Query 036802
Match_columns 180
No_of_seqs 120 out of 455
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 05:38:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036802.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036802hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489 Transcription factor z 99.8 2.6E-20 5.5E-25 160.0 3.0 70 24-98 155-224 (261)
2 KOG0484 Transcription factor P 99.8 3.9E-20 8.4E-25 144.6 1.3 70 24-98 13-82 (125)
3 KOG0487 Transcription factor A 99.8 4.1E-19 8.9E-24 157.5 5.6 75 21-100 228-302 (308)
4 KOG0488 Transcription factor B 99.8 7E-19 1.5E-23 155.3 5.5 70 24-98 168-237 (309)
5 PF00046 Homeobox: Homeobox do 99.7 4.8E-19 1E-23 117.9 2.6 57 29-90 1-57 (57)
6 KOG0842 Transcription factor t 99.7 1.7E-18 3.7E-23 153.5 6.1 71 25-100 150-220 (307)
7 KOG0843 Transcription factor E 99.7 3E-18 6.5E-23 143.5 4.6 64 27-95 101-164 (197)
8 KOG0492 Transcription factor M 99.7 1.2E-17 2.7E-22 142.9 5.1 66 26-96 142-207 (246)
9 KOG0494 Transcription factor C 99.6 9.5E-17 2.1E-21 141.4 4.8 63 28-95 141-203 (332)
10 smart00389 HOX Homeodomain. DN 99.6 7.6E-17 1.7E-21 106.0 3.0 56 29-89 1-56 (56)
11 KOG0848 Transcription factor C 99.6 4.3E-17 9.3E-22 143.6 2.1 84 5-96 178-262 (317)
12 KOG0844 Transcription factor E 99.6 8.8E-17 1.9E-21 144.2 4.0 67 26-97 179-245 (408)
13 KOG2251 Homeobox transcription 99.6 1.7E-16 3.7E-21 135.9 5.1 68 23-95 32-99 (228)
14 KOG0483 Transcription factor H 99.6 6.8E-17 1.5E-21 135.8 2.2 82 29-120 51-132 (198)
15 cd00086 homeodomain Homeodomai 99.6 1.6E-16 3.5E-21 104.6 3.3 58 29-91 1-58 (59)
16 KOG0485 Transcription factor N 99.6 1.9E-16 4.1E-21 136.6 3.5 67 24-95 100-166 (268)
17 KOG0850 Transcription factor D 99.6 5E-16 1.1E-20 133.9 5.0 72 25-101 119-190 (245)
18 TIGR01565 homeo_ZF_HD homeobox 99.6 1.6E-15 3.4E-20 106.0 5.3 52 29-85 2-57 (58)
19 KOG0493 Transcription factor E 99.6 6E-16 1.3E-20 136.5 3.4 67 24-95 242-308 (342)
20 COG5576 Homeodomain-containing 99.6 2.1E-15 4.6E-20 122.5 5.5 70 24-98 47-116 (156)
21 KOG4577 Transcription factor L 99.5 6E-15 1.3E-19 131.7 4.3 67 24-95 163-229 (383)
22 KOG0491 Transcription factor B 99.5 5.3E-15 1.1E-19 123.2 -0.7 64 28-96 100-163 (194)
23 KOG0486 Transcription factor P 99.4 1.1E-13 2.3E-18 124.1 4.3 75 17-96 99-175 (351)
24 KOG3802 Transcription factor O 99.4 1.3E-13 2.9E-18 125.9 4.9 62 27-93 293-354 (398)
25 KOG0490 Transcription factor, 99.4 1.3E-13 2.9E-18 111.4 3.2 64 25-93 57-120 (235)
26 KOG0847 Transcription factor, 99.2 8.8E-12 1.9E-16 108.3 1.5 65 28-97 167-231 (288)
27 KOG0849 Transcription factor P 99.1 3.1E-11 6.8E-16 108.3 3.3 69 24-97 172-240 (354)
28 KOG1168 Transcription factor A 99.0 3.5E-10 7.6E-15 101.5 3.5 66 25-95 306-371 (385)
29 KOG0490 Transcription factor, 98.5 7.3E-08 1.6E-12 77.9 3.9 67 22-93 147-213 (235)
30 KOG2252 CCAAT displacement pro 98.4 2.3E-07 5E-12 88.3 3.1 60 24-88 416-475 (558)
31 KOG0775 Transcription factor S 98.3 4.4E-07 9.5E-12 80.8 3.9 49 37-90 185-233 (304)
32 KOG0774 Transcription factor P 98.1 1.6E-06 3.4E-11 77.4 3.5 64 28-95 188-253 (334)
33 PF05920 Homeobox_KN: Homeobox 98.1 3.9E-07 8.5E-12 59.2 -0.6 33 51-87 8-40 (40)
34 KOG1146 Homeobox protein [Gene 97.7 3.2E-05 7E-10 79.8 3.9 66 25-95 900-965 (1406)
35 KOG0773 Transcription factor M 96.4 0.0029 6.3E-08 55.6 3.5 67 26-96 237-305 (342)
36 KOG3623 Homeobox transcription 95.0 0.013 2.8E-07 58.7 2.1 52 40-96 568-619 (1007)
37 KOG1146 Homeobox protein [Gene 93.1 0.14 2.9E-06 54.1 5.1 103 21-132 698-800 (1406)
38 PF11569 Homez: Homeodomain le 91.0 0.067 1.4E-06 37.6 0.1 42 40-86 10-51 (56)
39 PF04218 CENP-B_N: CENP-B N-te 88.5 0.4 8.7E-06 32.3 2.3 47 29-85 1-47 (53)
40 smart00340 HALZ homeobox assoc 86.5 0.085 1.8E-06 35.6 -1.9 42 94-140 2-43 (44)
41 cd06171 Sigma70_r4 Sigma70, re 79.1 0.94 2E-05 27.4 0.8 43 34-86 10-52 (55)
42 PF04967 HTH_10: HTH DNA bindi 78.3 2 4.4E-05 29.5 2.4 39 35-77 1-40 (53)
43 PF01527 HTH_Tnp_1: Transposas 71.7 1.7 3.8E-05 29.6 0.7 42 30-81 2-44 (76)
44 PF08281 Sigma70_r4_2: Sigma-7 68.1 1.9 4.1E-05 27.9 0.2 39 35-83 11-49 (54)
45 PRK09642 RNA polymerase sigma 67.2 4.5 9.7E-05 30.9 2.2 49 36-94 108-156 (160)
46 COG3413 Predicted DNA binding 65.2 7.6 0.00016 32.2 3.3 40 34-77 155-195 (215)
47 PF04545 Sigma70_r4: Sigma-70, 63.7 4.1 9E-05 26.1 1.2 38 34-81 4-41 (50)
48 cd00569 HTH_Hin_like Helix-tur 62.5 7.8 0.00017 20.6 2.1 38 34-81 5-42 (42)
49 PRK09652 RNA polymerase sigma 60.0 5.9 0.00013 30.1 1.7 47 34-90 128-174 (182)
50 TIGR02937 sigma70-ECF RNA poly 60.0 5.9 0.00013 28.3 1.6 46 34-89 110-155 (158)
51 KOG3755 SATB1 matrix attachmen 58.9 1.9 4.1E-05 43.0 -1.5 70 25-94 688-760 (769)
52 PRK09646 RNA polymerase sigma 58.9 8.3 0.00018 30.8 2.4 46 35-90 143-188 (194)
53 PF13936 HTH_38: Helix-turn-he 56.3 4.4 9.6E-05 26.1 0.4 38 33-80 3-40 (44)
54 smart00027 EH Eps15 homology d 55.9 12 0.00027 26.9 2.7 45 33-81 2-50 (96)
55 PRK09644 RNA polymerase sigma 55.4 8.7 0.00019 29.6 1.9 51 35-95 109-159 (165)
56 TIGR02948 SigW_bacill RNA poly 55.0 8.1 0.00018 30.0 1.7 46 35-90 137-182 (187)
57 PRK12512 RNA polymerase sigma 52.5 11 0.00025 29.4 2.2 50 35-94 132-181 (184)
58 PF02796 HTH_7: Helix-turn-hel 52.3 6.2 0.00013 25.3 0.6 39 33-81 4-42 (45)
59 PRK03975 tfx putative transcri 51.4 8.8 0.00019 31.1 1.4 53 33-96 5-57 (141)
60 PRK12519 RNA polymerase sigma 50.5 9.1 0.0002 30.2 1.4 46 35-90 142-187 (194)
61 PF06056 Terminase_5: Putative 50.0 7.1 0.00015 27.0 0.6 28 44-81 7-34 (58)
62 TIGR02989 Sig-70_gvs1 RNA poly 49.0 11 0.00025 28.4 1.6 38 34-81 111-148 (159)
63 PF10925 DUF2680: Protein of u 48.6 12 0.00025 26.3 1.5 42 35-81 1-42 (59)
64 PRK09639 RNA polymerase sigma 48.2 14 0.0003 28.1 2.1 45 35-90 113-157 (166)
65 PRK11924 RNA polymerase sigma 48.1 13 0.00029 28.1 1.9 47 35-91 126-172 (179)
66 PRK06930 positive control sigm 47.7 14 0.00031 30.2 2.2 52 34-95 114-165 (170)
67 PRK06759 RNA polymerase factor 47.7 12 0.00026 28.2 1.6 43 35-87 107-149 (154)
68 TIGR02985 Sig70_bacteroi1 RNA 47.6 14 0.0003 27.4 1.9 45 35-89 114-158 (161)
69 PRK09413 IS2 repressor TnpA; R 47.5 15 0.00032 28.0 2.1 39 32-80 10-49 (121)
70 smart00421 HTH_LUXR helix_turn 47.4 16 0.00034 22.4 1.9 38 34-82 3-40 (58)
71 PRK12526 RNA polymerase sigma 47.3 15 0.00032 29.9 2.1 46 35-90 154-199 (206)
72 PRK05602 RNA polymerase sigma 46.9 15 0.00033 28.8 2.1 48 36-93 130-177 (186)
73 PRK09637 RNA polymerase sigma 46.6 14 0.00029 29.5 1.8 46 34-89 106-151 (181)
74 PRK12530 RNA polymerase sigma 45.8 15 0.00034 29.2 2.0 48 36-93 136-183 (189)
75 PRK12541 RNA polymerase sigma 45.4 12 0.00027 28.6 1.4 47 34-90 112-158 (161)
76 PRK12515 RNA polymerase sigma 44.9 18 0.00039 28.5 2.3 48 34-91 131-178 (189)
77 TIGR02959 SigZ RNA polymerase 43.4 16 0.00035 28.5 1.8 47 34-90 100-146 (170)
78 TIGR02983 SigE-fam_strep RNA p 42.8 16 0.00036 27.7 1.7 45 36-90 112-156 (162)
79 PRK12538 RNA polymerase sigma 42.3 14 0.0003 31.1 1.3 31 60-94 191-221 (233)
80 TIGR02939 RpoE_Sigma70 RNA pol 42.3 14 0.0003 28.7 1.3 28 59-90 157-184 (190)
81 PF13873 Myb_DNA-bind_5: Myb/S 42.1 34 0.00073 23.6 3.1 60 33-92 3-76 (78)
82 PRK12546 RNA polymerase sigma 41.7 19 0.0004 29.1 1.9 51 35-95 114-164 (188)
83 PRK09047 RNA polymerase factor 41.4 22 0.00047 26.9 2.2 39 35-83 107-145 (161)
84 PRK12514 RNA polymerase sigma 40.9 24 0.00053 27.4 2.4 45 36-90 131-175 (179)
85 PRK12537 RNA polymerase sigma 40.3 25 0.00053 27.7 2.4 43 35-87 134-176 (182)
86 PRK04217 hypothetical protein; 40.3 17 0.00036 28.4 1.4 50 31-90 39-88 (110)
87 PF13865 FoP_duplication: C-te 40.1 1.3E+02 0.0029 21.5 6.0 18 30-47 35-53 (74)
88 PRK09647 RNA polymerase sigma 39.9 24 0.00053 28.8 2.4 32 60-95 158-189 (203)
89 PRK12531 RNA polymerase sigma 39.8 25 0.00054 28.0 2.4 45 36-90 143-187 (194)
90 PRK11923 algU RNA polymerase s 39.0 20 0.00044 28.2 1.7 30 59-92 157-186 (193)
91 KOG3755 SATB1 matrix attachmen 38.8 17 0.00038 36.5 1.6 68 22-93 348-416 (769)
92 PF12323 HTH_OrfB_IS605: Helix 38.3 21 0.00046 22.8 1.4 21 29-49 5-25 (46)
93 TIGR02952 Sig70_famx2 RNA poly 38.3 22 0.00048 27.0 1.8 37 35-81 123-159 (170)
94 TIGR02999 Sig-70_X6 RNA polyme 38.3 22 0.00048 27.6 1.8 45 35-89 135-179 (183)
95 PF10668 Phage_terminase: Phag 36.6 11 0.00023 26.8 -0.2 18 59-80 25-42 (60)
96 KOG3623 Homeobox transcription 36.3 17 0.00038 37.4 1.2 63 28-95 626-688 (1007)
97 PRK09648 RNA polymerase sigma 36.3 20 0.00044 28.2 1.4 39 34-82 139-177 (189)
98 PF08880 QLQ: QLQ; InterPro: 35.8 31 0.00067 22.1 1.9 14 34-47 2-15 (37)
99 PF13551 HTH_29: Winged helix- 35.5 51 0.0011 23.3 3.2 52 29-81 52-108 (112)
100 PF00196 GerE: Bacterial regul 35.2 12 0.00025 24.7 -0.2 44 34-88 3-46 (58)
101 PRK00118 putative DNA-binding 34.7 31 0.00068 26.6 2.1 51 35-95 18-68 (104)
102 PRK12532 RNA polymerase sigma 34.7 29 0.00062 27.5 2.0 49 35-93 137-185 (195)
103 cd02413 40S_S3_KH K homology R 34.7 26 0.00056 25.6 1.6 27 56-82 49-75 (81)
104 PRK12543 RNA polymerase sigma 34.5 27 0.00058 27.4 1.7 35 59-97 136-170 (179)
105 PRK12545 RNA polymerase sigma 34.1 33 0.00071 27.7 2.2 48 36-93 141-188 (201)
106 TIGR02957 SigX4 RNA polymerase 34.0 18 0.00039 31.0 0.8 47 35-91 109-155 (281)
107 PRK09645 RNA polymerase sigma 34.0 37 0.0008 26.2 2.4 44 35-88 119-162 (173)
108 PRK06811 RNA polymerase factor 33.8 29 0.00062 27.5 1.8 39 35-83 132-170 (189)
109 TIGR02954 Sig70_famx3 RNA poly 33.2 34 0.00073 26.3 2.1 45 34-88 119-163 (169)
110 PRK12536 RNA polymerase sigma 32.8 30 0.00066 27.1 1.8 28 59-90 148-175 (181)
111 PRK12516 RNA polymerase sigma 32.5 35 0.00075 27.4 2.1 50 35-94 117-166 (187)
112 PRK07037 extracytoplasmic-func 32.3 33 0.00071 26.1 1.9 37 35-81 110-146 (163)
113 PRK12540 RNA polymerase sigma 32.2 42 0.0009 26.8 2.5 50 35-94 112-161 (182)
114 PRK12524 RNA polymerase sigma 32.0 31 0.00068 27.5 1.8 27 60-90 156-182 (196)
115 cd06170 LuxR_C_like C-terminal 31.8 35 0.00076 21.0 1.7 37 35-82 1-37 (57)
116 PRK13919 putative RNA polymera 31.8 37 0.00081 26.4 2.2 41 35-85 136-176 (186)
117 PRK12522 RNA polymerase sigma 31.1 41 0.00089 26.0 2.3 27 60-90 139-165 (173)
118 PRK12520 RNA polymerase sigma 30.7 41 0.0009 26.5 2.3 51 35-95 132-182 (191)
119 PHA02955 hypothetical protein; 30.5 52 0.0011 28.8 3.0 44 37-84 60-103 (213)
120 PF00424 REV: REV protein (ant 30.1 71 0.0015 24.5 3.3 39 40-98 14-53 (91)
121 PRK12513 RNA polymerase sigma 29.3 18 0.00038 28.6 -0.1 30 59-92 158-187 (194)
122 PTZ00183 centrin; Provisional 29.2 1.7E+02 0.0036 21.6 5.2 39 29-67 5-47 (158)
123 PRK12539 RNA polymerase sigma 29.0 39 0.00084 26.6 1.9 46 34-89 131-176 (184)
124 PRK12547 RNA polymerase sigma 28.3 41 0.00088 26.0 1.8 45 35-89 113-157 (164)
125 PRK12528 RNA polymerase sigma 28.0 43 0.00093 25.5 1.9 38 35-82 114-151 (161)
126 PRK12533 RNA polymerase sigma 27.8 36 0.00079 28.3 1.6 47 36-92 136-182 (216)
127 PRK09651 RNA polymerase sigma 27.8 44 0.00095 26.1 1.9 44 34-89 119-162 (172)
128 COG4367 Uncharacterized protei 27.1 45 0.00098 25.9 1.8 39 34-77 2-40 (97)
129 PRK08295 RNA polymerase factor 26.9 47 0.001 26.3 2.0 44 35-89 156-199 (208)
130 PF07638 Sigma70_ECF: ECF sigm 26.7 44 0.00094 26.9 1.8 45 36-90 137-181 (185)
131 PRK12518 RNA polymerase sigma 25.9 21 0.00046 27.5 -0.2 29 59-91 139-167 (175)
132 PRK12511 RNA polymerase sigma 25.7 48 0.001 26.5 1.9 39 34-82 111-149 (182)
133 PRK12523 RNA polymerase sigma 25.7 49 0.0011 25.6 1.9 38 36-83 121-158 (172)
134 PRK09480 slmA division inhibit 25.6 48 0.001 25.5 1.8 36 44-85 20-55 (194)
135 PF13050 DUF3911: Protein of u 25.6 21 0.00046 26.4 -0.2 10 126-135 13-22 (77)
136 PF13565 HTH_32: Homeodomain-l 25.5 1.9E+02 0.004 19.5 4.6 41 36-80 32-76 (77)
137 PRK15369 two component system 25.3 38 0.00083 25.0 1.1 43 34-87 149-191 (211)
138 PRK12542 RNA polymerase sigma 25.2 48 0.001 26.0 1.7 39 35-83 123-161 (185)
139 PRK09636 RNA polymerase sigma 25.0 44 0.00095 28.6 1.6 28 60-91 135-162 (293)
140 PF07750 GcrA: GcrA cell cycle 24.5 86 0.0019 25.7 3.1 33 34-75 2-34 (162)
141 PRK09641 RNA polymerase sigma 24.4 45 0.00098 25.8 1.4 28 59-90 155-182 (187)
142 PRK06986 fliA flagellar biosyn 24.1 42 0.00092 27.7 1.3 46 36-91 186-231 (236)
143 PRK12535 RNA polymerase sigma 24.0 57 0.0012 26.4 2.0 50 35-94 134-183 (196)
144 PRK12529 RNA polymerase sigma 23.7 54 0.0012 25.8 1.8 39 35-83 128-166 (178)
145 PRK10100 DNA-binding transcrip 23.7 42 0.0009 28.0 1.2 47 34-91 155-201 (216)
146 PRK12544 RNA polymerase sigma 22.9 62 0.0014 26.5 2.1 48 35-92 149-196 (206)
147 TIGR02947 SigH_actino RNA poly 22.6 30 0.00065 27.4 0.1 30 59-92 150-179 (193)
148 PRK10651 transcriptional regul 22.5 46 0.001 25.0 1.1 46 34-90 155-200 (216)
149 PRK09638 RNA polymerase sigma 22.4 32 0.00069 26.5 0.2 25 59-89 145-169 (176)
150 TIGR03001 Sig-70_gmx1 RNA poly 22.2 66 0.0014 27.4 2.1 33 59-95 180-212 (244)
151 TIGR02943 Sig70_famx1 RNA poly 22.2 68 0.0015 25.6 2.1 47 35-91 132-178 (188)
152 PRK09649 RNA polymerase sigma 21.6 55 0.0012 26.0 1.4 19 60-82 150-168 (185)
153 TIGR02479 FliA_WhiG RNA polyme 21.4 52 0.0011 26.9 1.3 46 34-89 175-220 (224)
154 TIGR02960 SigX5 RNA polymerase 20.3 61 0.0013 27.7 1.6 46 36-91 144-189 (324)
155 PRK08583 RNA polymerase sigma 20.2 70 0.0015 26.8 1.9 44 34-87 205-248 (257)
No 1
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.79 E-value=2.6e-20 Score=159.95 Aligned_cols=70 Identities=19% Similarity=0.246 Sum_probs=63.3
Q ss_pred CCCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhccc
Q 036802 24 SDTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSVD 98 (180)
Q Consensus 24 ~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~d 98 (180)
.....||.||.||..||-+||..|.. ++|.++.+|.+||..|. |+|+||||||||||||+||..+.....
T Consensus 155 ~~~~~kR~RtayT~~QllELEkEFhf-N~YLtR~RRiEiA~~L~----LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 155 TGGKSKRRRTAFTRYQLLELEKEFHF-NKYLTRSRRIEIAHALN----LTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred ccCCCCCCCcccchhhhhhhhhhhcc-ccccchHHHHHHHhhcc----hhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 34457889999999999999999998 49999999999999996 999999999999999999988777554
No 2
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.78 E-value=3.9e-20 Score=144.56 Aligned_cols=70 Identities=24% Similarity=0.355 Sum_probs=64.2
Q ss_pred CCCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhccc
Q 036802 24 SDTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSVD 98 (180)
Q Consensus 24 ~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~d 98 (180)
.....+|.||+||..||++||++|.. ++||+...|++||-++. |+|.+|||||||||||-|++.+...+.
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~E-THYPDIYTREEiA~kid----LTEARVQVWFQNRRAKfRKQEr~a~~~ 82 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAE-THYPDIYTREEIALKID----LTEARVQVWFQNRRAKFRKQERAAIAK 82 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHh-hcCCcchhHHHHHHhhh----hhHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 46667889999999999999999998 59999999999999997 999999999999999999998877653
No 3
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.76 E-value=4.1e-19 Score=157.54 Aligned_cols=75 Identities=21% Similarity=0.267 Sum_probs=65.9
Q ss_pred CCCCCCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhccccc
Q 036802 21 NDNSDTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSVDYD 100 (180)
Q Consensus 21 ~gs~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~d~~ 100 (180)
.++.....|++|...|+.|+.+||+.|-.| .|++.+.|.+|++.|. |+|+||+|||||||+|+||.-|+...++.
T Consensus 228 ~~~~~~~~RKKRcPYTK~QtlELEkEFlfN-~YitkeKR~ElSr~lN----LTeRQVKIWFQNRRMK~KK~~re~r~~~~ 302 (308)
T KOG0487|consen 228 NASSARRGRKKRCPYTKHQTLELEKEFLFN-MYITKEKRLELSRTLN----LTERQVKIWFQNRRMKEKKVNRENRLKEL 302 (308)
T ss_pred ccccccccccccCCchHHHHHHHHHHHHHH-HHHhHHHHHHHHHhcc----cchhheeeeehhhhhHHhhhhhhhhcccc
Confidence 344556677799999999999999999985 8999999999999996 99999999999999999999987665544
No 4
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.75 E-value=7e-19 Score=155.33 Aligned_cols=70 Identities=16% Similarity=0.208 Sum_probs=63.7
Q ss_pred CCCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhccc
Q 036802 24 SDTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSVD 98 (180)
Q Consensus 24 ~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~d 98 (180)
.++..|+.||.||..||..||..|+.. +|.+..+|.+||..|+ |++.||++||||||+||||+......+
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~Q-KYLS~~DR~~LA~~Lg----LTdaQVKtWfQNRRtKWKrq~a~g~~~ 237 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQ-KYLSVADRIELAASLG----LTDAQVKTWFQNRRTKWKRQTAEGGEL 237 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHh-hcccHHHHHHHHHHcC----CchhhHHHHHhhhhHHHHHHHHhhhcc
Confidence 356677799999999999999999985 9999999999999997 999999999999999999998885443
No 5
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.75 E-value=4.8e-19 Score=117.88 Aligned_cols=57 Identities=32% Similarity=0.549 Sum_probs=54.4
Q ss_pred CccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 29 KCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 29 kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
+|+|+.||++|+.+||.+|.. ++||+.+++..||..|+ |+..+|++||||||+++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~-~~~p~~~~~~~la~~l~----l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE-NPYPSKEEREELAKELG----LTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH-SSSCHHHHHHHHHHHHT----SSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH-hcccccccccccccccc----ccccccccCHHHhHHHhCc
Confidence 579999999999999999999 59999999999999996 9999999999999999986
No 6
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.74 E-value=1.7e-18 Score=153.54 Aligned_cols=71 Identities=18% Similarity=0.288 Sum_probs=64.9
Q ss_pred CCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhccccc
Q 036802 25 DTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSVDYD 100 (180)
Q Consensus 25 ~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~d~~ 100 (180)
....||+|.-||+.|+-+||+.|.++ +|.+..+|++||..|. |+++||||||||||+|-||++.+..++..
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQ-RYLSAPERE~LA~~Lr----LT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQ-RYLSAPEREHLASSLR----LTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhh-hccccHhHHHHHHhcC----CCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 44667799999999999999999985 9999999999999997 99999999999999999999998876544
No 7
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.72 E-value=3e-18 Score=143.54 Aligned_cols=64 Identities=22% Similarity=0.317 Sum_probs=60.7
Q ss_pred CCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 27 GTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 27 ~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
.++|.||.||++||..||..|+.+ +|....+|++||..|+ |++.||+|||||||.|.||++.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~-~Yvvg~eR~~LA~~L~----LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGN-QYVVGAERKQLAQSLS----LSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcC-CeeechHHHHHHHHcC----CChhHhhhhhhhhhHHHHHHHHHh
Confidence 788999999999999999999884 8999999999999997 999999999999999999988774
No 8
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.70 E-value=1.2e-17 Score=142.87 Aligned_cols=66 Identities=21% Similarity=0.285 Sum_probs=60.8
Q ss_pred CCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhc
Q 036802 26 TGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVS 96 (180)
Q Consensus 26 ~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~ 96 (180)
+..|++||.||+.||..||+-|.+. +|.++++|.+++.-|. |++.||+|||||||||.||.++...
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrek-qYLSiaEraefSsSL~----LTeTqVKIWFQNRRAKaKRlQeae~ 207 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREK-QYLSIAERAEFSSSLE----LTETQVKIWFQNRRAKAKRLQEAEL 207 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHh-hhhhHHHHHhhhhhhh----hhhhheehhhhhhhHHHHHHHHHHH
Confidence 4456799999999999999999985 8999999999999997 9999999999999999999887763
No 9
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.65 E-value=9.5e-17 Score=141.36 Aligned_cols=63 Identities=21% Similarity=0.305 Sum_probs=56.1
Q ss_pred CCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 28 TKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 28 ~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
+|+-||.||..|+..||+.|... +||+..-|+-||..+. |+|.+|+||||||||||||..+.-
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkea-HYPDv~Are~la~kte----lpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEA-HYPDVYAREMLADKTE----LPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhc-cCccHHHHHHHhhhcc----CchhhhhHHhhhhhHHhhhhhhhc
Confidence 33349999999999999999985 9999999998888885 999999999999999999977654
No 10
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.65 E-value=7.6e-17 Score=105.96 Aligned_cols=56 Identities=27% Similarity=0.473 Sum_probs=52.0
Q ss_pred CccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHH
Q 036802 29 KCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARER 89 (180)
Q Consensus 29 kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReK 89 (180)
++.|+.||++|+.+||..|..+ +||+.+++.+||..|+ |+..+|++||+|||++.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~-~~P~~~~~~~la~~~~----l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKN-PYPSREEREELAAKLG----LSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHC----cCHHHHHHhHHHHhhccC
Confidence 3578899999999999999985 8999999999999997 999999999999999864
No 11
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.64 E-value=4.3e-17 Score=143.61 Aligned_cols=84 Identities=27% Similarity=0.370 Sum_probs=69.6
Q ss_pred ccccchhcccccCCCCCCCCCCCCC-ccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCc
Q 036802 5 ISGFYVKAGHVRAGNGNDNSDTGTK-CGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQN 83 (180)
Q Consensus 5 ~s~~~~~~~~~~~gg~~gs~~~~~k-R~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQN 83 (180)
..+|+.+.++. |.| +.+..+.+ +-|..+|..|.-+||+.|..+ +|+++.++.+||..|+ |+|+||+|||||
T Consensus 178 ~~dwmrkpa~~--~~g-~~~KtRTkDKYRvVYTDhQRLELEKEfh~S-ryITirRKSELA~~Lg----LsERQVKIWFQN 249 (317)
T KOG0848|consen 178 PYDWMRKPAQP--GTG-QNVKTRTKDKYRVVYTDHQRLELEKEFHTS-RYITIRRKSELAATLG----LSERQVKIWFQN 249 (317)
T ss_pred hhhhhhccccc--CCC-CCceeecccceeEEecchhhhhhhhhhccc-cceeeehhHHHHHhhC----ccHhhhhHhhhh
Confidence 46788887763 222 33333333 489999999999999999984 9999999999999997 999999999999
Q ss_pred chhhHHHhhhhhc
Q 036802 84 HKARERQKRRKVS 96 (180)
Q Consensus 84 RRAReKRk~r~~~ 96 (180)
|||||||..++..
T Consensus 250 RRAKERK~nKKk~ 262 (317)
T KOG0848|consen 250 RRAKERKDNKKKR 262 (317)
T ss_pred hhHHHHHHHHHHH
Confidence 9999998877764
No 12
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.64 E-value=8.8e-17 Score=144.17 Aligned_cols=67 Identities=19% Similarity=0.287 Sum_probs=60.3
Q ss_pred CCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhcc
Q 036802 26 TGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSV 97 (180)
Q Consensus 26 ~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~ 97 (180)
+.-||-||.||.|||..||+.|-.. -|.++.+|-+||..|+ |+|..|+|||||||+|.||++-....
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrE-NYVSRprRcELAAaLN----LPEtTIKVWFQNRRMKDKRQRlamaW 245 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRE-NYVSRPRRCELAAALN----LPETTIKVWFQNRRMKDKRQRLAMAW 245 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHh-ccccCchhhhHHHhhC----CCcceeehhhhhchhhhhhhhhhccC
Confidence 3457899999999999999999765 4999999999999996 99999999999999999998877653
No 13
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.64 E-value=1.7e-16 Score=135.91 Aligned_cols=68 Identities=22% Similarity=0.395 Sum_probs=63.3
Q ss_pred CCCCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 23 NSDTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 23 s~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
+++.+.+|.||+||-.||.+||.+|.+ +.||+...|++||.+|+ |+|.+|+|||.|||||.|+++++.
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~k-TqYPDv~~rEelAlkln----LpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAK-TQYPDVFMREELALKLN----LPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHh-hcCccHHHHHHHHHHhC----CchhhhhhhhccccchhhHhhhhh
Confidence 566777889999999999999999999 58999999999999996 999999999999999999998874
No 14
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.63 E-value=6.8e-17 Score=135.83 Aligned_cols=82 Identities=30% Similarity=0.507 Sum_probs=70.5
Q ss_pred CccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhccccccccccccc
Q 036802 29 KCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSVDYDHQKDLIRH 108 (180)
Q Consensus 29 kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~d~~~~~~~~~~ 108 (180)
.++.-.||.+|+..||..|+.+ .|...+++.+||.+|+ |.++||.|||||||||||.++.+. ||+. |..+
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~-~~L~p~~K~~LAk~Lg----L~pRQVavWFQNRRARwK~kqlE~--d~~~---Lk~~ 120 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESE-KKLEPERKKKLAKELG----LQPRQVAVWFQNRRARWKTKQLEK--DYES---LKRQ 120 (198)
T ss_pred ccccccccHHHHHHhHHhhccc-cccChHHHHHHHHhhC----CChhHHHHHHhhccccccchhhhh--hHHH---HHHH
Confidence 3455567999999999999985 7999999999999997 999999999999999999988777 6553 7778
Q ss_pred cCCCCcchhhhc
Q 036802 109 VDKISSPKREAH 120 (180)
Q Consensus 109 ~~~~~~~~~~~~ 120 (180)
+++++.++..+-
T Consensus 121 ~~~l~~~~~~Lq 132 (198)
T KOG0483|consen 121 LESLRSENDRLQ 132 (198)
T ss_pred HHHHhhhhhHHH
Confidence 888888887553
No 15
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.63 E-value=1.6e-16 Score=104.63 Aligned_cols=58 Identities=26% Similarity=0.450 Sum_probs=54.0
Q ss_pred CccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHh
Q 036802 29 KCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQK 91 (180)
Q Consensus 29 kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk 91 (180)
++.|+.|+++|+.+||..|.. ++||+.+++.+||..++ |+..+|++||+|||++.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~-~~~P~~~~~~~la~~~~----l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEK-NPYPSREEREELAKELG----LTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHHC----cCHHHHHHHHHHHHHHHhcc
Confidence 357899999999999999999 58999999999999997 99999999999999999874
No 16
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.62 E-value=1.9e-16 Score=136.62 Aligned_cols=67 Identities=22% Similarity=0.256 Sum_probs=61.0
Q ss_pred CCCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 24 SDTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 24 ~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
+..+.|+.||.|+..|+..||..|+-. +|.+.++|.-||..|. |+|.||+|||||||-||||+-...
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~k-rYLSsaeRa~LA~sLq----LTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELK-RYLSSAERAGLAASLQ----LTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHH-hhhhHHHHhHHHHhhh----hhhhhhhhhhhhhhHHHHHHHhhh
Confidence 344677899999999999999999985 8999999999999997 999999999999999999986544
No 17
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.61 E-value=5e-16 Score=133.94 Aligned_cols=72 Identities=17% Similarity=0.240 Sum_probs=65.3
Q ss_pred CCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhcccccc
Q 036802 25 DTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSVDYDH 101 (180)
Q Consensus 25 ~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~d~~~ 101 (180)
++..|++||.++.-||+.|.+.|++ +.|.-..+|.+||..|+ |+..||||||||||.|-||..++.+.+-++
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQk-TQYLALPERAeLAAsLG----LTQTQVKIWFQNrRSK~KKl~k~g~~~~e~ 190 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQ-TQYLALPERAELAASLG----LTQTQVKIWFQNRRSKFKKLKKQGSGPVEG 190 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhh-cchhcCcHHHHHHHHhC----CchhHhhhhhhhhHHHHHHHHhcCCCcccc
Confidence 4667779999999999999999998 58999999999999997 999999999999999999999977665444
No 18
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.59 E-value=1.6e-15 Score=105.95 Aligned_cols=52 Identities=19% Similarity=0.282 Sum_probs=49.5
Q ss_pred CccCCCCCHHHHHHHHHHHhcCCCC----CCHHHHHHHHHHhcccCCCCCCcceeccCcch
Q 036802 29 KCGRWNPTSEQVKVLTDLFTSGLRT----PSTDQIQKISTQLSFYGKIESKNVFYWFQNHK 85 (180)
Q Consensus 29 kR~Rt~fT~eQL~~LE~~F~~~~~y----Ps~~~r~eLA~~L~~~g~L~e~qVqvWFQNRR 85 (180)
+|.||.||++|+..||..|+.. +| |+..+|.+||..|+ |++.+|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~-~y~~~~~~~~~r~~la~~lg----l~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKL-GWKLKDKRREEVREFCEEIG----VTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHc-CCCCCCCCHHHHHHHHHHhC----CCHHHeeeecccCC
Confidence 7899999999999999999984 99 99999999999997 99999999999975
No 19
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.59 E-value=6e-16 Score=136.53 Aligned_cols=67 Identities=24% Similarity=0.363 Sum_probs=60.3
Q ss_pred CCCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 24 SDTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 24 ~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
..+..||+||.||.|||+.|...|+.+ +|.+..+|++||.+|+ |+|.||+|||||+|||-||.--..
T Consensus 242 ~~~eeKRPRTAFtaeQL~RLK~EF~en-RYlTEqRRQ~La~ELg----LNEsQIKIWFQNKRAKiKKsTgsk 308 (342)
T KOG0493|consen 242 SSKEEKRPRTAFTAEQLQRLKAEFQEN-RYLTEQRRQELAQELG----LNESQIKIWFQNKRAKIKKSTGSK 308 (342)
T ss_pred ccchhcCccccccHHHHHHHHHHHhhh-hhHHHHHHHHHHHHhC----cCHHHhhHHhhhhhhhhhhccCCC
Confidence 345668899999999999999999994 9999999999999997 999999999999999999865443
No 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.58 E-value=2.1e-15 Score=122.55 Aligned_cols=70 Identities=33% Similarity=0.430 Sum_probs=59.6
Q ss_pred CCCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhccc
Q 036802 24 SDTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSVD 98 (180)
Q Consensus 24 ~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~d 98 (180)
+....++.|..-|.+|+.+|++.|..+ +||+...|.+|+..|+ |+++.|++|||||||++|++......+
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~-p~Ps~~~r~~L~~~ln----m~~ksVqIWFQNkR~~~k~~~~~~~~~ 116 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEIN-PYPSSITRIKLSLLLN----MPPKSVQIWFQNKRAKEKKKRSGKVEQ 116 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccC-CCCCHHHHHHHHHhcC----CChhhhhhhhchHHHHHHHhcccchhc
Confidence 334444555555999999999999994 9999999999999996 999999999999999999988775443
No 21
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.52 E-value=6e-15 Score=131.69 Aligned_cols=67 Identities=22% Similarity=0.460 Sum_probs=58.8
Q ss_pred CCCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 24 SDTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 24 ~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
+....+|+||++|..||+.|...|... +.|-+--|++|+.+. +|+.++||||||||||||||.++..
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~S-pKPARHVREQLsseT----GLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTS-PKPARHVREQLSSET----GLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCC-CchhHHHHHHhhhcc----CcceeehhhhhhhhhHHHHhhhhhc
Confidence 556788999999999999999999874 899987777777766 4999999999999999999987654
No 22
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.46 E-value=5.3e-15 Score=123.23 Aligned_cols=64 Identities=25% Similarity=0.369 Sum_probs=59.4
Q ss_pred CCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhc
Q 036802 28 TKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVS 96 (180)
Q Consensus 28 ~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~ 96 (180)
.++.|+.|+..||..||+.|+.. +|.+..+|++||..|+ |+++||+.||||||+|.||.++...
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~Q-rYLS~~e~~ELan~L~----LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQ-RYLSTPERQELANALS----LSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhhhcccccCccccccHHHHhhh-hhcccHHHHHHHHHhh----hhHHHHHHHHHHHHHHHHHHHhccC
Confidence 44589999999999999999975 8999999999999997 9999999999999999999988764
No 23
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.42 E-value=1.1e-13 Score=124.15 Aligned_cols=75 Identities=25% Similarity=0.392 Sum_probs=66.5
Q ss_pred CCCCCCCCCC--CCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhh
Q 036802 17 AGNGNDNSDT--GTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRK 94 (180)
Q Consensus 17 ~gg~~gs~~~--~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~ 94 (180)
.|++..+..+ +.+|.|+-||..||++||..|.. ++||+-+.|++||.-.. |+|++|.|||.||||||||..|.
T Consensus 99 ~gn~~~~~kki~KqrrQrthFtSqqlqele~tF~r-NrypdMstrEEIavwtN----lTE~rvrvwfknrrakwrkrErN 173 (351)
T KOG0486|consen 99 MGNEDPNKKKISKQRRQRTHFTSQQLQELEATFQR-NRYPDMSTREEIAVWTN----LTEARVRVWFKNRRAKWRKRERN 173 (351)
T ss_pred cCCCCcccchhhhhhhhhhhhHHHHHHHHHHHHhh-ccCCccchhhHHHhhcc----ccchhhhhhcccchhhhhhhhhh
Confidence 4555555566 78899999999999999999998 59999999999999875 99999999999999999998887
Q ss_pred hc
Q 036802 95 VS 96 (180)
Q Consensus 95 ~~ 96 (180)
..
T Consensus 174 ~~ 175 (351)
T KOG0486|consen 174 QQ 175 (351)
T ss_pred HH
Confidence 76
No 24
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.42 E-value=1.3e-13 Score=125.89 Aligned_cols=62 Identities=21% Similarity=0.353 Sum_probs=58.7
Q ss_pred CCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhh
Q 036802 27 GTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRR 93 (180)
Q Consensus 27 ~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r 93 (180)
+.|++||.++.-...+||..|..+ +.|+.++|..||++|+ |+..+|+|||+|||.|+||...
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~n-pKPt~qEIt~iA~~L~----leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKN-PKPTSQEITHIAESLQ----LEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhC-CCCCHHHHHHHHHHhc----cccceEEEEeeccccccccCCC
Confidence 667799999999999999999995 9999999999999997 9999999999999999999877
No 25
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.40 E-value=1.3e-13 Score=111.36 Aligned_cols=64 Identities=25% Similarity=0.396 Sum_probs=59.2
Q ss_pred CCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhh
Q 036802 25 DTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRR 93 (180)
Q Consensus 25 ~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r 93 (180)
....+|.|+.||..|+.+||++|... +||+...|+.+|..+. +++..|+||||||||+++++.+
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~----~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLT----GDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCC----CCeeeeehhhhhhcHhhhhhhc
Confidence 45778899999999999999999985 9999999999988886 9999999999999999999886
No 26
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.16 E-value=8.8e-12 Score=108.31 Aligned_cols=65 Identities=22% Similarity=0.293 Sum_probs=58.9
Q ss_pred CCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhcc
Q 036802 28 TKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSV 97 (180)
Q Consensus 28 ~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~ 97 (180)
.+..|.+|+-.||..||..|++ ++||--.+|.++|..|+ +++.+|+|||||||.||||+....-.
T Consensus 167 rk~srPTf~g~qi~~le~~feq-tkylaG~~ra~lA~~lg----mteSqvkVWFQNRRTKWRKkhAaEma 231 (288)
T KOG0847|consen 167 RKQSRPTFTGHQIYQLERKFEQ-TKYLAGADRAQLAQELN----MTESQVKVWFQNRRTKWRKKHAAEMA 231 (288)
T ss_pred ccccCCCccchhhhhhhhhhhh-hhcccchhHHHhhcccc----ccHHHHHHHHhcchhhhhhhhccchh
Confidence 3458899999999999999998 59999999999999997 89999999999999999998876643
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.12 E-value=3.1e-11 Score=108.31 Aligned_cols=69 Identities=22% Similarity=0.362 Sum_probs=61.8
Q ss_pred CCCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhcc
Q 036802 24 SDTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSV 97 (180)
Q Consensus 24 ~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~ 97 (180)
.....+|.|++||++|+..||+.|..+ +||+...|++||.+.+ +++.+|+|||||||+|++|.....+.
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt-~yP~i~~Re~La~~i~----l~e~riqvwf~nrra~~rr~~~~~s~ 240 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRT-PYPDIVGRETLAKETG----LPEPRVQVWFQNRRAKWRRQHRDCSK 240 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCC-CCCchhhHHHHhhhcc----CCchHHHHHHhhhhhhhhhccccccc
Confidence 355666789999999999999999985 7999999999999996 99999999999999999999976553
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.96 E-value=3.5e-10 Score=101.54 Aligned_cols=66 Identities=21% Similarity=0.400 Sum_probs=59.4
Q ss_pred CCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 25 DTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 25 ~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
+...||+||.+-....+.||.+|..+ +.|+.+.|..||++|. |...+|.|||+|.|.|+||.++-.
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQ-PRPS~EkIAaIAekLD----LKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQ-PRPSGEKIAAIAEKLD----LKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred ccccccccccccCcccccHHHHhccC-CCCchhHHHHHHHhhh----hhhceEEEEeeccHHHHHHhhhhh
Confidence 44567899999999999999999985 9999999999999997 888999999999999999965543
No 29
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.53 E-value=7.3e-08 Score=77.95 Aligned_cols=67 Identities=24% Similarity=0.470 Sum_probs=60.0
Q ss_pred CCCCCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhh
Q 036802 22 DNSDTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRR 93 (180)
Q Consensus 22 gs~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r 93 (180)
+......++.|+.++..|+..|+..|... ++|+...+.+|+..++ +++..|++||||+|++.++...
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~P~~~~~~~l~~~~~----~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 147 GPSNKKPRRPRTTFTENQLEVLETVFRAT-PKPDADDREQLAEETG----LSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCCccccCCCccccccchhHhhhhcccCC-CCCchhhHHHHHHhcC----CChhhhhhhcccHHHHHHhhcc
Confidence 34456777899999999999999999985 8999999999999986 9999999999999999998766
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.36 E-value=2.3e-07 Score=88.28 Aligned_cols=60 Identities=30% Similarity=0.356 Sum_probs=55.0
Q ss_pred CCCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhH
Q 036802 24 SDTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARE 88 (180)
Q Consensus 24 ~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRARe 88 (180)
.....|++|.+||..|++.|-.+|.. +++|+.+..+.|+.+|+ |....|.+||.|-|-|.
T Consensus 416 ~~~~~KKPRlVfTd~QkrTL~aiFke-~~RPS~Emq~tIS~qL~----L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 416 KMLQTKKPRLVFTDIQKRTLQAIFKE-NKRPSREMQETISQQLN----LELSTVINFFMNARRRS 475 (558)
T ss_pred ccccCCCceeeecHHHHHHHHHHHhc-CCCCCHHHHHHHHHHhC----CcHHHHHHHHHhhhhhc
Confidence 35567889999999999999999998 59999999999999996 99999999999988876
No 31
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.32 E-value=4.4e-07 Score=80.79 Aligned_cols=49 Identities=18% Similarity=0.426 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 37 SEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 37 ~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
..=...|.+.|.. ++||+..++.+||+..+ |+..||-+||.|||.|+|-
T Consensus 185 ekSR~~LrewY~~-~~YPsp~eKReLA~aTg----Lt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 185 EKSRSLLREWYLQ-NPYPSPREKRELAEATG----LTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred HhhHHHHHHHHhc-CCCCChHHHHHHHHHhC----Cchhhhhhhhhhhhhhhhh
Confidence 3346799999998 59999999999999886 9999999999999999993
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.15 E-value=1.6e-06 Score=77.39 Aligned_cols=64 Identities=22% Similarity=0.361 Sum_probs=56.4
Q ss_pred CCccCCCCCHHHHHHHHHHHh--cCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 28 TKCGRWNPTSEQVKVLTDLFT--SGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 28 ~kR~Rt~fT~eQL~~LE~~F~--~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
.+|+|.+|++.--.+|.++|- .+++||+.+..++||.+.+ |+..||-+||-|+|.|-||--..-
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCn----ItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCN----ITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcC----ceehhhccccccceeehhhhhhhh
Confidence 568999999999999999995 3469999999999998875 999999999999999999865443
No 33
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.12 E-value=3.9e-07 Score=59.19 Aligned_cols=33 Identities=24% Similarity=0.504 Sum_probs=27.7
Q ss_pred CCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhh
Q 036802 51 LRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKAR 87 (180)
Q Consensus 51 ~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAR 87 (180)
+|||+.+++++||.+.+ |+..||.+||-|.|.|
T Consensus 8 nPYPs~~ek~~L~~~tg----ls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 8 NPYPSKEEKEELAKQTG----LSRKQISNWFINARRR 40 (40)
T ss_dssp SGS--HHHHHHHHHHHT----S-HHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHcC----CCHHHHHHHHHHhHcc
Confidence 59999999999999986 9999999999999976
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.68 E-value=3.2e-05 Score=79.81 Aligned_cols=66 Identities=18% Similarity=0.429 Sum_probs=58.4
Q ss_pred CCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 25 DTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 25 ~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
.-+.++.|+.++..||++|..+|... .||.-++.+-+-..+. ++.++|++||||-|+|.|+.....
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~q-~~~~~~~~E~l~~~~~----~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEAQ-RTPTMQECEVLEEPIG----LPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhhc-cCChHHHHHhhccccc----CCcchhHHhhhhhhhhhhhhhhcc
Confidence 55667799999999999999999985 8999999888877775 899999999999999999987754
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.41 E-value=0.0029 Score=55.64 Aligned_cols=67 Identities=18% Similarity=0.187 Sum_probs=52.2
Q ss_pred CCCCccCCCCCHHHHHHHHHHHhcC--CCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhc
Q 036802 26 TGTKCGRWNPTSEQVKVLTDLFTSG--LRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVS 96 (180)
Q Consensus 26 ~~~kR~Rt~fT~eQL~~LE~~F~~~--~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~ 96 (180)
....|++..+-++...+|....... .+||+..+...||.+.+ |+..||.+||-|.|-|..+-.....
T Consensus 237 ~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TG----Ls~~Qv~NWFINaR~R~w~p~~~~~ 305 (342)
T KOG0773|consen 237 QSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTG----LSRPQVSNWFINARVRLWKPMIEEM 305 (342)
T ss_pred cCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcC----CCcccCCchhhhcccccCCchHHHH
Confidence 4466777899999999998765431 27999998887777765 9999999999999988776555443
No 36
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=95.02 E-value=0.013 Score=58.74 Aligned_cols=52 Identities=25% Similarity=0.437 Sum_probs=47.4
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhc
Q 036802 40 VKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVS 96 (180)
Q Consensus 40 L~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~ 96 (180)
+..|..+|..+ ..|+.++..+||.+++ |+-+.|+.||+|+++.+.+-.|.-+
T Consensus 568 ~sllkayyaln-~~ps~eelskia~qvg----lp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYALN-GLPSEEELSKIAQQVG----LPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHhc-CCCCHHHHHHHHHHhc----ccHHHHHHHHHhhhhhhhhhccCcc
Confidence 78899999985 8999999999999997 9999999999999999998876655
No 37
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=93.12 E-value=0.14 Score=54.08 Aligned_cols=103 Identities=17% Similarity=0.260 Sum_probs=78.7
Q ss_pred CCCCCCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhccccc
Q 036802 21 NDNSDTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSVDYD 100 (180)
Q Consensus 21 ~gs~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~d~~ 100 (180)
+++-.-..++.|.+.-++++.+|=..|..+ -.|+..-+..|..... .+.+++++||+|-+.|.++.+ ...|..
T Consensus 698 ~~~~~~~~~~~~~~~~~~aa~~l~~a~~~~-~sps~k~~~civcd~~----st~~l~~l~~h~~~~rs~ke~--v~g~~~ 770 (1406)
T KOG1146|consen 698 GESLSPRDKLLRLTILPEAAMILGRAYMQD-NSPSLKVFDCIVCDVF----STDRLDQLWFHNTRERSRKEQ--VPGDVP 770 (1406)
T ss_pred CCCCCcccccCcccccHHHHhhhhhcccCC-CCHHHHHHHHhhhhhh----hhhhHHHHhhcchhhhhhhhc--ccCCCC
Confidence 666677778899999999999999999986 5999988888777664 688889999999999999988 333433
Q ss_pred cccccccccCCCCcchhhhccchHHHHHHhhc
Q 036802 101 HQKDLIRHVDKISSPKREAHDEPERVIETLQL 132 (180)
Q Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~e~l~~ 132 (180)
. -.+++|.+-.+-+-.++++-++-+-.+++
T Consensus 771 ~--c~l~~y~t~~kanfqlh~Ktdkh~qk~~~ 800 (1406)
T KOG1146|consen 771 S--CKLKPYATNTKANFQLHNKTDKHVQKYQL 800 (1406)
T ss_pred c--ceecccccccchhhhhhcccchhhhccch
Confidence 2 46778887655555555666666655554
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=91.04 E-value=0.067 Score=37.64 Aligned_cols=42 Identities=12% Similarity=0.369 Sum_probs=29.4
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchh
Q 036802 40 VKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKA 86 (180)
Q Consensus 40 L~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRA 86 (180)
++-|+++|... +.+...+...|..+-+ |+..+|+.||--|..
T Consensus 10 ~~pL~~Yy~~h-~~L~E~DL~~L~~kS~----ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKH-KQLQEEDLDELCDKSR----MSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT-----TTHHHHHHHHTT------HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHc-CCccHhhHHHHHHHHC----CCHHHHHHHHHHhcc
Confidence 45699999984 8999999999999886 999999999976543
No 39
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=88.49 E-value=0.4 Score=32.31 Aligned_cols=47 Identities=17% Similarity=0.196 Sum_probs=35.1
Q ss_pred CccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcch
Q 036802 29 KCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHK 85 (180)
Q Consensus 29 kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRR 85 (180)
+|+|..+|-+|.-.+=..++.| . ...+||.+++ |+..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g-~-----s~~~ia~~fg----v~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG-E-----SKRDIAREFG----VSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT-T------HHHHHHHHT------CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcC-C-----CHHHHHHHhC----CCHHHHHHHHHhHH
Confidence 5789999999998888889876 2 3458999997 99999999998863
No 40
>smart00340 HALZ homeobox associated leucin zipper.
Probab=86.45 E-value=0.085 Score=35.58 Aligned_cols=42 Identities=19% Similarity=0.353 Sum_probs=32.7
Q ss_pred hhccccccccccccccCCCCcchhhhccchHHHHHHhhcCCCCCCCC
Q 036802 94 KVSVDYDHQKDLIRHVDKISSPKREAHDEPERVIETLQLFPLNSFDD 140 (180)
Q Consensus 94 ~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~l~~~p~~~~~~ 140 (180)
+.+.|++. |.+||++|+.+++.| +.+..++..|...| ..|++
T Consensus 2 QTEvdCe~---LKrcce~LteeNrRL-~ke~~eLralk~~~-~~~m~ 43 (44)
T smart00340 2 QTEVDCEL---LKRCCESLTEENRRL-QKEVQELRALKLSP-PLYMQ 43 (44)
T ss_pred chHHHHHH---HHHHHHHHHHHHHHH-HHHHHHHHhcccCC-ccccc
Confidence 34557774 888999999999998 77777788888877 56664
No 41
>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=79.08 E-value=0.94 Score=27.39 Aligned_cols=43 Identities=16% Similarity=0.173 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchh
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKA 86 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRA 86 (180)
.+++.|..+++..|..+ ++ ..+||..++ ++...|+.|.+.-+.
T Consensus 10 ~l~~~~~~~~~~~~~~~--~~----~~~ia~~~~----~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG--LS----YEEIAEILG----ISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC--CC----HHHHHHHHC----cCHHHHHHHHHHHHH
Confidence 35888999999998654 33 347899996 899999988765443
No 42
>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=78.32 E-value=2 Score=29.50 Aligned_cols=39 Identities=21% Similarity=0.388 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhcCC-CCCCHHHHHHHHHHhcccCCCCCCcc
Q 036802 35 PTSEQVKVLTDLFTSGL-RTPSTDQIQKISTQLSFYGKIESKNV 77 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~-~yPs~~~r~eLA~~L~~~g~L~e~qV 77 (180)
+|+.|.++|...|..|- .+|-.....+||++|+ |+..-|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lg----is~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELG----ISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhC----CCHHHH
Confidence 58999999999999863 3466667889999997 776554
No 43
>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=71.66 E-value=1.7 Score=29.55 Aligned_cols=42 Identities=14% Similarity=0.313 Sum_probs=27.1
Q ss_pred ccCCCCCHHHHHHHHHHH-hcCCCCCCHHHHHHHHHHhcccCCCCCCcceecc
Q 036802 30 CGRWNPTSEQVKVLTDLF-TSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWF 81 (180)
Q Consensus 30 R~Rt~fT~eQL~~LE~~F-~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWF 81 (180)
+.|..||+++...+=..+ ..+ ..+.+||.+++ |+...|..|=
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g------~sv~~va~~~g----i~~~~l~~W~ 44 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG------ESVSEVAREYG----ISPSTLYNWR 44 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH------CHHHHHHHHHT----S-HHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC------CceEeeecccc----cccccccHHH
Confidence 467778998877666555 443 55678999996 9999999994
No 44
>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=68.12 E-value=1.9 Score=27.88 Aligned_cols=39 Identities=15% Similarity=0.169 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCc
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQN 83 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQN 83 (180)
.++.|..++.-.|-.+ ++. .+||..++ +++..|++|.+.
T Consensus 11 L~~~~r~i~~l~~~~g--~s~----~eIa~~l~----~s~~~v~~~l~r 49 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG--MSY----AEIAEILG----ISESTVKRRLRR 49 (54)
T ss_dssp S-HHHHHHHHHHHTS-----H----HHHHHHCT----S-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC--cCH----HHHHHHHC----cCHHHHHHHHHH
Confidence 5788888898888775 443 38899996 999999998764
No 45
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=67.21 E-value=4.5 Score=30.88 Aligned_cols=49 Identities=16% Similarity=0.148 Sum_probs=30.9
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhh
Q 036802 36 TSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRK 94 (180)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~ 94 (180)
++.|..++.-.|-.+ ++ .++||..|+ +++..|+++...=|.+.|+.-..
T Consensus 108 p~~~r~v~~l~~~~g--~s----~~EIA~~lg----is~~tV~~~l~Rar~~Lr~~l~~ 156 (160)
T PRK09642 108 PENYRDVVLAHYLEE--KS----YQEIALQEK----IEVKTVEMKLYRARKWIKKHWKE 156 (160)
T ss_pred CHHHHHHHHHHHHhC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHhh
Confidence 444555555544443 22 348899996 99999999887655555554433
No 46
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=65.19 E-value=7.6 Score=32.16 Aligned_cols=40 Identities=20% Similarity=0.379 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHhcCC-CCCCHHHHHHHHHHhcccCCCCCCcc
Q 036802 34 NPTSEQVKVLTDLFTSGL-RTPSTDQIQKISTQLSFYGKIESKNV 77 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~-~yPs~~~r~eLA~~L~~~g~L~e~qV 77 (180)
.+|+.|+++|...|..|- -||-.....+||++|| |+...+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lG----ISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELG----ISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhC----CCHHHH
Confidence 799999999999999863 4566777889999997 776554
No 47
>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=63.75 E-value=4.1 Score=26.12 Aligned_cols=38 Identities=16% Similarity=0.250 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceecc
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWF 81 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWF 81 (180)
.+++.|..+|...|..+ ++ -.+||..|+ ++...|+.+-
T Consensus 4 ~L~~~er~vi~~~y~~~--~t----~~eIa~~lg----~s~~~V~~~~ 41 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG--LT----LEEIAERLG----ISRSTVRRIL 41 (50)
T ss_dssp TS-HHHHHHHHHHHTST---S----HHHHHHHHT----SCHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC--CC----HHHHHHHHC----CcHHHHHHHH
Confidence 46899999999999654 32 348899997 8988887654
No 48
>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=62.50 E-value=7.8 Score=20.59 Aligned_cols=38 Identities=18% Similarity=0.462 Sum_probs=26.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceecc
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWF 81 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWF 81 (180)
.++.++...+...|..+ + ...+||..++ ++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~--~----s~~~ia~~~~----is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG--E----SVAEIARRLG----VSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC--C----CHHHHHHHHC----CCHHHHHHhC
Confidence 35777887777778653 3 2347888886 8888888773
No 49
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=60.04 E-value=5.9 Score=30.14 Aligned_cols=47 Identities=13% Similarity=-0.001 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
.+++.|..+|.-.|-.+ ++.. +||..|+ ++...|+.|.+.=+.+-|+
T Consensus 128 ~L~~~~r~vl~l~~~~~--~s~~----eIA~~lg----is~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLREIEG--LSYE----EIAEIMG----CPIGTVRSRIFRAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CCHH----HHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 46777888888776554 4333 7899997 9999999988744444333
No 50
>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=60.01 E-value=5.9 Score=28.35 Aligned_cols=46 Identities=17% Similarity=0.208 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHH
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARER 89 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReK 89 (180)
.+++.|..++...|-.+ ++. .+||..|+ +++..|..|.+.=+.|-|
T Consensus 110 ~L~~~~~~ii~~~~~~g--~s~----~eIA~~l~----~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG--LSY----KEIAEILG----ISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhcC--CCH----HHHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 45788888887776553 433 38899996 899999988765544443
No 51
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=58.94 E-value=1.9 Score=43.01 Aligned_cols=70 Identities=19% Similarity=0.159 Sum_probs=45.9
Q ss_pred CCCCCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcc---cCCCCCCcceeccCcchhhHHHhhhh
Q 036802 25 DTGTKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSF---YGKIESKNVFYWFQNHKARERQKRRK 94 (180)
Q Consensus 25 ~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~---~g~L~e~qVqvWFQNRRAReKRk~r~ 94 (180)
...+|+.|..|=.+|.-.+......-+.-|+--.+.+-.+++-. .-+.++++|+.||.|||+++|+.+-.
T Consensus 688 ~~~pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 688 LDLPKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hcccHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhcc
Confidence 55666777777777766655444332466766666665555431 11246789999999999999986544
No 52
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=58.94 E-value=8.3 Score=30.76 Aligned_cols=46 Identities=17% Similarity=0.200 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
+++.|..+|.-.|-.+ ++ .++||+.|+ ++..+|+++...=|.+.|+
T Consensus 143 L~~~~r~vl~l~~~~~--~s----~~EIA~~Lg----is~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 143 LTDTQRESVTLAYYGG--LT----YREVAERLA----VPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHhC----CChHhHHHHHHHHHHHHHH
Confidence 4566666666655443 32 348899997 9999998887544444443
No 53
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=56.27 E-value=4.4 Score=26.08 Aligned_cols=38 Identities=21% Similarity=0.231 Sum_probs=18.4
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceec
Q 036802 33 WNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYW 80 (180)
Q Consensus 33 t~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvW 80 (180)
..+|.+|...++.++..+ + ...+||+.|+ .+...|..|
T Consensus 3 ~~Lt~~eR~~I~~l~~~G--~----s~~~IA~~lg----~s~sTV~re 40 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG--M----SIREIAKRLG----RSRSTVSRE 40 (44)
T ss_dssp ---------HHHHHHCS---------HHHHHHHTT------HHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC--C----CHHHHHHHHC----cCcHHHHHH
Confidence 357999999999999775 2 3347999997 676666544
No 54
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=55.87 E-value=12 Score=26.88 Aligned_cols=45 Identities=16% Similarity=0.163 Sum_probs=29.8
Q ss_pred CCCCHHHHHHHHHHHhc----CCCCCCHHHHHHHHHHhcccCCCCCCcceecc
Q 036802 33 WNPTSEQVKVLTDLFTS----GLRTPSTDQIQKISTQLSFYGKIESKNVFYWF 81 (180)
Q Consensus 33 t~fT~eQL~~LE~~F~~----~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWF 81 (180)
|.+|++|+..|..+|.. ++.+.+..+..++-..+ ++++..|..+|
T Consensus 2 ~~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~----~~~~~ev~~i~ 50 (96)
T smart00027 2 WAISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKS----GLPQTLLAKIW 50 (96)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHc----CCCHHHHHHHH
Confidence 78899999999999975 23456666655554443 25655555444
No 55
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=55.36 E-value=8.7 Score=29.60 Aligned_cols=51 Identities=4% Similarity=-0.046 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
+++.|..++.-.|-.+ ++ .++||..|+ +++..|++|.+-=|.+.|+.-...
T Consensus 109 L~~~~r~v~~l~~~~g--~s----~~eIA~~lg----is~~tv~~~l~Rar~~Lr~~l~~~ 159 (165)
T PRK09644 109 LPVIEAQAILLCDVHE--LT----YEEAASVLD----LKLNTYKSHLFRGRKRLKALLKEE 159 (165)
T ss_pred CCHHHHHHHHhHHHhc--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHhh
Confidence 3445555555444332 22 348899997 899999998876666666554443
No 56
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=55.02 E-value=8.1 Score=29.96 Aligned_cols=46 Identities=13% Similarity=0.121 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
+++.|..++.-.|-.+ ++ .++||..|+ +++.+|+++.+.=|.+.|.
T Consensus 137 L~~~~r~v~~l~~~~g--~s----~~eIA~~lg----is~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 137 LPPKYRMVIVLKYMED--LS----LKEISEILD----LPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCHHHhHHhhhHHhcC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 4445555555544332 22 348899996 8999999998655555544
No 57
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=52.46 E-value=11 Score=29.37 Aligned_cols=50 Identities=20% Similarity=0.194 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRK 94 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~ 94 (180)
+++.|..+|.-.|-.+ ++ -.+||..|+ |+...|+++...=|.+.|.+-+.
T Consensus 132 L~~~~r~v~~l~~~~g--~s----~~eIA~~l~----is~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12512 132 LPPRQRDVVQSISVEG--AS----IKETAAKLS----MSEGAVRVALHRGLAALAAKFRS 181 (184)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHhC----CCHHHHHHHHHHHHHHHHHHhhc
Confidence 3445555555554333 21 347899996 99999999887766666655443
No 58
>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=52.29 E-value=6.2 Score=25.34 Aligned_cols=39 Identities=21% Similarity=0.491 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceecc
Q 036802 33 WNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWF 81 (180)
Q Consensus 33 t~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWF 81 (180)
..++++|++.+-+++..+ + .+.+||..++ |+...|+-++
T Consensus 4 ~~~~~~~~~~i~~l~~~G--~----si~~IA~~~g----vsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEG--M----SIAEIAKQFG----VSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT--------HHHHHHHTT----S-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCC--C----CHHHHHHHHC----cCHHHHHHHH
Confidence 347888999999999875 3 3558999996 8887777543
No 59
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=51.43 E-value=8.8 Score=31.13 Aligned_cols=53 Identities=21% Similarity=0.152 Sum_probs=39.5
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhc
Q 036802 33 WNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVS 96 (180)
Q Consensus 33 t~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~ 96 (180)
..+|+.|.++|.-. ..+ +. .++||..|+ ++...|..|-++-+.+.++...-..
T Consensus 5 ~~Lt~rqreVL~lr-~~G--lT----q~EIAe~LG----iS~~tVs~ie~ra~kkLr~~~~tl~ 57 (141)
T PRK03975 5 SFLTERQIEVLRLR-ERG--LT----QQEIADILG----TSRANVSSIEKRARENIEKARETLA 57 (141)
T ss_pred cCCCHHHHHHHHHH-HcC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46799999999884 454 32 238999997 9999999999976666666555543
No 60
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=50.50 E-value=9.1 Score=30.19 Aligned_cols=46 Identities=20% Similarity=0.153 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
+++.|..++.-.|-.+ ++ ..+||..|+ ++...|++|.+.=|.+-|+
T Consensus 142 L~~~~~~v~~l~~~~g--~s----~~EIA~~lg----is~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 142 LPESQRQVLELAYYEG--LS----QSEIAKRLG----IPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHhhhhhhhhhcC--CC----HHHHHHHhC----CCHHHHHHHHHHHHHHHHH
Confidence 3555666665555443 22 348899997 8999999999655544444
No 61
>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=49.99 E-value=7.1 Score=26.98 Aligned_cols=28 Identities=21% Similarity=0.512 Sum_probs=21.1
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceecc
Q 036802 44 TDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWF 81 (180)
Q Consensus 44 E~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWF 81 (180)
..+|-.+ |+.. +||..|+ ++.+.|+.|=
T Consensus 7 ~~LY~~G--~~~~----eIA~~Lg----~~~~TV~~W~ 34 (58)
T PF06056_consen 7 RSLYLQG--WSIK----EIAEELG----VPRSTVYSWK 34 (58)
T ss_pred HHHHHcC--CCHH----HHHHHHC----CChHHHHHHH
Confidence 3456554 5544 8999997 8999999994
No 62
>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=48.97 E-value=11 Score=28.36 Aligned_cols=38 Identities=16% Similarity=0.202 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceecc
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWF 81 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWF 81 (180)
.+++.|..++.-.|-.+ ++. .+||+.|+ |+...|+++.
T Consensus 111 ~L~~~~r~v~~l~~~~g--~~~----~eIA~~l~----is~~tv~~~l 148 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG--VSL----TALAEQLG----RTVNAVYKAL 148 (159)
T ss_pred HCCHHHHHHHHHHHhcC--CCH----HHHHHHhC----CCHHHHHHHH
Confidence 36777777777766554 433 38899996 9999999764
No 63
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=48.61 E-value=12 Score=26.26 Aligned_cols=42 Identities=19% Similarity=0.139 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceecc
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWF 81 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWF 81 (180)
+|++|+..|+.+|.. . .+.+.+|-.+.-.+|-|+..+=..|-
T Consensus 1 lT~~Qk~el~~l~~q-m----~e~kK~~idk~Ve~G~iTqeqAd~ik 42 (59)
T PF10925_consen 1 LTDQQKKELKALYKQ-M----LELKKQIIDKYVEAGVITQEQADAIK 42 (59)
T ss_pred CCHHHHHHHHHHHHH-H----HHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 589999999999987 2 46777888888889999987755443
No 64
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=48.15 E-value=14 Score=28.14 Aligned_cols=45 Identities=27% Similarity=0.240 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
+++.|..+|.-.| .+ ++. .+||..|+ +++..|+++...=|.+.|+
T Consensus 113 L~~~~r~il~l~~-~g--~s~----~eIA~~lg----is~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 113 MTERDRTVLLLRF-SG--YSY----KEIAEALG----IKESSVGTTLARAKKKFRK 157 (166)
T ss_pred CCHHHHHHHHHHH-cC--CCH----HHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 5666777777777 54 433 37899996 9999999888544444443
No 65
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=48.06 E-value=13 Score=28.13 Aligned_cols=47 Identities=15% Similarity=0.144 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQK 91 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk 91 (180)
+++.+..+|.-.|-.+ ++ ..+||..|+ ++...|..|..-=|.+.|+.
T Consensus 126 L~~~~r~i~~l~~~~~--~~----~~eIA~~lg----is~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 126 LPVKQREVFLLRYVEG--LS----YREIAEILG----VPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CCHHHHHHhhHHHHcC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHH
Confidence 4555555555555443 22 248899997 99999999887655555543
No 66
>PRK06930 positive control sigma-like factor; Validated
Probab=47.67 E-value=14 Score=30.15 Aligned_cols=52 Identities=13% Similarity=0.077 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
.+++.+..++.-.|..+ .+. .+||..|+ ++...|+++...=+.+-++.-...
T Consensus 114 ~L~~rer~V~~L~~~eg--~s~----~EIA~~lg----iS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG--LSY----SEIADYLN----IKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred hCCHHHHHHHHHHHHcC--CCH----HHHHHHHC----cCHHHHHHHHHHHHHHHHHHHHHh
Confidence 56777778887766554 332 37899996 999999999876666666554433
No 67
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=47.67 E-value=12 Score=28.17 Aligned_cols=43 Identities=9% Similarity=0.216 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKAR 87 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAR 87 (180)
+++.|..++.-.|-.+ ++ ..+||..|+ ++...|++|...=+.+
T Consensus 107 L~~~~r~ii~l~~~~~--~s----~~EIA~~l~----is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 107 LDEKEKYIIFERFFVG--KT----MGEIALETE----MTYYQVRWIYRQALEK 149 (154)
T ss_pred CCHHHHHHHHHHHhcC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHH
Confidence 4566666666666554 22 458899996 9999999887543333
No 68
>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=47.60 E-value=14 Score=27.44 Aligned_cols=45 Identities=20% Similarity=0.188 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHH
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARER 89 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReK 89 (180)
+++.+..+|.-.|-.+ ++. .+||..|+ +++..|+++...=|.+.|
T Consensus 114 L~~~~r~il~l~~~~~--~~~----~eIA~~lg----is~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 114 LPEQCRKIFILSRFEG--KSY----KEIAEELG----ISVKTVEYHISKALKELR 158 (161)
T ss_pred CCHHHHHHHHHHHHcC--CCH----HHHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 4566666666655443 333 37888886 899999877654444433
No 69
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=47.49 E-value=15 Score=28.03 Aligned_cols=39 Identities=18% Similarity=0.514 Sum_probs=27.6
Q ss_pred CCCCCHHH-HHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceec
Q 036802 32 RWNPTSEQ-VKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYW 80 (180)
Q Consensus 32 Rt~fT~eQ-L~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvW 80 (180)
|..+|.++ +.++..++..+ ++- .+||.+++ |+...|+.|
T Consensus 10 rr~ys~EfK~~aV~~~~~~g--~sv----~evA~e~g----Is~~tl~~W 49 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG--MTV----SLVARQHG----VAASQLFLW 49 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC--CCH----HHHHHHHC----cCHHHHHHH
Confidence 44457766 45666677654 433 37899997 999999999
No 70
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=47.40 E-value=16 Score=22.41 Aligned_cols=38 Identities=26% Similarity=0.305 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccC
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQ 82 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQ 82 (180)
.+|+.|..++... ..+ + ...+||..|+ ++...|+.|.+
T Consensus 3 ~l~~~e~~i~~~~-~~g--~----s~~eia~~l~----is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRLL-AEG--L----TNKEIAERLG----ISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHHH-HcC--C----CHHHHHHHHC----CCHHHHHHHHH
Confidence 4688999988764 443 3 2357899996 89999988766
No 71
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=47.26 E-value=15 Score=29.86 Aligned_cols=46 Identities=13% Similarity=0.135 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
+++.|..+|.-.|-.+ +. .++||..|+ +++..|+++.+.=+.+.++
T Consensus 154 L~~~~r~vl~l~~~~g--~s----~~EIA~~lg----is~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 154 LPEAQQTVVKGVYFQE--LS----QEQLAQQLN----VPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 3445555665444333 22 348899997 9999998877544444443
No 72
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=46.88 E-value=15 Score=28.83 Aligned_cols=48 Identities=8% Similarity=0.068 Sum_probs=29.7
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhh
Q 036802 36 TSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRR 93 (180)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r 93 (180)
++.|..++.-.|-.+ ++ ..+||..|+ ++...|+++...=|.+.|+...
T Consensus 130 ~~~~r~i~~l~~~~g--~s----~~EIA~~lg----is~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 130 PERQREAIVLQYYQG--LS----NIEAAAVMD----ISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CHHHHHHhhHHHhcC--CC----HHHHHHHhC----cCHHHHHHHHHHHHHHHHHHHH
Confidence 455555555544343 22 247889996 9999999988555555444433
No 73
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=46.64 E-value=14 Score=29.50 Aligned_cols=46 Identities=11% Similarity=0.099 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHH
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARER 89 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReK 89 (180)
.+++.|..+|.-.|-.+ ++- .+||..|+ ++...|++.+..=|.+.|
T Consensus 106 ~L~~~~r~i~~l~~~~g--~~~----~EIA~~lg----is~~tV~~~l~Rar~~Lr 151 (181)
T PRK09637 106 ALPEKYAEALRLTELEG--LSQ----KEIAEKLG----LSLSGAKSRVQRGRVKLK 151 (181)
T ss_pred hCCHHHHHHHHHHHhcC--CCH----HHHHHHhC----CCHHHHHHHHHHHHHHHH
Confidence 45666666666665443 333 37899996 899999988864333333
No 74
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=45.80 E-value=15 Score=29.22 Aligned_cols=48 Identities=10% Similarity=0.073 Sum_probs=30.8
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhh
Q 036802 36 TSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRR 93 (180)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r 93 (180)
++.|..++.-.|-.+ ++ .++||..|+ +++..|+++...=|.+.|....
T Consensus 136 p~~~R~v~~L~~~~g--~s----~~EIA~~lg----is~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 136 PAQQARVFMMREYLE--LS----SEQICQECD----ISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred CHHHHHHHhHHHHcC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHH
Confidence 445555555555443 22 348899997 9999999987655555444433
No 75
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=45.38 E-value=12 Score=28.55 Aligned_cols=47 Identities=13% Similarity=0.036 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
.+++.|..+|.-.|-.+ ++. .+||..|+ ++...|+++-..=|.+.|+
T Consensus 112 ~L~~~~r~v~~l~~~~~--~s~----~eIA~~lg----is~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG--FSY----KEIAEMTG----LSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhcC--CCH----HHHHHHHC----CCHHHHHHHHHHHHHHHHh
Confidence 36667777777766553 433 38899996 8999998877655544443
No 76
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=44.89 E-value=18 Score=28.53 Aligned_cols=48 Identities=4% Similarity=0.112 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHh
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQK 91 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk 91 (180)
.+++.|..+|+-.|-.+ ++ ..+||+.|+ +++..|++....=|.+.|+.
T Consensus 131 ~L~~~~r~vl~l~~~~~--~s----~~eIA~~lg----is~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE--KS----VEEVGEIVG----IPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHHcC--CC----HHHHHHHHC----cCHHHHHHHHHHHHHHHHHH
Confidence 45566666666655443 32 347899997 89999998775544444443
No 77
>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=43.38 E-value=16 Score=28.55 Aligned_cols=47 Identities=13% Similarity=0.119 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
.+++.|..+|.-.|-.+ ++- .+||..|+ |++..|+++-+-=|.+.++
T Consensus 100 ~L~~~~r~v~~l~~~~g--~s~----~eIA~~lg----is~~tV~~~l~Rar~~Lr~ 146 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG--LSQ----QEIAEKLG----LSLSGAKSRVQRGRKKLKE 146 (170)
T ss_pred hCCHHHHHHHHHHHHcC--CCH----HHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 56777777777777554 433 38899997 9999999877544444444
No 78
>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=42.75 E-value=16 Score=27.73 Aligned_cols=45 Identities=18% Similarity=0.171 Sum_probs=30.3
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 36 TSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
++.|..+|.-.|-.+ ++. ++||..|+ ++...|+++-..=|.+-|+
T Consensus 112 ~~~~r~i~~l~~~~g--~s~----~eIA~~lg----is~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 112 PARQRAVVVLRYYED--LSE----AQVAEALG----ISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CHHHHHHhhhHHHhc--CCH----HHHHHHhC----CCHHHHHHHHHHHHHHHHH
Confidence 566666776666443 333 37899996 9999999876655555444
No 79
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=42.33 E-value=14 Score=31.13 Aligned_cols=31 Identities=13% Similarity=0.150 Sum_probs=23.4
Q ss_pred HHHHHHhcccCCCCCCcceeccCcchhhHHHhhhh
Q 036802 60 QKISTQLSFYGKIESKNVFYWFQNHKARERQKRRK 94 (180)
Q Consensus 60 ~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~ 94 (180)
++||..|+ +++..|+++.+.=|.+.|+.-..
T Consensus 191 ~EIA~~Lg----is~~tVk~~l~RAr~kLr~~l~~ 221 (233)
T PRK12538 191 GEIAEVMD----TTVAAVESLLKRGRQQLRDLLRR 221 (233)
T ss_pred HHHHHHHC----cCHHHHHHHHHHHHHHHHHHHHH
Confidence 48899996 99999998887666666655443
No 80
>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=42.26 E-value=14 Score=28.70 Aligned_cols=28 Identities=7% Similarity=-0.044 Sum_probs=20.0
Q ss_pred HHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 59 IQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 59 r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
-.+||..|+ |++..|+++...=|.+.|+
T Consensus 157 ~~EIA~~lg----is~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 157 YEDIARIMD----CPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred HHHHHHHHC----cCHHHHHHHHHHHHHHHHH
Confidence 458899996 8999999888544444443
No 81
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=42.07 E-value=34 Score=23.64 Aligned_cols=60 Identities=18% Similarity=0.202 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHHhcC-----CCCCCHHH-------HHHHHHHhcccCCC--CCCcceeccCcchhhHHHhh
Q 036802 33 WNPTSEQVKVLTDLFTSG-----LRTPSTDQ-------IQKISTQLSFYGKI--ESKNVFYWFQNHKARERQKR 92 (180)
Q Consensus 33 t~fT~eQL~~LE~~F~~~-----~~yPs~~~-------r~eLA~~L~~~g~L--~e~qVqvWFQNRRAReKRk~ 92 (180)
-+||++|..+|-+++... +...+... =++||..|...++. +..+|+..++|=+++.|++.
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk~~ 76 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKKKL 76 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 357999999999887652 01111111 14788999876664 12346667777777777654
No 82
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=41.65 E-value=19 Score=29.09 Aligned_cols=51 Identities=16% Similarity=0.036 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
+++.|..+|.-.|-.+ ++ ..+||..|+ |+...|+++.+-=|.+.|+.-...
T Consensus 114 Lp~~~r~v~~L~~~~g--~s----~~EIA~~Lg----iS~~tVk~~l~Rar~~Lr~~l~~~ 164 (188)
T PRK12546 114 LPDEQREALILVGASG--FS----YEEAAEMCG----VAVGTVKSRANRARARLAELLQLE 164 (188)
T ss_pred CCHHHhHHhhhHHhcC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHhcc
Confidence 3455555555554433 33 348899997 999999999876666665544433
No 83
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=41.37 E-value=22 Score=26.87 Aligned_cols=39 Identities=5% Similarity=0.009 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCc
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQN 83 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQN 83 (180)
+++.|..++.-.|-.+ ++ ..+||..|+ ++...|++....
T Consensus 107 Lp~~~r~v~~l~~~~g--~s----~~EIA~~lg----is~~tV~~~l~r 145 (161)
T PRK09047 107 LPARQREAFLLRYWED--MD----VAETAAAMG----CSEGSVKTHCSR 145 (161)
T ss_pred CCHHHHHHHHHHHHhc--CC----HHHHHHHHC----CCHHHHHHHHHH
Confidence 3445555555555443 33 348899997 899999876653
No 84
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=40.92 E-value=24 Score=27.39 Aligned_cols=45 Identities=7% Similarity=0.289 Sum_probs=28.0
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 36 TSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
++.|..++.-.|-.+ ++ .++||..|+ +++..|+++.+.=|.+.|+
T Consensus 131 ~~~~r~i~~l~~~~g--~s----~~eIA~~lg----is~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 131 EKDRAAAVRRAYLEG--LS----YKELAERHD----VPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CHHHHHHHHHHHHcC--CC----HHHHHHHHC----CChHHHHHHHHHHHHHHHH
Confidence 444555555555433 22 458899997 9999998887654444443
No 85
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=40.34 E-value=25 Score=27.66 Aligned_cols=43 Identities=12% Similarity=0.223 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKAR 87 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAR 87 (180)
+++.|..++.-.|-.+ ++ ..+||+.|+ |+...|++|-+.=|.+
T Consensus 134 L~~~~r~i~~l~~~~~--~s----~~eIA~~lg----is~~tV~~~l~ra~~~ 176 (182)
T PRK12537 134 LEPARRNCILHAYVDG--CS----HAEIAQRLG----APLGTVKAWIKRSLKA 176 (182)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHHC----CChhhHHHHHHHHHHH
Confidence 3445555555555443 22 348899997 9999999876543333
No 86
>PRK04217 hypothetical protein; Provisional
Probab=40.28 E-value=17 Score=28.36 Aligned_cols=50 Identities=12% Similarity=0.102 Sum_probs=36.7
Q ss_pred cCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 31 GRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 31 ~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
+=-.+|++|..++...|..+ + ..++||+.|+ |+...|+...+.-+.+.+.
T Consensus 39 p~~~Lt~eereai~l~~~eG--l----S~~EIAk~LG----IS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 39 PPIFMTYEEFEALRLVDYEG--L----TQEEAGKRMG----VSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred CcccCCHHHHHHHHHHHHcC--C----CHHHHHHHHC----cCHHHHHHHHHHHHHHHHH
Confidence 34467999999999888765 2 3457899996 8999999777655544443
No 87
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=40.15 E-value=1.3e+02 Score=21.50 Aligned_cols=18 Identities=17% Similarity=0.141 Sum_probs=14.2
Q ss_pred ccCCCCCHHHHH-HHHHHH
Q 036802 30 CGRWNPTSEQVK-VLTDLF 47 (180)
Q Consensus 30 R~Rt~fT~eQL~-~LE~~F 47 (180)
+.+...|.|||- +|+.+.
T Consensus 35 ~~~~~kT~EeLDaELD~Ym 53 (74)
T PF13865_consen 35 RKKPPKTAEELDAELDAYM 53 (74)
T ss_pred CCCCCCCHHHHHHHHHHHH
Confidence 348889999994 688777
No 88
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=39.88 E-value=24 Score=28.82 Aligned_cols=32 Identities=13% Similarity=0.132 Sum_probs=23.6
Q ss_pred HHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 60 QKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 60 ~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
++||+.|+ +++..|+++...=|.+.++.-...
T Consensus 158 ~EIA~~Lg----is~~tV~~~l~RArk~Lr~~l~~~ 189 (203)
T PRK09647 158 EEIAATLG----VKLGTVRSRIHRGRQQLRAALAAH 189 (203)
T ss_pred HHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHHh
Confidence 47899996 999999998876666666544443
No 89
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=39.77 E-value=25 Score=28.00 Aligned_cols=45 Identities=18% Similarity=0.214 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 36 TSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
++.|..++.-.|-.+ ++ .++||+.|+ ++...|++....=|.+.|+
T Consensus 143 p~~~r~v~~l~~~eg--~s----~~EIA~~lg----is~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 143 PKAQRDVLQAVYLEE--LP----HQQVAEMFD----IPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred CHHHHHHHHHHHHcC--CC----HHHHHHHhC----cCHHHHHHHHHHHHHHHHH
Confidence 444555555544443 22 348899997 9999997666443333333
No 90
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=38.95 E-value=20 Score=28.19 Aligned_cols=30 Identities=7% Similarity=-0.008 Sum_probs=22.5
Q ss_pred HHHHHHHhcccCCCCCCcceeccCcchhhHHHhh
Q 036802 59 IQKISTQLSFYGKIESKNVFYWFQNHKARERQKR 92 (180)
Q Consensus 59 r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~ 92 (180)
-++||+.|+ +++..|++..+.=|.+.|+.-
T Consensus 157 ~~eIA~~lg----is~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 157 YEDIASVMQ----CPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 358899996 999999888776666665543
No 91
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=38.84 E-value=17 Score=36.52 Aligned_cols=68 Identities=13% Similarity=0.085 Sum_probs=41.0
Q ss_pred CCCCCCCCccCCCCCH-HHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhh
Q 036802 22 DNSDTGTKCGRWNPTS-EQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRR 93 (180)
Q Consensus 22 gs~~~~~kR~Rt~fT~-eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r 93 (180)
+++..+++-+|+.|-+ .|+-.|...|.. |..+++..--.+|+.---+-.+.-++||||=|+--+|+..
T Consensus 348 ~~~~H~Pp~pRa~~~P~~ql~~lq~~fs~----~~~qQv~d~~~rl~~sqav~gr~~~N~~q~~~s~~~raE~ 416 (769)
T KOG3755|consen 348 QGLNHPPPYPRAQLKPGFQLNLLQSEFSE----PIYQQVRDELKRLDESQAVFGRVAFNRTQGLLSEILRAEE 416 (769)
T ss_pred cccCCCCCCchhhcCccccchhhhhhhcc----HHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhhccccchhc
Confidence 3344556667998777 699999999964 3444433333333311111123346899999998777543
No 92
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=38.33 E-value=21 Score=22.79 Aligned_cols=21 Identities=33% Similarity=0.283 Sum_probs=16.5
Q ss_pred CccCCCCCHHHHHHHHHHHhc
Q 036802 29 KCGRWNPTSEQVKVLTDLFTS 49 (180)
Q Consensus 29 kR~Rt~fT~eQL~~LE~~F~~ 49 (180)
.+-|..||++|...|+..|..
T Consensus 5 ~k~rl~Pt~~Q~~~L~~~~~~ 25 (46)
T PF12323_consen 5 YKYRLYPTKEQEEKLERWFGA 25 (46)
T ss_pred eEEEEecCHHHHHHHHHHHHH
Confidence 346778888888888888865
No 93
>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=38.31 E-value=22 Score=27.00 Aligned_cols=37 Identities=22% Similarity=0.193 Sum_probs=23.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceecc
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWF 81 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWF 81 (180)
+++.|..+|.-.|-.+ ++ ..+||+.|+ +++..|++..
T Consensus 123 L~~~~r~vl~l~~~~g--~s----~~eIA~~l~----is~~tv~~~l 159 (170)
T TIGR02952 123 LTPKQQHVIALRFGQN--LP----IAEVARILG----KTEGAVKILQ 159 (170)
T ss_pred CCHHHHHHHHHHHhcC--CC----HHHHHHHHC----CCHHHHHHHH
Confidence 4455555555544333 22 348899996 8999888654
No 94
>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=38.27 E-value=22 Score=27.58 Aligned_cols=45 Identities=18% Similarity=0.197 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHH
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARER 89 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReK 89 (180)
+++.|..++.-.|-.+ ++ .++||..|+ |++..|++..+.=|.+.|
T Consensus 135 Lp~~~r~v~~l~~~~g--~s----~~EIA~~lg----is~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG--LT----VEEIAELLG----VSVRTVERDWRFARAWLA 179 (183)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHhC----CCHHHHHHHHHHHHHHHH
Confidence 4555555555555443 22 348899997 999999988765444433
No 95
>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=36.56 E-value=11 Score=26.75 Aligned_cols=18 Identities=17% Similarity=0.589 Sum_probs=15.7
Q ss_pred HHHHHHHhcccCCCCCCcceec
Q 036802 59 IQKISTQLSFYGKIESKNVFYW 80 (180)
Q Consensus 59 r~eLA~~L~~~g~L~e~qVqvW 80 (180)
-.+||++|+ +++.+|..|
T Consensus 25 lkdIA~~Lg----vs~~tIr~W 42 (60)
T PF10668_consen 25 LKDIAEKLG----VSESTIRKW 42 (60)
T ss_pred HHHHHHHHC----CCHHHHHHH
Confidence 347999997 999999988
No 96
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=36.35 E-value=17 Score=37.38 Aligned_cols=63 Identities=17% Similarity=0.167 Sum_probs=44.4
Q ss_pred CCccCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 28 TKCGRWNPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 28 ~kR~Rt~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
+.+.|+....++-..|-.+++.+ --|+..+-.-++..|. ..+.+|.|||+||+.+.+...-..
T Consensus 626 p~kv~sp~k~~dq~ql~~a~elq-~s~~n~~~pl~~t~~~----n~~pv~ev~dhsrsstpsp~pl~l 688 (1007)
T KOG3623|consen 626 PVKVRSPIKEEDQQQLKQAYELQ-ASPSNDEFPLIATRLQ----NDPPVVEVWDHSRSSTPSPMPLFL 688 (1007)
T ss_pred CccccCCCCccchhhhHhhhhcc-cCccCcccchhhhhcc----CCCcchhhcccCCCCCCCCCcccc
Confidence 33466777777777888888765 3455555455666675 677888999999999887655443
No 97
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=36.31 E-value=20 Score=28.16 Aligned_cols=39 Identities=10% Similarity=0.021 Sum_probs=25.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccC
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQ 82 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQ 82 (180)
.+++.|..++.-.|-.+ + ..++||..|+ ++...|+++..
T Consensus 139 ~L~~~~r~i~~l~~~~g--~----s~~EIA~~lg----is~~tV~~~l~ 177 (189)
T PRK09648 139 TLPEKQREILILRVVVG--L----SAEETAEAVG----STPGAVRVAQH 177 (189)
T ss_pred hCCHHHHHHHHHHHHcC--C----CHHHHHHHHC----CCHHHHHHHHH
Confidence 34555566666555443 2 2458899996 89999998774
No 98
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=35.79 E-value=31 Score=22.15 Aligned_cols=14 Identities=21% Similarity=0.126 Sum_probs=11.8
Q ss_pred CCCHHHHHHHHHHH
Q 036802 34 NPTSEQVKVLTDLF 47 (180)
Q Consensus 34 ~fT~eQL~~LE~~F 47 (180)
.||++|+..|+.--
T Consensus 2 ~FT~~Ql~~L~~Qi 15 (37)
T PF08880_consen 2 PFTPAQLQELRAQI 15 (37)
T ss_pred CCCHHHHHHHHHHH
Confidence 59999999999743
No 99
>PF13551 HTH_29: Winged helix-turn helix
Probab=35.46 E-value=51 Score=23.31 Aligned_cols=52 Identities=12% Similarity=0.047 Sum_probs=29.5
Q ss_pred CccCCCCCHHHHHHHHHHHhcCCCCCC--HHHHHHHHHHh-cccC--CCCCCcceecc
Q 036802 29 KCGRWNPTSEQVKVLTDLFTSGLRTPS--TDQIQKISTQL-SFYG--KIESKNVFYWF 81 (180)
Q Consensus 29 kR~Rt~fT~eQL~~LE~~F~~~~~yPs--~~~r~eLA~~L-~~~g--~L~e~qVqvWF 81 (180)
.+++..+|++|...|.+++... +... .-....|+..| .... .++...|..|+
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~~-p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L 108 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLREN-PPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRIL 108 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHC-CCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHH
Confidence 3445558999999999999874 2111 12234555544 2222 25555566554
No 100
>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=35.16 E-value=12 Score=24.75 Aligned_cols=44 Identities=20% Similarity=0.200 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhH
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARE 88 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRARe 88 (180)
.+|+.++.+|.-+... +.. .+||..|+ ++++.|+++..|=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G---~~~----~eIA~~l~----is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG---MSN----KEIAEELG----ISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTT---S-H----HHHHHHHT----SHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhc---CCc----chhHHhcC----cchhhHHHHHHHHHHHh
Confidence 5899999999988853 333 38999996 89999998776554443
No 101
>PRK00118 putative DNA-binding protein; Validated
Probab=34.75 E-value=31 Score=26.60 Aligned_cols=51 Identities=10% Similarity=0.171 Sum_probs=36.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
+++.|..++.-.|..+ ++ ..+||..++ ++...|+.|...-|.+.|..-...
T Consensus 18 L~ekqRevl~L~y~eg--~S----~~EIAe~lG----IS~~TV~r~L~RArkkLr~~~~~~ 68 (104)
T PRK00118 18 LTEKQRNYMELYYLDD--YS----LGEIAEEFN----VSRQAVYDNIKRTEKLLEDYEEKL 68 (104)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHHC----cCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4778888888877765 33 337899996 999999999876665555544433
No 102
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=34.74 E-value=29 Score=27.52 Aligned_cols=49 Identities=16% Similarity=0.102 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRR 93 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r 93 (180)
+++.|..++.-.|-.+ +. ..+||+.|+ ++...|+++...=|.+.|+.-.
T Consensus 137 L~~~~r~i~~L~~~~g--~s----~~EIA~~lg----is~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 137 LPENTARVFTLKEILG--FS----SDEIQQMCG----ISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred CCHHHHHHhhhHHHhC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHH
Confidence 4555666666554443 22 348899997 9999999887766666665543
No 103
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=34.73 E-value=26 Score=25.57 Aligned_cols=27 Identities=7% Similarity=0.089 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhcccCCCCCCcceeccC
Q 036802 56 TDQIQKISTQLSFYGKIESKNVFYWFQ 82 (180)
Q Consensus 56 ~~~r~eLA~~L~~~g~L~e~qVqvWFQ 82 (180)
...+.+|...|....+|++.+|.+|+.
T Consensus 49 G~~i~~L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 49 GRRIRELTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred chhHHHHHHHHHHHhCCCCCeEEEEEE
Confidence 356788888888888899999999985
No 104
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=34.48 E-value=27 Score=27.39 Aligned_cols=35 Identities=20% Similarity=0.161 Sum_probs=26.4
Q ss_pred HHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhcc
Q 036802 59 IQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSV 97 (180)
Q Consensus 59 r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~ 97 (180)
.++||+.|+ |++..|++..+.=|.+.|+.-.....
T Consensus 136 ~~EIA~~lg----is~~tV~~~l~ra~~~Lr~~l~~~~~ 170 (179)
T PRK12543 136 QEEIAQLLQ----IPIGTVKSRIHAALKKLRQKEQIEEI 170 (179)
T ss_pred HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 357899996 99999998887777777766555543
No 105
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=34.13 E-value=33 Score=27.70 Aligned_cols=48 Identities=15% Similarity=0.094 Sum_probs=29.5
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhh
Q 036802 36 TSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRR 93 (180)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r 93 (180)
++.|..++.-.|-.+ ++ ..+||..|+ +++..|++....=|.+.|+.-.
T Consensus 141 p~~~r~v~~L~~~eg--~s----~~EIA~~lg----is~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 141 PEQIGRVFMMREFLD--FE----IDDICTELT----LTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred CHHHHHHHHHHHHcC--CC----HHHHHHHHC----cCHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444333 22 348899996 9999999887655555555443
No 106
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=34.01 E-value=18 Score=31.00 Aligned_cols=47 Identities=9% Similarity=0.013 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQK 91 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk 91 (180)
+++.|..++.-.|-.+ ++ ..+||+.|+ +++..|+.+.+.=|.+.|..
T Consensus 109 L~~~~R~v~~L~~~~g--~s----~~EIA~~lg----~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 109 LSPLERAVFVLREVFD--YP----YEEIASIVG----KSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHhh
Confidence 4455555555544333 22 347899997 89999999987666666554
No 107
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=33.97 E-value=37 Score=26.15 Aligned_cols=44 Identities=18% Similarity=0.168 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhH
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARE 88 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRARe 88 (180)
+++.|..+|.-.|-.+ ++. .+||+.|+ +++..|++....=|.+.
T Consensus 119 L~~~~r~vl~L~~~~g--~s~----~EIA~~lg----is~~tV~~~l~ra~~~L 162 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG--WST----AQIAADLG----IPEGTVKSRLHYALRAL 162 (173)
T ss_pred CCHHHHHHHHHHHHcC--CCH----HHHHHHHC----cCHHHHHHHHHHHHHHH
Confidence 4455666666655443 333 48899997 89999987664333333
No 108
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=33.78 E-value=29 Score=27.55 Aligned_cols=39 Identities=10% Similarity=0.198 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCc
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQN 83 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQN 83 (180)
+++.|..++.-.|-.+ ++ ..+||+.|+ ++...|++.-+-
T Consensus 132 L~~~~r~i~~l~~~~g--~s----~~EIAe~lg----is~~~V~~~l~R 170 (189)
T PRK06811 132 LEKLDREIFIRRYLLG--EK----IEEIAKKLG----LTRSAIDNRLSR 170 (189)
T ss_pred CCHHHHHHHHHHHHcc--CC----HHHHHHHHC----CCHHHHHHHHHH
Confidence 4566666666555443 32 247899996 899888876543
No 109
>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=33.25 E-value=34 Score=26.34 Aligned_cols=45 Identities=7% Similarity=0.066 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhH
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARE 88 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRARe 88 (180)
.+++.|.+++.-.|-.+ ++ .++||..|+ |++..|+++..-=|.+.
T Consensus 119 ~L~~~~r~i~~l~~~~g--~s----~~eiA~~lg----is~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD--LT----IKEIAEVMN----KPEGTVKTYLHRALKKL 163 (169)
T ss_pred hCCHHHhHHHHHHHHcC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHH
Confidence 35566667776666554 22 347899997 99999987654333333
No 110
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=32.79 E-value=30 Score=27.13 Aligned_cols=28 Identities=4% Similarity=-0.063 Sum_probs=20.9
Q ss_pred HHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 59 IQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 59 r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
.++||..|+ |++..|++....=|.+.|+
T Consensus 148 ~~EIA~~l~----is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 148 VAETAQLTG----LSESAVKVGIHRGLKALAA 175 (181)
T ss_pred HHHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 458899997 9999999888655554444
No 111
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=32.46 E-value=35 Score=27.36 Aligned_cols=50 Identities=8% Similarity=0.003 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRK 94 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~ 94 (180)
+++.|..++.-.|-.+ ++. .+||+.|+ |++..|+++...=|.+.|+....
T Consensus 117 Lp~~~r~i~~L~~~~g--~s~----~EIA~~Lg----is~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 117 LPDDQREAIILVGASG--FAY----EEAAEICG----CAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred CCHHHHHHHHHHHHcC--CCH----HHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHh
Confidence 3555666666655443 333 38899997 99999999887666666655443
No 112
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=32.25 E-value=33 Score=26.08 Aligned_cols=37 Identities=11% Similarity=0.123 Sum_probs=23.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceecc
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWF 81 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWF 81 (180)
+++.|..+|.-.|-.+ ++ .++||+.|+ ++...|+..-
T Consensus 110 L~~~~r~v~~l~~~~~--~s----~~EIA~~lg----is~~tV~~~l 146 (163)
T PRK07037 110 LPARTRYAFEMYRLHG--ET----QKDIARELG----VSPTLVNFMI 146 (163)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHHC----CCHHHHHHHH
Confidence 3455555555555443 22 348899997 9999999753
No 113
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=32.18 E-value=42 Score=26.78 Aligned_cols=50 Identities=8% Similarity=-0.030 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRK 94 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~ 94 (180)
+++.|..++.-.|-.+ +. ..+||+.|+ +++..|++...-=|.+.|+....
T Consensus 112 Lp~~~R~v~~L~~~~g--~s----~~EIA~~Lg----is~~tV~~~l~RAr~~Lr~~l~~ 161 (182)
T PRK12540 112 LPQDQREALILVGASG--FS----YEDAAAICG----CAVGTIKSRVNRARSKLSALLYV 161 (182)
T ss_pred CCHHHHHHhhHHHHcC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHh
Confidence 4555666666655443 22 348899997 89999998776544444444443
No 114
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=32.05 E-value=31 Score=27.47 Aligned_cols=27 Identities=15% Similarity=0.032 Sum_probs=19.6
Q ss_pred HHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 60 QKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 60 ~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
.+||+.|+ ++...|+++..-=|.+.|+
T Consensus 156 ~eIA~~lg----is~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 156 PEIAEVME----IGVEAVESLTARGKRALAA 182 (196)
T ss_pred HHHHHHHC----cCHHHHHHHHHHHHHHHHH
Confidence 47899996 9999999888644444433
No 115
>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=31.78 E-value=35 Score=21.03 Aligned_cols=37 Identities=27% Similarity=0.274 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccC
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQ 82 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQ 82 (180)
+++.|..++.-++ .+ + ...+||..++ ++...|+.|..
T Consensus 1 l~~~e~~i~~~~~-~~--~----s~~eia~~l~----~s~~tv~~~~~ 37 (57)
T cd06170 1 LTPREREVLRLLA-EG--K----TNKEIADILG----ISEKTVKTHLR 37 (57)
T ss_pred CCHHHHHHHHHHH-cC--C----CHHHHHHHHC----CCHHHHHHHHH
Confidence 3677888887654 33 3 2347888886 89999988874
No 116
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=31.76 E-value=37 Score=26.44 Aligned_cols=41 Identities=12% Similarity=0.131 Sum_probs=25.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcch
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHK 85 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRR 85 (180)
+++.|..+|.-.|-.+ +. -++||..|+ ++...|+++-+.=|
T Consensus 136 L~~~~r~vl~l~~~~~--~s----~~eIA~~lg----is~~~V~~~l~ra~ 176 (186)
T PRK13919 136 LSPEERRVIEVLYYQG--YT----HREAAQLLG----LPLGTLKTRARRAL 176 (186)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHHC----cCHHHHHHHHHHHH
Confidence 4555555555444332 22 247899996 89999987665433
No 117
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=31.11 E-value=41 Score=26.03 Aligned_cols=27 Identities=26% Similarity=0.334 Sum_probs=19.6
Q ss_pred HHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 60 QKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 60 ~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
++||+.|+ ++...|+++...=|.+-++
T Consensus 139 ~EIA~~lg----is~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 139 KEMSEILN----IPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred HHHHHHhC----CCHHHHHHHHHHHHHHHHH
Confidence 48899996 8999999877544444443
No 118
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=30.71 E-value=41 Score=26.52 Aligned_cols=51 Identities=14% Similarity=0.063 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
+++.|..++.-.|-.+ ++ .++||..|+ +++..|++....=|.+.|+.-...
T Consensus 132 Lp~~~r~v~~l~~~~g--~s----~~EIA~~lg----is~~tV~~~l~Rar~~Lr~~l~~~ 182 (191)
T PRK12520 132 LPPRTGRVFMMREWLE--LE----TEEICQELQ----ITATNAWVLLYRARMRLRECLDLH 182 (191)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666666655443 33 348899997 999999988765555555544443
No 119
>PHA02955 hypothetical protein; Provisional
Probab=30.50 E-value=52 Score=28.81 Aligned_cols=44 Identities=7% Similarity=0.140 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcc
Q 036802 37 SEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNH 84 (180)
Q Consensus 37 ~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNR 84 (180)
..|+..|=+.|....-..+.+++.++|++|+ ++-..|..||++.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lg----I~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIG----INIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhC----CChhhccCcccch
Confidence 3455555555544223467789999999997 7776688999874
No 120
>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=30.06 E-value=71 Score=24.55 Aligned_cols=39 Identities=26% Similarity=0.419 Sum_probs=23.9
Q ss_pred HHHHHHHHhcCCCCCCHHH-HHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhhccc
Q 036802 40 VKVLTDLFTSGLRTPSTDQ-IQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKVSVD 98 (180)
Q Consensus 40 L~~LE~~F~~~~~yPs~~~-r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~~~d 98 (180)
+++..-+|+. ++||+.+- ++ |. -|||-||++.+++...-
T Consensus 14 vRiIk~Lyqs-nPyP~~~GTr~--aR-----------------RnRRRRWR~rq~QI~~l 53 (91)
T PF00424_consen 14 VRIIKILYQS-NPYPSPEGTRQ--AR-----------------RNRRRRWRARQRQIRAL 53 (91)
T ss_dssp HHHHHHHHHT-S-S--S-S-HH--HH-----------------HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcc-ccCCCCCCccc--cc-----------------cchhhhHHHHHHHHHHH
Confidence 4566778877 59997542 21 11 28999999999988654
No 121
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=29.28 E-value=18 Score=28.63 Aligned_cols=30 Identities=10% Similarity=0.117 Sum_probs=21.8
Q ss_pred HHHHHHHhcccCCCCCCcceeccCcchhhHHHhh
Q 036802 59 IQKISTQLSFYGKIESKNVFYWFQNHKARERQKR 92 (180)
Q Consensus 59 r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~ 92 (180)
..+||+.|+ |+...|+++...=|.+.|+.-
T Consensus 158 ~~EIA~~lg----is~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 158 LEEIAELTG----VPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 458899996 999999877665555555443
No 122
>PTZ00183 centrin; Provisional
Probab=29.23 E-value=1.7e+02 Score=21.62 Aligned_cols=39 Identities=21% Similarity=0.237 Sum_probs=28.9
Q ss_pred CccCCCCCHHHHHHHHHHHhc----CCCCCCHHHHHHHHHHhc
Q 036802 29 KCGRWNPTSEQVKVLTDLFTS----GLRTPSTDQIQKISTQLS 67 (180)
Q Consensus 29 kR~Rt~fT~eQL~~LE~~F~~----~~~yPs~~~r~eLA~~L~ 67 (180)
+..+..++++|+..|+..|.. ++.+.+..+...+...++
T Consensus 5 ~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g 47 (158)
T PTZ00183 5 RSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLG 47 (158)
T ss_pred ccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhC
Confidence 346788999999999999973 335677777666665553
No 123
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=29.01 E-value=39 Score=26.58 Aligned_cols=46 Identities=7% Similarity=-0.005 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHH
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARER 89 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReK 89 (180)
.+++.|..+++-.|-.+ ++ ..+||+.|+ ++...|+.+...-|.+.|
T Consensus 131 ~L~~~~r~v~~l~~~~g--~s----~~eIA~~lg----is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG--LS----VAEAATRSG----MSESAVKVSVHRGLKALA 176 (184)
T ss_pred hCCHHHHHHHHHHHHcC--Cc----HHHHHHHHC----cCHHHHHHHHHHHHHHHH
Confidence 45666666666555443 22 347899997 899999987754444443
No 124
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=28.30 E-value=41 Score=25.96 Aligned_cols=45 Identities=9% Similarity=0.054 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHH
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARER 89 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReK 89 (180)
+++.|..++.-.|-.+ +. ..+||..|+ |++..|+++...=|.+-|
T Consensus 113 L~~~~r~v~~l~~~~g--~s----~~eIA~~lg----is~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 113 LSADQREAIILIGASG--FS----YEDAAAICG----CAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHhC----CCHHHHHHHHHHHHHHHH
Confidence 4455555565555443 22 347899997 899999987754444333
No 125
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=27.99 E-value=43 Score=25.53 Aligned_cols=38 Identities=16% Similarity=0.102 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccC
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQ 82 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQ 82 (180)
+++.|..++.-.|-.+ ++. .+||+.|+ ++...|+++-.
T Consensus 114 L~~~~r~v~~L~~~~g--~s~----~EIA~~l~----is~~tV~~~l~ 151 (161)
T PRK12528 114 LPPLVKRAFLLAQVDG--LGY----GEIATELG----ISLATVKRYLN 151 (161)
T ss_pred CCHHHHHHHHHHHHcC--CCH----HHHHHHHC----CCHHHHHHHHH
Confidence 4556777777666554 333 37888896 89988887653
No 126
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=27.84 E-value=36 Score=28.32 Aligned_cols=47 Identities=13% Similarity=0.032 Sum_probs=28.5
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhh
Q 036802 36 TSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKR 92 (180)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~ 92 (180)
++.|..+|.-.|-.+ ++ .++||..|+ |++..|+++-..=|.+.++.-
T Consensus 136 p~~~R~v~~L~y~eg--~s----~~EIAe~Lg----iS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 136 PVEYREVLVLRELED--MS----YREIAAIAD----VPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHhHhhhHHhcC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 344445555544432 33 348899996 999999887765444444443
No 127
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=27.81 E-value=44 Score=26.07 Aligned_cols=44 Identities=16% Similarity=0.167 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHH
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARER 89 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReK 89 (180)
.+++.|..++.-.|-.+ ++ ..+||+.|+ ++...|+++. .||+.+
T Consensus 119 ~L~~~~r~i~~l~~~~g--~s----~~EIA~~lg----is~~tV~~~l--~Ra~~~ 162 (172)
T PRK09651 119 GLNGKTREAFLLSQLDG--LT----YSEIAHKLG----VSVSSVKKYV--AKATEH 162 (172)
T ss_pred hCCHHHhHHhhhhhccC--CC----HHHHHHHhC----CCHHHHHHHH--HHHHHH
Confidence 34555555555555443 22 358899996 8999998876 344433
No 128
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.08 E-value=45 Score=25.93 Aligned_cols=39 Identities=13% Similarity=0.049 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcc
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNV 77 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qV 77 (180)
+++++|.++-...|+.+ .-.+.-..++||..|+ +++..|
T Consensus 2 SLn~eq~~~Tk~elqan-~el~~LS~~~iA~~Ln----~t~~~l 40 (97)
T COG4367 2 SLNPEQKQRTKQELQAN-FELCPLSDEEIATALN----WTEVKL 40 (97)
T ss_pred CCCHHHHHHHHHHHHHh-hhhccccHHHHHHHhC----CCHHHH
Confidence 57899998877777763 4555566778999996 666544
No 129
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=26.87 E-value=47 Score=26.29 Aligned_cols=44 Identities=20% Similarity=0.213 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHH
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARER 89 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReK 89 (180)
+++.+..+|.- |-.+ +. ..+||..|+ ++...|++....-|.+.|
T Consensus 156 L~~~~r~vl~l-~~e~--~s----~~EIA~~lg----is~~tV~~~l~rar~~Lr 199 (208)
T PRK08295 156 LSELEKEVLEL-YLDG--KS----YQEIAEELN----RHVKSIDNALQRVKRKLE 199 (208)
T ss_pred CCHHHHHHHHH-HHcc--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 34455555555 3332 32 347899996 899999865544333333
No 130
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=26.69 E-value=44 Score=26.88 Aligned_cols=45 Identities=22% Similarity=0.333 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 36 TSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
.+.|.++++-.|-.| | ...+||..|+ |+++.|+...+.=|++-++
T Consensus 137 ~~~~~~~v~l~~~~G--l----s~~EIA~~lg----iS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 137 DPRQRRVVELRFFEG--L----SVEEIAERLG----ISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CHHHHHHHHHHHHCC--C----CHHHHHHHHC----cCHHHHHHHHHHHHHHHHH
Confidence 344444444444443 2 2457899996 9999999777655554443
No 131
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=25.87 E-value=21 Score=27.49 Aligned_cols=29 Identities=17% Similarity=0.097 Sum_probs=21.8
Q ss_pred HHHHHHHhcccCCCCCCcceeccCcchhhHHHh
Q 036802 59 IQKISTQLSFYGKIESKNVFYWFQNHKARERQK 91 (180)
Q Consensus 59 r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk 91 (180)
-++||..|+ +++..|++.+..=|.+-|+.
T Consensus 139 ~~eIA~~lg----~s~~tv~~~l~Rar~~L~~~ 167 (175)
T PRK12518 139 QKEIAEILN----IPVGTVKSRLFYARRQLRKF 167 (175)
T ss_pred HHHHHHHHC----CCHHHHHHHHHHHHHHHHHH
Confidence 458999997 89999998886555555544
No 132
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=25.70 E-value=48 Score=26.48 Aligned_cols=39 Identities=18% Similarity=0.135 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccC
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQ 82 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQ 82 (180)
.+++.|..+++-.|-.+ ++. .+||..|+ |+...|+++-+
T Consensus 111 ~Lp~~~R~v~~L~~~eg--~s~----~EIA~~lg----is~~tV~~~l~ 149 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG--LSY----QEAAAVLG----IPIGTLMSRIG 149 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CCH----HHHHHHhC----cCHHHHHHHHH
Confidence 45566666666655443 333 48899997 99999998874
No 133
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=25.68 E-value=49 Score=25.65 Aligned_cols=38 Identities=13% Similarity=0.153 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCc
Q 036802 36 TSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQN 83 (180)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQN 83 (180)
++.|..++.-.|-.+ ++. .+||+.|+ +++..|+++..+
T Consensus 121 p~~~r~v~~L~~~~g--~s~----~EIA~~lg----is~~tV~~~l~r 158 (172)
T PRK12523 121 SSKARAAFLYNRLDG--MGH----AEIAERLG----VSVSRVRQYLAQ 158 (172)
T ss_pred CHHHHHHHHHHHHcC--CCH----HHHHHHHC----CCHHHHHHHHHH
Confidence 445555555555443 332 37889996 899999988744
No 134
>PRK09480 slmA division inhibitor protein; Provisional
Probab=25.62 E-value=48 Score=25.53 Aligned_cols=36 Identities=8% Similarity=0.248 Sum_probs=27.9
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcch
Q 036802 44 TDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHK 85 (180)
Q Consensus 44 E~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRR 85 (180)
..+|... +. ....+.+||++.+ ++...++.+|.|+-
T Consensus 20 ~~l~~~~-~G-~~~ti~~Ia~~ag----vs~gt~Y~~F~~K~ 55 (194)
T PRK09480 20 AQMLESP-PG-ERITTAKLAARVG----VSEAALYRHFPSKA 55 (194)
T ss_pred HHHHHhc-CC-CccCHHHHHHHhC----CCHhHHHHHCCCHH
Confidence 3455442 35 6777889999986 99999999999976
No 135
>PF13050 DUF3911: Protein of unknown function (DUF3911)
Probab=25.62 E-value=21 Score=26.40 Aligned_cols=10 Identities=70% Similarity=1.016 Sum_probs=8.7
Q ss_pred HHHHhhcCCC
Q 036802 126 VIETLQLFPL 135 (180)
Q Consensus 126 ~~e~l~~~p~ 135 (180)
||||||||-|
T Consensus 13 vvemlqlfdl 22 (77)
T PF13050_consen 13 VVEMLQLFDL 22 (77)
T ss_pred HHHHHHHHHH
Confidence 4999999976
No 136
>PF13565 HTH_32: Homeodomain-like domain
Probab=25.46 E-value=1.9e+02 Score=19.47 Aligned_cols=41 Identities=15% Similarity=0.076 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCC----CCCCcceec
Q 036802 36 TSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGK----IESKNVFYW 80 (180)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~----L~e~qVqvW 80 (180)
+++|.+.|.++...+ +.-+.. +|+..|....+ ++...|..|
T Consensus 32 ~~e~~~~i~~~~~~~-p~wt~~---~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEH-PRWTPR---EIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhC-CCCCHH---HHHHHHHHHhCCCCCccHhHHHHh
Confidence 788889999999874 444544 45555554333 255555543
No 137
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=25.31 E-value=38 Score=24.99 Aligned_cols=43 Identities=28% Similarity=0.198 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhh
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKAR 87 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAR 87 (180)
.+|+.+.++|.- +..+ +. ..+||+.|+ ++++.|.++.+|=+.|
T Consensus 149 ~lt~~e~~vl~l-~~~g--~~----~~~Ia~~l~----~s~~tv~~~~~~~~~k 191 (211)
T PRK15369 149 LLTPRERQILKL-ITEG--YT----NRDIAEQLS----ISIKTVETHRLNMMRK 191 (211)
T ss_pred CCCHHHHHHHHH-HHCC--CC----HHHHHHHhC----CCHHHHHHHHHHHHHH
Confidence 489999999987 5554 43 358899996 8999999987764333
No 138
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=25.18 E-value=48 Score=26.02 Aligned_cols=39 Identities=21% Similarity=0.165 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCc
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQN 83 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQN 83 (180)
+++.|..++.-.|-.+ ++ ..+||..|+ +++..|++....
T Consensus 123 L~~~~r~i~~l~~~~g--~s----~~EIA~~lg----is~~tVk~~l~R 161 (185)
T PRK12542 123 LNESNRQVFKYKVFYN--LT----YQEISSVMG----ITEANVRKQFER 161 (185)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHHC----CCHHHHHHHHHH
Confidence 3455556665544443 22 347899996 999999986643
No 139
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=25.04 E-value=44 Score=28.64 Aligned_cols=28 Identities=11% Similarity=0.092 Sum_probs=21.5
Q ss_pred HHHHHHhcccCCCCCCcceeccCcchhhHHHh
Q 036802 60 QKISTQLSFYGKIESKNVFYWFQNHKARERQK 91 (180)
Q Consensus 60 ~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk 91 (180)
++||+.|+ +++..|+...+.=|.+.++.
T Consensus 135 ~EIA~~lg----~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 135 DEIASTLG----RSPAACRQLASRARKHVRAA 162 (293)
T ss_pred HHHHHHHC----CCHHHHHHHHHHHHHHHHhh
Confidence 48899996 89999999887555555543
No 140
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=24.50 E-value=86 Score=25.71 Aligned_cols=33 Identities=33% Similarity=0.498 Sum_probs=25.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCC
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESK 75 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~ 75 (180)
..|.|+++.|.+++..|. |. .+||.+|+ +++-.
T Consensus 2 ~Wtde~~~~L~~lw~~G~---Sa---sqIA~~lg---~vsRn 34 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGL---SA---SQIARQLG---GVSRN 34 (162)
T ss_pred CCCHHHHHHHHHHHHcCC---CH---HHHHHHhC---Ccchh
Confidence 359999999999999873 33 47889997 35544
No 141
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=24.44 E-value=45 Score=25.76 Aligned_cols=28 Identities=18% Similarity=0.217 Sum_probs=19.9
Q ss_pred HHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 59 IQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 59 r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
.++||..|+ ++...|.++...=|.+.|+
T Consensus 155 ~~eIA~~lg----is~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 155 LKEISEILD----LPVGTVKTRIHRGREALRK 182 (187)
T ss_pred HHHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 358899996 8999998776555554443
No 142
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=24.11 E-value=42 Score=27.74 Aligned_cols=46 Identities=15% Similarity=0.209 Sum_probs=30.8
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHh
Q 036802 36 TSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQK 91 (180)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk 91 (180)
++.|..++.-.|..+ + ...+||..|+ |+...|+++...=+.+.|+.
T Consensus 186 ~~~~r~vl~l~~~~g--~----s~~EIA~~lg----is~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 186 PEREQLVLSLYYQEE--L----NLKEIGAVLG----VSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CHHHHHHHHhHhccC--C----CHHHHHHHHC----CCHHHHHHHHHHHHHHHHHH
Confidence 445555555555443 2 2458899996 99999999887666666553
No 143
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=23.95 E-value=57 Score=26.36 Aligned_cols=50 Identities=8% Similarity=-0.019 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRK 94 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~ 94 (180)
+++.|..++.-.|-.+ +. ..+||+.|+ ++...|+++...=|.+.|+...+
T Consensus 134 Lp~~~r~v~~l~~~~g--~s----~~EIAe~lg----is~~tV~~~l~Rar~~Lr~~l~~ 183 (196)
T PRK12535 134 LPPERREALILTQVLG--YT----YEEAAKIAD----VRVGTIRSRVARARADLIAATAT 183 (196)
T ss_pred CCHHHHHHhhhHHHhC--CC----HHHHHHHhC----CCHHHHHHHHHHHHHHHHHHhcc
Confidence 4445555555555443 22 348899996 89999998885555544444333
No 144
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=23.73 E-value=54 Score=25.77 Aligned_cols=39 Identities=13% Similarity=0.104 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCc
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQN 83 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQN 83 (180)
+++.|..++.-.|-.+ ++ .++||..|+ +++..|++....
T Consensus 128 Lp~~~R~v~~L~~~~g--~s----~~EIA~~lg----is~~tVk~~l~r 166 (178)
T PRK12529 128 LRPRVKQAFLMATLDG--MK----QKDIAQALD----IALPTVKKYIHQ 166 (178)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHHC----CCHHHHHHHHHH
Confidence 4455555555555443 22 347899996 899999987763
No 145
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=23.69 E-value=42 Score=28.04 Aligned_cols=47 Identities=21% Similarity=0.187 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHh
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQK 91 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk 91 (180)
.+|+.|+++|+-+.. | +.+. +||+.|+ +++..|+++..|=..|..-+
T Consensus 155 ~Lt~rE~~Vl~l~~~-G--~s~~----eIA~~L~----iS~~TVk~~~~~i~~Kl~v~ 201 (216)
T PRK10100 155 LLTHREKEILNKLRI-G--ASNN----EIARSLF----ISENTVKTHLYNLFKKIAVK 201 (216)
T ss_pred CCCHHHHHHHHHHHc-C--CCHH----HHHHHhC----CCHHHHHHHHHHHHHHhCCC
Confidence 489999999999986 4 4443 8899996 99999999887766555443
No 146
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.89 E-value=62 Score=26.49 Aligned_cols=48 Identities=10% Similarity=0.036 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHhh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQKR 92 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~ 92 (180)
+++.|..++.-.|-.+ ++ ..+||..|+ ++...|+++.+-=|.+.|+.-
T Consensus 149 L~~~~r~v~~L~~~~g--~s----~~EIAe~lg----is~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 149 LPAKYARVFMMREFIE--LE----TNEICHAVD----LSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHHC----cCHHHHHHHHHHHHHHHHHHH
Confidence 3445555555555443 22 248899996 899999987765555555443
No 147
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=22.63 E-value=30 Score=27.36 Aligned_cols=30 Identities=10% Similarity=0.168 Sum_probs=22.5
Q ss_pred HHHHHHHhcccCCCCCCcceeccCcchhhHHHhh
Q 036802 59 IQKISTQLSFYGKIESKNVFYWFQNHKARERQKR 92 (180)
Q Consensus 59 r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~ 92 (180)
..+||..|+ |++..|+++.+-=|.+.|+.-
T Consensus 150 ~~EIA~~lg----is~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 150 YKEIAEIMG----TPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 468999997 999999998765555555443
No 148
>PRK10651 transcriptional regulator NarL; Provisional
Probab=22.52 E-value=46 Score=25.02 Aligned_cols=46 Identities=17% Similarity=0.240 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHH
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQ 90 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKR 90 (180)
.+|+.+.++|+-+. .+ +++. +||.+|+ ++++.|++..+|=|.|..-
T Consensus 155 ~Lt~rE~~vl~~l~-~g--~~~~----~ia~~l~----is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 155 QLTPRERDILKLIA-QG--LPNK----MIARRLD----ITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred cCCHHHHHHHHHHH-cC--CCHH----HHHHHcC----CCHHHHHHHHHHHHHHcCC
Confidence 49999999998766 33 4444 7889986 8999998887776665543
No 149
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=22.37 E-value=32 Score=26.50 Aligned_cols=25 Identities=16% Similarity=0.185 Sum_probs=18.3
Q ss_pred HHHHHHHhcccCCCCCCcceeccCcchhhHH
Q 036802 59 IQKISTQLSFYGKIESKNVFYWFQNHKARER 89 (180)
Q Consensus 59 r~eLA~~L~~~g~L~e~qVqvWFQNRRAReK 89 (180)
.++||..|+ ++...|+++.. ||+.+
T Consensus 145 ~~eIA~~l~----is~~~V~~~l~--ra~~~ 169 (176)
T PRK09638 145 YEEIAKMLN----IPEGTVKSRVH--HGIKQ 169 (176)
T ss_pred HHHHHHHHC----CChhHHHHHHH--HHHHH
Confidence 458899997 89999987764 44443
No 150
>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=22.23 E-value=66 Score=27.40 Aligned_cols=33 Identities=15% Similarity=0.395 Sum_probs=25.6
Q ss_pred HHHHHHHhcccCCCCCCcceeccCcchhhHHHhhhhh
Q 036802 59 IQKISTQLSFYGKIESKNVFYWFQNHKARERQKRRKV 95 (180)
Q Consensus 59 r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk~r~~ 95 (180)
.++||..|+ |++..|+++...=|.+-|+.-+..
T Consensus 180 ~~EIA~~Lg----is~~TVk~rl~RAr~~Lr~~l~~~ 212 (244)
T TIGR03001 180 MDRIGAMYQ----VHRSTVSRWVAQARERLLERTRRR 212 (244)
T ss_pred HHHHHHHHC----cCHHHHHHHHHHHHHHHHHHHHHH
Confidence 458899997 999999999987777666655444
No 151
>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=22.17 E-value=68 Score=25.58 Aligned_cols=47 Identities=15% Similarity=0.145 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHh
Q 036802 35 PTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQK 91 (180)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk 91 (180)
+++.|..++.-.|-.+ + ..++||+.|+ ++...|+++...=|.+.|+.
T Consensus 132 L~~~~r~v~~l~~~~g--~----s~~EIA~~lg----is~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 132 LPEQTARVFMMREVLG--F----ESDEICQELE----ISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred CCHHHHHHHHHHHHhC--C----CHHHHHHHhC----CCHHHHHHHHHHHHHHHHHH
Confidence 3445555555555443 2 2358899997 89999987665444444443
No 152
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=21.64 E-value=55 Score=25.98 Aligned_cols=19 Identities=0% Similarity=-0.142 Sum_probs=15.6
Q ss_pred HHHHHHhcccCCCCCCcceeccC
Q 036802 60 QKISTQLSFYGKIESKNVFYWFQ 82 (180)
Q Consensus 60 ~eLA~~L~~~g~L~e~qVqvWFQ 82 (180)
.+||..|+ +++..|+++-.
T Consensus 150 ~EIA~~lg----is~~tVk~~l~ 168 (185)
T PRK09649 150 ADAAAVCG----CPVGTIRSRVA 168 (185)
T ss_pred HHHHHHHC----CCHHHHHHHHH
Confidence 47899996 89999998763
No 153
>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=21.41 E-value=52 Score=26.92 Aligned_cols=46 Identities=13% Similarity=0.153 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHH
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARER 89 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReK 89 (180)
.+++.|..+|...|..+ + ..++||..|+ ++...|+.+...=+.+.|
T Consensus 175 ~L~~~~r~il~l~y~~~--~----s~~eIA~~lg----is~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE--L----NLKEIGEVLG----LTESRVSQIHSQALKKLR 220 (224)
T ss_pred hCCHHHHHHHHHHHhCC--C----CHHHHHHHhC----CCHHHHHHHHHHHHHHHH
Confidence 35677777777777554 2 2358899996 899888877654443333
No 154
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=20.30 E-value=61 Score=27.71 Aligned_cols=46 Identities=17% Similarity=0.021 Sum_probs=28.0
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhhHHHh
Q 036802 36 TSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKARERQK 91 (180)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAReKRk 91 (180)
++.|..++.-.|-.+ ++ .++||..|+ +++..|++..+-=|.+.|+.
T Consensus 144 p~~~R~v~~L~~~~g--~s----~~EIA~~lg----is~~tV~~~l~Rar~~Lr~~ 189 (324)
T TIGR02960 144 PPRQRAVLLLRDVLG--WR----AAETAELLG----TSTASVNSALQRARATLDEV 189 (324)
T ss_pred CHHHhhHhhhHHHhC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHh
Confidence 444444444444333 22 248899997 99999998776544444443
No 155
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=20.18 E-value=70 Score=26.79 Aligned_cols=44 Identities=9% Similarity=0.102 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcccCCCCCCcceeccCcchhh
Q 036802 34 NPTSEQVKVLTDLFTSGLRTPSTDQIQKISTQLSFYGKIESKNVFYWFQNHKAR 87 (180)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~~~r~eLA~~L~~~g~L~e~qVqvWFQNRRAR 87 (180)
.+++.|..+|.-.|-.+ ++ ..+||..|+ |+...|+.|-..=+.+
T Consensus 205 ~L~~~~r~vl~l~~~~g--~s----~~eIA~~l~----is~~tV~~~~~ra~~k 248 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN--LS----QKETGERLG----ISQMHVSRLQRQAIKK 248 (257)
T ss_pred hCCHHHHHHHHHHHhCC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHH
Confidence 35777777888777554 32 248899997 9999998776433333
Done!