Query psy16970
Match_columns 257
No_of_seqs 219 out of 524
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 18:23:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16970.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16970hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00686 DM13 Domain present 100.0 3.3E-41 7.2E-46 270.4 11.8 106 139-244 2-108 (108)
2 KOG4731|consensus 100.0 3.5E-29 7.6E-34 239.0 11.5 159 97-256 117-283 (512)
3 PF10517 DM13: Electron transf 99.9 2.6E-27 5.7E-32 188.8 8.8 99 137-237 7-107 (108)
4 KOG4731|consensus 99.9 1.1E-26 2.4E-31 221.9 10.0 117 129-246 31-150 (512)
5 PF01498 HTH_Tnp_Tc3_2: Transp 99.6 2.2E-16 4.8E-21 116.4 3.4 72 11-98 1-72 (72)
6 PF13592 HTH_33: Winged helix- 96.2 0.0083 1.8E-07 42.9 4.5 43 21-63 2-44 (60)
7 PF13551 HTH_29: Winged helix- 95.0 0.062 1.3E-06 41.3 5.4 48 7-54 59-112 (112)
8 cd00131 PAX Paired Box domain 94.6 0.077 1.7E-06 43.6 5.4 45 8-52 78-126 (128)
9 PF13404 HTH_AsnC-type: AsnC-t 94.4 0.1 2.2E-06 35.0 4.7 38 9-52 3-40 (42)
10 PF13565 HTH_32: Homeodomain-l 94.3 0.08 1.7E-06 38.7 4.4 43 8-50 33-77 (77)
11 PF13276 HTH_21: HTH-like doma 94.0 0.17 3.6E-06 35.8 5.4 50 12-61 8-58 (60)
12 smart00351 PAX Paired Box doma 91.7 0.29 6.4E-06 39.9 4.5 43 8-51 78-125 (125)
13 PF08461 HTH_12: Ribonuclease 91.6 0.63 1.4E-05 34.1 5.8 55 14-69 3-61 (66)
14 TIGR01529 argR_whole arginine 91.5 0.42 9E-06 40.3 5.3 42 14-56 7-48 (146)
15 PF13412 HTH_24: Winged helix- 91.3 0.57 1.2E-05 31.3 4.9 38 9-52 3-40 (48)
16 PRK11179 DNA-binding transcrip 90.7 0.48 1E-05 39.6 5.0 39 8-52 8-46 (153)
17 PF01710 HTH_Tnp_IS630: Transp 90.5 0.55 1.2E-05 37.9 5.0 46 10-61 58-103 (119)
18 PRK11169 leucine-responsive tr 90.2 0.5 1.1E-05 40.0 4.7 40 8-53 13-52 (164)
19 PF01316 Arg_repressor: Argini 89.1 0.93 2E-05 33.9 4.9 46 11-57 7-52 (70)
20 PRK00441 argR arginine repress 87.6 1.2 2.7E-05 37.7 5.3 46 11-57 6-51 (149)
21 COG3415 Transposase and inacti 87.1 1.6 3.4E-05 36.8 5.6 55 11-65 68-122 (138)
22 PF08279 HTH_11: HTH domain; 87.0 1.3 2.8E-05 30.3 4.2 35 13-53 4-39 (55)
23 smart00344 HTH_ASNC helix_turn 86.9 1 2.2E-05 34.8 4.1 40 9-54 3-42 (108)
24 cd07153 Fur_like Ferric uptake 86.5 1.6 3.5E-05 34.1 5.1 46 10-56 2-51 (116)
25 PRK03341 arginine repressor; P 86.3 1.5 3.3E-05 37.9 5.2 46 11-57 17-62 (168)
26 PRK05066 arginine repressor; P 86.2 1.7 3.7E-05 37.2 5.4 46 11-57 11-57 (156)
27 PHA02517 putative transposase 85.7 1.6 3.4E-05 39.3 5.3 48 12-60 33-81 (277)
28 PRK04280 arginine repressor; P 85.3 1.9 4.1E-05 36.5 5.2 46 11-57 6-51 (148)
29 COG1438 ArgR Arginine represso 84.9 1.9 4.1E-05 36.9 5.1 47 10-57 7-53 (150)
30 PF08220 HTH_DeoR: DeoR-like h 84.3 2.2 4.8E-05 30.0 4.4 36 12-53 3-38 (57)
31 PF07592 DDE_Tnp_ISAZ013: Rhod 83.5 1.3 2.9E-05 42.0 3.9 44 23-67 24-67 (311)
32 PRK09462 fur ferric uptake reg 81.7 3.2 7E-05 34.4 5.2 44 8-52 16-61 (148)
33 PF01475 FUR: Ferric uptake re 81.7 2.5 5.5E-05 33.5 4.3 47 9-56 8-58 (120)
34 COG0735 Fur Fe2+/Zn2+ uptake r 79.0 4.3 9.4E-05 33.9 5.1 44 8-52 20-64 (145)
35 COG1522 Lrp Transcriptional re 77.2 4.9 0.00011 32.7 4.8 40 8-53 7-46 (154)
36 PRK09954 putative kinase; Prov 75.6 3.4 7.4E-05 38.7 3.9 53 9-67 3-55 (362)
37 PRK11639 zinc uptake transcrip 75.6 4.9 0.00011 34.4 4.6 48 8-56 25-76 (169)
38 PF01418 HTH_6: Helix-turn-hel 75.5 6.1 0.00013 29.3 4.5 45 9-59 16-64 (77)
39 PRK14702 insertion element IS2 75.5 6.5 0.00014 35.9 5.6 48 13-60 16-67 (262)
40 PRK09409 IS2 transposase TnpB; 74.7 7.9 0.00017 36.0 6.0 48 14-61 56-107 (301)
41 TIGR00122 birA_repr_reg BirA b 73.9 7 0.00015 28.0 4.4 36 11-53 2-37 (69)
42 smart00550 Zalpha Z-DNA-bindin 73.7 8.6 0.00019 28.0 4.9 43 9-57 6-53 (68)
43 PF02796 HTH_7: Helix-turn-hel 71.7 7.6 0.00016 25.9 3.8 33 12-52 12-44 (45)
44 PF13542 HTH_Tnp_ISL3: Helix-t 70.7 10 0.00022 25.4 4.4 38 7-52 13-50 (52)
45 PRK10906 DNA-binding transcrip 69.5 8.3 0.00018 35.0 4.8 42 10-57 6-50 (252)
46 PRK13509 transcriptional repre 68.2 9.1 0.0002 34.6 4.8 37 11-53 7-43 (251)
47 PRK10434 srlR DNA-bindng trans 67.5 8.5 0.00018 34.9 4.5 37 10-52 6-42 (256)
48 COG1349 GlpR Transcriptional r 67.3 9.3 0.0002 34.7 4.7 43 10-58 6-51 (253)
49 smart00420 HTH_DEOR helix_turn 67.2 16 0.00035 23.7 4.7 34 13-52 4-37 (53)
50 PF13551 HTH_29: Winged helix- 65.7 27 0.00059 26.4 6.4 57 13-76 3-68 (112)
51 PF04967 HTH_10: HTH DNA bindi 65.2 17 0.00036 25.7 4.6 41 7-53 2-47 (53)
52 PF12840 HTH_20: Helix-turn-he 63.8 20 0.00044 25.0 5.0 43 8-56 9-54 (61)
53 PF01978 TrmB: Sugar-specific 62.5 11 0.00023 26.9 3.4 45 9-59 8-55 (68)
54 PRK10411 DNA-binding transcrip 61.8 14 0.00031 33.2 4.8 37 11-53 6-42 (240)
55 TIGR02844 spore_III_D sporulat 61.5 16 0.00035 28.0 4.3 34 13-53 10-43 (80)
56 PF02954 HTH_8: Bacterial regu 59.2 22 0.00048 23.3 4.2 36 11-52 6-41 (42)
57 PF13384 HTH_23: Homeodomain-l 58.6 19 0.0004 23.9 3.8 36 9-52 5-40 (50)
58 PF13936 HTH_38: Helix-turn-he 56.4 16 0.00034 24.4 3.1 34 12-52 10-43 (44)
59 PRK09802 DNA-binding transcrip 56.4 18 0.00038 33.2 4.5 36 11-52 19-54 (269)
60 smart00351 PAX Paired Box doma 56.4 44 0.00096 27.0 6.4 79 7-108 19-103 (125)
61 COG0536 Obg Predicted GTPase [ 55.5 34 0.00074 33.3 6.3 73 139-228 36-109 (369)
62 PF00356 LacI: Bacterial regul 54.4 36 0.00078 23.1 4.7 23 25-53 1-23 (46)
63 smart00686 DM13 Domain present 54.4 8.7 0.00019 31.0 1.9 24 106-129 85-108 (108)
64 PRK11886 bifunctional biotin-- 54.1 23 0.0005 32.9 4.9 43 7-55 2-47 (319)
65 PRK10681 DNA-binding transcrip 53.0 24 0.00052 31.9 4.7 39 10-54 8-46 (252)
66 PF12728 HTH_17: Helix-turn-he 52.3 29 0.00062 23.1 4.0 30 24-59 2-31 (51)
67 PRK04424 fatty acid biosynthes 51.5 21 0.00045 30.9 3.9 42 10-57 8-49 (185)
68 COG3763 Uncharacterized protei 50.2 45 0.00098 25.2 4.9 42 10-52 25-66 (71)
69 PF12802 MarR_2: MarR family; 49.8 53 0.0011 22.3 5.1 44 9-58 5-53 (62)
70 smart00421 HTH_LUXR helix_turn 49.5 51 0.0011 21.3 4.8 35 11-53 8-42 (58)
71 PRK06474 hypothetical protein; 49.4 36 0.00077 29.4 5.0 46 7-57 9-58 (178)
72 PF03965 Penicillinase_R: Peni 49.4 36 0.00077 26.8 4.7 61 12-74 6-74 (115)
73 PRK11302 DNA-binding transcrip 48.0 33 0.00071 30.8 4.8 46 8-59 15-64 (284)
74 COG1321 TroR Mn-dependent tran 46.5 48 0.001 28.1 5.3 52 14-71 15-69 (154)
75 PF08280 HTH_Mga: M protein tr 45.3 33 0.00072 24.1 3.5 36 13-54 9-44 (59)
76 PF10045 DUF2280: Uncharacteri 45.2 32 0.00069 27.8 3.7 42 5-48 3-44 (104)
77 cd00090 HTH_ARSR Arsenical Res 43.9 66 0.0014 21.6 4.9 37 9-52 7-43 (78)
78 PF03672 UPF0154: Uncharacteri 43.1 74 0.0016 23.5 5.1 43 9-52 17-59 (64)
79 smart00346 HTH_ICLR helix_turn 42.9 53 0.0011 24.1 4.5 40 13-58 9-52 (91)
80 cd00131 PAX Paired Box domain 42.5 86 0.0019 25.6 6.0 82 7-111 19-106 (128)
81 PF14420 Clr5: Clr5 domain 39.7 1.1E+02 0.0024 21.2 5.4 37 20-56 17-53 (54)
82 smart00418 HTH_ARSR helix_turn 39.3 63 0.0014 21.2 4.1 31 15-52 3-33 (66)
83 PF09339 HTH_IclR: IclR helix- 39.2 44 0.00096 22.5 3.3 33 14-52 8-41 (52)
84 TIGR02702 SufR_cyano iron-sulf 39.1 60 0.0013 28.2 4.9 44 10-59 2-48 (203)
85 PF01022 HTH_5: Bacterial regu 38.7 77 0.0017 21.0 4.4 36 10-52 3-38 (47)
86 PF05043 Mga: Mga helix-turn-h 38.0 55 0.0012 24.2 3.9 38 10-53 17-54 (87)
87 TIGR01764 excise DNA binding d 37.9 72 0.0016 20.2 4.1 30 24-59 2-31 (49)
88 PF13518 HTH_28: Helix-turn-he 37.8 84 0.0018 20.5 4.5 34 11-52 2-35 (52)
89 COG3355 Predicted transcriptio 37.6 71 0.0015 26.6 4.8 44 10-59 29-75 (126)
90 PRK00430 fis global DNA-bindin 36.7 71 0.0015 25.0 4.5 16 40-55 79-94 (95)
91 PF00626 Gelsolin: Gelsolin re 36.2 27 0.0006 24.7 1.9 23 144-179 16-38 (76)
92 PF12990 DUF3874: Domain of un 35.8 37 0.00079 25.6 2.6 41 22-62 24-67 (73)
93 COG1737 RpiR Transcriptional r 35.5 58 0.0013 29.8 4.4 50 8-59 17-66 (281)
94 smart00347 HTH_MARR helix_turn 35.4 97 0.0021 22.4 4.9 44 8-57 9-55 (101)
95 TIGR02698 CopY_TcrY copper tra 35.1 1.2E+02 0.0025 24.8 5.7 59 14-74 9-75 (130)
96 PRK04217 hypothetical protein; 35.1 83 0.0018 25.4 4.7 37 10-53 46-82 (110)
97 cd03488 Topoisomer_IB_N_htopoI 34.5 1.3E+02 0.0027 27.4 6.2 74 148-237 125-214 (215)
98 PRK10014 DNA-binding transcrip 34.0 68 0.0015 28.9 4.6 27 22-54 5-31 (342)
99 cd03489 Topoisomer_IB_N_Ldtopo 33.9 1.3E+02 0.0028 27.2 6.2 74 148-237 122-211 (212)
100 PF04545 Sigma70_r4: Sigma-70, 33.7 1.2E+02 0.0025 20.1 4.6 26 21-52 18-43 (50)
101 cd06170 LuxR_C_like C-terminal 33.3 1.3E+02 0.0028 19.4 4.9 33 13-53 7-39 (57)
102 PF09862 DUF2089: Protein of u 33.3 89 0.0019 25.5 4.6 37 9-52 36-72 (113)
103 cd00660 Topoisomer_IB_N Topois 33.1 1.4E+02 0.003 27.1 6.2 74 148-237 125-214 (215)
104 PF00292 PAX: 'Paired box' dom 32.5 99 0.0021 25.7 4.8 44 7-50 77-124 (125)
105 PRK01905 DNA-binding protein F 32.3 98 0.0021 22.9 4.5 16 40-55 61-76 (77)
106 PRK11557 putative DNA-binding 32.1 46 0.001 29.9 3.1 49 8-62 11-63 (278)
107 PF11972 HTH_13: HTH DNA bindi 31.7 1.1E+02 0.0024 21.9 4.4 37 13-55 3-39 (54)
108 PF13309 HTH_22: HTH domain 31.4 63 0.0014 23.2 3.2 43 7-51 22-64 (64)
109 TIGR03879 near_KaiC_dom probab 31.4 1E+02 0.0023 23.2 4.4 36 12-53 21-56 (73)
110 PRK00523 hypothetical protein; 30.9 1.4E+02 0.0031 22.6 5.0 43 10-53 26-68 (72)
111 COG3682 Predicted transcriptio 30.8 1.9E+02 0.0041 24.0 6.2 60 12-73 9-76 (123)
112 COG2345 Predicted transcriptio 30.6 1.1E+02 0.0023 27.8 5.1 43 4-52 6-48 (218)
113 PRK12297 obgE GTPase CgtA; Rev 30.0 97 0.0021 30.6 5.2 63 139-218 35-98 (424)
114 PHA00738 putative HTH transcri 29.7 1.2E+02 0.0026 24.7 4.8 46 7-58 10-58 (108)
115 COG3413 Predicted DNA binding 29.7 93 0.002 27.2 4.6 41 7-53 157-202 (215)
116 COG3415 Transposase and inacti 29.6 2.2E+02 0.0047 24.0 6.5 59 11-76 10-74 (138)
117 PF13730 HTH_36: Helix-turn-he 29.5 78 0.0017 21.2 3.3 26 22-53 24-49 (55)
118 PRK10141 DNA-binding transcrip 29.3 1.3E+02 0.0028 24.5 5.0 45 7-57 14-61 (117)
119 PRK15482 transcriptional regul 29.0 60 0.0013 29.4 3.4 47 8-60 15-65 (285)
120 PF13463 HTH_27: Winged helix 28.7 1.1E+02 0.0025 20.9 4.1 40 11-56 5-48 (68)
121 smart00155 PLDc Phospholipase 28.5 65 0.0014 19.1 2.4 19 147-165 8-26 (28)
122 TIGR02944 suf_reg_Xantho FeS a 28.4 1.1E+02 0.0024 24.3 4.5 50 1-56 2-55 (130)
123 PRK12298 obgE GTPase CgtA; Rev 28.3 1.1E+02 0.0023 29.8 5.1 63 139-218 36-99 (390)
124 TIGR02729 Obg_CgtA Obg family 27.7 1.2E+02 0.0026 28.7 5.2 63 140-219 35-98 (329)
125 PRK05472 redox-sensing transcr 27.6 85 0.0019 27.4 4.0 42 11-58 18-61 (213)
126 TIGR01884 cas_HTH CRISPR locus 27.6 1.4E+02 0.003 25.8 5.3 45 9-59 143-190 (203)
127 PF04703 FaeA: FaeA-like prote 27.3 1E+02 0.0022 22.4 3.7 34 14-53 5-39 (62)
128 cd00569 HTH_Hin_like Helix-tur 27.0 1.2E+02 0.0026 16.7 4.3 30 12-49 12-41 (42)
129 PF04552 Sigma54_DBD: Sigma-54 27.0 89 0.0019 26.8 3.9 47 12-59 107-156 (160)
130 PF12561 TagA: ToxR activated 26.5 1.4E+02 0.0031 25.2 4.8 62 149-226 34-101 (135)
131 PRK10703 DNA-binding transcrip 26.5 95 0.002 28.0 4.2 24 24-53 2-25 (341)
132 PF02650 HTH_WhiA: WhiA C-term 26.3 1.1E+02 0.0024 23.5 3.9 37 12-52 43-79 (85)
133 PRK12299 obgE GTPase CgtA; Rev 26.2 1.2E+02 0.0027 28.6 5.1 64 139-219 35-99 (335)
134 PRK11337 DNA-binding transcrip 25.4 71 0.0015 28.9 3.2 46 9-60 28-77 (292)
135 PRK12296 obgE GTPase CgtA; Rev 25.3 1.3E+02 0.0027 30.6 5.1 63 139-218 37-100 (500)
136 PRK01844 hypothetical protein; 25.1 2.1E+02 0.0046 21.7 5.1 43 10-53 25-67 (72)
137 PF10668 Phage_terminase: Phag 25.1 1.7E+02 0.0037 21.2 4.5 29 18-52 17-45 (60)
138 COG3711 BglG Transcriptional a 25.0 1.2E+02 0.0026 29.5 4.9 39 9-53 5-43 (491)
139 PF01047 MarR: MarR family; I 25.0 1.2E+02 0.0027 20.3 3.7 40 13-58 7-49 (59)
140 PF13358 DDE_3: DDE superfamil 24.4 42 0.00092 25.9 1.3 22 106-127 1-26 (146)
141 PF08281 Sigma70_r4_2: Sigma-7 24.3 1.5E+02 0.0033 19.6 4.0 36 11-53 15-50 (54)
142 COG1693 Repressor of nif and g 24.3 1.7E+02 0.0036 28.1 5.3 55 14-69 11-69 (325)
143 PF01325 Fe_dep_repress: Iron 24.2 1.7E+02 0.0036 20.7 4.3 39 14-58 13-54 (60)
144 cd00092 HTH_CRP helix_turn_hel 24.2 2.3E+02 0.0051 19.1 5.0 31 21-57 23-56 (67)
145 TIGR01610 phage_O_Nterm phage 23.8 1.7E+02 0.0036 22.5 4.5 42 6-53 23-71 (95)
146 cd03490 Topoisomer_IB_N_1 Topo 23.7 2.7E+02 0.0058 25.4 6.3 74 148-237 124-216 (217)
147 cd04762 HTH_MerR-trunc Helix-T 23.6 1.4E+02 0.003 18.6 3.5 27 25-57 2-28 (49)
148 smart00262 GEL Gelsolin homolo 23.5 80 0.0017 23.3 2.6 27 142-181 22-48 (90)
149 PRK14987 gluconate operon tran 23.4 1.2E+02 0.0026 27.3 4.3 27 22-54 4-30 (331)
150 PRK10509 bacterioferritin-asso 23.4 1.6E+02 0.0035 21.3 4.1 45 9-53 9-53 (64)
151 PRK03902 manganese transport t 23.3 1.4E+02 0.0031 24.2 4.3 53 13-71 12-67 (142)
152 PRK00118 putative DNA-binding 22.7 1.9E+02 0.0041 23.1 4.7 38 9-53 20-57 (104)
153 TIGR02787 codY_Gpos GTP-sensin 22.2 1.4E+02 0.0029 27.8 4.3 43 11-59 185-231 (251)
154 PRK09863 putative frv operon r 22.1 1.2E+02 0.0027 30.5 4.5 34 13-53 8-41 (584)
155 PF04218 CENP-B_N: CENP-B N-te 22.1 1.1E+02 0.0025 21.0 3.0 38 7-52 8-45 (53)
156 TIGR02395 rpoN_sigma RNA polym 21.8 1.9E+02 0.0042 28.5 5.6 37 24-61 392-428 (429)
157 cd08685 C2_RGS-like C2 domain 21.5 2.8E+02 0.006 21.8 5.5 87 147-240 15-105 (119)
158 smart00345 HTH_GNTR helix_turn 21.4 1.1E+02 0.0023 20.2 2.7 22 25-52 22-43 (60)
159 PF07508 Recombinase: Recombin 21.3 2.2E+02 0.0048 21.1 4.8 54 10-65 6-64 (102)
160 PHA02701 ORF020 dsRNA-binding 21.1 1.7E+02 0.0036 26.0 4.5 36 11-52 6-42 (183)
161 PRK10727 DNA-binding transcrip 20.7 1.6E+02 0.0034 26.8 4.4 25 24-54 2-26 (343)
162 smart00354 HTH_LACI helix_turn 20.7 2.4E+02 0.0052 20.1 4.6 22 25-52 2-23 (70)
163 TIGR00738 rrf2_super rrf2 fami 20.4 1.7E+02 0.0037 23.1 4.1 50 1-56 1-55 (132)
No 1
>smart00686 DM13 Domain present in fly proteins (CG14681, CG12492, CG6217), worm H06A10.1 and Arabidopsis thaliana MBG8.9.
Probab=100.00 E-value=3.3e-41 Score=270.35 Aligned_cols=106 Identities=56% Similarity=1.021 Sum_probs=102.3
Q ss_pred cccccccccEEEEeCceEEecCeeccCCCCceEEEecCCCCCCCC-CceecCCCCCCCcCccccCceEEEEcCCCceeec
Q psy16970 139 GVHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQ-GIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFE 217 (257)
Q Consensus 139 ~~H~v~sg~V~ivD~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~-G~~vpde~g~~~~L~~Y~~~~i~l~LP~~~ti~d 217 (257)
.+||++|++|+|+|+|||+|.+|+|||+|||||||+|.++.|+.. |+++|||.|.+++|++|+||+|+|+||+++||+|
T Consensus 2 ~~h~v~g~~V~i~d~~Tl~I~~FsydG~~pD~yF~~g~~~~p~~~~G~~v~de~g~~~~l~~y~~e~ivl~LP~~~ti~d 81 (108)
T smart00686 2 LQHGVSSDPVEIVDAKTLRIPNFSYDGSGPDAYFWVGAGSRPDNEGGKKVPDEYGYCNPLRRYHNEDIVLRLPESLTIDD 81 (108)
T ss_pred CcccccceeEEEEeCCEEEEcceeccCCCCcEEEEeccCCCCCCcCCeEcCCccCCcccccceeCCEEEEECCCCCeEec
Confidence 479998777999999999999999999999999999999999986 9999999998888999999999999999999999
Q ss_pred cCeEEEeccccccCeeeEEcCCCCCCC
Q psy16970 218 IGHFGVWCEAFTVDFGHIQIPANVNMP 244 (257)
Q Consensus 218 i~w~SVwc~~~~~nFG~V~ip~~~~~P 244 (257)
|+||||||.++++|||||.||+++++|
T Consensus 82 i~w~SV~~~~~~~nFG~V~ip~~~~~p 108 (108)
T smart00686 82 IKWFSVWCLKTAHNFGHVLFPENLNIP 108 (108)
T ss_pred CCEEEEEccccCCcceeEEccCCCCCC
Confidence 999999999999999999999999998
No 2
>KOG4731|consensus
Probab=99.96 E-value=3.5e-29 Score=238.98 Aligned_cols=159 Identities=37% Similarity=0.590 Sum_probs=143.2
Q ss_pred ccCChhhhccccccCCCccccceeEeCCCCCCCCCcccccccc-ccccccccEEEEeCceEEecCeeccCCCC-ceEEEe
Q psy16970 97 MHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAG-VHGVSSDPIVIVDAQTLLVPNFSYDGEAP-DAKFWV 174 (257)
Q Consensus 97 ~~w~~~~w~~vvwsdEsk~~fGsVwrp~ge~~Pkpq~Ig~l~~-~H~v~sg~V~ivD~~Tl~i~~FsydG~gP-d~yfw~ 174 (257)
+.|+..+|. .||+.++..+||+|..|.+.+.|+.+..++++. .||++|++++|+|++||+|.+|+|+|+++ +-||.+
T Consensus 117 ~t~de~kw~-sv~~l~ta~nfg~Vv~pee~d~P~~es~~~~s~~~~~v~SdnieviDarTlki~~Fsy~g~~~~~~y~~A 195 (512)
T KOG4731|consen 117 KTIDEIKWF-SVWDLPTASNFGDVVIPEESDTPKAESPPSFSNGVYGVSSDNIEVIDARTLKIPCFSYDGKYRPRWYFNA 195 (512)
T ss_pred ceeeheeeE-EEEEccCCCcccceeccCCCCCccccCCcccccCccccccCCeeEeccceeeeccccccCccCCceEEec
Confidence 557777774 789999999999988999999999999999964 89999999999999999999999999755 555555
Q ss_pred cCCCCCCCCCce------ecCCCCCCCcCccccCceEEEEcCCCceeeccCeEEEeccccccCeeeEEcCCCCCCCCccc
Q psy16970 175 GTGPHPSPQGIR------VPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPANVNMPPSLK 248 (257)
Q Consensus 175 g~~~~p~~~G~~------vpde~g~~~~L~~Y~~~~i~l~LP~~~ti~di~w~SVwc~~~~~nFG~V~ip~~~~~P~~~~ 248 (257)
|.|+.|+.+|-+ .+++.|+..+|+.|+++||+|+||++.||+||.||||||..+.+|||||.+|.++++|++.+
T Consensus 196 G~G~~~s~~s~kk~ai~~~~~~~~~~~sl~~~n~k~Ivl~Lped~tIfDI~wIsV~c~ky~~dfGhv~v~~d~n~e~~~~ 275 (512)
T KOG4731|consen 196 GRGDIPSSASGKKLAIMAFDDEKGYETSLRMYNAKDIVLELPEDGTIFDIDWISVYCVKYVVDFGHVLVPPDLNVEPSPP 275 (512)
T ss_pred cccCcccccccceeeeecccccccCCchhHhhccceEEEECCCCCcEEeeceEEEEEEEEeeccceeecCCccccCcCCC
Confidence 999999987665 68999999999999999999999999999999999999999999999999999999999988
Q ss_pred cCCCCCCC
Q psy16970 249 MLGVSPQY 256 (257)
Q Consensus 249 ~~~~~~~~ 256 (257)
.++.-+++
T Consensus 276 ~v~si~~s 283 (512)
T KOG4731|consen 276 YVPSINNS 283 (512)
T ss_pred ccCccccc
Confidence 88655543
No 3
>PF10517 DM13: Electron transfer DM13; InterPro: IPR019545 This domain of unknown function is present in proteins of Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana. In some proteins it is found in either one or two copies, N-terminal to the DOMON domain. Proteins with the DM13 and DOMON domains include Skeletor, which is part of a macromolecular complex that forms the spindle matrix []. The DM13 domain is also a component of a novel electron-transfer system potentially involved in oxidative modification of animal cell-surface proteins []. It contains a nearly absolutely conserved cysteine, which could be involved in a redox reaction, either as a naked thiol group or through binding a prosthetic group like heme [].
Probab=99.94 E-value=2.6e-27 Score=188.76 Aligned_cols=99 Identities=42% Similarity=0.899 Sum_probs=91.1
Q ss_pred cccccccccccEEEEeCceEEecCeeccCC-CCceEEEecCCCCCCCCCceec-CCCCCCCcCccccCceEEEEcCCCce
Q psy16970 137 LAGVHGVSSDPIVIVDAQTLLVPNFSYDGE-APDAKFWVGTGPHPSPQGIRVP-DENGKEEPLRRYNRKTIVLTLPGELT 214 (257)
Q Consensus 137 l~~~H~v~sg~V~ivD~~Tl~i~~FsydG~-gPd~yfw~g~~~~p~~~G~~vp-de~g~~~~L~~Y~~~~i~l~LP~~~t 214 (257)
++..|++ +|+|+|+|+||+.+.+|+|+|. |||+|||++++..|+..|++++ ++.+...+|+.| +++++++||++++
T Consensus 7 ~~~~h~v-sG~v~i~d~~t~~i~~f~f~~~~gPD~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~LP~~~~ 84 (108)
T PF10517_consen 7 LSGGHGV-SGTVTIVDGKTFLIFNFNFDGSQGPDLYFWLGKGPSPTPDGFIIPSDEYVSLGPLKSY-NGDQTYTLPAGVD 84 (108)
T ss_pred cCCCcee-eEEEEEeCCCeEEEecccccCCCCCCEEEEEECCCCCCCcccccccccceeeeccccc-CCCEEEECCCCCC
Confidence 3446888 5899999999999999999995 8999999999988888888877 677788999999 8999999999999
Q ss_pred eeccCeEEEeccccccCeeeEEc
Q psy16970 215 VFEIGHFGVWCEAFTVDFGHIQI 237 (257)
Q Consensus 215 i~di~w~SVwc~~~~~nFG~V~i 237 (257)
++||+||||||++|+++||||.|
T Consensus 85 ~~d~~~v~IwC~~f~~~FG~a~l 107 (108)
T PF10517_consen 85 LDDYKWVSIWCEKFSVNFGHAPL 107 (108)
T ss_pred HHHCCEEEEEehhcCceeeEEEe
Confidence 99999999999999999999987
No 4
>KOG4731|consensus
Probab=99.94 E-value=1.1e-26 Score=221.88 Aligned_cols=117 Identities=34% Similarity=0.612 Sum_probs=108.2
Q ss_pred CCCcccccccc-ccccccccEEEEeCceEEecCeeccCCCCceEEEecCCCCCCCCC-ceecCCCCCCCcC-ccccCceE
Q psy16970 129 PRPQKIGQLAG-VHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQG-IRVPDENGKEEPL-RRYNRKTI 205 (257)
Q Consensus 129 Pkpq~Ig~l~~-~H~v~sg~V~ivD~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~G-~~vpde~g~~~~L-~~Y~~~~i 205 (257)
..-.++|+|+. +|+++ |.|++||+|||+|.+|+|+|.+||+|||+|.+.+|+..| +..++|+|++..| ++|+|+++
T Consensus 31 y~G~~lGels~lehqVs-G~Vf~Vns~t~qI~nF~~~~~~~d~~fw~~~sn~psn~gi~~~~~e~G~t~~l~~~~~N~~~ 109 (512)
T KOG4731|consen 31 YYGVYLGELSSLEHQVS-GDVFAVNSTTFQIVNFNYDGGPPDVFFWGGMSNRPSNEGIRHNDDEYGSTQSLNRTYKNKDF 109 (512)
T ss_pred ccceeeeeccccccccc-eeEEEEeeeEEEEEEeccCCCCCceEEEeccCCCCCCccccccccccccccccceecccccE
Confidence 34567888976 78885 899999999999999999999999999999999999999 6678999999987 78999999
Q ss_pred EEEcCCCceeeccCeEEEeccccccCeeeEEcCCCCCCCCc
Q psy16970 206 VLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPANVNMPPS 246 (257)
Q Consensus 206 ~l~LP~~~ti~di~w~SVwc~~~~~nFG~V~ip~~~~~P~~ 246 (257)
+|+||+++||++|+|+||||..++.|||||.||.+++.|.+
T Consensus 110 ~v~lp~~~t~de~kw~sv~~l~ta~nfg~Vv~pee~d~P~~ 150 (512)
T KOG4731|consen 110 TVRLPENKTIDEIKWFSVWDLPTASNFGDVVIPEESDTPKA 150 (512)
T ss_pred EEEcCCCceeeheeeEEEEEccCCCcccceeccCCCCCccc
Confidence 99999999999999999999999999999999999999944
No 5
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=99.62 E-value=2.2e-16 Score=116.41 Aligned_cols=72 Identities=33% Similarity=0.451 Sum_probs=42.5
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccccCCCcchHHHHhhhhhhhccccccccchh
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPELSIRNQRARSRKVENVVLKPVLGQI 90 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~~~p~l~~~~~~~r~~~~~~~~~~~~~~~~ 90 (257)
+|+|++.+.+||+.|+.+|+.+|++. |..||..||+|.|++.|++++...++|+||+.|+++|++
T Consensus 1 ~r~I~~~v~~~p~~s~~~i~~~l~~~-~~~vS~~TI~r~L~~~g~~~~~~~~kP~Ls~~~~~~Rl~-------------- 65 (72)
T PF01498_consen 1 DRRIVRMVRRNPRISAREIAQELQEA-GISVSKSTIRRRLREAGLKKRKARKKPFLSPKHKKKRLE-------------- 65 (72)
T ss_dssp ---------------HHHHHHHT----T--S-HHHHHHHHHHT-EEEETTEEEES--HHHHHHHHH--------------
T ss_pred CcHHHHHHHHCCCCCHHHHHHHHHHc-cCCcCHHHHHHHHHHcCccccccccCCCCCHHHHHHHHH--------------
Confidence 58899999999999999999999998 899999999999999999999999999999999999999
Q ss_pred hhhhhccc
Q psy16970 91 YIYIYHMH 98 (257)
Q Consensus 91 ~~a~~h~~ 98 (257)
||++|+|
T Consensus 66 -fA~~h~~ 72 (72)
T PF01498_consen 66 -FAKEHLD 72 (72)
T ss_dssp -HH-----
T ss_pred -HhhhccC
Confidence 9999985
No 6
>PF13592 HTH_33: Winged helix-turn helix
Probab=96.25 E-value=0.0083 Score=42.94 Aligned_cols=43 Identities=12% Similarity=0.007 Sum_probs=39.2
Q ss_pred CcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccccC
Q psy16970 21 NCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRA 63 (257)
Q Consensus 21 ~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~~~ 63 (257)
+.+-|+.+|+..+....|+.+|.++|++.|++.|+..++++..
T Consensus 2 ~~~wt~~~i~~~I~~~fgv~ys~~~v~~lL~r~G~s~~kp~~~ 44 (60)
T PF13592_consen 2 GGRWTLKEIAAYIEEEFGVKYSPSGVYRLLKRLGFSYQKPRPR 44 (60)
T ss_pred CCcccHHHHHHHHHHHHCCEEcHHHHHHHHHHcCCccccCCCC
Confidence 4567899999999999999999999999999999999888765
No 7
>PF13551 HTH_29: Winged helix-turn helix
Probab=94.96 E-value=0.062 Score=41.35 Aligned_cols=48 Identities=15% Similarity=0.104 Sum_probs=39.7
Q ss_pred CchhhHHHHHHHhhCc-----ccCHHHHHHHH-HhccCccccHHHHHHHHHhcC
Q psy16970 7 ASMNDRFIVSQVLRNC-----FATALEVRQEL-QDVRKVHLNEGTVRIRLNENN 54 (257)
Q Consensus 7 ~~~~~r~i~r~v~~~~-----~~ta~~i~~~l-~~~~g~~~s~~Tvrr~L~~~~ 54 (257)
++.+...|+..+.++| ..|..+|+..| ....|+.+|.+||+|.|++.|
T Consensus 59 ~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~G 112 (112)
T PF13551_consen 59 SEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILKRAG 112 (112)
T ss_pred CHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHHHCc
Confidence 3445567777777777 57899999987 888889999999999999986
No 8
>cd00131 PAX Paired Box domain
Probab=94.60 E-value=0.077 Score=43.65 Aligned_cols=45 Identities=16% Similarity=-0.054 Sum_probs=36.9
Q ss_pred chhhHHHHHHHhhCcccCHHHHHHHHHhccC----ccccHHHHHHHHHh
Q psy16970 8 SMNDRFIVSQVLRNCFATALEVRQELQDVRK----VHLNEGTVRIRLNE 52 (257)
Q Consensus 8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g----~~~s~~Tvrr~L~~ 52 (257)
....+.|+..+.++|.+|+.|++++|.+.+. +.+|.+||.|.|+.
T Consensus 78 ~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 78 PEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 3456778888999999999999999876531 36799999999875
No 9
>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=94.36 E-value=0.1 Score=35.02 Aligned_cols=38 Identities=32% Similarity=0.337 Sum_probs=31.4
Q ss_pred hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
..|+.|++...+|+..+..+|.+++ .+|+.||++|+++
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l------glS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL------GLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH------TS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH------CcCHHHHHHHHHH
Confidence 4689999999999999999999987 5899999999875
No 10
>PF13565 HTH_32: Homeodomain-like domain
Probab=94.27 E-value=0.08 Score=38.67 Aligned_cols=43 Identities=16% Similarity=0.097 Sum_probs=37.3
Q ss_pred chhhHHHHHHHhhCcccCHHHHHHHHHhccCccc--cHHHHHHHH
Q psy16970 8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHL--NEGTVRIRL 50 (257)
Q Consensus 8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~--s~~Tvrr~L 50 (257)
+.....|+..+..+|.-|..+|+..|....|+.+ |.+||+|.|
T Consensus 33 ~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L 77 (77)
T PF13565_consen 33 PEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL 77 (77)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence 4445788888899999999999999999888766 999999976
No 11
>PF13276 HTH_21: HTH-like domain
Probab=93.97 E-value=0.17 Score=35.76 Aligned_cols=50 Identities=18% Similarity=0.141 Sum_probs=40.9
Q ss_pred HHHHHHHhhC-cccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccc
Q psy16970 12 RFIVSQVLRN-CFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLH 61 (257)
Q Consensus 12 r~i~r~v~~~-~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~ 61 (257)
..|......+ +..-+..|..+|+..+|..+|..||+|.+++.||.++..+
T Consensus 8 ~~I~~i~~~~~~~yG~rri~~~L~~~~~~~v~~krV~RlM~~~gL~~~~rr 58 (60)
T PF13276_consen 8 ELIKEIFKESKPTYGYRRIWAELRREGGIRVSRKRVRRLMREMGLRSKRRR 58 (60)
T ss_pred HHHHHHHHHcCCCeehhHHHHHHhccCcccccHHHHHHHHHHcCCcccCCC
Confidence 3455555555 7788899999999998899999999999999999986544
No 12
>smart00351 PAX Paired Box domain.
Probab=91.68 E-value=0.29 Score=39.89 Aligned_cols=43 Identities=19% Similarity=0.018 Sum_probs=35.8
Q ss_pred chhhHHHHHHHhhCcccCHHHHHHHHHhccCccc-----cHHHHHHHHH
Q psy16970 8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHL-----NEGTVRIRLN 51 (257)
Q Consensus 8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~-----s~~Tvrr~L~ 51 (257)
.....+|+..+.++|..|+.||+++|.+. |+.+ |.+||.+.|.
T Consensus 78 ~~~~~~I~~~~~~~p~~t~~el~~~L~~~-gv~~~~~~Ps~sti~~~l~ 125 (125)
T smart00351 78 PKVVKKIADYKQENPGIFAWEIRDRLLSE-GVCDKDNVPSVSSINRILR 125 (125)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHc-CCCcCCCCCChhhHHHhhC
Confidence 45567888889999999999999999864 4666 9999998873
No 13
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=91.65 E-value=0.63 Score=34.07 Aligned_cols=55 Identities=22% Similarity=0.192 Sum_probs=38.4
Q ss_pred HHHHHh-hCcccCHHHHHHHHHhccCccccHHHHHHHHHh---cCCcccccccCCCcchH
Q psy16970 14 IVSQVL-RNCFATALEVRQELQDVRKVHLNEGTVRIRLNE---NNLTAKRLHRAPELSIR 69 (257)
Q Consensus 14 i~r~v~-~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~---~~l~~~~~~~~p~l~~~ 69 (257)
|.+.+. .+--+++.+|.+.|+.. |..+|+.||||+|+. .|+..++...--.||.+
T Consensus 3 IL~~L~~~~~P~g~~~l~~~L~~~-g~~~se~avRrrLr~me~~Glt~~~g~~G~~iT~~ 61 (66)
T PF08461_consen 3 ILRILAESDKPLGRKQLAEELKLR-GEELSEEAVRRRLRAMERDGLTRKVGRQGRIITEK 61 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhc-ChhhhHHHHHHHHHHHHHCCCccccCCcccccCHH
Confidence 444443 34459999999999988 699999999999985 55555444444445543
No 14
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=91.51 E-value=0.42 Score=40.28 Aligned_cols=42 Identities=19% Similarity=0.163 Sum_probs=37.0
Q ss_pred HHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCc
Q psy16970 14 IVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLT 56 (257)
Q Consensus 14 i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~ 56 (257)
|...+..++..|+.||.+.|+..+ ..+|..||+|-|++.|+-
T Consensus 7 i~~Li~~~~i~tqeeL~~~L~~~G-~~vsqaTIsRdL~elglv 48 (146)
T TIGR01529 7 IKEIITEEKISTQEELVALLKAEG-IEVTQATVSRDLRELGAV 48 (146)
T ss_pred HHHHHHcCCCCCHHHHHHHHHHhC-CCcCHHHHHHHHHHcCCE
Confidence 555668889999999999998764 999999999999999985
No 15
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=91.34 E-value=0.57 Score=31.35 Aligned_cols=38 Identities=24% Similarity=0.225 Sum_probs=31.2
Q ss_pred hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
..++.|+..+..+|..|..||++.+ .+|.+||++.|++
T Consensus 3 ~~~~~Il~~l~~~~~~t~~ela~~~------~is~~tv~~~l~~ 40 (48)
T PF13412_consen 3 ETQRKILNYLRENPRITQKELAEKL------GISRSTVNRYLKK 40 (48)
T ss_dssp HHHHHHHHHHHHCTTS-HHHHHHHH------TS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHh------CCCHHHHHHHHHH
Confidence 3578899999999999999999987 4799999988875
No 16
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=90.75 E-value=0.48 Score=39.62 Aligned_cols=39 Identities=21% Similarity=0.377 Sum_probs=34.9
Q ss_pred chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
...|+.|+.+..+|+..|..+|+++| .+|+.||++|+++
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l------glS~~tV~~Ri~r 46 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF------GVSPGTIHVRVEK 46 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHH
Confidence 35799999999999999999999998 5899999988765
No 17
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=90.48 E-value=0.55 Score=37.86 Aligned_cols=46 Identities=22% Similarity=0.153 Sum_probs=39.0
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccc
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLH 61 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~ 61 (257)
+...|...|..+|.+|..|++..| .||.+||.+.|++.|+..++..
T Consensus 58 d~~~L~~~v~~~pd~tl~Ela~~l------~Vs~~ti~~~Lkrlg~t~KK~~ 103 (119)
T PF01710_consen 58 DRDELKALVEENPDATLRELAERL------GVSPSTIWRALKRLGITRKKKT 103 (119)
T ss_pred cHHHHHHHHHHCCCcCHHHHHHHc------CCCHHHHHHHHHHcCchhccCc
Confidence 455688888999999999999876 3799999999999999976554
No 18
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=90.17 E-value=0.5 Score=40.00 Aligned_cols=40 Identities=15% Similarity=0.194 Sum_probs=35.0
Q ss_pred chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
...|+.|+++..+|+..|..||.+++ .+|+.||++|+++.
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l------glS~~tv~~Ri~rL 52 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV------GLSPTPCLERVRRL 52 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH------CcCHHHHHHHHHHH
Confidence 34699999999999999999999987 58999999887753
No 19
>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=89.14 E-value=0.93 Score=33.88 Aligned_cols=46 Identities=13% Similarity=0.198 Sum_probs=33.6
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA 57 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~ 57 (257)
...|...+..++..|=.||...|... |+.++..||.|-|++.|+..
T Consensus 7 ~~~I~~li~~~~i~sQ~eL~~~L~~~-Gi~vTQaTiSRDLkeL~~vK 52 (70)
T PF01316_consen 7 QELIKELISEHEISSQEELVELLEEE-GIEVTQATISRDLKELGAVK 52 (70)
T ss_dssp HHHHHHHHHHS---SHHHHHHHHHHT-T-T--HHHHHHHHHHHT-EE
T ss_pred HHHHHHHHHHCCcCCHHHHHHHHHHc-CCCcchhHHHHHHHHcCcEE
Confidence 34567777889999999999999997 59999999999999999764
No 20
>PRK00441 argR arginine repressor; Provisional
Probab=87.64 E-value=1.2 Score=37.65 Aligned_cols=46 Identities=20% Similarity=0.230 Sum_probs=40.8
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA 57 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~ 57 (257)
...|.+.+.++...|-.|+.+.|+..| ..+|..||||=|++.++..
T Consensus 6 ~~~I~~ll~~~~~~~q~eL~~~L~~~G-~~vSqaTisRDl~~L~lvK 51 (149)
T PRK00441 6 HAKILEIINSKEIETQEELAEELKKMG-FDVTQATVSRDIKELKLIK 51 (149)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHHhcC-CCcCHHHHHHHHHHcCcEE
Confidence 456778888899999999999999875 9999999999999999774
No 21
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=87.11 E-value=1.6 Score=36.77 Aligned_cols=55 Identities=27% Similarity=0.161 Sum_probs=45.5
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccccCCC
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPE 65 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~~~p~ 65 (257)
...++..+.+...-|..+++..|+...|+.++.+.|++.||+.||..++++..+.
T Consensus 68 q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~~v~~~l~~~GlsykK~~~~~~ 122 (138)
T COG3415 68 QLEILLERLREKDWTLKELVEELGLEFGVWYHASAVRRLLHELGLSYKKPRWTPA 122 (138)
T ss_pred HHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHHHHHHHHHHcCCCcCCCCCCcc
Confidence 3455556656666999999999998889999999999999999999887776653
No 22
>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=86.97 E-value=1.3 Score=30.27 Aligned_cols=35 Identities=26% Similarity=0.222 Sum_probs=25.9
Q ss_pred HHHHHH-hhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 13 FIVSQV-LRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 13 ~i~r~v-~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
.|+... ..+...|+.+++++| .||.+||++-++..
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l------~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEEL------GVSRRTIRRDIKEL 39 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHC------TS-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHh------CCCHHHHHHHHHHH
Confidence 344444 556669999999987 58999999988764
No 23
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=86.86 E-value=1 Score=34.80 Aligned_cols=40 Identities=20% Similarity=0.266 Sum_probs=34.7
Q ss_pred hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcC
Q psy16970 9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENN 54 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~ 54 (257)
..|+.|++.+.+++..|..+|..++ .+|+.||++++++..
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l------~~s~~tv~~~l~~L~ 42 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV------GLSPSTVHNRVKRLE 42 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH------CcCHHHHHHHHHHHH
Confidence 4689999999999999999999987 589999999887643
No 24
>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=86.50 E-value=1.6 Score=34.15 Aligned_cols=46 Identities=24% Similarity=0.229 Sum_probs=35.1
Q ss_pred hhHHHHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCc
Q psy16970 10 NDRFIVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLT 56 (257)
Q Consensus 10 ~~r~i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~ 56 (257)
++..|+..+.. +...||.||.+.|+..+ ..+|..||+|.|. +.|+-
T Consensus 2 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~-~~i~~~TVYR~L~~L~~~Gli 51 (116)
T cd07153 2 QRLAILEVLLESDGHLTAEEIYERLRKKG-PSISLATVYRTLELLEEAGLV 51 (116)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHhcC-CCCCHHHHHHHHHHHHhCCCE
Confidence 45566777755 45699999999998865 7899999999765 45554
No 25
>PRK03341 arginine repressor; Provisional
Probab=86.29 E-value=1.5 Score=37.94 Aligned_cols=46 Identities=20% Similarity=0.226 Sum_probs=40.7
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA 57 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~ 57 (257)
...|.+.+.+++..|-.||...|+..| +.+|..||+|-|++.++..
T Consensus 17 ~~~I~~li~~~~i~tQ~eL~~~L~~~G-i~vTQaTiSRDl~eL~~~K 62 (168)
T PRK03341 17 QARIVAILSRQSVRSQAELAALLADEG-IEVTQATLSRDLDELGAVK 62 (168)
T ss_pred HHHHHHHHHHCCCccHHHHHHHHHHcC-CcccHHHHHHHHHHhcCEe
Confidence 456778888999999999999999875 9999999999999998764
No 26
>PRK05066 arginine repressor; Provisional
Probab=86.25 E-value=1.7 Score=37.20 Aligned_cols=46 Identities=15% Similarity=0.148 Sum_probs=40.8
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCcc-ccHHHHHHHHHhcCCcc
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVH-LNEGTVRIRLNENNLTA 57 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~-~s~~Tvrr~L~~~~l~~ 57 (257)
+..|.+.+..++..|=.||.+.|+..| .. ++..||.|-|++.|+..
T Consensus 11 ~~~I~~iI~~~~I~tQeeL~~~L~~~G-i~~vTQATiSRDikeL~lvK 57 (156)
T PRK05066 11 VKAFKALLKEEKFGSQGEIVTALQEQG-FDNINQSKVSRMLTKFGAVR 57 (156)
T ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHCC-CCeecHHHHHHHHHHcCCEE
Confidence 356778888899999999999999985 88 99999999999999874
No 27
>PHA02517 putative transposase OrfB; Reviewed
Probab=85.75 E-value=1.6 Score=39.32 Aligned_cols=48 Identities=15% Similarity=0.030 Sum_probs=38.7
Q ss_pred HHHHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCccccc
Q psy16970 12 RFIVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRL 60 (257)
Q Consensus 12 r~i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~ 60 (257)
..|++...+ ++...+..|..+|+.. |..+|..||+|.|++.||.+...
T Consensus 33 ~~I~~i~~~~~~~~G~r~I~~~L~~~-g~~vs~~tV~Rim~~~gl~~~~~ 81 (277)
T PHA02517 33 SEILRVYDENHQVYGVRKVWRQLNRE-GIRVARCTVGRLMKELGLAGVLR 81 (277)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHhc-CcccCHHHHHHHHHHcCCceEec
Confidence 445555544 5788999999999876 58999999999999999986543
No 28
>PRK04280 arginine repressor; Provisional
Probab=85.31 E-value=1.9 Score=36.55 Aligned_cols=46 Identities=20% Similarity=0.183 Sum_probs=40.9
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA 57 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~ 57 (257)
...|.+.+..++..|=.||.+.|+..| ..++..||.|-|++.|+-.
T Consensus 6 ~~~I~~iI~~~~I~tQeeL~~~L~~~G-i~vTQATiSRDikeL~lvK 51 (148)
T PRK04280 6 HIKIREIITNNEIETQDELVDRLREEG-FNVTQATVSRDIKELHLVK 51 (148)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHcC-CCeehHHHHHHHHHcCCEE
Confidence 346778888899999999999999985 9999999999999999774
No 29
>COG1438 ArgR Arginine repressor [Transcription]
Probab=84.92 E-value=1.9 Score=36.86 Aligned_cols=47 Identities=21% Similarity=0.217 Sum_probs=41.6
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA 57 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~ 57 (257)
-...|.+.+.++...|=.||...|++.| ..++..||.|-|++.|+..
T Consensus 7 R~~~Ik~iI~~~~i~TQ~Elv~~L~~~G-i~vTQaTvSRDlkelglvK 53 (150)
T COG1438 7 RLELIKEIITEEKISTQEELVELLQEEG-IEVTQATVSRDLKELGLVK 53 (150)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHcC-CeEehHHHHHHHHHcCCEE
Confidence 3467778889999999999999999987 7799999999999999875
No 30
>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=84.30 E-value=2.2 Score=30.01 Aligned_cols=36 Identities=22% Similarity=0.239 Sum_probs=30.9
Q ss_pred HHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 12 RFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 12 r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
..|+..+..+...|..|+.+.+ .+|..||||=|+..
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~------~VS~~TiRRDl~~L 38 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEF------GVSEMTIRRDLNKL 38 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHH------CcCHHHHHHHHHHH
Confidence 4678888999999999999987 58999999988753
No 31
>PF07592 DDE_Tnp_ISAZ013: Rhodopirellula transposase DDE domain; InterPro: IPR011518 These transposases are found in the planctomycete Rhodopirellula baltica, the cyanobacterium Nostoc, and the Gram-positive bacterium Streptomyces. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=83.49 E-value=1.3 Score=41.97 Aligned_cols=44 Identities=16% Similarity=0.095 Sum_probs=36.7
Q ss_pred ccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccccCCCcc
Q psy16970 23 FATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPELS 67 (257)
Q Consensus 23 ~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~~~p~l~ 67 (257)
..|+.+|+++|... |..+|..||++.|++.||.-+..+|.-+.+
T Consensus 24 ~~S~~~la~~L~~~-G~~vS~~tV~~lL~~lGYsLq~n~Kt~~g~ 67 (311)
T PF07592_consen 24 RKSTRKLAEELRRQ-GHPVSARTVARLLNRLGYSLQANRKTKEGK 67 (311)
T ss_pred eccHHHHHHHHHHc-CCCccHHHHHHHHHHcCcchhhhhcccCCC
Confidence 37889999999665 599999999999999999988777654443
No 32
>PRK09462 fur ferric uptake regulator; Provisional
Probab=81.71 E-value=3.2 Score=34.39 Aligned_cols=44 Identities=18% Similarity=0.170 Sum_probs=35.3
Q ss_pred chhhHHHHHHHhhC--cccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 8 SMNDRFIVSQVLRN--CFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 8 ~~~~r~i~r~v~~~--~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
..++..|+..+... ...||.||-+.|+..+ ..+|..||+|.|..
T Consensus 16 T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~-~~i~~aTVYR~L~~ 61 (148)
T PRK09462 16 TLPRLKILEVLQEPDNHHVSAEDLYKRLIDMG-EEIGLATVYRVLNQ 61 (148)
T ss_pred CHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhC-CCCCHHHHHHHHHH
Confidence 35667777777653 4799999999998866 78999999999864
No 33
>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=81.65 E-value=2.5 Score=33.47 Aligned_cols=47 Identities=21% Similarity=0.145 Sum_probs=33.8
Q ss_pred hhhHHHHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCc
Q psy16970 9 MNDRFIVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLT 56 (257)
Q Consensus 9 ~~~r~i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~ 56 (257)
.++..|+..+.. +...||.||.+.|+..+ ..+|..||+|.|. +.|+-
T Consensus 8 ~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~-~~is~~TVYR~L~~L~e~Gli 58 (120)
T PF01475_consen 8 PQRLAILELLKESPEHLTAEEIYDKLRKKG-PRISLATVYRTLDLLEEAGLI 58 (120)
T ss_dssp HHHHHHHHHHHHHSSSEEHHHHHHHHHHTT-TT--HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHhhhcc-CCcCHHHHHHHHHHHHHCCeE
Confidence 355666666644 45899999999999654 8999999999876 45544
No 34
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=78.97 E-value=4.3 Score=33.92 Aligned_cols=44 Identities=18% Similarity=0.139 Sum_probs=34.9
Q ss_pred chhhHHHHHHHhhC-cccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 8 SMNDRFIVSQVLRN-CFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 8 ~~~~r~i~r~v~~~-~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
..++..|+..+.+. ...||.+|-.+|+..+ ..+|..||+|.|+.
T Consensus 20 T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~-p~islaTVYr~L~~ 64 (145)
T COG0735 20 TPQRLAVLELLLEADGHLSAEELYEELREEG-PGISLATVYRTLKL 64 (145)
T ss_pred CHHHHHHHHHHHhcCCCCCHHHHHHHHHHhC-CCCCHhHHHHHHHH
Confidence 34566677777543 4599999999999865 89999999999874
No 35
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=77.23 E-value=4.9 Score=32.71 Aligned_cols=40 Identities=20% Similarity=0.196 Sum_probs=34.7
Q ss_pred chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
...|++|+....+|...+-.+|+++| .+|+.|+++|+.+.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l------glS~~~v~~Ri~~L 46 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV------GLSPSTVLRRIKRL 46 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH------CCCHHHHHHHHHHH
Confidence 46789999999999999999999987 48999999887653
No 36
>PRK09954 putative kinase; Provisional
Probab=75.64 E-value=3.4 Score=38.71 Aligned_cols=53 Identities=15% Similarity=0.139 Sum_probs=39.7
Q ss_pred hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccccCCCcc
Q psy16970 9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPELS 67 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~~~p~l~ 67 (257)
..+..|++.+++|++.|..||.+.|. +|+.||+++|++..-.+....+...|.
T Consensus 3 ~~~~~il~~l~~~~~~s~~~la~~l~------~s~~~v~~~i~~L~~~g~i~~~~~~l~ 55 (362)
T PRK09954 3 NREKEILAILRRNPLIQQNEIADILQ------ISRSRVAAHIMDLMRKGRIKGKGYILT 55 (362)
T ss_pred hHHHHHHHHHHHCCCCCHHHHHHHHC------CCHHHHHHHHHHHHHCCCcCCcEEEEc
Confidence 35677999999999999999999984 899999998885443333344444443
No 37
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=75.58 E-value=4.9 Score=34.38 Aligned_cols=48 Identities=13% Similarity=0.083 Sum_probs=37.3
Q ss_pred chhhHHHHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCc
Q psy16970 8 SMNDRFIVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLT 56 (257)
Q Consensus 8 ~~~~r~i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~ 56 (257)
..++..|+..+.. +...||.||-+.|...+ ..+|..||+|.|. +.|+-
T Consensus 25 T~qR~~IL~~l~~~~~hlSa~eI~~~L~~~~-~~is~aTVYRtL~~L~e~Glv 76 (169)
T PRK11639 25 TPQRLEVLRLMSLQPGAISAYDLLDLLREAE-PQAKPPTVYRALDFLLEQGFV 76 (169)
T ss_pred CHHHHHHHHHHHhcCCCCCHHHHHHHHHhhC-CCCCcchHHHHHHHHHHCCCE
Confidence 4566677777754 34789999999999876 7899999999886 45554
No 38
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=75.50 E-value=6.1 Score=29.29 Aligned_cols=45 Identities=13% Similarity=0.174 Sum_probs=32.7
Q ss_pred hhhHHHHHHHhhCc----ccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccc
Q psy16970 9 MNDRFIVSQVLRNC----FATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKR 59 (257)
Q Consensus 9 ~~~r~i~r~v~~~~----~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~ 59 (257)
..++.|...+..+| ..|..||++.+ .+|..||.|-.++.|+.+..
T Consensus 16 ~~e~~Ia~yil~~~~~~~~~si~elA~~~------~vS~sti~Rf~kkLG~~gf~ 64 (77)
T PF01418_consen 16 PTEKKIADYILENPDEIAFMSISELAEKA------GVSPSTIVRFCKKLGFSGFK 64 (77)
T ss_dssp HHHHHHHHHHHH-HHHHCT--HHHHHHHC------TS-HHHHHHHHHHCTTTCHH
T ss_pred HHHHHHHHHHHhCHHHHHHccHHHHHHHc------CCCHHHHHHHHHHhCCCCHH
Confidence 34577888887775 57888877764 68999999999999999854
No 39
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=75.45 E-value=6.5 Score=35.86 Aligned_cols=48 Identities=17% Similarity=-0.011 Sum_probs=37.7
Q ss_pred HHHHHHhhCcccCHHHHHHHHHhcc---Cc-cccHHHHHHHHHhcCCccccc
Q psy16970 13 FIVSQVLRNCFATALEVRQELQDVR---KV-HLNEGTVRIRLNENNLTAKRL 60 (257)
Q Consensus 13 ~i~r~v~~~~~~ta~~i~~~l~~~~---g~-~~s~~Tvrr~L~~~~l~~~~~ 60 (257)
.|.....+++..-+..|..+|...+ |. .+|+.||.|.+++.||.+++.
T Consensus 16 ~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~v~~krV~rlmr~~gL~~~~r 67 (262)
T PRK14702 16 RIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRLMRQNALLLERK 67 (262)
T ss_pred HHHHHHHhCcccChHHHHHHHHhhhcccCccccCHHHHHHHHHHhCCccccC
Confidence 3444446678888999999998853 45 499999999999999997544
No 40
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=74.70 E-value=7.9 Score=36.03 Aligned_cols=48 Identities=17% Similarity=0.003 Sum_probs=37.6
Q ss_pred HHHHHhhCcccCHHHHHHHHHhcc---Cc-cccHHHHHHHHHhcCCcccccc
Q psy16970 14 IVSQVLRNCFATALEVRQELQDVR---KV-HLNEGTVRIRLNENNLTAKRLH 61 (257)
Q Consensus 14 i~r~v~~~~~~ta~~i~~~l~~~~---g~-~~s~~Tvrr~L~~~~l~~~~~~ 61 (257)
|.......+..-+..|..+|+..+ |. .+|..||+|.+++.||.+++.+
T Consensus 56 I~~i~~~~~~yG~Rri~~~L~~~g~~~g~~~v~~k~V~RlMr~~Gl~~~~~~ 107 (301)
T PRK09409 56 IHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQNALLLERKP 107 (301)
T ss_pred HHHHHHhCccCCHHHHHHHHHhhhcccCccccCHHHHHHHHHHcCCcccccC
Confidence 444435568888999999998763 45 5999999999999999976543
No 41
>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=73.93 E-value=7 Score=28.00 Aligned_cols=36 Identities=6% Similarity=0.045 Sum_probs=27.5
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
|..|++... +...|..++.+.+ .+|.+||++.+...
T Consensus 2 ~~~il~~L~-~~~~~~~eLa~~l------~vS~~tv~~~l~~L 37 (69)
T TIGR00122 2 PLRLLALLA-DNPFSGEKLGEAL------GMSRTAVNKHIQTL 37 (69)
T ss_pred hHHHHHHHH-cCCcCHHHHHHHH------CCCHHHHHHHHHHH
Confidence 567777755 5557899999887 58999999887653
No 42
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=73.74 E-value=8.6 Score=27.96 Aligned_cols=43 Identities=19% Similarity=0.123 Sum_probs=32.8
Q ss_pred hhhHHHHHHHhhCcc--cCHHHHHHHHHhccCccccHHHHHHHHHh---cCCcc
Q psy16970 9 MNDRFIVSQVLRNCF--ATALEVRQELQDVRKVHLNEGTVRIRLNE---NNLTA 57 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~--~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~---~~l~~ 57 (257)
...+.|+..+.+++. .|+.||..+|. ++..+|+|.|.. .|+-.
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lg------l~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLG------LPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHC------CCHHHHHHHHHHHHHCCCEE
Confidence 456778888888766 99999999984 788899988764 55543
No 43
>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=71.71 E-value=7.6 Score=25.91 Aligned_cols=33 Identities=18% Similarity=0.161 Sum_probs=21.9
Q ss_pred HHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 12 RFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 12 r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
..++... .+. .|..+|+.++ .||.+||+|.|++
T Consensus 12 ~~i~~l~-~~G-~si~~IA~~~------gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 12 EEIKELY-AEG-MSIAEIAKQF------GVSRSTVYRYLNK 44 (45)
T ss_dssp HHHHHHH-HTT---HHHHHHHT------TS-HHHHHHHHCC
T ss_pred HHHHHHH-HCC-CCHHHHHHHH------CcCHHHHHHHHhc
Confidence 4444444 444 8889998886 5899999999975
No 44
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=70.69 E-value=10 Score=25.42 Aligned_cols=38 Identities=18% Similarity=0.260 Sum_probs=28.4
Q ss_pred CchhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 7 ASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 7 ~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
|.+....|..++... .|.++|++++ .+|..||+|.+++
T Consensus 13 T~~~~~~i~~~~~~~--~s~~~vA~~~------~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 13 TKRLEQYILKLLRES--RSFKDVAREL------GVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHHHHhhc--CCHHHHHHHH------CCCHHHHHHHHHh
Confidence 345556666666554 7888888886 6899999999875
No 45
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=69.48 E-value=8.3 Score=35.01 Aligned_cols=42 Identities=19% Similarity=0.270 Sum_probs=34.5
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHH---HHHhcCCcc
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRI---RLNENNLTA 57 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr---~L~~~~l~~ 57 (257)
-...|+..+.++...+..||.+.| .||..|||| .|.+.|+-.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l------~vS~~TiRRdL~~Le~~g~l~ 50 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHF------SVSPQTIRRDLNDLAEQNKIL 50 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHh------CCCHHHHHHHHHHHHHCCCEE
Confidence 456788888999999999999987 589999999 556677643
No 46
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=68.19 E-value=9.1 Score=34.62 Aligned_cols=37 Identities=19% Similarity=0.273 Sum_probs=31.8
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
...|+..+.++++.+..|+.+.+ .+|+.||||-|++.
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~~l------~vS~~TirRdL~~L 43 (251)
T PRK13509 7 HQILLELLAQLGFVTVEKVIERL------GISPATARRDINKL 43 (251)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHH------CcCHHHHHHHHHHH
Confidence 45688888999999999999987 48999999998853
No 47
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=67.45 E-value=8.5 Score=34.92 Aligned_cols=37 Identities=16% Similarity=0.108 Sum_probs=31.8
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
-.+.|+..+.++...+..|+.+.| .+|+.||||-|.+
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l------~VS~~TIRRDL~~ 42 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYF------DTTGTTIRKDLVI 42 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHH------CCCHHHHHHHHHH
Confidence 356788888899999999999988 5899999998875
No 48
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=67.30 E-value=9.3 Score=34.69 Aligned_cols=43 Identities=19% Similarity=0.211 Sum_probs=35.2
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHH---HHHhcCCccc
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRI---RLNENNLTAK 58 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr---~L~~~~l~~~ 58 (257)
-++.|+..+.++..++..|+.+.+ .||+.|||| .|.+.|+--|
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~------~VS~~TIRRDL~~Le~~g~l~R 51 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELF------GVSEMTIRRDLNELEEQGLLLR 51 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHh------CCCHHHHHHhHHHHHHCCcEEE
Confidence 356789999999999999999887 599999999 6666775543
No 49
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=67.18 E-value=16 Score=23.65 Aligned_cols=34 Identities=24% Similarity=0.236 Sum_probs=26.8
Q ss_pred HHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 13 FIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 13 ~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
.|+..+.+++..|..++.+.+ .++.+|+++.|..
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l------~~s~~tv~~~l~~ 37 (53)
T smart00420 4 QILELLAQQGKVSVEELAELL------GVSEMTIRRDLNK 37 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHH------CCCHHHHHHHHHH
Confidence 355566667789999999987 4799999988865
No 50
>PF13551 HTH_29: Winged helix-turn helix
Probab=65.68 E-value=27 Score=26.38 Aligned_cols=57 Identities=19% Similarity=0.151 Sum_probs=36.3
Q ss_pred HHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh---cCC---cc--cccccCCC-cchHHHHhhhh
Q psy16970 13 FIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE---NNL---TA--KRLHRAPE-LSIRNQRARSR 76 (257)
Q Consensus 13 ~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~---~~l---~~--~~~~~~p~-l~~~~~~~r~~ 76 (257)
.++..+..+.. |..++++.+ .+|.+||++.++. .|+ .. ++..+.+- |++.++..=.+
T Consensus 3 ~~l~l~~~g~~-~~~~ia~~l------g~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~ 68 (112)
T PF13551_consen 3 QILLLLAEGVS-TIAEIARRL------GISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIE 68 (112)
T ss_pred HHHHHHHcCCC-cHHHHHHHH------CcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHH
Confidence 34555544433 788888876 4899999998886 552 22 12223333 88888876666
No 51
>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=65.16 E-value=17 Score=25.74 Aligned_cols=41 Identities=17% Similarity=0.131 Sum_probs=31.4
Q ss_pred CchhhHHHHHHHhhC-----cccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 7 ASMNDRFIVSQVLRN-----CFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 7 ~~~~~r~i~r~v~~~-----~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
|+++...+..+.... ..+|..||+.+| .||.+|+..+|++.
T Consensus 2 T~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~l------gis~st~~~~LRra 47 (53)
T PF04967_consen 2 TDRQREILKAAYELGYFDVPRRITLEELAEEL------GISKSTVSEHLRRA 47 (53)
T ss_pred CHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHh------CCCHHHHHHHHHHH
Confidence 456666676666554 468899999987 58999999999764
No 52
>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=63.85 E-value=20 Score=24.99 Aligned_cols=43 Identities=26% Similarity=0.246 Sum_probs=32.9
Q ss_pred chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCc
Q psy16970 8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLT 56 (257)
Q Consensus 8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~ 56 (257)
.-.++.|++.+..+.-.|+.||.+++. ++.+|+++.|+ +.|+-
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~------~~~~t~s~hL~~L~~aGli 54 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELG------ISQSTVSYHLKKLEEAGLI 54 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHT------S-HHHHHHHHHHHHHTTSE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHC------CCHHHHHHHHHHHHHCCCe
Confidence 356778888887788899999999984 78899997765 45554
No 53
>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=62.52 E-value=11 Score=26.88 Aligned_cols=45 Identities=31% Similarity=0.354 Sum_probs=33.3
Q ss_pred hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCcccc
Q psy16970 9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLTAKR 59 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~~~~ 59 (257)
.....+...+..+...|+.||...+ .++++||++.|+ +.|+-.+.
T Consensus 8 ~~E~~vy~~Ll~~~~~t~~eIa~~l------~i~~~~v~~~L~~L~~~GlV~~~ 55 (68)
T PF01978_consen 8 ENEAKVYLALLKNGPATAEEIAEEL------GISRSTVYRALKSLEEKGLVERE 55 (68)
T ss_dssp HHHHHHHHHHHHHCHEEHHHHHHHH------TSSHHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCEEEE
Confidence 4455666677788889999999998 478899997766 46655443
No 54
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=61.79 E-value=14 Score=33.22 Aligned_cols=37 Identities=27% Similarity=0.347 Sum_probs=31.7
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
...|+..+.++...+..|+.+.| .+|+.||||-|.+.
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l------~VS~~TiRRdL~~L 42 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQL------NVSKETIRRDLNEL 42 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHH------CcCHHHHHHHHHHH
Confidence 35578888899999999999998 48999999998864
No 55
>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=61.52 E-value=16 Score=27.96 Aligned_cols=34 Identities=21% Similarity=0.172 Sum_probs=27.5
Q ss_pred HHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 13 FIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 13 ~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
.|+..+.+ ...|..+|+.++ .+|..||+|.|+..
T Consensus 10 ~I~e~l~~-~~~ti~dvA~~~------gvS~~TVsr~L~~~ 43 (80)
T TIGR02844 10 EIGKYIVE-TKATVRETAKVF------GVSKSTVHKDVTER 43 (80)
T ss_pred HHHHHHHH-CCCCHHHHHHHh------CCCHHHHHHHhcCC
Confidence 45666666 999999999886 58999999999653
No 56
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=59.19 E-value=22 Score=23.27 Aligned_cols=36 Identities=17% Similarity=0.327 Sum_probs=24.8
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
.+.++.++.+.+.-+-.+.++.| .+|++|++++|++
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L------gisr~tL~~klkk 41 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL------GISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH------TS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH------CCCHHHHHHHHHh
Confidence 34555666666666777777777 4899999999975
No 57
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=58.57 E-value=19 Score=23.87 Aligned_cols=36 Identities=14% Similarity=0.076 Sum_probs=21.8
Q ss_pred hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
..+..++..... ..|..+|++.| .+|.+||++-+++
T Consensus 5 ~~R~~ii~l~~~--G~s~~~ia~~l------gvs~~Tv~~w~kr 40 (50)
T PF13384_consen 5 ERRAQIIRLLRE--GWSIREIAKRL------GVSRSTVYRWIKR 40 (50)
T ss_dssp -----HHHHHHH--T--HHHHHHHH------TS-HHHHHHHHT-
T ss_pred hHHHHHHHHHHC--CCCHHHHHHHH------CcCHHHHHHHHHH
Confidence 344556666655 78899999987 5899999998876
No 58
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=56.44 E-value=16 Score=24.36 Aligned_cols=34 Identities=21% Similarity=0.180 Sum_probs=19.7
Q ss_pred HHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 12 RFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 12 r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
|..+..... -..|..+|+..| .+|.+||+|-|++
T Consensus 10 R~~I~~l~~-~G~s~~~IA~~l------g~s~sTV~relkR 43 (44)
T PF13936_consen 10 RNQIEALLE-QGMSIREIAKRL------GRSRSTVSRELKR 43 (44)
T ss_dssp --HHHHHHC-S---HHHHHHHT------T--HHHHHHHHHH
T ss_pred HHHHHHHHH-cCCCHHHHHHHH------CcCcHHHHHHHhc
Confidence 333444433 448889999987 4799999999876
No 59
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=56.40 E-value=18 Score=33.19 Aligned_cols=36 Identities=11% Similarity=0.064 Sum_probs=30.3
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
...|+..+.+++..|..|+.+.| .||+.||||=|..
T Consensus 19 ~~~Il~~L~~~~~vtv~eLa~~l------~VS~~TIRRDL~~ 54 (269)
T PRK09802 19 REQIIQRLRQQGSVQVNDLSALY------GVSTVTIRNDLAF 54 (269)
T ss_pred HHHHHHHHHHcCCEeHHHHHHHH------CCCHHHHHHHHHH
Confidence 45677888889999999999998 5899999997654
No 60
>smart00351 PAX Paired Box domain.
Probab=56.35 E-value=44 Score=27.04 Aligned_cols=79 Identities=10% Similarity=0.025 Sum_probs=48.9
Q ss_pred CchhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh---cCCccccc--ccCCC-cchHHHHhhhhhhhc
Q psy16970 7 ASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE---NNLTAKRL--HRAPE-LSIRNQRARSRKVEN 80 (257)
Q Consensus 7 ~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~---~~l~~~~~--~~~p~-l~~~~~~~r~~~~~~ 80 (257)
+...+.+|+..+.. ..|..+|+..+ .+|..||++.+++ .|....++ ..+|. ++..+...=++
T Consensus 19 s~~~R~riv~~~~~--G~s~~~iA~~~------gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~---- 86 (125)
T smart00351 19 PDEERQRIVELAQN--GVRPCDISRQL------CVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIAD---- 86 (125)
T ss_pred CHHHHHHHHHHHHc--CCCHHHHHHHH------CcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHH----
Confidence 34466778877753 35888888876 5899999988775 45433322 22343 44444433333
Q ss_pred cccccccchhhhhhhcccCChhhhcccc
Q psy16970 81 VVLKPVLGQIYIYIYHMHWTPAQQANVL 108 (257)
Q Consensus 81 ~~~~~~~~~~~~a~~h~~w~~~~w~~vv 108 (257)
+..+|-+||..+=+..+
T Consensus 87 -----------~~~~~p~~t~~el~~~L 103 (125)
T smart00351 87 -----------YKQENPGIFAWEIRDRL 103 (125)
T ss_pred -----------HHHHCCCCCHHHHHHHH
Confidence 67888888876554444
No 61
>COG0536 Obg Predicted GTPase [General function prediction only]
Probab=55.45 E-value=34 Score=33.29 Aligned_cols=73 Identities=18% Similarity=0.239 Sum_probs=46.8
Q ss_pred cccccccccEEEE-eCceEEecCeeccCCCCceEEEecCCCCCCCCCceecCCCCCCCcCccccCceEEEEcCCCceeec
Q psy16970 139 GVHGVSSDPIVIV-DAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFE 217 (257)
Q Consensus 139 ~~H~v~sg~V~iv-D~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~G~~vpde~g~~~~L~~Y~~~~i~l~LP~~~ti~d 217 (257)
+-.|..+|.|+++ |...=.+.+|.|. -+|-+.+|. +|.......=+|+|++|++|.|.++.|
T Consensus 36 GGdGG~GGsV~~~ad~~l~TL~d~r~~-----~~f~A~~G~------------~G~~~~~~G~~G~Dl~i~VP~GT~v~d 98 (369)
T COG0536 36 GGDGGRGGSVIFEADENLNTLIDFRYK-----KHFKAENGE------------NGMGRNRTGAKGKDLVIKVPVGTVVRD 98 (369)
T ss_pred CCCCCCCceEEEEEcCCcccHhhhccc-----eEEEccCCC------------CCCCCCCCCCCCCceEEEcCCCCEEEe
Confidence 3566777777766 6666667788885 344333321 111111223468999999999999999
Q ss_pred cCeEEEecccc
Q psy16970 218 IGHFGVWCEAF 228 (257)
Q Consensus 218 i~w~SVwc~~~ 228 (257)
.+-=.|.+.-.
T Consensus 99 ~~t~e~i~Dl~ 109 (369)
T COG0536 99 EDTGELLADLT 109 (369)
T ss_pred CCCCeEehhhc
Confidence 88766665543
No 62
>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=54.41 E-value=36 Score=23.15 Aligned_cols=23 Identities=26% Similarity=0.277 Sum_probs=17.7
Q ss_pred CHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 25 TALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 25 ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
|.+||++++ .+|..||.|.|+..
T Consensus 1 Ti~dIA~~a------gvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 1 TIKDIAREA------GVSKSTVSRVLNGP 23 (46)
T ss_dssp CHHHHHHHH------TSSHHHHHHHHTTC
T ss_pred CHHHHHHHH------CcCHHHHHHHHhCC
Confidence 456666665 58999999999876
No 63
>smart00686 DM13 Domain present in fly proteins (CG14681, CG12492, CG6217), worm H06A10.1 and Arabidopsis thaliana MBG8.9.
Probab=54.39 E-value=8.7 Score=30.97 Aligned_cols=24 Identities=25% Similarity=0.530 Sum_probs=21.2
Q ss_pred cccccCCCccccceeEeCCCCCCC
Q psy16970 106 NVLFSDEPRVNFGDVRIPKGFDFP 129 (257)
Q Consensus 106 ~vvwsdEsk~~fGsVwrp~ge~~P 129 (257)
-+|||...+.+||+|..|++...|
T Consensus 85 ~SV~~~~~~~nFG~V~ip~~~~~p 108 (108)
T smart00686 85 FSVWCLKTAHNFGHVLFPENLNIP 108 (108)
T ss_pred EEEEccccCCcceeEEccCCCCCC
Confidence 479999999999999999887755
No 64
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=54.13 E-value=23 Score=32.89 Aligned_cols=43 Identities=14% Similarity=0.155 Sum_probs=34.4
Q ss_pred CchhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCC
Q psy16970 7 ASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNL 55 (257)
Q Consensus 7 ~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l 55 (257)
|...++.|++.+.+++..+..+|++++ .+|+.||++.|+ +.|+
T Consensus 2 ~~~r~~~il~~L~~~~~~s~~~LA~~l------gvsr~tV~~~l~~L~~~G~ 47 (319)
T PRK11886 2 TYTVMLQLLSLLADGDFHSGEQLGEEL------GISRAAIWKHIQTLEEWGL 47 (319)
T ss_pred cccHHHHHHHHHHcCCCcCHHHHHHHH------CCCHHHHHHHHHHHHHCCC
Confidence 344578888988889999999998876 589999987655 5666
No 65
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=53.00 E-value=24 Score=31.89 Aligned_cols=39 Identities=18% Similarity=0.118 Sum_probs=33.4
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcC
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENN 54 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~ 54 (257)
-...|+..+.++..++..|+.+.| .||+.||||=|....
T Consensus 8 R~~~I~~~l~~~~~v~v~eLa~~~------~VS~~TIRRDL~~Le 46 (252)
T PRK10681 8 RIGQLLQALKRSDKLHLKDAAALL------GVSEMTIRRDLNAHS 46 (252)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHh------CCCHHHHHHHHHHhh
Confidence 355788888999999999999988 589999999998754
No 66
>PF12728 HTH_17: Helix-turn-helix domain
Probab=52.35 E-value=29 Score=23.15 Aligned_cols=30 Identities=17% Similarity=0.192 Sum_probs=24.0
Q ss_pred cCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccc
Q psy16970 24 ATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKR 59 (257)
Q Consensus 24 ~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~ 59 (257)
.|..|+++.| .+|..||++.+++-++.+.+
T Consensus 2 lt~~e~a~~l------~is~~tv~~~~~~g~i~~~~ 31 (51)
T PF12728_consen 2 LTVKEAAELL------GISRSTVYRWIRQGKIPPFK 31 (51)
T ss_pred CCHHHHHHHH------CcCHHHHHHHHHcCCCCeEE
Confidence 5777888777 58999999999888887653
No 67
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=51.55 E-value=21 Score=30.93 Aligned_cols=42 Identities=17% Similarity=0.225 Sum_probs=34.8
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA 57 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~ 57 (257)
-...|+..+.+++..+..++.+.+ .+|..||||=|.+..-.+
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~------~vS~~TiRRDl~~L~~~g 49 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKF------GVSIQTIRLDRMELGIPE 49 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHH------CcCHHHHHHHHHHHhcch
Confidence 345677888999999999999987 589999999988766555
No 68
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.18 E-value=45 Score=25.17 Aligned_cols=42 Identities=10% Similarity=0.052 Sum_probs=35.2
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
.++.+.++.++||.++..-|+.-+...| ...|+..|....++
T Consensus 25 ark~~~k~lk~NPpine~~iR~M~~qmG-qKpSe~kI~Qvm~~ 66 (71)
T COG3763 25 ARKQMKKQLKDNPPINEEMIRMMMAQMG-QKPSEKKINQVMRS 66 (71)
T ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHhC-CCchHHHHHHHHHH
Confidence 4678889999999999999988887765 78899888877765
No 69
>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=49.76 E-value=53 Score=22.30 Aligned_cols=44 Identities=16% Similarity=0.163 Sum_probs=30.5
Q ss_pred hhhHHHHHHHhhCcc--cCHHHHHHHHHhccCccccHHHHHHHHH---hcCCccc
Q psy16970 9 MNDRFIVSQVLRNCF--ATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLTAK 58 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~--~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~~~ 58 (257)
...-.++..+...+. .|+.||.+.+. ++.+||.+.++ +.||-.+
T Consensus 5 ~~q~~vL~~l~~~~~~~~t~~~la~~l~------~~~~~vs~~v~~L~~~Glv~r 53 (62)
T PF12802_consen 5 PSQFRVLMALARHPGEELTQSELAERLG------ISKSTVSRIVKRLEKKGLVER 53 (62)
T ss_dssp HHHHHHHHHHHHSTTSGEEHHHHHHHHT------S-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHC------cCHHHHHHHHHHHHHCCCEEE
Confidence 345567777777777 89999999985 67777776554 5665543
No 70
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=49.50 E-value=51 Score=21.27 Aligned_cols=35 Identities=23% Similarity=0.254 Sum_probs=25.2
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
++.++..+. ...+..+|.+.+ .+|..||++++++.
T Consensus 8 e~~i~~~~~--~g~s~~eia~~l------~is~~tv~~~~~~~ 42 (58)
T smart00421 8 EREVLRLLA--EGLTNKEIAERL------GISEKTVKTHLSNI 42 (58)
T ss_pred HHHHHHHHH--cCCCHHHHHHHH------CCCHHHHHHHHHHH
Confidence 344555553 336889999887 47999999998854
No 71
>PRK06474 hypothetical protein; Provisional
Probab=49.44 E-value=36 Score=29.40 Aligned_cols=46 Identities=20% Similarity=0.184 Sum_probs=34.5
Q ss_pred CchhhHHHHHHHhhCcc-cCHHHHHHHHHhccCccccHHHHHHHHH---hcCCcc
Q psy16970 7 ASMNDRFIVSQVLRNCF-ATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLTA 57 (257)
Q Consensus 7 ~~~~~r~i~r~v~~~~~-~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~~ 57 (257)
+...+.+|+..+..++. .|+.+|.+.|. .++..||+|.|+ +.|+-.
T Consensus 9 a~p~R~~Il~~L~~~~~~~ta~el~~~l~-----~is~aTvYrhL~~L~e~GLI~ 58 (178)
T PRK06474 9 MHPVRMKICQVLMRNKEGLTPLELVKILK-----DVPQATLYRHLQTMVDSGILH 58 (178)
T ss_pred CCHHHHHHHHHHHhCCCCCCHHHHHHHhc-----CCCHHHHHHHHHHHHHCCCEE
Confidence 34567788888877654 99999999885 488899997664 566554
No 72
>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=49.41 E-value=36 Score=26.84 Aligned_cols=61 Identities=23% Similarity=0.199 Sum_probs=39.9
Q ss_pred HHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHH---HHHHhcCCccccc-----ccCCCcchHHHHhh
Q psy16970 12 RFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVR---IRLNENNLTAKRL-----HRAPELSIRNQRAR 74 (257)
Q Consensus 12 r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvr---r~L~~~~l~~~~~-----~~~p~l~~~~~~~r 74 (257)
..|++.+=+.+..|+.||...|.+.. ..+..||+ ++|.+.|+-.+.. ...|.++...-.++
T Consensus 6 ~~IM~~lW~~~~~t~~eI~~~l~~~~--~~~~sTv~t~L~rL~~Kg~l~~~~~gr~~~Y~p~is~~e~~~~ 74 (115)
T PF03965_consen 6 LEIMEILWESGEATVREIHEALPEER--SWAYSTVQTLLNRLVEKGFLTREKIGRAYVYSPLISREEYLAQ 74 (115)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHHCTTS--S--HHHHHHHHHHHHHTTSEEEEEETTCEEEEESSSHHHHHHH
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHhcc--ccchhHHHHHHHHHHhCCceeEeecCCceEEEeCCcHHHHHHH
Confidence 34555553444499999999998863 55666666 6677788765543 34588888765554
No 73
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=47.98 E-value=33 Score=30.78 Aligned_cols=46 Identities=13% Similarity=0.069 Sum_probs=36.9
Q ss_pred chhhHHHHHHHhhCcc----cCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccc
Q psy16970 8 SMNDRFIVSQVLRNCF----ATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKR 59 (257)
Q Consensus 8 ~~~~r~i~r~v~~~~~----~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~ 59 (257)
....++|.+-+..||. .|..+|+++. .+|..||-|-.++.|+.+..
T Consensus 15 t~~e~~Ia~yil~n~~~v~~~si~~lA~~~------~vS~aTv~Rf~kklG~~gf~ 64 (284)
T PRK11302 15 SKSERKVAEVILASPQTAIHSSIATLAKMA------NVSEPTVNRFCRSLDTKGFP 64 (284)
T ss_pred CHHHHHHHHHHHhCHHHHHhcCHHHHHHHh------CCCHHHHHHHHHHcCCCCHH
Confidence 3567788888888865 5777777664 69999999999999999875
No 74
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=46.48 E-value=48 Score=28.11 Aligned_cols=52 Identities=17% Similarity=0.204 Sum_probs=41.5
Q ss_pred HHHHHhhCcccCHHHHHHHHHhccCccccHHHH---HHHHHhcCCcccccccCCCcchHHH
Q psy16970 14 IVSQVLRNCFATALEVRQELQDVRKVHLNEGTV---RIRLNENNLTAKRLHRAPELSIRNQ 71 (257)
Q Consensus 14 i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tv---rr~L~~~~l~~~~~~~~p~l~~~~~ 71 (257)
|........++...+|+..|+ |+..|| -++|.+.||--+.+.+.-.||.+=+
T Consensus 15 Iy~l~~~~~~~~~~diA~~L~------Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~ 69 (154)
T COG1321 15 IYELLEEKGFARTKDIAERLK------VSPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGR 69 (154)
T ss_pred HHHHHhccCcccHHHHHHHhC------CCcHHHHHHHHHHHHCCCeEEecCCCeEEChhhH
Confidence 444555788999999999985 677777 7889999999999999999995443
No 75
>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=45.28 E-value=33 Score=24.06 Aligned_cols=36 Identities=28% Similarity=0.433 Sum_probs=27.8
Q ss_pred HHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcC
Q psy16970 13 FIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENN 54 (257)
Q Consensus 13 ~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~ 54 (257)
.|+.....++..|..|++..| .+|++||++.+++.+
T Consensus 9 ~Ll~~L~~~~~~~~~ela~~l------~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 9 KLLELLLKNKWITLKELAKKL------NISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHTSBBHHHHHHHC------TS-HHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCcHHHHHHHH------CCCHHHHHHHHHHHH
Confidence 455555558889999999887 589999999998754
No 76
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=45.22 E-value=32 Score=27.79 Aligned_cols=42 Identities=21% Similarity=0.341 Sum_probs=35.3
Q ss_pred cCCchhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHH
Q psy16970 5 SGASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRI 48 (257)
Q Consensus 5 ~~~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr 48 (257)
.-+.....+|++.+ -||-|..++...++...|+.||++.|-.
T Consensus 3 ~L~~~vK~FIVQ~L--AcfdTPs~v~~aVk~eFgi~vsrQqve~ 44 (104)
T PF10045_consen 3 ALKKEVKAFIVQSL--ACFDTPSEVAEAVKEEFGIDVSRQQVES 44 (104)
T ss_pred CccHHHHHHHHHHH--HhhCCHHHHHHHHHHHhCCccCHHHHHH
Confidence 34556678888886 5999999999999999999999998864
No 77
>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=43.91 E-value=66 Score=21.61 Aligned_cols=37 Identities=24% Similarity=0.232 Sum_probs=27.0
Q ss_pred hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
.....|+..+...+ .+..|+.+.+ .++..||++.|+.
T Consensus 7 ~~~~~il~~l~~~~-~~~~ei~~~~------~i~~~~i~~~l~~ 43 (78)
T cd00090 7 PTRLRILRLLLEGP-LTVSELAERL------GLSQSTVSRHLKK 43 (78)
T ss_pred hHHHHHHHHHHHCC-cCHHHHHHHH------CcCHhHHHHHHHH
Confidence 44556666666677 8999988876 4678888877764
No 78
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=43.09 E-value=74 Score=23.52 Aligned_cols=43 Identities=9% Similarity=0.156 Sum_probs=35.6
Q ss_pred hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
-.++++..+..+||-++...|+.-....| ...|+..|++.++.
T Consensus 17 ~ar~~~~k~l~~NPpine~mir~M~~QMG-~kpSekqi~Q~m~~ 59 (64)
T PF03672_consen 17 IARKYMEKQLKENPPINEKMIRAMMMQMG-RKPSEKQIKQMMRS 59 (64)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHhC-CCccHHHHHHHHHH
Confidence 35678888899999999999988887765 88899999887765
No 79
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=42.92 E-value=53 Score=24.07 Aligned_cols=40 Identities=18% Similarity=0.144 Sum_probs=29.2
Q ss_pred HHHHHHhhC-cccCHHHHHHHHHhccCccccHHHHHHHHHh---cCCccc
Q psy16970 13 FIVSQVLRN-CFATALEVRQELQDVRKVHLNEGTVRIRLNE---NNLTAK 58 (257)
Q Consensus 13 ~i~r~v~~~-~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~---~~l~~~ 58 (257)
.|+..+.+. +..|..||.+++ .++..||+|.|+. .|+-.+
T Consensus 9 ~Il~~l~~~~~~~t~~~ia~~l------~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 9 AVLRALAEEPGGLTLAELAERL------GLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHHhCCCCcCHHHHHHHh------CCCHHHHHHHHHHHHHCCCeee
Confidence 355556555 679999999988 4799999998864 555543
No 80
>cd00131 PAX Paired Box domain
Probab=42.49 E-value=86 Score=25.55 Aligned_cols=82 Identities=11% Similarity=0.022 Sum_probs=51.9
Q ss_pred CchhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh---cCCcccccc--cCCC-cchHHHHhhhhhhhc
Q psy16970 7 ASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE---NNLTAKRLH--RAPE-LSIRNQRARSRKVEN 80 (257)
Q Consensus 7 ~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~---~~l~~~~~~--~~p~-l~~~~~~~r~~~~~~ 80 (257)
|...+.+|+..+.. -.|..+|+..+ .||..||++.+++ .|--.-++. +.|. ++..+...-.+
T Consensus 19 S~d~R~rIv~~~~~--G~s~~~iA~~~------~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~---- 86 (128)
T cd00131 19 PDSIRQRIVELAQS--GIRPCDISRQL------RVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEI---- 86 (128)
T ss_pred CHHHHHHHHHHHHc--CCCHHHHHHHH------CcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHH----
Confidence 34467778877753 36888998876 5899999988775 332222221 2233 45555444444
Q ss_pred cccccccchhhhhhhcccCChhhhccccccC
Q psy16970 81 VVLKPVLGQIYIYIYHMHWTPAQQANVLFSD 111 (257)
Q Consensus 81 ~~~~~~~~~~~~a~~h~~w~~~~w~~vvwsd 111 (257)
++.+|-+.|..+-+..+|.+
T Consensus 87 -----------~v~~~p~~Tl~El~~~L~~~ 106 (128)
T cd00131 87 -----------YKQENPGMFAWEIRDRLLQE 106 (128)
T ss_pred -----------HHHHCCCCCHHHHHHHHHHc
Confidence 67888888877777777744
No 81
>PF14420 Clr5: Clr5 domain
Probab=39.72 E-value=1.1e+02 Score=21.23 Aligned_cols=37 Identities=11% Similarity=0.069 Sum_probs=32.0
Q ss_pred hCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCc
Q psy16970 20 RNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLT 56 (257)
Q Consensus 20 ~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~ 56 (257)
-+...|..+|.+.+....|...|.++-+++|.+=|+.
T Consensus 17 ~~e~~tl~~v~~~M~~~~~F~at~rqy~~r~~~Wg~~ 53 (54)
T PF14420_consen 17 IDENKTLEEVMEIMKEEHGFKATKRQYKRRFKKWGFR 53 (54)
T ss_pred HhCCCcHHHHHHHHHHHhCCCcCHHHHHHHHHHcCCC
Confidence 3566899999999999989999999999999876654
No 82
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=39.32 E-value=63 Score=21.16 Aligned_cols=31 Identities=19% Similarity=0.182 Sum_probs=22.4
Q ss_pred HHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 15 VSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 15 ~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
+..+. +...|..+|.+.+. +|..|+++.|++
T Consensus 3 l~~l~-~~~~~~~~i~~~l~------is~~~v~~~l~~ 33 (66)
T smart00418 3 LKLLA-EGELCVCELAEILG------LSQSTVSHHLKK 33 (66)
T ss_pred HHHhh-cCCccHHHHHHHHC------CCHHHHHHHHHH
Confidence 34444 55578999998874 688888877765
No 83
>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=39.20 E-value=44 Score=22.54 Aligned_cols=33 Identities=24% Similarity=0.203 Sum_probs=23.3
Q ss_pred HHHHHhhCcc-cCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 14 IVSQVLRNCF-ATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 14 i~r~v~~~~~-~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
|++.+.+.+. .|..||.+++ .+++.|++|.|+.
T Consensus 8 iL~~l~~~~~~~t~~eia~~~------gl~~stv~r~L~t 41 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIARAL------GLPKSTVHRLLQT 41 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHHHH------TS-HHHHHHHHHH
T ss_pred HHHHHHcCCCCCCHHHHHHHH------CcCHHHHHHHHHH
Confidence 4455544444 6999999987 4788999998874
No 84
>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=39.08 E-value=60 Score=28.16 Aligned_cols=44 Identities=25% Similarity=0.302 Sum_probs=33.3
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh---cCCcccc
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE---NNLTAKR 59 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~---~~l~~~~ 59 (257)
+++.|+..+.+....|..+|...| .++..||++.|.+ .|+-.++
T Consensus 2 tr~~IL~~L~~~~~~t~~eLA~~l------gis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 2 TKEDILSYLLKQGQATAAALAEAL------AISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeEEe
Confidence 356778777766669999999988 4788999988765 6666544
No 85
>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=38.70 E-value=77 Score=20.96 Aligned_cols=36 Identities=25% Similarity=0.239 Sum_probs=26.6
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
.+..|+..+..++ .++.||.+.+ .+|..||++.|..
T Consensus 3 ~R~~Il~~L~~~~-~~~~el~~~l------~~s~~~vs~hL~~ 38 (47)
T PF01022_consen 3 TRLRILKLLSEGP-LTVSELAEEL------GLSQSTVSHHLKK 38 (47)
T ss_dssp HHHHHHHHHTTSS-EEHHHHHHHH------TS-HHHHHHHHHH
T ss_pred HHHHHHHHHHhCC-CchhhHHHhc------cccchHHHHHHHH
Confidence 4567777777755 8888999987 4789999977653
No 86
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 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 []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=38.01 E-value=55 Score=24.19 Aligned_cols=38 Identities=13% Similarity=0.251 Sum_probs=27.7
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
..=.|...+..++..|..++++++ .+|++|++|.+++.
T Consensus 17 ~~~~ll~~ll~~~~~s~~~la~~~------~iS~sti~~~i~~l 54 (87)
T PF05043_consen 17 LNYQLLKLLLNNEYVSIEDLAEEL------FISRSTIYRDIKKL 54 (87)
T ss_dssp HHHHHHHHHHH-SEEEHHHHHHHH------T--HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHH------CCCHHHHHHHHHHH
Confidence 344566677788999999999987 58999999988764
No 87
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=37.85 E-value=72 Score=20.18 Aligned_cols=30 Identities=30% Similarity=0.277 Sum_probs=22.6
Q ss_pred cCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccc
Q psy16970 24 ATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKR 59 (257)
Q Consensus 24 ~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~ 59 (257)
.|..|+++.| .+|++|+++.+++-.+.+.+
T Consensus 2 lt~~e~a~~l------gis~~ti~~~~~~g~i~~~~ 31 (49)
T TIGR01764 2 LTVEEAAEYL------GVSKDTVYRLIHEGELPAYR 31 (49)
T ss_pred CCHHHHHHHH------CCCHHHHHHHHHcCCCCeEE
Confidence 4667777766 58999999999876666543
No 88
>PF13518 HTH_28: Helix-turn-helix domain
Probab=37.84 E-value=84 Score=20.48 Aligned_cols=34 Identities=21% Similarity=0.203 Sum_probs=24.8
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
+..++..+.++ . |..+++.++ .||.+||++-++.
T Consensus 2 r~~iv~~~~~g-~-s~~~~a~~~------gis~~tv~~w~~~ 35 (52)
T PF13518_consen 2 RLQIVELYLEG-E-SVREIAREF------GISRSTVYRWIKR 35 (52)
T ss_pred HHHHHHHHHcC-C-CHHHHHHHH------CCCHhHHHHHHHH
Confidence 34567777743 3 989988887 4689999887754
No 89
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=37.57 E-value=71 Score=26.58 Aligned_cols=44 Identities=20% Similarity=0.129 Sum_probs=30.7
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCcccc
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLTAKR 59 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~~~~ 59 (257)
+-.-+...+..+.-.|..+|++.|+ .+++||.|.|+ +.|+--|.
T Consensus 29 Dv~v~~~LL~~~~~~tvdelae~ln------r~rStv~rsl~~L~~~GlV~Re 75 (126)
T COG3355 29 DVEVYKALLEENGPLTVDELAEILN------RSRSTVYRSLQNLLEAGLVERE 75 (126)
T ss_pred HHHHHHHHHhhcCCcCHHHHHHHHC------ccHHHHHHHHHHHHHcCCeeee
Confidence 3334444443677899999999985 68999998766 47766543
No 90
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=36.71 E-value=71 Score=24.95 Aligned_cols=16 Identities=31% Similarity=0.617 Sum_probs=13.5
Q ss_pred cccHHHHHHHHHhcCC
Q psy16970 40 HLNEGTVRIRLNENNL 55 (257)
Q Consensus 40 ~~s~~Tvrr~L~~~~l 55 (257)
.+|++|++++|++.|+
T Consensus 79 GIsRsTL~rKLkr~gi 94 (95)
T PRK00430 79 GINRGTLRKKLKKYGM 94 (95)
T ss_pred CCCHHHHHHHHHHhCC
Confidence 5799999999988775
No 91
>PF00626 Gelsolin: Gelsolin repeat; InterPro: IPR007123 Gelsolin is a cytoplasmic, calcium-regulated, actin-modulating protein that binds to the barbed ends of actin filaments, preventing monomer exchange (end-blocking or capping) []. It can promote nucleation (the assembly of monomers into filaments), as well as sever existing filaments. In addition, this protein binds with high affinity to fibronectin. Plasma gelsolin and cytoplasmic gelsolin are derived from a single gene by alternate initiation sites and differential splicing. Sequence comparisons indicate an evolutionary relationship between gelsolin, villin, fragmin and severin []. Six large repeating segments occur in gelsolin and villin, and 3 similar segments in severin and fragmin. While the multiple repeats have yet to be related to any known function of the actin-severing proteins, the superfamily appears to have evolved from an ancestral sequence of 120 to 130 amino acid residues [].; PDB: 3FG6_F 1RGI_G 2FGH_A 1D0N_B 3EGD_B 2NUP_B 2NUT_B 3EGX_B 1JHW_A 1J72_A ....
Probab=36.20 E-value=27 Score=24.70 Aligned_cols=23 Identities=30% Similarity=0.510 Sum_probs=17.7
Q ss_pred ccccEEEEeCceEEecCeeccCCCCceEEEecCCCC
Q psy16970 144 SSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPH 179 (257)
Q Consensus 144 ~sg~V~ivD~~Tl~i~~FsydG~gPd~yfw~g~~~~ 179 (257)
.++.+||+|... ..|.|.|..+.
T Consensus 16 ~s~~~yIld~~~-------------~i~vW~G~~~~ 38 (76)
T PF00626_consen 16 NSDDCYILDCGY-------------EIFVWVGKKSS 38 (76)
T ss_dssp ETTSEEEEEESS-------------EEEEEEHTTSH
T ss_pred CCCCEEEEEeCC-------------CcEEEEeccCC
Confidence 456799987655 79999999843
No 92
>PF12990 DUF3874: Domain of unknonw function from B. Theta Gene description (DUF3874); InterPro: IPR024450 This domain of unknown function if found in uncharacterised proteins from Bacteroides thetaiotaomicron and other Bacteroidetes.
Probab=35.81 E-value=37 Score=25.61 Aligned_cols=41 Identities=17% Similarity=0.164 Sum_probs=30.3
Q ss_pred cccCHHHHHHHHHhccCccccHHHH---HHHHHhcCCccccccc
Q psy16970 22 CFATALEVRQELQDVRKVHLNEGTV---RIRLNENNLTAKRLHR 62 (257)
Q Consensus 22 ~~~ta~~i~~~l~~~~g~~~s~~Tv---rr~L~~~~l~~~~~~~ 62 (257)
-..||.||-+.|+...+..++..++ -|.|...|+..++..+
T Consensus 24 e~lsa~~If~~L~k~~~~~l~~~~~~~FGriL~~~gi~~khT~~ 67 (73)
T PF12990_consen 24 EWLSAAEIFERLQKKSPAALRGSNPNHFGRILQKLGIPRKHTRK 67 (73)
T ss_pred eeecHHHHHHHHHHhCccccccCCHHHHHHHHHHcCCCccccCC
Confidence 4579999999999876665554444 5899999988765543
No 93
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=35.45 E-value=58 Score=29.80 Aligned_cols=50 Identities=20% Similarity=0.103 Sum_probs=37.7
Q ss_pred chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccc
Q psy16970 8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKR 59 (257)
Q Consensus 8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~ 59 (257)
...+|+|...+..||..-+..=.++|... .+||+.||-|-.++.|+.+..
T Consensus 17 t~~er~iA~yil~~~~~~~~~si~elA~~--a~VS~aTv~Rf~~kLGf~Gf~ 66 (281)
T COG1737 17 TKSERKIADYILANPDEVALLSIAELAER--AGVSPATVVRFARKLGFEGFS 66 (281)
T ss_pred CHHHHHHHHHHHhCHHHHHHHHHHHHHHH--hCCCHHHHHHHHHHcCCCCHH
Confidence 34678888899888775555445555543 378999999999999999864
No 94
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=35.39 E-value=97 Score=22.45 Aligned_cols=44 Identities=14% Similarity=0.174 Sum_probs=31.5
Q ss_pred chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCcc
Q psy16970 8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLTA 57 (257)
Q Consensus 8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~~ 57 (257)
....-.|+..+..++..|..+|.+.+. ++..||.+.|+ +.|+-.
T Consensus 9 ~~~~~~il~~l~~~~~~~~~~la~~~~------~s~~~i~~~l~~L~~~g~v~ 55 (101)
T smart00347 9 TPTQFLVLRILYEEGPLSVSELAKRLG------VSPSTVTRVLDRLEKKGLIR 55 (101)
T ss_pred CHHHHHHHHHHHHcCCcCHHHHHHHHC------CCchhHHHHHHHHHHCCCeE
Confidence 455667778887788899999988874 56777776554 566554
No 95
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=35.13 E-value=1.2e+02 Score=24.84 Aligned_cols=59 Identities=10% Similarity=0.115 Sum_probs=38.4
Q ss_pred HHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHH---HHhcCCccc-----ccccCCCcchHHHHhh
Q psy16970 14 IVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIR---LNENNLTAK-----RLHRAPELSIRNQRAR 74 (257)
Q Consensus 14 i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~---L~~~~l~~~-----~~~~~p~l~~~~~~~r 74 (257)
|+..+-.....|+.||...|.+.. .++..||+.. |.+.|+-.+ .....|.++...-.++
T Consensus 9 VM~vlW~~~~~t~~eI~~~l~~~~--~~~~tTv~T~L~rL~~KG~v~~~k~gr~~~Y~p~vs~ee~~~~ 75 (130)
T TIGR02698 9 VMRVVWTLGETTSRDIIRILAEKK--DWSDSTIKTLLGRLVDKGCLTTEKEGRKFIYTALVSEDEAVEN 75 (130)
T ss_pred HHHHHHcCCCCCHHHHHHHHhhcc--CCcHHHHHHHHHHHHHCCceeeecCCCcEEEEecCCHHHHHHH
Confidence 555554455689999999997643 4666676654 777886543 2344677777665443
No 96
>PRK04217 hypothetical protein; Provisional
Probab=35.11 E-value=83 Score=25.42 Aligned_cols=37 Identities=19% Similarity=0.046 Sum_probs=26.5
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
+.+.++..... -..|..||++.| .+|..||+++|++.
T Consensus 46 eereai~l~~~-eGlS~~EIAk~L------GIS~sTV~r~L~RA 82 (110)
T PRK04217 46 EEFEALRLVDY-EGLTQEEAGKRM------GVSRGTVWRALTSA 82 (110)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHH------CcCHHHHHHHHHHH
Confidence 33455555432 346999999987 58999999999864
No 97
>cd03488 Topoisomer_IB_N_htopoI_like Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.
Probab=34.53 E-value=1.3e+02 Score=27.41 Aligned_cols=74 Identities=26% Similarity=0.436 Sum_probs=47.2
Q ss_pred EEEEeCceEEecCeeccCCCCceEEEecCCCCCCCCCceecCCCCCCCcC-ccccCceEEEE---------cCCCceeec
Q psy16970 148 IVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPL-RRYNRKTIVLT---------LPGELTVFE 217 (257)
Q Consensus 148 V~ivD~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~G~~vpde~g~~~~L-~~Y~~~~i~l~---------LP~~~ti~d 217 (257)
.-+||...-+|+||.-.. |.+| -|.|.-|.. | .| ++-.=+||+|. -|.|..|.+
T Consensus 125 ~~~vDG~kekVgNfrvEP--PgLF--rGRG~HPK~-G-----------~lK~Rv~PedVtINigkda~vP~pp~Gh~Wke 188 (215)
T cd03488 125 FCILDGHKEKVGNFRIEP--PGLF--RGRGAHPKT-G-----------KLKRRIMPEDIIINIGKDAKVPEPPPGHKWKE 188 (215)
T ss_pred EEEECCEEEeeCCcccCC--Cccc--cCCCCCCCC-C-----------ccccccChhhEEEecCCCCCCCccCCCCCcce
Confidence 447899999999999854 3333 344444442 2 22 12222566663 466788876
Q ss_pred ------cCeEEEeccccccCeeeEEc
Q psy16970 218 ------IGHFGVWCEAFTVDFGHIQI 237 (257)
Q Consensus 218 ------i~w~SVwc~~~~~nFG~V~i 237 (257)
++||+-|-+.-+-+|=-|.|
T Consensus 189 V~HDntVtWLA~W~enIn~~~KYV~L 214 (215)
T cd03488 189 VRHDNTVTWLASWTENINGSIKYVML 214 (215)
T ss_pred eecCCCceEEEEeEeccCCceeEEEe
Confidence 68999998887766666654
No 98
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=34.02 E-value=68 Score=28.93 Aligned_cols=27 Identities=19% Similarity=0.091 Sum_probs=21.7
Q ss_pred cccCHHHHHHHHHhccCccccHHHHHHHHHhcC
Q psy16970 22 CFATALEVRQELQDVRKVHLNEGTVRIRLNENN 54 (257)
Q Consensus 22 ~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~ 54 (257)
...|.+||+++. .||..||+|.|+..+
T Consensus 5 ~~~Ti~dIA~~a------gVS~~TVSr~Ln~~~ 31 (342)
T PRK10014 5 KKITIHDVALAA------GVSVSTVSLVLSGKG 31 (342)
T ss_pred CCCcHHHHHHHh------CCCHHHHHHHHCCCC
Confidence 457888988876 589999999998644
No 99
>cd03489 Topoisomer_IB_N_LdtopoI_like Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human
Probab=33.87 E-value=1.3e+02 Score=27.25 Aligned_cols=74 Identities=23% Similarity=0.422 Sum_probs=47.1
Q ss_pred EEEEeCceEEecCeeccCCCCceEEEecCCCCCCCCCceecCCCCCCCcC-ccccCceEEEE---------cCCCceeec
Q psy16970 148 IVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPL-RRYNRKTIVLT---------LPGELTVFE 217 (257)
Q Consensus 148 V~ivD~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~G~~vpde~g~~~~L-~~Y~~~~i~l~---------LP~~~ti~d 217 (257)
.-+||...-+|+||.-.. |.+| -|.|.-|.. | .| ++-.=+||+|. -|.|..|.+
T Consensus 122 ~~~vDG~kekVgNFrvEP--PgLF--rGRG~HPK~-G-----------~lK~Rv~PedVtINigkda~vP~pp~Gh~Wke 185 (212)
T cd03489 122 WCVWDGVKEQVANFRVEP--PGLF--RGRGEHPKM-G-----------KLKKRIQPEDITINIGKGAPIPECPAGHKWKE 185 (212)
T ss_pred EEEECCEEEeeCCcccCC--Cccc--ccCCCCCCC-c-----------ccccccChhheEEecCCCCCCCccCCCCCcce
Confidence 447899999999999854 3333 344444442 2 22 12222566663 456778866
Q ss_pred ------cCeEEEeccccccCeeeEEc
Q psy16970 218 ------IGHFGVWCEAFTVDFGHIQI 237 (257)
Q Consensus 218 ------i~w~SVwc~~~~~nFG~V~i 237 (257)
++||+-|-+.-+-+|=-|.|
T Consensus 186 V~HDntVtWLA~W~enIn~~~KYV~L 211 (212)
T cd03489 186 VKHDNTVTWLAMWRDPIAGNFKYVML 211 (212)
T ss_pred eecCCCceEEEEeEeccCCceeEEEe
Confidence 68999998887766666554
No 100
>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=33.68 E-value=1.2e+02 Score=20.10 Aligned_cols=26 Identities=27% Similarity=0.160 Sum_probs=20.4
Q ss_pred CcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 21 NCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 21 ~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
....|..||...+ .+|.+||++++++
T Consensus 18 ~~~~t~~eIa~~l------g~s~~~V~~~~~~ 43 (50)
T PF04545_consen 18 FEGLTLEEIAERL------GISRSTVRRILKR 43 (50)
T ss_dssp TST-SHHHHHHHH------TSCHHHHHHHHHH
T ss_pred cCCCCHHHHHHHH------CCcHHHHHHHHHH
Confidence 4457889999987 4799999998875
No 101
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=33.27 E-value=1.3e+02 Score=19.40 Aligned_cols=33 Identities=21% Similarity=0.158 Sum_probs=23.9
Q ss_pred HHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 13 FIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 13 ~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
.++.... ...|..+|.+.+ .+|.+||++++++.
T Consensus 7 ~i~~~~~--~~~s~~eia~~l------~~s~~tv~~~~~~~ 39 (57)
T cd06170 7 EVLRLLA--EGKTNKEIADIL------GISEKTVKTHLRNI 39 (57)
T ss_pred HHHHHHH--cCCCHHHHHHHH------CCCHHHHHHHHHHH
Confidence 3444443 347999999886 47999999998754
No 102
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=33.26 E-value=89 Score=25.53 Aligned_cols=37 Identities=24% Similarity=0.293 Sum_probs=27.7
Q ss_pred hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
.++..+++...++ .-+.+|+..+| .+|..|||.||.+
T Consensus 36 ~E~~~Fi~~Fi~~-rGnlKe~e~~l------giSYPTvR~rLd~ 72 (113)
T PF09862_consen 36 PEQLEFIKLFIKN-RGNLKEMEKEL------GISYPTVRNRLDK 72 (113)
T ss_pred HHHHHHHHHHHHh-cCCHHHHHHHH------CCCcHHHHHHHHH
Confidence 4455566666553 47888998887 5899999999986
No 103
>cd00660 Topoisomer_IB_N Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I diffe
Probab=33.13 E-value=1.4e+02 Score=27.12 Aligned_cols=74 Identities=27% Similarity=0.429 Sum_probs=47.2
Q ss_pred EEEEeCceEEecCeeccCCCCceEEEecCCCCCCCCCceecCCCCCCCcC-ccccCceEEEE---------cCCCceeec
Q psy16970 148 IVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPL-RRYNRKTIVLT---------LPGELTVFE 217 (257)
Q Consensus 148 V~ivD~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~G~~vpde~g~~~~L-~~Y~~~~i~l~---------LP~~~ti~d 217 (257)
.-+||...-+|+||.-.. |.+| -|.|.-|.. | .| ++-.=+||+|. -|.|..|.+
T Consensus 125 ~~~vDG~kekVgNfrvEP--PgLF--rGRG~HPK~-G-----------~lK~Rv~PedVtINigkda~vP~pp~Gh~Wke 188 (215)
T cd00660 125 YCLVDGHKEKVGNFRIEP--PGLF--RGRGEHPKM-G-----------KLKRRIMPEDITINIGKDAPVPEPPAGHKWKE 188 (215)
T ss_pred EEEECCEEEeeCCcccCC--Cccc--ccCCCCCCC-C-----------ccccccChhhEEEecCCCCCCCccCCCCCcce
Confidence 457899999999999854 3333 344444442 2 22 12223566663 456777766
Q ss_pred ------cCeEEEeccccccCeeeEEc
Q psy16970 218 ------IGHFGVWCEAFTVDFGHIQI 237 (257)
Q Consensus 218 ------i~w~SVwc~~~~~nFG~V~i 237 (257)
++||+-|-+.-+-+|=-|.|
T Consensus 189 V~HDntVtWLA~W~enIn~~~KYV~L 214 (215)
T cd00660 189 VRHDNTVTWLASWKENINGQFKYVML 214 (215)
T ss_pred eecCCCceEEEEeEeccCCceeEEEe
Confidence 68999998887766666554
No 104
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=32.45 E-value=99 Score=25.69 Aligned_cols=44 Identities=16% Similarity=-0.047 Sum_probs=29.4
Q ss_pred CchhhHHHHHHHhhCcccCHHHHHHHHHhccCc----cccHHHHHHHH
Q psy16970 7 ASMNDRFIVSQVLRNCFATALEVRQELQDVRKV----HLNEGTVRIRL 50 (257)
Q Consensus 7 ~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~----~~s~~Tvrr~L 50 (257)
++....+|......||.+.|-||++.|-..+-. .-|.++|.|.|
T Consensus 77 tp~v~~~I~~~k~enP~ifawEiR~~L~~~gvc~~~~~PsvssInRil 124 (125)
T PF00292_consen 77 TPEVVEKIEQYKRENPTIFAWEIRDRLIADGVCDRSNVPSVSSINRIL 124 (125)
T ss_dssp -HCHHHHHHHHHHH-TTS-HHHHHHHHHHTTSS-TTTS--HHHHHHHH
T ss_pred ChHHHHHHHHHHhcCCCcchHHHHHHHHHcCCCCCCCCCCHHHHHHhh
Confidence 445667888888999999999999999876522 23566776665
No 105
>PRK01905 DNA-binding protein Fis; Provisional
Probab=32.25 E-value=98 Score=22.92 Aligned_cols=16 Identities=31% Similarity=0.576 Sum_probs=13.1
Q ss_pred cccHHHHHHHHHhcCC
Q psy16970 40 HLNEGTVRIRLNENNL 55 (257)
Q Consensus 40 ~~s~~Tvrr~L~~~~l 55 (257)
.+|++|++++|++.|+
T Consensus 61 GIsrstL~rklkk~gi 76 (77)
T PRK01905 61 GINRNTLRKKLQQHGL 76 (77)
T ss_pred CCCHHHHHHHHHHhCC
Confidence 5788999999988764
No 106
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=32.09 E-value=46 Score=29.87 Aligned_cols=49 Identities=10% Similarity=0.046 Sum_probs=37.8
Q ss_pred chhhHHHHHHHhhCcc----cCHHHHHHHHHhccCccccHHHHHHHHHhcCCccccccc
Q psy16970 8 SMNDRFIVSQVLRNCF----ATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHR 62 (257)
Q Consensus 8 ~~~~r~i~r~v~~~~~----~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~~ 62 (257)
....+.|.+-+..||. .|..||+++. .+|+.||.|-.++.|+.+..--+
T Consensus 11 t~~e~~ia~yil~n~~~v~~~si~elA~~~------~vS~aTv~Rf~kklG~~Gf~efk 63 (278)
T PRK11557 11 AQSDRKLADYLLLQPDTARHLSSQQLANEA------GVSQSSVVKFAQKLGYKGFPALK 63 (278)
T ss_pred CHHHHHHHHHHHhCHHHHHhcCHHHHHHHh------CCCHHHHHHHHHHcCCCCHHHHH
Confidence 3456788888888864 5666776664 68999999999999999875433
No 107
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=31.73 E-value=1.1e+02 Score=21.86 Aligned_cols=37 Identities=19% Similarity=0.208 Sum_probs=31.4
Q ss_pred HHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCC
Q psy16970 13 FIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNL 55 (257)
Q Consensus 13 ~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l 55 (257)
.++..+...|..|+..+.++|+ +|.++..+.+.+.|+
T Consensus 3 ~Lidll~~~P~Vsa~mva~~L~------vT~~~A~~li~eLg~ 39 (54)
T PF11972_consen 3 RLIDLLLSRPLVSAPMVAKELG------VTPQAAQRLIAELGL 39 (54)
T ss_pred HHHHHHHhCccccHHHHHHHhC------CCHHHHHHHHHHhhc
Confidence 3566778889999999999984 799999999888776
No 108
>PF13309 HTH_22: HTH domain
Probab=31.42 E-value=63 Score=23.24 Aligned_cols=43 Identities=14% Similarity=0.099 Sum_probs=25.0
Q ss_pred CchhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHH
Q psy16970 7 ASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLN 51 (257)
Q Consensus 7 ~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~ 51 (257)
+..++..|++...+...--.+.-...+... ..+|+.||+|.|+
T Consensus 22 ~~~~k~~iV~~L~~~G~F~lKgav~~vA~~--L~iS~~TVY~YLr 64 (64)
T PF13309_consen 22 SKEEKKEIVRQLYEKGIFLLKGAVEYVAEK--LGISRATVYRYLR 64 (64)
T ss_pred CHHHHHHHHHHHHHCCCcccCcHHHHHHHH--HCCCHHHHHHHcC
Confidence 345566677777666543333322333222 2689999998874
No 109
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=31.40 E-value=1e+02 Score=23.20 Aligned_cols=36 Identities=28% Similarity=0.206 Sum_probs=26.5
Q ss_pred HHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 12 RFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 12 r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
+.+....+.....|..||++.| .+|.+||+.+++..
T Consensus 21 r~af~L~R~~eGlS~kEIAe~L------GIS~~TVk~~l~~~ 56 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEEL------GRTEQTVRNHLKGE 56 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHH------CcCHHHHHHHHhcC
Confidence 3444444444668999999988 58999999999853
No 110
>PRK00523 hypothetical protein; Provisional
Probab=30.91 E-value=1.4e+02 Score=22.55 Aligned_cols=43 Identities=12% Similarity=0.103 Sum_probs=35.4
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
.++++..+.++||-++-.-|+.-....| ...|+..|++..+..
T Consensus 26 ark~~~k~l~~NPpine~mir~M~~QMG-qKPSekki~Q~m~~m 68 (72)
T PRK00523 26 SKKMFKKQIRENPPITENMIRAMYMQMG-RKPSESQIKQVMRSV 68 (72)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHHHHhC-CCccHHHHHHHHHHH
Confidence 4677888899999999888888877665 788999999887654
No 111
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=30.84 E-value=1.9e+02 Score=24.01 Aligned_cols=60 Identities=23% Similarity=0.212 Sum_probs=40.5
Q ss_pred HHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHH---HHHHhcCCcc-----cccccCCCcchHHHHh
Q psy16970 12 RFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVR---IRLNENNLTA-----KRLHRAPELSIRNQRA 73 (257)
Q Consensus 12 r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvr---r~L~~~~l~~-----~~~~~~p~l~~~~~~~ 73 (257)
.-+++.+=....+|+.||..+|.... ..|.+||+ +||-+.|+-. ++-...|+++...-++
T Consensus 9 ~eVM~ilW~~~~~t~~eI~~~l~~~~--ews~sTV~TLl~RL~KKg~l~~~kdgr~~~y~pL~~~~~~~~ 76 (123)
T COG3682 9 WEVMEILWSRGPATVREIIEELPADR--EWSYSTVKTLLNRLVKKGLLTRKKDGRAFRYSPLLTRDQYVA 76 (123)
T ss_pred HHHHHHHHHcCCccHHHHHHHHhhcc--cccHHHHHHHHHHHHhccchhhhhcCCeeeeecccCHHHHHH
Confidence 34555555556799999999999864 67777777 5666677543 2334468888765444
No 112
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=30.58 E-value=1.1e+02 Score=27.83 Aligned_cols=43 Identities=21% Similarity=0.226 Sum_probs=36.7
Q ss_pred ccCCchhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 4 ASGASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 4 ~~~~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
++.+..+++.|+...++..-.|+.|+.++| .+|..+||+.|..
T Consensus 6 ~~~~~~tr~~il~lL~~~g~~sa~elA~~L------gis~~avR~HL~~ 48 (218)
T COG2345 6 ADPSGSTRERILELLKKSGPVSADELAEEL------GISPMAVRRHLDD 48 (218)
T ss_pred cCCCccHHHHHHHHHhccCCccHHHHHHHh------CCCHHHHHHHHHH
Confidence 445667888999999988889999999998 4899999998875
No 113
>PRK12297 obgE GTPase CgtA; Reviewed
Probab=29.99 E-value=97 Score=30.55 Aligned_cols=63 Identities=21% Similarity=0.380 Sum_probs=39.4
Q ss_pred cccccccccEEEE-eCceEEecCeeccCCCCceEEEecCCCCCCCCCceecCCCCCCCcCccccCceEEEEcCCCceeec
Q psy16970 139 GVHGVSSDPIVIV-DAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFE 217 (257)
Q Consensus 139 ~~H~v~sg~V~iv-D~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~G~~vpde~g~~~~L~~Y~~~~i~l~LP~~~ti~d 217 (257)
+-.|..+|.|+++ |...-.+.+|.|. -+|-+..|. .|.......-+|+|++|++|-|..+.|
T Consensus 35 gG~GG~GG~v~~~~~~~~~tl~~~~~~-----~~~~a~~G~------------~g~~~~~~G~~g~d~~i~vP~Gt~v~~ 97 (424)
T PRK12297 35 GGDGGKGGSVIFVADEGLRTLLDFRYK-----RHFKAENGE------------NGMGKNMHGRNGEDLIIKVPVGTVVKD 97 (424)
T ss_pred CCCCCCCCEEEEEECCCcChhhhhcCc-----cEEEcCCCC------------CCCCCCCCCCCCCeeEEecCCCCEEEE
Confidence 3466677778877 5555566777774 233333321 111122334578999999999999988
Q ss_pred c
Q psy16970 218 I 218 (257)
Q Consensus 218 i 218 (257)
.
T Consensus 98 ~ 98 (424)
T PRK12297 98 A 98 (424)
T ss_pred C
Confidence 4
No 114
>PHA00738 putative HTH transcription regulator
Probab=29.72 E-value=1.2e+02 Score=24.66 Aligned_cols=46 Identities=26% Similarity=0.225 Sum_probs=35.3
Q ss_pred CchhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHH---HhcCCccc
Q psy16970 7 ASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRL---NENNLTAK 58 (257)
Q Consensus 7 ~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L---~~~~l~~~ 58 (257)
+...+|.|+..+...+..++.+|...+ .+|..||.+-| .++||-..
T Consensus 10 ~dptRr~IL~lL~~~e~~~V~eLae~l------~lSQptVS~HLKvLreAGLV~s 58 (108)
T PHA00738 10 AKILRRKILELIAENYILSASLISHTL------LLSYTTVLRHLKILNEQGYIEL 58 (108)
T ss_pred CCHHHHHHHHHHHHcCCccHHHHHHhh------CCCHHHHHHHHHHHHHCCceEE
Confidence 356788999999887778888888766 58999999665 56776643
No 115
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=29.68 E-value=93 Score=27.22 Aligned_cols=41 Identities=10% Similarity=0.058 Sum_probs=33.4
Q ss_pred CchhhHHHHHHHhhC-----cccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 7 ASMNDRFIVSQVLRN-----CFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 7 ~~~~~r~i~r~v~~~-----~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
|+++.+.|..+.... ..+|+.||+.+| .||++|+...|+++
T Consensus 157 TdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~l------GISkst~~ehLRrA 202 (215)
T COG3413 157 TDRQLEVLRLAYKMGYFDYPRRVSLKDLAKEL------GISKSTLSEHLRRA 202 (215)
T ss_pred CHHHHHHHHHHHHcCCCCCCccCCHHHHHHHh------CCCHHHHHHHHHHH
Confidence 677777787777665 568999999987 58999999999765
No 116
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.65 E-value=2.2e+02 Score=23.96 Aligned_cols=59 Identities=19% Similarity=0.107 Sum_probs=37.2
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcC---C--ccc-ccccCCCcchHHHHhhhh
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENN---L--TAK-RLHRAPELSIRNQRARSR 76 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~---l--~~~-~~~~~p~l~~~~~~~r~~ 76 (257)
+++++-.+.. --.|..+++..+ .+|..||++-+++-. + ... +..+...|+..+...=+.
T Consensus 10 R~~~~~~~~~-~G~S~re~Ak~~------gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e 74 (138)
T COG3415 10 RERVVDAVVG-EGLSCREAAKRF------GVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLE 74 (138)
T ss_pred HHHHHHHHHH-cCccHHHHHHHh------CccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHH
Confidence 3334444333 447888888876 488999998877644 3 333 345566777776666555
No 117
>PF13730 HTH_36: Helix-turn-helix domain
Probab=29.53 E-value=78 Score=21.20 Aligned_cols=26 Identities=23% Similarity=0.461 Sum_probs=20.5
Q ss_pred cccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 22 CFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 22 ~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
|+.|-.+|+..+ .+|++||++.+++-
T Consensus 24 ~~pS~~~la~~~------g~s~~Tv~~~i~~L 49 (55)
T PF13730_consen 24 CFPSQETLAKDL------GVSRRTVQRAIKEL 49 (55)
T ss_pred CCcCHHHHHHHH------CcCHHHHHHHHHHH
Confidence 777878887776 57899999988753
No 118
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=29.32 E-value=1.3e+02 Score=24.45 Aligned_cols=45 Identities=13% Similarity=0.047 Sum_probs=33.9
Q ss_pred CchhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHH---HHhcCCcc
Q psy16970 7 ASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIR---LNENNLTA 57 (257)
Q Consensus 7 ~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~---L~~~~l~~ 57 (257)
+.-.++.|+..+......++.||.+.+ .++..||.+. |.++|+-.
T Consensus 14 adptRl~IL~~L~~~~~~~v~ela~~l------~lsqstvS~HL~~L~~AGLV~ 61 (117)
T PRK10141 14 SDETRLGIVLLLRESGELCVCDLCTAL------DQSQPKISRHLALLRESGLLL 61 (117)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHH------CcCHHHHHHHHHHHHHCCceE
Confidence 455678888888776668999998876 4688899865 55688664
No 119
>PRK15482 transcriptional regulator MurR; Provisional
Probab=29.01 E-value=60 Score=29.39 Aligned_cols=47 Identities=9% Similarity=0.065 Sum_probs=36.4
Q ss_pred chhhHHHHHHHhhCcc----cCHHHHHHHHHhccCccccHHHHHHHHHhcCCccccc
Q psy16970 8 SMNDRFIVSQVLRNCF----ATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRL 60 (257)
Q Consensus 8 ~~~~r~i~r~v~~~~~----~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~ 60 (257)
....++|.+.+..||. .|..||+++. .+|..||-|-.++.|+.+..-
T Consensus 15 t~~e~~Ia~yIl~n~~~v~~~si~elA~~~------~vS~aTv~Rf~kkLGf~Gf~e 65 (285)
T PRK15482 15 TENEQKIADFLRANVSELKSVSSRKMAKQL------GISQSSIVKFAQKLGAQGFTE 65 (285)
T ss_pred CHHHHHHHHHHHhCHHHHHhcCHHHHHHHh------CCCHHHHHHHHHHhCCCCHHH
Confidence 3457788888888865 5666666554 689999999999999998753
No 120
>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=28.69 E-value=1.1e+02 Score=20.93 Aligned_cols=40 Identities=15% Similarity=0.211 Sum_probs=25.9
Q ss_pred hHHHHHHHh-hCcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCc
Q psy16970 11 DRFIVSQVL-RNCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLT 56 (257)
Q Consensus 11 ~r~i~r~v~-~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~ 56 (257)
.-.++..+. .+...|..+|...+. ++..||.+.++ +.||-
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~~~------~~~~~vs~~i~~L~~~glv 48 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAERLG------ISKSTVSRIIKKLEEKGLV 48 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHHTT--------HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHccCCCcCHHHHHHHHC------cCHHHHHHHHHHHHHCCCE
Confidence 445666666 788899999999875 57778777665 45655
No 121
>smart00155 PLDc Phospholipase D. Active site motifs. Phosphatidylcholine-hydrolyzing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, aspartic acid, and/or asparagine residues which may contribute to the active site. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not be
Probab=28.54 E-value=65 Score=19.10 Aligned_cols=19 Identities=26% Similarity=0.489 Sum_probs=16.4
Q ss_pred cEEEEeCceEEecCeeccC
Q psy16970 147 PIVIVDAQTLLVPNFSYDG 165 (257)
Q Consensus 147 ~V~ivD~~Tl~i~~FsydG 165 (257)
.++++|++...|++++++.
T Consensus 8 K~~v~D~~~~~iGs~N~~~ 26 (28)
T smart00155 8 KLMIVDDEIAYIGSANLDG 26 (28)
T ss_pred EEEEEcCCEEEEeCccCCC
Confidence 3789999999999998875
No 122
>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=28.42 E-value=1.1e+02 Score=24.33 Aligned_cols=50 Identities=16% Similarity=0.139 Sum_probs=33.1
Q ss_pred CccccCCchhhHHHHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCc
Q psy16970 1 MRIASGASMNDRFIVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLT 56 (257)
Q Consensus 1 ~~~~~~~~~~~r~i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~ 56 (257)
|++...+..--+.+...... ++..|..||.+.+ .+|..++++.|+ +.|+-
T Consensus 2 m~ls~~~~yal~~l~~la~~~~~~~s~~eia~~l------~is~~~v~~~l~~L~~~Gli 55 (130)
T TIGR02944 2 LKISKLTDYATLVLTTLAQNDSQPYSAAEIAEQT------GLNAPTVSKILKQLSLAGIV 55 (130)
T ss_pred CccchHHhHHHHHHHHHHhCCCCCccHHHHHHHH------CcCHHHHHHHHHHHHHCCcE
Confidence 45555555555555555443 4678999999887 578888887654 56655
No 123
>PRK12298 obgE GTPase CgtA; Reviewed
Probab=28.30 E-value=1.1e+02 Score=29.79 Aligned_cols=63 Identities=17% Similarity=0.322 Sum_probs=38.1
Q ss_pred cccccccccEEEE-eCceEEecCeeccCCCCceEEEecCCCCCCCCCceecCCCCCCCcCccccCceEEEEcCCCceeec
Q psy16970 139 GVHGVSSDPIVIV-DAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFE 217 (257)
Q Consensus 139 ~~H~v~sg~V~iv-D~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~G~~vpde~g~~~~L~~Y~~~~i~l~LP~~~ti~d 217 (257)
+-.|..+|.|+++ |.+.--+.+|.|. -+|-+..|. .|.......-+|+|++|++|-|..+.|
T Consensus 36 gg~GG~Gg~v~~~~~~~~~~l~~~~~~-----~~~~a~~G~------------~g~~~~~~g~~g~d~~i~vP~gt~v~~ 98 (390)
T PRK12298 36 GGDGGDGGDVYLEADENLNTLIDYRFE-----RHFRAERGQ------------NGQGRDCTGKRGKDITIKVPVGTRVID 98 (390)
T ss_pred CCCCCCCCEEEEEECCCcChhhhhcCC-----ceEEcCCCC------------CCCCCCCCCCCCCceEEEcCCCCEEEe
Confidence 3566777778877 4444455666663 233333321 111122344579999999999999987
Q ss_pred c
Q psy16970 218 I 218 (257)
Q Consensus 218 i 218 (257)
.
T Consensus 99 ~ 99 (390)
T PRK12298 99 A 99 (390)
T ss_pred C
Confidence 4
No 124
>TIGR02729 Obg_CgtA Obg family GTPase CgtA. This model describes a univeral, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. This GTPase, related to the nucleolar protein Obg, is designated CgtA in bacteria. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure. Recent work done in Vibrio cholerae shows an essential role in the stringent response, in which RelA-dependent ability to synthesize the alarmone ppGpp is required for deletion of this GTPase to be lethal.
Probab=27.74 E-value=1.2e+02 Score=28.66 Aligned_cols=63 Identities=19% Similarity=0.346 Sum_probs=37.5
Q ss_pred ccccccccEEEE-eCceEEecCeeccCCCCceEEEecCCCCCCCCCceecCCCCCCCcCccccCceEEEEcCCCceeecc
Q psy16970 140 VHGVSSDPIVIV-DAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEI 218 (257)
Q Consensus 140 ~H~v~sg~V~iv-D~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~G~~vpde~g~~~~L~~Y~~~~i~l~LP~~~ti~di 218 (257)
-.|..+|.|++. |.+.-.+.+|.|. -+|-+..|. .|.......-+|+|++|++|-|..+.|.
T Consensus 35 g~gg~gg~v~~~~~~~~~~l~~~~~~-----~~~~a~~g~------------~g~~~~~~g~~g~d~~~~vp~gt~v~~~ 97 (329)
T TIGR02729 35 GDGGRGGSVILEADENLNTLLDFRYQ-----RHFKAENGE------------NGMGKNRTGKNGEDLVIKVPVGTVVYDA 97 (329)
T ss_pred CCCCCCCEEEEEECCCcChhhhccCC-----cEEEcCCCC------------CCCCCCCCCCCCCceEEEeCCCCEEEEC
Confidence 456667778877 4444455666553 123233221 1111223445799999999999999885
Q ss_pred C
Q psy16970 219 G 219 (257)
Q Consensus 219 ~ 219 (257)
+
T Consensus 98 ~ 98 (329)
T TIGR02729 98 D 98 (329)
T ss_pred C
Confidence 3
No 125
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=27.59 E-value=85 Score=27.35 Aligned_cols=42 Identities=12% Similarity=0.073 Sum_probs=32.9
Q ss_pred hHHHHHHHhhCc--ccCHHHHHHHHHhccCccccHHHHHHHHHhcCCccc
Q psy16970 11 DRFIVSQVLRNC--FATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAK 58 (257)
Q Consensus 11 ~r~i~r~v~~~~--~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~ 58 (257)
..+|+..+.+.. ++|..|+.+.+ .+|..||||=|...+..++
T Consensus 18 ~~~il~~l~~~~~~~vs~~~L~~~~------~v~~~tirrDl~~l~~~G~ 61 (213)
T PRK05472 18 YYRYLKELKEEGVERVSSKELAEAL------GVDSAQIRKDLSYFGEFGK 61 (213)
T ss_pred HHHHHHHHHHcCCcEEeHHHHHHHh------CcCHHHHHHHHHHHHhcCC
Confidence 345666777776 99999998886 4788999999998877663
No 126
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=27.55 E-value=1.4e+02 Score=25.84 Aligned_cols=45 Identities=11% Similarity=0.144 Sum_probs=32.7
Q ss_pred hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh---cCCcccc
Q psy16970 9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE---NNLTAKR 59 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~---~~l~~~~ 59 (257)
.....|+..+.+++..|..|+.+.+ .+|..|++|.|.+ .|+-.+.
T Consensus 143 ~~~~~IL~~l~~~g~~s~~eia~~l------~is~stv~r~L~~Le~~GlI~r~ 190 (203)
T TIGR01884 143 REELKVLEVLKAEGEKSVKNIAKKL------GKSLSTISRHLRELEKKGLVEQK 190 (203)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHH------CcCHHHHHHHHHHHHHCCCEEEE
Confidence 3445677777776778999999887 4789999988775 4555443
No 127
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=27.31 E-value=1e+02 Score=22.36 Aligned_cols=34 Identities=21% Similarity=0.141 Sum_probs=22.5
Q ss_pred HHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 14 IVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 14 i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
|+.-+.. +...|+.||++.+ .+|..|+|+.|...
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~------gls~~~aR~yL~~L 39 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADAL------GLSIYQARYYLEKL 39 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHH------TS-HHHHHHHHHHH
T ss_pred HHHHHHHcCCCCCHHHHHHHh------CCCHHHHHHHHHHH
Confidence 4444444 5557888999987 47888999887653
No 128
>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=27.05 E-value=1.2e+02 Score=16.68 Aligned_cols=30 Identities=10% Similarity=0.042 Sum_probs=19.1
Q ss_pred HHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHH
Q psy16970 12 RFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIR 49 (257)
Q Consensus 12 r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~ 49 (257)
..|+... .+. .|..++..++ .++..||++.
T Consensus 12 ~~i~~~~-~~~-~s~~~ia~~~------~is~~tv~~~ 41 (42)
T cd00569 12 EEARRLL-AAG-ESVAEIARRL------GVSRSTLYRY 41 (42)
T ss_pred HHHHHHH-HcC-CCHHHHHHHH------CCCHHHHHHh
Confidence 3444443 333 4888888766 4788898875
No 129
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=27.02 E-value=89 Score=26.78 Aligned_cols=47 Identities=13% Similarity=0.092 Sum_probs=29.2
Q ss_pred HHHHHHHhhC---cccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccc
Q psy16970 12 RFIVSQVLRN---CFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKR 59 (257)
Q Consensus 12 r~i~r~v~~~---~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~ 59 (257)
..|...+... .-.|=.+|.+.|...| +.||++||-..-++.|+-...
T Consensus 107 ~~i~~lI~~Ed~~~PlSD~~i~~~L~~~g-i~isRRTVaKYR~~L~Ip~s~ 156 (160)
T PF04552_consen 107 ARIKELIEEEDKKKPLSDQEIAELLKEEG-IKISRRTVAKYREELGIPSSS 156 (160)
T ss_dssp HHHHHHHTTS-TTS---HHHHHHHHTTTT-S---HHHHHHHHHHHT-S-SH
T ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHHHcC-CCccHHHHHHHHHHcCCCChh
Confidence 3555555442 3467789999999877 999999999998888887643
No 130
>PF12561 TagA: ToxR activated gene A lipoprotein; InterPro: IPR022218 This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found in association with PF10462 from PFAM. There is a conserved GAG sequence motif. This family is a bacterial lipoprotein.
Probab=26.53 E-value=1.4e+02 Score=25.18 Aligned_cols=62 Identities=11% Similarity=0.172 Sum_probs=39.2
Q ss_pred EEEeCceEEecCeec-cCCCCceEEEecCCCCCCCCCceecCCCCCCCcCccccCceEEEEcCCC-----ceeeccCeEE
Q psy16970 149 VIVDAQTLLVPNFSY-DGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGE-----LTVFEIGHFG 222 (257)
Q Consensus 149 ~ivD~~Tl~i~~Fsy-dG~gPd~yfw~g~~~~p~~~G~~vpde~g~~~~L~~Y~~~~i~l~LP~~-----~ti~di~w~S 222 (257)
+-+|....+|-.|+| ...|..+-|.+.....- .+ .=.|++|....-+. -.+.|+.|||
T Consensus 34 m~v~~~~~~iCrFtf~~~ng~~~~fvG~V~~~~----~~------------C~~g~di~~~~ng~~~~~~S~~ndye~LS 97 (135)
T PF12561_consen 34 MRVNGEQEYICRFTFTAANGDSANFVGYVDTSN----YR------------CEGGSDIYWRINGSREPMVSALNDYEWLS 97 (135)
T ss_pred hhcCCcccceeEEEeecCCCCEEEEEEeEcCCC----Ce------------EcCCCcEEEEecCCCccccccccccEEEe
Confidence 556788889999999 66777677766654110 11 01234444444222 3678999999
Q ss_pred Eecc
Q psy16970 223 VWCE 226 (257)
Q Consensus 223 Vwc~ 226 (257)
+|-.
T Consensus 98 ~~g~ 101 (135)
T PF12561_consen 98 LYGP 101 (135)
T ss_pred ccCC
Confidence 9976
No 131
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=26.47 E-value=95 Score=28.05 Aligned_cols=24 Identities=25% Similarity=0.253 Sum_probs=18.5
Q ss_pred cCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 24 ATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 24 ~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
.|.+||++++ .||..||+|.|+..
T Consensus 2 ~Ti~dIA~~a------gVS~~TVSrvLn~~ 25 (341)
T PRK10703 2 ATIKDVAKRA------GVSTTTVSHVINKT 25 (341)
T ss_pred CCHHHHHHHh------CCCHHHHHHHHcCC
Confidence 3677887776 58899999999754
No 132
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=26.31 E-value=1.1e+02 Score=23.54 Aligned_cols=37 Identities=24% Similarity=0.207 Sum_probs=24.6
Q ss_pred HHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 12 RFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 12 r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
+.+...=..+|..|..|+.+.+.. ++|+++|..+|++
T Consensus 43 ~~~a~lRl~~Pd~SL~EL~~~~~~----~iSKSgvnhrlrK 79 (85)
T PF02650_consen 43 REFAELRLENPDASLKELGELLEP----PISKSGVNHRLRK 79 (85)
T ss_dssp HHHHHHHHH-TTS-HHHHHHTT------T--HHHHHHHHHH
T ss_pred HHHHHHHHHCccccHHHHHHHHcC----cCcHHHHHHHHHH
Confidence 344444577899999999998875 8999999988875
No 133
>PRK12299 obgE GTPase CgtA; Reviewed
Probab=26.20 E-value=1.2e+02 Score=28.65 Aligned_cols=64 Identities=20% Similarity=0.367 Sum_probs=38.4
Q ss_pred cccccccccEEEE-eCceEEecCeeccCCCCceEEEecCCCCCCCCCceecCCCCCCCcCccccCceEEEEcCCCceeec
Q psy16970 139 GVHGVSSDPIVIV-DAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFE 217 (257)
Q Consensus 139 ~~H~v~sg~V~iv-D~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~G~~vpde~g~~~~L~~Y~~~~i~l~LP~~~ti~d 217 (257)
+-.|..+|.|++. |.+.-.+.+|.|. -+|=+..|. .|.......-+|+|++|++|-|..+.|
T Consensus 35 gg~gg~gg~v~~~~~~~~~~l~~~~~~-----~~~~a~~g~------------~g~~~~~~g~~g~d~~~~vp~gt~v~~ 97 (335)
T PRK12299 35 GGDGGRGGSVILEADENLNTLIDFRYK-----RHFKAENGE------------NGMGRNRTGKSGKDLVLKVPVGTQIYD 97 (335)
T ss_pred CCCCCCCCEEEEEECCCcChhhhhcCc-----cEEECCCCC------------CCCCCCCCCCCCCceEEEeCCCCEEEE
Confidence 3466667778877 4444456666663 233233221 111122334578999999999999987
Q ss_pred cC
Q psy16970 218 IG 219 (257)
Q Consensus 218 i~ 219 (257)
..
T Consensus 98 ~~ 99 (335)
T PRK12299 98 AD 99 (335)
T ss_pred CC
Confidence 53
No 134
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=25.40 E-value=71 Score=28.92 Aligned_cols=46 Identities=11% Similarity=0.080 Sum_probs=35.9
Q ss_pred hhhHHHHHHHhhCcc----cCHHHHHHHHHhccCccccHHHHHHHHHhcCCccccc
Q psy16970 9 MNDRFIVSQVLRNCF----ATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRL 60 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~----~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~ 60 (257)
..++.|.+.+.+||. .|..+|+++. .+|..||-|-.++.|+.+..-
T Consensus 28 ~~e~~Ia~yil~~~~~v~~~si~~lA~~~------~vS~aTi~Rf~kkLGf~gf~e 77 (292)
T PRK11337 28 PLESRVVEWLLKPGDLSEATALKDIAEAL------AVSEAMIVKVAKKLGFSGFRN 77 (292)
T ss_pred HHHHHHHHHHHhCHHHHHhcCHHHHHHHh------CCChHHHHHHHHHcCCCCHHH
Confidence 456788888888865 5666666654 699999999999999998653
No 135
>PRK12296 obgE GTPase CgtA; Reviewed
Probab=25.31 E-value=1.3e+02 Score=30.58 Aligned_cols=63 Identities=21% Similarity=0.318 Sum_probs=39.5
Q ss_pred cccccccccEEEE-eCceEEecCeeccCCCCceEEEecCCCCCCCCCceecCCCCCCCcCccccCceEEEEcCCCceeec
Q psy16970 139 GVHGVSSDPIVIV-DAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFE 217 (257)
Q Consensus 139 ~~H~v~sg~V~iv-D~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~G~~vpde~g~~~~L~~Y~~~~i~l~LP~~~ti~d 217 (257)
+-.|..+|.|+++ |.+.-.+.+|.|.. +|-+..|.. |.......-+|+|++|++|-|..+.|
T Consensus 37 GG~GG~GG~v~~~~~~~~~tl~~~~~~~-----~~~a~~G~~------------G~~~~~~G~~g~d~~i~VP~Gt~v~~ 99 (500)
T PRK12296 37 GGNGGRGGSVVLVVDPQVTTLLDFHFRP-----HRKATNGKP------------GMGDNRDGAAGEDLVLPVPDGTVVLD 99 (500)
T ss_pred CCCCCCCCEEEEEECCCcCchHHhccCc-----eEECCCCCC------------CCCCCCCCCCCCceEEecCCCcEEEc
Confidence 3466666778776 66666677888752 333333211 11112234568999999999999976
Q ss_pred c
Q psy16970 218 I 218 (257)
Q Consensus 218 i 218 (257)
-
T Consensus 100 ~ 100 (500)
T PRK12296 100 E 100 (500)
T ss_pred C
Confidence 3
No 136
>PRK01844 hypothetical protein; Provisional
Probab=25.13 E-value=2.1e+02 Score=21.67 Aligned_cols=43 Identities=2% Similarity=0.087 Sum_probs=35.2
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
.++.+..+.++||-++-.-|+.-....| ...|+..|++..+..
T Consensus 25 ark~~~k~lk~NPpine~mir~Mm~QMG-qkPSekki~Q~m~~m 67 (72)
T PRK01844 25 ARKYMMNYLQKNPPINEQMLKMMMMQMG-QKPSQKKINQMMSAM 67 (72)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHhC-CCccHHHHHHHHHHH
Confidence 4678888999999999888888777665 788999998877654
No 137
>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=25.05 E-value=1.7e+02 Score=21.23 Aligned_cols=29 Identities=17% Similarity=0.152 Sum_probs=22.4
Q ss_pred HhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 18 VLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 18 v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
...+...+..||+.+| .||..||++-=.+
T Consensus 17 ~~~~g~i~lkdIA~~L------gvs~~tIr~WK~~ 45 (60)
T PF10668_consen 17 KESNGKIKLKDIAEKL------GVSESTIRKWKSR 45 (60)
T ss_pred HHhCCCccHHHHHHHH------CCCHHHHHHHhhh
Confidence 3456788999999998 4899999975443
No 138
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=25.01 E-value=1.2e+02 Score=29.54 Aligned_cols=39 Identities=18% Similarity=0.339 Sum_probs=31.2
Q ss_pred hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
+....+......++..|..++++.| .||.+||++.+...
T Consensus 5 ~~~~~l~~l~~~~~~~~~~~la~~l------~vS~Rti~~~i~~I 43 (491)
T COG3711 5 RREQLLLLLLLKNPLLTIKELAEQL------GVSRRTIRYDIKKI 43 (491)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHh------CccHHHHHHHHHHH
Confidence 3445566677889999999999987 58999999987643
No 139
>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=25.00 E-value=1.2e+02 Score=20.33 Aligned_cols=40 Identities=20% Similarity=0.226 Sum_probs=26.8
Q ss_pred HHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCccc
Q psy16970 13 FIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLTAK 58 (257)
Q Consensus 13 ~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~~~ 58 (257)
.++..+.+++..|..+|...+. ++.+|+.+.++ +.||-.+
T Consensus 7 ~iL~~l~~~~~~~~~~la~~~~------~~~~~~t~~i~~L~~~g~I~r 49 (59)
T PF01047_consen 7 RILRILYENGGITQSELAEKLG------ISRSTVTRIIKRLEKKGLIER 49 (59)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHT------S-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHcCCCCHHHHHHHHC------CChhHHHHHHHHHHHCCCEEe
Confidence 4556666677799999999874 57777776554 4555443
No 140
>PF13358 DDE_3: DDE superfamily endonuclease
Probab=24.44 E-value=42 Score=25.89 Aligned_cols=22 Identities=41% Similarity=0.508 Sum_probs=17.6
Q ss_pred cccccCCCccccc----eeEeCCCCC
Q psy16970 106 NVLFSDEPRVNFG----DVRIPKGFD 127 (257)
Q Consensus 106 ~vvwsdEsk~~fG----sVwrp~ge~ 127 (257)
+++|.||+.++.. ..|.+.|+.
T Consensus 1 ~vv~~DE~~~~~~~~~~~~w~~~g~~ 26 (146)
T PF13358_consen 1 RVVFSDESGFNLRPRRGRGWSPKGER 26 (146)
T ss_pred CEEEEeCCCCccCCCCCceEeeCCce
Confidence 4799999999863 388888865
No 141
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=24.29 E-value=1.5e+02 Score=19.63 Aligned_cols=36 Identities=25% Similarity=0.163 Sum_probs=21.5
Q ss_pred hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
.|.++...-- -..|..||.+.+ .+|.+||++.+++.
T Consensus 15 ~r~i~~l~~~-~g~s~~eIa~~l------~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 15 QREIFLLRYF-QGMSYAEIAEIL------GISESTVKRRLRRA 50 (54)
T ss_dssp HHHHHHHHHT-S---HHHHHHHC------TS-HHHHHHHHHHH
T ss_pred HHHHHHHHHH-HCcCHHHHHHHH------CcCHHHHHHHHHHH
Confidence 3444444322 347788888887 58999999998763
No 142
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=24.26 E-value=1.7e+02 Score=28.06 Aligned_cols=55 Identities=24% Similarity=0.193 Sum_probs=38.9
Q ss_pred HHHHH-hhCcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCcccccccCCCcchH
Q psy16970 14 IVSQV-LRNCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLTAKRLHRAPELSIR 69 (257)
Q Consensus 14 i~r~v-~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~~~~~~~~p~l~~~ 69 (257)
|++.. ..+.-..|+.|+.||+.. |..+++++||-.|+ +.||..|..-....||.+
T Consensus 11 Il~il~esd~plgak~Ia~el~kR-Gy~igeRavRYhlk~lderglt~kvgyagr~iTe~ 69 (325)
T COG1693 11 ILRILAESDEPLGAKIIALELRKR-GYNIGERAVRYHLKKLDERGLTRKVGYAGREITEK 69 (325)
T ss_pred HHHHHHhcCCccchHHHHHHHHhc-ccchhHHHHHHHHHHHhhccchhhccccceeehHh
Confidence 34443 334468999999999987 59999999996554 567776655555556553
No 143
>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=24.23 E-value=1.7e+02 Score=20.72 Aligned_cols=39 Identities=21% Similarity=0.179 Sum_probs=26.0
Q ss_pred HHHHHhhCcccCHHHHHHHHHhccCccccHHHHH---HHHHhcCCccc
Q psy16970 14 IVSQVLRNCFATALEVRQELQDVRKVHLNEGTVR---IRLNENNLTAK 58 (257)
Q Consensus 14 i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvr---r~L~~~~l~~~ 58 (257)
|......+..++..+|++.|+ +|..||. ++|.+.||--+
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~------vs~~tvt~ml~~L~~~GlV~~ 54 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLG------VSPPTVTEMLKRLAEKGLVEY 54 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHT------S-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHcCCCCccHHHHHHHHC------CChHHHHHHHHHHHHCCCEEe
Confidence 444445678899999999985 5566655 56666776543
No 144
>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=24.18 E-value=2.3e+02 Score=19.11 Aligned_cols=31 Identities=29% Similarity=0.247 Sum_probs=22.1
Q ss_pred CcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCcc
Q psy16970 21 NCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLTA 57 (257)
Q Consensus 21 ~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~~ 57 (257)
++..|..||.+.+ .+|..||.+.|+ +.|+-.
T Consensus 23 ~~~~s~~ela~~~------g~s~~tv~r~l~~L~~~g~i~ 56 (67)
T cd00092 23 QLPLTRQEIADYL------GLTRETVSRTLKELEEEGLIS 56 (67)
T ss_pred cCCcCHHHHHHHH------CCCHHHHHHHHHHHHHCCCEE
Confidence 3567888888876 478999988665 455544
No 145
>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=23.81 E-value=1.7e+02 Score=22.45 Aligned_cols=42 Identities=12% Similarity=0.021 Sum_probs=29.0
Q ss_pred CCchhhHHHHHHHh-------hCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 6 GASMNDRFIVSQVL-------RNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 6 ~~~~~~r~i~r~v~-------~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
-+.+.-+.|+.... .....|..||+..+ .+++.||.|.|++.
T Consensus 23 l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~------g~sr~tVsr~L~~L 71 (95)
T TIGR01610 23 LSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELT------GLSRTHVSDAIKSL 71 (95)
T ss_pred CCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHH------CcCHHHHHHHHHHH
Confidence 35566666666664 45678888877765 57889999877654
No 146
>cd03490 Topoisomer_IB_N_1 Topoisomer_IB_N_1: A subgroup of the N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB. Topo IB proteins include the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanoso
Probab=23.67 E-value=2.7e+02 Score=25.38 Aligned_cols=74 Identities=18% Similarity=0.278 Sum_probs=46.5
Q ss_pred EEEEeCceEEecCeeccCCCCceEEEecCCCCCCCCCceecCCCCCCCcC-ccccCceEEEEc---------C---CCce
Q psy16970 148 IVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPL-RRYNRKTIVLTL---------P---GELT 214 (257)
Q Consensus 148 V~ivD~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~G~~vpde~g~~~~L-~~Y~~~~i~l~L---------P---~~~t 214 (257)
.-+||...-+|+||.-.. |.+| -|.|.-|.. | .| ++-.=+||+|.+ | .|+.
T Consensus 124 ~~~vDG~kekVgNfriEP--PgLF--rGRG~HPK~-G-----------~lK~RV~PedVtINigkda~vP~~p~~~~GH~ 187 (217)
T cd03490 124 YALVDWIREKVSSNKLEP--PGLF--KGRGEHPKQ-G-----------LLKSRIFPEDVILNISKDAPVPKVTNFMEGHS 187 (217)
T ss_pred EEEECCEEEeeCCcccCC--Cccc--ccCCCCCCC-C-----------ccccccChhheEEecCCCCCCCcCCCCCCCCc
Confidence 447899999999999864 3333 344544442 2 22 112225555533 2 6777
Q ss_pred eec------cCeEEEeccccccCeeeEEc
Q psy16970 215 VFE------IGHFGVWCEAFTVDFGHIQI 237 (257)
Q Consensus 215 i~d------i~w~SVwc~~~~~nFG~V~i 237 (257)
|.+ ++||+-|-+.-+-+|=-|.|
T Consensus 188 WkeV~HDntVtWLA~W~enIn~~~KYV~L 216 (217)
T cd03490 188 WKDIYHDNSVTWLAYYKDSINDQFKYMFL 216 (217)
T ss_pred cceeecCCCceEEEEeecCCCCceeEEEe
Confidence 866 68999998887766666654
No 147
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=23.55 E-value=1.4e+02 Score=18.61 Aligned_cols=27 Identities=30% Similarity=0.336 Sum_probs=19.1
Q ss_pred CHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970 25 TALEVRQELQDVRKVHLNEGTVRIRLNENNLTA 57 (257)
Q Consensus 25 ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~ 57 (257)
|..|+++.| .+|.+|+++...+-.+.+
T Consensus 2 s~~e~a~~l------gvs~~tl~~~~~~g~~~~ 28 (49)
T cd04762 2 TTKEAAELL------GVSPSTLRRWVKEGKLKA 28 (49)
T ss_pred CHHHHHHHH------CcCHHHHHHHHHcCCCCc
Confidence 455666655 589999998887755543
No 148
>smart00262 GEL Gelsolin homology domain. Gelsolin/severin/villin homology domain. Calcium-binding and actin-binding. Both intra- and extracellular domains.
Probab=23.55 E-value=80 Score=23.30 Aligned_cols=27 Identities=22% Similarity=0.471 Sum_probs=20.3
Q ss_pred ccccccEEEEeCceEEecCeeccCCCCceEEEecCCCCCC
Q psy16970 142 GVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPS 181 (257)
Q Consensus 142 ~v~sg~V~ivD~~Tl~i~~FsydG~gPd~yfw~g~~~~p~ 181 (257)
...++.+||+|. +.+.|.|.|....+.
T Consensus 22 ~L~s~d~fild~-------------~~~iyvW~G~~as~~ 48 (90)
T smart00262 22 SLNSGDCYILDT-------------GSEIYVWVGKKSSQD 48 (90)
T ss_pred HCCCCCEEEEEC-------------CCEEEEEECCCCCHH
Confidence 345678999885 347999999987655
No 149
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=23.41 E-value=1.2e+02 Score=27.27 Aligned_cols=27 Identities=15% Similarity=0.052 Sum_probs=21.3
Q ss_pred cccCHHHHHHHHHhccCccccHHHHHHHHHhcC
Q psy16970 22 CFATALEVRQELQDVRKVHLNEGTVRIRLNENN 54 (257)
Q Consensus 22 ~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~ 54 (257)
...|-+||++.. .||..||+|.|+..+
T Consensus 4 ~~~ti~dIA~~a------gVS~~TVSrvLn~~~ 30 (331)
T PRK14987 4 KRPVLQDVADRV------GVTKMTVSRFLRNPE 30 (331)
T ss_pred CCCcHHHHHHHh------CCCHHHhhhhhCCCC
Confidence 357888888876 589999999997654
No 150
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=23.40 E-value=1.6e+02 Score=21.25 Aligned_cols=45 Identities=11% Similarity=0.020 Sum_probs=35.2
Q ss_pred hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
-.++.|.+++..+.-.|..+|.+.|.--.+---+..++++.|.+.
T Consensus 9 Vtd~~I~~ai~~~g~~s~~~l~~~~~~g~~CG~C~~~i~~il~~~ 53 (64)
T PRK10509 9 VSDKKIRQAVRQFHPQSFQQLRKFVPVGNQCGKCIRAAREVMQDE 53 (64)
T ss_pred CCHHHHHHHHHHcCCCCHHHHHHhcCCCCCccchHHHHHHHHHHH
Confidence 357788888887777788999998887666677788888888664
No 151
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=23.32 E-value=1.4e+02 Score=24.15 Aligned_cols=53 Identities=11% Similarity=0.159 Sum_probs=34.9
Q ss_pred HHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHH---HhcCCcccccccCCCcchHHH
Q psy16970 13 FIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRL---NENNLTAKRLHRAPELSIRNQ 71 (257)
Q Consensus 13 ~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L---~~~~l~~~~~~~~p~l~~~~~ 71 (257)
.|.+....+...+..+|...|. +|..||.+.| .+.|+--+...+.-.||+.=+
T Consensus 12 ~I~~l~~~~~~~~~~ela~~l~------vs~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~ 67 (142)
T PRK03902 12 QIYLLIEEKGYARVSDIAEALS------VHPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGK 67 (142)
T ss_pred HHHHHHhcCCCcCHHHHHHHhC------CChhHHHHHHHHHHHCCCEEEecCceEEECHHHH
Confidence 3444556678889999998874 5677777655 667776554445556666543
No 152
>PRK00118 putative DNA-binding protein; Validated
Probab=22.69 E-value=1.9e+02 Score=23.14 Aligned_cols=38 Identities=11% Similarity=0.025 Sum_probs=27.3
Q ss_pred hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
...+.++.... -...|..||++.+ .+|++||++++++.
T Consensus 20 ekqRevl~L~y-~eg~S~~EIAe~l------GIS~~TV~r~L~RA 57 (104)
T PRK00118 20 EKQRNYMELYY-LDDYSLGEIAEEF------NVSRQAVYDNIKRT 57 (104)
T ss_pred HHHHHHHHHHH-HcCCCHHHHHHHH------CcCHHHHHHHHHHH
Confidence 34455554443 3468889999887 58999999999864
No 153
>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=22.22 E-value=1.4e+02 Score=27.81 Aligned_cols=43 Identities=9% Similarity=0.149 Sum_probs=31.8
Q ss_pred hHHHHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHHh---cCCcccc
Q psy16970 11 DRFIVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLNE---NNLTAKR 59 (257)
Q Consensus 11 ~r~i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~---~~l~~~~ 59 (257)
-..|+++... |...+..+++..+ .+|+.+|++++++ .|+-..+
T Consensus 185 v~~IL~~L~~~egrlse~eLAerl------GVSRs~ireAlrkLE~aGvIe~r 231 (251)
T TIGR02787 185 VEHIFEELDGNEGLLVASKIADRV------GITRSVIVNALRKLESAGVIESR 231 (251)
T ss_pred HHHHHHHhccccccccHHHHHHHH------CCCHHHHHHHHHHHHHCCCEEec
Confidence 3567777777 5899999998886 5899999977664 5544333
No 154
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=22.10 E-value=1.2e+02 Score=30.48 Aligned_cols=34 Identities=18% Similarity=0.047 Sum_probs=25.7
Q ss_pred HHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970 13 FIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN 53 (257)
Q Consensus 13 ~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~ 53 (257)
.|+.... +...|+.++++.| .||.+||||-+.+.
T Consensus 8 ~iL~~L~-~~~~t~~~LA~~l------~VS~RTIr~dI~~i 41 (584)
T PRK09863 8 KIVDLLE-QQDRSGGELAQQL------GVSRRTIVRDIAYI 41 (584)
T ss_pred HHHHHHH-cCCCCHHHHHHHh------CCCHHHHHHHHHHH
Confidence 3445544 4568999999987 59999999987743
No 155
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=22.06 E-value=1.1e+02 Score=21.02 Aligned_cols=38 Identities=13% Similarity=0.169 Sum_probs=26.4
Q ss_pred CchhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 7 ASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 7 ~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
|..+.-.|+..+..++ +..+|+.++ .|+.+||+..+..
T Consensus 8 Tl~eK~~iI~~~e~g~--s~~~ia~~f------gv~~sTv~~I~K~ 45 (53)
T PF04218_consen 8 TLEEKLEIIKRLEEGE--SKRDIAREF------GVSRSTVSTILKN 45 (53)
T ss_dssp -HHHHHHHHHHHHCTT---HHHHHHHH------T--CCHHHHHHHC
T ss_pred CHHHHHHHHHHHHcCC--CHHHHHHHh------CCCHHHHHHHHHh
Confidence 5566777888887776 788888887 4788899988764
No 156
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=21.79 E-value=1.9e+02 Score=28.52 Aligned_cols=37 Identities=11% Similarity=0.142 Sum_probs=30.4
Q ss_pred cCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccc
Q psy16970 24 ATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLH 61 (257)
Q Consensus 24 ~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~ 61 (257)
.|=.+|...|+.. |+.|+++||-..-.+.|+-..+.|
T Consensus 392 lSD~~I~~~L~~~-Gi~IaRRTVaKYRe~L~Ip~s~~R 428 (429)
T TIGR02395 392 LSDQKIAELLKEK-GIKIARRTVAKYREELGIPSSSKR 428 (429)
T ss_pred CCHHHHHHHHHhc-CCCeehHHHHHHHHHcCCCccccC
Confidence 6778999999987 599999999998888888764443
No 157
>cd08685 C2_RGS-like C2 domain of the Regulator Of G-Protein Signaling (RGS) family. This CD contains members of the regulator of G-protein signaling (RGS) family. RGS is a GTPase activating protein which inhibits G-protein mediated signal transduction. The protein is largely cytosolic, but G-protein activation leads to translocation of this protein to the plasma membrane. A nuclear form of this protein has also been described, but its sequence has not been identified. There are multiple alternatively spliced transcript variants in this family with some members having additional domains (ex. PDZ and RGS) downstream of the C2 domain. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind pho
Probab=21.48 E-value=2.8e+02 Score=21.82 Aligned_cols=87 Identities=8% Similarity=0.050 Sum_probs=46.1
Q ss_pred cEEEEeCceEEecCeeccCCCCceEEEecCCCCCCCCCceecCCCCCCCcCccccCceEEEEcCCCceeeccCeEEEecc
Q psy16970 147 PIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCE 226 (257)
Q Consensus 147 ~V~ivD~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~G~~vpde~g~~~~L~~Y~~~~i~l~LP~~~ti~di~w~SVwc~ 226 (257)
.|.|+.++-|.- .|+..+|.|.=+.-.+.+.....+ ... -...-+.+.=||++.+.++.+. ..+.-.|+||..
T Consensus 15 ~V~Vi~ar~L~~----~~~g~~dpYVkv~l~p~~~~~~~~-kT~-v~~~t~~P~~nE~F~f~v~~~~-~~~~l~v~V~~~ 87 (119)
T cd08685 15 TLHVLEAKGLRS----TNSGTCNSYVKISLSPDKEVRFRQ-KTS-TVPDSANPLFHETFSFDVNERD-YQKRLLVTVWNK 87 (119)
T ss_pred EEEEEEEECCCC----CCCCCCCeeEEEEEEeCCCCcceE-eCc-cccCCCCCccccEEEEEcChHH-hCCEEEEEEECC
Confidence 366665554432 233456777766654433221110 000 0001122334799999998654 222235999997
Q ss_pred ccc----cCeeeEEcCCC
Q psy16970 227 AFT----VDFGHIQIPAN 240 (257)
Q Consensus 227 ~~~----~nFG~V~ip~~ 240 (257)
... .-.|.+.||-.
T Consensus 88 ~~~~~~~~~lG~~~i~l~ 105 (119)
T cd08685 88 LSKSRDSGLLGCMSFGVK 105 (119)
T ss_pred CCCcCCCEEEEEEEecHH
Confidence 542 23899999863
No 158
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=21.41 E-value=1.1e+02 Score=20.16 Aligned_cols=22 Identities=27% Similarity=0.347 Sum_probs=17.2
Q ss_pred CHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 25 TALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 25 ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
|..++.+.+ .+|..||++.|+.
T Consensus 22 s~~~la~~~------~vs~~tv~~~l~~ 43 (60)
T smart00345 22 SERELAAQL------GVSRTTVREALSR 43 (60)
T ss_pred CHHHHHHHH------CCCHHHHHHHHHH
Confidence 777877776 5799999987764
No 159
>PF07508 Recombinase: Recombinase; InterPro: IPR011109 This domain is usually found associated with IPR006119 from INTERPRO in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=21.33 E-value=2.2e+02 Score=21.10 Aligned_cols=54 Identities=20% Similarity=0.115 Sum_probs=37.2
Q ss_pred hhHHHHHHHhhCcccCHHHHHHHHHhcc-----CccccHHHHHHHHHhcCCcccccccCCC
Q psy16970 10 NDRFIVSQVLRNCFATALEVRQELQDVR-----KVHLNEGTVRIRLNENNLTAKRLHRAPE 65 (257)
Q Consensus 10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~-----g~~~s~~Tvrr~L~~~~l~~~~~~~~p~ 65 (257)
--+.|...+. -..+..+|.+.|++.+ |..-+.+||++.|..--+.|.....+..
T Consensus 6 vVr~if~~~~--~g~s~~~I~~~ln~~gi~~~~~~~W~~~~v~~iL~np~y~G~~~~~~~~ 64 (102)
T PF07508_consen 6 VVREIFELYL--EGYSLRQIARELNEKGIPTPRGKKWSKSTVRRILRNPAYAGYRVYNKRE 64 (102)
T ss_pred HHHHHHHHHH--cCCCHHHHHHHHHhcCCccccCCcccHHHHHHHHhhhhccceEEeeecc
Confidence 3456666665 4578889999998865 2234788999999987777755544433
No 160
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=21.10 E-value=1.7e+02 Score=25.96 Aligned_cols=36 Identities=14% Similarity=0.138 Sum_probs=27.8
Q ss_pred hHHHHHHHhhCc-ccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 11 DRFIVSQVLRNC-FATALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 11 ~r~i~r~v~~~~-~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
.++|....+++. ..||.+|..+|. ++..+|-|+|..
T Consensus 6 ~~~i~~~l~~~~~~~~a~~i~k~l~------i~k~~vNr~LY~ 42 (183)
T PHA02701 6 ASLILTLLSSSGDKLPAKRIAKELG------ISKHEANRCLYR 42 (183)
T ss_pred HHHHHHHHHhcCCCCcHHHHHHHhC------ccHHHHHHHHHH
Confidence 356666666665 699999999984 688899998764
No 161
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=20.69 E-value=1.6e+02 Score=26.77 Aligned_cols=25 Identities=24% Similarity=0.185 Sum_probs=18.1
Q ss_pred cCHHHHHHHHHhccCccccHHHHHHHHHhcC
Q psy16970 24 ATALEVRQELQDVRKVHLNEGTVRIRLNENN 54 (257)
Q Consensus 24 ~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~ 54 (257)
.|.+||++.. .||..||.|.|+..+
T Consensus 2 ~ti~dIA~~a------GVS~~TVSrvLn~~~ 26 (343)
T PRK10727 2 ATIKDVARLA------GVSVATVSRVINNSP 26 (343)
T ss_pred CCHHHHHHHh------CCCHHHHHHHhCCCC
Confidence 3667777765 488889999887643
No 162
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=20.67 E-value=2.4e+02 Score=20.12 Aligned_cols=22 Identities=27% Similarity=0.212 Sum_probs=14.6
Q ss_pred CHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970 25 TALEVRQELQDVRKVHLNEGTVRIRLNE 52 (257)
Q Consensus 25 ta~~i~~~l~~~~g~~~s~~Tvrr~L~~ 52 (257)
|..||++.+ .+|..||.|.|+.
T Consensus 2 t~~~iA~~~------gvS~~TVSr~ln~ 23 (70)
T smart00354 2 TIKDVARLA------GVSKATVSRVLNG 23 (70)
T ss_pred CHHHHHHHH------CCCHHHHHHHHCC
Confidence 345555554 4788888888754
No 163
>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=20.44 E-value=1.7e+02 Score=23.06 Aligned_cols=50 Identities=12% Similarity=0.169 Sum_probs=30.8
Q ss_pred CccccCCchhhHHHHHHHhh--CcccCHHHHHHHHHhccCccccHHHHHHHH---HhcCCc
Q psy16970 1 MRIASGASMNDRFIVSQVLR--NCFATALEVRQELQDVRKVHLNEGTVRIRL---NENNLT 56 (257)
Q Consensus 1 ~~~~~~~~~~~r~i~r~v~~--~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L---~~~~l~ 56 (257)
|++...+..--+.+...... .+..|+.+|...+ .++..+|++.| .+.|+-
T Consensus 1 M~ls~~~~~al~~l~~la~~~~~~~~s~~eia~~~------~i~~~~v~~il~~L~~~gli 55 (132)
T TIGR00738 1 MKLTKKTEYALRALLDLALNPDEGPVSVKEIAERQ------GISRSYLEKILRTLRRAGLV 55 (132)
T ss_pred CcCccHHHHHHHHHHHHHhCCCCCcCcHHHHHHHH------CcCHHHHHHHHHHHHHCCcE
Confidence 44444444444445555443 2368999999887 46788888665 456654
Done!