Query 044959
Match_columns 159
No_of_seqs 187 out of 333
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 08:28:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044959.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044959hhsearch_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 1.4E-38 3E-43 214.9 2.9 52 1-52 1-53 (53)
2 PF04770 ZF-HD_dimer: ZF-HD pr 100.0 2E-37 4.3E-42 214.4 2.9 53 1-53 5-58 (60)
3 TIGR01565 homeo_ZF_HD homeobox 99.9 3.3E-27 7.1E-32 161.8 5.9 58 75-132 1-58 (58)
4 KOG0843 Transcription factor E 99.7 1.8E-17 3.8E-22 136.7 2.3 63 74-140 101-163 (197)
5 PF00046 Homeobox: Homeobox do 99.7 2.3E-17 5E-22 107.6 1.1 56 76-135 1-56 (57)
6 KOG0489 Transcription factor z 99.6 2.5E-17 5.5E-22 138.7 1.2 63 73-139 157-219 (261)
7 KOG0493 Transcription factor E 99.6 2.9E-16 6.3E-21 136.3 3.4 58 76-137 247-304 (342)
8 KOG0488 Transcription factor B 99.6 3E-16 6.6E-21 136.0 3.5 61 73-137 170-230 (309)
9 KOG0484 Transcription factor P 99.6 5.8E-16 1.3E-20 119.4 0.7 62 71-136 13-74 (125)
10 KOG0842 Transcription factor t 99.6 1.8E-15 4E-20 131.9 3.8 65 72-140 150-214 (307)
11 smart00389 HOX Homeodomain. DN 99.5 1.1E-14 2.4E-19 93.8 4.8 56 76-135 1-56 (56)
12 KOG2251 Homeobox transcription 99.5 7.1E-15 1.5E-19 123.9 4.7 67 70-140 32-98 (228)
13 KOG0485 Transcription factor N 99.5 3.8E-15 8.3E-20 126.5 2.2 66 72-141 101-166 (268)
14 KOG0494 Transcription factor C 99.5 8.7E-15 1.9E-19 127.0 3.3 60 75-138 141-200 (332)
15 cd00086 homeodomain Homeodomai 99.5 2.6E-14 5.7E-19 92.2 4.0 58 76-137 1-58 (59)
16 KOG0850 Transcription factor D 99.5 1.2E-14 2.6E-19 123.4 2.2 63 73-139 120-182 (245)
17 KOG3802 Transcription factor O 99.4 8.1E-14 1.7E-18 125.1 4.9 64 72-139 291-354 (398)
18 KOG0492 Transcription factor M 99.4 5.1E-14 1.1E-18 118.9 3.2 62 74-139 143-204 (246)
19 KOG0844 Transcription factor E 99.4 4E-14 8.6E-19 125.2 1.6 62 75-140 181-242 (408)
20 KOG0487 Transcription factor A 99.4 7E-14 1.5E-18 122.1 2.9 62 73-138 233-294 (308)
21 KOG4577 Transcription factor L 99.4 9.6E-14 2.1E-18 122.1 3.1 64 71-138 163-226 (383)
22 KOG0491 Transcription factor B 99.2 8.7E-13 1.9E-17 108.3 -1.0 65 74-142 99-163 (194)
23 KOG0483 Transcription factor H 99.2 6.9E-12 1.5E-16 103.7 3.8 65 75-143 50-114 (198)
24 COG5576 Homeodomain-containing 99.2 9.7E-12 2.1E-16 99.3 3.0 67 70-140 46-112 (156)
25 KOG0490 Transcription factor, 99.2 7.3E-12 1.6E-16 99.0 1.8 63 72-138 57-119 (235)
26 KOG0486 Transcription factor P 99.1 1.9E-11 4.2E-16 107.9 2.7 64 74-142 111-174 (351)
27 KOG0848 Transcription factor C 99.1 1.8E-11 3.8E-16 106.6 0.4 59 74-136 198-256 (317)
28 KOG0847 Transcription factor, 99.0 8.2E-11 1.8E-15 100.7 1.8 69 72-144 164-232 (288)
29 KOG1168 Transcription factor A 99.0 1E-10 2.2E-15 103.3 0.5 62 71-136 305-366 (385)
30 KOG0849 Transcription factor P 98.9 1.1E-09 2.4E-14 96.5 4.4 63 72-138 173-235 (354)
31 KOG2252 CCAAT displacement pro 98.4 5.3E-07 1.1E-11 84.3 5.6 59 72-134 417-475 (558)
32 KOG0490 Transcription factor, 98.3 1.9E-07 4.1E-12 73.9 1.3 64 71-138 149-212 (235)
33 KOG1146 Homeobox protein [Gene 97.9 5.9E-06 1.3E-10 83.5 3.1 75 74-153 902-976 (1406)
34 PF05920 Homeobox_KN: Homeobox 97.7 8.5E-06 1.8E-10 52.0 0.1 33 100-132 7-39 (40)
35 KOG0775 Transcription factor S 97.4 0.00015 3.3E-09 63.8 4.5 55 78-136 170-233 (304)
36 KOG0774 Transcription factor P 97.3 0.00026 5.6E-09 62.4 3.9 64 75-139 188-251 (334)
37 PF04218 CENP-B_N: CENP-B N-te 96.7 0.0028 6.1E-08 42.1 4.1 47 76-131 1-47 (53)
38 PF01527 HTH_Tnp_1: Transposas 96.4 0.0033 7.1E-08 42.4 2.7 47 77-131 2-48 (76)
39 KOG0773 Transcription factor M 95.8 0.01 2.2E-07 51.1 3.8 61 74-136 238-299 (342)
40 PF11569 Homez: Homeodomain le 94.5 0.027 5.9E-07 38.9 2.1 41 88-132 11-51 (56)
41 KOG3623 Homeobox transcription 94.0 0.055 1.2E-06 53.6 3.8 58 79-141 561-619 (1007)
42 cd00569 HTH_Hin_like Helix-tur 93.6 0.16 3.4E-06 27.1 3.7 40 79-127 3-42 (42)
43 cd06171 Sigma70_r4 Sigma70, re 91.6 0.12 2.6E-06 30.8 1.5 45 81-134 10-54 (55)
44 PRK09413 IS2 repressor TnpA; R 90.1 0.27 5.8E-06 36.9 2.6 44 78-129 9-52 (121)
45 PF02796 HTH_7: Helix-turn-hel 89.8 0.27 5.7E-06 31.2 2.0 41 79-128 3-43 (45)
46 PF04967 HTH_10: HTH DNA bindi 88.9 0.44 9.5E-06 32.2 2.7 42 82-125 1-42 (53)
47 COG2963 Transposase and inacti 87.8 1.1 2.3E-05 32.8 4.4 48 79-134 5-53 (116)
48 PF00196 GerE: Bacterial regul 86.0 0.25 5.5E-06 32.2 0.2 45 81-135 3-47 (58)
49 smart00421 HTH_LUXR helix_turn 86.0 0.44 9.4E-06 29.0 1.3 45 81-135 3-47 (58)
50 PF06163 DUF977: Bacterial pro 85.9 0.62 1.3E-05 37.0 2.4 45 81-129 4-49 (127)
51 PF08281 Sigma70_r4_2: Sigma-7 84.8 1.4 3.1E-05 27.9 3.3 41 82-131 11-51 (54)
52 TIGR02989 Sig-70_gvs1 RNA poly 84.7 0.39 8.4E-06 35.6 0.7 47 80-136 110-157 (159)
53 PF13936 HTH_38: Helix-turn-he 84.5 0.49 1.1E-05 30.0 1.0 42 79-129 2-43 (44)
54 PRK06759 RNA polymerase factor 81.8 0.66 1.4E-05 34.3 0.9 30 107-136 123-152 (154)
55 PRK03975 tfx putative transcri 81.6 0.47 1E-05 37.7 0.1 51 80-140 5-55 (141)
56 cd06170 LuxR_C_like C-terminal 81.2 1.7 3.7E-05 26.6 2.5 43 82-134 1-43 (57)
57 PRK09646 RNA polymerase sigma 80.7 0.52 1.1E-05 36.9 0.1 30 107-136 159-188 (194)
58 PRK10403 transcriptional regul 80.4 0.99 2.1E-05 33.3 1.4 47 80-136 152-198 (215)
59 PRK12541 RNA polymerase sigma 79.8 0.68 1.5E-05 34.8 0.4 31 107-137 129-159 (161)
60 PRK09644 RNA polymerase sigma 79.4 0.62 1.3E-05 35.3 0.1 47 81-137 108-155 (165)
61 PRK12526 RNA polymerase sigma 79.1 0.6 1.3E-05 37.1 -0.1 31 107-137 170-200 (206)
62 PF13551 HTH_29: Winged helix- 79.1 4.6 9.9E-05 28.2 4.5 54 75-128 51-109 (112)
63 PF13518 HTH_28: Helix-turn-he 78.6 1.3 2.8E-05 27.4 1.4 25 108-132 14-38 (52)
64 PF04545 Sigma70_r4: Sigma-70, 78.4 1.7 3.6E-05 27.4 1.9 40 81-129 4-43 (50)
65 TIGR02985 Sig70_bacteroi1 RNA 78.2 0.78 1.7E-05 33.5 0.3 29 108-136 131-159 (161)
66 PRK12512 RNA polymerase sigma 77.8 0.7 1.5E-05 35.5 -0.0 31 107-137 148-178 (184)
67 PRK12537 RNA polymerase sigma 77.8 0.85 1.8E-05 35.2 0.4 30 107-136 150-179 (182)
68 PF09607 BrkDBD: Brinker DNA-b 77.3 3.1 6.8E-05 29.0 3.1 45 79-128 3-47 (58)
69 cd04762 HTH_MerR-trunc Helix-T 77.0 1.9 4.2E-05 25.5 1.8 25 109-133 3-27 (49)
70 PRK04217 hypothetical protein; 76.8 0.92 2E-05 34.7 0.3 48 80-136 41-88 (110)
71 PRK09652 RNA polymerase sigma 76.3 0.76 1.7E-05 34.3 -0.2 47 81-136 128-174 (182)
72 PRK12530 RNA polymerase sigma 76.1 0.81 1.8E-05 35.8 -0.1 30 107-136 151-180 (189)
73 TIGR02939 RpoE_Sigma70 RNA pol 76.0 0.6 1.3E-05 35.6 -0.8 33 104-136 152-184 (190)
74 TIGR03879 near_KaiC_dom probab 75.6 2.8 6.1E-05 30.1 2.6 27 105-131 31-57 (73)
75 KOG3755 SATB1 matrix attachmen 75.5 2.2 4.7E-05 41.9 2.5 61 74-137 646-709 (769)
76 PRK10072 putative transcriptio 75.4 3.9 8.5E-05 30.4 3.4 23 109-131 49-71 (96)
77 PRK12514 RNA polymerase sigma 75.2 0.98 2.1E-05 34.5 0.1 29 108-136 147-175 (179)
78 TIGR02948 SigW_bacill RNA poly 74.8 0.98 2.1E-05 34.3 0.1 31 106-136 152-182 (187)
79 PRK09648 RNA polymerase sigma 74.8 0.94 2E-05 35.0 -0.1 48 79-136 137-185 (189)
80 PF01381 HTH_3: Helix-turn-hel 74.4 3 6.5E-05 26.1 2.2 22 109-130 12-33 (55)
81 cd04761 HTH_MerR-SF Helix-Turn 74.1 1.9 4.1E-05 26.4 1.2 25 109-133 3-27 (49)
82 PRK15369 two component system 74.0 1.8 3.9E-05 31.4 1.3 46 80-135 148-193 (211)
83 PRK09726 antitoxin HipB; Provi 74.0 7.7 0.00017 27.4 4.5 42 81-130 7-49 (88)
84 PF13443 HTH_26: Cro/C1-type H 73.9 1.9 4E-05 27.9 1.2 24 108-131 12-35 (63)
85 PF13384 HTH_23: Homeodomain-l 73.8 1.9 4.1E-05 26.9 1.2 23 107-129 18-40 (50)
86 PRK09642 RNA polymerase sigma 73.5 1.1 2.5E-05 33.4 0.1 29 108-136 124-152 (160)
87 TIGR03070 couple_hipB transcri 72.9 6.7 0.00014 24.1 3.5 23 109-131 18-40 (58)
88 PRK05602 RNA polymerase sigma 72.7 0.99 2.1E-05 34.8 -0.4 30 108-137 146-175 (186)
89 COG3413 Predicted DNA binding 72.4 3.5 7.7E-05 33.4 2.8 43 81-125 155-197 (215)
90 PRK12515 RNA polymerase sigma 72.2 1.2 2.6E-05 34.5 -0.0 47 80-136 130-177 (189)
91 PRK06424 transcription factor; 71.9 2.9 6.3E-05 33.2 2.1 53 75-132 68-123 (144)
92 PRK12539 RNA polymerase sigma 71.8 1.3 2.8E-05 34.3 0.1 31 106-136 147-177 (184)
93 PRK09390 fixJ response regulat 71.7 2 4.2E-05 31.1 1.0 28 109-136 159-186 (202)
94 PRK09047 RNA polymerase factor 71.5 1.4 3E-05 32.7 0.2 29 108-136 124-152 (161)
95 PF13411 MerR_1: MerR HTH fami 71.3 2.4 5.2E-05 27.8 1.3 23 109-131 3-25 (69)
96 TIGR02959 SigZ RNA polymerase 70.9 1.3 2.9E-05 34.0 -0.1 30 108-137 118-147 (170)
97 PF10668 Phage_terminase: Phag 70.9 2.4 5.3E-05 29.5 1.3 23 106-128 22-44 (60)
98 PRK00118 putative DNA-binding 70.8 1.3 2.8E-05 33.6 -0.1 47 81-136 17-63 (104)
99 TIGR00270 conserved hypothetic 70.7 1.4 3E-05 35.2 0.0 24 108-131 84-107 (154)
100 PRK12519 RNA polymerase sigma 70.7 1 2.2E-05 34.9 -0.7 33 104-136 155-187 (194)
101 TIGR02983 SigE-fam_strep RNA p 70.6 1.3 2.9E-05 33.0 -0.1 29 108-136 128-156 (162)
102 TIGR01764 excise DNA binding d 70.4 3 6.4E-05 25.0 1.5 26 108-133 3-28 (49)
103 TIGR02950 SigM_subfam RNA poly 70.4 1.3 2.8E-05 32.7 -0.2 35 102-136 117-151 (154)
104 PRK06811 RNA polymerase factor 70.1 1.9 4.1E-05 33.6 0.7 33 108-140 149-181 (189)
105 TIGR03541 reg_near_HchA LuxR f 70.0 1.2 2.6E-05 36.6 -0.5 48 79-136 169-216 (232)
106 TIGR02999 Sig-70_X6 RNA polyme 69.1 1.6 3.4E-05 33.3 0.0 30 107-136 151-180 (183)
107 PRK10651 transcriptional regul 68.9 3 6.4E-05 30.8 1.5 46 81-136 155-200 (216)
108 PRK09649 RNA polymerase sigma 68.9 1.9 4E-05 33.7 0.4 30 107-136 147-176 (185)
109 PRK12524 RNA polymerase sigma 68.7 1.5 3.3E-05 34.3 -0.2 30 108-137 154-183 (196)
110 PRK12547 RNA polymerase sigma 68.5 1.8 3.9E-05 32.9 0.2 31 106-136 128-158 (164)
111 PRK12543 RNA polymerase sigma 68.3 1.7 3.8E-05 33.4 0.1 30 107-136 134-163 (179)
112 PRK09645 RNA polymerase sigma 68.2 1.7 3.7E-05 32.9 0.1 29 108-136 136-164 (173)
113 PRK09935 transcriptional regul 67.8 3.4 7.4E-05 30.6 1.6 45 81-135 149-193 (210)
114 PRK12533 RNA polymerase sigma 67.6 1.3 2.8E-05 36.2 -0.8 33 105-137 149-181 (216)
115 PRK12520 RNA polymerase sigma 67.6 1.8 3.8E-05 33.6 0.0 30 107-136 148-177 (191)
116 PRK11511 DNA-binding transcrip 67.1 5.5 0.00012 29.8 2.6 42 84-130 8-49 (127)
117 PRK12528 RNA polymerase sigma 67.0 5.2 0.00011 30.0 2.5 25 108-132 131-155 (161)
118 PRK12546 RNA polymerase sigma 67.0 1.6 3.5E-05 34.5 -0.3 31 106-136 129-159 (188)
119 PRK12516 RNA polymerase sigma 66.7 1.8 3.9E-05 34.1 -0.1 31 107-137 133-163 (187)
120 PRK08295 RNA polymerase factor 66.5 1.8 3.9E-05 33.7 -0.1 30 107-136 171-200 (208)
121 PRK10360 DNA-binding transcrip 66.3 3.3 7.3E-05 30.6 1.3 46 80-135 136-181 (196)
122 PF13022 HTH_Tnp_1_2: Helix-tu 66.2 4.4 9.6E-05 32.7 2.0 51 79-131 8-59 (142)
123 PF12728 HTH_17: Helix-turn-he 66.2 3.9 8.4E-05 25.7 1.4 24 109-132 4-27 (51)
124 TIGR00721 tfx DNA-binding prot 66.1 2.2 4.8E-05 33.7 0.3 48 79-136 4-51 (137)
125 PRK12535 RNA polymerase sigma 66.0 1.9 4.1E-05 34.3 -0.1 38 107-144 150-187 (196)
126 PRK10430 DNA-binding transcrip 65.7 9.2 0.0002 30.4 3.8 47 79-130 156-202 (239)
127 PRK12529 RNA polymerase sigma 65.5 5.7 0.00012 30.7 2.5 27 108-134 145-171 (178)
128 PF06056 Terminase_5: Putative 65.2 4.1 8.8E-05 27.7 1.4 27 108-136 15-41 (58)
129 PRK12536 RNA polymerase sigma 64.9 2 4.4E-05 33.1 -0.1 33 104-136 143-175 (181)
130 TIGR02954 Sig70_famx3 RNA poly 64.7 2.4 5.1E-05 32.1 0.2 29 108-136 137-165 (169)
131 TIGR02937 sigma70-ECF RNA poly 64.4 2.5 5.4E-05 29.6 0.3 47 81-136 110-156 (158)
132 TIGR02957 SigX4 RNA polymerase 64.1 2.9 6.2E-05 35.1 0.6 31 108-138 126-156 (281)
133 PRK09639 RNA polymerase sigma 64.0 2.1 4.5E-05 32.0 -0.2 29 108-136 129-157 (166)
134 TIGR02607 antidote_HigA addict 63.9 8.5 0.00018 25.7 2.8 23 109-131 21-43 (78)
135 PRK07037 extracytoplasmic-func 63.7 6.6 0.00014 29.3 2.5 29 108-136 127-155 (163)
136 PRK08241 RNA polymerase factor 63.5 3.7 8E-05 34.9 1.2 33 106-138 169-201 (339)
137 cd00093 HTH_XRE Helix-turn-hel 63.1 5.5 0.00012 22.9 1.6 23 109-131 15-37 (58)
138 PRK13919 putative RNA polymera 62.7 2.6 5.5E-05 32.3 0.1 29 108-136 153-181 (186)
139 PRK09651 RNA polymerase sigma 62.5 5.1 0.00011 30.7 1.7 30 105-134 134-163 (172)
140 PRK11924 RNA polymerase sigma 62.5 2.3 5.1E-05 31.6 -0.2 31 106-136 141-171 (179)
141 TIGR03020 EpsA transcriptional 62.4 4 8.6E-05 34.8 1.2 48 79-136 188-235 (247)
142 PHA00542 putative Cro-like pro 62.4 9.9 0.00021 26.8 3.1 46 75-131 11-56 (82)
143 PRK12542 RNA polymerase sigma 62.3 2.4 5.2E-05 32.7 -0.1 30 108-137 140-169 (185)
144 PRK12531 RNA polymerase sigma 62.3 2.6 5.6E-05 32.9 0.0 30 107-136 158-187 (194)
145 PF13309 HTH_22: HTH domain 62.1 13 0.00029 25.3 3.5 44 78-124 17-60 (64)
146 PRK12545 RNA polymerase sigma 61.9 2.5 5.5E-05 33.4 -0.0 31 106-136 155-185 (201)
147 PRK09480 slmA division inhibit 61.9 8.9 0.00019 29.0 2.9 27 105-131 29-55 (194)
148 PHA02893 hypothetical protein; 61.7 3 6.5E-05 31.3 0.3 21 23-43 57-77 (88)
149 PRK06930 positive control sigm 61.6 2.5 5.4E-05 33.9 -0.1 46 81-136 114-160 (170)
150 TIGR02952 Sig70_famx2 RNA poly 61.3 2.8 6.2E-05 31.2 0.1 30 107-136 139-168 (170)
151 PRK12511 RNA polymerase sigma 60.9 2.7 5.8E-05 33.0 -0.1 31 106-136 127-157 (182)
152 COG2197 CitB Response regulato 60.8 7.9 0.00017 31.4 2.6 46 80-135 147-192 (211)
153 PRK12532 RNA polymerase sigma 60.6 2.8 6E-05 32.6 -0.0 30 107-136 153-182 (195)
154 PF08914 Myb_DNA-bind_2: Rap1 60.4 15 0.00033 25.5 3.6 47 79-126 2-49 (65)
155 PRK09637 RNA polymerase sigma 60.0 2.8 6E-05 32.7 -0.1 30 107-136 123-152 (181)
156 PF12844 HTH_19: Helix-turn-he 59.8 13 0.00027 24.0 3.0 24 108-131 14-37 (64)
157 PRK06704 RNA polymerase factor 59.7 2.2 4.7E-05 35.7 -0.8 30 108-137 134-163 (228)
158 smart00351 PAX Paired Box doma 59.7 13 0.00027 28.2 3.4 42 81-131 17-58 (125)
159 PRK12544 RNA polymerase sigma 59.4 3.1 6.7E-05 33.5 0.0 29 108-136 166-194 (206)
160 COG2944 Predicted transcriptio 59.3 9.6 0.00021 29.2 2.7 40 82-132 44-83 (104)
161 cd01104 HTH_MlrA-CarA Helix-Tu 59.3 5.2 0.00011 26.1 1.1 21 109-129 3-23 (68)
162 PRK12522 RNA polymerase sigma 59.1 3.2 6.9E-05 31.6 0.0 32 105-136 134-165 (173)
163 TIGR02943 Sig70_famx1 RNA poly 58.6 3.3 7.1E-05 32.5 0.0 31 106-136 147-177 (188)
164 TIGR02859 spore_sigH RNA polym 58.6 3.7 7.9E-05 31.6 0.3 31 106-136 165-195 (198)
165 cd04763 HTH_MlrA-like Helix-Tu 58.0 5.8 0.00013 26.3 1.2 21 109-129 3-23 (68)
166 PRK12538 RNA polymerase sigma 57.9 2.7 5.8E-05 34.7 -0.6 32 105-136 186-217 (233)
167 PF01710 HTH_Tnp_IS630: Transp 57.8 21 0.00045 26.6 4.3 39 81-128 2-40 (119)
168 PRK09647 RNA polymerase sigma 57.2 3.5 7.5E-05 33.1 -0.0 31 108-138 156-186 (203)
169 PRK12523 RNA polymerase sigma 57.1 9.5 0.00021 29.0 2.4 29 106-134 135-163 (172)
170 PRK11923 algU RNA polymerase s 56.6 3.1 6.8E-05 32.1 -0.4 33 104-136 152-184 (193)
171 PRK12525 RNA polymerase sigma 56.2 11 0.00023 28.7 2.5 26 108-133 136-161 (168)
172 PRK09641 RNA polymerase sigma 55.9 3.4 7.4E-05 31.4 -0.2 33 104-136 150-182 (187)
173 cd01392 HTH_LacI Helix-turn-he 55.9 5.7 0.00012 24.6 0.8 21 111-131 2-22 (52)
174 PF00249 Myb_DNA-binding: Myb- 55.7 42 0.0009 20.9 4.8 34 79-119 1-34 (48)
175 PRK09636 RNA polymerase sigma 55.2 6.1 0.00013 33.1 1.1 32 108-139 133-164 (293)
176 PF13551 HTH_29: Winged helix- 55.0 6.4 0.00014 27.4 1.0 24 108-131 14-37 (112)
177 PRK10100 DNA-binding transcrip 55.0 6.6 0.00014 32.1 1.3 46 80-135 154-199 (216)
178 PRK12540 RNA polymerase sigma 55.0 3.7 8.1E-05 32.1 -0.2 34 106-139 127-160 (182)
179 PF00376 MerR: MerR family reg 55.0 7 0.00015 24.3 1.1 21 109-129 2-22 (38)
180 PRK08301 sporulation sigma fac 54.9 3.7 8E-05 33.1 -0.2 32 105-136 197-228 (234)
181 PRK09483 response regulator; P 54.6 7.6 0.00017 29.1 1.5 46 80-135 147-192 (217)
182 PF08279 HTH_11: HTH domain; 54.3 8.8 0.00019 24.3 1.5 21 107-127 16-36 (55)
183 PRK12513 RNA polymerase sigma 53.1 1.6 3.5E-05 33.8 -2.5 35 103-137 152-186 (194)
184 PF13565 HTH_32: Homeodomain-l 52.7 10 0.00022 25.3 1.7 46 75-126 26-76 (77)
185 PF04936 DUF658: Protein of un 52.3 9 0.00019 32.1 1.6 31 106-136 14-44 (186)
186 PRK06986 fliA flagellar biosyn 52.2 3.9 8.5E-05 33.1 -0.5 32 105-136 199-230 (236)
187 PRK11475 DNA-binding transcrip 51.0 14 0.0003 30.2 2.5 46 80-135 133-178 (207)
188 PRK09415 RNA polymerase factor 51.0 4 8.7E-05 31.5 -0.6 29 108-136 145-173 (179)
189 PRK13558 bacterio-opsin activa 50.3 14 0.0003 34.0 2.7 41 79-124 605-648 (665)
190 smart00530 HTH_XRE Helix-turn- 50.2 13 0.00028 21.1 1.7 23 109-131 13-35 (56)
191 PRK11891 aspartate carbamoyltr 49.6 15 0.00032 34.1 2.8 38 83-128 1-38 (429)
192 cd04774 HTH_YfmP Helix-Turn-He 49.6 16 0.00035 26.5 2.5 33 109-143 3-35 (96)
193 PF13698 DUF4156: Domain of un 49.3 7.9 0.00017 28.4 0.8 14 6-19 54-67 (93)
194 TIGR02479 FliA_WhiG RNA polyme 49.3 5.5 0.00012 32.0 -0.1 47 81-136 175-221 (224)
195 PHA01976 helix-turn-helix prot 49.2 13 0.00027 24.2 1.7 24 108-131 17-40 (67)
196 cd04764 HTH_MlrA-like_sg1 Heli 48.6 10 0.00023 24.9 1.2 23 109-131 3-25 (67)
197 PF11516 DUF3220: Protein of u 48.6 5.7 0.00012 30.1 -0.1 10 121-130 31-40 (106)
198 PRK05657 RNA polymerase sigma 48.6 5.8 0.00013 34.6 -0.0 51 81-136 262-312 (325)
199 PRK12534 RNA polymerase sigma 48.4 7.7 0.00017 29.8 0.7 31 106-136 153-183 (187)
200 PRK12527 RNA polymerase sigma 48.2 7 0.00015 29.2 0.4 30 107-136 122-151 (159)
201 TIGR02154 PhoB phosphate regul 48.2 13 0.00028 27.7 1.8 54 80-136 153-208 (226)
202 PRK10188 DNA-binding transcrip 47.9 11 0.00025 31.2 1.6 49 78-136 176-224 (240)
203 PF13730 HTH_36: Helix-turn-he 47.8 57 0.0012 20.4 4.6 43 81-128 2-47 (55)
204 TIGR02984 Sig-70_plancto1 RNA 47.7 6.3 0.00014 29.8 0.1 47 81-136 140-186 (189)
205 PRK13890 conjugal transfer pro 47.2 27 0.00059 26.4 3.5 18 104-121 45-62 (120)
206 PRK12518 RNA polymerase sigma 47.2 2 4.4E-05 32.4 -2.7 35 102-136 132-166 (175)
207 smart00422 HTH_MERR helix_turn 47.1 11 0.00025 24.5 1.2 20 109-128 3-22 (70)
208 PRK10840 transcriptional regul 47.1 17 0.00038 28.1 2.5 46 80-135 149-194 (216)
209 PF12651 RHH_3: Ribbon-helix-h 47.1 13 0.00029 23.7 1.5 24 75-98 2-25 (44)
210 PF08280 HTH_Mga: M protein tr 47.0 21 0.00045 23.6 2.5 40 84-131 5-44 (59)
211 TIGR03001 Sig-70_gmx1 RNA poly 46.7 6.2 0.00013 32.9 -0.1 30 107-136 178-207 (244)
212 TIGR02846 spore_sigmaK RNA pol 46.6 6.4 0.00014 31.9 -0.0 51 80-135 173-223 (227)
213 PHA02535 P terminase ATPase su 46.5 28 0.00062 33.6 4.2 46 80-136 1-46 (581)
214 TIGR02531 yecD_yerC TrpR-relat 46.3 13 0.00028 27.3 1.5 22 107-128 51-72 (88)
215 PF01726 LexA_DNA_bind: LexA D 46.1 34 0.00075 23.5 3.6 38 81-124 3-44 (65)
216 PRK09638 RNA polymerase sigma 46.0 3 6.4E-05 31.6 -2.0 34 103-136 139-172 (176)
217 PRK08583 RNA polymerase sigma 45.8 6.4 0.00014 32.3 -0.2 28 108-135 223-250 (257)
218 KOG1146 Homeobox protein [Gene 45.6 24 0.00052 37.5 3.7 63 72-138 702-764 (1406)
219 PF12123 Amidase02_C: N-acetyl 45.6 22 0.00047 23.5 2.4 19 82-100 24-42 (45)
220 PF05344 DUF746: Domain of Unk 45.4 17 0.00037 25.9 2.0 35 88-128 1-35 (65)
221 TIGR02980 SigBFG RNA polymeras 45.3 7.3 0.00016 31.2 0.1 47 80-135 177-223 (227)
222 TIGR02947 SigH_actino RNA poly 45.3 2.6 5.7E-05 32.7 -2.4 36 101-136 142-177 (193)
223 PRK02220 4-oxalocrotonate taut 45.0 28 0.00061 22.3 2.9 33 83-129 13-45 (61)
224 PF06252 DUF1018: Protein of u 45.0 23 0.00049 26.5 2.7 28 76-103 16-43 (119)
225 PF13743 Thioredoxin_5: Thiore 44.8 20 0.00044 28.4 2.5 42 86-130 85-127 (176)
226 PRK05803 sporulation sigma fac 44.7 7.2 0.00016 31.6 -0.0 32 105-136 194-225 (233)
227 TIGR02960 SigX5 RNA polymerase 44.7 7.9 0.00017 32.4 0.2 33 107-139 159-191 (324)
228 PRK10336 DNA-binding transcrip 44.6 21 0.00046 26.6 2.5 51 80-136 148-203 (219)
229 PRK09643 RNA polymerase sigma 44.4 7.2 0.00016 30.6 -0.1 31 107-137 151-181 (192)
230 PRK15411 rcsA colanic acid cap 44.3 19 0.00041 28.9 2.3 45 81-135 137-181 (207)
231 PRK07670 RNA polymerase sigma 44.0 7.5 0.00016 32.0 -0.0 31 106-136 217-247 (251)
232 PRK09640 RNA polymerase sigma 43.9 4.3 9.4E-05 31.4 -1.4 53 84-136 122-180 (188)
233 PF12802 MarR_2: MarR family; 43.8 17 0.00037 23.0 1.7 37 82-124 3-39 (62)
234 PF05077 DUF678: Protein of un 42.1 10 0.00022 27.7 0.4 11 33-43 55-65 (74)
235 PRK11922 RNA polymerase sigma 41.8 4.4 9.6E-05 32.8 -1.7 36 103-138 162-197 (231)
236 PRK09706 transcriptional repre 41.0 38 0.00083 25.4 3.4 17 104-120 45-61 (135)
237 PRK09975 DNA-binding transcrip 40.2 25 0.00055 27.2 2.4 30 103-132 28-57 (213)
238 TIGR02366 DHAK_reg probable di 40.0 28 0.00061 26.2 2.6 27 103-129 20-46 (176)
239 PF02954 HTH_8: Bacterial regu 39.6 33 0.00071 21.2 2.4 34 86-127 6-39 (42)
240 PF12824 MRP-L20: Mitochondria 39.3 72 0.0016 25.9 5.0 42 78-125 82-123 (164)
241 PF12244 DUF3606: Protein of u 39.1 26 0.00056 23.6 2.0 20 105-124 19-38 (57)
242 TIGR02835 spore_sigmaE RNA pol 39.1 9.4 0.0002 31.0 -0.2 31 106-136 198-228 (234)
243 PHA02955 hypothetical protein; 38.9 42 0.00091 28.8 3.7 43 84-129 60-102 (213)
244 PRK15479 transcriptional regul 38.2 30 0.00066 25.7 2.5 51 80-136 147-202 (221)
245 PF01361 Tautomerase: Tautomer 38.1 41 0.00089 21.6 2.8 33 83-129 12-44 (60)
246 KOG3623 Homeobox transcription 37.9 31 0.00067 35.1 3.1 64 72-139 623-686 (1007)
247 smart00529 HTH_DTXR Helix-turn 37.8 70 0.0015 21.9 4.2 31 81-117 66-96 (96)
248 PF04539 Sigma70_r3: Sigma-70 37.8 13 0.00027 25.1 0.3 25 105-129 19-43 (78)
249 COG3040 Blc Bacterial lipocali 37.8 35 0.00075 28.5 2.9 26 78-103 139-165 (174)
250 TIGR02941 Sigma_B RNA polymera 37.4 9.9 0.00022 31.2 -0.3 47 81-136 205-251 (255)
251 cd00029 C1 Protein kinase C co 36.6 15 0.00032 22.5 0.5 31 15-50 11-41 (50)
252 cd04768 HTH_BmrR-like Helix-Tu 36.4 21 0.00045 25.7 1.3 21 109-129 3-23 (96)
253 smart00109 C1 Protein kinase C 36.3 19 0.00041 21.6 0.9 23 16-42 12-34 (49)
254 TIGR02394 rpoS_proteo RNA poly 36.2 16 0.00034 30.8 0.7 33 104-136 240-272 (285)
255 cd04766 HTH_HspR Helix-Turn-He 36.1 21 0.00045 25.3 1.2 21 109-129 4-24 (91)
256 PF07022 Phage_CI_repr: Bacter 36.1 11 0.00023 25.5 -0.3 23 108-130 14-37 (66)
257 PRK09958 DNA-binding transcrip 36.0 24 0.00052 26.2 1.6 46 80-135 142-187 (204)
258 PF05572 Peptidase_M43: Pregna 36.0 28 0.0006 27.5 2.0 17 78-94 137-153 (154)
259 cd01106 HTH_TipAL-Mta Helix-Tu 35.6 22 0.00047 25.6 1.3 23 109-131 3-25 (103)
260 cd01105 HTH_GlnR-like Helix-Tu 35.5 21 0.00046 25.3 1.2 19 109-127 4-22 (88)
261 PRK10955 DNA-binding transcrip 35.4 28 0.00062 26.2 2.0 53 81-136 156-210 (232)
262 PRK12517 RNA polymerase sigma 35.3 38 0.00082 26.5 2.7 30 107-136 145-174 (188)
263 cd08315 Death_TRAILR_DR4_DR5 D 35.2 40 0.00086 24.8 2.7 30 103-132 16-45 (96)
264 PF08880 QLQ: QLQ; InterPro: 35.2 32 0.00068 21.7 1.8 12 81-92 2-13 (37)
265 PRK01271 4-oxalocrotonate taut 34.9 45 0.00099 23.8 2.8 34 82-129 13-46 (76)
266 PF00325 Crp: Bacterial regula 34.9 21 0.00046 21.9 1.0 17 108-124 4-20 (32)
267 cd00592 HTH_MerR-like Helix-Tu 34.4 23 0.0005 25.0 1.3 23 109-131 3-25 (100)
268 cd04789 HTH_Cfa Helix-Turn-Hel 34.2 23 0.0005 25.8 1.3 35 108-144 3-37 (102)
269 PRK13870 transcriptional regul 34.2 25 0.00053 29.2 1.6 47 80-136 172-218 (234)
270 PF04297 UPF0122: Putative hel 34.1 38 0.00082 25.7 2.4 40 81-129 17-56 (101)
271 PRK06288 RNA polymerase sigma 33.5 13 0.00028 30.9 -0.2 30 107-136 229-258 (268)
272 PF01710 HTH_Tnp_IS630: Transp 33.4 60 0.0013 24.2 3.4 48 81-138 56-103 (119)
273 KOG0705 GTPase-activating prot 33.3 17 0.00038 35.8 0.6 37 15-52 514-551 (749)
274 PF05121 GvpK: Gas vesicle pro 33.2 89 0.0019 23.5 4.2 36 80-123 40-75 (88)
275 cd04773 HTH_TioE_rpt2 Second H 32.8 25 0.00055 25.8 1.3 23 109-131 3-25 (108)
276 PRK11083 DNA-binding response 32.8 30 0.00066 25.8 1.7 51 80-136 153-208 (228)
277 cd04780 HTH_MerR-like_sg5 Heli 32.3 26 0.00055 25.5 1.2 21 109-129 3-23 (95)
278 PRK15008 HTH-type transcriptio 32.0 41 0.00088 26.5 2.4 29 104-132 36-64 (212)
279 PF03374 ANT: Phage antirepres 32.0 37 0.00081 24.4 2.0 33 104-136 22-54 (111)
280 cd01107 HTH_BmrR Helix-Turn-He 31.9 27 0.00058 25.6 1.3 23 109-131 3-25 (108)
281 cd04775 HTH_Cfa-like Helix-Tur 31.8 27 0.00058 25.4 1.2 33 109-143 4-36 (102)
282 PRK02289 4-oxalocrotonate taut 31.8 59 0.0013 21.3 2.8 34 82-129 12-45 (60)
283 PF01257 2Fe-2S_thioredx: Thio 31.8 63 0.0014 25.0 3.4 34 87-124 16-49 (145)
284 cd01109 HTH_YyaN Helix-Turn-He 31.7 27 0.00059 25.5 1.3 21 109-129 3-23 (113)
285 smart00027 EH Eps15 homology d 31.7 1.2E+02 0.0026 21.2 4.6 47 82-128 4-51 (96)
286 PF13011 LZ_Tnp_IS481: leucine 31.5 79 0.0017 23.4 3.7 58 81-146 8-74 (85)
287 PF07750 GcrA: GcrA cell cycle 31.5 44 0.00095 26.9 2.6 36 81-125 2-38 (162)
288 TIGR03209 P21_Cbot clostridium 30.9 49 0.0011 24.2 2.5 17 108-124 125-141 (142)
289 TIGR01610 phage_O_Nterm phage 30.6 74 0.0016 22.9 3.4 44 80-124 21-65 (95)
290 cd01279 HTH_HspR-like Helix-Tu 30.4 29 0.00062 25.2 1.2 22 109-130 4-25 (98)
291 TIGR03826 YvyF flagellar opero 30.4 55 0.0012 26.0 2.9 30 106-135 46-75 (137)
292 TIGR03830 CxxCG_CxxCG_HTH puta 30.3 47 0.001 24.0 2.4 44 76-130 59-102 (127)
293 PRK09191 two-component respons 30.0 37 0.0008 26.7 1.9 33 106-138 104-136 (261)
294 cd04782 HTH_BltR Helix-Turn-He 29.9 30 0.00065 24.9 1.2 21 109-129 3-23 (97)
295 cd00131 PAX Paired Box domain 29.9 42 0.00091 25.6 2.1 42 81-131 17-58 (128)
296 PF13189 Cytidylate_kin2: Cyti 29.8 21 0.00045 28.1 0.4 39 91-131 17-55 (179)
297 PRK08359 transcription factor; 29.8 57 0.0012 26.9 3.0 50 76-132 72-124 (176)
298 cd04767 HTH_HspR-like_MBC Heli 29.8 29 0.00063 26.8 1.2 23 108-130 3-25 (120)
299 TIGR01958 nuoE_fam NADH-quinon 29.4 86 0.0019 24.3 3.8 35 86-124 18-52 (148)
300 PRK04140 hypothetical protein; 29.2 67 0.0015 28.7 3.5 37 88-132 129-165 (317)
301 cd04788 HTH_NolA-AlbR Helix-Tu 29.2 31 0.00068 24.7 1.2 34 109-144 3-37 (96)
302 cd02259 Peptidase_C39_like Pep 29.0 80 0.0017 21.9 3.3 44 76-125 17-60 (122)
303 PF01485 IBR: IBR domain; Int 28.9 41 0.00089 21.3 1.6 31 20-50 25-61 (64)
304 PRK00215 LexA repressor; Valid 28.9 45 0.00097 26.5 2.2 45 82-129 2-47 (205)
305 PF06413 Neugrin: Neugrin; In 28.7 67 0.0015 27.3 3.3 42 79-126 8-49 (225)
306 cd02425 Peptidase_C39F A sub-f 28.4 89 0.0019 21.9 3.5 44 76-125 22-65 (126)
307 PF02042 RWP-RK: RWP-RK domain 28.4 41 0.0009 22.7 1.6 16 104-119 27-42 (52)
308 cd02421 Peptidase_C39_likeD A 28.3 73 0.0016 22.5 3.0 43 77-125 18-60 (124)
309 PF10410 DnaB_bind: DnaB-helic 28.2 1.5E+02 0.0032 18.7 4.2 38 83-123 17-59 (59)
310 cd00491 4Oxalocrotonate_Tautom 27.9 80 0.0017 19.8 2.9 34 83-130 12-45 (58)
311 TIGR02051 MerR Hg(II)-responsi 27.8 33 0.00071 25.8 1.2 34 109-144 2-36 (124)
312 PRK10668 DNA-binding transcrip 27.8 54 0.0012 25.4 2.5 30 103-132 28-57 (215)
313 PF13223 DUF4031: Protein of u 27.7 46 0.00099 24.6 1.9 21 105-129 22-42 (83)
314 PF00440 TetR_N: Bacterial reg 27.7 25 0.00054 21.9 0.4 36 90-130 5-40 (47)
315 PF12763 EF-hand_4: Cytoskelet 27.6 40 0.00086 25.2 1.6 46 81-126 3-49 (104)
316 PRK07539 NADH dehydrogenase su 27.5 95 0.0021 24.3 3.8 34 87-124 25-58 (154)
317 PF04492 Phage_rep_O: Bacterio 27.2 85 0.0019 23.4 3.3 46 78-124 26-72 (100)
318 PRK04841 transcriptional regul 26.7 36 0.00079 32.2 1.5 46 80-135 837-882 (903)
319 cd01110 HTH_SoxR Helix-Turn-He 26.6 36 0.00077 26.3 1.2 35 108-144 3-37 (139)
320 PRK09943 DNA-binding transcrip 26.5 91 0.002 24.4 3.5 48 76-123 15-66 (185)
321 TIGR02885 spore_sigF RNA polym 26.5 23 0.0005 28.4 0.2 45 81-134 183-227 (231)
322 PRK01964 4-oxalocrotonate taut 26.5 78 0.0017 20.7 2.7 34 83-130 13-46 (64)
323 CHL00148 orf27 Ycf27; Reviewed 26.4 53 0.0011 24.9 2.1 51 80-136 160-217 (240)
324 COG1427 Predicted periplasmic 26.4 79 0.0017 27.7 3.4 50 80-136 179-228 (252)
325 PF05930 Phage_AlpA: Prophage 26.4 33 0.00072 22.0 0.9 22 109-130 6-27 (51)
326 PRK10219 DNA-binding transcrip 26.2 62 0.0014 22.9 2.4 38 85-127 5-42 (107)
327 cd01108 HTH_CueR Helix-Turn-He 26.2 38 0.00082 25.5 1.3 24 109-132 3-26 (127)
328 cd04781 HTH_MerR-like_sg6 Heli 26.1 38 0.00082 25.2 1.2 21 109-129 3-23 (120)
329 PLN03119 putative ADP-ribosyla 26.1 59 0.0013 32.0 2.8 28 21-48 29-57 (648)
330 COG0289 DapB Dihydrodipicolina 26.1 57 0.0012 28.8 2.5 19 80-98 101-119 (266)
331 PRK12461 UDP-N-acetylglucosami 26.0 99 0.0021 26.2 3.9 50 78-128 196-247 (255)
332 PRK10643 DNA-binding transcrip 25.9 69 0.0015 23.8 2.6 54 80-136 148-203 (222)
333 cd08319 Death_RAIDD Death doma 25.9 1.1E+02 0.0023 22.1 3.5 37 89-133 4-40 (83)
334 cd02417 Peptidase_C39_likeA A 25.9 1.1E+02 0.0024 21.4 3.5 42 78-125 19-60 (121)
335 cd01111 HTH_MerD Helix-Turn-He 25.7 39 0.00085 25.0 1.3 21 109-129 3-23 (107)
336 PF06569 DUF1128: Protein of u 25.7 1.2E+02 0.0025 22.0 3.6 38 80-118 31-68 (71)
337 cd01282 HTH_MerR-like_sg3 Heli 25.6 40 0.00086 24.9 1.3 32 109-142 3-34 (112)
338 PRK09635 sigI RNA polymerase s 25.6 28 0.00061 29.8 0.5 31 108-138 136-166 (290)
339 cd04772 HTH_TioE_rpt1 First He 25.6 40 0.00086 24.5 1.2 21 109-129 3-23 (99)
340 cd04779 HTH_MerR-like_sg4 Heli 25.6 38 0.00082 26.3 1.2 34 109-144 3-36 (134)
341 smart00354 HTH_LACI helix_turn 25.6 48 0.001 22.3 1.6 24 109-132 3-26 (70)
342 PRK07408 RNA polymerase sigma 25.5 59 0.0013 27.0 2.4 31 106-136 219-249 (256)
343 PRK08215 sporulation sigma fac 25.4 22 0.00047 29.4 -0.2 47 80-135 208-254 (258)
344 PF10925 DUF2680: Protein of u 25.3 70 0.0015 21.9 2.3 41 82-126 1-41 (59)
345 TIGR03787 marine_sort_RR prote 25.3 84 0.0018 23.7 3.0 54 79-136 154-207 (227)
346 PRK11552 putative DNA-binding 25.2 64 0.0014 26.0 2.5 28 107-134 33-60 (225)
347 PF09832 DUF2059: Uncharacteri 25.2 67 0.0014 21.1 2.2 19 78-96 13-31 (64)
348 PF00130 C1_1: Phorbol esters/ 25.1 44 0.00095 21.0 1.3 23 17-42 13-35 (53)
349 PF13560 HTH_31: Helix-turn-he 25.1 47 0.001 21.6 1.4 25 108-132 16-40 (64)
350 COG1309 AcrR Transcriptional r 25.0 53 0.0012 22.7 1.8 28 104-131 30-57 (201)
351 PRK07122 RNA polymerase sigma 24.9 21 0.00046 30.0 -0.3 30 106-135 231-260 (264)
352 PTZ00397 macrophage migration 24.9 93 0.002 22.7 3.1 35 83-131 70-104 (116)
353 cd08577 PI-PLCc_GDPD_SF_unchar 24.7 1.2E+02 0.0027 25.3 4.2 43 77-119 174-222 (228)
354 cd04770 HTH_HMRTR Helix-Turn-H 24.6 42 0.00092 24.7 1.3 21 109-129 3-23 (123)
355 cd04776 HTH_GnyR Helix-Turn-He 24.6 42 0.00091 25.2 1.2 20 109-128 3-22 (118)
356 PRK13719 conjugal transfer tra 24.4 42 0.0009 28.7 1.3 51 76-136 138-188 (217)
357 PF13720 Acetyltransf_11: Udp 24.3 84 0.0018 22.4 2.7 44 78-122 24-67 (83)
358 PRK00745 4-oxalocrotonate taut 24.3 89 0.0019 20.0 2.6 33 83-129 13-45 (62)
359 PRK10710 DNA-binding transcrip 24.2 70 0.0015 24.2 2.4 51 80-136 159-214 (240)
360 TIGR00013 taut 4-oxalocrotonat 24.2 1E+02 0.0022 19.8 2.9 34 83-130 13-46 (63)
361 TIGR02054 MerD mercuric resist 24.2 43 0.00094 25.6 1.3 22 108-129 5-26 (120)
362 smart00661 RPOL9 RNA polymeras 24.0 48 0.001 20.7 1.3 25 20-44 5-29 (52)
363 TIGR02044 CueR Cu(I)-responsiv 24.0 43 0.00094 25.1 1.2 22 109-130 3-24 (127)
364 cd04275 ZnMc_pappalysin_like Z 23.8 52 0.0011 27.6 1.8 18 77-94 207-224 (225)
365 TIGR02043 ZntR Zn(II)-responsi 23.8 44 0.00096 25.3 1.3 21 109-129 4-24 (131)
366 TIGR03613 RutR pyrimidine util 23.6 63 0.0014 24.7 2.1 29 104-132 26-54 (202)
367 PRK06437 hypothetical protein; 23.6 8.5 0.00019 26.4 -2.5 34 99-133 13-46 (67)
368 PRK10856 cytoskeletal protein 23.5 1.1E+02 0.0023 27.3 3.7 37 88-132 17-53 (331)
369 COG0789 SoxR Predicted transcr 23.4 47 0.001 23.9 1.3 19 109-127 3-21 (124)
370 PRK05988 formate dehydrogenase 23.4 1.2E+02 0.0027 24.0 3.8 36 85-124 24-59 (156)
371 cd04765 HTH_MlrA-like_sg2 Heli 23.4 45 0.00099 24.3 1.2 21 109-129 3-23 (99)
372 PRK05572 sporulation sigma fac 23.3 64 0.0014 26.5 2.2 47 80-135 201-247 (252)
373 COG5484 Uncharacterized conser 23.3 47 0.001 29.6 1.5 30 103-134 16-45 (279)
374 cd08318 Death_NMPP84 Death dom 23.3 1.3E+02 0.0029 21.3 3.6 34 81-125 4-37 (86)
375 cd04787 HTH_HMRTR_unk Helix-Tu 22.9 47 0.001 25.1 1.3 29 109-139 3-31 (133)
376 cd04784 HTH_CadR-PbrR Helix-Tu 22.8 47 0.001 24.8 1.2 22 109-130 3-24 (127)
377 PRK09514 zntR zinc-responsive 22.7 47 0.001 25.6 1.2 21 109-129 4-24 (140)
378 TIGR02047 CadR-PbrR Cd(II)/Pb( 22.7 48 0.001 25.0 1.2 22 109-130 3-24 (127)
379 cd08777 Death_RIP1 Death Domai 22.4 1.3E+02 0.0028 21.6 3.4 18 108-125 15-32 (86)
380 cd04783 HTH_MerR1 Helix-Turn-H 22.3 49 0.0011 24.7 1.2 21 109-129 3-23 (126)
381 PF00165 HTH_AraC: Bacterial r 22.2 42 0.00091 20.2 0.7 24 105-128 7-30 (42)
382 PRK15201 fimbriae regulatory p 22.1 74 0.0016 27.1 2.4 46 81-136 133-178 (198)
383 PF11869 DUF3389: Protein of u 22.0 55 0.0012 24.0 1.4 24 97-120 51-74 (75)
384 KOG2767 Translation initiation 22.0 28 0.00062 32.3 -0.1 12 35-46 118-129 (400)
385 PRK13500 transcriptional activ 21.8 71 0.0015 27.0 2.3 42 84-130 205-246 (312)
386 cd01670 Death Death Domain: a 21.8 1.1E+02 0.0024 20.3 2.8 25 107-131 11-35 (79)
387 cd00131 PAX Paired Box domain 21.7 3.2E+02 0.007 20.7 5.6 46 80-130 74-127 (128)
388 COG1595 RpoE DNA-directed RNA 21.6 16 0.00035 28.1 -1.5 30 107-136 144-173 (182)
389 COG4802 FtrB Ferredoxin-thiore 21.6 1.5E+02 0.0032 23.2 3.7 52 84-136 3-58 (110)
390 COG1476 Predicted transcriptio 21.5 53 0.0012 23.4 1.2 22 108-129 16-37 (68)
391 smart00857 Resolvase Resolvase 21.3 72 0.0016 23.3 1.9 18 84-101 18-35 (148)
392 TIGR02684 dnstrm_HI1420 probab 21.0 1E+02 0.0022 22.5 2.6 35 87-131 34-68 (89)
393 PF00382 TFIIB: Transcription 21.0 50 0.0011 22.1 0.9 38 109-146 1-42 (71)
394 TIGR02997 Sig70-cyanoRpoD RNA 20.8 58 0.0013 27.7 1.5 30 105-134 268-297 (298)
395 cd02423 Peptidase_C39G A sub-f 20.7 1.7E+02 0.0037 20.5 3.7 40 80-125 27-66 (129)
396 PF07037 DUF1323: Putative tra 20.7 49 0.0011 26.2 1.0 26 109-136 3-28 (122)
397 PF08220 HTH_DeoR: DeoR-like h 20.6 61 0.0013 21.2 1.3 21 105-125 13-33 (57)
398 cd04785 HTH_CadR-PbrR-like Hel 20.4 57 0.0012 24.5 1.2 23 109-131 3-25 (126)
399 PF01343 Peptidase_S49: Peptid 20.3 1.6E+02 0.0034 22.6 3.7 46 77-129 75-120 (154)
400 TIGR02393 RpoD_Cterm RNA polym 20.3 47 0.001 27.0 0.8 32 105-136 195-226 (238)
401 cd04769 HTH_MerR2 Helix-Turn-H 20.2 58 0.0013 24.0 1.2 21 109-129 3-23 (116)
402 PF11737 DUF3300: Protein of u 20.2 61 0.0013 28.2 1.5 48 82-136 1-50 (237)
403 PF07638 Sigma70_ECF: ECF sigm 20.1 90 0.0019 24.5 2.4 26 108-133 153-178 (185)
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=1.4e-38 Score=214.85 Aligned_cols=52 Identities=63% Similarity=1.258 Sum_probs=49.9
Q ss_pred CcHHHhhhhhhccCCccccCcccccc-CCCCCCcccccccccccccccccccc
Q 044959 1 SYRECRRNHAASIGRYAYDGCGEFLK-AGKDGTKEAFHCAACGCHRSFHRKEL 52 (159)
Q Consensus 1 ~Y~eC~~Nhaa~~G~~~~DgC~ef~~-~~~~~~~~~l~CaaCgcHRnFHr~~~ 52 (159)
.|+||||||||+||||+||||||||| +|+++++++|+||||||||||||||+
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 59999999999999999999999999 68899999999999999999999984
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=2e-37 Score=214.38 Aligned_cols=53 Identities=66% Similarity=1.305 Sum_probs=51.2
Q ss_pred CcHHHhhhhhhccCCccccCccccccC-CCCCCccccccccccccccccccccc
Q 044959 1 SYRECRRNHAASIGRYAYDGCGEFLKA-GKDGTKEAFHCAACGCHRSFHRKELS 53 (159)
Q Consensus 1 ~Y~eC~~Nhaa~~G~~~~DgC~ef~~~-~~~~~~~~l~CaaCgcHRnFHr~~~~ 53 (159)
.|+||+||||++||||+||||+||||+ |+++++++|+|||||||||||||+++
T Consensus 5 ~Y~EC~kNHAa~~Gg~a~DGCgEFm~~~g~eg~~~al~CaACgCHRnFHRre~~ 58 (60)
T PF04770_consen 5 RYRECLKNHAASIGGHAVDGCGEFMPSPGEEGTPEALKCAACGCHRNFHRREVE 58 (60)
T ss_pred eHHHHHhhHhHhhCCcccccccccccCCCCCCCcccceecccCcchhcccCCcC
Confidence 499999999999999999999999999 88999999999999999999999974
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=99.94 E-value=3.3e-27 Score=161.84 Aligned_cols=58 Identities=59% Similarity=1.064 Sum_probs=56.7
Q ss_pred CCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccC
Q 044959 75 AKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 75 kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
+||+||+||++|+++|++||+++||+|++||..+|++||.+|||++.||||||||||+
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
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.67 E-value=1.8e-17 Score=136.66 Aligned_cols=63 Identities=22% Similarity=0.287 Sum_probs=59.7
Q ss_pred CCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCCC
Q 044959 74 KAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVP 140 (159)
Q Consensus 74 ~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~ 140 (159)
+.||.||.||.+|+.+||..|+.+ +|....+|++||..|+|++.+|||||||||.|.||.+..
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 679999999999999999999997 899999999999999999999999999999999986655
No 5
>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=99.65 E-value=2.3e-17 Score=107.63 Aligned_cols=56 Identities=30% Similarity=0.512 Sum_probs=53.3
Q ss_pred CCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 76 KTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 76 KR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
||.||.||.+|+..|+++|+.. +||+..++++||.+|||+..+|++||+|+|.+.|
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~----~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 56 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQEN----PYPSKEEREELAKELGLTERQVKNWFQNRRRKEK 56 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHS----SSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHh----ccccccccccccccccccccccccCHHHhHHHhC
Confidence 7899999999999999999986 8999999999999999999999999999998765
No 6
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.65 E-value=2.5e-17 Score=138.68 Aligned_cols=63 Identities=17% Similarity=0.182 Sum_probs=58.9
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCC
Q 044959 73 YKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRV 139 (159)
Q Consensus 73 ~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~ 139 (159)
+..||.||.||..|+.+||..|..+ +|++...|.|+|..|.|++++|||||||||+||||...
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN----~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFN----KYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccc----cccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence 4579999999999999999999998 89999999999999999999999999999999997443
No 7
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.61 E-value=2.9e-16 Score=136.34 Aligned_cols=58 Identities=22% Similarity=0.377 Sum_probs=55.8
Q ss_pred CCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 76 KTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 76 KR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
||.||.||.|||++|+..|..+ .|+.+..||+|+.||||.+.+|||||||.|+|.||.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~en----RYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQEN----RYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred cCccccccHHHHHHHHHHHhhh----hhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 8999999999999999999887 799999999999999999999999999999999984
No 8
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.61 E-value=3e-16 Score=135.99 Aligned_cols=61 Identities=18% Similarity=0.280 Sum_probs=57.8
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 73 YKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 73 ~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
.++|+.||.||..|+.+||.-|+++ +|.+..+|.+||..|||+..|||+||||||+|||+-
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~Q----KYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq 230 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQ----KYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQ 230 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHh----hcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHH
Confidence 4568899999999999999999997 899999999999999999999999999999999974
No 9
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.56 E-value=5.8e-16 Score=119.37 Aligned_cols=62 Identities=19% Similarity=0.266 Sum_probs=56.1
Q ss_pred CCCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 71 KNYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 71 ~~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..++.+|.||.||.-||.+||..|... +|||.-.+++||..|.|++..|+|||||||+|++|
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ET----HYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRK 74 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAET----HYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRK 74 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhh----cCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHH
Confidence 345679999999999999999955554 89999999999999999999999999999999986
No 10
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.56 E-value=1.8e-15 Score=131.89 Aligned_cols=65 Identities=15% Similarity=0.264 Sum_probs=59.7
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCCC
Q 044959 72 NYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVP 140 (159)
Q Consensus 72 ~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~ 140 (159)
..+|||.|-.||+-|.-+||.-|..+ .|++..||++||+.|+||..||||||||+|+|.||.+..
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQ----RYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~d 214 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQ----RYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKD 214 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhh----hccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhh
Confidence 45789999999999999999988776 799999999999999999999999999999999986544
No 11
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.53 E-value=1.1e-14 Score=93.80 Aligned_cols=56 Identities=27% Similarity=0.433 Sum_probs=52.5
Q ss_pred CCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 76 KTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 76 KR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
++.||.||++|+..|+++|+.. +||+..++++||.++||+..+|++||+|+|.+.+
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 5788999999999999999997 7999999999999999999999999999998764
No 12
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.53 E-value=7.1e-15 Score=123.86 Aligned_cols=67 Identities=18% Similarity=0.209 Sum_probs=60.5
Q ss_pred CCCCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCCC
Q 044959 70 HKNYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVP 140 (159)
Q Consensus 70 ~~~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~ 140 (159)
....+.+|-||.||.+|++.||..|++. ||||...++++|..|+|++.+|||||.|||+|+++.+..
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kT----qYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKT----QYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhh----cCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 3445679999999999999999988887 999999999999999999999999999999999875543
No 13
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.51 E-value=3.8e-15 Score=126.54 Aligned_cols=66 Identities=15% Similarity=0.233 Sum_probs=60.7
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCCCc
Q 044959 72 NYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPE 141 (159)
Q Consensus 72 ~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~~ 141 (159)
..+|||.||.||..|...||..||.- .|++..+|.-||..|.|++.||||||||||+|||++....
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~k----rYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELK----RYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHH----hhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 34899999999999999999999885 7999999999999999999999999999999999865443
No 14
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.50 E-value=8.7e-15 Score=127.00 Aligned_cols=60 Identities=15% Similarity=0.192 Sum_probs=55.1
Q ss_pred CCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 75 AKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 75 kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
+|++||.||..|+++||+.|... +|||...++-|+..+.|++..|+|||||||+||+|+-
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkea----HYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEA----HYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhc----cCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 45569999999999999988776 8999999999999999999999999999999998753
No 15
>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=99.49 E-value=2.6e-14 Score=92.19 Aligned_cols=58 Identities=28% Similarity=0.457 Sum_probs=54.3
Q ss_pred CCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 76 KTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 76 KR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
++.|+.||.+|+..|+++|+.. +||+..++++||.++||+..+|++||+|+|.+.++.
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 4788999999999999999996 799999999999999999999999999999998763
No 16
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.48 E-value=1.2e-14 Score=123.37 Aligned_cols=63 Identities=21% Similarity=0.308 Sum_probs=58.0
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCC
Q 044959 73 YKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRV 139 (159)
Q Consensus 73 ~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~ 139 (159)
.+.|+.||+|+.-||+.|..-|++. ||+-..||.+||..|||+..+|||||||||-|+||-..
T Consensus 120 KK~RKPRTIYSS~QLqaL~rRFQkT----QYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 120 KKVRKPRTIYSSLQLQALNRRFQQT----QYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred ccccCCcccccHHHHHHHHHHHhhc----chhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 3458899999999999999999997 99999999999999999999999999999999987433
No 17
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.44 E-value=8.1e-14 Score=125.06 Aligned_cols=64 Identities=16% Similarity=0.362 Sum_probs=59.9
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCC
Q 044959 72 NYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRV 139 (159)
Q Consensus 72 ~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~ 139 (159)
.++|||+||.|+.-.+..||.+|.++ ++|+..+|-+||++|+|.+.||+|||+|||+|.|+.-.
T Consensus 291 ~~RkRKKRTSie~~vr~aLE~~F~~n----pKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 291 QSRKRKKRTSIEVNVRGALEKHFLKN----PKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccccceeHHHHHHHHHHHHhC----CCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 34789999999999999999999998 89999999999999999999999999999999998443
No 18
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.44 E-value=5.1e-14 Score=118.88 Aligned_cols=62 Identities=21% Similarity=0.319 Sum_probs=55.7
Q ss_pred CCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCC
Q 044959 74 KAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRV 139 (159)
Q Consensus 74 ~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~ 139 (159)
..|+.||.||..||..||.-|..- ||++.+++.+|+..|.|++.+|||||||||+|.|+-+.
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrek----qYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREK----QYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHh----hhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 358899999999999999965553 89999999999999999999999999999999987443
No 19
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.42 E-value=4e-14 Score=125.21 Aligned_cols=62 Identities=18% Similarity=0.294 Sum_probs=56.7
Q ss_pred CCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCCC
Q 044959 75 AKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVP 140 (159)
Q Consensus 75 kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~ 140 (159)
-+|.||.||.||+-+||+.|-+- .|.+...|=|||..|+|++.+|||||||||+|-|+.|..
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrE----NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYRE----NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHh----ccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 49999999999999999955443 699999999999999999999999999999999998765
No 20
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.42 E-value=7e-14 Score=122.12 Aligned_cols=62 Identities=18% Similarity=0.250 Sum_probs=57.6
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 73 YKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 73 ~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
.+-|++|-.+|..|+.+||..|-.+ .|.+.+.|-||++.|+|+++||||||||||+|.||..
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN----~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFN----MYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHH----HHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 4568889999999999999988777 8999999999999999999999999999999999965
No 21
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.41 E-value=9.6e-14 Score=122.09 Aligned_cols=64 Identities=19% Similarity=0.370 Sum_probs=57.6
Q ss_pred CCCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 71 KNYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 71 ~~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
+....||+||.+|+.|||.|+...... .+|-.-+|++|++++||+.+||+|||||||+|.|+-+
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~S----pKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTS----PKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCC----CchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence 456789999999999999999977553 7899999999999999999999999999999998643
No 22
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.23 E-value=8.7e-13 Score=108.34 Aligned_cols=65 Identities=14% Similarity=0.284 Sum_probs=59.0
Q ss_pred CCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCCCcc
Q 044959 74 KAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEK 142 (159)
Q Consensus 74 ~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~~~ 142 (159)
++++.||.|+..|+.-|++.||.. .|++-.+++||++-|+|++.+||.||||+|+|.||....+-
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Q----rYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQ----RYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred HhhhhcccccCccccccHHHHhhh----hhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 468899999999999999999987 79999999999999999999999999999999998554443
No 23
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.22 E-value=6.9e-12 Score=103.75 Aligned_cols=65 Identities=22% Similarity=0.377 Sum_probs=57.0
Q ss_pred CCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCCCccc
Q 044959 75 AKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEKC 143 (159)
Q Consensus 75 kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~~~~ 143 (159)
.+++.-.||.+|...||.-|+.. .|........||.+|||.++||+|||||||++||.++...-+
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~----~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~ 114 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESE----KKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDY 114 (198)
T ss_pred cccccccccHHHHHHhHHhhccc----cccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhH
Confidence 35555579999999999988876 789999999999999999999999999999999988765443
No 24
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.19 E-value=9.7e-12 Score=99.33 Aligned_cols=67 Identities=19% Similarity=0.205 Sum_probs=60.6
Q ss_pred CCCCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCCC
Q 044959 70 HKNYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVP 140 (159)
Q Consensus 70 ~~~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~ 140 (159)
..++..++.|+.-|.+|+..|+..|+.. +||+..++..|+..|+|+++.||+||||+|++.|+.+.-
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~----p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEIN----PYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccC----CCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 3455678888889999999999999998 899999999999999999999999999999999876554
No 25
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.18 E-value=7.3e-12 Score=99.01 Aligned_cols=63 Identities=16% Similarity=0.141 Sum_probs=59.5
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 72 NYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 72 ~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
..+++|.||.||..|++.|+..|++. +|||...++.++..+++++..|+|||||+|+++++..
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 45789999999999999999999997 9999999999999999999999999999999999755
No 26
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.13 E-value=1.9e-11 Score=107.92 Aligned_cols=64 Identities=19% Similarity=0.259 Sum_probs=59.2
Q ss_pred CCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCCCcc
Q 044959 74 KAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEK 142 (159)
Q Consensus 74 ~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~~~ 142 (159)
+++|.||-||..|+++||..|.++ .|||-+.++|||.-++|++..|+|||.|||+||+| |+-|.
T Consensus 111 KqrrQrthFtSqqlqele~tF~rN----rypdMstrEEIavwtNlTE~rvrvwfknrrakwrk-rErN~ 174 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRN----RYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK-RERNQ 174 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhc----cCCccchhhHHHhhccccchhhhhhcccchhhhhh-hhhhH
Confidence 568999999999999999999997 79999999999999999999999999999999998 44443
No 27
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.09 E-value=1.8e-11 Score=106.64 Aligned_cols=59 Identities=14% Similarity=0.301 Sum_probs=54.0
Q ss_pred CCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 74 KAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 74 ~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-|-+.|..+|..|+-+||+.|.-. .|.+.....|||..|||++++|||||||||+|.+|
T Consensus 198 TkDKYRvVYTDhQRLELEKEfh~S----ryITirRKSELA~~LgLsERQVKIWFQNRRAKERK 256 (317)
T KOG0848|consen 198 TKDKYRVVYTDHQRLELEKEFHTS----RYITIRRKSELAATLGLSERQVKIWFQNRRAKERK 256 (317)
T ss_pred cccceeEEecchhhhhhhhhhccc----cceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHH
Confidence 366788899999999999988775 78999999999999999999999999999999875
No 28
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.02 E-value=8.2e-11 Score=100.72 Aligned_cols=69 Identities=20% Similarity=0.280 Sum_probs=61.7
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCCCcccc
Q 044959 72 NYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEKCR 144 (159)
Q Consensus 72 ~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~~~~~ 144 (159)
.+++|-.|-.|+-.|+..|+.-||.. +|+-..++.++|..+|+++.++||||||||.||+|+--.+.++
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqt----kylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmas 232 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQT----KYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMAS 232 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhh----hcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhh
Confidence 35688899999999999999999987 8999999999999999999999999999999999865544443
No 29
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.98 E-value=1e-10 Score=103.30 Aligned_cols=62 Identities=19% Similarity=0.404 Sum_probs=57.5
Q ss_pred CCCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 71 KNYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 71 ~~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.++-|||+||.+-+..|..||+||..+ ..|+.+.|..+|++|.|+..||+|||+|.|+|.|+
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQ----PRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQ----PRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred CccccccccccccCcccccHHHHhccC----CCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 356799999999999999999999775 56999999999999999999999999999999998
No 30
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.91 E-value=1.1e-09 Score=96.47 Aligned_cols=63 Identities=16% Similarity=0.237 Sum_probs=58.1
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 72 NYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 72 ~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
....+|.||+||++|++.|++-|++. +||+...+++|+.+||+++..|+|||+|+|+++++..
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt----~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRT----PYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccccchHHHHHHHhcCC----CCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 34467779999999999999999997 7999999999999999999999999999999998865
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.36 E-value=5.3e-07 Score=84.34 Aligned_cols=59 Identities=19% Similarity=0.235 Sum_probs=54.7
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCC
Q 044959 72 NYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRP 134 (159)
Q Consensus 72 ~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~ 134 (159)
....||.|+.||..||+.|..+|... ++|+.+..+.|+.+|||...+|..||+|-|.+.
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFke~----~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFKEN----KRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHhcC----CCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 34568999999999999999999987 899999999999999999999999999988874
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.32 E-value=1.9e-07 Score=73.93 Aligned_cols=64 Identities=22% Similarity=0.423 Sum_probs=58.0
Q ss_pred CCCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 71 KNYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 71 ~~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
.....++.||.|+..|++.|...|... .+|+...+++|+..+|++..+|+|||+|+|.+.++..
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRAT----PKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCC----CCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 345679999999999999999988765 7899999999999999999999999999999998753
No 33
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.92 E-value=5.9e-06 Score=83.54 Aligned_cols=75 Identities=16% Similarity=0.311 Sum_probs=63.2
Q ss_pred CCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCCCcccccccchhhhh
Q 044959 74 KAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEKCRAASVVGVKN 153 (159)
Q Consensus 74 ~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~~~~~~~~~~~~~~ 153 (159)
.+++.||.|+..|+..|..+++.. .++...+.+.+-..|++..+||.|||||+|.+.++-.. |..+.++--|+++
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q----~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~-n~~~~ss~~~s~s 976 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQ----RTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL-NGTAASSTGGSSS 976 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhc----cCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh-ccccccccccccC
Confidence 468999999999999999999996 57889999999999999999999999999999999666 4444444444443
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=97.70 E-value=8.5e-06 Score=52.01 Aligned_cols=33 Identities=27% Similarity=0.509 Sum_probs=27.7
Q ss_pred CCCCCCHHHHHHHHHHhCCCccchhhhhccccC
Q 044959 100 KPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 100 ~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
.-+||+.++.++||.++||+..+|..||-|.|.
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRr 39 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARR 39 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHc
Confidence 457999999999999999999999999999874
No 35
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=97.45 E-value=0.00015 Score=63.77 Aligned_cols=55 Identities=22% Similarity=0.311 Sum_probs=46.8
Q ss_pred CCccCCHHH---------HHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 78 KRTKITEEQ---------KSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 78 ~RTkFT~eQ---------kekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
+||+..-|| +..|.+++.+. +||+..+..+||+.+||+..||-.||.|||++.+.
T Consensus 170 PrTIWDGEet~yCFKekSR~~LrewY~~~----~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 170 PRTIWDGEETVYCFKEKSRSLLREWYLQN----PYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred CCccccCceeeeehhHhhHHHHHHHHhcC----CCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 466655555 46788888776 89999999999999999999999999999999983
No 36
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=97.27 E-value=0.00026 Score=62.44 Aligned_cols=64 Identities=17% Similarity=0.215 Sum_probs=56.5
Q ss_pred CCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCC
Q 044959 75 AKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRV 139 (159)
Q Consensus 75 kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~ 139 (159)
.+|+|.-|+..-.+.|.++|-.. -..+||++++.++||.+-||+..++-.||-|.|.++||..+
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h-~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSH-LSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHh-cCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence 47889999999999999977653 24578999999999999999999999999999999988544
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=96.71 E-value=0.0028 Score=42.08 Aligned_cols=47 Identities=23% Similarity=0.318 Sum_probs=37.4
Q ss_pred CCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 76 KTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 76 KR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
||.|+.+|-+|+-++...++.- + -..++|.++||++.+|.-|+.|+.
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 6899999999999999999773 2 688999999999999999998853
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=96.35 E-value=0.0033 Score=42.37 Aligned_cols=47 Identities=26% Similarity=0.307 Sum_probs=35.1
Q ss_pred CCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 77 TKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 77 R~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
+.|+.||+|++..+...+.. +...+.++|.++||++.+|-.|..--+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~--------~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE--------SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHH--------HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH--------CCCceEeeecccccccccccHHHHHHh
Confidence 57899999999999987733 346899999999999999999987665
No 39
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.81 E-value=0.01 Score=51.14 Aligned_cols=61 Identities=18% Similarity=0.235 Sum_probs=52.8
Q ss_pred CCCCCCccCCHHHHHHHHH-HHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 74 KAKTKRTKITEEQKSKMRR-FADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 74 ~kKR~RTkFT~eQkekLe~-ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.++|.+..|..+....|+. .|+-+- -.||++.+...|+.++||++.+|..||-|.|-+..+
T Consensus 238 ~~~r~~~~lP~~a~~ilr~Wl~~h~~--~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 238 SKWRPQRGLPKEAVSILRAWLFEHLL--HPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHhcc--CCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 3678888999999999999 666542 268999999999999999999999999999988764
No 40
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=94.52 E-value=0.027 Score=38.92 Aligned_cols=41 Identities=12% Similarity=0.408 Sum_probs=30.0
Q ss_pred HHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccC
Q 044959 88 SKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 88 ekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
+-|++++.+. +.+.+..+++||...||+-.+|+.||--+..
T Consensus 11 ~pL~~Yy~~h----~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 11 QPLEDYYLKH----KQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp HHHHHHHHHT--------TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred HHHHHHHHHc----CCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 4589999886 5788899999999999999999999976544
No 41
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.01 E-value=0.055 Score=53.58 Aligned_cols=58 Identities=21% Similarity=0.429 Sum_probs=47.4
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCC-CCc
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVR-VPE 141 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~-~~~ 141 (159)
-.-|++. +..|..++..+| .|+.++...|+..+||+..|||+||+|.++...... .|.
T Consensus 561 ~k~~~~p-~sllkayyaln~----~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 561 SKQFNHP-TSLLKAYYALNG----LPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred ccccCCc-HHHHHHHHHhcC----CCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence 3445555 778888887774 799999999999999999999999999999887654 444
No 42
>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=93.58 E-value=0.16 Score=27.09 Aligned_cols=40 Identities=28% Similarity=0.439 Sum_probs=30.5
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhh
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWL 127 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWF 127 (159)
+..|+.+++..+...++ .|| .+.++|.++|+++.+|..|+
T Consensus 3 ~~~~~~~~~~~i~~~~~-~~~--------s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLA-AGE--------SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHH-cCC--------CHHHHHHHHCCCHHHHHHhC
Confidence 34578888888777664 232 57788999999999999885
No 43
>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=91.56 E-value=0.12 Score=30.83 Aligned_cols=45 Identities=13% Similarity=0.196 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRP 134 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~ 134 (159)
.++++|.+.+..++. +.....++|.++|++..+|+.|.+.-+.++
T Consensus 10 ~l~~~~~~~~~~~~~---------~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 10 KLPEREREVILLRFG---------EGLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred hCCHHHHHHHHHHHh---------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 467888887777652 223577889999999999999998766544
No 44
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=90.12 E-value=0.27 Score=36.92 Aligned_cols=44 Identities=16% Similarity=0.234 Sum_probs=34.5
Q ss_pred CCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcc
Q 044959 78 KRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 78 ~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
.|..||.|++..+-...-.. ...+.++|.++||+..+|--|..-
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~--------g~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEP--------GMTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcC--------CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 35669999988777655332 346788999999999999999765
No 45
>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=89.79 E-value=0.27 Score=31.21 Aligned_cols=41 Identities=17% Similarity=0.387 Sum_probs=29.7
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhc
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLN 128 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFq 128 (159)
+.+++.+|.+.+.+.... ...+.++|..+||++.+|.-++.
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 346888888887776643 25789999999999999987764
No 46
>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=88.92 E-value=0.44 Score=32.18 Aligned_cols=42 Identities=14% Similarity=0.294 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhh
Q 044959 82 ITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKV 125 (159)
Q Consensus 82 FT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKV 125 (159)
+|+.|++.|....+. |+ ..+|-....++||++|||++.+|--
T Consensus 1 LT~~Q~e~L~~A~~~-GY-fd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYEL-GY-FDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHc-CC-CCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 588999998886654 41 1226688999999999999988753
No 47
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=87.84 E-value=1.1 Score=32.81 Aligned_cols=48 Identities=21% Similarity=0.260 Sum_probs=39.3
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCC-CccchhhhhccccCCC
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGI-TRKMFKVWLNNNRRRP 134 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl-~r~VvKVWFqNrR~k~ 134 (159)
|.+||.|-|..+-++....| ..+.++|.++|| +..++..|...-+...
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g--------~sv~~vAr~~gv~~~~~l~~W~~~~~~~~ 53 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGG--------DTVSEVAREFGIVSATQLYKWRIQLQKGG 53 (116)
T ss_pred cccCCHHHHHHHHHHHHhcC--------ccHHHHHHHhCCCChHHHHHHHHHHHHcc
Confidence 89999999999988775543 279999999996 9999999988544433
No 48
>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=86.02 E-value=0.25 Score=32.19 Aligned_cols=45 Identities=20% Similarity=0.256 Sum_probs=36.7
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
.||+.|++.|.-.++-. ...++|.++||+..+|+.+..|=+.|++
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 68999999999888543 6788999999999999999988776654
No 49
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=85.96 E-value=0.44 Score=29.03 Aligned_cols=45 Identities=24% Similarity=0.321 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
.+|++|++.+..++ .| ....++|..+||++.+|+.|.+.-+.+++
T Consensus 3 ~l~~~e~~i~~~~~--~g--------~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVLRLLA--EG--------LTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHHHH--cC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 57888888765543 22 15688999999999999999986655553
No 50
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=85.92 E-value=0.62 Score=36.97 Aligned_cols=45 Identities=16% Similarity=0.406 Sum_probs=35.4
Q ss_pred cCCHHHHHHHHH-HHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcc
Q 044959 81 KITEEQKSKMRR-FADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 81 kFT~eQkekLe~-ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
.||+||+++|.. .-|-+ ......++.+++..+|+++.++++-|.+
T Consensus 4 ~~T~eer~eLk~rIvElV----Re~GRiTi~ql~~~TGasR~Tvk~~lre 49 (127)
T PF06163_consen 4 VFTPEEREELKARIVELV----REHGRITIKQLVAKTGASRNTVKRYLRE 49 (127)
T ss_pred cCCHHHHHHHHHHHHHHH----HHcCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 699999999987 33333 3455678999999999999999887743
No 51
>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=84.76 E-value=1.4 Score=27.86 Aligned_cols=41 Identities=17% Similarity=0.177 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 82 ITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 82 FT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
++++|.+.+.-++ .+.-..+++|..+|++...|++|++.-|
T Consensus 11 L~~~~r~i~~l~~---------~~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRY---------FQGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHH---------TS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH---------HHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4566666665533 3455788999999999999999998644
No 52
>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=84.68 E-value=0.39 Score=35.62 Aligned_cols=47 Identities=17% Similarity=0.181 Sum_probs=34.8
Q ss_pred ccCCHHHHHHHHH-HHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRR-FADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~-ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..++++|++.+.- +++ .-..+++|..+||++.+|+++++.-|.+++.
T Consensus 110 ~~L~~~~r~v~~l~~~~----------g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQR----------GVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhc----------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 3466666666665 332 2357889999999999999999988877654
No 53
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=84.46 E-value=0.49 Score=30.02 Aligned_cols=42 Identities=12% Similarity=0.264 Sum_probs=21.7
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcc
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
...||.+|+..++.+-+ ...-+.++|..||+++.+|--++..
T Consensus 2 ~~~Lt~~eR~~I~~l~~---------~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLE---------QGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ----------HHHHHHC---------S---HHHHHHHTT--HHHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHH---------cCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 35789999999888753 2346778999999999999887754
No 54
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=81.80 E-value=0.66 Score=34.31 Aligned_cols=30 Identities=10% Similarity=0.060 Sum_probs=26.1
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|++..+|++|++.-+.++++
T Consensus 123 ~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 123 KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 357899999999999999999988777765
No 55
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=81.61 E-value=0.47 Score=37.73 Aligned_cols=51 Identities=18% Similarity=0.133 Sum_probs=40.6
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVP 140 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~ 140 (159)
+.+|+.|++.|.-++ .|| ..+++|..+|+++.+|+.|.++-+.++++.+..
T Consensus 5 ~~Lt~rqreVL~lr~--~Gl--------Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLRE--RGL--------TQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHHH--cCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 568999999987754 232 467899999999999999999988887765443
No 56
>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=81.18 E-value=1.7 Score=26.59 Aligned_cols=43 Identities=26% Similarity=0.370 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCC
Q 044959 82 ITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRP 134 (159)
Q Consensus 82 FT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~ 134 (159)
+|..|++.+.-++ .| ...+++|..+||++.+|+.|.+--+.+.
T Consensus 1 l~~~e~~i~~~~~--~~--------~s~~eia~~l~~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 1 LTPREREVLRLLA--EG--------KTNKEIADILGISEKTVKTHLRNIMRKL 43 (57)
T ss_pred CCHHHHHHHHHHH--cC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 3667777654443 22 1568889999999999999998544433
No 57
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=80.70 E-value=0.52 Score=36.86 Aligned_cols=30 Identities=7% Similarity=0.008 Sum_probs=26.2
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|+.+|++..+|+++++.-|.++++
T Consensus 159 ~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 159 LTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred CCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 367899999999999999999988877765
No 58
>PRK10403 transcriptional regulator NarP; Provisional
Probab=80.39 E-value=0.99 Score=33.25 Aligned_cols=47 Identities=17% Similarity=0.206 Sum_probs=38.4
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..+|+.+++.|.-+++- ...+++++.|++++++|++.++|=+.|++-
T Consensus 152 ~~Lt~~e~~vl~~~~~g----------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 152 SVLTERELDVLHELAQG----------LSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred ccCCHHHHHHHHHHHCC----------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 46899999988877643 245788999999999999999998888753
No 59
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=79.78 E-value=0.68 Score=34.77 Aligned_cols=31 Identities=13% Similarity=0.202 Sum_probs=27.3
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
-..+++|..+|+++.+|+++.+.-|.++++.
T Consensus 129 ~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 129 FSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 3678999999999999999999998888764
No 60
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=79.41 E-value=0.62 Score=35.25 Aligned_cols=47 Identities=9% Similarity=0.066 Sum_probs=34.6
Q ss_pred cCCHHHHHHHHH-HHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 81 KITEEQKSKMRR-FADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 81 kFT~eQkekLe~-ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
.++++|++.+.- +++. -..+++|..+|++..+|++|++--|.++++.
T Consensus 108 ~L~~~~r~v~~l~~~~g----------~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 108 TLPVIEAQAILLCDVHE----------LTYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred hCCHHHHHHHHhHHHhc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 445556655543 3332 3578999999999999999999988887653
No 61
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=79.10 E-value=0.6 Score=37.12 Aligned_cols=31 Identities=6% Similarity=-0.045 Sum_probs=26.6
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
-..+++|..+||+..+|+++++.-+.++++.
T Consensus 170 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 170 LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3678999999999999999999888777653
No 62
>PF13551 HTH_29: Winged helix-turn helix
Probab=79.06 E-value=4.6 Score=28.17 Aligned_cols=54 Identities=15% Similarity=0.252 Sum_probs=34.1
Q ss_pred CCCCCccCCHHHHHHHHHHHHHhCCCC-CCCCHHHHHH-HHH---HhCCCccchhhhhc
Q 044959 75 AKTKRTKITEEQKSKMRRFADKLGWKP-QRHDEEEVGK-FCG---EVGITRKMFKVWLN 128 (159)
Q Consensus 75 kKR~RTkFT~eQkekLe~ffek~GW~i-q~~d~~~r~e-fc~---eiGl~r~VvKVWFq 128 (159)
..|+++.+|++|.+.|.+++....-.- ...+...+.+ +.+ .+.|+..+|.-|++
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 456666699999999999998842110 0123344444 312 34678888888875
No 63
>PF13518 HTH_28: Helix-turn-helix domain
Probab=78.57 E-value=1.3 Score=27.45 Aligned_cols=25 Identities=28% Similarity=0.562 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCCccchhhhhccccC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
.+.++|.++||++.+|..|.+.-+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 6788999999999999999976443
No 64
>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=78.42 E-value=1.7 Score=27.44 Aligned_cols=40 Identities=13% Similarity=0.225 Sum_probs=30.2
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcc
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
.++++|++.+...|- ..-..+++|..+|+++..|+.+...
T Consensus 4 ~L~~~er~vi~~~y~---------~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 4 QLPPREREVIRLRYF---------EGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp TS-HHHHHHHHHHHT---------ST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc---------CCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 478899999888661 2235788999999999999988654
No 65
>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=78.21 E-value=0.78 Score=33.45 Aligned_cols=29 Identities=14% Similarity=0.204 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+.++|..+||++.+|+++.+.-|.++++
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 57789999999999999999887776654
No 66
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=77.79 E-value=0.7 Score=35.45 Aligned_cols=31 Identities=6% Similarity=0.107 Sum_probs=26.9
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
-..+++|..+|++..+|+++++.-|.+++..
T Consensus 148 ~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 148 ASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999999988887754
No 67
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=77.77 E-value=0.85 Score=35.23 Aligned_cols=30 Identities=10% Similarity=0.214 Sum_probs=25.4
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+||+..+|++|++.-+.++++
T Consensus 150 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 150 CSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 357889999999999999999987766654
No 68
>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=77.32 E-value=3.1 Score=28.98 Aligned_cols=45 Identities=20% Similarity=0.310 Sum_probs=30.1
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhc
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLN 128 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFq 128 (159)
|-.||.+=|-+..++|++. .........-|.+.||+++.|+-|.+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~-----~nc~~~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKD-----NNCKGNQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH------TTTTT-HHHHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHc-----cchhhhHHHHHHHhCccHHHHHHHHH
Confidence 6689999999999999874 33333445678999999999999986
No 69
>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=77.05 E-value=1.9 Score=25.53 Aligned_cols=25 Identities=8% Similarity=0.405 Sum_probs=21.7
Q ss_pred HHHHHHHhCCCccchhhhhccccCC
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRRR 133 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~k 133 (159)
+.++|..+||++.+|.-|..+..-.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 5789999999999999999986643
No 70
>PRK04217 hypothetical protein; Provisional
Probab=76.77 E-value=0.92 Score=34.70 Aligned_cols=48 Identities=15% Similarity=0.100 Sum_probs=37.2
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-++|.+|++.+...+.. .-.++++|+.+||++.+|+..++.-+.+++.
T Consensus 41 ~~Lt~eereai~l~~~e---------GlS~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 41 IFMTYEEFEALRLVDYE---------GLTQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred ccCCHHHHHHHHHHHHc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35789998777654422 1278899999999999999999988777754
No 71
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=76.33 E-value=0.76 Score=34.29 Aligned_cols=47 Identities=9% Similarity=0.054 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.++++|++.+.-++ .+.-...++|..+|+++.+|+.|++.-+.++++
T Consensus 128 ~L~~~~r~vl~l~~---------~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLRE---------IEGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHH---------HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46666666665432 122356789999999999999999977776654
No 72
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=76.08 E-value=0.81 Score=35.81 Aligned_cols=30 Identities=20% Similarity=0.267 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|+++.+||++++--|.++++
T Consensus 151 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 151 LSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999988777654
No 73
>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=76.00 E-value=0.6 Score=35.61 Aligned_cols=33 Identities=3% Similarity=-0.097 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 104 HDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 104 ~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
...-..+++|..+|++..+|+++++.-|.++++
T Consensus 152 ~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 152 LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 344467899999999999999999988887765
No 74
>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=75.57 E-value=2.8 Score=30.13 Aligned_cols=27 Identities=15% Similarity=0.267 Sum_probs=23.0
Q ss_pred CHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
..-.+.++|..+||++.+|++|+++..
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 445788999999999999999998643
No 75
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=75.48 E-value=2.2 Score=41.89 Aligned_cols=61 Identities=21% Similarity=0.344 Sum_probs=56.4
Q ss_pred CCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHH---HHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 74 KAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEE---VGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 74 ~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~---r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
-++|+||+++-|-+..+.+|+...| -|||... +.-|...++++++++---|+|.|+-.+.+
T Consensus 646 ~~p~~~~~isge~~~~~qs~i~~~g---l~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~~ 709 (769)
T KOG3755|consen 646 HKPRKRTKISGEALGILQSFITDVG---LYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKHH 709 (769)
T ss_pred cCccccceecccchHHHHHHHHHhc---cCchhhcccccchhhhhhcccHHHHHHhhhcceeecchh
Confidence 3799999999999999999999988 7899888 99999999999999999999999877754
No 76
>PRK10072 putative transcriptional regulator; Provisional
Probab=75.37 E-value=3.9 Score=30.42 Aligned_cols=23 Identities=22% Similarity=0.515 Sum_probs=21.2
Q ss_pred HHHHHHHhCCCccchhhhhcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR 131 (159)
..+||..+||+..+|.-|.+.+|
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 78999999999999999998775
No 77
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=75.19 E-value=0.98 Score=34.49 Aligned_cols=29 Identities=7% Similarity=0.210 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..+++|..+|++..+|+++++.-|.++++
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 57899999999999999999987776654
No 78
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=74.82 E-value=0.98 Score=34.34 Aligned_cols=31 Identities=6% Similarity=0.074 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.-..+++|+.+|+++.+|+++++.-|.+++.
T Consensus 152 g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 152 DLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999999987777654
No 79
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=74.76 E-value=0.94 Score=34.99 Aligned_cols=48 Identities=15% Similarity=0.053 Sum_probs=34.6
Q ss_pred CccCCHHHHHHHHH-HHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 79 RTKITEEQKSKMRR-FADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 79 RTkFT~eQkekLe~-ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
=..+++.|++.+.- +++ ....+++|..+||+..+|+++++.-+.++++
T Consensus 137 l~~L~~~~r~i~~l~~~~----------g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 137 LDTLPEKQREILILRVVV----------GLSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred HHhCCHHHHHHHHHHHHc----------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34555666665554 332 2357899999999999999999887776654
No 80
>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=74.38 E-value=3 Score=26.14 Aligned_cols=22 Identities=18% Similarity=0.291 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCccchhhhhccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNr 130 (159)
..+||..+|+++.+|.-|+.+.
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~ 33 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGK 33 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTS
T ss_pred HHHHHHHhCCCcchhHHHhcCC
Confidence 3789999999999999999883
No 81
>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=74.10 E-value=1.9 Score=26.36 Aligned_cols=25 Identities=8% Similarity=0.235 Sum_probs=21.3
Q ss_pred HHHHHHHhCCCccchhhhhccccCC
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRRR 133 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~k 133 (159)
+.++|..+||++.+|+.|..+-.-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~l~ 27 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGLLS 27 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 5789999999999999998776543
No 82
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=74.04 E-value=1.8 Score=31.40 Aligned_cols=46 Identities=11% Similarity=0.113 Sum_probs=36.9
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..+|+.|++.|.-+.+- + ..+++|+.++++.++|+++.+|=+.|+.
T Consensus 148 ~~lt~~e~~vl~l~~~g------~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKLITEG------Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHHHHCC------C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 35899988888776532 2 2578889999999999999999888776
No 83
>PRK09726 antitoxin HipB; Provisional
Probab=74.02 E-value=7.7 Score=27.37 Aligned_cols=42 Identities=19% Similarity=0.374 Sum_probs=29.7
Q ss_pred cCCHHHH-HHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccc
Q 044959 81 KITEEQK-SKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 81 kFT~eQk-ekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNr 130 (159)
.+++.++ +.|..+-+..|| ..++||..+||+..+|.-|..+.
T Consensus 7 ~~~~~~l~~~lk~~R~~~gl--------tq~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 7 IYSPTQLANAMKLVRQQNGW--------TQSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred ccCHHHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHCCC
Confidence 4556666 455556666554 36788999999999999998864
No 84
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=73.92 E-value=1.9 Score=27.94 Aligned_cols=24 Identities=21% Similarity=0.324 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCCccchhhhhcccc
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
.+.+||+.+||++.+|.-|++++.
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 578899999999999999999773
No 85
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=73.84 E-value=1.9 Score=26.89 Aligned_cols=23 Identities=13% Similarity=0.455 Sum_probs=17.9
Q ss_pred HHHHHHHHHhCCCccchhhhhcc
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqN 129 (159)
..+.++|..+||++.+|.-|...
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 36789999999999999999865
No 86
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=73.54 E-value=1.1 Score=33.42 Aligned_cols=29 Identities=14% Similarity=0.031 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..+++|..+|++..+|++.++.-|.++++
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56799999999999999999988777654
No 87
>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=72.85 E-value=6.7 Score=24.14 Aligned_cols=23 Identities=9% Similarity=0.141 Sum_probs=20.1
Q ss_pred HHHHHHHhCCCccchhhhhcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR 131 (159)
.++||..+||+..+|.-|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 68899999999999999987653
No 88
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=72.74 E-value=0.99 Score=34.79 Aligned_cols=30 Identities=13% Similarity=0.066 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
..+++|..+|++..+|+++++.-|.++++.
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999999888877763
No 89
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=72.41 E-value=3.5 Score=33.40 Aligned_cols=43 Identities=16% Similarity=0.263 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhh
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKV 125 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKV 125 (159)
.+|..|++.|...++. |+ -.+|-....++||+++||++.++.-
T Consensus 155 ~LTdrQ~~vL~~A~~~-GY-Fd~PR~~~l~dLA~~lGISkst~~e 197 (215)
T COG3413 155 DLTDRQLEVLRLAYKM-GY-FDYPRRVSLKDLAKELGISKSTLSE 197 (215)
T ss_pred cCCHHHHHHHHHHHHc-CC-CCCCccCCHHHHHHHhCCCHHHHHH
Confidence 8999999999886643 41 1236678999999999999988753
No 90
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=72.20 E-value=1.2 Score=34.49 Aligned_cols=47 Identities=15% Similarity=0.250 Sum_probs=35.0
Q ss_pred ccCCHHHHHHHHH-HHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRR-FADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~-ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..++++|++.|.- +++. -..+++|..+||+..+|++-++.-|.++++
T Consensus 130 ~~L~~~~r~vl~l~~~~~----------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 130 AKLSPAHREIIDLVYYHE----------KSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3556666666644 3433 257889999999999999999988887765
No 91
>PRK06424 transcription factor; Provisional
Probab=71.92 E-value=2.9 Score=33.21 Aligned_cols=53 Identities=8% Similarity=0.125 Sum_probs=35.5
Q ss_pred CCCCCccCCHHHHHHHHHHHHHhCCCCCCCC---HHHHHHHHHHhCCCccchhhhhccccC
Q 044959 75 AKTKRTKITEEQKSKMRRFADKLGWKPQRHD---EEEVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 75 kKR~RTkFT~eQkekLe~ffek~GW~iq~~d---~~~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
++|.|.. ..+..+.++.|.+.+ ...- .-..++||..+|++...|.-|..+.+.
T Consensus 68 ~~~~~d~-~~~~~~~~~~~g~~I----r~lRe~~GLSQ~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 68 KKYKKKA-SDEDLDIVEDYAELV----KNARERLSMSQADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred CCccCcc-cHHHHHHHHHHHHHH----HHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCC
Confidence 3444454 455557777777664 1111 123679999999999999999987754
No 92
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=71.80 E-value=1.3 Score=34.26 Aligned_cols=31 Identities=13% Similarity=0.149 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.-..+++|..+|++..+|+.+++.-|.++++
T Consensus 147 g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 147 GLSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999999988877765
No 93
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=71.69 E-value=2 Score=31.13 Aligned_cols=28 Identities=11% Similarity=0.144 Sum_probs=24.7
Q ss_pred HHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.++++.++|++..+|++++++=+.|++.
T Consensus 159 ~~~ia~~l~~s~~tv~~~~~~~~~kl~~ 186 (202)
T PRK09390 159 NKVIARDLDISPRTVEVYRANVMTKMQA 186 (202)
T ss_pred hHHHHHHcCCCHHHHHHHHHHHHHHHcc
Confidence 5668899999999999999999888864
No 94
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=71.47 E-value=1.4 Score=32.69 Aligned_cols=29 Identities=10% Similarity=0.140 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..+++|..+|++..+|++.++--|.++++
T Consensus 124 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 124 DVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999877766654
No 95
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=71.29 E-value=2.4 Score=27.82 Aligned_cols=23 Identities=4% Similarity=0.231 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCccchhhhhcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR 131 (159)
+.++|..+||++.+|+.|-..--
T Consensus 3 i~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTTS
T ss_pred HHHHHHHHCcCHHHHHHHHHhcC
Confidence 57899999999999999976554
No 96
>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=70.91 E-value=1.3 Score=33.97 Aligned_cols=30 Identities=10% Similarity=0.189 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
..+++|..+|++..+|+++++--|.++++.
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 578899999999999999999888887764
No 97
>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=70.91 E-value=2.4 Score=29.47 Aligned_cols=23 Identities=9% Similarity=0.446 Sum_probs=19.6
Q ss_pred HHHHHHHHHHhCCCccchhhhhc
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLN 128 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFq 128 (159)
.-...+||.+|||+..+|+.|=.
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhh
Confidence 44677899999999999999954
No 98
>PRK00118 putative DNA-binding protein; Validated
Probab=70.76 E-value=1.3 Score=33.57 Aligned_cols=47 Identities=17% Similarity=0.249 Sum_probs=34.3
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+++.|++.+.-.+. ....+.++|..+|+++.+|+.|++.-|.++++
T Consensus 17 ~L~ekqRevl~L~y~---------eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYL---------DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHH---------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 356777777755332 23367889999999999999999876665543
No 99
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=70.71 E-value=1.4 Score=35.24 Aligned_cols=24 Identities=8% Similarity=0.068 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCCccchhhhhcccc
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
..++||..+|+++.+|.-|-++.+
T Consensus 84 SqeeLA~~lgvs~s~IsriE~G~~ 107 (154)
T TIGR00270 84 SQEQLAKKIQEKESLIKKIENAEI 107 (154)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCC
Confidence 478999999999999999997764
No 100
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=70.70 E-value=1 Score=34.86 Aligned_cols=33 Identities=9% Similarity=0.024 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 104 HDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 104 ~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+.-...++|..+|++..+|++|++.-|.++++
T Consensus 155 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 155 YEGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 344567899999999999999999887776654
No 101
>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=70.65 E-value=1.3 Score=33.02 Aligned_cols=29 Identities=17% Similarity=0.152 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..+++|..+|+++.+|+++.+.-|.++++
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 56789999999999999999988887765
No 102
>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=70.43 E-value=3 Score=24.97 Aligned_cols=26 Identities=8% Similarity=0.155 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCCccchhhhhccccCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRR 133 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k 133 (159)
.+++.|..+||++.+|.-|..+.+-.
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHEGELP 28 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHcCCCC
Confidence 36789999999999999999776533
No 103
>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=70.41 E-value=1.3 Score=32.65 Aligned_cols=35 Identities=11% Similarity=0.044 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 102 QRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 102 q~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.|.+.-..+++|..+|++..+|+++++--|.++++
T Consensus 117 ~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 117 REFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34556678999999999999999999877666543
No 104
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=70.13 E-value=1.9 Score=33.56 Aligned_cols=33 Identities=15% Similarity=0.350 Sum_probs=28.5
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVP 140 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~ 140 (159)
..+++|..+|++..+|++..+--|.++++...+
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~~ 181 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKLN 181 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcccC
Confidence 568999999999999999999988888875543
No 105
>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=70.04 E-value=1.2 Score=36.59 Aligned_cols=48 Identities=17% Similarity=0.246 Sum_probs=39.3
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
...+|+.|++.|.-.++ | ....++|..+||++++|+.+++|=+.|++-
T Consensus 169 ~~~Lt~re~evl~~~a~--G--------~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 169 AGVLSEREREVLAWTAL--G--------RRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred hccCCHHHHHHHHHHHC--C--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 45789999998887652 2 256778899999999999999999998874
No 106
>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=69.13 E-value=1.6 Score=33.31 Aligned_cols=30 Identities=10% Similarity=0.023 Sum_probs=25.2
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|++..+||+.++.-|.++++
T Consensus 151 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 151 LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 356889999999999999999987766653
No 107
>PRK10651 transcriptional regulator NarL; Provisional
Probab=68.90 E-value=3 Score=30.84 Aligned_cols=46 Identities=15% Similarity=0.207 Sum_probs=37.6
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+|+.|.+.|.-+++-. ..+++|.+++++..+|++..+|=+.|+.-
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 49999999988777321 35677889999999999999998888853
No 108
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=68.87 E-value=1.9 Score=33.68 Aligned_cols=30 Identities=7% Similarity=0.027 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|++..+|+++++--|.++++
T Consensus 147 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 147 LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 356899999999999999999999888887
No 109
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=68.68 E-value=1.5 Score=34.33 Aligned_cols=30 Identities=7% Similarity=0.047 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
..+++|+.+||+..+|+++++--|.++++.
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 468899999999999999999888887753
No 110
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=68.54 E-value=1.8 Score=32.86 Aligned_cols=31 Identities=13% Similarity=0.026 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.-..+++|..+|+++.+|+++++--|.+++.
T Consensus 128 g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 128 GFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999999987776654
No 111
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=68.26 E-value=1.7 Score=33.40 Aligned_cols=30 Identities=7% Similarity=-0.023 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|++..+|++.++.-|.++++
T Consensus 134 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 134 YSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999988877764
No 112
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=68.20 E-value=1.7 Score=32.89 Aligned_cols=29 Identities=17% Similarity=0.204 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..+++|..+|+++.+|++.++.-|.++++
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999988777765
No 113
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=67.79 E-value=3.4 Score=30.57 Aligned_cols=45 Identities=7% Similarity=0.056 Sum_probs=37.2
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
.+|+.+.+.|.-+++- -..+++|.+|+++.++|+++..+=|.|+.
T Consensus 149 ~lt~re~~vl~~l~~g----------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVTILRYLVSG----------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHHHHHHHHcC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 4788888777766533 36789999999999999999999998886
No 114
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=67.64 E-value=1.3 Score=36.23 Aligned_cols=33 Identities=12% Similarity=0.159 Sum_probs=28.2
Q ss_pred CHHHHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
+.-..+++|..+||+..+|+++++.-|.++++.
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 344678999999999999999999988888763
No 115
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=67.60 E-value=1.8 Score=33.63 Aligned_cols=30 Identities=30% Similarity=0.261 Sum_probs=26.5
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|++..+|++.++.-|.++++
T Consensus 148 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (191)
T PRK12520 148 LETEEICQELQITATNAWVLLYRARMRLRE 177 (191)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 457899999999999999999988887765
No 116
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=67.10 E-value=5.5 Score=29.84 Aligned_cols=42 Identities=5% Similarity=0.087 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccc
Q 044959 84 EEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 84 ~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNr 130 (159)
..-+.++.++-+. ++.+.-.++++|..+||++.+|.-+|...
T Consensus 8 ~~~i~~~~~~I~~-----~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIED-----NLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHH-----hcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445667777766 35556789999999999999999888753
No 117
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=66.97 E-value=5.2 Score=29.99 Aligned_cols=25 Identities=28% Similarity=0.428 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCccchhhhhccccC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
..+++|..+|++..+|+++++.-+.
T Consensus 131 s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5688999999999999999876543
No 118
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=66.96 E-value=1.6 Score=34.55 Aligned_cols=31 Identities=16% Similarity=0.069 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.-..+++|..+||+..+|+++++--|.++++
T Consensus 129 g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 129 GFSYEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3457899999999999999999998888775
No 119
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=66.66 E-value=1.8 Score=34.06 Aligned_cols=31 Identities=16% Similarity=0.103 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
-..+++|..+||+..+||++++.-|.++++.
T Consensus 133 ~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~ 163 (187)
T PRK12516 133 FAYEEAAEICGCAVGTIKSRVNRARQRLQEI 163 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999999998888753
No 120
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=66.45 E-value=1.8 Score=33.66 Aligned_cols=30 Identities=13% Similarity=0.090 Sum_probs=25.7
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|+++.+|++-++.-|.++++
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 357889999999999999999988777665
No 121
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=66.34 E-value=3.3 Score=30.58 Aligned_cols=46 Identities=17% Similarity=0.288 Sum_probs=38.5
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..+|+.+.+.|.-+++-. ..+++|.+++++.++|++..++=+.|+.
T Consensus 136 ~~Lt~~E~~il~~l~~g~----------~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 136 DPLTKRERQVAEKLAQGM----------AVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred cCCCHHHHHHHHHHHCCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 368999999988888431 5778899999999999999999888775
No 122
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=66.24 E-value=4.4 Score=32.73 Aligned_cols=51 Identities=20% Similarity=0.375 Sum_probs=31.5
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCC-CHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRH-DEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~-d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
-.++|.+|+..-.-.++.- -+... .....+++|+++||++.+|=-|.+-++
T Consensus 8 e~~L~~~Q~kAa~ll~~ne--~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~ 59 (142)
T PF13022_consen 8 EAKLTLQQRKAAQLLVENE--LMPENGERRTQAEIAEEVGISRSTLYRWRQQNK 59 (142)
T ss_dssp HTTS-HHHHHHHHHHHHHH--HS------S-HHHHHHHHTS-HHHHHHHHHH-H
T ss_pred HHHcCHHHHHHHHHHHHHH--HhhhccccchHHHHHHHhCCCHHHHHHHHhcCH
Confidence 3578899998655544432 01122 346789999999999999999997554
No 123
>PF12728 HTH_17: Helix-turn-helix domain
Probab=66.20 E-value=3.9 Score=25.70 Aligned_cols=24 Identities=21% Similarity=0.430 Sum_probs=20.9
Q ss_pred HHHHHHHhCCCccchhhhhccccC
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
++|+|+.|||++.+|.-|.++..-
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 678999999999999999976643
No 124
>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=66.11 E-value=2.2 Score=33.74 Aligned_cols=48 Identities=17% Similarity=0.070 Sum_probs=39.8
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-+.+|..|++.+.-++ .|| ..+++|..+|+++..|+.+.+.-+.++++
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 4678999999988764 332 67899999999999999999998888775
No 125
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=66.00 E-value=1.9 Score=34.29 Aligned_cols=38 Identities=3% Similarity=-0.007 Sum_probs=31.2
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCCCCCCcccc
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEKCR 144 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~~~~~ 144 (159)
-..+++|..+||+..+|+++++.-|.++++.-.++-.+
T Consensus 150 ~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~ 187 (196)
T PRK12535 150 YTYEEAAKIADVRVGTIRSRVARARADLIAATATGQAS 187 (196)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccch
Confidence 35789999999999999999999998888755554433
No 126
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=65.65 E-value=9.2 Score=30.43 Aligned_cols=47 Identities=15% Similarity=0.163 Sum_probs=37.9
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccc
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNr 130 (159)
...+|+.+++.|..+.+.+ +...-..+++|+++++++.+|+.-+.+=
T Consensus 156 ~~~Lt~re~~~l~~~i~~~-----~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 156 PKGLTPQTLRTLCQWIDAH-----QDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCCCCHHHHHHHHHHHHhC-----CCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 4468999988888877652 4445578999999999999999998876
No 127
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=65.49 E-value=5.7 Score=30.68 Aligned_cols=27 Identities=7% Similarity=0.073 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRP 134 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~ 134 (159)
..+++|..+|++..+||+.++.-+.+.
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~ 171 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTC 171 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 578999999999999999998655444
No 128
>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=65.18 E-value=4.1 Score=27.67 Aligned_cols=27 Identities=19% Similarity=0.396 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+.++|..|||++.+|..|-+ |.+|..
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 357899999999999999975 444443
No 129
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=64.92 E-value=2 Score=33.10 Aligned_cols=33 Identities=12% Similarity=0.134 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 104 HDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 104 ~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+.-..+++|..+|+++.+|++.++.-|.++++
T Consensus 143 ~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 143 LEGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344567899999999999999999988877765
No 130
>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=64.71 E-value=2.4 Score=32.10 Aligned_cols=29 Identities=7% Similarity=0.138 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..+++|+.+||+..+|+++.+--|.++++
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 57889999999999999999877766554
No 131
>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=64.39 E-value=2.5 Score=29.62 Aligned_cols=47 Identities=15% Similarity=0.148 Sum_probs=32.8
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+++.|++.+...+ ......+++|.++||++.+|..+.+.-+.++++
T Consensus 110 ~L~~~~~~ii~~~~---------~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRY---------LEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHH---------hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45666666654432 122356799999999999999998876665543
No 132
>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=64.08 E-value=2.9 Score=35.14 Aligned_cols=31 Identities=16% Similarity=0.168 Sum_probs=27.5
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
..+++|..+|+++.+|++.++.-|.+++..+
T Consensus 126 s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~ 156 (281)
T TIGR02957 126 PYEEIASIVGKSEANCRQLVSRARRHLDARR 156 (281)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 4678999999999999999999999988744
No 133
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=64.02 E-value=2.1 Score=32.01 Aligned_cols=29 Identities=10% Similarity=0.145 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..+++|..+|++..+|+++++.-|.++++
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56889999999999999999887776654
No 134
>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=63.91 E-value=8.5 Score=25.68 Aligned_cols=23 Identities=17% Similarity=0.430 Sum_probs=18.5
Q ss_pred HHHHHHHhCCCccchhhhhcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR 131 (159)
.++||..+||++.+|--|+.+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46888888998888888887653
No 135
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=63.70 E-value=6.6 Score=29.30 Aligned_cols=29 Identities=7% Similarity=0.147 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..+++|+.+|++..+|++.++--+.++++
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46889999999999999998766655543
No 136
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=63.51 E-value=3.7 Score=34.88 Aligned_cols=33 Identities=6% Similarity=-0.070 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
.-..+++|..+|++..+||+.++.-|.++++.+
T Consensus 169 g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~ 201 (339)
T PRK08241 169 GWSAAEVAELLDTSVAAVNSALQRARATLAERG 201 (339)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcC
Confidence 346789999999999999999999999998843
No 137
>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=63.11 E-value=5.5 Score=22.88 Aligned_cols=23 Identities=17% Similarity=0.338 Sum_probs=20.2
Q ss_pred HHHHHHHhCCCccchhhhhcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR 131 (159)
..+||..+|+++.+|..|+.+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 35899999999999999998864
No 138
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=62.69 E-value=2.6 Score=32.31 Aligned_cols=29 Identities=10% Similarity=0.007 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..+++|..+|++..+|+++++.-|.+++.
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56789999999999999999887776654
No 139
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=62.51 E-value=5.1 Score=30.70 Aligned_cols=30 Identities=10% Similarity=0.201 Sum_probs=23.9
Q ss_pred CHHHHHHHHHHhCCCccchhhhhccccCCC
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLNNNRRRP 134 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFqNrR~k~ 134 (159)
..-..+++|..+|++..+|+++++.-+.++
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~ 163 (172)
T PRK09651 134 DGLTYSEIAHKLGVSVSSVKKYVAKATEHC 163 (172)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 344578999999999999999997655443
No 140
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=62.49 E-value=2.3 Score=31.56 Aligned_cols=31 Identities=13% Similarity=0.065 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.-..+++|..+|+++.+|+.|++--|.++++
T Consensus 141 ~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 141 GLSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3456899999999999999999887776654
No 141
>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=62.45 E-value=4 Score=34.78 Aligned_cols=48 Identities=15% Similarity=0.102 Sum_probs=39.3
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
...+|+.|++.|.-.++- ....++|..|||++.+||.++.|=+.|++-
T Consensus 188 ~~~LT~RE~evl~l~a~G----------~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVRDG----------KTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHHCC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 457999999999976622 245678899999999999999998888764
No 142
>PHA00542 putative Cro-like protein
Probab=62.36 E-value=9.9 Score=26.85 Aligned_cols=46 Identities=4% Similarity=0.070 Sum_probs=32.2
Q ss_pred CCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 75 AKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 75 kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
.+..+.++.+.++.. +.+..|| ...++|..+||++.+|.-|..+..
T Consensus 11 ~Rp~~~~~~~~~l~~---~l~~~gl--------Tq~elA~~lgIs~~tIsr~e~g~~ 56 (82)
T PHA00542 11 TIPAAYTQRPDELVC---ALIRAGW--------SQEQIADATDVSQPTICRIYSGRH 56 (82)
T ss_pred cCCcccCcCHHHHHH---HHHHCCC--------CHHHHHHHHCcCHHHHHHHHcCCC
Confidence 344556666665543 3344443 567899999999999999998763
No 143
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=62.30 E-value=2.4 Score=32.72 Aligned_cols=30 Identities=17% Similarity=0.245 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
..+++|..+|++..+|++.++.-|.++++.
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 568999999999999999999888887664
No 144
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=62.25 E-value=2.6 Score=32.95 Aligned_cols=30 Identities=10% Similarity=-0.099 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|++..+|++-++.-|.++++
T Consensus 158 ~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 158 LPHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 367899999999999999999988777664
No 145
>PF13309 HTH_22: HTH domain
Probab=62.15 E-value=13 Score=25.31 Aligned_cols=44 Identities=18% Similarity=0.220 Sum_probs=34.2
Q ss_pred CCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchh
Q 044959 78 KRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFK 124 (159)
Q Consensus 78 ~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvK 124 (159)
....+|.+++..+-......| -..=...++.+|+.|||++.+|=
T Consensus 17 ~~~~l~~~~k~~iV~~L~~~G---~F~lKgav~~vA~~L~iS~~TVY 60 (64)
T PF13309_consen 17 PPSRLSKEEKKEIVRQLYEKG---IFLLKGAVEYVAEKLGISRATVY 60 (64)
T ss_pred ChhhCCHHHHHHHHHHHHHCC---CcccCcHHHHHHHHHCCCHHHHH
Confidence 345678888888888777766 33456789999999999998873
No 146
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=61.90 E-value=2.5 Score=33.42 Aligned_cols=31 Identities=26% Similarity=0.384 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.-..+++|..+|++..+||+.++.-|.++++
T Consensus 155 g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 185 (201)
T PRK12545 155 DFEIDDICTELTLTANHCSVLLYRARTRLRT 185 (201)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3457899999999999999999988887765
No 147
>PRK09480 slmA division inhibitor protein; Provisional
Probab=61.87 E-value=8.9 Score=28.99 Aligned_cols=27 Identities=11% Similarity=0.256 Sum_probs=25.4
Q ss_pred CHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
+...++++|.+.||++.+|=-+|.|+.
T Consensus 29 ~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 29 ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 788999999999999999999999965
No 148
>PHA02893 hypothetical protein; Provisional
Probab=61.71 E-value=3 Score=31.31 Aligned_cols=21 Identities=33% Similarity=0.812 Sum_probs=14.1
Q ss_pred ccccCCCCCCccccccccccc
Q 044959 23 EFLKAGKDGTKEAFHCAACGC 43 (159)
Q Consensus 23 ef~~~~~~~~~~~l~CaaCgc 43 (159)
+|.+.|.-+....|.|+|||-
T Consensus 57 ~~~~~Gk~~~~~tL~CaACGS 77 (88)
T PHA02893 57 DYLNIGKAFSNSNIKCIACGS 77 (88)
T ss_pred HHHhccccCCCCceeehhhch
Confidence 455555434456799999983
No 149
>PRK06930 positive control sigma-like factor; Validated
Probab=61.62 E-value=2.5 Score=33.89 Aligned_cols=46 Identities=9% Similarity=0.084 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHH-HHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 81 KITEEQKSKMRR-FADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 81 kFT~eQkekLe~-ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+|+.+++.+.- +++- ....++|..+||+..+|+++++.-+.++++
T Consensus 114 ~L~~rer~V~~L~~~eg----------~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG----------LSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 466666666554 3332 257889999999999999999988777654
No 150
>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=61.29 E-value=2.8 Score=31.22 Aligned_cols=30 Identities=10% Similarity=0.077 Sum_probs=24.1
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|++..+|++.++--|.++++
T Consensus 139 ~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 139 LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356899999999999999998766655543
No 151
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=60.91 E-value=2.7 Score=33.04 Aligned_cols=31 Identities=10% Similarity=0.020 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.-..+++|..+||+..+|+++++--|.++++
T Consensus 127 g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 157 (182)
T PRK12511 127 GLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157 (182)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 3457899999999999999999887777664
No 152
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=60.76 E-value=7.9 Score=31.42 Aligned_cols=46 Identities=20% Similarity=0.249 Sum_probs=37.5
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..||+.|.+.|.-+++=. ...++|.+|++++++||+-.+|==.|+.
T Consensus 147 ~~LT~RE~eVL~lla~G~----------snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 147 ELLTPRELEVLRLLAEGL----------SNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCCHHHHHHHHHHHCCC----------CHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 479999999999988332 4578999999999999998888555554
No 153
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=60.58 E-value=2.8 Score=32.61 Aligned_cols=30 Identities=10% Similarity=0.117 Sum_probs=25.7
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|++..+|++.++.-|.++++
T Consensus 153 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 182 (195)
T PRK12532 153 FSSDEIQQMCGISTSNYHTIMHRARESLRQ 182 (195)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999987777664
No 154
>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=60.39 E-value=15 Score=25.54 Aligned_cols=47 Identities=19% Similarity=0.269 Sum_probs=24.5
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCC-HHHHHHHHHHhCCCccchhhh
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHD-EEEVGKFCGEVGITRKMFKVW 126 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d-~~~r~efc~eiGl~r~VvKVW 126 (159)
||.||.+.=+.|.+|.....+.-.... ...-++|+ +..+++++-+-|
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le-~~~~t~HtwQSw 49 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELE-EKHPTRHTWQSW 49 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHH-HS-SSS--SHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHH-HHcCCCCCHHHH
Confidence 899999999999998865433222223 34555554 446778888877
No 155
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=59.96 E-value=2.8 Score=32.74 Aligned_cols=30 Identities=10% Similarity=0.085 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|++..+|+..++.-|.++++
T Consensus 123 ~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 123 LSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 356889999999999999999988877765
No 156
>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=59.85 E-value=13 Score=24.03 Aligned_cols=24 Identities=21% Similarity=0.325 Sum_probs=16.9
Q ss_pred HHHHHHHHhCCCccchhhhhcccc
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
...+||..+|+++.+|.-|-.+++
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc
Confidence 366777788888888888877755
No 157
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=59.75 E-value=2.2 Score=35.71 Aligned_cols=30 Identities=17% Similarity=0.200 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
..+|+|..+|+++.+||++++--|.++++.
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~ 163 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTV 163 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 568999999999999999999999988764
No 158
>smart00351 PAX Paired Box domain.
Probab=59.72 E-value=13 Score=28.20 Aligned_cols=42 Identities=10% Similarity=0.186 Sum_probs=34.0
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
.+|.|+++++..+++ .|. ...++|..+||++.+|.-|.+--+
T Consensus 17 ~~s~~~R~riv~~~~-~G~--------s~~~iA~~~gvs~~tV~kwi~r~~ 58 (125)
T smart00351 17 PLPDEERQRIVELAQ-NGV--------RPCDISRQLCVSHGCVSKILGRYY 58 (125)
T ss_pred CCCHHHHHHHHHHHH-cCC--------CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 488999999998875 341 456889999999999999988543
No 159
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=59.42 E-value=3.1 Score=33.47 Aligned_cols=29 Identities=24% Similarity=0.352 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..+++|..+|++..+|++.++--|.++++
T Consensus 166 s~~EIAe~lgis~~tV~~~l~RAr~~Lr~ 194 (206)
T PRK12544 166 ETNEICHAVDLSVSNLNVLLYRARLRLRE 194 (206)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999988877765
No 160
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=59.33 E-value=9.6 Score=29.23 Aligned_cols=40 Identities=10% Similarity=0.277 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccC
Q 044959 82 ITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 82 FT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
+|+.++..|.+-..- -..+||..||++..+|+-|=|+++.
T Consensus 44 ls~~eIk~iRe~~~l-----------SQ~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLGL-----------SQPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhCC-----------CHHHHHHHHCCCHHHHHHHHcCCcC
Confidence 888888888775522 3578999999999999999998863
No 161
>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=59.26 E-value=5.2 Score=26.09 Aligned_cols=21 Identities=14% Similarity=0.526 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|+.+||+..+|+.|.+.
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 578999999999999999864
No 162
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=59.14 E-value=3.2 Score=31.61 Aligned_cols=32 Identities=13% Similarity=0.106 Sum_probs=26.1
Q ss_pred CHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
+.-..+++|+.+|++..+|++.++.-|.++++
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 34456899999999999999999887776653
No 163
>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=58.63 E-value=3.3 Score=32.46 Aligned_cols=31 Identities=23% Similarity=0.237 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.-..+++|..+|++..+|++.++--|.++++
T Consensus 147 g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~ 177 (188)
T TIGR02943 147 GFESDEICQELEISTSNCHVLLYRARLSLRA 177 (188)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999999887776654
No 164
>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=58.59 E-value=3.7 Score=31.59 Aligned_cols=31 Identities=10% Similarity=0.056 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.-..+++|..+|++..+|++.++--|.++++
T Consensus 165 ~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 165 GKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999999877776654
No 165
>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=57.96 E-value=5.8 Score=26.34 Aligned_cols=21 Identities=19% Similarity=0.536 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|+.+||+..+|+.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 578999999999999999764
No 166
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=57.88 E-value=2.7 Score=34.68 Aligned_cols=32 Identities=13% Similarity=0.153 Sum_probs=27.4
Q ss_pred CHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..-..+++|..+|++..+|++.++.-|.++++
T Consensus 186 eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 186 ENMSNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 33456899999999999999999998888875
No 167
>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=57.83 E-value=21 Score=26.64 Aligned_cols=39 Identities=13% Similarity=0.363 Sum_probs=31.6
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhc
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLN 128 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFq 128 (159)
.+|.|=++++.++++.- .-+.+.|...+|++.+|.-||.
T Consensus 2 aYS~DlR~rVl~~~~~g---------~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 2 AYSLDLRQRVLAYIEKG---------KSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CCCHHHHHHHHHHHHcc---------chHHHHHHHhCcHHHHHHHHHH
Confidence 35677788888877662 2567789999999999999999
No 168
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=57.18 E-value=3.5 Score=33.08 Aligned_cols=31 Identities=6% Similarity=0.170 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
..+++|+.+|+++.+|+++++--|.++++.-
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999999988887643
No 169
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=57.14 E-value=9.5 Score=29.02 Aligned_cols=29 Identities=10% Similarity=0.205 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRP 134 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~ 134 (159)
.-..+++|+.+|++..+|+++++.-+.++
T Consensus 135 g~s~~EIA~~lgis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 135 GMGHAEIAERLGVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34678999999999999999998766554
No 170
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=56.57 E-value=3.1 Score=32.11 Aligned_cols=33 Identities=6% Similarity=-0.058 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 104 HDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 104 ~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
...-..+++|+.+|++..+|++.++.-|.++++
T Consensus 152 ~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 152 FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 334457899999999999999999988877764
No 171
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=56.16 E-value=11 Score=28.74 Aligned_cols=26 Identities=4% Similarity=0.095 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCCccchhhhhccccCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRR 133 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k 133 (159)
..+++|..+|+++.+|+.++.+-+..
T Consensus 136 s~~EIA~~l~is~~tV~~~l~ra~~~ 161 (168)
T PRK12525 136 TYVEIGERLGVSLSRIHQYMVEAFKC 161 (168)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 57899999999999999999776544
No 172
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=55.92 E-value=3.4 Score=31.36 Aligned_cols=33 Identities=6% Similarity=0.075 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 104 HDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 104 ~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
......+++|..+|++..+|++..+.-|.++++
T Consensus 150 ~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 150 IEDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344567899999999999999999988877764
No 173
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=55.91 E-value=5.7 Score=24.64 Aligned_cols=21 Identities=14% Similarity=0.208 Sum_probs=19.3
Q ss_pred HHHHHhCCCccchhhhhcccc
Q 044959 111 KFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 111 efc~eiGl~r~VvKVWFqNrR 131 (159)
+||..+||+..+|.-|++|+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 689999999999999999875
No 174
>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=55.66 E-value=42 Score=20.92 Aligned_cols=34 Identities=26% Similarity=0.222 Sum_probs=25.1
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCC
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGIT 119 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~ 119 (159)
|-.||+|+-+.|.+...+.|- + .-..+|..++.+
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~-----~--~W~~Ia~~~~~~ 34 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGK-----D--NWKKIAKRMPGG 34 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTT-----T--HHHHHHHHHSSS
T ss_pred CCCCCHHHHHHHHHHHHHhCC-----c--HHHHHHHHcCCC
Confidence 567999999999999988751 1 677888888833
No 175
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=55.20 E-value=6.1 Score=33.14 Aligned_cols=32 Identities=9% Similarity=0.159 Sum_probs=28.3
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVPVRV 139 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~ 139 (159)
..+++|+.+|+++.+||+.++.-|.++++...
T Consensus 133 s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 133 PFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 46789999999999999999999999987554
No 176
>PF13551 HTH_29: Winged helix-turn helix
Probab=55.02 E-value=6.4 Score=27.43 Aligned_cols=24 Identities=25% Similarity=0.624 Sum_probs=21.6
Q ss_pred HHHHHHHHhCCCccchhhhhcccc
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
.+.++|..+|+++.+|.-|.+.=+
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 689999999999999999998743
No 177
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=55.01 E-value=6.6 Score=32.12 Aligned_cols=46 Identities=15% Similarity=0.192 Sum_probs=38.0
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..+|+-|++.|.-.++ | ...+++|+++++++++||.+..|=..|+.
T Consensus 154 ~~Lt~rE~~Vl~l~~~--G--------~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 154 ALLTHREKEILNKLRI--G--------ASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCCHHHHHHHHHHHc--C--------CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3599999999988884 3 14578899999999999999998877665
No 178
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=54.99 E-value=3.7 Score=32.12 Aligned_cols=34 Identities=12% Similarity=0.026 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRV 139 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~ 139 (159)
.-..+++|..+|+++.+|++.++--|.++++.-.
T Consensus 127 g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 127 GFSYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3457899999999999999999999888876544
No 179
>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=54.96 E-value=7 Score=24.29 Aligned_cols=21 Identities=10% Similarity=0.444 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|+.+||+.++|+.|-.-
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 568999999999999999764
No 180
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=54.85 E-value=3.7 Score=33.09 Aligned_cols=32 Identities=13% Similarity=0.151 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
++-..+++|..+||+..+|+++++.-+.++++
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44467899999999999999999887777654
No 181
>PRK09483 response regulator; Provisional
Probab=54.61 E-value=7.6 Score=29.15 Aligned_cols=46 Identities=11% Similarity=0.199 Sum_probs=37.1
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..||+-+++.|.-+++ | ....++|..++++.++|+.-.+|=+.|+.
T Consensus 147 ~~Lt~rE~~vl~~~~~--G--------~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIMLMITK--G--------QKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHHHHHHC--C--------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 5699999999876652 2 13448999999999999999999888885
No 182
>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=54.35 E-value=8.8 Score=24.25 Aligned_cols=21 Identities=14% Similarity=0.348 Sum_probs=16.6
Q ss_pred HHHHHHHHHhCCCccchhhhh
Q 044959 107 EEVGKFCGEVGITRKMFKVWL 127 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWF 127 (159)
-..++||+++||++++|+-=+
T Consensus 16 it~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHH
T ss_pred cCHHHHHHHhCCCHHHHHHHH
Confidence 578899999999999987543
No 183
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=53.11 E-value=1.6 Score=33.80 Aligned_cols=35 Identities=14% Similarity=0.223 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 103 RHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 103 ~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
+.+.-..+++|..+|++..+|+++++.-|.++++.
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 152 EHGDLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34456789999999999999999999988887753
No 184
>PF13565 HTH_32: Homeodomain-like domain
Probab=52.73 E-value=10 Score=25.32 Aligned_cols=46 Identities=20% Similarity=0.233 Sum_probs=29.4
Q ss_pred CCCCCccCCHHHHHHHHHHHHHhCCCCCCCC-HHHHHHHHHHhCC----Cccchhhh
Q 044959 75 AKTKRTKITEEQKSKMRRFADKLGWKPQRHD-EEEVGKFCGEVGI----TRKMFKVW 126 (159)
Q Consensus 75 kKR~RTkFT~eQkekLe~ffek~GW~iq~~d-~~~r~efc~eiGl----~r~VvKVW 126 (159)
.-|+|+ +.+|.+.|.+..... +..+ ....+.|..+.|+ +..+|.-|
T Consensus 26 ~Grp~~--~~e~~~~i~~~~~~~----p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 26 PGRPRK--DPEQRERIIALIEEH----PRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred CCCCCC--cHHHHHHHHHHHHhC----CCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 445555 899989999988774 2334 4556667776664 55555443
No 185
>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=52.33 E-value=9 Score=32.15 Aligned_cols=31 Identities=13% Similarity=0.392 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-.++++|+..++|++.+|-+|+.|-+...++
T Consensus 14 tgt~~e~~~~~~VS~~sv~~WiKNG~~~~~a 44 (186)
T PF04936_consen 14 TGTIDELADYFDVSRTSVSVWIKNGKDPKRA 44 (186)
T ss_pred cccHHHHHHHHccCHHHHHHHHHcCCCcccc
Confidence 4578999999999999999999999887765
No 186
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=52.16 E-value=3.9 Score=33.15 Aligned_cols=32 Identities=9% Similarity=0.138 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
+.-..+++|..+||+..+|+++++.-+.++++
T Consensus 199 ~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 199 EELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34467899999999999999999988777654
No 187
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=50.98 E-value=14 Score=30.16 Aligned_cols=46 Identities=7% Similarity=0.062 Sum_probs=38.4
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..+|+-|++.|.-+++=. ...++|.+++|++++|+.-..|=-.|+.
T Consensus 133 ~~LT~RE~eVL~ll~~G~----------snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 133 RMLSPTEREILRFMSRGY----------SMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred CCCCHHHHHHHHHHHCCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 469999999999988432 5678999999999999998888766665
No 188
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=50.98 E-value=4 Score=31.45 Aligned_cols=29 Identities=10% Similarity=0.189 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..+++|..+|++..+|+.+++--|.++++
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999877766653
No 189
>PRK13558 bacterio-opsin activator; Provisional
Probab=50.28 E-value=14 Score=33.96 Aligned_cols=41 Identities=20% Similarity=0.336 Sum_probs=34.5
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCC---CCHHHHHHHHHHhCCCccchh
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQR---HDEEEVGKFCGEVGITRKMFK 124 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~---~d~~~r~efc~eiGl~r~VvK 124 (159)
...+|..|.+.|+..++. | | |-....+++|.+|||++.+|-
T Consensus 605 ~~~lt~~q~e~l~~a~~~-g----yf~~pr~~~~~e~a~~l~is~~t~~ 648 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVS-G----YFEWPRRVEGEELAESMGISRSTFH 648 (665)
T ss_pred hhhCCHHHHHHHHHHHHc-C----CCCCCccCCHHHHHHHhCCCHHHHH
Confidence 357999999999987655 3 5 778899999999999998874
No 190
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=50.25 E-value=13 Score=21.06 Aligned_cols=23 Identities=17% Similarity=0.352 Sum_probs=19.6
Q ss_pred HHHHHHHhCCCccchhhhhcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR 131 (159)
..+|+..+|++..+|..|..++.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 56899999999999999987653
No 191
>PRK11891 aspartate carbamoyltransferase; Provisional
Probab=49.64 E-value=15 Score=34.07 Aligned_cols=38 Identities=24% Similarity=0.482 Sum_probs=30.4
Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhc
Q 044959 83 TEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLN 128 (159)
Q Consensus 83 T~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFq 128 (159)
|..|-+-|.+.-..+| -.+++||+.|||+.+++-.|+-
T Consensus 1 ~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~l~~wl~ 38 (429)
T PRK11891 1 TVPQQAFLRDAMRRLN--------MTREAFANRIGVSRRALDTWLL 38 (429)
T ss_pred ChhHHHHHHHHHHHhC--------CCHHHHHHHhCCcHHhHHhhcC
Confidence 4567777777776764 2689999999999999999974
No 192
>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=49.62 E-value=16 Score=26.48 Aligned_cols=33 Identities=18% Similarity=0.314 Sum_probs=24.1
Q ss_pred HHHHHHHhCCCccchhhhhccccCCCCCCCCCccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEKC 143 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~~~~ 143 (159)
+.++|..+||+..+|+.|... --..+.+..+..
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~--Gll~p~r~~~g~ 35 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEI--GLVSPERSEGRY 35 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC--CCCCCCcCCCCC
Confidence 678999999999999999864 333344544443
No 193
>PF13698 DUF4156: Domain of unknown function (DUF4156)
Probab=49.32 E-value=7.9 Score=28.37 Aligned_cols=14 Identities=36% Similarity=0.363 Sum_probs=12.4
Q ss_pred hhhhhhccCCcccc
Q 044959 6 RRNHAASIGRYAYD 19 (159)
Q Consensus 6 ~~Nhaa~~G~~~~D 19 (159)
|||.||.+||.+|=
T Consensus 54 lrNeAa~lGgntV~ 67 (93)
T PF13698_consen 54 LRNEAAKLGGNTVV 67 (93)
T ss_pred HHHHHHHhCCCEEE
Confidence 79999999998774
No 194
>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=49.26 E-value=5.5 Score=31.98 Aligned_cols=47 Identities=9% Similarity=0.140 Sum_probs=33.4
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+++.|++.+..++ ...-..+++|..+|++..+|+.+++.-+.++++
T Consensus 175 ~L~~~~r~il~l~y---------~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYY---------YEELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHH---------hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 35566666665533 122356899999999999999999877666553
No 195
>PHA01976 helix-turn-helix protein
Probab=49.15 E-value=13 Score=24.24 Aligned_cols=24 Identities=8% Similarity=0.261 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCccchhhhhcccc
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
..++||..+||++.+|.-|....+
T Consensus 17 t~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 17 SAPELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 367899999999999999987653
No 196
>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=48.61 E-value=10 Score=24.94 Aligned_cols=23 Identities=4% Similarity=0.229 Sum_probs=19.8
Q ss_pred HHHHHHHhCCCccchhhhhcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR 131 (159)
+.++|+.+||+..+|+.|-..-.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~g~ 25 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKEFN 25 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHhcC
Confidence 56899999999999999987633
No 197
>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=48.58 E-value=5.7 Score=30.09 Aligned_cols=10 Identities=40% Similarity=0.704 Sum_probs=7.8
Q ss_pred cchhhhhccc
Q 044959 121 KMFKVWLNNN 130 (159)
Q Consensus 121 ~VvKVWFqNr 130 (159)
.-|||||||-
T Consensus 31 gdvkvwmqnl 40 (106)
T PF11516_consen 31 GDVKVWMQNL 40 (106)
T ss_dssp HHHHHHHHHH
T ss_pred ccHHHHHHHH
Confidence 3489999993
No 198
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=48.55 E-value=5.8 Score=34.61 Aligned_cols=51 Identities=18% Similarity=0.253 Sum_probs=38.0
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+++.|++.|...| | +.+...-..+++|..+||++.+|+++.+.-+.++++
T Consensus 262 ~L~~~~R~vl~lry---g--L~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~ 312 (325)
T PRK05657 262 ELNDKQREVLARRF---G--LLGYEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312 (325)
T ss_pred cCCHHHHHHHHHHh---c--cCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45566666665544 1 124455677999999999999999999998888875
No 199
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=48.36 E-value=7.7 Score=29.75 Aligned_cols=31 Identities=6% Similarity=0.122 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.-..+++|..+||++.+|++-.+.-|.+++.
T Consensus 153 g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 153 GITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 3467899999999999999998877766653
No 200
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=48.17 E-value=7 Score=29.21 Aligned_cols=30 Identities=13% Similarity=0.181 Sum_probs=24.4
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|+++.+|++.++.-+.+++.
T Consensus 122 ~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~ 151 (159)
T PRK12527 122 LSHQQIAEHLGISRSLVEKHIVNAMKHCRV 151 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 356899999999999999999876665543
No 201
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.
Probab=48.15 E-value=13 Score=27.70 Aligned_cols=54 Identities=11% Similarity=0.152 Sum_probs=40.6
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHH--HHHHHHhCCCccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEV--GKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r--~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..+|+.|.+.|.-+++..| +-.+.+++ ..++.+++++.++|++-+.+=|.|+..
T Consensus 153 ~~Lt~~E~~il~~l~~~~~---~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (226)
T TIGR02154 153 LSLGPTEFRLLHFFMTHPE---RVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNP 208 (226)
T ss_pred EEcCHHHHHHHHHHHhCCC---ceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhcc
Confidence 4699999999998887543 22333332 334788999999999999999988864
No 202
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=47.86 E-value=11 Score=31.22 Aligned_cols=49 Identities=8% Similarity=0.119 Sum_probs=39.0
Q ss_pred CCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 78 KRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 78 ~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
....+|+-|++.|.=.++-. .-.++|..|||++++|+.=+.|=+.|+.-
T Consensus 176 ~~~~LT~rE~evl~~~a~G~----------t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 176 PEMNFSKREKEILKWTAEGK----------TSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred CCCCCCHHHHHHHHHHHcCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 34578888888877776332 45688999999999999999999998873
No 203
>PF13730 HTH_36: Helix-turn-helix domain
Probab=47.85 E-value=57 Score=20.42 Aligned_cols=43 Identities=12% Similarity=0.132 Sum_probs=29.2
Q ss_pred cCCHHHHHHHHHHHHH---hCCCCCCCCHHHHHHHHHHhCCCccchhhhhc
Q 044959 81 KITEEQKSKMRRFADK---LGWKPQRHDEEEVGKFCGEVGITRKMFKVWLN 128 (159)
Q Consensus 81 kFT~eQkekLe~ffek---~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFq 128 (159)
.+|+.++-.+..++.. .|| -+| -++.||..+|+++++|+-++.
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~--~~p---S~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGG--CFP---SQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCC--CCc---CHHHHHHHHCcCHHHHHHHHH
Confidence 4566666666554433 332 344 478899999999999988764
No 204
>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=47.69 E-value=6.3 Score=29.85 Aligned_cols=47 Identities=6% Similarity=0.020 Sum_probs=32.2
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+++.|++.+.-. |.+....+++|..+||++.+|++=++.-|.++++
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 3455555555442 2234467899999999999999888776666553
No 205
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=47.24 E-value=27 Score=26.39 Aligned_cols=18 Identities=0% Similarity=-0.079 Sum_probs=9.6
Q ss_pred CCHHHHHHHHHHhCCCcc
Q 044959 104 HDEEEVGKFCGEVGITRK 121 (159)
Q Consensus 104 ~d~~~r~efc~eiGl~r~ 121 (159)
|+.+.+..||+.+||+..
T Consensus 45 ps~~~l~kIa~aL~v~~~ 62 (120)
T PRK13890 45 PSLKVMEAIADALETPLP 62 (120)
T ss_pred CCHHHHHHHHHHHCCCHH
Confidence 455555555555555443
No 206
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=47.24 E-value=2 Score=32.44 Aligned_cols=35 Identities=14% Similarity=0.062 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 102 QRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 102 q~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.|.+.-..+++|..+|++..+|++.++.-|.++++
T Consensus 132 ~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 132 HDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred hHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34455568999999999999999999988888765
No 207
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=47.13 E-value=11 Score=24.46 Aligned_cols=20 Identities=10% Similarity=0.404 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCccchhhhhc
Q 044959 109 VGKFCGEVGITRKMFKVWLN 128 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFq 128 (159)
+.++|+.+||++.+|+.|..
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 57899999999999999976
No 208
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=47.10 E-value=17 Score=28.12 Aligned_cols=46 Identities=11% Similarity=0.109 Sum_probs=37.6
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..+|+-|++.|.-.++= ..-.++|++++|+.++|+.-..|=-.|+.
T Consensus 149 ~~Lt~rE~evl~~~~~G----------~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 149 KRLSPKESEVLRLFAEG----------FLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred ccCCHHHHHHHHHHHCC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 35999999999888732 25678999999999999998888777765
No 209
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=47.07 E-value=13 Score=23.73 Aligned_cols=24 Identities=17% Similarity=0.311 Sum_probs=21.8
Q ss_pred CCCCCccCCHHHHHHHHHHHHHhC
Q 044959 75 AKTKRTKITEEQKSKMRRFADKLG 98 (159)
Q Consensus 75 kKR~RTkFT~eQkekLe~ffek~G 98 (159)
++|+-+.++.++.++|..++++.|
T Consensus 2 r~r~t~~l~~el~~~L~~ls~~t~ 25 (44)
T PF12651_consen 2 RKRFTFSLDKELYEKLKELSEETG 25 (44)
T ss_pred ceEEEEecCHHHHHHHHHHHHHHC
Confidence 578888999999999999999986
No 210
>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=46.98 E-value=21 Score=23.59 Aligned_cols=40 Identities=13% Similarity=0.224 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 84 EEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 84 ~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
..|++.|+-+.+ .+|- ...++|..+|+++++|+.-+.+=+
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 457777777776 5443 466999999999999987665543
No 211
>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=46.68 E-value=6.2 Score=32.94 Aligned_cols=30 Identities=13% Similarity=0.305 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+||+..+||++++.-|.++++
T Consensus 178 ~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~ 207 (244)
T TIGR03001 178 LSMDRIGAMYQVHRSTVSRWVAQARERLLE 207 (244)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999988877764
No 212
>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=46.61 E-value=6.4 Score=31.87 Aligned_cols=51 Identities=6% Similarity=0.016 Sum_probs=33.1
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..+++.|++.|.-.+-- ...++-..+++|..+|+++.+|+++.+.-+.+++
T Consensus 173 ~~L~~~~r~il~l~y~~-----~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr 223 (227)
T TIGR02846 173 SVLDGREREVIEMRYGL-----GDGRRKTQREIAKILGISRSYVSRIEKRALMKLY 223 (227)
T ss_pred HhCCHHHHHHHHHHHcC-----CCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34556666665553300 0013346889999999999999999876555544
No 213
>PHA02535 P terminase ATPase subunit; Provisional
Probab=46.50 E-value=28 Score=33.64 Aligned_cols=46 Identities=17% Similarity=0.380 Sum_probs=35.1
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
+.||+|-+.+-.....+ || .+.++|++|||++.+|..|- +|.+|..
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 46899988777765544 65 46799999999999999994 4566654
No 214
>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=46.26 E-value=13 Score=27.26 Aligned_cols=22 Identities=9% Similarity=0.060 Sum_probs=19.5
Q ss_pred HHHHHHHHHhCCCccchhhhhc
Q 044959 107 EEVGKFCGEVGITRKMFKVWLN 128 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFq 128 (159)
....++|..+||++.+|..|..
T Consensus 51 ~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 51 KTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3678899999999999999876
No 215
>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=46.11 E-value=34 Score=23.46 Aligned_cols=38 Identities=18% Similarity=0.350 Sum_probs=23.5
Q ss_pred cCCHHHHHHHHH---HHHHhCCCCCCCCHHHHHHHHHHhCCC-ccchh
Q 044959 81 KITEEQKSKMRR---FADKLGWKPQRHDEEEVGKFCGEVGIT-RKMFK 124 (159)
Q Consensus 81 kFT~eQkekLe~---ffek~GW~iq~~d~~~r~efc~eiGl~-r~VvK 124 (159)
.+|+-|.+.|+- |-++.| |+ ..+.+||+.+|++ ..+|.
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G----~~--Pt~rEIa~~~g~~S~~tv~ 44 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENG----YP--PTVREIAEALGLKSTSTVQ 44 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHS----S-----HHHHHHHHTSSSHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcC----CC--CCHHHHHHHhCCCChHHHH
Confidence 478888877765 555654 43 4889999999997 55554
No 216
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=46.02 E-value=3 Score=31.58 Aligned_cols=34 Identities=6% Similarity=-0.028 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 103 RHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 103 ~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
|...-..+++|..+|++...|+++++.-|.++++
T Consensus 139 ~~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 139 HYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred hhcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 3445567899999999999999999888777654
No 217
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=45.80 E-value=6.4 Score=32.31 Aligned_cols=28 Identities=7% Similarity=0.029 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..+++|..+||++.+|+.|.+.-+.+++
T Consensus 223 s~~eIA~~l~is~~tV~~~~~ra~~kLr 250 (257)
T PRK08583 223 SQKETGERLGISQMHVSRLQRQAIKKLR 250 (257)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4689999999999999999987766654
No 218
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=45.64 E-value=24 Score=37.47 Aligned_cols=63 Identities=17% Similarity=0.155 Sum_probs=51.7
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 72 NYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 72 ~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
..+-|+.|+..-.++...|-..+... .-|+..+.+-|--+...+.++..+||||.+.+..+-.
T Consensus 702 ~~~~~~~~~~~~~~aa~~l~~a~~~~----~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 702 SPRDKLLRLTILPEAAMILGRAYMQD----NSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CcccccCcccccHHHHhhhhhcccCC----CCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 34579999999999999887744222 3477889999999999999999999999999988755
No 219
>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=45.63 E-value=22 Score=23.52 Aligned_cols=19 Identities=21% Similarity=0.606 Sum_probs=14.4
Q ss_pred CCHHHHHHHHHHHHHhCCC
Q 044959 82 ITEEQKSKMRRFADKLGWK 100 (159)
Q Consensus 82 FT~eQkekLe~ffek~GW~ 100 (159)
++..|+++|.+++++.||-
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 4689999999999999994
No 220
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=45.39 E-value=17 Score=25.86 Aligned_cols=35 Identities=20% Similarity=0.361 Sum_probs=28.4
Q ss_pred HHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhc
Q 044959 88 SKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLN 128 (159)
Q Consensus 88 ekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFq 128 (159)
++|..|.--+||.+ -+.+.|..||++..+|.-|.-
T Consensus 1 ~~~~~fIrlLs~~~------s~~~Aa~~lG~~~~~v~~wv~ 35 (65)
T PF05344_consen 1 EKARAFIRLLSQQI------SVAQAADRLGTDPGTVRRWVR 35 (65)
T ss_pred CcHHHHHHHhcccc------cHHHHHHHHCcCHHHHHHHHH
Confidence 36778888887665 477889999999999999964
No 221
>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=45.26 E-value=7.3 Score=31.17 Aligned_cols=47 Identities=9% Similarity=0.135 Sum_probs=33.7
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..+++.|++.+.-.+. .....+++|..+||++.+|+.|.+.-+.+++
T Consensus 177 ~~L~~~~r~vl~l~y~---------~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 177 AALPERERRILLLRFF---------EDKTQSEIAERLGISQMHVSRLLRRALKKLR 223 (227)
T ss_pred HcCCHHHHHHHHHHHh---------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3566777776666431 2336889999999999999999876555544
No 222
>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=45.26 E-value=2.6 Score=32.69 Aligned_cols=36 Identities=8% Similarity=0.001 Sum_probs=30.3
Q ss_pred CCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 101 PQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 101 iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
+.|.+.-..+++|..+||+..+|+++++--|.++++
T Consensus 142 L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 177 (193)
T TIGR02947 142 LADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRK 177 (193)
T ss_pred ehhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345556678999999999999999999988888775
No 223
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=45.03 E-value=28 Score=22.34 Aligned_cols=33 Identities=21% Similarity=0.255 Sum_probs=25.7
Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcc
Q 044959 83 TEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 83 T~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
|.|||++|-+-. -+.++..+|+++.-+.|.|..
T Consensus 13 s~eqk~~l~~~i--------------t~~l~~~~~~p~~~v~V~i~e 45 (61)
T PRK02220 13 TEEQLKALVKDV--------------TAAVSKNTGAPAEHIHVIINE 45 (61)
T ss_pred CHHHHHHHHHHH--------------HHHHHHHhCcChhhEEEEEEE
Confidence 799999887644 346889999988888777754
No 224
>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=44.99 E-value=23 Score=26.46 Aligned_cols=28 Identities=29% Similarity=0.499 Sum_probs=22.4
Q ss_pred CCCCccCCHHHHHHHHHHHHHhCCCCCC
Q 044959 76 KTKRTKITEEQKSKMRRFADKLGWKPQR 103 (159)
Q Consensus 76 KR~RTkFT~eQkekLe~ffek~GW~iq~ 103 (159)
|+.=+..|..|++++.+++++.||+.++
T Consensus 16 k~S~k~lt~~el~~vl~~l~~~G~k~~~ 43 (119)
T PF06252_consen 16 KSSSKDLTEAELEKVLDELKRLGFKPPK 43 (119)
T ss_pred hhhHHHCCHHHHHHHHHHHHHccCcCcc
Confidence 3444568999999999999999997554
No 225
>PF13743 Thioredoxin_5: Thioredoxin; PDB: 3KZQ_C.
Probab=44.77 E-value=20 Score=28.39 Aligned_cols=42 Identities=21% Similarity=0.200 Sum_probs=28.3
Q ss_pred HHHHHHHHH-HHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccc
Q 044959 86 QKSKMRRFA-DKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 86 QkekLe~ff-ek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNr 130 (159)
=+.+|.+.. ... ..+-+.+.+.++|+++||+...|+..|+..
T Consensus 85 fL~~lQ~a~~~~~---~~~s~~~~l~~iA~~~gLD~~~F~~d~~S~ 127 (176)
T PF13743_consen 85 FLRALQEALFLEG---KNYSDEELLLEIAEELGLDVEMFKEDLHSD 127 (176)
T ss_dssp HHHHHHHHHHTS------TTSHHHHHHHHHHTT--HHHHHHHHTSH
T ss_pred HHHHHHHHHHhcC---CCCCHHHHHHHHHHHhCCCHHHHHHHHhCh
Confidence 356666633 221 245667999999999999999999998754
No 226
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=44.75 E-value=7.2 Score=31.63 Aligned_cols=32 Identities=13% Similarity=0.185 Sum_probs=25.7
Q ss_pred CHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.....+++|..+||++.+|+++.+.-+.++++
T Consensus 194 e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~ 225 (233)
T PRK05803 194 KEKTQREIAKALGISRSYVSRIEKRALKKLFK 225 (233)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34468899999999999999998776666554
No 227
>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=44.72 E-value=7.9 Score=32.42 Aligned_cols=33 Identities=12% Similarity=-0.000 Sum_probs=28.1
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRV 139 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~ 139 (159)
-..+++|..+|++..+|++.++--|.++++.-.
T Consensus 159 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 159 WRAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 356899999999999999999988888876544
No 228
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=44.62 E-value=21 Score=26.57 Aligned_cols=51 Identities=10% Similarity=0.074 Sum_probs=40.7
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhC-----CCccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVG-----ITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiG-----l~r~VvKVWFqNrR~k~kk 136 (159)
..+|+.+.+.|.-+++..| ..-.+++++..+. ++.++|++.+.+=|.|+..
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 4699999999998886532 2234568888886 9999999999999999863
No 229
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=44.38 E-value=7.2 Score=30.55 Aligned_cols=31 Identities=16% Similarity=0.168 Sum_probs=25.6
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVPV 137 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~ 137 (159)
-..+++|..+||+..+|++=++.-|.++++.
T Consensus 151 ~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~ 181 (192)
T PRK09643 151 YSVADAARMLGVAEGTVKSRCARGRARLAEL 181 (192)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999888777777653
No 230
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=44.25 E-value=19 Score=28.94 Aligned_cols=45 Identities=13% Similarity=0.178 Sum_probs=37.3
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
.+|+-|++.|.-.++=. .-.++|++++|++++|+.-..|=..|++
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 49999999998888432 4578999999999999998887766665
No 231
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=44.04 E-value=7.5 Score=31.97 Aligned_cols=31 Identities=3% Similarity=-0.068 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
+-..+++|..+||+..+|+++++.-+.+++.
T Consensus 217 ~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 217 ELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3357899999999999999999887766653
No 232
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=43.95 E-value=4.3 Score=31.44 Aligned_cols=53 Identities=9% Similarity=0.018 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHhCCC------CCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 84 EEQKSKMRRFADKLGWK------PQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 84 ~eQkekLe~ffek~GW~------iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.++.+.|....+.+.=+ +.|...-..+++|..+||+..+|+++++.-|.++++
T Consensus 122 ~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 122 PEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLRE 180 (188)
T ss_pred HHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34555566555554211 112334567899999999999999999988777654
No 233
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=43.77 E-value=17 Score=23.02 Aligned_cols=37 Identities=16% Similarity=0.235 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchh
Q 044959 82 ITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFK 124 (159)
Q Consensus 82 FT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvK 124 (159)
||..|...|......- ++.-...+||..+++++.++.
T Consensus 3 lt~~q~~vL~~l~~~~------~~~~t~~~la~~l~~~~~~vs 39 (62)
T PF12802_consen 3 LTPSQFRVLMALARHP------GEELTQSELAERLGISKSTVS 39 (62)
T ss_dssp STHHHHHHHHHHHHST------TSGEEHHHHHHHHTS-HHHHH
T ss_pred cCHHHHHHHHHHHHCC------CCCcCHHHHHHHHCcCHHHHH
Confidence 7889999998887542 223588899999999988764
No 234
>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=42.14 E-value=10 Score=27.73 Aligned_cols=11 Identities=36% Similarity=1.072 Sum_probs=9.0
Q ss_pred ccccccccccc
Q 044959 33 KEAFHCAACGC 43 (159)
Q Consensus 33 ~~~l~CaaCgc 43 (159)
...|.|+|||-
T Consensus 55 ~~tLsCsACGS 65 (74)
T PF05077_consen 55 GNTLSCSACGS 65 (74)
T ss_pred CCeEeehhccc
Confidence 46799999983
No 235
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=41.79 E-value=4.4 Score=32.82 Aligned_cols=36 Identities=19% Similarity=0.180 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 103 RHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 103 ~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
|...-..+++|+.+|++..+|++.++.-|.++++.-
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 445567889999999999999999999998888743
No 236
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=41.03 E-value=38 Score=25.40 Aligned_cols=17 Identities=0% Similarity=-0.035 Sum_probs=8.5
Q ss_pred CCHHHHHHHHHHhCCCc
Q 044959 104 HDEEEVGKFCGEVGITR 120 (159)
Q Consensus 104 ~d~~~r~efc~eiGl~r 120 (159)
|+...+..||..+||+.
T Consensus 45 p~~~~l~~la~~l~vs~ 61 (135)
T PRK09706 45 PTGKNLFALAKALQCSP 61 (135)
T ss_pred CCHHHHHHHHHHHCcCH
Confidence 44444555555555543
No 237
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=40.19 E-value=25 Score=27.17 Aligned_cols=30 Identities=10% Similarity=0.178 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhccccC
Q 044959 103 RHDEEEVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 103 ~~d~~~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
..+...++++|++.||++.+|-.+|.|+-.
T Consensus 28 G~~~~ti~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 28 GVSNTTLNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred CcccCCHHHHHHHcCCCHHHHHHHcCCHHH
Confidence 367789999999999999999999988765
No 238
>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=40.02 E-value=28 Score=26.22 Aligned_cols=27 Identities=15% Similarity=0.230 Sum_probs=23.0
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhcc
Q 044959 103 RHDEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 103 ~~d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
.-+.-.|+++|++.||++.+|=.-|.+
T Consensus 20 ~~~~ITV~~I~~~AgvsR~TFY~hF~d 46 (176)
T TIGR02366 20 AFSKISVSDIMSTAQIRRQTFYNHFQD 46 (176)
T ss_pred CCccCCHHHHHHHhCCCHHHHHHHCCC
Confidence 466789999999999999998776665
No 239
>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=39.57 E-value=33 Score=21.21 Aligned_cols=34 Identities=26% Similarity=0.354 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhh
Q 044959 86 QKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWL 127 (159)
Q Consensus 86 QkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWF 127 (159)
+++.|.+..++.||. +.+-|..|||++.+|.--|
T Consensus 6 E~~~i~~aL~~~~gn--------~~~aA~~Lgisr~tL~~kl 39 (42)
T PF02954_consen 6 EKQLIRQALERCGGN--------VSKAARLLGISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHTTT---------HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHhCCC--------HHHHHHHHCCCHHHHHHHH
Confidence 445556666665543 5789999999999986544
No 240
>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=39.25 E-value=72 Score=25.89 Aligned_cols=42 Identities=14% Similarity=0.240 Sum_probs=34.6
Q ss_pred CCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhh
Q 044959 78 KRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKV 125 (159)
Q Consensus 78 ~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKV 125 (159)
+...+|+||+++|...=. +-|..-.|..||.+.||++.-|.+
T Consensus 82 k~y~Lt~e~i~Eir~LR~------~DP~~wTr~~LAkkF~~S~~fV~~ 123 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRA------EDPEKWTRKKLAKKFNCSPLFVSM 123 (164)
T ss_pred ccccCCHHHHHHHHHHHH------cCchHhhHHHHHHHhCCCHHHHHH
Confidence 457899999999998653 357778999999999999876654
No 241
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=39.11 E-value=26 Score=23.63 Aligned_cols=20 Identities=20% Similarity=0.408 Sum_probs=10.7
Q ss_pred CHHHHHHHHHHhCCCccchh
Q 044959 105 DEEEVGKFCGEVGITRKMFK 124 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvK 124 (159)
+..+|+-+|.++||++.+|+
T Consensus 19 e~~ev~ywa~~~gvt~~~L~ 38 (57)
T PF12244_consen 19 EPYEVRYWAKRFGVTEEQLR 38 (57)
T ss_pred CHHHHHHHHHHHCcCHHHHH
Confidence 34455555555555555543
No 242
>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=39.10 E-value=9.4 Score=31.04 Aligned_cols=31 Identities=13% Similarity=0.129 Sum_probs=24.9
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
+-..+++|..+||+..+|+++++--+.++++
T Consensus 198 g~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~ 228 (234)
T TIGR02835 198 EKTQKEVADMLGISQSYISRLEKRILKRLKK 228 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3467889999999999999999876665543
No 243
>PHA02955 hypothetical protein; Provisional
Probab=38.87 E-value=42 Score=28.81 Aligned_cols=43 Identities=14% Similarity=0.133 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcc
Q 044959 84 EEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 84 ~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
..|++.|.+-+.+. +....++++++++.+||++-.++.-||.+
T Consensus 60 ~~sf~lli~a~~Et---~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 60 EKNFQLLIEALIET---IENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHH---HHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 46777777744443 25578999999999999999988888876
No 244
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=38.24 E-value=30 Score=25.70 Aligned_cols=51 Identities=6% Similarity=0.120 Sum_probs=40.4
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhC-----CCccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVG-----ITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiG-----l~r~VvKVWFqNrR~k~kk 136 (159)
-.+|+-|.+.|.-++...| ..-.+++++.++. ++.++|++.+.+=|.|+..
T Consensus 147 ~~Lt~~E~~il~~l~~~~~------~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~~ 202 (221)
T PRK15479 147 LALTPREQALLTVLMYRRT------RPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQG 202 (221)
T ss_pred EecCHHHHHHHHHHHhCCC------CcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcCC
Confidence 4699999999999985532 2335777887775 9999999999999988863
No 245
>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=38.13 E-value=41 Score=21.63 Aligned_cols=33 Identities=21% Similarity=0.276 Sum_probs=24.0
Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcc
Q 044959 83 TEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 83 T~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
|.|||++|-+-.- +-+.+.+|+++..+-|.|+-
T Consensus 12 ~~e~K~~l~~~it--------------~~~~~~lg~~~~~i~V~i~E 44 (60)
T PF01361_consen 12 TAEQKRELAEAIT--------------DAVVEVLGIPPERISVVIEE 44 (60)
T ss_dssp -HHHHHHHHHHHH--------------HHHHHHHTS-GGGEEEEEEE
T ss_pred CHHHHHHHHHHHH--------------HHHHHHhCcCCCeEEEEEEE
Confidence 8899988776543 34778899999999888764
No 246
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=37.91 E-value=31 Score=35.06 Aligned_cols=64 Identities=14% Similarity=0.287 Sum_probs=45.9
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCCC
Q 044959 72 NYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRV 139 (159)
Q Consensus 72 ~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~ 139 (159)
+.++-+-|+....++-..|...++-. --+...+---.+.++.....|+.||+|+|+.+-++...
T Consensus 623 g~~p~kv~sp~k~~dq~ql~~a~elq----~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl 686 (1007)
T KOG3623|consen 623 GERPVKVRSPIKEEDQQQLKQAYELQ----ASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPL 686 (1007)
T ss_pred CCCCccccCCCCccchhhhHhhhhcc----cCccCcccchhhhhccCCCcchhhcccCCCCCCCCCcc
Confidence 44566777888888777777766553 12444444455666899999999999999999887543
No 247
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=37.84 E-value=70 Score=21.94 Aligned_cols=31 Identities=13% Similarity=0.112 Sum_probs=20.0
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVG 117 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiG 117 (159)
.|+.++++.|...++. ..+++..+.+|+-||
T Consensus 66 ~~~~~e~~~l~~~l~~------~~~~~~~~~~~~~~~ 96 (96)
T smart00529 66 GVDEEEVHEEAERLEH------VLSDELEDRLDRFLG 96 (96)
T ss_pred CCCHHHHHHHHHHHHc------cCCHHHHHHHHHHhC
Confidence 4666666666665544 466777777776664
No 248
>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=37.76 E-value=13 Score=25.06 Aligned_cols=25 Identities=20% Similarity=0.271 Sum_probs=18.2
Q ss_pred CHHHHHHHHHHhCCCccchhhhhcc
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
.....+++|..+||+..-|.-.++-
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHh
Confidence 3567788999999999999877764
No 249
>COG3040 Blc Bacterial lipocalin [Cell envelope biogenesis, outer membrane]
Probab=37.75 E-value=35 Score=28.53 Aligned_cols=26 Identities=23% Similarity=0.459 Sum_probs=23.2
Q ss_pred CCcc-CCHHHHHHHHHHHHHhCCCCCC
Q 044959 78 KRTK-ITEEQKSKMRRFADKLGWKPQR 103 (159)
Q Consensus 78 ~RTk-FT~eQkekLe~ffek~GW~iq~ 103 (159)
.||. .+++++++|.+.+..+||-+..
T Consensus 139 sRtP~~s~~~~~~ml~~ak~~Gfdv~~ 165 (174)
T COG3040 139 SRTPTLSQETLKRMLEIAKRRGFDVSK 165 (174)
T ss_pred ecCCCCCHHHHHHHHHHHHHcCCCcce
Confidence 4888 9999999999999999987654
No 250
>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=37.37 E-value=9.9 Score=31.17 Aligned_cols=47 Identities=11% Similarity=0.075 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+++.|++.+.-.+. ..-...++|..+||+..+|+.+++.-+.++++
T Consensus 205 ~L~~~~r~ii~l~~~---------~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFE---------ENLSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHc---------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 445555555554331 22246899999999999999999876665543
No 251
>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=36.64 E-value=15 Score=22.47 Aligned_cols=31 Identities=23% Similarity=0.391 Sum_probs=21.0
Q ss_pred CccccCccccccCCCCCCcccccccccccccccccc
Q 044959 15 RYAYDGCGEFLKAGKDGTKEAFHCAACGCHRSFHRK 50 (159)
Q Consensus 15 ~~~~DgC~ef~~~~~~~~~~~l~CaaCgcHRnFHr~ 50 (159)
...=+-|+++|+.. ...+++|..| ..+.|.+
T Consensus 11 ~~~C~~C~~~i~~~---~~~~~~C~~C--~~~~H~~ 41 (50)
T cd00029 11 PTFCDVCRKSIWGL---FKQGLRCSWC--KVKCHKK 41 (50)
T ss_pred CCChhhcchhhhcc---ccceeEcCCC--CCchhhh
Confidence 33457799999864 3578999888 4455543
No 252
>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=36.37 E-value=21 Score=25.69 Aligned_cols=21 Identities=14% Similarity=0.441 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|..+||+.++|+.|-..
T Consensus 3 i~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 678999999999999999976
No 253
>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=36.26 E-value=19 Score=21.62 Aligned_cols=23 Identities=13% Similarity=0.302 Sum_probs=17.1
Q ss_pred ccccCccccccCCCCCCcccccccccc
Q 044959 16 YAYDGCGEFLKAGKDGTKEAFHCAACG 42 (159)
Q Consensus 16 ~~~DgC~ef~~~~~~~~~~~l~CaaCg 42 (159)
..=+.|+++|+... .+++|+.|+
T Consensus 12 ~~C~~C~~~i~~~~----~~~~C~~C~ 34 (49)
T smart00109 12 TKCCVCRKSIWGSF----QGLRCSWCK 34 (49)
T ss_pred CCccccccccCcCC----CCcCCCCCC
Confidence 34588999998643 479999874
No 254
>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=36.18 E-value=16 Score=30.78 Aligned_cols=33 Identities=15% Similarity=0.210 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 104 HDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 104 ~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
...-..+++|..+||+..+|+.+++.-+.++++
T Consensus 240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~ 272 (285)
T TIGR02394 240 YEPATLEEVAAEVGLTRERVRQIQVEALKKLRR 272 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 444567899999999999999999988877765
No 255
>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=36.12 E-value=21 Score=25.26 Aligned_cols=21 Identities=5% Similarity=0.150 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|..+||+..+|+.|...
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 678999999999999999874
No 256
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=36.05 E-value=11 Score=25.51 Aligned_cols=23 Identities=13% Similarity=0.423 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCccchh-hhhccc
Q 044959 108 EVGKFCGEVGITRKMFK-VWLNNN 130 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvK-VWFqNr 130 (159)
...+||+.+||+...|. .|...+
T Consensus 14 ~~~~lA~~lgis~st~s~~~~~r~ 37 (66)
T PF07022_consen 14 SDKELAERLGISKSTLSNNWKKRG 37 (66)
T ss_dssp SCHHHHCCTT--HHHHH-HHHHSS
T ss_pred CHHHHHHHhCcCHHHhhHHHHhCC
Confidence 44689999999999999 998643
No 257
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=36.00 E-value=24 Score=26.16 Aligned_cols=46 Identities=13% Similarity=0.159 Sum_probs=38.4
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..+|+.+.+.|.-+++-. ..++++..++++.++|++-..+=|.|+.
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 459999998888887432 3678899999999999999999888875
No 258
>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=35.96 E-value=28 Score=27.47 Aligned_cols=17 Identities=24% Similarity=0.176 Sum_probs=12.4
Q ss_pred CCccCCHHHHHHHHHHH
Q 044959 78 KRTKITEEQKSKMRRFA 94 (159)
Q Consensus 78 ~RTkFT~eQkekLe~ff 94 (159)
-++.||+.|+++|..+-
T Consensus 137 c~~~FT~gQ~~RM~~~l 153 (154)
T PF05572_consen 137 CMNMFTPGQVARMRAVL 153 (154)
T ss_dssp G--B-BHHHHHHHHHHH
T ss_pred cccccCHHHHHHHHHHh
Confidence 78999999999998764
No 259
>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=35.57 E-value=22 Score=25.63 Aligned_cols=23 Identities=13% Similarity=0.250 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCccchhhhhcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR 131 (159)
+.++|+.+||+..+|+.|..+--
T Consensus 3 i~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 57899999999999999987544
No 260
>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=35.47 E-value=21 Score=25.28 Aligned_cols=19 Identities=16% Similarity=0.601 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCccchhhhh
Q 044959 109 VGKFCGEVGITRKMFKVWL 127 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWF 127 (159)
+.++|+.+||+.++|+.|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5789999999999999993
No 261
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=35.44 E-value=28 Score=26.23 Aligned_cols=53 Identities=17% Similarity=0.207 Sum_probs=42.5
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHH--HHHHHHhCCCccchhhhhccccCCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEV--GKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r--~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+|..+.+.|.-+++..| +-.+.+.+ +.++.++.++.++|+++..+=|.|+..
T Consensus 156 ~Lt~~E~~~l~~l~~~~~---~v~sr~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~~ 210 (232)
T PRK10955 156 ELTGTEFTLLYLLAQHLG---QVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPD 210 (232)
T ss_pred cCCHHHHHHHHHHHhCCC---ceEcHHHHHHHHhCCCCCCCCcCHHHHHHHHHHhccc
Confidence 699999999999997764 33444443 457788899999999999999999964
No 262
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=35.28 E-value=38 Score=26.51 Aligned_cols=30 Identities=7% Similarity=-0.003 Sum_probs=24.7
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|++..+|+++++--|.++++
T Consensus 145 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (188)
T PRK12517 145 FSGEEIAEILDLNKNTVMTRLFRARNQLKE 174 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356899999999999999999876666554
No 263
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=35.17 E-value=40 Score=24.80 Aligned_cols=30 Identities=13% Similarity=0.193 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhccccC
Q 044959 103 RHDEEEVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 103 ~~d~~~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
........+|+++|||++..|..=-.+++.
T Consensus 16 ~V~~~~Wk~laR~LGLse~~I~~i~~~~~~ 45 (96)
T cd08315 16 EVPFDSWNRLMRQLGLSENEIDVAKANERV 45 (96)
T ss_pred HCCHHHHHHHHHHcCCCHHHHHHHHHHCCC
Confidence 345678899999999999999888777776
No 264
>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=35.16 E-value=32 Score=21.70 Aligned_cols=12 Identities=25% Similarity=0.315 Sum_probs=11.2
Q ss_pred cCCHHHHHHHHH
Q 044959 81 KITEEQKSKMRR 92 (159)
Q Consensus 81 kFT~eQkekLe~ 92 (159)
.||++|++.|+.
T Consensus 2 ~FT~~Ql~~L~~ 13 (37)
T PF08880_consen 2 PFTPAQLQELRA 13 (37)
T ss_pred CCCHHHHHHHHH
Confidence 699999999998
No 265
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=34.94 E-value=45 Score=23.77 Aligned_cols=34 Identities=15% Similarity=0.158 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcc
Q 044959 82 ITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 82 FT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
.|.|||++|-+-.-+ .+++.+|.++.+|.|.|+-
T Consensus 13 ~s~EqK~~La~~iT~--------------a~~~~lg~~~e~v~V~I~e 46 (76)
T PRK01271 13 LDEEQKAALAADITD--------------VIIRHLNSKDSSISIALQQ 46 (76)
T ss_pred CCHHHHHHHHHHHHH--------------HHHHHhCcCcceEEEEEEE
Confidence 479999988765433 4788899999999988763
No 266
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=34.89 E-value=21 Score=21.88 Aligned_cols=17 Identities=18% Similarity=0.306 Sum_probs=12.9
Q ss_pred HHHHHHHHhCCCccchh
Q 044959 108 EVGKFCGEVGITRKMFK 124 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvK 124 (159)
.++++|+.+|+++.+|-
T Consensus 4 tr~diA~~lG~t~ETVS 20 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVS 20 (32)
T ss_dssp -HHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHhCCcHHHHH
Confidence 47899999999998763
No 267
>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=34.41 E-value=23 Score=24.96 Aligned_cols=23 Identities=9% Similarity=0.371 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCccchhhhhcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR 131 (159)
+.++|+.+||++.+|+.|-...-
T Consensus 3 ~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 57899999999999999987544
No 268
>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=34.22 E-value=23 Score=25.78 Aligned_cols=35 Identities=14% Similarity=0.204 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCCCCCCcccc
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEKCR 144 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~~~~~ 144 (159)
.+.++|+.+||+.++|+.|-.. --..+.+.++.-+
T Consensus 3 ~i~eva~~~gvs~~tlR~ye~~--Gll~~~r~~~g~R 37 (102)
T cd04789 3 TISELAEKAGISRSTLLYYEKL--GLITGTRNANGYR 37 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC--CCCCCCcCCCCCe
Confidence 3678999999999999999875 3334445554443
No 269
>PRK13870 transcriptional regulator TraR; Provisional
Probab=34.21 E-value=25 Score=29.19 Aligned_cols=47 Identities=13% Similarity=0.142 Sum_probs=33.8
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
..||+-++|.|.=.++= ..-.|+|.-|||++++|+.=+.|-+.|+.-
T Consensus 172 ~~LT~RE~E~L~W~A~G----------KT~~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 172 AWLDPKEATYLRWIAVG----------KTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred CCCCHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 34555555555544411 234578999999999999999999999864
No 270
>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=34.10 E-value=38 Score=25.69 Aligned_cols=40 Identities=18% Similarity=0.346 Sum_probs=27.9
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcc
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
-+|..|++.|+-++ .++--..++|..+||++..|--|++-
T Consensus 17 LLT~kQ~~~l~lyy---------~eDlSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 17 LLTEKQREILELYY---------EEDLSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp GS-HHHHHHHHHHC---------TS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HCCHHHHHHHHHHH---------ccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 47888988887654 45567889999999999998877653
No 271
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=33.48 E-value=13 Score=30.91 Aligned_cols=30 Identities=7% Similarity=-0.007 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-..+++|..+|++..+|+..++.-+.++++
T Consensus 229 ~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 258 (268)
T PRK06288 229 LTLKEIGKVLGVTESRISQLHTKAVLQLRA 258 (268)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 357899999999999999998877666554
No 272
>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=33.37 E-value=60 Score=24.16 Aligned_cols=48 Identities=10% Similarity=0.160 Sum_probs=34.0
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
++. .+.|.++-+. +||... .|+|..+||+..+|-..++--....||..
T Consensus 56 Kid---~~~L~~~v~~------~pd~tl-~Ela~~l~Vs~~ti~~~Lkrlg~t~KK~~ 103 (119)
T PF01710_consen 56 KID---RDELKALVEE------NPDATL-RELAERLGVSPSTIWRALKRLGITRKKKT 103 (119)
T ss_pred ccc---HHHHHHHHHH------CCCcCH-HHHHHHcCCCHHHHHHHHHHcCchhccCc
Confidence 664 3456666554 566544 47899999999999888887777777644
No 273
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=33.28 E-value=17 Score=35.82 Aligned_cols=37 Identities=22% Similarity=0.338 Sum_probs=27.4
Q ss_pred CccccCccccccCCCCCCccccccccc-ccccccccccc
Q 044959 15 RYAYDGCGEFLKAGKDGTKEAFHCAAC-GCHRSFHRKEL 52 (159)
Q Consensus 15 ~~~~DgC~ef~~~~~~~~~~~l~CaaC-gcHRnFHr~~~ 52 (159)
++.+| |+---|.-..-..++|.|.-| |||||++....
T Consensus 514 ~~c~d-c~~~n~~wAslnlg~l~cieCsgihr~lgt~lS 551 (749)
T KOG0705|consen 514 SHCVD-CGTPNPKWASLNLGVLMCIECSGIHRNLGTHLS 551 (749)
T ss_pred ceeee-cCCCCcccccccCCeEEEEEchhhhhhhhhhhh
Confidence 35666 766555545667889999988 89999997654
No 274
>PF05121 GvpK: Gas vesicle protein K ; InterPro: IPR007805 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in liquid to access oxygen and/or light. Proteins containing this domain are involved in the formation of gas vesicles [].; GO: 0031412 gas vesicle organization
Probab=33.19 E-value=89 Score=23.46 Aligned_cols=36 Identities=28% Similarity=0.469 Sum_probs=30.1
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccch
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMF 123 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~Vv 123 (159)
-..|.+|.++|-.-..++ +..+.++|...||+..-+
T Consensus 40 G~Lse~qiErlG~tLm~L--------e~~~~~l~~~~gl~~~dL 75 (88)
T PF05121_consen 40 GSLSEEQIERLGETLMKL--------EEAMEELCERFGLTPEDL 75 (88)
T ss_pred CCCCHHHHHHHHHHHHHH--------HHHHHHHHHHcCCCHHHh
Confidence 468999999998877665 778999999999987644
No 275
>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=32.79 E-value=25 Score=25.81 Aligned_cols=23 Identities=13% Similarity=0.485 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCccchhhhhcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR 131 (159)
+.++|+.+||+.++|+.|-..--
T Consensus 3 i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 67899999999999999987643
No 276
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=32.77 E-value=30 Score=25.82 Aligned_cols=51 Identities=6% Similarity=-0.077 Sum_probs=41.2
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCC-----ccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGIT-----RKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~-----r~VvKVWFqNrR~k~kk 136 (159)
..+|+-+.+.|.-+++.. ...-.++++++.+..+ .++|++...+=|.|++.
T Consensus 153 ~~Lt~~E~~il~~l~~~~------~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (228)
T PRK11083 153 LTLTRYEFLLLKTLLLSP------GRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA 208 (228)
T ss_pred eecCHHHHHHHHHHHhCC------CceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence 469999999999999652 2234678888888886 88999999999999864
No 277
>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=32.35 E-value=26 Score=25.46 Aligned_cols=21 Identities=14% Similarity=0.385 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|..+||+.++|+.|..-
T Consensus 3 I~eva~~~gvs~~tlR~Ye~~ 23 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLRE 23 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 678999999999999999873
No 278
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=32.04 E-value=41 Score=26.51 Aligned_cols=29 Identities=3% Similarity=0.204 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhccccC
Q 044959 104 HDEEEVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 104 ~d~~~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
.+...+.++|...||++..|-.-|.|+..
T Consensus 36 y~~~s~~dIA~~aGvs~gtiY~hF~sKe~ 64 (212)
T PRK15008 36 FHGTRLEQIAELAGVSKTNLLYYFPSKEA 64 (212)
T ss_pred cccCCHHHHHHHhCcCHHHHHHHCCCHHH
Confidence 56678999999999999999999988754
No 279
>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=32.00 E-value=37 Score=24.40 Aligned_cols=33 Identities=15% Similarity=0.149 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 104 HDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 104 ~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+.-.+.++|..|||++..|--|+..++.-.+.
T Consensus 22 ~~~~ti~~~AK~L~i~~~~l~~~Lr~~g~l~~~ 54 (111)
T PF03374_consen 22 DGLYTIREAAKLLGIGRNKLFQWLREKGWLYRR 54 (111)
T ss_pred CCCccHHHHHHHhCCCHHHHHHHHHhCCceEEC
Confidence 456789999999999999999999998887773
No 280
>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=31.94 E-value=27 Score=25.55 Aligned_cols=23 Identities=13% Similarity=0.265 Sum_probs=20.1
Q ss_pred HHHHHHHhCCCccchhhhhcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR 131 (159)
+.++|+.+||+.++|+.|-...-
T Consensus 3 i~eva~~~gis~~tlR~ye~~GL 25 (108)
T cd01107 3 IGEFAKLSNLSIKALRYYDKIGL 25 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 67899999999999999988633
No 281
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=31.77 E-value=27 Score=25.39 Aligned_cols=33 Identities=12% Similarity=0.236 Sum_probs=24.2
Q ss_pred HHHHHHHhCCCccchhhhhccccCCCCCCCCCccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEKC 143 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~~~~ 143 (159)
+.++|+.+||+.++|+.|-.- --..+.+.++.-
T Consensus 4 i~eva~~~gvs~~tLR~ye~~--Gll~~~r~~~g~ 36 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYESI--GLIPSARSEANY 36 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC--CCCCCCCCCCCC
Confidence 678999999999999999874 333444544443
No 282
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=31.77 E-value=59 Score=21.28 Aligned_cols=34 Identities=18% Similarity=0.264 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcc
Q 044959 82 ITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 82 FT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
.|.|||++|-+-. -+.++..+|+++..|.|-|..
T Consensus 12 rs~EqK~~L~~~i--------------t~a~~~~~~~p~~~v~V~i~e 45 (60)
T PRK02289 12 RSQEQKNALAREV--------------TEVVSRIAKAPKEAIHVFIND 45 (60)
T ss_pred CCHHHHHHHHHHH--------------HHHHHHHhCcCcceEEEEEEE
Confidence 3799999887644 345788899999998887754
No 283
>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=31.76 E-value=63 Score=24.98 Aligned_cols=34 Identities=15% Similarity=0.227 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchh
Q 044959 87 KSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFK 124 (159)
Q Consensus 87 kekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvK 124 (159)
+..|...-+..| |.+++.++++|..+||+...|.
T Consensus 16 l~~L~~~Q~~~g----~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 16 LPILHEVQEEYG----YIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHS----S--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHcC----CCCHHHHHHHHHHHCCCHHHHH
Confidence 455666667765 8999999999999999998765
No 284
>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=31.73 E-value=27 Score=25.55 Aligned_cols=21 Identities=5% Similarity=0.335 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|..+||+.++|+.|-..
T Consensus 3 i~e~a~~~gvs~~tlr~ye~~ 23 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEKE 23 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 678999999999999999764
No 285
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=31.72 E-value=1.2e+02 Score=21.21 Aligned_cols=47 Identities=15% Similarity=0.180 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHHHhCC-CCCCCCHHHHHHHHHHhCCCccchhhhhc
Q 044959 82 ITEEQKSKMRRFADKLGW-KPQRHDEEEVGKFCGEVGITRKMFKVWLN 128 (159)
Q Consensus 82 FT~eQkekLe~ffek~GW-~iq~~d~~~r~efc~eiGl~r~VvKVWFq 128 (159)
+|.+|+..+...|...-= .-.+.+..++.++-..+|++...++-+|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 688999999987766410 01246678888888889999888877774
No 286
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=31.50 E-value=79 Score=23.37 Aligned_cols=58 Identities=24% Similarity=0.501 Sum_probs=41.0
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCC---------CCCCCCCcccccc
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRR---------PVPVRVPEKCRAA 146 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k---------~kk~~~~~~~~~~ 146 (159)
.+|+.....|-.---..|| -+.+.|.+.||++.++.-|..--|+- .++++.|+.+...
T Consensus 8 ~Lt~~gR~~lv~~vv~~g~--------~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~~t~~~ 74 (85)
T PF13011_consen 8 RLTPRGRLRLVRRVVEQGW--------PVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSRPHRSPRRTPPE 74 (85)
T ss_pred CCCHHHHHHHHHHHHHcCC--------cHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCCCCCCCccCCHH
Confidence 4678888887775544444 46789999999999999998654432 3456666666543
No 287
>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=31.49 E-value=44 Score=26.86 Aligned_cols=36 Identities=14% Similarity=0.310 Sum_probs=26.7
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhC-CCccchhh
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVG-ITRKMFKV 125 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiG-l~r~VvKV 125 (159)
..|.|+++.|.++... .. ...++|.+|| |++..|--
T Consensus 2 ~Wtde~~~~L~~lw~~------G~---SasqIA~~lg~vsRnAViG 38 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE------GL---SASQIARQLGGVSRNAVIG 38 (162)
T ss_pred CCCHHHHHHHHHHHHc------CC---CHHHHHHHhCCcchhhhhh
Confidence 3689999999997744 23 4567888999 89886653
No 288
>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=30.95 E-value=49 Score=24.22 Aligned_cols=17 Identities=12% Similarity=0.112 Sum_probs=14.8
Q ss_pred HHHHHHHHhCCCccchh
Q 044959 108 EVGKFCGEVGITRKMFK 124 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvK 124 (159)
..+++|..+|++..+|+
T Consensus 125 s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 125 KEIDIAKKLHISRQSVY 141 (142)
T ss_pred CHHHHHHHHCcCHHhhc
Confidence 56789999999999886
No 289
>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=30.60 E-value=74 Score=22.86 Aligned_cols=44 Identities=11% Similarity=0.283 Sum_probs=31.2
Q ss_pred ccCCHHHHHHHHHHHHH-hCCCCCCCCHHHHHHHHHHhCCCccchh
Q 044959 80 TKITEEQKSKMRRFADK-LGWKPQRHDEEEVGKFCGEVGITRKMFK 124 (159)
Q Consensus 80 TkFT~eQkekLe~ffek-~GW~iq~~d~~~r~efc~eiGl~r~VvK 124 (159)
..+++.|...|...+++ .||.. ..+.-...+||+.+|+++.+|.
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~-~~~~is~~eLa~~~g~sr~tVs 65 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNK-KQDRVTATVIAELTGLSRTHVS 65 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccc-cCCccCHHHHHHHHCcCHHHHH
Confidence 34677888888887763 36663 2344457799999999998764
No 290
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=30.40 E-value=29 Score=25.15 Aligned_cols=22 Identities=14% Similarity=0.220 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCccchhhhhccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNr 130 (159)
+.++|+.+||+..+|+.|...-
T Consensus 4 i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 5789999999999999998754
No 291
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=30.39 E-value=55 Score=25.99 Aligned_cols=30 Identities=17% Similarity=0.370 Sum_probs=25.8
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
...+.++++.+||+..+|+.|..--|--..
T Consensus 46 ~ati~eV~e~tgVs~~~I~~~IreGRL~~~ 75 (137)
T TIGR03826 46 QATVSEIVEETGVSEKLILKFIREGRLQLK 75 (137)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHcCCeecc
Confidence 378899999999999999999987776554
No 292
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=30.29 E-value=47 Score=24.03 Aligned_cols=44 Identities=11% Similarity=0.127 Sum_probs=30.3
Q ss_pred CCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccc
Q 044959 76 KTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 76 KR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNr 130 (159)
++..-.++..++..+.... | . ...+||..+|++..+|.-|....
T Consensus 59 ~~~~~~~~~~~i~~~r~~~---g-----l---tq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 59 RKVDGLLTPPEIRRIRKKL---G-----L---SQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred HHccCCcCHHHHHHHHHHc---C-----C---CHHHHHHHhCCCHHHHHHHHCCC
Confidence 4455566777666554433 2 1 34579999999999999997655
No 293
>PRK09191 two-component response regulator; Provisional
Probab=29.96 E-value=37 Score=26.70 Aligned_cols=33 Identities=12% Similarity=0.065 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
.-..+++|..+|++..+||+-++--+.+++...
T Consensus 104 ~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~ 136 (261)
T PRK09191 104 GFSVEEAAEILGVDPAEAEALLDDARAEIARQV 136 (261)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccC
Confidence 335788999999999999999998777776543
No 294
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=29.91 E-value=30 Score=24.89 Aligned_cols=21 Identities=19% Similarity=0.349 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|+.+||+..+|+.|-..
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDKI 23 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 678999999999999999764
No 295
>cd00131 PAX Paired Box domain
Probab=29.87 E-value=42 Score=25.62 Aligned_cols=42 Identities=10% Similarity=0.189 Sum_probs=33.5
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
.+|.+..+++...++. | ....++|..+||++.+|.-|.+--+
T Consensus 17 ~lS~d~R~rIv~~~~~-G--------~s~~~iA~~~~Vs~~tV~r~i~r~~ 58 (128)
T cd00131 17 PLPDSIRQRIVELAQS-G--------IRPCDISRQLRVSHGCVSKILNRYY 58 (128)
T ss_pred cCCHHHHHHHHHHHHc-C--------CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5788999999887753 3 2456779999999999999998654
No 296
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=29.79 E-value=21 Score=28.06 Aligned_cols=39 Identities=28% Similarity=0.404 Sum_probs=18.5
Q ss_pred HHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 91 RRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 91 e~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
+..|+++| +.+-|.+.+.+.|.+.|+++..|..|-....
T Consensus 17 ~~LA~~Lg--~~~~d~~ii~~~a~~~~~~~~~~~~~~e~~~ 55 (179)
T PF13189_consen 17 ERLAEKLG--YPYYDREIIEEAAKESGISEEEFEEFDEKKP 55 (179)
T ss_dssp HHHHHHCT----EE-HHHHHHCT------------SS-HHH
T ss_pred HHHHHHcC--CccCCHHHHHHHHHHccCCHHHHHHHhcccc
Confidence 45889997 4568889999999999999999988776544
No 297
>PRK08359 transcription factor; Validated
Probab=29.79 E-value=57 Score=26.94 Aligned_cols=50 Identities=10% Similarity=0.181 Sum_probs=32.2
Q ss_pred CCCCccCCHHHHHHHHHHHHHhCCCCCCCC---HHHHHHHHHHhCCCccchhhhhccccC
Q 044959 76 KTKRTKITEEQKSKMRRFADKLGWKPQRHD---EEEVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 76 KR~RTkFT~eQkekLe~ffek~GW~iq~~d---~~~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
+|.|..| -.+.+++|.+++ ...- .-..++||..|||++.+|.-|=.+.+.
T Consensus 72 ~~~~d~~---~~elv~dy~~rI----keaRe~kglSQeeLA~~lgvs~stI~~iE~G~~~ 124 (176)
T PRK08359 72 RRERPLY---TEDIVEDYAERV----YEAIQKSGLSYEELSHEVGLSVNDLRRIAHGEYE 124 (176)
T ss_pred CCcccch---HHHHHHHHHHHH----HHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCcC
Confidence 3445557 225556666554 1110 124678999999999999998877653
No 298
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=29.78 E-value=29 Score=26.83 Aligned_cols=23 Identities=13% Similarity=0.453 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCCccchhhhhccc
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNr 130 (159)
.+.++|..+||+.++|+.|-+..
T Consensus 3 sI~eVA~~~GVs~~TLR~wE~~G 25 (120)
T cd04767 3 PIGVVAELLNIHPETLRIWERHG 25 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCC
Confidence 36789999999999999999863
No 299
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=29.38 E-value=86 Score=24.33 Aligned_cols=35 Identities=11% Similarity=0.088 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchh
Q 044959 86 QKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFK 124 (159)
Q Consensus 86 QkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvK 124 (159)
-+..|...-+..| |.+.+.++.+|+.+||+...|.
T Consensus 18 li~~L~~vQ~~~G----~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 18 IMPALMIAQEQKG----WVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHhC----CCCHHHHHHHHHHhCcCHHHHH
Confidence 3455555666665 7999999999999999985543
No 300
>PRK04140 hypothetical protein; Provisional
Probab=29.24 E-value=67 Score=28.65 Aligned_cols=37 Identities=22% Similarity=0.519 Sum_probs=24.6
Q ss_pred HHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccC
Q 044959 88 SKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 88 ekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
+.|..+-++.||. ..+||+.+||++.+|.-|-++.+.
T Consensus 129 erLk~lRe~~GlS--------q~eLA~~lGVSr~tIskyE~G~~~ 165 (317)
T PRK04140 129 DVLREAREELGLS--------LGELASELGVSRRTISKYENGGMN 165 (317)
T ss_pred HHHHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 4444455555544 467888888888888888876543
No 301
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=29.22 E-value=31 Score=24.74 Aligned_cols=34 Identities=15% Similarity=0.278 Sum_probs=24.1
Q ss_pred HHHHHHHhCCCccchhhhhccccCCCCC-CCCCcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRRRPVP-VRVPEKCR 144 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~k~kk-~~~~~~~~ 144 (159)
+.++|+.+||+.++|+.|-.. --..+ .+.++.-+
T Consensus 3 i~eva~~~gvs~~tlR~ye~~--Gll~p~~r~~~gyR 37 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDHI--GLLSPSQRTEGGHR 37 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC--CCCCCCccCCCCce
Confidence 578999999999999999863 34433 24444433
No 302
>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=29.04 E-value=80 Score=21.85 Aligned_cols=44 Identities=9% Similarity=0.104 Sum_probs=31.8
Q ss_pred CCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhh
Q 044959 76 KTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKV 125 (159)
Q Consensus 76 KR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKV 125 (159)
+.....++.+++.. ..+|.-...+...+.++|+.+|++-+.+++
T Consensus 17 ~~~g~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~gl~~~~~~~ 60 (122)
T cd02259 17 RYFGIPVRRDVLLN------AQQRRQQGLSLADLVSLANKLGLTAQGVKL 60 (122)
T ss_pred HHcCCCCCHHHHHH------HHhhccCCCCHHHHHHHHHHcCCeeeEEEc
Confidence 34456677887732 233444568899999999999999888764
No 303
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=28.87 E-value=41 Score=21.28 Aligned_cols=31 Identities=19% Similarity=0.659 Sum_probs=16.4
Q ss_pred CccccccCCCCCCcccccccccc------cccccccc
Q 044959 20 GCGEFLKAGKDGTKEAFHCAACG------CHRSFHRK 50 (159)
Q Consensus 20 gC~ef~~~~~~~~~~~l~CaaCg------cHRnFHr~ 50 (159)
+|+.++............|.+|+ |...+|..
T Consensus 25 ~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~ 61 (64)
T PF01485_consen 25 DCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEG 61 (64)
T ss_dssp ST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTT
T ss_pred CCcccEEecCCCCCCeeECCCCCCcCccccCcccCCC
Confidence 68888876443333248899886 66667653
No 304
>PRK00215 LexA repressor; Validated
Probab=28.86 E-value=45 Score=26.46 Aligned_cols=45 Identities=11% Similarity=0.198 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCC-Cccchhhhhcc
Q 044959 82 ITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGI-TRKMFKVWLNN 129 (159)
Q Consensus 82 FT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl-~r~VvKVWFqN 129 (159)
+|+.|.+.|+-..+.. .+......+.+||..+|+ ++.++..+++-
T Consensus 2 lt~~q~~il~~i~~~~---~~~~~~~s~~ela~~~~~~~~~tv~~~l~~ 47 (205)
T PRK00215 2 LTKRQQEILDFIRDHI---EETGYPPSRREIADALGLRSPSAVHEHLKA 47 (205)
T ss_pred CCHHHHHHHHHHHHHH---HHhCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 5889999888776431 011222358899999999 88888777554
No 305
>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=28.66 E-value=67 Score=27.34 Aligned_cols=42 Identities=12% Similarity=0.239 Sum_probs=34.5
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhh
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVW 126 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVW 126 (159)
..++|.++++.+...... .|+.-.++.||+..+|++.+|+-=
T Consensus 8 ~k~Ls~~~~~~ir~L~~~------~p~~~t~~~Lae~F~vspe~irrI 49 (225)
T PF06413_consen 8 PKKLSREAMEQIRYLHKE------DPEEWTVERLAESFKVSPEAIRRI 49 (225)
T ss_pred CCCCCHHHHHHHHHHHHh------CccccCHHHHHhhCCCCHHHHHHH
Confidence 446899999998887654 677788999999999999988743
No 306
>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=28.44 E-value=89 Score=21.90 Aligned_cols=44 Identities=14% Similarity=0.140 Sum_probs=33.4
Q ss_pred CCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhh
Q 044959 76 KTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKV 125 (159)
Q Consensus 76 KR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKV 125 (159)
+.+...++.+++.. ..+|..+..+...+.++++.+||+-+.+++
T Consensus 22 ~~~~~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~gl~~~~~~~ 65 (126)
T cd02425 22 NYFGYKVSLNELRE------KYELGRDGLSLSYLKQLLEEYGFKCKVYKI 65 (126)
T ss_pred HHhCCCCCHHHHHH------hccCCCCCcCHHHHHHHHHHCCCcceEEEE
Confidence 34556677777653 235666778999999999999999988875
No 307
>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=28.43 E-value=41 Score=22.73 Aligned_cols=16 Identities=19% Similarity=0.418 Sum_probs=7.7
Q ss_pred CCHHHHHHHHHHhCCC
Q 044959 104 HDEEEVGKFCGEVGIT 119 (159)
Q Consensus 104 ~d~~~r~efc~eiGl~ 119 (159)
.+.......|.++||+
T Consensus 27 v~~T~LKr~CR~~GI~ 42 (52)
T PF02042_consen 27 VSVTTLKRRCRRLGIP 42 (52)
T ss_pred CCHHHHHHHHHHcCCC
Confidence 3444445555555543
No 308
>cd02421 Peptidase_C39_likeD 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 not conserved in this sub-family.
Probab=28.31 E-value=73 Score=22.48 Aligned_cols=43 Identities=7% Similarity=0.088 Sum_probs=32.4
Q ss_pred CCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhh
Q 044959 77 TKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKV 125 (159)
Q Consensus 77 R~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKV 125 (159)
.+.-.++.+|+. ...||.....+...+.+.|+.+|++-+.+++
T Consensus 18 ~~g~~~~~~~l~------~~~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~ 60 (124)
T cd02421 18 QFGKPASRDSLV------AGLPLDDGRLSPALFPRAAARAGLSARVVRR 60 (124)
T ss_pred HhCCCCCHHHHH------hcCCCCCCCcCHHHHHHHHHHCCCcceeeeC
Confidence 344566777765 3456655668899999999999999988876
No 309
>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=28.17 E-value=1.5e+02 Score=18.71 Aligned_cols=38 Identities=24% Similarity=0.278 Sum_probs=21.9
Q ss_pred CHHHHHHHHHHHHHhCCCCCC-CCH----HHHHHHHHHhCCCccch
Q 044959 83 TEEQKSKMRRFADKLGWKPQR-HDE----EEVGKFCGEVGITRKMF 123 (159)
Q Consensus 83 T~eQkekLe~ffek~GW~iq~-~d~----~~r~efc~eiGl~r~Vv 123 (159)
|++++.++...+... +.. ++. .-++++|+.+||+..++
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 566666666533332 223 453 45678999999998764
No 310
>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=27.88 E-value=80 Score=19.76 Aligned_cols=34 Identities=18% Similarity=0.204 Sum_probs=25.5
Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccc
Q 044959 83 TEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 83 T~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNr 130 (159)
|.|||++|-+-. -+.++..+|+++..+-|.|+..
T Consensus 12 t~eqk~~l~~~i--------------~~~l~~~~g~~~~~v~V~i~e~ 45 (58)
T cd00491 12 TDEQKRELIERV--------------TEAVSEILGAPEATIVVIIDEM 45 (58)
T ss_pred CHHHHHHHHHHH--------------HHHHHHHhCcCcccEEEEEEEe
Confidence 588988876633 3457888999999888887653
No 311
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=27.84 E-value=33 Score=25.77 Aligned_cols=34 Identities=15% Similarity=0.298 Sum_probs=23.4
Q ss_pred HHHHHHHhCCCccchhhhhccccCCCC-CCCCCcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRRRPV-PVRVPEKCR 144 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~k~k-k~~~~~~~~ 144 (159)
+.+||..+||+.++|+.|-+ .--.+ +.+.++..+
T Consensus 2 I~e~a~~~gvs~~tlR~Ye~--~GLl~~~~r~~~g~R 36 (124)
T TIGR02051 2 IGELAKAAGVNVETIRYYER--KGLLPEPDRPEGGYR 36 (124)
T ss_pred HHHHHHHHCcCHHHHHHHHH--CCCCCCCccCCCCCE
Confidence 57899999999999999944 34443 234444443
No 312
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=27.84 E-value=54 Score=25.41 Aligned_cols=30 Identities=13% Similarity=0.206 Sum_probs=26.1
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhccccC
Q 044959 103 RHDEEEVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 103 ~~d~~~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
..+...++++|.+.||++..|--+|-|+-.
T Consensus 28 G~~~~t~~~Ia~~agvs~~tlY~~F~sKe~ 57 (215)
T PRK10668 28 GVSATSLADIAKAAGVTRGAIYWHFKNKSD 57 (215)
T ss_pred CcccCCHHHHHHHhCCChHHHHHHCCCHHH
Confidence 456778999999999999999999987654
No 313
>PF13223 DUF4031: Protein of unknown function (DUF4031)
Probab=27.74 E-value=46 Score=24.60 Aligned_cols=21 Identities=24% Similarity=0.710 Sum_probs=16.7
Q ss_pred CHHHHHHHHHHhCCCccchhhhhcc
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
+.+|...||..|||++ -|||.
T Consensus 22 t~~ELHafA~riGv~r----r~fq~ 42 (83)
T PF13223_consen 22 TLDELHAFAARIGVPR----RWFQR 42 (83)
T ss_pred CHHHHHHHHHHcCCCH----HHHcC
Confidence 3677788888899988 58887
No 314
>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=27.74 E-value=25 Score=21.87 Aligned_cols=36 Identities=8% Similarity=0.244 Sum_probs=26.7
Q ss_pred HHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccc
Q 044959 90 MRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 90 Le~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNr 130 (159)
-.+.+.+.| .+...+.++|+++||++..|---|.|+
T Consensus 5 a~~l~~~~G-----~~~~s~~~Ia~~~gvs~~~~y~~f~~k 40 (47)
T PF00440_consen 5 ALELFAEKG-----YEAVSIRDIARRAGVSKGSFYRYFPSK 40 (47)
T ss_dssp HHHHHHHHH-----TTTSSHHHHHHHHTSCHHHHHHHCSSH
T ss_pred HHHHHHHhC-----HHhCCHHHHHHHHccchhhHHHHcCCH
Confidence 344444543 455678899999999999998888764
No 315
>PF12763 EF-hand_4: Cytoskeletal-regulatory complex EF hand; PDB: 2QPT_A 2KSP_A 2KFG_A 2JQ6_A 2KFH_A 2KFF_A 1IQ3_A 3FIA_A 2KHN_A 2KGR_A ....
Probab=27.65 E-value=40 Score=25.20 Aligned_cols=46 Identities=20% Similarity=0.447 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchh-hh
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFK-VW 126 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvK-VW 126 (159)
++|++++++-..+|+.+.=.-.+.+..+..+|=..-||+..+++ ||
T Consensus 3 ~ls~~e~~~y~~~F~~l~~~~g~isg~~a~~~f~~S~L~~~~L~~IW 49 (104)
T PF12763_consen 3 KLSPEEKQKYDQIFQSLDPQDGKISGDQAREFFMKSGLPRDVLAQIW 49 (104)
T ss_dssp --SCCHHHHHHHHHHCTSSSTTEEEHHHHHHHHHHTTSSHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHhcCCCCCeEeHHHHHHHHHHcCCCHHHHHHHH
Confidence 57889999999999876411223557778888889999988886 77
No 316
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=27.53 E-value=95 Score=24.29 Aligned_cols=34 Identities=9% Similarity=0.178 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchh
Q 044959 87 KSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFK 124 (159)
Q Consensus 87 kekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvK 124 (159)
+..|...-+..| |.+.+.++.+|+.+||+...|-
T Consensus 25 l~~L~~vQ~~~g----~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 25 IPALKIVQEQRG----WVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHhC----CCCHHHHHHHHHHhCcCHHHHH
Confidence 444555556665 7999999999999999987653
No 317
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=27.20 E-value=85 Score=23.44 Aligned_cols=46 Identities=17% Similarity=0.362 Sum_probs=35.3
Q ss_pred CCccCCHHHHHHHHHHHHH-hCCCCCCCCHHHHHHHHHHhCCCccchh
Q 044959 78 KRTKITEEQKSKMRRFADK-LGWKPQRHDEEEVGKFCGEVGITRKMFK 124 (159)
Q Consensus 78 ~RTkFT~eQkekLe~ffek-~GW~iq~~d~~~r~efc~eiGl~r~VvK 124 (159)
-+..||.-|+..|.....+ -||. ++-|.-...+|+..+|+++..|.
T Consensus 26 ~~~dls~rq~ki~~ai~RkTyG~n-Kk~d~Is~sq~~e~tg~~~~~V~ 72 (100)
T PF04492_consen 26 LRADLSGRQLKILLAIIRKTYGWN-KKMDRISNSQIAEMTGLSRDHVS 72 (100)
T ss_pred HhccccHHHHHHHHHHHHHccCCC-CccceeeHHHHHHHHCcCHHHHH
Confidence 3567889999888886655 5776 55667778899999999887663
No 318
>PRK04841 transcriptional regulator MalT; Provisional
Probab=26.71 E-value=36 Score=32.15 Aligned_cols=46 Identities=11% Similarity=0.160 Sum_probs=39.0
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..+|+-+++.|.-+++-. .-+++|.+++|+..+||..+.|=..|++
T Consensus 837 ~~lt~~e~~v~~~~~~g~----------~~~~ia~~l~~s~~tv~~h~~~~~~kl~ 882 (903)
T PRK04841 837 SPLTQREWQVLGLIYSGY----------SNEQIAGELDVAATTIKTHIRNLYQKLG 882 (903)
T ss_pred CCCCHHHHHHHHHHHcCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 459999999998888543 4678999999999999999999777775
No 319
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=26.58 E-value=36 Score=26.30 Aligned_cols=35 Identities=14% Similarity=0.212 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCCCCCCcccc
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEKCR 144 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~~~~~ 144 (159)
.+.++|+.+||+..+|+.|-.--= ..+.|..+..+
T Consensus 3 ~I~EvA~~~Gvs~~tLRyYE~~GL--l~p~r~~~g~R 37 (139)
T cd01110 3 SVGEVAKRSGVAVSALHFYEQKGL--IASWRNAGNQR 37 (139)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCC--CCCCcCCCCCe
Confidence 367999999999999999987633 34445555443
No 320
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=26.54 E-value=91 Score=24.43 Aligned_cols=48 Identities=6% Similarity=0.144 Sum_probs=30.0
Q ss_pred CCCCccCCHHHHHHHHHH----HHHhCCCCCCCCHHHHHHHHHHhCCCccch
Q 044959 76 KTKRTKITEEQKSKMRRF----ADKLGWKPQRHDEEEVGKFCGEVGITRKMF 123 (159)
Q Consensus 76 KR~RTkFT~eQkekLe~f----fek~GW~iq~~d~~~r~efc~eiGl~r~Vv 123 (159)
.|.+..+|++++.++... .-+.--....|+...+..+|..+||+...|
T Consensus 15 ~R~~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~~l 66 (185)
T PRK09943 15 IRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEF 66 (185)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHH
Confidence 455667777776665421 111000124688999999999999996643
No 321
>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=26.53 E-value=23 Score=28.42 Aligned_cols=45 Identities=9% Similarity=0.114 Sum_probs=31.1
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRP 134 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~ 134 (159)
++++.|++.+.-.+ .+....+++|..+||++..|..+.+.-..++
T Consensus 183 ~L~~~e~~i~~~~~---------~~~~t~~eIA~~lgis~~~V~~~~~~al~~L 227 (231)
T TIGR02885 183 KLDERERQIIMLRY---------FKDKTQTEVANMLGISQVQVSRLEKKVLKKM 227 (231)
T ss_pred cCCHHHHHHHHHHH---------HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 55666666665543 1233689999999999999998876544443
No 322
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=26.48 E-value=78 Score=20.68 Aligned_cols=34 Identities=15% Similarity=0.249 Sum_probs=25.9
Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccc
Q 044959 83 TEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 83 T~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNr 130 (159)
|.|||++|-+-. -+.++..+|+++.-+-|.+...
T Consensus 13 t~eqk~~l~~~i--------------t~~l~~~lg~p~~~v~V~i~e~ 46 (64)
T PRK01964 13 PEEKIKNLIREV--------------TEAISATLDVPKERVRVIVNEV 46 (64)
T ss_pred CHHHHHHHHHHH--------------HHHHHHHhCcChhhEEEEEEEc
Confidence 789998887643 3457888999999888877643
No 323
>CHL00148 orf27 Ycf27; Reviewed
Probab=26.43 E-value=53 Score=24.91 Aligned_cols=51 Identities=18% Similarity=0.176 Sum_probs=40.1
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHh-------CCCccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEV-------GITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~ei-------Gl~r~VvKVWFqNrR~k~kk 136 (159)
..+|.-+.+.|.-+++..| ..-.+++++..| +++.++|+|...+=|.|+..
T Consensus 160 ~~Lt~~E~~il~~l~~~~~------~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~ 217 (240)
T CHL00148 160 IRLTGMEFSLLELLISKSG------EIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED 217 (240)
T ss_pred EEcCHHHHHHHHHHHHCCC------EEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence 4599999999988885422 234677788877 48999999999999999974
No 324
>COG1427 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=26.39 E-value=79 Score=27.67 Aligned_cols=50 Identities=12% Similarity=0.076 Sum_probs=38.8
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
+.+-+-++++|+.-... ++ .+.+++.|..+||++.+++-.|.|-|+.+..
T Consensus 179 ~~~~~~~~~~~~~~~~~------~~-~ei~~~~a~~lglp~~~~~eYy~~~~Y~l~~ 228 (252)
T COG1427 179 KPFYKRALLEFEETKAK------FP-AEILKEAAKRLGLPRSDVEEYYTNIRYSLGT 228 (252)
T ss_pred CCchhhhHHHHHHHHHh------hh-HHHHHHHHHHcCCCHHHHHHHHHHheeecCH
Confidence 45556666666654433 23 8899999999999999999999999988764
No 325
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=26.37 E-value=33 Score=21.96 Aligned_cols=22 Identities=9% Similarity=0.302 Sum_probs=18.7
Q ss_pred HHHHHHHhCCCccchhhhhccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNr 130 (159)
+.++++.+||++.+|--|+.+.
T Consensus 6 ~~ev~~~~g~s~~ti~~~~k~g 27 (51)
T PF05930_consen 6 IKEVAELLGVSRSTIYRLIKDG 27 (51)
T ss_dssp HHHHHHHHSS-HHHHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHhcc
Confidence 5788999999999999999865
No 326
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=26.24 E-value=62 Score=22.86 Aligned_cols=38 Identities=5% Similarity=0.096 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhh
Q 044959 85 EQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWL 127 (159)
Q Consensus 85 eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWF 127 (159)
+-++++..+-+.. +...-.++++|..+|++++.|.-=|
T Consensus 5 ~~~~~~~~~i~~~-----~~~~~~~~~lA~~~~~S~~~l~r~f 42 (107)
T PRK10219 5 KIIQTLIAWIDEH-----IDQPLNIDVVAKKSGYSKWYLQRMF 42 (107)
T ss_pred HHHHHHHHHHHHh-----cCCCCCHHHHHHHHCCCHHHHHHHH
Confidence 3456666666663 4344678899999999988775444
No 327
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=26.22 E-value=38 Score=25.46 Aligned_cols=24 Identities=17% Similarity=0.290 Sum_probs=20.4
Q ss_pred HHHHHHHhCCCccchhhhhccccC
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
+.++|+.+||+.++|+.|-..---
T Consensus 3 I~e~a~~~gvs~~tlRyYe~~GLl 26 (127)
T cd01108 3 IGEAAKLTGLSAKMIRYYEEIGLI 26 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCC
Confidence 678999999999999999876433
No 328
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. 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, an
Probab=26.12 E-value=38 Score=25.17 Aligned_cols=21 Identities=5% Similarity=0.321 Sum_probs=19.2
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|..+||+.++|+.|-.-
T Consensus 3 IgevA~~~gvs~~tlRyYe~~ 23 (120)
T cd04781 3 IAEVARQSGLPASTLRYYEEK 23 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 678999999999999999875
No 329
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=26.08 E-value=59 Score=32.02 Aligned_cols=28 Identities=36% Similarity=0.563 Sum_probs=19.2
Q ss_pred ccccccCCCCCCccccccccc-ccccccc
Q 044959 21 CGEFLKAGKDGTKEAFHCAAC-GCHRSFH 48 (159)
Q Consensus 21 C~ef~~~~~~~~~~~l~CaaC-gcHRnFH 48 (159)
|+..-|.=..-+.+.+.|..| |.||+|=
T Consensus 29 Cgs~~P~WASiNlGIFICi~CSGIHRsLG 57 (648)
T PLN03119 29 CNSLGPQYVCTTFWTFVCMACSGIHREFT 57 (648)
T ss_pred CCCCCCCceeeccceEEeccchhhhccCC
Confidence 666555544455677888776 7899984
No 330
>COG0289 DapB Dihydrodipicolinate reductase [Amino acid transport and metabolism]
Probab=26.06 E-value=57 Score=28.77 Aligned_cols=19 Identities=47% Similarity=0.531 Sum_probs=17.4
Q ss_pred ccCCHHHHHHHHHHHHHhC
Q 044959 80 TKITEEQKSKMRRFADKLG 98 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~G 98 (159)
|=||.+|+++|.+++++.+
T Consensus 101 TGf~~e~~~~l~~~a~~v~ 119 (266)
T COG0289 101 TGFTEEQLEKLREAAEKVP 119 (266)
T ss_pred CCCCHHHHHHHHHHHhhCC
Confidence 7899999999999999864
No 331
>PRK12461 UDP-N-acetylglucosamine acyltransferase; Provisional
Probab=26.04 E-value=99 Score=26.18 Aligned_cols=50 Identities=6% Similarity=0.116 Sum_probs=35.8
Q ss_pred CCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccc--hhhhhc
Q 044959 78 KRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKM--FKVWLN 128 (159)
Q Consensus 78 ~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~V--vKVWFq 128 (159)
.|--||+|+++.|++.|..+ |+...+-.+.++++.+++.-++.+ |--++.
T Consensus 196 ~r~g~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~ 247 (255)
T PRK12461 196 RRRGFSSRAIRALKRAYKII-YRSGLSVQQAVAELELQQFESPEVEELIDFIK 247 (255)
T ss_pred hhcCCCHHHHHHHHHHHHHH-HhcCCCHHHHHHHHHHhccCCHHHHHHHHHHH
Confidence 67789999999999988765 343444567788888877765554 445553
No 332
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=25.95 E-value=69 Score=23.76 Aligned_cols=54 Identities=15% Similarity=0.130 Sum_probs=39.2
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHH--HHHHhCCCccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGK--FCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~e--fc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-.+|+.+.+.|.-++...| +..+.+...+ +..+++++.++|++..++=|.|+..
T Consensus 148 ~~Lt~~E~~il~~l~~~~g---~~~~~~~~~~~~~~~~~~~~~~tv~~~i~~lr~Kl~~ 203 (222)
T PRK10643 148 LILTPKEFALLSRLMLKAG---SPVHREILYQDIYNWDDEPSSNTLEVHIHNLRDKVGK 203 (222)
T ss_pred EecCHHHHHHHHHHHhCCC---ceEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhCCC
Confidence 4699999999988887654 2223443333 2246789999999999999999863
No 333
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=25.89 E-value=1.1e+02 Score=22.14 Aligned_cols=37 Identities=16% Similarity=0.303 Sum_probs=29.4
Q ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCC
Q 044959 89 KMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRR 133 (159)
Q Consensus 89 kLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k 133 (159)
.|...+..+| ..-+.+|.+||++...|...-++++..
T Consensus 4 ~L~~la~~LG--------~~W~~Lar~Lgls~~~I~~i~~~~p~~ 40 (83)
T cd08319 4 ELNQLAQRLG--------PEWEQVLLDLGLSQTDIYRCKENHPHN 40 (83)
T ss_pred HHHHHHHHHh--------hhHHHHHHHcCCCHHHHHHHHHhCCCC
Confidence 3455676665 477889999999999999999988765
No 334
>cd02417 Peptidase_C39_likeA A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. 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 this
Probab=25.88 E-value=1.1e+02 Score=21.41 Aligned_cols=42 Identities=14% Similarity=0.182 Sum_probs=31.4
Q ss_pred CCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhh
Q 044959 78 KRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKV 125 (159)
Q Consensus 78 ~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKV 125 (159)
+...++.+++.. .++|.....+...+.+.++.+|++-+.+++
T Consensus 19 ~g~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~ 60 (121)
T cd02417 19 HGIAADPEQLRH------EFGLAGEPFNSTELLLAAKSLGLKAKAVRQ 60 (121)
T ss_pred cCCCCCHHHHHH------HhcCCCCCCCHHHHHHHHHHcCCeeEEEec
Confidence 445567777764 334555668899999999999999888875
No 335
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=25.71 E-value=39 Score=24.99 Aligned_cols=21 Identities=10% Similarity=0.374 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+-++|..+||+.++|+.|-..
T Consensus 3 Ige~A~~~gvs~~tlR~ye~~ 23 (107)
T cd01111 3 ISQLALDAGVSVHIVRDYLLR 23 (107)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 578999999999999999876
No 336
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=25.70 E-value=1.2e+02 Score=22.01 Aligned_cols=38 Identities=13% Similarity=0.253 Sum_probs=27.4
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGI 118 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl 118 (159)
..|+.++-+.|.+..+-+= +-..-+..+++.|+.+||-
T Consensus 31 ~~f~~~~yedl~diy~~V~-~K~~fS~sEm~aI~~ELG~ 68 (71)
T PF06569_consen 31 EDFSEEKYEDLKDIYEMVM-SKDSFSPSEMQAIAEELGQ 68 (71)
T ss_pred HhCChhhHHHHHHHHHHHH-hccCCCHHHHHHHHHHHHh
Confidence 4688888888888766651 1123568999999999983
No 337
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.64 E-value=40 Score=24.87 Aligned_cols=32 Identities=16% Similarity=0.419 Sum_probs=23.7
Q ss_pred HHHHHHHhCCCccchhhhhccccCCCCCCCCCcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEK 142 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~~~ 142 (159)
+.++|..+||+..+|+.|-.-. -.++.|..+.
T Consensus 3 i~eva~~~gvs~~tlR~Ye~~G--Ll~p~r~~~g 34 (112)
T cd01282 3 IGELAARTGVSVRSLRYYEEQG--LLVPERSANG 34 (112)
T ss_pred HHHHHHHHCCCHHHHHHHHHCC--CCCCCcCCCC
Confidence 6789999999999999998753 3344444444
No 338
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=25.63 E-value=28 Score=29.76 Aligned_cols=31 Identities=13% Similarity=0.176 Sum_probs=27.5
Q ss_pred HHHHHHHHhCCCccchhhhhccccCCCCCCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRRPVPVR 138 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k~kk~~ 138 (159)
..+++|..+|+++..|++.++--|.+++..+
T Consensus 136 s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 136 PYQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 4678999999999999999999999888754
No 339
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=25.62 E-value=40 Score=24.45 Aligned_cols=21 Identities=5% Similarity=0.200 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|..+||+..+|+.|-..
T Consensus 3 i~e~A~~~gvs~~tlR~Ye~~ 23 (99)
T cd04772 3 TVDLARAIGLSPQTVRNYESL 23 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 578999999999999999653
No 340
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.58 E-value=38 Score=26.32 Aligned_cols=34 Identities=18% Similarity=0.387 Sum_probs=25.3
Q ss_pred HHHHHHHhCCCccchhhhhccccCCCCCCCCCcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEKCR 144 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~~~~~~ 144 (159)
+.++|..+||+.++|+.|...- -.++.+.+++.+
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~G--Ll~p~r~~~g~R 36 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNLG--LLTPERSDSNYR 36 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC--CCCCccCCCCCe
Confidence 5789999999999999998654 444555555443
No 341
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=25.56 E-value=48 Score=22.35 Aligned_cols=24 Identities=21% Similarity=0.329 Sum_probs=20.6
Q ss_pred HHHHHHHhCCCccchhhhhccccC
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
..++|+.+||+..+|--+++++..
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln~~~~ 26 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLNGNGR 26 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCCC
Confidence 568999999999999999987654
No 342
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=25.48 E-value=59 Score=27.01 Aligned_cols=31 Identities=6% Similarity=0.021 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.-..+++|..+||++.+|+.+++--+.++++
T Consensus 219 ~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~ 249 (256)
T PRK07408 219 DLTQKEAAERLGISPVTVSRRVKKGLDQLKK 249 (256)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4467899999999999999998866665543
No 343
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=25.44 E-value=22 Score=29.38 Aligned_cols=47 Identities=11% Similarity=0.066 Sum_probs=32.9
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..+++.|++.+...+- +.....++|..+||+..+|+...++-..+++
T Consensus 208 ~~L~~~er~vi~~~~~---------~~~t~~eIA~~lgis~~~V~~~~~~al~kLr 254 (258)
T PRK08215 208 KKLNDREKLILNLRFF---------QGKTQMEVAEEIGISQAQVSRLEKAALKHMR 254 (258)
T ss_pred HcCCHHHHHHHHHHHh---------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3577777766666441 2235789999999999999988776554443
No 344
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=25.34 E-value=70 Score=21.92 Aligned_cols=41 Identities=15% Similarity=0.268 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhh
Q 044959 82 ITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVW 126 (159)
Q Consensus 82 FT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVW 126 (159)
+|.+|+.+|.+|+... --.-...|++....=-||..+=..|
T Consensus 1 lT~~Qk~el~~l~~qm----~e~kK~~idk~Ve~G~iTqeqAd~i 41 (59)
T PF10925_consen 1 LTDQQKKELKALYKQM----LELKKQIIDKYVEAGVITQEQADAI 41 (59)
T ss_pred CCHHHHHHHHHHHHHH----HHHHHHHHHHHHHcCCCCHHHHHHH
Confidence 5899999999988763 1222344555444444444443333
No 345
>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.
Probab=25.27 E-value=84 Score=23.72 Aligned_cols=54 Identities=7% Similarity=0.126 Sum_probs=40.3
Q ss_pred CccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 79 RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 79 RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
...+|+-+.+.|.-+++..| +-.+.+++.+ +..++++.++|++...+=|.|+..
T Consensus 154 ~~~Lt~~E~~il~~l~~~~g---~v~s~~~i~~-~~~~~~~~~tv~~~v~rlr~Kl~~ 207 (227)
T TIGR03787 154 PIDLTVTEFWMVHALAKHPG---HVKSRQQLMD-AAKIVVDDSTITSHIKRIRKKFQA 207 (227)
T ss_pred EecCCHHHHHHHHHHHhCCC---ccccHHHHHH-HhhhcCCccCHHHHHHHHHHHhcc
Confidence 36799999999999996543 2234444422 337889999999999999999974
No 346
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=25.24 E-value=64 Score=26.04 Aligned_cols=28 Identities=4% Similarity=0.096 Sum_probs=25.3
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRP 134 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~ 134 (159)
..++++|+..||++.+|-.+|.|+..-+
T Consensus 33 ~s~~~IA~~AGvsk~tiy~~F~sKe~L~ 60 (225)
T PRK11552 33 ATTRDIAAQAGQNIAAITYYFGSKEDLY 60 (225)
T ss_pred CCHHHHHHHhCCCHHHHHHHcCCHHHHH
Confidence 7899999999999999999999877644
No 347
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=25.17 E-value=67 Score=21.07 Aligned_cols=19 Identities=21% Similarity=0.274 Sum_probs=15.2
Q ss_pred CCccCCHHHHHHHHHHHHH
Q 044959 78 KRTKITEEQKSKMRRFADK 96 (159)
Q Consensus 78 ~RTkFT~eQkekLe~ffek 96 (159)
....||.++++.|.+|++.
T Consensus 13 y~~~ft~~El~~i~~FY~S 31 (64)
T PF09832_consen 13 YAEHFTEEELDAILAFYES 31 (64)
T ss_dssp HHHHS-HHHHHHHHHHHHS
T ss_pred HHHHCCHHHHHHHHHHHCC
Confidence 3467999999999999965
No 348
>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=25.15 E-value=44 Score=20.99 Aligned_cols=23 Identities=35% Similarity=0.833 Sum_probs=16.2
Q ss_pred cccCccccccCCCCCCcccccccccc
Q 044959 17 AYDGCGEFLKAGKDGTKEAFHCAACG 42 (159)
Q Consensus 17 ~~DgC~ef~~~~~~~~~~~l~CaaCg 42 (159)
-=|-|+++|.. ....+++|..|+
T Consensus 13 ~C~~C~~~i~g---~~~~g~~C~~C~ 35 (53)
T PF00130_consen 13 YCDVCGKFIWG---LGKQGYRCSWCG 35 (53)
T ss_dssp B-TTSSSBECS---SSSCEEEETTTT
T ss_pred CCcccCcccCC---CCCCeEEECCCC
Confidence 34779999954 235679999775
No 349
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=25.06 E-value=47 Score=21.60 Aligned_cols=25 Identities=8% Similarity=0.217 Sum_probs=20.9
Q ss_pred HHHHHHHHhCCCccchhhhhccccC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
..+++|..+|++...|.-|.+.++.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 5789999999999999999998775
No 350
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=25.05 E-value=53 Score=22.72 Aligned_cols=28 Identities=7% Similarity=0.181 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 104 HDEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 104 ~d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
-+...+.++|+++||++..|-..|.|+.
T Consensus 30 ~~~~t~~~Ia~~agvs~~~~Y~~f~~K~ 57 (201)
T COG1309 30 YAATTVDEIAKAAGVSKGTLYRHFPSKE 57 (201)
T ss_pred cCCCCHHHHHHHhCCCcchhHHHcCCHH
Confidence 4556789999999999999999999875
No 351
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=24.92 E-value=21 Score=29.97 Aligned_cols=30 Identities=17% Similarity=0.141 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 106 EEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 106 ~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
.-..+++|..+||++.+|+.+++.-+.+++
T Consensus 231 ~~t~~EIA~~lgis~~~V~~~~~ral~kLr 260 (264)
T PRK07122 231 SMTQTQIAERVGISQMHVSRLLAKTLARLR 260 (264)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 345789999999999999999887665544
No 352
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=24.89 E-value=93 Score=22.74 Aligned_cols=35 Identities=3% Similarity=0.071 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 83 TEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 83 T~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
|.||+++|-+.. -+.|.+.+||++..|-|-|++..
T Consensus 70 ~~e~k~~l~~~i--------------~~~l~~~lgi~~~rv~I~f~~~~ 104 (116)
T PTZ00397 70 SRSNNSSIAAAI--------------TKILASHLKVKSERVYIEFKDCS 104 (116)
T ss_pred CHHHHHHHHHHH--------------HHHHHHHhCcCcccEEEEEEECC
Confidence 589998876632 34578899999999999998864
No 353
>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=24.67 E-value=1.2e+02 Score=25.31 Aligned_cols=43 Identities=26% Similarity=0.310 Sum_probs=26.5
Q ss_pred CCCccCCHHHHHHHHHH---HHHhCCCCCC---CCHHHHHHHHHHhCCC
Q 044959 77 TKRTKITEEQKSKMRRF---ADKLGWKPQR---HDEEEVGKFCGEVGIT 119 (159)
Q Consensus 77 R~RTkFT~eQkekLe~f---fek~GW~iq~---~d~~~r~efc~eiGl~ 119 (159)
..+-.|+.+|+++|.++ +.+.|+++.+ ++..+.-+.+-+.||+
T Consensus 174 ~~~g~~~~~q~~~l~~~v~~a~~~Gl~vr~Wtv~~~~~~~~~l~~~GVd 222 (228)
T cd08577 174 NGKGDTPEDEKEKLKSIIDKAHARGKKVRFWGTPDRPNVWKTLMELGVD 222 (228)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEccCChHHHHHHHHHhCCC
Confidence 33456999999999986 5666766665 2223333444455653
No 354
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal 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=24.62 E-value=42 Score=24.69 Aligned_cols=21 Identities=10% Similarity=0.382 Sum_probs=18.6
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|..+||+.++|+.|-.-
T Consensus 3 I~eva~~~gvs~~tLRyYe~~ 23 (123)
T cd04770 3 IGELAKAAGVSPDTIRYYERI 23 (123)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 678999999999999998764
No 355
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=24.61 E-value=42 Score=25.15 Aligned_cols=20 Identities=10% Similarity=0.419 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCccchhhhhc
Q 044959 109 VGKFCGEVGITRKMFKVWLN 128 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFq 128 (159)
+.++|..+||+.++|+.|=.
T Consensus 3 Igeva~~~gvs~~tlRyYe~ 22 (118)
T cd04776 3 ISELAREFDVTPRTLRFYED 22 (118)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 67899999999999999954
No 356
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=24.40 E-value=42 Score=28.72 Aligned_cols=51 Identities=12% Similarity=-0.055 Sum_probs=42.4
Q ss_pred CCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 76 KTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 76 KR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
+.+=..+|+.|++.|.-.++=. ..+++|++++|+.++||.-..|=..|+.-
T Consensus 138 ~~~~~~LS~RE~eVL~Lia~G~----------SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILYSFGF----------SHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred hhccCCCCHHHHHHHHHHHCCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 5566789999999999988543 56789999999999999988887777764
No 357
>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=24.34 E-value=84 Score=22.44 Aligned_cols=44 Identities=20% Similarity=0.240 Sum_probs=28.2
Q ss_pred CCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccc
Q 044959 78 KRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKM 122 (159)
Q Consensus 78 ~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~V 122 (159)
+|--||.+|...|.+.+..+ ++-...-.+.++++-++..-++.+
T Consensus 24 rR~Gfs~~~i~~l~~ayr~l-~~~~~~~~~a~~~l~~~~~~~~~v 67 (83)
T PF13720_consen 24 RRRGFSKEEISALRRAYRIL-FRSGLTLEEALEELEEEYPDSPEV 67 (83)
T ss_dssp HHTTS-HHHHHHHHHHHHHH-HTSSS-HHHHHHHHHHHTTSCHHH
T ss_pred HHcCCCHHHHHHHHHHHHHH-HhCCCCHHHHHHHHHHhccCCHHH
Confidence 36679999999999988776 222223366777776665554443
No 358
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=24.33 E-value=89 Score=20.01 Aligned_cols=33 Identities=18% Similarity=0.179 Sum_probs=25.4
Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcc
Q 044959 83 TEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 83 T~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
|.|||+.|-+.. -+.++..+|++..-+-|.|..
T Consensus 13 s~eqk~~l~~~i--------------t~~l~~~~~~p~~~v~V~i~e 45 (62)
T PRK00745 13 TVEQKRKLVEEI--------------TRVTVETLGCPPESVDIIITD 45 (62)
T ss_pred CHHHHHHHHHHH--------------HHHHHHHcCCChhHEEEEEEE
Confidence 789998876643 345788899999888887764
No 359
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=24.25 E-value=70 Score=24.23 Aligned_cols=51 Identities=10% Similarity=0.126 Sum_probs=40.7
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhC-----CCccchhhhhccccCCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVG-----ITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiG-----l~r~VvKVWFqNrR~k~kk 136 (159)
..+|+.+.+.|.-+++.. ...-.++++++++. ++.++|++-+.+=|.|+..
T Consensus 159 ~~Lt~~e~~il~~l~~~~------~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~ 214 (240)
T PRK10710 159 LDLTPAEFRLLKTLSHEP------GKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES 214 (240)
T ss_pred eecCHHHHHHHHHHHhCC------CceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence 469999999999888642 22345678888887 9999999999999999864
No 360
>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=24.22 E-value=1e+02 Score=19.75 Aligned_cols=34 Identities=18% Similarity=0.218 Sum_probs=25.8
Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccc
Q 044959 83 TEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 83 T~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNr 130 (159)
|.|||+.|-+.. -+.++..+|+++..+-|.+...
T Consensus 13 t~eqK~~l~~~i--------------t~~l~~~lg~~~~~v~V~i~e~ 46 (63)
T TIGR00013 13 TDEQKRQLIEGV--------------TEAMAETLGANLESIVVIIDEM 46 (63)
T ss_pred CHHHHHHHHHHH--------------HHHHHHHhCCCcccEEEEEEEc
Confidence 789998876643 3567888999998888877643
No 361
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=24.20 E-value=43 Score=25.61 Aligned_cols=22 Identities=9% Similarity=0.415 Sum_probs=19.8
Q ss_pred HHHHHHHHhCCCccchhhhhcc
Q 044959 108 EVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqN 129 (159)
.+.++|..+||+.++|+.|-..
T Consensus 5 tI~elA~~~gvs~~tlR~Ye~~ 26 (120)
T TIGR02054 5 TISRLAEDAGVSVHVVRDYLLR 26 (120)
T ss_pred cHHHHHHHHCcCHHHHHHHHHC
Confidence 4789999999999999999765
No 362
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.02 E-value=48 Score=20.72 Aligned_cols=25 Identities=32% Similarity=0.763 Sum_probs=15.5
Q ss_pred CccccccCCCCCCcccccccccccc
Q 044959 20 GCGEFLKAGKDGTKEAFHCAACGCH 44 (159)
Q Consensus 20 gC~ef~~~~~~~~~~~l~CaaCgcH 44 (159)
-||..|...+.....-+.|..||=|
T Consensus 5 ~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 5 KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCccccccCCCCCEEECCcCCCe
Confidence 4788776543222236789999943
No 363
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=23.95 E-value=43 Score=25.10 Aligned_cols=22 Identities=18% Similarity=0.487 Sum_probs=19.3
Q ss_pred HHHHHHHhCCCccchhhhhccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNr 130 (159)
+.++|..+||+.++|+.|-+.-
T Consensus 3 I~e~a~~~gvs~~tlRyYe~~G 24 (127)
T TIGR02044 3 IGQVAKLTGLSSKMIRYYEEKG 24 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 6789999999999999998643
No 364
>cd04275 ZnMc_pappalysin_like Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor. This model includes pappalysins and related metalloprotease domains from all three kingdoms of life. The three-dimensional structure of an archaeal representative, ulilysin, has been solved.
Probab=23.78 E-value=52 Score=27.64 Aligned_cols=18 Identities=22% Similarity=0.350 Sum_probs=15.1
Q ss_pred CCCccCCHHHHHHHHHHH
Q 044959 77 TKRTKITEEQKSKMRRFA 94 (159)
Q Consensus 77 R~RTkFT~eQkekLe~ff 94 (159)
.-+..||+.|+++|....
T Consensus 207 ~C~~~FT~~Q~~RM~~~~ 224 (225)
T cd04275 207 SCMNEFTPGQVTRMRSYL 224 (225)
T ss_pred chhcccCHHHHHHHHHHh
Confidence 357899999999998754
No 365
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=23.75 E-value=44 Score=25.34 Aligned_cols=21 Identities=19% Similarity=0.510 Sum_probs=19.3
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|..+||+.++|+.|-..
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~ 24 (131)
T TIGR02043 4 IGELAKLCGVTSDTLRFYEKN 24 (131)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 678999999999999999966
No 366
>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=23.62 E-value=63 Score=24.71 Aligned_cols=29 Identities=3% Similarity=0.194 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhccccC
Q 044959 104 HDEEEVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 104 ~d~~~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
.+...+.++|++.||++..|-..|.|+-.
T Consensus 26 ~~~~s~~~IA~~agvs~~~lY~hF~sKe~ 54 (202)
T TIGR03613 26 FHGTSLEQIAELAGVSKTNLLYYFPSKDA 54 (202)
T ss_pred cccCCHHHHHHHhCCCHHHHHHHcCCHHH
Confidence 56678999999999999999999987643
No 367
>PRK06437 hypothetical protein; Provisional
Probab=23.57 E-value=8.5 Score=26.36 Aligned_cols=34 Identities=15% Similarity=0.152 Sum_probs=27.1
Q ss_pred CCCCCCCHHHHHHHHHHhCCCccchhhhhccccCC
Q 044959 99 WKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRR 133 (159)
Q Consensus 99 W~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k 133 (159)
|..+.++...+.+|..++|++...+-|. .|.+.-
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 5566666778999999999999999887 665544
No 368
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=23.50 E-value=1.1e+02 Score=27.28 Aligned_cols=37 Identities=8% Similarity=0.168 Sum_probs=24.4
Q ss_pred HHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccC
Q 044959 88 SKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRR 132 (159)
Q Consensus 88 ekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~ 132 (159)
++|++.=+++||. ++++|..|+|++.+|.-|-.+++.
T Consensus 17 ~~Lr~aRe~~GlS--------q~~vA~~l~l~~~~I~~iE~g~~~ 53 (331)
T PRK10856 17 ERLRQAREQLGLT--------QQAVAERLCLKVSTVRDIEEDKAP 53 (331)
T ss_pred HHHHHHHHHcCCC--------HHHHHHHHCCCHHHHHHHHCCCCC
Confidence 3445555555543 567788888888888888877653
No 369
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=23.38 E-value=47 Score=23.92 Aligned_cols=19 Identities=11% Similarity=0.440 Sum_probs=16.8
Q ss_pred HHHHHHHhCCCccchhhhh
Q 044959 109 VGKFCGEVGITRKMFKVWL 127 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWF 127 (159)
+-++|..+||+.++|+-|=
T Consensus 3 I~eva~~~gvs~~tLRyYE 21 (124)
T COG0789 3 IGEVAKLTGVSVRTLRFYE 21 (124)
T ss_pred HHHHHHHhCCCHHHHHHHH
Confidence 5688999999999999994
No 370
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=23.38 E-value=1.2e+02 Score=24.03 Aligned_cols=36 Identities=14% Similarity=0.231 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchh
Q 044959 85 EQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFK 124 (159)
Q Consensus 85 eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvK 124 (159)
.-+..|...-+..| |.+.+.++.+|..+||+...|.
T Consensus 24 ~li~~L~~vQ~~~G----~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 24 ALLPILHAIQDEFG----YVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHHcC----CCCHHHHHHHHHHhCCCHHHHH
Confidence 34556666666765 7999999999999999987654
No 371
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=23.35 E-value=45 Score=24.31 Aligned_cols=21 Identities=14% Similarity=0.588 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|..+||+..+|+.|-++
T Consensus 3 i~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 3 IGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 568999999999999999766
No 372
>PRK05572 sporulation sigma factor SigF; Validated
Probab=23.34 E-value=64 Score=26.48 Aligned_cols=47 Identities=6% Similarity=0.063 Sum_probs=33.5
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCC
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPV 135 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~k 135 (159)
..+++.|++.+..++ .+.....++|..+||+...|..+.+.-..+++
T Consensus 201 ~~L~~~~~~v~~l~~---------~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr 247 (252)
T PRK05572 201 RELDERERLIVYLRY---------FKDKTQSEVAKRLGISQVQVSRLEKKILKQMK 247 (252)
T ss_pred HcCCHHHHHHHHHHH---------hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 456777777766644 12346789999999999999998776554443
No 373
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=23.28 E-value=47 Score=29.60 Aligned_cols=30 Identities=13% Similarity=0.275 Sum_probs=24.3
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhccccCCC
Q 044959 103 RHDEEEVGKFCGEVGITRKMFKVWLNNNRRRP 134 (159)
Q Consensus 103 ~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~ 134 (159)
|...--+.++|+.+||++.+|+-|- +|..|
T Consensus 16 yl~gmk~~dIAeklGvspntiksWK--rr~gW 45 (279)
T COG5484 16 YLKGMKLKDIAEKLGVSPNTIKSWK--RRDGW 45 (279)
T ss_pred HHhhccHHHHHHHhCCChHHHHHHH--HhcCC
Confidence 4445567899999999999999996 46666
No 374
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=23.27 E-value=1.3e+02 Score=21.34 Aligned_cols=34 Identities=26% Similarity=0.398 Sum_probs=23.0
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhh
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKV 125 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKV 125 (159)
..|.+|++.+ +..+| ....+||.+||++...|.-
T Consensus 4 ~~t~~~l~~i---a~~iG--------~~Wk~Lar~LGls~~dI~~ 37 (86)
T cd08318 4 PVTGEQITVF---ANKLG--------EDWKTLAPHLEMKDKEIRA 37 (86)
T ss_pred CCCHHHHHHH---HHHHh--------hhHHHHHHHcCCCHHHHHH
Confidence 3577777764 44442 4677788888888776654
No 375
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal 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. This subgroup lacks one of the c
Probab=22.91 E-value=47 Score=25.13 Aligned_cols=29 Identities=17% Similarity=0.268 Sum_probs=21.5
Q ss_pred HHHHHHHhCCCccchhhhhccccCCCCCCCC
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRRRPVPVRV 139 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~k~kk~~~ 139 (159)
+-++|..+||+.++|+.|-. .--.++.+.
T Consensus 3 IgE~A~~~gvs~~TLRyYE~--~GLl~p~r~ 31 (133)
T cd04787 3 VKELANAAGVTPDTVRFYTR--IGLLRPTRD 31 (133)
T ss_pred HHHHHHHHCcCHHHHHHHHH--CCCCCCCcC
Confidence 67899999999999999963 333444343
No 376
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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=22.83 E-value=47 Score=24.75 Aligned_cols=22 Identities=9% Similarity=0.382 Sum_probs=19.6
Q ss_pred HHHHHHHhCCCccchhhhhccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNr 130 (159)
+-+||+.+||+.++|+.|-.--
T Consensus 3 IgevA~~~gvs~~tLRyYe~~G 24 (127)
T cd04784 3 IGELAKKTGCSVETIRYYEKEG 24 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 6789999999999999998754
No 377
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=22.75 E-value=47 Score=25.61 Aligned_cols=21 Identities=10% Similarity=0.335 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+-++|+.+||+.++|+.|-..
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~ 24 (140)
T PRK09514 4 IGELAKLAEVTPDTLRFYEKQ 24 (140)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 678999999999999999765
No 378
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=22.73 E-value=48 Score=25.04 Aligned_cols=22 Identities=9% Similarity=0.462 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCccchhhhhccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNr 130 (159)
+.++|..+||+.++|+.|-..-
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~~G 24 (127)
T TIGR02047 3 IGELAQKTGVSVETIRFYEKQG 24 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 6789999999999999997653
No 379
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=22.40 E-value=1.3e+02 Score=21.62 Aligned_cols=18 Identities=11% Similarity=0.202 Sum_probs=8.9
Q ss_pred HHHHHHHHhCCCccchhh
Q 044959 108 EVGKFCGEVGITRKMFKV 125 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKV 125 (159)
...+||.+||++...|+.
T Consensus 15 ~Wk~lar~LG~s~~eI~~ 32 (86)
T cd08777 15 KWKRCARKLGFTESEIEE 32 (86)
T ss_pred HHHHHHHHcCCCHHHHHH
Confidence 444555555555544444
No 380
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.26 E-value=49 Score=24.72 Aligned_cols=21 Identities=10% Similarity=0.428 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|..+||+.++|+.|-+-
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~~ 23 (126)
T cd04783 3 IGELAKAAGVNVETIRYYQRR 23 (126)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 678999999999999999543
No 381
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=22.18 E-value=42 Score=20.24 Aligned_cols=24 Identities=8% Similarity=0.259 Sum_probs=13.3
Q ss_pred CHHHHHHHHHHhCCCccchhhhhc
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLN 128 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFq 128 (159)
..-.++++|..+|+++..|..=|+
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk 30 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFK 30 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345667777777777766665554
No 382
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=22.13 E-value=74 Score=27.13 Aligned_cols=46 Identities=7% Similarity=0.084 Sum_probs=37.6
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 81 KITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 81 kFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+|+-|++.|.-.++=. ...++|.+++|++++|+.-..+=..|+.-
T Consensus 133 ~LSpRErEVLrLLAqGk----------TnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 133 HFSVTERHLLKLIASGY----------HLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCHHHHHHHHHHHCCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 39999999999988432 46789999999999999888776666653
No 383
>PF11869 DUF3389: Protein of unknown function (DUF3389); InterPro: IPR021811 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Probab=22.03 E-value=55 Score=24.01 Aligned_cols=24 Identities=25% Similarity=0.527 Sum_probs=20.2
Q ss_pred hCCCCCCCCHHHHHHHHHHhCCCc
Q 044959 97 LGWKPQRHDEEEVGKFCGEVGITR 120 (159)
Q Consensus 97 ~GW~iq~~d~~~r~efc~eiGl~r 120 (159)
.-|.++--+++..+++++++|+.-
T Consensus 51 vkWSikLD~eeQL~~ia~~lGi~i 74 (75)
T PF11869_consen 51 VKWSIKLDNEEQLQAIAEELGIDI 74 (75)
T ss_pred eEEEEEcCCHHHHHHHHHHhCccc
Confidence 348888888999999999999863
No 384
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=22.02 E-value=28 Score=32.29 Aligned_cols=12 Identities=33% Similarity=0.982 Sum_probs=10.2
Q ss_pred cccccccccccc
Q 044959 35 AFHCAACGCHRS 46 (159)
Q Consensus 35 ~l~CaaCgcHRn 46 (159)
++.|.|||++-+
T Consensus 118 ~~~CkACG~r~~ 129 (400)
T KOG2767|consen 118 SLKCKACGFRSD 129 (400)
T ss_pred hhHHHHcCCccc
Confidence 689999999854
No 385
>PRK13500 transcriptional activator RhaR; Provisional
Probab=21.84 E-value=71 Score=27.02 Aligned_cols=42 Identities=14% Similarity=0.243 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccc
Q 044959 84 EEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNN 130 (159)
Q Consensus 84 ~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNr 130 (159)
.+++.++.++-+. +|-+.-.++++|+.+|++++.|.-.|...
T Consensus 205 ~~~l~~i~~yI~~-----~~~e~isl~~lA~~~~iS~~~L~r~FK~~ 246 (312)
T PRK13500 205 ETLLDKLITRLAA-----SLKSPFALDKFCDEASCSERVLRQQFRQQ 246 (312)
T ss_pred HHHHHHHHHHHHH-----cccCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4566777777766 36666789999999999999998888653
No 386
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=21.83 E-value=1.1e+02 Score=20.25 Aligned_cols=25 Identities=12% Similarity=0.226 Sum_probs=17.8
Q ss_pred HHHHHHHHHhCCCccchhhhhcccc
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
....+||..||++...|+..=++++
T Consensus 11 ~~W~~la~~Lgl~~~~I~~i~~~~~ 35 (79)
T cd01670 11 KDWKKLARKLGLSDGEIDQIEEDNP 35 (79)
T ss_pred hHHHHHHHHhCCCHHHHHHHHHhCC
Confidence 5667777777777777777666664
No 387
>cd00131 PAX Paired Box domain
Probab=21.72 E-value=3.2e+02 Score=20.72 Aligned_cols=46 Identities=15% Similarity=0.076 Sum_probs=29.7
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCC-HHHHHHHHHHhCC-------Cccchhhhhccc
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHD-EEEVGKFCGEVGI-------TRKMFKVWLNNN 130 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d-~~~r~efc~eiGl-------~r~VvKVWFqNr 130 (159)
.+.|.++.+.++.+.+.. +..+ .+..++|.. -|| +..+|--||+|.
T Consensus 74 r~~~~~~~~~i~~~v~~~----p~~Tl~El~~~L~~-~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 74 RVATPEVVKKIEIYKQEN----PGMFAWEIRDRLLQ-EGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CcCCHHHHHHHHHHHHHC----CCCCHHHHHHHHHH-cCCcccCCCCCHHHHHHHHHhc
Confidence 356778888888877764 2333 344455553 366 888888887763
No 388
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=21.64 E-value=16 Score=28.15 Aligned_cols=30 Identities=17% Similarity=0.181 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 107 EEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 107 ~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-.-+++|..+||+..+||.+++--|.++++
T Consensus 144 ls~~EIA~~l~i~~~tVks~l~ra~~~l~~ 173 (182)
T COG1595 144 LSYEEIAEILGISVGTVKSRLHRARKKLRE 173 (182)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345789999999999999999987776654
No 389
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=21.56 E-value=1.5e+02 Score=23.19 Aligned_cols=52 Identities=17% Similarity=0.209 Sum_probs=38.5
Q ss_pred HHHHHHH----HHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 84 EEQKSKM----RRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 84 ~eQkekL----e~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.+.+++| +++|++.||++ .||.+....+..-|-..+..+=.|..--|.-..+
T Consensus 3 ~e~l~~my~~~eq~AeksG~~l-npD~e~~~~v~~gL~~~ke~yG~~~CPCRl~~g~ 58 (110)
T COG4802 3 DEELNKMYRFTEQYAEKSGYRL-NPDREFTAEVLRGLASNKERYGYPSCPCRLVTGK 58 (110)
T ss_pred HHHHHHHHHHHHHHHHhcCcee-CCCHHHHHHHHHHHHHhHHHhCCCCCCeecccCC
Confidence 4556666 45788999987 4788888888888877778887787776665443
No 390
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=21.48 E-value=53 Score=23.40 Aligned_cols=22 Identities=14% Similarity=0.202 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCCccchhhhhcc
Q 044959 108 EVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqN 129 (159)
..++||..+||+++++--|=.+
T Consensus 16 tQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 16 TQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred CHHHHHHHcCcCHHHHHHHHcC
Confidence 5689999999999999776443
No 391
>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=21.35 E-value=72 Score=23.33 Aligned_cols=18 Identities=33% Similarity=0.669 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHhCCCC
Q 044959 84 EEQKSKMRRFADKLGWKP 101 (159)
Q Consensus 84 ~eQkekLe~ffek~GW~i 101 (159)
..|++.+++|+.+.||.+
T Consensus 18 ~~Q~~~~~~~a~~~g~~i 35 (148)
T smart00857 18 ERQLEALRAYAKANGWEV 35 (148)
T ss_pred HHHHHHHHHHHHHCCCEE
Confidence 579999999999999986
No 392
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=20.99 E-value=1e+02 Score=22.47 Aligned_cols=35 Identities=14% Similarity=0.235 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcccc
Q 044959 87 KSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 87 kekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR 131 (159)
...+..+-+..||. +||+.+||++.+|--|+.+..
T Consensus 34 ~~~l~~~r~~~glS----------qLAe~~GIs~stLs~iE~g~~ 68 (89)
T TIGR02684 34 AHALGYIARARGMT----------QLARKTGLSRESLYKALSGKG 68 (89)
T ss_pred HHHHHHHHHHCChH----------HHHHHHCCCHHHHHHHHcCCC
Confidence 34455555554432 499999999999999996653
No 393
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=20.97 E-value=50 Score=22.06 Aligned_cols=38 Identities=21% Similarity=0.409 Sum_probs=20.3
Q ss_pred HHHHHHHhCCCccchh---hhhcc-ccCCCCCCCCCcccccc
Q 044959 109 VGKFCGEVGITRKMFK---VWLNN-NRRRPVPVRVPEKCRAA 146 (159)
Q Consensus 109 r~efc~eiGl~r~VvK---VWFqN-rR~k~kk~~~~~~~~~~ 146 (159)
+++||+.|||+..|.+ .+++. ...++-+.|.|..-.+|
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA 42 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAA 42 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHH
Confidence 4688999999987764 23332 34455555555544443
No 394
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=20.78 E-value=58 Score=27.69 Aligned_cols=30 Identities=7% Similarity=0.132 Sum_probs=23.7
Q ss_pred CHHHHHHHHHHhCCCccchhhhhccccCCC
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLNNNRRRP 134 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFqNrR~k~ 134 (159)
+....+++|..+||++..|+...+.-+.|+
T Consensus 268 ~~~Tl~EIa~~lgiS~erVrq~~~rAl~kL 297 (298)
T TIGR02997 268 EPLTLAEIGRRLNLSRERVRQIEAKALRKL 297 (298)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 345789999999999999998877554443
No 395
>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=20.69 E-value=1.7e+02 Score=20.53 Aligned_cols=40 Identities=13% Similarity=0.297 Sum_probs=28.5
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhh
Q 044959 80 TKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKV 125 (159)
Q Consensus 80 TkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKV 125 (159)
-.++.+++.. ..+|.-...+...+.++++.+|+.-+.+++
T Consensus 27 ~~~~~~~l~~------~~~~~~~~~s~~~l~~~a~~~Gl~~~~~~~ 66 (129)
T cd02423 27 INITEQEVLK------LMLIRSEGFSMLDLKRYAEALGLKANGYRL 66 (129)
T ss_pred CCCCHHHHHH------HhCcccCCcCHHHHHHHHHHCCCcceEEEc
Confidence 5566776643 234444567888889999999988888765
No 396
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=20.68 E-value=49 Score=26.24 Aligned_cols=26 Identities=12% Similarity=0.285 Sum_probs=21.8
Q ss_pred HHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
-+|||..+|+++++|--|. |+..|+.
T Consensus 3 ~eELA~~tG~srQTINrWv--RkegW~T 28 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWV--RKEGWKT 28 (122)
T ss_pred HHHHHHHhCccHHHHHHHH--HhcCcee
Confidence 3789999999999999998 5566654
No 397
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=20.59 E-value=61 Score=21.23 Aligned_cols=21 Identities=14% Similarity=0.316 Sum_probs=17.5
Q ss_pred CHHHHHHHHHHhCCCccchhh
Q 044959 105 DEEEVGKFCGEVGITRKMFKV 125 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKV 125 (159)
+.-.++++|+.+||++.+++-
T Consensus 13 ~~~s~~ela~~~~VS~~TiRR 33 (57)
T PF08220_consen 13 GKVSVKELAEEFGVSEMTIRR 33 (57)
T ss_pred CCEEHHHHHHHHCcCHHHHHH
Confidence 445788999999999999874
No 398
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.39 E-value=57 Score=24.48 Aligned_cols=23 Identities=9% Similarity=0.317 Sum_probs=19.7
Q ss_pred HHHHHHHhCCCccchhhhhcccc
Q 044959 109 VGKFCGEVGITRKMFKVWLNNNR 131 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqNrR 131 (159)
+.++|+.+||+.++|+.|-..-=
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~~Gl 25 (126)
T cd04785 3 IGELARRTGVNVETIRYYESIGL 25 (126)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 67899999999999999986443
No 399
>PF01343 Peptidase_S49: Peptidase family S49 peptidase classification.; InterPro: IPR002142 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. The domain defines sequences in viruses, archaea, bacteria and plants. These sequences are variously annotated in the different taxonomic groups, examples are: Viruses: capsid protein Archaea: proteinase IV homolog Bacteria: proteinase IV, sohB, SppA, pfaP, putative protease Plants: SppA, protease IV This group also contains proteins classified as non-peptidase homologues that either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases. Related proteins, non-peptidase homologs and unclassified S49 members are also to be found in IPR002810 from INTERPRO.; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3RST_B 3BEZ_D 3BF0_A.
Probab=20.27 E-value=1.6e+02 Score=22.62 Aligned_cols=46 Identities=15% Similarity=0.283 Sum_probs=34.5
Q ss_pred CCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhcc
Q 044959 77 TKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 77 R~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqN 129 (159)
=.|+.+|+++++.|++....+ -..-++.+++.-|++...++-|+.+
T Consensus 75 ~~~~~~s~~~r~~~~~~l~~~-------~~~f~~~Va~~R~~~~~~v~~~~~~ 120 (154)
T PF01343_consen 75 FPRDPMSEEERENLQELLDEL-------YDQFVNDVAEGRGLSPDDVEEIADG 120 (154)
T ss_dssp CTTSS--HHHHHHHHHHHHHH-------HHHHHHHHHHHHTS-HHHHHCHHCC
T ss_pred CcCCCCCHHHHHHHHHHHHHH-------HHHHHHHHHHccCCCHHHHHHHHhh
Confidence 468999999999999877664 2556777788889999999888876
No 400
>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=20.26 E-value=47 Score=27.03 Aligned_cols=32 Identities=13% Similarity=0.121 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959 105 DEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 105 d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk 136 (159)
.....+++|..+||+...|+.+.+.-..|++.
T Consensus 195 ~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~ 226 (238)
T TIGR02393 195 RPHTLEEVGKEFNVTRERIRQIESKALRKLRH 226 (238)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 34568999999999999999999988888875
No 401
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=20.24 E-value=58 Score=24.00 Aligned_cols=21 Identities=19% Similarity=0.555 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCccchhhhhcc
Q 044959 109 VGKFCGEVGITRKMFKVWLNN 129 (159)
Q Consensus 109 r~efc~eiGl~r~VvKVWFqN 129 (159)
+.++|..+||+.+++..|-.-
T Consensus 3 ige~a~~~gvs~~tLryYe~~ 23 (116)
T cd04769 3 IGELAQQTGVTIKAIRLYEEK 23 (116)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 678999999999999999865
No 402
>PF11737 DUF3300: Protein of unknown function (DUF3300); InterPro: IPR021728 This hypothetical bacterial gene product has a long hydrophobic segment and is thus likely to be a membrane protein.
Probab=20.20 E-value=61 Score=28.18 Aligned_cols=48 Identities=13% Similarity=0.058 Sum_probs=31.4
Q ss_pred CCHHHHHHHHH-HHHHhCCCCCCCCHHHHHHHHHHh-CCCccchhhhhccccCCCCC
Q 044959 82 ITEEQKSKMRR-FADKLGWKPQRHDEEEVGKFCGEV-GITRKMFKVWLNNNRRRPVP 136 (159)
Q Consensus 82 FT~eQkekLe~-ffek~GW~iq~~d~~~r~efc~ei-Gl~r~VvKVWFqNrR~k~kk 136 (159)
||++||+.|.+ .| -|||.-.-+=|...+ -+.--.-.-|...|+.....
T Consensus 1 fs~~qL~qlvAPIA-------LYPD~LlaqiL~ASTYPleVv~A~rw~~~n~~l~g~ 50 (237)
T PF11737_consen 1 FSAAQLDQLVAPIA-------LYPDPLLAQILMASTYPLEVVQAARWLQQNPGLKGD 50 (237)
T ss_pred CCHHHHHHHhcchh-------cCchHHHHHHHHhccCcHHHHHHHHHHHHCcCcchh
Confidence 89999999999 77 589875544444333 23333345798887754443
No 403
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=20.11 E-value=90 Score=24.52 Aligned_cols=26 Identities=19% Similarity=0.354 Sum_probs=20.9
Q ss_pred HHHHHHHHhCCCccchhhhhccccCC
Q 044959 108 EVGKFCGEVGITRKMFKVWLNNNRRR 133 (159)
Q Consensus 108 ~r~efc~eiGl~r~VvKVWFqNrR~k 133 (159)
.++++|..+||++++|+-.++.-|.+
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~ 178 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAW 178 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46789999999999998877665543
Done!