Query 016517
Match_columns 388
No_of_seqs 75 out of 77
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:33:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016517.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016517hhsearch_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 93.7 0.13 2.8E-06 40.3 4.7 50 80-131 4-54 (68)
2 PRK13239 alkylmercury lyase; P 93.5 0.13 2.9E-06 49.0 5.3 56 81-143 21-76 (206)
3 PF09339 HTH_IclR: IclR helix- 93.1 0.11 2.3E-06 38.2 3.2 39 86-124 7-45 (52)
4 PF06163 DUF977: Bacterial pro 92.7 0.25 5.5E-06 44.3 5.5 52 81-135 11-63 (127)
5 COG3355 Predicted transcriptio 92.4 0.93 2E-05 40.5 8.7 85 85-173 30-119 (126)
6 smart00346 HTH_ICLR helix_turn 92.1 1.2 2.5E-05 35.0 8.1 78 85-165 8-89 (91)
7 PF12324 HTH_15: Helix-turn-he 90.9 0.3 6.4E-06 40.5 3.7 50 83-138 25-74 (77)
8 PRK06266 transcription initiat 90.1 1.7 3.6E-05 40.3 8.4 83 81-166 21-106 (178)
9 PF04703 FaeA: FaeA-like prote 89.7 0.44 9.6E-06 37.6 3.6 53 84-138 2-56 (62)
10 PF13412 HTH_24: Winged helix- 89.5 0.8 1.7E-05 32.7 4.6 41 83-124 4-44 (48)
11 PF12840 HTH_20: Helix-turn-he 88.9 0.97 2.1E-05 34.0 4.9 53 80-135 8-60 (61)
12 TIGR00373 conserved hypothetic 88.9 2.6 5.7E-05 38.2 8.5 80 86-168 18-100 (158)
13 cd00090 HTH_ARSR Arsenical Res 87.6 3.8 8.3E-05 29.5 7.2 60 79-142 4-64 (78)
14 PF08220 HTH_DeoR: DeoR-like h 87.0 1.4 3E-05 33.4 4.7 40 84-124 2-41 (57)
15 smart00418 HTH_ARSR helix_turn 86.4 1.9 4.1E-05 30.4 5.0 49 87-139 2-50 (66)
16 smart00420 HTH_DEOR helix_turn 85.8 2.7 5.8E-05 29.2 5.4 47 84-133 2-48 (53)
17 TIGR02844 spore_III_D sporulat 85.7 0.94 2E-05 37.4 3.4 34 83-118 7-40 (80)
18 PF08784 RPA_C: Replication pr 85.0 1.7 3.8E-05 35.7 4.7 44 81-124 46-92 (102)
19 PF09743 DUF2042: Uncharacteri 84.9 1.8 3.9E-05 42.7 5.5 57 80-138 53-109 (272)
20 KOG3341 RNA polymerase II tran 84.2 2.6 5.6E-05 41.4 6.1 84 68-152 159-245 (249)
21 PF08279 HTH_11: HTH domain; 83.8 3.5 7.7E-05 30.0 5.4 44 85-129 3-46 (55)
22 PF08221 HTH_9: RNA polymerase 80.6 3.6 7.8E-05 31.9 4.7 38 85-123 16-53 (62)
23 PF12802 MarR_2: MarR family; 79.5 4.4 9.5E-05 29.7 4.7 41 84-124 7-48 (62)
24 PF04583 Baculo_p74: Baculovir 79.5 8.1 0.00017 38.3 7.7 54 143-196 62-120 (249)
25 PRK15466 carboxysome structura 79.2 3.6 7.9E-05 38.5 5.0 41 84-124 111-151 (166)
26 PF01978 TrmB: Sugar-specific 79.1 5.5 0.00012 30.4 5.2 51 86-139 12-62 (68)
27 PF01726 LexA_DNA_bind: LexA D 78.1 3.4 7.5E-05 32.5 3.9 45 85-131 13-58 (65)
28 PF04539 Sigma70_r3: Sigma-70 76.8 3.1 6.8E-05 32.2 3.3 51 85-135 8-58 (78)
29 cd07377 WHTH_GntR Winged helix 73.5 5.9 0.00013 28.7 3.9 48 82-131 5-57 (66)
30 smart00345 HTH_GNTR helix_turn 72.4 5.3 0.00012 28.4 3.4 38 94-133 16-54 (60)
31 COG2512 Predicted membrane-ass 71.8 5.2 0.00011 39.3 4.2 46 77-123 191-236 (258)
32 smart00753 PAM PCI/PINT associ 71.5 13 0.00028 29.2 5.7 66 81-146 8-73 (88)
33 smart00088 PINT motif in prote 71.5 13 0.00028 29.2 5.7 66 81-146 8-73 (88)
34 PRK09802 DNA-binding transcrip 71.4 9.6 0.00021 37.0 5.9 53 80-135 15-67 (269)
35 TIGR02702 SufR_cyano iron-sulf 71.2 6.3 0.00014 36.3 4.4 46 83-131 2-47 (203)
36 PRK10434 srlR DNA-bindng trans 70.9 21 0.00046 34.3 8.1 43 81-124 4-46 (256)
37 cd00092 HTH_CRP helix_turn_hel 70.2 21 0.00044 26.3 6.3 39 96-136 24-62 (67)
38 PF13404 HTH_AsnC-type: AsnC-t 69.2 9.5 0.00021 27.6 4.1 38 83-121 4-41 (42)
39 PRK12423 LexA repressor; Provi 68.2 11 0.00024 34.9 5.4 52 82-135 6-62 (202)
40 PRK04424 fatty acid biosynthes 66.7 8.6 0.00019 35.5 4.3 46 82-130 7-52 (185)
41 PF06969 HemN_C: HemN C-termin 65.5 15 0.00032 27.7 4.7 52 83-135 7-64 (66)
42 PF01022 HTH_5: Bacterial regu 65.1 11 0.00025 27.1 3.8 39 83-123 3-41 (47)
43 smart00347 HTH_MARR helix_turn 64.6 63 0.0014 24.9 8.5 48 84-134 12-59 (101)
44 PF00392 GntR: Bacterial regul 64.4 5.9 0.00013 30.0 2.4 37 93-131 19-56 (64)
45 cd07153 Fur_like Ferric uptake 64.4 23 0.00051 29.1 6.1 59 83-141 2-65 (116)
46 smart00344 HTH_ASNC helix_turn 62.8 14 0.00029 30.2 4.4 41 83-124 4-44 (108)
47 COG1349 GlpR Transcriptional r 60.9 41 0.0009 32.4 8.0 63 80-147 3-71 (253)
48 PF04405 ScdA_N: Domain of Unk 60.0 7.8 0.00017 30.0 2.3 38 84-121 12-55 (56)
49 PF02002 TFIIE_alpha: TFIIE al 59.4 13 0.00029 30.8 3.8 78 85-165 16-96 (105)
50 TIGR02431 pcaR_pcaU beta-ketoa 58.8 12 0.00026 35.1 3.9 44 86-131 13-56 (248)
51 PF00356 LacI: Bacterial regul 58.0 7.5 0.00016 28.8 1.9 21 99-119 1-21 (46)
52 COG2345 Predicted transcriptio 57.9 21 0.00045 34.7 5.3 50 75-125 4-53 (218)
53 PF03640 Lipoprotein_15: Secre 57.2 9.5 0.00021 28.6 2.3 22 124-145 6-27 (48)
54 COG1675 TFA1 Transcription ini 57.1 55 0.0012 30.9 7.8 83 85-170 21-106 (176)
55 PHA02943 hypothetical protein; 57.0 55 0.0012 30.8 7.6 78 83-169 9-87 (165)
56 PRK10681 DNA-binding transcrip 56.8 18 0.00039 34.7 4.7 41 82-123 7-47 (252)
57 PF00356 LacI: Bacterial regul 55.8 8.7 0.00019 28.5 1.9 22 77-98 24-45 (46)
58 PRK15090 DNA-binding transcrip 55.2 64 0.0014 30.6 8.1 45 86-133 18-62 (257)
59 PRK10411 DNA-binding transcrip 55.0 82 0.0018 30.1 8.8 47 82-131 4-50 (240)
60 PRK10906 DNA-binding transcrip 54.6 21 0.00045 34.4 4.7 42 82-124 5-46 (252)
61 PRK11569 transcriptional repre 54.3 17 0.00037 35.0 4.1 46 86-133 32-77 (274)
62 PRK10163 DNA-binding transcrip 54.3 17 0.00037 35.0 4.1 47 86-134 29-75 (271)
63 smart00419 HTH_CRP helix_turn_ 53.9 14 0.0003 25.4 2.6 37 95-133 6-42 (48)
64 PF01325 Fe_dep_repress: Iron 52.6 30 0.00065 26.7 4.5 32 93-124 18-49 (60)
65 PRK13509 transcriptional repre 52.3 21 0.00046 34.2 4.4 42 82-124 5-46 (251)
66 PF10025 DUF2267: Uncharacteri 52.2 8.8 0.00019 33.1 1.7 79 100-178 6-99 (125)
67 PF10717 ODV-E18: Occlusion-de 52.0 30 0.00066 29.4 4.7 28 179-206 26-54 (85)
68 PRK09480 slmA division inhibit 51.9 13 0.00028 32.4 2.6 33 80-112 8-45 (194)
69 PRK09834 DNA-binding transcrip 51.1 21 0.00045 34.1 4.1 48 86-135 15-63 (263)
70 PF13463 HTH_27: Winged helix 51.0 25 0.00054 26.0 3.8 45 85-131 6-50 (68)
71 PRK10014 DNA-binding transcrip 50.0 11 0.00024 35.6 2.1 26 95-120 4-29 (342)
72 PF08279 HTH_11: HTH domain; 50.0 7.9 0.00017 28.1 0.9 29 272-300 1-29 (55)
73 PRK00135 scpB segregation and 49.7 44 0.00095 31.5 5.9 56 85-141 6-66 (188)
74 TIGR00498 lexA SOS regulatory 49.7 26 0.00057 31.8 4.4 48 82-131 6-58 (199)
75 PF01047 MarR: MarR family; I 49.3 36 0.00078 24.8 4.3 39 85-124 6-44 (59)
76 PF14257 DUF4349: Domain of un 49.3 51 0.0011 31.6 6.4 79 85-174 149-234 (262)
77 PF15145 DUF4577: Domain of un 49.0 7 0.00015 35.0 0.6 30 172-201 62-91 (128)
78 PTZ00326 phenylalanyl-tRNA syn 48.7 72 0.0016 34.5 8.0 80 81-162 5-84 (494)
79 COG1414 IclR Transcriptional r 48.5 24 0.00052 33.8 4.1 47 86-134 8-54 (246)
80 COG3695 Predicted methylated D 48.2 27 0.00059 30.6 4.0 60 81-140 5-70 (103)
81 PHA02701 ORF020 dsRNA-binding 48.0 25 0.00053 33.5 4.0 87 83-171 5-127 (183)
82 PRK11014 transcriptional repre 47.8 22 0.00048 31.0 3.5 43 82-124 10-52 (141)
83 PLN02853 Probable phenylalanyl 47.1 79 0.0017 34.3 8.0 79 82-162 3-81 (492)
84 PF03965 Penicillinase_R: Peni 46.4 73 0.0016 26.8 6.3 78 83-167 4-85 (115)
85 COG2846 Regulator of cell morp 46.2 15 0.00033 35.7 2.4 32 94-125 31-62 (221)
86 PF03297 Ribosomal_S25: S25 ri 45.2 36 0.00079 29.6 4.3 59 81-140 44-102 (105)
87 PRK10992 iron-sulfur cluster r 45.0 20 0.00044 34.2 3.0 42 85-126 16-63 (220)
88 PF04157 EAP30: EAP30/Vps36 fa 44.7 31 0.00068 32.5 4.2 43 82-124 174-217 (223)
89 PLN03083 E3 UFM1-protein ligas 44.1 35 0.00075 39.0 5.0 62 80-147 58-119 (803)
90 PRK10141 DNA-binding transcrip 43.8 2.2E+02 0.0049 24.9 9.4 60 79-141 13-72 (117)
91 cd06445 ATase The DNA repair p 43.2 39 0.00085 27.0 4.0 55 84-138 2-62 (79)
92 PRK11179 DNA-binding transcrip 43.1 44 0.00095 29.5 4.7 41 83-124 10-50 (153)
93 PHA03093 EEV glycoprotein; Pro 42.8 45 0.00098 31.9 4.9 30 164-194 30-59 (185)
94 PF06224 HTH_42: Winged helix 42.2 57 0.0012 31.6 5.7 57 87-145 172-230 (327)
95 PRK11050 manganese transport r 42.0 2E+02 0.0044 25.6 8.7 56 85-144 40-95 (152)
96 PRK09492 treR trehalose repres 41.9 16 0.00034 34.2 1.8 24 96-119 3-26 (315)
97 PRK09526 lacI lac repressor; R 41.6 17 0.00037 34.4 2.0 24 96-119 4-27 (342)
98 PF01035 DNA_binding_1: 6-O-me 41.4 36 0.00077 27.8 3.5 57 82-138 2-64 (85)
99 PRK05472 redox-sensing transcr 41.1 42 0.00092 31.1 4.4 40 82-121 16-56 (213)
100 PF05331 DUF742: Protein of un 40.8 36 0.00077 30.0 3.7 45 87-135 45-91 (114)
101 TIGR00589 ogt O-6-methylguanin 40.5 60 0.0013 26.6 4.7 56 82-138 2-64 (80)
102 smart00531 TFIIE Transcription 40.3 1.3E+02 0.0028 26.8 7.2 78 87-167 6-89 (147)
103 PF01853 MOZ_SAS: MOZ/SAS fami 39.6 35 0.00077 32.6 3.7 39 84-122 135-175 (188)
104 COG1609 PurR Transcriptional r 39.4 74 0.0016 31.5 6.1 59 78-136 26-98 (333)
105 PRK14987 gluconate operon tran 39.2 18 0.0004 34.2 1.8 25 95-119 3-27 (331)
106 PLN03238 probable histone acet 39.2 34 0.00074 34.7 3.7 56 84-145 210-265 (290)
107 PRK07598 RNA polymerase sigma 39.0 1.2E+02 0.0025 32.1 7.7 87 92-178 273-364 (415)
108 PF00165 HTH_AraC: Bacterial r 38.6 25 0.00054 24.5 1.9 28 93-120 4-31 (42)
109 PF01316 Arg_repressor: Argini 38.4 85 0.0018 25.4 5.2 46 83-144 21-67 (70)
110 PRK03902 manganese transport t 38.1 2.6E+02 0.0056 24.2 8.6 42 86-130 12-53 (142)
111 TIGR02405 trehalos_R_Ecol treh 38.0 21 0.00045 33.7 1.9 23 97-119 1-23 (311)
112 PF09012 FeoC: FeoC like trans 38.0 47 0.001 25.7 3.6 40 89-130 6-45 (69)
113 TIGR02787 codY_Gpos GTP-sensin 37.9 38 0.00083 33.8 3.7 45 87-133 188-232 (251)
114 COG1321 TroR Mn-dependent tran 37.9 54 0.0012 29.8 4.5 50 86-136 14-69 (154)
115 PF10771 DUF2582: Protein of u 37.8 59 0.0013 26.1 4.1 52 86-140 12-63 (65)
116 PRK11552 putative DNA-binding 37.5 30 0.00065 32.1 2.8 33 82-114 13-49 (225)
117 TIGR02944 suf_reg_Xantho FeS a 36.7 55 0.0012 27.9 4.1 44 87-132 14-58 (130)
118 PRK04172 pheS phenylalanyl-tRN 36.7 1.6E+02 0.0035 31.1 8.4 72 83-157 7-78 (489)
119 PF03640 Lipoprotein_15: Secre 36.3 18 0.00039 27.1 1.0 24 312-335 4-27 (48)
120 PHA01815 hypothetical protein 35.9 1.4E+02 0.0031 23.1 5.8 24 158-181 12-35 (55)
121 PF09105 SelB-wing_1: Elongati 35.9 1E+02 0.0023 24.2 5.1 43 87-129 7-49 (61)
122 TIGR02698 CopY_TcrY copper tra 35.8 2E+02 0.0044 25.1 7.6 75 84-165 6-84 (130)
123 PF04967 HTH_10: HTH DNA bindi 35.4 76 0.0017 24.4 4.3 36 85-120 6-46 (53)
124 PRK14996 TetR family transcrip 34.9 27 0.00059 30.8 2.1 30 84-113 10-44 (192)
125 PRK15008 HTH-type transcriptio 34.7 33 0.00071 31.1 2.6 33 81-113 17-54 (212)
126 TIGR03826 YvyF flagellar opero 34.0 64 0.0014 29.3 4.3 53 85-143 33-86 (137)
127 PRK10703 DNA-binding transcrip 33.7 26 0.00056 33.3 1.8 22 98-119 2-23 (341)
128 TIGR01481 ccpA catabolite cont 33.5 26 0.00057 33.0 1.8 22 98-119 2-23 (329)
129 KOG3970 Predicted E3 ubiquitin 33.4 90 0.002 31.3 5.5 45 150-197 220-272 (299)
130 PF07245 Phlebovirus_G2: Phleb 33.2 38 0.00083 36.5 3.2 16 134-149 421-436 (507)
131 TIGR01884 cas_HTH CRISPR locus 33.2 1.5E+02 0.0033 27.3 6.7 47 84-133 145-191 (203)
132 PF11772 EpuA: DNA-directed RN 33.0 23 0.00051 26.8 1.1 25 258-282 22-46 (47)
133 smart00874 B5 tRNA synthetase 32.7 53 0.0012 25.0 3.1 52 97-150 5-56 (71)
134 PRK09334 30S ribosomal protein 32.4 1.1E+02 0.0024 26.0 5.1 59 79-140 24-84 (86)
135 PRK10344 DNA-binding transcrip 32.0 60 0.0013 28.0 3.5 34 84-119 10-43 (92)
136 PRK09975 DNA-binding transcrip 31.8 37 0.00079 30.3 2.4 32 82-113 11-47 (213)
137 PHA02673 ORF109 EEV glycoprote 31.7 92 0.002 29.3 5.0 25 165-190 28-52 (161)
138 cd00131 PAX Paired Box domain 31.6 80 0.0017 27.6 4.4 49 77-130 16-64 (128)
139 PF10668 Phage_terminase: Phag 31.5 64 0.0014 25.6 3.4 34 82-115 7-40 (60)
140 PF02796 HTH_7: Helix-turn-hel 31.5 37 0.0008 24.4 1.9 32 87-118 11-42 (45)
141 PRK13239 alkylmercury lyase; P 31.3 38 0.00082 32.7 2.5 56 269-332 20-75 (206)
142 PRK10727 DNA-binding transcrip 31.0 29 0.00064 33.1 1.7 22 98-119 2-23 (343)
143 KOG4251 Calcium binding protei 30.8 30 0.00065 35.1 1.8 59 265-323 275-336 (362)
144 smart00421 HTH_LUXR helix_turn 30.7 94 0.002 21.3 3.9 46 78-127 3-48 (58)
145 PF01475 FUR: Ferric uptake re 30.3 1.7E+02 0.0036 24.5 6.0 62 82-143 8-74 (120)
146 PRK06474 hypothetical protein; 30.3 90 0.0019 28.8 4.7 56 77-134 6-62 (178)
147 PRK11169 leucine-responsive tr 30.2 76 0.0016 28.4 4.1 42 83-125 15-56 (164)
148 PRK10339 DNA-binding transcrip 30.0 26 0.00056 33.2 1.2 22 98-119 2-23 (327)
149 PRK10401 DNA-binding transcrip 29.8 33 0.00072 32.8 1.9 22 98-119 2-23 (346)
150 COG1802 GntR Transcriptional r 29.3 31 0.00067 31.9 1.5 59 81-141 23-82 (230)
151 PF14947 HTH_45: Winged helix- 29.1 82 0.0018 25.0 3.7 37 88-124 9-46 (77)
152 cd00569 HTH_Hin_like Helix-tur 29.0 98 0.0021 18.2 3.4 34 79-115 6-39 (42)
153 PF10975 DUF2802: Protein of u 29.0 38 0.00081 27.3 1.8 29 88-116 35-63 (70)
154 TIGR03613 RutR pyrimidine util 28.4 44 0.00096 29.5 2.3 32 82-113 8-44 (202)
155 smart00351 PAX Paired Box doma 28.2 1.2E+02 0.0026 26.3 4.9 47 73-122 12-58 (125)
156 PRK05441 murQ N-acetylmuramic 27.6 71 0.0015 31.7 3.8 43 84-130 250-292 (299)
157 TIGR00738 rrf2_super rrf2 fami 27.6 97 0.0021 26.1 4.1 43 87-131 13-57 (132)
158 PF11625 DUF3253: Protein of u 27.6 1.4E+02 0.0031 25.1 5.0 65 81-149 6-77 (83)
159 PF00802 Glycoprotein_G: Pneum 27.1 21 0.00045 35.6 0.0 16 161-176 3-18 (263)
160 PF05055 DUF677: Protein of un 26.9 1.9E+02 0.0041 29.8 6.8 78 108-191 116-205 (336)
161 PRK11303 DNA-binding transcrip 26.6 41 0.0009 31.6 1.9 23 98-120 1-23 (328)
162 PF00325 Crp: Bacterial regula 26.6 72 0.0016 22.4 2.6 28 97-124 2-29 (32)
163 PF02295 z-alpha: Adenosine de 26.1 90 0.0019 24.7 3.4 43 82-125 4-48 (66)
164 PRK10668 DNA-binding transcrip 26.0 53 0.0011 29.4 2.4 32 82-113 11-47 (215)
165 PF11268 DUF3071: Protein of u 25.9 75 0.0016 29.8 3.4 33 82-116 56-88 (170)
166 TIGR02393 RpoD_Cterm RNA polym 25.8 2.6E+02 0.0056 26.2 7.0 27 93-119 99-125 (238)
167 PF13542 HTH_Tnp_ISL3: Helix-t 25.8 90 0.0019 22.3 3.1 37 81-120 14-50 (52)
168 PF07790 DUF1628: Protein of u 25.8 1.2E+02 0.0027 23.9 4.2 21 177-197 7-27 (80)
169 PF05158 RNA_pol_Rpc34: RNA po 25.7 2.1E+02 0.0044 29.2 6.7 71 81-152 8-82 (327)
170 PF07845 DUF1636: Protein of u 25.7 67 0.0015 28.3 2.9 32 255-287 66-97 (116)
171 PF15581 Imm35: Immunity prote 25.5 1.2E+02 0.0026 26.2 4.2 33 107-139 44-77 (93)
172 PRK09526 lacI lac repressor; R 25.2 1.6E+02 0.0034 28.0 5.5 56 77-132 30-99 (342)
173 PF00440 TetR_N: Bacterial reg 25.1 49 0.0011 23.6 1.7 28 87-114 5-33 (47)
174 PF12324 HTH_15: Helix-turn-he 24.9 33 0.00071 28.6 0.7 49 273-328 26-74 (77)
175 TIGR01610 phage_O_Nterm phage 24.8 1.6E+02 0.0034 24.3 4.8 31 94-124 44-74 (95)
176 PF04545 Sigma70_r4: Sigma-70, 24.8 1.8E+02 0.0039 20.7 4.6 41 77-120 3-43 (50)
177 PF13384 HTH_23: Homeodomain-l 24.4 80 0.0017 22.3 2.6 38 81-121 4-41 (50)
178 PRK00441 argR arginine repress 24.4 2.1E+02 0.0046 26.0 5.9 56 84-145 6-67 (149)
179 TIGR00274 N-acetylmuramic acid 24.4 90 0.0019 31.1 3.8 43 84-130 245-287 (291)
180 PRK11041 DNA-binding transcrip 24.2 55 0.0012 30.3 2.2 23 77-99 2-24 (309)
181 PRK07405 RNA polymerase sigma 24.1 2.4E+02 0.0052 28.2 6.8 86 91-178 178-270 (317)
182 PF13693 HTH_35: Winged helix- 24.1 46 0.001 27.6 1.5 33 84-118 4-36 (78)
183 PRK07122 RNA polymerase sigma 23.9 2.4E+02 0.0053 27.2 6.6 44 78-121 117-167 (264)
184 PRK14987 gluconate operon tran 23.9 2.2E+02 0.0049 26.9 6.3 56 77-132 30-99 (331)
185 PRK11202 DNA-binding transcrip 23.5 60 0.0013 29.4 2.3 32 81-112 10-47 (203)
186 TIGR02417 fruct_sucro_rep D-fr 23.2 53 0.0012 31.0 1.9 21 99-119 1-21 (327)
187 PRK11161 fumarate/nitrate redu 23.2 84 0.0018 28.6 3.1 53 80-134 153-219 (235)
188 TIGR02997 Sig70-cyanoRpoD RNA 22.9 3.2E+02 0.007 26.7 7.3 30 92-121 172-201 (298)
189 PF02082 Rrf2: Transcriptional 22.8 1.5E+02 0.0033 23.5 4.2 44 87-132 13-58 (83)
190 PRK05949 RNA polymerase sigma 22.7 2.8E+02 0.006 28.0 6.9 86 91-178 188-280 (327)
191 TIGR00122 birA_repr_reg BirA b 22.6 2.3E+02 0.005 21.5 5.0 36 86-123 4-39 (69)
192 PRK10014 DNA-binding transcrip 22.5 2.4E+02 0.0052 26.7 6.2 23 77-99 31-53 (342)
193 PRK09210 RNA polymerase sigma 22.5 3E+02 0.0066 28.0 7.3 85 92-178 227-319 (367)
194 smart00354 HTH_LACI helix_turn 22.5 61 0.0013 25.1 1.8 21 98-118 1-21 (70)
195 TIGR02337 HpaR homoprotocatech 22.5 1.3E+02 0.0027 25.1 3.8 45 85-132 31-75 (118)
196 PRK08215 sporulation sigma fac 22.4 2.1E+02 0.0045 27.2 5.7 44 78-121 113-163 (258)
197 PF04079 DUF387: Putative tran 22.4 1.6E+02 0.0034 27.1 4.7 43 93-136 9-54 (159)
198 PF12387 Peptidase_C74: Pestiv 22.3 52 0.0011 31.6 1.6 25 316-340 11-35 (200)
199 COG1386 scpB Chromosome segreg 22.3 1.9E+02 0.0042 27.3 5.4 51 85-135 10-65 (184)
200 PLN00104 MYST -like histone ac 22.2 96 0.0021 33.3 3.7 38 84-121 361-398 (450)
201 PRK00215 LexA repressor; Valid 22.2 1.4E+02 0.0029 27.3 4.3 48 84-133 6-58 (205)
202 PF13518 HTH_28: Helix-turn-he 22.2 1.7E+02 0.0038 20.4 4.0 36 84-122 2-37 (52)
203 PF10075 PCI_Csn8: COP9 signal 22.1 1.4E+02 0.003 26.0 4.1 61 77-143 77-137 (143)
204 PF13038 DUF3899: Domain of un 22.1 94 0.002 25.3 2.9 33 163-195 58-90 (92)
205 PRK00441 argR arginine repress 22.1 90 0.002 28.3 3.1 64 270-335 3-67 (149)
206 COG5346 Predicted membrane pro 22.0 4.2E+02 0.0092 24.3 7.2 27 101-128 42-68 (136)
207 PRK11534 DNA-binding transcrip 21.7 70 0.0015 29.3 2.4 41 93-135 26-67 (224)
208 PHA01976 helix-turn-helix prot 21.7 1.2E+02 0.0027 22.5 3.3 32 81-114 1-32 (67)
209 PRK10402 DNA-binding transcrip 21.7 1.9E+02 0.0042 26.5 5.2 51 81-133 149-203 (226)
210 COG1349 GlpR Transcriptional r 21.5 52 0.0011 31.7 1.5 31 269-300 3-33 (253)
211 TIGR03384 betaine_BetI transcr 21.5 54 0.0012 28.3 1.5 33 82-114 8-45 (189)
212 COG4565 CitB Response regulato 21.5 1.8E+02 0.0038 28.8 5.1 69 73-141 145-219 (224)
213 PF01399 PCI: PCI domain; Int 21.5 2.3E+02 0.0049 22.1 5.0 50 76-125 39-88 (105)
214 PRK04217 hypothetical protein; 21.3 1.6E+02 0.0035 25.7 4.3 43 76-122 40-83 (110)
215 COG0640 ArsR Predicted transcr 21.2 2E+02 0.0044 21.3 4.4 58 80-140 23-80 (110)
216 PF06971 Put_DNA-bind_N: Putat 21.1 1.4E+02 0.003 22.8 3.4 33 86-118 16-49 (50)
217 PRK10703 DNA-binding transcrip 21.1 2E+02 0.0043 27.3 5.3 56 77-132 26-95 (341)
218 PF13744 HTH_37: Helix-turn-he 21.0 1.8E+02 0.0038 23.2 4.2 38 95-132 29-78 (80)
219 TIGR03338 phnR_burk phosphonat 20.8 78 0.0017 28.6 2.4 58 82-141 19-77 (212)
220 PRK11303 DNA-binding transcrip 20.8 1.9E+02 0.0042 27.2 5.1 22 78-99 29-50 (328)
221 PF00376 MerR: MerR family reg 20.8 62 0.0013 23.0 1.4 16 99-114 1-16 (38)
222 PF13730 HTH_36: Helix-turn-he 20.7 1E+02 0.0022 22.3 2.6 25 99-123 27-51 (55)
223 PF14451 Ub-Mut7C: Mut7-C ubiq 20.7 92 0.002 25.7 2.6 49 93-144 28-77 (81)
224 TIGR03652 FeS_repair_RIC iron- 20.6 96 0.0021 29.2 3.0 41 85-125 9-55 (216)
225 PF12298 Bot1p: Eukaryotic mit 20.6 1.5E+02 0.0032 27.8 4.3 43 79-124 17-59 (172)
226 PF05781 MRVI1: MRVI1 protein; 20.3 2.9E+02 0.0062 30.6 6.8 44 152-198 456-499 (538)
227 COG1522 Lrp Transcriptional re 20.1 1.9E+02 0.004 24.7 4.5 43 82-125 8-50 (154)
228 cd02106 Band_7 The band 7 doma 20.0 1.7E+02 0.0036 23.0 3.9 70 80-151 50-119 (121)
No 1
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=93.68 E-value=0.13 Score=40.31 Aligned_cols=50 Identities=16% Similarity=0.242 Sum_probs=43.0
Q ss_pred CchhhHHHHHHHHhcCC-ceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 016517 80 PADVRNRAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (388)
Q Consensus 80 ~~~~~~~im~Ave~lg~-rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqV 131 (388)
+.....+|++++.+.|. .+|+.|+|.+.|++...+.+.|..|..+ |-++-
T Consensus 4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~--G~V~~ 54 (68)
T smart00550 4 QDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK--GKVCK 54 (68)
T ss_pred chHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEe
Confidence 34567899999999988 6999999999999999999999999876 44443
No 2
>PRK13239 alkylmercury lyase; Provisional
Probab=93.48 E-value=0.13 Score=49.05 Aligned_cols=56 Identities=18% Similarity=0.284 Sum_probs=47.7
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCh
Q 016517 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (388)
Q Consensus 81 ~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~ 143 (388)
..+.-.|++.+. .|.-||+.|+|+.+|.+.+++++.|.+|. ..+.+++|+|+- ||-
T Consensus 21 ~~~~~~llr~la-~G~pvt~~~lA~~~~~~~~~v~~~L~~l~-----~~~~d~~g~iv~-~pl 76 (206)
T PRK13239 21 ATLLVPLLRLLA-KGRPVSVTTLAAALGWPVEEVEAVLEAMP-----DTEYDEDGRIIG-YGL 76 (206)
T ss_pred hHHHHHHHHHHH-cCCCCCHHHHHHHhCCCHHHHHHHHHhCC-----CeEECCCCCEEe-ccc
Confidence 356778899988 99999999999999999999999999985 347899999975 643
No 3
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=93.11 E-value=0.11 Score=38.24 Aligned_cols=39 Identities=23% Similarity=0.434 Sum_probs=35.1
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 86 ~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
+|++++.+.+...|+.|+|.++|++...+.+-|..|...
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 689999999999999999999999999999999998763
No 4
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=92.65 E-value=0.25 Score=44.25 Aligned_cols=52 Identities=27% Similarity=0.412 Sum_probs=44.1
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC-C
Q 016517 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-G 135 (388)
Q Consensus 81 ~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVses-G 135 (388)
+.+..+|++.|++. +|+|++|+++.+|++.+.+++-|..|.+ .|+|..+.. |
T Consensus 11 ~eLk~rIvElVRe~-GRiTi~ql~~~TGasR~Tvk~~lreLVa--~G~l~~~G~~G 63 (127)
T PF06163_consen 11 EELKARIVELVREH-GRITIKQLVAKTGASRNTVKRYLRELVA--RGDLYRHGRSG 63 (127)
T ss_pred HHHHHHHHHHHHHc-CCccHHHHHHHHCCCHHHHHHHHHHHHH--cCCeEeCCCcc
Confidence 45667888888775 5899999999999999999999999985 588888776 6
No 5
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=92.41 E-value=0.93 Score=40.53 Aligned_cols=85 Identities=21% Similarity=0.246 Sum_probs=68.4
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE---ec-cCCcEEEEc-ChhhHHHHhhhhHHHhHH
Q 016517 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE---VS-DEGDVLYVF-PNNYRAKLAAKSFRLKVE 159 (388)
Q Consensus 85 ~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLq---Vs-esGdIlY~F-P~~fRs~l~~Ks~r~rlq 159 (388)
-.++.++-+.++..|+-|+|..-+++...|+++|+.|... |-++ ++ +.|-..|.+ |.++-. ..+-....++
T Consensus 30 v~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~--GlV~Rek~~~~~Ggy~yiY~~i~~ee--~k~~i~~~l~ 105 (126)
T COG3355 30 VEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA--GLVEREKVNLKGGGYYYLYKPIDPEE--IKKKILKDLD 105 (126)
T ss_pred HHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHc--CCeeeeeeccCCCceeEEEecCCHHH--HHHHHHHHHH
Confidence 3566677668899999999999999999999999999875 3332 34 789999999 888877 3666777888
Q ss_pred HHHHHHhhhhhHHH
Q 016517 160 PVIDKAKAAAEYSI 173 (388)
Q Consensus 160 ~~~~k~w~v~~yli 173 (388)
+|.+++.+.+..+.
T Consensus 106 ~w~~~~~~~i~~~~ 119 (126)
T COG3355 106 EWYDKMKQLIEEFE 119 (126)
T ss_pred HHHHHHHHHHHHHh
Confidence 88888887766543
No 6
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=92.08 E-value=1.2 Score=35.03 Aligned_cols=78 Identities=21% Similarity=0.369 Sum_probs=54.1
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc-ChhhH---HHHhhhhHHHhHHH
Q 016517 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF-PNNYR---AKLAAKSFRLKVEP 160 (388)
Q Consensus 85 ~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~F-P~~fR---s~l~~Ks~r~rlq~ 160 (388)
-+|++.+.+.+..+|+.|+|...|++...+.+-|..|.+ .|-|+-...+. .|.. |+.++ ..+.+.+++....+
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~--~g~l~~~~~~~-~y~l~~~~~~~~~~~~~~~~l~~~~~~ 84 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE--LGYVEQDGQNG-RYRLGPKVLELGQSYLSSLDLREVAKP 84 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeeecCCCC-ceeecHHHHHHHHHHHhcCCHHHHHHH
Confidence 457888887766899999999999999999999999976 48887764333 3554 33222 22333456666666
Q ss_pred HHHHH
Q 016517 161 VIDKA 165 (388)
Q Consensus 161 ~~~k~ 165 (388)
.++.+
T Consensus 85 ~l~~l 89 (91)
T smart00346 85 VLEEL 89 (91)
T ss_pred HHHHH
Confidence 65543
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=90.87 E-value=0.3 Score=40.45 Aligned_cols=50 Identities=22% Similarity=0.353 Sum_probs=36.1
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEE
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL 138 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIl 138 (388)
+--.+++.+.+ |.-||+.++|+.+|.+++++.++|.++. ..|-+++|.||
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 33446666666 9999999999999999999998887775 37888888886
No 8
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=90.12 E-value=1.7 Score=40.33 Aligned_cols=83 Identities=18% Similarity=0.141 Sum_probs=59.2
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcC---CceEeccCCcEEEEcChhhHHHHhhhhHHHh
Q 016517 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTD---GFLEVSDEGDVLYVFPNNYRAKLAAKSFRLK 157 (388)
Q Consensus 81 ~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~---GhLqVsesGdIlY~FP~~fRs~l~~Ks~r~r 157 (388)
.+..-+|++++...| .+|..|+|...|++.+++++.|..|..+-= -.....++|-+.|.+=-+...+ ....+.+
T Consensus 21 ~~~~~~Vl~~L~~~g-~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i--~d~ik~~ 97 (178)
T PRK06266 21 DEEGFEVLKALIKKG-EVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKL--PEIIKKK 97 (178)
T ss_pred CccHhHHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHH--HHHHHHH
Confidence 445578999999888 699999999999999999999999998851 1223346888999775555552 2333444
Q ss_pred HHHHHHHHh
Q 016517 158 VEPVIDKAK 166 (388)
Q Consensus 158 lq~~~~k~w 166 (388)
+....+++.
T Consensus 98 ~~~~~~klk 106 (178)
T PRK06266 98 KMEELKKLK 106 (178)
T ss_pred HHHHHHHHH
Confidence 444444443
No 9
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=89.71 E-value=0.44 Score=37.57 Aligned_cols=53 Identities=21% Similarity=0.362 Sum_probs=41.0
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc--CCcEE
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD--EGDVL 138 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVse--sGdIl 138 (388)
.++|++.+++...-+|..|||...|++..+|+.=|..|..+ |.++-++ .|-..
T Consensus 2 ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~e--G~V~~~~~~rG~~~ 56 (62)
T PF04703_consen 2 KEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKE--GKVERSPVRRGKST 56 (62)
T ss_dssp HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHC--TSEEEES-SSSSS-
T ss_pred cHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEecCCCCcce
Confidence 36799999998899999999999999999999999998775 4666544 35443
No 10
>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=89.46 E-value=0.8 Score=32.74 Aligned_cols=41 Identities=17% Similarity=0.324 Sum_probs=34.0
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
.+.+|++.+.+.+ ++|+.|+|...|++...+.+.|..|..+
T Consensus 4 ~~~~Il~~l~~~~-~~t~~ela~~~~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 4 TQRKILNYLRENP-RITQKELAEKLGISRSTVNRYLKKLEEK 44 (48)
T ss_dssp HHHHHHHHHHHCT-TS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHcC-CCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 4578999999955 5999999999999999999999998764
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=88.91 E-value=0.97 Score=34.05 Aligned_cols=53 Identities=26% Similarity=0.439 Sum_probs=44.5
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC
Q 016517 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (388)
Q Consensus 80 ~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesG 135 (388)
....|-+|++.+ ..+...|++++|...|++.+.+-.-|..|.. .|-+++..+|
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 346788899998 6788899999999999999999999999987 5778877766
No 12
>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=88.86 E-value=2.6 Score=38.21 Aligned_cols=80 Identities=23% Similarity=0.230 Sum_probs=59.7
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCC---ceEeccCCcEEEEcChhhHHHHhhhhHHHhHHHHH
Q 016517 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG---FLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVI 162 (388)
Q Consensus 86 ~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~G---hLqVsesGdIlY~FP~~fRs~l~~Ks~r~rlq~~~ 162 (388)
.|++|+-..| -+|..|+|...|++++++++.|..|..+-=. +.+-.++|-+.|.+=-++..+ -...+.++....
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-EFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKA--LDVLKRKLEETA 94 (158)
T ss_pred HHHHHHhccC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHH--HHHHHHHHHHHH
Confidence 4678877666 6999999999999999999999999988633 556677899999975577774 334455555555
Q ss_pred HHHhhh
Q 016517 163 DKAKAA 168 (388)
Q Consensus 163 ~k~w~v 168 (388)
+++..-
T Consensus 95 ~~lk~~ 100 (158)
T TIGR00373 95 KKLREK 100 (158)
T ss_pred HHHHHH
Confidence 555443
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=87.57 E-value=3.8 Score=29.48 Aligned_cols=60 Identities=25% Similarity=0.424 Sum_probs=46.7
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC-cEEEEcC
Q 016517 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG-DVLYVFP 142 (388)
Q Consensus 79 l~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesG-dIlY~FP 142 (388)
+....+..|+.++.+.+ ++..|+|...|++...+.+.|..|.+. |.+....++ ...|.+.
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 999999999999999999999999764 677765544 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=87.00 E-value=1.4 Score=33.36 Aligned_cols=40 Identities=13% Similarity=0.298 Sum_probs=36.1
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
+..|++.+++. +.+|+.|+|..-|+|...+++.|..|+..
T Consensus 2 ~~~Il~~l~~~-~~~s~~ela~~~~VS~~TiRRDl~~L~~~ 41 (57)
T PF08220_consen 2 QQQILELLKEK-GKVSVKELAEEFGVSEMTIRRDLNKLEKQ 41 (57)
T ss_pred HHHHHHHHHHc-CCEEHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 46789999886 58999999999999999999999999875
No 15
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=86.42 E-value=1.9 Score=30.40 Aligned_cols=49 Identities=20% Similarity=0.391 Sum_probs=39.1
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEE
Q 016517 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY 139 (388)
Q Consensus 87 im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY 139 (388)
|+..+. ...+|+.|++...|++...+.+.|..|.++ |-+.....|...|
T Consensus 2 il~~l~--~~~~~~~~i~~~l~is~~~v~~~l~~L~~~--g~i~~~~~~~~~~ 50 (66)
T smart00418 2 ILKLLA--EGELCVCELAEILGLSQSTVSHHLKKLREA--GLVESRREGKRVY 50 (66)
T ss_pred HHHHhh--cCCccHHHHHHHHCCCHHHHHHHHHHHHHC--CCeeeeecCCEEE
Confidence 567776 667899999999999999999999999975 6777666454433
No 16
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=85.75 E-value=2.7 Score=29.20 Aligned_cols=47 Identities=15% Similarity=0.319 Sum_probs=38.3
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVse 133 (388)
+..+++.+.+.+ .+|+.|+|...|++...+.+.|..|..+ |.++-..
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 5999999999999999999999998876 5565443
No 17
>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=85.75 E-value=0.94 Score=37.41 Aligned_cols=34 Identities=12% Similarity=0.081 Sum_probs=30.9
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHH
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL 118 (388)
-+..|++.+.+ +.+|+.|||..+|+|...+.+.|
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 99999999999999999998866
No 18
>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=85.02 E-value=1.7 Score=35.74 Aligned_cols=44 Identities=20% Similarity=0.459 Sum_probs=37.6
Q ss_pred chhhHHHHHHHHh---cCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 81 ADVRNRAMDAVDA---CNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 81 ~~~~~~im~Ave~---lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
..++.+|+++++. ..-.|.+.+||.+.|++.++++++|..|..+
T Consensus 46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~e 92 (102)
T PF08784_consen 46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNE 92 (102)
T ss_dssp -HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhC
Confidence 4578999999998 5667999999999999999999999999875
No 19
>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=84.86 E-value=1.8 Score=42.74 Aligned_cols=57 Identities=18% Similarity=0.367 Sum_probs=49.6
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEE
Q 016517 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL 138 (388)
Q Consensus 80 ~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIl 138 (388)
|.-++..|.+.+...|+|+++.|++..-|++.+..|+.+..++.+-. +++.. .||++
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 45678899999999999999999999999999999999999999877 56544 68864
No 20
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=84.22 E-value=2.6 Score=41.37 Aligned_cols=84 Identities=17% Similarity=0.313 Sum_probs=70.2
Q ss_pred cCCCcccccCCCCchhh---HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChh
Q 016517 68 VGPGRIVESDKLPADVR---NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (388)
Q Consensus 68 ~~~~~~~~~~~l~~~~~---~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~ 144 (388)
++.||.----++|..++ ..|+++++.+|| ||+.-+-+.-|-.-.-|.++|..|.++.=+-+.-...+|..|=||..
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 45566655566676655 579999999999 99999999999999999999999999988888888899999999999
Q ss_pred hHHHHhhh
Q 016517 145 YRAKLAAK 152 (388)
Q Consensus 145 fRs~l~~K 152 (388)
|-..+...
T Consensus 238 ~~~~~~q~ 245 (249)
T KOG3341|consen 238 FTDQYAQR 245 (249)
T ss_pred hhHHHhhh
Confidence 97755443
No 21
>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=83.77 E-value=3.5 Score=29.97 Aligned_cols=44 Identities=9% Similarity=0.174 Sum_probs=34.7
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCce
Q 016517 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFL 129 (388)
Q Consensus 85 ~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhL 129 (388)
.+|++.+.+.+..+|..++|.+.|+|...+++.|..| .+.+..+
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L-~~~~~~I 46 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKEL-REWGIPI 46 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHH-HHTT-EE
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHH-HHCCCeE
Confidence 5788888666666999999999999999999999999 4444333
No 22
>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=80.59 E-value=3.6 Score=31.94 Aligned_cols=38 Identities=21% Similarity=0.366 Sum_probs=30.6
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 016517 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (388)
Q Consensus 85 ~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAa 123 (388)
.+|.+.+-+.| |.|+.+++..++|+.++++++|..|..
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 56777776666 999999999999999999999999875
No 23
>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=79.51 E-value=4.4 Score=29.68 Aligned_cols=41 Identities=15% Similarity=0.255 Sum_probs=35.0
Q ss_pred hHHHHHHHHhcCCc-eeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 84 RNRAMDAVDACNRR-VTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 84 ~~~im~Ave~lg~r-vTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
+-+++-++...+.. +|+.|+|...|++...+.+.+..|...
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~ 48 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKK 48 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34678889888887 999999999999999999999988764
No 24
>PF04583 Baculo_p74: Baculoviridae p74 conserved region; InterPro: IPR007663 Baculoviruses are distinct from other virus families in that there are two viral phenotypes: budded virus (BV) and occlusion-derived virus (ODV). BVs disseminate viral infection throughout the tissues of the host and ODVs transmit baculovirus between insect hosts. GFP tagging experiments implicate p74 as an ODV envelope protein [, ].; GO: 0019058 viral infectious cycle
Probab=79.48 E-value=8.1 Score=38.30 Aligned_cols=54 Identities=19% Similarity=0.369 Sum_probs=40.6
Q ss_pred hhhHHHHhhhhHHHhH-----HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016517 143 NNYRAKLAAKSFRLKV-----EPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAIL 196 (388)
Q Consensus 143 ~~fRs~l~~Ks~r~rl-----q~~~~k~w~v~~yliRVsFGi~LIaSIvLv~~aI~all 196 (388)
+.+-.++.+..+|..+ +-+.+-+-++++.+.|+...-+=|+.|+|++++|+-++
T Consensus 62 ~~vt~rlLgetyKaav~h~~nr~aIkt~s~vAkal~r~~~~AaSVvgi~Li~~ti~Dlv 120 (249)
T PF04583_consen 62 RRVTVRLLGETYKAAVVHQLNRIAIKTVSTVAKALTRIAIAAASVVGIVLIFLTIADLV 120 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455666666555543 33455577889999999999999999999999998766
No 25
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=79.24 E-value=3.6 Score=38.52 Aligned_cols=41 Identities=24% Similarity=0.404 Sum_probs=36.8
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
.+.++.-+-...+..|.|+||+.-|.++++|+.+|..|-+|
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 151 (166)
T PRK15466 111 ADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSA 151 (166)
T ss_pred HHHHHHHHHHHHccccHHHHHHHhCCcHHHHHHHHHHHHhc
Confidence 46667777888899999999999999999999999999886
No 26
>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=79.09 E-value=5.5 Score=30.36 Aligned_cols=51 Identities=22% Similarity=0.324 Sum_probs=40.7
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEE
Q 016517 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY 139 (388)
Q Consensus 86 ~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY 139 (388)
+|..++- ..+.+|+.|+|..+|++...+.+.|..|... |-++..+...-+|
T Consensus 12 ~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~--GlV~~~~~~~~~Y 62 (68)
T PF01978_consen 12 KVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK--GLVEREEGRPKVY 62 (68)
T ss_dssp HHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT--TSEEEEEECCEEE
T ss_pred HHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEcCceEEE
Confidence 4555555 5678999999999999999999999999875 7777777554444
No 27
>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=78.06 E-value=3.4 Score=32.49 Aligned_cols=45 Identities=22% Similarity=0.362 Sum_probs=34.0
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCC-HHHHHHHHHHHHhhcCCceEe
Q 016517 85 NRAMDAVDACNRRVTIGDVAGKAGLK-LNEAQKALQALAADTDGFLEV 131 (388)
Q Consensus 85 ~~im~Ave~lg~rvTvgDVAa~aGL~-l~~Ae~aL~aLAaD~~GhLqV 131 (388)
.-|.+.+++.|+-.|+.|+|...|++ .+.|++-|.+|... |.|+-
T Consensus 13 ~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~k--G~I~r 58 (65)
T PF01726_consen 13 EFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERK--GYIRR 58 (65)
T ss_dssp HHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHT--TSEEE
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC--cCccC
Confidence 34455667799999999999999997 99999999999853 55553
No 28
>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=76.78 E-value=3.1 Score=32.21 Aligned_cols=51 Identities=24% Similarity=0.232 Sum_probs=33.7
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC
Q 016517 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (388)
Q Consensus 85 ~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesG 135 (388)
..+.+--.++|...|..+||...|+++++.++.|.....-..=++.+..++
T Consensus 8 ~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~ 58 (78)
T PF04539_consen 8 RARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDED 58 (78)
T ss_dssp HHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSS
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCC
Confidence 344445567899999999999999999999887776544334444454443
No 29
>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=73.49 E-value=5.9 Score=28.74 Aligned_cols=48 Identities=21% Similarity=0.372 Sum_probs=35.3
Q ss_pred hhhHHHHHHHHhcC----Cc-eeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 016517 82 DVRNRAMDAVDACN----RR-VTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (388)
Q Consensus 82 ~~~~~im~Ave~lg----~r-vTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqV 131 (388)
++.+.|.+.+.... .. .|+.|+|...|++...+.++|..|+. .|-|+.
T Consensus 5 ~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~--~G~i~~ 57 (66)
T cd07377 5 QIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEA--EGLVER 57 (66)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEe
Confidence 45566666655432 22 45999999999999999999999987 345553
No 30
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=72.36 E-value=5.3 Score=28.40 Aligned_cols=38 Identities=18% Similarity=0.359 Sum_probs=31.8
Q ss_pred cCCce-eehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 016517 94 CNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (388)
Q Consensus 94 lg~rv-TvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVse 133 (388)
-|.++ |+.|+|..-|++...+.++|..|..+ |-|+...
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 36677 89999999999999999999999975 5666443
No 31
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=71.75 E-value=5.2 Score=39.33 Aligned_cols=46 Identities=20% Similarity=0.293 Sum_probs=39.5
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 016517 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (388)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAa 123 (388)
..|+.+. ..||+++..+|+|+|+.|+..+.|+|...+=+.|+.|..
T Consensus 191 ~~L~~~e-~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk 236 (258)
T COG2512 191 YDLNEDE-KEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEK 236 (258)
T ss_pred CCCCHHH-HHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHh
Confidence 3444444 468999999999999999999999999999999999865
No 32
>smart00753 PAM PCI/PINT associated module.
Probab=71.53 E-value=13 Score=29.24 Aligned_cols=66 Identities=14% Similarity=0.164 Sum_probs=48.5
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhhH
Q 016517 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYR 146 (388)
Q Consensus 81 ~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~fR 146 (388)
...+.+.+..+-+--..+|..++|...+++.+++|..|..+..+..=+-.++....+++.-....|
T Consensus 8 ~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00753 8 RKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred HHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 445666666666677789999999999999999999999998886323345565566666555444
No 33
>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=71.53 E-value=13 Score=29.24 Aligned_cols=66 Identities=14% Similarity=0.164 Sum_probs=48.5
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhhH
Q 016517 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYR 146 (388)
Q Consensus 81 ~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~fR 146 (388)
...+.+.+..+-+--..+|..++|...+++.+++|..|..+..+..=+-.++....+++.-....|
T Consensus 8 ~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00088 8 RKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred HHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 445666666666677789999999999999999999999998886323345565566666555444
No 34
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=71.35 E-value=9.6 Score=37.02 Aligned_cols=53 Identities=15% Similarity=0.250 Sum_probs=43.7
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC
Q 016517 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (388)
Q Consensus 80 ~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesG 135 (388)
..+-+.+|++.+++.|. +|+.|+|..-|+|...+++.|..|.+. |.++-..-|
T Consensus 15 ~~eR~~~Il~~L~~~~~-vtv~eLa~~l~VS~~TIRRDL~~Le~~--G~l~r~~GG 67 (269)
T PRK09802 15 TSERREQIIQRLRQQGS-VQVNDLSALYGVSTVTIRNDLAFLEKQ--GIAVRAYGG 67 (269)
T ss_pred HHHHHHHHHHHHHHcCC-EeHHHHHHHHCCCHHHHHHHHHHHHhC--CCeEEEeCC
Confidence 34667888999999876 999999999999999999999999664 666555444
No 35
>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=71.15 E-value=6.3 Score=36.31 Aligned_cols=46 Identities=13% Similarity=0.263 Sum_probs=40.3
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqV 131 (388)
.|.+|+..+.+.|. +|+.|+|...|++...+.+.|..|.++ |-++-
T Consensus 2 tr~~IL~~L~~~~~-~t~~eLA~~lgis~~tV~~~L~~Le~~--GlV~r 47 (203)
T TIGR02702 2 TKEDILSYLLKQGQ-ATAAALAEALAISPQAVRRHLKDLETE--GLIEY 47 (203)
T ss_pred HHHHHHHHHHHcCC-CCHHHHHHHHCcCHHHHHHHHHHHHHC--CCeEE
Confidence 47899999998876 999999999999999999999999875 55553
No 36
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=70.87 E-value=21 Score=34.28 Aligned_cols=43 Identities=9% Similarity=0.102 Sum_probs=38.2
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 81 ~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
..-+.+|++.+++.| ++|+.|+|..-|+|...+++.|..|+..
T Consensus 4 ~eR~~~Il~~L~~~~-~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 4 RQRQAAILEYLQKQG-KTSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred HHHHHHHHHHHHHcC-CEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 356788899988865 6999999999999999999999999876
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=70.24 E-value=21 Score=26.26 Aligned_cols=39 Identities=21% Similarity=0.385 Sum_probs=33.5
Q ss_pred CceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCc
Q 016517 96 RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD 136 (388)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGd 136 (388)
..+|..|+|...|++...+.+.|..|..+ |-|+....|.
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~--g~i~~~~~~~ 62 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEE--GLISRRGRGK 62 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEecCCCe
Confidence 56899999999999999999999999886 7777766453
No 38
>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=69.20 E-value=9.5 Score=27.61 Aligned_cols=38 Identities=13% Similarity=0.297 Sum_probs=29.9
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHH
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (388)
+..+|++++.+- .|.+..++|.+.|++-.++.+-+..|
T Consensus 4 ~D~~Il~~Lq~d-~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 4 LDRKILRLLQED-GRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHH--TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHc-CCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 456788888766 88999999999999999999888765
No 39
>PRK12423 LexA repressor; Provisional
Probab=68.23 E-value=11 Score=34.85 Aligned_cols=52 Identities=23% Similarity=0.357 Sum_probs=41.0
Q ss_pred hhhHHHHH----HHHhcCCceeehhhhhhcCC-CHHHHHHHHHHHHhhcCCceEeccCC
Q 016517 82 DVRNRAMD----AVDACNRRVTIGDVAGKAGL-KLNEAQKALQALAADTDGFLEVSDEG 135 (388)
Q Consensus 82 ~~~~~im~----Ave~lg~rvTvgDVAa~aGL-~l~~Ae~aL~aLAaD~~GhLqVsesG 135 (388)
..|.+|++ .+++.|+.-|+.++|.+.|+ +.+.+.+.|.+|+.. |.|+++..+
T Consensus 6 ~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~--G~l~~~~~~ 62 (202)
T PRK12423 6 PKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEA--GLIEVVPNQ 62 (202)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC--CCEEecCCC
Confidence 34555555 45557888999999999996 899999999999874 788887764
No 40
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=66.66 E-value=8.6 Score=35.47 Aligned_cols=46 Identities=13% Similarity=0.163 Sum_probs=39.5
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 016517 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (388)
Q Consensus 82 ~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLq 130 (388)
.-+.+|++.+.+.| .+|+.|+|..-|+|...+++.|..|+.+ |.|+
T Consensus 7 ~R~~~Il~~l~~~~-~~~~~~La~~~~vS~~TiRRDl~~L~~~--g~~~ 52 (185)
T PRK04424 7 ERQKALQELIEENP-FITDEELAEKFGVSIQTIRLDRMELGIP--ELRE 52 (185)
T ss_pred HHHHHHHHHHHHCC-CEEHHHHHHHHCcCHHHHHHHHHHHhcc--hHHH
Confidence 56677888888854 6999999999999999999999999876 6655
No 41
>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=65.50 E-value=15 Score=27.67 Aligned_cols=52 Identities=25% Similarity=0.490 Sum_probs=38.2
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHH-HHHHHHHHhh-----cCCceEeccCC
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEA-QKALQALAAD-----TDGFLEVSDEG 135 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~A-e~aL~aLAaD-----~~GhLqVsesG 135 (388)
.++.+|..+.. ..++.+.++..+.|.++.+. .+.|..+.++ .+++|.+|+.|
T Consensus 7 ~~e~i~~~LR~-~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~~~~~l~lT~~G 64 (66)
T PF06969_consen 7 LREYIMLGLRC-NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLLEIDGGRLRLTEKG 64 (66)
T ss_dssp HHHHHHHHHHH-HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE-SSEEEE-TTT
T ss_pred HHHHHHHHHHh-HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEEeCCEEEECccc
Confidence 45677777765 67899999999999987666 7778888886 37788888877
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=65.07 E-value=11 Score=27.07 Aligned_cols=39 Identities=21% Similarity=0.348 Sum_probs=34.0
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAa 123 (388)
.|-+|+.++.+ +..|+.|+|...|++...+.+-|..|-.
T Consensus 3 ~R~~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 3 TRLRILKLLSE--GPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHh--CCCchhhHHHhccccchHHHHHHHHHHH
Confidence 57789999999 6799999999999999999999988864
No 43
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=64.60 E-value=63 Score=24.88 Aligned_cols=48 Identities=10% Similarity=0.232 Sum_probs=41.1
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVses 134 (388)
.-.|+..+...+ .+|+.|+|...+++...+.+.|..|... |-++..++
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 456788888876 6999999999999999999999999986 77776654
No 44
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=64.45 E-value=5.9 Score=30.00 Aligned_cols=37 Identities=24% Similarity=0.425 Sum_probs=28.8
Q ss_pred hcCCce-eehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 016517 93 ACNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (388)
Q Consensus 93 ~lg~rv-TvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqV 131 (388)
+.|.++ |..++|.+-|+|...++++|..|+++ |.|+.
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~--g~i~~ 56 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRLEAE--GLIER 56 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHT--TSEEE
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHC--CcEEE
Confidence 356788 99999999999999999999999976 44443
No 45
>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=64.40 E-value=23 Score=29.14 Aligned_cols=59 Identities=12% Similarity=0.129 Sum_probs=45.6
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~a-----GL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~F 141 (388)
.|..|++++.+.+.-+|+.||..+. ++++..+=+.|..|+..-==+=-..++|...|..
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 5788999999999889999999877 6899999999999987632222233356677764
No 46
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=62.77 E-value=14 Score=30.17 Aligned_cols=41 Identities=15% Similarity=0.414 Sum_probs=36.5
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
...+|+.++.+. .++|..++|.+.|++...+.+.|..|.++
T Consensus 4 ~D~~il~~L~~~-~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 4 IDRKILEELQKD-ARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred HHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 456888998886 48999999999999999999999999886
No 47
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=60.94 E-value=41 Score=32.41 Aligned_cols=63 Identities=14% Similarity=0.278 Sum_probs=48.6
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh------cCCceEeccCCcEEEEcChhhHH
Q 016517 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD------TDGFLEVSDEGDVLYVFPNNYRA 147 (388)
Q Consensus 80 ~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD------~~GhLqVsesGdIlY~FP~~fRs 147 (388)
+..-+.+|++-|++ .+.++|.|+|..-|.|..++++.|..|+.. +||-.-.+...+. |..-|.
T Consensus 3 ~~eR~~~Il~~l~~-~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~hGGa~~~~~~~~~----~~~~r~ 71 (253)
T COG1349 3 KEERHQKILELLKE-KGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVHGGAVLPDSESEY----PFSERK 71 (253)
T ss_pred hHHHHHHHHHHHHH-cCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEeCCEecCCCcccc----cHHHHH
Confidence 34567788999988 568999999999999999999999999986 4555555555444 555554
No 48
>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=60.04 E-value=7.8 Score=29.95 Aligned_cols=38 Identities=21% Similarity=0.287 Sum_probs=31.9
Q ss_pred hHHHHHHHHhc------CCceeehhhhhhcCCCHHHHHHHHHHH
Q 016517 84 RNRAMDAVDAC------NRRVTIGDVAGKAGLKLNEAQKALQAL 121 (388)
Q Consensus 84 ~~~im~Ave~l------g~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (388)
.|+..+.+++. |+..|+.+++.+.||++++.-++|.+|
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 45667777774 678999999999999999999998875
No 49
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=59.38 E-value=13 Score=30.77 Aligned_cols=78 Identities=24% Similarity=0.235 Sum_probs=39.5
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEec---cCCcEEEEcChhhHHHHhhhhHHHhHHHH
Q 016517 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS---DEGDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (388)
Q Consensus 85 ~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVs---esGdIlY~FP~~fRs~l~~Ks~r~rlq~~ 161 (388)
-.||+++-..| .+|=.|+|..+|++.+++++-|..|..+-=-..+.. +.|-..|.+==|++.+ -...+.++...
T Consensus 16 ~~Il~~L~~~~-~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~i~~~~~--~~~ik~r~~~~ 92 (105)
T PF02002_consen 16 VRILDALLRKG-ELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWYIDYDQI--IDVIKYRIYKM 92 (105)
T ss_dssp HHHHHHHHHH---B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE-THHHH-------------
T ss_pred HHHHHHHHHcC-CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEEEcHHHH--HHHHHHHHHHH
Confidence 46899998776 489999999999999999999999998865444432 2354456664455542 22234444444
Q ss_pred HHHH
Q 016517 162 IDKA 165 (388)
Q Consensus 162 ~~k~ 165 (388)
.+++
T Consensus 93 ~~~l 96 (105)
T PF02002_consen 93 REKL 96 (105)
T ss_dssp ----
T ss_pred HHHH
Confidence 4443
No 50
>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=58.79 E-value=12 Score=35.14 Aligned_cols=44 Identities=30% Similarity=0.416 Sum_probs=36.7
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 016517 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (388)
Q Consensus 86 ~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqV 131 (388)
+|++++.+.+..+|+.|+|.++||+...+-+=|..|.+ -|.|+-
T Consensus 13 ~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~--~G~l~~ 56 (248)
T TIGR02431 13 AVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE--LGYVTS 56 (248)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEe
Confidence 46777777778899999999999999999999988865 467764
No 51
>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=58.02 E-value=7.5 Score=28.84 Aligned_cols=21 Identities=33% Similarity=0.528 Sum_probs=18.7
Q ss_pred eehhhhhhcCCCHHHHHHHHH
Q 016517 99 TIGDVAGKAGLKLNEAQKALQ 119 (388)
Q Consensus 99 TvgDVAa~aGL~l~~Ae~aL~ 119 (388)
|+.|||..+|+|...+-+.|.
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 788999999999999987774
No 52
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=57.93 E-value=21 Score=34.69 Aligned_cols=50 Identities=16% Similarity=0.281 Sum_probs=43.3
Q ss_pred ccCCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 016517 75 ESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (388)
Q Consensus 75 ~~~~l~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~ 125 (388)
+..+.++..+.+|+..+.+.| .+|++|+|.+-|++...|++-|..|.++.
T Consensus 4 ~~~~~~~~tr~~il~lL~~~g-~~sa~elA~~Lgis~~avR~HL~~Le~~G 53 (218)
T COG2345 4 MLADPSGSTRERILELLKKSG-PVSADELAEELGISPMAVRRHLDDLEAEG 53 (218)
T ss_pred cccCCCccHHHHHHHHHhccC-CccHHHHHHHhCCCHHHHHHHHHHHHhCc
Confidence 456778888999988887766 58999999999999999999999998764
No 53
>PF03640 Lipoprotein_15: Secreted repeat of unknown function; InterPro: IPR005297 This repeat is found in tandem in a set of lipoproteins. The alignment contains a Y-X4-D motif.
Probab=57.21 E-value=9.5 Score=28.57 Aligned_cols=22 Identities=32% Similarity=0.543 Sum_probs=19.3
Q ss_pred hcCCceEeccCCcEEEEcChhh
Q 016517 124 DTDGFLEVSDEGDVLYVFPNNY 145 (388)
Q Consensus 124 D~~GhLqVsesGdIlY~FP~~f 145 (388)
...|..||+.+|-.||.|.+|-
T Consensus 6 ~~dG~~~~~~~G~~LY~f~~D~ 27 (48)
T PF03640_consen 6 RADGTIQVDYNGMPLYYFDKDS 27 (48)
T ss_pred eCCCCEEECCCCCEEEEECCCC
Confidence 3469999999999999998875
No 54
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=57.12 E-value=55 Score=30.91 Aligned_cols=83 Identities=25% Similarity=0.246 Sum_probs=60.7
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc--CCceEe-ccCCcEEEEcChhhHHHHhhhhHHHhHHHH
Q 016517 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DGFLEV-SDEGDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (388)
Q Consensus 85 ~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~--~GhLqV-sesGdIlY~FP~~fRs~l~~Ks~r~rlq~~ 161 (388)
-.|++++...| -+|=-++|...|+.++++++.|.+|-.+- ..+=+. .++|...|..=-+++.++ -..+.+....
T Consensus 21 ~~v~~~l~~kg-e~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~~~~~~~y~w~~~~~~v~--~~l~~~~~~~ 97 (176)
T COG1675 21 VLVVDALLEKG-ELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDEESGWEEYTWYINYEKVL--EVLKGKKRKI 97 (176)
T ss_pred hHHHHHHHhcC-CcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCCCcEEEEEEechHHHH--HHHHHHHHHH
Confidence 46789999988 99999999999999999999999887664 222333 458889998877777743 3344555555
Q ss_pred HHHHhhhhh
Q 016517 162 IDKAKAAAE 170 (388)
Q Consensus 162 ~~k~w~v~~ 170 (388)
++++...+.
T Consensus 98 le~Lk~~le 106 (176)
T COG1675 98 LEKLKRKLE 106 (176)
T ss_pred HHHHHHHHH
Confidence 566555544
No 55
>PHA02943 hypothetical protein; Provisional
Probab=57.02 E-value=55 Score=30.84 Aligned_cols=78 Identities=21% Similarity=0.201 Sum_probs=54.2
Q ss_pred hhHHHHHHHHh-cCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhhHHHHhhhhHHHhHHHH
Q 016517 83 VRNRAMDAVDA-CNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (388)
Q Consensus 83 ~~~~im~Ave~-lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~fRs~l~~Ks~r~rlq~~ 161 (388)
+.+|+.+.+|= ..+-.|..+||...|+|-.+|+-.|.-|..+ |.++--+-|-..|.+=.+ .+ +.+. +..+
T Consensus 9 v~~R~~eILE~Lk~G~~TtseIAkaLGlS~~qa~~~LyvLErE--G~VkrV~~G~~tyw~l~~-da-----y~~~-v~~~ 79 (165)
T PHA02943 9 VHTRMIKTLRLLADGCKTTSRIANKLGVSHSMARNALYQLAKE--GMVLKVEIGRAAIWCLDE-DA-----YTNL-VFEI 79 (165)
T ss_pred HHHHHHHHHHHHhcCCccHHHHHHHHCCCHHHHHHHHHHHHHc--CceEEEeecceEEEEECh-HH-----HHHH-HHHH
Confidence 44555555555 5555779999999999999999999988765 666666799888887444 11 1111 5566
Q ss_pred HHHHhhhh
Q 016517 162 IDKAKAAA 169 (388)
Q Consensus 162 ~~k~w~v~ 169 (388)
.+-+|+.+
T Consensus 80 ~Relwrlv 87 (165)
T PHA02943 80 KRELWRLV 87 (165)
T ss_pred HHHHHHHH
Confidence 66666643
No 56
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=56.85 E-value=18 Score=34.68 Aligned_cols=41 Identities=17% Similarity=0.283 Sum_probs=36.3
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 016517 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (388)
Q Consensus 82 ~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAa 123 (388)
.-+.+|++-+++.| ++|+.|+|..-|+|..++++.|..|..
T Consensus 7 eR~~~I~~~l~~~~-~v~v~eLa~~~~VS~~TIRRDL~~Le~ 47 (252)
T PRK10681 7 ERIGQLLQALKRSD-KLHLKDAAALLGVSEMTIRRDLNAHSA 47 (252)
T ss_pred HHHHHHHHHHHHcC-CCcHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 46678899888865 599999999999999999999999884
No 57
>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=55.83 E-value=8.7 Score=28.50 Aligned_cols=22 Identities=18% Similarity=0.412 Sum_probs=19.4
Q ss_pred CCCCchhhHHHHHHHHhcCCce
Q 016517 77 DKLPADVRNRAMDAVDACNRRV 98 (388)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~rv 98 (388)
.++..+.+++|+++++++||+.
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 58
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=55.17 E-value=64 Score=30.56 Aligned_cols=45 Identities=13% Similarity=0.269 Sum_probs=35.3
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 016517 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (388)
Q Consensus 86 ~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVse 133 (388)
+|++++.+. ..+|+.|+|.++||+...+-+=|..|.. -|.|+-++
T Consensus 18 ~IL~~l~~~-~~l~l~eia~~lgl~kstv~Rll~tL~~--~G~l~~~~ 62 (257)
T PRK15090 18 GILQALGEE-REIGITELSQRVMMSKSTVYRFLQTMKT--LGYVAQEG 62 (257)
T ss_pred HHHHHhhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 456666654 4699999999999999999998888876 46776543
No 59
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=55.04 E-value=82 Score=30.14 Aligned_cols=47 Identities=13% Similarity=0.157 Sum_probs=40.0
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 016517 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (388)
Q Consensus 82 ~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqV 131 (388)
+-+.+|++.+++.+ .+|+.|+|..-|+|...+++.|..|.. .|.|+-
T Consensus 4 ~R~~~Il~~l~~~~-~~~~~eLa~~l~VS~~TiRRdL~~L~~--~~~l~r 50 (240)
T PRK10411 4 ARQQAIVDLLLNHT-SLTTEALAEQLNVSKETIRRDLNELQT--QGKILR 50 (240)
T ss_pred HHHHHHHHHHHHcC-CCcHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEE
Confidence 34577899998765 899999999999999999999999988 366664
No 60
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=54.58 E-value=21 Score=34.43 Aligned_cols=42 Identities=12% Similarity=0.202 Sum_probs=37.3
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 82 ~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
.-+.+|++.+++.| .+|+.|+|..-|+|..++++.|..|..+
T Consensus 5 ~R~~~Il~~l~~~~-~~~~~ela~~l~vS~~TiRRdL~~Le~~ 46 (252)
T PRK10906 5 QRHDAIIELVKQQG-YVSTEELVEHFSVSPQTIRRDLNDLAEQ 46 (252)
T ss_pred HHHHHHHHHHHHcC-CEeHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 45778899997655 7999999999999999999999999985
No 61
>PRK11569 transcriptional repressor IclR; Provisional
Probab=54.31 E-value=17 Score=35.00 Aligned_cols=46 Identities=20% Similarity=0.413 Sum_probs=38.7
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 016517 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (388)
Q Consensus 86 ~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVse 133 (388)
+|++++.+.+..+|+.|+|..+||+...+-+=|..|.. -|.|+-++
T Consensus 32 ~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~--~G~l~~~~ 77 (274)
T PRK11569 32 KLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ--QGFVRQVG 77 (274)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 56888888788899999999999999999999888875 47776543
No 62
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=54.28 E-value=17 Score=34.99 Aligned_cols=47 Identities=15% Similarity=0.273 Sum_probs=39.5
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC
Q 016517 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (388)
Q Consensus 86 ~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVses 134 (388)
+|++++.+.+...|+.|+|..+|++...+-+=|..|.+. |.|+-+++
T Consensus 29 ~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~--G~l~~~~~ 75 (271)
T PRK10163 29 AILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAA--DFVYQDSQ 75 (271)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEcCC
Confidence 568888888888999999999999999999988888764 77766543
No 63
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=53.89 E-value=14 Score=25.41 Aligned_cols=37 Identities=19% Similarity=0.328 Sum_probs=30.6
Q ss_pred CCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 016517 95 NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (388)
Q Consensus 95 g~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVse 133 (388)
...+|+.|+|...|++...+.+.|..|.+ .|.|+...
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~--~g~l~~~~ 42 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEK--EGLISREG 42 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEEeC
Confidence 34678899999999999999999999987 46666543
No 64
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=52.56 E-value=30 Score=26.66 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=28.5
Q ss_pred hcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 93 ~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
+.+..|+..|+|...|++...|-..|..|+.+
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 37899999999999999999999999999864
No 65
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=52.29 E-value=21 Score=34.18 Aligned_cols=42 Identities=14% Similarity=0.219 Sum_probs=37.3
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 82 ~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
.-+.+|++.+++ .+.+|+.|+|...|+|...+++.|..|.+.
T Consensus 5 ~R~~~Il~~l~~-~~~~~~~ela~~l~vS~~TirRdL~~Le~~ 46 (251)
T PRK13509 5 QRHQILLELLAQ-LGFVTVEKVIERLGISPATARRDINKLDES 46 (251)
T ss_pred HHHHHHHHHHHH-cCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 456788999986 678999999999999999999999999764
No 66
>PF10025 DUF2267: Uncharacterized conserved protein (DUF2267); InterPro: IPR018727 This entry contains proteins that have no known function. ; PDB: 2YSK_A.
Probab=52.24 E-value=8.8 Score=33.07 Aligned_cols=79 Identities=23% Similarity=0.314 Sum_probs=58.3
Q ss_pred ehhhhhhcCC-CHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhhHHHHhh------hhHHHhHHHHHHHHhh-----
Q 016517 100 IGDVAGKAGL-KLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAA------KSFRLKVEPVIDKAKA----- 167 (388)
Q Consensus 100 vgDVAa~aGL-~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~fRs~l~~------Ks~r~rlq~~~~k~w~----- 167 (388)
+.+|+.++|+ +.++|++++++...--+-+|.+.+.-++.=.-|...|..|.. ..-+..+++|+..+..
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 4689999999 999999999999999999999999999999999999999954 2233668888888777
Q ss_pred ---hhhHHHHHHHH
Q 016517 168 ---AAEYSIRVLFG 178 (388)
Q Consensus 168 ---v~~yliRVsFG 178 (388)
-..+++|.-|.
T Consensus 86 ~~~~a~~~~~aV~~ 99 (125)
T PF10025_consen 86 DEDDAERLARAVFA 99 (125)
T ss_dssp TEE-HHHHHHHHHH
T ss_pred CcccHHHHHHHHHH
Confidence 44555555544
No 67
>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=52.04 E-value=30 Score=29.40 Aligned_cols=28 Identities=25% Similarity=0.418 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHHHH-hcCCCCCCCC
Q 016517 179 TALIASIVIVFTAIIAIL-SSKSDDDDRG 206 (388)
Q Consensus 179 i~LIaSIvLv~~aI~all-ss~s~~d~~~ 206 (388)
+++.+=|+||.++.++++ .++|++++.+
T Consensus 26 ~lMtILivLVIIiLlImlfqsSS~~~~s~ 54 (85)
T PF10717_consen 26 TLMTILIVLVIIILLIMLFQSSSNGNSSS 54 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCCCCCC
Confidence 333333445544444444 4445444444
No 68
>PRK09480 slmA division inhibitor protein; Provisional
Probab=51.87 E-value=13 Score=32.42 Aligned_cols=33 Identities=18% Similarity=0.396 Sum_probs=25.1
Q ss_pred CchhhHHHHHHH----H-hcCCceeehhhhhhcCCCHH
Q 016517 80 PADVRNRAMDAV----D-ACNRRVTIGDVAGKAGLKLN 112 (388)
Q Consensus 80 ~~~~~~~im~Av----e-~lg~rvTvgDVAa~aGL~l~ 112 (388)
+.+.|++|++|. . +.|..+|+.|||.++|++..
T Consensus 8 ~~~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~g 45 (194)
T PRK09480 8 KGERREQILQALAQMLESPPGERITTAKLAARVGVSEA 45 (194)
T ss_pred chhHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHh
Confidence 345677888773 2 33689999999999998864
No 69
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=51.05 E-value=21 Score=34.12 Aligned_cols=48 Identities=21% Similarity=0.401 Sum_probs=38.4
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc-CC
Q 016517 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EG 135 (388)
Q Consensus 86 ~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVse-sG 135 (388)
+|++++...+..+|+.|+|.+.|++...+-+-|..|.. -|.|+-++ +|
T Consensus 15 ~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~--~g~v~~~~~~~ 63 (263)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE--EGYVRRSASDD 63 (263)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEecCCC
Confidence 45677766677799999999999999999999999875 47776543 44
No 70
>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=51.02 E-value=25 Score=26.04 Aligned_cols=45 Identities=18% Similarity=0.352 Sum_probs=34.2
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 016517 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (388)
Q Consensus 85 ~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqV 131 (388)
-.||..+...+...|+.|+|...|++...+-+.|..|... |-|+-
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~--glv~~ 50 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEK--GLVEK 50 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHT--TSEEE
T ss_pred HHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEe
Confidence 4578888888899999999999999999999999999876 66643
No 71
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=50.03 E-value=11 Score=35.63 Aligned_cols=26 Identities=31% Similarity=0.456 Sum_probs=23.0
Q ss_pred CCceeehhhhhhcCCCHHHHHHHHHH
Q 016517 95 NRRVTIGDVAGKAGLKLNEAQKALQA 120 (388)
Q Consensus 95 g~rvTvgDVAa~aGL~l~~Ae~aL~a 120 (388)
..++|+.|||..+|+|..++-++|..
T Consensus 4 ~~~~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 4 AKKITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHHHCC
Confidence 45799999999999999999888864
No 72
>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=49.96 E-value=7.9 Score=28.13 Aligned_cols=29 Identities=34% Similarity=0.367 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhcCCeEeeeeccCccCCCC
Q 016517 272 RWKLIGEYIASNGGVVTAEELAPYLDIDR 300 (388)
Q Consensus 272 RWk~Ig~~Ir~N~GvV~AEQLAPyLD~~~ 300 (388)
|++.|..++.++++-|+++|||-.|+...
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~vS~ 29 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELGVSR 29 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCTS-H
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhCCCH
Confidence 67788888877777799999999999763
No 73
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=49.68 E-value=44 Score=31.50 Aligned_cols=56 Identities=20% Similarity=0.261 Sum_probs=42.8
Q ss_pred HHHHHHHHhc-CC-ceeehhhhhhcCCCHHHHHHHHHHHHhhcC---CceEeccCCcEEEEc
Q 016517 85 NRAMDAVDAC-NR-RVTIGDVAGKAGLKLNEAQKALQALAADTD---GFLEVSDEGDVLYVF 141 (388)
Q Consensus 85 ~~im~Ave~l-g~-rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~---GhLqVsesGdIlY~F 141 (388)
.++++|+-=. |- .+|+.++|...|++..+++..|..|..++. .-+++.+.|+- |.|
T Consensus 6 ~~~iEA~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~-y~l 66 (188)
T PRK00135 6 KSIIEALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDV-YKL 66 (188)
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCE-EEE
Confidence 3455555444 55 499999999999999999999999999984 34787776654 655
No 74
>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=49.65 E-value=26 Score=31.80 Aligned_cols=48 Identities=25% Similarity=0.439 Sum_probs=39.1
Q ss_pred hhhHHHHHHHHh----cCCceeehhhhhhcCCC-HHHHHHHHHHHHhhcCCceEe
Q 016517 82 DVRNRAMDAVDA----CNRRVTIGDVAGKAGLK-LNEAQKALQALAADTDGFLEV 131 (388)
Q Consensus 82 ~~~~~im~Ave~----lg~rvTvgDVAa~aGL~-l~~Ae~aL~aLAaD~~GhLqV 131 (388)
+.+.+|++.+.+ .++..|+.|+|...|++ .+.+.+.|..|..+ |.|+-
T Consensus 6 ~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~--g~i~~ 58 (199)
T TIGR00498 6 ARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERK--GYIER 58 (199)
T ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHC--CCEec
Confidence 456677777763 57779999999999998 99999999999886 66653
No 75
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=49.33 E-value=36 Score=24.77 Aligned_cols=39 Identities=15% Similarity=0.251 Sum_probs=33.6
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 85 ~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
=.+|..+.+.|. +|+.|+|...|++...+-+.+..|..+
T Consensus 6 ~~iL~~l~~~~~-~~~~~la~~~~~~~~~~t~~i~~L~~~ 44 (59)
T PF01047_consen 6 FRILRILYENGG-ITQSELAEKLGISRSTVTRIIKRLEKK 44 (59)
T ss_dssp HHHHHHHHHHSS-EEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHcCC-CCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence 357888988888 999999999999999999999988764
No 76
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=49.27 E-value=51 Score=31.56 Aligned_cols=79 Identities=11% Similarity=0.158 Sum_probs=38.5
Q ss_pred HHHHHHHHhcCCceeehhhhhhcC------CCHHHHHHHHHHHHhhc-CCceEeccCCcEEEEcChhhHHHHhhhhHHHh
Q 016517 85 NRAMDAVDACNRRVTIGDVAGKAG------LKLNEAQKALQALAADT-DGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLK 157 (388)
Q Consensus 85 ~~im~Ave~lg~rvTvgDVAa~aG------L~l~~Ae~aL~aLAaD~-~GhLqVsesGdIlY~FP~~fRs~l~~Ks~r~r 157 (388)
+|+.+-+++-+ |+.|+.+--. -.+++.+..+..|...+ =.++.++=... ..... .+.++-.+
T Consensus 149 ~rl~~ll~ka~---~~~d~l~ie~~L~~v~~eIe~~~~~~~~l~~~v~~sti~i~l~~~------~~~~~--~~~~~~~~ 217 (262)
T PF14257_consen 149 ERLLELLEKAK---TVEDLLEIERELSRVRSEIEQLEGQLKYLDDRVDYSTITISLYEP------ESIKP--ESPSFGSR 217 (262)
T ss_pred HHHHHHHHhcC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhceEEEEEEEEec------CCCCC--CCCCcchH
Confidence 33444444333 7777765222 14555666666666665 34443321111 00001 23455555
Q ss_pred HHHHHHHHhhhhhHHHH
Q 016517 158 VEPVIDKAKAAAEYSIR 174 (388)
Q Consensus 158 lq~~~~k~w~v~~yliR 174 (388)
+...+...|..+..++.
T Consensus 218 ~~~al~~~~~~~~~~~~ 234 (262)
T PF14257_consen 218 FRDALKNGWNALVSFLS 234 (262)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 55666666766666653
No 77
>PF15145 DUF4577: Domain of unknown function (DUF4577)
Probab=49.02 E-value=7 Score=34.97 Aligned_cols=30 Identities=23% Similarity=0.211 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 016517 172 SIRVLFGTALIASIVIVFTAIIAILSSKSD 201 (388)
Q Consensus 172 liRVsFGi~LIaSIvLv~~aI~allss~s~ 201 (388)
+|=|.+.++||+|++||...|+.|+.-.+.
T Consensus 62 lffvglii~LivSLaLVsFvIFLiiQTgnk 91 (128)
T PF15145_consen 62 LFFVGLIIVLIVSLALVSFVIFLIIQTGNK 91 (128)
T ss_pred ehHHHHHHHHHHHHHHHHHHHHheeeccch
Confidence 344678899999999999999988854333
No 78
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=48.65 E-value=72 Score=34.51 Aligned_cols=80 Identities=10% Similarity=0.105 Sum_probs=67.5
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhhHHHHhhhhHHHhHHH
Q 016517 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEP 160 (388)
Q Consensus 81 ~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~fRs~l~~Ks~r~rlq~ 160 (388)
+....+|++++++.+..++..++|...|++.+++.+++..|.+. |-++|.+.=...|+--..=+..+++-+.=.++-.
T Consensus 5 ~~~e~~iL~~l~~~~~~~~~~~la~~~~~~~~~v~~~~~~L~~k--g~v~~~~~~~~~~~LT~eG~~~~~~G~PE~rl~~ 82 (494)
T PTZ00326 5 ELEENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESA--NYITTEMKKSNTWTLTEEGEDYLKNGSPEYRLWQ 82 (494)
T ss_pred hHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhC--CCEEEEEEEEEEEEECHHHHHHHHcCCHHHHHHH
Confidence 45678899999986666899999999999999999999999997 7999999999999999988888888665555444
Q ss_pred HH
Q 016517 161 VI 162 (388)
Q Consensus 161 ~~ 162 (388)
++
T Consensus 83 ~l 84 (494)
T PTZ00326 83 KL 84 (494)
T ss_pred Hh
Confidence 43
No 79
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=48.49 E-value=24 Score=33.81 Aligned_cols=47 Identities=21% Similarity=0.381 Sum_probs=38.5
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC
Q 016517 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (388)
Q Consensus 86 ~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVses 134 (388)
+|++++.+.+..+|+.|+|.++|++.+.+-+=|..|.. -|-++-+++
T Consensus 8 ~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~--~G~v~~d~~ 54 (246)
T COG1414 8 AILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVE--LGYVEQDPE 54 (246)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CCCEEEcCC
Confidence 57888888666689999999999999999998888875 466665553
No 80
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=48.25 E-value=27 Score=30.62 Aligned_cols=60 Identities=25% Similarity=0.358 Sum_probs=46.6
Q ss_pred chhhHHHHHHHHhc--CCceeehhhhhhcCCC--HHHHHHHHHHHHhhc--CCceEeccCCcEEEE
Q 016517 81 ADVRNRAMDAVDAC--NRRVTIGDVAGKAGLK--LNEAQKALQALAADT--DGFLEVSDEGDVLYV 140 (388)
Q Consensus 81 ~~~~~~im~Ave~l--g~rvTvgDVAa~aGL~--l~~Ae~aL~aLAaD~--~GhLqVsesGdIlY~ 140 (388)
.+.++++.+.|.+. |+-.|-||||.-+|++ ..++-+.|..|-.++ .-|=-|+..|.|--.
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 35678888888875 6778999999999999 778888888665544 677778888877543
No 81
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=48.00 E-value=25 Score=33.55 Aligned_cols=87 Identities=14% Similarity=0.217 Sum_probs=61.7
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEec----------------------cCC-----
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS----------------------DEG----- 135 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVs----------------------esG----- 135 (388)
--.+|++.+.+.|-++|.-++|.+-||+..++.+.|-.|-... .+-++ ++.
T Consensus 5 ~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~--~v~~~~~~pP~W~~~~~~~~~~~~~~~~~~~~~~~ 82 (183)
T PHA02701 5 CASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLESD--AVSCEDGCPPLWSVECEPDEKKEEGSGSDTEPMET 82 (183)
T ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhcC--cEecCCCCCCccccccCCCCCcccccccccCcccc
Confidence 3478999999999779999999999999999999999997542 12111 011
Q ss_pred ----cEEE-----EcChhhHHHHhhhhHHHhHHHHHHHHhhhhhH
Q 016517 136 ----DVLY-----VFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEY 171 (388)
Q Consensus 136 ----dIlY-----~FP~~fRs~l~~Ks~r~rlq~~~~k~w~v~~y 171 (388)
+=+| +-|..+=-.+..++++-+||+|.++-++...|
T Consensus 83 ~~~~~~~f~~~~d~~~~~~i~~~k~~DpKS~LQE~~Q~~~~~l~Y 127 (183)
T PHA02701 83 EAGCDTLFGGDIDVLTVSAVMRLKTLNPVSAVNEFCMRTHRPLEF 127 (183)
T ss_pred cccccccccCccccccHHHhhcCCCCCccHHHHHHHHhcCCCCeE
Confidence 1122 34555555566677888888888887655444
No 82
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=47.80 E-value=22 Score=30.97 Aligned_cols=43 Identities=21% Similarity=0.190 Sum_probs=36.1
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 82 ~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
+++..|+.+...-|..+++.++|.+.|+|..-++++|..|..+
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 4566666666666778999999999999999999999999875
No 83
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=47.14 E-value=79 Score=34.29 Aligned_cols=79 Identities=15% Similarity=0.189 Sum_probs=67.4
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhhHHHHhhhhHHHhHHHH
Q 016517 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (388)
Q Consensus 82 ~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~fRs~l~~Ks~r~rlq~~ 161 (388)
+...+|+++++..+..++..++|...|++.+++.+++..|.+. |-+++.+.=+..|+--..=+..+++-+.-.++-.+
T Consensus 3 ~~e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k--g~v~~~~~~~~~~~LT~eG~~~l~~G~PE~rl~~~ 80 (492)
T PLN02853 3 MAEEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGF--RYVDAQDIKRETWVLTEEGKKYAAEGSPEVQLFAA 80 (492)
T ss_pred hHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhC--CCEEEEEEEEEEEEECHHHHHHHHcCCHHHHHHHH
Confidence 4568899999987766899999999999999999999999997 69999999999999998888888876665555444
Q ss_pred H
Q 016517 162 I 162 (388)
Q Consensus 162 ~ 162 (388)
+
T Consensus 81 l 81 (492)
T PLN02853 81 V 81 (492)
T ss_pred H
Confidence 4
No 84
>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=46.40 E-value=73 Score=26.78 Aligned_cols=78 Identities=15% Similarity=0.197 Sum_probs=54.2
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcC----CCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhhHHHHhhhhHHHhH
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAG----LKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKV 158 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aG----L~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~fRs~l~~Ks~r~rl 158 (388)
.-..||+.+=++|. +|+.||..... ++.+.+..-|..|.. -|.|++...|---+-.|---|. .+.+..+
T Consensus 4 ~E~~IM~~lW~~~~-~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~--Kg~l~~~~~gr~~~Y~p~is~~----e~~~~~~ 76 (115)
T PF03965_consen 4 LELEIMEILWESGE-ATVREIHEALPEERSWAYSTVQTLLNRLVE--KGFLTREKIGRAYVYSPLISRE----EYLAQEL 76 (115)
T ss_dssp HHHHHHHHHHHHSS-EEHHHHHHHHCTTSS--HHHHHHHHHHHHH--TTSEEEEEETTCEEEEESSSHH----HHHHHHH
T ss_pred HHHHHHHHHHhCCC-CCHHHHHHHHHhccccchhHHHHHHHHHHh--CCceeEeecCCceEEEeCCcHH----HHHHHHH
Confidence 34679999999999 99999997644 668888777777776 6999999988754444544444 2344455
Q ss_pred HHHHHHHhh
Q 016517 159 EPVIDKAKA 167 (388)
Q Consensus 159 q~~~~k~w~ 167 (388)
+.+++++..
T Consensus 77 ~~~l~~~~~ 85 (115)
T PF03965_consen 77 RQFLDRLFD 85 (115)
T ss_dssp HHHHHHHST
T ss_pred HHHHHHHhC
Confidence 566665543
No 85
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=46.22 E-value=15 Score=35.72 Aligned_cols=32 Identities=31% Similarity=0.606 Sum_probs=30.0
Q ss_pred cCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 016517 94 CNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (388)
Q Consensus 94 lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~ 125 (388)
+|+.+|+.+.|.+.|+.+++.++.|.+|....
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 79999999999999999999999999998754
No 86
>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=45.22 E-value=36 Score=29.61 Aligned_cols=59 Identities=14% Similarity=0.124 Sum_probs=41.0
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEE
Q 016517 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (388)
Q Consensus 81 ~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~ 140 (388)
.+.=+++.+-|-+. .-+|+.-||.+-+++...|+++|..|++.--=.+=+-..+-.||.
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 559999999999999999999999999864333334445666664
No 87
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=44.99 E-value=20 Score=34.22 Aligned_cols=42 Identities=21% Similarity=0.334 Sum_probs=34.7
Q ss_pred HHHHHHHHh------cCCceeehhhhhhcCCCHHHHHHHHHHHHhhcC
Q 016517 85 NRAMDAVDA------CNRRVTIGDVAGKAGLKLNEAQKALQALAADTD 126 (388)
Q Consensus 85 ~~im~Ave~------lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~ 126 (388)
++..+.+++ +|+..|+++++.+.|++.++.-++|.++++...
T Consensus 16 p~~~~vf~~~~idfCcgG~~~l~ea~~~~~i~~~~~~~~l~~~~~~~~ 63 (220)
T PRK10992 16 PRATALFREYDLDFCCGGKQTLARAAARKNLDIDVIEARLAALQEQPI 63 (220)
T ss_pred ccHHHHHHHcCCcccCCCCchHHHHHHHcCCCHHHHHHHHHHHHhccc
Confidence 444555665 578999999999999999999999999986663
No 88
>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=44.69 E-value=31 Score=32.49 Aligned_cols=43 Identities=23% Similarity=0.386 Sum_probs=36.1
Q ss_pred hhhHHHHHHH-HhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 82 DVRNRAMDAV-DACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 82 ~~~~~im~Av-e~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
....+|++.+ +..++.+|+.++|...|.+..-|+..|..+..+
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 6668889999 888999999999999999999999999885543
No 89
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=44.08 E-value=35 Score=38.97 Aligned_cols=62 Identities=21% Similarity=0.358 Sum_probs=48.2
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhhHH
Q 016517 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA 147 (388)
Q Consensus 80 ~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~fRs 147 (388)
|..++..|++-+. .|+||.+-|++..-|+.+.-+|+.+..++.+- .++.. ..|||+ ..+|=.
T Consensus 58 ~~qL~~EI~~El~-~gGRvnlvdLa~~LnVD~~hiEr~~~~iv~~d-~~~~l-~~GeLi---t~~Yld 119 (803)
T PLN03083 58 QDQLRNEIEAEIK-KLGRVSLVDLADTIGVDLYHVERQAQQVVSDD-PGLML-VQGEII---SQSYWD 119 (803)
T ss_pred HHHHHHHHHHHHH-hCCCeeHHHHhhhcCCCHHHHHHHHHHHhcCC-CceEE-ecCEec---chHHHH
Confidence 4457788888884 58999999999999999999999999998885 44443 467764 445533
No 90
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=43.83 E-value=2.2e+02 Score=24.90 Aligned_cols=60 Identities=13% Similarity=0.139 Sum_probs=46.4
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 016517 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (388)
Q Consensus 79 l~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~F 141 (388)
|....|-+|+..+... +.+||+|+|...|++...+-+-|..|.. -|-+.....|.-+|-.
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 4556788899888653 4699999999999999999999988864 3667777777655443
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=43.17 E-value=39 Score=27.04 Aligned_cols=55 Identities=20% Similarity=0.175 Sum_probs=42.7
Q ss_pred hHHHHHHHHh--cCCceeehhhhhhcCC--CHHHHHHHHHHHHh--hcCCceEeccCCcEE
Q 016517 84 RNRAMDAVDA--CNRRVTIGDVAGKAGL--KLNEAQKALQALAA--DTDGFLEVSDEGDVL 138 (388)
Q Consensus 84 ~~~im~Ave~--lg~rvTvgDVAa~aGL--~l~~Ae~aL~aLAa--D~~GhLqVsesGdIl 138 (388)
+.++.+++.+ .|.-+|-+|||..+|. ....+-.+|.+.-. +..+|==|+.+|.+.
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 4567777776 5677899999999999 46677777776654 678998899888876
No 92
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=43.06 E-value=44 Score=29.51 Aligned_cols=41 Identities=10% Similarity=0.193 Sum_probs=35.4
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
...+|++++.+- +|.+..++|.+.|+|...+.+-+..|-++
T Consensus 10 ~D~~Il~~Lq~d-~R~s~~eiA~~lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 10 LDRGILEALMEN-ARTPYAELAKQFGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 556777777665 89999999999999999999999999765
No 93
>PHA03093 EEV glycoprotein; Provisional
Probab=42.79 E-value=45 Score=31.91 Aligned_cols=30 Identities=13% Similarity=0.241 Sum_probs=22.0
Q ss_pred HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 016517 164 KAKAAAEYSIRVLFGTALIASIVIVFTAIIA 194 (388)
Q Consensus 164 k~w~v~~yliRVsFGi~LIaSIvLv~~aI~a 194 (388)
|..+.+..+|||++.|.+| |+++|.++++.
T Consensus 30 kk~r~i~i~~RisiiiSIl-sL~~i~~~LAl 59 (185)
T PHA03093 30 KKVKCIGICIRISIIISIL-SLIAITATLAL 59 (185)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 6778889999999998887 55555544443
No 94
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=42.23 E-value=57 Score=31.65 Aligned_cols=57 Identities=30% Similarity=0.411 Sum_probs=43.2
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC-CcE-EEEcChhh
Q 016517 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-GDV-LYVFPNNY 145 (388)
Q Consensus 87 im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVses-GdI-lY~FP~~f 145 (388)
+-+.+...| -+|+.|+|.-+||+..+++++|..|.+ .|.=.+|+-+ |.- .|.-|.+-
T Consensus 172 v~Ryl~~~G-Pat~~d~a~w~gl~~~~~r~~l~~l~~-~~~L~~v~~~~G~~~~~~~~~~~ 230 (327)
T PF06224_consen 172 VRRYLRAYG-PATLADFAWWSGLPKTQARRALAQLVE-EGELVEVEVEGGKEPLYDLPEDL 230 (327)
T ss_pred HHHHHHHcC-CccHHHHHHHhccCHHHHHHHHHhhcc-CCcEEEEEEcCcceeEEechhhh
Confidence 344555555 899999999999999999998877764 3344566666 776 99988765
No 95
>PRK11050 manganese transport regulator MntR; Provisional
Probab=42.01 E-value=2e+02 Score=25.61 Aligned_cols=56 Identities=21% Similarity=0.325 Sum_probs=41.4
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChh
Q 016517 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (388)
Q Consensus 85 ~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~ 144 (388)
..|+.++.. +...|+.|+|...|++...+.+.|..|.++ |-++....+ -++.-+.+
T Consensus 40 ~~I~~~l~~-~~~~t~~eLA~~l~is~stVsr~l~~Le~~--GlI~r~~~~-~v~LT~~G 95 (152)
T PRK11050 40 ELIADLIAE-VGEARQVDIAARLGVSQPTVAKMLKRLARD--GLVEMRPYR-GVFLTPEG 95 (152)
T ss_pred HHHHHHHHh-cCCCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEecCC-ceEECchH
Confidence 456667765 567999999999999999999999999987 677654432 34444433
No 96
>PRK09492 treR trehalose repressor; Provisional
Probab=41.89 E-value=16 Score=34.21 Aligned_cols=24 Identities=25% Similarity=0.448 Sum_probs=21.3
Q ss_pred CceeehhhhhhcCCCHHHHHHHHH
Q 016517 96 RRVTIGDVAGKAGLKLNEAQKALQ 119 (388)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~Ae~aL~ 119 (388)
.++|+.|||..+|+|..++-+.|.
T Consensus 3 ~~~ti~dIA~~agVS~~TVSrvLn 26 (315)
T PRK09492 3 NKLTIKDIARLSGVGKSTVSRVLN 26 (315)
T ss_pred CCCcHHHHHHHhCCCHHHHhHHhC
Confidence 468999999999999998888776
No 97
>PRK09526 lacI lac repressor; Reviewed
Probab=41.56 E-value=17 Score=34.37 Aligned_cols=24 Identities=33% Similarity=0.462 Sum_probs=21.2
Q ss_pred CceeehhhhhhcCCCHHHHHHHHH
Q 016517 96 RRVTIGDVAGKAGLKLNEAQKALQ 119 (388)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~Ae~aL~ 119 (388)
.++|+.|||.+||+|..++-+.|.
T Consensus 4 ~~~ti~dIA~~aGVS~~TVSrvLn 27 (342)
T PRK09526 4 KPVTLYDVARYAGVSYQTVSRVLN 27 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHhc
Confidence 468999999999999998877775
No 98
>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=41.36 E-value=36 Score=27.84 Aligned_cols=57 Identities=19% Similarity=0.207 Sum_probs=44.5
Q ss_pred hhhHHHHHHHHhcC--CceeehhhhhhcC--CCHHHHHHHHHH--HHhhcCCceEeccCCcEE
Q 016517 82 DVRNRAMDAVDACN--RRVTIGDVAGKAG--LKLNEAQKALQA--LAADTDGFLEVSDEGDVL 138 (388)
Q Consensus 82 ~~~~~im~Ave~lg--~rvTvgDVAa~aG--L~l~~Ae~aL~a--LAaD~~GhLqVsesGdIl 138 (388)
+.+.++.+++.+.. .-+|-||||..+| -....+-.+|.. +.....+|==|+.+|.+-
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 5688899999999 666677777766 556779999999999875
No 99
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=41.06 E-value=42 Score=31.08 Aligned_cols=40 Identities=18% Similarity=0.258 Sum_probs=36.4
Q ss_pred hhhHHHHHHHHhcC-CceeehhhhhhcCCCHHHHHHHHHHH
Q 016517 82 DVRNRAMDAVDACN-RRVTIGDVAGKAGLKLNEAQKALQAL 121 (388)
Q Consensus 82 ~~~~~im~Ave~lg-~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (388)
....+|++.+.+.| -+|++.++|..+|++..++++.|..|
T Consensus 16 ~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l 56 (213)
T PRK05472 16 PLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYF 56 (213)
T ss_pred HHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHH
Confidence 44678899999987 69999999999999999999999999
No 100
>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=40.81 E-value=36 Score=29.99 Aligned_cols=45 Identities=22% Similarity=0.509 Sum_probs=33.0
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc--CCceEeccCC
Q 016517 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DGFLEVSDEG 135 (388)
Q Consensus 87 im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~--~GhLqVsesG 135 (388)
--+.++-|....+|+|||+..+|++..++ -|++|- .|+|+|....
T Consensus 45 ~~~Il~lC~~~~SVAEiAA~L~lPlgVvr----VLvsDL~~~G~v~v~~p~ 91 (114)
T PF05331_consen 45 HRAILELCRRPLSVAEIAARLGLPLGVVR----VLVSDLADAGLVRVRAPA 91 (114)
T ss_pred HHHHHHHHCCCccHHHHHHhhCCCchhhh----hhHHHHHhCCCEEEeCCC
Confidence 33444555559999999999999999984 444554 7899887654
No 101
>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=40.52 E-value=60 Score=26.58 Aligned_cols=56 Identities=13% Similarity=0.128 Sum_probs=42.0
Q ss_pred hhhHHHHHHHHhc--CCceeehhhhhhcCCCHHHHHHHHHHHHh-----hcCCceEeccCCcEE
Q 016517 82 DVRNRAMDAVDAC--NRRVTIGDVAGKAGLKLNEAQKALQALAA-----DTDGFLEVSDEGDVL 138 (388)
Q Consensus 82 ~~~~~im~Ave~l--g~rvTvgDVAa~aGL~l~~Ae~aL~aLAa-----D~~GhLqVsesGdIl 138 (388)
+.+.+|.+++.+- |.-+|-||||..+|.+- -++.--.+|+. ...+|==|+.+|.+-
T Consensus 2 ~f~~~V~~~l~~IP~G~v~TYg~iA~~~g~p~-~~RaVg~al~~np~~~~iPcHRVv~s~G~l~ 64 (80)
T TIGR00589 2 PFQQRVWQALRTIPYGETKSYGQLAARIGNPK-AVRAVGGANGRNPLAILVPCHRVIGKNGSLT 64 (80)
T ss_pred hHHHHHHHHHhCCCCCCcCCHHHHHHHhCCCC-hHHHHHHHHHhCCCCCCCCCceeECCCCCCC
Confidence 4678899999987 67788899999999753 23333344444 468999999999975
No 102
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=40.27 E-value=1.3e+02 Score=26.82 Aligned_cols=78 Identities=22% Similarity=0.192 Sum_probs=51.4
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcC--C--ceEec-cCC-cEEEEcChhhHHHHhhhhHHHhHHH
Q 016517 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTD--G--FLEVS-DEG-DVLYVFPNNYRAKLAAKSFRLKVEP 160 (388)
Q Consensus 87 im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~--G--hLqVs-esG-dIlY~FP~~fRs~l~~Ks~r~rlq~ 160 (388)
||+++-+.| -+|-.|+|...|++++++++.|..|-.|-- . .-+-+ ++| -..|.|==|++.+. -..+.++..
T Consensus 6 v~d~L~~~~-~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~--~vik~r~~~ 82 (147)
T smart00531 6 VLDALMRNG-CVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLL--DVVKYKLDK 82 (147)
T ss_pred ehHHHHhcC-CcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHH--HHHHHHHHH
Confidence 577777766 699999999999999999999999988542 1 22223 345 46777755665532 234444444
Q ss_pred HHHHHhh
Q 016517 161 VIDKAKA 167 (388)
Q Consensus 161 ~~~k~w~ 167 (388)
..+++..
T Consensus 83 ~~~~L~~ 89 (147)
T smart00531 83 MRKRLED 89 (147)
T ss_pred HHHHHHH
Confidence 4444443
No 103
>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=39.60 E-value=35 Score=32.56 Aligned_cols=39 Identities=18% Similarity=0.382 Sum_probs=33.8
Q ss_pred hHHHHHHHHhcCCc--eeehhhhhhcCCCHHHHHHHHHHHH
Q 016517 84 RNRAMDAVDACNRR--VTIGDVAGKAGLKLNEAQKALQALA 122 (388)
Q Consensus 84 ~~~im~Ave~lg~r--vTvgDVAa~aGL~l~~Ae~aL~aLA 122 (388)
+..|++.+.+...+ +|+.|++.+||+..+++-..|+.|-
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 9999999999999999988888763
No 104
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=39.42 E-value=74 Score=31.47 Aligned_cols=59 Identities=15% Similarity=0.195 Sum_probs=42.8
Q ss_pred CCCchhhHHHHHHHHhcCCceeehhhhhhcC--------------CCHHHHHHHHHHHHhhcCCceEeccCCc
Q 016517 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAG--------------LKLNEAQKALQALAADTDGFLEVSDEGD 136 (388)
Q Consensus 78 ~l~~~~~~~im~Ave~lg~rvTvgDVAa~aG--------------L~l~~Ae~aL~aLAaD~~GhLqVsesGd 136 (388)
++..+.|+||++++|++||+....--+.+++ ---.+.-+++...+.+.|=++-+..+.+
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 7899999999999999999965554443443 2345556777777887777777666543
No 105
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=39.23 E-value=18 Score=34.22 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=21.5
Q ss_pred CCceeehhhhhhcCCCHHHHHHHHH
Q 016517 95 NRRVTIGDVAGKAGLKLNEAQKALQ 119 (388)
Q Consensus 95 g~rvTvgDVAa~aGL~l~~Ae~aL~ 119 (388)
..++|+.|||..+|+|..++-+.|.
T Consensus 3 ~~~~ti~dIA~~agVS~~TVSrvLn 27 (331)
T PRK14987 3 KKRPVLQDVADRVGVTKMTVSRFLR 27 (331)
T ss_pred CCCCcHHHHHHHhCCCHHHhhhhhC
Confidence 3479999999999999998887774
No 106
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=39.21 E-value=34 Score=34.71 Aligned_cols=56 Identities=16% Similarity=0.259 Sum_probs=41.9
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhh
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNY 145 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~f 145 (388)
+..|++++.+.+..+|+.|++..||+..+++-.+|+.| |.|.+-..+-+++. +++.
T Consensus 210 ~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l-----~~l~~~~g~~~i~~-~~~~ 265 (290)
T PLN03238 210 TRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL-----NLIKYWKGQHVIHV-DQRV 265 (290)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC-----CcEEEECCcEEEEe-CHHH
Confidence 46788898888899999999999999999998877755 55655444444444 4443
No 107
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=39.00 E-value=1.2e+02 Score=32.14 Aligned_cols=87 Identities=17% Similarity=0.202 Sum_probs=53.5
Q ss_pred HhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCc-----EEEEcChhhHHHHhhhhHHHhHHHHHHHHh
Q 016517 92 DACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-----VLYVFPNNYRAKLAAKSFRLKVEPVIDKAK 166 (388)
Q Consensus 92 e~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGd-----IlY~FP~~fRs~l~~Ks~r~rlq~~~~k~w 166 (388)
.++|...|+.+||...|+++++.+..|.....-..-+..|.+++| ++-.-..+--..+.....+..++.+++.+-
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 457888999999999999999998776653322233333433333 221111122233334456666777777777
Q ss_pred hhhhHHHHHHHH
Q 016517 167 AAAEYSIRVLFG 178 (388)
Q Consensus 167 ~v~~yliRVsFG 178 (388)
.-=.-+++..||
T Consensus 353 ~reR~VI~LRyg 364 (415)
T PRK07598 353 SRERDVIRMRFG 364 (415)
T ss_pred HHHHHHHHHHHh
Confidence 776777777776
No 108
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=38.58 E-value=25 Score=24.49 Aligned_cols=28 Identities=18% Similarity=0.356 Sum_probs=18.5
Q ss_pred hcCCceeehhhhhhcCCCHHHHHHHHHH
Q 016517 93 ACNRRVTIGDVAGKAGLKLNEAQKALQA 120 (388)
Q Consensus 93 ~lg~rvTvgDVAa~aGL~l~~Ae~aL~a 120 (388)
.+....||.|||...|++...-.+..+.
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 4556799999999999988776665544
No 109
>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=38.38 E-value=85 Score=25.35 Aligned_cols=46 Identities=22% Similarity=0.455 Sum_probs=30.1
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEec-cCCcEEEEcChh
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS-DEGDVLYVFPNN 144 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVs-esGdIlY~FP~~ 144 (388)
-++.+++.+++.|..||.+-|+ +.|..| |-..|. ++|.-+|..|.+
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 3678888888888888877654 445544 445666 799999999975
No 110
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=38.06 E-value=2.6e+02 Score=24.25 Aligned_cols=42 Identities=17% Similarity=0.212 Sum_probs=33.8
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 016517 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (388)
Q Consensus 86 ~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLq 130 (388)
.|.... ..++.+|+.|+|...|++...+.+.|..|..+ |-++
T Consensus 12 ~I~~l~-~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~--Gli~ 53 (142)
T PRK03902 12 QIYLLI-EEKGYARVSDIAEALSVHPSSVTKMVQKLDKD--EYLI 53 (142)
T ss_pred HHHHHH-hcCCCcCHHHHHHHhCCChhHHHHHHHHHHHC--CCEE
Confidence 344433 45667799999999999999999999999887 6665
No 111
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=38.04 E-value=21 Score=33.70 Aligned_cols=23 Identities=30% Similarity=0.482 Sum_probs=20.6
Q ss_pred ceeehhhhhhcCCCHHHHHHHHH
Q 016517 97 RVTIGDVAGKAGLKLNEAQKALQ 119 (388)
Q Consensus 97 rvTvgDVAa~aGL~l~~Ae~aL~ 119 (388)
++|+.|||..+|+|..++-++|.
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhC
Confidence 47999999999999999988884
No 112
>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=37.99 E-value=47 Score=25.67 Aligned_cols=40 Identities=18% Similarity=0.335 Sum_probs=28.3
Q ss_pred HHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 016517 89 DAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (388)
Q Consensus 89 ~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLq 130 (388)
...-+.++++|++|+|...|++.+.++.-|..|-. -|.++
T Consensus 6 ~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~--kG~I~ 45 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAREFGISPEAVEAMLEQLIR--KGYIR 45 (69)
T ss_dssp HHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHC--CTSCE
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCcEE
Confidence 34445788999999999999999999888777754 34444
No 113
>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=37.91 E-value=38 Score=33.75 Aligned_cols=45 Identities=18% Similarity=0.344 Sum_probs=36.2
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 016517 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (388)
Q Consensus 87 im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVse 133 (388)
|++++.+..+|++-.++|.+-|+|......+++.|.++ |-+++-.
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 33344444579999999999999999999999999874 7777776
No 114
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=37.87 E-value=54 Score=29.83 Aligned_cols=50 Identities=12% Similarity=0.155 Sum_probs=40.2
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc------CCceEeccCCc
Q 016517 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT------DGFLEVSDEGD 136 (388)
Q Consensus 86 ~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~------~GhLqVsesGd 136 (388)
.|-...+ .++.++++|+|..-+++...+.+.|..|+++- .|.++.|+.|+
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~ 69 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGR 69 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCeEEChhhH
Confidence 3444455 77889999999999999999999999999863 56666777775
No 115
>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=37.82 E-value=59 Score=26.08 Aligned_cols=52 Identities=21% Similarity=0.337 Sum_probs=43.0
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEE
Q 016517 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (388)
Q Consensus 86 ~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~ 140 (388)
.|-+++.. .+..|+.+++..+|++-.++..||==||.+ +.+++.+.++.+|+
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 45667777 678999999999999999999999888875 78888888887775
No 116
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=37.50 E-value=30 Score=32.15 Aligned_cols=33 Identities=18% Similarity=0.314 Sum_probs=26.2
Q ss_pred hhhHHHHHH----HHhcCCceeehhhhhhcCCCHHHH
Q 016517 82 DVRNRAMDA----VDACNRRVTIGDVAGKAGLKLNEA 114 (388)
Q Consensus 82 ~~~~~im~A----ve~lg~rvTvgDVAa~aGL~l~~A 114 (388)
+.|.+|++| +-+.||.+|+.|||.+||++....
T Consensus 13 ~~r~~Il~aA~~lF~~~Gy~~s~~~IA~~AGvsk~ti 49 (225)
T PRK11552 13 QAKQQLIAAALAQFGEYGLHATTRDIAAQAGQNIAAI 49 (225)
T ss_pred HHHHHHHHHHHHHHHHhCccCCHHHHHHHhCCCHHHH
Confidence 566677665 456799999999999999987654
No 117
>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=36.73 E-value=55 Score=27.86 Aligned_cols=44 Identities=16% Similarity=0.329 Sum_probs=34.3
Q ss_pred HHHHHHhc-CCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEec
Q 016517 87 AMDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (388)
Q Consensus 87 im~Ave~l-g~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVs 132 (388)
+|..+-+. +.++|+.|+|.+.|++...+++-|..|.. .|-++..
T Consensus 14 ~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~--~Gli~~~ 58 (130)
T TIGR02944 14 VLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSL--AGIVTSK 58 (130)
T ss_pred HHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHH--CCcEEec
Confidence 44455443 56799999999999999999999999987 4556543
No 118
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=36.66 E-value=1.6e+02 Score=31.13 Aligned_cols=72 Identities=17% Similarity=0.270 Sum_probs=55.7
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhhHHHHhhhhHHHh
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLK 157 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~fRs~l~~Ks~r~r 157 (388)
...+++.++...+ .+|..|+|.+.|++...+.+.+..|.+. |-+++.+.=...|.--..=++.+.+-+...+
T Consensus 7 ~e~~vL~~L~~~~-~~s~~eLA~~l~l~~~tVt~~i~~Le~k--GlV~~~~~~~~~i~LTeeG~~~~~~g~pE~r 78 (489)
T PRK04172 7 NEKKVLKALKELK-EATLEELAEKLGLPPEAVMRAAEWLEEK--GLVKVEERVEEVYVLTEEGKKYAEEGLPERR 78 (489)
T ss_pred HHHHHHHHHHhCC-CCCHHHHHHHhCcCHHHHHHHHHHHHhC--CCEEEEeeeEEEEEECHHHHHHHHhcCHHHH
Confidence 4578899998766 6999999999999999999999999997 7888876544555556665666665444444
No 119
>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=36.26 E-value=18 Score=27.11 Aligned_cols=24 Identities=33% Similarity=0.462 Sum_probs=20.0
Q ss_pred hhhcCCccccCCCcCEEEecCccc
Q 016517 312 LLRFDGQPEIDEEGNILYRFPSFQ 335 (388)
Q Consensus 312 L~rF~G~PeVse~G~IVY~FPeLq 335 (388)
+.+-||...++.+|..||+|..=+
T Consensus 4 v~~~dG~~~~~~~G~~LY~f~~D~ 27 (48)
T PF03640_consen 4 VTRADGTIQVDYNGMPLYYFDKDS 27 (48)
T ss_pred EEeCCCCEEECCCCCEEEEECCCC
Confidence 456789999999999999997533
No 120
>PHA01815 hypothetical protein
Probab=35.93 E-value=1.4e+02 Score=23.12 Aligned_cols=24 Identities=21% Similarity=0.232 Sum_probs=16.2
Q ss_pred HHHHHHHHhhhhhHHHHHHHHHHH
Q 016517 158 VEPVIDKAKAAAEYSIRVLFGTAL 181 (388)
Q Consensus 158 lq~~~~k~w~v~~yliRVsFGi~L 181 (388)
+-+++-.+--....-+|||||+..
T Consensus 12 llaflitliilmt~~irvsfgvlf 35 (55)
T PHA01815 12 LLAFLITLIILMTLHIRVSFGVLF 35 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555566777999999754
No 121
>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=35.90 E-value=1e+02 Score=24.22 Aligned_cols=43 Identities=26% Similarity=0.306 Sum_probs=32.1
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCce
Q 016517 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFL 129 (388)
Q Consensus 87 im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhL 129 (388)
+-+.+....-+..-.+.|+++.|++++.++-|+..|+...-.|
T Consensus 7 laqiiqehregldwqeaatraslsleetrkllqsmaaagqvtl 49 (61)
T PF09105_consen 7 LAQIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQVTL 49 (61)
T ss_dssp HHHHHHC-TT-EEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHccCcHHHHHHHhhccHHHHHHHHHHHHhcCceEE
Confidence 3566777888888899999999999999999999988765444
No 122
>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=35.84 E-value=2e+02 Score=25.12 Aligned_cols=75 Identities=13% Similarity=0.093 Sum_probs=51.9
Q ss_pred hHHHHHHHHhcCCceeehhhhhhc----CCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhhHHHHhhhhHHHhHH
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKA----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVE 159 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~a----GL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~fRs~l~~Ks~r~rlq 159 (388)
.-.||+.+=+.| .+|+.||.... |++.+.+..-|..|.. -|.|+...+|-.-+-.|--=|.- +.+..++
T Consensus 6 E~~VM~vlW~~~-~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~--KG~v~~~k~gr~~~Y~p~vs~ee----~~~~~~~ 78 (130)
T TIGR02698 6 EWEVMRVVWTLG-ETTSRDIIRILAEKKDWSDSTIKTLLGRLVD--KGCLTTEKEGRKFIYTALVSEDE----AVENAAQ 78 (130)
T ss_pred HHHHHHHHHcCC-CCCHHHHHHHHhhccCCcHHHHHHHHHHHHH--CCceeeecCCCcEEEEecCCHHH----HHHHHHH
Confidence 346899998776 68999977764 7888999888888876 68899888888544345433332 3344455
Q ss_pred HHHHHH
Q 016517 160 PVIDKA 165 (388)
Q Consensus 160 ~~~~k~ 165 (388)
.+++++
T Consensus 79 ~~~~~~ 84 (130)
T TIGR02698 79 ELFSRI 84 (130)
T ss_pred HHHHHH
Confidence 555543
No 123
>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=35.41 E-value=76 Score=24.40 Aligned_cols=36 Identities=17% Similarity=0.300 Sum_probs=27.3
Q ss_pred HHHHHHHHhcCC-----ceeehhhhhhcCCCHHHHHHHHHH
Q 016517 85 NRAMDAVDACNR-----RVTIGDVAGKAGLKLNEAQKALQA 120 (388)
Q Consensus 85 ~~im~Ave~lg~-----rvTvgDVAa~aGL~l~~Ae~aL~a 120 (388)
.+++.+.=..|| ++|+.|+|..-|++...+..-|+.
T Consensus 6 ~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 6 REILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred HHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 344444445555 899999999999999998777764
No 124
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=34.89 E-value=27 Score=30.82 Aligned_cols=30 Identities=20% Similarity=0.199 Sum_probs=23.2
Q ss_pred hHHHHHH----HHhcCCc-eeehhhhhhcCCCHHH
Q 016517 84 RNRAMDA----VDACNRR-VTIGDVAGKAGLKLNE 113 (388)
Q Consensus 84 ~~~im~A----ve~lg~r-vTvgDVAa~aGL~l~~ 113 (388)
|.+|++| +.+.||. +|+.|||.++|++...
T Consensus 10 R~~Il~aA~~lf~e~G~~~tSi~~Ia~~aGvsk~~ 44 (192)
T PRK14996 10 REVILQAAMRVALAEGFAAMTVRRIASEAQVAAGQ 44 (192)
T ss_pred HHHHHHHHHHHHHhcChhhccHHHHHHHhCCCcHH
Confidence 5566555 5667887 8999999999998653
No 125
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=34.66 E-value=33 Score=31.15 Aligned_cols=33 Identities=12% Similarity=0.202 Sum_probs=25.1
Q ss_pred chhhHHHHHH----HHhcCCc-eeehhhhhhcCCCHHH
Q 016517 81 ADVRNRAMDA----VDACNRR-VTIGDVAGKAGLKLNE 113 (388)
Q Consensus 81 ~~~~~~im~A----ve~lg~r-vTvgDVAa~aGL~l~~ 113 (388)
.+.|++|++| +.+.||. +|+.|||.++|++...
T Consensus 17 ~~~r~~IL~AA~~lf~e~Gy~~~s~~dIA~~aGvs~gt 54 (212)
T PRK15008 17 SAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTN 54 (212)
T ss_pred HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHH
Confidence 3456666554 6678987 8999999999998754
No 126
>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=34.01 E-value=64 Score=29.26 Aligned_cols=53 Identities=13% Similarity=0.261 Sum_probs=40.2
Q ss_pred HHHHHHHHhcC-CceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCh
Q 016517 85 NRAMDAVDACN-RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (388)
Q Consensus 85 ~~im~Ave~lg-~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~ 143 (388)
.+|-+.++... .++|+.+||..+|++..+..+=+. .|.|++++...+-|.=.+
T Consensus 33 ~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~Ir------eGRL~~~~~~nl~~~CE~ 86 (137)
T TIGR03826 33 EKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIR------EGRLQLKHFPNLGYPCER 86 (137)
T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHH------cCCeeccCCCCCcCcccc
Confidence 44555565443 369999999999999999866555 499999998887775543
No 127
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=33.69 E-value=26 Score=33.29 Aligned_cols=22 Identities=32% Similarity=0.487 Sum_probs=19.3
Q ss_pred eeehhhhhhcCCCHHHHHHHHH
Q 016517 98 VTIGDVAGKAGLKLNEAQKALQ 119 (388)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL~ 119 (388)
+|+.|||.++|+|..++-+.|.
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn 23 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVIN 23 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 6999999999999998877775
No 128
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=33.48 E-value=26 Score=32.96 Aligned_cols=22 Identities=36% Similarity=0.539 Sum_probs=19.0
Q ss_pred eeehhhhhhcCCCHHHHHHHHH
Q 016517 98 VTIGDVAGKAGLKLNEAQKALQ 119 (388)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL~ 119 (388)
+|+.|||..||+|..++-+.|.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn 23 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVN 23 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhC
Confidence 6899999999999988877664
No 129
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.43 E-value=90 Score=31.30 Aligned_cols=45 Identities=27% Similarity=0.219 Sum_probs=31.0
Q ss_pred hhhhHHHhHHHHHHHHhhhh--------hHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 016517 150 AAKSFRLKVEPVIDKAKAAA--------EYSIRVLFGTALIASIVIVFTAIIAILS 197 (388)
Q Consensus 150 ~~Ks~r~rlq~~~~k~w~v~--------~yliRVsFGi~LIaSIvLv~~aI~alls 197 (388)
.+|+-|.---.|.++.|+.. ...=|.+|.|+|- +|-|++|+++++
T Consensus 220 dnKY~RRp~~~w~~rl~R~~~g~s~rP~~~~~ra~fli~lg---vLafi~~i~lM~ 272 (299)
T KOG3970|consen 220 DNKYKRRPTMDWMRRLWRAKHGGSGRPQEAKKRALFLIFLG---VLAFITIIMLMK 272 (299)
T ss_pred cchhhcCChHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHH---HHHHHHHHHHHH
Confidence 45777777888888888753 3355667665543 677888888883
No 130
>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=33.21 E-value=38 Score=36.54 Aligned_cols=16 Identities=25% Similarity=0.453 Sum_probs=12.8
Q ss_pred CCcEEEEcChhhHHHH
Q 016517 134 EGDVLYVFPNNYRAKL 149 (388)
Q Consensus 134 sGdIlY~FP~~fRs~l 149 (388)
+|.++|.-+.+-|..-
T Consensus 421 ~G~L~~~~~f~~r~~~ 436 (507)
T PF07245_consen 421 KGTLIYLGPFDDRNYT 436 (507)
T ss_pred EEEEEecccccccccc
Confidence 6899999998877643
No 131
>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=33.18 E-value=1.5e+02 Score=27.32 Aligned_cols=47 Identities=19% Similarity=0.368 Sum_probs=38.8
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVse 133 (388)
.-+|+..+.+.| .+|+.|+|...|++...+.+.|..|... |-++...
T Consensus 145 ~~~IL~~l~~~g-~~s~~eia~~l~is~stv~r~L~~Le~~--GlI~r~~ 191 (203)
T TIGR01884 145 ELKVLEVLKAEG-EKSVKNIAKKLGKSLSTISRHLRELEKK--GLVEQKG 191 (203)
T ss_pred HHHHHHHHHHcC-CcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEc
Confidence 457788887765 5899999999999999999999999865 6666554
No 132
>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=33.03 E-value=23 Score=26.82 Aligned_cols=25 Identities=24% Similarity=0.650 Sum_probs=21.5
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHHh
Q 016517 258 VFGEGDPNQGIEEKRWKLIGEYIAS 282 (388)
Q Consensus 258 vFGDGDPN~dlEerRWk~Ig~~Ir~ 282 (388)
+.|||||-+=+..+-||.|-..+..
T Consensus 22 viG~G~p~~vf~~~tW~hi~d~~~g 46 (47)
T PF11772_consen 22 VIGDGNPFDVFSPDTWQHIIDFFTG 46 (47)
T ss_pred eeCCCCHHHhCCHHHHHHHHHHHcC
Confidence 4799999999999999999887753
No 133
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=32.70 E-value=53 Score=25.04 Aligned_cols=52 Identities=21% Similarity=0.260 Sum_probs=38.2
Q ss_pred ceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhhHHHHh
Q 016517 97 RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLA 150 (388)
Q Consensus 97 rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~fRs~l~ 150 (388)
.++..++..-.|+++.. .++..+....|...+.+++++.+.+.+.-||.=+.
T Consensus 5 ~~~~~~i~~llG~~i~~--~ei~~~L~~lg~~~~~~~~~~~~~v~~P~~R~Di~ 56 (71)
T smart00874 5 TLRRERINRLLGLDLSA--EEIEEILKRLGFEVEVSGDDDTLEVTVPSYRFDIL 56 (71)
T ss_pred EecHHHHHHHHCCCCCH--HHHHHHHHHCCCeEEecCCCCeEEEECCCCccccC
Confidence 35667888889987763 44677777778877776667888888888886433
No 134
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=32.43 E-value=1.1e+02 Score=25.96 Aligned_cols=59 Identities=31% Similarity=0.409 Sum_probs=44.4
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCce-Eecc-CCcEEEE
Q 016517 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFL-EVSD-EGDVLYV 140 (388)
Q Consensus 79 l~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhL-qVse-sGdIlY~ 140 (388)
++.+.-+++++-|-+ -.-+|+.-||.+-+++.+.|+++|+.|... |.+ .|+. +.-.||+
T Consensus 24 ~dk~t~dkl~kEV~~-~K~ITps~lserlkI~~SlAr~~Lr~L~~k--G~Ik~V~~~~~q~IYt 84 (86)
T PRK09334 24 LDEELLKRVAKEVKK-EKIVTPYTLASKYGIKISVAKKVLRELEKR--GVLVLYSKNRRTPIYV 84 (86)
T ss_pred cCHHHHHHHHHHhcc-CcEEcHHHHHHHhcchHHHHHHHHHHHHHC--CCEEEEecCCCeEEec
Confidence 556677788888877 455899999999999999999999999864 444 2333 3555553
No 135
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=31.98 E-value=60 Score=28.05 Aligned_cols=34 Identities=12% Similarity=0.191 Sum_probs=29.9
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHH
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~ 119 (388)
+..|+-|+++.| .|+..++.++||+-+....+|.
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 467899999988 7999999999999999888874
No 136
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=31.80 E-value=37 Score=30.28 Aligned_cols=32 Identities=16% Similarity=0.257 Sum_probs=24.0
Q ss_pred hhhHHHHHH----HHhcCC-ceeehhhhhhcCCCHHH
Q 016517 82 DVRNRAMDA----VDACNR-RVTIGDVAGKAGLKLNE 113 (388)
Q Consensus 82 ~~~~~im~A----ve~lg~-rvTvgDVAa~aGL~l~~ 113 (388)
..|.+|++| +.+.|+ .+|+.|||.++|++...
T Consensus 11 ~~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t 47 (213)
T PRK09975 11 KTRQELIETAIAQFALRGVSNTTLNDIADAANVTRGA 47 (213)
T ss_pred HHHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHH
Confidence 345556555 567786 69999999999998654
No 137
>PHA02673 ORF109 EEV glycoprotein; Provisional
Probab=31.70 E-value=92 Score=29.33 Aligned_cols=25 Identities=16% Similarity=0.289 Sum_probs=17.0
Q ss_pred HhhhhhHHHHHHHHHHHHHHHHHHHH
Q 016517 165 AKAAAEYSIRVLFGTALIASIVIVFT 190 (388)
Q Consensus 165 ~w~v~~yliRVsFGi~LIaSIvLv~~ 190 (388)
+.+.+..+|||+..|.+| |++++.+
T Consensus 28 ~~R~i~l~~Ri~~~iSIi-sL~~l~v 52 (161)
T PHA02673 28 IRRYIKLFFRLMAAIAII-VLAILVV 52 (161)
T ss_pred HHHHHHHHHHHHHHHHHH-HHHHHHH
Confidence 356778899999988776 4443333
No 138
>cd00131 PAX Paired Box domain
Probab=31.63 E-value=80 Score=27.65 Aligned_cols=49 Identities=16% Similarity=0.279 Sum_probs=39.4
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 016517 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (388)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLq 130 (388)
--|+.+.|.+|+.+++ ...+..+||.+.|++.+.+.+-+..-.. .|+++
T Consensus 16 ~~lS~d~R~rIv~~~~---~G~s~~~iA~~~~Vs~~tV~r~i~r~~e--~G~v~ 64 (128)
T cd00131 16 RPLPDSIRQRIVELAQ---SGIRPCDISRQLRVSHGCVSKILNRYYE--TGSIR 64 (128)
T ss_pred CcCCHHHHHHHHHHHH---cCCCHHHHHHHHCcCHHHHHHHHHHHHH--cCCcC
Confidence 4578899999999987 2479999999999999999887776654 33444
No 139
>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=31.52 E-value=64 Score=25.64 Aligned_cols=34 Identities=21% Similarity=0.404 Sum_probs=29.9
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHH
Q 016517 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQ 115 (388)
Q Consensus 82 ~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae 115 (388)
.-|+.+-+--...++.+++-|||.+.|++..+++
T Consensus 7 p~rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr 40 (60)
T PF10668_consen 7 PNRDKAFEIYKESNGKIKLKDIAEKLGVSESTIR 40 (60)
T ss_pred cCHHHHHHHHHHhCCCccHHHHHHHHCCCHHHHH
Confidence 3577888888899999999999999999998875
No 140
>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=31.45 E-value=37 Score=24.42 Aligned_cols=32 Identities=13% Similarity=0.225 Sum_probs=20.9
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHH
Q 016517 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (388)
Q Consensus 87 im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL 118 (388)
+-++++-+..+.|+.|||...|++.....+-|
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 34444444455999999999999999886654
No 141
>PRK13239 alkylmercury lyase; Provisional
Probab=31.32 E-value=38 Score=32.67 Aligned_cols=56 Identities=25% Similarity=0.252 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHHHhcCCeEeeeeccCccCCCCCCCCchhhhhHhhhcCCccccCCCcCEEEecC
Q 016517 269 EEKRWKLIGEYIASNGGVVTAEELAPYLDIDRTMSDESYVLPVLLRFDGQPEIDEEGNILYRFP 332 (388)
Q Consensus 269 EerRWk~Ig~~Ir~N~GvV~AEQLAPyLD~~~~~~~E~ymLpvL~rF~G~PeVse~G~IVY~FP 332 (388)
+.+=|..|-+.+. +|..|+-++||.-+++ +++.+..+|..+. ..+.+++|+||= ||
T Consensus 20 ~~~~~~~llr~la-~G~pvt~~~lA~~~~~-----~~~~v~~~L~~l~-~~~~d~~g~iv~-~p 75 (206)
T PRK13239 20 TATLLVPLLRLLA-KGRPVSVTTLAAALGW-----PVEEVEAVLEAMP-DTEYDEDGRIIG-YG 75 (206)
T ss_pred chHHHHHHHHHHH-cCCCCCHHHHHHHhCC-----CHHHHHHHHHhCC-CeEECCCCCEEe-cc
Confidence 3455788889988 9999999999998774 5667888888876 448999999986 54
No 142
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=31.05 E-value=29 Score=33.11 Aligned_cols=22 Identities=32% Similarity=0.483 Sum_probs=19.2
Q ss_pred eeehhhhhhcCCCHHHHHHHHH
Q 016517 98 VTIGDVAGKAGLKLNEAQKALQ 119 (388)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL~ 119 (388)
+|+.|||..||+|..++-+.|.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 2 ATIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CCHHHHHHHhCCCHHHHHHHhC
Confidence 6999999999999998877764
No 143
>KOG4251 consensus Calcium binding protein [General function prediction only]
Probab=30.84 E-value=30 Score=35.06 Aligned_cols=59 Identities=29% Similarity=0.339 Sum_probs=42.3
Q ss_pred CCChHHHHHHHHHHHHHhc-CCeEeeeeccCccCCCC--CCCCchhhhhHhhhcCCccccCC
Q 016517 265 NQGIEEKRWKLIGEYIASN-GGVVTAEELAPYLDIDR--TMSDESYVLPVLLRFDGQPEIDE 323 (388)
Q Consensus 265 N~dlEerRWk~Ig~~Ir~N-~GvV~AEQLAPyLD~~~--~~~~E~ymLpvL~rF~G~PeVse 323 (388)
..++-++|-|..-..|-+| .|.||||||--|+|..+ ....|-...-+++.-|+....|.
T Consensus 275 ddnwvkdRkkEFeElIDsNhDGivTaeELe~y~dP~n~~~alne~~~~ma~~d~n~~~~Ls~ 336 (362)
T KOG4251|consen 275 DDNWVKDRKKEFEELIDSNHDGIVTAEELEDYVDPQNFRLALNEVNDIMALTDANNDEKLSL 336 (362)
T ss_pred HHHHHHHHHHHHHHHhhcCCccceeHHHHHhhcCchhhhhhHHHHHHHHhhhccCCCcccCH
Confidence 3458889999999999765 79999999999999654 12245444555666666655553
No 144
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=30.70 E-value=94 Score=21.30 Aligned_cols=46 Identities=13% Similarity=0.213 Sum_probs=32.7
Q ss_pred CCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCC
Q 016517 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG 127 (388)
Q Consensus 78 ~l~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~G 127 (388)
.|+..-+. ++..+ -.+.+..++|...|++...+.+-+..+-...+.
T Consensus 3 ~l~~~e~~-i~~~~---~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~ 48 (58)
T smart00421 3 SLTPRERE-VLRLL---AEGLTNKEIAERLGISEKTVKTHLSNIMRKLGV 48 (58)
T ss_pred CCCHHHHH-HHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 45554443 44443 234699999999999999999988887665543
No 145
>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=30.35 E-value=1.7e+02 Score=24.46 Aligned_cols=62 Identities=13% Similarity=0.127 Sum_probs=45.5
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCh
Q 016517 82 DVRNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (388)
Q Consensus 82 ~~~~~im~Ave~lg~rvTvgDVAa~a-----GL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~ 143 (388)
..|..|++.+.+.+.-+|+.||.... .+++..+=+.|..|...-=-+=-..++|...|.+-.
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 46889999999999999999988754 588899999999988754222223346778887754
No 146
>PRK06474 hypothetical protein; Provisional
Probab=30.26 E-value=90 Score=28.76 Aligned_cols=56 Identities=18% Similarity=0.180 Sum_probs=46.0
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhc-CCCHHHHHHHHHHHHhhcCCceEeccC
Q 016517 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKA-GLKLNEAQKALQALAADTDGFLEVSDE 134 (388)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~rvTvgDVAa~a-GL~l~~Ae~aL~aLAaD~~GhLqVses 134 (388)
+-|....|.+|++++...+...|+.|++... +++...+=+-|..|+. .|-|++.+.
T Consensus 6 ~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e--~GLI~~~~~ 62 (178)
T PRK06474 6 EILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVD--SGILHVVKE 62 (178)
T ss_pred HhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH--CCCEEEeec
Confidence 3466788999999999887669999999988 6888888888988876 477776654
No 147
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=30.19 E-value=76 Score=28.40 Aligned_cols=42 Identities=10% Similarity=0.255 Sum_probs=35.4
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 016517 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (388)
Q Consensus 83 ~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~ 125 (388)
...+|++++ +.+.|.|..|+|.+.|||-..+.+-+..|-.+-
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 456677754 578899999999999999999999999997653
No 148
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=30.00 E-value=26 Score=33.24 Aligned_cols=22 Identities=32% Similarity=0.508 Sum_probs=20.1
Q ss_pred eeehhhhhhcCCCHHHHHHHHH
Q 016517 98 VTIGDVAGKAGLKLNEAQKALQ 119 (388)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL~ 119 (388)
+|+-|||..||+|..++-+.|.
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln 23 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLN 23 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhc
Confidence 6999999999999999988884
No 149
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=29.81 E-value=33 Score=32.79 Aligned_cols=22 Identities=36% Similarity=0.602 Sum_probs=19.4
Q ss_pred eeehhhhhhcCCCHHHHHHHHH
Q 016517 98 VTIGDVAGKAGLKLNEAQKALQ 119 (388)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL~ 119 (388)
+|+.|||..+|+|..++-+.|.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHC
Confidence 6999999999999998877774
No 150
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=29.31 E-value=31 Score=31.91 Aligned_cols=59 Identities=20% Similarity=0.374 Sum_probs=47.1
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc-CCcEEEEc
Q 016517 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYVF 141 (388)
Q Consensus 81 ~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVse-sGdIlY~F 141 (388)
..++++||+--=+-|.+++..++|.+-|+|..-++.+|..|++| |-|++.. .|-.|=.+
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 45666666666667999999999999999999999999999986 6677664 46555555
No 151
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=29.06 E-value=82 Score=25.04 Aligned_cols=37 Identities=19% Similarity=0.230 Sum_probs=26.8
Q ss_pred HHHHHhc-CCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 88 MDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 88 m~Ave~l-g~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
++-++.+ ....+..+++..++|+-..+++-|..|...
T Consensus 9 ~~IL~~l~~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~ 46 (77)
T PF14947_consen 9 FDILKILSKGGAKKTEIMYKANLNYSTLKKYLKELEEK 46 (77)
T ss_dssp HHHHHHH-TT-B-HHHHHTTST--HHHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCCCHHHHHHHhCcCHHHHHHHHHHHHHC
Confidence 4444444 778888999999999999999999999865
No 152
>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=29.05 E-value=98 Score=18.22 Aligned_cols=34 Identities=12% Similarity=0.219 Sum_probs=23.9
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHH
Q 016517 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQ 115 (388)
Q Consensus 79 l~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae 115 (388)
++.+.+..++...+ .| .|+.++|...|++...+.
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 44555666666654 23 399999999999887664
No 153
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=28.98 E-value=38 Score=27.29 Aligned_cols=29 Identities=17% Similarity=0.318 Sum_probs=23.8
Q ss_pred HHHHHhcCCceeehhhhhhcCCCHHHHHH
Q 016517 88 MDAVDACNRRVTIGDVAGKAGLKLNEAQK 116 (388)
Q Consensus 88 m~Ave~lg~rvTvgDVAa~aGL~l~~Ae~ 116 (388)
-+|++-...++++.+|+...||+..|||-
T Consensus 35 ~~A~klv~~Ga~~~el~~~CgL~~aEAeL 63 (70)
T PF10975_consen 35 SQAIKLVRQGASVEELMEECGLSRAEAEL 63 (70)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHH
Confidence 45666666779999999999999999953
No 154
>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=28.39 E-value=44 Score=29.51 Aligned_cols=32 Identities=13% Similarity=0.212 Sum_probs=24.1
Q ss_pred hhhHHHHH----HHHhcCCc-eeehhhhhhcCCCHHH
Q 016517 82 DVRNRAMD----AVDACNRR-VTIGDVAGKAGLKLNE 113 (388)
Q Consensus 82 ~~~~~im~----Ave~lg~r-vTvgDVAa~aGL~l~~ 113 (388)
..|.+|++ .+.+.||. +|+.|||.++|++...
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 45556654 46677886 8999999999998754
No 155
>smart00351 PAX Paired Box domain.
Probab=28.24 E-value=1.2e+02 Score=26.28 Aligned_cols=47 Identities=19% Similarity=0.233 Sum_probs=37.7
Q ss_pred ccccCCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHH
Q 016517 73 IVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALA 122 (388)
Q Consensus 73 ~~~~~~l~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLA 122 (388)
++-.-.++++.|.+|+.+++ . +.+..+||.+.|++...+.+-+..-.
T Consensus 12 ~~~~~~~s~~~R~riv~~~~-~--G~s~~~iA~~~gvs~~tV~kwi~r~~ 58 (125)
T smart00351 12 FVNGRPLPDEERQRIVELAQ-N--GVRPCDISRQLCVSHGCVSKILGRYY 58 (125)
T ss_pred ecCCCCCCHHHHHHHHHHHH-c--CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 33344599999999999987 3 35888999999999999988777653
No 156
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=27.63 E-value=71 Score=31.73 Aligned_cols=43 Identities=33% Similarity=0.415 Sum_probs=36.1
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLq 130 (388)
.+...+++++.+|.|-++=+...+|++..+|++.|. +++|||.
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 355678899999999999999999999999976654 6788875
No 157
>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=27.61 E-value=97 Score=26.05 Aligned_cols=43 Identities=21% Similarity=0.352 Sum_probs=32.7
Q ss_pred HHHHHHhc--CCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 016517 87 AMDAVDAC--NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (388)
Q Consensus 87 im~Ave~l--g~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqV 131 (388)
+|-.+.+. +..+|..++|...|++...+++-|..|.. .|-|..
T Consensus 13 ~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~--~gli~~ 57 (132)
T TIGR00738 13 ALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRR--AGLVES 57 (132)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH--CCcEEe
Confidence 34444444 34799999999999999999999999986 344544
No 158
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=27.61 E-value=1.4e+02 Score=25.13 Aligned_cols=65 Identities=23% Similarity=0.364 Sum_probs=43.7
Q ss_pred chhhHHHHHHHHhcCCceee--hhhhhhcCCC-----HHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhhHHHH
Q 016517 81 ADVRNRAMDAVDACNRRVTI--GDVAGKAGLK-----LNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKL 149 (388)
Q Consensus 81 ~~~~~~im~Ave~lg~rvTv--gDVAa~aGL~-----l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~fRs~l 149 (388)
..+...|++.+.+.|..-|+ .|||-.-|=+ ...++++-..|+. .|.++++-.|..| =|.+||..+
T Consensus 6 ~~l~~~Il~ll~~R~~~ktiCPSevARal~~~~WR~lm~~vR~~A~~L~~--~G~i~I~qkG~~V--dp~~~rGpi 77 (83)
T PF11625_consen 6 ARLEAAILALLAARGPGKTICPSEVARALGPDDWRDLMPPVRAAARRLAR--AGRIEITQKGKPV--DPETFRGPI 77 (83)
T ss_dssp HHHHHHHHHHHHHS-TT--B-HHHHHHHH-TTS-GGGHHHHHHHHHHHHH--TTSEEEEETTEE----TTT--S--
T ss_pred HHHHHHHHHHHHhcCCCCccCHHHHHHHHCchhhHHHHHHHHHHHHHHHH--CCcEEEEECCEec--CcccCcCCe
Confidence 35667888999999888777 7999887754 6677777777775 5999999999988 577776644
No 159
>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=27.11 E-value=21 Score=35.63 Aligned_cols=16 Identities=13% Similarity=0.096 Sum_probs=0.0
Q ss_pred HHHHHhhhhhHHHHHH
Q 016517 161 VIDKAKAAAEYSIRVL 176 (388)
Q Consensus 161 ~~~k~w~v~~yliRVs 176 (388)
-++|+|..+.||+=++
T Consensus 3 tl~~~w~~~~~~i~~~ 18 (263)
T PF00802_consen 3 TLEKTWDTLNHLIVIS 18 (263)
T ss_dssp ----------------
T ss_pred hHHHhHhhhcceehhh
Confidence 4678899888887544
No 160
>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=26.87 E-value=1.9e+02 Score=29.76 Aligned_cols=78 Identities=19% Similarity=0.225 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHHHHh-hcCCceEeccCCcEEEEcChhhHHHHhh-hhHHHhHHHHHHHH----------hhhhhHHHHH
Q 016517 108 GLKLNEAQKALQALAA-DTDGFLEVSDEGDVLYVFPNNYRAKLAA-KSFRLKVEPVIDKA----------KAAAEYSIRV 175 (388)
Q Consensus 108 GL~l~~Ae~aL~aLAa-D~~GhLqVsesGdIlY~FP~~fRs~l~~-Ks~r~rlq~~~~k~----------w~v~~yliRV 175 (388)
|.+-+.-.+.|..|.+ +.-|+-= +++. |+.+|+.+-.. .++..+|+.-.+|+ .++.-.++=+
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 4455555566666665 2222211 1111 78899988665 23444444333332 2333334444
Q ss_pred HHHHHHHHHHHHHHHH
Q 016517 176 LFGTALIASIVIVFTA 191 (388)
Q Consensus 176 sFGi~LIaSIvLv~~a 191 (388)
+|...+|+|+|+..+|
T Consensus 190 a~~aV~i~svv~aa~a 205 (336)
T PF05055_consen 190 AFVAVAIASVVAAAHA 205 (336)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 5666677777766653
No 161
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=26.61 E-value=41 Score=31.63 Aligned_cols=23 Identities=17% Similarity=0.341 Sum_probs=19.2
Q ss_pred eeehhhhhhcCCCHHHHHHHHHH
Q 016517 98 VTIGDVAGKAGLKLNEAQKALQA 120 (388)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL~a 120 (388)
+|+.|||..+|+|..++-+.|..
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Confidence 38899999999999888777753
No 162
>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=26.58 E-value=72 Score=22.37 Aligned_cols=28 Identities=25% Similarity=0.331 Sum_probs=21.8
Q ss_pred ceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 97 RVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 97 rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
..|-.|+|...|++.+.+-+.|..|..+
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 3577899999999999999999888654
No 163
>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=26.08 E-value=90 Score=24.72 Aligned_cols=43 Identities=21% Similarity=0.303 Sum_probs=36.1
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCC--HHHHHHHHHHHHhhc
Q 016517 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLK--LNEAQKALQALAADT 125 (388)
Q Consensus 82 ~~~~~im~Ave~lg~rvTvgDVAa~aGL~--l~~Ae~aL~aLAaD~ 125 (388)
+..++|.++++.+| ..|.-.+|-.-||+ ..++.+.|-.|....
T Consensus 4 ~~ee~Il~~L~~~g-~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g 48 (66)
T PF02295_consen 4 DLEEKILDFLKELG-GSTATAIAKALGLSVPKKEVNRVLYRLEKQG 48 (66)
T ss_dssp HHHHHHHHHHHHHT-SSEEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred hHHHHHHHHHHhcC-CccHHHHHHHhCcchhHHHHHHHHHHHHHCC
Confidence 45689999999999 88888888877877 799999999997653
No 164
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=26.04 E-value=53 Score=29.40 Aligned_cols=32 Identities=16% Similarity=0.293 Sum_probs=24.1
Q ss_pred hhhHHHH----HHHHhcCCc-eeehhhhhhcCCCHHH
Q 016517 82 DVRNRAM----DAVDACNRR-VTIGDVAGKAGLKLNE 113 (388)
Q Consensus 82 ~~~~~im----~Ave~lg~r-vTvgDVAa~aGL~l~~ 113 (388)
+.|.+|+ +.+.+.||. +|+.|||..+|++...
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 4455554 456688995 7899999999998654
No 165
>PF11268 DUF3071: Protein of unknown function (DUF3071); InterPro: IPR021421 Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=25.90 E-value=75 Score=29.77 Aligned_cols=33 Identities=21% Similarity=0.381 Sum_probs=28.2
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHH
Q 016517 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQK 116 (388)
Q Consensus 82 ~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~ 116 (388)
.++||-+|+.=+.| .|+.|||..+|++++.+++
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 77899999877665 7999999999999998753
No 166
>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=25.83 E-value=2.6e+02 Score=26.18 Aligned_cols=27 Identities=15% Similarity=0.240 Sum_probs=23.8
Q ss_pred hcCCceeehhhhhhcCCCHHHHHHHHH
Q 016517 93 ACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (388)
Q Consensus 93 ~lg~rvTvgDVAa~aGL~l~~Ae~aL~ 119 (388)
++|...|+.+||.+.|++.+++++.+.
T Consensus 99 ~~g~~pt~~eia~~l~~~~~~v~~~~~ 125 (238)
T TIGR02393 99 ELGREPTDEELAERMGMPAEKVREIKK 125 (238)
T ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 468999999999999999999977654
No 167
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=25.82 E-value=90 Score=22.25 Aligned_cols=37 Identities=11% Similarity=0.239 Sum_probs=26.8
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHH
Q 016517 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQA 120 (388)
Q Consensus 81 ~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~a 120 (388)
..+...|++.+.+ ..|+.+||...|++-+.+++-+..
T Consensus 14 ~~~~~~i~~~~~~---~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 14 KRLEQYILKLLRE---SRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHHHhh---cCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3344455544444 379999999999999999876654
No 168
>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=25.77 E-value=1.2e+02 Score=23.94 Aligned_cols=21 Identities=19% Similarity=0.572 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 016517 177 FGTALIASIVIVFTAIIAILS 197 (388)
Q Consensus 177 FGi~LIaSIvLv~~aI~alls 197 (388)
+|++|++.|+++..++++...
T Consensus 7 iGviLliaitVilaavv~~~~ 27 (80)
T PF07790_consen 7 IGVILLIAITVILAAVVGAFV 27 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 688999999999988887763
No 169
>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=25.75 E-value=2.1e+02 Score=29.22 Aligned_cols=71 Identities=18% Similarity=0.209 Sum_probs=50.5
Q ss_pred chhhHHHHHHHHhc--CCceeehhhhhh-cCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc-ChhhHHHHhhh
Q 016517 81 ADVRNRAMDAVDAC--NRRVTIGDVAGK-AGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF-PNNYRAKLAAK 152 (388)
Q Consensus 81 ~~~~~~im~Ave~l--g~rvTvgDVAa~-aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~F-P~~fRs~l~~K 152 (388)
.++.++|.+.+.+. +..+|..|+... .++++.+...+|+.|.++---.|-. .+|.++|.. ++.-.+++.+-
T Consensus 8 ~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~-~~~~l~~~~~~~~~a~k~~~l 82 (327)
T PF05158_consen 8 SELEKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLK-KGGGLSYKAVSEEEAKKLKGL 82 (327)
T ss_dssp HHHHHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE--SSSEEEEE--SSS-----SS
T ss_pred HHHHHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEE-cCCEEEEEEeCHHHHhhhcCC
Confidence 35778999999998 999999999998 8899999999999999987666555 567799987 44444555553
No 170
>PF07845 DUF1636: Protein of unknown function (DUF1636); InterPro: IPR012863 The sequences featured in this family are derived from a number of hypothetical prokaryotic proteins. The region in question is approximately 130 amino acids long.
Probab=25.72 E-value=67 Score=28.26 Aligned_cols=32 Identities=31% Similarity=0.667 Sum_probs=25.9
Q ss_pred hhcccCCCCCCCChHHHHHHHHHHHHHhcCCeE
Q 016517 255 FSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVV 287 (388)
Q Consensus 255 FSFvFGDGDPN~dlEerRWk~Ig~~Ir~N~GvV 287 (388)
.+|||||=||.++.+.- -+-..+|..+..|.|
T Consensus 66 ~tYlfGdl~p~~~a~~i-l~~a~~Y~~s~dG~v 97 (116)
T PF07845_consen 66 WTYLFGDLDPDEDAEDI-LAFAALYAASPDGLV 97 (116)
T ss_pred cEEEEecCCcccCHHHH-HHHHHHHHhCCCCcc
Confidence 48999999999887766 566678889999944
No 171
>PF15581 Imm35: Immunity protein 35
Probab=25.51 E-value=1.2e+02 Score=26.22 Aligned_cols=33 Identities=27% Similarity=0.471 Sum_probs=30.0
Q ss_pred cCCCHHHHHHHHHHHHhhc-CCceEeccCCcEEE
Q 016517 107 AGLKLNEAQKALQALAADT-DGFLEVSDEGDVLY 139 (388)
Q Consensus 107 aGL~l~~Ae~aL~aLAaD~-~GhLqVsesGdIlY 139 (388)
-||+-.|+++-|.+.|+.- ++..+|-.+|+++.
T Consensus 44 RGl~~~qV~~kl~ava~~~~~~~~vvKkE~~~Iw 77 (93)
T PF15581_consen 44 RGLPEEQVLYKLEAVAAKGPEAKIVVKKEGNIIW 77 (93)
T ss_pred cCCCHHHHHHHHHHHHhcCCCcceEEEecCCeEE
Confidence 5999999999999999887 89999999998875
No 172
>PRK09526 lacI lac repressor; Reviewed
Probab=25.19 E-value=1.6e+02 Score=27.96 Aligned_cols=56 Identities=18% Similarity=0.155 Sum_probs=36.6
Q ss_pred CCCCchhhHHHHHHHHhcCCceeeh--hhhh-hcC--------C---CHHHHHHHHHHHHhhcCCceEec
Q 016517 77 DKLPADVRNRAMDAVDACNRRVTIG--DVAG-KAG--------L---KLNEAQKALQALAADTDGFLEVS 132 (388)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~rvTvg--DVAa-~aG--------L---~l~~Ae~aL~aLAaD~~GhLqVs 132 (388)
.++..+.|++|+++++++||..... .++. +++ + --.+.-+++.+.|.+.|-++.+.
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 4688999999999999999965321 1111 111 1 12455677778888888777653
No 173
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=25.14 E-value=49 Score=23.59 Aligned_cols=28 Identities=25% Similarity=0.342 Sum_probs=21.0
Q ss_pred HHHHHHhcCC-ceeehhhhhhcCCCHHHH
Q 016517 87 AMDAVDACNR-RVTIGDVAGKAGLKLNEA 114 (388)
Q Consensus 87 im~Ave~lg~-rvTvgDVAa~aGL~l~~A 114 (388)
..+.+.+.|+ .+|+.|||.++|++....
T Consensus 5 a~~l~~~~G~~~~s~~~Ia~~~gvs~~~~ 33 (47)
T PF00440_consen 5 ALELFAEKGYEAVSIRDIARRAGVSKGSF 33 (47)
T ss_dssp HHHHHHHHHTTTSSHHHHHHHHTSCHHHH
T ss_pred HHHHHHHhCHHhCCHHHHHHHHccchhhH
Confidence 4455566665 589999999999997654
No 174
>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=24.85 E-value=33 Score=28.63 Aligned_cols=49 Identities=29% Similarity=0.348 Sum_probs=34.5
Q ss_pred HHHHHHHHHhcCCeEeeeeccCccCCCCCCCCchhhhhHhhhcCCccccCCCcCEE
Q 016517 273 WKLIGEYIASNGGVVTAEELAPYLDIDRTMSDESYVLPVLLRFDGQPEIDEEGNIL 328 (388)
Q Consensus 273 Wk~Ig~~Ir~N~GvV~AEQLAPyLD~~~~~~~E~ymLpvL~rF~G~PeVse~G~IV 328 (388)
|..+-+.+.. |.-|+.++||.=++++. +-+-.+|...- ..|.+++|+||
T Consensus 26 ~r~LLr~LA~-G~PVt~~~LA~a~g~~~-----e~v~~~L~~~p-~tEyD~~GrIV 74 (77)
T PF12324_consen 26 LRPLLRLLAK-GQPVTVEQLAAALGWPV-----EEVRAALAAMP-DTEYDDQGRIV 74 (77)
T ss_dssp HHHHHHHHTT-TS-B-HHHHHHHHT--H-----HHHHHHHHH-T-TSEEETTSEEE
T ss_pred HHHHHHHHHc-CCCcCHHHHHHHHCCCH-----HHHHHHHHhCC-CceEcCCCCee
Confidence 6777788877 99999999999999753 33555666654 47889999998
No 175
>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=24.83 E-value=1.6e+02 Score=24.35 Aligned_cols=31 Identities=29% Similarity=0.325 Sum_probs=28.2
Q ss_pred cCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 94 CNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 94 lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
....+|..|+|..+|++...+.++|..|..+
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~ 74 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARR 74 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 5678899999999999999999999999875
No 176
>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=24.79 E-value=1.8e+02 Score=20.75 Aligned_cols=41 Identities=20% Similarity=0.321 Sum_probs=28.8
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHH
Q 016517 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQA 120 (388)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~a 120 (388)
+.||..-+.-|.... ....|..|||..-|+|...+.+-+..
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 77889999999999999999765443
No 177
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.43 E-value=80 Score=22.33 Aligned_cols=38 Identities=11% Similarity=0.231 Sum_probs=23.0
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHH
Q 016517 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (388)
Q Consensus 81 ~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (388)
+..|-.++..+.+ +.|+.+||...|++.+.+.+=+...
T Consensus 4 ~~~R~~ii~l~~~---G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 4 EERRAQIIRLLRE---GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp ------HHHHHHH---T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred hhHHHHHHHHHHC---CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 4556677777777 8899999999999999997665543
No 178
>PRK00441 argR arginine repressor; Provisional
Probab=24.39 E-value=2.1e+02 Score=25.96 Aligned_cols=56 Identities=13% Similarity=0.295 Sum_probs=42.2
Q ss_pred hHHHHHHHHhcCCceeehhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEe-ccCCcEEEEcChhh
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEV-SDEGDVLYVFPNNY 145 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~a-----GL~l~~Ae~aL~aLAaD~~GhLqV-sesGdIlY~FP~~f 145 (388)
+..|.+.+.+ ....|+.|++..- +.+-..+.+.|.+| |-.+| +++|.-.|..|.+-
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 4556666666 5566999999875 67777788888888 44677 58999999998864
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=24.38 E-value=90 Score=31.06 Aligned_cols=43 Identities=26% Similarity=0.295 Sum_probs=36.6
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLq 130 (388)
.++..+++++.+|.|-++=+...+|++..+|++.|. +++|||.
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 466788999999999999999999999999976654 6788875
No 180
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=24.17 E-value=55 Score=30.34 Aligned_cols=23 Identities=22% Similarity=0.221 Sum_probs=20.4
Q ss_pred CCCCchhhHHHHHHHHhcCCcee
Q 016517 77 DKLPADVRNRAMDAVDACNRRVT 99 (388)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~rvT 99 (388)
+++..+.|+||+++++++||+--
T Consensus 2 ~~Vs~~Tr~rV~~~a~elgY~pn 24 (309)
T PRK11041 2 EKVSQATRQRVEQAVLEVGYSPQ 24 (309)
T ss_pred CcCCHHHHHHHHHHHHHHCCCcC
Confidence 56788999999999999999864
No 181
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=24.12 E-value=2.4e+02 Score=28.15 Aligned_cols=86 Identities=21% Similarity=0.283 Sum_probs=48.1
Q ss_pred HHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE--eccCCcE-EEEc-C---hhhHHHHhhhhHHHhHHHHHH
Q 016517 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE--VSDEGDV-LYVF-P---NNYRAKLAAKSFRLKVEPVID 163 (388)
Q Consensus 91 ve~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLq--VsesGdI-lY~F-P---~~fRs~l~~Ks~r~rlq~~~~ 163 (388)
..++|...|+.++|...|++.++++..+.....+. .|. +.++++. +..+ | .+--..+.....+..++..++
T Consensus 178 ~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~--SLd~~~~~~~~~~l~~~~~d~~~~pe~~~~~~~~~~~l~~al~ 255 (317)
T PRK07405 178 SQQLGRAATIGELAEELELTPKQVREYLERARQPL--SLDLRVGDNQDTELGELLEDTGASPEDFATQSSLQLDLERLME 255 (317)
T ss_pred HHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCe--eecCCCCCCCCccHHHhhcCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999999987765433221 222 2222221 1111 1 111222334455666666666
Q ss_pred HHhhhhhHHHHHHHH
Q 016517 164 KAKAAAEYSIRVLFG 178 (388)
Q Consensus 164 k~w~v~~yliRVsFG 178 (388)
.+-.--.-+++..||
T Consensus 256 ~L~~rer~Vi~lr~g 270 (317)
T PRK07405 256 DLTPQQKEVIALRFG 270 (317)
T ss_pred cCCHHHHHHHHHHhh
Confidence 555544555665655
No 182
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=24.09 E-value=46 Score=27.61 Aligned_cols=33 Identities=21% Similarity=0.307 Sum_probs=25.6
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHH
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL 118 (388)
+..|+-++++.| .|+.++|.++||+-+....+|
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 467888998887 799999999999998887766
No 183
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=23.94 E-value=2.4e+02 Score=27.21 Aligned_cols=44 Identities=23% Similarity=0.272 Sum_probs=32.3
Q ss_pred CCCchhhHHH---HHH----HHhcCCceeehhhhhhcCCCHHHHHHHHHHH
Q 016517 78 KLPADVRNRA---MDA----VDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (388)
Q Consensus 78 ~l~~~~~~~i---m~A----ve~lg~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (388)
++|...++.+ .++ -.++|...|..+||...|++.++.++.+.+.
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 4676655432 222 2367889999999999999999998877653
No 184
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=23.93 E-value=2.2e+02 Score=26.92 Aligned_cols=56 Identities=9% Similarity=0.104 Sum_probs=35.5
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhc-----------CCC---HHHHHHHHHHHHhhcCCceEec
Q 016517 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKA-----------GLK---LNEAQKALQALAADTDGFLEVS 132 (388)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~rvTvgDVAa~a-----------GL~---l~~Ae~aL~aLAaD~~GhLqVs 132 (388)
.++..+.|+||+++++++||+.-..--+.++ .++ -.+.-+++..-|.+.|-++.+.
T Consensus 30 ~~vs~~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~ 99 (331)
T PRK14987 30 EQVSVALRGKIAAALDELGYIPNRAPDILSNATSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQTMLA 99 (331)
T ss_pred CCCCHHHHHHHHHHHHHhCCCccHHHHHHhhCCCCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEEEEe
Confidence 4678899999999999999964221111111 111 3445567777777777666553
No 185
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=23.49 E-value=60 Score=29.36 Aligned_cols=32 Identities=22% Similarity=0.333 Sum_probs=23.7
Q ss_pred chhhHHHHHHH-----HhcCC-ceeehhhhhhcCCCHH
Q 016517 81 ADVRNRAMDAV-----DACNR-RVTIGDVAGKAGLKLN 112 (388)
Q Consensus 81 ~~~~~~im~Av-----e~lg~-rvTvgDVAa~aGL~l~ 112 (388)
...|++|++|. .+.|| .+|+.|||.++|++..
T Consensus 10 ~~~R~~Il~aA~~~l~~~~G~~~~si~~IA~~Agvs~~ 47 (203)
T PRK11202 10 EKTRRALIDAAFSQLSAERSFSSLSLREVAREAGIAPT 47 (203)
T ss_pred HHHHHHHHHHHHHHHHhcCCcccCCHHHHHHHhCCCcc
Confidence 35677877654 34476 7999999999998753
No 186
>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=23.16 E-value=53 Score=30.97 Aligned_cols=21 Identities=29% Similarity=0.414 Sum_probs=18.3
Q ss_pred eehhhhhhcCCCHHHHHHHHH
Q 016517 99 TIGDVAGKAGLKLNEAQKALQ 119 (388)
Q Consensus 99 TvgDVAa~aGL~l~~Ae~aL~ 119 (388)
|+.|||..||+|..++-+.|.
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn 21 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVIN 21 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHc
Confidence 678999999999998887774
No 187
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=23.15 E-value=84 Score=28.60 Aligned_cols=53 Identities=19% Similarity=0.310 Sum_probs=40.3
Q ss_pred CchhhHHHHHHHHhcC--------------CceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC
Q 016517 80 PADVRNRAMDAVDACN--------------RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (388)
Q Consensus 80 ~~~~~~~im~Ave~lg--------------~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVses 134 (388)
..++++|+...+..+. ..+|..|+|...|++...+.+.|..|..+ |-++....
T Consensus 153 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~~--g~I~~~~~ 219 (235)
T PRK11161 153 KKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKS--GMLAVKGK 219 (235)
T ss_pred CCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHHC--CCEEecCC
Confidence 3567788877776542 34788999999999999999999988764 56665543
No 188
>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=22.90 E-value=3.2e+02 Score=26.70 Aligned_cols=30 Identities=17% Similarity=0.206 Sum_probs=25.5
Q ss_pred HhcCCceeehhhhhhcCCCHHHHHHHHHHH
Q 016517 92 DACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (388)
Q Consensus 92 e~lg~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (388)
..+|...|..++|...|++.++++..+...
T Consensus 172 ~~~~~~pt~~eia~~l~~~~~~v~~~~~~~ 201 (298)
T TIGR02997 172 QKLGRTPSEAEIAEALELEPEQVRELLQRA 201 (298)
T ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 457888999999999999999998776543
No 189
>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=22.81 E-value=1.5e+02 Score=23.46 Aligned_cols=44 Identities=23% Similarity=0.287 Sum_probs=31.0
Q ss_pred HHHHHHhcCC--ceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEec
Q 016517 87 AMDAVDACNR--RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (388)
Q Consensus 87 im~Ave~lg~--rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVs 132 (388)
+|-.+...+. .+|+.|+|.+.|++...+++-|..|.. .|-|+..
T Consensus 13 ~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~--~Gli~s~ 58 (83)
T PF02082_consen 13 ILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKK--AGLIESS 58 (83)
T ss_dssp HHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEE
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhh--CCeeEec
Confidence 3444443333 399999999999999999999999987 3445443
No 190
>PRK05949 RNA polymerase sigma factor; Validated
Probab=22.71 E-value=2.8e+02 Score=27.99 Aligned_cols=86 Identities=16% Similarity=0.206 Sum_probs=48.5
Q ss_pred HHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE--eccCCc-----EEEEcChhhHHHHhhhhHHHhHHHHHH
Q 016517 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE--VSDEGD-----VLYVFPNNYRAKLAAKSFRLKVEPVID 163 (388)
Q Consensus 91 ve~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLq--VsesGd-----IlY~FP~~fRs~l~~Ks~r~rlq~~~~ 163 (388)
..++|...|+.++|...|++.++++..+. .+.+. -.|. +.++++ ++=.-..+--..+.....+..++.+++
T Consensus 188 ~~~lgr~pt~~eiA~~l~i~~~~v~~~~~-~~~~~-~SLd~~~~~~~~~~l~~~l~d~~~~pe~~~~~~~~~~~L~~~L~ 265 (327)
T PRK05949 188 SQKLGRSATPAEIAKELELEPSQIREYLS-MARQP-ISLDVRVGDNQDTELSELLEDEGPSPDQYITQELLRQDLNNLLA 265 (327)
T ss_pred HHHhCCCCCHHHHHHHhCcCHHHHHHHHH-Hhccc-cccCCCcCCCCCccHHhhcCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 35679999999999999999999977553 33221 1111 222222 221111111223344455666777776
Q ss_pred HHhhhhhHHHHHHHH
Q 016517 164 KAKAAAEYSIRVLFG 178 (388)
Q Consensus 164 k~w~v~~yliRVsFG 178 (388)
.+-.-=..+++..||
T Consensus 266 ~L~~rer~Vi~lr~g 280 (327)
T PRK05949 266 ELTPQQREVLTLRFG 280 (327)
T ss_pred hCCHHHHHHHHHHhc
Confidence 666655566665555
No 191
>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=22.62 E-value=2.3e+02 Score=21.52 Aligned_cols=36 Identities=14% Similarity=0.211 Sum_probs=29.6
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 016517 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (388)
Q Consensus 86 ~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAa 123 (388)
+|++.+.. ...|+.++|.+.|++...+.+.|..|-+
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 45666553 3578999999999999999999999955
No 192
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=22.54 E-value=2.4e+02 Score=26.74 Aligned_cols=23 Identities=9% Similarity=0.149 Sum_probs=20.5
Q ss_pred CCCCchhhHHHHHHHHhcCCcee
Q 016517 77 DKLPADVRNRAMDAVDACNRRVT 99 (388)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~rvT 99 (388)
.++..+.|++|+++++++||.-.
T Consensus 31 ~~vs~~tr~~V~~~a~elgY~p~ 53 (342)
T PRK10014 31 GRISTATGERVNQAIEELGFVRN 53 (342)
T ss_pred CCCCHHHHHHHHHHHHHhCCCcC
Confidence 46889999999999999999764
No 193
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=22.53 E-value=3e+02 Score=28.01 Aligned_cols=85 Identities=22% Similarity=0.314 Sum_probs=46.5
Q ss_pred HhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE--eccCCcE-EEEcCh-----hhHHHHhhhhHHHhHHHHHH
Q 016517 92 DACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE--VSDEGDV-LYVFPN-----NYRAKLAAKSFRLKVEPVID 163 (388)
Q Consensus 92 e~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLq--VsesGdI-lY~FP~-----~fRs~l~~Ks~r~rlq~~~~ 163 (388)
..+|...|+.+||...|++.++++..+. ++.+. -.|+ +.++++. +..|-. +--..+.....+..++.++.
T Consensus 227 ~~lgr~pt~~EiA~~l~~~~~~v~~~~~-~~~~~-~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~l~ 304 (367)
T PRK09210 227 QELGREPTPEEIAEEMDMPPEKVREILK-IAQEP-VSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLD 304 (367)
T ss_pred HHhCCCCCHHHHHHHhCcCHHHHHHHHH-HhcCC-CCcCCCCCCCCcchhhhhccCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 4579999999999999999999976554 44321 1222 2233321 222210 11122234445556666666
Q ss_pred HHhhhhhHHHHHHHH
Q 016517 164 KAKAAAEYSIRVLFG 178 (388)
Q Consensus 164 k~w~v~~yliRVsFG 178 (388)
.+-.-=..+++--||
T Consensus 305 ~L~~rEr~Vl~lryg 319 (367)
T PRK09210 305 TLTDREENVLRLRFG 319 (367)
T ss_pred hCCHHHHHHHHHHhc
Confidence 554444444544444
No 194
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=22.47 E-value=61 Score=25.10 Aligned_cols=21 Identities=38% Similarity=0.452 Sum_probs=17.5
Q ss_pred eeehhhhhhcCCCHHHHHHHH
Q 016517 98 VTIGDVAGKAGLKLNEAQKAL 118 (388)
Q Consensus 98 vTvgDVAa~aGL~l~~Ae~aL 118 (388)
+|+.|+|.++|++...+-+.|
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~l 21 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVL 21 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 478899999999999986655
No 195
>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=22.46 E-value=1.3e+02 Score=25.09 Aligned_cols=45 Identities=16% Similarity=0.167 Sum_probs=37.5
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEec
Q 016517 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (388)
Q Consensus 85 ~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVs 132 (388)
=.|+.++.+.+ ..|+.|+|...|++...+-+.|..|..+ |-++-.
T Consensus 31 ~~iL~~l~~~~-~~t~~ela~~~~~~~~tvs~~l~~Le~~--GlI~r~ 75 (118)
T TIGR02337 31 WRILRILAEQG-SMEFTQLANQACILRPSLTGILARLERD--GLVTRL 75 (118)
T ss_pred HHHHHHHHHcC-CcCHHHHHHHhCCCchhHHHHHHHHHHC--CCEEec
Confidence 36788887754 6999999999999999999999999877 666654
No 196
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=22.43 E-value=2.1e+02 Score=27.19 Aligned_cols=44 Identities=18% Similarity=0.307 Sum_probs=32.1
Q ss_pred CCCchhhHHH---HHHH----HhcCCceeehhhhhhcCCCHHHHHHHHHHH
Q 016517 78 KLPADVRNRA---MDAV----DACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (388)
Q Consensus 78 ~l~~~~~~~i---m~Av----e~lg~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (388)
++|...+... .++. .++|...|+.++|...|++..+..+.+...
T Consensus 113 rip~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~ 163 (258)
T PRK08215 113 RVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAI 163 (258)
T ss_pred EecHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhc
Confidence 5666555443 2232 467889999999999999999998877543
No 197
>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=22.40 E-value=1.6e+02 Score=27.07 Aligned_cols=43 Identities=30% Similarity=0.413 Sum_probs=33.0
Q ss_pred hcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc---CCceEeccCCc
Q 016517 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADT---DGFLEVSDEGD 136 (388)
Q Consensus 93 ~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~---~GhLqVsesGd 136 (388)
-.|..||+.++|...| +.+++++.|..|..++ +.-|++-+.|+
T Consensus 9 ~s~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~ 54 (159)
T PF04079_consen 9 ASGEPVSIEELAEILG-SEDEVEEALEELQEEYNEEDRGLELVEVGG 54 (159)
T ss_dssp H-SS-B-HHHHHHHCT--HHHHHHHHHHHHHHHHHCT-SEEEEEETT
T ss_pred HcCCCCCHHHHHHHhC-CHHHHHHHHHHHHHHhccCCCCEEEEEECC
Confidence 3556799999999999 9999999999999999 66777777554
No 198
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=22.28 E-value=52 Score=31.61 Aligned_cols=25 Identities=36% Similarity=0.571 Sum_probs=20.2
Q ss_pred CCccccCCCcCEEEecCccchhhhh
Q 016517 316 DGQPEIDEEGNILYRFPSFQRTAAS 340 (388)
Q Consensus 316 ~G~PeVse~G~IVY~FPeLq~TA~~ 340 (388)
+--=|+++.|+-||-||+.|.+.+.
T Consensus 11 ~~iyd~~~~~EgVylfPS~qk~~~~ 35 (200)
T PF12387_consen 11 NSIYDIDESGEGVYLFPSRQKGGSC 35 (200)
T ss_pred cceeeecCCCceEEEccccccCCCC
Confidence 3445788999999999999988643
No 199
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=22.26 E-value=1.9e+02 Score=27.29 Aligned_cols=51 Identities=20% Similarity=0.210 Sum_probs=38.6
Q ss_pred HHHHHHH-HhcCCceeehhhhhhcCC-CHHHHHHHHHHHHhhc---CCceEeccCC
Q 016517 85 NRAMDAV-DACNRRVTIGDVAGKAGL-KLNEAQKALQALAADT---DGFLEVSDEG 135 (388)
Q Consensus 85 ~~im~Av-e~lg~rvTvgDVAa~aGL-~l~~Ae~aL~aLAaD~---~GhLqVsesG 135 (388)
.+++.|+ =..+..+|+.++|...|+ +..++...|..|..++ |-.|++..+|
T Consensus 10 ~~~vEall~a~~~pls~~~L~~il~~~~~~~~~~~l~~l~~~y~~rg~~L~~~~~~ 65 (184)
T COG1386 10 KALIEALLFAGGEPLSLKELAEILGIVSADAIIDALAELKEEYEDRGLELVEVAEG 65 (184)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCeeEEEEcCc
Confidence 4444444 455669999999999999 8888999999999887 4456655554
No 200
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=22.20 E-value=96 Score=33.32 Aligned_cols=38 Identities=13% Similarity=0.298 Sum_probs=34.4
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHH
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aL 121 (388)
+..|++.+.+....+|+.|++..||+..+++-.+|+.|
T Consensus 361 ~~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l 398 (450)
T PLN00104 361 TRVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSL 398 (450)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 46788888888889999999999999999998888876
No 201
>PRK00215 LexA repressor; Validated
Probab=22.19 E-value=1.4e+02 Score=27.34 Aligned_cols=48 Identities=19% Similarity=0.351 Sum_probs=36.6
Q ss_pred hHHHHHHH----HhcCCceeehhhhhhcCC-CHHHHHHHHHHHHhhcCCceEecc
Q 016517 84 RNRAMDAV----DACNRRVTIGDVAGKAGL-KLNEAQKALQALAADTDGFLEVSD 133 (388)
Q Consensus 84 ~~~im~Av----e~lg~rvTvgDVAa~aGL-~l~~Ae~aL~aLAaD~~GhLqVse 133 (388)
+..+++.+ ++.+...|+.|+|...|+ +...+.+-|..|... |.|+-..
T Consensus 6 q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~--g~i~~~~ 58 (205)
T PRK00215 6 QQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERK--GFIRRDP 58 (205)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC--CCEEeCC
Confidence 34455555 456888999999999999 999999988888654 6665543
No 202
>PF13518 HTH_28: Helix-turn-helix domain
Probab=22.16 E-value=1.7e+02 Score=20.41 Aligned_cols=36 Identities=8% Similarity=0.183 Sum_probs=26.7
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHH
Q 016517 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALA 122 (388)
Q Consensus 84 ~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLA 122 (388)
+-+|++.+.+ |. |+.++|.+-|++..++.+=+...-
T Consensus 2 r~~iv~~~~~-g~--s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 2 RLQIVELYLE-GE--SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHHHHHc-CC--CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 3467777773 43 999999999999998866555443
No 203
>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=22.13 E-value=1.4e+02 Score=25.97 Aligned_cols=61 Identities=16% Similarity=0.303 Sum_probs=39.1
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCh
Q 016517 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (388)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~ 143 (388)
..+-.+.|.+|.+.+++.=..+++.++|.-.|++. .+|..++.+.| =+++++|.++...|+
T Consensus 77 ~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg~~~----~el~~~~~~~g--W~~d~~~~~~~~~~~ 137 (143)
T PF10075_consen 77 PGFEDTIRERIAHLISKAYSSISLSDLAEMLGLSE----EELEKFIKSRG--WTVDGDGVLFPPNPE 137 (143)
T ss_dssp TTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTTS-H----HHHHHHHHHHT---EE-----EE---HH
T ss_pred HHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhCCCH----HHHHHHHHHcC--CEECCCccEEecCCc
Confidence 45667899999999999999999999999999993 36677777763 455566666555554
No 204
>PF13038 DUF3899: Domain of unknown function (DUF3899)
Probab=22.08 E-value=94 Score=25.27 Aligned_cols=33 Identities=18% Similarity=0.304 Sum_probs=18.3
Q ss_pred HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016517 163 DKAKAAAEYSIRVLFGTALIASIVIVFTAIIAI 195 (388)
Q Consensus 163 ~k~w~v~~yliRVsFGi~LIaSIvLv~~aI~al 195 (388)
++-++--.+.+.-|....|+++++++.++|++.
T Consensus 58 ~~~~~~~~~~~~~~~~~~ll~~~ll~l~~iil~ 90 (92)
T PF13038_consen 58 DKKLKKEKYRVSRWTYPLLLIGLLLILLSIILS 90 (92)
T ss_pred hHHHHHhhhHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444455555555566666666666665543
No 205
>PRK00441 argR arginine repressor; Provisional
Probab=22.08 E-value=90 Score=28.29 Aligned_cols=64 Identities=23% Similarity=0.120 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHhcCCeEeeeeccCccCCCCCCCCchhhhhHhhhcCCcccc-CCCcCEEEecCccc
Q 016517 270 EKRWKLIGEYIASNGGVVTAEELAPYLDIDRTMSDESYVLPVLLRFDGQPEI-DEEGNILYRFPSFQ 335 (388)
Q Consensus 270 erRWk~Ig~~Ir~N~GvV~AEQLAPyLD~~~~~~~E~ymLpvL~rF~G~PeV-se~G~IVY~FPeLq 335 (388)
++|.+.|-++|++ +|+++-+||+-.|-...-.-.+.-+-+=|... |-.+| +++|+-.|..|.=+
T Consensus 3 ~~R~~~I~~ll~~-~~~~~q~eL~~~L~~~G~~vSqaTisRDl~~L-~lvKv~~~~G~~~Y~l~~~~ 67 (149)
T PRK00441 3 VSRHAKILEIINS-KEIETQEELAEELKKMGFDVTQATVSRDIKEL-KLIKVLSNDGKYKYATISKT 67 (149)
T ss_pred HHHHHHHHHHHHH-cCCCcHHHHHHHHHhcCCCcCHHHHHHHHHHc-CcEEeECCCCCEEEEeCccc
Confidence 4689999999988 56789999999983211011333343434333 45666 68999999988633
No 206
>COG5346 Predicted membrane protein [Function unknown]
Probab=21.95 E-value=4.2e+02 Score=24.34 Aligned_cols=27 Identities=11% Similarity=0.112 Sum_probs=15.8
Q ss_pred hhhhhhcCCCHHHHHHHHHHHHhhcCCc
Q 016517 101 GDVAGKAGLKLNEAQKALQALAADTDGF 128 (388)
Q Consensus 101 gDVAa~aGL~l~~Ae~aL~aLAaD~~Gh 128 (388)
-|++..-.+=.+.+ +.+.+.|....+|
T Consensus 42 ~~l~qYnsI~pnt~-~rimaMAekEQah 68 (136)
T COG5346 42 DLLSQYNSIYPNTL-QRIMAMAEKEQAH 68 (136)
T ss_pred HHHHHHHhhcCCHH-HHHHHHHHHHHHH
Confidence 34555555555666 5567777776543
No 207
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=21.73 E-value=70 Score=29.32 Aligned_cols=41 Identities=17% Similarity=0.352 Sum_probs=34.4
Q ss_pred hcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc-CC
Q 016517 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EG 135 (388)
Q Consensus 93 ~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVse-sG 135 (388)
+-|.+++..++|.+-|+|..-++.+|..|.++ |-+++.. .|
T Consensus 26 ~pG~~L~e~eLae~lgVSRtpVREAL~~L~~e--Glv~~~~~~G 67 (224)
T PRK11534 26 QPDEKLRMSLLTSRYALGVGPLREALSQLVAE--RLVTVVNQKG 67 (224)
T ss_pred CCCCcCCHHHHHHHHCCChHHHHHHHHHHHHC--CCEEEeCCCc
Confidence 34789999999999999999999999999864 7777554 45
No 208
>PHA01976 helix-turn-helix protein
Probab=21.69 E-value=1.2e+02 Score=22.46 Aligned_cols=32 Identities=13% Similarity=0.158 Sum_probs=23.7
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHH
Q 016517 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEA 114 (388)
Q Consensus 81 ~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~A 114 (388)
|+.-.++-++-++.| .|..|+|...|++....
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 455667766666655 79999999999986554
No 209
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=21.66 E-value=1.9e+02 Score=26.51 Aligned_cols=51 Identities=18% Similarity=0.147 Sum_probs=39.8
Q ss_pred chhhHHHHHHHHhc----CCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 016517 81 ADVRNRAMDAVDAC----NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (388)
Q Consensus 81 ~~~~~~im~Ave~l----g~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVse 133 (388)
.++++|+...+..+ ....|..|+|...|++...+-+.|..|..+ |-+++..
T Consensus 149 ~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~--G~I~~~~ 203 (226)
T PRK10402 149 FPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQD--GYLKKSK 203 (226)
T ss_pred ChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHC--CCEEeeC
Confidence 46788888887653 233588999999999999999999999875 5566643
No 210
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=21.55 E-value=52 Score=31.75 Aligned_cols=31 Identities=32% Similarity=0.464 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHhcCCeEeeeeccCccCCCC
Q 016517 269 EEKRWKLIGEYIASNGGVVTAEELAPYLDIDR 300 (388)
Q Consensus 269 EerRWk~Ig~~Ir~N~GvV~AEQLAPyLD~~~ 300 (388)
.++|++.|.+++++ +|.|+.+||+-.+++..
T Consensus 3 ~~eR~~~Il~~l~~-~g~v~v~eLa~~~~VS~ 33 (253)
T COG1349 3 KEERHQKILELLKE-KGKVSVEELAELFGVSE 33 (253)
T ss_pred hHHHHHHHHHHHHH-cCcEEHHHHHHHhCCCH
Confidence 46789999999998 67899999999999874
No 211
>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=21.48 E-value=54 Score=28.33 Aligned_cols=33 Identities=21% Similarity=0.297 Sum_probs=23.7
Q ss_pred hhhHHHH----HHHHhcCC-ceeehhhhhhcCCCHHHH
Q 016517 82 DVRNRAM----DAVDACNR-RVTIGDVAGKAGLKLNEA 114 (388)
Q Consensus 82 ~~~~~im----~Ave~lg~-rvTvgDVAa~aGL~l~~A 114 (388)
.-|++|+ +.+.+.|| .+|+.|||.++|++....
T Consensus 8 ~rr~~Il~aA~~lf~~~G~~~~s~~~IA~~agvsk~~l 45 (189)
T TIGR03384 8 IRRAELIDATIESIGERGSLDVTIAQIARRAGVSSGII 45 (189)
T ss_pred HHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCCHHHH
Confidence 3445554 45566775 688999999999987543
No 212
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=21.47 E-value=1.8e+02 Score=28.78 Aligned_cols=69 Identities=16% Similarity=0.229 Sum_probs=51.5
Q ss_pred ccccCCCCchhh----HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcC--CceEeccCCcEEEEc
Q 016517 73 IVESDKLPADVR----NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTD--GFLEVSDEGDVLYVF 141 (388)
Q Consensus 73 ~~~~~~l~~~~~----~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~--GhLqVsesGdIlY~F 141 (388)
...-+.||.-++ .+|+++++..+...|.-++|...|+|--.|++=|.-|++-.- ..|+-...|.+.|.+
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 455566774444 467888888899999999999999999999999999998653 333333466666554
No 213
>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=21.47 E-value=2.3e+02 Score=22.12 Aligned_cols=50 Identities=18% Similarity=0.312 Sum_probs=41.1
Q ss_pred cCCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 016517 76 SDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (388)
Q Consensus 76 ~~~l~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~ 125 (388)
.+.|...++.+.+..+-+--.++++.++|...+++.+++|.-|..+..+-
T Consensus 39 ~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~ 88 (105)
T PF01399_consen 39 VEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLISNG 88 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHHCC
Confidence 34555667777787888888899999999999999999999999888765
No 214
>PRK04217 hypothetical protein; Provisional
Probab=21.32 E-value=1.6e+02 Score=25.73 Aligned_cols=43 Identities=12% Similarity=0.132 Sum_probs=29.3
Q ss_pred cCCCCchhhHHHHHHHHhcC-CceeehhhhhhcCCCHHHHHHHHHHHH
Q 016517 76 SDKLPADVRNRAMDAVDACN-RRVTIGDVAGKAGLKLNEAQKALQALA 122 (388)
Q Consensus 76 ~~~l~~~~~~~im~Ave~lg-~rvTvgDVAa~aGL~l~~Ae~aL~aLA 122 (388)
..+|+.+-+ +++.... ...|+.|||...|++.+.+.+-|....
T Consensus 40 ~~~Lt~eer----eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RAr 83 (110)
T PRK04217 40 PIFMTYEEF----EALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSAR 83 (110)
T ss_pred cccCCHHHH----HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 445555543 4444444 556999999999999998877665433
No 215
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=21.16 E-value=2e+02 Score=21.26 Aligned_cols=58 Identities=21% Similarity=0.361 Sum_probs=43.6
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEE
Q 016517 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (388)
Q Consensus 80 ~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~ 140 (388)
....|-+|+..+.+. ...|+.+++...|++...+...|..|-.. |-+....+|...|.
T Consensus 23 ~~~~r~~il~~l~~~-~~~~~~~l~~~~~~~~~~v~~hL~~L~~~--glv~~~~~~~~~~~ 80 (110)
T COG0640 23 ADPTRLEILSLLAEG-GELTVGELAEALGLSQSTVSHHLKVLREA--GLVELRREGRLRLY 80 (110)
T ss_pred CCHHHHHHHHHHHhc-CCccHHHHHHHHCCChhHHHHHHHHHHHC--CCeEEEecccEEEE
Confidence 334678888888887 78899999999999999999999987654 33444555555443
No 216
>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=21.09 E-value=1.4e+02 Score=22.77 Aligned_cols=33 Identities=21% Similarity=0.344 Sum_probs=24.1
Q ss_pred HHHHHHHhcCC-ceeehhhhhhcCCCHHHHHHHH
Q 016517 86 RAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKAL 118 (388)
Q Consensus 86 ~im~Ave~lg~-rvTvgDVAa~aGL~l~~Ae~aL 118 (388)
++++.++..|. +|+-.++|...|++..++++.|
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 34566666665 7788899999999999999876
No 217
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=21.06 E-value=2e+02 Score=27.32 Aligned_cols=56 Identities=14% Similarity=0.099 Sum_probs=36.5
Q ss_pred CCCCchhhHHHHHHHHhcCCceee-------------hhhhhhc-CCCHHHHHHHHHHHHhhcCCceEec
Q 016517 77 DKLPADVRNRAMDAVDACNRRVTI-------------GDVAGKA-GLKLNEAQKALQALAADTDGFLEVS 132 (388)
Q Consensus 77 ~~l~~~~~~~im~Ave~lg~rvTv-------------gDVAa~a-GL~l~~Ae~aL~aLAaD~~GhLqVs 132 (388)
.+++.+.|++|+++++++||..-. |=+.... ..--.+.-+++...|.+.|-++.+.
T Consensus 26 ~~vs~~tr~~V~~~a~elgY~pn~~a~~l~~~~~~~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~ 95 (341)
T PRK10703 26 RFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAPYFAEIIEAVEKNCYQKGYTLILC 95 (341)
T ss_pred CCCCHHHHHHHHHHHHHHCCCcCHHHHHHhhCCCCeEEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEE
Confidence 368899999999999999997632 2111111 1223445577777788777665543
No 218
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=20.99 E-value=1.8e+02 Score=23.17 Aligned_cols=38 Identities=18% Similarity=0.318 Sum_probs=26.1
Q ss_pred CCceeehhhhhhcCCCHHHHHH------------HHHHHHhhcCCceEec
Q 016517 95 NRRVTIGDVAGKAGLKLNEAQK------------ALQALAADTDGFLEVS 132 (388)
Q Consensus 95 g~rvTvgDVAa~aGL~l~~Ae~------------aL~aLAaD~~GhLqVs 132 (388)
....|..|+|...|++-...-+ .|..++...|+++++.
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 4667778888888874
No 219
>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=20.85 E-value=78 Score=28.64 Aligned_cols=58 Identities=14% Similarity=0.280 Sum_probs=42.5
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc-CCcEEEEc
Q 016517 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYVF 141 (388)
Q Consensus 82 ~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVse-sGdIlY~F 141 (388)
.++.+|++--=+-|.+++-.++|.+-|+|..-++.+|..|+++ |-|++.. .|-.|-.+
T Consensus 19 ~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~e--Glv~~~~~~G~~V~~~ 77 (212)
T TIGR03338 19 EIERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEA--GLVRNEKNRGVFVREI 77 (212)
T ss_pred HHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHC--CCEEEecCCCeEEecC
Confidence 3444444443456888999999999999999999999999864 7777654 45544444
No 220
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=20.82 E-value=1.9e+02 Score=27.19 Aligned_cols=22 Identities=14% Similarity=0.214 Sum_probs=19.7
Q ss_pred CCCchhhHHHHHHHHhcCCcee
Q 016517 78 KLPADVRNRAMDAVDACNRRVT 99 (388)
Q Consensus 78 ~l~~~~~~~im~Ave~lg~rvT 99 (388)
+++.+.|+||+++++++||+..
T Consensus 29 ~Vs~~tr~rV~~~a~elgY~pn 50 (328)
T PRK11303 29 RVSDKTVEKVMAVVREHNYHPN 50 (328)
T ss_pred CcCHHHHHHHHHHHHHhCCCCC
Confidence 5889999999999999999753
No 221
>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=20.81 E-value=62 Score=22.97 Aligned_cols=16 Identities=38% Similarity=0.468 Sum_probs=13.1
Q ss_pred eehhhhhhcCCCHHHH
Q 016517 99 TIGDVAGKAGLKLNEA 114 (388)
Q Consensus 99 TvgDVAa~aGL~l~~A 114 (388)
|+|+||..+|++....
T Consensus 1 ti~e~A~~~gvs~~tl 16 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTL 16 (38)
T ss_dssp EHHHHHHHHTS-HHHH
T ss_pred CHHHHHHHHCCCHHHH
Confidence 7899999999998765
No 222
>PF13730 HTH_36: Helix-turn-helix domain
Probab=20.72 E-value=1e+02 Score=22.26 Aligned_cols=25 Identities=20% Similarity=0.320 Sum_probs=22.8
Q ss_pred eehhhhhhcCCCHHHHHHHHHHHHh
Q 016517 99 TIGDVAGKAGLKLNEAQKALQALAA 123 (388)
Q Consensus 99 TvgDVAa~aGL~l~~Ae~aL~aLAa 123 (388)
+...+|...|++.+.++++|..|..
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5789999999999999999999875
No 223
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=20.69 E-value=92 Score=25.71 Aligned_cols=49 Identities=24% Similarity=0.271 Sum_probs=32.8
Q ss_pred hcCCceeehhhhhhcCCCHHHHHHHHHH-HHhhcCCceEeccCCcEEEEcChh
Q 016517 93 ACNRRVTIGDVAGKAGLKLNEAQKALQA-LAADTDGFLEVSDEGDVLYVFPNN 144 (388)
Q Consensus 93 ~lg~rvTvgDVAa~aGL~l~~Ae~aL~a-LAaD~~GhLqVsesGdIlY~FP~~ 144 (388)
.+....|++|+....|++..|+..-|.. -..+-+ .+=.+||.|.+||..
T Consensus 28 ~~~~~~tvkd~IEsLGVP~tEV~~i~vNG~~v~~~---~~~~~Gd~v~V~P~~ 77 (81)
T PF14451_consen 28 PFDGGATVKDVIESLGVPHTEVGLILVNGRPVDFD---YRLKDGDRVAVYPVF 77 (81)
T ss_pred ecCCCCcHHHHHHHcCCChHHeEEEEECCEECCCc---ccCCCCCEEEEEecc
Confidence 5677899999999999999998322100 000001 234589999999853
No 224
>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=20.58 E-value=96 Score=29.18 Aligned_cols=41 Identities=22% Similarity=0.323 Sum_probs=32.3
Q ss_pred HHHHHHHHhc------CCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 016517 85 NRAMDAVDAC------NRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (388)
Q Consensus 85 ~~im~Ave~l------g~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~ 125 (388)
|+..+.+.+. |+..|+.+++...|+++++.-++|.++++..
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 4455555554 4567999999999999999999999998544
No 225
>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=20.58 E-value=1.5e+02 Score=27.80 Aligned_cols=43 Identities=21% Similarity=0.381 Sum_probs=37.1
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 016517 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (388)
Q Consensus 79 l~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD 124 (388)
|+.++|..|.+-+.+.|. |+-.||.+-|+++.-+ .|++.|-..
T Consensus 17 lse~~r~~Iy~~~~~~~~--sv~~vS~~ygi~~~RV-~AIvrLkei 59 (172)
T PF12298_consen 17 LSEELREQIYEDVMQDGK--SVREVSQKYGIKIQRV-EAIVRLKEI 59 (172)
T ss_pred CCHHHHHHHHHHHHhCCC--CHHHHHHHhCCCHHHH-HHHHHHHHH
Confidence 677899999999998888 9999999999999999 666666543
No 226
>PF05781 MRVI1: MRVI1 protein; InterPro: IPR008677 This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene []. IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP []. Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins [].
Probab=20.29 E-value=2.9e+02 Score=30.55 Aligned_cols=44 Identities=16% Similarity=0.230 Sum_probs=21.2
Q ss_pred hhHHHhHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 016517 152 KSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSS 198 (388)
Q Consensus 152 Ks~r~rlq~~~~k~w~v~~yliRVsFGi~LIaSIvLv~~aI~allss 198 (388)
++.-.+++.|+.-++..+-=+-|+ +-+.+.+++|+.+|+.++.+
T Consensus 456 ~s~~srves~~~~Lk~s~pKanK~---LWIsvAliVLLAaLlSfLtg 499 (538)
T PF05781_consen 456 SSRYSRVESWASYLKTSFPKANKV---LWISVALIVLLAALLSFLTG 499 (538)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHhc
Confidence 344445666666555444433343 22333344555555556543
No 227
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=20.11 E-value=1.9e+02 Score=24.73 Aligned_cols=43 Identities=16% Similarity=0.367 Sum_probs=36.4
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 016517 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (388)
Q Consensus 82 ~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~ 125 (388)
+...+|++.+++-+. .+..++|.+.|+|...+..-+..|-.+-
T Consensus 8 ~~D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L~~~G 50 (154)
T COG1522 8 DIDRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIKRLEEEG 50 (154)
T ss_pred HHHHHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 345678888776655 9999999999999999999999998765
No 228
>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=20.05 E-value=1.7e+02 Score=22.95 Aligned_cols=70 Identities=17% Similarity=0.133 Sum_probs=46.1
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcChhhHHHHhh
Q 016517 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAA 151 (388)
Q Consensus 80 ~~~~~~~im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAaD~~GhLqVsesGdIlY~FP~~fRs~l~~ 151 (388)
..-+++.+..+++......++-++.+...-=.+..+.+|..-...+| +++..=+---..||.++++.+..
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 45677888888888888889888855432112222344444444455 88887766667889888776554
Done!