Query 048824
Match_columns 209
No_of_seqs 164 out of 312
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 13:48:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048824.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048824hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01566 ZF_HD_prot_N ZF-HD h 100.0 1.2E-36 2.7E-41 212.6 2.4 48 23-70 1-53 (53)
2 PF04770 ZF-HD_dimer: ZF-HD pr 100.0 1.7E-36 3.7E-41 217.3 2.9 53 20-72 2-59 (60)
3 TIGR01565 homeo_ZF_HD homeobox 99.9 8.4E-27 1.8E-31 165.9 6.4 58 129-186 1-58 (58)
4 PF00046 Homeobox: Homeobox do 99.5 2.4E-15 5.2E-20 102.1 0.3 57 130-190 1-57 (57)
5 KOG0484 Transcription factor P 99.5 2E-15 4.3E-20 120.6 -1.4 60 127-191 15-75 (125)
6 KOG2251 Homeobox transcription 99.5 3E-14 6.4E-19 124.8 4.7 63 126-192 34-96 (228)
7 KOG3802 Transcription factor O 99.5 1.4E-13 3E-18 128.5 8.3 69 126-198 291-359 (398)
8 KOG0843 Transcription factor E 99.4 3.1E-14 6.8E-19 122.0 2.6 63 128-194 101-163 (197)
9 KOG0494 Transcription factor C 99.4 8.2E-14 1.8E-18 125.5 4.1 61 128-192 140-200 (332)
10 KOG4577 Transcription factor L 99.4 6.8E-14 1.5E-18 127.6 2.5 63 126-192 164-226 (383)
11 KOG0493 Transcription factor E 99.4 1.3E-13 2.9E-18 124.3 2.5 59 130-193 247-306 (342)
12 smart00389 HOX Homeodomain. DN 99.3 1.4E-12 3E-17 87.5 3.2 56 130-189 1-56 (56)
13 cd00086 homeodomain Homeodomai 99.3 2E-12 4.4E-17 86.8 2.4 58 130-191 1-58 (59)
14 KOG0485 Transcription factor N 99.3 1.8E-12 4E-17 114.4 2.2 64 125-192 100-163 (268)
15 KOG0488 Transcription factor B 99.2 2.5E-12 5.5E-17 116.4 1.7 62 127-192 170-231 (309)
16 KOG0489 Transcription factor z 99.2 3.2E-12 7E-17 112.5 1.6 66 127-196 157-222 (261)
17 KOG0844 Transcription factor E 99.2 4.5E-12 9.8E-17 116.5 1.2 60 129-193 181-241 (408)
18 KOG0842 Transcription factor t 99.2 3.4E-11 7.4E-16 109.6 5.5 65 126-195 150-215 (307)
19 KOG0492 Transcription factor M 99.1 3.2E-11 6.9E-16 105.9 3.1 58 130-192 145-203 (246)
20 KOG0490 Transcription factor, 99.1 5.1E-11 1.1E-15 98.5 3.9 63 126-192 57-119 (235)
21 KOG0850 Transcription factor D 99.0 6.5E-11 1.4E-15 104.7 2.1 60 128-191 121-180 (245)
22 KOG1168 Transcription factor A 99.0 7.8E-11 1.7E-15 107.8 2.5 63 126-193 306-369 (385)
23 KOG0486 Transcription factor P 99.0 1.2E-10 2.6E-15 106.9 2.1 61 128-192 111-171 (351)
24 COG5576 Homeodomain-containing 98.9 1.1E-09 2.3E-14 91.2 3.0 65 126-194 48-112 (156)
25 KOG0849 Transcription factor P 98.8 2E-09 4.4E-14 98.9 3.3 61 128-192 175-235 (354)
26 KOG0848 Transcription factor C 98.7 1.5E-09 3.2E-14 98.3 -0.2 60 129-192 199-258 (317)
27 KOG0487 Transcription factor A 98.7 7.9E-09 1.7E-13 94.4 4.1 60 129-193 235-295 (308)
28 KOG0483 Transcription factor H 98.7 5.9E-09 1.3E-13 90.0 1.8 58 131-192 52-109 (198)
29 KOG0847 Transcription factor, 98.5 2E-08 4.4E-13 89.4 0.3 62 127-192 165-226 (288)
30 KOG0491 Transcription factor B 98.5 8.6E-09 1.9E-13 88.1 -2.8 61 128-192 99-159 (194)
31 KOG1146 Homeobox protein [Gene 98.3 7.3E-07 1.6E-11 93.4 4.6 61 128-192 902-962 (1406)
32 KOG0490 Transcription factor, 98.2 6.8E-07 1.5E-11 74.0 2.2 64 126-193 150-213 (235)
33 KOG2252 CCAAT displacement pro 98.1 1.9E-06 4E-11 84.0 4.0 56 128-187 419-474 (558)
34 PF05920 Homeobox_KN: Homeobox 96.8 0.0002 4.4E-09 47.5 -1.2 34 154-187 7-40 (40)
35 KOG0774 Transcription factor P 96.4 0.0033 7.1E-08 57.8 3.7 62 130-192 189-250 (334)
36 KOG0775 Transcription factor S 96.0 0.0078 1.7E-07 55.3 4.1 56 132-191 170-234 (304)
37 PF04218 CENP-B_N: CENP-B N-te 95.9 0.0062 1.4E-07 42.1 2.3 47 130-185 1-47 (53)
38 PF01527 HTH_Tnp_1: Transposas 95.6 0.007 1.5E-07 42.5 1.6 47 131-185 2-48 (76)
39 KOG0773 Transcription factor M 94.7 0.035 7.7E-07 50.0 4.0 63 127-191 237-300 (342)
40 KOG3623 Homeobox transcription 93.7 0.043 9.3E-07 56.4 2.5 54 134-192 562-615 (1007)
41 cd00569 HTH_Hin_like Helix-tur 90.9 0.22 4.9E-06 27.7 2.2 40 133-181 3-42 (42)
42 cd06171 Sigma70_r4 Sigma70, re 90.2 0.055 1.2E-06 33.8 -0.9 45 135-188 10-54 (55)
43 PF04967 HTH_10: HTH DNA bindi 89.6 0.27 5.9E-06 34.6 2.2 41 136-178 1-41 (53)
44 PF02796 HTH_7: Helix-turn-hel 87.5 0.094 2E-06 34.7 -1.3 41 133-182 3-43 (45)
45 PF08281 Sigma70_r4_2: Sigma-7 85.2 0.17 3.7E-06 33.7 -1.0 44 135-187 10-53 (54)
46 PRK09413 IS2 repressor TnpA; R 84.7 0.62 1.3E-05 36.5 1.9 43 133-183 10-52 (121)
47 PF11569 Homez: Homeodomain le 84.7 0.29 6.4E-06 35.2 0.0 40 143-186 12-51 (56)
48 PF13936 HTH_38: Helix-turn-he 84.6 0.18 4E-06 33.4 -1.0 42 133-183 2-43 (44)
49 COG2963 Transposase and inacti 84.2 0.9 2E-05 34.7 2.6 49 133-189 5-54 (116)
50 PRK09646 RNA polymerase sigma 81.8 0.18 4E-06 41.2 -2.2 50 135-193 142-191 (194)
51 smart00421 HTH_LUXR helix_turn 80.6 0.45 9.7E-06 30.3 -0.3 45 135-189 3-47 (58)
52 PRK06759 RNA polymerase factor 80.4 0.3 6.4E-06 37.9 -1.4 48 135-191 106-153 (154)
53 TIGR02989 Sig-70_gvs1 RNA poly 79.7 0.4 8.7E-06 37.2 -0.9 47 134-190 110-157 (159)
54 PF06163 DUF977: Bacterial pro 78.8 0.82 1.8E-05 37.8 0.6 44 135-182 4-48 (127)
55 PF13443 HTH_26: Cro/C1-type H 78.5 0.91 2E-05 30.8 0.7 24 162-185 12-35 (63)
56 PF13384 HTH_23: Homeodomain-l 78.4 0.83 1.8E-05 29.8 0.5 23 162-184 19-41 (50)
57 PRK12533 RNA polymerase sigma 78.4 0.23 5E-06 42.4 -2.8 40 160-199 150-189 (216)
58 PF00196 GerE: Bacterial regul 78.4 0.39 8.4E-06 32.7 -1.2 45 135-189 3-47 (58)
59 PF04545 Sigma70_r4: Sigma-70, 76.0 0.28 6E-06 32.5 -2.4 45 135-188 4-48 (50)
60 PRK12537 RNA polymerase sigma 75.6 0.64 1.4E-05 37.6 -0.9 30 162-191 151-180 (182)
61 PRK06424 transcription factor; 75.4 1.8 4E-05 35.8 1.8 56 129-186 68-123 (144)
62 PRK09652 RNA polymerase sigma 75.4 0.33 7.2E-06 37.9 -2.5 48 135-191 128-175 (182)
63 TIGR02939 RpoE_Sigma70 RNA pol 75.3 0.32 6.8E-06 38.9 -2.7 33 160-192 154-186 (190)
64 TIGR02983 SigE-fam_strep RNA p 75.1 0.35 7.6E-06 37.9 -2.4 33 162-194 128-160 (162)
65 PRK03975 tfx putative transcri 73.6 0.64 1.4E-05 38.5 -1.3 47 134-190 5-51 (141)
66 PRK10403 transcriptional regul 73.6 1.1 2.3E-05 34.6 0.0 48 134-191 152-199 (215)
67 PF13022 HTH_Tnp_1_2: Helix-tu 73.5 1.3 2.9E-05 37.2 0.5 54 131-185 6-59 (142)
68 PRK04217 hypothetical protein; 73.5 0.45 9.8E-06 37.9 -2.2 49 135-192 42-90 (110)
69 PRK12526 RNA polymerase sigma 73.5 0.35 7.6E-06 40.2 -2.9 49 135-192 153-201 (206)
70 PRK12512 RNA polymerase sigma 73.2 0.4 8.7E-06 38.5 -2.6 49 135-192 131-179 (184)
71 PRK09644 RNA polymerase sigma 73.1 0.4 8.7E-06 37.9 -2.5 49 134-192 107-156 (165)
72 PRK12541 RNA polymerase sigma 72.3 0.5 1.1E-05 37.2 -2.2 49 135-192 112-160 (161)
73 KOG3755 SATB1 matrix attachmen 72.1 1.8 3.9E-05 44.1 1.1 61 128-191 646-709 (769)
74 PRK12539 RNA polymerase sigma 72.0 0.48 1E-05 38.3 -2.4 51 134-193 130-180 (184)
75 PRK09648 RNA polymerase sigma 71.9 0.45 9.7E-06 38.5 -2.6 51 131-191 135-186 (189)
76 PRK00118 putative DNA-binding 71.1 0.47 1E-05 37.5 -2.5 47 135-190 17-63 (104)
77 TIGR02985 Sig70_bacteroi1 RNA 71.0 0.82 1.8E-05 34.9 -1.2 46 135-190 113-159 (161)
78 PRK12530 RNA polymerase sigma 70.9 0.46 1E-05 38.9 -2.7 47 135-190 134-180 (189)
79 PRK02220 4-oxalocrotonate taut 70.5 8.8 0.00019 25.9 4.0 34 137-184 13-46 (61)
80 TIGR03070 couple_hipB transcri 70.3 2.2 4.7E-05 27.6 0.9 35 143-185 6-40 (58)
81 PRK12514 RNA polymerase sigma 70.2 0.56 1.2E-05 37.5 -2.4 30 162-191 147-176 (179)
82 COG3413 Predicted DNA binding 69.6 3.5 7.5E-05 35.0 2.2 42 135-178 155-196 (215)
83 TIGR02960 SigX5 RNA polymerase 69.2 0.92 2E-05 39.8 -1.4 35 161-195 159-193 (324)
84 PRK10072 putative transcriptio 68.9 2.4 5.1E-05 33.0 1.0 35 144-186 38-72 (96)
85 PRK05602 RNA polymerase sigma 68.0 0.84 1.8E-05 36.8 -1.8 47 136-192 129-176 (186)
86 TIGR02937 sigma70-ECF RNA poly 68.0 0.81 1.8E-05 33.7 -1.7 47 135-190 110-156 (158)
87 PRK12519 RNA polymerase sigma 67.9 0.61 1.3E-05 37.8 -2.6 32 159-190 156-187 (194)
88 TIGR00270 conserved hypothetic 67.5 1.2 2.7E-05 37.0 -0.9 24 162-185 84-107 (154)
89 PF13551 HTH_29: Winged helix- 67.3 4.9 0.00011 29.4 2.3 54 129-182 51-109 (112)
90 PRK11924 RNA polymerase sigma 67.1 0.66 1.4E-05 36.1 -2.5 32 160-191 141-172 (179)
91 PRK12547 RNA polymerase sigma 67.0 0.64 1.4E-05 36.9 -2.6 48 135-191 112-159 (164)
92 KOG3623 Homeobox transcription 66.8 5.8 0.00013 41.5 3.4 67 126-197 623-690 (1007)
93 PRK09480 slmA division inhibit 66.6 3.9 8.4E-05 32.4 1.8 47 138-185 9-55 (194)
94 PRK09642 RNA polymerase sigma 66.3 0.69 1.5E-05 36.2 -2.5 47 135-191 106-153 (160)
95 PRK09639 RNA polymerase sigma 66.1 0.78 1.7E-05 35.9 -2.3 48 134-191 111-158 (166)
96 PRK06811 RNA polymerase factor 65.9 0.87 1.9E-05 37.1 -2.1 49 134-192 130-179 (189)
97 TIGR02948 SigW_bacill RNA poly 65.9 0.71 1.5E-05 36.8 -2.5 46 135-190 136-182 (187)
98 TIGR02607 antidote_HigA addict 65.8 2.9 6.3E-05 29.3 0.8 21 164-184 22-42 (78)
99 cd06170 LuxR_C_like C-terminal 65.7 2 4.3E-05 27.5 0.0 44 136-189 1-44 (57)
100 cd04762 HTH_MerR-trunc Helix-T 65.5 2 4.2E-05 26.7 -0.1 24 163-186 3-26 (49)
101 PRK09726 antitoxin HipB; Provi 65.2 4.8 0.0001 29.7 1.9 21 163-183 28-48 (88)
102 TIGR02999 Sig-70_X6 RNA polyme 65.1 0.8 1.7E-05 36.5 -2.4 47 136-191 135-181 (183)
103 PRK12513 RNA polymerase sigma 64.8 0.46 1E-05 38.6 -3.9 35 158-192 153-187 (194)
104 TIGR02959 SigZ RNA polymerase 64.6 0.8 1.7E-05 36.8 -2.5 50 134-192 99-148 (170)
105 PF01381 HTH_3: Helix-turn-hel 64.6 3.3 7.1E-05 27.2 0.9 24 162-185 11-34 (55)
106 PRK09390 fixJ response regulat 64.5 1.7 3.8E-05 32.9 -0.5 46 136-191 142-187 (202)
107 PRK12536 RNA polymerase sigma 64.3 0.75 1.6E-05 37.1 -2.7 34 158-191 143-176 (181)
108 PRK15369 two component system 64.3 2 4.2E-05 32.7 -0.3 47 134-190 148-194 (211)
109 PRK12520 RNA polymerase sigma 63.7 0.88 1.9E-05 36.9 -2.4 49 135-192 131-179 (191)
110 TIGR02950 SigM_subfam RNA poly 63.6 1.3 2.9E-05 34.1 -1.3 34 157-190 118-151 (154)
111 PRK09645 RNA polymerase sigma 63.5 1.4 3.1E-05 34.9 -1.2 48 135-192 118-166 (173)
112 PRK09649 RNA polymerase sigma 63.5 0.93 2E-05 37.0 -2.3 31 161-191 147-177 (185)
113 PRK15008 HTH-type transcriptio 63.1 4.2 9.1E-05 33.6 1.4 48 138-186 17-64 (212)
114 PRK12546 RNA polymerase sigma 63.0 0.91 2E-05 37.6 -2.5 32 161-192 130-161 (188)
115 PRK12516 RNA polymerase sigma 62.9 0.96 2.1E-05 37.2 -2.4 33 161-193 133-165 (187)
116 PRK13919 putative RNA polymera 62.6 0.96 2.1E-05 36.3 -2.4 50 134-192 134-183 (186)
117 PF13518 HTH_28: Helix-turn-he 62.6 1.8 3.9E-05 28.0 -0.6 25 162-186 14-38 (52)
118 PRK09047 RNA polymerase factor 62.5 0.83 1.8E-05 35.5 -2.7 48 134-191 105-153 (161)
119 PRK12522 RNA polymerase sigma 62.1 1 2.2E-05 35.9 -2.3 32 160-191 135-166 (173)
120 PRK12524 RNA polymerase sigma 61.9 1 2.2E-05 36.9 -2.4 50 134-193 135-185 (196)
121 PRK12515 RNA polymerase sigma 60.9 1.6 3.5E-05 35.4 -1.4 50 133-192 129-179 (189)
122 PRK12545 RNA polymerase sigma 60.8 1.1 2.4E-05 37.1 -2.3 32 161-192 156-187 (201)
123 PF12651 RHH_3: Ribbon-helix-h 60.8 7.2 0.00016 26.1 2.0 38 129-166 2-39 (44)
124 PRK12535 RNA polymerase sigma 60.7 1.7 3.6E-05 36.2 -1.4 35 161-195 150-184 (196)
125 PRK12543 RNA polymerase sigma 60.0 1.1 2.5E-05 36.0 -2.4 29 162-190 135-163 (179)
126 PF13698 DUF4156: Domain of un 59.8 4.1 8.8E-05 31.2 0.7 16 27-42 53-68 (93)
127 PRK09975 DNA-binding transcrip 59.6 3.7 8.1E-05 33.3 0.5 45 141-186 13-57 (213)
128 PRK12529 RNA polymerase sigma 59.5 1.3 2.7E-05 35.9 -2.2 47 135-191 127-174 (178)
129 PF12844 HTH_19: Helix-turn-he 59.2 4.8 0.0001 27.3 0.9 23 163-185 15-37 (64)
130 cd00491 4Oxalocrotonate_Tautom 59.2 24 0.00052 23.3 4.4 35 137-185 12-46 (58)
131 PHA01976 helix-turn-helix prot 59.1 4.8 0.0001 27.5 1.0 18 158-175 42-59 (67)
132 TIGR02954 Sig70_famx3 RNA poly 58.2 2.2 4.7E-05 33.8 -1.0 47 135-191 119-166 (169)
133 PRK09637 RNA polymerase sigma 58.0 1.4 3E-05 36.1 -2.3 49 135-192 106-154 (181)
134 TIGR01764 excise DNA binding d 57.5 2.7 5.9E-05 26.3 -0.5 24 162-185 3-26 (49)
135 PRK12532 RNA polymerase sigma 57.4 1.2 2.6E-05 36.3 -2.7 31 162-192 154-184 (195)
136 PRK09641 RNA polymerase sigma 57.3 1.2 2.5E-05 35.5 -2.7 32 160-191 152-183 (187)
137 PRK08295 RNA polymerase factor 57.0 2 4.2E-05 35.0 -1.5 48 134-191 154-201 (208)
138 cd04761 HTH_MerR-SF Helix-Turn 57.0 2.6 5.6E-05 26.9 -0.7 24 163-186 3-26 (49)
139 TIGR03879 near_KaiC_dom probab 56.8 3.1 6.8E-05 31.2 -0.3 28 159-186 31-58 (73)
140 TIGR00721 tfx DNA-binding prot 56.7 2.4 5.2E-05 35.0 -1.0 48 133-190 4-51 (137)
141 PRK02289 4-oxalocrotonate taut 56.7 28 0.0006 23.9 4.5 33 137-183 13-45 (60)
142 TIGR02952 Sig70_famx2 RNA poly 56.6 1.6 3.4E-05 34.1 -2.1 47 135-190 122-168 (170)
143 PRK12531 RNA polymerase sigma 56.4 1.3 2.9E-05 36.2 -2.6 48 135-192 141-189 (194)
144 PRK07037 extracytoplasmic-func 56.2 1.3 2.8E-05 34.7 -2.6 47 135-191 109-156 (163)
145 PRK12511 RNA polymerase sigma 56.2 1.4 3E-05 36.2 -2.5 48 135-191 111-158 (182)
146 TIGR03541 reg_near_HchA LuxR f 56.1 3.7 8E-05 35.2 -0.0 49 133-191 169-217 (232)
147 PRK09651 RNA polymerase sigma 55.9 1.7 3.6E-05 34.9 -2.1 47 133-188 117-163 (172)
148 PRK10651 transcriptional regul 55.4 3.5 7.5E-05 31.9 -0.3 46 135-190 155-200 (216)
149 cd00093 HTH_XRE Helix-turn-hel 55.3 5.7 0.00012 23.9 0.7 21 164-184 16-36 (58)
150 PRK08301 sporulation sigma fac 55.2 2.1 4.5E-05 36.2 -1.7 52 135-191 178-229 (234)
151 PF13411 MerR_1: MerR HTH fami 54.9 2.9 6.3E-05 28.7 -0.7 22 163-184 3-24 (69)
152 PF06056 Terminase_5: Putative 54.8 5.2 0.00011 28.3 0.5 21 162-182 15-35 (58)
153 PRK06930 positive control sigm 54.7 2.3 4.9E-05 35.7 -1.5 47 135-191 114-161 (170)
154 TIGR02479 FliA_WhiG RNA polyme 54.6 1.9 4.1E-05 36.2 -2.0 49 134-191 174-222 (224)
155 KOG1146 Homeobox protein [Gene 54.2 9.9 0.00021 41.7 2.7 61 126-192 702-764 (1406)
156 TIGR00013 taut 4-oxalocrotonat 54.0 32 0.0007 23.2 4.4 34 137-184 13-46 (63)
157 PRK12523 RNA polymerase sigma 53.9 1.8 3.9E-05 34.6 -2.2 48 134-190 118-165 (172)
158 PRK12544 RNA polymerase sigma 53.2 2.7 5.8E-05 35.4 -1.3 30 162-191 166-195 (206)
159 PRK10360 DNA-binding transcrip 53.2 4.5 9.8E-05 31.3 0.0 47 134-190 136-182 (196)
160 PRK12527 RNA polymerase sigma 53.1 1.2 2.6E-05 35.0 -3.3 49 136-193 106-154 (159)
161 PRK09636 RNA polymerase sigma 52.9 2.7 5.9E-05 36.9 -1.4 50 135-193 115-164 (293)
162 PRK06986 fliA flagellar biosyn 52.9 2.1 4.6E-05 36.3 -2.0 34 159-192 199-232 (236)
163 PRK11923 algU RNA polymerase s 52.8 1.7 3.6E-05 35.2 -2.6 32 160-191 154-185 (193)
164 PRK12528 RNA polymerase sigma 52.8 1.9 4.1E-05 33.9 -2.2 45 134-188 112-157 (161)
165 PRK01964 4-oxalocrotonate taut 52.5 29 0.00064 23.8 4.1 35 137-185 13-47 (64)
166 TIGR02943 Sig70_famx1 RNA poly 52.3 1.7 3.6E-05 35.7 -2.7 48 135-191 131-178 (188)
167 PRK12540 RNA polymerase sigma 52.3 1.7 3.7E-05 35.6 -2.6 33 161-193 128-160 (182)
168 PHA00542 putative Cro-like pro 52.2 11 0.00025 27.7 2.1 45 130-185 12-56 (82)
169 PRK09935 transcriptional regul 52.2 4.4 9.6E-05 31.4 -0.2 46 135-190 149-194 (210)
170 PF12728 HTH_17: Helix-turn-he 51.6 3.8 8.2E-05 26.9 -0.5 25 162-186 3-27 (51)
171 PRK10668 DNA-binding transcrip 51.4 6.4 0.00014 32.1 0.6 48 138-186 10-57 (215)
172 PRK09647 RNA polymerase sigma 51.3 2.9 6.3E-05 35.1 -1.4 31 162-192 156-186 (203)
173 PF01361 Tautomerase: Tautomer 51.3 32 0.0007 23.1 4.1 34 137-184 12-45 (60)
174 PRK12538 RNA polymerase sigma 51.3 1.6 3.4E-05 37.7 -3.1 33 160-192 187-219 (233)
175 PRK12525 RNA polymerase sigma 51.2 2 4.2E-05 34.3 -2.4 47 134-189 117-163 (168)
176 PTZ00397 macrophage migration 51.0 34 0.00075 26.2 4.6 36 137-186 70-105 (116)
177 PRK12542 RNA polymerase sigma 50.9 1.8 3.8E-05 35.0 -2.7 49 134-192 121-170 (185)
178 PF10668 Phage_terminase: Phag 50.4 4.4 9.6E-05 29.4 -0.4 24 159-182 21-44 (60)
179 PRK10100 DNA-binding transcrip 50.4 5.6 0.00012 34.0 0.2 47 134-190 154-200 (216)
180 PF13309 HTH_22: HTH domain 50.2 18 0.00038 25.8 2.7 42 133-177 18-59 (64)
181 TIGR03020 EpsA transcriptional 50.1 5.3 0.00011 35.5 -0.0 49 133-191 188-236 (247)
182 PF12824 MRP-L20: Mitochondria 50.0 29 0.00062 29.5 4.4 41 132-178 82-122 (164)
183 PHA02535 P terminase ATPase su 49.6 12 0.00025 37.8 2.2 46 134-190 1-46 (581)
184 PRK11891 aspartate carbamoyltr 49.1 12 0.00025 36.3 2.1 43 137-187 1-43 (429)
185 PRK09640 RNA polymerase sigma 49.1 0.81 1.8E-05 37.2 -4.9 53 139-191 123-181 (188)
186 PRK00745 4-oxalocrotonate taut 49.1 35 0.00075 23.0 3.9 34 137-184 13-46 (62)
187 TIGR02984 Sig-70_plancto1 RNA 49.0 2.4 5.2E-05 33.7 -2.2 47 135-190 140-186 (189)
188 TIGR02947 SigH_actino RNA poly 48.8 1.4 3.1E-05 35.8 -3.6 38 155-192 142-179 (193)
189 PRK08241 RNA polymerase factor 48.0 5 0.00011 35.7 -0.5 31 161-191 170-200 (339)
190 PRK05657 RNA polymerase sigma 47.7 4.1 8.8E-05 37.2 -1.1 53 135-192 262-314 (325)
191 PRK08359 transcription factor; 47.6 8.8 0.00019 33.0 0.9 24 162-185 100-123 (176)
192 TIGR02957 SigX4 RNA polymerase 47.5 4.3 9.2E-05 35.7 -1.0 32 162-193 126-157 (281)
193 PF13565 HTH_32: Homeodomain-l 47.2 20 0.00043 25.0 2.6 39 129-173 26-65 (77)
194 PRK13558 bacterio-opsin activa 46.6 14 0.0003 35.6 2.1 43 133-177 605-647 (665)
195 TIGR02859 spore_sigH RNA polym 46.3 4.4 9.5E-05 32.6 -1.0 31 161-191 166-196 (198)
196 PF04297 UPF0122: Putative hel 46.1 10 0.00022 30.0 1.0 41 135-184 17-57 (101)
197 PF02954 HTH_8: Bacterial regu 45.4 21 0.00046 23.1 2.3 32 140-179 6-37 (42)
198 PRK06704 RNA polymerase factor 45.4 3.6 7.8E-05 35.9 -1.8 31 162-192 134-164 (228)
199 PF08279 HTH_11: HTH domain; 45.4 7.4 0.00016 25.7 0.1 19 161-179 16-34 (55)
200 PRK05803 sporulation sigma fac 45.2 3.8 8.3E-05 34.8 -1.6 51 135-190 175-225 (233)
201 PRK09415 RNA polymerase factor 44.8 2.3 4.9E-05 34.4 -2.9 47 134-190 126-173 (179)
202 PRK07670 RNA polymerase sigma 44.7 3.6 7.8E-05 35.4 -1.9 47 135-190 201-247 (251)
203 smart00351 PAX Paired Box doma 44.6 12 0.00026 29.6 1.3 42 136-186 18-59 (125)
204 PF00249 Myb_DNA-binding: Myb- 44.5 35 0.00076 22.3 3.3 35 133-174 1-35 (48)
205 PRK11511 DNA-binding transcrip 44.3 10 0.00022 29.7 0.7 42 138-184 8-49 (127)
206 PF04936 DUF658: Protein of un 44.0 6.6 0.00014 34.2 -0.4 35 158-192 12-46 (186)
207 TIGR02366 DHAK_reg probable di 43.9 12 0.00027 29.5 1.2 27 157-183 20-46 (176)
208 TIGR02846 spore_sigmaK RNA pol 43.6 4 8.6E-05 34.6 -1.8 53 134-191 173-225 (227)
209 PRK09706 transcriptional repre 43.6 11 0.00024 29.6 0.9 18 158-175 45-62 (135)
210 PRK12534 RNA polymerase sigma 43.4 3.5 7.7E-05 33.1 -2.0 48 134-190 136-183 (187)
211 PRK01271 4-oxalocrotonate taut 43.1 58 0.0013 24.3 4.6 34 136-183 13-46 (76)
212 PRK11552 putative DNA-binding 42.8 14 0.00031 31.2 1.5 29 158-187 31-59 (225)
213 TIGR02980 SigBFG RNA polymeras 42.8 3.4 7.4E-05 34.6 -2.3 48 134-190 177-224 (227)
214 cd01104 HTH_MlrA-CarA Helix-Tu 42.7 6.2 0.00013 26.9 -0.6 21 163-183 3-23 (68)
215 PF09607 BrkDBD: Brinker DNA-b 42.2 13 0.00028 27.0 1.0 46 133-183 3-48 (58)
216 PHA02893 hypothetical protein; 41.9 8.5 0.00018 30.1 -0.0 10 52-61 68-77 (88)
217 TIGR03001 Sig-70_gmx1 RNA poly 41.7 3.1 6.6E-05 36.3 -2.8 32 161-192 178-209 (244)
218 PRK08583 RNA polymerase sigma 41.4 3.7 8E-05 35.3 -2.3 48 135-191 205-252 (257)
219 PF03227 GILT: Gamma interfero 41.2 4.6 9.9E-05 31.1 -1.6 55 1-57 35-102 (108)
220 COG3040 Blc Bacterial lipocali 41.1 27 0.00058 30.4 2.9 26 132-157 139-165 (174)
221 smart00109 C1 Protein kinase C 41.0 16 0.00034 23.0 1.2 28 38-67 12-39 (49)
222 TIGR03613 RutR pyrimidine util 41.0 9.6 0.00021 30.7 0.2 47 138-185 7-53 (202)
223 COG2197 CitB Response regulato 41.0 12 0.00025 31.9 0.7 46 134-189 147-192 (211)
224 PF13551 HTH_29: Winged helix- 40.7 5.9 0.00013 28.9 -1.0 25 162-186 14-38 (112)
225 PF00376 MerR: MerR family reg 40.5 6.3 0.00014 25.6 -0.8 21 163-183 2-22 (38)
226 PF14552 Tautomerase_2: Tautom 40.4 46 0.001 24.9 3.8 32 137-182 41-72 (82)
227 PRK09638 RNA polymerase sigma 40.2 2.1 4.5E-05 34.0 -3.8 33 159-191 141-173 (176)
228 PRK00432 30S ribosomal protein 39.8 14 0.0003 25.6 0.8 19 43-61 26-45 (50)
229 PF02042 RWP-RK: RWP-RK domain 39.8 51 0.0011 23.2 3.7 35 135-174 4-43 (52)
230 cd04763 HTH_MlrA-like Helix-Tu 39.3 7.6 0.00017 26.9 -0.6 21 163-183 3-23 (68)
231 COG1476 Predicted transcriptio 38.5 20 0.00044 26.6 1.5 30 143-180 5-34 (68)
232 COG4802 FtrB Ferredoxin-thiore 38.5 31 0.00068 28.0 2.7 55 137-192 2-60 (110)
233 TIGR02941 Sigma_B RNA polymera 38.4 5.2 0.00011 34.4 -1.9 48 135-191 205-252 (255)
234 TIGR02394 rpoS_proteo RNA poly 38.3 8 0.00017 34.0 -0.7 53 134-191 221-273 (285)
235 PRK09643 RNA polymerase sigma 38.2 3.9 8.5E-05 33.5 -2.6 31 162-192 152-182 (192)
236 PRK11922 RNA polymerase sigma 38.1 2.7 5.8E-05 35.7 -3.6 35 158-192 163-197 (231)
237 PRK09483 response regulator; P 37.9 9.2 0.0002 30.1 -0.4 47 133-189 146-192 (217)
238 PF12802 MarR_2: MarR family; 37.6 16 0.00035 24.2 0.8 36 136-177 3-38 (62)
239 smart00529 HTH_DTXR Helix-turn 37.5 66 0.0014 23.1 4.1 31 135-171 66-96 (96)
240 PRK13890 conjugal transfer pro 37.4 16 0.00035 28.9 0.9 21 157-177 44-64 (120)
241 PRK14996 TetR family transcrip 37.1 22 0.00047 28.6 1.6 29 158-186 26-54 (192)
242 PF00440 TetR_N: Bacterial reg 36.9 9.1 0.0002 25.0 -0.5 35 145-184 6-40 (47)
243 COG1309 AcrR Transcriptional r 36.6 31 0.00066 25.1 2.2 28 158-185 30-57 (201)
244 PF12123 Amidase02_C: N-acetyl 36.4 35 0.00077 23.5 2.4 19 136-154 24-42 (45)
245 PF01726 LexA_DNA_bind: LexA D 36.4 73 0.0016 22.8 4.1 37 135-177 3-43 (65)
246 cd00029 C1 Protein kinase C co 36.3 14 0.00031 23.5 0.4 29 38-68 12-41 (50)
247 PF03374 ANT: Phage antirepres 36.0 18 0.00039 27.3 1.0 42 146-190 13-54 (111)
248 cd01392 HTH_LacI Helix-turn-he 35.8 7.1 0.00015 25.3 -1.1 21 165-185 2-22 (52)
249 PRK12518 RNA polymerase sigma 35.2 4.9 0.00011 31.8 -2.4 36 157-192 133-168 (175)
250 PF09894 DUF2121: Uncharacteri 35.1 35 0.00076 30.1 2.7 45 137-190 27-71 (194)
251 PRK10336 DNA-binding transcrip 34.9 19 0.00042 28.1 1.0 51 134-190 148-203 (219)
252 PF05077 DUF678: Protein of un 34.7 16 0.00034 27.9 0.5 10 52-61 56-65 (74)
253 PRK10188 DNA-binding transcrip 34.6 14 0.00031 32.0 0.3 49 132-190 176-224 (240)
254 PF05572 Peptidase_M43: Pregna 34.0 30 0.00064 28.5 2.0 18 132-149 137-154 (154)
255 PF01710 HTH_Tnp_IS630: Transp 33.4 33 0.00073 26.7 2.1 41 136-186 3-43 (119)
256 PRK10430 DNA-binding transcrip 32.8 26 0.00056 29.2 1.5 48 132-184 155-202 (239)
257 cd02259 Peptidase_C39_like Pep 32.6 84 0.0018 22.8 4.1 44 130-179 17-60 (122)
258 PRK15479 transcriptional regul 32.5 23 0.0005 27.6 1.1 50 135-190 148-202 (221)
259 cd02425 Peptidase_C39F A sub-f 32.3 97 0.0021 22.8 4.4 44 130-179 22-65 (126)
260 PF06252 DUF1018: Protein of u 31.5 43 0.00094 26.1 2.5 25 132-156 18-42 (119)
261 TIGR02835 spore_sigmaE RNA pol 31.4 8.6 0.00019 32.7 -1.6 53 134-191 177-229 (234)
262 PRK04140 hypothetical protein; 31.4 22 0.00049 33.0 1.0 22 163-184 142-163 (317)
263 PRK10856 cytoskeletal protein 30.9 25 0.00053 32.6 1.1 36 142-185 17-52 (331)
264 KOG2767 Translation initiation 30.9 16 0.00034 35.3 -0.1 14 53-66 118-131 (400)
265 COG0289 DapB Dihydrodipicolina 30.8 41 0.00089 30.9 2.5 19 134-152 101-119 (266)
266 cd04764 HTH_MlrA-like_sg1 Heli 30.4 13 0.00028 25.6 -0.6 21 163-183 3-23 (67)
267 PRK11083 DNA-binding response 30.2 20 0.00044 28.1 0.4 52 134-191 153-209 (228)
268 PRK09943 DNA-binding transcrip 30.2 25 0.00054 28.9 1.0 47 129-177 14-66 (185)
269 smart00422 HTH_MERR helix_turn 30.0 13 0.00029 25.2 -0.6 20 163-182 3-22 (70)
270 PF13189 Cytidylate_kin2: Cyti 29.8 20 0.00044 29.4 0.4 40 144-185 16-55 (179)
271 PRK12517 RNA polymerase sigma 29.7 6.1 0.00013 32.5 -2.7 31 162-192 146-176 (188)
272 PF08914 Myb_DNA-bind_2: Rap1 29.6 48 0.001 24.1 2.2 47 133-180 2-49 (65)
273 PRK06288 RNA polymerase sigma 29.4 6.8 0.00015 34.1 -2.6 48 135-191 212-259 (268)
274 cd08353 Glo_EDI_BRP_like_7 Thi 29.3 80 0.0017 23.7 3.5 44 139-182 12-55 (142)
275 COG1813 Predicted transcriptio 29.2 23 0.00051 30.4 0.6 45 128-182 63-114 (165)
276 PF10410 DnaB_bind: DnaB-helic 29.0 1.3E+02 0.0028 19.9 4.2 38 137-177 17-59 (59)
277 PF13720 Acetyltransf_11: Udp 29.0 66 0.0014 24.0 3.0 41 133-174 25-65 (83)
278 PF13011 LZ_Tnp_IS481: leucine 28.9 39 0.00084 26.1 1.7 44 135-186 8-51 (85)
279 PF07750 GcrA: GcrA cell cycle 28.8 58 0.0013 27.4 2.9 35 136-179 3-38 (162)
280 TIGR02885 spore_sigF RNA polym 28.7 7.9 0.00017 32.6 -2.3 48 134-190 182-229 (231)
281 PF13730 HTH_36: Helix-turn-he 28.6 25 0.00054 23.2 0.6 44 134-182 1-47 (55)
282 PRK11475 DNA-binding transcrip 28.5 18 0.00039 30.8 -0.2 47 133-189 132-178 (207)
283 PRK07122 RNA polymerase sigma 28.4 9.4 0.0002 33.6 -1.9 47 135-190 215-261 (264)
284 cd04774 HTH_YfmP Helix-Turn-He 28.3 15 0.00033 27.8 -0.6 22 162-183 2-23 (96)
285 PF00356 LacI: Bacterial regul 28.3 83 0.0018 21.2 3.1 22 134-155 24-45 (46)
286 PF05344 DUF746: Domain of Unk 28.0 21 0.00045 26.5 0.1 38 142-185 1-38 (65)
287 PF13223 DUF4031: Protein of u 27.8 35 0.00076 26.3 1.3 21 159-183 22-42 (83)
288 PF01710 HTH_Tnp_IS630: Transp 27.7 31 0.00067 26.9 1.1 51 132-192 53-103 (119)
289 PF11516 DUF3220: Protein of u 27.4 9.8 0.00021 29.9 -1.8 10 176-185 32-41 (106)
290 PF08688 ASD1: Apx/Shroom doma 27.3 2E+02 0.0043 25.1 6.0 15 129-143 123-137 (182)
291 PRK05572 sporulation sigma fac 27.1 9.8 0.00021 32.7 -2.0 50 132-190 199-248 (252)
292 PRK12461 UDP-N-acetylglucosami 27.0 81 0.0017 27.9 3.7 44 132-176 196-239 (255)
293 PF11976 Rad60-SLD: Ubiquitin- 26.8 77 0.0017 21.8 2.9 27 160-186 24-51 (72)
294 cd08577 PI-PLCc_GDPD_SF_unchar 26.5 1.1E+02 0.0025 26.7 4.5 42 132-173 175-222 (228)
295 PRK07408 RNA polymerase sigma 26.0 9.6 0.00021 33.2 -2.3 32 160-191 219-250 (256)
296 PRK10840 transcriptional regul 25.9 21 0.00047 28.9 -0.1 45 135-189 150-194 (216)
297 smart00530 HTH_XRE Helix-turn- 25.4 20 0.00043 21.2 -0.3 24 162-185 12-35 (56)
298 PRK09191 two-component respons 25.4 14 0.00031 30.5 -1.3 32 161-192 105-136 (261)
299 PF02943 FeThRed_B: Ferredoxin 25.3 1.5E+02 0.0032 23.7 4.5 26 142-168 8-33 (108)
300 PF06413 Neugrin: Neugrin; In 25.3 52 0.0011 29.2 2.2 39 134-178 9-47 (225)
301 PF08280 HTH_Mga: M protein tr 25.3 44 0.00095 23.0 1.4 40 138-185 5-44 (59)
302 cd02423 Peptidase_C39G A sub-f 25.2 1.5E+02 0.0032 21.8 4.3 40 134-179 27-66 (129)
303 PF13560 HTH_31: Helix-turn-he 25.1 32 0.00068 23.5 0.6 17 158-174 42-58 (64)
304 PRK03988 translation initiatio 25.0 31 0.00067 28.5 0.6 14 53-66 123-136 (138)
305 COG2944 Predicted transcriptio 24.8 21 0.00045 28.6 -0.4 40 136-186 44-83 (104)
306 PF14106 DUF4279: Domain of un 24.8 1.7E+02 0.0037 21.9 4.7 42 137-186 53-94 (118)
307 PF01873 eIF-5_eIF-2B: Domain 24.7 26 0.00057 28.4 0.2 11 53-63 114-124 (125)
308 TIGR02531 yecD_yerC TrpR-relat 24.5 31 0.00066 26.4 0.5 22 161-182 51-72 (88)
309 TIGR01958 nuoE_fam NADH-quinon 24.5 1.2E+02 0.0025 24.7 3.9 32 139-174 17-48 (148)
310 cd04768 HTH_BmrR-like Helix-Tu 24.5 20 0.00044 26.9 -0.5 22 162-183 2-23 (96)
311 PRK15411 rcsA colanic acid cap 24.5 21 0.00045 30.0 -0.5 45 135-189 137-181 (207)
312 PF00130 C1_1: Phorbol esters/ 24.3 43 0.00094 22.0 1.1 28 39-68 13-41 (53)
313 smart00857 Resolvase Resolvase 24.2 62 0.0013 24.8 2.2 18 138-155 18-35 (148)
314 PF01257 2Fe-2S_thioredx: Thio 24.1 74 0.0016 25.7 2.7 33 140-176 15-47 (145)
315 PRK09635 sigI RNA polymerase s 24.0 16 0.00034 32.7 -1.3 32 162-193 136-167 (290)
316 cd01763 Sumo Small ubiquitin-r 23.1 95 0.0021 22.8 2.9 28 161-188 36-63 (87)
317 TIGR03209 P21_Cbot clostridium 22.8 40 0.00086 25.9 0.8 18 161-178 124-141 (142)
318 PF13743 Thioredoxin_5: Thiore 22.8 45 0.00098 27.6 1.2 30 156-185 99-128 (176)
319 cd01106 HTH_TipAL-Mta Helix-Tu 22.8 22 0.00049 26.7 -0.5 23 163-185 3-25 (103)
320 TIGR01610 phage_O_Nterm phage 22.8 86 0.0019 23.6 2.6 44 133-177 20-64 (95)
321 PRK08215 sporulation sigma fac 22.7 12 0.00027 32.3 -2.2 48 134-190 208-255 (258)
322 PF01113 DapB_N: Dihydrodipico 22.6 34 0.00074 26.6 0.4 20 134-153 99-118 (124)
323 COG0484 DnaJ DnaJ-class molecu 22.3 87 0.0019 30.1 3.1 20 133-152 333-352 (371)
324 cd01107 HTH_BmrR Helix-Turn-He 22.1 25 0.00055 26.9 -0.4 22 162-183 2-23 (108)
325 TIGR00311 aIF-2beta translatio 21.9 37 0.00079 27.9 0.5 13 53-65 118-130 (133)
326 cd02420 Peptidase_C39D A sub-f 21.9 1.7E+02 0.0038 21.6 4.1 42 132-179 24-65 (125)
327 PRK09958 DNA-binding transcrip 21.9 29 0.00064 26.9 -0.1 46 134-189 142-187 (204)
328 cd04766 HTH_HspR Helix-Turn-He 21.9 24 0.00051 26.1 -0.6 22 162-183 3-24 (91)
329 PF14794 DUF4479: Domain of un 21.8 84 0.0018 23.3 2.4 23 133-155 45-67 (73)
330 COG1961 PinR Site-specific rec 21.8 1E+02 0.0022 25.9 3.2 50 138-187 18-77 (222)
331 cd04789 HTH_Cfa Helix-Turn-Hel 21.8 24 0.00052 26.8 -0.5 22 162-183 3-24 (102)
332 cd04780 HTH_MerR-like_sg5 Heli 21.7 24 0.00052 26.8 -0.6 20 163-182 3-22 (95)
333 PF02969 TAF: TATA box binding 21.7 1.5E+02 0.0032 21.7 3.6 28 141-170 6-33 (66)
334 TIGR02393 RpoD_Cterm RNA polym 21.3 25 0.00055 30.0 -0.6 52 135-191 176-227 (238)
335 TIGR03384 betaine_BetI transcr 21.2 57 0.0012 25.5 1.5 44 140-184 9-52 (189)
336 cd00131 PAX Paired Box domain 21.1 55 0.0012 26.1 1.3 38 136-182 18-55 (128)
337 cd01105 HTH_GlnR-like Helix-Tu 21.1 25 0.00054 26.1 -0.6 19 162-180 3-21 (88)
338 PF01402 RHH_1: Ribbon-helix-h 20.9 1.4E+02 0.003 18.4 2.9 18 135-152 5-22 (39)
339 COG1595 RpoE DNA-directed RNA 20.7 13 0.00029 30.0 -2.3 31 162-192 145-175 (182)
340 PF04539 Sigma70_r3: Sigma-70 20.6 22 0.00048 25.0 -0.9 23 160-182 20-42 (78)
341 cd01109 HTH_YyaN Helix-Turn-He 20.5 28 0.0006 26.7 -0.5 21 163-183 3-23 (113)
342 PRK12336 translation initiatio 20.5 40 0.00087 29.1 0.5 18 53-70 119-136 (201)
343 cd04773 HTH_TioE_rpt2 Second H 20.4 28 0.0006 26.8 -0.5 22 163-184 3-24 (108)
344 PF08880 QLQ: QLQ; InterPro: 20.4 78 0.0017 20.8 1.7 12 135-146 2-13 (37)
345 cd00592 HTH_MerR-like Helix-Tu 20.4 27 0.00058 25.8 -0.5 22 163-184 3-24 (100)
346 KOG3341 RNA polymerase II tran 20.1 95 0.002 28.4 2.7 36 142-177 43-80 (249)
347 PRK06437 hypothetical protein; 20.0 23 0.00049 25.3 -1.0 34 153-187 13-46 (67)
No 1
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
Probab=100.00 E-value=1.2e-36 Score=212.60 Aligned_cols=48 Identities=79% Similarity=1.448 Sum_probs=44.6
Q ss_pred eehHhhhhhhhhcCCccccccccccc-CCCC----cccccccccccccccccc
Q 048824 23 NYKECMKNHAASIGGHANDGCCEFMP-RADD----SLTCAACGCHRNFHRREV 70 (209)
Q Consensus 23 ~Y~eC~kNhaa~~Gg~~~DGC~Efm~-~~~~----~l~CaaCgCHRnFHr~e~ 70 (209)
+|+||||||||+|||||||||||||| ++++ +|+||||||||||||||+
T Consensus 1 ~Y~EC~kNHAa~~Gg~a~DGCgEFmps~g~~~~~~al~CaACgCHRnFHRre~ 53 (53)
T TIGR01566 1 LYKECLKNHAASIGGHALDGCGEFMPSSGEEGDPESLTCAACGCHRNFHRKEP 53 (53)
T ss_pred CHHHHHHhhHHHhCCcccccccccccCCCCCCCCcceeeeecCcccccccCCC
Confidence 69999999999999999999999999 4543 999999999999999984
No 2
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=100.00 E-value=1.7e-36 Score=217.34 Aligned_cols=53 Identities=72% Similarity=1.445 Sum_probs=49.1
Q ss_pred CeeeehHhhhhhhhhcCCcccccccccccC-CC----Ccccccccccccccccccccc
Q 048824 20 NIINYKECMKNHAASIGGHANDGCCEFMPR-AD----DSLTCAACGCHRNFHRREVRG 72 (209)
Q Consensus 20 ~~v~Y~eC~kNhaa~~Gg~~~DGC~Efm~~-~~----~~l~CaaCgCHRnFHr~e~~~ 72 (209)
..|+|+||+|||||+||||+||||+||||+ ++ ++|+||||||||||||||+++
T Consensus 2 ~~v~Y~EC~kNHAa~~Gg~a~DGCgEFm~~~g~eg~~~al~CaACgCHRnFHRre~~~ 59 (60)
T PF04770_consen 2 KVVRYRECLKNHAASIGGHAVDGCGEFMPSPGEEGTPEALKCAACGCHRNFHRREVEG 59 (60)
T ss_pred CceeHHHHHhhHhHhhCCcccccccccccCCCCCCCcccceecccCcchhcccCCcCC
Confidence 479999999999999999999999999999 54 399999999999999999864
No 3
>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=99.93 E-value=8.4e-27 Score=165.94 Aligned_cols=58 Identities=55% Similarity=1.078 Sum_probs=56.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 129 SKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 129 kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
+||+||+||++|+++|++|||++||+|+++|..+|++||++|||++.||||||||||+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k~ 58 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNKK 58 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCCC
Confidence 5899999999999999999999999999999999999999999999999999999985
No 4
>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=99.51 E-value=2.4e-15 Score=102.15 Aligned_cols=57 Identities=25% Similarity=0.486 Sum_probs=53.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 130 KRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 130 KR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
||.||.||.+|++.|+++|+.. ++|+..++++||.+|||+...|++||+|+|++.||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~----~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQEN----PYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHS----SSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHh----ccccccccccccccccccccccccCHHHhHHHhCc
Confidence 6899999999999999988874 58999999999999999999999999999998764
No 5
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.49 E-value=2e-15 Score=120.64 Aligned_cols=60 Identities=23% Similarity=0.397 Sum_probs=55.4
Q ss_pred CCCCCCCCCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 127 GKSKRQRTKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 127 ~~kKR~RTkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
.+.+|-||+||.-|+..|+. |+|.. |||.-++|+||..|.|++..|||||||||+|++|+
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ETH-----YPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAETH-----YPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhhc-----CCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 45689999999999999998 88874 99999999999999999999999999999999765
No 6
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.48 E-value=3e-14 Score=124.77 Aligned_cols=63 Identities=21% Similarity=0.407 Sum_probs=57.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 126 TGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 126 ~~~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
..+.+|-||+||.+|+|.|+++|++ .||||..++|++|.+|.|.+.+|||||.|||+|.+++.
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~k----TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq 96 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAK----TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQ 96 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHh----hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhh
Confidence 4566999999999999999997666 47999999999999999999999999999999998765
No 7
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.46 E-value=1.4e-13 Score=128.49 Aligned_cols=69 Identities=10% Similarity=0.305 Sum_probs=62.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCCCCC
Q 048824 126 TGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKDESASQ 198 (209)
Q Consensus 126 ~~~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~~~~~~ 198 (209)
.+||||+||.|+--.+..|+.+|++. +||+..+|-+||++|++.+.||+|||+|||+|+||-.+..+..
T Consensus 291 ~~RkRKKRTSie~~vr~aLE~~F~~n----pKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~~~~~~ 359 (398)
T KOG3802|consen 291 QSRKRKKRTSIEVNVRGALEKHFLKN----PKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITPFPSAG 359 (398)
T ss_pred cccccccccceeHHHHHHHHHHHHhC----CCCCHHHHHHHHHHhccccceEEEEeeccccccccCCCCccCC
Confidence 34789999999999999999999994 6999999999999999999999999999999999988733333
No 8
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.44 E-value=3.1e-14 Score=122.01 Aligned_cols=63 Identities=29% Similarity=0.372 Sum_probs=57.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCC
Q 048824 128 KSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKDE 194 (209)
Q Consensus 128 ~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~~ 194 (209)
+.||.||.||.||+.+|+..||.. +|---.++++||..|+|++..|||||||||.|.||....
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~----~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGN----QYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcC----CeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 679999999999999999998985 477788999999999999999999999999999987654
No 9
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.43 E-value=8.2e-14 Score=125.46 Aligned_cols=61 Identities=18% Similarity=0.300 Sum_probs=54.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 128 KSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 128 ~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
++|++||.||..|+++|++.|... +|||...++-|+..+.|.+..|+|||||||+||+|+.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkea----HYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEA----HYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhc----cCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 345679999999999999844443 4999999999999999999999999999999999875
No 10
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.41 E-value=6.8e-14 Score=127.56 Aligned_cols=63 Identities=24% Similarity=0.408 Sum_probs=55.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 126 TGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 126 ~~~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
....||.||+||+.|+|.|+..... ..||-.-++|+|++|+||+.+||||||||||+|+||-.
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~----SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNT----SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcC----CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence 3457999999999999999986544 35788999999999999999999999999999998644
No 11
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.38 E-value=1.3e-13 Score=124.25 Aligned_cols=59 Identities=25% Similarity=0.502 Sum_probs=54.2
Q ss_pred CCCCCCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 130 KRQRTKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 130 KR~RTkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
||.||.||.|||++|+. |-|.. |..+..+++|+.||||.+..||+||||.|+|.||...
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enR-----YlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENR-----YLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhh-----hHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 89999999999999998 65553 8999999999999999999999999999999999763
No 12
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.30 E-value=1.4e-12 Score=87.47 Aligned_cols=56 Identities=21% Similarity=0.410 Sum_probs=51.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 048824 130 KRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASH 189 (209)
Q Consensus 130 KR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~k 189 (209)
|+.||.||.+|++.|++++++. .+|+..++++|+.++||+...|++||+|+|.+.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~----~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKN----PYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhC----CCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 4688999999999999988875 3899999999999999999999999999998864
No 13
>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=99.27 E-value=2e-12 Score=86.83 Aligned_cols=58 Identities=24% Similarity=0.473 Sum_probs=53.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 130 KRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 130 KR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
++.|+.|+.+|++.|+++|+.. .+|+..++++||.++||+...|++||+|+|.+.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~----~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKN----PYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhC----CCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 4688999999999999988884 589999999999999999999999999999998764
No 14
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.26 E-value=1.8e-12 Score=114.43 Aligned_cols=64 Identities=17% Similarity=0.282 Sum_probs=58.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 125 ATGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 125 ~~~~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+..+|||.||.|+..|.-.||.-||.- .|.+..++.-||..|.|++-.||+||||||+||||+.
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~k----rYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELK----RYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHH----hhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 356899999999999999999977763 4789999999999999999999999999999999986
No 15
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.23 E-value=2.5e-12 Score=116.40 Aligned_cols=62 Identities=18% Similarity=0.304 Sum_probs=56.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 127 GKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 127 ~~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
.++|+.||.||..|+..||.-||+. .|....++.+||..|||+-..||+||||||.||||+.
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~Q----KYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQ----KYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHh----hcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 4568899999999999999987883 4699999999999999999999999999999999876
No 16
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.21 E-value=3.2e-12 Score=112.45 Aligned_cols=66 Identities=20% Similarity=0.288 Sum_probs=56.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCCC
Q 048824 127 GKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKDESA 196 (209)
Q Consensus 127 ~~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~~~~ 196 (209)
...||.||.||.+|+-+||.-|.- ..|.....+-|||..|.|+++.|||||||||.|+||.....+
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhf----N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHF----NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhcc----ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 347999999999999999984443 247889999999999999999999999999999997764443
No 17
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.19 E-value=4.5e-12 Score=116.45 Aligned_cols=60 Identities=22% Similarity=0.394 Sum_probs=53.9
Q ss_pred CCCCCCCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 129 SKRQRTKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 129 kKR~RTkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
-||.||.||-||+.+|+. |+.. +|-+.-.+=|||..|+|.+.+|||||||||.|.||+.-
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrE-----NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYRE-----NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHh-----ccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 489999999999999997 7444 57888899999999999999999999999999999863
No 18
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.16 E-value=3.4e-11 Score=109.63 Aligned_cols=65 Identities=17% Similarity=0.367 Sum_probs=56.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCcccC-CCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCC
Q 048824 126 TGKSKRQRTKFTQEQKDKMLEFAERIGWRMQ-RQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKDES 195 (209)
Q Consensus 126 ~~~kKR~RTkFT~EQkekM~~faEk~GW~iq-kpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~~~ 195 (209)
..+|||.|--||+-|.-+||.= |+.| |.+.-|||+||+.|.|+.-.||+||||+|+|-||+..+.
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERR-----FrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERR-----FRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred cccccccccccchhHHHHHHHH-----HHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhh
Confidence 3468889999999999999973 2333 599999999999999999999999999999999988554
No 19
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.11 E-value=3.2e-11 Score=105.91 Aligned_cols=58 Identities=22% Similarity=0.428 Sum_probs=53.7
Q ss_pred CCCCCCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 130 KRQRTKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 130 KR~RTkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
|+.||-||..|+..|+. |-|| ||.+++++.+|+..|.|++-.||+||||||+|.||-.
T Consensus 145 RkPRtPFTtqQLlaLErkfrek-----qYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 145 RKPRTPFTTQQLLALERKFREK-----QYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCHHHHHHHHHHHhHh-----hhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 77999999999999998 7666 6999999999999999999999999999999998744
No 20
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.11 E-value=5.1e-11 Score=98.47 Aligned_cols=63 Identities=16% Similarity=0.205 Sum_probs=58.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 126 TGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 126 ~~~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
..++||.||+||.+|++.|+..+++. ++||...++.++..+++++..|+|||||+|++++++.
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~----h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKV----HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCC----CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 34679999999999999999988885 7999999999999999999999999999999999876
No 21
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.05 E-value=6.5e-11 Score=104.68 Aligned_cols=60 Identities=15% Similarity=0.282 Sum_probs=54.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 128 KSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 128 ~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
+.|+.||.|+.-||+.|..=|++ .||.-..+|.+||..|||+...||+||||||-|+||-
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQk----TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQ----TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhh----cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 44779999999999999996676 5788889999999999999999999999999998864
No 22
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.04 E-value=7.8e-11 Score=107.81 Aligned_cols=63 Identities=22% Similarity=0.506 Sum_probs=56.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCcccCC-CCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 126 TGKSKRQRTKFTQEQKDKMLEFAERIGWRMQR-QDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 126 ~~~kKR~RTkFT~EQkekM~~faEk~GW~iqk-pd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
.+-|||+||.+-+.+|..|++| |.+|. |+.+-|..+|++|.|++.||+|||+|.|+|.||...
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEay-----FavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAY-----FAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccccCcccccHHHH-----hccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 4568999999999999999998 55665 899999999999999999999999999999998653
No 23
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.00 E-value=1.2e-10 Score=106.86 Aligned_cols=61 Identities=23% Similarity=0.367 Sum_probs=57.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 128 KSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 128 ~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+++|.||-||..|++.||..|.+. .|||.+++|+||..+.|++..|+|||.|||+||+|+.
T Consensus 111 KqrrQrthFtSqqlqele~tF~rN----rypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRN----RYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhc----cCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 568999999999999999987775 4899999999999999999999999999999999986
No 24
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.87 E-value=1.1e-09 Score=91.22 Aligned_cols=65 Identities=12% Similarity=0.220 Sum_probs=57.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCC
Q 048824 126 TGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKDE 194 (209)
Q Consensus 126 ~~~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~~ 194 (209)
++..|+.|+.-|.+|+..|+..|+.. .+|+..++..|+..|+|+.+.||+||||+|++.|+....
T Consensus 48 s~~~~~~r~R~t~~Q~~vL~~~F~i~----p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 48 SSPPKSKRRRTTDEQLMVLEREFEIN----PYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCcCcccceechHHHHHHHHHHhccC----CCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 44567788888999999999998874 579999999999999999999999999999999876643
No 25
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.82 E-value=2e-09 Score=98.86 Aligned_cols=61 Identities=25% Similarity=0.436 Sum_probs=56.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 128 KSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 128 ~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+.+|.||+||++|++.|++.|++. +|||...+++++.+||+.+..|+|||+|+|++++|..
T Consensus 175 ~~rr~rtsft~~Q~~~le~~f~rt----~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 175 GGRRNRTSFSPSQLEALEECFQRT----PYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccchHHHHHHHhcCC----CCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 457779999999999999988885 5999999999999999999999999999999999988
No 26
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.74 E-value=1.5e-09 Score=98.33 Aligned_cols=60 Identities=12% Similarity=0.273 Sum_probs=50.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 129 SKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 129 kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
|-+.|-..|..|+-+||.-|-- ..|..+....|||.-|||+++.||+||||||+|+||..
T Consensus 199 kDKYRvVYTDhQRLELEKEfh~----SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFHT----SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred ccceeEEecchhhhhhhhhhcc----ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 5568888999999999973222 23677788899999999999999999999999998655
No 27
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.73 E-value=7.9e-09 Score=94.36 Aligned_cols=60 Identities=12% Similarity=0.304 Sum_probs=51.8
Q ss_pred CCCCCCCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 129 SKRQRTKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 129 kKR~RTkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
-|++|--.|..|+-+||. |+=.. |...+-+-||++.|+|+++.|||||||||-|+||-..
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN~-----YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFNM-----YITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHHH-----HHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 355677889999999997 54442 7899999999999999999999999999999998763
No 28
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.69 E-value=5.9e-09 Score=89.97 Aligned_cols=58 Identities=16% Similarity=0.330 Sum_probs=48.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 131 RQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 131 R~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+..-+||.||...|+.-|+.. .+..-.....||.++||..+.|+|||||||++||.+.
T Consensus 52 ~kk~Rlt~eQ~~~LE~~F~~~----~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 52 GKKRRLTSEQVKFLEKSFESE----KKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred cccccccHHHHHHhHHhhccc----cccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 334469999999999854542 3677788999999999999999999999999999765
No 29
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.52 E-value=2e-08 Score=89.37 Aligned_cols=62 Identities=21% Similarity=0.367 Sum_probs=56.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 127 GKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 127 ~~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+++|-.|-+|+-.|+..|+.-+|.. +|+--.++.++|..+|+.+..+||||||||.||+|+-
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqt----kylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQT----KYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhh----hcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 5688899999999999999977773 5788889999999999999999999999999999876
No 30
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.48 E-value=8.6e-09 Score=88.14 Aligned_cols=61 Identities=16% Similarity=0.343 Sum_probs=54.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 128 KSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 128 ~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
++++.||.|+..|+.-|++-||.- .|.+..+++||++-|+|+...||.||||+|.|.||..
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Q----rYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQ----RYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred HhhhhcccccCccccccHHHHhhh----hhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 467799999999999999977753 2688999999999999999999999999999998755
No 31
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=98.26 E-value=7.3e-07 Score=93.41 Aligned_cols=61 Identities=18% Similarity=0.279 Sum_probs=55.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 128 KSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 128 ~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
.+++.||.|+.+|+..|+.|+++- -++.+.++|-+-..|++..+||+|||+|+|++.+|..
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q----~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQ----RTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhc----cCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 478999999999999999998884 2577889999999999999999999999999998865
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.20 E-value=6.8e-07 Score=73.96 Aligned_cols=64 Identities=25% Similarity=0.461 Sum_probs=56.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 126 TGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 126 ~~~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
..+.+|.||.|+..|++.+...+.. ..+|+...+++++..+|+...||+|||+|+|.+.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRA----TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccC----CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 4567999999999999999986554 457999999999999999999999999999999987654
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.13 E-value=1.9e-06 Score=83.98 Aligned_cols=56 Identities=14% Similarity=0.234 Sum_probs=51.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccccc
Q 048824 128 KSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNA 187 (209)
Q Consensus 128 ~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k 187 (209)
.-||.|+.||..||+.|..+|... ++|+.++.+.|+..|||+..+|..||+|.|-+
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~----~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR 474 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKEN----KRPSREMQETISQQLNLELSTVINFFMNARRR 474 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcC----CCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence 358899999999999999987663 57999999999999999999999999998887
No 34
>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=96.75 E-value=0.0002 Score=47.51 Aligned_cols=34 Identities=12% Similarity=0.328 Sum_probs=28.0
Q ss_pred ccCCCCHHHHHHHHHHhCCCCceeeeeccccccc
Q 048824 154 RMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNA 187 (209)
Q Consensus 154 ~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k 187 (209)
.-.||+.++.++||.++||++..|..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4468999999999999999999999999998853
No 35
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=96.37 E-value=0.0033 Score=57.77 Aligned_cols=62 Identities=11% Similarity=0.268 Sum_probs=54.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 130 KRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 130 KR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+|+|--|+..-.|+|.++|-.. -...||++++.++||.+-+|+...+-.||-|.|-+.||..
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h-~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSH-LSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHh-cCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 7888999999999999966654 3456799999999999999999999999999999988764
No 36
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=96.00 E-value=0.0078 Score=55.33 Aligned_cols=56 Identities=13% Similarity=0.252 Sum_probs=44.4
Q ss_pred CCCCCCHHH---------HHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 132 QRTKFTQEQ---------KDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 132 ~RTkFT~EQ---------kekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
.||...-|| +..|++++-+ ..||.-.+..+||+.+||+.-.|-.||.|||++.|-.
T Consensus 170 PrTIWDGEet~yCFKekSR~~LrewY~~----~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~ 234 (304)
T KOG0775|consen 170 PRTIWDGEETVYCFKEKSRSLLREWYLQ----NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA 234 (304)
T ss_pred CCccccCceeeeehhHhhHHHHHHHHhc----CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence 477766666 3455665444 3579999999999999999999999999999998733
No 37
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.87 E-value=0.0062 Score=42.11 Aligned_cols=47 Identities=26% Similarity=0.392 Sum_probs=37.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 130 KRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 130 KR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
||.|+.+|-+||-.+...+|.- . -+.++|.++||++.+|.-|+.|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g------~---s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG------E---SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT------T----HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcC------C---CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 6899999999999999987772 2 688999999999999999998864
No 38
>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=95.56 E-value=0.007 Score=42.54 Aligned_cols=47 Identities=19% Similarity=0.355 Sum_probs=34.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 131 RQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 131 R~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
+.|+.||.|+|..+...+..-| ..|.++|.+.||+..+|..|..--+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g--------~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG--------ESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH--------CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC--------CceEeeecccccccccccHHHHHHh
Confidence 5689999999999998764433 4899999999999999999987655
No 39
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=94.73 E-value=0.035 Score=49.99 Aligned_cols=63 Identities=13% Similarity=0.166 Sum_probs=53.6
Q ss_pred CCCCCCCCCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 127 GKSKRQRTKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 127 ~~kKR~RTkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
..++|.+..|..+...+|++ .++.+- -.||++.+...|+.++||++..|..||-|.|-+..+-
T Consensus 237 ~~~~r~~~~lP~~a~~ilr~Wl~~h~~--~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 237 QSKWRPQRGLPKEAVSILRAWLFEHLL--HPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred cCCCCCCCCCCHHHHHHHHHHHHHhcc--CCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 34788889999999999998 666543 3578888888999999999999999999999887653
No 40
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.66 E-value=0.043 Score=56.38 Aligned_cols=54 Identities=15% Similarity=0.350 Sum_probs=44.9
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
--|++- ++.|++++...| -+.+++...|+..+||...|||+||.|.++......
T Consensus 562 k~~~~p-~sllkayyaln~----~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 562 KQFNHP-TSLLKAYYALNG----LPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred cccCCc-HHHHHHHHHhcC----CCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 345555 777888766655 499999999999999999999999999999987655
No 41
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=90.92 E-value=0.22 Score=27.70 Aligned_cols=40 Identities=23% Similarity=0.372 Sum_probs=29.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeec
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWM 181 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWf 181 (209)
+..|+.+++..+....+. || .+.++|.++||++.+|..|+
T Consensus 3 ~~~~~~~~~~~i~~~~~~-~~--------s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLAA-GE--------SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHHc-CC--------CHHHHHHHHCCCHHHHHHhC
Confidence 345788888877776432 32 67889999999999988875
No 42
>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=90.22 E-value=0.055 Score=33.80 Aligned_cols=45 Identities=11% Similarity=0.303 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNAS 188 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~ 188 (209)
.++.+|++.+..++. +....+++|.++|++..+|+.|.+.-+.+.
T Consensus 10 ~l~~~~~~~~~~~~~---------~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 10 KLPEREREVILLRFG---------EGLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred hCCHHHHHHHHHHHh---------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 567888888877632 223678889999999999999998776654
No 43
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=89.60 E-value=0.27 Score=34.57 Aligned_cols=41 Identities=17% Similarity=0.473 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceee
Q 048824 136 FTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLK 178 (209)
Q Consensus 136 FT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~K 178 (209)
+|..|++.|....+ .|| -..|....++++|+++||++.+|-
T Consensus 1 LT~~Q~e~L~~A~~-~GY-fd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYE-LGY-FDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHH-cCC-CCCCCcCCHHHHHHHhCCCHHHHH
Confidence 58899999887544 465 334778899999999999987763
No 44
>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=87.47 E-value=0.094 Score=34.72 Aligned_cols=41 Identities=17% Similarity=0.417 Sum_probs=28.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecc
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMH 182 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfh 182 (209)
+.+++.+|.+.+.+..+. ...+.++|.++||++.+|.-++.
T Consensus 3 p~~~~~~~~~~i~~l~~~---------G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 3 PPKLSKEQIEEIKELYAE---------GMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSSHCCHHHHHHHHHT---------T--HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCCCHHHHHHHHHHHHC---------CCCHHHHHHHHCcCHHHHHHHHh
Confidence 346788777777775333 15799999999999999876654
No 45
>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=85.18 E-value=0.17 Score=33.66 Aligned_cols=44 Identities=9% Similarity=0.240 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccccc
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNA 187 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k 187 (209)
.++.+|++.+.-+ +-+....+++|..+|++...|++|++.-|.+
T Consensus 10 ~L~~~~r~i~~l~---------~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLR---------YFQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHH---------HTS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHH---------HHHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 3567777777764 3455588999999999999999999876543
No 46
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=84.74 E-value=0.62 Score=36.50 Aligned_cols=43 Identities=19% Similarity=0.322 Sum_probs=33.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccc
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhN 183 (209)
|.+||.|.|..+-...-..| ..+.++|.++||+..+|--|..-
T Consensus 10 rr~ys~EfK~~aV~~~~~~g--------~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG--------MTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC--------CCHHHHHHHHCcCHHHHHHHHHH
Confidence 56699999887766433333 37889999999999999999654
No 47
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=84.66 E-value=0.29 Score=35.20 Aligned_cols=40 Identities=8% Similarity=0.355 Sum_probs=28.4
Q ss_pred HHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 143 KMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 143 kM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
-|++|+.+.+ ...+..+++||.+.|++-..|+.||--+..
T Consensus 12 pL~~Yy~~h~----~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 12 PLEDYYLKHK----QLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp HHHHHHHHT--------TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred HHHHHHHHcC----CccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 4888866654 477889999999999999999999976544
No 48
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=84.61 E-value=0.18 Score=33.40 Aligned_cols=42 Identities=10% Similarity=0.308 Sum_probs=20.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccc
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhN 183 (209)
.+.||.+|+..++.+- ..-..+.++|..||+++.+|--|+.+
T Consensus 2 ~~~Lt~~eR~~I~~l~---------~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 2 YKHLTPEERNQIEALL---------EQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ----------HHHHHH---------CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred ccchhhhHHHHHHHHH---------HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 3578999999998872 22347788999999999998776654
No 49
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=84.24 E-value=0.9 Score=34.69 Aligned_cols=49 Identities=20% Similarity=0.306 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCC-CCceeeeecccccccCC
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGV-KRHVLKVWMHNNKNASH 189 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv-~r~V~KVWfhNnR~k~k 189 (209)
|.+||.|-|..+-+++...| ..|.++|.++|| +...+..|...-+....
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g--------~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~ 54 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGG--------DTVSEVAREFGIVSATQLYKWRIQLQKGGG 54 (116)
T ss_pred cccCCHHHHHHHHHHHHhcC--------ccHHHHHHHhCCCChHHHHHHHHHHHHccc
Confidence 89999999999998866644 179999999996 99999999886555443
No 50
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=81.77 E-value=0.18 Score=41.21 Aligned_cols=50 Identities=10% Similarity=0.084 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
.++..|++.+.-. +-+.-..+++|+.+|++..+|+++++.-|.++++...
T Consensus 142 ~L~~~~r~vl~l~---------~~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~ 191 (194)
T PRK09646 142 ALTDTQRESVTLA---------YYGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCLG 191 (194)
T ss_pred hCCHHHHHHHHHH---------HHcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHhc
Confidence 4566666666442 1222367899999999999999999999998887653
No 51
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=80.60 E-value=0.45 Score=30.30 Aligned_cols=45 Identities=13% Similarity=0.253 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASH 189 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~k 189 (209)
.+|.+|++.+..++ .|+ ..+++|..+||++.+|+.|.+.-+.+++
T Consensus 3 ~l~~~e~~i~~~~~--~g~--------s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVLRLLA--EGL--------TNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHHHH--cCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 57888888765543 232 5689999999999999999987666554
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=80.42 E-value=0.3 Score=37.86 Aligned_cols=48 Identities=6% Similarity=-0.002 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
++++.|++.+... +-+....+++|+.+|++..+|++|++.-+.++++.
T Consensus 106 ~L~~~~r~ii~l~---------~~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 106 VLDEKEKYIIFER---------FFVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred hCCHHHHHHHHHH---------HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 4556666665442 12233689999999999999999999988887764
No 53
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=79.69 E-value=0.4 Score=37.19 Aligned_cols=47 Identities=11% Similarity=0.201 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 134 TKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 134 TkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
.+++++|++.+.- |++. ...+++|..+||+..+|+++++.-|.+++.
T Consensus 110 ~~L~~~~r~v~~l~~~~g----------~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRG----------VSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhcC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 4677777777776 4332 367899999999999999999998888765
No 54
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=78.76 E-value=0.82 Score=37.79 Aligned_cols=44 Identities=18% Similarity=0.492 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecc
Q 048824 135 KFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMH 182 (209)
Q Consensus 135 kFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfh 182 (209)
.||+||+++|.. .-|-+ ......++.+++..+|+++.++++-|.
T Consensus 4 ~~T~eer~eLk~rIvElV----Re~GRiTi~ql~~~TGasR~Tvk~~lr 48 (127)
T PF06163_consen 4 VFTPEEREELKARIVELV----REHGRITIKQLVAKTGASRNTVKRYLR 48 (127)
T ss_pred cCCHHHHHHHHHHHHHHH----HHcCCccHHHHHHHHCCCHHHHHHHHH
Confidence 599999999987 33332 235677999999999999999887654
No 55
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=78.51 E-value=0.91 Score=30.75 Aligned_cols=24 Identities=13% Similarity=0.333 Sum_probs=17.3
Q ss_pred HHHHHHHHhCCCCceeeeeccccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
.+.+||+++||++.+|.-|++++.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 677888999999999999988763
No 56
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=78.41 E-value=0.83 Score=29.82 Aligned_cols=23 Identities=17% Similarity=0.564 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCCCceeeeecccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNn 184 (209)
.+.++|..+||++.+|.-|...-
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT--
T ss_pred CHHHHHHHHCcCHHHHHHHHHHc
Confidence 78899999999999999998653
No 57
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=78.39 E-value=0.23 Score=42.38 Aligned_cols=40 Identities=5% Similarity=0.040 Sum_probs=34.1
Q ss_pred HHHHHHHHHHhCCCCceeeeecccccccCCCCCCCCCCCC
Q 048824 160 DVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKDESASQS 199 (209)
Q Consensus 160 ~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~~~~~~~ 199 (209)
....+++|..+||+..+|+++++.-|.++++.....+..+
T Consensus 150 g~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~~~~~ 189 (216)
T PRK12533 150 DMSYREIAAIADVPVGTVMSRLARARRRLAALLGGASAAQ 189 (216)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchhh
Confidence 3467899999999999999999999999998876665543
No 58
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=78.35 E-value=0.39 Score=32.70 Aligned_cols=45 Identities=11% Similarity=0.202 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASH 189 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~k 189 (209)
.||..|++.|.-+++-. ..+++|.++||+..+|+.+..|=+.|++
T Consensus 3 ~LT~~E~~vl~~l~~G~----------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM----------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-----------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcC----------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 58999999998875553 6789999999999999999988777654
No 59
>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=75.95 E-value=0.28 Score=32.47 Aligned_cols=45 Identities=7% Similarity=0.222 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNAS 188 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~ 188 (209)
.++.+|++.+...+ -.....+++|+.+|+++..|+.+...-..++
T Consensus 4 ~L~~~er~vi~~~y---------~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 4 QLPPREREVIRLRY---------FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TS-HHHHHHHHHHH---------TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh---------cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 47889999998852 2334688999999999999988876554443
No 60
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=75.57 E-value=0.64 Score=37.59 Aligned_cols=30 Identities=13% Similarity=0.323 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
..+++|+.+||+..+|++|++.-|.++++.
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 678999999999999999999988877653
No 61
>PRK06424 transcription factor; Provisional
Probab=75.38 E-value=1.8 Score=35.82 Aligned_cols=56 Identities=13% Similarity=0.163 Sum_probs=36.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 129 SKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 129 kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
++|.|..| .+..+.+..|++++-...... .-..++||..+|+++..|.-|..+.+.
T Consensus 68 ~~~~~d~~-~~~~~~~~~~g~~Ir~lRe~~-GLSQ~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 68 KKYKKKAS-DEDLDIVEDYAELVKNARERL-SMSQADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred CCccCccc-HHHHHHHHHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHCCCCC
Confidence 34455554 455577777776642111111 124789999999999999999988754
No 62
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=75.35 E-value=0.33 Score=37.94 Aligned_cols=48 Identities=6% Similarity=0.173 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
.++++|++.+.-+ +-+....+++|..+|+++.+|+.|++.-+.++++.
T Consensus 128 ~L~~~~r~vl~l~---------~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLR---------EIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHH---------HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5677777777653 12223678999999999999999999888877653
No 63
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=75.31 E-value=0.32 Score=38.89 Aligned_cols=33 Identities=6% Similarity=0.098 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 160 DVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 160 ~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
....+++|+.+|++..+|+++++.-|.++++..
T Consensus 154 ~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 154 GLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 346789999999999999999999999887654
No 64
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=75.10 E-value=0.35 Score=37.85 Aligned_cols=33 Identities=12% Similarity=0.137 Sum_probs=29.0
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCCCCC
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKNASHRRKDE 194 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~~ 194 (209)
..+++|+.+|++..+|+++.+.-|.++++....
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 160 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRELLEE 160 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 578999999999999999999999998876543
No 65
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=73.64 E-value=0.64 Score=38.54 Aligned_cols=47 Identities=11% Similarity=0.140 Sum_probs=38.6
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
+.+|..|++.|.-++ .|| ..+++|..+|+++.+|+.|.++.+.++++
T Consensus 5 ~~Lt~rqreVL~lr~--~Gl--------Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 5 SFLTERQIEVLRLRE--RGL--------TQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred cCCCHHHHHHHHHHH--cCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 568899999987753 344 67899999999999999999988877654
No 66
>PRK10403 transcriptional regulator NarP; Provisional
Probab=73.59 E-value=1.1 Score=34.65 Aligned_cols=48 Identities=19% Similarity=0.284 Sum_probs=39.5
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
..+|..+++.|.-+++. ...+++++.+|+++++|++.++|=+.|+.-+
T Consensus 152 ~~Lt~~e~~vl~~~~~g----------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 152 SVLTERELDVLHELAQG----------LSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred ccCCHHHHHHHHHHHCC----------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 46999999998877543 2467889999999999999999988887654
No 67
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=73.52 E-value=1.3 Score=37.17 Aligned_cols=54 Identities=22% Similarity=0.331 Sum_probs=33.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 131 RQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 131 R~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
+.-.++|.+|+..-.-.++.- +-+..-+.-+.+++|+++||++.+|=-|.+-++
T Consensus 6 ~le~~L~~~Q~kAa~ll~~ne-~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~ 59 (142)
T PF13022_consen 6 ELEAKLTLQQRKAAQLLVENE-LMPENGERRTQAEIAEEVGISRSTLYRWRQQNK 59 (142)
T ss_dssp HHHTTS-HHHHHHHHHHHHHH-HS------S-HHHHHHHHTS-HHHHHHHHHH-H
T ss_pred HHHHHcCHHHHHHHHHHHHHH-HhhhccccchHHHHHHHhCCCHHHHHHHHhcCH
Confidence 344578999999766655552 111112456889999999999999999997665
No 68
>PRK04217 hypothetical protein; Provisional
Probab=73.49 E-value=0.45 Score=37.93 Aligned_cols=49 Identities=10% Similarity=0.079 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
++|.+|++.+...+. +.-.++++|+.+||++.+|+..++.-+.+++...
T Consensus 42 ~Lt~eereai~l~~~---------eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 42 FMTYEEFEALRLVDY---------EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cCCHHHHHHHHHHHH---------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 578899877765421 1227889999999999999999998888776543
No 69
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=73.46 E-value=0.35 Score=40.23 Aligned_cols=49 Identities=10% Similarity=0.104 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
.++.+|++.+.-. +-+.-..+++|+.+||+..+|+++++.-+.++++..
T Consensus 153 ~L~~~~r~vl~l~---------~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGV---------YFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHH---------HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3555666666542 122236889999999999999999999998887654
No 70
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=73.17 E-value=0.4 Score=38.50 Aligned_cols=49 Identities=10% Similarity=0.216 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
.++.++++.+.-+ +-+....+++|..+||+..+|+++++.-|.++++..
T Consensus 131 ~L~~~~r~v~~l~---------~~~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSI---------SVEGASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHH---------HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 4556666666653 122236789999999999999999999999887654
No 71
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=73.12 E-value=0.4 Score=37.95 Aligned_cols=49 Identities=6% Similarity=0.064 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 134 TKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 134 TkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
-+++.+|++.+.- +.+. ...+++|.++|++..+|++|++.-|.++++..
T Consensus 107 ~~L~~~~r~v~~l~~~~g----------~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE----------LTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4566777777664 3333 26789999999999999999999998887644
No 72
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=72.29 E-value=0.5 Score=37.18 Aligned_cols=49 Identities=12% Similarity=0.222 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
.++..|++.+.-. +-..-..+++|..+|++..+|+++.+.-|.++++..
T Consensus 112 ~L~~~~r~v~~l~---------~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 112 SLPLERRNVLLLR---------DYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred HCCHHHHHHhhhH---------HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhc
Confidence 4666666666542 122236789999999999999999999999887653
No 73
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=72.08 E-value=1.8 Score=44.12 Aligned_cols=61 Identities=16% Similarity=0.345 Sum_probs=54.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHH---HHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 128 KSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVA---LNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 128 ~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~---ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
-++|+||+++-|-+..+.+|+...|- +||..+ +.-|...+.+.++++-..|+|.|.-.+++
T Consensus 646 ~~p~~~~~isge~~~~~qs~i~~~gl---~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~~ 709 (769)
T KOG3755|consen 646 HKPRKRTKISGEALGILQSFITDVGL---YPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKHH 709 (769)
T ss_pred cCccccceecccchHHHHHHHHHhcc---CchhhcccccchhhhhhcccHHHHHHhhhcceeecchh
Confidence 37999999999999999999999884 788888 99999999999999999999998866643
No 74
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=72.01 E-value=0.48 Score=38.35 Aligned_cols=51 Identities=10% Similarity=0.199 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
.+++++|++.+.-+ +-+.-..+++|+.+|++..+|+.+++.-|.++++...
T Consensus 130 ~~L~~~~r~v~~l~---------~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12539 130 ARLPEKMRLAIQAV---------KLEGLSVAEAATRSGMSESAVKVSVHRGLKALAALIG 180 (184)
T ss_pred HhCCHHHHHHHHHH---------HHcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHh
Confidence 34666666666642 1223368899999999999999999999988876543
No 75
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=71.92 E-value=0.45 Score=38.50 Aligned_cols=51 Identities=10% Similarity=0.158 Sum_probs=39.2
Q ss_pred CCCCCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 131 RQRTKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 131 R~RTkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
+.-..++..|++.+.- |.+ ....+++|..+||+..+|+++++.-|.++++.
T Consensus 135 ~~l~~L~~~~r~i~~l~~~~----------g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 135 ELLDTLPEKQREILILRVVV----------GLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred HHHHhCCHHHHHHHHHHHHc----------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3445677777777775 333 23689999999999999999999888887764
No 76
>PRK00118 putative DNA-binding protein; Validated
Probab=71.07 E-value=0.47 Score=37.49 Aligned_cols=47 Identities=19% Similarity=0.273 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
+++..|++.+.-+. -....+.++|..+||++.+|+.|++.-|.+.++
T Consensus 17 ~L~ekqRevl~L~y---------~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYY---------LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHH---------HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35677888776532 223378889999999999999999877766543
No 77
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=71.02 E-value=0.82 Score=34.89 Aligned_cols=46 Identities=9% Similarity=0.213 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 135 KFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 135 kFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
+++.++++.+.- +.+ .-.++++|..+||++.+|+++.+.-|.++++
T Consensus 113 ~L~~~~r~il~l~~~~----------~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----------GKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHc----------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 445666666554 322 2267889999999999999999988887765
No 78
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=70.91 E-value=0.46 Score=38.89 Aligned_cols=47 Identities=13% Similarity=0.207 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
+++..|++.+.-+ +-..-..+++|..+|++..+|+++++.-|.++++
T Consensus 134 ~Lp~~~R~v~~L~---------~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 134 HLPAQQARVFMMR---------EYLELSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred hCCHHHHHHHhHH---------HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4556666666652 1122368999999999999999999988887765
No 79
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=70.52 E-value=8.8 Score=25.90 Aligned_cols=34 Identities=15% Similarity=0.211 Sum_probs=27.0
Q ss_pred CHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 048824 137 TQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 137 T~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNn 184 (209)
|.|||++|.+- .-+.++..+|++..-+.|+|...
T Consensus 13 s~eqk~~l~~~--------------it~~l~~~~~~p~~~v~V~i~e~ 46 (61)
T PRK02220 13 TEEQLKALVKD--------------VTAAVSKNTGAPAEHIHVIINEM 46 (61)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCcChhhEEEEEEEe
Confidence 79999998864 55678999999887777777654
No 80
>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=70.28 E-value=2.2 Score=27.62 Aligned_cols=35 Identities=9% Similarity=0.113 Sum_probs=25.0
Q ss_pred HHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 143 KMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 143 kM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
.|..+-++.|| ..++||..+||+..+|.-|..+++
T Consensus 6 ~l~~~r~~~gl--------tq~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 6 LVRARRKALGL--------TQADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHCCCC
Confidence 45555566665 367888888888888888886653
No 81
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=70.20 E-value=0.56 Score=37.52 Aligned_cols=30 Identities=7% Similarity=0.255 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
..+++|+.+|++...|+++++.-|.++|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999988887764
No 82
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=69.59 E-value=3.5 Score=34.98 Aligned_cols=42 Identities=19% Similarity=0.412 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceee
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLK 178 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~K 178 (209)
.+|..|++.|... -+.|| -.+|.....++||+++||++.+|.
T Consensus 155 ~LTdrQ~~vL~~A-~~~GY-Fd~PR~~~l~dLA~~lGISkst~~ 196 (215)
T COG3413 155 DLTDRQLEVLRLA-YKMGY-FDYPRRVSLKDLAKELGISKSTLS 196 (215)
T ss_pred cCCHHHHHHHHHH-HHcCC-CCCCccCCHHHHHHHhCCCHHHHH
Confidence 8999999998864 34575 334778999999999999998763
No 83
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=69.16 E-value=0.92 Score=39.75 Aligned_cols=35 Identities=3% Similarity=0.013 Sum_probs=31.0
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCCCCCC
Q 048824 161 VALNQFCNEVGVKRHVLKVWMHNNKNASHRRKDES 195 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~~~ 195 (209)
-..+++|+.+|++..+|++.++--|.++++.....
T Consensus 159 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 193 (324)
T TIGR02960 159 WRAAETAELLGTSTASVNSALQRARATLDEVGPSA 193 (324)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccc
Confidence 36789999999999999999999999999877644
No 84
>PRK10072 putative transcriptional regulator; Provisional
Probab=68.91 E-value=2.4 Score=32.96 Aligned_cols=35 Identities=17% Similarity=0.423 Sum_probs=27.7
Q ss_pred HHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 144 MLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 144 M~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
++++-+++|| ..++||..+||+..+|.-|.+.+|.
T Consensus 38 ik~LR~~~gl--------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 38 FEQLRKGTGL--------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred HHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 4444566676 4789999999999999999988763
No 85
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=68.03 E-value=0.84 Score=36.82 Aligned_cols=47 Identities=6% Similarity=0.173 Sum_probs=35.3
Q ss_pred CCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 136 FTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 136 FT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+++++++.+.- |++. ...+++|..+||+..+|+++++.-|.++++..
T Consensus 129 L~~~~r~i~~l~~~~g----------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 129 LPERQREAIVLQYYQG----------LSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CCHHHHHHhhHHHhcC----------CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 45556665543 3333 25789999999999999999999998888754
No 86
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=67.96 E-value=0.81 Score=33.66 Aligned_cols=47 Identities=6% Similarity=0.210 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
+++..|++.+..+.- .....+++|+++||++.+|+.|.+.-+.+.++
T Consensus 110 ~L~~~~~~ii~~~~~---------~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYL---------EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHh---------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 567777777655311 12267799999999999999999887777664
No 87
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=67.87 E-value=0.61 Score=37.77 Aligned_cols=32 Identities=6% Similarity=0.154 Sum_probs=27.3
Q ss_pred CHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 159 DDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 159 d~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
+....+++|..+|++..+|++|++.-|.++++
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 34468899999999999999999988877765
No 88
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=67.50 E-value=1.2 Score=37.04 Aligned_cols=24 Identities=13% Similarity=0.185 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCCCceeeeeccccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
..++||..+||++.+|.-|-.+.+
T Consensus 84 SqeeLA~~lgvs~s~IsriE~G~~ 107 (154)
T TIGR00270 84 SQEQLAKKIQEKESLIKKIENAEI 107 (154)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCC
Confidence 578899999999999999987654
No 89
>PF13551 HTH_29: Winged helix-turn helix
Probab=67.31 E-value=4.9 Score=29.36 Aligned_cols=54 Identities=17% Similarity=0.265 Sum_probs=31.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCcc-cCCCCHHHHHH-H-HHH--hCCCCceeeeecc
Q 048824 129 SKRQRTKFTQEQKDKMLEFAERIGWR-MQRQDDVALNQ-F-CNE--VGVKRHVLKVWMH 182 (209)
Q Consensus 129 kKR~RTkFT~EQkekM~~faEk~GW~-iqkpd~~~ve~-f-c~e--iGv~r~V~KVWfh 182 (209)
..|.++.+|.+|++.+.+++....-. ........+.+ + .+. +.|+..+|.-|++
T Consensus 51 ~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 51 GGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 45666669999999999988874211 00122334443 3 222 3566666666654
No 90
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=67.09 E-value=0.66 Score=36.14 Aligned_cols=32 Identities=9% Similarity=0.181 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 160 DVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 160 ~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
....+++|..+|+++.+|+.|++--|.++++.
T Consensus 141 ~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 141 GLSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999999888877653
No 91
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=66.97 E-value=0.64 Score=36.93 Aligned_cols=48 Identities=8% Similarity=0.165 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
++++.|++.+.-+ +-+.-..+++|..+||+..+|+++++.-|.+++..
T Consensus 112 ~L~~~~r~v~~l~---------~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 112 LLSADQREAIILI---------GASGFSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred hCCHHHHHHHHHH---------HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4455555555442 22334689999999999999999999888877653
No 92
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=66.75 E-value=5.8 Score=41.52 Aligned_cols=67 Identities=12% Similarity=0.227 Sum_probs=48.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCcccCC-CCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCCCC
Q 048824 126 TGKSKRQRTKFTQEQKDKMLEFAERIGWRMQR-QDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKDESAS 197 (209)
Q Consensus 126 ~~~kKR~RTkFT~EQkekM~~faEk~GW~iqk-pd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~~~~~ 197 (209)
+.++-|.|+-...++-..|.+. |..|. +...+.--.+.++.....|+.||+|||+.+-++-.-..++
T Consensus 623 g~~p~kv~sp~k~~dq~ql~~a-----~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl~lts 690 (1007)
T KOG3623|consen 623 GERPVKVRSPIKEEDQQQLKQA-----YELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPLFLTS 690 (1007)
T ss_pred CCCCccccCCCCccchhhhHhh-----hhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCcccccc
Confidence 3456678888888888888877 44444 3333444456668999999999999999998886644443
No 93
>PRK09480 slmA division inhibitor protein; Provisional
Probab=66.58 E-value=3.9 Score=32.43 Aligned_cols=47 Identities=13% Similarity=0.214 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 138 QEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 138 ~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
.+.++++.+-|.++=+.-.. +...++++|.+.||++.+|=-+|.|..
T Consensus 9 ~~~r~~Il~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 9 GERREQILQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred hhHHHHHHHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 55556666655554122224 788999999999999999999999865
No 94
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=66.32 E-value=0.69 Score=36.24 Aligned_cols=47 Identities=6% Similarity=0.208 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
+++..|++.+.- +.+. -..+++|..+||+..+|+++++.-|.++++.
T Consensus 106 ~Lp~~~r~v~~l~~~~g----------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE----------KSYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred hCCHHHHHHHHHHHHhC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 355566666544 3222 2578999999999999999999988887754
No 95
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=66.11 E-value=0.78 Score=35.94 Aligned_cols=48 Identities=15% Similarity=0.244 Sum_probs=36.6
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
.+++.+|++.|.-+. .| -..+++|..+||+..+|+++++.-|.++|+.
T Consensus 111 ~~L~~~~r~il~l~~--~g--------~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 111 AKMTERDRTVLLLRF--SG--------YSYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred HcCCHHHHHHHHHHH--cC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 346677777766543 23 2678999999999999999999888877653
No 96
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=65.93 E-value=0.87 Score=37.09 Aligned_cols=49 Identities=6% Similarity=0.297 Sum_probs=38.1
Q ss_pred CCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 134 TKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 134 TkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
.+++++|++.+.- |.+. ...+++|+.+|++..+|++.++--|.+++++.
T Consensus 130 ~~L~~~~r~i~~l~~~~g----------~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLG----------EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred HhCCHHHHHHHHHHHHcc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 3566777776654 3332 26789999999999999999999999988875
No 97
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=65.90 E-value=0.71 Score=36.77 Aligned_cols=46 Identities=13% Similarity=0.302 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 135 KFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 135 kFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
+++..|++.+.- +++ ....+++|+.+|++..+|+++++.-|.+++.
T Consensus 136 ~L~~~~r~v~~l~~~~----------g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME----------DLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCHHHhHHhhhHHhc----------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 566666666554 333 3468899999999999999999988887765
No 98
>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=65.77 E-value=2.9 Score=29.28 Aligned_cols=21 Identities=19% Similarity=0.376 Sum_probs=11.7
Q ss_pred HHHHHHhCCCCceeeeecccc
Q 048824 164 NQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 164 e~fc~eiGv~r~V~KVWfhNn 184 (209)
++||..+||++..|--|+.++
T Consensus 22 ~~lA~~~gis~~tis~~~~g~ 42 (78)
T TIGR02607 22 RALAKALGVSRSTLSRIVNGR 42 (78)
T ss_pred HHHHHHhCCCHHHHHHHHcCC
Confidence 455555565555555555443
No 99
>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=65.70 E-value=2 Score=27.50 Aligned_cols=44 Identities=14% Similarity=0.243 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 048824 136 FTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASH 189 (209)
Q Consensus 136 FT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~k 189 (209)
++..|++.+.-++ .| ...+++|..+||++.+|+.|.+.-+.+..
T Consensus 1 l~~~e~~i~~~~~--~~--------~s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 1 LTPREREVLRLLA--EG--------KTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred CCHHHHHHHHHHH--cC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 3567777654442 22 26788999999999999999886554444
No 100
>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=65.47 E-value=2 Score=26.69 Aligned_cols=24 Identities=21% Similarity=0.430 Sum_probs=21.1
Q ss_pred HHHHHHHhCCCCceeeeecccccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
++++|..+||++.+|.-|..+.+-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 678999999999999999987654
No 101
>PRK09726 antitoxin HipB; Provisional
Probab=65.18 E-value=4.8 Score=29.72 Aligned_cols=21 Identities=14% Similarity=0.469 Sum_probs=10.0
Q ss_pred HHHHHHHhCCCCceeeeeccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhN 183 (209)
.++||..+||+...|.-|..+
T Consensus 28 q~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENN 48 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCC
Confidence 344444455554444444443
No 102
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=65.12 E-value=0.8 Score=36.55 Aligned_cols=47 Identities=6% Similarity=-0.031 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 136 FTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 136 FT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
++..|++.+.-. +-+....+++|..+|++..+|++.++.-|.++++.
T Consensus 135 Lp~~~r~v~~l~---------~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELR---------FFAGLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHH---------HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 555666655542 22233678999999999999999999988887653
No 103
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=64.79 E-value=0.46 Score=38.57 Aligned_cols=35 Identities=14% Similarity=0.203 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 158 QDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 158 pd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
-+....+++|+++||+..+|+++++.-|.++++..
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34557899999999999999999999998887643
No 104
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=64.56 E-value=0.8 Score=36.80 Aligned_cols=50 Identities=6% Similarity=0.137 Sum_probs=36.8
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
.+++.+|++.+.-+. -..-..+++|.++|++..+|+++++.-|.++++..
T Consensus 99 ~~L~~~~r~v~~l~~---------~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 99 KELPDEYREAIRLTE---------LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred HhCCHHHHHHHHHHH---------HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 356677776666531 12236789999999999999999998888877543
No 105
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=64.55 E-value=3.3 Score=27.17 Aligned_cols=24 Identities=8% Similarity=0.347 Sum_probs=16.2
Q ss_pred HHHHHHHHhCCCCceeeeeccccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
...+||..+||++.+|.-|+.+++
T Consensus 11 s~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 11 SQKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHhCCCcchhHHHhcCCC
Confidence 347778888888888877777743
No 106
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=64.53 E-value=1.7 Score=32.90 Aligned_cols=46 Identities=7% Similarity=0.189 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 136 FTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 136 FT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
+|.-+.+.|..+++.. ..++++.++|++..++++++++=+.|++..
T Consensus 142 l~~~e~~vl~~~~~~~----------~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~ 187 (202)
T PRK09390 142 LSERERQVMDGLVAGL----------SNKVIARDLDISPRTVEVYRANVMTKMQAG 187 (202)
T ss_pred hhhhHHHHHHHHHccC----------chHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence 5555556655443321 356788999999999999999988887654
No 107
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=64.28 E-value=0.75 Score=37.13 Aligned_cols=34 Identities=15% Similarity=0.259 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 158 QDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 158 pd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
-+....+++|..+||++.+|++.++.-|.++++.
T Consensus 143 ~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 143 LEGLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3345678999999999999999999999888764
No 108
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=64.25 E-value=2 Score=32.74 Aligned_cols=47 Identities=6% Similarity=0.065 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
..+|..+++.|.-+++.. ..+++|++++++.++|++|.+|=+.|+.-
T Consensus 148 ~~lt~~e~~vl~l~~~g~----------~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 148 PLLTPRERQILKLITEGY----------TNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred cCCCHHHHHHHHHHHCCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 459999999988764431 35788899999999999999998887753
No 109
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=63.72 E-value=0.88 Score=36.94 Aligned_cols=49 Identities=6% Similarity=0.080 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+++.+|++.+.-. +-+....+++|..+|++..+|++.++.-|.++++..
T Consensus 131 ~Lp~~~r~v~~l~---------~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 131 RLPPRTGRVFMMR---------EWLELETEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred hCCHHHHHHHHHH---------HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3555555555442 222336899999999999999999999998887643
No 110
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=63.59 E-value=1.3 Score=34.07 Aligned_cols=34 Identities=3% Similarity=0.115 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 157 RQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 157 kpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
+-+....+++|+.+||+..+|+++++--|.++++
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3445678999999999999999999988877664
No 111
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=63.53 E-value=1.4 Score=34.91 Aligned_cols=48 Identities=13% Similarity=0.243 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 135 KFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 135 kFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+++..|++.|.- +.+. -..+++|..+|++..+|+++++.-|.++++.-
T Consensus 118 ~L~~~~r~vl~L~~~~g----------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRG----------WSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 356667776665 3333 25789999999999999999999888887654
No 112
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=63.51 E-value=0.93 Score=37.00 Aligned_cols=31 Identities=6% Similarity=0.090 Sum_probs=27.9
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 161 VALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
-..+++|..+|++..+|+++++.-|.++++.
T Consensus 147 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 177 (185)
T PRK09649 147 LSYADAAAVCGCPVGTIRSRVARARDALLAD 177 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 3678999999999999999999999998873
No 113
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=63.06 E-value=4.2 Score=33.61 Aligned_cols=48 Identities=17% Similarity=0.209 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 138 QEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 138 ~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
.+.++++.+-|..+ +.-+.-+...+.++|.+.||++..|-.-|.|+..
T Consensus 17 ~~~r~~IL~AA~~l-f~e~Gy~~~s~~dIA~~aGvs~gtiY~hF~sKe~ 64 (212)
T PRK15008 17 SAKKKAILSAALDT-FSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEA 64 (212)
T ss_pred HHHHHHHHHHHHHH-HHHhCcccCCHHHHHHHhCcCHHHHHHHCCCHHH
Confidence 45566666544443 2222466778999999999999999999987653
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=62.98 E-value=0.91 Score=37.57 Aligned_cols=32 Identities=9% Similarity=0.055 Sum_probs=28.1
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 161 VALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
...+++|..+||+..+|+++++.-|.++++..
T Consensus 130 ~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 130 FSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999998887644
No 115
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=62.89 E-value=0.96 Score=37.24 Aligned_cols=33 Identities=9% Similarity=0.095 Sum_probs=28.8
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 161 VALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
...+++|..+||+..+|+++++.-|.++++...
T Consensus 133 ~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 133 FAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 367899999999999999999999998876553
No 116
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=62.65 E-value=0.96 Score=36.28 Aligned_cols=50 Identities=8% Similarity=0.046 Sum_probs=35.8
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
..++..|++.+.-. +-+.-..+++|+.+|++..+|+++++.-|.++++..
T Consensus 134 ~~L~~~~r~vl~l~---------~~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 134 KALSPEERRVIEVL---------YYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred HhCCHHHHHHHHHH---------HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34556666665532 122235789999999999999999999888877654
No 117
>PF13518 HTH_28: Helix-turn-helix domain
Probab=62.64 E-value=1.8 Score=27.99 Aligned_cols=25 Identities=16% Similarity=0.563 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCCCceeeeecccccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
.+.++|.++||++.+|..|...-+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 7888999999999999999976543
No 118
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=62.48 E-value=0.83 Score=35.52 Aligned_cols=48 Identities=15% Similarity=0.249 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 134 TKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 134 TkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
-+++.+|++.+.- +.+. -..+++|+.+||+..+|++.++.-|.++++.
T Consensus 105 ~~Lp~~~r~v~~l~~~~g----------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 105 QKLPARQREAFLLRYWED----------MDVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred HhCCHHHHHHHHHHHHhc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4566667766665 3332 2578999999999999999999888877654
No 119
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=62.13 E-value=1 Score=35.95 Aligned_cols=32 Identities=6% Similarity=0.135 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 160 DVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 160 ~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
....+++|+.+|++..+|+++++.-|.++++.
T Consensus 135 ~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 135 QYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34578999999999999999999888877653
No 120
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=61.85 E-value=1 Score=36.95 Aligned_cols=50 Identities=8% Similarity=0.092 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 134 TKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 134 TkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
..++.+|++.+.- +++. -..+++|+.+||+..+|+++++--|.++++...
T Consensus 135 ~~L~~~~r~i~~L~~~~g----------~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 135 AALPERQRQAVVLRHIEG----------LSNPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3566667666655 3222 257899999999999999999999998887543
No 121
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=60.89 E-value=1.6 Score=35.38 Aligned_cols=50 Identities=10% Similarity=0.161 Sum_probs=38.7
Q ss_pred CCCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 133 RTKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 133 RTkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
-..++.+|++.|.- +.+. ...+++|..+||+..+|++.++.-|.++++..
T Consensus 129 l~~L~~~~r~vl~l~~~~~----------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 129 LAKLSPAHREIIDLVYYHE----------KSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred HHhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34677777777754 4333 26789999999999999999999988887643
No 122
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=60.82 E-value=1.1 Score=37.07 Aligned_cols=32 Identities=9% Similarity=0.234 Sum_probs=27.9
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 161 VALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
...+++|..+|++..+||+.++.-|.++++..
T Consensus 156 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 156 FEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 36789999999999999999999888887644
No 123
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=60.82 E-value=7.2 Score=26.10 Aligned_cols=38 Identities=24% Similarity=0.298 Sum_probs=27.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHH
Q 048824 129 SKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQF 166 (209)
Q Consensus 129 kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~f 166 (209)
|||+-+.++.|+.++|..++++.|-.+.+-=++.++.|
T Consensus 2 r~r~t~~l~~el~~~L~~ls~~t~i~~S~Ll~eAle~~ 39 (44)
T PF12651_consen 2 RKRFTFSLDKELYEKLKELSEETGIPKSKLLREALEDY 39 (44)
T ss_pred ceEEEEecCHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 67888999999999999999998732222224444444
No 124
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=60.68 E-value=1.7 Score=36.19 Aligned_cols=35 Identities=3% Similarity=0.019 Sum_probs=30.5
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCCCCCC
Q 048824 161 VALNQFCNEVGVKRHVLKVWMHNNKNASHRRKDES 195 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~~~ 195 (209)
...+++|+.+||+..+|+++++.-|.++++..++.
T Consensus 150 ~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 150 YTYEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 36899999999999999999999999988766554
No 125
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=60.02 E-value=1.1 Score=36.01 Aligned_cols=29 Identities=7% Similarity=0.113 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
..+++|+.+||+..+|++.++.-|+++++
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 67899999999999999999998888765
No 126
>PF13698 DUF4156: Domain of unknown function (DUF4156)
Probab=59.82 E-value=4.1 Score=31.22 Aligned_cols=16 Identities=31% Similarity=0.412 Sum_probs=13.7
Q ss_pred hhhhhhhhcCCccccc
Q 048824 27 CMKNHAASIGGHANDG 42 (209)
Q Consensus 27 C~kNhaa~~Gg~~~DG 42 (209)
=|||.||.|||.+|-+
T Consensus 53 dlrNeAa~lGgntV~~ 68 (93)
T PF13698_consen 53 DLRNEAAKLGGNTVVL 68 (93)
T ss_pred HHHHHHHHhCCCEEEE
Confidence 4899999999988853
No 127
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=59.61 E-value=3.7 Score=33.32 Aligned_cols=45 Identities=16% Similarity=0.310 Sum_probs=32.4
Q ss_pred HHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 141 KDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 141 kekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
++++.+-|.++ |.-+.-+...++++|.+.||++.+|-.+|.|+..
T Consensus 13 r~~Il~aa~~l-f~~~G~~~~ti~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 13 RQELIETAIAQ-FALRGVSNTTLNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred HHHHHHHHHHH-HHHcCcccCCHHHHHHHcCCCHHHHHHHcCCHHH
Confidence 44455444433 2223467889999999999999999999988654
No 128
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=59.47 E-value=1.3 Score=35.90 Aligned_cols=47 Identities=9% Similarity=0.147 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
+++++|++.+.- +.+ .-..+++|..+||+..+||+.++.-+.+...+
T Consensus 127 ~Lp~~~R~v~~L~~~~----------g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLD----------GMKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHc----------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 456666666554 322 23678999999999999999999776665444
No 129
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=59.21 E-value=4.8 Score=27.26 Aligned_cols=23 Identities=9% Similarity=0.339 Sum_probs=11.8
Q ss_pred HHHHHHHhCCCCceeeeeccccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
..+||..+|+++..|.-|..+++
T Consensus 15 ~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 15 QKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHHCcCHHHHHHHHCCCc
Confidence 44555555555555555555543
No 130
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=59.18 E-value=24 Score=23.27 Aligned_cols=35 Identities=20% Similarity=0.277 Sum_probs=28.3
Q ss_pred CHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 137 TQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 137 T~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
|.|||++|-+- .-+.++..+|+++..+-|.|+...
T Consensus 12 t~eqk~~l~~~--------------i~~~l~~~~g~~~~~v~V~i~e~~ 46 (58)
T cd00491 12 TDEQKRELIER--------------VTEAVSEILGAPEATIVVIIDEMP 46 (58)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCcCcccEEEEEEEeC
Confidence 58999988764 566788899999999999987643
No 131
>PHA01976 helix-turn-helix protein
Probab=59.10 E-value=4.8 Score=27.49 Aligned_cols=18 Identities=17% Similarity=0.265 Sum_probs=10.0
Q ss_pred CCHHHHHHHHHHhCCCCc
Q 048824 158 QDDVALNQFCNEVGVKRH 175 (209)
Q Consensus 158 pd~~~ve~fc~eiGv~r~ 175 (209)
|+...+.++|+.+||+..
T Consensus 42 p~~~~l~~ia~~l~v~~~ 59 (67)
T PHA01976 42 PNLKTLLRLADALGVTLD 59 (67)
T ss_pred CCHHHHHHHHHHHCcCHH
Confidence 455555566666555543
No 132
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=58.15 E-value=2.2 Score=33.79 Aligned_cols=47 Identities=6% Similarity=0.275 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
+++..|++.+.- |++. ...+++|+.+||+..+|+++.+--|.++++.
T Consensus 119 ~L~~~~r~i~~l~~~~g----------~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD----------LTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455666666644 3332 2678999999999999999999888877653
No 133
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=57.97 E-value=1.4 Score=36.07 Aligned_cols=49 Identities=4% Similarity=0.081 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+++.+|++.+.-. +-....++++|..+||+..+|++.++.-|.++++..
T Consensus 106 ~L~~~~r~i~~l~---------~~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLT---------ELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHH---------HhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4555555555432 122236789999999999999999998888877543
No 134
>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=57.54 E-value=2.7 Score=26.29 Aligned_cols=24 Identities=13% Similarity=0.340 Sum_probs=20.1
Q ss_pred HHHHHHHHhCCCCceeeeeccccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
.+++.|..+||++.+|.-|..+.+
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHcCC
Confidence 467889999999999999987664
No 135
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=57.38 E-value=1.2 Score=36.30 Aligned_cols=31 Identities=10% Similarity=0.184 Sum_probs=27.5
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
..+++|..+|++..+|+++++.-|.++++..
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999888887654
No 136
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=57.25 E-value=1.2 Score=35.53 Aligned_cols=32 Identities=16% Similarity=0.360 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 160 DVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 160 ~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
....+++|..+||+..+|+++.+.-|.++++.
T Consensus 152 ~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 152 DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999999998887753
No 137
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=57.01 E-value=2 Score=35.03 Aligned_cols=48 Identities=6% Similarity=0.120 Sum_probs=35.6
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
..++..+++.+.-+.+. -..+++|+.+||+..+|++.++.-|.++++.
T Consensus 154 ~~L~~~~r~vl~l~~e~----------~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 154 ELLSELEKEVLELYLDG----------KSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred HhCCHHHHHHHHHHHcc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34555666665444333 3678999999999999999999888887754
No 138
>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=56.99 E-value=2.6 Score=26.93 Aligned_cols=24 Identities=13% Similarity=0.213 Sum_probs=20.5
Q ss_pred HHHHHHHhCCCCceeeeecccccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
+.++|..+||+..+|+.|..+..-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~l 26 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGLL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCC
Confidence 678999999999999999766643
No 139
>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=56.82 E-value=3.1 Score=31.17 Aligned_cols=28 Identities=7% Similarity=0.255 Sum_probs=23.5
Q ss_pred CHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 159 DDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 159 d~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
+...++++|..+||+..+|++|+++...
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~ 58 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETK 58 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence 3447889999999999999999997543
No 140
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=56.71 E-value=2.4 Score=35.01 Aligned_cols=48 Identities=13% Similarity=0.109 Sum_probs=39.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
.|.+|..|++.+.-++ .|| ..+++|..+|+++..|+.|.+.-+.++++
T Consensus 4 ~~~Lte~qr~VL~Lr~--~Gl--------Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KGL--------SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH--cCC--------CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4678999999988753 343 67899999999999999999988888764
No 141
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=56.68 E-value=28 Score=23.92 Aligned_cols=33 Identities=15% Similarity=0.280 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccc
Q 048824 137 TQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 137 T~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhN 183 (209)
|.|||++|-+- .-+.++..+|++...|.|.|..
T Consensus 13 s~EqK~~L~~~--------------it~a~~~~~~~p~~~v~V~i~e 45 (60)
T PRK02289 13 SQEQKNALARE--------------VTEVVSRIAKAPKEAIHVFIND 45 (60)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCcCcceEEEEEEE
Confidence 79999998764 5567888999999999998865
No 142
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=56.62 E-value=1.6 Score=34.15 Aligned_cols=47 Identities=11% Similarity=0.125 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
.++..|++.+.-. +-.....+++|+.+||+..+|++.++--|.++|+
T Consensus 122 ~L~~~~r~vl~l~---------~~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALR---------FGQNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHH---------HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4556666665552 1222367899999999999999999877777765
No 143
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=56.37 E-value=1.3 Score=36.17 Aligned_cols=48 Identities=10% Similarity=0.174 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 135 KFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 135 kFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
.++++|++.|.- +.+. -..+++|+.+||+..+|++.++.-|.++++..
T Consensus 141 ~Lp~~~r~v~~l~~~eg----------~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 141 RLPKAQRDVLQAVYLEE----------LPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 445566666554 3333 36789999999999999999999888877644
No 144
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=56.21 E-value=1.3 Score=34.65 Aligned_cols=47 Identities=6% Similarity=0.104 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
+++.++++.|.- |++. ...+++|+++||+..+|+++++--+.++++.
T Consensus 109 ~L~~~~r~v~~l~~~~~----------~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 109 ELPARTRYAFEMYRLHG----------ETQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455556665543 3222 2578999999999999999988777766654
No 145
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=56.16 E-value=1.4 Score=36.22 Aligned_cols=48 Identities=10% Similarity=0.142 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
+++..|++.+.-+ +-+....+++|..+||+..+|+++++--|.++++.
T Consensus 111 ~Lp~~~R~v~~L~---------~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 111 DLPEEQRAALHLV---------AIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred hCCHHHHHHHHHH---------HHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 4666666666542 12233688999999999999999999888877653
No 146
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=56.13 E-value=3.7 Score=35.24 Aligned_cols=49 Identities=6% Similarity=0.155 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
..+||..|+|.|.-.+ .| ...+++|..+||+.++|+.++.|-+.|++-+
T Consensus 169 ~~~Lt~re~evl~~~a--~G--------~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~ 217 (232)
T TIGR03541 169 AGVLSEREREVLAWTA--LG--------RRQADIAAILGISERTVENHLRSARRKLGVA 217 (232)
T ss_pred hccCCHHHHHHHHHHH--CC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence 4579999999988764 23 2667889999999999999999999888754
No 147
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=55.92 E-value=1.7 Score=34.93 Aligned_cols=47 Identities=11% Similarity=0.255 Sum_probs=32.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccC
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNAS 188 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~ 188 (209)
-.+++.+|++.+.-. +-.....+++|+.+||+..+|+++++.-+.+.
T Consensus 117 l~~L~~~~r~i~~l~---------~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~ 163 (172)
T PRK09651 117 LDGLNGKTREAFLLS---------QLDGLTYSEIAHKLGVSVSSVKKYVAKATEHC 163 (172)
T ss_pred HHhCCHHHhHHhhhh---------hccCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 345566666665432 23333678999999999999999998766543
No 148
>PRK10651 transcriptional regulator NarL; Provisional
Probab=55.37 E-value=3.5 Score=31.95 Aligned_cols=46 Identities=11% Similarity=0.195 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
.||..+++.|.-+++-. ..+++|.+++++..+|++...|=+.|+.-
T Consensus 155 ~Lt~rE~~vl~~l~~g~----------~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 155 QLTPRERDILKLIAQGL----------PNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred cCCHHHHHHHHHHHcCC----------CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 49999999998775431 45677889999999999999998888754
No 149
>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=55.26 E-value=5.7 Score=23.88 Aligned_cols=21 Identities=14% Similarity=0.368 Sum_probs=12.7
Q ss_pred HHHHHHhCCCCceeeeecccc
Q 048824 164 NQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 164 e~fc~eiGv~r~V~KVWfhNn 184 (209)
.+||..+|+++..|..|+.++
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 16 EELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcCC
Confidence 356666666666666666554
No 150
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=55.17 E-value=2.1 Score=36.15 Aligned_cols=52 Identities=8% Similarity=0.127 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
+++..|++.+.-.+. +..-+.-..+++|+.+||+..+|+++++.-+.++|+.
T Consensus 178 ~Lp~~~R~v~~L~y~-----l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 178 KLSDREKQIMELRFG-----LNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHhc-----cCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455566666554310 0113344688999999999999999999988887764
No 151
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=54.88 E-value=2.9 Score=28.67 Aligned_cols=22 Identities=14% Similarity=0.370 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCCceeeeecccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhNn 184 (209)
+.++|..+||+.++|+.|-..-
T Consensus 3 i~eva~~~gvs~~tlr~y~~~g 24 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREG 24 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTT
T ss_pred HHHHHHHHCcCHHHHHHHHHhc
Confidence 6789999999999999996543
No 152
>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=54.84 E-value=5.2 Score=28.33 Aligned_cols=21 Identities=24% Similarity=0.635 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCCCceeeeecc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMH 182 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfh 182 (209)
.+.++|.+|||++.+|.-|-.
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 467899999999999999964
No 153
>PRK06930 positive control sigma-like factor; Validated
Probab=54.67 E-value=2.3 Score=35.65 Aligned_cols=47 Identities=11% Similarity=0.237 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
+++..+++.+.- |++- ...+++|..+||+..+|+++++.-+.++++.
T Consensus 114 ~L~~rer~V~~L~~~eg----------~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG----------LSYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 577777777665 4333 2678999999999999999999988887654
No 154
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=54.60 E-value=1.9 Score=36.22 Aligned_cols=49 Identities=4% Similarity=0.128 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
.+++..|++.+..++ -+....+++|..+||+..+|+.+++.-+.++++.
T Consensus 174 ~~L~~~~r~il~l~y---------~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 174 ESLSEREQLVLSLYY---------YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred HhCCHHHHHHHHHHH---------hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 356777777776632 2223679999999999999999999888877654
No 155
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=54.17 E-value=9.9 Score=41.75 Aligned_cols=61 Identities=16% Similarity=0.205 Sum_probs=52.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCcccCC--CCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 126 TGKSKRQRTKFTQEQKDKMLEFAERIGWRMQR--QDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 126 ~~~kKR~RTkFT~EQkekM~~faEk~GW~iqk--pd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+.+-|+.|+.+-.|+...|-. |.|+. +...+...|-.+.+.+.++..+||||.+.+.+|-.
T Consensus 702 ~~~~~~~~~~~~~~aa~~l~~------a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 702 SPRDKLLRLTILPEAAMILGR------AYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CcccccCcccccHHHHhhhhh------cccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 456799999999999988875 33544 66889999999999999999999999999988765
No 156
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=54.05 E-value=32 Score=23.18 Aligned_cols=34 Identities=21% Similarity=0.308 Sum_probs=28.3
Q ss_pred CHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 048824 137 TQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 137 T~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNn 184 (209)
|.|||++|..- .-+.++..+|++...+-|.+...
T Consensus 13 t~eqK~~l~~~--------------it~~l~~~lg~~~~~v~V~i~e~ 46 (63)
T TIGR00013 13 TDEQKRQLIEG--------------VTEAMAETLGANLESIVVIIDEM 46 (63)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCCCcccEEEEEEEc
Confidence 79999998764 56778999999999999888754
No 157
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=53.87 E-value=1.8 Score=34.55 Aligned_cols=48 Identities=13% Similarity=0.226 Sum_probs=34.3
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
..++.+|++.+.-. +-+.-..+++|+.+|++..+|++++++-+.+.+.
T Consensus 118 ~~Lp~~~r~v~~L~---------~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 118 GKLSSKARAAFLYN---------RLDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred HhCCHHHHHHHHHH---------HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44556666665542 2223367899999999999999999987776654
No 158
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=53.21 E-value=2.7 Score=35.37 Aligned_cols=30 Identities=17% Similarity=0.255 Sum_probs=26.8
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
..+++|..+|++..+|+++++.-|.++++.
T Consensus 166 s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 166 ETNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999988887764
No 159
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=53.17 E-value=4.5 Score=31.31 Aligned_cols=47 Identities=15% Similarity=0.237 Sum_probs=39.0
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
..+|..+.+.|.-+++-. ..++++.+++++.++|++..+|=+.|+.-
T Consensus 136 ~~Lt~~E~~il~~l~~g~----------~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~ 182 (196)
T PRK10360 136 DPLTKRERQVAEKLAQGM----------AVKEIAAELGLSPKTVHVHRANLMEKLGV 182 (196)
T ss_pred cCCCHHHHHHHHHHHCCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 369999999998887542 57888999999999999999998887653
No 160
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=53.06 E-value=1.2 Score=34.95 Aligned_cols=49 Identities=14% Similarity=0.276 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 136 FTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 136 FT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
++.++++.+.-. +-+....+++|.++|++..+|++.++.-+.++++...
T Consensus 106 L~~~~r~v~~l~---------~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 106 LPPACRDSFLLR---------KLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred CCHHHHHHHHHH---------HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 555555555442 2233367899999999999999999988777765443
No 161
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=52.91 E-value=2.7 Score=36.87 Aligned_cols=50 Identities=6% Similarity=0.145 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
+++++|++.+.-. +-..-..+++|+.+|++..++++.++.-|.++++..+
T Consensus 115 ~L~~~~R~v~~L~---------~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 115 RLSPLERAAFLLH---------DVFGVPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred hCCHHHHHHHHHH---------HHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 3556666665432 1112257899999999999999999999999998654
No 162
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=52.88 E-value=2.1 Score=36.31 Aligned_cols=34 Identities=12% Similarity=0.163 Sum_probs=28.8
Q ss_pred CHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 159 DDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 159 d~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+....+++|..+||+..+|+++++.-+.++++..
T Consensus 199 ~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 199 EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3346899999999999999999999888877643
No 163
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=52.83 E-value=1.7 Score=35.21 Aligned_cols=32 Identities=3% Similarity=0.137 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 160 DVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 160 ~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
...++++|+.+||+..+|++.++.-|.++++.
T Consensus 154 g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 154 GLSYEDIASVMQCPVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34679999999999999999999988887764
No 164
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=52.83 E-value=1.9 Score=33.87 Aligned_cols=45 Identities=11% Similarity=0.210 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccC
Q 048824 134 TKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNAS 188 (209)
Q Consensus 134 TkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~ 188 (209)
.+++.+|++.+.- +++. ...+++|+.+|++..+|+++++.-+.++
T Consensus 112 ~~L~~~~r~v~~L~~~~g----------~s~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 112 DGLPPLVKRAFLLAQVDG----------LGYGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred HHCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4566677777654 3333 2678999999999999999988765543
No 165
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=52.47 E-value=29 Score=23.79 Aligned_cols=35 Identities=9% Similarity=0.204 Sum_probs=28.1
Q ss_pred CHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 137 TQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 137 T~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
|.|||++|.+- .-+.++..+|++...+-|.+....
T Consensus 13 t~eqk~~l~~~--------------it~~l~~~lg~p~~~v~V~i~e~~ 47 (64)
T PRK01964 13 PEEKIKNLIRE--------------VTEAISATLDVPKERVRVIVNEVP 47 (64)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCcChhhEEEEEEEcC
Confidence 78999998764 456688899999999998886543
No 166
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=52.33 E-value=1.7 Score=35.70 Aligned_cols=48 Identities=6% Similarity=0.121 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
+++..|++.+.-. +-+....+++|+++|++..+|+++++.-|.++++.
T Consensus 131 ~L~~~~r~v~~l~---------~~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 131 HLPEQTARVFMMR---------EVLGFESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred hCCHHHHHHHHHH---------HHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4556666665542 22233688999999999999999999888877653
No 167
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=52.32 E-value=1.7 Score=35.63 Aligned_cols=33 Identities=6% Similarity=0.007 Sum_probs=28.9
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 161 VALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
-..+++|+.+|++..+|++.++--|.++++.-.
T Consensus 128 ~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 128 FSYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 368899999999999999999999998876653
No 168
>PHA00542 putative Cro-like protein
Probab=52.23 E-value=11 Score=27.71 Aligned_cols=45 Identities=11% Similarity=0.107 Sum_probs=31.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 130 KRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 130 KR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
+..+.++.+.++. .+.+..|| ...++|..+||++.+|--|..+..
T Consensus 12 Rp~~~~~~~~~l~---~~l~~~gl--------Tq~elA~~lgIs~~tIsr~e~g~~ 56 (82)
T PHA00542 12 IPAAYTQRPDELV---CALIRAGW--------SQEQIADATDVSQPTICRIYSGRH 56 (82)
T ss_pred CCcccCcCHHHHH---HHHHHCCC--------CHHHHHHHHCcCHHHHHHHHcCCC
Confidence 4455666655443 33355565 677899999999999999998763
No 169
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=52.18 E-value=4.4 Score=31.42 Aligned_cols=46 Identities=2% Similarity=0.008 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
.+|.-+.+.|.-+++- ...+++|.+++++.++|+++..+=|.|+.-
T Consensus 149 ~lt~re~~vl~~l~~g----------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~ 194 (210)
T PRK09935 149 VLSNREVTILRYLVSG----------LSNKEIADQLLLSNKTVSAHKSNIYGKLGL 194 (210)
T ss_pred cCCHHHHHHHHHHHcC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 4888888888776544 267899999999999999999998888753
No 170
>PF12728 HTH_17: Helix-turn-helix domain
Probab=51.64 E-value=3.8 Score=26.90 Aligned_cols=25 Identities=16% Similarity=0.452 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCCceeeeecccccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
.++++|+.+||++.+|.-|.++.+-
T Consensus 3 t~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 3688999999999999999876643
No 171
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=51.42 E-value=6.4 Score=32.10 Aligned_cols=48 Identities=23% Similarity=0.385 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 138 QEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 138 ~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
++-++++.+-|.++ |.-+.-+...++++|.+.||++..|--+|-|+-.
T Consensus 10 ~~~R~~Il~AA~~l-f~e~G~~~~t~~~Ia~~agvs~~tlY~~F~sKe~ 57 (215)
T PRK10668 10 QETRQHILDAALRL-FSQQGVSATSLADIAKAAGVTRGAIYWHFKNKSD 57 (215)
T ss_pred HHHHHHHHHHHHHH-HHHcCcccCCHHHHHHHhCCChHHHHHHCCCHHH
Confidence 55566666544444 2223466778999999999999999999987654
No 172
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=51.34 E-value=2.9 Score=35.07 Aligned_cols=31 Identities=13% Similarity=0.278 Sum_probs=27.7
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
..+++|+.+|++..+|+++++.-|.++++..
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999999887654
No 173
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=51.33 E-value=32 Score=23.14 Aligned_cols=34 Identities=21% Similarity=0.279 Sum_probs=25.4
Q ss_pred CHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 048824 137 TQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 137 T~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNn 184 (209)
|.|||++|-+- .-+-+.+.+|+++..+.|.|+.-
T Consensus 12 ~~e~K~~l~~~--------------it~~~~~~lg~~~~~i~V~i~E~ 45 (60)
T PF01361_consen 12 TAEQKRELAEA--------------ITDAVVEVLGIPPERISVVIEEV 45 (60)
T ss_dssp -HHHHHHHHHH--------------HHHHHHHHHTS-GGGEEEEEEEE
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCcCCCeEEEEEEEE
Confidence 78999887754 44567888999999999988753
No 174
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=51.30 E-value=1.6 Score=37.67 Aligned_cols=33 Identities=0% Similarity=0.064 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 160 DVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 160 ~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
....+++|+.+||+..+|+++++.-|.++++..
T Consensus 187 g~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 187 NMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 345689999999999999999999998887643
No 175
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=51.24 E-value=2 Score=34.31 Aligned_cols=47 Identities=9% Similarity=0.161 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASH 189 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~k 189 (209)
.+++..|++.+.-+ +-+.-..+++|..+|++..+|+.++.+.+.+.+
T Consensus 117 ~~L~~~~r~v~~L~---------~~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 117 DGLSGKARAAFLMS---------QLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred HhCCHHHHHHHHHH---------HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45667777766652 122236889999999999999999987765543
No 176
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=51.04 E-value=34 Score=26.21 Aligned_cols=36 Identities=6% Similarity=0.107 Sum_probs=29.2
Q ss_pred CHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 137 TQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 137 T~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
+.||+++|-+- .-+.|.+.+||+...|-|-|++...
T Consensus 70 ~~e~k~~l~~~--------------i~~~l~~~lgi~~~rv~I~f~~~~~ 105 (116)
T PTZ00397 70 SRSNNSSIAAA--------------ITKILASHLKVKSERVYIEFKDCSA 105 (116)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCcCcccEEEEEEECCh
Confidence 57999887753 4556788999999999999998754
No 177
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=50.92 E-value=1.8 Score=35.02 Aligned_cols=49 Identities=2% Similarity=0.110 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 134 TKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 134 TkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
.+++.+|++.+.- +.+. -..+++|..+|++..+|++.++.-|.++++..
T Consensus 121 ~~L~~~~r~i~~l~~~~g----------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 121 KELNESNRQVFKYKVFYN----------LTYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3456666666654 3333 36789999999999999999998888876543
No 178
>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=50.42 E-value=4.4 Score=29.37 Aligned_cols=24 Identities=17% Similarity=0.571 Sum_probs=20.2
Q ss_pred CHHHHHHHHHHhCCCCceeeeecc
Q 048824 159 DDVALNQFCNEVGVKRHVLKVWMH 182 (209)
Q Consensus 159 d~~~ve~fc~eiGv~r~V~KVWfh 182 (209)
......+||++|||+..+|+.|=.
T Consensus 21 g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 21 GKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred CCccHHHHHHHHCCCHHHHHHHhh
Confidence 345678899999999999999954
No 179
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=50.40 E-value=5.6 Score=34.05 Aligned_cols=47 Identities=13% Similarity=0.129 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
..+|+-|++.|.-.+. || ..+++|++++|+.+++|.+..|-..|+.-
T Consensus 154 ~~Lt~rE~~Vl~l~~~--G~--------s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 154 ALLTHREKEILNKLRI--GA--------SNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCCHHHHHHHHHHHc--CC--------CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3599999999998766 53 56789999999999999999987777653
No 180
>PF13309 HTH_22: HTH domain
Probab=50.19 E-value=18 Score=25.77 Aligned_cols=42 Identities=14% Similarity=0.253 Sum_probs=31.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCcee
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVL 177 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~ 177 (209)
...++.+++..+-..-+..|. ..=...|+..|+.+||++.+|
T Consensus 18 ~~~l~~~~k~~iV~~L~~~G~---F~lKgav~~vA~~L~iS~~TV 59 (64)
T PF13309_consen 18 PSRLSKEEKKEIVRQLYEKGI---FLLKGAVEYVAEKLGISRATV 59 (64)
T ss_pred hhhCCHHHHHHHHHHHHHCCC---cccCcHHHHHHHHHCCCHHHH
Confidence 356778888887776666663 233459999999999999875
No 181
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=50.14 E-value=5.3 Score=35.54 Aligned_cols=49 Identities=10% Similarity=0.147 Sum_probs=40.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
...+|..|++.|.-.++ | + ..+++|..+||++++||+++.|-+.|++-.
T Consensus 188 ~~~LT~RE~evl~l~a~--G----~----s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~ 236 (247)
T TIGR03020 188 AGLITAREAEILAWVRD--G----K----TNEEIAAILGISSLTVKNHLQHIFKKLDVR 236 (247)
T ss_pred ccCCCHHHHHHHHHHHC--C----C----CHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence 45799999999997643 3 2 567889999999999999999988887644
No 182
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=50.03 E-value=29 Score=29.46 Aligned_cols=41 Identities=5% Similarity=0.164 Sum_probs=33.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceee
Q 048824 132 QRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLK 178 (209)
Q Consensus 132 ~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~K 178 (209)
....+|.|++++|..+= .+.|..-.|..||.+.||+..-|.
T Consensus 82 k~y~Lt~e~i~Eir~LR------~~DP~~wTr~~LAkkF~~S~~fV~ 122 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLR------AEDPEKWTRKKLAKKFNCSPLFVS 122 (164)
T ss_pred ccccCCHHHHHHHHHHH------HcCchHhhHHHHHHHhCCCHHHHH
Confidence 45789999999999972 235778899999999999876554
No 183
>PHA02535 P terminase ATPase subunit; Provisional
Probab=49.64 E-value=12 Score=37.78 Aligned_cols=46 Identities=15% Similarity=0.449 Sum_probs=36.0
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
++||.|-|........+ || .+.++|+++||+.++|.-|- +|.+|..
T Consensus 1 ~~yt~EfK~~Av~Ly~~-G~--------sv~eIA~~LGv~~~Tl~~W~--kr~~w~~ 46 (581)
T PHA02535 1 TAYDDDVRRAAKFLYWQ-GW--------TVAEIAEELGLKSRTIYSWK--ERDGWRD 46 (581)
T ss_pred CCCCHHHHHHHHHHHHc-CC--------CHHHHHHHhCCChhHHHHHh--ccccccc
Confidence 46899988888876666 77 67899999999999999994 3444443
No 184
>PRK11891 aspartate carbamoyltransferase; Provisional
Probab=49.13 E-value=12 Score=36.29 Aligned_cols=43 Identities=23% Similarity=0.468 Sum_probs=33.1
Q ss_pred CHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccccc
Q 048824 137 TQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNA 187 (209)
Q Consensus 137 T~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k 187 (209)
|..|-+-|.+.-..+|- ++++||+.|||++++|..|+--.-..
T Consensus 1 ~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~l~~wl~p~~~~ 43 (429)
T PRK11891 1 TVPQQAFLRDAMRRLNM--------TREAFANRIGVSRRALDTWLLPDDSQ 43 (429)
T ss_pred ChhHHHHHHHHHHHhCC--------CHHHHHHHhCCcHHhHHhhcCCCCch
Confidence 34677777777677762 78999999999999999998544333
No 185
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=49.12 E-value=0.81 Score=37.15 Aligned_cols=53 Identities=4% Similarity=0.094 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHhCcc------cCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 139 EQKDKMLEFAERIGWR------MQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 139 EQkekM~~faEk~GW~------iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
++.+.|.+..+++.=+ +.+-.....+++|..+||+..+|++|++.-|.++++.
T Consensus 123 ~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 123 EERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred HHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4445555555554311 1122334679999999999999999999988887754
No 186
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=49.09 E-value=35 Score=23.02 Aligned_cols=34 Identities=21% Similarity=0.248 Sum_probs=27.8
Q ss_pred CHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 048824 137 TQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 137 T~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNn 184 (209)
|.|||+.|-+- .-+.++..+|++...+.|.|...
T Consensus 13 s~eqk~~l~~~--------------it~~l~~~~~~p~~~v~V~i~e~ 46 (62)
T PRK00745 13 TVEQKRKLVEE--------------ITRVTVETLGCPPESVDIIITDV 46 (62)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHcCCChhHEEEEEEEc
Confidence 79999988764 45668899999999999988654
No 187
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=48.95 E-value=2.4 Score=33.71 Aligned_cols=47 Identities=4% Similarity=0.134 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
+++..|++.+.-. +-+....+++|+.+||+..+|++=++.-|.++++
T Consensus 140 ~L~~~~r~vi~l~---------~~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 140 KLPEDYREVILLR---------HLEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCHHHHHHHHHH---------HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4677777776652 2234478899999999999999988877777664
No 188
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=48.80 E-value=1.4 Score=35.82 Aligned_cols=38 Identities=8% Similarity=0.206 Sum_probs=31.4
Q ss_pred cCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 155 MQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 155 iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+.+-+....+++|..+||+..+|+++++.-|.++++..
T Consensus 142 L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 142 LADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred ehhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34445567899999999999999999999988887644
No 189
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=47.96 E-value=5 Score=35.69 Aligned_cols=31 Identities=3% Similarity=0.044 Sum_probs=28.4
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 161 VALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
-..+++|+.+|++..+||+.++.-|.++++.
T Consensus 170 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 200 (339)
T PRK08241 170 WSAAEVAELLDTSVAAVNSALQRARATLAER 200 (339)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHhhc
Confidence 3678999999999999999999999999984
No 190
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=47.69 E-value=4.1 Score=37.17 Aligned_cols=53 Identities=11% Similarity=0.208 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+++..|++.|...+ | +.+-+....+++|..+||++.+|+++.+.-+.++|+.-
T Consensus 262 ~L~~~~R~vl~lry---g--L~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRF---G--LLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHh---c--cCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 45566666655421 1 12344557899999999999999999999998887643
No 191
>PRK08359 transcription factor; Validated
Probab=47.57 E-value=8.8 Score=33.03 Aligned_cols=24 Identities=21% Similarity=0.365 Sum_probs=19.2
Q ss_pred HHHHHHHHhCCCCceeeeeccccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
..++||..+||++.+|.-|=.+.+
T Consensus 100 SQeeLA~~lgvs~stI~~iE~G~~ 123 (176)
T PRK08359 100 SYEELSHEVGLSVNDLRRIAHGEY 123 (176)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCc
Confidence 567888888888888888877665
No 192
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=47.46 E-value=4.3 Score=35.68 Aligned_cols=32 Identities=9% Similarity=0.162 Sum_probs=28.7
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
..+++|+.+|++..+++++++.-|.+++...+
T Consensus 126 s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 126 PYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 57899999999999999999999999987543
No 193
>PF13565 HTH_32: Homeodomain-like domain
Probab=47.19 E-value=20 Score=24.98 Aligned_cols=39 Identities=21% Similarity=0.446 Sum_probs=25.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHh-CcccCCCCHHHHHHHHHHhCCC
Q 048824 129 SKRQRTKFTQEQKDKMLEFAERI-GWRMQRQDDVALNQFCNEVGVK 173 (209)
Q Consensus 129 kKR~RTkFT~EQkekM~~faEk~-GW~iqkpd~~~ve~fc~eiGv~ 173 (209)
.-|.|+ +.|+.+.|.++.+.. .| --....+.|..+.|++
T Consensus 26 ~Grp~~--~~e~~~~i~~~~~~~p~w----t~~~i~~~L~~~~g~~ 65 (77)
T PF13565_consen 26 PGRPRK--DPEQRERIIALIEEHPRW----TPREIAEYLEEEFGIS 65 (77)
T ss_pred CCCCCC--cHHHHHHHHHHHHhCCCC----CHHHHHHHHHHHhCCC
Confidence 344555 899988888876653 33 2245777778877754
No 194
>PRK13558 bacterio-opsin activator; Provisional
Probab=46.57 E-value=14 Score=35.61 Aligned_cols=43 Identities=14% Similarity=0.295 Sum_probs=34.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCcee
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVL 177 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~ 177 (209)
...+|..|.|.|+...+. || -..|.+...+++|.++||++.+|
T Consensus 605 ~~~lt~~q~e~l~~a~~~-gy-f~~pr~~~~~e~a~~l~is~~t~ 647 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVS-GY-FEWPRRVEGEELAESMGISRSTF 647 (665)
T ss_pred hhhCCHHHHHHHHHHHHc-CC-CCCCccCCHHHHHHHhCCCHHHH
Confidence 357999999998875444 64 22277889999999999999876
No 195
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=46.30 E-value=4.4 Score=32.61 Aligned_cols=31 Identities=3% Similarity=0.051 Sum_probs=26.9
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 161 VALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
...+++|+.+|++..+|+++++--|.++++.
T Consensus 166 ~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~ 196 (198)
T TIGR02859 166 KSYQEIACDLNRHVKSIDNALQRVKRKLEKY 196 (198)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 3678999999999999999999888887653
No 196
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=46.15 E-value=10 Score=30.03 Aligned_cols=41 Identities=17% Similarity=0.412 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNn 184 (209)
-+|..|++.|.-+ +-++--+.++|..+||+|+.|--|+.--
T Consensus 17 LLT~kQ~~~l~ly---------y~eDlSlsEIAe~~~iSRqaV~d~ikr~ 57 (101)
T PF04297_consen 17 LLTEKQREILELY---------YEEDLSLSEIAEELGISRQAVYDSIKRA 57 (101)
T ss_dssp GS-HHHHHHHHHH---------CTS---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred HCCHHHHHHHHHH---------HccCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4789999999887 6777789999999999999887666543
No 197
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=45.44 E-value=21 Score=23.11 Aligned_cols=32 Identities=22% Similarity=0.297 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeee
Q 048824 140 QKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKV 179 (209)
Q Consensus 140 QkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KV 179 (209)
+++.|.+.-++.|| .+.+-|..+||++.+|.-
T Consensus 6 E~~~i~~aL~~~~g--------n~~~aA~~Lgisr~tL~~ 37 (42)
T PF02954_consen 6 EKQLIRQALERCGG--------NVSKAARLLGISRRTLYR 37 (42)
T ss_dssp HHHHHHHHHHHTTT---------HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHHhCC--------CHHHHHHHHCCCHHHHHH
Confidence 45566666677666 467899999999988753
No 198
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=45.43 E-value=3.6 Score=35.93 Aligned_cols=31 Identities=10% Similarity=0.173 Sum_probs=27.9
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
..+++|+.+|++..+||++++.-|.++++..
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l 164 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTVS 164 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999999988654
No 199
>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=45.43 E-value=7.4 Score=25.73 Aligned_cols=19 Identities=21% Similarity=0.574 Sum_probs=15.4
Q ss_pred HHHHHHHHHhCCCCceeee
Q 048824 161 VALNQFCNEVGVKRHVLKV 179 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KV 179 (209)
-..++||+++||++++|+-
T Consensus 16 it~~eLa~~l~vS~rTi~~ 34 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRR 34 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHH
T ss_pred cCHHHHHHHhCCCHHHHHH
Confidence 5789999999999988753
No 200
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=45.24 E-value=3.8 Score=34.77 Aligned_cols=51 Identities=6% Similarity=0.104 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
++++.|++.+.-+. -+..-+....+++|+.+||+..+|++|.+..+.++++
T Consensus 175 ~Lp~~~R~i~~l~y-----~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~ 225 (233)
T PRK05803 175 ILDEREKEVIEMRY-----GLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225 (233)
T ss_pred hCCHHHHHHHHHHh-----CCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45566666666531 0111233468899999999999999998877777664
No 201
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=44.84 E-value=2.3 Score=34.39 Aligned_cols=47 Identities=11% Similarity=0.299 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHH-HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 134 TKFTQEQKDKMLE-FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 134 TkFT~EQkekM~~-faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
.+++..|++.+.- +.+. ...+++|..+||+..+|+.+++--|+++++
T Consensus 126 ~~L~~~~r~v~~l~~~~g----------~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 126 MSLPIKYREVIYLFYYEE----------LSIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred HhCCHHHhhHhHhHHhcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3566667666554 3333 267899999999999999999988877764
No 202
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=44.68 E-value=3.6 Score=35.39 Aligned_cols=47 Identities=4% Similarity=0.126 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
+++..|++.+.-. +-.....+++|..+||+..+|+++++.-+.++|+
T Consensus 201 ~L~~~~r~vl~l~---------~~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 201 QLSEKEQLVISLF---------YKEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred cCCHHHHHHHHHH---------HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3556666666542 2233467999999999999999999988887765
No 203
>smart00351 PAX Paired Box domain.
Probab=44.63 E-value=12 Score=29.56 Aligned_cols=42 Identities=12% Similarity=0.233 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 136 FTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 136 FT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
++.|+++++..+++ -|+ ...++|..+||++.+|..|.+.-+.
T Consensus 18 ~s~~~R~riv~~~~-~G~--------s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 18 LPDEERQRIVELAQ-NGV--------RPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCHHHHHHHHHHHH-cCC--------CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 88999999998765 342 4568899999999999999986543
No 204
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=44.54 E-value=35 Score=22.26 Aligned_cols=35 Identities=23% Similarity=0.392 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCC
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKR 174 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r 174 (209)
|-.||.|+-++|.+...+.|-. .-..+|..++..+
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~-------~W~~Ia~~~~~~R 35 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKD-------NWKKIAKRMPGGR 35 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTT-------HHHHHHHHHSSSS
T ss_pred CCCCCHHHHHHHHHHHHHhCCc-------HHHHHHHHcCCCC
Confidence 5679999999999999997722 4566777777433
No 205
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=44.28 E-value=10 Score=29.71 Aligned_cols=42 Identities=12% Similarity=0.232 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 048824 138 QEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 138 ~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNn 184 (209)
..-.+++.+|-+.. ..+.-.++++|..+||++..|.-+|...
T Consensus 8 ~~~i~~~~~~I~~~-----~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIEDN-----LESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHHh-----cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 33445666665553 3345688999999999999998888653
No 206
>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=44.02 E-value=6.6 Score=34.24 Aligned_cols=35 Identities=17% Similarity=0.468 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 158 QDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 158 pd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
-.-.++++|+..++|++..+-+|+.|-+...+++.
T Consensus 12 ~~tgt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~ 46 (186)
T PF04936_consen 12 KATGTIDELADYFDVSRTSVSVWIKNGKDPKRAKP 46 (186)
T ss_pred cccccHHHHHHHHccCHHHHHHHHHcCCCcccccc
Confidence 34468999999999999999999999998887765
No 207
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=43.93 E-value=12 Score=29.49 Aligned_cols=27 Identities=4% Similarity=0.239 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHHHhCCCCceeeeeccc
Q 048824 157 RQDDVALNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 157 kpd~~~ve~fc~eiGv~r~V~KVWfhN 183 (209)
.-+.-.|+++|++.||+|.+|=.-|.|
T Consensus 20 ~~~~ITV~~I~~~AgvsR~TFY~hF~d 46 (176)
T TIGR02366 20 AFSKISVSDIMSTAQIRRQTFYNHFQD 46 (176)
T ss_pred CCccCCHHHHHHHhCCCHHHHHHHCCC
Confidence 366789999999999999998766665
No 208
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=43.60 E-value=4 Score=34.62 Aligned_cols=53 Identities=4% Similarity=0.020 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
..++..|++.|.-.+- ...-+.-..+++|+.+|++..+|+++.+.-+.+++++
T Consensus 173 ~~L~~~~r~il~l~y~-----~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 173 SVLDGREREVIEMRYG-----LGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred HhCCHHHHHHHHHHHc-----CCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4566777777665310 0001334689999999999999999988877776653
No 209
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=43.60 E-value=11 Score=29.61 Aligned_cols=18 Identities=6% Similarity=0.032 Sum_probs=13.1
Q ss_pred CCHHHHHHHHHHhCCCCc
Q 048824 158 QDDVALNQFCNEVGVKRH 175 (209)
Q Consensus 158 pd~~~ve~fc~eiGv~r~ 175 (209)
|+...+..||.-+||+..
T Consensus 45 p~~~~l~~la~~l~vs~~ 62 (135)
T PRK09706 45 PTGKNLFALAKALQCSPT 62 (135)
T ss_pred CCHHHHHHHHHHHCcCHH
Confidence 666777777777777764
No 210
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=43.37 E-value=3.5 Score=33.13 Aligned_cols=48 Identities=4% Similarity=0.160 Sum_probs=34.2
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
..++..|++.+.... -.....+++|..+||+..+|++.++.-|.+++.
T Consensus 136 ~~L~~~~r~i~~l~~---------~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 136 AELEPPRSELIRTAF---------FEGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred HhCCHHHHHHHHHHH---------HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 345555555554421 222367899999999999999999988887764
No 211
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=43.10 E-value=58 Score=24.26 Aligned_cols=34 Identities=12% Similarity=0.186 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccc
Q 048824 136 FTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 136 FT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhN 183 (209)
.|.|||++|-+- .-+.+++-+|.+..++.|.|.-
T Consensus 13 ~s~EqK~~La~~--------------iT~a~~~~lg~~~e~v~V~I~e 46 (76)
T PRK01271 13 LDEEQKAALAAD--------------ITDVIIRHLNSKDSSISIALQQ 46 (76)
T ss_pred CCHHHHHHHHHH--------------HHHHHHHHhCcCcceEEEEEEE
Confidence 479999988753 3456788899999999998864
No 212
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=42.83 E-value=14 Score=31.16 Aligned_cols=29 Identities=3% Similarity=0.177 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHhCCCCceeeeeccccccc
Q 048824 158 QDDVALNQFCNEVGVKRHVLKVWMHNNKNA 187 (209)
Q Consensus 158 pd~~~ve~fc~eiGv~r~V~KVWfhNnR~k 187 (209)
-+ ..++++|.+.||++.+|-.+|-|+..-
T Consensus 31 y~-~s~~~IA~~AGvsk~tiy~~F~sKe~L 59 (225)
T PRK11552 31 LH-ATTRDIAAQAGQNIAAITYYFGSKEDL 59 (225)
T ss_pred cc-CCHHHHHHHhCCCHHHHHHHcCCHHHH
Confidence 44 789999999999999999999987653
No 213
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=42.82 E-value=3.4 Score=34.62 Aligned_cols=48 Identities=6% Similarity=0.155 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
..++..|++.+.-.+ -+...++++|..+||+..+|+.|.+.-+.++++
T Consensus 177 ~~L~~~~r~vl~l~y---------~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 177 AALPERERRILLLRF---------FEDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred HcCCHHHHHHHHHHH---------hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467777777776642 123368999999999999999999877766654
No 214
>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=42.75 E-value=6.2 Score=26.94 Aligned_cols=21 Identities=19% Similarity=0.487 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCCceeeeeccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhN 183 (209)
+.++|..+||+..+|+.|.+.
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 578999999999999999864
No 215
>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=42.16 E-value=13 Score=27.01 Aligned_cols=46 Identities=24% Similarity=0.362 Sum_probs=29.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccc
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhN 183 (209)
|-.||.+=|-+..++|++.+ ........-|.+.||+++.|+-|.+-
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~-----nc~~~~RAaarkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDN-----NCKGNQRAAARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp -----HHHHHHHHHHHHH-T-----TTTT-HHHHHHHTTS-HHHHHHHHTT
T ss_pred ccccChHHHHHHHHHHHHcc-----chhhhHHHHHHHhCccHHHHHHHHHH
Confidence 56789998888889988853 32333455789999999999999763
No 216
>PHA02893 hypothetical protein; Provisional
Probab=41.90 E-value=8.5 Score=30.12 Aligned_cols=10 Identities=40% Similarity=1.185 Sum_probs=8.5
Q ss_pred Cccccccccc
Q 048824 52 DSLTCAACGC 61 (209)
Q Consensus 52 ~~l~CaaCgC 61 (209)
..|.|+|||-
T Consensus 68 ~tL~CaACGS 77 (88)
T PHA02893 68 SNIKCIACGS 77 (88)
T ss_pred Cceeehhhch
Confidence 4799999993
No 217
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=41.68 E-value=3.1 Score=36.34 Aligned_cols=32 Identities=13% Similarity=0.335 Sum_probs=27.7
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 161 VALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
-..+++|..+||+..+||++++.-|.++++..
T Consensus 178 ~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 178 LSMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 36789999999999999999999988877543
No 218
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=41.41 E-value=3.7 Score=35.30 Aligned_cols=48 Identities=4% Similarity=0.061 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
.++..|++.+.-. +-+.-..+++|..+||+..+|++|.+.-+.++++.
T Consensus 205 ~L~~~~r~vl~l~---------~~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCT---------FIENLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHH---------HhCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3556666665542 11223578999999999999999999888877654
No 219
>PF03227 GILT: Gamma interferon inducible lysosomal thiol reductase (GILT); InterPro: IPR004911 This family includes the two characterised human gamma-interferon-inducible lysosomal thiol reductase (GILT) sequences [, ]. It also contains several other eukaryotic putative proteins with similarity to GILT []. The aligned region contains three conserved cysteine residues. In addition, the two GILT sequences possess a C-X(2)-C motif that is shared by some of the other sequences in the family. This motif is thought to be associated with disulphide bond reduction.
Probab=41.25 E-value=4.6 Score=31.14 Aligned_cols=55 Identities=22% Similarity=0.400 Sum_probs=29.9
Q ss_pred CCCccccCCCCCCCCCCCCCeee----ehHhh--------hhhhhhcCC-cccccccccccCCCCccccc
Q 048824 1 MDLSLVPYKHQRPHPQQEPNIIN----YKECM--------KNHAASIGG-HANDGCCEFMPRADDSLTCA 57 (209)
Q Consensus 1 ~~ls~~p~~~~~~~~~~~~~~v~----Y~eC~--------kNhaa~~Gg-~~~DGC~Efm~~~~~~l~Ca 57 (209)
|||+||||+......... .+. =.||. -+|.-...- .-+-.|.+.-....++..||
T Consensus 35 ~~l~lvP~G~a~~~~~~~--~~~CqHG~~EC~gN~~q~C~l~~~~~~~~~~~~i~Cm~~~~~~~~~~~Ca 102 (108)
T PF03227_consen 35 MNLTLVPFGNAKVSSSGN--EFTCQHGPDECYGNKLQACALKHLPDTNAALPFIACMESSQDFPKAIKCA 102 (108)
T ss_pred EEEEEEEEeccEEecCCc--eeecCCcHHHHHcCHHHHhHHHhcCChhhhcCEEEEEcCCCCCchhhhhH
Confidence 799999999776544322 121 13555 444443322 24456776665544444454
No 220
>COG3040 Blc Bacterial lipocalin [Cell envelope biogenesis, outer membrane]
Probab=41.13 E-value=27 Score=30.42 Aligned_cols=26 Identities=38% Similarity=0.653 Sum_probs=23.2
Q ss_pred CCCC-CCHHHHHHHHHHHHHhCcccCC
Q 048824 132 QRTK-FTQEQKDKMLEFAERIGWRMQR 157 (209)
Q Consensus 132 ~RTk-FT~EQkekM~~faEk~GW~iqk 157 (209)
.||- .+++++++|.+-|+++||.+.+
T Consensus 139 sRtP~~s~~~~~~ml~~ak~~Gfdv~~ 165 (174)
T COG3040 139 SRTPTLSQETLKRMLEIAKRRGFDVSK 165 (174)
T ss_pred ecCCCCCHHHHHHHHHHHHHcCCCcce
Confidence 5888 9999999999999999997654
No 221
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=41.04 E-value=16 Score=23.02 Aligned_cols=28 Identities=18% Similarity=0.275 Sum_probs=19.9
Q ss_pred cccccccccccCCCCccccccccccccccc
Q 048824 38 HANDGCCEFMPRADDSLTCAACGCHRNFHR 67 (209)
Q Consensus 38 ~~~DGC~Efm~~~~~~l~CaaCgCHRnFHr 67 (209)
..=+.|+++|.....+++|..|+ ...|.
T Consensus 12 ~~C~~C~~~i~~~~~~~~C~~C~--~~~H~ 39 (49)
T smart00109 12 TKCCVCRKSIWGSFQGLRCSWCK--VKCHK 39 (49)
T ss_pred CCccccccccCcCCCCcCCCCCC--chHHH
Confidence 34588999998654689999874 44443
No 222
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=41.01 E-value=9.6 Score=30.65 Aligned_cols=47 Identities=15% Similarity=0.225 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 138 QEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 138 ~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
.+.++++.+-|..+ +.-+.-+...++++|++.||++..|-..|.|+-
T Consensus 7 ~~~r~~Il~aA~~l-f~e~G~~~~s~~~IA~~agvs~~~lY~hF~sKe 53 (202)
T TIGR03613 7 EAKRKAILSAALDT-FSRFGFHGTSLEQIAELAGVSKTNLLYYFPSKD 53 (202)
T ss_pred HHHHHHHHHHHHHH-HHHhCcccCCHHHHHHHhCCCHHHHHHHcCCHH
Confidence 34555555433332 111235667899999999999999999988753
No 223
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=40.97 E-value=12 Score=31.87 Aligned_cols=46 Identities=13% Similarity=0.146 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASH 189 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~k 189 (209)
..||+.|.+.|.-+++= | ...++|.+++|++++||+-.+|==.|+.
T Consensus 147 ~~LT~RE~eVL~lla~G--~--------snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 147 ELLTPRELEVLRLLAEG--L--------SNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCCHHHHHHHHHHHCC--C--------CHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 47999999999988553 2 5678999999999999998877555443
No 224
>PF13551 HTH_29: Winged helix-turn helix
Probab=40.66 E-value=5.9 Score=28.91 Aligned_cols=25 Identities=12% Similarity=0.557 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCCCceeeeecccccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
.+.++|..+||++.+|.-|.++=+.
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~ 38 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYRE 38 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHc
Confidence 6899999999999999999987443
No 225
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=40.48 E-value=6.3 Score=25.60 Aligned_cols=21 Identities=14% Similarity=0.387 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCCceeeeeccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhN 183 (209)
+.++|+.+||+.++|+.|-..
T Consensus 2 i~e~A~~~gvs~~tlR~ye~~ 22 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYERE 22 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHHT
T ss_pred HHHHHHHHCCCHHHHHHHHHC
Confidence 568999999999999999654
No 226
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=40.37 E-value=46 Score=24.94 Aligned_cols=32 Identities=13% Similarity=0.305 Sum_probs=21.7
Q ss_pred CHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecc
Q 048824 137 TQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMH 182 (209)
Q Consensus 137 T~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfh 182 (209)
|.|||++|.+. .++.|+.++||+..=|-|=+.
T Consensus 41 s~e~K~~ly~~--------------l~~~L~~~~gi~p~Dv~I~l~ 72 (82)
T PF14552_consen 41 STEQKKALYRA--------------LAERLAEKLGIRPEDVMIVLV 72 (82)
T ss_dssp -HHHHHHHHHH--------------HHHHHHHHH---GGGEEEEEE
T ss_pred CHHHHHHHHHH--------------HHHHHHHHcCCCHHHEEEEEE
Confidence 48999998875 677889999999876665443
No 227
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=40.23 E-value=2.1 Score=33.96 Aligned_cols=33 Identities=6% Similarity=0.155 Sum_probs=28.3
Q ss_pred CHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 159 DDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 159 d~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
.....+++|+.+|++...|+++++.-|.++++.
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 445689999999999999999999988887754
No 228
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=39.79 E-value=14 Score=25.60 Aligned_cols=19 Identities=37% Similarity=0.870 Sum_probs=16.4
Q ss_pred ccc-cccCCCCccccccccc
Q 048824 43 CCE-FMPRADDSLTCAACGC 61 (209)
Q Consensus 43 C~E-fm~~~~~~l~CaaCgC 61 (209)
||. ||....+.+.|..||=
T Consensus 26 Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 26 CGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred CCcchheccCCcEECCCcCC
Confidence 777 9998889999999973
No 229
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=39.76 E-value=51 Score=23.25 Aligned_cols=35 Identities=26% Similarity=0.478 Sum_probs=24.5
Q ss_pred CCCHHHHHH-----HHHHHHHhCcccCCCCHHHHHHHHHHhCCCC
Q 048824 135 KFTQEQKDK-----MLEFAERIGWRMQRQDDVALNQFCNEVGVKR 174 (209)
Q Consensus 135 kFT~EQkek-----M~~faEk~GW~iqkpd~~~ve~fc~eiGv~r 174 (209)
.||-|+++. +.+.|..+| -....+.+.|.++||.+
T Consensus 4 ~lt~~~L~~~fhlp~~eAA~~Lg-----v~~T~LKr~CR~~GI~R 43 (52)
T PF02042_consen 4 SLTLEDLSQYFHLPIKEAAKELG-----VSVTTLKRRCRRLGIPR 43 (52)
T ss_pred ccCHHHHHHHhCCCHHHHHHHhC-----CCHHHHHHHHHHcCCCC
Confidence 456666654 345667775 66788889999999875
No 230
>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=39.31 E-value=7.6 Score=26.93 Aligned_cols=21 Identities=29% Similarity=0.661 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCCceeeeeccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhN 183 (209)
+.++|+.+||+..+|+.|...
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 678999999999999999754
No 231
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=38.47 E-value=20 Score=26.63 Aligned_cols=30 Identities=23% Similarity=0.429 Sum_probs=22.4
Q ss_pred HHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeee
Q 048824 143 KMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVW 180 (209)
Q Consensus 143 kM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVW 180 (209)
+++++-+++|+ .-++||..+||+|+++--|
T Consensus 5 k~k~~R~~~~l--------tQ~elA~~vgVsRQTi~~i 34 (68)
T COG1476 5 KLKELRAELGL--------TQEELAKLVGVSRQTIIAI 34 (68)
T ss_pred HHHHHHHHhCc--------CHHHHHHHcCcCHHHHHHH
Confidence 56666666664 5688999999999887554
No 232
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=38.46 E-value=31 Score=27.98 Aligned_cols=55 Identities=15% Similarity=0.242 Sum_probs=39.7
Q ss_pred CHHHHHHHHH----HHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 137 TQEQKDKMLE----FAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 137 T~EQkekM~~----faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+.+.+++|.. +|||.||++. ||.+....+..-|-..+..+-.|.+--|.-..+..
T Consensus 2 ~~e~l~~my~~~eq~AeksG~~ln-pD~e~~~~v~~gL~~~ke~yG~~~CPCRl~~g~ee 60 (110)
T COG4802 2 SDEELNKMYRFTEQYAEKSGYRLN-PDREFTAEVLRGLASNKERYGYPSCPCRLVTGKEE 60 (110)
T ss_pred cHHHHHHHHHHHHHHHHhcCceeC-CCHHHHHHHHHHHHHhHHHhCCCCCCeecccCCHH
Confidence 3566777754 7889999875 78888888888777777777777777666554433
No 233
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=38.37 E-value=5.2 Score=34.37 Aligned_cols=48 Identities=4% Similarity=0.093 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
+++..|++.+.-.+ -+....+++|..+||+..+|+.+++.-+.++++.
T Consensus 205 ~L~~~~r~ii~l~~---------~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 205 ILSEREKSIIHCTF---------EENLSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred cCCHHHHHHHHHHH---------cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 45666666665532 2223568999999999999999998887777653
No 234
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=38.30 E-value=8 Score=34.05 Aligned_cols=53 Identities=15% Similarity=0.256 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
.+++..|++.|.-++ | +.+-..-..+++|..+||+..+|+.+++.-+.++++.
T Consensus 221 ~~Lp~~~R~Vl~l~y---g--L~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~ 273 (285)
T TIGR02394 221 AELNERQREVLARRF---G--LLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRI 273 (285)
T ss_pred HcCCHHHHHHHHHHh---C--CCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 345566666655431 1 2234445789999999999999999999888887654
No 235
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=38.20 E-value=3.9 Score=33.54 Aligned_cols=31 Identities=10% Similarity=0.075 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
..+++|+.+||+..+|++=++.-|.++++..
T Consensus 152 s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 152 SVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 6789999999999999998888787776543
No 236
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=38.15 E-value=2.7 Score=35.66 Aligned_cols=35 Identities=9% Similarity=0.299 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 158 QDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 158 pd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
-.....+++|+.+||+..+|++.++.-|.++|+..
T Consensus 163 ~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 163 VEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34457899999999999999999999999988765
No 237
>PRK09483 response regulator; Provisional
Probab=37.85 E-value=9.2 Score=30.10 Aligned_cols=47 Identities=9% Similarity=0.188 Sum_probs=36.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASH 189 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~k 189 (209)
-..||.-+++.|.-+++ | ....++|++++++.++|+.-.+|=+.|+.
T Consensus 146 ~~~Lt~rE~~vl~~~~~--G--------~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 146 FASLSERELQIMLMITK--G--------QKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred ccccCHHHHHHHHHHHC--C--------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 35699999999976532 2 14558999999999999988888777764
No 238
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=37.56 E-value=16 Score=24.23 Aligned_cols=36 Identities=11% Similarity=0.351 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCcee
Q 048824 136 FTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVL 177 (209)
Q Consensus 136 FT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~ 177 (209)
||..|...|..+.+.- .+.-.+.+||..+|+++.++
T Consensus 3 lt~~q~~vL~~l~~~~------~~~~t~~~la~~l~~~~~~v 38 (62)
T PF12802_consen 3 LTPSQFRVLMALARHP------GEELTQSELAERLGISKSTV 38 (62)
T ss_dssp STHHHHHHHHHHHHST------TSGEEHHHHHHHHTS-HHHH
T ss_pred cCHHHHHHHHHHHHCC------CCCcCHHHHHHHHCcCHHHH
Confidence 7888999988876552 22358899999999988654
No 239
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=37.50 E-value=66 Score=23.14 Aligned_cols=31 Identities=16% Similarity=0.100 Sum_probs=22.6
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVG 171 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiG 171 (209)
.|+.++++.+....++ .-+++..+.+|+.||
T Consensus 66 ~~~~~e~~~l~~~l~~------~~~~~~~~~~~~~~~ 96 (96)
T smart00529 66 GVDEEEVHEEAERLEH------VLSDELEDRLDRFLG 96 (96)
T ss_pred CCCHHHHHHHHHHHHc------cCCHHHHHHHHHHhC
Confidence 5777777777775555 377788888888775
No 240
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=37.38 E-value=16 Score=28.89 Aligned_cols=21 Identities=5% Similarity=0.083 Sum_probs=16.2
Q ss_pred CCCHHHHHHHHHHhCCCCcee
Q 048824 157 RQDDVALNQFCNEVGVKRHVL 177 (209)
Q Consensus 157 kpd~~~ve~fc~eiGv~r~V~ 177 (209)
.|+.+.+++||+.+||+...|
T Consensus 44 ~ps~~~l~kIa~aL~v~~~~L 64 (120)
T PRK13890 44 NPSLKVMEAIADALETPLPLL 64 (120)
T ss_pred CCCHHHHHHHHHHHCCCHHHH
Confidence 477888888888888877644
No 241
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=37.11 E-value=22 Score=28.61 Aligned_cols=29 Identities=7% Similarity=0.101 Sum_probs=25.1
Q ss_pred CCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 158 QDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 158 pd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
-....++++|.+.||++..|--+|.|+..
T Consensus 26 ~~~tSi~~Ia~~aGvsk~~lY~~F~sK~~ 54 (192)
T PRK14996 26 FAAMTVRRIASEAQVAAGQVHHHFSSAGE 54 (192)
T ss_pred hhhccHHHHHHHhCCCcHHHHHHcCCHHH
Confidence 46678999999999999999999987644
No 242
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=36.88 E-value=9.1 Score=24.98 Aligned_cols=35 Identities=17% Similarity=0.366 Sum_probs=26.1
Q ss_pred HHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 048824 145 LEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 145 ~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNn 184 (209)
.+.+.+.| .+...++++|+++||++..|---|.|+
T Consensus 6 ~~l~~~~G-----~~~~s~~~Ia~~~gvs~~~~y~~f~~k 40 (47)
T PF00440_consen 6 LELFAEKG-----YEAVSIRDIARRAGVSKGSFYRYFPSK 40 (47)
T ss_dssp HHHHHHHH-----TTTSSHHHHHHHHTSCHHHHHHHCSSH
T ss_pred HHHHHHhC-----HHhCCHHHHHHHHccchhhHHHHcCCH
Confidence 34444555 455678999999999999988777764
No 243
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=36.56 E-value=31 Score=25.14 Aligned_cols=28 Identities=11% Similarity=0.243 Sum_probs=24.3
Q ss_pred CCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 158 QDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 158 pd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
-+...+.++|+++||++..|-.+|.|..
T Consensus 30 ~~~~t~~~Ia~~agvs~~~~Y~~f~~K~ 57 (201)
T COG1309 30 YAATTVDEIAKAAGVSKGTLYRHFPSKE 57 (201)
T ss_pred cCCCCHHHHHHHhCCCcchhHHHcCCHH
Confidence 4556789999999999999999999875
No 244
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=36.41 E-value=35 Score=23.49 Aligned_cols=19 Identities=21% Similarity=0.606 Sum_probs=14.3
Q ss_pred CCHHHHHHHHHHHHHhCcc
Q 048824 136 FTQEQKDKMLEFAERIGWR 154 (209)
Q Consensus 136 FT~EQkekM~~faEk~GW~ 154 (209)
++..|+++|.++.++.||-
T Consensus 24 ~s~~~L~k~~~wld~rgWw 42 (45)
T PF12123_consen 24 LSDAELDKFTAWLDERGWW 42 (45)
T ss_dssp --HHHHHHHHHHHHHTT--
T ss_pred CCHHHHHHHHHHHHhcCcE
Confidence 4589999999999999994
No 245
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=36.36 E-value=73 Score=22.83 Aligned_cols=37 Identities=19% Similarity=0.421 Sum_probs=22.9
Q ss_pred CCCHHHHHHHHH---HHHHhCcccCCCCHHHHHHHHHHhCCC-Ccee
Q 048824 135 KFTQEQKDKMLE---FAERIGWRMQRQDDVALNQFCNEVGVK-RHVL 177 (209)
Q Consensus 135 kFT~EQkekM~~---faEk~GW~iqkpd~~~ve~fc~eiGv~-r~V~ 177 (209)
.+|.-|++.|.- |-++.|+ + -.+.+||+.+|++ ..++
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~----~--Pt~rEIa~~~g~~S~~tv 43 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGY----P--PTVREIAEALGLKSTSTV 43 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS---------HHHHHHHHTSSSHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcCC----C--CCHHHHHHHhCCCChHHH
Confidence 578888887764 6666663 2 2789999999997 4433
No 246
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=36.28 E-value=14 Score=23.54 Aligned_cols=29 Identities=21% Similarity=0.416 Sum_probs=20.5
Q ss_pred cccccccccccCC-CCcccccccccccccccc
Q 048824 38 HANDGCCEFMPRA-DDSLTCAACGCHRNFHRR 68 (209)
Q Consensus 38 ~~~DGC~Efm~~~-~~~l~CaaCgCHRnFHr~ 68 (209)
..=+-|+++|... ..+++|..| ..+.|.+
T Consensus 12 ~~C~~C~~~i~~~~~~~~~C~~C--~~~~H~~ 41 (50)
T cd00029 12 TFCDVCRKSIWGLFKQGLRCSWC--KVKCHKK 41 (50)
T ss_pred CChhhcchhhhccccceeEcCCC--CCchhhh
Confidence 3457799999865 359999888 4555543
No 247
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=36.03 E-value=18 Score=27.29 Aligned_cols=42 Identities=17% Similarity=0.334 Sum_probs=33.3
Q ss_pred HHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 146 EFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 146 ~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
+|++.. +...+.-.+.++|..+||.+..|--|+..++--.++
T Consensus 13 ~~~d~~---~~~~~~~ti~~~AK~L~i~~~~l~~~Lr~~g~l~~~ 54 (111)
T PF03374_consen 13 EFYDAF---VDSDGLYTIREAAKLLGIGRNKLFQWLREKGWLYRR 54 (111)
T ss_pred HHHHHH---HcCCCCccHHHHHHHhCCCHHHHHHHHHhCCceEEC
Confidence 366664 334567899999999999999999999988777663
No 248
>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=35.81 E-value=7.1 Score=25.29 Aligned_cols=21 Identities=10% Similarity=0.192 Sum_probs=19.0
Q ss_pred HHHHHhCCCCceeeeeccccc
Q 048824 165 QFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 165 ~fc~eiGv~r~V~KVWfhNnR 185 (209)
+||..+||+..+|-.|++|+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 689999999999999999874
No 249
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=35.21 E-value=4.9 Score=31.80 Aligned_cols=36 Identities=6% Similarity=0.110 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 157 RQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 157 kpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
+-+....+++|..+|++..+|++.++.-|.++++..
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 334446899999999999999999999998887643
No 250
>PF09894 DUF2121: Uncharacterized protein conserved in archaea (DUF2121); InterPro: IPR016754 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. They do show distant similarity to NTPases and to nucleic acid binding enzymes.
Probab=35.12 E-value=35 Score=30.13 Aligned_cols=45 Identities=20% Similarity=0.391 Sum_probs=31.3
Q ss_pred CHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 137 TQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 137 T~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
..++.++|++- | |.=.-.++++..+.|.|+||+ +|++..|.|-++
T Consensus 27 ~~~~re~LEee---L-YsG~IktdeEL~kkA~Elgv~-----i~I~D~r~KV~~ 71 (194)
T PF09894_consen 27 DEEKREKLEEE---L-YSGKIKTDEELLKKAEELGVK-----IKITDDREKVRK 71 (194)
T ss_pred CHHHHHHHHHH---H-hCCccCCHHHHHHHHHHcCCE-----EEEecCchheEE
Confidence 35677888762 1 111127799999999999987 777777776554
No 251
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=34.92 E-value=19 Score=28.11 Aligned_cols=51 Identities=8% Similarity=0.078 Sum_probs=40.5
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhC-----CCCceeeeecccccccCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVG-----VKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiG-----v~r~V~KVWfhNnR~k~kk 190 (209)
..+|..+.+.|.-+++..| ....+++++.++. ++.++|++.+.|=|.|+..
T Consensus 148 ~~Lt~~E~~il~~l~~~~~------~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~~ 203 (219)
T PRK10336 148 LTLKPKEFALLELLMRNAG------RVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLGS 203 (219)
T ss_pred EecCHHHHHHHHHHHhCCC------ccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcCC
Confidence 4699999999998877633 2235668888886 9999999999998888763
No 252
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=34.73 E-value=16 Score=27.86 Aligned_cols=10 Identities=50% Similarity=1.411 Sum_probs=8.6
Q ss_pred Cccccccccc
Q 048824 52 DSLTCAACGC 61 (209)
Q Consensus 52 ~~l~CaaCgC 61 (209)
+.|.|+|||-
T Consensus 56 ~tLsCsACGS 65 (74)
T PF05077_consen 56 NTLSCSACGS 65 (74)
T ss_pred CeEeehhccc
Confidence 5899999994
No 253
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=34.61 E-value=14 Score=32.02 Aligned_cols=49 Identities=10% Similarity=0.169 Sum_probs=40.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 132 QRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 132 ~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
.+..||.-|+|.|.=.++- | .-.++|..+||+.++|+.-+.|-+.|+.-
T Consensus 176 ~~~~LT~rE~evl~~~a~G------~----t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 176 PEMNFSKREKEILKWTAEG------K----TSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred CCCCCCHHHHHHHHHHHcC------C----CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 4568999999999876543 2 56789999999999999999998888763
No 254
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=34.04 E-value=30 Score=28.55 Aligned_cols=18 Identities=28% Similarity=0.215 Sum_probs=12.9
Q ss_pred CCCCCCHHHHHHHHHHHH
Q 048824 132 QRTKFTQEQKDKMLEFAE 149 (209)
Q Consensus 132 ~RTkFT~EQkekM~~faE 149 (209)
-++.||+.|+++|..+-|
T Consensus 137 c~~~FT~gQ~~RM~~~l~ 154 (154)
T PF05572_consen 137 CMNMFTPGQVARMRAVLE 154 (154)
T ss_dssp G--B-BHHHHHHHHHHHH
T ss_pred cccccCHHHHHHHHHHhC
Confidence 789999999999998643
No 255
>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=33.43 E-value=33 Score=26.71 Aligned_cols=41 Identities=20% Similarity=0.607 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 136 FTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 136 FT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
.|.+=++++.++.++ | ..+.+.|...+|++.+|.-||. ++.
T Consensus 3 YS~DlR~rVl~~~~~-g--------~s~~eaa~~F~VS~~Tv~~W~k-~~~ 43 (119)
T PF01710_consen 3 YSLDLRQRVLAYIEK-G--------KSIREAAKRFGVSRNTVYRWLK-RKE 43 (119)
T ss_pred CCHHHHHHHHHHHHc-c--------chHHHHHHHhCcHHHHHHHHHH-hcc
Confidence 356667788887666 2 1677889999999999999999 443
No 256
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=32.80 E-value=26 Score=29.19 Aligned_cols=48 Identities=8% Similarity=0.173 Sum_probs=36.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 048824 132 QRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 132 ~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNn 184 (209)
....+|..+++.+..+.+.. .......+++|+++|++..+|+.-+.+=
T Consensus 155 ~~~~Lt~re~~~l~~~i~~~-----~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 155 LPKGLTPQTLRTLCQWIDAH-----QDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCCCCCHHHHHHHHHHHHhC-----CCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 44568999988888776542 2233477999999999999999887754
No 257
>cd02259 Peptidase_C39_like Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.
Probab=32.62 E-value=84 Score=22.80 Aligned_cols=44 Identities=14% Similarity=0.095 Sum_probs=31.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeee
Q 048824 130 KRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKV 179 (209)
Q Consensus 130 KR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KV 179 (209)
+.+...++.+++.. ..+|.-...+...+.++|+.+|++-+.+++
T Consensus 17 ~~~g~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~gl~~~~~~~ 60 (122)
T cd02259 17 RYFGIPVRRDVLLN------AQQRRQQGLSLADLVSLANKLGLTAQGVKL 60 (122)
T ss_pred HHcCCCCCHHHHHH------HHhhccCCCCHHHHHHHHHHcCCeeeEEEc
Confidence 44566777887732 334444568888999999999998888765
No 258
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=32.54 E-value=23 Score=27.65 Aligned_cols=50 Identities=14% Similarity=0.203 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhC-----CCCceeeeecccccccCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVG-----VKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiG-----v~r~V~KVWfhNnR~k~kk 190 (209)
.+|+-|.+.|.-++...| .....+++++++. ++.++|++++.+=|.|+..
T Consensus 148 ~Lt~~E~~il~~l~~~~~------~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~~ 202 (221)
T PRK15479 148 ALTPREQALLTVLMYRRT------RPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQG 202 (221)
T ss_pred ecCHHHHHHHHHHHhCCC------CcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcCC
Confidence 599999999998877643 2335777887775 8999999999998888753
No 259
>cd02425 Peptidase_C39F A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=32.33 E-value=97 Score=22.76 Aligned_cols=44 Identities=18% Similarity=0.130 Sum_probs=33.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeee
Q 048824 130 KRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKV 179 (209)
Q Consensus 130 KR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KV 179 (209)
+.+...++.+++.. ..+|.-+..+...+.++++++|++-+++++
T Consensus 22 ~~~~~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~gl~~~~~~~ 65 (126)
T cd02425 22 NYFGYKVSLNELRE------KYELGRDGLSLSYLKQLLEEYGFKCKVYKI 65 (126)
T ss_pred HHhCCCCCHHHHHH------hccCCCCCcCHHHHHHHHHHCCCcceEEEE
Confidence 45666777777643 235666678899999999999999988876
No 260
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=31.51 E-value=43 Score=26.08 Aligned_cols=25 Identities=20% Similarity=0.461 Sum_probs=17.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcccC
Q 048824 132 QRTKFTQEQKDKMLEFAERIGWRMQ 156 (209)
Q Consensus 132 ~RTkFT~EQkekM~~faEk~GW~iq 156 (209)
.=+..|..|++++.++++++||+.+
T Consensus 18 S~k~lt~~el~~vl~~l~~~G~k~~ 42 (119)
T PF06252_consen 18 SSKDLTEAELEKVLDELKRLGFKPP 42 (119)
T ss_pred hHHHCCHHHHHHHHHHHHHccCcCc
Confidence 4456777778887777777787543
No 261
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=31.42 E-value=8.6 Score=32.73 Aligned_cols=53 Identities=8% Similarity=0.088 Sum_probs=35.9
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
..++..|++.+.-..- +..-..-..+++|+.+||+..+|+++++.-+.++|+.
T Consensus 177 ~~Lp~~~R~ii~L~~~-----l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 177 AKLNDREKKIMELRFG-----LVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred HhCCHHHHHHHHHHHc-----cCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3466666666664310 0001234678999999999999999998877776653
No 262
>PRK04140 hypothetical protein; Provisional
Probab=31.40 E-value=22 Score=33.01 Aligned_cols=22 Identities=23% Similarity=0.540 Sum_probs=11.4
Q ss_pred HHHHHHHhCCCCceeeeecccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhNn 184 (209)
..+||+.+||++.+|.-|-.+.
T Consensus 142 q~eLA~~lGVSr~tIskyE~G~ 163 (317)
T PRK04140 142 LGELASELGVSRRTISKYENGG 163 (317)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 3455555555555555555443
No 263
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=30.89 E-value=25 Score=32.64 Aligned_cols=36 Identities=8% Similarity=0.219 Sum_probs=19.0
Q ss_pred HHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 142 DKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 142 ekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
++|++.-|++|| .++++|..|+|++.+|.-|-.+++
T Consensus 17 ~~Lr~aRe~~Gl--------Sq~~vA~~l~l~~~~I~~iE~g~~ 52 (331)
T PRK10856 17 ERLRQAREQLGL--------TQQAVAERLCLKVSTVRDIEEDKA 52 (331)
T ss_pred HHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHCCCC
Confidence 334445555554 245555555555555555555543
No 264
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=30.88 E-value=16 Score=35.30 Aligned_cols=14 Identities=43% Similarity=0.992 Sum_probs=11.4
Q ss_pred cccccccccccccc
Q 048824 53 SLTCAACGCHRNFH 66 (209)
Q Consensus 53 ~l~CaaCgCHRnFH 66 (209)
+++|+||||+-+--
T Consensus 118 ~~~CkACG~r~~~d 131 (400)
T KOG2767|consen 118 SLKCKACGFRSDMD 131 (400)
T ss_pred hhHHHHcCCccccc
Confidence 78999999985543
No 265
>COG0289 DapB Dihydrodipicolinate reductase [Amino acid transport and metabolism]
Probab=30.76 E-value=41 Score=30.94 Aligned_cols=19 Identities=47% Similarity=0.611 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHHHHHHHhC
Q 048824 134 TKFTQEQKDKMLEFAERIG 152 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~G 152 (209)
|=||.||+++|.+++|+.+
T Consensus 101 TGf~~e~~~~l~~~a~~v~ 119 (266)
T COG0289 101 TGFTEEQLEKLREAAEKVP 119 (266)
T ss_pred CCCCHHHHHHHHHHHhhCC
Confidence 7899999999999999976
No 266
>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=30.38 E-value=13 Score=25.58 Aligned_cols=21 Identities=24% Similarity=0.545 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCCceeeeeccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhN 183 (209)
+.++|+.+||+..+|+.|..+
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 578899999999999999765
No 267
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=30.21 E-value=20 Score=28.09 Aligned_cols=52 Identities=8% Similarity=-0.033 Sum_probs=41.7
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCC-----CceeeeecccccccCCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVK-----RHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~-----r~V~KVWfhNnR~k~kk~ 191 (209)
-.+|.-+.+.|.-+++..| ..-..+++++.++.+ .++|++..++=|.|++..
T Consensus 153 ~~Lt~~E~~il~~l~~~~~------~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~~ 209 (228)
T PRK11083 153 LTLTRYEFLLLKTLLLSPG------RVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRAI 209 (228)
T ss_pred eecCHHHHHHHHHHHhCCC------ceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhccC
Confidence 4699999999999988632 234678899999886 789999999999998643
No 268
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=30.20 E-value=25 Score=28.88 Aligned_cols=47 Identities=11% Similarity=0.093 Sum_probs=31.6
Q ss_pred CCCCCCCCCHHHHHHHHH----HHHHhCcc--cCCCCHHHHHHHHHHhCCCCcee
Q 048824 129 SKRQRTKFTQEQKDKMLE----FAERIGWR--MQRQDDVALNQFCNEVGVKRHVL 177 (209)
Q Consensus 129 kKR~RTkFT~EQkekM~~----faEk~GW~--iqkpd~~~ve~fc~eiGv~r~V~ 177 (209)
+.|.+..+|++++.+... +.-+ |. ...|+...+.++|..+||+..-|
T Consensus 14 ~~R~~~glt~~elA~~~gis~~~is~--~E~g~~~p~~~~l~~ia~~l~v~~~~l 66 (185)
T PRK09943 14 EIRQQQGLSQRRAAELSGLTHSAIST--IEQDKVSPAISTLQKLLKVYGLSLSEF 66 (185)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHH--HHcCCCCCCHHHHHHHHHHhCCCHHHH
Confidence 456677788877666542 1111 22 23588999999999999997653
No 269
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=30.01 E-value=13 Score=25.25 Aligned_cols=20 Identities=15% Similarity=0.345 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCCceeeeecc
Q 048824 163 LNQFCNEVGVKRHVLKVWMH 182 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfh 182 (209)
+.++|+.+||+..+|+.|..
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 67899999999999999965
No 270
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=29.79 E-value=20 Score=29.39 Aligned_cols=40 Identities=15% Similarity=0.313 Sum_probs=19.1
Q ss_pred HHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 144 MLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 144 M~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
=+..|+++|++ +-|.+.+++.|.+.||++..|..|-....
T Consensus 16 a~~LA~~Lg~~--~~d~~ii~~~a~~~~~~~~~~~~~~e~~~ 55 (179)
T PF13189_consen 16 AERLAEKLGYP--YYDREIIEEAAKESGISEEEFEEFDEKKP 55 (179)
T ss_dssp HHHHHHHCT----EE-HHHHHHCT------------SS-HHH
T ss_pred HHHHHHHcCCc--cCCHHHHHHHHHHccCCHHHHHHHhcccc
Confidence 35689999964 46779999999999999999988877654
No 271
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=29.67 E-value=6.1 Score=32.46 Aligned_cols=31 Identities=3% Similarity=0.125 Sum_probs=26.8
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
..+++|+.+||+..+|+++++--|.++++..
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 6789999999999999999998888776543
No 272
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=29.62 E-value=48 Score=24.05 Aligned_cols=47 Identities=19% Similarity=0.384 Sum_probs=24.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCcc-cCCCCHHHHHHHHHHhCCCCceeeee
Q 048824 133 RTKFTQEQKDKMLEFAERIGWR-MQRQDDVALNQFCNEVGVKRHVLKVW 180 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~-iqkpd~~~ve~fc~eiGv~r~V~KVW 180 (209)
||.||.|.=+.|..|..+..+. ..--....=++|+.+ .+++++-|-|
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~-~~t~HtwQSw 49 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEK-HPTRHTWQSW 49 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS--SSS--SHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH-cCCCCCHHHH
Confidence 8999999999999988543222 222334566666554 4667776666
No 273
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=29.37 E-value=6.8 Score=34.11 Aligned_cols=48 Identities=10% Similarity=0.224 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
.+++.|++.|.-. +-+....+++|..+||+..+|+..++.-+.++++.
T Consensus 212 ~L~~~~r~vl~l~---------~~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 212 TLPEREKKVLILY---------YYEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred hCCHHHHHHHHHH---------HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4556666665542 12233679999999999999999998877776653
No 274
>cd08353 Glo_EDI_BRP_like_7 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins.
Probab=29.32 E-value=80 Score=23.65 Aligned_cols=44 Identities=9% Similarity=0.161 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecc
Q 048824 139 EQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMH 182 (209)
Q Consensus 139 EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfh 182 (209)
..+++..+|++++||++.......-..+...+|++...+.+||-
T Consensus 12 ~Dl~~s~~FY~~LG~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l 55 (142)
T cd08353 12 RDLEAAIAFFLELGLELEGRAEIEGEWADRVTGLDGVRVEIAML 55 (142)
T ss_pred CCHHHHHHHHHHcCCEEccccccChHHHHHhcCCCCceEEEEEE
Confidence 46788899999999987553221113345567887666676663
No 275
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=29.15 E-value=23 Score=30.44 Aligned_cols=45 Identities=13% Similarity=0.278 Sum_probs=30.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHH-------HhCcccCCCCHHHHHHHHHHhCCCCceeeeecc
Q 048824 128 KSKRQRTKFTQEQKDKMLEFAE-------RIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMH 182 (209)
Q Consensus 128 ~kKR~RTkFT~EQkekM~~faE-------k~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfh 182 (209)
.+++.|++ .+-.+..++|++ +.|| -.++||.+|+++..||+-|=+
T Consensus 63 ~~~~~~~~--d~~~elvedY~e~Ir~ARE~~G~--------SqedLA~ki~ek~svI~~iE~ 114 (165)
T COG1813 63 PRRERRDN--DELPELVEDYGERIREAREKRGL--------SQEDLAAKLKEKVSVIRRIER 114 (165)
T ss_pred ccccCCcc--chHHHHHHHHHHHHHHHHHHcCC--------CHHHHHHHhcccHHHHHHHHh
Confidence 35666666 333344444654 5666 578999999999999987744
No 276
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=29.02 E-value=1.3e+02 Score=19.87 Aligned_cols=38 Identities=18% Similarity=0.410 Sum_probs=21.5
Q ss_pred CHHHHHHHHHHHHHhCcccCC-CC----HHHHHHHHHHhCCCCcee
Q 048824 137 TQEQKDKMLEFAERIGWRMQR-QD----DVALNQFCNEVGVKRHVL 177 (209)
Q Consensus 137 T~EQkekM~~faEk~GW~iqk-pd----~~~ve~fc~eiGv~r~V~ 177 (209)
|.|+|-++.+-+..+ |.. +| +.-++++|+.+||+...|
T Consensus 17 ~~egk~~~~~~~~~~---i~~i~~~i~r~~y~~~la~~~~i~~~~L 59 (59)
T PF10410_consen 17 TPEGKAEAVREAAPL---IAQIPDPIERELYIRELAERLGISEDAL 59 (59)
T ss_dssp SHHHHHHHHHHHHHH---HTT--SHHHHHHHHHHHHHHCT-SSTT-
T ss_pred CHHHHHHHHHHHHHH---HHHCCCHHHHHHHHHHHHHHhCcCcccC
Confidence 456665555533332 222 45 466789999999998654
No 277
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=28.99 E-value=66 Score=24.01 Aligned_cols=41 Identities=17% Similarity=0.169 Sum_probs=28.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCC
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKR 174 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r 174 (209)
|--||.++...|+..+..+ |+-...-++.++++-++.+-+.
T Consensus 25 R~Gfs~~~i~~l~~ayr~l-~~~~~~~~~a~~~l~~~~~~~~ 65 (83)
T PF13720_consen 25 RRGFSKEEISALRRAYRIL-FRSGLTLEEALEELEEEYPDSP 65 (83)
T ss_dssp HTTS-HHHHHHHHHHHHHH-HTSSS-HHHHHHHHHHHTTSCH
T ss_pred HcCCCHHHHHHHHHHHHHH-HhCCCCHHHHHHHHHHhccCCH
Confidence 6679999999999987777 6555455777777777655443
No 278
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=28.86 E-value=39 Score=26.09 Aligned_cols=44 Identities=18% Similarity=0.453 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
.+|......|-.---.-|| .+.+.|.+.||++.++..|..--|+
T Consensus 8 ~Lt~~gR~~lv~~vv~~g~--------~~a~aA~~~gVS~~Ta~kW~~Ryra 51 (85)
T PF13011_consen 8 RLTPRGRLRLVRRVVEQGW--------PVAHAAAEFGVSRRTAYKWLARYRA 51 (85)
T ss_pred CCCHHHHHHHHHHHHHcCC--------cHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4677788877764333355 5789999999999999999965554
No 279
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=28.82 E-value=58 Score=27.35 Aligned_cols=35 Identities=17% Similarity=0.378 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhC-CCCceeee
Q 048824 136 FTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVG-VKRHVLKV 179 (209)
Q Consensus 136 FT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiG-v~r~V~KV 179 (209)
.|.|++++|.++... -....+||.+|| |+++.|--
T Consensus 3 Wtde~~~~L~~lw~~---------G~SasqIA~~lg~vsRnAViG 38 (162)
T PF07750_consen 3 WTDERVERLRKLWAE---------GLSASQIARQLGGVSRNAVIG 38 (162)
T ss_pred CCHHHHHHHHHHHHc---------CCCHHHHHHHhCCcchhhhhh
Confidence 689999999997322 225678899999 99985543
No 280
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=28.67 E-value=7.9 Score=32.58 Aligned_cols=48 Identities=8% Similarity=0.124 Sum_probs=34.1
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
.+++..+++.+.-.+ -+....+++|..+||+...|..+.+.-..++++
T Consensus 182 ~~L~~~e~~i~~~~~---------~~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 182 SKLDERERQIIMLRY---------FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred HcCCHHHHHHHHHHH---------HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 366667776666532 123478999999999999999887766665543
No 281
>PF13730 HTH_36: Helix-turn-helix domain
Probab=28.59 E-value=25 Score=23.16 Aligned_cols=44 Identities=16% Similarity=0.215 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHHHHHH---HhCcccCCCCHHHHHHHHHHhCCCCceeeeecc
Q 048824 134 TKFTQEQKDKMLEFAE---RIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMH 182 (209)
Q Consensus 134 TkFT~EQkekM~~faE---k~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfh 182 (209)
|.+|..++-.+..++. +.|| -+| -++.||..+|+++++|+-++.
T Consensus 1 ~~Ls~~~~~v~~~l~~~~~~~~~--~~p---S~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 1 KNLSPTAKLVYLYLASYANKNGG--CFP---SQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCCCHHHHHHHHHHHHhcCCCCC--CCc---CHHHHHHHHCcCHHHHHHHHH
Confidence 3466677766655333 3332 233 478899999999999887654
No 282
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=28.48 E-value=18 Score=30.84 Aligned_cols=47 Identities=4% Similarity=0.093 Sum_probs=37.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASH 189 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~k 189 (209)
.+.+|.-|+|.|.-+++=. ...++|++++|+.++|+.-..|=-.|+.
T Consensus 132 ~~~LT~RE~eVL~ll~~G~----------snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 132 SRMLSPTEREILRFMSRGY----------SMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred cCCCCHHHHHHHHHHHCCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 3569999999999886542 5788999999999999987777655553
No 283
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=28.44 E-value=9.4 Score=33.57 Aligned_cols=47 Identities=6% Similarity=0.131 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
+++..|++.|... +-+....+++|+.+||+...|+.|++.-+.++++
T Consensus 215 ~L~~rer~vl~l~---------y~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 215 ALPERERTVLVLR---------FFESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred cCCHHHHHHHHHH---------hcCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3455555555542 2233467999999999999999999887777664
No 284
>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=28.32 E-value=15 Score=27.85 Aligned_cols=22 Identities=14% Similarity=0.403 Sum_probs=19.3
Q ss_pred HHHHHHHHhCCCCceeeeeccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhN 183 (209)
.+.++|..+||+.++|+.|...
T Consensus 2 ~I~e~a~~~gvs~~tLR~ye~~ 23 (96)
T cd04774 2 KVDEVAKRLGLTKRTLKYYEEI 23 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 3678999999999999999764
No 285
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=28.28 E-value=83 Score=21.22 Aligned_cols=22 Identities=32% Similarity=0.724 Sum_probs=18.8
Q ss_pred CCCCHHHHHHHHHHHHHhCccc
Q 048824 134 TKFTQEQKDKMLEFAERIGWRM 155 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~i 155 (209)
-.++++-+++.++.++++||+.
T Consensus 24 ~~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 24 PRVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp SSSTHHHHHHHHHHHHHHTB-S
T ss_pred CCCCHHHHHHHHHHHHHHCCCC
Confidence 4788999999999999999863
No 286
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=28.03 E-value=21 Score=26.51 Aligned_cols=38 Identities=13% Similarity=0.360 Sum_probs=29.9
Q ss_pred HHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 142 DKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 142 ekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
++|..|.--+||.+ .+.+.|.+||++..++.-|.--=|
T Consensus 1 ~~~~~fIrlLs~~~------s~~~Aa~~lG~~~~~v~~wv~~fR 38 (65)
T PF05344_consen 1 EKARAFIRLLSQQI------SVAQAADRLGTDPGTVRRWVRMFR 38 (65)
T ss_pred CcHHHHHHHhcccc------cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46778888888765 467889999999999999975433
No 287
>PF13223 DUF4031: Protein of unknown function (DUF4031)
Probab=27.79 E-value=35 Score=26.28 Aligned_cols=21 Identities=29% Similarity=0.648 Sum_probs=15.7
Q ss_pred CHHHHHHHHHHhCCCCceeeeeccc
Q 048824 159 DDVALNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 159 d~~~ve~fc~eiGv~r~V~KVWfhN 183 (209)
+.++...||..|||+++ |||+
T Consensus 22 t~~ELHafA~riGv~rr----~fq~ 42 (83)
T PF13223_consen 22 TLDELHAFAARIGVPRR----WFQR 42 (83)
T ss_pred CHHHHHHHHHHcCCCHH----HHcC
Confidence 35677777888888884 7777
No 288
>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=27.67 E-value=31 Score=26.90 Aligned_cols=51 Identities=14% Similarity=0.257 Sum_probs=34.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 132 QRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 132 ~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
.+.++.. +.|+++.+. +||... .|+|..+||+..+|-..++--.-+.||+.
T Consensus 53 ~~~Kid~---~~L~~~v~~------~pd~tl-~Ela~~l~Vs~~ti~~~Lkrlg~t~KK~~ 103 (119)
T PF01710_consen 53 GRKKIDR---DELKALVEE------NPDATL-RELAERLGVSPSTIWRALKRLGITRKKKT 103 (119)
T ss_pred ccccccH---HHHHHHHHH------CCCcCH-HHHHHHcCCCHHHHHHHHHHcCchhccCc
Confidence 3336644 456666555 466544 57899999999998777776666666655
No 289
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=27.45 E-value=9.8 Score=29.95 Aligned_cols=10 Identities=50% Similarity=0.906 Sum_probs=7.5
Q ss_pred eeeeeccccc
Q 048824 176 VLKVWMHNNK 185 (209)
Q Consensus 176 V~KVWfhNnR 185 (209)
-+||||||--
T Consensus 32 dvkvwmqnle 41 (106)
T PF11516_consen 32 DVKVWMQNLE 41 (106)
T ss_dssp HHHHHHHHHH
T ss_pred cHHHHHHHHH
Confidence 4689999853
No 290
>PF08688 ASD1: Apx/Shroom domain ASD1; InterPro: IPR014800 Cell shape changes require the coordination of actin and microtubule cytoskeletons. The Shroom family is a small group of related proteins that are defined by sequence similarity and in most cases by some link to the actin cytoskeleton. The Shroom (Shrm) protein family is found only in animals. Proteins of this family are predicted to be utilised in multiple morphogenic and developmental processes across animal phyla to regulate cells shape or intracellular architecture in an actin and myosin-dependent manner []. While the founding member of the Shrm family is Shrm1 (formerly Apx), it appears that this protein is found only in Xenopus []. In mice and humans, the Shrm family of proteins consists of: Shrm2 (formerly Apxl), a protein involved in the morphogenesis, maintenance, and/or function of vascular endothelial cells. Shrm3 (formerly Shroom), a protein necessary for neural tube closure in vertebrate development as deficiency in Shrm results in spina bifida. Shrm3 is also conserved in some invertebrates, as orthologues can be found in sea urchins. Shrm4, a regulator of cyto-skeletal architecture that may play an important role in vertebrate development. It is implicated in X-linked mental retardation in humans. This protein family is based on the conservation of a specific arrangement of an N-terminal PDZ domain, a centrally positioned sequence motif termed ASD1 (Apx/Shrm Domain 1) and a C-terminal motif termed ASD2 [, , ]. Shrm2 and Shrm3 contain all three domains, while Shrm4 contains the PDZ and ASD2 domains, but lacks a discernible ASD1 element. To date, the ASD1 and ASD2 elements have only been found in Shrm-related proteins and do not appear in combination with other conserved domains. ASD1 is required for targeting actin, while ASD2 is capable of eliciting an actomyosin based constriction event [, ]. ASD2 is the most highly conserved sequence element shared by Shrm1, Shrm2, Shrm3, and Shrm4. It possesses a well conserved series of leucine residues that exhibit spacing consistent with that of a leucine zipper motif []. This region is found in the actin binding protein Shroom. ASD1 has been implicated directly in F-actin binding.
Probab=27.28 E-value=2e+02 Score=25.14 Aligned_cols=15 Identities=33% Similarity=0.450 Sum_probs=10.5
Q ss_pred CCCCCCCCCHHHHHH
Q 048824 129 SKRQRTKFTQEQKDK 143 (209)
Q Consensus 129 kKR~RTkFT~EQkek 143 (209)
+---|-.||.|||.+
T Consensus 123 RiGgRkRlTaEQKkr 137 (182)
T PF08688_consen 123 RIGGRKRLTAEQKKR 137 (182)
T ss_pred cccccccCCHHHhhh
Confidence 344555699999965
No 291
>PRK05572 sporulation sigma factor SigF; Validated
Probab=27.05 E-value=9.8 Score=32.75 Aligned_cols=50 Identities=4% Similarity=0.016 Sum_probs=36.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 132 QRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 132 ~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
.-.+++..|++.+..++ -+....+++|..+||+...|.+|.+.-..++++
T Consensus 199 ~l~~L~~~~~~v~~l~~---------~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 199 AIRELDERERLIVYLRY---------FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred HHHcCCHHHHHHHHHHH---------hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 33467777777776642 233477999999999999999988877666654
No 292
>PRK12461 UDP-N-acetylglucosamine acyltransferase; Provisional
Probab=27.00 E-value=81 Score=27.93 Aligned_cols=44 Identities=14% Similarity=0.070 Sum_probs=33.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCce
Q 048824 132 QRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHV 176 (209)
Q Consensus 132 ~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V 176 (209)
.|--||.|+.+.|++.+..+ |+....-++.++++.+++.-+..+
T Consensus 196 ~r~g~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 239 (255)
T PRK12461 196 RRRGFSSRAIRALKRAYKII-YRSGLSVQQAVAELELQQFESPEV 239 (255)
T ss_pred hhcCCCHHHHHHHHHHHHHH-HhcCCCHHHHHHHHHHhccCCHHH
Confidence 56789999999999977766 666666678888888877655543
No 293
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=26.85 E-value=77 Score=21.79 Aligned_cols=27 Identities=7% Similarity=0.443 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhCCCC-ceeeeecccccc
Q 048824 160 DVALNQFCNEVGVKR-HVLKVWMHNNKN 186 (209)
Q Consensus 160 ~~~ve~fc~eiGv~r-~V~KVWfhNnR~ 186 (209)
...++.||.+.|++. ..++.+|...+=
T Consensus 24 ~~l~~~~~~~~~i~~~~~~~l~fdG~~L 51 (72)
T PF11976_consen 24 SKLIEKYCEKKGIPPEESIRLIFDGKRL 51 (72)
T ss_dssp HHHHHHHHHHHTTTT-TTEEEEETTEEE
T ss_pred HHHHHHHHHhhCCCccceEEEEECCEEc
Confidence 678899999999999 999999988764
No 294
>cd08577 PI-PLCc_GDPD_SF_unchar3 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues.
Probab=26.51 E-value=1.1e+02 Score=26.71 Aligned_cols=42 Identities=19% Similarity=0.267 Sum_probs=25.2
Q ss_pred CCCCCCHHHHHHHHHH---HHHhCcccCC---CCHHHHHHHHHHhCCC
Q 048824 132 QRTKFTQEQKDKMLEF---AERIGWRMQR---QDDVALNQFCNEVGVK 173 (209)
Q Consensus 132 ~RTkFT~EQkekM~~f---aEk~GW~iqk---pd~~~ve~fc~eiGv~ 173 (209)
.+-.|+.+|+++|+++ |.+.|+++.. ++...+-+.+.+.||+
T Consensus 175 ~~g~~~~~q~~~l~~~v~~a~~~Gl~vr~Wtv~~~~~~~~~l~~~GVd 222 (228)
T cd08577 175 GKGDTPEDEKEKLKSIIDKAHARGKKVRFWGTPDRPNVWKTLMELGVD 222 (228)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCEEEEEccCChHHHHHHHHHhCCC
Confidence 3446999999999986 5555666544 2323333344445654
No 295
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=25.99 E-value=9.6 Score=33.17 Aligned_cols=32 Identities=6% Similarity=0.177 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 160 DVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 160 ~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
....+++|..+||+..+|+.+++--+.++++.
T Consensus 219 ~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 219 DLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34679999999999999999998877776653
No 296
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=25.85 E-value=21 Score=28.93 Aligned_cols=45 Identities=7% Similarity=0.148 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASH 189 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~k 189 (209)
.+|+-|+|.|.-.++= + ...++|++++|+.++|+.-..|=..|+.
T Consensus 150 ~Lt~rE~evl~~~~~G--~--------s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 150 RLSPKESEVLRLFAEG--F--------LVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred cCCHHHHHHHHHHHCC--C--------CHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 5999999999987533 2 5678999999999999988877666654
No 297
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=25.44 E-value=20 Score=21.24 Aligned_cols=24 Identities=17% Similarity=0.363 Sum_probs=19.6
Q ss_pred HHHHHHHHhCCCCceeeeeccccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
...+|+..+|++...|..|..+++
T Consensus 12 s~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 12 TQEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCC
Confidence 356899999999999999977653
No 298
>PRK09191 two-component response regulator; Provisional
Probab=25.42 E-value=14 Score=30.46 Aligned_cols=32 Identities=9% Similarity=0.205 Sum_probs=26.8
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 161 VALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
...+++|..+|++..+|++.++.-|.++++..
T Consensus 105 ~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~ 136 (261)
T PRK09191 105 FSVEEAAEILGVDPAEAEALLDDARAEIARQV 136 (261)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHhccC
Confidence 36889999999999999999988777776544
No 299
>PF02943 FeThRed_B: Ferredoxin thioredoxin reductase catalytic beta chain; InterPro: IPR004209 Ferredoxin thioredoxin reductase is a [4FE-4S] protein present in organisms performing oxygenic photosynthesis, and plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit alpha and subunit beta. Subunit alpha is the variable subunit, and beta is the catalytic chain []. The structure of the beta subunit has been determined and found to fold around the FeS cluster [].; GO: 0008937 ferredoxin-NAD(P) reductase activity, 0055114 oxidation-reduction process; PDB: 2PUK_E 2PVD_A 2PVG_A 2PUO_A 2PU9_A 1DJ7_A 2PVO_A.
Probab=25.31 E-value=1.5e+02 Score=23.72 Aligned_cols=26 Identities=15% Similarity=0.437 Sum_probs=15.3
Q ss_pred HHHHHHHHHhCcccCCCCHHHHHHHHH
Q 048824 142 DKMLEFAERIGWRMQRQDDVALNQFCN 168 (209)
Q Consensus 142 ekM~~faEk~GW~iqkpd~~~ve~fc~ 168 (209)
+.++.+|++.||.++ ||.+.+..+-.
T Consensus 8 ~~~~~~a~~~G~~~N-pD~~~~~~v~~ 33 (108)
T PF02943_consen 8 KFLEKYAEKSGYKLN-PDEEVTDDVLE 33 (108)
T ss_dssp HHHHHHHHHTT-B-B-SSHHHHHHHHH
T ss_pred HHHHHHHHHhCCEEC-CCHHHHHHHHH
Confidence 444558899999876 56655555444
No 300
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=25.29 E-value=52 Score=29.24 Aligned_cols=39 Identities=8% Similarity=0.285 Sum_probs=32.9
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceee
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLK 178 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~K 178 (209)
.++|.++++.+..+... .|+.-.++.||+..+|+..+|+
T Consensus 9 k~Ls~~~~~~ir~L~~~------~p~~~t~~~Lae~F~vspe~ir 47 (225)
T PF06413_consen 9 KKLSREAMEQIRYLHKE------DPEEWTVERLAESFKVSPEAIR 47 (225)
T ss_pred CCCCHHHHHHHHHHHHh------CccccCHHHHHhhCCCCHHHHH
Confidence 36889999998887555 5888899999999999998886
No 301
>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=25.28 E-value=44 Score=23.04 Aligned_cols=40 Identities=10% Similarity=0.227 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 138 QEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 138 ~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
..|++.|+-+.+ .+|- .++++|+++|++.++|+.-+.+=+
T Consensus 5 ~rq~~Ll~~L~~-~~~~-------~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWI-------TLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHH-HTSB-------BHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHc-CCCC-------cHHHHHHHHCCCHHHHHHHHHHHH
Confidence 346677777666 5552 567999999999999886555433
No 302
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=25.18 E-value=1.5e+02 Score=21.84 Aligned_cols=40 Identities=15% Similarity=0.242 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeee
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKV 179 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KV 179 (209)
-.++.+++.. .++|.-...+...+.++|+++|++-+.+++
T Consensus 27 ~~~~~~~l~~------~~~~~~~~~s~~~l~~~a~~~Gl~~~~~~~ 66 (129)
T cd02423 27 INITEQEVLK------LMLIRSEGFSMLDLKRYAEALGLKANGYRL 66 (129)
T ss_pred CCCCHHHHHH------HhCcccCCcCHHHHHHHHHHCCCcceEEEc
Confidence 5566666543 223444456777777777888877777664
No 303
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=25.09 E-value=32 Score=23.50 Aligned_cols=17 Identities=18% Similarity=0.327 Sum_probs=7.6
Q ss_pred CCHHHHHHHHHHhCCCC
Q 048824 158 QDDVALNQFCNEVGVKR 174 (209)
Q Consensus 158 pd~~~ve~fc~eiGv~r 174 (209)
++...+..||.-+|++.
T Consensus 42 p~~~~l~~l~~~l~~~~ 58 (64)
T PF13560_consen 42 PSPDTLQRLARALGVPP 58 (64)
T ss_dssp -BHHHHHHHHHHTT--H
T ss_pred CCHHHHHHHHHHHCcCH
Confidence 44555555555555543
No 304
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=24.96 E-value=31 Score=28.52 Aligned_cols=14 Identities=36% Similarity=0.847 Sum_probs=11.8
Q ss_pred cccccccccccccc
Q 048824 53 SLTCAACGCHRNFH 66 (209)
Q Consensus 53 ~l~CaaCgCHRnFH 66 (209)
.|+|.|||-+|...
T Consensus 123 ~l~C~ACGa~~~V~ 136 (138)
T PRK03988 123 VLKCEACGAETPVK 136 (138)
T ss_pred EEEcccCCCCCcCC
Confidence 68999999998753
No 305
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=24.82 E-value=21 Score=28.58 Aligned_cols=40 Identities=18% Similarity=0.369 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 136 FTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 136 FT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
++..+.+.|.+- +| - -...||..+||+..+|+.|=++++.
T Consensus 44 ls~~eIk~iRe~---~~-----l---SQ~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREK---LG-----L---SQPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHH---hC-----C---CHHHHHHHHCCCHHHHHHHHcCCcC
Confidence 788888777752 22 1 3578999999999999999998864
No 306
>PF14106 DUF4279: Domain of unknown function (DUF4279)
Probab=24.81 E-value=1.7e+02 Score=21.91 Aligned_cols=42 Identities=5% Similarity=0.209 Sum_probs=32.1
Q ss_pred CHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 048824 137 TQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKN 186 (209)
Q Consensus 137 T~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~ 186 (209)
-.+|++.|.+ ++ .+..+.+.+|+++.++...++-+|+.+...
T Consensus 53 l~~~l~~ll~---~L-----~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~ 94 (118)
T PF14106_consen 53 LEDHLEELLD---RL-----EPKREIIKELKEKYNLEIQFFCYFSSISGG 94 (118)
T ss_pred HHHHHHHHHH---HH-----cccHHHHHHHHHhcCcceEEEEEEEecCCC
Confidence 4466666554 33 588999999999999998888899865543
No 307
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=24.71 E-value=26 Score=28.40 Aligned_cols=11 Identities=55% Similarity=1.147 Sum_probs=9.7
Q ss_pred ccccccccccc
Q 048824 53 SLTCAACGCHR 63 (209)
Q Consensus 53 ~l~CaaCgCHR 63 (209)
.|+|.|||..|
T Consensus 114 ~l~C~aCGa~~ 124 (125)
T PF01873_consen 114 FLKCKACGASR 124 (125)
T ss_dssp EEEETTTSCEE
T ss_pred EEEecccCCcC
Confidence 68999999876
No 308
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=24.55 E-value=31 Score=26.44 Aligned_cols=22 Identities=9% Similarity=0.083 Sum_probs=19.5
Q ss_pred HHHHHHHHHhCCCCceeeeecc
Q 048824 161 VALNQFCNEVGVKRHVLKVWMH 182 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KVWfh 182 (209)
..+.++|..+||++.+|..|..
T Consensus 51 ~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 51 KTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3778899999999999999776
No 309
>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=24.52 E-value=1.2e+02 Score=24.67 Aligned_cols=32 Identities=16% Similarity=0.313 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCC
Q 048824 139 EQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKR 174 (209)
Q Consensus 139 EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r 174 (209)
.-+..|.+..+..|| -+.+.++.+|+.+||+.
T Consensus 17 ~li~~L~~vQ~~~G~----i~~~~~~~iA~~l~~~~ 48 (148)
T TIGR01958 17 AIMPALMIAQEQKGW----VTPEAIAAVAEMLGIPP 48 (148)
T ss_pred HHHHHHHHHHHHhCC----CCHHHHHHHHHHhCcCH
Confidence 456777788888885 78889999999999976
No 310
>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=24.50 E-value=20 Score=26.89 Aligned_cols=22 Identities=18% Similarity=0.347 Sum_probs=19.5
Q ss_pred HHHHHHHHhCCCCceeeeeccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhN 183 (209)
.+.++|..+||+.++|+.|-..
T Consensus 2 ti~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 2 TIGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 3678999999999999999865
No 311
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=24.46 E-value=21 Score=30.02 Aligned_cols=45 Identities=9% Similarity=0.129 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASH 189 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~k 189 (209)
.+|.-|+|.|.-.++=. ..+++|+++||+.++|+.-..|=..|++
T Consensus 137 ~LT~RE~eVL~lla~G~----------snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESSMLRMWMAGQ----------GTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHHHHHHHHcCC----------CHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 49999999998875542 5678999999999999887776666554
No 312
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=24.33 E-value=43 Score=22.01 Aligned_cols=28 Identities=25% Similarity=0.560 Sum_probs=18.1
Q ss_pred ccccccccccC-CCCcccccccccccccccc
Q 048824 39 ANDGCCEFMPR-ADDSLTCAACGCHRNFHRR 68 (209)
Q Consensus 39 ~~DGC~Efm~~-~~~~l~CaaCgCHRnFHr~ 68 (209)
-=|-|+++|.. +..+++|..|+ ...|.+
T Consensus 13 ~C~~C~~~i~g~~~~g~~C~~C~--~~~H~~ 41 (53)
T PF00130_consen 13 YCDVCGKFIWGLGKQGYRCSWCG--LVCHKK 41 (53)
T ss_dssp B-TTSSSBECSSSSCEEEETTTT---EEETT
T ss_pred CCcccCcccCCCCCCeEEECCCC--ChHhhh
Confidence 34779999964 33599999775 344443
No 313
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=24.15 E-value=62 Score=24.81 Aligned_cols=18 Identities=22% Similarity=0.625 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHhCccc
Q 048824 138 QEQKDKMLEFAERIGWRM 155 (209)
Q Consensus 138 ~EQkekM~~faEk~GW~i 155 (209)
..|++.+++||++.||.+
T Consensus 18 ~~Q~~~~~~~a~~~g~~i 35 (148)
T smart00857 18 ERQLEALRAYAKANGWEV 35 (148)
T ss_pred HHHHHHHHHHHHHCCCEE
Confidence 589999999999999986
No 314
>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=24.06 E-value=74 Score=25.72 Aligned_cols=33 Identities=18% Similarity=0.292 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCce
Q 048824 140 QKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHV 176 (209)
Q Consensus 140 QkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V 176 (209)
-+..|.+..+..|| -+.+.++++|+.+||+...
T Consensus 15 ll~~L~~~Q~~~g~----i~~~~~~~iA~~l~i~~~~ 47 (145)
T PF01257_consen 15 LLPILHEVQEEYGY----IPEEALEEIAEALGIPPAE 47 (145)
T ss_dssp HHHHHHHHHHHHSS------HHHHHHHHHHHTS-HHH
T ss_pred HHHHHHHHHHHcCC----CCHHHHHHHHHHHCCCHHH
Confidence 46778888899884 8889999999999998653
No 315
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=24.03 E-value=16 Score=32.74 Aligned_cols=32 Identities=9% Similarity=0.214 Sum_probs=28.6
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~~ 193 (209)
..+++|+.+|++...+++.++.-|.+++...+
T Consensus 136 s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~ 167 (290)
T PRK09635 136 PYQQIATTIGSQASTCRQLAHRARRKINESRI 167 (290)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCC
Confidence 57899999999999999999999999987543
No 316
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=23.07 E-value=95 Score=22.83 Aligned_cols=28 Identities=7% Similarity=0.366 Sum_probs=21.6
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccC
Q 048824 161 VALNQFCNEVGVKRHVLKVWMHNNKNAS 188 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~KVWfhNnR~k~ 188 (209)
...+.+|+..||+...++-||..++=..
T Consensus 36 ~l~~~y~~~~gi~~~~~rf~f~G~~L~~ 63 (87)
T cd01763 36 KLMEAYCQRQGLSMNSVRFLFDGQRIRD 63 (87)
T ss_pred HHHHHHHHHhCCCccceEEEECCeECCC
Confidence 3456677888899999999998876554
No 317
>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=22.82 E-value=40 Score=25.88 Aligned_cols=18 Identities=6% Similarity=0.154 Sum_probs=15.5
Q ss_pred HHHHHHHHHhCCCCceee
Q 048824 161 VALNQFCNEVGVKRHVLK 178 (209)
Q Consensus 161 ~~ve~fc~eiGv~r~V~K 178 (209)
-..+++|..+|++..+|+
T Consensus 124 ~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 124 MKEIDIAKKLHISRQSVY 141 (142)
T ss_pred CCHHHHHHHHCcCHHhhc
Confidence 367899999999998876
No 318
>PF13743 Thioredoxin_5: Thioredoxin; PDB: 3KZQ_C.
Probab=22.79 E-value=45 Score=27.61 Aligned_cols=30 Identities=20% Similarity=0.379 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 048824 156 QRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 156 qkpd~~~ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
++.+++++.++|+++||+...|+..|+..-
T Consensus 99 ~~s~~~~l~~iA~~~gLD~~~F~~d~~S~~ 128 (176)
T PF13743_consen 99 NYSDEELLLEIAEELGLDVEMFKEDLHSDE 128 (176)
T ss_dssp -TTSHHHHHHHHHHTT--HHHHHHHHTSHH
T ss_pred CCCHHHHHHHHHHHhCCCHHHHHHHHhChH
Confidence 346679999999999999999998887653
No 319
>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=22.79 E-value=22 Score=26.74 Aligned_cols=23 Identities=13% Similarity=0.172 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCCceeeeeccccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHNNK 185 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhNnR 185 (209)
+.++|..+||+..+|+.|..+-.
T Consensus 3 i~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 67899999999999999976543
No 320
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=22.76 E-value=86 Score=23.56 Aligned_cols=44 Identities=18% Similarity=0.361 Sum_probs=30.6
Q ss_pred CCCCCHHHHHHHHHHHHH-hCcccCCCCHHHHHHHHHHhCCCCcee
Q 048824 133 RTKFTQEQKDKMLEFAER-IGWRMQRQDDVALNQFCNEVGVKRHVL 177 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk-~GW~iqkpd~~~ve~fc~eiGv~r~V~ 177 (209)
...++..|...|...+++ .||.. ..+.-..++||+.+|+++.++
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~-~~~~is~~eLa~~~g~sr~tV 64 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNK-KQDRVTATVIAELTGLSRTHV 64 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccc-cCCccCHHHHHHHHCcCHHHH
Confidence 345677788888887763 37653 234455779999999998765
No 321
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=22.70 E-value=12 Score=32.25 Aligned_cols=48 Identities=8% Similarity=0.050 Sum_probs=34.9
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHR 190 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk 190 (209)
.+++..+++.+...+ -+....+++|..+||+..+|+.+.++-..++++
T Consensus 208 ~~L~~~er~vi~~~~---------~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 208 KKLNDREKLILNLRF---------FQGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred HcCCHHHHHHHHHHH---------hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 367777777766532 122368899999999999999888877666654
No 322
>PF01113 DapB_N: Dihydrodipicolinate reductase, N-terminus; InterPro: IPR000846 Dihydrodipicolinate reductase catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5-tetrahydrodipicolinate [, , ]. In Escherichia coli and Mycobacterium tuberculosis, dihydrodipicolinate reductase has equal specificity for NADH and NADPH, however in Thermotoga maritima there it has a greater affinity for NADPH []. In addition, the enzyme is inhibited by high concentrations of its substrate, which consequently acts as a feedback control on the lysine biosynthesis pathway. In T. maritima, the enzyme also lacks N-terminal and C-terminal loops which are present in enzyme of the former two organisms. This entry represents the N-terminal domain of dihydrodipicolinate reductase which binds the dinucleotide NAD(P)H.; GO: 0008839 dihydrodipicolinate reductase activity, 0009089 lysine biosynthetic process via diaminopimelate, 0055114 oxidation-reduction process; PDB: 3QY9_D 1VM6_C 1ARZ_A 1DIH_A 1DRW_A 1DRV_A 1DRU_A 2DAP_A 1DAP_B 3DAP_A ....
Probab=22.61 E-value=34 Score=26.60 Aligned_cols=20 Identities=40% Similarity=0.544 Sum_probs=16.6
Q ss_pred CCCCHHHHHHHHHHHHHhCc
Q 048824 134 TKFTQEQKDKMLEFAERIGW 153 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW 153 (209)
|=|+.||++.|++++++.++
T Consensus 99 TG~~~~~~~~l~~~a~~~~v 118 (124)
T PF01113_consen 99 TGFSDEQIDELEELAKKIPV 118 (124)
T ss_dssp SSSHHHHHHHHHHHTTTSEE
T ss_pred CCCCHHHHHHHHHHhccCCE
Confidence 55789999999999888654
No 323
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=22.28 E-value=87 Score=30.06 Aligned_cols=20 Identities=35% Similarity=0.632 Sum_probs=17.2
Q ss_pred CCCCCHHHHHHHHHHHHHhC
Q 048824 133 RTKFTQEQKDKMLEFAERIG 152 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~G 152 (209)
-+.+|.+|++.|++|++..+
T Consensus 333 P~~ls~~q~~lL~~~~~~~~ 352 (371)
T COG0484 333 PKNLSDEQKELLEEFAKSLG 352 (371)
T ss_pred CCCCCHHHHHHHHHHHHhhc
Confidence 35699999999999999863
No 324
>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=22.11 E-value=25 Score=26.88 Aligned_cols=22 Identities=9% Similarity=0.231 Sum_probs=19.4
Q ss_pred HHHHHHHHhCCCCceeeeeccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhN 183 (209)
.+.++|..+||+.++|+.|-..
T Consensus 2 ~i~eva~~~gis~~tlR~ye~~ 23 (108)
T cd01107 2 TIGEFAKLSNLSIKALRYYDKI 23 (108)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 3678999999999999999865
No 325
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=21.89 E-value=37 Score=27.92 Aligned_cols=13 Identities=38% Similarity=0.912 Sum_probs=10.7
Q ss_pred ccccccccccccc
Q 048824 53 SLTCAACGCHRNF 65 (209)
Q Consensus 53 ~l~CaaCgCHRnF 65 (209)
.|+|.|||-+|.-
T Consensus 118 ~l~C~ACGa~~~v 130 (133)
T TIGR00311 118 LLKCEACGAKAPL 130 (133)
T ss_pred EEecccCCCCCcc
Confidence 5899999988753
No 326
>cd02420 Peptidase_C39D A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=21.87 E-value=1.7e+02 Score=21.56 Aligned_cols=42 Identities=12% Similarity=0.021 Sum_probs=26.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeee
Q 048824 132 QRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKV 179 (209)
Q Consensus 132 ~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KV 179 (209)
+.-.++.+++.. .++|.....+...+.++++.+|++-+.+++
T Consensus 24 ~g~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~ 65 (125)
T cd02420 24 YGRYVPLSELRI------ACGVSRDGSNASNLLKAAREYGLTAKGYKK 65 (125)
T ss_pred cCCCCCHHHHHH------HcCCCCCCCCHHHHHHHHHHcCcccceEec
Confidence 444556666542 334544446777788888888887777764
No 327
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=21.86 E-value=29 Score=26.92 Aligned_cols=46 Identities=4% Similarity=0.065 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 048824 134 TKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASH 189 (209)
Q Consensus 134 TkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~k 189 (209)
..+|..+.+.|.-+++-. ..++++..++++.++|++-..|=|.|+.
T Consensus 142 ~~lt~~E~~vl~~l~~g~----------~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 142 DSLSKQEISVMRYILDGK----------DNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred ccCCHHHHHHHHHHHcCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 459999999888876542 3678899999999999999888887764
No 328
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=21.86 E-value=24 Score=26.10 Aligned_cols=22 Identities=9% Similarity=0.228 Sum_probs=19.3
Q ss_pred HHHHHHHHhCCCCceeeeeccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhN 183 (209)
.+.++|..+||+..+|+.|...
T Consensus 3 ~i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 3 VISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 4678999999999999999764
No 329
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=21.84 E-value=84 Score=23.32 Aligned_cols=23 Identities=22% Similarity=0.312 Sum_probs=14.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCccc
Q 048824 133 RTKFTQEQKDKMLEFAERIGWRM 155 (209)
Q Consensus 133 RTkFT~EQkekM~~faEk~GW~i 155 (209)
.=++|.||+++|.+..++.||..
T Consensus 45 ~V~Lt~eqv~~LN~~l~~~Gf~~ 67 (73)
T PF14794_consen 45 QVFLTEEQVAKLNQALQKAGFDE 67 (73)
T ss_dssp -----HHHHHHHHHHHHHTT---
T ss_pred CEEcCHHHHHHHHHHHHHcCCCc
Confidence 34689999999999999999753
No 330
>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]
Probab=21.80 E-value=1e+02 Score=25.94 Aligned_cols=50 Identities=14% Similarity=0.298 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHhCcccCCCC----------HHHHHHHHHHhCCCCceeeeeccccccc
Q 048824 138 QEQKDKMLEFAERIGWRMQRQD----------DVALNQFCNEVGVKRHVLKVWMHNNKNA 187 (209)
Q Consensus 138 ~EQkekM~~faEk~GW~iqkpd----------~~~ve~fc~eiGv~r~V~KVWfhNnR~k 187 (209)
.-|++.|++|+.+.||.+-+.| ....+++.+.|.-.+.+|-||=-+|-.+
T Consensus 18 ~~Q~~~l~~~~~~~g~~~~~~~~~sg~~~~~~Rp~l~~ll~~i~~g~d~lvV~~lDRL~R 77 (222)
T COG1961 18 DNQREALEAYAKNKGCEIVFEDKDSGSSSGKNRPGLQRLLEDIEEGKDTLVVYKLDRLGR 77 (222)
T ss_pred HHHHHHHHHHHHhCCCEEEEEeecCCccCCCCCHHHHHHHHHHHcCCcEEEEEEechhhc
Confidence 7899999999999999954322 4578888888876668888886665544
No 331
>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=21.80 E-value=24 Score=26.85 Aligned_cols=22 Identities=14% Similarity=0.388 Sum_probs=19.0
Q ss_pred HHHHHHHHhCCCCceeeeeccc
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhN 183 (209)
.+.++|+.+||+.++|+.|-..
T Consensus 3 ~i~eva~~~gvs~~tlR~ye~~ 24 (102)
T cd04789 3 TISELAEKAGISRSTLLYYEKL 24 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 4678999999999999998764
No 332
>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=21.70 E-value=24 Score=26.76 Aligned_cols=20 Identities=15% Similarity=0.458 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCCceeeeecc
Q 048824 163 LNQFCNEVGVKRHVLKVWMH 182 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfh 182 (209)
+.++|..+||+.++|+.|..
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 67899999999999999976
No 333
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=21.66 E-value=1.5e+02 Score=21.74 Aligned_cols=28 Identities=21% Similarity=0.462 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhCcccCCCCHHHHHHHHHHh
Q 048824 141 KDKMLEFAERIGWRMQRQDDVALNQFCNEV 170 (209)
Q Consensus 141 kekM~~faEk~GW~iqkpd~~~ve~fc~ei 170 (209)
.+.++.+||.+| |...+++..+.||+++
T Consensus 6 ~esvk~iAes~G--i~~l~de~a~~La~dv 33 (66)
T PF02969_consen 6 QESVKDIAESLG--ISNLSDEAAKALAEDV 33 (66)
T ss_dssp HHHHHHHHHHTT-----B-HHHHHHHHHHH
T ss_pred HHHHHHHHHHcC--CCCCCHHHHHHHHHHH
Confidence 467788999999 6667778888888776
No 334
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=21.34 E-value=25 Score=29.96 Aligned_cols=52 Identities=12% Similarity=0.130 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824 135 KFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR 191 (209)
Q Consensus 135 kFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~ 191 (209)
.++..|++.|.-.+ | +..-.....+++|..+||+...|+.+.+.-..|+|..
T Consensus 176 ~L~~~er~vl~l~y---g--l~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 176 TLTERERKVLRMRY---G--LLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred hCCHHHHHHHHHHh---C--CCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 34555555555431 1 1112445789999999999999999998888887754
No 335
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=21.25 E-value=57 Score=25.55 Aligned_cols=44 Identities=11% Similarity=0.257 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 048824 140 QKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 140 QkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNn 184 (209)
-++++.+-|.++ +.-+.-....++++|++.||++..|---|-|.
T Consensus 9 rr~~Il~aA~~l-f~~~G~~~~s~~~IA~~agvsk~~ly~~F~sK 52 (189)
T TIGR03384 9 RRAELIDATIES-IGERGSLDVTIAQIARRAGVSSGIISHYFGGK 52 (189)
T ss_pred HHHHHHHHHHHH-HHhcCcccCCHHHHHHHhCCCHHHHHHHcCCH
Confidence 344555444433 11223557789999999999999887777543
No 336
>cd00131 PAX Paired Box domain
Probab=21.10 E-value=55 Score=26.11 Aligned_cols=38 Identities=11% Similarity=0.263 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecc
Q 048824 136 FTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMH 182 (209)
Q Consensus 136 FT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfh 182 (209)
+|.+..+++..+++ -|. ...++|..+||++.+|.-|.+
T Consensus 18 lS~d~R~rIv~~~~-~G~--------s~~~iA~~~~Vs~~tV~r~i~ 55 (128)
T cd00131 18 LPDSIRQRIVELAQ-SGI--------RPCDISRQLRVSHGCVSKILN 55 (128)
T ss_pred CCHHHHHHHHHHHH-cCC--------CHHHHHHHHCcCHHHHHHHHH
No 337
>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=21.07 E-value=25 Score=26.07 Aligned_cols=19 Identities=21% Similarity=0.557 Sum_probs=17.3
Q ss_pred HHHHHHHHhCCCCceeeee
Q 048824 162 ALNQFCNEVGVKRHVLKVW 180 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVW 180 (209)
.+.++|..+||+.++|+.|
T Consensus 3 ti~evA~~~gvs~~tLR~y 21 (88)
T cd01105 3 GIGEVSKLTGVSPRQLRYW 21 (88)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 3678999999999999999
No 338
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=20.89 E-value=1.4e+02 Score=18.39 Aligned_cols=18 Identities=22% Similarity=0.534 Sum_probs=15.2
Q ss_pred CCCHHHHHHHHHHHHHhC
Q 048824 135 KFTQEQKDKMLEFAERIG 152 (209)
Q Consensus 135 kFT~EQkekM~~faEk~G 152 (209)
+|+.++.++|.+.|++.|
T Consensus 5 ~l~~~~~~~l~~~a~~~g 22 (39)
T PF01402_consen 5 RLPDELYERLDELAKELG 22 (39)
T ss_dssp EEEHHHHHHHHHHHHHHT
T ss_pred EeCHHHHHHHHHHHHHHC
Confidence 467889999999999987
No 339
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=20.66 E-value=13 Score=29.98 Aligned_cols=31 Identities=10% Similarity=0.262 Sum_probs=26.8
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCCC
Q 048824 162 ALNQFCNEVGVKRHVLKVWMHNNKNASHRRK 192 (209)
Q Consensus 162 ~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~~ 192 (209)
..+++|+.+||+..+||.|++--|.++++..
T Consensus 145 s~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 145 SYEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999998888877654
No 340
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=20.56 E-value=22 Score=24.95 Aligned_cols=23 Identities=9% Similarity=0.293 Sum_probs=16.2
Q ss_pred HHHHHHHHHHhCCCCceeeeecc
Q 048824 160 DVALNQFCNEVGVKRHVLKVWMH 182 (209)
Q Consensus 160 ~~~ve~fc~eiGv~r~V~KVWfh 182 (209)
.-..+++|..+||+..-|+-.++
T Consensus 20 ~Pt~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 20 EPTDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp --BHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCHHHHHHHHcccHHHHHHHHH
Confidence 45778899999999887776654
No 341
>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=20.53 E-value=28 Score=26.69 Aligned_cols=21 Identities=10% Similarity=0.406 Sum_probs=18.5
Q ss_pred HHHHHHHhCCCCceeeeeccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHN 183 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhN 183 (209)
+.++|..+||+.++|+.|-..
T Consensus 3 i~e~a~~~gvs~~tlr~ye~~ 23 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEKE 23 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 678999999999999999653
No 342
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=20.48 E-value=40 Score=29.11 Aligned_cols=18 Identities=44% Similarity=0.995 Sum_probs=14.6
Q ss_pred cccccccccccccccccc
Q 048824 53 SLTCAACGCHRNFHRREV 70 (209)
Q Consensus 53 ~l~CaaCgCHRnFHr~e~ 70 (209)
.|+|.|||-+|.-+..-.
T Consensus 119 ~l~C~aCGa~~~v~~~~~ 136 (201)
T PRK12336 119 MLRCDACGAHRPVKKRKA 136 (201)
T ss_pred EEEcccCCCCcccccccc
Confidence 689999999988875543
No 343
>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=20.43 E-value=28 Score=26.77 Aligned_cols=22 Identities=18% Similarity=0.527 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCCceeeeecccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhNn 184 (209)
+.++|..+||+.++|+.|..+-
T Consensus 3 i~eva~~~gvs~~tlR~ye~~G 24 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKEG 24 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 6789999999999999997653
No 344
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=20.38 E-value=78 Score=20.77 Aligned_cols=12 Identities=25% Similarity=0.335 Sum_probs=11.0
Q ss_pred CCCHHHHHHHHH
Q 048824 135 KFTQEQKDKMLE 146 (209)
Q Consensus 135 kFT~EQkekM~~ 146 (209)
.||.+|++.|+.
T Consensus 2 ~FT~~Ql~~L~~ 13 (37)
T PF08880_consen 2 PFTPAQLQELRA 13 (37)
T ss_pred CCCHHHHHHHHH
Confidence 599999999997
No 345
>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=20.36 E-value=27 Score=25.76 Aligned_cols=22 Identities=14% Similarity=0.354 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCCceeeeecccc
Q 048824 163 LNQFCNEVGVKRHVLKVWMHNN 184 (209)
Q Consensus 163 ve~fc~eiGv~r~V~KVWfhNn 184 (209)
+.++|+.+||+..+|+.|-...
T Consensus 3 ~~eva~~~gi~~~tlr~~~~~G 24 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEEKG 24 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 6789999999999999997654
No 346
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=20.11 E-value=95 Score=28.41 Aligned_cols=36 Identities=17% Similarity=0.403 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCcccCCCC--HHHHHHHHHHhCCCCcee
Q 048824 142 DKMLEFAERIGWRMQRQD--DVALNQFCNEVGVKRHVL 177 (209)
Q Consensus 142 ekM~~faEk~GW~iqkpd--~~~ve~fc~eiGv~r~V~ 177 (209)
+.|++||.+.-=.|++.. ...-++.|..|||++-+.
T Consensus 43 ~~LeeFA~kH~~ei~knsqFR~~Fq~Mca~IGvDPlas 80 (249)
T KOG3341|consen 43 EALEEFARKHKTEIRKNSQFRNQFQEMCASIGVDPLAS 80 (249)
T ss_pred HHHHHHHHHHHHHHhhCHHHHHHHHHHHHHcCCCcccc
Confidence 456779888766666655 467789999999997553
No 347
>PRK06437 hypothetical protein; Provisional
Probab=20.03 E-value=23 Score=25.32 Aligned_cols=34 Identities=12% Similarity=0.251 Sum_probs=26.4
Q ss_pred cccCCCCHHHHHHHHHHhCCCCceeeeeccccccc
Q 048824 153 WRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNA 187 (209)
Q Consensus 153 W~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k 187 (209)
|..+.++...+.+|..++|++...+-|+ .|.+--
T Consensus 13 ~~~~i~~~~tv~dLL~~Lgi~~~~vaV~-vNg~iv 46 (67)
T PRK06437 13 KTIEIDHELTVNDIIKDLGLDEEEYVVI-VNGSPV 46 (67)
T ss_pred eEEEcCCCCcHHHHHHHcCCCCccEEEE-ECCEEC
Confidence 4455556678999999999999999888 666544
Done!