Query 036145
Match_columns 375
No_of_seqs 164 out of 507
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 09:53:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036145.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036145hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0487 Transcription factor A 99.8 4.3E-20 9.3E-25 180.0 4.1 66 54-124 233-298 (308)
2 KOG0489 Transcription factor z 99.8 2.4E-20 5.3E-25 176.6 1.2 67 54-125 157-223 (261)
3 KOG0484 Transcription factor P 99.8 1.1E-19 2.3E-24 155.2 1.0 71 50-125 11-81 (125)
4 KOG0492 Transcription factor M 99.8 5.2E-19 1.1E-23 165.4 5.6 75 49-128 135-211 (246)
5 KOG0488 Transcription factor B 99.7 8.7E-19 1.9E-23 170.5 3.5 71 50-125 166-236 (309)
6 KOG0843 Transcription factor E 99.7 4.3E-18 9.4E-23 156.1 4.3 64 55-123 101-164 (197)
7 KOG0842 Transcription factor t 99.7 6.7E-18 1.4E-22 164.7 5.1 67 53-124 150-216 (307)
8 PF00046 Homeobox: Homeobox do 99.7 8.9E-18 1.9E-22 123.1 1.8 57 57-118 1-57 (57)
9 KOG2251 Homeobox transcription 99.7 3.2E-17 6.9E-22 153.8 5.8 76 43-123 24-99 (228)
10 KOG0494 Transcription factor C 99.6 3.5E-16 7.5E-21 150.6 5.7 65 55-124 140-204 (332)
11 KOG0850 Transcription factor D 99.6 4.9E-16 1.1E-20 146.8 3.9 64 55-123 121-184 (245)
12 smart00389 HOX Homeodomain. DN 99.6 6.3E-16 1.4E-20 112.0 2.9 56 57-117 1-56 (56)
13 KOG0848 Transcription factor C 99.6 5.7E-16 1.2E-20 149.3 3.4 64 55-123 198-261 (317)
14 cd00086 homeodomain Homeodomai 99.6 1.1E-15 2.3E-20 111.0 2.7 58 57-119 1-58 (59)
15 KOG0493 Transcription factor E 99.5 2.6E-15 5.5E-20 144.8 2.8 61 56-121 246-306 (342)
16 KOG0485 Transcription factor N 99.5 3.4E-15 7.3E-20 140.9 3.5 67 56-127 104-170 (268)
17 KOG0844 Transcription factor E 99.5 3E-15 6.6E-20 146.7 2.0 64 55-123 180-243 (408)
18 COG5576 Homeodomain-containing 99.5 8.3E-15 1.8E-19 131.1 4.6 69 51-124 46-114 (156)
19 TIGR01565 homeo_ZF_HD homeobox 99.5 2.2E-14 4.7E-19 110.2 5.5 52 57-113 2-57 (58)
20 KOG0486 Transcription factor P 99.5 3.6E-14 7.8E-19 139.2 5.2 66 54-124 110-175 (351)
21 KOG0483 Transcription factor H 99.5 2.3E-14 4.9E-19 132.8 2.8 63 56-123 50-112 (198)
22 KOG0491 Transcription factor B 99.4 9E-15 1.9E-19 133.3 -2.5 70 50-124 94-163 (194)
23 KOG3802 Transcription factor O 99.4 1.8E-13 4E-18 137.2 5.3 62 55-121 293-354 (398)
24 KOG4577 Transcription factor L 99.4 2.2E-13 4.8E-18 133.0 3.7 70 53-127 164-233 (383)
25 KOG0490 Transcription factor, 99.4 2E-13 4.4E-18 122.1 3.0 64 53-121 57-120 (235)
26 KOG0849 Transcription factor P 99.2 1.1E-11 2.4E-16 122.7 3.6 76 44-124 164-239 (354)
27 KOG0847 Transcription factor, 99.1 1E-11 2.2E-16 117.9 0.8 63 57-124 168-230 (288)
28 KOG1168 Transcription factor A 98.9 1.3E-09 2.7E-14 107.1 3.2 62 56-122 309-370 (385)
29 KOG0775 Transcription factor S 98.5 2.7E-07 5.8E-12 90.1 7.8 63 50-117 161-232 (304)
30 KOG0490 Transcription factor, 98.3 3.6E-07 7.8E-12 82.0 2.8 64 53-121 150-213 (235)
31 KOG2252 CCAAT displacement pro 98.2 8E-07 1.7E-11 93.0 3.0 67 53-124 417-483 (558)
32 KOG0774 Transcription factor P 98.1 9.6E-06 2.1E-10 79.4 7.6 69 55-127 187-257 (334)
33 PF05920 Homeobox_KN: Homeobox 97.6 7.2E-06 1.6E-10 58.8 -1.0 32 80-115 9-40 (40)
34 KOG1146 Homeobox protein [Gene 97.4 9.7E-05 2.1E-09 83.9 4.0 67 50-121 896-963 (1406)
35 KOG0773 Transcription factor M 94.6 0.02 4.4E-07 56.0 2.4 65 56-124 239-305 (342)
36 KOG3623 Homeobox transcription 94.1 0.022 4.9E-07 62.6 1.6 55 63-123 564-618 (1007)
37 PF11569 Homez: Homeodomain le 90.2 0.055 1.2E-06 42.1 -1.1 43 68-115 10-52 (56)
38 PF04218 CENP-B_N: CENP-B N-te 86.5 0.63 1.4E-05 34.9 2.6 47 57-113 1-47 (53)
39 PF00577 Usher: Outer membrane 81.3 0.57 1.2E-05 48.6 0.6 25 316-340 98-125 (552)
40 PF04967 HTH_10: HTH DNA bindi 80.2 2.2 4.8E-05 32.6 3.3 38 63-105 1-40 (53)
41 cd06171 Sigma70_r4 Sigma70, re 77.5 1 2.2E-05 30.4 0.7 44 62-115 10-53 (55)
42 KOG3755 SATB1 matrix attachmen 68.5 0.99 2.1E-05 49.3 -1.6 67 55-122 690-760 (769)
43 COG3413 Predicted DNA binding 67.9 5.5 0.00012 36.8 3.3 47 62-115 155-203 (215)
44 PRK15248 fimbrial outer membra 65.1 4.5 9.8E-05 45.2 2.6 37 316-352 285-330 (853)
45 PRK15207 long polar fimbrial o 64.1 4.7 0.0001 45.1 2.5 37 316-352 302-347 (842)
46 PRK15213 fimbrial outer membra 63.4 4.7 0.0001 44.6 2.3 25 316-340 273-300 (797)
47 PRK09828 putative fimbrial out 61.7 8.4 0.00018 43.1 3.8 37 316-352 294-339 (865)
48 PRK15217 fimbrial outer membra 61.1 5.8 0.00013 44.2 2.5 25 316-340 272-299 (826)
49 PF01527 HTH_Tnp_1: Transposas 59.7 4.7 0.0001 30.6 1.1 42 58-109 2-44 (76)
50 PRK15294 putative fimbrial out 59.0 6.8 0.00015 43.7 2.6 37 316-352 289-334 (845)
51 PRK09642 RNA polymerase sigma 57.8 5.7 0.00012 33.8 1.4 51 63-123 107-157 (160)
52 PRK15298 fimbrial outer membra 57.1 7.1 0.00015 43.7 2.3 37 316-352 293-338 (848)
53 PF04545 Sigma70_r4: Sigma-70, 56.6 4.8 0.0001 28.9 0.6 38 62-109 4-41 (50)
54 cd00569 HTH_Hin_like Helix-tur 56.6 13 0.00027 22.2 2.5 40 60-109 3-42 (42)
55 PRK15223 pilin outer membrane 56.5 8.1 0.00018 43.1 2.6 37 316-352 284-329 (836)
56 PRK07696 sulfur carrier protei 56.4 12 0.00027 29.1 2.9 50 319-370 1-55 (67)
57 PRK03975 tfx putative transcri 56.1 6.2 0.00014 35.6 1.4 52 61-123 5-56 (141)
58 PRK15198 outer membrane usher 55.7 8.2 0.00018 43.3 2.5 25 316-340 287-314 (860)
59 PRK09652 RNA polymerase sigma 55.7 6.9 0.00015 33.3 1.6 49 62-120 128-176 (182)
60 KOG3623 Homeobox transcription 55.3 6.9 0.00015 44.1 1.8 65 55-124 625-689 (1007)
61 PRK05863 sulfur carrier protei 55.3 16 0.00035 28.0 3.4 49 319-371 1-54 (65)
62 PRK15193 outer membrane usher 54.9 8.4 0.00018 43.4 2.4 25 316-340 306-333 (876)
63 KOG1146 Homeobox protein [Gene 53.5 13 0.00028 44.1 3.6 59 57-120 706-764 (1406)
64 PRK09646 RNA polymerase sigma 51.0 9.2 0.0002 34.1 1.7 40 62-111 142-181 (194)
65 PRK15304 putative fimbrial out 50.5 11 0.00024 41.9 2.4 37 316-352 270-315 (801)
66 PF13551 HTH_29: Winged helix- 49.0 17 0.00037 28.9 2.7 53 56-109 51-108 (112)
67 PRK12519 RNA polymerase sigma 48.7 8.4 0.00018 34.0 1.0 48 63-120 142-189 (194)
68 PRK12512 RNA polymerase sigma 48.5 9.5 0.00021 33.3 1.3 51 62-122 131-181 (184)
69 PRK09644 RNA polymerase sigma 48.0 9.4 0.0002 32.9 1.2 53 62-124 108-160 (165)
70 TIGR02948 SigW_bacill RNA poly 47.5 8.5 0.00018 33.4 0.8 49 62-120 136-184 (187)
71 PRK11924 RNA polymerase sigma 47.4 12 0.00026 31.7 1.7 50 62-121 125-174 (179)
72 TIGR02989 Sig-70_gvs1 RNA poly 46.9 17 0.00036 30.7 2.5 38 62-109 111-148 (159)
73 PRK09413 IS2 repressor TnpA; R 44.8 18 0.00039 30.8 2.4 43 58-110 8-51 (121)
74 PRK15255 fimbrial outer membra 44.6 16 0.00034 41.0 2.5 38 316-353 284-329 (829)
75 TIGR02937 sigma70-ECF RNA poly 44.5 11 0.00025 30.1 1.1 46 62-117 110-155 (158)
76 PRK12526 RNA polymerase sigma 44.5 13 0.00028 33.7 1.5 46 62-117 153-198 (206)
77 PF08281 Sigma70_r4_2: Sigma-7 44.4 8.4 0.00018 27.7 0.3 39 63-111 11-49 (54)
78 PRK15235 outer membrane fimbri 43.5 17 0.00037 40.6 2.6 38 316-353 268-317 (814)
79 PRK06759 RNA polymerase factor 43.4 11 0.00023 31.8 0.8 40 62-111 106-145 (154)
80 PRK12515 RNA polymerase sigma 43.3 14 0.00031 32.5 1.7 50 61-120 130-179 (189)
81 PRK08053 sulfur carrier protei 42.9 27 0.00058 26.8 2.9 50 319-371 1-55 (66)
82 PF13936 HTH_38: Helix-turn-he 42.8 7.9 0.00017 27.8 -0.1 38 60-107 2-39 (44)
83 PRK05659 sulfur carrier protei 41.6 29 0.00064 26.1 2.9 49 319-370 1-54 (66)
84 PRK04217 hypothetical protein; 41.2 16 0.00034 31.8 1.5 60 46-119 30-89 (110)
85 smart00027 EH Eps15 homology d 41.0 21 0.00046 28.7 2.2 46 61-110 2-51 (96)
86 KOG0048 Transcription factor, 40.3 29 0.00062 33.0 3.2 63 50-124 48-115 (238)
87 PRK12538 RNA polymerase sigma 39.9 14 0.0003 34.8 1.0 49 63-121 172-220 (233)
88 COG3188 FimD P pilus assembly 39.7 22 0.00048 40.1 2.8 37 316-352 289-334 (835)
89 PRK12514 RNA polymerase sigma 38.9 19 0.00041 31.3 1.7 46 63-118 130-175 (179)
90 PRK09647 RNA polymerase sigma 38.8 19 0.00041 32.9 1.7 51 62-122 138-188 (203)
91 PRK09639 RNA polymerase sigma 38.8 19 0.00041 30.7 1.6 48 62-120 112-159 (166)
92 PRK05602 RNA polymerase sigma 38.2 16 0.00036 32.0 1.2 48 63-120 129-176 (186)
93 PF00196 GerE: Bacterial regul 38.1 13 0.00027 27.5 0.4 45 62-117 3-47 (58)
94 PF02796 HTH_7: Helix-turn-hel 37.9 11 0.00023 27.1 -0.0 38 61-108 4-41 (45)
95 PF13510 Fer2_4: 2Fe-2S iron-s 37.8 28 0.0006 28.0 2.3 34 317-350 2-35 (82)
96 PF13873 Myb_DNA-bind_5: Myb/S 36.9 21 0.00046 27.6 1.5 61 60-120 2-76 (78)
97 TIGR02939 RpoE_Sigma70 RNA pol 36.4 15 0.00032 31.9 0.7 47 63-119 139-185 (190)
98 smart00421 HTH_LUXR helix_turn 36.4 18 0.00039 24.8 1.0 38 62-110 3-40 (58)
99 PRK13558 bacterio-opsin activa 35.7 33 0.00071 36.0 3.1 41 60-105 605-647 (665)
100 TIGR02983 SigE-fam_strep RNA p 34.9 18 0.00038 30.8 0.9 46 63-118 111-156 (162)
101 COG2104 ThiS Sulfur transfer p 34.5 61 0.0013 25.9 3.8 43 318-361 2-49 (68)
102 PRK09047 RNA polymerase factor 33.8 23 0.00049 30.0 1.3 39 62-110 106-144 (161)
103 PRK15284 putative fimbrial out 33.6 42 0.00091 38.0 3.7 38 316-353 304-349 (881)
104 PRK07440 hypothetical protein; 33.2 62 0.0013 25.5 3.6 46 317-363 3-53 (70)
105 TIGR02959 SigZ RNA polymerase 33.1 26 0.00056 30.6 1.6 42 62-113 100-141 (170)
106 PRK12543 RNA polymerase sigma 32.6 30 0.00066 30.3 2.0 52 63-124 118-169 (179)
107 TIGR02954 Sig70_famx3 RNA poly 32.4 24 0.00053 30.4 1.3 39 62-110 119-157 (169)
108 PF13565 HTH_32: Homeodomain-l 32.0 87 0.0019 23.8 4.2 37 57-99 27-63 (77)
109 TIGR02999 Sig-70_X6 RNA polyme 31.9 25 0.00055 30.5 1.3 45 63-117 135-179 (183)
110 PRK12532 RNA polymerase sigma 31.9 27 0.00058 31.0 1.5 50 62-121 136-185 (195)
111 PRK09637 RNA polymerase sigma 31.9 27 0.00058 31.1 1.5 39 62-110 106-144 (181)
112 PRK07037 extracytoplasmic-func 31.8 25 0.00054 29.9 1.3 37 62-108 109-145 (163)
113 PRK12531 RNA polymerase sigma 31.8 27 0.00058 31.1 1.5 38 62-109 141-178 (194)
114 cd01668 TGS_RelA_SpoT TGS_RelA 31.7 54 0.0012 23.4 2.9 47 319-371 1-54 (60)
115 cd02413 40S_S3_KH K homology R 31.7 40 0.00086 27.5 2.4 26 85-110 50-75 (81)
116 cd06170 LuxR_C_like C-terminal 31.7 26 0.00055 24.3 1.1 37 63-110 1-37 (57)
117 PRK12536 RNA polymerase sigma 31.7 23 0.00049 31.2 1.0 47 64-120 131-177 (181)
118 PRK06930 positive control sigm 31.4 27 0.00058 31.9 1.4 51 62-122 114-164 (170)
119 PF12824 MRP-L20: Mitochondria 30.6 1.3E+02 0.0029 27.8 5.8 44 59-109 82-125 (164)
120 PRK15273 putative fimbrial out 30.6 32 0.00069 39.0 2.1 37 316-352 282-326 (881)
121 PF12323 HTH_OrfB_IS605: Helix 30.4 34 0.00073 24.5 1.6 23 57-79 5-27 (46)
122 PRK09645 RNA polymerase sigma 30.4 31 0.00066 29.8 1.6 47 62-118 118-164 (173)
123 PF10925 DUF2680: Protein of u 30.2 50 0.0011 25.8 2.6 41 63-108 1-41 (59)
124 PHA03256 BDLF3; Provisional 30.2 1E+02 0.0023 25.7 4.5 44 46-95 2-45 (77)
125 TIGR02985 Sig70_bacteroi1 RNA 30.0 26 0.00057 29.0 1.1 40 62-111 113-152 (161)
126 PRK06986 fliA flagellar biosyn 29.9 25 0.00054 32.5 1.0 48 63-120 185-232 (236)
127 PRK13919 putative RNA polymera 29.8 29 0.00064 30.2 1.4 46 62-117 135-180 (186)
128 PRK12539 RNA polymerase sigma 29.8 31 0.00067 30.4 1.6 47 61-117 130-176 (184)
129 PRK12537 RNA polymerase sigma 29.2 36 0.00079 29.9 1.9 39 62-110 133-171 (182)
130 PF14453 ThiS-like: ThiS-like 29.1 57 0.0012 25.6 2.7 38 319-356 1-40 (57)
131 PRK09648 RNA polymerase sigma 29.1 29 0.00062 30.6 1.2 39 61-109 138-176 (189)
132 PRK12530 RNA polymerase sigma 28.8 33 0.00071 30.6 1.6 47 62-118 134-180 (189)
133 PRK00118 putative DNA-binding 28.4 34 0.00073 29.5 1.5 51 63-123 18-68 (104)
134 TIGR02943 Sig70_famx1 RNA poly 27.8 36 0.00078 30.4 1.6 49 62-120 131-179 (188)
135 PRK12546 RNA polymerase sigma 27.6 28 0.00062 31.3 1.0 51 62-122 113-163 (188)
136 PRK10100 DNA-binding transcrip 27.6 28 0.0006 32.5 0.9 51 62-123 155-205 (216)
137 PRK12513 RNA polymerase sigma 27.5 17 0.00036 32.2 -0.6 47 63-119 140-186 (194)
138 PRK12533 RNA polymerase sigma 27.3 26 0.00055 32.6 0.6 47 62-118 134-180 (216)
139 PRK12541 RNA polymerase sigma 27.2 27 0.00058 29.9 0.7 46 62-117 112-157 (161)
140 PF07638 Sigma70_ECF: ECF sigm 27.1 30 0.00064 31.1 1.0 48 63-120 136-183 (185)
141 PRK06083 sulfur carrier protei 27.0 73 0.0016 26.3 3.1 51 317-370 17-72 (84)
142 PRK12520 RNA polymerase sigma 27.0 38 0.00083 29.9 1.6 49 62-120 131-179 (191)
143 PF00424 REV: REV protein (ant 26.3 54 0.0012 28.1 2.3 39 68-126 14-53 (91)
144 PRK09643 RNA polymerase sigma 25.9 38 0.00083 30.2 1.5 36 62-107 134-169 (192)
145 PRK12545 RNA polymerase sigma 25.8 40 0.00088 30.4 1.6 48 63-120 140-187 (201)
146 PF06312 Neurexophilin: Neurex 25.6 48 0.001 32.2 2.1 34 313-352 83-120 (219)
147 PRK09480 slmA division inhibit 25.6 51 0.0011 28.5 2.1 36 72-113 20-55 (194)
148 PRK11923 algU RNA polymerase s 25.6 36 0.00077 30.0 1.2 30 88-121 158-187 (193)
149 PRK06288 RNA polymerase sigma 25.2 42 0.00091 31.9 1.7 50 62-121 212-261 (268)
150 PRK10651 transcriptional regul 25.2 40 0.00088 28.4 1.4 50 62-122 155-204 (216)
151 PRK08295 RNA polymerase factor 24.9 38 0.00083 30.0 1.3 46 62-122 155-200 (208)
152 PLN02917 CMP-KDO synthetase 24.9 41 0.00089 32.9 1.6 27 148-174 2-36 (293)
153 KOG3755 SATB1 matrix attachmen 24.7 63 0.0014 36.1 3.0 63 54-124 352-419 (769)
154 PRK12547 RNA polymerase sigma 24.6 38 0.00083 29.2 1.2 45 62-116 112-156 (164)
155 TIGR02952 Sig70_famx2 RNA poly 24.4 38 0.00082 28.8 1.1 46 62-121 122-167 (170)
156 PF08880 QLQ: QLQ; InterPro: 24.3 59 0.0013 23.3 1.9 13 62-74 2-14 (37)
157 PRK09651 RNA polymerase sigma 24.3 44 0.00096 29.1 1.5 38 62-109 119-156 (172)
158 PRK12516 RNA polymerase sigma 24.2 44 0.00096 29.9 1.5 49 62-120 116-164 (187)
159 PF11033 ComJ: Competence prot 24.2 99 0.0022 27.8 3.7 61 299-365 30-104 (125)
160 COG4367 Uncharacterized protei 24.0 48 0.001 28.6 1.6 40 62-106 2-41 (97)
161 PRK12522 RNA polymerase sigma 24.0 48 0.001 28.7 1.7 46 63-118 120-165 (173)
162 PF05132 RNA_pol_Rpc4: RNA pol 23.5 87 0.0019 27.3 3.2 31 317-350 78-108 (131)
163 PRK12542 RNA polymerase sigma 23.5 37 0.00081 29.8 0.9 49 62-120 122-170 (185)
164 PF08144 CPL: CPL (NUC119) dom 23.3 1.2E+02 0.0026 27.3 4.1 39 57-95 16-55 (148)
165 PRK06811 RNA polymerase factor 23.0 43 0.00094 29.7 1.2 39 62-110 131-169 (189)
166 PRK12544 RNA polymerase sigma 23.0 50 0.0011 30.3 1.6 50 62-121 148-197 (206)
167 PF10668 Phage_terminase: Phag 23.0 23 0.0005 28.0 -0.5 17 88-108 26-42 (60)
168 TIGR03001 Sig-70_gmx1 RNA poly 22.9 48 0.001 31.5 1.6 51 63-123 162-212 (244)
169 PTZ00183 centrin; Provisional 22.8 2.1E+02 0.0046 23.7 5.3 37 56-92 4-44 (158)
170 PRK12518 RNA polymerase sigma 22.6 20 0.00044 30.8 -0.9 30 87-120 139-168 (175)
171 PRK12535 RNA polymerase sigma 22.3 42 0.00091 30.4 1.0 51 62-122 133-183 (196)
172 TIGR02947 SigH_actino RNA poly 22.2 31 0.00068 30.5 0.2 49 63-121 132-180 (193)
173 PRK12527 RNA polymerase sigma 22.1 47 0.001 28.3 1.2 38 63-110 106-143 (159)
174 PRK06944 sulfur carrier protei 22.0 60 0.0013 24.3 1.6 41 319-360 1-45 (65)
175 PF09136 Glucodextran_B: Gluco 21.6 59 0.0013 27.6 1.7 23 313-335 24-46 (89)
176 PRK06488 sulfur carrier protei 21.6 1.1E+02 0.0025 23.1 3.1 43 319-363 1-48 (65)
177 PF03672 UPF0154: Uncharacteri 21.2 87 0.0019 25.3 2.5 35 68-105 19-53 (64)
178 PRK09641 RNA polymerase sigma 21.2 45 0.00098 28.9 1.0 46 63-118 137-182 (187)
179 PRK15369 two component system 21.0 46 0.00099 27.6 0.9 45 62-117 149-193 (211)
180 PF13364 BetaGal_dom4_5: Beta- 21.0 1.2E+02 0.0025 25.6 3.4 25 314-338 60-97 (111)
181 PRK09638 RNA polymerase sigma 20.6 28 0.0006 30.0 -0.5 27 87-117 145-171 (176)
182 PRK12529 RNA polymerase sigma 20.5 52 0.0011 29.0 1.2 45 62-116 127-171 (178)
183 PRK10360 DNA-binding transcrip 20.5 58 0.0013 27.5 1.4 45 62-117 137-181 (196)
184 PRK14711 ureE urease accessory 20.2 39 0.00085 32.1 0.4 10 5-14 114-123 (191)
185 TIGR03541 reg_near_HchA LuxR f 20.2 53 0.0011 30.7 1.2 52 59-121 168-219 (232)
186 TIGR02479 FliA_WhiG RNA polyme 20.1 52 0.0011 30.1 1.2 44 62-115 175-218 (224)
No 1
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.79 E-value=4.3e-20 Score=179.97 Aligned_cols=66 Identities=24% Similarity=0.280 Sum_probs=61.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhH
Q 036145 54 SPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 54 sp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q 124 (375)
+..||+|+.+|+.|+.+||++|..|+ |+++++|.+|++.|+ |+|+||||||||||+|+||--|+..
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~-YitkeKR~ElSr~lN----LTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNM-YITKEKRLELSRTLN----LTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHH-HHhHHHHHHHHHhcc----cchhheeeeehhhhhHHhhhhhhhh
Confidence 45689999999999999999999997 999999999999997 9999999999999999999876443
No 2
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.78 E-value=2.4e-20 Score=176.57 Aligned_cols=67 Identities=21% Similarity=0.241 Sum_probs=62.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhHh
Q 036145 54 SPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQN 125 (375)
Q Consensus 54 sp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q~ 125 (375)
...||.|+.||.+||.+||++|..|+ |.++.+|.+||..|. |+|+||||||||||+|+||..+....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~-YLtR~RRiEiA~~L~----LtErQIKIWFQNRRMK~Kk~~k~~~~ 223 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNK-YLTRSRRIEIAHALN----LTERQIKIWFQNRRMKWKKENKAKSS 223 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhcccc-ccchHHHHHHHhhcc----hhHHHHHHHHHHHHHHHHHhhccccc
Confidence 34699999999999999999999996 999999999999997 99999999999999999998877654
No 3
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.76 E-value=1.1e-19 Score=155.21 Aligned_cols=71 Identities=23% Similarity=0.351 Sum_probs=66.5
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhHh
Q 036145 50 CEERSPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQN 125 (375)
Q Consensus 50 ~~~rsp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q~ 125 (375)
..++++.||-|++||..||.+||++|.+.+ ||+...|++||.+|. |+|++|+|||||||||.||++|..-.
T Consensus 11 l~ekrKQRRIRTTFTS~QLkELErvF~ETH-YPDIYTREEiA~kid----LTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 11 LTEKRKQRRIRTTFTSAQLKELERVFAETH-YPDIYTREEIALKID----LTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred hhHHHHhhhhhhhhhHHHHHHHHHHHHhhc-CCcchhHHHHHHhhh----hhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 678899999999999999999999999997 999999999999998 99999999999999999998886543
No 4
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.76 E-value=5.2e-19 Score=165.38 Aligned_cols=75 Identities=25% Similarity=0.379 Sum_probs=68.3
Q ss_pred CCCCCC--CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhHhH
Q 036145 49 GCEERS--PEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQNS 126 (375)
Q Consensus 49 ~~~~rs--p~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q~~ 126 (375)
.|..|+ +.|++||.||..||..||+.|.+.. |.++.||.+++..|. |+|.||||||||||||.||.++.+-++
T Consensus 135 ~C~LrKhk~nRkPRtPFTtqQLlaLErkfrekq-YLSiaEraefSsSL~----LTeTqVKIWFQNRRAKaKRlQeae~Ek 209 (246)
T KOG0492|consen 135 TCTLRKHKPNRKPRTPFTTQQLLALERKFREKQ-YLSIAERAEFSSSLE----LTETQVKIWFQNRRAKAKRLQEAELEK 209 (246)
T ss_pred cchhcccCCCCCCCCCCCHHHHHHHHHHHhHhh-hhhHHHHHhhhhhhh----hhhhheehhhhhhhHHHHHHHHHHHHH
Confidence 588655 8899999999999999999999997 999999999999998 999999999999999999998877654
Q ss_pred hh
Q 036145 127 KQ 128 (375)
Q Consensus 127 ~~ 128 (375)
-+
T Consensus 210 ~k 211 (246)
T KOG0492|consen 210 LK 211 (246)
T ss_pred hh
Confidence 43
No 5
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=8.7e-19 Score=170.50 Aligned_cols=71 Identities=24% Similarity=0.234 Sum_probs=65.3
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhHh
Q 036145 50 CEERSPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQN 125 (375)
Q Consensus 50 ~~~rsp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q~ 125 (375)
+...+++||.|+.||..||.+||+.|++.+ |.+..+|.+||++|+ |+|.|||+||||||+||||...+...
T Consensus 166 ~~~pkK~RksRTaFT~~Ql~~LEkrF~~QK-YLS~~DR~~LA~~Lg----LTdaQVKtWfQNRRtKWKrq~a~g~~ 236 (309)
T KOG0488|consen 166 RSTPKKRRKSRTAFSDHQLFELEKRFEKQK-YLSVADRIELAASLG----LTDAQVKTWFQNRRTKWKRQTAEGGE 236 (309)
T ss_pred cCCCcccccchhhhhHHHHHHHHHHHHHhh-cccHHHHHHHHHHcC----CchhhHHHHHhhhhHHHHHHHHhhhc
Confidence 455578899999999999999999999996 999999999999997 99999999999999999999887543
No 6
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.71 E-value=4.3e-18 Score=156.11 Aligned_cols=64 Identities=25% Similarity=0.370 Sum_probs=60.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhh
Q 036145 55 PEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHI 123 (375)
Q Consensus 55 p~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~ 123 (375)
+++|.||.||++||..||.+|+.++ |....||++||..|+ |+|.||||||||||.|.||.+.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~-Yvvg~eR~~LA~~L~----LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQ-YVVGAERKQLAQSLS----LSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCC-eeechHHHHHHHHcC----CChhHhhhhhhhhhHHHHHHHHHh
Confidence 6789999999999999999999997 999999999999997 999999999999999999987664
No 7
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.71 E-value=6.7e-18 Score=164.66 Aligned_cols=67 Identities=22% Similarity=0.300 Sum_probs=62.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhH
Q 036145 53 RSPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 53 rsp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q 124 (375)
.++.||+|.-||+.|.-+||+.|...+ |.+..||++||..|. |++.||||||||||+|.||++.+..
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQR-YLSAPERE~LA~~Lr----LT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQR-YLSAPEREHLASSLR----LTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhh-ccccHhHHHHHHhcC----CCchheeeeeecchhhhhhhhhhhh
Confidence 346689999999999999999999996 999999999999997 9999999999999999999987665
No 8
>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=99.68 E-value=8.9e-18 Score=123.10 Aligned_cols=57 Identities=28% Similarity=0.532 Sum_probs=54.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhh
Q 036145 57 PKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKH 118 (375)
Q Consensus 57 ~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KR 118 (375)
+|+|+.||++|+.+||++|..++ ||+.+++++||.+|+ |++.+|++||||||+|+||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~-~p~~~~~~~la~~l~----l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENP-YPSKEEREELAKELG----LTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSS-SCHHHHHHHHHHHHT----SSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhc-ccccccccccccccc----ccccccccCHHHhHHHhCc
Confidence 58999999999999999999996 999999999999997 9999999999999999986
No 9
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.68 E-value=3.2e-17 Score=153.85 Aligned_cols=76 Identities=18% Similarity=0.339 Sum_probs=68.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhh
Q 036145 43 SYTTVPGCEERSPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRH 122 (375)
Q Consensus 43 ~~~s~p~~~~rsp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~ 122 (375)
+...+|--.-+++.||.||+||..||++||.+|++.+ |||...|++||.+|+ |.|.+|+|||.|||+|.|+++++
T Consensus 24 ~~~~vP~~~~pRkqRRERTtFtr~QlevLe~LF~kTq-YPDv~~rEelAlkln----LpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 24 PKPGVPYSSGPRKQRRERTTFTRKQLEVLEALFAKTQ-YPDVFMREELALKLN----LPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred cCCCCCcCccchhcccccceecHHHHHHHHHHHHhhc-CccHHHHHHHHHHhC----CchhhhhhhhccccchhhHhhhh
Confidence 3344554566778899999999999999999999997 999999999999997 99999999999999999998886
Q ss_pred h
Q 036145 123 I 123 (375)
Q Consensus 123 ~ 123 (375)
.
T Consensus 99 q 99 (228)
T KOG2251|consen 99 Q 99 (228)
T ss_pred h
Confidence 5
No 10
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.62 E-value=3.5e-16 Score=150.55 Aligned_cols=65 Identities=17% Similarity=0.234 Sum_probs=58.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhH
Q 036145 55 PEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 55 p~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q 124 (375)
++|+-||.||..||++||+.|.+.+ |||...|+-||.++. |.|.+|+||||||||||||+++.--
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaH-YPDv~Are~la~kte----lpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAH-YPDVYAREMLADKTE----LPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhcc-CccHHHHHHHhhhcc----CchhhhhHHhhhhhHHhhhhhhhcC
Confidence 3344499999999999999999997 999999999988886 9999999999999999999887543
No 11
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.59 E-value=4.9e-16 Score=146.83 Aligned_cols=64 Identities=27% Similarity=0.292 Sum_probs=60.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhh
Q 036145 55 PEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHI 123 (375)
Q Consensus 55 p~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~ 123 (375)
+-|++||.++.-||+.|.+.|+++. |+-..||.+||..|+ |+..||||||||||.|.||..++-
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQkTQ-YLALPERAeLAAsLG----LTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQTQ-YLALPERAELAASLG----LTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhhcc-hhcCcHHHHHHHHhC----CchhHhhhhhhhhHHHHHHHHhcC
Confidence 4589999999999999999999997 999999999999997 999999999999999999998843
No 12
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.58 E-value=6.3e-16 Score=111.96 Aligned_cols=56 Identities=34% Similarity=0.552 Sum_probs=52.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhh
Q 036145 57 PKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSK 117 (375)
Q Consensus 57 ~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~K 117 (375)
++.|+.|+++|+.+||+.|+.++ ||+.+++.+||++|+ |+..+|++||+|||+|.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~-~P~~~~~~~la~~~~----l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNP-YPSREEREELAAKLG----LSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHC----cCHHHHHHhHHHHhhccC
Confidence 47889999999999999999997 999999999999997 999999999999999875
No 13
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.58 E-value=5.7e-16 Score=149.31 Aligned_cols=64 Identities=22% Similarity=0.268 Sum_probs=58.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhh
Q 036145 55 PEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHI 123 (375)
Q Consensus 55 p~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~ 123 (375)
..-|-|..+|..|..+||++|..++ |.++.++.+||.-|+ |+|||||||||||||||||..++.
T Consensus 198 TkDKYRvVYTDhQRLELEKEfh~Sr-yITirRKSELA~~Lg----LsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 198 TKDKYRVVYTDHQRLELEKEFHTSR-YITIRRKSELAATLG----LSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred cccceeEEecchhhhhhhhhhcccc-ceeeehhHHHHHhhC----ccHhhhhHhhhhhhHHHHHHHHHH
Confidence 3357889999999999999999996 999999999999997 999999999999999999866554
No 14
>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=99.57 E-value=1.1e-15 Score=111.03 Aligned_cols=58 Identities=31% Similarity=0.521 Sum_probs=54.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhh
Q 036145 57 PKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHK 119 (375)
Q Consensus 57 ~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk 119 (375)
++.|..|+++|+.+||+.|+.++ ||+.+++.+||++|+ |++++|++||+|||++.|+.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~-~P~~~~~~~la~~~~----l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNP-YPSREEREELAKELG----LTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHC----cCHHHHHHHHHHHHHHHhcc
Confidence 47899999999999999999997 999999999999997 99999999999999999875
No 15
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.53 E-value=2.6e-15 Score=144.79 Aligned_cols=61 Identities=21% Similarity=0.416 Sum_probs=57.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 56 EPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 56 ~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
++|+||.||.|||++|..+|++++ |....+|++||.+|+ |.|.||||||||+|+|.||.--
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enR-YlTEqRRQ~La~ELg----LNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENR-YLTEQRRQELAQELG----LNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhh-hHHHHHHHHHHHHhC----cCHHHhhHHhhhhhhhhhhccC
Confidence 478999999999999999999996 999999999999997 9999999999999999987544
No 16
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.53 E-value=3.4e-15 Score=140.92 Aligned_cols=67 Identities=27% Similarity=0.291 Sum_probs=61.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhHhHh
Q 036145 56 EPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQNSK 127 (375)
Q Consensus 56 ~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q~~~ 127 (375)
-+|.||.|+..|+..||..|+..+ |.+..||.-||++|+ |+|.||||||||||-|+||+...+.+..
T Consensus 104 KKktRTvFSraQV~qLEs~Fe~kr-YLSsaeRa~LA~sLq----LTETQVKIWFQNRRnKwKRq~aad~ea~ 170 (268)
T KOG0485|consen 104 KKKTRTVFSRAQVFQLESTFELKR-YLSSAERAGLAASLQ----LTETQVKIWFQNRRNKWKRQYAADLEAA 170 (268)
T ss_pred cccchhhhhHHHHHHHHHHHHHHh-hhhHHHHhHHHHhhh----hhhhhhhhhhhhhhHHHHHHHhhhhhhh
Confidence 368999999999999999999996 999999999999998 9999999999999999999987665444
No 17
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.52 E-value=3e-15 Score=146.66 Aligned_cols=64 Identities=25% Similarity=0.294 Sum_probs=59.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhh
Q 036145 55 PEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHI 123 (375)
Q Consensus 55 p~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~ 123 (375)
--||-||.||.|||.+||++|-+.. |.++.+|-+||..|+ |.|..|||||||||+|.||++-.+
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrEN-YVSRprRcELAAaLN----LPEtTIKVWFQNRRMKDKRQRlam 243 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYREN-YVSRPRRCELAAALN----LPETTIKVWFQNRRMKDKRQRLAM 243 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhc-cccCchhhhHHHhhC----CCcceeehhhhhchhhhhhhhhhc
Confidence 3489999999999999999999996 999999999999997 999999999999999999988765
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.52 E-value=8.3e-15 Score=131.12 Aligned_cols=69 Identities=25% Similarity=0.357 Sum_probs=62.7
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhH
Q 036145 51 EERSPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 51 ~~rsp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q 124 (375)
...++.+++|.+-|.+|+.+||++|+.++ ||+..+|.+|+..|+ |+++.|++||||||+|+|++.....
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p-~Ps~~~r~~L~~~ln----m~~ksVqIWFQNkR~~~k~~~~~~~ 114 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINP-YPSSITRIKLSLLLN----MPPKSVQIWFQNKRAKEKKKRSGKV 114 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCC-CCCHHHHHHHHHhcC----CChhhhhhhhchHHHHHHHhcccch
Confidence 34467799999999999999999999997 899999999999997 9999999999999999998876543
No 19
>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=99.51 E-value=2.2e-14 Score=110.18 Aligned_cols=52 Identities=19% Similarity=0.217 Sum_probs=50.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCC----CCHHHHHHHHHHHhhcCCCCCCceeeccCcch
Q 036145 57 PKPRWNPKPEQIRILESIFNSGMVN----PPRDEIRRIRAQLQEYGQVGDANVFYWFQNRK 113 (375)
Q Consensus 57 ~R~Rt~FT~eQL~~LE~~F~~~~~y----Ps~~eR~qLA~~L~~~g~LtE~qVkvWFQNRR 113 (375)
+|.||.||++|++.||+.|+.+. | |+..+|++||.+|+ |++++|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~-y~~~~~~~~~r~~la~~lg----l~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLG-WKLKDKRREEVREFCEEIG----VTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHhC----CCHHHeeeecccCC
Confidence 79999999999999999999996 9 99999999999997 99999999999975
No 20
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.47 E-value=3.6e-14 Score=139.17 Aligned_cols=66 Identities=24% Similarity=0.388 Sum_probs=62.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhH
Q 036145 54 SPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 54 sp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q 124 (375)
+++||.|+.||..||++||..|..+. ||+...|++||.-.+ |+|++|+|||.|||+|+||++|..+
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNr-ypdMstrEEIavwtN----lTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNR-YPDMSTREEIAVWTN----LTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhcc-CCccchhhHHHhhcc----ccchhhhhhcccchhhhhhhhhhHH
Confidence 37899999999999999999999996 999999999999886 9999999999999999999999877
No 21
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.46 E-value=2.3e-14 Score=132.80 Aligned_cols=63 Identities=25% Similarity=0.381 Sum_probs=58.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhh
Q 036145 56 EPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHI 123 (375)
Q Consensus 56 ~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~ 123 (375)
..++..+||.+|+..||+.|+.+. |...+++.+||++|+ |.++||.|||||||||+|.|+-+.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~-~L~p~~K~~LAk~Lg----L~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEK-KLEPERKKKLAKELG----LQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred cccccccccHHHHHHhHHhhcccc-ccChHHHHHHHHhhC----CChhHHHHHHhhccccccchhhhh
Confidence 467778899999999999999997 899999999999997 999999999999999999887655
No 22
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.42 E-value=9e-15 Score=133.29 Aligned_cols=70 Identities=24% Similarity=0.292 Sum_probs=63.7
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhH
Q 036145 50 CEERSPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 50 ~~~rsp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q 124 (375)
|.....+++.|+.|+..||..||+.|+..+ |.+..+|.+||..|+ |+|+|||.||||||+|.||.+|..+
T Consensus 94 ~~~~~~r~K~Rtvfs~~ql~~l~~rFe~Qr-YLS~~e~~ELan~L~----LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 94 ARLHCRRRKARTVFSDPQLSGLEKRFERQR-YLSTPERQELANALS----LSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhHHHHhhhhcccccCccccccHHHHhhhh-hcccHHHHHHHHHhh----hhHHHHHHHHHHHHHHHHHHHhccC
Confidence 333446789999999999999999999996 999999999999998 9999999999999999999988766
No 23
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.40 E-value=1.8e-13 Score=137.20 Aligned_cols=62 Identities=27% Similarity=0.336 Sum_probs=58.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 55 PEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 55 p~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
+.||+||.+....+..||+.|.+|+ .|+.+||.+||++|+ |+..+|+|||+|||.|+||-..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~np-KPt~qEIt~iA~~L~----leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNP-KPTSQEITHIAESLQ----LEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCC-CCCHHHHHHHHHHhc----cccceEEEEeeccccccccCCC
Confidence 6689999999999999999999998 599999999999997 9999999999999999999766
No 24
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.38 E-value=2.2e-13 Score=132.98 Aligned_cols=70 Identities=20% Similarity=0.409 Sum_probs=60.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhHhHh
Q 036145 53 RSPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQNSK 127 (375)
Q Consensus 53 rsp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q~~~ 127 (375)
-.+.+|+||++|..||+.|...|+..+ .|-+--|++|+.+.+ |+.++|||||||||||+||.+++.-..+
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~Sp-KPARHVREQLsseTG----LDMRVVQVWFQNRRAKEKRLKKDAGR~R 233 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNTSP-KPARHVREQLSSETG----LDMRVVQVWFQNRRAKEKRLKKDAGRTR 233 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcCCC-chhHHHHHHhhhccC----cceeehhhhhhhhhHHHHhhhhhcchhH
Confidence 346799999999999999999999997 599887777776664 9999999999999999999998775433
No 25
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.37 E-value=2e-13 Score=122.06 Aligned_cols=64 Identities=22% Similarity=0.242 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 53 RSPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 53 rsp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
....+|.|+.|+..|+++||++|+..+ ||+...|+.+|..+. ++|.+|++||||||+|++++++
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h-~Pd~~~r~~la~~~~----~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVH-LPCFACRECLALLLT----GDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCC-cCccchHHHHhhcCC----CCeeeeehhhhhhcHhhhhhhc
Confidence 456799999999999999999999996 999999998888886 9999999999999999999987
No 26
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.18 E-value=1.1e-11 Score=122.71 Aligned_cols=76 Identities=21% Similarity=0.318 Sum_probs=68.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhh
Q 036145 44 YTTVPGCEERSPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHI 123 (375)
Q Consensus 44 ~~s~p~~~~rsp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~ 123 (375)
+...|++...+..+|.|+.|+++|++.||+.|+.++ ||+...|++||.+++ |+|.+|++||+|||+|.||..++.
T Consensus 164 ~~~~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~-yP~i~~Re~La~~i~----l~e~riqvwf~nrra~~rr~~~~~ 238 (354)
T KOG0849|consen 164 DEEPPGYALQRGGRRNRTSFSPSQLEALEECFQRTP-YPDIVGRETLAKETG----LPEPRVQVWFQNRRAKWRRQHRDC 238 (354)
T ss_pred ccccccccccccccccccccccchHHHHHHHhcCCC-CCchhhHHHHhhhcc----CCchHHHHHHhhhhhhhhhccccc
Confidence 344556777778889999999999999999999998 999999999999987 999999999999999999999876
Q ss_pred H
Q 036145 124 Q 124 (375)
Q Consensus 124 q 124 (375)
.
T Consensus 239 s 239 (354)
T KOG0849|consen 239 S 239 (354)
T ss_pred c
Confidence 6
No 27
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.13 E-value=1e-11 Score=117.94 Aligned_cols=63 Identities=22% Similarity=0.292 Sum_probs=57.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhH
Q 036145 57 PKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 57 ~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q 124 (375)
...|.+|+-.||..||+.|+..+ ||-..+|.++|..|+ ++|.+|+|||||||.|+|||...+-
T Consensus 168 k~srPTf~g~qi~~le~~feqtk-ylaG~~ra~lA~~lg----mteSqvkVWFQNRRTKWRKkhAaEm 230 (288)
T KOG0847|consen 168 KQSRPTFTGHQIYQLERKFEQTK-YLAGADRAQLAQELN----MTESQVKVWFQNRRTKWRKKHAAEM 230 (288)
T ss_pred cccCCCccchhhhhhhhhhhhhh-cccchhHHHhhcccc----ccHHHHHHHHhcchhhhhhhhccch
Confidence 45688899999999999999996 999999999999997 9999999999999999999876543
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.85 E-value=1.3e-09 Score=107.11 Aligned_cols=62 Identities=24% Similarity=0.369 Sum_probs=57.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhh
Q 036145 56 EPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRH 122 (375)
Q Consensus 56 ~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~ 122 (375)
.+|+||.+-.-..+.||.+|...++ |+.++|..||++|. |...+|+|||+|.|.|.||.++.
T Consensus 309 kKRKRTSIAAPEKRsLEayFavQPR-PS~EkIAaIAekLD----LKKNVVRVWFCNQRQKQKRm~~S 370 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAVQPR-PSGEKIAAIAEKLD----LKKNVVRVWFCNQRQKQKRMKRS 370 (385)
T ss_pred cccccccccCcccccHHHHhccCCC-CchhHHHHHHHhhh----hhhceEEEEeeccHHHHHHhhhh
Confidence 3799999999999999999999985 99999999999998 99999999999999999995553
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.51 E-value=2.7e-07 Score=90.14 Aligned_cols=63 Identities=24% Similarity=0.335 Sum_probs=54.2
Q ss_pred CCCCCCCCCCCCCCCHHH---------HHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhh
Q 036145 50 CEERSPEPKPRWNPKPEQ---------IRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSK 117 (375)
Q Consensus 50 ~~~rsp~~R~Rt~FT~eQ---------L~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~K 117 (375)
+.-|++=|-+||...-|| ...|.+.|..++ ||+.+++++||+..+ |+..||-+||.|||.|+|
T Consensus 161 YRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~-YPsp~eKReLA~aTg----Lt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 161 YRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNP-YPSPREKRELAEATG----LTITQVSNWFKNRRQRDR 232 (304)
T ss_pred ceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCC-CCChHHHHHHHHHhC----Cchhhhhhhhhhhhhhhh
Confidence 455666788888766665 578999999997 999999999988876 999999999999999988
No 30
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.30 E-value=3.6e-07 Score=81.99 Aligned_cols=64 Identities=22% Similarity=0.488 Sum_probs=58.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 53 RSPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 53 rsp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
..+.++.|+.++..|+..|+..|..+. ||+...+++|+..++ +.++.|++||||+|++.|+...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~P~~~~~~~l~~~~~----~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATP-KPDADDREQLAEETG----LSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCC-CCchhhHHHHHHhcC----CChhhhhhhcccHHHHHHhhcc
Confidence 346689999999999999999999997 899988898888886 9999999999999999998877
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.19 E-value=8e-07 Score=92.97 Aligned_cols=67 Identities=28% Similarity=0.325 Sum_probs=58.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhH
Q 036145 53 RSPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 53 rsp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q 124 (375)
.-..+|+|+.||..|++.|-.+|+.++ +|+++..+.|+.+|+ |....|.+||.|-|.|.+-+....+
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFke~~-RPS~Emq~tIS~qL~----L~~sTV~NfFmNaRRRsl~~~~~dd 483 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFKENK-RPSREMQETISQQLN----LELSTVINFFMNARRRSLDKKVDDD 483 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHhcCC-CCCHHHHHHHHHHhC----CcHHHHHHHHHhhhhhccccccccC
Confidence 345578899999999999999999997 799999999999997 9999999999999988755544444
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.07 E-value=9.6e-06 Score=79.35 Aligned_cols=69 Identities=22% Similarity=0.317 Sum_probs=59.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcC--CCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhHhHh
Q 036145 55 PEPKPRWNPKPEQIRILESIFNSG--MVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQNSK 127 (375)
Q Consensus 55 p~~R~Rt~FT~eQL~~LE~~F~~~--~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q~~~ 127 (375)
..||+|.+|++.--++|.++|-.. .+||+.+.+++||++.+ |+-.||-+||-|+|.|-||.....++.+
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCn----ItvsQvsnwfgnkrIrykK~~~k~~ee~ 257 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCN----ITVSQVSNWFGNKRIRYKKNMGKNQEEA 257 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcC----ceehhhccccccceeehhhhhhhhhhhh
Confidence 458999999999999999999643 34999999999998886 9999999999999999999776555433
No 33
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=97.64 E-value=7.2e-06 Score=58.83 Aligned_cols=32 Identities=22% Similarity=0.475 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhh
Q 036145 80 VNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSR 115 (375)
Q Consensus 80 ~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK 115 (375)
+||+.+++++|+++.+ |+.+||..||-|.|.|
T Consensus 9 PYPs~~ek~~L~~~tg----ls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 9 PYPSKEEKEELAKQTG----LSRKQISNWFINARRR 40 (40)
T ss_dssp GS--HHHHHHHHHHHT----S-HHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHcC----CCHHHHHHHHHHhHcc
Confidence 4999999999999886 9999999999999976
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.45 E-value=9.7e-05 Score=83.86 Aligned_cols=67 Identities=16% Similarity=0.270 Sum_probs=57.7
Q ss_pred CCCCC-CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 50 CEERS-PEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 50 ~~~rs-p~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
|..+. ..|+.|+.++.+||++|..+|.... ||..++.+.+-+.++ +..+.|.+||||-|+|+|+...
T Consensus 896 ~~~~~~~r~a~~~~~~d~qlk~i~~~~~~q~-~~~~~~~E~l~~~~~----~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 896 GVPDGMGRRAYRTQESDLQLKIIKACYEAQR-TPTMQECEVLEEPIG----LPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred ccchhhhhhhhccchhHHHHHHHHHHHhhcc-CChHHHHHhhccccc----CCcchhHHhhhhhhhhhhhhhh
Confidence 44433 4579999999999999999999995 899998887777775 8999999999999999998766
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=94.64 E-value=0.02 Score=55.95 Aligned_cols=65 Identities=20% Similarity=0.234 Sum_probs=51.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcC--CCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhH
Q 036145 56 EPKPRWNPKPEQIRILESIFNSG--MVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 56 ~~R~Rt~FT~eQL~~LE~~F~~~--~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q 124 (375)
..|++..+-++...+|+.-.... ..||+..++..|+++.+ |+..||.+||-|.|-|..+-...+-
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TG----Ls~~Qv~NWFINaR~R~w~p~~~~~ 305 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTG----LSRPQVSNWFINARVRLWKPMIEEM 305 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcC----CCcccCCchhhhcccccCCchHHHH
Confidence 45777789999999998766552 24899988876766665 9999999999999999887665443
No 36
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.14 E-value=0.022 Score=62.59 Aligned_cols=55 Identities=18% Similarity=0.270 Sum_probs=47.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHI 123 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~ 123 (375)
|+.- +..|..+|..|. .|+.++-.+||.+++ |.-+.|+.||+++|+++.+-.|.-
T Consensus 564 ~~~p-~sllkayyaln~-~ps~eelskia~qvg----lp~~vvk~wfE~~~a~e~sv~rsp 618 (1007)
T KOG3623|consen 564 FNHP-TSLLKAYYALNG-LPSEEELSKIAQQVG----LPFAVVKAWFEDEEAEEMSVERSP 618 (1007)
T ss_pred cCCc-HHHHHHHHHhcC-CCCHHHHHHHHHHhc----ccHHHHHHHHHhhhhhhhhhccCc
Confidence 4433 789999999997 799999999999997 999999999999999988777643
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=90.16 E-value=0.055 Score=42.14 Aligned_cols=43 Identities=16% Similarity=0.317 Sum_probs=29.2
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhh
Q 036145 68 IRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSR 115 (375)
Q Consensus 68 L~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK 115 (375)
++-||++|.... .+...+...|.++-+ |+..+|+.||--|+.+
T Consensus 10 ~~pL~~Yy~~h~-~L~E~DL~~L~~kS~----ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKHK-QLQEEDLDELCDKSR----MSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT-----TTHHHHHHHHTT------HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHcC-CccHhhHHHHHHHHC----CCHHHHHHHHHHhccc
Confidence 566999999996 798888888877765 9999999999766543
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=86.54 E-value=0.63 Score=34.89 Aligned_cols=47 Identities=17% Similarity=0.168 Sum_probs=36.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcch
Q 036145 57 PKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRK 113 (375)
Q Consensus 57 ~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRR 113 (375)
+|+|..+|.+|...+=+.++.+. ...+||++++ ++..+|..|..||.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~------s~~~ia~~fg----v~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE------SKRDIAREFG----VSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT-------HHHHHHHHT------CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC------CHHHHHHHhC----CCHHHHHHHHHhHH
Confidence 58999999999999999999984 3567899997 99999999998864
No 39
>PF00577 Usher: Outer membrane usher protein; InterPro: IPR000015 In Gram-negative bacteria the biogenesis of fimbriae (or pili) requires a two- component assembly and transport system which is composed of a periplasmic chaperone (see PDOC00552 from PROSITEDOC) and an outer membrane protein which has been termed a molecular 'usher' [, , ]. The usher protein is rather large (from 86 to 100 kDa) and seems to be mainly composed of membrane-spanning beta-sheets, a structure reminiscent of porins. Although the degree of sequence similarity of these proteins is not very high, they share a number of characteristics. One of these is the presence of two pairs of cysteines, the first one located in the N-terminal part and the second at the C-terminal extremity that are probably involved in disulphide bonds. The best conserved region is located in the central part of these proteins.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2VQI_B 3FIP_A 3RFZ_E 3OHN_A 3FCG_B.
Probab=81.35 E-value=0.57 Score=48.57 Aligned_cols=25 Identities=24% Similarity=0.490 Sum_probs=19.8
Q ss_pred cceEEEEecce---eeeeccccchhhhh
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVREA 340 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~~ 340 (375)
.++++|++||+ ...||+|||+++..
T Consensus 98 ~s~V~v~qnG~~iy~~~VppGpF~i~dl 125 (552)
T PF00577_consen 98 PSTVEVYQNGRLIYSTNVPPGPFEIDDL 125 (552)
T ss_dssp SEEEEEEETTEEEEEEEE-SEEEEE-SS
T ss_pred ccEEEEEECCEEEEEEEeCCCCEEecCc
Confidence 58999999995 57899999999854
No 40
>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=80.18 E-value=2.2 Score=32.59 Aligned_cols=38 Identities=21% Similarity=0.361 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhcCCCC--CCHHHHHHHHHHHhhcCCCCCCce
Q 036145 63 PKPEQIRILESIFNSGMVN--PPRDEIRRIRAQLQEYGQVGDANV 105 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~y--Ps~~eR~qLA~~L~~~g~LtE~qV 105 (375)
+|+.|.++|+..|+.+ +| |-.....+||++|+ |+..-|
T Consensus 1 LT~~Q~e~L~~A~~~G-Yfd~PR~~tl~elA~~lg----is~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELG-YFDVPRRITLEELAEELG----ISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcC-CCCCCCcCCHHHHHHHhC----CCHHHH
Confidence 5899999999999999 45 77778889999997 776544
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=77.53 E-value=1 Score=30.41 Aligned_cols=44 Identities=11% Similarity=0.179 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSR 115 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK 115 (375)
.+++++.++|+..|..+. . ..+||++|+ ++...|+.|...-|.+
T Consensus 10 ~l~~~~~~~~~~~~~~~~--~----~~~ia~~~~----~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEGL--S----YEEIAEILG----ISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcCC--C----HHHHHHHHC----cCHHHHHHHHHHHHHH
Confidence 367889999999987763 2 357899987 9999998887655444
No 42
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=68.48 E-value=0.99 Score=49.32 Aligned_cols=67 Identities=12% Similarity=0.056 Sum_probs=41.9
Q ss_pred CCCCCCCCCCHHHHHHHHHH-HhcCCCCCCHHHHHHHHHHHhhc---CCCCCCceeeccCcchhhhhhhhhh
Q 036145 55 PEPKPRWNPKPEQIRILESI-FNSGMVNPPRDEIRRIRAQLQEY---GQVGDANVFYWFQNRKSRSKHKLRH 122 (375)
Q Consensus 55 p~~R~Rt~FT~eQL~~LE~~-F~~~~~yPs~~eR~qLA~~L~~~---g~LtE~qVkvWFQNRRAK~KRk~r~ 122 (375)
-++|.|.+|=.+|.-++... |.+++ .+..-.+.+-.+++... -...+++|+.||.|||+++||.+-.
T Consensus 690 ~pk~~~~k~f~~~~~ev~~~w~~k~~-s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 690 LPKKTIIKFFQNQRYEVKHHWKLKTR-SGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred ccHHHHHHhhhcceeecchhheeccc-CchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhcc
Confidence 45677777766666555443 44443 46665555544444210 0136789999999999999987643
No 43
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=67.95 E-value=5.5 Score=36.80 Aligned_cols=47 Identities=15% Similarity=0.319 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHhcCCCC--CCHHHHHHHHHHHhhcCCCCCCceeeccCcchhh
Q 036145 62 NPKPEQIRILESIFNSGMVN--PPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSR 115 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~y--Ps~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK 115 (375)
.+|+.|+++|...|..+ +| |-+...++||++|+ |+..-+ |..=|||-
T Consensus 155 ~LTdrQ~~vL~~A~~~G-YFd~PR~~~l~dLA~~lG----ISkst~--~ehLRrAe 203 (215)
T COG3413 155 DLTDRQLEVLRLAYKMG-YFDYPRRVSLKDLAKELG----ISKSTL--SEHLRRAE 203 (215)
T ss_pred cCCHHHHHHHHHHHHcC-CCCCCccCCHHHHHHHhC----CCHHHH--HHHHHHHH
Confidence 89999999999999999 44 77778889999997 766544 33334443
No 44
>PRK15248 fimbrial outer membrane usher protein StbC; Provisional
Probab=65.08 E-value=4.5 Score=45.21 Aligned_cols=37 Identities=27% Similarity=0.481 Sum_probs=27.1
Q ss_pred cceEEEEecce---eeeeccccchhhhhc-----CC-ceEEEecCC
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVREAF-----GE-DAVLINSSG 352 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~~F-----G~-davLihssG 352 (375)
.|++||+.||. ...||+|||.+.... || +|++....|
T Consensus 285 ~A~V~V~QnG~~iY~t~VppGPF~I~dl~~~~~~GdL~VtV~EadG 330 (853)
T PRK15248 285 SAHVVVKQLGKVIYETNVPPGPFYIDDLYNTRYQGDLEVEVIEASG 330 (853)
T ss_pred ccEEEEEECCEEEEEeEcCCCCeEeccCcCCCCCceEEEEEEECCC
Confidence 58999999995 678999999987652 33 334445566
No 45
>PRK15207 long polar fimbrial outer membrane usher protein LpfC; Provisional
Probab=64.10 E-value=4.7 Score=45.07 Aligned_cols=37 Identities=19% Similarity=0.413 Sum_probs=27.0
Q ss_pred cceEEEEecce---eeeeccccchhhhhc-----CC-ceEEEecCC
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVREAF-----GE-DAVLINSSG 352 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~~F-----G~-davLihssG 352 (375)
.|+++|+.||. ...||+|||.+.... || +|++..+.|
T Consensus 302 ~A~V~V~QnG~~iY~t~VppGPF~I~dl~~~~~~GdL~VtV~EadG 347 (842)
T PRK15207 302 NAEVSIEQNGYVIYRTFVQPGAFEINDLYPTSNSGDLTVIIKEADG 347 (842)
T ss_pred CcEEEEEECCEEEEEEEeCCCCeEeccccCCCCCceEEEEEEeCCC
Confidence 58999999994 568999999998662 33 334445566
No 46
>PRK15213 fimbrial outer membrane usher protein PefC; Provisional
Probab=63.38 E-value=4.7 Score=44.58 Aligned_cols=25 Identities=32% Similarity=0.458 Sum_probs=21.2
Q ss_pred cceEEEEecce---eeeeccccchhhhh
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVREA 340 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~~ 340 (375)
.|+++|++||. ...||+|||.+...
T Consensus 273 ~A~V~V~QnG~~iy~t~VppGpF~I~dl 300 (797)
T PRK15213 273 PSRVTISQNGYTLYSEVVPAGPFQLDDV 300 (797)
T ss_pred CcEEEEEECCEEEEEEEeCCCCeEeccC
Confidence 58999999994 57899999988744
No 47
>PRK09828 putative fimbrial outer membrane usher protein; Provisional
Probab=61.68 E-value=8.4 Score=43.11 Aligned_cols=37 Identities=19% Similarity=0.368 Sum_probs=28.0
Q ss_pred cceEEEEecce---eeeeccccchhhhh----cC-C-ceEEEecCC
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVREA----FG-E-DAVLINSSG 352 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~~----FG-~-davLihssG 352 (375)
.|++||+.||. ...||+|||.+... .| | +|++.-+.|
T Consensus 294 nA~V~V~QnG~~iy~t~VppGPF~I~Dl~~~g~ggdL~VtV~EadG 339 (865)
T PRK09828 294 NAKVTITQSGYKIYETTVPPGAFVIDDLSPSGYGSDLIVTIEEADG 339 (865)
T ss_pred CcEEEEEECCEEEEEeEcCCCceEecccccCCCCCcEEEEEEECCC
Confidence 58999999994 56899999998766 45 4 444455667
No 48
>PRK15217 fimbrial outer membrane usher protein; Provisional
Probab=61.13 E-value=5.8 Score=44.17 Aligned_cols=25 Identities=32% Similarity=0.396 Sum_probs=21.6
Q ss_pred cceEEEEecce---eeeeccccchhhhh
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVREA 340 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~~ 340 (375)
.|++||+.||. ...||+|||.+...
T Consensus 272 nA~V~V~QnG~~iy~t~VppGPF~I~dl 299 (826)
T PRK15217 272 NALVTIEQNGFVVYQKEVPPGPFAIADL 299 (826)
T ss_pred CcEEEEEECCEEEEEEEeCCCCeEeccc
Confidence 58999999994 57899999998765
No 49
>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=59.66 E-value=4.7 Score=30.59 Aligned_cols=42 Identities=14% Similarity=0.309 Sum_probs=27.6
Q ss_pred CCCCCCCHHHHHHHHHHH-hcCCCCCCHHHHHHHHHHHhhcCCCCCCceeecc
Q 036145 58 KPRWNPKPEQIRILESIF-NSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWF 109 (375)
Q Consensus 58 R~Rt~FT~eQL~~LE~~F-~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWF 109 (375)
++|..||+|+...+=..+ ..+. .+.+||++++ |+...+..|=
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g~------sv~~va~~~g----i~~~~l~~W~ 44 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESGE------SVSEVAREYG----ISPSTLYNWR 44 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHHC------HHHHHHHHHT----S-HHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCCC------ceEeeecccc----cccccccHHH
Confidence 578899999887766666 5542 5678999997 9999999994
No 50
>PRK15294 putative fimbrial outer membrane usher protein SthC; Provisional
Probab=58.99 E-value=6.8 Score=43.74 Aligned_cols=37 Identities=32% Similarity=0.427 Sum_probs=27.2
Q ss_pred cceEEEEecce---eeeeccccchhhhh----c-CC-ceEEEecCC
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVREA----F-GE-DAVLINSSG 352 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~~----F-G~-davLihssG 352 (375)
.|++||+.||. ...||+|||.+... . || +|++.-..|
T Consensus 289 nA~V~V~QnG~~iY~t~VppGPF~I~Dl~~~~~~GdL~VtV~EadG 334 (845)
T PRK15294 289 SAQVTVEQNGYTIYKTNVPAGPFAINDLYPTGGSGDLYVTIKESDG 334 (845)
T ss_pred CcEEEEEECCEEEEEeEeCCCCeEeccccCCCCCceEEEEEEeCCC
Confidence 58999999994 57899999988765 2 43 344445566
No 51
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=57.80 E-value=5.7 Score=33.83 Aligned_cols=51 Identities=8% Similarity=-0.009 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHI 123 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~ 123 (375)
+++.|.++++-.|..+. + .++||+.|+ +++..|+++...=|.|.|+..+.+
T Consensus 107 Lp~~~r~v~~l~~~~g~--s----~~EIA~~lg----is~~tV~~~l~Rar~~Lr~~l~~~ 157 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK--S----YQEIALQEK----IEVKTVEMKLYRARKWIKKHWKEE 157 (160)
T ss_pred CCHHHHHHHHHHHHhCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHhhh
Confidence 55667777777766663 2 357899997 999999988876666666665443
No 52
>PRK15298 fimbrial outer membrane usher protein StiC; Provisional
Probab=57.05 E-value=7.1 Score=43.73 Aligned_cols=37 Identities=27% Similarity=0.476 Sum_probs=27.1
Q ss_pred cceEEEEecce---eeeeccccchhhhhc-----CC-ceEEEecCC
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVREAF-----GE-DAVLINSSG 352 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~~F-----G~-davLihssG 352 (375)
.|++||+.||. ...||+|||.+.... || +|++.-+.|
T Consensus 293 ~A~V~V~QnG~~iy~t~VppGPF~I~Dl~~~~~~GdL~VtV~EadG 338 (848)
T PRK15298 293 NAQVIVRQNGYIAYQTAVSPGEFEINDMFPTGSNGDYDVTVKEADG 338 (848)
T ss_pred CcEEEEEECCEEEEEeEeCCCCeEeccCcCCCCCceEEEEEEEcCC
Confidence 58999999994 578999999887652 33 344445566
No 53
>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=56.64 E-value=4.8 Score=28.86 Aligned_cols=38 Identities=13% Similarity=0.299 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeecc
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWF 109 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWF 109 (375)
.++++|.++|+..|..+. . -.+||+.|+ +++..|+.+-
T Consensus 4 ~L~~~er~vi~~~y~~~~--t----~~eIa~~lg----~s~~~V~~~~ 41 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEGL--T----LEEIAERLG----ISRSTVRRIL 41 (50)
T ss_dssp TS-HHHHHHHHHHHTST---S----HHHHHHHHT----SCHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCC--C----HHHHHHHHC----CcHHHHHHHH
Confidence 468999999999997764 2 357999997 8988887553
No 54
>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=56.63 E-value=13 Score=22.18 Aligned_cols=40 Identities=20% Similarity=0.370 Sum_probs=27.3
Q ss_pred CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeecc
Q 036145 60 RWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWF 109 (375)
Q Consensus 60 Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWF 109 (375)
+..++.++...+...|..+. ...+|+++++ ++...|..|.
T Consensus 3 ~~~~~~~~~~~i~~~~~~~~------s~~~ia~~~~----is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLAAGE------SVAEIARRLG----VSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHhC
Confidence 34467788887777787552 2357888886 7877777763
No 55
>PRK15223 pilin outer membrane usher protein SafC; Provisional
Probab=56.50 E-value=8.1 Score=43.08 Aligned_cols=37 Identities=30% Similarity=0.478 Sum_probs=27.2
Q ss_pred cceEEEEecc---eeeeeccccchhhhhc-----CC-ceEEEecCC
Q 036145 316 AARSTVFIND---VAFEVVAGPFNVREAF-----GE-DAVLINSSG 352 (375)
Q Consensus 316 ~a~~tVfIn~---vafeV~~GpfnVr~~F-----G~-davLihssG 352 (375)
.|++||+.|| -...||+|||-+.... || +|++.-+.|
T Consensus 284 nA~V~V~QnG~~IY~t~VppGPF~I~Dl~~~~~~GdL~VtV~EadG 329 (836)
T PRK15223 284 QARVEVKQNGYTIYNTTVAPGPFALRDLSVTDSSGDLHVTVWEADG 329 (836)
T ss_pred CcEEEEEECCEEEEEEEeCCCCeEeccccccCCCceEEEEEEEcCC
Confidence 5899999999 4678999999887552 33 344455566
No 56
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=56.41 E-value=12 Score=29.08 Aligned_cols=50 Identities=18% Similarity=0.173 Sum_probs=38.1
Q ss_pred EEEEecceeeeeccccchhhhh---cC--CceEEEecCCcceecccccccccccccc
Q 036145 319 STVFINDVAFEVVAGPFNVREA---FG--EDAVLINSSGQPVLTNEWGVTLQSLNHG 370 (375)
Q Consensus 319 ~tVfIn~vafeV~~GpfnVr~~---FG--~davLihssG~pv~tne~Gvtl~sLqhG 370 (375)
|+|.|||.+++++.+...|++. +| ..-+.|--.|+.||-++|.-+. |+.|
T Consensus 1 m~I~vNG~~~~~~~~~~tv~~lL~~l~~~~~~vav~vN~~iv~r~~w~~~~--L~~g 55 (67)
T PRK07696 1 MNLKINGNQIEVPESVKTVAELLTHLELDNKIVVVERNKDILQKDDHTDTS--VFDG 55 (67)
T ss_pred CEEEECCEEEEcCCCcccHHHHHHHcCCCCCeEEEEECCEEeCHHHcCcee--cCCC
Confidence 5899999999999887777743 33 4566677789999999997664 4444
No 57
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=56.05 E-value=6.2 Score=35.56 Aligned_cols=52 Identities=17% Similarity=0.123 Sum_probs=38.9
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhh
Q 036145 61 WNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHI 123 (375)
Q Consensus 61 t~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~ 123 (375)
..+|+.|+++|+. +..+. ..++||+.|+ ++...|+.|-.+.|.|.|+...-.
T Consensus 5 ~~Lt~rqreVL~l-r~~Gl------Tq~EIAe~LG----iS~~tVs~ie~ra~kkLr~~~~tl 56 (141)
T PRK03975 5 SFLTERQIEVLRL-RERGL------TQQEIADILG----TSRANVSSIEKRARENIEKARETL 56 (141)
T ss_pred cCCCHHHHHHHHH-HHcCC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4679999999988 45553 2358999997 999999999886666655554443
No 58
>PRK15198 outer membrane usher protein FimD; Provisional
Probab=55.74 E-value=8.2 Score=43.29 Aligned_cols=25 Identities=28% Similarity=0.317 Sum_probs=21.5
Q ss_pred cceEEEEecc---eeeeeccccchhhhh
Q 036145 316 AARSTVFIND---VAFEVVAGPFNVREA 340 (375)
Q Consensus 316 ~a~~tVfIn~---vafeV~~GpfnVr~~ 340 (375)
.|++||++|| -...||+|||-+...
T Consensus 287 ~A~V~V~QnG~~iYst~VppGPF~I~Dl 314 (860)
T PRK15198 287 AAKLTIRQNGYVIYQSYVSPGAFAITDL 314 (860)
T ss_pred CcEEEEEECCEEEEEeEeCCCCeEeccc
Confidence 5899999999 457899999988755
No 59
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=55.70 E-value=6.9 Score=33.29 Aligned_cols=49 Identities=12% Similarity=0.007 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
.+++.|.++|+-.|-.+. + ..+||+.|+ +++..|+.|...=|.|.|+..
T Consensus 128 ~L~~~~r~vl~l~~~~~~--s----~~eIA~~lg----is~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREIEGL--S----YEEIAEIMG----CPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 588889999998877763 2 247899997 999999988774444444433
No 60
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=55.33 E-value=6.9 Score=44.08 Aligned_cols=65 Identities=23% Similarity=0.227 Sum_probs=50.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhH
Q 036145 55 PEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 55 p~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q 124 (375)
++.|.|....+++-..|-.+++-+. .|...+-.-++.+|. ..+.+|.+||++|+.+.+.---..-
T Consensus 625 ~p~kv~sp~k~~dq~ql~~a~elq~-s~~n~~~pl~~t~~~----n~~pv~ev~dhsrsstpsp~pl~lt 689 (1007)
T KOG3623|consen 625 RPVKVRSPIKEEDQQQLKQAYELQA-SPSNDEFPLIATRLQ----NDPPVVEVWDHSRSSTPSPMPLFLT 689 (1007)
T ss_pred CCccccCCCCccchhhhHhhhhccc-CccCcccchhhhhcc----CCCcchhhcccCCCCCCCCCccccc
Confidence 4457888999999999999999986 477766666666665 6778889999999999886554443
No 61
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=55.27 E-value=16 Score=28.05 Aligned_cols=49 Identities=24% Similarity=0.425 Sum_probs=37.4
Q ss_pred EEEEecceeeeeccccchhhh---hcC--CceEEEecCCcceeccccccccccccccc
Q 036145 319 STVFINDVAFEVVAGPFNVRE---AFG--EDAVLINSSGQPVLTNEWGVTLQSLNHGA 371 (375)
Q Consensus 319 ~tVfIn~vafeV~~GpfnVr~---~FG--~davLihssG~pv~tne~Gvtl~sLqhGa 371 (375)
|+|.|||.+++++. +..|.+ .+| .+.+-|--.|+.|+-.+|. + . |+.|-
T Consensus 1 m~i~vNG~~~~~~~-~~tl~~ll~~l~~~~~~vav~~N~~iv~r~~~~-~-~-L~~gD 54 (65)
T PRK05863 1 MIVVVNEEQVEVDE-QTTVAALLDSLGFPEKGIAVAVDWSVLPRSDWA-T-K-LRDGA 54 (65)
T ss_pred CEEEECCEEEEcCC-CCcHHHHHHHcCCCCCcEEEEECCcCcChhHhh-h-h-cCCCC
Confidence 58999999999986 466763 344 4566677789999999998 4 3 77774
No 62
>PRK15193 outer membrane usher protein; Provisional
Probab=54.87 E-value=8.4 Score=43.37 Aligned_cols=25 Identities=24% Similarity=0.303 Sum_probs=21.4
Q ss_pred cceEEEEecce---eeeeccccchhhhh
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVREA 340 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~~ 340 (375)
.|++||+.||+ ...||+|||-+...
T Consensus 306 nA~V~V~QnG~~iY~t~VPpGPF~I~Dl 333 (876)
T PRK15193 306 NAQVTIKQNGYTIYQTYVSPGAFEISDL 333 (876)
T ss_pred CcEEEEEECCEEEEEEEeCCCCeEeccC
Confidence 58999999994 56899999988755
No 63
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=53.52 E-value=13 Score=44.12 Aligned_cols=59 Identities=22% Similarity=0.279 Sum_probs=49.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 57 PKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 57 ~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
.+.|...=++++.+|=+.|..+. .|+...+.-|....- .+++.+++||+|-|.|+++..
T Consensus 706 ~~~~~~~~~~aa~~l~~a~~~~~-sps~k~~~civcd~~----st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 706 KLLRLTILPEAAMILGRAYMQDN-SPSLKVFDCIVCDVF----STDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccCcccccHHHHhhhhhcccCCC-CHHHHHHHHhhhhhh----hhhhHHHHhhcchhhhhhhhc
Confidence 45566666699999999999997 799988877766654 788999999999999998765
No 64
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=51.04 E-value=9.2 Score=34.06 Aligned_cols=40 Identities=15% Similarity=0.175 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCc
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQN 111 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQN 111 (375)
.+++.|.++|+-.|..+. ..++||+.|+ +++..|+.+...
T Consensus 142 ~L~~~~r~vl~l~~~~~~------s~~EIA~~Lg----is~~tVk~~l~r 181 (194)
T PRK09646 142 ALTDTQRESVTLAYYGGL------TYREVAERLA----VPLGTVKTRMRD 181 (194)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHhC----CChHhHHHHHHH
Confidence 467778888877776663 2357999997 999999776633
No 65
>PRK15304 putative fimbrial outer membrane usher protein; Provisional
Probab=50.46 E-value=11 Score=41.92 Aligned_cols=37 Identities=19% Similarity=0.319 Sum_probs=27.4
Q ss_pred cceEEEEecce---eeeeccccchhhhh----c-CC-ceEEEecCC
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVREA----F-GE-DAVLINSSG 352 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~~----F-G~-davLihssG 352 (375)
.|++||+.||+ ...||+|||.+... . || +|++.-+.|
T Consensus 270 nA~V~V~QnG~~iY~t~VppGPF~I~Dl~~~~~~GdL~V~V~EadG 315 (801)
T PRK15304 270 QARVEIRQSGQLIYSTLVPAGAFTLDDVPVINGNTDLNVTVVETDG 315 (801)
T ss_pred CcEEEEEECCEEEEEeEcCCCCeEeccccCCCCCccEEEEEEEcCC
Confidence 48999999994 56899999998866 2 33 344455577
No 66
>PF13551 HTH_29: Winged helix-turn helix
Probab=49.03 E-value=17 Score=28.90 Aligned_cols=53 Identities=17% Similarity=0.105 Sum_probs=33.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCC--HHHHHHHHHHH-hhcCC--CCCCceeecc
Q 036145 56 EPKPRWNPKPEQIRILESIFNSGMVNPP--RDEIRRIRAQL-QEYGQ--VGDANVFYWF 109 (375)
Q Consensus 56 ~~R~Rt~FT~eQL~~LE~~F~~~~~yPs--~~eR~qLA~~L-~~~g~--LtE~qVkvWF 109 (375)
+.+++..++++|++.|++++...+.+ . .-....|++.| .+..+ ++...|..|+
T Consensus 51 ~g~~~~~l~~~~~~~l~~~~~~~p~~-g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L 108 (112)
T PF13551_consen 51 GGRPRKRLSEEQRAQLIELLRENPPE-GRSRWTLEELAEWLIEEEFGIDVSPSTIRRIL 108 (112)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHCCCC-CCCcccHHHHHHHHHHhccCccCCHHHHHHHH
Confidence 34556569999999999999988521 1 12345667665 33333 4555555554
No 67
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=48.72 E-value=8.4 Score=33.95 Aligned_cols=48 Identities=17% Similarity=0.147 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
+++++.++|+-.|-.+. ..++||+.|+ +++..|+.|...-|.|.|+..
T Consensus 142 L~~~~~~v~~l~~~~g~------s~~EIA~~lg----is~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 142 LPESQRQVLELAYYEGL------SQSEIAKRLG----IPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred CCHHHhhhhhhhhhcCC------CHHHHHHHhC----CCHHHHHHHHHHHHHHHHHHH
Confidence 56777777777766663 2357899997 999999999865555555443
No 68
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=48.50 E-value=9.5 Score=33.34 Aligned_cols=51 Identities=22% Similarity=0.272 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRH 122 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~ 122 (375)
.+++++.++|.-.|-.+. .-++||+.|+ ++...|+.+...=|.|.|++.+.
T Consensus 131 ~L~~~~r~v~~l~~~~g~------s~~eIA~~l~----is~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12512 131 TLPPRQRDVVQSISVEGA------SIKETAAKLS----MSEGAVRVALHRGLAALAAKFRS 181 (184)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHhC----CCHHHHHHHHHHHHHHHHHHhhc
Confidence 456667777777766663 1357899997 99999998887666666665543
No 69
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=48.05 E-value=9.4 Score=32.86 Aligned_cols=53 Identities=8% Similarity=-0.061 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhH
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q 124 (375)
.++++|.++|.-.|-.+. ..++||+.|+ +++..|+.|.+-=|.|.|+..+++.
T Consensus 108 ~L~~~~r~v~~l~~~~g~------s~~eIA~~lg----is~~tv~~~l~Rar~~Lr~~l~~~~ 160 (165)
T PRK09644 108 TLPVIEAQAILLCDVHEL------TYEEAASVLD----LKLNTYKSHLFRGRKRLKALLKEEK 160 (165)
T ss_pred hCCHHHHHHHHhHHHhcC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHhhh
Confidence 456777777776655552 2357899987 9999998887766666666555444
No 70
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=47.50 E-value=8.5 Score=33.37 Aligned_cols=49 Identities=10% Similarity=0.166 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
.+++.+.++|+-.|-.+. + .++||+.|+ +++..|+++.+.=|.|.|+..
T Consensus 136 ~L~~~~r~v~~l~~~~g~--s----~~eIA~~lg----is~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMEDL--S----LKEISEILD----LPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHhcCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHh
Confidence 466777777777665553 2 357899997 999999988865555555543
No 71
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=47.37 E-value=12 Score=31.72 Aligned_cols=50 Identities=16% Similarity=0.131 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
.+++.+.++|...|..+. .-.+||+.|+ +++..|+.|..-=|.|.|+..+
T Consensus 125 ~L~~~~r~i~~l~~~~~~------~~~eIA~~lg----is~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 125 ALPVKQREVFLLRYVEGL------SYREIAEILG----VPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred hCCHHHHHHhhHHHHcCC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHH
Confidence 356666667776666653 2357888887 9999999887665555555443
No 72
>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=46.85 E-value=17 Score=30.68 Aligned_cols=38 Identities=16% Similarity=0.219 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeecc
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWF 109 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWF 109 (375)
.+++.|.++++-.|-.+. + .++||+.|+ |++..|+++.
T Consensus 111 ~L~~~~r~v~~l~~~~g~--~----~~eIA~~l~----is~~tv~~~l 148 (159)
T TIGR02989 111 KLPERQRELLQLRYQRGV--S----LTALAEQLG----RTVNAVYKAL 148 (159)
T ss_pred HCCHHHHHHHHHHHhcCC--C----HHHHHHHhC----CCHHHHHHHH
Confidence 477888888888776663 2 357899997 9999999653
No 73
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=44.77 E-value=18 Score=30.80 Aligned_cols=43 Identities=21% Similarity=0.453 Sum_probs=30.7
Q ss_pred CCCCCCCHHHH-HHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccC
Q 036145 58 KPRWNPKPEQI-RILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQ 110 (375)
Q Consensus 58 R~Rt~FT~eQL-~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQ 110 (375)
++|.+||.|.. +++..++..+. + ..+||++++ |+...|+.|-.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~--s----v~evA~e~g----Is~~tl~~W~r 51 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGM--T----VSLVARQHG----VAASQLFLWRK 51 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCC--C----HHHHHHHHC----cCHHHHHHHHH
Confidence 44566777764 46666777663 2 347899997 99999999943
No 74
>PRK15255 fimbrial outer membrane usher protein StdB; Provisional
Probab=44.60 E-value=16 Score=40.96 Aligned_cols=38 Identities=32% Similarity=0.441 Sum_probs=27.6
Q ss_pred cceEEEEecc---eeeeeccccchhhhhc----CC-ceEEEecCCc
Q 036145 316 AARSTVFIND---VAFEVVAGPFNVREAF----GE-DAVLINSSGQ 353 (375)
Q Consensus 316 ~a~~tVfIn~---vafeV~~GpfnVr~~F----G~-davLihssG~ 353 (375)
.|+++|++|| -...||+|||-+...- || ||++.-+.|.
T Consensus 284 nA~V~V~QnG~~iY~t~VppGPF~I~Dlp~~~~GdL~V~V~EadG~ 329 (829)
T PRK15255 284 NAQVTVSQNGRILYQTRVSPGPFELPDLSQNISGNLDVSVRESDGS 329 (829)
T ss_pred CcEEEEEECCEEEEEeEeCCCCeEeccCCCCCCccEEEEEEEcCCC
Confidence 5899999999 4678999999775442 43 4455556775
No 75
>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=44.48 E-value=11 Score=30.07 Aligned_cols=46 Identities=11% Similarity=0.182 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSK 117 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~K 117 (375)
.+++.|.++|...|-.+. + ..+||++|+ +++..|+.|...=|.|.|
T Consensus 110 ~L~~~~~~ii~~~~~~g~--s----~~eIA~~l~----~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLEGL--S----YKEIAEILG----ISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhcCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 467888888877766652 2 347899997 999999877665444444
No 76
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=44.47 E-value=13 Score=33.73 Aligned_cols=46 Identities=13% Similarity=0.143 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSK 117 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~K 117 (375)
.++++|.++|.-.|-.+. ..++||+.|+ +++..|+.+...=|.+.|
T Consensus 153 ~L~~~~r~vl~l~~~~g~------s~~EIA~~lg----is~~tV~~~l~Ra~~~Lr 198 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQEL------SQEQLAQQLN----VPLGTVKSRLRLALAKLK 198 (206)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 356677777776666663 2457899997 999999776644443333
No 77
>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=44.43 E-value=8.4 Score=27.72 Aligned_cols=39 Identities=18% Similarity=0.186 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCc
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQN 111 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQN 111 (375)
.++.|.++++-.|-.+. ..++||+.|+ +++..|+.|.+.
T Consensus 11 L~~~~r~i~~l~~~~g~------s~~eIa~~l~----~s~~~v~~~l~r 49 (54)
T PF08281_consen 11 LPERQREIFLLRYFQGM------SYAEIAEILG----ISESTVKRRLRR 49 (54)
T ss_dssp S-HHHHHHHHHHHTS---------HHHHHHHCT----S-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHCc------CHHHHHHHHC----cCHHHHHHHHHH
Confidence 57888999999998884 2457899987 999999988753
No 78
>PRK15235 outer membrane fimbrial usher protein SefC; Provisional
Probab=43.49 E-value=17 Score=40.62 Aligned_cols=38 Identities=26% Similarity=0.367 Sum_probs=27.2
Q ss_pred cceEEEEecce---eeeeccccchhhh-------h-cCC-ceEEEecCCc
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVRE-------A-FGE-DAVLINSSGQ 353 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~-------~-FG~-davLihssG~ 353 (375)
.|++||++||. ...||+|||.+.. . -|| ||++....|.
T Consensus 268 nA~V~V~QnG~~iY~t~VppGPF~I~d~p~~dl~~~~GdL~V~V~EadG~ 317 (814)
T PRK15235 268 NATVEVRQNGYLIYSTSVPPGQFEIGREQIADLGVGVGVLDVSIYEKNGQ 317 (814)
T ss_pred CcEEEEEECCEEEEEEEeCCCCeEecCcccccCCCCcceEEEEEEEcCCC
Confidence 58999999994 5689999999962 2 254 3444555673
No 79
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=43.43 E-value=11 Score=31.76 Aligned_cols=40 Identities=13% Similarity=0.130 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCc
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQN 111 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQN 111 (375)
.+++.|.++++-.|-.+. ..++||+.|+ +++..|+.|...
T Consensus 106 ~L~~~~r~ii~l~~~~~~------s~~EIA~~l~----is~~tV~~~~~r 145 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGK------TMGEIALETE----MTYYQVRWIYRQ 145 (154)
T ss_pred hCCHHHHHHHHHHHhcCC------CHHHHHHHHC----CCHHHHHHHHHH
Confidence 456777788877777764 2467899997 999999977543
No 80
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=43.32 E-value=14 Score=32.52 Aligned_cols=50 Identities=8% Similarity=0.159 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 61 WNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 61 t~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
-.++++|.++|+-.|..+. + .++||+.|+ +++..|++....=|.|.|+..
T Consensus 130 ~~L~~~~r~vl~l~~~~~~--s----~~eIA~~lg----is~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 130 AKLSPAHREIIDLVYYHEK--S----VEEVGEIVG----IPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred HhCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----cCHHHHHHHHHHHHHHHHHHH
Confidence 3577888888888777763 2 357899997 999999977654444444443
No 81
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=42.87 E-value=27 Score=26.80 Aligned_cols=50 Identities=18% Similarity=0.388 Sum_probs=36.1
Q ss_pred EEEEecceeeeeccccchhh---hhcCCc--eEEEecCCcceeccccccccccccccc
Q 036145 319 STVFINDVAFEVVAGPFNVR---EAFGED--AVLINSSGQPVLTNEWGVTLQSLNHGA 371 (375)
Q Consensus 319 ~tVfIn~vafeV~~GpfnVr---~~FG~d--avLihssG~pv~tne~Gvtl~sLqhGa 371 (375)
|+|.|||.+++++.+ ..|. +.+|-+ .+-|=-.|+.|+-++|.-+. |+-|.
T Consensus 1 m~i~vNg~~~~~~~~-~tl~~ll~~l~~~~~~vaVavN~~iv~r~~w~~~~--L~~gD 55 (66)
T PRK08053 1 MQILFNDQPMQCAAG-QTVHELLEQLNQLQPGAALAINQQIIPREQWAQHI--VQDGD 55 (66)
T ss_pred CEEEECCeEEEcCCC-CCHHHHHHHcCCCCCcEEEEECCEEeChHHcCccc--cCCCC
Confidence 579999999999875 4444 555543 56667789999999998763 55443
No 82
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=42.76 E-value=7.9 Score=27.82 Aligned_cols=38 Identities=26% Similarity=0.371 Sum_probs=17.6
Q ss_pred CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceee
Q 036145 60 RWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFY 107 (375)
Q Consensus 60 Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkv 107 (375)
...+|.+|...++..++.+. ...+||+.|+ .+..-|..
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~------s~~~IA~~lg----~s~sTV~r 39 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGM------SIREIAKRLG----RSRSTVSR 39 (44)
T ss_dssp ----------HHHHHHCS---------HHHHHHHTT------HHHHHH
T ss_pred ccchhhhHHHHHHHHHHcCC------CHHHHHHHHC----cCcHHHHH
Confidence 35689999999999998884 2457999997 55555543
No 83
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=41.64 E-value=29 Score=26.10 Aligned_cols=49 Identities=22% Similarity=0.262 Sum_probs=33.3
Q ss_pred EEEEecceeeeeccccchhhh---hcC--CceEEEecCCcceecccccccccccccc
Q 036145 319 STVFINDVAFEVVAGPFNVRE---AFG--EDAVLINSSGQPVLTNEWGVTLQSLNHG 370 (375)
Q Consensus 319 ~tVfIn~vafeV~~GpfnVr~---~FG--~davLihssG~pv~tne~Gvtl~sLqhG 370 (375)
++|.|||.+++++.| ..|++ .+| .+-+.|--.|+.|+-.+|--+. |+.|
T Consensus 1 m~i~vNG~~~~~~~~-~tl~~lL~~l~~~~~~vav~vNg~iv~r~~~~~~~--l~~g 54 (66)
T PRK05659 1 MNIQLNGEPRELPDG-ESVAALLAREGLAGRRVAVEVNGEIVPRSQHASTA--LREG 54 (66)
T ss_pred CEEEECCeEEEcCCC-CCHHHHHHhcCCCCCeEEEEECCeEeCHHHcCccc--CCCC
Confidence 579999999999985 56663 445 3344444568888888876543 4444
No 84
>PRK04217 hypothetical protein; Provisional
Probab=41.25 E-value=16 Score=31.75 Aligned_cols=60 Identities=12% Similarity=0.175 Sum_probs=42.4
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhh
Q 036145 46 TVPGCEERSPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHK 119 (375)
Q Consensus 46 s~p~~~~rsp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk 119 (375)
+.|.|-...| =-.++++|+++++..|..+. ..++||+.|+ ++...|+.....-|.+.|..
T Consensus 30 ~~~~~~~~~p----~~~Lt~eereai~l~~~eGl------S~~EIAk~LG----IS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 30 AIPPVGPPKP----PIFMTYEEFEALRLVDYEGL------TQEEAGKRMG----VSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred CCCCccCCCC----cccCCHHHHHHHHHHHHcCC------CHHHHHHHHC----cCHHHHHHHHHHHHHHHHHH
Confidence 3444654444 34689999999999988773 3467999997 99999997776555554443
No 85
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=41.00 E-value=21 Score=28.67 Aligned_cols=46 Identities=17% Similarity=0.193 Sum_probs=30.5
Q ss_pred CCCCHHHHHHHHHHHhcCC----CCCCHHHHHHHHHHHhhcCCCCCCceeeccC
Q 036145 61 WNPKPEQIRILESIFNSGM----VNPPRDEIRRIRAQLQEYGQVGDANVFYWFQ 110 (375)
Q Consensus 61 t~FT~eQL~~LE~~F~~~~----~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQ 110 (375)
|-+|.+|+..|.++|..-. .+.+.++ |.+.|.. .++++..|..+|.
T Consensus 2 ~~ls~~~~~~l~~~F~~~D~d~~G~Is~~e---l~~~l~~-~~~~~~ev~~i~~ 51 (96)
T smart00027 2 WAISPEDKAKYEQIFRSLDKNQDGTVTGAQ---AKPILLK-SGLPQTLLAKIWN 51 (96)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCCCeEeHHH---HHHHHHH-cCCCHHHHHHHHH
Confidence 7789999999999998732 2344444 4444443 2377777776663
No 86
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=40.29 E-value=29 Score=32.98 Aligned_cols=63 Identities=21% Similarity=0.177 Sum_probs=45.6
Q ss_pred CCCCC----CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcee-eccCcchhhhhhhhhhhH
Q 036145 50 CEERS----PEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVF-YWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 50 ~~~rs----p~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVk-vWFQNRRAK~KRk~r~~q 124 (375)
|.+|= +|.=+|-.||+|.-++|-+....-- + +-..||+.|. |=+|..|| +| ..+.|||.+.+.
T Consensus 48 CRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~G---N--rWs~IA~~LP---GRTDNeIKN~W----nt~lkkkl~~~~ 115 (238)
T KOG0048|consen 48 CRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLG---N--RWSLIAGRLP---GRTDNEVKNHW----NTHLKKKLLKMG 115 (238)
T ss_pred HHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHC---c--HHHHHHhhCC---CcCHHHHHHHH----HHHHHHHHHHcC
Confidence 65543 4445588999998888888777642 2 3788999997 78888999 66 666677776654
No 87
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=39.90 E-value=14 Score=34.77 Aligned_cols=49 Identities=14% Similarity=0.097 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
+.+.|.++|+-.|-.+. ..++||+.|+ +++..|+.+.+.=|.|.|+..+
T Consensus 172 Lp~~~R~v~~L~~~eg~------s~~EIA~~Lg----is~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 172 LPEQQRIAVILSYHENM------SNGEIAEVMD----TTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CCHHHHHHhhhHHhcCC------CHHHHHHHHC----cCHHHHHHHHHHHHHHHHHHHH
Confidence 34556666666665553 2357899997 9999999887666666665554
No 88
>COG3188 FimD P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=39.69 E-value=22 Score=40.11 Aligned_cols=37 Identities=32% Similarity=0.499 Sum_probs=28.9
Q ss_pred cceEEEEecce---eeeeccccchhhhhc-----CC-ceEEEecCC
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVREAF-----GE-DAVLINSSG 352 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~~F-----G~-davLihssG 352 (375)
.|++||+.||. ...||.|||-+...+ || ||++..+.|
T Consensus 289 nA~V~V~QnG~~IY~t~VppGpF~I~dl~~~~~~GdL~V~V~EadG 334 (835)
T COG3188 289 NARVTVSQNGYVIYQTTVPPGPFEINDLPPTSGSGDLDVTVKEADG 334 (835)
T ss_pred CcEEEEEECCEEEEEeecCCCCeEeccccccCCCceEEEEEEECCC
Confidence 58999999994 468999999999877 55 445555666
No 89
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=38.88 E-value=19 Score=31.32 Aligned_cols=46 Identities=7% Similarity=0.221 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKH 118 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KR 118 (375)
..++|.++|.-.|-.+. ..++||+.|+ +++..|+++.+.=|.+.|+
T Consensus 130 L~~~~r~i~~l~~~~g~------s~~eIA~~lg----is~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 130 LEKDRAAAVRRAYLEGL------SYKELAERHD----VPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHHHHHcCC------CHHHHHHHHC----CChHHHHHHHHHHHHHHHH
Confidence 45666667776666553 2467899997 9999998766544444433
No 90
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=38.83 E-value=19 Score=32.93 Aligned_cols=51 Identities=18% Similarity=0.100 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRH 122 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~ 122 (375)
.+++.|.+++.-.|-.+. + .++||+.|+ +++..|+.+...=|.|.|+..+.
T Consensus 138 ~L~~~~r~v~~L~~~~g~--s----~~EIA~~Lg----is~~tV~~~l~RArk~Lr~~l~~ 188 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEGL--S----YEEIAATLG----VKLGTVRSRIHRGRQQLRAALAA 188 (203)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHH
Confidence 355566666666665553 2 357888887 99999998776555555544443
No 91
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=38.80 E-value=19 Score=30.69 Aligned_cols=48 Identities=17% Similarity=0.186 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
.+++.|..+|.-.| .+. + .++||+.|+ +++..|+.+...=|.+.|+..
T Consensus 112 ~L~~~~r~il~l~~-~g~--s----~~eIA~~lg----is~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF-SGY--S----YKEIAEALG----IKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH-cCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 46778888888888 663 2 357899997 999999988754444444443
No 92
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=38.19 E-value=16 Score=32.00 Aligned_cols=48 Identities=8% Similarity=0.068 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
+++.+.++|+-.|-.+. + .++||+.|+ ++...|+.+...=|.|.|+..
T Consensus 129 L~~~~r~i~~l~~~~g~--s----~~EIA~~lg----is~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 129 LPERQREAIVLQYYQGL--S----NIEAAAVMD----ISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CCHHHHHHhhHHHhcCC--C----HHHHHHHhC----cCHHHHHHHHHHHHHHHHHHH
Confidence 46666777777665553 1 357888887 999999987754444444433
No 93
>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=38.09 E-value=13 Score=27.47 Aligned_cols=45 Identities=9% Similarity=0.092 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSK 117 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~K 117 (375)
.+|+.++++|+-+..... ..+||++|+ ++++.|+++..|=+.|.+
T Consensus 3 ~LT~~E~~vl~~l~~G~~-------~~eIA~~l~----is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMS-------NKEIAEELG----ISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS--------HHHHHHHHT----SHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcCC-------cchhHHhcC----cchhhHHHHHHHHHHHhC
Confidence 589999999998877653 468999997 999999987666555544
No 94
>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=37.94 E-value=11 Score=27.09 Aligned_cols=38 Identities=26% Similarity=0.444 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeec
Q 036145 61 WNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYW 108 (375)
Q Consensus 61 t~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvW 108 (375)
..++++|++.+-+.+..+. .+.+||++++ ++...|+.+
T Consensus 4 ~~~~~~~~~~i~~l~~~G~------si~~IA~~~g----vsr~TvyR~ 41 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEGM------SIAEIAKQFG----VSRSTVYRY 41 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT--------HHHHHHHTT----S-HHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCCC------CHHHHHHHHC----cCHHHHHHH
Confidence 4578889999999999984 3568999987 887777644
No 95
>PF13510 Fer2_4: 2Fe-2S iron-sulfur cluster binding domain; PDB: 1Y56_A 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 2GAG_A 2GAH_A.
Probab=37.81 E-value=28 Score=28.02 Aligned_cols=34 Identities=15% Similarity=0.102 Sum_probs=21.2
Q ss_pred ceEEEEecceeeeeccccchhhhhcCCceEEEec
Q 036145 317 ARSTVFINDVAFEVVAGPFNVREAFGEDAVLINS 350 (375)
Q Consensus 317 a~~tVfIn~vafeV~~GpfnVr~~FG~davLihs 350 (375)
..|+|.|||.+++++.|===+.++......+.|.
T Consensus 2 ~~v~i~idG~~v~~~~G~til~al~~~gi~ip~~ 35 (82)
T PF13510_consen 2 KMVTITIDGKPVEVPPGETILEALLAAGIDIPRL 35 (82)
T ss_dssp EEEEEEETTEEEEEEET-BHHHHHHHTT--B-EE
T ss_pred CEEEEEECCEEEEEcCCCHHHHHHHHCCCeEEEe
Confidence 4699999999999999864444444444433333
No 96
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=36.94 E-value=21 Score=27.62 Aligned_cols=61 Identities=23% Similarity=0.163 Sum_probs=38.1
Q ss_pred CCCCCHHHHHHHHHHHhcCCC-----CCCHH---HH----HHHHHHHhhcCCC--CCCceeeccCcchhhhhhhh
Q 036145 60 RWNPKPEQIRILESIFNSGMV-----NPPRD---EI----RRIRAQLQEYGQV--GDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 60 Rt~FT~eQL~~LE~~F~~~~~-----yPs~~---eR----~qLA~~L~~~g~L--tE~qVkvWFQNRRAK~KRk~ 120 (375)
.-+||.+|+.+|-++++..+. ..+.. .+ ++|+..|+..++. +-.+++..+.|=+.+.|++.
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk~~ 76 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKKKL 76 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 357999999999988877421 11111 11 4688999876663 22335566666666666654
No 97
>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=36.45 E-value=15 Score=31.93 Aligned_cols=47 Identities=6% Similarity=-0.059 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHK 119 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk 119 (375)
+++++.++|.-.|-.+. .-++||+.|+ +++..|+++...=|.|.|+.
T Consensus 139 L~~~~r~v~~l~~~~~~------s~~EIA~~lg----is~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 139 LPEDLRTAITLRELEGL------SYEDIARIMD----CPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CCHHHhhhhhhhhhcCC------CHHHHHHHHC----cCHHHHHHHHHHHHHHHHHH
Confidence 34555555555554442 2357888887 99999987774444444433
No 98
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=36.40 E-value=18 Score=24.83 Aligned_cols=38 Identities=16% Similarity=0.327 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccC
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQ 110 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQ 110 (375)
.+++.++++++. +..+. ...+||+.|+ ++...|+.|.+
T Consensus 3 ~l~~~e~~i~~~-~~~g~------s~~eia~~l~----is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRL-LAEGL------TNKEIAERLG----ISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHH-HHcCC------CHHHHHHHHC----CCHHHHHHHHH
Confidence 468889998877 44442 2367898887 99999987766
No 99
>PRK13558 bacterio-opsin activator; Provisional
Probab=35.69 E-value=33 Score=36.03 Aligned_cols=41 Identities=17% Similarity=0.254 Sum_probs=34.5
Q ss_pred CCCCCHHHHHHHHHHHhcCCCC--CCHHHHHHHHHHHhhcCCCCCCce
Q 036145 60 RWNPKPEQIRILESIFNSGMVN--PPRDEIRRIRAQLQEYGQVGDANV 105 (375)
Q Consensus 60 Rt~FT~eQL~~LE~~F~~~~~y--Ps~~eR~qLA~~L~~~g~LtE~qV 105 (375)
+..+|+.|.+.|+..|+.+ +| |-...-++||++|+ |+..-+
T Consensus 605 ~~~lt~~q~e~l~~a~~~g-yf~~pr~~~~~e~a~~l~----is~~t~ 647 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVSG-YFEWPRRVEGEELAESMG----ISRSTF 647 (665)
T ss_pred hhhCCHHHHHHHHHHHHcC-CCCCCccCCHHHHHHHhC----CCHHHH
Confidence 4579999999999999999 56 77778889999997 776554
No 100
>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=34.94 E-value=18 Score=30.81 Aligned_cols=46 Identities=9% Similarity=0.086 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKH 118 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KR 118 (375)
++++|.++|+-.|-.+. . .++||+.|+ +++..|+.+-..=|.|.|+
T Consensus 111 L~~~~r~i~~l~~~~g~--s----~~eIA~~lg----is~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 111 LPARQRAVVVLRYYEDL--S----EAQVAEALG----ISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CCHHHHHHhhhHHHhcC--C----HHHHHHHhC----CCHHHHHHHHHHHHHHHHH
Confidence 46777777777776663 2 357888887 9999999776554444444
No 101
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=34.52 E-value=61 Score=25.89 Aligned_cols=43 Identities=21% Similarity=0.433 Sum_probs=34.9
Q ss_pred eEEEEecceeeeeccccchhhhh-----cCCceEEEecCCcceeccccc
Q 036145 318 RSTVFINDVAFEVVAGPFNVREA-----FGEDAVLINSSGQPVLTNEWG 361 (375)
Q Consensus 318 ~~tVfIn~vafeV~~GpfnVr~~-----FG~davLihssG~pv~tne~G 361 (375)
.|||-+||-+.|++.+ ..|.+. |.++-+.+--.|++||-.+|-
T Consensus 2 ~m~i~~ng~~~e~~~~-~tv~dLL~~l~~~~~~vav~vNg~iVpr~~~~ 49 (68)
T COG2104 2 PMTIQLNGKEVEIAEG-TTVADLLAQLGLNPEGVAVAVNGEIVPRSQWA 49 (68)
T ss_pred cEEEEECCEEEEcCCC-CcHHHHHHHhCCCCceEEEEECCEEccchhhh
Confidence 5899999999999997 555433 677888889999999977763
No 102
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=33.78 E-value=23 Score=29.97 Aligned_cols=39 Identities=10% Similarity=0.050 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccC
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQ 110 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQ 110 (375)
.+.+.|.+++.-.|-.+. + .++||+.|+ +++..|++...
T Consensus 106 ~Lp~~~r~v~~l~~~~g~--s----~~EIA~~lg----is~~tV~~~l~ 144 (161)
T PRK09047 106 KLPARQREAFLLRYWEDM--D----VAETAAAMG----CSEGSVKTHCS 144 (161)
T ss_pred hCCHHHHHHHHHHHHhcC--C----HHHHHHHHC----CCHHHHHHHHH
Confidence 456677777777666663 2 357899997 99999986554
No 103
>PRK15284 putative fimbrial outer membrane usher protein StfC; Provisional
Probab=33.64 E-value=42 Score=38.03 Aligned_cols=38 Identities=29% Similarity=0.392 Sum_probs=27.8
Q ss_pred cceEEEEecce---eeeeccccchhhhhc----CC-ceEEEecCCc
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVREAF----GE-DAVLINSSGQ 353 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~~F----G~-davLihssG~ 353 (375)
.|++||+.||. ...||+|||-+...- || +|++.-+.|.
T Consensus 304 nA~VtV~QnG~~IY~t~VppGPF~I~Dl~~~~~GdL~VtV~EadG~ 349 (881)
T PRK15284 304 TAKVTVSQMGRVIYETQVPAGPFRIQDIGDSVSGTLHVRIEEQNGQ 349 (881)
T ss_pred CcEEEEEECCEEEEEEEcCCCCceeccCCCCCCCcEEEEEEECCCC
Confidence 58999999994 568999999876542 44 3445556775
No 104
>PRK07440 hypothetical protein; Provisional
Probab=33.17 E-value=62 Score=25.49 Aligned_cols=46 Identities=15% Similarity=0.227 Sum_probs=35.3
Q ss_pred ceEEEEecceeeeeccccchhhhh---c--CCceEEEecCCcceeccccccc
Q 036145 317 ARSTVFINDVAFEVVAGPFNVREA---F--GEDAVLINSSGQPVLTNEWGVT 363 (375)
Q Consensus 317 a~~tVfIn~vafeV~~GpfnVr~~---F--G~davLihssG~pv~tne~Gvt 363 (375)
.+|+|.|||.+.|++.| ..|.+. + -.+.|.|=-.|+.|+-++|.=+
T Consensus 3 ~~m~i~vNG~~~~~~~~-~tl~~lL~~l~~~~~~vav~~N~~iv~r~~w~~~ 53 (70)
T PRK07440 3 NPITLQVNGETRTCSSG-TSLPDLLQQLGFNPRLVAVEYNGEILHRQFWEQT 53 (70)
T ss_pred CceEEEECCEEEEcCCC-CCHHHHHHHcCCCCCeEEEEECCEEeCHHHcCce
Confidence 36999999999999875 666643 3 3456777778999999999755
No 105
>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=33.14 E-value=26 Score=30.62 Aligned_cols=42 Identities=12% Similarity=0.048 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcch
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRK 113 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRR 113 (375)
.+++.|..+|+-.|-.+. + .++||+.|+ +++..|+++-+-=|
T Consensus 100 ~L~~~~r~v~~l~~~~g~--s----~~eIA~~lg----is~~tV~~~l~Rar 141 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGL--S----QQEIAEKLG----LSLSGAKSRVQRGR 141 (170)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----CCHHHHHHHHHHHH
Confidence 678888888888887773 2 357899997 99999987664333
No 106
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=32.63 E-value=30 Score=30.29 Aligned_cols=52 Identities=10% Similarity=-0.008 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhH
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q 124 (375)
+.+.|.+++.-.|-.+. ..++||+.|+ +++..|+.....=|.|.|+...+..
T Consensus 118 Lp~~~r~i~~l~~~e~~------s~~EIA~~lg----is~~tV~~~l~ra~~~Lr~~l~~~~ 169 (179)
T PRK12543 118 LPYKLRQVIILRYLHDY------SQEEIAQLLQ----IPIGTVKSRIHAALKKLRQKEQIEE 169 (179)
T ss_pred CCHHHHHHHHHHHHccC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555566666555542 2357888887 9999999887777777766655544
No 107
>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=32.44 E-value=24 Score=30.35 Aligned_cols=39 Identities=8% Similarity=0.134 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccC
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQ 110 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQ 110 (375)
.+.+.|.+++...|-.+. + .++||+.|+ +++..|+++..
T Consensus 119 ~L~~~~r~i~~l~~~~g~--s----~~eiA~~lg----is~~tv~~~l~ 157 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHDL--T----IKEIAEVMN----KPEGTVKTYLH 157 (169)
T ss_pred hCCHHHhHHHHHHHHcCC--C----HHHHHHHHC----CCHHHHHHHHH
Confidence 567778888888877774 2 357899997 99999986544
No 108
>PF13565 HTH_32: Homeodomain-like domain
Probab=32.01 E-value=87 Score=23.76 Aligned_cols=37 Identities=24% Similarity=0.217 Sum_probs=25.1
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCC
Q 036145 57 PKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQ 99 (375)
Q Consensus 57 ~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~ 99 (375)
-|+|. ++++.+.|.+.+..++ .-+. .+|+..|....+
T Consensus 27 Grp~~--~~e~~~~i~~~~~~~p-~wt~---~~i~~~L~~~~g 63 (77)
T PF13565_consen 27 GRPRK--DPEQRERIIALIEEHP-RWTP---REIAEYLEEEFG 63 (77)
T ss_pred CCCCC--cHHHHHHHHHHHHhCC-CCCH---HHHHHHHHHHhC
Confidence 34455 7888899999999885 3443 456777765544
No 109
>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=31.95 E-value=25 Score=30.50 Aligned_cols=45 Identities=20% Similarity=0.227 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSK 117 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~K 117 (375)
+.+.|.++++-.|-.+. ..++||+.|+ +++..|++....=|.+.|
T Consensus 135 Lp~~~r~v~~l~~~~g~------s~~EIA~~lg----is~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGL------TVEEIAELLG----VSVRTVERDWRFARAWLA 179 (183)
T ss_pred CCHHHHHHHHHHHHcCC------CHHHHHHHhC----CCHHHHHHHHHHHHHHHH
Confidence 66777777777777764 2357899997 999999977654444433
No 110
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=31.95 E-value=27 Score=30.99 Aligned_cols=50 Identities=12% Similarity=0.128 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
.+.+.|.++|+-.|-.+. ..++||+.|+ ++...|+.+...=|.+.|+..+
T Consensus 136 ~L~~~~r~i~~L~~~~g~------s~~EIA~~lg----is~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 136 NLPENTARVFTLKEILGF------SSDEIQQMCG----ISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred hCCHHHHHHhhhHHHhCC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHH
Confidence 456777777776666663 2357899997 9999999877655555555443
No 111
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=31.89 E-value=27 Score=31.09 Aligned_cols=39 Identities=13% Similarity=0.039 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccC
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQ 110 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQ 110 (375)
.++++|.++|+-.|-.+. + .++||..|+ +++..|+..+.
T Consensus 106 ~L~~~~r~i~~l~~~~g~--~----~~EIA~~lg----is~~tV~~~l~ 144 (181)
T PRK09637 106 ALPEKYAEALRLTELEGL--S----QKEIAEKLG----LSLSGAKSRVQ 144 (181)
T ss_pred hCCHHHHHHHHHHHhcCC--C----HHHHHHHhC----CCHHHHHHHHH
Confidence 567778888887777763 2 357888887 99999987775
No 112
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=31.84 E-value=25 Score=29.94 Aligned_cols=37 Identities=16% Similarity=0.080 Sum_probs=26.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeec
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYW 108 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvW 108 (375)
.+++++.++|+-.|-.+. + .++||++|+ ++...|+.+
T Consensus 109 ~L~~~~r~v~~l~~~~~~--s----~~EIA~~lg----is~~tV~~~ 145 (163)
T PRK07037 109 ELPARTRYAFEMYRLHGE--T----QKDIARELG----VSPTLVNFM 145 (163)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----CCHHHHHHH
Confidence 456666777776666663 2 357899997 999999975
No 113
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=31.79 E-value=27 Score=31.12 Aligned_cols=38 Identities=11% Similarity=0.212 Sum_probs=27.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeecc
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWF 109 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWF 109 (375)
.+.++|.++|.-.|-.+. + -++||+.|+ ++...|++..
T Consensus 141 ~Lp~~~r~v~~l~~~eg~--s----~~EIA~~lg----is~~tVk~rl 178 (194)
T PRK12531 141 RLPKAQRDVLQAVYLEEL--P----HQQVAEMFD----IPLGTVKSRL 178 (194)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHhC----cCHHHHHHHH
Confidence 355677777777666663 2 357899997 9999996554
No 114
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
Probab=31.74 E-value=54 Score=23.36 Aligned_cols=47 Identities=26% Similarity=0.314 Sum_probs=29.5
Q ss_pred EEEEe-cceeeeeccc--cchhhhhc----CCceEEEecCCcceeccccccccccccccc
Q 036145 319 STVFI-NDVAFEVVAG--PFNVREAF----GEDAVLINSSGQPVLTNEWGVTLQSLNHGA 371 (375)
Q Consensus 319 ~tVfI-n~vafeV~~G--pfnVr~~F----G~davLihssG~pv~tne~Gvtl~sLqhGa 371 (375)
|-||+ ||-.++|+.| ..++.+.. ..+++.+.-.|+.+..+ ++|.+|.
T Consensus 1 ~~~~~~~g~~~~~~~~~t~~~~~~~~~~~~~~~~va~~vng~~vdl~------~~l~~~~ 54 (60)
T cd01668 1 IYVFTPKGEIIELPAGATVLDFAYAIHTEIGNRCVGAKVNGKLVPLS------TVLKDGD 54 (60)
T ss_pred CEEECCCCCEEEcCCCCCHHHHHHHHChHhhhheEEEEECCEECCCC------CCCCCCC
Confidence 35777 8888888876 34433322 24667777788877655 4555554
No 115
>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=31.68 E-value=40 Score=27.49 Aligned_cols=26 Identities=15% Similarity=0.211 Sum_probs=23.0
Q ss_pred HHHHHHHHHHhhcCCCCCCceeeccC
Q 036145 85 DEIRRIRAQLQEYGQVGDANVFYWFQ 110 (375)
Q Consensus 85 ~eR~qLA~~L~~~g~LtE~qVkvWFQ 110 (375)
.++++|...|.+..+|.+.++.+|+.
T Consensus 50 ~~i~~L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 50 RRIRELTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred hhHHHHHHHHHHHhCCCCCeEEEEEE
Confidence 56788999999889999999999985
No 116
>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=31.68 E-value=26 Score=24.32 Aligned_cols=37 Identities=16% Similarity=0.257 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccC
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQ 110 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQ 110 (375)
+++.|.++++.++ .+. ...+||+.|+ ++...|+.|..
T Consensus 1 l~~~e~~i~~~~~-~~~------s~~eia~~l~----~s~~tv~~~~~ 37 (57)
T cd06170 1 LTPREREVLRLLA-EGK------TNKEIADILG----ISEKTVKTHLR 37 (57)
T ss_pred CCHHHHHHHHHHH-cCC------CHHHHHHHHC----CCHHHHHHHHH
Confidence 3667888887754 332 2457888886 89998988764
No 117
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=31.67 E-value=23 Score=31.16 Aligned_cols=47 Identities=9% Similarity=0.015 Sum_probs=29.7
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 64 KPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 64 T~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
++.|..++.-.|-.+. ..++||+.|+ +++..|++....-|.|.|+..
T Consensus 131 ~~~~r~v~~l~~~~g~------s~~EIA~~l~----is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 131 PDRQRLPIVHVKLEGL------SVAETAQLTG----LSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred CHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHHHHh
Confidence 3344444444444442 3467899997 999999988866555555543
No 118
>PRK06930 positive control sigma-like factor; Validated
Probab=31.37 E-value=27 Score=31.88 Aligned_cols=51 Identities=8% Similarity=0.098 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRH 122 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~ 122 (375)
.+++.+.++|.-.|..+. . ..+||+.|+ +++..|+.+...-|.|.|+..+.
T Consensus 114 ~L~~rer~V~~L~~~eg~--s----~~EIA~~lg----iS~~tVk~~l~Ra~~kLr~~l~~ 164 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGL--S----YSEIADYLN----IKKSTVQSMIERAEKKIARQINE 164 (170)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----cCHHHHHHHHHHHHHHHHHHHHH
Confidence 688888888888777764 2 357899997 99999999887666666665543
No 119
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=30.62 E-value=1.3e+02 Score=27.76 Aligned_cols=44 Identities=11% Similarity=0.207 Sum_probs=35.5
Q ss_pred CCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeecc
Q 036145 59 PRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWF 109 (375)
Q Consensus 59 ~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWF 109 (375)
+...+|+|+++++-++=.++ |..-.|.+||++.+ ++.--|.+=-
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D---P~~wTr~~LAkkF~----~S~~fV~~v~ 125 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED---PEKWTRKKLAKKFN----CSPLFVSMVA 125 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC---chHhhHHHHHHHhC----CCHHHHHHhc
Confidence 45789999999999999987 77888999999987 6665555433
No 120
>PRK15273 putative fimbrial outer membrane usher protein SteB; Provisional
Probab=30.59 E-value=32 Score=39.01 Aligned_cols=37 Identities=24% Similarity=0.399 Sum_probs=26.9
Q ss_pred cceEEEEecce---eeeeccccchhhhhc----CC-ceEEEecCC
Q 036145 316 AARSTVFINDV---AFEVVAGPFNVREAF----GE-DAVLINSSG 352 (375)
Q Consensus 316 ~a~~tVfIn~v---afeV~~GpfnVr~~F----G~-davLihssG 352 (375)
.|++||++||. ...||+|||-+...- || +|++.-+.|
T Consensus 282 nA~VtV~QnG~~IY~t~VPpGPF~I~DLp~~~~GdL~V~V~EadG 326 (881)
T PRK15273 282 NAKVKVSWQGRVLYETQVPAGPFRIQDLNQSVSGTLHVTVEEQNG 326 (881)
T ss_pred CcEEEEEECCEEEEEeEeCCCCeEecCCCCCCCccEEEEEEEcCC
Confidence 58999999994 568999999776442 43 344555566
No 121
>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=30.44 E-value=34 Score=24.49 Aligned_cols=23 Identities=35% Similarity=0.277 Sum_probs=19.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCC
Q 036145 57 PKPRWNPKPEQIRILESIFNSGM 79 (375)
Q Consensus 57 ~R~Rt~FT~eQL~~LE~~F~~~~ 79 (375)
.+-|..||++|.+.|++.|....
T Consensus 5 ~k~rl~Pt~~Q~~~L~~~~~~~R 27 (46)
T PF12323_consen 5 YKYRLYPTKEQEEKLERWFGACR 27 (46)
T ss_pred eEEEEecCHHHHHHHHHHHHHHH
Confidence 45688999999999999998774
No 122
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=30.42 E-value=31 Score=29.78 Aligned_cols=47 Identities=17% Similarity=0.210 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKH 118 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KR 118 (375)
.+++.|.++|+-.|-.+. + .++||+.|+ +++..|+.+...=|.+.|+
T Consensus 118 ~L~~~~r~vl~L~~~~g~--s----~~EIA~~lg----is~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRGW--S----TAQIAADLG----IPEGTVKSRLHYALRALRL 164 (173)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----cCHHHHHHHHHHHHHHHHH
Confidence 356777788888776663 2 357899997 9999998765444444333
No 123
>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=30.17 E-value=50 Score=25.82 Aligned_cols=41 Identities=12% Similarity=0.156 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeec
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYW 108 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvW 108 (375)
+|++|+.+|+.+|..-- +.|.+|-.+.-++|-|+..+=..|
T Consensus 1 lT~~Qk~el~~l~~qm~-----e~kK~~idk~Ve~G~iTqeqAd~i 41 (59)
T PF10925_consen 1 LTDQQKKELKALYKQML-----ELKKQIIDKYVEAGVITQEQADAI 41 (59)
T ss_pred CCHHHHHHHHHHHHHHH-----HHHHHHHHHHHHcCCCCHHHHHHH
Confidence 58999999999998862 677888888888999998775544
No 124
>PHA03256 BDLF3; Provisional
Probab=30.17 E-value=1e+02 Score=25.67 Aligned_cols=44 Identities=23% Similarity=0.287 Sum_probs=34.3
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHh
Q 036145 46 TVPGCEERSPEPKPRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQ 95 (375)
Q Consensus 46 s~p~~~~rsp~~R~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~ 95 (375)
|.|+|+++. .|+|...+.+-...+-..|... =+..+.++++.|+
T Consensus 2 sapgcs~~~--sK~~~~IsE~df~~~~~ff~rp----Lp~lVaevska~~ 45 (77)
T PHA03256 2 SAPGCSERQ--DKKRGTIGEREFGELLSWDPTD----LPRTVARVYVAVG 45 (77)
T ss_pred CCCCccccc--cccCCccCHHHHHHHHHHcCCc----HHHHHHHHHHHhc
Confidence 458999776 4678899999999999988764 3456777888776
No 125
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=30.00 E-value=26 Score=29.04 Aligned_cols=40 Identities=15% Similarity=0.132 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCc
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQN 111 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQN 111 (375)
.+++.+.++|+-.|-.+. + ..+||+.|+ +++..|+.+...
T Consensus 113 ~L~~~~r~il~l~~~~~~--~----~~eIA~~lg----is~~tv~~~~~r 152 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEGK--S----YKEIAEELG----ISVKTVEYHISK 152 (161)
T ss_pred HCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----CCHHHHHHHHHH
Confidence 456677777777665552 2 347888887 999999865543
No 126
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=29.90 E-value=25 Score=32.53 Aligned_cols=48 Identities=17% Similarity=0.246 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
+.+.|.++|...|..+. ..++||+.|+ +++..|+.+...=|.|.|+..
T Consensus 185 L~~~~r~vl~l~~~~g~------s~~EIA~~lg----is~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 185 LPEREQLVLSLYYQEEL------NLKEIGAVLG----VSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CCHHHHHHHHhHhccCC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 46677777777776663 2457899997 999999988876666666544
No 127
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=29.84 E-value=29 Score=30.24 Aligned_cols=46 Identities=22% Similarity=0.247 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSK 117 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~K 117 (375)
.+++.+.++|.-.|-.+. .-++||+.|+ +++..|+.+-+.=|.|.|
T Consensus 135 ~L~~~~r~vl~l~~~~~~------s~~eIA~~lg----is~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 135 ALSPEERRVIEVLYYQGY------THREAAQLLG----LPLGTLKTRARRALSRLK 180 (186)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHHC----cCHHHHHHHHHHHHHHHH
Confidence 456777777776655553 1357888887 999999876544333333
No 128
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=29.81 E-value=31 Score=30.38 Aligned_cols=47 Identities=4% Similarity=-0.015 Sum_probs=32.1
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhh
Q 036145 61 WNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSK 117 (375)
Q Consensus 61 t~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~K 117 (375)
..+++.|.++|+-.|-.+. ..++||+.|+ ++...|+.+...-|.|.|
T Consensus 130 ~~L~~~~r~v~~l~~~~g~------s~~eIA~~lg----is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12539 130 ARLPEKMRLAIQAVKLEGL------SVAEAATRSG----MSESAVKVSVHRGLKALA 176 (184)
T ss_pred HhCCHHHHHHHHHHHHcCC------cHHHHHHHHC----cCHHHHHHHHHHHHHHHH
Confidence 3567777788887666663 2457899997 999999877643333333
No 129
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=29.18 E-value=36 Score=29.89 Aligned_cols=39 Identities=15% Similarity=0.251 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccC
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQ 110 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQ 110 (375)
.+++.|.++++..|-.+. ..++||+.|+ +++..|++|-.
T Consensus 133 ~L~~~~r~i~~l~~~~~~------s~~eIA~~lg----is~~tV~~~l~ 171 (182)
T PRK12537 133 QLEPARRNCILHAYVDGC------SHAEIAQRLG----APLGTVKAWIK 171 (182)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHHC----CChhhHHHHHH
Confidence 355667777777776663 2457999997 99999987654
No 130
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=29.14 E-value=57 Score=25.59 Aligned_cols=38 Identities=21% Similarity=0.300 Sum_probs=30.1
Q ss_pred EEEEecceeeeeccc--cchhhhhcCCceEEEecCCccee
Q 036145 319 STVFINDVAFEVVAG--PFNVREAFGEDAVLINSSGQPVL 356 (375)
Q Consensus 319 ~tVfIn~vafeV~~G--pfnVr~~FG~davLihssG~pv~ 356 (375)
|-++|||...++..+ -+.+|..++.|+-++=..|=|+-
T Consensus 1 M~I~vN~k~~~~~~~~tl~~lr~~~k~~~DI~I~NGF~~~ 40 (57)
T PF14453_consen 1 MKIKVNEKEIETEENTTLFELRKESKPDADIVILNGFPTK 40 (57)
T ss_pred CEEEECCEEEEcCCCcCHHHHHHhhCCCCCEEEEcCcccC
Confidence 358999999999987 79999999777766666665543
No 131
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=29.08 E-value=29 Score=30.58 Aligned_cols=39 Identities=13% Similarity=-0.076 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeecc
Q 036145 61 WNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWF 109 (375)
Q Consensus 61 t~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWF 109 (375)
-.+.+.|.++++-.|-.+. ..++||+.|+ +++..|+.+.
T Consensus 138 ~~L~~~~r~i~~l~~~~g~------s~~EIA~~lg----is~~tV~~~l 176 (189)
T PRK09648 138 DTLPEKQREILILRVVVGL------SAEETAEAVG----STPGAVRVAQ 176 (189)
T ss_pred HhCCHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHHH
Confidence 3567777888887776663 2467899997 9999998766
No 132
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=28.85 E-value=33 Score=30.58 Aligned_cols=47 Identities=9% Similarity=0.093 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKH 118 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KR 118 (375)
.+++.|.++|.-.|-.+. ..++||+.|+ +++..|+++...=|.+.|+
T Consensus 134 ~Lp~~~R~v~~L~~~~g~------s~~EIA~~lg----is~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 134 HLPAQQARVFMMREYLEL------SSEQICQECD----ISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred hCCHHHHHHHhHHHHcCC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 356677777777776663 2468999997 9999999886544444333
No 133
>PRK00118 putative DNA-binding protein; Validated
Probab=28.45 E-value=34 Score=29.46 Aligned_cols=51 Identities=10% Similarity=0.132 Sum_probs=38.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHI 123 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~ 123 (375)
.++.|.+++...|..+. ...+||+.++ +++..|+.|...-|.+.|.-....
T Consensus 18 L~ekqRevl~L~y~eg~------S~~EIAe~lG----IS~~TV~r~L~RArkkLr~~~~~~ 68 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY------SLGEIAEEFN----VSRQAVYDNIKRTEKLLEDYEEKL 68 (104)
T ss_pred CCHHHHHHHHHHHHcCC------CHHHHHHHHC----cCHHHHHHHHHHHHHHHHHHHHHH
Confidence 57788999988888874 2357899997 999999998876666666554444
No 134
>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=27.79 E-value=36 Score=30.39 Aligned_cols=49 Identities=14% Similarity=0.148 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
.+.+.|.++|.-.|-.+. ..++||+.|+ ++...|+.+...=|.|.|+..
T Consensus 131 ~L~~~~r~v~~l~~~~g~------s~~EIA~~lg----is~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 131 HLPEQTARVFMMREVLGF------ESDEICQELE----ISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred hCCHHHHHHHHHHHHhCC------CHHHHHHHhC----CCHHHHHHHHHHHHHHHHHHH
Confidence 456777777777776664 2468899997 999999766554444444443
No 135
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=27.62 E-value=28 Score=31.32 Aligned_cols=51 Identities=18% Similarity=0.055 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRH 122 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~ 122 (375)
.++++|.++|.-.|-.+. + .++||+.|+ +++..|+++.+-=|.+.|+....
T Consensus 113 ~Lp~~~r~v~~L~~~~g~--s----~~EIA~~Lg----iS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 113 QLPDEQREALILVGASGF--S----YEEAAEMCG----VAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred hCCHHHhHHhhhHHhcCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHhc
Confidence 356667777777666552 2 357888887 99999999887666666655443
No 136
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=27.59 E-value=28 Score=32.47 Aligned_cols=51 Identities=18% Similarity=0.082 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHI 123 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~ 123 (375)
.+|+.|+++|+-+.. +. . .++||++|+ ++++.|+.+..|=..|..-+-|-+
T Consensus 155 ~Lt~rE~~Vl~l~~~-G~--s----~~eIA~~L~----iS~~TVk~~~~~i~~Kl~v~nr~e 205 (216)
T PRK10100 155 LLTHREKEILNKLRI-GA--S----NNEIARSLF----ISENTVKTHLYNLFKKIAVKNRTQ 205 (216)
T ss_pred CCCHHHHHHHHHHHc-CC--C----HHHHHHHhC----CCHHHHHHHHHHHHHHhCCCCHHH
Confidence 489999999999988 42 3 358999997 999999999888777776555543
No 137
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=27.51 E-value=17 Score=32.19 Aligned_cols=47 Identities=13% Similarity=0.063 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHK 119 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk 119 (375)
+++.+.++|+-.|-.+. ..++||++|+ |+...|+.+...=|.|.|+.
T Consensus 140 L~~~~r~i~~l~~~~g~------s~~EIA~~lg----is~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 140 LPDEQREVFLLREHGDL------ELEEIAELTG----VPEETVKSRLRYALQKLREL 186 (194)
T ss_pred CCHhHhhheeeehccCC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHHHH
Confidence 44555555555554442 2457999997 99999986554444444433
No 138
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=27.34 E-value=26 Score=32.65 Aligned_cols=47 Identities=19% Similarity=0.070 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKH 118 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KR 118 (375)
.+.+.|.++|.-.|-.+. + .++||+.|+ |++..|+.+-..=|.|.|+
T Consensus 134 ~Lp~~~R~v~~L~y~eg~--s----~~EIAe~Lg----iS~~tVk~~L~RAr~~Lr~ 180 (216)
T PRK12533 134 KLPVEYREVLVLRELEDM--S----YREIAAIAD----VPVGTVMSRLARARRRLAA 180 (216)
T ss_pred cCCHHHHhHhhhHHhcCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 345566677777666653 2 357899997 9999998766543333333
No 139
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=27.23 E-value=27 Score=29.88 Aligned_cols=46 Identities=15% Similarity=0.065 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSK 117 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~K 117 (375)
.+++.|..+|+-.|-.+. + .++||+.|+ +++..|+.+-..=|.|.|
T Consensus 112 ~L~~~~r~v~~l~~~~~~--s----~~eIA~~lg----is~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 112 SLPLERRNVLLLRDYYGF--S----YKEIAEMTG----LSLAKVKIELHRGRKETK 157 (161)
T ss_pred HCCHHHHHHhhhHHhcCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 477888888888777763 2 357899997 999988876554443333
No 140
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=27.13 E-value=30 Score=31.13 Aligned_cols=48 Identities=21% Similarity=0.386 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
..+++.+++|-.|-.+. ..++||+.|+ ++++.|+...+.=|++.+++.
T Consensus 136 l~~~~~~~v~l~~~~Gl------s~~EIA~~lg----iS~~tV~r~l~~aR~~l~~~l 183 (185)
T PF07638_consen 136 LDPRQRRVVELRFFEGL------SVEEIAERLG----ISERTVRRRLRRARAWLRREL 183 (185)
T ss_pred cCHHHHHHHHHHHHCCC------CHHHHHHHHC----cCHHHHHHHHHHHHHHHHHHh
Confidence 45555566666555551 2357888886 999999977766665555443
No 141
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=27.03 E-value=73 Score=26.29 Aligned_cols=51 Identities=25% Similarity=0.349 Sum_probs=37.5
Q ss_pred ceEEEEecceeeeeccccchhhh---hcC--CceEEEecCCcceecccccccccccccc
Q 036145 317 ARSTVFINDVAFEVVAGPFNVRE---AFG--EDAVLINSSGQPVLTNEWGVTLQSLNHG 370 (375)
Q Consensus 317 a~~tVfIn~vafeV~~GpfnVr~---~FG--~davLihssG~pv~tne~Gvtl~sLqhG 370 (375)
..|+|.|||.+++++.+ ..|.+ .+| ...|-|=-.|+.||-++|.-++ |+.|
T Consensus 17 ~~m~I~VNG~~~~~~~~-~tl~~LL~~l~~~~~~vAVevNg~iVpr~~w~~t~--L~eg 72 (84)
T PRK06083 17 VLITISINDQSIQVDIS-SSLAQIIAQLSLPELGCVFAINNQVVPRSEWQSTV--LSSG 72 (84)
T ss_pred ceEEEEECCeEEEcCCC-CcHHHHHHHcCCCCceEEEEECCEEeCHHHcCccc--CCCC
Confidence 46999999999999874 55663 344 3455666689999999998764 4444
No 142
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=26.98 E-value=38 Score=29.90 Aligned_cols=49 Identities=16% Similarity=0.160 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
.+++.|.++++-.|-.+. + .++||+.|+ +++..|++....=|.|.|+..
T Consensus 131 ~Lp~~~r~v~~l~~~~g~--s----~~EIA~~lg----is~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 131 RLPPRTGRVFMMREWLEL--E----TEEICQELQ----ITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 366778888887776663 2 357899997 999999976654444444433
No 143
>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=26.30 E-value=54 Score=28.06 Aligned_cols=39 Identities=23% Similarity=0.470 Sum_probs=24.0
Q ss_pred HHHHHHHHhcCCCCCCHH-HHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhhHhH
Q 036145 68 IRILESIFNSGMVNPPRD-EIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHIQNS 126 (375)
Q Consensus 68 L~~LE~~F~~~~~yPs~~-eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~q~~ 126 (375)
+++..-+|+.|+ ||..+ .|.. + -|||-|+|+++++...-
T Consensus 14 vRiIk~LyqsnP-yP~~~GTr~a--R-----------------RnRRRRWR~rq~QI~~l 53 (91)
T PF00424_consen 14 VRIIKILYQSNP-YPSPEGTRQA--R-----------------RNRRRRWRARQRQIRAL 53 (91)
T ss_dssp HHHHHHHHHTS--S--S-S-HHH--H-----------------HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcccc-CCCCCCcccc--c-----------------cchhhhHHHHHHHHHHH
Confidence 456677888996 88754 2221 1 28999999999888753
No 144
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=25.86 E-value=38 Score=30.23 Aligned_cols=36 Identities=19% Similarity=0.118 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceee
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFY 107 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkv 107 (375)
.+.++|.++|+-.|-.+. ..++||+.|+ +++..|++
T Consensus 134 ~Lp~~~r~i~~l~~~~g~------s~~EIA~~lg----~s~~tV~~ 169 (192)
T PRK09643 134 RLPVEQRAALVAVDMQGY------SVADAARMLG----VAEGTVKS 169 (192)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHHC----cCHHHHHH
Confidence 356778888887776663 2357899997 99999954
No 145
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=25.82 E-value=40 Score=30.38 Aligned_cols=48 Identities=13% Similarity=0.048 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
+.+.|.++|+-.|-.+. + .++||+.|+ +++..|++....=|.+.|+..
T Consensus 140 Lp~~~r~v~~L~~~eg~--s----~~EIA~~lg----is~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 140 LPEQIGRVFMMREFLDF--E----IDDICTELT----LTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CCHHHHHHHHHHHHcCC--C----HHHHHHHHC----cCHHHHHHHHHHHHHHHHHHH
Confidence 55566666666666653 2 357899997 999999987654444444443
No 146
>PF06312 Neurexophilin: Neurexophilin
Probab=25.62 E-value=48 Score=32.16 Aligned_cols=34 Identities=29% Similarity=0.399 Sum_probs=26.3
Q ss_pred CCCcceEEEEecc---eeeeecc-ccchhhhhcCCceEEEecCC
Q 036145 313 HGGAARSTVFIND---VAFEVVA-GPFNVREAFGEDAVLINSSG 352 (375)
Q Consensus 313 ~~~~a~~tVfIn~---vafeV~~-GpfnVr~~FG~davLihssG 352 (375)
.|++++|+.+-|| |-|-... |-.+|+ +.|||++=
T Consensus 83 ag~~G~V~Dh~NGTYtv~F~L~W~G~v~vs------V~LVHPSE 120 (219)
T PF06312_consen 83 AGAAGKVTDHGNGTYTVSFPLLWPGQVSVS------VSLVHPSE 120 (219)
T ss_pred ccceEEEEECCCCeEEEEEEeecCceEEEE------EEEEcchh
Confidence 3567899999999 6666655 888887 88999864
No 147
>PRK09480 slmA division inhibitor protein; Provisional
Probab=25.57 E-value=51 Score=28.45 Aligned_cols=36 Identities=17% Similarity=0.333 Sum_probs=27.8
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcch
Q 036145 72 ESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRK 113 (375)
Q Consensus 72 E~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRR 113 (375)
.++|.... . ......+||++.+ ++...++.+|.|+.
T Consensus 20 ~~l~~~~~-G-~~~ti~~Ia~~ag----vs~gt~Y~~F~~K~ 55 (194)
T PRK09480 20 AQMLESPP-G-ERITTAKLAARVG----VSEAALYRHFPSKA 55 (194)
T ss_pred HHHHHhcC-C-CccCHHHHHHHhC----CCHhHHHHHCCCHH
Confidence 44565543 4 5667788999987 99999999999966
No 148
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=25.55 E-value=36 Score=29.99 Aligned_cols=30 Identities=13% Similarity=0.076 Sum_probs=22.1
Q ss_pred HHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 88 RRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 88 ~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
++||+.|+ +++..|++..+.=|.|.|+..+
T Consensus 158 ~eIA~~lg----is~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 158 EDIASVMQ----CPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred HHHHHHHC----CCHHHHHHHHHHHHHHHHHHHH
Confidence 57888887 9999998777665655555544
No 149
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=25.19 E-value=42 Score=31.87 Aligned_cols=50 Identities=12% Similarity=0.179 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
.+.+.+.++|+..|..+. ..++||+.|+ +++..|+.....=|.|.|+..+
T Consensus 212 ~L~~~~r~vl~l~~~~~~------s~~eIA~~lg----is~~tV~~~~~ra~~~Lr~~l~ 261 (268)
T PRK06288 212 TLPEREKKVLILYYYEDL------TLKEIGKVLG----VTESRISQLHTKAVLQLRAKLA 261 (268)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHHC----cCHHHHHHHHHHHHHHHHHHHH
Confidence 577788888888887764 2457899987 9999998665554444444443
No 150
>PRK10651 transcriptional regulator NarL; Provisional
Probab=25.16 E-value=40 Score=28.41 Aligned_cols=50 Identities=24% Similarity=0.302 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRH 122 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~ 122 (375)
.+|+.+.++|+-+. .+ ++. ++||++|+ ++++.|++..+|=|.|..-+-|.
T Consensus 155 ~Lt~rE~~vl~~l~-~g--~~~----~~ia~~l~----is~~tV~~~~~~l~~Kl~~~~~~ 204 (216)
T PRK10651 155 QLTPRERDILKLIA-QG--LPN----KMIARRLD----ITESTVKVHVKHMLKKMKLKSRV 204 (216)
T ss_pred cCCHHHHHHHHHHH-cC--CCH----HHHHHHcC----CCHHHHHHHHHHHHHHcCCCCHH
Confidence 49999999998765 43 232 57888886 99999998888777776654443
No 151
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=24.94 E-value=38 Score=30.00 Aligned_cols=46 Identities=20% Similarity=0.175 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRH 122 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~ 122 (375)
.+++.+.++|.. |-.+. . -++||+.|+ ++...|++ |..|.|++.|+
T Consensus 155 ~L~~~~r~vl~l-~~e~~--s----~~EIA~~lg----is~~tV~~----~l~rar~~Lr~ 200 (208)
T PRK08295 155 LLSELEKEVLEL-YLDGK--S----YQEIAEELN----RHVKSIDN----ALQRVKRKLEK 200 (208)
T ss_pred hCCHHHHHHHHH-HHccC--C----HHHHHHHHC----CCHHHHHH----HHHHHHHHHHH
Confidence 455666666666 44442 2 357898887 99999975 55555555544
No 152
>PLN02917 CMP-KDO synthetase
Probab=24.87 E-value=41 Score=32.91 Aligned_cols=27 Identities=41% Similarity=0.444 Sum_probs=14.5
Q ss_pred CCCCCCCCCCCCCCC--------CCccccccCCCc
Q 036145 148 PSSSSSSSEKSSPTT--------GSIKRLSLSSPN 174 (375)
Q Consensus 148 ~sssssss~~sS~~~--------~~~~~~~~~~~~ 174 (375)
||||||||+.||.|. .....+.+|+++
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 36 (293)
T PLN02917 2 PSSSSSSSSSSSTKSWIVHGIVAGAAIAAAIGAGA 36 (293)
T ss_pred CcccCCccccccchhHHhhhhcccccceeeccCch
Confidence 455555555566554 233445566665
No 153
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=24.74 E-value=63 Score=36.10 Aligned_cols=63 Identities=24% Similarity=0.289 Sum_probs=43.2
Q ss_pred CCCCCCCCCCCH-HHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCC----CceeeccCcchhhhhhhhhhhH
Q 036145 54 SPEPKPRWNPKP-EQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGD----ANVFYWFQNRKSRSKHKLRHIQ 124 (375)
Q Consensus 54 sp~~R~Rt~FT~-eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE----~qVkvWFQNRRAK~KRk~r~~q 124 (375)
-||+-+|..|.| +|+--|...|... -++++..+|.+.. .++ +.-++||||-|+--+|++.+-.
T Consensus 352 H~Pp~pRa~~~P~~ql~~lq~~fs~~-------~~qQv~d~~~rl~-~sqav~gr~~~N~~q~~~s~~~raE~~~~ 419 (769)
T KOG3755|consen 352 HPPPYPRAQLKPGFQLNLLQSEFSEP-------IYQQVRDELKRLD-ESQAVFGRVAFNRTQGLLSEILRAEEDPH 419 (769)
T ss_pred CCCCCchhhcCccccchhhhhhhccH-------HHHHHHHHHHHhh-hhhhhhhhhhhhhhhhhhccccchhcccc
Confidence 466777999888 6999999999872 3455555554321 222 2235899999999888776553
No 154
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=24.56 E-value=38 Score=29.23 Aligned_cols=45 Identities=13% Similarity=0.017 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRS 116 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~ 116 (375)
.+++.|.++|.-.|-.+. ..++||+.|+ +++..|+.+...=|.|.
T Consensus 112 ~L~~~~r~v~~l~~~~g~------s~~eIA~~lg----is~~tV~~~l~Rar~~L 156 (164)
T PRK12547 112 LLSADQREAIILIGASGF------SYEDAAAICG----CAVGTIKSRVSRARNRL 156 (164)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHhC----CCHHHHHHHHHHHHHHH
Confidence 456667777777666663 2457899997 99999987664433333
No 155
>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=24.36 E-value=38 Score=28.79 Aligned_cols=46 Identities=22% Similarity=0.293 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
.+++.|.++|.-.|-.+. + .++||+.|+ +++..|+.. ..|-|++.|
T Consensus 122 ~L~~~~r~vl~l~~~~g~--s----~~eIA~~l~----is~~tv~~~----l~ra~~~Lr 167 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQNL--P----IAEVARILG----KTEGAVKIL----QFRAIKKLA 167 (170)
T ss_pred hCCHHHHHHHHHHHhcCC--C----HHHHHHHHC----CCHHHHHHH----HHHHHHHHH
Confidence 566667777777665553 2 357888887 999999754 444444444
No 156
>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=24.33 E-value=59 Score=23.34 Aligned_cols=13 Identities=23% Similarity=0.281 Sum_probs=11.4
Q ss_pred CCCHHHHHHHHHH
Q 036145 62 NPKPEQIRILESI 74 (375)
Q Consensus 62 ~FT~eQL~~LE~~ 74 (375)
.||++|+.+||.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 5999999999964
No 157
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=24.31 E-value=44 Score=29.14 Aligned_cols=38 Identities=13% Similarity=0.063 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeecc
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWF 109 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWF 109 (375)
.++++|.+++.-.|-.+. ..++||+.|+ +++..|+++.
T Consensus 119 ~L~~~~r~i~~l~~~~g~------s~~EIA~~lg----is~~tV~~~l 156 (172)
T PRK09651 119 GLNGKTREAFLLSQLDGL------TYSEIAHKLG----VSVSSVKKYV 156 (172)
T ss_pred hCCHHHhHHhhhhhccCC------CHHHHHHHhC----CCHHHHHHHH
Confidence 567777777777666663 2467899997 9999998776
No 158
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=24.23 E-value=44 Score=29.93 Aligned_cols=49 Identities=10% Similarity=0.036 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
.+.+.|.++|.-.|-.+. + .++||+.|+ +++..|+++...=|.+.|+..
T Consensus 116 ~Lp~~~r~i~~L~~~~g~--s----~~EIA~~Lg----is~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 116 QLPDDQREAIILVGASGF--A----YEEAAEICG----CAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 346667777777666663 2 357899997 999999987655554444443
No 159
>PF11033 ComJ: Competence protein J (ComJ); InterPro: IPR020354 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. The proteins in this entry play a role in the competence of cells to be transformed. They inhibit the activity of the DNA-entry nuclease. DNA-entry nuclease inhibitor is a subunit of a 75 kDa protein complex, which governs binding and entry of donor DNA. The complex is a tetramer of two subunits of the DNA-entry nuclease and two subunits of a competence-specific protein ComJ. Only the complex is able to bind ds- and ss-DNA []. It is found in the plasma membrane.
Probab=24.17 E-value=99 Score=27.80 Aligned_cols=61 Identities=21% Similarity=0.327 Sum_probs=38.7
Q ss_pred ccCCCccCCCCccC--CCCcceEEEEecc------------eeeeeccccchhhhhcCCceEEEecCCcceecccccccc
Q 036145 299 IQGAGVEESDPVVG--HGGAARSTVFIND------------VAFEVVAGPFNVREAFGEDAVLINSSGQPVLTNEWGVTL 364 (375)
Q Consensus 299 ~qg~~~~~~~~~~~--~~~~a~~tVfIn~------------vafeV~~GpfnVr~~FG~davLihssG~pv~tne~Gvtl 364 (375)
.||+......++.+ +..++.|+|-+|. |||+|.-+.++|..++.+. +.+ +||-.+|.++.
T Consensus 30 ~qG~a~~~g~VsFeai~D~~a~V~v~~~~~~~~~~~~R~i~VPF~V~~d~i~V~Svls~~-~~~-----~ip~G~Y~Lv~ 103 (125)
T PF11033_consen 30 EQGYAWADGAVSFEAISDGAAEVEVTLNEKFEAEDAQRTISVPFTVKGDGIEVSSVLSEK-LSF-----DIPKGDYQLVF 103 (125)
T ss_pred hCcceecCCcEEEeeecCCeEEEEEEeCCcccCccceEEEEeeEEEcCCCEEEEEeecCc-EEE-----ecCCCcEEEEE
Confidence 36655444344444 2335677777776 8999999999999888885 333 34444555444
Q ss_pred c
Q 036145 365 Q 365 (375)
Q Consensus 365 ~ 365 (375)
+
T Consensus 104 ~ 104 (125)
T PF11033_consen 104 Q 104 (125)
T ss_pred E
Confidence 3
No 160
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.00 E-value=48 Score=28.63 Aligned_cols=40 Identities=13% Similarity=0.066 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcee
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVF 106 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVk 106 (375)
.+++||+++-.+.|+.+- -...-..++||++|+ .++..|.
T Consensus 2 SLn~eq~~~Tk~elqan~-el~~LS~~~iA~~Ln----~t~~~le 41 (97)
T COG4367 2 SLNPEQKQRTKQELQANF-ELCPLSDEEIATALN----WTEVKLE 41 (97)
T ss_pred CCCHHHHHHHHHHHHHhh-hhccccHHHHHHHhC----CCHHHHH
Confidence 478999988777777774 355556788999997 7765543
No 161
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=24.00 E-value=48 Score=28.72 Aligned_cols=46 Identities=11% Similarity=0.148 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKH 118 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KR 118 (375)
+++++.++++-.|-.+. .-++||+.|+ +++..|+.+...=|.|.|+
T Consensus 120 L~~~~r~i~~l~~~~~~------s~~EIA~~lg----is~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 120 LNEKYKTVLVLYYYEQY------SYKEMSEILN----IPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred CCHHHHHHHHHHHHcCC------CHHHHHHHhC----CCHHHHHHHHHHHHHHHHH
Confidence 34444455555554442 2357888887 9999998766544444333
No 162
>PF05132 RNA_pol_Rpc4: RNA polymerase III RPC4; InterPro: IPR007811 This family comprises a specific subunit for Pol III, the tRNA specific polymerase.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006383 transcription from RNA polymerase III promoter, 0005666 DNA-directed RNA polymerase III complex
Probab=23.54 E-value=87 Score=27.26 Aligned_cols=31 Identities=29% Similarity=0.491 Sum_probs=27.7
Q ss_pred ceEEEEecceeeeeccccchhhhhcCCceEEEec
Q 036145 317 ARSTVFINDVAFEVVAGPFNVREAFGEDAVLINS 350 (375)
Q Consensus 317 a~~tVfIn~vafeV~~GpfnVr~~FG~davLihs 350 (375)
+++++-|+|+.|+|-.|- ...|=+++|.|+.
T Consensus 78 Gkv~l~iG~~~~dV~~G~---~~~FlQevv~i~~ 108 (131)
T PF05132_consen 78 GKVTLKIGGVVFDVSPGT---QCSFLQEVVAIDE 108 (131)
T ss_pred CcEEEEECCEEEEecCCC---CCCchheEEEeec
Confidence 589999999999999985 4469999999998
No 163
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=23.53 E-value=37 Score=29.81 Aligned_cols=49 Identities=12% Similarity=0.213 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
.+++.|.+++.-.|-.+. ..++||+.|+ +++..|+.....=|.|.|+..
T Consensus 122 ~L~~~~r~i~~l~~~~g~------s~~EIA~~lg----is~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 122 ELNESNRQVFKYKVFYNL------TYQEISSVMG----ITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 456677777777666663 2357899997 999999986654444444433
No 164
>PF08144 CPL: CPL (NUC119) domain; InterPro: IPR012959 This C-terminal domain is found in Penguin-like proteins (CPL) and is associated with Pumilio like repeats [].; GO: 0003723 RNA binding
Probab=23.32 E-value=1.2e+02 Score=27.27 Aligned_cols=39 Identities=18% Similarity=0.238 Sum_probs=29.1
Q ss_pred CCCCCCCCHHHHHHHHHHH-hcCCCCCCHHHHHHHHHHHh
Q 036145 57 PKPRWNPKPEQIRILESIF-NSGMVNPPRDEIRRIRAQLQ 95 (375)
Q Consensus 57 ~R~Rt~FT~eQL~~LE~~F-~~~~~yPs~~eR~qLA~~L~ 95 (375)
+|-+..|+|+++++|++.- +...+.+...+|++|.+.+.
T Consensus 16 ~~d~~~f~p~~i~~L~~~d~~~tSKKd~~~Rr~ELl~~~s 55 (148)
T PF08144_consen 16 PRDPRYFSPEIIKLLKEGDRNATSKKDPEVRRKELLEAIS 55 (148)
T ss_pred CCCcccCCHHHHHHHhhhcccccccCCHHHHHHHHHHHhh
Confidence 5678889999999999887 22223477778888877664
No 165
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=23.04 E-value=43 Score=29.67 Aligned_cols=39 Identities=13% Similarity=0.110 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccC
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQ 110 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQ 110 (375)
.++++|..+|.-.|-.+. + .++||+.|+ ++...|+..-+
T Consensus 131 ~L~~~~r~i~~l~~~~g~--s----~~EIAe~lg----is~~~V~~~l~ 169 (189)
T PRK06811 131 DLEKLDREIFIRRYLLGE--K----IEEIAKKLG----LTRSAIDNRLS 169 (189)
T ss_pred hCCHHHHHHHHHHHHccC--C----HHHHHHHHC----CCHHHHHHHHH
Confidence 466777777776665553 2 357888887 89988875443
No 166
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.97 E-value=50 Score=30.27 Aligned_cols=50 Identities=10% Similarity=0.041 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
.+++.|.++++-.|-.+. + .++||+.|+ +++..|+++.+.=|.+.|+..+
T Consensus 148 ~L~~~~r~v~~L~~~~g~--s----~~EIAe~lg----is~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 148 GLPAKYARVFMMREFIEL--E----TNEICHAVD----LSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----cCHHHHHHHHHHHHHHHHHHHH
Confidence 455666667776666663 2 357888887 9999999776655555554443
No 167
>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=22.96 E-value=23 Score=27.98 Aligned_cols=17 Identities=24% Similarity=0.597 Sum_probs=15.4
Q ss_pred HHHHHHHhhcCCCCCCceeec
Q 036145 88 RRIRAQLQEYGQVGDANVFYW 108 (375)
Q Consensus 88 ~qLA~~L~~~g~LtE~qVkvW 108 (375)
.+||++|+ +++.+|+.|
T Consensus 26 kdIA~~Lg----vs~~tIr~W 42 (60)
T PF10668_consen 26 KDIAEKLG----VSESTIRKW 42 (60)
T ss_pred HHHHHHHC----CCHHHHHHH
Confidence 57999997 999999988
No 168
>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=22.86 E-value=48 Score=31.53 Aligned_cols=51 Identities=24% Similarity=0.353 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRHI 123 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~~ 123 (375)
+.+.|.+++.-.|..+. ..++||+.|+ +++..|+.+...=|.+.|+..+..
T Consensus 162 Lp~~~R~v~~L~~~eg~------S~~EIA~~Lg----is~~TVk~rl~RAr~~Lr~~l~~~ 212 (244)
T TIGR03001 162 LSERERHLLRLHFVDGL------SMDRIGAMYQ----VHRSTVSRWVAQARERLLERTRRR 212 (244)
T ss_pred CCHHHHHHHHHHHHcCC------CHHHHHHHHC----cCHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455666666665553 2467899997 999999999877666666655443
No 169
>PTZ00183 centrin; Provisional
Probab=22.82 E-value=2.1e+02 Score=23.66 Aligned_cols=37 Identities=11% Similarity=-0.008 Sum_probs=25.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCC----CCCCHHHHHHHHH
Q 036145 56 EPKPRWNPKPEQIRILESIFNSGM----VNPPRDEIRRIRA 92 (375)
Q Consensus 56 ~~R~Rt~FT~eQL~~LE~~F~~~~----~yPs~~eR~qLA~ 92 (375)
.+-.|..++++|+++|+++|..-. .+.+..+-..+.+
T Consensus 4 ~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~ 44 (158)
T PTZ00183 4 RRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMR 44 (158)
T ss_pred cccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHH
Confidence 355678899999999999998532 2455544444333
No 170
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=22.57 E-value=20 Score=30.83 Aligned_cols=30 Identities=13% Similarity=0.079 Sum_probs=21.7
Q ss_pred HHHHHHHHhhcCCCCCCceeeccCcchhhhhhhh
Q 036145 87 IRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKL 120 (375)
Q Consensus 87 R~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~ 120 (375)
-++||+.|+ +++..|+..+..=|.|.|+..
T Consensus 139 ~~eIA~~lg----~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 139 QKEIAEILN----IPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 468899997 999999988755555544443
No 171
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=22.31 E-value=42 Score=30.37 Aligned_cols=51 Identities=10% Similarity=-0.042 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLRH 122 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r~ 122 (375)
.+.+.|.+++.-.|-.+. ..++||+.|+ +++..|+++...=|.+.|+...+
T Consensus 133 ~Lp~~~r~v~~l~~~~g~------s~~EIAe~lg----is~~tV~~~l~Rar~~Lr~~l~~ 183 (196)
T PRK12535 133 ALPPERREALILTQVLGY------TYEEAAKIAD----VRVGTIRSRVARARADLIAATAT 183 (196)
T ss_pred cCCHHHHHHhhhHHHhCC------CHHHHHHHhC----CCHHHHHHHHHHHHHHHHHHhcc
Confidence 466667777777776663 2357899997 99999998775444444444443
No 172
>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=22.23 E-value=31 Score=30.51 Aligned_cols=49 Identities=10% Similarity=0.057 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
+.+.|.+++.-.|-.+. ..++||+.|+ +++..|+++...=|.+.|+...
T Consensus 132 Lp~~~r~i~~L~~~~g~------s~~EIA~~lg----is~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 132 LPEEFRQAVYLADVEGF------AYKEIAEIMG----TPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred CCHHHhhheeehhhcCC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444442 3468999997 9999999887666666555544
No 173
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=22.13 E-value=47 Score=28.30 Aligned_cols=38 Identities=13% Similarity=0.018 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccC
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQ 110 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQ 110 (375)
+.+++.++|+-.|-.+. ..++||+.|+ +++..|+..-.
T Consensus 106 L~~~~r~v~~l~~~~~~------s~~eIA~~lg----is~~tv~~~l~ 143 (159)
T PRK12527 106 LPPACRDSFLLRKLEGL------SHQQIAEHLG----ISRSLVEKHIV 143 (159)
T ss_pred CCHHHHHHHHHHHHcCC------CHHHHHHHhC----CCHHHHHHHHH
Confidence 56666677776666653 2357888887 99998886554
No 174
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=22.00 E-value=60 Score=24.27 Aligned_cols=41 Identities=17% Similarity=0.311 Sum_probs=24.0
Q ss_pred EEEEecceeeeeccccchhh---hhcCCc-eEEEecCCcceecccc
Q 036145 319 STVFINDVAFEVVAGPFNVR---EAFGED-AVLINSSGQPVLTNEW 360 (375)
Q Consensus 319 ~tVfIn~vafeV~~GpfnVr---~~FG~d-avLihssG~pv~tne~ 360 (375)
|+|.|||..++++.| ..|. +.+|-+ .+.|=-.|+.|+-.+|
T Consensus 1 m~i~vNg~~~~~~~~-~tl~~ll~~l~~~~~~~v~vN~~~v~~~~~ 45 (65)
T PRK06944 1 MDIQLNQQTLSLPDG-ATVADALAAYGARPPFAVAVNGDFVARTQH 45 (65)
T ss_pred CEEEECCEEEECCCC-CcHHHHHHhhCCCCCeEEEECCEEcCchhc
Confidence 579999999999876 3444 444332 2333334555544443
No 175
>PF09136 Glucodextran_B: Glucodextranase, domain B; InterPro: IPR015219 The glucodextranase B domain adopts a structure consisting of seven/eight-strand antiparallel beta-sheets, in a Greek-key topology, similar to the immunoglobulin beta-sandwich fold. It acts as a cell wall anchor, interacting with the S-layer present in the cell wall of Gram-positive bacteria by hydrophobic interactions. In glucodextranase, domain B is buried in the S-layer, and a flexible linker located between domain B and the catalytic unit confers motion to the catalytic unit, which is capable of efficient hydrolysis of the substrates located close to the cell surface []. ; PDB: 1UG9_A 1ULV_A.
Probab=21.64 E-value=59 Score=27.60 Aligned_cols=23 Identities=26% Similarity=0.185 Sum_probs=16.1
Q ss_pred CCCcceEEEEecceeeeeccccc
Q 036145 313 HGGAARSTVFINDVAFEVVAGPF 335 (375)
Q Consensus 313 ~~~~a~~tVfIn~vafeV~~Gpf 335 (375)
...++++-|.+||..||.|+-|-
T Consensus 24 tt~a~kv~~~vng~~~e~pvt~~ 46 (89)
T PF09136_consen 24 TTNAAKVYVSVNGNKTEAPVTPA 46 (89)
T ss_dssp EE-SSEEEEEETTEEEEE--B--
T ss_pred cccceEEEEEeCCcEEecceeec
Confidence 44578999999999999998753
No 176
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=21.60 E-value=1.1e+02 Score=23.07 Aligned_cols=43 Identities=12% Similarity=0.143 Sum_probs=30.7
Q ss_pred EEEEecceeeeeccccchhh---hhcCC--ceEEEecCCcceeccccccc
Q 036145 319 STVFINDVAFEVVAGPFNVR---EAFGE--DAVLINSSGQPVLTNEWGVT 363 (375)
Q Consensus 319 ~tVfIn~vafeV~~GpfnVr---~~FG~--davLihssG~pv~tne~Gvt 363 (375)
|+|.|||.++++.. .+|. +.+|- +.+.|=-.|+.|+-++|.=+
T Consensus 1 m~i~~Ng~~~~~~~--~tl~~Ll~~l~~~~~~vavavN~~iv~~~~~~~~ 48 (65)
T PRK06488 1 MKLFVNGETLQTEA--TTLALLLAELDYEGNWLATAVNGELVHKEARAQF 48 (65)
T ss_pred CEEEECCeEEEcCc--CcHHHHHHHcCCCCCeEEEEECCEEcCHHHcCcc
Confidence 58999999999943 4555 34443 35556667889998888764
No 177
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=21.21 E-value=87 Score=25.25 Aligned_cols=35 Identities=11% Similarity=0.174 Sum_probs=24.2
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCce
Q 036145 68 IRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANV 105 (375)
Q Consensus 68 L~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qV 105 (375)
.+.+|+++.+|++ .+.+.++.+..+.++ ..+|++|
T Consensus 19 r~~~~k~l~~NPp-ine~mir~M~~QMG~--kpSekqi 53 (64)
T PF03672_consen 19 RKYMEKQLKENPP-INEKMIRAMMMQMGR--KPSEKQI 53 (64)
T ss_pred HHHHHHHHHHCCC-CCHHHHHHHHHHhCC--CccHHHH
Confidence 3568899999873 688877777777763 2455554
No 178
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=21.18 E-value=45 Score=28.86 Aligned_cols=46 Identities=7% Similarity=0.086 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhh
Q 036145 63 PKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKH 118 (375)
Q Consensus 63 FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KR 118 (375)
+++.+.++|.-.|-.+. ..++||+.|+ ++...|+++...=|.|.|+
T Consensus 137 L~~~~r~il~l~~~~~~------s~~eIA~~lg----is~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 137 LPEKYRTVIVLKYIEDL------SLKEISEILD----LPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCHHHHHHhhhHHhhCC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 44555555555544442 2357888887 9998887665544444443
No 179
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=21.00 E-value=46 Score=27.57 Aligned_cols=45 Identities=22% Similarity=0.181 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSK 117 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~K 117 (375)
.+|+.+.++|+- +.++. . .++||++|+ ++++.|+.|.+|=|.|..
T Consensus 149 ~lt~~e~~vl~l-~~~g~--~----~~~Ia~~l~----~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEGY--T----NRDIAEQLS----ISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCCC--C----HHHHHHHhC----CCHHHHHHHHHHHHHHhC
Confidence 489999999998 66663 3 468899986 999999998777555543
No 180
>PF13364 BetaGal_dom4_5: Beta-galactosidase jelly roll domain; PDB: 1TG7_A 1XC6_A 3OGS_A 3OGV_A 3OGR_A 3OG2_A.
Probab=21.00 E-value=1.2e+02 Score=25.65 Aligned_cols=25 Identities=36% Similarity=0.599 Sum_probs=17.4
Q ss_pred CCcceEEEEecc-------------eeeeeccccchhh
Q 036145 314 GGAARSTVFIND-------------VAFEVVAGPFNVR 338 (375)
Q Consensus 314 ~~~a~~tVfIn~-------------vafeV~~GpfnVr 338 (375)
|.+.+..||||| .-|.||.|=++-+
T Consensus 60 g~~~~~~vwVNG~~~G~~~~~~g~q~tf~~p~~il~~~ 97 (111)
T PF13364_consen 60 GNAFRASVWVNGWFLGSYWPGIGPQTTFSVPAGILKYG 97 (111)
T ss_dssp STTEEEEEEETTEEEEEEETTTECCEEEEE-BTTBTTC
T ss_pred CCceEEEEEECCEEeeeecCCCCccEEEEeCceeecCC
Confidence 446789999999 4677777655553
No 181
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=20.61 E-value=28 Score=30.04 Aligned_cols=27 Identities=11% Similarity=0.128 Sum_probs=18.7
Q ss_pred HHHHHHHHhhcCCCCCCceeeccCcchhhhh
Q 036145 87 IRRIRAQLQEYGQVGDANVFYWFQNRKSRSK 117 (375)
Q Consensus 87 R~qLA~~L~~~g~LtE~qVkvWFQNRRAK~K 117 (375)
.++||+.|+ +++..|+.+...=|.|.|
T Consensus 145 ~~eIA~~l~----is~~~V~~~l~ra~~~l~ 171 (176)
T PRK09638 145 YEEIAKMLN----IPEGTVKSRVHHGIKQLR 171 (176)
T ss_pred HHHHHHHHC----CChhHHHHHHHHHHHHHH
Confidence 467899997 999999877643333333
No 182
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=20.53 E-value=52 Score=28.96 Aligned_cols=45 Identities=13% Similarity=0.153 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRS 116 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~ 116 (375)
.+.++|..+++-.|-.+. ..++||+.|+ +++..|+.....-+.+.
T Consensus 127 ~Lp~~~R~v~~L~~~~g~------s~~EIA~~lg----is~~tVk~~l~rAl~~~ 171 (178)
T PRK12529 127 TLRPRVKQAFLMATLDGM------KQKDIAQALD----IALPTVKKYIHQAYVTC 171 (178)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHHHHHHHHHH
Confidence 466777777777776663 2357899997 99999998776444433
No 183
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=20.47 E-value=58 Score=27.46 Aligned_cols=45 Identities=13% Similarity=0.141 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSK 117 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~K 117 (375)
.+|+.+.++|+-+... | .+++||++|+ ++++.|++..+|=|.|..
T Consensus 137 ~Lt~~E~~il~~l~~g---~----~~~~Ia~~l~----~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQG---M----AVKEIAAELG----LSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCC---C----CHHHHHHHhC----CCHHHHHHHHHHHHHHhC
Confidence 5899999999886653 2 4678999986 899999876665555443
No 184
>PRK14711 ureE urease accessory protein UreE; Provisional
Probab=20.25 E-value=39 Score=32.08 Aligned_cols=10 Identities=40% Similarity=1.149 Sum_probs=7.6
Q ss_pred CCCCCccccc
Q 036145 5 NRNWPSMFKS 14 (375)
Q Consensus 5 nrhWPsmfks 14 (375)
|||||-+|+-
T Consensus 114 NRH~p~~i~~ 123 (191)
T PRK14711 114 NQHWPAVVKE 123 (191)
T ss_pred CCcceeEEcC
Confidence 8888888863
No 185
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=20.21 E-value=53 Score=30.73 Aligned_cols=52 Identities=12% Similarity=0.038 Sum_probs=39.4
Q ss_pred CCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhhhhhhhh
Q 036145 59 PRWNPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSRSKHKLR 121 (375)
Q Consensus 59 ~Rt~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK~KRk~r 121 (375)
....+|+.|+++|.-. ..+. .-.+||+.|+ |+++.|+.+..|=|.|.+.+-|
T Consensus 168 ~~~~Lt~re~evl~~~-a~G~------t~~eIa~~l~----is~~Tv~~~l~~~~~kl~~~~~ 219 (232)
T TIGR03541 168 EAGVLSEREREVLAWT-ALGR------RQADIAAILG----ISERTVENHLRSARRKLGVATT 219 (232)
T ss_pred hhccCCHHHHHHHHHH-HCCC------CHHHHHHHHC----cCHHHHHHHHHHHHHHHCCCCH
Confidence 3457899999999986 4553 2357898997 9999999988877777665444
No 186
>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=20.08 E-value=52 Score=30.10 Aligned_cols=44 Identities=9% Similarity=0.159 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccCcchhh
Q 036145 62 NPKPEQIRILESIFNSGMVNPPRDEIRRIRAQLQEYGQVGDANVFYWFQNRKSR 115 (375)
Q Consensus 62 ~FT~eQL~~LE~~F~~~~~yPs~~eR~qLA~~L~~~g~LtE~qVkvWFQNRRAK 115 (375)
.+++.|.++|+..|..+. ..++||+.|+ ++...|+.+...=|.|
T Consensus 175 ~L~~~~r~il~l~y~~~~------s~~eIA~~lg----is~~tV~~~~~ra~~~ 218 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEEL------NLKEIGEVLG----LTESRVSQIHSQALKK 218 (224)
T ss_pred hCCHHHHHHHHHHHhCCC------CHHHHHHHhC----CCHHHHHHHHHHHHHH
Confidence 467888888888887764 2367888887 8998887665433333
Done!