Query psy8538
Match_columns 64
No_of_seqs 123 out of 1048
Neff 7.3
Searched_HMMs 46136
Date Fri Aug 16 21:27:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8538.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8538hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0848|consensus 99.7 2.3E-18 5E-23 113.2 1.5 48 2-49 214-261 (317)
2 KOG0487|consensus 99.7 1.7E-18 3.7E-23 115.4 0.4 51 2-52 250-300 (308)
3 KOG0842|consensus 99.7 5.3E-18 1.1E-22 113.0 2.7 51 2-53 168-218 (307)
4 KOG0488|consensus 99.7 3.9E-18 8.5E-23 113.8 1.6 58 2-61 187-244 (309)
5 KOG0489|consensus 99.7 9.6E-19 2.1E-23 114.3 -1.7 51 2-52 174-224 (261)
6 KOG0843|consensus 99.7 1.8E-17 3.9E-22 103.8 1.6 48 2-49 117-164 (197)
7 KOG0484|consensus 99.6 7E-17 1.5E-21 94.1 0.2 55 2-56 32-86 (125)
8 KOG0485|consensus 99.6 6E-17 1.3E-21 104.3 -0.7 45 1-45 118-162 (268)
9 KOG0850|consensus 99.6 1.8E-16 3.8E-21 102.3 0.3 47 1-47 136-182 (245)
10 KOG0492|consensus 99.6 6.1E-16 1.3E-20 99.0 1.2 45 1-45 158-202 (246)
11 KOG0483|consensus 99.6 1.5E-15 3.2E-20 96.4 1.9 48 1-48 64-111 (198)
12 PF00046 Homeobox: Homeobox do 99.5 4.8E-16 1E-20 80.6 -2.6 43 2-44 15-57 (57)
13 smart00389 HOX Homeodomain. DN 99.5 5.9E-15 1.3E-19 75.8 0.1 43 1-43 14-56 (56)
14 cd00086 homeodomain Homeodomai 99.5 4.3E-15 9.3E-20 76.8 -0.5 45 1-45 14-58 (59)
15 COG5576 Homeodomain-containing 99.5 1.1E-14 2.4E-19 89.6 1.1 44 2-45 66-109 (156)
16 KOG2251|consensus 99.4 6.8E-14 1.5E-18 89.8 2.7 47 2-48 52-98 (228)
17 KOG0494|consensus 99.4 3.3E-14 7.2E-19 93.6 1.0 48 2-49 156-203 (332)
18 KOG0491|consensus 99.4 2.7E-14 6E-19 88.8 -1.1 47 2-48 115-161 (194)
19 KOG0844|consensus 99.4 1.2E-13 2.6E-18 92.7 1.3 47 2-49 196-242 (408)
20 KOG0493|consensus 99.3 2.1E-13 4.6E-18 90.0 0.2 44 2-45 261-304 (342)
21 TIGR01565 homeo_ZF_HD homeobox 99.3 1.3E-12 2.7E-17 69.0 2.6 38 2-39 16-57 (58)
22 KOG3802|consensus 99.2 4.2E-12 9E-17 87.0 2.8 47 1-47 308-354 (398)
23 KOG0847|consensus 99.2 1.1E-12 2.5E-17 84.9 -0.2 45 1-45 181-225 (288)
24 KOG4577|consensus 99.2 4.4E-12 9.5E-17 84.8 1.0 47 2-48 182-228 (383)
25 KOG0486|consensus 99.1 2.5E-11 5.5E-16 81.5 2.7 56 2-58 127-182 (351)
26 KOG0775|consensus 99.1 2.3E-11 4.9E-16 80.5 1.9 43 2-44 191-233 (304)
27 KOG0490|consensus 99.1 1.8E-11 3.8E-16 77.1 0.6 46 1-46 74-119 (235)
28 KOG0849|consensus 98.8 7.8E-10 1.7E-14 75.2 0.7 46 1-46 190-235 (354)
29 PF05920 Homeobox_KN: Homeobox 98.7 8.9E-10 1.9E-14 54.2 -1.8 32 8-39 7-38 (40)
30 KOG1168|consensus 98.6 1.4E-08 3E-13 68.2 1.7 47 2-48 324-370 (385)
31 KOG0774|consensus 98.1 2.2E-06 4.7E-11 57.1 2.9 44 2-45 203-249 (334)
32 KOG0490|consensus 97.8 7.3E-06 1.6E-10 51.5 0.9 44 2-45 168-211 (235)
33 PF11569 Homez: Homeodomain le 97.3 2.4E-05 5.1E-10 41.0 -1.2 39 2-40 13-51 (56)
34 KOG2252|consensus 97.1 0.00021 4.6E-09 51.3 1.0 40 2-41 435-474 (558)
35 KOG0773|consensus 96.9 0.00044 9.6E-09 46.4 1.5 37 9-45 264-300 (342)
36 KOG1146|consensus 96.7 0.00061 1.3E-08 53.0 1.1 41 5-45 921-961 (1406)
37 KOG3623|consensus 94.5 0.0093 2E-07 44.8 -0.2 44 2-45 571-614 (1007)
38 PF10668 Phage_terminase: Phag 86.6 0.21 4.6E-06 26.4 0.1 18 17-34 25-42 (60)
39 PF04218 CENP-B_N: CENP-B N-te 81.8 0.43 9.4E-06 24.2 -0.0 24 16-39 24-47 (53)
40 PF13518 HTH_28: Helix-turn-he 78.1 0.65 1.4E-05 22.5 -0.1 23 17-39 15-37 (52)
41 PRK10072 putative transcriptio 77.5 1.6 3.4E-05 24.9 1.4 24 17-40 49-72 (96)
42 PF06056 Terminase_5: Putative 74.1 1.2 2.6E-05 23.0 0.3 21 17-37 16-36 (58)
43 cd04761 HTH_MerR-SF Helix-Turn 70.8 1.1 2.3E-05 21.4 -0.4 22 18-39 4-25 (49)
44 PF13384 HTH_23: Homeodomain-l 69.0 1.1 2.3E-05 21.7 -0.6 23 17-39 20-42 (50)
45 PF13411 MerR_1: MerR HTH fami 64.3 2 4.4E-05 21.9 -0.1 21 18-38 4-24 (69)
46 cd02413 40S_S3_KH K homology R 63.9 6.1 0.00013 21.7 1.7 21 16-36 55-75 (81)
47 TIGR03879 near_KaiC_dom probab 62.5 0.54 1.2E-05 25.7 -2.6 34 6-39 24-57 (73)
48 cd04762 HTH_MerR-trunc Helix-T 62.4 2.4 5.3E-05 19.6 -0.1 22 18-39 4-25 (49)
49 COG2944 Predicted transcriptio 59.2 6 0.00013 23.0 1.2 40 18-60 61-100 (104)
50 PF13443 HTH_26: Cro/C1-type H 58.1 2.7 5.9E-05 21.1 -0.3 23 17-39 13-35 (63)
51 cd04764 HTH_MlrA-like_sg1 Heli 57.4 3.3 7.2E-05 21.2 -0.1 20 18-37 4-23 (67)
52 PF09607 BrkDBD: Brinker DNA-b 55.9 1.9 4.1E-05 22.6 -1.1 17 20-36 31-47 (58)
53 cd01392 HTH_LacI Helix-turn-he 55.8 2.7 5.8E-05 20.3 -0.6 22 19-40 2-23 (52)
54 PF00376 MerR: MerR family reg 51.1 3.3 7.2E-05 19.5 -0.6 19 18-36 3-21 (38)
55 cd01104 HTH_MlrA-CarA Helix-Tu 50.1 5.4 0.00012 20.2 0.0 20 18-37 4-23 (68)
56 PF08281 Sigma70_r4_2: Sigma-7 50.0 2.5 5.5E-05 20.7 -1.2 23 15-37 27-49 (54)
57 PF01381 HTH_3: Helix-turn-hel 49.6 5.5 0.00012 19.3 0.0 23 17-39 12-34 (55)
58 cd04763 HTH_MlrA-like Helix-Tu 49.1 5.3 0.00012 20.5 -0.1 20 18-37 4-23 (68)
59 TIGR01764 excise DNA binding d 48.8 5.3 0.00012 18.5 -0.1 22 18-39 5-26 (49)
60 TIGR03070 couple_hipB transcri 48.0 7.9 0.00017 18.5 0.4 23 17-39 18-40 (58)
61 smart00422 HTH_MERR helix_turn 46.9 6 0.00013 20.1 -0.1 20 18-37 4-23 (70)
62 PF01527 HTH_Tnp_1: Transposas 45.8 5.8 0.00013 20.5 -0.3 22 16-37 25-46 (76)
63 cd00093 HTH_XRE Helix-turn-hel 44.9 8.5 0.00018 17.4 0.3 22 18-39 16-37 (58)
64 PRK09643 RNA polymerase sigma 44.7 16 0.00034 22.4 1.5 40 17-62 153-192 (192)
65 PF12728 HTH_17: Helix-turn-he 42.9 7.3 0.00016 18.8 -0.2 22 18-39 5-26 (51)
66 cd00569 HTH_Hin_like Helix-tur 42.7 9.8 0.00021 15.5 0.3 18 17-34 24-41 (42)
67 cd06171 Sigma70_r4 Sigma70, re 42.6 6 0.00013 18.2 -0.5 21 17-37 29-49 (55)
68 COG5484 Uncharacterized conser 41.4 12 0.00025 25.3 0.6 22 16-37 21-42 (279)
69 PHA00542 putative Cro-like pro 39.4 22 0.00047 19.2 1.4 40 17-56 34-75 (82)
70 PHA01976 helix-turn-helix prot 38.9 12 0.00027 18.8 0.3 23 17-39 18-40 (67)
71 TIGR02607 antidote_HigA addict 38.5 12 0.00027 19.3 0.3 23 17-39 21-43 (78)
72 PF14229 DUF4332: Domain of un 38.3 15 0.00032 21.5 0.6 23 12-34 27-49 (122)
73 PHA02955 hypothetical protein; 36.7 41 0.00089 22.0 2.5 28 11-38 76-103 (213)
74 PF13404 HTH_AsnC-type: AsnC-t 36.2 12 0.00026 17.9 0.0 16 17-32 20-35 (42)
75 PF04936 DUF658: Protein of un 36.1 13 0.00028 23.6 0.2 28 16-43 16-43 (186)
76 cd01106 HTH_TipAL-Mta Helix-Tu 36.0 11 0.00023 21.1 -0.2 22 18-39 4-25 (103)
77 smart00530 HTH_XRE Helix-turn- 36.0 16 0.00035 16.2 0.5 23 17-39 13-35 (56)
78 COG1905 NuoE NADH:ubiquinone o 35.8 25 0.00054 21.9 1.4 31 2-32 31-61 (160)
79 PRK09413 IS2 repressor TnpA; R 35.7 12 0.00025 21.6 -0.1 21 17-37 32-52 (121)
80 PF13542 HTH_Tnp_ISL3: Helix-t 35.6 10 0.00022 18.2 -0.3 19 17-35 30-48 (52)
81 PRK13890 conjugal transfer pro 35.3 15 0.00033 21.3 0.4 23 17-39 21-43 (120)
82 PF01710 HTH_Tnp_IS630: Transp 35.2 9.7 0.00021 22.0 -0.5 21 17-37 21-41 (119)
83 PF06971 Put_DNA-bind_N: Putat 35.1 12 0.00026 18.9 -0.1 15 18-32 32-46 (50)
84 cd01105 HTH_GlnR-like Helix-Tu 34.9 11 0.00023 20.6 -0.3 18 18-35 5-22 (88)
85 PF14549 P22_Cro: DNA-binding 34.6 9.9 0.00022 19.8 -0.5 17 18-34 13-29 (60)
86 PF13551 HTH_29: Winged helix- 33.5 9.8 0.00021 20.8 -0.6 23 17-39 15-37 (112)
87 PRK09706 transcriptional repre 33.3 17 0.00037 21.2 0.3 24 17-40 21-44 (135)
88 PF08279 HTH_11: HTH domain; 33.1 12 0.00027 18.1 -0.2 16 17-32 18-33 (55)
89 cd06170 LuxR_C_like C-terminal 33.0 14 0.0003 17.4 -0.0 20 17-36 18-37 (57)
90 cd04766 HTH_HspR Helix-Turn-He 32.9 15 0.00032 20.0 0.1 22 17-38 4-25 (91)
91 cd01798 parkin_N amino-termina 32.4 34 0.00073 17.5 1.4 28 15-42 23-50 (70)
92 PRK05988 formate dehydrogenase 32.1 27 0.00059 21.3 1.1 25 8-32 35-59 (156)
93 cd08313 Death_TNFR1 Death doma 32.1 37 0.0008 18.6 1.6 19 14-32 11-29 (80)
94 cd01796 DDI1_N DNA damage indu 31.4 35 0.00076 17.7 1.4 26 15-40 24-49 (71)
95 PF03584 Herpes_ICP4_N: Herpes 31.4 92 0.002 19.8 3.4 46 15-61 61-106 (173)
96 PTZ00044 ubiquitin; Provisiona 31.3 34 0.00074 17.6 1.3 28 15-42 25-52 (76)
97 PF08765 Mor: Mor transcriptio 30.8 16 0.00034 20.8 -0.1 17 16-32 74-90 (108)
98 PF05269 Phage_CII: Bacterioph 30.4 32 0.00069 19.5 1.1 19 18-36 27-45 (91)
99 cd01793 Fubi Fubi ubiquitin-li 30.0 39 0.00084 17.5 1.4 28 16-43 24-51 (74)
100 TIGR01958 nuoE_fam NADH-quinon 29.9 30 0.00065 20.7 1.0 24 9-32 29-52 (148)
101 smart00421 HTH_LUXR helix_turn 29.8 17 0.00037 17.0 -0.1 21 17-37 21-41 (58)
102 cd00592 HTH_MerR-like Helix-Tu 29.8 17 0.00037 19.9 -0.1 21 18-38 4-24 (100)
103 PF07471 Phage_Nu1: Phage DNA 29.8 16 0.00036 22.6 -0.1 21 17-37 5-25 (164)
104 cd04789 HTH_Cfa Helix-Turn-Hel 29.7 15 0.00033 20.6 -0.3 22 17-38 4-25 (102)
105 cd04775 HTH_Cfa-like Helix-Tur 29.4 16 0.00034 20.5 -0.3 21 17-37 4-24 (102)
106 cd04788 HTH_NolA-AlbR Helix-Tu 29.2 16 0.00034 20.3 -0.3 21 18-38 4-24 (96)
107 PF08280 HTH_Mga: M protein tr 29.2 16 0.00034 18.5 -0.2 16 18-33 23-38 (59)
108 TIGR03830 CxxCG_CxxCG_HTH puta 28.9 49 0.0011 18.6 1.8 22 18-39 82-103 (127)
109 cd04774 HTH_YfmP Helix-Turn-He 28.9 19 0.00041 20.0 0.1 21 18-38 4-24 (96)
110 cd01769 UBL Ubiquitin-like dom 28.8 42 0.00092 16.4 1.4 25 15-39 22-46 (69)
111 cd04779 HTH_MerR-like_sg4 Heli 28.7 14 0.00031 22.0 -0.5 22 18-39 4-25 (134)
112 cd04768 HTH_BmrR-like Helix-Tu 28.4 18 0.00039 20.0 -0.1 21 18-38 4-24 (96)
113 TIGR03826 YvyF flagellar opero 28.0 18 0.00038 22.0 -0.2 29 16-44 48-76 (137)
114 PRK07539 NADH dehydrogenase su 27.8 34 0.00074 20.6 1.0 25 8-32 34-58 (154)
115 PF13560 HTH_31: Helix-turn-he 27.6 19 0.00041 18.1 -0.1 24 17-40 17-40 (64)
116 cd04773 HTH_TioE_rpt2 Second H 27.6 23 0.00049 20.1 0.2 21 18-38 4-24 (108)
117 PF08452 DNAP_B_exo_N: DNA pol 27.2 23 0.0005 15.0 0.1 7 33-39 7-13 (22)
118 cd04780 HTH_MerR-like_sg5 Heli 27.0 18 0.00039 20.1 -0.3 20 18-37 4-23 (95)
119 PRK11511 DNA-binding transcrip 26.9 16 0.00035 21.1 -0.5 23 16-38 27-49 (127)
120 PRK09726 antitoxin HipB; Provi 26.8 27 0.00059 18.9 0.4 23 17-39 28-50 (88)
121 cd01109 HTH_YyaN Helix-Turn-He 26.7 20 0.00043 20.3 -0.1 20 18-37 4-23 (113)
122 cd01111 HTH_MerD Helix-Turn-He 26.1 19 0.00042 20.5 -0.3 21 18-38 4-24 (107)
123 cd04782 HTH_BltR Helix-Turn-He 26.0 19 0.00042 19.9 -0.3 21 18-38 4-24 (97)
124 cd01107 HTH_BmrR Helix-Turn-He 25.7 22 0.00047 20.1 -0.1 21 18-38 4-24 (108)
125 cd08306 Death_FADD Fas-associa 25.6 27 0.00059 19.1 0.3 21 17-37 16-36 (86)
126 cd01803 Ubiquitin Ubiquitin. U 24.6 50 0.0011 16.7 1.2 26 14-39 24-49 (76)
127 COG0789 SoxR Predicted transcr 24.5 23 0.00049 20.0 -0.2 18 18-35 4-21 (124)
128 TIGR02054 MerD mercuric resist 24.5 26 0.00057 20.5 0.1 21 17-37 6-26 (120)
129 PF04545 Sigma70_r4: Sigma-70, 24.2 21 0.00046 17.1 -0.3 18 17-34 23-40 (50)
130 cd01797 NIRF_N amino-terminal 24.0 55 0.0012 17.4 1.3 29 15-43 27-55 (78)
131 PRK07571 bidirectional hydroge 23.7 47 0.001 20.7 1.1 25 8-32 48-72 (169)
132 cd04765 HTH_MlrA-like_sg2 Heli 23.7 25 0.00053 19.7 -0.1 20 18-37 4-23 (99)
133 PF01257 2Fe-2S_thioredx: Thio 23.7 24 0.00052 21.1 -0.2 25 8-32 25-49 (145)
134 PF13730 HTH_36: Helix-turn-he 23.3 13 0.00029 18.0 -1.2 20 16-35 27-46 (55)
135 cd04767 HTH_HspR-like_MBC Heli 23.3 23 0.00051 20.9 -0.3 22 17-38 4-25 (120)
136 PRK06759 RNA polymerase factor 23.2 26 0.00057 20.1 -0.1 21 17-37 125-145 (154)
137 PF09292 Neil1-DNA_bind: Endon 23.2 29 0.00064 16.7 0.1 6 32-37 27-32 (39)
138 PRK12537 RNA polymerase sigma 22.9 38 0.00082 20.3 0.6 20 17-36 152-171 (182)
139 cd01794 DC_UbP_C dendritic cel 22.9 61 0.0013 16.9 1.3 28 16-43 24-51 (70)
140 PF05848 CtsR: Firmicute trans 22.7 42 0.00091 20.7 0.8 18 16-33 27-44 (152)
141 cd08318 Death_NMPP84 Death dom 22.7 32 0.00069 18.8 0.2 16 18-33 22-37 (86)
142 PRK11924 RNA polymerase sigma 22.6 26 0.00057 20.4 -0.2 21 17-37 144-164 (179)
143 PF12200 DUF3597: Domain of un 22.6 83 0.0018 19.0 2.0 17 12-28 83-99 (127)
144 cd01807 GDX_N ubiquitin-like d 22.4 59 0.0013 16.8 1.2 28 16-43 26-53 (74)
145 cd01282 HTH_MerR-like_sg3 Heli 22.2 26 0.00056 19.9 -0.2 21 18-38 4-24 (112)
146 PRK13182 racA polar chromosome 21.7 32 0.00068 21.6 0.1 21 18-38 4-24 (175)
147 PF07022 Phage_CI_repr: Bacter 21.6 9.8 0.00021 19.7 -1.9 21 17-37 15-36 (66)
148 TIGR02051 MerR Hg(II)-responsi 21.6 26 0.00057 20.3 -0.3 17 18-34 3-19 (124)
149 cd01812 BAG1_N Ubiquitin-like 21.5 65 0.0014 16.1 1.3 25 15-39 24-48 (71)
150 smart00351 PAX Paired Box doma 21.2 24 0.00053 20.5 -0.5 21 17-37 36-56 (125)
151 PF07037 DUF1323: Putative tra 21.1 28 0.00062 20.8 -0.2 20 18-37 4-23 (122)
152 PF06505 XylR_N: Activator of 21.1 37 0.00081 19.5 0.3 21 20-40 2-22 (103)
153 KOG3755|consensus 21.1 13 0.00029 28.0 -1.9 19 27-45 739-757 (769)
154 COG2197 CitB Response regulato 21.0 47 0.001 20.9 0.7 20 18-37 167-186 (211)
155 PF09581 Spore_III_AF: Stage I 20.9 49 0.0011 20.2 0.8 19 16-34 169-187 (188)
156 cd01279 HTH_HspR-like Helix-Tu 20.9 28 0.0006 19.4 -0.3 22 17-38 4-25 (98)
157 TIGR03629 arch_S13P archaeal r 20.6 79 0.0017 19.2 1.6 29 11-39 51-79 (144)
158 cd01108 HTH_CueR Helix-Turn-He 20.6 31 0.00066 20.0 -0.1 21 18-38 4-24 (127)
159 cd04776 HTH_GnyR Helix-Turn-He 20.6 29 0.00062 20.0 -0.3 18 18-35 4-21 (118)
160 cd08316 Death_FAS_TNFRSF6 Deat 20.4 82 0.0018 17.8 1.6 21 12-32 18-38 (97)
161 PRK09514 zntR zinc-responsive 20.3 29 0.00063 20.6 -0.3 22 17-38 4-25 (140)
162 cd01806 Nedd8 Nebb8-like ubiq 20.3 95 0.0021 15.6 1.8 27 14-40 24-50 (76)
163 PF12244 DUF3606: Protein of u 20.2 58 0.0013 16.6 0.9 18 15-32 21-38 (57)
164 TIGR03209 P21_Cbot clostridium 20.1 55 0.0012 18.6 0.9 15 18-32 127-141 (142)
165 cd04772 HTH_TioE_rpt1 First He 20.0 30 0.00066 19.3 -0.2 21 18-38 4-24 (99)
166 PF02796 HTH_7: Helix-turn-hel 20.0 25 0.00054 16.7 -0.5 20 16-35 23-42 (45)
167 cd08804 Death_ank2 Death domai 20.0 42 0.00091 18.3 0.3 16 18-33 19-34 (84)
No 1
>KOG0848|consensus
Probab=99.71 E-value=2.3e-18 Score=113.20 Aligned_cols=48 Identities=48% Similarity=0.562 Sum_probs=45.1
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHH
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIV 49 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~ 49 (64)
||++|+.++|+++..+.+||.-|+|+|+||+|||||||+|+|+..+..
T Consensus 214 LEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 214 LEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred hhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 899999999999999999999999999999999999999999885544
No 2
>KOG0487|consensus
Probab=99.70 E-value=1.7e-18 Score=115.41 Aligned_cols=51 Identities=25% Similarity=0.309 Sum_probs=46.5
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHHHHH
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFL 52 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~ 52 (64)
||++|..|.|++.+.|.+|++.|+|+++||+|||||||-|+|++.+.....
T Consensus 250 LEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~ 300 (308)
T KOG0487|consen 250 LEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK 300 (308)
T ss_pred HHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence 899999999999999999999999999999999999999999885544443
No 3
>KOG0842|consensus
Probab=99.70 E-value=5.3e-18 Score=113.03 Aligned_cols=51 Identities=24% Similarity=0.230 Sum_probs=46.1
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHHHHHH
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLE 53 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~~ 53 (64)
||+.|...+|++..+|++||..|+||++||+|||||||.|.||. ...+..+
T Consensus 168 LERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~-~~dk~~~ 218 (307)
T KOG0842|consen 168 LERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQ-QKDKALE 218 (307)
T ss_pred HHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhh-hhhhhhh
Confidence 89999999999999999999999999999999999999999998 4444433
No 4
>KOG0488|consensus
Probab=99.70 E-value=3.9e-18 Score=113.84 Aligned_cols=58 Identities=24% Similarity=0.277 Sum_probs=49.8
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHHHHHHHhcCCCCC
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKVHGDGRN 61 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~~~~~~~g~~ 61 (64)
||+.|++..|++..+|++||..|||+..||++||||||+|+|+.. . ...+.....|+.
T Consensus 187 LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~-a-~g~~~~~~~~~~ 244 (309)
T KOG0488|consen 187 LEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT-A-EGGELLYQAGNS 244 (309)
T ss_pred HHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH-H-hhhccccccccc
Confidence 899999999999999999999999999999999999999999993 2 355555555544
No 5
>KOG0489|consensus
Probab=99.69 E-value=9.6e-19 Score=114.32 Aligned_cols=51 Identities=27% Similarity=0.368 Sum_probs=46.6
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHHHHH
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFL 52 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~ 52 (64)
||++|+.|+|++...|.+||..|+|+|+||+|||||||.|+|+..+.....
T Consensus 174 LEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 174 LEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred hhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 899999999999999999999999999999999999999999885555443
No 6
>KOG0843|consensus
Probab=99.67 E-value=1.8e-17 Score=103.82 Aligned_cols=48 Identities=25% Similarity=0.221 Sum_probs=44.9
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHH
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIV 49 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~ 49 (64)
||.+|..++|....+|+.||..|+|++.||+|||||||+|.|+.....
T Consensus 117 LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 117 LEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred HHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 899999999999999999999999999999999999999999885443
No 7
>KOG0484|consensus
Probab=99.61 E-value=7e-17 Score=94.09 Aligned_cols=55 Identities=15% Similarity=0.073 Sum_probs=49.7
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHHHHHHHhc
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKVH 56 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~~~~~ 56 (64)
||+.|...+||++..|++||.+++|++..|||||||||++-+++.+.+.......
T Consensus 32 LErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~~~~ 86 (125)
T KOG0484|consen 32 LERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKMAAK 86 (125)
T ss_pred HHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHhhhh
Confidence 7999999999999999999999999999999999999999998877776655544
No 8
>KOG0485|consensus
Probab=99.61 E-value=6e-17 Score=104.27 Aligned_cols=45 Identities=27% Similarity=0.285 Sum_probs=43.7
Q ss_pred CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538 1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT 45 (64)
Q Consensus 1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~ 45 (64)
+||.+|...+|++..+|..||.+|.|+++||+|||||||+|+||.
T Consensus 118 qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 118 QLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred HHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 489999999999999999999999999999999999999999998
No 9
>KOG0850|consensus
Probab=99.59 E-value=1.8e-16 Score=102.29 Aligned_cols=47 Identities=26% Similarity=0.346 Sum_probs=43.4
Q ss_pred CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHH
Q psy8538 1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAI 47 (64)
Q Consensus 1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~ 47 (64)
||.+.|+.++|+--.+|.+||..|||+.+||+|||||||.|-|+..+
T Consensus 136 aL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 136 ALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred HHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 57889999999999999999999999999999999999999886633
No 10
>KOG0492|consensus
Probab=99.56 E-value=6.1e-16 Score=98.95 Aligned_cols=45 Identities=24% Similarity=0.330 Sum_probs=43.3
Q ss_pred CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538 1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT 45 (64)
Q Consensus 1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~ 45 (64)
.||+-|...+|++++++.+++..|.|+++||+|||||||++.||.
T Consensus 158 aLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 158 ALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred HHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 389999999999999999999999999999999999999999987
No 11
>KOG0483|consensus
Probab=99.55 E-value=1.5e-15 Score=96.43 Aligned_cols=48 Identities=23% Similarity=0.238 Sum_probs=44.5
Q ss_pred CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHH
Q psy8538 1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAII 48 (64)
Q Consensus 1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~ 48 (64)
+||..|..+.++.+..+..||+.|||.++||.|||||||+++|.....
T Consensus 64 ~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 64 FLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred HhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 589999999999999999999999999999999999999999977433
No 12
>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=99.50 E-value=4.8e-16 Score=80.57 Aligned_cols=43 Identities=28% Similarity=0.325 Sum_probs=40.6
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN 44 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~ 44 (64)
||..|..++||+..++..||..+||+..+|++||+|+|.++|+
T Consensus 15 L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 15 LEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp HHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 8899999999999999999999999999999999999987763
No 13
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.47 E-value=5.9e-15 Score=75.84 Aligned_cols=43 Identities=33% Similarity=0.341 Sum_probs=40.0
Q ss_pred CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCccccc
Q psy8538 1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNN 43 (64)
Q Consensus 1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k 43 (64)
.||..|..++||+..++..||..+||+..+|+.||+|+|.+.+
T Consensus 14 ~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 14 ELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 3889999999999999999999999999999999999997653
No 14
>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=99.47 E-value=4.3e-15 Score=76.77 Aligned_cols=45 Identities=29% Similarity=0.333 Sum_probs=41.6
Q ss_pred CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538 1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT 45 (64)
Q Consensus 1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~ 45 (64)
.||..|..++||+..++..||..+||++.+|++||+|+|.+.++.
T Consensus 14 ~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 14 ELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 388999999999999999999999999999999999999877653
No 15
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.47 E-value=1.1e-14 Score=89.59 Aligned_cols=44 Identities=14% Similarity=0.150 Sum_probs=41.9
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT 45 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~ 45 (64)
|+..|..++||+...+..|+..++|+++.|+|||||+|++.|..
T Consensus 66 L~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~ 109 (156)
T COG5576 66 LEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109 (156)
T ss_pred HHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHh
Confidence 78999999999999999999999999999999999999988765
No 16
>KOG2251|consensus
Probab=99.43 E-value=6.8e-14 Score=89.83 Aligned_cols=47 Identities=19% Similarity=0.134 Sum_probs=44.1
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHH
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAII 48 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~ 48 (64)
||..|..+.||+...+++||.+|+|++.+|+|||.|||+|.++...-
T Consensus 52 Le~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 52 LEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred HHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 78999999999999999999999999999999999999999987443
No 17
>KOG0494|consensus
Probab=99.42 E-value=3.3e-14 Score=93.63 Aligned_cols=48 Identities=15% Similarity=0.099 Sum_probs=45.0
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHH
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIV 49 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~ 49 (64)
||+.|...+||+...|+-||.++.|++..|+|||||||+|+++.++..
T Consensus 156 LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 156 LEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred HHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 799999999999999999999999999999999999999999886544
No 18
>KOG0491|consensus
Probab=99.39 E-value=2.7e-14 Score=88.77 Aligned_cols=47 Identities=28% Similarity=0.322 Sum_probs=43.7
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHH
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAII 48 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~ 48 (64)
||+.|+..+|++..++.+||..|+|+++||+.||||||.|.|+..+.
T Consensus 115 l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~ 161 (194)
T KOG0491|consen 115 LEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN 161 (194)
T ss_pred cHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 79999999999999999999999999999999999999998887333
No 19
>KOG0844|consensus
Probab=99.37 E-value=1.2e-13 Score=92.68 Aligned_cols=47 Identities=21% Similarity=0.306 Sum_probs=44.1
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHH
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIV 49 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~ 49 (64)
||++|-+..|.+...|-+||..|+|++..|+|||||||.|+||+ +++
T Consensus 196 LEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ-Rla 242 (408)
T KOG0844|consen 196 LEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ-RLA 242 (408)
T ss_pred HHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh-hhh
Confidence 89999999999999999999999999999999999999999998 543
No 20
>KOG0493|consensus
Probab=99.33 E-value=2.1e-13 Score=89.99 Aligned_cols=44 Identities=32% Similarity=0.453 Sum_probs=40.9
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT 45 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~ 45 (64)
|..+|+.++|++...|.+||.+|+|.+.||+|||||+|+|-|+.
T Consensus 261 LK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 261 LKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred HHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 56789999999999999999999999999999999999987754
No 21
>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=99.31 E-value=1.3e-12 Score=69.05 Aligned_cols=38 Identities=8% Similarity=0.016 Sum_probs=36.4
Q ss_pred chhhhccCCC----CCHHHHHHHHHHhCCCCCcccccccCCc
Q psy8538 2 DSLEFHYSRY----ITIRRKAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 2 ~e~~F~~~~~----p~~~~r~~La~~l~l~~~qV~vWFqNrR 39 (64)
||..|..++| |+...+.+||..+||++.+|+|||||.+
T Consensus 16 Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 16 MRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred HHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 7889999999 9999999999999999999999999975
No 22
>KOG3802|consensus
Probab=99.24 E-value=4.2e-12 Score=87.00 Aligned_cols=47 Identities=17% Similarity=0.051 Sum_probs=44.5
Q ss_pred CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHH
Q psy8538 1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAI 47 (64)
Q Consensus 1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~ 47 (64)
.||+.|..|+.|+..++..||.+|+|-...|+|||+|||.++||...
T Consensus 308 aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 308 ALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 38999999999999999999999999999999999999999999844
No 23
>KOG0847|consensus
Probab=99.23 E-value=1.1e-12 Score=84.88 Aligned_cols=45 Identities=22% Similarity=0.281 Sum_probs=42.6
Q ss_pred CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538 1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT 45 (64)
Q Consensus 1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~ 45 (64)
.||..|....|+-.+++.+||..+|+++.||+|||||||+++++.
T Consensus 181 ~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKk 225 (288)
T KOG0847|consen 181 QLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKK 225 (288)
T ss_pred hhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhh
Confidence 378999999999999999999999999999999999999999876
No 24
>KOG4577|consensus
Probab=99.19 E-value=4.4e-12 Score=84.77 Aligned_cols=47 Identities=13% Similarity=0.049 Sum_probs=42.4
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHH
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAII 48 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~ 48 (64)
|...|...+.|..+.|++|+.++||..+.|||||||||+|+||.++-
T Consensus 182 LK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 182 LKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred HHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 45678889999999999999999999999999999999999988443
No 25
>KOG0486|consensus
Probab=99.14 E-value=2.5e-11 Score=81.48 Aligned_cols=56 Identities=20% Similarity=0.172 Sum_probs=49.2
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHHHHHHHhcCC
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKVHGD 58 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~~~~~~~ 58 (64)
||..|++++||+...|+++|.-++|++..|.|||.|||+++++.++-.. .|.+.++
T Consensus 127 le~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~-ae~~k~~ 182 (351)
T KOG0486|consen 127 LEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ-AELAKGG 182 (351)
T ss_pred HHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH-HHhhhcC
Confidence 6888999999999999999999999999999999999999998866655 5555444
No 26
>KOG0775|consensus
Probab=99.12 E-value=2.3e-11 Score=80.47 Aligned_cols=43 Identities=23% Similarity=0.157 Sum_probs=40.1
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN 44 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~ 44 (64)
|...|..++||+..++.+||+.+||+..||-.||.|||.++|.
T Consensus 191 LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 191 LREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred HHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 5667899999999999999999999999999999999998883
No 27
>KOG0490|consensus
Probab=99.10 E-value=1.8e-11 Score=77.11 Aligned_cols=46 Identities=13% Similarity=-0.031 Sum_probs=43.5
Q ss_pred CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchH
Q psy8538 1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTA 46 (64)
Q Consensus 1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~ 46 (64)
+||+.|...+||+...++.||..+++++..|+|||||+|+++++..
T Consensus 74 ~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 74 ELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred HHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 5899999999999999999999999999999999999999999774
No 28
>KOG0849|consensus
Probab=98.83 E-value=7.8e-10 Score=75.19 Aligned_cols=46 Identities=20% Similarity=0.156 Sum_probs=43.2
Q ss_pred CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchH
Q psy8538 1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTA 46 (64)
Q Consensus 1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~ 46 (64)
+||+.|..++||+...|+.||.++++++..|+|||+|+|++.++..
T Consensus 190 ~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 190 ALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred HHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 5899999999999999999999999999999999999999888773
No 29
>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=98.69 E-value=8.9e-10 Score=54.21 Aligned_cols=32 Identities=28% Similarity=0.291 Sum_probs=27.2
Q ss_pred cCCCCCHHHHHHHHHHhCCCCCcccccccCCc
Q psy8538 8 YSRYITIRRKAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 8 ~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR 39 (64)
.++||+..++..||..+||+..||..||-|-|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaR 38 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINAR 38 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhH
Confidence 47899999999999999999999999999976
No 30
>KOG1168|consensus
Probab=98.62 E-value=1.4e-08 Score=68.21 Aligned_cols=47 Identities=15% Similarity=0.021 Sum_probs=43.5
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHH
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAII 48 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~ 48 (64)
||.+|...+.|+.+....+|.+|+|....|+|||.|.|.|.||++..
T Consensus 324 LEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~S 370 (385)
T KOG1168|consen 324 LEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRS 370 (385)
T ss_pred HHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhh
Confidence 78999999999999999999999999999999999999999987443
No 31
>KOG0774|consensus
Probab=98.12 E-value=2.2e-06 Score=57.11 Aligned_cols=44 Identities=18% Similarity=0.061 Sum_probs=37.6
Q ss_pred chhhh---ccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538 2 DSLEF---HYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT 45 (64)
Q Consensus 2 ~e~~F---~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~ 45 (64)
|...| ..++||+...+++||+++|++..||..||.|.|-+-|+.
T Consensus 203 LneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 203 LNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 44556 468999999999999999999999999999998766544
No 32
>KOG0490|consensus
Probab=97.79 E-value=7.3e-06 Score=51.54 Aligned_cols=44 Identities=18% Similarity=0.144 Sum_probs=39.6
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT 45 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~ 45 (64)
++..|..+.+|+...+..|+..+|+++..|++||||++.+.++.
T Consensus 168 ~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~ 211 (235)
T KOG0490|consen 168 LETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH 211 (235)
T ss_pred hhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence 35568889999999999999999999999999999999888765
No 33
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.33 E-value=2.4e-05 Score=41.00 Aligned_cols=39 Identities=15% Similarity=0.010 Sum_probs=28.9
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcc
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTT 40 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~ 40 (64)
|+..|...+++...+...|+.+.+|+..||+.||--+..
T Consensus 13 L~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 13 LEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp HHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred HHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 788899889998899999999999999999999976653
No 34
>KOG2252|consensus
Probab=97.06 E-value=0.00021 Score=51.29 Aligned_cols=40 Identities=10% Similarity=-0.022 Sum_probs=36.6
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCccc
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTV 41 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~ 41 (64)
|-.+|+.+++|+.+....|+.+|+|....|..||-|-|.+
T Consensus 435 L~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR 474 (558)
T KOG2252|consen 435 LQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRR 474 (558)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence 5678999999999999999999999999999999997644
No 35
>KOG0773|consensus
Probab=96.92 E-value=0.00044 Score=46.45 Aligned_cols=37 Identities=24% Similarity=0.081 Sum_probs=32.4
Q ss_pred CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538 9 SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT 45 (64)
Q Consensus 9 ~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~ 45 (64)
.+||+..++..||.++||+..||..||-|.|-+....
T Consensus 264 ~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 264 HPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred CCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 5899999999999999999999999999977655433
No 36
>KOG1146|consensus
Probab=96.73 E-value=0.00061 Score=53.03 Aligned_cols=41 Identities=15% Similarity=0.233 Sum_probs=36.4
Q ss_pred hhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538 5 EFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT 45 (64)
Q Consensus 5 ~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~ 45 (64)
.|....||...+.+.|...++++.+.|++||||-|.+.+..
T Consensus 921 ~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~ 961 (1406)
T KOG1146|consen 921 CYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKA 961 (1406)
T ss_pred HHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhh
Confidence 45667788888888999999999999999999999988876
No 37
>KOG3623|consensus
Probab=94.54 E-value=0.0093 Score=44.82 Aligned_cols=44 Identities=9% Similarity=0.038 Sum_probs=39.2
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT 45 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~ 45 (64)
|...|..|..|+..+-..+|.+.||+..-|+.||++.++.+...
T Consensus 571 lkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv 614 (1007)
T KOG3623|consen 571 LKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSV 614 (1007)
T ss_pred HHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhh
Confidence 45578999999999999999999999999999999998766655
No 38
>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=86.57 E-value=0.21 Score=26.35 Aligned_cols=18 Identities=33% Similarity=0.453 Sum_probs=16.1
Q ss_pred HHHHHHHhCCCCCccccc
Q psy8538 17 KAELANSLGLSERQVRCP 34 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vW 34 (64)
-..+|.+||+++.+|..|
T Consensus 25 lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKW 42 (60)
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 346899999999999999
No 39
>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=81.81 E-value=0.43 Score=24.17 Aligned_cols=24 Identities=21% Similarity=0.293 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCCCCcccccccCCc
Q psy8538 16 RKAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~vWFqNrR 39 (64)
....||..+|++..+|..|..|+.
T Consensus 24 s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 24 SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp -HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 356899999999999999988864
No 40
>PF13518 HTH_28: Helix-turn-helix domain
Probab=78.05 E-value=0.65 Score=22.47 Aligned_cols=23 Identities=22% Similarity=0.218 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCCCcccccccCCc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR 39 (64)
..++|..+|++..+|..|.+.-+
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHH
Confidence 45689999999999999976543
No 41
>PRK10072 putative transcriptional regulator; Provisional
Probab=77.51 E-value=1.6 Score=24.89 Aligned_cols=24 Identities=21% Similarity=0.180 Sum_probs=20.9
Q ss_pred HHHHHHHhCCCCCcccccccCCcc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLTT 40 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR~ 40 (64)
..+||..+|++...|..|.+.++.
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 457899999999999999998874
No 42
>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=74.13 E-value=1.2 Score=23.05 Aligned_cols=21 Identities=24% Similarity=0.313 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCCCcccccccC
Q psy8538 17 KAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqN 37 (64)
..++|..||++...|..|-+-
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred HHHHHHHHCCChHHHHHHHHh
Confidence 457899999999999999553
No 43
>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=70.75 E-value=1.1 Score=21.37 Aligned_cols=22 Identities=27% Similarity=0.215 Sum_probs=18.8
Q ss_pred HHHHHHhCCCCCcccccccCCc
Q psy8538 18 AELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNrR 39 (64)
.++|..+|+++..|..|.+...
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHCCC
Confidence 4789999999999999977654
No 44
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=68.97 E-value=1.1 Score=21.71 Aligned_cols=23 Identities=26% Similarity=0.228 Sum_probs=16.8
Q ss_pred HHHHHHHhCCCCCcccccccCCc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR 39 (64)
..++|..+|++...|..|...-+
T Consensus 20 ~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 20 IREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHHHCcCHHHHHHHHHHcc
Confidence 45789999999999999976543
No 45
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=64.33 E-value=2 Score=21.94 Aligned_cols=21 Identities=29% Similarity=0.338 Sum_probs=17.6
Q ss_pred HHHHHHhCCCCCcccccccCC
Q psy8538 18 AELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNr 38 (64)
.++|+.+|++..+|+.|=...
T Consensus 4 ~eva~~~gvs~~tlr~y~~~g 24 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYEREG 24 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHHTT
T ss_pred HHHHHHHCcCHHHHHHHHHhc
Confidence 478999999999999995543
No 46
>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=63.89 E-value=6.1 Score=21.67 Aligned_cols=21 Identities=10% Similarity=0.078 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCCCCccccccc
Q psy8538 16 RKAELANSLGLSERQVRCPHH 36 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~vWFq 36 (64)
-+..|...++|.+.+|++|+.
T Consensus 55 L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 55 LTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHHhCCCCCeEEEEEE
Confidence 445788999999999999985
No 47
>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=62.52 E-value=0.54 Score=25.72 Aligned_cols=34 Identities=26% Similarity=0.238 Sum_probs=23.6
Q ss_pred hccCCCCCHHHHHHHHHHhCCCCCcccccccCCc
Q psy8538 6 FHYSRYITIRRKAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 6 F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR 39 (64)
|...+|...-...++|..+|+|+..|+.|+.+.-
T Consensus 24 f~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 24 AALAREEAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 4333332333456899999999999999987543
No 48
>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=62.35 E-value=2.4 Score=19.60 Aligned_cols=22 Identities=27% Similarity=0.190 Sum_probs=19.0
Q ss_pred HHHHHHhCCCCCcccccccCCc
Q psy8538 18 AELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNrR 39 (64)
.++|..+|++...|..|.++..
T Consensus 4 ~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 4 KEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHcCC
Confidence 5789999999999999987754
No 49
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=59.24 E-value=6 Score=23.05 Aligned_cols=40 Identities=20% Similarity=0.174 Sum_probs=28.9
Q ss_pred HHHHHHhCCCCCcccccccCCcccccchHHHHHHHHHhcCCCC
Q psy8538 18 AELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKVHGDGR 60 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~~~~~~~g~ 60 (64)
..+|..+|++...|+.|=|+|+ ++..........+..+|.
T Consensus 61 ~vFA~~L~vs~~Tv~~WEqGr~---kPsg~AlkLL~ivq~~p~ 100 (104)
T COG2944 61 PVFARYLGVSVSTVRKWEQGRK---KPSGAALKLLRIVQNHPL 100 (104)
T ss_pred HHHHHHHCCCHHHHHHHHcCCc---CCCCHHHHHHHHHHhcch
Confidence 3578889999999999999998 666555555555544443
No 50
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=58.13 E-value=2.7 Score=21.08 Aligned_cols=23 Identities=17% Similarity=0.208 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCCCcccccccCCc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR 39 (64)
...||+.+|++..+|..|+.++.
T Consensus 13 ~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 13 QKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp HHHHHHHHT--HHHHHHHHTTT-
T ss_pred HHHHHHHHCcCHHHHHHHHhccc
Confidence 45799999999999999999873
No 51
>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=57.38 E-value=3.3 Score=21.21 Aligned_cols=20 Identities=15% Similarity=0.371 Sum_probs=17.4
Q ss_pred HHHHHHhCCCCCcccccccC
Q psy8538 18 AELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqN 37 (64)
.++|+.+|+++..|+.|-+.
T Consensus 4 ~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999764
No 52
>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=55.95 E-value=1.9 Score=22.64 Aligned_cols=17 Identities=35% Similarity=0.341 Sum_probs=14.1
Q ss_pred HHHHhCCCCCccccccc
Q psy8538 20 LANSLGLSERQVRCPHH 36 (64)
Q Consensus 20 La~~l~l~~~qV~vWFq 36 (64)
.|.++|+++.+|+-|-+
T Consensus 31 aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 31 AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp HHHHTTS-HHHHHHHHT
T ss_pred HHHHhCccHHHHHHHHH
Confidence 49999999999999954
No 53
>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=55.77 E-value=2.7 Score=20.28 Aligned_cols=22 Identities=18% Similarity=0.176 Sum_probs=19.5
Q ss_pred HHHHHhCCCCCcccccccCCcc
Q psy8538 19 ELANSLGLSERQVRCPHHQLTT 40 (64)
Q Consensus 19 ~La~~l~l~~~qV~vWFqNrR~ 40 (64)
+||..+|++...|..|+.+...
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~~ 23 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKPR 23 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCCC
Confidence 5899999999999999998863
No 54
>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=51.13 E-value=3.3 Score=19.51 Aligned_cols=19 Identities=37% Similarity=0.522 Sum_probs=14.5
Q ss_pred HHHHHHhCCCCCccccccc
Q psy8538 18 AELANSLGLSERQVRCPHH 36 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFq 36 (64)
.++|+.+|++.+.|+.|=+
T Consensus 3 ~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 4689999999999888843
No 55
>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=50.06 E-value=5.4 Score=20.21 Aligned_cols=20 Identities=20% Similarity=0.267 Sum_probs=17.4
Q ss_pred HHHHHHhCCCCCcccccccC
Q psy8538 18 AELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqN 37 (64)
.++|+.+|++...|..|-+.
T Consensus 4 ~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 4 GAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999763
No 56
>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=49.97 E-value=2.5 Score=20.67 Aligned_cols=23 Identities=35% Similarity=0.414 Sum_probs=16.5
Q ss_pred HHHHHHHHHhCCCCCcccccccC
Q psy8538 15 RRKAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 15 ~~r~~La~~l~l~~~qV~vWFqN 37 (64)
-.-.++|..+|+++..|+.|.+.
T Consensus 27 ~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 27 MSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp --HHHHHHHCTS-HHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHH
Confidence 34567899999999999887653
No 57
>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=49.58 E-value=5.5 Score=19.29 Aligned_cols=23 Identities=26% Similarity=0.354 Sum_probs=19.3
Q ss_pred HHHHHHHhCCCCCcccccccCCc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR 39 (64)
..+||..+|++...|..|..+.+
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 36799999999999999999855
No 58
>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=49.12 E-value=5.3 Score=20.51 Aligned_cols=20 Identities=20% Similarity=0.247 Sum_probs=17.4
Q ss_pred HHHHHHhCCCCCcccccccC
Q psy8538 18 AELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqN 37 (64)
.++|+.+|+++..|+.|.+.
T Consensus 4 ~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 4 GEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999764
No 59
>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=48.82 E-value=5.3 Score=18.52 Aligned_cols=22 Identities=32% Similarity=0.265 Sum_probs=18.1
Q ss_pred HHHHHHhCCCCCcccccccCCc
Q psy8538 18 AELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNrR 39 (64)
.++|..+|++...|..|.+...
T Consensus 5 ~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 5 EEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHCCCHHHHHHHHHcCC
Confidence 4678999999999999986654
No 60
>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=48.00 E-value=7.9 Score=18.53 Aligned_cols=23 Identities=26% Similarity=0.312 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCCCcccccccCCc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR 39 (64)
..+||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 35799999999999999987775
No 61
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=46.88 E-value=6 Score=20.07 Aligned_cols=20 Identities=30% Similarity=0.355 Sum_probs=16.7
Q ss_pred HHHHHHhCCCCCcccccccC
Q psy8538 18 AELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqN 37 (64)
.++|+.+|+++..|..|-..
T Consensus 4 ~eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 4 GEVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999543
No 62
>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=45.83 E-value=5.8 Score=20.52 Aligned_cols=22 Identities=23% Similarity=0.237 Sum_probs=17.0
Q ss_pred HHHHHHHHhCCCCCcccccccC
Q psy8538 16 RKAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~vWFqN 37 (64)
....+|..+|+++.++..|-.-
T Consensus 25 sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 25 SVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHH
T ss_pred ceEeeecccccccccccHHHHH
Confidence 4567899999999999999543
No 63
>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=44.94 E-value=8.5 Score=17.40 Aligned_cols=22 Identities=27% Similarity=0.338 Sum_probs=19.2
Q ss_pred HHHHHHhCCCCCcccccccCCc
Q psy8538 18 AELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNrR 39 (64)
..+|..+|+++..|..|..+..
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 16 EELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcCCC
Confidence 4789999999999999988765
No 64
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=44.67 E-value=16 Score=22.37 Aligned_cols=40 Identities=25% Similarity=0.302 Sum_probs=26.0
Q ss_pred HHHHHHHhCCCCCcccccccCCcccccchHHHHHHHHHhcCCCCCC
Q psy8538 17 KAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKVHGDGRNS 62 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~~~~~~~g~~s 62 (64)
-.++|..+|++...|++= -.|++ .++.+..+...++||.|
T Consensus 153 ~~EIA~~lg~s~~tV~~r--l~rar----~~Lr~~l~~~~~~~~~~ 192 (192)
T PRK09643 153 VADAARMLGVAEGTVKSR--CARGR----ARLAELLGYLRAGGNAS 192 (192)
T ss_pred HHHHHHHHCcCHHHHHHH--HHHHH----HHHHHHHHHhcCCCCCC
Confidence 457899999999988641 12221 24566666777777754
No 65
>PF12728 HTH_17: Helix-turn-helix domain
Probab=42.88 E-value=7.3 Score=18.78 Aligned_cols=22 Identities=32% Similarity=0.157 Sum_probs=18.3
Q ss_pred HHHHHHhCCCCCcccccccCCc
Q psy8538 18 AELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNrR 39 (64)
.++|..||++...|..|.....
T Consensus 5 ~e~a~~l~is~~tv~~~~~~g~ 26 (51)
T PF12728_consen 5 KEAAELLGISRSTVYRWIRQGK 26 (51)
T ss_pred HHHHHHHCcCHHHHHHHHHcCC
Confidence 4689999999999999986653
No 66
>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=42.70 E-value=9.8 Score=15.52 Aligned_cols=18 Identities=33% Similarity=0.355 Sum_probs=12.6
Q ss_pred HHHHHHHhCCCCCccccc
Q psy8538 17 KAELANSLGLSERQVRCP 34 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vW 34 (64)
...+|..+|++...|..|
T Consensus 24 ~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 24 VAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 346778888887776655
No 67
>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=42.62 E-value=6 Score=18.22 Aligned_cols=21 Identities=38% Similarity=0.509 Sum_probs=16.8
Q ss_pred HHHHHHHhCCCCCcccccccC
Q psy8538 17 KAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqN 37 (64)
...+|..+|++...|..|...
T Consensus 29 ~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 29 YEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 456799999999999887654
No 68
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=41.41 E-value=12 Score=25.34 Aligned_cols=22 Identities=18% Similarity=0.412 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCCCCcccccccC
Q psy8538 16 RKAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~vWFqN 37 (64)
.-..+|.++|+++.+|+-|-+.
T Consensus 21 k~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 21 KLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred cHHHHHHHhCCChHHHHHHHHh
Confidence 3457899999999999999543
No 69
>PHA00542 putative Cro-like protein
Probab=39.45 E-value=22 Score=19.24 Aligned_cols=40 Identities=5% Similarity=0.031 Sum_probs=26.0
Q ss_pred HHHHHHHhCCCCCcccccccCCc--ccccchHHHHHHHHHhc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLT--TVNNNTAIIVSFLEKVH 56 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR--~~~k~~~~~~~~~~~~~ 56 (64)
..+||..+|++...|..|...+. ........++.+.....
T Consensus 34 q~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~~~~~ 75 (82)
T PHA00542 34 QEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLVLNLD 75 (82)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHHHhc
Confidence 34689999999999999988763 33333334444444443
No 70
>PHA01976 helix-turn-helix protein
Probab=38.87 E-value=12 Score=18.79 Aligned_cols=23 Identities=13% Similarity=0.101 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCCCcccccccCCc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR 39 (64)
..+||..+|++...|..|-...+
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 45799999999999999987654
No 71
>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=38.45 E-value=12 Score=19.30 Aligned_cols=23 Identities=22% Similarity=0.190 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCCCcccccccCCc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR 39 (64)
...||..+|++...|..|..+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 35799999999999999998765
No 72
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=38.26 E-value=15 Score=21.47 Aligned_cols=23 Identities=35% Similarity=0.276 Sum_probs=20.2
Q ss_pred CCHHHHHHHHHHhCCCCCccccc
Q psy8538 12 ITIRRKAELANSLGLSERQVRCP 34 (64)
Q Consensus 12 p~~~~r~~La~~l~l~~~qV~vW 34 (64)
++...|..||.+++++...|..|
T Consensus 27 ~~~~~r~~La~~~~i~~~~l~~w 49 (122)
T PF14229_consen 27 DTPLGRKALAKKLGISERNLLKW 49 (122)
T ss_pred CCHHHHHHHHHhcCCCHHHHHHH
Confidence 55667888999999999999999
No 73
>PHA02955 hypothetical protein; Provisional
Probab=36.69 E-value=41 Score=21.98 Aligned_cols=28 Identities=11% Similarity=0.227 Sum_probs=23.3
Q ss_pred CCCHHHHHHHHHHhCCCCCcccccccCC
Q psy8538 11 YITIRRKAELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 11 ~p~~~~r~~La~~l~l~~~qV~vWFqNr 38 (64)
-++..++..++..+|+....|..||.+-
T Consensus 76 ~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 76 NFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred hCCHHHHHHHHHHhCCChhhccCcccch
Confidence 3667889999999999997778888773
No 74
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=36.24 E-value=12 Score=17.92 Aligned_cols=16 Identities=69% Similarity=0.827 Sum_probs=11.6
Q ss_pred HHHHHHHhCCCCCccc
Q psy8538 17 KAELANSLGLSERQVR 32 (64)
Q Consensus 17 r~~La~~l~l~~~qV~ 32 (64)
-.+||..+|+++..|.
T Consensus 20 ~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 20 YAELAEELGLSESTVR 35 (42)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCcCHHHHH
Confidence 3478999999987654
No 75
>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=36.12 E-value=13 Score=23.57 Aligned_cols=28 Identities=18% Similarity=0.080 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCCCcccccccCCccccc
Q psy8538 16 RKAELANSLGLSERQVRCPHHQLTTVNN 43 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~vWFqNrR~~~k 43 (64)
...+|+.-+++|..+|-+|..|.+.-.+
T Consensus 16 t~~e~~~~~~VS~~sv~~WiKNG~~~~~ 43 (186)
T PF04936_consen 16 TIDELADYFDVSRTSVSVWIKNGKDPKR 43 (186)
T ss_pred cHHHHHHHHccCHHHHHHHHHcCCCccc
Confidence 4678999999999999999999876443
No 76
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=36.03 E-value=11 Score=21.07 Aligned_cols=22 Identities=23% Similarity=0.170 Sum_probs=18.4
Q ss_pred HHHHHHhCCCCCcccccccCCc
Q psy8538 18 AELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNrR 39 (64)
.++|+.+|++...|+.|..+.-
T Consensus 4 ~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 4 GEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred HHHHHHHCcCHHHHHHHHHCCC
Confidence 4689999999999999976643
No 77
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=35.99 E-value=16 Score=16.25 Aligned_cols=23 Identities=26% Similarity=0.326 Sum_probs=19.2
Q ss_pred HHHHHHHhCCCCCcccccccCCc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR 39 (64)
...+|..+|++...|..|-.+..
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 34789999999999999977664
No 78
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=35.81 E-value=25 Score=21.93 Aligned_cols=31 Identities=16% Similarity=0.209 Sum_probs=25.4
Q ss_pred chhhhccCCCCCHHHHHHHHHHhCCCCCccc
Q psy8538 2 DSLEFHYSRYITIRRKAELANSLGLSERQVR 32 (64)
Q Consensus 2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~ 32 (64)
|...+....|.+......+|..||++...|.
T Consensus 31 L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 31 LHIAQEQFGWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred HHHHHHHhCCCCHHHHHHHHHHhCCCHHHhe
Confidence 5556667779999999999999999987664
No 79
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=35.70 E-value=12 Score=21.65 Aligned_cols=21 Identities=19% Similarity=0.120 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCCCcccccccC
Q psy8538 17 KAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqN 37 (64)
...+|.++|+++.+|..|.+-
T Consensus 32 v~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 32 VSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 457899999999999999654
No 80
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=35.62 E-value=10 Score=18.21 Aligned_cols=19 Identities=32% Similarity=0.300 Sum_probs=15.2
Q ss_pred HHHHHHHhCCCCCcccccc
Q psy8538 17 KAELANSLGLSERQVRCPH 35 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWF 35 (64)
...+|+.+|++...|...|
T Consensus 30 ~~~vA~~~~vs~~TV~ri~ 48 (52)
T PF13542_consen 30 FKDVARELGVSWSTVRRIF 48 (52)
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 4578999999998887665
No 81
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=35.32 E-value=15 Score=21.34 Aligned_cols=23 Identities=22% Similarity=0.121 Sum_probs=20.6
Q ss_pred HHHHHHHhCCCCCcccccccCCc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR 39 (64)
+.+||..+|++...|..|.+++.
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 45799999999999999999886
No 82
>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=35.17 E-value=9.7 Score=21.98 Aligned_cols=21 Identities=24% Similarity=0.170 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCCCcccccccC
Q psy8538 17 KAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqN 37 (64)
..++|..++++...|..|++.
T Consensus 21 ~~eaa~~F~VS~~Tv~~W~k~ 41 (119)
T PF01710_consen 21 IREAAKRFGVSRNTVYRWLKR 41 (119)
T ss_pred HHHHHHHhCcHHHHHHHHHHh
Confidence 456799999999999999993
No 83
>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=35.08 E-value=12 Score=18.85 Aligned_cols=15 Identities=53% Similarity=0.809 Sum_probs=11.5
Q ss_pred HHHHHHhCCCCCccc
Q psy8538 18 AELANSLGLSERQVR 32 (64)
Q Consensus 18 ~~La~~l~l~~~qV~ 32 (64)
.+||..+|+++.||+
T Consensus 32 ~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 32 QELAEALGITPAQVR 46 (50)
T ss_dssp HHHHHHHTS-HHHHH
T ss_pred HHHHHHHCCCHHHhc
Confidence 368999999998875
No 84
>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=34.93 E-value=11 Score=20.63 Aligned_cols=18 Identities=33% Similarity=0.433 Sum_probs=15.9
Q ss_pred HHHHHHhCCCCCcccccc
Q psy8538 18 AELANSLGLSERQVRCPH 35 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWF 35 (64)
.++|+.+|++..+++.|-
T Consensus 5 ~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 5 GEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 478999999999999993
No 85
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=34.56 E-value=9.9 Score=19.80 Aligned_cols=17 Identities=35% Similarity=0.429 Sum_probs=14.8
Q ss_pred HHHHHHhCCCCCccccc
Q psy8538 18 AELANSLGLSERQVRCP 34 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vW 34 (64)
..||+.||++...|--|
T Consensus 13 ~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 13 SKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHCCCHHHHHHh
Confidence 47899999999999999
No 86
>PF13551 HTH_29: Winged helix-turn helix
Probab=33.54 E-value=9.8 Score=20.77 Aligned_cols=23 Identities=35% Similarity=0.353 Sum_probs=19.3
Q ss_pred HHHHHHHhCCCCCcccccccCCc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR 39 (64)
..++|..+|++...|..|.+.-+
T Consensus 15 ~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 15 IAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHH
Confidence 56789999999999999977633
No 87
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=33.31 E-value=17 Score=21.18 Aligned_cols=24 Identities=17% Similarity=0.137 Sum_probs=20.7
Q ss_pred HHHHHHHhCCCCCcccccccCCcc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLTT 40 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR~ 40 (64)
..+||..+|++...|..|..+.+.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 357899999999999999988763
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=33.10 E-value=12 Score=18.14 Aligned_cols=16 Identities=50% Similarity=0.787 Sum_probs=11.7
Q ss_pred HHHHHHHhCCCCCccc
Q psy8538 17 KAELANSLGLSERQVR 32 (64)
Q Consensus 17 r~~La~~l~l~~~qV~ 32 (64)
..+||..+++|.+.|.
T Consensus 18 ~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 18 AKELAEELGVSRRTIR 33 (55)
T ss_dssp HHHHHHHCTS-HHHHH
T ss_pred HHHHHHHhCCCHHHHH
Confidence 3478999999987664
No 89
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=33.00 E-value=14 Score=17.43 Aligned_cols=20 Identities=35% Similarity=0.579 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCCCccccccc
Q psy8538 17 KAELANSLGLSERQVRCPHH 36 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFq 36 (64)
..++|..++++...|..|..
T Consensus 18 ~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 18 NKEIADILGISEKTVKTHLR 37 (57)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 45789999999999988765
No 90
>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=32.93 E-value=15 Score=20.05 Aligned_cols=22 Identities=14% Similarity=0.034 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCCCcccccccCC
Q psy8538 17 KAELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNr 38 (64)
..++|..+|++...|..|-+..
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~G 25 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERLG 25 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3478999999999999997654
No 91
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=32.44 E-value=34 Score=17.48 Aligned_cols=28 Identities=21% Similarity=0.178 Sum_probs=22.6
Q ss_pred HHHHHHHHHhCCCCCcccccccCCcccc
Q psy8538 15 RRKAELANSLGLSERQVRCPHHQLTTVN 42 (64)
Q Consensus 15 ~~r~~La~~l~l~~~qV~vWFqNrR~~~ 42 (64)
.-+..++.+.|++..+...+|.++.-.+
T Consensus 23 ~lK~~i~~~~gi~~~~q~Li~~G~~L~d 50 (70)
T cd01798 23 QLKEVVAKRQGVPPDQLRVIFAGKELRN 50 (70)
T ss_pred HHHHHHHHHHCCCHHHeEEEECCeECCC
Confidence 3456799999999999999999876443
No 92
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=32.13 E-value=27 Score=21.35 Aligned_cols=25 Identities=24% Similarity=0.280 Sum_probs=21.5
Q ss_pred cCCCCCHHHHHHHHHHhCCCCCccc
Q psy8538 8 YSRYITIRRKAELANSLGLSERQVR 32 (64)
Q Consensus 8 ~~~~p~~~~r~~La~~l~l~~~qV~ 32 (64)
...|++......+|..+|+++.+|.
T Consensus 35 ~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 35 EFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 4568999999999999999988765
No 93
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=32.06 E-value=37 Score=18.61 Aligned_cols=19 Identities=37% Similarity=0.592 Sum_probs=14.9
Q ss_pred HHHHHHHHHHhCCCCCccc
Q psy8538 14 IRRKAELANSLGLSERQVR 32 (64)
Q Consensus 14 ~~~r~~La~~l~l~~~qV~ 32 (64)
...=..+++++||++.+|.
T Consensus 11 ~~~wk~~~R~LGlse~~Id 29 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIE 29 (80)
T ss_pred HHHHHHHHHHcCCCHHHHH
Confidence 3455679999999998875
No 94
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=31.42 E-value=35 Score=17.68 Aligned_cols=26 Identities=15% Similarity=-0.013 Sum_probs=21.0
Q ss_pred HHHHHHHHHhCCCCCcccccccCCcc
Q psy8538 15 RRKAELANSLGLSERQVRCPHHQLTT 40 (64)
Q Consensus 15 ~~r~~La~~l~l~~~qV~vWFqNrR~ 40 (64)
.-+..++...|++..+.+.||..+--
T Consensus 24 ~lK~~I~~~~gip~~~q~Li~~Gk~L 49 (71)
T cd01796 24 NFKALCEAESGIPASQQQLIYNGREL 49 (71)
T ss_pred HHHHHHHHHhCCCHHHeEEEECCeEc
Confidence 34567899999999999999987643
No 95
>PF03584 Herpes_ICP4_N: Herpesvirus ICP4-like protein N-terminal region; InterPro: IPR005206 The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection. ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer. ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the N-terminal region that contains sites for DNA binding and homodimerisation [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0042025 host cell nucleus
Probab=31.38 E-value=92 Score=19.75 Aligned_cols=46 Identities=15% Similarity=0.226 Sum_probs=31.8
Q ss_pred HHHHHHHHHhCCCCCcccccccCCcccccchHHHHHHHHHhcCCCCC
Q psy8538 15 RRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKVHGDGRN 61 (64)
Q Consensus 15 ~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~~~~~~~g~~ 61 (64)
.+-..|.+.+-.+...+-.|.||-+--.... .+..++.+..+.+.+
T Consensus 61 kQy~aLv~~~~~~~~~~m~wlq~~Kls~~d~-~L~~~cqk~~~~~~~ 106 (173)
T PF03584_consen 61 KQYEALVRLIYTPDRDAMAWLQNPKLSPADQ-ALNQFCQKFRGGGRS 106 (173)
T ss_pred HHHHHHHHHHhcccHHHHHHhcCCCcCchHH-HHHHHHHHhccCCCC
Confidence 3445677777667888999999988655444 777777666555554
No 96
>PTZ00044 ubiquitin; Provisional
Probab=31.28 E-value=34 Score=17.61 Aligned_cols=28 Identities=18% Similarity=0.195 Sum_probs=22.1
Q ss_pred HHHHHHHHHhCCCCCcccccccCCcccc
Q psy8538 15 RRKAELANSLGLSERQVRCPHHQLTTVN 42 (64)
Q Consensus 15 ~~r~~La~~l~l~~~qV~vWFqNrR~~~ 42 (64)
.-+..++...|++..+.+.||..+--.+
T Consensus 25 ~lK~~i~~~~gi~~~~q~L~~~g~~L~d 52 (76)
T PTZ00044 25 QVKMALQEKEGIDVKQIRLIYSGKQMSD 52 (76)
T ss_pred HHHHHHHHHHCCCHHHeEEEECCEEccC
Confidence 3456799999999999999998765443
No 97
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=30.81 E-value=16 Score=20.79 Aligned_cols=17 Identities=53% Similarity=0.657 Sum_probs=11.6
Q ss_pred HHHHHHHHhCCCCCccc
Q psy8538 16 RKAELANSLGLSERQVR 32 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~ 32 (64)
...+||.++|||+++|.
T Consensus 74 n~~eLA~kyglS~r~I~ 90 (108)
T PF08765_consen 74 NVRELARKYGLSERQIY 90 (108)
T ss_dssp -HHHHHHHHT--HHHHH
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 35689999999998764
No 98
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=30.42 E-value=32 Score=19.50 Aligned_cols=19 Identities=16% Similarity=0.345 Sum_probs=16.4
Q ss_pred HHHHHHhCCCCCccccccc
Q psy8538 18 AELANSLGLSERQVRCPHH 36 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFq 36 (64)
..+|..+|+++.+|-.|..
T Consensus 27 ~~vA~~~Gv~eStISR~k~ 45 (91)
T PF05269_consen 27 KKVAEAMGVDESTISRWKN 45 (91)
T ss_dssp HHHHHHHTSSTTTHHHHHH
T ss_pred HHHHHHhCCCHHHHHHHHh
Confidence 4689999999999999954
No 99
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=30.02 E-value=39 Score=17.52 Aligned_cols=28 Identities=14% Similarity=0.058 Sum_probs=22.6
Q ss_pred HHHHHHHHhCCCCCcccccccCCccccc
Q psy8538 16 RKAELANSLGLSERQVRCPHHQLTTVNN 43 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~vWFqNrR~~~k 43 (64)
-+..++...|++..+...+|.++.-.+-
T Consensus 24 lK~~i~~~~gip~~~q~Li~~Gk~L~D~ 51 (74)
T cd01793 24 IKAHVAGLEGIDVEDQVLLLAGVPLEDD 51 (74)
T ss_pred HHHHHHhhhCCCHHHEEEEECCeECCCC
Confidence 4567899999999999999998765444
No 100
>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=29.90 E-value=30 Score=20.71 Aligned_cols=24 Identities=25% Similarity=0.282 Sum_probs=20.6
Q ss_pred CCCCCHHHHHHHHHHhCCCCCccc
Q psy8538 9 SRYITIRRKAELANSLGLSERQVR 32 (64)
Q Consensus 9 ~~~p~~~~r~~La~~l~l~~~qV~ 32 (64)
..|++......+|..+|++..+|.
T Consensus 29 ~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 29 KGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred hCCCCHHHHHHHHHHhCcCHHHHH
Confidence 458999999999999999987765
No 101
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=29.81 E-value=17 Score=16.98 Aligned_cols=21 Identities=33% Similarity=0.555 Sum_probs=16.8
Q ss_pred HHHHHHHhCCCCCcccccccC
Q psy8538 17 KAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqN 37 (64)
..++|..+|++...|..|...
T Consensus 21 ~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 21 NKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHHH
Confidence 457899999999998877553
No 102
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, 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=29.80 E-value=17 Score=19.91 Aligned_cols=21 Identities=33% Similarity=0.401 Sum_probs=17.5
Q ss_pred HHHHHHhCCCCCcccccccCC
Q psy8538 18 AELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNr 38 (64)
.++|..+|+++..|..|-+..
T Consensus 4 ~eva~~~gi~~~tlr~~~~~G 24 (100)
T cd00592 4 GEVAKLLGVSVRTLRYYEEKG 24 (100)
T ss_pred HHHHHHHCcCHHHHHHHHHCC
Confidence 468999999999999996554
No 103
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 This entry is represented by the Bacteriophage lambda, Nu1, terminase small subunit. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA [].; PDB: 1J9I_A.
Probab=29.75 E-value=16 Score=22.63 Aligned_cols=21 Identities=43% Similarity=0.514 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCCCcccccccC
Q psy8538 17 KAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqN 37 (64)
+.+||..+|+|+..|.-|-.+
T Consensus 5 k~~lA~i~gvS~~ti~~W~~~ 25 (164)
T PF07471_consen 5 KKELAEIFGVSERTIDKWQRQ 25 (164)
T ss_dssp HHHHHHHTT--HHHHHHHTTT
T ss_pred HHHHHHHHCCCHHHHHHHHHC
Confidence 568999999999999999765
No 104
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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 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=29.68 E-value=15 Score=20.58 Aligned_cols=22 Identities=23% Similarity=0.178 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCCCcccccccCC
Q psy8538 17 KAELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNr 38 (64)
..++|+.+|++...|..|-+..
T Consensus 4 i~eva~~~gvs~~tlR~ye~~G 25 (102)
T cd04789 4 ISELAEKAGISRSTLLYYEKLG 25 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3478999999999999886653
No 105
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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 N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=29.39 E-value=16 Score=20.52 Aligned_cols=21 Identities=10% Similarity=0.184 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCCCcccccccC
Q psy8538 17 KAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqN 37 (64)
..++|+.+|+|...+..|-+.
T Consensus 4 i~eva~~~gvs~~tLR~ye~~ 24 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYESI 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999988664
No 106
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively 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 C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=29.19 E-value=16 Score=20.26 Aligned_cols=21 Identities=38% Similarity=0.366 Sum_probs=17.9
Q ss_pred HHHHHHhCCCCCcccccccCC
Q psy8538 18 AELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNr 38 (64)
.++|+.+|++...|..|-+..
T Consensus 4 ~eva~~~gvs~~tlR~ye~~G 24 (96)
T cd04788 4 GELARRTGLSVRTLHHYDHIG 24 (96)
T ss_pred HHHHHHHCcCHHHHHHHHHCC
Confidence 478999999999999997654
No 107
>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=29.16 E-value=16 Score=18.48 Aligned_cols=16 Identities=44% Similarity=0.671 Sum_probs=12.1
Q ss_pred HHHHHHhCCCCCcccc
Q psy8538 18 AELANSLGLSERQVRC 33 (64)
Q Consensus 18 ~~La~~l~l~~~qV~v 33 (64)
.+||..+|+|++.|+.
T Consensus 23 ~ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 23 KELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHCTS-HHHHHH
T ss_pred HHHHHHHCCCHHHHHH
Confidence 3789999999987754
No 108
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=28.87 E-value=49 Score=18.61 Aligned_cols=22 Identities=18% Similarity=-0.004 Sum_probs=18.8
Q ss_pred HHHHHHhCCCCCcccccccCCc
Q psy8538 18 AELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNrR 39 (64)
.+||..+|++...|.-|-....
T Consensus 82 ~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 82 REAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred HHHHHHhCCCHHHHHHHHCCCC
Confidence 4789999999999999976665
No 109
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.86 E-value=19 Score=20.05 Aligned_cols=21 Identities=29% Similarity=0.406 Sum_probs=17.9
Q ss_pred HHHHHHhCCCCCcccccccCC
Q psy8538 18 AELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNr 38 (64)
.++|+.+|++...|..|....
T Consensus 4 ~e~a~~~gvs~~tLR~ye~~G 24 (96)
T cd04774 4 DEVAKRLGLTKRTLKYYEEIG 24 (96)
T ss_pred HHHHHHHCcCHHHHHHHHHCC
Confidence 478999999999999997653
No 110
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=28.77 E-value=42 Score=16.38 Aligned_cols=25 Identities=24% Similarity=0.149 Sum_probs=19.9
Q ss_pred HHHHHHHHHhCCCCCcccccccCCc
Q psy8538 15 RRKAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 15 ~~r~~La~~l~l~~~qV~vWFqNrR 39 (64)
.-+..++..++++...+..+|..+-
T Consensus 22 ~lK~~i~~~~~~~~~~~~l~~~g~~ 46 (69)
T cd01769 22 ELKAKIAAKEGVPPEQQRLIYAGKI 46 (69)
T ss_pred HHHHHHHHHHCcChHHEEEEECCcC
Confidence 3456789999999999999887643
No 111
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=28.68 E-value=14 Score=22.03 Aligned_cols=22 Identities=23% Similarity=0.241 Sum_probs=19.0
Q ss_pred HHHHHHhCCCCCcccccccCCc
Q psy8538 18 AELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNrR 39 (64)
.++|+.+|++.+.|..|.+..-
T Consensus 4 ~e~a~~~gvs~~TLR~Ye~~GL 25 (134)
T cd04779 4 GQLAHLAGVSKRTIDYYTNLGL 25 (134)
T ss_pred HHHHHHHCcCHHHHHHHHHCCC
Confidence 4789999999999999987653
No 112
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=28.44 E-value=18 Score=20.04 Aligned_cols=21 Identities=29% Similarity=0.243 Sum_probs=18.3
Q ss_pred HHHHHHhCCCCCcccccccCC
Q psy8538 18 AELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNr 38 (64)
.++|+.+|++...+..|-+..
T Consensus 4 ~eva~~~gvs~~tLRyye~~G 24 (96)
T cd04768 4 GEFAKLAGVSIRTLRHYDDIG 24 (96)
T ss_pred HHHHHHHCcCHHHHHHHHHCC
Confidence 478999999999999998764
No 113
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=28.01 E-value=18 Score=21.97 Aligned_cols=29 Identities=14% Similarity=0.081 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538 16 RKAELANSLGLSERQVRCPHHQLTTVNNN 44 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~vWFqNrR~~~k~ 44 (64)
...+++..+|+++.+|..|....|-.-..
T Consensus 48 ti~eV~e~tgVs~~~I~~~IreGRL~~~~ 76 (137)
T TIGR03826 48 TVSEIVEETGVSEKLILKFIREGRLQLKH 76 (137)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCeeccC
Confidence 35688999999999999999988854443
No 114
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=27.83 E-value=34 Score=20.64 Aligned_cols=25 Identities=16% Similarity=0.254 Sum_probs=21.3
Q ss_pred cCCCCCHHHHHHHHHHhCCCCCccc
Q psy8538 8 YSRYITIRRKAELANSLGLSERQVR 32 (64)
Q Consensus 8 ~~~~p~~~~r~~La~~l~l~~~qV~ 32 (64)
.-.|++......+|..+|++..+|.
T Consensus 34 ~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 34 QRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 3468999999999999999988765
No 115
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=27.65 E-value=19 Score=18.10 Aligned_cols=24 Identities=29% Similarity=0.365 Sum_probs=20.4
Q ss_pred HHHHHHHhCCCCCcccccccCCcc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLTT 40 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR~ 40 (64)
..++|..+|++...|..|-..++.
T Consensus 17 ~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 17 QAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred HHHHHHHHCcCHHHHHHHHCCCCC
Confidence 457899999999999999998885
No 116
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. 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. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=27.61 E-value=23 Score=20.09 Aligned_cols=21 Identities=29% Similarity=0.322 Sum_probs=18.2
Q ss_pred HHHHHHhCCCCCcccccccCC
Q psy8538 18 AELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNr 38 (64)
.++|+.+|++...|..|-+..
T Consensus 4 ~eva~~~gvs~~tlR~ye~~G 24 (108)
T cd04773 4 GELAHLLGVPPSTLRHWEKEG 24 (108)
T ss_pred HHHHHHHCcCHHHHHHHHHCC
Confidence 478999999999999997764
No 117
>PF08452 DNAP_B_exo_N: DNA polymerase family B exonuclease domain, N-terminal; InterPro: IPR013660 This domain is found in viral DNA polymerases to the N terminus of DNA polymerase family B exonuclease domains (IPR006133 from INTERPRO). ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=27.17 E-value=23 Score=14.95 Aligned_cols=7 Identities=0% Similarity=-0.453 Sum_probs=5.9
Q ss_pred ccccCCc
Q psy8538 33 CPHHQLT 39 (64)
Q Consensus 33 vWFqNrR 39 (64)
.||.++.
T Consensus 7 NWFE~~g 13 (22)
T PF08452_consen 7 NWFESRG 13 (22)
T ss_pred ehhhhCC
Confidence 6999986
No 118
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=27.02 E-value=18 Score=20.14 Aligned_cols=20 Identities=20% Similarity=0.318 Sum_probs=16.4
Q ss_pred HHHHHHhCCCCCcccccccC
Q psy8538 18 AELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqN 37 (64)
.++|+.+|++...|..|=..
T Consensus 4 ~eva~~~gvs~~tlR~Ye~~ 23 (95)
T cd04780 4 SELSKRSGVSVATIKYYLRE 23 (95)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 47899999999999888554
No 119
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=26.88 E-value=16 Score=21.10 Aligned_cols=23 Identities=9% Similarity=0.117 Sum_probs=19.6
Q ss_pred HHHHHHHHhCCCCCcccccccCC
Q psy8538 16 RKAELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~vWFqNr 38 (64)
...+||..+|++++.+..+|+.-
T Consensus 27 sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 27 SLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHH
Confidence 45689999999999999998864
No 120
>PRK09726 antitoxin HipB; Provisional
Probab=26.82 E-value=27 Score=18.88 Aligned_cols=23 Identities=17% Similarity=0.352 Sum_probs=19.7
Q ss_pred HHHHHHHhCCCCCcccccccCCc
Q psy8538 17 KAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNrR 39 (64)
..+||..+|++...|..|..+.+
T Consensus 28 q~elA~~~gvs~~tis~~e~g~~ 50 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNPD 50 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCCC
Confidence 45789999999999999988754
No 121
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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 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=26.67 E-value=20 Score=20.30 Aligned_cols=20 Identities=30% Similarity=0.421 Sum_probs=16.8
Q ss_pred HHHHHHhCCCCCcccccccC
Q psy8538 18 AELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqN 37 (64)
.++|+.+|++.+.|..|-+.
T Consensus 4 ~e~a~~~gvs~~tlr~ye~~ 23 (113)
T cd01109 4 KEVAEKTGLSADTLRYYEKE 23 (113)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 47899999999999988554
No 122
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which 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 N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=26.12 E-value=19 Score=20.46 Aligned_cols=21 Identities=29% Similarity=0.129 Sum_probs=17.7
Q ss_pred HHHHHHhCCCCCcccccccCC
Q psy8538 18 AELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNr 38 (64)
.++|+.+|++...|+.|-...
T Consensus 4 ge~A~~~gvs~~tlR~ye~~G 24 (107)
T cd01111 4 SQLALDAGVSVHIVRDYLLRG 24 (107)
T ss_pred HHHHHHHCcCHHHHHHHHHCC
Confidence 478999999999999996653
No 123
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.99 E-value=19 Score=19.92 Aligned_cols=21 Identities=19% Similarity=0.143 Sum_probs=17.7
Q ss_pred HHHHHHhCCCCCcccccccCC
Q psy8538 18 AELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNr 38 (64)
.++|+.+|++...+..|-+..
T Consensus 4 ~eva~~~gvs~~tlR~ye~~G 24 (97)
T cd04782 4 GEFAKLCGISKQTLFHYDKIG 24 (97)
T ss_pred HHHHHHHCcCHHHHHHHHHCC
Confidence 478999999999999996654
No 124
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.72 E-value=22 Score=20.08 Aligned_cols=21 Identities=24% Similarity=0.146 Sum_probs=17.8
Q ss_pred HHHHHHhCCCCCcccccccCC
Q psy8538 18 AELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNr 38 (64)
.++|+.+|++...|..|-...
T Consensus 4 ~eva~~~gis~~tlR~ye~~G 24 (108)
T cd01107 4 GEFAKLSNLSIKALRYYDKIG 24 (108)
T ss_pred HHHHHHHCcCHHHHHHHHHcC
Confidence 478999999999999997663
No 125
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=25.64 E-value=27 Score=19.12 Aligned_cols=21 Identities=33% Similarity=0.433 Sum_probs=15.9
Q ss_pred HHHHHHHhCCCCCcccccccC
Q psy8538 17 KAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqN 37 (64)
=..||+.||+++.+|..--.+
T Consensus 16 Wk~laR~LGlse~~Id~i~~~ 36 (86)
T cd08306 16 WRKLARKLGLSETKIESIEEA 36 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHH
Confidence 357899999999998754433
No 126
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=24.61 E-value=50 Score=16.73 Aligned_cols=26 Identities=19% Similarity=0.147 Sum_probs=20.3
Q ss_pred HHHHHHHHHHhCCCCCcccccccCCc
Q psy8538 14 IRRKAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 14 ~~~r~~La~~l~l~~~qV~vWFqNrR 39 (64)
..-+..++..++++...++.||.++-
T Consensus 24 ~~lK~~i~~~~g~~~~~q~L~~~g~~ 49 (76)
T cd01803 24 ENVKAKIQDKEGIPPDQQRLIFAGKQ 49 (76)
T ss_pred HHHHHHHHHHhCCCHHHeEEEECCEE
Confidence 34556789999999999999986553
No 127
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=24.48 E-value=23 Score=19.96 Aligned_cols=18 Identities=33% Similarity=0.410 Sum_probs=14.7
Q ss_pred HHHHHHhCCCCCcccccc
Q psy8538 18 AELANSLGLSERQVRCPH 35 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWF 35 (64)
.++|+.+|++.+.++-|=
T Consensus 4 ~eva~~~gvs~~tLRyYE 21 (124)
T COG0789 4 GEVAKLTGVSVRTLRFYE 21 (124)
T ss_pred HHHHHHhCCCHHHHHHHH
Confidence 468889999999888873
No 128
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=24.47 E-value=26 Score=20.52 Aligned_cols=21 Identities=29% Similarity=0.213 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCCCcccccccC
Q psy8538 17 KAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqN 37 (64)
..++|+.+|++...|+.|-+.
T Consensus 6 I~elA~~~gvs~~tlR~Ye~~ 26 (120)
T TIGR02054 6 ISRLAEDAGVSVHVVRDYLLR 26 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 567999999999999998654
No 129
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=24.18 E-value=21 Score=17.07 Aligned_cols=18 Identities=39% Similarity=0.492 Sum_probs=14.3
Q ss_pred HHHHHHHhCCCCCccccc
Q psy8538 17 KAELANSLGLSERQVRCP 34 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vW 34 (64)
-.++|..+|+|...|..+
T Consensus 23 ~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 23 LEEIAERLGISRSTVRRI 40 (50)
T ss_dssp HHHHHHHHTSCHHHHHHH
T ss_pred HHHHHHHHCCcHHHHHHH
Confidence 457899999999877654
No 130
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=23.97 E-value=55 Score=17.43 Aligned_cols=29 Identities=3% Similarity=-0.012 Sum_probs=23.2
Q ss_pred HHHHHHHHHhCCCCCcccccccCCccccc
Q psy8538 15 RRKAELANSLGLSERQVRCPHHQLTTVNN 43 (64)
Q Consensus 15 ~~r~~La~~l~l~~~qV~vWFqNrR~~~k 43 (64)
.-+..++...|++..+.+.+|.++--.+-
T Consensus 27 ~lK~~i~~~~gi~~~~QrLi~~Gk~L~D~ 55 (78)
T cd01797 27 ELREKIQELFNVEPECQRLFYRGKQMEDG 55 (78)
T ss_pred HHHHHHHHHhCCCHHHeEEEeCCEECCCC
Confidence 44567889999999999999988765554
No 131
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=23.74 E-value=47 Score=20.69 Aligned_cols=25 Identities=20% Similarity=0.107 Sum_probs=21.3
Q ss_pred cCCCCCHHHHHHHHHHhCCCCCccc
Q psy8538 8 YSRYITIRRKAELANSLGLSERQVR 32 (64)
Q Consensus 8 ~~~~p~~~~r~~La~~l~l~~~qV~ 32 (64)
...|++......+|..+|++..+|.
T Consensus 48 ~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 48 LFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 3468999999999999999988765
No 132
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), 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. 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.
Probab=23.72 E-value=25 Score=19.75 Aligned_cols=20 Identities=30% Similarity=0.398 Sum_probs=16.9
Q ss_pred HHHHHHhCCCCCcccccccC
Q psy8538 18 AELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqN 37 (64)
.++|+.+|+++..+..|-++
T Consensus 4 ~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 4 GEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred HHHHHHHCcCHHHHHHHHHH
Confidence 47899999999999999654
No 133
>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=23.72 E-value=24 Score=21.07 Aligned_cols=25 Identities=28% Similarity=0.376 Sum_probs=18.5
Q ss_pred cCCCCCHHHHHHHHHHhCCCCCccc
Q psy8538 8 YSRYITIRRKAELANSLGLSERQVR 32 (64)
Q Consensus 8 ~~~~p~~~~r~~La~~l~l~~~qV~ 32 (64)
.-.|++......+|..+|+++.+|.
T Consensus 25 ~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 25 EYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 3458899999999999999998875
No 134
>PF13730 HTH_36: Helix-turn-helix domain
Probab=23.30 E-value=13 Score=18.03 Aligned_cols=20 Identities=35% Similarity=0.491 Sum_probs=15.3
Q ss_pred HHHHHHHHhCCCCCcccccc
Q psy8538 16 RKAELANSLGLSERQVRCPH 35 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~vWF 35 (64)
-...||..+|++.+.|+.+.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i 46 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAI 46 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 35678999999988776554
No 135
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). 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 spe
Probab=23.28 E-value=23 Score=20.89 Aligned_cols=22 Identities=14% Similarity=0.072 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCCCcccccccCC
Q psy8538 17 KAELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNr 38 (64)
..++|..+|++...+..|-+..
T Consensus 4 I~eVA~~~GVs~~TLR~wE~~G 25 (120)
T cd04767 4 IGVVAELLNIHPETLRIWERHG 25 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3578999999999999997653
No 136
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=23.24 E-value=26 Score=20.15 Aligned_cols=21 Identities=29% Similarity=0.178 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCCCcccccccC
Q psy8538 17 KAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqN 37 (64)
..++|..+|++...|..+...
T Consensus 125 ~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 125 MGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred HHHHHHHHCCCHHHHHHHHHH
Confidence 567899999999999887543
No 137
>PF09292 Neil1-DNA_bind: Endonuclease VIII-like 1, DNA bind; InterPro: IPR015371 This domain is predominantly found in Endonuclease VIII-like 1 proteins and adopts a glucocorticoid receptor-like fold. Structural analysis reveals a zincless finger motif that is required for glycosylase activity []. ; PDB: 1TDH_A.
Probab=23.21 E-value=29 Score=16.68 Aligned_cols=6 Identities=0% Similarity=-0.341 Sum_probs=4.7
Q ss_pred cccccC
Q psy8538 32 RCPHHQ 37 (64)
Q Consensus 32 ~vWFqN 37 (64)
.||||.
T Consensus 27 TiWFqG 32 (39)
T PF09292_consen 27 TIWFQG 32 (39)
T ss_dssp EEEESS
T ss_pred EEEeeC
Confidence 589985
No 138
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=22.94 E-value=38 Score=20.31 Aligned_cols=20 Identities=30% Similarity=0.307 Sum_probs=16.2
Q ss_pred HHHHHHHhCCCCCccccccc
Q psy8538 17 KAELANSLGLSERQVRCPHH 36 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFq 36 (64)
-.++|..+|+|...|+++..
T Consensus 152 ~~eIA~~lgis~~tV~~~l~ 171 (182)
T PRK12537 152 HAEIAQRLGAPLGTVKAWIK 171 (182)
T ss_pred HHHHHHHHCCChhhHHHHHH
Confidence 45789999999999987643
No 139
>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein. DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.
Probab=22.85 E-value=61 Score=16.88 Aligned_cols=28 Identities=14% Similarity=0.042 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCCCcccccccCCccccc
Q psy8538 16 RKAELANSLGLSERQVRCPHHQLTTVNN 43 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~vWFqNrR~~~k 43 (64)
-+..++...|++..+.+.||..+--.+-
T Consensus 24 lK~~I~~~~gi~~~~q~Li~~G~~L~D~ 51 (70)
T cd01794 24 LKKQLQAAEGVDPCCQRWFFSGKLLTDK 51 (70)
T ss_pred HHHHHHHHhCCCHHHeEEEECCeECCCC
Confidence 4456888899999999999987765443
No 140
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=22.73 E-value=42 Score=20.75 Aligned_cols=18 Identities=22% Similarity=0.361 Sum_probs=14.1
Q ss_pred HHHHHHHHhCCCCCcccc
Q psy8538 16 RKAELANSLGLSERQVRC 33 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~v 33 (64)
+|.+||.++++-|.||..
T Consensus 27 qR~eLA~~F~CvPSQINY 44 (152)
T PF05848_consen 27 QRNELAERFNCVPSQINY 44 (152)
T ss_dssp -HHHHHHHTTS-THHHHH
T ss_pred eHHHHHHHhCCchhhhhe
Confidence 578999999999999864
No 141
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=22.72 E-value=32 Score=18.81 Aligned_cols=16 Identities=25% Similarity=0.549 Sum_probs=13.3
Q ss_pred HHHHHHhCCCCCcccc
Q psy8538 18 AELANSLGLSERQVRC 33 (64)
Q Consensus 18 ~~La~~l~l~~~qV~v 33 (64)
..||..||+++..|..
T Consensus 22 k~Lar~LGls~~dI~~ 37 (86)
T cd08318 22 KTLAPHLEMKDKEIRA 37 (86)
T ss_pred HHHHHHcCCCHHHHHH
Confidence 4689999999988764
No 142
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=22.62 E-value=26 Score=20.40 Aligned_cols=21 Identities=24% Similarity=0.328 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCCCcccccccC
Q psy8538 17 KAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqN 37 (64)
-.++|..+|++...|..|...
T Consensus 144 ~~eIA~~lgis~~tv~~~~~r 164 (179)
T PRK11924 144 YREIAEILGVPVGTVKSRLRR 164 (179)
T ss_pred HHHHHHHHCCCHHHHHHHHHH
Confidence 457899999999999887543
No 143
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=22.62 E-value=83 Score=18.98 Aligned_cols=17 Identities=29% Similarity=0.509 Sum_probs=11.9
Q ss_pred CCHHHHHHHHHHhCCCC
Q psy8538 12 ITIRRKAELANSLGLSE 28 (64)
Q Consensus 12 p~~~~r~~La~~l~l~~ 28 (64)
.+...|.+||.++|++.
T Consensus 83 SSl~aRkeLA~eL~~~~ 99 (127)
T PF12200_consen 83 SSLAARKELAKELGYTG 99 (127)
T ss_dssp -SHHHHHHHHHHHT---
T ss_pred CCHHHHHHHHHHhCCCC
Confidence 56788999999999887
No 144
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=22.41 E-value=59 Score=16.76 Aligned_cols=28 Identities=18% Similarity=0.184 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCCCCcccccccCCccccc
Q psy8538 16 RKAELANSLGLSERQVRCPHHQLTTVNN 43 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~vWFqNrR~~~k 43 (64)
-+..++...|++..+.+.+|..+.-.+-
T Consensus 26 lK~~i~~~~gi~~~~q~L~~~G~~L~d~ 53 (74)
T cd01807 26 LKKLVSEHLNVPEEQQRLLFKGKALADD 53 (74)
T ss_pred HHHHHHHHHCCCHHHeEEEECCEECCCC
Confidence 4567899999999999998887765443
No 145
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=22.22 E-value=26 Score=19.92 Aligned_cols=21 Identities=38% Similarity=0.387 Sum_probs=17.5
Q ss_pred HHHHHHhCCCCCcccccccCC
Q psy8538 18 AELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNr 38 (64)
.++|+.+|+|...|..|-+..
T Consensus 4 ~eva~~~gvs~~tlR~Ye~~G 24 (112)
T cd01282 4 GELAARTGVSVRSLRYYEEQG 24 (112)
T ss_pred HHHHHHHCCCHHHHHHHHHCC
Confidence 478999999999999986653
No 146
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=21.66 E-value=32 Score=21.58 Aligned_cols=21 Identities=33% Similarity=0.339 Sum_probs=17.9
Q ss_pred HHHHHHhCCCCCcccccccCC
Q psy8538 18 AELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNr 38 (64)
.++|+.+|++...|..|....
T Consensus 4 ~evA~~lGVS~~TLRrw~k~g 24 (175)
T PRK13182 4 PFVAKKLGVSPKTVQRWVKQL 24 (175)
T ss_pred HHHHHHHCcCHHHHHHHHHcC
Confidence 468999999999999997653
No 147
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=21.64 E-value=9.8 Score=19.70 Aligned_cols=21 Identities=29% Similarity=0.396 Sum_probs=15.6
Q ss_pred HHHHHHHhCCCCCccc-ccccC
Q psy8538 17 KAELANSLGLSERQVR-CPHHQ 37 (64)
Q Consensus 17 r~~La~~l~l~~~qV~-vWFqN 37 (64)
..+||..+|++...|. .|...
T Consensus 15 ~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHHS
T ss_pred HHHHHHHhCcCHHHhhHHHHhC
Confidence 3578999999999999 88753
No 148
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=21.57 E-value=26 Score=20.27 Aligned_cols=17 Identities=29% Similarity=0.456 Sum_probs=14.8
Q ss_pred HHHHHHhCCCCCccccc
Q psy8538 18 AELANSLGLSERQVRCP 34 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vW 34 (64)
.++|+.+|++...|..|
T Consensus 3 ~e~a~~~gvs~~tlR~Y 19 (124)
T TIGR02051 3 GELAKAAGVNVETIRYY 19 (124)
T ss_pred HHHHHHHCcCHHHHHHH
Confidence 46899999999999888
No 149
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=21.46 E-value=65 Score=16.11 Aligned_cols=25 Identities=20% Similarity=0.130 Sum_probs=20.0
Q ss_pred HHHHHHHHHhCCCCCcccccccCCc
Q psy8538 15 RRKAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 15 ~~r~~La~~l~l~~~qV~vWFqNrR 39 (64)
.-+..++..+|++....+.+|..+.
T Consensus 24 ~lK~~i~~~~gi~~~~q~L~~~g~~ 48 (71)
T cd01812 24 DLKKMLAPVTGVEPRDQKLIFKGKE 48 (71)
T ss_pred HHHHHHHHhhCCChHHeEEeeCCcc
Confidence 3456788999999999999987554
No 150
>smart00351 PAX Paired Box domain.
Probab=21.24 E-value=24 Score=20.52 Aligned_cols=21 Identities=14% Similarity=0.098 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCCCcccccccC
Q psy8538 17 KAELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqN 37 (64)
..++|+.+|++...|..|.+.
T Consensus 36 ~~~iA~~~gvs~~tV~kwi~r 56 (125)
T smart00351 36 PCDISRQLCVSHGCVSKILGR 56 (125)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 347899999999999999764
No 151
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=21.11 E-value=28 Score=20.83 Aligned_cols=20 Identities=25% Similarity=0.243 Sum_probs=17.2
Q ss_pred HHHHHHhCCCCCcccccccC
Q psy8538 18 AELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqN 37 (64)
++||..+|++...|.-|..-
T Consensus 4 eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 4 EELAELTGYSRQTINRWVRK 23 (122)
T ss_pred HHHHHHhCccHHHHHHHHHh
Confidence 58999999999999999743
No 152
>PF06505 XylR_N: Activator of aromatic catabolism; InterPro: IPR010523 This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators in several proteobacteria, including activators of phenol degradation such as XylR. It is found adjacent to IPR004096 from INTERPRO.
Probab=21.10 E-value=37 Score=19.48 Aligned_cols=21 Identities=19% Similarity=0.025 Sum_probs=17.4
Q ss_pred HHHHhCCCCCcccccccCCcc
Q psy8538 20 LANSLGLSERQVRCPHHQLTT 40 (64)
Q Consensus 20 La~~l~l~~~qV~vWFqNrR~ 40 (64)
|...+..++.+=.|||.+.|.
T Consensus 2 L~~~L~F~p~~G~Iwl~~~Rm 22 (103)
T PF06505_consen 2 LRELLRFSPEDGRIWLNGQRM 22 (103)
T ss_pred hHHheeEeCCCCeEEECCEEE
Confidence 566778888899999999884
No 153
>KOG3755|consensus
Probab=21.05 E-value=13 Score=28.05 Aligned_cols=19 Identities=5% Similarity=-0.029 Sum_probs=16.6
Q ss_pred CCCcccccccCCcccccch
Q psy8538 27 SERQVRCPHHQLTTVNNNT 45 (64)
Q Consensus 27 ~~~qV~vWFqNrR~~~k~~ 45 (64)
..+.|+.||.|||..+++.
T Consensus 739 ~~kn~~~~fk~~~ee~~~~ 757 (769)
T KOG3755|consen 739 ESKNVQFWFKVRREEEKRL 757 (769)
T ss_pred hhcchHHHHHHHHHHHhhh
Confidence 5678999999999988876
No 154
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=20.95 E-value=47 Score=20.88 Aligned_cols=20 Identities=35% Similarity=0.491 Sum_probs=15.8
Q ss_pred HHHHHHhCCCCCcccccccC
Q psy8538 18 AELANSLGLSERQVRCPHHQ 37 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqN 37 (64)
.++|.+|+++++.|+.--.|
T Consensus 167 keIA~~L~iS~~TVk~h~~~ 186 (211)
T COG2197 167 KEIAEELNLSEKTVKTHVSN 186 (211)
T ss_pred HHHHHHHCCCHhHHHHHHHH
Confidence 35789999999999875544
No 155
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=20.92 E-value=49 Score=20.16 Aligned_cols=19 Identities=32% Similarity=0.363 Sum_probs=16.0
Q ss_pred HHHHHHHHhCCCCCccccc
Q psy8538 16 RKAELANSLGLSERQVRCP 34 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~vW 34 (64)
-+..||..+|+++.+|.|+
T Consensus 169 i~~~la~~~~i~~~~I~V~ 187 (188)
T PF09581_consen 169 IKQYLADFYGISPEQIKVY 187 (188)
T ss_pred HHHHHHHHhCCCHHHeEEe
Confidence 4557999999999999886
No 156
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, 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 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=20.89 E-value=28 Score=19.40 Aligned_cols=22 Identities=18% Similarity=0.149 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCCCcccccccCC
Q psy8538 17 KAELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNr 38 (64)
..++|+.+|++...+..|-+..
T Consensus 4 i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3478999999999999996654
No 157
>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=20.63 E-value=79 Score=19.23 Aligned_cols=29 Identities=10% Similarity=0.019 Sum_probs=19.8
Q ss_pred CCCHHHHHHHHHHhCCCCCcccccccCCc
Q psy8538 11 YITIRRKAELANSLGLSERQVRCPHHQLT 39 (64)
Q Consensus 11 ~p~~~~r~~La~~l~l~~~qV~vWFqNrR 39 (64)
.++..+...|...+.=..-.|..||=||+
T Consensus 51 ~Lt~~qi~~l~~~i~~~~~~iP~w~~Nr~ 79 (144)
T TIGR03629 51 YLDDEEIEKLEEAVENYEYGIPSWLLNRR 79 (144)
T ss_pred cCCHHHHHHHHHHHHhccccCCHHHhhcc
Confidence 36666677777666434455888999976
No 158
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=20.63 E-value=31 Score=20.04 Aligned_cols=21 Identities=29% Similarity=0.254 Sum_probs=17.1
Q ss_pred HHHHHHhCCCCCcccccccCC
Q psy8538 18 AELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNr 38 (64)
.++|+.+|++...|..|-+..
T Consensus 4 ~e~a~~~gvs~~tlRyYe~~G 24 (127)
T cd01108 4 GEAAKLTGLSAKMIRYYEEIG 24 (127)
T ss_pred HHHHHHHCcCHHHHHHHHHCC
Confidence 468999999999999886553
No 159
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. 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=20.60 E-value=29 Score=20.03 Aligned_cols=18 Identities=28% Similarity=0.449 Sum_probs=14.8
Q ss_pred HHHHHHhCCCCCcccccc
Q psy8538 18 AELANSLGLSERQVRCPH 35 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWF 35 (64)
.++|+.+|+|...|..|=
T Consensus 4 geva~~~gvs~~tlRyYe 21 (118)
T cd04776 4 SELAREFDVTPRTLRFYE 21 (118)
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 468899999999888873
No 160
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=20.40 E-value=82 Score=17.82 Aligned_cols=21 Identities=24% Similarity=0.469 Sum_probs=15.7
Q ss_pred CCHHHHHHHHHHhCCCCCccc
Q psy8538 12 ITIRRKAELANSLGLSERQVR 32 (64)
Q Consensus 12 p~~~~r~~La~~l~l~~~qV~ 32 (64)
.+...-.++|+++||++..|.
T Consensus 18 ~~~~~wK~faR~lglse~~Id 38 (97)
T cd08316 18 MTLKDVKKFVRKSGLSEPKID 38 (97)
T ss_pred cCHHHHHHHHHHcCCCHHHHH
Confidence 344555678999999988775
No 161
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=20.35 E-value=29 Score=20.61 Aligned_cols=22 Identities=23% Similarity=0.146 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCCCcccccccCC
Q psy8538 17 KAELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 17 r~~La~~l~l~~~qV~vWFqNr 38 (64)
..++|+.+|++...|..|-...
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~G 25 (140)
T PRK09514 4 IGELAKLAEVTPDTLRFYEKQG 25 (140)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999997653
No 162
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=20.33 E-value=95 Score=15.62 Aligned_cols=27 Identities=19% Similarity=0.122 Sum_probs=21.1
Q ss_pred HHHHHHHHHHhCCCCCcccccccCCcc
Q psy8538 14 IRRKAELANSLGLSERQVRCPHHQLTT 40 (64)
Q Consensus 14 ~~~r~~La~~l~l~~~qV~vWFqNrR~ 40 (64)
..-+..++...|++....+.+|..+.-
T Consensus 24 ~~lK~~i~~~~g~~~~~qrL~~~g~~L 50 (76)
T cd01806 24 ERIKERVEEKEGIPPQQQRLIYSGKQM 50 (76)
T ss_pred HHHHHHHhHhhCCChhhEEEEECCeEc
Confidence 344567889999999999999886643
No 163
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=20.17 E-value=58 Score=16.56 Aligned_cols=18 Identities=28% Similarity=0.390 Sum_probs=13.3
Q ss_pred HHHHHHHHHhCCCCCccc
Q psy8538 15 RRKAELANSLGLSERQVR 32 (64)
Q Consensus 15 ~~r~~La~~l~l~~~qV~ 32 (64)
.+..-+|+++|+|+.+++
T Consensus 21 ~ev~ywa~~~gvt~~~L~ 38 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLR 38 (57)
T ss_pred HHHHHHHHHHCcCHHHHH
Confidence 455678899998887654
No 164
>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=20.05 E-value=55 Score=18.65 Aligned_cols=15 Identities=27% Similarity=0.430 Sum_probs=10.7
Q ss_pred HHHHHHhCCCCCccc
Q psy8538 18 AELANSLGLSERQVR 32 (64)
Q Consensus 18 ~~La~~l~l~~~qV~ 32 (64)
.++|..+|+|+..|+
T Consensus 127 ~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 127 IDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHHHHCcCHHhhc
Confidence 467888888877664
No 165
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. 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. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=20.04 E-value=30 Score=19.26 Aligned_cols=21 Identities=33% Similarity=0.392 Sum_probs=17.2
Q ss_pred HHHHHHhCCCCCcccccccCC
Q psy8538 18 AELANSLGLSERQVRCPHHQL 38 (64)
Q Consensus 18 ~~La~~l~l~~~qV~vWFqNr 38 (64)
.++|+.+|++...|..|-+..
T Consensus 4 ~e~A~~~gvs~~tlR~Ye~~G 24 (99)
T cd04772 4 VDLARAIGLSPQTVRNYESLG 24 (99)
T ss_pred HHHHHHHCcCHHHHHHHHHcC
Confidence 478999999999999886553
No 166
>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=20.02 E-value=25 Score=16.72 Aligned_cols=20 Identities=30% Similarity=0.286 Sum_probs=13.5
Q ss_pred HHHHHHHHhCCCCCcccccc
Q psy8538 16 RKAELANSLGLSERQVRCPH 35 (64)
Q Consensus 16 ~r~~La~~l~l~~~qV~vWF 35 (64)
...++|+.+|++...|..++
T Consensus 23 si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 23 SIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp -HHHHHHHTTS-HHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 35678999999888776543
No 167
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=20.00 E-value=42 Score=18.32 Aligned_cols=16 Identities=38% Similarity=0.557 Sum_probs=13.0
Q ss_pred HHHHHHhCCCCCcccc
Q psy8538 18 AELANSLGLSERQVRC 33 (64)
Q Consensus 18 ~~La~~l~l~~~qV~v 33 (64)
.+||.++|+++..|..
T Consensus 19 k~LAr~Lg~se~dI~~ 34 (84)
T cd08804 19 TELARELDFTEEQIHQ 34 (84)
T ss_pred HHHHHHcCCCHHHHHH
Confidence 5689999999887764
Done!