Query 021250
Match_columns 315
No_of_seqs 293 out of 1531
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 08:47:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021250.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021250hhsearch_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 7.8E-22 1.7E-26 178.5 8.0 105 54-164 47-151 (198)
2 KOG0489 Transcription factor z 99.7 1.7E-17 3.7E-22 155.9 4.6 63 55-117 157-219 (261)
3 KOG0842 Transcription factor t 99.7 2.7E-17 5.9E-22 157.2 4.8 69 56-124 150-220 (307)
4 KOG0488 Transcription factor B 99.7 2.7E-16 5.9E-21 151.2 9.4 55 64-118 179-233 (309)
5 KOG0487 Transcription factor A 99.6 2.4E-16 5.2E-21 150.8 4.1 63 57-119 235-297 (308)
6 KOG0843 Transcription factor E 99.6 8.7E-16 1.9E-20 136.4 5.8 64 56-119 101-164 (197)
7 PF00046 Homeobox: Homeobox do 99.6 2.4E-15 5.3E-20 109.1 6.3 57 58-114 1-57 (57)
8 KOG0484 Transcription factor P 99.6 1.4E-15 3.1E-20 124.5 5.4 59 59-117 19-77 (125)
9 KOG0485 Transcription factor N 99.6 1.6E-15 3.5E-20 138.2 5.3 59 58-116 103-163 (268)
10 KOG0850 Transcription factor D 99.5 4.7E-15 1E-19 136.0 5.7 59 57-115 122-180 (245)
11 KOG0492 Transcription factor M 99.5 2.4E-14 5.2E-19 129.8 7.0 61 57-117 144-204 (246)
12 KOG0494 Transcription factor C 99.5 2.4E-14 5.1E-19 133.5 7.0 57 64-120 148-204 (332)
13 KOG0493 Transcription factor E 99.5 3.4E-14 7.3E-19 132.5 8.0 62 58-119 247-308 (342)
14 KOG0848 Transcription factor C 99.5 9.5E-15 2.1E-19 136.5 4.1 54 64-117 206-259 (317)
15 KOG2251 Homeobox transcription 99.5 3.6E-14 7.8E-19 129.6 5.2 64 56-119 36-99 (228)
16 cd00086 homeodomain Homeodomai 99.4 1.7E-13 3.8E-18 98.9 6.4 57 59-115 2-58 (59)
17 smart00389 HOX Homeodomain. DN 99.4 2E-13 4.3E-18 98.1 5.8 55 59-113 2-56 (56)
18 KOG0844 Transcription factor E 99.4 1E-13 2.2E-18 131.8 3.0 63 56-118 180-242 (408)
19 COG5576 Homeodomain-containing 99.4 3.3E-13 7.3E-18 118.4 5.8 65 55-119 49-113 (156)
20 KOG4577 Transcription factor L 99.4 4E-13 8.6E-18 126.9 4.9 96 53-149 163-258 (383)
21 KOG0491 Transcription factor B 99.4 2.3E-13 5E-18 119.6 2.2 58 62-119 105-162 (194)
22 TIGR01565 homeo_ZF_HD homeobox 99.3 1.1E-12 2.5E-17 97.4 4.5 52 58-109 2-57 (58)
23 KOG0486 Transcription factor P 99.3 2.3E-12 5.1E-17 122.9 5.0 57 64-120 119-175 (351)
24 KOG0847 Transcription factor, 99.2 7.7E-12 1.7E-16 114.5 4.1 63 55-117 165-227 (288)
25 KOG3802 Transcription factor O 99.2 1.6E-11 3.5E-16 120.4 3.2 60 56-115 293-352 (398)
26 KOG0490 Transcription factor, 99.0 1.1E-10 2.3E-15 105.5 3.0 62 56-117 59-120 (235)
27 KOG0849 Transcription factor P 98.8 3.3E-09 7.1E-14 104.1 5.6 61 57-117 176-236 (354)
28 KOG1168 Transcription factor A 98.7 5.1E-09 1.1E-13 99.5 2.0 65 52-116 304-368 (385)
29 KOG0775 Transcription factor S 98.6 3.9E-08 8.4E-13 92.9 4.6 51 64-114 183-233 (304)
30 PF05920 Homeobox_KN: Homeobox 98.2 1.5E-06 3.3E-11 60.0 3.1 34 78-111 7-40 (40)
31 KOG0774 Transcription factor P 98.1 1.5E-06 3.3E-11 81.9 2.6 59 57-115 188-249 (334)
32 KOG0490 Transcription factor, 97.8 3.1E-05 6.7E-10 69.9 4.6 61 57-117 153-213 (235)
33 PF02183 HALZ: Homeobox associ 97.6 5.4E-05 1.2E-09 53.7 3.5 44 115-164 1-44 (45)
34 KOG2252 CCAAT displacement pro 97.6 9.1E-05 2E-09 76.0 6.3 56 57-112 420-475 (558)
35 KOG1146 Homeobox protein [Gene 97.1 0.00039 8.5E-09 77.3 4.5 63 56-118 902-964 (1406)
36 PF11569 Homez: Homeodomain le 96.2 0.0041 8.8E-08 46.1 2.6 42 68-109 9-50 (56)
37 KOG0773 Transcription factor M 95.9 0.0064 1.4E-07 59.1 3.6 57 61-117 243-302 (342)
38 PF04218 CENP-B_N: CENP-B N-te 92.6 0.33 7.1E-06 35.2 5.2 47 58-109 1-47 (53)
39 KOG3623 Homeobox transcription 92.6 0.16 3.5E-06 54.4 4.9 52 64-116 564-615 (1007)
40 PRK09413 IS2 repressor TnpA; R 90.0 1.9 4E-05 36.0 7.9 43 60-107 9-52 (121)
41 KOG4196 bZIP transcription fac 86.7 6.9 0.00015 33.9 9.2 90 62-170 22-119 (135)
42 PF02183 HALZ: Homeobox associ 85.7 0.7 1.5E-05 32.7 2.4 36 123-164 2-37 (45)
43 PF04967 HTH_10: HTH DNA bindi 76.2 3.3 7.3E-05 30.3 3.1 40 64-103 1-42 (53)
44 PF01527 HTH_Tnp_1: Transposas 74.1 2.2 4.7E-05 31.8 1.8 44 59-106 2-45 (76)
45 PF04545 Sigma70_r4: Sigma-70, 73.9 8 0.00017 26.8 4.6 39 63-106 4-42 (50)
46 cd06171 Sigma70_r4 Sigma70, re 71.1 6.1 0.00013 26.2 3.3 42 64-110 11-52 (55)
47 cd00569 HTH_Hin_like Helix-tur 68.8 12 0.00026 22.0 4.1 39 62-105 4-42 (42)
48 PF13443 HTH_26: Cro/C1-type H 62.5 10 0.00023 27.1 3.3 40 86-125 12-51 (63)
49 COG3413 Predicted DNA binding 61.4 13 0.00028 33.8 4.5 49 63-113 155-205 (215)
50 smart00340 HALZ homeobox assoc 58.9 9.3 0.0002 27.0 2.3 26 129-160 8-33 (44)
51 PF08281 Sigma70_r4_2: Sigma-7 57.0 21 0.00045 24.9 4.0 39 64-107 11-49 (54)
52 KOG4005 Transcription factor X 55.8 25 0.00055 33.5 5.4 52 106-163 82-135 (292)
53 PF00170 bZIP_1: bZIP transcri 54.9 28 0.00061 25.6 4.6 30 121-150 28-57 (64)
54 PRK03975 tfx putative transcri 54.8 32 0.0007 30.0 5.6 48 61-114 4-51 (141)
55 PF10668 Phage_terminase: Phag 53.1 9.3 0.0002 28.8 1.7 19 86-104 24-42 (60)
56 PF13936 HTH_38: Helix-turn-he 52.4 14 0.00031 25.4 2.4 40 62-106 3-42 (44)
57 PF10224 DUF2205: Predicted co 49.7 40 0.00087 26.8 4.9 47 111-163 15-61 (80)
58 PF06156 DUF972: Protein of un 49.4 28 0.00061 29.0 4.2 46 115-166 11-56 (107)
59 PF09607 BrkDBD: Brinker DNA-b 49.1 33 0.00072 25.7 4.1 44 61-106 3-47 (58)
60 PF00170 bZIP_1: bZIP transcri 48.0 45 0.00098 24.5 4.8 38 112-149 26-63 (64)
61 PF00424 REV: REV protein (ant 45.1 32 0.00069 28.1 3.7 33 69-117 14-48 (91)
62 PF00196 GerE: Bacterial regul 45.1 43 0.00092 23.8 4.1 44 63-112 3-46 (58)
63 PRK09642 RNA polymerase sigma 44.4 53 0.0011 27.6 5.3 46 64-114 107-152 (160)
64 COG4467 Regulator of replicati 43.5 47 0.001 28.0 4.6 44 115-164 11-54 (114)
65 cd04761 HTH_MerR-SF Helix-Turn 43.5 19 0.00042 24.2 2.0 22 87-108 3-24 (49)
66 PRK13169 DNA replication intia 42.9 41 0.00088 28.2 4.2 45 115-165 11-55 (110)
67 PRK09652 RNA polymerase sigma 42.8 51 0.0011 27.8 5.0 41 64-109 129-169 (182)
68 TIGR02937 sigma70-ECF RNA poly 42.5 52 0.0011 26.1 4.8 43 64-111 111-153 (158)
69 KOG4571 Activating transcripti 41.0 44 0.00094 32.7 4.6 46 111-163 241-286 (294)
70 PF13518 HTH_28: Helix-turn-he 40.9 28 0.00061 23.7 2.6 22 86-107 14-35 (52)
71 PRK09646 RNA polymerase sigma 40.4 59 0.0013 28.5 5.1 45 64-113 143-187 (194)
72 PRK06759 RNA polymerase factor 40.3 55 0.0012 27.1 4.7 42 64-110 107-148 (154)
73 PF02796 HTH_7: Helix-turn-hel 40.1 41 0.00088 23.1 3.2 38 63-105 5-42 (45)
74 cd04766 HTH_HspR Helix-Turn-He 39.3 1.2E+02 0.0026 23.6 6.3 22 87-108 4-25 (91)
75 PRK11924 RNA polymerase sigma 39.2 69 0.0015 26.9 5.2 45 64-113 126-170 (179)
76 PRK12526 RNA polymerase sigma 39.1 64 0.0014 28.7 5.2 45 64-113 154-198 (206)
77 PRK04217 hypothetical protein; 38.9 80 0.0017 26.4 5.4 44 63-111 42-85 (110)
78 smart00421 HTH_LUXR helix_turn 37.8 70 0.0015 21.3 4.2 37 64-106 4-40 (58)
79 PRK12514 RNA polymerase sigma 37.0 49 0.0011 28.4 4.0 45 64-113 130-174 (179)
80 KOG0709 CREB/ATF family transc 36.5 2.3E+02 0.005 29.5 9.2 82 62-150 219-310 (472)
81 PRK12530 RNA polymerase sigma 35.5 94 0.002 27.2 5.6 45 64-113 135-179 (189)
82 PF13384 HTH_23: Homeodomain-l 35.3 29 0.00063 23.7 1.9 22 85-106 18-39 (50)
83 TIGR03879 near_KaiC_dom probab 35.1 19 0.00041 28.1 1.0 35 73-107 21-55 (73)
84 PRK09644 RNA polymerase sigma 35.1 94 0.002 26.3 5.4 45 64-113 109-153 (165)
85 PRK12512 RNA polymerase sigma 35.1 80 0.0017 27.1 5.1 46 64-114 132-177 (184)
86 PRK12519 RNA polymerase sigma 34.7 63 0.0014 28.0 4.4 45 64-113 142-186 (194)
87 KOG1146 Homeobox protein [Gene 34.7 51 0.0011 38.3 4.5 53 64-116 712-764 (1406)
88 PRK00118 putative DNA-binding 34.5 2E+02 0.0043 23.8 7.0 42 64-110 18-59 (104)
89 PF06056 Terminase_5: Putative 34.3 29 0.00063 25.6 1.8 27 86-114 15-41 (58)
90 TIGR02985 Sig70_bacteroi1 RNA 34.3 83 0.0018 25.7 4.9 43 64-111 114-156 (161)
91 PRK10072 putative transcriptio 34.3 25 0.00054 28.6 1.6 42 63-111 32-73 (96)
92 PF08280 HTH_Mga: M protein tr 34.0 42 0.00092 24.3 2.7 34 67-104 6-39 (59)
93 PF06005 DUF904: Protein of un 33.8 91 0.002 24.1 4.6 35 116-150 22-56 (72)
94 PF07888 CALCOCO1: Calcium bin 33.7 1.7E+02 0.0036 31.2 7.8 41 120-166 418-458 (546)
95 PRK09648 RNA polymerase sigma 33.3 88 0.0019 27.1 5.0 39 64-107 140-178 (189)
96 cd04762 HTH_MerR-trunc Helix-T 33.1 36 0.00079 22.2 2.0 24 87-110 3-26 (49)
97 PRK12515 RNA polymerase sigma 32.9 1.1E+02 0.0023 26.6 5.5 46 64-114 132-177 (189)
98 smart00340 HALZ homeobox assoc 32.5 52 0.0011 23.3 2.7 33 115-147 1-33 (44)
99 TIGR02989 Sig-70_gvs1 RNA poly 32.5 89 0.0019 25.9 4.8 38 64-106 112-149 (159)
100 TIGR02959 SigZ RNA polymerase 31.7 94 0.002 26.6 4.9 38 64-106 101-138 (170)
101 KOG4005 Transcription factor X 31.7 2E+02 0.0043 27.7 7.2 46 115-166 100-145 (292)
102 PRK09639 RNA polymerase sigma 31.7 1.2E+02 0.0026 25.4 5.5 44 64-113 113-156 (166)
103 PRK13729 conjugal transfer pil 31.6 1.5E+02 0.0032 31.0 6.9 44 113-162 77-120 (475)
104 PRK12546 RNA polymerase sigma 31.3 72 0.0016 28.2 4.2 45 64-113 114-158 (188)
105 TIGR02999 Sig-70_X6 RNA polyme 30.8 1E+02 0.0023 26.3 5.1 43 64-111 135-177 (183)
106 PRK05602 RNA polymerase sigma 30.6 93 0.002 26.9 4.7 43 64-111 129-171 (186)
107 KOG0709 CREB/ATF family transc 30.6 1.5E+02 0.0034 30.8 6.8 84 81-165 220-312 (472)
108 PF06005 DUF904: Protein of un 30.5 1.1E+02 0.0023 23.8 4.4 36 115-150 14-49 (72)
109 PF13411 MerR_1: MerR HTH fami 30.4 36 0.00078 24.7 1.8 21 87-107 3-23 (69)
110 TIGR02948 SigW_bacill RNA poly 30.2 95 0.002 26.5 4.7 45 64-113 137-181 (187)
111 PRK12541 RNA polymerase sigma 30.0 74 0.0016 26.7 3.9 42 64-110 113-154 (161)
112 TIGR02943 Sig70_famx1 RNA poly 29.4 1.5E+02 0.0031 26.0 5.8 46 64-114 132-177 (188)
113 KOG3119 Basic region leucine z 29.3 76 0.0017 30.3 4.2 26 134-165 223-248 (269)
114 PRK06811 RNA polymerase factor 28.9 1E+02 0.0022 26.9 4.7 46 64-114 132-177 (189)
115 PRK09047 RNA polymerase factor 28.6 1.2E+02 0.0027 25.1 5.0 39 64-107 107-145 (161)
116 smart00338 BRLZ basic region l 28.6 2.1E+02 0.0045 20.9 5.7 36 121-162 28-63 (65)
117 PRK12538 RNA polymerase sigma 28.5 1.2E+02 0.0027 27.8 5.4 45 64-113 172-216 (233)
118 TIGR02939 RpoE_Sigma70 RNA pol 28.5 91 0.002 26.7 4.3 27 85-111 155-181 (190)
119 COG4367 Uncharacterized protei 28.4 70 0.0015 26.2 3.2 38 64-101 3-40 (97)
120 cd06170 LuxR_C_like C-terminal 28.3 98 0.0021 20.8 3.7 36 65-106 2-37 (57)
121 smart00338 BRLZ basic region l 27.9 1.4E+02 0.0029 22.0 4.5 36 114-149 28-63 (65)
122 PRK07037 extracytoplasmic-func 27.0 1.3E+02 0.0029 25.1 4.9 38 64-106 110-147 (163)
123 PF15058 Speriolin_N: Sperioli 26.9 30 0.00064 32.0 1.0 39 127-165 6-44 (200)
124 cd04764 HTH_MlrA-like_sg1 Heli 26.7 46 0.00099 24.3 1.8 21 87-107 3-23 (67)
125 PF01381 HTH_3: Helix-turn-hel 26.6 42 0.00091 23.1 1.5 23 87-109 12-34 (55)
126 PRK11546 zraP zinc resistance 26.4 1.1E+02 0.0024 26.9 4.3 45 117-167 66-110 (143)
127 PF12824 MRP-L20: Mitochondria 26.3 2.6E+02 0.0056 24.9 6.8 45 60-106 82-126 (164)
128 cd04763 HTH_MlrA-like Helix-Tu 26.2 45 0.00098 24.4 1.7 21 87-107 3-23 (68)
129 COG2944 Predicted transcriptio 26.2 86 0.0019 26.2 3.4 40 64-110 44-83 (104)
130 PRK06288 RNA polymerase sigma 26.1 1.3E+02 0.0029 28.0 5.2 45 64-113 213-257 (268)
131 PRK10403 transcriptional regul 26.1 82 0.0018 26.4 3.5 44 63-112 153-196 (215)
132 PRK12532 RNA polymerase sigma 26.0 1.5E+02 0.0033 25.8 5.3 46 64-114 137-182 (195)
133 PRK06930 positive control sigm 26.0 1.6E+02 0.0035 26.0 5.5 46 64-114 115-160 (170)
134 PRK00888 ftsB cell division pr 25.9 79 0.0017 26.0 3.2 23 128-150 36-58 (105)
135 PF08172 CASP_C: CASP C termin 25.7 1.3E+02 0.0028 28.6 5.1 49 109-163 90-138 (248)
136 PRK12537 RNA polymerase sigma 25.5 1.5E+02 0.0033 25.5 5.2 41 64-109 134-174 (182)
137 PF00376 MerR: MerR family reg 25.3 46 0.001 22.4 1.4 18 88-105 3-20 (38)
138 PRK12543 RNA polymerase sigma 25.1 2.2E+02 0.0047 24.5 6.1 46 64-114 118-163 (179)
139 PRK06986 fliA flagellar biosyn 25.1 1E+02 0.0022 28.0 4.2 46 64-114 185-230 (236)
140 TIGR02983 SigE-fam_strep RNA p 25.0 1.5E+02 0.0032 24.8 4.8 45 64-113 111-155 (162)
141 PF07716 bZIP_2: Basic region 24.8 1.6E+02 0.0034 20.9 4.3 17 134-150 33-49 (54)
142 cd01392 HTH_LacI Helix-turn-he 24.3 81 0.0018 21.4 2.6 21 89-109 2-22 (52)
143 COG2963 Transposase and inacti 24.2 1.4E+02 0.0031 24.0 4.5 42 61-106 5-47 (116)
144 TIGR02954 Sig70_famx3 RNA poly 24.1 1.6E+02 0.0035 24.9 5.0 39 64-107 120-158 (169)
145 PRK12547 RNA polymerase sigma 24.1 1.6E+02 0.0035 24.9 5.0 42 64-110 113-154 (164)
146 TIGR03001 Sig-70_gmx1 RNA poly 23.8 2E+02 0.0043 26.7 5.9 48 64-116 162-209 (244)
147 TIGR02479 FliA_WhiG RNA polyme 23.7 1.1E+02 0.0025 27.4 4.2 42 64-110 176-217 (224)
148 cd01104 HTH_MlrA-CarA Helix-Tu 23.6 64 0.0014 23.3 2.1 20 87-106 3-22 (68)
149 cd00093 HTH_XRE Helix-turn-hel 23.6 56 0.0012 20.9 1.6 23 87-109 15-37 (58)
150 cd01106 HTH_TipAL-Mta Helix-Tu 23.4 3.7E+02 0.008 21.3 6.7 35 61-108 36-70 (103)
151 cd04779 HTH_MerR-like_sg4 Heli 23.3 4.6E+02 0.01 22.3 7.6 36 61-109 35-70 (134)
152 PRK09637 RNA polymerase sigma 23.3 1.5E+02 0.0033 25.7 4.8 38 64-106 107-144 (181)
153 PF13551 HTH_29: Winged helix- 23.3 2.1E+02 0.0046 22.1 5.2 43 64-106 58-109 (112)
154 TIGR02952 Sig70_famx2 RNA poly 22.7 1.8E+02 0.0039 24.3 5.0 38 64-106 123-160 (170)
155 PHA02955 hypothetical protein; 22.6 98 0.0021 29.0 3.5 42 66-107 60-102 (213)
156 PRK09935 transcriptional regul 22.6 1.1E+02 0.0024 25.7 3.6 43 63-111 149-191 (210)
157 PRK08301 sporulation sigma fac 22.4 1.7E+02 0.0036 26.5 5.0 47 64-111 179-225 (234)
158 PRK15369 two component system 22.3 1.8E+02 0.0039 23.9 4.9 43 63-111 149-191 (211)
159 PRK12536 RNA polymerase sigma 22.1 1.9E+02 0.004 24.9 5.1 45 64-113 130-174 (181)
160 PRK10360 DNA-binding transcrip 22.1 1.1E+02 0.0025 25.5 3.7 43 63-111 137-179 (196)
161 PRK12524 RNA polymerase sigma 22.0 1.7E+02 0.0037 25.6 4.8 38 64-106 137-174 (196)
162 PRK13919 putative RNA polymera 22.0 1.9E+02 0.0042 24.7 5.1 38 64-106 136-173 (186)
163 PRK05657 RNA polymerase sigma 22.0 1.5E+02 0.0033 28.8 4.9 49 64-113 263-311 (325)
164 PF04297 UPF0122: Putative hel 21.9 3.3E+02 0.0071 22.5 6.1 52 64-122 18-69 (101)
165 PRK12518 RNA polymerase sigma 21.8 1E+02 0.0022 26.2 3.3 32 83-114 135-166 (175)
166 PRK12544 RNA polymerase sigma 21.6 2.4E+02 0.0052 25.3 5.8 46 64-114 149-194 (206)
167 PRK09651 RNA polymerase sigma 21.4 1.8E+02 0.0039 24.9 4.8 38 64-106 120-157 (172)
168 PRK06704 RNA polymerase factor 21.4 1.9E+02 0.0041 26.9 5.2 27 86-112 134-160 (228)
169 smart00027 EH Eps15 homology d 21.2 1.9E+02 0.004 22.6 4.4 43 64-106 4-51 (96)
170 PRK08583 RNA polymerase sigma 21.0 1.4E+02 0.003 27.6 4.2 42 64-110 206-247 (257)
171 TIGR03070 couple_hipB transcri 20.9 63 0.0014 22.0 1.5 23 87-109 18-40 (58)
172 PRK12529 RNA polymerase sigma 20.8 2.1E+02 0.0045 24.7 5.1 43 64-111 128-170 (178)
173 PRK09645 RNA polymerase sigma 20.5 2.2E+02 0.0048 24.0 5.1 38 64-106 119-156 (173)
174 KOG0483 Transcription factor H 20.3 75 0.0016 29.3 2.2 39 121-165 107-145 (198)
175 PRK09649 RNA polymerase sigma 20.3 1.8E+02 0.004 25.2 4.7 38 64-106 131-168 (185)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.85 E-value=7.8e-22 Score=178.50 Aligned_cols=105 Identities=59% Similarity=0.873 Sum_probs=94.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHHHHHHHhhhhhHHhh
Q 021250 54 GGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKANYDALKL 133 (315)
Q Consensus 54 ~~~~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~~~~~lk~~~~~l~~ 133 (315)
+....+|++|||.+|+..||..|+.+.++.+.+|..||+.|||.+|||+|||||||||||.++++.++..||..++.++.
T Consensus 47 ~~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~ 126 (198)
T KOG0483|consen 47 GSKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRS 126 (198)
T ss_pred ccccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhh
Confidence 34466778889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccchHHHHHHHHhhhhccccchhhhhhccc
Q 021250 134 NYDSLQHDNEALLKETIVHETDHQNKATLDR 164 (315)
Q Consensus 134 ~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~~ 164 (315)
+++.|+.++..|.+++. .++..+..
T Consensus 127 ~~~~Lq~e~~eL~~~~~------~~~~~~~~ 151 (198)
T KOG0483|consen 127 ENDRLQSEVQELVAELS------SLKREMQK 151 (198)
T ss_pred hhhHHHHHHHHHHHHHh------hhhhhhcc
Confidence 88888888888888887 56555543
No 2
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.68 E-value=1.7e-17 Score=155.93 Aligned_cols=63 Identities=33% Similarity=0.688 Sum_probs=57.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHH
Q 021250 55 GHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (315)
Q Consensus 55 ~~~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (315)
+..||.|+.||..|+.+||+.|..|+|+++.+|.+||..|.|++|||||||||||+||||..+
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence 345555666999999999999999999999999999999999999999999999999998644
No 3
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.67 E-value=2.7e-17 Score=157.16 Aligned_cols=69 Identities=38% Similarity=0.587 Sum_probs=61.4
Q ss_pred CCCCCCCC--CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHHHHHHH
Q 021250 56 HVSEKKRR--LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVL 124 (315)
Q Consensus 56 ~~krkrrR--fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~~~~~l 124 (315)
.++|||+| ||..|+.+||+.|..++|++..+|++||..|+|+++||||||||||-|.||+++++.+..+
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 34455555 9999999999999999999999999999999999999999999999999999887765543
No 4
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.66 E-value=2.7e-16 Score=151.21 Aligned_cols=55 Identities=44% Similarity=0.723 Sum_probs=53.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~ 118 (315)
||..||..||+.|++.+|++..+|.+||+.|||+..||++||||||+|||+...+
T Consensus 179 FT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 179 FSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred hhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 9999999999999999999999999999999999999999999999999997554
No 5
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.61 E-value=2.4e-16 Score=150.76 Aligned_cols=63 Identities=33% Similarity=0.502 Sum_probs=56.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHH
Q 021250 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (315)
Q Consensus 57 ~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~ 119 (315)
.||||.-+|..|+.+||+.|-.|.|++.+.|.+|++.|+|++|||+|||||||+|.||..++.
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 445555599999999999999999999999999999999999999999999999999876533
No 6
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.60 E-value=8.7e-16 Score=136.39 Aligned_cols=64 Identities=34% Similarity=0.487 Sum_probs=58.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHH
Q 021250 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (315)
Q Consensus 56 ~~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~ 119 (315)
+.||.|+.||.+|+..||..|+.++|....+|++||+.|+|++.||+|||||||.|.||.+.+.
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 3444455599999999999999999999999999999999999999999999999999987754
No 7
>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=99.59 E-value=2.4e-15 Score=109.10 Aligned_cols=57 Identities=42% Similarity=0.647 Sum_probs=54.1
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 58 krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
+++|++||.+|+..|+..|..++||+..++..||..|||+..+|++||+|||+++|+
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 456778999999999999999999999999999999999999999999999999885
No 8
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.58 E-value=1.4e-15 Score=124.53 Aligned_cols=59 Identities=27% Similarity=0.497 Sum_probs=54.2
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHH
Q 021250 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (315)
Q Consensus 59 rkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (315)
+-|+.||..||..||+.|...+||++-.|++||.++.|++.+|+|||||||||.|++..
T Consensus 19 RIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 19 RIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred hhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 33444999999999999999999999999999999999999999999999999998644
No 9
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.57 E-value=1.6e-15 Score=138.20 Aligned_cols=59 Identities=42% Similarity=0.684 Sum_probs=54.7
Q ss_pred CCCCCC--CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHH
Q 021250 58 SEKKRR--LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (315)
Q Consensus 58 krkrrR--fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (315)
||||+| |+..|+..||..|+..+|++..+|..||+.|.|++.||+|||||||.|||++-
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 445555 99999999999999999999999999999999999999999999999999863
No 10
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.55 E-value=4.7e-15 Score=135.99 Aligned_cols=59 Identities=36% Similarity=0.587 Sum_probs=53.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHH
Q 021250 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (315)
Q Consensus 57 ~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkk 115 (315)
.||.|+.++.-||..|.+.|+++.|+-..+|.+||..|||+..||+|||||||.|.||.
T Consensus 122 ~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 122 VRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred ccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 33444559999999999999999999999999999999999999999999999999874
No 11
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.51 E-value=2.4e-14 Score=129.80 Aligned_cols=61 Identities=31% Similarity=0.491 Sum_probs=55.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHH
Q 021250 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (315)
Q Consensus 57 ~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (315)
.|+.|+-||..||..||+.|...+|+++.+|.+++..|.|++.||+|||||||||.||-|.
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 3444555999999999999999999999999999999999999999999999999998554
No 12
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.51 E-value=2.4e-14 Score=133.46 Aligned_cols=57 Identities=30% Similarity=0.533 Sum_probs=53.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERD 120 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~~ 120 (315)
||..|+..||+.|+..+||+...|+-||.++.|++.+|+||||||||||||+...-.
T Consensus 148 FT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 148 FTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred hhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 999999999999999999999999999999999999999999999999999765443
No 13
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.51 E-value=3.4e-14 Score=132.54 Aligned_cols=62 Identities=32% Similarity=0.610 Sum_probs=56.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHH
Q 021250 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (315)
Q Consensus 58 krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~ 119 (315)
||.|+.||.+||..|+..|+.++|++..+|++||.+|||.+.||+|||||+|+|.||..-.+
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgsk 308 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSK 308 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCC
Confidence 44455599999999999999999999999999999999999999999999999999865543
No 14
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.50 E-value=9.5e-15 Score=136.52 Aligned_cols=54 Identities=41% Similarity=0.602 Sum_probs=51.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (315)
+|..|..+||+.|..++|.++.+|.+||.-|||++|||+|||||||||+||..+
T Consensus 206 YTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred ecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999998544
No 15
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.47 E-value=3.6e-14 Score=129.58 Aligned_cols=64 Identities=27% Similarity=0.436 Sum_probs=58.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHH
Q 021250 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (315)
Q Consensus 56 ~~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~ 119 (315)
+.+|.|++||..|+.+||..|.+..||+...|++||.+|+|.+.+|+|||+|||+|+|+++..+
T Consensus 36 kqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 36 KQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred hcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 3445566699999999999999999999999999999999999999999999999999876643
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=1.7e-13 Score=98.94 Aligned_cols=57 Identities=46% Similarity=0.738 Sum_probs=53.2
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHH
Q 021250 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (315)
Q Consensus 59 rkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkk 115 (315)
+++..++..|+..|+..|..++||+..++..||..+||++++|++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 445669999999999999999999999999999999999999999999999998763
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.43 E-value=2e-13 Score=98.11 Aligned_cols=55 Identities=45% Similarity=0.792 Sum_probs=51.2
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 59 rkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+.+.+|+.+|+..|+..|..++||+..++..||..+||+..||++||+|||++.|
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 3456699999999999999999999999999999999999999999999998754
No 18
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.40 E-value=1e-13 Score=131.76 Aligned_cols=63 Identities=33% Similarity=0.551 Sum_probs=58.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHH
Q 021250 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (315)
Q Consensus 56 ~~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~ 118 (315)
+-||-|+.||.+||..||+.|-+.+|.+..+|.+||..|+|++..|+|||||||+|+||+.+.
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 445556669999999999999999999999999999999999999999999999999998775
No 19
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.40 E-value=3.3e-13 Score=118.42 Aligned_cols=65 Identities=32% Similarity=0.573 Sum_probs=59.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHH
Q 021250 55 GHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (315)
Q Consensus 55 ~~~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~ 119 (315)
...+++|+|.|..|+.+|+..|+.++||+...|..|+..|+|+++-|+|||||||++.|++....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence 45677788899999999999999999999999999999999999999999999999999876543
No 20
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.37 E-value=4e-13 Score=126.91 Aligned_cols=96 Identities=22% Similarity=0.336 Sum_probs=79.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHHHHHHHhhhhhHHh
Q 021250 53 SGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKANYDALK 132 (315)
Q Consensus 53 ~~~~~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~~~~~lk~~~~~l~ 132 (315)
..+..||.|+.+|+.||+.|+..|+..++|....|++|+.++||.-|.|||||||||||.||-+...-...|.+-+..++
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK 242 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMK 242 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhh
Confidence 34556777888999999999999999999999999999999999999999999999999999877777778888887777
Q ss_pred hhccchHHHHHHHHhhh
Q 021250 133 LNYDSLQHDNEALLKET 149 (315)
Q Consensus 133 ~~~~sl~~en~~L~~E~ 149 (315)
.. .+-+.++..=..|+
T Consensus 243 ~s-gs~r~ekdsd~sel 258 (383)
T KOG4577|consen 243 RS-GSSRAEKDSDDSEL 258 (383)
T ss_pred cc-CCcccccccccCcc
Confidence 66 44455544423344
No 21
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.35 E-value=2.3e-13 Score=119.61 Aligned_cols=58 Identities=38% Similarity=0.548 Sum_probs=54.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHH
Q 021250 62 RRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (315)
Q Consensus 62 rRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~ 119 (315)
+.|+..|+..||+.|+..+|++..+|.+||..|+|+++||+.||||||+|.||.++..
T Consensus 105 tvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 105 TVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred ccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 3499999999999999999999999999999999999999999999999999876644
No 22
>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=99.33 E-value=1.1e-12 Score=97.37 Aligned_cols=52 Identities=15% Similarity=0.360 Sum_probs=49.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHhCCCcchhhhHhhhhH
Q 021250 58 SEKKRRLSVDQVKALEKNFEVENK----LEPERKVKLAQELGLQPRQVAVWFQNRR 109 (315)
Q Consensus 58 krkrrRfT~~Ql~~LE~~F~~~~y----ps~~~r~eLA~~LgLserQVqVWFQNRR 109 (315)
++.|+.||.+|+..||..|+.+.| |+...+.+||..|||++++|+|||||.+
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 566777999999999999999999 9999999999999999999999999964
No 23
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.29 E-value=2.3e-12 Score=122.85 Aligned_cols=57 Identities=26% Similarity=0.559 Sum_probs=54.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERD 120 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~~ 120 (315)
||..|+..||..|++++||+...|++||..++|++.+|+|||.|||+||||+.+...
T Consensus 119 FtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 119 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 999999999999999999999999999999999999999999999999999766444
No 24
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.21 E-value=7.7e-12 Score=114.52 Aligned_cols=63 Identities=37% Similarity=0.675 Sum_probs=56.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHH
Q 021250 55 GHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (315)
Q Consensus 55 ~~~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (315)
|+++..|..|+..||..||..|+..+|+-...|.+||-.+|+++.||+|||||||+||||+.-
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 444444445999999999999999999999999999999999999999999999999998643
No 25
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.15 E-value=1.6e-11 Score=120.40 Aligned_cols=60 Identities=32% Similarity=0.443 Sum_probs=54.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHH
Q 021250 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (315)
Q Consensus 56 ~~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkk 115 (315)
++||||+.|....+..||+.|.+|++|+..++..||.+|+|...+|+|||+|||.|.||.
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~ 352 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRI 352 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccC
Confidence 345555559999999999999999999999999999999999999999999999999873
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.03 E-value=1.1e-10 Score=105.46 Aligned_cols=62 Identities=27% Similarity=0.318 Sum_probs=56.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHH
Q 021250 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (315)
Q Consensus 56 ~~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (315)
..++.|+.|+..|+.+||+.|+..+||+...|+.||..+++++..|+|||||||+||++...
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 34555566999999999999999999999999999999999999999999999999998653
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.84 E-value=3.3e-09 Score=104.11 Aligned_cols=61 Identities=34% Similarity=0.570 Sum_probs=55.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHH
Q 021250 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (315)
Q Consensus 57 ~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (315)
.+++|+.|+..|+..||+.|++++||+...|++||.+++|++..|+|||+|||+++++...
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred ccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 3444566999999999999999999999999999999999999999999999999998644
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.70 E-value=5.1e-09 Score=99.46 Aligned_cols=65 Identities=28% Similarity=0.495 Sum_probs=58.8
Q ss_pred cCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHH
Q 021250 52 ESGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (315)
Q Consensus 52 ~~~~~~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (315)
..++.+||||+.+.+...+.||.+|...+.|+.+.+..||.+|+|....|+|||+|.|.|.||.+
T Consensus 304 ~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 304 LPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred cCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 34566777788899999999999999999999999999999999999999999999999988843
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.60 E-value=3.9e-08 Score=92.85 Aligned_cols=51 Identities=29% Similarity=0.428 Sum_probs=47.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
|...-..+|..+|..++||++.+|.+||+.+||+..||-.||.|||.|+|.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 666778899999999999999999999999999999999999999999883
No 30
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.17 E-value=1.5e-06 Score=59.97 Aligned_cols=34 Identities=35% Similarity=0.556 Sum_probs=28.9
Q ss_pred hcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHH
Q 021250 78 VENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (315)
Q Consensus 78 ~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK 111 (315)
.++||+.+++..||..+||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4689999999999999999999999999999875
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.10 E-value=1.5e-06 Score=81.88 Aligned_cols=59 Identities=29% Similarity=0.461 Sum_probs=53.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHH
Q 021250 57 VSEKKRRLSVDQVKALEKNFE---VENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (315)
Q Consensus 57 ~krkrrRfT~~Ql~~LE~~F~---~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkk 115 (315)
.+||||.|+..-..+|..+|. .++||+.+.+++||+++|++..||-.||.|+|-+.||.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 456777799999999999997 57899999999999999999999999999999998873
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.75 E-value=3.1e-05 Score=69.89 Aligned_cols=61 Identities=31% Similarity=0.573 Sum_probs=54.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHH
Q 021250 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (315)
Q Consensus 57 ~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (315)
.++.++.++..|+..|+..|....+|+...+.+|+..+|++++.|++||||+|++.++...
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3444455899999999999999999999999999999999999999999999999988644
No 33
>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=97.64 E-value=5.4e-05 Score=53.66 Aligned_cols=44 Identities=55% Similarity=0.763 Sum_probs=41.2
Q ss_pred HHHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhccc
Q 021250 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDR 164 (315)
Q Consensus 115 kq~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~~ 164 (315)
+|++++|..|+..|+.|+.+|++|.++|+.|++|+. .|+.+|..
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~------~L~~kl~~ 44 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQ------ELKEKLQM 44 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHhhcC
Confidence 478999999999999999999999999999999999 99988753
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.63 E-value=9.1e-05 Score=75.98 Aligned_cols=56 Identities=21% Similarity=0.280 Sum_probs=50.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHH
Q 021250 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARW 112 (315)
Q Consensus 57 ~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~ 112 (315)
.||.|.-||..|...|..+|+.+++|+.+..+.|+..|||....|.+||-|-|.|.
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 34444449999999999999999999999999999999999999999999988764
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.15 E-value=0.00039 Score=77.30 Aligned_cols=63 Identities=27% Similarity=0.380 Sum_probs=57.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHH
Q 021250 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (315)
Q Consensus 56 ~~krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~ 118 (315)
.++.+|++++..||..|...|....+|...+.+.|...+++..+.|+|||||-|+|.|+..+.
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n 964 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLN 964 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhc
Confidence 356667789999999999999999999999999999999999999999999999999987664
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.18 E-value=0.0041 Score=46.14 Aligned_cols=42 Identities=24% Similarity=0.421 Sum_probs=31.2
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhH
Q 021250 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (315)
Q Consensus 68 Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRR 109 (315)
-+..|+++|...+.+.......|..+.+|+..||+.||-.|+
T Consensus 9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 356799999999999999999999999999999999997554
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.95 E-value=0.0064 Score=59.08 Aligned_cols=57 Identities=28% Similarity=0.366 Sum_probs=47.7
Q ss_pred CCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHH
Q 021250 61 KRRLSVDQVKALEKNFEV---ENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (315)
Q Consensus 61 rrRfT~~Ql~~LE~~F~~---~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (315)
++.|....+.+|+.+... .+||+...+..||+++||+..||.+||-|.|-|..+-..
T Consensus 243 ~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 243 QRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 334999999999977433 469999999999999999999999999999887766444
No 38
>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=92.61 E-value=0.33 Score=35.17 Aligned_cols=47 Identities=21% Similarity=0.412 Sum_probs=34.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhH
Q 021250 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (315)
Q Consensus 58 krkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRR 109 (315)
+++|+.+|.++-..+-..++... ....||+++|++..+|..|..|+.
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 35566699998888877787765 578899999999999999998753
No 39
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=92.59 E-value=0.16 Score=54.41 Aligned_cols=52 Identities=21% Similarity=0.345 Sum_probs=46.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (315)
|+.. +.+|..+|..|..|+.++...+|...||+.+.|++||+++++....-.
T Consensus 564 ~~~p-~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 564 FNHP-TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred cCCc-HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 4433 788999999999999999999999999999999999999999876544
No 40
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=90.00 E-value=1.9 Score=35.99 Aligned_cols=43 Identities=21% Similarity=0.402 Sum_probs=29.2
Q ss_pred CCCCCCHHHHH-HHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhh
Q 021250 60 KKRRLSVDQVK-ALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (315)
Q Consensus 60 krrRfT~~Ql~-~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQN 107 (315)
+++++|.++.. ++...+.. . ....++|+++|+++.+|..|.+.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~-g----~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEP-G----MTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcC-C----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 35668877644 44333432 2 24567899999999999999653
No 41
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=86.72 E-value=6.9 Score=33.89 Aligned_cols=90 Identities=23% Similarity=0.224 Sum_probs=60.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHh-CCCcchhhhHhhhhHHHH-------HHHHHHHHHHHHhhhhhHHhh
Q 021250 62 RRLSVDQVKALEKNFEVENKLEPERKVKLAQEL-GLQPRQVAVWFQNRRARW-------KTKQLERDYGVLKANYDALKL 133 (315)
Q Consensus 62 rRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~L-gLserQVqVWFQNRRaK~-------Kkkq~~~~~~~lk~~~~~l~~ 133 (315)
.+|+.++|..+ . ..+|=+.| |++...|-.|=|.||+-. -+-+.-.+...|...+..|..
T Consensus 22 d~lsDd~Lvsm------------S-VReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~q 88 (135)
T KOG4196|consen 22 DRLSDDELVSM------------S-VRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQ 88 (135)
T ss_pred CCcCHHHHHHh------------h-HHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56999988876 2 23344444 899999999999887532 122223344556666667777
Q ss_pred hccchHHHHHHHHhhhhccccchhhhhhcccccchhH
Q 021250 134 NYDSLQHDNEALLKETIVHETDHQNKATLDRDQESDD 170 (315)
Q Consensus 134 ~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~~~~~~s~ 170 (315)
+.+.|..++.++..|+. .++.+...-....+
T Consensus 89 qv~~L~~e~s~~~~E~d------a~k~k~e~l~~~~~ 119 (135)
T KOG4196|consen 89 QVEKLKEENSRLRRELD------AYKSKYEALQNSAV 119 (135)
T ss_pred HHHHHHHHHHHHHHHHH------HHHHHHHHHHhhhh
Confidence 77788888888888888 78887765554444
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=85.75 E-value=0.7 Score=32.74 Aligned_cols=36 Identities=39% Similarity=0.600 Sum_probs=30.6
Q ss_pred HHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhccc
Q 021250 123 VLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDR 164 (315)
Q Consensus 123 ~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~~ 164 (315)
.+...|+.|+..|+.|..++++|..|+. .|++.+..
T Consensus 2 QlE~Dy~~LK~~yd~Lk~~~~~L~~E~~------~L~aev~~ 37 (45)
T PF02183_consen 2 QLERDYDALKASYDSLKAEYDSLKKENE------KLRAEVQE 37 (45)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHH
Confidence 3567889999999999999999999998 88887753
No 43
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=76.16 E-value=3.3 Score=30.26 Aligned_cols=40 Identities=25% Similarity=0.264 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHhCCCcchhhh
Q 021250 64 LSVDQVKALEKNFEVENK--LEPERKVKLAQELGLQPRQVAV 103 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~y--ps~~~r~eLA~~LgLserQVqV 103 (315)
+|..|..+|...|+..-| |-.....+||.+||+++..|..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 688999999999998876 5556688999999999987654
No 44
>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=74.07 E-value=2.2 Score=31.84 Aligned_cols=44 Identities=23% Similarity=0.379 Sum_probs=28.2
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 59 rkrrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
+++++||+++...+-..+... ......+|+++||++.++..|-.
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 356679998877665555221 25678899999999999999954
No 45
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=73.93 E-value=8 Score=26.83 Aligned_cols=39 Identities=13% Similarity=0.176 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
.+++.+..+|...|.. ...-.++|..+|++...|+.+..
T Consensus 4 ~L~~~er~vi~~~y~~-----~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE-----GLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHHTS-----T-SHHHHHHHHTSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC-----CCCHHHHHHHHCCcHHHHHHHHH
Confidence 3788899999999932 24567899999999999988754
No 46
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=71.09 E-value=6.1 Score=26.17 Aligned_cols=42 Identities=14% Similarity=0.128 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRa 110 (315)
++..+..++...|... ....++|..+|++...|..|....+.
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6778888887777422 24567899999999999999865443
No 47
>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=68.80 E-value=12 Score=21.99 Aligned_cols=39 Identities=13% Similarity=0.329 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHh
Q 021250 62 RRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWF 105 (315)
Q Consensus 62 rRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWF 105 (315)
+.++.++...+...|... . ...++|..+|++...|..|.
T Consensus 4 ~~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 346777777776666532 1 45678999999999888773
No 48
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=62.52 E-value=10 Score=27.14 Aligned_cols=40 Identities=15% Similarity=0.204 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHHHHHHHh
Q 021250 86 RKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLK 125 (315)
Q Consensus 86 ~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~~~~~lk 125 (315)
....||+.+|++..+|..|+.++.....-..+.+-...|.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~ 51 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALN 51 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcC
Confidence 4678999999999999999988766666555544444443
No 49
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=61.40 E-value=13 Score=33.79 Aligned_cols=49 Identities=24% Similarity=0.269 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 63 RLSVDQVKALEKNFEVENK--LEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~y--ps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
.||..|+.+|..+|...-| |-.....+||+++|+++..+. .-=|||..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~--ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLS--EHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH--HHHHHHHHH
Confidence 4999999999999998875 666678899999999997643 334555433
No 50
>smart00340 HALZ homeobox associated leucin zipper.
Probab=58.93 E-value=9.3 Score=26.98 Aligned_cols=26 Identities=35% Similarity=0.397 Sum_probs=20.3
Q ss_pred hHHhhhccchHHHHHHHHhhhhccccchhhhh
Q 021250 129 DALKLNYDSLQHDNEALLKETIVHETDHQNKA 160 (315)
Q Consensus 129 ~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~ 160 (315)
+.|+.-+++|..+|.+|++|+. +|+.
T Consensus 8 e~LKrcce~LteeNrRL~ke~~------eLra 33 (44)
T smart00340 8 ELLKRCCESLTEENRRLQKEVQ------ELRA 33 (44)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH------HHHh
Confidence 3445566777889999999999 8886
No 51
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=56.95 E-value=21 Score=24.88 Aligned_cols=39 Identities=15% Similarity=0.147 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQN 107 (315)
+++.+..++.-.|-.. -.-.++|..+|+++..|+.|.+.
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 5666666766655433 46778999999999999999863
No 52
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=55.84 E-value=25 Score=33.55 Aligned_cols=52 Identities=29% Similarity=0.366 Sum_probs=34.7
Q ss_pred hhhHHHHHHH--HHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhcc
Q 021250 106 QNRRARWKTK--QLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLD 163 (315)
Q Consensus 106 QNRRaK~Kkk--q~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~ 163 (315)
|+-|-|.|-+ .++.+..-|..+++.|..+++.|+..|+.|..++. +|..+|.
T Consensus 82 QtaRDrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~------el~~~le 135 (292)
T KOG4005|consen 82 QTARDRKKARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNH------ELDSELE 135 (292)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH------HHHHHHH
Confidence 5555554443 33444556777888888888888888888877776 6666554
No 53
>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=54.88 E-value=28 Score=25.62 Aligned_cols=30 Identities=23% Similarity=0.281 Sum_probs=15.4
Q ss_pred HHHHhhhhhHHhhhccchHHHHHHHHhhhh
Q 021250 121 YGVLKANYDALKLNYDSLQHDNEALLKETI 150 (315)
Q Consensus 121 ~~~lk~~~~~l~~~~~sl~~en~~L~~E~~ 150 (315)
...|......|...++.|..++..|..++.
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~L~~~~~ 57 (64)
T PF00170_consen 28 IEELEEKVEELESENEELKKELEQLKKEIQ 57 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444455555555555555555555554
No 54
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=54.81 E-value=32 Score=30.00 Aligned_cols=48 Identities=19% Similarity=0.178 Sum_probs=35.4
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 61 rrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
...+|+.|..+|... ... ....++|..||++...|..|-+..+.+.|+
T Consensus 4 ~~~Lt~rqreVL~lr-~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ERG-----LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345899999999773 222 345689999999999999998755544443
No 55
>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=53.11 E-value=9.3 Score=28.78 Aligned_cols=19 Identities=21% Similarity=0.604 Sum_probs=16.9
Q ss_pred HHHHHHHHhCCCcchhhhH
Q 021250 86 RKVKLAQELGLQPRQVAVW 104 (315)
Q Consensus 86 ~r~eLA~~LgLserQVqVW 104 (315)
.-.+||.+||+++.+|+.|
T Consensus 24 ~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 3557899999999999999
No 56
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=52.43 E-value=14 Score=25.43 Aligned_cols=40 Identities=18% Similarity=0.231 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 62 RRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 62 rRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
+.||.+|...++..+... ....+||+.||.++..|..+..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 458899999999887644 4566799999999999987763
No 57
>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=49.74 E-value=40 Score=26.77 Aligned_cols=47 Identities=17% Similarity=0.202 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhcc
Q 021250 111 RWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLD 163 (315)
Q Consensus 111 K~Kkkq~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~ 163 (315)
+..+..+.++...|+.....|....+..+.+++.|..|+. .|...+.
T Consensus 15 ~e~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~------~Lq~YI~ 61 (80)
T PF10224_consen 15 KEEKEELIQEILELQDSLEALSDRVEEVKEENEKLESENE------YLQQYIG 61 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHH
Confidence 3344456666777777777788888888888888888887 7777664
No 58
>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=49.36 E-value=28 Score=28.96 Aligned_cols=46 Identities=26% Similarity=0.335 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhccccc
Q 021250 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDRDQ 166 (315)
Q Consensus 115 kq~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~~~~ 166 (315)
.++++....+-.....|+.....+..+|..|..|+. .|+.+|....
T Consensus 11 ~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~------~Lr~~l~~~~ 56 (107)
T PF06156_consen 11 DQLEQQLGQLLEELEELKKQLQELLEENARLRIENE------HLRERLEELE 56 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHh
Confidence 456677777788888888888889999999999999 9999987654
No 59
>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=49.09 E-value=33 Score=25.74 Aligned_cols=44 Identities=18% Similarity=0.341 Sum_probs=22.3
Q ss_pred CCCCCHHH-HHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 61 KRRLSVDQ-VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 61 rrRfT~~Q-l~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
|+.|+..- |.+++..+..+ .--...|. -|+++|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~-nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDN-NCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-T-TTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHcc-chhhhHHH-HHHHhCccHHHHHHHHH
Confidence 34466543 45555444333 22222333 49999999999999953
No 60
>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=47.97 E-value=45 Score=24.51 Aligned_cols=38 Identities=21% Similarity=0.304 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhh
Q 021250 112 WKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKET 149 (315)
Q Consensus 112 ~Kkkq~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~ 149 (315)
..-..++.....|...++.|......|..+...|..++
T Consensus 26 ~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 26 QYIEELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 33445666777788888888888888888888887765
No 61
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=45.12 E-value=32 Score=28.08 Aligned_cols=33 Identities=30% Similarity=0.662 Sum_probs=19.9
Q ss_pred HHHHHHHHhhcCCCCHH--HHHHHHHHhCCCcchhhhHhhhhHHHHHHHHH
Q 021250 69 VKALEKNFEVENKLEPE--RKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (315)
Q Consensus 69 l~~LE~~F~~~~yps~~--~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (315)
+....-.|+.++||... .+.. .|||.+|++.+.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~aR----------------RnRRRRWR~rq~ 48 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQAR----------------RNRRRRWRARQR 48 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HHHH----------------HHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccccc----------------cchhhhHHHHHH
Confidence 44556668999998754 2222 689999998765
No 62
>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=45.08 E-value=43 Score=23.84 Aligned_cols=44 Identities=16% Similarity=0.191 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHH
Q 021250 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARW 112 (315)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~ 112 (315)
+||+.++.+|.-...-. ...++|..+|++++.|..+..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 47888888887766533 467899999999999998876555443
No 63
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=44.35 E-value=53 Score=27.55 Aligned_cols=46 Identities=13% Similarity=0.122 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
+++.+..++...|-.. -.-.++|..+|+++..|++....-|.+-|+
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5666666665554333 235689999999999999988644444443
No 64
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=43.54 E-value=47 Score=28.00 Aligned_cols=44 Identities=34% Similarity=0.405 Sum_probs=37.6
Q ss_pred HHHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhccc
Q 021250 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDR 164 (315)
Q Consensus 115 kq~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~~ 164 (315)
..++....++-++...++....++-.+|..|+.|+. .|+.+|..
T Consensus 11 ~~le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe------~LR~RL~~ 54 (114)
T COG4467 11 DNLEEQLGVLLAELGGLKQHLGSLVEENTALRLENE------KLRERLGE 54 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHH------HHHHHhCC
Confidence 356667777888888888888899999999999999 99999987
No 65
>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=43.47 E-value=19 Score=24.22 Aligned_cols=22 Identities=18% Similarity=0.208 Sum_probs=18.7
Q ss_pred HHHHHHHhCCCcchhhhHhhhh
Q 021250 87 KVKLAQELGLQPRQVAVWFQNR 108 (315)
Q Consensus 87 r~eLA~~LgLserQVqVWFQNR 108 (315)
..++|+.+|++++.|+.|.++.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999997654
No 66
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=42.92 E-value=41 Score=28.24 Aligned_cols=45 Identities=31% Similarity=0.364 Sum_probs=36.8
Q ss_pred HHHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhcccc
Q 021250 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDRD 165 (315)
Q Consensus 115 kq~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~~~ 165 (315)
.++++....+-.....|+.....+..+|..|+.|+. -|+.+|...
T Consensus 11 ~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~------~Lr~~l~~~ 55 (110)
T PRK13169 11 DDLEQNLGVLLKELGALKKQLAELLEENTALRLEND------KLRERLEEL 55 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHh
Confidence 456677777777888888888888899999999998 899998753
No 67
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=42.85 E-value=51 Score=27.75 Aligned_cols=41 Identities=15% Similarity=0.012 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRR 109 (315)
+++.+..+|...|-.. ..-.++|..+|+++..|+.|...-|
T Consensus 129 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~ 169 (182)
T PRK09652 129 LPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAR 169 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 7777777777665322 2456899999999999999886333
No 68
>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=42.48 E-value=52 Score=26.12 Aligned_cols=43 Identities=16% Similarity=0.167 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK 111 (315)
+++.|..++...|-. .....++|..+|+++..|..+...-+.+
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKK 153 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 666666666554432 2345689999999999999887644443
No 69
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=41.04 E-value=44 Score=32.67 Aligned_cols=46 Identities=17% Similarity=0.232 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhcc
Q 021250 111 RWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLD 163 (315)
Q Consensus 111 K~Kkkq~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~ 163 (315)
|+|.|++ .+...+-.+.+.|-..++.|+.+...|.+|+. +||+-+.
T Consensus 241 RYRqKkR-ae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~------ylKqli~ 286 (294)
T KOG4571|consen 241 RYRQKKR-AEKEALLGELEGLEKRNEELKDQASELEREIR------YLKQLIL 286 (294)
T ss_pred HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHH
Confidence 4443333 44455556677788888888889999999999 8888654
No 70
>PF13518 HTH_28: Helix-turn-helix domain
Probab=40.86 E-value=28 Score=23.67 Aligned_cols=22 Identities=23% Similarity=0.520 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCCcchhhhHhhh
Q 021250 86 RKVKLAQELGLQPRQVAVWFQN 107 (315)
Q Consensus 86 ~r~eLA~~LgLserQVqVWFQN 107 (315)
...++|.++|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 4567999999999999999863
No 71
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=40.43 E-value=59 Score=28.50 Aligned_cols=45 Identities=13% Similarity=0.119 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.+..+|...|-.. ..-.++|..||++...|+++...-|.+-|
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence 7777777776655333 34678999999999999998854444433
No 72
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=40.30 E-value=55 Score=27.11 Aligned_cols=42 Identities=17% Similarity=0.101 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRa 110 (315)
+++.+..++...|-.. ....++|..+|++...|+.|...-|.
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6777777776655433 34678999999999999998753333
No 73
>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=40.07 E-value=41 Score=23.09 Aligned_cols=38 Identities=16% Similarity=0.367 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHh
Q 021250 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWF 105 (315)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWF 105 (315)
.++.+|+..+...+... ....+||+.+|++...|..++
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 37777777777777655 347789999999999987765
No 74
>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=39.31 E-value=1.2e+02 Score=23.64 Aligned_cols=22 Identities=14% Similarity=0.208 Sum_probs=18.6
Q ss_pred HHHHHHHhCCCcchhhhHhhhh
Q 021250 87 KVKLAQELGLQPRQVAVWFQNR 108 (315)
Q Consensus 87 r~eLA~~LgLserQVqVWFQNR 108 (315)
..++|+.+|++++.|+.|-+..
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~G 25 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERLG 25 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999998654
No 75
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=39.17 E-value=69 Score=26.85 Aligned_cols=45 Identities=18% Similarity=0.172 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.+..+|...|-. ...-.+||..+|+++..|..|..--|.+.|
T Consensus 126 L~~~~r~i~~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 126 LPVKQREVFLLRYVE-----GLSYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 555555555554432 234578999999999999999864444444
No 76
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=39.11 E-value=64 Score=28.72 Aligned_cols=45 Identities=20% Similarity=0.149 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.|..+|...|-. .....++|..+|+++..|+++...-|.+.+
T Consensus 154 L~~~~r~vl~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 198 (206)
T PRK12526 154 LPEAQQTVVKGVYFQ-----ELSQEQLAQQLNVPLGTVKSRLRLALAKLK 198 (206)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 566666666544422 234678999999999999988754444433
No 77
>PRK04217 hypothetical protein; Provisional
Probab=38.92 E-value=80 Score=26.39 Aligned_cols=44 Identities=11% Similarity=0.079 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHH
Q 021250 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (315)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK 111 (315)
.++.+|..++...|...- ...+||+.+|++...|...+..-|.+
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkk 85 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKK 85 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 489999888877765443 56789999999999999877644433
No 78
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=37.79 E-value=70 Score=21.34 Aligned_cols=37 Identities=16% Similarity=0.214 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
++..+...+...+ .. ....++|..+|++...|..|.+
T Consensus 4 l~~~e~~i~~~~~-~g-----~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 4 LTPREREVLRLLA-EG-----LTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 6777888775533 22 2457899999999999998865
No 79
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=37.00 E-value=49 Score=28.37 Aligned_cols=45 Identities=16% Similarity=0.302 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.+..+|...|- ......++|..+|+++..|+++...-|.+-|
T Consensus 130 L~~~~r~i~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 130 LEKDRAAAVRRAYL-----EGLSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 56666655555542 2234678999999999999998864444443
No 80
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=36.52 E-value=2.3e+02 Score=29.52 Aligned_cols=82 Identities=15% Similarity=0.267 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHH-HhhcC-CCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHHH--------HHHHhhhhhHH
Q 021250 62 RRLSVDQVKALEKN-FEVEN-KLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERD--------YGVLKANYDAL 131 (315)
Q Consensus 62 rRfT~~Ql~~LE~~-F~~~~-yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~~--------~~~lk~~~~~l 131 (315)
-++|.+....|.+. |-... +|-...-+++-+ +|+.=.+|+|...-.+++.++ +...-+++..|
T Consensus 219 L~LteeEkrLL~kEG~slPs~lPLTKaEEriLK-------rvRRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqeL 291 (472)
T KOG0709|consen 219 LVLTEEEKRLLTKEGYSLPSKLPLTKAEERILK-------RVRRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQEL 291 (472)
T ss_pred eeccHHHHHHHHhccCcCcccCCchHHHHHHHH-------HHHHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHHH
Confidence 34888888888765 33333 344443333333 344444555533322222222 22223333444
Q ss_pred hhhccchHHHHHHHHhhhh
Q 021250 132 KLNYDSLQHDNEALLKETI 150 (315)
Q Consensus 132 ~~~~~sl~~en~~L~~E~~ 150 (315)
+.....|..+|+.|.+++.
T Consensus 292 ~kkV~~Le~~N~sLl~qL~ 310 (472)
T KOG0709|consen 292 QKKVEELELSNRSLLAQLK 310 (472)
T ss_pred HHHHHHHhhccHHHHHHHH
Confidence 4444444444555555554
No 81
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=35.48 E-value=94 Score=27.18 Aligned_cols=45 Identities=16% Similarity=0.200 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.+..++.-.|-.. ....++|..+|+++..|+++...-|.+-|
T Consensus 135 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr 179 (189)
T PRK12530 135 LPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQ 179 (189)
T ss_pred CCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5666666666554332 24678999999999999998754443333
No 82
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=35.27 E-value=29 Score=23.72 Aligned_cols=22 Identities=23% Similarity=0.412 Sum_probs=17.3
Q ss_pred HHHHHHHHHhCCCcchhhhHhh
Q 021250 85 ERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 85 ~~r~eLA~~LgLserQVqVWFQ 106 (315)
....++|+.+|++...|..|.+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4567899999999999999975
No 83
>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=35.13 E-value=19 Score=28.12 Aligned_cols=35 Identities=17% Similarity=0.229 Sum_probs=25.7
Q ss_pred HHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhh
Q 021250 73 EKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (315)
Q Consensus 73 E~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQN 107 (315)
+..|...++...-...+||..+|+++..|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 33455444444456788999999999999999853
No 84
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=35.10 E-value=94 Score=26.26 Aligned_cols=45 Identities=20% Similarity=0.040 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.+..++...|-. .....++|..+|+++..|++|.+.-|.+-|
T Consensus 109 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr 153 (165)
T PRK09644 109 LPVIEAQAILLCDVH-----ELTYEEAASVLDLKLNTYKSHLFRGRKRLK 153 (165)
T ss_pred CCHHHHHHHHhHHHh-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 566666655543322 234678999999999999998864444433
No 85
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=35.07 E-value=80 Score=27.15 Aligned_cols=46 Identities=15% Similarity=0.047 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
+++.+..+|...|-.. ..-.+||..+|++...|+.++..-|.+-|.
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 132 LPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 6777777776655433 346789999999999999988655555443
No 86
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=34.74 E-value=63 Score=28.05 Aligned_cols=45 Identities=20% Similarity=0.261 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.+..+|...| .......++|..+|++...|+.|...-|.+-|
T Consensus 142 L~~~~~~v~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 142 LPESQRQVLELAY-----YEGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CCHHHhhhhhhhh-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4555555554443 22345678999999999999999864444433
No 87
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=34.65 E-value=51 Score=38.30 Aligned_cols=53 Identities=17% Similarity=0.231 Sum_probs=49.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (315)
+-.+++..|-++|-.+.-|+.+.+.-|....+.+.+++.+||+|-|.|.++.+
T Consensus 712 ~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 712 ILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 55699999999999999999999999999999999999999999999988766
No 88
>PRK00118 putative DNA-binding protein; Validated
Probab=34.51 E-value=2e+02 Score=23.81 Aligned_cols=42 Identities=14% Similarity=0.113 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRa 110 (315)
++..|..++...|... ....+||..+|+++..|..|...-|.
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArk 59 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEK 59 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5677777776665543 24567999999999999999864333
No 89
>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=34.35 E-value=29 Score=25.63 Aligned_cols=27 Identities=30% Similarity=0.625 Sum_probs=21.1
Q ss_pred HHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 86 RKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 86 ~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
...+||..||++.+.|..|-+ |-+|..
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 456899999999999999964 555443
No 90
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=34.34 E-value=83 Score=25.75 Aligned_cols=43 Identities=16% Similarity=0.103 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK 111 (315)
++..+..+|...|-. .....++|..+|+++..|+.+...-|.+
T Consensus 114 L~~~~r~il~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 114 LPEQCRKIFILSRFE-----GKSYKEIAEELGISVKTVEYHISKALKE 156 (161)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 555566666554422 2345679999999999999887543333
No 91
>PRK10072 putative transcriptional regulator; Provisional
Probab=34.30 E-value=25 Score=28.63 Aligned_cols=42 Identities=21% Similarity=0.280 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHH
Q 021250 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (315)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK 111 (315)
+.+...+..|...-.. ...+||+.+|++...|..|.+.+|.-
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 3467777777443322 26789999999999999999877653
No 92
>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=34.00 E-value=42 Score=24.34 Aligned_cols=34 Identities=24% Similarity=0.285 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhH
Q 021250 67 DQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVW 104 (315)
Q Consensus 67 ~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVW 104 (315)
.|+..|+-.+. +...+.. +||..+|++++.|+.-
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~ 39 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKND 39 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHH
Confidence 57888888888 6666554 8999999999988654
No 93
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=33.79 E-value=91 Score=24.13 Aligned_cols=35 Identities=29% Similarity=0.348 Sum_probs=18.0
Q ss_pred HHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhhh
Q 021250 116 QLERDYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (315)
Q Consensus 116 q~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~ 150 (315)
.++.+...|+..+..+...+..|..+|+.|+.+-.
T Consensus 22 ~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~ 56 (72)
T PF06005_consen 22 LLQMENEELKEKNNELKEENEELKEENEQLKQERN 56 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 34444555555555555555555555555555443
No 94
>PF07888 CALCOCO1: Calcium binding and coiled-coil domain (CALCOCO1) like; InterPro: IPR012852 Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein expressed by Mus musculus (CoCoA, Q8CGU1 from SWISSPROT). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (Q61026 from SWISSPROT), and thus enhances transcriptional activation by a number of nuclear receptors. CoCoA has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region [].
Probab=33.72 E-value=1.7e+02 Score=31.18 Aligned_cols=41 Identities=20% Similarity=0.260 Sum_probs=28.8
Q ss_pred HHHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhccccc
Q 021250 120 DYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDRDQ 166 (315)
Q Consensus 120 ~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~~~~ 166 (315)
+...|++....+..+...+..+++.|...+. .|..+|....
T Consensus 418 el~Elks~lrv~qkEKEql~~EkQeL~~yi~------~Le~r~~~~~ 458 (546)
T PF07888_consen 418 ELQELKSSLRVAQKEKEQLQEEKQELLEYIE------RLEQRLDKVA 458 (546)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHhh
Confidence 3444566666666677777778888888887 8888887654
No 95
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=33.26 E-value=88 Score=27.08 Aligned_cols=39 Identities=23% Similarity=0.150 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQN 107 (315)
+++.|..++...|-.. ....+||..+|++...|+.+...
T Consensus 140 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~R 178 (189)
T PRK09648 140 LPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHR 178 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 6777777777655433 34678999999999999988743
No 96
>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=33.10 E-value=36 Score=22.21 Aligned_cols=24 Identities=21% Similarity=0.502 Sum_probs=20.2
Q ss_pred HHHHHHHhCCCcchhhhHhhhhHH
Q 021250 87 KVKLAQELGLQPRQVAVWFQNRRA 110 (315)
Q Consensus 87 r~eLA~~LgLserQVqVWFQNRRa 110 (315)
..++|+.+|++++.|..|.++.+.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467899999999999999876543
No 97
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=32.89 E-value=1.1e+02 Score=26.64 Aligned_cols=46 Identities=13% Similarity=0.171 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
+++.+..+|.-.|-.. ..-.++|..+|+++..|++-...-|.+.|+
T Consensus 132 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 132 LSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 6677777776654322 245688999999999999877544444443
No 98
>smart00340 HALZ homeobox associated leucin zipper.
Probab=32.53 E-value=52 Score=23.28 Aligned_cols=33 Identities=30% Similarity=0.312 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhhhhhHHhhhccchHHHHHHHHh
Q 021250 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLK 147 (315)
Q Consensus 115 kq~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~ 147 (315)
||.+-+.+.||...+.|..++..|+++.+.|++
T Consensus 1 KQTEvdCe~LKrcce~LteeNrRL~ke~~eLra 33 (44)
T smart00340 1 KQTEVDCELLKRCCESLTEENRRLQKEVQELRA 33 (44)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 356777888888888888888888888777765
No 99
>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=32.46 E-value=89 Score=25.93 Aligned_cols=38 Identities=21% Similarity=0.198 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
+++.+..++...|- ....-.++|..+|++...|+++..
T Consensus 112 L~~~~r~v~~l~~~-----~g~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 112 LPERQRELLQLRYQ-----RGVSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 66666666666443 223567899999999999998764
No 100
>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=31.71 E-value=94 Score=26.62 Aligned_cols=38 Identities=18% Similarity=0.123 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
+++.+..+|.-.|-.. ....++|..+|+++..|+++..
T Consensus 101 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 101 LPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 6677777776655333 3467899999999999998765
No 101
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=31.70 E-value=2e+02 Score=27.72 Aligned_cols=46 Identities=24% Similarity=0.249 Sum_probs=31.8
Q ss_pred HHHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhccccc
Q 021250 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDRDQ 166 (315)
Q Consensus 115 kq~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~~~~ 166 (315)
+.+..+...|...++.|+..+.+|..+|..|..++. .|++.|....
T Consensus 100 ~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~le------~~~~~l~~~~ 145 (292)
T KOG4005|consen 100 KDLTEENEILQNENDSLRAINESLLAKNHELDSELE------LLRQELAELK 145 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH------HHHHHHHhhH
Confidence 445666777777777777777777777777777776 6666665443
No 102
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=31.65 E-value=1.2e+02 Score=25.36 Aligned_cols=44 Identities=14% Similarity=0.265 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.+..+|.-.| .. ..-.+||..+|+++..|+.+...-|.+.|
T Consensus 113 L~~~~r~il~l~~-~g-----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr 156 (166)
T PRK09639 113 MTERDRTVLLLRF-SG-----YSYKEIAEALGIKESSVGTTLARAKKKFR 156 (166)
T ss_pred CCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6677777776666 32 24567999999999999998754444333
No 103
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=31.57 E-value=1.5e+02 Score=31.04 Aligned_cols=44 Identities=16% Similarity=0.230 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhc
Q 021250 113 KTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATL 162 (315)
Q Consensus 113 Kkkq~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L 162 (315)
|...++++++.++++.+.+......+++..+.|..|+. .|+.++
T Consensus 77 kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~------~Lk~Ql 120 (475)
T PRK13729 77 TAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNA------ALAEQV 120 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHH------HHHHHH
Confidence 44556666666666666555555556666666777777 777776
No 104
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=31.35 E-value=72 Score=28.18 Aligned_cols=45 Identities=22% Similarity=0.038 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.|..+|.-.|-. .....++|..||++...|+++...-|.+-|
T Consensus 114 Lp~~~r~v~~L~~~~-----g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr 158 (188)
T PRK12546 114 LPDEQREALILVGAS-----GFSYEEAAEMCGVAVGTVKSRANRARARLA 158 (188)
T ss_pred CCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 666666666554332 234568999999999999998864444443
No 105
>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=30.75 E-value=1e+02 Score=26.27 Aligned_cols=43 Identities=23% Similarity=0.216 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK 111 (315)
+++.|..++.-.|-.. -.-.++|..||+++..|++....-|.+
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAW 177 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4455555554443322 245688999999999999987644443
No 106
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=30.65 E-value=93 Score=26.85 Aligned_cols=43 Identities=12% Similarity=0.117 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK 111 (315)
+++.+..+|...|-. ...-.+||..+|++...|+.+...-|.+
T Consensus 129 L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~~ 171 (186)
T PRK05602 129 LPERQREAIVLQYYQ-----GLSNIEAAAVMDISVDALESLLARGRRA 171 (186)
T ss_pred CCHHHHHHhhHHHhc-----CCCHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence 566666666554422 2345689999999999999987544433
No 107
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=30.59 E-value=1.5e+02 Score=30.76 Aligned_cols=84 Identities=20% Similarity=0.213 Sum_probs=48.7
Q ss_pred CCCHHHHHHHHHH-------hCCCcchhhhHhhhhHHHHHHHHHHHHHHHHhh-hhhHHhhhccchHHHHHHHHhhhh-c
Q 021250 81 KLEPERKVKLAQE-------LGLQPRQVAVWFQNRRARWKTKQLERDYGVLKA-NYDALKLNYDSLQHDNEALLKETI-V 151 (315)
Q Consensus 81 yps~~~r~eLA~~-------LgLserQVqVWFQNRRaK~Kkkq~~~~~~~lk~-~~~~l~~~~~sl~~en~~L~~E~~-v 151 (315)
+++.+++..|.++ |-|+.++=++-=+ =|.|.|+|+..++-..-|. -.+.|...+.....+|+.|++++. .
T Consensus 220 ~LteeEkrLL~kEG~slPs~lPLTKaEEriLKr-vRRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqeL~kkV~~L 298 (472)
T KOG0709|consen 220 VLTEEEKRLLTKEGYSLPSKLPLTKAEERILKR-VRRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQELQKKVEEL 298 (472)
T ss_pred eccHHHHHHHHhccCcCcccCCchHHHHHHHHH-HHHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHHHHHHHHHH
Confidence 4666777766654 3456666555433 3445566666665554444 446777777777778888777764 1
Q ss_pred cccchhhhhhcccc
Q 021250 152 HETDHQNKATLDRD 165 (315)
Q Consensus 152 ~~~~~~Lk~~L~~~ 165 (315)
...+..|-++|.+-
T Consensus 299 e~~N~sLl~qL~kl 312 (472)
T KOG0709|consen 299 ELSNRSLLAQLKKL 312 (472)
T ss_pred hhccHHHHHHHHHH
Confidence 11333555555443
No 108
>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=30.46 E-value=1.1e+02 Score=23.78 Aligned_cols=36 Identities=25% Similarity=0.342 Sum_probs=23.4
Q ss_pred HHHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhhh
Q 021250 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (315)
Q Consensus 115 kq~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~ 150 (315)
.+.-..+..|+...+.|+..+..+..++..|..++.
T Consensus 14 ~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~ 49 (72)
T PF06005_consen 14 QQAVETIALLQMENEELKEKNNELKEENEELKEENE 49 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 344455666666666676666666666777777666
No 109
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=30.41 E-value=36 Score=24.69 Aligned_cols=21 Identities=19% Similarity=0.366 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCcchhhhHhhh
Q 021250 87 KVKLAQELGLQPRQVAVWFQN 107 (315)
Q Consensus 87 r~eLA~~LgLserQVqVWFQN 107 (315)
..++|+.+|+++++|+.|=+.
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 357899999999999999643
No 110
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=30.18 E-value=95 Score=26.52 Aligned_cols=45 Identities=13% Similarity=0.114 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.+..+|...|- ....-.++|..+|+++..|+++...-|.+-|
T Consensus 137 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 137 LPPKYRMVIVLKYM-----EDLSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred CCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 66666666655433 2334678999999999999998864444333
No 111
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=30.03 E-value=74 Score=26.73 Aligned_cols=42 Identities=17% Similarity=0.117 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRa 110 (315)
+++.|..+|.-.|-.. ..-.++|..+|++...|+.+...-|.
T Consensus 113 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~ 154 (161)
T PRK12541 113 LPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRK 154 (161)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6666666665544322 34568999999999999988753333
No 112
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=29.42 E-value=1.5e+02 Score=26.00 Aligned_cols=46 Identities=13% Similarity=0.143 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
+++.+..+|.-.|-.. ....+||..+|++...|++....-|.+-|+
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~ 177 (188)
T TIGR02943 132 LPEQTARVFMMREVLG-----FESDEICQELEISTSNCHVLLYRARLSLRA 177 (188)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 6666666666654333 346789999999999999877544444443
No 113
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=29.25 E-value=76 Score=30.31 Aligned_cols=26 Identities=31% Similarity=0.267 Sum_probs=14.4
Q ss_pred hccchHHHHHHHHhhhhccccchhhhhhcccc
Q 021250 134 NYDSLQHDNEALLKETIVHETDHQNKATLDRD 165 (315)
Q Consensus 134 ~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~~~ 165 (315)
....|.+||+.|+.++. +|+..|..-
T Consensus 223 r~~~leken~~lr~~v~------~l~~el~~~ 248 (269)
T KOG3119|consen 223 RVAELEKENEALRTQVE------QLKKELATL 248 (269)
T ss_pred HHHHHHHHHHHHHHHHH------HHHHHHHHH
Confidence 33445556666666666 565555443
No 114
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=28.85 E-value=1e+02 Score=26.89 Aligned_cols=46 Identities=15% Similarity=0.266 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
+++.+..++.-.|-.. ....++|..+|++...|+...+.-|.+-|+
T Consensus 132 L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 132 LEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6677777766554322 345789999999999998876544444333
No 115
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=28.62 E-value=1.2e+02 Score=25.08 Aligned_cols=39 Identities=15% Similarity=0.125 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQN 107 (315)
+++.|..++.-.|-.. ..-.++|..||++...|++....
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~r 145 (161)
T PRK09047 107 LPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSR 145 (161)
T ss_pred CCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 6777777776654332 23578999999999999987653
No 116
>smart00338 BRLZ basic region leucin zipper.
Probab=28.58 E-value=2.1e+02 Score=20.92 Aligned_cols=36 Identities=22% Similarity=0.272 Sum_probs=21.2
Q ss_pred HHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhc
Q 021250 121 YGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATL 162 (315)
Q Consensus 121 ~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L 162 (315)
...|......|...+..|..+...|..|+. .|+..+
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~~------~lk~~~ 63 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRELE------KLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHh
Confidence 444555555566666666666666666666 565544
No 117
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=28.51 E-value=1.2e+02 Score=27.80 Aligned_cols=45 Identities=13% Similarity=0.135 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
++..|..+|.-.|-. ...-.+||..||++...|++....-|.+-|
T Consensus 172 Lp~~~R~v~~L~~~e-----g~s~~EIA~~Lgis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 172 LPEQQRIAVILSYHE-----NMSNGEIAEVMDTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred CCHHHHHHhhhHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 455555554444322 234678999999999999998764444443
No 118
>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=28.45 E-value=91 Score=26.71 Aligned_cols=27 Identities=11% Similarity=-0.018 Sum_probs=20.8
Q ss_pred HHHHHHHHHhCCCcchhhhHhhhhHHH
Q 021250 85 ERKVKLAQELGLQPRQVAVWFQNRRAR 111 (315)
Q Consensus 85 ~~r~eLA~~LgLserQVqVWFQNRRaK 111 (315)
..-.++|..+|+++..|+++...-|.+
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREA 181 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 456789999999999999987533333
No 119
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.45 E-value=70 Score=26.15 Aligned_cols=38 Identities=16% Similarity=0.246 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQV 101 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQV 101 (315)
++++|.+.-...|+.+--+++-..+++|.+|++++--|
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 67888888888888888888888999999999988544
No 120
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=28.33 E-value=98 Score=20.77 Aligned_cols=36 Identities=17% Similarity=0.257 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 65 SVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 65 T~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
+..|...+...+ .. ....++|..+|++...|..|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 455666665433 11 2457889999999999998874
No 121
>smart00338 BRLZ basic region leucin zipper.
Probab=27.94 E-value=1.4e+02 Score=21.95 Aligned_cols=36 Identities=31% Similarity=0.390 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhh
Q 021250 114 TKQLERDYGVLKANYDALKLNYDSLQHDNEALLKET 149 (315)
Q Consensus 114 kkq~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~ 149 (315)
...++.....|...+..|......+..++..|..++
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345566666777777777777777777777776654
No 122
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=26.96 E-value=1.3e+02 Score=25.10 Aligned_cols=38 Identities=26% Similarity=0.296 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
+++.+..+|.-.|-.. ....++|..+|++...|+....
T Consensus 110 L~~~~r~v~~l~~~~~-----~s~~EIA~~lgis~~tV~~~l~ 147 (163)
T PRK07037 110 LPARTRYAFEMYRLHG-----ETQKDIARELGVSPTLVNFMIR 147 (163)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 5566666665544322 2467899999999999998754
No 123
>PF15058 Speriolin_N: Speriolin N terminus
Probab=26.93 E-value=30 Score=31.95 Aligned_cols=39 Identities=28% Similarity=0.438 Sum_probs=25.8
Q ss_pred hhhHHhhhccchHHHHHHHHhhhhccccchhhhhhcccc
Q 021250 127 NYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDRD 165 (315)
Q Consensus 127 ~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~~~ 165 (315)
.|+.+.+..+.+-.||+.|++++.+--.+|+||.-|.+.
T Consensus 6 ~yeGlrhqierLv~ENeeLKKlVrLirEN~eLksaL~ea 44 (200)
T PF15058_consen 6 NYEGLRHQIERLVRENEELKKLVRLIRENHELKSALGEA 44 (200)
T ss_pred chHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455555556666677777777776666666888876544
No 124
>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=26.72 E-value=46 Score=24.26 Aligned_cols=21 Identities=10% Similarity=0.365 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCcchhhhHhhh
Q 021250 87 KVKLAQELGLQPRQVAVWFQN 107 (315)
Q Consensus 87 r~eLA~~LgLserQVqVWFQN 107 (315)
..++|+.+|++++.|+.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999764
No 125
>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=26.63 E-value=42 Score=23.15 Aligned_cols=23 Identities=22% Similarity=0.404 Sum_probs=19.2
Q ss_pred HHHHHHHhCCCcchhhhHhhhhH
Q 021250 87 KVKLAQELGLQPRQVAVWFQNRR 109 (315)
Q Consensus 87 r~eLA~~LgLserQVqVWFQNRR 109 (315)
..+||+.+|+++..|..|..++|
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 47899999999999999998754
No 126
>PRK11546 zraP zinc resistance protein; Provisional
Probab=26.36 E-value=1.1e+02 Score=26.88 Aligned_cols=45 Identities=20% Similarity=0.152 Sum_probs=29.6
Q ss_pred HHHHHHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhcccccc
Q 021250 117 LERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDRDQE 167 (315)
Q Consensus 117 ~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~~~~~ 167 (315)
++++.-..+.++.+|......-.+....|.+|+. .|+.+|.+.+.
T Consensus 66 LRqqL~aKr~ELnALl~~~~pD~~kI~aL~kEI~------~Lr~kL~e~r~ 110 (143)
T PRK11546 66 LRQQLVSKRYEYNALLTANPPDSSKINAVAKEME------NLRQSLDELRV 110 (143)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH------HHHHHHHHHHH
Confidence 3333444445556666666666666778889998 89988876654
No 127
>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=26.34 E-value=2.6e+02 Score=24.95 Aligned_cols=45 Identities=20% Similarity=0.239 Sum_probs=35.9
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 60 KKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 60 krrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
++..+|++++..+.+.-..+ |..-.+..||+++|+++.-|.+=..
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~ 126 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAP 126 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcC
Confidence 34459999999998876655 5667899999999999988877554
No 128
>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=26.24 E-value=45 Score=24.40 Aligned_cols=21 Identities=19% Similarity=0.412 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCcchhhhHhhh
Q 021250 87 KVKLAQELGLQPRQVAVWFQN 107 (315)
Q Consensus 87 r~eLA~~LgLserQVqVWFQN 107 (315)
..++|+.+|++++.|+.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999764
No 129
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=26.17 E-value=86 Score=26.17 Aligned_cols=40 Identities=28% Similarity=0.472 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRa 110 (315)
+++.++..+.+.+... ...+|+.||++...|+.|=|+|+.
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 8899999998877644 457899999999999999998764
No 130
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=26.09 E-value=1.3e+02 Score=28.01 Aligned_cols=45 Identities=11% Similarity=0.146 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.+..+|...|... ....++|..+|++...|+.....-+.+-|
T Consensus 213 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 257 (268)
T PRK06288 213 LPEREKKVLILYYYED-----LTLKEIGKVLGVTESRISQLHTKAVLQLR 257 (268)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 6777777777766432 34678999999999999877654444333
No 131
>PRK10403 transcriptional regulator NarP; Provisional
Probab=26.08 E-value=82 Score=26.36 Aligned_cols=44 Identities=16% Similarity=0.172 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHH
Q 021250 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARW 112 (315)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~ 112 (315)
.+|..+..+|+..... ..+.+||..++++++.|++...|=|.|-
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl 196 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKL 196 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 3888888888765432 3457889999999999999887655543
No 132
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=25.99 E-value=1.5e+02 Score=25.79 Aligned_cols=46 Identities=9% Similarity=0.105 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
+++.+..++.-.|-.. ..-.++|..+|++...|+.....-|.+-|+
T Consensus 137 L~~~~r~i~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 182 (195)
T PRK12532 137 LPENTARVFTLKEILG-----FSSDEIQQMCGISTSNYHTIMHRARESLRQ 182 (195)
T ss_pred CCHHHHHHhhhHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5555655555443222 235789999999999999987644444333
No 133
>PRK06930 positive control sigma-like factor; Validated
Probab=25.96 E-value=1.6e+02 Score=26.03 Aligned_cols=46 Identities=9% Similarity=0.046 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
+++.+..++.-.|-.. ..-.++|..+|+++..|+.+...-|.+-++
T Consensus 115 L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 115 LTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 7777777776654332 245689999999999999998655444443
No 134
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=25.89 E-value=79 Score=26.00 Aligned_cols=23 Identities=22% Similarity=0.200 Sum_probs=13.7
Q ss_pred hhHHhhhccchHHHHHHHHhhhh
Q 021250 128 YDALKLNYDSLQHDNEALLKETI 150 (315)
Q Consensus 128 ~~~l~~~~~sl~~en~~L~~E~~ 150 (315)
...++.+...++++|+.|..|+.
T Consensus 36 ~~~~~~e~~~l~~~n~~L~~eI~ 58 (105)
T PRK00888 36 VAAQQQTNAKLKARNDQLFAEID 58 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444555667777777776
No 135
>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=25.68 E-value=1.3e+02 Score=28.56 Aligned_cols=49 Identities=20% Similarity=0.251 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhcc
Q 021250 109 RARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLD 163 (315)
Q Consensus 109 RaK~Kkkq~~~~~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~ 163 (315)
|-|.|-..++++...+++....|+.+.++|+.+|..|=+.+. .|...-.
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiR------ylqSY~~ 138 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIR------YLQSYNN 138 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHhhCcc
Confidence 556667788888888888888999999999999988888887 7766543
No 136
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=25.49 E-value=1.5e+02 Score=25.47 Aligned_cols=41 Identities=17% Similarity=0.272 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRR 109 (315)
+++.+..++...|-.+ ....++|..+|++...|++|...-|
T Consensus 134 L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~ 174 (182)
T PRK12537 134 LEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSL 174 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHH
Confidence 5666666555554322 3466899999999999999875333
No 137
>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=25.28 E-value=46 Score=22.37 Aligned_cols=18 Identities=28% Similarity=0.482 Sum_probs=15.1
Q ss_pred HHHHHHhCCCcchhhhHh
Q 021250 88 VKLAQELGLQPRQVAVWF 105 (315)
Q Consensus 88 ~eLA~~LgLserQVqVWF 105 (315)
-++|+.+|++.+.|+.|=
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 478999999999999994
No 138
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=25.13 E-value=2.2e+02 Score=24.47 Aligned_cols=46 Identities=11% Similarity=0.089 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
+++.+..++.-.|-.. ..-.++|..+|++...|++....-|.+.|+
T Consensus 118 Lp~~~r~i~~l~~~e~-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 118 LPYKLRQVIILRYLHD-----YSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5555555555443222 245689999999999999887655555444
No 139
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=25.11 E-value=1e+02 Score=27.99 Aligned_cols=46 Identities=13% Similarity=0.154 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
+++.+..+|...|-. ...-.++|..+|++...|+.+...-|.+-|+
T Consensus 185 L~~~~r~vl~l~~~~-----g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 185 LPEREQLVLSLYYQE-----ELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CCHHHHHHHHhHhcc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 566666666665532 2356789999999999999998655555444
No 140
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=24.95 E-value=1.5e+02 Score=24.80 Aligned_cols=45 Identities=18% Similarity=0.211 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.+..+|...|-. ...-.++|..+|++...|+.+-..-|.+-|
T Consensus 111 L~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 155 (162)
T TIGR02983 111 LPARQRAVVVLRYYE-----DLSEAQVAEALGISVGTVKSRLSRALARLR 155 (162)
T ss_pred CCHHHHHHhhhHHHh-----cCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 566666666655532 234567999999999999998764444433
No 141
>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=24.75 E-value=1.6e+02 Score=20.95 Aligned_cols=17 Identities=29% Similarity=0.440 Sum_probs=8.6
Q ss_pred hccchHHHHHHHHhhhh
Q 021250 134 NYDSLQHDNEALLKETI 150 (315)
Q Consensus 134 ~~~sl~~en~~L~~E~~ 150 (315)
....|..+|..|..++.
T Consensus 33 ~~~~L~~en~~L~~~i~ 49 (54)
T PF07716_consen 33 EVQELEEENEQLRQEIA 49 (54)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33444455555555554
No 142
>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=24.33 E-value=81 Score=21.44 Aligned_cols=21 Identities=14% Similarity=0.272 Sum_probs=18.7
Q ss_pred HHHHHhCCCcchhhhHhhhhH
Q 021250 89 KLAQELGLQPRQVAVWFQNRR 109 (315)
Q Consensus 89 eLA~~LgLserQVqVWFQNRR 109 (315)
+||..+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998874
No 143
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.23 E-value=1.4e+02 Score=24.03 Aligned_cols=42 Identities=14% Similarity=0.222 Sum_probs=31.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCC-CcchhhhHhh
Q 021250 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGL-QPRQVAVWFQ 106 (315)
Q Consensus 61 rrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgL-serQVqVWFQ 106 (315)
+++|+.+....+-+.+....+ ....+|+++|+ ...++..|-+
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 566999877666555554443 57789999996 9999998864
No 144
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=24.15 E-value=1.6e+02 Score=24.86 Aligned_cols=39 Identities=10% Similarity=0.110 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQN 107 (315)
++..+..++...|-.. ....++|..||+++..|+++..-
T Consensus 120 L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~R 158 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHR 158 (169)
T ss_pred CCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 6666666666655333 34568999999999999987643
No 145
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=24.10 E-value=1.6e+02 Score=24.88 Aligned_cols=42 Identities=19% Similarity=-0.003 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRa 110 (315)
+++.+..++.-.|-.. ..-.++|..+|+++..|+++...-|.
T Consensus 113 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~ 154 (164)
T PRK12547 113 LSADQREAIILIGASG-----FSYEDAAAICGCAVGTIKSRVSRARN 154 (164)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 6666777666654322 24668999999999999998753333
No 146
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=23.84 E-value=2e+02 Score=26.73 Aligned_cols=48 Identities=17% Similarity=0.219 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (315)
+++.+..++.-.|-.. ..-.++|..+|++...|+++...-|.+-|+.-
T Consensus 162 Lp~~~R~v~~L~~~eg-----~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 162 LSERERHLLRLHFVDG-----LSMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5555555554444322 24678999999999999999976666555543
No 147
>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=23.73 E-value=1.1e+02 Score=27.42 Aligned_cols=42 Identities=19% Similarity=0.154 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRa 110 (315)
+++.+..+|...|-.. ....++|..+|++...|+.+...-+.
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~ 217 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALK 217 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 7788888887776433 24578999999999999987653333
No 148
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=23.60 E-value=64 Score=23.26 Aligned_cols=20 Identities=20% Similarity=0.414 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCcchhhhHhh
Q 021250 87 KVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 87 r~eLA~~LgLserQVqVWFQ 106 (315)
..++|+.+|+++..|+.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999975
No 149
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=23.56 E-value=56 Score=20.93 Aligned_cols=23 Identities=22% Similarity=0.387 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCcchhhhHhhhhH
Q 021250 87 KVKLAQELGLQPRQVAVWFQNRR 109 (315)
Q Consensus 87 r~eLA~~LgLserQVqVWFQNRR 109 (315)
...+|+.+|+++..|..|..+++
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45789999999999999987653
No 150
>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=23.40 E-value=3.7e+02 Score=21.31 Aligned_cols=35 Identities=14% Similarity=0.364 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhh
Q 021250 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNR 108 (315)
Q Consensus 61 rrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNR 108 (315)
.+.|+..++..|.... ..+.+|++-.+|+-++...
T Consensus 36 ~R~y~~~di~~l~~i~-------------~lr~~g~~l~~i~~~~~~~ 70 (103)
T cd01106 36 YRLYTEEDLERLQQIL-------------FLKELGFSLKEIKELLKDP 70 (103)
T ss_pred ceeeCHHHHHHHHHHH-------------HHHHcCCCHHHHHHHHHcC
Confidence 3459999999985543 3456788888888877654
No 151
>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=23.34 E-value=4.6e+02 Score=22.33 Aligned_cols=36 Identities=8% Similarity=0.022 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhH
Q 021250 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (315)
Q Consensus 61 rrRfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRR 109 (315)
.+.|+..++..|... ...+.+|++-..|+.++.+..
T Consensus 35 ~R~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~~~ 70 (134)
T cd04779 35 YRYYDETALDRLQLI-------------EHLKGQRLSLAEIKDQLEEVQ 70 (134)
T ss_pred CeeECHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHHhhc
Confidence 445999999988433 223567777777776665543
No 152
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=23.31 E-value=1.5e+02 Score=25.72 Aligned_cols=38 Identities=21% Similarity=0.133 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
+++.+..+|...|-. .....++|..+|+++..|+..+.
T Consensus 107 L~~~~r~i~~l~~~~-----g~~~~EIA~~lgis~~tV~~~l~ 144 (181)
T PRK09637 107 LPEKYAEALRLTELE-----GLSQKEIAEKLGLSLSGAKSRVQ 144 (181)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHhCCCHHHHHHHHH
Confidence 566666666554322 23466899999999999988775
No 153
>PF13551 HTH_29: Winged helix-turn helix
Probab=23.27 E-value=2.1e+02 Score=22.13 Aligned_cols=43 Identities=19% Similarity=0.231 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHHhhcCC-----CCHHHHHH-H-HHHh--CCCcchhhhHhh
Q 021250 64 LSVDQVKALEKNFEVENK-----LEPERKVK-L-AQEL--GLQPRQVAVWFQ 106 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~y-----ps~~~r~e-L-A~~L--gLserQVqVWFQ 106 (315)
+++++...|.+.+...+. .+.....+ | .... .+++..|..|+.
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 899999999999998763 33333332 3 2232 467788887764
No 154
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=22.70 E-value=1.8e+02 Score=24.30 Aligned_cols=38 Identities=18% Similarity=0.162 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
+++.+..+|.-.|-.. ..-.++|..||+++..|+....
T Consensus 123 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 123 LTPKQQHVIALRFGQN-----LPIAEVARILGKTEGAVKILQF 160 (170)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 6666666666544322 3456899999999999988653
No 155
>PHA02955 hypothetical protein; Provisional
Probab=22.64 E-value=98 Score=28.97 Aligned_cols=42 Identities=7% Similarity=0.132 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHhhc-CCCCHHHHHHHHHHhCCCcchhhhHhhh
Q 021250 66 VDQVKALEKNFEVE-NKLEPERKVKLAQELGLQPRQVAVWFQN 107 (315)
Q Consensus 66 ~~Ql~~LE~~F~~~-~yps~~~r~eLA~~LgLserQVqVWFQN 107 (315)
..|+..|-+.|... ..+++++|.++|++||+....|..||.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 45677777777655 6788999999999999998777888864
No 156
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=22.57 E-value=1.1e+02 Score=25.69 Aligned_cols=43 Identities=21% Similarity=0.131 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHH
Q 021250 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (315)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK 111 (315)
.+|..+..+|....+. ..+.+||.+++++.+.|+++..+=|.|
T Consensus 149 ~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~k 191 (210)
T PRK09935 149 VLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGK 191 (210)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 3788888888654333 457789999999999999987654444
No 157
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=22.35 E-value=1.7e+02 Score=26.47 Aligned_cols=47 Identities=21% Similarity=0.237 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK 111 (315)
+++.|..++.-.|.. .+...-.-.++|..+|++...|+.+...-|.+
T Consensus 179 Lp~~~R~v~~L~y~l-~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~ 225 (234)
T PRK08301 179 LSDREKQIMELRFGL-NGGEEKTQKEVADMLGISQSYISRLEKRIIKR 225 (234)
T ss_pred CCHHHHHHHHHHhcc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 777777777766621 11223346789999999999999876533333
No 158
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=22.32 E-value=1.8e+02 Score=23.94 Aligned_cols=43 Identities=14% Similarity=0.129 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHH
Q 021250 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (315)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK 111 (315)
.+|+.+..+|.- +..+ + ...++|..++++++.|+.+.++=|.|
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~k 191 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRK 191 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 388888888876 3332 2 25689999999999999988764443
No 159
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=22.14 E-value=1.9e+02 Score=24.94 Aligned_cols=45 Identities=22% Similarity=0.061 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.+..++...| .......++|..+|+++..|++....-|.+.|
T Consensus 130 L~~~~r~v~~l~~-----~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr 174 (181)
T PRK12536 130 LPDRQRLPIVHVK-----LEGLSVAETAQLTGLSESAVKVGIHRGLKALA 174 (181)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4444444443333 22234678999999999999998864444444
No 160
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=22.13 E-value=1.1e+02 Score=25.47 Aligned_cols=43 Identities=28% Similarity=0.280 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHH
Q 021250 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (315)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK 111 (315)
.+|+.+...|+-..+. ..+.+||..++++++.|++..++=|.|
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEK 179 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4777777777665542 257788999999999998877654443
No 161
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=22.03 E-value=1.7e+02 Score=25.59 Aligned_cols=38 Identities=13% Similarity=0.023 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
+++.+..++.-.|-. ...-.+||..+|++...|+.+..
T Consensus 137 L~~~~r~i~~L~~~~-----g~s~~eIA~~lgis~~tV~~~l~ 174 (196)
T PRK12524 137 LPERQRQAVVLRHIE-----GLSNPEIAEVMEIGVEAVESLTA 174 (196)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHH
Confidence 555555555444332 22356899999999999999885
No 162
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=22.01 E-value=1.9e+02 Score=24.71 Aligned_cols=38 Identities=21% Similarity=0.166 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
++..+..+|.-.|-. ...-.++|..+|++...|+.+..
T Consensus 136 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 136 LSPEERRVIEVLYYQ-----GYTHREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHH
Confidence 566666666544422 23456889999999999998765
No 163
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=21.96 E-value=1.5e+02 Score=28.84 Aligned_cols=49 Identities=22% Similarity=0.268 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~K 113 (315)
+++.|..+|...|... +.......+||..+|++...|+.+...-+.+-|
T Consensus 263 L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr 311 (325)
T PRK05657 263 LNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311 (325)
T ss_pred CCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 8888888888877332 233445678999999999999998764444443
No 164
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=21.95 E-value=3.3e+02 Score=22.51 Aligned_cols=52 Identities=29% Similarity=0.359 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHHHHHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYG 122 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kkkq~~~~~~ 122 (315)
+|..|...|+-+|..+ -.-.++|..+|++..-|--|.+ |++.+-..-+...+
T Consensus 18 LT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ik--r~~~~L~~yE~kL~ 69 (101)
T PF04297_consen 18 LTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDSIK--RAEKKLEEYEEKLG 69 (101)
T ss_dssp S-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHH--HHHHHHHHHHHHH-
T ss_pred CCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHHh
Confidence 7889999998777654 3567899999999999998884 55544433433333
No 165
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=21.82 E-value=1e+02 Score=26.16 Aligned_cols=32 Identities=16% Similarity=0.149 Sum_probs=23.8
Q ss_pred CHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 83 EPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 83 s~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
....-.++|..+|+++..|++.+..-|.+-|+
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33456789999999999999988654444443
No 166
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=21.62 E-value=2.4e+02 Score=25.26 Aligned_cols=46 Identities=13% Similarity=0.178 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHHHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK~Kk 114 (315)
+++.|..++.-.|-.. ....++|..+|++...|++....-|.+-|+
T Consensus 149 L~~~~r~v~~L~~~~g-----~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~ 194 (206)
T PRK12544 149 LPAKYARVFMMREFIE-----LETNEICHAVDLSVSNLNVLLYRARLRLRE 194 (206)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 6666666665554332 235789999999999999987644444333
No 167
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=21.42 E-value=1.8e+02 Score=24.88 Aligned_cols=38 Identities=18% Similarity=0.204 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
+++.|..++.-.| .......+||..+|++...|+++..
T Consensus 120 L~~~~r~i~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK09651 120 LNGKTREAFLLSQ-----LDGLTYSEIAHKLGVSVSSVKKYVA 157 (172)
T ss_pred CCHHHhHHhhhhh-----ccCCCHHHHHHHhCCCHHHHHHHHH
Confidence 5555555544332 2233467899999999999999874
No 168
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=21.41 E-value=1.9e+02 Score=26.85 Aligned_cols=27 Identities=15% Similarity=0.126 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCcchhhhHhhhhHHHH
Q 021250 86 RKVKLAQELGLQPRQVAVWFQNRRARW 112 (315)
Q Consensus 86 ~r~eLA~~LgLserQVqVWFQNRRaK~ 112 (315)
.-.++|..+|+++..|+++...-|.+-
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~L 160 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRL 160 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 356899999999999999875444333
No 169
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=21.24 E-value=1.9e+02 Score=22.56 Aligned_cols=43 Identities=14% Similarity=0.173 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHhhc-----CCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 64 LSVDQVKALEKNFEVE-----NKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~-----~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
++.+|+..|...|..- .+.+..+...+-+.+|+++..|..+|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 6788999999998852 356777766666667888877776663
No 170
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=21.04 E-value=1.4e+02 Score=27.57 Aligned_cols=42 Identities=14% Similarity=0.145 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRa 110 (315)
+++.+..+|...|-.. ..-.++|..+|+++..|+.|...-+.
T Consensus 206 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~ 247 (257)
T PRK08583 206 LSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIK 247 (257)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7777777777766332 24578999999999999988653333
No 171
>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=20.87 E-value=63 Score=21.99 Aligned_cols=23 Identities=17% Similarity=0.127 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCcchhhhHhhhhH
Q 021250 87 KVKLAQELGLQPRQVAVWFQNRR 109 (315)
Q Consensus 87 r~eLA~~LgLserQVqVWFQNRR 109 (315)
..+||..+|+++..|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46899999999999999987664
No 172
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=20.80 E-value=2.1e+02 Score=24.69 Aligned_cols=43 Identities=14% Similarity=0.075 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhhhhHHH
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQNRRaK 111 (315)
+++.|..++.-.|-.. -.-.++|..||+++..|+.....-+.+
T Consensus 128 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~rAl~~ 170 (178)
T PRK12529 128 LRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIHQAYVT 170 (178)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 6777777776654432 245689999999999999887644433
No 173
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=20.46 E-value=2.2e+02 Score=24.05 Aligned_cols=38 Identities=18% Similarity=0.278 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
+++.+..+|.-.|-.. ..-.+||..||+++..|+....
T Consensus 119 L~~~~r~vl~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ 156 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG-----WSTAQIAADLGIPEGTVKSRLH 156 (173)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHH
Confidence 6677777776654332 2357899999999999998764
No 174
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=20.28 E-value=75 Score=29.29 Aligned_cols=39 Identities=28% Similarity=0.364 Sum_probs=32.8
Q ss_pred HHHHhhhhhHHhhhccchHHHHHHHHhhhhccccchhhhhhcccc
Q 021250 121 YGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDRD 165 (315)
Q Consensus 121 ~~~lk~~~~~l~~~~~sl~~en~~L~~E~~v~~~~~~Lk~~L~~~ 165 (315)
...+...|+.|+..++++..++..|+.|+. +|+..+...
T Consensus 107 ~kqlE~d~~~Lk~~~~~l~~~~~~Lq~e~~------eL~~~~~~~ 145 (198)
T KOG0483|consen 107 TKQLEKDYESLKRQLESLRSENDRLQSEVQ------ELVAELSSL 145 (198)
T ss_pred chhhhhhHHHHHHHHHHHhhhhhHHHHHHH------HHHHHHhhh
Confidence 344556799999999999999999999999 888877643
No 175
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=20.26 E-value=1.8e+02 Score=25.22 Aligned_cols=38 Identities=18% Similarity=0.044 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcchhhhHhh
Q 021250 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (315)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yps~~~r~eLA~~LgLserQVqVWFQ 106 (315)
+++.|..++.-.|-.. -.-.+||..+|+++..|+++..
T Consensus 131 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~ 168 (185)
T PRK09649 131 LTTDQREALLLTQLLG-----LSYADAAAVCGCPVGTIRSRVA 168 (185)
T ss_pred CCHHHhHHhhhHHHcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 5566665555444322 2457899999999999998774
Done!