Query 022049
Match_columns 303
No_of_seqs 75 out of 77
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:38:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022049.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022049hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00550 Zalpha Z-DNA-bindin 94.9 0.054 1.2E-06 41.0 4.7 46 80-125 4-50 (68)
2 COG3355 Predicted transcriptio 94.5 0.29 6.4E-06 42.3 8.8 86 85-172 30-118 (126)
3 PRK13239 alkylmercury lyase; P 94.5 0.066 1.4E-06 49.4 5.2 56 81-143 21-76 (206)
4 PF09339 HTH_IclR: IclR helix- 94.0 0.067 1.4E-06 38.0 3.3 39 86-124 7-45 (52)
5 PRK06266 transcription initiat 93.5 0.45 9.8E-06 42.6 8.4 84 81-167 21-107 (178)
6 TIGR00373 conserved hypothetic 93.3 0.56 1.2E-05 41.1 8.5 80 86-168 18-100 (158)
7 smart00346 HTH_ICLR helix_turn 93.3 0.67 1.5E-05 35.1 8.0 78 85-165 8-89 (91)
8 PF04703 FaeA: FaeA-like prote 92.9 0.17 3.6E-06 38.7 4.1 54 84-139 2-57 (62)
9 PF12324 HTH_15: Helix-turn-he 92.6 0.19 4E-06 40.3 4.2 49 84-138 26-74 (77)
10 PF13412 HTH_24: Winged helix- 92.6 0.27 5.9E-06 33.9 4.6 41 83-124 4-44 (48)
11 PF06163 DUF977: Bacterial pro 92.1 0.25 5.3E-06 43.0 4.6 51 81-134 11-61 (127)
12 PF08220 HTH_DeoR: DeoR-like h 91.9 0.38 8.2E-06 35.2 4.8 41 84-125 2-42 (57)
13 cd00090 HTH_ARSR Arsenical Res 91.5 1.4 3.1E-05 30.6 7.3 60 79-142 4-64 (78)
14 KOG3341 RNA polymerase II tran 91.4 0.49 1.1E-05 44.9 6.1 84 68-152 159-245 (249)
15 PF12840 HTH_20: Helix-turn-he 91.3 0.53 1.1E-05 34.3 5.0 53 80-135 8-60 (61)
16 PF08784 RPA_C: Replication pr 90.0 0.64 1.4E-05 37.0 4.8 45 81-125 46-93 (102)
17 PF08279 HTH_11: HTH domain; 89.9 1.2 2.5E-05 31.4 5.6 46 84-130 2-47 (55)
18 smart00420 HTH_DEOR helix_turn 89.8 1.1 2.5E-05 30.0 5.4 47 84-133 2-48 (53)
19 smart00418 HTH_ARSR helix_turn 89.8 0.92 2E-05 30.9 4.9 51 87-141 2-53 (66)
20 TIGR02844 spore_III_D sporulat 88.5 0.52 1.1E-05 37.6 3.3 34 83-118 7-40 (80)
21 PF09743 DUF2042: Uncharacteri 86.9 1.3 2.9E-05 42.2 5.6 57 80-138 53-109 (272)
22 PF01726 LexA_DNA_bind: LexA D 86.6 1.1 2.3E-05 34.2 3.9 38 87-124 15-53 (65)
23 PF01978 TrmB: Sugar-specific 85.3 2.4 5.3E-05 31.2 5.2 52 85-139 11-62 (68)
24 PF12802 MarR_2: MarR family; 85.2 2.1 4.5E-05 30.3 4.7 42 84-125 7-49 (62)
25 PRK15466 carboxysome structura 85.2 1.7 3.6E-05 39.4 5.0 42 84-125 111-152 (166)
26 PF08221 HTH_9: RNA polymerase 85.1 1.7 3.7E-05 32.6 4.3 38 85-123 16-53 (62)
27 PF04539 Sigma70_r3: Sigma-70 84.8 1.1 2.4E-05 33.5 3.2 52 84-135 7-58 (78)
28 PRK10434 srlR DNA-bindng trans 82.6 7 0.00015 36.2 8.2 43 81-124 4-46 (256)
29 PRK09802 DNA-binding transcrip 82.5 8 0.00017 36.3 8.6 54 80-136 15-68 (269)
30 COG2512 Predicted membrane-ass 81.3 2.3 4.9E-05 40.4 4.5 47 77-124 191-237 (258)
31 cd07377 WHTH_GntR Winged helix 80.7 3.1 6.6E-05 29.1 4.0 48 82-131 5-57 (66)
32 COG2345 Predicted transcriptio 80.6 3.3 7.1E-05 38.8 5.2 50 75-125 4-53 (218)
33 TIGR02702 SufR_cyano iron-sulf 79.6 3 6.4E-05 37.1 4.5 45 83-130 2-46 (203)
34 COG1349 GlpR Transcriptional r 79.6 9.5 0.00021 35.5 7.9 63 80-147 3-71 (253)
35 PF13404 HTH_AsnC-type: AsnC-t 79.4 3.8 8.2E-05 28.7 4.0 38 83-121 4-41 (42)
36 PRK04424 fatty acid biosynthes 79.4 2.8 6.1E-05 37.3 4.3 46 82-130 7-52 (185)
37 PF06969 HemN_C: HemN C-termin 78.8 4.7 0.0001 29.3 4.6 53 83-136 7-65 (66)
38 cd07153 Fur_like Ferric uptake 78.3 7.6 0.00017 30.9 6.1 59 83-141 2-65 (116)
39 smart00753 PAM PCI/PINT associ 78.0 7.6 0.00016 29.5 5.7 66 81-146 8-73 (88)
40 smart00088 PINT motif in prote 78.0 7.6 0.00016 29.5 5.7 66 81-146 8-73 (88)
41 smart00345 HTH_GNTR helix_turn 77.7 3.6 7.8E-05 28.2 3.6 38 94-133 16-54 (60)
42 PF04583 Baculo_p74: Baculovir 76.8 9.7 0.00021 36.6 7.2 108 83-196 8-120 (249)
43 smart00344 HTH_ASNC helix_turn 76.4 4.9 0.00011 31.6 4.4 42 83-125 4-45 (108)
44 smart00347 HTH_MARR helix_turn 76.3 29 0.00062 25.8 8.4 48 84-134 12-59 (101)
45 PRK12423 LexA repressor; Provi 75.9 6 0.00013 35.4 5.3 52 82-135 6-62 (202)
46 cd00092 HTH_CRP helix_turn_hel 74.5 15 0.00032 26.0 6.1 38 96-135 24-61 (67)
47 PF02002 TFIIE_alpha: TFIIE al 73.6 9.9 0.00021 30.4 5.5 78 85-165 16-96 (105)
48 PF00392 GntR: Bacterial regul 72.9 3.5 7.5E-05 30.1 2.6 33 93-125 19-52 (64)
49 PF01022 HTH_5: Bacterial regu 72.7 8.4 0.00018 26.8 4.4 40 83-124 3-42 (47)
50 COG1675 TFA1 Transcription ini 72.4 26 0.00057 31.9 8.5 82 85-169 21-105 (176)
51 PRK10411 DNA-binding transcrip 71.6 31 0.00066 31.9 9.0 47 82-131 4-50 (240)
52 PRK13509 transcriptional repre 70.3 6.9 0.00015 36.2 4.5 42 82-124 5-46 (251)
53 PRK10141 DNA-binding transcrip 70.1 55 0.0012 27.7 9.4 60 79-141 13-72 (117)
54 PRK10906 DNA-binding transcrip 69.3 8.6 0.00019 35.7 4.9 42 82-124 5-46 (252)
55 PRK09334 30S ribosomal protein 69.3 11 0.00024 30.8 4.9 61 79-140 24-84 (86)
56 PF00356 LacI: Bacterial regul 68.1 3.9 8.4E-05 29.3 1.9 22 77-98 24-45 (46)
57 PHA02943 hypothetical protein; 68.0 36 0.00079 31.0 8.3 60 83-144 9-69 (165)
58 PRK10681 DNA-binding transcrip 67.9 13 0.00029 34.3 5.8 42 81-123 6-47 (252)
59 TIGR02431 pcaR_pcaU beta-ketoa 66.5 7.8 0.00017 35.1 3.9 43 86-130 13-55 (248)
60 PF03965 Penicillinase_R: Peni 65.7 60 0.0013 26.3 8.6 78 83-167 4-85 (115)
61 PF04405 ScdA_N: Domain of Unk 65.3 5.7 0.00012 29.7 2.4 38 84-121 12-55 (56)
62 PF03297 Ribosomal_S25: S25 ri 64.7 17 0.00037 30.6 5.3 59 81-140 44-102 (105)
63 PF13463 HTH_27: Winged helix 63.9 13 0.00028 26.6 4.0 41 85-125 6-46 (68)
64 PTZ00326 phenylalanyl-tRNA syn 63.7 33 0.00072 35.8 8.2 80 81-162 5-84 (494)
65 TIGR00498 lexA SOS regulatory 63.7 12 0.00026 32.8 4.5 47 82-130 6-57 (199)
66 PF01047 MarR: MarR family; I 63.5 16 0.00034 25.7 4.3 40 85-125 6-45 (59)
67 PRK00135 scpB segregation and 63.4 18 0.00038 32.9 5.6 56 85-141 6-66 (188)
68 PF04157 EAP30: EAP30/Vps36 fa 62.6 12 0.00025 34.1 4.3 43 82-124 174-217 (223)
69 smart00419 HTH_CRP helix_turn_ 62.5 8.7 0.00019 25.5 2.7 35 96-132 7-41 (48)
70 PRK11569 transcriptional repre 62.5 11 0.00023 35.0 4.2 45 86-132 32-76 (274)
71 PRK11014 transcriptional repre 62.0 10 0.00023 31.8 3.7 43 82-124 10-52 (141)
72 PRK10163 DNA-binding transcrip 62.0 11 0.00024 34.9 4.2 47 85-133 28-74 (271)
73 PF01325 Fe_dep_repress: Iron 61.8 18 0.00039 26.9 4.5 33 92-124 17-49 (60)
74 PLN02853 Probable phenylalanyl 61.6 38 0.00082 35.4 8.2 79 82-162 3-81 (492)
75 PF14257 DUF4349: Domain of un 60.9 27 0.00059 32.2 6.5 45 85-132 149-200 (262)
76 PF00356 LacI: Bacterial regul 60.6 6.4 0.00014 28.2 1.8 21 99-119 1-21 (46)
77 PF03640 Lipoprotein_15: Secre 60.5 7.5 0.00016 28.1 2.2 22 124-145 6-27 (48)
78 PRK09834 DNA-binding transcrip 59.3 13 0.00029 34.1 4.2 52 86-141 15-67 (263)
79 smart00531 TFIIE Transcription 58.6 49 0.0011 28.4 7.2 77 87-166 6-88 (147)
80 PF09105 SelB-wing_1: Elongati 57.6 31 0.00067 26.2 5.1 43 87-129 7-49 (61)
81 PRK09480 slmA division inhibit 57.3 9.5 0.00021 32.0 2.6 33 81-113 9-46 (194)
82 PRK11179 DNA-binding transcrip 57.0 21 0.00045 30.4 4.7 42 83-125 10-51 (153)
83 COG1414 IclR Transcriptional r 55.5 17 0.00036 33.7 4.1 46 86-133 8-53 (246)
84 TIGR02787 codY_Gpos GTP-sensin 55.4 15 0.00032 35.4 3.8 46 86-133 187-232 (251)
85 PRK10014 DNA-binding transcrip 55.4 7.5 0.00016 35.4 1.8 26 95-120 4-29 (342)
86 PF06224 HTH_42: Winged helix 55.3 29 0.00063 32.4 5.7 62 82-145 167-230 (327)
87 COG1609 PurR Transcriptional r 54.7 33 0.00072 32.7 6.1 59 78-136 26-98 (333)
88 PF01316 Arg_repressor: Argini 53.9 37 0.0008 26.5 5.2 46 83-144 21-67 (70)
89 COG1321 TroR Mn-dependent tran 53.5 23 0.0005 31.1 4.5 49 87-136 15-69 (154)
90 PF10717 ODV-E18: Occlusion-de 53.1 23 0.0005 29.1 4.1 20 186-205 33-53 (85)
91 PRK05472 redox-sensing transcr 53.0 22 0.00047 31.8 4.4 40 82-121 16-56 (213)
92 PRK07598 RNA polymerase sigma 52.8 61 0.0013 33.0 7.9 87 92-178 273-364 (415)
93 PHA02701 ORF020 dsRNA-binding 52.6 21 0.00045 32.9 4.2 84 83-168 5-124 (183)
94 TIGR00589 ogt O-6-methylguanin 52.4 31 0.00066 27.3 4.6 57 82-139 2-65 (80)
95 PF01035 DNA_binding_1: 6-O-me 51.9 21 0.00046 28.1 3.7 58 82-139 2-65 (85)
96 PRK04172 pheS phenylalanyl-tRN 51.9 76 0.0016 32.4 8.5 72 83-157 7-78 (489)
97 PRK15090 DNA-binding transcrip 51.9 18 0.0004 33.0 3.8 44 86-132 18-61 (257)
98 PLN03238 probable histone acet 51.4 26 0.00057 34.4 4.9 55 84-144 210-264 (290)
99 PF08279 HTH_11: HTH domain; 51.3 8.1 0.00018 27.0 1.1 28 272-299 1-28 (55)
100 cd06445 ATase The DNA repair p 50.5 26 0.00056 27.1 3.9 55 84-138 2-62 (79)
101 PF01475 FUR: Ferric uptake re 50.4 58 0.0013 26.2 6.1 62 82-143 8-74 (120)
102 COG3695 Predicted methylated D 50.0 25 0.00053 29.9 3.9 60 81-140 5-70 (103)
103 PF10771 DUF2582: Protein of u 49.9 36 0.00077 26.4 4.5 52 86-140 12-63 (65)
104 TIGR02944 suf_reg_Xantho FeS a 49.5 28 0.00061 28.6 4.2 43 87-131 14-57 (130)
105 PLN03083 E3 UFM1-protein ligas 49.3 27 0.00058 38.5 5.0 56 80-138 58-113 (803)
106 PF14947 HTH_45: Winged helix- 49.0 29 0.00063 26.6 3.9 38 88-125 9-47 (77)
107 TIGR02698 CopY_TcrY copper tra 48.9 1.3E+02 0.0028 25.4 8.1 75 84-165 6-84 (130)
108 PF09012 FeoC: FeoC like trans 48.1 27 0.00059 26.0 3.6 34 92-125 9-42 (69)
109 PRK10992 iron-sulfur cluster r 47.1 18 0.00039 33.4 2.9 42 85-126 16-63 (220)
110 PF14451 Ub-Mut7C: Mut7-C ubiq 47.1 18 0.00038 28.9 2.5 49 93-144 28-77 (81)
111 TIGR03826 YvyF flagellar opero 47.0 31 0.00067 30.2 4.2 53 85-143 33-86 (137)
112 PRK11050 manganese transport r 47.0 1.7E+02 0.0037 25.1 8.8 46 85-133 40-85 (152)
113 PF01853 MOZ_SAS: MOZ/SAS fami 47.0 23 0.0005 32.6 3.6 38 84-121 135-174 (188)
114 PRK09526 lacI lac repressor; R 46.8 13 0.00028 33.9 1.9 24 96-119 4-27 (342)
115 PF04967 HTH_10: HTH DNA bindi 46.2 43 0.00093 24.9 4.3 38 84-121 5-47 (53)
116 PF10975 DUF2802: Protein of u 46.0 14 0.00031 28.7 1.8 29 88-116 35-63 (70)
117 COG2846 Regulator of cell morp 46.0 16 0.00035 34.5 2.4 32 94-125 31-62 (221)
118 PRK09492 treR trehalose repres 45.9 12 0.00025 33.8 1.5 25 96-120 3-27 (315)
119 COG1459 PulF Type II secretory 45.1 66 0.0014 32.4 6.7 87 95-184 52-178 (397)
120 PF10025 DUF2267: Uncharacteri 45.1 16 0.00035 30.3 2.1 68 100-167 6-80 (125)
121 PF15581 Imm35: Immunity prote 44.9 39 0.00086 28.2 4.2 33 107-139 44-77 (93)
122 PRK15008 HTH-type transcriptio 44.6 17 0.00037 31.7 2.3 32 82-113 18-54 (212)
123 smart00874 B5 tRNA synthetase 44.3 27 0.00058 25.7 3.0 50 97-148 5-54 (71)
124 PF11268 DUF3071: Protein of u 43.6 26 0.00057 31.6 3.4 33 82-116 56-88 (170)
125 COG4565 CitB Response regulato 43.6 45 0.00099 31.7 5.0 69 73-141 145-219 (224)
126 PRK14996 TetR family transcrip 43.4 17 0.00037 31.0 2.0 30 84-113 10-44 (192)
127 TIGR01884 cas_HTH CRISPR locus 43.1 87 0.0019 27.8 6.5 47 84-133 145-191 (203)
128 TIGR02405 trehalos_R_Ecol treh 42.9 16 0.00035 33.2 1.9 23 97-119 1-23 (311)
129 PRK11552 putative DNA-binding 42.9 19 0.00041 32.3 2.3 33 82-114 13-49 (225)
130 TIGR00738 rrf2_super rrf2 fami 42.1 43 0.00094 27.1 4.2 38 87-124 13-52 (132)
131 PRK03902 manganese transport t 41.9 2.1E+02 0.0045 23.9 8.7 43 85-130 11-53 (142)
132 PF11772 EpuA: DNA-directed RN 41.6 15 0.00031 27.0 1.2 25 258-282 22-46 (47)
133 PRK06474 hypothetical protein; 41.5 49 0.0011 29.4 4.7 56 77-134 6-62 (178)
134 PRK05441 murQ N-acetylmuramic 41.4 28 0.00061 33.3 3.4 44 84-131 250-293 (299)
135 PF05158 RNA_pol_Rpc34: RNA po 41.3 82 0.0018 30.9 6.6 70 82-152 9-82 (327)
136 PF07245 Phlebovirus_G2: Phleb 41.3 26 0.00057 36.5 3.4 16 134-149 421-436 (507)
137 PRK14987 gluconate operon tran 41.1 84 0.0018 28.6 6.3 57 77-133 30-100 (331)
138 PRK10344 DNA-binding transcrip 40.6 37 0.0008 28.3 3.5 34 84-119 10-43 (92)
139 PF02796 HTH_7: Helix-turn-hel 40.6 22 0.00048 24.6 1.9 31 88-118 12-42 (45)
140 COG1802 GntR Transcriptional r 40.3 18 0.00038 32.3 1.8 60 81-142 23-83 (230)
141 PRK14987 gluconate operon tran 40.3 17 0.00037 33.1 1.7 25 95-119 3-27 (331)
142 PRK09526 lacI lac repressor; R 40.1 76 0.0016 28.9 5.8 56 77-132 30-99 (342)
143 KOG0860 Synaptobrevin/VAMP-lik 40.1 90 0.0019 27.0 5.8 13 110-122 58-70 (116)
144 PF13542 HTH_Tnp_ISL3: Helix-t 40.0 39 0.00085 23.3 3.1 38 80-120 13-50 (52)
145 smart00421 HTH_LUXR helix_turn 39.3 59 0.0013 21.5 3.9 46 78-127 3-48 (58)
146 PRK10014 DNA-binding transcrip 39.3 92 0.002 28.4 6.2 54 77-130 31-98 (342)
147 PRK10703 DNA-binding transcrip 39.2 18 0.00038 33.1 1.6 22 98-119 2-23 (341)
148 PRK11041 DNA-binding transcrip 39.0 22 0.00048 31.7 2.2 55 77-131 2-70 (309)
149 PF11625 DUF3253: Protein of u 38.8 81 0.0018 25.7 5.1 65 81-149 6-77 (83)
150 PRK09975 DNA-binding transcrip 38.6 25 0.00055 30.1 2.4 32 82-113 11-47 (213)
151 PF02082 Rrf2: Transcriptional 38.4 60 0.0013 24.9 4.2 44 87-132 13-58 (83)
152 COG1522 Lrp Transcriptional re 38.2 61 0.0013 26.7 4.5 51 82-133 8-61 (154)
153 COG0640 ArsR Predicted transcr 37.9 1.3E+02 0.0029 21.4 5.8 59 80-141 23-81 (110)
154 PF05331 DUF742: Protein of un 37.6 49 0.0011 28.2 3.9 46 85-135 46-91 (114)
155 TIGR00274 N-acetylmuramic acid 37.5 37 0.0008 32.6 3.5 43 84-130 245-287 (291)
156 PF10668 Phage_terminase: Phag 37.3 46 0.001 25.5 3.3 34 82-115 7-40 (60)
157 TIGR03613 RutR pyrimidine util 37.3 25 0.00053 29.9 2.1 32 82-113 8-44 (202)
158 TIGR01481 ccpA catabolite cont 37.3 19 0.00042 32.6 1.5 22 98-119 2-23 (329)
159 PF00165 HTH_AraC: Bacterial r 37.1 30 0.00064 23.2 2.1 27 94-120 5-31 (42)
160 PRK07405 RNA polymerase sigma 37.0 1.1E+02 0.0025 29.3 6.8 31 91-121 178-208 (317)
161 cd00569 HTH_Hin_like Helix-tur 36.8 53 0.0012 18.7 3.0 34 79-115 6-39 (42)
162 PRK09954 putative kinase; Prov 36.2 57 0.0012 31.0 4.5 49 83-132 4-55 (362)
163 smart00351 PAX Paired Box doma 36.0 85 0.0018 26.2 5.1 48 73-123 12-59 (125)
164 PF15145 DUF4577: Domain of un 35.9 15 0.00033 31.9 0.6 28 172-199 62-89 (128)
165 PF07070 Spo0M: SpoOM protein; 35.6 43 0.00094 31.3 3.6 49 56-104 109-157 (218)
166 PRK07122 RNA polymerase sigma 35.5 1.3E+02 0.0028 28.1 6.6 44 78-121 117-167 (264)
167 PF13545 HTH_Crp_2: Crp-like h 35.3 56 0.0012 23.8 3.5 33 97-131 28-60 (76)
168 cd00131 PAX Paired Box domain 35.1 72 0.0016 26.9 4.5 44 77-123 16-59 (128)
169 PRK10703 DNA-binding transcrip 34.7 88 0.0019 28.6 5.4 56 77-132 26-95 (341)
170 PRK00441 argR arginine repress 34.7 1.1E+02 0.0024 26.8 5.7 57 83-145 5-67 (149)
171 PF02295 z-alpha: Adenosine de 34.6 54 0.0012 25.0 3.4 44 82-126 4-49 (66)
172 TIGR02417 fruct_sucro_rep D-fr 34.6 1.1E+02 0.0024 27.7 6.0 55 78-132 28-96 (327)
173 PRK09210 RNA polymerase sigma 34.6 1.6E+02 0.0035 28.9 7.4 28 92-119 227-254 (367)
174 PRK05949 RNA polymerase sigma 34.4 1.5E+02 0.0033 28.7 7.2 86 91-178 188-280 (327)
175 TIGR02393 RpoD_Cterm RNA polym 34.2 1.8E+02 0.0039 26.2 7.2 28 92-119 98-125 (238)
176 PF04545 Sigma70_r4: Sigma-70, 33.9 1.1E+02 0.0023 21.1 4.6 41 77-120 3-43 (50)
177 PF04079 DUF387: Putative tran 33.8 83 0.0018 27.9 4.9 43 93-136 9-54 (159)
178 PRK10727 DNA-binding transcrip 33.7 23 0.0005 32.6 1.4 22 98-119 2-23 (343)
179 PRK11303 DNA-binding transcrip 33.6 88 0.0019 28.3 5.2 55 78-132 29-97 (328)
180 PRK10339 DNA-binding transcrip 33.6 21 0.00045 32.6 1.2 22 98-119 2-23 (327)
181 PRK10668 DNA-binding transcrip 33.6 33 0.00073 29.5 2.4 32 82-113 11-47 (215)
182 TIGR02337 HpaR homoprotocatech 33.3 65 0.0014 25.8 3.9 45 85-132 31-75 (118)
183 TIGR00122 birA_repr_reg BirA b 33.2 1.1E+02 0.0023 22.5 4.7 36 86-123 4-39 (69)
184 PRK11169 leucine-responsive tr 33.0 70 0.0015 27.6 4.2 42 83-125 15-56 (164)
185 TIGR02997 Sig70-cyanoRpoD RNA 33.0 1.9E+02 0.0042 27.2 7.5 30 92-121 172-201 (298)
186 PRK10423 transcriptional repre 32.4 1.1E+02 0.0024 27.6 5.5 56 77-132 23-92 (327)
187 PRK10401 DNA-binding transcrip 32.2 29 0.00063 31.9 1.9 22 98-119 2-23 (346)
188 PRK00215 LexA repressor; Valid 31.8 77 0.0017 27.9 4.4 47 84-132 6-57 (205)
189 TIGR01610 phage_O_Nterm phage 31.8 1.1E+02 0.0023 24.4 4.8 32 94-125 44-75 (95)
190 PF13730 HTH_36: Helix-turn-he 31.6 50 0.0011 23.0 2.6 26 99-124 27-52 (55)
191 PF00325 Crp: Bacterial regula 31.6 54 0.0012 22.2 2.6 27 98-124 3-29 (32)
192 PRK09492 treR trehalose repres 31.5 1.4E+02 0.0029 26.9 6.0 22 77-98 29-50 (315)
193 PRK10513 sugar phosphate phosp 31.4 1.9E+02 0.0042 25.9 6.9 60 79-144 21-80 (270)
194 COG1386 scpB Chromosome segreg 31.3 1.1E+02 0.0025 27.8 5.4 53 85-137 10-67 (184)
195 PRK10402 DNA-binding transcrip 31.3 1.1E+02 0.0025 26.9 5.4 50 81-132 149-202 (226)
196 PF00440 TetR_N: Bacterial reg 31.3 33 0.00072 23.6 1.6 28 87-114 5-33 (47)
197 PRK11534 DNA-binding transcrip 31.2 41 0.00089 29.7 2.6 48 93-144 26-74 (224)
198 PF13384 HTH_23: Homeodomain-l 31.2 52 0.0011 22.4 2.6 40 80-122 3-42 (50)
199 PF06971 Put_DNA-bind_N: Putat 31.0 70 0.0015 23.5 3.3 33 86-118 16-49 (50)
200 COG0735 Fur Fe2+/Zn2+ uptake r 31.0 1.9E+02 0.0041 24.9 6.5 64 81-144 20-88 (145)
201 PRK11753 DNA-binding transcrip 30.9 91 0.002 26.6 4.6 46 80-125 138-196 (211)
202 PF13693 HTH_35: Winged helix- 30.9 32 0.0007 27.5 1.7 33 84-118 4-36 (78)
203 PRK08215 sporulation sigma fac 30.6 1.4E+02 0.003 27.3 5.9 44 78-121 113-163 (258)
204 TIGR03697 NtcA_cyano global ni 30.4 1.3E+02 0.0027 25.3 5.3 50 81-132 113-176 (193)
205 TIGR01481 ccpA catabolite cont 30.0 39 0.00085 30.6 2.3 56 77-132 26-95 (329)
206 TIGR02405 trehalos_R_Ecol treh 30.0 1.6E+02 0.0035 26.7 6.3 56 77-132 26-95 (311)
207 PHA01815 hypothetical protein 29.9 2.4E+02 0.0052 21.2 5.9 27 158-184 12-38 (55)
208 PF00957 Synaptobrevin: Synapt 29.9 1.4E+02 0.003 23.1 5.1 12 154-165 50-61 (89)
209 PRK11161 fumarate/nitrate redu 29.8 56 0.0012 28.6 3.2 51 81-133 154-218 (235)
210 PRK03573 transcriptional regul 29.7 83 0.0018 25.9 4.0 41 85-125 34-74 (144)
211 PRK11414 colanic acid/biofilm 29.7 1.8E+02 0.0038 25.7 6.3 52 93-147 30-81 (221)
212 TIGR03338 phnR_burk phosphonat 29.5 47 0.001 28.9 2.6 58 83-142 20-78 (212)
213 PF14394 DUF4423: Domain of un 29.5 81 0.0018 28.0 4.1 45 80-124 22-68 (171)
214 PRK11303 DNA-binding transcrip 29.3 33 0.00071 31.1 1.7 23 98-120 1-23 (328)
215 TIGR02010 IscR iron-sulfur clu 29.2 91 0.002 26.0 4.2 30 95-124 23-52 (135)
216 PLN00104 MYST -like histone ac 28.6 64 0.0014 33.5 3.7 38 84-121 361-398 (450)
217 PF07106 TBPIP: Tat binding pr 28.5 1.6E+02 0.0035 25.5 5.7 57 84-142 3-62 (169)
218 PRK07921 RNA polymerase sigma 28.5 2.3E+02 0.005 27.6 7.3 42 78-119 163-211 (324)
219 PRK03837 transcriptional regul 28.4 92 0.002 27.6 4.3 60 82-144 17-81 (241)
220 PRK11202 DNA-binding transcrip 28.3 44 0.00096 29.1 2.3 32 81-112 10-47 (203)
221 PRK04984 fatty acid metabolism 28.3 90 0.002 27.8 4.2 54 83-138 12-71 (239)
222 PF13518 HTH_28: Helix-turn-he 28.0 1.4E+02 0.003 20.1 4.3 37 84-123 2-38 (52)
223 TIGR03384 betaine_BetI transcr 28.0 35 0.00076 28.4 1.5 33 82-114 8-45 (189)
224 PF05055 DUF677: Protein of un 28.0 2E+02 0.0044 28.6 6.9 78 108-191 116-205 (336)
225 KOG3970 Predicted E3 ubiquitin 27.8 1.4E+02 0.003 29.2 5.5 45 150-197 220-272 (299)
226 KOG4251 Calcium binding protei 27.7 35 0.00076 33.6 1.6 38 263-300 273-311 (362)
227 PRK10727 DNA-binding transcrip 27.7 45 0.00098 30.6 2.3 56 77-132 26-95 (343)
228 PRK12570 N-acetylmuramic acid- 27.6 59 0.0013 31.2 3.1 44 84-131 246-289 (296)
229 PF11548 Receptor_IA-2: Protei 27.5 20 0.00043 29.7 -0.0 27 92-118 52-78 (91)
230 PRK04280 arginine repressor; P 27.4 1.3E+02 0.0029 26.3 5.0 48 82-145 19-67 (148)
231 PRK00453 rpsF 30S ribosomal pr 27.3 62 0.0013 26.2 2.8 39 248-291 1-41 (108)
232 PF09756 DDRGK: DDRGK domain; 27.3 1.6E+02 0.0035 27.0 5.7 65 83-148 100-164 (188)
233 PF08280 HTH_Mga: M protein tr 27.3 93 0.002 22.7 3.5 44 85-129 8-51 (59)
234 COG4901 Ribosomal protein S25 27.2 75 0.0016 27.2 3.3 27 98-124 60-86 (107)
235 PRK10339 DNA-binding transcrip 27.2 44 0.00095 30.5 2.1 23 78-100 29-51 (327)
236 PHA01976 helix-turn-helix prot 27.0 89 0.0019 22.4 3.3 32 81-114 1-32 (67)
237 PF07499 RuvA_C: RuvA, C-termi 26.7 1.1E+02 0.0023 21.6 3.6 29 82-123 1-29 (47)
238 PRK04217 hypothetical protein; 26.6 1.2E+02 0.0025 25.7 4.3 45 76-124 40-85 (110)
239 cd02106 Band_7 The band 7 doma 26.1 1.3E+02 0.0028 22.7 4.3 70 80-151 50-119 (121)
240 PF01399 PCI: PCI domain; Int 26.1 1.7E+02 0.0037 21.9 4.9 57 76-132 39-95 (105)
241 PF07845 DUF1636: Protein of u 26.1 64 0.0014 27.4 2.8 34 255-289 66-99 (116)
242 PF07381 DUF1495: Winged helix 25.8 79 0.0017 25.9 3.1 48 81-128 8-56 (90)
243 TIGR02417 fruct_sucro_rep D-fr 25.6 42 0.00091 30.5 1.7 21 99-119 1-21 (327)
244 TIGR02844 spore_III_D sporulat 25.5 34 0.00075 27.3 1.0 31 267-299 2-32 (80)
245 smart00354 HTH_LACI helix_turn 25.4 45 0.00097 24.9 1.5 21 98-118 1-21 (70)
246 COG1654 BirA Biotin operon rep 25.3 2.5E+02 0.0054 22.5 5.8 54 81-135 2-57 (79)
247 PF13443 HTH_26: Cro/C1-type H 25.0 95 0.0021 22.0 3.1 28 87-116 2-29 (63)
248 COG2103 Predicted sugar phosph 24.6 98 0.0021 30.6 4.0 43 84-130 248-290 (298)
249 COG1308 EGD2 Transcription fac 24.5 62 0.0013 28.2 2.4 23 98-120 83-108 (122)
250 PLN03239 histone acetyltransfe 24.5 86 0.0019 31.6 3.7 59 84-147 268-329 (351)
251 PRK10401 DNA-binding transcrip 24.2 1.8E+02 0.0038 26.8 5.5 56 77-132 26-95 (346)
252 PF09743 DUF2042: Uncharacteri 24.1 1.4E+02 0.003 28.7 4.9 59 84-147 118-176 (272)
253 PRK08392 hypothetical protein; 24.1 90 0.0019 27.9 3.5 56 67-127 146-204 (215)
254 PF00462 Glutaredoxin: Glutare 24.0 2.2E+02 0.0048 19.8 4.9 33 85-122 13-45 (60)
255 KOG2587 RNA polymerase III (C) 23.8 2.8E+02 0.0061 29.7 7.3 88 85-172 22-114 (551)
256 PF09753 Use1: Membrane fusion 23.7 1.5E+02 0.0032 27.5 4.9 13 155-167 215-227 (251)
257 PRK00767 transcriptional regul 23.6 65 0.0014 27.0 2.4 34 81-114 8-46 (197)
258 PF12298 Bot1p: Eukaryotic mit 23.5 1.2E+02 0.0027 27.3 4.2 43 79-124 17-59 (172)
259 PRK10225 DNA-binding transcrip 23.5 72 0.0016 28.8 2.8 48 92-141 27-76 (257)
260 PF00376 MerR: MerR family reg 23.4 50 0.0011 22.6 1.3 17 99-115 1-17 (38)
261 PF03460 NIR_SIR_ferr: Nitrite 23.3 1.1E+02 0.0024 22.3 3.3 30 110-140 22-52 (69)
262 PRK11104 hemG protoporphyrinog 23.0 56 0.0012 28.6 1.9 36 247-282 129-169 (177)
263 COG5346 Predicted membrane pro 22.8 5E+02 0.011 23.1 7.6 61 102-187 43-107 (136)
264 PF08006 DUF1700: Protein of u 22.7 5.1E+02 0.011 22.5 9.7 39 78-116 16-59 (181)
265 PF08100 Dimerisation: Dimeris 22.6 1.3E+02 0.0028 22.1 3.4 24 85-108 9-33 (51)
266 PRK14999 histidine utilization 22.3 73 0.0016 28.7 2.5 58 81-141 15-77 (241)
267 PF13038 DUF3899: Domain of un 22.3 1E+02 0.0022 24.1 3.1 26 170-195 65-90 (92)
268 TIGR03652 FeS_repair_RIC iron- 22.2 84 0.0018 28.5 2.9 31 95-125 25-55 (216)
269 COG4189 Predicted transcriptio 22.2 1.6E+02 0.0035 29.0 4.9 66 78-144 19-96 (308)
270 TIGR02018 his_ut_repres histid 22.1 1.5E+02 0.0032 26.4 4.4 54 83-138 6-65 (230)
271 PRK15126 thiamin pyrimidine py 22.0 2.3E+02 0.005 25.6 5.7 53 79-140 20-72 (272)
272 PHA00738 putative HTH transcri 22.0 3.5E+02 0.0075 23.2 6.3 57 82-141 12-68 (108)
273 PF14493 HTH_40: Helix-turn-he 21.9 1.2E+02 0.0025 23.8 3.3 72 88-166 4-78 (91)
274 PRK11512 DNA-binding transcrip 21.8 1.5E+02 0.0032 24.6 4.1 47 83-132 41-87 (144)
275 TIGR02812 fadR_gamma fatty aci 21.7 77 0.0017 28.2 2.5 56 83-140 15-72 (235)
276 COG1609 PurR Transcriptional r 21.7 54 0.0012 31.2 1.7 22 98-119 1-22 (333)
277 cd06171 Sigma70_r4 Sigma70, re 21.5 1.6E+02 0.0035 18.7 3.5 26 96-121 25-50 (55)
278 TIGR02325 C_P_lyase_phnF phosp 21.4 1.7E+02 0.0036 25.9 4.6 44 82-125 12-60 (238)
279 PRK11511 DNA-binding transcrip 21.3 1.4E+02 0.0029 24.7 3.8 36 85-120 12-48 (127)
280 PF13744 HTH_37: Helix-turn-he 21.3 2.4E+02 0.0052 21.6 4.9 43 88-132 24-78 (80)
281 TIGR01557 myb_SHAQKYF myb-like 21.3 1.9E+02 0.004 21.6 4.1 39 81-119 8-51 (57)
282 PF02932 Neur_chan_memb: Neuro 21.3 3E+02 0.0065 21.9 5.6 38 149-186 197-234 (237)
283 PF10075 PCI_Csn8: COP9 signal 21.2 1.5E+02 0.0033 24.8 4.1 61 77-143 77-137 (143)
284 PRK13719 conjugal transfer tra 21.1 1.5E+02 0.0032 28.1 4.3 51 77-127 138-188 (217)
285 cd07977 TFIIE_beta_winged_heli 20.9 1.9E+02 0.0042 22.6 4.3 35 85-119 12-48 (75)
286 PF07790 DUF1628: Protein of u 20.8 1.9E+02 0.0041 22.0 4.2 21 177-197 7-27 (80)
287 COG5027 SAS2 Histone acetyltra 20.8 1.1E+02 0.0024 31.3 3.6 39 84-122 317-356 (395)
288 PRK10857 DNA-binding transcrip 20.7 95 0.0021 27.4 2.9 32 93-124 21-52 (164)
289 PRK10421 DNA-binding transcrip 20.4 86 0.0019 28.4 2.6 52 85-138 13-66 (253)
290 PRK10870 transcriptional repre 20.2 1.5E+02 0.0033 26.0 4.0 42 84-125 57-99 (176)
291 PRK10219 DNA-binding transcrip 20.2 1.6E+02 0.0035 23.0 3.8 38 84-121 7-45 (107)
292 PRK00377 cbiT cobalt-precorrin 20.2 77 0.0017 27.7 2.2 46 67-112 134-179 (198)
293 PRK07406 RNA polymerase sigma 20.1 3.9E+02 0.0084 26.8 7.3 42 78-119 213-261 (373)
294 TIGR02850 spore_sigG RNA polym 20.1 1.5E+02 0.0032 27.1 4.1 46 77-122 109-161 (254)
295 PRK10820 DNA-binding transcrip 20.0 2E+02 0.0043 29.6 5.3 71 67-140 32-105 (520)
No 1
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=94.88 E-value=0.054 Score=40.99 Aligned_cols=46 Identities=15% Similarity=0.252 Sum_probs=41.3
Q ss_pred CchhhHHHHHHHHhcCC-ceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 80 PADVRNRAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 80 ~~~~~~~im~Ave~~g~-rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
+....++|++++.+.|. .+|+.|+|.+.|++...+.+.|..|..+.
T Consensus 4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G 50 (68)
T smart00550 4 QDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKG 50 (68)
T ss_pred chHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 34567899999999988 59999999999999999999999998873
No 2
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=94.50 E-value=0.29 Score=42.25 Aligned_cols=86 Identities=19% Similarity=0.162 Sum_probs=68.6
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc-CCceEee-ccccEEEEc-ChhhHHHHhhhhHHHhHHHH
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT-DGFLEVS-DEGDVLYVF-PNNYRAKLAAKSFRLKVEPV 161 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~-~G~LeVs-esGdIlYvF-P~~fRs~l~~Ks~r~rlq~~ 161 (303)
-.+++++-+.++..|+-|+|..-+++.+.|+++|+.|.... ==.-+++ +.|-..|.+ |.++-. -.+-.+..+++|
T Consensus 30 v~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee--~k~~i~~~l~~w 107 (126)
T COG3355 30 VEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEE--IKKKILKDLDEW 107 (126)
T ss_pred HHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHH--HHHHHHHHHHHH
Confidence 45677777678889999999999999999999999999875 1222344 789999999 988887 356677788999
Q ss_pred HHHHhhhhHHH
Q 022049 162 IDKAKAAAEYS 172 (303)
Q Consensus 162 ~~k~w~v~~yl 172 (303)
.+++...+...
T Consensus 108 ~~~~~~~i~~~ 118 (126)
T COG3355 108 YDKMKQLIEEF 118 (126)
T ss_pred HHHHHHHHHHH
Confidence 88887775543
No 3
>PRK13239 alkylmercury lyase; Provisional
Probab=94.47 E-value=0.066 Score=49.42 Aligned_cols=56 Identities=18% Similarity=0.284 Sum_probs=47.5
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcCh
Q 022049 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~ 143 (303)
..+.-.|++.+. .|.-||+.|+|+.+|.+.+++++.|.+|. ..+..++|+|+- ||-
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 346677888888 99999999999999999999999999985 447889999875 544
No 4
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=93.98 E-value=0.067 Score=37.99 Aligned_cols=39 Identities=23% Similarity=0.434 Sum_probs=35.4
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
+|++++.+.+...|+.|+|.++|++...+.+-|..|.+.
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 678999999999999999999999999999999999864
No 5
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=93.47 E-value=0.45 Score=42.58 Aligned_cols=84 Identities=18% Similarity=0.141 Sum_probs=60.7
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCc---eEeeccccEEEEcChhhHHHHhhhhHHHh
Q 022049 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGF---LEVSDEGDVLYVFPNNYRAKLAAKSFRLK 157 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~---LeVsesGdIlYvFP~~fRs~l~~Ks~r~r 157 (303)
.+..-+|++++.++| .+|..|+|...|++.+++++.|..|..+.=.. .+..+.|-+.|.+--+...+ ....+.+
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 445678999999988 69999999999999999999999999987322 23335788999776555553 2333444
Q ss_pred HHHHHHHHhh
Q 022049 158 VEPVIDKAKA 167 (303)
Q Consensus 158 lq~~~~k~w~ 167 (303)
+....++++.
T Consensus 98 ~~~~~~klk~ 107 (178)
T PRK06266 98 KMEELKKLKE 107 (178)
T ss_pred HHHHHHHHHH
Confidence 4555555443
No 6
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=93.33 E-value=0.56 Score=41.09 Aligned_cols=80 Identities=23% Similarity=0.230 Sum_probs=60.8
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCC---ceEeeccccEEEEcChhhHHHHhhhhHHHhHHHHH
Q 022049 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG---FLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVI 162 (303)
Q Consensus 86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G---~LeVsesGdIlYvFP~~fRs~l~~Ks~r~rlq~~~ 162 (303)
.||+|+-.+| -+|..|+|...|++++++++.|..|..+.=. +.+-.++|-+.|.+=-++..+ -...+.++....
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 5788888777 5999999999999999999999999998854 555667888999985577774 334444555555
Q ss_pred HHHhhh
Q 022049 163 DKAKAA 168 (303)
Q Consensus 163 ~k~w~v 168 (303)
++++.-
T Consensus 95 ~~lk~~ 100 (158)
T TIGR00373 95 KKLREK 100 (158)
T ss_pred HHHHHH
Confidence 555433
No 7
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=93.29 E-value=0.67 Score=35.09 Aligned_cols=78 Identities=19% Similarity=0.335 Sum_probs=53.0
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChh-hH---HHHhhhhHHHhHHH
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN-YR---AKLAAKSFRLKVEP 160 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~-fR---s~l~~Ks~r~rlq~ 160 (303)
-+|++.+.+.+..+|+.|+|...|++...+.+-|..|.+. |-|+-..++. .|..-.. ++ ..+.+..+.....+
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~--g~l~~~~~~~-~y~l~~~~~~~~~~~~~~~~l~~~~~~ 84 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQEL--GYVEQDGQNG-RYRLGPKVLELGQSYLSSLDLREVAKP 84 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC--CCeeecCCCC-ceeecHHHHHHHHHHHhcCCHHHHHHH
Confidence 4578888887668999999999999999999999999764 7777654332 3555332 22 22333445555555
Q ss_pred HHHHH
Q 022049 161 VIDKA 165 (303)
Q Consensus 161 ~~~k~ 165 (303)
+++.+
T Consensus 85 ~l~~l 89 (91)
T smart00346 85 VLEEL 89 (91)
T ss_pred HHHHH
Confidence 55543
No 8
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=92.90 E-value=0.17 Score=38.66 Aligned_cols=54 Identities=20% Similarity=0.356 Sum_probs=41.6
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec--cccEEE
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD--EGDVLY 139 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse--sGdIlY 139 (303)
.++|++.+++.+.-+|..|||...|++..+|+.=|..|..+. .++-++ .|-..|
T Consensus 2 ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG--~V~~~~~~rG~~~~ 57 (62)
T PF04703_consen 2 KEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEG--KVERSPVRRGKSTY 57 (62)
T ss_dssp HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCT--SEEEES-SSSSS-E
T ss_pred cHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCC--CEEEecCCCCccee
Confidence 367999999988889999999999999999999999998764 556544 355433
No 9
>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=92.63 E-value=0.19 Score=40.31 Aligned_cols=49 Identities=22% Similarity=0.348 Sum_probs=35.9
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEE
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL 138 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIl 138 (303)
--.+++.+.+ |.-||+.++|+.+|.+.++++++|.++. ..|-.++|.||
T Consensus 26 ~r~LLr~LA~-G~PVt~~~LA~a~g~~~e~v~~~L~~~p-----~tEyD~~GrIV 74 (77)
T PF12324_consen 26 LRPLLRLLAK-GQPVTVEQLAAALGWPVEEVRAALAAMP-----DTEYDDQGRIV 74 (77)
T ss_dssp HHHHHHHHTT-TS-B-HHHHHHHHT--HHHHHHHHHH-T-----TSEEETTSEEE
T ss_pred HHHHHHHHHc-CCCcCHHHHHHHHCCCHHHHHHHHHhCC-----CceEcCCCCee
Confidence 3445666665 9999999999999999999999988775 47888888887
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=92.61 E-value=0.27 Score=33.94 Aligned_cols=41 Identities=17% Similarity=0.324 Sum_probs=34.6
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
.+.+|++.+.+.+. .|+.|+|...|+|...+.+.|..|..+
T Consensus 4 ~~~~Il~~l~~~~~-~t~~ela~~~~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 4 TQRKILNYLRENPR-ITQKELAEKLGISRSTVNRYLKKLEEK 44 (48)
T ss_dssp HHHHHHHHHHHCTT-S-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHcCC-CCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 46789999999655 999999999999999999999999865
No 11
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=92.09 E-value=0.25 Score=42.96 Aligned_cols=51 Identities=25% Similarity=0.386 Sum_probs=43.2
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecc
Q 022049 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVses 134 (303)
+++..+|++.|+++| |+|++|++..+|++.+.+++-|..|++ .|+|..+..
T Consensus 11 ~eLk~rIvElVRe~G-RiTi~ql~~~TGasR~Tvk~~lreLVa--~G~l~~~G~ 61 (127)
T PF06163_consen 11 EELKARIVELVREHG-RITIKQLVAKTGASRNTVKRYLRELVA--RGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHcC-CccHHHHHHHHCCCHHHHHHHHHHHHH--cCCeEeCCC
Confidence 556778899998876 699999999999999999999999986 467776554
No 12
>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=91.88 E-value=0.38 Score=35.20 Aligned_cols=41 Identities=12% Similarity=0.294 Sum_probs=36.9
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
+..|++.+++.| .+|+.|+|..-|+|...+++.|..|+...
T Consensus 2 ~~~Il~~l~~~~-~~s~~ela~~~~VS~~TiRRDl~~L~~~g 42 (57)
T PF08220_consen 2 QQQILELLKEKG-KVSVKELAEEFGVSEMTIRRDLNKLEKQG 42 (57)
T ss_pred HHHHHHHHHHcC-CEEHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 467899998875 69999999999999999999999998864
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=91.52 E-value=1.4 Score=30.56 Aligned_cols=60 Identities=25% Similarity=0.424 Sum_probs=47.1
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccc-cEEEEcC
Q 022049 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG-DVLYVFP 142 (303)
Q Consensus 79 l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesG-dIlYvFP 142 (303)
+....+..|++++.+.+ ++..|+|...|++...+.+.|..|.+. |.+....++ ...|.+.
T Consensus 4 ~~~~~~~~il~~l~~~~--~~~~ei~~~~~i~~~~i~~~l~~L~~~--g~i~~~~~~~~~~~~~~ 64 (78)
T cd00090 4 LSDPTRLRILRLLLEGP--LTVSELAERLGLSQSTVSRHLKKLEEA--GLVESRREGRRVYYSLT 64 (78)
T ss_pred ccChHHHHHHHHHHHCC--cCHHHHHHHHCcCHhHHHHHHHHHHHC--CCeEEEEeccEEEEEeC
Confidence 34456778899888866 999999999999999999999999775 567665544 4566665
No 14
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=91.44 E-value=0.49 Score=44.86 Aligned_cols=84 Identities=17% Similarity=0.313 Sum_probs=70.1
Q ss_pred cCCCcccccCCCCchhh---HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChh
Q 022049 68 VGPGRIVESDKLPADVR---NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (303)
Q Consensus 68 ~~~~~~~~~~~l~~~~~---~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~ 144 (303)
++.||.----++|.+++ ..|+++++.+|| ||+.-+-+.-|-.-.-|+++|..|.++.=+-+.-...+|..|-||..
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 44556555556666554 579999999999 99999999999999999999999999999999988999999999999
Q ss_pred hHHHHhhh
Q 022049 145 YRAKLAAK 152 (303)
Q Consensus 145 fRs~l~~K 152 (303)
|-..+...
T Consensus 238 ~~~~~~q~ 245 (249)
T KOG3341|consen 238 FTDQYAQR 245 (249)
T ss_pred hhHHHhhh
Confidence 97754443
No 15
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=91.26 E-value=0.53 Score=34.27 Aligned_cols=53 Identities=26% Similarity=0.439 Sum_probs=44.2
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccc
Q 022049 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (303)
Q Consensus 80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesG 135 (303)
....|-+|++.+ ..+...|++++|...|++...+..-|..|.. .|-+++.++|
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 345788899999 5677799999999999999999999999987 5778887776
No 16
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=89.96 E-value=0.64 Score=36.98 Aligned_cols=45 Identities=20% Similarity=0.440 Sum_probs=38.1
Q ss_pred chhhHHHHHHHHh---cCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 81 ADVRNRAMDAVDA---CNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 81 ~~~~~~im~Ave~---~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
..++.+|++.++. ..-.|.+.+|+.+.|++.++++++|..|..+.
T Consensus 46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG 93 (102)
T PF08784_consen 46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEG 93 (102)
T ss_dssp -HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCC
Confidence 4578999999998 56679999999999999999999999999863
No 17
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=89.90 E-value=1.2 Score=31.37 Aligned_cols=46 Identities=11% Similarity=0.172 Sum_probs=35.6
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~Le 130 (303)
+.+|++.+.+.+..+|..++|.+.|+|...+++.|..|-+. +..++
T Consensus 2 ~~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~-~~~I~ 47 (55)
T PF08279_consen 2 QKQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREW-GIPIE 47 (55)
T ss_dssp HHHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHT-T-EEE
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC-CCeEE
Confidence 35788889666666999999999999999999999999444 44443
No 18
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=89.85 E-value=1.1 Score=29.97 Aligned_cols=47 Identities=15% Similarity=0.319 Sum_probs=38.5
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse 133 (303)
+..+++.+.+.+ .+|+.|+|...|++...+.+.|..|..+ |.++-..
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 356888888776 4999999999999999999999999886 5555433
No 19
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=89.77 E-value=0.92 Score=30.86 Aligned_cols=51 Identities=22% Similarity=0.406 Sum_probs=39.6
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecccc-EEEEc
Q 022049 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-VLYVF 141 (303)
Q Consensus 87 im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGd-IlYvF 141 (303)
|+..+. ...+|+.|++...|++...+.+.|..|.++ |-++....|. ..|.+
T Consensus 2 il~~l~--~~~~~~~~i~~~l~is~~~v~~~l~~L~~~--g~i~~~~~~~~~~~~~ 53 (66)
T smart00418 2 ILKLLA--EGELCVCELAEILGLSQSTVSHHLKKLREA--GLVESRREGKRVYYSL 53 (66)
T ss_pred HHHHhh--cCCccHHHHHHHHCCCHHHHHHHHHHHHHC--CCeeeeecCCEEEEEE
Confidence 567776 566899999999999999999999999986 5666555454 44443
No 20
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=88.52 E-value=0.52 Score=37.63 Aligned_cols=34 Identities=12% Similarity=0.081 Sum_probs=31.0
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHH
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL 118 (303)
-+..|++.+.+ +.+|+.|||..+|+|...+.+.|
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 46788999999 88999999999999999999877
No 21
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=86.95 E-value=1.3 Score=42.17 Aligned_cols=57 Identities=18% Similarity=0.367 Sum_probs=49.4
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEE
Q 022049 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL 138 (303)
Q Consensus 80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIl 138 (303)
|.-++..|.+.+..+|+|+++.|++..-|+..+..|+.+..++.+-. +++.. .||++
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 45677899999999999999999999999999999999999998877 55544 68864
No 22
>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=86.64 E-value=1.1 Score=34.16 Aligned_cols=38 Identities=24% Similarity=0.336 Sum_probs=30.6
Q ss_pred HHHHHHhcCCceeehhhhhhcCCC-HHHHHHHHHHHHhh
Q 022049 87 AMDAVDACNRRVTIGDVAGKAGLK-LNEAQKALQALAAD 124 (303)
Q Consensus 87 im~Ave~~g~rvTvgDVAa~aGLs-l~eAe~aL~aLAad 124 (303)
|.+.+++.||-.|+.|+|...|++ .+.+++-|.+|..+
T Consensus 15 I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~k 53 (65)
T PF01726_consen 15 IREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERK 53 (65)
T ss_dssp HHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHT
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 445567799999999999999997 99999999999865
No 23
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=85.34 E-value=2.4 Score=31.15 Aligned_cols=52 Identities=21% Similarity=0.316 Sum_probs=40.4
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEE
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY 139 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlY 139 (303)
.+|..++- ..+.+|+.|+|..+|++...+.+.|..|... |-++..+...-+|
T Consensus 11 ~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~--GlV~~~~~~~~~Y 62 (68)
T PF01978_consen 11 AKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK--GLVEREEGRPKVY 62 (68)
T ss_dssp HHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT--TSEEEEEECCEEE
T ss_pred HHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEcCceEEE
Confidence 35566665 4567999999999999999999999999986 6677776443333
No 24
>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=85.22 E-value=2.1 Score=30.27 Aligned_cols=42 Identities=14% Similarity=0.240 Sum_probs=36.1
Q ss_pred hHHHHHHHHhcCCc-eeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 84 RNRAMDAVDACNRR-VTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 84 ~~~im~Ave~~g~r-vTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
+-+++-++...+.. +|+.|+|...|++...+.+.+..|.++.
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~G 49 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKG 49 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 34678899888887 9999999999999999999999998764
No 25
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=85.20 E-value=1.7 Score=39.42 Aligned_cols=42 Identities=24% Similarity=0.385 Sum_probs=36.3
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
.+.++.-+-...+..|.|+||+.-|.++++++.+|..|-+|.
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 (166)
T PRK15466 111 ADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAG 152 (166)
T ss_pred HHHHHHHHHHHHccccHHHHHHHhCCcHHHHHHHHHHHHhcc
Confidence 355566667778899999999999999999999999998874
No 26
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=85.13 E-value=1.7 Score=32.55 Aligned_cols=38 Identities=21% Similarity=0.366 Sum_probs=30.6
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAa 123 (303)
.+|.+.+-+.| |.|+.+++..++|+.++++++|..|.+
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 46677776666 899999999999999999999999975
No 27
>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=84.78 E-value=1.1 Score=33.52 Aligned_cols=52 Identities=23% Similarity=0.230 Sum_probs=34.8
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccc
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesG 135 (303)
+..+.+.-.++|...|..+||...|+++++.++.|.....-..=++.+..++
T Consensus 7 ~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~ 58 (78)
T PF04539_consen 7 ERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDED 58 (78)
T ss_dssp HHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSS
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCC
Confidence 3344455568899999999999999999999888876544334444454443
No 28
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=82.58 E-value=7 Score=36.23 Aligned_cols=43 Identities=9% Similarity=0.102 Sum_probs=38.5
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
.+-+.+|++.+++.| ++|+.|+|..-|+|...+++.|..|+..
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 356788899998876 5999999999999999999999999876
No 29
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=82.49 E-value=8 Score=36.26 Aligned_cols=54 Identities=15% Similarity=0.244 Sum_probs=44.4
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecccc
Q 022049 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD 136 (303)
Q Consensus 80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGd 136 (303)
..+-+.+|++.+++.|. +|+.|+|..-|+|...+++.|..|.+. |-++-..-|-
T Consensus 15 ~~eR~~~Il~~L~~~~~-vtv~eLa~~l~VS~~TIRRDL~~Le~~--G~l~r~~GGa 68 (269)
T PRK09802 15 TSERREQIIQRLRQQGS-VQVNDLSALYGVSTVTIRNDLAFLEKQ--GIAVRAYGGA 68 (269)
T ss_pred HHHHHHHHHHHHHHcCC-EeHHHHHHHHCCCHHHHHHHHHHHHhC--CCeEEEeCCE
Confidence 34667888999999887 999999999999999999999999664 5665555443
No 30
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=81.26 E-value=2.3 Score=40.44 Aligned_cols=47 Identities=19% Similarity=0.285 Sum_probs=40.4
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
..|+.+. ..||++++.+|+|+|+.|+..+.|+|...+=+.|+.|...
T Consensus 191 ~~L~~~e-~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~ 237 (258)
T COG2512 191 YDLNEDE-KEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKR 237 (258)
T ss_pred CCCCHHH-HHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhC
Confidence 3444444 4689999999999999999999999999999999999764
No 31
>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=80.68 E-value=3.1 Score=29.14 Aligned_cols=48 Identities=21% Similarity=0.369 Sum_probs=35.0
Q ss_pred hhhHHHHHHHHhc----CCc-eeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 022049 82 DVRNRAMDAVDAC----NRR-VTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (303)
Q Consensus 82 ~~~~~im~Ave~~----g~r-vTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeV 131 (303)
++.+.+.+.+... |.. .|+.|+|...|+|...+.++|..|+.. |-|+.
T Consensus 5 ~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~--G~i~~ 57 (66)
T cd07377 5 QIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAE--GLVER 57 (66)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEe
Confidence 4456666665543 222 459999999999999999999999984 34543
No 32
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=80.63 E-value=3.3 Score=38.76 Aligned_cols=50 Identities=16% Similarity=0.281 Sum_probs=45.2
Q ss_pred ccCCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 75 ESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 75 ~~~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
++.+.++..+.+|+..+++.|. +|++|+|.+-||+...|++-|..|.++.
T Consensus 4 ~~~~~~~~tr~~il~lL~~~g~-~sa~elA~~Lgis~~avR~HL~~Le~~G 53 (218)
T COG2345 4 MLADPSGSTRERILELLKKSGP-VSADELAEELGISPMAVRRHLDDLEAEG 53 (218)
T ss_pred cccCCCccHHHHHHHHHhccCC-ccHHHHHHHhCCCHHHHHHHHHHHHhCc
Confidence 4567788899999999888876 8999999999999999999999999876
No 33
>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=79.62 E-value=3 Score=37.10 Aligned_cols=45 Identities=13% Similarity=0.276 Sum_probs=39.9
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~Le 130 (303)
.|.+|+..+.+.|. +|+.|+|...|++...+.+.|..|.++ |-++
T Consensus 2 tr~~IL~~L~~~~~-~t~~eLA~~lgis~~tV~~~L~~Le~~--GlV~ 46 (203)
T TIGR02702 2 TKEDILSYLLKQGQ-ATAAALAEALAISPQAVRRHLKDLETE--GLIE 46 (203)
T ss_pred HHHHHHHHHHHcCC-CCHHHHHHHHCcCHHHHHHHHHHHHHC--CCeE
Confidence 57899999998876 999999999999999999999999886 4444
No 34
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=79.61 E-value=9.5 Score=35.45 Aligned_cols=63 Identities=14% Similarity=0.263 Sum_probs=48.0
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc------CCceEeeccccEEEEcChhhHH
Q 022049 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT------DGFLEVSDEGDVLYVFPNNYRA 147 (303)
Q Consensus 80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~------~G~LeVsesGdIlYvFP~~fRs 147 (303)
+..-+.+|++-|++.| .+++.|+|..-|.|...+++.|..|+... ||-.-.+...+. |..-|.
T Consensus 3 ~~eR~~~Il~~l~~~g-~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~hGGa~~~~~~~~~----~~~~r~ 71 (253)
T COG1349 3 KEERHQKILELLKEKG-KVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVHGGAVLPDSESEY----PFSERK 71 (253)
T ss_pred hHHHHHHHHHHHHHcC-cEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEeCCEecCCCcccc----cHHHHH
Confidence 3456788999999966 59999999999999999999999999863 555444444444 444554
No 35
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=79.40 E-value=3.8 Score=28.68 Aligned_cols=38 Identities=13% Similarity=0.297 Sum_probs=30.3
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHH
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aL 121 (303)
...+|++++++. .|.+..++|...|+|-.++.+-+..|
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 456788888777 78999999999999999999888776
No 36
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=79.37 E-value=2.8 Score=37.27 Aligned_cols=46 Identities=13% Similarity=0.163 Sum_probs=39.5
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~Le 130 (303)
.-+.+|++.+.+.| .+|+.|+|..-|+|...+++.|..|+.+ |.|+
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 56678888998866 5999999999999999999999999887 5444
No 37
>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=78.85 E-value=4.7 Score=29.30 Aligned_cols=53 Identities=25% Similarity=0.479 Sum_probs=39.5
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHH-HHHHHHHHhh-----cCCceEeecccc
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEA-QKALQALAAD-----TDGFLEVSDEGD 136 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eA-e~aL~aLAad-----~~G~LeVsesGd 136 (303)
.++.+|-.+.. ..++...++..+.|.++.+. .+.|..+.++ .+++|.+|+.|-
T Consensus 7 ~~e~i~~~LR~-~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~~~~~l~lT~~G~ 65 (66)
T PF06969_consen 7 LREYIMLGLRC-NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLLEIDGGRLRLTEKGR 65 (66)
T ss_dssp HHHHHHHHHHH-HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE-SSEEEE-TTTG
T ss_pred HHHHHHHHHHh-HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEEeCCEEEECcccC
Confidence 46777888876 55699999999999997776 7779988886 378888888873
No 38
>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=78.30 E-value=7.6 Score=30.87 Aligned_cols=59 Identities=12% Similarity=0.129 Sum_probs=47.2
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeeccccEEEEc
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~a-----GLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvF 141 (303)
.|..|++++.+.+.-+|+.||..+. ++++..+=+.|..|++..--+=-..++|...|..
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 5788999999998889999999875 7899999999999998765443334456677765
No 39
>smart00753 PAM PCI/PINT associated module.
Probab=78.05 E-value=7.6 Score=29.46 Aligned_cols=66 Identities=14% Similarity=0.164 Sum_probs=48.4
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhH
Q 022049 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYR 146 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fR 146 (303)
...+.+.+..+-+--..+|..++|...+++.+++|..|..+..+..=+-.++.....++.-....|
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 345566666666667789999999999999999999999999887433345565556665555444
No 40
>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=78.05 E-value=7.6 Score=29.46 Aligned_cols=66 Identities=14% Similarity=0.164 Sum_probs=48.4
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhH
Q 022049 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYR 146 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fR 146 (303)
...+.+.+..+-+--..+|..++|...+++.+++|..|..+..+..=+-.++.....++.-....|
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 345566666666667789999999999999999999999999887433345565556665555444
No 41
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=77.72 E-value=3.6 Score=28.22 Aligned_cols=38 Identities=18% Similarity=0.359 Sum_probs=31.5
Q ss_pred cCCce-eehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 022049 94 CNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (303)
Q Consensus 94 ~g~rv-TvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse 133 (303)
-|.++ |..|+|...|+|...++++|..|.++ |-|+...
T Consensus 16 ~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~--g~i~~~~ 54 (60)
T smart00345 16 PGDKLPSERELAAQLGVSRTTVREALSRLEAE--GLVQRRP 54 (60)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEec
Confidence 35667 89999999999999999999999986 4565443
No 42
>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=76.80 E-value=9.7 Score=36.56 Aligned_cols=108 Identities=16% Similarity=0.246 Sum_probs=58.4
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHHHhhhhHHHhHH---
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVE--- 159 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~l~~Ks~r~rlq--- 159 (303)
+..-|.|.+|.+. .+..+++.-|. +..+.+|..+..+.--.|= -.=...+-...+.+-.++.+..+|..+.
T Consensus 8 le~II~~Fled~~---~i~~I~~d~Gf--d~l~~~lk~mlkkin~~li-P~Lk~~ll~~s~~vt~rlLgetyKaav~h~~ 81 (249)
T PF04583_consen 8 LEDIISQFLEDHA---LIMSIATDLGF--DVLESALKSMLKKINTKLI-PALKRMLLSTSRRVTVRLLGETYKAAVVHQL 81 (249)
T ss_pred HHHHHHHHHHhhH---HHHHHHHHHhH--HHHHHHHHHHHHHHHHHHH-HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Confidence 4445667777643 34555655553 3334444444332211100 0000111122244555566655554322
Q ss_pred --HHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022049 160 --PVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAIL 196 (303)
Q Consensus 160 --~~~~k~w~v~~yliRVsFGi~LIaSIvlv~~aIiail 196 (303)
-..+-+-.++..+.|+...-+-|+-|+|++++|+-++
T Consensus 82 nr~aIkt~s~vAkal~r~~~~AaSVvgi~Li~~ti~Dlv 120 (249)
T PF04583_consen 82 NRIAIKTVSTVAKALTRIAIAAASVVGIVLIFLTIADLV 120 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2333447788899999999999999999999987665
No 43
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=76.42 E-value=4.9 Score=31.58 Aligned_cols=42 Identities=14% Similarity=0.398 Sum_probs=37.4
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
...+|+.++.+.+ +.|..|+|.+.|++...+.+.|..|.++.
T Consensus 4 ~D~~il~~L~~~~-~~~~~~la~~l~~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 4 IDRKILEELQKDA-RISLAELAKKVGLSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHHHHHhC-CCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 4568899998865 79999999999999999999999999864
No 44
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=76.33 E-value=29 Score=25.79 Aligned_cols=48 Identities=10% Similarity=0.232 Sum_probs=40.9
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecc
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVses 134 (303)
.-.|+..+..++ .+|+.|+|...+++...+.+.|..|.++ |-++..++
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 5999999999999999999999999996 67766654
No 45
>PRK12423 LexA repressor; Provisional
Probab=75.89 E-value=6 Score=35.35 Aligned_cols=52 Identities=23% Similarity=0.346 Sum_probs=41.0
Q ss_pred hhhHHHHHH----HHhcCCceeehhhhhhcCC-CHHHHHHHHHHHHhhcCCceEeeccc
Q 022049 82 DVRNRAMDA----VDACNRRVTIGDVAGKAGL-KLNEAQKALQALAADTDGFLEVSDEG 135 (303)
Q Consensus 82 ~~~~~im~A----ve~~g~rvTvgDVAa~aGL-sl~eAe~aL~aLAad~~G~LeVsesG 135 (303)
..|.++.++ +++.|+.-|+.|+|.+.|+ +.+.+++.|.+|+.+ |.|+++..+
T Consensus 6 ~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~--G~l~~~~~~ 62 (202)
T PRK12423 6 PKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEA--GLIEVVPNQ 62 (202)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC--CCEEecCCC
Confidence 345555554 5557888999999999995 899999999999975 678877664
No 46
>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=74.49 E-value=15 Score=26.03 Aligned_cols=38 Identities=21% Similarity=0.391 Sum_probs=32.9
Q ss_pred CceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccc
Q 022049 96 RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (303)
Q Consensus 96 ~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesG 135 (303)
..+|..|+|...|++...+.+.|..|..+ |-|+....|
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~--g~i~~~~~~ 61 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEE--GLISRRGRG 61 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEecCCC
Confidence 56899999999999999999999999886 777766545
No 47
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=73.58 E-value=9.9 Score=30.40 Aligned_cols=78 Identities=24% Similarity=0.235 Sum_probs=41.6
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecc---ccEEEEcChhhHHHHhhhhHHHhHHHH
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE---GDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVses---GdIlYvFP~~fRs~l~~Ks~r~rlq~~ 161 (303)
-.||+++-..|. +|-.|+|..+|++.+++++.|..|..+.=-+.+-..+ |-..|.+==|++.+ -...+.++...
T Consensus 16 ~~Il~~L~~~~~-l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~i~~~~~--~~~ik~r~~~~ 92 (105)
T PF02002_consen 16 VRILDALLRKGE-LTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWYIDYDQI--IDVIKYRIYKM 92 (105)
T ss_dssp HHHHHHHHHH---B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE-THHHH-------------
T ss_pred HHHHHHHHHcCC-cCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEEEcHHHH--HHHHHHHHHHH
Confidence 468999988765 8999999999999999999999999998766665443 44556665555553 22234444444
Q ss_pred HHHH
Q 022049 162 IDKA 165 (303)
Q Consensus 162 ~~k~ 165 (303)
.+++
T Consensus 93 ~~~l 96 (105)
T PF02002_consen 93 REKL 96 (105)
T ss_dssp ----
T ss_pred HHHH
Confidence 4444
No 48
>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=72.90 E-value=3.5 Score=30.13 Aligned_cols=33 Identities=21% Similarity=0.335 Sum_probs=27.2
Q ss_pred hcCCce-eehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 93 ACNRRV-TIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 93 ~~g~rv-TvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
+.|.++ |..++|..-|+|...++++|..|+++.
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g 52 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRLEAEG 52 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCC
Confidence 456778 999999999999999999999999863
No 49
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=72.70 E-value=8.4 Score=26.76 Aligned_cols=40 Identities=20% Similarity=0.336 Sum_probs=34.6
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
.|-+|+.++.+ +..|+.|+|...|++...+.+-|..|-..
T Consensus 3 ~R~~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL~~L~~~ 42 (47)
T PF01022_consen 3 TRLRILKLLSE--GPLTVSELAEELGLSQSTVSHHLKKLREA 42 (47)
T ss_dssp HHHHHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHh--CCCchhhHHHhccccchHHHHHHHHHHHC
Confidence 57789999998 66999999999999999999999988654
No 50
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=72.44 E-value=26 Score=31.91 Aligned_cols=82 Identities=24% Similarity=0.212 Sum_probs=61.4
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCc--eEee-ccccEEEEcChhhHHHHhhhhHHHhHHHH
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGF--LEVS-DEGDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~--LeVs-esGdIlYvFP~~fRs~l~~Ks~r~rlq~~ 161 (303)
-.+.+++.+.| -+|=-++|...|+.++++++.|.+|-.+.-.. =+.+ ++|...|..=-+++.++. ..+.+....
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-ELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDEESGWEEYTWYINYEKVLE--VLKGKKRKI 97 (176)
T ss_pred hHHHHHHHhcC-CcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCCCcEEEEEEechHHHHH--HHHHHHHHH
Confidence 46788998888 89999999999999999999999998876433 3333 588899988888887533 344455555
Q ss_pred HHHHhhhh
Q 022049 162 IDKAKAAA 169 (303)
Q Consensus 162 ~~k~w~v~ 169 (303)
+++++..+
T Consensus 98 le~Lk~~l 105 (176)
T COG1675 98 LEKLKRKL 105 (176)
T ss_pred HHHHHHHH
Confidence 56655553
No 51
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=71.63 E-value=31 Score=31.87 Aligned_cols=47 Identities=13% Similarity=0.157 Sum_probs=40.2
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeV 131 (303)
+-+.+|++.+++.+ .+|+.|+|..-|+|...+++.|..|... |.|+-
T Consensus 4 ~R~~~Il~~l~~~~-~~~~~eLa~~l~VS~~TiRRdL~~L~~~--~~l~r 50 (240)
T PRK10411 4 ARQQAIVDLLLNHT-SLTTEALAEQLNVSKETIRRDLNELQTQ--GKILR 50 (240)
T ss_pred HHHHHHHHHHHHcC-CCcHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEE
Confidence 34677899999766 7999999999999999999999999883 66654
No 52
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=70.34 E-value=6.9 Score=36.18 Aligned_cols=42 Identities=14% Similarity=0.231 Sum_probs=37.1
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
..+.+|++.+++. +.+|+.|+|...|+|...+++.|..|.+.
T Consensus 5 ~R~~~Il~~l~~~-~~~~~~ela~~l~vS~~TirRdL~~Le~~ 46 (251)
T PRK13509 5 QRHQILLELLAQL-GFVTVEKVIERLGISPATARRDINKLDES 46 (251)
T ss_pred HHHHHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4677889999975 56999999999999999999999999764
No 53
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=70.07 E-value=55 Score=27.69 Aligned_cols=60 Identities=13% Similarity=0.139 Sum_probs=47.5
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEc
Q 022049 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (303)
Q Consensus 79 l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvF 141 (303)
|....|-+|++.+... +.+|++|+|...|++...+-+-|..|.. -|-+....+|.-+|..
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 4556788899888654 4699999999999999999999998865 4677778788755544
No 54
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=69.35 E-value=8.6 Score=35.71 Aligned_cols=42 Identities=12% Similarity=0.202 Sum_probs=37.6
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
.-+.+|++.+++.| .+|+.|+|..-|+|...+++.|..|.++
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 46778899997766 6999999999999999999999999985
No 55
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=69.29 E-value=11 Score=30.78 Aligned_cols=61 Identities=26% Similarity=0.281 Sum_probs=45.5
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEE
Q 022049 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (303)
Q Consensus 79 l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYv 140 (303)
++.+.-+++++-|.+.-+ +|+.-||.+-+++.+.|+++|+.|....-=.+-+-...-.||+
T Consensus 24 ~dk~t~dkl~kEV~~~K~-ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt 84 (86)
T PRK09334 24 LDEELLKRVAKEVKKEKI-VTPYTLASKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYV 84 (86)
T ss_pred cCHHHHHHHHHHhccCcE-EcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEec
Confidence 566777888888887544 9999999999999999999999998764322222234556664
No 56
>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=68.14 E-value=3.9 Score=29.32 Aligned_cols=22 Identities=18% Similarity=0.412 Sum_probs=19.4
Q ss_pred CCCCchhhHHHHHHHHhcCCce
Q 022049 77 DKLPADVRNRAMDAVDACNRRV 98 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rv 98 (303)
+++..+.+++|+++++++||+.
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 57
>PHA02943 hypothetical protein; Provisional
Probab=68.03 E-value=36 Score=30.97 Aligned_cols=60 Identities=22% Similarity=0.279 Sum_probs=45.6
Q ss_pred hhHHHHHHHHh-cCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChh
Q 022049 83 VRNRAMDAVDA-CNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (303)
Q Consensus 83 ~~~~im~Ave~-~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~ 144 (303)
+.+|+.+.+|- ..+-.|..+||-..|+|-.+|+-.|..|..+ |-++--+-|...|.+=.+
T Consensus 9 v~~R~~eILE~Lk~G~~TtseIAkaLGlS~~qa~~~LyvLErE--G~VkrV~~G~~tyw~l~~ 69 (165)
T PHA02943 9 VHTRMIKTLRLLADGCKTTSRIANKLGVSHSMARNALYQLAKE--GMVLKVEIGRAAIWCLDE 69 (165)
T ss_pred HHHHHHHHHHHHhcCCccHHHHHHHHCCCHHHHHHHHHHHHHc--CceEEEeecceEEEEECh
Confidence 44555555555 4555779999999999999999999988775 556666799888877544
No 58
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=67.92 E-value=13 Score=34.27 Aligned_cols=42 Identities=17% Similarity=0.274 Sum_probs=37.3
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 022049 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAa 123 (303)
..-+.+|++-++++|. +|+.|+|..-|.|...+++.|..|..
T Consensus 6 ~eR~~~I~~~l~~~~~-v~v~eLa~~~~VS~~TIRRDL~~Le~ 47 (252)
T PRK10681 6 DERIGQLLQALKRSDK-LHLKDAAALLGVSEMTIRRDLNAHSA 47 (252)
T ss_pred HHHHHHHHHHHHHcCC-CcHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 3467788999998776 99999999999999999999999885
No 59
>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=66.45 E-value=7.8 Score=35.12 Aligned_cols=43 Identities=30% Similarity=0.433 Sum_probs=36.4
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 022049 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (303)
Q Consensus 86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~Le 130 (303)
+|++++.+.+..+|+.|+|..+||+...+-+=|..|.+. |.|+
T Consensus 13 ~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~--G~l~ 55 (248)
T TIGR02431 13 AVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVEL--GYVT 55 (248)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEE
Confidence 467777777788999999999999999999999999765 4565
No 60
>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=65.68 E-value=60 Score=26.30 Aligned_cols=78 Identities=15% Similarity=0.208 Sum_probs=55.8
Q ss_pred hhHHHHHHHHhcCCceeehhhhhh----cCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHHHhhhhHHHhH
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGK----AGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKV 158 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~----aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~l~~Ks~r~rl 158 (303)
.-..||+.+=++|. +|+.||... -+++.+.++.-|..|.. -|.|++...|---+..|---|.- +.+..+
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--KGFLTREKIGRAYVYSPLISREE----YLAQEL 76 (115)
T ss_dssp HHHHHHHHHHHHSS-EEHHHHHHHHCTTSS--HHHHHHHHHHHHH--TTSEEEEEETTCEEEEESSSHHH----HHHHHH
T ss_pred HHHHHHHHHHhCCC-CCHHHHHHHHHhccccchhHHHHHHHHHHh--CCceeEeecCCceEEEeCCcHHH----HHHHHH
Confidence 34679999999999 999999965 35778888888888887 58999999888655556555443 344455
Q ss_pred HHHHHHHhh
Q 022049 159 EPVIDKAKA 167 (303)
Q Consensus 159 q~~~~k~w~ 167 (303)
+.+++++..
T Consensus 77 ~~~l~~~~~ 85 (115)
T PF03965_consen 77 RQFLDRLFD 85 (115)
T ss_dssp HHHHHHHST
T ss_pred HHHHHHHhC
Confidence 555555543
No 61
>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=65.34 E-value=5.7 Score=29.66 Aligned_cols=38 Identities=21% Similarity=0.287 Sum_probs=31.4
Q ss_pred hHHHHHHHHhc------CCceeehhhhhhcCCCHHHHHHHHHHH
Q 022049 84 RNRAMDAVDAC------NRRVTIGDVAGKAGLKLNEAQKALQAL 121 (303)
Q Consensus 84 ~~~im~Ave~~------g~rvTvgDVAa~aGLsl~eAe~aL~aL 121 (303)
.|+..+.++++ |+..|+.+++.+.||++++.-++|.+|
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 35566666664 577999999999999999999999875
No 62
>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=64.74 E-value=17 Score=30.56 Aligned_cols=59 Identities=14% Similarity=0.124 Sum_probs=43.3
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEE
Q 022049 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYv 140 (303)
.+.-+++++-|.+. .-+|+.-||.+-+++...|+++|+.|++..-=.+=+-..+-.||.
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 44445555555554 349999999999999999999999999876544444455667774
No 63
>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=63.90 E-value=13 Score=26.56 Aligned_cols=41 Identities=15% Similarity=0.277 Sum_probs=32.3
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
-.||..+...+...|+.|+|...|++...+-+.|..|....
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~g 46 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKG 46 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 45788888788899999999999999999999999999874
No 64
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=63.68 E-value=33 Score=35.78 Aligned_cols=80 Identities=10% Similarity=0.105 Sum_probs=67.3
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHHHhhhhHHHhHHH
Q 022049 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEP 160 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~l~~Ks~r~rlq~ 160 (303)
+....+|++++++.+...+..++|...|++.+++.+++..|.++ |-++|.+.=...|+-...=+..+++-+.-.++-.
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 6899999999999999998998888665555443
Q ss_pred HH
Q 022049 161 VI 162 (303)
Q Consensus 161 ~~ 162 (303)
.+
T Consensus 83 ~l 84 (494)
T PTZ00326 83 KL 84 (494)
T ss_pred Hh
Confidence 33
No 65
>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=63.68 E-value=12 Score=32.81 Aligned_cols=47 Identities=26% Similarity=0.462 Sum_probs=38.6
Q ss_pred hhhHHHHHHHHh----cCCceeehhhhhhcCCC-HHHHHHHHHHHHhhcCCceE
Q 022049 82 DVRNRAMDAVDA----CNRRVTIGDVAGKAGLK-LNEAQKALQALAADTDGFLE 130 (303)
Q Consensus 82 ~~~~~im~Ave~----~g~rvTvgDVAa~aGLs-l~eAe~aL~aLAad~~G~Le 130 (303)
+.+.+|++++.+ .|+..|+.|+|...|++ ...+.+.|..|..+ |.|+
T Consensus 6 ~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~--g~i~ 57 (199)
T TIGR00498 6 ARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERK--GYIE 57 (199)
T ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHC--CCEe
Confidence 456677777763 57789999999999998 99999999999987 4444
No 66
>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=63.45 E-value=16 Score=25.69 Aligned_cols=40 Identities=15% Similarity=0.236 Sum_probs=34.8
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
=.+|..+.+.|. +|+.|+|...|++...+-+.+..|..+.
T Consensus 6 ~~iL~~l~~~~~-~~~~~la~~~~~~~~~~t~~i~~L~~~g 45 (59)
T PF01047_consen 6 FRILRILYENGG-ITQSELAEKLGISRSTVTRIIKRLEKKG 45 (59)
T ss_dssp HHHHHHHHHHSS-EEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCC-CCHHHHHHHHCCChhHHHHHHHHHHHCC
Confidence 467888999888 9999999999999999999999998764
No 67
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=63.44 E-value=18 Score=32.93 Aligned_cols=56 Identities=20% Similarity=0.275 Sum_probs=43.1
Q ss_pred HHHHHHHH-hcCC-ceeehhhhhhcCCCHHHHHHHHHHHHhhcC---CceEeeccccEEEEc
Q 022049 85 NRAMDAVD-ACNR-RVTIGDVAGKAGLKLNEAQKALQALAADTD---GFLEVSDEGDVLYVF 141 (303)
Q Consensus 85 ~~im~Ave-~~g~-rvTvgDVAa~aGLsl~eAe~aL~aLAad~~---G~LeVsesGdIlYvF 141 (303)
+++++|+- -.|- .+|+.++|...|++.+++++.|..|..++. .-+++.+.|+- |.|
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 34455553 4455 499999999999999999999999999984 35888886664 555
No 68
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=62.60 E-value=12 Score=34.13 Aligned_cols=43 Identities=23% Similarity=0.386 Sum_probs=36.6
Q ss_pred hhhHHHHHHH-HhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 82 DVRNRAMDAV-DACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 82 ~~~~~im~Av-e~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
....+|++.+ +..++.+|+.++|...|.+..-|+..|..+..+
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 6678899999 788889999999999999999999999996654
No 69
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=62.46 E-value=8.7 Score=25.49 Aligned_cols=35 Identities=20% Similarity=0.342 Sum_probs=29.4
Q ss_pred CceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 022049 96 RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 96 ~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs 132 (303)
..+|+.|+|...|++...+.+.|..|.++ |-|+..
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~~--g~l~~~ 41 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEKE--GLISRE 41 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEe
Confidence 45788999999999999999999999884 555544
No 70
>PRK11569 transcriptional repressor IclR; Provisional
Probab=62.45 E-value=11 Score=35.02 Aligned_cols=45 Identities=20% Similarity=0.421 Sum_probs=38.1
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 022049 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs 132 (303)
+|++++.+.+..+|+.|+|..+||+...+-+=|..|.+. |-|+-.
T Consensus 32 ~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~--G~l~~~ 76 (274)
T PRK11569 32 KLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQ--GFVRQV 76 (274)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEc
Confidence 568888887888999999999999999999999999764 566543
No 71
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=62.03 E-value=10 Score=31.82 Aligned_cols=43 Identities=21% Similarity=0.190 Sum_probs=36.2
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
+++..|+.+....|..+++.++|.+.|+|..-++++|..|..+
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 72
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=61.98 E-value=11 Score=34.92 Aligned_cols=47 Identities=15% Similarity=0.241 Sum_probs=39.4
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse 133 (303)
-+|++++.+.+...|+.|+|..+|++...+-+=|..|.+. |.|+=++
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~--G~l~~~~ 74 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAA--DFVYQDS 74 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEcC
Confidence 3568888888888999999999999999999999999875 6665554
No 73
>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=61.77 E-value=18 Score=26.92 Aligned_cols=33 Identities=21% Similarity=0.264 Sum_probs=29.2
Q ss_pred HhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 92 DACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 92 e~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
.+.+..|+..|+|...|++...|-+.|..|+.+
T Consensus 17 ~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~ 49 (60)
T PF01325_consen 17 SEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEK 49 (60)
T ss_dssp HHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HcCCCCccHHHHHHHHCCChHHHHHHHHHHHHC
Confidence 347899999999999999999999999999875
No 74
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=61.59 E-value=38 Score=35.41 Aligned_cols=79 Identities=15% Similarity=0.189 Sum_probs=66.8
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHHHhhhhHHHhHHHH
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~l~~Ks~r~rlq~~ 161 (303)
+...+|+++++..+...+..++|...|++.+++.+++..|.++ |-+++.+.=+..|+-...=+..+++-+.-.++-.+
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 4568899999987766899999999999999999999999998 68999999999999999888888876655554444
Q ss_pred H
Q 022049 162 I 162 (303)
Q Consensus 162 ~ 162 (303)
+
T Consensus 81 l 81 (492)
T PLN02853 81 V 81 (492)
T ss_pred H
Confidence 3
No 75
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=60.87 E-value=27 Score=32.15 Aligned_cols=45 Identities=13% Similarity=0.252 Sum_probs=24.4
Q ss_pred HHHHHHHHhcCCceeehhhhhhcC------CCHHHHHHHHHHHHhhc-CCceEee
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAG------LKLNEAQKALQALAADT-DGFLEVS 132 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aG------Lsl~eAe~aL~aLAad~-~G~LeVs 132 (303)
+|..+-+++.+ |+.|+..--. -.+++.+..+..|.... -.++.++
T Consensus 149 ~rl~~ll~ka~---~~~d~l~ie~~L~~v~~eIe~~~~~~~~l~~~v~~sti~i~ 200 (262)
T PF14257_consen 149 ERLLELLEKAK---TVEDLLEIERELSRVRSEIEQLEGQLKYLDDRVDYSTITIS 200 (262)
T ss_pred HHHHHHHHhcC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhceEEEEEE
Confidence 33444444333 7887764222 14566666666666666 4555544
No 76
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=60.59 E-value=6.4 Score=28.20 Aligned_cols=21 Identities=33% Similarity=0.528 Sum_probs=18.7
Q ss_pred eehhhhhhcCCCHHHHHHHHH
Q 022049 99 TIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 99 TvgDVAa~aGLsl~eAe~aL~ 119 (303)
|+.|||..+|+|...+-+.|.
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 77
>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=60.47 E-value=7.5 Score=28.13 Aligned_cols=22 Identities=32% Similarity=0.543 Sum_probs=19.2
Q ss_pred hcCCceEeeccccEEEEcChhh
Q 022049 124 DTDGFLEVSDEGDVLYVFPNNY 145 (303)
Q Consensus 124 d~~G~LeVsesGdIlYvFP~~f 145 (303)
...|..+|+.+|-.||.|.+|-
T Consensus 6 ~~dG~~~~~~~G~~LY~f~~D~ 27 (48)
T PF03640_consen 6 RADGTIQVDYNGMPLYYFDKDS 27 (48)
T ss_pred eCCCCEEECCCCCEEEEECCCC
Confidence 3469999999999999998875
No 78
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=59.31 E-value=13 Score=34.12 Aligned_cols=52 Identities=19% Similarity=0.406 Sum_probs=39.9
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-cccEEEEc
Q 022049 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYVF 141 (303)
Q Consensus 86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse-sGdIlYvF 141 (303)
+|++++...+..+|+.|+|.+.|++...+-+-|..|.+. |-|+-.+ +|. |.-
T Consensus 15 ~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~--g~v~~~~~~~~--Y~L 67 (263)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEE--GYVRRSASDDS--FRL 67 (263)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEecCCCc--EEE
Confidence 456677677777999999999999999999999999764 5665443 443 544
No 79
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=58.56 E-value=49 Score=28.38 Aligned_cols=77 Identities=21% Similarity=0.190 Sum_probs=52.5
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcC--CceE--ee-ccc-cEEEEcChhhHHHHhhhhHHHhHHH
Q 022049 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTD--GFLE--VS-DEG-DVLYVFPNNYRAKLAAKSFRLKVEP 160 (303)
Q Consensus 87 im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~--G~Le--Vs-esG-dIlYvFP~~fRs~l~~Ks~r~rlq~ 160 (303)
||+++-+.| -+|-.|+|...|++++++++.|..|-.|-- .+-+ -. ++| -..|.|==|++.+. -..+.++..
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 678887776 699999999999999999999999998553 2222 22 345 47777766666642 234444555
Q ss_pred HHHHHh
Q 022049 161 VIDKAK 166 (303)
Q Consensus 161 ~~~k~w 166 (303)
..+++.
T Consensus 83 ~~~~L~ 88 (147)
T smart00531 83 MRKRLE 88 (147)
T ss_pred HHHHHH
Confidence 555544
No 80
>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=57.62 E-value=31 Score=26.24 Aligned_cols=43 Identities=26% Similarity=0.306 Sum_probs=33.3
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCce
Q 022049 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFL 129 (303)
Q Consensus 87 im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~L 129 (303)
+.|.+.++.-...-.+.|+++.|+++|.++-|+..|+...-+|
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 3567788888889999999999999999999999998876554
No 81
>PRK09480 slmA division inhibitor protein; Provisional
Probab=57.30 E-value=9.5 Score=31.99 Aligned_cols=33 Identities=18% Similarity=0.402 Sum_probs=25.1
Q ss_pred chhhHHHHHHH----H-hcCCceeehhhhhhcCCCHHH
Q 022049 81 ADVRNRAMDAV----D-ACNRRVTIGDVAGKAGLKLNE 113 (303)
Q Consensus 81 ~~~~~~im~Av----e-~~g~rvTvgDVAa~aGLsl~e 113 (303)
.+.+++|++|. . +.|..+|+.|||.++|++...
T Consensus 9 ~~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt 46 (194)
T PRK09480 9 GERREQILQALAQMLESPPGERITTAKLAARVGVSEAA 46 (194)
T ss_pred hhHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhH
Confidence 45677777773 3 336899999999999998643
No 82
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=57.01 E-value=21 Score=30.40 Aligned_cols=42 Identities=10% Similarity=0.180 Sum_probs=37.2
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
...+|++++++. +|.+..++|.+.|+|...+++-+..|-++.
T Consensus 10 ~D~~Il~~Lq~d-~R~s~~eiA~~lglS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 10 LDRGILEALMEN-ARTPYAELAKQFGVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 566778888776 889999999999999999999999998765
No 83
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=55.51 E-value=17 Score=33.66 Aligned_cols=46 Identities=20% Similarity=0.364 Sum_probs=37.9
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 022049 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (303)
Q Consensus 86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse 133 (303)
+|++++.+.+..+|+.|+|.++|++.+.+.+-|..|... |-++-++
T Consensus 8 ~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~--G~v~~d~ 53 (246)
T COG1414 8 AILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVEL--GYVEQDP 53 (246)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHC--CCEEEcC
Confidence 578888886677899999999999999999999999764 5555544
No 84
>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=55.44 E-value=15 Score=35.39 Aligned_cols=46 Identities=17% Similarity=0.341 Sum_probs=37.4
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 022049 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (303)
Q Consensus 86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse 133 (303)
+|++++++..+|++-.++|.+-|+|....+++++.|.++ |-+++..
T Consensus 187 ~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~a--GvIe~r~ 232 (251)
T TIGR02787 187 HIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESA--GVIESRS 232 (251)
T ss_pred HHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEecc
Confidence 344444554679999999999999999999999999875 6777776
No 85
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=55.37 E-value=7.5 Score=35.42 Aligned_cols=26 Identities=31% Similarity=0.456 Sum_probs=23.0
Q ss_pred CCceeehhhhhhcCCCHHHHHHHHHH
Q 022049 95 NRRVTIGDVAGKAGLKLNEAQKALQA 120 (303)
Q Consensus 95 g~rvTvgDVAa~aGLsl~eAe~aL~a 120 (303)
..++|+.|||..+|+|...+-++|..
T Consensus 4 ~~~~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 4 AKKITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHHHCC
Confidence 45799999999999999999888864
No 86
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=55.30 E-value=29 Score=32.40 Aligned_cols=62 Identities=27% Similarity=0.391 Sum_probs=46.5
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecc-ccE-EEEcChhh
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-GDV-LYVFPNNY 145 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVses-GdI-lYvFP~~f 145 (303)
+..+-+-..+...| -+|+.|+|.-+||+..+++++|..|.++ +.=.+|+-+ |.- .|.-|.+-
T Consensus 167 a~~~Lv~Ryl~~~G-Pat~~d~a~w~gl~~~~~r~~l~~l~~~-~~L~~v~~~~G~~~~~~~~~~~ 230 (327)
T PF06224_consen 167 ALAELVRRYLRAYG-PATLADFAWWSGLPKTQARRALAQLVEE-GELVEVEVEGGKEPLYDLPEDL 230 (327)
T ss_pred HHHHHHHHHHHHcC-CccHHHHHHHhccCHHHHHHHHHhhccC-CcEEEEEEcCcceeEEechhhh
Confidence 34444556677777 5999999999999999999998888653 333566655 776 89888765
No 87
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=54.74 E-value=33 Score=32.68 Aligned_cols=59 Identities=15% Similarity=0.195 Sum_probs=43.3
Q ss_pred CCCchhhHHHHHHHHhcCCceeehhhhhhcC--------------CCHHHHHHHHHHHHhhcCCceEeecccc
Q 022049 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAG--------------LKLNEAQKALQALAADTDGFLEVSDEGD 136 (303)
Q Consensus 78 ~l~~~~~~~im~Ave~~g~rvTvgDVAa~aG--------------Lsl~eAe~aL~aLAad~~G~LeVsesGd 136 (303)
++..+.|+||++++|++||+....--+.+++ ---.+.-+++...+++.|=++-+....+
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 7899999999999999999955543333333 2455666788888888888877766543
No 88
>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=53.93 E-value=37 Score=26.48 Aligned_cols=46 Identities=22% Similarity=0.455 Sum_probs=29.5
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee-ccccEEEEcChh
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS-DEGDVLYVFPNN 144 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs-esGdIlYvFP~~ 144 (303)
.++.+++.+++.|..||.+-|+ +.|..| |-..|. ++|..+|..|.+
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 4677788888888888776554 445554 446677 799999999975
No 89
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=53.52 E-value=23 Score=31.10 Aligned_cols=49 Identities=12% Similarity=0.159 Sum_probs=40.2
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc------CCceEeecccc
Q 022049 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT------DGFLEVSDEGD 136 (303)
Q Consensus 87 im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~------~G~LeVsesGd 136 (303)
|-...+ .++.++++|+|..-+++...+.+.|..|+++. .+.++.|+.|+
T Consensus 15 Iy~l~~-~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~ 69 (154)
T COG1321 15 IYELLE-EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGR 69 (154)
T ss_pred HHHHHh-ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCeEEChhhH
Confidence 333444 77789999999999999999999999999875 56677777775
No 90
>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=53.14 E-value=23 Score=29.12 Aligned_cols=20 Identities=25% Similarity=0.451 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHh-cCCCCCCC
Q 022049 186 VIVFTAIIAILS-SKSDDDDR 205 (303)
Q Consensus 186 vlv~~aIiails-s~s~~d~~ 205 (303)
+||++..+++++ ++|++++.
T Consensus 33 vLVIIiLlImlfqsSS~~~~s 53 (85)
T PF10717_consen 33 VLVIIILLIMLFQSSSNGNSS 53 (85)
T ss_pred HHHHHHHHHHHHhccCCCCCC
Confidence 343333344444 55544433
No 91
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=53.05 E-value=22 Score=31.79 Aligned_cols=40 Identities=18% Similarity=0.258 Sum_probs=36.3
Q ss_pred hhhHHHHHHHHhcC-CceeehhhhhhcCCCHHHHHHHHHHH
Q 022049 82 DVRNRAMDAVDACN-RRVTIGDVAGKAGLKLNEAQKALQAL 121 (303)
Q Consensus 82 ~~~~~im~Ave~~g-~rvTvgDVAa~aGLsl~eAe~aL~aL 121 (303)
....+|++.+.+.| -++++.|+|..+|++..++++.|..|
T Consensus 16 ~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l 56 (213)
T PRK05472 16 PLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYF 56 (213)
T ss_pred HHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHH
Confidence 44678899999988 68999999999999999999999999
No 92
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=52.82 E-value=61 Score=33.02 Aligned_cols=87 Identities=17% Similarity=0.202 Sum_probs=52.6
Q ss_pred HhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecccc-----EEEEcChhhHHHHhhhhHHHhHHHHHHHHh
Q 022049 92 DACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-----VLYVFPNNYRAKLAAKSFRLKVEPVIDKAK 166 (303)
Q Consensus 92 e~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGd-----IlYvFP~~fRs~l~~Ks~r~rlq~~~~k~w 166 (303)
.++|...|+.+||...|++.++.++.|.....-..-+..|.+++| ++-....+--..+.....+..|+.++..+.
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 467889999999999999999998877654322233333433333 221111122233334455666777777776
Q ss_pred hhhHHHHHHHHH
Q 022049 167 AAAEYSIRVLFG 178 (303)
Q Consensus 167 ~v~~yliRVsFG 178 (303)
.-=.-+|+..||
T Consensus 353 ~reR~VI~LRyg 364 (415)
T PRK07598 353 SRERDVIRMRFG 364 (415)
T ss_pred HHHHHHHHHHHh
Confidence 655556666665
No 93
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=52.59 E-value=21 Score=32.93 Aligned_cols=84 Identities=13% Similarity=0.197 Sum_probs=59.7
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec----------------------cccE---
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD----------------------EGDV--- 137 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse----------------------sGdI--- 137 (303)
--.+|++.++++|-++|.-+||.+-||+..++.+.|-.|.... .+-+++ +.+.
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 3468999999999779999999999999999999999997643 121110 1111
Q ss_pred ------EE-----EcChhhHHHHhhhhHHHhHHHHHHHHhhh
Q 022049 138 ------LY-----VFPNNYRAKLAAKSFRLKVEPVIDKAKAA 168 (303)
Q Consensus 138 ------lY-----vFP~~fRs~l~~Ks~r~rlq~~~~k~w~v 168 (303)
+| +-|..+=-.+..++++-+||+|.++-+..
T Consensus 83 ~~~~~~~f~~~~d~~~~~~i~~~k~~DpKS~LQE~~Q~~~~~ 124 (183)
T PHA02701 83 EAGCDTLFGGDIDVLTVSAVMRLKTLNPVSAVNEFCMRTHRP 124 (183)
T ss_pred cccccccccCccccccHHHhhcCCCCCccHHHHHHHHhcCCC
Confidence 22 34555555556677888888888876554
No 94
>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=52.44 E-value=31 Score=27.29 Aligned_cols=57 Identities=12% Similarity=0.103 Sum_probs=43.4
Q ss_pred hhhHHHHHHHHhc--CCceeehhhhhhcCCCHHHHHHHHHHHHh-----hcCCceEeeccccEEE
Q 022049 82 DVRNRAMDAVDAC--NRRVTIGDVAGKAGLKLNEAQKALQALAA-----DTDGFLEVSDEGDVLY 139 (303)
Q Consensus 82 ~~~~~im~Ave~~--g~rvTvgDVAa~aGLsl~eAe~aL~aLAa-----d~~G~LeVsesGdIlY 139 (303)
+.+.+|.+++++- |.-+|-+|||..+|.+- -++.--.+|+. ...||==|+.+|.+--
T Consensus 2 ~f~~~V~~~l~~IP~G~v~TYg~iA~~~g~p~-~~RaVg~al~~np~~~~iPcHRVv~s~G~l~~ 65 (80)
T TIGR00589 2 PFQQRVWQALRTIPYGETKSYGQLAARIGNPK-AVRAVGGANGRNPLAILVPCHRVIGKNGSLTG 65 (80)
T ss_pred hHHHHHHHHHhCCCCCCcCCHHHHHHHhCCCC-hHHHHHHHHHhCCCCCCCCCceeECCCCCCCC
Confidence 4678899999987 66788899999999653 24444455555 4689999999999753
No 95
>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=51.95 E-value=21 Score=28.09 Aligned_cols=58 Identities=19% Similarity=0.180 Sum_probs=45.2
Q ss_pred hhhHHHHHHHHhcC--CceeehhhhhhcC--CCHHHHHHHHHH--HHhhcCCceEeeccccEEE
Q 022049 82 DVRNRAMDAVDACN--RRVTIGDVAGKAG--LKLNEAQKALQA--LAADTDGFLEVSDEGDVLY 139 (303)
Q Consensus 82 ~~~~~im~Ave~~g--~rvTvgDVAa~aG--Lsl~eAe~aL~a--LAad~~G~LeVsesGdIlY 139 (303)
+.+.++.+++.+.. .-+|-+|||..+| -....+-.+|.. +.....+|==|+.+|.+-.
T Consensus 2 ~f~~~V~~~v~~IP~G~v~TYg~iA~~~g~p~~ar~Vg~al~~np~~~~iP~HRVv~~~G~l~~ 65 (85)
T PF01035_consen 2 PFQRRVWEAVRQIPYGKVTTYGEIARLLGRPKAARAVGSALARNPIPIIIPCHRVVNSDGSLGG 65 (85)
T ss_dssp HHHHHHHHHHTTS-TT-BEEHHHHHHHTT-TTCHHHHHHHHHTSSCTTTSGGGGEEBTTSBECT
T ss_pred hHHHHHHHHHHcCCCCceEeHHHHHHHHhhcccHHHHHHHhccccccCCCCeEEEECCCCCcCC
Confidence 46788899998865 5688899999999 666677777766 5567799999999999753
No 96
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=51.94 E-value=76 Score=32.36 Aligned_cols=72 Identities=17% Similarity=0.270 Sum_probs=56.2
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHHHhhhhHHHh
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLK 157 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~l~~Ks~r~r 157 (303)
.+.++++++...+ .+|..|+|.+.|++...+.+.+..|.++ |-+++.+.=...|.-...=++.+++-+...+
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 4578899998776 6999999999999999999999999998 6777776544566666666666665444333
No 97
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=51.86 E-value=18 Score=32.98 Aligned_cols=44 Identities=14% Similarity=0.274 Sum_probs=35.0
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 022049 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs 132 (303)
+|++++.+. ..+|+.|+|..+||+...+-+=|..|.+. |.|+-.
T Consensus 18 ~IL~~l~~~-~~l~l~eia~~lgl~kstv~Rll~tL~~~--G~l~~~ 61 (257)
T PRK15090 18 GILQALGEE-REIGITELSQRVMMSKSTVYRFLQTMKTL--GYVAQE 61 (257)
T ss_pred HHHHHhhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEc
Confidence 456666654 36999999999999999999999999875 556544
No 98
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=51.41 E-value=26 Score=34.36 Aligned_cols=55 Identities=16% Similarity=0.271 Sum_probs=41.6
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChh
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~ 144 (303)
+..|++++.+.+..+|+.|++..||+..+++-.+|+.| +.|.+-..+-+++. +++
T Consensus 210 ~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l-----~~l~~~~g~~~i~~-~~~ 264 (290)
T PLN03238 210 TRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL-----NLIKYWKGQHVIHV-DQR 264 (290)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC-----CcEEEECCcEEEEe-CHH
Confidence 46788998888899999999999999999998887755 55555444444444 443
No 99
>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=51.34 E-value=8.1 Score=27.04 Aligned_cols=28 Identities=32% Similarity=0.324 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhcCCeEeeecccCccCCC
Q 022049 272 RWKLIGEYIASNGGVVTAEELAPYLDID 299 (303)
Q Consensus 272 Rwq~Ig~~Ir~N~GvV~AEQlAPyLD~~ 299 (303)
|++.|..++.++++-|+++|||-.|+..
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~vS 28 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELGVS 28 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCTS-
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhCCC
Confidence 5677888897777779999999888754
No 100
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=50.48 E-value=26 Score=27.09 Aligned_cols=55 Identities=20% Similarity=0.175 Sum_probs=42.8
Q ss_pred hHHHHHHHHh--cCCceeehhhhhhcCC--CHHHHHHHHHHHHh--hcCCceEeeccccEE
Q 022049 84 RNRAMDAVDA--CNRRVTIGDVAGKAGL--KLNEAQKALQALAA--DTDGFLEVSDEGDVL 138 (303)
Q Consensus 84 ~~~im~Ave~--~g~rvTvgDVAa~aGL--sl~eAe~aL~aLAa--d~~G~LeVsesGdIl 138 (303)
+.++.++|++ .|.-+|-+|||..+|. ....+-.+|.+.-. +..+|==|+.+|.+.
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 4677777776 5667889999999999 46677777766654 578998889888876
No 101
>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=50.37 E-value=58 Score=26.24 Aligned_cols=62 Identities=13% Similarity=0.135 Sum_probs=47.8
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhh-----cCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcCh
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGK-----AGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~-----aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~ 143 (303)
..|..|++.+.+.+.-+|+.||... -.+++..+=+.|..|....=-+--..++|...|.+-.
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 4688899999999999999999864 3688899999999999876444444456778888754
No 102
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=50.04 E-value=25 Score=29.89 Aligned_cols=60 Identities=25% Similarity=0.358 Sum_probs=47.1
Q ss_pred chhhHHHHHHHHhc--CCceeehhhhhhcCCC--HHHHHHHHHHHHhhc--CCceEeeccccEEEE
Q 022049 81 ADVRNRAMDAVDAC--NRRVTIGDVAGKAGLK--LNEAQKALQALAADT--DGFLEVSDEGDVLYV 140 (303)
Q Consensus 81 ~~~~~~im~Ave~~--g~rvTvgDVAa~aGLs--l~eAe~aL~aLAad~--~G~LeVsesGdIlYv 140 (303)
.+.++++.+.|.+. |+-.|-||||.-+|++ ..++-+.|..|-.++ ..|=-|+.+|.|--.
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 35678888888765 6778999999999999 778888888665554 778888888887543
No 103
>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=49.86 E-value=36 Score=26.36 Aligned_cols=52 Identities=21% Similarity=0.337 Sum_probs=43.2
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEE
Q 022049 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (303)
Q Consensus 86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYv 140 (303)
.|-+++.. ++..|+.+++..+|++-.++..||==||.+ +.+++.+.++.+|+
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 46677777 668999999999999999999999999876 67888888777775
No 104
>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=49.49 E-value=28 Score=28.56 Aligned_cols=43 Identities=16% Similarity=0.325 Sum_probs=33.9
Q ss_pred HHHHHHh-cCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 022049 87 AMDAVDA-CNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (303)
Q Consensus 87 im~Ave~-~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeV 131 (303)
+|..+-+ .+.++|+.|+|.+.|+|...+++-|..|.+. |-++.
T Consensus 14 ~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~--Gli~~ 57 (130)
T TIGR02944 14 VLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLA--GIVTS 57 (130)
T ss_pred HHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHC--CcEEe
Confidence 4445544 3567999999999999999999999999884 45554
No 105
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=49.31 E-value=27 Score=38.54 Aligned_cols=56 Identities=21% Similarity=0.349 Sum_probs=45.7
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEE
Q 022049 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL 138 (303)
Q Consensus 80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIl 138 (303)
|..++..|++-+. .|+||.+-|++..-++.++-+|+.+..++++- .++.. ..|||+
T Consensus 58 ~~qL~~EI~~El~-~gGRvnlvdLa~~LnVD~~hiEr~~~~iv~~d-~~~~l-~~GeLi 113 (803)
T PLN03083 58 QDQLRNEIEAEIK-KLGRVSLVDLADTIGVDLYHVERQAQQVVSDD-PGLML-VQGEII 113 (803)
T ss_pred HHHHHHHHHHHHH-hCCCeeHHHHhhhcCCCHHHHHHHHHHHhcCC-CceEE-ecCEec
Confidence 4457788888884 58999999999999999999999999998885 44443 567764
No 106
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=48.95 E-value=29 Score=26.60 Aligned_cols=38 Identities=18% Similarity=0.214 Sum_probs=27.3
Q ss_pred HHHHHhc-CCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 88 MDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 88 m~Ave~~-g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
++-++.+ ....+..+++..++|+-..+++-|..|....
T Consensus 9 ~~IL~~l~~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~g 47 (77)
T PF14947_consen 9 FDILKILSKGGAKKTEIMYKANLNYSTLKKYLKELEEKG 47 (77)
T ss_dssp HHHHHHH-TT-B-HHHHHTTST--HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCc
Confidence 3434444 6778888999999999999999999998764
No 107
>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=48.85 E-value=1.3e+02 Score=25.42 Aligned_cols=75 Identities=13% Similarity=0.096 Sum_probs=53.1
Q ss_pred hHHHHHHHHhcCCceeehhhhhh----cCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHHHhhhhHHHhHH
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGK----AGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVE 159 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~----aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~l~~Ks~r~rlq 159 (303)
.-.||+.+=+.| .+|+.||... .|++.+.+..-|..|.. -|.|+...+|-.-+.+|--=|.- +.+..++
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 456899998776 5899997765 47889999888888877 57899888898555555444442 3344455
Q ss_pred HHHHHH
Q 022049 160 PVIDKA 165 (303)
Q Consensus 160 ~~~~k~ 165 (303)
.+++++
T Consensus 79 ~~~~~~ 84 (130)
T TIGR02698 79 ELFSRI 84 (130)
T ss_pred HHHHHH
Confidence 555544
No 108
>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=48.14 E-value=27 Score=26.04 Aligned_cols=34 Identities=18% Similarity=0.254 Sum_probs=26.2
Q ss_pred HhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 92 DACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 92 e~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
-+.++++|++|+|..-+++.+.++.-|..|....
T Consensus 9 l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG 42 (69)
T PF09012_consen 9 LRERGRVSLAELAREFGISPEAVEAMLEQLIRKG 42 (69)
T ss_dssp HHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCT
T ss_pred HHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 3456789999999999999999999988887653
No 109
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=47.14 E-value=18 Score=33.35 Aligned_cols=42 Identities=21% Similarity=0.334 Sum_probs=34.1
Q ss_pred HHHHHHHHh------cCCceeehhhhhhcCCCHHHHHHHHHHHHhhcC
Q 022049 85 NRAMDAVDA------CNRRVTIGDVAGKAGLKLNEAQKALQALAADTD 126 (303)
Q Consensus 85 ~~im~Ave~------~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~ 126 (303)
++..+..++ +|+..|+++++.+.|++.++.-++|.++++...
T Consensus 16 p~~~~vf~~~~idfCcgG~~~l~ea~~~~~i~~~~~~~~l~~~~~~~~ 63 (220)
T PRK10992 16 PRATALFREYDLDFCCGGKQTLARAAARKNLDIDVIEARLAALQEQPI 63 (220)
T ss_pred ccHHHHHHHcCCcccCCCCchHHHHHHHcCCCHHHHHHHHHHHHhccc
Confidence 344445555 578999999999999999999999999986653
No 110
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=47.08 E-value=18 Score=28.85 Aligned_cols=49 Identities=20% Similarity=0.190 Sum_probs=32.7
Q ss_pred hcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCce-EeeccccEEEEcChh
Q 022049 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFL-EVSDEGDVLYVFPNN 144 (303)
Q Consensus 93 ~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~L-eVsesGdIlYvFP~~ 144 (303)
......|++|+..+.|++..|+..-|. .-....+ .+=++||-|.+||..
T Consensus 28 ~~~~~~tvkd~IEsLGVP~tEV~~i~v---NG~~v~~~~~~~~Gd~v~V~P~~ 77 (81)
T PF14451_consen 28 PFDGGATVKDVIESLGVPHTEVGLILV---NGRPVDFDYRLKDGDRVAVYPVF 77 (81)
T ss_pred ecCCCCcHHHHHHHcCCChHHeEEEEE---CCEECCCcccCCCCCEEEEEecc
Confidence 567789999999999999999932221 0000000 122699999999863
No 111
>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=47.00 E-value=31 Score=30.22 Aligned_cols=53 Identities=11% Similarity=0.234 Sum_probs=41.3
Q ss_pred HHHHHHHHhcCC-ceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcCh
Q 022049 85 NRAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (303)
Q Consensus 85 ~~im~Ave~~g~-rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~ 143 (303)
++|-+.++++.. ++|+.+||..+|++..+..+=+. .|.|++++.-++-|.=.+
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 566777776654 69999999999999999876655 489999987777765443
No 112
>PRK11050 manganese transport regulator MntR; Provisional
Probab=46.96 E-value=1.7e+02 Score=25.09 Aligned_cols=46 Identities=24% Similarity=0.335 Sum_probs=37.3
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse 133 (303)
..|+.++.. +...|+.|+|...|++...+.+.|..|.++ |-++...
T Consensus 40 ~~I~~~l~~-~~~~t~~eLA~~l~is~stVsr~l~~Le~~--GlI~r~~ 85 (152)
T PRK11050 40 ELIADLIAE-VGEARQVDIAARLGVSQPTVAKMLKRLARD--GLVEMRP 85 (152)
T ss_pred HHHHHHHHh-cCCCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEec
Confidence 456667765 457899999999999999999999999987 5666544
No 113
>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=46.96 E-value=23 Score=32.65 Aligned_cols=38 Identities=18% Similarity=0.388 Sum_probs=33.2
Q ss_pred hHHHHHHHHhcCCc--eeehhhhhhcCCCHHHHHHHHHHH
Q 022049 84 RNRAMDAVDACNRR--VTIGDVAGKAGLKLNEAQKALQAL 121 (303)
Q Consensus 84 ~~~im~Ave~~g~r--vTvgDVAa~aGLsl~eAe~aL~aL 121 (303)
+..|++.+.+...+ +|+.|++.+||+..+++-..|+.|
T Consensus 135 ~~~i~~~L~~~~~~~~isi~~is~~Tgi~~~DIi~tL~~l 174 (188)
T PF01853_consen 135 RRVILEYLLEFKGKKSISIKDISQETGIRPEDIISTLQQL 174 (188)
T ss_dssp HHHHHHHHHHTSSE--EEHHHHHHHH-BTHHHHHHHHHHT
T ss_pred HHHHHHHHHhcCCCCeEEHHHHHHHHCCCHHHHHHHHHHC
Confidence 57889999888885 999999999999999999988876
No 114
>PRK09526 lacI lac repressor; Reviewed
Probab=46.76 E-value=13 Score=33.92 Aligned_cols=24 Identities=33% Similarity=0.462 Sum_probs=21.2
Q ss_pred CceeehhhhhhcCCCHHHHHHHHH
Q 022049 96 RRVTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 96 ~rvTvgDVAa~aGLsl~eAe~aL~ 119 (303)
.++|+.|||..+|+|...+-+.|.
T Consensus 4 ~~~ti~dIA~~aGVS~~TVSrvLn 27 (342)
T PRK09526 4 KPVTLYDVARYAGVSYQTVSRVLN 27 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHhc
Confidence 468999999999999998877776
No 115
>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=46.16 E-value=43 Score=24.86 Aligned_cols=38 Identities=16% Similarity=0.287 Sum_probs=28.5
Q ss_pred hHHHHHHHHhcCC-----ceeehhhhhhcCCCHHHHHHHHHHH
Q 022049 84 RNRAMDAVDACNR-----RVTIGDVAGKAGLKLNEAQKALQAL 121 (303)
Q Consensus 84 ~~~im~Ave~~g~-----rvTvgDVAa~aGLsl~eAe~aL~aL 121 (303)
+.+++++.=+.|| ++|+.|+|..-|+|...+..-|+.-
T Consensus 5 Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 5 QREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred HHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3445555555555 8999999999999999987777653
No 116
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=46.05 E-value=14 Score=28.69 Aligned_cols=29 Identities=17% Similarity=0.318 Sum_probs=23.0
Q ss_pred HHHHHhcCCceeehhhhhhcCCCHHHHHH
Q 022049 88 MDAVDACNRRVTIGDVAGKAGLKLNEAQK 116 (303)
Q Consensus 88 m~Ave~~g~rvTvgDVAa~aGLsl~eAe~ 116 (303)
=+|++-...++++.||+..+|||..||+-
T Consensus 35 ~~A~klv~~Ga~~~el~~~CgL~~aEAeL 63 (70)
T PF10975_consen 35 SQAIKLVRQGASVEELMEECGLSRAEAEL 63 (70)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHH
Confidence 34555555679999999999999999953
No 117
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=45.98 E-value=16 Score=34.50 Aligned_cols=32 Identities=31% Similarity=0.606 Sum_probs=30.0
Q ss_pred cCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 94 CNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 94 ~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
+|+.+|+.+.|.+.|+.+++.++.|.+|....
T Consensus 31 CGG~~~L~~Aa~~k~l~~~~i~a~L~~l~~~~ 62 (221)
T COG2846 31 CGGKVTLERAAAEKGLDIDEIEARLNALQQEP 62 (221)
T ss_pred cCChHHHHHHHHHcCCCHHHHHHHHHHHHhcc
Confidence 79999999999999999999999999998765
No 118
>PRK09492 treR trehalose repressor; Provisional
Probab=45.86 E-value=12 Score=33.80 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=21.5
Q ss_pred CceeehhhhhhcCCCHHHHHHHHHH
Q 022049 96 RRVTIGDVAGKAGLKLNEAQKALQA 120 (303)
Q Consensus 96 ~rvTvgDVAa~aGLsl~eAe~aL~a 120 (303)
.++|+.|||..+|+|...+-++|..
T Consensus 3 ~~~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 3 NKLTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CCCcHHHHHHHhCCCHHHHhHHhCC
Confidence 3689999999999999988887763
No 119
>COG1459 PulF Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=45.12 E-value=66 Score=32.42 Aligned_cols=87 Identities=34% Similarity=0.420 Sum_probs=53.2
Q ss_pred CCceeehhhhh---------hcCCCHHHHHHHHHHHHhhcCC-ce--------EeeccccEEE--------EcChhhHHH
Q 022049 95 NRRVTIGDVAG---------KAGLKLNEAQKALQALAADTDG-FL--------EVSDEGDVLY--------VFPNNYRAK 148 (303)
Q Consensus 95 g~rvTvgDVAa---------~aGLsl~eAe~aL~aLAad~~G-~L--------eVsesGdIlY--------vFP~~fRs~ 148 (303)
..+++..|++. ++|+++.|| |..|+..+.. .+ +-=++|.-++ +||+.+++-
T Consensus 52 ~~~~~~~~l~~f~~qLa~Ll~aG~pL~~a---L~~l~~q~~~~~~~~~l~~i~~~l~~G~sls~al~~~~~~F~~~~~~~ 128 (397)
T COG1459 52 FKRISKKDLALFTRQLATLLKAGLPLYEA---LEILADQAPNPKLKQVLTSILEELESGKSLSEALAQLPGVFPDLYVAM 128 (397)
T ss_pred cCCCCHHHHHHHHHHHHHHHHCCCcHHHH---HHHHHHhCCCHHHHHHHHHHHHHHHCCCcHHHHHHhCcccCCHHHHHH
Confidence 45577777763 699999988 4444444433 11 1114566544 499999987
Q ss_pred Hhh--------------hhHHHhHHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 022049 149 LAA--------------KSFRLKVEPVIDKAKAAAEYSIRVLFGTALIAS 184 (303)
Q Consensus 149 l~~--------------Ks~r~rlq~~~~k~w~v~~yliRVsFGi~LIaS 184 (303)
++. -...++.++..+|+++++.|=.=+-+..++|..
T Consensus 129 v~~gE~~G~L~~~l~~la~y~e~~~~lr~Ki~~Al~YP~vll~v~~~v~~ 178 (397)
T COG1459 129 VAAGERSGNLDEVLQRLAKYLEKQAALRKKIKSALIYPLVLLVVALVVVL 178 (397)
T ss_pred HHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 764 124556677788999999997544333333333
No 120
>PF10025 DUF2267: Uncharacterized conserved protein (DUF2267); InterPro: IPR018727 This entry contains proteins that have no known function. ; PDB: 2YSK_A.
Probab=45.05 E-value=16 Score=30.34 Aligned_cols=68 Identities=21% Similarity=0.302 Sum_probs=52.3
Q ss_pred ehhhhhhcCC-CHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHHHhh-----h-hHHHhHHHHHHHHhh
Q 022049 100 IGDVAGKAGL-KLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAA-----K-SFRLKVEPVIDKAKA 167 (303)
Q Consensus 100 vgDVAa~aGL-sl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~l~~-----K-s~r~rlq~~~~k~w~ 167 (303)
+.+|+..+|+ +.++|++++++...--+-+|.+.+.-++.=..|...|..|.. . .-+..+++|+..+..
T Consensus 6 l~~V~~~~~l~~~~~A~~a~~avL~~L~~rL~~~ea~~La~qLP~~l~~~l~~gw~~~~~~~~~~~~eF~~rVa~ 80 (125)
T PF10025_consen 6 LDEVRERAGLPDREEAYRATRAVLHTLRERLPPEEAADLAAQLPMELRGILYEGWRPSEGPGRFDLDEFLARVAE 80 (125)
T ss_dssp HHHHHHHHT---HHHHHHHHHHHHHHHHTTS-HHHHHHHHTTS-HHHHHHHHTT--TTS-----SHHHHHHHHHH
T ss_pred HHHHHHHhCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHhCCHHHHHHHHhcccCCCCCCCCCHHHHHHHHHH
Confidence 4678999999 899999999999999999999999999999999999999954 1 223567888887755
No 121
>PF15581 Imm35: Immunity protein 35
Probab=44.91 E-value=39 Score=28.16 Aligned_cols=33 Identities=27% Similarity=0.471 Sum_probs=30.3
Q ss_pred cCCCHHHHHHHHHHHHhhc-CCceEeeccccEEE
Q 022049 107 AGLKLNEAQKALQALAADT-DGFLEVSDEGDVLY 139 (303)
Q Consensus 107 aGLsl~eAe~aL~aLAad~-~G~LeVsesGdIlY 139 (303)
-||+-.|+++-|.+.|+.. ++..+|-.+|+++.
T Consensus 44 RGl~~~qV~~kl~ava~~~~~~~~vvKkE~~~Iw 77 (93)
T PF15581_consen 44 RGLPEEQVLYKLEAVAAKGPEAKIVVKKEGNIIW 77 (93)
T ss_pred cCCCHHHHHHHHHHHHhcCCCcceEEEecCCeEE
Confidence 6999999999999999988 89999999999775
No 122
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=44.58 E-value=17 Score=31.73 Aligned_cols=32 Identities=13% Similarity=0.197 Sum_probs=24.9
Q ss_pred hhhHHHHHH----HHhcCCc-eeehhhhhhcCCCHHH
Q 022049 82 DVRNRAMDA----VDACNRR-VTIGDVAGKAGLKLNE 113 (303)
Q Consensus 82 ~~~~~im~A----ve~~g~r-vTvgDVAa~aGLsl~e 113 (303)
+.|++|++| +.+.||. +|+.|||.++|++...
T Consensus 18 ~~r~~IL~AA~~lf~e~Gy~~~s~~dIA~~aGvs~gt 54 (212)
T PRK15008 18 AKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTN 54 (212)
T ss_pred HHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHH
Confidence 456666555 5678887 8999999999999754
No 123
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=44.27 E-value=27 Score=25.72 Aligned_cols=50 Identities=22% Similarity=0.260 Sum_probs=37.0
Q ss_pred ceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHH
Q 022049 97 RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAK 148 (303)
Q Consensus 97 rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~ 148 (303)
.++..++..-.|++++. .++..+....|...+.+++++.+.+.++-||.=
T Consensus 5 ~~~~~~i~~llG~~i~~--~ei~~~L~~lg~~~~~~~~~~~~~v~~P~~R~D 54 (71)
T smart00874 5 TLRRERINRLLGLDLSA--EEIEEILKRLGFEVEVSGDDDTLEVTVPSYRFD 54 (71)
T ss_pred EecHHHHHHHHCCCCCH--HHHHHHHHHCCCeEEecCCCCeEEEECCCCccc
Confidence 35667888888988763 456777777788777766677888888888863
No 124
>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=43.64 E-value=26 Score=31.63 Aligned_cols=33 Identities=21% Similarity=0.381 Sum_probs=28.9
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHH
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQK 116 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~ 116 (303)
.++||-+|+.=+.| .|+.|||..+|++++.++.
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 77899999988776 7999999999999998753
No 125
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=43.55 E-value=45 Score=31.69 Aligned_cols=69 Identities=17% Similarity=0.222 Sum_probs=52.7
Q ss_pred ccccCCCCchhh----HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe--eccccEEEEc
Q 022049 73 IVESDKLPADVR----NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV--SDEGDVLYVF 141 (303)
Q Consensus 73 ~~~~~~l~~~~~----~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeV--sesGdIlYvF 141 (303)
...-+.||.-++ ..|+++++..+...|.-++|...|+|-..|++=|.-|++-.--..++ ...|.+.|.+
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 445566664433 56788888888999999999999999999999999999877444333 3577776654
No 126
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=43.36 E-value=17 Score=30.96 Aligned_cols=30 Identities=20% Similarity=0.199 Sum_probs=23.4
Q ss_pred hHHHHHH----HHhcCCc-eeehhhhhhcCCCHHH
Q 022049 84 RNRAMDA----VDACNRR-VTIGDVAGKAGLKLNE 113 (303)
Q Consensus 84 ~~~im~A----ve~~g~r-vTvgDVAa~aGLsl~e 113 (303)
|++|++| +.++||. +|+.|||.++|+|...
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 5666655 4667887 8999999999998654
No 127
>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=43.07 E-value=87 Score=27.84 Aligned_cols=47 Identities=19% Similarity=0.368 Sum_probs=38.9
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse 133 (303)
+-+++..+.++| .+|+.|+|...|++...+.+.|..|..+ |-++...
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 457788888765 4899999999999999999999999876 6665554
No 128
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=42.88 E-value=16 Score=33.16 Aligned_cols=23 Identities=30% Similarity=0.482 Sum_probs=20.5
Q ss_pred ceeehhhhhhcCCCHHHHHHHHH
Q 022049 97 RVTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 97 rvTvgDVAa~aGLsl~eAe~aL~ 119 (303)
++|+.|||..+|+|...+-++|.
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhC
Confidence 47999999999999999888884
No 129
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=42.87 E-value=19 Score=32.26 Aligned_cols=33 Identities=18% Similarity=0.314 Sum_probs=26.3
Q ss_pred hhhHHHHHHH----HhcCCceeehhhhhhcCCCHHHH
Q 022049 82 DVRNRAMDAV----DACNRRVTIGDVAGKAGLKLNEA 114 (303)
Q Consensus 82 ~~~~~im~Av----e~~g~rvTvgDVAa~aGLsl~eA 114 (303)
+.|++|++|. .+.||.+|+.|||.++|++....
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 5667776664 56799999999999999997653
No 130
>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=42.12 E-value=43 Score=27.14 Aligned_cols=38 Identities=18% Similarity=0.284 Sum_probs=30.7
Q ss_pred HHHHHHhc--CCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 87 AMDAVDAC--NRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 87 im~Ave~~--g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
+|-.+.+. +..+|..++|...|++...+++-|..|...
T Consensus 13 ~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 13 ALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRA 52 (132)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34444444 347999999999999999999999999874
No 131
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=41.94 E-value=2.1e+02 Score=23.93 Aligned_cols=43 Identities=16% Similarity=0.235 Sum_probs=33.8
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~Le 130 (303)
+.|...++ .++.+|+.|+|...|++...+...|..|..+ |-++
T Consensus 11 ~~I~~l~~-~~~~~~~~ela~~l~vs~~svs~~l~~L~~~--Gli~ 53 (142)
T PRK03902 11 EQIYLLIE-EKGYARVSDIAEALSVHPSSVTKMVQKLDKD--EYLI 53 (142)
T ss_pred HHHHHHHh-cCCCcCHHHHHHHhCCChhHHHHHHHHHHHC--CCEE
Confidence 33444444 4566799999999999999999999999988 5555
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=41.62 E-value=15 Score=27.00 Aligned_cols=25 Identities=24% Similarity=0.650 Sum_probs=21.8
Q ss_pred ccCCCCCCCchHHHHHHHHHHHHHh
Q 022049 258 VFGEGDPNQGIEEKRWKLIGEYIAS 282 (303)
Q Consensus 258 vFGDGDPN~dlEerRwq~Ig~~Ir~ 282 (303)
+.|||||-+-+...-||.|-..+..
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 4799999999999999999887754
No 133
>PRK06474 hypothetical protein; Provisional
Probab=41.47 E-value=49 Score=29.37 Aligned_cols=56 Identities=18% Similarity=0.180 Sum_probs=45.8
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhc-CCCHHHHHHHHHHHHhhcCCceEeecc
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKA-GLKLNEAQKALQALAADTDGFLEVSDE 134 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTvgDVAa~a-GLsl~eAe~aL~aLAad~~G~LeVses 134 (303)
+-|.-..|.+|++.+.+.+...|+.|++... +++...+=+-|..|+.. |-|++.+.
T Consensus 6 ~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~--GLI~~~~~ 62 (178)
T PRK06474 6 EILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDS--GILHVVKE 62 (178)
T ss_pred HhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHC--CCEEEeec
Confidence 3466778999999999887669999999987 78888888899999864 56666554
No 134
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=41.44 E-value=28 Score=33.32 Aligned_cols=44 Identities=32% Similarity=0.393 Sum_probs=36.7
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeV 131 (303)
.+.+.+++++.+|.|-++=+...+|++..+|++.|. +.+|||+.
T Consensus 250 ~~~a~~~l~~~~~~vk~a~~~~~~~~~~~~a~~~l~----~~~g~~~~ 293 (299)
T PRK05441 250 REEAEAALEAADGSVKLAIVMILTGLDAAEAKALLA----RHGGFLRK 293 (299)
T ss_pred HHHHHHHHHHhCCCcHHHHHHHHhCCCHHHHHHHHH----HcCCCHHH
Confidence 456788999999999999999999999999977665 57888753
No 135
>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=41.34 E-value=82 Score=30.91 Aligned_cols=70 Identities=19% Similarity=0.207 Sum_probs=50.4
Q ss_pred hhhHHHHHHHHhc--CCceeehhhhhh-cCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEc-ChhhHHHHhhh
Q 022049 82 DVRNRAMDAVDAC--NRRVTIGDVAGK-AGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF-PNNYRAKLAAK 152 (303)
Q Consensus 82 ~~~~~im~Ave~~--g~rvTvgDVAa~-aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvF-P~~fRs~l~~K 152 (303)
++.+++++.+.++ +..+|..|+... .++++.+...+|+.|.++.--.|-. .+|.++|.. ++.-.+++.+-
T Consensus 9 ~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~-~~~~l~~~~~~~~~a~k~~~l 82 (327)
T PF05158_consen 9 ELEKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLK-KGGGLSYKAVSEEEAKKLKGL 82 (327)
T ss_dssp HHHHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE--SSSEEEEE--SSS-----SS
T ss_pred HHHHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEE-cCCEEEEEEeCHHHHhhhcCC
Confidence 4778999999998 999999999988 8999999999999999987766666 566699987 34444545543
No 136
>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=41.27 E-value=26 Score=36.49 Aligned_cols=16 Identities=25% Similarity=0.453 Sum_probs=12.9
Q ss_pred cccEEEEcChhhHHHH
Q 022049 134 EGDVLYVFPNNYRAKL 149 (303)
Q Consensus 134 sGdIlYvFP~~fRs~l 149 (303)
+|.++|.-+.+-|..-
T Consensus 421 ~G~L~~~~~f~~r~~~ 436 (507)
T PF07245_consen 421 KGTLIYLGPFDDRNYT 436 (507)
T ss_pred EEEEEecccccccccc
Confidence 6899999998877643
No 137
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=41.08 E-value=84 Score=28.64 Aligned_cols=57 Identities=9% Similarity=0.105 Sum_probs=36.5
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhc-----------CCC---HHHHHHHHHHHHhhcCCceEeec
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKA-----------GLK---LNEAQKALQALAADTDGFLEVSD 133 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTvgDVAa~a-----------GLs---l~eAe~aL~aLAad~~G~LeVse 133 (303)
.++..+.|++|+++++++||+.-..--+.++ .++ ..+.-+++..-|.+.|-++.+..
T Consensus 30 ~~vs~~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~ 100 (331)
T PRK14987 30 EQVSVALRGKIAAALDELGYIPNRAPDILSNATSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQTMLAH 100 (331)
T ss_pred CCCCHHHHHHHHHHHHHhCCCccHHHHHHhhCCCCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEEEEec
Confidence 4678899999999999999964221101111 121 34556677777777777766543
No 138
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=40.62 E-value=37 Score=28.33 Aligned_cols=34 Identities=12% Similarity=0.191 Sum_probs=30.0
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHH
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~ 119 (303)
+..|+-|+++.| .|+..++.++||+-+....+|.
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 467889999998 7999999999999999988874
No 139
>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=40.56 E-value=22 Score=24.64 Aligned_cols=31 Identities=13% Similarity=0.240 Sum_probs=20.0
Q ss_pred HHHHHhcCCceeehhhhhhcCCCHHHHHHHH
Q 022049 88 MDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (303)
Q Consensus 88 m~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL 118 (303)
-++++-+..+.|+.|||...|+|.....+-|
T Consensus 12 ~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 12 EEIKELYAEGMSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHHHTT--HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3334444444999999999999999887655
No 140
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=40.32 E-value=18 Score=32.31 Aligned_cols=60 Identities=20% Similarity=0.370 Sum_probs=47.1
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-cccEEEEcC
Q 022049 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYVFP 142 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse-sGdIlYvFP 142 (303)
..++++||.--=+-|.+++..++|.+-|+|..-++++|..|+++ |=|++.. .|-.|=.+.
T Consensus 23 ~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~e--Glv~~~p~rG~~V~~~~ 83 (230)
T COG1802 23 EELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAE--GLVEIEPNRGAFVAPLS 83 (230)
T ss_pred HHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHC--CCeEecCCCCCeeCCCC
Confidence 45566666666667999999999999999999999999999987 4555554 566665553
No 141
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=40.27 E-value=17 Score=33.12 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=21.3
Q ss_pred CCceeehhhhhhcCCCHHHHHHHHH
Q 022049 95 NRRVTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 95 g~rvTvgDVAa~aGLsl~eAe~aL~ 119 (303)
..++|+.|||..+|+|...+-+.|.
T Consensus 3 ~~~~ti~dIA~~agVS~~TVSrvLn 27 (331)
T PRK14987 3 KKRPVLQDVADRVGVTKMTVSRFLR 27 (331)
T ss_pred CCCCcHHHHHHHhCCCHHHhhhhhC
Confidence 3469999999999999988877774
No 142
>PRK09526 lacI lac repressor; Reviewed
Probab=40.14 E-value=76 Score=28.93 Aligned_cols=56 Identities=18% Similarity=0.155 Sum_probs=37.4
Q ss_pred CCCCchhhHHHHHHHHhcCCceeeh--hhhh-hcC--------C---CHHHHHHHHHHHHhhcCCceEee
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTIG--DVAG-KAG--------L---KLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTvg--DVAa-~aG--------L---sl~eAe~aL~aLAad~~G~LeVs 132 (303)
.++..+.|++|+++++++||..-.. .++. +++ + -..+.-+++.+.|.+.|-++.+.
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 4688999999999999999964321 1111 011 1 12456677888888888777763
No 143
>KOG0860 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.05 E-value=90 Score=27.02 Aligned_cols=13 Identities=31% Similarity=0.409 Sum_probs=6.0
Q ss_pred CHHHHHHHHHHHH
Q 022049 110 KLNEAQKALQALA 122 (303)
Q Consensus 110 sl~eAe~aL~aLA 122 (303)
.|++-+.-=.+|.
T Consensus 58 kL~~L~drad~L~ 70 (116)
T KOG0860|consen 58 KLDELDDRADQLQ 70 (116)
T ss_pred hHHHHHHHHHHHH
Confidence 5555544444443
No 144
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=40.05 E-value=39 Score=23.26 Aligned_cols=38 Identities=11% Similarity=0.236 Sum_probs=28.4
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHH
Q 022049 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQA 120 (303)
Q Consensus 80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~a 120 (303)
...+...|++.+.+. .|+.+||...|++-+.++.-+..
T Consensus 13 T~~~~~~i~~~~~~~---~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 13 TKRLEQYILKLLRES---RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHHHHhhc---CCHHHHHHHHCCCHHHHHHHHHh
Confidence 334455555555544 79999999999999999887764
No 145
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=39.35 E-value=59 Score=21.50 Aligned_cols=46 Identities=13% Similarity=0.213 Sum_probs=33.1
Q ss_pred CCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCC
Q 022049 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG 127 (303)
Q Consensus 78 ~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G 127 (303)
.|+...+. ++..+. ...+..|+|...|++...+++-+..+-.+.+.
T Consensus 3 ~l~~~e~~-i~~~~~---~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~ 48 (58)
T smart00421 3 SLTPRERE-VLRLLA---EGLTNKEIAERLGISEKTVKTHLSNIMRKLGV 48 (58)
T ss_pred CCCHHHHH-HHHHHH---cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 45554444 554442 33699999999999999999998887666554
No 146
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=39.25 E-value=92 Score=28.39 Aligned_cols=54 Identities=13% Similarity=0.122 Sum_probs=34.1
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhcC-----------CC---HHHHHHHHHHHHhhcCCceE
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------LK---LNEAQKALQALAADTDGFLE 130 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aG-----------Ls---l~eAe~aL~aLAad~~G~Le 130 (303)
.++..+.|++|+++++++||.....--+.+++ ++ -.+..+++..-|.+.|-.+-
T Consensus 31 ~~vs~~tr~~V~~~a~elgY~p~~~a~~l~~~~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~ 98 (342)
T PRK10014 31 GRISTATGERVNQAIEELGFVRNRQASALRGGQSGVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVF 98 (342)
T ss_pred CCCCHHHHHHHHHHHHHhCCCcCHHHHhhccCCCCEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEE
Confidence 46889999999999999999764321111111 11 24555667676766655443
No 147
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=39.16 E-value=18 Score=33.11 Aligned_cols=22 Identities=32% Similarity=0.487 Sum_probs=19.4
Q ss_pred eeehhhhhhcCCCHHHHHHHHH
Q 022049 98 VTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 98 vTvgDVAa~aGLsl~eAe~aL~ 119 (303)
+|+.|||.++|+|...+-++|.
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn 23 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVIN 23 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 6999999999999998877775
No 148
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=39.03 E-value=22 Score=31.70 Aligned_cols=55 Identities=16% Similarity=0.137 Sum_probs=35.2
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhc-----------CC---CHHHHHHHHHHHHhhcCCceEe
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKA-----------GL---KLNEAQKALQALAADTDGFLEV 131 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTvgDVAa~a-----------GL---sl~eAe~aL~aLAad~~G~LeV 131 (303)
+++..+.|+||+++++++||+--..--+.++ .+ -..+..+++..-+.+.|-.+.+
T Consensus 2 ~~Vs~~Tr~rV~~~a~elgY~pn~~a~~l~~~~~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~ 70 (309)
T PRK11041 2 EKVSQATRQRVEQAVLEVGYSPQSLGRNLKRNESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYLVLI 70 (309)
T ss_pred CcCCHHHHHHHHHHHHHHCCCcCHHHHHhhcCCCcEEEEEeCCCcCccHHHHHHHHHHHHHHCCCEEEE
Confidence 5688899999999999999986433111111 11 2344556666666666655544
No 149
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=38.85 E-value=81 Score=25.71 Aligned_cols=65 Identities=23% Similarity=0.364 Sum_probs=42.7
Q ss_pred chhhHHHHHHHHhcCCceee--hhhhhhcCCC-----HHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHHH
Q 022049 81 ADVRNRAMDAVDACNRRVTI--GDVAGKAGLK-----LNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKL 149 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTv--gDVAa~aGLs-----l~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~l 149 (303)
..+...|++.+.+.|..-|+ .|||-.-+=+ ...++++-..|+. .|.++++-.|..| =|.+||..+
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 34667888888888887777 7999765433 6677777777776 5899999999987 567776644
No 150
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=38.57 E-value=25 Score=30.14 Aligned_cols=32 Identities=16% Similarity=0.257 Sum_probs=24.1
Q ss_pred hhhHHHHHH----HHhcCC-ceeehhhhhhcCCCHHH
Q 022049 82 DVRNRAMDA----VDACNR-RVTIGDVAGKAGLKLNE 113 (303)
Q Consensus 82 ~~~~~im~A----ve~~g~-rvTvgDVAa~aGLsl~e 113 (303)
..|.+|++| +.+.|| .+|+.|||.++|++...
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 467886 69999999999999754
No 151
>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=38.44 E-value=60 Score=24.86 Aligned_cols=44 Identities=23% Similarity=0.287 Sum_probs=31.2
Q ss_pred HHHHHHhcCC--ceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 022049 87 AMDAVDACNR--RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 87 im~Ave~~g~--rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs 132 (303)
+|-.+...+. .+|+.|+|...|++...+++-|..|... |-|+..
T Consensus 13 ~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~--Gli~s~ 58 (83)
T PF02082_consen 13 ILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA--GLIESS 58 (83)
T ss_dssp HHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT--TSEEEE
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC--CeeEec
Confidence 3444433333 3999999999999999999999999874 345444
No 152
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=38.25 E-value=61 Score=26.69 Aligned_cols=51 Identities=14% Similarity=0.261 Sum_probs=41.6
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc---CCceEeec
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT---DGFLEVSD 133 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~---~G~LeVse 133 (303)
+...+|++.+++.+. .+..++|.+.|+|...+.+-+..|-.+. +-+..++.
T Consensus 8 ~~D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~ 61 (154)
T COG1522 8 DIDRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDP 61 (154)
T ss_pred HHHHHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECH
Confidence 355678888887766 9999999999999999999999999887 44555553
No 153
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=37.88 E-value=1.3e+02 Score=21.39 Aligned_cols=59 Identities=19% Similarity=0.259 Sum_probs=44.5
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEc
Q 022049 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (303)
Q Consensus 80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvF 141 (303)
....|.+|+..+.+. ...++.+++...|++...+...|..|-...- ++...+|...|..
T Consensus 23 ~~~~r~~il~~l~~~-~~~~~~~l~~~~~~~~~~v~~hL~~L~~~gl--v~~~~~~~~~~~~ 81 (110)
T COG0640 23 ADPTRLEILSLLAEG-GELTVGELAEALGLSQSTVSHHLKVLREAGL--VELRREGRLRLYR 81 (110)
T ss_pred CCHHHHHHHHHHHhc-CCccHHHHHHHHCCChhHHHHHHHHHHHCCC--eEEEecccEEEEe
Confidence 334778888888877 7789999999999999999999999766543 3335566654443
No 154
>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=37.60 E-value=49 Score=28.15 Aligned_cols=46 Identities=17% Similarity=0.370 Sum_probs=33.4
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccc
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesG 135 (303)
.+|++-+++ ..+|+|||+..+|++..++==+-.|++ .|+|+|....
T Consensus 46 ~~Il~lC~~---~~SVAEiAA~L~lPlgVvrVLvsDL~~--~G~v~v~~p~ 91 (114)
T PF05331_consen 46 RAILELCRR---PLSVAEIAARLGLPLGVVRVLVSDLAD--AGLVRVRAPA 91 (114)
T ss_pred HHHHHHHCC---CccHHHHHHhhCCCchhhhhhHHHHHh--CCCEEEeCCC
Confidence 455555555 899999999999999999544444433 6888887653
No 155
>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=37.47 E-value=37 Score=32.55 Aligned_cols=43 Identities=26% Similarity=0.295 Sum_probs=36.9
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~Le 130 (303)
.+++.+++++.+|.|-++=+...+|++..+|++.|. +.+|||.
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 567889999999999999999999999999977664 6778775
No 156
>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=37.33 E-value=46 Score=25.52 Aligned_cols=34 Identities=21% Similarity=0.404 Sum_probs=29.8
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHH
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQ 115 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe 115 (303)
.-|+.+-+.-.++++.+++-|||.+-|++..+++
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 3567788888899999999999999999998875
No 157
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=37.27 E-value=25 Score=29.95 Aligned_cols=32 Identities=16% Similarity=0.231 Sum_probs=24.1
Q ss_pred hhhHHHHHH----HHhcCCc-eeehhhhhhcCCCHHH
Q 022049 82 DVRNRAMDA----VDACNRR-VTIGDVAGKAGLKLNE 113 (303)
Q Consensus 82 ~~~~~im~A----ve~~g~r-vTvgDVAa~aGLsl~e 113 (303)
..|++|++| +.+.||. +|+.|||.++|+|...
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 455566554 5677776 8999999999998754
No 158
>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=37.26 E-value=19 Score=32.59 Aligned_cols=22 Identities=36% Similarity=0.539 Sum_probs=18.6
Q ss_pred eeehhhhhhcCCCHHHHHHHHH
Q 022049 98 VTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 98 vTvgDVAa~aGLsl~eAe~aL~ 119 (303)
+|+.|||..||+|...+-+.|.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn 23 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVN 23 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhC
Confidence 6899999999999988776664
No 159
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=37.10 E-value=30 Score=23.21 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=17.8
Q ss_pred cCCceeehhhhhhcCCCHHHHHHHHHH
Q 022049 94 CNRRVTIGDVAGKAGLKLNEAQKALQA 120 (303)
Q Consensus 94 ~g~rvTvgDVAa~aGLsl~eAe~aL~a 120 (303)
.....|+.|||...|+|..--.+..+.
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFKK 31 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHHH
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 455689999999999988776665544
No 160
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=37.05 E-value=1.1e+02 Score=29.32 Aligned_cols=31 Identities=23% Similarity=0.324 Sum_probs=26.5
Q ss_pred HHhcCCceeehhhhhhcCCCHHHHHHHHHHH
Q 022049 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (303)
Q Consensus 91 ve~~g~rvTvgDVAa~aGLsl~eAe~aL~aL 121 (303)
..++|...|+.++|...|++.++++..+...
T Consensus 178 ~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~ 208 (317)
T PRK07405 178 SQQLGRAATIGELAEELELTPKQVREYLERA 208 (317)
T ss_pred HHHhCCCCCHHHHHHHhCcCHHHHHHHHHHc
Confidence 3567899999999999999999998876644
No 161
>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=36.80 E-value=53 Score=18.65 Aligned_cols=34 Identities=12% Similarity=0.219 Sum_probs=23.7
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHH
Q 022049 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQ 115 (303)
Q Consensus 79 l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe 115 (303)
++.+.+..+++..+ .| .|+.++|...|++...+.
T Consensus 6 ~~~~~~~~i~~~~~-~~--~s~~~ia~~~~is~~tv~ 39 (42)
T cd00569 6 LTPEQIEEARRLLA-AG--ESVAEIARRLGVSRSTLY 39 (42)
T ss_pred CCHHHHHHHHHHHH-cC--CCHHHHHHHHCCCHHHHH
Confidence 44555566666654 33 399999999999877664
No 162
>PRK09954 putative kinase; Provisional
Probab=36.15 E-value=57 Score=31.01 Aligned_cols=49 Identities=4% Similarity=0.008 Sum_probs=40.2
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc---CCceEee
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT---DGFLEVS 132 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~---~G~LeVs 132 (303)
...+|++.+++.+ ++|..|+|.+-|+|...+.+-|..|-++. +...++.
T Consensus 4 ~~~~il~~l~~~~-~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~ 55 (362)
T PRK09954 4 REKEILAILRRNP-LIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKGYILT 55 (362)
T ss_pred HHHHHHHHHHHCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEc
Confidence 3457889998877 89999999999999999999999999854 3444443
No 163
>smart00351 PAX Paired Box domain.
Probab=36.05 E-value=85 Score=26.21 Aligned_cols=48 Identities=19% Similarity=0.238 Sum_probs=38.6
Q ss_pred ccccCCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 022049 73 IVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (303)
Q Consensus 73 ~~~~~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAa 123 (303)
++-.-.++++.|.+|+.+++ .| .+..+||.+.|++...+.+-+..-..
T Consensus 12 ~~~~~~~s~~~R~riv~~~~-~G--~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 12 FVNGRPLPDEERQRIVELAQ-NG--VRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred ecCCCCCCHHHHHHHHHHHH-cC--CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33344599999999999987 33 58889999999999999888877543
No 164
>PF15145 DUF4577: Domain of unknown function (DUF4577)
Probab=35.95 E-value=15 Score=31.94 Aligned_cols=28 Identities=25% Similarity=0.209 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 022049 172 SIRVLFGTALIASIVIVFTAIIAILSSK 199 (303)
Q Consensus 172 liRVsFGi~LIaSIvlv~~aIiailss~ 199 (303)
+|=|.+.++||+|+.||...|+.|+.-+
T Consensus 62 lffvglii~LivSLaLVsFvIFLiiQTg 89 (128)
T PF15145_consen 62 LFFVGLIIVLIVSLALVSFVIFLIIQTG 89 (128)
T ss_pred ehHHHHHHHHHHHHHHHHHHHHheeecc
Confidence 3347889999999999999998887543
No 165
>PF07070 Spo0M: SpoOM protein; InterPro: IPR009776 This family consists of several bacterial SpoOM proteins which are thought to control sporulation in Bacillus subtilis.Spo0M exerts certain negative effects on sporulation and its gene expression is controlled by sigmaH [].
Probab=35.61 E-value=43 Score=31.27 Aligned_cols=49 Identities=20% Similarity=0.302 Sum_probs=40.5
Q ss_pred eeeecccccccccCCCcccccCCCCchhhHHHHHHHHhcCCceeehhhh
Q 022049 56 PVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVA 104 (303)
Q Consensus 56 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~im~Ave~~g~rvTvgDVA 104 (303)
+-.+.++|...++-|+..=.-.=+|....+++++|++++|.|..-.|+-
T Consensus 109 v~l~T~LdI~~avD~~D~D~i~V~P~p~~~~vl~A~~~LGF~~~~~d~e 157 (218)
T PF07070_consen 109 VWLRTGLDIAGAVDPGDLDPIEVEPLPAQQAVLDALERLGFRLRSADCE 157 (218)
T ss_pred EEEEEEEEeCCCCCCCCceeEEEeCCHHHHHHHHHHHhcCceEEeeeee
Confidence 4466777877888888877777789999999999999999998877653
No 166
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=35.48 E-value=1.3e+02 Score=28.07 Aligned_cols=44 Identities=23% Similarity=0.272 Sum_probs=32.4
Q ss_pred CCCchhhHHH---HHH----HHhcCCceeehhhhhhcCCCHHHHHHHHHHH
Q 022049 78 KLPADVRNRA---MDA----VDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (303)
Q Consensus 78 ~l~~~~~~~i---m~A----ve~~g~rvTvgDVAa~aGLsl~eAe~aL~aL 121 (303)
++|...++.+ .++ -.++|...|..|||...|++.++.++.+.+.
T Consensus 117 r~Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~ 167 (264)
T PRK07122 117 KVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAG 167 (264)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 4666655432 222 2467899999999999999999998877653
No 167
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=35.28 E-value=56 Score=23.82 Aligned_cols=33 Identities=21% Similarity=0.368 Sum_probs=27.6
Q ss_pred ceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 022049 97 RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (303)
Q Consensus 97 rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeV 131 (303)
.+|..|+|..+|++...+.+.|..|..+. -+++
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g--~I~~ 60 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEG--IIEV 60 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTT--SEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCC--CEEE
Confidence 35778999999999999999999998864 4443
No 168
>cd00131 PAX Paired Box domain
Probab=35.15 E-value=72 Score=26.92 Aligned_cols=44 Identities=16% Similarity=0.267 Sum_probs=37.7
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAa 123 (303)
--|+.+.|.+|+.+++. ..+..+||.+.|++...+.+-+..-..
T Consensus 16 ~~lS~d~R~rIv~~~~~---G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 16 RPLPDSIRQRIVELAQS---GIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CcCCHHHHHHHHHHHHc---CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45788999999999873 379999999999999999888877665
No 169
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=34.71 E-value=88 Score=28.58 Aligned_cols=56 Identities=14% Similarity=0.092 Sum_probs=37.4
Q ss_pred CCCCchhhHHHHHHHHhcCCceee-------------hhhhhh-cCCCHHHHHHHHHHHHhhcCCceEee
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTI-------------GDVAGK-AGLKLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTv-------------gDVAa~-aGLsl~eAe~aL~aLAad~~G~LeVs 132 (303)
.+++.+.+++|+++++++||..-. |=+... ...--.+.-+++...|++.|-++.+.
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 211111 11234456677888888887666554
No 170
>PRK00441 argR arginine repressor; Provisional
Probab=34.68 E-value=1.1e+02 Score=26.79 Aligned_cols=57 Identities=12% Similarity=0.260 Sum_probs=42.6
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEe-eccccEEEEcChhh
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEV-SDEGDVLYVFPNNY 145 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~a-----GLsl~eAe~aL~aLAad~~G~LeV-sesGdIlYvFP~~f 145 (303)
.+..|.+.+++.+ ..|+.|++..- +.+-..+.+.|.+| |-.+| +++|.-.|..|.+-
T Consensus 5 R~~~I~~ll~~~~-~~~q~eL~~~L~~~G~~vSqaTisRDl~~L-----~lvKv~~~~G~~~Y~l~~~~ 67 (149)
T PRK00441 5 RHAKILEIINSKE-IETQEELAEELKKMGFDVTQATVSRDIKEL-----KLIKVLSNDGKYKYATISKT 67 (149)
T ss_pred HHHHHHHHHHHcC-CCcHHHHHHHHHhcCCCcCHHHHHHHHHHc-----CcEEeECCCCCEEEEeCccc
Confidence 3456667776655 46999999874 66677778888887 45677 47999999998864
No 171
>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=34.64 E-value=54 Score=25.04 Aligned_cols=44 Identities=20% Similarity=0.300 Sum_probs=36.4
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCC--HHHHHHHHHHHHhhcC
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLK--LNEAQKALQALAADTD 126 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLs--l~eAe~aL~aLAad~~ 126 (303)
+..++|.++++.+| ..|.-.+|-.-||+ ..++.+.|-.|.....
T Consensus 4 ~~ee~Il~~L~~~g-~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~ 49 (66)
T PF02295_consen 4 DLEEKILDFLKELG-GSTATAIAKALGLSVPKKEVNRVLYRLEKQGK 49 (66)
T ss_dssp HHHHHHHHHHHHHT-SSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred hHHHHHHHHHHhcC-CccHHHHHHHhCcchhHHHHHHHHHHHHHCCC
Confidence 45689999999999 77888888777776 7999999999987643
No 172
>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=34.59 E-value=1.1e+02 Score=27.71 Aligned_cols=55 Identities=18% Similarity=0.238 Sum_probs=36.2
Q ss_pred CCCchhhHHHHHHHHhcCCceeehhhhhhcC-----------C---CHHHHHHHHHHHHhhcCCceEee
Q 022049 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------L---KLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 78 ~l~~~~~~~im~Ave~~g~rvTvgDVAa~aG-----------L---sl~eAe~aL~aLAad~~G~LeVs 132 (303)
+++.+.|++|+++++++||+....--+.+++ + --.+..+++...|.+.|-++.+.
T Consensus 28 ~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~ 96 (327)
T TIGR02417 28 RISQETVERVMAVVREQGYQPNIHAASLRAGRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIA 96 (327)
T ss_pred ccCHHHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEE
Confidence 5889999999999999999753221111111 1 13445667777777777777664
No 173
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=34.58 E-value=1.6e+02 Score=28.94 Aligned_cols=28 Identities=14% Similarity=0.236 Sum_probs=24.8
Q ss_pred HhcCCceeehhhhhhcCCCHHHHHHHHH
Q 022049 92 DACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 92 e~~g~rvTvgDVAa~aGLsl~eAe~aL~ 119 (303)
+++|...|+.+||...|++.++++..+.
T Consensus 227 ~~lgr~pt~~EiA~~l~~~~~~v~~~~~ 254 (367)
T PRK09210 227 QELGREPTPEEIAEEMDMPPEKVREILK 254 (367)
T ss_pred HHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 5679999999999999999999977654
No 174
>PRK05949 RNA polymerase sigma factor; Validated
Probab=34.41 E-value=1.5e+02 Score=28.74 Aligned_cols=86 Identities=16% Similarity=0.206 Sum_probs=46.8
Q ss_pred HHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE--eecccc-----EEEEcChhhHHHHhhhhHHHhHHHHHH
Q 022049 91 VDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE--VSDEGD-----VLYVFPNNYRAKLAAKSFRLKVEPVID 163 (303)
Q Consensus 91 ve~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~Le--VsesGd-----IlYvFP~~fRs~l~~Ks~r~rlq~~~~ 163 (303)
..++|...|+.++|...|++.++++..+. .+.+. -.|. +.++++ ++=.-..+--..+.....+..++.+++
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 36679999999999999999999977654 33221 1111 122222 221111111223344455556666666
Q ss_pred HHhhhhHHHHHHHHH
Q 022049 164 KAKAAAEYSIRVLFG 178 (303)
Q Consensus 164 k~w~v~~yliRVsFG 178 (303)
.+-.-=..+|+-.||
T Consensus 266 ~L~~rer~Vi~lr~g 280 (327)
T PRK05949 266 ELTPQQREVLTLRFG 280 (327)
T ss_pred hCCHHHHHHHHHHhc
Confidence 654444444554444
No 175
>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=34.23 E-value=1.8e+02 Score=26.24 Aligned_cols=28 Identities=14% Similarity=0.242 Sum_probs=24.4
Q ss_pred HhcCCceeehhhhhhcCCCHHHHHHHHH
Q 022049 92 DACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 92 e~~g~rvTvgDVAa~aGLsl~eAe~aL~ 119 (303)
+++|...|+.+||...|++.+++++.+.
T Consensus 98 ~~~g~~pt~~eia~~l~~~~~~v~~~~~ 125 (238)
T TIGR02393 98 QELGREPTDEELAERMGMPAEKVREIKK 125 (238)
T ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3578999999999999999999987654
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=33.90 E-value=1.1e+02 Score=21.10 Aligned_cols=41 Identities=20% Similarity=0.321 Sum_probs=28.4
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHH
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQA 120 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~a 120 (303)
+.||..-+.-+..-. ....|..|||..-|+|...+++-+..
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 456665555553333 67789999999999999999765544
No 177
>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=33.81 E-value=83 Score=27.86 Aligned_cols=43 Identities=30% Similarity=0.413 Sum_probs=33.6
Q ss_pred hcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc---CCceEeecccc
Q 022049 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADT---DGFLEVSDEGD 136 (303)
Q Consensus 93 ~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~---~G~LeVsesGd 136 (303)
-.|..||+.++|...| +.+++++.|..|..++ +.-|++-+.|+
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 4556699999999999 9999999999999999 77788887665
No 178
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=33.68 E-value=23 Score=32.58 Aligned_cols=22 Identities=32% Similarity=0.483 Sum_probs=19.0
Q ss_pred eeehhhhhhcCCCHHHHHHHHH
Q 022049 98 VTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 98 vTvgDVAa~aGLsl~eAe~aL~ 119 (303)
+|+.|||..||+|...+-+.|.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 2 ATIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CCHHHHHHHhCCCHHHHHHHhC
Confidence 6999999999999988877764
No 179
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=33.64 E-value=88 Score=28.32 Aligned_cols=55 Identities=16% Similarity=0.124 Sum_probs=34.0
Q ss_pred CCCchhhHHHHHHHHhcCCceeehhhhhhc-----------CC---CHHHHHHHHHHHHhhcCCceEee
Q 022049 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKA-----------GL---KLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 78 ~l~~~~~~~im~Ave~~g~rvTvgDVAa~a-----------GL---sl~eAe~aL~aLAad~~G~LeVs 132 (303)
+++.+.|++|+++++++||+....--+.++ .+ --.+.-+++..-|.+.|-++.+.
T Consensus 29 ~Vs~~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~ 97 (328)
T PRK11303 29 RVSDKTVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIA 97 (328)
T ss_pred CcCHHHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEE
Confidence 588999999999999999975332111111 11 12334456666666666665553
No 180
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=33.63 E-value=21 Score=32.59 Aligned_cols=22 Identities=32% Similarity=0.508 Sum_probs=20.1
Q ss_pred eeehhhhhhcCCCHHHHHHHHH
Q 022049 98 VTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 98 vTvgDVAa~aGLsl~eAe~aL~ 119 (303)
+|+-|||..+|+|...+-++|.
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln 23 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLN 23 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhc
Confidence 6999999999999999988885
No 181
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=33.58 E-value=33 Score=29.52 Aligned_cols=32 Identities=19% Similarity=0.345 Sum_probs=24.1
Q ss_pred hhhHHHHH----HHHhcCCc-eeehhhhhhcCCCHHH
Q 022049 82 DVRNRAMD----AVDACNRR-VTIGDVAGKAGLKLNE 113 (303)
Q Consensus 82 ~~~~~im~----Ave~~g~r-vTvgDVAa~aGLsl~e 113 (303)
+.|++|++ .+.+.||. +|+.|||.++|++...
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 44555554 45788995 7899999999998754
No 182
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=33.34 E-value=65 Score=25.81 Aligned_cols=45 Identities=16% Similarity=0.167 Sum_probs=37.6
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs 132 (303)
=.++.++.+.+ ..|+.|+|...|++...+-+.|..|..+ |-++-.
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 36788887765 5999999999999999999999999887 555544
No 183
>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=33.16 E-value=1.1e+02 Score=22.51 Aligned_cols=36 Identities=17% Similarity=0.243 Sum_probs=29.5
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 022049 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (303)
Q Consensus 86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAa 123 (303)
++++.+.. + ..|+.++|.+.|+|...+++.+..|-+
T Consensus 4 ~il~~L~~-~-~~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 4 RLLALLAD-N-PFSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HHHHHHHc-C-CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45666553 3 478999999999999999999999965
No 184
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=33.01 E-value=70 Score=27.60 Aligned_cols=42 Identities=10% Similarity=0.264 Sum_probs=35.6
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
...+|+++++ .+.|.|..|+|.+.|+|-..+.+-++.|-.+.
T Consensus 15 ~D~~IL~~Lq-~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~G 56 (164)
T PRK11169 15 IDRNILNELQ-KDGRISNVELSKRVGLSPTPCLERVRRLERQG 56 (164)
T ss_pred HHHHHHHHhc-cCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 4566777654 56789999999999999999999999998765
No 185
>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=33.00 E-value=1.9e+02 Score=27.18 Aligned_cols=30 Identities=17% Similarity=0.206 Sum_probs=25.7
Q ss_pred HhcCCceeehhhhhhcCCCHHHHHHHHHHH
Q 022049 92 DACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (303)
Q Consensus 92 e~~g~rvTvgDVAa~aGLsl~eAe~aL~aL 121 (303)
+++|...|..++|...|++.+++++.+...
T Consensus 172 ~~~~~~pt~~eia~~l~~~~~~v~~~~~~~ 201 (298)
T TIGR02997 172 QKLGRTPSEAEIAEALELEPEQVRELLQRA 201 (298)
T ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 557888999999999999999998876643
No 186
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=32.40 E-value=1.1e+02 Score=27.64 Aligned_cols=56 Identities=9% Similarity=0.053 Sum_probs=36.9
Q ss_pred CCCCchhhHHHHHHHHhcCCceee-------------hhhhhh-cCCCHHHHHHHHHHHHhhcCCceEee
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTI-------------GDVAGK-AGLKLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTv-------------gDVAa~-aGLsl~eAe~aL~aLAad~~G~LeVs 132 (303)
.++..+.|+||+++++++||..-. |=|... ..---.+..+++...+.+.|-++.+.
T Consensus 23 ~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~ 92 (327)
T PRK10423 23 RFVSEAITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPFYSELVRGVERSCFERGYSLVLC 92 (327)
T ss_pred CCCCHHHHHHHHHHHHHHCCCccHHHHHHhhCCCCeEEEEeCCCCCCcHHHHHHHHHHHHHHcCCEEEEE
Confidence 468899999999999999996522 111111 11124456677888888877666553
No 187
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=32.19 E-value=29 Score=31.93 Aligned_cols=22 Identities=36% Similarity=0.602 Sum_probs=19.2
Q ss_pred eeehhhhhhcCCCHHHHHHHHH
Q 022049 98 VTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 98 vTvgDVAa~aGLsl~eAe~aL~ 119 (303)
+|+.|||..+|+|...+-+.|.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHC
Confidence 6999999999999998777774
No 188
>PRK00215 LexA repressor; Validated
Probab=31.84 E-value=77 Score=27.88 Aligned_cols=47 Identities=19% Similarity=0.364 Sum_probs=36.3
Q ss_pred hHHHHHHH----HhcCCceeehhhhhhcCC-CHHHHHHHHHHHHhhcCCceEee
Q 022049 84 RNRAMDAV----DACNRRVTIGDVAGKAGL-KLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 84 ~~~im~Av----e~~g~rvTvgDVAa~aGL-sl~eAe~aL~aLAad~~G~LeVs 132 (303)
+..+++.+ ++.|...|+.|+|...|+ +...+.+-|..|..+ |.|+-.
T Consensus 6 q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~--g~i~~~ 57 (205)
T PRK00215 6 QQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERK--GFIRRD 57 (205)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC--CCEEeC
Confidence 44555555 456888999999999999 999999999998765 455444
No 189
>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=31.82 E-value=1.1e+02 Score=24.42 Aligned_cols=32 Identities=28% Similarity=0.313 Sum_probs=28.8
Q ss_pred cCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 94 CNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 94 ~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
....+|..|+|..+|++...+.++|..|..+.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~G 75 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRR 75 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 56678999999999999999999999998864
No 190
>PF13730 HTH_36: Helix-turn-helix domain
Probab=31.61 E-value=50 Score=22.97 Aligned_cols=26 Identities=19% Similarity=0.314 Sum_probs=23.5
Q ss_pred eehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 99 TIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 99 TvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
+...+|..+|++.+.++++|..|...
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~ 52 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEK 52 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 56899999999999999999999764
No 191
>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=31.57 E-value=54 Score=22.21 Aligned_cols=27 Identities=26% Similarity=0.354 Sum_probs=21.7
Q ss_pred eeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 98 VTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 98 vTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
.|-.|+|...|++.+.+-+.|..|..+
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~ 29 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQ 29 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHc
Confidence 577899999999999999999988765
No 192
>PRK09492 treR trehalose repressor; Provisional
Probab=31.54 E-value=1.4e+02 Score=26.94 Aligned_cols=22 Identities=9% Similarity=0.176 Sum_probs=19.8
Q ss_pred CCCCchhhHHHHHHHHhcCCce
Q 022049 77 DKLPADVRNRAMDAVDACNRRV 98 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rv 98 (303)
.++..+.|++|+++++++||..
T Consensus 29 ~~vs~~tr~rV~~~a~elgY~p 50 (315)
T PRK09492 29 SGVSEETRERVEAVINQHGFSP 50 (315)
T ss_pred CCCCHHHHHHHHHHHHHHCCCc
Confidence 4688999999999999999965
No 193
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=31.45 E-value=1.9e+02 Score=25.85 Aligned_cols=60 Identities=17% Similarity=0.269 Sum_probs=40.4
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChh
Q 022049 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (303)
Q Consensus 79 l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~ 144 (303)
++... .++++.+++.|..+.++ ||=+...++.-+..|--+....--|+.+|-.||.+..+
T Consensus 21 i~~~~-~~ai~~l~~~G~~~~ia-----TGR~~~~~~~~~~~l~~~~~~~~~I~~NGa~i~~~~~~ 80 (270)
T PRK10513 21 ISPAV-KQAIAAARAKGVNVVLT-----TGRPYAGVHRYLKELHMEQPGDYCITNNGALVQKAADG 80 (270)
T ss_pred cCHHH-HHHHHHHHHCCCEEEEe-----cCCChHHHHHHHHHhCCCCCCCeEEEcCCeEEEECCCC
Confidence 55444 45577778889988775 88888888766666543322234688899988876433
No 194
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=31.35 E-value=1.1e+02 Score=27.80 Aligned_cols=53 Identities=19% Similarity=0.157 Sum_probs=40.1
Q ss_pred HHHHHHH-HhcCCceeehhhhhhcCC-CHHHHHHHHHHHHhhc---CCceEeeccccE
Q 022049 85 NRAMDAV-DACNRRVTIGDVAGKAGL-KLNEAQKALQALAADT---DGFLEVSDEGDV 137 (303)
Q Consensus 85 ~~im~Av-e~~g~rvTvgDVAa~aGL-sl~eAe~aL~aLAad~---~G~LeVsesGdI 137 (303)
.+++.|+ =..+..||+.++|...|+ +..++...|..|..++ |-.|++.++|==
T Consensus 10 ~~~vEall~a~~~pls~~~L~~il~~~~~~~~~~~l~~l~~~y~~rg~~L~~~~~~~r 67 (184)
T COG1386 10 KALIEALLFAGGEPLSLKELAEILGIVSADAIIDALAELKEEYEDRGLELVEVAEGWR 67 (184)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCeeEEEEcCcee
Confidence 4444444 566779999999999999 8899999999999887 445666665533
No 195
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=31.32 E-value=1.1e+02 Score=26.95 Aligned_cols=50 Identities=18% Similarity=0.147 Sum_probs=38.9
Q ss_pred chhhHHHHHHHHhc----CCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 022049 81 ADVRNRAMDAVDAC----NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 81 ~~~~~~im~Ave~~----g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs 132 (303)
.++++|+.+.+... ....|..|+|...|++.+.+-+.|..|..+ |-+++.
T Consensus 149 ~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~--G~I~~~ 202 (226)
T PRK10402 149 FPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQD--GYLKKS 202 (226)
T ss_pred ChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHC--CCEEee
Confidence 36788888887643 233588999999999999999999999876 445553
No 196
>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=31.26 E-value=33 Score=23.59 Aligned_cols=28 Identities=25% Similarity=0.342 Sum_probs=20.6
Q ss_pred HHHHHHhcCC-ceeehhhhhhcCCCHHHH
Q 022049 87 AMDAVDACNR-RVTIGDVAGKAGLKLNEA 114 (303)
Q Consensus 87 im~Ave~~g~-rvTvgDVAa~aGLsl~eA 114 (303)
..+-+.+.|+ .+|+.|||.++|++....
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 4455555555 589999999999997654
No 197
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=31.20 E-value=41 Score=29.70 Aligned_cols=48 Identities=17% Similarity=0.270 Sum_probs=37.0
Q ss_pred hcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-cccEEEEcChh
Q 022049 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYVFPNN 144 (303)
Q Consensus 93 ~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse-sGdIlYvFP~~ 144 (303)
+-|.+++..++|.+-|+|..-+++||..|.++ |-|++.. .|- |+=+-+
T Consensus 26 ~pG~~L~e~eLae~lgVSRtpVREAL~~L~~e--Glv~~~~~~G~--~V~~~~ 74 (224)
T PRK11534 26 QPDEKLRMSLLTSRYALGVGPLREALSQLVAE--RLVTVVNQKGY--RVASMS 74 (224)
T ss_pred CCCCcCCHHHHHHHHCCChHHHHHHHHHHHHC--CCEEEeCCCce--EeCCCC
Confidence 34789999999999999999999999999965 6666554 453 444433
No 198
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=31.18 E-value=52 Score=22.44 Aligned_cols=40 Identities=10% Similarity=0.218 Sum_probs=23.4
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHH
Q 022049 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALA 122 (303)
Q Consensus 80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLA 122 (303)
.+..|-.++..+.+ +.|+.+||...|+|.+.+.+=+..-.
T Consensus 3 ~~~~R~~ii~l~~~---G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 3 SEERRAQIIRLLRE---GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -------HHHHHHH---T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred chhHHHHHHHHHHC---CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 34556677888877 78999999999999999977665544
No 199
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=31.02 E-value=70 Score=23.51 Aligned_cols=33 Identities=21% Similarity=0.344 Sum_probs=24.3
Q ss_pred HHHHHHHhcCC-ceeehhhhhhcCCCHHHHHHHH
Q 022049 86 RAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKAL 118 (303)
Q Consensus 86 ~im~Ave~~g~-rvTvgDVAa~aGLsl~eAe~aL 118 (303)
++++.+++.|. +|+-.++|...|++-.++++.|
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 45666666665 6777799999999999999987
No 200
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=31.00 E-value=1.9e+02 Score=24.88 Aligned_cols=64 Identities=11% Similarity=0.141 Sum_probs=46.6
Q ss_pred chhhHHHHHHHHhcCCceeehhhhh-----hcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChh
Q 022049 81 ADVRNRAMDAVDACNRRVTIGDVAG-----KAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTvgDVAa-----~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~ 144 (303)
...|.+|++.+.+.+...|+-||=. .-++|+.++=+.|..|+...==+--..++|...|.....
T Consensus 20 T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y~~~~~ 88 (145)
T COG0735 20 TPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRYELNSE 88 (145)
T ss_pred CHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEEecCCC
Confidence 4567788888888877788887753 367899999999999987543333334466788877654
No 201
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=30.90 E-value=91 Score=26.59 Aligned_cols=46 Identities=15% Similarity=0.177 Sum_probs=35.4
Q ss_pred CchhhHHHHHHHHhc----C---------CceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 80 PADVRNRAMDAVDAC----N---------RRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 80 ~~~~~~~im~Ave~~----g---------~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
..+.++|+.+.+..+ + .++|..|+|...|++...+-+.|..|.++.
T Consensus 138 ~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~~g 196 (211)
T PRK11753 138 FLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLEDQG 196 (211)
T ss_pred hcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 456667777655321 1 367889999999999999999999998765
No 202
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=30.88 E-value=32 Score=27.54 Aligned_cols=33 Identities=21% Similarity=0.307 Sum_probs=25.9
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHH
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL 118 (303)
+..|+-++++.| .|+.++|-++||+-+....+|
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 467888999888 799999999999998887766
No 203
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=30.61 E-value=1.4e+02 Score=27.35 Aligned_cols=44 Identities=18% Similarity=0.320 Sum_probs=32.1
Q ss_pred CCCchhhHHHHH---H----HHhcCCceeehhhhhhcCCCHHHHHHHHHHH
Q 022049 78 KLPADVRNRAMD---A----VDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (303)
Q Consensus 78 ~l~~~~~~~im~---A----ve~~g~rvTvgDVAa~aGLsl~eAe~aL~aL 121 (303)
++|...+....+ + -.++|...|+.++|...|++.++..+.+...
T Consensus 113 rip~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~ 163 (258)
T PRK08215 113 RVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAI 163 (258)
T ss_pred EecHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhc
Confidence 566555543322 2 2467889999999999999999998877543
No 204
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=30.41 E-value=1.3e+02 Score=25.28 Aligned_cols=50 Identities=14% Similarity=0.173 Sum_probs=37.4
Q ss_pred chhhHHHHHHHH----hcC----------CceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 022049 81 ADVRNRAMDAVD----ACN----------RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 81 ~~~~~~im~Ave----~~g----------~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs 132 (303)
.+.++|+...+. +.| ..+|..|+|...|++.+.+-+.|..|..+ |-++++
T Consensus 113 ~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~--g~I~~~ 176 (193)
T TIGR03697 113 RDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKK--KLISIH 176 (193)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHC--CCEEec
Confidence 456677776653 222 45789999999999999999999999876 444444
No 205
>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=30.03 E-value=39 Score=30.61 Aligned_cols=56 Identities=9% Similarity=0.119 Sum_probs=35.3
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhc--------------CCCHHHHHHHHHHHHhhcCCceEee
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKA--------------GLKLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTvgDVAa~a--------------GLsl~eAe~aL~aLAad~~G~LeVs 132 (303)
.++..+.|++|+++++++||+.-..--+.++ .-=..+..+++...|.+.|-++.+.
T Consensus 26 ~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~ 95 (329)
T TIGR01481 26 PNVKPATRKKVLEVIKRLDYRPNAVARGLASKRTTTVGVIIPDISNIYYAELARGIEDIATMYKYNIILS 95 (329)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCHHHHHHhhCCCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEE
Confidence 4688999999999999999975322111111 1113344566667777777666553
No 206
>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=29.97 E-value=1.6e+02 Score=26.71 Aligned_cols=56 Identities=14% Similarity=0.068 Sum_probs=35.0
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhcC-----------C---CHHHHHHHHHHHHhhcCCceEee
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAG-----------L---KLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aG-----------L---sl~eAe~aL~aLAad~~G~LeVs 132 (303)
.++..+.|++|+++++++||.....--+.+++ + -..+.-+++..-+.+.|-++-+.
T Consensus 26 ~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~ 95 (311)
T TIGR02405 26 PKVSIETRERVEQVIQQSGFVPSKSARAMRGGSDKVVAVIVSRLDSPSENLAVSGMLPVFYTAGYDPIIM 95 (311)
T ss_pred CCCCHHHHHHHHHHHHHHCCCcCHHHHHhhcCCCCEEEEEeCCcccccHHHHHHHHHHHHHHCCCeEEEe
Confidence 46889999999999999999753221110111 1 12344566677777777776553
No 207
>PHA01815 hypothetical protein
Probab=29.94 E-value=2.4e+02 Score=21.25 Aligned_cols=27 Identities=19% Similarity=0.181 Sum_probs=18.1
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 022049 158 VEPVIDKAKAAAEYSIRVLFGTALIAS 184 (303)
Q Consensus 158 lq~~~~k~w~v~~yliRVsFGi~LIaS 184 (303)
+-+++-.+--....-+|||||+....-
T Consensus 12 llaflitliilmt~~irvsfgvlftt~ 38 (55)
T PHA01815 12 LLAFLITLIILMTLHIRVSFGVLFTTL 38 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555555566677999999866544
No 208
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain []. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins []. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.; GO: 0016192 vesicle-mediated transport, 0016021 integral to membrane; PDB: 3EGX_C 2NUP_C 3EGD_C 2NUT_C 1IOU_A 1H8M_A 3B5N_A 3ZYM_A 2NPS_A 1SFC_E ....
Probab=29.86 E-value=1.4e+02 Score=23.10 Aligned_cols=12 Identities=17% Similarity=0.307 Sum_probs=4.6
Q ss_pred HHHhHHHHHHHH
Q 022049 154 FRLKVEPVIDKA 165 (303)
Q Consensus 154 ~r~rlq~~~~k~ 165 (303)
|+.+...+-++.
T Consensus 50 F~k~a~~l~r~~ 61 (89)
T PF00957_consen 50 FKKNAKKLKRKM 61 (89)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 333333333333
No 209
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=29.84 E-value=56 Score=28.64 Aligned_cols=51 Identities=20% Similarity=0.318 Sum_probs=39.0
Q ss_pred chhhHHHHHHHHhcC--------------CceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 022049 81 ADVRNRAMDAVDACN--------------RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (303)
Q Consensus 81 ~~~~~~im~Ave~~g--------------~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse 133 (303)
.++++|+...+.++. ..+|..|+|...|++...+-+.|..|..+ |-++...
T Consensus 154 ~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~~--g~I~~~~ 218 (235)
T PRK11161 154 KNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKS--GMLAVKG 218 (235)
T ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHHC--CCEEecC
Confidence 466788877775532 34788999999999999999999998875 4555444
No 210
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=29.72 E-value=83 Score=25.94 Aligned_cols=41 Identities=10% Similarity=0.097 Sum_probs=35.8
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
-.++.++...+...|+.|+|...|++...+-+.+..|-.+.
T Consensus 34 ~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~G 74 (144)
T PRK03573 34 WVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKG 74 (144)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCC
Confidence 36788888877778999999999999999999999998764
No 211
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=29.66 E-value=1.8e+02 Score=25.74 Aligned_cols=52 Identities=19% Similarity=0.217 Sum_probs=38.2
Q ss_pred hcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHH
Q 022049 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA 147 (303)
Q Consensus 93 ~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs 147 (303)
+-|.+.+..++|.+-|+|-.-+++||..|.++ |-|++.... -.++-+-+...
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVREAL~~L~~e--GLV~~~~~~-g~~v~~~~~~~ 81 (221)
T PRK11414 30 KPGARLITKNLAEQLGMSITPVREALLRLVSV--NALSVAPAQ-AFTVPEVSKRQ 81 (221)
T ss_pred CCCCccCHHHHHHHHCCCchhHHHHHHHHHHC--CCEEecCCC-ceeecCCCHHH
Confidence 45788888999999999999999999999864 566665432 24555544433
No 212
>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=29.54 E-value=47 Score=28.95 Aligned_cols=58 Identities=14% Similarity=0.267 Sum_probs=41.8
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-cccEEEEcC
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYVFP 142 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse-sGdIlYvFP 142 (303)
++++|+.--=+-|.+++-.++|.+-|+|..-++++|..|+++ |-|++.. .|-.|-.++
T Consensus 20 l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~e--Glv~~~~~~G~~V~~~~ 78 (212)
T TIGR03338 20 IERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEA--GLVRNEKNRGVFVREIS 78 (212)
T ss_pred HHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHC--CCEEEecCCCeEEecCC
Confidence 334444433345888898999999999999999999999965 5677664 455544443
No 213
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=29.52 E-value=81 Score=28.00 Aligned_cols=45 Identities=9% Similarity=-0.039 Sum_probs=38.2
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhc--CCCHHHHHHHHHHHHhh
Q 022049 80 PADVRNRAMDAVDACNRRVTIGDVAGKA--GLKLNEAQKALQALAAD 124 (303)
Q Consensus 80 ~~~~~~~im~Ave~~g~rvTvgDVAa~a--GLsl~eAe~aL~aLAad 124 (303)
..-..+.|-..++-.++..+++.+|... +++.+|++++|..|..-
T Consensus 22 ~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~ 68 (171)
T PF14394_consen 22 SSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKL 68 (171)
T ss_pred hhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHC
Confidence 3445667777888888888999999999 99999999999999763
No 214
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=29.28 E-value=33 Score=31.08 Aligned_cols=23 Identities=17% Similarity=0.341 Sum_probs=18.7
Q ss_pred eeehhhhhhcCCCHHHHHHHHHH
Q 022049 98 VTIGDVAGKAGLKLNEAQKALQA 120 (303)
Q Consensus 98 vTvgDVAa~aGLsl~eAe~aL~a 120 (303)
+|+.|||..+|+|...+-+.|..
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Confidence 38889999999999888777753
No 215
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=29.20 E-value=91 Score=26.03 Aligned_cols=30 Identities=20% Similarity=0.390 Sum_probs=24.9
Q ss_pred CCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 95 NRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 95 g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
+..+|+.++|.+.++|....++-|..|...
T Consensus 23 ~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 23 TGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 345888999999999999998888888764
No 216
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=28.57 E-value=64 Score=33.49 Aligned_cols=38 Identities=13% Similarity=0.298 Sum_probs=34.4
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHH
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aL 121 (303)
+..|++.+.+....+|+.|++..||+..+++-.+|+.|
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 56788899888889999999999999999998888876
No 217
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=28.49 E-value=1.6e+02 Score=25.47 Aligned_cols=57 Identities=19% Similarity=0.300 Sum_probs=47.8
Q ss_pred hHHHHHHHHhcCCceeehhhhhh--cCCCHHHHHHHHHHHHhhcCCceEeecccc-EEEEcC
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGK--AGLKLNEAQKALQALAADTDGFLEVSDEGD-VLYVFP 142 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~--aGLsl~eAe~aL~aLAad~~G~LeVsesGd-IlYvFP 142 (303)
...|.+-+++.+.-.++.||..- .+++...++++|..|+.+ |.|.+-.-|- .||...
T Consensus 3 e~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~--g~i~~K~~GKqkiY~~~ 62 (169)
T PF07106_consen 3 EDAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEE--GKIVEKEYGKQKIYFAN 62 (169)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhC--CCeeeeeecceEEEeeC
Confidence 36788999999999999999974 479999999999999987 7788888887 556554
No 218
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=28.45 E-value=2.3e+02 Score=27.62 Aligned_cols=42 Identities=17% Similarity=0.279 Sum_probs=31.1
Q ss_pred CCCchhhHHHH---HH----HHhcCCceeehhhhhhcCCCHHHHHHHHH
Q 022049 78 KLPADVRNRAM---DA----VDACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 78 ~l~~~~~~~im---~A----ve~~g~rvTvgDVAa~aGLsl~eAe~aL~ 119 (303)
+||...++.+- ++ -.++|...|+.+||...|++.+++++.+.
T Consensus 163 rlP~~~~~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~ 211 (324)
T PRK07921 163 RLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLE 211 (324)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 57766654332 22 25679999999999999999999987654
No 219
>PRK03837 transcriptional regulator NanR; Provisional
Probab=28.37 E-value=92 Score=27.63 Aligned_cols=60 Identities=20% Similarity=0.305 Sum_probs=40.6
Q ss_pred hhhHHHHHHHHhc----CCce-eehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChh
Q 022049 82 DVRNRAMDAVDAC----NRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (303)
Q Consensus 82 ~~~~~im~Ave~~----g~rv-TvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~ 144 (303)
.+-..|.+.+... |-+. +..|+|.+-|+|..-+++||..|.++ |-+++.. |-=.|+-+.+
T Consensus 17 ~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~e--Glv~~~~-~~G~~V~~~~ 81 (241)
T PRK03837 17 EVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRK--GLVQISH-GERARVSRPS 81 (241)
T ss_pred HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEec-CCceeEecCC
Confidence 3334444444443 5556 88899999999999999999999965 5566643 3334555433
No 220
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=28.34 E-value=44 Score=29.12 Aligned_cols=32 Identities=22% Similarity=0.333 Sum_probs=23.6
Q ss_pred chhhHHHHHHH-----HhcCC-ceeehhhhhhcCCCHH
Q 022049 81 ADVRNRAMDAV-----DACNR-RVTIGDVAGKAGLKLN 112 (303)
Q Consensus 81 ~~~~~~im~Av-----e~~g~-rvTvgDVAa~aGLsl~ 112 (303)
...|++|++|. .+.|| .+|+.|||.++|++..
T Consensus 10 ~~~R~~Il~aA~~~l~~~~G~~~~si~~IA~~Agvs~~ 47 (203)
T PRK11202 10 EKTRRALIDAAFSQLSAERSFSSLSLREVAREAGIAPT 47 (203)
T ss_pred HHHHHHHHHHHHHHHHhcCCcccCCHHHHHHHhCCCcc
Confidence 35677777654 34576 7999999999999753
No 221
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=28.28 E-value=90 Score=27.78 Aligned_cols=54 Identities=15% Similarity=0.259 Sum_probs=38.8
Q ss_pred hhHHHHHHHHhc----CCce-eehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-cccEE
Q 022049 83 VRNRAMDAVDAC----NRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVL 138 (303)
Q Consensus 83 ~~~~im~Ave~~----g~rv-TvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse-sGdIl 138 (303)
.-+.|.+.+... |.+. |-.++|.+-|+|-..+++||..|.++ |-|++.. .|-.|
T Consensus 12 ~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~e--Glv~~~~g~G~~V 71 (239)
T PRK04984 12 AEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARD--GWLTIQHGKPTKV 71 (239)
T ss_pred HHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEeCCCeeEe
Confidence 344455555443 6677 78899999999999999999999976 5566543 45444
No 222
>PF13518 HTH_28: Helix-turn-helix domain
Probab=27.98 E-value=1.4e+02 Score=20.10 Aligned_cols=37 Identities=8% Similarity=0.179 Sum_probs=27.6
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAa 123 (303)
+-+|++.+.+ |. |+.++|.+-|++..++..=+...-.
T Consensus 2 r~~iv~~~~~-g~--s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 2 RLQIVELYLE-GE--SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHHc-CC--CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3466777773 43 9999999999999998666655443
No 223
>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=27.97 E-value=35 Score=28.36 Aligned_cols=33 Identities=24% Similarity=0.317 Sum_probs=23.5
Q ss_pred hhhHHHHH----HHHhcCC-ceeehhhhhhcCCCHHHH
Q 022049 82 DVRNRAMD----AVDACNR-RVTIGDVAGKAGLKLNEA 114 (303)
Q Consensus 82 ~~~~~im~----Ave~~g~-rvTvgDVAa~aGLsl~eA 114 (303)
.-|++|++ .+.+.|| .+|+.|||.++|++....
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 34455544 4566775 688999999999987543
No 224
>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=27.97 E-value=2e+02 Score=28.55 Aligned_cols=78 Identities=19% Similarity=0.231 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHh-hcCCceEeeccccEEEEcChhhHHHHhhh-hHHHhHHHHHHHH----------hhhhHHHHHH
Q 022049 108 GLKLNEAQKALQALAA-DTDGFLEVSDEGDVLYVFPNNYRAKLAAK-SFRLKVEPVIDKA----------KAAAEYSIRV 175 (303)
Q Consensus 108 GLsl~eAe~aL~aLAa-d~~G~LeVsesGdIlYvFP~~fRs~l~~K-s~r~rlq~~~~k~----------w~v~~yliRV 175 (303)
|.+-+.-.+.|.+|.+ +.-|.-= +++. |+..|+.+-..- ++..+|+.-.+|+ .++.-.+|=.
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 4444555566666665 2222111 1111 789999886662 3444444333322 2232333334
Q ss_pred HHHHHHHHHHHHHHHH
Q 022049 176 LFGTALIASIVIVFTA 191 (303)
Q Consensus 176 sFGi~LIaSIvlv~~a 191 (303)
.|..++|+|+++..+|
T Consensus 190 a~~aV~i~svv~aa~a 205 (336)
T PF05055_consen 190 AFVAVAIASVVAAAHA 205 (336)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 5666677776665553
No 225
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.75 E-value=1.4e+02 Score=29.17 Aligned_cols=45 Identities=27% Similarity=0.219 Sum_probs=29.5
Q ss_pred hhhhHHHhHHHHHHHHhhhh--------HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022049 150 AAKSFRLKVEPVIDKAKAAA--------EYSIRVLFGTALIASIVIVFTAIIAILS 197 (303)
Q Consensus 150 ~~Ks~r~rlq~~~~k~w~v~--------~yliRVsFGi~LIaSIvlv~~aIiails 197 (303)
.+||-|.---.|.+++|+.. ...=|.+|.++| -+|-|++|++++.
T Consensus 220 dnKY~RRp~~~w~~rl~R~~~g~s~rP~~~~~ra~fli~l---gvLafi~~i~lM~ 272 (299)
T KOG3970|consen 220 DNKYKRRPTMDWMRRLWRAKHGGSGRPQEAKKRALFLIFL---GVLAFITIIMLMK 272 (299)
T ss_pred cchhhcCChHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHH---HHHHHHHHHHHHH
Confidence 46777776777777777652 334456665444 3567889998885
No 226
>KOG4251 consensus Calcium binding protein [General function prediction only]
Probab=27.74 E-value=35 Score=33.62 Aligned_cols=38 Identities=42% Similarity=0.529 Sum_probs=31.4
Q ss_pred CCCCchHHHHHHHHHHHHHhc-CCeEeeecccCccCCCC
Q 022049 263 DPNQGIEEKRWKLIGEYIASN-GGVVTAEELAPYLDIDR 300 (303)
Q Consensus 263 DPN~dlEerRwq~Ig~~Ir~N-~GvV~AEQlAPyLD~~~ 300 (303)
|=..+|-++|.+++-++|-+| .|.||||||--|.|...
T Consensus 273 diddnwvkdRkkEFeElIDsNhDGivTaeELe~y~dP~n 311 (362)
T KOG4251|consen 273 DIDDNWVKDRKKEFEELIDSNHDGIVTAEELEDYVDPQN 311 (362)
T ss_pred chHHHHHHHHHHHHHHHhhcCCccceeHHHHHhhcCchh
Confidence 334567889999999999765 69999999999988653
No 227
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=27.73 E-value=45 Score=30.65 Aligned_cols=56 Identities=18% Similarity=0.155 Sum_probs=35.4
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhh-----------cCC---CHHHHHHHHHHHHhhcCCceEee
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGK-----------AGL---KLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTvgDVAa~-----------aGL---sl~eAe~aL~aLAad~~G~LeVs 132 (303)
.++..+.|+||+++++++||+.-..-=+.+ ..+ -..+.-+++...|.+.|-++.+.
T Consensus 26 ~~Vs~~tr~rV~~~a~elgY~pn~~ar~l~~~~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~~~~~ 95 (343)
T PRK10727 26 PKASEASRLAVHSAMESLSYHPNANARALAQQSTETVGLVVGDVSDPFFGAMVKAVEQVAYHTGNFLLIG 95 (343)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCHHHHhhhhCCCCeEEEEeCCCCcchHHHHHHHHHHHHHHcCCEEEEE
Confidence 367899999999999999997533110000 111 13345567777777777666543
No 228
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=27.63 E-value=59 Score=31.20 Aligned_cols=44 Identities=23% Similarity=0.415 Sum_probs=35.4
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeV 131 (303)
.+++.+++++.+|.|-++=+...+|++..+|++.|. +.+|||+.
T Consensus 246 ~~~a~~~l~~~~~~vk~ai~~~~~~~~~~~a~~~l~----~~~~~~~~ 289 (296)
T PRK12570 246 EDEAKELLKESDNDVKLAILMILTGMDVEQARAALS----HADGFLRK 289 (296)
T ss_pred HHHHHHHHHHhCCccHHHHHHHHhCCCHHHHHHHHH----HcCChHHH
Confidence 355678899999999999999999999999977665 56777653
No 229
>PF11548 Receptor_IA-2: Protein-tyrosine phosphatase receptor IA-2; InterPro: IPR021613 IA-2 is a protein-tyrosine phosphatase receptor that upon exocytosis, the cytoplasmic domain is cleaved and moves to the nucleus where it enhances transcription of the insulin gene. The mature exodomain of IA-2 participates in adhesion to the extracellular matrix and is self-proteolyzed in vitro by reactive oxygen species which may be a new shedding mechanism. ; PDB: 2QT7_B 3N01_B 3N4W_B 3NG8_A.
Probab=27.48 E-value=20 Score=29.70 Aligned_cols=27 Identities=30% Similarity=0.268 Sum_probs=16.8
Q ss_pred HhcCCceeehhhhhhcCCCHHHHHHHH
Q 022049 92 DACNRRVTIGDVAGKAGLKLNEAQKAL 118 (303)
Q Consensus 92 e~~g~rvTvgDVAa~aGLsl~eAe~aL 118 (303)
+++.+++|.+|||.+++...++-|+++
T Consensus 52 ~~N~~n~taadVa~~a~~~K~~Le~~t 78 (91)
T PF11548_consen 52 RPNNKNLTAADVAKQAVDNKNQLEKET 78 (91)
T ss_dssp ---TT---HHHHHHHHHHTHHHHHHHH
T ss_pred ccCcCCCCHHHHHHHHHHhHHHHHHhh
Confidence 456789999999999998777666543
No 230
>PRK04280 arginine repressor; Provisional
Probab=27.43 E-value=1.3e+02 Score=26.26 Aligned_cols=48 Identities=19% Similarity=0.373 Sum_probs=34.5
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe-eccccEEEEcChhh
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV-SDEGDVLYVFPNNY 145 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeV-sesGdIlYvFP~~f 145 (303)
..++.+++.+++.|..||.+-|+ +.|..| |-++| +++|...|..|.+-
T Consensus 19 ~tQeeL~~~L~~~Gi~vTQATiS-----------RDikeL-----~lvKv~~~~G~~~Y~lp~~~ 67 (148)
T PRK04280 19 ETQDELVDRLREEGFNVTQATVS-----------RDIKEL-----HLVKVPLPDGRYKYSLPADQ 67 (148)
T ss_pred CCHHHHHHHHHHcCCCeehHHHH-----------HHHHHc-----CCEEeecCCCcEEEeecccc
Confidence 34788888888888888877554 333333 44566 47899999999874
No 231
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=27.30 E-value=62 Score=26.25 Aligned_cols=39 Identities=26% Similarity=0.325 Sum_probs=25.1
Q ss_pred cchhhhhhhcccCCCCCCCchHHH--HHHHHHHHHHhcCCeEeeec
Q 022049 248 MNFIKSVFSFVFGEGDPNQGIEEK--RWKLIGEYIASNGGVVTAEE 291 (303)
Q Consensus 248 mnFlEsVFSFvFGDGDPN~dlEer--Rwq~Ig~~Ir~N~GvV~AEQ 291 (303)
|+.+|.+|-+ +|+..-|+. --+.+..+|.++||.|...|
T Consensus 1 M~~YE~~~il-----~~~~~~~~~~~~~~~~~~~i~~~gg~i~~~~ 41 (108)
T PRK00453 1 MRKYEIVFIL-----RPDLSEEQVKALVERFKGVITENGGTIHKVE 41 (108)
T ss_pred CCceeEEEEE-----CCCCCHHHHHHHHHHHHHHHHHCCCEEEEEe
Confidence 5667777654 444332222 23558889999999997655
No 232
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=27.30 E-value=1.6e+02 Score=27.05 Aligned_cols=65 Identities=18% Similarity=0.306 Sum_probs=39.1
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHH
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAK 148 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~ 148 (303)
+-...++.++.+- -|.+.|+|+.-||+..++-.-+..|-++..=+==+++.|--||+=|..+.++
T Consensus 100 lL~~Fi~yIK~~K-vv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE~~~v 164 (188)
T PF09756_consen 100 LLQEFINYIKEHK-VVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEEMEAV 164 (188)
T ss_dssp HHHHHHHHHHH-S-EE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE---------
T ss_pred HHHHHHHHHHHcc-eeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHHHHHH
Confidence 5556677776654 4888999999999999999999999998844434578999999999988874
No 233
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=27.26 E-value=93 Score=22.66 Aligned_cols=44 Identities=11% Similarity=0.160 Sum_probs=34.9
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCce
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFL 129 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~L 129 (303)
-+++..+-+ ....|+.|+|.+.|+|.-..+..+..|=...+..+
T Consensus 8 ~~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L~~~f~~~~ 51 (59)
T PF08280_consen 8 LKLLELLLK-NKWITLKELAKKLNISERTIKNDINELNEFFPENI 51 (59)
T ss_dssp HHHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT--TCC
T ss_pred HHHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHHHHhhhhc
Confidence 457888877 78899999999999999999999999987664433
No 234
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=27.22 E-value=75 Score=27.19 Aligned_cols=27 Identities=26% Similarity=0.244 Sum_probs=24.9
Q ss_pred eeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 98 VTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 98 vTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
||+-.+|++.|++...|+..|+.|...
T Consensus 60 VTpy~la~r~gI~~SvAr~vLR~Leee 86 (107)
T COG4901 60 VTPYVLASRYGINGSVARIVLRHLEEE 86 (107)
T ss_pred ecHHHHHHHhccchHHHHHHHHHHHhC
Confidence 899999999999999999999999653
No 235
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=27.16 E-value=44 Score=30.53 Aligned_cols=23 Identities=4% Similarity=0.286 Sum_probs=20.2
Q ss_pred CCCchhhHHHHHHHHhcCCceee
Q 022049 78 KLPADVRNRAMDAVDACNRRVTI 100 (303)
Q Consensus 78 ~l~~~~~~~im~Ave~~g~rvTv 100 (303)
++..+.|++|++++|++||+.-.
T Consensus 29 ~vs~~tr~rV~~~a~~lgY~pn~ 51 (327)
T PRK10339 29 NVKEETKHRILEIAEKLEYKTSS 51 (327)
T ss_pred CcCHHHHHHHHHHHHHhCCCCch
Confidence 48899999999999999997553
No 236
>PHA01976 helix-turn-helix protein
Probab=26.98 E-value=89 Score=22.39 Aligned_cols=32 Identities=13% Similarity=0.158 Sum_probs=23.9
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHH
Q 022049 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEA 114 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eA 114 (303)
|+.-.++.++-++.| .|..|+|...|++....
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 455667766666665 79999999999986555
No 237
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=26.75 E-value=1.1e+02 Score=21.60 Aligned_cols=29 Identities=31% Similarity=0.302 Sum_probs=20.1
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAa 123 (303)
|..+.+++|+..+|| +..|+++++..+..
T Consensus 1 d~~~d~~~AL~~LGy-------------~~~e~~~av~~~~~ 29 (47)
T PF07499_consen 1 DALEDALEALISLGY-------------SKAEAQKAVSKLLE 29 (47)
T ss_dssp HHHHHHHHHHHHTTS--------------HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHcCC-------------CHHHHHHHHHHhhc
Confidence 356778888888888 56666676666654
No 238
>PRK04217 hypothetical protein; Provisional
Probab=26.59 E-value=1.2e+02 Score=25.68 Aligned_cols=45 Identities=11% Similarity=0.127 Sum_probs=29.9
Q ss_pred cCCCCchhhHHHHHHHHhcC-CceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 76 SDKLPADVRNRAMDAVDACN-RRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 76 ~~~l~~~~~~~im~Ave~~g-~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
..+|+.+-+ +++.... ...|+.|||...|+|.+.+.+-|......
T Consensus 40 ~~~Lt~eer----eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkk 85 (110)
T PRK04217 40 PIFMTYEEF----EALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKK 85 (110)
T ss_pred cccCCHHHH----HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 445555543 3333333 45699999999999999887776644433
No 239
>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=26.13 E-value=1.3e+02 Score=22.69 Aligned_cols=70 Identities=17% Similarity=0.133 Sum_probs=46.0
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHHHhh
Q 022049 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAA 151 (303)
Q Consensus 80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~l~~ 151 (303)
..-+++.+..+++......++-++.+...-=.+..+.+|..-...+| +++..=+--=..||.++++.+..
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 45677788888888888888888865433112223444444455554 88887766667888888776554
No 240
>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=26.13 E-value=1.7e+02 Score=21.95 Aligned_cols=57 Identities=16% Similarity=0.226 Sum_probs=43.9
Q ss_pred cCCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 022049 76 SDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 76 ~~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs 132 (303)
.+.|....+.+.+..+-+.-.++++.++|...+++.+++|.-|..+..+..=+-..+
T Consensus 39 ~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID 95 (105)
T PF01399_consen 39 VEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLISNGLIKAKID 95 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEE
T ss_pred HHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHHCCCEEEEEE
Confidence 345556677777777778888999999999999999999999999888764333333
No 241
>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=26.12 E-value=64 Score=27.40 Aligned_cols=34 Identities=29% Similarity=0.594 Sum_probs=26.5
Q ss_pred hhcccCCCCCCCchHHHHHHHHHHHHHhcCCeEee
Q 022049 255 FSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTA 289 (303)
Q Consensus 255 FSFvFGDGDPN~dlEerRwq~Ig~~Ir~N~GvV~A 289 (303)
.+|||||=||+++.+.. -+-..+|..+..|.|--
T Consensus 66 ~tYlfGdl~p~~~a~~i-l~~a~~Y~~s~dG~vp~ 99 (116)
T PF07845_consen 66 WTYLFGDLDPDEDAEDI-LAFAALYAASPDGLVPW 99 (116)
T ss_pred cEEEEecCCcccCHHHH-HHHHHHHHhCCCCcccc
Confidence 57999999999877776 34567788888887753
No 242
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=25.82 E-value=79 Score=25.95 Aligned_cols=48 Identities=13% Similarity=0.147 Sum_probs=41.9
Q ss_pred chhhHHHHHHHHhc-CCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCc
Q 022049 81 ADVRNRAMDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGF 128 (303)
Q Consensus 81 ~~~~~~im~Ave~~-g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~ 128 (303)
+.+|.+|+..+-+. +...++.|+|..+|++...+..+|......+.++
T Consensus 8 S~~R~~vl~~L~~~yp~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e 56 (90)
T PF07381_consen 8 SKVRKKVLEYLCSIYPEPAYPSEIARSVGSDYSNVLGALRGDGKRYNKE 56 (90)
T ss_pred HHHHHHHHHHHHHcCCCcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcc
Confidence 45788999999888 8999999999999999999999999877776654
No 243
>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=25.60 E-value=42 Score=30.47 Aligned_cols=21 Identities=29% Similarity=0.414 Sum_probs=17.4
Q ss_pred eehhhhhhcCCCHHHHHHHHH
Q 022049 99 TIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 99 TvgDVAa~aGLsl~eAe~aL~ 119 (303)
|+.|||..||+|...+-+.|.
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn 21 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVIN 21 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHc
Confidence 678999999998888877774
No 244
>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=25.51 E-value=34 Score=27.33 Aligned_cols=31 Identities=29% Similarity=0.341 Sum_probs=25.2
Q ss_pred chHHHHHHHHHHHHHhcCCeEeeecccCccCCC
Q 022049 267 GIEEKRWKLIGEYIASNGGVVTAEELAPYLDID 299 (303)
Q Consensus 267 dlEerRwq~Ig~~Ir~N~GvV~AEQlAPyLD~~ 299 (303)
|.-+.|..+|.++|++ |.++..|||-.++.-
T Consensus 2 ~~~~~R~~~I~e~l~~--~~~ti~dvA~~~gvS 32 (80)
T TIGR02844 2 DYIEERVLEIGKYIVE--TKATVRETAKVFGVS 32 (80)
T ss_pred CcHHHHHHHHHHHHHH--CCCCHHHHHHHhCCC
Confidence 3445677889999999 999999999877653
No 245
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=25.35 E-value=45 Score=24.93 Aligned_cols=21 Identities=38% Similarity=0.452 Sum_probs=17.2
Q ss_pred eeehhhhhhcCCCHHHHHHHH
Q 022049 98 VTIGDVAGKAGLKLNEAQKAL 118 (303)
Q Consensus 98 vTvgDVAa~aGLsl~eAe~aL 118 (303)
+|+.|+|..+|+|...+-+.|
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~l 21 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVL 21 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 477899999999998886655
No 246
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=25.31 E-value=2.5e+02 Score=22.47 Aligned_cols=54 Identities=17% Similarity=0.152 Sum_probs=42.8
Q ss_pred chhhHHHHHHHHhcCCceeeh-hhhhhcCCCHHHHHHHHHHHHhhcCCceEeecc-c
Q 022049 81 ADVRNRAMDAVDACNRRVTIG-DVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-G 135 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~rvTvg-DVAa~aGLsl~eAe~aL~aLAad~~G~LeVses-G 135 (303)
++.+..++..+..+++...-| ++|++.|+|-..+.+.+++|= +.|-.++...+ |
T Consensus 2 ~~~~~~~~~ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr-~~G~~I~s~~~kG 57 (79)
T COG1654 2 KDTSQMLLLLLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLR-EEGVDIESVRGKG 57 (79)
T ss_pred cchHHHHHHHHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHH-HhCCceEecCCCc
Confidence 566778888888888877777 889999999999999999998 55555555443 5
No 247
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=24.98 E-value=95 Score=21.97 Aligned_cols=28 Identities=18% Similarity=0.204 Sum_probs=17.9
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHH
Q 022049 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQK 116 (303)
Q Consensus 87 im~Ave~~g~rvTvgDVAa~aGLsl~eAe~ 116 (303)
+-+.+++.|. |+.|+|.++|++..+..+
T Consensus 2 L~~~m~~~~i--t~~~La~~~gis~~tl~~ 29 (63)
T PF13443_consen 2 LKELMAERGI--TQKDLARKTGISRSTLSR 29 (63)
T ss_dssp HHHHHHHTT----HHHHHHHHT--HHHHHH
T ss_pred HHHHHHHcCC--CHHHHHHHHCcCHHHHHH
Confidence 3455666665 999999999999877644
No 248
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=24.63 E-value=98 Score=30.61 Aligned_cols=43 Identities=26% Similarity=0.370 Sum_probs=35.8
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~Le 130 (303)
++.+++++++.|+.|-++=|...+|++.++|++.|. .++|+|+
T Consensus 248 ~~~A~~~L~~~~~~vK~AIvm~~~~~~a~~A~~~L~----~~~g~lr 290 (298)
T COG2103 248 AEEAEALLEEAGGNVKLAIVMLLTGLSAEEAKRLLE----RAGGFLR 290 (298)
T ss_pred HHHHHHHHHHcCCccHhHHHHHHhCCCHHHHHHHHH----HccChHH
Confidence 466788899999999999999999999999987664 4566653
No 249
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=24.50 E-value=62 Score=28.23 Aligned_cols=23 Identities=35% Similarity=0.492 Sum_probs=18.4
Q ss_pred eeehhh---hhhcCCCHHHHHHHHHH
Q 022049 98 VTIGDV---AGKAGLKLNEAQKALQA 120 (303)
Q Consensus 98 vTvgDV---Aa~aGLsl~eAe~aL~a 120 (303)
++-.|| +.+||.|-++|.+||.+
T Consensus 83 i~eeDIkLV~eQa~VsreeA~kAL~e 108 (122)
T COG1308 83 ISEEDIKLVMEQAGVSREEAIKALEE 108 (122)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 455554 57999999999999975
No 250
>PLN03239 histone acetyltransferase; Provisional
Probab=24.49 E-value=86 Score=31.65 Aligned_cols=59 Identities=17% Similarity=0.144 Sum_probs=40.8
Q ss_pred hHHHHHHHHhcC---CceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHH
Q 022049 84 RNRAMDAVDACN---RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA 147 (303)
Q Consensus 84 ~~~im~Ave~~g---~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs 147 (303)
+..|++.+.+.. ..+|+.|++..||+..+++-.+|+.| |-|.....+.+|+.=+...+.
T Consensus 268 ~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l-----~~l~~~~g~~~i~~~~~~l~~ 329 (351)
T PLN03239 268 GSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQL-----GILKFINGIYFIAAEKGLLEE 329 (351)
T ss_pred HHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHC-----CcEEEECCeEEEEeCHHHHHH
Confidence 467778776653 46999999999999999998888876 344433333455554444444
No 251
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=24.23 E-value=1.8e+02 Score=26.84 Aligned_cols=56 Identities=23% Similarity=0.283 Sum_probs=36.2
Q ss_pred CCCCchhhHHHHHHHHhcCCcee-------------ehhhhhh-cCCCHHHHHHHHHHHHhhcCCceEee
Q 022049 77 DKLPADVRNRAMDAVDACNRRVT-------------IGDVAGK-AGLKLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvT-------------vgDVAa~-aGLsl~eAe~aL~aLAad~~G~LeVs 132 (303)
.++..+.|++|+++++++||+.- +|=+... ..---.+.-+++...+.+.|-++-+.
T Consensus 26 ~~Vs~~tr~kV~~~a~elgY~pn~~a~~l~~~~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~~~~~ 95 (346)
T PRK10401 26 ALVSADTREAVMKAVSELGYRPNANAQALATQVSDTIGVVVMDVSDAFFGALVKAVDLVAQQHQKYVLIG 95 (346)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCHHHHHhhcCCCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEE
Confidence 46889999999999999999742 2222211 11123445567777777777766553
No 252
>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=24.14 E-value=1.4e+02 Score=28.69 Aligned_cols=59 Identities=20% Similarity=0.293 Sum_probs=40.5
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHH
Q 022049 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA 147 (303)
Q Consensus 84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs 147 (303)
-+.|-+.++++ +.+|++|.|.+-.|+.+-.++.+..- .-|..++.--+|+.+|. .-|-+
T Consensus 118 ~~Eine~Lqe~-G~vsi~eLa~~~~Lp~efl~~~li~~--~lg~~I~g~~d~~~lyT--~ayv~ 176 (272)
T PF09743_consen 118 AEEINEKLQES-GQVSISELAKQYDLPSEFLKEELISK--RLGKIIKGRLDGDVLYT--EAYVA 176 (272)
T ss_pred HHHHHHHHHHc-CeEeHHHHHHhcCCcHHHHHHHHhhh--hcCcceeEEEeCCEEec--HHHHH
Confidence 34444445555 56999999999999999887444332 45777888888886654 44444
No 253
>PRK08392 hypothetical protein; Provisional
Probab=24.06 E-value=90 Score=27.92 Aligned_cols=56 Identities=11% Similarity=0.033 Sum_probs=35.6
Q ss_pred ccCCCcccccCCCCchhhHHHHHHHHhcCCceeehhhh---hhcCCCHHHHHHHHHHHHhhcCC
Q 022049 67 GVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVA---GKAGLKLNEAQKALQALAADTDG 127 (303)
Q Consensus 67 ~~~~~~~~~~~~l~~~~~~~im~Ave~~g~rvTvgDVA---a~aGLsl~eAe~aL~aLAad~~G 127 (303)
.++-|-.+|-+....-+.+.+++.+.+.|.++|+|.=| ..-| ..++| .+++.+.|-
T Consensus 146 ~~~~g~~lEiNt~~~~p~~~~l~~~~~~G~~~~igSDAH~~~~vg-~~~~a----~~~~~~~g~ 204 (215)
T PRK08392 146 AEAYGKAFEISSRYRVPDLEFIRECIKRGIKLTFASDAHRPEDVG-NVSWS----LKVFKKAGG 204 (215)
T ss_pred HHHhCCEEEEeCCCCCCCHHHHHHHHHcCCEEEEeCCCCChHHCC-cHHHH----HHHHHHcCC
Confidence 34556667766544456678999999999999999333 2345 24444 445555543
No 254
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=24.04 E-value=2.2e+02 Score=19.82 Aligned_cols=33 Identities=24% Similarity=0.257 Sum_probs=27.2
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHH
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALA 122 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLA 122 (303)
.++.+.++++|...+.-||.... +++++|.++.
T Consensus 13 ~~~~~~L~~~~i~y~~~dv~~~~-----~~~~~l~~~~ 45 (60)
T PF00462_consen 13 KKAKEFLDEKGIPYEEVDVDEDE-----EAREELKELS 45 (60)
T ss_dssp HHHHHHHHHTTBEEEEEEGGGSH-----HHHHHHHHHH
T ss_pred HHHHHHHHHcCCeeeEcccccch-----hHHHHHHHHc
Confidence 46788889999999999998875 7777777776
No 255
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=23.82 E-value=2.8e+02 Score=29.67 Aligned_cols=88 Identities=14% Similarity=0.114 Sum_probs=55.9
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc--CCceEeeccccEEEEc---ChhhHHHHhhhhHHHhHH
Q 022049 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DGFLEVSDEGDVLYVF---PNNYRAKLAAKSFRLKVE 159 (303)
Q Consensus 85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~--~G~LeVsesGdIlYvF---P~~fRs~l~~Ks~r~rlq 159 (303)
.+|+.++-++|.--..-=++..+|++.+.++++|..|.+-. ..++....+|+++|.. -+-.+-..-+|+-..--+
T Consensus 22 akV~~~Llr~G~lss~~~~~~~t~i~~~kVk~aL~sLiQh~~V~y~~~~~~~g~vt~Y~~~~~ei~hilry~r~~~i~~~ 101 (551)
T KOG2587|consen 22 AKVGEHLLRTGRLSSLRVIAKDTGISLDKVKKALVSLIQHNCVSYQVHTRNSGKVTTYEAQCSEILHILRYPRYIYITKT 101 (551)
T ss_pred HHHHHHHHHcCCcchhHHHHhhcCCChHHHHHHHHHHHHhcceEEEEecCCCCceEEEEehhhHHHHHHhcccceeeHHH
Confidence 46778888887655566678899999999999999998865 4455555688887654 333333323343333334
Q ss_pred HHHHHHhhhhHHH
Q 022049 160 PVIDKAKAAAEYS 172 (303)
Q Consensus 160 ~~~~k~w~v~~yl 172 (303)
+.-+.+..+..+|
T Consensus 102 ~~~q~~~sIv~~L 114 (551)
T KOG2587|consen 102 LYSQTAESIVEEL 114 (551)
T ss_pred HhhhHHHHHHHHH
Confidence 4444444444444
No 256
>PF09753 Use1: Membrane fusion protein Use1; InterPro: IPR019150 This entry represents a family of proteins, approximately 300 residues in length, involved in vesicle transport. They have a single C-terminal transmembrane domain and a SNARE [soluble NSF (N-ethylmaleimide-sensitive fusion protein) attachment protein receptor] domain of approximately 60 residues. The SNARE domains are essential for membrane fusion and are conserved from yeasts to humans. Use1 is one of the three protein subunits that make up the SNARE complex and it is specifically required for Golgi-endoplasmic reticulum retrograde transport [].
Probab=23.66 E-value=1.5e+02 Score=27.45 Aligned_cols=13 Identities=8% Similarity=0.026 Sum_probs=7.6
Q ss_pred HHhHHHHHHHHhh
Q 022049 155 RLKVEPVIDKAKA 167 (303)
Q Consensus 155 r~rlq~~~~k~w~ 167 (303)
..||++..++-|+
T Consensus 215 ~~rl~~~~~~~~~ 227 (251)
T PF09753_consen 215 SKRLKEHSSKSWG 227 (251)
T ss_pred HHHHHHHHHhccc
Confidence 4456666666555
No 257
>PRK00767 transcriptional regulator BetI; Validated
Probab=23.56 E-value=65 Score=27.01 Aligned_cols=34 Identities=24% Similarity=0.303 Sum_probs=24.4
Q ss_pred chhhHHHHHH----HHhcCCc-eeehhhhhhcCCCHHHH
Q 022049 81 ADVRNRAMDA----VDACNRR-VTIGDVAGKAGLKLNEA 114 (303)
Q Consensus 81 ~~~~~~im~A----ve~~g~r-vTvgDVAa~aGLsl~eA 114 (303)
...|++|+++ +.+.||. +|+.|||.++|++.-..
T Consensus 8 ~~~r~~Il~aA~~lf~~~G~~~~s~~~Ia~~aGvs~gsl 46 (197)
T PRK00767 8 PIRRQQLIDATLRAIGEVGLLDATIAQIARRAGVSTGII 46 (197)
T ss_pred hhHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCHHHH
Confidence 3456666554 4677775 78899999999987543
No 258
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=23.48 E-value=1.2e+02 Score=27.34 Aligned_cols=43 Identities=21% Similarity=0.381 Sum_probs=36.6
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 79 l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
|+.++|..|.+-+.+.|. |+-.||.+-|+++.-+ .|++.|-..
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 566666543
No 259
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=23.46 E-value=72 Score=28.85 Aligned_cols=48 Identities=19% Similarity=0.180 Sum_probs=35.8
Q ss_pred HhcCCce-eehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-cccEEEEc
Q 022049 92 DACNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYVF 141 (303)
Q Consensus 92 e~~g~rv-TvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse-sGdIlYvF 141 (303)
=+-|-++ |..++|.+-|+|..-+++||..|.++ |-+++.. .|-.|=.+
T Consensus 27 l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~e--GlV~~~~~~G~~V~~~ 76 (257)
T PRK10225 27 YNPGERLPPEREIAEMLDVTRTVVREALIMLEIK--GLVEVRRGAGIYVLDS 76 (257)
T ss_pred CCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEecCCEEEEeCC
Confidence 3446677 68899999999999999999999975 5565443 45444433
No 260
>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=23.38 E-value=50 Score=22.59 Aligned_cols=17 Identities=35% Similarity=0.470 Sum_probs=13.3
Q ss_pred eehhhhhhcCCCHHHHH
Q 022049 99 TIGDVAGKAGLKLNEAQ 115 (303)
Q Consensus 99 TvgDVAa~aGLsl~eAe 115 (303)
|++|||..+|++....+
T Consensus 1 ti~e~A~~~gvs~~tlR 17 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLR 17 (38)
T ss_dssp EHHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 68999999999987653
No 261
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=23.35 E-value=1.1e+02 Score=22.28 Aligned_cols=30 Identities=13% Similarity=0.247 Sum_probs=23.9
Q ss_pred CHHHHHHHHHHHHhhcC-CceEeeccccEEEE
Q 022049 110 KLNEAQKALQALAADTD-GFLEVSDEGDVLYV 140 (303)
Q Consensus 110 sl~eAe~aL~aLAad~~-G~LeVsesGdIlYv 140 (303)
+.++. ++|..+|.+++ |++.+|....+...
T Consensus 22 ~~~~l-~~la~ia~~yg~~~irlT~~Q~l~l~ 52 (69)
T PF03460_consen 22 SAEQL-RALAEIAEKYGDGEIRLTTRQNLQLR 52 (69)
T ss_dssp EHHHH-HHHHHHHHHHSTSEEEEETTSCEEEE
T ss_pred CHHHH-HHHHHHHHHhCCCeEEECCCCeEEEe
Confidence 33444 78899999998 99999999886654
No 262
>PRK11104 hemG protoporphyrinogen oxidase; Provisional
Probab=23.00 E-value=56 Score=28.64 Aligned_cols=36 Identities=14% Similarity=0.448 Sum_probs=29.0
Q ss_pred ccchhhh-hhh----cccCCCCCCCchHHHHHHHHHHHHHh
Q 022049 247 KMNFIKS-VFS----FVFGEGDPNQGIEEKRWKLIGEYIAS 282 (303)
Q Consensus 247 emnFlEs-VFS----FvFGDGDPN~dlEerRwq~Ig~~Ir~ 282 (303)
+|||+|- +.- -.=|+.||+.+.|.+.|++|-++.+.
T Consensus 129 k~~f~~r~~~~~i~k~~~~~~~~~~~~~~~dw~~v~~fa~~ 169 (177)
T PRK11104 129 RYRWFDRFMIKLIMKMTGGETDTSKEVEYTDWEQVANFARE 169 (177)
T ss_pred cCCHHHHHHHHHHHHHcCCCCCCCCceeeCCHHHHHHHHHH
Confidence 5999994 443 35578999999999999999988764
No 263
>COG5346 Predicted membrane protein [Function unknown]
Probab=22.77 E-value=5e+02 Score=23.13 Aligned_cols=61 Identities=16% Similarity=0.286 Sum_probs=31.4
Q ss_pred hhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHHHhhhhHHHh----HHHHHHHHhhhhHHHHHHHH
Q 022049 102 DVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLK----VEPVIDKAKAAAEYSIRVLF 177 (303)
Q Consensus 102 DVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~l~~Ks~r~r----lq~~~~k~w~v~~yliRVsF 177 (303)
|++..--+=.+.+ +.+-+.|.+..+| |.....|..+.+ +++.+.++-. .-|
T Consensus 43 ~l~qYnsI~pnt~-~rimaMAekEQah-----------------rH~~~~k~~~~q~r~~~~~~~tril~-------liF 97 (136)
T COG5346 43 LLSQYNSIYPNTL-QRIMAMAEKEQAH-----------------RHAIDLKNLKIQRRGQLYAKLTRILL-------LIF 97 (136)
T ss_pred HHHHHHhhcCCHH-HHHHHHHHHHHHH-----------------HHHHHHhhhHHHHHHHHHHHHHHHHH-------HHH
Confidence 4444444444455 4566777766543 555555544332 3444433322 246
Q ss_pred HHHHHHHHHH
Q 022049 178 GTALIASIVI 187 (303)
Q Consensus 178 Gi~LIaSIvl 187 (303)
|+.||.||..
T Consensus 98 gi~LVvsi~~ 107 (136)
T COG5346 98 GIFLVVSIFP 107 (136)
T ss_pred HHHHHHHHHH
Confidence 7777777655
No 264
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=22.66 E-value=5.1e+02 Score=22.50 Aligned_cols=39 Identities=15% Similarity=0.279 Sum_probs=26.8
Q ss_pred CCCchhhHHHHHHHHhc-----CCceeehhhhhhcCCCHHHHHH
Q 022049 78 KLPADVRNRAMDAVDAC-----NRRVTIGDVAGKAGLKLNEAQK 116 (303)
Q Consensus 78 ~l~~~~~~~im~Ave~~-----g~rvTvgDVAa~aGLsl~eAe~ 116 (303)
+||.+.++.+|+-.+++ --+.|-.||.++-|=|.+-|++
T Consensus 16 ~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~ 59 (181)
T PF08006_consen 16 KLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIARE 59 (181)
T ss_pred cCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHH
Confidence 68999999998776543 2235778888888855555544
No 265
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=22.55 E-value=1.3e+02 Score=22.12 Aligned_cols=24 Identities=8% Similarity=0.196 Sum_probs=19.8
Q ss_pred HHHHHHHHhcC-CceeehhhhhhcC
Q 022049 85 NRAMDAVDACN-RRVTIGDVAGKAG 108 (303)
Q Consensus 85 ~~im~Ave~~g-~rvTvgDVAa~aG 108 (303)
-.|-|++.+.| .-+|+.|+|++..
T Consensus 9 LgI~dii~~~g~~~ls~~eia~~l~ 33 (51)
T PF08100_consen 9 LGIPDIIHNAGGGPLSLSEIAARLP 33 (51)
T ss_dssp TTHHHHHHHHTTS-BEHHHHHHTST
T ss_pred cCcHHHHHHcCCCCCCHHHHHHHcC
Confidence 35678898887 9999999999887
No 266
>PRK14999 histidine utilization repressor; Provisional
Probab=22.27 E-value=73 Score=28.68 Aligned_cols=58 Identities=17% Similarity=0.306 Sum_probs=39.6
Q ss_pred chhhHHHHHHHHhc----CCce-eehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEc
Q 022049 81 ADVRNRAMDAVDAC----NRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (303)
Q Consensus 81 ~~~~~~im~Ave~~----g~rv-TvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvF 141 (303)
..+...|.+.++.. |-+. |-.++|.+-|+|...+++||..|+.+. -| ....|.=.||=
T Consensus 15 ~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eG--li-~r~~GkGTfV~ 77 (241)
T PRK14999 15 ETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEG--WL-VRLQGVGTFVA 77 (241)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCC--CE-EEecCcEEEEC
Confidence 34445566666554 4455 778999999999999999999999874 34 33334334443
No 267
>PF13038 DUF3899: Domain of unknown function (DUF3899)
Probab=22.26 E-value=1e+02 Score=24.14 Aligned_cols=26 Identities=15% Similarity=0.327 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022049 170 EYSIRVLFGTALIASIVIVFTAIIAI 195 (303)
Q Consensus 170 ~yliRVsFGi~LIaSIvlv~~aIiai 195 (303)
.+.+.-|....|++.++++.++|++.
T Consensus 65 ~~~~~~~~~~~ll~~~ll~l~~iil~ 90 (92)
T PF13038_consen 65 KYRVSRWTYPLLLIGLLLILLSIILS 90 (92)
T ss_pred hhHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444455555555556656665554
No 268
>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=22.25 E-value=84 Score=28.48 Aligned_cols=31 Identities=23% Similarity=0.391 Sum_probs=27.2
Q ss_pred CCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 95 NRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 95 g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
|+..|+.+++...|+++++.-++|.++++..
T Consensus 25 ~g~~~l~~a~~~~g~d~~~~l~~ln~~~~~~ 55 (216)
T TIGR03652 25 GGNVSLAEACKEKGLDPDEILAELNALQQEP 55 (216)
T ss_pred CCcchHHHHHHHcCCCHHHHHHHHHHHHhcc
Confidence 4567999999999999999999999998544
No 269
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=22.21 E-value=1.6e+02 Score=28.96 Aligned_cols=66 Identities=15% Similarity=0.282 Sum_probs=51.6
Q ss_pred CCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh------------cCCceEeeccccEEEEcChh
Q 022049 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD------------TDGFLEVSDEGDVLYVFPNN 144 (303)
Q Consensus 78 ~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad------------~~G~LeVsesGdIlYvFP~~ 144 (303)
.|.+.+|-+|++-+.+.|. ..|-++|..-||+-...-..+..|-.. ..-.+-.+..+||+-.||..
T Consensus 19 alaS~vRv~Il~lL~~k~p-lNvneiAe~lgLpqst~s~~ik~Le~aGlirT~t~karkG~QKiC~s~~~ei~i~F~~r 96 (308)
T COG4189 19 ALASKVRVAILQLLHRKGP-LNVNEIAEALGLPQSTMSANIKVLEKAGLIRTETVKARKGSQKICISTTDEIEINFPDR 96 (308)
T ss_pred HHHHHHHHHHHHHHHHhCC-CCHHHHHHHhCCchhhhhhhHHHHHhcCceeeeeeccccCceeEeEeecceEEEecCCC
Confidence 4667889999999988775 688999999999999988888777543 22334456788999999874
No 270
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=22.14 E-value=1.5e+02 Score=26.45 Aligned_cols=54 Identities=17% Similarity=0.369 Sum_probs=37.5
Q ss_pred hhHHHHHHHHhc----CCce-eehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee-ccccEE
Q 022049 83 VRNRAMDAVDAC----NRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS-DEGDVL 138 (303)
Q Consensus 83 ~~~~im~Ave~~----g~rv-TvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs-esGdIl 138 (303)
+...+.+.++.. |-+. |-.++|.+-|+|...+++||..|+.+ |-|+-- -.|-.|
T Consensus 6 i~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~e--Gli~r~~G~GtfV 65 (230)
T TIGR02018 6 IKQDILERIRSGEWPPGHRIPSEHELVAQYGCSRMTVNRALRELTDA--GLLERRQGVGTFV 65 (230)
T ss_pred HHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEecCCEEEE
Confidence 345556666554 3344 77799999999999999999999998 444332 244433
No 271
>PRK15126 thiamin pyrimidine pyrophosphate hydrolase; Provisional
Probab=22.05 E-value=2.3e+02 Score=25.55 Aligned_cols=53 Identities=19% Similarity=0.234 Sum_probs=36.9
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEE
Q 022049 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (303)
Q Consensus 79 l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYv 140 (303)
++.. ..++++.+++.|..++++ ||=+...++.-+..|.-+ + .-|+.+|-++|.
T Consensus 20 i~~~-~~~ai~~l~~~G~~~~ia-----TGR~~~~~~~~~~~l~~~--~-~~I~~NGa~I~~ 72 (272)
T PRK15126 20 LGEK-TLSTLARLRERDITLTFA-----TGRHVLEMQHILGALSLD--A-YLITGNGTRVHS 72 (272)
T ss_pred CCHH-HHHHHHHHHHCCCEEEEE-----CCCCHHHHHHHHHHcCCC--C-cEEecCCcEEEc
Confidence 4544 345566677789888875 888898887777666433 2 247888888886
No 272
>PHA00738 putative HTH transcription regulator
Probab=21.96 E-value=3.5e+02 Score=23.18 Aligned_cols=57 Identities=19% Similarity=0.346 Sum_probs=46.8
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEc
Q 022049 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (303)
Q Consensus 82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvF 141 (303)
..|-+|++.+.+ +...+++|++...+++...+-+=|..|-. -|-+++..+|--+|.-
T Consensus 12 ptRr~IL~lL~~-~e~~~V~eLae~l~lSQptVS~HLKvLre--AGLV~srK~Gr~vyY~ 68 (108)
T PHA00738 12 ILRRKILELIAE-NYILSASLISHTLLLSYTTVLRHLKILNE--QGYIELYKEGRTLYAK 68 (108)
T ss_pred HHHHHHHHHHHH-cCCccHHHHHHhhCCCHHHHHHHHHHHHH--CCceEEEEECCEEEEE
Confidence 467788888865 44599999999999999999898888854 4788999999866653
No 273
>PF14493 HTH_40: Helix-turn-helix domain
Probab=21.91 E-value=1.2e+02 Score=23.76 Aligned_cols=72 Identities=14% Similarity=0.203 Sum_probs=46.5
Q ss_pred HHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHHHhhhh---HHHhHHHHHHH
Q 022049 88 MDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKS---FRLKVEPVIDK 164 (303)
Q Consensus 88 m~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~l~~Ks---~r~rlq~~~~k 164 (303)
+...+-...+-|+.|||.+-||+.+....-|..++.... .+.+.+ .+|....+.+..-. -..+++++.+.
T Consensus 4 ~~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~-~~~~~~------~l~~e~~~~I~~~~~~~~~~~lk~i~e~ 76 (91)
T PF14493_consen 4 QITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGE-PLDIEE------LLSEEEIKQIEDAIEKLGSEKLKPIKEA 76 (91)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCC-CCCHHH------hCCHHHHHHHHHHHHHcCcccHHHHHHH
Confidence 344444456789999999999999999999999887733 344432 15665554433311 11456666666
Q ss_pred Hh
Q 022049 165 AK 166 (303)
Q Consensus 165 ~w 166 (303)
+-
T Consensus 77 l~ 78 (91)
T PF14493_consen 77 LP 78 (91)
T ss_pred CC
Confidence 54
No 274
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=21.77 E-value=1.5e+02 Score=24.65 Aligned_cols=47 Identities=13% Similarity=0.226 Sum_probs=36.9
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 022049 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (303)
Q Consensus 83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs 132 (303)
.+=.++..+... ..+|+.|+|...|++...+-+.|..|..+ |-++-.
T Consensus 41 ~q~~vL~~l~~~-~~~t~~eLa~~l~i~~~tvsr~l~~Le~~--GlI~R~ 87 (144)
T PRK11512 41 AQFKVLCSIRCA-ACITPVELKKVLSVDLGALTRMLDRLVCK--GWVERL 87 (144)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEec
Confidence 345678888654 46999999999999999999999999775 444433
No 275
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=21.74 E-value=77 Score=28.22 Aligned_cols=56 Identities=14% Similarity=0.179 Sum_probs=40.9
Q ss_pred hhHHHHHHHHhcCCce-eehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-cccEEEE
Q 022049 83 VRNRAMDAVDACNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVLYV 140 (303)
Q Consensus 83 ~~~~im~Ave~~g~rv-TvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse-sGdIlYv 140 (303)
++.+|+.--=+-|-+. |-.|+|.+-|+|-.-++.||..|.++ |-|++.. .|-.|-.
T Consensus 15 l~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~e--GlV~~~~~~G~~V~~ 72 (235)
T TIGR02812 15 IVESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARD--GWLTIQHGKPTKVNN 72 (235)
T ss_pred HHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEeCCCccEecC
Confidence 3444444334457788 78899999999999999999999976 6777664 5644433
No 276
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=21.66 E-value=54 Score=31.24 Aligned_cols=22 Identities=36% Similarity=0.441 Sum_probs=19.2
Q ss_pred eeehhhhhhcCCCHHHHHHHHH
Q 022049 98 VTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 98 vTvgDVAa~aGLsl~eAe~aL~ 119 (303)
+|+.|||..+|+|...+-+.|+
T Consensus 1 ~TikDVA~~AGVS~sTVSrvln 22 (333)
T COG1609 1 ATIKDVAKLAGVSKATVSRVLN 22 (333)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 5899999999999999877765
No 277
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=21.52 E-value=1.6e+02 Score=18.74 Aligned_cols=26 Identities=12% Similarity=0.249 Sum_probs=21.8
Q ss_pred CceeehhhhhhcCCCHHHHHHHHHHH
Q 022049 96 RRVTIGDVAGKAGLKLNEAQKALQAL 121 (303)
Q Consensus 96 ~rvTvgDVAa~aGLsl~eAe~aL~aL 121 (303)
...|..|||...|++.....+.+...
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45799999999999999998777654
No 278
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=21.40 E-value=1.7e+02 Score=25.95 Aligned_cols=44 Identities=14% Similarity=0.231 Sum_probs=33.0
Q ss_pred hhhHHHHHHHHhcCC----ce-eehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 82 DVRNRAMDAVDACNR----RV-TIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 82 ~~~~~im~Ave~~g~----rv-TvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
.+.+.+.+.++..-+ +. |-.++|.+-|+|...+++||..|..+.
T Consensus 12 ~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eG 60 (238)
T TIGR02325 12 QIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERG 60 (238)
T ss_pred HHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 344555566655433 33 777999999999999999999999874
No 279
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=21.33 E-value=1.4e+02 Score=24.72 Aligned_cols=36 Identities=11% Similarity=0.269 Sum_probs=27.6
Q ss_pred HHHHHHHHhc-CCceeehhhhhhcCCCHHHHHHHHHH
Q 022049 85 NRAMDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQA 120 (303)
Q Consensus 85 ~~im~Ave~~-g~rvTvgDVAa~aGLsl~eAe~aL~a 120 (303)
.++++.++++ ....|+.|+|...|++....++-+..
T Consensus 12 ~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 12 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5677777554 46689999999999999887655544
No 280
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=21.29 E-value=2.4e+02 Score=21.56 Aligned_cols=43 Identities=16% Similarity=0.278 Sum_probs=27.9
Q ss_pred HHHHHhcCCceeehhhhhhcCCCHHHHHH------------HHHHHHhhcCCceEee
Q 022049 88 MDAVDACNRRVTIGDVAGKAGLKLNEAQK------------ALQALAADTDGFLEVS 132 (303)
Q Consensus 88 m~Ave~~g~rvTvgDVAa~aGLsl~eAe~------------aL~aLAad~~G~LeVs 132 (303)
-+.+++ ...|..|+|...|++-...-+ .|..++...|++++++
T Consensus 24 ~~~~~~--~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~~v~i~ 78 (80)
T PF13744_consen 24 RELREE--RGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGGRVEIV 78 (80)
T ss_dssp HHHHHC--CT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTEEEEEE
T ss_pred HHHHHH--cCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCCeEEEe
Confidence 334444 458999999999998766532 4566777788888874
No 281
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=21.27 E-value=1.9e+02 Score=21.64 Aligned_cols=39 Identities=23% Similarity=0.292 Sum_probs=29.9
Q ss_pred chhhHHHHHHHHhcCC--ceeehhhhh---hcCCCHHHHHHHHH
Q 022049 81 ADVRNRAMDAVDACNR--RVTIGDVAG---KAGLKLNEAQKALQ 119 (303)
Q Consensus 81 ~~~~~~im~Ave~~g~--rvTvgDVAa---~aGLsl~eAe~aL~ 119 (303)
.+...+-++|++.+|. .+|+..|+. .++|+..+++.=|+
T Consensus 8 ~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~Q 51 (57)
T TIGR01557 8 EDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQ 51 (57)
T ss_pred HHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHH
Confidence 4566788999999997 678877765 46778888876554
No 282
>PF02932 Neur_chan_memb: Neurotransmitter-gated ion-channel transmembrane region ion channel family signature gamma-aminobutyric acid (GABA) receptor signature nicotinic acetylcholine receptor signature; InterPro: IPR006029 Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily: Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits []. Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits []. Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known []. Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) []. Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) []. These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ]. This domain represents four transmembrane helices of a variety of neurotransmitter-gated ion-channels.; GO: 0006811 ion transport, 0016020 membrane; PDB: 1DXZ_A 3MRA_A 1EQ8_C 1OED_C 2PR9_P 1A11_A 1CEK_A 2BG9_E 2KSR_A 2K59_B ....
Probab=21.26 E-value=3e+02 Score=21.86 Aligned_cols=38 Identities=16% Similarity=0.151 Sum_probs=23.3
Q ss_pred HhhhhHHHhHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Q 022049 149 LAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIV 186 (303)
Q Consensus 149 l~~Ks~r~rlq~~~~k~w~v~~yliRVsFGi~LIaSIv 186 (303)
++++.-..+.++-|+.+..++--++|+-|-++.++.-+
T Consensus 197 ~~~~~~~~~~~~ew~~~A~viDR~~~~~F~i~f~~~~i 234 (237)
T PF02932_consen 197 LREQDEEEEIKEEWKFVAMVIDRLFRILFPIAFILFNI 234 (237)
T ss_dssp HHHHHHHHHHHHHHHSTSHHHHHHHHHHHHHHHHHHHH
T ss_pred cccccccccccccccccHHHHHHHHHHHHHHHHHHHHh
Confidence 44555555566667777777777777766665554433
No 283
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=21.22 E-value=1.5e+02 Score=24.77 Aligned_cols=61 Identities=16% Similarity=0.303 Sum_probs=38.5
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcCh
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~ 143 (303)
+.+-.+.|++|.+.+++.=..+++.++|.-.|++- ++|..++.+.| =+++++|.++...|+
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 45677899999999999999999999999999993 36666766664 344566665554444
No 284
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=21.09 E-value=1.5e+02 Score=28.05 Aligned_cols=51 Identities=6% Similarity=-0.061 Sum_probs=42.9
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCC
Q 022049 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG 127 (303)
Q Consensus 77 ~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G 127 (303)
......+.+|=.+.++-...+.|..|+|.+.+++...++.-+..+..+.|.
T Consensus 138 ~~~~~~LS~RE~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred hhccCCCCHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 344456667777888888889999999999999999999999998888763
No 285
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=20.88 E-value=1.9e+02 Score=22.62 Aligned_cols=35 Identities=11% Similarity=0.204 Sum_probs=28.4
Q ss_pred HHHHHHHHhcC-CceeehhhhhhcC-CCHHHHHHHHH
Q 022049 85 NRAMDAVDACN-RRVTIGDVAGKAG-LKLNEAQKALQ 119 (303)
Q Consensus 85 ~~im~Ave~~g-~rvTvgDVAa~aG-Lsl~eAe~aL~ 119 (303)
-.|++-+++.+ .-+|+.||...+. +.+..+...++
T Consensus 12 ~~aV~ymK~r~~~Plt~~EIl~~ls~~d~~~~~~~~L 48 (75)
T cd07977 12 AKIVDYMKKRHQHPLTLDEILDYLSLLDIGPKLKEWL 48 (75)
T ss_pred HHHHHHHHhcCCCCccHHHHHHHHhccCccHHHHHHH
Confidence 45778888999 9999999999999 88887754433
No 286
>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=20.84 E-value=1.9e+02 Score=22.02 Aligned_cols=21 Identities=19% Similarity=0.572 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 022049 177 FGTALIASIVIVFTAIIAILS 197 (303)
Q Consensus 177 FGi~LIaSIvlv~~aIiails 197 (303)
+|++|+..|.++.+++++...
T Consensus 7 iGviLliaitVilaavv~~~~ 27 (80)
T PF07790_consen 7 IGVILLIAITVILAAVVGAFV 27 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 688888888888888877765
No 287
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=20.76 E-value=1.1e+02 Score=31.29 Aligned_cols=39 Identities=15% Similarity=0.349 Sum_probs=35.5
Q ss_pred hHHHHHHHHhcCCcee-ehhhhhhcCCCHHHHHHHHHHHH
Q 022049 84 RNRAMDAVDACNRRVT-IGDVAGKAGLKLNEAQKALQALA 122 (303)
Q Consensus 84 ~~~im~Ave~~g~rvT-vgDVAa~aGLsl~eAe~aL~aLA 122 (303)
++.+.+.+-+.+...| +-|+|..||++.+++=..|.+|-
T Consensus 317 ~~~v~~~L~k~~~~~~~I~~Is~~TgM~~dDVI~tLe~L~ 356 (395)
T COG5027 317 SEIVAKLLLKMDKEITDINEISKETGMSTDDVIHTLEALN 356 (395)
T ss_pred HHHHHHHHHhcCcccccHHHHHhhhCCchhhHHHHHHHhc
Confidence 4788999999999999 99999999999999998888774
No 288
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=20.66 E-value=95 Score=27.39 Aligned_cols=32 Identities=16% Similarity=0.341 Sum_probs=27.5
Q ss_pred hcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (303)
Q Consensus 93 ~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad 124 (303)
..+..+|+.|+|.+.|+|..-.++-|..|...
T Consensus 21 ~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~a 52 (164)
T PRK10857 21 SEAGPVPLADISERQGISLSYLEQLFSRLRKN 52 (164)
T ss_pred CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34457999999999999999999999999865
No 289
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=20.44 E-value=86 Score=28.35 Aligned_cols=52 Identities=17% Similarity=0.219 Sum_probs=37.0
Q ss_pred HHHHHHHHhcCCce-eehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec-cccEE
Q 022049 85 NRAMDAVDACNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EGDVL 138 (303)
Q Consensus 85 ~~im~Ave~~g~rv-TvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse-sGdIl 138 (303)
..|++--=+-|.++ +-.|+|.+-|+|..-+++||..|.++ |-+++-. .|-.|
T Consensus 13 ~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~--GlV~~~~~~G~~V 66 (253)
T PRK10421 13 ALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSE--GVLLSRRGGGTFI 66 (253)
T ss_pred HHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEeCCCeEEE
Confidence 33333333447788 68899999999999999999999975 5555443 45433
No 290
>PRK10870 transcriptional repressor MprA; Provisional
Probab=20.24 E-value=1.5e+02 Score=26.02 Aligned_cols=42 Identities=12% Similarity=0.124 Sum_probs=36.1
Q ss_pred hHHHHHHHHhc-CCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049 84 RNRAMDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (303)
Q Consensus 84 ~~~im~Ave~~-g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~ 125 (303)
+=.+|..+... ++.+|+.|+|...|++...+-+.+..|..+.
T Consensus 57 q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kG 99 (176)
T PRK10870 57 LFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRG 99 (176)
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 55778888764 6789999999999999999999999998764
No 291
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=20.23 E-value=1.6e+02 Score=23.04 Aligned_cols=38 Identities=18% Similarity=0.221 Sum_probs=28.3
Q ss_pred hHHHHHHHHhc-CCceeehhhhhhcCCCHHHHHHHHHHH
Q 022049 84 RNRAMDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQAL 121 (303)
Q Consensus 84 ~~~im~Ave~~-g~rvTvgDVAa~aGLsl~eAe~aL~aL 121 (303)
-.++.+.++.+ ...+|+.|+|...|+|....++...+.
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34556666544 556999999999999998887766654
No 292
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=20.16 E-value=77 Score=27.65 Aligned_cols=46 Identities=20% Similarity=0.243 Sum_probs=30.4
Q ss_pred ccCCCcccccCCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHH
Q 022049 67 GVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLN 112 (303)
Q Consensus 67 ~~~~~~~~~~~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~ 112 (303)
.++|||.+-.+-..-+.-.++++.++++|..+.+-++....|.++.
T Consensus 134 ~LkpgG~lv~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~~~ 179 (198)
T PRK00377 134 IIKKGGRIVIDAILLETVNNALSALENIGFNLEITEVIIAKGMKTK 179 (198)
T ss_pred HcCCCcEEEEEeecHHHHHHHHHHHHHcCCCeEEEEEehhhccccc
Confidence 5677777665555555556777777777777777777766665543
No 293
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=20.12 E-value=3.9e+02 Score=26.80 Aligned_cols=42 Identities=12% Similarity=0.238 Sum_probs=30.4
Q ss_pred CCCchhhHH---HHHHH----HhcCCceeehhhhhhcCCCHHHHHHHHH
Q 022049 78 KLPADVRNR---AMDAV----DACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (303)
Q Consensus 78 ~l~~~~~~~---im~Av----e~~g~rvTvgDVAa~aGLsl~eAe~aL~ 119 (303)
+||...... +.++. .++|...|+.+||...|++.++++..+.
T Consensus 213 RlP~~~~~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~ 261 (373)
T PRK07406 213 RLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAK 261 (373)
T ss_pred eCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 577665532 23333 4578889999999999999999976543
No 294
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=20.08 E-value=1.5e+02 Score=27.13 Aligned_cols=46 Identities=17% Similarity=0.300 Sum_probs=34.0
Q ss_pred CCCCchhhHHH---HHH----HHhcCCceeehhhhhhcCCCHHHHHHHHHHHH
Q 022049 77 DKLPADVRNRA---MDA----VDACNRRVTIGDVAGKAGLKLNEAQKALQALA 122 (303)
Q Consensus 77 ~~l~~~~~~~i---m~A----ve~~g~rvTvgDVAa~aGLsl~eAe~aL~aLA 122 (303)
.++|...++.+ .++ ..++|...|..+||...|++.++.+..+....
T Consensus 109 ir~p~~~~~~~~~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~ 161 (254)
T TIGR02850 109 IRVSRSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQ 161 (254)
T ss_pred ccCchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcC
Confidence 36777665443 222 35679999999999999999999988776643
No 295
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=20.01 E-value=2e+02 Score=29.60 Aligned_cols=71 Identities=17% Similarity=0.189 Sum_probs=57.5
Q ss_pred ccCCCc--ccccCCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc-CCceEeeccccEEEE
Q 022049 67 GVGPGR--IVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT-DGFLEVSDEGDVLYV 140 (303)
Q Consensus 67 ~~~~~~--~~~~~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~-~G~LeVsesGdIlYv 140 (303)
-|-|.| -++.+.+..+.-..+|..+++..+ |-||-.-.-++.++-++.|.++.+-. .|-+-|+.+|.|++.
T Consensus 32 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g---v~~~~~~~~~~~e~e~~~L~aIL~sm~eGVi~vD~~G~I~~i 105 (520)
T PRK10820 32 EIDPIGRIYLNFAELEFESFSSLMAEIRRIAG---VTDVRTVPFMPSEREHRALSALLEALPEPVLSIDMKGKVELA 105 (520)
T ss_pred EEcCCCeEEEeCCCcChhhHHHHHHHHhcCCC---ccchhhhccChHHHHHHHHHHHHHhCCCcEEEECCCCeeeHh
Confidence 444544 466777777777778888877766 77888888899999999999998876 799999999999985
Done!