Query psy9614
Match_columns 103
No_of_seqs 180 out of 1005
Neff 8.1
Searched_HMMs 46136
Date Sat Aug 17 00:16:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9614.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9614hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.9 8.4E-24 1.8E-28 130.5 -0.8 70 10-79 10-79 (125)
2 KOG0850|consensus 99.9 2.8E-22 6.1E-27 138.5 3.5 71 11-81 116-186 (245)
3 KOG0488|consensus 99.8 1.4E-21 3E-26 142.0 4.4 71 8-78 163-233 (309)
4 KOG2251|consensus 99.8 3.7E-21 8E-26 132.3 5.2 68 12-79 32-99 (228)
5 KOG0489|consensus 99.8 3.4E-21 7.4E-26 137.3 2.3 69 14-82 156-224 (261)
6 KOG0842|consensus 99.8 1.6E-20 3.4E-25 135.4 5.7 73 13-85 149-221 (307)
7 KOG0843|consensus 99.8 1.3E-20 2.9E-25 126.2 4.0 64 16-79 101-164 (197)
8 KOG0494|consensus 99.8 7.8E-20 1.7E-24 128.6 4.0 67 15-81 138-205 (332)
9 KOG0487|consensus 99.8 1.6E-19 3.5E-24 130.3 4.5 65 13-77 231-295 (308)
10 KOG0485|consensus 99.8 2.1E-19 4.5E-24 123.7 1.9 65 13-77 100-164 (268)
11 PF00046 Homeobox: Homeobox do 99.8 1.9E-19 4.2E-24 101.0 1.0 57 18-74 1-57 (57)
12 KOG0492|consensus 99.7 9.1E-19 2E-23 119.7 3.4 65 14-78 141-205 (246)
13 TIGR01565 homeo_ZF_HD homeobox 99.7 7.8E-18 1.7E-22 94.8 5.8 52 18-69 2-57 (58)
14 KOG0848|consensus 99.7 1.7E-18 3.8E-23 122.1 0.6 67 12-78 194-260 (317)
15 KOG0493|consensus 99.7 1.1E-17 2.3E-22 118.0 3.9 75 3-77 222-306 (342)
16 KOG0844|consensus 99.7 4.7E-18 1E-22 122.0 1.1 72 13-84 177-248 (408)
17 smart00389 HOX Homeodomain. DN 99.7 6.9E-17 1.5E-21 89.9 3.4 55 19-73 2-56 (56)
18 KOG0486|consensus 99.7 5.5E-17 1.2E-21 116.6 3.1 65 16-80 111-175 (351)
19 cd00086 homeodomain Homeodomai 99.6 1.2E-16 2.5E-21 89.7 2.9 57 19-75 2-58 (59)
20 KOG3802|consensus 99.6 2.6E-16 5.6E-21 116.2 5.4 62 16-77 293-354 (398)
21 COG5576 Homeodomain-containing 99.6 2.4E-16 5.1E-21 104.8 3.9 66 13-78 47-112 (156)
22 KOG0491|consensus 99.6 2.8E-17 6.2E-22 108.9 -1.5 70 16-85 99-168 (194)
23 KOG4577|consensus 99.6 8.3E-16 1.8E-20 109.8 3.1 68 13-80 163-230 (383)
24 KOG0483|consensus 99.6 8.8E-16 1.9E-20 105.4 2.9 61 18-78 51-111 (198)
25 KOG0847|consensus 99.5 4.3E-15 9.3E-20 102.7 1.4 65 14-78 164-228 (288)
26 KOG0490|consensus 99.5 1.5E-14 3.3E-19 100.4 3.7 64 14-77 57-120 (235)
27 KOG0849|consensus 99.4 3.5E-13 7.5E-18 99.8 3.3 67 11-77 170-236 (354)
28 KOG1168|consensus 99.2 5.7E-12 1.2E-16 90.4 1.5 63 16-78 308-370 (385)
29 KOG0775|consensus 99.1 9.7E-11 2.1E-15 83.3 4.5 54 24-77 183-236 (304)
30 KOG0774|consensus 98.7 8E-09 1.7E-13 73.4 3.4 61 17-77 188-251 (334)
31 KOG2252|consensus 98.6 5E-08 1.1E-12 75.1 4.9 60 13-72 416-475 (558)
32 KOG0490|consensus 98.5 4.5E-08 9.7E-13 67.9 2.4 66 12-77 148-213 (235)
33 PF05920 Homeobox_KN: Homeobox 98.5 9.4E-09 2E-13 53.8 -1.4 33 38-70 7-39 (40)
34 KOG1146|consensus 98.0 4.1E-06 8.9E-11 70.0 3.2 64 16-79 902-965 (1406)
35 KOG0773|consensus 97.3 0.00038 8.3E-09 51.3 4.1 61 15-75 237-300 (342)
36 PF11569 Homez: Homeodomain le 97.1 0.00013 2.8E-09 40.6 0.1 43 28-70 9-51 (56)
37 KOG3623|consensus 96.9 0.0009 2E-08 53.9 3.0 57 29-85 568-624 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 95.1 0.024 5.2E-07 31.0 2.5 46 18-68 1-46 (53)
39 PF04967 HTH_10: HTH DNA bindi 91.0 0.26 5.6E-06 27.1 2.4 38 24-61 1-40 (53)
40 PF01527 HTH_Tnp_1: Transposas 82.9 1.1 2.4E-05 25.4 2.0 43 19-66 2-45 (76)
41 KOG1146|consensus 82.6 1.4 3.1E-05 38.2 3.2 63 14-76 702-764 (1406)
42 COG3413 Predicted DNA binding 79.2 1.9 4E-05 29.8 2.4 39 23-61 155-195 (215)
43 PF10668 Phage_terminase: Phag 75.5 0.87 1.9E-05 25.7 -0.1 20 46-65 24-43 (60)
44 cd06171 Sigma70_r4 Sigma70, re 72.3 1.7 3.7E-05 22.1 0.6 41 23-68 10-50 (55)
45 cd00569 HTH_Hin_like Helix-tur 68.0 9.4 0.0002 17.0 2.8 37 23-64 5-41 (42)
46 PF04545 Sigma70_r4: Sigma-70, 66.2 3.9 8.5E-05 21.3 1.2 38 23-65 4-41 (50)
47 PF08281 Sigma70_r4_2: Sigma-7 64.8 2.6 5.6E-05 22.3 0.3 38 24-66 11-48 (54)
48 PF09607 BrkDBD: Brinker DNA-b 62.7 8.8 0.00019 21.5 2.2 45 21-66 3-47 (58)
49 PF13936 HTH_38: Helix-turn-he 61.5 5.3 0.00012 20.6 1.2 39 22-65 3-41 (44)
50 PRK03975 tfx putative transcri 57.4 3.6 7.8E-05 27.0 0.1 49 21-75 4-52 (141)
51 PRK09413 IS2 repressor TnpA; R 55.5 21 0.00045 22.4 3.4 41 21-66 10-51 (121)
52 TIGR03879 near_KaiC_dom probab 53.5 2.2 4.8E-05 24.9 -1.2 34 34-67 22-55 (73)
53 PF06056 Terminase_5: Putative 53.0 4.8 0.00011 22.3 0.1 21 46-66 15-35 (58)
54 cd04761 HTH_MerR-SF Helix-Turn 52.9 3.7 8E-05 21.0 -0.3 22 47-68 3-24 (49)
55 PF04936 DUF658: Protein of un 50.3 4.6 0.0001 27.4 -0.3 34 45-78 15-48 (186)
56 PF13411 MerR_1: MerR HTH fami 49.9 5.5 0.00012 22.0 0.0 20 47-66 3-22 (69)
57 PF08280 HTH_Mga: M protein tr 49.8 14 0.00031 20.1 1.8 33 27-63 6-38 (59)
58 PRK06759 RNA polymerase factor 49.7 6.7 0.00014 24.9 0.4 27 46-72 124-150 (154)
59 PRK10072 putative transcriptio 48.6 6.5 0.00014 24.1 0.2 41 23-70 32-72 (96)
60 COG4367 Uncharacterized protei 46.9 20 0.00044 21.8 2.2 37 24-60 3-39 (97)
61 PRK09646 RNA polymerase sigma 46.6 7.4 0.00016 26.0 0.3 29 46-74 160-188 (194)
62 PF13518 HTH_28: Helix-turn-he 46.0 7.6 0.00016 20.0 0.2 23 46-68 14-36 (52)
63 PF13384 HTH_23: Homeodomain-l 44.0 5.8 0.00013 20.5 -0.5 23 45-67 18-40 (50)
64 PRK12526 RNA polymerase sigma 43.9 7.4 0.00016 26.4 -0.1 29 46-74 171-199 (206)
65 PRK09480 slmA division inhibit 42.9 19 0.00042 23.5 1.9 36 34-70 21-56 (194)
66 PRK13558 bacterio-opsin activa 41.4 25 0.00054 28.0 2.5 40 22-61 606-647 (665)
67 PRK00118 putative DNA-binding 41.1 9.3 0.0002 23.8 0.1 47 23-74 17-63 (104)
68 KOG3623|consensus 41.0 43 0.00092 28.2 3.7 60 19-78 628-687 (1007)
69 PRK09652 RNA polymerase sigma 40.6 8.8 0.00019 24.8 -0.1 28 46-73 146-173 (182)
70 PF00376 MerR: MerR family reg 40.3 7.5 0.00016 19.5 -0.4 18 48-65 3-20 (38)
71 PRK05602 RNA polymerase sigma 40.1 8.3 0.00018 25.5 -0.3 32 46-77 146-177 (186)
72 PF00196 GerE: Bacterial regul 39.7 14 0.00031 19.8 0.7 43 23-71 3-45 (58)
73 PF02796 HTH_7: Helix-turn-hel 39.7 29 0.00064 17.7 1.9 38 23-65 5-42 (45)
74 PRK12514 RNA polymerase sigma 39.1 11 0.00025 24.6 0.3 28 46-73 147-174 (179)
75 TIGR02989 Sig-70_gvs1 RNA poly 39.0 13 0.00028 23.6 0.5 25 46-70 129-153 (159)
76 TIGR02937 sigma70-ECF RNA poly 38.3 11 0.00024 23.1 0.1 26 46-71 128-153 (158)
77 PRK09642 RNA polymerase sigma 37.8 12 0.00026 24.0 0.2 29 46-74 124-152 (160)
78 cd04764 HTH_MlrA-like_sg1 Heli 37.5 11 0.00023 20.9 -0.1 21 47-67 3-23 (67)
79 cd04762 HTH_MerR-trunc Helix-T 36.9 9.9 0.00021 18.9 -0.2 24 47-70 3-26 (49)
80 PHA02955 hypothetical protein; 36.8 66 0.0014 22.7 3.7 44 26-69 60-104 (213)
81 PRK12512 RNA polymerase sigma 36.3 13 0.00027 24.5 0.1 29 46-74 149-177 (184)
82 smart00421 HTH_LUXR helix_turn 35.7 46 0.001 16.7 2.4 39 23-67 3-41 (58)
83 PRK11924 RNA polymerase sigma 35.2 13 0.00028 23.9 0.0 28 46-73 143-170 (179)
84 cd01392 HTH_LacI Helix-turn-he 34.8 8.6 0.00019 19.9 -0.7 21 49-69 2-22 (52)
85 PRK12519 RNA polymerase sigma 34.7 10 0.00022 25.2 -0.5 30 44-73 157-186 (194)
86 PRK09648 RNA polymerase sigma 34.6 13 0.00029 24.5 0.1 26 46-71 157-182 (189)
87 COG1905 NuoE NADH:ubiquinone o 34.2 66 0.0014 21.6 3.3 36 26-61 25-60 (160)
88 PF08279 HTH_11: HTH domain; 34.1 38 0.00082 17.6 1.8 31 30-63 4-34 (55)
89 COG2963 Transposase and inacti 33.9 58 0.0013 19.9 2.9 42 21-66 5-47 (116)
90 TIGR02999 Sig-70_X6 RNA polyme 33.8 13 0.00029 24.3 -0.1 27 46-72 152-178 (183)
91 PRK09644 RNA polymerase sigma 33.7 11 0.00025 24.3 -0.4 30 46-75 126-155 (165)
92 TIGR02985 Sig70_bacteroi1 RNA 33.7 15 0.00033 23.1 0.2 26 46-71 131-156 (161)
93 cd04763 HTH_MlrA-like Helix-Tu 33.5 13 0.00028 20.6 -0.1 20 47-66 3-22 (68)
94 cd01104 HTH_MlrA-CarA Helix-Tu 33.2 13 0.00029 20.3 -0.1 20 47-66 3-22 (68)
95 PRK05988 formate dehydrogenase 33.2 66 0.0014 21.3 3.2 35 28-62 25-59 (156)
96 PRK07539 NADH dehydrogenase su 32.9 65 0.0014 21.1 3.1 35 28-62 24-58 (154)
97 TIGR03629 arch_S13P archaeal r 32.2 43 0.00094 22.0 2.2 10 61-70 71-80 (144)
98 PF08880 QLQ: QLQ; InterPro: 32.0 52 0.0011 16.5 2.0 15 23-37 2-16 (37)
99 PF01710 HTH_Tnp_IS630: Transp 31.9 39 0.00084 21.1 1.9 38 24-66 3-40 (119)
100 PRK04217 hypothetical protein; 31.7 17 0.00038 22.8 0.2 48 21-73 40-87 (110)
101 PRK12537 RNA polymerase sigma 31.3 21 0.00046 23.5 0.6 25 46-70 151-175 (182)
102 TIGR01958 nuoE_fam NADH-quinon 30.8 74 0.0016 20.6 3.1 35 28-62 18-52 (148)
103 PRK12511 RNA polymerase sigma 30.7 19 0.00042 23.9 0.3 30 46-75 129-158 (182)
104 TIGR02959 SigZ RNA polymerase 30.6 17 0.00038 23.7 0.1 30 46-75 118-147 (170)
105 PF01381 HTH_3: Helix-turn-hel 30.2 15 0.00033 19.1 -0.2 23 47-69 12-34 (55)
106 PRK09639 RNA polymerase sigma 30.2 17 0.00036 23.3 -0.0 29 46-74 129-157 (166)
107 PRK12530 RNA polymerase sigma 30.2 17 0.00037 24.2 0.0 29 46-74 152-180 (189)
108 PRK12515 RNA polymerase sigma 30.0 15 0.00034 24.3 -0.2 30 46-75 149-178 (189)
109 TIGR02948 SigW_bacill RNA poly 29.6 16 0.00034 23.9 -0.2 29 45-73 153-181 (187)
110 PRK12541 RNA polymerase sigma 29.5 18 0.00039 23.2 0.0 27 46-72 130-156 (161)
111 KOG3755|consensus 28.8 21 0.00045 29.2 0.2 62 16-77 646-711 (769)
112 PRK12535 RNA polymerase sigma 28.4 21 0.00046 24.0 0.2 33 46-78 151-183 (196)
113 PRK11552 putative DNA-binding 28.3 35 0.00076 23.5 1.3 40 31-72 21-60 (225)
114 PRK06811 RNA polymerase factor 28.3 29 0.00063 23.0 0.9 31 46-76 149-179 (189)
115 TIGR02939 RpoE_Sigma70 RNA pol 28.0 13 0.00028 24.4 -0.9 30 45-74 155-184 (190)
116 TIGR02954 Sig70_famx3 RNA poly 28.0 22 0.00048 23.0 0.2 26 46-71 137-162 (169)
117 PRK12538 RNA polymerase sigma 27.8 8.9 0.00019 26.8 -1.8 30 46-75 189-218 (233)
118 TIGR03070 couple_hipB transcri 27.7 25 0.00053 18.1 0.4 23 47-69 18-40 (58)
119 cd02413 40S_S3_KH K homology R 27.6 50 0.0011 19.4 1.7 21 46-66 55-75 (81)
120 PRK09047 RNA polymerase factor 27.3 22 0.00048 22.6 0.2 28 46-73 124-151 (161)
121 PRK07571 bidirectional hydroge 27.0 95 0.0021 20.9 3.2 32 31-62 41-72 (169)
122 PRK12536 RNA polymerase sigma 26.7 21 0.00045 23.5 -0.1 29 46-74 147-175 (181)
123 cd06170 LuxR_C_like C-terminal 26.6 71 0.0015 16.1 2.1 36 25-66 2-37 (57)
124 PRK06930 positive control sigm 26.5 21 0.00046 23.9 -0.0 47 23-74 114-160 (170)
125 PF13412 HTH_24: Winged helix- 26.3 64 0.0014 16.3 1.8 34 25-62 2-35 (48)
126 PRK12516 RNA polymerase sigma 26.2 25 0.00053 23.5 0.2 32 46-77 134-165 (187)
127 PF01257 2Fe-2S_thioredx: Thio 26.2 69 0.0015 20.7 2.3 34 29-62 16-49 (145)
128 PF13443 HTH_26: Cro/C1-type H 26.2 73 0.0016 16.9 2.1 21 48-68 14-34 (63)
129 smart00422 HTH_MERR helix_turn 26.1 21 0.00046 19.5 -0.1 20 47-66 3-22 (70)
130 PRK12547 RNA polymerase sigma 26.1 21 0.00045 23.1 -0.1 28 46-73 130-157 (164)
131 TIGR02983 SigE-fam_strep RNA p 25.5 23 0.0005 22.6 -0.0 29 46-74 128-156 (162)
132 TIGR01764 excise DNA binding d 25.2 22 0.00048 17.6 -0.1 25 47-71 4-28 (49)
133 PRK12543 RNA polymerase sigma 25.0 25 0.00054 23.1 0.1 30 46-75 135-164 (179)
134 KOG0773|consensus 24.5 27 0.00059 25.7 0.2 42 37-78 117-158 (342)
135 PF07750 GcrA: GcrA cell cycle 24.3 1.2E+02 0.0027 20.1 3.3 32 23-59 2-34 (162)
136 TIGR02952 Sig70_famx2 RNA poly 24.3 26 0.00056 22.5 0.0 21 46-66 140-160 (170)
137 PRK09637 RNA polymerase sigma 24.2 26 0.00057 23.2 0.1 29 46-74 124-152 (181)
138 PRK12546 RNA polymerase sigma 24.2 23 0.00049 23.8 -0.2 31 46-76 131-161 (188)
139 PRK06424 transcription factor; 24.1 47 0.001 21.8 1.2 24 47-70 100-123 (144)
140 COG2944 Predicted transcriptio 23.9 54 0.0012 20.5 1.4 40 24-70 44-83 (104)
141 PRK06986 fliA flagellar biosyn 23.8 24 0.00052 24.4 -0.2 29 46-74 202-230 (236)
142 PRK09645 RNA polymerase sigma 23.8 28 0.00061 22.5 0.1 29 46-74 136-164 (173)
143 PRK12529 RNA polymerase sigma 23.8 73 0.0016 20.8 2.2 25 46-70 145-169 (178)
144 TIGR00721 tfx DNA-binding prot 23.7 68 0.0015 20.9 1.9 48 21-74 4-51 (137)
145 PRK12532 RNA polymerase sigma 23.6 24 0.00051 23.5 -0.3 30 46-75 154-183 (195)
146 smart00027 EH Eps15 homology d 23.3 91 0.002 18.3 2.4 44 23-66 3-51 (96)
147 PRK12539 RNA polymerase sigma 23.0 30 0.00065 22.8 0.2 29 45-73 148-176 (184)
148 cd00093 HTH_XRE Helix-turn-hel 22.9 30 0.00065 16.8 0.1 22 47-68 15-36 (58)
149 PF14549 P22_Cro: DNA-binding 22.9 21 0.00045 19.9 -0.5 18 47-64 12-29 (60)
150 PRK12524 RNA polymerase sigma 22.9 28 0.00061 23.2 0.0 30 46-75 154-183 (196)
151 PF01325 Fe_dep_repress: Iron 22.7 26 0.00056 19.3 -0.2 37 25-61 3-39 (60)
152 PRK12544 RNA polymerase sigma 22.4 24 0.00053 24.0 -0.4 30 46-75 166-195 (206)
153 PRK07037 extracytoplasmic-func 22.3 31 0.00067 22.0 0.1 21 46-66 127-147 (163)
154 PF13309 HTH_22: HTH domain 22.2 1.2E+02 0.0027 16.7 2.6 38 24-61 21-59 (64)
155 cd01105 HTH_GlnR-like Helix-Tu 22.1 28 0.0006 20.5 -0.1 19 47-65 4-22 (88)
156 PRK12528 RNA polymerase sigma 22.1 75 0.0016 20.2 1.9 21 46-66 131-151 (161)
157 PHA01976 helix-turn-helix prot 22.0 33 0.00072 18.6 0.2 23 47-69 18-40 (67)
158 cd04766 HTH_HspR Helix-Turn-He 21.8 29 0.00062 20.5 -0.1 21 47-67 4-24 (91)
159 TIGR02607 antidote_HigA addict 21.4 35 0.00075 19.1 0.2 23 47-69 21-43 (78)
160 PRK08583 RNA polymerase sigma 21.4 32 0.00069 24.1 0.0 28 46-73 223-250 (257)
161 PF12728 HTH_17: Helix-turn-he 21.4 28 0.00062 17.9 -0.2 24 47-70 4-27 (51)
162 PF12802 MarR_2: MarR family; 21.3 63 0.0014 17.0 1.2 36 24-61 3-38 (62)
163 PRK09649 RNA polymerase sigma 21.2 32 0.00069 22.8 0.0 29 46-74 148-176 (185)
164 PRK13919 putative RNA polymera 21.2 34 0.00074 22.4 0.1 26 46-71 153-178 (186)
165 PF01726 LexA_DNA_bind: LexA D 20.9 1.5E+02 0.0033 16.5 2.8 33 23-57 3-38 (65)
166 TIGR03209 P21_Cbot clostridium 20.8 1.3E+02 0.0028 18.6 2.8 16 47-62 126-141 (142)
167 PRK09651 RNA polymerase sigma 20.6 60 0.0013 21.1 1.3 21 46-66 137-157 (172)
168 PF06971 Put_DNA-bind_N: Putat 20.5 32 0.00069 18.5 -0.1 16 47-62 31-46 (50)
169 TIGR02479 FliA_WhiG RNA polyme 20.4 33 0.00071 23.5 -0.1 25 46-70 193-217 (224)
170 PF14229 DUF4332: Domain of un 20.2 50 0.0011 20.8 0.8 25 41-65 26-50 (122)
171 COG5484 Uncharacterized conser 20.2 40 0.00087 24.6 0.3 26 45-72 20-45 (279)
172 PRK12531 RNA polymerase sigma 20.1 35 0.00077 22.7 0.1 28 46-73 159-186 (194)
No 1
>KOG0484|consensus
Probab=99.87 E-value=8.4e-24 Score=130.48 Aligned_cols=70 Identities=46% Similarity=0.710 Sum_probs=65.0
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccccc
Q psy9614 10 SANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQ 79 (103)
Q Consensus 10 ~~~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~ 79 (103)
+-...++++|-||.|+..||..||+.|...+||++-+|++||..++|++.+|||||||||+|+||+++..
T Consensus 10 ~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 10 GLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred ChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 3345688999999999999999999999999999999999999999999999999999999999988763
No 2
>KOG0850|consensus
Probab=99.85 E-value=2.8e-22 Score=138.48 Aligned_cols=71 Identities=28% Similarity=0.440 Sum_probs=66.4
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccccccc
Q psy9614 11 ANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQIV 81 (103)
Q Consensus 11 ~~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~~~ 81 (103)
++.++|.|+.||.|+..||..|.+.|++++|.-.++|.+||+.|||+..||+|||||||.|.||..+.+..
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~ 186 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSG 186 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCC
Confidence 56788999999999999999999999999999999999999999999999999999999999998885433
No 3
>KOG0488|consensus
Probab=99.84 E-value=1.4e-21 Score=141.97 Aligned_cols=71 Identities=32% Similarity=0.483 Sum_probs=65.9
Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccccc
Q psy9614 8 PGSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKV 78 (103)
Q Consensus 8 ~~~~~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~ 78 (103)
++..+.++|.|+.||.||..|+..||..|+...|.+..+|.+||+.|||+..||++||||||+||||....
T Consensus 163 ~~~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 163 PYQRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CcccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 34456678999999999999999999999999999999999999999999999999999999999997655
No 4
>KOG2251|consensus
Probab=99.83 E-value=3.7e-21 Score=132.30 Aligned_cols=68 Identities=51% Similarity=0.690 Sum_probs=65.3
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccccc
Q psy9614 12 NKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQ 79 (103)
Q Consensus 12 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~ 79 (103)
+.+++.||.||.|+..|+.+||..|.+.+|||...|++||.+|+|++.+|+|||+|||+|+|+++...
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 67899999999999999999999999999999999999999999999999999999999999988764
No 5
>KOG0489|consensus
Probab=99.82 E-value=3.4e-21 Score=137.32 Aligned_cols=69 Identities=28% Similarity=0.388 Sum_probs=63.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccccccccc
Q psy9614 14 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQIVV 82 (103)
Q Consensus 14 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~~~~ 82 (103)
..+.+|.||.||..|+..||+.|..|.|.+...|.+||..|.|+++||+|||||||+||||..+.....
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 345799999999999999999999999999999999999999999999999999999999987766544
No 6
>KOG0842|consensus
Probab=99.82 E-value=1.6e-20 Score=135.43 Aligned_cols=73 Identities=27% Similarity=0.327 Sum_probs=66.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccccccccCCC
Q psy9614 13 KPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQIVVTSD 85 (103)
Q Consensus 13 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~~~~~~~ 85 (103)
..+++|+.|..||..|+.+||+.|....|.+.++|+.||..|.|++.||||||||||.|.||.+.........
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~ 221 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALL 221 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhccc
Confidence 4567888899999999999999999999999999999999999999999999999999999998876554443
No 7
>KOG0843|consensus
Probab=99.81 E-value=1.3e-20 Score=126.17 Aligned_cols=64 Identities=34% Similarity=0.397 Sum_probs=61.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccccc
Q psy9614 16 KIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQ 79 (103)
Q Consensus 16 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~ 79 (103)
+.+|.||.|+.+|+..||..|+.++|....+|+.||..|+|++.||+|||||||.|.||.+...
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 7889999999999999999999999999999999999999999999999999999999987664
No 8
>KOG0494|consensus
Probab=99.79 E-value=7.8e-20 Score=128.60 Aligned_cols=67 Identities=43% Similarity=0.625 Sum_probs=61.0
Q ss_pred CCCCCC-CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccccccc
Q psy9614 15 RKIRRS-RTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQIV 81 (103)
Q Consensus 15 ~~~rr~-Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~~~ 81 (103)
+++||. ||.||..|+..||..|...+|||...|+.||..+.|++.+|+|||||||+||||.++....
T Consensus 138 k~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~ 205 (332)
T KOG0494|consen 138 KKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGG 205 (332)
T ss_pred ccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCc
Confidence 334444 9999999999999999999999999999999999999999999999999999999887543
No 9
>KOG0487|consensus
Probab=99.78 E-value=1.6e-19 Score=130.28 Aligned_cols=65 Identities=23% Similarity=0.280 Sum_probs=61.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccc
Q psy9614 13 KPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEK 77 (103)
Q Consensus 13 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~ 77 (103)
..+..|++|..||..|+..||+.|..|.|.+...|.+|++.|+|+++||+|||||||+|+||..+
T Consensus 231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 45778889999999999999999999999999999999999999999999999999999999875
No 10
>KOG0485|consensus
Probab=99.76 E-value=2.1e-19 Score=123.68 Aligned_cols=65 Identities=25% Similarity=0.366 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccc
Q psy9614 13 KPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEK 77 (103)
Q Consensus 13 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~ 77 (103)
+..++++.||+|+..|+..||..|+...|.+..+|..||+.|.|++.||+|||||||.||||+-.
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 34577889999999999999999999999999999999999999999999999999999999754
No 11
>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=99.75 E-value=1.9e-19 Score=100.95 Aligned_cols=57 Identities=35% Similarity=0.453 Sum_probs=54.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccc
Q psy9614 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 18 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
++.|+.||.+|+.+|+..|..++||+..++..||..+||+..+|++||+|+|+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999875
No 12
>KOG0492|consensus
Probab=99.74 E-value=9.1e-19 Score=119.73 Aligned_cols=65 Identities=31% Similarity=0.454 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccccc
Q psy9614 14 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKV 78 (103)
Q Consensus 14 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~ 78 (103)
.+..|++||.||..||..||+-|...+|.++.+|.+++..|.|++.||+|||||||+|.||.+..
T Consensus 141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQea 205 (246)
T KOG0492|consen 141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEA 205 (246)
T ss_pred cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHH
Confidence 35567789999999999999999999999999999999999999999999999999999997764
No 13
>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=99.73 E-value=7.8e-18 Score=94.83 Aligned_cols=52 Identities=15% Similarity=0.206 Sum_probs=50.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHhcCCCcccceecccccc
Q psy9614 18 RRSRTTFTTYQLHQLERAFDKTQY----PDVFTREDLASRLDLSEARVQVNSDSQI 69 (103)
Q Consensus 18 rr~Rt~~s~~q~~~Le~~F~~~~~----p~~~~r~~La~~l~l~~~~V~vWFqNrR 69 (103)
+|.||.||.+|+..|+..|+.++| |+...+.+||..+||++.+|+|||||.+
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 789999999999999999999999 9999999999999999999999999975
No 14
>KOG0848|consensus
Probab=99.70 E-value=1.7e-18 Score=122.13 Aligned_cols=67 Identities=25% Similarity=0.359 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccccc
Q psy9614 12 NKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKV 78 (103)
Q Consensus 12 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~ 78 (103)
++-+.+.+.|.+||..|...||+.|.-++|.++..+.+||.-|||+++||+|||||||+|+||..+.
T Consensus 194 ~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 194 VKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK 260 (317)
T ss_pred ceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence 3455566779999999999999999999999999999999999999999999999999999986554
No 15
>KOG0493|consensus
Probab=99.70 E-value=1.1e-17 Score=117.98 Aligned_cols=75 Identities=28% Similarity=0.434 Sum_probs=64.8
Q ss_pred cccCCCCCCCCCCC----------CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccc
Q psy9614 3 FYFFPPGSANKPRK----------IRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTL 72 (103)
Q Consensus 3 ~~~~~~~~~~~~~~----------~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~ 72 (103)
.|+..|+++++.++ -+|+||.||.+||..|...|+.+.|.+...|..||.+|+|.+.||+|||||+|+|.
T Consensus 222 RYSDRPSsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKi 301 (342)
T KOG0493|consen 222 RYSDRPSSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKI 301 (342)
T ss_pred cccCCCCCCcccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhh
Confidence 36666777654322 34679999999999999999999999999999999999999999999999999999
Q ss_pred ccccc
Q psy9614 73 GSNEK 77 (103)
Q Consensus 73 rr~~~ 77 (103)
||--.
T Consensus 302 KKsTg 306 (342)
T KOG0493|consen 302 KKSTG 306 (342)
T ss_pred hhccC
Confidence 88544
No 16
>KOG0844|consensus
Probab=99.69 E-value=4.7e-18 Score=122.02 Aligned_cols=72 Identities=25% Similarity=0.292 Sum_probs=65.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccccccccCC
Q psy9614 13 KPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQIVVTS 84 (103)
Q Consensus 13 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~~~~~~ 84 (103)
.+.+.||.||.||.+|+..||+.|-+..|-+.+.|.+||..|+|++..|+|||||||+|+||+.....+..+
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWPhp 248 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWPHP 248 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCCCC
Confidence 456789999999999999999999999999999999999999999999999999999999998776555444
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.66 E-value=6.9e-17 Score=89.92 Aligned_cols=55 Identities=42% Similarity=0.596 Sum_probs=52.0
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccc
Q psy9614 19 RSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLG 73 (103)
Q Consensus 19 r~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~r 73 (103)
+.|+.|+..++.+|+..|..++||+..++..||..+||+..+|++||+|+|++.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 5678899999999999999999999999999999999999999999999998754
No 18
>KOG0486|consensus
Probab=99.65 E-value=5.5e-17 Score=116.62 Aligned_cols=65 Identities=42% Similarity=0.592 Sum_probs=62.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccccccc
Q psy9614 16 KIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQI 80 (103)
Q Consensus 16 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~~ 80 (103)
|++|.||.|+..|+..||..|+++.||+...|+++|..++|++.+|+|||.|||+||||+++-..
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 78899999999999999999999999999999999999999999999999999999999887543
No 19
>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=99.64 E-value=1.2e-16 Score=89.66 Aligned_cols=57 Identities=39% Similarity=0.582 Sum_probs=53.9
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccc
Q psy9614 19 RSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSN 75 (103)
Q Consensus 19 r~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~ 75 (103)
+.++.|+..++.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 467899999999999999999999999999999999999999999999999998764
No 20
>KOG3802|consensus
Probab=99.64 E-value=2.6e-16 Score=116.17 Aligned_cols=62 Identities=21% Similarity=0.170 Sum_probs=60.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccc
Q psy9614 16 KIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEK 77 (103)
Q Consensus 16 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~ 77 (103)
++|++||.|......+||.+|.+|+.|+..++..||.+|+|...+|+|||||||+|.||-..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 77889999999999999999999999999999999999999999999999999999999776
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.63 E-value=2.4e-16 Score=104.80 Aligned_cols=66 Identities=24% Similarity=0.268 Sum_probs=60.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccccc
Q psy9614 13 KPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKV 78 (103)
Q Consensus 13 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~ 78 (103)
.....++.|++.+..|+.+|++.|..++||+...+..|+..++|+++.|+|||||+|++.|+....
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 345567778888999999999999999999999999999999999999999999999999987655
No 22
>KOG0491|consensus
Probab=99.61 E-value=2.8e-17 Score=108.92 Aligned_cols=70 Identities=27% Similarity=0.392 Sum_probs=62.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccccccccCCC
Q psy9614 16 KIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQIVVTSD 85 (103)
Q Consensus 16 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~~~~~~~ 85 (103)
+.++.||+|+..|+..|++.|+...|.+..++.+||..|+|++.||+.||||||+|.||.++.....++.
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~nS~ 168 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKNSN 168 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCCCC
Confidence 3456799999999999999999999999999999999999999999999999999999988765543433
No 23
>KOG4577|consensus
Probab=99.58 E-value=8.3e-16 Score=109.81 Aligned_cols=68 Identities=28% Similarity=0.257 Sum_probs=62.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccccccc
Q psy9614 13 KPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQI 80 (103)
Q Consensus 13 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~~ 80 (103)
+....+|+||.+|..||+.|...|...+.|....|+.|+.++||.-++|||||||||+|+||..+.++
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence 34557899999999999999999999999999999999999999999999999999999998777643
No 24
>KOG0483|consensus
Probab=99.58 E-value=8.8e-16 Score=105.36 Aligned_cols=61 Identities=18% Similarity=0.244 Sum_probs=56.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccccc
Q psy9614 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKV 78 (103)
Q Consensus 18 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~ 78 (103)
.+...+|+.+|+..||..|+...+.....+..||..|||.++||.||||||||+||.++..
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 4455689999999999999999999999999999999999999999999999999987654
No 25
>KOG0847|consensus
Probab=99.51 E-value=4.3e-15 Score=102.72 Aligned_cols=65 Identities=31% Similarity=0.419 Sum_probs=60.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccccc
Q psy9614 14 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKV 78 (103)
Q Consensus 14 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~ 78 (103)
+.+++..|..|+..|+..|+..|+..+|+-.+++.+||..+|+++.+|+|||||||.||||+...
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 45667778899999999999999999999999999999999999999999999999999987543
No 26
>KOG0490|consensus
Probab=99.50 E-value=1.5e-14 Score=100.38 Aligned_cols=64 Identities=38% Similarity=0.358 Sum_probs=61.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccc
Q psy9614 14 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEK 77 (103)
Q Consensus 14 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~ 77 (103)
..++++.|+.|+..|+..|++.|+..+||+...++.||..+++++..|+|||||+|+++++..+
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 4678999999999999999999999999999999999999999999999999999999998875
No 27
>KOG0849|consensus
Probab=99.36 E-value=3.5e-13 Score=99.85 Aligned_cols=67 Identities=37% Similarity=0.517 Sum_probs=62.5
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccc
Q psy9614 11 ANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEK 77 (103)
Q Consensus 11 ~~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~ 77 (103)
....++.+|.||.|+..|+..|+..|+.++||++..|+.||.++++++..|+|||+|+|++++|...
T Consensus 170 ~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 170 YALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred ccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 3456777888999999999999999999999999999999999999999999999999999999884
No 28
>KOG1168|consensus
Probab=99.19 E-value=5.7e-12 Score=90.38 Aligned_cols=63 Identities=22% Similarity=0.205 Sum_probs=58.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccccc
Q psy9614 16 KIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKV 78 (103)
Q Consensus 16 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~ 78 (103)
-++|+||.+..-....||.+|...+.|+.+.+..+|.+|+|...+|+|||+|.|+|.||....
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~S 370 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRS 370 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhh
Confidence 357889999999999999999999999999999999999999999999999999999885543
No 29
>KOG0775|consensus
Probab=99.10 E-value=9.7e-11 Score=83.32 Aligned_cols=54 Identities=15% Similarity=0.138 Sum_probs=48.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccc
Q psy9614 24 FTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEK 77 (103)
Q Consensus 24 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~ 77 (103)
|-..-...|..+|..++||+..++.+||+++||+..||-+||+|||+++|-...
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a 236 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA 236 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence 334556799999999999999999999999999999999999999999995443
No 30
>KOG0774|consensus
Probab=98.74 E-value=8e-09 Score=73.41 Aligned_cols=61 Identities=21% Similarity=0.279 Sum_probs=56.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHhcCCCcccceecccccccccccccc
Q psy9614 17 IRRSRTTFTTYQLHQLERAFD---KTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEK 77 (103)
Q Consensus 17 ~rr~Rt~~s~~q~~~Le~~F~---~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~ 77 (103)
.+|+|..|+..-..+|..+|. .++||+....++||.+++++..||-.||.|+|-+.+|...
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence 467888999999999999995 4899999999999999999999999999999999998654
No 31
>KOG2252|consensus
Probab=98.62 E-value=5e-08 Score=75.09 Aligned_cols=60 Identities=20% Similarity=0.214 Sum_probs=55.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccc
Q psy9614 13 KPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTL 72 (103)
Q Consensus 13 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~ 72 (103)
.....+++|.+||..|...|..+|..+++|+....+.|+.+|+|....|.+||.|-|.+.
T Consensus 416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 334567779999999999999999999999999999999999999999999999988774
No 32
>KOG0490|consensus
Probab=98.53 E-value=4.5e-08 Score=67.86 Aligned_cols=66 Identities=39% Similarity=0.461 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccc
Q psy9614 12 NKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEK 77 (103)
Q Consensus 12 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~ 77 (103)
....+.++.|+.+...|+..+...|..+++|+...+..|+..+|++...|++||+|+|++.++...
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 345678889999999999999999999999999999999999999999999999999999987654
No 33
>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=98.50 E-value=9.4e-09 Score=53.76 Aligned_cols=33 Identities=21% Similarity=0.233 Sum_probs=28.0
Q ss_pred hcCCCCHHHHHHHHHhcCCCcccceeccccccc
Q psy9614 38 KTQYPDVFTREDLASRLDLSEARVQVNSDSQIP 70 (103)
Q Consensus 38 ~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~ 70 (103)
.++||+..++..||..+||+..||..||-|.|.
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 479999999999999999999999999999875
No 34
>KOG1146|consensus
Probab=98.01 E-value=4.1e-06 Score=70.03 Aligned_cols=64 Identities=17% Similarity=0.153 Sum_probs=58.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccccc
Q psy9614 16 KIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQ 79 (103)
Q Consensus 16 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~ 79 (103)
..+..|+.++..|+..+...|....+|...+.+.|-..++++.+.|+|||||-|++.++.....
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 4567899999999999999999999999999999999999999999999999999999876543
No 35
>KOG0773|consensus
Probab=97.26 E-value=0.00038 Score=51.34 Aligned_cols=61 Identities=16% Similarity=0.045 Sum_probs=50.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHhcCCCcccceecccccccccccc
Q psy9614 15 RKIRRSRTTFTTYQLHQLERAFDK---TQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSN 75 (103)
Q Consensus 15 ~~~rr~Rt~~s~~q~~~Le~~F~~---~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~ 75 (103)
....+.+..+......+|+.+... .+||+..+...||.++||+..||.+||-|.|-+.-+-
T Consensus 237 ~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 237 QSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred cCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 335556668999999999988433 5799999999999999999999999999998876543
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.10 E-value=0.00013 Score=40.64 Aligned_cols=43 Identities=14% Similarity=0.140 Sum_probs=31.2
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccc
Q psy9614 28 QLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIP 70 (103)
Q Consensus 28 q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~ 70 (103)
.+..|+.+|....++...+...|+.+.+|+..+|+.||-.+..
T Consensus 9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 3566999999999999999999999999999999999976544
No 37
>KOG3623|consensus
Probab=96.86 E-value=0.0009 Score=53.94 Aligned_cols=57 Identities=14% Similarity=0.068 Sum_probs=50.0
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccccccccCCC
Q psy9614 29 LHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQIVVTSD 85 (103)
Q Consensus 29 ~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~~~~~~~ 85 (103)
+..|..+|..|..|+..+...+|.+.||+...|+.||.+.++.....++.-...++.
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps~psg~ 624 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPSQPSGE 624 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCccCCCCC
Confidence 778999999999999999999999999999999999999999988877655433333
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=95.09 E-value=0.024 Score=31.02 Aligned_cols=46 Identities=15% Similarity=0.335 Sum_probs=34.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccc
Q psy9614 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQ 68 (103)
Q Consensus 18 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNr 68 (103)
++.|..+|-++...+-..++.+. ....+|..+|++..+|..|..|+
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 46788999988888888888776 57789999999999999998875
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=91.02 E-value=0.26 Score=27.07 Aligned_cols=38 Identities=32% Similarity=0.450 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHhcCCCcccc
Q psy9614 24 FTTYQLHQLERAFDKTQY--PDVFTREDLASRLDLSEARV 61 (103)
Q Consensus 24 ~s~~q~~~Le~~F~~~~~--p~~~~r~~La~~l~l~~~~V 61 (103)
+|+.|..+|...+..+-| |-.....+||..+|++...|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 578999999999998765 66677889999999987554
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=82.90 E-value=1.1 Score=25.38 Aligned_cols=43 Identities=14% Similarity=0.162 Sum_probs=28.1
Q ss_pred CCCCCCCHHHHHHHHHHH-hhcCCCCHHHHHHHHHhcCCCcccceeccc
Q psy9614 19 RSRTTFTTYQLHQLERAF-DKTQYPDVFTREDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 19 r~Rt~~s~~q~~~Le~~F-~~~~~p~~~~r~~La~~l~l~~~~V~vWFq 66 (103)
+.|..||+++...+-..+ ..+ .....+|..+||+...+..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHH
Confidence 456789988877666555 333 3678899999999999999964
No 41
>KOG1146|consensus
Probab=82.63 E-value=1.4 Score=38.23 Aligned_cols=63 Identities=11% Similarity=0.019 Sum_probs=56.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccc
Q psy9614 14 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNE 76 (103)
Q Consensus 14 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~ 76 (103)
+...++.+..+-.+++.+|-++|-.+..|+...+.-|......+.+.+.+||+|-+.+.++..
T Consensus 702 ~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 702 SPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 344566778888899999999999999999999999999999999999999999999998876
No 42
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=79.19 E-value=1.9 Score=29.81 Aligned_cols=39 Identities=28% Similarity=0.428 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHhcCCCcccc
Q psy9614 23 TFTTYQLHQLERAFDKTQY--PDVFTREDLASRLDLSEARV 61 (103)
Q Consensus 23 ~~s~~q~~~Le~~F~~~~~--p~~~~r~~La~~l~l~~~~V 61 (103)
-+|+.|+.+|..+|..+=| |-......||..+|++...+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 6999999999999998754 76777889999999987543
No 43
>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=75.52 E-value=0.87 Score=25.65 Aligned_cols=20 Identities=25% Similarity=0.400 Sum_probs=17.1
Q ss_pred HHHHHHHhcCCCcccceecc
Q psy9614 46 TREDLASRLDLSEARVQVNS 65 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWF 65 (103)
.-..+|..||+++.+|..|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 34578999999999999994
No 44
>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=72.31 E-value=1.7 Score=22.08 Aligned_cols=41 Identities=15% Similarity=0.185 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccc
Q psy9614 23 TFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQ 68 (103)
Q Consensus 23 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNr 68 (103)
.+++.+..++...|..+. ....+|..+|++...|..|...-
T Consensus 10 ~l~~~~~~~~~~~~~~~~-----~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 10 KLPEREREVILLRFGEGL-----SYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred hCCHHHHHHHHHHHhcCC-----CHHHHHHHHCcCHHHHHHHHHHH
Confidence 356777777777664332 45677999999999998887543
No 45
>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=68.03 E-value=9.4 Score=17.03 Aligned_cols=37 Identities=19% Similarity=0.292 Sum_probs=24.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceec
Q psy9614 23 TFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVN 64 (103)
Q Consensus 23 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vW 64 (103)
.++..+...+...+.... ....+|..++++...|..|
T Consensus 5 ~~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHh
Confidence 356666666666665322 4557788999988777666
No 46
>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=66.18 E-value=3.9 Score=21.34 Aligned_cols=38 Identities=18% Similarity=0.239 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecc
Q psy9614 23 TFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNS 65 (103)
Q Consensus 23 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWF 65 (103)
.+++.+..+|...|..+ ..-.++|..+|++...|+.+.
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~ 41 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRIL 41 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHH
Confidence 46788899999888333 246788999999998887654
No 47
>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=64.82 E-value=2.6 Score=22.30 Aligned_cols=38 Identities=16% Similarity=0.137 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccc
Q psy9614 24 FTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 24 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFq 66 (103)
+++.+..++.-.|-.+. ...++|..+|++...|+.|..
T Consensus 11 L~~~~r~i~~l~~~~g~-----s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 11 LPERQREIFLLRYFQGM-----SYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHCc-----CHHHHHHHHCcCHHHHHHHHH
Confidence 45566666665554433 677899999999999999875
No 48
>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=62.68 E-value=8.8 Score=21.46 Aligned_cols=45 Identities=16% Similarity=0.120 Sum_probs=21.4
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccc
Q psy9614 21 RTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 21 Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFq 66 (103)
|..|+.......-.+|....---...| ..|.++|+++.+|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHH-HHHHHhCccHHHHHHHHH
Confidence 445665443333333433322222223 349999999999999964
No 49
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=61.47 E-value=5.3 Score=20.59 Aligned_cols=39 Identities=21% Similarity=0.296 Sum_probs=18.8
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecc
Q psy9614 22 TTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNS 65 (103)
Q Consensus 22 t~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWF 65 (103)
..+|..+...++..+..+ ....++|..+|++...|..+.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHH
Confidence 467888888888876644 356678999999987775543
No 50
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=57.41 E-value=3.6 Score=27.03 Aligned_cols=49 Identities=18% Similarity=0.215 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccc
Q psy9614 21 RTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSN 75 (103)
Q Consensus 21 Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~ 75 (103)
...+++.|..+|.. +..+ ....++|..+|++...|..|-..-+.+.++.
T Consensus 4 ~~~Lt~rqreVL~l-r~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~ 52 (141)
T PRK03975 4 ESFLTERQIEVLRL-RERG-----LTQQEIADILGTSRANVSSIEKRARENIEKA 52 (141)
T ss_pred ccCCCHHHHHHHHH-HHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35789999999977 3322 2466899999999999999988766665543
No 51
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=55.50 E-value=21 Score=22.38 Aligned_cols=41 Identities=15% Similarity=0.164 Sum_probs=27.9
Q ss_pred CCCCCHHHHHH-HHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccc
Q psy9614 21 RTTFTTYQLHQ-LERAFDKTQYPDVFTREDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 21 Rt~~s~~q~~~-Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFq 66 (103)
|..|+.++... +...+. +.. ....+|..+||+...|..|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~-~g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFE-PGM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHc-CCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 45678776543 333333 322 456789999999999999954
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=53.51 E-value=2.2 Score=24.93 Aligned_cols=34 Identities=18% Similarity=0.091 Sum_probs=24.7
Q ss_pred HHHhhcCCCCHHHHHHHHHhcCCCcccceecccc
Q psy9614 34 RAFDKTQYPDVFTREDLASRLDLSEARVQVNSDS 67 (103)
Q Consensus 34 ~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqN 67 (103)
..|....+-......++|..+|++...|+.|+.+
T Consensus 22 ~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 22 AAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 3344444434446788999999999999999864
No 53
>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=53.04 E-value=4.8 Score=22.27 Aligned_cols=21 Identities=19% Similarity=0.292 Sum_probs=18.0
Q ss_pred HHHHHHHhcCCCcccceeccc
Q psy9614 46 TREDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFq 66 (103)
...++|..||++...|..|-+
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 456789999999999999964
No 54
>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=52.90 E-value=3.7 Score=20.99 Aligned_cols=22 Identities=14% Similarity=0.077 Sum_probs=18.2
Q ss_pred HHHHHHhcCCCcccceeccccc
Q psy9614 47 REDLASRLDLSEARVQVNSDSQ 68 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFqNr 68 (103)
..++|..+|++...|+.|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999997544
No 55
>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=50.27 E-value=4.6 Score=27.36 Aligned_cols=34 Identities=24% Similarity=0.165 Sum_probs=29.3
Q ss_pred HHHHHHHHhcCCCcccceeccccccccccccccc
Q psy9614 45 FTREDLASRLDLSEARVQVNSDSQIPTLGSNEKV 78 (103)
Q Consensus 45 ~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~ 78 (103)
-+..+|+.-++++..+|-+|..|-+...+....-
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~y 48 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPKY 48 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccchh
Confidence 3577899999999999999999999988876554
No 56
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=49.89 E-value=5.5 Score=21.97 Aligned_cols=20 Identities=15% Similarity=0.215 Sum_probs=17.0
Q ss_pred HHHHHHhcCCCcccceeccc
Q psy9614 47 REDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFq 66 (103)
..++|..+|++...|+.|=.
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999954
No 57
>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=49.78 E-value=14 Score=20.08 Aligned_cols=33 Identities=27% Similarity=0.414 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCccccee
Q psy9614 27 YQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63 (103)
Q Consensus 27 ~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~v 63 (103)
.|+..|+-.+. +...+.. +||..+|++++.|+.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHH
Confidence 46778888888 6555544 899999999887764
No 58
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=49.70 E-value=6.7 Score=24.93 Aligned_cols=27 Identities=11% Similarity=0.138 Sum_probs=20.8
Q ss_pred HHHHHHHhcCCCcccceeccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTL 72 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~ 72 (103)
...++|..+|++...|+.+...-+.+.
T Consensus 124 s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 124 TMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 467889999999999999876444433
No 59
>PRK10072 putative transcriptional regulator; Provisional
Probab=48.65 E-value=6.5 Score=24.07 Aligned_cols=41 Identities=22% Similarity=0.246 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccc
Q psy9614 23 TFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIP 70 (103)
Q Consensus 23 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~ 70 (103)
..+...+..|..... -...+||..+|++...|..|...+|.
T Consensus 32 ~~~~~eik~LR~~~g-------lTQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTG-------LKIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcC-------CCHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 346666666643222 13678999999999999999987764
No 60
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.93 E-value=20 Score=21.81 Aligned_cols=37 Identities=14% Similarity=0.218 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCccc
Q psy9614 24 FTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEAR 60 (103)
Q Consensus 24 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~ 60 (103)
++++|...-...|+.+--.+.-...++|..|++++-.
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~ 39 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVK 39 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHH
Confidence 5677777666666655555556677889999887643
No 61
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=46.60 E-value=7.4 Score=26.05 Aligned_cols=29 Identities=21% Similarity=0.264 Sum_probs=22.4
Q ss_pred HHHHHHHhcCCCcccceeccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
...++|..+|++...|+++...-|.+.++
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 45788999999999999988655555443
No 62
>PF13518 HTH_28: Helix-turn-helix domain
Probab=45.96 E-value=7.6 Score=20.03 Aligned_cols=23 Identities=13% Similarity=0.137 Sum_probs=18.9
Q ss_pred HHHHHHHhcCCCcccceeccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQ 68 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNr 68 (103)
....+|..+|++..+|..|.+.-
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHH
Confidence 35568999999999999997543
No 63
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=44.01 E-value=5.8 Score=20.52 Aligned_cols=23 Identities=22% Similarity=0.289 Sum_probs=17.1
Q ss_pred HHHHHHHHhcCCCcccceecccc
Q psy9614 45 FTREDLASRLDLSEARVQVNSDS 67 (103)
Q Consensus 45 ~~r~~La~~l~l~~~~V~vWFqN 67 (103)
....++|..+|++...|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 35678899999999999999753
No 64
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=43.95 E-value=7.4 Score=26.43 Aligned_cols=29 Identities=21% Similarity=0.302 Sum_probs=22.3
Q ss_pred HHHHHHHhcCCCcccceeccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
...++|..+|++...|+++...-+.+.++
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45788999999999999887655555444
No 65
>PRK09480 slmA division inhibitor protein; Provisional
Probab=42.89 E-value=19 Score=23.51 Aligned_cols=36 Identities=22% Similarity=0.254 Sum_probs=29.4
Q ss_pred HHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccc
Q psy9614 34 RAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIP 70 (103)
Q Consensus 34 ~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~ 70 (103)
..|...+. .......+|...|++...+-.+|.|+-.
T Consensus 21 ~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 21 QMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 34555556 7888999999999999999999998753
No 66
>PRK13558 bacterio-opsin activator; Provisional
Probab=41.37 E-value=25 Score=27.97 Aligned_cols=40 Identities=25% Similarity=0.427 Sum_probs=34.1
Q ss_pred CCCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHhcCCCcccc
Q psy9614 22 TTFTTYQLHQLERAFDKTQY--PDVFTREDLASRLDLSEARV 61 (103)
Q Consensus 22 t~~s~~q~~~Le~~F~~~~~--p~~~~r~~La~~l~l~~~~V 61 (103)
..+|..|..+|+..|..+-| |-...-.+||..||++...+
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~ 647 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTF 647 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 47999999999999998876 76778899999999987543
No 67
>PRK00118 putative DNA-binding protein; Validated
Probab=41.06 E-value=9.3 Score=23.77 Aligned_cols=47 Identities=17% Similarity=0.129 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccc
Q psy9614 23 TFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 23 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
.+++.|..++...|..+. ...++|..+|++...|..|...-+.+.+.
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 456667777766555443 46678999999999999988755555444
No 68
>KOG3623|consensus
Probab=41.05 E-value=43 Score=28.19 Aligned_cols=60 Identities=20% Similarity=0.179 Sum_probs=40.4
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccccc
Q psy9614 19 RSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKV 78 (103)
Q Consensus 19 r~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~ 78 (103)
+.++.....+-..|..+++....++-.+-...+..+...+.+|.|||++|+..-+.....
T Consensus 628 kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl~ 687 (1007)
T KOG3623|consen 628 KVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPLF 687 (1007)
T ss_pred cccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCccc
Confidence 344556666666677777666655555444455557777788999999999887765443
No 69
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=40.60 E-value=8.8 Score=24.80 Aligned_cols=28 Identities=14% Similarity=0.081 Sum_probs=21.1
Q ss_pred HHHHHHHhcCCCcccceecccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLG 73 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~r 73 (103)
...++|..+|++...|..|...-+.+.+
T Consensus 146 s~~eIA~~lgis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVRSRIFRAREALR 173 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567899999999999998764444433
No 70
>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=40.34 E-value=7.5 Score=19.52 Aligned_cols=18 Identities=17% Similarity=0.220 Sum_probs=14.3
Q ss_pred HHHHHhcCCCcccceecc
Q psy9614 48 EDLASRLDLSEARVQVNS 65 (103)
Q Consensus 48 ~~La~~l~l~~~~V~vWF 65 (103)
.++|..+|++...|+.|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 468999999999998883
No 71
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=40.09 E-value=8.3 Score=25.47 Aligned_cols=32 Identities=13% Similarity=0.071 Sum_probs=24.4
Q ss_pred HHHHHHHhcCCCcccceecccccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSNEK 77 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~ 77 (103)
.-.++|..+|++...|+.+...-|.+.++...
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988766666555433
No 72
>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=39.72 E-value=14 Score=19.77 Aligned_cols=43 Identities=19% Similarity=0.271 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccc
Q psy9614 23 TFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPT 71 (103)
Q Consensus 23 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k 71 (103)
.||+.+..+|.-...-. ...++|..+++++..|..+..+=+.|
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHH
Confidence 57888888876654422 36788999999999988876554444
No 73
>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=39.69 E-value=29 Score=17.70 Aligned_cols=38 Identities=11% Similarity=0.246 Sum_probs=24.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecc
Q psy9614 23 TFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNS 65 (103)
Q Consensus 23 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWF 65 (103)
.++..+...+...+.... ....+|..+|++...|.-++
T Consensus 5 ~~~~~~~~~i~~l~~~G~-----si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEGM-----SIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHHHHHH
Confidence 456656666666666552 47788999999987765443
No 74
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=39.13 E-value=11 Score=24.59 Aligned_cols=28 Identities=18% Similarity=0.208 Sum_probs=21.5
Q ss_pred HHHHHHHhcCCCcccceecccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLG 73 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~r 73 (103)
...++|..+|++...|+++...-|.+.|
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 4678899999999999988765444443
No 75
>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=38.96 E-value=13 Score=23.65 Aligned_cols=25 Identities=16% Similarity=-0.001 Sum_probs=19.1
Q ss_pred HHHHHHHhcCCCcccceeccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIP 70 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~ 70 (103)
...++|..+|++...|.++...-|.
T Consensus 129 ~~~eIA~~l~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 129 SLTALAEQLGRTVNAVYKALSRLRV 153 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4678899999999999887653333
No 76
>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=38.33 E-value=11 Score=23.10 Aligned_cols=26 Identities=15% Similarity=0.161 Sum_probs=19.8
Q ss_pred HHHHHHHhcCCCcccceecccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPT 71 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k 71 (103)
...++|..+|++...|..+...-+.+
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKK 153 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45688999999999998887644443
No 77
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=37.76 E-value=12 Score=24.00 Aligned_cols=29 Identities=7% Similarity=0.053 Sum_probs=21.9
Q ss_pred HHHHHHHhcCCCcccceeccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
...++|..+|++...|++....-|.+.|+
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34678999999999999987655555444
No 78
>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=37.46 E-value=11 Score=20.86 Aligned_cols=21 Identities=0% Similarity=0.117 Sum_probs=17.5
Q ss_pred HHHHHHhcCCCcccceecccc
Q psy9614 47 REDLASRLDLSEARVQVNSDS 67 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFqN 67 (103)
..++|..+|++...++.|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999653
No 79
>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=36.92 E-value=9.9 Score=18.87 Aligned_cols=24 Identities=13% Similarity=0.050 Sum_probs=19.5
Q ss_pred HHHHHHhcCCCcccceeccccccc
Q psy9614 47 REDLASRLDLSEARVQVNSDSQIP 70 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFqNrR~ 70 (103)
..++|..+|++...|..|.++..-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 357899999999999999876544
No 80
>PHA02955 hypothetical protein; Provisional
Probab=36.77 E-value=66 Score=22.68 Aligned_cols=44 Identities=9% Similarity=0.138 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHhhc-CCCCHHHHHHHHHhcCCCcccceecccccc
Q psy9614 26 TYQLHQLERAFDKT-QYPDVFTREDLASRLDLSEARVQVNSDSQI 69 (103)
Q Consensus 26 ~~q~~~Le~~F~~~-~~p~~~~r~~La~~l~l~~~~V~vWFqNrR 69 (103)
..++..|-+.|... .-.+..++..+++++|+....|..||.+.-
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~ 104 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDL 104 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchh
Confidence 35566666666554 456778899999999998877888997653
No 81
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=36.29 E-value=13 Score=24.51 Aligned_cols=29 Identities=24% Similarity=0.407 Sum_probs=22.7
Q ss_pred HHHHHHHhcCCCcccceeccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
.-.++|..+|++...|+.+...-+.+.+.
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45788999999999999988765555544
No 82
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=35.74 E-value=46 Score=16.72 Aligned_cols=39 Identities=23% Similarity=0.324 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccc
Q psy9614 23 TFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDS 67 (103)
Q Consensus 23 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqN 67 (103)
.++..+..++...+ .+ ....++|..+|++...|..|...
T Consensus 3 ~l~~~e~~i~~~~~-~g-----~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLA-EG-----LTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 46777777775532 22 24577899999999999888653
No 83
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=35.18 E-value=13 Score=23.93 Aligned_cols=28 Identities=14% Similarity=0.133 Sum_probs=21.7
Q ss_pred HHHHHHHhcCCCcccceecccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLG 73 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~r 73 (103)
...++|..+|++...|..|..--+.+.+
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4578899999999999998865554444
No 84
>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=34.83 E-value=8.6 Score=19.90 Aligned_cols=21 Identities=24% Similarity=0.178 Sum_probs=18.3
Q ss_pred HHHHhcCCCcccceecccccc
Q psy9614 49 DLASRLDLSEARVQVNSDSQI 69 (103)
Q Consensus 49 ~La~~l~l~~~~V~vWFqNrR 69 (103)
+||..+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 579999999999999998774
No 85
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=34.67 E-value=10 Score=25.18 Aligned_cols=30 Identities=17% Similarity=0.316 Sum_probs=22.8
Q ss_pred HHHHHHHHHhcCCCcccceecccccccccc
Q psy9614 44 VFTREDLASRLDLSEARVQVNSDSQIPTLG 73 (103)
Q Consensus 44 ~~~r~~La~~l~l~~~~V~vWFqNrR~k~r 73 (103)
.....++|..+|++...|++|...-+.+.+
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 345678899999999999999865554444
No 86
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=34.59 E-value=13 Score=24.54 Aligned_cols=26 Identities=15% Similarity=0.254 Sum_probs=19.8
Q ss_pred HHHHHHHhcCCCcccceecccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPT 71 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k 71 (103)
...++|..+|++...|+++...-+.+
T Consensus 157 s~~EIA~~lgis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHRALAR 182 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 46788999999999998876543433
No 87
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=34.23 E-value=66 Score=21.62 Aligned_cols=36 Identities=22% Similarity=0.212 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccc
Q psy9614 26 TYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARV 61 (103)
Q Consensus 26 ~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 61 (103)
..-+..|........|.+......+|..||++...|
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 445677888888888999999999999999987544
No 88
>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=34.10 E-value=38 Score=17.65 Aligned_cols=31 Identities=19% Similarity=0.310 Sum_probs=18.4
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHhcCCCccccee
Q psy9614 30 HQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63 (103)
Q Consensus 30 ~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~v 63 (103)
.+|.-.+....+ ....+||..++++.+.|..
T Consensus 4 ~il~~L~~~~~~---it~~eLa~~l~vS~rTi~~ 34 (55)
T PF08279_consen 4 QILKLLLESKEP---ITAKELAEELGVSRRTIRR 34 (55)
T ss_dssp HHHHHHHHTTTS---BEHHHHHHHCTS-HHHHHH
T ss_pred HHHHHHHHcCCC---cCHHHHHHHhCCCHHHHHH
Confidence 344444344443 3456899999999877653
No 89
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.91 E-value=58 Score=19.87 Aligned_cols=42 Identities=10% Similarity=0.048 Sum_probs=31.2
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCC-Ccccceeccc
Q psy9614 21 RTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDL-SEARVQVNSD 66 (103)
Q Consensus 21 Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l-~~~~V~vWFq 66 (103)
|..||.+....+-..+....+ ....+|..+|+ ...++..|-.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 678998877666655554443 57789999996 8888888853
No 90
>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=33.83 E-value=13 Score=24.29 Aligned_cols=27 Identities=26% Similarity=0.156 Sum_probs=20.2
Q ss_pred HHHHHHHhcCCCcccceeccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTL 72 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~ 72 (103)
...++|..+|++...|++....-|.+.
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~L 178 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWL 178 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 456789999999999998776444443
No 91
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=33.68 E-value=11 Score=24.29 Aligned_cols=30 Identities=27% Similarity=0.097 Sum_probs=22.9
Q ss_pred HHHHHHHhcCCCcccceecccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSN 75 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~ 75 (103)
...++|..+|++...|++|.+--|.+.++.
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999887555555443
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=33.67 E-value=15 Score=23.05 Aligned_cols=26 Identities=15% Similarity=0.282 Sum_probs=19.4
Q ss_pred HHHHHHHhcCCCcccceecccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPT 71 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k 71 (103)
...++|..+|+++..|+.+...-+.+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKE 156 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45678999999999998876544433
No 93
>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=33.52 E-value=13 Score=20.56 Aligned_cols=20 Identities=5% Similarity=-0.039 Sum_probs=17.3
Q ss_pred HHHHHHhcCCCcccceeccc
Q psy9614 47 REDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFq 66 (103)
..++|+.+|++...++.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999975
No 94
>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=33.21 E-value=13 Score=20.31 Aligned_cols=20 Identities=10% Similarity=-0.001 Sum_probs=17.2
Q ss_pred HHHHHHhcCCCcccceeccc
Q psy9614 47 REDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFq 66 (103)
..++|..+|++...+..|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999974
No 95
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=33.18 E-value=66 Score=21.28 Aligned_cols=35 Identities=29% Similarity=0.208 Sum_probs=27.2
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccce
Q psy9614 28 QLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 62 (103)
Q Consensus 28 q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~ 62 (103)
-+.+|...=+...|.+......+|..+|++...|.
T Consensus 25 li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 25 LLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 35556555566779999999999999999986654
No 96
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=32.90 E-value=65 Score=21.11 Aligned_cols=35 Identities=14% Similarity=0.134 Sum_probs=26.4
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccce
Q psy9614 28 QLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 62 (103)
Q Consensus 28 q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~ 62 (103)
-+.+|...=+...|.+......+|..++++...|-
T Consensus 24 ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 24 VIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34455555556679999999999999999986654
No 97
>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=32.18 E-value=43 Score=22.01 Aligned_cols=10 Identities=0% Similarity=-0.276 Sum_probs=6.6
Q ss_pred ceeccccccc
Q psy9614 61 VQVNSDSQIP 70 (103)
Q Consensus 61 V~vWFqNrR~ 70 (103)
|..||-||+.
T Consensus 71 iP~w~~Nr~~ 80 (144)
T TIGR03629 71 IPSWLLNRRK 80 (144)
T ss_pred CCHHHhhccc
Confidence 5568888553
No 98
>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=31.97 E-value=52 Score=16.49 Aligned_cols=15 Identities=33% Similarity=0.394 Sum_probs=12.2
Q ss_pred CCCHHHHHHHHHHHh
Q psy9614 23 TFTTYQLHQLERAFD 37 (103)
Q Consensus 23 ~~s~~q~~~Le~~F~ 37 (103)
.||..|+..|+.-..
T Consensus 2 ~FT~~Ql~~L~~Qi~ 16 (37)
T PF08880_consen 2 PFTPAQLQELRAQIL 16 (37)
T ss_pred CCCHHHHHHHHHHHH
Confidence 689999999987543
No 99
>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=31.87 E-value=39 Score=21.06 Aligned_cols=38 Identities=13% Similarity=0.121 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccc
Q psy9614 24 FTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 24 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFq 66 (103)
||-+-....-.++..+. ...++|..++|+...|..|++
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 34444444445565544 456679999999999999998
No 100
>PRK04217 hypothetical protein; Provisional
Probab=31.72 E-value=17 Score=22.80 Aligned_cols=48 Identities=17% Similarity=0.092 Sum_probs=35.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccc
Q psy9614 21 RTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLG 73 (103)
Q Consensus 21 Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~r 73 (103)
-..++..+..++...|...- ...++|..+|++...|...+..-+.+.+
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLr 87 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVA 87 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 35678888888877665443 5678999999999999887765555544
No 101
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=31.32 E-value=21 Score=23.47 Aligned_cols=25 Identities=16% Similarity=0.242 Sum_probs=19.3
Q ss_pred HHHHHHHhcCCCcccceeccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIP 70 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~ 70 (103)
...++|..+|++...|+++...-+.
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHH
Confidence 4577899999999999988654333
No 102
>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=30.78 E-value=74 Score=20.64 Aligned_cols=35 Identities=14% Similarity=0.064 Sum_probs=26.2
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccce
Q psy9614 28 QLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 62 (103)
Q Consensus 28 q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~ 62 (103)
-+.+|...=+...|.+......+|..+|++...|.
T Consensus 18 li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 18 IMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34555555455679999999999999999876543
No 103
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=30.71 E-value=19 Score=23.94 Aligned_cols=30 Identities=10% Similarity=0.078 Sum_probs=22.4
Q ss_pred HHHHHHHhcCCCcccceecccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSN 75 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~ 75 (103)
...++|..+|++...|+++..--|.+.++.
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999876555554443
No 104
>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=30.58 E-value=17 Score=23.71 Aligned_cols=30 Identities=17% Similarity=0.223 Sum_probs=22.7
Q ss_pred HHHHHHHhcCCCcccceecccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSN 75 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~ 75 (103)
...++|..+|++...|+++...-|.+.+..
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999876555555543
No 105
>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=30.22 E-value=15 Score=19.11 Aligned_cols=23 Identities=17% Similarity=0.371 Sum_probs=18.4
Q ss_pred HHHHHHhcCCCcccceecccccc
Q psy9614 47 REDLASRLDLSEARVQVNSDSQI 69 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFqNrR 69 (103)
..+||..+|++...|.-|..+.+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 47899999999999999987643
No 106
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=30.16 E-value=17 Score=23.34 Aligned_cols=29 Identities=14% Similarity=0.214 Sum_probs=21.3
Q ss_pred HHHHHHHhcCCCcccceeccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
...++|..+|++...|+.+...-+.+.|+
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999887544444443
No 107
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=30.16 E-value=17 Score=24.19 Aligned_cols=29 Identities=17% Similarity=0.194 Sum_probs=21.9
Q ss_pred HHHHHHHhcCCCcccceeccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
...++|..+|+++..|+++...-|.+.|+
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46788999999999999987644444443
No 108
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=29.96 E-value=15 Score=24.27 Aligned_cols=30 Identities=13% Similarity=0.130 Sum_probs=22.4
Q ss_pred HHHHHHHhcCCCcccceecccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSN 75 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~ 75 (103)
...++|..+|++...|++-...-|.+.++.
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999988776555555543
No 109
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=29.60 E-value=16 Score=23.92 Aligned_cols=29 Identities=17% Similarity=0.251 Sum_probs=21.9
Q ss_pred HHHHHHHHhcCCCcccceecccccccccc
Q psy9614 45 FTREDLASRLDLSEARVQVNSDSQIPTLG 73 (103)
Q Consensus 45 ~~r~~La~~l~l~~~~V~vWFqNrR~k~r 73 (103)
....++|..+|++...|+++...-|.+.+
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35578899999999999998865554444
No 110
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=29.50 E-value=18 Score=23.20 Aligned_cols=27 Identities=19% Similarity=0.202 Sum_probs=19.6
Q ss_pred HHHHHHHhcCCCcccceeccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTL 72 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~ 72 (103)
...++|..+|++...|+++...-|.+.
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L 156 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKET 156 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 456789999999988888765444443
No 111
>KOG3755|consensus
Probab=28.82 E-value=21 Score=29.19 Aligned_cols=62 Identities=23% Similarity=0.213 Sum_probs=49.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhh-cCCCCHHH---HHHHHHhcCCCcccceecccccccccccccc
Q psy9614 16 KIRRSRTTFTTYQLHQLERAFDK-TQYPDVFT---REDLASRLDLSEARVQVNSDSQIPTLGSNEK 77 (103)
Q Consensus 16 ~~rr~Rt~~s~~q~~~Le~~F~~-~~~p~~~~---r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~ 77 (103)
...+.|+.++.+-+..|..+... .=||+... ..-|...++++...+--.|+|.|...+....
T Consensus 646 ~~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~~w~ 711 (769)
T KOG3755|consen 646 HKPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKHHWK 711 (769)
T ss_pred cCccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecchhhe
Confidence 35677888888888888777543 55788777 7889999999999999999999988765443
No 112
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=28.44 E-value=21 Score=24.03 Aligned_cols=33 Identities=15% Similarity=0.096 Sum_probs=25.0
Q ss_pred HHHHHHHhcCCCcccceeccccccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSNEKV 78 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~ 78 (103)
...++|..+|++...|+++...-|.+.|+....
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~ 183 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAATAT 183 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 457889999999999999887666666654443
No 113
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=28.30 E-value=35 Score=23.47 Aligned_cols=40 Identities=15% Similarity=0.056 Sum_probs=32.0
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccc
Q psy9614 31 QLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTL 72 (103)
Q Consensus 31 ~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~ 72 (103)
.-...|....|- .....+|+..|++...|-.+|.|+..-.
T Consensus 21 aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~ 60 (225)
T PRK11552 21 AALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLY 60 (225)
T ss_pred HHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHH
Confidence 334458877776 5788899999999999999999986643
No 114
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=28.26 E-value=29 Score=22.99 Aligned_cols=31 Identities=19% Similarity=0.292 Sum_probs=23.4
Q ss_pred HHHHHHHhcCCCcccceeccccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSNE 76 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~ 76 (103)
...++|..+|++...|++..+--|.+.+++.
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 4578899999999999988765555555543
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=28.03 E-value=13 Score=24.45 Aligned_cols=30 Identities=17% Similarity=0.159 Sum_probs=22.5
Q ss_pred HHHHHHHHhcCCCcccceeccccccccccc
Q psy9614 45 FTREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 45 ~~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
..-.++|..+|++...|+++...-|.+.|+
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 346788999999999999987655544443
No 116
>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=28.00 E-value=22 Score=22.97 Aligned_cols=26 Identities=15% Similarity=0.236 Sum_probs=19.2
Q ss_pred HHHHHHHhcCCCcccceecccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPT 71 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k 71 (103)
...++|..+|++...|+++..--|.+
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKK 162 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45678999999999988876533333
No 117
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=27.82 E-value=8.9 Score=26.81 Aligned_cols=30 Identities=17% Similarity=0.123 Sum_probs=23.7
Q ss_pred HHHHHHHhcCCCcccceecccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSN 75 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~ 75 (103)
...++|..+|++...|++....-|.+.|+.
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~ 218 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDL 218 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999887666666554
No 118
>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=27.65 E-value=25 Score=18.13 Aligned_cols=23 Identities=13% Similarity=0.098 Sum_probs=19.4
Q ss_pred HHHHHHhcCCCcccceecccccc
Q psy9614 47 REDLASRLDLSEARVQVNSDSQI 69 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFqNrR 69 (103)
...||..+|++...|.-|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 56899999999999999986654
No 119
>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=27.65 E-value=50 Score=19.38 Aligned_cols=21 Identities=14% Similarity=0.333 Sum_probs=17.3
Q ss_pred HHHHHHHhcCCCcccceeccc
Q psy9614 46 TREDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFq 66 (103)
-+..|...++|..-+|.+|+.
T Consensus 55 L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 55 LTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHHhCCCCCeEEEEEE
Confidence 355678888999999999984
No 120
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=27.31 E-value=22 Score=22.58 Aligned_cols=28 Identities=18% Similarity=0.234 Sum_probs=20.5
Q ss_pred HHHHHHHhcCCCcccceecccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLG 73 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~r 73 (103)
...++|..+|++...|++....-+.+.+
T Consensus 124 s~~EIA~~lgis~~tV~~~l~ra~~~Lr 151 (161)
T PRK09047 124 DVAETAAAMGCSEGSVKTHCSRATHALA 151 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3578899999999999887654444433
No 121
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=27.04 E-value=95 Score=20.91 Aligned_cols=32 Identities=25% Similarity=0.153 Sum_probs=23.2
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHhcCCCcccce
Q psy9614 31 QLERAFDKTQYPDVFTREDLASRLDLSEARVQ 62 (103)
Q Consensus 31 ~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~ 62 (103)
+|...=+...|.+......+|..+|++...|.
T Consensus 41 ~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 41 VLHKAQELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 33333344568889999999999999876543
No 122
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=26.65 E-value=21 Score=23.51 Aligned_cols=29 Identities=24% Similarity=0.288 Sum_probs=22.3
Q ss_pred HHHHHHHhcCCCcccceeccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
...++|..+|++...|++....-|.+.++
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45788999999999999887655555544
No 123
>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=26.57 E-value=71 Score=16.07 Aligned_cols=36 Identities=22% Similarity=0.181 Sum_probs=24.3
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccc
Q psy9614 25 TTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 25 s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFq 66 (103)
+..+..++...+ .. ....++|..++++...|..|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 455556654432 11 2456789999999999998875
No 124
>PRK06930 positive control sigma-like factor; Validated
Probab=26.46 E-value=21 Score=23.89 Aligned_cols=47 Identities=11% Similarity=0.065 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccc
Q psy9614 23 TFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 23 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
.+++.+..++.-.|..+. .-.++|..+|++...|+.+...-+.+.++
T Consensus 114 ~L~~rer~V~~L~~~eg~-----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGL-----SYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345555555554433222 45678999999999999988765555544
No 125
>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=26.32 E-value=64 Score=16.29 Aligned_cols=34 Identities=24% Similarity=0.294 Sum_probs=20.1
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccce
Q psy9614 25 TTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 62 (103)
Q Consensus 25 s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~ 62 (103)
+..+..+|....+ ++. ....+||..+|++...|.
T Consensus 2 ~~~~~~Il~~l~~-~~~---~t~~ela~~~~is~~tv~ 35 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPR---ITQKELAEKLGISRSTVN 35 (48)
T ss_dssp -HHHHHHHHHHHH-CTT---S-HHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHHHHHH-cCC---CCHHHHHHHhCCCHHHHH
Confidence 3456666755555 333 356688999999876554
No 126
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=26.19 E-value=25 Score=23.50 Aligned_cols=32 Identities=9% Similarity=0.020 Sum_probs=24.7
Q ss_pred HHHHHHHhcCCCcccceecccccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSNEK 77 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~ 77 (103)
...++|..+|++...|++....-|.+.++...
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988766666665443
No 127
>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=26.18 E-value=69 Score=20.73 Aligned_cols=34 Identities=24% Similarity=0.235 Sum_probs=23.7
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccce
Q psy9614 29 LHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 62 (103)
Q Consensus 29 ~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~ 62 (103)
+.+|...=+...|.+......+|..++++..+|.
T Consensus 16 l~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 16 LPILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 4555555566779999999999999999987654
No 128
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=26.18 E-value=73 Score=16.92 Aligned_cols=21 Identities=19% Similarity=0.305 Sum_probs=9.5
Q ss_pred HHHHHhcCCCcccceeccccc
Q psy9614 48 EDLASRLDLSEARVQVNSDSQ 68 (103)
Q Consensus 48 ~~La~~l~l~~~~V~vWFqNr 68 (103)
..||..+|++...|..|+.++
T Consensus 14 ~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 14 KDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp HHHHHHHT--HHHHHHHHTTT
T ss_pred HHHHHHHCcCHHHHHHHHhcc
Confidence 345555555555555555443
No 129
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=26.12 E-value=21 Score=19.50 Aligned_cols=20 Identities=10% Similarity=0.044 Sum_probs=16.6
Q ss_pred HHHHHHhcCCCcccceeccc
Q psy9614 47 REDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFq 66 (103)
..++|..+|++...|+.|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35689999999999999954
No 130
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=26.06 E-value=21 Score=23.08 Aligned_cols=28 Identities=14% Similarity=0.086 Sum_probs=20.8
Q ss_pred HHHHHHHhcCCCcccceecccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLG 73 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~r 73 (103)
...++|..+|++...|+++...-|.+.+
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4578899999999999988764444433
No 131
>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=25.51 E-value=23 Score=22.62 Aligned_cols=29 Identities=17% Similarity=0.259 Sum_probs=21.7
Q ss_pred HHHHHHHhcCCCcccceeccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
.-.++|..+|++...|+++-..-+.+.++
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999887655555443
No 132
>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=25.16 E-value=22 Score=17.61 Aligned_cols=25 Identities=20% Similarity=0.033 Sum_probs=18.9
Q ss_pred HHHHHHhcCCCcccceecccccccc
Q psy9614 47 REDLASRLDLSEARVQVNSDSQIPT 71 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFqNrR~k 71 (103)
..++|..+|++...|..|..+.+-.
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGELP 28 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCCCC
Confidence 4567889999999999887655433
No 133
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=24.96 E-value=25 Score=23.05 Aligned_cols=30 Identities=17% Similarity=0.315 Sum_probs=23.0
Q ss_pred HHHHHHHhcCCCcccceecccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSN 75 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~ 75 (103)
...++|..+|++...|++....-+.+.++.
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 164 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQK 164 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999998877666665543
No 134
>KOG0773|consensus
Probab=24.49 E-value=27 Score=25.71 Aligned_cols=42 Identities=19% Similarity=0.137 Sum_probs=35.0
Q ss_pred hhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccccc
Q psy9614 37 DKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKV 78 (103)
Q Consensus 37 ~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~ 78 (103)
..++||+......++....++..+|.+||-|-+.+.....+.
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~ 158 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKM 158 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCC
Confidence 448899999999999999999999999999888776655444
No 135
>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=24.34 E-value=1.2e+02 Score=20.13 Aligned_cols=32 Identities=16% Similarity=0.361 Sum_probs=23.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcC-CCcc
Q psy9614 23 TFTTYQLHQLERAFDKTQYPDVFTREDLASRLD-LSEA 59 (103)
Q Consensus 23 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~-l~~~ 59 (103)
.+|.+.+..|.+.+.... ...++|.+|| ++..
T Consensus 2 ~Wtde~~~~L~~lw~~G~-----SasqIA~~lg~vsRn 34 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGL-----SASQIARQLGGVSRN 34 (162)
T ss_pred CCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCcchh
Confidence 367889999999887655 4556778887 6654
No 136
>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=24.26 E-value=26 Score=22.46 Aligned_cols=21 Identities=19% Similarity=0.156 Sum_probs=16.3
Q ss_pred HHHHHHHhcCCCcccceeccc
Q psy9614 46 TREDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFq 66 (103)
...++|..+|++...|++...
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQF 160 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 457789999999988877653
No 137
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=24.24 E-value=26 Score=23.20 Aligned_cols=29 Identities=17% Similarity=0.245 Sum_probs=22.2
Q ss_pred HHHHHHHhcCCCcccceeccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
...++|..+|++...|+..+..-|.+.++
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45788999999999999888655555444
No 138
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=24.22 E-value=23 Score=23.75 Aligned_cols=31 Identities=13% Similarity=0.102 Sum_probs=24.5
Q ss_pred HHHHHHHhcCCCcccceeccccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSNE 76 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~ 76 (103)
...++|..+|++...|+++...-|.+.|+..
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578899999999999999876666665543
No 139
>PRK06424 transcription factor; Provisional
Probab=24.05 E-value=47 Score=21.81 Aligned_cols=24 Identities=13% Similarity=0.160 Sum_probs=19.9
Q ss_pred HHHHHHhcCCCcccceeccccccc
Q psy9614 47 REDLASRLDLSEARVQVNSDSQIP 70 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFqNrR~ 70 (103)
..+||..+|++...|.-|-.+.+.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 568999999999999999876654
No 140
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=23.95 E-value=54 Score=20.45 Aligned_cols=40 Identities=10% Similarity=0.159 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccc
Q psy9614 24 FTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIP 70 (103)
Q Consensus 24 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~ 70 (103)
+++.++..+...+.-. ...+|.-||++...|+.|=|+|+.
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 6777777776655433 346799999999999999887654
No 141
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=23.81 E-value=24 Score=24.42 Aligned_cols=29 Identities=24% Similarity=0.335 Sum_probs=22.9
Q ss_pred HHHHHHHhcCCCcccceeccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
...++|..+|++...|+.+...-+.+.|+
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56788999999999999988765555544
No 142
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=23.81 E-value=28 Score=22.52 Aligned_cols=29 Identities=17% Similarity=0.268 Sum_probs=21.0
Q ss_pred HHHHHHHhcCCCcccceeccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
...++|..+|+++..|+.....-+.+.++
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35788999999999998876544444443
No 143
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=23.80 E-value=73 Score=20.85 Aligned_cols=25 Identities=20% Similarity=0.270 Sum_probs=19.1
Q ss_pred HHHHHHHhcCCCcccceeccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIP 70 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~ 70 (103)
...++|..+|+++..|++....-+.
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~ 169 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYV 169 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4578899999999999887654333
No 144
>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=23.70 E-value=68 Score=20.91 Aligned_cols=48 Identities=21% Similarity=0.310 Sum_probs=35.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccc
Q psy9614 21 RTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 21 Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
.+.++..|..+|.-. ..+. ...++|..+|++...|..+-..-+.+.++
T Consensus 4 ~~~Lte~qr~VL~Lr-~~Gl-----Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKGL-----SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHH-HcCC-----CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 367889999999774 2222 56789999999999999887665555553
No 145
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=23.55 E-value=24 Score=23.50 Aligned_cols=30 Identities=7% Similarity=0.098 Sum_probs=22.9
Q ss_pred HHHHHHHhcCCCcccceecccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSN 75 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~ 75 (103)
...++|..+|++...|++....-|.+.|+.
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999876555555543
No 146
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=23.33 E-value=91 Score=18.28 Aligned_cols=44 Identities=7% Similarity=0.003 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHhhc-----CCCCHHHHHHHHHhcCCCcccceeccc
Q psy9614 23 TFTTYQLHQLERAFDKT-----QYPDVFTREDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 23 ~~s~~q~~~Le~~F~~~-----~~p~~~~r~~La~~l~l~~~~V~vWFq 66 (103)
.++..++..+...|... .+.+..+...+-..+|++...|.-.|.
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 36788899999888652 356666666666667887776666653
No 147
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=23.00 E-value=30 Score=22.79 Aligned_cols=29 Identities=24% Similarity=0.385 Sum_probs=21.6
Q ss_pred HHHHHHHHhcCCCcccceecccccccccc
Q psy9614 45 FTREDLASRLDLSEARVQVNSDSQIPTLG 73 (103)
Q Consensus 45 ~~r~~La~~l~l~~~~V~vWFqNrR~k~r 73 (103)
....++|..+|++...|+.+...-+.+.+
T Consensus 148 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 176 (184)
T PRK12539 148 LSVAEAATRSGMSESAVKVSVHRGLKALA 176 (184)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 35678899999999999988754444444
No 148
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=22.89 E-value=30 Score=16.85 Aligned_cols=22 Identities=23% Similarity=0.445 Sum_probs=18.1
Q ss_pred HHHHHHhcCCCcccceeccccc
Q psy9614 47 REDLASRLDLSEARVQVNSDSQ 68 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFqNr 68 (103)
...+|..+|++...|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 4578999999999999887665
No 149
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=22.89 E-value=21 Score=19.90 Aligned_cols=18 Identities=28% Similarity=0.250 Sum_probs=15.1
Q ss_pred HHHHHHhcCCCcccceec
Q psy9614 47 REDLASRLDLSEARVQVN 64 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vW 64 (103)
...||..||++...|--|
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 150
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=22.87 E-value=28 Score=23.23 Aligned_cols=30 Identities=10% Similarity=0.168 Sum_probs=23.1
Q ss_pred HHHHHHHhcCCCcccceecccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSN 75 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~ 75 (103)
.-.++|..+|++...|+++..--|.+.++.
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999987555555543
No 151
>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=22.73 E-value=26 Score=19.30 Aligned_cols=37 Identities=22% Similarity=0.286 Sum_probs=23.1
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccc
Q psy9614 25 TTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARV 61 (103)
Q Consensus 25 s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 61 (103)
|+..-..|+..|....--.......||..++++...|
T Consensus 3 t~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tv 39 (60)
T PF01325_consen 3 TESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTV 39 (60)
T ss_dssp SCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHH
T ss_pred CcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHH
Confidence 3444566777776654333445667899999887554
No 152
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.40 E-value=24 Score=24.01 Aligned_cols=30 Identities=17% Similarity=0.137 Sum_probs=22.8
Q ss_pred HHHHHHHhcCCCcccceecccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGSN 75 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr~ 75 (103)
...++|..+|++...|++....-|.+.|+.
T Consensus 166 s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 166 ETNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999876555555544
No 153
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=22.28 E-value=31 Score=22.03 Aligned_cols=21 Identities=29% Similarity=0.338 Sum_probs=17.2
Q ss_pred HHHHHHHhcCCCcccceeccc
Q psy9614 46 TREDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFq 66 (103)
...++|..+|++...|+....
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ 147 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIR 147 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 457889999999999988654
No 154
>PF13309 HTH_22: HTH domain
Probab=22.23 E-value=1.2e+02 Score=16.72 Aligned_cols=38 Identities=18% Similarity=0.204 Sum_probs=25.0
Q ss_pred CCHHH-HHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccc
Q psy9614 24 FTTYQ-LHQLERAFDKTQYPDVFTREDLASRLDLSEARV 61 (103)
Q Consensus 24 ~s~~q-~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 61 (103)
++..+ +.++...++.+-|--......+|..||++...|
T Consensus 21 l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TV 59 (64)
T PF13309_consen 21 LSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATV 59 (64)
T ss_pred CCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHH
Confidence 34433 445555566666666677788899999987654
No 155
>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=22.14 E-value=28 Score=20.53 Aligned_cols=19 Identities=5% Similarity=0.043 Sum_probs=16.4
Q ss_pred HHHHHHhcCCCcccceecc
Q psy9614 47 REDLASRLDLSEARVQVNS 65 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWF 65 (103)
..++|..+|++...++.|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4578999999999999993
No 156
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=22.12 E-value=75 Score=20.21 Aligned_cols=21 Identities=24% Similarity=0.259 Sum_probs=16.7
Q ss_pred HHHHHHHhcCCCcccceeccc
Q psy9614 46 TREDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFq 66 (103)
.-.++|..+|++...|+++..
T Consensus 131 s~~EIA~~l~is~~tV~~~l~ 151 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLN 151 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 456789999999998888654
No 157
>PHA01976 helix-turn-helix protein
Probab=22.03 E-value=33 Score=18.59 Aligned_cols=23 Identities=9% Similarity=0.088 Sum_probs=18.8
Q ss_pred HHHHHHhcCCCcccceecccccc
Q psy9614 47 REDLASRLDLSEARVQVNSDSQI 69 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFqNrR 69 (103)
..+||..+|++...|..|-...+
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56799999999999999975543
No 158
>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=21.83 E-value=29 Score=20.48 Aligned_cols=21 Identities=5% Similarity=-0.072 Sum_probs=17.7
Q ss_pred HHHHHHhcCCCcccceecccc
Q psy9614 47 REDLASRLDLSEARVQVNSDS 67 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFqN 67 (103)
..++|..+|++...|+.|-..
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999643
No 159
>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=21.40 E-value=35 Score=19.07 Aligned_cols=23 Identities=17% Similarity=0.160 Sum_probs=19.4
Q ss_pred HHHHHHhcCCCcccceecccccc
Q psy9614 47 REDLASRLDLSEARVQVNSDSQI 69 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFqNrR 69 (103)
...||..+|++...|..|...++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999986654
No 160
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=21.39 E-value=32 Score=24.13 Aligned_cols=28 Identities=21% Similarity=0.319 Sum_probs=21.0
Q ss_pred HHHHHHHhcCCCcccceecccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLG 73 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~r 73 (103)
...++|..+|++...|+.|...-+.+.|
T Consensus 223 s~~eIA~~l~is~~tV~~~~~ra~~kLr 250 (257)
T PRK08583 223 SQKETGERLGISQMHVSRLQRQAIKKLR 250 (257)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4578899999999999988754444433
No 161
>PF12728 HTH_17: Helix-turn-helix domain
Probab=21.39 E-value=28 Score=17.91 Aligned_cols=24 Identities=17% Similarity=0.003 Sum_probs=18.6
Q ss_pred HHHHHHhcCCCcccceeccccccc
Q psy9614 47 REDLASRLDLSEARVQVNSDSQIP 70 (103)
Q Consensus 47 r~~La~~l~l~~~~V~vWFqNrR~ 70 (103)
..++|..||++...|..|.+...-
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 356788999999999998865544
No 162
>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=21.31 E-value=63 Score=17.00 Aligned_cols=36 Identities=28% Similarity=0.316 Sum_probs=23.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccc
Q psy9614 24 FTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARV 61 (103)
Q Consensus 24 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 61 (103)
++..|..+|...+..... .....+||..++++...|
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~v 38 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTV 38 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHH
Confidence 577888888777665443 225667888888876544
No 163
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=21.23 E-value=32 Score=22.79 Aligned_cols=29 Identities=10% Similarity=0.014 Sum_probs=21.4
Q ss_pred HHHHHHHhcCCCcccceeccccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLGS 74 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~rr 74 (103)
...++|..+|++...|++....-|.+.++
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45788999999999999887544444443
No 164
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=21.19 E-value=34 Score=22.40 Aligned_cols=26 Identities=15% Similarity=0.238 Sum_probs=19.3
Q ss_pred HHHHHHHhcCCCcccceecccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPT 71 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k 71 (103)
...++|..+|++...|+++...-|.+
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~ 178 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSR 178 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 45678999999999998876544433
No 165
>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=20.90 E-value=1.5e+02 Score=16.50 Aligned_cols=33 Identities=30% Similarity=0.387 Sum_probs=19.8
Q ss_pred CCCHHHHHHHHHH---HhhcCCCCHHHHHHHHHhcCCC
Q psy9614 23 TFTTYQLHQLERA---FDKTQYPDVFTREDLASRLDLS 57 (103)
Q Consensus 23 ~~s~~q~~~Le~~---F~~~~~p~~~~r~~La~~l~l~ 57 (103)
.+|..|..+|+-. ...+.|| +...+||..+|+.
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~--Pt~rEIa~~~g~~ 38 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYP--PTVREIAEALGLK 38 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSS
T ss_pred CCCHHHHHHHHHHHHHHHHcCCC--CCHHHHHHHhCCC
Confidence 3567777766543 4667776 4667889999986
No 166
>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=20.75 E-value=1.3e+02 Score=18.63 Aligned_cols=16 Identities=31% Similarity=0.449 Sum_probs=11.0
Q ss_pred HHHHHHhcCCCcccce
Q psy9614 47 REDLASRLDLSEARVQ 62 (103)
Q Consensus 47 r~~La~~l~l~~~~V~ 62 (103)
-.++|..+|++...|+
T Consensus 126 ~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 126 EIDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHHHHHCcCHHhhc
Confidence 4567778888776654
No 167
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.64 E-value=60 Score=21.08 Aligned_cols=21 Identities=24% Similarity=0.302 Sum_probs=17.4
Q ss_pred HHHHHHHhcCCCcccceeccc
Q psy9614 46 TREDLASRLDLSEARVQVNSD 66 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFq 66 (103)
...++|..+|++...|+++..
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVA 157 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 467889999999999988764
No 168
>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=20.51 E-value=32 Score=18.47 Aligned_cols=16 Identities=31% Similarity=0.561 Sum_probs=12.2
Q ss_pred HHHHHHhcCCCcccce
Q psy9614 47 REDLASRLDLSEARVQ 62 (103)
Q Consensus 47 r~~La~~l~l~~~~V~ 62 (103)
-.+||..+|++..||+
T Consensus 31 S~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 31 SQELAEALGITPAQVR 46 (50)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCCCHHHhc
Confidence 4578999999988875
No 169
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=20.43 E-value=33 Score=23.49 Aligned_cols=25 Identities=20% Similarity=0.328 Sum_probs=18.8
Q ss_pred HHHHHHHhcCCCcccceeccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIP 70 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~ 70 (103)
...++|..+|++...|+.+...-+.
T Consensus 193 s~~eIA~~lgis~~tV~~~~~ra~~ 217 (224)
T TIGR02479 193 NLKEIGEVLGLTESRVSQIHSQALK 217 (224)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4578899999999988887654333
No 170
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=20.20 E-value=50 Score=20.83 Aligned_cols=25 Identities=24% Similarity=0.209 Sum_probs=21.3
Q ss_pred CCCHHHHHHHHHhcCCCcccceecc
Q psy9614 41 YPDVFTREDLASRLDLSEARVQVNS 65 (103)
Q Consensus 41 ~p~~~~r~~La~~l~l~~~~V~vWF 65 (103)
.++...|..||..++++...|.-|-
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~ 50 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWV 50 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHH
Confidence 3566778889999999999999994
No 171
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=20.18 E-value=40 Score=24.56 Aligned_cols=26 Identities=15% Similarity=0.224 Sum_probs=21.5
Q ss_pred HHHHHHHHhcCCCcccceeccccccccc
Q psy9614 45 FTREDLASRLDLSEARVQVNSDSQIPTL 72 (103)
Q Consensus 45 ~~r~~La~~l~l~~~~V~vWFqNrR~k~ 72 (103)
-.-.++|..+||++.+|+.|= +|..|
T Consensus 20 mk~~dIAeklGvspntiksWK--rr~gW 45 (279)
T COG5484 20 MKLKDIAEKLGVSPNTIKSWK--RRDGW 45 (279)
T ss_pred ccHHHHHHHhCCChHHHHHHH--HhcCC
Confidence 356789999999999999995 46666
No 172
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=20.12 E-value=35 Score=22.68 Aligned_cols=28 Identities=14% Similarity=0.223 Sum_probs=20.0
Q ss_pred HHHHHHHhcCCCcccceecccccccccc
Q psy9614 46 TREDLASRLDLSEARVQVNSDSQIPTLG 73 (103)
Q Consensus 46 ~r~~La~~l~l~~~~V~vWFqNrR~k~r 73 (103)
.-.++|..+|++...|++-...-+.+.+
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr 186 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLR 186 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 4567899999999999876654444433
Done!