~l~----~~~g~~~ 292 (299)
T PRK05441 250 REEAEAALEAADGSVKLAIVMILTGLDAAEAKALLA----RHGGFLR 292 (299)
T ss_pred HHHHHHHHHHhCCCcHHHHHHHHhCCCHHHHHHHHH----HcCCCHH
Confidence 355778899999999999999999999999977664 5777765
No 120
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=41.48 E-value=88 Score=25.36 Aligned_cols=60 Identities=27% Similarity=0.297 Sum_probs=44.8
Q ss_pred CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc-CCcEEEE
Q 023574 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYV 140 (280)
Q Consensus 79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse-sGEIlYv 140 (280)
++.+.-+++++-|-+ -.-+|+.-|+.+-++....|+++|..|....-=. .|+. ..-.||.
T Consensus 24 ~dk~t~dkl~kEV~~-~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik-~V~~~~~q~IYt 84 (86)
T PRK09334 24 LDEELLKRVAKEVKK-EKIVTPYTLASKYGIKISVAKKVLRELEKRGVLV-LYSKNRRTPIYV 84 (86)
T ss_pred cCHHHHHHHHHHhcc-CcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEE-EEecCCCeEEec
Confidence 556677788877776 4568999999999999999999999998753222 3333 3566664
No 121
>PRK09526 lacI lac repressor; Reviewed
Probab=41.37 E-value=20 Score=32.19 Aligned_cols=48 Identities=23% Similarity=0.219 Sum_probs=33.1
Q ss_pred CceehhhhhhhcCCCHHHHHHHHH--------------HHHhhcC-------CceEeccCCcEEEEcCc
Q 023574 96 RRVTIGDVAGKAGLKLNEAQKALQ--------------ALAADTD-------GFLEVSDEGDVLYVFPN 143 (280)
Q Consensus 96 ~RvTvGDVAa~aGL~L~~Ae~aL~--------------aLAsD~~-------GhLqVsesGEIlYvFP~ 143 (280)
.++|+.|||.++|+|...+-+.|. +.|.+.| -.|.-..++-|-.++|.
T Consensus 4 ~~~ti~dIA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvv~~~ 72 (342)
T PRK09526 4 KPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPNRVAQQLAGKQSLTIGLATTS 72 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHhcCCCCCCHHHHHHHHHHHHHHCCCcCHHHHHhhcCCCceEEEEeCC
Confidence 468999999999999998887773 2333321 12444456778888874
No 122
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=40.37 E-value=20 Score=32.27 Aligned_cols=24 Identities=25% Similarity=0.423 Sum_probs=21.0
Q ss_pred CCceehhhhhhhcCCCHHHHHHHH
Q 023574 95 NRRVTIGDVAGKAGLKLNEAQKAL 118 (280)
Q Consensus 95 g~RvTvGDVAa~aGL~L~~Ae~aL 118 (280)
..++|+.|||..+|+|...+-+.|
T Consensus 3 ~~~~ti~dIA~~agVS~~TVSrvL 26 (331)
T PRK14987 3 KKRPVLQDVADRVGVTKMTVSRFL 26 (331)
T ss_pred CCCCcHHHHHHHhCCCHHHhhhhh
Confidence 347999999999999998887777
No 123
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.31 E-value=64 Score=31.06 Aligned_cols=44 Identities=27% Similarity=0.223 Sum_probs=30.3
Q ss_pred hhhhHHHhHHHHHHHhhhhh--------hhHhhHHHHHHHHHHHHHHHHHHHHHH
Q 023574 150 AAKSFRLKVEPVIDKAKAAA--------EYSIRVLFGTALIASIVIVFTAIIAIL 196 (280)
Q Consensus 150 ~~Ks~r~rl~~~~~k~w~v~--------~yliRisFGi~LIaSivLv~~aIiail 196 (280)
.|||-|.---.|.+++|+.. ...=|.+|-|+|- +|-|++|+++|
T Consensus 220 dnKY~RRp~~~w~~rl~R~~~g~s~rP~~~~~ra~fli~lg---vLafi~~i~lM 271 (299)
T KOG3970|consen 220 DNKYKRRPTMDWMRRLWRAKHGGSGRPQEAKKRALFLIFLG---VLAFITIIMLM 271 (299)
T ss_pred cchhhcCChHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHH---HHHHHHHHHHH
Confidence 45777766777777777653 3355777766664 67778888887
No 124
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=40.02 E-value=56 Score=28.33 Aligned_cols=46 Identities=13% Similarity=0.117 Sum_probs=39.6
Q ss_pred HHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc------CCceEeccCCc
Q 023574 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT------DGFLEVSDEGD 136 (280)
Q Consensus 91 ve~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~------~GhLqVsesGE 136 (280)
+.+.++.++++|+|..-+++...+.+.|..|+.+. .+.++.|+.|+
T Consensus 18 l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~ 69 (154)
T COG1321 18 LLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGR 69 (154)
T ss_pred HHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCeEEChhhH
Confidence 33478899999999999999999999999999873 67778888886
No 125
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=39.02 E-value=58 Score=27.74 Aligned_cols=42 Identities=10% Similarity=0.255 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~ 125 (280)
...+|++++ +.++|.|..|+|.+.|+|-..+.+-+..|-.+.
T Consensus 15 ~D~~IL~~L-q~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~G 56 (164)
T PRK11169 15 IDRNILNEL-QKDGRISNVELSKRVGLSPTPCLERVRRLERQG 56 (164)
T ss_pred HHHHHHHHh-ccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 456777755 568899999999999999999999999998874
No 126
>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=38.97 E-value=1.3e+02 Score=26.41 Aligned_cols=48 Identities=19% Similarity=0.347 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse 133 (280)
.+.+++..+.+.| ..|+.|+|...|++...+.+.|..|..+ |-++...
T Consensus 144 ~~~~IL~~l~~~g-~~s~~eia~~l~is~stv~r~L~~Le~~--GlI~r~~ 191 (203)
T TIGR01884 144 EELKVLEVLKAEG-EKSVKNIAKKLGKSLSTISRHLRELEKK--GLVEQKG 191 (203)
T ss_pred HHHHHHHHHHHcC-CcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEc
Confidence 3457888887765 5899999999999999999999999866 5555543
No 127
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=38.82 E-value=48 Score=24.07 Aligned_cols=51 Identities=22% Similarity=0.273 Sum_probs=36.1
Q ss_pred ceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHH
Q 023574 97 RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKL 149 (280)
Q Consensus 97 RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fRs~l 149 (280)
.++..++..-.|++++. +++..+....|...+.+++++.+.+.++-||.=+
T Consensus 5 ~~~~~~i~~llG~~i~~--~ei~~~L~~lg~~~~~~~~~~~~~v~~P~~R~Di 55 (71)
T smart00874 5 TLRRERINRLLGLDLSA--EEIEEILKRLGFEVEVSGDDDTLEVTVPSYRFDI 55 (71)
T ss_pred EecHHHHHHHHCCCCCH--HHHHHHHHHCCCeEEecCCCCeEEEECCCCcccc
Confidence 35667788888877763 3456666666777777666778888888888644
No 128
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI 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 Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=38.57 E-value=23 Score=31.72 Aligned_cols=23 Identities=30% Similarity=0.482 Sum_probs=20.3
Q ss_pred ceehhhhhhhcCCCHHHHHHHHH
Q 023574 97 RVTIGDVAGKAGLKLNEAQKALQ 119 (280)
Q Consensus 97 RvTvGDVAa~aGL~L~~Ae~aL~ 119 (280)
++|+.|||..+|+|...+-++|.
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhC
Confidence 47999999999999998888883
No 129
>PHA01815 hypothetical protein
Probab=38.47 E-value=1.2e+02 Score=22.63 Aligned_cols=25 Identities=20% Similarity=0.215 Sum_probs=16.1
Q ss_pred HHHHHHHhhhhhhhHhhHHHHHHHH
Q 023574 158 VEPVIDKAKAAAEYSIRVLFGTALI 182 (280)
Q Consensus 158 l~~~~~k~w~v~~yliRisFGi~LI 182 (280)
+-+++-.+--....-+|+|||+..-
T Consensus 12 llaflitliilmt~~irvsfgvlft 36 (55)
T PHA01815 12 LLAFLITLIILMTLHIRVSFGVLFT 36 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444445555556679999997643
No 130
>PRK11050 manganese transport regulator MntR; Provisional
Probab=38.24 E-value=2.5e+02 Score=23.81 Aligned_cols=46 Identities=24% Similarity=0.335 Sum_probs=37.0
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse 133 (280)
..|+.++.. ++..|+.|+|...|++...+.+.|..|..+ |-++...
T Consensus 40 ~~I~~~l~~-~~~~t~~eLA~~l~is~stVsr~l~~Le~~--GlI~r~~ 85 (152)
T PRK11050 40 ELIADLIAE-VGEARQVDIAARLGVSQPTVAKMLKRLARD--GLVEMRP 85 (152)
T ss_pred HHHHHHHHh-cCCCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEec
Confidence 456667765 567899999999999999999999999987 5665543
No 131
>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=38.10 E-value=86 Score=23.01 Aligned_cols=37 Identities=16% Similarity=0.305 Sum_probs=28.7
Q ss_pred HHHHHHHHHHcCC-----ceehhhhhhhcCCCHHHHHHHHHH
Q 023574 84 RNRAMDAVDACNR-----RVTIGDVAGKAGLKLNEAQKALQA 120 (280)
Q Consensus 84 ~~~im~Ave~lg~-----RvTvGDVAa~aGL~L~~Ae~aL~a 120 (280)
+.+++++.=+.|| ++|+.|+|..-|++...+.+-|+.
T Consensus 5 Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 5 QREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred HHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 4455555556665 899999999999999998877754
No 132
>PRK06474 hypothetical protein; Provisional
Probab=37.75 E-value=74 Score=27.92 Aligned_cols=56 Identities=18% Similarity=0.180 Sum_probs=45.2
Q ss_pred CCCCchHHHHHHHHHHHcCCceehhhhhhhc-CCCHHHHHHHHHHHHhhcCCceEeccC
Q 023574 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKA-GLKLNEAQKALQALAADTDGFLEVSDE 134 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvTvGDVAa~a-GL~L~~Ae~aL~aLAsD~~GhLqVses 134 (280)
+-|.-..|.+|++++...+...|+.||+..- +++...+=+-|..|+.. |-+++.+.
T Consensus 6 ~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~--GLI~~~~~ 62 (178)
T PRK06474 6 EILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDS--GILHVVKE 62 (178)
T ss_pred HhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHC--CCEEEeec
Confidence 3466788999999999987679999999988 68888888888888764 66666554
No 133
>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=37.49 E-value=63 Score=27.99 Aligned_cols=53 Identities=11% Similarity=0.203 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHcCC-ceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 023574 83 VRNRAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (280)
Q Consensus 83 ~~~~im~Ave~lg~-RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvF 141 (280)
.=.+|-+.|+.... ++|+.+|+..+|++..+..+=+. .|.|++++.-.+-|.=
T Consensus 31 ~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~Ir------eGRL~~~~~~nl~~~C 84 (137)
T TIGR03826 31 EFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIR------EGRLQLKHFPNLGYPC 84 (137)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHH------cCCeeccCCCCCcCcc
Confidence 33566667775543 69999999999999998866554 4889998876666644
No 134
>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=37.30 E-value=46 Score=25.13 Aligned_cols=43 Identities=21% Similarity=0.303 Sum_probs=35.7
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhcCCC--HHHHHHHHHHHHhhc
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLK--LNEAQKALQALAADT 125 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~--L~~Ae~aL~aLAsD~ 125 (280)
+..++|+++++.+| ..|.-.+|..-||+ ..++.+.|-.|....
T Consensus 4 ~~ee~Il~~L~~~g-~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g 48 (66)
T PF02295_consen 4 DLEEKILDFLKELG-GSTATAIAKALGLSVPKKEVNRVLYRLEKQG 48 (66)
T ss_dssp HHHHHHHHHHHHHT-SSEEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred hHHHHHHHHHHhcC-CccHHHHHHHhCcchhHHHHHHHHHHHHHCC
Confidence 56789999999999 77777777777766 799999999987764
No 135
>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=37.02 E-value=97 Score=24.35 Aligned_cols=31 Identities=29% Similarity=0.325 Sum_probs=28.6
Q ss_pred cCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 94 CNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 94 lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
....+|..|+|...|++-..+.++|..|..+
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~ 74 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARR 74 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 5678999999999999999999999999886
No 136
>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=36.66 E-value=67 Score=25.68 Aligned_cols=38 Identities=18% Similarity=0.284 Sum_probs=30.7
Q ss_pred HHHHHHHc--CCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 87 AMDAVDAC--NRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 87 im~Ave~l--g~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
+|-.+.+. +..+|..++|...|++...+++-|..|...
T Consensus 13 ~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 13 ALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRA 52 (132)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 44455444 347999999999999999999999999864
No 137
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=36.65 E-value=56 Score=27.00 Aligned_cols=33 Identities=12% Similarity=0.195 Sum_probs=29.6
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHH
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL 118 (280)
+..|.-|+++.| .|+..++.++||+-+....+|
T Consensus 10 ~adI~AaL~KrG--~sLa~lsr~~Gls~~TL~nAL 42 (92)
T PRK10344 10 PADIIAGLRKKG--TSMAAESRRNGLSSSTLANAL 42 (92)
T ss_pred HHHHHHHHHHcC--CcHHHHHHHcCCChHHHHHHH
Confidence 356888999988 799999999999999999998
No 138
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=36.57 E-value=1e+02 Score=27.82 Aligned_cols=55 Identities=16% Similarity=0.153 Sum_probs=41.3
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCC-CHHHHHHHHHHHHhhc---CCceEeccCC
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGL-KLNEAQKALQALAADT---DGFLEVSDEG 135 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL-~L~~Ae~aL~aLAsD~---~GhLqVsesG 135 (280)
|.....+.-++=..+..+|+.++|...|+ +..++..+|..|..++ |-.|++..+|
T Consensus 7 ~~~~~~vEall~a~~~pls~~~L~~il~~~~~~~~~~~l~~l~~~y~~rg~~L~~~~~~ 65 (184)
T COG1386 7 MELKALIEALLFAGGEPLSLKELAEILGIVSADAIIDALAELKEEYEDRGLELVEVAEG 65 (184)
T ss_pred hhHHHHHHHHHHhcCCCCCHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCeeEEEEcCc
Confidence 34444445555666779999999999999 8888999999999885 4456666654
No 139
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=36.55 E-value=1.3e+02 Score=26.56 Aligned_cols=55 Identities=16% Similarity=0.138 Sum_probs=36.2
Q ss_pred CCCCchHHHHHHHHHHHcCCceehhhhhhhcC-----------C---CHHHHHHHHHHHHhhcCCceEe
Q 023574 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------L---KLNEAQKALQALAADTDGFLEV 131 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aG-----------L---~L~~Ae~aL~aLAsD~~GhLqV 131 (280)
+++..+.++||+++++++||+--..--+.+++ + --.+..+++..-|.+.|-.|.+
T Consensus 2 ~~Vs~~Tr~rV~~~a~elgY~pn~~a~~l~~~~~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~ 70 (309)
T PRK11041 2 EKVSQATRQRVEQAVLEVGYSPQSLGRNLKRNESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYLVLI 70 (309)
T ss_pred CcCCHHHHHHHHHHHHHHCCCcCHHHHHhhcCCCcEEEEEeCCCcCccHHHHHHHHHHHHHHCCCEEEE
Confidence 56888999999999999999875442222221 1 2344556666666666666554
No 140
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=36.46 E-value=32 Score=30.44 Aligned_cols=32 Identities=19% Similarity=0.332 Sum_probs=25.2
Q ss_pred hHHHHHHHH----HHHcCCceehhhhhhhcCCCHHH
Q 023574 82 DVRNRAMDA----VDACNRRVTIGDVAGKAGLKLNE 113 (280)
Q Consensus 82 ~~~~~im~A----ve~lg~RvTvGDVAa~aGL~L~~ 113 (280)
+.+.+|++| +-+.||.+|+.|||.++|++...
T Consensus 13 ~~r~~Il~aA~~lF~~~Gy~~s~~~IA~~AGvsk~t 48 (225)
T PRK11552 13 QAKQQLIAAALAQFGEYGLHATTRDIAAQAGQNIAA 48 (225)
T ss_pred HHHHHHHHHHHHHHHHhCccCCHHHHHHHhCCCHHH
Confidence 556666655 45679889999999999998765
No 141
>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=36.43 E-value=2.5e+02 Score=23.36 Aligned_cols=77 Identities=14% Similarity=0.111 Sum_probs=52.4
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhc----CCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHhhhhHHHh
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKA----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLK 157 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~a----GL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fRs~l~~Ks~r~r 157 (280)
+..-.||+.+=+.| ..|+.||...- |++-..+..-|..|.. -|.|+...+|-.-+..|--=|. .+.+..
T Consensus 4 ~~E~~VM~vlW~~~-~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~--KG~v~~~k~gr~~~Y~p~vs~e----e~~~~~ 76 (130)
T TIGR02698 4 DAEWEVMRVVWTLG-ETTSRDIIRILAEKKDWSDSTIKTLLGRLVD--KGCLTTEKEGRKFIYTALVSED----EAVENA 76 (130)
T ss_pred HHHHHHHHHHHcCC-CCCHHHHHHHHhhccCCcHHHHHHHHHHHHH--CCceeeecCCCcEEEEecCCHH----HHHHHH
Confidence 34567999998776 58999977653 7788888888888876 5788888888854434432222 334445
Q ss_pred HHHHHHHh
Q 023574 158 VEPVIDKA 165 (280)
Q Consensus 158 l~~~~~k~ 165 (280)
++.+.+++
T Consensus 77 ~~~~~~~~ 84 (130)
T TIGR02698 77 AQELFSRI 84 (130)
T ss_pred HHHHHHHH
Confidence 66665554
No 142
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=36.31 E-value=52 Score=31.20 Aligned_cols=43 Identities=26% Similarity=0.295 Sum_probs=36.6
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLq 130 (280)
.++..+++++.+|.|-++=+...+|++..+|++.|. +.+|||.
T Consensus 245 ~~~a~~~l~~~~~~vk~Ai~~~~~~~~~~~a~~~l~----~~~g~~~ 287 (291)
T TIGR00274 245 KELAEQTLLAADQNVKLAIVMILSTLSASEAKVLLD----RHGGFLR 287 (291)
T ss_pred HHHHHHHHHHhCCCcHHHHHHHHhCCCHHHHHHHHH----HcCCcHH
Confidence 466889999999999999999999999999977664 6777775
No 143
>PLN02343 allene oxide cyclase
Probab=35.94 E-value=12 Score=34.88 Aligned_cols=13 Identities=31% Similarity=0.851 Sum_probs=11.9
Q ss_pred chheehhhcccCC
Q 023574 249 NFIKSVFSFVFGE 261 (280)
Q Consensus 249 nFlEsVFSFvFGD 261 (280)
.=+||+|||-|||
T Consensus 125 DryEa~ySfyfGD 137 (229)
T PLN02343 125 DRYEAIYSFYFGD 137 (229)
T ss_pred ceeEEEEEEEecC
Confidence 5689999999999
No 144
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=35.84 E-value=38 Score=29.19 Aligned_cols=32 Identities=9% Similarity=0.178 Sum_probs=24.3
Q ss_pred hHHHHHHH----HHHHcCCc-eehhhhhhhcCCCHHH
Q 023574 82 DVRNRAMD----AVDACNRR-VTIGDVAGKAGLKLNE 113 (280)
Q Consensus 82 ~~~~~im~----Ave~lg~R-vTvGDVAa~aGL~L~~ 113 (280)
+.+++|++ .+.+.|+. +|+.|||.++|++...
T Consensus 18 ~~r~~IL~AA~~lf~e~Gy~~~s~~dIA~~aGvs~gt 54 (212)
T PRK15008 18 AKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTN 54 (212)
T ss_pred HHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHH
Confidence 45566655 45678877 8999999999988654
No 145
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=35.70 E-value=35 Score=22.60 Aligned_cols=26 Identities=19% Similarity=0.392 Sum_probs=17.0
Q ss_pred cCCceehhhhhhhcCCCHHHHHHHHH
Q 023574 94 CNRRVTIGDVAGKAGLKLNEAQKALQ 119 (280)
Q Consensus 94 lg~RvTvGDVAa~aGL~L~~Ae~aL~ 119 (280)
.....||.|||...|++...-.+...
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk 30 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFK 30 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHH
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45678999999999998776655544
No 146
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=35.47 E-value=26 Score=31.54 Aligned_cols=46 Identities=22% Similarity=0.281 Sum_probs=31.7
Q ss_pred eehhhhhhhcCCCHHHHHHHHH--------------HHHhhcC-------CceEeccCCcEEEEcCc
Q 023574 98 VTIGDVAGKAGLKLNEAQKALQ--------------ALAADTD-------GFLEVSDEGDVLYVFPN 143 (280)
Q Consensus 98 vTvGDVAa~aGL~L~~Ae~aL~--------------aLAsD~~-------GhLqVsesGEIlYvFP~ 143 (280)
+|+.|||.++|+|...+-++|. +.|.+.| -.|.-.++..|..++|.
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~~V~~~a~elgY~pn~~a~~l~~~~~~~i~vi~~~ 68 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATS 68 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcCHHHHHHhhCCCCeEEEEeCC
Confidence 6999999999999998877773 3444432 12444455677777775
No 147
>PRK09526 lacI lac repressor; Reviewed
Probab=35.47 E-value=1.3e+02 Score=27.15 Aligned_cols=56 Identities=13% Similarity=0.017 Sum_probs=38.0
Q ss_pred CCCCchHHHHHHHHHHHcCCceehhhhhhhcC--------------CCHHHHHHHHHHHHhhcCCceEec
Q 023574 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG--------------LKLNEAQKALQALAADTDGFLEVS 132 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aG--------------L~L~~Ae~aL~aLAsD~~GhLqVs 132 (280)
.++..+.+++|+++++++||.....=-+.+.+ ---.+..+++.+.|.+.|-+|.+.
T Consensus 30 ~~vs~~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvv~~~~~~~~~~~~~~gi~~~a~~~g~~~~i~ 99 (342)
T PRK09526 30 SHVSAKTREKVEAAMAELNYVPNRVAQQLAGKQSLTIGLATTSLALHAPSQIAAAIKSRADQLGYSVVIS 99 (342)
T ss_pred CCCCHHHHHHHHHHHHHHCCCcCHHHHHhhcCCCceEEEEeCCCCcccHHHHHHHHHHHHHHCCCEEEEE
Confidence 46899999999999999999754221111111 112455677888888888887763
No 148
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=35.43 E-value=64 Score=27.92 Aligned_cols=51 Identities=20% Similarity=0.318 Sum_probs=38.6
Q ss_pred chHHHHHHHHHHHcC--------------CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 023574 81 ADVRNRAMDAVDACN--------------RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (280)
Q Consensus 81 ~~~~~~im~Ave~lg--------------~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse 133 (280)
.++++|+...+.++. ..+|..|+|...|++...+-+.|..|..+ |-++...
T Consensus 154 ~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~~--g~I~~~~ 218 (235)
T PRK11161 154 KNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKS--GMLAVKG 218 (235)
T ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHHC--CCEEecC
Confidence 466788877776532 34789999999999999999999988775 4444443
No 149
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=34.69 E-value=33 Score=28.84 Aligned_cols=29 Identities=21% Similarity=0.186 Sum_probs=22.1
Q ss_pred HHHHHHH----HHHcCCc-eehhhhhhhcCCCHH
Q 023574 84 RNRAMDA----VDACNRR-VTIGDVAGKAGLKLN 112 (280)
Q Consensus 84 ~~~im~A----ve~lg~R-vTvGDVAa~aGL~L~ 112 (280)
|.+|++| +.+.|+. +|+.|||.++|++..
T Consensus 10 R~~Il~aA~~lf~e~G~~~tSi~~Ia~~aGvsk~ 43 (192)
T PRK14996 10 REVILQAAMRVALAEGFAAMTVRRIASEAQVAAG 43 (192)
T ss_pred HHHHHHHHHHHHHhcChhhccHHHHHHHhCCCcH
Confidence 5555554 5567887 899999999998754
No 150
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=34.15 E-value=2.2e+02 Score=28.77 Aligned_cols=65 Identities=18% Similarity=0.330 Sum_probs=49.2
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHh
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLA 150 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fRs~l~ 150 (280)
.+.++++++...+ .+|..|+|.+.|++...+-+++..|.++ |-+++.+.-...|.-...=+..+.
T Consensus 7 ~e~~vL~~L~~~~-~~s~~eLA~~l~l~~~tVt~~i~~Le~k--GlV~~~~~~~~~i~LTeeG~~~~~ 71 (489)
T PRK04172 7 NEKKVLKALKELK-EATLEELAEKLGLPPEAVMRAAEWLEEK--GLVKVEERVEEVYVLTEEGKKYAE 71 (489)
T ss_pred HHHHHHHHHHhCC-CCCHHHHHHHhCcCHHHHHHHHHHHHhC--CCEEEEeeeEEEEEECHHHHHHHH
Confidence 4578899998766 6999999999999999999999999998 677776654444444444344443
No 151
>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=34.03 E-value=33 Score=23.47 Aligned_cols=32 Identities=13% Similarity=0.225 Sum_probs=20.5
Q ss_pred HHHHHHHcCCceehhhhhhhcCCCHHHHHHHH
Q 023574 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (280)
Q Consensus 87 im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL 118 (280)
+.++++-+....|+.|||...|++.....+-|
T Consensus 11 ~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 11 IEEIKELYAEGMSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHHHHTT--HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 33444444444999999999999998886654
No 152
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=33.72 E-value=1.6e+02 Score=26.44 Aligned_cols=57 Identities=9% Similarity=0.105 Sum_probs=36.5
Q ss_pred CCCCchHHHHHHHHHHHcCCceehhhhhhhcC-----------CC---HHHHHHHHHHHHhhcCCceEecc
Q 023574 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------LK---LNEAQKALQALAADTDGFLEVSD 133 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aG-----------L~---L~~Ae~aL~aLAsD~~GhLqVse 133 (280)
.++..+.|+||+++++++||+.-..--+.+++ ++ ..+.-+++..-|.+.|-++.+..
T Consensus 30 ~~vs~~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~ 100 (331)
T PRK14987 30 EQVSVALRGKIAAALDELGYIPNRAPDILSNATSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQTMLAH 100 (331)
T ss_pred CCCCHHHHHHHHHHHHHhCCCccHHHHHHhhCCCCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEEEEec
Confidence 46788999999999999999753321111111 11 34455667777777776766543
No 153
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=33.63 E-value=1.9e+02 Score=26.63 Aligned_cols=44 Identities=20% Similarity=0.245 Sum_probs=32.4
Q ss_pred CCCchHHHHH---HH----HHHHcCCceehhhhhhhcCCCHHHHHHHHHHH
Q 023574 78 KLPADVRNRA---MD----AVDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (280)
Q Consensus 78 ~l~~~~~~~i---m~----Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aL 121 (280)
++|...++.+ .+ .-.++|...|..|||...|++.++.++.+.+.
T Consensus 117 r~Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~ 167 (264)
T PRK07122 117 KVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAG 167 (264)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 4666655433 22 23467888999999999999999998877653
No 154
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=33.43 E-value=1.7e+02 Score=20.50 Aligned_cols=58 Identities=19% Similarity=0.316 Sum_probs=43.5
Q ss_pred CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEE
Q 023574 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (280)
Q Consensus 80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYv 140 (280)
....+.+|+..+.+. ...|+.+++...+++...+...|..|-... -++...+|...|.
T Consensus 23 ~~~~r~~il~~l~~~-~~~~~~~l~~~~~~~~~~v~~hL~~L~~~g--lv~~~~~~~~~~~ 80 (110)
T COG0640 23 ADPTRLEILSLLAEG-GELTVGELAEALGLSQSTVSHHLKVLREAG--LVELRREGRLRLY 80 (110)
T ss_pred CCHHHHHHHHHHHhc-CCccHHHHHHHHCCChhHHHHHHHHHHHCC--CeEEEecccEEEE
Confidence 344778888888887 778999999999999999999998876553 3333555555443
No 155
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=33.35 E-value=76 Score=21.51 Aligned_cols=37 Identities=11% Similarity=0.241 Sum_probs=27.2
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHH
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQA 120 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~a 120 (280)
..+...|++.+... .|+.|||...|++-+.++.-+..
T Consensus 14 ~~~~~~i~~~~~~~---~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 14 KRLEQYILKLLRES---RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHHHhhc---CCHHHHHHHHCCCHHHHHHHHHh
Confidence 34445555554443 79999999999999999877654
No 156
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=33.31 E-value=30 Score=30.90 Aligned_cols=46 Identities=26% Similarity=0.299 Sum_probs=31.1
Q ss_pred eehhhhhhhcCCCHHHHHHHH--------------HHHHhhcCC-------ceEeccCCcEEEEcCc
Q 023574 98 VTIGDVAGKAGLKLNEAQKAL--------------QALAADTDG-------FLEVSDEGDVLYVFPN 143 (280)
Q Consensus 98 vTvGDVAa~aGL~L~~Ae~aL--------------~aLAsD~~G-------hLqVsesGEIlYvFP~ 143 (280)
+|+.|||..||+|...+-+.| .+.|.+.|= .|.-.+++-|..++|.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvv~~~ 68 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNGNPNVKPATRKKVLEVIKRLDYRPNAVARGLASKRTTTVGVIIPD 68 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHhhCCCCEEEEEeCC
Confidence 689999999999998887776 334444321 2333456777777774
No 157
>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=33.09 E-value=74 Score=22.88 Aligned_cols=28 Identities=18% Similarity=0.318 Sum_probs=25.5
Q ss_pred ceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 97 RVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 97 RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
.+|..|+|..+|++...+.+.|..|..+
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~ 55 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDE 55 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3578899999999999999999999887
No 158
>PF11772 EpuA: DNA-directed RNA polymerase subunit beta; InterPro: IPR024596 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 entry represents the short 60-residue long bacterial family that is the beta subunit of the DNA-directed RNA polymerase, likely to be 2.7.7.6 from EC It is membrane-bound and is referred to by the name EpuA.
Probab=32.89 E-value=19 Score=26.08 Aligned_cols=19 Identities=26% Similarity=0.746 Sum_probs=16.8
Q ss_pred ccCCCCCCCchHHHHHHHh
Q 023574 258 VFGEGDPNQGIEEKRWKLV 276 (280)
Q Consensus 258 vFGDGDPN~~lEerRWq~i 276 (280)
|.|||||-+=++.+-||.|
T Consensus 22 viG~G~p~~vf~~~tW~hi 40 (47)
T PF11772_consen 22 VIGDGNPFDVFSPDTWQHI 40 (47)
T ss_pred eeCCCCHHHhCCHHHHHHH
Confidence 4799999999999999976
No 159
>PF05055 DUF677: Protein of unknown function (DUF677); InterPro: IPR007749 This entry contains proteins belonging to the UPF0496 family, found in plants. This family includes AT14A like proteins from Arabidopsis thaliana. At14a contains a small domain that has sequence similarities to integrins from fungi, insects and humans. Transcripts of At14a are found in all Arabidopsis tissues and the protein localises partly to the plasma membrane [].
Probab=32.56 E-value=1.3e+02 Score=29.48 Aligned_cols=51 Identities=20% Similarity=0.216 Sum_probs=27.3
Q ss_pred cCcchHHHHhh-hhHHHhHHHHHHHhh----------hhhhhHhhHHHHHHHHHHHHHHHHH
Q 023574 141 FPNNYRAKLAA-KSFRLKVEPVIDKAK----------AAAEYSIRVLFGTALIASIVIVFTA 191 (280)
Q Consensus 141 FP~~fRs~l~~-Ks~r~rl~~~~~k~w----------~v~~yliRisFGi~LIaSivLv~~a 191 (280)
|+.+|+.+-.. .++..+|+.-.+|+- ++.-.++=++|..++|+|+|+..++
T Consensus 144 ~~~~F~~i~~~~~~Ll~kL~~~k~Kl~kklk~~r~~~kvs~v~fvaa~~aV~i~svv~aa~a 205 (336)
T PF05055_consen 144 FFHQFQSIHDQQSSLLEKLDSRKKKLRKKLKLVRTWRKVSNVCFVAAFVAVAIASVVAAAHA 205 (336)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHh
Confidence 78899988655 334444443333322 2333334445666666666666553
No 160
>PHA02673 ORF109 EEV glycoprotein; Provisional
Probab=32.34 E-value=85 Score=28.29 Aligned_cols=27 Identities=15% Similarity=0.293 Sum_probs=17.5
Q ss_pred hhhhhhHhhHHHHHHHHHHHHHHHHHHH
Q 023574 166 KAAAEYSIRVLFGTALIASIVIVFTAII 193 (280)
Q Consensus 166 w~v~~yliRisFGi~LIaSivLv~~aIi 193 (280)
-+.+..++||+..|.+| |.+++.++++
T Consensus 29 ~R~i~l~~Ri~~~iSIi-sL~~l~v~La 55 (161)
T PHA02673 29 RRYIKLFFRLMAAIAII-VLAILVVILA 55 (161)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHHHHHH
Confidence 45667789999888877 4444444443
No 161
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=32.17 E-value=49 Score=26.22 Aligned_cols=33 Identities=21% Similarity=0.307 Sum_probs=25.8
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHH
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL 118 (280)
+..|+-++++.| .|+.++|.+.||+-+....+|
T Consensus 4 ~adI~AaL~krG--~sL~~lsr~~Gl~~~tl~nal 36 (78)
T PF13693_consen 4 RADIKAALRKRG--TSLAALSREAGLSSSTLRNAL 36 (78)
T ss_dssp HHHHHHHHCTTS----HHHHHHHHSS-HHHHHHTT
T ss_pred HHHHHHHHHHcC--CCHHHHHHHcCCCHHHHHHHH
Confidence 356788888877 799999999999999998887
No 162
>PRK00441 argR arginine repressor; Provisional
Probab=32.16 E-value=1.7e+02 Score=25.37 Aligned_cols=56 Identities=13% Similarity=0.295 Sum_probs=40.9
Q ss_pred HHHHHHHHHHcCCceehhhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEe-ccCCcEEEEcCcch
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEV-SDEGDVLYVFPNNY 145 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~a-----GL~L~~Ae~aL~aLAsD~~GhLqV-sesGEIlYvFP~~f 145 (280)
+..|.+.+++ ....|+.|++..- +.+-..+.+.|.+| |-.+| +++|.-.|..|..-
T Consensus 6 ~~~I~~ll~~-~~~~~q~eL~~~L~~~G~~vSqaTisRDl~~L-----~lvKv~~~~G~~~Y~l~~~~ 67 (149)
T PRK00441 6 HAKILEIINS-KEIETQEELAEELKKMGFDVTQATVSRDIKEL-----KLIKVLSNDGKYKYATISKT 67 (149)
T ss_pred HHHHHHHHHH-cCCCcHHHHHHHHHhcCCCcCHHHHHHHHHHc-----CcEEeECCCCCEEEEeCccc
Confidence 4455665655 5667999998874 56777778888877 44677 46899999998754
No 163
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=31.97 E-value=1.1e+02 Score=24.85 Aligned_cols=51 Identities=14% Similarity=0.261 Sum_probs=42.5
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc---CCceEecc
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT---DGFLEVSD 133 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~---~GhLqVse 133 (280)
+...+|++.+++.+. .+..++|.+-|+|...+.+-+..|-.+. +=+..|+.
T Consensus 8 ~~D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~ 61 (154)
T COG1522 8 DIDRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDP 61 (154)
T ss_pred HHHHHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECH
Confidence 456788888887666 9999999999999999999999999885 55666664
No 164
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=31.85 E-value=2.4e+02 Score=25.08 Aligned_cols=28 Identities=14% Similarity=0.242 Sum_probs=24.4
Q ss_pred HHcCCceehhhhhhhcCCCHHHHHHHHH
Q 023574 92 DACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (280)
Q Consensus 92 e~lg~RvTvGDVAa~aGL~L~~Ae~aL~ 119 (280)
.++|...|+.+||.+.|++.+++++.+.
T Consensus 98 ~~~g~~pt~~eia~~l~~~~~~v~~~~~ 125 (238)
T TIGR02393 98 QELGREPTDEELAERMGMPAEKVREIKK 125 (238)
T ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3568999999999999999999987654
No 165
>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=31.65 E-value=1e+02 Score=23.30 Aligned_cols=44 Identities=23% Similarity=0.287 Sum_probs=31.3
Q ss_pred HHHHHHHcCC--ceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEec
Q 023574 87 AMDAVDACNR--RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (280)
Q Consensus 87 im~Ave~lg~--RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVs 132 (280)
+|-.+...+. .+|+.|+|.+.|++...+++-|..|... |-++..
T Consensus 13 ~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~--Gli~s~ 58 (83)
T PF02082_consen 13 ILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA--GLIESS 58 (83)
T ss_dssp HHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT--TSEEEE
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC--CeeEec
Confidence 4444444433 3999999999999999999999999874 334443
No 166
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=31.55 E-value=1.8e+02 Score=26.15 Aligned_cols=54 Identities=13% Similarity=0.101 Sum_probs=34.5
Q ss_pred CCCCchHHHHHHHHHHHcCCceehhhhhhhcC-----------C---CHHHHHHHHHHHHhhcCCceE
Q 023574 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------L---KLNEAQKALQALAADTDGFLE 130 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aG-----------L---~L~~Ae~aL~aLAsD~~GhLq 130 (280)
.++..+.+++|+++++++||.....--+.+++ + --.+..+++..-|.+.|-.+-
T Consensus 31 ~~vs~~tr~~V~~~a~elgY~p~~~a~~l~~~~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~ 98 (342)
T PRK10014 31 GRISTATGERVNQAIEELGFVRNRQASALRGGQSGVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVF 98 (342)
T ss_pred CCCCHHHHHHHHHHHHHhCCCcCHHHHhhccCCCCEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEE
Confidence 46899999999999999999865432222222 1 123455666666666655443
No 167
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=31.46 E-value=99 Score=17.19 Aligned_cols=34 Identities=12% Similarity=0.219 Sum_probs=23.2
Q ss_pred CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHH
Q 023574 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQ 115 (280)
Q Consensus 79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae 115 (280)
++++.+..+++..+ .+ .|+.++|...|++...+.
T Consensus 6 ~~~~~~~~i~~~~~-~~--~s~~~ia~~~~is~~tv~ 39 (42)
T cd00569 6 LTPEQIEEARRLLA-AG--ESVAEIARRLGVSRSTLY 39 (42)
T ss_pred CCHHHHHHHHHHHH-cC--CCHHHHHHHHCCCHHHHH
Confidence 44555556666654 23 399999999999877654
No 168
>PF07245 Phlebovirus_G2: Phlebovirus glycoprotein G2; InterPro: IPR009878 This domain is found in several Phlebovirus glycoprotein G2 sequences. Members of the Bunyaviridae family acquire an envelope by budding through the lipid bilayer of the Golgi complex. The budding compartment is thought to be determined by the accumulation of the two heterodimeric membrane glycoproteins G1 and G2 in the Golgi [].
Probab=31.39 E-value=43 Score=34.62 Aligned_cols=16 Identities=25% Similarity=0.453 Sum_probs=12.2
Q ss_pred CCcEEEEcCcchHHHH
Q 023574 134 EGDVLYVFPNNYRAKL 149 (280)
Q Consensus 134 sGEIlYvFP~~fRs~l 149 (280)
+|.++|.-+.+-|...
T Consensus 421 ~G~L~~~~~f~~r~~~ 436 (507)
T PF07245_consen 421 KGTLIYLGPFDDRNYT 436 (507)
T ss_pred EEEEEecccccccccc
Confidence 5889999988776543
No 169
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=31.32 E-value=1.1e+02 Score=26.84 Aligned_cols=49 Identities=29% Similarity=0.375 Sum_probs=35.8
Q ss_pred HHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc---CCceEeccCCcEEEEc
Q 023574 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT---DGFLEVSDEGDVLYVF 141 (280)
Q Consensus 91 ve~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~---~GhLqVsesGEIlYvF 141 (280)
+=-.|.-+|+.++|...+ +.++++++|..|..++ +.-|++-+.|+- |.|
T Consensus 7 LF~s~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~-y~l 58 (159)
T PF04079_consen 7 LFASGEPVSIEELAEILG-SEDEVEEALEELQEEYNEEDRGLELVEVGGG-YRL 58 (159)
T ss_dssp HHH-SS-B-HHHHHHHCT--HHHHHHHHHHHHHHHHHCT-SEEEEEETTE-EEE
T ss_pred HHHcCCCCCHHHHHHHhC-CHHHHHHHHHHHHHHhccCCCCEEEEEECCE-EEE
Confidence 334566799999999999 9999999999999998 667888877654 444
No 170
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=31.32 E-value=52 Score=27.82 Aligned_cols=31 Identities=16% Similarity=0.251 Sum_probs=23.0
Q ss_pred HHHHHHH----HHHHcCC-ceehhhhhhhcCCCHHH
Q 023574 83 VRNRAMD----AVDACNR-RVTIGDVAGKAGLKLNE 113 (280)
Q Consensus 83 ~~~~im~----Ave~lg~-RvTvGDVAa~aGL~L~~ 113 (280)
.+.+|++ .+.+.|+ .+|+.|||..+|++...
T Consensus 12 ~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t 47 (213)
T PRK09975 12 TRQELIETAIAQFALRGVSNTTLNDIADAANVTRGA 47 (213)
T ss_pred HHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHH
Confidence 3455554 4567786 69999999999988654
No 171
>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=31.21 E-value=1.5e+02 Score=21.49 Aligned_cols=36 Identities=14% Similarity=0.211 Sum_probs=29.8
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh
Q 023574 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (280)
Q Consensus 86 ~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAs 123 (280)
+|++.+.. ...|+.++|.+-|++...+++.|..|-+
T Consensus 4 ~il~~L~~--~~~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 4 RLLALLAD--NPFSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HHHHHHHc--CCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56666553 3578999999999999999999999965
No 172
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=30.78 E-value=58 Score=25.65 Aligned_cols=48 Identities=21% Similarity=0.215 Sum_probs=32.7
Q ss_pred HcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCce-EeccCCcEEEEcCc
Q 023574 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFL-EVSDEGDVLYVFPN 143 (280)
Q Consensus 93 ~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhL-qVsesGEIlYvFP~ 143 (280)
......|++|+..+-|++..|+..-|+ .-....+ .+=++||-|.+||.
T Consensus 28 ~~~~~~tvkd~IEsLGVP~tEV~~i~v---NG~~v~~~~~~~~Gd~v~V~P~ 76 (81)
T PF14451_consen 28 PFDGGATVKDVIESLGVPHTEVGLILV---NGRPVDFDYRLKDGDRVAVYPV 76 (81)
T ss_pred ecCCCCcHHHHHHHcCCChHHeEEEEE---CCEECCCcccCCCCCEEEEEec
Confidence 567889999999999999999843221 0001111 23357999999985
No 173
>PF07070 Spo0M: SpoOM protein; InterPro: IPR009776 This family consists of several bacterial SpoOM proteins which are thought to control sporulation in Bacillus subtilis.Spo0M exerts certain negative effects on sporulation and its gene expression is controlled by sigmaH [].
Probab=30.57 E-value=58 Score=30.12 Aligned_cols=48 Identities=21% Similarity=0.308 Sum_probs=39.9
Q ss_pred eeeecccccccccCCCcccccCCCCchHHHHHHHHHHHcCCceehhhh
Q 023574 56 PVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDV 103 (280)
Q Consensus 56 ~~~~~~~~~~~~~~~~~~v~~~~l~~~~~~~im~Ave~lg~RvTvGDV 103 (280)
+-.+.++|...++-|+..=.-.=+|....+++++|++++|.+.--.|+
T Consensus 109 v~l~T~LdI~~avD~~D~D~i~V~P~p~~~~vl~A~~~LGF~~~~~d~ 156 (218)
T PF07070_consen 109 VWLRTGLDIAGAVDPGDLDPIEVEPLPAQQAVLDALERLGFRLRSADC 156 (218)
T ss_pred EEEEEEEEeCCCCCCCCceeEEEeCCHHHHHHHHHHHhcCceEEeeee
Confidence 446677787888888888777778999999999999999999876665
No 174
>cd00131 PAX Paired Box domain
Probab=30.30 E-value=1.2e+02 Score=25.22 Aligned_cols=44 Identities=16% Similarity=0.267 Sum_probs=37.7
Q ss_pred CCCCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh
Q 023574 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAs 123 (280)
--|+.+.|.+|+.+++. ..+..+||.+.|++...+.+-+.....
T Consensus 16 ~~lS~d~R~rIv~~~~~---G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 16 RPLPDSIRQRIVELAQS---GIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CcCCHHHHHHHHHHHHc---CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45888999999999872 479999999999999999888877665
No 175
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=30.28 E-value=35 Score=30.95 Aligned_cols=46 Identities=22% Similarity=0.243 Sum_probs=31.2
Q ss_pred eehhhhhhhcCCCHHHHHHHH--------------HHHHhhcC-------CceEeccCCcEEEEcCc
Q 023574 98 VTIGDVAGKAGLKLNEAQKAL--------------QALAADTD-------GFLEVSDEGDVLYVFPN 143 (280)
Q Consensus 98 vTvGDVAa~aGL~L~~Ae~aL--------------~aLAsD~~-------GhLqVsesGEIlYvFP~ 143 (280)
+|+.|||..||+|...+-+.| .+.|.+.| -.|.-..++-|-.++|.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~elgY~pn~~ar~l~~~~~~~Igvi~~~ 68 (343)
T PRK10727 2 ATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNANARALAQQSTETVGLVVGD 68 (343)
T ss_pred CCHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHhhhhCCCCeEEEEeCC
Confidence 599999999999998887777 23343322 13444456677777763
No 176
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=30.28 E-value=1.3e+02 Score=28.45 Aligned_cols=69 Identities=16% Similarity=0.223 Sum_probs=52.5
Q ss_pred ccccCCCCc----hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc--CCceEeccCCcEEEEc
Q 023574 73 IVESDKLPA----DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DGFLEVSDEGDVLYVF 141 (280)
Q Consensus 73 ~v~~~~l~~----~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~--~GhLqVsesGEIlYvF 141 (280)
...-+.||. ..-..|+++++..+...|.-++|...|+|--.|++=|.-|++-. .+.|+-..-|.+.|.+
T Consensus 145 ~~~~~~LPkGi~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~i~yG~vGRP~r~Y 219 (224)
T COG4565 145 EQPPDDLPKGLDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILEAEIHYGKVGRPERRY 219 (224)
T ss_pred ccCcccCCCCcCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeEEeeccccCCcceee
Confidence 444556663 33457788889888999999999999999999999999999875 3444444557776655
No 177
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=30.10 E-value=29 Score=31.24 Aligned_cols=22 Identities=32% Similarity=0.508 Sum_probs=19.8
Q ss_pred eehhhhhhhcCCCHHHHHHHHH
Q 023574 98 VTIGDVAGKAGLKLNEAQKALQ 119 (280)
Q Consensus 98 vTvGDVAa~aGL~L~~Ae~aL~ 119 (280)
+|+-|||..+|+|...+-++|.
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln 23 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLN 23 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhc
Confidence 6999999999999999988884
No 178
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=30.07 E-value=2.4e+02 Score=27.38 Aligned_cols=29 Identities=14% Similarity=0.249 Sum_probs=25.2
Q ss_pred HHHcCCceehhhhhhhcCCCHHHHHHHHH
Q 023574 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (280)
Q Consensus 91 ve~lg~RvTvGDVAa~aGL~L~~Ae~aL~ 119 (280)
.+++|...|+.+||...|++.+++++.+.
T Consensus 226 ~~~lgr~pt~~EiA~~l~~~~~~v~~~~~ 254 (367)
T PRK09210 226 LQELGREPTPEEIAEEMDMPPEKVREILK 254 (367)
T ss_pred HHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 35579999999999999999999977664
No 179
>PHA00738 putative HTH transcription regulator
Probab=29.99 E-value=2.2e+02 Score=24.14 Aligned_cols=58 Identities=19% Similarity=0.338 Sum_probs=46.6
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvF 141 (280)
...|.+|++.+.+ +...+++|++...+++...+-+=|..|-. -|-+++..+|--+|.-
T Consensus 11 dptRr~IL~lL~~-~e~~~V~eLae~l~lSQptVS~HLKvLre--AGLV~srK~Gr~vyY~ 68 (108)
T PHA00738 11 KILRRKILELIAE-NYILSASLISHTLLLSYTTVLRHLKILNE--QGYIELYKEGRTLYAK 68 (108)
T ss_pred CHHHHHHHHHHHH-cCCccHHHHHHhhCCCHHHHHHHHHHHHH--CCceEEEEECCEEEEE
Confidence 3567888988865 55699999999999999999888887743 5788888888877754
No 180
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=29.98 E-value=1.8e+02 Score=30.73 Aligned_cols=88 Identities=15% Similarity=0.132 Sum_probs=57.9
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc--CCceEeccCCcEEEEcCcc--hHHHHh-hhhHHHhHH
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DGFLEVSDEGDVLYVFPNN--YRAKLA-AKSFRLKVE 159 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~--~GhLqVsesGEIlYvFP~~--fRs~l~-~Ks~r~rl~ 159 (280)
.+++..+-+.|.--..-=++..+|++.+.++++|..|.+.. ..|+...-+|+++|..-.+ --.+|+ +|+-..--+
T Consensus 22 akV~~~Llr~G~lss~~~~~~~t~i~~~kVk~aL~sLiQh~~V~y~~~~~~~g~vt~Y~~~~~ei~hilry~r~~~i~~~ 101 (551)
T KOG2587|consen 22 AKVGEHLLRTGRLSSLRVIAKDTGISLDKVKKALVSLIQHNCVSYQVHTRNSGKVTTYEAQCSEILHILRYPRYIYITKT 101 (551)
T ss_pred HHHHHHHHHcCCcchhHHHHhhcCCChHHHHHHHHHHHHhcceEEEEecCCCCceEEEEehhhHHHHHHhcccceeeHHH
Confidence 46777777877666577788999999999999999999983 6666666679998765322 222333 233333344
Q ss_pred HHHHHhhhhhhhH
Q 023574 160 PVIDKAKAAAEYS 172 (280)
Q Consensus 160 ~~~~k~w~v~~yl 172 (280)
+.-+++..+..++
T Consensus 102 ~~~q~~~sIv~~L 114 (551)
T KOG2587|consen 102 LYSQTAESIVEEL 114 (551)
T ss_pred HhhhHHHHHHHHH
Confidence 4444454444444
No 181
>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=29.97 E-value=1.8e+02 Score=19.71 Aligned_cols=40 Identities=20% Similarity=0.334 Sum_probs=28.8
Q ss_pred CCCCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHH
Q 023574 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~ 119 (280)
+.||..-+.-|.... ....|..|||..-|++...+.+-+.
T Consensus 3 ~~L~~~er~vi~~~y---~~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 3 DQLPPREREVIRLRY---FEGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp CTS-HHHHHHHHHHH---TST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred hhCCHHHHHHHHHHh---cCCCCHHHHHHHHCCcHHHHHHHHH
Confidence 456666665554444 7788999999999999999976553
No 182
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=29.84 E-value=38 Score=30.78 Aligned_cols=21 Identities=38% Similarity=0.620 Sum_probs=18.9
Q ss_pred eehhhhhhhcCCCHHHHHHHH
Q 023574 98 VTIGDVAGKAGLKLNEAQKAL 118 (280)
Q Consensus 98 vTvGDVAa~aGL~L~~Ae~aL 118 (280)
+|+.|||..+|+|...+-++|
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvL 22 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVL 22 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHH
Confidence 699999999999999887777
No 183
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=29.79 E-value=45 Score=27.96 Aligned_cols=32 Identities=16% Similarity=0.256 Sum_probs=23.4
Q ss_pred hHHHHHH----HHHHHcCCc-eehhhhhhhcCCCHHH
Q 023574 82 DVRNRAM----DAVDACNRR-VTIGDVAGKAGLKLNE 113 (280)
Q Consensus 82 ~~~~~im----~Ave~lg~R-vTvGDVAa~aGL~L~~ 113 (280)
+.+.+|+ +.+.+.|+. +|+.|||.++|++...
T Consensus 8 ~~r~~Il~aA~~lf~e~G~~~~s~~~IA~~agvs~~~ 44 (202)
T TIGR03613 8 AKRKAILSAALDTFSRFGFHGTSLEQIAELAGVSKTN 44 (202)
T ss_pred HHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHH
Confidence 4455554 445667776 9999999999988653
No 184
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=29.44 E-value=96 Score=27.22 Aligned_cols=55 Identities=13% Similarity=0.027 Sum_probs=42.9
Q ss_pred CCchHHHHHHHHHHHcCCceehhhhhhhc--CCCHHHHHHHHHHHHhh------cCCceEecc
Q 023574 79 LPADVRNRAMDAVDACNRRVTIGDVAGKA--GLKLNEAQKALQALAAD------TDGFLEVSD 133 (280)
Q Consensus 79 l~~~~~~~im~Ave~lg~RvTvGDVAa~a--GL~L~~Ae~aL~aLAsD------~~GhLqVse 133 (280)
...-..+.|...++-.++..+++.+|... +++.++++++|..|..- .+|...+++
T Consensus 21 ~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~ 83 (171)
T PF14394_consen 21 YSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTD 83 (171)
T ss_pred HhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEEec
Confidence 34445677778888888888999999999 99999999999888753 344555554
No 185
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=29.37 E-value=71 Score=32.82 Aligned_cols=39 Identities=13% Similarity=0.288 Sum_probs=34.5
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHH
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALA 122 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLA 122 (280)
...|++.+.+....+|+.|++..||+..++.-.+|+.|-
T Consensus 361 ~~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l~ 399 (450)
T PLN00104 361 TRVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSLN 399 (450)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 467888888888899999999999999999988887763
No 186
>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=29.27 E-value=84 Score=22.79 Aligned_cols=27 Identities=11% Similarity=0.218 Sum_probs=22.0
Q ss_pred hHHHHHHHHHHHcC-CceehhhhhhhcC
Q 023574 82 DVRNRAMDAVDACN-RRVTIGDVAGKAG 108 (280)
Q Consensus 82 ~~~~~im~Ave~lg-~RvTvGDVAa~aG 108 (280)
++.-.|-+++.+.| .-+|+.|+|++..
T Consensus 6 aveLgI~dii~~~g~~~ls~~eia~~l~ 33 (51)
T PF08100_consen 6 AVELGIPDIIHNAGGGPLSLSEIAARLP 33 (51)
T ss_dssp HHHTTHHHHHHHHTTS-BEHHHHHHTST
T ss_pred HHHcCcHHHHHHcCCCCCCHHHHHHHcC
Confidence 45566788999998 9999999999887
No 187
>PRK05949 RNA polymerase sigma factor; Validated
Probab=29.14 E-value=2.3e+02 Score=27.17 Aligned_cols=29 Identities=17% Similarity=0.221 Sum_probs=25.1
Q ss_pred HHHcCCceehhhhhhhcCCCHHHHHHHHH
Q 023574 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (280)
Q Consensus 91 ve~lg~RvTvGDVAa~aGL~L~~Ae~aL~ 119 (280)
..++|...|+.++|...|++.++++..+.
T Consensus 188 ~~~lgr~pt~~eiA~~l~i~~~~v~~~~~ 216 (327)
T PRK05949 188 SQKLGRSATPAEIAKELELEPSQIREYLS 216 (327)
T ss_pred HHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 35679999999999999999999977654
No 188
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=28.87 E-value=2e+02 Score=25.76 Aligned_cols=56 Identities=18% Similarity=0.214 Sum_probs=36.8
Q ss_pred CCCchHHHHHHHHHHHcCCceehhhhhhhcC-----------C---CHHHHHHHHHHHHhhcCCceEecc
Q 023574 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------L---KLNEAQKALQALAADTDGFLEVSD 133 (280)
Q Consensus 78 ~l~~~~~~~im~Ave~lg~RvTvGDVAa~aG-----------L---~L~~Ae~aL~aLAsD~~GhLqVse 133 (280)
+++.+.+++|+++++++||.....--+.+++ + --.+..+++...|.+.|-++.+..
T Consensus 28 ~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~ 97 (327)
T TIGR02417 28 RISQETVERVMAVVREQGYQPNIHAASLRAGRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIAC 97 (327)
T ss_pred ccCHHHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEe
Confidence 5889999999999999999764332122222 1 124455667777777777776643
No 189
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=28.79 E-value=74 Score=30.16 Aligned_cols=44 Identities=23% Similarity=0.311 Sum_probs=33.0
Q ss_pred CCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEE
Q 023574 95 NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (280)
Q Consensus 95 g~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYv 140 (280)
.+.+|++|+|.+-.|+.+-.++.+..- .-|..++.--+|+++|.
T Consensus 128 ~G~vsi~eLa~~~~Lp~efl~~~li~~--~lg~~I~g~~d~~~lyT 171 (272)
T PF09743_consen 128 SGQVSISELAKQYDLPSEFLKEELISK--RLGKIIKGRLDGDVLYT 171 (272)
T ss_pred cCeEeHHHHHHhcCCcHHHHHHHHhhh--hcCcceeEEEeCCEEec
Confidence 378999999999999999887444332 45677777777886553
No 190
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=28.76 E-value=2.9e+02 Score=25.74 Aligned_cols=30 Identities=17% Similarity=0.206 Sum_probs=25.6
Q ss_pred HHcCCceehhhhhhhcCCCHHHHHHHHHHH
Q 023574 92 DACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (280)
Q Consensus 92 e~lg~RvTvGDVAa~aGL~L~~Ae~aL~aL 121 (280)
.++|...|..++|...|++.++.++.+...
T Consensus 172 ~~~~~~pt~~eia~~l~~~~~~v~~~~~~~ 201 (298)
T TIGR02997 172 QKLGRTPSEAEIAEALELEPEQVRELLQRA 201 (298)
T ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 457888999999999999999998876543
No 191
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=28.54 E-value=65 Score=30.55 Aligned_cols=42 Identities=24% Similarity=0.445 Sum_probs=34.0
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLq 130 (280)
++..+++++.+|.|-++=+...+|++.++|++.|. +.+|||+
T Consensus 247 ~~a~~~l~~~~~~vk~ai~~~~~~~~~~~a~~~l~----~~~~~~~ 288 (296)
T PRK12570 247 DEAKELLKESDNDVKLAILMILTGMDVEQARAALS----HADGFLR 288 (296)
T ss_pred HHHHHHHHHhCCccHHHHHHHHhCCCHHHHHHHHH----HcCChHH
Confidence 55678899999999999999999999999977664 4566664
No 192
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=28.39 E-value=1.2e+02 Score=19.67 Aligned_cols=45 Identities=13% Similarity=0.243 Sum_probs=31.8
Q ss_pred CCCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcC
Q 023574 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTD 126 (280)
Q Consensus 78 ~l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~ 126 (280)
.|+..-.. ++..+. ...+..|+|...|++...+.+-+..+-...+
T Consensus 3 ~l~~~e~~-i~~~~~---~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPRERE-VLRLLA---EGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHH-HHHHHH---cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 45554443 444432 3469999999999999999998887765544
No 193
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=28.32 E-value=2.4e+02 Score=26.84 Aligned_cols=31 Identities=23% Similarity=0.324 Sum_probs=26.4
Q ss_pred HHHcCCceehhhhhhhcCCCHHHHHHHHHHH
Q 023574 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (280)
Q Consensus 91 ve~lg~RvTvGDVAa~aGL~L~~Ae~aL~aL 121 (280)
..++|...|+.+||...|++.++++..+...
T Consensus 178 ~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~ 208 (317)
T PRK07405 178 SQQLGRAATIGELAEELELTPKQVREYLERA 208 (317)
T ss_pred HHHhCCCCCHHHHHHHhCcCHHHHHHHHHHc
Confidence 3567889999999999999999998877643
No 194
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=28.31 E-value=1.9e+02 Score=21.46 Aligned_cols=58 Identities=16% Similarity=0.227 Sum_probs=44.5
Q ss_pred cCCCCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 023574 76 SDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (280)
Q Consensus 76 ~~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse 133 (280)
.+.|...++.+.+..+-+.-.++++.++|...+++.+++|.-|..+..+.-=+-..+.
T Consensus 39 ~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~ 96 (105)
T PF01399_consen 39 VEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLISNGLIKAKIDQ 96 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEET
T ss_pred HHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHHCCCEEEEEEC
Confidence 3455666777888888888899999999999999999999999888777533333343
No 195
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=28.28 E-value=2.2e+02 Score=25.33 Aligned_cols=56 Identities=9% Similarity=-0.016 Sum_probs=36.8
Q ss_pred CCCCchHHHHHHHHHHHcCCceehhhhhhhcC--------------CCHHHHHHHHHHHHhhcCCceEec
Q 023574 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG--------------LKLNEAQKALQALAADTDGFLEVS 132 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aG--------------L~L~~Ae~aL~aLAsD~~GhLqVs 132 (280)
.++..+.++||+++++++||..-..--+.+++ .--.+..+++...+.+.|-++.+.
T Consensus 23 ~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~ 92 (327)
T PRK10423 23 RFVSEAITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPFYSELVRGVERSCFERGYSLVLC 92 (327)
T ss_pred CCCCHHHHHHHHHHHHHHCCCccHHHHHHhhCCCCeEEEEeCCCCCCcHHHHHHHHHHHHHHcCCEEEEE
Confidence 46889999999999999999753221111111 123455677777777777666553
No 196
>smart00351 PAX Paired Box domain.
Probab=28.18 E-value=1.6e+02 Score=24.21 Aligned_cols=48 Identities=19% Similarity=0.228 Sum_probs=38.5
Q ss_pred ccccCCCCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh
Q 023574 73 IVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (280)
Q Consensus 73 ~v~~~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAs 123 (280)
++-.-.++++.|.+|+.+++ . ..+..+||.+-|++...+.+-+.....
T Consensus 12 ~~~~~~~s~~~R~riv~~~~-~--G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 12 FVNGRPLPDEERQRIVELAQ-N--GVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred ecCCCCCCHHHHHHHHHHHH-c--CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34444599999999999987 3 358899999999999999888876543
No 197
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=28.07 E-value=41 Score=29.59 Aligned_cols=59 Identities=20% Similarity=0.377 Sum_probs=45.9
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC-CcEEEEc
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-GDVLYVF 141 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses-GEIlYvF 141 (280)
..++.+|+.--=+-|.+++..++|.+-|+|..-+++||..|++| |=|++..+ |-.|=.+
T Consensus 23 ~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~e--Glv~~~p~rG~~V~~~ 82 (230)
T COG1802 23 EELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAE--GLVEIEPNRGAFVAPL 82 (230)
T ss_pred HHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHC--CCeEecCCCCCeeCCC
Confidence 34555555555566999999999999999999999999999987 55666654 6665555
No 198
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=27.84 E-value=81 Score=26.73 Aligned_cols=58 Identities=21% Similarity=0.192 Sum_probs=38.3
Q ss_pred CCCCchHHHHHH-HHHHHcCCceehhhhhhhcCCCHHHHHHHHH-HHHhhcCCceEeccCCcEE
Q 023574 77 DKLPADVRNRAM-DAVDACNRRVTIGDVAGKAGLKLNEAQKALQ-ALAADTDGFLEVSDEGDVL 138 (280)
Q Consensus 77 ~~l~~~~~~~im-~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~-aLAsD~~GhLqVsesGEIl 138 (280)
++||+.-+.-+. ..++ ..+..|||...|++...++..|. ++..----.|-.+..||++
T Consensus 130 ~~L~~~~r~i~~l~~~~----g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~~~~~~~~~~ 189 (189)
T PRK06811 130 NDLEKLDREIFIRRYLL----GEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKLNISLGGEVI 189 (189)
T ss_pred HhCCHHHHHHHHHHHHc----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcccCcccCCccC
Confidence 456665554442 3333 47889999999999999988873 3333334566677777764
No 199
>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=27.79 E-value=1e+02 Score=22.36 Aligned_cols=33 Identities=21% Similarity=0.344 Sum_probs=23.6
Q ss_pred HHHHHHHHcCC-ceehhhhhhhcCCCHHHHHHHH
Q 023574 86 RAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKAL 118 (280)
Q Consensus 86 ~im~Ave~lg~-RvTvGDVAa~aGL~L~~Ae~aL 118 (280)
++++.++..|. +++-.++|...|++-.++++.|
T Consensus 16 r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 16 RYLEQLKEEGVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHcCCeeECHHHHHHHHCCCHHHhcccC
Confidence 34555555554 7888899999999999999987
No 200
>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=27.61 E-value=1.3e+02 Score=21.71 Aligned_cols=42 Identities=12% Similarity=0.188 Sum_probs=34.6
Q ss_pred HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcC
Q 023574 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTD 126 (280)
Q Consensus 84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~ 126 (280)
+-++++.+-+ ...+|+.|+|.+.|++--..+..+..|=...+
T Consensus 7 q~~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L~~~f~ 48 (59)
T PF08280_consen 7 QLKLLELLLK-NKWITLKELAKKLNISERTIKNDINELNEFFP 48 (59)
T ss_dssp HHHHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT--
T ss_pred HHHHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHHHHhh
Confidence 4567888888 89999999999999999999999998876653
No 201
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=27.60 E-value=1.9e+02 Score=25.76 Aligned_cols=55 Identities=18% Similarity=0.163 Sum_probs=34.3
Q ss_pred CCCchHHHHHHHHHHHcCCceehhhhhhhcC-----------C---CHHHHHHHHHHHHhhcCCceEec
Q 023574 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------L---KLNEAQKALQALAADTDGFLEVS 132 (280)
Q Consensus 78 ~l~~~~~~~im~Ave~lg~RvTvGDVAa~aG-----------L---~L~~Ae~aL~aLAsD~~GhLqVs 132 (280)
+++.+.+++|+++++++||+....--+.+++ + --.+.-+++..-|.+.|-++.+.
T Consensus 29 ~Vs~~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~ 97 (328)
T PRK11303 29 RVSDKTVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIA 97 (328)
T ss_pred CcCHHHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEE
Confidence 5889999999999999999764332222221 1 12333455666666666666553
No 202
>PHA01976 helix-turn-helix protein
Probab=27.47 E-value=1e+02 Score=21.74 Aligned_cols=32 Identities=13% Similarity=0.158 Sum_probs=23.7
Q ss_pred chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHH
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEA 114 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~A 114 (280)
|++-.++-++-++.| .|..|+|...|++....
T Consensus 1 m~~~~rl~~~R~~~g--lt~~~lA~~~gvs~~~v 32 (67)
T PHA01976 1 MSFAIQLIKARNARA--WSAPELSRRAGVRHSLI 32 (67)
T ss_pred CcHHHHHHHHHHHcC--CCHHHHHHHhCCCHHHH
Confidence 455667766666555 79999999999886554
No 203
>KOG0860 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.38 E-value=1.8e+02 Score=24.97 Aligned_cols=33 Identities=18% Similarity=0.228 Sum_probs=16.2
Q ss_pred hhHHHhHHHHHHHhhhhhhhHhhHHHHHHHHHHHHHHHHHH
Q 023574 152 KSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAI 192 (280)
Q Consensus 152 Ks~r~rl~~~~~k~w~v~~yliRisFGi~LIaSivLv~~aI 192 (280)
...+++=+-||+.+ |.-..+.+|+.|+|+++.|
T Consensus 79 ~A~klkrk~wWkn~--------Km~~il~~v~~i~l~iiii 111 (116)
T KOG0860|consen 79 TAVKLKRKMWWKNC--------KMRIILGLVIIILLVVIII 111 (116)
T ss_pred HHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHH
Confidence 34444445566554 4444555555444444433
No 204
>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=27.34 E-value=1.8e+02 Score=24.04 Aligned_cols=50 Identities=14% Similarity=0.173 Sum_probs=36.8
Q ss_pred chHHHHHHHHHH----HcC----------CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEec
Q 023574 81 ADVRNRAMDAVD----ACN----------RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (280)
Q Consensus 81 ~~~~~~im~Ave----~lg----------~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVs 132 (280)
.++++|+...+. +.| ..+|..|+|...|++...+-+.|..|..+ |-++++
T Consensus 113 ~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~--g~I~~~ 176 (193)
T TIGR03697 113 RDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKK--KLISIH 176 (193)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHC--CCEEec
Confidence 356677766653 222 35799999999999999999999999876 344443
No 205
>PRK09954 putative kinase; Provisional
Probab=27.27 E-value=1.2e+02 Score=28.58 Aligned_cols=50 Identities=4% Similarity=0.026 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc---CCceEecc
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT---DGFLEVSD 133 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~---~GhLqVse 133 (280)
...+|++.+++.+ ++|..|+|.+-|++...+.+-|..|-.+. +...++++
T Consensus 4 ~~~~il~~l~~~~-~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~ 56 (362)
T PRK09954 4 REKEILAILRRNP-LIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTE 56 (362)
T ss_pred HHHHHHHHHHHCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcC
Confidence 4467888888765 89999999999999999999999999863 44445544
No 206
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=27.14 E-value=1.7e+02 Score=25.57 Aligned_cols=49 Identities=16% Similarity=0.135 Sum_probs=38.2
Q ss_pred chHHHHHHHHHHHc----CCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023574 81 ADVRNRAMDAVDAC----NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (280)
Q Consensus 81 ~~~~~~im~Ave~l----g~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqV 131 (280)
.++++|+...+... ....|..|+|...|++.+.+-+.|..|..+ |-+++
T Consensus 149 ~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~--G~I~~ 201 (226)
T PRK10402 149 FPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQD--GYLKK 201 (226)
T ss_pred ChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHC--CCEEe
Confidence 36788888887653 233688999999999999999999999876 44444
No 207
>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=27.00 E-value=83 Score=21.06 Aligned_cols=27 Identities=26% Similarity=0.354 Sum_probs=21.5
Q ss_pred eehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 98 VTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 98 vTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
.|-.|+|...|++.+.+-+.|..|..+
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~ 29 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQ 29 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHc
Confidence 577899999999999999999888764
No 208
>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=26.79 E-value=1.1e+02 Score=23.26 Aligned_cols=33 Identities=21% Similarity=0.423 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHH
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQ 115 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae 115 (280)
-|..+-+.-...++..|+-|||.+-|++..+++
T Consensus 8 ~rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr 40 (60)
T PF10668_consen 8 NRDKAFEIYKESNGKIKLKDIAEKLGVSESTIR 40 (60)
T ss_pred CHHHHHHHHHHhCCCccHHHHHHHHCCCHHHHH
Confidence 466777777889999999999999999988875
No 209
>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=26.70 E-value=1.2e+02 Score=24.03 Aligned_cols=45 Identities=16% Similarity=0.167 Sum_probs=36.5
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEec
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVs 132 (280)
-.++.++...+ ..|+.|+|...|++...+-+.|..|..+ |-++-.
T Consensus 31 ~~iL~~l~~~~-~~t~~ela~~~~~~~~tvs~~l~~Le~~--GlI~r~ 75 (118)
T TIGR02337 31 WRILRILAEQG-SMEFTQLANQACILRPSLTGILARLERD--GLVTRL 75 (118)
T ss_pred HHHHHHHHHcC-CcCHHHHHHHhCCCchhHHHHHHHHHHC--CCEEec
Confidence 36788887754 6999999999999999999999999877 555543
No 210
>PF09753 Use1: Membrane fusion protein Use1; InterPro: IPR019150 This entry represents a family of proteins, approximately 300 residues in length, involved in vesicle transport. They have a single C-terminal transmembrane domain and a SNARE [soluble NSF (N-ethylmaleimide-sensitive fusion protein) attachment protein receptor] domain of approximately 60 residues. The SNARE domains are essential for membrane fusion and are conserved from yeasts to humans. Use1 is one of the three protein subunits that make up the SNARE complex and it is specifically required for Golgi-endoplasmic reticulum retrograde transport [].
Probab=26.70 E-value=1.3e+02 Score=27.49 Aligned_cols=16 Identities=13% Similarity=0.003 Sum_probs=10.3
Q ss_pred hhHHHhHHHHHHHhhh
Q 023574 152 KSFRLKVEPVIDKAKA 167 (280)
Q Consensus 152 Ks~r~rl~~~~~k~w~ 167 (280)
+.-..||++..++-|+
T Consensus 212 ~~~~~rl~~~~~~~~~ 227 (251)
T PF09753_consen 212 KRESKRLKEHSSKSWG 227 (251)
T ss_pred HHHHHHHHHHHHhccc
Confidence 3445567777777766
No 211
>PF13730 HTH_36: Helix-turn-helix domain
Probab=26.61 E-value=81 Score=21.62 Aligned_cols=26 Identities=19% Similarity=0.314 Sum_probs=23.6
Q ss_pred ehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 99 TIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 99 TvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
+...+|...|++.+.++++|..|...
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~ 52 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEK 52 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 67899999999999999999999764
No 212
>PF12263 DUF3611: Protein of unknown function (DUF3611); InterPro: IPR022051 This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 180 and 205 amino acids in length. There are two completely conserved residues (W and G) that may be functionally important.
Probab=26.57 E-value=1.2e+02 Score=27.52 Aligned_cols=38 Identities=18% Similarity=0.187 Sum_probs=28.5
Q ss_pred HHHHHHhhhhhhhHhhHHHHHHHHHHHHHHHHHHHHHH
Q 023574 159 EPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAIL 196 (280)
Q Consensus 159 ~~~~~k~w~v~~yliRisFGi~LIaSivLv~~aIiail 196 (280)
.+-.+++.+.+..+-+++|-+.|+..+|-..+.+++.+
T Consensus 4 ~~~~~~~a~~lr~~Gwi~FW~QlvLgvVs~~iL~F~~~ 41 (183)
T PF12263_consen 4 PPALQRIARALRRLGWIGFWIQLVLGVVSAVILLFANL 41 (183)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34456667777778899999999988887666666655
No 213
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=26.53 E-value=1.4e+02 Score=25.10 Aligned_cols=46 Identities=15% Similarity=0.177 Sum_probs=34.7
Q ss_pred CchHHHHHHHHHHHc----C---------CceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574 80 PADVRNRAMDAVDAC----N---------RRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (280)
Q Consensus 80 ~~~~~~~im~Ave~l----g---------~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~ 125 (280)
..+...|+...+..+ + .++|.-|+|...|++...+-+.|..|..+.
T Consensus 138 ~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~~g 196 (211)
T PRK11753 138 FLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLEDQG 196 (211)
T ss_pred hcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 345666776654321 1 268889999999999999999999998773
No 214
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=26.42 E-value=71 Score=27.15 Aligned_cols=28 Identities=18% Similarity=0.262 Sum_probs=21.7
Q ss_pred HHHHHHHHcCCc-eehhhhhhhcCCCHHH
Q 023574 86 RAMDAVDACNRR-VTIGDVAGKAGLKLNE 113 (280)
Q Consensus 86 ~im~Ave~lg~R-vTvGDVAa~aGL~L~~ 113 (280)
..++.+.+.|+. +|+.|||..+|++...
T Consensus 19 AA~~lf~e~G~~~~t~~~Ia~~agvs~~t 47 (215)
T PRK10668 19 AALRLFSQQGVSATSLADIAKAAGVTRGA 47 (215)
T ss_pred HHHHHHHHcCcccCCHHHHHHHhCCChHH
Confidence 345556788985 7899999999988654
No 215
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=26.34 E-value=3.1e+02 Score=23.27 Aligned_cols=64 Identities=11% Similarity=0.141 Sum_probs=45.1
Q ss_pred chHHHHHHHHHHHcCCceehhhhhh-----hcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcc
Q 023574 81 ADVRNRAMDAVDACNRRVTIGDVAG-----KAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~RvTvGDVAa-----~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~ 144 (280)
...|.+|++.+.+.+...|+-||=. .-++++.++=+.|..|+...==+--..++|...|..+..
T Consensus 20 T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y~~~~~ 88 (145)
T COG0735 20 TPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRYELNSE 88 (145)
T ss_pred CHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEEecCCC
Confidence 4567788999998888888887754 245889999999999876533333333356788876544
No 216
>PF07790 DUF1628: Protein of unknown function (DUF1628); InterPro: IPR012859 The sequences making up this family are derived from hypothetical proteins of unknown function expressed by various archaeal species. The region in question is approximately 160 residues long.
Probab=26.30 E-value=1.3e+02 Score=22.65 Aligned_cols=21 Identities=19% Similarity=0.572 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 023574 177 FGTALIASIVIVFTAIIAILS 197 (280)
Q Consensus 177 FGi~LIaSivLv~~aIiails 197 (280)
+|++|++.++++..++++...
T Consensus 7 iGviLliaitVilaavv~~~~ 27 (80)
T PF07790_consen 7 IGVILLIAITVILAAVVGAFV 27 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 689999999988888876653
No 217
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=26.14 E-value=49 Score=29.57 Aligned_cols=22 Identities=18% Similarity=0.348 Sum_probs=17.9
Q ss_pred eehhhhhhhcCCCHHHHHHHHH
Q 023574 98 VTIGDVAGKAGLKLNEAQKALQ 119 (280)
Q Consensus 98 vTvGDVAa~aGL~L~~Ae~aL~ 119 (280)
+|+.|||..+|+|...+-+.|.
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn 22 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVIN 22 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 3888999999999887777763
No 218
>PRK00215 LexA repressor; Validated
Probab=26.12 E-value=1.2e+02 Score=26.25 Aligned_cols=58 Identities=17% Similarity=0.291 Sum_probs=39.8
Q ss_pred HHHHHHHH----HHcCCceehhhhhhhcCC-CHHHHHHHHHHHHhhcCCceEeccC-CcEEEEcCc
Q 023574 84 RNRAMDAV----DACNRRVTIGDVAGKAGL-KLNEAQKALQALAADTDGFLEVSDE-GDVLYVFPN 143 (280)
Q Consensus 84 ~~~im~Av----e~lg~RvTvGDVAa~aGL-~L~~Ae~aL~aLAsD~~GhLqVses-GEIlYvFP~ 143 (280)
+..+++.+ ++.+...|+.|+|...|+ +...+.+-|..|..+ |.|+-..+ +..+-+.|.
T Consensus 6 q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~--g~i~~~~~~~r~~~l~~~ 69 (205)
T PRK00215 6 QQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERK--GFIRRDPGRSRAIEVAAP 69 (205)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC--CCEEeCCCCcceEEeccc
Confidence 44555555 456888999999999999 999999888888765 44544432 334444333
No 219
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=26.10 E-value=1.3e+02 Score=27.44 Aligned_cols=64 Identities=20% Similarity=0.429 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc--CCceEeccCCcEEEEcCcchHHHH
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DGFLEVSDEGDVLYVFPNNYRAKL 149 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~--~GhLqVsesGEIlYvFP~~fRs~l 149 (280)
+-...++.++. ..-|.+.|+|+.-||+..++-.-+..|-++. .|-+ ++.|--||+=|.-+.++.
T Consensus 100 lL~~Fi~yIK~-~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~--DdrGkfIyIs~eE~~~va 165 (188)
T PF09756_consen 100 LLQEFINYIKE-HKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVI--DDRGKFIYISEEEMEAVA 165 (188)
T ss_dssp HHHHHHHHHHH--SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE---TT--EEE----------
T ss_pred HHHHHHHHHHH-cceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeE--cCCCCeEEecHHHHHHHH
Confidence 55566677765 4678899999999999999999999999885 5554 778999999999888854
No 220
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=25.98 E-value=1.2e+02 Score=28.19 Aligned_cols=39 Identities=26% Similarity=0.428 Sum_probs=30.9
Q ss_pred HHHHHHHHH------cCCceehhhhh-hhcCCCHHHHHHHHHHHHh
Q 023574 85 NRAMDAVDA------CNRRVTIGDVA-GKAGLKLNEAQKALQALAA 123 (280)
Q Consensus 85 ~~im~Ave~------lg~RvTvGDVA-a~aGL~L~~Ae~aL~aLAs 123 (280)
|+..+.+++ +|+..|+.+++ ...|+++++.-++|.+++.
T Consensus 16 P~aa~VF~~~gIdfCcgg~~tLeeA~~~~~gld~~~ll~eLn~~~~ 61 (224)
T PRK13276 16 PKAADIFRSVGIDFCCGGQVSIEAASLEKKNVDLNELLQRLNDVEQ 61 (224)
T ss_pred ccHHHHHHHcCCCcCCCCChhHHHHHHHHcCCCHHHHHHHHHHHhh
Confidence 344445555 45678999999 9999999999999999963
No 221
>PRK09492 treR trehalose repressor; Provisional
Probab=25.82 E-value=2.5e+02 Score=24.95 Aligned_cols=23 Identities=9% Similarity=0.190 Sum_probs=20.4
Q ss_pred CCCCchHHHHHHHHHHHcCCcee
Q 023574 77 DKLPADVRNRAMDAVDACNRRVT 99 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvT 99 (280)
.++..+.+++|+++++++||...
T Consensus 29 ~~vs~~tr~rV~~~a~elgY~pn 51 (315)
T PRK09492 29 SGVSEETRERVEAVINQHGFSPS 51 (315)
T ss_pred CCCCHHHHHHHHHHHHHHCCCcC
Confidence 46889999999999999999764
No 222
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=25.80 E-value=1.8e+02 Score=27.52 Aligned_cols=65 Identities=22% Similarity=0.396 Sum_probs=46.8
Q ss_pred CCCCchHHH-HHHHHHHH---cCCceehhhhhhhcC-------CCHHHHHHHHHHHHhhcCCceEeccC-C-cEEEEcC
Q 023574 77 DKLPADVRN-RAMDAVDA---CNRRVTIGDVAGKAG-------LKLNEAQKALQALAADTDGFLEVSDE-G-DVLYVFP 142 (280)
Q Consensus 77 ~~l~~~~~~-~im~Ave~---lg~RvTvGDVAa~aG-------L~L~~Ae~aL~aLAsD~~GhLqVses-G-EIlYvFP 142 (280)
+.||+.+=- .+++..++ ....+++.|++...| |+-++..+.|..|+..+ |+++++++ | +.||.-.
T Consensus 196 ~~l~~~i~~YaL~~~~~~~~~~~~sis~~~L~~~~~sPGriF~L~~~~l~~~L~~l~~~~-g~i~~~~TaGl~qv~~~~ 273 (286)
T PF13182_consen 196 PNLPPEIFLYALLDFAERESPGRNSISFDELLNEPGSPGRIFKLDEESLAERLEQLEEIY-GFISWSDTAGLDQVYLKD 273 (286)
T ss_pred CCCCHHHHHHHHHHHHHHhCCCCcEEEHHHHhcCCCCcceEeccCHHHHHHHHHHHHhhc-CcEEEEEcCCCeEEEecc
Confidence 455554333 23454433 456678889987655 88999999999999999 99999998 5 4666654
No 223
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=25.40 E-value=1.5e+02 Score=26.64 Aligned_cols=57 Identities=12% Similarity=0.046 Sum_probs=37.3
Q ss_pred CCCCchHHHHHHHHHHHcCCceehh-------------hhhhh-cCCCHHHHHHHHHHHHhhcCCceEecc
Q 023574 77 DKLPADVRNRAMDAVDACNRRVTIG-------------DVAGK-AGLKLNEAQKALQALAADTDGFLEVSD 133 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvTvG-------------DVAa~-aGL~L~~Ae~aL~aLAsD~~GhLqVse 133 (280)
.+++.+.+++|+++++++||..-.. =+... ...--.+.-+++...|.+.|-++.+..
T Consensus 26 ~~vs~~tr~~V~~~a~elgY~pn~~a~~l~~~~~~~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~ 96 (341)
T PRK10703 26 RFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAPYFAEIIEAVEKNCYQKGYTLILCN 96 (341)
T ss_pred CCCCHHHHHHHHHHHHHHCCCcCHHHHHHhhCCCCeEEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEEe
Confidence 3688999999999999999986332 11111 112234555677777887776665543
No 224
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=25.11 E-value=4.6e+02 Score=22.80 Aligned_cols=50 Identities=20% Similarity=0.236 Sum_probs=37.7
Q ss_pred HcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC-CcEEEEcCcchH
Q 023574 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-GDVLYVFPNNYR 146 (280)
Q Consensus 93 ~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses-GEIlYvFP~~fR 146 (280)
+-|.+.+..++|.+-|+|-.-+++||..|.++ |-|++... | .|+-+-+..
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVREAL~~L~~e--GLV~~~~~~g--~~v~~~~~~ 80 (221)
T PRK11414 30 KPGARLITKNLAEQLGMSITPVREALLRLVSV--NALSVAPAQA--FTVPEVSKR 80 (221)
T ss_pred CCCCccCHHHHHHHHCCCchhHHHHHHHHHHC--CCEEecCCCc--eeecCCCHH
Confidence 34688888999999999999999999999864 55666554 4 455544433
No 225
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=25.11 E-value=79 Score=28.33 Aligned_cols=41 Identities=22% Similarity=0.323 Sum_probs=32.0
Q ss_pred HHHHHHHHHc------CCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574 85 NRAMDAVDAC------NRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (280)
Q Consensus 85 ~~im~Ave~l------g~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~ 125 (280)
|+..+.+.+. |+..|+.+++...|+++++.-++|.+++...
T Consensus 9 p~~~~vf~~~gid~cc~g~~~l~~a~~~~g~d~~~~l~~ln~~~~~~ 55 (216)
T TIGR03652 9 PRAARIFRKYGIDFCCGGNVSLAEACKEKGLDPDEILAELNALQQEP 55 (216)
T ss_pred ccHHHHHHHcCCCccCCCcchHHHHHHHcCCCHHHHHHHHHHHHhcc
Confidence 3444555554 4567999999999999999999999998543
No 226
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=25.09 E-value=1.5e+02 Score=30.15 Aligned_cols=72 Identities=17% Similarity=0.179 Sum_probs=57.8
Q ss_pred ccCCCc--ccccCCCCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh-cCCceEeccCCcEEEEc
Q 023574 67 GVGPGR--IVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD-TDGFLEVSDEGDVLYVF 141 (280)
Q Consensus 67 ~~~~~~--~v~~~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD-~~GhLqVsesGEIlYvF 141 (280)
-|-|.| -++.+.+..+.-..+|..+++..+ |-||-.-.-++.++-++.|.++.+- ..|-+-|+.+|.|+|.=
T Consensus 32 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g---v~~~~~~~~~~~e~e~~~L~aIL~sm~eGVi~vD~~G~I~~iN 106 (520)
T PRK10820 32 EIDPIGRIYLNFAELEFESFSSLMAEIRRIAG---VTDVRTVPFMPSEREHRALSALLEALPEPVLSIDMKGKVELAN 106 (520)
T ss_pred EEcCCCeEEEeCCCcChhhHHHHHHHHhcCCC---ccchhhhccChHHHHHHHHHHHHHhCCCcEEEECCCCeeeHhH
Confidence 444544 466777777777788888877777 7788888889999999999988877 58999999999998753
No 227
>PLN03239 histone acetyltransferase; Provisional
Probab=25.04 E-value=97 Score=30.96 Aligned_cols=59 Identities=17% Similarity=0.144 Sum_probs=39.9
Q ss_pred HHHHHHHHHHcC---CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHH
Q 023574 84 RNRAMDAVDACN---RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA 147 (280)
Q Consensus 84 ~~~im~Ave~lg---~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fRs 147 (280)
+.+|++.+.+.. ..+|+.|++..||+..++.-.+|..| |-|.....+.+|+.=+...+.
T Consensus 268 ~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l-----~~l~~~~g~~~i~~~~~~l~~ 329 (351)
T PLN03239 268 GSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQL-----GILKFINGIYFIAAEKGLLEE 329 (351)
T ss_pred HHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHC-----CcEEEECCeEEEEeCHHHHHH
Confidence 456777776653 46999999999999999998888766 344433334445544433333
No 228
>PF11268 DUF3071: Protein of unknown function (DUF3071); InterPro: IPR021421 Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=25.01 E-value=85 Score=28.09 Aligned_cols=33 Identities=21% Similarity=0.381 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHH
Q 023574 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQK 116 (280)
Q Consensus 82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~ 116 (280)
.++||-+++.=+.| .|+.|||..+|++++.++.
T Consensus 56 ~L~PReIQarIRaG--as~eeVA~~~G~~~~rV~r 88 (170)
T PF11268_consen 56 SLRPREIQARIRAG--ASAEEVAEEAGVPVERVRR 88 (170)
T ss_pred CCCHHHHHHHHHCC--CCHHHHHHHhCCCHHHhhh
Confidence 66788888877765 7999999999999998753
No 229
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=24.79 E-value=55 Score=26.84 Aligned_cols=27 Identities=22% Similarity=0.406 Sum_probs=20.1
Q ss_pred HHHHHHHcCC-ceehhhhhhhcCCCHHH
Q 023574 87 AMDAVDACNR-RVTIGDVAGKAGLKLNE 113 (280)
Q Consensus 87 im~Ave~lg~-RvTvGDVAa~aGL~L~~ 113 (280)
.++.+.+.|+ .+|+.|||..+|++...
T Consensus 17 A~~lf~~~G~~~~s~~~IA~~agvsk~~ 44 (189)
T TIGR03384 17 TIESIGERGSLDVTIAQIARRAGVSSGI 44 (189)
T ss_pred HHHHHHhcCcccCCHHHHHHHhCCCHHH
Confidence 3445566775 68899999999987643
No 230
>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=24.53 E-value=1.4e+02 Score=24.57 Aligned_cols=29 Identities=21% Similarity=0.398 Sum_probs=23.1
Q ss_pred CceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 96 RRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 96 ~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
..+|+.++|.+.+++....++-|..|...
T Consensus 24 ~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 24 GPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45888888888888888888888777654
No 231
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=24.51 E-value=62 Score=28.91 Aligned_cols=56 Identities=9% Similarity=0.111 Sum_probs=36.7
Q ss_pred CCCCchHHHHHHHHHHHcCCceehhhhhhhcC--------------CCHHHHHHHHHHHHhhcCCceEec
Q 023574 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG--------------LKLNEAQKALQALAADTDGFLEVS 132 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aG--------------L~L~~Ae~aL~aLAsD~~GhLqVs 132 (280)
.++..+.+++|++++|++||+.-..--+.+++ .=-.+..+++...|.+.|-++.+.
T Consensus 26 ~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~ 95 (329)
T TIGR01481 26 PNVKPATRKKVLEVIKRLDYRPNAVARGLASKRTTTVGVIIPDISNIYYAELARGIEDIATMYKYNIILS 95 (329)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCHHHHHHhhCCCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEE
Confidence 46889999999999999999764322121111 113344566677777777777653
No 232
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=24.37 E-value=62 Score=23.86 Aligned_cols=21 Identities=38% Similarity=0.452 Sum_probs=17.3
Q ss_pred eehhhhhhhcCCCHHHHHHHH
Q 023574 98 VTIGDVAGKAGLKLNEAQKAL 118 (280)
Q Consensus 98 vTvGDVAa~aGL~L~~Ae~aL 118 (280)
+|+.|+|.++|++...+-+.|
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~l 21 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVL 21 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 478899999999998886655
No 233
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=24.14 E-value=72 Score=25.54 Aligned_cols=57 Identities=11% Similarity=0.189 Sum_probs=46.5
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHH-----HhhcCCceEeccCCcEEEEc
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQAL-----AADTDGFLEVSDEGDVLYVF 141 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aL-----AsD~~GhLqVsesGEIlYvF 141 (280)
..+++.+++....--..++....|+++++-+..+..+ ....|..+..+++|.+-..|
T Consensus 19 ~dVl~Vl~~~~~~~~~~~l~~G~Gl~l~~le~~f~~F~I~A~v~~~g~~~~lN~~G~i~~~F 80 (89)
T PF05379_consen 19 QDVLAVLSRKCGEELLEELWSGEGLDLEDLEELFELFDICAHVNFGGETFVLNEEGRIKGSF 80 (89)
T ss_pred HHHHHHHHhccCHHHHHHHHcCCCcCHHHHHHHHHHcCeEEEEEECCEEEEECCCCcEEEEE
Confidence 4678888998888889999999999999998877543 33457788888999987666
No 234
>PRK10617 cytochrome c-type protein NapC; Provisional
Probab=24.09 E-value=1.5e+02 Score=27.16 Aligned_cols=21 Identities=29% Similarity=0.464 Sum_probs=17.9
Q ss_pred ehhhcccCCCCCCCchHHHHH
Q 023574 253 SVFSFVFGEGDPNQGIEEKRW 273 (280)
Q Consensus 253 sVFSFvFGDGDPN~~lEerRW 273 (280)
=||.++||+-|-.+++|++|.
T Consensus 109 dv~~~~~~~idt~ekfe~~r~ 129 (200)
T PRK10617 109 ELYGKIFGVIDTPQKFEAHRL 129 (200)
T ss_pred HHHHHhhcCCCChHHHHHhHH
Confidence 489999999888899998873
No 235
>PRK03837 transcriptional regulator NanR; Provisional
Probab=24.04 E-value=1.5e+02 Score=25.87 Aligned_cols=63 Identities=21% Similarity=0.314 Sum_probs=42.3
Q ss_pred CCchHHHHHHHHHHHc----CCce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcc
Q 023574 79 LPADVRNRAMDAVDAC----NRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (280)
Q Consensus 79 l~~~~~~~im~Ave~l----g~Rv-TvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~ 144 (280)
+...+-..|.+.+... |.+. +..|+|.+-|+|..-+++||..|.++ |-+++.. |-=.||-+.+
T Consensus 14 ~~~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~e--Glv~~~~-~~G~~V~~~~ 81 (241)
T PRK03837 14 LSEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRK--GLVQISH-GERARVSRPS 81 (241)
T ss_pred HHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEec-CCceeEecCC
Confidence 3334444444444443 5566 88999999999999999999999965 5566644 3334555433
No 236
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=23.76 E-value=3.6e+02 Score=25.97 Aligned_cols=42 Identities=17% Similarity=0.300 Sum_probs=31.2
Q ss_pred CCCchHHHHHH-------HHHHHcCCceehhhhhhhcCCCHHHHHHHHH
Q 023574 78 KLPADVRNRAM-------DAVDACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (280)
Q Consensus 78 ~l~~~~~~~im-------~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~ 119 (280)
+||......+- +.-.++|...|+.+||...|++.+++++.+.
T Consensus 163 rlP~~~~~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~ 211 (324)
T PRK07921 163 RLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLE 211 (324)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 57766654432 2234578999999999999999999987654
No 237
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=23.75 E-value=74 Score=30.94 Aligned_cols=75 Identities=19% Similarity=0.214 Sum_probs=51.9
Q ss_pred chHHHHHHHHHHHc--CCceehhhhhhhcCCCH--HHHHHHH--HHHHhhcCCceEeccCCcEEEEcCcchHHHHhhhhH
Q 023574 81 ADVRNRAMDAVDAC--NRRVTIGDVAGKAGLKL--NEAQKAL--QALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSF 154 (280)
Q Consensus 81 ~~~~~~im~Ave~l--g~RvTvGDVAa~aGL~L--~~Ae~aL--~aLAsD~~GhLqVsesGEIlYvFP~~fRs~l~~Ks~ 154 (280)
++.+.++.+++.+. |.-+|=||||...|-+. -.+-.|+ +.++-...+|=-|..+|.| .+|+.-+..|.+
T Consensus 269 t~f~~~v~~~l~~ip~G~~~tY~~~a~~~g~p~a~ravg~a~~~np~~~~iPchRvv~~~g~l-----~g~~~g~~~k~~ 343 (353)
T PRK15435 269 TAFQQQVWQALRTIPCGETVSYQQLANAIGKPKAVRAVASACAANKLAIVIPCHRVVRGDGAL-----SGYRWGVSRKAQ 343 (353)
T ss_pred CHHHHHHHHHHhcCCCCCcCcHHHHHHHhCCCChHHHHHHHHHhCCCCcccCCceeECCCCCc-----CCCCCcHHHHHH
Confidence 56889999999998 56677789999999764 2222333 2223345799999999998 345555555666
Q ss_pred HHhHHH
Q 023574 155 RLKVEP 160 (280)
Q Consensus 155 r~rl~~ 160 (280)
.+.+|.
T Consensus 344 Ll~~e~ 349 (353)
T PRK15435 344 LLRREA 349 (353)
T ss_pred HHHHhc
Confidence 666654
No 238
>cd02106 Band_7 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions. Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins. Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins. Prokaryotic HflK/C plays a role i
Probab=23.61 E-value=1.5e+02 Score=21.97 Aligned_cols=69 Identities=17% Similarity=0.136 Sum_probs=43.2
Q ss_pred CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHh
Q 023574 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLA 150 (280)
Q Consensus 80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fRs~l~ 150 (280)
..-+++.+..+++......++-++.....-=.+..+++|..-...+| +++..=+--=..+|.+++..+.
T Consensus 50 ~~~i~~~~~~~~~~~~~~~~~~~~~~~r~~i~~~v~~~l~~~~~~~G--i~i~~v~i~~i~~~~~~~~ai~ 118 (121)
T cd02106 50 EEALRQLAQSALRSVIGKMTLDELLEDRDEIAAEVREALQEDLDKYG--IEVVDVRIKDIDPPEEVQEAME 118 (121)
T ss_pred HHHHHHHHHHHHHHHHccccHHHHHhhHHHHHHHHHHHHHHHHHhcC--CEEEEEEEEecCCCHHHHHHHH
Confidence 45678888899999999999999954322111222333333333344 8887765555677888776553
No 239
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI 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 Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=23.54 E-value=3.1e+02 Score=24.52 Aligned_cols=56 Identities=13% Similarity=0.030 Sum_probs=35.2
Q ss_pred CCCCchHHHHHHHHHHHcCCceehhhhhhhcC--------------CCHHHHHHHHHHHHhhcCCceEec
Q 023574 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG--------------LKLNEAQKALQALAADTDGFLEVS 132 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aG--------------L~L~~Ae~aL~aLAsD~~GhLqVs 132 (280)
.++..+.+++|+++++++||.....=-+.+++ .--.+.-+++..-+.+.|-++-+.
T Consensus 26 ~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~ 95 (311)
T TIGR02405 26 PKVSIETRERVEQVIQQSGFVPSKSARAMRGGSDKVVAVIVSRLDSPSENLAVSGMLPVFYTAGYDPIIM 95 (311)
T ss_pred CCCCHHHHHHHHHHHHHHCCCcCHHHHHhhcCCCCEEEEEeCCcccccHHHHHHHHHHHHHHCCCeEEEe
Confidence 46889999999999999999764321111111 112334456666666677776654
No 240
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=23.48 E-value=1.5e+02 Score=24.13 Aligned_cols=40 Identities=10% Similarity=0.109 Sum_probs=34.8
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
-.++.++...++..|+.|+|...|++...+-+.+..|-.+
T Consensus 34 ~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~ 73 (144)
T PRK03573 34 WVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEK 73 (144)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHC
Confidence 3678888888778999999999999999998888888766
No 241
>PRK03887 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=23.30 E-value=83 Score=28.57 Aligned_cols=56 Identities=9% Similarity=0.082 Sum_probs=42.7
Q ss_pred chHHHHHHHHH-HHc--CCceehhhhhhhcCCCHHHHHHHHHH--HHhhcCCceEeccCCc
Q 023574 81 ADVRNRAMDAV-DAC--NRRVTIGDVAGKAGLKLNEAQKALQA--LAADTDGFLEVSDEGD 136 (280)
Q Consensus 81 ~~~~~~im~Av-e~l--g~RvTvGDVAa~aGL~L~~Ae~aL~a--LAsD~~GhLqVsesGE 136 (280)
++.+.++.+++ ++. |...|-||+|..+|.+...+-.+|.+ ++-...||==|+.+|.
T Consensus 91 T~Fq~rV~~~Lv~~IP~G~v~TYgqIA~~~G~aaRAVG~Al~~NP~~i~IPCHRVV~s~G~ 151 (175)
T PRK03887 91 TPFERKVYEWLTKNVKRGEVITYGELAKALNTSPRAVGGAMKRNPYPIIVPCHRVVGRKNP 151 (175)
T ss_pred CHHHHHHHHHHHHhCCCCCCCcHHHHHHHHCchHHHHHHHHHhCCCCCccCCeeEECCCCC
Confidence 67889999965 445 88899999999999765555555533 3345789999999994
No 242
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=23.14 E-value=1.6e+02 Score=25.87 Aligned_cols=55 Identities=15% Similarity=0.227 Sum_probs=39.1
Q ss_pred hHHHHHHHHHHHc----CCce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc-CCcEE
Q 023574 82 DVRNRAMDAVDAC----NRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVL 138 (280)
Q Consensus 82 ~~~~~im~Ave~l----g~Rv-TvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse-sGEIl 138 (280)
.+-..|.+.+... |.+. |-.++|.+-|+|-..+++||..|.++ |-|++.. .|-.|
T Consensus 11 ~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~e--Glv~~~~g~G~~V 71 (239)
T PRK04984 11 FAEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARD--GWLTIQHGKPTKV 71 (239)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEeCCCeeEe
Confidence 3444455555443 6677 78899999999999999999999976 5566544 25443
No 243
>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=23.10 E-value=2.6e+02 Score=23.55 Aligned_cols=40 Identities=18% Similarity=0.256 Sum_probs=34.2
Q ss_pred eehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEE
Q 023574 98 VTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY 139 (280)
Q Consensus 98 vTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlY 139 (280)
.|..++|...+-++++++.||..|- --|=+|+.++|.+--
T Consensus 54 y~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~~ed~~i~i 93 (121)
T PF09681_consen 54 YTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEIDEDGVIYI 93 (121)
T ss_pred CcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEecCCeEEe
Confidence 5788899999999999999998887 368899999987744
No 244
>PRK08392 hypothetical protein; Provisional
Probab=22.93 E-value=82 Score=27.84 Aligned_cols=35 Identities=9% Similarity=-0.059 Sum_probs=25.7
Q ss_pred ccCCCcccccCCCCchHHHHHHHHHHHcCCceehh
Q 023574 67 GVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIG 101 (280)
Q Consensus 67 ~~~~~~~v~~~~l~~~~~~~im~Ave~lg~RvTvG 101 (280)
.++-|-.+|-+....-+.+.+++.+.+.|.++|+|
T Consensus 146 ~~~~g~~lEiNt~~~~p~~~~l~~~~~~G~~~~ig 180 (215)
T PRK08392 146 AEAYGKAFEISSRYRVPDLEFIRECIKRGIKLTFA 180 (215)
T ss_pred HHHhCCEEEEeCCCCCCCHHHHHHHHHcCCEEEEe
Confidence 34556666655444455678999999999999998
No 245
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=22.92 E-value=1.1e+02 Score=20.55 Aligned_cols=40 Identities=10% Similarity=0.218 Sum_probs=23.1
Q ss_pred CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHH
Q 023574 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALA 122 (280)
Q Consensus 80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLA 122 (280)
.+..|-.++..+.+ ..|+.+||..-|++...+.+=+....
T Consensus 3 ~~~~R~~ii~l~~~---G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 3 SEERRAQIIRLLRE---GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -------HHHHHHH---T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred chhHHHHHHHHHHC---CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 34556667777777 88999999999999999977665543
No 246
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=22.90 E-value=79 Score=27.20 Aligned_cols=31 Identities=23% Similarity=0.338 Sum_probs=22.6
Q ss_pred chHHHHHHHHH-----HHcCC-ceehhhhhhhcCCCH
Q 023574 81 ADVRNRAMDAV-----DACNR-RVTIGDVAGKAGLKL 111 (280)
Q Consensus 81 ~~~~~~im~Av-----e~lg~-RvTvGDVAa~aGL~L 111 (280)
...|++|+++. .+.|+ .+|+.|||.++|++.
T Consensus 10 ~~~R~~Il~aA~~~l~~~~G~~~~si~~IA~~Agvs~ 46 (203)
T PRK11202 10 EKTRRALIDAAFSQLSAERSFSSLSLREVAREAGIAP 46 (203)
T ss_pred HHHHHHHHHHHHHHHHhcCCcccCCHHHHHHHhCCCc
Confidence 35567777654 24465 789999999999764
No 247
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=22.68 E-value=62 Score=28.96 Aligned_cols=20 Identities=30% Similarity=0.423 Sum_probs=16.5
Q ss_pred ehhhhhhhcCCCHHHHHHHH
Q 023574 99 TIGDVAGKAGLKLNEAQKAL 118 (280)
Q Consensus 99 TvGDVAa~aGL~L~~Ae~aL 118 (280)
|+.|||..||+|...+-+.|
T Consensus 1 ti~dIA~~aGVS~~TVSrvL 20 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVI 20 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHH
Confidence 67899999998888777776
No 248
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=22.44 E-value=4.4e+02 Score=21.65 Aligned_cols=38 Identities=18% Similarity=0.231 Sum_probs=31.8
Q ss_pred HHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 023574 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (280)
Q Consensus 91 ve~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLq 130 (280)
+...++.+|+.|+|..-|++...+-..|..|..+ |-++
T Consensus 16 l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~--Gli~ 53 (142)
T PRK03902 16 LIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKD--EYLI 53 (142)
T ss_pred HHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHC--CCEE
Confidence 4445677899999999999999999999999887 5554
No 249
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=22.42 E-value=1.4e+02 Score=20.85 Aligned_cols=28 Identities=18% Similarity=0.204 Sum_probs=17.8
Q ss_pred HHHHHHHcCCceehhhhhhhcCCCHHHHHH
Q 023574 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQK 116 (280)
Q Consensus 87 im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~ 116 (280)
|-+.+++.|. |+.|+|.++|++..+..+
T Consensus 2 L~~~m~~~~i--t~~~La~~~gis~~tl~~ 29 (63)
T PF13443_consen 2 LKELMAERGI--TQKDLARKTGISRSTLSR 29 (63)
T ss_dssp HHHHHHHTT----HHHHHHHHT--HHHHHH
T ss_pred HHHHHHHcCC--CHHHHHHHHCcCHHHHHH
Confidence 4455666665 999999999998877644
No 250
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=22.26 E-value=73 Score=28.90 Aligned_cols=56 Identities=18% Similarity=0.144 Sum_probs=35.8
Q ss_pred CCCCchHHHHHHHHHHHcCCceehhhhhhhcC-----------C---CHHHHHHHHHHHHhhcCCceEec
Q 023574 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------L---KLNEAQKALQALAADTDGFLEVS 132 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aG-----------L---~L~~Ae~aL~aLAsD~~GhLqVs 132 (280)
.++..+.|+||+++++++||+.-..-=+.+++ + --.+.-+++...|.+.|-++.+.
T Consensus 26 ~~Vs~~tr~rV~~~a~elgY~pn~~ar~l~~~~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~~~~~ 95 (343)
T PRK10727 26 PKASEASRLAVHSAMESLSYHPNANARALAQQSTETVGLVVGDVSDPFFGAMVKAVEQVAYHTGNFLLIG 95 (343)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCHHHHhhhhCCCCeEEEEeCCCCcchHHHHHHHHHHHHHHcCCEEEEE
Confidence 36889999999999999999764321111111 1 12344566777777777666553
No 251
>TIGR02161 napC_nirT periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family. Nearly every member of this subfamily is NapC, a predicted membrane-anchored four-heme c-type cytochrome that forms one component of the periplasmic nitrate reductase along with NapA, NapB, NapD, NapE, and NapF subunits. A single known exception at this time is NirT, which is instead a component of a nitrite reductase. This family excludes TorC subunits of trimethylamine N-oxide (TMAO) reductases.
Probab=22.25 E-value=1.4e+02 Score=26.81 Aligned_cols=23 Identities=30% Similarity=0.557 Sum_probs=19.5
Q ss_pred ehhhcccCCCCCCCchHHHHHHH
Q 023574 253 SVFSFVFGEGDPNQGIEEKRWKL 275 (280)
Q Consensus 253 sVFSFvFGDGDPN~~lEerRWq~ 275 (280)
=||.++||+-|..+++||.|+++
T Consensus 100 dv~~~~~g~~~~~~k~~~~r~~~ 122 (185)
T TIGR02161 100 EVWGHLFGTIDTREKFEAHRLEL 122 (185)
T ss_pred HHHHhHccCCCCHHHHHHhHHHH
Confidence 48899999988888899988775
No 252
>PF00802 Glycoprotein_G: Pneumovirus attachment glycoprotein G; InterPro: IPR000925 This family includes attachment proteins from respiratory synctial virus. Glycoprotein G has not been shown to have any neuraminidase or haemagglutinin activity. The amino terminus is thought to be cytoplasmic, and the carboxyl terminus extracellular. The extracellular region contains four completely conserved cysteine residues.; GO: 0019062 virion attachment to host cell surface receptor, 0016020 membrane; PDB: 1BRV_A.
Probab=22.24 E-value=29 Score=33.22 Aligned_cols=16 Identities=13% Similarity=0.096 Sum_probs=0.0
Q ss_pred HHHHhhhhhhhHhhHH
Q 023574 161 VIDKAKAAAEYSIRVL 176 (280)
Q Consensus 161 ~~~k~w~v~~yliRis 176 (280)
-++++|..+-|+|=++
T Consensus 3 tl~~~w~~~~~~i~~~ 18 (263)
T PF00802_consen 3 TLEKTWDTLNHLIVIS 18 (263)
T ss_dssp ----------------
T ss_pred hHHHhHhhhcceehhh
Confidence 3678888888887654
No 253
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=22.15 E-value=2e+02 Score=25.32 Aligned_cols=44 Identities=18% Similarity=0.215 Sum_probs=34.3
Q ss_pred chHHHHHHHHHHHc----C------CceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 81 ADVRNRAMDAVDAC----N------RRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 81 ~~~~~~im~Ave~l----g------~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
.+++.|+.+.+.++ | -.+|..|+|...|++.+.+-+.|..|-.+
T Consensus 153 ~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 153 KTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 45667777766553 2 24688999999999999999999988765
No 254
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=21.97 E-value=1.7e+02 Score=25.65 Aligned_cols=73 Identities=25% Similarity=0.369 Sum_probs=54.0
Q ss_pred chHHHHHHHHHHHcCC--ceehhhhhhhcCCCHHHHHHHH-HHHHhh-----cCCceEeccCCcEEEEcCcchHHHHhhh
Q 023574 81 ADVRNRAMDAVDACNR--RVTIGDVAGKAGLKLNEAQKAL-QALAAD-----TDGFLEVSDEGDVLYVFPNNYRAKLAAK 152 (280)
Q Consensus 81 ~~~~~~im~Ave~lg~--RvTvGDVAa~aGL~L~~Ae~aL-~aLAsD-----~~GhLqVsesGEIlYvFP~~fRs~l~~K 152 (280)
.+.+.++.+++.+..+ ..|-+|+|.+.|.+ .|.+|. .|+.+- ..||==|..+|++ -+|+.-+.-|
T Consensus 87 t~Fq~~Vw~aL~~IP~Get~TY~eiA~~ig~p--~a~rAVG~A~~~NPl~IiIPCHRVig~~G~L-----~Gy~~G~~~K 159 (168)
T COG0350 87 TGFQGRVWQALREIPYGETVTYGEIARRLGRP--TAVRAVGNANGANPLPIIIPCHRVIGADGDL-----GGYAGGLERK 159 (168)
T ss_pred ChHHHHHHHHHhcCCCCCcEeHHHHHHHhCCC--cHHHHHHHHhccCCceEEecCeEeEcCCCCc-----cCccchHHHH
Confidence 5789999999998755 56778999999972 222222 344444 7899999999999 6777777777
Q ss_pred hHHHhHHH
Q 023574 153 SFRLKVEP 160 (280)
Q Consensus 153 s~r~rl~~ 160 (280)
.+.+++|.
T Consensus 160 ~~LL~~E~ 167 (168)
T COG0350 160 KWLLELEG 167 (168)
T ss_pred HHHHHhhc
Confidence 77776653
No 255
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=21.87 E-value=67 Score=21.73 Aligned_cols=16 Identities=38% Similarity=0.468 Sum_probs=13.0
Q ss_pred ehhhhhhhcCCCHHHH
Q 023574 99 TIGDVAGKAGLKLNEA 114 (280)
Q Consensus 99 TvGDVAa~aGL~L~~A 114 (280)
|+||||..+|++.+..
T Consensus 1 ti~e~A~~~gvs~~tl 16 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTL 16 (38)
T ss_dssp EHHHHHHHHTS-HHHH
T ss_pred CHHHHHHHHCCCHHHH
Confidence 7899999999998765
No 256
>PRK12702 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=21.80 E-value=1.2e+02 Score=29.58 Aligned_cols=28 Identities=25% Similarity=0.375 Sum_probs=22.7
Q ss_pred ceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 97 RVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 97 RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
..|+.+|+.-|||+.++|++|.+.-.++
T Consensus 123 d~t~~ei~~~TGL~~~~A~~A~~Re~SE 150 (302)
T PRK12702 123 DWTASELAAATGIPLEEAERAQKREYSE 150 (302)
T ss_pred hCCHHHHHHHhCcCHHHHHHHHhccCCc
Confidence 4689999999999999998887654433
No 257
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=21.67 E-value=90 Score=27.20 Aligned_cols=40 Identities=18% Similarity=0.366 Sum_probs=33.9
Q ss_pred cCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC-C
Q 023574 94 CNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-G 135 (280)
Q Consensus 94 lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses-G 135 (280)
-|.+++..++|.+-|+|..-+++||..|+++ |-+++... |
T Consensus 27 pG~~L~e~eLae~lgVSRtpVREAL~~L~~e--Glv~~~~~~G 67 (224)
T PRK11534 27 PDEKLRMSLLTSRYALGVGPLREALSQLVAE--RLVTVVNQKG 67 (224)
T ss_pred CCCcCCHHHHHHHHCCChHHHHHHHHHHHHC--CCEEEeCCCc
Confidence 3779999999999999999999999999965 66666553 5
No 258
>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=21.56 E-value=1.8e+02 Score=26.02 Aligned_cols=43 Identities=21% Similarity=0.381 Sum_probs=36.4
Q ss_pred CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
|+.+++..|.+-+.+.|. |+-.||.+-|+++.-+ .|++.|-..
T Consensus 17 lse~~r~~Iy~~~~~~~~--sv~~vS~~ygi~~~RV-~AIvrLkei 59 (172)
T PF12298_consen 17 LSEELREQIYEDVMQDGK--SVREVSQKYGIKIQRV-EAIVRLKEI 59 (172)
T ss_pred CCHHHHHHHHHHHHhCCC--CHHHHHHHhCCCHHHH-HHHHHHHHH
Confidence 678899999999988887 9999999999999999 566666543
No 259
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=21.51 E-value=1.8e+02 Score=20.08 Aligned_cols=35 Identities=14% Similarity=0.214 Sum_probs=23.6
Q ss_pred HHHHHHHHHcCC-ceehhhhhhhcCC-CHHHHHHHHH
Q 023574 85 NRAMDAVDACNR-RVTIGDVAGKAGL-KLNEAQKALQ 119 (280)
Q Consensus 85 ~~im~Ave~lg~-RvTvGDVAa~aGL-~L~~Ae~aL~ 119 (280)
.++.++++.+.. ..|+.|||...|+ +...-.+...
T Consensus 37 ~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk 73 (84)
T smart00342 37 RRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFK 73 (84)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 345555555444 5999999999999 7766555443
No 260
>KOG3830 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.39 E-value=96 Score=32.38 Aligned_cols=41 Identities=17% Similarity=0.336 Sum_probs=37.4
Q ss_pred CCCCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHH
Q 023574 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKA 117 (280)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~a 117 (280)
+++|.+-++-+.+.+.-...-.|+-|+|..+|+++.++=.-
T Consensus 283 ~~vP~d~np~l~~li~~~sp~~slqdma~~agisi~evf~L 323 (542)
T KOG3830|consen 283 KRVPLDQNPLLSSLIAIVSPNLSLQDMANRAGISISEVFIL 323 (542)
T ss_pred cCCCCccchHHHHHHHHhCccccHHHHhhhcCCCHHHHHHH
Confidence 47899999999999999999999999999999999998443
No 261
>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=21.29 E-value=93 Score=26.74 Aligned_cols=57 Identities=14% Similarity=0.272 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC-CcEEEEc
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-GDVLYVF 141 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses-GEIlYvF 141 (280)
++.+|+.--=+-|.+.+-.++|.+-|+|-.-+++||..|+++ |-|++... |-.|-.+
T Consensus 20 l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~e--Glv~~~~~~G~~V~~~ 77 (212)
T TIGR03338 20 IERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEA--GLVRNEKNRGVFVREI 77 (212)
T ss_pred HHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHC--CCEEEecCCCeEEecC
Confidence 333333333345888899999999999999999999999965 56776653 6544443
No 262
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=21.12 E-value=74 Score=28.66 Aligned_cols=23 Identities=4% Similarity=0.286 Sum_probs=20.4
Q ss_pred CCCchHHHHHHHHHHHcCCceeh
Q 023574 78 KLPADVRNRAMDAVDACNRRVTI 100 (280)
Q Consensus 78 ~l~~~~~~~im~Ave~lg~RvTv 100 (280)
++..+.+++|++++|++||+.-.
T Consensus 29 ~vs~~tr~rV~~~a~~lgY~pn~ 51 (327)
T PRK10339 29 NVKEETKHRILEIAEKLEYKTSS 51 (327)
T ss_pred CcCHHHHHHHHHHHHHhCCCCch
Confidence 48899999999999999997654
No 263
>PF13038 DUF3899: Domain of unknown function (DUF3899)
Probab=21.08 E-value=99 Score=23.93 Aligned_cols=32 Identities=19% Similarity=0.333 Sum_probs=17.2
Q ss_pred HHhhhhhhhHhhHHHHHHHHHHHHHHHHHHHH
Q 023574 163 DKAKAAAEYSIRVLFGTALIASIVIVFTAIIA 194 (280)
Q Consensus 163 ~k~w~v~~yliRisFGi~LIaSivLv~~aIia 194 (280)
.+-++--.+.+.-|.-..|+++++++.++|++
T Consensus 58 ~~~~~~~~~~~~~~~~~~ll~~~ll~l~~iil 89 (92)
T PF13038_consen 58 DKKLKKEKYRVSRWTYPLLLIGLLLILLSIIL 89 (92)
T ss_pred hHHHHHhhhHhHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444555555556666666666655554
No 264
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=20.92 E-value=3e+02 Score=24.79 Aligned_cols=44 Identities=18% Similarity=0.310 Sum_probs=32.0
Q ss_pred CCCchHHHHHHH-------HHHHcCCceehhhhhhhcCCCHHHHHHHHHHH
Q 023574 78 KLPADVRNRAMD-------AVDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (280)
Q Consensus 78 ~l~~~~~~~im~-------Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aL 121 (280)
++|...+....+ ...++|...|+.++|...|++.++..+.+...
T Consensus 113 rip~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~ 163 (258)
T PRK08215 113 RVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAI 163 (258)
T ss_pred EecHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhc
Confidence 556555443322 23467889999999999999999998877543
No 265
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=20.91 E-value=2.8e+02 Score=20.93 Aligned_cols=38 Identities=18% Similarity=0.318 Sum_probs=25.6
Q ss_pred CCceehhhhhhhcCCCHHHHHH------------HHHHHHhhcCCceEec
Q 023574 95 NRRVTIGDVAGKAGLKLNEAQK------------ALQALAADTDGFLEVS 132 (280)
Q Consensus 95 g~RvTvGDVAa~aGL~L~~Ae~------------aL~aLAsD~~GhLqVs 132 (280)
....|..|+|...|++-...-+ .|..++...|+++++.
T Consensus 29 ~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~~v~i~ 78 (80)
T PF13744_consen 29 ERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGGRVEIV 78 (80)
T ss_dssp CCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTEEEEEE
T ss_pred HcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCCeEEEe
Confidence 3568999999999988666533 3466777778888874
No 266
>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=20.90 E-value=2.5e+02 Score=21.74 Aligned_cols=34 Identities=12% Similarity=0.225 Sum_probs=28.2
Q ss_pred HHHHHHHHHcC-CceehhhhhhhcC-CCHHHHHHHH
Q 023574 85 NRAMDAVDACN-RRVTIGDVAGKAG-LKLNEAQKAL 118 (280)
Q Consensus 85 ~~im~Ave~lg-~RvTvGDVAa~aG-L~L~~Ae~aL 118 (280)
-.|++.+++.+ .-+|+.||....+ +.+..+...+
T Consensus 12 ~~aV~ymK~r~~~Plt~~EIl~~ls~~d~~~~~~~~ 47 (75)
T cd07977 12 AKIVDYMKKRHQHPLTLDEILDYLSLLDIGPKLKEW 47 (75)
T ss_pred HHHHHHHHhcCCCCccHHHHHHHHhccCccHHHHHH
Confidence 46788889999 9999999999999 8888765443
No 267
>PF13518 HTH_28: Helix-turn-helix domain
Probab=20.89 E-value=2.4e+02 Score=18.62 Aligned_cols=36 Identities=6% Similarity=0.140 Sum_probs=26.2
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh
Q 023574 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (280)
Q Consensus 85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAs 123 (280)
.+|++.+.+ |. |+.++|.+-|++..++..=+...-.
T Consensus 3 ~~iv~~~~~-g~--s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 3 LQIVELYLE-GE--SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHc-CC--CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 456666663 33 9999999999999888666554443
No 268
>TIGR02161 napC_nirT periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family. Nearly every member of this subfamily is NapC, a predicted membrane-anchored four-heme c-type cytochrome that forms one component of the periplasmic nitrate reductase along with NapA, NapB, NapD, NapE, and NapF subunits. A single known exception at this time is NirT, which is instead a component of a nitrite reductase. This family excludes TorC subunits of trimethylamine N-oxide (TMAO) reductases.
Probab=20.89 E-value=49 Score=29.73 Aligned_cols=12 Identities=33% Similarity=0.664 Sum_probs=6.2
Q ss_pred hHHHHHHHHHHH
Q 023574 174 RVLFGTALIASI 185 (280)
Q Consensus 174 RisFGi~LIaSi 185 (280)
++++|++|++.+
T Consensus 14 ~~~~~~ll~~g~ 25 (185)
T TIGR02161 14 RLALGTLLLGGF 25 (185)
T ss_pred HHHHHHHHHHHH
Confidence 345566555443
No 269
>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=20.66 E-value=2.3e+02 Score=17.75 Aligned_cols=26 Identities=12% Similarity=0.249 Sum_probs=21.5
Q ss_pred CceehhhhhhhcCCCHHHHHHHHHHH
Q 023574 96 RRVTIGDVAGKAGLKLNEAQKALQAL 121 (280)
Q Consensus 96 ~RvTvGDVAa~aGL~L~~Ae~aL~aL 121 (280)
...|..|||...|++.....+.+...
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 55799999999999999997776543
No 270
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=20.64 E-value=3.8e+02 Score=23.64 Aligned_cols=59 Identities=17% Similarity=0.259 Sum_probs=37.8
Q ss_pred CCCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcC
Q 023574 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFP 142 (280)
Q Consensus 78 ~l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP 142 (280)
.++... .++++.+++.|..+.+. ||=+...++.-+..|.-+..+.--|+.+|-+||...
T Consensus 20 ~i~~~~-~~ai~~l~~~G~~~~ia-----TGR~~~~~~~~~~~l~~~~~~~~~I~~NGa~i~~~~ 78 (270)
T PRK10513 20 TISPAV-KQAIAAARAKGVNVVLT-----TGRPYAGVHRYLKELHMEQPGDYCITNNGALVQKAA 78 (270)
T ss_pred ccCHHH-HHHHHHHHHCCCEEEEe-----cCCChHHHHHHHHHhCCCCCCCeEEEcCCeEEEECC
Confidence 355554 45566678889887764 898888887666655433222235777777777653
No 271
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=20.34 E-value=2.1e+02 Score=27.62 Aligned_cols=42 Identities=19% Similarity=0.366 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD 124 (280)
.+-+|+--+-...+++-+.|+|.+-|+++.-+-.-+..|..+
T Consensus 11 t~fqIL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~e 52 (260)
T COG1497 11 TRFQILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKE 52 (260)
T ss_pred hHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhc
Confidence 456777778888999999999999999999998888998876
No 272
>PF14493 HTH_40: Helix-turn-helix domain
Probab=20.32 E-value=1.5e+02 Score=22.91 Aligned_cols=80 Identities=15% Similarity=0.220 Sum_probs=49.9
Q ss_pred HHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHhhh---hHHHhHHHHHHHh
Q 023574 89 DAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAK---SFRLKVEPVIDKA 165 (280)
Q Consensus 89 ~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fRs~l~~K---s~r~rl~~~~~k~ 165 (280)
..++-.....|+.|||.+-||+.+..+.=|..++... -.+.+++ + +|......+..- .-..+++++.+.+
T Consensus 5 ~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g-~~~~~~~---~---l~~e~~~~I~~~~~~~~~~~lk~i~e~l 77 (91)
T PF14493_consen 5 ITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESG-EPLDIEE---L---LSEEEIKQIEDAIEKLGSEKLKPIKEAL 77 (91)
T ss_pred HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhC-CCCCHHH---h---CCHHHHHHHHHHHHHcCcccHHHHHHHC
Confidence 3444555679999999999999999999998888763 2344442 1 455544433221 1114677777776
Q ss_pred h-hhhhhHhhH
Q 023574 166 K-AAAEYSIRV 175 (280)
Q Consensus 166 w-~v~~yliRi 175 (280)
- .+-+.-+|+
T Consensus 78 ~~~~sy~~iRl 88 (91)
T PF14493_consen 78 PGDYSYFEIRL 88 (91)
T ss_pred CCCCCHHHHHH
Confidence 6 333344444
No 273
>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=20.28 E-value=3.1e+02 Score=20.78 Aligned_cols=53 Identities=11% Similarity=0.223 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC-cEEE
Q 023574 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG-DVLY 139 (280)
Q Consensus 83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesG-EIlY 139 (280)
.--.+++.+++.+.-+|+.|+...+.+.++..-..++. -.=.++++.+| --.|
T Consensus 6 ql~~~VeymK~r~~Plt~~eI~d~l~~d~~~~~~~~Lk----~npKI~~d~~~~~f~f 59 (65)
T PF02186_consen 6 QLAKAVEYMKKRDHPLTLEEILDYLSLDIGKKLKQWLK----NNPKIEYDPDGNTFSF 59 (65)
T ss_dssp HHHHHHHHHHHH-S-B-HHHHHHHHTSSS-HHHHHHHH----H-TTEEEE-TT-CEEE
T ss_pred HHHHHHHHHHhcCCCcCHHHHHHHHcCCCCHHHHHHHH----cCCCEEEecCCCEEEe
Confidence 34567888999999999999999999988766554444 55567888776 4444
No 274
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=20.22 E-value=87 Score=27.04 Aligned_cols=23 Identities=39% Similarity=0.497 Sum_probs=18.3
Q ss_pred eehhh---hhhhcCCCHHHHHHHHHH
Q 023574 98 VTIGD---VAGKAGLKLNEAQKALQA 120 (280)
Q Consensus 98 vTvGD---VAa~aGL~L~~Ae~aL~a 120 (280)
++-.| |+.|||.|-++|.+||.+
T Consensus 83 i~eeDIkLV~eQa~VsreeA~kAL~e 108 (122)
T COG1308 83 ISEEDIKLVMEQAGVSREEAIKALEE 108 (122)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 45555 456999999999999964
No 275
>PF11548 Receptor_IA-2: Protein-tyrosine phosphatase receptor IA-2; InterPro: IPR021613 IA-2 is a protein-tyrosine phosphatase receptor that upon exocytosis, the cytoplasmic domain is cleaved and moves to the nucleus where it enhances transcription of the insulin gene. The mature exodomain of IA-2 participates in adhesion to the extracellular matrix and is self-proteolyzed in vitro by reactive oxygen species which may be a new shedding mechanism. ; PDB: 2QT7_B 3N01_B 3N4W_B 3NG8_A.
Probab=20.06 E-value=39 Score=27.70 Aligned_cols=27 Identities=30% Similarity=0.268 Sum_probs=17.2
Q ss_pred HHcCCceehhhhhhhcCCCHHHHHHHH
Q 023574 92 DACNRRVTIGDVAGKAGLKLNEAQKAL 118 (280)
Q Consensus 92 e~lg~RvTvGDVAa~aGL~L~~Ae~aL 118 (280)
+...+.+|.+|||.+++...++-|+++
T Consensus 52 ~~N~~n~taadVa~~a~~~K~~Le~~t 78 (91)
T PF11548_consen 52 RPNNKNLTAADVAKQAVDNKNQLEKET 78 (91)
T ss_dssp ---TT---HHHHHHHHHHTHHHHHHHH
T ss_pred ccCcCCCCHHHHHHHHHHhHHHHHHhh
Confidence 345678999999999998877776654
Done!