Query 042627
Match_columns 237
No_of_seqs 315 out of 1588
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 08:03:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042627.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042627hhsearch_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 1.1E-25 2.3E-30 193.8 10.4 117 88-206 48-169 (198)
2 KOG0489 Transcription factor z 99.7 2.9E-18 6.2E-23 153.7 3.6 61 87-147 156-218 (261)
3 KOG0843 Transcription factor E 99.7 1.5E-17 3.2E-22 140.3 5.1 62 89-150 101-164 (197)
4 KOG0488 Transcription factor B 99.7 2.3E-17 5E-22 151.1 6.4 61 88-148 170-232 (309)
5 KOG0842 Transcription factor t 99.7 1E-16 2.2E-21 145.9 7.9 66 89-154 152-219 (307)
6 KOG0484 Transcription factor P 99.7 2.9E-17 6.2E-22 127.7 3.7 62 87-148 14-77 (125)
7 KOG0487 Transcription factor A 99.7 3.6E-17 7.8E-22 148.9 3.7 62 88-149 233-296 (308)
8 KOG0485 Transcription factor N 99.6 7.5E-16 1.6E-20 133.5 9.3 61 87-147 101-163 (268)
9 KOG2251 Homeobox transcription 99.6 5E-16 1.1E-20 134.7 4.8 63 87-149 34-98 (228)
10 PF00046 Homeobox: Homeobox do 99.6 7.8E-16 1.7E-20 106.6 4.6 55 91-145 1-57 (57)
11 KOG0494 Transcription factor C 99.6 1.6E-15 3.4E-20 134.4 6.9 60 91-150 142-203 (332)
12 KOG0850 Transcription factor D 99.6 2.2E-15 4.7E-20 131.5 5.4 61 86-146 118-180 (245)
13 KOG0492 Transcription factor M 99.6 2.9E-15 6.3E-20 129.0 5.6 60 89-148 143-204 (246)
14 KOG0848 Transcription factor C 99.5 5.4E-15 1.2E-19 131.5 3.1 55 93-147 202-258 (317)
15 KOG0493 Transcription factor E 99.5 1.5E-14 3.2E-19 128.4 3.8 61 90-150 246-308 (342)
16 cd00086 homeodomain Homeodomai 99.5 8.8E-14 1.9E-18 96.0 4.8 56 91-146 1-58 (59)
17 smart00389 HOX Homeodomain. DN 99.4 7.9E-14 1.7E-18 95.7 4.1 54 91-144 1-56 (56)
18 TIGR01565 homeo_ZF_HD homeobox 99.4 1.1E-13 2.5E-18 97.6 4.7 50 91-140 2-57 (58)
19 COG5576 Homeodomain-containing 99.4 1.3E-13 2.9E-18 115.1 5.7 65 85-149 46-112 (156)
20 KOG0844 Transcription factor E 99.4 1.1E-13 2.5E-18 125.1 2.8 61 89-149 180-242 (408)
21 KOG0486 Transcription factor P 99.4 2.6E-13 5.6E-18 123.0 4.4 63 89-151 111-175 (351)
22 KOG4577 Transcription factor L 99.4 3.6E-13 7.7E-18 121.1 4.7 63 87-149 164-228 (383)
23 KOG0491 Transcription factor B 99.4 1.2E-13 2.7E-18 115.3 0.5 61 89-149 99-161 (194)
24 KOG0847 Transcription factor, 99.3 5.2E-13 1.1E-17 116.1 2.8 63 86-148 163-227 (288)
25 KOG3802 Transcription factor O 99.3 2.4E-12 5.2E-17 120.1 4.0 60 88-147 292-353 (398)
26 KOG0490 Transcription factor, 99.2 1.1E-11 2.4E-16 106.9 3.5 61 87-147 57-119 (235)
27 smart00340 HALZ homeobox assoc 99.2 4E-11 8.6E-16 78.5 4.5 44 146-191 1-44 (44)
28 KOG0849 Transcription factor P 99.0 2.9E-10 6.3E-15 106.2 4.8 62 87-148 173-236 (354)
29 KOG1168 Transcription factor A 98.8 3.4E-09 7.3E-14 95.8 3.0 61 87-147 306-368 (385)
30 KOG0775 Transcription factor S 98.5 8E-08 1.7E-12 86.3 4.1 49 97-145 183-233 (304)
31 KOG0774 Transcription factor P 98.4 8.2E-07 1.8E-11 79.5 7.7 57 90-146 188-249 (334)
32 KOG0490 Transcription factor, 98.0 6.4E-06 1.4E-10 71.0 4.2 62 87-148 150-213 (235)
33 PF05920 Homeobox_KN: Homeobox 97.9 5.3E-06 1.1E-10 54.3 1.3 32 111-142 7-40 (40)
34 KOG2252 CCAAT displacement pro 97.8 2.6E-05 5.7E-10 75.9 5.0 61 84-144 414-476 (558)
35 PF02183 HALZ: Homeobox associ 97.3 0.00052 1.1E-08 46.1 4.7 35 146-180 1-35 (45)
36 KOG1146 Homeobox protein [Gene 97.0 0.00041 8.8E-09 73.5 3.0 60 89-148 902-963 (1406)
37 PF11569 Homez: Homeodomain le 96.3 0.002 4.4E-08 45.2 1.6 39 102-140 10-50 (56)
38 KOG0773 Transcription factor M 95.5 0.011 2.3E-07 54.8 3.0 56 90-145 239-299 (342)
39 PF04218 CENP-B_N: CENP-B N-te 94.2 0.1 2.2E-06 35.8 4.5 47 91-140 1-47 (53)
40 PRK09413 IS2 repressor TnpA; R 93.8 0.57 1.2E-05 37.1 8.7 43 92-138 8-52 (121)
41 KOG3623 Homeobox transcription 93.2 0.074 1.6E-06 54.2 3.3 46 102-147 568-615 (1007)
42 PF02183 HALZ: Homeobox associ 92.2 0.38 8.1E-06 32.2 4.6 32 148-179 10-41 (45)
43 KOG4196 bZIP transcription fac 91.4 1.5 3.2E-05 35.8 8.1 73 95-178 22-109 (135)
44 PRK00888 ftsB cell division pr 87.8 1.4 2.9E-05 34.6 5.3 47 131-178 16-62 (105)
45 PF07716 bZIP_2: Basic region 83.7 4.1 8.9E-05 27.7 5.5 29 150-178 25-53 (54)
46 KOG3119 Basic region leucine z 82.0 4.4 9.5E-05 36.7 6.5 31 151-181 223-253 (269)
47 PF04967 HTH_10: HTH DNA bindi 79.9 2.8 6.1E-05 28.9 3.5 36 97-132 1-40 (53)
48 PF00170 bZIP_1: bZIP transcri 77.3 13 0.00028 25.9 6.4 26 153-178 29-54 (64)
49 PF04545 Sigma70_r4: Sigma-70, 75.9 5.8 0.00012 26.1 4.1 38 96-137 4-42 (50)
50 PF01527 HTH_Tnp_1: Transposas 74.4 1.1 2.3E-05 31.9 0.1 43 92-137 2-45 (76)
51 PF04977 DivIC: Septum formati 74.2 10 0.00022 27.0 5.3 30 147-176 21-50 (80)
52 PF00170 bZIP_1: bZIP transcri 74.2 15 0.00032 25.7 6.0 35 145-179 28-62 (64)
53 PF01166 TSC22: TSC-22/dip/bun 73.9 6.5 0.00014 27.8 4.0 32 149-180 13-44 (59)
54 PF06156 DUF972: Protein of un 72.7 11 0.00023 29.7 5.5 36 145-180 17-52 (107)
55 KOG4571 Activating transcripti 70.7 9.3 0.0002 35.2 5.3 30 151-180 256-285 (294)
56 TIGR02209 ftsL_broad cell divi 69.9 15 0.00032 26.7 5.5 32 147-178 28-59 (85)
57 cd06171 Sigma70_r4 Sigma70, re 67.8 6.4 0.00014 24.7 2.8 41 96-140 10-51 (55)
58 PRK03975 tfx putative transcri 67.3 11 0.00023 31.2 4.6 47 94-144 4-50 (141)
59 smart00338 BRLZ basic region l 65.8 31 0.00066 24.1 6.2 25 154-178 30-54 (65)
60 COG3413 Predicted DNA binding 65.4 10 0.00022 32.7 4.4 47 96-144 155-205 (215)
61 PRK13169 DNA replication intia 65.4 17 0.00037 28.8 5.2 35 146-180 18-52 (110)
62 PF06005 DUF904: Protein of un 64.2 32 0.0007 25.1 6.1 32 148-179 23-54 (72)
63 PF13443 HTH_26: Cro/C1-type H 63.7 6.4 0.00014 26.8 2.3 36 118-153 13-48 (63)
64 cd01106 HTH_TipAL-Mta Helix-Tu 63.5 49 0.0011 25.0 7.4 65 94-177 36-100 (103)
65 KOG4005 Transcription factor X 61.2 18 0.0004 32.7 5.2 7 90-96 54-60 (292)
66 KOG1146 Homeobox protein [Gene 61.1 29 0.00064 38.2 7.5 57 91-147 445-503 (1406)
67 KOG3335 Predicted coiled-coil 59.2 32 0.0007 29.6 6.1 52 128-179 84-135 (181)
68 PF09607 BrkDBD: Brinker DNA-b 58.5 14 0.00029 26.2 3.1 44 94-137 3-47 (58)
69 PF10668 Phage_terminase: Phag 56.7 5.4 0.00012 28.4 0.9 19 118-136 25-43 (60)
70 PF00196 GerE: Bacterial regul 56.4 12 0.00026 25.3 2.6 46 96-145 3-48 (58)
71 PF08961 DUF1875: Domain of un 55.6 3.9 8.4E-05 36.4 0.0 40 141-180 120-159 (243)
72 PF12824 MRP-L20: Mitochondria 55.5 84 0.0018 26.5 8.1 48 93-140 82-129 (164)
73 cd00569 HTH_Hin_like Helix-tur 55.4 27 0.00058 19.3 3.8 38 96-136 5-42 (42)
74 smart00338 BRLZ basic region l 54.7 60 0.0013 22.5 6.1 35 146-180 29-63 (65)
75 PF08172 CASP_C: CASP C termin 54.5 29 0.00064 31.2 5.5 39 140-178 90-128 (248)
76 PF06005 DUF904: Protein of un 52.8 57 0.0012 23.8 5.8 27 148-174 30-56 (72)
77 PRK13922 rod shape-determining 52.3 31 0.00068 30.7 5.3 36 145-180 71-109 (276)
78 PF15058 Speriolin_N: Sperioli 52.0 23 0.00049 30.9 4.1 27 151-177 6-32 (200)
79 TIGR02449 conserved hypothetic 51.3 47 0.001 23.9 5.1 25 153-177 10-34 (65)
80 KOG4571 Activating transcripti 51.1 41 0.0009 31.1 5.9 35 145-179 243-277 (294)
81 PRK14127 cell division protein 50.7 35 0.00076 27.0 4.7 35 146-180 33-67 (109)
82 PF00424 REV: REV protein (ant 49.6 26 0.00056 27.0 3.7 34 102-150 14-50 (91)
83 cd04781 HTH_MerR-like_sg6 Heli 49.2 1.3E+02 0.0027 23.5 8.0 69 93-178 34-102 (120)
84 KOG4403 Cell surface glycoprot 49.1 36 0.00079 33.3 5.4 43 133-175 229-274 (575)
85 PF10224 DUF2205: Predicted co 48.7 73 0.0016 23.9 5.9 34 145-178 25-58 (80)
86 smart00421 HTH_LUXR helix_turn 47.8 35 0.00076 21.7 3.8 39 96-138 3-41 (58)
87 PF07716 bZIP_2: Basic region 46.9 66 0.0014 21.6 5.1 24 149-172 31-54 (54)
88 TIGR00219 mreC rod shape-deter 46.9 43 0.00092 30.5 5.3 35 146-180 69-107 (283)
89 cd01109 HTH_YyaN Helix-Turn-He 46.8 1E+02 0.0022 23.7 6.8 72 94-178 36-107 (113)
90 PRK00118 putative DNA-binding 46.5 66 0.0014 25.2 5.6 56 97-158 18-74 (104)
91 PF14197 Cep57_CLD_2: Centroso 46.4 53 0.0012 23.8 4.8 24 154-177 44-67 (69)
92 PF10226 DUF2216: Uncharacteri 46.1 47 0.001 28.9 5.1 23 157-179 55-77 (195)
93 PRK10072 putative transcriptio 46.0 21 0.00045 27.5 2.7 42 96-142 32-73 (96)
94 cd04779 HTH_MerR-like_sg4 Heli 45.3 1.3E+02 0.0028 24.3 7.5 73 93-176 34-107 (134)
95 COG4467 Regulator of replicati 44.5 49 0.0011 26.3 4.6 35 146-180 18-52 (114)
96 KOG4797 Transcriptional regula 44.5 49 0.0011 26.4 4.6 32 149-180 66-97 (123)
97 PF11365 DUF3166: Protein of u 43.0 56 0.0012 25.4 4.7 31 149-179 14-44 (96)
98 KOG1924 RhoA GTPase effector D 42.5 1.9E+02 0.0041 30.8 9.5 31 146-176 470-500 (1102)
99 cd04770 HTH_HMRTR Helix-Turn-H 41.4 1.5E+02 0.0034 22.9 7.2 73 93-178 35-107 (123)
100 KOG0709 CREB/ATF family transc 41.3 90 0.0019 30.7 6.8 80 94-180 218-316 (472)
101 PF04999 FtsL: Cell division p 41.1 74 0.0016 23.8 5.1 29 150-178 42-70 (97)
102 cd04761 HTH_MerR-SF Helix-Turn 40.9 13 0.00029 23.6 0.8 23 118-140 3-25 (49)
103 PF13518 HTH_28: Helix-turn-he 40.3 15 0.00033 23.7 1.0 21 118-138 15-35 (52)
104 PRK00888 ftsB cell division pr 39.9 55 0.0012 25.4 4.3 39 134-172 25-63 (105)
105 TIGR03752 conj_TIGR03752 integ 39.5 53 0.0011 32.4 4.9 16 163-178 115-130 (472)
106 PF08281 Sigma70_r4_2: Sigma-7 39.1 37 0.0008 22.3 2.8 38 97-138 11-49 (54)
107 PF03980 Nnf1: Nnf1 ; InterPr 38.8 58 0.0013 25.0 4.3 30 149-178 79-108 (109)
108 cd04777 HTH_MerR-like_sg1 Heli 38.3 1.1E+02 0.0023 23.3 5.7 33 96-139 36-68 (107)
109 TIGR00721 tfx DNA-binding prot 37.8 97 0.0021 25.4 5.6 45 94-142 4-48 (137)
110 TIGR03879 near_KaiC_dom probab 37.4 15 0.00032 27.1 0.7 34 106-139 21-56 (73)
111 cd04775 HTH_Cfa-like Helix-Tur 37.4 1.8E+02 0.0039 22.0 7.3 65 93-178 35-99 (102)
112 TIGR02051 MerR Hg(II)-responsi 37.2 1.9E+02 0.004 22.7 7.1 71 93-178 34-104 (124)
113 cd04765 HTH_MlrA-like_sg2 Heli 37.0 70 0.0015 24.4 4.4 37 93-139 35-71 (99)
114 PF12808 Mto2_bdg: Micro-tubul 37.0 80 0.0017 21.8 4.2 28 151-178 23-50 (52)
115 PRK12514 RNA polymerase sigma 36.9 51 0.0011 26.8 3.9 42 97-142 130-172 (179)
116 cd04783 HTH_MerR1 Helix-Turn-H 36.0 2E+02 0.0044 22.4 7.1 70 94-178 36-105 (126)
117 TIGR02894 DNA_bind_RsfA transc 35.9 84 0.0018 26.6 5.0 27 151-177 105-131 (161)
118 PF14775 NYD-SP28_assoc: Sperm 35.8 98 0.0021 21.7 4.7 21 160-180 36-56 (60)
119 PF05377 FlaC_arch: Flagella a 35.7 1.1E+02 0.0024 21.4 4.8 30 149-178 6-35 (55)
120 PF10883 DUF2681: Protein of u 35.4 1.1E+02 0.0024 23.3 5.2 38 134-178 21-58 (87)
121 PRK15422 septal ring assembly 35.2 1.1E+02 0.0024 22.9 5.0 13 157-169 25-37 (79)
122 COG2944 Predicted transcriptio 34.7 42 0.00091 26.4 2.9 41 96-141 43-83 (104)
123 PRK12526 RNA polymerase sigma 34.0 61 0.0013 27.4 4.1 38 97-138 154-192 (206)
124 PF13936 HTH_38: Helix-turn-he 33.9 24 0.00052 22.9 1.2 39 94-136 2-41 (44)
125 cd06170 LuxR_C_like C-terminal 33.9 67 0.0015 20.4 3.4 35 98-137 2-37 (57)
126 KOG4343 bZIP transcription fac 33.7 85 0.0018 31.6 5.4 24 155-178 307-330 (655)
127 COG3074 Uncharacterized protei 33.7 1.3E+02 0.0028 22.2 5.0 16 157-172 46-61 (79)
128 cd04769 HTH_MerR2 Helix-Turn-H 33.6 1.5E+02 0.0032 22.9 5.9 73 94-178 35-107 (116)
129 PRK09652 RNA polymerase sigma 33.5 55 0.0012 26.1 3.6 43 96-144 128-171 (182)
130 TIGR03752 conj_TIGR03752 integ 33.5 61 0.0013 32.0 4.3 16 165-180 110-125 (472)
131 PF13411 MerR_1: MerR HTH fami 33.3 21 0.00046 24.5 0.9 21 118-138 3-23 (69)
132 COG2963 Transposase and inacti 33.3 2.2E+02 0.0047 21.7 7.8 42 94-137 5-47 (116)
133 PRK10884 SH3 domain-containing 33.2 1.2E+02 0.0026 26.5 5.8 30 149-178 138-167 (206)
134 PRK05657 RNA polymerase sigma 33.1 63 0.0014 29.9 4.3 43 96-138 262-305 (325)
135 PF07989 Microtub_assoc: Micro 32.9 85 0.0018 23.0 4.1 44 132-178 21-64 (75)
136 PRK09646 RNA polymerase sigma 32.9 63 0.0014 26.9 3.9 39 96-138 142-181 (194)
137 PF14662 CCDC155: Coiled-coil 32.8 1.2E+02 0.0025 26.5 5.5 43 137-179 82-124 (193)
138 KOG1962 B-cell receptor-associ 32.7 1E+02 0.0022 27.4 5.2 32 149-180 178-209 (216)
139 KOG4343 bZIP transcription fac 32.6 82 0.0018 31.8 5.1 31 149-179 308-338 (655)
140 TIGR02937 sigma70-ECF RNA poly 32.6 62 0.0014 24.4 3.6 43 96-142 110-153 (158)
141 COG3074 Uncharacterized protei 32.3 1.1E+02 0.0025 22.5 4.6 17 158-174 26-42 (79)
142 cd04766 HTH_HspR Helix-Turn-He 32.2 1.5E+02 0.0033 21.8 5.5 33 94-136 36-68 (91)
143 PF07407 Seadorna_VP6: Seadorn 32.2 67 0.0014 30.5 4.2 25 154-178 36-60 (420)
144 PF10883 DUF2681: Protein of u 31.6 2.1E+02 0.0044 21.8 6.1 17 156-172 29-45 (87)
145 PF09726 Macoilin: Transmembra 31.6 97 0.0021 32.0 5.6 37 142-178 544-580 (697)
146 TIGR02047 CadR-PbrR Cd(II)/Pb( 31.5 2.4E+02 0.0051 22.3 6.9 73 93-178 35-107 (127)
147 PF02796 HTH_7: Helix-turn-hel 31.3 48 0.001 21.4 2.3 38 96-136 5-42 (45)
148 PF14775 NYD-SP28_assoc: Sperm 30.9 1.7E+02 0.0037 20.5 5.2 48 128-175 11-58 (60)
149 PF10367 Vps39_2: Vacuolar sor 30.9 1.1E+02 0.0023 22.7 4.5 36 161-204 53-88 (109)
150 PF07407 Seadorna_VP6: Seadorn 30.7 47 0.001 31.5 2.9 25 148-172 37-61 (420)
151 PRK11511 DNA-binding transcrip 30.5 61 0.0013 25.5 3.3 36 103-138 12-48 (127)
152 PRK13922 rod shape-determining 30.5 93 0.002 27.7 4.8 21 154-174 73-93 (276)
153 KOG2483 Upstream transcription 30.3 1.1E+02 0.0024 27.4 5.1 39 139-177 101-139 (232)
154 TIGR02989 Sig-70_gvs1 RNA poly 30.3 71 0.0015 25.2 3.7 38 96-137 111-149 (159)
155 PF04618 HD-ZIP_N: HD-ZIP prot 30.3 2.8E+02 0.0061 22.0 6.9 18 1-19 1-18 (111)
156 TIGR02948 SigW_bacill RNA poly 30.1 70 0.0015 26.0 3.7 39 96-138 136-175 (187)
157 PF08826 DMPK_coil: DMPK coile 30.1 2E+02 0.0044 20.4 6.0 24 155-178 37-60 (61)
158 PRK15422 septal ring assembly 29.7 1.3E+02 0.0028 22.6 4.6 15 159-173 48-62 (79)
159 PF12269 zf-CpG_bind_C: CpG bi 29.7 1.7E+02 0.0037 26.3 6.2 11 129-139 10-20 (236)
160 TIGR02894 DNA_bind_RsfA transc 29.6 1.7E+02 0.0038 24.8 5.9 33 146-178 107-139 (161)
161 PRK06759 RNA polymerase factor 29.2 72 0.0016 25.0 3.5 39 96-138 106-145 (154)
162 PRK10884 SH3 domain-containing 29.0 1.6E+02 0.0036 25.6 5.9 24 155-178 137-160 (206)
163 cd07429 Cby_like Chibby, a nuc 28.8 1.2E+02 0.0025 24.1 4.5 26 154-179 76-101 (108)
164 PRK12512 RNA polymerase sigma 28.7 86 0.0019 25.6 4.0 45 96-144 131-176 (184)
165 TIGR02985 Sig70_bacteroi1 RNA 28.6 88 0.0019 24.3 3.9 38 97-138 114-152 (161)
166 PRK09642 RNA polymerase sigma 28.6 1.1E+02 0.0024 24.2 4.6 25 118-142 125-149 (160)
167 cd04785 HTH_CadR-PbrR-like Hel 28.4 2.9E+02 0.0063 21.6 7.0 72 94-178 36-107 (126)
168 PF06056 Terminase_5: Putative 28.3 32 0.00068 24.0 1.1 25 118-144 16-40 (58)
169 PF13551 HTH_29: Winged helix- 28.1 1.2E+02 0.0026 22.3 4.4 46 92-137 53-109 (112)
170 PRK11924 RNA polymerase sigma 27.9 76 0.0017 25.2 3.5 38 97-138 126-164 (179)
171 cd01107 HTH_BmrR Helix-Turn-He 27.8 2.8E+02 0.006 21.1 7.5 67 94-178 37-103 (108)
172 PF04977 DivIC: Septum formati 27.6 1.4E+02 0.0031 20.8 4.6 22 148-169 29-50 (80)
173 PRK04217 hypothetical protein; 27.6 1E+02 0.0022 24.3 4.0 40 96-138 42-81 (110)
174 cd04763 HTH_MlrA-like Helix-Tu 27.5 29 0.00063 24.1 0.8 21 118-138 3-23 (68)
175 KOG3119 Basic region leucine z 27.2 1.5E+02 0.0031 26.9 5.5 38 140-180 208-245 (269)
176 TIGR02043 ZntR Zn(II)-responsi 27.1 3E+02 0.0065 21.8 6.8 73 94-178 37-109 (131)
177 COG4367 Uncharacterized protei 27.0 77 0.0017 24.5 3.0 37 96-132 2-40 (97)
178 cd04764 HTH_MlrA-like_sg1 Heli 26.9 31 0.00066 23.8 0.8 21 118-138 3-23 (67)
179 PF11594 Med28: Mediator compl 26.6 1.3E+02 0.0028 23.8 4.3 15 130-144 18-32 (106)
180 PF06210 DUF1003: Protein of u 26.4 1.9E+02 0.004 22.7 5.3 38 137-178 57-94 (108)
181 PF13384 HTH_23: Homeodomain-l 26.3 31 0.00068 22.2 0.8 20 118-137 20-39 (50)
182 COG2919 Septum formation initi 26.0 1.4E+02 0.003 23.5 4.6 33 147-179 54-86 (117)
183 PRK09975 DNA-binding transcrip 25.9 65 0.0014 26.8 2.8 42 102-143 17-59 (213)
184 PRK12519 RNA polymerase sigma 25.9 80 0.0017 26.0 3.3 25 118-144 160-184 (194)
185 cd04784 HTH_CadR-PbrR Helix-Tu 25.9 2.7E+02 0.0059 21.7 6.3 72 94-178 36-107 (127)
186 PRK10100 DNA-binding transcrip 25.5 78 0.0017 27.3 3.3 47 96-146 155-201 (216)
187 PRK05602 RNA polymerase sigma 25.4 88 0.0019 25.6 3.5 37 97-137 129-166 (186)
188 PRK10360 DNA-binding transcrip 25.3 88 0.0019 24.9 3.4 45 96-144 137-181 (196)
189 PF00376 MerR: MerR family reg 25.3 36 0.00077 21.6 0.8 18 119-136 3-20 (38)
190 KOG3623 Homeobox transcription 25.3 58 0.0012 34.1 2.7 59 89-147 625-685 (1007)
191 KOG0150 Spliceosomal protein F 25.2 1.6E+02 0.0034 27.7 5.2 13 132-144 16-28 (336)
192 PF01486 K-box: K-box region; 25.1 1.2E+02 0.0025 23.0 3.9 44 130-174 56-99 (100)
193 COG3416 Uncharacterized protei 25.0 5E+02 0.011 23.2 9.0 18 97-114 1-18 (233)
194 PF08280 HTH_Mga: M protein tr 24.9 60 0.0013 22.2 2.0 33 100-134 6-38 (59)
195 PRK08301 sporulation sigma fac 24.8 1.1E+02 0.0025 26.1 4.2 42 96-137 178-220 (234)
196 PRK09047 RNA polymerase factor 24.7 1.2E+02 0.0027 23.8 4.1 38 96-137 106-144 (161)
197 PF00440 TetR_N: Bacterial reg 24.7 58 0.0013 21.0 1.8 36 105-140 5-41 (47)
198 PHA03308 transcriptional regul 24.2 1.1E+02 0.0023 32.3 4.4 18 87-104 1291-1308(1463)
199 PF07334 IFP_35_N: Interferon- 24.2 1.1E+02 0.0023 22.8 3.3 12 163-174 6-17 (76)
200 PRK10651 transcriptional regul 24.2 88 0.0019 25.0 3.2 46 96-145 155-200 (216)
201 PRK10403 transcriptional regul 24.1 88 0.0019 24.9 3.2 45 96-144 153-197 (215)
202 cd04762 HTH_MerR-trunc Helix-T 24.1 39 0.00084 20.9 0.9 24 118-141 3-26 (49)
203 PF11167 DUF2953: Protein of u 23.8 14 0.0003 24.9 -1.4 18 1-18 3-20 (53)
204 PF14645 Chibby: Chibby family 23.7 1.6E+02 0.0035 23.4 4.5 30 149-178 70-99 (116)
205 cd04787 HTH_HMRTR_unk Helix-Tu 23.6 3.7E+02 0.0081 21.2 8.2 72 94-178 36-107 (133)
206 cd01392 HTH_LacI Helix-turn-he 23.5 41 0.00089 21.7 0.9 21 120-140 2-22 (52)
207 PRK09644 RNA polymerase sigma 23.5 1.5E+02 0.0032 23.7 4.4 21 118-138 127-147 (165)
208 PF13730 HTH_36: Helix-turn-he 23.2 1.4E+02 0.0031 19.4 3.6 40 97-136 3-46 (55)
209 PF15136 UPF0449: Uncharacteri 23.1 2.2E+02 0.0047 22.2 4.9 28 147-174 68-95 (97)
210 PRK14872 rod shape-determining 23.1 1.5E+02 0.0032 28.1 4.8 17 155-171 62-78 (337)
211 PRK09639 RNA polymerase sigma 23.0 1.2E+02 0.0027 24.0 3.9 43 96-144 112-154 (166)
212 PF13565 HTH_32: Homeodomain-l 22.9 2.7E+02 0.0058 19.3 5.5 32 98-129 32-66 (77)
213 PF07926 TPR_MLP1_2: TPR/MLP1/ 22.7 1.9E+02 0.0041 23.1 4.8 32 145-176 100-131 (132)
214 TIGR02479 FliA_WhiG RNA polyme 22.7 1.2E+02 0.0026 25.9 3.9 38 96-137 175-213 (224)
215 TIGR02393 RpoD_Cterm RNA polym 22.7 1.2E+02 0.0026 26.3 4.0 43 96-138 176-219 (238)
216 KOG3863 bZIP transcription fac 22.5 4.7E+02 0.01 26.8 8.4 60 119-178 484-546 (604)
217 PF07047 OPA3: Optic atrophy 3 22.4 1.2E+02 0.0026 24.5 3.6 43 132-177 90-132 (134)
218 TIGR02859 spore_sigH RNA polym 22.4 1.2E+02 0.0027 24.7 3.9 20 118-137 168-187 (198)
219 PRK06986 fliA flagellar biosyn 22.3 1.2E+02 0.0025 26.2 3.8 44 97-144 185-229 (236)
220 PF01381 HTH_3: Helix-turn-hel 22.2 38 0.00082 22.1 0.6 23 118-140 12-34 (55)
221 KOG3755 SATB1 matrix attachmen 22.2 39 0.00084 34.5 0.8 21 128-148 739-759 (769)
222 PRK14872 rod shape-determining 22.0 1.1E+02 0.0023 29.0 3.7 33 146-178 60-95 (337)
223 PRK09648 RNA polymerase sigma 21.9 1.3E+02 0.0029 24.6 3.9 43 96-144 139-182 (189)
224 PF08279 HTH_11: HTH domain; 21.8 89 0.0019 20.4 2.4 31 102-133 3-33 (55)
225 KOG0999 Microtubule-associated 21.7 1.5E+02 0.0033 30.1 4.8 47 133-179 146-192 (772)
226 TIGR02959 SigZ RNA polymerase 21.7 1.5E+02 0.0033 24.0 4.2 38 96-137 100-138 (170)
227 PF07047 OPA3: Optic atrophy 3 21.6 1.9E+02 0.004 23.4 4.6 42 130-171 92-133 (134)
228 PRK08295 RNA polymerase factor 21.6 1.4E+02 0.003 24.8 4.0 20 118-137 173-192 (208)
229 cd02413 40S_S3_KH K homology R 21.3 60 0.0013 24.0 1.5 20 118-137 56-75 (81)
230 TIGR02999 Sig-70_X6 RNA polyme 21.3 1.6E+02 0.0035 23.8 4.3 40 97-140 135-175 (183)
231 cd01108 HTH_CueR Helix-Turn-He 21.3 4.1E+02 0.0088 20.8 6.8 73 94-179 36-108 (127)
232 TIGR02209 ftsL_broad cell divi 21.2 1.9E+02 0.0041 20.7 4.2 41 131-171 19-59 (85)
233 TIGR02939 RpoE_Sigma70 RNA pol 21.1 1.1E+02 0.0023 24.9 3.2 25 118-144 157-181 (190)
234 PF06785 UPF0242: Uncharacteri 21.1 2.4E+02 0.0052 26.9 5.7 40 139-178 137-176 (401)
235 KOG4378 Nuclear protein COP1 [ 20.7 1.6E+02 0.0035 29.6 4.6 11 135-145 599-609 (673)
236 PRK06930 positive control sigm 20.6 1.5E+02 0.0032 24.9 3.9 45 96-144 114-159 (170)
237 PF07412 Geminin: Geminin; In 20.6 2E+02 0.0042 25.3 4.7 32 148-179 123-154 (200)
238 KOG0483 Transcription factor H 20.6 3.6E+02 0.0077 23.5 6.4 59 146-207 115-173 (198)
239 cd00093 HTH_XRE Helix-turn-hel 20.5 49 0.0011 20.1 0.8 23 118-140 15-37 (58)
240 TIGR03070 couple_hipB transcri 20.3 49 0.0011 21.3 0.8 23 118-140 18-40 (58)
241 KOG4005 Transcription factor X 20.3 1.8E+02 0.004 26.4 4.6 15 87-101 54-68 (292)
242 TIGR03826 YvyF flagellar opero 20.2 1.1E+02 0.0023 25.2 2.9 28 117-144 47-75 (137)
243 TIGR02394 rpoS_proteo RNA poly 20.2 1.5E+02 0.0034 26.4 4.3 42 96-137 222-264 (285)
244 PRK12538 RNA polymerase sigma 20.2 1.5E+02 0.0032 25.8 4.0 21 118-138 190-210 (233)
245 PF01726 LexA_DNA_bind: LexA D 20.0 1.2E+02 0.0026 21.5 2.8 37 96-132 3-43 (65)
246 PRK12546 RNA polymerase sigma 20.0 1.4E+02 0.003 24.9 3.7 21 118-138 132-152 (188)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.93 E-value=1.1e-25 Score=193.81 Aligned_cols=117 Identities=45% Similarity=0.587 Sum_probs=104.3
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHH
Q 042627 88 NISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDE 165 (237)
Q Consensus 88 ~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~e 165 (237)
....+++.+|+.+|+..||..|+.+.++.+ +..||++|||.+|||+|||||||||||.+|.+.+|+.||.+++.|..+
T Consensus 48 ~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~ 127 (198)
T KOG0483|consen 48 SKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSE 127 (198)
T ss_pred cccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhh
Confidence 345677889999999999999999999998 899999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCchhhccc-cCc--CCCCCCCCCCC
Q 042627 166 NKRLKKELQELQSAKAGASSPLFIQLQ-KAA--TCPSCEKIMRT 206 (237)
Q Consensus 166 n~~l~~e~~~l~~~~~~~~~~~~~~~~-~~~--~CpsC~~~~~~ 206 (237)
+++|+.|+++|++.... ...+++.. ... .|++|.....+
T Consensus 128 ~~~Lq~e~~eL~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~ 169 (198)
T KOG0483|consen 128 NDRLQSEVQELVAELSS--LKREMQKSPENTLTMCPNSESSSSV 169 (198)
T ss_pred hhHHHHHHHHHHHHHhh--hhhhhccCcccccccCccccccCCc
Confidence 99999999999998865 56776663 222 39999966654
No 2
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.71 E-value=2.9e-18 Score=153.66 Aligned_cols=61 Identities=34% Similarity=0.495 Sum_probs=57.4
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHH
Q 042627 87 INISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147 (237)
Q Consensus 87 ~~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq 147 (237)
.++.||.||.||..|+.+||+.|..++|++. |.+||..|.|+++||||||||||+||||..
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 3467999999999999999999999999999 899999999999999999999999999764
No 3
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.69 E-value=1.5e-17 Score=140.34 Aligned_cols=62 Identities=37% Similarity=0.482 Sum_probs=58.8
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHhHH
Q 042627 89 ISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQNEV 150 (237)
Q Consensus 89 ~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~ 150 (237)
+.||.||.|+.+|+..||..|+.++|... |++||+.|+|++.||||||||||+|.||++.+.
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 67899999999999999999999999887 999999999999999999999999999988764
No 4
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.69 E-value=2.3e-17 Score=151.06 Aligned_cols=61 Identities=30% Similarity=0.405 Sum_probs=57.1
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHh
Q 042627 88 NISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQN 148 (237)
Q Consensus 88 ~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~ 148 (237)
.++|+.||.||..|+..||+.|++.+|++. |.+||+.|||+..|||+||||||+||||+..
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 566778999999999999999999999998 9999999999999999999999999998654
No 5
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.67 E-value=1e-16 Score=145.92 Aligned_cols=66 Identities=33% Similarity=0.540 Sum_probs=59.7
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHH
Q 042627 89 ISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEF 154 (237)
Q Consensus 89 ~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~ 154 (237)
++||.|..|+..|+.+||+.|+..+|++. |++||..|.|++.||||||||||-|.||++.+..++.
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred cccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 45555667999999999999999999998 9999999999999999999999999999987766554
No 6
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.67 E-value=2.9e-17 Score=127.70 Aligned_cols=62 Identities=27% Similarity=0.422 Sum_probs=57.9
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHh
Q 042627 87 INISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQN 148 (237)
Q Consensus 87 ~~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~ 148 (237)
..++||-|+.||..|+.+||+.|.+.+||+. |++||.++.|++.+|+|||||||+|.|++..
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 4477899999999999999999999999999 9999999999999999999999999997543
No 7
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.66 E-value=3.6e-17 Score=148.89 Aligned_cols=62 Identities=34% Similarity=0.521 Sum_probs=57.6
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHhH
Q 042627 88 NISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQNE 149 (237)
Q Consensus 88 ~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~ 149 (237)
...|+||.-+|+.|+.+||+.|..|.|++. |.+|++.|+|++|||||||||||.|+||..+|
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 466888999999999999999999999999 89999999999999999999999999987643
No 8
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.64 E-value=7.5e-16 Score=133.48 Aligned_cols=61 Identities=33% Similarity=0.478 Sum_probs=56.5
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHH
Q 042627 87 INISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147 (237)
Q Consensus 87 ~~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq 147 (237)
+.++||.||.|+..|+..||..|+...|++. |..||.+|.|++.||||||||||.||||+-
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 3466788999999999999999999999998 999999999999999999999999999863
No 9
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.61 E-value=5e-16 Score=134.73 Aligned_cols=63 Identities=32% Similarity=0.488 Sum_probs=59.0
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHhH
Q 042627 87 INISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQNE 149 (237)
Q Consensus 87 ~~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~ 149 (237)
..+.||.||+|+..|+.+||..|.+.+||+. |++||.+|+|.+.+|+|||.|||+|+|+++..
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 4477999999999999999999999999999 99999999999999999999999999987653
No 10
>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=99.60 E-value=7.8e-16 Score=106.61 Aligned_cols=55 Identities=42% Similarity=0.653 Sum_probs=52.9
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHH
Q 042627 91 GRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKL 145 (237)
Q Consensus 91 rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Kr 145 (237)
||+|+.||.+|+..|+.+|..++||+. ++.||..|||+..+|++||+|||+++|+
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 578999999999999999999999999 8999999999999999999999999985
No 11
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.59 E-value=1.6e-15 Score=134.44 Aligned_cols=60 Identities=28% Similarity=0.401 Sum_probs=55.1
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHhHH
Q 042627 91 GRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQNEV 150 (237)
Q Consensus 91 rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~ 150 (237)
|+.||.||..|+..||+.|++.+||+. |+-||.++.|.+.+|+|||||||+||||++.+-
T Consensus 142 Rh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 142 RHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred ccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 344899999999999999999999999 999999999999999999999999999876543
No 12
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.57 E-value=2.2e-15 Score=131.46 Aligned_cols=61 Identities=28% Similarity=0.382 Sum_probs=56.0
Q ss_pred CCCCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHH
Q 042627 86 RINISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLK 146 (237)
Q Consensus 86 ~~~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krk 146 (237)
...|.|+.||.|+.-||..|.+.|++++|+-. |.+||..|||+..||||||||||.|.||.
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 34456778999999999999999999999887 99999999999999999999999999974
No 13
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.56 E-value=2.9e-15 Score=129.04 Aligned_cols=60 Identities=32% Similarity=0.493 Sum_probs=56.2
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHh
Q 042627 89 ISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQN 148 (237)
Q Consensus 89 ~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~ 148 (237)
..|+.|+.||..|+..||+.|++.+|+++ |.+++..|.|++.||||||||||+|.||.|+
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 34677999999999999999999999999 9999999999999999999999999998764
No 14
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.51 E-value=5.4e-15 Score=131.46 Aligned_cols=55 Identities=36% Similarity=0.532 Sum_probs=51.2
Q ss_pred CCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHH
Q 042627 93 KKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147 (237)
Q Consensus 93 ~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq 147 (237)
-|.++|..|..+||+.|...+|.++ +.+||.-|+|++|||||||||||||+||..
T Consensus 202 YRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 202 YRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred eeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 3667999999999999999999998 789999999999999999999999999764
No 15
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.49 E-value=1.5e-14 Score=128.38 Aligned_cols=61 Identities=33% Similarity=0.544 Sum_probs=56.1
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHhHH
Q 042627 90 SGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQNEV 150 (237)
Q Consensus 90 ~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~ 150 (237)
.||.||.||.+||..|+..|+.+.|++. |++||.+|+|.+.||||||||+|+|.|+-..-+
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgsk 308 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSK 308 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCC
Confidence 3778999999999999999999999998 899999999999999999999999999765443
No 16
>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=99.45 E-value=8.8e-14 Score=96.01 Aligned_cols=56 Identities=43% Similarity=0.640 Sum_probs=52.2
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHH
Q 042627 91 GRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLK 146 (237)
Q Consensus 91 rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krk 146 (237)
++.+..|+.+|+.+|+.+|..++||+. +..||.++||+..||++||+|||++.++.
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 356788999999999999999999999 89999999999999999999999998863
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.44 E-value=7.9e-14 Score=95.67 Aligned_cols=54 Identities=44% Similarity=0.630 Sum_probs=50.1
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHH
Q 042627 91 GRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 91 rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
++.|++|+.+|+.+|+..|..++||+. +..||..+||+..||+.||+|||++.|
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 356778999999999999999999999 999999999999999999999998764
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=99.44 E-value=1.1e-13 Score=97.57 Aligned_cols=50 Identities=18% Similarity=0.358 Sum_probs=48.0
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCC----CCH--HHHHHHHhCCCCccchhhccchH
Q 042627 91 GRKKLRLTIEQSRLLEDSFKLHTT----LNS--KQALAEQLNLEPRQVEVWFQNRR 140 (237)
Q Consensus 91 rR~Rt~~t~~Ql~~LE~~F~~~~~----p~~--r~~LA~~LgL~~rQVkvWFQNRR 140 (237)
||.||.||.+|+..||.+|+..+| |+. +++||..|||++++|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 789999999999999999999999 998 99999999999999999999964
No 19
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.44 E-value=1.3e-13 Score=115.11 Aligned_cols=65 Identities=34% Similarity=0.513 Sum_probs=58.9
Q ss_pred CCCCCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHhH
Q 042627 85 KRINISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQNE 149 (237)
Q Consensus 85 ~~~~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~ 149 (237)
+..+..+++|++.|.+|+.+|+..|+.++||+. |..|+..++|+++-|+|||||||++.|++...
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 344567888999999999999999999999999 99999999999999999999999999987643
No 20
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.39 E-value=1.1e-13 Score=125.08 Aligned_cols=61 Identities=33% Similarity=0.440 Sum_probs=56.8
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHhH
Q 042627 89 ISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQNE 149 (237)
Q Consensus 89 ~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~ 149 (237)
.-||-||.||.+||..||+.|-+..|.+. |.+||..|+|.+..|||||||||.|+||++..
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 45889999999999999999999999888 89999999999999999999999999998753
No 21
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.38 E-value=2.6e-13 Score=123.05 Aligned_cols=63 Identities=27% Similarity=0.444 Sum_probs=58.2
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHhHHH
Q 042627 89 ISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVD 151 (237)
Q Consensus 89 ~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~ 151 (237)
|+||.|+.|+.+|+.+||..|.++.||+. |++||...+|++.+|+|||.|||+|||+++.-..
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 56788999999999999999999999999 9999999999999999999999999998665443
No 22
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.37 E-value=3.6e-13 Score=121.11 Aligned_cols=63 Identities=27% Similarity=0.456 Sum_probs=58.2
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHhH
Q 042627 87 INISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQNE 149 (237)
Q Consensus 87 ~~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~ 149 (237)
+...||.||.+|+.|++.|+..|...++|.. |++|+.++||..|+|||||||||||+||-+..
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 4467899999999999999999999999998 99999999999999999999999999976643
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.35 E-value=1.2e-13 Score=115.27 Aligned_cols=61 Identities=33% Similarity=0.472 Sum_probs=56.1
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHhH
Q 042627 89 ISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQNE 149 (237)
Q Consensus 89 ~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~ 149 (237)
+.++-|+.|+..|+..||+.|+...|++. +.+||..|+|++.|||.||||||.|.||.+..
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~ 161 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN 161 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 45667999999999999999999999987 99999999999999999999999999987653
No 24
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.33 E-value=5.2e-13 Score=116.12 Aligned_cols=63 Identities=32% Similarity=0.436 Sum_probs=57.3
Q ss_pred CCCCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHh
Q 042627 86 RINISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQN 148 (237)
Q Consensus 86 ~~~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~ 148 (237)
.+++++..|..|+-.|+..||..|+..+|+-. +.+||..+|+.+.||+|||||||+|||++.-
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 45666777888999999999999999999987 9999999999999999999999999998653
No 25
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.27 E-value=2.4e-12 Score=120.10 Aligned_cols=60 Identities=30% Similarity=0.430 Sum_probs=56.6
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHH
Q 042627 88 NISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147 (237)
Q Consensus 88 ~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq 147 (237)
+++|||||.|.......||++|..|++|+. +..||.+|+|...+|+|||.|||.|.||..
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 377889999999999999999999999999 899999999999999999999999999854
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.18 E-value=1.1e-11 Score=106.94 Aligned_cols=61 Identities=30% Similarity=0.358 Sum_probs=57.3
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHH
Q 042627 87 INISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147 (237)
Q Consensus 87 ~~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq 147 (237)
..+.+|.|+.|+..|+.+||+.|...+||+. ++.||..+++++..|+|||||||++|+++.
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 4567899999999999999999999999999 999999999999999999999999999765
No 27
>smart00340 HALZ homeobox associated leucin zipper.
Probab=99.17 E-value=4e-11 Score=78.49 Aligned_cols=44 Identities=64% Similarity=1.109 Sum_probs=41.0
Q ss_pred HHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHhcCCCCchhhcc
Q 042627 146 KQNEVDCEFLKKCCESLTDENKRLKKELQELQSAKAGASSPLFIQL 191 (237)
Q Consensus 146 kq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~~~~~~~~~~~~ 191 (237)
||+++||+.||+||+.|.+||.+|++|+++|++++++ +|+|+++
T Consensus 1 KQTEvdCe~LKrcce~LteeNrRL~ke~~eLralk~~--~~~~m~~ 44 (44)
T smart00340 1 KQTEVDCELLKRCCESLTEENRRLQKEVQELRALKLS--PPLYMQH 44 (44)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC--CcccccC
Confidence 5899999999999999999999999999999999987 7888864
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.00 E-value=2.9e-10 Score=106.20 Aligned_cols=62 Identities=27% Similarity=0.438 Sum_probs=57.6
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHh
Q 042627 87 INISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQN 148 (237)
Q Consensus 87 ~~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~ 148 (237)
..+.+|.|++|+..|+..||+.|++++||+. |++||.++++.+..|+|||+|||++++|...
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 4466788999999999999999999999999 9999999999999999999999999998753
No 29
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.77 E-value=3.4e-09 Score=95.79 Aligned_cols=61 Identities=30% Similarity=0.445 Sum_probs=56.0
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHH
Q 042627 87 INISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147 (237)
Q Consensus 87 ~~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq 147 (237)
++.+|||||.+.......||.+|...+.|+. +..||++|.|...+|+|||.|.|.|.||..
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 4457899999999999999999999999998 788999999999999999999999988753
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.51 E-value=8e-08 Score=86.26 Aligned_cols=49 Identities=31% Similarity=0.468 Sum_probs=44.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHH
Q 042627 97 LTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKL 145 (237)
Q Consensus 97 ~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Kr 145 (237)
|...-...|.++|..++||++ +.+||+.+||+..||-.||.|||.|+|.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 455567799999999999999 8999999999999999999999999993
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.41 E-value=8.2e-07 Score=79.51 Aligned_cols=57 Identities=30% Similarity=0.473 Sum_probs=52.8
Q ss_pred CCCCCccCCHHHHHHHHHHHhh---CCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHH
Q 042627 90 SGRKKLRLTIEQSRLLEDSFKL---HTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLK 146 (237)
Q Consensus 90 ~rR~Rt~~t~~Ql~~LE~~F~~---~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krk 146 (237)
.+|||+.|+..-.++|..+|.. ++||+. +++||++++++..||-.||.|+|-+.|+-
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 4889999999999999999975 889998 99999999999999999999999999863
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.99 E-value=6.4e-06 Score=71.01 Aligned_cols=62 Identities=31% Similarity=0.517 Sum_probs=56.5
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHh
Q 042627 87 INISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQN 148 (237)
Q Consensus 87 ~~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~ 148 (237)
..+.++.|+.+...|+..++..|...++|+. ++.|+..+|+.++.|++||||+|++.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3466788899999999999999999999987 9999999999999999999999999997643
No 33
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=97.87 E-value=5.3e-06 Score=54.30 Aligned_cols=32 Identities=34% Similarity=0.538 Sum_probs=26.4
Q ss_pred hCCCCCH--HHHHHHHhCCCCccchhhccchHHH
Q 042627 111 LHTTLNS--KQALAEQLNLEPRQVEVWFQNRRAR 142 (237)
Q Consensus 111 ~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak 142 (237)
.++||+. +++||.++||+..||..||-|.|.|
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 3789998 9999999999999999999999865
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.78 E-value=2.6e-05 Score=75.94 Aligned_cols=61 Identities=28% Similarity=0.371 Sum_probs=55.3
Q ss_pred CCCCCCCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHH
Q 042627 84 SKRINISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 84 ~~~~~~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
.+.....||.|.+||..|...|..+|+.+++|+. .+.|+.+|+|...-|..||-|-|.|.+
T Consensus 414 ~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 414 DDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred ccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 4556677889999999999999999999999999 888999999999999999999887753
No 35
>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=97.30 E-value=0.00052 Score=46.05 Aligned_cols=35 Identities=40% Similarity=0.434 Sum_probs=32.7
Q ss_pred HHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHh
Q 042627 146 KQNEVDCEFLKKCCESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 146 kq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~ 180 (237)
+|.+.+|+.||++|+.|..++++|++|++.|++..
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 47899999999999999999999999999999865
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.01 E-value=0.00041 Score=73.49 Aligned_cols=60 Identities=23% Similarity=0.354 Sum_probs=54.4
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHHh
Q 042627 89 ISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQN 148 (237)
Q Consensus 89 ~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~ 148 (237)
.+++.|++++..|+..|..+|....|+.. .+.|...+++..+.|+|||||-|++.|+...
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 45778999999999999999999999888 7789999999999999999999999986543
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.32 E-value=0.002 Score=45.15 Aligned_cols=39 Identities=28% Similarity=0.474 Sum_probs=28.6
Q ss_pred HHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchH
Q 042627 102 SRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRR 140 (237)
Q Consensus 102 l~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRR 140 (237)
+..|+++|..++++.. ...|..+.+|+..||+.||--|+
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 4569999999999988 99999999999999999996543
No 38
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.48 E-value=0.011 Score=54.77 Aligned_cols=56 Identities=30% Similarity=0.284 Sum_probs=45.5
Q ss_pred CCCCCccCCHHHHHHHHHHHhh---CCCCCH--HHHHHHHhCCCCccchhhccchHHHHHH
Q 042627 90 SGRKKLRLTIEQSRLLEDSFKL---HTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKL 145 (237)
Q Consensus 90 ~rR~Rt~~t~~Ql~~LE~~F~~---~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Kr 145 (237)
..|.+..|......+|+.+... ++||+. +..||+++||+..||..||-|.|-|..+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 3445567899999999987444 568887 7799999999999999999998877553
No 39
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=94.22 E-value=0.1 Score=35.81 Aligned_cols=47 Identities=21% Similarity=0.320 Sum_probs=36.0
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchH
Q 042627 91 GRKKLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRR 140 (237)
Q Consensus 91 rR~Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRR 140 (237)
||+|..+|-++-..+-..++... ...+||+++|+...+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~---s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE---SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT----HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC---CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 57889999999888888887765 478899999999999999998853
No 40
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=93.75 E-value=0.57 Score=37.12 Aligned_cols=43 Identities=21% Similarity=0.323 Sum_probs=29.5
Q ss_pred CCCccCCHHHHHHH-HHHHhhCCCCCH-HHHHHHHhCCCCccchhhccc
Q 042627 92 RKKLRLTIEQSRLL-EDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 92 R~Rt~~t~~Ql~~L-E~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQN 138 (237)
++|.+|+.++.... ...+. ... ..++|+++|+++.+|..|.+-
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~----~g~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE----PGMTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34566888765433 33333 222 788999999999999999643
No 41
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.23 E-value=0.074 Score=54.17 Aligned_cols=46 Identities=22% Similarity=0.374 Sum_probs=42.3
Q ss_pred HHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHH
Q 042627 102 SRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147 (237)
Q Consensus 102 l~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq 147 (237)
+..|..+|..|..|.. ...+|.+.||..+.|++||+++++....-+
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 7789999999999998 788999999999999999999999987655
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=92.16 E-value=0.38 Score=32.22 Aligned_cols=32 Identities=34% Similarity=0.476 Sum_probs=28.9
Q ss_pred hHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHH
Q 042627 148 NEVDCEFLKKCCESLTDENKRLKKELQELQSA 179 (237)
Q Consensus 148 ~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~ 179 (237)
.+..++.|+..++.|..||+.|+.|+..|+..
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 45679999999999999999999999999874
No 43
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=91.36 E-value=1.5 Score=35.83 Aligned_cols=73 Identities=29% Similarity=0.332 Sum_probs=50.7
Q ss_pred ccCCHHHHHHHHHHHhhCCCCCHHHHHHHH-hCCCCccchhhccchHH----------HHHHHHhHH----HHHHHHHHh
Q 042627 95 LRLTIEQSRLLEDSFKLHTTLNSKQALAEQ-LNLEPRQVEVWFQNRRA----------RTKLKQNEV----DCEFLKKCC 159 (237)
Q Consensus 95 t~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~-LgL~~rQVkvWFQNRRa----------k~Krkq~~~----~~~~Lk~~~ 159 (237)
.+|+.+++..|- ..+|=+. -|++...|-.|=|.||+ +.||-+.+. +...|.++.
T Consensus 22 d~lsDd~LvsmS-----------VReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~qqv 90 (135)
T KOG4196|consen 22 DRLSDDELVSMS-----------VRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQQV 90 (135)
T ss_pred CCcCHHHHHHhh-----------HHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678998887663 2333333 47888888888888886 334444444 444467778
Q ss_pred HhhHHHHHHHHHHHHHHHH
Q 042627 160 ESLTDENKRLKKELQELQS 178 (237)
Q Consensus 160 ~~l~~en~~l~~e~~~l~~ 178 (237)
+.|.+||.+++.|+..++.
T Consensus 91 ~~L~~e~s~~~~E~da~k~ 109 (135)
T KOG4196|consen 91 EKLKEENSRLRRELDAYKS 109 (135)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 8888888888888888776
No 44
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=87.81 E-value=1.4 Score=34.55 Aligned_cols=47 Identities=17% Similarity=0.286 Sum_probs=32.6
Q ss_pred cchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 131 QVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 131 QVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
++..||.+.-- .+..+.+.+.+.+++..+.++++|++|+.|+..|+.
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 56688865421 122344456677788888888888888888888876
No 45
>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=83.73 E-value=4.1 Score=27.71 Aligned_cols=29 Identities=28% Similarity=0.447 Sum_probs=22.1
Q ss_pred HHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 150 VDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 150 ~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
.....|......|..+|..|+.++..|..
T Consensus 25 ~~~~~le~~~~~L~~en~~L~~~i~~L~~ 53 (54)
T PF07716_consen 25 QREEELEQEVQELEEENEQLRQEIAQLER 53 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34455667788889999999998888764
No 46
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=81.99 E-value=4.4 Score=36.74 Aligned_cols=31 Identities=32% Similarity=0.296 Sum_probs=24.0
Q ss_pred HHHHHHHHhHhhHHHHHHHHHHHHHHHHHhc
Q 042627 151 DCEFLKKCCESLTDENKRLKKELQELQSAKA 181 (237)
Q Consensus 151 ~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~~ 181 (237)
....|.++++.|+.+.++|++|+..|+.+..
T Consensus 223 r~~~leken~~lr~~v~~l~~el~~~~~~~~ 253 (269)
T KOG3119|consen 223 RVAELEKENEALRTQVEQLKKELATLRRLFL 253 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445777888888888888888888888764
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=79.91 E-value=2.8 Score=28.93 Aligned_cols=36 Identities=28% Similarity=0.326 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCH----HHHHHHHhCCCCccc
Q 042627 97 LTIEQSRLLEDSFKLHTTLNS----KQALAEQLNLEPRQV 132 (237)
Q Consensus 97 ~t~~Ql~~LE~~F~~~~~p~~----r~~LA~~LgL~~rQV 132 (237)
+|..|..+|...|+..-|-.+ ..+||.+||++..-|
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 588999999999999877444 789999999998654
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=77.27 E-value=13 Score=25.94 Aligned_cols=26 Identities=46% Similarity=0.610 Sum_probs=12.2
Q ss_pred HHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 153 EFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 153 ~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
+.|...+..|..+|..|+.++..|..
T Consensus 29 ~~Le~~~~~L~~en~~L~~~~~~L~~ 54 (64)
T PF00170_consen 29 EELEEKVEELESENEELKKELEQLKK 54 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444455555555544444443
No 49
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=75.86 E-value=5.8 Score=26.07 Aligned_cols=38 Identities=13% Similarity=0.214 Sum_probs=29.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhcc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQ 137 (237)
.+++.+..+|...| +-.. -.++|..+|++...|+.+..
T Consensus 4 ~L~~~er~vi~~~y----~~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRY----FEGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHH----TST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh----cCCCCHHHHHHHHCCcHHHHHHHHH
Confidence 47888999999999 3344 88999999999998887653
No 50
>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=74.42 E-value=1.1 Score=31.88 Aligned_cols=43 Identities=16% Similarity=0.247 Sum_probs=27.9
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhcc
Q 042627 92 RKKLRLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 92 R~Rt~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQ 137 (237)
++|.+||.++...+-..+... .. ..++|+++||++.+|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~---g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES---GESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH---HCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC---CCceEeeecccccccccccHHHH
Confidence 467889998887776666211 12 88999999999999999964
No 51
>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=74.23 E-value=10 Score=26.98 Aligned_cols=30 Identities=37% Similarity=0.442 Sum_probs=25.7
Q ss_pred HhHHHHHHHHHHhHhhHHHHHHHHHHHHHH
Q 042627 147 QNEVDCEFLKKCCESLTDENKRLKKELQEL 176 (237)
Q Consensus 147 q~~~~~~~Lk~~~~~l~~en~~l~~e~~~l 176 (237)
+.+.+...|+...+.++.+|+.|+.+++.|
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 455667888899999999999999999888
No 52
>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=74.17 E-value=15 Score=25.67 Aligned_cols=35 Identities=37% Similarity=0.422 Sum_probs=28.9
Q ss_pred HHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHH
Q 042627 145 LKQNEVDCEFLKKCCESLTDENKRLKKELQELQSA 179 (237)
Q Consensus 145 rkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~ 179 (237)
..+.+.....|...++.|..++..|+.+++.|...
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e 62 (64)
T PF00170_consen 28 IEELEEKVEELESENEELKKELEQLKKEIQSLKSE 62 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34456677779999999999999999999999864
No 53
>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=73.91 E-value=6.5 Score=27.85 Aligned_cols=32 Identities=25% Similarity=0.338 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHh
Q 042627 149 EVDCEFLKKCCESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 149 ~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~ 180 (237)
+++-+.||..+..|.+.|.+|+.|+.-||...
T Consensus 13 rEEVevLK~~I~eL~~~n~~Le~EN~~Lk~~~ 44 (59)
T PF01166_consen 13 REEVEVLKEQIAELEERNSQLEEENNLLKQNA 44 (59)
T ss_dssp TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 45678899999999999999999999999965
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=72.73 E-value=11 Score=29.73 Aligned_cols=36 Identities=36% Similarity=0.322 Sum_probs=30.4
Q ss_pred HHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHh
Q 042627 145 LKQNEVDCEFLKKCCESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 145 rkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~ 180 (237)
..+.-.+...||.....|.+||.+|+-|++.|+...
T Consensus 17 l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l 52 (107)
T PF06156_consen 17 LGQLLEELEELKKQLQELLEENARLRIENEHLRERL 52 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345666788899999999999999999999999864
No 55
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=70.67 E-value=9.3 Score=35.24 Aligned_cols=30 Identities=30% Similarity=0.379 Sum_probs=15.4
Q ss_pred HHHHHHHHhHhhHHHHHHHHHHHHHHHHHh
Q 042627 151 DCEFLKKCCESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 151 ~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~ 180 (237)
+++.|-+.++.|++.-..|.+|++.||.+.
T Consensus 256 e~~~Le~rN~~LK~qa~~lerEI~ylKqli 285 (294)
T KOG4571|consen 256 ELEGLEKRNEELKDQASELEREIRYLKQLI 285 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444555555555555555555543
No 56
>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=69.87 E-value=15 Score=26.73 Aligned_cols=32 Identities=25% Similarity=0.243 Sum_probs=25.1
Q ss_pred HhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 147 QNEVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 147 q~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
+...+...+++..+.++.||++|+.|...|..
T Consensus 28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~ 59 (85)
T TIGR02209 28 QLNNELQKLQLEIDKLQKEWRDLQLEVAELSR 59 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 55566677788888888999999988887765
No 57
>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=67.81 E-value=6.4 Score=24.71 Aligned_cols=41 Identities=15% Similarity=0.147 Sum_probs=30.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccchH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQNRR 140 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQNRR 140 (237)
.++..+..++...|... . ..++|..+|++...|..|...-+
T Consensus 10 ~l~~~~~~~~~~~~~~~----~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 10 KLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred hCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46777777777776422 2 78889999999999999886543
No 58
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=67.25 E-value=11 Score=31.23 Aligned_cols=47 Identities=21% Similarity=0.107 Sum_probs=35.4
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHH
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
...+++.|..+|...++--. ..++|..||++...|+.|.+..+.+.|
T Consensus 4 ~~~Lt~rqreVL~lr~~GlT----q~EIAe~LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 4 ESFLTERQIEVLRLRERGLT----QQEIADILGTSRANVSSIEKRARENIE 50 (141)
T ss_pred ccCCCHHHHHHHHHHHcCCC----HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45689999999977432211 789999999999999999875554444
No 59
>smart00338 BRLZ basic region leucin zipper.
Probab=65.79 E-value=31 Score=24.06 Aligned_cols=25 Identities=44% Similarity=0.615 Sum_probs=12.9
Q ss_pred HHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 154 FLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 154 ~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
.|......|..+|..|+.++..|..
T Consensus 30 ~Le~~~~~L~~en~~L~~~~~~l~~ 54 (65)
T smart00338 30 ELERKVEQLEAENERLKKEIERLRR 54 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455555555555555555544
No 60
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=65.42 E-value=10 Score=32.66 Aligned_cols=47 Identities=26% Similarity=0.219 Sum_probs=36.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH----HHHHHHHhCCCCccchhhccchHHHHH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS----KQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~----r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
.+|..|+.+|...|+..-|-.+ ..+||++||+++.- +|..=|||..|
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 6999999999999999877443 78999999999854 44445555544
No 61
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=65.38 E-value=17 Score=28.83 Aligned_cols=35 Identities=26% Similarity=0.167 Sum_probs=29.3
Q ss_pred HHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHh
Q 042627 146 KQNEVDCEFLKKCCESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 146 kq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~ 180 (237)
.+.-.+...||.....|.+||..|+-|++.|+...
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 45556778889999999999999999999999865
No 62
>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=64.17 E-value=32 Score=25.13 Aligned_cols=32 Identities=31% Similarity=0.415 Sum_probs=18.4
Q ss_pred hHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHH
Q 042627 148 NEVDCEFLKKCCESLTDENKRLKKELQELQSA 179 (237)
Q Consensus 148 ~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~ 179 (237)
.+.+.+.|+..+..|.++|..|+.++++|+..
T Consensus 23 Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e 54 (72)
T PF06005_consen 23 LQMENEELKEKNNELKEENEELKEENEQLKQE 54 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555666666666666653
No 63
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=63.65 E-value=6.4 Score=26.78 Aligned_cols=36 Identities=11% Similarity=0.169 Sum_probs=22.3
Q ss_pred HHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHH
Q 042627 118 KQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCE 153 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~ 153 (237)
..+||+.+|++...|..||.++...........=+.
T Consensus 13 ~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~ 48 (63)
T PF13443_consen 13 QKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAK 48 (63)
T ss_dssp HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHH
Confidence 678999999999999999998865655544433333
No 64
>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=63.48 E-value=49 Score=25.02 Aligned_cols=65 Identities=18% Similarity=0.218 Sum_probs=40.9
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHH
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKEL 173 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~ 173 (237)
+..|+.+++..|...+. .+.+|++..+|+-++.... ..-.+.|+.....|.++..+|+.-.
T Consensus 36 ~R~y~~~di~~l~~i~~-----------lr~~g~~l~~i~~~~~~~~--------~~~~~~l~~~~~~l~~~i~~l~~~~ 96 (103)
T cd01106 36 YRLYTEEDLERLQQILF-----------LKELGFSLKEIKELLKDPS--------EDLLEALREQKELLEEKKERLDKLI 96 (103)
T ss_pred ceeeCHHHHHHHHHHHH-----------HHHcCCCHHHHHHHHHcCc--------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45699999998875433 4567888888888886543 2233445555555666666665555
Q ss_pred HHHH
Q 042627 174 QELQ 177 (237)
Q Consensus 174 ~~l~ 177 (237)
+.|.
T Consensus 97 ~~l~ 100 (103)
T cd01106 97 KTID 100 (103)
T ss_pred HHHH
Confidence 5443
No 65
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=61.21 E-value=18 Score=32.65 Aligned_cols=7 Identities=43% Similarity=0.591 Sum_probs=3.0
Q ss_pred CCCCCcc
Q 042627 90 SGRKKLR 96 (237)
Q Consensus 90 ~rR~Rt~ 96 (237)
++|||.|
T Consensus 54 ~~rKr~R 60 (292)
T KOG4005|consen 54 PKRKRRR 60 (292)
T ss_pred hHHHHHh
Confidence 3444443
No 66
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=61.09 E-value=29 Score=38.15 Aligned_cols=57 Identities=18% Similarity=0.070 Sum_probs=47.6
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHH
Q 042627 91 GRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147 (237)
Q Consensus 91 rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq 147 (237)
+-.+++++.-|...|..+|+...+|.- ...++.-|++..|.+-.||++++.++....
T Consensus 445 ~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~ 503 (1406)
T KOG1146|consen 445 LLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNH 503 (1406)
T ss_pred hhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhcccc
Confidence 345678888999999999988777765 888999999999999999999888887433
No 67
>KOG3335 consensus Predicted coiled-coil protein [General function prediction only]
Probab=59.21 E-value=32 Score=29.59 Aligned_cols=52 Identities=25% Similarity=0.282 Sum_probs=43.7
Q ss_pred CCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHH
Q 042627 128 EPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQSA 179 (237)
Q Consensus 128 ~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~ 179 (237)
..-...+|-+-|-.+.|..+.+.+.+.|+...+.|..+-+++++++.+|...
T Consensus 84 g~lv~Ey~R~~~~e~~kee~~~~e~~elr~~~~~l~~~i~~~~~~~~~L~~~ 135 (181)
T KOG3335|consen 84 GVLVFEYWRQARKERKKEEKRKQEIMELRLKVEKLENAIAELTKFFSQLHSK 135 (181)
T ss_pred eeeeehhHHhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445678888888888888888889999999999999999999999999753
No 68
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=58.47 E-value=14 Score=26.19 Aligned_cols=44 Identities=20% Similarity=0.265 Sum_probs=23.3
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhcc
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQ 137 (237)
|..|+.......-.+|.....-.. ....|+++|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHH
Confidence 456766554444444544333222 34459999999999999953
No 69
>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=56.70 E-value=5.4 Score=28.35 Aligned_cols=19 Identities=21% Similarity=0.489 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCCccchhhc
Q 042627 118 KQALAEQLNLEPRQVEVWF 136 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWF 136 (237)
..+||.+||+++.+|+.|=
T Consensus 25 lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHHCCCHHHHHHHh
Confidence 7889999999999999994
No 70
>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=56.37 E-value=12 Score=25.29 Aligned_cols=46 Identities=15% Similarity=0.151 Sum_probs=35.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKL 145 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Kr 145 (237)
.||..+..+|.-...-.. ..++|..++++++.|+.+..+=+.|..-
T Consensus 3 ~LT~~E~~vl~~l~~G~~----~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMS----NKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-----HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhcCC----cchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 578888888887766544 8899999999999999988766666543
No 71
>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=55.61 E-value=3.9 Score=36.40 Aligned_cols=40 Identities=25% Similarity=0.450 Sum_probs=0.0
Q ss_pred HHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHh
Q 042627 141 ARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 141 ak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~ 180 (237)
.|.+....+.....|++..+.|..||++|++|++.|++.+
T Consensus 120 dKT~IEEQ~T~I~dLrrlVe~L~aeNErLr~EnkqL~ae~ 159 (243)
T PF08961_consen 120 DKTRIEEQATKIADLRRLVEFLLAENERLRRENKQLKAEN 159 (243)
T ss_dssp ----------------------------------------
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555556667788888888888888888888888765
No 72
>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=55.47 E-value=84 Score=26.52 Aligned_cols=48 Identities=21% Similarity=0.174 Sum_probs=37.2
Q ss_pred CCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchH
Q 042627 93 KKLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRR 140 (237)
Q Consensus 93 ~Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRR 140 (237)
+...++++++.++.+.-..++.--.+..||+++|++..-|.+=..--.
T Consensus 82 k~y~Lt~e~i~Eir~LR~~DP~~wTr~~LAkkF~~S~~fV~~v~~~~~ 129 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAEDPEKWTRKKLAKKFNCSPLFVSMVAPAPK 129 (164)
T ss_pred ccccCCHHHHHHHHHHHHcCchHhhHHHHHHHhCCCHHHHHHhcCCCH
Confidence 456899999999998888775433399999999999887776654433
No 73
>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=55.44 E-value=27 Score=19.27 Aligned_cols=38 Identities=18% Similarity=0.180 Sum_probs=26.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWF 136 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWF 136 (237)
.++.++...+...|.... ...++|..++++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~~---s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAGE---SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcCC---CHHHHHHHHCCCHHHHHHhC
Confidence 456666666666665321 27788999999988887774
No 74
>smart00338 BRLZ basic region leucin zipper.
Probab=54.75 E-value=60 Score=22.51 Aligned_cols=35 Identities=34% Similarity=0.413 Sum_probs=28.2
Q ss_pred HHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHh
Q 042627 146 KQNEVDCEFLKKCCESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 146 kq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~ 180 (237)
...+.....|...++.|..+...|..++..|+...
T Consensus 29 ~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 29 EELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34566777788889999999999999999888754
No 75
>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=54.54 E-value=29 Score=31.17 Aligned_cols=39 Identities=21% Similarity=0.185 Sum_probs=26.5
Q ss_pred HHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 140 RARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 140 Rak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
|.|.|-.+.|++...++.....|+.|.+.|+++|-+|-.
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYE 128 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYE 128 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 555566666666666666777777777777777666655
No 76
>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=52.76 E-value=57 Score=23.84 Aligned_cols=27 Identities=33% Similarity=0.336 Sum_probs=12.3
Q ss_pred hHHHHHHHHHHhHhhHHHHHHHHHHHH
Q 042627 148 NEVDCEFLKKCCESLTDENKRLKKELQ 174 (237)
Q Consensus 148 ~~~~~~~Lk~~~~~l~~en~~l~~e~~ 174 (237)
.+.++..|+...+.|..||.+|+.+..
T Consensus 30 Lke~n~~L~~e~~~L~~en~~L~~e~~ 56 (72)
T PF06005_consen 30 LKEKNNELKEENEELKEENEQLKQERN 56 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444445555555444433
No 77
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=52.35 E-value=31 Score=30.74 Aligned_cols=36 Identities=25% Similarity=0.130 Sum_probs=25.9
Q ss_pred HHHhHHHHHHHHHHhHhhHHHHH---HHHHHHHHHHHHh
Q 042627 145 LKQNEVDCEFLKKCCESLTDENK---RLKKELQELQSAK 180 (237)
Q Consensus 145 rkq~~~~~~~Lk~~~~~l~~en~---~l~~e~~~l~~~~ 180 (237)
.++.+++++.|+++...|+.++. .+++|+++|+.+.
T Consensus 71 ~~~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL 109 (276)
T PRK13922 71 LFDLREENEELKKELLELESRLQELEQLEAENARLRELL 109 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34556677778877777776666 6688888888754
No 78
>PF15058 Speriolin_N: Speriolin N terminus
Probab=52.02 E-value=23 Score=30.93 Aligned_cols=27 Identities=33% Similarity=0.401 Sum_probs=14.1
Q ss_pred HHHHHHHHhHhhHHHHHHHHHHHHHHH
Q 042627 151 DCEFLKKCCESLTDENKRLKKELQELQ 177 (237)
Q Consensus 151 ~~~~Lk~~~~~l~~en~~l~~e~~~l~ 177 (237)
.|+-|+.+++.|..||++|+++++-++
T Consensus 6 ~yeGlrhqierLv~ENeeLKKlVrLir 32 (200)
T PF15058_consen 6 NYEGLRHQIERLVRENEELKKLVRLIR 32 (200)
T ss_pred chHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence 344555555556666665555444333
No 79
>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=51.33 E-value=47 Score=23.95 Aligned_cols=25 Identities=28% Similarity=0.373 Sum_probs=11.3
Q ss_pred HHHHHHhHhhHHHHHHHHHHHHHHH
Q 042627 153 EFLKKCCESLTDENKRLKKELQELQ 177 (237)
Q Consensus 153 ~~Lk~~~~~l~~en~~l~~e~~~l~ 177 (237)
+.|-..|+.|+.||..|+.++..+.
T Consensus 10 e~Li~~~~~L~~EN~~Lr~q~~~~~ 34 (65)
T TIGR02449 10 EHLLEYLERLKSENRLLRAQEKTWR 34 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444444444443
No 80
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=51.08 E-value=41 Score=31.09 Aligned_cols=35 Identities=26% Similarity=0.300 Sum_probs=29.0
Q ss_pred HHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHH
Q 042627 145 LKQNEVDCEFLKKCCESLTDENKRLKKELQELQSA 179 (237)
Q Consensus 145 rkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~ 179 (237)
|++.+.+.+.|--+++.|..+|++|+.++++|--.
T Consensus 243 RqKkRae~E~l~ge~~~Le~rN~~LK~qa~~lerE 277 (294)
T KOG4571|consen 243 RQKKRAEKEALLGELEGLEKRNEELKDQASELERE 277 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556778889999999999999999999888653
No 81
>PRK14127 cell division protein GpsB; Provisional
Probab=50.75 E-value=35 Score=27.01 Aligned_cols=35 Identities=34% Similarity=0.385 Sum_probs=29.3
Q ss_pred HHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHh
Q 042627 146 KQNEVDCEFLKKCCESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 146 kq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~ 180 (237)
.+-..+++.|......|++++.+|+.++.++....
T Consensus 33 d~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~ 67 (109)
T PRK14127 33 DDVIKDYEAFQKEIEELQQENARLKAQVDELTKQV 67 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 35667888888899999999999999998888855
No 82
>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=49.65 E-value=26 Score=26.98 Aligned_cols=34 Identities=24% Similarity=0.423 Sum_probs=20.1
Q ss_pred HHHHHHHHhhCCCCCH---HHHHHHHhCCCCccchhhccchHHHHHHHHhHH
Q 042627 102 SRLLEDSFKLHTTLNS---KQALAEQLNLEPRQVEVWFQNRRARTKLKQNEV 150 (237)
Q Consensus 102 l~~LE~~F~~~~~p~~---r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~ 150 (237)
+.+..-.|+.++||.. +.. + .|||.+||+.|.+.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~a--R-------------RnRRRRWR~rq~QI 50 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQA--R-------------RNRRRRWRARQRQI 50 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HHH--H-------------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCcccc--c-------------cchhhhHHHHHHHH
Confidence 3345556888999876 221 1 58999999876543
No 83
>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=49.20 E-value=1.3e+02 Score=23.51 Aligned_cols=69 Identities=14% Similarity=0.156 Sum_probs=44.8
Q ss_pred CCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHH
Q 042627 93 KKLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKE 172 (237)
Q Consensus 93 ~Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e 172 (237)
.+..|+..++..|.. ....+.+|++-.+|+.+|.+.... ....+.+....+.+.++.++|+.-
T Consensus 34 gyR~Y~~~~l~~l~~-----------I~~lr~~G~~L~eI~~~l~~~~~~------~~~~~~l~~~~~~l~~~i~~l~~~ 96 (120)
T cd04781 34 LRRQYDPQVLDRLAL-----------IALGRAAGFSLDEIQAMLSHDGKP------PIDRQLLKAKAAELDQQIQRLQAM 96 (120)
T ss_pred CceecCHHHHHHHHH-----------HHHHHHcCCCHHHHHHHHhccCCc------HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456789999988863 344778888888888888764311 112244555666666666666666
Q ss_pred HHHHHH
Q 042627 173 LQELQS 178 (237)
Q Consensus 173 ~~~l~~ 178 (237)
...|..
T Consensus 97 ~~~L~~ 102 (120)
T cd04781 97 RELLRH 102 (120)
T ss_pred HHHHHH
Confidence 666654
No 84
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=49.11 E-value=36 Score=33.35 Aligned_cols=43 Identities=37% Similarity=0.568 Sum_probs=29.4
Q ss_pred hhhc---cchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHH
Q 042627 133 EVWF---QNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQE 175 (237)
Q Consensus 133 kvWF---QNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~ 175 (237)
-+|| ||+.+|.+-.+.-.+++-|+..-+.|.+=.++|.+...+
T Consensus 229 gcw~ay~Qnk~akehv~km~kdle~Lq~aEqsl~dlQk~Lekar~e 274 (575)
T KOG4403|consen 229 GCWFAYRQNKKAKEHVNKMMKDLEGLQRAEQSLEDLQKRLEKAREE 274 (575)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4688 999999988888778887777665555444444444333
No 85
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=48.75 E-value=73 Score=23.87 Aligned_cols=34 Identities=26% Similarity=0.319 Sum_probs=25.7
Q ss_pred HHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 145 LKQNEVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 145 rkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
.+..+..+..|-...+.++.|+++|..|++-|..
T Consensus 25 i~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~ 58 (80)
T PF10224_consen 25 ILELQDSLEALSDRVEEVKEENEKLESENEYLQQ 58 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566667777778888888888888888876
No 86
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=47.78 E-value=35 Score=21.65 Aligned_cols=39 Identities=21% Similarity=0.277 Sum_probs=28.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQN 138 (237)
.++..+..++..++... ...++|..++++...|..|.+.
T Consensus 3 ~l~~~e~~i~~~~~~g~----s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLAEGL----TNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHH
Confidence 46777777775543211 1789999999999999888763
No 87
>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=46.92 E-value=66 Score=21.64 Aligned_cols=24 Identities=29% Similarity=0.364 Sum_probs=12.5
Q ss_pred HHHHHHHHHHhHhhHHHHHHHHHH
Q 042627 149 EVDCEFLKKCCESLTDENKRLKKE 172 (237)
Q Consensus 149 ~~~~~~Lk~~~~~l~~en~~l~~e 172 (237)
+.....|...+..|..++..|+.|
T Consensus 31 e~~~~~L~~en~~L~~~i~~L~~E 54 (54)
T PF07716_consen 31 EQEVQELEEENEQLRQEIAQLERE 54 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc
Confidence 333444555555565555555543
No 88
>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=46.90 E-value=43 Score=30.53 Aligned_cols=35 Identities=17% Similarity=0.069 Sum_probs=23.0
Q ss_pred HHhHHHHHHHHHHhHhhHHHHH----HHHHHHHHHHHHh
Q 042627 146 KQNEVDCEFLKKCCESLTDENK----RLKKELQELQSAK 180 (237)
Q Consensus 146 kq~~~~~~~Lk~~~~~l~~en~----~l~~e~~~l~~~~ 180 (237)
.+.++|++.||++...+..+.. .+++|+++|+.+.
T Consensus 69 ~~l~~EN~~Lr~e~~~l~~~~~~~~~~l~~EN~rLr~LL 107 (283)
T TIGR00219 69 NNLEYENYKLRQELLKKNQQLEILTQNLKQENVRLRELL 107 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3466777778777655533332 3788888888864
No 89
>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=46.81 E-value=1e+02 Score=23.68 Aligned_cols=72 Identities=18% Similarity=0.162 Sum_probs=43.1
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHH
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKEL 173 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~ 173 (237)
...|+.+++..|.. ....+.+|++-.+|+..+........ ........|....+.+.++...|+..+
T Consensus 36 yR~Y~~~~l~~l~~-----------I~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~l~~~~ 102 (113)
T cd01109 36 IRDFTEEDLEWLEF-----------IKCLRNTGMSIKDIKEYAELRREGDS--TIPERLELLEEHREELEEQIAELQETL 102 (113)
T ss_pred CccCCHHHHHHHHH-----------HHHHHHcCCCHHHHHHHHHHHccCCc--cHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34689999888863 23367788888888888865432111 012223455566666666666666555
Q ss_pred HHHHH
Q 042627 174 QELQS 178 (237)
Q Consensus 174 ~~l~~ 178 (237)
..|..
T Consensus 103 ~~l~~ 107 (113)
T cd01109 103 AYLDY 107 (113)
T ss_pred HHHHH
Confidence 55543
No 90
>PRK00118 putative DNA-binding protein; Validated
Probab=46.51 E-value=66 Score=25.16 Aligned_cols=56 Identities=21% Similarity=0.210 Sum_probs=36.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHH
Q 042627 97 LTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKC 158 (237)
Q Consensus 97 ~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~ 158 (237)
++..|..++...|.. .. ..++|..+|+++..|..|.. |++.+.++.......+++.
T Consensus 18 L~ekqRevl~L~y~e----g~S~~EIAe~lGIS~~TV~r~L~--RArkkLr~~~~~~~~~~~~ 74 (104)
T PRK00118 18 LTEKQRNYMELYYLD----DYSLGEIAEEFNVSRQAVYDNIK--RTEKLLEDYEEKLHLYEKF 74 (104)
T ss_pred CCHHHHHHHHHHHHc----CCCHHHHHHHHCcCHHHHHHHHH--HHHHHHHHHHHHHChHHHH
Confidence 456666666555443 22 78899999999999999986 4444444444444444443
No 91
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=46.38 E-value=53 Score=23.76 Aligned_cols=24 Identities=38% Similarity=0.455 Sum_probs=16.0
Q ss_pred HHHHHhHhhHHHHHHHHHHHHHHH
Q 042627 154 FLKKCCESLTDENKRLKKELQELQ 177 (237)
Q Consensus 154 ~Lk~~~~~l~~en~~l~~e~~~l~ 177 (237)
..-..+..|+.|++.|++|+++++
T Consensus 44 ~a~~e~~~Lk~E~e~L~~el~~~r 67 (69)
T PF14197_consen 44 DAYEENNKLKEENEALRKELEELR 67 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Confidence 344456677777777777776655
No 92
>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=46.14 E-value=47 Score=28.92 Aligned_cols=23 Identities=26% Similarity=0.406 Sum_probs=18.5
Q ss_pred HHhHhhHHHHHHHHHHHHHHHHH
Q 042627 157 KCCESLTDENKRLKKELQELQSA 179 (237)
Q Consensus 157 ~~~~~l~~en~~l~~e~~~l~~~ 179 (237)
.++..|++.|++||.++++|+.+
T Consensus 55 ~EIR~LKe~NqkLqedNqELRdL 77 (195)
T PF10226_consen 55 NEIRGLKEVNQKLQEDNQELRDL 77 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35567888899999999999875
No 93
>PRK10072 putative transcriptional regulator; Provisional
Probab=45.99 E-value=21 Score=27.50 Aligned_cols=42 Identities=17% Similarity=0.200 Sum_probs=30.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRAR 142 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak 142 (237)
+.+...+..|....... ..+||+.+|++...|..|.+.+|.-
T Consensus 32 ~~~~~eik~LR~~~glT-----Q~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 32 TTSFTEFEQLRKGTGLK-----IDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred cCChHHHHHHHHHcCCC-----HHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 34666666664432222 7899999999999999999887643
No 94
>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=45.32 E-value=1.3e+02 Score=24.31 Aligned_cols=73 Identities=8% Similarity=0.011 Sum_probs=39.9
Q ss_pred CCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHH-HHHHHHhHHHHHHHHHHhHhhHHHHHHHHH
Q 042627 93 KKLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRA-RTKLKQNEVDCEFLKKCCESLTDENKRLKK 171 (237)
Q Consensus 93 ~Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRa-k~Krkq~~~~~~~Lk~~~~~l~~en~~l~~ 171 (237)
.+..|+..++..|..... .+.+|++-..|+-++.+... .....+.....+.+....+.+......|+.
T Consensus 34 g~R~Y~~~~l~~l~~I~~-----------lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~i~~Le~~l~~L~~ 102 (134)
T cd04779 34 NYRYYDETALDRLQLIEH-----------LKGQRLSLAEIKDQLEEVQRSDKEQREVAQEVQLVCDQIDGLEHRLKQLKP 102 (134)
T ss_pred CCeeECHHHHHHHHHHHH-----------HHHCCCCHHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355789999888865322 35667776677766655442 122223333444455555555555555544
Q ss_pred HHHHH
Q 042627 172 ELQEL 176 (237)
Q Consensus 172 e~~~l 176 (237)
-.+.|
T Consensus 103 ~~~~l 107 (134)
T cd04779 103 IASQT 107 (134)
T ss_pred HHHHH
Confidence 44444
No 95
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=44.50 E-value=49 Score=26.34 Aligned_cols=35 Identities=26% Similarity=0.182 Sum_probs=29.7
Q ss_pred HHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHh
Q 042627 146 KQNEVDCEFLKKCCESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 146 kq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~ 180 (237)
-++-.+...||+....+.+||..|+-|+..||...
T Consensus 18 ~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL 52 (114)
T COG4467 18 GVLLAELGGLKQHLGSLVEENTALRLENEKLRERL 52 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHh
Confidence 34556677889999999999999999999999864
No 96
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=44.49 E-value=49 Score=26.40 Aligned_cols=32 Identities=25% Similarity=0.335 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHh
Q 042627 149 EVDCEFLKKCCESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 149 ~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~ 180 (237)
+++-+.||.++..|.+.|.+|++|+.=|+...
T Consensus 66 REEVe~Lk~qI~eL~er~~~Le~EN~lLk~~~ 97 (123)
T KOG4797|consen 66 REEVEVLKEQIRELEERNSALERENSLLKTLA 97 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 45678899999999999999999999999864
No 97
>PF11365 DUF3166: Protein of unknown function (DUF3166); InterPro: IPR021507 This eukaryotic family of proteins has no known function.
Probab=43.05 E-value=56 Score=25.37 Aligned_cols=31 Identities=39% Similarity=0.590 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhHhhHHHHHHHHHHHHHHHHH
Q 042627 149 EVDCEFLKKCCESLTDENKRLKKELQELQSA 179 (237)
Q Consensus 149 ~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~ 179 (237)
+++-+.|++....+..+|++|..|+.+++..
T Consensus 14 EEEa~LlRRkl~ele~eN~~l~~EL~kyk~~ 44 (96)
T PF11365_consen 14 EEEAELLRRKLSELEDENKQLTEELNKYKSK 44 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5677889999999999999999999999984
No 98
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=42.52 E-value=1.9e+02 Score=30.76 Aligned_cols=31 Identities=19% Similarity=0.198 Sum_probs=12.9
Q ss_pred HHhHHHHHHHHHHhHhhHHHHHHHHHHHHHH
Q 042627 146 KQNEVDCEFLKKCCESLTDENKRLKKELQEL 176 (237)
Q Consensus 146 kq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l 176 (237)
+..++.-..+.+.++..--..+..+.|++.+
T Consensus 470 eeseqkA~e~~kk~~ke~ta~qe~qael~k~ 500 (1102)
T KOG1924|consen 470 EESEQKAAELEKKFDKELTARQEAQAELQKH 500 (1102)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence 3334344445455544433333344444333
No 99
>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=41.37 E-value=1.5e+02 Score=22.86 Aligned_cols=73 Identities=11% Similarity=-0.018 Sum_probs=43.1
Q ss_pred CCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHH
Q 042627 93 KKLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKE 172 (237)
Q Consensus 93 ~Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e 172 (237)
....|+.+++..|... ...+.+|++-..|+..|....... .....-...|....+.+.++.+.|+.-
T Consensus 35 gyR~Y~~~~i~~l~~I-----------~~lr~~G~sl~eI~~~l~~~~~~~--~~~~~~~~~l~~~~~~l~~~i~~l~~~ 101 (123)
T cd04770 35 GYRLYGEADLARLRFI-----------RRAQALGFSLAEIRELLSLRDDGA--APCAEVRALLEEKLAEVEAKIAELQAL 101 (123)
T ss_pred CCccCCHHHHHHHHHH-----------HHHHHCCCCHHHHHHHHHhhhcCC--CCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3557899999888642 336788888888888886544310 001112344555555566666666555
Q ss_pred HHHHHH
Q 042627 173 LQELQS 178 (237)
Q Consensus 173 ~~~l~~ 178 (237)
.+.|..
T Consensus 102 ~~~l~~ 107 (123)
T cd04770 102 RAELAG 107 (123)
T ss_pred HHHHHH
Confidence 555554
No 100
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=41.29 E-value=90 Score=30.75 Aligned_cols=80 Identities=25% Similarity=0.339 Sum_probs=47.2
Q ss_pred CccCCHHHHHHHHHH-HhhCC-CCCH-H-HHHHHHhCCCCccchhhccchHHHHHHHHhHH---------------HHHH
Q 042627 94 KLRLTIEQSRLLEDS-FKLHT-TLNS-K-QALAEQLNLEPRQVEVWFQNRRARTKLKQNEV---------------DCEF 154 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~-F~~~~-~p~~-r-~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~---------------~~~~ 154 (237)
-.+++.+....|.+. |.... +|-. . +++- .+|+.=.+|+|.+--.++++. ++..
T Consensus 218 ~L~LteeEkrLL~kEG~slPs~lPLTKaEEriL-------KrvRRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqe 290 (472)
T KOG0709|consen 218 PLVLTEEEKRLLTKEGYSLPSKLPLTKAEERIL-------KRVRRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQE 290 (472)
T ss_pred ceeccHHHHHHHHhccCcCcccCCchHHHHHHH-------HHHHHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHH
Confidence 346788887777664 32222 2322 2 2222 245555567776543223322 3344
Q ss_pred HHHHhHhhHHHHHHHHHHHHHHHHHh
Q 042627 155 LKKCCESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 155 Lk~~~~~l~~en~~l~~e~~~l~~~~ 180 (237)
|++..+.|..+|+.|..+++.|.+..
T Consensus 291 L~kkV~~Le~~N~sLl~qL~klQt~v 316 (472)
T KOG0709|consen 291 LQKKVEELELSNRSLLAQLKKLQTLV 316 (472)
T ss_pred HHHHHHHHhhccHHHHHHHHHHHHHH
Confidence 77788888888888888888888754
No 101
>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=41.07 E-value=74 Score=23.75 Aligned_cols=29 Identities=34% Similarity=0.501 Sum_probs=22.0
Q ss_pred HHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 150 VDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 150 ~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
.+.+.++++.+.|.+||.+|+-|...|.+
T Consensus 42 ~~l~~l~~~~~~l~~e~~~L~lE~~~l~~ 70 (97)
T PF04999_consen 42 YELQQLEKEIDQLQEENERLRLEIATLSS 70 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 34666777777888888888888887775
No 102
>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=40.89 E-value=13 Score=23.64 Aligned_cols=23 Identities=13% Similarity=0.121 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCCccchhhccchH
Q 042627 118 KQALAEQLNLEPRQVEVWFQNRR 140 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQNRR 140 (237)
..++|+.+|++++.|+.|.+.-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 35789999999999999976543
No 103
>PF13518 HTH_28: Helix-turn-helix domain
Probab=40.28 E-value=15 Score=23.70 Aligned_cols=21 Identities=14% Similarity=0.431 Sum_probs=18.7
Q ss_pred HHHHHHHhCCCCccchhhccc
Q 042627 118 KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQN 138 (237)
..++|.++|++..+|..|.+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHH
Confidence 778999999999999999853
No 104
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=39.88 E-value=55 Score=25.45 Aligned_cols=39 Identities=18% Similarity=0.104 Sum_probs=30.2
Q ss_pred hhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHH
Q 042627 134 VWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKE 172 (237)
Q Consensus 134 vWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e 172 (237)
-|+..+..+.+..+.+.+++.++..++.|..|.+.|+..
T Consensus 25 G~~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~ 63 (105)
T PRK00888 25 GILDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGG 63 (105)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCc
Confidence 455666666677777888888888888999988888773
No 105
>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=39.50 E-value=53 Score=32.41 Aligned_cols=16 Identities=50% Similarity=0.557 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHHHHHH
Q 042627 163 TDENKRLKKELQELQS 178 (237)
Q Consensus 163 ~~en~~l~~e~~~l~~ 178 (237)
.+|.++|+.++++++.
T Consensus 115 ~~~~~ql~~~~~~~~~ 130 (472)
T TIGR03752 115 TKEIEQLKSERQQLQG 130 (472)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3344444444444433
No 106
>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=39.11 E-value=37 Score=22.27 Aligned_cols=38 Identities=16% Similarity=0.142 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccc
Q 042627 97 LTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 97 ~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQN 138 (237)
+++.+..++...|-.. . ..++|..+|+++..|+.|.+.
T Consensus 11 L~~~~r~i~~l~~~~g----~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG----MSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp S-HHHHHHHHHHHTS-------HHHHHHHCTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC----cCHHHHHHHHCcCHHHHHHHHHH
Confidence 4555655655544322 2 789999999999999999863
No 107
>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=38.79 E-value=58 Score=24.97 Aligned_cols=30 Identities=30% Similarity=0.398 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 149 EVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 149 ~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
....+.|+..++.+..+|..|..++++++.
T Consensus 79 ~~~~~~L~~~l~~l~~eN~~L~~~i~~~r~ 108 (109)
T PF03980_consen 79 KKEREQLNARLQELEEENEALAEEIQEQRK 108 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 345567888999999999999999988764
No 108
>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=38.35 E-value=1.1e+02 Score=23.28 Aligned_cols=33 Identities=12% Similarity=0.019 Sum_probs=25.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccch
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNR 139 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNR 139 (237)
+|+..++..|. ....++.+|++-.+|+.+|...
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 58888887775 3445888999999999999753
No 109
>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=37.84 E-value=97 Score=25.41 Aligned_cols=45 Identities=22% Similarity=0.133 Sum_probs=32.2
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHH
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRAR 142 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak 142 (237)
.+.++..|..+|.-.++--. ..++|..+|++...|+.|-+.-|.+
T Consensus 4 ~~~Lte~qr~VL~Lr~~GlT----q~EIAe~LgiS~stV~~~e~ra~kk 48 (137)
T TIGR00721 4 KTFLTERQIKVLELREKGLS----QKEIAKELKTTRANVSAIEKRAMEN 48 (137)
T ss_pred cCCCCHHHHHHHHHHHcCCC----HHHHHHHHCcCHHHHHHHHHhHHHH
Confidence 45688999998877422111 8899999999999888876533333
No 110
>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=37.40 E-value=15 Score=27.09 Aligned_cols=34 Identities=18% Similarity=0.202 Sum_probs=24.9
Q ss_pred HHHHhhCCCCCH--HHHHHHHhCCCCccchhhccch
Q 042627 106 EDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNR 139 (237)
Q Consensus 106 E~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNR 139 (237)
+..|....+... ..+||..+|+++..|+.|+.+.
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 334544444333 8999999999999999998643
No 111
>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=37.36 E-value=1.8e+02 Score=21.97 Aligned_cols=65 Identities=17% Similarity=0.135 Sum_probs=40.9
Q ss_pred CCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHH
Q 042627 93 KKLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKE 172 (237)
Q Consensus 93 ~Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e 172 (237)
....|+.+++..|...- ..+.+|++-..|+..+.... ..+.+..+.+.+.++...|+..
T Consensus 35 g~R~Y~~~dl~~l~~I~-----------~l~~~G~~l~ei~~~~~~~~----------~~~~l~~~~~~l~~~i~~l~~~ 93 (102)
T cd04775 35 NYRLYSEADLSRLEKIV-----------FLQAGGLPLEEIAGCLAQPH----------VQAILEERLQSLNREIQRLRQQ 93 (102)
T ss_pred CCeeeCHHHHHHHHHHH-----------HHHHCCCCHHHHHHHHcCCc----------HHHHHHHHHHHHHHHHHHHHHH
Confidence 35578999998886532 24667777777777665432 1244555556666666666666
Q ss_pred HHHHHH
Q 042627 173 LQELQS 178 (237)
Q Consensus 173 ~~~l~~ 178 (237)
...|..
T Consensus 94 ~~~l~~ 99 (102)
T cd04775 94 QQVLAA 99 (102)
T ss_pred HHHHHH
Confidence 655554
No 112
>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=37.19 E-value=1.9e+02 Score=22.74 Aligned_cols=71 Identities=13% Similarity=0.032 Sum_probs=40.0
Q ss_pred CCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHH
Q 042627 93 KKLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKE 172 (237)
Q Consensus 93 ~Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e 172 (237)
....|+..++..|.. ....+.+|++-..|+.+|..... .....-.+.+....+.+.++...|+.-
T Consensus 34 g~R~Y~~~~l~~l~~-----------I~~l~~~G~sl~eI~~~l~~~~~----~~~~~~~~~l~~~~~~l~~~i~~L~~~ 98 (124)
T TIGR02051 34 GYRRYPEETVKRLRF-----------IKRAQELGFSLEEIGGLLGLVDG----THCREMYELASRKLKSVQAKMADLLRI 98 (124)
T ss_pred CCEeECHHHHHHHHH-----------HHHHHHCCCCHHHHHHHHhcccC----CCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355688998888853 23367888888888888865432 001111233444444555555555554
Q ss_pred HHHHHH
Q 042627 173 LQELQS 178 (237)
Q Consensus 173 ~~~l~~ 178 (237)
...|..
T Consensus 99 ~~~L~~ 104 (124)
T TIGR02051 99 ERLLEE 104 (124)
T ss_pred HHHHHH
Confidence 444444
No 113
>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=37.00 E-value=70 Score=24.35 Aligned_cols=37 Identities=8% Similarity=-0.056 Sum_probs=25.7
Q ss_pred CCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccch
Q 042627 93 KKLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNR 139 (237)
Q Consensus 93 ~Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNR 139 (237)
.+..|+.+++..|... ..|.+.+|++-..|+.++.+.
T Consensus 35 g~R~Yt~~di~~l~~I----------~~llr~~G~~l~~i~~~l~~~ 71 (99)
T cd04765 35 GRRYYRPKDVELLLLI----------KHLLYEKGYTIEGAKQALKED 71 (99)
T ss_pred CCeeeCHHHHHHHHHH----------HHHHHHCCCCHHHHHHHHHhc
Confidence 3557999999888642 334567788888877777643
No 114
>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=37.00 E-value=80 Score=21.79 Aligned_cols=28 Identities=36% Similarity=0.445 Sum_probs=21.0
Q ss_pred HHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 151 DCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 151 ~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
+.......+..|..||..|+.++.-++.
T Consensus 23 d~~~a~~rl~~l~~EN~~Lr~eL~~~r~ 50 (52)
T PF12808_consen 23 DRSAARKRLSKLEGENRLLRAELERLRS 50 (52)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4445667777888999999888877664
No 115
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=36.93 E-value=51 Score=26.83 Aligned_cols=42 Identities=12% Similarity=0.290 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccchHHH
Q 042627 97 LTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQNRRAR 142 (237)
Q Consensus 97 ~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQNRRak 142 (237)
+++.+..++.-.|- -.. .+++|..+|+++..|+++...=|.+
T Consensus 130 L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 130 LEKDRAAAVRRAYL----EGLSYKELAERHDVPLNTMRTWLRRSLLK 172 (179)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCCChHHHHHHHHHHHHH
Confidence 45555555544441 222 8899999999999999987643333
No 116
>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=35.99 E-value=2e+02 Score=22.44 Aligned_cols=70 Identities=13% Similarity=0.081 Sum_probs=41.9
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHH
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKEL 173 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~ 173 (237)
...|+.+++..|.. ....+.+|++-.+|+-+|...... ....-.+.|+...+.+.++..+|+.-.
T Consensus 36 yR~Y~~~~l~~l~~-----------I~~lr~~G~sL~eI~~~l~~~~~~----~~~~~~~~l~~~~~~l~~~i~~L~~~~ 100 (126)
T cd04783 36 YRRYPEETVTRLRF-----------IKRAQELGFTLDEIAELLELDDGT----DCSEARELAEQKLAEVDEKIADLQRMR 100 (126)
T ss_pred CeecCHHHHHHHHH-----------HHHHHHcCCCHHHHHHHHhcccCC----CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55689999988863 334688899888888888654321 011112334445555555555555555
Q ss_pred HHHHH
Q 042627 174 QELQS 178 (237)
Q Consensus 174 ~~l~~ 178 (237)
..|..
T Consensus 101 ~~l~~ 105 (126)
T cd04783 101 ASLQE 105 (126)
T ss_pred HHHHH
Confidence 55554
No 117
>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=35.87 E-value=84 Score=26.64 Aligned_cols=27 Identities=44% Similarity=0.564 Sum_probs=12.2
Q ss_pred HHHHHHHHhHhhHHHHHHHHHHHHHHH
Q 042627 151 DCEFLKKCCESLTDENKRLKKELQELQ 177 (237)
Q Consensus 151 ~~~~Lk~~~~~l~~en~~l~~e~~~l~ 177 (237)
+++.|+.....|+.+|+.|++++..|.
T Consensus 105 e~~~l~~e~~~l~~~~e~Le~e~~~L~ 131 (161)
T TIGR02894 105 ENERLKNQNESLQKRNEELEKELEKLR 131 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444444444443
No 118
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=35.83 E-value=98 Score=21.73 Aligned_cols=21 Identities=29% Similarity=0.412 Sum_probs=15.7
Q ss_pred HhhHHHHHHHHHHHHHHHHHh
Q 042627 160 ESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 160 ~~l~~en~~l~~e~~~l~~~~ 180 (237)
..|..|++.|++||.+|+.+.
T Consensus 36 ~~l~~e~~~L~~qN~eLr~lL 56 (60)
T PF14775_consen 36 AALIQEKESLEQQNEELRSLL 56 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 346777888888888888754
No 119
>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=35.66 E-value=1.1e+02 Score=21.35 Aligned_cols=30 Identities=10% Similarity=0.329 Sum_probs=15.4
Q ss_pred HHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 149 EVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 149 ~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
+.+...+.....+++.||+.+..+++++..
T Consensus 6 En~~~~~~~~i~tvk~en~~i~~~ve~i~e 35 (55)
T PF05377_consen 6 ENELPRIESSINTVKKENEEISESVEKIEE 35 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444555555555555555555543
No 120
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=35.42 E-value=1.1e+02 Score=23.30 Aligned_cols=38 Identities=18% Similarity=0.396 Sum_probs=19.7
Q ss_pred hhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 134 VWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 134 vWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
+|||=++++.+ .+.|..+++.|..|....+.|+...+.
T Consensus 21 ~~~k~~ka~~~-------~~kL~~en~qlk~Ek~~~~~qvkn~~v 58 (87)
T PF10883_consen 21 LWWKVKKAKKQ-------NAKLQKENEQLKTEKAVAETQVKNAKV 58 (87)
T ss_pred HHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56655554444 455555555555555555555444443
No 121
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=35.16 E-value=1.1e+02 Score=22.93 Aligned_cols=13 Identities=31% Similarity=0.378 Sum_probs=4.7
Q ss_pred HHhHhhHHHHHHH
Q 042627 157 KCCESLTDENKRL 169 (237)
Q Consensus 157 ~~~~~l~~en~~l 169 (237)
-..+.|+++|..|
T Consensus 25 mEieELKekn~~L 37 (79)
T PRK15422 25 MEIEELKEKNNSL 37 (79)
T ss_pred HHHHHHHHHHHHH
Confidence 3333333333333
No 122
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=34.67 E-value=42 Score=26.42 Aligned_cols=41 Identities=20% Similarity=0.376 Sum_probs=35.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRA 141 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRa 141 (237)
.++..++..+.+.+... ....|+.||++..-|+-|=|+|+.
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 38888999988877655 688999999999999999998764
No 123
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=33.96 E-value=61 Score=27.36 Aligned_cols=38 Identities=21% Similarity=0.257 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccc
Q 042627 97 LTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 97 ~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQN 138 (237)
++..+..+|...|- -.. ..++|..+|++...|+++...
T Consensus 154 L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~l~R 192 (206)
T PRK12526 154 LPEAQQTVVKGVYF----QELSQEQLAQQLNVPLGTVKSRLRL 192 (206)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45555555554331 122 789999999999999888753
No 124
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=33.93 E-value=24 Score=22.89 Aligned_cols=39 Identities=18% Similarity=0.129 Sum_probs=19.9
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhc
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWF 136 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWF 136 (237)
...||.+|...++..+... . ..+||+.||.+..-|..|.
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G----~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG----MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ----------HHHHHHCS-------HHHHHHHTT--HHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC----CCHHHHHHHHCcCcHHHHHHH
Confidence 3568888888888887633 2 6789999999988777664
No 125
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=33.85 E-value=67 Score=20.43 Aligned_cols=35 Identities=14% Similarity=0.258 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhcc
Q 042627 98 TIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 98 t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQ 137 (237)
+..+..++...+. .. ..++|+.++++...|+.|..
T Consensus 2 ~~~e~~i~~~~~~-----~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLAE-----GKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHH
Confidence 4455555544331 23 78899999999999998875
No 126
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=33.73 E-value=85 Score=31.64 Aligned_cols=24 Identities=38% Similarity=0.462 Sum_probs=13.7
Q ss_pred HHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 155 LKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 155 Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
|+...+.|..||+.|++|+..|+.
T Consensus 307 Le~rLq~ll~Ene~Lk~ENatLk~ 330 (655)
T KOG4343|consen 307 LEARLQALLSENEQLKKENATLKR 330 (655)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHH
Confidence 455555555666666666655554
No 127
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.70 E-value=1.3e+02 Score=22.22 Aligned_cols=16 Identities=44% Similarity=0.551 Sum_probs=6.5
Q ss_pred HHhHhhHHHHHHHHHH
Q 042627 157 KCCESLTDENKRLKKE 172 (237)
Q Consensus 157 ~~~~~l~~en~~l~~e 172 (237)
...+.|..||++|+.|
T Consensus 46 ~~reaL~~eneqlk~e 61 (79)
T COG3074 46 HQREALERENEQLKEE 61 (79)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3333444444444433
No 128
>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=33.63 E-value=1.5e+02 Score=22.92 Aligned_cols=73 Identities=14% Similarity=0.089 Sum_probs=42.5
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHH
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKEL 173 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~ 173 (237)
...|+..++..|... ...+.+|++-.+|+..|....... ......-.+.|....+.+.++...|+...
T Consensus 35 yR~Y~~~d~~~l~~I-----------~~lr~~G~sl~eI~~~l~~~~~~~-~~~~~~~~~~l~~~~~~l~~~i~~l~~~~ 102 (116)
T cd04769 35 YRVYDAQHVECLRFI-----------KEARQLGFTLAELKAIFAGHEGRA-VLPWPHLQQALEDKKQEIRAQITELQQLL 102 (116)
T ss_pred ceeeCHHHHHHHHHH-----------HHHHHcCCCHHHHHHHHhccccCC-cCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456888888887642 236778888888888887655432 00111112345555555555555555555
Q ss_pred HHHHH
Q 042627 174 QELQS 178 (237)
Q Consensus 174 ~~l~~ 178 (237)
+.|..
T Consensus 103 ~~l~~ 107 (116)
T cd04769 103 ARLDA 107 (116)
T ss_pred HHHHH
Confidence 55544
No 129
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=33.48 E-value=55 Score=26.14 Aligned_cols=43 Identities=19% Similarity=0.038 Sum_probs=31.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccchHHHHH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
.+++.+..+|...|-. .. -.++|..+|++...|+.|.. |++.+
T Consensus 128 ~L~~~~r~vl~l~~~~----~~s~~eIA~~lgis~~tV~~~l~--ra~~~ 171 (182)
T PRK09652 128 SLPEELRTAITLREIE----GLSYEEIAEIMGCPIGTVRSRIF--RAREA 171 (182)
T ss_pred hCCHHHHHHHHHHHHc----CCCHHHHHHHHCCCHHHHHHHHH--HHHHH
Confidence 4677777777665421 22 78999999999999999886 44444
No 130
>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=33.46 E-value=61 Score=31.96 Aligned_cols=16 Identities=38% Similarity=0.698 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHHHh
Q 042627 165 ENKRLKKELQELQSAK 180 (237)
Q Consensus 165 en~~l~~e~~~l~~~~ 180 (237)
+..++++|.++|+...
T Consensus 110 ~~~~~~~~~~ql~~~~ 125 (472)
T TIGR03752 110 ETQELTKEIEQLKSER 125 (472)
T ss_pred hhHHHHHHHHHHHHHH
Confidence 3444444666665543
No 131
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=33.30 E-value=21 Score=24.53 Aligned_cols=21 Identities=14% Similarity=0.330 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCCccchhhccc
Q 042627 118 KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQN 138 (237)
..++|+.+|++.+.|+.|=+.
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 132
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.27 E-value=2.2e+02 Score=21.68 Aligned_cols=42 Identities=10% Similarity=0.098 Sum_probs=31.4
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCC-CCccchhhcc
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNL-EPRQVEVWFQ 137 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL-~~rQVkvWFQ 137 (237)
+.+|+.+....+-+.+....+ ...++|+++|+ ...++..|-+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~--sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD--TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc--cHHHHHHHhCCCChHHHHHHHH
Confidence 778999877666655554332 27889999996 9999998864
No 133
>PRK10884 SH3 domain-containing protein; Provisional
Probab=33.24 E-value=1.2e+02 Score=26.51 Aligned_cols=30 Identities=13% Similarity=0.051 Sum_probs=15.4
Q ss_pred HHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 149 EVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 149 ~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
+.+++.|+.+.+.++.|++.|+.+++.++.
T Consensus 138 ~~~n~~L~~~l~~~~~~~~~l~~~~~~~~~ 167 (206)
T PRK10884 138 KEENQKLKNQLIVAQKKVDAANLQLDDKQR 167 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444555555555555555555555543
No 134
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=33.06 E-value=63 Score=29.85 Aligned_cols=43 Identities=19% Similarity=0.192 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQN 138 (237)
.++..|..+|...|-...+-.. .++||..+|++...|+.+...
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~r 305 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVE 305 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 5788888888888754444444 899999999999999988753
No 135
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=32.93 E-value=85 Score=23.03 Aligned_cols=44 Identities=30% Similarity=0.315 Sum_probs=19.0
Q ss_pred chhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 132 VEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 132 VkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
++|.|-..|... ......+.+-+++-.|..+...|++++++++.
T Consensus 21 LrI~fLee~l~~---~~~~~~~~~~keNieLKve~~~L~~el~~~~~ 64 (75)
T PF07989_consen 21 LRIYFLEERLQK---LGPESIEELLKENIELKVEVESLKRELQEKKK 64 (75)
T ss_pred HHHHHHHHHHHh---cccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456665554441 11222222333333355555555555555443
No 136
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=32.87 E-value=63 Score=26.86 Aligned_cols=39 Identities=18% Similarity=0.134 Sum_probs=27.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQN 138 (237)
.++..+..+|...|-.. . -.++|..||++...|+++...
T Consensus 142 ~L~~~~r~vl~l~~~~~----~s~~EIA~~Lgis~~tVk~~l~r 181 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG----LTYREVAERLAVPLGTVKTRMRD 181 (194)
T ss_pred hCCHHHHHHHHHHHHcC----CCHHHHHHHhCCChHhHHHHHHH
Confidence 46666666665544221 2 789999999999999988753
No 137
>PF14662 CCDC155: Coiled-coil region of CCDC155
Probab=32.76 E-value=1.2e+02 Score=26.54 Aligned_cols=43 Identities=28% Similarity=0.293 Sum_probs=31.1
Q ss_pred cchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHH
Q 042627 137 QNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQSA 179 (237)
Q Consensus 137 QNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~ 179 (237)
+||+.-...++.+.+...|-...++|.+||.++..+...++..
T Consensus 82 ~~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl~~e~~~lk~~ 124 (193)
T PF14662_consen 82 ENRSLLAQARQLEKEQQSLVAEIETLQEENGKLLAERDGLKKR 124 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhHHHH
Confidence 4566666667777777788888888888888777776666653
No 138
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=32.72 E-value=1e+02 Score=27.37 Aligned_cols=32 Identities=38% Similarity=0.437 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHh
Q 042627 149 EVDCEFLKKCCESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 149 ~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~ 180 (237)
+.+...|+++.+.+..|-++|..+.+.|+..-
T Consensus 178 ~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i 209 (216)
T KOG1962|consen 178 QKKVDALKKQSEGLQDEYDRLLEEYSKLQEQI 209 (216)
T ss_pred HHHHHHHHHHHHHcccHHHHHHHHHHHHHHHH
Confidence 44556677777777777777777777777643
No 139
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=32.61 E-value=82 Score=31.76 Aligned_cols=31 Identities=39% Similarity=0.415 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhHhhHHHHHHHHHHHHHHHHH
Q 042627 149 EVDCEFLKKCCESLTDENKRLKKELQELQSA 179 (237)
Q Consensus 149 ~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~ 179 (237)
+....+|-++++.|+.||..|++++..|...
T Consensus 308 e~rLq~ll~Ene~Lk~ENatLk~qL~~l~~E 338 (655)
T KOG4343|consen 308 EARLQALLSENEQLKKENATLKRQLDELVSE 338 (655)
T ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHhhc
Confidence 5667778889999999999999999888774
No 140
>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=32.59 E-value=62 Score=24.39 Aligned_cols=43 Identities=16% Similarity=0.209 Sum_probs=28.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccchHHH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQNRRAR 142 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQNRRak 142 (237)
.+++.+..++...|-. .. ..++|..+|+++..|+.|...-+.+
T Consensus 110 ~L~~~~~~ii~~~~~~----g~s~~eIA~~l~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GLSYKEIAEILGISVGTVKRRLKRARKK 153 (158)
T ss_pred hCCHHHHHHHhhHHhc----CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 3456666665544321 22 7899999999999999887643333
No 141
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.25 E-value=1.1e+02 Score=22.50 Aligned_cols=17 Identities=35% Similarity=0.507 Sum_probs=6.7
Q ss_pred HhHhhHHHHHHHHHHHH
Q 042627 158 CCESLTDENKRLKKELQ 174 (237)
Q Consensus 158 ~~~~l~~en~~l~~e~~ 174 (237)
..+.|.++|..|..|++
T Consensus 26 EieELKEknn~l~~e~q 42 (79)
T COG3074 26 EIEELKEKNNSLSQEVQ 42 (79)
T ss_pred HHHHHHHHhhHhHHHHH
Confidence 33444444443333333
No 142
>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=32.23 E-value=1.5e+02 Score=21.81 Aligned_cols=33 Identities=18% Similarity=0.179 Sum_probs=21.6
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhc
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWF 136 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWF 136 (237)
...|+..++..|... ..|...+|++...|+.-+
T Consensus 36 ~R~y~~~dv~~l~~i----------~~L~~d~g~~l~~i~~~l 68 (91)
T cd04766 36 TRRYSERDIERLRRI----------QRLTQELGVNLAGVKRIL 68 (91)
T ss_pred CeeECHHHHHHHHHH----------HHHHHHcCCCHHHHHHHH
Confidence 446899999888653 344555777776665444
No 143
>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=32.23 E-value=67 Score=30.49 Aligned_cols=25 Identities=36% Similarity=0.434 Sum_probs=11.8
Q ss_pred HHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 154 FLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 154 ~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
.|+.+++.|+.||..|+.++.+|.+
T Consensus 36 aLr~EN~~LKkEN~~Lk~eVerLE~ 60 (420)
T PF07407_consen 36 ALRMENHSLKKENNDLKIEVERLEN 60 (420)
T ss_pred hHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444444444443
No 144
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=31.57 E-value=2.1e+02 Score=21.83 Aligned_cols=17 Identities=47% Similarity=0.546 Sum_probs=7.2
Q ss_pred HHHhHhhHHHHHHHHHH
Q 042627 156 KKCCESLTDENKRLKKE 172 (237)
Q Consensus 156 k~~~~~l~~en~~l~~e 172 (237)
+++++.|..||++|+.|
T Consensus 29 ~~~~~kL~~en~qlk~E 45 (87)
T PF10883_consen 29 KKQNAKLQKENEQLKTE 45 (87)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33344444444444443
No 145
>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=31.55 E-value=97 Score=32.04 Aligned_cols=37 Identities=27% Similarity=0.388 Sum_probs=22.5
Q ss_pred HHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 142 RTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 142 k~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
|.|+++.+.|+..|+.......++...|+.|+++|+.
T Consensus 544 r~r~~~lE~E~~~lr~elk~kee~~~~~e~~~~~lr~ 580 (697)
T PF09726_consen 544 RQRRRQLESELKKLRRELKQKEEQIRELESELQELRK 580 (697)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455666666777766666666666666666555544
No 146
>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=31.54 E-value=2.4e+02 Score=22.26 Aligned_cols=73 Identities=10% Similarity=0.068 Sum_probs=42.8
Q ss_pred CCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHH
Q 042627 93 KKLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKE 172 (237)
Q Consensus 93 ~Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e 172 (237)
....|+.+++..|.. ....+.+|++-.+|+-.|.....-.. ....-.+.|+...+.+..+...|+..
T Consensus 35 gyR~Y~~~~l~~l~~-----------I~~lr~lG~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~L~~~ 101 (127)
T TIGR02047 35 NYRVYTVGHVERLAF-----------IRNCRTLDMSLAEIRQLLRYQDKPEK--SCSDVNALLDEHISHVRARIIKLQAL 101 (127)
T ss_pred CCCcCCHHHHHHHHH-----------HHHHHHcCCCHHHHHHHHHhhhCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355789999888864 23367888888888887753211100 00112334555666666666666665
Q ss_pred HHHHHH
Q 042627 173 LQELQS 178 (237)
Q Consensus 173 ~~~l~~ 178 (237)
...|..
T Consensus 102 ~~~L~~ 107 (127)
T TIGR02047 102 IEQLVD 107 (127)
T ss_pred HHHHHH
Confidence 555554
No 147
>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=31.34 E-value=48 Score=21.42 Aligned_cols=38 Identities=18% Similarity=0.249 Sum_probs=26.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWF 136 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWF 136 (237)
.++.++...+...+... ....++|+.+|++...|.-++
T Consensus 5 ~~~~~~~~~i~~l~~~G---~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG---MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-----HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC---CCHHHHHHHHCcCHHHHHHHH
Confidence 46776777777777654 128899999999998877655
No 148
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=30.94 E-value=1.7e+02 Score=20.53 Aligned_cols=48 Identities=19% Similarity=0.261 Sum_probs=29.2
Q ss_pred CCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHH
Q 042627 128 EPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQE 175 (237)
Q Consensus 128 ~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~ 175 (237)
++..+++|=.=-..-.|--..-.+...|..+.+.|+.+|..|+.-+++
T Consensus 11 p~~~~~~W~~L~~~l~rY~~vL~~R~~l~~e~~~L~~qN~eLr~lLkq 58 (60)
T PF14775_consen 11 PDEKIRLWDALENFLKRYNKVLLDRAALIQEKESLEQQNEELRSLLKQ 58 (60)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455566664333333333344455566777888899999888876554
No 149
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=30.93 E-value=1.1e+02 Score=22.68 Aligned_cols=36 Identities=33% Similarity=0.541 Sum_probs=23.3
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCchhhccccCcCCCCCCCCC
Q 042627 161 SLTDENKRLKKELQELQSAKAGASSPLFIQLQKAATCPSCEKIM 204 (237)
Q Consensus 161 ~l~~en~~l~~e~~~l~~~~~~~~~~~~~~~~~~~~CpsC~~~~ 204 (237)
.++.++.+++.++..++.. +..+...+.|+.|+..=
T Consensus 53 l~~~~~~~~~~~l~~~~~~--------~v~i~~~~~C~vC~k~l 88 (109)
T PF10367_consen 53 LLKSENLQLKYELVKLRSR--------SVVITESTKCSVCGKPL 88 (109)
T ss_pred HHHhHHHHHHHHHHhhcCc--------eEEECCCCCccCcCCcC
Confidence 3455666666665554443 34566778899999865
No 150
>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=30.74 E-value=47 Score=31.48 Aligned_cols=25 Identities=32% Similarity=0.291 Sum_probs=16.2
Q ss_pred hHHHHHHHHHHhHhhHHHHHHHHHH
Q 042627 148 NEVDCEFLKKCCESLTDENKRLKKE 172 (237)
Q Consensus 148 ~~~~~~~Lk~~~~~l~~en~~l~~e 172 (237)
.++|+..||++++.|+.|-.+|+.+
T Consensus 37 Lr~EN~~LKkEN~~Lk~eVerLE~e 61 (420)
T PF07407_consen 37 LRMENHSLKKENNDLKIEVERLENE 61 (420)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 4556667777777777766666444
No 151
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=30.53 E-value=61 Score=25.48 Aligned_cols=36 Identities=8% Similarity=0.070 Sum_probs=25.3
Q ss_pred HHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccc
Q 042627 103 RLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 103 ~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQN 138 (237)
..+..+...+..-.. ..+||..+|++++.+..+|+.
T Consensus 12 ~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 12 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 334444444433334 899999999999999999964
No 152
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=30.48 E-value=93 Score=27.70 Aligned_cols=21 Identities=33% Similarity=0.292 Sum_probs=8.7
Q ss_pred HHHHHhHhhHHHHHHHHHHHH
Q 042627 154 FLKKCCESLTDENKRLKKELQ 174 (237)
Q Consensus 154 ~Lk~~~~~l~~en~~l~~e~~ 174 (237)
.++++++.|++|+.+|+.++.
T Consensus 73 ~l~~en~~L~~e~~~l~~~~~ 93 (276)
T PRK13922 73 DLREENEELKKELLELESRLQ 93 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444444444
No 153
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=30.33 E-value=1.1e+02 Score=27.35 Aligned_cols=39 Identities=26% Similarity=0.365 Sum_probs=31.2
Q ss_pred hHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHH
Q 042627 139 RRARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQ 177 (237)
Q Consensus 139 RRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~ 177 (237)
+|++.-.+..+.......+..+.|..|+..|++++.+|.
T Consensus 101 ~kA~~~i~~l~~~~~~~~~~~e~l~~e~~~l~~rl~ql~ 139 (232)
T KOG2483|consen 101 DKALEHIQSLERKSATQQQDIEDLSRENRKLKARLEQLS 139 (232)
T ss_pred hhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 466666666777777777888999999999999998877
No 154
>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=30.32 E-value=71 Score=25.16 Aligned_cols=38 Identities=29% Similarity=0.245 Sum_probs=26.6
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhcc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQ 137 (237)
.+++.+..++...|- ... ..++|..+|++...|+++..
T Consensus 111 ~L~~~~r~v~~l~~~----~g~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 111 KLPERQRELLQLRYQ----RGVSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred HCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 356666666655332 122 78999999999999998764
No 155
>PF04618 HD-ZIP_N: HD-ZIP protein N terminus; InterPro: IPR006712 Homeodomain leucine zipper (HDZip) genes encode putative transcription factors that are unique to plants. This observation suggests that homeobox-leucine zipper genes evolved after the divergence of plants and animals, perhaps to mediate specific regulatory events []. This domain is the N-terminal of plant homeobox-leucine zipper proteins. Its function is unknown.; GO: 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=30.27 E-value=2.8e+02 Score=22.02 Aligned_cols=18 Identities=33% Similarity=0.588 Sum_probs=8.3
Q ss_pred CCcccccccccccccccCC
Q 042627 1 MAAAEECNTGLCLGLGVGE 19 (237)
Q Consensus 1 ~~~~~~~~~gl~lglg~~~ 19 (237)
|+..|. +-||+|+||++.
T Consensus 1 m~~~~d-~LGLsLSLg~~~ 18 (111)
T PF04618_consen 1 MMEKKD-GLGLSLSLGFAG 18 (111)
T ss_pred CCCCCC-cceeeeeccCCC
Confidence 555322 344544555544
No 156
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=30.15 E-value=70 Score=25.95 Aligned_cols=39 Identities=13% Similarity=0.136 Sum_probs=27.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQN 138 (237)
.+++.+..++...|-. .. -.++|..+|+++..|+++++.
T Consensus 136 ~L~~~~r~v~~l~~~~----g~s~~eIA~~lgis~~~v~~~l~R 175 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME----DLSLKEISEILDLPVGTVKTRIHR 175 (187)
T ss_pred hCCHHHhHHhhhHHhc----CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4555555555543321 22 789999999999999998853
No 157
>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=30.14 E-value=2e+02 Score=20.36 Aligned_cols=24 Identities=46% Similarity=0.572 Sum_probs=14.6
Q ss_pred HHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 155 LKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 155 Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
....+..|..+...|++++.++++
T Consensus 37 aE~rn~eL~~ei~~L~~e~ee~r~ 60 (61)
T PF08826_consen 37 AEKRNRELEQEIERLKKEMEELRS 60 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhc
Confidence 344555667777777777766654
No 158
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=29.68 E-value=1.3e+02 Score=22.61 Aligned_cols=15 Identities=40% Similarity=0.501 Sum_probs=7.2
Q ss_pred hHhhHHHHHHHHHHH
Q 042627 159 CESLTDENKRLKKEL 173 (237)
Q Consensus 159 ~~~l~~en~~l~~e~ 173 (237)
.+.|..||.+|+.|.
T Consensus 48 r~~L~~en~qLk~E~ 62 (79)
T PRK15422 48 REELERENNHLKEQQ 62 (79)
T ss_pred HHHHHHHHHHHHHHH
Confidence 334455555555543
No 159
>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=29.65 E-value=1.7e+02 Score=26.31 Aligned_cols=11 Identities=18% Similarity=0.712 Sum_probs=8.6
Q ss_pred Cccchhhccch
Q 042627 129 PRQVEVWFQNR 139 (237)
Q Consensus 129 ~rQVkvWFQNR 139 (237)
|.+|+-||.+-
T Consensus 10 PqRIQEw~~~p 20 (236)
T PF12269_consen 10 PQRIQEWQLSP 20 (236)
T ss_pred hHHHHHhcCCC
Confidence 77888998763
No 160
>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=29.65 E-value=1.7e+02 Score=24.76 Aligned_cols=33 Identities=24% Similarity=0.339 Sum_probs=20.0
Q ss_pred HHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 146 KQNEVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 146 kq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
+..+.+...|+..++.|..|+..|++++..+..
T Consensus 107 ~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~e 139 (161)
T TIGR02894 107 ERLKNQNESLQKRNEELEKELEKLRQRLSTIEE 139 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555566666666677777666666555543
No 161
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=29.16 E-value=72 Score=25.03 Aligned_cols=39 Identities=13% Similarity=0.166 Sum_probs=27.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQN 138 (237)
.+++.+..++...|-. .. ..++|..+|++...|+.|...
T Consensus 106 ~L~~~~r~ii~l~~~~----~~s~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 106 VLDEKEKYIIFERFFV----GKTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred hCCHHHHHHHHHHHhc----CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4566666666544422 12 789999999999999998753
No 162
>PRK10884 SH3 domain-containing protein; Provisional
Probab=29.02 E-value=1.6e+02 Score=25.63 Aligned_cols=24 Identities=17% Similarity=0.156 Sum_probs=12.6
Q ss_pred HHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 155 LKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 155 Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
|+.+++.|.+|...++.+++.|.+
T Consensus 137 L~~~n~~L~~~l~~~~~~~~~l~~ 160 (206)
T PRK10884 137 LKEENQKLKNQLIVAQKKVDAANL 160 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555555555555555555444
No 163
>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=28.85 E-value=1.2e+02 Score=24.09 Aligned_cols=26 Identities=35% Similarity=0.363 Sum_probs=16.1
Q ss_pred HHHHHhHhhHHHHHHHHHHHHHHHHH
Q 042627 154 FLKKCCESLTDENKRLKKELQELQSA 179 (237)
Q Consensus 154 ~Lk~~~~~l~~en~~l~~e~~~l~~~ 179 (237)
.||+.+..|.+||..|+-+++-|...
T Consensus 76 rlkkk~~~LeEENNlLklKievLLDM 101 (108)
T cd07429 76 RLKKKNQQLEEENNLLKLKIEVLLDM 101 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555677777777776666653
No 164
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=28.66 E-value=86 Score=25.55 Aligned_cols=45 Identities=16% Similarity=0.108 Sum_probs=30.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccchHHHHH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
.++..+..++...|-. .. -.+||..||++...|+.++..=|.+.|
T Consensus 131 ~L~~~~r~v~~l~~~~----g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 131 TLPPRQRDVVQSISVE----GASIKETAAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred hCCHHHHHHHHHHHHc----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3555565566554332 12 789999999999999998864444443
No 165
>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=28.57 E-value=88 Score=24.29 Aligned_cols=38 Identities=18% Similarity=0.177 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccc
Q 042627 97 LTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 97 ~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQN 138 (237)
++..+..+|.-.|- ... ..++|..+|+++..|+.+...
T Consensus 114 L~~~~r~il~l~~~----~~~~~~eIA~~lgis~~tv~~~~~r 152 (161)
T TIGR02985 114 LPEQCRKIFILSRF----EGKSYKEIAEELGISVKTVEYHISK 152 (161)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45555555554332 122 788999999999999987753
No 166
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=28.55 E-value=1.1e+02 Score=24.19 Aligned_cols=25 Identities=28% Similarity=0.253 Sum_probs=20.3
Q ss_pred HHHHHHHhCCCCccchhhccchHHH
Q 042627 118 KQALAEQLNLEPRQVEVWFQNRRAR 142 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQNRRak 142 (237)
-.++|..+|+++..|++++..=|.+
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKW 149 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 6899999999999999988643333
No 167
>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=28.44 E-value=2.9e+02 Score=21.63 Aligned_cols=72 Identities=8% Similarity=0.009 Sum_probs=40.4
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHH
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKEL 173 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~ 173 (237)
...|+.+++..|... ...+.+|++-.+|+.+|.-..... .....-...|....+.+.++...|+.-.
T Consensus 36 ~R~Y~~~~l~~l~~I-----------~~lr~~G~sL~eI~~~l~~~~~~~--~~~~~~~~~l~~~~~~l~~~i~~L~~~~ 102 (126)
T cd04785 36 YRLYGAAHVERLRFI-----------RRARDLGFSLEEIRALLALSDRPD--RSCAEADAIARAHLADVRARIADLRRLE 102 (126)
T ss_pred ccccCHHHHHHHHHH-----------HHHHHCCCCHHHHHHHHhhhhcCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456899999888643 336778888888888775322110 0011112334455555555555555555
Q ss_pred HHHHH
Q 042627 174 QELQS 178 (237)
Q Consensus 174 ~~l~~ 178 (237)
..|..
T Consensus 103 ~~L~~ 107 (126)
T cd04785 103 AELKR 107 (126)
T ss_pred HHHHH
Confidence 55544
No 168
>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=28.34 E-value=32 Score=23.98 Aligned_cols=25 Identities=24% Similarity=0.377 Sum_probs=20.6
Q ss_pred HHHHHHHhCCCCccchhhccchHHHHH
Q 042627 118 KQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
..++|..||++.+.|..|-+ |.+|.
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~--r~~W~ 40 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD--RYKWD 40 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH--hhCcc
Confidence 78899999999999999964 44444
No 169
>PF13551 HTH_29: Winged helix-turn helix
Probab=28.07 E-value=1.2e+02 Score=22.27 Aligned_cols=46 Identities=24% Similarity=0.301 Sum_probs=28.8
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCC---H-HHHHHHHh-------CCCCccchhhcc
Q 042627 92 RKKLRLTIEQSRLLEDSFKLHTTLN---S-KQALAEQL-------NLEPRQVEVWFQ 137 (237)
Q Consensus 92 R~Rt~~t~~Ql~~LE~~F~~~~~p~---~-r~~LA~~L-------gL~~rQVkvWFQ 137 (237)
+.+..++.++...|.+.+...+... . ...|+..| .++...|..|++
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 3344489999999999999876321 1 33444332 355666666653
No 170
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=27.91 E-value=76 Score=25.22 Aligned_cols=38 Identities=16% Similarity=0.195 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccc
Q 042627 97 LTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 97 ~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQN 138 (237)
+++.+..++...|-. .. ..++|..+|+++..|+.|...
T Consensus 126 L~~~~r~i~~l~~~~----~~~~~eIA~~lgis~~tv~~~~~r 164 (179)
T PRK11924 126 LPVKQREVFLLRYVE----GLSYREIAEILGVPVGTVKSRLRR 164 (179)
T ss_pred CCHHHHHHhhHHHHc----CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 445555555444321 22 689999999999999999864
No 171
>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=27.82 E-value=2.8e+02 Score=21.15 Aligned_cols=67 Identities=15% Similarity=0.152 Sum_probs=42.9
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHH
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKEL 173 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~ 173 (237)
...|+..++..|... ...+.+|++-..|+-.|..... ..-...++...+.+.++...|+...
T Consensus 37 yR~Y~~~~i~~l~~I-----------~~lr~~G~sl~~i~~l~~~~~~-------~~~~~~l~~~~~~l~~~i~~l~~~~ 98 (108)
T cd01107 37 YRYYSAEQLERLNRI-----------KYLRDLGFPLEEIKEILDADND-------DELRKLLREKLAELEAEIEELQRIL 98 (108)
T ss_pred ccccCHHHHHHHHHH-----------HHHHHcCCCHHHHHHHHhcCCH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456888888888632 2357788888888888876553 2233445556666666666666655
Q ss_pred HHHHH
Q 042627 174 QELQS 178 (237)
Q Consensus 174 ~~l~~ 178 (237)
+.|..
T Consensus 99 ~~l~~ 103 (108)
T cd01107 99 RLLED 103 (108)
T ss_pred HHHHH
Confidence 55544
No 172
>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=27.60 E-value=1.4e+02 Score=20.81 Aligned_cols=22 Identities=41% Similarity=0.383 Sum_probs=11.1
Q ss_pred hHHHHHHHHHHhHhhHHHHHHH
Q 042627 148 NEVDCEFLKKCCESLTDENKRL 169 (237)
Q Consensus 148 ~~~~~~~Lk~~~~~l~~en~~l 169 (237)
.+.+.+.++...+.|..+.+.|
T Consensus 29 l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 29 LQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 3444444555555555555555
No 173
>PRK04217 hypothetical protein; Provisional
Probab=27.58 E-value=1e+02 Score=24.31 Aligned_cols=40 Identities=10% Similarity=-0.024 Sum_probs=29.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQN 138 (237)
.++.+|..++...|...- ...+||+.+|++...|+..+..
T Consensus 42 ~Lt~eereai~l~~~eGl---S~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL---TQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred cCCHHHHHHHHHHHHcCC---CHHHHHHHHCcCHHHHHHHHHH
Confidence 467788777766653321 1788999999999988877653
No 174
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=27.48 E-value=29 Score=24.05 Aligned_cols=21 Identities=14% Similarity=0.343 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCCccchhhccc
Q 042627 118 KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQN 138 (237)
..++|+.+|++++.|+.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999764
No 175
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=27.20 E-value=1.5e+02 Score=26.91 Aligned_cols=38 Identities=26% Similarity=0.433 Sum_probs=24.0
Q ss_pred HHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHh
Q 042627 140 RARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQSAK 180 (237)
Q Consensus 140 Rak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~ 180 (237)
|.|.++++.+ ..+......|..||+.|+.++.+|+...
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 3444444443 3344455667888888888888888743
No 176
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=27.15 E-value=3e+02 Score=21.78 Aligned_cols=73 Identities=14% Similarity=0.060 Sum_probs=41.0
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHH
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKEL 173 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~ 173 (237)
...|+.+++..|... ...+.+|++-.+|+.+|........ .....-.+.|....+.+.++...|+.-.
T Consensus 37 yR~Y~~~~l~~l~~I-----------~~lr~~G~sl~eI~~~l~~~~~~~~-~~~~~~~~~l~~~~~~l~~~i~~L~~~~ 104 (131)
T TIGR02043 37 YRLYTDEDQKRLRFI-----------LKAKELGFTLDEIKELLSIKLDATE-HSCAEVKAIVDAKLELVDEKINELTKIR 104 (131)
T ss_pred ceecCHHHHHHHHHH-----------HHHHHcCCCHHHHHHHHHhhccCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 557899998888643 2367788888888888864311000 0011223344555555555555555554
Q ss_pred HHHHH
Q 042627 174 QELQS 178 (237)
Q Consensus 174 ~~l~~ 178 (237)
..|..
T Consensus 105 ~~L~~ 109 (131)
T TIGR02043 105 RSLKK 109 (131)
T ss_pred HHHHH
Confidence 44444
No 177
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.99 E-value=77 Score=24.46 Aligned_cols=37 Identities=19% Similarity=0.246 Sum_probs=29.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQV 132 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQV 132 (237)
.++++|...-...|+.+--+.. .+++|..|++++-.|
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 3678888887888887777777 899999999887543
No 178
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=26.85 E-value=31 Score=23.83 Aligned_cols=21 Identities=10% Similarity=0.352 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCCccchhhccc
Q 042627 118 KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQN 138 (237)
..++|+.+|++++.|+.|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999764
No 179
>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=26.59 E-value=1.3e+02 Score=23.82 Aligned_cols=15 Identities=33% Similarity=0.594 Sum_probs=12.2
Q ss_pred ccchhhccchHHHHH
Q 042627 130 RQVEVWFQNRRARTK 144 (237)
Q Consensus 130 rQVkvWFQNRRak~K 144 (237)
||.+.||-.+|.--.
T Consensus 18 Rq~e~~FlqKr~~LS 32 (106)
T PF11594_consen 18 RQMEAFFLQKRFELS 32 (106)
T ss_pred HHHHHHHHHHHHHHH
Confidence 678999999888764
No 180
>PF06210 DUF1003: Protein of unknown function (DUF1003); InterPro: IPR010406 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=26.40 E-value=1.9e+02 Score=22.74 Aligned_cols=38 Identities=29% Similarity=0.395 Sum_probs=20.6
Q ss_pred cchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 137 QNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 137 QNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
|||-++.-+.+.+.+++. +.....|.+.|+.++.++..
T Consensus 57 QNRq~~~dr~ra~~D~~i----nl~ae~ei~~l~~~l~~l~~ 94 (108)
T PF06210_consen 57 QNRQAARDRLRAELDYQI----NLKAEQEIERLHRKLDALRE 94 (108)
T ss_pred hhHhHHHHHHHHHHHHHH----HHHhHHHHHHHHHHHHHHHH
Confidence 677665545555555554 22334555555555555554
No 181
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=26.30 E-value=31 Score=22.22 Aligned_cols=20 Identities=20% Similarity=0.468 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCCccchhhcc
Q 042627 118 KQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQ 137 (237)
..++|+.+|++...|..|.+
T Consensus 20 ~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 20 IREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 78999999999999999975
No 182
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=26.02 E-value=1.4e+02 Score=23.50 Aligned_cols=33 Identities=21% Similarity=0.268 Sum_probs=22.2
Q ss_pred HhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHH
Q 042627 147 QNEVDCEFLKKCCESLTDENKRLKKELQELQSA 179 (237)
Q Consensus 147 q~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~ 179 (237)
+...+.+.+++.++.|..++..|..|+..|+.-
T Consensus 54 ~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 54 QLQRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 344455566777777777777777777777653
No 183
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=25.95 E-value=65 Score=26.76 Aligned_cols=42 Identities=17% Similarity=0.178 Sum_probs=34.2
Q ss_pred HHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccchHHHH
Q 042627 102 SRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQNRRART 143 (237)
Q Consensus 102 l~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQNRRak~ 143 (237)
+....+.|.+..|... ..+||+..|++..-+-.+|.+|-.-.
T Consensus 17 l~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~~F~sKe~Ll 59 (213)
T PRK09975 17 IETAIAQFALRGVSNTTLNDIADAANVTRGAIYWHFENKTQLF 59 (213)
T ss_pred HHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHHHcCCHHHHH
Confidence 3344555778888887 99999999999999999999987643
No 184
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=25.89 E-value=80 Score=25.99 Aligned_cols=25 Identities=16% Similarity=0.229 Sum_probs=20.9
Q ss_pred HHHHHHHhCCCCccchhhccchHHHHH
Q 042627 118 KQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
..++|..+|++...|++|+. |++.+
T Consensus 160 ~~EIA~~lgis~~tV~~~l~--Ra~~~ 184 (194)
T PRK12519 160 QSEIAKRLGIPLGTVKARAR--QGLLK 184 (194)
T ss_pred HHHHHHHhCCCHHHHHHHHH--HHHHH
Confidence 78999999999999999985 44444
No 185
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.86 E-value=2.7e+02 Score=21.71 Aligned_cols=72 Identities=10% Similarity=0.011 Sum_probs=40.3
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHH
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKEL 173 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~ 173 (237)
...|+.+++..|.. ....+.+|++-.+|+..|........ ....-...|....+.+.++...|+.-.
T Consensus 36 yR~Y~~~~l~~l~~-----------I~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~L~~~~ 102 (127)
T cd04784 36 YRLYDEEHLERLLF-----------IRRCRSLDMSLDEIRTLLQLQDDPEA--SCAEVNALIDEHLAHVRARIAELQALE 102 (127)
T ss_pred CeecCHHHHHHHHH-----------HHHHHHcCCCHHHHHHHHHhhhcCCC--cHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45789999888863 33467788888888887764321100 011122344445555555555555544
Q ss_pred HHHHH
Q 042627 174 QELQS 178 (237)
Q Consensus 174 ~~l~~ 178 (237)
..|..
T Consensus 103 ~~L~~ 107 (127)
T cd04784 103 KQLQA 107 (127)
T ss_pred HHHHH
Confidence 44444
No 186
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=25.54 E-value=78 Score=27.34 Aligned_cols=47 Identities=17% Similarity=0.155 Sum_probs=38.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLK 146 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krk 146 (237)
.+|+.+.++|+-..+-.. ..++|..|+++++.|+.+..+=..|..-+
T Consensus 155 ~Lt~rE~~Vl~l~~~G~s----~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~ 201 (216)
T PRK10100 155 LLTHREKEILNKLRIGAS----NNEIARSLFISENTVKTHLYNLFKKIAVK 201 (216)
T ss_pred CCCHHHHHHHHHHHcCCC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 489999999987766322 78999999999999999998877776643
No 187
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=25.36 E-value=88 Score=25.61 Aligned_cols=37 Identities=11% Similarity=0.112 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHHH-hhCCCCCHHHHHHHHhCCCCccchhhcc
Q 042627 97 LTIEQSRLLEDSF-KLHTTLNSKQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 97 ~t~~Ql~~LE~~F-~~~~~p~~r~~LA~~LgL~~rQVkvWFQ 137 (237)
+++.+..++...| .... -.++|..+|++...|+.+..
T Consensus 129 L~~~~r~i~~l~~~~g~s----~~EIA~~lgis~~tV~~~l~ 166 (186)
T PRK05602 129 LPERQREAIVLQYYQGLS----NIEAAAVMDISVDALESLLA 166 (186)
T ss_pred CCHHHHHHhhHHHhcCCC----HHHHHHHhCcCHHHHHHHHH
Confidence 4555555554433 2111 78999999999999999875
No 188
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=25.33 E-value=88 Score=24.88 Aligned_cols=45 Identities=22% Similarity=0.245 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
.+|+.+..+|+-.+..- .+++||..++++.+.|++..++=|.|..
T Consensus 137 ~Lt~~E~~il~~l~~g~----~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQGM----AVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCCC----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 58888888887766431 2889999999999999988876665543
No 189
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=25.33 E-value=36 Score=21.58 Aligned_cols=18 Identities=22% Similarity=0.423 Sum_probs=14.9
Q ss_pred HHHHHHhCCCCccchhhc
Q 042627 119 QALAEQLNLEPRQVEVWF 136 (237)
Q Consensus 119 ~~LA~~LgL~~rQVkvWF 136 (237)
.++|+.+|++.+.|+.|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 478999999999999984
No 190
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=25.29 E-value=58 Score=34.09 Aligned_cols=59 Identities=19% Similarity=0.317 Sum_probs=42.4
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCH--HHHHHHHhCCCCccchhhccchHHHHHHHH
Q 042627 89 ISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147 (237)
Q Consensus 89 ~~rR~Rt~~t~~Ql~~LE~~F~~~~~p~~--r~~LA~~LgL~~rQVkvWFQNRRak~Krkq 147 (237)
...+.++....++-..|...|+.+-.+.. ...++..|...+..|+|||++|+..-+...
T Consensus 625 ~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~p 685 (1007)
T KOG3623|consen 625 RPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMP 685 (1007)
T ss_pred CCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCc
Confidence 34455666777777788888888776665 333344477888999999999998877544
No 191
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=25.19 E-value=1.6e+02 Score=27.75 Aligned_cols=13 Identities=15% Similarity=0.705 Sum_probs=10.6
Q ss_pred chhhccchHHHHH
Q 042627 132 VEVWFQNRRARTK 144 (237)
Q Consensus 132 VkvWFQNRRak~K 144 (237)
.+|||+|.|+..+
T Consensus 16 CKiWi~dN~~Sv~ 28 (336)
T KOG0150|consen 16 CKIWIKDNPASVR 28 (336)
T ss_pred hhhhhcCChHHHH
Confidence 5899999888754
No 192
>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=25.14 E-value=1.2e+02 Score=22.97 Aligned_cols=44 Identities=27% Similarity=0.314 Sum_probs=26.1
Q ss_pred ccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHH
Q 042627 130 RQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQ 174 (237)
Q Consensus 130 rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~ 174 (237)
.++..|...=|++. .+....+...|++.-..|.++|..|+.++.
T Consensus 56 ~~Le~aL~~VR~rK-~~~l~~~i~~l~~ke~~l~~en~~L~~~~~ 99 (100)
T PF01486_consen 56 QQLESALKRVRSRK-DQLLMEQIEELKKKERELEEENNQLRQKIE 99 (100)
T ss_pred HhhhhhHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34444443333332 234456667777777778888888877654
No 193
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.01 E-value=5e+02 Score=23.18 Aligned_cols=18 Identities=33% Similarity=0.464 Sum_probs=14.8
Q ss_pred CCHHHHHHHHHHHhhCCC
Q 042627 97 LTIEQSRLLEDSFKLHTT 114 (237)
Q Consensus 97 ~t~~Ql~~LE~~F~~~~~ 114 (237)
.|++....||.+|.+-+.
T Consensus 1 MtpeE~qlle~lf~rlk~ 18 (233)
T COG3416 1 MTPEEKQLLENLFHRLKK 18 (233)
T ss_pred CCHHHHHHHHHHHHHHhh
Confidence 378889999999998654
No 194
>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=24.86 E-value=60 Score=22.18 Aligned_cols=33 Identities=30% Similarity=0.416 Sum_probs=23.2
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchh
Q 042627 100 EQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEV 134 (237)
Q Consensus 100 ~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkv 134 (237)
.|+..|+-.|. ..+.+ ..+||..+|++.+.|+.
T Consensus 6 rq~~Ll~~L~~-~~~~~-~~ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWIT-LKELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHHH-HTSBB-HHHHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHHc-CCCCc-HHHHHHHHCCCHHHHHH
Confidence 56778887787 44333 56999999999977654
No 195
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=24.76 E-value=1.1e+02 Score=26.13 Aligned_cols=42 Identities=14% Similarity=0.260 Sum_probs=28.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhcc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQ 137 (237)
.+++.+..++.-.|-...+-.. -.++|..+|++...|+.+..
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~ 220 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3566666666665522112233 88999999999999988764
No 196
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=24.70 E-value=1.2e+02 Score=23.80 Aligned_cols=38 Identities=11% Similarity=0.022 Sum_probs=26.3
Q ss_pred cCCHHHHHHHHHHHh-hCCCCCHHHHHHHHhCCCCccchhhcc
Q 042627 96 RLTIEQSRLLEDSFK-LHTTLNSKQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~-~~~~p~~r~~LA~~LgL~~rQVkvWFQ 137 (237)
.++..+..++.-.|- .-. ..++|..||++...|++...
T Consensus 106 ~Lp~~~r~v~~l~~~~g~s----~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 106 KLPARQREAFLLRYWEDMD----VAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred hCCHHHHHHHHHHHHhcCC----HHHHHHHHCCCHHHHHHHHH
Confidence 355666666555432 221 78999999999999998765
No 197
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=24.67 E-value=58 Score=20.95 Aligned_cols=36 Identities=8% Similarity=0.090 Sum_probs=28.8
Q ss_pred HHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccchH
Q 042627 105 LEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQNRR 140 (237)
Q Consensus 105 LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQNRR 140 (237)
-.+.|.+..|-.. ...||+++|++..-+-..|.|+-
T Consensus 5 a~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 5 ALELFAEKGYEAVSIRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp HHHHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred HHHHHHHhCHHhCCHHHHHHHHccchhhHHHHcCCHH
Confidence 3455666666666 89999999999999999998753
No 198
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=24.25 E-value=1.1e+02 Score=32.30 Aligned_cols=18 Identities=22% Similarity=0.134 Sum_probs=13.7
Q ss_pred CCCCCCCCccCCHHHHHH
Q 042627 87 INISGRKKLRLTIEQSRL 104 (237)
Q Consensus 87 ~~~~rR~Rt~~t~~Ql~~ 104 (237)
++.+||.|.++..+|...
T Consensus 1291 g~~KKRGRK~LPpe~Ka~ 1308 (1463)
T PHA03308 1291 GGGKRRGRQRLPIRDRVY 1308 (1463)
T ss_pred CCccccCCCCCChHHhhh
Confidence 445677888999998766
No 199
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=24.24 E-value=1.1e+02 Score=22.83 Aligned_cols=12 Identities=58% Similarity=0.886 Sum_probs=4.5
Q ss_pred HHHHHHHHHHHH
Q 042627 163 TDENKRLKKELQ 174 (237)
Q Consensus 163 ~~en~~l~~e~~ 174 (237)
.+||.+|+.+++
T Consensus 6 ~eEn~~Lk~eiq 17 (76)
T PF07334_consen 6 QEENARLKEEIQ 17 (76)
T ss_pred HHHHHHHHHHHH
Confidence 333333333333
No 200
>PRK10651 transcriptional regulator NarL; Provisional
Probab=24.15 E-value=88 Score=24.95 Aligned_cols=46 Identities=20% Similarity=0.249 Sum_probs=36.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKL 145 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Kr 145 (237)
.+|+.+..+|+-..+.-. ..++|++++++.+.|++..++=|.|-..
T Consensus 155 ~Lt~rE~~vl~~l~~g~~----~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 155 QLTPRERDILKLIAQGLP----NKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred cCCHHHHHHHHHHHcCCC----HHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 489999988876553212 7888999999999999998877777653
No 201
>PRK10403 transcriptional regulator NarP; Provisional
Probab=24.11 E-value=88 Score=24.86 Aligned_cols=45 Identities=20% Similarity=0.233 Sum_probs=35.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
.+|..+..+|+....... ..+||+.++++++.|++..+|=|.|-.
T Consensus 153 ~Lt~~e~~vl~~~~~g~s----~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 153 VLTERELDVLHELAQGLS----NKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred cCCHHHHHHHHHHHCCCC----HHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 588888888876554311 889999999999999998877666654
No 202
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=24.10 E-value=39 Score=20.86 Aligned_cols=24 Identities=21% Similarity=0.501 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCCccchhhccchHH
Q 042627 118 KQALAEQLNLEPRQVEVWFQNRRA 141 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQNRRa 141 (237)
..++|+.+|++.+.|..|.++.+.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 367899999999999999876554
No 203
>PF11167 DUF2953: Protein of unknown function (DUF2953); InterPro: IPR021338 This family of proteins has no known function.
Probab=23.76 E-value=14 Score=24.86 Aligned_cols=18 Identities=22% Similarity=0.412 Sum_probs=14.4
Q ss_pred CCcccccccccccccccC
Q 042627 1 MAAAEECNTGLCLGLGVG 18 (237)
Q Consensus 1 ~~~~~~~~~gl~lglg~~ 18 (237)
+|++|.+.||++.|+-.+
T Consensus 3 ~G~~Daa~Tgi~~G~l~~ 20 (53)
T PF11167_consen 3 IGLGDAADTGILYGLLWA 20 (53)
T ss_pred eeccCHHHHHHHHHHHHH
Confidence 478999999998887554
No 204
>PF14645 Chibby: Chibby family
Probab=23.69 E-value=1.6e+02 Score=23.39 Aligned_cols=30 Identities=27% Similarity=0.304 Sum_probs=20.2
Q ss_pred HHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 149 EVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 149 ~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
..+...+++.+..|++||..|+-+++-|-+
T Consensus 70 ~~~~~~l~~~n~~L~EENN~Lklk~elLlD 99 (116)
T PF14645_consen 70 GEENQRLRKENQQLEEENNLLKLKIELLLD 99 (116)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555666677777777777777766655
No 205
>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=23.63 E-value=3.7e+02 Score=21.23 Aligned_cols=72 Identities=11% Similarity=0.015 Sum_probs=42.4
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHH
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKEL 173 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~ 173 (237)
...|+.+++..|.. ....+.+|++-.+|+-+|......... ...-.+.|+...+.+.++..+|+.-.
T Consensus 36 yR~Y~~~~~~~l~~-----------I~~lr~~G~sL~eI~~~l~~~~~~~~~--~~~~~~~l~~~~~~l~~~i~~l~~~~ 102 (133)
T cd04787 36 YRLYSEKDLSRLRF-----------ILSARQLGFSLKDIKEILSHADQGESP--CPMVRRLIEQRLAETERRIKELLKLR 102 (133)
T ss_pred eeeCCHHHHHHHHH-----------HHHHHHcCCCHHHHHHHHhhhccCCCc--HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44789999888853 334678899988888888753321100 01123445555555666666665555
Q ss_pred HHHHH
Q 042627 174 QELQS 178 (237)
Q Consensus 174 ~~l~~ 178 (237)
+.|..
T Consensus 103 ~~l~~ 107 (133)
T cd04787 103 DRMQQ 107 (133)
T ss_pred HHHHH
Confidence 55543
No 206
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=23.46 E-value=41 Score=21.67 Aligned_cols=21 Identities=10% Similarity=0.126 Sum_probs=19.1
Q ss_pred HHHHHhCCCCccchhhccchH
Q 042627 120 ALAEQLNLEPRQVEVWFQNRR 140 (237)
Q Consensus 120 ~LA~~LgL~~rQVkvWFQNRR 140 (237)
+||+.+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999884
No 207
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=23.46 E-value=1.5e+02 Score=23.75 Aligned_cols=21 Identities=14% Similarity=0.112 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCCccchhhccc
Q 042627 118 KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQN 138 (237)
.+++|..+|++...|++|.+.
T Consensus 127 ~~eIA~~lgis~~tv~~~l~R 147 (165)
T PRK09644 127 YEEAASVLDLKLNTYKSHLFR 147 (165)
T ss_pred HHHHHHHHCCCHHHHHHHHHH
Confidence 789999999999999998763
No 208
>PF13730 HTH_36: Helix-turn-helix domain
Probab=23.24 E-value=1.4e+02 Score=19.43 Aligned_cols=40 Identities=15% Similarity=0.087 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHHHhh---CCCCCH-HHHHHHHhCCCCccchhhc
Q 042627 97 LTIEQSRLLEDSFKL---HTTLNS-KQALAEQLNLEPRQVEVWF 136 (237)
Q Consensus 97 ~t~~Ql~~LE~~F~~---~~~p~~-r~~LA~~LgL~~rQVkvWF 136 (237)
+++.+..++-..+.. ...--+ ...||..+|++.+.|+-+.
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i 46 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAI 46 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 455555555544433 222222 8899999999988887665
No 209
>PF15136 UPF0449: Uncharacterised protein family UPF0449
Probab=23.14 E-value=2.2e+02 Score=22.20 Aligned_cols=28 Identities=25% Similarity=0.489 Sum_probs=19.2
Q ss_pred HhHHHHHHHHHHhHhhHHHHHHHHHHHH
Q 042627 147 QNEVDCEFLKKCCESLTDENKRLKKELQ 174 (237)
Q Consensus 147 q~~~~~~~Lk~~~~~l~~en~~l~~e~~ 174 (237)
+.++-+..|++.|+.|+.-.+.|++++.
T Consensus 68 rLqqa~~~Lkkk~e~L~~age~Le~~i~ 95 (97)
T PF15136_consen 68 RLQQARDQLKKKCEELRQAGEELERDIE 95 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444456677778888887877777654
No 210
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=23.06 E-value=1.5e+02 Score=28.08 Aligned_cols=17 Identities=18% Similarity=0.055 Sum_probs=6.7
Q ss_pred HHHHhHhhHHHHHHHHH
Q 042627 155 LKKCCESLTDENKRLKK 171 (237)
Q Consensus 155 Lk~~~~~l~~en~~l~~ 171 (237)
|+.+++.|++||.+|+.
T Consensus 62 L~~EN~~Lk~Ena~L~~ 78 (337)
T PRK14872 62 LETENFLLKERIALLEE 78 (337)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33333334444444433
No 211
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=23.04 E-value=1.2e+02 Score=23.96 Aligned_cols=43 Identities=26% Similarity=0.302 Sum_probs=29.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
.++..+..+|.-.| ... ...++|..+|++...|+.+.. |++.+
T Consensus 112 ~L~~~~r~il~l~~-~g~---s~~eIA~~lgis~~tV~~~i~--ra~~~ 154 (166)
T PRK09639 112 KMTERDRTVLLLRF-SGY---SYKEIAEALGIKESSVGTTLA--RAKKK 154 (166)
T ss_pred cCCHHHHHHHHHHH-cCC---CHHHHHHHHCCCHHHHHHHHH--HHHHH
Confidence 35666666665555 211 078999999999999998874 44443
No 212
>PF13565 HTH_32: Homeodomain-like domain
Probab=22.91 E-value=2.7e+02 Score=19.27 Aligned_cols=32 Identities=16% Similarity=0.178 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHHhhCCCCCH---HHHHHHHhCCCC
Q 042627 98 TIEQSRLLEDSFKLHTTLNS---KQALAEQLNLEP 129 (237)
Q Consensus 98 t~~Ql~~LE~~F~~~~~p~~---r~~LA~~LgL~~ 129 (237)
+.++...+.+.+..++..+. ...|..++|+..
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISV 66 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC
Confidence 67777899999998876665 567888877543
No 213
>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [, , ]. TPR is thought to be a component of nuclear pore complex- attached intranuclear filaments [], and is implicated in nuclear protein import []. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex []. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity []. ; GO: 0006606 protein import into nucleus, 0005643 nuclear pore
Probab=22.75 E-value=1.9e+02 Score=23.07 Aligned_cols=32 Identities=31% Similarity=0.377 Sum_probs=24.2
Q ss_pred HHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHH
Q 042627 145 LKQNEVDCEFLKKCCESLTDENKRLKKELQEL 176 (237)
Q Consensus 145 rkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l 176 (237)
+...+.+...++..++.|..+|.-|+.+++.+
T Consensus 100 k~~le~e~~~~~~r~~dL~~QN~lLh~QlE~l 131 (132)
T PF07926_consen 100 KEQLEKELSELEQRIEDLNEQNKLLHDQLESL 131 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 45556677778888888888888888887653
No 214
>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=22.66 E-value=1.2e+02 Score=25.90 Aligned_cols=38 Identities=16% Similarity=0.143 Sum_probs=28.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhcc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQ 137 (237)
.++..+..+|...|- -.. ..++|..+|++...|+.+..
T Consensus 175 ~L~~~~r~il~l~y~----~~~s~~eIA~~lgis~~tV~~~~~ 213 (224)
T TIGR02479 175 SLSEREQLVLSLYYY----EELNLKEIGEVLGLTESRVSQIHS 213 (224)
T ss_pred hCCHHHHHHHHHHHh----CCCCHHHHHHHhCCCHHHHHHHHH
Confidence 467777777777662 222 78999999999999988764
No 215
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=22.65 E-value=1.2e+02 Score=26.25 Aligned_cols=43 Identities=12% Similarity=0.184 Sum_probs=32.6
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQN 138 (237)
.++..+..+|...|-...+-.. ..++|..+|++...|+.+...
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~ 219 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESK 219 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 5678888888887744333334 889999999999999887653
No 216
>KOG3863 consensus bZIP transcription factor NRF1 [Transcription]
Probab=22.55 E-value=4.7e+02 Score=26.76 Aligned_cols=60 Identities=27% Similarity=0.244 Sum_probs=33.4
Q ss_pred HHHHHHhCCCCc-cchhhccchHHHH--HHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 119 QALAEQLNLEPR-QVEVWFQNRRART--KLKQNEVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 119 ~~LA~~LgL~~r-QVkvWFQNRRak~--Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
++|+..-++..| -=||=-||+|.|. +..+.+.+.+.|++.-+.|..|...+.+.+.+++.
T Consensus 484 ~QLslIrDIRRRgKNkvAAQnCRKRKLd~I~nLE~ev~~l~~eKeqLl~Er~~~d~~L~~~kq 546 (604)
T KOG3863|consen 484 EQLSLIRDIRRRGKNKVAAQNCRKRKLDCILNLEDEVEKLQKEKEQLLRERDELDSTLGVMKQ 546 (604)
T ss_pred HHHHHhhccccccccchhccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444433 1245556766653 45555666666666666666666666666655555
No 217
>PF07047 OPA3: Optic atrophy 3 protein (OPA3); InterPro: IPR010754 OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity []. This family consists of several optic atrophy 3 (OPA3) proteins and related proteins from other eukaryotic species, the function is unknown.
Probab=22.38 E-value=1.2e+02 Score=24.50 Aligned_cols=43 Identities=19% Similarity=0.239 Sum_probs=19.9
Q ss_pred chhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHH
Q 042627 132 VEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQ 177 (237)
Q Consensus 132 VkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~ 177 (237)
.-++|-..|+..|-...+. .++...+.|+.+...|+.++++++
T Consensus 90 ~li~~E~~Rs~~ke~~Ke~---~~~~~l~~L~~~i~~L~~~~~~~~ 132 (134)
T PF07047_consen 90 GLIIYEYWRSARKEAKKEE---ELQERLEELEERIEELEEQVEKQQ 132 (134)
T ss_pred HHHHHHHHHHHhhHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455655555544322222 222344445555555555555443
No 218
>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=22.38 E-value=1.2e+02 Score=24.74 Aligned_cols=20 Identities=25% Similarity=0.260 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCCccchhhcc
Q 042627 118 KQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQ 137 (237)
..++|..+|++...|++++.
T Consensus 168 ~~eIA~~l~~s~~tV~~~l~ 187 (198)
T TIGR02859 168 YQEIACDLNRHVKSIDNALQ 187 (198)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 78999999999999998765
No 219
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=22.27 E-value=1.2e+02 Score=26.23 Aligned_cols=44 Identities=11% Similarity=0.126 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccchHHHHH
Q 042627 97 LTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 97 ~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
+++.+..++...|- -.. ..++|..+|++...|+.+...=|.+.|
T Consensus 185 L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr 229 (236)
T PRK06986 185 LPEREQLVLSLYYQ----EELNLKEIGAVLGVSESRVSQIHSQAIKRLR 229 (236)
T ss_pred CCHHHHHHHHhHhc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45555555555442 222 789999999999999998864444433
No 220
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=22.24 E-value=38 Score=22.09 Aligned_cols=23 Identities=22% Similarity=0.362 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCCccchhhccchH
Q 042627 118 KQALAEQLNLEPRQVEVWFQNRR 140 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQNRR 140 (237)
..+||+.+|+++..|.-|..+++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 67899999999999999998744
No 221
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=22.16 E-value=39 Score=34.47 Aligned_cols=21 Identities=33% Similarity=0.651 Sum_probs=17.5
Q ss_pred CCccchhhccchHHHHHHHHh
Q 042627 128 EPRQVEVWFQNRRARTKLKQN 148 (237)
Q Consensus 128 ~~rQVkvWFQNRRak~Krkq~ 148 (237)
...-|+.||.|||+++|+.+.
T Consensus 739 ~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 739 ESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred hhcchHHHHHHHHHHHhhhhc
Confidence 567799999999999987654
No 222
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=21.96 E-value=1.1e+02 Score=28.96 Aligned_cols=33 Identities=15% Similarity=0.060 Sum_probs=19.1
Q ss_pred HHhHHHHHHHHHHhHhhHHHHHHHH---HHHHHHHH
Q 042627 146 KQNEVDCEFLKKCCESLTDENKRLK---KELQELQS 178 (237)
Q Consensus 146 kq~~~~~~~Lk~~~~~l~~en~~l~---~e~~~l~~ 178 (237)
...+++++.|+++...|+.+..+++ .|+..|+.
T Consensus 60 ~~L~~EN~~Lk~Ena~L~~~l~~~e~l~~En~~Lr~ 95 (337)
T PRK14872 60 LVLETENFLLKERIALLEERLKSYEEANQTPPLFSE 95 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556677777777777755555433 44444443
No 223
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=21.89 E-value=1.3e+02 Score=24.60 Aligned_cols=43 Identities=23% Similarity=0.206 Sum_probs=29.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccchHHHHH
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
.+++.|..++...|-. .. .+++|..+|++...|+++.. |++.+
T Consensus 139 ~L~~~~r~i~~l~~~~----g~s~~EIA~~lgis~~tV~~~l~--Ra~~~ 182 (189)
T PRK09648 139 TLPEKQREILILRVVV----GLSAEETAEAVGSTPGAVRVAQH--RALAR 182 (189)
T ss_pred hCCHHHHHHHHHHHHc----CCCHHHHHHHHCCCHHHHHHHHH--HHHHH
Confidence 4566666666654432 12 78999999999999998874 44444
No 224
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=21.83 E-value=89 Score=20.44 Aligned_cols=31 Identities=19% Similarity=0.303 Sum_probs=18.7
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHhCCCCccch
Q 042627 102 SRLLEDSFKLHTTLNSKQALAEQLNLEPRQVE 133 (237)
Q Consensus 102 l~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVk 133 (237)
..+|...+.... +-...+||..|+++.+-|+
T Consensus 3 ~~il~~L~~~~~-~it~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 3 KQILKLLLESKE-PITAKELAEELGVSRRTIR 33 (55)
T ss_dssp HHHHHHHHHTTT-SBEHHHHHHHCTS-HHHHH
T ss_pred HHHHHHHHHcCC-CcCHHHHHHHhCCCHHHHH
Confidence 344444444443 3228999999999986554
No 225
>KOG0999 consensus Microtubule-associated protein Bicaudal-D [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.74 E-value=1.5e+02 Score=30.14 Aligned_cols=47 Identities=30% Similarity=0.319 Sum_probs=33.5
Q ss_pred hhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHH
Q 042627 133 EVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQSA 179 (237)
Q Consensus 133 kvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~ 179 (237)
.+=-|.+|.|.-.+...-.-..|-..|..|.+||-.||+++..|+..
T Consensus 146 ~~E~qR~rlr~elKe~KfRE~RllseYSELEEENIsLQKqVs~LR~s 192 (772)
T KOG0999|consen 146 AVEDQRRRLRDELKEYKFREARLLSEYSELEEENISLQKQVSNLRQS 192 (772)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHhhh
Confidence 34456777777666665555567777888888888888888887763
No 226
>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=21.73 E-value=1.5e+02 Score=23.95 Aligned_cols=38 Identities=21% Similarity=0.115 Sum_probs=26.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhcc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQ 137 (237)
.+++.+..+|.-.|-. .. ..++|..+|+++..|+++.+
T Consensus 100 ~L~~~~r~v~~l~~~~----g~s~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 100 ELPDEYREAIRLTELE----GLSQQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred hCCHHHHHHHHHHHHc----CCCHHHHHHHHCCCHHHHHHHHH
Confidence 4566666666654422 12 78999999999999988764
No 227
>PF07047 OPA3: Optic atrophy 3 protein (OPA3); InterPro: IPR010754 OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity []. This family consists of several optic atrophy 3 (OPA3) proteins and related proteins from other eukaryotic species, the function is unknown.
Probab=21.60 E-value=1.9e+02 Score=23.36 Aligned_cols=42 Identities=19% Similarity=0.247 Sum_probs=34.9
Q ss_pred ccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHH
Q 042627 130 RQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKK 171 (237)
Q Consensus 130 rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~ 171 (237)
--..+|=+.+..+.|....+++.+.|....+.|..+.+++++
T Consensus 92 i~~E~~Rs~~ke~~Ke~~~~~~l~~L~~~i~~L~~~~~~~~~ 133 (134)
T PF07047_consen 92 IIYEYWRSARKEAKKEEELQERLEELEERIEELEEQVEKQQE 133 (134)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 345678888888888888889999999999999988887764
No 228
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=21.55 E-value=1.4e+02 Score=24.76 Aligned_cols=20 Identities=30% Similarity=0.383 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCCccchhhcc
Q 042627 118 KQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQ 137 (237)
-.++|..+|+++..|++.+.
T Consensus 173 ~~EIA~~lgis~~tV~~~l~ 192 (208)
T PRK08295 173 YQEIAEELNRHVKSIDNALQ 192 (208)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 78999999999999987554
No 229
>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=21.32 E-value=60 Score=24.02 Aligned_cols=20 Identities=15% Similarity=0.363 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCCccchhhcc
Q 042627 118 KQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQ 137 (237)
+..|.+.++|..-||.|||.
T Consensus 56 ~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 56 TSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHhCCCCCeEEEEEE
Confidence 67789999999999999985
No 230
>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=21.30 E-value=1.6e+02 Score=23.78 Aligned_cols=40 Identities=25% Similarity=0.252 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhccchH
Q 042627 97 LTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQNRR 140 (237)
Q Consensus 97 ~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQNRR 140 (237)
+++.+..++.-.|-. .. -.++|..||+++..|++....=|
T Consensus 135 Lp~~~r~v~~l~~~~----g~s~~EIA~~lgis~~tVk~~l~Rar 175 (183)
T TIGR02999 135 VDPRQAEVVELRFFA----GLTVEEIAELLGVSVRTVERDWRFAR 175 (183)
T ss_pred CCHHHHHHHHHHHHc----CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 455555544444322 12 78999999999999999876433
No 231
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=21.26 E-value=4.1e+02 Score=20.81 Aligned_cols=73 Identities=11% Similarity=0.004 Sum_probs=42.4
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHhCCCCccchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHH
Q 042627 94 KLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKKEL 173 (237)
Q Consensus 94 Rt~~t~~Ql~~LE~~F~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~ 173 (237)
...|+.+++..|... ...+.+|++-.+|+.+|........ ....-...|+...+.+.++...|+.-.
T Consensus 36 ~R~Y~~~~~~~l~~I-----------~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~L~~~~ 102 (127)
T cd01108 36 YRVYNQRDIEELRFI-----------RRARDLGFSLEEIRELLALWRDPSR--ASADVKALALEHIAELERKIAELQAMR 102 (127)
T ss_pred ceecCHHHHHHHHHH-----------HHHHHcCCCHHHHHHHHHHHhCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556899988888642 3357788888888887753221100 011123445556666666666666655
Q ss_pred HHHHHH
Q 042627 174 QELQSA 179 (237)
Q Consensus 174 ~~l~~~ 179 (237)
+.|...
T Consensus 103 ~~l~~~ 108 (127)
T cd01108 103 RTLQQL 108 (127)
T ss_pred HHHHHH
Confidence 555543
No 232
>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=21.22 E-value=1.9e+02 Score=20.73 Aligned_cols=41 Identities=22% Similarity=0.261 Sum_probs=26.6
Q ss_pred cchhhccchHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHH
Q 042627 131 QVEVWFQNRRARTKLKQNEVDCEFLKKCCESLTDENKRLKK 171 (237)
Q Consensus 131 QVkvWFQNRRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~ 171 (237)
-|..+++.|.......+.+.+.+.++..++.|+.|...|..
T Consensus 19 ~v~~~~~~~~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~ 59 (85)
T TIGR02209 19 VVSAQHQTRQLNNELQKLQLEIDKLQKEWRDLQLEVAELSR 59 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 34444555555555666666777777777777777777655
No 233
>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=21.09 E-value=1.1e+02 Score=24.92 Aligned_cols=25 Identities=20% Similarity=0.190 Sum_probs=20.4
Q ss_pred HHHHHHHhCCCCccchhhccchHHHHH
Q 042627 118 KQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
-.++|..+|+++..|+++.. |++.+
T Consensus 157 ~~EIA~~lgis~~tv~~~l~--rar~~ 181 (190)
T TIGR02939 157 YEDIARIMDCPVGTVRSRIF--RAREA 181 (190)
T ss_pred HHHHHHHHCcCHHHHHHHHH--HHHHH
Confidence 78999999999999998874 44444
No 234
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=21.07 E-value=2.4e+02 Score=26.93 Aligned_cols=40 Identities=23% Similarity=0.370 Sum_probs=28.3
Q ss_pred hHHHHHHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHH
Q 042627 139 RRARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQS 178 (237)
Q Consensus 139 RRak~Krkq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~ 178 (237)
++.+.+.++.+...+.++++|....+|...|-+|+.+..+
T Consensus 137 ~~~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE~la 176 (401)
T PF06785_consen 137 RHLREENQCLQLQLDALQQECGEKEEESQTLNRELAEALA 176 (401)
T ss_pred HHHHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHHHHH
Confidence 3455566666777777888887777888888777766554
No 235
>KOG4378 consensus Nuclear protein COP1 [Signal transduction mechanisms]
Probab=20.70 E-value=1.6e+02 Score=29.64 Aligned_cols=11 Identities=27% Similarity=0.404 Sum_probs=6.4
Q ss_pred hccchHHHHHH
Q 042627 135 WFQNRRARTKL 145 (237)
Q Consensus 135 WFQNRRak~Kr 145 (237)
=|+|+|-..-+
T Consensus 599 ~fs~q~~q~~~ 609 (673)
T KOG4378|consen 599 TFSNQRLQANK 609 (673)
T ss_pred hhHHHHHHHHh
Confidence 46777665443
No 236
>PRK06930 positive control sigma-like factor; Validated
Probab=20.65 E-value=1.5e+02 Score=24.90 Aligned_cols=45 Identities=13% Similarity=0.096 Sum_probs=31.0
Q ss_pred cCCHHHHHHHHHHH-hhCCCCCHHHHHHHHhCCCCccchhhccchHHHHH
Q 042627 96 RLTIEQSRLLEDSF-KLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F-~~~~~p~~r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
.+++.+..++.-.| ..-. -.++|..+|++...|+.+...-|.+.+
T Consensus 114 ~L~~rer~V~~L~~~eg~s----~~EIA~~lgiS~~tVk~~l~Ra~~kLr 159 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGLS----YSEIADYLNIKKSTVQSMIERAEKKIA 159 (170)
T ss_pred hCCHHHHHHHHHHHHcCCC----HHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 46777766666543 2222 789999999999999998864444433
No 237
>PF07412 Geminin: Geminin; InterPro: IPR022786 This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle []. ; GO: 0008156 negative regulation of DNA replication; PDB: 1T6F_B 2LP0_B 1UII_B 2WVR_B 2ZXX_B.
Probab=20.60 E-value=2e+02 Score=25.30 Aligned_cols=32 Identities=31% Similarity=0.275 Sum_probs=24.4
Q ss_pred hHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHH
Q 042627 148 NEVDCEFLKKCCESLTDENKRLKKELQELQSA 179 (237)
Q Consensus 148 ~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~ 179 (237)
.-++++.|....+.+.+|...|+.|+.+|+.+
T Consensus 123 aL~ENe~Lh~~ie~~~eEi~~lk~en~~L~el 154 (200)
T PF07412_consen 123 ALEENEKLHKEIEQKDEEIAKLKEENEELKEL 154 (200)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566777778888888888888888887764
No 238
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=20.58 E-value=3.6e+02 Score=23.53 Aligned_cols=59 Identities=17% Similarity=0.135 Sum_probs=42.2
Q ss_pred HHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHhcCCCCchhhccccCcCCCCCCCCCCCC
Q 042627 146 KQNEVDCEFLKKCCESLTDENKRLKKELQELQSAKAGASSPLFIQLQKAATCPSCEKIMRTS 207 (237)
Q Consensus 146 kq~~~~~~~Lk~~~~~l~~en~~l~~e~~~l~~~~~~~~~~~~~~~~~~~~CpsC~~~~~~~ 207 (237)
.-.+..++.|+.+++.|+.|+..|+.++..++...- ......+.....|..+.....-.
T Consensus 115 ~~Lk~~~~~l~~~~~~Lq~e~~eL~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~ 173 (198)
T KOG0483|consen 115 ESLKRQLESLRSENDRLQSEVQELVAELSSLKREMQ---KSPENTLTMCPNSESSSSVSDEN 173 (198)
T ss_pred HHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhc---cCcccccccCccccccCCccccc
Confidence 344567888999999999999999999888777542 22455666777777777655433
No 239
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=20.53 E-value=49 Score=20.06 Aligned_cols=23 Identities=22% Similarity=0.351 Sum_probs=20.2
Q ss_pred HHHHHHHhCCCCccchhhccchH
Q 042627 118 KQALAEQLNLEPRQVEVWFQNRR 140 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQNRR 140 (237)
..++|+.+++++..|..|..+++
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 67899999999999999988764
No 240
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=20.28 E-value=49 Score=21.31 Aligned_cols=23 Identities=13% Similarity=0.082 Sum_probs=20.6
Q ss_pred HHHHHHHhCCCCccchhhccchH
Q 042627 118 KQALAEQLNLEPRQVEVWFQNRR 140 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQNRR 140 (237)
..+||..+|++...|.-|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 68899999999999999997764
No 241
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=20.26 E-value=1.8e+02 Score=26.40 Aligned_cols=15 Identities=20% Similarity=0.131 Sum_probs=9.9
Q ss_pred CCCCCCCCccCCHHH
Q 042627 87 INISGRKKLRLTIEQ 101 (237)
Q Consensus 87 ~~~~rR~Rt~~t~~Q 101 (237)
..++|+.-..++.+.
T Consensus 54 ~~rKr~RL~HLS~EE 68 (292)
T KOG4005|consen 54 PKRKRRRLDHLSWEE 68 (292)
T ss_pred hHHHHHhhcccCHHH
Confidence 445666777787764
No 242
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=20.23 E-value=1.1e+02 Score=25.18 Aligned_cols=28 Identities=11% Similarity=0.252 Sum_probs=23.6
Q ss_pred H-HHHHHHHhCCCCccchhhccchHHHHH
Q 042627 117 S-KQALAEQLNLEPRQVEVWFQNRRARTK 144 (237)
Q Consensus 117 ~-r~~LA~~LgL~~rQVkvWFQNRRak~K 144 (237)
. ..+++..+|++..+|..|...-|-...
T Consensus 47 ati~eV~e~tgVs~~~I~~~IreGRL~~~ 75 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIREGRLQLK 75 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCeecc
Confidence 5 899999999999999999876665443
No 243
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=20.21 E-value=1.5e+02 Score=26.40 Aligned_cols=42 Identities=19% Similarity=0.178 Sum_probs=31.6
Q ss_pred cCCHHHHHHHHHHHhhCCCCCH-HHHHHHHhCCCCccchhhcc
Q 042627 96 RLTIEQSRLLEDSFKLHTTLNS-KQALAEQLNLEPRQVEVWFQ 137 (237)
Q Consensus 96 ~~t~~Ql~~LE~~F~~~~~p~~-r~~LA~~LgL~~rQVkvWFQ 137 (237)
.++..+..+|.-.|....+-.. -.++|..||++...|+.+..
T Consensus 222 ~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~ 264 (285)
T TIGR02394 222 ELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQV 264 (285)
T ss_pred cCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHH
Confidence 5777888888777733333334 88999999999999998764
No 244
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=20.17 E-value=1.5e+02 Score=25.84 Aligned_cols=21 Identities=19% Similarity=0.275 Sum_probs=18.5
Q ss_pred HHHHHHHhCCCCccchhhccc
Q 042627 118 KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQN 138 (237)
-.++|..||++...|+++.+.
T Consensus 190 ~~EIA~~Lgis~~tVk~~l~R 210 (233)
T PRK12538 190 NGEIAEVMDTTVAAVESLLKR 210 (233)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 689999999999999988753
No 245
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=20.03 E-value=1.2e+02 Score=21.45 Aligned_cols=37 Identities=27% Similarity=0.254 Sum_probs=22.5
Q ss_pred cCCHHHHHHHHH---HHhhCCCCCHHHHHHHHhCCC-Cccc
Q 042627 96 RLTIEQSRLLED---SFKLHTTLNSKQALAEQLNLE-PRQV 132 (237)
Q Consensus 96 ~~t~~Ql~~LE~---~F~~~~~p~~r~~LA~~LgL~-~rQV 132 (237)
.+|..|..+|+- +...+.||....+||+.+|+. ..-|
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv 43 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTV 43 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHH
Confidence 367777777654 456677876688999999997 4433
No 246
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=20.01 E-value=1.4e+02 Score=24.91 Aligned_cols=21 Identities=14% Similarity=0.034 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCCccchhhccc
Q 042627 118 KQALAEQLNLEPRQVEVWFQN 138 (237)
Q Consensus 118 r~~LA~~LgL~~rQVkvWFQN 138 (237)
..++|..||++...|+++++.
T Consensus 132 ~~EIA~~LgiS~~tVk~~l~R 152 (188)
T PRK12546 132 YEEAAEMCGVAVGTVKSRANR 152 (188)
T ss_pred HHHHHHHHCCCHHHHHHHHHH
Confidence 789999999999999998863
Done!