Query 023862
Match_columns 276
No_of_seqs 73 out of 75
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 07:11:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023862.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023862hhsearch_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 95.5 0.034 7.4E-07 41.5 5.2 46 80-125 4-50 (68)
2 PRK13239 alkylmercury lyase; P 95.0 0.048 1E-06 49.7 5.7 53 81-139 21-73 (206)
3 COG3355 Predicted transcriptio 95.0 0.27 5.8E-06 42.0 9.7 86 85-172 30-118 (126)
4 PF09339 HTH_IclR: IclR helix- 94.7 0.043 9.3E-07 38.4 3.5 40 85-124 6-45 (52)
5 PF04703 FaeA: FaeA-like prote 94.0 0.11 2.4E-06 39.1 4.7 53 85-139 3-57 (62)
6 smart00346 HTH_ICLR helix_turn 93.9 0.48 1E-05 35.3 8.0 54 85-141 8-61 (91)
7 PF12324 HTH_15: Helix-turn-he 93.6 0.13 2.7E-06 40.8 4.5 50 83-138 25-74 (77)
8 PF13412 HTH_24: Winged helix- 93.6 0.21 4.5E-06 34.1 5.1 42 82-124 3-44 (48)
9 PRK06266 transcription initiat 93.5 0.58 1.3E-05 41.3 8.9 66 81-147 21-89 (178)
10 TIGR00373 conserved hypothetic 93.4 0.67 1.5E-05 40.0 9.0 78 86-166 18-98 (158)
11 PF12840 HTH_20: Helix-turn-he 93.3 0.26 5.5E-06 35.4 5.4 53 80-135 8-60 (61)
12 PF06163 DUF977: Bacterial pro 92.6 0.24 5.2E-06 42.5 5.1 51 81-134 11-61 (127)
13 cd00090 HTH_ARSR Arsenical Res 92.1 1.3 2.9E-05 30.2 7.5 60 79-142 4-64 (78)
14 PF08220 HTH_DeoR: DeoR-like h 92.1 0.43 9.3E-06 34.4 5.2 41 84-125 2-42 (57)
15 KOG3341 RNA polymerase II tran 91.9 0.45 9.8E-06 44.6 6.4 84 68-152 159-245 (249)
16 smart00418 HTH_ARSR helix_turn 91.9 0.54 1.2E-05 31.5 5.3 50 87-140 2-51 (66)
17 PF08279 HTH_11: HTH domain; 91.8 0.8 1.7E-05 31.7 6.2 46 84-130 2-47 (55)
18 smart00420 HTH_DEOR helix_turn 91.5 0.85 1.8E-05 30.1 5.8 47 84-133 2-48 (53)
19 PF08784 RPA_C: Replication pr 91.3 0.5 1.1E-05 37.0 5.3 45 81-125 46-93 (102)
20 TIGR02844 spore_III_D sporulat 90.2 0.4 8.7E-06 37.8 3.8 34 83-118 7-40 (80)
21 PF09743 DUF2042: Uncharacteri 90.2 0.75 1.6E-05 43.2 6.2 57 80-138 53-109 (272)
22 PF01978 TrmB: Sugar-specific 89.3 1.5 3.3E-05 31.8 6.0 53 84-139 10-62 (68)
23 PRK15466 carboxysome structura 88.4 1 2.3E-05 40.2 5.4 42 84-125 111-152 (166)
24 PF01726 LexA_DNA_bind: LexA D 88.0 1 2.2E-05 33.8 4.5 40 85-124 13-53 (65)
25 PF04539 Sigma70_r3: Sigma-70 87.7 0.78 1.7E-05 33.8 3.6 53 84-136 7-59 (78)
26 PF12802 MarR_2: MarR family; 87.6 1.9 4.1E-05 30.0 5.4 43 83-125 6-49 (62)
27 PF08221 HTH_9: RNA polymerase 86.4 2 4.2E-05 31.8 5.1 38 85-123 16-53 (62)
28 smart00088 PINT motif in prote 85.2 4.2 9.1E-05 30.4 6.5 68 80-147 7-74 (88)
29 smart00753 PAM PCI/PINT associ 85.2 4.2 9.1E-05 30.4 6.5 68 80-147 7-74 (88)
30 PRK10434 srlR DNA-bindng trans 84.3 6.8 0.00015 35.8 8.7 50 81-133 4-53 (256)
31 PRK09802 DNA-binding transcrip 84.2 3.2 6.9E-05 38.3 6.5 54 80-136 15-68 (269)
32 cd07377 WHTH_GntR Winged helix 84.1 2.5 5.5E-05 29.1 4.6 49 81-131 4-57 (66)
33 COG2512 Predicted membrane-ass 83.9 2 4.4E-05 40.2 5.2 46 78-124 192-237 (258)
34 cd07153 Fur_like Ferric uptake 83.2 5.4 0.00012 31.2 6.6 59 83-141 2-65 (116)
35 PF13404 HTH_AsnC-type: AsnC-t 82.6 3.3 7.2E-05 28.6 4.6 39 82-121 3-41 (42)
36 PRK04424 fatty acid biosynthes 82.5 2.5 5.3E-05 37.1 4.9 43 81-124 6-48 (185)
37 cd00092 HTH_CRP helix_turn_hel 82.4 8.1 0.00017 27.0 6.7 38 96-135 24-61 (67)
38 smart00345 HTH_GNTR helix_turn 82.2 2.5 5.4E-05 28.6 3.8 38 94-133 16-54 (60)
39 PF06969 HemN_C: HemN C-termin 82.1 4.2 9.1E-05 29.1 5.2 53 83-136 7-65 (66)
40 TIGR02702 SufR_cyano iron-sulf 81.5 2.8 6.1E-05 36.7 4.9 41 83-124 2-42 (203)
41 PHA02943 hypothetical protein; 81.4 11 0.00024 33.8 8.5 79 82-169 8-87 (165)
42 PF01022 HTH_5: Bacterial regu 80.2 4.6 9.9E-05 27.7 4.6 41 82-124 2-42 (47)
43 smart00344 HTH_ASNC helix_turn 79.5 4.4 9.6E-05 31.3 4.9 42 83-125 4-45 (108)
44 PRK12423 LexA repressor; Provi 79.3 5.7 0.00012 34.9 6.1 52 82-135 6-62 (202)
45 PRK10141 DNA-binding transcrip 78.5 18 0.00039 30.2 8.4 60 79-141 13-72 (117)
46 PRK00135 scpB segregation and 76.7 7.2 0.00016 34.9 6.0 59 82-141 4-66 (188)
47 COG1349 GlpR Transcriptional r 76.1 5.7 0.00012 36.4 5.3 57 80-137 3-65 (253)
48 COG2345 Predicted transcriptio 74.9 7.3 0.00016 36.0 5.7 66 75-141 4-71 (218)
49 PF00392 GntR: Bacterial regul 74.0 3.6 7.9E-05 29.6 2.9 41 85-125 7-52 (64)
50 PF02002 TFIIE_alpha: TFIIE al 73.9 12 0.00026 29.4 6.0 78 85-165 16-96 (105)
51 PRK13509 transcriptional repre 73.7 6.5 0.00014 35.8 5.0 43 81-124 4-46 (251)
52 PF04405 ScdA_N: Domain of Unk 73.7 3.5 7.7E-05 30.4 2.7 38 84-121 12-55 (56)
53 COG1675 TFA1 Transcription ini 73.1 23 0.0005 31.8 8.2 82 85-169 21-105 (176)
54 PF03965 Penicillinase_R: Peni 73.1 35 0.00076 27.2 8.6 79 82-167 3-85 (115)
55 PF13463 HTH_27: Winged helix 72.5 9.1 0.0002 26.9 4.6 44 83-126 4-47 (68)
56 PRK10906 DNA-binding transcrip 72.4 8 0.00017 35.4 5.3 42 82-124 5-46 (252)
57 TIGR02431 pcaR_pcaU beta-ketoa 72.2 5.8 0.00013 35.4 4.3 44 86-131 13-56 (248)
58 PRK10411 DNA-binding transcrip 72.0 38 0.00082 30.8 9.5 54 82-139 4-57 (240)
59 smart00347 HTH_MARR helix_turn 70.9 38 0.00083 24.7 9.1 48 84-134 12-59 (101)
60 PF04157 EAP30: EAP30/Vps36 fa 70.8 7.8 0.00017 34.7 4.8 43 82-124 174-217 (223)
61 PRK10681 DNA-binding transcrip 69.9 8.2 0.00018 35.1 4.8 42 81-123 6-47 (252)
62 PRK11569 transcriptional repre 69.6 7.6 0.00017 35.5 4.5 47 85-133 31-77 (274)
63 smart00419 HTH_CRP helix_turn_ 69.0 6.4 0.00014 25.8 3.0 35 96-132 7-41 (48)
64 PRK10163 DNA-binding transcrip 68.6 8.1 0.00017 35.3 4.5 48 85-134 28-75 (271)
65 PF10717 ODV-E18: Occlusion-de 68.5 8 0.00017 31.4 3.9 26 171-196 18-43 (85)
66 TIGR00498 lexA SOS regulatory 68.4 10 0.00022 32.7 4.9 47 82-130 6-57 (199)
67 PF00356 LacI: Bacterial regul 67.6 4.8 0.0001 28.5 2.2 21 99-119 1-21 (46)
68 PF01047 MarR: MarR family; I 67.3 18 0.00039 25.0 5.1 42 83-125 4-45 (59)
69 PRK09834 DNA-binding transcrip 66.1 10 0.00022 34.4 4.6 52 86-141 15-67 (263)
70 PF06224 HTH_42: Winged helix 65.0 19 0.00041 33.1 6.2 61 83-145 168-230 (327)
71 PF01325 Fe_dep_repress: Iron 65.0 18 0.00039 26.5 4.9 32 93-124 18-49 (60)
72 COG1414 IclR Transcriptional r 64.7 11 0.00023 34.3 4.5 47 85-133 7-53 (246)
73 PF14947 HTH_45: Winged helix- 63.9 13 0.00029 28.1 4.2 38 86-125 10-47 (77)
74 COG3695 Predicted methylated D 63.8 13 0.00029 31.1 4.5 60 81-140 5-70 (103)
75 PF03640 Lipoprotein_15: Secre 63.7 4.1 8.8E-05 29.1 1.3 22 124-145 6-27 (48)
76 PF00356 LacI: Bacterial regul 63.0 6.2 0.00013 27.9 2.1 22 77-98 24-45 (46)
77 PF03297 Ribosomal_S25: S25 ri 62.4 23 0.00049 29.4 5.6 59 81-140 44-102 (105)
78 PLN03083 E3 UFM1-protein ligas 62.3 15 0.00032 39.9 5.6 56 80-138 58-113 (803)
79 PF11625 DUF3253: Protein of u 62.1 23 0.00049 28.5 5.3 66 81-150 6-78 (83)
80 PRK10014 DNA-binding transcrip 62.1 5.7 0.00012 35.6 2.2 26 95-120 4-29 (342)
81 PF01475 FUR: Ferric uptake re 61.8 40 0.00087 26.8 6.8 62 82-143 8-74 (120)
82 PF01035 DNA_binding_1: 6-O-me 61.6 14 0.0003 28.7 4.1 57 82-138 2-64 (85)
83 PRK11014 transcriptional repre 61.6 12 0.00027 30.9 4.0 43 82-124 10-52 (141)
84 smart00531 TFIIE Transcription 61.2 58 0.0013 27.5 8.0 63 87-150 6-74 (147)
85 PRK09480 slmA division inhibit 61.2 9.2 0.0002 31.5 3.2 32 81-112 9-45 (194)
86 PRK09334 30S ribosomal protein 61.1 28 0.0006 28.1 5.7 61 79-140 24-84 (86)
87 COG1321 TroR Mn-dependent tran 61.0 17 0.00037 31.4 4.8 45 92-136 19-69 (154)
88 PRK05472 redox-sensing transcr 60.6 17 0.00036 32.0 4.8 41 81-121 15-56 (213)
89 PTZ00326 phenylalanyl-tRNA syn 60.3 44 0.00095 34.4 8.3 71 81-153 5-75 (494)
90 PF09012 FeoC: FeoC like trans 59.7 17 0.00037 26.7 4.0 37 89-125 6-42 (69)
91 cd06445 ATase The DNA repair p 59.4 19 0.00041 27.4 4.3 55 84-138 2-62 (79)
92 PF09105 SelB-wing_1: Elongati 59.1 38 0.00082 25.6 5.7 45 85-129 5-49 (61)
93 PF01316 Arg_repressor: Argini 58.9 35 0.00077 26.2 5.7 46 83-144 21-67 (70)
94 COG1609 PurR Transcriptional r 58.7 34 0.00073 32.1 6.8 59 78-136 26-98 (333)
95 PRK11179 DNA-binding transcrip 58.6 23 0.00049 29.7 5.1 42 83-125 10-51 (153)
96 COG2846 Regulator of cell morp 58.5 8.9 0.00019 35.8 2.8 32 94-125 31-62 (221)
97 PHA02701 ORF020 dsRNA-binding 58.2 19 0.00042 32.7 4.9 90 82-171 4-127 (183)
98 PF07106 TBPIP: Tat binding pr 58.0 34 0.00074 29.2 6.1 57 83-141 2-60 (169)
99 PRK15090 DNA-binding transcrip 57.9 14 0.00031 33.1 4.0 51 86-141 18-69 (257)
100 PLN02853 Probable phenylalanyl 57.7 51 0.0011 34.1 8.2 70 82-153 3-72 (492)
101 PRK07598 RNA polymerase sigma 57.6 55 0.0012 32.9 8.4 87 92-178 273-364 (415)
102 PRK10992 iron-sulfur cluster r 57.5 11 0.00024 34.2 3.3 42 85-126 16-63 (220)
103 PF14257 DUF4349: Domain of un 57.0 96 0.0021 28.2 9.2 68 99-174 160-234 (262)
104 TIGR00589 ogt O-6-methylguanin 56.7 29 0.00063 27.0 5.1 58 82-139 2-65 (80)
105 PF10771 DUF2582: Protein of u 56.6 26 0.00056 26.8 4.6 52 86-140 12-63 (65)
106 TIGR02698 CopY_TcrY copper tra 56.5 1E+02 0.0022 25.7 8.5 77 82-165 4-84 (130)
107 PLN03238 probable histone acet 56.5 20 0.00043 34.7 4.9 53 84-141 210-262 (290)
108 TIGR02787 codY_Gpos GTP-sensin 56.4 16 0.00035 34.7 4.2 45 87-133 188-232 (251)
109 TIGR01884 cas_HTH CRISPR locus 55.0 54 0.0012 28.7 7.0 49 82-133 143-191 (203)
110 PRK11050 manganese transport r 54.8 1.2E+02 0.0027 25.6 9.0 46 85-133 40-85 (152)
111 PF04967 HTH_10: HTH DNA bindi 54.7 33 0.00072 25.1 4.8 39 83-121 4-47 (53)
112 PF10717 ODV-E18: Occlusion-de 54.6 18 0.00039 29.4 3.6 28 177-204 27-54 (85)
113 TIGR02944 suf_reg_Xantho FeS a 54.6 25 0.00054 28.4 4.5 45 86-132 13-58 (130)
114 PF05331 DUF742: Protein of un 53.9 21 0.00046 29.9 4.1 49 85-135 43-91 (114)
115 PRK09492 treR trehalose repres 53.8 8.5 0.00018 34.1 1.9 24 96-119 3-26 (315)
116 TIGR03826 YvyF flagellar opero 53.6 25 0.00055 30.3 4.6 54 84-143 32-86 (137)
117 PF10025 DUF2267: Uncharacteri 53.4 8.3 0.00018 31.6 1.6 80 100-179 6-100 (125)
118 PF01853 MOZ_SAS: MOZ/SAS fami 53.3 19 0.00042 32.7 4.1 39 84-122 135-175 (188)
119 PRK09526 lacI lac repressor; R 53.2 10 0.00022 34.0 2.3 48 96-143 4-72 (342)
120 PRK11169 leucine-responsive tr 53.0 26 0.00057 29.8 4.6 42 83-125 15-56 (164)
121 PHA03093 EEV glycoprotein; Pro 52.8 26 0.00057 32.0 4.8 32 164-196 30-61 (185)
122 PF15581 Imm35: Immunity prote 52.5 26 0.00057 28.9 4.3 33 107-139 44-77 (93)
123 PF05158 RNA_pol_Rpc34: RNA po 52.4 57 0.0012 31.5 7.3 60 81-141 8-70 (327)
124 PRK14987 gluconate operon tran 51.2 11 0.00024 33.8 2.2 25 95-119 3-27 (331)
125 COG0640 ArsR Predicted transcr 50.6 84 0.0018 22.0 6.3 59 80-141 23-81 (110)
126 PF10975 DUF2802: Protein of u 50.5 13 0.00028 28.5 2.2 29 88-116 35-63 (70)
127 PF00165 HTH_AraC: Bacterial r 49.6 16 0.00035 24.2 2.3 28 93-120 4-31 (42)
128 TIGR02405 trehalos_R_Ecol treh 49.6 11 0.00025 33.6 2.0 23 97-119 1-23 (311)
129 PF02796 HTH_7: Helix-turn-hel 49.6 15 0.00033 25.1 2.2 32 87-118 11-42 (45)
130 PHA01815 hypothetical protein 49.4 69 0.0015 23.8 5.7 25 158-182 12-36 (55)
131 PF15145 DUF4577: Domain of un 49.4 6.9 0.00015 33.6 0.5 36 172-207 62-97 (128)
132 TIGR00738 rrf2_super rrf2 fami 47.5 38 0.00083 27.0 4.6 43 87-131 13-57 (132)
133 PRK06474 hypothetical protein; 47.2 43 0.00094 29.3 5.2 56 77-134 6-62 (178)
134 PRK10703 DNA-binding transcrip 47.0 13 0.00028 33.4 1.9 46 98-143 2-68 (341)
135 smart00421 HTH_LUXR helix_turn 46.7 44 0.00095 21.8 4.1 46 78-127 3-48 (58)
136 PRK11041 DNA-binding transcrip 46.6 73 0.0016 27.9 6.6 55 77-131 2-70 (309)
137 COG4565 CitB Response regulato 46.3 50 0.0011 31.1 5.6 69 73-141 145-219 (224)
138 TIGR01610 phage_O_Nterm phage 46.2 58 0.0013 25.6 5.3 32 94-125 44-75 (95)
139 PF13542 HTH_Tnp_ISL3: Helix-t 46.1 37 0.00079 23.0 3.7 38 81-121 14-51 (52)
140 COG1386 scpB Chromosome segreg 46.0 61 0.0013 29.1 6.0 91 81-186 7-101 (184)
141 PF02295 z-alpha: Adenosine de 46.0 28 0.0006 26.3 3.3 44 82-126 4-49 (66)
142 PF08006 DUF1700: Protein of u 45.8 1.9E+02 0.0042 24.7 10.0 42 78-119 16-62 (181)
143 PRK03902 manganese transport t 45.5 1.7E+02 0.0037 24.0 8.8 38 91-130 16-53 (142)
144 PRK11161 fumarate/nitrate redu 45.4 37 0.0008 29.3 4.4 51 81-133 154-218 (235)
145 PRK05441 murQ N-acetylmuramic 45.4 26 0.00055 33.1 3.7 43 84-130 250-292 (299)
146 smart00874 B5 tRNA synthetase 45.2 34 0.00074 24.8 3.6 51 97-149 5-55 (71)
147 TIGR00122 birA_repr_reg BirA b 45.1 67 0.0015 23.2 5.2 36 86-123 4-39 (69)
148 PRK11552 putative DNA-binding 45.0 24 0.00051 31.1 3.3 32 82-113 13-48 (225)
149 TIGR01481 ccpA catabolite cont 44.8 14 0.00031 32.8 1.9 46 98-143 2-68 (329)
150 PRK00441 argR arginine repress 44.7 81 0.0018 27.2 6.4 56 84-145 6-67 (149)
151 PRK09526 lacI lac repressor; R 44.7 76 0.0017 28.4 6.5 56 77-132 30-99 (342)
152 PRK07122 RNA polymerase sigma 44.6 1E+02 0.0022 28.3 7.4 44 78-121 117-167 (264)
153 TIGR02393 RpoD_Cterm RNA polym 44.6 1.2E+02 0.0027 26.8 7.8 29 92-120 98-126 (238)
154 PRK04172 pheS phenylalanyl-tRN 44.3 1.3E+02 0.0027 30.4 8.5 66 83-151 7-72 (489)
155 PRK15008 HTH-type transcriptio 44.1 21 0.00046 30.7 2.8 32 82-113 18-54 (212)
156 PRK14987 gluconate operon tran 43.7 95 0.002 27.8 6.9 57 77-133 30-100 (331)
157 PF04545 Sigma70_r4: Sigma-70, 43.6 82 0.0018 21.4 5.1 41 77-120 3-43 (50)
158 PF13545 HTH_Crp_2: Crp-like h 43.5 43 0.00094 24.0 4.0 33 97-131 28-60 (76)
159 cd00131 PAX Paired Box domain 43.5 56 0.0012 27.2 5.1 44 77-123 16-59 (128)
160 COG1522 Lrp Transcriptional re 43.5 56 0.0012 26.5 5.0 51 82-133 8-61 (154)
161 PF10668 Phage_terminase: Phag 43.5 40 0.00087 25.5 3.8 33 83-115 8-40 (60)
162 PRK05949 RNA polymerase sigma 43.4 1.1E+02 0.0024 29.3 7.6 87 91-178 188-280 (327)
163 PRK14996 TetR family transcrip 43.2 20 0.00044 30.0 2.5 29 84-112 10-43 (192)
164 PF04079 DUF387: Putative tran 43.2 57 0.0012 28.5 5.3 49 91-141 7-58 (159)
165 cd00569 HTH_Hin_like Helix-tur 43.0 51 0.0011 18.4 3.5 34 79-115 6-39 (42)
166 PF07245 Phlebovirus_G2: Phleb 42.9 23 0.0005 36.4 3.2 18 134-151 421-438 (507)
167 PRK10014 DNA-binding transcrip 42.5 98 0.0021 27.7 6.8 54 77-130 31-98 (342)
168 PRK09210 RNA polymerase sigma 42.4 1.2E+02 0.0027 29.2 7.9 87 91-178 226-319 (367)
169 PF02082 Rrf2: Transcriptional 42.4 56 0.0012 24.6 4.6 44 87-132 13-58 (83)
170 PRK07405 RNA polymerase sigma 42.0 1.1E+02 0.0024 28.9 7.5 88 91-178 178-270 (317)
171 COG1802 GntR Transcriptional r 41.6 18 0.0004 31.7 2.0 59 81-141 23-82 (230)
172 PF06971 Put_DNA-bind_N: Putat 41.4 47 0.001 24.1 3.8 33 86-118 16-49 (50)
173 TIGR02997 Sig70-cyanoRpoD RNA 41.3 1.5E+02 0.0031 27.6 7.9 86 92-177 172-262 (298)
174 PRK10727 DNA-binding transcrip 41.1 17 0.00037 32.9 1.8 46 98-143 2-68 (343)
175 PRK10339 DNA-binding transcrip 40.8 16 0.00034 32.8 1.5 22 98-119 2-23 (327)
176 PRK09975 DNA-binding transcrip 40.6 27 0.00058 29.5 2.8 31 83-113 12-47 (213)
177 smart00351 PAX Paired Box doma 40.6 78 0.0017 26.0 5.5 48 73-123 12-59 (125)
178 PRK10344 DNA-binding transcrip 40.5 46 0.00099 27.5 4.0 34 84-119 10-43 (92)
179 TIGR00274 N-acetylmuramic acid 40.3 41 0.0009 31.7 4.3 43 84-130 245-287 (291)
180 PRK10401 DNA-binding transcrip 40.0 19 0.00041 32.6 1.9 46 98-143 2-68 (346)
181 PHA02673 ORF109 EEV glycoprote 40.0 58 0.0013 29.3 4.9 30 166-196 29-58 (161)
182 TIGR02337 HpaR homoprotocatech 39.6 61 0.0013 25.6 4.5 47 83-132 29-75 (118)
183 PF08100 Dimerisation: Dimeris 39.0 47 0.001 24.1 3.4 27 82-108 6-33 (51)
184 PRK10402 DNA-binding transcrip 38.8 87 0.0019 27.3 5.8 50 81-132 149-202 (226)
185 PF13730 HTH_36: Helix-turn-he 38.8 39 0.00086 23.2 3.0 26 99-124 27-52 (55)
186 TIGR01481 ccpA catabolite cont 38.7 1.1E+02 0.0023 27.3 6.4 56 77-132 26-95 (329)
187 PF08280 HTH_Mga: M protein tr 38.6 90 0.002 22.4 4.9 44 84-128 7-50 (59)
188 PRK09954 putative kinase; Prov 38.4 59 0.0013 30.4 4.9 42 83-125 4-45 (362)
189 PRK10423 transcriptional repre 38.4 1.2E+02 0.0027 26.8 6.8 56 77-132 23-92 (327)
190 TIGR03697 NtcA_cyano global ni 38.3 97 0.0021 25.5 5.7 50 81-132 113-176 (193)
191 PF14394 DUF4423: Domain of un 37.9 58 0.0013 28.5 4.5 45 79-123 21-67 (171)
192 PF13384 HTH_23: Homeodomain-l 37.8 43 0.00094 22.5 3.0 40 80-122 3-42 (50)
193 TIGR02417 fruct_sucro_rep D-fr 37.6 1.2E+02 0.0026 27.0 6.6 56 78-133 28-97 (327)
194 PRK03573 transcriptional regul 37.4 70 0.0015 26.0 4.7 42 84-125 33-74 (144)
195 PRK07921 RNA polymerase sigma 37.4 1.6E+02 0.0035 28.2 7.8 42 78-119 163-211 (324)
196 TIGR03613 RutR pyrimidine util 37.3 29 0.00064 29.0 2.5 32 82-113 8-44 (202)
197 PF14451 Ub-Mut7C: Mut7-C ubiq 37.1 39 0.00085 26.5 3.0 49 93-143 28-76 (81)
198 PRK11303 DNA-binding transcrip 36.9 1.1E+02 0.0025 27.1 6.3 55 78-132 29-97 (328)
199 COG0735 Fur Fe2+/Zn2+ uptake r 36.7 1.4E+02 0.003 25.3 6.5 64 81-144 20-88 (145)
200 PRK11753 DNA-binding transcrip 36.4 81 0.0017 26.5 5.0 46 80-125 138-196 (211)
201 PRK11303 DNA-binding transcrip 36.3 24 0.00053 31.4 2.0 23 98-120 1-23 (328)
202 PF00325 Crp: Bacterial regula 35.8 49 0.0011 22.1 2.9 28 97-124 2-29 (32)
203 PRK00215 LexA repressor; Valid 35.6 70 0.0015 27.7 4.7 58 84-143 6-69 (205)
204 KOG3970 Predicted E3 ubiquitin 35.4 85 0.0018 30.2 5.4 44 150-196 220-271 (299)
205 PF05055 DUF677: Protein of un 35.3 1.2E+02 0.0025 29.8 6.5 78 108-191 116-205 (336)
206 PRK11414 colanic acid/biofilm 35.0 2.8E+02 0.0061 24.1 8.3 52 93-147 30-81 (221)
207 PHA00738 putative HTH transcri 34.8 1.7E+02 0.0037 24.7 6.6 58 81-141 11-68 (108)
208 PRK08215 sporulation sigma fac 34.4 1.4E+02 0.0029 26.9 6.4 30 92-121 134-163 (258)
209 PRK09492 treR trehalose repres 34.2 1.5E+02 0.0033 26.2 6.6 55 77-131 29-97 (315)
210 PLN00104 MYST -like histone ac 34.2 53 0.0012 33.6 4.2 39 84-122 361-399 (450)
211 PHA01976 helix-turn-helix prot 33.8 71 0.0015 22.6 3.7 32 81-114 1-32 (67)
212 PRK04984 fatty acid metabolism 33.7 80 0.0017 27.6 4.8 55 82-138 11-71 (239)
213 PRK03837 transcriptional regul 33.5 83 0.0018 27.4 4.8 63 79-144 14-81 (241)
214 TIGR02010 IscR iron-sulfur clu 33.3 82 0.0018 25.9 4.5 29 96-124 24-52 (135)
215 PF11268 DUF3071: Protein of u 33.1 54 0.0012 29.3 3.6 33 82-116 56-88 (170)
216 PRK10668 DNA-binding transcrip 33.0 47 0.001 28.1 3.1 32 82-113 11-47 (215)
217 PF01399 PCI: PCI domain; Int 32.9 1.5E+02 0.0032 21.9 5.5 58 76-133 39-96 (105)
218 smart00354 HTH_LACI helix_turn 32.8 32 0.0007 25.3 1.9 21 98-118 1-21 (70)
219 TIGR03652 FeS_repair_RIC iron- 32.7 51 0.0011 29.4 3.4 41 85-125 9-55 (216)
220 TIGR02405 trehalos_R_Ecol treh 32.1 1.8E+02 0.004 25.9 6.9 56 77-132 26-95 (311)
221 PLN02343 allene oxide cyclase 32.0 12 0.00025 35.0 -0.7 14 248-261 124-137 (229)
222 PRK12570 N-acetylmuramic acid- 32.0 52 0.0011 31.1 3.5 43 84-130 246-288 (296)
223 PRK10703 DNA-binding transcrip 31.9 1E+02 0.0022 27.7 5.2 57 77-133 26-96 (341)
224 PRK11534 DNA-binding transcrip 31.8 46 0.00099 28.9 2.9 49 93-145 26-75 (224)
225 TIGR02417 fruct_sucro_rep D-fr 31.8 32 0.00069 30.7 2.0 21 99-119 1-21 (327)
226 PF13518 HTH_28: Helix-turn-he 31.8 1.4E+02 0.003 19.8 4.7 37 84-123 2-38 (52)
227 PRK11202 DNA-binding transcrip 31.6 44 0.00096 28.6 2.8 31 81-111 10-46 (203)
228 TIGR03338 phnR_burk phosphonat 31.4 47 0.001 28.5 2.9 57 83-141 20-77 (212)
229 TIGR03384 betaine_BetI transcr 31.3 36 0.00077 27.8 2.1 31 82-112 8-43 (189)
230 PF09756 DDRGK: DDRGK domain; 31.2 93 0.002 28.2 4.8 64 83-147 100-163 (188)
231 PF11772 EpuA: DNA-directed RN 31.0 13 0.00029 26.9 -0.5 19 258-276 22-40 (47)
232 PF07790 DUF1628: Protein of u 30.9 97 0.0021 23.3 4.2 21 177-197 7-27 (80)
233 PRK09391 fixK transcriptional 30.8 1.1E+02 0.0024 26.8 5.2 53 81-135 153-215 (230)
234 PF00376 MerR: MerR family reg 30.4 38 0.00083 22.9 1.7 17 99-115 1-17 (38)
235 PRK14999 histidine utilization 30.2 90 0.002 27.6 4.6 59 81-142 15-78 (241)
236 PF09743 DUF2042: Uncharacteri 30.0 71 0.0015 30.2 4.1 44 95-140 128-171 (272)
237 PF11548 Receptor_IA-2: Protei 30.0 20 0.00043 29.3 0.4 27 92-118 52-78 (91)
238 PF13693 HTH_35: Winged helix- 29.9 37 0.00081 26.8 1.9 33 84-118 4-36 (78)
239 cd06171 Sigma70_r4 Sigma70, re 29.9 1.2E+02 0.0027 19.0 4.1 26 96-121 25-50 (55)
240 PLN03239 histone acetyltransfe 29.9 71 0.0015 31.8 4.1 59 84-147 268-329 (351)
241 PRK04217 hypothetical protein; 29.8 1.1E+02 0.0023 25.6 4.6 45 76-124 40-85 (110)
242 COG1654 BirA Biotin operon rep 29.8 1.9E+02 0.0042 22.8 5.8 54 81-135 2-57 (79)
243 PRK04280 arginine repressor; P 29.6 1.4E+02 0.003 25.8 5.4 48 82-145 19-67 (148)
244 PF02186 TFIIE_beta: TFIIE bet 29.2 1.5E+02 0.0032 22.5 4.9 53 83-139 6-59 (65)
245 cd07977 TFIIE_beta_winged_heli 29.2 1.5E+02 0.0032 23.0 5.0 35 85-119 12-48 (75)
246 PF07070 Spo0M: SpoOM protein; 29.2 62 0.0013 29.8 3.4 48 56-103 109-156 (218)
247 smart00342 HTH_ARAC helix_turn 28.7 1.1E+02 0.0025 21.1 4.1 37 85-121 37-75 (84)
248 PF07381 DUF1495: Winged helix 28.7 83 0.0018 25.5 3.7 48 81-128 8-56 (90)
249 PF13744 HTH_37: Helix-turn-he 28.7 1.5E+02 0.0034 22.3 5.0 38 95-132 29-78 (80)
250 COG1308 EGD2 Transcription fac 28.6 49 0.0011 28.5 2.4 23 98-120 83-108 (122)
251 PF14493 HTH_40: Helix-turn-he 28.4 84 0.0018 24.2 3.6 72 88-166 4-78 (91)
252 PF12298 Bot1p: Eukaryotic mit 28.4 1.2E+02 0.0027 27.0 5.1 45 78-125 16-60 (172)
253 PF13443 HTH_26: Cro/C1-type H 28.4 93 0.002 21.7 3.5 28 87-116 2-29 (63)
254 PRK10513 sugar phosphate phosp 28.2 2.4E+02 0.0053 24.8 6.9 60 78-143 20-79 (270)
255 PRK10286 O-6-alkylguanine-DNA: 28.0 82 0.0018 28.1 3.9 74 81-159 87-166 (171)
256 PRK08392 hypothetical protein; 28.0 61 0.0013 28.6 3.1 35 67-101 146-180 (215)
257 PRK12702 mannosyl-3-phosphogly 28.0 80 0.0017 30.8 4.1 28 97-124 123-150 (302)
258 PRK11512 DNA-binding transcrip 27.6 1.4E+02 0.0031 24.3 5.0 42 83-125 41-82 (144)
259 KOG2587 RNA polymerase III (C) 27.6 2.1E+02 0.0046 30.2 7.2 89 85-173 22-115 (551)
260 COG3413 Predicted DNA binding 27.5 1.3E+02 0.0029 26.5 5.1 39 82-120 158-201 (215)
261 PRK07406 RNA polymerase sigma 27.4 2.9E+02 0.0062 27.3 7.8 100 78-178 213-325 (373)
262 COG1497 Predicted transcriptio 27.4 1.3E+02 0.0029 28.9 5.3 91 82-193 10-101 (260)
263 TIGR02018 his_ut_repres histid 27.3 1.3E+02 0.0028 26.4 5.0 55 83-140 6-65 (230)
264 cd02106 Band_7 The band 7 doma 27.3 1.2E+02 0.0027 22.4 4.2 70 80-151 50-119 (121)
265 KOG0860 Synaptobrevin/VAMP-lik 27.3 2.2E+02 0.0048 24.4 6.1 33 152-192 79-111 (116)
266 PF09753 Use1: Membrane fusion 27.2 1.3E+02 0.0028 27.5 5.1 14 154-167 214-227 (251)
267 TIGR02716 C20_methyl_CrtF C-20 27.1 41 0.00089 30.8 1.9 44 79-124 7-50 (306)
268 PRK10617 cytochrome c-type pro 26.7 1.3E+02 0.0029 27.4 5.0 22 252-273 108-129 (200)
269 PRK06811 RNA polymerase factor 26.7 86 0.0019 26.5 3.6 58 77-138 130-189 (189)
270 COG1609 PurR Transcriptional r 26.6 44 0.00094 31.4 2.0 22 98-119 1-22 (333)
271 COG4189 Predicted transcriptio 26.4 1.5E+02 0.0033 28.8 5.5 66 78-144 19-96 (308)
272 PRK13719 conjugal transfer tra 26.3 1.1E+02 0.0024 28.5 4.5 51 77-127 138-188 (217)
273 TIGR02325 C_P_lyase_phnF phosp 26.3 1.4E+02 0.0031 25.9 5.0 57 81-140 11-72 (238)
274 PRK11511 DNA-binding transcrip 26.3 1.2E+02 0.0025 24.8 4.2 37 85-121 12-49 (127)
275 PRK10870 transcriptional repre 25.9 1.4E+02 0.003 25.8 4.9 43 83-125 56-99 (176)
276 PF00802 Glycoprotein_G: Pneum 25.5 23 0.0005 33.8 0.0 16 161-176 3-18 (263)
277 COG1725 Predicted transcriptio 25.3 3.5E+02 0.0076 23.1 7.0 69 99-170 37-107 (125)
278 TIGR01557 myb_SHAQKYF myb-like 25.3 1.8E+02 0.0038 21.5 4.6 39 81-119 8-51 (57)
279 PRK10219 DNA-binding transcrip 25.3 1.4E+02 0.0031 23.0 4.4 38 84-121 7-45 (107)
280 PRK10727 DNA-binding transcrip 25.2 59 0.0013 29.4 2.5 56 77-132 26-95 (343)
281 PRK10225 DNA-binding transcrip 25.1 72 0.0016 28.4 3.0 47 93-141 28-76 (257)
282 PF03460 NIR_SIR_ferr: Nitrite 25.1 1E+02 0.0023 22.1 3.4 31 109-140 21-52 (69)
283 PF09681 Phage_rep_org_N: N-te 24.7 2.5E+02 0.0053 23.6 6.0 42 97-140 53-94 (121)
284 TIGR00331 hrcA heat shock gene 24.6 1.3E+02 0.0028 29.0 4.8 63 85-149 9-73 (337)
285 PF13038 DUF3899: Domain of un 24.6 73 0.0016 24.6 2.6 32 163-194 58-89 (92)
286 TIGR02850 spore_sigG RNA polym 24.5 1.2E+02 0.0027 27.2 4.4 46 77-122 109-161 (254)
287 TIGR02161 napC_nirT periplasmi 24.4 1.3E+02 0.0028 27.0 4.5 24 252-275 99-122 (185)
288 PRK13276 cell wall biosynthesi 24.4 78 0.0017 29.4 3.2 38 85-122 16-60 (224)
289 PF13411 MerR_1: MerR HTH fami 24.4 67 0.0015 22.7 2.2 44 99-147 2-45 (69)
290 KOG2747 Histone acetyltransfer 24.3 1.1E+02 0.0024 30.9 4.4 39 84-122 315-354 (396)
291 PRK10820 DNA-binding transcrip 24.3 1.5E+02 0.0033 29.9 5.4 72 67-141 32-106 (520)
292 PHA03103 double-strand RNA-bin 24.3 1.5E+02 0.0033 26.9 4.9 45 81-125 9-55 (183)
293 COG2103 Predicted sugar phosph 24.2 1.2E+02 0.0025 29.8 4.4 42 84-129 248-289 (298)
294 PRK10339 DNA-binding transcrip 24.1 59 0.0013 29.2 2.3 23 78-100 29-51 (327)
295 PRK03887 methylated-DNA--prote 23.8 1.3E+02 0.0027 27.3 4.3 56 81-136 91-151 (175)
296 PF04492 Phage_rep_O: Bacterio 23.8 95 0.0021 25.3 3.2 39 86-124 36-81 (100)
297 COG2207 AraC AraC-type DNA-bin 23.6 1.5E+02 0.0033 22.1 4.2 41 81-122 20-61 (127)
298 PRK10401 DNA-binding transcrip 23.4 3.2E+02 0.0068 24.8 6.9 56 77-132 26-95 (346)
299 KOG3233 RNA polymerase III, su 23.1 2.2E+02 0.0048 27.9 6.0 67 77-144 6-73 (297)
300 PRK00767 transcriptional regul 23.1 81 0.0018 26.0 2.8 32 81-112 8-44 (197)
301 TIGR02812 fadR_gamma fatty aci 23.1 78 0.0017 27.7 2.8 54 84-139 16-71 (235)
302 KOG0793 Protein tyrosine phosp 22.7 2.5E+02 0.0054 31.2 6.8 23 93-115 549-571 (1004)
303 TIGR02313 HpaI-NOT-DapA 2,4-di 22.7 1.3E+02 0.0028 28.0 4.3 59 67-128 38-97 (294)
304 PRK11104 hemG protoporphyrinog 22.1 34 0.00074 29.5 0.4 30 247-276 129-163 (177)
305 PRK10421 DNA-binding transcrip 21.9 86 0.0019 27.9 2.9 39 93-133 21-60 (253)
306 PF01710 HTH_Tnp_IS630: Transp 21.8 1.5E+02 0.0033 24.0 4.1 50 80-135 4-53 (119)
307 PRK05066 arginine repressor; P 21.8 2.3E+02 0.0051 24.7 5.4 47 83-145 25-73 (156)
308 PF13551 HTH_29: Winged helix- 21.8 1.8E+02 0.0039 21.9 4.3 27 99-125 14-40 (112)
309 PF00196 GerE: Bacterial regul 21.7 1.2E+02 0.0026 21.2 3.1 44 84-127 5-48 (58)
310 KOG3830 Uncharacterized conser 21.6 97 0.0021 32.3 3.5 50 77-126 283-332 (542)
311 PRK09764 DNA-binding transcrip 21.6 1.8E+02 0.004 25.7 4.9 44 82-125 9-57 (240)
312 PRK10857 DNA-binding transcrip 21.6 98 0.0021 26.9 3.1 31 94-124 22-52 (164)
313 PRK11886 bifunctional biotin-- 21.5 1.5E+02 0.0032 27.7 4.5 38 85-123 7-44 (319)
314 TIGR02404 trehalos_R_Bsub treh 21.5 2E+02 0.0043 25.2 5.0 43 83-125 5-52 (233)
315 TIGR02885 spore_sigF RNA polym 21.4 3.1E+02 0.0068 23.9 6.2 43 78-120 87-136 (231)
316 PF10075 PCI_Csn8: COP9 signal 21.3 1.2E+02 0.0027 24.9 3.6 60 77-142 77-136 (143)
317 PRK07408 RNA polymerase sigma 21.3 2.1E+02 0.0046 25.9 5.3 32 89-120 121-152 (256)
318 COG5340 Predicted transcriptio 21.2 1.4E+02 0.0031 28.7 4.3 55 79-135 12-66 (269)
319 PF15615 TerB-C: TerB-C domain 21.1 2.7E+02 0.0059 23.5 5.6 68 78-148 73-142 (144)
320 PRK06369 nac nascent polypepti 21.0 80 0.0017 26.8 2.4 24 97-120 74-100 (115)
321 COG1438 ArgR Arginine represso 21.0 1.5E+02 0.0032 26.2 4.1 81 83-180 22-104 (150)
322 COG4901 Ribosomal protein S25 20.9 1E+02 0.0022 26.1 2.9 43 82-124 41-86 (107)
323 PRK09392 ftrB transcriptional 20.9 2.5E+02 0.0055 24.2 5.5 46 80-125 146-201 (236)
324 COG5027 SAS2 Histone acetyltra 20.8 1.3E+02 0.0028 30.5 4.0 40 84-123 317-357 (395)
325 COG1378 Predicted transcriptio 20.7 6.4E+02 0.014 23.4 8.4 53 96-151 29-84 (247)
326 PF05584 Sulfolobus_pRN: Sulfo 20.7 2.4E+02 0.0052 22.2 4.8 42 82-125 5-46 (72)
327 PRK09464 pdhR transcriptional 20.5 94 0.002 27.5 2.8 38 94-133 30-68 (254)
328 TIGR02224 recomb_XerC tyrosine 20.4 2.1E+02 0.0046 24.4 4.9 69 113-183 180-251 (295)
329 PRK10079 phosphonate metabolis 20.4 1.1E+02 0.0023 27.2 3.1 39 99-140 37-75 (241)
330 PRK15126 thiamin pyrimidine py 20.3 3E+02 0.0065 24.4 6.0 53 79-140 20-72 (272)
331 PRK03170 dihydrodipicolinate s 20.3 3.2E+02 0.0068 25.1 6.3 91 69-171 41-133 (292)
332 PF00462 Glutaredoxin: Glutare 20.3 2.6E+02 0.0056 19.2 4.5 33 85-122 13-45 (60)
333 PF13630 SdpI: SdpI/YhfL prote 20.2 3.5E+02 0.0075 19.6 5.7 33 156-188 17-49 (76)
334 KOG2927 Membrane component of 20.2 2.1E+02 0.0045 28.9 5.3 16 126-141 161-181 (372)
335 cd06170 LuxR_C_like C-terminal 20.1 2.3E+02 0.005 18.4 4.1 31 96-126 14-44 (57)
336 PRK10046 dpiA two-component re 20.1 2.4E+02 0.0053 24.2 5.2 56 86-141 166-223 (225)
No 1
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=95.50 E-value=0.034 Score=41.47 Aligned_cols=46 Identities=15% Similarity=0.252 Sum_probs=41.6
Q ss_pred CchhhHHHHHHHHHcCC-ceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 80 PADVRNRAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 80 ~~~~~~rim~Ave~lg~-rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
+..++.+|++++.+.|. .+|+.|+|.+.|++...+.+.|..|..+.
T Consensus 4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G 50 (68)
T smart00550 4 QDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKG 50 (68)
T ss_pred chHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 34677899999999988 69999999999999999999999998873
No 2
>PRK13239 alkylmercury lyase; Provisional
Probab=95.05 E-value=0.048 Score=49.67 Aligned_cols=53 Identities=19% Similarity=0.297 Sum_probs=46.3
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEE
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY 139 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlY 139 (276)
..+.-.|++.+. .|.-||+.|+|+.+|.+.+++++.|.+|. ..+..++|+|+-
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 347899999974
No 3
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=95.00 E-value=0.27 Score=41.96 Aligned_cols=86 Identities=19% Similarity=0.162 Sum_probs=68.5
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc-CCceEee-cCccEEEEc-CcchHHHhhhhhHHHhHHHH
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT-DGFLEVS-DEGDVLYVF-PNNYRAKLAAKSFRLKVEPV 161 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~-~GhLeVS-esGDIlYvF-P~nfRs~L~~Ks~r~rl~~~ 161 (276)
-.++.++-+.++..|+-|+|..-+++...|+++|+.|.... ==.-+++ +.|---|.+ |.++-. -.+-.+..+++|
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 VEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEE--IKKKILKDLDEW 107 (126)
T ss_pred HHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHH--HHHHHHHHHHHH
Confidence 45677777789999999999999999999999999999875 1223344 789999999 888876 455567778888
Q ss_pred HHHHhhhhhhH
Q 023862 162 IDKAKAAAEYS 172 (276)
Q Consensus 162 ~~k~w~v~~Yl 172 (276)
.+++...+..+
T Consensus 108 ~~~~~~~i~~~ 118 (126)
T COG3355 108 YDKMKQLIEEF 118 (126)
T ss_pred HHHHHHHHHHH
Confidence 88888776554
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=94.69 E-value=0.043 Score=38.43 Aligned_cols=40 Identities=23% Similarity=0.398 Sum_probs=35.9
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
-+|++++.+.+...|+.|+|.++|++...+.+-|..|.+.
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 3689999999999999999999999999999999999864
No 5
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=94.04 E-value=0.11 Score=39.13 Aligned_cols=53 Identities=23% Similarity=0.394 Sum_probs=41.5
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec--CccEEE
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD--EGDVLY 139 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe--sGDIlY 139 (276)
++|++.+++.+.-+|..|||...|++..+|+.=|..|..+ |.++-++ .|-..|
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 6799999998889999999999999999999999999876 4555544 355443
No 6
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=93.90 E-value=0.48 Score=35.35 Aligned_cols=54 Identities=20% Similarity=0.346 Sum_probs=43.1
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF 141 (276)
.+|++.+.+.++.+|+.|+|...|++...+.+-|..|.+ .|-|+-...+. .|..
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~--~g~l~~~~~~~-~y~l 61 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE--LGYVEQDGQNG-RYRL 61 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeeecCCCC-ceee
Confidence 467888888767899999999999999999999999976 47777654333 3555
No 7
>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=0.13 Score=40.77 Aligned_cols=50 Identities=22% Similarity=0.353 Sum_probs=36.3
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEE
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL 138 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIl 138 (276)
+--.+++.+.+ |.-||+.++|+++|.++++++++|.++. ..|-.++|.||
T Consensus 25 L~r~LLr~LA~-G~PVt~~~LA~a~g~~~e~v~~~L~~~p-----~tEyD~~GrIV 74 (77)
T PF12324_consen 25 LLRPLLRLLAK-GQPVTVEQLAAALGWPVEEVRAALAAMP-----DTEYDDQGRIV 74 (77)
T ss_dssp HHHHHHHHHTT-TS-B-HHHHHHHHT--HHHHHHHHHH-T-----TSEEETTSEEE
T ss_pred HHHHHHHHHHc-CCCcCHHHHHHHHCCCHHHHHHHHHhCC-----CceEcCCCCee
Confidence 33445666665 9999999999999999999999988875 47888888887
No 8
>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=93.61 E-value=0.21 Score=34.06 Aligned_cols=42 Identities=17% Similarity=0.338 Sum_probs=35.0
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
+.+.+|++++.+.+ ++|+.|+|...|++...+.+.|..|..+
T Consensus 3 ~~~~~Il~~l~~~~-~~t~~ela~~~~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 3 ETQRKILNYLRENP-RITQKELAEKLGISRSTVNRYLKKLEEK 44 (48)
T ss_dssp HHHHHHHHHHHHCT-TS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHcC-CCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 35678999999955 5999999999999999999999999765
No 9
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=93.46 E-value=0.58 Score=41.32 Aligned_cols=66 Identities=18% Similarity=0.154 Sum_probs=52.2
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCc---eEeecCccEEEEcCcchHH
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGF---LEVSDEGDVLYVFPNNYRA 147 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~Gh---LeVSesGDIlYvFP~nfRs 147 (276)
.+..-+|++++.+.| .+|..|+|...|++.+++++.|..|..+.=.. .+..++|-+.|.+==+...
T Consensus 21 ~~~~~~Vl~~L~~~g-~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~ 89 (178)
T PRK06266 21 DEEGFEVLKALIKKG-EVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEK 89 (178)
T ss_pred CccHhHHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHH
Confidence 445578999999888 69999999999999999999999999987322 3333688899977444444
No 10
>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=93.38 E-value=0.67 Score=39.99 Aligned_cols=78 Identities=24% Similarity=0.261 Sum_probs=58.2
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCC---ceEeecCccEEEEcCcchHHHhhhhhHHHhHHHHH
Q 023862 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG---FLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVI 162 (276)
Q Consensus 86 rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~G---hLeVSesGDIlYvFP~nfRs~L~~Ks~r~rl~~~~ 162 (276)
.|++|+-..| .+|..|+|...|++++++++.|..|..+.=. +.+-.++|-+.|.+=-|+..+... .+.++....
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-EFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKALDV--LKRKLEETA 94 (158)
T ss_pred HHHHHHhccC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHHHH--HHHHHHHHH
Confidence 5677777666 6999999999999999999999999999854 666777899999974477764443 333334444
Q ss_pred HHHh
Q 023862 163 DKAK 166 (276)
Q Consensus 163 ~k~w 166 (276)
+++.
T Consensus 95 ~~lk 98 (158)
T TIGR00373 95 KKLR 98 (158)
T ss_pred HHHH
Confidence 4443
No 11
>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=93.30 E-value=0.26 Score=35.39 Aligned_cols=53 Identities=26% Similarity=0.439 Sum_probs=45.1
Q ss_pred CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCc
Q 023862 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (276)
Q Consensus 80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesG 135 (276)
....|-+|++.+ ..+...|++++|...|++...+..-|..|.. .|-+++.++|
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 7788899999999999999999999999987 5778887776
No 12
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=92.61 E-value=0.24 Score=42.49 Aligned_cols=51 Identities=25% Similarity=0.377 Sum_probs=42.8
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecC
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSes 134 (276)
+++..+|++.|++. +|+|++|++..+|++.+.+++-|..|++ .|+|..+..
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 56677888888765 5899999999999999999999999986 567776654
No 13
>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=92.07 E-value=1.3 Score=30.24 Aligned_cols=60 Identities=25% Similarity=0.424 Sum_probs=46.6
Q ss_pred CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCc-cEEEEcC
Q 023862 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG-DVLYVFP 142 (276)
Q Consensus 79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesG-DIlYvFP 142 (276)
+..+.+..|++++.+.+ ++..|+|...|++...+.+.|..|.+. |.+....++ ...|.+.
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 34456778899888866 999999999999999999999999775 567665544 4555554
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=92.06 E-value=0.43 Score=34.42 Aligned_cols=41 Identities=12% Similarity=0.282 Sum_probs=36.7
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
+..|++.+++. +.+|+.|+|..-|+|...+++.|..|+...
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 689999999999999999999999998764
No 15
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=91.91 E-value=0.45 Score=44.56 Aligned_cols=84 Identities=17% Similarity=0.313 Sum_probs=70.6
Q ss_pred cCCCcccccCCCCchhh---HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcc
Q 023862 68 VGPGRIVESDKLPADVR---NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (276)
Q Consensus 68 ~~~~~~v~~~~l~~~~~---~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~n 144 (276)
++.||.----++|-+++ ..|+++++.+|| ||+.-+-+.-|-.-.-|.++|..|.++.=+-+--...+|-.|-||.+
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 44556655566776665 579999999999 99999999999999999999999999998888888899999999999
Q ss_pred hHHHhhhh
Q 023862 145 YRAKLAAK 152 (276)
Q Consensus 145 fRs~L~~K 152 (276)
|-......
T Consensus 238 ~~~~~~q~ 245 (249)
T KOG3341|consen 238 FTDQYAQR 245 (249)
T ss_pred hhHHHhhh
Confidence 97755443
No 16
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=91.89 E-value=0.54 Score=31.50 Aligned_cols=50 Identities=20% Similarity=0.376 Sum_probs=39.4
Q ss_pred HHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (276)
Q Consensus 87 im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv 140 (276)
|+..+. ...+|+.|++...|++...+.+.|..|.++ |-++....|.-.|.
T Consensus 2 il~~l~--~~~~~~~~i~~~l~is~~~v~~~l~~L~~~--g~i~~~~~~~~~~~ 51 (66)
T smart00418 2 ILKLLA--EGELCVCELAEILGLSQSTVSHHLKKLREA--GLVESRREGKRVYY 51 (66)
T ss_pred HHHHhh--cCCccHHHHHHHHCCCHHHHHHHHHHHHHC--CCeeeeecCCEEEE
Confidence 566776 667899999999999999999999999986 66666564544443
No 17
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=91.83 E-value=0.8 Score=31.75 Aligned_cols=46 Identities=11% Similarity=0.172 Sum_probs=36.0
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLe 130 (276)
+.+|++.+.+.+..+|..++|.+.|+|...+++.|..|-+. +..++
T Consensus 2 ~~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~-~~~I~ 47 (55)
T PF08279_consen 2 QKQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREW-GIPIE 47 (55)
T ss_dssp HHHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHT-T-EEE
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC-CCeEE
Confidence 35788899666666999999999999999999999999444 44443
No 18
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=91.53 E-value=0.85 Score=30.14 Aligned_cols=47 Identities=15% Similarity=0.319 Sum_probs=38.4
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
+..+++.+.+.+ .+|+.|+|...|++...+.+.|..|..+ |.++-..
T Consensus 2 ~~~il~~l~~~~-~~s~~~l~~~l~~s~~tv~~~l~~L~~~--g~i~~~~ 48 (53)
T smart00420 2 QQQILELLAQQG-KVSVEELAELLGVSEMTIRRDLNKLEEQ--GLLTRVH 48 (53)
T ss_pred HHHHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEee
Confidence 356788888765 5999999999999999999999999886 5555433
No 19
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=91.33 E-value=0.5 Score=37.00 Aligned_cols=45 Identities=20% Similarity=0.440 Sum_probs=38.2
Q ss_pred chhhHHHHHHHHH---cCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 81 ADVRNRAMDAVDA---CNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 81 ~~~~~rim~Ave~---lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
..++.+|+++++. ..-.+.+.+||.+.|++.++++++|..|..+.
T Consensus 46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG 93 (102)
T PF08784_consen 46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEG 93 (102)
T ss_dssp -HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCC
Confidence 4578899999998 56679999999999999999999999999863
No 20
>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=90.23 E-value=0.4 Score=37.77 Aligned_cols=34 Identities=12% Similarity=0.081 Sum_probs=31.0
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHH
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL 118 (276)
-+.+|++.+.+ +.+|+.|||..+|+|...+.+.|
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 45788999999 99999999999999999998877
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=90.23 E-value=0.75 Score=43.21 Aligned_cols=57 Identities=18% Similarity=0.367 Sum_probs=49.6
Q ss_pred CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEE
Q 023862 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL 138 (276)
Q Consensus 80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIl 138 (276)
|..++.+|.+.+...|||+++.|++..-|+..+..|+.+..++.+-. +++.. .||++
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 45678899999999999999999999999999999999999998877 56544 68864
No 22
>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=89.29 E-value=1.5 Score=31.76 Aligned_cols=53 Identities=21% Similarity=0.312 Sum_probs=41.7
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEE
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY 139 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlY 139 (276)
..++..++- ..+.+|+.|+|..+|++...+.+.|..|... |-++..+...-+|
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 345666665 5778999999999999999999999999886 6677776443333
No 23
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=88.42 E-value=1 Score=40.22 Aligned_cols=42 Identities=24% Similarity=0.385 Sum_probs=37.1
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
.+.++.-+-...+..|.|+||+.-|.++++++.+|..|-+|.
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 (166)
T PRK15466 111 ADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAG 152 (166)
T ss_pred HHHHHHHHHHHHccccHHHHHHHhCCcHHHHHHHHHHHHhcc
Confidence 456677777888999999999999999999999999998863
No 24
>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=88.00 E-value=1 Score=33.77 Aligned_cols=40 Identities=23% Similarity=0.300 Sum_probs=32.1
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCC-HHHHHHHHHHHHhh
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLK-LNEAQKALQALAAD 124 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~-l~~Ae~aL~aLAsD 124 (276)
.-|.+.+++.|+-.|+.|+|...|++ .+.|++-|.+|..+
T Consensus 13 ~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~k 53 (65)
T PF01726_consen 13 EFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERK 53 (65)
T ss_dssp HHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 44556677899999999999999997 99999999999865
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=87.72 E-value=0.78 Score=33.81 Aligned_cols=53 Identities=25% Similarity=0.255 Sum_probs=35.9
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCcc
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD 136 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGD 136 (276)
+..+.+.-.++|...|..+||...|+++++.++.|.....-..=++.+..+++
T Consensus 7 ~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~ 59 (78)
T PF04539_consen 7 ERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDD 59 (78)
T ss_dssp HHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSS
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCC
Confidence 34445556688999999999999999999998888765544444555555433
No 26
>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=87.57 E-value=1.9 Score=30.02 Aligned_cols=43 Identities=14% Similarity=0.227 Sum_probs=37.3
Q ss_pred hhHHHHHHHHHcCCc-eehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 83 VRNRAMDAVDACNRR-VTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 83 ~~~rim~Ave~lg~r-vTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
.+-+++.++...+.. +|+.|+|...|++...+.+.+..|.++.
T Consensus 6 ~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~G 49 (62)
T PF12802_consen 6 SQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKG 49 (62)
T ss_dssp HHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 356789999999887 9999999999999999999999998764
No 27
>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=86.41 E-value=2 Score=31.82 Aligned_cols=38 Identities=21% Similarity=0.366 Sum_probs=30.3
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAs 123 (276)
.+|.+.+-+.| +.|+.+++..++|+.++++++|..|.+
T Consensus 16 ~~V~~~Ll~~G-~ltl~~i~~~t~l~~~~Vk~~L~~LiQ 53 (62)
T PF08221_consen 16 AKVGEVLLSRG-RLTLREIVRRTGLSPKQVKKALVVLIQ 53 (62)
T ss_dssp HHHHHHHHHC--SEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcC-CcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46667776655 999999999999999999999999976
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=85.17 E-value=4.2 Score=30.39 Aligned_cols=68 Identities=13% Similarity=0.155 Sum_probs=51.3
Q ss_pred CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHH
Q 023862 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA 147 (276)
Q Consensus 80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs 147 (276)
-...+.+.+..+-+--..+|..++|...+++.+++|..|..+..+..=+-.++.....++.--...|.
T Consensus 7 ~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~ 74 (88)
T smart00088 7 QRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR 74 (88)
T ss_pred HHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh
Confidence 34455666666666678899999999999999999999999999874444567766677666555553
No 29
>smart00753 PAM PCI/PINT associated module.
Probab=85.17 E-value=4.2 Score=30.39 Aligned_cols=68 Identities=13% Similarity=0.155 Sum_probs=51.3
Q ss_pred CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHH
Q 023862 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA 147 (276)
Q Consensus 80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs 147 (276)
-...+.+.+..+-+--..+|..++|...+++.+++|..|..+..+..=+-.++.....++.--...|.
T Consensus 7 ~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~ 74 (88)
T smart00753 7 QRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR 74 (88)
T ss_pred HHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh
Confidence 34455666666666678899999999999999999999999999874444567766677666555553
No 30
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=84.34 E-value=6.8 Score=35.78 Aligned_cols=50 Identities=10% Similarity=0.089 Sum_probs=41.2
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
.+-+.+|++.+++.| ++|+.|+|..-|+|...+++.|..|+.. |.|+-.-
T Consensus 4 ~eR~~~Il~~L~~~~-~v~v~eLa~~l~VS~~TIRRDL~~Le~~--g~l~r~~ 53 (256)
T PRK10434 4 RQRQAAILEYLQKQG-KTSVEELAQYFDTTGTTIRKDLVILEHA--GTVIRTY 53 (256)
T ss_pred HHHHHHHHHHHHHcC-CEEHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEEE
Confidence 456788899888855 6999999999999999999999999876 4444433
No 31
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=84.17 E-value=3.2 Score=38.30 Aligned_cols=54 Identities=15% Similarity=0.244 Sum_probs=44.8
Q ss_pred CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCcc
Q 023862 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD 136 (276)
Q Consensus 80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGD 136 (276)
..+-+.+|++.+++.+. +|+.|+|..-|+|...+++.|..|.+. |-++-..-|-
T Consensus 15 ~~eR~~~Il~~L~~~~~-vtv~eLa~~l~VS~~TIRRDL~~Le~~--G~l~r~~GGa 68 (269)
T PRK09802 15 TSERREQIIQRLRQQGS-VQVNDLSALYGVSTVTIRNDLAFLEKQ--GIAVRAYGGA 68 (269)
T ss_pred HHHHHHHHHHHHHHcCC-EeHHHHHHHHCCCHHHHHHHHHHHHhC--CCeEEEeCCE
Confidence 35677888999999776 999999999999999999999999664 6666555554
No 32
>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=84.06 E-value=2.5 Score=29.10 Aligned_cols=49 Identities=20% Similarity=0.365 Sum_probs=35.8
Q ss_pred chhhHHHHHHHHHcC----Cc-eehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023862 81 ADVRNRAMDAVDACN----RR-VTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (276)
Q Consensus 81 ~~~~~rim~Ave~lg----~r-vTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeV 131 (276)
.++...+.+.+.... .. .|+.|+|...|++...+.++|..|++. |-|+.
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 345566666655432 22 459999999999999999999999984 34543
No 33
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=83.89 E-value=2 Score=40.15 Aligned_cols=46 Identities=20% Similarity=0.328 Sum_probs=40.0
Q ss_pred CCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 78 ~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
.|+.+ ...||++++.+|+|+|+.|+..+.|+|...+=+.|+.|...
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 35789999999999999999999999999999999999764
No 34
>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=83.20 E-value=5.4 Score=31.24 Aligned_cols=59 Identities=12% Similarity=0.129 Sum_probs=48.1
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~a-----GL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF 141 (276)
.|..|++++.+.+.-+|+.||..+. ++++..+=+.|..|++..=-+=-..++|...|..
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 4788999999999899999999887 6899999999999998765444344456677765
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=82.56 E-value=3.3 Score=28.58 Aligned_cols=39 Identities=13% Similarity=0.313 Sum_probs=30.9
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHH
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (276)
++..+|++++.+. .|.+..++|.+.|++-.++.+-+..|
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 3556788888776 88999999999999999999888776
No 36
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=82.48 E-value=2.5 Score=37.10 Aligned_cols=43 Identities=14% Similarity=0.194 Sum_probs=37.7
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
.+-+.+|++.+.+ .+.+|+.|+|..-|.|...+++.|..|+.+
T Consensus 6 ~~R~~~Il~~l~~-~~~~~~~~La~~~~vS~~TiRRDl~~L~~~ 48 (185)
T PRK04424 6 KERQKALQELIEE-NPFITDEELAEKFGVSIQTIRLDRMELGIP 48 (185)
T ss_pred HHHHHHHHHHHHH-CCCEEHHHHHHHHCcCHHHHHHHHHHHhcc
Confidence 3566778888888 456999999999999999999999999887
No 37
>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=82.40 E-value=8.1 Score=26.96 Aligned_cols=38 Identities=21% Similarity=0.391 Sum_probs=33.1
Q ss_pred CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCc
Q 023862 96 RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (276)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesG 135 (276)
..+|..|+|...|++...+.+.|..|.++ |-|+....|
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 777766545
No 38
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=82.15 E-value=2.5 Score=28.57 Aligned_cols=38 Identities=18% Similarity=0.359 Sum_probs=31.6
Q ss_pred cCCce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862 94 CNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 94 lg~rv-TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
.|.++ |..|+|...|++...++++|..|.++ |-|+...
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 35667 89999999999999999999999986 4565443
No 39
>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=82.12 E-value=4.2 Score=29.12 Aligned_cols=53 Identities=25% Similarity=0.479 Sum_probs=39.2
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHH-HHHHHHHHhh-----cCCceEeecCcc
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEA-QKALQALAAD-----TDGFLEVSDEGD 136 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~A-e~aL~aLAsD-----~~GhLeVSesGD 136 (276)
.++.+|-.+.. ..++...++..+.|.++.+. .+.|..+.++ .+++|.+|+.|-
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 45667777765 67899999999999997766 7779888886 378888888873
No 40
>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=81.51 E-value=2.8 Score=36.68 Aligned_cols=41 Identities=10% Similarity=0.182 Sum_probs=37.8
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
.+.+|+..+.+.|. +|+.|+|...|++...+.+.|..|.++
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 999999999999999999999999886
No 41
>PHA02943 hypothetical protein; Provisional
Probab=81.44 E-value=11 Score=33.83 Aligned_cols=79 Identities=19% Similarity=0.187 Sum_probs=55.8
Q ss_pred hhhHHHHHHHHH-cCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHhhhhhHHHhHHH
Q 023862 82 DVRNRAMDAVDA-CNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEP 160 (276)
Q Consensus 82 ~~~~rim~Ave~-lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L~~Ks~r~rl~~ 160 (276)
.+.+|+.+.+|- ..+-.|..+||-..|+|-.+||-.|..|..+ |.++--+-|-..|.+=.+ ..+... ..+
T Consensus 8 ~v~~R~~eILE~Lk~G~~TtseIAkaLGlS~~qa~~~LyvLErE--G~VkrV~~G~~tyw~l~~------day~~~-v~~ 78 (165)
T PHA02943 8 TVHTRMIKTLRLLADGCKTTSRIANKLGVSHSMARNALYQLAKE--GMVLKVEIGRAAIWCLDE------DAYTNL-VFE 78 (165)
T ss_pred HHHHHHHHHHHHHhcCCccHHHHHHHHCCCHHHHHHHHHHHHHc--CceEEEeecceEEEEECh------HHHHHH-HHH
Confidence 455666666665 5566789999999999999999999988765 556666799988888444 222222 566
Q ss_pred HHHHHhhhh
Q 023862 161 VIDKAKAAA 169 (276)
Q Consensus 161 ~~~k~w~v~ 169 (276)
+.+-+|+.+
T Consensus 79 ~~Relwrlv 87 (165)
T PHA02943 79 IKRELWRLV 87 (165)
T ss_pred HHHHHHHHH
Confidence 666666643
No 42
>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=80.19 E-value=4.6 Score=27.70 Aligned_cols=41 Identities=20% Similarity=0.323 Sum_probs=35.3
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
..|-+|+.++.+ +..|+.|+|...|++...+.+-|..|-..
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 77999999999999999999999988654
No 43
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=79.50 E-value=4.4 Score=31.33 Aligned_cols=42 Identities=14% Similarity=0.396 Sum_probs=37.5
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
...+|+.++.+. ++.|..|+|.+.|++...+.+.|..|.++.
T Consensus 4 ~D~~il~~L~~~-~~~~~~~la~~l~~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 4 IDRKILEELQKD-ARISLAELAKKVGLSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 457889999886 489999999999999999999999999864
No 44
>PRK12423 LexA repressor; Provisional
Probab=79.25 E-value=5.7 Score=34.93 Aligned_cols=52 Identities=23% Similarity=0.346 Sum_probs=41.0
Q ss_pred hhhHHHHHH----HHHcCCceehhhhhhhcCC-CHHHHHHHHHHHHhhcCCceEeecCc
Q 023862 82 DVRNRAMDA----VDACNRRVTIGDVAGKAGL-KLNEAQKALQALAADTDGFLEVSDEG 135 (276)
Q Consensus 82 ~~~~rim~A----ve~lg~rvTvgDVAa~aGL-~l~~Ae~aL~aLAsD~~GhLeVSesG 135 (276)
..|.+|+++ +++.|+..|+.|+|.+.|+ +...+++.|.+|+.. |.|+++..+
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 345555554 4556888899999999995 899999999999975 778887664
No 45
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=78.45 E-value=18 Score=30.16 Aligned_cols=60 Identities=13% Similarity=0.139 Sum_probs=48.4
Q ss_pred CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (276)
Q Consensus 79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF 141 (276)
|....|-+|+..+... +.+|++|+|.+.|++...+-+-|..|.. -|-++...+|.-+|..
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 5567788999988653 4699999999999999999999998865 4677777788766655
No 46
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=76.66 E-value=7.2 Score=34.91 Aligned_cols=59 Identities=19% Similarity=0.249 Sum_probs=44.8
Q ss_pred hhhHHHHHHHHHcCC-ceehhhhhhhcCCCHHHHHHHHHHHHhhcCC---ceEeecCccEEEEc
Q 023862 82 DVRNRAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKALQALAADTDG---FLEVSDEGDVLYVF 141 (276)
Q Consensus 82 ~~~~rim~Ave~lg~-rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~G---hLeVSesGDIlYvF 141 (276)
.....|+-++=-.|. .+|+.++|...|++.++++.+|..|..+|.. -+++.+.|+- |.|
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 333344444445565 4999999999999999999999999999843 4888887665 776
No 47
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=76.06 E-value=5.7 Score=36.36 Aligned_cols=57 Identities=12% Similarity=0.267 Sum_probs=45.6
Q ss_pred CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh------cCCceEeecCccE
Q 023862 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD------TDGFLEVSDEGDV 137 (276)
Q Consensus 80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD------~~GhLeVSesGDI 137 (276)
+.+-+.+|++.|++ .+.++|.|+|..-|.|..++++.|..|+.. +||-.-.+...+.
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 44567888999988 568999999999999999999999999986 3555555554444
No 48
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=74.87 E-value=7.3 Score=36.01 Aligned_cols=66 Identities=14% Similarity=0.192 Sum_probs=50.3
Q ss_pred ccCCCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcC--CceEeecCccEEEEc
Q 023862 75 ESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTD--GFLEVSDEGDVLYVF 141 (276)
Q Consensus 75 ~~~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~--GhLeVSesGDIlYvF 141 (276)
+..+.++..+.+|+..+++.| .+|++|+|.+-|++...|++-|..|.++.- -..+=..-|-..+.|
T Consensus 4 ~~~~~~~~tr~~il~lL~~~g-~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y 71 (218)
T COG2345 4 MLADPSGSTRERILELLKKSG-PVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLY 71 (218)
T ss_pred cccCCCccHHHHHHHHHhccC-CccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceee
Confidence 456778888999988887765 579999999999999999999999998862 222222236666555
No 49
>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=73.97 E-value=3.6 Score=29.59 Aligned_cols=41 Identities=20% Similarity=0.302 Sum_probs=31.0
Q ss_pred HHHHHHHHH----cCCce-ehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 85 NRAMDAVDA----CNRRV-TIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 85 ~rim~Ave~----lg~rv-TvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
..|.+.+.. .|.++ |..++|..-|+|...++++|..|+++.
T Consensus 7 ~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g 52 (64)
T PF00392_consen 7 DQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEG 52 (64)
T ss_dssp HHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCC
Confidence 344444444 56678 999999999999999999999999863
No 50
>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=73.88 E-value=12 Score=29.44 Aligned_cols=78 Identities=24% Similarity=0.250 Sum_probs=40.8
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecC---ccEEEEcCcchHHHhhhhhHHHhHHHH
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE---GDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSes---GDIlYvFP~nfRs~L~~Ks~r~rl~~~ 161 (276)
-.||+++-..| .+|-.|+|..+|++..++++.|..|..+.=-+.+-..+ |-..|.+==|++.+. ...+.++...
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 58999999999999999999999999998766654443 444455544555432 2233444444
Q ss_pred HHHH
Q 023862 162 IDKA 165 (276)
Q Consensus 162 ~~k~ 165 (276)
.+++
T Consensus 93 ~~~l 96 (105)
T PF02002_consen 93 REKL 96 (105)
T ss_dssp ----
T ss_pred HHHH
Confidence 4443
No 51
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=73.69 E-value=6.5 Score=35.81 Aligned_cols=43 Identities=16% Similarity=0.233 Sum_probs=37.9
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
.+-+.+|++.+++ .+.+|+.|+|...|+|...+++.|..|.+.
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 3567788999986 688999999999999999999999999764
No 52
>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=73.67 E-value=3.5 Score=30.37 Aligned_cols=38 Identities=21% Similarity=0.287 Sum_probs=32.1
Q ss_pred hHHHHHHHHHc------CCceehhhhhhhcCCCHHHHHHHHHHH
Q 023862 84 RNRAMDAVDAC------NRRVTIGDVAGKAGLKLNEAQKALQAL 121 (276)
Q Consensus 84 ~~rim~Ave~l------g~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (276)
.|+..+.+++. |+..|+.+++.+.|+++++.-++|.+|
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 688999999999999999999999875
No 53
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=73.08 E-value=23 Score=31.82 Aligned_cols=82 Identities=24% Similarity=0.214 Sum_probs=59.3
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCC--ceEe-ecCccEEEEcCcchHHHhhhhhHHHhHHHH
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG--FLEV-SDEGDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~G--hLeV-SesGDIlYvFP~nfRs~L~~Ks~r~rl~~~ 161 (276)
-.|.+++...| .+|=-++|...|+.++++++.|.+|-.+.-. +=+. .++|...|..=-+++.++.. ++.+....
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-ELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDEESGWEEYTWYINYEKVLEV--LKGKKRKI 97 (176)
T ss_pred hHHHHHHHhcC-CcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCCCcEEEEEEechHHHHHH--HHHHHHHH
Confidence 46788999888 9999999999999999999999999887633 3333 34888988886677765443 33344444
Q ss_pred HHHHhhhh
Q 023862 162 IDKAKAAA 169 (276)
Q Consensus 162 ~~k~w~v~ 169 (276)
++++...+
T Consensus 98 le~Lk~~l 105 (176)
T COG1675 98 LEKLKRKL 105 (176)
T ss_pred HHHHHHHH
Confidence 44444443
No 54
>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=73.07 E-value=35 Score=27.25 Aligned_cols=79 Identities=16% Similarity=0.214 Sum_probs=56.3
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcC----CCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHhhhhhHHHh
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAG----LKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLK 157 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aG----L~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L~~Ks~r~r 157 (276)
+....||+.+=++|. +|+.||..... ++.+.++.-|..|.. -|.|++...|---+..|--=+. .+.+..
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 99999997765 568888888888887 5899999988754444433222 345555
Q ss_pred HHHHHHHHhh
Q 023862 158 VEPVIDKAKA 167 (276)
Q Consensus 158 l~~~~~k~w~ 167 (276)
++.+++++..
T Consensus 76 ~~~~l~~~~~ 85 (115)
T PF03965_consen 76 LRQFLDRLFD 85 (115)
T ss_dssp HHHHHHHHST
T ss_pred HHHHHHHHhC
Confidence 6666666544
No 55
>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=72.50 E-value=9.1 Score=26.95 Aligned_cols=44 Identities=14% Similarity=0.226 Sum_probs=34.3
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcC
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTD 126 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~ 126 (276)
.+..||..+...+...|+.|+|...|++...+-+.|..|....=
T Consensus 4 ~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~gl 47 (68)
T PF13463_consen 4 PQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGL 47 (68)
T ss_dssp HHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 35678888888899999999999999999999999999998743
No 56
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=72.40 E-value=8 Score=35.38 Aligned_cols=42 Identities=12% Similarity=0.191 Sum_probs=37.4
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
+-+.+|++.+++. +.+|+.|+|..-++|..++++.|..|.++
T Consensus 5 ~R~~~Il~~l~~~-~~~~~~ela~~l~vS~~TiRRdL~~Le~~ 46 (252)
T PRK10906 5 QRHDAIIELVKQQ-GYVSTEELVEHFSVSPQTIRRDLNDLAEQ 46 (252)
T ss_pred HHHHHHHHHHHHc-CCEeHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 5677889999665 47999999999999999999999999985
No 57
>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=72.21 E-value=5.8 Score=35.39 Aligned_cols=44 Identities=30% Similarity=0.416 Sum_probs=37.0
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023862 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (276)
Q Consensus 86 rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeV 131 (276)
+|++++.+.+..+|+.|+|.++|++...+-+=|..|.+. |.|+=
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 567777777888999999999999999999999999764 56653
No 58
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=71.99 E-value=38 Score=30.81 Aligned_cols=54 Identities=15% Similarity=0.219 Sum_probs=42.9
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEE
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY 139 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlY 139 (276)
+-+.+|++.+++.+ .+|+.|+|..-|+|...+++.|..|.. .|.|+-. .|-.+|
T Consensus 4 ~R~~~Il~~l~~~~-~~~~~eLa~~l~VS~~TiRRdL~~L~~--~~~l~r~-~Gga~~ 57 (240)
T PRK10411 4 ARQQAIVDLLLNHT-SLTTEALAEQLNVSKETIRRDLNELQT--QGKILRN-HGRAKY 57 (240)
T ss_pred HHHHHHHHHHHHcC-CCcHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEe-cCeEEE
Confidence 44677899998755 899999999999999999999999988 3667643 444433
No 59
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=70.89 E-value=38 Score=24.70 Aligned_cols=48 Identities=10% Similarity=0.232 Sum_probs=41.2
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecC
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSes 134 (276)
...|+..+...+ .+|+.|+|...+++...+.+.|..|.++ |-++..++
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 567889998876 6999999999999999999999999986 67766654
No 60
>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=70.75 E-value=7.8 Score=34.67 Aligned_cols=43 Identities=23% Similarity=0.386 Sum_probs=37.0
Q ss_pred hhhHHHHHHH-HHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 82 DVRNRAMDAV-DACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 82 ~~~~rim~Av-e~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
....+|++.+ +..++.+|+.++|...|.+..-|+..|..+..+
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 6778899999 888999999999999999999999999986654
No 61
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=69.86 E-value=8.2 Score=35.11 Aligned_cols=42 Identities=17% Similarity=0.274 Sum_probs=36.8
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAs 123 (276)
.+-+.+|++.+++.| ++|+.|+|..-|.|...+++.|..|..
T Consensus 6 ~eR~~~I~~~l~~~~-~v~v~eLa~~~~VS~~TIRRDL~~Le~ 47 (252)
T PRK10681 6 DERIGQLLQALKRSD-KLHLKDAAALLGVSEMTIRRDLNAHSA 47 (252)
T ss_pred HHHHHHHHHHHHHcC-CCcHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 356778899888855 599999999999999999999999884
No 62
>PRK11569 transcriptional repressor IclR; Provisional
Probab=69.56 E-value=7.6 Score=35.45 Aligned_cols=47 Identities=19% Similarity=0.383 Sum_probs=39.4
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
-+|++++.+.+..+|+.|+|..+|++...+.+=|..|.+. |-|+-.+
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 4678888888888999999999999999999999999764 6665443
No 63
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=69.04 E-value=6.4 Score=25.75 Aligned_cols=35 Identities=20% Similarity=0.342 Sum_probs=29.6
Q ss_pred CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 023862 96 RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (276)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS 132 (276)
..+|+.|+|...|++...+.+.|..|.++ |-|+..
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 555544
No 64
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=68.56 E-value=8.1 Score=35.30 Aligned_cols=48 Identities=15% Similarity=0.248 Sum_probs=40.3
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecC
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSes 134 (276)
-+|++++.+.+...|+.|+|..+|++...+-+=|..|.+. |.|+-+++
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 4678888888888999999999999999999999999875 66755543
No 65
>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=68.47 E-value=8 Score=31.39 Aligned_cols=26 Identities=19% Similarity=0.171 Sum_probs=11.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023862 171 YSIRVLFGTALIASIVIVFTAIIAIL 196 (276)
Q Consensus 171 YliRIsFGi~LIaSIvLv~~aI~ail 196 (276)
|+-++.=-+++.+=|+||.+++++++
T Consensus 18 ~~~~l~pn~lMtILivLVIIiLlIml 43 (85)
T PF10717_consen 18 NLNGLNPNTLMTILIVLVIIILLIML 43 (85)
T ss_pred cccccChhHHHHHHHHHHHHHHHHHH
Confidence 33344333444444455555554555
No 66
>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=68.42 E-value=10 Score=32.66 Aligned_cols=47 Identities=26% Similarity=0.462 Sum_probs=38.6
Q ss_pred hhhHHHHHHHHH----cCCceehhhhhhhcCCC-HHHHHHHHHHHHhhcCCceE
Q 023862 82 DVRNRAMDAVDA----CNRRVTIGDVAGKAGLK-LNEAQKALQALAADTDGFLE 130 (276)
Q Consensus 82 ~~~~rim~Ave~----lg~rvTvgDVAa~aGL~-l~~Ae~aL~aLAsD~~GhLe 130 (276)
+.+.+|++.+.+ .++..|+.|+|...|++ ...+.+.|..|..+ |.|+
T Consensus 6 ~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~--g~i~ 57 (199)
T TIGR00498 6 ARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERK--GYIE 57 (199)
T ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHC--CCEe
Confidence 456777777764 57779999999999998 99999999999987 4444
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=67.56 E-value=4.8 Score=28.47 Aligned_cols=21 Identities=33% Similarity=0.528 Sum_probs=18.8
Q ss_pred ehhhhhhhcCCCHHHHHHHHH
Q 023862 99 TIGDVAGKAGLKLNEAQKALQ 119 (276)
Q Consensus 99 TvgDVAa~aGL~l~~Ae~aL~ 119 (276)
|+.|||..+|+|...+-+.|.
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 789999999999999987774
No 68
>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=67.34 E-value=18 Score=25.02 Aligned_cols=42 Identities=14% Similarity=0.229 Sum_probs=36.1
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
.+-.+|..+.+.++ +|+.|+|...|++...+-+.+..|..+.
T Consensus 4 ~q~~iL~~l~~~~~-~~~~~la~~~~~~~~~~t~~i~~L~~~g 45 (59)
T PF01047_consen 4 SQFRILRILYENGG-ITQSELAEKLGISRSTVTRIIKRLEKKG 45 (59)
T ss_dssp HHHHHHHHHHHHSS-EEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHcCC-CCHHHHHHHHCCChhHHHHHHHHHHHCC
Confidence 35678999999888 9999999999999999999999998764
No 69
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=66.11 E-value=10 Score=34.40 Aligned_cols=52 Identities=19% Similarity=0.406 Sum_probs=40.3
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-CccEEEEc
Q 023862 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYVF 141 (276)
Q Consensus 86 rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe-sGDIlYvF 141 (276)
+|++++...+..+|+.|+|.+.|++...+-+-|..|.+. |-|+-.+ +|. |.-
T Consensus 15 ~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~--g~v~~~~~~~~--Y~L 67 (263)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEE--GYVRRSASDDS--FRL 67 (263)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEecCCCc--EEE
Confidence 456777677777999999999999999999999999764 6665443 443 554
No 70
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=65.01 E-value=19 Score=33.06 Aligned_cols=61 Identities=28% Similarity=0.398 Sum_probs=45.4
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecC-ccE-EEEcCcch
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-GDV-LYVFPNNY 145 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSes-GDI-lYvFP~nf 145 (276)
..+-+.+.+...| -+|+.|+|--+||+..+++++|..|.++ +.=.+|+-+ |.- .|.-|.+-
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 3344455666665 8999999999999999999998888652 333566665 776 88888765
No 71
>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=64.99 E-value=18 Score=26.54 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=28.8
Q ss_pred HcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 93 ~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
+.+..|+..|+|...|++...|-+.|..|+.+
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 72
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=64.65 E-value=11 Score=34.35 Aligned_cols=47 Identities=19% Similarity=0.335 Sum_probs=38.5
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
-+|++++.+.+..+|+.|+|.++|++...+.+-|..|... |-++-++
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~--G~v~~d~ 53 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVEL--GYVEQDP 53 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHC--CCEEEcC
Confidence 3678888886666899999999999999999999999764 5555444
No 73
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=63.89 E-value=13 Score=28.05 Aligned_cols=38 Identities=16% Similarity=0.198 Sum_probs=27.6
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 86 rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
.|++.++ .+..+..+++.+++|+-..+++-|..|....
T Consensus 10 ~IL~~l~--~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~g 47 (77)
T PF14947_consen 10 DILKILS--KGGAKKTEIMYKANLNYSTLKKYLKELEEKG 47 (77)
T ss_dssp HHHHHH---TT-B-HHHHHTTST--HHHHHHHHHHHHHTT
T ss_pred HHHHHHH--cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCc
Confidence 4444544 7888899999999999999999999998764
No 74
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=63.78 E-value=13 Score=31.06 Aligned_cols=60 Identities=25% Similarity=0.358 Sum_probs=48.0
Q ss_pred chhhHHHHHHHHHc--CCceehhhhhhhcCCC--HHHHHHHHHHHHhhc--CCceEeecCccEEEE
Q 023862 81 ADVRNRAMDAVDAC--NRRVTIGDVAGKAGLK--LNEAQKALQALAADT--DGFLEVSDEGDVLYV 140 (276)
Q Consensus 81 ~~~~~rim~Ave~l--g~rvTvgDVAa~aGL~--l~~Ae~aL~aLAsD~--~GhLeVSesGDIlYv 140 (276)
.+..+++.+.|.+. |+-.|-||||.-+|++ ..++-+.|..|-.++ .-|=-|+..|.|--.
T Consensus 5 def~~~v~~vv~~IP~GkV~TYGdIA~laG~p~~ARqVG~il~~l~~~s~lPWhRVvns~G~isl~ 70 (103)
T COG3695 5 DEFTQRVLDVVAAIPEGKVSTYGDIAKLAGLPRAARQVGRILKHLPEGSDLPWHRVVNSDGRISLP 70 (103)
T ss_pred hHHHHHHHHHHHhCCCCceeeHHHHHHHhCCChhHHHHHHHHhhCCCCCCCChhheecCCCcccCC
Confidence 35677888888875 6779999999999999 888888888766554 788888888887543
No 75
>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=63.67 E-value=4.1 Score=29.13 Aligned_cols=22 Identities=32% Similarity=0.543 Sum_probs=18.9
Q ss_pred hcCCceEeecCccEEEEcCcch
Q 023862 124 DTDGFLEVSDEGDVLYVFPNNY 145 (276)
Q Consensus 124 D~~GhLeVSesGDIlYvFP~nf 145 (276)
...|..||+.+|-.||.|.+|=
T Consensus 6 ~~dG~~~~~~~G~~LY~f~~D~ 27 (48)
T PF03640_consen 6 RADGTIQVDYNGMPLYYFDKDS 27 (48)
T ss_pred eCCCCEEECCCCCEEEEECCCC
Confidence 3469999999999999997764
No 76
>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=63.00 E-value=6.2 Score=27.90 Aligned_cols=22 Identities=18% Similarity=0.412 Sum_probs=19.4
Q ss_pred CCCCchhhHHHHHHHHHcCCce
Q 023862 77 DKLPADVRNRAMDAVDACNRRV 98 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rv 98 (276)
+++..+.+++|+++++++||+.
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 77
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=62.36 E-value=23 Score=29.42 Aligned_cols=59 Identities=14% Similarity=0.124 Sum_probs=43.1
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv 140 (276)
.+.=+++++-|-+. .-+|+..||.+-+++...|+++|+.|++..-=.+=+-..+-.||.
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 569999999999999999999999999876555555556667774
No 78
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=62.27 E-value=15 Score=39.92 Aligned_cols=56 Identities=21% Similarity=0.349 Sum_probs=45.8
Q ss_pred CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEE
Q 023862 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL 138 (276)
Q Consensus 80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIl 138 (276)
|..++.+|++-+. .||||.+-|++..-++.++-+|+.+..++.+- .++.. ..|||+
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 4456778888884 58999999999999999999999999998885 44444 578875
No 79
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=62.14 E-value=23 Score=28.51 Aligned_cols=66 Identities=23% Similarity=0.356 Sum_probs=45.8
Q ss_pred chhhHHHHHHHHHcCCceeh--hhhhhhcCCC-----HHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHhh
Q 023862 81 ADVRNRAMDAVDACNRRVTI--GDVAGKAGLK-----LNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLA 150 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTv--gDVAa~aGL~-----l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L~ 150 (276)
..+...|++.+.+.+..-|+ .|||-.-+-+ ..+++++-..|+. .|.++++-.|..| =|.+||..+|
T Consensus 6 ~~l~~~Il~ll~~R~~~ktiCPSevARal~~~~WR~lm~~vR~~A~~L~~--~G~i~I~qkG~~V--dp~~~rGpiR 78 (83)
T PF11625_consen 6 ARLEAAILALLAARGPGKTICPSEVARALGPDDWRDLMPPVRAAARRLAR--AGRIEITQKGKPV--DPETFRGPIR 78 (83)
T ss_dssp HHHHHHHHHHHHHS-TT--B-HHHHHHHH-TTS-GGGHHHHHHHHHHHHH--TTSEEEEETTEE----TTT--S--E
T ss_pred HHHHHHHHHHHHhcCCCCccCHHHHHHHHCchhhHHHHHHHHHHHHHHHH--CCcEEEEECCEec--CcccCcCCeE
Confidence 45678889999999887777 7999888755 7778888888876 5899999999988 5777776543
No 80
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=62.11 E-value=5.7 Score=35.56 Aligned_cols=26 Identities=31% Similarity=0.456 Sum_probs=22.9
Q ss_pred CCceehhhhhhhcCCCHHHHHHHHHH
Q 023862 95 NRRVTIGDVAGKAGLKLNEAQKALQA 120 (276)
Q Consensus 95 g~rvTvgDVAa~aGL~l~~Ae~aL~a 120 (276)
..++|+.|||..+|+|...+-++|..
T Consensus 4 ~~~~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 4 AKKITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHHHCC
Confidence 45799999999999999999888864
No 81
>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=61.80 E-value=40 Score=26.76 Aligned_cols=62 Identities=13% Similarity=0.127 Sum_probs=48.6
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCc
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~a-----GL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~ 143 (276)
..|..|++++.+.+.-+|+.||.... .+++..+=+.|..|....=-+=-..++|...|.+-.
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 46889999999999999999987765 588999999999999877554444557888888743
No 82
>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=61.64 E-value=14 Score=28.71 Aligned_cols=57 Identities=19% Similarity=0.207 Sum_probs=45.9
Q ss_pred hhhHHHHHHHHHcC--CceehhhhhhhcC--CCHHHHHHHHHH--HHhhcCCceEeecCccEE
Q 023862 82 DVRNRAMDAVDACN--RRVTIGDVAGKAG--LKLNEAQKALQA--LAADTDGFLEVSDEGDVL 138 (276)
Q Consensus 82 ~~~~rim~Ave~lg--~rvTvgDVAa~aG--L~l~~Ae~aL~a--LAsD~~GhLeVSesGDIl 138 (276)
+.+.++.+++.+.. .-+|-+|||..+| -....+-.+|.. +.....+|==|+.+|.+-
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 777778788877 666779999999999975
No 83
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=61.62 E-value=12 Score=30.91 Aligned_cols=43 Identities=21% Similarity=0.190 Sum_probs=35.2
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
+++..|..+....|..+++.++|.+.|+|..-++++|..|..+
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 4555566665556678999999999999999999999999875
No 84
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=61.24 E-value=58 Score=27.53 Aligned_cols=63 Identities=24% Similarity=0.168 Sum_probs=45.1
Q ss_pred HHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcC--CceE--ee-cCc-cEEEEcCcchHHHhh
Q 023862 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTD--GFLE--VS-DEG-DVLYVFPNNYRAKLA 150 (276)
Q Consensus 87 im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~--GhLe--VS-esG-DIlYvFP~nfRs~L~ 150 (276)
||+++-+.| -+|-.|+|...|++++++++.|..|-.|-- .+-+ -. ++| -..|.|==|++.+..
T Consensus 6 v~d~L~~~~-~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~ 74 (147)
T smart00531 6 VLDALMRNG-CVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLD 74 (147)
T ss_pred ehHHHHhcC-CcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHH
Confidence 577777765 799999999999999999999999998543 2222 22 245 467766456665443
No 85
>PRK09480 slmA division inhibitor protein; Provisional
Probab=61.23 E-value=9.2 Score=31.52 Aligned_cols=32 Identities=19% Similarity=0.415 Sum_probs=24.2
Q ss_pred chhhHHHHHHH----H-HcCCceehhhhhhhcCCCHH
Q 023862 81 ADVRNRAMDAV----D-ACNRRVTIGDVAGKAGLKLN 112 (276)
Q Consensus 81 ~~~~~rim~Av----e-~lg~rvTvgDVAa~aGL~l~ 112 (276)
.+.+.+|++|+ . +.|..+|+.|||.++|++..
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 45677777773 2 33689999999999997753
No 86
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=61.05 E-value=28 Score=28.14 Aligned_cols=61 Identities=26% Similarity=0.312 Sum_probs=45.6
Q ss_pred CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (276)
Q Consensus 79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv 140 (276)
++.+.-+++++-|.+ -.-+|+.-||.+-+++.+.|+++|+.|....-=.+-+-...-.||.
T Consensus 24 ~dk~t~dkl~kEV~~-~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt 84 (86)
T PRK09334 24 LDEELLKRVAKEVKK-EKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYV 84 (86)
T ss_pred cCHHHHHHHHHHhcc-CcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEec
Confidence 556677788887776 4568999999999999999999999998764333333334556663
No 87
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=61.02 E-value=17 Score=31.45 Aligned_cols=45 Identities=13% Similarity=0.107 Sum_probs=38.8
Q ss_pred HHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc------CCceEeecCcc
Q 023862 92 DACNRRVTIGDVAGKAGLKLNEAQKALQALAADT------DGFLEVSDEGD 136 (276)
Q Consensus 92 e~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~------~GhLeVSesGD 136 (276)
.+.++.++++|+|..-+++...+.+.|+.|+++. .+.++.|+.|+
T Consensus 19 ~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~ 69 (154)
T COG1321 19 LEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGR 69 (154)
T ss_pred HhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCeEEChhhH
Confidence 3478899999999999999999999999999874 56677777776
No 88
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=60.65 E-value=17 Score=32.04 Aligned_cols=41 Identities=17% Similarity=0.242 Sum_probs=36.7
Q ss_pred chhhHHHHHHHHHcC-CceehhhhhhhcCCCHHHHHHHHHHH
Q 023862 81 ADVRNRAMDAVDACN-RRVTIGDVAGKAGLKLNEAQKALQAL 121 (276)
Q Consensus 81 ~~~~~rim~Ave~lg-~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (276)
.....+|++.+.+.| -++++.|+|..+|++..++++.|..|
T Consensus 15 ~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l 56 (213)
T PRK05472 15 LPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYF 56 (213)
T ss_pred hHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHH
Confidence 345678899999977 69999999999999999999999999
No 89
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=60.27 E-value=44 Score=34.44 Aligned_cols=71 Identities=11% Similarity=0.129 Sum_probs=62.1
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHhhhhh
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKS 153 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L~~Ks 153 (276)
+....+|++++++.+...+..++|.+.|++.+++.+++..|.++ |-++|.+.=...|+-...=+..+++-+
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 689999999999999887777777744
No 90
>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=59.73 E-value=17 Score=26.74 Aligned_cols=37 Identities=16% Similarity=0.218 Sum_probs=28.1
Q ss_pred HHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 89 DAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 89 ~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
+..-+.++++|++|+|..-+++.+.++.-|..|....
T Consensus 6 ~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG 42 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKG 42 (69)
T ss_dssp HHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCT
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 3444567899999999999999999999888887653
No 91
>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=59.38 E-value=19 Score=27.45 Aligned_cols=55 Identities=20% Similarity=0.175 Sum_probs=43.5
Q ss_pred hHHHHHHHHH--cCCceehhhhhhhcCC--CHHHHHHHHHHHHh--hcCCceEeecCccEE
Q 023862 84 RNRAMDAVDA--CNRRVTIGDVAGKAGL--KLNEAQKALQALAA--DTDGFLEVSDEGDVL 138 (276)
Q Consensus 84 ~~rim~Ave~--lg~rvTvgDVAa~aGL--~l~~Ae~aL~aLAs--D~~GhLeVSesGDIl 138 (276)
+.++.+++++ .|.-+|-+|||..+|. ....+-.+|.+.-. +..+|==|+.+|.+.
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 3566677766 5777899999999999 57777788777655 679998999988886
No 92
>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=59.12 E-value=38 Score=25.56 Aligned_cols=45 Identities=24% Similarity=0.281 Sum_probs=34.0
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCce
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFL 129 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhL 129 (276)
+-+-+.+........-.+.|+++.|++++.++-|+..|+...-.|
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 334567778888889999999999999999999999998876554
No 93
>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=58.90 E-value=35 Score=26.22 Aligned_cols=46 Identities=22% Similarity=0.455 Sum_probs=31.3
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee-cCccEEEEcCcc
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS-DEGDVLYVFPNN 144 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS-esGDIlYvFP~n 144 (276)
-+..+++.+++.|..||.+-|+ +.|..| |-..|. ++|.-+|..|.+
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 4678889999999988887654 555555 446777 799999999875
No 94
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=58.67 E-value=34 Score=32.11 Aligned_cols=59 Identities=15% Similarity=0.195 Sum_probs=45.5
Q ss_pred CCCchhhHHHHHHHHHcCCceehhhhhhhcC--------------CCHHHHHHHHHHHHhhcCCceEeecCcc
Q 023862 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAG--------------LKLNEAQKALQALAADTDGFLEVSDEGD 136 (276)
Q Consensus 78 ~l~~~~~~rim~Ave~lg~rvTvgDVAa~aG--------------L~l~~Ae~aL~aLAsD~~GhLeVSesGD 136 (276)
++..+.|+||++++|++||+....--+.+++ ---.+.-+++...+++.|=++-+..+.+
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 7899999999999999999977765555555 2345666788888888888877766554
No 95
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=58.56 E-value=23 Score=29.72 Aligned_cols=42 Identities=10% Similarity=0.180 Sum_probs=37.5
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
...+|++++.+. +|.+..++|.+.|+|...+++-++.|-++.
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 667888888766 899999999999999999999999998765
No 96
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=58.53 E-value=8.9 Score=35.76 Aligned_cols=32 Identities=31% Similarity=0.606 Sum_probs=30.1
Q ss_pred cCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 94 CNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 94 lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
+||.+|+.+.|.+.|+.+++.++.|.+|....
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 79999999999999999999999999998765
No 97
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=58.17 E-value=19 Score=32.68 Aligned_cols=90 Identities=14% Similarity=0.225 Sum_probs=62.9
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCC-----c-----eEee----------cCcc-----
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG-----F-----LEVS----------DEGD----- 136 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~G-----h-----LeVS----------esGD----- 136 (276)
+-..+|++.+++.|-++|.-+||.+-|++..++.+.|-.|.....= + ++-. ++.+
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 4457899999999977999999999999999999999999754211 0 0000 0111
Q ss_pred ----EEE-----EcCcchHHHhhhhhHHHhHHHHHHHHhhhhhh
Q 023862 137 ----VLY-----VFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEY 171 (276)
Q Consensus 137 ----IlY-----vFP~nfRs~L~~Ks~r~rl~~~~~k~w~v~~Y 171 (276)
=+| +-|..+--.+..+..+-+||||.++-+....|
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 122 34555555566677888899999887665544
No 98
>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=57.99 E-value=34 Score=29.21 Aligned_cols=57 Identities=19% Similarity=0.271 Sum_probs=48.2
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhc--CCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKA--GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~a--GL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF 141 (276)
....|.+.+++.+.-.++.||..-- +++...++++|..|+.+ |.|.+-.-|--.+.|
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 3567999999999999999999877 58999999999999987 777777777665554
No 99
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=57.87 E-value=14 Score=33.11 Aligned_cols=51 Identities=14% Similarity=0.311 Sum_probs=38.4
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee-cCccEEEEc
Q 023862 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS-DEGDVLYVF 141 (276)
Q Consensus 86 rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS-esGDIlYvF 141 (276)
+|++++.+. ..+|+.|+|.++|++...+-+=|..|.+. |.|+-. ++|. |.-
T Consensus 18 ~IL~~l~~~-~~l~l~eia~~lgl~kstv~Rll~tL~~~--G~l~~~~~~~~--Y~l 69 (257)
T PRK15090 18 GILQALGEE-REIGITELSQRVMMSKSTVYRFLQTMKTL--GYVAQEGESEK--YSL 69 (257)
T ss_pred HHHHHhhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEcCCCCc--EEe
Confidence 456666654 46999999999999999999999999865 557544 3442 554
No 100
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=57.70 E-value=51 Score=34.06 Aligned_cols=70 Identities=17% Similarity=0.207 Sum_probs=61.0
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHhhhhh
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKS 153 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L~~Ks 153 (276)
+...+|+++++..+..++..++|...|++.+++.+++..|+++ |-++|.+.=+..|+-...=+..+++-+
T Consensus 3 ~~e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k--g~v~~~~~~~~~~~LT~eG~~~l~~G~ 72 (492)
T PLN02853 3 MAEEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGF--RYVDAQDIKRETWVLTEEGKKYAAEGS 72 (492)
T ss_pred hHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhC--CCEEEEEEEEEEEEECHHHHHHHHcCC
Confidence 5678999999987766899999999999999999999999998 689999988999998877777777643
No 101
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=57.65 E-value=55 Score=32.87 Aligned_cols=87 Identities=17% Similarity=0.202 Sum_probs=54.5
Q ss_pred HHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCcc-----EEEEcCcchHHHhhhhhHHHhHHHHHHHHh
Q 023862 92 DACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-----VLYVFPNNYRAKLAAKSFRLKVEPVIDKAK 166 (276)
Q Consensus 92 e~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGD-----IlYvFP~nfRs~L~~Ks~r~rl~~~~~k~w 166 (276)
.++|...|+.+||...|+++++.+..|.....-..-+..|.+++| ++-.-..+--..+.....+..|+.++..+-
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 457888999999999999999998877654332233344444433 221111122233334455666777777777
Q ss_pred hhhhhHHHHHHH
Q 023862 167 AAAEYSIRVLFG 178 (276)
Q Consensus 167 ~v~~YliRIsFG 178 (276)
.-=.-+++..||
T Consensus 353 ~reR~VI~LRyg 364 (415)
T PRK07598 353 SRERDVIRMRFG 364 (415)
T ss_pred HHHHHHHHHHHh
Confidence 766777777765
No 102
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=57.52 E-value=11 Score=34.15 Aligned_cols=42 Identities=21% Similarity=0.334 Sum_probs=34.6
Q ss_pred HHHHHHHHH------cCCceehhhhhhhcCCCHHHHHHHHHHHHhhcC
Q 023862 85 NRAMDAVDA------CNRRVTIGDVAGKAGLKLNEAQKALQALAADTD 126 (276)
Q Consensus 85 ~rim~Ave~------lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~ 126 (276)
++..+.+++ +||..|+++++.+.|++.++.-.+|.++++...
T Consensus 16 p~~~~vf~~~~idfCcgG~~~l~ea~~~~~i~~~~~~~~l~~~~~~~~ 63 (220)
T PRK10992 16 PRATALFREYDLDFCCGGKQTLARAAARKNLDIDVIEARLAALQEQPI 63 (220)
T ss_pred ccHHHHHHHcCCcccCCCCchHHHHHHHcCCCHHHHHHHHHHHHhccc
Confidence 344455555 579999999999999999999999999986653
No 103
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=57.01 E-value=96 Score=28.15 Aligned_cols=68 Identities=12% Similarity=0.100 Sum_probs=35.3
Q ss_pred ehhhhhhhcC------CCHHHHHHHHHHHHhhc-CCceEeecCccEEEEcCcchHHHhhhhhHHHhHHHHHHHHhhhhhh
Q 023862 99 TIGDVAGKAG------LKLNEAQKALQALAADT-DGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEY 171 (276)
Q Consensus 99 TvgDVAa~aG------L~l~~Ae~aL~aLAsD~-~GhLeVSesGDIlYvFP~nfRs~L~~Ks~r~rl~~~~~k~w~v~~Y 171 (276)
|+.|+..--. -.+++.+..+..|.... -.++.++=...- ..-. .+.++-.++...+...|..+..
T Consensus 160 ~~~d~l~ie~~L~~v~~eIe~~~~~~~~l~~~v~~sti~i~l~~~~------~~~~--~~~~~~~~~~~al~~~~~~~~~ 231 (262)
T PF14257_consen 160 TVEDLLEIERELSRVRSEIEQLEGQLKYLDDRVDYSTITISLYEPE------SIKP--ESPSFGSRFRDALKNGWNALVS 231 (262)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhceEEEEEEEEecC------CCCC--CCCCcchHHHHHHHHHHHHHHH
Confidence 7777654332 35666667777777766 455544322210 0000 3334445555556666666665
Q ss_pred HHH
Q 023862 172 SIR 174 (276)
Q Consensus 172 liR 174 (276)
++.
T Consensus 232 ~~~ 234 (262)
T PF14257_consen 232 FLS 234 (262)
T ss_pred HHH
Confidence 544
No 104
>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=56.72 E-value=29 Score=27.04 Aligned_cols=58 Identities=14% Similarity=0.098 Sum_probs=42.9
Q ss_pred hhhHHHHHHHHHc--CCceehhhhhhhcCCCH--HHHHHHHHHH--HhhcCCceEeecCccEEE
Q 023862 82 DVRNRAMDAVDAC--NRRVTIGDVAGKAGLKL--NEAQKALQAL--AADTDGFLEVSDEGDVLY 139 (276)
Q Consensus 82 ~~~~rim~Ave~l--g~rvTvgDVAa~aGL~l--~~Ae~aL~aL--AsD~~GhLeVSesGDIlY 139 (276)
+.+.+|.+++++- |..+|-||||..+|.+- ..+-.+|... .-...+|==|+.+|+|--
T Consensus 2 ~f~~~V~~~l~~IP~G~v~TYg~iA~~~g~p~~~RaVg~al~~np~~~~iPcHRVv~s~G~l~~ 65 (80)
T TIGR00589 2 PFQQRVWQALRTIPYGETKSYGQLAARIGNPKAVRAVGGANGRNPLAILVPCHRVIGKNGSLTG 65 (80)
T ss_pred hHHHHHHHHHhCCCCCCcCCHHHHHHHhCCCChHHHHHHHHHhCCCCCCCCCceeECCCCCCCC
Confidence 4678899999987 67788999999999753 3443444332 234689999999999853
No 105
>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=56.64 E-value=26 Score=26.80 Aligned_cols=52 Identities=21% Similarity=0.337 Sum_probs=43.3
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (276)
Q Consensus 86 rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv 140 (276)
.|-+++.. ++..|+.+++..+|++-.++..||==||.+ +.+++.+.++.+|+
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 35667777 678999999999999999999999999876 67888888888876
No 106
>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=56.52 E-value=1e+02 Score=25.69 Aligned_cols=77 Identities=14% Similarity=0.111 Sum_probs=53.7
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhc----CCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHhhhhhHHHh
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKA----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLK 157 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~a----GL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L~~Ks~r~r 157 (276)
+....||+.+=+.| .+|+.||.... |++-..+..-|..|.. -|.|+...+|-.-+..|--=| ..+.+..
T Consensus 4 ~~E~~VM~vlW~~~-~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~--KG~v~~~k~gr~~~Y~p~vs~----ee~~~~~ 76 (130)
T TIGR02698 4 DAEWEVMRVVWTLG-ETTSRDIIRILAEKKDWSDSTIKTLLGRLVD--KGCLTTEKEGRKFIYTALVSE----DEAVENA 76 (130)
T ss_pred HHHHHHHHHHHcCC-CCCHHHHHHHHhhccCCcHHHHHHHHHHHHH--CCceeeecCCCcEEEEecCCH----HHHHHHH
Confidence 34567999998766 58999977764 7888999888888877 578998888985444443222 2334445
Q ss_pred HHHHHHHH
Q 023862 158 VEPVIDKA 165 (276)
Q Consensus 158 l~~~~~k~ 165 (276)
++.+.+++
T Consensus 77 ~~~~~~~~ 84 (130)
T TIGR02698 77 AQELFSRI 84 (130)
T ss_pred HHHHHHHH
Confidence 66665554
No 107
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=56.51 E-value=20 Score=34.70 Aligned_cols=53 Identities=17% Similarity=0.251 Sum_probs=41.2
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF 141 (276)
+..|++++.+.+..+|+.|++..||+..+++-.+|+.| +.|.+-..+-++++=
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 46788888888899999999999999999998877755 556655555555543
No 108
>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=56.36 E-value=16 Score=34.74 Aligned_cols=45 Identities=18% Similarity=0.344 Sum_probs=36.4
Q ss_pred HHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 87 im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
|++.+.+..+|++-.++|.+-|+|.....++++.|.+. |-+++..
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 34444444579999999999999999999999999875 6777776
No 109
>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=55.04 E-value=54 Score=28.69 Aligned_cols=49 Identities=18% Similarity=0.338 Sum_probs=39.9
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
..+.+|+..+.+.| .+|+.|+|...|++...+.+.|..|..+ |-++...
T Consensus 143 ~~~~~IL~~l~~~g-~~s~~eia~~l~is~stv~r~L~~Le~~--GlI~r~~ 191 (203)
T TIGR01884 143 REELKVLEVLKAEG-EKSVKNIAKKLGKSLSTISRHLRELEKK--GLVEQKG 191 (203)
T ss_pred HHHHHHHHHHHHcC-CcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEc
Confidence 34557888888765 5899999999999999999999999866 6665554
No 110
>PRK11050 manganese transport regulator MntR; Provisional
Probab=54.75 E-value=1.2e+02 Score=25.58 Aligned_cols=46 Identities=24% Similarity=0.335 Sum_probs=37.3
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
..|+.++.. ++..|+.|+|...|++...+.+.|..|.++ |-++...
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 455666665 567899999999999999999999999987 5666544
No 111
>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=54.70 E-value=33 Score=25.13 Aligned_cols=39 Identities=15% Similarity=0.262 Sum_probs=30.4
Q ss_pred hhHHHHHHHHHcCC-----ceehhhhhhhcCCCHHHHHHHHHHH
Q 023862 83 VRNRAMDAVDACNR-----RVTIGDVAGKAGLKLNEAQKALQAL 121 (276)
Q Consensus 83 ~~~rim~Ave~lg~-----rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (276)
-+.+++++.-+.|| ++|+.|+|..-|++...+..-|+.-
T Consensus 4 ~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 4 RQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 34556666666666 8999999999999999987777653
No 112
>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=54.61 E-value=18 Score=29.43 Aligned_cols=28 Identities=21% Similarity=0.331 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCC
Q 023862 177 FGTALIASIVIVFTAIIAILSSKSDDDD 204 (276)
Q Consensus 177 FGi~LIaSIvLv~~aI~ailss~s~~D~ 204 (276)
++++||+=++|+.+.+....||.+++++
T Consensus 27 lMtILivLVIIiLlImlfqsSS~~~~s~ 54 (85)
T PF10717_consen 27 LMTILIVLVIIILLIMLFQSSSNGNSSS 54 (85)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCCCCC
Confidence 6889999999999999999988766654
No 113
>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=54.60 E-value=25 Score=28.42 Aligned_cols=45 Identities=16% Similarity=0.306 Sum_probs=34.9
Q ss_pred HHHHHHHHc-CCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 023862 86 RAMDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (276)
Q Consensus 86 rim~Ave~l-g~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS 132 (276)
++|..+-+. +.++|+.|+|.+.|++...+++-|..|.+. |-++..
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~--Gli~~~ 58 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLA--GIVTSK 58 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHC--CcEEec
Confidence 345555443 567999999999999999999999999884 455543
No 114
>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=53.88 E-value=21 Score=29.89 Aligned_cols=49 Identities=20% Similarity=0.438 Sum_probs=33.9
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCc
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesG 135 (276)
++--+.++-|....+|+|||+..+|++..++==+-.|++ .|+++|....
T Consensus 43 pE~~~Il~lC~~~~SVAEiAA~L~lPlgVvrVLvsDL~~--~G~v~v~~p~ 91 (114)
T PF05331_consen 43 PEHRAILELCRRPLSVAEIAARLGLPLGVVRVLVSDLAD--AGLVRVRAPA 91 (114)
T ss_pred HHHHHHHHHHCCCccHHHHHHhhCCCchhhhhhHHHHHh--CCCEEEeCCC
Confidence 333344455555999999999999999998433333332 6888887754
No 115
>PRK09492 treR trehalose repressor; Provisional
Probab=53.75 E-value=8.5 Score=34.05 Aligned_cols=24 Identities=25% Similarity=0.448 Sum_probs=20.9
Q ss_pred CceehhhhhhhcCCCHHHHHHHHH
Q 023862 96 RRVTIGDVAGKAGLKLNEAQKALQ 119 (276)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~Ae~aL~ 119 (276)
.++|+.|||..+|+|...+-++|.
T Consensus 3 ~~~ti~dIA~~agVS~~TVSrvLn 26 (315)
T PRK09492 3 NKLTIKDIARLSGVGKSTVSRVLN 26 (315)
T ss_pred CCCcHHHHHHHhCCCHHHHhHHhC
Confidence 468999999999999988877776
No 116
>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=53.61 E-value=25 Score=30.34 Aligned_cols=54 Identities=11% Similarity=0.210 Sum_probs=41.5
Q ss_pred hHHHHHHHHHcCC-ceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCc
Q 023862 84 RNRAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (276)
Q Consensus 84 ~~rim~Ave~lg~-rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~ 143 (276)
=.+|-+.+++... .+|+.+||..+|++..+..+=++ .|.|++++.-.+-|.=.+
T Consensus 32 f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~Ir------eGRL~~~~~~nl~~~CE~ 86 (137)
T TIGR03826 32 FEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIR------EGRLQLKHFPNLGYPCER 86 (137)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHH------cCCeeccCCCCCcCcccc
Confidence 3556677776544 69999999999999999876655 489999998777775433
No 117
>PF10025 DUF2267: Uncharacterized conserved protein (DUF2267); InterPro: IPR018727 This entry contains proteins that have no known function. ; PDB: 2YSK_A.
Probab=53.41 E-value=8.3 Score=31.57 Aligned_cols=80 Identities=23% Similarity=0.312 Sum_probs=58.8
Q ss_pred hhhhhhhcCC-CHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHhhh------hhHHHhHHHHHHHHhh-----
Q 023862 100 IGDVAGKAGL-KLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAA------KSFRLKVEPVIDKAKA----- 167 (276)
Q Consensus 100 vgDVAa~aGL-~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L~~------Ks~r~rl~~~~~k~w~----- 167 (276)
+.+|+..+|+ +.++|++++++...--+-+|.+.+.-++.=..|.-.|..+.. ..-+..+++|+..+..
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 5689999999 999999999999999999999999999999999999999954 2233568888887776
Q ss_pred ---hhhhHHHHHHHH
Q 023862 168 ---AAEYSIRVLFGT 179 (276)
Q Consensus 168 ---v~~YliRIsFGi 179 (276)
-..+++|.-|.+
T Consensus 86 ~~~~a~~~~~aV~~~ 100 (125)
T PF10025_consen 86 DEDDAERLARAVFAA 100 (125)
T ss_dssp TEE-HHHHHHHHHHH
T ss_pred CcccHHHHHHHHHHH
Confidence 455666655544
No 118
>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=53.33 E-value=19 Score=32.70 Aligned_cols=39 Identities=18% Similarity=0.382 Sum_probs=33.8
Q ss_pred hHHHHHHHHHcCCc--eehhhhhhhcCCCHHHHHHHHHHHH
Q 023862 84 RNRAMDAVDACNRR--VTIGDVAGKAGLKLNEAQKALQALA 122 (276)
Q Consensus 84 ~~rim~Ave~lg~r--vTvgDVAa~aGL~l~~Ae~aL~aLA 122 (276)
+..|++++.+.... +|+.|++.+||+..+++-.+|+.|-
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 57889999999885 9999999999999999998888763
No 119
>PRK09526 lacI lac repressor; Reviewed
Probab=53.24 E-value=10 Score=33.95 Aligned_cols=48 Identities=21% Similarity=0.201 Sum_probs=33.3
Q ss_pred CceehhhhhhhcCCCHHHHHHHHHH--------------HHhhcC-------CceEeecCccEEEEcCc
Q 023862 96 RRVTIGDVAGKAGLKLNEAQKALQA--------------LAADTD-------GFLEVSDEGDVLYVFPN 143 (276)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~Ae~aL~a--------------LAsD~~-------GhLeVSesGDIlYvFP~ 143 (276)
.++|+.|||.+||+|...+-+.|.. .|.+.| -.|.-..++-|-.++|.
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 4689999999999999888777752 222221 12455567778888874
No 120
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=53.03 E-value=26 Score=29.76 Aligned_cols=42 Identities=10% Similarity=0.255 Sum_probs=36.5
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
...+|++++ +.++|.|..|+|.+.|+|-..+.+-++.|-++.
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 566778755 568899999999999999999999999998765
No 121
>PHA03093 EEV glycoprotein; Provisional
Probab=52.80 E-value=26 Score=31.99 Aligned_cols=32 Identities=16% Similarity=0.247 Sum_probs=24.3
Q ss_pred HHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023862 164 KAKAAAEYSIRVLFGTALIASIVIVFTAIIAIL 196 (276)
Q Consensus 164 k~w~v~~YliRIsFGi~LIaSIvLv~~aI~ail 196 (276)
|..+.+...|||+..|.+| |.++|.++++..+
T Consensus 30 kk~r~i~i~~RisiiiSIl-sL~~i~~~LAlql 61 (185)
T PHA03093 30 KKVKCIGICIRISIIISIL-SLIAITATLALQL 61 (185)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Confidence 6677888999999999988 6666666665443
No 122
>PF15581 Imm35: Immunity protein 35
Probab=52.54 E-value=26 Score=28.87 Aligned_cols=33 Identities=27% Similarity=0.471 Sum_probs=30.3
Q ss_pred cCCCHHHHHHHHHHHHhhc-CCceEeecCccEEE
Q 023862 107 AGLKLNEAQKALQALAADT-DGFLEVSDEGDVLY 139 (276)
Q Consensus 107 aGL~l~~Ae~aL~aLAsD~-~GhLeVSesGDIlY 139 (276)
-||+-+|+++-|.+.|+.. ++..+|-.+|++|.
T Consensus 44 RGl~~~qV~~kl~ava~~~~~~~~vvKkE~~~Iw 77 (93)
T PF15581_consen 44 RGLPEEQVLYKLEAVAAKGPEAKIVVKKEGNIIW 77 (93)
T ss_pred cCCCHHHHHHHHHHHHhcCCCcceEEEecCCeEE
Confidence 4899999999999999987 99999999999886
No 123
>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=52.44 E-value=57 Score=31.50 Aligned_cols=60 Identities=18% Similarity=0.227 Sum_probs=49.5
Q ss_pred chhhHHHHHHHHHc--CCceehhhhhhh-cCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862 81 ADVRNRAMDAVDAC--NRRVTIGDVAGK-AGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (276)
Q Consensus 81 ~~~~~rim~Ave~l--g~rvTvgDVAa~-aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF 141 (276)
.++..+|++.+.+. +..+|..|+... .++++.+...+|+.|.++.--.|-. ..|.++|..
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 999999999999 7899999999999999998777766 667799987
No 124
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=51.24 E-value=11 Score=33.81 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=21.1
Q ss_pred CCceehhhhhhhcCCCHHHHHHHHH
Q 023862 95 NRRVTIGDVAGKAGLKLNEAQKALQ 119 (276)
Q Consensus 95 g~rvTvgDVAa~aGL~l~~Ae~aL~ 119 (276)
..++|+.|||..+|+|...+-+.|.
T Consensus 3 ~~~~ti~dIA~~agVS~~TVSrvLn 27 (331)
T PRK14987 3 KKRPVLQDVADRVGVTKMTVSRFLR 27 (331)
T ss_pred CCCCcHHHHHHHhCCCHHHhhhhhC
Confidence 4579999999999999988877763
No 125
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=50.62 E-value=84 Score=22.03 Aligned_cols=59 Identities=19% Similarity=0.231 Sum_probs=44.9
Q ss_pred CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (276)
Q Consensus 80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF 141 (276)
....+.+|+..+.+. ...|+.+++...+++...+...|..|-...-- +...+|...|..
T Consensus 23 ~~~~r~~il~~l~~~-~~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv--~~~~~~~~~~~~ 81 (110)
T COG0640 23 ADPTRLEILSLLAEG-GELTVGELAEALGLSQSTVSHHLKVLREAGLV--ELRREGRLRLYR 81 (110)
T ss_pred CCHHHHHHHHHHHhc-CCccHHHHHHHHCCChhHHHHHHHHHHHCCCe--EEEecccEEEEe
Confidence 344788888888887 78899999999999999999999997665433 335566554443
No 126
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=50.48 E-value=13 Score=28.48 Aligned_cols=29 Identities=17% Similarity=0.318 Sum_probs=23.7
Q ss_pred HHHHHHcCCceehhhhhhhcCCCHHHHHH
Q 023862 88 MDAVDACNRRVTIGDVAGKAGLKLNEAQK 116 (276)
Q Consensus 88 m~Ave~lg~rvTvgDVAa~aGL~l~~Ae~ 116 (276)
-+|++-...++++.||+..+||+..|||-
T Consensus 35 ~~A~klv~~Ga~~~el~~~CgL~~aEAeL 63 (70)
T PF10975_consen 35 SQAIKLVRQGASVEELMEECGLSRAEAEL 63 (70)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHH
Confidence 35566666779999999999999999953
No 127
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=49.61 E-value=16 Score=24.19 Aligned_cols=28 Identities=18% Similarity=0.356 Sum_probs=18.7
Q ss_pred HcCCceehhhhhhhcCCCHHHHHHHHHH
Q 023862 93 ACNRRVTIGDVAGKAGLKLNEAQKALQA 120 (276)
Q Consensus 93 ~lg~rvTvgDVAa~aGL~l~~Ae~aL~a 120 (276)
......|+.|||..+|++...-.+..++
T Consensus 4 ~~~~~~~l~~iA~~~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 4 NLQQKLTLEDIAEQAGFSPSYFSRLFKK 31 (42)
T ss_dssp TT-SS--HHHHHHHHTS-HHHHHHHHHH
T ss_pred cccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3456789999999999988777666554
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=49.60 E-value=11 Score=33.58 Aligned_cols=23 Identities=30% Similarity=0.482 Sum_probs=20.3
Q ss_pred ceehhhhhhhcCCCHHHHHHHHH
Q 023862 97 RVTIGDVAGKAGLKLNEAQKALQ 119 (276)
Q Consensus 97 rvTvgDVAa~aGL~l~~Ae~aL~ 119 (276)
++|+.|||..+|+|...+-++|.
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhC
Confidence 47999999999999998888874
No 129
>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=49.57 E-value=15 Score=25.14 Aligned_cols=32 Identities=13% Similarity=0.225 Sum_probs=21.2
Q ss_pred HHHHHHHcCCceehhhhhhhcCCCHHHHHHHH
Q 023862 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (276)
Q Consensus 87 im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL 118 (276)
+.++++-+..+.|+.|||...|++.....+-|
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 44444444455999999999999999887655
No 130
>PHA01815 hypothetical protein
Probab=49.39 E-value=69 Score=23.82 Aligned_cols=25 Identities=20% Similarity=0.215 Sum_probs=17.3
Q ss_pred HHHHHHHHhhhhhhHHHHHHHHHHH
Q 023862 158 VEPVIDKAKAAAEYSIRVLFGTALI 182 (276)
Q Consensus 158 l~~~~~k~w~v~~YliRIsFGi~LI 182 (276)
|-+++-.+--....-+|+|||+..-
T Consensus 12 llaflitliilmt~~irvsfgvlft 36 (55)
T PHA01815 12 LLAFLITLIILMTLHIRVSFGVLFT 36 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555566667789999997543
No 131
>PF15145 DUF4577: Domain of unknown function (DUF4577)
Probab=49.36 E-value=6.9 Score=33.61 Aligned_cols=36 Identities=28% Similarity=0.264 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCC
Q 023862 172 SIRVLFGTALIASIVIVFTAIIAILSSKSDDDDRGR 207 (276)
Q Consensus 172 liRIsFGi~LIaSIvLv~~aI~ailss~s~~D~~~r 207 (276)
+|=|.+-++|++|.+||...|+.|+.-.+.=|+=+|
T Consensus 62 lffvglii~LivSLaLVsFvIFLiiQTgnkMddvSr 97 (128)
T PF15145_consen 62 LFFVGLIIVLIVSLALVSFVIFLIIQTGNKMDDVSR 97 (128)
T ss_pred ehHHHHHHHHHHHHHHHHHHHHheeeccchHHHHHH
Confidence 444778899999999999999988755554444333
No 132
>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=47.48 E-value=38 Score=27.02 Aligned_cols=43 Identities=21% Similarity=0.352 Sum_probs=33.2
Q ss_pred HHHHHHHc--CCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023862 87 AMDAVDAC--NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (276)
Q Consensus 87 im~Ave~l--g~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeV 131 (276)
+|-.+.+. +..+|..++|...|++...+++-|..|... |-|+.
T Consensus 13 ~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~--gli~~ 57 (132)
T TIGR00738 13 ALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRA--GLVES 57 (132)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC--CcEEe
Confidence 45555444 347999999999999999999999999874 34544
No 133
>PRK06474 hypothetical protein; Provisional
Probab=47.22 E-value=43 Score=29.29 Aligned_cols=56 Identities=18% Similarity=0.180 Sum_probs=46.2
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhc-CCCHHHHHHHHHHHHhhcCCceEeecC
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKA-GLKLNEAQKALQALAADTDGFLEVSDE 134 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~a-GL~l~~Ae~aL~aLAsD~~GhLeVSes 134 (276)
+-|.-..|.+|++++...+...|+.|++... +++...+=+-|..|+.. |-+++.+.
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 3466788999999999987679999999998 68999998899999864 66666554
No 134
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=46.96 E-value=13 Score=33.40 Aligned_cols=46 Identities=22% Similarity=0.281 Sum_probs=31.8
Q ss_pred eehhhhhhhcCCCHHHHHHHHH--------------HHHhhcC-------CceEeecCccEEEEcCc
Q 023862 98 VTIGDVAGKAGLKLNEAQKALQ--------------ALAADTD-------GFLEVSDEGDVLYVFPN 143 (276)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL~--------------aLAsD~~-------GhLeVSesGDIlYvFP~ 143 (276)
+|+.|||.++|+|...+-++|. +.|.+.| -.|...++..|...+|.
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 6999999999999988777765 3333332 12444556677777775
No 135
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=46.70 E-value=44 Score=21.76 Aligned_cols=46 Identities=13% Similarity=0.213 Sum_probs=32.9
Q ss_pred CCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCC
Q 023862 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG 127 (276)
Q Consensus 78 ~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~G 127 (276)
.|+..-+. ++..+. ...+..|||...|++...+++-+..+-.+.+.
T Consensus 3 ~l~~~e~~-i~~~~~---~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~ 48 (58)
T smart00421 3 SLTPRERE-VLRLLA---EGLTNKEIAERLGISEKTVKTHLSNIMRKLGV 48 (58)
T ss_pred CCCHHHHH-HHHHHH---cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 45544443 554442 34699999999999999999998887666553
No 136
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=46.65 E-value=73 Score=27.92 Aligned_cols=55 Identities=16% Similarity=0.138 Sum_probs=37.2
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcC-----------C---CHHHHHHHHHHHHhhcCCceEe
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------L---KLNEAQKALQALAADTDGFLEV 131 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aG-----------L---~l~~Ae~aL~aLAsD~~GhLeV 131 (276)
+++..+.++||+++++++||+--..--+.+++ + --.+..+++..-|.+.|-.|.+
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 56888999999999999999875442222222 1 1344556777777777766654
No 137
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=46.35 E-value=50 Score=31.06 Aligned_cols=69 Identities=16% Similarity=0.242 Sum_probs=53.3
Q ss_pred ccccCCCCch----hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc--CCceEeecCccEEEEc
Q 023862 73 IVESDKLPAD----VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DGFLEVSDEGDVLYVF 141 (276)
Q Consensus 73 ~v~~~~l~~~----~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~--~GhLeVSesGDIlYvF 141 (276)
...-+.||.- .-..|+++++..+...|..++|.+.|+|--.|++=|.-|++-. .+.++-...|.+.|.+
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 4445566633 3356788888889999999999999999999999999999887 3444444577777765
No 138
>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=46.22 E-value=58 Score=25.56 Aligned_cols=32 Identities=28% Similarity=0.313 Sum_probs=29.0
Q ss_pred cCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 94 CNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 94 lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
....+|..|+|..+|++...+.++|..|..+.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~G 75 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRR 75 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 56789999999999999999999999998764
No 139
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=46.07 E-value=37 Score=23.05 Aligned_cols=38 Identities=11% Similarity=0.235 Sum_probs=27.9
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHH
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (276)
..+...|++.+.+. .|+.+||...|++-+.++.-+...
T Consensus 14 ~~~~~~i~~~~~~~---~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 14 KRLEQYILKLLRES---RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHHHHHhhc---CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 34445555555444 799999999999999998877653
No 140
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=46.02 E-value=61 Score=29.11 Aligned_cols=91 Identities=13% Similarity=0.087 Sum_probs=56.6
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCC-CHHHHHHHHHHHHhhc---CCceEeecCccEEEEcCcchHHHhhhhhHHH
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGL-KLNEAQKALQALAADT---DGFLEVSDEGDVLYVFPNNYRAKLAAKSFRL 156 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL-~l~~Ae~aL~aLAsD~---~GhLeVSesGDIlYvFP~nfRs~L~~Ks~r~ 156 (276)
|.....+.-++=..+..+|+.++|...|+ +..++..+|..|..++ |-.|++..+|==+|. +.
T Consensus 7 ~~~~~~vEall~a~~~pls~~~L~~il~~~~~~~~~~~l~~l~~~y~~rg~~L~~~~~~~r~~t--------------~~ 72 (184)
T COG1386 7 MELKALIEALLFAGGEPLSLKELAEILGIVSADAIIDALAELKEEYEDRGLELVEVAEGWRLQT--------------KQ 72 (184)
T ss_pred hhHHHHHHHHHHhcCCCCCHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCeeEEEEcCceeEEe--------------hH
Confidence 33334444455566779999999999999 8999999999999887 445666655422222 23
Q ss_pred hHHHHHHHHhhhhhhHHHHHHHHHHHHHHH
Q 023862 157 KVEPVIDKAKAAAEYSIRVLFGTALIASIV 186 (276)
Q Consensus 157 rl~~~~~k~w~v~~YliRIsFGi~LIaSIv 186 (276)
...++.++++..-.. -+.|=+.+-+++|+
T Consensus 73 ~~~~~~~~l~~~~~~-~~LSraalEtLAiI 101 (184)
T COG1386 73 EYAEYLEKLQEQRPK-RELSRAALETLAII 101 (184)
T ss_pred HHHHHHHHHhccccc-ccccHHHHHHHHHH
Confidence 344555555554444 22444445444433
No 141
>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=46.00 E-value=28 Score=26.29 Aligned_cols=44 Identities=20% Similarity=0.300 Sum_probs=36.4
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCC--HHHHHHHHHHHHhhcC
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLK--LNEAQKALQALAADTD 126 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~--l~~Ae~aL~aLAsD~~ 126 (276)
+..++|+++++.+| ..|.-.+|..-||+ ..++.+.|-.|.....
T Consensus 4 ~~ee~Il~~L~~~g-~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~ 49 (66)
T PF02295_consen 4 DLEEKILDFLKELG-GSTATAIAKALGLSVPKKEVNRVLYRLEKQGK 49 (66)
T ss_dssp HHHHHHHHHHHHHT-SSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred hHHHHHHHHHHhcC-CccHHHHHHHhCcchhHHHHHHHHHHHHHCCC
Confidence 56789999999999 77777777777766 7999999999987643
No 142
>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=45.77 E-value=1.9e+02 Score=24.75 Aligned_cols=42 Identities=17% Similarity=0.283 Sum_probs=29.6
Q ss_pred CCCchhhHHHHHHHHHc-----CCceehhhhhhhcCCCHHHHHHHHH
Q 023862 78 KLPADVRNRAMDAVDAC-----NRRVTIGDVAGKAGLKLNEAQKALQ 119 (276)
Q Consensus 78 ~l~~~~~~rim~Ave~l-----g~rvTvgDVAa~aGL~l~~Ae~aL~ 119 (276)
+||.+.++++++..++. -.+.|-.||.++-|=|.+-|++-+.
T Consensus 16 ~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~ 62 (181)
T PF08006_consen 16 KLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILA 62 (181)
T ss_pred cCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHH
Confidence 68999888888766543 2345777888888877777755443
No 143
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=45.54 E-value=1.7e+02 Score=24.03 Aligned_cols=38 Identities=18% Similarity=0.231 Sum_probs=32.2
Q ss_pred HHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 023862 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (276)
Q Consensus 91 ve~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLe 130 (276)
+...++.+|+.|+|...|++...+-+.|..|..+ |-++
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 4445677899999999999999999999999988 5554
No 144
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=45.41 E-value=37 Score=29.28 Aligned_cols=51 Identities=20% Similarity=0.318 Sum_probs=39.2
Q ss_pred chhhHHHHHHHHHcC--------------CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862 81 ADVRNRAMDAVDACN--------------RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 81 ~~~~~rim~Ave~lg--------------~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
.++++|+...+.++. ..+|..|+|...|++...+-+.|..|..+ |-++.+.
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 466788877776542 34789999999999999999999988775 4555544
No 145
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=45.36 E-value=26 Score=33.10 Aligned_cols=43 Identities=33% Similarity=0.415 Sum_probs=36.4
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLe 130 (276)
.++..+++++.+|.|-++=+...+|++..+|++.|. +++|||+
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 455788999999999999999999999999977665 5788775
No 146
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=45.19 E-value=34 Score=24.79 Aligned_cols=51 Identities=22% Similarity=0.273 Sum_probs=36.1
Q ss_pred ceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHh
Q 023862 97 RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKL 149 (276)
Q Consensus 97 rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L 149 (276)
.++..++..-.|++++. .++..+....|...+.+++++.+.+.++-||.=+
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 35667888888977653 3456666666777777666788888888888633
No 147
>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=45.06 E-value=67 Score=23.24 Aligned_cols=36 Identities=14% Similarity=0.211 Sum_probs=29.8
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh
Q 023862 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (276)
Q Consensus 86 rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAs 123 (276)
+|++.+.. ...|+.++|.+.|++...+++.+..|-+
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 46666553 3578999999999999999999999965
No 148
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=44.97 E-value=24 Score=31.11 Aligned_cols=32 Identities=19% Similarity=0.332 Sum_probs=25.3
Q ss_pred hhhHHHHHHH----HHcCCceehhhhhhhcCCCHHH
Q 023862 82 DVRNRAMDAV----DACNRRVTIGDVAGKAGLKLNE 113 (276)
Q Consensus 82 ~~~~rim~Av----e~lg~rvTvgDVAa~aGL~l~~ 113 (276)
+.|.+|++|. -+.||.+|+.|||.+||++...
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 5666676654 5679889999999999988765
No 149
>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=44.78 E-value=14 Score=32.85 Aligned_cols=46 Identities=26% Similarity=0.316 Sum_probs=30.9
Q ss_pred eehhhhhhhcCCCHHHHHHHHH--------------HHHhhcCC-------ceEeecCccEEEEcCc
Q 023862 98 VTIGDVAGKAGLKLNEAQKALQ--------------ALAADTDG-------FLEVSDEGDVLYVFPN 143 (276)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL~--------------aLAsD~~G-------hLeVSesGDIlYvFP~ 143 (276)
+|+.|||..||+|...+-+.|+ +.|.+.|= .|.-.+++-|..++|.
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 6899999999999987766653 33433331 2334456778788874
No 150
>PRK00441 argR arginine repressor; Provisional
Probab=44.72 E-value=81 Score=27.20 Aligned_cols=56 Identities=13% Similarity=0.295 Sum_probs=43.2
Q ss_pred hHHHHHHHHHcCCceehhhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEe-ecCccEEEEcCcch
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEV-SDEGDVLYVFPNNY 145 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~a-----GL~l~~Ae~aL~aLAsD~~GhLeV-SesGDIlYvFP~nf 145 (276)
+..|.+.+++ ....|+.|++..- +.+-..+.+.|.+| +-.+| +++|.-.|..|.+-
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 4555666665 5667999999885 78888889999888 45677 57999999998864
No 151
>PRK09526 lacI lac repressor; Reviewed
Probab=44.69 E-value=76 Score=28.41 Aligned_cols=56 Identities=14% Similarity=0.052 Sum_probs=38.5
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcC-----------C---CHHHHHHHHHHHHhhcCCceEee
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------L---KLNEAQKALQALAADTDGFLEVS 132 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aG-----------L---~l~~Ae~aL~aLAsD~~GhLeVS 132 (276)
.++..+.+++|+++++++||..-..--+.+++ + --.+.-+++.+.|.+.|-+|.+.
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 46899999999999999999754321111111 1 12456678888888888887764
No 152
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=44.62 E-value=1e+02 Score=28.27 Aligned_cols=44 Identities=20% Similarity=0.245 Sum_probs=32.4
Q ss_pred CCCchhhHHH---HH----HHHHcCCceehhhhhhhcCCCHHHHHHHHHHH
Q 023862 78 KLPADVRNRA---MD----AVDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (276)
Q Consensus 78 ~l~~~~~~ri---m~----Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (276)
++|...+..+ .+ .-.++|...|..|||...|++.+++++.+.+.
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 4666655432 22 23467889999999999999999998877653
No 153
>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=44.59 E-value=1.2e+02 Score=26.85 Aligned_cols=29 Identities=14% Similarity=0.225 Sum_probs=24.8
Q ss_pred HHcCCceehhhhhhhcCCCHHHHHHHHHH
Q 023862 92 DACNRRVTIGDVAGKAGLKLNEAQKALQA 120 (276)
Q Consensus 92 e~lg~rvTvgDVAa~aGL~l~~Ae~aL~a 120 (276)
.++|...|+.+||.+.|++.+++++.+..
T Consensus 98 ~~~g~~pt~~eia~~l~~~~~~v~~~~~~ 126 (238)
T TIGR02393 98 QELGREPTDEELAERMGMPAEKVREIKKI 126 (238)
T ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 35689999999999999999999876543
No 154
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=44.26 E-value=1.3e+02 Score=30.37 Aligned_cols=66 Identities=18% Similarity=0.325 Sum_probs=50.6
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHhhh
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAA 151 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L~~ 151 (276)
.+.++++++...+ .+|..|+|.+.|++...+-+.+..|.++ |-+++.+.=...|.-...=+..+.+
T Consensus 7 ~e~~vL~~L~~~~-~~s~~eLA~~l~l~~~tVt~~i~~Le~k--GlV~~~~~~~~~i~LTeeG~~~~~~ 72 (489)
T PRK04172 7 NEKKVLKALKELK-EATLEELAEKLGLPPEAVMRAAEWLEEK--GLVKVEERVEEVYVLTEEGKKYAEE 72 (489)
T ss_pred HHHHHHHHHHhCC-CCCHHHHHHHhCcCHHHHHHHHHHHHhC--CCEEEEeeeEEEEEECHHHHHHHHh
Confidence 5678999998766 6999999999999999999999999998 6777766434444444444444444
No 155
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=44.14 E-value=21 Score=30.68 Aligned_cols=32 Identities=13% Similarity=0.197 Sum_probs=24.3
Q ss_pred hhhHHHHHH----HHHcCCc-eehhhhhhhcCCCHHH
Q 023862 82 DVRNRAMDA----VDACNRR-VTIGDVAGKAGLKLNE 113 (276)
Q Consensus 82 ~~~~rim~A----ve~lg~r-vTvgDVAa~aGL~l~~ 113 (276)
+.|.+|++| +.+.||. +|+.|||.++|++...
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 456666554 5677877 8999999999988643
No 156
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=43.67 E-value=95 Score=27.84 Aligned_cols=57 Identities=9% Similarity=0.105 Sum_probs=37.4
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcC-----------CC---HHHHHHHHHHHHhhcCCceEeec
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------LK---LNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aG-----------L~---l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
.++..+.|++|+++++++||+.-..--+.+++ ++ -.+.-+++..-|.+.|-++.+..
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 34556677777777777766543
No 157
>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=43.62 E-value=82 Score=21.38 Aligned_cols=41 Identities=20% Similarity=0.321 Sum_probs=29.2
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHH
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQA 120 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~a 120 (276)
+.||..-+.-|.... ....|..|||..-|+|...+.+-+..
T Consensus 3 ~~L~~~er~vi~~~y---~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 3 DQLPPREREVIRLRY---FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp CTS-HHHHHHHHHHH---TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred hhCCHHHHHHHHHHh---cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 456666665554444 77889999999999999999765544
No 158
>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=43.55 E-value=43 Score=24.03 Aligned_cols=33 Identities=21% Similarity=0.368 Sum_probs=27.8
Q ss_pred ceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023862 97 RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (276)
Q Consensus 97 rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeV 131 (276)
.+|..|+|..+|++...+.+.|..|..+. -+++
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g--~I~~ 60 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEG--IIEV 60 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTT--SEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCC--CEEE
Confidence 45788999999999999999999998864 4443
No 159
>cd00131 PAX Paired Box domain
Probab=43.52 E-value=56 Score=27.16 Aligned_cols=44 Identities=16% Similarity=0.257 Sum_probs=37.9
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAs 123 (276)
--|+.+.|.+|+.+++ ...+..+||.+.|++...+.+-+..-..
T Consensus 16 ~~lS~d~R~rIv~~~~---~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 16 RPLPDSIRQRIVELAQ---SGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CcCCHHHHHHHHHHHH---cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4588899999999987 2479999999999999999888887665
No 160
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=43.47 E-value=56 Score=26.46 Aligned_cols=51 Identities=14% Similarity=0.261 Sum_probs=42.0
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc---CCceEeec
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT---DGFLEVSD 133 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~---~GhLeVSe 133 (276)
+...+|++.+++.+. .+..++|.+.|+|...+..-+..|-.+. +-+..++.
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 9999999999999999999999999887 44555553
No 161
>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=43.45 E-value=40 Score=25.51 Aligned_cols=33 Identities=21% Similarity=0.423 Sum_probs=29.1
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHH
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQ 115 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae 115 (276)
-|..+-+.-...++.+++-|||.+-|++..+++
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 467777788899999999999999999998875
No 162
>PRK05949 RNA polymerase sigma factor; Validated
Probab=43.41 E-value=1.1e+02 Score=29.29 Aligned_cols=87 Identities=15% Similarity=0.182 Sum_probs=48.6
Q ss_pred HHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc-CCceEeecCcc-----EEEEcCcchHHHhhhhhHHHhHHHHHHH
Q 023862 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT-DGFLEVSDEGD-----VLYVFPNNYRAKLAAKSFRLKVEPVIDK 164 (276)
Q Consensus 91 ve~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~-~GhLeVSesGD-----IlYvFP~nfRs~L~~Ks~r~rl~~~~~k 164 (276)
..++|...|+.++|...|++.++++..+. .+.+. .=+-.+.++++ ++=.-..+--..+.....+..++++++.
T Consensus 188 ~~~lgr~pt~~eiA~~l~i~~~~v~~~~~-~~~~~~SLd~~~~~~~~~~l~~~l~d~~~~pe~~~~~~~~~~~L~~~L~~ 266 (327)
T PRK05949 188 SQKLGRSATPAEIAKELELEPSQIREYLS-MARQPISLDVRVGDNQDTELSELLEDEGPSPDQYITQELLRQDLNNLLAE 266 (327)
T ss_pred HHHhCCCCCHHHHHHHhCcCHHHHHHHHH-HhccccccCCCcCCCCCccHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 36679999999999999999999977654 33221 10111222222 2211111122333444555566776666
Q ss_pred HhhhhhhHHHHHHH
Q 023862 165 AKAAAEYSIRVLFG 178 (276)
Q Consensus 165 ~w~v~~YliRIsFG 178 (276)
+-.-=..+|+..||
T Consensus 267 L~~rer~Vi~lr~g 280 (327)
T PRK05949 267 LTPQQREVLTLRFG 280 (327)
T ss_pred CCHHHHHHHHHHhc
Confidence 66555556665554
No 163
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=43.19 E-value=20 Score=29.96 Aligned_cols=29 Identities=21% Similarity=0.186 Sum_probs=22.1
Q ss_pred hHHHHHH----HHHcCCc-eehhhhhhhcCCCHH
Q 023862 84 RNRAMDA----VDACNRR-VTIGDVAGKAGLKLN 112 (276)
Q Consensus 84 ~~rim~A----ve~lg~r-vTvgDVAa~aGL~l~ 112 (276)
|.+|+++ +.+.|+. +|+.|||.++|++..
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 5556555 5567887 899999999998754
No 164
>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=43.16 E-value=57 Score=28.47 Aligned_cols=49 Identities=29% Similarity=0.375 Sum_probs=35.7
Q ss_pred HHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc---CCceEeecCccEEEEc
Q 023862 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT---DGFLEVSDEGDVLYVF 141 (276)
Q Consensus 91 ve~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~---~GhLeVSesGDIlYvF 141 (276)
+=-.|..||+.++|...+ +.+++++.|..|..++ +.-|++-+.|+- |.|
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 9999999999999999 666777776553 444
No 165
>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=42.99 E-value=51 Score=18.41 Aligned_cols=34 Identities=12% Similarity=0.219 Sum_probs=23.7
Q ss_pred CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHH
Q 023862 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQ 115 (276)
Q Consensus 79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae 115 (276)
++++.+..+++..+ .+ .|+.++|...|++...+.
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 44555566666654 23 399999999999887664
No 166
>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=42.86 E-value=23 Score=36.43 Aligned_cols=18 Identities=22% Similarity=0.421 Sum_probs=13.4
Q ss_pred CccEEEEcCcchHHHhhh
Q 023862 134 EGDVLYVFPNNYRAKLAA 151 (276)
Q Consensus 134 sGDIlYvFP~nfRs~L~~ 151 (276)
+|.|+|.-+.|-|....+
T Consensus 421 ~G~L~~~~~f~~r~~~~~ 438 (507)
T PF07245_consen 421 KGTLIYLGPFDDRNYTGG 438 (507)
T ss_pred EEEEEeccccccccccCc
Confidence 689999998877654433
No 167
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=42.47 E-value=98 Score=27.72 Aligned_cols=54 Identities=13% Similarity=0.122 Sum_probs=35.6
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcC-----------CC---HHHHHHHHHHHHhhcCCceE
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------LK---LNEAQKALQALAADTDGFLE 130 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aG-----------L~---l~~Ae~aL~aLAsD~~GhLe 130 (276)
.++..+.+++|+++++++||.....--+.+++ ++ -.+..+++..-|.+.|-++-
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 46889999999999999999865432222222 11 23555667777776665543
No 168
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=42.42 E-value=1.2e+02 Score=29.24 Aligned_cols=87 Identities=20% Similarity=0.271 Sum_probs=47.0
Q ss_pred HHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc-CCceEeecCccE-EEEcCc-----chHHHhhhhhHHHhHHHHHH
Q 023862 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT-DGFLEVSDEGDV-LYVFPN-----NYRAKLAAKSFRLKVEPVID 163 (276)
Q Consensus 91 ve~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~-~GhLeVSesGDI-lYvFP~-----nfRs~L~~Ks~r~rl~~~~~ 163 (276)
.+++|...|+.+||...|++.++++..+. ++.+. .=+-.|.++++. +..|-. +--..+....++..|+.++.
T Consensus 226 ~~~lgr~pt~~EiA~~l~~~~~~v~~~~~-~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~l~ 304 (367)
T PRK09210 226 LQELGREPTPEEIAEEMDMPPEKVREILK-IAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLD 304 (367)
T ss_pred HHHhCCCCCHHHHHHHhCcCHHHHHHHHH-HhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 35579999999999999999999977654 44321 111112233321 222211 11122233445555666665
Q ss_pred HHhhhhhhHHHHHHH
Q 023862 164 KAKAAAEYSIRVLFG 178 (276)
Q Consensus 164 k~w~v~~YliRIsFG 178 (276)
.+-.-=..+++--||
T Consensus 305 ~L~~rEr~Vl~lryg 319 (367)
T PRK09210 305 TLTDREENVLRLRFG 319 (367)
T ss_pred hCCHHHHHHHHHHhc
Confidence 554444444444444
No 169
>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=42.40 E-value=56 Score=24.62 Aligned_cols=44 Identities=23% Similarity=0.287 Sum_probs=31.7
Q ss_pred HHHHHHHcCC--ceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 023862 87 AMDAVDACNR--RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (276)
Q Consensus 87 im~Ave~lg~--rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS 132 (276)
+|-.+...+. .+|+.|+|.+.|++...+++-|..|... |-++..
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 345444
No 170
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=42.05 E-value=1.1e+02 Score=28.91 Aligned_cols=88 Identities=20% Similarity=0.256 Sum_probs=48.0
Q ss_pred HHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccE-EEEc-Cc---chHHHhhhhhHHHhHHHHHHHH
Q 023862 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDV-LYVF-PN---NYRAKLAAKSFRLKVEPVIDKA 165 (276)
Q Consensus 91 ve~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDI-lYvF-P~---nfRs~L~~Ks~r~rl~~~~~k~ 165 (276)
..++|...|+.++|...|++.++++..+.....+..=+-.+.++++. +..+ |. +--..+.....+..|+..++.+
T Consensus 178 ~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~~~pe~~~~~~~~~~~l~~al~~L 257 (317)
T PRK07405 178 SQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPEDFATQSSLQLDLERLMEDL 257 (317)
T ss_pred HHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHcC
Confidence 35678999999999999999999988776543222111112222221 1111 11 1222333444555566666555
Q ss_pred hhhhhhHHHHHHH
Q 023862 166 KAAAEYSIRVLFG 178 (276)
Q Consensus 166 w~v~~YliRIsFG 178 (276)
-.--.-+++..||
T Consensus 258 ~~rer~Vi~lr~g 270 (317)
T PRK07405 258 TPQQKEVIALRFG 270 (317)
T ss_pred CHHHHHHHHHHhh
Confidence 5444455555554
No 171
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=41.64 E-value=18 Score=31.69 Aligned_cols=59 Identities=20% Similarity=0.374 Sum_probs=45.9
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-CccEEEEc
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYVF 141 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe-sGDIlYvF 141 (276)
..++.+||.--=+-|.+++..++|.+-|+|..-+++||..|++| |=|++.. .|-.|=.+
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 44556666665667999999999999999999999999999987 4555554 46655555
No 172
>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=41.39 E-value=47 Score=24.11 Aligned_cols=33 Identities=21% Similarity=0.344 Sum_probs=24.2
Q ss_pred HHHHHHHHcCC-ceehhhhhhhcCCCHHHHHHHH
Q 023862 86 RAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKAL 118 (276)
Q Consensus 86 rim~Ave~lg~-rvTvgDVAa~aGL~l~~Ae~aL 118 (276)
++++.+++.|. +|+-.++|..+|++..|+++.|
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 34555666555 7788899999999999999987
No 173
>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=41.30 E-value=1.5e+02 Score=27.59 Aligned_cols=86 Identities=17% Similarity=0.193 Sum_probs=46.4
Q ss_pred HHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCcc-----EEEEcCcchHHHhhhhhHHHhHHHHHHHHh
Q 023862 92 DACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-----VLYVFPNNYRAKLAAKSFRLKVEPVIDKAK 166 (276)
Q Consensus 92 e~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGD-----IlYvFP~nfRs~L~~Ks~r~rl~~~~~k~w 166 (276)
.++|...|..++|...|++.++++..+.....+..=+-.+.++++ ++-.-..+--..+..+..+..++..++++-
T Consensus 172 ~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~~pe~~~~~~~~~~~L~~~L~~L~ 251 (298)
T TIGR02997 172 QKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGESPEEQVERESLRQDLESLLAELT 251 (298)
T ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCCCCCHHHHHHHHHHHHHHHHHHHcCC
Confidence 457888999999999999999998876654322221111222221 121111222333444445555666665554
Q ss_pred hhhhhHHHHHH
Q 023862 167 AAAEYSIRVLF 177 (276)
Q Consensus 167 ~v~~YliRIsF 177 (276)
.--.-+++-.|
T Consensus 252 ~rer~Vi~lr~ 262 (298)
T TIGR02997 252 PRERQVLRLRF 262 (298)
T ss_pred HHHHHHHHHHh
Confidence 44444444444
No 174
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=41.08 E-value=17 Score=32.86 Aligned_cols=46 Identities=22% Similarity=0.239 Sum_probs=30.9
Q ss_pred eehhhhhhhcCCCHHHHHHHHH--------------HHHhhcC-------CceEeecCccEEEEcCc
Q 023862 98 VTIGDVAGKAGLKLNEAQKALQ--------------ALAADTD-------GFLEVSDEGDVLYVFPN 143 (276)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL~--------------aLAsD~~-------GhLeVSesGDIlYvFP~ 143 (276)
+|+.|||..||+|...+-+.|. +.|.+.| -.|.-..++-|-.++|.
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 6999999999999888766664 2333332 23444556777777763
No 175
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=40.81 E-value=16 Score=32.83 Aligned_cols=22 Identities=32% Similarity=0.508 Sum_probs=19.9
Q ss_pred eehhhhhhhcCCCHHHHHHHHH
Q 023862 98 VTIGDVAGKAGLKLNEAQKALQ 119 (276)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL~ 119 (276)
+|+-|||..||+|...+-++|.
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln 23 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLN 23 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhc
Confidence 6999999999999999988875
No 176
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=40.63 E-value=27 Score=29.49 Aligned_cols=31 Identities=16% Similarity=0.260 Sum_probs=23.0
Q ss_pred hhHHHHHH----HHHcCC-ceehhhhhhhcCCCHHH
Q 023862 83 VRNRAMDA----VDACNR-RVTIGDVAGKAGLKLNE 113 (276)
Q Consensus 83 ~~~rim~A----ve~lg~-rvTvgDVAa~aGL~l~~ 113 (276)
.+.+|++| +.+.|+ .+|+.|||.++|++...
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 34555554 567786 69999999999988643
No 177
>smart00351 PAX Paired Box domain.
Probab=40.55 E-value=78 Score=26.05 Aligned_cols=48 Identities=19% Similarity=0.228 Sum_probs=38.7
Q ss_pred ccccCCCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh
Q 023862 73 IVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (276)
Q Consensus 73 ~v~~~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAs 123 (276)
++-.-.++++.|.+|+.+++ . ..+..+||.+.|++...+.+-+..-..
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 358899999999999999888877543
No 178
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=40.53 E-value=46 Score=27.48 Aligned_cols=34 Identities=12% Similarity=0.191 Sum_probs=29.7
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHH
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~ 119 (276)
+..|+-++++.| .|+..++.++||+-+....+|.
T Consensus 10 ~adI~AaL~KrG--~sLa~lsr~~Gls~~TL~nAL~ 43 (92)
T PRK10344 10 PADIIAGLRKKG--TSMAAESRRNGLSSSTLANALS 43 (92)
T ss_pred HHHHHHHHHHcC--CcHHHHHHHcCCChHHHHHHHc
Confidence 467888999988 7999999999999999988884
No 179
>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=40.26 E-value=41 Score=31.74 Aligned_cols=43 Identities=26% Similarity=0.295 Sum_probs=37.1
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLe 130 (276)
.++..+++++.+|.|-++=+...+|++..+|++.|. +.+|||.
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 467889999999999999999999999999977665 6778775
No 180
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=39.95 E-value=19 Score=32.58 Aligned_cols=46 Identities=22% Similarity=0.270 Sum_probs=31.1
Q ss_pred eehhhhhhhcCCCHHHHHHHHH--------------HHHhhcCC-------ceEeecCccEEEEcCc
Q 023862 98 VTIGDVAGKAGLKLNEAQKALQ--------------ALAADTDG-------FLEVSDEGDVLYVFPN 143 (276)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL~--------------aLAsD~~G-------hLeVSesGDIlYvFP~ 143 (276)
+|+.|||..+|+|...+-++|. +.|.+.|= .|.-..++-|..++|.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~kV~~~a~elgY~pn~~a~~l~~~~~~~Igvi~~~ 68 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPNANAQALATQVSDTIGVVVMD 68 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHhhcCCCCEEEEEeCC
Confidence 6999999999999987777664 33333321 2444456677777773
No 181
>PHA02673 ORF109 EEV glycoprotein; Provisional
Probab=39.95 E-value=58 Score=29.26 Aligned_cols=30 Identities=17% Similarity=0.286 Sum_probs=20.0
Q ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023862 166 KAAAEYSIRVLFGTALIASIVIVFTAIIAIL 196 (276)
Q Consensus 166 w~v~~YliRIsFGi~LIaSIvLv~~aI~ail 196 (276)
-+.+..++||+..|.+| |.+++.++++.-+
T Consensus 29 ~R~i~l~~Ri~~~iSIi-sL~~l~v~LaL~l 58 (161)
T PHA02673 29 RRYIKLFFRLMAAIAII-VLAILVVILALAL 58 (161)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Confidence 56677889999988877 5555444444333
No 182
>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=39.57 E-value=61 Score=25.56 Aligned_cols=47 Identities=15% Similarity=0.160 Sum_probs=38.4
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS 132 (276)
.+-.|+.++.+.+ ..|+.|+|...|++...+-+.|..|..+ |-++-.
T Consensus 29 ~q~~iL~~l~~~~-~~t~~ela~~~~~~~~tvs~~l~~Le~~--GlI~r~ 75 (118)
T TIGR02337 29 QQWRILRILAEQG-SMEFTQLANQACILRPSLTGILARLERD--GLVTRL 75 (118)
T ss_pred HHHHHHHHHHHcC-CcCHHHHHHHhCCCchhHHHHHHHHHHC--CCEEec
Confidence 3457888888754 6999999999999999999999999887 555543
No 183
>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=39.02 E-value=47 Score=24.09 Aligned_cols=27 Identities=11% Similarity=0.218 Sum_probs=22.2
Q ss_pred hhhHHHHHHHHHcC-CceehhhhhhhcC
Q 023862 82 DVRNRAMDAVDACN-RRVTIGDVAGKAG 108 (276)
Q Consensus 82 ~~~~rim~Ave~lg-~rvTvgDVAa~aG 108 (276)
++.-.|-+++.+.| +.+|+.|+|++..
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 44556789999998 9999999999988
No 184
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=38.77 E-value=87 Score=27.25 Aligned_cols=50 Identities=18% Similarity=0.147 Sum_probs=39.1
Q ss_pred chhhHHHHHHHHHc----CCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 023862 81 ADVRNRAMDAVDAC----NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (276)
Q Consensus 81 ~~~~~rim~Ave~l----g~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS 132 (276)
.+++.|+.+.+... ....|..|+|...|++.+.+-+.|..|..+ |-+++.
T Consensus 149 ~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~--G~I~~~ 202 (226)
T PRK10402 149 FPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQD--GYLKKS 202 (226)
T ss_pred ChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHC--CCEEee
Confidence 36788888887653 233688999999999999999999999876 445553
No 185
>PF13730 HTH_36: Helix-turn-helix domain
Probab=38.76 E-value=39 Score=23.15 Aligned_cols=26 Identities=19% Similarity=0.314 Sum_probs=23.7
Q ss_pred ehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 99 TIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 99 TvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
+...+|..+|++.+.++++|..|...
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 186
>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=38.69 E-value=1.1e+02 Score=27.32 Aligned_cols=56 Identities=9% Similarity=0.111 Sum_probs=37.3
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcC-----------C---CHHHHHHHHHHHHhhcCCceEee
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------L---KLNEAQKALQALAADTDGFLEVS 132 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aG-----------L---~l~~Ae~aL~aLAsD~~GhLeVS 132 (276)
.++..+.+++|+++++++||+.-..--+.+++ + =-.+..+++...|.+.|-++.+.
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 46889999999999999999764322222221 1 12344567777778777777653
No 187
>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=38.58 E-value=90 Score=22.42 Aligned_cols=44 Identities=11% Similarity=0.150 Sum_probs=35.7
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCc
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGF 128 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~Gh 128 (276)
+-++++.+-+ ....|+.|+|.+.|+|.-..++.+..|-...+..
T Consensus 7 q~~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L~~~f~~~ 50 (59)
T PF08280_consen 7 QLKLLELLLK-NKWITLKELAKKLNISERTIKNDINELNEFFPEN 50 (59)
T ss_dssp HHHHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT--TC
T ss_pred HHHHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHHHHhhhh
Confidence 3567888888 8899999999999999999999999998766433
No 188
>PRK09954 putative kinase; Provisional
Probab=38.37 E-value=59 Score=30.40 Aligned_cols=42 Identities=5% Similarity=0.053 Sum_probs=37.1
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
...+|++.+++.+ ++|..|+|.+-|++...+.+-|..|-++.
T Consensus 4 ~~~~il~~l~~~~-~~s~~~la~~l~~s~~~v~~~i~~L~~~g 45 (362)
T PRK09954 4 REKEILAILRRNP-LIQQNEIADILQISRSRVAAHIMDLMRKG 45 (362)
T ss_pred HHHHHHHHHHHCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 3457889888776 89999999999999999999999999854
No 189
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=38.37 E-value=1.2e+02 Score=26.80 Aligned_cols=56 Identities=9% Similarity=-0.016 Sum_probs=37.6
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcC--------------CCHHHHHHHHHHHHhhcCCceEee
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG--------------LKLNEAQKALQALAADTDGFLEVS 132 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aG--------------L~l~~Ae~aL~aLAsD~~GhLeVS 132 (276)
.++..+.+++|+++++++||..-..--+.+++ ---.+.-+++...+.+.|-++.+.
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 46889999999999999999753321111111 113456677888888877776553
No 190
>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=38.28 E-value=97 Score=25.53 Aligned_cols=50 Identities=14% Similarity=0.173 Sum_probs=37.3
Q ss_pred chhhHHHHHHHH----HcC----------CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 023862 81 ADVRNRAMDAVD----ACN----------RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (276)
Q Consensus 81 ~~~~~rim~Ave----~lg----------~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS 132 (276)
.++++|+...+. +.| ..+|..|+|.-.|++.+.+-+.|..|..+ |-++++
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 444444
No 191
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=37.87 E-value=58 Score=28.49 Aligned_cols=45 Identities=9% Similarity=-0.009 Sum_probs=38.5
Q ss_pred CCchhhHHHHHHHHHcCCceehhhhhhhc--CCCHHHHHHHHHHHHh
Q 023862 79 LPADVRNRAMDAVDACNRRVTIGDVAGKA--GLKLNEAQKALQALAA 123 (276)
Q Consensus 79 l~~~~~~rim~Ave~lg~rvTvgDVAa~a--GL~l~~Ae~aL~aLAs 123 (276)
...-..+.|...++-.++..+++.+|.+. +++.+|++++|..|..
T Consensus 21 ~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~ 67 (171)
T PF14394_consen 21 YSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEK 67 (171)
T ss_pred HhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence 34445677788888888888999999999 9999999999999976
No 192
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=37.84 E-value=43 Score=22.49 Aligned_cols=40 Identities=10% Similarity=0.218 Sum_probs=23.5
Q ss_pred CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHH
Q 023862 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALA 122 (276)
Q Consensus 80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLA 122 (276)
.+..|-.++..+.+ +.|+.+||...|++...+.+=+..-.
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 34556677777777 88999999999999999977666543
No 193
>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=37.57 E-value=1.2e+02 Score=27.02 Aligned_cols=56 Identities=18% Similarity=0.214 Sum_probs=37.7
Q ss_pred CCCchhhHHHHHHHHHcCCceehhhhhhhcC-----------C---CHHHHHHHHHHHHhhcCCceEeec
Q 023862 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------L---KLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 78 ~l~~~~~~rim~Ave~lg~rvTvgDVAa~aG-----------L---~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
+++.+.+++|+++++++||.....--+.+++ + --.+.-+++...|.+.|-++.+..
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 5889999999999999999764332222222 1 124455677777777777776643
No 194
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=37.40 E-value=70 Score=25.95 Aligned_cols=42 Identities=10% Similarity=0.100 Sum_probs=36.9
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
+..++.++...+...|+.|+|...|++...+-+.+..|-.+.
T Consensus 33 q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~G 74 (144)
T PRK03573 33 HWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKG 74 (144)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCC
Confidence 457889998888789999999999999999999999997764
No 195
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=37.39 E-value=1.6e+02 Score=28.18 Aligned_cols=42 Identities=17% Similarity=0.300 Sum_probs=31.2
Q ss_pred CCCchhhHHHH-------HHHHHcCCceehhhhhhhcCCCHHHHHHHHH
Q 023862 78 KLPADVRNRAM-------DAVDACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (276)
Q Consensus 78 ~l~~~~~~rim-------~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~ 119 (276)
+||......+- +.-.++|...|+.+||...|++.+++++.+.
T Consensus 163 rlP~~~~~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~ 211 (324)
T PRK07921 163 RLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLE 211 (324)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 57766654332 2234578999999999999999999987654
No 196
>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=37.31 E-value=29 Score=28.99 Aligned_cols=32 Identities=13% Similarity=0.212 Sum_probs=23.5
Q ss_pred hhhHHHHH----HHHHcCCc-eehhhhhhhcCCCHHH
Q 023862 82 DVRNRAMD----AVDACNRR-VTIGDVAGKAGLKLNE 113 (276)
Q Consensus 82 ~~~~rim~----Ave~lg~r-vTvgDVAa~aGL~l~~ 113 (276)
+.+.+|++ .+.+.|+. +|+.|||.++|++...
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 45555554 45667776 9999999999987643
No 197
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=37.09 E-value=39 Score=26.52 Aligned_cols=49 Identities=22% Similarity=0.259 Sum_probs=32.8
Q ss_pred HcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCc
Q 023862 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (276)
Q Consensus 93 ~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~ 143 (276)
......|++|+..+.|++..|+..-|.. -..-+.=.+=++||-|.+||.
T Consensus 28 ~~~~~~tvkd~IEsLGVP~tEV~~i~vN--G~~v~~~~~~~~Gd~v~V~P~ 76 (81)
T PF14451_consen 28 PFDGGATVKDVIESLGVPHTEVGLILVN--GRPVDFDYRLKDGDRVAVYPV 76 (81)
T ss_pred ecCCCCcHHHHHHHcCCChHHeEEEEEC--CEECCCcccCCCCCEEEEEec
Confidence 5678899999999999999998432210 000000123358999999985
No 198
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=36.95 E-value=1.1e+02 Score=27.14 Aligned_cols=55 Identities=18% Similarity=0.170 Sum_probs=35.4
Q ss_pred CCCchhhHHHHHHHHHcCCceehhhhhhhcC-----------CC---HHHHHHHHHHHHhhcCCceEee
Q 023862 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------LK---LNEAQKALQALAADTDGFLEVS 132 (276)
Q Consensus 78 ~l~~~~~~rim~Ave~lg~rvTvgDVAa~aG-----------L~---l~~Ae~aL~aLAsD~~GhLeVS 132 (276)
+++.+.|++|+++++++||+....--+.+++ ++ -.+.-+++..-|.+.|-++.+.
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 5889999999999999999865432222222 11 2334456666677766666553
No 199
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=36.65 E-value=1.4e+02 Score=25.27 Aligned_cols=64 Identities=11% Similarity=0.153 Sum_probs=47.1
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhh-----cCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcc
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGK-----AGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~-----aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~n 144 (276)
...|.+|++.+.+.+...|+-||=.+ -++++.++=+.|..|+...==+--..++|...|..+..
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 45678889999999888998877433 34999999999999987544444444466788877554
No 200
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=36.40 E-value=81 Score=26.47 Aligned_cols=46 Identities=15% Similarity=0.177 Sum_probs=35.0
Q ss_pred CchhhHHHHHHHHHc----C---------CceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 80 PADVRNRAMDAVDAC----N---------RRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 80 ~~~~~~rim~Ave~l----g---------~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
..+.+.|+.+.+..+ + .++|..|+|...|++...+-+.|..|.++.
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 345667776654321 1 368889999999999999999999998765
No 201
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=36.32 E-value=24 Score=31.35 Aligned_cols=23 Identities=17% Similarity=0.341 Sum_probs=18.5
Q ss_pred eehhhhhhhcCCCHHHHHHHHHH
Q 023862 98 VTIGDVAGKAGLKLNEAQKALQA 120 (276)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL~a 120 (276)
+|+.|||..||+|...+-+.|..
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Confidence 38899999999998877766653
No 202
>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=35.77 E-value=49 Score=22.12 Aligned_cols=28 Identities=25% Similarity=0.331 Sum_probs=22.2
Q ss_pred ceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 97 RVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 97 rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
..|-.|+|...|++.+.+-+.|..|..+
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~~~ 29 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLERQ 29 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHHHc
Confidence 3577899999999999999999988765
No 203
>PRK00215 LexA repressor; Validated
Probab=35.62 E-value=70 Score=27.67 Aligned_cols=58 Identities=17% Similarity=0.281 Sum_probs=40.3
Q ss_pred hHHHHHHHH----HcCCceehhhhhhhcCC-CHHHHHHHHHHHHhhcCCceEeec-CccEEEEcCc
Q 023862 84 RNRAMDAVD----ACNRRVTIGDVAGKAGL-KLNEAQKALQALAADTDGFLEVSD-EGDVLYVFPN 143 (276)
Q Consensus 84 ~~rim~Ave----~lg~rvTvgDVAa~aGL-~l~~Ae~aL~aLAsD~~GhLeVSe-sGDIlYvFP~ 143 (276)
+.++++.+. +.+...|+.|+|...|+ +...+.+-|..|..+ |.|+-.. .+..+-+.|+
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 455565554 56888999999999999 999999999998765 4444333 2333444333
No 204
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.35 E-value=85 Score=30.22 Aligned_cols=44 Identities=27% Similarity=0.223 Sum_probs=31.2
Q ss_pred hhhhHHHhHHHHHHHHhhhh--------hhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023862 150 AAKSFRLKVEPVIDKAKAAA--------EYSIRVLFGTALIASIVIVFTAIIAIL 196 (276)
Q Consensus 150 ~~Ks~r~rl~~~~~k~w~v~--------~YliRIsFGi~LIaSIvLv~~aI~ail 196 (276)
.|||-|.---+|.+++|+.. ...=|.+|.|+|- +|-|++|+++|
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 56887777888888888754 3355677766654 66777888887
No 205
>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=35.29 E-value=1.2e+02 Score=29.79 Aligned_cols=78 Identities=19% Similarity=0.225 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHHh-hcCCceEeecCccEEEEcCcchHHHhhh-hhHHHhHHHHHHHHh----------hhhhhHHHH
Q 023862 108 GLKLNEAQKALQALAA-DTDGFLEVSDEGDVLYVFPNNYRAKLAA-KSFRLKVEPVIDKAK----------AAAEYSIRV 175 (276)
Q Consensus 108 GL~l~~Ae~aL~aLAs-D~~GhLeVSesGDIlYvFP~nfRs~L~~-Ks~r~rl~~~~~k~w----------~v~~YliRI 175 (276)
|.+-+.-.+.|.+|.+ +.-|+-= +++. |+.+|+.+-.. .++..+|+.-.+|+- ++.-.++=+
T Consensus 116 g~~~~~~~~tl~eL~~F~~~~NPF---s~~~---~~~~F~~i~~~~~~Ll~kL~~~k~Kl~kklk~~r~~~kvs~v~fva 189 (336)
T PF05055_consen 116 GVSQKKYDKTLEELKKFKAAGNPF---SDEE---FFHQFQSIHDQQSSLLEKLDSRKKKLRKKLKLVRTWRKVSNVCFVA 189 (336)
T ss_pred cccchhHHHHHHHHHhhhhcCCCC---Cchh---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Confidence 4445555566777765 2222211 1221 78899988776 224444443333222 333344444
Q ss_pred HHHHHHHHHHHHHHHH
Q 023862 176 LFGTALIASIVIVFTA 191 (276)
Q Consensus 176 sFGi~LIaSIvLv~~a 191 (276)
.|..++|+|+|+..++
T Consensus 190 a~~aV~i~svv~aa~a 205 (336)
T PF05055_consen 190 AFVAVAIASVVAAAHA 205 (336)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 5666666666666553
No 206
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=35.02 E-value=2.8e+02 Score=24.06 Aligned_cols=52 Identities=19% Similarity=0.217 Sum_probs=38.4
Q ss_pred HcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHH
Q 023862 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA 147 (276)
Q Consensus 93 ~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs 147 (276)
+-|.+.+..++|.+-|+|-.-++.||..|.++ |-|++.... -.++-+-+...
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVREAL~~L~~e--GLV~~~~~~-g~~v~~~~~~~ 81 (221)
T PRK11414 30 KPGARLITKNLAEQLGMSITPVREALLRLVSV--NALSVAPAQ-AFTVPEVSKRQ 81 (221)
T ss_pred CCCCccCHHHHHHHHCCCchhHHHHHHHHHHC--CCEEecCCC-ceeecCCCHHH
Confidence 34688888999999999999999999999864 566665432 24555444433
No 207
>PHA00738 putative HTH transcription regulator
Probab=34.82 E-value=1.7e+02 Score=24.73 Aligned_cols=58 Identities=19% Similarity=0.338 Sum_probs=48.2
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF 141 (276)
...|-+|++.+.+ +...+++|++...+++...+-+=|..|-. -|-+++..+|--+|.-
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 3567889998865 44699999999999999999888888854 5788999999888765
No 208
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=34.43 E-value=1.4e+02 Score=26.94 Aligned_cols=30 Identities=20% Similarity=0.279 Sum_probs=26.0
Q ss_pred HHcCCceehhhhhhhcCCCHHHHHHHHHHH
Q 023862 92 DACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (276)
Q Consensus 92 e~lg~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (276)
.++|...|+.++|...|++.+++.+.+...
T Consensus 134 ~~~~r~p~~~eia~~l~v~~~~v~~~~~~~ 163 (258)
T PRK08215 134 NENSKEPTVEEIAKELEVPREEVVFALDAI 163 (258)
T ss_pred HHhCCCCCHHHHHHHHCcCHHHHHHHHHhc
Confidence 467889999999999999999998877543
No 209
>PRK09492 treR trehalose repressor; Provisional
Probab=34.21 E-value=1.5e+02 Score=26.21 Aligned_cols=55 Identities=11% Similarity=0.059 Sum_probs=34.4
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcC-----------C---CHHHHHHHHHHHHhhcCCceEe
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------L---KLNEAQKALQALAADTDGFLEV 131 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aG-----------L---~l~~Ae~aL~aLAsD~~GhLeV 131 (276)
.++..+.+++|+++++++||..-..--+.+.+ + --.+.-+++..-+.+.|-++-+
T Consensus 29 ~~vs~~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~~~ 97 (315)
T PRK09492 29 SGVSEETRERVEAVINQHGFSPSKSARAMRGQSDKVVGIIVSRLDSLSENQAVRTMLPAFYEQGYDPII 97 (315)
T ss_pred CCCCHHHHHHHHHHHHHHCCCcCHHHHHhhcCCCCeEEEEecCCcCcccHHHHHHHHHHHHHcCCeEEE
Confidence 46889999999999999999764322111111 1 1234445666666666665544
No 210
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=34.18 E-value=53 Score=33.60 Aligned_cols=39 Identities=13% Similarity=0.288 Sum_probs=34.8
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHH
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALA 122 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLA 122 (276)
+..|++.+.+....+|+.|++..||+..+++=.+|+.|-
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 467888998888999999999999999999988888763
No 211
>PHA01976 helix-turn-helix protein
Probab=33.82 E-value=71 Score=22.56 Aligned_cols=32 Identities=13% Similarity=0.158 Sum_probs=23.7
Q ss_pred chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHH
Q 023862 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEA 114 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~A 114 (276)
|++-.++-++-++.| .|+.|+|...|++....
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 455667766655555 79999999999986555
No 212
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=33.74 E-value=80 Score=27.63 Aligned_cols=55 Identities=15% Similarity=0.227 Sum_probs=39.3
Q ss_pred hhhHHHHHHHHHc----CCce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-CccEE
Q 023862 82 DVRNRAMDAVDAC----NRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVL 138 (276)
Q Consensus 82 ~~~~rim~Ave~l----g~rv-TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe-sGDIl 138 (276)
.+-..|.+.+... |.+. |-.++|.+-|+|-..+++||..|.++ |-|++.. .|-.|
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 3444555555444 6677 78899999999999999999999975 5566543 45444
No 213
>PRK03837 transcriptional regulator NanR; Provisional
Probab=33.55 E-value=83 Score=27.43 Aligned_cols=63 Identities=21% Similarity=0.314 Sum_probs=42.7
Q ss_pred CCchhhHHHHHHHHHc----CCce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcc
Q 023862 79 LPADVRNRAMDAVDAC----NRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (276)
Q Consensus 79 l~~~~~~rim~Ave~l----g~rv-TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~n 144 (276)
+...+-..|.+.+... |.+. +..|+|.+-|+|..-+++||..|.++ |-+++.. |-=.|+-+.+
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 3334444444444444 4556 88999999999999999999999965 5566643 3335555433
No 214
>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=33.26 E-value=82 Score=25.90 Aligned_cols=29 Identities=21% Similarity=0.398 Sum_probs=24.0
Q ss_pred CceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 96 RRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
..+|+.++|.+.++|...+++-|..|...
T Consensus 24 ~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 24 GPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 35888899999999999998888888764
No 215
>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=33.13 E-value=54 Score=29.26 Aligned_cols=33 Identities=21% Similarity=0.381 Sum_probs=27.5
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHH
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQK 116 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~ 116 (276)
.++||-+|+.=+.| .|+.|||..+|++++.++.
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 67788888876655 7999999999999998753
No 216
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=32.98 E-value=47 Score=28.14 Aligned_cols=32 Identities=16% Similarity=0.293 Sum_probs=23.6
Q ss_pred hhhHHH----HHHHHHcCCc-eehhhhhhhcCCCHHH
Q 023862 82 DVRNRA----MDAVDACNRR-VTIGDVAGKAGLKLNE 113 (276)
Q Consensus 82 ~~~~ri----m~Ave~lg~r-vTvgDVAa~aGL~l~~ 113 (276)
+.|.+| ++.+.+.|+. +|+.|||..+|++...
T Consensus 11 ~~R~~Il~AA~~lf~e~G~~~~t~~~Ia~~agvs~~t 47 (215)
T PRK10668 11 ETRQHILDAALRLFSQQGVSATSLADIAKAAGVTRGA 47 (215)
T ss_pred HHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCChHH
Confidence 444555 4556678885 7899999999987653
No 217
>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=32.91 E-value=1.5e+02 Score=21.93 Aligned_cols=58 Identities=16% Similarity=0.227 Sum_probs=45.4
Q ss_pred cCCCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862 76 SDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 76 ~~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
.+.|...++.+.+..+-+.-.++++.++|...+++.+++|.-|..+..+..=+-+.+.
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 3455666777778788888889999999999999999999999999887644444443
No 218
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=32.84 E-value=32 Score=25.32 Aligned_cols=21 Identities=38% Similarity=0.452 Sum_probs=17.2
Q ss_pred eehhhhhhhcCCCHHHHHHHH
Q 023862 98 VTIGDVAGKAGLKLNEAQKAL 118 (276)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL 118 (276)
+|+.|+|.++|++...+-+.|
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~l 21 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVL 21 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 478899999999998886654
No 219
>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=32.65 E-value=51 Score=29.43 Aligned_cols=41 Identities=22% Similarity=0.323 Sum_probs=32.2
Q ss_pred HHHHHHHHHc------CCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 85 NRAMDAVDAC------NRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 85 ~rim~Ave~l------g~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
|+..+.+.+. |+..|+.+++...|+++++.-++|.++++..
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 3444555544 4668999999999999999999999998544
No 220
>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=32.10 E-value=1.8e+02 Score=25.90 Aligned_cols=56 Identities=14% Similarity=0.068 Sum_probs=36.0
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcC-----------C---CHHHHHHHHHHHHhhcCCceEee
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------L---KLNEAQKALQALAADTDGFLEVS 132 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aG-----------L---~l~~Ae~aL~aLAsD~~GhLeVS 132 (276)
.++..+.+++|+++++++||.....=-+.+++ + --.+.-+++..-+.+.|-++-+.
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 1 12334566777777777776654
No 221
>PLN02343 allene oxide cyclase
Probab=32.04 E-value=12 Score=35.01 Aligned_cols=14 Identities=29% Similarity=0.707 Sum_probs=12.3
Q ss_pred cchhhhhhhcccCC
Q 023862 248 MNFIKSVFSFVFGE 261 (276)
Q Consensus 248 mnFlEaVFSFvFGD 261 (276)
=.=+||+|||-|||
T Consensus 124 gDryEa~ySfyfGD 137 (229)
T PLN02343 124 GDRYEAIYSFYFGD 137 (229)
T ss_pred CceeEEEEEEEecC
Confidence 35689999999999
No 222
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=32.01 E-value=52 Score=31.14 Aligned_cols=43 Identities=23% Similarity=0.438 Sum_probs=35.4
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLe 130 (276)
.++..+++++.+|.|-++=+...+|++.++|++.|. +++|||+
T Consensus 246 ~~~a~~~l~~~~~~vk~ai~~~~~~~~~~~a~~~l~----~~~~~~~ 288 (296)
T PRK12570 246 EDEAKELLKESDNDVKLAILMILTGMDVEQARAALS----HADGFLR 288 (296)
T ss_pred HHHHHHHHHHhCCccHHHHHHHHhCCCHHHHHHHHH----HcCChHH
Confidence 355778899999999999999999999999977665 5577765
No 223
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=31.89 E-value=1e+02 Score=27.70 Aligned_cols=57 Identities=12% Similarity=0.046 Sum_probs=37.8
Q ss_pred CCCCchhhHHHHHHHHHcCCceehh-------------hhhhh-cCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIG-------------DVAGK-AGLKLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvg-------------DVAa~-aGL~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
.+++.+.+++|+++++++||..-.. =+... ...--.+.-+++...|++.|-++.+..
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 3688999999999999999986432 11111 012234556788888888887765543
No 224
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=31.83 E-value=46 Score=28.94 Aligned_cols=49 Identities=16% Similarity=0.266 Sum_probs=37.6
Q ss_pred HcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-CccEEEEcCcch
Q 023862 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYVFPNNY 145 (276)
Q Consensus 93 ~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe-sGDIlYvFP~nf 145 (276)
+-|.+++..++|.+-|+|..-++.||..|+++ |-+++.. .| .||=+-+.
T Consensus 26 ~pG~~L~e~eLae~lgVSRtpVREAL~~L~~e--Glv~~~~~~G--~~V~~~~~ 75 (224)
T PRK11534 26 QPDEKLRMSLLTSRYALGVGPLREALSQLVAE--RLVTVVNQKG--YRVASMSE 75 (224)
T ss_pred CCCCcCCHHHHHHHHCCChHHHHHHHHHHHHC--CCEEEeCCCc--eEeCCCCH
Confidence 34779999999999999999999999999965 6676654 45 34444343
No 225
>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=31.83 E-value=32 Score=30.72 Aligned_cols=21 Identities=29% Similarity=0.414 Sum_probs=17.2
Q ss_pred ehhhhhhhcCCCHHHHHHHHH
Q 023862 99 TIGDVAGKAGLKLNEAQKALQ 119 (276)
Q Consensus 99 TvgDVAa~aGL~l~~Ae~aL~ 119 (276)
|+.|||..||+|...+-+.|.
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn 21 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVIN 21 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHc
Confidence 678999999998888777764
No 226
>PF13518 HTH_28: Helix-turn-helix domain
Probab=31.75 E-value=1.4e+02 Score=19.81 Aligned_cols=37 Identities=8% Similarity=0.179 Sum_probs=27.2
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAs 123 (276)
+.+|++.+.+ |. |+.++|.+-|++..++..=+...-.
T Consensus 2 r~~iv~~~~~-g~--s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 2 RLQIVELYLE-GE--SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHHc-CC--CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3456677763 33 9999999999999998666655443
No 227
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=31.62 E-value=44 Score=28.64 Aligned_cols=31 Identities=23% Similarity=0.293 Sum_probs=22.8
Q ss_pred chhhHHHHHHHH-----HcCC-ceehhhhhhhcCCCH
Q 023862 81 ADVRNRAMDAVD-----ACNR-RVTIGDVAGKAGLKL 111 (276)
Q Consensus 81 ~~~~~rim~Ave-----~lg~-rvTvgDVAa~aGL~l 111 (276)
...|++|+++.. +.|+ .+|+.|||.++|++.
T Consensus 10 ~~~R~~Il~aA~~~l~~~~G~~~~si~~IA~~Agvs~ 46 (203)
T PRK11202 10 EKTRRALIDAAFSQLSAERSFSSLSLREVAREAGIAP 46 (203)
T ss_pred HHHHHHHHHHHHHHHHhcCCcccCCHHHHHHHhCCCc
Confidence 356777776653 3465 789999999999764
No 228
>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=31.45 E-value=47 Score=28.47 Aligned_cols=57 Identities=14% Similarity=0.269 Sum_probs=41.3
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-CccEEEEc
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYVF 141 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe-sGDIlYvF 141 (276)
++.+|++--=+-|.+.+-.++|.+-|+|..-++.||..|+++ |-|++.. .|-.|-.+
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 334444433345888899999999999999999999999965 6677665 45444443
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=31.33 E-value=36 Score=27.82 Aligned_cols=31 Identities=26% Similarity=0.374 Sum_probs=22.1
Q ss_pred hhhHHHHH----HHHHcCC-ceehhhhhhhcCCCHH
Q 023862 82 DVRNRAMD----AVDACNR-RVTIGDVAGKAGLKLN 112 (276)
Q Consensus 82 ~~~~rim~----Ave~lg~-rvTvgDVAa~aGL~l~ 112 (276)
.-+++|++ .+.+.|+ .+|+.|||.++|++..
T Consensus 8 ~rr~~Il~aA~~lf~~~G~~~~s~~~IA~~agvsk~ 43 (189)
T TIGR03384 8 IRRAELIDATIESIGERGSLDVTIAQIARRAGVSSG 43 (189)
T ss_pred HHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCCHH
Confidence 34455554 4556675 6889999999998764
No 230
>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=31.15 E-value=93 Score=28.22 Aligned_cols=64 Identities=19% Similarity=0.342 Sum_probs=39.7
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHH
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA 147 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs 147 (276)
+-...++.++. ..-|.+.|+|+.-||+..++-.-+..|-++..=+==+++.|--||+=|.-+.+
T Consensus 100 lL~~Fi~yIK~-~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE~~~ 163 (188)
T PF09756_consen 100 LLQEFINYIKE-HKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEEMEA 163 (188)
T ss_dssp HHHHHHHHHHH--SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--------
T ss_pred HHHHHHHHHHH-cceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHHHHH
Confidence 55666777765 46788999999999999999999999999884444458899999998888776
No 231
>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=30.97 E-value=13 Score=26.88 Aligned_cols=19 Identities=26% Similarity=0.746 Sum_probs=15.8
Q ss_pred ccCCCCCCCchhhhhhhcC
Q 023862 258 VFGEGDPNQGIEEKRWKLV 276 (276)
Q Consensus 258 vFGDGDPNa~lEErRwq~i 276 (276)
+.|||||-+=++.+-||.|
T Consensus 22 viG~G~p~~vf~~~tW~hi 40 (47)
T PF11772_consen 22 VIGDGNPFDVFSPDTWQHI 40 (47)
T ss_pred eeCCCCHHHhCCHHHHHHH
Confidence 4689999999999999864
No 232
>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=30.91 E-value=97 Score=23.30 Aligned_cols=21 Identities=19% Similarity=0.572 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 023862 177 FGTALIASIVIVFTAIIAILS 197 (276)
Q Consensus 177 FGi~LIaSIvLv~~aI~ails 197 (276)
+|++|++.|+++..++++...
T Consensus 7 iGviLliaitVilaavv~~~~ 27 (80)
T PF07790_consen 7 IGVILLIAITVILAAVVGAFV 27 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 689999999999988886663
No 233
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=30.80 E-value=1.1e+02 Score=26.79 Aligned_cols=53 Identities=19% Similarity=0.265 Sum_probs=38.2
Q ss_pred chhhHHHHHHHHHc----C------CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCc
Q 023862 81 ADVRNRAMDAVDAC----N------RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (276)
Q Consensus 81 ~~~~~rim~Ave~l----g------~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesG 135 (276)
.+++.|+.+.+.++ | -.+|..|+|...|++.+.+-+.|..|-.+ |-+++...|
T Consensus 153 ~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~--GlI~~~~~~ 215 (230)
T PRK09391 153 KTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDR--GLIGLSGAR 215 (230)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHC--CcEEecCCc
Confidence 45667777766553 2 24688999999999999999999998765 344444333
No 234
>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=30.39 E-value=38 Score=22.87 Aligned_cols=17 Identities=35% Similarity=0.470 Sum_probs=13.6
Q ss_pred ehhhhhhhcCCCHHHHH
Q 023862 99 TIGDVAGKAGLKLNEAQ 115 (276)
Q Consensus 99 TvgDVAa~aGL~l~~Ae 115 (276)
|++|||..+|++....+
T Consensus 1 ti~e~A~~~gvs~~tlR 17 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLR 17 (38)
T ss_dssp EHHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 78999999999987653
No 235
>PRK14999 histidine utilization repressor; Provisional
Probab=30.21 E-value=90 Score=27.63 Aligned_cols=59 Identities=17% Similarity=0.298 Sum_probs=41.1
Q ss_pred chhhHHHHHHHHHc----CCce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcC
Q 023862 81 ADVRNRAMDAVDAC----NRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFP 142 (276)
Q Consensus 81 ~~~~~rim~Ave~l----g~rv-TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP 142 (276)
..+...|.+.++.. |-+. |-.++|.+-|+|...+++||..|+.+. -| +...|.=.||=+
T Consensus 15 ~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eG--li-~r~~GkGTfV~~ 78 (241)
T PRK14999 15 ETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEG--WL-VRLQGVGTFVAE 78 (241)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCC--CE-EEecCcEEEECC
Confidence 44455666666653 4445 788999999999999999999999874 34 334444445543
No 236
>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=30.02 E-value=71 Score=30.18 Aligned_cols=44 Identities=23% Similarity=0.311 Sum_probs=33.6
Q ss_pred CCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862 95 NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (276)
Q Consensus 95 g~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv 140 (276)
.+.+|++|.|.+-.|+.+-.++.+..- .-|..++.--+|+.+|.
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 45777787778886653
No 237
>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=29.98 E-value=20 Score=29.33 Aligned_cols=27 Identities=30% Similarity=0.268 Sum_probs=17.6
Q ss_pred HHcCCceehhhhhhhcCCCHHHHHHHH
Q 023862 92 DACNRRVTIGDVAGKAGLKLNEAQKAL 118 (276)
Q Consensus 92 e~lg~rvTvgDVAa~aGL~l~~Ae~aL 118 (276)
++..+.+|.+|||.+++...++-|+++
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 446788999999999998888777654
No 238
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=29.92 E-value=37 Score=26.84 Aligned_cols=33 Identities=21% Similarity=0.307 Sum_probs=25.1
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHH
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL 118 (276)
+..|+-++++.| .|+.++|-++||+-+....+|
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 356788888777 799999999999998887766
No 239
>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=29.89 E-value=1.2e+02 Score=19.02 Aligned_cols=26 Identities=12% Similarity=0.249 Sum_probs=22.0
Q ss_pred CceehhhhhhhcCCCHHHHHHHHHHH
Q 023862 96 RRVTIGDVAGKAGLKLNEAQKALQAL 121 (276)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (276)
...|..|||...|++...+.+.+...
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 55799999999999999998777654
No 240
>PLN03239 histone acetyltransferase; Provisional
Probab=29.85 E-value=71 Score=31.79 Aligned_cols=59 Identities=17% Similarity=0.144 Sum_probs=40.4
Q ss_pred hHHHHHHHHHcC---CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHH
Q 023862 84 RNRAMDAVDACN---RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA 147 (276)
Q Consensus 84 ~~rim~Ave~lg---~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs 147 (276)
+.+|++.+.+.. ..+|+.|++..||+..+++-.+|+.| |-|.....+.+|+.=+...+.
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 466777776653 46999999999999999998888876 444444444445544333333
No 241
>PRK04217 hypothetical protein; Provisional
Probab=29.85 E-value=1.1e+02 Score=25.56 Aligned_cols=45 Identities=11% Similarity=0.127 Sum_probs=30.1
Q ss_pred cCCCCchhhHHHHHHHHHcC-CceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 76 SDKLPADVRNRAMDAVDACN-RRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 76 ~~~l~~~~~~rim~Ave~lg-~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
..+|+.+-+ +++.... ...|+.|||...|++.+.+.+-|......
T Consensus 40 ~~~Lt~eer----eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkk 85 (110)
T PRK04217 40 PIFMTYEEF----EALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKK 85 (110)
T ss_pred cccCCHHHH----HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 445665553 3333333 55699999999999999887776654433
No 242
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=29.76 E-value=1.9e+02 Score=22.77 Aligned_cols=54 Identities=17% Similarity=0.152 Sum_probs=41.9
Q ss_pred chhhHHHHHHHHHcCCceehh-hhhhhcCCCHHHHHHHHHHHHhhcCCceEeecC-c
Q 023862 81 ADVRNRAMDAVDACNRRVTIG-DVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-G 135 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~rvTvg-DVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSes-G 135 (276)
++.+..++..+..+++...-| ++|++.|++-..+.+.+++|= +.|-.++...+ |
T Consensus 2 ~~~~~~~~~ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr-~~G~~I~s~~~kG 57 (79)
T COG1654 2 KDTSQMLLLLLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLR-EEGVDIESVRGKG 57 (79)
T ss_pred cchHHHHHHHHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHH-HhCCceEecCCCc
Confidence 456677888888888876666 899999999999999999998 44555544443 5
No 243
>PRK04280 arginine repressor; Provisional
Probab=29.62 E-value=1.4e+02 Score=25.81 Aligned_cols=48 Identities=19% Similarity=0.373 Sum_probs=35.7
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe-ecCccEEEEcCcch
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV-SDEGDVLYVFPNNY 145 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeV-SesGDIlYvFP~nf 145 (276)
..++.+++.+++.|..||++-|. +.|..| |-.+| +++|.-.|..|.+-
T Consensus 19 ~tQeeL~~~L~~~Gi~vTQATiS-----------RDikeL-----~lvKv~~~~G~~~Y~lp~~~ 67 (148)
T PRK04280 19 ETQDELVDRLREEGFNVTQATVS-----------RDIKEL-----HLVKVPLPDGRYKYSLPADQ 67 (148)
T ss_pred CCHHHHHHHHHHcCCCeehHHHH-----------HHHHHc-----CCEEeecCCCcEEEeecccc
Confidence 34788999999999999887554 444444 44566 47899999999864
No 244
>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=29.24 E-value=1.5e+02 Score=22.47 Aligned_cols=53 Identities=11% Similarity=0.223 Sum_probs=35.4
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCc-cEEE
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG-DVLY 139 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesG-DIlY 139 (276)
.=-.|++.+++.+.-+|+.|+...+.++++..-..++. -.=.+++..+| .-.|
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 33567889999999999999999999998866554444 55678888776 4444
No 245
>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=29.21 E-value=1.5e+02 Score=22.97 Aligned_cols=35 Identities=11% Similarity=0.204 Sum_probs=29.3
Q ss_pred HHHHHHHHHcC-CceehhhhhhhcC-CCHHHHHHHHH
Q 023862 85 NRAMDAVDACN-RRVTIGDVAGKAG-LKLNEAQKALQ 119 (276)
Q Consensus 85 ~rim~Ave~lg-~rvTvgDVAa~aG-L~l~~Ae~aL~ 119 (276)
-.|++.+++.+ .-+|+.||...+. +.+..+...++
T Consensus 12 ~~aV~ymK~r~~~Plt~~EIl~~ls~~d~~~~~~~~L 48 (75)
T cd07977 12 AKIVDYMKKRHQHPLTLDEILDYLSLLDIGPKLKEWL 48 (75)
T ss_pred HHHHHHHHhcCCCCccHHHHHHHHhccCccHHHHHHH
Confidence 46788899999 9999999999999 88887765443
No 246
>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=29.18 E-value=62 Score=29.85 Aligned_cols=48 Identities=21% Similarity=0.308 Sum_probs=39.8
Q ss_pred eeeecccccccccCCCcccccCCCCchhhHHHHHHHHHcCCceehhhh
Q 023862 56 PVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDV 103 (276)
Q Consensus 56 ~~~~~~~~~~~~~~~~~~v~~~~l~~~~~~rim~Ave~lg~rvTvgDV 103 (276)
+-.+.++|...++-|+..=.-.=+|.....++++|++++|.+.--.|+
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 446677787888888887777778999999999999999999876665
No 247
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=28.73 E-value=1.1e+02 Score=21.09 Aligned_cols=37 Identities=16% Similarity=0.235 Sum_probs=25.1
Q ss_pred HHHHHHHHHcCC-ceehhhhhhhcCC-CHHHHHHHHHHH
Q 023862 85 NRAMDAVDACNR-RVTIGDVAGKAGL-KLNEAQKALQAL 121 (276)
Q Consensus 85 ~rim~Ave~lg~-rvTvgDVAa~aGL-~l~~Ae~aL~aL 121 (276)
.++.++++.+.. ..|+.|||..+|+ +...-.+.....
T Consensus 37 ~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 37 RRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 344455555444 5999999999999 877665555443
No 248
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=28.71 E-value=83 Score=25.46 Aligned_cols=48 Identities=13% Similarity=0.147 Sum_probs=42.2
Q ss_pred chhhHHHHHHHHHc-CCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCc
Q 023862 81 ADVRNRAMDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGF 128 (276)
Q Consensus 81 ~~~~~rim~Ave~l-g~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~Gh 128 (276)
+.+|.+|+..+.+. +...++.|+|..+|.+...+..+|.-....+.++
T Consensus 8 S~~R~~vl~~L~~~yp~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e 56 (90)
T PF07381_consen 8 SKVRKKVLEYLCSIYPEPAYPSEIARSVGSDYSNVLGALRGDGKRYNKE 56 (90)
T ss_pred HHHHHHHHHHHHHcCCCcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcc
Confidence 46788999999999 9999999999999999999999998877766654
No 249
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=28.66 E-value=1.5e+02 Score=22.30 Aligned_cols=38 Identities=18% Similarity=0.318 Sum_probs=26.0
Q ss_pred CCceehhhhhhhcCCCHHHHHH------------HHHHHHhhcCCceEee
Q 023862 95 NRRVTIGDVAGKAGLKLNEAQK------------ALQALAADTDGFLEVS 132 (276)
Q Consensus 95 g~rvTvgDVAa~aGL~l~~Ae~------------aL~aLAsD~~GhLeVS 132 (276)
....|..|+|...|++-..+-+ .|..++...|+++++.
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 3568999999999988665532 4566777788888874
No 250
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=28.61 E-value=49 Score=28.50 Aligned_cols=23 Identities=39% Similarity=0.497 Sum_probs=18.7
Q ss_pred eehhh---hhhhcCCCHHHHHHHHHH
Q 023862 98 VTIGD---VAGKAGLKLNEAQKALQA 120 (276)
Q Consensus 98 vTvgD---VAa~aGL~l~~Ae~aL~a 120 (276)
++-.| |+.|||.|-++|.+||.+
T Consensus 83 i~eeDIkLV~eQa~VsreeA~kAL~e 108 (122)
T COG1308 83 ISEEDIKLVMEQAGVSREEAIKALEE 108 (122)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 44444 578999999999999975
No 251
>PF14493 HTH_40: Helix-turn-helix domain
Probab=28.42 E-value=84 Score=24.22 Aligned_cols=72 Identities=14% Similarity=0.209 Sum_probs=46.4
Q ss_pred HHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHhhhhhH---HHhHHHHHHH
Q 023862 88 MDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSF---RLKVEPVIDK 164 (276)
Q Consensus 88 m~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L~~Ks~---r~rl~~~~~k 164 (276)
+...+-...+-|+.|||.+-||+.+..+.-|..++.... .+.+++ .+|......+..-.- ..+|+++.+.
T Consensus 4 ~~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~-~~~~~~------~l~~e~~~~I~~~~~~~~~~~lk~i~e~ 76 (91)
T PF14493_consen 4 QITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGE-PLDIEE------LLSEEEIKQIEDAIEKLGSEKLKPIKEA 76 (91)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCC-CCCHHH------hCCHHHHHHHHHHHHHcCcccHHHHHHH
Confidence 344455556799999999999999999999999887743 244331 145554443333111 1356666666
Q ss_pred Hh
Q 023862 165 AK 166 (276)
Q Consensus 165 ~w 166 (276)
+-
T Consensus 77 l~ 78 (91)
T PF14493_consen 77 LP 78 (91)
T ss_pred CC
Confidence 55
No 252
>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=28.40 E-value=1.2e+02 Score=26.98 Aligned_cols=45 Identities=20% Similarity=0.351 Sum_probs=37.9
Q ss_pred CCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 78 ~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
-|+.+++..|.+-+.+.|. |+-.||.+-|+++.-+ .|++.|-...
T Consensus 16 ~lse~~r~~Iy~~~~~~~~--sv~~vS~~ygi~~~RV-~AIvrLkeiE 60 (172)
T PF12298_consen 16 VLSEELREQIYEDVMQDGK--SVREVSQKYGIKIQRV-EAIVRLKEIE 60 (172)
T ss_pred cCCHHHHHHHHHHHHhCCC--CHHHHHHHhCCCHHHH-HHHHHHHHHH
Confidence 3678899999999998888 9999999999999999 6666665543
No 253
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=28.38 E-value=93 Score=21.65 Aligned_cols=28 Identities=18% Similarity=0.204 Sum_probs=17.7
Q ss_pred HHHHHHHcCCceehhhhhhhcCCCHHHHHH
Q 023862 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQK 116 (276)
Q Consensus 87 im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~ 116 (276)
+-+.+++.|. |+.|+|.++|++..+..+
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 3455566665 999999999999877644
No 254
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=28.19 E-value=2.4e+02 Score=24.77 Aligned_cols=60 Identities=17% Similarity=0.267 Sum_probs=40.0
Q ss_pred CCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCc
Q 023862 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (276)
Q Consensus 78 ~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~ 143 (276)
.++... .++++.+++.|..+.+. ||=+...++.-+..|.-+....--|+.+|-+||....
T Consensus 20 ~i~~~~-~~ai~~l~~~G~~~~ia-----TGR~~~~~~~~~~~l~~~~~~~~~I~~NGa~i~~~~~ 79 (270)
T PRK10513 20 TISPAV-KQAIAAARAKGVNVVLT-----TGRPYAGVHRYLKELHMEQPGDYCITNNGALVQKAAD 79 (270)
T ss_pred ccCHHH-HHHHHHHHHCCCEEEEe-----cCCChHHHHHHHHHhCCCCCCCeEEEcCCeEEEECCC
Confidence 355544 45677778889887764 8988888877666664332223457888888887543
No 255
>PRK10286 O-6-alkylguanine-DNA:cysteine-protein methyltransferase; Provisional
Probab=28.01 E-value=82 Score=28.08 Aligned_cols=74 Identities=11% Similarity=0.159 Sum_probs=52.5
Q ss_pred chhhHHHHHHHHHc--CCceehhhhhhhcCCC--HHHHHHHHHH--HHhhcCCceEeecCccEEEEcCcchHHHhhhhhH
Q 023862 81 ADVRNRAMDAVDAC--NRRVTIGDVAGKAGLK--LNEAQKALQA--LAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSF 154 (276)
Q Consensus 81 ~~~~~rim~Ave~l--g~rvTvgDVAa~aGL~--l~~Ae~aL~a--LAsD~~GhLeVSesGDIlYvFP~nfRs~L~~Ks~ 154 (276)
.+.+.+|.+++.+. |.-+|-||+|...|-+ ...+-.++.+ +.-...||==|..+|.+-- | +.=+..|.+
T Consensus 87 t~fq~~V~~~l~~IP~G~~~tYg~iA~~~g~p~aaRaVG~A~~~Np~~i~iPCHRVv~~~G~l~g-y----~gG~~~K~~ 161 (171)
T PRK10286 87 TPFQREVWQTLRTIPCGQVMHYGQLAEQLGRPGAARAVGAANGSNPISIVVPCHRVIGRNGTMTG-Y----AGGVQRKEW 161 (171)
T ss_pred CHHHHHHHHHHHcCCCCCcEeHHHHHHHhCCCChHHHHHHHHHhCCCCCccCCceEECCCCCcCC-C----CCcHHHHHH
Confidence 46789999999998 7778889999999975 3444444422 3445689999999999863 3 222444666
Q ss_pred HHhHH
Q 023862 155 RLKVE 159 (276)
Q Consensus 155 r~rl~ 159 (276)
.+.+|
T Consensus 162 LL~~E 166 (171)
T PRK10286 162 LLRHE 166 (171)
T ss_pred HHHHc
Confidence 66555
No 256
>PRK08392 hypothetical protein; Provisional
Probab=28.01 E-value=61 Score=28.55 Aligned_cols=35 Identities=9% Similarity=-0.059 Sum_probs=25.8
Q ss_pred ccCCCcccccCCCCchhhHHHHHHHHHcCCceehh
Q 023862 67 GVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIG 101 (276)
Q Consensus 67 ~~~~~~~v~~~~l~~~~~~rim~Ave~lg~rvTvg 101 (276)
.++-|-.+|-+....-+.+.+++.+.++|.++|+|
T Consensus 146 ~~~~g~~lEiNt~~~~p~~~~l~~~~~~G~~~~ig 180 (215)
T PRK08392 146 AEAYGKAFEISSRYRVPDLEFIRECIKRGIKLTFA 180 (215)
T ss_pred HHHhCCEEEEeCCCCCCCHHHHHHHHHcCCEEEEe
Confidence 34556666665444456678999999999999998
No 257
>PRK12702 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=27.99 E-value=80 Score=30.76 Aligned_cols=28 Identities=25% Similarity=0.375 Sum_probs=23.2
Q ss_pred ceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 97 RVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 97 rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
..|+.+||+-|||+.++|++|.+.-.++
T Consensus 123 d~t~~ei~~~TGL~~~~A~~A~~Re~SE 150 (302)
T PRK12702 123 DWTASELAAATGIPLEEAERAQKREYSE 150 (302)
T ss_pred hCCHHHHHHHhCcCHHHHHHHHhccCCc
Confidence 4689999999999999999887764443
No 258
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=27.63 E-value=1.4e+02 Score=24.33 Aligned_cols=42 Identities=10% Similarity=0.147 Sum_probs=35.4
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
.+..++..+.. .+.+|+.|+|...|++...+=+.|..|..+.
T Consensus 41 ~q~~vL~~l~~-~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~G 82 (144)
T PRK11512 41 AQFKVLCSIRC-AACITPVELKKVLSVDLGALTRMLDRLVCKG 82 (144)
T ss_pred HHHHHHHHHHH-cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 46778888865 4569999999999999999999999987653
No 259
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=27.57 E-value=2.1e+02 Score=30.15 Aligned_cols=89 Identities=13% Similarity=0.122 Sum_probs=59.1
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc--CCceEeecCccEEEEcC---cchHHHhhhhhHHHhHH
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DGFLEVSDEGDVLYVFP---NNYRAKLAAKSFRLKVE 159 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~--~GhLeVSesGDIlYvFP---~nfRs~L~~Ks~r~rl~ 159 (276)
.+++..+-+.|.--..-=++..+|++.+.++++|..|.+-. ..++....+|+++|..- +-.+-..-+|+-..--+
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 45677777777666577789999999999999999999865 55555666899887652 22332223344444445
Q ss_pred HHHHHHhhhhhhHH
Q 023862 160 PVIDKAKAAAEYSI 173 (276)
Q Consensus 160 ~~~~k~w~v~~Yli 173 (276)
+.-+++-.++.+|+
T Consensus 102 ~~~q~~~sIv~~Ll 115 (551)
T KOG2587|consen 102 LYSQTAESIVEELL 115 (551)
T ss_pred HhhhHHHHHHHHHH
Confidence 55555555555553
No 260
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=27.49 E-value=1.3e+02 Score=26.47 Aligned_cols=39 Identities=18% Similarity=0.251 Sum_probs=31.3
Q ss_pred hhhHHHHHHHHHcCC-----ceehhhhhhhcCCCHHHHHHHHHH
Q 023862 82 DVRNRAMDAVDACNR-----RVTIGDVAGKAGLKLNEAQKALQA 120 (276)
Q Consensus 82 ~~~~rim~Ave~lg~-----rvTvgDVAa~aGL~l~~Ae~aL~a 120 (276)
+-+.++++..=+.|| ++|+.|+|.+-|++...+++-|+.
T Consensus 158 drQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRr 201 (215)
T COG3413 158 DRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRR 201 (215)
T ss_pred HHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHH
Confidence 445667777777776 899999999999999988766654
No 261
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=27.43 E-value=2.9e+02 Score=27.30 Aligned_cols=100 Identities=16% Similarity=0.189 Sum_probs=52.7
Q ss_pred CCCchhhHHH---HHH----HHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh-cCCceEeecCcc-EEEEc-Cc---c
Q 023862 78 KLPADVRNRA---MDA----VDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD-TDGFLEVSDEGD-VLYVF-PN---N 144 (276)
Q Consensus 78 ~l~~~~~~ri---m~A----ve~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD-~~GhLeVSesGD-IlYvF-P~---n 144 (276)
+||......+ .++ -.++|...|+.+||...|++.++++..+. ++.. ..=+-.+.++++ .+..+ +. +
T Consensus 213 RlP~~~~~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~-~~~~~~SLd~~i~~~~~~~l~d~l~d~~~~ 291 (373)
T PRK07406 213 RLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAK-SAQLPISLETPIGKEEDSRLGDFIEADGET 291 (373)
T ss_pred eCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-hcCCCcccCCCCCCCCcccHHHhcCCCCCC
Confidence 5776665322 333 34568889999999999999999976544 3321 111112222222 11111 21 1
Q ss_pred hHHHhhhhhHHHhHHHHHHHHhhhhhhHHHHHHH
Q 023862 145 YRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFG 178 (276)
Q Consensus 145 fRs~L~~Ks~r~rl~~~~~k~w~v~~YliRIsFG 178 (276)
--..+.....+..|..+++.+-.-=..+++--||
T Consensus 292 pee~~~~~~~~~~L~~aL~~L~~rEr~IL~lryg 325 (373)
T PRK07406 292 PEDDVAKNLLREDLEGVLATLSPRERDVLRLRYG 325 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence 1233333445555666666555555555555554
No 262
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=27.41 E-value=1.3e+02 Score=28.87 Aligned_cols=91 Identities=22% Similarity=0.319 Sum_probs=58.8
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcC-cchHHHhhhhhHHHhHHH
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFP-NNYRAKLAAKSFRLKVEP 160 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP-~nfRs~L~~Ks~r~rl~~ 160 (276)
..+-+|+--+-...+++-+.|+|.+-|+++.-+-.-+..|.++. +.+. +|.-=|+-. ++++-.+++-+ -++.
T Consensus 10 ~t~fqIL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG--~i~~--~gR~~Y~iTkkG~e~l~~~~~---dlr~ 82 (260)
T COG1497 10 LTRFQILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKEG--LIEK--EGRGEYEITKKGAEWLLEQLS---DLRR 82 (260)
T ss_pred chHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhcc--ceee--cCCeeEEEehhHHHHHHHHHH---HHHH
Confidence 34567777888888999999999999999999988999998763 3333 444444432 23444333322 1222
Q ss_pred HHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 023862 161 VIDKAKAAAEYSIRVLFGTALIASIVIVFTAII 193 (276)
Q Consensus 161 ~~~k~w~v~~YliRIsFGi~LIaSIvLv~~aI~ 193 (276)
+.+. +.++...+-++.||+
T Consensus 83 f~~e--------------v~~~l~~~~vw~AIA 101 (260)
T COG1497 83 FSEE--------------VELVLDYVMVWTAIA 101 (260)
T ss_pred HHHH--------------HHHHHhhHHHHHHhh
Confidence 2222 134556777888887
No 263
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=27.33 E-value=1.3e+02 Score=26.38 Aligned_cols=55 Identities=18% Similarity=0.389 Sum_probs=38.1
Q ss_pred hhHHHHHHHHHc----CCce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862 83 VRNRAMDAVDAC----NRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (276)
Q Consensus 83 ~~~rim~Ave~l----g~rv-TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv 140 (276)
+...|.+.++.. |.+. |-.++|.+-|+|-..+++||..|+.+ |-|+ ...|-=.||
T Consensus 6 i~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~e--Gli~-r~~G~GtfV 65 (230)
T TIGR02018 6 IKQDILERIRSGEWPPGHRIPSEHELVAQYGCSRMTVNRALRELTDA--GLLE-RRQGVGTFV 65 (230)
T ss_pred HHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEE-EecCCEEEE
Confidence 445556666553 3344 77799999999999999999999998 4443 333333444
No 264
>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=27.32 E-value=1.2e+02 Score=22.42 Aligned_cols=70 Identities=17% Similarity=0.133 Sum_probs=45.6
Q ss_pred CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHhhh
Q 023862 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAA 151 (276)
Q Consensus 80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L~~ 151 (276)
..-++..+..+++......++-++.+...-=.+..+.+|..-...+| +++..=+--=..+|.+++..+..
T Consensus 50 ~~~i~~~~~~~~~~~~~~~~~~~~~~~r~~i~~~v~~~l~~~~~~~G--i~i~~v~i~~i~~~~~~~~ai~~ 119 (121)
T cd02106 50 EEALRQLAQSALRSVIGKMTLDELLEDRDEIAAEVREALQEDLDKYG--IEVVDVRIKDIDPPEEVQEAMED 119 (121)
T ss_pred HHHHHHHHHHHHHHHHccccHHHHHhhHHHHHHHHHHHHHHHHHhcC--CEEEEEEEEecCCCHHHHHHHHh
Confidence 45677888888888888889999954432222233444444444454 88887665566788887765543
No 265
>KOG0860 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.31 E-value=2.2e+02 Score=24.35 Aligned_cols=33 Identities=18% Similarity=0.228 Sum_probs=16.6
Q ss_pred hhHHHhHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 023862 152 KSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAI 192 (276)
Q Consensus 152 Ks~r~rl~~~~~k~w~v~~YliRIsFGi~LIaSIvLv~~aI 192 (276)
..-+++=+-||+.+ |....+.+|+.|+|+++.|
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 44455555566654 3444555554444444433
No 266
>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=27.22 E-value=1.3e+02 Score=27.50 Aligned_cols=14 Identities=7% Similarity=-0.069 Sum_probs=9.2
Q ss_pred HHHhHHHHHHHHhh
Q 023862 154 FRLKVEPVIDKAKA 167 (276)
Q Consensus 154 ~r~rl~~~~~k~w~ 167 (276)
-..||++..++-|+
T Consensus 214 ~~~rl~~~~~~~~~ 227 (251)
T PF09753_consen 214 ESKRLKEHSSKSWG 227 (251)
T ss_pred HHHHHHHHHHhccc
Confidence 34467777777666
No 267
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=27.12 E-value=41 Score=30.81 Aligned_cols=44 Identities=11% Similarity=0.122 Sum_probs=34.8
Q ss_pred CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
|-.+++..|-+++.+ +..|+.|+|+++|++..-++.=|++|++-
T Consensus 7 l~aa~~Lglfd~L~~--gp~t~~eLA~~~~~~~~~~~~lL~~L~~l 50 (306)
T TIGR02716 7 MKAAIELDLFSHMAE--GPKDLATLAADTGSVPPRLEMLLETLRQM 50 (306)
T ss_pred HHHHHHcCcHHHHhc--CCCCHHHHHHHcCCChHHHHHHHHHHHhC
Confidence 334555666677755 46799999999999999999999999864
No 268
>PRK10617 cytochrome c-type protein NapC; Provisional
Probab=26.74 E-value=1.3e+02 Score=27.42 Aligned_cols=22 Identities=32% Similarity=0.492 Sum_probs=18.3
Q ss_pred hhhhhcccCCCCCCCchhhhhh
Q 023862 252 KSVFSFVFGEGDPNQGIEEKRW 273 (276)
Q Consensus 252 EaVFSFvFGDGDPNa~lEErRw 273 (276)
.=||.++||+-|-..++|++|.
T Consensus 108 ~dv~~~~~~~idt~ekfe~~r~ 129 (200)
T PRK10617 108 KELYGKIFGVIDTPQKFEAHRL 129 (200)
T ss_pred hHHHHHhhcCCCChHHHHHhHH
Confidence 3589999999888889998873
No 269
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=26.66 E-value=86 Score=26.51 Aligned_cols=58 Identities=21% Similarity=0.190 Sum_probs=38.1
Q ss_pred CCCCchhhHHHH-HHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc-CCceEeecCccEE
Q 023862 77 DKLPADVRNRAM-DAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT-DGFLEVSDEGDVL 138 (276)
Q Consensus 77 ~~l~~~~~~rim-~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~-~GhLeVSesGDIl 138 (276)
++||+.-+.-+. ..++ ..+..|||...|++...++..|...-..- --.|-.+..||++
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 47899999999999999987766433332 4456677777753
No 270
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=26.56 E-value=44 Score=31.37 Aligned_cols=22 Identities=36% Similarity=0.441 Sum_probs=18.6
Q ss_pred eehhhhhhhcCCCHHHHHHHHH
Q 023862 98 VTIGDVAGKAGLKLNEAQKALQ 119 (276)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL~ 119 (276)
+|+.|||..||+|..++-+.|+
T Consensus 1 ~TikDVA~~AGVS~sTVSrvln 22 (333)
T COG1609 1 ATIKDVAKLAGVSKATVSRVLN 22 (333)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 5899999999999988866664
No 271
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=26.36 E-value=1.5e+02 Score=28.76 Aligned_cols=66 Identities=15% Similarity=0.286 Sum_probs=51.8
Q ss_pred CCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh------------hcCCceEeecCccEEEEcCcc
Q 023862 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA------------DTDGFLEVSDEGDVLYVFPNN 144 (276)
Q Consensus 78 ~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAs------------D~~GhLeVSesGDIlYvFP~n 144 (276)
.|.+.+|-+|++.+.++|. ..|-+||..-||+-...-..+..|-. +..-.+-.+..+||+-.||..
T Consensus 19 alaS~vRv~Il~lL~~k~p-lNvneiAe~lgLpqst~s~~ik~Le~aGlirT~t~karkG~QKiC~s~~~ei~i~F~~r 96 (308)
T COG4189 19 ALASKVRVAILQLLHRKGP-LNVNEIAEALGLPQSTMSANIKVLEKAGLIRTETVKARKGSQKICISTTDEIEINFPDR 96 (308)
T ss_pred HHHHHHHHHHHHHHHHhCC-CCHHHHHHHhCCchhhhhhhHHHHHhcCceeeeeeccccCceeEeEeecceEEEecCCC
Confidence 4668899999999988774 67899999999999998777777743 223345567789999999763
No 272
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=26.32 E-value=1.1e+02 Score=28.48 Aligned_cols=51 Identities=6% Similarity=-0.061 Sum_probs=43.4
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCC
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG 127 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~G 127 (276)
......+.+|=.+.++-...+.|..|||.+.+++..+++.-+..+-.+.|.
T Consensus 138 ~~~~~~LS~RE~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred hhccCCCCHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 344456677778888889999999999999999999999999999888763
No 273
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=26.26 E-value=1.4e+02 Score=25.91 Aligned_cols=57 Identities=16% Similarity=0.315 Sum_probs=38.1
Q ss_pred chhhHHHHHHHHHcC----Cce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862 81 ADVRNRAMDAVDACN----RRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (276)
Q Consensus 81 ~~~~~rim~Ave~lg----~rv-TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv 140 (276)
..+...|.+.++..- -+. |-.++|.+-|+|...+++||..|+.+. -|+ ...|-=.||
T Consensus 11 ~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eG--li~-r~~G~GtfV 72 (238)
T TIGR02325 11 RQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERG--LLR-AEQGRGTFV 72 (238)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCC--CEE-EecCCEEEE
Confidence 344455555555532 233 777999999999999999999999874 333 334444454
No 274
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=26.26 E-value=1.2e+02 Score=24.75 Aligned_cols=37 Identities=11% Similarity=0.237 Sum_probs=28.4
Q ss_pred HHHHHHHHHc-CCceehhhhhhhcCCCHHHHHHHHHHH
Q 023862 85 NRAMDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQAL 121 (276)
Q Consensus 85 ~rim~Ave~l-g~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (276)
.++++.+++. ....|+.|+|...|++....++-+.+.
T Consensus 12 ~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 12 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4666777554 466899999999999998887766554
No 275
>PRK10870 transcriptional repressor MprA; Provisional
Probab=25.92 E-value=1.4e+02 Score=25.81 Aligned_cols=43 Identities=12% Similarity=0.121 Sum_probs=37.1
Q ss_pred hhHHHHHHHHHc-CCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 83 VRNRAMDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 83 ~~~rim~Ave~l-g~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
.+-.++..+... ++.+|+.|+|...|++...+-+.+..|..+.
T Consensus 56 ~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kG 99 (176)
T PRK10870 56 TLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRG 99 (176)
T ss_pred HHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 467888888865 5789999999999999999999999998764
No 276
>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=25.49 E-value=23 Score=33.82 Aligned_cols=16 Identities=13% Similarity=0.096 Sum_probs=0.0
Q ss_pred HHHHHhhhhhhHHHHH
Q 023862 161 VIDKAKAAAEYSIRVL 176 (276)
Q Consensus 161 ~~~k~w~v~~YliRIs 176 (276)
-++|+|..+-|||=++
T Consensus 3 tl~~~w~~~~~~i~~~ 18 (263)
T PF00802_consen 3 TLEKTWDTLNHLIVIS 18 (263)
T ss_dssp ----------------
T ss_pred hHHHhHhhhcceehhh
Confidence 3678888888887665
No 277
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=25.35 E-value=3.5e+02 Score=23.14 Aligned_cols=69 Identities=25% Similarity=0.368 Sum_probs=46.2
Q ss_pred ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcc--hHHHhhhhhHHHhHHHHHHHHhhhhh
Q 023862 99 TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN--YRAKLAAKSFRLKVEPVIDKAKAAAE 170 (276)
Q Consensus 99 TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~n--fRs~L~~Ks~r~rl~~~~~k~w~v~~ 170 (276)
++-++|..+|++.+.++++.+.|-.+ |.++ +..|-=.|+=+.+ -..-.+..-+...++++...+....+
T Consensus 37 SvRelA~~~~VNpnTv~raY~eLE~e--G~i~-t~rg~G~fV~~~~~~~~~~~~~~~~~~~l~~~I~~~~~~G~ 107 (125)
T COG1725 37 SVRELAKDLGVNPNTVQRAYQELERE--GIVE-TKRGKGTFVTEDAKEILDQLKRELAEEELEEFIEEAKALGL 107 (125)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHC--CCEE-EecCeeEEEcCCchhhHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 47789999999999999999999765 4444 3344445554332 23333445566678888777766544
No 278
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=25.32 E-value=1.8e+02 Score=21.49 Aligned_cols=39 Identities=23% Similarity=0.289 Sum_probs=29.5
Q ss_pred chhhHHHHHHHHHcCC--ceehhhhhhh---cCCCHHHHHHHHH
Q 023862 81 ADVRNRAMDAVDACNR--RVTIGDVAGK---AGLKLNEAQKALQ 119 (276)
Q Consensus 81 ~~~~~rim~Ave~lg~--rvTvgDVAa~---aGL~l~~Ae~aL~ 119 (276)
.+...+.++|++.+|. .+|...|+.. ++|+..++++=|+
T Consensus 8 ~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~Q 51 (57)
T TIGR01557 8 EDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQ 51 (57)
T ss_pred HHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHH
Confidence 4667788999999997 6777777654 6678888766554
No 279
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=25.30 E-value=1.4e+02 Score=22.95 Aligned_cols=38 Identities=18% Similarity=0.221 Sum_probs=28.8
Q ss_pred hHHHHHHHHHc-CCceehhhhhhhcCCCHHHHHHHHHHH
Q 023862 84 RNRAMDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQAL 121 (276)
Q Consensus 84 ~~rim~Ave~l-g~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (276)
-.++.+.++.. ...+|+.|+|.+.|++....++...+.
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34555555544 556999999999999999888777765
No 280
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=25.15 E-value=59 Score=29.40 Aligned_cols=56 Identities=18% Similarity=0.164 Sum_probs=36.5
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcC-----------CC---HHHHHHHHHHHHhhcCCceEee
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------LK---LNEAQKALQALAADTDGFLEVS 132 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aG-----------L~---l~~Ae~aL~aLAsD~~GhLeVS 132 (276)
.++..+.|+||+++++++||+.-..-=+.+++ ++ -.+.-+++...|.+.|-++.+.
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 11 2345567777777777766553
No 281
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=25.09 E-value=72 Score=28.38 Aligned_cols=47 Identities=19% Similarity=0.204 Sum_probs=35.3
Q ss_pred HcCCce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-CccEEEEc
Q 023862 93 ACNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYVF 141 (276)
Q Consensus 93 ~lg~rv-TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe-sGDIlYvF 141 (276)
+-|.++ |..++|.+-|+|..-++.||..|.++ |-+++.. .|-.|=.+
T Consensus 28 ~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~e--GlV~~~~~~G~~V~~~ 76 (257)
T PRK10225 28 NPGERLPPEREIAEMLDVTRTVVREALIMLEIK--GLVEVRRGAGIYVLDS 76 (257)
T ss_pred CCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEecCCEEEEeCC
Confidence 446677 68899999999999999999999975 5565443 45444333
No 282
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=25.07 E-value=1e+02 Score=22.08 Aligned_cols=31 Identities=13% Similarity=0.269 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHHHHhhcC-CceEeecCccEEEE
Q 023862 109 LKLNEAQKALQALAADTD-GFLEVSDEGDVLYV 140 (276)
Q Consensus 109 L~l~~Ae~aL~aLAsD~~-GhLeVSesGDIlYv 140 (276)
++.++. ++|..+|.+++ |++.+|....|...
T Consensus 21 i~~~~l-~~la~ia~~yg~~~irlT~~Q~l~l~ 52 (69)
T PF03460_consen 21 ISAEQL-RALAEIAEKYGDGEIRLTTRQNLQLR 52 (69)
T ss_dssp EEHHHH-HHHHHHHHHHSTSEEEEETTSCEEEE
T ss_pred ECHHHH-HHHHHHHHHhCCCeEEECCCCeEEEe
Confidence 344555 78999999997 99999999887665
No 283
>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=24.72 E-value=2.5e+02 Score=23.61 Aligned_cols=42 Identities=17% Similarity=0.218 Sum_probs=35.5
Q ss_pred ceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862 97 RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (276)
Q Consensus 97 rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv 140 (276)
-.|..++|....-++++++.||..|-. -|=+|+.++|.+--.
T Consensus 53 py~~e~LA~~~~~~~~~V~~AL~~f~k--~glIe~~ed~~i~i~ 94 (121)
T PF09681_consen 53 PYTAEMLALEFDRPVDTVRLALAVFQK--LGLIEIDEDGVIYIP 94 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEEecCCeEEee
Confidence 357889999999999999999999874 688999999876544
No 284
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=24.65 E-value=1.3e+02 Score=29.03 Aligned_cols=63 Identities=16% Similarity=0.170 Sum_probs=47.9
Q ss_pred HHHHHHHHHcCCceehhhhhhh--cCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHh
Q 023862 85 NRAMDAVDACNRRVTIGDVAGK--AGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKL 149 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~--aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L 149 (276)
..|++..-+.++.|+..++|.+ -|+|...+++.|.+|.+ .|.|+=.-.|-.---..++||--.
T Consensus 9 ~aIV~~~l~~~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~--~G~l~~~h~sagript~kGYR~yv 73 (337)
T TIGR00331 9 KAIVEEYIKTGQPVGSKTLLEKYNLGLSSATIRNDMADLED--LGFIEKPHTSSGRIPTDKGYRYYV 73 (337)
T ss_pred HHHHHHHHhcCCCcCHHHHHhhcCCCCChHHHHHHHHHHHH--CCCccCCCCCCCcCcChhHHHHHH
Confidence 3455666778999999999999 99999999999999987 456655555555555566666533
No 285
>PF13038 DUF3899: Domain of unknown function (DUF3899)
Probab=24.59 E-value=73 Score=24.61 Aligned_cols=32 Identities=19% Similarity=0.333 Sum_probs=18.0
Q ss_pred HHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 023862 163 DKAKAAAEYSIRVLFGTALIASIVIVFTAIIA 194 (276)
Q Consensus 163 ~k~w~v~~YliRIsFGi~LIaSIvLv~~aI~a 194 (276)
++-++--.+.+.-|....|+++++++.++|++
T Consensus 58 ~~~~~~~~~~~~~~~~~~ll~~~ll~l~~iil 89 (92)
T PF13038_consen 58 DKKLKKEKYRVSRWTYPLLLIGLLLILLSIIL 89 (92)
T ss_pred hHHHHHhhhHhHHHHHHHHHHHHHHHHHHHHH
Confidence 34444445555556666666666666666554
No 286
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=24.51 E-value=1.2e+02 Score=27.20 Aligned_cols=46 Identities=17% Similarity=0.288 Sum_probs=34.3
Q ss_pred CCCCchhhHHH---H----HHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHH
Q 023862 77 DKLPADVRNRA---M----DAVDACNRRVTIGDVAGKAGLKLNEAQKALQALA 122 (276)
Q Consensus 77 ~~l~~~~~~ri---m----~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLA 122 (276)
.++|...+..+ . +...++|...|..+||...|++.++.+..+....
T Consensus 109 ir~p~~~~~~~~~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~ 161 (254)
T TIGR02850 109 IRVSRSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQ 161 (254)
T ss_pred ccCchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcC
Confidence 36777665443 2 2245679999999999999999999988776653
No 287
>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=24.44 E-value=1.3e+02 Score=26.99 Aligned_cols=24 Identities=33% Similarity=0.578 Sum_probs=19.7
Q ss_pred hhhhhcccCCCCCCCchhhhhhhc
Q 023862 252 KSVFSFVFGEGDPNQGIEEKRWKL 275 (276)
Q Consensus 252 EaVFSFvFGDGDPNa~lEErRwq~ 275 (276)
.=||.++||+-|...++||.|+++
T Consensus 99 kdv~~~~~g~~~~~~k~~~~r~~~ 122 (185)
T TIGR02161 99 KEVWGHLFGTIDTREKFEAHRLEL 122 (185)
T ss_pred HHHHHhHccCCCCHHHHHHhHHHH
Confidence 348999999988888899988764
No 288
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=24.40 E-value=78 Score=29.38 Aligned_cols=38 Identities=26% Similarity=0.441 Sum_probs=30.7
Q ss_pred HHHHHHHHH------cCCceehhhhh-hhcCCCHHHHHHHHHHHH
Q 023862 85 NRAMDAVDA------CNRRVTIGDVA-GKAGLKLNEAQKALQALA 122 (276)
Q Consensus 85 ~rim~Ave~------lg~rvTvgDVA-a~aGL~l~~Ae~aL~aLA 122 (276)
|+..+.+++ +|+..|+.+++ ...|+++++.-++|.+++
T Consensus 16 P~aa~VF~~~gIdfCcgg~~tLeeA~~~~~gld~~~ll~eLn~~~ 60 (224)
T PRK13276 16 PKAADIFRSVGIDFCCGGQVSIEAASLEKKNVDLNELLQRLNDVE 60 (224)
T ss_pred ccHHHHHHHcCCCcCCCCChhHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 344445555 45678999999 999999999999999996
No 289
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=24.36 E-value=67 Score=22.75 Aligned_cols=44 Identities=16% Similarity=0.073 Sum_probs=26.7
Q ss_pred ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHH
Q 023862 99 TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA 147 (276)
Q Consensus 99 TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs 147 (276)
|++|||..+|++.+..+. -....-=.-..+++|.-.|.. .+...
T Consensus 2 ti~eva~~~gvs~~tlr~----y~~~gll~~~~~~~g~r~y~~-~dv~~ 45 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRY----YEREGLLPPPRDENGYRYYSE-EDVER 45 (69)
T ss_dssp EHHHHHHHTTTTHHHHHH----HHHTTSSTTBESTTSSEEE-H-HHHHH
T ss_pred cHHHHHHHHCcCHHHHHH----HHHhcCcccccccCceeeccH-HHHHH
Confidence 889999999999877643 333332222225678866665 34433
No 290
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=24.28 E-value=1.1e+02 Score=30.92 Aligned_cols=39 Identities=15% Similarity=0.367 Sum_probs=35.0
Q ss_pred hHHHHHHHHHcCCc-eehhhhhhhcCCCHHHHHHHHHHHH
Q 023862 84 RNRAMDAVDACNRR-VTIGDVAGKAGLKLNEAQKALQALA 122 (276)
Q Consensus 84 ~~rim~Ave~lg~r-vTvgDVAa~aGL~l~~Ae~aL~aLA 122 (276)
+..|++.+.+++.. +|+-|++..||+..+++=..|+.|-
T Consensus 315 ~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 315 RCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred HHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 46789999998877 9999999999999999999988874
No 291
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=24.27 E-value=1.5e+02 Score=29.92 Aligned_cols=72 Identities=17% Similarity=0.172 Sum_probs=57.9
Q ss_pred ccCCCc--ccccCCCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc-CCceEeecCccEEEEc
Q 023862 67 GVGPGR--IVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT-DGFLEVSDEGDVLYVF 141 (276)
Q Consensus 67 ~~~~~~--~v~~~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~-~GhLeVSesGDIlYvF 141 (276)
-|-|.| -++.+.+..+.-..+|..+++..+ |-||-.-.-++.++-++.|.++.+-. .|-+-|+.+|.|++.=
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 466777777777778888877776 77888888899999999999998776 8999999999999853
No 292
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=24.25 E-value=1.5e+02 Score=26.89 Aligned_cols=45 Identities=18% Similarity=0.234 Sum_probs=36.4
Q ss_pred chhhHHHHHHHHHcC--CceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 81 ADVRNRAMDAVDACN--RRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 81 ~~~~~rim~Ave~lg--~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
++.-+-+++.|+.+| ...|.-|+|.+-|++..++.+.|-.|....
T Consensus 9 ~~~~~lv~~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~ 55 (183)
T PHA03103 9 VDIYELVKKEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQREG 55 (183)
T ss_pred HHHHHHHHHHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhcC
Confidence 344455677777765 588999999999999999999999998753
No 293
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=24.16 E-value=1.2e+02 Score=29.75 Aligned_cols=42 Identities=26% Similarity=0.376 Sum_probs=35.1
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCce
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFL 129 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhL 129 (276)
++..+.++++.++.|-++=|...+|++.++|++.|. .++|+|
T Consensus 248 ~~~A~~~L~~~~~~vK~AIvm~~~~~~a~~A~~~L~----~~~g~l 289 (298)
T COG2103 248 AEEAEALLEEAGGNVKLAIVMLLTGLSAEEAKRLLE----RAGGFL 289 (298)
T ss_pred HHHHHHHHHHcCCccHhHHHHHHhCCCHHHHHHHHH----HccChH
Confidence 456778899999999999999999999999987764 456655
No 294
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=24.05 E-value=59 Score=29.18 Aligned_cols=23 Identities=4% Similarity=0.286 Sum_probs=20.5
Q ss_pred CCCchhhHHHHHHHHHcCCceeh
Q 023862 78 KLPADVRNRAMDAVDACNRRVTI 100 (276)
Q Consensus 78 ~l~~~~~~rim~Ave~lg~rvTv 100 (276)
++..+.|++|++++|++||+.-.
T Consensus 29 ~vs~~tr~rV~~~a~~lgY~pn~ 51 (327)
T PRK10339 29 NVKEETKHRILEIAEKLEYKTSS 51 (327)
T ss_pred CcCHHHHHHHHHHHHHhCCCCch
Confidence 48899999999999999997664
No 295
>PRK03887 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=23.82 E-value=1.3e+02 Score=27.35 Aligned_cols=56 Identities=9% Similarity=0.064 Sum_probs=42.5
Q ss_pred chhhHHHHHHH-HHc--CCceehhhhhhhcCCCHHHHHHHHHHH--HhhcCCceEeecCcc
Q 023862 81 ADVRNRAMDAV-DAC--NRRVTIGDVAGKAGLKLNEAQKALQAL--AADTDGFLEVSDEGD 136 (276)
Q Consensus 81 ~~~~~rim~Av-e~l--g~rvTvgDVAa~aGL~l~~Ae~aL~aL--AsD~~GhLeVSesGD 136 (276)
++.+.++.+++ ++- |..+|=||+|..+|.+...+=.+|.+. +-...||==|+.+|.
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 888999999999998655555555543 335689999999994
No 296
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=23.77 E-value=95 Score=25.29 Aligned_cols=39 Identities=23% Similarity=0.277 Sum_probs=32.6
Q ss_pred HHHHHHHHc-------CCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 86 RAMDAVDAC-------NRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 86 rim~Ave~l-------g~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
+|+.|+-++ ..++|...+|..+|++.+.+.++|..|...
T Consensus 36 ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~ 81 (100)
T PF04492_consen 36 KILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRR 81 (100)
T ss_pred HHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 555555544 568999999999999999999999999875
No 297
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=23.55 E-value=1.5e+02 Score=22.10 Aligned_cols=41 Identities=17% Similarity=0.333 Sum_probs=30.1
Q ss_pred chhhHHHHHHHHH-cCCceehhhhhhhcCCCHHHHHHHHHHHH
Q 023862 81 ADVRNRAMDAVDA-CNRRVTIGDVAGKAGLKLNEAQKALQALA 122 (276)
Q Consensus 81 ~~~~~rim~Ave~-lg~rvTvgDVAa~aGL~l~~Ae~aL~aLA 122 (276)
+... ++.+.++. .....|+.|||...|++.....+.+....
T Consensus 20 ~~~~-~~~~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~~~~ 61 (127)
T COG2207 20 RRLA-RALDYIEENLAEPLTLEDLARRLGMSRRTLSRLFKKET 61 (127)
T ss_pred HHHH-HHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3455 77777776 23338999999999999988877766443
No 298
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=23.39 E-value=3.2e+02 Score=24.75 Aligned_cols=56 Identities=21% Similarity=0.249 Sum_probs=36.1
Q ss_pred CCCCchhhHHHHHHHHHcCCceeh-------------hhhhhhc-CCCHHHHHHHHHHHHhhcCCceEee
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTI-------------GDVAGKA-GLKLNEAQKALQALAADTDGFLEVS 132 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTv-------------gDVAa~a-GL~l~~Ae~aL~aLAsD~~GhLeVS 132 (276)
.++..+.|++|+++++++||..-. |=+.... .-=-.+.-+++...+.+.|-++.+.
T Consensus 26 ~~Vs~~tr~kV~~~a~elgY~pn~~a~~l~~~~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~~~~~ 95 (346)
T PRK10401 26 ALVSADTREAVMKAVSELGYRPNANAQALATQVSDTIGVVVMDVSDAFFGALVKAVDLVAQQHQKYVLIG 95 (346)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCHHHHHhhcCCCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEE
Confidence 468899999999999999997532 2111110 0112345567777777777776553
No 299
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=23.14 E-value=2.2e+02 Score=27.93 Aligned_cols=67 Identities=15% Similarity=0.167 Sum_probs=53.5
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcC-CCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcc
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-LKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aG-L~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~n 144 (276)
+-+|.+.+..+++.+++.+-.+|.-|+..+.| ++..+...+|+.|.+...=.|.=..+ .++|.=|..
T Consensus 6 ~~~~~e~~~~~~~~~~~~p~git~q~L~~~~p~~~~~~~~salN~lLs~~~l~llr~~~-~l~yr~~d~ 73 (297)
T KOG3233|consen 6 LALPVEIENILIQIVKQIPEGITQQELQSEMPQISATDRASALNILLSRGLLDLLRQNT-GLVYRAKDP 73 (297)
T ss_pred ccChHHHHHHHHHHHHhccccccHHHHHHHcCCCcHHHHHHHHHHHHhcCcchhhccCC-cceEeccCc
Confidence 45788888999999999999999999999987 99999999999999876554443333 466665443
No 300
>PRK00767 transcriptional regulator BetI; Validated
Probab=23.09 E-value=81 Score=26.00 Aligned_cols=32 Identities=25% Similarity=0.358 Sum_probs=22.8
Q ss_pred chhhHHHHHH----HHHcCCc-eehhhhhhhcCCCHH
Q 023862 81 ADVRNRAMDA----VDACNRR-VTIGDVAGKAGLKLN 112 (276)
Q Consensus 81 ~~~~~rim~A----ve~lg~r-vTvgDVAa~aGL~l~ 112 (276)
..-|++|+++ +.+.|+. +|+.|||.++|++..
T Consensus 8 ~~~r~~Il~aA~~lf~~~G~~~~s~~~Ia~~aGvs~g 44 (197)
T PRK00767 8 PIRRQQLIDATLRAIGEVGLLDATIAQIARRAGVSTG 44 (197)
T ss_pred hhHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCHH
Confidence 3456666654 4566764 789999999998754
No 301
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=23.08 E-value=78 Score=27.71 Aligned_cols=54 Identities=15% Similarity=0.180 Sum_probs=39.7
Q ss_pred hHHHHHHHHHcCCce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-CccEEE
Q 023862 84 RNRAMDAVDACNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLY 139 (276)
Q Consensus 84 ~~rim~Ave~lg~rv-TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe-sGDIlY 139 (276)
+.+|++--=+-|.+. |-.|+|.+-|+|-.-++.||..|.++ |-+++.. .|-.|-
T Consensus 16 ~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~e--GlV~~~~~~G~~V~ 71 (235)
T TIGR02812 16 VESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARD--GWLTIQHGKPTKVN 71 (235)
T ss_pred HHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEeCCCccEec
Confidence 333433333457778 78999999999999999999999976 7777665 464443
No 302
>KOG0793 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=22.70 E-value=2.5e+02 Score=31.22 Aligned_cols=23 Identities=26% Similarity=0.141 Sum_probs=17.9
Q ss_pred HcCCceehhhhhhhcCCCHHHHH
Q 023862 93 ACNRRVTIGDVAGKAGLKLNEAQ 115 (276)
Q Consensus 93 ~lg~rvTvgDVAa~aGL~l~~Ae 115 (276)
+..+++|++|||.+++...++.|
T Consensus 549 ~n~q~~t~edVa~a~~~~k~~ie 571 (1004)
T KOG0793|consen 549 ANVQNVTTEDVAKATVDNKDKLE 571 (1004)
T ss_pred cccccccHHHHHHHHHhhHHHHH
Confidence 45578899999999998866543
No 303
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=22.68 E-value=1.3e+02 Score=28.03 Aligned_cols=59 Identities=22% Similarity=0.299 Sum_probs=41.3
Q ss_pred ccCCCcccccCCCCchhhHHHHH-HHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCc
Q 023862 67 GVGPGRIVESDKLPADVRNRAMD-AVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGF 128 (276)
Q Consensus 67 ~~~~~~~v~~~~l~~~~~~rim~-Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~Gh 128 (276)
.+-.|..=|--.|..+-|.++++ +++..++|++| ++--.+.+..++ -++-..|.+.|++
T Consensus 38 i~v~GstGE~~~Ls~~Er~~l~~~~~~~~~g~~pv--i~gv~~~~t~~a-i~~a~~A~~~Gad 97 (294)
T TIGR02313 38 ISVGGTSGEPGSLTLEERKQAIENAIDQIAGRIPF--APGTGALNHDET-LELTKFAEEAGAD 97 (294)
T ss_pred EEECccCcccccCCHHHHHHHHHHHHHHhCCCCcE--EEECCcchHHHH-HHHHHHHHHcCCC
Confidence 34567788999999999999998 56777777765 344444677766 4455556666653
No 304
>PRK11104 hemG protoporphyrinogen oxidase; Provisional
Probab=22.09 E-value=34 Score=29.54 Aligned_cols=30 Identities=20% Similarity=0.453 Sum_probs=23.5
Q ss_pred ccchhh-hhhh----cccCCCCCCCchhhhhhhcC
Q 023862 247 KMNFIK-SVFS----FVFGEGDPNQGIEEKRWKLV 276 (276)
Q Consensus 247 ~mnFlE-aVFS----FvFGDGDPNa~lEErRwq~i 276 (276)
+|||++ .+.- -.=|+-||+.+.|.+.|++|
T Consensus 129 k~~f~~r~~~~~i~k~~~~~~~~~~~~~~~dw~~v 163 (177)
T PRK11104 129 RYRWFDRFMIKLIMKMTGGETDTSKEVEYTDWEQV 163 (177)
T ss_pred cCCHHHHHHHHHHHHHcCCCCCCCCceeeCCHHHH
Confidence 499999 4443 34478999999999999875
No 305
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=21.92 E-value=86 Score=27.89 Aligned_cols=39 Identities=21% Similarity=0.296 Sum_probs=32.0
Q ss_pred HcCCce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862 93 ACNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 93 ~lg~rv-TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
+-|.++ |-.|+|.+-|+|..-++.||..|.++ |-+++-.
T Consensus 21 ~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~--GlV~~~~ 60 (253)
T PRK10421 21 EAGMKLPAERQLAMQLGVSRNSLREALAKLVSE--GVLLSRR 60 (253)
T ss_pred CCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEeC
Confidence 447788 68899999999999999999999975 5555443
No 306
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.81 E-value=1.5e+02 Score=24.05 Aligned_cols=50 Identities=24% Similarity=0.407 Sum_probs=39.3
Q ss_pred CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCc
Q 023862 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (276)
Q Consensus 80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesG 135 (276)
+.|+|.+|++++++ |. +..++|..=+++.+.+..=+. ..-.|.++....|
T Consensus 4 S~DlR~rVl~~~~~-g~--s~~eaa~~F~VS~~Tv~~W~k---~~~~G~~~~k~r~ 53 (119)
T PF01710_consen 4 SLDLRQRVLAYIEK-GK--SIREAAKRFGVSRNTVYRWLK---RKETGDLEPKPRG 53 (119)
T ss_pred CHHHHHHHHHHHHc-cc--hHHHHHHHhCcHHHHHHHHHH---hcccccccccccc
Confidence 56899999999998 33 899999999999999976555 4446677666655
No 307
>PRK05066 arginine repressor; Provisional
Probab=21.77 E-value=2.3e+02 Score=24.72 Aligned_cols=47 Identities=13% Similarity=0.315 Sum_probs=34.3
Q ss_pred hhHHHHHHHHHcCCc-eehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee-cCccEEEEcCcch
Q 023862 83 VRNRAMDAVDACNRR-VTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS-DEGDVLYVFPNNY 145 (276)
Q Consensus 83 ~~~rim~Ave~lg~r-vTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS-esGDIlYvFP~nf 145 (276)
.++.+++.+++.|.. ||++=|+ +.|..| |-.+|. ++|.-.|..|.+-
T Consensus 25 tQeeL~~~L~~~Gi~~vTQATiS-----------RDikeL-----~lvKv~~~~G~~~Y~l~~~~ 73 (156)
T PRK05066 25 SQGEIVTALQEQGFDNINQSKVS-----------RMLTKF-----GAVRTRNAKMEMVYCLPAEL 73 (156)
T ss_pred CHHHHHHHHHHCCCCeecHHHHH-----------HHHHHc-----CCEEeeCCCCCEEEEeCCCC
Confidence 478888889999988 8876553 444444 446664 7899999998854
No 308
>PF13551 HTH_29: Winged helix-turn helix
Probab=21.76 E-value=1.8e+02 Score=21.86 Aligned_cols=27 Identities=19% Similarity=0.298 Sum_probs=24.0
Q ss_pred ehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 99 TIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 99 TvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
|+.++|...|++...+.+-+.....+.
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 899999999999999999888877554
No 309
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=21.67 E-value=1.2e+02 Score=21.18 Aligned_cols=44 Identities=7% Similarity=0.163 Sum_probs=35.2
Q ss_pred hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCC
Q 023862 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG 127 (276)
Q Consensus 84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~G 127 (276)
.++=++.++-+..+.|..+||..-|++...+..-+..+..+.|.
T Consensus 5 T~~E~~vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 5 TERELEVLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp -HHHHHHHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred CHHHHHHHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 34556677788889999999999999999999999988877654
No 310
>KOG3830 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.63 E-value=97 Score=32.30 Aligned_cols=50 Identities=16% Similarity=0.252 Sum_probs=42.3
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcC
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTD 126 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~ 126 (276)
+++|.+-++-+.+.+.-...-.|+-|+|..+|+++.|+=+-..-|..=+.
T Consensus 283 ~~vP~d~np~l~~li~~~sp~~slqdma~~agisi~evf~La~HLv~W~K 332 (542)
T KOG3830|consen 283 KRVPLDQNPLLSSLIAIVSPNLSLQDMANRAGISISEVFILAKHLVYWRK 332 (542)
T ss_pred cCCCCccchHHHHHHHHhCccccHHHHhhhcCCCHHHHHHHHHHHHHHHh
Confidence 47899999999999999999999999999999999998665555554333
No 311
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=21.57 E-value=1.8e+02 Score=25.73 Aligned_cols=44 Identities=14% Similarity=0.236 Sum_probs=33.5
Q ss_pred hhhHHHHHHHHHc----CCce-ehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 82 DVRNRAMDAVDAC----NRRV-TIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 82 ~~~~rim~Ave~l----g~rv-TvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
.+...|.+.++.. |-++ |-.++|.+-|+|...+++||..|+.+.
T Consensus 9 qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eG 57 (240)
T PRK09764 9 QIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQ 57 (240)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4445555555553 4455 678999999999999999999999873
No 312
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=21.55 E-value=98 Score=26.91 Aligned_cols=31 Identities=16% Similarity=0.340 Sum_probs=26.6
Q ss_pred cCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 94 CNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 94 lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
.+..+|+.|+|.+.|+|..-.++-|..|...
T Consensus 22 ~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~a 52 (164)
T PRK10857 22 EAGPVPLADISERQGISLSYLEQLFSRLRKN 52 (164)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3457999999999999999999999998764
No 313
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=21.49 E-value=1.5e+02 Score=27.66 Aligned_cols=38 Identities=11% Similarity=0.091 Sum_probs=32.3
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAs 123 (276)
.+|++.+.+ +.+++..|+|.+-|++...+.+.|..|.+
T Consensus 7 ~~il~~L~~-~~~~s~~~LA~~lgvsr~tV~~~l~~L~~ 44 (319)
T PRK11886 7 LQLLSLLAD-GDFHSGEQLGEELGISRAAIWKHIQTLEE 44 (319)
T ss_pred HHHHHHHHc-CCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 356666654 67889999999999999999999999984
No 314
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=21.45 E-value=2e+02 Score=25.20 Aligned_cols=43 Identities=12% Similarity=0.139 Sum_probs=31.9
Q ss_pred hhHHHHHHHHHcCCc-----eehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 83 VRNRAMDAVDACNRR-----VTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 83 ~~~rim~Ave~lg~r-----vTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
+...|.+.++...+. -|-.++|.+-|+|...+++||..|+++.
T Consensus 5 i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eG 52 (233)
T TIGR02404 5 IYQDLEQKITHGQYKEGDYLPSEHELMDQYGASRETVRKALNLLTEAG 52 (233)
T ss_pred HHHHHHHHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 345555555543332 2567899999999999999999999874
No 315
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=21.38 E-value=3.1e+02 Score=23.94 Aligned_cols=43 Identities=23% Similarity=0.268 Sum_probs=30.9
Q ss_pred CCCchhhHHH---HHHH----HHcCCceehhhhhhhcCCCHHHHHHHHHH
Q 023862 78 KLPADVRNRA---MDAV----DACNRRVTIGDVAGKAGLKLNEAQKALQA 120 (276)
Q Consensus 78 ~l~~~~~~ri---m~Av----e~lg~rvTvgDVAa~aGL~l~~Ae~aL~a 120 (276)
++|..++..+ .++. .++|...|+.++|...|++.+++...+..
T Consensus 87 ~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~ 136 (231)
T TIGR02885 87 KVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALES 136 (231)
T ss_pred ECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5666554333 2222 34689999999999999999999877654
No 316
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=21.35 E-value=1.2e+02 Score=24.87 Aligned_cols=60 Identities=17% Similarity=0.302 Sum_probs=37.9
Q ss_pred CCCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcC
Q 023862 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFP 142 (276)
Q Consensus 77 ~~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP 142 (276)
+.+-.++|.+|.+.+++.=..+++.++|.-.|++.+ +|.+++.+.| =+++++|.++...|
T Consensus 77 ~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg~~~~----el~~~~~~~g--W~~d~~~~~~~~~~ 136 (143)
T PF10075_consen 77 PGFEDTIRERIAHLISKAYSSISLSDLAEMLGLSEE----ELEKFIKSRG--WTVDGDGVLFPPNP 136 (143)
T ss_dssp TTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTTS-HH----HHHHHHHHHT---EE-----EE---H
T ss_pred HHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhCCCHH----HHHHHHHHcC--CEECCCccEEecCC
Confidence 456778999999999999999999999999999933 5666666664 34456665554444
No 317
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=21.31 E-value=2.1e+02 Score=25.90 Aligned_cols=32 Identities=22% Similarity=0.176 Sum_probs=26.3
Q ss_pred HHHHHcCCceehhhhhhhcCCCHHHHHHHHHH
Q 023862 89 DAVDACNRRVTIGDVAGKAGLKLNEAQKALQA 120 (276)
Q Consensus 89 ~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~a 120 (276)
+..+++|...|..+||...|++.++.++.+.+
T Consensus 121 ~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~ 152 (256)
T PRK07408 121 ELRQELGRQPTDQEIAQALDISLEEWQEIKLA 152 (256)
T ss_pred HHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHH
Confidence 34456789999999999999999999776543
No 318
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=21.17 E-value=1.4e+02 Score=28.66 Aligned_cols=55 Identities=22% Similarity=0.213 Sum_probs=38.5
Q ss_pred CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCc
Q 023862 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (276)
Q Consensus 79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesG 135 (276)
+.|.--++....+.+.-+-+|+-|||...|++.++++..+-.|-. .|-|+==+.|
T Consensus 12 ~~m~~~e~l~~laae~hkiiTirdvae~~ev~~n~lr~lasrLek--kG~LeRi~rG 66 (269)
T COG5340 12 LSMRESELLSHLAAEGHKIITIRDVAETLEVAPNTLRELASRLEK--KGWLERILRG 66 (269)
T ss_pred hhHHHHHHHHHHHHHhCceEEeHHhhhhccCCHHHHHHHHhhhhh--cchhhhhcCc
Confidence 456655666666677778899999999999999888665554432 4555554454
No 319
>PF15615 TerB-C: TerB-C domain
Probab=21.08 E-value=2.7e+02 Score=23.51 Aligned_cols=68 Identities=21% Similarity=0.237 Sum_probs=51.9
Q ss_pred CCCchhhHHHHHHHHHcCC--ceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHH
Q 023862 78 KLPADVRNRAMDAVDACNR--RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAK 148 (276)
Q Consensus 78 ~l~~~~~~rim~Ave~lg~--rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~ 148 (276)
.|.. -..++++++-+.+. |.-+.++|...||-++-+=..++..|-|+-|..=+.. ||.+++- .+|+..
T Consensus 73 gLd~-~~~~lL~~Ll~~~~w~r~e~~~~a~~~glm~~~~ie~INE~afd~~gd~vie~-~d~i~I~-~dy~e~ 142 (144)
T PF15615_consen 73 GLDE-EHSALLRALLSRESWSREELEDIARDHGLMPDGAIESINEKAFDYFGDPVIEG-DDPIEIN-EDYREE 142 (144)
T ss_pred CCCH-HHHHHHHHHHhCCCccHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCeeEeC-CCCceEc-HHHHHh
Confidence 4544 33455666655544 5667799999999999999999999999999987777 9988887 355543
No 320
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=21.01 E-value=80 Score=26.78 Aligned_cols=24 Identities=38% Similarity=0.519 Sum_probs=19.0
Q ss_pred ceehhh---hhhhcCCCHHHHHHHHHH
Q 023862 97 RVTIGD---VAGKAGLKLNEAQKALQA 120 (276)
Q Consensus 97 rvTvgD---VAa~aGL~l~~Ae~aL~a 120 (276)
.++-.| |+.|||.+-++|.+||.+
T Consensus 74 ~i~~edI~lv~~q~gvs~~~A~~AL~~ 100 (115)
T PRK06369 74 EIPEEDIELVAEQTGVSEEEARKALEE 100 (115)
T ss_pred CCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 355444 578999999999999974
No 321
>COG1438 ArgR Arginine repressor [Transcription]
Probab=20.98 E-value=1.5e+02 Score=26.21 Aligned_cols=81 Identities=16% Similarity=0.289 Sum_probs=55.5
Q ss_pred hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee-cCccEEEEcCcchHHHhhhhhHHHhHHHH
Q 023862 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS-DEGDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (276)
Q Consensus 83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS-esGDIlYvFP~nfRs~L~~Ks~r~rl~~~ 161 (276)
.++++.+.+++.|..||++-|+ +.|..| |-.+|- ++|.-+|..|.+-.....++.. ..++..
T Consensus 22 TQ~Elv~~L~~~Gi~vTQaTvS-----------RDlkel-----glvKv~~~~g~~~Y~l~~~~~~~~~~~~~-~~~~~~ 84 (150)
T COG1438 22 TQEELVELLQEEGIEVTQATVS-----------RDLKEL-----GLVKVRNEKGTYVYSLPAELGVPPTSKLK-RYLKDL 84 (150)
T ss_pred CHHHHHHHHHHcCCeEehHHHH-----------HHHHHc-----CCEEecCCCCcEEEEeCCccCCCchhhHH-HHHHHH
Confidence 3688888899999888877654 455554 456776 6999999999988876666554 445666
Q ss_pred HHHHhhhhhh-HHHHHHHHH
Q 023862 162 IDKAKAAAEY-SIRVLFGTA 180 (276)
Q Consensus 162 ~~k~w~v~~Y-liRIsFGi~ 180 (276)
...+.....+ ++|..=|.+
T Consensus 85 v~~vd~~~~~ivlkT~PG~A 104 (150)
T COG1438 85 VLSIDRNGNLIVLKTSPGAA 104 (150)
T ss_pred heeeccCCcEEEEEeCCchH
Confidence 6555555443 456655544
No 322
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=20.93 E-value=1e+02 Score=26.07 Aligned_cols=43 Identities=23% Similarity=0.257 Sum_probs=31.6
Q ss_pred hhhHHHHHHHHHc---CCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862 82 DVRNRAMDAVDAC---NRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (276)
Q Consensus 82 ~~~~rim~Ave~l---g~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD 124 (276)
.+.+.+.+.+.+- -.-||+-.+|++.|++...|+..|+.|...
T Consensus 41 ~vdee~~~ki~KEV~~~r~VTpy~la~r~gI~~SvAr~vLR~Leee 86 (107)
T COG4901 41 TVDEELLDKIRKEVPRERVVTPYVLASRYGINGSVARIVLRHLEEE 86 (107)
T ss_pred hccHHHHHHHHHhcccceeecHHHHHHHhccchHHHHHHHHHHHhC
Confidence 3344444444432 234899999999999999999999999653
No 323
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=20.88 E-value=2.5e+02 Score=24.19 Aligned_cols=46 Identities=15% Similarity=0.081 Sum_probs=34.2
Q ss_pred CchhhHHHHHHHHHcC----C--c----eehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 80 PADVRNRAMDAVDACN----R--R----VTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 80 ~~~~~~rim~Ave~lg----~--r----vTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
-.+++.|+.+.+.++. . . .|..|+|...|++.+.+-+.|..|..+.
T Consensus 146 ~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~~g 201 (236)
T PRK09392 146 LRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALASHG 201 (236)
T ss_pred cCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHhCC
Confidence 3467777777775432 2 1 2347999999999999999999988765
No 324
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=20.82 E-value=1.3e+02 Score=30.46 Aligned_cols=40 Identities=15% Similarity=0.334 Sum_probs=35.6
Q ss_pred hHHHHHHHHHcCCcee-hhhhhhhcCCCHHHHHHHHHHHHh
Q 023862 84 RNRAMDAVDACNRRVT-IGDVAGKAGLKLNEAQKALQALAA 123 (276)
Q Consensus 84 ~~rim~Ave~lg~rvT-vgDVAa~aGL~l~~Ae~aL~aLAs 123 (276)
...+.+.+-+.+...| +-|+|..||++.+++=..|.+|--
T Consensus 317 ~~~v~~~L~k~~~~~~~I~~Is~~TgM~~dDVI~tLe~L~i 357 (395)
T COG5027 317 SEIVAKLLLKMDKEITDINEISKETGMSTDDVIHTLEALNI 357 (395)
T ss_pred HHHHHHHHHhcCcccccHHHHHhhhCCchhhHHHHHHHhcc
Confidence 4678899999999999 999999999999999988887743
No 325
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=20.71 E-value=6.4e+02 Score=23.38 Aligned_cols=53 Identities=19% Similarity=0.315 Sum_probs=39.6
Q ss_pred CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc---CcchHHHhhh
Q 023862 96 RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF---PNNYRAKLAA 151 (276)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF---P~nfRs~L~~ 151 (276)
+..|..|||..+|+|-..+=.-|..|..+ |..++. .|.....= |+....+.+.
T Consensus 29 g~~tA~eis~~sgvP~~kvY~vl~sLe~k--G~v~~~-~g~P~~y~av~p~~~i~~~~~ 84 (247)
T COG1378 29 GEATAKEISEASGVPRPKVYDVLRSLEKK--GLVEVI-EGRPKKYRAVPPEELIERIKE 84 (247)
T ss_pred CCccHHHHHHHcCCCchhHHHHHHHHHHC--CCEEee-CCCCceEEeCCHHHHHHHHHH
Confidence 67899999999999999999999999875 677777 56554433 5554444443
No 326
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=20.71 E-value=2.4e+02 Score=22.23 Aligned_cols=42 Identities=19% Similarity=0.209 Sum_probs=35.9
Q ss_pred hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (276)
Q Consensus 82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~ 125 (276)
++..+|+-.+.+. -.|+.++-.++|++-++.---|..||...
T Consensus 5 t~~~~IL~~ls~~--c~TLeeL~ekTgi~k~~LlV~LsrL~k~G 46 (72)
T PF05584_consen 5 TVTQKILIILSKR--CCTLEELEEKTGISKNTLLVYLSRLAKRG 46 (72)
T ss_pred hHHHHHHHHHHhc--cCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4566777777766 89999999999999999999999999764
No 327
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=20.50 E-value=94 Score=27.54 Aligned_cols=38 Identities=18% Similarity=0.238 Sum_probs=31.5
Q ss_pred cCCce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862 94 CNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (276)
Q Consensus 94 lg~rv-TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe 133 (276)
-|.++ |-.|+|.+-|+|-.-++.||..|.++ |-+++..
T Consensus 30 pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~e--Glv~~~~ 68 (254)
T PRK09464 30 PGEKLPPERELAKQFDVSRPSLREAIQRLEAK--GLLLRRQ 68 (254)
T ss_pred CCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEec
Confidence 36677 78899999999999999999999876 5555544
No 328
>TIGR02224 recomb_XerC tyrosine recombinase XerC. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK.
Probab=20.42 E-value=2.1e+02 Score=24.37 Aligned_cols=69 Identities=25% Similarity=0.320 Sum_probs=41.0
Q ss_pred HHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHhhhhhHHHhHHHHHHHHh---hhhhhHHHHHHHHHHHH
Q 023862 113 EAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAK---AAAEYSIRVLFGTALIA 183 (276)
Q Consensus 113 ~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L~~Ks~r~rl~~~~~k~w---~v~~YliRIsFGi~LIa 183 (276)
++.+.|..+.......+.-...++ |+|+..-...+..+++...++.+.+++. .+-.+-+|-+|++.+..
T Consensus 180 ~~~~~l~~~~~~~~~~~~~~~~~~--~lf~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRht~~t~~~~ 251 (295)
T TIGR02224 180 YAKDALQAYLEARREKLLASEGQD--ALFLNRRGGRLTPRGVQYRLQQLVAKAGLPKHVHPHALRHSFATHLLE 251 (295)
T ss_pred HHHHHHHHHHHHhhhccchhcCCC--eeEEeCCCCCCCHHHHHHHHHHHHHHcCCCCCcChHHHHHHHHHHHHH
Confidence 333455555443333332222222 6676544445556677778888887774 35689999999988753
No 329
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=20.39 E-value=1.1e+02 Score=27.19 Aligned_cols=39 Identities=13% Similarity=0.258 Sum_probs=28.9
Q ss_pred ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862 99 TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (276)
Q Consensus 99 TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv 140 (276)
|-.++|.+-|+|-..+++||..|+++. -|+ ...|-=.||
T Consensus 37 sE~eLa~~~~VSR~TVR~Al~~L~~eG--li~-r~~G~GtfV 75 (241)
T PRK10079 37 AEQQLAARYEVNRHTLRRAIDQLVEKG--WVQ-RRQGVGVLV 75 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCC--CEE-EecCCEEEE
Confidence 445899999999999999999999874 333 333333454
No 330
>PRK15126 thiamin pyrimidine pyrophosphate hydrolase; Provisional
Probab=20.34 E-value=3e+02 Score=24.45 Aligned_cols=53 Identities=19% Similarity=0.234 Sum_probs=37.0
Q ss_pred CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (276)
Q Consensus 79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv 140 (276)
++.. +.++++.+.+.|..+++. ||=+...++.-+..|.-+ + .-|+.+|-++|.
T Consensus 20 i~~~-~~~ai~~l~~~G~~~~ia-----TGR~~~~~~~~~~~l~~~--~-~~I~~NGa~I~~ 72 (272)
T PRK15126 20 LGEK-TLSTLARLRERDITLTFA-----TGRHVLEMQHILGALSLD--A-YLITGNGTRVHS 72 (272)
T ss_pred CCHH-HHHHHHHHHHCCCEEEEE-----CCCCHHHHHHHHHHcCCC--C-cEEecCCcEEEc
Confidence 5555 345566677788888764 898998887777666433 2 247888888886
No 331
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=20.29 E-value=3.2e+02 Score=25.07 Aligned_cols=91 Identities=21% Similarity=0.241 Sum_probs=54.1
Q ss_pred CCCcccccCCCCchhhHHHHH-HHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHH
Q 023862 69 GPGRIVESDKLPADVRNRAMD-AVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA 147 (276)
Q Consensus 69 ~~~~~v~~~~l~~~~~~rim~-Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs 147 (276)
-.|..=|.-.|..+-|.++++ +++..++|+++ ++-..+.+.+++ .++-..|.+.|++ -+.+.|+-|-
T Consensus 41 ~~Gs~GE~~~ls~~Er~~~~~~~~~~~~~~~~v--i~gv~~~~~~~~-i~~a~~a~~~G~d--------~v~~~pP~~~- 108 (292)
T PRK03170 41 VVGTTGESPTLTHEEHEELIRAVVEAVNGRVPV--IAGTGSNSTAEA-IELTKFAEKAGAD--------GALVVTPYYN- 108 (292)
T ss_pred ECCcCCccccCCHHHHHHHHHHHHHHhCCCCcE--EeecCCchHHHH-HHHHHHHHHcCCC--------EEEECCCcCC-
Confidence 357777899999999999987 55555666543 233334677777 5566667777763 3444444432
Q ss_pred HhhhhhHHHhHHHHHHHH-hhhhhh
Q 023862 148 KLAAKSFRLKVEPVIDKA-KAAAEY 171 (276)
Q Consensus 148 ~L~~Ks~r~rl~~~~~k~-w~v~~Y 171 (276)
....+.+....+++.+.+ -.+..|
T Consensus 109 ~~~~~~i~~~~~~ia~~~~~pv~lY 133 (292)
T PRK03170 109 KPTQEGLYQHFKAIAEATDLPIILY 133 (292)
T ss_pred CCCHHHHHHHHHHHHhcCCCCEEEE
Confidence 123344555555555554 234444
No 332
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=20.26 E-value=2.6e+02 Score=19.17 Aligned_cols=33 Identities=24% Similarity=0.257 Sum_probs=26.9
Q ss_pred HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHH
Q 023862 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALA 122 (276)
Q Consensus 85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLA 122 (276)
.++.+.+++.|-..+.-||.... +++++|.++.
T Consensus 13 ~~~~~~L~~~~i~y~~~dv~~~~-----~~~~~l~~~~ 45 (60)
T PF00462_consen 13 KKAKEFLDEKGIPYEEVDVDEDE-----EAREELKELS 45 (60)
T ss_dssp HHHHHHHHHTTBEEEEEEGGGSH-----HHHHHHHHHH
T ss_pred HHHHHHHHHcCCeeeEcccccch-----hHHHHHHHHc
Confidence 45778889999999999998876 7777777776
No 333
>PF13630 SdpI: SdpI/YhfL protein family
Probab=20.19 E-value=3.5e+02 Score=19.58 Aligned_cols=33 Identities=24% Similarity=0.119 Sum_probs=20.7
Q ss_pred HhHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHH
Q 023862 156 LKVEPVIDKAKAAAEYSIRVLFGTALIASIVIV 188 (276)
Q Consensus 156 ~rl~~~~~k~w~v~~YliRIsFGi~LIaSIvLv 188 (276)
++-++.|+++-+....+.-+.-.+++++++++.
T Consensus 17 ~~s~~~W~~a~r~~g~~~~~~Gi~~~~~~~~~~ 49 (76)
T PF13630_consen 17 MKSDENWKKAHRFAGKIFIIGGIVLLIIGIIIL 49 (76)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445677777777666666665555666666543
No 334
>KOG2927 consensus Membrane component of ER protein translocation complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.17 E-value=2.1e+02 Score=28.91 Aligned_cols=16 Identities=44% Similarity=0.659 Sum_probs=12.0
Q ss_pred CCceEeec-----CccEEEEc
Q 023862 126 DGFLEVSD-----EGDVLYVF 141 (276)
Q Consensus 126 ~GhLeVSe-----sGDIlYvF 141 (276)
--+|++-+ +||-.||+
T Consensus 161 ~~~l~i~~dQ~F~d~de~YVW 181 (372)
T KOG2927|consen 161 KFELEIHDDQAFQDGDEHYVW 181 (372)
T ss_pred ccceeeccchhhcccCceEEE
Confidence 55666655 68999999
No 335
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=20.14 E-value=2.3e+02 Score=18.45 Aligned_cols=31 Identities=13% Similarity=0.170 Sum_probs=25.8
Q ss_pred CceehhhhhhhcCCCHHHHHHHHHHHHhhcC
Q 023862 96 RRVTIGDVAGKAGLKLNEAQKALQALAADTD 126 (276)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~ 126 (276)
...|..|||...|++...++..+..+-.+.+
T Consensus 14 ~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 14 EGKTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 4469999999999999999999887765543
No 336
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=20.13 E-value=2.4e+02 Score=24.17 Aligned_cols=56 Identities=13% Similarity=0.038 Sum_probs=40.7
Q ss_pred HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc--CCceEeecCccEEEEc
Q 023862 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DGFLEVSDEGDVLYVF 141 (276)
Q Consensus 86 rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~--~GhLeVSesGDIlYvF 141 (276)
+|++.+.+.....|..+||.+.|+|..++++=+.-|++-. --.+.-...|..-+.|
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~~~~grp~~~~ 223 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEIVHGKVGRPQRIY 223 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEeecCCCCCcCeec
Confidence 6777776554468999999999999999999999888755 2333334455554444
Done!