Query psy15969
Match_columns 111
No_of_seqs 157 out of 1168
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 17:40:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15969.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15969hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00046 Homeobox: Homeobox do 99.7 1.3E-17 2.8E-22 98.4 2.8 53 45-97 1-53 (57)
2 KOG0489|consensus 99.7 8.2E-18 1.8E-22 126.8 2.0 64 41-108 156-219 (261)
3 KOG0488|consensus 99.7 2.3E-17 5E-22 127.0 4.5 65 39-107 167-231 (309)
4 KOG0842|consensus 99.7 6.2E-17 1.4E-21 124.0 5.1 65 40-108 149-213 (307)
5 KOG0843|consensus 99.7 3.8E-17 8.2E-22 116.6 3.5 60 43-106 101-160 (197)
6 TIGR01565 homeo_ZF_HD homeobox 99.6 3.9E-16 8.5E-21 93.3 5.8 52 45-96 2-57 (58)
7 KOG0484|consensus 99.6 2E-17 4.4E-22 108.9 0.2 63 41-107 14-76 (125)
8 KOG0850|consensus 99.6 1.5E-16 3.3E-21 117.1 3.5 64 40-107 118-181 (245)
9 KOG2251|consensus 99.6 8.8E-16 1.9E-20 112.5 4.5 65 39-107 32-96 (228)
10 smart00389 HOX Homeodomain. DN 99.6 2.1E-15 4.5E-20 88.3 4.6 52 46-97 2-53 (56)
11 KOG0485|consensus 99.6 6.6E-16 1.4E-20 113.2 2.6 65 40-108 100-164 (268)
12 cd00086 homeodomain Homeodomai 99.6 2.8E-15 6.2E-20 88.2 4.3 52 46-97 2-53 (59)
13 KOG0487|consensus 99.6 2.1E-15 4.6E-20 115.6 3.7 63 41-107 232-294 (308)
14 KOG0492|consensus 99.5 7E-15 1.5E-19 107.2 3.5 61 42-106 142-202 (246)
15 KOG0494|consensus 99.5 1.3E-14 2.8E-19 108.8 3.2 60 45-108 142-201 (332)
16 COG5576 Homeodomain-containing 99.5 2.6E-14 5.7E-19 100.7 4.2 62 37-98 44-105 (156)
17 KOG4577|consensus 99.5 1.6E-14 3.4E-19 109.9 1.9 79 24-106 142-225 (383)
18 KOG3802|consensus 99.4 1.3E-13 2.7E-18 108.3 5.9 62 43-108 293-354 (398)
19 KOG0848|consensus 99.4 3E-14 6.5E-19 107.1 1.1 57 46-106 201-257 (317)
20 KOG0493|consensus 99.4 1.1E-13 2.4E-18 104.1 4.1 58 44-105 246-303 (342)
21 KOG0491|consensus 99.4 3.8E-14 8.3E-19 100.1 -0.9 62 44-105 100-161 (194)
22 KOG0483|consensus 99.4 4.1E-13 8.8E-18 97.8 3.9 59 44-106 50-108 (198)
23 KOG0844|consensus 99.3 2E-13 4.3E-18 104.6 1.2 62 41-106 178-239 (408)
24 KOG2252|consensus 99.3 6E-12 1.3E-16 102.1 5.7 82 26-108 403-484 (558)
25 KOG0486|consensus 99.3 2.8E-12 6E-17 98.3 3.1 62 43-108 111-172 (351)
26 KOG0847|consensus 99.2 3.3E-12 7.2E-17 94.1 2.2 66 39-108 162-227 (288)
27 KOG0490|consensus 99.2 1.6E-11 3.4E-16 89.5 2.4 63 41-107 57-119 (235)
28 KOG0849|consensus 99.1 5.8E-11 1.3E-15 93.1 4.2 73 31-107 163-235 (354)
29 KOG0775|consensus 99.0 2.7E-10 5.9E-15 86.1 4.6 56 52-107 184-239 (304)
30 KOG1168|consensus 99.0 2E-10 4.3E-15 87.7 2.4 65 38-106 303-367 (385)
31 PF05920 Homeobox_KN: Homeobox 98.7 2E-09 4.4E-14 59.8 0.0 33 65-97 7-39 (40)
32 KOG0774|consensus 98.6 4.2E-08 9.2E-13 74.1 3.6 60 44-107 188-250 (334)
33 KOG0490|consensus 98.1 1.7E-06 3.7E-11 62.9 2.9 58 40-97 149-206 (235)
34 PF11569 Homez: Homeodomain le 97.4 7.6E-05 1.7E-09 44.2 1.3 42 56-97 10-51 (56)
35 KOG1146|consensus 97.2 0.00018 3.9E-09 64.1 2.4 55 43-97 902-956 (1406)
36 KOG0773|consensus 97.2 0.00042 9.2E-09 53.8 4.1 55 44-98 239-296 (342)
37 KOG3623|consensus 95.4 0.013 2.7E-07 50.4 2.9 42 56-97 568-609 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 95.3 0.034 7.4E-07 32.2 3.7 46 45-95 1-46 (53)
39 PF04967 HTH_10: HTH DNA bindi 89.5 0.47 1E-05 27.6 2.8 40 51-90 1-42 (53)
40 PF01527 HTH_Tnp_1: Transposas 85.3 0.38 8.2E-06 28.9 0.7 44 47-94 3-46 (76)
41 cd00569 HTH_Hin_like Helix-tur 81.0 3.9 8.5E-05 19.4 3.5 38 50-92 5-42 (42)
42 PF04545 Sigma70_r4: Sigma-70, 79.0 2.1 4.6E-05 23.7 2.3 40 50-94 4-43 (50)
43 PF08281 Sigma70_r4_2: Sigma-7 78.2 2 4.4E-05 24.0 2.0 41 51-96 11-51 (54)
44 PF10668 Phage_terminase: Phag 75.9 1.1 2.5E-05 26.7 0.5 21 73-93 24-44 (60)
45 COG3413 Predicted DNA binding 74.2 3.4 7.5E-05 29.9 2.8 40 50-89 155-196 (215)
46 cd06171 Sigma70_r4 Sigma70, re 73.5 3.4 7.3E-05 21.9 2.1 43 50-97 10-52 (55)
47 PRK09413 IS2 repressor TnpA; R 69.1 12 0.00025 24.8 4.3 43 48-94 10-52 (121)
48 PF13936 HTH_38: Helix-turn-he 68.0 2.9 6.3E-05 22.9 1.0 40 49-93 3-42 (44)
49 PF00196 GerE: Bacterial regul 67.0 5.5 0.00012 22.7 2.1 42 50-97 3-44 (58)
50 PRK12512 RNA polymerase sigma 65.7 4.4 9.5E-05 28.1 1.7 25 73-97 149-173 (184)
51 PF06056 Terminase_5: Putative 63.8 3.8 8.2E-05 24.1 1.0 21 73-93 15-35 (58)
52 TIGR03879 near_KaiC_dom probab 63.1 1.8 3.8E-05 26.9 -0.6 32 63-94 24-55 (73)
53 PF13518 HTH_28: Helix-turn-he 61.4 3.9 8.5E-05 22.4 0.7 24 73-96 14-37 (52)
54 KOG3623|consensus 61.0 10 0.00023 33.3 3.4 59 39-97 621-679 (1007)
55 cd04761 HTH_MerR-SF Helix-Turn 59.7 4.2 9.1E-05 21.9 0.6 23 74-96 3-25 (49)
56 PF09607 BrkDBD: Brinker DNA-b 58.5 14 0.0003 22.0 2.7 44 48-93 3-47 (58)
57 PF13384 HTH_23: Homeodomain-l 56.0 5.1 0.00011 21.9 0.5 22 73-94 19-40 (50)
58 PF08280 HTH_Mga: M protein tr 55.4 10 0.00023 21.9 1.9 36 54-93 6-41 (59)
59 PRK06759 RNA polymerase factor 54.7 9.7 0.00021 25.4 1.9 25 73-97 124-148 (154)
60 COG1905 NuoE NADH:ubiquinone o 54.5 26 0.00056 24.9 4.0 36 53-88 25-60 (160)
61 PRK10072 putative transcriptio 53.8 6.7 0.00015 25.4 0.9 40 51-97 33-72 (96)
62 KOG0773|consensus 53.5 8.8 0.00019 29.7 1.7 39 61-99 114-152 (342)
63 PF02796 HTH_7: Helix-turn-hel 51.6 14 0.00029 20.2 1.8 39 49-92 4-42 (45)
64 PF13411 MerR_1: MerR HTH fami 51.2 7.2 0.00016 22.6 0.7 21 74-94 3-23 (69)
65 KOG1146|consensus 50.5 19 0.0004 33.5 3.4 56 44-99 705-760 (1406)
66 smart00421 HTH_LUXR helix_turn 50.4 20 0.00043 19.2 2.5 42 50-97 3-44 (58)
67 PRK03975 tfx putative transcri 49.4 12 0.00026 26.0 1.7 44 48-97 4-47 (141)
68 PF00376 MerR: MerR family reg 48.5 8.4 0.00018 20.5 0.6 20 74-93 2-21 (38)
69 PF13565 HTH_32: Homeodomain-l 48.2 55 0.0012 19.2 5.7 34 52-85 32-66 (77)
70 cd04762 HTH_MerR-trunc Helix-T 48.1 8.5 0.00018 20.2 0.6 24 74-97 3-26 (49)
71 PRK09642 RNA polymerase sigma 47.4 9.7 0.00021 25.6 1.0 25 73-97 124-148 (160)
72 PRK00118 putative DNA-binding 47.4 20 0.00044 23.5 2.4 43 50-97 17-59 (104)
73 COG4367 Uncharacterized protei 46.8 24 0.00052 22.8 2.6 39 50-88 2-40 (97)
74 PRK05988 formate dehydrogenase 46.6 34 0.00073 23.9 3.6 36 54-89 24-59 (156)
75 PRK09646 RNA polymerase sigma 46.3 15 0.00032 25.8 1.8 25 73-97 160-184 (194)
76 PRK09652 RNA polymerase sigma 46.0 14 0.00029 25.0 1.5 25 73-97 146-170 (182)
77 PF01726 LexA_DNA_bind: LexA D 45.8 30 0.00064 20.6 2.8 39 50-90 3-45 (65)
78 COG2944 Predicted transcriptio 44.6 27 0.00059 23.1 2.7 41 50-97 43-83 (104)
79 cd01392 HTH_LacI Helix-turn-he 44.4 7.4 0.00016 21.3 -0.0 21 76-96 2-22 (52)
80 COG2963 Transposase and inacti 44.4 41 0.00088 21.7 3.6 43 48-94 5-48 (116)
81 TIGR02989 Sig-70_gvs1 RNA poly 44.2 18 0.00039 24.1 1.9 26 72-97 128-153 (159)
82 PF12802 MarR_2: MarR family; 43.2 19 0.00041 20.2 1.6 37 51-89 3-39 (62)
83 PRK11924 RNA polymerase sigma 42.9 16 0.00035 24.6 1.5 25 73-97 143-167 (179)
84 TIGR01958 nuoE_fam NADH-quinon 42.8 41 0.00089 23.0 3.6 36 54-89 17-52 (148)
85 PRK07539 NADH dehydrogenase su 42.5 41 0.0009 23.2 3.6 36 54-89 23-58 (154)
86 PRK12526 RNA polymerase sigma 42.0 18 0.00039 25.8 1.7 25 73-97 171-195 (206)
87 cd04764 HTH_MlrA-like_sg1 Heli 41.7 13 0.00028 21.6 0.8 21 74-94 3-23 (67)
88 cd00131 PAX Paired Box domain 41.0 1.1E+02 0.0023 20.5 5.3 45 50-94 75-126 (128)
89 PRK12514 RNA polymerase sigma 40.5 22 0.00048 24.3 1.9 25 73-97 147-171 (179)
90 PRK12523 RNA polymerase sigma 39.9 22 0.00048 24.3 1.9 25 73-97 137-161 (172)
91 TIGR02937 sigma70-ECF RNA poly 39.4 21 0.00045 22.8 1.6 25 73-97 128-152 (158)
92 TIGR02985 Sig70_bacteroi1 RNA 39.2 23 0.00051 23.3 1.9 25 73-97 131-155 (161)
93 PF01257 2Fe-2S_thioredx: Thio 38.3 38 0.00082 23.1 2.8 35 55-89 15-49 (145)
94 PHA02955 hypothetical protein; 38.2 57 0.0012 24.3 3.8 43 53-95 60-103 (213)
95 cd04763 HTH_MlrA-like Helix-Tu 38.1 14 0.00031 21.5 0.6 21 74-94 3-23 (68)
96 PRK09480 slmA division inhibit 38.1 30 0.00066 23.6 2.3 35 60-95 20-54 (194)
97 PRK04217 hypothetical protein; 38.0 39 0.00085 22.4 2.7 45 48-97 40-84 (110)
98 TIGR02999 Sig-70_X6 RNA polyme 37.6 32 0.0007 23.5 2.4 25 73-97 152-176 (183)
99 PRK09648 RNA polymerase sigma 37.5 22 0.00049 24.6 1.6 25 73-97 157-181 (189)
100 PF01047 MarR: MarR family; I 37.4 24 0.00051 19.7 1.4 38 51-92 1-38 (59)
101 PRK12537 RNA polymerase sigma 37.3 46 0.00099 22.9 3.1 25 73-97 151-175 (182)
102 TIGR02959 SigZ RNA polymerase 37.2 25 0.00055 24.1 1.8 25 73-97 118-142 (170)
103 cd06170 LuxR_C_like C-terminal 37.2 28 0.00061 18.7 1.7 37 52-94 2-38 (57)
104 PRK07571 bidirectional hydroge 37.2 71 0.0015 22.7 4.1 34 56-89 39-72 (169)
105 PRK09644 RNA polymerase sigma 37.0 22 0.00048 24.1 1.5 25 73-97 126-150 (165)
106 cd01104 HTH_MlrA-CarA Helix-Tu 36.9 17 0.00036 21.0 0.7 21 74-94 3-23 (68)
107 smart00027 EH Eps15 homology d 36.9 58 0.0013 20.2 3.3 44 50-93 3-51 (96)
108 PRK09639 RNA polymerase sigma 36.4 23 0.00051 23.7 1.5 25 73-97 129-153 (166)
109 PRK12519 RNA polymerase sigma 36.2 18 0.0004 25.1 1.0 27 71-97 157-183 (194)
110 PRK13558 bacterio-opsin activa 35.9 37 0.0008 28.3 2.9 41 49-89 606-648 (665)
111 TIGR03070 couple_hipB transcri 35.8 18 0.00039 19.7 0.7 23 74-96 18-40 (58)
112 PRK12529 RNA polymerase sigma 35.3 41 0.00089 23.2 2.6 25 73-97 145-169 (178)
113 PRK12528 RNA polymerase sigma 35.1 41 0.0009 22.5 2.6 24 73-96 131-154 (161)
114 PF13730 HTH_36: Helix-turn-he 34.7 21 0.00044 19.8 0.9 43 50-93 2-47 (55)
115 TIGR02939 RpoE_Sigma70 RNA pol 33.9 17 0.00036 25.0 0.5 28 70-97 153-180 (190)
116 TIGR02948 SigW_bacill RNA poly 33.8 26 0.00056 24.0 1.4 27 71-97 152-178 (187)
117 PF13443 HTH_26: Cro/C1-type H 33.8 64 0.0014 18.1 2.9 20 68-87 37-56 (63)
118 PRK12530 RNA polymerase sigma 33.6 39 0.00085 23.6 2.3 25 73-97 152-176 (189)
119 PRK05602 RNA polymerase sigma 33.6 20 0.00044 24.8 0.8 25 73-97 146-170 (186)
120 PF08880 QLQ: QLQ; InterPro: 33.6 43 0.00093 17.9 1.9 14 49-62 1-14 (37)
121 PRK06930 positive control sigm 33.4 29 0.00062 24.5 1.6 43 50-97 114-156 (170)
122 PRK09649 RNA polymerase sigma 33.2 32 0.00069 24.0 1.8 25 73-97 148-172 (185)
123 PRK09047 RNA polymerase factor 32.7 50 0.0011 21.9 2.7 25 73-97 124-148 (161)
124 PRK12541 RNA polymerase sigma 32.4 29 0.00063 23.3 1.5 25 73-97 130-154 (161)
125 PF07750 GcrA: GcrA cell cycle 32.2 78 0.0017 22.3 3.7 34 50-88 2-36 (162)
126 PRK11511 DNA-binding transcrip 32.1 37 0.0008 22.4 1.9 25 70-94 24-48 (127)
127 PF04297 UPF0122: Putative hel 32.0 30 0.00066 22.7 1.4 40 50-94 17-56 (101)
128 PRK12515 RNA polymerase sigma 32.0 35 0.00075 23.7 1.8 25 73-97 149-173 (189)
129 PRK12524 RNA polymerase sigma 31.8 48 0.001 23.2 2.6 25 73-97 154-178 (196)
130 PRK12547 RNA polymerase sigma 31.3 46 0.00099 22.5 2.3 25 73-97 130-154 (164)
131 COG0735 Fur Fe2+/Zn2+ uptake r 31.2 1.4E+02 0.003 20.4 4.7 34 49-82 17-50 (145)
132 TIGR02983 SigE-fam_strep RNA p 31.2 32 0.0007 23.0 1.5 25 73-97 128-152 (162)
133 PF06569 DUF1128: Protein of u 31.1 1.3E+02 0.0028 18.5 4.0 33 50-82 32-67 (71)
134 PRK09637 RNA polymerase sigma 31.1 33 0.00071 23.9 1.6 26 72-97 123-148 (181)
135 TIGR01764 excise DNA binding d 30.5 24 0.00053 18.4 0.7 23 74-96 4-26 (49)
136 PF01325 Fe_dep_repress: Iron 30.3 17 0.00037 21.2 0.0 41 52-92 3-43 (60)
137 PF13412 HTH_24: Winged helix- 30.2 66 0.0014 17.2 2.5 37 52-92 2-38 (48)
138 PF13551 HTH_29: Winged helix- 29.8 1.4E+02 0.003 18.4 5.0 46 48-93 55-109 (112)
139 PRK12546 RNA polymerase sigma 29.3 32 0.0007 24.2 1.3 25 73-97 131-155 (188)
140 PF08279 HTH_11: HTH domain; 29.3 35 0.00077 18.8 1.2 33 56-91 3-35 (55)
141 PF12728 HTH_17: Helix-turn-he 28.9 26 0.00056 19.1 0.6 22 74-95 4-25 (51)
142 PRK07037 extracytoplasmic-func 28.8 69 0.0015 21.4 2.9 25 73-97 127-151 (163)
143 PF01710 HTH_Tnp_IS630: Transp 28.7 67 0.0015 21.0 2.7 38 51-93 3-40 (119)
144 smart00422 HTH_MERR helix_turn 28.6 28 0.00061 20.0 0.8 20 74-93 3-22 (70)
145 PRK09645 RNA polymerase sigma 28.5 69 0.0015 21.6 2.8 25 73-97 136-160 (173)
146 PRK00215 LexA repressor; Valid 28.4 38 0.00082 24.1 1.6 41 51-93 2-46 (205)
147 PRK13919 putative RNA polymera 28.1 61 0.0013 22.2 2.5 25 73-97 153-177 (186)
148 PRK09651 RNA polymerase sigma 27.8 48 0.001 22.6 2.0 24 72-95 136-159 (172)
149 PHA01976 helix-turn-helix prot 27.1 32 0.0007 19.7 0.8 22 74-95 18-39 (67)
150 TIGR03209 P21_Cbot clostridium 26.8 1E+02 0.0022 20.1 3.4 17 73-89 125-141 (142)
151 TIGR02952 Sig70_famx2 RNA poly 26.7 47 0.001 22.2 1.7 25 72-96 139-163 (170)
152 PRK12536 RNA polymerase sigma 26.7 45 0.00097 23.0 1.6 25 73-97 147-171 (181)
153 TIGR02954 Sig70_famx3 RNA poly 26.6 77 0.0017 21.3 2.8 25 73-97 137-161 (169)
154 cd04766 HTH_HspR Helix-Turn-He 26.6 31 0.00068 21.4 0.8 21 74-94 4-24 (91)
155 TIGR02607 antidote_HigA addict 26.5 33 0.00071 20.2 0.8 23 74-96 21-43 (78)
156 PF09862 DUF2089: Protein of u 26.5 1.1E+02 0.0023 20.5 3.3 36 49-89 32-67 (113)
157 PRK11639 zinc uptake transcrip 26.3 2E+02 0.0044 20.0 4.9 34 50-83 23-56 (169)
158 PRK12543 RNA polymerase sigma 26.1 47 0.001 22.8 1.7 25 73-97 135-159 (179)
159 PRK06811 RNA polymerase factor 26.1 52 0.0011 22.9 1.9 25 73-97 149-173 (189)
160 PRK12532 RNA polymerase sigma 26.0 61 0.0013 22.5 2.3 25 73-97 154-178 (195)
161 PRK12511 RNA polymerase sigma 25.8 73 0.0016 22.2 2.6 25 73-97 129-153 (182)
162 TIGR00721 tfx DNA-binding prot 25.7 86 0.0019 21.6 2.8 44 48-97 4-47 (137)
163 PRK12525 RNA polymerase sigma 25.7 69 0.0015 21.7 2.4 25 73-97 136-160 (168)
164 PF04936 DUF658: Protein of un 25.5 36 0.00077 24.5 0.9 26 72-97 15-40 (186)
165 TIGR02957 SigX4 RNA polymerase 25.5 63 0.0014 24.2 2.4 24 74-97 127-150 (281)
166 PRK11552 putative DNA-binding 25.2 55 0.0012 23.6 2.0 39 56-96 19-57 (225)
167 cd01106 HTH_TipAL-Mta Helix-Tu 25.2 33 0.00073 21.8 0.7 23 74-96 3-25 (103)
168 PF14549 P22_Cro: DNA-binding 25.1 30 0.00066 20.4 0.4 18 74-91 12-29 (60)
169 PRK12539 RNA polymerase sigma 25.0 82 0.0018 21.7 2.8 26 72-97 148-173 (184)
170 PRK09706 transcriptional repre 25.0 33 0.00071 22.9 0.7 23 74-96 21-43 (135)
171 PRK03573 transcriptional regul 25.0 1.6E+02 0.0035 19.4 4.1 37 50-89 28-64 (144)
172 PRK08583 RNA polymerase sigma 24.9 80 0.0017 23.2 2.8 25 73-97 223-247 (257)
173 PRK10430 DNA-binding transcrip 24.9 64 0.0014 23.1 2.2 45 50-95 158-202 (239)
174 TIGR03629 arch_S13P archaeal r 24.9 75 0.0016 22.1 2.4 16 50-65 51-66 (144)
175 PRK12535 RNA polymerase sigma 24.6 48 0.001 23.4 1.5 25 73-97 151-175 (196)
176 TIGR02980 SigBFG RNA polymeras 24.5 84 0.0018 22.5 2.8 42 51-97 179-220 (227)
177 PF01381 HTH_3: Helix-turn-hel 24.5 1.1E+02 0.0024 16.5 2.8 20 66-85 33-52 (55)
178 cd01105 HTH_GlnR-like Helix-Tu 24.3 36 0.00079 21.1 0.7 20 74-93 4-23 (88)
179 PRK12516 RNA polymerase sigma 24.3 73 0.0016 22.3 2.4 25 73-97 134-158 (187)
180 TIGR01889 Staph_reg_Sar staphy 24.2 97 0.0021 19.7 2.8 40 50-89 22-61 (109)
181 cd02413 40S_S3_KH K homology R 24.2 63 0.0014 20.0 1.8 20 74-93 56-75 (81)
182 COG1846 MarR Transcriptional r 24.2 1.2E+02 0.0026 18.6 3.3 38 51-92 20-57 (126)
183 PRK12538 RNA polymerase sigma 24.0 41 0.0009 24.6 1.1 25 73-97 189-213 (233)
184 PRK06986 fliA flagellar biosyn 23.9 47 0.001 24.1 1.4 25 73-97 202-226 (236)
185 PRK09636 RNA polymerase sigma 23.9 71 0.0015 24.0 2.4 25 73-97 133-157 (293)
186 PRK12542 RNA polymerase sigma 23.6 73 0.0016 21.9 2.3 25 73-97 140-164 (185)
187 PF13022 HTH_Tnp_1_2: Helix-tu 23.3 56 0.0012 22.8 1.6 23 71-93 34-56 (142)
188 PRK12513 RNA polymerase sigma 23.2 12 0.00027 26.0 -1.8 29 69-97 153-181 (194)
189 PF06971 Put_DNA-bind_N: Putat 23.0 39 0.00085 19.2 0.6 17 73-89 30-46 (50)
190 PRK12545 RNA polymerase sigma 22.7 82 0.0018 22.2 2.4 25 73-97 157-181 (201)
191 PRK09647 RNA polymerase sigma 22.7 60 0.0013 23.1 1.7 25 73-97 156-180 (203)
192 PRK14996 TetR family transcrip 22.6 90 0.002 21.4 2.6 38 57-95 15-52 (192)
193 PRK12520 RNA polymerase sigma 22.5 82 0.0018 21.8 2.4 25 73-97 149-173 (191)
194 PF00325 Crp: Bacterial regula 22.2 50 0.0011 17.1 0.9 18 73-90 4-21 (32)
195 TIGR02943 Sig70_famx1 RNA poly 22.2 86 0.0019 21.8 2.4 25 73-97 149-173 (188)
196 PRK10403 transcriptional regul 22.1 60 0.0013 21.7 1.6 43 49-97 152-194 (215)
197 COG5484 Uncharacterized conser 22.0 42 0.00091 25.8 0.8 23 71-93 19-41 (279)
198 PRK12522 RNA polymerase sigma 21.9 89 0.0019 21.2 2.4 25 73-97 137-161 (173)
199 PRK12373 NADH dehydrogenase su 21.9 1.6E+02 0.0034 24.0 4.1 34 56-89 40-73 (400)
200 cd04774 HTH_YfmP Helix-Turn-He 21.9 43 0.00094 21.2 0.7 22 74-95 3-24 (96)
201 TIGR03001 Sig-70_gmx1 RNA poly 21.7 85 0.0018 23.2 2.4 25 73-97 179-203 (244)
202 cd04768 HTH_BmrR-like Helix-Tu 21.7 46 0.00099 21.0 0.8 22 74-95 3-24 (96)
203 PRK12534 RNA polymerase sigma 21.5 1.3E+02 0.0029 20.5 3.3 25 73-97 155-179 (187)
204 PF12793 SgrR_N: Sugar transpo 21.4 77 0.0017 21.0 1.9 33 55-89 5-37 (115)
205 PRK15369 two component system 21.4 94 0.002 20.5 2.4 43 49-97 148-190 (211)
206 PRK09643 RNA polymerase sigma 21.3 1.2E+02 0.0025 21.2 2.9 22 73-94 152-173 (192)
207 TIGR02885 spore_sigF RNA polym 21.3 1E+02 0.0023 22.1 2.8 23 72-94 200-222 (231)
208 TIGR02941 Sigma_B RNA polymera 21.1 61 0.0013 23.8 1.5 42 51-97 206-247 (255)
209 PRK09462 fur ferric uptake reg 21.0 2.7E+02 0.0059 18.7 4.7 34 49-82 13-47 (148)
210 PRK09641 RNA polymerase sigma 20.8 61 0.0013 22.1 1.4 27 71-97 152-178 (187)
211 PRK12531 RNA polymerase sigma 20.6 1E+02 0.0022 21.5 2.5 25 73-97 159-183 (194)
212 PF13309 HTH_22: HTH domain 20.5 1.6E+02 0.0035 17.2 3.0 36 55-90 26-61 (64)
213 PRK05572 sporulation sigma fac 20.4 1.1E+02 0.0023 22.5 2.7 40 51-95 203-242 (252)
214 PF10078 DUF2316: Uncharacteri 20.3 50 0.0011 21.2 0.8 30 56-89 12-41 (89)
215 PRK12533 RNA polymerase sigma 20.0 82 0.0018 22.8 2.0 25 73-97 152-176 (216)
216 PRK08301 sporulation sigma fac 20.0 42 0.00091 24.2 0.4 26 72-97 199-224 (234)
No 1
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.69 E-value=1.3e-17 Score=98.42 Aligned_cols=53 Identities=42% Similarity=0.617 Sum_probs=51.4
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 45 KKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 45 rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
++.|+.||++|+.+|+.+|..++||+..++..||..|||+..+|.+||+|+|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~ 53 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRR 53 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHH
Confidence 46789999999999999999999999999999999999999999999999999
No 2
>KOG0489|consensus
Probab=99.68 E-value=8.2e-18 Score=126.84 Aligned_cols=64 Identities=28% Similarity=0.444 Sum_probs=60.1
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccCC
Q psy15969 41 SSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDDP 108 (111)
Q Consensus 41 ~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~~ 108 (111)
....+|.||.||..|+.+||..|..|.|.+...+.+||..|.|+++||+|||||||+ |||++..
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRM----K~Kk~~k 219 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRM----KWKKENK 219 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHH----HHHHhhc
Confidence 455788999999999999999999999999999999999999999999999999999 9997653
No 3
>KOG0488|consensus
Probab=99.68 E-value=2.3e-17 Score=127.02 Aligned_cols=65 Identities=31% Similarity=0.475 Sum_probs=60.6
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccC
Q psy15969 39 DQSSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDD 107 (111)
Q Consensus 39 ~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~ 107 (111)
....+.++.||+||..|+..||..|+...|.+..+|.+||..|||+..||++||||||+ |||++.
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRt----KWKrq~ 231 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRT----KWKRQT 231 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhH----HHHHHH
Confidence 33467788899999999999999999999999999999999999999999999999999 999863
No 4
>KOG0842|consensus
Probab=99.67 E-value=6.2e-17 Score=123.98 Aligned_cols=65 Identities=28% Similarity=0.366 Sum_probs=59.6
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccCC
Q psy15969 40 QSSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDDP 108 (111)
Q Consensus 40 ~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~~ 108 (111)
....+|+.|..||..|+.+||..|....|.+..+|+.||..|.|+..||+|||||+|. |.||...
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRY----K~KR~~~ 213 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRY----KTKRQQK 213 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchh----hhhhhhh
Confidence 3556777899999999999999999999999999999999999999999999999999 8877643
No 5
>KOG0843|consensus
Probab=99.66 E-value=3.8e-17 Score=116.57 Aligned_cols=60 Identities=30% Similarity=0.342 Sum_probs=56.9
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCccccccc
Q psy15969 43 TPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDD 106 (111)
Q Consensus 43 ~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~ 106 (111)
.+++.||.||++|+..||..|+.++|....++..||..|+|++.||+|||||||+ |.++.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRt----k~kr~ 160 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRT----KHKRM 160 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhH----HHHHH
Confidence 6788999999999999999999999999999999999999999999999999999 66654
No 6
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.64 E-value=3.9e-16 Score=93.32 Aligned_cols=52 Identities=15% Similarity=0.263 Sum_probs=50.3
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCC----CCHHHHHHHHHHhCCCcccccccccccc
Q psy15969 45 KKPRLVFTDLQRRTLQAIFKETKR----PSKEMQVTIARQLGLEPTTVGNFFMNAR 96 (111)
Q Consensus 45 rr~Rt~ft~~ql~~Le~~F~~~~~----ps~~~r~~LA~~lgL~~~qVkvWFqNrR 96 (111)
++.||.||++|+..|+.+|+.++| |+..++.+||..+||+..+|+|||||..
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 678999999999999999999999 9999999999999999999999999975
No 7
>KOG0484|consensus
Probab=99.64 E-value=2e-17 Score=108.94 Aligned_cols=63 Identities=27% Similarity=0.440 Sum_probs=58.8
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccC
Q psy15969 41 SSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDD 107 (111)
Q Consensus 41 ~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~ 107 (111)
..+.++-||.||..||..||.+|...+||++-.+++||..++|++..|+|||||||+ |+++++
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRA----KfRKQE 76 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRA----KFRKQE 76 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHH----HHHHHH
Confidence 456788899999999999999999999999999999999999999999999999999 887754
No 8
>KOG0850|consensus
Probab=99.63 E-value=1.5e-16 Score=117.07 Aligned_cols=64 Identities=30% Similarity=0.466 Sum_probs=58.7
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccC
Q psy15969 40 QSSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDD 107 (111)
Q Consensus 40 ~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~ 107 (111)
...+.|+.||.|+..||..|...|+.++|+-..+|.+||..|||+..||+|||||||. |+|+..
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRS----K~KKl~ 181 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRS----KFKKLK 181 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHH----HHHHHH
Confidence 3556788999999999999999999999999999999999999999999999999999 666543
No 9
>KOG2251|consensus
Probab=99.59 E-value=8.8e-16 Score=112.47 Aligned_cols=65 Identities=28% Similarity=0.408 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccC
Q psy15969 39 DQSSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDD 107 (111)
Q Consensus 39 ~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~ 107 (111)
......+|.||.|+-.|+.+||.+|...+||+...+++||..|+|.+..|+|||.|||+ |++++.
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRA----K~r~qq 96 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRA----KCRRQQ 96 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccc----hhhHhh
Confidence 45667889999999999999999999999999999999999999999999999999999 887754
No 10
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.58 E-value=2.1e-15 Score=88.26 Aligned_cols=52 Identities=33% Similarity=0.466 Sum_probs=50.0
Q ss_pred CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 46 KPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 46 r~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
+.++.|+++++..|+.+|..++||+..++..||..+||+..+|.+||+|+|.
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~ 53 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRA 53 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhh
Confidence 4577899999999999999999999999999999999999999999999998
No 11
>KOG0485|consensus
Probab=99.58 E-value=6.6e-16 Score=113.24 Aligned_cols=65 Identities=31% Similarity=0.400 Sum_probs=60.5
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccCC
Q psy15969 40 QSSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDDP 108 (111)
Q Consensus 40 ~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~~ 108 (111)
+....++.||+|+..|+..||..|+...|.+..++.-||..|.|++.||+|||||||. |||+...
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRn----KwKRq~a 164 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRN----KWKRQYA 164 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhH----HHHHHHh
Confidence 3446778999999999999999999999999999999999999999999999999999 9998754
No 12
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.57 E-value=2.8e-15 Score=88.24 Aligned_cols=52 Identities=33% Similarity=0.474 Sum_probs=50.1
Q ss_pred CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 46 KPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 46 r~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
+.++.|+..++.+|+.+|..++||+..++..||..+||+..+|.+||+|+|.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~ 53 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRA 53 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4578999999999999999999999999999999999999999999999999
No 13
>KOG0487|consensus
Probab=99.56 E-value=2.1e-15 Score=115.61 Aligned_cols=63 Identities=27% Similarity=0.287 Sum_probs=58.6
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccC
Q psy15969 41 SSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDD 107 (111)
Q Consensus 41 ~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~ 107 (111)
....|++|-.+|..|+.+||..|..|.|++.+.|.+|+..|+|+++||+|||||||+ |.|+..
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRM----K~KK~~ 294 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRM----KEKKVN 294 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhh----HHhhhh
Confidence 356778899999999999999999999999999999999999999999999999999 877754
No 14
>KOG0492|consensus
Probab=99.52 E-value=7e-15 Score=107.18 Aligned_cols=61 Identities=31% Similarity=0.333 Sum_probs=56.8
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCccccccc
Q psy15969 42 STPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDD 106 (111)
Q Consensus 42 ~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~ 106 (111)
...+.+||.||..||..||.-|...+|.++.++.+++..|.|++.||+|||||||+ +.++.
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRA----KaKRl 202 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRA----KAKRL 202 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhH----HHHHH
Confidence 34577899999999999999999999999999999999999999999999999999 76664
No 15
>KOG0494|consensus
Probab=99.49 E-value=1.3e-14 Score=108.84 Aligned_cols=60 Identities=27% Similarity=0.463 Sum_probs=56.2
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccCC
Q psy15969 45 KKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDDP 108 (111)
Q Consensus 45 rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~~ 108 (111)
+..||+||..|+..||..|...+||+...++.||..++|.+..|+|||||||+ ||++.+.
T Consensus 142 Rh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRA----KWRk~Ek 201 (332)
T KOG0494|consen 142 RHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRA----KWRKTEK 201 (332)
T ss_pred ccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhH----Hhhhhhh
Confidence 34499999999999999999999999999999999999999999999999999 9998654
No 16
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.49 E-value=2.6e-14 Score=100.68 Aligned_cols=62 Identities=32% Similarity=0.407 Sum_probs=56.9
Q ss_pred CCCCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccC
Q psy15969 37 SQDQSSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRR 98 (111)
Q Consensus 37 ~~~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R 98 (111)
.++..+..++.|+..|..|+.+|+..|..++||+...+..|+..++|++..|++||||+|+.
T Consensus 44 ~~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~ 105 (156)
T COG5576 44 KQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAK 105 (156)
T ss_pred cccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHH
Confidence 34555667778899999999999999999999999999999999999999999999999993
No 17
>KOG4577|consensus
Probab=99.46 E-value=1.6e-14 Score=109.86 Aligned_cols=79 Identities=24% Similarity=0.402 Sum_probs=70.3
Q ss_pred hhhhhcccCCCCCCCC-----CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccC
Q psy15969 24 KKKTCKRKEEPDISQD-----QSSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRR 98 (111)
Q Consensus 24 ~r~~~~~~e~~~~~~~-----~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R 98 (111)
.|.+|+.+++++..-. +....+|+||.||..||+.|...|...+-|....++.|+.++||.-+.|+|||||||+
T Consensus 142 ~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRA- 220 (383)
T KOG4577|consen 142 ARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRA- 220 (383)
T ss_pred ceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhH-
Confidence 4678999888774443 5667889999999999999999999999999999999999999999999999999999
Q ss_pred Cccccccc
Q psy15969 99 SMDKWKDD 106 (111)
Q Consensus 99 ~~~K~kr~ 106 (111)
|+++.
T Consensus 221 ---KEKRL 225 (383)
T KOG4577|consen 221 ---KEKRL 225 (383)
T ss_pred ---HHHhh
Confidence 77654
No 18
>KOG3802|consensus
Probab=99.45 E-value=1.3e-13 Score=108.31 Aligned_cols=62 Identities=29% Similarity=0.351 Sum_probs=58.6
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccCC
Q psy15969 43 TPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDDP 108 (111)
Q Consensus 43 ~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~~ 108 (111)
.+|+.||+|.......||.+|..|+.|+..++..||..|+|....|+|||||||+ |.|+..+
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQ----keKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQ----KEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeecccc----ccccCCC
Confidence 5688899999999999999999999999999999999999999999999999999 8887654
No 19
>KOG0848|consensus
Probab=99.43 E-value=3e-14 Score=107.14 Aligned_cols=57 Identities=33% Similarity=0.444 Sum_probs=53.3
Q ss_pred CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCccccccc
Q psy15969 46 KPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDD 106 (111)
Q Consensus 46 r~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~ 106 (111)
+-|.++|+.|..+||..|..+.|.++....+||.-|||+++||+|||||||+ |++++
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRA----KERK~ 257 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRA----KERKD 257 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhH----HHHHH
Confidence 4477999999999999999999999999999999999999999999999999 76654
No 20
>KOG0493|consensus
Probab=99.43 E-value=1.1e-13 Score=104.06 Aligned_cols=58 Identities=33% Similarity=0.518 Sum_probs=54.4
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccc
Q psy15969 44 PKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKD 105 (111)
Q Consensus 44 ~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr 105 (111)
-+|+||.||.+||..|...|+.|.|.+...+.+||.+|||.+.||+|||||.|+ |-++
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRA----KiKK 303 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRA----KIKK 303 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhh----hhhh
Confidence 357899999999999999999999999999999999999999999999999999 5554
No 21
>KOG0491|consensus
Probab=99.38 E-value=3.8e-14 Score=100.13 Aligned_cols=62 Identities=27% Similarity=0.387 Sum_probs=55.5
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccc
Q psy15969 44 PKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKD 105 (111)
Q Consensus 44 ~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr 105 (111)
.++.|++|+..|+..|+..|+...|.+..++.+||..|+|++.||+.||||+|+..++..+.
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~ 161 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN 161 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 45679999999999999999999999999999999999999999999999999954444333
No 22
>KOG0483|consensus
Probab=99.37 E-value=4.1e-13 Score=97.78 Aligned_cols=59 Identities=31% Similarity=0.515 Sum_probs=54.0
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCccccccc
Q psy15969 44 PKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDD 106 (111)
Q Consensus 44 ~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~ 106 (111)
.......|+.+|+..||..|+.+.+..+..+..||..|||.++||.|||||||+ +|+..
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRA----RwK~k 108 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRA----RWKTK 108 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccc----cccch
Confidence 444566899999999999999999999999999999999999999999999999 77654
No 23
>KOG0844|consensus
Probab=99.35 E-value=2e-13 Score=104.56 Aligned_cols=62 Identities=27% Similarity=0.290 Sum_probs=57.1
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCccccccc
Q psy15969 41 SSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDD 106 (111)
Q Consensus 41 ~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~ 106 (111)
..+-+|-||.||.+|+..||..|-...|.+...+.+||..|+|++..|+|||||||+ |.|++
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRM----KDKRQ 239 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRM----KDKRQ 239 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchh----hhhhh
Confidence 345678899999999999999999999999999999999999999999999999999 66665
No 24
>KOG2252|consensus
Probab=99.27 E-value=6e-12 Score=102.11 Aligned_cols=82 Identities=68% Similarity=0.968 Sum_probs=73.7
Q ss_pred hhhcccCCCCCCCCCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccc
Q psy15969 26 KTCKRKEEPDISQDQSSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKD 105 (111)
Q Consensus 26 ~~~~~~e~~~~~~~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr 105 (111)
++|++.++ +.+.+.....+++|.+||+.|...|..+|..+++|+.++.+.|+..|||....|.+||.|.|.|.+.+|..
T Consensus 403 ~a~kRke~-ep~~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl~~~~~ 481 (558)
T KOG2252|consen 403 KACKRKEQ-EPTDDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSLDKKVD 481 (558)
T ss_pred HHhhhccc-CCCccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhccccccc
Confidence 34999998 45567777888899999999999999999999999999999999999999999999999999998888776
Q ss_pred cCC
Q psy15969 106 DDP 108 (111)
Q Consensus 106 ~~~ 108 (111)
+..
T Consensus 482 dd~ 484 (558)
T KOG2252|consen 482 DDS 484 (558)
T ss_pred cCc
Confidence 654
No 25
>KOG0486|consensus
Probab=99.26 E-value=2.8e-12 Score=98.34 Aligned_cols=62 Identities=27% Similarity=0.452 Sum_probs=59.0
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccCC
Q psy15969 43 TPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDDP 108 (111)
Q Consensus 43 ~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~~ 108 (111)
++++.|+.|+..|+..||..|.+|.||+-..+++||..++|++..|.|||.|||+ +|++.+.
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrra----kwrkrEr 172 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRA----KWRKRER 172 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchh----hhhhhhh
Confidence 5788999999999999999999999999999999999999999999999999999 9988654
No 26
>KOG0847|consensus
Probab=99.23 E-value=3.3e-12 Score=94.11 Aligned_cols=66 Identities=26% Similarity=0.423 Sum_probs=60.2
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccCC
Q psy15969 39 DQSSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDDP 108 (111)
Q Consensus 39 ~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~~ 108 (111)
+..++.+..|..|+..|+..|+..|+...|+-.+++.+||..+||++.+|.|||||||+ ||++.-.
T Consensus 162 ~kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRT----KWRKkhA 227 (288)
T KOG0847|consen 162 NLNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRT----KWRKKHA 227 (288)
T ss_pred CcCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchh----hhhhhhc
Confidence 34466777888999999999999999999999999999999999999999999999999 9998643
No 27
>KOG0490|consensus
Probab=99.15 E-value=1.6e-11 Score=89.45 Aligned_cols=63 Identities=22% Similarity=0.222 Sum_probs=58.9
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccC
Q psy15969 41 SSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDD 107 (111)
Q Consensus 41 ~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~ 107 (111)
....++.|+.|+..|++.|+..|+.++||+...++.||..+++++..|++||||+|+ +|++..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrra----k~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRA----KDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcH----hhhhhh
Confidence 346788999999999999999999999999999999999999999999999999999 888765
No 28
>KOG0849|consensus
Probab=99.11 E-value=5.8e-11 Score=93.12 Aligned_cols=73 Identities=25% Similarity=0.383 Sum_probs=63.2
Q ss_pred cCCCCCCCCCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccC
Q psy15969 31 KEEPDISQDQSSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDD 107 (111)
Q Consensus 31 ~e~~~~~~~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~ 107 (111)
+++..++.......++.|+.|+..|+..|+..|+.++||++..++.||..+|+++..|++||+|+|+ +|++..
T Consensus 163 ~~~~~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra----~~rr~~ 235 (354)
T KOG0849|consen 163 DDEEPPGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRA----KWRRQH 235 (354)
T ss_pred CccccccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhh----hhhhcc
Confidence 3344444444666778899999999999999999999999999999999999999999999999999 777765
No 29
>KOG0775|consensus
Probab=99.03 E-value=2.7e-10 Score=86.10 Aligned_cols=56 Identities=25% Similarity=0.360 Sum_probs=49.0
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccC
Q psy15969 52 TDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDD 107 (111)
Q Consensus 52 t~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~ 107 (111)
-..-..+|.++|..|+||++.+..+||..+||+..||-+||.|||+|++....+..
T Consensus 184 KekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ak~~ 239 (304)
T KOG0775|consen 184 KEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAAKNS 239 (304)
T ss_pred hHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcccccc
Confidence 34457899999999999999999999999999999999999999998876555443
No 30
>KOG1168|consensus
Probab=98.99 E-value=2e-10 Score=87.70 Aligned_cols=65 Identities=31% Similarity=0.386 Sum_probs=59.3
Q ss_pred CCCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCCccccccc
Q psy15969 38 QDQSSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDD 106 (111)
Q Consensus 38 ~~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~ 106 (111)
--.....+|.||++.......||.+|...+.|+.+.+..||..|+|....|+|||||.|+ |.++.
T Consensus 303 l~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQ----KQKRm 367 (385)
T KOG1168|consen 303 LLPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQ----KQKRM 367 (385)
T ss_pred ccCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHH----HHHHh
Confidence 344566788999999999999999999999999999999999999999999999999999 77764
No 31
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.73 E-value=2e-09 Score=59.77 Aligned_cols=33 Identities=42% Similarity=0.686 Sum_probs=28.4
Q ss_pred hCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 65 ETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 65 ~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.+|||+..++..||..+||+..||.+||-|.|.
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRr 39 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARR 39 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHc
Confidence 479999999999999999999999999999886
No 32
>KOG0774|consensus
Probab=98.59 E-value=4.2e-08 Score=74.13 Aligned_cols=60 Identities=25% Similarity=0.417 Sum_probs=53.3
Q ss_pred CCCCCCcCCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCcccccccccccccCCcccccccC
Q psy15969 44 PKKPRLVFTDLQRRTLQAIFK---ETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRSMDKWKDDD 107 (111)
Q Consensus 44 ~rr~Rt~ft~~ql~~Le~~F~---~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~~~K~kr~~ 107 (111)
.+|.|..|+...-++|..+|. .|+||+....++||..+|++..||.+||.|.|- .+++..
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrI----rykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRI----RYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhcccccccee----ehhhhh
Confidence 356788999999999999996 579999999999999999999999999999999 555543
No 33
>KOG0490|consensus
Probab=98.13 E-value=1.7e-06 Score=62.86 Aligned_cols=58 Identities=28% Similarity=0.570 Sum_probs=54.3
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 40 QSSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 40 ~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.....++.++.|+..++..|...|..+++|+......|+..+|++...|++||+|.+.
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~ 206 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRA 206 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHH
Confidence 3456777899999999999999999999999999999999999999999999999998
No 34
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.39 E-value=7.6e-05 Score=44.17 Aligned_cols=42 Identities=12% Similarity=0.188 Sum_probs=31.5
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 56 RRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 56 l~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
+..|+.+|....++...+...|+...+|+..||+.||-.+..
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 567999999999999999999999999999999999976544
No 35
>KOG1146|consensus
Probab=97.24 E-value=0.00018 Score=64.14 Aligned_cols=55 Identities=22% Similarity=0.367 Sum_probs=52.2
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 43 TPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 43 ~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
..+..|+.++..||..|..+|....||...+.+.|...+++....|++||||.|+
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~ 956 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARA 956 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhh
Confidence 3567899999999999999999999999999999999999999999999999999
No 36
>KOG0773|consensus
Probab=97.22 E-value=0.00042 Score=53.80 Aligned_cols=55 Identities=29% Similarity=0.399 Sum_probs=46.6
Q ss_pred CCCCCCcCCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCcccccccccccccC
Q psy15969 44 PKKPRLVFTDLQRRTLQAIFK---ETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRR 98 (111)
Q Consensus 44 ~rr~Rt~ft~~ql~~Le~~F~---~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R 98 (111)
..+....|......+|..++. ..+||+..+...||..+||+..||.+||-|.|-|
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R 296 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVR 296 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccc
Confidence 445566888888889887733 2579999999999999999999999999999885
No 37
>KOG3623|consensus
Probab=95.42 E-value=0.013 Score=50.40 Aligned_cols=42 Identities=29% Similarity=0.371 Sum_probs=40.4
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 56 RRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 56 l~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
+.+|..+|..|.+|+..+...+|...||+...|+.||.+.++
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a 609 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEA 609 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhh
Confidence 788999999999999999999999999999999999999887
No 38
>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=95.28 E-value=0.034 Score=32.18 Aligned_cols=46 Identities=24% Similarity=0.332 Sum_probs=34.8
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccc
Q psy15969 45 KKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNA 95 (111)
Q Consensus 45 rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNr 95 (111)
++.|..+|.++...+-..++.+. ....||..+|++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 35788999998888888888775 57789999999999999999885
No 39
>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=89.51 E-value=0.47 Score=27.62 Aligned_cols=40 Identities=30% Similarity=0.423 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhCCCcccccc
Q psy15969 51 FTDLQRRTLQAIFKETKR--PSKEMQVTIARQLGLEPTTVGN 90 (111)
Q Consensus 51 ft~~ql~~Le~~F~~~~~--ps~~~r~~LA~~lgL~~~qVkv 90 (111)
+|+.|..+|...|...-| |-.....+||..+|++...|..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 588999999999987654 6667788999999999876543
No 40
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. 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; PDB: 2JN6_A 2RN7_A.
Probab=85.28 E-value=0.38 Score=28.85 Aligned_cols=44 Identities=23% Similarity=0.279 Sum_probs=29.1
Q ss_pred CCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccc
Q psy15969 47 PRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 47 ~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqN 94 (111)
.+..||+++...+-..+.. +......+|..+||+..+|..|-.-
T Consensus 3 ~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHHH
Confidence 4678999887777666522 2246888999999999999999753
No 41
>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=80.97 E-value=3.9 Score=19.40 Aligned_cols=38 Identities=21% Similarity=0.299 Sum_probs=26.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFF 92 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWF 92 (111)
.++......+...|... + ....+|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 46666666666666532 2 45677889999988888774
No 42
>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=79.04 E-value=2.1 Score=23.70 Aligned_cols=40 Identities=20% Similarity=0.269 Sum_probs=30.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqN 94 (111)
.+++.+..+|...|..+ ....++|..+|++...|..+...
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHH
Confidence 57888999999998333 35788999999999999887654
No 43
>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=78.25 E-value=2 Score=24.02 Aligned_cols=41 Identities=24% Similarity=0.270 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccc
Q psy15969 51 FTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNAR 96 (111)
Q Consensus 51 ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR 96 (111)
+++.+..++...|-.+ -...++|..+|++...|..|...-+
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5566666666655444 3678899999999999999987544
No 44
>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=75.95 E-value=1.1 Score=26.72 Aligned_cols=21 Identities=24% Similarity=0.343 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCCccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFq 93 (111)
....||..||+++.+|..|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 456789999999999999953
No 45
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=74.23 E-value=3.4 Score=29.95 Aligned_cols=40 Identities=25% Similarity=0.352 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHHHhhCC--CCCHHHHHHHHHHhCCCccccc
Q psy15969 50 VFTDLQRRTLQAIFKETK--RPSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~--~ps~~~r~~LA~~lgL~~~qVk 89 (111)
.+|+.|+.+|...|...- ||-.....+||..+|++...+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ 196 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLS 196 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH
Confidence 799999999999999764 5777788999999999987643
No 46
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=73.51 E-value=3.4 Score=21.94 Aligned_cols=43 Identities=23% Similarity=0.244 Sum_probs=31.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.+++.+..++...|..+ .....+|..+|++...|..|...-+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35677777777766433 24667799999999999999865443
No 47
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=69.10 E-value=12 Score=24.81 Aligned_cols=43 Identities=16% Similarity=0.040 Sum_probs=29.9
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccc
Q psy15969 48 RLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 48 Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqN 94 (111)
+..||.++....-.....+.+ ....+|..+|++..+|..|..-
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 567888876544443333332 3567899999999999999754
No 48
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=68.03 E-value=2.9 Score=22.92 Aligned_cols=40 Identities=23% Similarity=0.275 Sum_probs=20.6
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccc
Q psy15969 49 LVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 49 t~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFq 93 (111)
..||.++...++..+... ....+||..+|.+...|..+..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 457888888888876644 3566799999999998877653
No 49
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=66.98 E-value=5.5 Score=22.69 Aligned_cols=42 Identities=19% Similarity=0.233 Sum_probs=32.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.||+.++.+|.....-. ...++|..+|+++..|..+..+-+.
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHH
Confidence 68888999887776544 4778899999999999988876544
No 50
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=65.75 E-value=4.4 Score=28.08 Aligned_cols=25 Identities=12% Similarity=0.010 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+++..-+.
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~ 173 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLA 173 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4678999999999999999987776
No 51
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=63.79 E-value=3.8 Score=24.06 Aligned_cols=21 Identities=29% Similarity=0.256 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCCccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFq 93 (111)
...+||..||++...|..|-.
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 366789999999999999975
No 52
>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=63.09 E-value=1.8 Score=26.88 Aligned_cols=32 Identities=22% Similarity=0.240 Sum_probs=23.7
Q ss_pred HhhCCCCCHHHHHHHHHHhCCCcccccccccc
Q psy15969 63 FKETKRPSKEMQVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 63 F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqN 94 (111)
|....|...-...+||..+|++...|.+|+.+
T Consensus 24 f~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 24 AALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 43333333445788999999999999999875
No 53
>PF13518 HTH_28: Helix-turn-helix domain
Probab=61.41 E-value=3.9 Score=22.35 Aligned_cols=24 Identities=29% Similarity=0.393 Sum_probs=19.5
Q ss_pred HHHHHHHHhCCCcccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNAR 96 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR 96 (111)
...++|..+|++..+|..|.+.-.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 355689999999999999987543
No 54
>KOG3623|consensus
Probab=61.01 E-value=10 Score=33.27 Aligned_cols=59 Identities=19% Similarity=0.240 Sum_probs=44.3
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 39 DQSSTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 39 ~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
+.+..+-+.++.+..++-.-|..+++.+..++..+...++..|......|.+||++++.
T Consensus 621 psg~~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrss 679 (1007)
T KOG3623|consen 621 PSGERPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSS 679 (1007)
T ss_pred CCCCCCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCC
Confidence 33444445566676777777888888877777777777777788888889999999887
No 55
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=59.70 E-value=4.2 Score=21.92 Aligned_cols=23 Identities=17% Similarity=0.209 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCcccccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMNAR 96 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqNrR 96 (111)
..++|..+|++...|..|..+-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 45789999999999999976543
No 56
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=58.54 E-value=14 Score=21.95 Aligned_cols=44 Identities=14% Similarity=0.184 Sum_probs=22.1
Q ss_pred CCcCCHHHH-HHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccc
Q psy15969 48 RLVFTDLQR-RTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 48 Rt~ft~~ql-~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFq 93 (111)
|.+|+.... .+++.+...+..- ...+ ..|..+|++..+|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~-~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCK-GNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTT-T-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchh-hhHH-HHHHHhCccHHHHHHHHH
Confidence 456776554 4444444433221 1223 348999999999999975
No 57
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=55.98 E-value=5.1 Score=21.93 Aligned_cols=22 Identities=27% Similarity=0.366 Sum_probs=17.3
Q ss_pred HHHHHHHHhCCCcccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqN 94 (111)
...++|..+|++...|..|...
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT-
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 5678899999999999999864
No 58
>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=55.38 E-value=10 Score=21.87 Aligned_cols=36 Identities=22% Similarity=0.288 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccc
Q psy15969 54 LQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 54 ~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFq 93 (111)
.|+..|+-.+. +...+.. +||..+|++...|+....
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHH
Confidence 46788888888 6666544 889999999988876543
No 59
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=54.72 E-value=9.7 Score=25.35 Aligned_cols=25 Identities=16% Similarity=0.016 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+|...-+.
T Consensus 124 s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 124 TMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678999999999999999876544
No 60
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=54.52 E-value=26 Score=24.92 Aligned_cols=36 Identities=19% Similarity=0.090 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccc
Q psy15969 53 DLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTV 88 (111)
Q Consensus 53 ~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qV 88 (111)
...+..|..++....|.+......+|..||++...|
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 456778888888889999999999999999997664
No 61
>PRK10072 putative transcriptional regulator; Provisional
Probab=53.85 E-value=6.7 Score=25.39 Aligned_cols=40 Identities=15% Similarity=0.003 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 51 FTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 51 ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.++..+..|...... ...+||..+|++...|..|...++.
T Consensus 33 ~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 356656666443322 2678899999999999999987654
No 62
>KOG0773|consensus
Probab=53.53 E-value=8.8 Score=29.72 Aligned_cols=39 Identities=33% Similarity=0.361 Sum_probs=33.5
Q ss_pred HHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCC
Q psy15969 61 AIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRS 99 (111)
Q Consensus 61 ~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~ 99 (111)
..-..++||+......|+....|+..+|.+||-|.+.+.
T Consensus 114 ~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~ 152 (342)
T KOG0773|consen 114 EEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRL 152 (342)
T ss_pred hhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHH
Confidence 334568999999999999999999999999999988743
No 63
>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=51.62 E-value=14 Score=20.16 Aligned_cols=39 Identities=21% Similarity=0.336 Sum_probs=26.6
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccc
Q psy15969 49 LVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFF 92 (111)
Q Consensus 49 t~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWF 92 (111)
..+++++++.+...+... .....||..+|++...|.-++
T Consensus 4 ~~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 356676666776666655 247789999999998877655
No 64
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=51.17 E-value=7.2 Score=22.64 Aligned_cols=21 Identities=24% Similarity=0.428 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCcccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqN 94 (111)
..++|..+|++..+|+.|-..
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999643
No 65
>KOG1146|consensus
Probab=50.51 E-value=19 Score=33.55 Aligned_cols=56 Identities=21% Similarity=0.156 Sum_probs=50.3
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccccCC
Q psy15969 44 PKKPRLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARRRS 99 (111)
Q Consensus 44 ~rr~Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~R~ 99 (111)
.+..++.+-++++..|-..|-.+..|+......|....+.+.+++.+||+|.+.|.
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs 760 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERS 760 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhh
Confidence 45567788889999999999999999999999999999999999999999998843
No 66
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=50.44 E-value=20 Score=19.19 Aligned_cols=42 Identities=26% Similarity=0.332 Sum_probs=29.6
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.+++.+..++..++. .+ ...++|..+|++...|..|...-+.
T Consensus 3 ~l~~~e~~i~~~~~~--g~----s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 3 SLTPREREVLRLLAE--GL----TNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCCHHHHHHHHHHHc--CC----CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 467777777755432 22 4577899999999999998765433
No 67
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=49.43 E-value=12 Score=25.98 Aligned_cols=44 Identities=25% Similarity=0.163 Sum_probs=33.9
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 48 RLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 48 Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.+.+|+.|..+|...+ .+ ....++|..+|++...|..|..+.+.
T Consensus 4 ~~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~k 47 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARE 47 (141)
T ss_pred ccCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3578999999997743 22 24668999999999999999876554
No 68
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=48.48 E-value=8.4 Score=20.54 Aligned_cols=20 Identities=25% Similarity=0.380 Sum_probs=15.3
Q ss_pred HHHHHHHhCCCccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFq 93 (111)
+.++|..+|++...|+.|=.
T Consensus 2 i~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 35789999999999998853
No 69
>PF13565 HTH_32: Homeodomain-like domain
Probab=48.22 E-value=55 Score=19.16 Aligned_cols=34 Identities=18% Similarity=0.265 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHH-HHHHhCCCc
Q psy15969 52 TDLQRRTLQAIFKETKRPSKEMQVT-IARQLGLEP 85 (111)
Q Consensus 52 t~~ql~~Le~~F~~~~~ps~~~r~~-LA~~lgL~~ 85 (111)
++++...|...+..++..+..+... |...+|+..
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISV 66 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC
Confidence 7788799999999888777777766 566667543
No 70
>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=48.11 E-value=8.5 Score=20.17 Aligned_cols=24 Identities=21% Similarity=0.392 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCccccccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
..++|..+|++...|..|..+..-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 457889999999999999876543
No 71
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=47.43 E-value=9.7 Score=25.62 Aligned_cols=25 Identities=32% Similarity=0.195 Sum_probs=20.9
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+.+..-|.
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~ 148 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARK 148 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3568899999999999998876665
No 72
>PRK00118 putative DNA-binding protein; Validated
Probab=47.42 E-value=20 Score=23.53 Aligned_cols=43 Identities=14% Similarity=0.213 Sum_probs=30.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.+++.+..++...|..+. ...+||..+|++...|..|....+.
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArk 59 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEK 59 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 456666677666555432 4667899999999999999875544
No 73
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.79 E-value=24 Score=22.84 Aligned_cols=39 Identities=10% Similarity=0.054 Sum_probs=28.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTV 88 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qV 88 (111)
+++++|...-...|+.|--.+....+++|..||.++..|
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 467788777777766666666667788899998876544
No 74
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=46.62 E-value=34 Score=23.93 Aligned_cols=36 Identities=25% Similarity=0.158 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccc
Q psy15969 54 LQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 54 ~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVk 89 (111)
.-+..|..+=+...|.+......+|..||++...|.
T Consensus 24 ~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 456666666667789999999999999999987754
No 75
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=46.33 E-value=15 Score=25.76 Aligned_cols=25 Identities=16% Similarity=0.076 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|+++...-+.
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~ 184 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLI 184 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHH
Confidence 4678899999999999999876665
No 76
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=45.98 E-value=14 Score=25.04 Aligned_cols=25 Identities=28% Similarity=0.222 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...++|..+|++...|..|...-+.
T Consensus 146 s~~eIA~~lgis~~tV~~~l~ra~~ 170 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVRSRIFRARE 170 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4568899999999999999875554
No 77
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=45.80 E-value=30 Score=20.59 Aligned_cols=39 Identities=33% Similarity=0.444 Sum_probs=23.0
Q ss_pred cCCHHHHHHHHHH---HhhCCCCCHHHHHHHHHHhCCC-cccccc
Q psy15969 50 VFTDLQRRTLQAI---FKETKRPSKEMQVTIARQLGLE-PTTVGN 90 (111)
Q Consensus 50 ~ft~~ql~~Le~~---F~~~~~ps~~~r~~LA~~lgL~-~~qVkv 90 (111)
.+|+-|..+|+-+ ...+.|| +...+||..+|+. ...|..
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~--Pt~rEIa~~~g~~S~~tv~~ 45 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYP--PTVREIAEALGLKSTSTVQR 45 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcCCC--CCHHHHHHHhCCCChHHHHH
Confidence 4667777666654 4567777 4677889999997 555543
No 78
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=44.56 E-value=27 Score=23.07 Aligned_cols=41 Identities=17% Similarity=0.287 Sum_probs=31.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.+++..+..|...+... ...+|..||++...|+.|=++++.
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 37777777777766543 456799999999999999988754
No 79
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=44.42 E-value=7.4 Score=21.29 Aligned_cols=21 Identities=29% Similarity=0.362 Sum_probs=18.2
Q ss_pred HHHHHhCCCcccccccccccc
Q psy15969 76 TIARQLGLEPTTVGNFFMNAR 96 (111)
Q Consensus 76 ~LA~~lgL~~~qVkvWFqNrR 96 (111)
+||..+|++...|..|+.+..
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 578999999999999998763
No 80
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.36 E-value=41 Score=21.67 Aligned_cols=43 Identities=14% Similarity=0.238 Sum_probs=32.9
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC-Ccccccccccc
Q psy15969 48 RLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGL-EPTTVGNFFMN 94 (111)
Q Consensus 48 Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL-~~~qVkvWFqN 94 (111)
+..||++....+-..+....+ ....+|..+|+ ...++..|-..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~ 48 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQ 48 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHH
Confidence 678999887766666555443 57789999996 99999988753
No 81
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=44.23 E-value=18 Score=24.11 Aligned_cols=26 Identities=23% Similarity=0.155 Sum_probs=20.9
Q ss_pred HHHHHHHHHhCCCccccccccccccc
Q psy15969 72 EMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 72 ~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
....+||..+|++...|.++...-|.
T Consensus 128 ~~~~eIA~~l~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 128 VSLTALAEQLGRTVNAVYKALSRLRV 153 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 35678999999999999988765544
No 82
>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=43.16 E-value=19 Score=20.21 Aligned_cols=37 Identities=30% Similarity=0.376 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccc
Q psy15969 51 FTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 51 ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVk 89 (111)
||+.|..+|..++....- .....+||..++++...|.
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs 39 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTVS 39 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHH
Confidence 688899999888776543 2256778888998876654
No 83
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=42.91 E-value=16 Score=24.56 Aligned_cols=25 Identities=32% Similarity=0.274 Sum_probs=21.1
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|..|...-+.
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~ 167 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQ 167 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578999999999999999876555
No 84
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=42.80 E-value=41 Score=23.04 Aligned_cols=36 Identities=19% Similarity=0.151 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccc
Q psy15969 54 LQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 54 ~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVk 89 (111)
.-+..|...=....|.+......+|..+|++...|.
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 445566665556679999999999999999987653
No 85
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=42.47 E-value=41 Score=23.21 Aligned_cols=36 Identities=17% Similarity=0.162 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccc
Q psy15969 54 LQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 54 ~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVk 89 (111)
.-+.+|...=..-.|.+......+|..+|++...|-
T Consensus 23 ~ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 23 AVIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 445666666566789999999999999999987754
No 86
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=41.97 E-value=18 Score=25.76 Aligned_cols=25 Identities=28% Similarity=0.142 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+++...+.
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~ 195 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALA 195 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678999999999999998876655
No 87
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=41.66 E-value=13 Score=21.62 Aligned_cols=21 Identities=14% Similarity=0.339 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCcccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqN 94 (111)
..++|..+|++...|..|-.+
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999764
No 88
>cd00131 PAX Paired Box domain
Probab=41.00 E-value=1.1e+02 Score=20.49 Aligned_cols=45 Identities=13% Similarity=0.003 Sum_probs=30.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC-------Ccccccccccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGL-------EPTTVGNFFMN 94 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL-------~~~qVkvWFqN 94 (111)
..++.+...+..+...++..+..+...+...-|+ +..+|--||++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 5567777777777788888887777665334455 66667666654
No 89
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=40.54 E-value=22 Score=24.34 Aligned_cols=25 Identities=8% Similarity=0.061 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+++..-+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~ 171 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLL 171 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHH
Confidence 4678999999999999999876554
No 90
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=39.90 E-value=22 Score=24.26 Aligned_cols=25 Identities=24% Similarity=0.418 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.-.+||..+|++...|.++...-+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~ 161 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLR 161 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578899999999999999876655
No 91
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=39.42 E-value=21 Score=22.81 Aligned_cols=25 Identities=32% Similarity=0.312 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|..+...-+.
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARK 152 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4668899999999999998876544
No 92
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=39.24 E-value=23 Score=23.25 Aligned_cols=25 Identities=28% Similarity=0.300 Sum_probs=20.0
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|..+...-+.
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALK 155 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4567899999999999988765544
No 93
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=38.25 E-value=38 Score=23.13 Aligned_cols=35 Identities=26% Similarity=0.247 Sum_probs=25.2
Q ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccc
Q psy15969 55 QRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 55 ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVk 89 (111)
-+..|..+=+.-.|.+......+|..+||+...|.
T Consensus 15 ll~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 15 LLPILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 45566666566789999999999999999987754
No 94
>PHA02955 hypothetical protein; Provisional
Probab=38.22 E-value=57 Score=24.27 Aligned_cols=43 Identities=16% Similarity=0.080 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHhhC-CCCCHHHHHHHHHHhCCCccccccccccc
Q psy15969 53 DLQRRTLQAIFKET-KRPSKEMQVTIARQLGLEPTTVGNFFMNA 95 (111)
Q Consensus 53 ~~ql~~Le~~F~~~-~~ps~~~r~~LA~~lgL~~~qVkvWFqNr 95 (111)
..++..|-..|... ...+..++..++..+|+....|..||.+-
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 34566666666554 45677889999999999998788898764
No 95
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=38.12 E-value=14 Score=21.51 Aligned_cols=21 Identities=14% Similarity=0.199 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCcccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqN 94 (111)
..++|..+|++...+..|...
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999763
No 96
>PRK09480 slmA division inhibitor protein; Provisional
Probab=38.06 E-value=30 Score=23.63 Aligned_cols=35 Identities=9% Similarity=0.231 Sum_probs=28.3
Q ss_pred HHHHhhCCCCCHHHHHHHHHHhCCCccccccccccc
Q psy15969 60 QAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNA 95 (111)
Q Consensus 60 e~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNr 95 (111)
...|...+. +......||...|++...+-.+|.|.
T Consensus 20 ~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K 54 (194)
T PRK09480 20 AQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSK 54 (194)
T ss_pred HHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCH
Confidence 334555556 77889999999999999999999885
No 97
>PRK04217 hypothetical protein; Provisional
Probab=38.01 E-value=39 Score=22.39 Aligned_cols=45 Identities=20% Similarity=0.199 Sum_probs=34.0
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 48 RLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 48 Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
-..++..+..++...|...- ...+||..+|++...|...+...+.
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArk 84 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARK 84 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45788889888877765443 5677999999999999888765444
No 98
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=37.62 E-value=32 Score=23.51 Aligned_cols=25 Identities=32% Similarity=0.240 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...++|..+|++...|.+....-+.
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARA 176 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4568899999999999998876554
No 99
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=37.52 E-value=22 Score=24.59 Aligned_cols=25 Identities=20% Similarity=0.077 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.++...-+.
T Consensus 157 s~~EIA~~lgis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHRALA 181 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678999999999999998765544
No 100
>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=37.40 E-value=24 Score=19.70 Aligned_cols=38 Identities=26% Similarity=0.392 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccc
Q psy15969 51 FTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFF 92 (111)
Q Consensus 51 ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWF 92 (111)
+|..|..+|...+...+ ....+||..++++...|..+.
T Consensus 1 lt~~q~~iL~~l~~~~~----~~~~~la~~~~~~~~~~t~~i 38 (59)
T PF01047_consen 1 LTPSQFRILRILYENGG----ITQSELAEKLGISRSTVTRII 38 (59)
T ss_dssp STHHHHHHHHHHHHHSS----EEHHHHHHHHTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCC----CCHHHHHHHHCCChhHHHHHH
Confidence 47788899988887665 234488999999887776554
No 101
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=37.28 E-value=46 Score=22.95 Aligned_cols=25 Identities=24% Similarity=0.325 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+|...-+.
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHH
Confidence 4678999999999999998875554
No 102
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=37.23 E-value=25 Score=24.08 Aligned_cols=25 Identities=28% Similarity=0.333 Sum_probs=20.1
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.++...-+.
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~ 142 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRK 142 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678899999999999988765444
No 103
>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=37.19 E-value=28 Score=18.67 Aligned_cols=37 Identities=27% Similarity=0.328 Sum_probs=25.2
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccc
Q psy15969 52 TDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 52 t~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqN 94 (111)
++.+..++..++ +. ....++|..+|++...|..|...
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 455556554433 22 24577889999999999998764
No 104
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=37.16 E-value=71 Score=22.71 Aligned_cols=34 Identities=21% Similarity=0.147 Sum_probs=25.1
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccc
Q psy15969 56 RRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 56 l~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVk 89 (111)
+..|..+=....|.+......+|..+||+...|.
T Consensus 39 i~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 39 IEVLHKAQELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 3444444455679999999999999999986643
No 105
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=37.04 E-value=22 Score=24.07 Aligned_cols=25 Identities=20% Similarity=0.215 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+|...-+.
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~ 150 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRK 150 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578999999999999999876665
No 106
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=36.90 E-value=17 Score=20.98 Aligned_cols=21 Identities=24% Similarity=0.322 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCcccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqN 94 (111)
..++|..+|++...|..|.+.
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999863
No 107
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=36.88 E-value=58 Score=20.19 Aligned_cols=44 Identities=14% Similarity=0.219 Sum_probs=31.9
Q ss_pred cCCHHHHHHHHHHHhh-----CCCCCHHHHHHHHHHhCCCccccccccc
Q psy15969 50 VFTDLQRRTLQAIFKE-----TKRPSKEMQVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~-----~~~ps~~~r~~LA~~lgL~~~qVkvWFq 93 (111)
.+|.+++..|...|.. +.+.+..+...+...+|++...|..+|.
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4678888888888764 3467777777766667888777776664
No 108
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=36.39 E-value=23 Score=23.75 Aligned_cols=25 Identities=28% Similarity=0.488 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|..+...-+.
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~ 153 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKK 153 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4677899999999999998865554
No 109
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=36.21 E-value=18 Score=25.09 Aligned_cols=27 Identities=26% Similarity=0.132 Sum_probs=22.0
Q ss_pred HHHHHHHHHHhCCCccccccccccccc
Q psy15969 71 KEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 71 ~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.....+||..+|++...|.+|+..-+.
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~ 183 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLL 183 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 345678999999999999999876555
No 110
>PRK13558 bacterio-opsin activator; Provisional
Probab=35.87 E-value=37 Score=28.27 Aligned_cols=41 Identities=22% Similarity=0.229 Sum_probs=34.5
Q ss_pred CcCCHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhCCCccccc
Q psy15969 49 LVFTDLQRRTLQAIFKETKR--PSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 49 t~ft~~ql~~Le~~F~~~~~--ps~~~r~~LA~~lgL~~~qVk 89 (111)
..+|+.|..+|+..|...-| |-.....+||..||++...+.
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~ 648 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFH 648 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH
Confidence 47999999999999997764 666778899999999987643
No 111
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=35.79 E-value=18 Score=19.71 Aligned_cols=23 Identities=13% Similarity=0.078 Sum_probs=19.6
Q ss_pred HHHHHHHhCCCcccccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMNAR 96 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqNrR 96 (111)
..+||..+|++...|..|..+..
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57789999999999999987653
No 112
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=35.27 E-value=41 Score=23.18 Aligned_cols=25 Identities=28% Similarity=0.291 Sum_probs=20.3
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+.+...+.
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~ 169 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYV 169 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678899999999999988775544
No 113
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=35.07 E-value=41 Score=22.52 Aligned_cols=24 Identities=29% Similarity=0.332 Sum_probs=19.3
Q ss_pred HHHHHHHHhCCCcccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNAR 96 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR 96 (111)
...+||..+|++...|.++...-+
T Consensus 131 s~~EIA~~l~is~~tV~~~l~ra~ 154 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLNKAA 154 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 457889999999999998876443
No 114
>PF13730 HTH_36: Helix-turn-helix domain
Probab=34.69 E-value=21 Score=19.79 Aligned_cols=43 Identities=16% Similarity=0.104 Sum_probs=28.1
Q ss_pred cCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCccccccccc
Q psy15969 50 VFTDLQRRTLQAIFKE---TKRPSKEMQVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~---~~~ps~~~r~~LA~~lgL~~~qVkvWFq 93 (111)
.+++....++...+.. +.. ..+....||..+|++...|..+..
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3566666666555432 222 333577889999999998887764
No 115
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. 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 RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=33.92 E-value=17 Score=25.02 Aligned_cols=28 Identities=25% Similarity=0.139 Sum_probs=22.6
Q ss_pred CHHHHHHHHHHhCCCccccccccccccc
Q psy15969 70 SKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 70 s~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
......+||..+|++...|.++...-|.
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar~ 180 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRARE 180 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3345678999999999999999876665
No 116
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=33.84 E-value=26 Score=23.99 Aligned_cols=27 Identities=22% Similarity=0.112 Sum_probs=21.9
Q ss_pred HHHHHHHHHHhCCCccccccccccccc
Q psy15969 71 KEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 71 ~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.....++|..+|++...|.+++..-+.
T Consensus 152 g~s~~eIA~~lgis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 152 DLSLKEISEILDLPVGTVKTRIHRGRE 178 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 345678999999999999999876555
No 117
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=33.82 E-value=64 Score=18.11 Aligned_cols=20 Identities=30% Similarity=0.436 Sum_probs=8.8
Q ss_pred CCCHHHHHHHHHHhCCCccc
Q psy15969 68 RPSKEMQVTIARQLGLEPTT 87 (111)
Q Consensus 68 ~ps~~~r~~LA~~lgL~~~q 87 (111)
.|+......||..||++...
T Consensus 37 ~~~~~~l~~ia~~l~~~~~e 56 (63)
T PF13443_consen 37 NPSLDTLEKIAKALNCSPEE 56 (63)
T ss_dssp ---HHHHHHHHHHHT--HHH
T ss_pred cccHHHHHHHHHHcCCCHHH
Confidence 55555666666666655544
No 118
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=33.60 E-value=39 Score=23.58 Aligned_cols=25 Identities=12% Similarity=0.208 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.++...-|.
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~ 176 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARL 176 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678999999999999999875554
No 119
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=33.60 E-value=20 Score=24.76 Aligned_cols=25 Identities=12% Similarity=0.294 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.++...-+.
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~ 170 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRR 170 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 4578899999999999998876665
No 120
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=33.57 E-value=43 Score=17.86 Aligned_cols=14 Identities=36% Similarity=0.278 Sum_probs=11.8
Q ss_pred CcCCHHHHHHHHHH
Q psy15969 49 LVFTDLQRRTLQAI 62 (111)
Q Consensus 49 t~ft~~ql~~Le~~ 62 (111)
+.||+.|+..|+.-
T Consensus 1 s~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 1 SPFTPAQLQELRAQ 14 (37)
T ss_pred CCCCHHHHHHHHHH
Confidence 46999999999874
No 121
>PRK06930 positive control sigma-like factor; Validated
Probab=33.41 E-value=29 Score=24.53 Aligned_cols=43 Identities=19% Similarity=0.153 Sum_probs=30.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.+++.+..++...|..+ ....++|..+|++...|+.++..-+.
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~ 156 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEK 156 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45666666665544322 24678899999999999999876655
No 122
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=33.20 E-value=32 Score=23.96 Aligned_cols=25 Identities=20% Similarity=0.076 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.++...-+.
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~ 172 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARD 172 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578999999999999998876555
No 123
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=32.66 E-value=50 Score=21.90 Aligned_cols=25 Identities=16% Similarity=0.110 Sum_probs=20.1
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+....-+.
T Consensus 124 s~~EIA~~lgis~~tV~~~l~ra~~ 148 (161)
T PRK09047 124 DVAETAAAMGCSEGSVKTHCSRATH 148 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3578899999999999988765554
No 124
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=32.36 E-value=29 Score=23.28 Aligned_cols=25 Identities=24% Similarity=0.179 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...++|..+|++...|.++...-+.
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~ 154 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRK 154 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578899999999999998876554
No 125
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=32.19 E-value=78 Score=22.25 Aligned_cols=34 Identities=32% Similarity=0.448 Sum_probs=25.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC-CCcccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLG-LEPTTV 88 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lg-L~~~qV 88 (111)
.+|++.+..|..++.... ...+||..|| ++..-|
T Consensus 2 ~Wtde~~~~L~~lw~~G~-----SasqIA~~lg~vsRnAV 36 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGL-----SASQIARQLGGVSRNAV 36 (162)
T ss_pred CCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCcchhhh
Confidence 578999999999987653 4566788888 666544
No 126
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=32.12 E-value=37 Score=22.43 Aligned_cols=25 Identities=12% Similarity=0.129 Sum_probs=20.6
Q ss_pred CHHHHHHHHHHhCCCcccccccccc
Q psy15969 70 SKEMQVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 70 s~~~r~~LA~~lgL~~~qVkvWFqN 94 (111)
......+||..+|++...+..+|..
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3356788999999999999998864
No 127
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=32.02 E-value=30 Score=22.67 Aligned_cols=40 Identities=25% Similarity=0.346 Sum_probs=28.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqN 94 (111)
.+|..|..+|+.+|..+ -...+||..+|++...|..|...
T Consensus 17 LLT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 17 LLTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp GS-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 47888888888776655 36788999999999888887753
No 128
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=32.00 E-value=35 Score=23.67 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...++|..+|++...|.+-+..-|.
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~ 173 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARK 173 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4578899999999999988776555
No 129
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=31.82 E-value=48 Score=23.17 Aligned_cols=25 Identities=16% Similarity=0.218 Sum_probs=20.9
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+++.--+.
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~ 178 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKR 178 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4578899999999999999876555
No 130
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=31.33 E-value=46 Score=22.52 Aligned_cols=25 Identities=20% Similarity=0.048 Sum_probs=20.9
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.++...-+.
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~ 154 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARN 154 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4678899999999999998876555
No 131
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=31.21 E-value=1.4e+02 Score=20.40 Aligned_cols=34 Identities=21% Similarity=0.174 Sum_probs=28.1
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC
Q psy15969 49 LVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLG 82 (111)
Q Consensus 49 t~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lg 82 (111)
-.+|+..+.+|+-+++...+|+..+.......-+
T Consensus 17 lr~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~ 50 (145)
T COG0735 17 LRLTPQRLAVLELLLEADGHLSAEELYEELREEG 50 (145)
T ss_pred CCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhC
Confidence 4588999999999999888899998888766544
No 132
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=31.19 E-value=32 Score=22.99 Aligned_cols=25 Identities=24% Similarity=0.266 Sum_probs=20.9
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...++|..+|++...|.++...-+.
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALA 152 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4678899999999999998876665
No 133
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=31.12 E-value=1.3e+02 Score=18.54 Aligned_cols=33 Identities=24% Similarity=0.354 Sum_probs=26.1
Q ss_pred cCCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhC
Q psy15969 50 VFTDLQRRTLQAIFK---ETKRPSKEMQVTIARQLG 82 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~---~~~~ps~~~r~~LA~~lg 82 (111)
.|+..+...|...|+ .-..+|+.+...||.+||
T Consensus 32 ~f~~~~yedl~diy~~V~~K~~fS~sEm~aI~~ELG 67 (71)
T PF06569_consen 32 DFSEEKYEDLKDIYEMVMSKDSFSPSEMQAIAEELG 67 (71)
T ss_pred hCChhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHH
Confidence 577777777777775 456789999999999997
No 134
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=31.08 E-value=33 Score=23.89 Aligned_cols=26 Identities=27% Similarity=0.222 Sum_probs=20.9
Q ss_pred HHHHHHHHHhCCCccccccccccccc
Q psy15969 72 EMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 72 ~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
....++|..+|++...|...+..-+.
T Consensus 123 ~~~~EIA~~lgis~~tV~~~l~Rar~ 148 (181)
T PRK09637 123 LSQKEIAEKLGLSLSGAKSRVQRGRV 148 (181)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34678999999999999988875554
No 135
>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=30.48 E-value=24 Score=18.43 Aligned_cols=23 Identities=22% Similarity=0.212 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCcccccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMNAR 96 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqNrR 96 (111)
..++|..+|++...|..|..+..
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 45678889999999999886543
No 136
>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=30.27 E-value=17 Score=21.19 Aligned_cols=41 Identities=27% Similarity=0.426 Sum_probs=26.6
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccc
Q psy15969 52 TDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFF 92 (111)
Q Consensus 52 t~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWF 92 (111)
|+..-..|+.+|....--.......||..+|++...|..-+
T Consensus 3 t~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml 43 (60)
T PF01325_consen 3 TESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEML 43 (60)
T ss_dssp SCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred CcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHH
Confidence 44555677777776543334456788999999988776543
No 137
>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=30.25 E-value=66 Score=17.19 Aligned_cols=37 Identities=27% Similarity=0.465 Sum_probs=22.7
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccc
Q psy15969 52 TDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFF 92 (111)
Q Consensus 52 t~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWF 92 (111)
+..+..+|...++ ++.. ...+||..+|++...|..-+
T Consensus 2 ~~~~~~Il~~l~~-~~~~---t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPRI---TQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp -HHHHHHHHHHHH-CTTS----HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHH-cCCC---CHHHHHHHhCCCHHHHHHHH
Confidence 3456677766665 4433 46678999999988765433
No 138
>PF13551 HTH_29: Winged helix-turn helix
Probab=29.77 E-value=1.4e+02 Score=18.36 Aligned_cols=46 Identities=22% Similarity=0.393 Sum_probs=30.0
Q ss_pred CCcCCHHHHHHHHHHHhhCC-----CCCHHHHHH-H-HHHhC--CCccccccccc
Q psy15969 48 RLVFTDLQRRTLQAIFKETK-----RPSKEMQVT-I-ARQLG--LEPTTVGNFFM 93 (111)
Q Consensus 48 Rt~ft~~ql~~Le~~F~~~~-----~ps~~~r~~-L-A~~lg--L~~~qVkvWFq 93 (111)
...+++++...|..++..++ ..+...... | ....| ++...|..|+.
T Consensus 55 ~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 55 RKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 33499999999999999876 344454444 3 33333 55666777664
No 139
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=29.26 E-value=32 Score=24.18 Aligned_cols=25 Identities=24% Similarity=0.065 Sum_probs=21.1
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...++|..+|++...|.+++..-+.
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~ 155 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARA 155 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578899999999999999876655
No 140
>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=29.26 E-value=35 Score=18.77 Aligned_cols=33 Identities=15% Similarity=0.289 Sum_probs=20.2
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccc
Q psy15969 56 RRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNF 91 (111)
Q Consensus 56 l~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvW 91 (111)
..+|...+..+.+. ...+||..+|++...|..-
T Consensus 3 ~~il~~L~~~~~~i---t~~eLa~~l~vS~rTi~~~ 35 (55)
T PF08279_consen 3 KQILKLLLESKEPI---TAKELAEELGVSRRTIRRD 35 (55)
T ss_dssp HHHHHHHHHTTTSB---EHHHHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHHcCCCc---CHHHHHHHhCCCHHHHHHH
Confidence 34444444544443 4567899999998887643
No 141
>PF12728 HTH_17: Helix-turn-helix domain
Probab=28.88 E-value=26 Score=19.11 Aligned_cols=22 Identities=23% Similarity=0.268 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCccccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMNA 95 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqNr 95 (111)
..++|..||++...|..|..+.
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 3567888899999999988654
No 142
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=28.79 E-value=69 Score=21.36 Aligned_cols=25 Identities=40% Similarity=0.489 Sum_probs=19.3
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...++|..+|++...|.......+.
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~ 151 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALV 151 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678899999999999987654433
No 143
>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=28.74 E-value=67 Score=21.05 Aligned_cols=38 Identities=18% Similarity=0.242 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccc
Q psy15969 51 FTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 51 ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFq 93 (111)
+|-+.....-.++.... ...++|..++++...|..||.
T Consensus 3 YS~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 3 YSLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CCHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 34444444555665543 456688999999999999998
No 144
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=28.56 E-value=28 Score=20.00 Aligned_cols=20 Identities=15% Similarity=0.137 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFq 93 (111)
..++|..+|++...|..|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35678899999999999964
No 145
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=28.47 E-value=69 Score=21.65 Aligned_cols=25 Identities=32% Similarity=0.313 Sum_probs=19.9
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.......+.
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~ 160 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALR 160 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4578899999999999988765544
No 146
>PRK00215 LexA repressor; Validated
Probab=28.41 E-value=38 Score=24.05 Aligned_cols=41 Identities=34% Similarity=0.430 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCC-Cccccccccc
Q psy15969 51 FTDLQRRTLQAIFK---ETKRPSKEMQVTIARQLGL-EPTTVGNFFM 93 (111)
Q Consensus 51 ft~~ql~~Le~~F~---~~~~ps~~~r~~LA~~lgL-~~~qVkvWFq 93 (111)
+|+.|..+|..... .+.++ ....+||..+|+ +...|..+..
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~--~s~~ela~~~~~~~~~tv~~~l~ 46 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYP--PSRREIADALGLRSPSAVHEHLK 46 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCC--CCHHHHHHHhCCCChHHHHHHHH
Confidence 57888888877753 23333 346688999999 8887776654
No 147
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=28.14 E-value=61 Score=22.20 Aligned_cols=25 Identities=24% Similarity=0.102 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.++...-+.
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~ 177 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALS 177 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4578899999999999988765554
No 148
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=27.76 E-value=48 Score=22.63 Aligned_cols=24 Identities=25% Similarity=0.375 Sum_probs=19.6
Q ss_pred HHHHHHHHHhCCCccccccccccc
Q psy15969 72 EMQVTIARQLGLEPTTVGNFFMNA 95 (111)
Q Consensus 72 ~~r~~LA~~lgL~~~qVkvWFqNr 95 (111)
....+||..+|++...|.++...-
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~Ra 159 (172)
T PRK09651 136 LTYSEIAHKLGVSVSSVKKYVAKA 159 (172)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Confidence 356789999999999999887543
No 149
>PHA01976 helix-turn-helix protein
Probab=27.11 E-value=32 Score=19.67 Aligned_cols=22 Identities=14% Similarity=0.308 Sum_probs=18.7
Q ss_pred HHHHHHHhCCCccccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMNA 95 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqNr 95 (111)
..+||..+|++...|..|....
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 5678999999999999998654
No 150
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=26.85 E-value=1e+02 Score=20.14 Aligned_cols=17 Identities=24% Similarity=0.385 Sum_probs=13.0
Q ss_pred HHHHHHHHhCCCccccc
Q psy15969 73 MQVTIARQLGLEPTTVG 89 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVk 89 (111)
...+||..+|++...|.
T Consensus 125 s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 125 KEIDIAKKLHISRQSVY 141 (142)
T ss_pred CHHHHHHHHCcCHHhhc
Confidence 35678889999887764
No 151
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=26.73 E-value=47 Score=22.21 Aligned_cols=25 Identities=24% Similarity=0.127 Sum_probs=19.0
Q ss_pred HHHHHHHHHhCCCcccccccccccc
Q psy15969 72 EMQVTIARQLGLEPTTVGNFFMNAR 96 (111)
Q Consensus 72 ~~r~~LA~~lgL~~~qVkvWFqNrR 96 (111)
....+||..+|++...|.+...--+
T Consensus 139 ~s~~eIA~~l~is~~tv~~~l~ra~ 163 (170)
T TIGR02952 139 LPIAEVARILGKTEGAVKILQFRAI 163 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3457889999999999888765433
No 152
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=26.71 E-value=45 Score=22.97 Aligned_cols=25 Identities=16% Similarity=0.080 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...++|..+|++...|.+....-+.
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~ 171 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLK 171 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578899999999999998876665
No 153
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=26.64 E-value=77 Score=21.35 Aligned_cols=25 Identities=20% Similarity=0.192 Sum_probs=19.9
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...++|..+|++...|.++...-+.
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~ 161 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALK 161 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678899999999999887765444
No 154
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=26.57 E-value=31 Score=21.42 Aligned_cols=21 Identities=19% Similarity=0.154 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCcccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqN 94 (111)
..++|..+|++...|..|-..
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999764
No 155
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=26.47 E-value=33 Score=20.20 Aligned_cols=23 Identities=22% Similarity=0.378 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCcccccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMNAR 96 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqNrR 96 (111)
...||..+|++...|..|+.+.+
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46799999999999999997653
No 156
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=26.47 E-value=1.1e+02 Score=20.52 Aligned_cols=36 Identities=17% Similarity=0.189 Sum_probs=21.0
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccc
Q psy15969 49 LVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 49 t~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVk 89 (111)
..++++|+..+..++.... ...+++..+|+++-.|+
T Consensus 32 ~~L~~E~~~Fi~~Fi~~rG-----nlKe~e~~lgiSYPTvR 67 (113)
T PF09862_consen 32 ARLSPEQLEFIKLFIKNRG-----NLKEMEKELGISYPTVR 67 (113)
T ss_pred hcCCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCcHHHH
Confidence 3678899888888765432 23344444455444443
No 157
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=26.26 E-value=2e+02 Score=20.02 Aligned_cols=34 Identities=12% Similarity=-0.004 Sum_probs=27.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGL 83 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL 83 (111)
.+|+..+.+|+.++....+++..+........+.
T Consensus 23 R~T~qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~ 56 (169)
T PRK11639 23 RLTPQRLEVLRLMSLQPGAISAYDLLDLLREAEP 56 (169)
T ss_pred CCCHHHHHHHHHHHhcCCCCCHHHHHHHHHhhCC
Confidence 5788888889888888788999888876666553
No 158
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=26.11 E-value=47 Score=22.82 Aligned_cols=25 Identities=28% Similarity=0.162 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+....-+.
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~ 159 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALK 159 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578899999999999988776655
No 159
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=26.07 E-value=52 Score=22.86 Aligned_cols=25 Identities=28% Similarity=0.449 Sum_probs=20.0
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+..+.-+.
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~ 173 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRK 173 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678899999999999888765544
No 160
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=25.99 E-value=61 Score=22.51 Aligned_cols=25 Identities=16% Similarity=0.234 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+....-+.
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~ 178 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARE 178 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578999999999999998876554
No 161
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=25.83 E-value=73 Score=22.20 Aligned_cols=25 Identities=24% Similarity=0.093 Sum_probs=20.3
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.++...-+.
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~ 153 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARA 153 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 4678899999999999998765544
No 162
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=25.68 E-value=86 Score=21.59 Aligned_cols=44 Identities=20% Similarity=0.127 Sum_probs=32.9
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 48 RLVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 48 Rt~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
-+.+|+.|..+|...+ .. ....++|..+|++...|..+-..-+.
T Consensus 4 ~~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~k 47 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAME 47 (137)
T ss_pred cCCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHH
Confidence 3578899999998742 22 25678899999999999888765444
No 163
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=25.67 E-value=69 Score=21.71 Aligned_cols=25 Identities=20% Similarity=0.434 Sum_probs=19.9
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...++|..+|++...|..+..+.+.
T Consensus 136 s~~EIA~~l~is~~tV~~~l~ra~~ 160 (168)
T PRK12525 136 TYVEIGERLGVSLSRIHQYMVEAFK 160 (168)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578899999999999988765443
No 164
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=25.49 E-value=36 Score=24.54 Aligned_cols=26 Identities=15% Similarity=0.202 Sum_probs=23.4
Q ss_pred HHHHHHHHHhCCCccccccccccccc
Q psy15969 72 EMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 72 ~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
..+.+|+.-++++..+|-+|..|-+.
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~ 40 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKD 40 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCC
Confidence 45788999999999999999999876
No 165
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=25.48 E-value=63 Score=24.21 Aligned_cols=24 Identities=25% Similarity=0.282 Sum_probs=21.0
Q ss_pred HHHHHHHhCCCccccccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
..+||..+|++...|...++.-|.
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~ 150 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARR 150 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHH
Confidence 568899999999999999987776
No 166
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=25.24 E-value=55 Score=23.59 Aligned_cols=39 Identities=21% Similarity=0.154 Sum_probs=31.2
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccc
Q psy15969 56 RRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNAR 96 (111)
Q Consensus 56 l~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR 96 (111)
+..-...|....|- .....||...|++...|-.+|.|.-
T Consensus 19 l~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe 57 (225)
T PRK11552 19 IAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKE 57 (225)
T ss_pred HHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHH
Confidence 34444568888877 5788899999999999999998854
No 167
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=25.17 E-value=33 Score=21.77 Aligned_cols=23 Identities=13% Similarity=0.040 Sum_probs=18.6
Q ss_pred HHHHHHHhCCCcccccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMNAR 96 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqNrR 96 (111)
..++|..+|++...|..|..+-.
T Consensus 3 i~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 45789999999999999976543
No 168
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=25.13 E-value=30 Score=20.39 Aligned_cols=18 Identities=33% Similarity=0.711 Sum_probs=15.2
Q ss_pred HHHHHHHhCCCccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNF 91 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvW 91 (111)
...||..||++...|..|
T Consensus 12 ~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 357899999999999999
No 169
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=25.00 E-value=82 Score=21.67 Aligned_cols=26 Identities=12% Similarity=0.050 Sum_probs=21.0
Q ss_pred HHHHHHHHHhCCCccccccccccccc
Q psy15969 72 EMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 72 ~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
....+||..+|++...|..+....+.
T Consensus 148 ~s~~eIA~~lgis~~tV~~~l~ra~~ 173 (184)
T PRK12539 148 LSVAEAATRSGMSESAVKVSVHRGLK 173 (184)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35678999999999999998865554
No 170
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=24.96 E-value=33 Score=22.87 Aligned_cols=23 Identities=9% Similarity=0.251 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCcccccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMNAR 96 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqNrR 96 (111)
...||..+|++...|..|..+.+
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~ 43 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDET 43 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46789999999999999998754
No 171
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=24.95 E-value=1.6e+02 Score=19.42 Aligned_cols=37 Identities=24% Similarity=0.370 Sum_probs=27.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVk 89 (111)
-+|+.|..+|..++..++..+ ..+||..+|++...|.
T Consensus 28 glt~~q~~vL~~l~~~~~~~t---~~eLa~~l~~~~~tvt 64 (144)
T PRK03573 28 ELTQTHWVTLHNIHQLPPEQS---QIQLAKAIGIEQPSLV 64 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCC---HHHHHHHhCCChhhHH
Confidence 478888888888876543333 3688999999887765
No 172
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=24.93 E-value=80 Score=23.18 Aligned_cols=25 Identities=20% Similarity=0.255 Sum_probs=20.7
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|..|...-+.
T Consensus 223 s~~eIA~~l~is~~tV~~~~~ra~~ 247 (257)
T PRK08583 223 SQKETGERLGISQMHVSRLQRQAIK 247 (257)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578999999999999999876554
No 173
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=24.92 E-value=64 Score=23.06 Aligned_cols=45 Identities=11% Similarity=0.093 Sum_probs=33.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNA 95 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNr 95 (111)
.+|+.++..|..+...+ +-....-.+||..++++..+|+..+.+-
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 47888877776665533 3334456789999999999999988754
No 174
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=24.88 E-value=75 Score=22.06 Aligned_cols=16 Identities=13% Similarity=0.204 Sum_probs=9.2
Q ss_pred cCCHHHHHHHHHHHhh
Q psy15969 50 VFTDLQRRTLQAIFKE 65 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~ 65 (111)
.+|.+|+..|..+.+.
T Consensus 51 ~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 51 YLDDEEIEKLEEAVEN 66 (144)
T ss_pred cCCHHHHHHHHHHHHh
Confidence 4566666666655543
No 175
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=24.62 E-value=48 Score=23.42 Aligned_cols=25 Identities=16% Similarity=0.066 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.++...-+.
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~ 175 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARA 175 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4578899999999999999876555
No 176
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=24.53 E-value=84 Score=22.46 Aligned_cols=42 Identities=29% Similarity=0.416 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 51 FTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 51 ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
+++.+..+|...|.. .....+||..+|++...|..|...-+.
T Consensus 179 L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~~ra~~ 220 (227)
T TIGR02980 179 LPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLLRRALK 220 (227)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 444444444444322 234678899999999999988754433
No 177
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=24.52 E-value=1.1e+02 Score=16.48 Aligned_cols=20 Identities=35% Similarity=0.647 Sum_probs=10.5
Q ss_pred CCCCCHHHHHHHHHHhCCCc
Q psy15969 66 TKRPSKEMQVTIARQLGLEP 85 (111)
Q Consensus 66 ~~~ps~~~r~~LA~~lgL~~ 85 (111)
...|+......||..+|++.
T Consensus 33 ~~~~~~~~~~~ia~~l~~~~ 52 (55)
T PF01381_consen 33 KRNPSLDTLKKIAKALGVSP 52 (55)
T ss_dssp SSTSBHHHHHHHHHHHTSEH
T ss_pred CCCCCHHHHHHHHHHHCCCH
Confidence 34455555555555555443
No 178
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=24.32 E-value=36 Score=21.13 Aligned_cols=20 Identities=10% Similarity=0.199 Sum_probs=16.8
Q ss_pred HHHHHHHhCCCccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFq 93 (111)
..++|..+|++..++..|-.
T Consensus 4 i~evA~~~gvs~~tLR~ye~ 23 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWEE 23 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999953
No 179
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=24.26 E-value=73 Score=22.27 Aligned_cols=25 Identities=20% Similarity=0.074 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..||++...|+++...-+.
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~ 158 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQ 158 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4568899999999999999876665
No 180
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=24.25 E-value=97 Score=19.74 Aligned_cols=40 Identities=10% Similarity=-0.022 Sum_probs=26.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccc
Q psy15969 50 VFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 50 ~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVk 89 (111)
.++..|..+|...+............+||..++++...|.
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs 61 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALV 61 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHH
Confidence 5788889888777632222234456778888888877664
No 181
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=24.24 E-value=63 Score=20.04 Aligned_cols=20 Identities=5% Similarity=0.152 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFq 93 (111)
...|...++|...+|.+|+.
T Consensus 56 ~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 56 TSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHhCCCCCeEEEEEE
Confidence 45577888999999999985
No 182
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=24.17 E-value=1.2e+02 Score=18.58 Aligned_cols=38 Identities=26% Similarity=0.392 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccc
Q psy15969 51 FTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFF 92 (111)
Q Consensus 51 ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWF 92 (111)
+++.|..+|...+....... ..||..++++...|....
T Consensus 20 lt~~q~~~L~~l~~~~~~~~----~~la~~l~i~~~~vt~~l 57 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITV----KELAERLGLDRSTVTRLL 57 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcH----HHHHHHHCCCHHHHHHHH
Confidence 78888888888777654332 888999999888776544
No 183
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=24.01 E-value=41 Score=24.63 Aligned_cols=25 Identities=16% Similarity=0.205 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+....-+.
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~ 213 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQ 213 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4578999999999999998876655
No 184
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=23.92 E-value=47 Score=24.09 Aligned_cols=25 Identities=20% Similarity=0.236 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|..+...-+.
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~ 226 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIK 226 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5678999999999999999877665
No 185
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=23.91 E-value=71 Score=24.00 Aligned_cols=25 Identities=28% Similarity=0.317 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|+..++.-|.
T Consensus 133 s~~EIA~~lg~s~~tVk~~l~RAr~ 157 (293)
T PRK09636 133 PFDEIASTLGRSPAACRQLASRARK 157 (293)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3568899999999999999987766
No 186
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=23.65 E-value=73 Score=21.91 Aligned_cols=25 Identities=24% Similarity=0.373 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+....-+.
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~ 164 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARK 164 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578899999999999998765554
No 187
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=23.28 E-value=56 Score=22.80 Aligned_cols=23 Identities=22% Similarity=0.374 Sum_probs=17.4
Q ss_pred HHHHHHHHHHhCCCccccccccc
Q psy15969 71 KEMQVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 71 ~~~r~~LA~~lgL~~~qVkvWFq 93 (111)
.....+||..+|++...+--|-+
T Consensus 34 r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 34 RRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp -S-HHHHHHHHTS-HHHHHHHHH
T ss_pred cchHHHHHHHhCCCHHHHHHHHh
Confidence 34578899999999999999974
No 188
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=23.24 E-value=12 Score=26.04 Aligned_cols=29 Identities=21% Similarity=0.068 Sum_probs=23.2
Q ss_pred CCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 69 PSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 69 ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.......+||..+|++...|.++...-+.
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~ 181 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQ 181 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34445688999999999999998876665
No 189
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=23.01 E-value=39 Score=19.20 Aligned_cols=17 Identities=29% Similarity=0.520 Sum_probs=12.4
Q ss_pred HHHHHHHHhCCCccccc
Q psy15969 73 MQVTIARQLGLEPTTVG 89 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVk 89 (111)
.-.+||..+|++..||+
T Consensus 30 SS~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 30 SSQELAEALGITPAQVR 46 (50)
T ss_dssp -HHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHHCCCHHHhc
Confidence 34678899999999885
No 190
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=22.73 E-value=82 Score=22.18 Aligned_cols=25 Identities=20% Similarity=0.211 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+....-|.
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~ 181 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRART 181 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4678899999999999988776555
No 191
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=22.71 E-value=60 Score=23.14 Aligned_cols=25 Identities=28% Similarity=0.271 Sum_probs=20.7
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.++...-+.
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk 180 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQ 180 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4568899999999999998876555
No 192
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=22.59 E-value=90 Score=21.45 Aligned_cols=38 Identities=13% Similarity=0.054 Sum_probs=29.2
Q ss_pred HHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccc
Q psy15969 57 RTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNA 95 (111)
Q Consensus 57 ~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNr 95 (111)
..-...|....|. ......||...|++...|-.+|.|+
T Consensus 15 ~aA~~lf~e~G~~-~tSi~~Ia~~aGvsk~~lY~~F~sK 52 (192)
T PRK14996 15 QAAMRVALAEGFA-AMTVRRIASEAQVAAGQVHHHFSSA 52 (192)
T ss_pred HHHHHHHHhcChh-hccHHHHHHHhCCCcHHHHHHcCCH
Confidence 3444457777774 4457888999999999999999875
No 193
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=22.53 E-value=82 Score=21.77 Aligned_cols=25 Identities=20% Similarity=0.216 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+....-|.
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~ 173 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARM 173 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578899999999999998776555
No 194
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=22.24 E-value=50 Score=17.06 Aligned_cols=18 Identities=39% Similarity=0.444 Sum_probs=12.7
Q ss_pred HHHHHHHHhCCCcccccc
Q psy15969 73 MQVTIARQLGLEPTTVGN 90 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkv 90 (111)
.+.+||..+|++...|.-
T Consensus 4 tr~diA~~lG~t~ETVSR 21 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSR 21 (32)
T ss_dssp -HHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHhCCcHHHHHH
Confidence 467899999999877653
No 195
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=22.17 E-value=86 Score=21.83 Aligned_cols=25 Identities=16% Similarity=0.223 Sum_probs=20.1
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+....-|.
T Consensus 149 s~~EIA~~lgis~~tvk~rl~Rar~ 173 (188)
T TIGR02943 149 ESDEICQELEISTSNCHVLLYRARL 173 (188)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5678999999999999887765544
No 196
>PRK10403 transcriptional regulator NarP; Provisional
Probab=22.15 E-value=60 Score=21.74 Aligned_cols=43 Identities=23% Similarity=0.197 Sum_probs=32.8
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 49 LVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 49 t~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
..+|+.+..+|..+... ....+||..++++...|.+...|=+.
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~ 194 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLR 194 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 35888888888765442 23567889999999999998887665
No 197
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=21.96 E-value=42 Score=25.84 Aligned_cols=23 Identities=26% Similarity=0.367 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhCCCccccccccc
Q psy15969 71 KEMQVTIARQLGLEPTTVGNFFM 93 (111)
Q Consensus 71 ~~~r~~LA~~lgL~~~qVkvWFq 93 (111)
.-....||..||+++.+|..|-+
T Consensus 19 gmk~~dIAeklGvspntiksWKr 41 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKR 41 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHH
Confidence 34567899999999999999975
No 198
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=21.93 E-value=89 Score=21.16 Aligned_cols=25 Identities=16% Similarity=0.090 Sum_probs=20.1
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.-.++|..+|++...|.+....-+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKK 161 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4578899999999999988765544
No 199
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=21.93 E-value=1.6e+02 Score=24.02 Aligned_cols=34 Identities=12% Similarity=-0.010 Sum_probs=25.9
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccc
Q psy15969 56 RRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 56 l~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVk 89 (111)
+.+|..+=....|.+...+..||..|||+...|-
T Consensus 40 IplL~~~Qe~~GyIp~~ai~~VAe~Lgvp~~~V~ 73 (400)
T PRK12373 40 IPLLMRAQEQEGWVTRAAIEKVADMLDMAYIRVL 73 (400)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 4444444455679999999999999999977654
No 200
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=21.87 E-value=43 Score=21.23 Aligned_cols=22 Identities=23% Similarity=0.268 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCccccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMNA 95 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqNr 95 (111)
..++|..+|++...|..|....
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~G 24 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEIG 24 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999998653
No 201
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=21.72 E-value=85 Score=23.24 Aligned_cols=25 Identities=20% Similarity=0.228 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|+++...-+.
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~ 203 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARE 203 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4678999999999999999876665
No 202
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.68 E-value=46 Score=20.99 Aligned_cols=22 Identities=14% Similarity=0.057 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCccccccccccc
Q psy15969 74 QVTIARQLGLEPTTVGNFFMNA 95 (111)
Q Consensus 74 r~~LA~~lgL~~~qVkvWFqNr 95 (111)
..++|..+|++...+..|....
T Consensus 3 i~eva~~~gvs~~tLRyye~~G 24 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDIG 24 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4678999999999999998653
No 203
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=21.50 E-value=1.3e+02 Score=20.51 Aligned_cols=25 Identities=12% Similarity=0.025 Sum_probs=19.1
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.+....-+.
T Consensus 155 s~~eIA~~lgis~~~v~~~l~Rar~ 179 (187)
T PRK12534 155 TYEELAARTDTPIGTVKSWIRRGLA 179 (187)
T ss_pred CHHHHHHHhCCChhHHHHHHHHHHH
Confidence 4578899999999998876654443
No 204
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=21.39 E-value=77 Score=20.97 Aligned_cols=33 Identities=15% Similarity=0.065 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccc
Q psy15969 55 QRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 55 ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVk 89 (111)
+...|...|. .-+......+||..+.++.+.++
T Consensus 5 ~y~~L~~~~~--~~~~~vtl~elA~~l~cS~Rn~r 37 (115)
T PF12793_consen 5 QYQRLWQHYG--GQPVEVTLDELAELLFCSRRNAR 37 (115)
T ss_pred HHHHHHHHcC--CCCcceeHHHHHHHhCCCHHHHH
Confidence 4455656665 45666788899999999987765
No 205
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=21.37 E-value=94 Score=20.50 Aligned_cols=43 Identities=30% Similarity=0.321 Sum_probs=32.6
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 49 LVFTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 49 t~ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
..+|+.+..+|..+ ..+ + ...++|..++++...|.++.+|-+.
T Consensus 148 ~~lt~~e~~vl~l~-~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~ 190 (211)
T PRK15369 148 PLLTPRERQILKLI-TEG-Y----TNRDIAEQLSISIKTVETHRLNMMR 190 (211)
T ss_pred cCCCHHHHHHHHHH-HCC-C----CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 35888888888763 332 2 2567889999999999999988665
No 206
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=21.29 E-value=1.2e+02 Score=21.20 Aligned_cols=22 Identities=27% Similarity=0.223 Sum_probs=16.6
Q ss_pred HHHHHHHHhCCCcccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqN 94 (111)
...+||..+|++...|.+=...
T Consensus 152 s~~EIA~~lg~s~~tV~~rl~r 173 (192)
T PRK09643 152 SVADAARMLGVAEGTVKSRCAR 173 (192)
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4568899999999988764433
No 207
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=21.28 E-value=1e+02 Score=22.08 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=17.9
Q ss_pred HHHHHHHHHhCCCcccccccccc
Q psy15969 72 EMQVTIARQLGLEPTTVGNFFMN 94 (111)
Q Consensus 72 ~~r~~LA~~lgL~~~qVkvWFqN 94 (111)
....+||..+|++...|..+-..
T Consensus 200 ~t~~eIA~~lgis~~~V~~~~~~ 222 (231)
T TIGR02885 200 KTQTEVANMLGISQVQVSRLEKK 222 (231)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 35778999999999888776543
No 208
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=21.06 E-value=61 Score=23.80 Aligned_cols=42 Identities=17% Similarity=0.296 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy15969 51 FTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 51 ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
+++.+..+|...|..+ ....+||..+|++...|..+...-+.
T Consensus 206 L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~ 247 (255)
T TIGR02941 206 LSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAIS 247 (255)
T ss_pred CCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3444444444444322 24578999999999999988765444
No 209
>PRK09462 fur ferric uptake regulator; Provisional
Probab=21.03 E-value=2.7e+02 Score=18.68 Aligned_cols=34 Identities=18% Similarity=0.107 Sum_probs=25.8
Q ss_pred CcCCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhC
Q psy15969 49 LVFTDLQRRTLQAIFKE-TKRPSKEMQVTIARQLG 82 (111)
Q Consensus 49 t~ft~~ql~~Le~~F~~-~~~ps~~~r~~LA~~lg 82 (111)
-.+|+....+|+.++.. ..+++..+........+
T Consensus 13 lr~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~ 47 (148)
T PRK09462 13 LKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMG 47 (148)
T ss_pred CCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhC
Confidence 35888999999998875 46889888877665544
No 210
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=20.83 E-value=61 Score=22.08 Aligned_cols=27 Identities=22% Similarity=0.112 Sum_probs=21.2
Q ss_pred HHHHHHHHHHhCCCccccccccccccc
Q psy15969 71 KEMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 71 ~~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
.....++|..+|++...|.+....-+.
T Consensus 152 ~~s~~eIA~~lgis~~~v~~~l~Rar~ 178 (187)
T PRK09641 152 DLSLKEISEILDLPVGTVKTRIHRGRE 178 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 334678999999999999888766555
No 211
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=20.57 E-value=1e+02 Score=21.47 Aligned_cols=25 Identities=16% Similarity=0.053 Sum_probs=19.9
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...++|..+|++...|.+-+..-+.
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~ 183 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVE 183 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 4578899999999999887765544
No 212
>PF13309 HTH_22: HTH domain
Probab=20.51 E-value=1.6e+02 Score=17.17 Aligned_cols=36 Identities=17% Similarity=0.242 Sum_probs=25.2
Q ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccc
Q psy15969 55 QRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGN 90 (111)
Q Consensus 55 ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkv 90 (111)
-+.++...++..-|--......+|..||++...|-.
T Consensus 26 k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~ 61 (64)
T PF13309_consen 26 KKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYR 61 (64)
T ss_pred HHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHH
Confidence 345555556656666667788899999999877644
No 213
>PRK05572 sporulation sigma factor SigF; Validated
Probab=20.41 E-value=1.1e+02 Score=22.52 Aligned_cols=40 Identities=15% Similarity=0.270 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccc
Q psy15969 51 FTDLQRRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVGNFFMNA 95 (111)
Q Consensus 51 ft~~ql~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVkvWFqNr 95 (111)
+++.+..+|...|.. .....+||..+|++...|..+-..-
T Consensus 203 L~~~~~~v~~l~~~~-----~~s~~eIA~~lgis~~~V~~~~~ra 242 (252)
T PRK05572 203 LDERERLIVYLRYFK-----DKTQSEVAKRLGISQVQVSRLEKKI 242 (252)
T ss_pred CCHHHHHHHHHHHhC-----CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 455555555555432 2356789999999999988776543
No 214
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=20.29 E-value=50 Score=21.17 Aligned_cols=30 Identities=33% Similarity=0.416 Sum_probs=19.2
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccc
Q psy15969 56 RRTLQAIFKETKRPSKEMQVTIARQLGLEPTTVG 89 (111)
Q Consensus 56 l~~Le~~F~~~~~ps~~~r~~LA~~lgL~~~qVk 89 (111)
...|.+.|....+. .+.+|..||++...|.
T Consensus 12 ~~ELq~nf~~~~ls----~~~ia~dL~~s~~~le 41 (89)
T PF10078_consen 12 RQELQANFELSGLS----LEQIAADLGTSPEHLE 41 (89)
T ss_pred HHHHHHHHHHcCCC----HHHHHHHhCCCHHHHH
Confidence 34566677766654 5667777777766554
No 215
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=20.01 E-value=82 Score=22.78 Aligned_cols=25 Identities=28% Similarity=0.129 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy15969 73 MQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 73 ~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
...+||..+|++...|.++...-+.
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~ 176 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARR 176 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578899999999999998876555
No 216
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=20.01 E-value=42 Score=24.24 Aligned_cols=26 Identities=15% Similarity=0.245 Sum_probs=21.1
Q ss_pred HHHHHHHHHhCCCccccccccccccc
Q psy15969 72 EMQVTIARQLGLEPTTVGNFFMNARR 97 (111)
Q Consensus 72 ~~r~~LA~~lgL~~~qVkvWFqNrR~ 97 (111)
-...++|..+|++...|.++...-+.
T Consensus 199 ~s~~EIA~~lgis~~tVk~~~~rA~~ 224 (234)
T PRK08301 199 KTQKEVADMLGISQSYISRLEKRIIK 224 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35678899999999999998766555
Done!