Query 026325
Match_columns 240
No_of_seqs 360 out of 1730
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 06:33:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026325.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026325hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.9 2.5E-25 5.5E-30 187.3 7.2 121 84-209 49-169 (198)
2 KOG0842 Transcription factor t 99.8 7.6E-19 1.6E-23 156.2 10.6 68 84-151 152-219 (307)
3 KOG0489 Transcription factor z 99.8 5.1E-20 1.1E-24 162.4 2.6 63 82-144 156-218 (261)
4 KOG0487 Transcription factor A 99.8 2.1E-19 4.6E-24 159.7 4.7 66 83-148 233-298 (308)
5 KOG0488 Transcription factor B 99.8 1.3E-18 2.7E-23 156.5 8.7 64 83-146 170-233 (309)
6 KOG0484 Transcription factor P 99.7 1.3E-18 2.9E-23 130.4 5.2 65 81-145 13-77 (125)
7 KOG0848 Transcription factor C 99.7 1.5E-17 3.2E-22 143.6 10.4 62 85-146 199-260 (317)
8 KOG0843 Transcription factor E 99.7 2.7E-18 5.8E-23 140.5 5.0 64 84-147 101-164 (197)
9 KOG0485 Transcription factor N 99.7 4.2E-17 9.2E-22 137.0 12.1 63 82-144 101-163 (268)
10 KOG0494 Transcription factor C 99.7 8.1E-18 1.8E-22 144.6 5.3 68 85-152 141-208 (332)
11 KOG0492 Transcription factor M 99.7 1.7E-17 3.7E-22 138.5 6.7 62 83-144 142-203 (246)
12 KOG0850 Transcription factor D 99.7 1E-17 2.2E-22 141.9 5.4 64 82-145 119-182 (245)
13 KOG2251 Homeobox transcription 99.7 2.5E-17 5.3E-22 139.0 4.8 67 81-147 33-99 (228)
14 KOG0493 Transcription factor E 99.7 1.4E-16 3.1E-21 137.1 8.6 92 52-143 211-304 (342)
15 PF00046 Homeobox: Homeobox do 99.7 3.3E-17 7.1E-22 111.7 3.7 57 86-142 1-57 (57)
16 KOG0844 Transcription factor E 99.6 3.2E-16 6.9E-21 137.5 3.9 68 81-148 177-244 (408)
17 KOG0486 Transcription factor P 99.6 5.3E-15 1.2E-19 130.4 7.4 73 84-156 111-183 (351)
18 TIGR01565 homeo_ZF_HD homeobox 99.6 5.1E-15 1.1E-19 101.3 5.5 53 85-137 1-57 (58)
19 smart00389 HOX Homeodomain. DN 99.5 3E-15 6.6E-20 101.2 3.4 56 86-141 1-56 (56)
20 cd00086 homeodomain Homeodomai 99.5 3.8E-15 8.3E-20 101.5 3.8 58 86-143 1-58 (59)
21 COG5576 Homeodomain-containing 99.5 1.5E-14 3.2E-19 118.2 5.5 66 82-147 48-113 (156)
22 KOG0491 Transcription factor B 99.5 3.9E-15 8.4E-20 120.4 -0.2 62 84-145 99-160 (194)
23 KOG3802 Transcription factor O 99.5 2.9E-14 6.2E-19 129.7 5.1 63 82-144 291-353 (398)
24 KOG4577 Transcription factor L 99.5 3.9E-14 8.4E-19 123.7 5.5 78 81-158 163-240 (383)
25 KOG0847 Transcription factor, 99.4 4.5E-14 9.8E-19 119.0 1.9 65 81-145 163-227 (288)
26 KOG0490 Transcription factor, 99.3 3.1E-12 6.6E-17 109.9 3.6 63 82-144 57-119 (235)
27 KOG0849 Transcription factor P 99.1 2.4E-11 5.3E-16 111.5 3.6 71 74-144 165-235 (354)
28 KOG1168 Transcription factor A 99.1 6.2E-11 1.3E-15 103.8 3.6 63 82-144 306-368 (385)
29 KOG0775 Transcription factor S 99.0 2.5E-10 5.4E-15 99.4 3.8 51 92-142 183-233 (304)
30 KOG0774 Transcription factor P 98.8 9.4E-09 2E-13 89.1 7.0 59 85-143 188-249 (334)
31 smart00340 HALZ homeobox assoc 98.8 1.3E-08 2.8E-13 64.0 4.6 42 143-184 1-42 (44)
32 PF05920 Homeobox_KN: Homeobox 98.5 2.7E-08 5.8E-13 63.2 0.2 34 106-139 7-40 (40)
33 KOG2252 CCAAT displacement pro 98.3 5.7E-07 1.2E-11 85.3 3.7 59 83-141 418-476 (558)
34 KOG0490 Transcription factor, 98.1 2.4E-06 5.2E-11 73.2 3.6 63 82-144 150-212 (235)
35 KOG1146 Homeobox protein [Gene 97.9 2.5E-05 5.3E-10 80.6 6.8 63 82-144 900-962 (1406)
36 KOG0773 Transcription factor M 97.2 0.00017 3.8E-09 65.9 2.3 60 85-144 239-301 (342)
37 PF11569 Homez: Homeodomain le 96.9 0.00023 5E-09 48.2 -0.1 41 97-137 10-50 (56)
38 PF02183 HALZ: Homeobox associ 96.2 0.0089 1.9E-07 38.8 4.0 35 143-177 1-35 (45)
39 KOG3623 Homeobox transcription 94.9 0.016 3.5E-07 57.4 2.3 48 97-144 568-615 (1007)
40 PRK09413 IS2 repressor TnpA; R 93.9 0.37 8.1E-06 37.5 7.7 81 87-171 8-102 (121)
41 PF04218 CENP-B_N: CENP-B N-te 93.8 0.072 1.6E-06 35.6 3.0 46 86-136 1-46 (53)
42 PF02183 HALZ: Homeobox associ 86.8 1.7 3.7E-05 28.1 4.4 32 145-176 10-41 (45)
43 KOG4196 bZIP transcription fac 84.1 9.3 0.0002 30.3 8.1 73 90-175 22-109 (135)
44 PRK00888 ftsB cell division pr 81.0 2.4 5.2E-05 32.3 3.8 47 128-175 16-62 (105)
45 PF04545 Sigma70_r4: Sigma-70, 73.1 2.8 6.2E-05 26.9 2.0 41 91-136 4-44 (50)
46 cd06171 Sigma70_r4 Sigma70, re 71.3 2.6 5.7E-05 26.2 1.5 43 91-138 10-52 (55)
47 PF04967 HTH_10: HTH DNA bindi 70.7 5.6 0.00012 26.6 3.0 38 92-129 1-40 (53)
48 PF00170 bZIP_1: bZIP transcri 69.2 22 0.00047 24.2 5.9 30 146-175 32-61 (64)
49 PF07716 bZIP_2: Basic region 69.2 22 0.00047 23.4 5.6 30 146-175 24-53 (54)
50 KOG3335 Predicted coiled-coil 67.7 20 0.00044 29.9 6.2 49 128-176 87-135 (181)
51 PF01527 HTH_Tnp_1: Transposas 67.0 4.1 8.8E-05 28.3 1.8 46 87-136 2-47 (76)
52 PRK03975 tfx putative transcri 64.6 8.1 0.00017 31.1 3.3 48 89-142 4-51 (141)
53 cd00569 HTH_Hin_like Helix-tur 63.8 8.7 0.00019 21.2 2.6 38 91-133 5-42 (42)
54 PF06156 DUF972: Protein of un 63.4 20 0.00044 27.4 5.2 34 143-176 18-51 (107)
55 KOG1146 Homeobox protein [Gene 63.2 8.5 0.00018 41.2 3.9 60 85-144 705-764 (1406)
56 PF13443 HTH_26: Cro/C1-type H 63.0 3 6.6E-05 27.9 0.5 40 114-153 12-51 (63)
57 PF08281 Sigma70_r4_2: Sigma-7 62.0 5 0.00011 26.0 1.4 42 92-138 11-52 (54)
58 KOG4571 Activating transcripti 60.9 20 0.00043 32.3 5.4 30 147-176 255-284 (294)
59 COG3413 Predicted DNA binding 60.8 7.7 0.00017 33.0 2.7 49 91-141 155-205 (215)
60 KOG3119 Basic region leucine z 60.5 17 0.00036 32.4 4.9 38 144-181 219-256 (269)
61 PF00424 REV: REV protein (ant 59.2 26 0.00057 26.1 4.9 36 97-146 14-49 (91)
62 KOG4005 Transcription factor X 58.9 22 0.00048 31.2 5.1 7 85-91 54-60 (292)
63 smart00338 BRLZ basic region l 58.3 41 0.00089 22.8 5.6 30 146-175 32-61 (65)
64 cd04787 HTH_HMRTR_unk Helix-Tu 56.9 66 0.0014 25.1 7.3 34 89-135 36-69 (133)
65 KOG4571 Activating transcripti 56.3 28 0.0006 31.4 5.5 32 144-175 245-276 (294)
66 KOG3755 SATB1 matrix attachmen 56.2 2.5 5.4E-05 41.5 -1.1 60 85-144 691-758 (769)
67 PRK12495 hypothetical protein; 56.1 44 0.00096 28.9 6.5 41 169-209 29-70 (226)
68 PRK00118 putative DNA-binding 53.9 23 0.00051 27.0 4.1 46 91-141 17-62 (104)
69 PRK13169 DNA replication intia 53.7 31 0.00068 26.6 4.8 35 143-177 18-52 (110)
70 PF09607 BrkDBD: Brinker DNA-b 53.3 8.6 0.00019 26.2 1.4 44 89-134 3-47 (58)
71 TIGR02209 ftsL_broad cell divi 53.2 38 0.00082 24.0 5.0 32 144-175 28-59 (85)
72 PF00196 GerE: Bacterial regul 52.3 8.4 0.00018 25.5 1.3 47 91-143 3-49 (58)
73 PF12824 MRP-L20: Mitochondria 52.2 84 0.0018 25.9 7.4 45 88-134 82-126 (164)
74 PF01166 TSC22: TSC-22/dip/bun 52.0 19 0.00041 24.6 2.9 31 146-176 13-43 (59)
75 PF00170 bZIP_1: bZIP transcri 51.9 62 0.0013 21.9 5.6 32 145-176 24-55 (64)
76 KOG0709 CREB/ATF family transc 51.9 58 0.0013 31.3 7.1 86 89-181 218-320 (472)
77 PRK09646 RNA polymerase sigma 51.1 16 0.00035 30.1 3.1 47 91-142 142-188 (194)
78 PF04977 DivIC: Septum formati 50.9 44 0.00095 23.1 5.0 30 144-173 21-50 (80)
79 cd01106 HTH_TipAL-Mta Helix-Tu 50.9 51 0.0011 24.4 5.5 65 89-174 36-100 (103)
80 PF10668 Phage_terminase: Phag 50.8 4.3 9.3E-05 27.9 -0.4 19 115-133 25-43 (60)
81 KOG3119 Basic region leucine z 50.0 54 0.0012 29.1 6.4 38 137-177 208-245 (269)
82 PF06005 DUF904: Protein of un 49.6 72 0.0016 22.6 5.8 29 146-174 24-52 (72)
83 smart00338 BRLZ basic region l 48.9 69 0.0015 21.7 5.5 30 146-175 25-54 (65)
84 cd04781 HTH_MerR-like_sg6 Heli 48.8 95 0.0021 23.7 6.9 69 88-175 34-102 (120)
85 PRK09642 RNA polymerase sigma 46.9 20 0.00044 28.3 2.9 46 92-142 107-152 (160)
86 PRK06759 RNA polymerase factor 46.5 14 0.00031 28.8 2.0 46 91-141 106-151 (154)
87 TIGR02449 conserved hypothetic 44.8 64 0.0014 22.5 4.7 19 152-170 12-30 (65)
88 PRK12526 RNA polymerase sigma 44.8 20 0.00043 29.9 2.7 46 92-142 154-199 (206)
89 PRK09652 RNA polymerase sigma 44.8 19 0.00041 28.6 2.5 46 91-141 128-173 (182)
90 PRK12512 RNA polymerase sigma 44.0 22 0.00048 28.8 2.8 47 91-142 131-177 (184)
91 PF07716 bZIP_2: Basic region 44.0 71 0.0015 20.9 4.8 25 145-169 30-54 (54)
92 PHA02955 hypothetical protein; 42.9 34 0.00073 29.5 3.7 43 94-136 60-103 (213)
93 PRK12514 RNA polymerase sigma 42.2 28 0.00061 28.0 3.2 46 92-142 130-175 (179)
94 TIGR02937 sigma70-ECF RNA poly 41.1 24 0.00052 26.6 2.5 46 91-141 110-155 (158)
95 COG4467 Regulator of replicati 41.0 53 0.0011 25.3 4.1 34 144-177 19-52 (114)
96 smart00421 HTH_LUXR helix_turn 40.9 27 0.00059 21.8 2.4 40 91-136 3-42 (58)
97 PRK11924 RNA polymerase sigma 40.8 25 0.00054 27.9 2.6 45 92-141 126-170 (179)
98 PRK12519 RNA polymerase sigma 40.7 20 0.00044 29.3 2.1 46 92-142 142-187 (194)
99 COG2963 Transposase and inacti 40.4 1.1E+02 0.0025 22.9 6.1 43 89-135 5-48 (116)
100 PRK04217 hypothetical protein; 40.2 29 0.00063 26.7 2.7 46 89-139 40-85 (110)
101 PF13936 HTH_38: Helix-turn-he 39.9 8.6 0.00019 24.3 -0.2 40 89-133 2-41 (44)
102 PRK10072 putative transcriptio 39.6 16 0.00034 27.4 1.1 42 91-139 32-73 (96)
103 PRK09644 RNA polymerase sigma 39.6 31 0.00068 27.4 3.0 47 91-142 108-154 (165)
104 PF08961 DUF1875: Domain of un 39.3 9.9 0.00021 32.9 0.0 37 141-177 123-159 (243)
105 PF10226 DUF2216: Uncharacteri 38.5 63 0.0014 27.4 4.6 23 156-178 57-79 (195)
106 PRK12515 RNA polymerase sigma 38.1 32 0.0007 28.0 2.9 47 91-142 131-177 (189)
107 KOG4403 Cell surface glycoprot 38.0 59 0.0013 31.1 4.8 37 131-167 230-269 (575)
108 KOG0999 Microtubule-associated 37.8 57 0.0012 32.2 4.8 53 126-178 142-194 (772)
109 TIGR02989 Sig-70_gvs1 RNA poly 37.8 27 0.0006 27.3 2.4 44 91-139 111-154 (159)
110 PRK09648 RNA polymerase sigma 37.6 30 0.00065 28.2 2.6 46 91-141 139-184 (189)
111 cd01109 HTH_YyaN Helix-Turn-He 37.3 86 0.0019 23.6 5.0 71 89-174 36-106 (113)
112 KOG4343 bZIP transcription fac 36.8 65 0.0014 31.6 5.0 29 147-175 309-337 (655)
113 PF14197 Cep57_CLD_2: Centroso 36.5 68 0.0015 22.5 3.9 22 153-174 46-67 (69)
114 TIGR02959 SigZ RNA polymerase 36.2 32 0.00069 27.7 2.5 42 91-137 100-141 (170)
115 PF01486 K-box: K-box region; 36.0 46 0.00099 24.7 3.2 44 127-171 56-99 (100)
116 TIGR02948 SigW_bacill RNA poly 36.0 29 0.00064 27.9 2.3 46 91-141 136-181 (187)
117 PRK13729 conjugal transfer pil 35.9 4.2E+02 0.0091 25.7 10.2 25 152-176 102-126 (475)
118 PRK05602 RNA polymerase sigma 35.6 31 0.00067 28.0 2.4 45 92-141 129-173 (186)
119 PF12269 zf-CpG_bind_C: CpG bi 35.5 1E+02 0.0022 27.1 5.6 81 126-208 10-95 (236)
120 PF05377 FlaC_arch: Flagella a 35.4 1.1E+02 0.0023 20.7 4.5 29 146-174 6-34 (55)
121 cd04779 HTH_MerR-like_sg4 Heli 35.2 1.3E+02 0.0029 23.7 5.9 16 88-103 34-49 (134)
122 PRK12537 RNA polymerase sigma 35.1 42 0.0009 27.2 3.1 45 92-141 134-178 (182)
123 TIGR00721 tfx DNA-binding prot 35.0 71 0.0015 25.6 4.3 47 89-141 4-50 (137)
124 TIGR02999 Sig-70_X6 RNA polyme 34.6 36 0.00078 27.4 2.6 45 92-141 135-179 (183)
125 TIGR02985 Sig70_bacteroi1 RNA 34.5 36 0.00078 26.3 2.6 45 92-141 114-158 (161)
126 TIGR02939 RpoE_Sigma70 RNA pol 34.3 27 0.00059 28.2 1.9 28 114-141 156-183 (190)
127 TIGR03879 near_KaiC_dom probab 34.3 6.7 0.00014 28.0 -1.5 34 103-136 23-56 (73)
128 PRK00888 ftsB cell division pr 34.0 72 0.0016 24.2 4.0 39 130-168 24-62 (105)
129 PF08172 CASP_C: CASP C termin 33.9 99 0.0022 27.2 5.4 38 137-174 90-127 (248)
130 PF06005 DUF904: Protein of un 33.8 1.4E+02 0.003 21.1 5.2 28 144-171 29-56 (72)
131 KOG4797 Transcriptional regula 33.8 85 0.0018 24.2 4.2 31 146-176 66-96 (123)
132 KOG0773 Transcription factor M 33.2 26 0.00055 31.9 1.7 38 105-142 117-154 (342)
133 PF08280 HTH_Mga: M protein tr 33.0 27 0.00058 23.4 1.4 32 95-130 6-37 (59)
134 COG4367 Uncharacterized protei 32.9 31 0.00067 25.6 1.7 38 92-129 3-40 (97)
135 PRK09047 RNA polymerase factor 32.9 42 0.00091 26.3 2.7 45 91-140 106-150 (161)
136 PRK12538 RNA polymerase sigma 32.5 46 0.00099 28.6 3.1 46 92-142 172-217 (233)
137 cd04766 HTH_HspR Helix-Turn-He 32.3 56 0.0012 23.6 3.1 21 115-135 4-24 (91)
138 PRK09639 RNA polymerase sigma 32.1 51 0.0011 25.9 3.1 45 91-141 112-156 (166)
139 PRK12541 RNA polymerase sigma 32.0 34 0.00074 27.0 2.1 46 91-141 112-157 (161)
140 PRK13922 rod shape-determining 32.0 87 0.0019 27.5 4.8 34 144-177 73-109 (276)
141 PRK12530 RNA polymerase sigma 31.8 52 0.0011 27.0 3.2 47 91-142 134-180 (189)
142 cd04761 HTH_MerR-SF Helix-Turn 31.7 12 0.00025 23.4 -0.6 22 115-136 3-24 (49)
143 PRK12546 RNA polymerase sigma 31.5 39 0.00084 27.9 2.4 47 91-142 113-159 (188)
144 TIGR00219 mreC rod shape-deter 31.2 91 0.002 27.9 4.8 34 144-177 70-107 (283)
145 PRK06930 positive control sigm 30.9 54 0.0012 27.0 3.1 47 91-142 114-160 (170)
146 PF06305 DUF1049: Protein of u 30.3 52 0.0011 22.2 2.5 13 161-173 55-67 (68)
147 PRK06811 RNA polymerase factor 30.3 42 0.00092 27.4 2.4 47 91-142 131-177 (189)
148 COG3074 Uncharacterized protei 30.2 1.1E+02 0.0023 21.8 4.0 30 141-170 33-62 (79)
149 PRK15422 septal ring assembly 30.0 1.3E+02 0.0029 21.7 4.5 24 147-170 39-62 (79)
150 cd04770 HTH_HMRTR Helix-Turn-H 29.9 1.6E+02 0.0034 22.4 5.5 73 88-175 35-107 (123)
151 cd02413 40S_S3_KH K homology R 29.8 47 0.001 24.0 2.3 20 115-134 56-75 (81)
152 PRK15422 septal ring assembly 29.6 1.5E+02 0.0033 21.5 4.8 27 146-172 17-43 (79)
153 COG3074 Uncharacterized protei 29.6 1.6E+02 0.0035 20.9 4.8 9 158-166 29-37 (79)
154 PRK09637 RNA polymerase sigma 29.4 48 0.001 27.0 2.6 44 91-139 106-149 (181)
155 TIGR02983 SigE-fam_strep RNA p 29.4 48 0.001 26.0 2.5 46 92-142 111-156 (162)
156 TIGR02954 Sig70_famx3 RNA poly 29.4 53 0.0012 26.1 2.8 46 91-141 119-164 (169)
157 PRK12543 RNA polymerase sigma 29.3 81 0.0018 25.4 3.9 46 92-142 118-163 (179)
158 PF04999 FtsL: Cell division p 29.2 1.1E+02 0.0024 22.3 4.3 29 147-175 42-70 (97)
159 PF06785 UPF0242: Uncharacteri 29.1 1.4E+02 0.0029 27.8 5.5 39 137-175 138-176 (401)
160 PF09726 Macoilin: Transmembra 29.0 2.2E+02 0.0047 29.1 7.5 39 138-176 543-581 (697)
161 PF03980 Nnf1: Nnf1 ; InterPr 28.7 1E+02 0.0022 23.1 4.1 30 146-175 79-108 (109)
162 cd06170 LuxR_C_like C-terminal 28.4 51 0.0011 20.6 2.1 36 93-134 2-37 (57)
163 TIGR02051 MerR Hg(II)-responsi 28.1 1.9E+02 0.0041 22.2 5.6 35 88-135 34-68 (124)
164 PRK12536 RNA polymerase sigma 27.9 55 0.0012 26.5 2.7 29 114-142 147-175 (181)
165 PRK07037 extracytoplasmic-func 27.7 57 0.0012 25.6 2.7 45 91-140 109-153 (163)
166 PRK13919 putative RNA polymera 27.7 60 0.0013 26.2 2.9 45 91-140 135-179 (186)
167 KOG4752 Ribosomal protein L41 27.7 1.2E+02 0.0025 16.9 3.0 8 137-144 2-9 (26)
168 PRK14127 cell division protein 27.6 1.5E+02 0.0032 22.8 4.8 35 144-178 34-68 (109)
169 PF12808 Mto2_bdg: Micro-tubul 27.5 1E+02 0.0023 20.5 3.4 25 150-174 25-49 (52)
170 PRK12547 RNA polymerase sigma 27.5 56 0.0012 25.9 2.6 46 91-141 112-157 (164)
171 TIGR03752 conj_TIGR03752 integ 27.5 1E+02 0.0022 29.8 4.7 17 158-174 120-136 (472)
172 cd04777 HTH_MerR-like_sg1 Heli 27.4 1.2E+02 0.0026 22.6 4.2 33 91-136 36-68 (107)
173 PF13518 HTH_28: Helix-turn-he 27.4 21 0.00046 22.5 0.1 21 115-135 15-35 (52)
174 PRK06986 fliA flagellar biosyn 27.2 50 0.0011 28.1 2.4 46 92-142 185-230 (236)
175 PRK10884 SH3 domain-containing 26.8 1.6E+02 0.0036 25.1 5.4 12 94-105 92-103 (206)
176 cd04775 HTH_Cfa-like Helix-Tur 26.6 1.9E+02 0.0041 21.4 5.2 16 88-103 35-50 (102)
177 cd04783 HTH_MerR1 Helix-Turn-H 26.5 1.9E+02 0.0042 22.1 5.4 35 89-136 36-70 (126)
178 PRK12524 RNA polymerase sigma 26.3 59 0.0013 26.7 2.6 45 92-141 137-181 (196)
179 PRK12532 RNA polymerase sigma 26.0 72 0.0016 26.1 3.1 46 92-142 137-182 (195)
180 TIGR02952 Sig70_famx2 RNA poly 25.9 61 0.0013 25.5 2.6 39 91-134 122-160 (170)
181 TIGR02894 DNA_bind_RsfA transc 25.8 1.4E+02 0.0031 24.6 4.6 25 149-173 106-130 (161)
182 PF06056 Terminase_5: Putative 25.6 22 0.00049 24.0 -0.1 26 115-142 16-41 (58)
183 KOG3584 cAMP response element 25.5 1E+02 0.0023 27.9 4.0 25 154-178 319-343 (348)
184 TIGR02943 Sig70_famx1 RNA poly 25.4 84 0.0018 25.7 3.4 47 91-142 131-177 (188)
185 KOG3623 Homeobox transcription 25.4 42 0.00092 34.2 1.8 60 86-145 627-686 (1007)
186 cd04765 HTH_MlrA-like_sg2 Heli 24.8 1.2E+02 0.0026 22.5 3.8 36 88-135 35-70 (99)
187 TIGR02479 FliA_WhiG RNA polyme 24.7 63 0.0014 27.2 2.5 46 91-141 175-220 (224)
188 PF15058 Speriolin_N: Sperioli 24.7 95 0.0021 26.4 3.5 25 147-172 19-43 (200)
189 PRK09645 RNA polymerase sigma 24.4 78 0.0017 25.2 2.9 44 92-140 119-162 (173)
190 PF02796 HTH_7: Helix-turn-hel 24.2 33 0.00072 21.5 0.6 38 91-133 5-42 (45)
191 PF07407 Seadorna_VP6: Seadorn 24.2 95 0.0021 28.7 3.6 19 155-173 40-58 (420)
192 PF10883 DUF2681: Protein of u 24.2 2.5E+02 0.0054 20.7 5.2 11 131-141 21-31 (87)
193 TIGR03001 Sig-70_gmx1 RNA poly 24.2 1.5E+02 0.0033 25.6 4.9 50 92-146 162-211 (244)
194 PF08826 DMPK_coil: DMPK coile 23.5 2.5E+02 0.0055 19.2 5.7 21 155-175 40-60 (61)
195 KOG2483 Upstream transcription 23.2 1.7E+02 0.0037 25.6 4.9 39 137-175 102-140 (232)
196 PRK08583 RNA polymerase sigma 23.1 72 0.0016 27.6 2.6 46 91-141 205-250 (257)
197 cd01107 HTH_BmrR Helix-Turn-He 23.0 2.8E+02 0.006 20.7 5.6 66 89-174 37-102 (108)
198 PRK12533 RNA polymerase sigma 22.9 66 0.0014 27.3 2.3 44 91-139 134-177 (216)
199 PRK08295 RNA polymerase factor 22.9 79 0.0017 25.9 2.8 44 92-141 156-199 (208)
200 PRK09649 RNA polymerase sigma 22.8 66 0.0014 26.2 2.2 46 91-141 130-175 (185)
201 PRK10100 DNA-binding transcrip 22.8 84 0.0018 26.7 2.9 48 91-144 155-202 (216)
202 PRK12539 RNA polymerase sigma 22.7 81 0.0017 25.5 2.7 46 91-141 131-176 (184)
203 PF02344 Myc-LZ: Myc leucine z 22.7 1.8E+02 0.004 17.3 3.9 24 152-175 6-29 (32)
204 PRK12545 RNA polymerase sigma 22.5 79 0.0017 26.2 2.7 46 91-141 139-184 (201)
205 COG1905 NuoE NADH:ubiquinone o 22.5 1E+02 0.0023 25.3 3.3 37 94-130 25-61 (160)
206 PRK12516 RNA polymerase sigma 22.5 80 0.0017 25.9 2.7 45 92-141 117-161 (187)
207 PF13411 MerR_1: MerR HTH fami 22.4 23 0.00049 23.9 -0.5 21 115-135 3-23 (69)
208 TIGR02980 SigBFG RNA polymeras 22.4 77 0.0017 26.7 2.6 46 91-141 178-223 (227)
209 PRK09647 RNA polymerase sigma 22.4 78 0.0017 26.4 2.6 46 91-141 138-183 (203)
210 PRK09480 slmA division inhibit 22.3 54 0.0012 26.4 1.6 38 100-138 19-56 (194)
211 PRK15369 two component system 22.0 97 0.0021 24.2 3.0 47 90-142 148-194 (211)
212 PRK10884 SH3 domain-containing 22.0 2.6E+02 0.0056 23.8 5.8 19 152-170 137-155 (206)
213 TIGR02859 spore_sigH RNA polym 22.0 79 0.0017 25.7 2.5 29 113-141 166-194 (198)
214 PRK10403 transcriptional regul 21.9 60 0.0013 25.8 1.8 48 91-144 153-200 (215)
215 PF14662 CCDC155: Coiled-coil 21.8 2.2E+02 0.0048 24.2 5.1 39 135-173 83-121 (193)
216 PRK09651 RNA polymerase sigma 21.8 74 0.0016 25.5 2.3 44 91-139 119-162 (172)
217 PRK12544 RNA polymerase sigma 21.7 83 0.0018 26.3 2.7 47 91-142 148-194 (206)
218 PF15397 DUF4618: Domain of un 21.5 1.8E+02 0.0039 25.8 4.8 35 153-187 199-233 (258)
219 PRK12529 RNA polymerase sigma 21.4 85 0.0018 25.3 2.6 45 91-140 127-171 (178)
220 PF04880 NUDE_C: NUDE protein, 21.4 77 0.0017 26.3 2.3 12 159-170 36-47 (166)
221 cd07429 Cby_like Chibby, a nuc 21.4 1.7E+02 0.0037 22.5 4.0 27 150-176 75-101 (108)
222 COG2944 Predicted transcriptio 21.3 56 0.0012 25.0 1.4 41 91-138 43-83 (104)
223 TIGR02047 CadR-PbrR Cd(II)/Pb( 21.2 2.7E+02 0.0058 21.5 5.3 34 88-134 35-68 (127)
224 PF13384 HTH_23: Homeodomain-l 21.2 22 0.00047 22.5 -0.8 22 114-135 19-40 (50)
225 cd04785 HTH_CadR-PbrR-like Hel 21.0 2.7E+02 0.0059 21.3 5.3 15 89-103 36-50 (126)
226 TIGR02947 SigH_actino RNA poly 21.0 45 0.00097 27.3 0.9 28 114-141 149-176 (193)
227 PF11365 DUF3166: Protein of u 21.0 2.1E+02 0.0045 21.6 4.3 31 146-176 14-44 (96)
228 PRK11923 algU RNA polymerase s 21.0 81 0.0017 25.6 2.4 28 114-141 156-183 (193)
229 PRK12511 RNA polymerase sigma 21.0 87 0.0019 25.6 2.6 44 91-139 111-154 (182)
230 PRK12542 RNA polymerase sigma 20.9 84 0.0018 25.4 2.5 46 91-141 122-167 (185)
231 PRK07670 RNA polymerase sigma 20.9 84 0.0018 27.1 2.6 45 92-141 202-246 (251)
232 PRK12523 RNA polymerase sigma 20.9 92 0.002 24.9 2.7 45 92-141 120-164 (172)
233 PRK12531 RNA polymerase sigma 20.8 1E+02 0.0022 25.2 3.0 44 91-139 141-184 (194)
234 PRK12518 RNA polymerase sigma 20.6 43 0.00094 26.7 0.7 29 114-142 138-166 (175)
235 PRK12520 RNA polymerase sigma 20.5 1.1E+02 0.0025 24.7 3.2 47 91-142 131-177 (191)
236 cd04769 HTH_MerR2 Helix-Turn-H 20.5 3E+02 0.0064 20.8 5.3 35 89-136 35-69 (116)
237 PTZ00454 26S protease regulato 20.4 2.3E+02 0.005 26.6 5.6 36 141-176 30-65 (398)
238 PF09730 BicD: Microtubule-ass 20.4 2E+02 0.0044 29.4 5.4 23 152-174 95-117 (717)
239 PRK10651 transcriptional regul 20.4 86 0.0019 24.9 2.5 47 91-143 155-201 (216)
240 PRK10360 DNA-binding transcrip 20.3 54 0.0012 25.9 1.2 45 91-141 137-181 (196)
241 PF11594 Med28: Mediator compl 20.1 1.1E+02 0.0023 23.6 2.6 14 127-140 18-31 (106)
242 PRK05657 RNA polymerase sigma 20.1 78 0.0017 28.8 2.3 51 91-142 262-312 (325)
243 KOG1962 B-cell receptor-associ 20.1 1.6E+02 0.0034 25.5 4.0 35 137-171 176-210 (216)
244 PF09744 Jnk-SapK_ap_N: JNK_SA 20.1 4.9E+02 0.011 21.2 7.1 14 96-109 34-47 (158)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.92 E-value=2.5e-25 Score=187.26 Aligned_cols=121 Identities=46% Similarity=0.657 Sum_probs=108.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHHHHHHHHHHhhchHHHH
Q 026325 84 GPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEMECEYLKRWFGSLTEQN 163 (240)
Q Consensus 84 ~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~~~~~l~~~~~~l~~e~ 163 (240)
+..+++.+|+.+|+..||..|+.+.++.+.++..||+.|||.+|||.|||||||||||.++.+.++++|+.+++.|..++
T Consensus 49 ~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~ 128 (198)
T KOG0483|consen 49 KGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEN 128 (198)
T ss_pred ccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhh
Confidence 35567789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccc
Q 026325 164 RRLQREVEELRAMKVGPPTVISPHSCEPLPASTLSMCPRCERVTTT 209 (240)
Q Consensus 164 ~~l~~e~~~l~~~~~~~~~~~~p~s~~~~p~~~~~~cp~c~~~~~~ 209 (240)
++|+.++.+|++........... .+.....+|+.|+.+...
T Consensus 129 ~~Lq~e~~eL~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~ 169 (198)
T KOG0483|consen 129 DRLQSEVQELVAELSSLKREMQK-----SPENTLTMCPNSESSSSV 169 (198)
T ss_pred hHHHHHHHHHHHHHhhhhhhhcc-----CcccccccCccccccCCc
Confidence 99999999999987655443321 267889999999966654
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.78 E-value=7.6e-19 Score=156.19 Aligned_cols=68 Identities=35% Similarity=0.605 Sum_probs=62.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHHHHHH
Q 026325 84 GPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEMECEY 151 (240)
Q Consensus 84 ~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~~~~~ 151 (240)
++||.|..|+..|+.+||+.|++.+|++..||+.||..|+|+++||||||||||-|.||++++++.+.
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred cccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 45566667999999999999999999999999999999999999999999999999999987776654
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.78 E-value=5.1e-20 Score=162.39 Aligned_cols=63 Identities=33% Similarity=0.568 Sum_probs=59.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 82 DGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 82 ~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
.++.||.|+.||..|+.+||+.|..|+|+++..|.+||..|.|+++||||||||||+||||.+
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhh
Confidence 346789999999999999999999999999999999999999999999999999999999865
No 4
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.77 E-value=2.1e-19 Score=159.75 Aligned_cols=66 Identities=33% Similarity=0.499 Sum_probs=61.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHHH
Q 026325 83 GGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEME 148 (240)
Q Consensus 83 ~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~~ 148 (240)
+..||||..+|+.|+.+||+.|..|.|++.+.|.+|++.|+|++|||||||||||+|+||..++..
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 457888999999999999999999999999999999999999999999999999999999875443
No 5
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.76 E-value=1.3e-18 Score=156.54 Aligned_cols=64 Identities=33% Similarity=0.452 Sum_probs=59.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhH
Q 026325 83 GGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTE 146 (240)
Q Consensus 83 ~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~ 146 (240)
.|+|+.|+.||..|+..||+.|++.+|++..+|.+||+.|||+..||++||||||+|||++..+
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 4667779999999999999999999999999999999999999999999999999999997644
No 6
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.75 E-value=1.3e-18 Score=130.39 Aligned_cols=65 Identities=29% Similarity=0.470 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHh
Q 026325 81 VDGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQT 145 (240)
Q Consensus 81 ~~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~ 145 (240)
...++||-|+.||..||.+||+.|...+||++..|++||.++.|++..|+|||||||+|.||+++
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 45678889999999999999999999999999999999999999999999999999999998653
No 7
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.73 E-value=1.5e-17 Score=143.55 Aligned_cols=62 Identities=32% Similarity=0.558 Sum_probs=57.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhH
Q 026325 85 PPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTE 146 (240)
Q Consensus 85 ~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~ 146 (240)
+-|.|.++|..|..+||+.|...+|+++..+.+||.-|+|++|||||||||||+|+||.+++
T Consensus 199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK 260 (317)
T ss_pred ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence 33567789999999999999999999999999999999999999999999999999987644
No 8
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.73 E-value=2.7e-18 Score=140.54 Aligned_cols=64 Identities=38% Similarity=0.538 Sum_probs=61.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHH
Q 026325 84 GPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEM 147 (240)
Q Consensus 84 ~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~ 147 (240)
+.||.||.|+.+|+..||..|+.++|..-.+|+.||..|+|++.||+|||||||.|.||++.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 7889999999999999999999999999999999999999999999999999999999988664
No 9
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.73 E-value=4.2e-17 Score=137.01 Aligned_cols=63 Identities=32% Similarity=0.503 Sum_probs=59.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 82 DGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 82 ~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
++++||.||+|+..|+..||..|+..+|++..+|..||++|.|++.||||||||||.|||++-
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 346777899999999999999999999999999999999999999999999999999999875
No 10
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.71 E-value=8.1e-18 Score=144.58 Aligned_cols=68 Identities=25% Similarity=0.377 Sum_probs=59.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHHHHHHH
Q 026325 85 PPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEMECEYL 152 (240)
Q Consensus 85 ~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~~~~~l 152 (240)
+|+.||.||..|+..||+.|+..+||+...|+.||.++.|.+.+|+|||||||+||||+++.--....
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~ 208 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTI 208 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchh
Confidence 33348999999999999999999999999999999999999999999999999999998765433333
No 11
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.70 E-value=1.7e-17 Score=138.53 Aligned_cols=62 Identities=32% Similarity=0.536 Sum_probs=58.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 83 GGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 83 ~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
...|+.|+.||..||..||+.|+..+|+++.+|.+++..|.|++.||||||||||+|.||-|
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 34677899999999999999999999999999999999999999999999999999999865
No 12
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.70 E-value=1e-17 Score=141.89 Aligned_cols=64 Identities=30% Similarity=0.433 Sum_probs=59.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHh
Q 026325 82 DGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQT 145 (240)
Q Consensus 82 ~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~ 145 (240)
..|.||.||.|+.-||..|.+.|+++.|+-..||.+||..|||+..||||||||||.|.||..+
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 3356667999999999999999999999999999999999999999999999999999998653
No 13
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.68 E-value=2.5e-17 Score=138.98 Aligned_cols=67 Identities=30% Similarity=0.482 Sum_probs=62.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHH
Q 026325 81 VDGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEM 147 (240)
Q Consensus 81 ~~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~ 147 (240)
..++.||.||.|+..|+++||..|.+..||+...|++||.+|+|.+.+|+|||+|||+|+|+++...
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 4567899999999999999999999999999999999999999999999999999999999877543
No 14
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.67 E-value=1.4e-16 Score=137.07 Aligned_cols=92 Identities=26% Similarity=0.451 Sum_probs=73.6
Q ss_pred CccCCCCCCCCCCCCCCCCCCCccccccC--CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcee
Q 026325 52 DTEWNNWNTATATTTGSGSMDDEEESCIN--VDGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQV 129 (240)
Q Consensus 52 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qV 129 (240)
..-|+.|+.++..+.-..+.......... .....||.|+.|+.+||..|+..|+.++|++...|.+||.+|+|.+.||
T Consensus 211 p~mwPAWVycTRYSDRPSsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQI 290 (342)
T KOG0493|consen 211 PSMWPAWVYCTRYSDRPSSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQI 290 (342)
T ss_pred ccccceeeeeecccCCCCCCcccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHh
Confidence 36688898888777655544332221111 1223567899999999999999999999999999999999999999999
Q ss_pred eecchhhhhHHHHH
Q 026325 130 EVWFQNRRARSKLK 143 (240)
Q Consensus 130 kvWFqNRR~k~Kkk 143 (240)
+|||||+|+|.||-
T Consensus 291 KIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 291 KIWFQNKRAKIKKS 304 (342)
T ss_pred hHHhhhhhhhhhhc
Confidence 99999999999874
No 15
>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=99.67 E-value=3.3e-17 Score=111.69 Aligned_cols=57 Identities=47% Similarity=0.723 Sum_probs=55.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 86 PRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 86 rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
||+|+.|+.+|+..|+.+|..++||+..+++.||..+||+..+|++||+|||+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999985
No 16
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.61 E-value=3.2e-16 Score=137.52 Aligned_cols=68 Identities=31% Similarity=0.498 Sum_probs=63.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHHH
Q 026325 81 VDGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEME 148 (240)
Q Consensus 81 ~~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~~ 148 (240)
.+..-||.||.||.+||..||+.|-+..|.++..|.+||..|+|.+..|||||||||+|+||++..+-
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlama 244 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMA 244 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhcc
Confidence 45567899999999999999999999999999999999999999999999999999999999887643
No 17
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.56 E-value=5.3e-15 Score=130.38 Aligned_cols=73 Identities=29% Similarity=0.479 Sum_probs=64.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHHHHHHHHHHh
Q 026325 84 GPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEMECEYLKRWF 156 (240)
Q Consensus 84 ~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~~~~~l~~~~ 156 (240)
|+||.|+.|+..|+.+||.+|+++.||+...|++||..++|++..|+|||.|||+||||.++....+..|..+
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~~k~~f 183 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELAKGGF 183 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHhhhcCC
Confidence 6788899999999999999999999999999999999999999999999999999999877655544444333
No 18
>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=99.56 E-value=5.1e-15 Score=101.31 Aligned_cols=53 Identities=13% Similarity=0.322 Sum_probs=50.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHhCCCCceeeecchhhh
Q 026325 85 PPRKKLRLSKEQSRLLEESFRHNHT----LNPKQKEELATQLKLKPRQVEVWFQNRR 137 (240)
Q Consensus 85 ~rr~R~~~t~~Q~~~Le~~F~~~~~----p~~~~r~~LA~~l~L~~~qVkvWFqNRR 137 (240)
+||.||.||.+|+..||..|..++| |+..++.+||..|||++++|+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3789999999999999999999999 9999999999999999999999999964
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.55 E-value=3e-15 Score=101.25 Aligned_cols=56 Identities=46% Similarity=0.684 Sum_probs=52.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 86 PRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 86 rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
++.|+.|+.+|+.+|+.+|..++||+..++..||..+||+..+|++||+|||++.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35677899999999999999999999999999999999999999999999998864
No 20
>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=99.54 E-value=3.8e-15 Score=101.54 Aligned_cols=58 Identities=45% Similarity=0.673 Sum_probs=54.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHH
Q 026325 86 PRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLK 143 (240)
Q Consensus 86 rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk 143 (240)
+++|..|+..|+.+|+.+|..++||+..++..||..+||++.+|++||+|||.+.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 3567899999999999999999999999999999999999999999999999998863
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.51 E-value=1.5e-14 Score=118.17 Aligned_cols=66 Identities=32% Similarity=0.532 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHH
Q 026325 82 DGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEM 147 (240)
Q Consensus 82 ~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~ 147 (240)
....+++|++.+.+|+.+|+..|+.++||+...|..|+..|+|+++-|+|||||||++.|++....
T Consensus 48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred CCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence 345788899999999999999999999999999999999999999999999999999999876443
No 22
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.48 E-value=3.9e-15 Score=120.37 Aligned_cols=62 Identities=34% Similarity=0.510 Sum_probs=58.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHh
Q 026325 84 GPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQT 145 (240)
Q Consensus 84 ~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~ 145 (240)
+++|-|++|+..|+..||+.|+..+|++..+|.+||..|+|++.||+.||||||+|.||.++
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r 160 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQR 160 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHh
Confidence 35667999999999999999999999999999999999999999999999999999998763
No 23
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.48 E-value=2.9e-14 Score=129.73 Aligned_cols=63 Identities=25% Similarity=0.404 Sum_probs=59.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 82 DGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 82 ~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
.+++|||||.|....+..||+.|.+|+.|+..++..||.+|+|.+..|+|||+|||.|+||..
T Consensus 291 ~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 291 QSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 347888999999999999999999999999999999999999999999999999999999854
No 24
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.48 E-value=3.9e-14 Score=123.66 Aligned_cols=78 Identities=26% Similarity=0.425 Sum_probs=69.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHHHHHHHHHHhhc
Q 026325 81 VDGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEMECEYLKRWFGS 158 (240)
Q Consensus 81 ~~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~~~~~l~~~~~~ 158 (240)
.++..||.||.+|..||+.|+..|+..+.|.+..|++|+.++||..|.|||||||||+|+||-++..-...|.+++.+
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrs 240 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRS 240 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHH
Confidence 345678999999999999999999999999999999999999999999999999999999998777666666555543
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.42 E-value=4.5e-14 Score=119.03 Aligned_cols=65 Identities=29% Similarity=0.522 Sum_probs=60.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHh
Q 026325 81 VDGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQT 145 (240)
Q Consensus 81 ~~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~ 145 (240)
.+++++..|..|+..|+..||..|+..+|+--.+|.+||..+|+++.||+|||||||.|||||..
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 45667777888999999999999999999999999999999999999999999999999998764
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.26 E-value=3.1e-12 Score=109.89 Aligned_cols=63 Identities=29% Similarity=0.335 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 82 DGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 82 ~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
..++|+.|+.|+..|+++||+.|.+.+||+...++.||..+++++..|+|||||||+||++++
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 446788999999999999999999999999999999999999999999999999999999865
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.14 E-value=2.4e-11 Score=111.55 Aligned_cols=71 Identities=32% Similarity=0.465 Sum_probs=63.0
Q ss_pred ccccccCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 74 EEESCINVDGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 74 ~~~~~~~~~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
+.........+.+|.|+.|+..|+..||+.|+.++||+...|+.||.++++++..|+|||+|||++|+|..
T Consensus 165 ~~~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 165 EEPPGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 33333344567788899999999999999999999999999999999999999999999999999999865
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.09 E-value=6.2e-11 Score=103.83 Aligned_cols=63 Identities=29% Similarity=0.449 Sum_probs=58.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 82 DGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 82 ~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
.+.+|||||.+-..+.+.||.+|...+.|+.+.+..||++|+|.+..|+|||+|.|+|.||.+
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 345789999999999999999999999999999999999999999999999999999988754
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.00 E-value=2.5e-10 Score=99.41 Aligned_cols=51 Identities=35% Similarity=0.571 Sum_probs=47.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
|...-..+|.+||..++||++.++.+||+.+||+..||-+||.|||+|+|-
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 556668899999999999999999999999999999999999999999984
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.82 E-value=9.4e-09 Score=89.09 Aligned_cols=59 Identities=37% Similarity=0.523 Sum_probs=55.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHH
Q 026325 85 PPRKKLRLSKEQSRLLEESFR---HNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLK 143 (240)
Q Consensus 85 ~rr~R~~~t~~Q~~~Le~~F~---~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk 143 (240)
.+|||+.|++...++|..+|. .++||+.+.+++||++.+++..||..||.|+|-+.||-
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 578999999999999999995 46999999999999999999999999999999999873
No 31
>smart00340 HALZ homeobox associated leucin zipper.
Probab=98.77 E-value=1.3e-08 Score=64.02 Aligned_cols=42 Identities=64% Similarity=0.985 Sum_probs=38.3
Q ss_pred HHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhccCCCCCCC
Q 026325 143 KQTEMECEYLKRWFGSLTEQNRRLQREVEELRAMKVGPPTVI 184 (240)
Q Consensus 143 k~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~~~~~~~~~ 184 (240)
||++.+|++||++++.|.+||++|++|+++||+++..++.++
T Consensus 1 KQTEvdCe~LKrcce~LteeNrRL~ke~~eLralk~~~~~~m 42 (44)
T smart00340 1 KQTEVDCELLKRCCESLTEENRRLQKEVQELRALKLSPPLYM 42 (44)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcccc
Confidence 478999999999999999999999999999999998776554
No 32
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.49 E-value=2.7e-08 Score=63.16 Aligned_cols=34 Identities=44% Similarity=0.646 Sum_probs=29.0
Q ss_pred hcCCCCHHHHHHHHHHhCCCCceeeecchhhhhH
Q 026325 106 HNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139 (240)
Q Consensus 106 ~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k 139 (240)
.++||+.++++.||.++||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4689999999999999999999999999999875
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.27 E-value=5.7e-07 Score=85.27 Aligned_cols=59 Identities=27% Similarity=0.362 Sum_probs=55.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 83 GGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 83 ~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
...||.|.+||..|++.|..+|+.+++|+.+..+.|+.+|+|....|.+||.|-|.|.+
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 35778899999999999999999999999999999999999999999999999988863
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.09 E-value=2.4e-06 Score=73.24 Aligned_cols=63 Identities=32% Similarity=0.584 Sum_probs=58.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 82 DGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 82 ~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
..+.++.|+.+...|+..|+..|....+|+...++.|+..+|+.++.|++||+|+|.+.++..
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 456778899999999999999999999999999999999999999999999999999999865
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.88 E-value=2.5e-05 Score=80.65 Aligned_cols=63 Identities=27% Similarity=0.404 Sum_probs=58.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 82 DGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 82 ~~~~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
.-+++++|++++..|+..|..+|....||...+.+.|...+++.++.|++||||-|+|.|+..
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 335788999999999999999999999999999999999999999999999999999998754
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.22 E-value=0.00017 Score=65.89 Aligned_cols=60 Identities=28% Similarity=0.237 Sum_probs=50.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 85 PPRKKLRLSKEQSRLLEESFRH---NHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 85 ~rr~R~~~t~~Q~~~Le~~F~~---~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
..|.+..|......+|+.|... .+||+..++..||+++||+..||.+||.|.|.|..+--
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence 4455567999999999998443 47999999999999999999999999999988766543
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.88 E-value=0.00023 Score=48.18 Aligned_cols=41 Identities=24% Similarity=0.472 Sum_probs=31.2
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhh
Q 026325 97 SRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRR 137 (240)
Q Consensus 97 ~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR 137 (240)
+..|+++|..++++...+...|..+.+|+..||+.||--|+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 45699999999999999999999999999999999997654
No 38
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=96.19 E-value=0.0089 Score=38.78 Aligned_cols=35 Identities=37% Similarity=0.435 Sum_probs=30.4
Q ss_pred HHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhcc
Q 026325 143 KQTEMECEYLKRWFGSLTEQNRRLQREVEELRAMK 177 (240)
Q Consensus 143 k~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~~ 177 (240)
||.+.++..|+.+++.|..+++.|++|++.|++..
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev 35 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEV 35 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999998888754
No 39
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.89 E-value=0.016 Score=57.38 Aligned_cols=48 Identities=21% Similarity=0.340 Sum_probs=44.5
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 97 SRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 97 ~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
+.+|..+|..|..|+.++...+|.+.||..+.|+.||+++++....-+
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 788999999999999999999999999999999999999998876544
No 40
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=93.85 E-value=0.37 Score=37.46 Aligned_cols=81 Identities=20% Similarity=0.224 Sum_probs=48.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhH--------------HHHHHhHHHHHHH
Q 026325 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR--------------SKLKQTEMECEYL 152 (240)
Q Consensus 87 r~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k--------------~Kkk~~~~~~~~l 152 (240)
++|.+|+.++....-..+..+.+ ...++|.++|++..+|..|.+--+.. ......+.++..|
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~L 83 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKEL 83 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHHH
Confidence 34566888775544333333332 35578999999999999996542211 0112234555566
Q ss_pred HHHhhchHHHHHHHHHHHH
Q 026325 153 KRWFGSLTEQNRRLQREVE 171 (240)
Q Consensus 153 ~~~~~~l~~e~~~l~~e~~ 171 (240)
++....|..|++-|++.+.
T Consensus 84 ~~el~~L~~E~diLKKa~~ 102 (121)
T PRK09413 84 QRLLGKKTMENELLKEAVE 102 (121)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 6666666666666666553
No 41
>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=93.82 E-value=0.072 Score=35.58 Aligned_cols=46 Identities=17% Similarity=0.312 Sum_probs=34.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhh
Q 026325 86 PRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNR 136 (240)
Q Consensus 86 rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNR 136 (240)
+|+|..+|-++...+-..++... ....||+++|+...+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 57888999998888877787665 46789999999999999999885
No 42
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=86.81 E-value=1.7 Score=28.09 Aligned_cols=32 Identities=31% Similarity=0.478 Sum_probs=28.4
Q ss_pred hHHHHHHHHHHhhchHHHHHHHHHHHHHHHhc
Q 026325 145 TEMECEYLKRWFGSLTEQNRRLQREVEELRAM 176 (240)
Q Consensus 145 ~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~ 176 (240)
....++.|+..++.|..||+.|+.++..|+..
T Consensus 10 LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~k 41 (45)
T PF02183_consen 10 LKASYDSLKAEYDSLKKENEKLRAEVQELKEK 41 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45678899999999999999999999999864
No 43
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=84.11 E-value=9.3 Score=30.32 Aligned_cols=73 Identities=29% Similarity=0.303 Sum_probs=49.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHH-HHhCCCCceeeecchhhhhH----------HHHH----HhHHHHHHHHH
Q 026325 90 LRLSKEQSRLLEESFRHNHTLNPKQKEELA-TQLKLKPRQVEVWFQNRRAR----------SKLK----QTEMECEYLKR 154 (240)
Q Consensus 90 ~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA-~~l~L~~~qVkvWFqNRR~k----------~Kkk----~~~~~~~~l~~ 154 (240)
.+|+.++|..|- .| +|= +.-|++...|-.|=|.||+- .|+- +.+.+...|.+
T Consensus 22 d~lsDd~LvsmS------------VR-eLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~q 88 (135)
T KOG4196|consen 22 DRLSDDELVSMS------------VR-ELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQ 88 (135)
T ss_pred CCcCHHHHHHhh------------HH-HHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678888877662 12 222 33377777777787777643 2332 33555667888
Q ss_pred HhhchHHHHHHHHHHHHHHHh
Q 026325 155 WFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 155 ~~~~l~~e~~~l~~e~~~l~~ 175 (240)
+.+.|.+||.+++.|+..++.
T Consensus 89 qv~~L~~e~s~~~~E~da~k~ 109 (135)
T KOG4196|consen 89 QVEKLKEENSRLRRELDAYKS 109 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 889999999999999887765
No 44
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=80.97 E-value=2.4 Score=32.33 Aligned_cols=47 Identities=17% Similarity=0.307 Sum_probs=27.6
Q ss_pred eeeecchhhhhHHHHHHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHh
Q 026325 128 QVEVWFQNRRARSKLKQTEMECEYLKRWFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 128 qVkvWFqNRR~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~ 175 (240)
++..||.+.-- .+-.+.+.+...++.....+..+|++|+.|+..|+.
T Consensus 16 ~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 16 QYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 34578855411 112233445556666667777777777777777764
No 45
>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=73.13 E-value=2.8 Score=26.92 Aligned_cols=41 Identities=15% Similarity=0.244 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhh
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNR 136 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNR 136 (240)
.+++.+..+|...|... ..-.++|..+|++...|+.+...-
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHH
Confidence 46788899999988333 235689999999998887665433
No 46
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=71.29 E-value=2.6 Score=26.23 Aligned_cols=43 Identities=16% Similarity=0.223 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhh
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRA 138 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~ 138 (240)
.++..+..++...|.... ...++|..+|++...|..|...-+.
T Consensus 10 ~l~~~~~~~~~~~~~~~~-----~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEGL-----SYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcCC-----CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 367777888877764332 3567899999999999888765443
No 47
>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=70.67 E-value=5.6 Score=26.58 Aligned_cols=38 Identities=24% Similarity=0.323 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHhCCCCcee
Q 026325 92 LSKEQSRLLEESFRHNH--TLNPKQKEELATQLKLKPRQV 129 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~--~p~~~~r~~LA~~l~L~~~qV 129 (240)
+|+.|.++|...|+..= +|-.....+||+.||++..-|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 57899999999998663 466667789999999988643
No 48
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=69.19 E-value=22 Score=24.16 Aligned_cols=30 Identities=23% Similarity=0.348 Sum_probs=16.5
Q ss_pred HHHHHHHHHHhhchHHHHHHHHHHHHHHHh
Q 026325 146 EMECEYLKRWFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 146 ~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~ 175 (240)
+..+..|...++.|..++..|..++..|..
T Consensus 32 e~~~~~L~~en~~L~~~~~~L~~~~~~L~~ 61 (64)
T PF00170_consen 32 EEKVEELESENEELKKELEQLKKEIQSLKS 61 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 444445555555566666666666555543
No 49
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=69.16 E-value=22 Score=23.41 Aligned_cols=30 Identities=27% Similarity=0.382 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhhchHHHHHHHHHHHHHHHh
Q 026325 146 EMECEYLKRWFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 146 ~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~ 175 (240)
......+......|..+|..|..++..|..
T Consensus 24 k~~~~~le~~~~~L~~en~~L~~~i~~L~~ 53 (54)
T PF07716_consen 24 KQREEELEQEVQELEEENEQLRQEIAQLER 53 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 344455666777888999999998888763
No 50
>KOG3335 consensus Predicted coiled-coil protein [General function prediction only]
Probab=67.75 E-value=20 Score=29.94 Aligned_cols=49 Identities=22% Similarity=0.265 Sum_probs=39.6
Q ss_pred eeeecchhhhhHHHHHHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhc
Q 026325 128 QVEVWFQNRRARSKLKQTEMECEYLKRWFGSLTEQNRRLQREVEELRAM 176 (240)
Q Consensus 128 qVkvWFqNRR~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~ 176 (240)
...+|.+-|-.+.|..+.+.+...|+...+.|..+.+++++.+.+|...
T Consensus 87 v~Ey~R~~~~e~~kee~~~~e~~elr~~~~~l~~~i~~~~~~~~~L~~~ 135 (181)
T KOG3335|consen 87 VFEYWRQARKERKKEEKRKQEIMELRLKVEKLENAIAELTKFFSQLHSK 135 (181)
T ss_pred eehhHHhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456777776777777778888889999999999999999999999743
No 51
>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=67.00 E-value=4.1 Score=28.26 Aligned_cols=46 Identities=20% Similarity=0.284 Sum_probs=29.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhh
Q 026325 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNR 136 (240)
Q Consensus 87 r~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNR 136 (240)
++|..|++++...+-..+.... ....++|+++|+++.+|..|-.--
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g----~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG----ESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH----CHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC----CceEeeecccccccccccHHHHHH
Confidence 4678899988777766662221 357789999999999998887533
No 52
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=64.60 E-value=8.1 Score=31.14 Aligned_cols=48 Identities=19% Similarity=0.141 Sum_probs=36.1
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 89 KLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 89 R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
...+++.|..+|...+ .. . ...++|..||++...|+.|..+.+.+.|+
T Consensus 4 ~~~Lt~rqreVL~lr~-~G--l---Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-RG--L---TQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHHH-cC--C---CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4578999999998743 22 1 35589999999999999999866555554
No 53
>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=63.79 E-value=8.7 Score=21.22 Aligned_cols=38 Identities=16% Similarity=0.209 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecc
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWF 133 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWF 133 (240)
.++.++...+...|... + ...++|+.+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 45666666666666532 2 35578999999888777663
No 54
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=63.37 E-value=20 Score=27.40 Aligned_cols=34 Identities=41% Similarity=0.377 Sum_probs=28.1
Q ss_pred HHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhc
Q 026325 143 KQTEMECEYLKRWFGSLTEQNRRLQREVEELRAM 176 (240)
Q Consensus 143 k~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~ 176 (240)
.....+...||.....|.+||.+|+-|+..||..
T Consensus 18 ~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~ 51 (107)
T PF06156_consen 18 GQLLEELEELKKQLQELLEENARLRIENEHLRER 51 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556677788888889999999999999988875
No 55
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=63.20 E-value=8.5 Score=41.22 Aligned_cols=60 Identities=20% Similarity=0.335 Sum_probs=54.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 85 PPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 85 ~rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
.++-|..+-.+++..|-++|-.+.-|+.+.+..|......+.+++.+||+|-|.|.++..
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 455667777899999999999999999999999999999999999999999999998876
No 56
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=62.95 E-value=3 Score=27.88 Aligned_cols=40 Identities=13% Similarity=0.206 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCCCceeeecchhhhhHHHHHHhHHHHHHHH
Q 026325 114 QKEELATQLKLKPRQVEVWFQNRRARSKLKQTEMECEYLK 153 (240)
Q Consensus 114 ~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~~~~~l~ 153 (240)
...+||+.+|++...|..||.++...........=+..|+
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~ 51 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALN 51 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcC
Confidence 3568999999999999999998866666555444444443
No 57
>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=62.02 E-value=5 Score=26.03 Aligned_cols=42 Identities=17% Similarity=0.228 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhh
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRA 138 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~ 138 (240)
+++.+..++...|-.. ..-.++|..+|+++..|+.|.+.-|.
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 5566666666655443 34678999999999999999875443
No 58
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=60.94 E-value=20 Score=32.30 Aligned_cols=30 Identities=30% Similarity=0.382 Sum_probs=18.0
Q ss_pred HHHHHHHHHhhchHHHHHHHHHHHHHHHhc
Q 026325 147 MECEYLKRWFGSLTEQNRRLQREVEELRAM 176 (240)
Q Consensus 147 ~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~ 176 (240)
.+++.|...++.|+++...|.+|++.|+.+
T Consensus 255 ge~~~Le~rN~~LK~qa~~lerEI~ylKql 284 (294)
T KOG4571|consen 255 GELEGLEKRNEELKDQASELEREIRYLKQL 284 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555566666666666666666654
No 59
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=60.82 E-value=7.7 Score=32.95 Aligned_cols=49 Identities=20% Similarity=0.244 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHhhc--CCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHN--HTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~--~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+|..|+++|...|... -||-.....+||++||+++.- +|..=||+..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHH
Confidence 69999999999999876 457777788999999998864 44444555444
No 60
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=60.46 E-value=17 Score=32.40 Aligned_cols=38 Identities=21% Similarity=0.279 Sum_probs=27.5
Q ss_pred HhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhccCCCC
Q 026325 144 QTEMECEYLKRWFGSLTEQNRRLQREVEELRAMKVGPP 181 (240)
Q Consensus 144 ~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~~~~~~ 181 (240)
+..+....|.++++.|..+.++|++|+..++......+
T Consensus 219 e~~~r~~~leken~~lr~~v~~l~~el~~~~~~~~~~~ 256 (269)
T KOG3119|consen 219 EMAHRVAELEKENEALRTQVEQLKKELATLRRLFLQLP 256 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 33455566777778888888888888888888765433
No 61
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=59.25 E-value=26 Score=26.11 Aligned_cols=36 Identities=25% Similarity=0.414 Sum_probs=19.6
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhH
Q 026325 97 SRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTE 146 (240)
Q Consensus 97 ~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~ 146 (240)
+.+..-.|+.++||...--.. | =.|||.+||+.+.+
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~Q 49 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQ 49 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHH
Confidence 344455588899997542211 1 16999999987644
No 62
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=58.92 E-value=22 Score=31.20 Aligned_cols=7 Identities=57% Similarity=0.956 Sum_probs=3.3
Q ss_pred CCCCCCC
Q 026325 85 PPRKKLR 91 (240)
Q Consensus 85 ~rr~R~~ 91 (240)
++|||.+
T Consensus 54 ~~rKr~R 60 (292)
T KOG4005|consen 54 PKRKRRR 60 (292)
T ss_pred hHHHHHh
Confidence 4455444
No 63
>smart00338 BRLZ basic region leucin zipper.
Probab=58.30 E-value=41 Score=22.80 Aligned_cols=30 Identities=33% Similarity=0.431 Sum_probs=14.3
Q ss_pred HHHHHHHHHHhhchHHHHHHHHHHHHHHHh
Q 026325 146 EMECEYLKRWFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 146 ~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~ 175 (240)
+.+...|......|..+...|..++..|+.
T Consensus 32 e~~~~~L~~en~~L~~~~~~l~~e~~~lk~ 61 (65)
T smart00338 32 ERKVEQLEAENERLKKEIERLRRELEKLKS 61 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444455555555555555443
No 64
>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=56.90 E-value=66 Score=25.12 Aligned_cols=34 Identities=15% Similarity=0.028 Sum_probs=21.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchh
Q 026325 89 KLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQN 135 (240)
Q Consensus 89 R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqN 135 (240)
.+.|+..++..|.. ....+.+|++-.+|+.+|..
T Consensus 36 yR~Y~~~~~~~l~~-------------I~~lr~~G~sL~eI~~~l~~ 69 (133)
T cd04787 36 YRLYSEKDLSRLRF-------------ILSARQLGFSLKDIKEILSH 69 (133)
T ss_pred eeeCCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhh
Confidence 34799999888843 23345666666666666654
No 65
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=56.31 E-value=28 Score=31.40 Aligned_cols=32 Identities=25% Similarity=0.288 Sum_probs=24.7
Q ss_pred HhHHHHHHHHHHhhchHHHHHHHHHHHHHHHh
Q 026325 144 QTEMECEYLKRWFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 144 ~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~ 175 (240)
+++.+.+.+--+++.|..+|++|+.++.+|..
T Consensus 245 KkRae~E~l~ge~~~Le~rN~~LK~qa~~ler 276 (294)
T KOG4571|consen 245 KKRAEKEALLGELEGLEKRNEELKDQASELER 276 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33556667777888899999999999887653
No 66
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=56.20 E-value=2.5 Score=41.54 Aligned_cols=60 Identities=15% Similarity=0.238 Sum_probs=0.0
Q ss_pred CCCCCCCCCHHHHHHHHH-HHhhcCCCCHHHHHHHHHHhC-------CCCceeeecchhhhhHHHHHH
Q 026325 85 PPRKKLRLSKEQSRLLEE-SFRHNHTLNPKQKEELATQLK-------LKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 85 ~rr~R~~~t~~Q~~~Le~-~F~~~~~p~~~~r~~LA~~l~-------L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
+|+++-+|-.+|...+.. ||.++..+......+--+++. ...+.|+.||.|||.++|+-+
T Consensus 691 pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 691 PKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
No 67
>PRK12495 hypothetical protein; Provisional
Probab=56.09 E-value=44 Score=28.95 Aligned_cols=41 Identities=17% Similarity=0.328 Sum_probs=24.5
Q ss_pred HHHHHHhccCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCccc
Q 026325 169 EVEELRAMKVGPPTVISPHSCEPLPAST-LSMCPRCERVTTT 209 (240)
Q Consensus 169 e~~~l~~~~~~~~~~~~p~s~~~~p~~~-~~~cp~c~~~~~~ 209 (240)
.+.+|--..........+.+-.|+|... ...|+.|..+...
T Consensus 29 ~ma~lL~~gatmsa~hC~~CG~PIpa~pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 29 RMSELLLQGATMTNAHCDECGDPIFRHDGQEFCPTCQQPVTE 70 (226)
T ss_pred HHHHHHHhhcccchhhcccccCcccCCCCeeECCCCCCcccc
Confidence 3333333344444455555666777653 4469999988764
No 68
>PRK00118 putative DNA-binding protein; Validated
Probab=53.88 E-value=23 Score=26.96 Aligned_cols=46 Identities=13% Similarity=0.147 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.++..|..++...|.... ...+||+.+|++...|..|...-|.+.|
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 356677777766655432 3567999999999999988875444444
No 69
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=53.75 E-value=31 Score=26.57 Aligned_cols=35 Identities=29% Similarity=0.244 Sum_probs=27.0
Q ss_pred HHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhcc
Q 026325 143 KQTEMECEYLKRWFGSLTEQNRRLQREVEELRAMK 177 (240)
Q Consensus 143 k~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~~ 177 (240)
...-.+...||.....+.+||.+|+-|++.||...
T Consensus 18 ~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l 52 (110)
T PRK13169 18 GVLLKELGALKKQLAELLEENTALRLENDKLRERL 52 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456677788888888899999999988888743
No 70
>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=53.32 E-value=8.6 Score=26.25 Aligned_cols=44 Identities=18% Similarity=0.331 Sum_probs=21.6
Q ss_pred CCCCCHHH-HHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecch
Q 026325 89 KLRLSKEQ-SRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQ 134 (240)
Q Consensus 89 R~~~t~~Q-~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFq 134 (240)
|..|+... |.+++..+. ...--..+|. -|.++|+.+++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~-~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEK-DNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH--TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHH-ccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 44566554 344444433 3222223344 49999999999988864
No 71
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=53.24 E-value=38 Score=24.04 Aligned_cols=32 Identities=34% Similarity=0.293 Sum_probs=21.1
Q ss_pred HhHHHHHHHHHHhhchHHHHHHHHHHHHHHHh
Q 026325 144 QTEMECEYLKRWFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 144 ~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~ 175 (240)
+...+...++...+.+..||.+|+.|+..|..
T Consensus 28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~ 59 (85)
T TIGR02209 28 QLNNELQKLQLEIDKLQKEWRDLQLEVAELSR 59 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 34455556666666777788888877776553
No 72
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=52.31 E-value=8.4 Score=25.48 Aligned_cols=47 Identities=15% Similarity=0.185 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLK 143 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk 143 (240)
.||+.++.+|.-...-. ...++|..++++++.|+.+..+=+.|..-.
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 57888888887776543 366899999999999998887776665543
No 73
>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=52.17 E-value=84 Score=25.91 Aligned_cols=45 Identities=18% Similarity=0.191 Sum_probs=35.1
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecch
Q 026325 88 KKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQ 134 (240)
Q Consensus 88 ~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFq 134 (240)
++..++++++.++.+.-..+ |..-.+..||+++|++..=|.+-..
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~ 126 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAP 126 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcC
Confidence 45689999999998876555 5666788999999998876665443
No 74
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=52.00 E-value=19 Score=24.57 Aligned_cols=31 Identities=32% Similarity=0.379 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhhchHHHHHHHHHHHHHHHhc
Q 026325 146 EMECEYLKRWFGSLTEQNRRLQREVEELRAM 176 (240)
Q Consensus 146 ~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~ 176 (240)
+.+.+.||.....|.++|.+|+.|+.-|+..
T Consensus 13 rEEVevLK~~I~eL~~~n~~Le~EN~~Lk~~ 43 (59)
T PF01166_consen 13 REEVEVLKEQIAELEERNSQLEEENNLLKQN 43 (59)
T ss_dssp TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3567788888899999999999999999985
No 75
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=51.95 E-value=62 Score=21.87 Aligned_cols=32 Identities=25% Similarity=0.341 Sum_probs=25.0
Q ss_pred hHHHHHHHHHHhhchHHHHHHHHHHHHHHHhc
Q 026325 145 TEMECEYLKRWFGSLTEQNRRLQREVEELRAM 176 (240)
Q Consensus 145 ~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~ 176 (240)
.......|......|..+|..|..++..|...
T Consensus 24 Kk~~~~~Le~~~~~L~~en~~L~~~~~~L~~~ 55 (64)
T PF00170_consen 24 KKQYIEELEEKVEELESENEELKKELEQLKKE 55 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556677788888999999999999888753
No 76
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=51.86 E-value=58 Score=31.28 Aligned_cols=86 Identities=20% Similarity=0.303 Sum_probs=46.1
Q ss_pred CCCCCHHHHHHHHHH-Hhhc-CCCCHHHHHHHHHHhCCCCceeeecchhhhhHH-HHHHhHH--------------HHHH
Q 026325 89 KLRLSKEQSRLLEES-FRHN-HTLNPKQKEELATQLKLKPRQVEVWFQNRRARS-KLKQTEM--------------ECEY 151 (240)
Q Consensus 89 R~~~t~~Q~~~Le~~-F~~~-~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~-Kkk~~~~--------------~~~~ 151 (240)
-.+++.+....|.+. |-.. .+|-...-+++-++. +.=.+|+|.+. +|++++. ++..
T Consensus 218 ~L~LteeEkrLL~kEG~slPs~lPLTKaEEriLKrv-------RRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqe 290 (472)
T KOG0709|consen 218 PLVLTEEEKRLLTKEGYSLPSKLPLTKAEERILKRV-------RRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQE 290 (472)
T ss_pred ceeccHHHHHHHHhccCcCcccCCchHHHHHHHHHH-------HHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHH
Confidence 567889998888876 4333 455544444554444 22234555332 2222221 2233
Q ss_pred HHHHhhchHHHHHHHHHHHHHHHhccCCCC
Q 026325 152 LKRWFGSLTEQNRRLQREVEELRAMKVGPP 181 (240)
Q Consensus 152 l~~~~~~l~~e~~~l~~e~~~l~~~~~~~~ 181 (240)
|++....|..+|+-|.+++.+|..+.....
T Consensus 291 L~kkV~~Le~~N~sLl~qL~klQt~v~q~a 320 (472)
T KOG0709|consen 291 LQKKVEELELSNRSLLAQLKKLQTLVIQVA 320 (472)
T ss_pred HHHHHHHHhhccHHHHHHHHHHHHHHhhcc
Confidence 455555666677777777777766544433
No 77
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=51.05 E-value=16 Score=30.10 Aligned_cols=47 Identities=15% Similarity=0.150 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
.++..+..+|...|-.. ..-.++|+.||++...|++|...-|.+.|+
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 46777777776655333 235689999999999998888655554443
No 78
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=50.93 E-value=44 Score=23.11 Aligned_cols=30 Identities=30% Similarity=0.419 Sum_probs=23.5
Q ss_pred HhHHHHHHHHHHhhchHHHHHHHHHHHHHH
Q 026325 144 QTEMECEYLKRWFGSLTEQNRRLQREVEEL 173 (240)
Q Consensus 144 ~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l 173 (240)
+...+...++.....+..+|+.|+.+++.|
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345566777788888888888888888887
No 79
>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=50.86 E-value=51 Score=24.44 Aligned_cols=65 Identities=15% Similarity=0.194 Sum_probs=34.9
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHHHHHHHHHHhhchHHHHHHHHH
Q 026325 89 KLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEMECEYLKRWFGSLTEQNRRLQR 168 (240)
Q Consensus 89 R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~ 168 (240)
+..|+..++..|..... .+.+|++..+|+.++.... ......+......|.++..+|+.
T Consensus 36 ~R~y~~~di~~l~~i~~-------------lr~~g~~l~~i~~~~~~~~--------~~~~~~l~~~~~~l~~~i~~l~~ 94 (103)
T cd01106 36 YRLYTEEDLERLQQILF-------------LKELGFSLKEIKELLKDPS--------EDLLEALREQKELLEEKKERLDK 94 (103)
T ss_pred ceeeCHHHHHHHHHHHH-------------HHHcCCCHHHHHHHHHcCc--------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45699999998866532 2334555555555554332 12223344444445555556655
Q ss_pred HHHHHH
Q 026325 169 EVEELR 174 (240)
Q Consensus 169 e~~~l~ 174 (240)
.++.|.
T Consensus 95 ~~~~l~ 100 (103)
T cd01106 95 LIKTID 100 (103)
T ss_pred HHHHHH
Confidence 555544
No 80
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=50.79 E-value=4.3 Score=27.91 Aligned_cols=19 Identities=16% Similarity=0.443 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCCceeeecc
Q 026325 115 KEELATQLKLKPRQVEVWF 133 (240)
Q Consensus 115 r~~LA~~l~L~~~qVkvWF 133 (240)
-.+||.+||+++.+|+.|=
T Consensus 25 lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHHCCCHHHHHHHh
Confidence 4578999999999998884
No 81
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=50.02 E-value=54 Score=29.13 Aligned_cols=38 Identities=29% Similarity=0.441 Sum_probs=21.5
Q ss_pred hhHHHHHHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhcc
Q 026325 137 RARSKLKQTEMECEYLKRWFGSLTEQNRRLQREVEELRAMK 177 (240)
Q Consensus 137 R~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~~ 177 (240)
|.|.|+|+.+ ..+......|..||+.|+.++++|+...
T Consensus 208 kSR~~~k~~~---~e~~~r~~~leken~~lr~~v~~l~~el 245 (269)
T KOG3119|consen 208 KSRDKRKQKE---DEMAHRVAELEKENEALRTQVEQLKKEL 245 (269)
T ss_pred HhhhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444433 3334445567777777777777776643
No 82
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=49.61 E-value=72 Score=22.58 Aligned_cols=29 Identities=41% Similarity=0.502 Sum_probs=13.3
Q ss_pred HHHHHHHHHHhhchHHHHHHHHHHHHHHH
Q 026325 146 EMECEYLKRWFGSLTEQNRRLQREVEELR 174 (240)
Q Consensus 146 ~~~~~~l~~~~~~l~~e~~~l~~e~~~l~ 174 (240)
+.++..|+.....|.++|..|+.++..|+
T Consensus 24 q~e~eeLke~n~~L~~e~~~L~~en~~L~ 52 (72)
T PF06005_consen 24 QMENEELKEKNNELKEENEELKEENEQLK 52 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 34444444444444444555555544444
No 83
>smart00338 BRLZ basic region leucin zipper.
Probab=48.85 E-value=69 Score=21.67 Aligned_cols=30 Identities=40% Similarity=0.571 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhhchHHHHHHHHHHHHHHHh
Q 026325 146 EMECEYLKRWFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 146 ~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~ 175 (240)
......|......|..+|..|..++..|..
T Consensus 25 k~~~~~Le~~~~~L~~en~~L~~~~~~l~~ 54 (65)
T smart00338 25 KAEIEELERKVEQLEAENERLKKEIERLRR 54 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566777888899999999999888775
No 84
>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=48.79 E-value=95 Score=23.71 Aligned_cols=69 Identities=17% Similarity=0.147 Sum_probs=35.4
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHHHHHHHHHHhhchHHHHHHHH
Q 026325 88 KKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEMECEYLKRWFGSLTEQNRRLQ 167 (240)
Q Consensus 88 ~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~ 167 (240)
....|+..++..|+. ....+.+|++-..|+.+|.+.... ......+......+.++.++|+
T Consensus 34 gyR~Y~~~~l~~l~~-------------I~~lr~~G~~L~eI~~~l~~~~~~------~~~~~~l~~~~~~l~~~i~~l~ 94 (120)
T cd04781 34 LRRQYDPQVLDRLAL-------------IALGRAAGFSLDEIQAMLSHDGKP------PIDRQLLKAKAAELDQQIQRLQ 94 (120)
T ss_pred CceecCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhccCCc------HHHHHHHHHHHHHHHHHHHHHH
Confidence 456799999888853 234555566666666655543210 0011223333334445555555
Q ss_pred HHHHHHHh
Q 026325 168 REVEELRA 175 (240)
Q Consensus 168 ~e~~~l~~ 175 (240)
.....|..
T Consensus 95 ~~~~~L~~ 102 (120)
T cd04781 95 AMRELLRH 102 (120)
T ss_pred HHHHHHHH
Confidence 55555544
No 85
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=46.86 E-value=20 Score=28.26 Aligned_cols=46 Identities=20% Similarity=0.234 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
+++.+..++...|-... .-.++|..+|+++..|++++..-|.+.|+
T Consensus 107 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK-----SYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CCHHHHHHHHHHHHhCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56666666655543332 24689999999999999888755555544
No 86
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=46.53 E-value=14 Score=28.82 Aligned_cols=46 Identities=15% Similarity=0.207 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..++...|-... ...++|..+|++...|+.|...-|.+.|
T Consensus 106 ~L~~~~r~ii~l~~~~~~-----s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGK-----TMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhcCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 466677777766554332 3678999999999999988775555444
No 87
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=44.81 E-value=64 Score=22.51 Aligned_cols=19 Identities=26% Similarity=0.429 Sum_probs=7.5
Q ss_pred HHHHhhchHHHHHHHHHHH
Q 026325 152 LKRWFGSLTEQNRRLQREV 170 (240)
Q Consensus 152 l~~~~~~l~~e~~~l~~e~ 170 (240)
|-..|..|..||..|+.++
T Consensus 12 Li~~~~~L~~EN~~Lr~q~ 30 (65)
T TIGR02449 12 LLEYLERLKSENRLLRAQE 30 (65)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3333333444444444333
No 88
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=44.81 E-value=20 Score=29.94 Aligned_cols=46 Identities=22% Similarity=0.289 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
+++.+..+|...|-.. ....++|..+|+++..|+++...-|.+.++
T Consensus 154 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 154 LPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5666666666544322 235689999999999998877655444443
No 89
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=44.75 E-value=19 Score=28.64 Aligned_cols=46 Identities=15% Similarity=0.050 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..+|...|-... ...++|..+|++...|+.|...-+.+.|
T Consensus 128 ~L~~~~r~vl~l~~~~~~-----s~~eIA~~lgis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 128 SLPEELRTAITLREIEGL-----SYEEIAEIMGCPIGTVRSRIFRAREALR 173 (182)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 477777777776653221 2458899999999999988874444433
No 90
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=44.02 E-value=22 Score=28.78 Aligned_cols=47 Identities=17% Similarity=0.133 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
.+++.+..+|...|-... .-.+||..+|++...|+.++..-|.+.|.
T Consensus 131 ~L~~~~r~v~~l~~~~g~-----s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 131 TLPPRQRDVVQSISVEGA-----SIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 466777777776654432 35689999999999999888766665554
No 91
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=44.00 E-value=71 Score=20.87 Aligned_cols=25 Identities=28% Similarity=0.279 Sum_probs=15.3
Q ss_pred hHHHHHHHHHHhhchHHHHHHHHHH
Q 026325 145 TEMECEYLKRWFGSLTEQNRRLQRE 169 (240)
Q Consensus 145 ~~~~~~~l~~~~~~l~~e~~~l~~e 169 (240)
.+.....|...+..|..++..|+.|
T Consensus 30 le~~~~~L~~en~~L~~~i~~L~~E 54 (54)
T PF07716_consen 30 LEQEVQELEEENEQLRQEIAQLERE 54 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3445555666666677776666654
No 92
>PHA02955 hypothetical protein; Provisional
Probab=42.88 E-value=34 Score=29.50 Aligned_cols=43 Identities=14% Similarity=0.231 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHhhc-CCCCHHHHHHHHHHhCCCCceeeecchhh
Q 026325 94 KEQSRLLEESFRHN-HTLNPKQKEELATQLKLKPRQVEVWFQNR 136 (240)
Q Consensus 94 ~~Q~~~Le~~F~~~-~~p~~~~r~~LA~~l~L~~~qVkvWFqNR 136 (240)
..++..|-+.|... .-+..++|.+++++||+....|..||.+.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 45677777777655 66888999999999999988789999764
No 93
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=42.19 E-value=28 Score=28.01 Aligned_cols=46 Identities=13% Similarity=0.303 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
+++.+..++.-.|-.. ...+++|..+|+++..|+++...-|.+.|+
T Consensus 130 L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 130 LEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 5556665555554322 235689999999999998888755555443
No 94
>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=41.09 E-value=24 Score=26.62 Aligned_cols=46 Identities=15% Similarity=0.248 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..++...|-.. ....++|..+|+++..|..|...-+.|.|
T Consensus 110 ~L~~~~~~ii~~~~~~g-----~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG-----LSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35566666665544322 23568999999999999877765444443
No 95
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=41.01 E-value=53 Score=25.30 Aligned_cols=34 Identities=38% Similarity=0.358 Sum_probs=28.7
Q ss_pred HhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhcc
Q 026325 144 QTEMECEYLKRWFGSLTEQNRRLQREVEELRAMK 177 (240)
Q Consensus 144 ~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~~ 177 (240)
.+-.+...+|+...++.+||-.|+-|+..||...
T Consensus 19 ~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL 52 (114)
T COG4467 19 VLLAELGGLKQHLGSLVEENTALRLENEKLRERL 52 (114)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHh
Confidence 4456677888999999999999999999999853
No 96
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=40.91 E-value=27 Score=21.83 Aligned_cols=40 Identities=18% Similarity=0.277 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhh
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNR 136 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNR 136 (240)
.++..+..++...+. . + ...++|..+|++...|..|...-
T Consensus 3 ~l~~~e~~i~~~~~~-g-~----s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPREREVLRLLAE-G-L----TNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHHHHc-C-C----CHHHHHHHHCCCHHHHHHHHHHH
Confidence 467777777765432 2 1 35688999999999988777643
No 97
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=40.80 E-value=25 Score=27.85 Aligned_cols=45 Identities=16% Similarity=0.160 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
+++.+..+|...|... ..-.+||..+|++...|+.|...-|.+.|
T Consensus 126 L~~~~r~i~~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 126 LPVKQREVFLLRYVEG-----LSYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CCHHHHHHhhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5555556665544322 23468999999999999988875555544
No 98
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=40.73 E-value=20 Score=29.27 Aligned_cols=46 Identities=17% Similarity=0.239 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
+++.+..+|...|-.. ....++|..+|++...|+.|+..-|.+.|+
T Consensus 142 L~~~~~~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 142 LPESQRQVLELAYYEG-----LSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHhhhhhhhhhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4555555555443222 235689999999999999998655554443
No 99
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.42 E-value=1.1e+02 Score=22.86 Aligned_cols=43 Identities=14% Similarity=0.156 Sum_probs=33.2
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCC-CCceeeecchh
Q 026325 89 KLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKL-KPRQVEVWFQN 135 (240)
Q Consensus 89 R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L-~~~qVkvWFqN 135 (240)
|.+|+.+....+-+.+....+ ....+|+++|+ ...++..|-+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~ 48 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQ 48 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHH
Confidence 778999988777666665554 46789999996 99988887653
No 100
>PRK04217 hypothetical protein; Provisional
Probab=40.17 E-value=29 Score=26.73 Aligned_cols=46 Identities=13% Similarity=0.076 Sum_probs=32.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhH
Q 026325 89 KLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139 (240)
Q Consensus 89 R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k 139 (240)
-..++.+|..++...|...- ...+||+.+|++...|+..+..-+.+
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkk 85 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKK 85 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 34588888888877764433 46689999999999887766543333
No 101
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=39.85 E-value=8.6 Score=24.31 Aligned_cols=40 Identities=18% Similarity=0.169 Sum_probs=18.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecc
Q 026325 89 KLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWF 133 (240)
Q Consensus 89 R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWF 133 (240)
...||.++...++..+.... -..+||+.||....-|..|.
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~-----s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGM-----SIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ----------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcCC-----CHHHHHHHHCcCcHHHHHHH
Confidence 35688888888888876442 35578999998887765544
No 102
>PRK10072 putative transcriptional regulator; Provisional
Probab=39.63 E-value=16 Score=27.43 Aligned_cols=42 Identities=17% Similarity=0.153 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k 139 (240)
+.+...+..|...... + ..+||+.+|++...|..|.+.+|.-
T Consensus 32 ~~~~~eik~LR~~~gl----T---Q~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL----K---IDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred cCChHHHHHHHHHcCC----C---HHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 4466667776543222 2 5689999999999999999987653
No 103
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=39.56 E-value=31 Score=27.39 Aligned_cols=47 Identities=23% Similarity=0.147 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
.+++.+..++.-.|-.. ....++|..+|+++..|++|.+.-|.+.|+
T Consensus 108 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 108 TLPVIEAQAILLCDVHE-----LTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred hCCHHHHHHHHhHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35666666665443222 235789999999999999888755555443
No 104
>PF08961 DUF1875: Domain of unknown function (DUF1875); InterPro: IPR015056 MIT can be found in the Nuclear receptor-binding factor 2, it has no known function. ; PDB: 2CRB_A.
Probab=39.30 E-value=9.9 Score=32.90 Aligned_cols=37 Identities=27% Similarity=0.434 Sum_probs=0.0
Q ss_pred HHHHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhcc
Q 026325 141 KLKQTEMECEYLKRWFGSLTEQNRRLQREVEELRAMK 177 (240)
Q Consensus 141 Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~~ 177 (240)
+..+....+..|++..+.|..||++|++|++.|++.+
T Consensus 123 ~IEEQ~T~I~dLrrlVe~L~aeNErLr~EnkqL~ae~ 159 (243)
T PF08961_consen 123 RIEEQATKIADLRRLVEFLLAENERLRRENKQLKAEN 159 (243)
T ss_dssp -------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344445556677777777788888888777777643
No 105
>PF10226 DUF2216: Uncharacterized conserved proteins (DUF2216); InterPro: IPR019359 Proteins in this entry are found in Metazoa and contain a coiled-coil domain. Some annotation suggests it might be PKR, the Hepatitis delta antigen-interacting protein A, but this could not be confirmed.
Probab=38.47 E-value=63 Score=27.36 Aligned_cols=23 Identities=35% Similarity=0.521 Sum_probs=16.5
Q ss_pred hhchHHHHHHHHHHHHHHHhccC
Q 026325 156 FGSLTEQNRRLQREVEELRAMKV 178 (240)
Q Consensus 156 ~~~l~~e~~~l~~e~~~l~~~~~ 178 (240)
+..|++.|++|+.++++||.+-+
T Consensus 57 IR~LKe~NqkLqedNqELRdLCC 79 (195)
T PF10226_consen 57 IRGLKEVNQKLQEDNQELRDLCC 79 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHc
Confidence 34577788888888888887533
No 106
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=38.09 E-value=32 Score=28.03 Aligned_cols=47 Identities=15% Similarity=0.249 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
.+++.+..+|+-.|-..- ...++|..+|+++..|++.+..-|.+.|+
T Consensus 131 ~L~~~~r~vl~l~~~~~~-----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 131 KLSPAHREIIDLVYYHEK-----SVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 466777777766543332 35689999999999998877655555443
No 107
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=38.00 E-value=59 Score=31.12 Aligned_cols=37 Identities=32% Similarity=0.565 Sum_probs=21.4
Q ss_pred ecc---hhhhhHHHHHHhHHHHHHHHHHhhchHHHHHHHH
Q 026325 131 VWF---QNRRARSKLKQTEMECEYLKRWFGSLTEQNRRLQ 167 (240)
Q Consensus 131 vWF---qNRR~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~ 167 (240)
+|| ||+.+|.+-++.-++.+.|++--.+|..-+++|.
T Consensus 230 cw~ay~Qnk~akehv~km~kdle~Lq~aEqsl~dlQk~Le 269 (575)
T KOG4403|consen 230 CWFAYRQNKKAKEHVNKMMKDLEGLQRAEQSLEDLQKRLE 269 (575)
T ss_pred hhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 488 8888887766666666665554333333333333
No 108
>KOG0999 consensus Microtubule-associated protein Bicaudal-D [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.82 E-value=57 Score=32.22 Aligned_cols=53 Identities=32% Similarity=0.371 Sum_probs=40.4
Q ss_pred CceeeecchhhhhHHHHHHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhccC
Q 026325 126 PRQVEVWFQNRRARSKLKQTEMECEYLKRWFGSLTEQNRRLQREVEELRAMKV 178 (240)
Q Consensus 126 ~~qVkvWFqNRR~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~~~ 178 (240)
...-.+=-|.+|.|.-.|..+-....|-..+..|.+||.-||+++..||...+
T Consensus 142 e~~~~~E~qR~rlr~elKe~KfRE~RllseYSELEEENIsLQKqVs~LR~sQV 194 (772)
T KOG0999|consen 142 ESNAAVEDQRRRLRDELKEYKFREARLLSEYSELEEENISLQKQVSNLRQSQV 194 (772)
T ss_pred hcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHhhhhh
Confidence 33334445778888877777777777888888899999999999999987443
No 109
>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=37.82 E-value=27 Score=27.28 Aligned_cols=44 Identities=25% Similarity=0.271 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k 139 (240)
.+++.+..++...|-.. ....++|..+|++...|+++...-|.+
T Consensus 111 ~L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKALSRLRVR 154 (159)
T ss_pred HCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 46677777776644322 236689999999999998776544443
No 110
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=37.62 E-value=30 Score=28.18 Aligned_cols=46 Identities=24% Similarity=0.185 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..++...|-.. ....+||..+|++...|+.+...-|.+.|
T Consensus 139 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 139 TLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLR 184 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 46777777777655443 23678999999999999887754444433
No 111
>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=37.26 E-value=86 Score=23.61 Aligned_cols=71 Identities=18% Similarity=0.161 Sum_probs=35.6
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHHHHHHHHHHhhchHHHHHHHHH
Q 026325 89 KLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEMECEYLKRWFGSLTEQNRRLQR 168 (240)
Q Consensus 89 R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~ 168 (240)
...|+.+++..|... ...+.+|++-.+|+..+........ ........+......+.++.+.|+.
T Consensus 36 yR~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (113)
T cd01109 36 IRDFTEEDLEWLEFI-------------KCLRNTGMSIKDIKEYAELRREGDS--TIPERLELLEEHREELEEQIAELQE 100 (113)
T ss_pred CccCCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHHHHccCCc--cHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346899998888543 2344556666665555543321110 0111223444444555555555555
Q ss_pred HHHHHH
Q 026325 169 EVEELR 174 (240)
Q Consensus 169 e~~~l~ 174 (240)
.+..|.
T Consensus 101 ~~~~l~ 106 (113)
T cd01109 101 TLAYLD 106 (113)
T ss_pred HHHHHH
Confidence 554444
No 112
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=36.81 E-value=65 Score=31.61 Aligned_cols=29 Identities=24% Similarity=0.283 Sum_probs=19.8
Q ss_pred HHHHHHHHHhhchHHHHHHHHHHHHHHHh
Q 026325 147 MECEYLKRWFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 147 ~~~~~l~~~~~~l~~e~~~l~~e~~~l~~ 175 (240)
...+.|-++++.|+.||..|++++..+-.
T Consensus 309 ~rLq~ll~Ene~Lk~ENatLk~qL~~l~~ 337 (655)
T KOG4343|consen 309 ARLQALLSENEQLKKENATLKRQLDELVS 337 (655)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Confidence 44455666777777777777777776654
No 113
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=36.48 E-value=68 Score=22.52 Aligned_cols=22 Identities=41% Similarity=0.515 Sum_probs=14.0
Q ss_pred HHHhhchHHHHHHHHHHHHHHH
Q 026325 153 KRWFGSLTEQNRRLQREVEELR 174 (240)
Q Consensus 153 ~~~~~~l~~e~~~l~~e~~~l~ 174 (240)
-..+..|..|++.|++|+++.+
T Consensus 46 ~~e~~~Lk~E~e~L~~el~~~r 67 (69)
T PF14197_consen 46 YEENNKLKEENEALRKELEELR 67 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHhh
Confidence 3344567777777777766654
No 114
>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=36.15 E-value=32 Score=27.69 Aligned_cols=42 Identities=19% Similarity=0.188 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhh
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRR 137 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR 137 (240)
.+++.+..+|.-.|-... ...++|..+|+++..|+++...-|
T Consensus 100 ~L~~~~r~v~~l~~~~g~-----s~~eIA~~lgis~~tV~~~l~Rar 141 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGL-----SQQEIAEKLGLSLSGAKSRVQRGR 141 (170)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467777777776654332 356899999999999887665333
No 115
>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development. The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=36.02 E-value=46 Score=24.69 Aligned_cols=44 Identities=30% Similarity=0.335 Sum_probs=27.7
Q ss_pred ceeeecchhhhhHHHHHHhHHHHHHHHHHhhchHHHHHHHHHHHH
Q 026325 127 RQVEVWFQNRRARSKLKQTEMECEYLKRWFGSLTEQNRRLQREVE 171 (240)
Q Consensus 127 ~qVkvWFqNRR~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~ 171 (240)
.++..|...=|++ |.+....+...++..-..+.++|..|+.++.
T Consensus 56 ~~Le~aL~~VR~r-K~~~l~~~i~~l~~ke~~l~~en~~L~~~~~ 99 (100)
T PF01486_consen 56 QQLESALKRVRSR-KDQLLMEQIEELKKKERELEEENNQLRQKIE 99 (100)
T ss_pred HhhhhhHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3445555444444 2334466677777777788888888887764
No 116
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=35.97 E-value=29 Score=27.93 Aligned_cols=46 Identities=13% Similarity=0.174 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..+|+..|-.. ..-.++|..+|+++..|++++..-|.+.|
T Consensus 136 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMED-----LSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred hCCHHHhHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 46666666666543322 23568999999999999888865555444
No 117
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=35.87 E-value=4.2e+02 Score=25.74 Aligned_cols=25 Identities=28% Similarity=0.304 Sum_probs=15.5
Q ss_pred HHHHhhchHHHHHHHHHHHHHHHhc
Q 026325 152 LKRWFGSLTEQNRRLQREVEELRAM 176 (240)
Q Consensus 152 l~~~~~~l~~e~~~l~~e~~~l~~~ 176 (240)
+....+.+..|+.+|+.+++.++..
T Consensus 102 le~KIkeLEaE~~~Lk~Ql~a~~~~ 126 (475)
T PRK13729 102 DQRRIEKLGQDNAALAEQVKALGAN 126 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhcC
Confidence 3444456677777777777555543
No 118
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=35.61 E-value=31 Score=28.03 Aligned_cols=45 Identities=13% Similarity=0.180 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
+++.+..+|...|-... .-.+||..+|++...|+.+...-|.+.|
T Consensus 129 L~~~~r~i~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~Rar~~Lr 173 (186)
T PRK05602 129 LPERQREAIVLQYYQGL-----SNIEAAAVMDISVDALESLLARGRRALR 173 (186)
T ss_pred CCHHHHHHhhHHHhcCC-----CHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 55666666655443221 3568999999999999887764444444
No 119
>PF12269 zf-CpG_bind_C: CpG binding protein zinc finger C terminal domain; InterPro: IPR022056 This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.
Probab=35.54 E-value=1e+02 Score=27.06 Aligned_cols=81 Identities=11% Similarity=0.251 Sum_probs=39.6
Q ss_pred Cceeeecchhh-----hhHHHHHHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCCC
Q 026325 126 PRQVEVWFQNR-----RARSKLKQTEMECEYLKRWFGSLTEQNRRLQREVEELRAMKVGPPTVISPHSCEPLPASTLSMC 200 (240)
Q Consensus 126 ~~qVkvWFqNR-----R~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~~~~~~~~~~p~s~~~~p~~~~~~c 200 (240)
+.+|+-||.+- ..+.+..+.+.+....+.....|.+....|..=+...+.............. ....-....|
T Consensus 10 PqRIQEw~~~p~~A~E~~r~~Le~Ir~kq~~v~~~l~eLe~~~~el~~~i~~~k~~~~~~~~~~~~~e--~~D~~~~~~C 87 (236)
T PF12269_consen 10 PQRIQEWQLSPCVAEEQNRKLLEEIRKKQQKVRNRLQELEKRFKELEAIIARAKQFTVDQDEEQNDDE--SEDDDLSIYC 87 (236)
T ss_pred hHHHHHhcCCCchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccccccccc--ccccceeeee
Confidence 66777787653 1122333334444444445555555555666655555554444322211110 0111123469
Q ss_pred CCCCCCcc
Q 026325 201 PRCERVTT 208 (240)
Q Consensus 201 p~c~~~~~ 208 (240)
..|++-.+
T Consensus 88 v~Cg~~i~ 95 (236)
T PF12269_consen 88 VTCGHEIP 95 (236)
T ss_pred eeCCCcCC
Confidence 99998544
No 120
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=35.45 E-value=1.1e+02 Score=20.70 Aligned_cols=29 Identities=17% Similarity=0.335 Sum_probs=14.0
Q ss_pred HHHHHHHHHHhhchHHHHHHHHHHHHHHH
Q 026325 146 EMECEYLKRWFGSLTEQNRRLQREVEELR 174 (240)
Q Consensus 146 ~~~~~~l~~~~~~l~~e~~~l~~e~~~l~ 174 (240)
+.+...+....+.++.||+.+..+++++.
T Consensus 6 En~~~~~~~~i~tvk~en~~i~~~ve~i~ 34 (55)
T PF05377_consen 6 ENELPRIESSINTVKKENEEISESVEKIE 34 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444444555555555555554443
No 121
>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=35.17 E-value=1.3e+02 Score=23.71 Aligned_cols=16 Identities=6% Similarity=-0.151 Sum_probs=12.0
Q ss_pred CCCCCCHHHHHHHHHH
Q 026325 88 KKLRLSKEQSRLLEES 103 (240)
Q Consensus 88 ~R~~~t~~Q~~~Le~~ 103 (240)
....|+..++..|...
T Consensus 34 g~R~Y~~~~l~~l~~I 49 (134)
T cd04779 34 NYRYYDETALDRLQLI 49 (134)
T ss_pred CCeeECHHHHHHHHHH
Confidence 3556999998888665
No 122
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=35.08 E-value=42 Score=27.22 Aligned_cols=45 Identities=13% Similarity=0.265 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
+++.+..++...|-... ...++|..+|++...|++|...-|.+.|
T Consensus 134 L~~~~r~i~~l~~~~~~-----s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 134 LEPARRNCILHAYVDGC-----SHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 55566665555443221 3568999999999999988765554444
No 123
>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=35.01 E-value=71 Score=25.55 Aligned_cols=47 Identities=21% Similarity=0.193 Sum_probs=33.6
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 89 KLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 89 R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+.++..|..+|+-.+ ... ...++|..+|++...|+.|-..-+.+.+
T Consensus 4 ~~~Lte~qr~VL~Lr~-~Gl-----Tq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-KGL-----SQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred cCCCCHHHHHHHHHHH-cCC-----CHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 4678899999998742 221 3568999999999988877665444444
No 124
>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=34.64 E-value=36 Score=27.40 Aligned_cols=45 Identities=27% Similarity=0.246 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
+++.+..++.-.|-... .-.++|..+|+++..|++....-|.+.|
T Consensus 135 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGL-----TVEEIAELLGVSVRTVERDWRFARAWLA 179 (183)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 66666666666554332 3568999999999999988765555444
No 125
>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=34.48 E-value=36 Score=26.33 Aligned_cols=45 Identities=18% Similarity=0.208 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
++..+..+|.-.|-.. ....++|..+|+++..|+.+...-|.+.|
T Consensus 114 L~~~~r~il~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 114 LPEQCRKIFILSRFEG-----KSYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4556666665544322 13567899999999998877664444433
No 126
>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=34.35 E-value=27 Score=28.21 Aligned_cols=28 Identities=14% Similarity=0.087 Sum_probs=20.9
Q ss_pred HHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 114 QKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 114 ~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.-.++|..+|+++..|+++...-|.+.|
T Consensus 156 s~~EIA~~lgis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3568999999999999888754444433
No 127
>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=34.29 E-value=6.7 Score=28.04 Aligned_cols=34 Identities=15% Similarity=0.121 Sum_probs=24.0
Q ss_pred HHhhcCCCCHHHHHHHHHHhCCCCceeeecchhh
Q 026325 103 SFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNR 136 (240)
Q Consensus 103 ~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNR 136 (240)
.|....|.......+||..+|+++..|+.|+.+.
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 3444433333346789999999999999998643
No 128
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=34.03 E-value=72 Score=24.18 Aligned_cols=39 Identities=13% Similarity=0.067 Sum_probs=30.3
Q ss_pred eecchhhhhHHHHHHhHHHHHHHHHHhhchHHHHHHHHH
Q 026325 130 EVWFQNRRARSKLKQTEMECEYLKRWFGSLTEQNRRLQR 168 (240)
Q Consensus 130 kvWFqNRR~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~ 168 (240)
.-|+..+..+.+....+.++..++..+..|..|...|+.
T Consensus 24 ~G~~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 24 NGILDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 346666667777777788888888888888888888876
No 129
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=33.94 E-value=99 Score=27.20 Aligned_cols=38 Identities=21% Similarity=0.189 Sum_probs=23.2
Q ss_pred hhHHHHHHhHHHHHHHHHHhhchHHHHHHHHHHHHHHH
Q 026325 137 RARSKLKQTEMECEYLKRWFGSLTEQNRRLQREVEELR 174 (240)
Q Consensus 137 R~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~ 174 (240)
|-|.|-.+.+.+...+++....|+.|...|++++.+|-
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLY 127 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLY 127 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444455566666666666677777777777665443
No 130
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=33.79 E-value=1.4e+02 Score=21.10 Aligned_cols=28 Identities=25% Similarity=0.257 Sum_probs=15.2
Q ss_pred HhHHHHHHHHHHhhchHHHHHHHHHHHH
Q 026325 144 QTEMECEYLKRWFGSLTEQNRRLQREVE 171 (240)
Q Consensus 144 ~~~~~~~~l~~~~~~l~~e~~~l~~e~~ 171 (240)
..+.++..+......|.++|.+|+.+..
T Consensus 29 eLke~n~~L~~e~~~L~~en~~L~~e~~ 56 (72)
T PF06005_consen 29 ELKEKNNELKEENEELKEENEQLKQERN 56 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 3344444555555556666666665544
No 131
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=33.78 E-value=85 Score=24.23 Aligned_cols=31 Identities=35% Similarity=0.441 Sum_probs=21.5
Q ss_pred HHHHHHHHHHhhchHHHHHHHHHHHHHHHhc
Q 026325 146 EMECEYLKRWFGSLTEQNRRLQREVEELRAM 176 (240)
Q Consensus 146 ~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~ 176 (240)
++|.+.||.....|.+.|.+|.+|+.-|+.+
T Consensus 66 REEVe~Lk~qI~eL~er~~~Le~EN~lLk~~ 96 (123)
T KOG4797|consen 66 REEVEVLKEQIRELEERNSALERENSLLKTL 96 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4556667777777777777777777766653
No 132
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=33.22 E-value=26 Score=31.92 Aligned_cols=38 Identities=39% Similarity=0.398 Sum_probs=33.7
Q ss_pred hhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 105 RHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 105 ~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
..+.|++..+...|+....|+-.+|.+||-|.|.+.+.
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~ 154 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKK 154 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence 35789999999999999999999999999998888665
No 133
>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=33.05 E-value=27 Score=23.36 Aligned_cols=32 Identities=34% Similarity=0.501 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceee
Q 026325 95 EQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVE 130 (240)
Q Consensus 95 ~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVk 130 (240)
.|+..|+-.|. +...+.. +||..+|++++.|+
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~ 37 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIK 37 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHH
Confidence 57788888888 6666654 89999999987653
No 134
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.87 E-value=31 Score=25.63 Aligned_cols=38 Identities=29% Similarity=0.406 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcee
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQV 129 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qV 129 (240)
+.++|...-...|+.+--.+.-..+++|.+|++++-.|
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 56778777777777776666677889999999887543
No 135
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=32.86 E-value=42 Score=26.26 Aligned_cols=45 Identities=11% Similarity=0.093 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARS 140 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~ 140 (240)
.+++.+..++.-.|-... .-.++|..||++...|++....-|.+.
T Consensus 106 ~Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~ra~~~L 150 (161)
T PRK09047 106 KLPARQREAFLLRYWEDM-----DVAETAAAMGCSEGSVKTHCSRATHAL 150 (161)
T ss_pred hCCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 466677666666543332 256899999999999887665433333
No 136
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=32.52 E-value=46 Score=28.62 Aligned_cols=46 Identities=20% Similarity=0.225 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
++..|..+|.-.|-.. ..-.+||..+|+++..|+++...-|.+.|+
T Consensus 172 Lp~~~R~v~~L~~~eg-----~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 172 LPEQQRIAVILSYHEN-----MSNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4555555544443222 235689999999999998887655555443
No 137
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=32.31 E-value=56 Score=23.65 Aligned_cols=21 Identities=10% Similarity=0.124 Sum_probs=15.3
Q ss_pred HHHHHHHhCCCCceeeecchh
Q 026325 115 KEELATQLKLKPRQVEVWFQN 135 (240)
Q Consensus 115 r~~LA~~l~L~~~qVkvWFqN 135 (240)
..++|+.+|++++.|+.|.+.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 346788888888888887643
No 138
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=32.06 E-value=51 Score=25.94 Aligned_cols=45 Identities=16% Similarity=0.267 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..+|.-.| ... .-.+||..+|++...|+.+...-|.+.|
T Consensus 112 ~L~~~~r~il~l~~-~g~-----s~~eIA~~lgis~~tV~~~i~ra~~~Lr 156 (166)
T PRK09639 112 KMTERDRTVLLLRF-SGY-----SYKEIAEALGIKESSVGTTLARAKKKFR 156 (166)
T ss_pred cCCHHHHHHHHHHH-cCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 36677777776666 332 3568999999999999888754444444
No 139
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=32.04 E-value=34 Score=26.98 Aligned_cols=46 Identities=20% Similarity=0.136 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.|..+|.-.|-.. ....++|..+|++...|+.+...-|.+.|
T Consensus 112 ~L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred HCCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 36666666666554332 13568999999999998887765554444
No 140
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=32.01 E-value=87 Score=27.48 Aligned_cols=34 Identities=26% Similarity=0.257 Sum_probs=21.6
Q ss_pred HhHHHHHHHHHHhhchHHHHH---HHHHHHHHHHhcc
Q 026325 144 QTEMECEYLKRWFGSLTEQNR---RLQREVEELRAMK 177 (240)
Q Consensus 144 ~~~~~~~~l~~~~~~l~~e~~---~l~~e~~~l~~~~ 177 (240)
+...+++.|+++...|..++. .+++|+++|+.+.
T Consensus 73 ~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL 109 (276)
T PRK13922 73 DLREENEELKKELLELESRLQELEQLEAENARLRELL 109 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445566666666666665555 5677777777653
No 141
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=31.80 E-value=52 Score=26.98 Aligned_cols=47 Identities=13% Similarity=0.193 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
.+++.+..++.-.|-... ...++|..+|+++..|+++...-|.+.|+
T Consensus 134 ~Lp~~~R~v~~L~~~~g~-----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 134 HLPAQQARVFMMREYLEL-----SSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred hCCHHHHHHHhHHHHcCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356666666666543322 35689999999999999988655544443
No 142
>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=31.66 E-value=12 Score=23.42 Aligned_cols=22 Identities=18% Similarity=0.176 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCCceeeecchhh
Q 026325 115 KEELATQLKLKPRQVEVWFQNR 136 (240)
Q Consensus 115 r~~LA~~l~L~~~qVkvWFqNR 136 (240)
..++|+.+|+++..|+.|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999997654
No 143
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=31.54 E-value=39 Score=27.90 Aligned_cols=47 Identities=23% Similarity=0.061 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
.+++.+..+|.-.|-.. ....++|..+|++...|++++..-|.+.|+
T Consensus 113 ~Lp~~~r~v~~L~~~~g-----~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 113 QLPDEQREALILVGASG-----FSYEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred hCCHHHhHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35666666665543322 235689999999999999988755555543
No 144
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=31.23 E-value=91 Score=27.86 Aligned_cols=34 Identities=24% Similarity=0.180 Sum_probs=19.4
Q ss_pred HhHHHHHHHHHHhhchHHHHH----HHHHHHHHHHhcc
Q 026325 144 QTEMECEYLKRWFGSLTEQNR----RLQREVEELRAMK 177 (240)
Q Consensus 144 ~~~~~~~~l~~~~~~l~~e~~----~l~~e~~~l~~~~ 177 (240)
+...|++.|+.+...+..+.. .+++|+++|+.+.
T Consensus 70 ~l~~EN~~Lr~e~~~l~~~~~~~~~~l~~EN~rLr~LL 107 (283)
T TIGR00219 70 NLEYENYKLRQELLKKNQQLEILTQNLKQENVRLRELL 107 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445666666666544422222 3677777777753
No 145
>PRK06930 positive control sigma-like factor; Validated
Probab=30.92 E-value=54 Score=27.00 Aligned_cols=47 Identities=13% Similarity=0.111 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
.+++.+..+|.-.|.... .-.++|..+|++...|+.+...-|.+.++
T Consensus 114 ~L~~rer~V~~L~~~eg~-----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGL-----SYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 477777777766543332 35688999999999999988766555554
No 146
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=30.35 E-value=52 Score=22.25 Aligned_cols=13 Identities=31% Similarity=0.728 Sum_probs=6.9
Q ss_pred HHHHHHHHHHHHH
Q 026325 161 EQNRRLQREVEEL 173 (240)
Q Consensus 161 ~e~~~l~~e~~~l 173 (240)
.+.+++++|++++
T Consensus 55 k~l~~le~e~~~l 67 (68)
T PF06305_consen 55 KELKKLEKELEQL 67 (68)
T ss_pred HHHHHHHHHHHhc
Confidence 3455555665554
No 147
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=30.29 E-value=42 Score=27.40 Aligned_cols=47 Identities=17% Similarity=0.265 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
.+++.+..++.-.|-.. ....++|+.+|++...|+...+.-|.+.|+
T Consensus 131 ~L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred hCCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46677777776554322 235689999999999887766554444444
No 148
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.21 E-value=1.1e+02 Score=21.77 Aligned_cols=30 Identities=20% Similarity=0.202 Sum_probs=13.5
Q ss_pred HHHHhHHHHHHHHHHhhchHHHHHHHHHHH
Q 026325 141 KLKQTEMECEYLKRWFGSLTEQNRRLQREV 170 (240)
Q Consensus 141 Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~ 170 (240)
|......+...+....+.|..||+.|+.|.
T Consensus 33 knn~l~~e~q~~q~~reaL~~eneqlk~e~ 62 (79)
T COG3074 33 KNNSLSQEVQNAQHQREALERENEQLKEEQ 62 (79)
T ss_pred HhhHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333344444444444555555555443
No 149
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=29.95 E-value=1.3e+02 Score=21.75 Aligned_cols=24 Identities=17% Similarity=0.198 Sum_probs=11.5
Q ss_pred HHHHHHHHHhhchHHHHHHHHHHH
Q 026325 147 MECEYLKRWFGSLTEQNRRLQREV 170 (240)
Q Consensus 147 ~~~~~l~~~~~~l~~e~~~l~~e~ 170 (240)
.+.+.++...+.|..+|.+|+.|.
T Consensus 39 ~e~~~~~~~r~~L~~en~qLk~E~ 62 (79)
T PRK15422 39 QEVQNAQHQREELERENNHLKEQQ 62 (79)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHH
Confidence 333333444444555555555554
No 150
>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=29.87 E-value=1.6e+02 Score=22.38 Aligned_cols=73 Identities=12% Similarity=0.020 Sum_probs=35.3
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHHHHHHHHHHhhchHHHHHHHH
Q 026325 88 KKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEMECEYLKRWFGSLTEQNRRLQ 167 (240)
Q Consensus 88 ~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~ 167 (240)
....|+.+++..|+.. ...+.+|++...|+..|.+...... ....-...+......+.++.++|+
T Consensus 35 gyR~Y~~~~i~~l~~I-------------~~lr~~G~sl~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~l~ 99 (123)
T cd04770 35 GYRLYGEADLARLRFI-------------RRAQALGFSLAEIRELLSLRDDGAA--PCAEVRALLEEKLAEVEAKIAELQ 99 (123)
T ss_pred CCccCCHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHHhhhcCCC--CHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457999999888543 2345555555555555544322100 001112233334444455555555
Q ss_pred HHHHHHHh
Q 026325 168 REVEELRA 175 (240)
Q Consensus 168 ~e~~~l~~ 175 (240)
.....|..
T Consensus 100 ~~~~~l~~ 107 (123)
T cd04770 100 ALRAELAG 107 (123)
T ss_pred HHHHHHHH
Confidence 54444443
No 151
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=29.84 E-value=47 Score=23.97 Aligned_cols=20 Identities=10% Similarity=0.267 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCCceeeecch
Q 026325 115 KEELATQLKLKPRQVEVWFQ 134 (240)
Q Consensus 115 r~~LA~~l~L~~~qVkvWFq 134 (240)
+..|.+.++|..-||.+||.
T Consensus 56 ~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 56 TSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHhCCCCCeEEEEEE
Confidence 56788999999999999995
No 152
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=29.64 E-value=1.5e+02 Score=21.48 Aligned_cols=27 Identities=26% Similarity=0.265 Sum_probs=13.0
Q ss_pred HHHHHHHHHHhhchHHHHHHHHHHHHH
Q 026325 146 EMECEYLKRWFGSLTEQNRRLQREVEE 172 (240)
Q Consensus 146 ~~~~~~l~~~~~~l~~e~~~l~~e~~~ 172 (240)
-.....|+-..+.|+++|..|.++++.
T Consensus 17 vdtI~LLqmEieELKekn~~L~~e~~~ 43 (79)
T PRK15422 17 IDTITLLQMEIEELKEKNNSLSQEVQN 43 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444555555555555555554433
No 153
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.57 E-value=1.6e+02 Score=20.88 Aligned_cols=9 Identities=44% Similarity=0.641 Sum_probs=3.3
Q ss_pred chHHHHHHH
Q 026325 158 SLTEQNRRL 166 (240)
Q Consensus 158 ~l~~e~~~l 166 (240)
.|+++|..|
T Consensus 29 ELKEknn~l 37 (79)
T COG3074 29 ELKEKNNSL 37 (79)
T ss_pred HHHHHhhHh
Confidence 333333333
No 154
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=29.40 E-value=48 Score=27.05 Aligned_cols=44 Identities=18% Similarity=0.194 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k 139 (240)
.+++.+..+|...|-.. ....++|..+|++...|+.++..-|.+
T Consensus 106 ~L~~~~r~i~~l~~~~g-----~~~~EIA~~lgis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 106 ALPEKYAEALRLTELEG-----LSQKEIAEKLGLSLSGAKSRVQRGRVK 149 (181)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 35666666665544322 235689999999999887777533333
No 155
>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=29.40 E-value=48 Score=26.04 Aligned_cols=46 Identities=15% Similarity=0.186 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
+++.+..+|...|-.. ..-.++|..+|++...|+.+...-|.+.|+
T Consensus 111 L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 111 LPARQRAVVVLRYYED-----LSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CCHHHHHHhhhHHHhc-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5566666666555322 235688999999999998877655555443
No 156
>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=29.40 E-value=53 Score=26.08 Aligned_cols=46 Identities=13% Similarity=0.208 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.++..+..++...|-.. ....++|..+|+++..|+++...-|.+.|
T Consensus 119 ~L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLK 164 (169)
T ss_pred hCCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35666666666554333 23568999999999998876654444433
No 157
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=29.28 E-value=81 Score=25.39 Aligned_cols=46 Identities=15% Similarity=0.219 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
+++.+..++.-.|-... ...+||..+|++...|++....-|.+.|+
T Consensus 118 Lp~~~r~i~~l~~~e~~-----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 118 LPYKLRQVIILRYLHDY-----SQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred CCHHHHHHHHHHHHccC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56666666655443322 35689999999999988777655555443
No 158
>PF04999 FtsL: Cell division protein FtsL; InterPro: IPR007082 In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein IPR007060 from INTERPRO [], however this interaction may be indirect [].; GO: 0007049 cell cycle, 0016021 integral to membrane
Probab=29.17 E-value=1.1e+02 Score=22.25 Aligned_cols=29 Identities=31% Similarity=0.459 Sum_probs=18.6
Q ss_pred HHHHHHHHHhhchHHHHHHHHHHHHHHHh
Q 026325 147 MECEYLKRWFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 147 ~~~~~l~~~~~~l~~e~~~l~~e~~~l~~ 175 (240)
.+...+++....+.+||.+|+-|...+..
T Consensus 42 ~~l~~l~~~~~~l~~e~~~L~lE~~~l~~ 70 (97)
T PF04999_consen 42 YELQQLEKEIDQLQEENERLRLEIATLSS 70 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 33555566666677777777777766554
No 159
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=29.09 E-value=1.4e+02 Score=27.77 Aligned_cols=39 Identities=23% Similarity=0.317 Sum_probs=27.7
Q ss_pred hhHHHHHHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHh
Q 026325 137 RARSKLKQTEMECEYLKRWFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 137 R~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~ 175 (240)
+.+...++.+...+.+.+.++...||.+.|.+|+.+..+
T Consensus 138 ~~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE~la 176 (401)
T PF06785_consen 138 HLREENQCLQLQLDALQQECGEKEEESQTLNRELAEALA 176 (401)
T ss_pred HHHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHHHHH
Confidence 455555666666777777887788888888887776554
No 160
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=29.05 E-value=2.2e+02 Score=29.05 Aligned_cols=39 Identities=36% Similarity=0.448 Sum_probs=28.4
Q ss_pred hHHHHHHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhc
Q 026325 138 ARSKLKQTEMECEYLKRWFGSLTEQNRRLQREVEELRAM 176 (240)
Q Consensus 138 ~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~ 176 (240)
.|.|+++.+.|+..|+.......++++.|..++++|+..
T Consensus 543 ~r~r~~~lE~E~~~lr~elk~kee~~~~~e~~~~~lr~~ 581 (697)
T PF09726_consen 543 CRQRRRQLESELKKLRRELKQKEEQIRELESELQELRKY 581 (697)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455667777888888887777777777777777766654
No 161
>PF03980 Nnf1: Nnf1 ; InterPro: IPR007128 NNF1 is an essential yeast gene required for proper spindle orientation, nucleolar and nuclear envelope structure and mRNA export [].
Probab=28.74 E-value=1e+02 Score=23.09 Aligned_cols=30 Identities=33% Similarity=0.430 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhhchHHHHHHHHHHHHHHHh
Q 026325 146 EMECEYLKRWFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 146 ~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~ 175 (240)
......|+.....+..+|..|..++.+++.
T Consensus 79 ~~~~~~L~~~l~~l~~eN~~L~~~i~~~r~ 108 (109)
T PF03980_consen 79 KKEREQLNARLQELEEENEALAEEIQEQRK 108 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 455667788888899999999999988764
No 162
>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=28.40 E-value=51 Score=20.61 Aligned_cols=36 Identities=17% Similarity=0.271 Sum_probs=24.3
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecch
Q 026325 93 SKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQ 134 (240)
Q Consensus 93 t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFq 134 (240)
+..+...+...+ .. ....++|+.++++...|+.|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 455566665443 22 1456889999999998888775
No 163
>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=28.15 E-value=1.9e+02 Score=22.23 Aligned_cols=35 Identities=14% Similarity=0.060 Sum_probs=21.7
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchh
Q 026325 88 KKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQN 135 (240)
Q Consensus 88 ~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqN 135 (240)
....|+..++..|.. ...++.+|++...|+.+|..
T Consensus 34 g~R~Y~~~~l~~l~~-------------I~~l~~~G~sl~eI~~~l~~ 68 (124)
T TIGR02051 34 GYRRYPEETVKRLRF-------------IKRAQELGFSLEEIGGLLGL 68 (124)
T ss_pred CCEeECHHHHHHHHH-------------HHHHHHCCCCHHHHHHHHhc
Confidence 345688888888843 23345666666666665543
No 164
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=27.93 E-value=55 Score=26.49 Aligned_cols=29 Identities=17% Similarity=0.014 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 114 QKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 114 ~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
...++|..+|++...|++....-|.+.|+
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35689999999999998888655555443
No 165
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=27.73 E-value=57 Score=25.62 Aligned_cols=45 Identities=16% Similarity=0.250 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARS 140 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~ 140 (240)
.+++.+..+|.-.|-... ...++|+.+|++...|+.+...-|.+.
T Consensus 109 ~L~~~~r~v~~l~~~~~~-----s~~EIA~~lgis~~tV~~~l~ra~~~l 153 (163)
T PRK07037 109 ELPARTRYAFEMYRLHGE-----TQKDIARELGVSPTLVNFMIRDALVHC 153 (163)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 356666666655443321 356899999999999987654333333
No 166
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=27.69 E-value=60 Score=26.17 Aligned_cols=45 Identities=22% Similarity=0.230 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARS 140 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~ 140 (240)
.++..+..+|.-.|-.. ..-.++|..+|++...|+.+...-|.+.
T Consensus 135 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~~V~~~l~ra~~~L 179 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG-----YTHREAAQLLGLPLGTLKTRARRALSRL 179 (186)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 36666666666544322 2356889999999998887665433333
No 167
>KOG4752 consensus Ribosomal protein L41 [Translation, ribosomal structure and biogenesis]
Probab=27.67 E-value=1.2e+02 Score=16.86 Aligned_cols=8 Identities=38% Similarity=0.492 Sum_probs=4.8
Q ss_pred hhHHHHHH
Q 026325 137 RARSKLKQ 144 (240)
Q Consensus 137 R~k~Kkk~ 144 (240)
|+||+++.
T Consensus 2 r~kwrkkr 9 (26)
T KOG4752|consen 2 RAKWRKKR 9 (26)
T ss_pred chHHHHHH
Confidence 56666654
No 168
>PRK14127 cell division protein GpsB; Provisional
Probab=27.56 E-value=1.5e+02 Score=22.84 Aligned_cols=35 Identities=23% Similarity=0.325 Sum_probs=26.5
Q ss_pred HhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhccC
Q 026325 144 QTEMECEYLKRWFGSLTEQNRRLQREVEELRAMKV 178 (240)
Q Consensus 144 ~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~~~ 178 (240)
+...+++.+......|.+++.+|+.++.++.....
T Consensus 34 ~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~ 68 (109)
T PRK14127 34 DVIKDYEAFQKEIEELQQENARLKAQVDELTKQVS 68 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 33456777777788888999999999888887443
No 169
>PF12808 Mto2_bdg: Micro-tubular organiser Mto1 C-term Mto2-binding region; InterPro: IPR024545 This domain occurs at the C terminus of microtubule organising proteins in both budding and fission fungi. In Schizosaccharomyces pombe it has been shown to interact with the Mto2p protein, an interaction which is critical for anchoring the cytokinetic actin ring to the medial region of the cell and for proper coordination of mitosis with cytokinesis [, ].
Probab=27.51 E-value=1e+02 Score=20.48 Aligned_cols=25 Identities=32% Similarity=0.497 Sum_probs=17.7
Q ss_pred HHHHHHhhchHHHHHHHHHHHHHHH
Q 026325 150 EYLKRWFGSLTEQNRRLQREVEELR 174 (240)
Q Consensus 150 ~~l~~~~~~l~~e~~~l~~e~~~l~ 174 (240)
.........|..||+.|+.++.-++
T Consensus 25 ~~a~~rl~~l~~EN~~Lr~eL~~~r 49 (52)
T PF12808_consen 25 SAARKRLSKLEGENRLLRAELERLR 49 (52)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445566678888888888887655
No 170
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=27.46 E-value=56 Score=25.94 Aligned_cols=46 Identities=15% Similarity=0.039 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..++.-.|-... .-.++|..+|+++..|+++...-|.+.|
T Consensus 112 ~L~~~~r~v~~l~~~~g~-----s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 112 LLSADQREAIILIGASGF-----SYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 366666666666543222 3568999999999999887764444443
No 171
>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=27.46 E-value=1e+02 Score=29.76 Aligned_cols=17 Identities=24% Similarity=0.499 Sum_probs=7.1
Q ss_pred chHHHHHHHHHHHHHHH
Q 026325 158 SLTEQNRRLQREVEELR 174 (240)
Q Consensus 158 ~l~~e~~~l~~e~~~l~ 174 (240)
.|.++.++++..+.+|.
T Consensus 120 ql~~~~~~~~~~l~~l~ 136 (472)
T TIGR03752 120 QLKSERQQLQGLIDQLQ 136 (472)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33444444444444443
No 172
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=27.39 E-value=1.2e+02 Score=22.58 Aligned_cols=33 Identities=12% Similarity=0.012 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhh
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNR 136 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNR 136 (240)
+|+...+..|. ....++.+|++-..|+.+|...
T Consensus 36 ~Y~~~~~~~l~-------------~I~~lr~~G~sL~eI~~~l~~~ 68 (107)
T cd04777 36 FFDEKCQDDLE-------------FILELKGLGFSLIEIQKIFSYK 68 (107)
T ss_pred ccCHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHHhc
Confidence 58888877663 4455777888888888888653
No 173
>PF13518 HTH_28: Helix-turn-helix domain
Probab=27.39 E-value=21 Score=22.50 Aligned_cols=21 Identities=19% Similarity=0.436 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCCceeeecchh
Q 026325 115 KEELATQLKLKPRQVEVWFQN 135 (240)
Q Consensus 115 r~~LA~~l~L~~~qVkvWFqN 135 (240)
..++|.++|++..+|..|.+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHH
Confidence 456899999999999999864
No 174
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=27.16 E-value=50 Score=28.14 Aligned_cols=46 Identities=13% Similarity=0.190 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
+++.+..+|...|... ....++|..+|++...|+.+...-+.+.|+
T Consensus 185 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 185 LPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5666666666655332 235689999999999999988766666554
No 175
>PRK10884 SH3 domain-containing protein; Provisional
Probab=26.80 E-value=1.6e+02 Score=25.07 Aligned_cols=12 Identities=17% Similarity=0.271 Sum_probs=5.9
Q ss_pred HHHHHHHHHHHh
Q 026325 94 KEQSRLLEESFR 105 (240)
Q Consensus 94 ~~Q~~~Le~~F~ 105 (240)
..++..|++...
T Consensus 92 ~~rlp~le~el~ 103 (206)
T PRK10884 92 RTRVPDLENQVK 103 (206)
T ss_pred HHHHHHHHHHHH
Confidence 345555555443
No 176
>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=26.59 E-value=1.9e+02 Score=21.40 Aligned_cols=16 Identities=19% Similarity=0.025 Sum_probs=11.8
Q ss_pred CCCCCCHHHHHHHHHH
Q 026325 88 KKLRLSKEQSRLLEES 103 (240)
Q Consensus 88 ~R~~~t~~Q~~~Le~~ 103 (240)
....|+..++..|...
T Consensus 35 g~R~Y~~~dl~~l~~I 50 (102)
T cd04775 35 NYRLYSEADLSRLEKI 50 (102)
T ss_pred CCeeeCHHHHHHHHHH
Confidence 3456999999888654
No 177
>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=26.52 E-value=1.9e+02 Score=22.14 Aligned_cols=35 Identities=14% Similarity=0.085 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhh
Q 026325 89 KLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNR 136 (240)
Q Consensus 89 R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNR 136 (240)
...|+.+++..|. .....+.+|++-..|+-+|...
T Consensus 36 yR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04783 36 YRRYPEETVTRLR-------------FIKRAQELGFTLDEIAELLELD 70 (126)
T ss_pred CeecCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhcc
Confidence 4569999988885 3334566777777777666543
No 178
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=26.35 E-value=59 Score=26.70 Aligned_cols=45 Identities=13% Similarity=0.113 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
+++.+..++.-.|-.. ..-.+||..+|++...|+.++..-|.+.|
T Consensus 137 L~~~~r~i~~L~~~~g-----~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr 181 (196)
T PRK12524 137 LPERQRQAVVLRHIEG-----LSNPEIAEVMEIGVEAVESLTARGKRALA 181 (196)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 5566655555543322 12568999999999999988864444443
No 179
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=26.02 E-value=72 Score=26.07 Aligned_cols=46 Identities=9% Similarity=0.133 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
+++.+..++.-.|-... .-.++|..+|++...|+.+...-|.+.|+
T Consensus 137 L~~~~r~i~~L~~~~g~-----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 182 (195)
T PRK12532 137 LPENTARVFTLKEILGF-----SSDEIQQMCGISTSNYHTIMHRARESLRQ 182 (195)
T ss_pred CCHHHHHHhhhHHHhCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55666666654433221 25689999999999999887655555444
No 180
>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=25.91 E-value=61 Score=25.51 Aligned_cols=39 Identities=21% Similarity=0.191 Sum_probs=26.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecch
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQ 134 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFq 134 (240)
.+++.+..+|.-.|-.. ..-.++|+.||+++..|+....
T Consensus 122 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQN-----LPIAEVARILGKTEGAVKILQF 160 (170)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 36666666666644322 2356889999999998876554
No 181
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=25.79 E-value=1.4e+02 Score=24.61 Aligned_cols=25 Identities=40% Similarity=0.494 Sum_probs=10.4
Q ss_pred HHHHHHHhhchHHHHHHHHHHHHHH
Q 026325 149 CEYLKRWFGSLTEQNRRLQREVEEL 173 (240)
Q Consensus 149 ~~~l~~~~~~l~~e~~~l~~e~~~l 173 (240)
+..|+.....|.++|..|.+++..|
T Consensus 106 ~~~l~~e~~~l~~~~e~Le~e~~~L 130 (161)
T TIGR02894 106 NERLKNQNESLQKRNEELEKELEKL 130 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333344444444444444444433
No 182
>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=25.59 E-value=22 Score=24.00 Aligned_cols=26 Identities=23% Similarity=0.304 Sum_probs=20.5
Q ss_pred HHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 115 KEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 115 r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
..+||..||++.+.|..|-+ |-+|..
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 56899999999999999975 445443
No 183
>KOG3584 consensus cAMP response element binding protein and related transcription factors [Transcription]
Probab=25.46 E-value=1e+02 Score=27.90 Aligned_cols=25 Identities=24% Similarity=0.376 Sum_probs=17.4
Q ss_pred HHhhchHHHHHHHHHHHHHHHhccC
Q 026325 154 RWFGSLTEQNRRLQREVEELRAMKV 178 (240)
Q Consensus 154 ~~~~~l~~e~~~l~~e~~~l~~~~~ 178 (240)
....-|..+|..|..|++.|+.+-+
T Consensus 319 NRVAVLENQNKaLIEELKtLKeLYc 343 (348)
T KOG3584|consen 319 NRVAVLENQNKALIEELKTLKELYC 343 (348)
T ss_pred hHHHHHhcccHHHHHHHHHHHHHhh
Confidence 3344577788888888888877633
No 184
>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=25.44 E-value=84 Score=25.69 Aligned_cols=47 Identities=13% Similarity=0.239 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
.+++.+..+|.-.|-... ...+||..+|++...|+.+...-|.+.|+
T Consensus 131 ~L~~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tvk~rl~Rar~~Lr~ 177 (188)
T TIGR02943 131 HLPEQTARVFMMREVLGF-----ESDEICQELEISTSNCHVLLYRARLSLRA 177 (188)
T ss_pred hCCHHHHHHHHHHHHhCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 456666666666544332 36789999999999998776644444443
No 185
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=25.41 E-value=42 Score=34.18 Aligned_cols=60 Identities=18% Similarity=0.303 Sum_probs=44.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHh
Q 026325 86 PRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQT 145 (240)
Q Consensus 86 rr~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~ 145 (240)
-|-++....++-..|...|..+-.+...+-..++..|...+..|++||++|+..-+....
T Consensus 627 ~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl 686 (1007)
T KOG3623|consen 627 VKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPL 686 (1007)
T ss_pred ccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCcc
Confidence 344556666667778888887776666666666777888889999999999988776543
No 186
>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=24.83 E-value=1.2e+02 Score=22.54 Aligned_cols=36 Identities=8% Similarity=-0.063 Sum_probs=21.5
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchh
Q 026325 88 KKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQN 135 (240)
Q Consensus 88 ~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqN 135 (240)
.+..|+.+++..|...- .|.+.+|++-..|+.++.+
T Consensus 35 g~R~Yt~~di~~l~~I~------------~llr~~G~~l~~i~~~l~~ 70 (99)
T cd04765 35 GRRYYRPKDVELLLLIK------------HLLYEKGYTIEGAKQALKE 70 (99)
T ss_pred CCeeeCHHHHHHHHHHH------------HHHHHCCCCHHHHHHHHHh
Confidence 35579999998885442 2344556655555555543
No 187
>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=24.71 E-value=63 Score=27.24 Aligned_cols=46 Identities=15% Similarity=0.186 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..+|...|-... ...++|..+|++...|+.+...-+.+.|
T Consensus 175 ~L~~~~r~il~l~y~~~~-----s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEEL-----NLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred hCCHHHHHHHHHHHhCCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 467777788877764332 3578999999999988777654444433
No 188
>PF15058 Speriolin_N: Speriolin N terminus
Probab=24.67 E-value=95 Score=26.39 Aligned_cols=25 Identities=32% Similarity=0.395 Sum_probs=11.3
Q ss_pred HHHHHHHHHhhchHHHHHHHHHHHHH
Q 026325 147 MECEYLKRWFGSLTEQNRRLQREVEE 172 (240)
Q Consensus 147 ~~~~~l~~~~~~l~~e~~~l~~e~~~ 172 (240)
.|++.||+... |..||.+|+..+.|
T Consensus 19 ~ENeeLKKlVr-LirEN~eLksaL~e 43 (200)
T PF15058_consen 19 RENEELKKLVR-LIRENHELKSALGE 43 (200)
T ss_pred hhhHHHHHHHH-HHHHHHHHHHHHHH
Confidence 34444444333 33455555555433
No 189
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=24.41 E-value=78 Score=25.17 Aligned_cols=44 Identities=18% Similarity=0.226 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARS 140 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~ 140 (240)
+++.+..+|.-.|-... ...+||..||+++..|+.+...-|.+.
T Consensus 119 L~~~~r~vl~L~~~~g~-----s~~EIA~~lgis~~tV~~~l~ra~~~L 162 (173)
T PRK09645 119 LSPEHRAVLVRSYYRGW-----STAQIAADLGIPEGTVKSRLHYALRAL 162 (173)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 66667777766543322 256899999999999887665433333
No 190
>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=24.23 E-value=33 Score=21.54 Aligned_cols=38 Identities=26% Similarity=0.357 Sum_probs=24.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecc
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWF 133 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWF 133 (240)
.++.++.+.+...+... + ...+||+.+|++...|.-|+
T Consensus 5 ~~~~~~~~~i~~l~~~G-~----si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-M----SIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHHHH
Confidence 46666666666677655 2 36789999999987765443
No 191
>PF07407 Seadorna_VP6: Seadornavirus VP6 protein; InterPro: IPR009982 This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Probab=24.18 E-value=95 Score=28.66 Aligned_cols=19 Identities=42% Similarity=0.393 Sum_probs=7.3
Q ss_pred HhhchHHHHHHHHHHHHHH
Q 026325 155 WFGSLTEQNRRLQREVEEL 173 (240)
Q Consensus 155 ~~~~l~~e~~~l~~e~~~l 173 (240)
++..|+.||..|+.++..|
T Consensus 40 EN~~LKkEN~~Lk~eVerL 58 (420)
T PF07407_consen 40 ENHSLKKENNDLKIEVERL 58 (420)
T ss_pred HhHHHHHHHHHHHHHHHHH
Confidence 3333333344443333333
No 192
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=24.17 E-value=2.5e+02 Score=20.71 Aligned_cols=11 Identities=18% Similarity=0.939 Sum_probs=6.1
Q ss_pred ecchhhhhHHH
Q 026325 131 VWFQNRRARSK 141 (240)
Q Consensus 131 vWFqNRR~k~K 141 (240)
+||+=++++.+
T Consensus 21 ~~~k~~ka~~~ 31 (87)
T PF10883_consen 21 LWWKVKKAKKQ 31 (87)
T ss_pred HHHHHHHHHHH
Confidence 56665555544
No 193
>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=24.16 E-value=1.5e+02 Score=25.63 Aligned_cols=50 Identities=18% Similarity=0.321 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTE 146 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~ 146 (240)
++..+..++.-.|-... ...++|..+|++...|+++...-|.+.|+.-..
T Consensus 162 Lp~~~R~v~~L~~~eg~-----S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~ 211 (244)
T TIGR03001 162 LSERERHLLRLHFVDGL-----SMDRIGAMYQVHRSTVSRWVAQARERLLERTRR 211 (244)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 55555555555443221 356899999999999999998777776665433
No 194
>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.
Probab=23.50 E-value=2.5e+02 Score=19.22 Aligned_cols=21 Identities=38% Similarity=0.548 Sum_probs=13.4
Q ss_pred HhhchHHHHHHHHHHHHHHHh
Q 026325 155 WFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 155 ~~~~l~~e~~~l~~e~~~l~~ 175 (240)
.+..|..+...|+.++++++.
T Consensus 40 rn~eL~~ei~~L~~e~ee~r~ 60 (61)
T PF08826_consen 40 RNRELEQEIERLKKEMEELRS 60 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHhhc
Confidence 444566777777777777664
No 195
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=23.24 E-value=1.7e+02 Score=25.56 Aligned_cols=39 Identities=21% Similarity=0.334 Sum_probs=29.7
Q ss_pred hhHHHHHHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHh
Q 026325 137 RARSKLKQTEMECEYLKRWFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 137 R~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~ 175 (240)
|++.-.+..+.......+..+.|..|+..|++++++|..
T Consensus 102 kA~~~i~~l~~~~~~~~~~~e~l~~e~~~l~~rl~ql~~ 140 (232)
T KOG2483|consen 102 KALEHIQSLERKSATQQQDIEDLSRENRKLKARLEQLSL 140 (232)
T ss_pred hHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 555556666666666677778899999999999988764
No 196
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=23.12 E-value=72 Score=27.55 Aligned_cols=46 Identities=15% Similarity=0.234 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..+|...|-... .-.++|..+|++...|+.|...-+.+.|
T Consensus 205 ~L~~~~r~vl~l~~~~g~-----s~~eIA~~l~is~~tV~~~~~ra~~kLr 250 (257)
T PRK08583 205 VLSDREKSIIQCTFIENL-----SQKETGERLGISQMHVSRLQRQAIKKLR 250 (257)
T ss_pred hCCHHHHHHHHHHHhCCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 467777777777653322 2468999999999999887765444444
No 197
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.95 E-value=2.8e+02 Score=20.67 Aligned_cols=66 Identities=17% Similarity=0.147 Sum_probs=33.6
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHHhHHHHHHHHHHhhchHHHHHHHHH
Q 026325 89 KLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEMECEYLKRWFGSLTEQNRRLQR 168 (240)
Q Consensus 89 R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~ 168 (240)
...|+...+..|... ...+.+|++...|+-+|..... ..-...+......+.++...|+.
T Consensus 37 yR~Y~~~~i~~l~~I-------------~~lr~~G~sl~~i~~l~~~~~~-------~~~~~~l~~~~~~l~~~i~~l~~ 96 (108)
T cd01107 37 YRYYSAEQLERLNRI-------------KYLRDLGFPLEEIKEILDADND-------DELRKLLREKLAELEAEIEELQR 96 (108)
T ss_pred ccccCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHhcCCH-------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 456888888887533 2234456665555555544332 11222334444444555555554
Q ss_pred HHHHHH
Q 026325 169 EVEELR 174 (240)
Q Consensus 169 e~~~l~ 174 (240)
..+.+.
T Consensus 97 ~~~~l~ 102 (108)
T cd01107 97 ILRLLE 102 (108)
T ss_pred HHHHHH
Confidence 444443
No 198
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=22.92 E-value=66 Score=27.29 Aligned_cols=44 Identities=18% Similarity=0.126 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k 139 (240)
.+++.+..+|...|-.. ..-.+||..||+++..|+++...-|.+
T Consensus 134 ~Lp~~~R~v~~L~y~eg-----~s~~EIAe~LgiS~~tVk~~L~RAr~~ 177 (216)
T PRK12533 134 KLPVEYREVLVLRELED-----MSYREIAAIADVPVGTVMSRLARARRR 177 (216)
T ss_pred cCCHHHHhHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 35566666666554332 125688999999999987766543333
No 199
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=22.86 E-value=79 Score=25.93 Aligned_cols=44 Identities=20% Similarity=0.276 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
+++.+..+|...|. ...-.+||..+|+++..|++.+..-|.+.|
T Consensus 156 L~~~~r~vl~l~~e------~~s~~EIA~~lgis~~tV~~~l~rar~~Lr 199 (208)
T PRK08295 156 LSELEKEVLELYLD------GKSYQEIAEELNRHVKSIDNALQRVKRKLE 199 (208)
T ss_pred CCHHHHHHHHHHHc------cCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 44555555544222 223568899999999999765554444433
No 200
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=22.80 E-value=66 Score=26.23 Aligned_cols=46 Identities=11% Similarity=-0.033 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.|..++.-.|-..- .-.+||..+|+++..|+++...-|.+.|
T Consensus 130 ~Lp~~~r~v~~L~~~~g~-----s~~EIA~~lgis~~tVk~~l~Rar~~Lr 175 (185)
T PRK09649 130 DLTTDQREALLLTQLLGL-----SYADAAAVCGCPVGTIRSRVARARDALL 175 (185)
T ss_pred hCCHHHhHHhhhHHHcCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 355666555555443221 2568999999999999887754444333
No 201
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.76 E-value=84 Score=26.68 Aligned_cols=48 Identities=17% Similarity=0.199 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
.+|+.+.++|+-..+-. .-.++|+.|+++++.|+.+..+-..|..-+.
T Consensus 155 ~Lt~rE~~Vl~l~~~G~------s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~n 202 (216)
T PRK10100 155 LLTHREKEILNKLRIGA------SNNEIARSLFISENTVKTHLYNLFKKIAVKN 202 (216)
T ss_pred CCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 48999999988776622 2457899999999999999988777766543
No 202
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=22.72 E-value=81 Score=25.54 Aligned_cols=46 Identities=15% Similarity=0.070 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..+++-.|-.. ....++|..+|++...|+.+...-|.+.|
T Consensus 131 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 176 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG-----LSVAEAATRSGMSESAVKVSVHRGLKALA 176 (184)
T ss_pred hCCHHHHHHHHHHHHcC-----CcHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 46677776776544322 23568999999999999887754444443
No 203
>PF02344 Myc-LZ: Myc leucine zipper domain; InterPro: IPR003327 This family consists of the leucine zipper dimerisation domain found in both cellular c-Myc proto-oncogenes and viral v-Myc oncogenes. Dimerisation via the leucine zipper motif with other basic helix-loop-helix-leucine zipper (b/HLH/lz) proteins is required for efficient DNA binding []. The Myc-Max dimer is a transactivating complex activating expression of growth related genes promoting cell proliferation. The dimerisation is facilitated via interdigitating leucine residues every 7th position of the alpha helix. Like charge repulsion of adjacent residues in this region preturbs the formation of homodimers with heterodimers being promoted by opposing charge attractions. It has been demonstrated that in transgenic mice the balance between oncogene-induced proliferation and apoptosis in a given tissue can be a critical determinant in the initiation and maintenance of the tumor [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1NKP_D 1A93_A 2A93_A.
Probab=22.69 E-value=1.8e+02 Score=17.31 Aligned_cols=24 Identities=25% Similarity=0.338 Sum_probs=13.2
Q ss_pred HHHHhhchHHHHHHHHHHHHHHHh
Q 026325 152 LKRWFGSLTEQNRRLQREVEELRA 175 (240)
Q Consensus 152 l~~~~~~l~~e~~~l~~e~~~l~~ 175 (240)
|...-+.|....+.|+..+++|+.
T Consensus 6 L~sekeqLrrr~eqLK~kLeqlrn 29 (32)
T PF02344_consen 6 LISEKEQLRRRREQLKHKLEQLRN 29 (32)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 344445556666666666666664
No 204
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=22.55 E-value=79 Score=26.16 Aligned_cols=46 Identities=17% Similarity=0.290 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..++.-.|-... .-.++|..+|+++..|++....-|.+.|
T Consensus 139 ~Lp~~~r~v~~L~~~eg~-----s~~EIA~~lgis~~tVk~~l~RAr~~Lr 184 (201)
T PRK12545 139 HLPEQIGRVFMMREFLDF-----EIDDICTELTLTANHCSVLLYRARTRLR 184 (201)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 355666666655443221 2568999999999999887664444443
No 205
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=22.54 E-value=1e+02 Score=25.31 Aligned_cols=37 Identities=24% Similarity=0.186 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceee
Q 026325 94 KEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVE 130 (240)
Q Consensus 94 ~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVk 130 (240)
..-+..|...+++..|........+|..||++...|.
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHhe
Confidence 4557888888999899999999999999999976543
No 206
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=22.50 E-value=80 Score=25.90 Aligned_cols=45 Identities=16% Similarity=0.058 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
+++.+..++.-.|-... .-.+||..||+++..|+++...-|.+.|
T Consensus 117 Lp~~~r~i~~L~~~~g~-----s~~EIA~~Lgis~~tVk~~l~Rar~~Lr 161 (187)
T PRK12516 117 LPDDQREAIILVGASGF-----AYEEAAEICGCAVGTIKSRVNRARQRLQ 161 (187)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 55666666555443221 2468899999999999887764444433
No 207
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=22.44 E-value=23 Score=23.89 Aligned_cols=21 Identities=19% Similarity=0.339 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCCceeeecchh
Q 026325 115 KEELATQLKLKPRQVEVWFQN 135 (240)
Q Consensus 115 r~~LA~~l~L~~~qVkvWFqN 135 (240)
..++|+.+|++...|+.|=+.
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999543
No 208
>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=22.43 E-value=77 Score=26.67 Aligned_cols=46 Identities=20% Similarity=0.320 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..+|...|... ....++|+.+|++...|+.|...-+.+.|
T Consensus 178 ~L~~~~r~vl~l~y~~~-----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 178 ALPERERRILLLRFFED-----KTQSEIAERLGISQMHVSRLLRRALKKLR 223 (227)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 47777777777766432 23568999999999999887754444433
No 209
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=22.42 E-value=78 Score=26.44 Aligned_cols=46 Identities=20% Similarity=0.122 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..++.-.|-.. ..-.++|..||+++..|+++...-|.+.|
T Consensus 138 ~L~~~~r~v~~L~~~~g-----~s~~EIA~~Lgis~~tV~~~l~RArk~Lr 183 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG-----LSYEEIAATLGVKLGTVRSRIHRGRQQLR 183 (203)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35555555554443222 12568899999999999887764444333
No 210
>PRK09480 slmA division inhibitor protein; Provisional
Probab=22.28 E-value=54 Score=26.36 Aligned_cols=38 Identities=11% Similarity=0.159 Sum_probs=29.8
Q ss_pred HHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhh
Q 026325 100 LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRA 138 (240)
Q Consensus 100 Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~ 138 (240)
....|...+. ......+||++.|++...+-.+|.|+-.
T Consensus 19 a~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 19 LAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 3344555545 6777889999999999999999999753
No 211
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=21.99 E-value=97 Score=24.21 Aligned_cols=47 Identities=17% Similarity=0.226 Sum_probs=34.8
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 90 LRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 90 ~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
..+++.+..+|+- +..+ + ...++|+.++++++.|+.|.+|=+.|..-
T Consensus 148 ~~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 148 PLLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred cCCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3488888888876 3332 2 25688999999999999998887666553
No 212
>PRK10884 SH3 domain-containing protein; Provisional
Probab=21.96 E-value=2.6e+02 Score=23.85 Aligned_cols=19 Identities=32% Similarity=0.150 Sum_probs=7.3
Q ss_pred HHHHhhchHHHHHHHHHHH
Q 026325 152 LKRWFGSLTEQNRRLQREV 170 (240)
Q Consensus 152 l~~~~~~l~~e~~~l~~e~ 170 (240)
|+..+..|.+|+..++.++
T Consensus 137 L~~~n~~L~~~l~~~~~~~ 155 (206)
T PRK10884 137 LKEENQKLKNQLIVAQKKV 155 (206)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3333333333333333333
No 213
>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=21.96 E-value=79 Score=25.67 Aligned_cols=29 Identities=17% Similarity=0.271 Sum_probs=21.0
Q ss_pred HHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 113 KQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 113 ~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
....+||..+|++...|++++..-|.+.|
T Consensus 166 ~s~~eIA~~l~~s~~tV~~~l~r~r~~L~ 194 (198)
T TIGR02859 166 KSYQEIACDLNRHVKSIDNALQRVKRKLE 194 (198)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34678999999999999876654444433
No 214
>PRK10403 transcriptional regulator NarP; Provisional
Probab=21.89 E-value=60 Score=25.76 Aligned_cols=48 Identities=17% Similarity=0.281 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk~ 144 (240)
.++..+..+|+..... ....+||+.++++++.|+++..|=|.|...+.
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~ 200 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 5888888888765432 23568899999999999998888777765443
No 215
>PF14662 CCDC155: Coiled-coil region of CCDC155
Probab=21.81 E-value=2.2e+02 Score=24.17 Aligned_cols=39 Identities=31% Similarity=0.316 Sum_probs=20.3
Q ss_pred hhhhHHHHHHhHHHHHHHHHHhhchHHHHHHHHHHHHHH
Q 026325 135 NRRARSKLKQTEMECEYLKRWFGSLTEQNRRLQREVEEL 173 (240)
Q Consensus 135 NRR~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l 173 (240)
||+--...++.+.+...|-...+.|.+||.++..+...+
T Consensus 83 ~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl~~e~~~l 121 (193)
T PF14662_consen 83 NRSLLAQARQLEKEQQSLVAEIETLQEENGKLLAERDGL 121 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhH
Confidence 444444444555555555555555555555555554443
No 216
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=21.80 E-value=74 Score=25.48 Aligned_cols=44 Identities=14% Similarity=0.109 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k 139 (240)
.+++.+..++.-.|-.. ....+||+.+|++...|+++...-+.+
T Consensus 119 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 119 GLNGKTREAFLLSQLDG-----LTYSEIAHKLGVSVSSVKKYVAKATEH 162 (172)
T ss_pred hCCHHHhHHhhhhhccC-----CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 35555555554433222 236789999999999998877533333
No 217
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=21.73 E-value=83 Score=26.33 Aligned_cols=47 Identities=15% Similarity=0.167 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
.+++.+..++.-.|-... ...+||..+|++...|+++...-|.+.|+
T Consensus 148 ~L~~~~r~v~~L~~~~g~-----s~~EIAe~lgis~~tV~~~l~RAr~~Lr~ 194 (206)
T PRK12544 148 GLPAKYARVFMMREFIEL-----ETNEICHAVDLSVSNLNVLLYRARLRLRE 194 (206)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 356666666665543332 25689999999999998877655555444
No 218
>PF15397 DUF4618: Domain of unknown function (DUF4618)
Probab=21.51 E-value=1.8e+02 Score=25.84 Aligned_cols=35 Identities=31% Similarity=0.395 Sum_probs=24.8
Q ss_pred HHHhhchHHHHHHHHHHHHHHHhccCCCCCCCCCC
Q 026325 153 KRWFGSLTEQNRRLQREVEELRAMKVGPPTVISPH 187 (240)
Q Consensus 153 ~~~~~~l~~e~~~l~~e~~~l~~~~~~~~~~~~p~ 187 (240)
+...+.+.++...|+.|+++|+.....+..++-+.
T Consensus 199 re~i~el~e~I~~L~~eV~~L~~~~~~~Re~iF~d 233 (258)
T PF15397_consen 199 REEIDELEEEIPQLRAEVEQLQAQAQDPREVIFAD 233 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcchHHHhhHH
Confidence 44456788888888999999988766555555443
No 219
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=21.40 E-value=85 Score=25.34 Aligned_cols=45 Identities=9% Similarity=0.141 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARS 140 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~ 140 (240)
.+++.|..++.-.|-... .-.++|..||+++..|+.....-+.+.
T Consensus 127 ~Lp~~~R~v~~L~~~~g~-----s~~EIA~~lgis~~tVk~~l~rAl~~~ 171 (178)
T PRK12529 127 TLRPRVKQAFLMATLDGM-----KQKDIAQALDIALPTVKKYIHQAYVTC 171 (178)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 467777777766554332 356899999999999988776444443
No 220
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=21.38 E-value=77 Score=26.26 Aligned_cols=12 Identities=33% Similarity=0.620 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHH
Q 026325 159 LTEQNRRLQREV 170 (240)
Q Consensus 159 l~~e~~~l~~e~ 170 (240)
|+.|.+.|++|+
T Consensus 36 LkDE~RDLKqEl 47 (166)
T PF04880_consen 36 LKDELRDLKQEL 47 (166)
T ss_dssp ------------
T ss_pred HHHHHHHHHHHH
Confidence 333333333333
No 221
>cd07429 Cby_like Chibby, a nuclear inhibitor of Wnt/beta-catenin mediated transcription, and similar proteins. Chibby(Cby) is a well-conserved nuclear protein that functions as part of the Wnt/beta-catenin signaling pathway. Specifically, Cby binds directly to beta-catenin by interacting with its central region, which harbors armadillo repeats. Cby-beta-catenin interactions may also involve 14-3-3 proteins. By competing with other binding partners of beta-catenin, the Tcf/Lef transcription factors, Cby inhibits transcriptional activation. Cby has been shown to play a role in adipocyte differentiation. The C-terminal region of Cby appears to contain an alpha-helical coiled-coil motif.
Probab=21.35 E-value=1.7e+02 Score=22.51 Aligned_cols=27 Identities=33% Similarity=0.299 Sum_probs=13.9
Q ss_pred HHHHHHhhchHHHHHHHHHHHHHHHhc
Q 026325 150 EYLKRWFGSLTEQNRRLQREVEELRAM 176 (240)
Q Consensus 150 ~~l~~~~~~l~~e~~~l~~e~~~l~~~ 176 (240)
..+++.+..|.|||.-|+-+++-|.++
T Consensus 75 ~rlkkk~~~LeEENNlLklKievLLDM 101 (108)
T cd07429 75 LRLKKKNQQLEEENNLLKLKIEVLLDM 101 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444556666555555555443
No 222
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=21.33 E-value=56 Score=24.96 Aligned_cols=41 Identities=22% Similarity=0.331 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhh
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRA 138 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~ 138 (240)
.+++.++..+.+.+... ...+|..||++..-|+.|=|+|+.
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 38889999998887654 457899999999999999999864
No 223
>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=21.22 E-value=2.7e+02 Score=21.48 Aligned_cols=34 Identities=6% Similarity=-0.008 Sum_probs=20.6
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecch
Q 026325 88 KKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQ 134 (240)
Q Consensus 88 ~R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFq 134 (240)
....|+..++..|... ...+.+|++-.+|+.+|.
T Consensus 35 gyR~Y~~~~l~~l~~I-------------~~lr~lG~sL~eI~~~l~ 68 (127)
T TIGR02047 35 NYRVYTVGHVERLAFI-------------RNCRTLDMSLAEIRQLLR 68 (127)
T ss_pred CCCcCCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHH
Confidence 3557899888888543 234555555555555553
No 224
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=21.16 E-value=22 Score=22.46 Aligned_cols=22 Identities=23% Similarity=0.430 Sum_probs=16.8
Q ss_pred HHHHHHHHhCCCCceeeecchh
Q 026325 114 QKEELATQLKLKPRQVEVWFQN 135 (240)
Q Consensus 114 ~r~~LA~~l~L~~~qVkvWFqN 135 (240)
...++|+.+|++...|..|.+.
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT-
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 3568899999999999999753
No 225
>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=21.02 E-value=2.7e+02 Score=21.34 Aligned_cols=15 Identities=7% Similarity=-0.206 Sum_probs=11.4
Q ss_pred CCCCCHHHHHHHHHH
Q 026325 89 KLRLSKEQSRLLEES 103 (240)
Q Consensus 89 R~~~t~~Q~~~Le~~ 103 (240)
...|+..++..|...
T Consensus 36 ~R~Y~~~~l~~l~~I 50 (126)
T cd04785 36 YRLYGAAHVERLRFI 50 (126)
T ss_pred ccccCHHHHHHHHHH
Confidence 456999999888654
No 226
>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=21.01 E-value=45 Score=27.27 Aligned_cols=28 Identities=14% Similarity=0.117 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 114 QKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 114 ~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.-.+||..+|+++..|+++...-|.+.|
T Consensus 149 s~~EIA~~lgis~~tVk~~l~Rar~~Lr 176 (193)
T TIGR02947 149 AYKEIAEIMGTPIGTVMSRLHRGRKQLR 176 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4578999999999999988875555444
No 227
>PF11365 DUF3166: Protein of unknown function (DUF3166); InterPro: IPR021507 This eukaryotic family of proteins has no known function.
Probab=21.00 E-value=2.1e+02 Score=21.56 Aligned_cols=31 Identities=29% Similarity=0.543 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhhchHHHHHHHHHHHHHHHhc
Q 026325 146 EMECEYLKRWFGSLTEQNRRLQREVEELRAM 176 (240)
Q Consensus 146 ~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~ 176 (240)
+.+...+++....+..+|++|..|+..++..
T Consensus 14 EEEa~LlRRkl~ele~eN~~l~~EL~kyk~~ 44 (96)
T PF11365_consen 14 EEEAELLRRKLSELEDENKQLTEELNKYKSK 44 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5666788889999999999999999998874
No 228
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=20.97 E-value=81 Score=25.63 Aligned_cols=28 Identities=14% Similarity=0.134 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 114 QKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 114 ~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.-.++|..+|+++..|++....-|.+.|
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr 183 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAID 183 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3568999999999999877664444433
No 229
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=20.97 E-value=87 Score=25.58 Aligned_cols=44 Identities=20% Similarity=0.101 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k 139 (240)
.+++.+..+|.-.|-... .-.++|..+|++...|+++...-|.+
T Consensus 111 ~Lp~~~R~v~~L~~~eg~-----s~~EIA~~lgis~~tV~~~l~Rar~~ 154 (182)
T PRK12511 111 DLPEEQRAALHLVAIEGL-----SYQEAAAVLGIPIGTLMSRIGRARAA 154 (182)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence 466667666666543321 35689999999999998877543333
No 230
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=20.93 E-value=84 Score=25.42 Aligned_cols=46 Identities=15% Similarity=0.263 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..++.-.|-.. ..-.+||..+|+++..|++....-|.+.|
T Consensus 122 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr 167 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN-----LTYQEISSVMGITEANVRKQFERARKRVQ 167 (185)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35666666666543322 13568999999999999987654444443
No 231
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=20.93 E-value=84 Score=27.10 Aligned_cols=45 Identities=13% Similarity=0.206 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
+++.+..++...|... ..-.++|..+|++...|+.++..-|.+.|
T Consensus 202 L~~~~r~vl~l~~~~~-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr 246 (251)
T PRK07670 202 LSEKEQLVISLFYKEE-----LTLTEIGQVLNLSTSRISQIHSKALFKLK 246 (251)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 5666777776655322 23568999999999999887765444443
No 232
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=20.90 E-value=92 Score=24.85 Aligned_cols=45 Identities=13% Similarity=0.116 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 92 ~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
+++.+..++.-.|-.. ..-.++|..+|++...|+++..+-+.+.+
T Consensus 120 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 120 LSSKARAAFLYNRLDG-----MGHAEIAERLGVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5566666665544322 13568899999999999888765544443
No 233
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=20.76 E-value=1e+02 Score=25.24 Aligned_cols=44 Identities=16% Similarity=0.261 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k 139 (240)
.+++.+..+|.-.|-... .-.++|..+|++...|++....-|.+
T Consensus 141 ~Lp~~~r~v~~l~~~eg~-----s~~EIA~~lgis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 141 RLPKAQRDVLQAVYLEEL-----PHQQVAEMFDIPLGTVKSRLRLAVEK 184 (194)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence 355666666665443221 35689999999999997665433333
No 234
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=20.57 E-value=43 Score=26.68 Aligned_cols=29 Identities=17% Similarity=0.197 Sum_probs=22.5
Q ss_pred HHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 114 QKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 114 ~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
.-+++|..+|+++..|++.+..-|.+.|+
T Consensus 138 s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 138 PQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35789999999999999888655555544
No 235
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=20.53 E-value=1.1e+02 Score=24.75 Aligned_cols=47 Identities=19% Similarity=0.237 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
.+++.+..++.-.|-.. ..-.+||..+|+++..|++....-|.+.|+
T Consensus 131 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE-----LETEEICQELQITATNAWVLLYRARMRLRE 177 (191)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 36666666666554332 125689999999999998877655554443
No 236
>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=20.48 E-value=3e+02 Score=20.77 Aligned_cols=35 Identities=14% Similarity=0.093 Sum_probs=19.9
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhh
Q 026325 89 KLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNR 136 (240)
Q Consensus 89 R~~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNR 136 (240)
...|+..++..|... ...+.+|++...|+.+|...
T Consensus 35 yR~Y~~~d~~~l~~I-------------~~lr~~G~sl~eI~~~l~~~ 69 (116)
T cd04769 35 YRVYDAQHVECLRFI-------------KEARQLGFTLAELKAIFAGH 69 (116)
T ss_pred ceeeCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHhcc
Confidence 456888888887543 22344555555555555433
No 237
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=20.43 E-value=2.3e+02 Score=26.61 Aligned_cols=36 Identities=22% Similarity=0.362 Sum_probs=24.5
Q ss_pred HHHHhHHHHHHHHHHhhchHHHHHHHHHHHHHHHhc
Q 026325 141 KLKQTEMECEYLKRWFGSLTEQNRRLQREVEELRAM 176 (240)
Q Consensus 141 Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~~l~~~ 176 (240)
+.++.+.+...+......+..|..+++.++..++..
T Consensus 30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 (398)
T PTZ00454 30 ELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQSV 65 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 334445555666666667777888888888888764
No 238
>PF09730 BicD: Microtubule-associated protein Bicaudal-D; InterPro: IPR018477 BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER) []. Glycogen synthase kinase-3beta (GSK-3beta) is required for the binding of BICD to dynein but not to dynactin, acting to maintain the anchoring of microtubules to the centromere []. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells [].; GO: 0006810 transport, 0005794 Golgi apparatus
Probab=20.41 E-value=2e+02 Score=29.36 Aligned_cols=23 Identities=35% Similarity=0.491 Sum_probs=10.7
Q ss_pred HHHHhhchHHHHHHHHHHHHHHH
Q 026325 152 LKRWFGSLTEQNRRLQREVEELR 174 (240)
Q Consensus 152 l~~~~~~l~~e~~~l~~e~~~l~ 174 (240)
+-+.|..|.+||..||++|.-|+
T Consensus 95 ll~dyselEeENislQKqvs~Lk 117 (717)
T PF09730_consen 95 LLQDYSELEEENISLQKQVSVLK 117 (717)
T ss_pred HhhhhHHHHHHHHHHHHHHHHHH
Confidence 33344445555555555444333
No 239
>PRK10651 transcriptional regulator NarL; Provisional
Probab=20.39 E-value=86 Score=24.87 Aligned_cols=47 Identities=19% Similarity=0.273 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLK 143 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kkk 143 (240)
.+++.+.++|+-..+. + ...++|++++++++.|++..+|=|.|..-+
T Consensus 155 ~Lt~rE~~vl~~l~~g--~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~ 201 (216)
T PRK10651 155 QLTPRERDILKLIAQG--L----PNKMIARRLDITESTVKVHVKHMLKKMKLK 201 (216)
T ss_pred cCCHHHHHHHHHHHcC--C----CHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 3899998888765432 1 245789999999999999988877776543
No 240
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=20.27 E-value=54 Score=25.94 Aligned_cols=45 Identities=24% Similarity=0.311 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~K 141 (240)
.+++.+..+|+-.+.. + .+.+||..++++++.|++..++=|.|..
T Consensus 137 ~Lt~~E~~il~~l~~g--~----~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQG--M----AVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCC--C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5788887777765542 2 4678899999999999887776665543
No 241
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=20.13 E-value=1.1e+02 Score=23.56 Aligned_cols=14 Identities=36% Similarity=0.615 Sum_probs=10.7
Q ss_pred ceeeecchhhhhHH
Q 026325 127 RQVEVWFQNRRARS 140 (240)
Q Consensus 127 ~qVkvWFqNRR~k~ 140 (240)
||.+.||-.+|.-.
T Consensus 18 Rq~e~~FlqKr~~L 31 (106)
T PF11594_consen 18 RQMEAFFLQKRFEL 31 (106)
T ss_pred HHHHHHHHHHHHHH
Confidence 55688998888765
No 242
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=20.10 E-value=78 Score=28.76 Aligned_cols=51 Identities=18% Similarity=0.195 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCceeeecchhhhhHHHH
Q 026325 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142 (240)
Q Consensus 91 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~LA~~l~L~~~qVkvWFqNRR~k~Kk 142 (240)
.+++.+..+|...|-... ......++||..+|++...|+.+...-+.|.|+
T Consensus 262 ~L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~ 312 (325)
T PRK05657 262 ELNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312 (325)
T ss_pred cCCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 578888888887763222 222346789999999999998887655555543
No 243
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=20.09 E-value=1.6e+02 Score=25.53 Aligned_cols=35 Identities=26% Similarity=0.405 Sum_probs=0.0
Q ss_pred hhHHHHHHhHHHHHHHHHHhhchHHHHHHHHHHHH
Q 026325 137 RARSKLKQTEMECEYLKRWFGSLTEQNRRLQREVE 171 (240)
Q Consensus 137 R~k~Kkk~~~~~~~~l~~~~~~l~~e~~~l~~e~~ 171 (240)
++..+....+...+.++.+++.|.+|+..|+.+++
T Consensus 176 ~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~ 210 (216)
T KOG1962|consen 176 KAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQIE 210 (216)
T ss_pred HHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHh
No 244
>PF09744 Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; InterPro: IPR019143 This entry represents the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have a RhoGEF domain (IPR000219 from INTERPRO) at their C-terminal end.
Probab=20.05 E-value=4.9e+02 Score=21.25 Aligned_cols=14 Identities=29% Similarity=0.228 Sum_probs=9.1
Q ss_pred HHHHHHHHHhhcCC
Q 026325 96 QSRLLEESFRHNHT 109 (240)
Q Consensus 96 Q~~~Le~~F~~~~~ 109 (240)
-+..|+.++..+.-
T Consensus 34 vLE~Le~~~~~n~~ 47 (158)
T PF09744_consen 34 VLELLESLASRNQE 47 (158)
T ss_pred HHHHHHHHHHhhhh
Confidence 45667777777663
Done!