Query 047211
Match_columns 282
No_of_seqs 143 out of 588
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 08:50:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047211.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047211hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489 Transcription factor z 99.8 2.4E-20 5.3E-25 171.2 1.0 68 36-108 157-224 (261)
2 KOG0487 Transcription factor A 99.8 1.7E-19 3.7E-24 170.3 4.9 70 31-105 228-297 (308)
3 KOG0488 Transcription factor B 99.7 6.7E-19 1.4E-23 166.0 4.8 73 31-108 165-237 (309)
4 KOG0843 Transcription factor E 99.7 7.5E-19 1.6E-23 155.7 4.7 65 36-105 100-164 (197)
5 KOG0842 Transcription factor t 99.7 2E-18 4.3E-23 163.0 6.2 71 35-110 150-220 (307)
6 PF00046 Homeobox: Homeobox do 99.7 1.5E-17 3.2E-22 118.2 2.3 57 39-100 1-57 (57)
7 KOG0485 Transcription factor N 99.7 3.4E-17 7.4E-22 149.2 4.3 76 28-108 94-169 (268)
8 KOG0484 Transcription factor P 99.7 2.6E-17 5.5E-22 135.9 2.1 72 34-110 13-84 (125)
9 KOG0848 Transcription factor C 99.6 6.1E-17 1.3E-21 150.9 3.6 64 38-106 199-262 (317)
10 KOG0492 Transcription factor M 99.6 1.5E-16 3.3E-21 144.1 5.9 70 37-111 143-212 (246)
11 KOG0493 Transcription factor E 99.6 3.6E-16 7.9E-21 145.7 4.0 64 34-102 242-305 (342)
12 KOG2251 Homeobox transcription 99.6 8.7E-16 1.9E-20 139.5 5.2 68 33-105 32-99 (228)
13 KOG0850 Transcription factor D 99.6 7.2E-16 1.6E-20 140.9 4.4 63 37-104 121-183 (245)
14 smart00389 HOX Homeodomain. DN 99.6 1E-15 2.2E-20 107.5 2.8 56 39-99 1-56 (56)
15 cd00086 homeodomain Homeodomai 99.5 2.4E-15 5.2E-20 105.9 2.9 58 39-101 1-58 (59)
16 KOG0494 Transcription factor C 99.5 3.2E-15 6.9E-20 139.3 3.9 62 39-105 141-203 (332)
17 COG5576 Homeodomain-containing 99.5 5.9E-15 1.3E-19 127.8 5.0 73 30-107 43-115 (156)
18 KOG0483 Transcription factor H 99.5 6.4E-15 1.4E-19 132.0 3.3 65 39-108 51-115 (198)
19 TIGR01565 homeo_ZF_HD homeobox 99.5 3E-14 6.5E-19 105.6 5.7 52 39-95 2-57 (58)
20 KOG0844 Transcription factor E 99.5 7E-15 1.5E-19 139.6 2.3 62 38-104 181-242 (408)
21 KOG4577 Transcription factor L 99.5 2.6E-14 5.6E-19 134.9 4.7 64 37-105 166-229 (383)
22 KOG3802 Transcription factor O 99.4 1.6E-13 3.5E-18 133.2 5.0 62 37-103 293-354 (398)
23 KOG0491 Transcription factor B 99.4 2E-14 4.4E-19 126.6 -1.3 66 37-107 99-164 (194)
24 KOG0486 Transcription factor P 99.4 1.3E-13 2.8E-18 131.0 3.9 67 37-108 111-177 (351)
25 KOG0490 Transcription factor, 99.3 1.9E-12 4E-17 112.5 3.4 64 35-103 57-120 (235)
26 KOG0847 Transcription factor, 99.3 1.3E-12 2.8E-17 119.8 1.3 67 37-108 166-232 (288)
27 KOG0849 Transcription factor P 99.1 5.8E-11 1.3E-15 114.0 2.6 65 38-107 176-240 (354)
28 KOG1168 Transcription factor A 98.9 6.2E-10 1.4E-14 105.7 3.7 64 35-103 306-369 (385)
29 KOG2252 CCAAT displacement pro 98.2 8.2E-07 1.8E-11 89.9 3.2 59 36-99 418-476 (558)
30 KOG0775 Transcription factor S 98.2 9.3E-07 2E-11 83.5 3.4 50 45-99 183-232 (304)
31 KOG0490 Transcription factor, 98.2 1.3E-06 2.7E-11 76.1 3.9 66 33-103 148-213 (235)
32 KOG0774 Transcription factor P 97.7 4E-05 8.7E-10 72.6 4.0 66 38-107 188-255 (334)
33 PF05920 Homeobox_KN: Homeobox 97.5 1.9E-05 4.1E-10 54.5 -0.8 33 60-97 8-40 (40)
34 KOG1146 Homeobox protein [Gene 97.1 0.00024 5.2E-09 78.2 2.9 61 38-103 903-963 (1406)
35 KOG0773 Transcription factor M 95.7 0.0076 1.7E-07 57.0 2.9 67 38-108 239-307 (342)
36 KOG3623 Homeobox transcription 95.1 0.0096 2.1E-07 63.2 1.6 51 50-105 568-618 (1007)
37 PF04218 CENP-B_N: CENP-B N-te 90.4 0.17 3.8E-06 36.4 1.8 47 39-95 1-47 (53)
38 PF11569 Homez: Homeodomain le 90.4 0.056 1.2E-06 40.4 -0.8 43 49-96 9-51 (56)
39 PRK08053 sulfur carrier protei 85.5 1.5 3.4E-05 32.3 4.2 58 221-280 1-62 (66)
40 PRK07696 sulfur carrier protei 80.4 3.3 7.1E-05 31.0 4.3 58 221-280 1-63 (67)
41 PF05132 RNA_pol_Rpc4: RNA pol 79.2 4.3 9.4E-05 34.0 5.1 34 216-252 75-108 (131)
42 PRK05659 sulfur carrier protei 78.8 4.3 9.4E-05 29.5 4.4 57 221-279 1-61 (66)
43 cd06171 Sigma70_r4 Sigma70, re 76.6 1.2 2.6E-05 29.0 0.8 44 44-97 10-53 (55)
44 PRK05863 sulfur carrier protei 74.7 6 0.00013 29.2 4.2 57 221-280 1-61 (65)
45 PRK06944 sulfur carrier protei 68.9 9 0.0002 27.6 4.0 57 221-279 1-60 (65)
46 PRK06083 sulfur carrier protei 67.5 9.1 0.0002 30.3 4.0 60 219-280 17-80 (84)
47 KOG3755 SATB1 matrix attachmen 67.4 1.2 2.6E-05 47.0 -1.2 66 35-103 688-759 (769)
48 PF14453 ThiS-like: ThiS-like 66.3 13 0.00028 27.9 4.4 54 221-280 1-56 (57)
49 PF13510 Fer2_4: 2Fe-2S iron-s 63.4 6 0.00013 30.6 2.3 33 220-252 3-35 (82)
50 PRK07440 hypothetical protein; 60.1 22 0.00048 26.9 4.8 59 220-280 4-66 (70)
51 PF01527 HTH_Tnp_1: Transposas 59.6 5.5 0.00012 29.1 1.4 41 40-90 2-43 (76)
52 PRK03975 tfx putative transcri 59.2 10 0.00022 33.0 3.1 55 42-107 4-58 (141)
53 PF05660 DUF807: Coxiella burn 58.6 3.9 8.3E-05 35.5 0.5 38 231-268 11-48 (142)
54 PF04545 Sigma70_r4: Sigma-70, 58.3 5.6 0.00012 27.4 1.2 40 44-93 4-43 (50)
55 PF04967 HTH_10: HTH DNA bindi 58.0 7.6 0.00016 28.5 1.9 40 45-88 1-41 (53)
56 PRK09652 RNA polymerase sigma 54.7 9.5 0.00021 31.3 2.2 50 44-103 128-177 (182)
57 cd00569 HTH_Hin_like Helix-tur 53.5 16 0.00034 20.9 2.5 38 44-91 5-42 (42)
58 cd02413 40S_S3_KH K homology R 53.2 12 0.00027 29.2 2.5 26 67-92 50-75 (81)
59 PRK06488 sulfur carrier protei 53.1 29 0.00062 25.3 4.3 57 221-279 1-60 (65)
60 TIGR01683 thiS thiamine biosyn 51.6 26 0.00057 25.5 3.9 56 223-280 1-60 (64)
61 PF00577 Usher: Outer membrane 51.5 11 0.00023 37.9 2.4 39 218-256 98-145 (552)
62 COG3413 Predicted DNA binding 50.6 10 0.00022 33.8 1.8 41 44-88 155-196 (215)
63 KOG3623 Homeobox transcription 50.6 9.3 0.0002 41.6 1.8 66 37-107 625-690 (1007)
64 cd01668 TGS_RelA_SpoT TGS_RelA 49.9 28 0.0006 23.9 3.6 49 222-276 2-57 (60)
65 PF02267 Rib_hydrolayse: ADP-r 49.7 11 0.00024 35.5 2.1 36 218-256 147-196 (243)
66 PF00424 REV: REV protein (ant 48.9 21 0.00045 29.3 3.2 40 50-108 14-53 (91)
67 KOG1146 Homeobox protein [Gene 48.9 15 0.00032 42.1 3.1 63 35-102 702-764 (1406)
68 PRK09646 RNA polymerase sigma 48.5 14 0.0003 31.8 2.3 47 44-100 142-188 (194)
69 PRK09642 RNA polymerase sigma 48.4 13 0.00028 30.5 2.0 49 45-103 107-155 (160)
70 PRK06759 RNA polymerase factor 45.8 10 0.00023 30.7 1.1 47 44-100 106-152 (154)
71 PF08281 Sigma70_r4_2: Sigma-7 45.7 8.3 0.00018 26.6 0.4 41 44-94 10-50 (54)
72 PRK12519 RNA polymerase sigma 44.5 15 0.00032 31.3 1.8 48 45-102 142-189 (194)
73 PRK12526 RNA polymerase sigma 44.0 16 0.00036 31.8 2.1 47 45-101 154-200 (206)
74 PRK11924 RNA polymerase sigma 43.5 18 0.00039 29.6 2.2 29 75-103 146-174 (179)
75 PF13873 Myb_DNA-bind_5: Myb/S 43.1 14 0.0003 27.5 1.3 60 43-102 3-76 (78)
76 COG2104 ThiS Sulfur transfer p 42.5 38 0.00083 25.9 3.6 44 220-263 2-49 (68)
77 cd00565 ThiS ThiaminS ubiquiti 41.6 47 0.001 24.2 3.9 57 222-280 1-61 (65)
78 PRK09828 putative fimbrial out 41.3 34 0.00073 37.1 4.3 39 218-256 294-341 (865)
79 COG3188 FimD P pilus assembly 40.9 33 0.00071 37.4 4.2 39 218-256 289-336 (835)
80 PF13551 HTH_29: Winged helix- 40.5 79 0.0017 24.1 5.2 53 38-91 51-108 (112)
81 TIGR02948 SigW_bacill RNA poly 40.4 18 0.00039 30.2 1.7 49 44-102 136-184 (187)
82 PRK12512 RNA polymerase sigma 40.3 20 0.00044 30.1 2.1 50 44-103 131-180 (184)
83 TIGR02937 sigma70-ECF RNA poly 39.9 18 0.00039 27.9 1.5 47 44-100 110-156 (158)
84 PF13565 HTH_32: Homeodomain-l 39.8 50 0.0011 24.1 3.8 39 38-82 26-64 (77)
85 PF13936 HTH_38: Helix-turn-he 39.3 10 0.00022 26.1 0.1 39 42-90 2-40 (44)
86 PRK09639 RNA polymerase sigma 38.9 25 0.00054 28.9 2.3 49 44-103 112-160 (166)
87 PRK12515 RNA polymerase sigma 37.9 25 0.00054 29.9 2.3 48 44-101 131-178 (189)
88 smart00421 HTH_LUXR helix_turn 37.2 12 0.00027 24.7 0.2 38 44-92 3-40 (58)
89 PF00196 GerE: Bacterial regul 37.2 9.9 0.00021 26.9 -0.3 45 44-99 3-47 (58)
90 PRK12538 RNA polymerase sigma 36.6 24 0.00051 32.0 2.0 31 75-105 192-222 (233)
91 PRK05602 RNA polymerase sigma 36.0 25 0.00054 29.7 1.9 47 46-102 130-176 (186)
92 PRK12514 RNA polymerase sigma 35.8 30 0.00064 29.0 2.3 47 45-101 130-176 (179)
93 PRK12543 RNA polymerase sigma 35.5 41 0.0009 28.4 3.2 36 75-110 138-173 (179)
94 TIGR02989 Sig-70_gvs1 RNA poly 35.1 23 0.0005 28.8 1.5 39 44-92 111-149 (159)
95 PRK10072 putative transcriptio 34.8 19 0.0004 29.3 0.9 41 44-96 32-72 (96)
96 PRK09644 RNA polymerase sigma 34.7 27 0.00059 28.9 1.9 51 44-104 108-158 (165)
97 COG2944 Predicted transcriptio 34.5 18 0.00039 30.2 0.8 40 45-96 44-83 (104)
98 PRK09637 RNA polymerase sigma 34.2 29 0.00063 29.7 2.1 39 44-92 106-144 (181)
99 cd06170 LuxR_C_like C-terminal 34.1 19 0.00042 24.0 0.8 37 45-92 1-37 (57)
100 PRK06930 positive control sigm 33.8 31 0.00067 30.3 2.2 51 44-104 114-164 (170)
101 KOG0048 Transcription factor, 33.5 47 0.001 30.3 3.4 58 38-106 58-115 (238)
102 TIGR02999 Sig-70_X6 RNA polyme 33.5 27 0.00059 29.2 1.8 46 45-100 135-180 (183)
103 PRK08295 RNA polymerase factor 33.1 21 0.00045 30.5 1.0 26 75-100 175-200 (208)
104 PRK04217 hypothetical protein; 32.8 34 0.00075 28.5 2.2 48 43-100 41-88 (110)
105 PF02796 HTH_7: Helix-turn-hel 31.8 19 0.00041 24.7 0.5 39 43-91 4-42 (45)
106 TIGR02959 SigZ RNA polymerase 31.8 37 0.0008 28.6 2.3 47 44-100 100-146 (170)
107 COG4276 Uncharacterized conser 31.6 23 0.00051 31.3 1.1 18 218-235 103-120 (153)
108 TIGR02939 RpoE_Sigma70 RNA pol 31.4 26 0.00057 29.3 1.3 29 74-102 158-186 (190)
109 PRK09047 RNA polymerase factor 30.4 39 0.00085 27.4 2.2 46 45-100 107-152 (161)
110 PRK12530 RNA polymerase sigma 30.3 40 0.00087 28.9 2.3 48 45-102 135-182 (189)
111 PRK12532 RNA polymerase sigma 30.3 39 0.00085 28.8 2.2 49 45-103 137-185 (195)
112 PRK12537 RNA polymerase sigma 30.3 41 0.00089 28.4 2.4 45 45-99 134-178 (182)
113 TIGR02983 SigE-fam_strep RNA p 30.3 32 0.00069 28.2 1.6 46 45-100 111-156 (162)
114 TIGR02985 Sig70_bacteroi1 RNA 29.9 34 0.00073 27.4 1.7 45 45-99 114-158 (161)
115 PRK12541 RNA polymerase sigma 29.6 28 0.00061 28.6 1.2 47 44-100 112-158 (161)
116 PF14009 DUF4228: Domain of un 29.3 33 0.00073 28.4 1.6 53 222-281 20-81 (181)
117 PRK09648 RNA polymerase sigma 29.2 36 0.00077 28.9 1.8 46 44-99 139-184 (189)
118 PHA02955 hypothetical protein; 28.7 70 0.0015 29.9 3.7 44 47-94 60-103 (213)
119 smart00027 EH Eps15 homology d 28.6 50 0.0011 25.5 2.4 48 43-91 2-50 (96)
120 PRK00118 putative DNA-binding 27.7 51 0.0011 27.2 2.4 49 45-103 18-66 (104)
121 PRK06986 fliA flagellar biosyn 27.0 37 0.0008 30.3 1.6 48 45-102 185-232 (236)
122 PRK07037 extracytoplasmic-func 26.9 45 0.00098 27.3 2.0 38 45-92 110-147 (163)
123 TIGR02954 Sig70_famx3 RNA poly 26.7 38 0.00083 28.1 1.5 47 44-100 119-165 (169)
124 PTZ00305 NADH:ubiquinone oxido 26.7 49 0.0011 32.2 2.4 22 220-241 68-92 (297)
125 cd01616 TGS The TGS domain, na 26.7 99 0.0021 20.1 3.3 46 222-273 3-54 (60)
126 PF08880 QLQ: QLQ; InterPro: 26.6 51 0.0011 22.6 1.8 13 44-56 2-14 (37)
127 PF12323 HTH_OrfB_IS605: Helix 26.6 29 0.00063 23.8 0.7 23 39-61 5-27 (46)
128 PRK12536 RNA polymerase sigma 26.5 42 0.00091 28.4 1.8 27 75-101 150-176 (181)
129 PRK15198 outer membrane usher 25.9 76 0.0016 34.6 3.9 38 218-255 287-333 (860)
130 PF10925 DUF2680: Protein of u 25.8 36 0.00078 25.5 1.0 41 45-90 1-41 (59)
131 PF10668 Phage_terminase: Phag 25.8 21 0.00046 27.0 -0.2 17 70-90 26-42 (60)
132 PRK15248 fimbrial outer membra 25.4 53 0.0011 35.7 2.6 38 218-255 285-331 (853)
133 PRK12539 RNA polymerase sigma 25.1 51 0.0011 28.0 2.0 47 44-100 131-177 (184)
134 PRK13919 putative RNA polymera 24.9 45 0.00098 28.0 1.6 47 44-100 135-181 (186)
135 PRK12520 RNA polymerase sigma 24.9 59 0.0013 27.6 2.4 50 45-104 132-181 (191)
136 PRK12546 RNA polymerase sigma 24.7 44 0.00095 29.0 1.6 31 74-104 133-163 (188)
137 TIGR03142 cytochro_ccmI cytoch 24.6 1.1E+02 0.0024 25.0 3.9 34 45-80 40-73 (117)
138 cd03113 CTGs CTP synthetase (C 24.6 34 0.00075 32.7 1.0 13 265-277 48-60 (255)
139 PRK11923 algU RNA polymerase s 24.5 51 0.0011 27.9 1.9 31 74-104 158-188 (193)
140 PRK06288 RNA polymerase sigma 24.3 58 0.0013 29.8 2.4 52 44-105 212-263 (268)
141 PRK12545 RNA polymerase sigma 24.0 65 0.0014 28.0 2.5 49 45-103 140-188 (201)
142 PRK15294 putative fimbrial out 23.7 88 0.0019 33.9 3.9 38 218-255 289-335 (845)
143 PRK12547 RNA polymerase sigma 23.6 55 0.0012 27.2 1.9 47 44-100 112-158 (164)
144 PRK15217 fimbrial outer membra 23.6 62 0.0013 35.0 2.7 38 218-255 272-318 (826)
145 PRK15213 fimbrial outer membra 23.2 64 0.0014 34.7 2.8 39 218-256 273-319 (797)
146 PRK11840 bifunctional sulfur c 23.2 97 0.0021 30.6 3.7 58 221-280 1-62 (326)
147 PRK09645 RNA polymerase sigma 23.1 65 0.0014 26.7 2.2 46 45-100 119-164 (173)
148 PRK12513 RNA polymerase sigma 23.0 30 0.00064 29.5 0.2 27 71-101 160-186 (194)
149 TIGR02943 Sig70_famx1 RNA poly 23.0 69 0.0015 27.5 2.5 49 45-103 132-180 (188)
150 PRK09413 IS2 repressor TnpA; R 22.9 69 0.0015 26.2 2.3 41 42-92 10-51 (121)
151 PRK12516 RNA polymerase sigma 22.8 66 0.0014 27.7 2.3 49 45-103 117-165 (187)
152 TIGR03001 Sig-70_gmx1 RNA poly 22.8 67 0.0015 29.4 2.4 31 75-105 182-212 (244)
153 PRK15207 long polar fimbrial o 22.6 67 0.0014 35.0 2.7 38 218-255 302-348 (842)
154 PF07638 Sigma70_ECF: ECF sigm 22.6 45 0.00097 28.8 1.2 28 74-101 155-182 (185)
155 PRK10100 DNA-binding transcrip 22.5 37 0.00081 30.5 0.7 50 44-104 155-204 (216)
156 PRK12531 RNA polymerase sigma 22.2 65 0.0014 27.6 2.1 37 45-91 142-178 (194)
157 PRK12533 RNA polymerase sigma 22.1 45 0.00099 29.8 1.2 48 45-102 135-182 (216)
158 PRK06811 RNA polymerase factor 22.1 54 0.0012 28.0 1.6 48 44-101 131-178 (189)
159 PRK12535 RNA polymerase sigma 21.9 46 0.00099 29.0 1.1 53 44-106 133-185 (196)
160 PRK12522 RNA polymerase sigma 21.8 80 0.0017 26.3 2.6 28 75-102 140-167 (173)
161 PRK15304 putative fimbrial out 21.8 1E+02 0.0022 33.3 3.9 37 219-255 271-316 (801)
162 KOG3755 SATB1 matrix attachmen 21.6 51 0.0011 35.4 1.6 66 30-104 347-417 (769)
163 cd01769 UBL Ubiquitin-like dom 21.6 72 0.0016 22.1 1.9 28 67-94 18-45 (69)
164 PF06418 CTP_synth_N: CTP synt 21.4 46 0.001 32.2 1.1 13 265-277 49-61 (276)
165 PRK10651 transcriptional regul 21.3 35 0.00076 27.8 0.3 51 44-105 155-205 (216)
166 TIGR02952 Sig70_famx2 RNA poly 21.3 61 0.0013 26.5 1.7 38 44-91 122-159 (170)
167 cd00131 PAX Paired Box domain 21.1 1E+02 0.0022 25.7 3.0 46 44-94 75-127 (128)
168 TIGR02947 SigH_actino RNA poly 21.1 45 0.00098 28.4 0.9 30 75-104 152-181 (193)
169 KOG3915 Transcription regulato 21.0 36 0.00077 35.6 0.3 44 69-113 540-583 (641)
170 PTZ00397 macrophage migration 20.8 71 0.0015 25.7 2.0 25 71-95 80-104 (116)
171 PRK12518 RNA polymerase sigma 20.3 30 0.00065 28.7 -0.3 28 75-102 141-168 (175)
172 PRK12529 RNA polymerase sigma 20.3 65 0.0014 27.3 1.7 45 44-98 127-171 (178)
173 PRK13558 bacterio-opsin activa 20.3 1.1E+02 0.0024 31.0 3.6 42 42-88 605-648 (665)
174 COG2132 SufI Putative multicop 20.2 1.6E+02 0.0035 29.1 4.7 35 244-280 228-262 (451)
175 cd04759 Rib_hydrolase ADP-ribo 20.2 99 0.0021 29.4 3.0 36 218-256 146-195 (242)
176 PRK09647 RNA polymerase sigma 20.0 85 0.0018 27.6 2.4 28 75-102 159-186 (203)
No 1
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.78 E-value=2.4e-20 Score=171.15 Aligned_cols=68 Identities=22% Similarity=0.350 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHHh
Q 047211 36 TEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQAS 108 (282)
Q Consensus 36 ~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~ 108 (282)
+..||.|+.||..||.+||++|..|+ |..+.+|.+||..| .|+|+||||||||||+||||+.+.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~-YLtR~RRiEiA~~L----~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNK-YLTRSRRIEIAHAL----NLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhcccc-ccchHHHHHHHhhc----chhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 34689999999999999999999999 59999999888888 7999999999999999999988776543
No 2
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.77 E-value=1.7e-19 Score=170.25 Aligned_cols=70 Identities=26% Similarity=0.339 Sum_probs=59.9
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHH
Q 047211 31 SAERSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQL 105 (282)
Q Consensus 31 ~~~~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~ 105 (282)
..+...+.||+|.-+|+.||.+||++|.-|+ |+++++|. ||++.++|+|+||||||||||+|+||..|+.
T Consensus 228 ~~~~~~~~RKKRcPYTK~QtlELEkEFlfN~-YitkeKR~----ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 228 NASSARRGRKKRCPYTKHQTLELEKEFLFNM-YITKEKRL----ELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccccccccccCCchHHHHHHHHHHHHHHH-HHhHHHHH----HHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 4455556788999999999999999999999 59999875 5555559999999999999999999998743
No 3
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.75 E-value=6.7e-19 Score=165.99 Aligned_cols=73 Identities=23% Similarity=0.316 Sum_probs=62.8
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHHh
Q 047211 31 SAERSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQAS 108 (282)
Q Consensus 31 ~~~~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~ 108 (282)
..+..+++||.|+.||..||..||+.|++.+ |.+..+|.+||+.| ||++.|||+||||||+||||...+..+.
T Consensus 165 ~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QK-YLS~~DR~~LA~~L----gLTdaQVKtWfQNRRtKWKrq~a~g~~~ 237 (309)
T KOG0488|consen 165 QRSTPKKRRKSRTAFSDHQLFELEKRFEKQK-YLSVADRIELAASL----GLTDAQVKTWFQNRRTKWKRQTAEGGEL 237 (309)
T ss_pred ccCCCcccccchhhhhHHHHHHHHHHHHHhh-cccHHHHHHHHHHc----CCchhhHHHHHhhhhHHHHHHHHhhhcc
Confidence 3344456788999999999999999999998 59999997777766 8999999999999999999999885544
No 4
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.75 E-value=7.5e-19 Score=155.75 Aligned_cols=65 Identities=34% Similarity=0.505 Sum_probs=57.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHH
Q 047211 36 TEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQL 105 (282)
Q Consensus 36 ~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~ 105 (282)
.++||.||.||++||..||.+|+.++| ..-.||++||..| +|+|.||||||||||+|.||++.+.
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Y-vvg~eR~~LA~~L----~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQY-VVGAERKQLAQSL----SLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCe-eechHHHHHHHHc----CCChhHhhhhhhhhhHHHHHHHHHh
Confidence 378999999999999999999999995 7777776666555 7999999999999999999988775
No 5
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.74 E-value=2e-18 Score=162.97 Aligned_cols=71 Identities=23% Similarity=0.293 Sum_probs=62.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHHhhh
Q 047211 35 STEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQASLA 110 (282)
Q Consensus 35 ~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~~~ 110 (282)
..++||+|..||+.|..+||+.|...+ |.+..||++||..| +|++.||||||||||.|.||++.++.....
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQR-YLSAPERE~LA~~L----rLT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQR-YLSAPEREHLASSL----RLTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhh-ccccHhHHHHHHhc----CCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 346788899999999999999999998 69999997777666 799999999999999999999988766533
No 6
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.67 E-value=1.5e-17 Score=118.17 Aligned_cols=57 Identities=33% Similarity=0.537 Sum_probs=53.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 39 VRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 39 kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
||+|+.||++|+.+||.+|..++ ||+.+++.+|+.+| ||++.+|++||||||+|+||
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-YPSKEEREELAKEL----GLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSS-SCHHHHHHHHHHHH----TSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhc-cccccccccccccc----cccccccccCHHHhHHHhCc
Confidence 57899999999999999999998 59999998888887 89999999999999999986
No 7
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.67 E-value=3.4e-17 Score=149.21 Aligned_cols=76 Identities=24% Similarity=0.308 Sum_probs=65.4
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHH
Q 047211 28 SRGSAERSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQA 107 (282)
Q Consensus 28 ~~~~~~~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~ 107 (282)
..+++...+|+||+||.|+..|+..||..|+..+ |.+..||.-||++| .|+|.||||||||||.||||+..-..+
T Consensus 94 sdg~~~g~~RKKktRTvFSraQV~qLEs~Fe~kr-YLSsaeRa~LA~sL----qLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 94 SDGNGLGDDRKKKTRTVFSRAQVFQLESTFELKR-YLSSAERAGLAASL----QLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred cCCCcccccccccchhhhhHHHHHHHHHHHHHHh-hhhHHHHhHHHHhh----hhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 3455667779999999999999999999999988 69999987777776 799999999999999999998765544
Q ss_pred h
Q 047211 108 S 108 (282)
Q Consensus 108 ~ 108 (282)
+
T Consensus 169 a 169 (268)
T KOG0485|consen 169 A 169 (268)
T ss_pred h
Confidence 3
No 8
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.66 E-value=2.6e-17 Score=135.92 Aligned_cols=72 Identities=29% Similarity=0.386 Sum_probs=61.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHHhhh
Q 047211 34 RSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQASLA 110 (282)
Q Consensus 34 ~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~~~ 110 (282)
|.+..+|.|++||..||.+||++|.+.. ||+.-.|.+||.+| .|+|..|+|||||||||-|+++|..-...+
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETH-YPDIYTREEiA~ki----dLTEARVQVWFQNRRAKfRKQEr~a~~~~~ 84 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETH-YPDIYTREEIALKI----DLTEARVQVWFQNRRAKFRKQERAAIAKMA 84 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhc-CCcchhHHHHHHhh----hhhHHHHHHHHHhhHHHHHHHHHHHHHHhh
Confidence 4556689999999999999999999988 59988776666555 899999999999999999999987765543
No 9
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.65 E-value=6.1e-17 Score=150.92 Aligned_cols=64 Identities=23% Similarity=0.292 Sum_probs=55.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHH
Q 047211 38 PVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQ 106 (282)
Q Consensus 38 ~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q 106 (282)
+-|-|..+|..|.-+||++|..++ |...+++. ||+..|+|+||||||||||||||+||..+++.
T Consensus 199 kDKYRvVYTDhQRLELEKEfh~Sr-yITirRKS----ELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFHTSR-YITIRRKS----ELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ccceeEEecchhhhhhhhhhcccc-ceeeehhH----HHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 356899999999999999999998 59887664 55555589999999999999999999888773
No 10
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.64 E-value=1.5e-16 Score=144.09 Aligned_cols=70 Identities=26% Similarity=0.333 Sum_probs=61.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHHhhhc
Q 047211 37 EPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQASLAG 111 (282)
Q Consensus 37 ~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~~~~ 111 (282)
.-|++|+.||..||..||+-|.+.+ |.+.+||.+....| .|++.||||||||||||.||.++.+-+..+.
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekq-YLSiaEraefSsSL----~LTeTqVKIWFQNRRAKaKRlQeae~Ek~km 212 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQ-YLSIAERAEFSSSL----ELTETQVKIWFQNRRAKAKRLQEAELEKLKM 212 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhh-hhhHHHHHhhhhhh----hhhhhheehhhhhhhHHHHHHHHHHHHHhhh
Confidence 3478999999999999999999998 59999986665555 7999999999999999999999888776543
No 11
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.60 E-value=3.6e-16 Score=145.71 Aligned_cols=64 Identities=22% Similarity=0.383 Sum_probs=56.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHH
Q 047211 34 RSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQ 102 (282)
Q Consensus 34 ~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~ 102 (282)
-..+.||+||.||.|||++|+.+|+.++ |....+|++|+.|| +|.|.||||||||+|+|.||--
T Consensus 242 ~~~eeKRPRTAFtaeQL~RLK~EF~enR-YlTEqRRQ~La~EL----gLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 242 SSKEEKRPRTAFTAEQLQRLKAEFQENR-YLTEQRRQELAQEL----GLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred ccchhcCccccccHHHHHHHHHHHhhhh-hHHHHHHHHHHHHh----CcCHHHhhHHhhhhhhhhhhcc
Confidence 3445689999999999999999999998 59988888777777 7999999999999999998753
No 12
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.59 E-value=8.7e-16 Score=139.54 Aligned_cols=68 Identities=26% Similarity=0.372 Sum_probs=59.5
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHH
Q 047211 33 ERSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQL 105 (282)
Q Consensus 33 ~~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~ 105 (282)
+...+.+|.||+||-+||++||.+|++.+ ||+...|++||.+ ++|.|.+|+|||.|||||+|+++++.
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTq-YPDv~~rEelAlk----lnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQ-YPDVFMREELALK----LNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhc-CccHHHHHHHHHH----hCCchhhhhhhhccccchhhHhhhhh
Confidence 45566789999999999999999999999 5999877555554 58999999999999999999999876
No 13
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.59 E-value=7.2e-16 Score=140.94 Aligned_cols=63 Identities=24% Similarity=0.321 Sum_probs=57.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHH
Q 047211 37 EPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQ 104 (282)
Q Consensus 37 ~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~ 104 (282)
+-||+||-|+--||+.|.+.|++++ |.-..||.+||..| ||+..||||||||||+|.||.+++
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQkTQ-YLALPERAeLAAsL----GLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQTQ-YLALPERAELAASL----GLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhhcc-hhcCcHHHHHHHHh----CCchhHhhhhhhhhHHHHHHHHhc
Confidence 3478999999999999999999999 59999998777777 899999999999999999999883
No 14
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.57 E-value=1e-15 Score=107.45 Aligned_cols=56 Identities=32% Similarity=0.513 Sum_probs=50.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhH
Q 047211 39 VRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSR 99 (282)
Q Consensus 39 kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~K 99 (282)
++.|+.|+++|+.+||..|..++ ||+.+++.+|+++| ||+..+|++||+|||+|.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~-~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNP-YPSREEREELAAKL----GLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHH----CcCHHHHHHhHHHHhhccC
Confidence 46788999999999999999999 69999998777777 8999999999999999875
No 15
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.54 E-value=2.4e-15 Score=105.89 Aligned_cols=58 Identities=34% Similarity=0.530 Sum_probs=52.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHH
Q 047211 39 VRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRR 101 (282)
Q Consensus 39 kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk 101 (282)
++.|..|+++|+.+||..|..++ ||+.+++.+|+++| ||++++|++||+|||++.|+.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~-~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNP-YPSREEREELAKEL----GLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHH----CcCHHHHHHHHHHHHHHHhcc
Confidence 36789999999999999999998 69999988777777 799999999999999998874
No 16
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.54 E-value=3.2e-15 Score=139.32 Aligned_cols=62 Identities=24% Similarity=0.370 Sum_probs=53.9
Q ss_pred CCC-CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHH
Q 047211 39 VRS-RWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQL 105 (282)
Q Consensus 39 kR~-Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~ 105 (282)
||. ||.||.-||++||+.|.+.. ||+.-.| +-|+-++.|.|.+|+||||||||||||+++.-
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaH-YPDv~Ar----e~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAH-YPDVYAR----EMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhcc-CccHHHH----HHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 444 89999999999999999998 5998765 56666678999999999999999999988764
No 17
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.53 E-value=5.9e-15 Score=127.78 Aligned_cols=73 Identities=23% Similarity=0.446 Sum_probs=62.8
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHH
Q 047211 30 GSAERSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQA 107 (282)
Q Consensus 30 ~~~~~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~ 107 (282)
+.+...+.++++|.+-|.+|+.+||++|+.++ ||+..+|.+|+..| +|+++.|++||||||+|+|+...-...
T Consensus 43 ~~~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p-~Ps~~~r~~L~~~l----nm~~ksVqIWFQNkR~~~k~~~~~~~~ 115 (156)
T COG5576 43 RKQDGSSPPKSKRRRTTDEQLMVLEREFEINP-YPSSITRIKLSLLL----NMPPKSVQIWFQNKRAKEKKKRSGKVE 115 (156)
T ss_pred hcccCCCcCcccceechHHHHHHHHHHhccCC-CCCHHHHHHHHHhc----CCChhhhhhhhchHHHHHHHhcccchh
Confidence 55666677888899999999999999999999 59999887666666 899999999999999999998766544
No 18
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.51 E-value=6.4e-15 Score=132.01 Aligned_cols=65 Identities=26% Similarity=0.366 Sum_probs=57.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHHh
Q 047211 39 VRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQAS 108 (282)
Q Consensus 39 kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~ 108 (282)
.++..+||.+|+..||..|+.+. +..++++.+||++| ||.++||.|||||||||||.++.+.+..
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~-~L~p~~K~~LAk~L----gL~pRQVavWFQNRRARwK~kqlE~d~~ 115 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEK-KLEPERKKKLAKEL----GLQPRQVAVWFQNRRARWKTKQLEKDYE 115 (198)
T ss_pred ccccccccHHHHHHhHHhhcccc-ccChHHHHHHHHhh----CCChhHHHHHHhhccccccchhhhhhHH
Confidence 34456789999999999999998 59998887776666 8999999999999999999999988775
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=99.50 E-value=3e-14 Score=105.63 Aligned_cols=52 Identities=15% Similarity=0.112 Sum_probs=47.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCC----CCHHHHHHHHHHHHhcCCCCCCceeecccccc
Q 047211 39 VRSRWTPKPEQILILESIFNSGMVN----PPKDETVRIRKLLEKFGSVGDANVFYWFQNRR 95 (282)
Q Consensus 39 kR~Rt~fT~eQL~~LE~~F~~~~~y----P~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRR 95 (282)
+|.||.||++|++.||..|+.+. | |+.++|.+|+.+| ||++++|||||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~-y~~~~~~~~~r~~la~~l----gl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLG-WKLKDKRREEVREFCEEI----GVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHh----CCCHHHeeeecccCC
Confidence 78999999999999999999998 8 9988887666666 899999999999965
No 20
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.49 E-value=7e-15 Score=139.56 Aligned_cols=62 Identities=26% Similarity=0.349 Sum_probs=54.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHH
Q 047211 38 PVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQ 104 (282)
Q Consensus 38 ~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~ 104 (282)
-||-||.||.|||.+||++|-+.. |.++.+|-+||..| +|.|..|||||||||+|.||+...
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrEN-YVSRprRcELAAaL----NLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYREN-YVSRPRRCELAAAL----NLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHhc-cccCchhhhHHHhh----CCCcceeehhhhhchhhhhhhhhh
Confidence 478999999999999999999988 58888775555555 899999999999999999987765
No 21
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.48 E-value=2.6e-14 Score=134.94 Aligned_cols=64 Identities=27% Similarity=0.421 Sum_probs=57.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHH
Q 047211 37 EPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQL 105 (282)
Q Consensus 37 ~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~ 105 (282)
..||+||++|..||+.|+..|+.. |.+. +.+|++|+..+||+.++|||||||||||+||-+++.
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~S---pKPA--RHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTS---PKPA--RHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCC---Cchh--HHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 458999999999999999999996 4444 368899999999999999999999999999988764
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.41 E-value=1.6e-13 Score=133.19 Aligned_cols=62 Identities=24% Similarity=0.294 Sum_probs=58.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 37 EPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 37 ~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
|+||+||.+....+..||+.|.+|++ |+.+||.+||++| +|+..+|+|||+|||-|+||-..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npK-Pt~qEIt~iA~~L----~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPK-PTSQEITHIAESL----QLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCC-CCHHHHHHHHHHh----ccccceEEEEeeccccccccCCC
Confidence 77889999999999999999999996 9999999999999 79999999999999999998654
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.40 E-value=2e-14 Score=126.61 Aligned_cols=66 Identities=27% Similarity=0.359 Sum_probs=59.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHH
Q 047211 37 EPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQA 107 (282)
Q Consensus 37 ~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~ 107 (282)
+++|.|+.|+..||..||+.|+..+ |.+..||++|+..| +|+++|||+||||||+|.||.+|..+.
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Qr-YLS~~e~~ELan~L----~LS~~QVKTWFQNrRMK~Kk~~r~~~p 164 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQR-YLSTPERQELANAL----SLSETQVKTWFQNRRMKHKKQQRNNQP 164 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhh-hcccHHHHHHHHHh----hhhHHHHHHHHHHHHHHHHHHHhccCC
Confidence 4567899999999999999999987 59999998777777 799999999999999999999887663
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.40 E-value=1.3e-13 Score=130.96 Aligned_cols=67 Identities=30% Similarity=0.432 Sum_probs=59.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHHh
Q 047211 37 EPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQAS 108 (282)
Q Consensus 37 ~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~ 108 (282)
+++|.|+.||-.||++||..|.+++ ||+-+.|++||--. +|+|.+|.|||.|||+||||++|..+..
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNr-ypdMstrEEIavwt----NlTE~rvrvwfknrrakwrkrErN~~ae 177 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNR-YPDMSTREEIAVWT----NLTEARVRVWFKNRRAKWRKRERNQQAE 177 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhcc-CCccchhhHHHhhc----cccchhhhhhcccchhhhhhhhhhHHHH
Confidence 6789999999999999999999998 59999876665554 8999999999999999999999988843
No 25
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.28 E-value=1.9e-12 Score=112.53 Aligned_cols=64 Identities=25% Similarity=0.257 Sum_probs=56.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 35 STEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 35 ~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
....+|.|+.|+..|+++||++|+..+ ||+...| ++|+..++++|..|++||||||+|+|++++
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h-~Pd~~~r----~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVH-LPCFACR----ECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCC-cCccchH----HHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 345688999999999999999999997 6998766 466666799999999999999999999988
No 26
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.25 E-value=1.3e-12 Score=119.83 Aligned_cols=67 Identities=28% Similarity=0.370 Sum_probs=57.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHHh
Q 047211 37 EPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQAS 108 (282)
Q Consensus 37 ~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~ 108 (282)
.++-.|.+|+..||..||..|+..+ ||--++|.++|..| |+++.||+|||||||+||||+...+...
T Consensus 166 ~rk~srPTf~g~qi~~le~~feqtk-ylaG~~ra~lA~~l----gmteSqvkVWFQNRRTKWRKkhAaEmas 232 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQTK-YLAGADRAQLAQEL----NMTESQVKVWFQNRRTKWRKKHAAEMAS 232 (288)
T ss_pred cccccCCCccchhhhhhhhhhhhhh-cccchhHHHhhccc----cccHHHHHHHHhcchhhhhhhhccchhh
Confidence 3456788999999999999999998 58888887666666 8999999999999999999988766554
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.06 E-value=5.8e-11 Score=113.98 Aligned_cols=65 Identities=31% Similarity=0.412 Sum_probs=56.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHH
Q 047211 38 PVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQA 107 (282)
Q Consensus 38 ~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~ 107 (282)
.+|.|++|+++|++.||+.|+.++ ||+...| ++|++..++++..|++||+|||+|+||..++..+
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~rt~-yP~i~~R----e~La~~i~l~e~riqvwf~nrra~~rr~~~~~s~ 240 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQRTP-YPDIVGR----ETLAKETGLPEPRVQVWFQNRRAKWRRQHRDCSK 240 (354)
T ss_pred ccccccccccchHHHHHHHhcCCC-CCchhhH----HHHhhhccCCchHHHHHHhhhhhhhhhccccccc
Confidence 356699999999999999999999 6998876 4555555899999999999999999999987653
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.92 E-value=6.2e-10 Score=105.66 Aligned_cols=64 Identities=25% Similarity=0.351 Sum_probs=57.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 35 STEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 35 ~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
.+++||+||.+-....+.||.+|...++ |+.+.+..||++| +|...+|+|||+|.|-|.||.++
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPR-PS~EkIAaIAekL----DLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPR-PSGEKIAAIAEKL----DLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCC-CchhHHHHHHHhh----hhhhceEEEEeeccHHHHHHhhh
Confidence 3467899999999999999999999997 9999998888888 79999999999999999998544
No 29
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.20 E-value=8.2e-07 Score=89.89 Aligned_cols=59 Identities=24% Similarity=0.306 Sum_probs=52.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhH
Q 047211 36 TEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSR 99 (282)
Q Consensus 36 ~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~K 99 (282)
-.+||+|..||..|++.|-.+|+.+++ |+++..+.|..+| +|....|.+||.|-|.|.+
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~R-PS~Emq~tIS~qL----~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKR-PSREMQETISQQL----NLELSTVINFFMNARRRSL 476 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCC-CCHHHHHHHHHHh----CCcHHHHHHHHHhhhhhcc
Confidence 356889999999999999999999995 9999887666666 8999999999999998873
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.20 E-value=9.3e-07 Score=83.51 Aligned_cols=50 Identities=26% Similarity=0.379 Sum_probs=42.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSR 99 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~K 99 (282)
|...-...|.+.|..++ ||+++++ ++|++.+||+..||-+||.|||-|.|
T Consensus 183 FKekSR~~LrewY~~~~-YPsp~eK----ReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNP-YPSPREK----RELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhcCC-CCChHHH----HHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 44445678999999999 5999987 56677779999999999999999888
No 31
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.19 E-value=1.3e-06 Score=76.12 Aligned_cols=66 Identities=30% Similarity=0.522 Sum_probs=56.3
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 33 ERSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 33 ~~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
......++.|+.++..|+..|+..|.... +|+.. ++++|+..++++++.|++||||+|++.|+...
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~P~~~----~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 148 PSNKKPRRPRTTFTENQLEVLETVFRATP-KPDAD----DREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCccccCCCccccccchhHhhhhcccCCC-CCchh----hHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 33456788999999999999999999988 48655 45677777799999999999999999999877
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=97.66 E-value=4e-05 Score=72.57 Aligned_cols=66 Identities=24% Similarity=0.311 Sum_probs=53.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcC--CCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHH
Q 047211 38 PVRSRWTPKPEQILILESIFNSG--MVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQA 107 (282)
Q Consensus 38 ~kR~Rt~fT~eQL~~LE~~F~~~--~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~ 107 (282)
.+|+|-.|++.--++|.++|-.. ..||+.+++ ++|+++.+|+-.||-.||-|+|-|.||-....+.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K----~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~e 255 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAK----EELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQE 255 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHH----HHHHHHcCceehhhccccccceeehhhhhhhhhh
Confidence 46789999999999999999863 235887766 4555566999999999999999999997765544
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=97.46 E-value=1.9e-05 Score=54.54 Aligned_cols=33 Identities=27% Similarity=0.492 Sum_probs=23.9
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchh
Q 047211 60 GMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSR 97 (282)
Q Consensus 60 ~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK 97 (282)
++ ||+.+|+.+|+.+ +||+.+||..||-|.|.|
T Consensus 8 nP-YPs~~ek~~L~~~----tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 8 NP-YPSKEEKEELAKQ----TGLSRKQISNWFINARRR 40 (40)
T ss_dssp SG-S--HHHHHHHHHH----HTS-HHHHHHHHHHHHHH
T ss_pred CC-CCCHHHHHHHHHH----cCCCHHHHHHHHHHhHcc
Confidence 45 6999988655555 589999999999999975
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.15 E-value=0.00024 Score=78.20 Aligned_cols=61 Identities=21% Similarity=0.338 Sum_probs=53.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 38 PVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 38 ~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
.++.|+.++..||.+|..+|.... ||.-++. +.|...+++..+.|.+||||-|+|.|+...
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~-~~~~~~~----E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQR-TPTMQEC----EVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhcc-CChHHHH----HhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 467899999999999999999976 5877665 566677789999999999999999998877
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.70 E-value=0.0076 Score=56.96 Aligned_cols=67 Identities=22% Similarity=0.248 Sum_probs=51.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcC-C-CCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHHh
Q 047211 38 PVRSRWTPKPEQILILESIFNSG-M-VNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQAS 108 (282)
Q Consensus 38 ~kR~Rt~fT~eQL~~LE~~F~~~-~-~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~ 108 (282)
.+|++..+-++...+|+.-.... . .||+.+++ ..|++.+||+..||.+||-|.|-|.++-.......
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K----~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~~~~ 307 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEK----LMLAKQTGLSRPQVSNWFINARVRLWKPMIEEMYL 307 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhc----cccchhcCCCcccCCchhhhcccccCCchHHHHHH
Confidence 45667788899999998764442 1 25887765 37888889999999999999999999877766554
No 36
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=95.12 E-value=0.0096 Score=63.19 Aligned_cols=51 Identities=18% Similarity=0.330 Sum_probs=45.8
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHH
Q 047211 50 ILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQL 105 (282)
Q Consensus 50 L~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~ 105 (282)
+..|..+|..|+. |+.++-.+|+.++ ||+-+.|+.||+++|+++.+..|.-
T Consensus 568 ~sllkayyaln~~-ps~eelskia~qv----glp~~vvk~wfE~~~a~e~sv~rsp 618 (1007)
T KOG3623|consen 568 TSLLKAYYALNGL-PSEEELSKIAQQV----GLPFAVVKAWFEDEEAEEMSVERSP 618 (1007)
T ss_pred HHHHHHHHHhcCC-CCHHHHHHHHHHh----cccHHHHHHHHHhhhhhhhhhccCc
Confidence 8899999999995 9999988888888 7999999999999999999887644
No 37
>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=90.45 E-value=0.17 Score=36.44 Aligned_cols=47 Identities=19% Similarity=0.142 Sum_probs=33.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccc
Q 047211 39 VRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRR 95 (282)
Q Consensus 39 kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRR 95 (282)
+|+|..+|.+|...+=..++.+. + ..+||.+ +|++..+|..|..||.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~---s---~~~ia~~----fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE---S---KRDIARE----FGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT-------HHHHHHH----HT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC---C---HHHHHHH----hCCCHHHHHHHHHhHH
Confidence 57899999999998888899874 2 2344455 5899999999998864
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=90.44 E-value=0.056 Score=40.41 Aligned_cols=43 Identities=19% Similarity=0.212 Sum_probs=28.0
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccch
Q 047211 49 QILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRS 96 (282)
Q Consensus 49 QL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRA 96 (282)
-++-|+.+|..... +...+. .+|-.+.+|+..||+.||--|+.
T Consensus 9 d~~pL~~Yy~~h~~-L~E~DL----~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQ-LQEEDL----DELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp --HHHHHHHHHT-----TTHH----HHHHHHTT--HHHHHHHHHHHS-
T ss_pred chHHHHHHHHHcCC-ccHhhH----HHHHHHHCCCHHHHHHHHHHhcc
Confidence 35679999999774 665543 67888889999999999976544
No 39
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=85.48 E-value=1.5 Score=32.35 Aligned_cols=58 Identities=16% Similarity=0.263 Sum_probs=45.2
Q ss_pred EEEEECCeeeeecCc--ccchhhccCCc--eEEEecCCCccccCCccccccccCCcceEEEeec
Q 047211 221 ITVFINGAPTEIPRG--PIDMKALFGQD--VVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSR 280 (282)
Q Consensus 221 ~tVfINgv~~EV~~G--p~dvr~~FG~d--avLvhSsG~pvptne~Gvt~~sLq~G~~Y~Lv~~ 280 (282)
|+|.|||.+++++.+ --+|-..+|-+ .+-|==.|++||-++|.=+ .|+.|...-+|+.
T Consensus 1 m~i~vNg~~~~~~~~~tl~~ll~~l~~~~~~vaVavN~~iv~r~~w~~~--~L~~gD~Ieii~~ 62 (66)
T PRK08053 1 MQILFNDQPMQCAAGQTVHELLEQLNQLQPGAALAINQQIIPREQWAQH--IVQDGDQILLFQV 62 (66)
T ss_pred CEEEECCeEEEcCCCCCHHHHHHHcCCCCCcEEEEECCEEeChHHcCcc--ccCCCCEEEEEEE
Confidence 579999999999875 35555666644 4666668999999999876 4999998888864
No 40
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=80.42 E-value=3.3 Score=31.00 Aligned_cols=58 Identities=16% Similarity=0.234 Sum_probs=43.3
Q ss_pred EEEEECCeeeeecCcccchh---hccCC--ceEEEecCCCccccCCccccccccCCcceEEEeec
Q 047211 221 ITVFINGAPTEIPRGPIDMK---ALFGQ--DVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSR 280 (282)
Q Consensus 221 ~tVfINgv~~EV~~Gp~dvr---~~FG~--davLvhSsG~pvptne~Gvt~~sLq~G~~Y~Lv~~ 280 (282)
|+|.|||.+++++.+...|. ..+|- ..|-|-=.|.+||-++|--+. |+.|...=+|+.
T Consensus 1 m~I~vNG~~~~~~~~~~tv~~lL~~l~~~~~~vav~vN~~iv~r~~w~~~~--L~~gD~iEIv~~ 63 (67)
T PRK07696 1 MNLKINGNQIEVPESVKTVAELLTHLELDNKIVVVERNKDILQKDDHTDTS--VFDGDQIEIVTF 63 (67)
T ss_pred CEEEECCEEEEcCCCcccHHHHHHHcCCCCCeEEEEECCEEeCHHHcCcee--cCCCCEEEEEEE
Confidence 58999999999998854454 44443 345555689999999998764 888887777653
No 41
>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=79.20 E-value=4.3 Score=33.98 Aligned_cols=34 Identities=26% Similarity=0.437 Sum_probs=30.7
Q ss_pred eeeceEEEEECCeeeeecCcccchhhccCCceEEEec
Q 047211 216 YQTGFITVFINGAPTEIPRGPIDMKALFGQDVVLVHS 252 (282)
Q Consensus 216 ~q~g~~tVfINgv~~EV~~Gp~dvr~~FG~davLvhS 252 (282)
|.+|++++-|.|+.|+|-.|. ...|=+++|.|+.
T Consensus 75 ~kSGkv~l~iG~~~~dV~~G~---~~~FlQevv~i~~ 108 (131)
T PF05132_consen 75 HKSGKVTLKIGGVVFDVSPGT---QCSFLQEVVAIDE 108 (131)
T ss_pred EeCCcEEEEECCEEEEecCCC---CCCchheEEEeec
Confidence 458999999999999999985 5689999999998
No 42
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=78.81 E-value=4.3 Score=29.47 Aligned_cols=57 Identities=26% Similarity=0.447 Sum_probs=40.0
Q ss_pred EEEEECCeeeeecCc--ccchhhccCC--ceEEEecCCCccccCCccccccccCCcceEEEee
Q 047211 221 ITVFINGAPTEIPRG--PIDMKALFGQ--DVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVS 279 (282)
Q Consensus 221 ~tVfINgv~~EV~~G--p~dvr~~FG~--davLvhSsG~pvptne~Gvt~~sLq~G~~Y~Lv~ 279 (282)
|+|.|||.+++++.| --|+-..+|- +-+-|-=.|.+||-.+|-- +.|+.|...=+++
T Consensus 1 m~i~vNG~~~~~~~~~tl~~lL~~l~~~~~~vav~vNg~iv~r~~~~~--~~l~~gD~vei~~ 61 (66)
T PRK05659 1 MNIQLNGEPRELPDGESVAALLAREGLAGRRVAVEVNGEIVPRSQHAS--TALREGDVVEIVH 61 (66)
T ss_pred CEEEECCeEEEcCCCCCHHHHHHhcCCCCCeEEEEECCeEeCHHHcCc--ccCCCCCEEEEEE
Confidence 579999999999886 3455566663 3333334699999888864 4588887766665
No 43
>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=76.62 E-value=1.2 Score=28.99 Aligned_cols=44 Identities=11% Similarity=0.178 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchh
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSR 97 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK 97 (282)
.+++++.++++..|..+. . ..+|+++| |++...|+.|...-|.+
T Consensus 10 ~l~~~~~~~~~~~~~~~~--~----~~~ia~~~----~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEGL--S----YEEIAEIL----GISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcCC--C----HHHHHHHH----CcCHHHHHHHHHHHHHH
Confidence 467889999999987653 2 23456666 89999999887655444
No 44
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=74.68 E-value=6 Score=29.24 Aligned_cols=57 Identities=16% Similarity=0.290 Sum_probs=42.2
Q ss_pred EEEEECCeeeeecCc--ccchhhccC--CceEEEecCCCccccCCccccccccCCcceEEEeec
Q 047211 221 ITVFINGAPTEIPRG--PIDMKALFG--QDVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSR 280 (282)
Q Consensus 221 ~tVfINgv~~EV~~G--p~dvr~~FG--~davLvhSsG~pvptne~Gvt~~sLq~G~~Y~Lv~~ 280 (282)
|+|.|||.+++++.+ --|+=..+| .+.+-|-=.|.+||-.+|. + . |+.|...-+|+.
T Consensus 1 m~i~vNG~~~~~~~~~tl~~ll~~l~~~~~~vav~~N~~iv~r~~~~-~-~-L~~gD~ieIv~~ 61 (65)
T PRK05863 1 MIVVVNEEQVEVDEQTTVAALLDSLGFPEKGIAVAVDWSVLPRSDWA-T-K-LRDGARLEVVTA 61 (65)
T ss_pred CEEEECCEEEEcCCCCcHHHHHHHcCCCCCcEEEEECCcCcChhHhh-h-h-cCCCCEEEEEee
Confidence 589999999999864 234445555 3345555589999999999 4 3 999988777754
No 45
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=68.89 E-value=9 Score=27.62 Aligned_cols=57 Identities=21% Similarity=0.354 Sum_probs=34.4
Q ss_pred EEEEECCeeeeecCcc--cchhhccCCc-eEEEecCCCccccCCccccccccCCcceEEEee
Q 047211 221 ITVFINGAPTEIPRGP--IDMKALFGQD-VVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVS 279 (282)
Q Consensus 221 ~tVfINgv~~EV~~Gp--~dvr~~FG~d-avLvhSsG~pvptne~Gvt~~sLq~G~~Y~Lv~ 279 (282)
|+|.|||.++++|.|- -++-+..|-+ .+.|==.|..||-.+|- -..|+.|...-+++
T Consensus 1 m~i~vNg~~~~~~~~~tl~~ll~~l~~~~~~~v~vN~~~v~~~~~~--~~~L~~gD~vei~~ 60 (65)
T PRK06944 1 MDIQLNQQTLSLPDGATVADALAAYGARPPFAVAVNGDFVARTQHA--ARALAAGDRLDLVQ 60 (65)
T ss_pred CEEEECCEEEECCCCCcHHHHHHhhCCCCCeEEEECCEEcCchhcc--cccCCCCCEEEEEe
Confidence 5799999999998762 4444555443 12222244555544433 34588887776665
No 46
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=67.52 E-value=9.1 Score=30.30 Aligned_cols=60 Identities=17% Similarity=0.227 Sum_probs=44.0
Q ss_pred ceEEEEECCeeeeecCcc--cchhhccCCc--eEEEecCCCccccCCccccccccCCcceEEEeec
Q 047211 219 GFITVFINGAPTEIPRGP--IDMKALFGQD--VVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSR 280 (282)
Q Consensus 219 g~~tVfINgv~~EV~~Gp--~dvr~~FG~d--avLvhSsG~pvptne~Gvt~~sLq~G~~Y~Lv~~ 280 (282)
..|+|.|||.+++++.+- -+|=..+|-+ .|-|==.|++||=++|.-+. |+.|...-+|..
T Consensus 17 ~~m~I~VNG~~~~~~~~~tl~~LL~~l~~~~~~vAVevNg~iVpr~~w~~t~--L~egD~IEIv~~ 80 (84)
T PRK06083 17 VLITISINDQSIQVDISSSLAQIIAQLSLPELGCVFAINNQVVPRSEWQSTV--LSSGDAISLFQA 80 (84)
T ss_pred ceEEEEECCeEEEcCCCCcHHHHHHHcCCCCceEEEEECCEEeCHHHcCccc--CCCCCEEEEEEE
Confidence 369999999999998752 2333455544 44444589999999998775 888888777653
No 47
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=67.42 E-value=1.2 Score=47.00 Aligned_cols=66 Identities=15% Similarity=0.142 Sum_probs=41.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHH-HhcCCCCCCHHHHHHHHHHH-----HhcCCCCCCceeecccccchhhHHHHH
Q 047211 35 STEPVRSRWTPKPEQILILESI-FNSGMVNPPKDETVRIRKLL-----EKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 35 ~~~~kR~Rt~fT~eQL~~LE~~-F~~~~~yP~~~eR~~Ia~eL-----a~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
.+.|||+|.+|=.+|..++... |.+++ .+.--...+-.+++ .+ ...+++|+.||.|||+++||.+-
T Consensus 688 ~~~pk~~~~k~f~~~~~ev~~~w~~k~~-s~s~~~v~eYkee~~~~~~~e--~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 688 LDLPKKTIIKFFQNQRYEVKHHWKLKTR-SGSWVDVAEYKEEELLMPYEE--KFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred hcccHHHHHHhhhcceeecchhheeccc-CchhHHHHHhhHHhhcchhhh--hhhhcchHHHHHHHHHHHhhhhc
Confidence 3457777777777777666544 44443 24433333333332 11 23678999999999999998764
No 48
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=66.33 E-value=13 Score=27.86 Aligned_cols=54 Identities=19% Similarity=0.367 Sum_probs=41.8
Q ss_pred EEEEECCeeeeecCc--ccchhhccCCceEEEecCCCccccCCccccccccCCcceEEEeec
Q 047211 221 ITVFINGAPTEIPRG--PIDMKALFGQDVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSR 280 (282)
Q Consensus 221 ~tVfINgv~~EV~~G--p~dvr~~FG~davLvhSsG~pvptne~Gvt~~sLq~G~~Y~Lv~~ 280 (282)
|.|+|||+..++.-+ -++||..++.|+=++==.|-|+-.| -.|+-|..-|||.+
T Consensus 1 M~I~vN~k~~~~~~~~tl~~lr~~~k~~~DI~I~NGF~~~~d------~~L~e~D~v~~Ikk 56 (57)
T PF14453_consen 1 MKIKVNEKEIETEENTTLFELRKESKPDADIVILNGFPTKED------IELKEGDEVFLIKK 56 (57)
T ss_pred CEEEECCEEEEcCCCcCHHHHHHhhCCCCCEEEEcCcccCCc------cccCCCCEEEEEeC
Confidence 468999999999776 6999999998776555566665554 36788888888775
No 49
>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=63.38 E-value=6 Score=30.60 Aligned_cols=33 Identities=27% Similarity=0.563 Sum_probs=20.3
Q ss_pred eEEEEECCeeeeecCcccchhhccCCceEEEec
Q 047211 220 FITVFINGAPTEIPRGPIDMKALFGQDVVLVHS 252 (282)
Q Consensus 220 ~~tVfINgv~~EV~~Gp~dvr~~FG~davLvhS 252 (282)
.++|.|||++++|+.|-==+.++...+.-+.|.
T Consensus 3 ~v~i~idG~~v~~~~G~til~al~~~gi~ip~~ 35 (82)
T PF13510_consen 3 MVTITIDGKPVEVPPGETILEALLAAGIDIPRL 35 (82)
T ss_dssp EEEEEETTEEEEEEET-BHHHHHHHTT--B-EE
T ss_pred EEEEEECCEEEEEcCCCHHHHHHHHCCCeEEEe
Confidence 689999999999998873334444433333344
No 50
>PRK07440 hypothetical protein; Provisional
Probab=60.11 E-value=22 Score=26.85 Aligned_cols=59 Identities=22% Similarity=0.252 Sum_probs=42.6
Q ss_pred eEEEEECCeeeeecCc--ccchhhccCC--ceEEEecCCCccccCCccccccccCCcceEEEeec
Q 047211 220 FITVFINGAPTEIPRG--PIDMKALFGQ--DVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSR 280 (282)
Q Consensus 220 ~~tVfINgv~~EV~~G--p~dvr~~FG~--davLvhSsG~pvptne~Gvt~~sLq~G~~Y~Lv~~ 280 (282)
+|+|.|||.+.|++.| --|+-..+|- ..|-|-=.|++||-++|.=+. |+-|...-+|+.
T Consensus 4 ~m~i~vNG~~~~~~~~~tl~~lL~~l~~~~~~vav~~N~~iv~r~~w~~~~--L~~gD~IEIv~~ 66 (70)
T PRK07440 4 PITLQVNGETRTCSSGTSLPDLLQQLGFNPRLVAVEYNGEILHRQFWEQTQ--VQPGDRLEIVTI 66 (70)
T ss_pred ceEEEECCEEEEcCCCCCHHHHHHHcCCCCCeEEEEECCEEeCHHHcCcee--cCCCCEEEEEEE
Confidence 6999999999999875 2333344443 456666689999999998654 777877766653
No 51
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=59.60 E-value=5.5 Score=29.12 Aligned_cols=41 Identities=20% Similarity=0.380 Sum_probs=24.0
Q ss_pred CCCCCCCHHHHHHHHHHH-hcCCCCCCHHHHHHHHHHHHhcCCCCCCceeec
Q 047211 40 RSRWTPKPEQILILESIF-NSGMVNPPKDETVRIRKLLEKFGSVGDANVFYW 90 (282)
Q Consensus 40 R~Rt~fT~eQL~~LE~~F-~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvW 90 (282)
++|..||+++...+-..+ ..+. ...++++++ ||++..+..|
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g~------sv~~va~~~----gi~~~~l~~W 43 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESGE------SVSEVAREY----GISPSTLYNW 43 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHHC------HHHHHHHHH----TS-HHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCCC------ceEeeeccc----ccccccccHH
Confidence 467889999887776666 4432 234455555 8999999988
No 52
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=59.17 E-value=10 Score=32.96 Aligned_cols=55 Identities=20% Similarity=0.181 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHH
Q 047211 42 RWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQA 107 (282)
Q Consensus 42 Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~ 107 (282)
...+|+.|+++|+.. ..+. + ..+||+.| |++...|+.|-.+.|.|.|+...-...
T Consensus 4 ~~~Lt~rqreVL~lr-~~Gl---T---q~EIAe~L----GiS~~tVs~ie~ra~kkLr~~~~tl~~ 58 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ERGL---T---QQEIADIL----GTSRANVSSIEKRARENIEKARETLAF 58 (141)
T ss_pred ccCCCHHHHHHHHHH-HcCC---C---HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346899999999984 4542 1 23566666 899999999999877777776666533
No 53
>PF05660 DUF807: Coxiella burnetii protein of unknown function (DUF807); InterPro: IPR008525 This family consists of several proteins of unknown function from Coxiella burnetii (the causative agent of a zoonotic disease called Q fever).
Probab=58.56 E-value=3.9 Score=35.54 Aligned_cols=38 Identities=32% Similarity=0.514 Sum_probs=34.3
Q ss_pred eecCcccchhhccCCceEEEecCCCccccCCccccccc
Q 047211 231 EIPRGPIDMKALFGQDVVLVHSSGVPIPTNEFGFLMQS 268 (282)
Q Consensus 231 EV~~Gp~dvr~~FG~davLvhSsG~pvptne~Gvt~~s 268 (282)
.+|.||||-+.-||.--.+.+..=+-+.|-||-||+-+
T Consensus 11 ~~~igpi~p~syfgn~gai~~p~I~k~aTGeytItfls 48 (142)
T PF05660_consen 11 QIPIGPIDPDSYFGNPGAIMDPEIEKIATGEYTITFLS 48 (142)
T ss_pred CcccCCcCchhccCCCccccChhhhhhccCceEEEEEe
Confidence 46899999999999999999999999999999988744
No 54
>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=58.31 E-value=5.6 Score=27.39 Aligned_cols=40 Identities=13% Similarity=0.204 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccc
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQN 93 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQN 93 (282)
.++++|.++|...|..+. + -.+|++.| |++...|+.|...
T Consensus 4 ~L~~~er~vi~~~y~~~~---t---~~eIa~~l----g~s~~~V~~~~~~ 43 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEGL---T---LEEIAERL----GISRSTVRRILKR 43 (50)
T ss_dssp TS-HHHHHHHHHHHTST----S---HHHHHHHH----TSCHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCC---C---HHHHHHHH----CCcHHHHHHHHHH
Confidence 468999999999997653 2 23466666 8999998866543
No 55
>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=57.97 E-value=7.6 Score=28.48 Aligned_cols=40 Identities=18% Similarity=0.188 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhcCCCC-CCHHHHHHHHHHHHhcCCCCCCcee
Q 047211 45 PKPEQILILESIFNSGMVN-PPKDETVRIRKLLEKFGSVGDANVF 88 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~y-P~~~eR~~Ia~eLa~~~~Lse~qVk 88 (282)
+|+.|.++|+..|+.+=|. |..-. .++|++.+||++..|-
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~t----l~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRIT----LEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCC----HHHHHHHhCCCHHHHH
Confidence 5899999999999998332 33332 3556666689876653
No 56
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=54.75 E-value=9.5 Score=31.29 Aligned_cols=50 Identities=12% Similarity=0.019 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
.+++.+.++|+..|-.+. +. .+|++.| |+++..|+.|...=|.|.|+..+
T Consensus 128 ~L~~~~r~vl~l~~~~~~--s~----~eIA~~l----gis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 128 SLPEELRTAITLREIEGL--SY----EEIAEIM----GCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred hCCHHHHHHHHHHHHcCC--CH----HHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 477788888887766553 22 2355555 89999999988855555554443
No 57
>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=53.50 E-value=16 Score=20.88 Aligned_cols=38 Identities=21% Similarity=0.396 Sum_probs=24.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecc
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWF 91 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWF 91 (282)
.++.++...+...|..+. + ..+|++++ +++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~~---s---~~~ia~~~----~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAGE---S---VAEIARRL----GVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcCC---C---HHHHHHHH----CCCHHHHHHhC
Confidence 466777777777776542 2 23455555 78888887773
No 58
>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=53.17 E-value=12 Score=29.18 Aligned_cols=26 Identities=12% Similarity=0.123 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHhcCCCCCCceeeccc
Q 047211 67 DETVRIRKLLEKFGSVGDANVFYWFQ 92 (282)
Q Consensus 67 ~eR~~Ia~eLa~~~~Lse~qVkvWFQ 92 (282)
.++.+|+++|.+.++|.+.+|.+|+.
T Consensus 50 ~~i~~L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 50 RRIRELTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred hhHHHHHHHHHHHhCCCCCeEEEEEE
Confidence 45778999999999999999999985
No 59
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=53.13 E-value=29 Score=25.28 Aligned_cols=57 Identities=14% Similarity=0.174 Sum_probs=40.4
Q ss_pred EEEEECCeeeeecC-cccchhhccCCc--eEEEecCCCccccCCccccccccCCcceEEEee
Q 047211 221 ITVFINGAPTEIPR-GPIDMKALFGQD--VVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVS 279 (282)
Q Consensus 221 ~tVfINgv~~EV~~-Gp~dvr~~FG~d--avLvhSsG~pvptne~Gvt~~sLq~G~~Y~Lv~ 279 (282)
|+|.|||.+++++. -.-++...+|-+ .+.|==.|++||-++|.= ..|+.|.-.-+|+
T Consensus 1 m~i~~Ng~~~~~~~~tl~~Ll~~l~~~~~~vavavN~~iv~~~~~~~--~~L~dgD~Ieiv~ 60 (65)
T PRK06488 1 MKLFVNGETLQTEATTLALLLAELDYEGNWLATAVNGELVHKEARAQ--FVLHEGDRIEILS 60 (65)
T ss_pred CEEEECCeEEEcCcCcHHHHHHHcCCCCCeEEEEECCEEcCHHHcCc--cccCCCCEEEEEE
Confidence 68999999999943 234555555544 455555789999988876 4588887766665
No 60
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=51.55 E-value=26 Score=25.47 Aligned_cols=56 Identities=25% Similarity=0.401 Sum_probs=39.6
Q ss_pred EEECCeeeeecCc--ccchhhccCC--ceEEEecCCCccccCCccccccccCCcceEEEeec
Q 047211 223 VFINGAPTEIPRG--PIDMKALFGQ--DVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSR 280 (282)
Q Consensus 223 VfINgv~~EV~~G--p~dvr~~FG~--davLvhSsG~pvptne~Gvt~~sLq~G~~Y~Lv~~ 280 (282)
|.|||..++++.+ --||...+|- +.+.|==.|++|+-++|--+ .|+.|...-+++.
T Consensus 1 i~iNg~~~~~~~~~tv~~ll~~l~~~~~~v~v~vN~~iv~~~~~~~~--~L~~gD~veii~~ 60 (64)
T TIGR01683 1 ITVNGEPVEVEDGLTLAALLESLGLDPRRVAVAVNGEIVPRSEWDDT--ILKEGDRIEIVTF 60 (64)
T ss_pred CEECCeEEEcCCCCcHHHHHHHcCCCCCeEEEEECCEEcCHHHcCce--ecCCCCEEEEEEe
Confidence 5799999999886 4666676663 34455557778877777654 5888887777653
No 61
>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=51.46 E-value=11 Score=37.93 Aligned_cols=39 Identities=31% Similarity=0.637 Sum_probs=24.5
Q ss_pred eceEEEEECCee---eeecCcccchhhc-----cCC-ceEEEecCCCc
Q 047211 218 TGFITVFINGAP---TEIPRGPIDMKAL-----FGQ-DVVLVHSSGVP 256 (282)
Q Consensus 218 ~g~~tVfINgv~---~EV~~Gp~dvr~~-----FG~-davLvhSsG~p 256 (282)
+.+++|++||+. ..||.|||++... -|| ++++.+..|+.
T Consensus 98 ~s~V~v~qnG~~iy~~~VppGpF~i~dlp~~~~~gdl~V~i~d~~G~~ 145 (552)
T PF00577_consen 98 PSTVEVYQNGRLIYSTNVPPGPFEIDDLPLISGSGDLQVVITDADGRE 145 (552)
T ss_dssp SEEEEEEETTEEEEEEEE-SEEEEE-SS-TTTTTSEEEEEEEETTS-E
T ss_pred ccEEEEEECCEEEEEEEeCCCCEEecCccccCCCceEEEEEEECCCCE
Confidence 468999999997 4789999987642 233 33444446653
No 62
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=50.63 E-value=10 Score=33.82 Aligned_cols=41 Identities=17% Similarity=0.210 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHHhcCCCC-CCHHHHHHHHHHHHhcCCCCCCcee
Q 047211 44 TPKPEQILILESIFNSGMVN-PPKDETVRIRKLLEKFGSVGDANVF 88 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~y-P~~~eR~~Ia~eLa~~~~Lse~qVk 88 (282)
.+|+.|+++|...|..+=|. |..-. .++||+.+||++..+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~----l~dLA~~lGISkst~~ 196 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVS----LKDLAKELGISKSTLS 196 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCC----HHHHHHHhCCCHHHHH
Confidence 79999999999999998221 43333 3556666689887653
No 63
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=50.61 E-value=9.3 Score=41.62 Aligned_cols=66 Identities=24% Similarity=0.233 Sum_probs=47.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHH
Q 047211 37 EPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQA 107 (282)
Q Consensus 37 ~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~ 107 (282)
++.|-|+....++-..|..+++.+-. |..++-.-++.+| ...+.+|.+||++|+.+.+.-....-.
T Consensus 625 ~p~kv~sp~k~~dq~ql~~a~elq~s-~~n~~~pl~~t~~----~n~~pv~ev~dhsrsstpsp~pl~lts 690 (1007)
T KOG3623|consen 625 RPVKVRSPIKEEDQQQLKQAYELQAS-PSNDEFPLIATRL----QNDPPVVEVWDHSRSSTPSPMPLFLTS 690 (1007)
T ss_pred CCccccCCCCccchhhhHhhhhcccC-ccCcccchhhhhc----cCCCcchhhcccCCCCCCCCCcccccc
Confidence 55667788888888899999988653 5555443344444 577888999999999998876554433
No 64
>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=49.85 E-value=28 Score=23.91 Aligned_cols=49 Identities=27% Similarity=0.433 Sum_probs=33.3
Q ss_pred EEEE-CCeeeeecCc--ccchhhc----cCCceEEEecCCCccccCCccccccccCCcceEE
Q 047211 222 TVFI-NGAPTEIPRG--PIDMKAL----FGQDVVLVHSSGVPIPTNEFGFLMQSLQHGESYF 276 (282)
Q Consensus 222 tVfI-Ngv~~EV~~G--p~dvr~~----FG~davLvhSsG~pvptne~Gvt~~sLq~G~~Y~ 276 (282)
-||+ ||...+++.| .-|+... +..+++.+.-.|+.++.+ ++|.+|...=
T Consensus 2 ~~~~~~g~~~~~~~~~t~~~~~~~~~~~~~~~~va~~vng~~vdl~------~~l~~~~~ve 57 (60)
T cd01668 2 YVFTPKGEIIELPAGATVLDFAYAIHTEIGNRCVGAKVNGKLVPLS------TVLKDGDIVE 57 (60)
T ss_pred EEECCCCCEEEcCCCCCHHHHHHHHChHhhhheEEEEECCEECCCC------CCCCCCCEEE
Confidence 4787 9999999877 3554433 234667777788888766 6677776543
No 65
>PF02267 Rib_hydrolayse: ADP-ribosyl cyclase; InterPro: IPR003193 CD38, the HUGO gene name, is also called T10 or ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase (3.2.2.5 from EC). CD38 is a novel enzyme capable of catalysing multiple reactions, including NAD glycohydrolase, ADP-ribosyl cyclase, cyclic ADP ribose hydrolase and base-exchange activities. Two of the enzymatic products, cyclic ADP-ribose (cADPR) and nicotinic acid adenine dinucleotide phosphate (NAADP), are calcium messengers in a wide variety of cells from protist, plant, and mammal to human. CD38 is a positive and negative regulator of cell activation and proliferation, depending on the cellular environment. It is involved in adhesion between human lymphocytes and endothelial cells and is involved in the metabolism of two calcium messengers, cADPR and NAADP. CD157 (also called BP-3/IF-7, BST-1 or Mo5) has ADP-ribosyl cyclase and cyclic ADP-ribose hydrolase activities. CD157 supports the growth of a pre-B cell line, DW34. Anti-CD157 mAb IF-7 has synergistic effects on anti-CD3-induced growth of T progenitor cells, and facilitates the development of [alpha][beta] TCR+ cells in foetal thymic organ culture system. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/).; GO: 0003953 NAD+ nucleosidase activity; PDB: 2EG9_B 1YH3_A 3DZF_C 2HCT_A 2O3R_A 3DZI_A 1ZVM_D 3I9M_B 2I66_B 2O3T_B ....
Probab=49.65 E-value=11 Score=35.53 Aligned_cols=36 Identities=33% Similarity=0.707 Sum_probs=29.7
Q ss_pred eceEEEEECCeeeeecCcccchhhccCC--------------ceEEEecCCCc
Q 047211 218 TGFITVFINGAPTEIPRGPIDMKALFGQ--------------DVVLVHSSGVP 256 (282)
Q Consensus 218 ~g~~tVfINgv~~EV~~Gp~dvr~~FG~--------------davLvhSsG~p 256 (282)
.|.++|+.|| .++.||||...+||+ .+.|||.-|.+
T Consensus 147 ~G~V~VmLNG---S~~~~af~~~S~Fg~vElpnL~~~kV~~l~i~vvh~~~~~ 196 (243)
T PF02267_consen 147 CGVVHVMLNG---SRPGGAFDNNSFFGSVELPNLNPDKVTRLEIWVVHDIEGP 196 (243)
T ss_dssp BEEEEEEEET---TSSTSSS-TTSHHHHCTGGGS-TTTEEEEEEEEEESSSSS
T ss_pred cceEEEEeeC---CCCCCCCCCcCcceeeecccCCccceeEEEEEEEecCCCC
Confidence 5899999999 578899999999996 47899987654
No 66
>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=48.92 E-value=21 Score=29.29 Aligned_cols=40 Identities=35% Similarity=0.516 Sum_probs=24.1
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHHh
Q 047211 50 ILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQAS 108 (282)
Q Consensus 50 L~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~ 108 (282)
+++..-.|+.|+ ||..+... ..= -|||-|||++++|...-
T Consensus 14 vRiIk~LyqsnP-yP~~~GTr---~aR---------------RnRRRRWR~rq~QI~~l 53 (91)
T PF00424_consen 14 VRIIKILYQSNP-YPSPEGTR---QAR---------------RNRRRRWRARQRQIRAL 53 (91)
T ss_dssp HHHHHHHHHTS--S--S-S-H---HHH---------------HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcccc-CCCCCCcc---ccc---------------cchhhhHHHHHHHHHHH
Confidence 455666788888 58765321 111 28999999999988764
No 67
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=48.88 E-value=15 Score=42.09 Aligned_cols=63 Identities=29% Similarity=0.277 Sum_probs=51.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHH
Q 047211 35 STEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQ 102 (282)
Q Consensus 35 ~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~ 102 (282)
.-+.++.|...=++++.+|=+.|..++ .|+...+..|-.+. ..++++++.||+|=|.|+++.+
T Consensus 702 ~~~~~~~~~~~~~~aa~~l~~a~~~~~-sps~k~~~civcd~----~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 702 SPRDKLLRLTILPEAAMILGRAYMQDN-SPSLKVFDCIVCDV----FSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CcccccCcccccHHHHhhhhhcccCCC-CHHHHHHHHhhhhh----hhhhhHHHHhhcchhhhhhhhc
Confidence 335567777777899999999999988 68877665555554 5889999999999999999887
No 68
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=48.51 E-value=14 Score=31.78 Aligned_cols=47 Identities=15% Similarity=0.084 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
.+++.|..+|...|-.+. . ..+|++.| |+++..|+.|...=|.+.|+
T Consensus 142 ~L~~~~r~vl~l~~~~~~--s----~~EIA~~L----gis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 142 ALTDTQRESVTLAYYGGL--T----YREVAERL----AVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHh----CCChHhHHHHHHHHHHHHHH
Confidence 456666777766655542 1 13455555 89999998877544444443
No 69
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=48.37 E-value=13 Score=30.54 Aligned_cols=49 Identities=6% Similarity=-0.090 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
+++.|.+++...|-.+. +. .+||+.| |+++..|+++...=|.+.|+..+
T Consensus 107 Lp~~~r~v~~l~~~~g~--s~----~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK--SY----QEIALQE----KIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred CCHHHHHHHHHHHHhCC--CH----HHHHHHH----CCCHHHHHHHHHHHHHHHHHHHh
Confidence 44555666665555543 11 2344554 89999999988766666665543
No 70
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=45.76 E-value=10 Score=30.71 Aligned_cols=47 Identities=13% Similarity=0.080 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
.+++.|.++++..|-.+. . ..+||+.| |+++..|+.|...=|.|.|+
T Consensus 106 ~L~~~~r~ii~l~~~~~~--s----~~EIA~~l----~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGK--T----MGEIALET----EMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcCC--C----HHHHHHHH----CCCHHHHHHHHHHHHHHHhh
Confidence 455667777766665553 1 23455555 89999999887655554443
No 71
>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=45.72 E-value=8.3 Score=26.64 Aligned_cols=41 Identities=12% Similarity=0.076 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccc
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNR 94 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNR 94 (282)
..++.+..++...|-.+. +. +++++.+|+++..|+.|.+.=
T Consensus 10 ~L~~~~r~i~~l~~~~g~--s~--------~eIa~~l~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQGM--SY--------AEIAEILGISESTVKRRLRRA 50 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----H--------HHHHHHCTS-HHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHCc--CH--------HHHHHHHCcCHHHHHHHHHHH
Confidence 356888888988888874 22 344444589999999998643
No 72
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=44.46 E-value=15 Score=31.28 Aligned_cols=48 Identities=19% Similarity=0.117 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQ 102 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~ 102 (282)
+++++.++|+..|-.+. + ..+||+.| |+++..|+.|...-|.|.|+..
T Consensus 142 L~~~~~~v~~l~~~~g~--s----~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 142 LPESQRQVLELAYYEGL--S----QSEIAKRL----GIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred CCHHHhhhhhhhhhcCC--C----HHHHHHHh----CCCHHHHHHHHHHHHHHHHHHH
Confidence 45566666666554442 1 12345555 8999999999976666665543
No 73
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=44.04 E-value=16 Score=31.81 Aligned_cols=47 Identities=9% Similarity=0.101 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRR 101 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk 101 (282)
++++|.++|...|-.+. + ..+||+.| |+++..|+.+...-|.+.|+.
T Consensus 154 L~~~~r~vl~l~~~~g~---s---~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 154 LPEAQQTVVKGVYFQEL---S---QEQLAQQL----NVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred CCHHHHHHHHHHHHcCC---C---HHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 45566666665554442 1 13455555 899999987775554444443
No 74
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=43.54 E-value=18 Score=29.56 Aligned_cols=29 Identities=14% Similarity=0.005 Sum_probs=20.0
Q ss_pred HHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 75 LLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 75 eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
++++.+|+++..|+.|..-=|.|.|+.-.
T Consensus 146 eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 146 EIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 44555589999999988766655555443
No 75
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=43.05 E-value=14 Score=27.50 Aligned_cols=60 Identities=15% Similarity=0.103 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHHHHhcCCCC-----CCH---HHH----HHHHHHHHhcCCC--CCCceeecccccchhhHHHH
Q 047211 43 WTPKPEQILILESIFNSGMVN-----PPK---DET----VRIRKLLEKFGSV--GDANVFYWFQNRRSRSRRRQ 102 (282)
Q Consensus 43 t~fT~eQL~~LE~~F~~~~~y-----P~~---~eR----~~Ia~eLa~~~~L--se~qVkvWFQNRRAK~KRk~ 102 (282)
.+||++|+.+|-.++...+.. .+. .++ .+|+..|...++. +..+++..+.|-+.+.|++.
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk~~ 76 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKKKL 76 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 478999999999988774210 111 111 2577777766553 22335555666666666553
No 76
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=42.49 E-value=38 Score=25.89 Aligned_cols=44 Identities=27% Similarity=0.441 Sum_probs=33.6
Q ss_pred eEEEEECCeeeeecCc--ccchhhc--cCCceEEEecCCCccccCCcc
Q 047211 220 FITVFINGAPTEIPRG--PIDMKAL--FGQDVVLVHSSGVPIPTNEFG 263 (282)
Q Consensus 220 ~~tVfINgv~~EV~~G--p~dvr~~--FG~davLvhSsG~pvptne~G 263 (282)
.|||.+||.+.|++.+ --|+=+. |.++-+.|-=.|++||-.+|-
T Consensus 2 ~m~i~~ng~~~e~~~~~tv~dLL~~l~~~~~~vav~vNg~iVpr~~~~ 49 (68)
T COG2104 2 PMTIQLNGKEVEIAEGTTVADLLAQLGLNPEGVAVAVNGEIVPRSQWA 49 (68)
T ss_pred cEEEEECCEEEEcCCCCcHHHHHHHhCCCCceEEEEECCEEccchhhh
Confidence 4899999999999986 2344333 556778888899999977763
No 77
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=41.55 E-value=47 Score=24.17 Aligned_cols=57 Identities=28% Similarity=0.473 Sum_probs=40.0
Q ss_pred EEEECCeeeeecCc--ccchhhccCCc--eEEEecCCCccccCCccccccccCCcceEEEeec
Q 047211 222 TVFINGAPTEIPRG--PIDMKALFGQD--VVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSR 280 (282)
Q Consensus 222 tVfINgv~~EV~~G--p~dvr~~FG~d--avLvhSsG~pvptne~Gvt~~sLq~G~~Y~Lv~~ 280 (282)
+|.|||.++|++.+ .-||-+.+|-+ -+.|-=.|.+|+-++|=-+ .|+.|....|++.
T Consensus 1 ~i~iNg~~~~~~~~~tv~~ll~~l~~~~~~i~V~vNg~~v~~~~~~~~--~L~~gD~V~ii~~ 61 (65)
T cd00565 1 KITVNGEPREVEEGATLAELLEELGLDPRGVAVALNGEIVPRSEWAST--PLQDGDRIEIVTA 61 (65)
T ss_pred CEEECCeEEEcCCCCCHHHHHHHcCCCCCcEEEEECCEEcCHHHcCce--ecCCCCEEEEEEe
Confidence 47899999999865 34555666543 3445567888888877544 5888887777653
No 78
>PRK09828 putative fimbrial outer membrane usher protein; Provisional
Probab=41.28 E-value=34 Score=37.12 Aligned_cols=39 Identities=23% Similarity=0.437 Sum_probs=28.9
Q ss_pred eceEEEEECCee---eeecCcccchhhc----cC-C-ceEEEecCCCc
Q 047211 218 TGFITVFINGAP---TEIPRGPIDMKAL----FG-Q-DVVLVHSSGVP 256 (282)
Q Consensus 218 ~g~~tVfINgv~---~EV~~Gp~dvr~~----FG-~-davLvhSsG~p 256 (282)
..++||+.||.. ..||.|||.+... .| | ++++..+.|..
T Consensus 294 nA~V~V~QnG~~iy~t~VppGPF~I~Dl~~~g~ggdL~VtV~EadG~~ 341 (865)
T PRK09828 294 NAKVTITQSGYKIYETTVPPGAFVIDDLSPSGYGSDLIVTIEEADGSK 341 (865)
T ss_pred CcEEEEEECCEEEEEeEcCCCceEecccccCCCCCcEEEEEEECCCCE
Confidence 468999999986 5799999977655 55 4 45556678863
No 79
>COG3188 FimD P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=40.88 E-value=33 Score=37.43 Aligned_cols=39 Identities=33% Similarity=0.542 Sum_probs=31.1
Q ss_pred eceEEEEECCee---eeecCcccchhhcc-----CC-ceEEEecCCCc
Q 047211 218 TGFITVFINGAP---TEIPRGPIDMKALF-----GQ-DVVLVHSSGVP 256 (282)
Q Consensus 218 ~g~~tVfINgv~---~EV~~Gp~dvr~~F-----G~-davLvhSsG~p 256 (282)
++++||+.||.. ..||.|||.+...+ || ||.+..+.|..
T Consensus 289 nA~V~V~QnG~~IY~t~VppGpF~I~dl~~~~~~GdL~V~V~EadGs~ 336 (835)
T COG3188 289 NARVTVSQNGYVIYQTTVPPGPFEINDLPPTSGSGDLDVTVKEADGSV 336 (835)
T ss_pred CcEEEEEECCEEEEEeecCCCCeEeccccccCCCceEEEEEEECCCCE
Confidence 468999999987 57999999998887 44 56666778864
No 80
>PF13551 HTH_29: Winged helix-turn helix
Probab=40.49 E-value=79 Score=24.07 Aligned_cols=53 Identities=15% Similarity=0.015 Sum_probs=32.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCC--HHHHHHHHHHH-HhcCC--CCCCceeecc
Q 047211 38 PVRSRWTPKPEQILILESIFNSGMVNPP--KDETVRIRKLL-EKFGS--VGDANVFYWF 91 (282)
Q Consensus 38 ~kR~Rt~fT~eQL~~LE~~F~~~~~yP~--~~eR~~Ia~eL-a~~~~--Lse~qVkvWF 91 (282)
+.+++..+++++++.|++.+...+.. + .-....|++.| .+..+ ++...|..|+
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 44555559999999999999986421 1 11234566665 44444 4555565554
No 81
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=40.36 E-value=18 Score=30.23 Aligned_cols=49 Identities=10% Similarity=0.122 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQ 102 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~ 102 (282)
.+++.+.++|+..|-.+. +. .+||+. +|+++..|+++.+.-|.|.|...
T Consensus 136 ~L~~~~r~v~~l~~~~g~--s~----~eIA~~----lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMEDL--SL----KEISEI----LDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHhcCC--CH----HHHHHH----HCCCHHHHHHHHHHHHHHHHHHh
Confidence 345555555555444432 11 234455 48999999999876666666543
No 82
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=40.35 E-value=20 Score=30.14 Aligned_cols=50 Identities=20% Similarity=0.082 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
.+++.+.++|...|-.+. +. +++++.+|++...|+.+...=|.|.|++.+
T Consensus 131 ~L~~~~r~v~~l~~~~g~---s~-------~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVEGA---SI-------KETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHcCC---CH-------HHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 345566666666554442 11 244444589999999988777777776554
No 83
>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=39.89 E-value=18 Score=27.90 Aligned_cols=47 Identities=15% Similarity=0.185 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
.+++.|.++|...|-.+. +. .+||++| |+++..|..|...=|.|.|+
T Consensus 110 ~L~~~~~~ii~~~~~~g~--s~----~eIA~~l----~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLEGL--SY----KEIAEIL----GISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhcCC--CH----HHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 456777777777655542 21 2455555 89999999887665555443
No 84
>PF13565 HTH_32: Homeodomain-like domain
Probab=39.81 E-value=50 Score=24.10 Aligned_cols=39 Identities=23% Similarity=0.159 Sum_probs=27.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCC
Q 047211 38 PVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSV 82 (282)
Q Consensus 38 ~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~L 82 (282)
+.|+|. ++++.+.|.+....++. -+. .+|+..|.+.+|+
T Consensus 26 ~Grp~~--~~e~~~~i~~~~~~~p~-wt~---~~i~~~L~~~~g~ 64 (77)
T PF13565_consen 26 PGRPRK--DPEQRERIIALIEEHPR-WTP---REIAEYLEEEFGI 64 (77)
T ss_pred CCCCCC--cHHHHHHHHHHHHhCCC-CCH---HHHHHHHHHHhCC
Confidence 334445 78888999999998642 343 4678888887764
No 85
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=39.35 E-value=10 Score=26.08 Aligned_cols=39 Identities=23% Similarity=0.201 Sum_probs=16.8
Q ss_pred CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeec
Q 047211 42 RWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYW 90 (282)
Q Consensus 42 Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvW 90 (282)
...+|.+|...++..++.+. + ..+||+.| |++...|..|
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~---s---~~~IA~~l----g~s~sTV~re 40 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGM---S---IREIAKRL----GRSRSTVSRE 40 (44)
T ss_dssp ----------HHHHHHCS---------HHHHHHHT----T--HHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcCC---C---HHHHHHHH----CcCcHHHHHH
Confidence 35688999999999998874 2 23466666 7887776554
No 86
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=38.86 E-value=25 Score=28.87 Aligned_cols=49 Identities=16% Similarity=0.148 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
.++++|..+|.-.| .+. +. .+||+.| |+++..|+.+...=|.+.|+...
T Consensus 112 ~L~~~~r~il~l~~-~g~--s~----~eIA~~l----gis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 112 KMTERDRTVLLLRF-SGY--SY----KEIAEAL----GIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred cCCHHHHHHHHHHH-cCC--CH----HHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 35666777777777 542 21 2345555 89999999988655555555444
No 87
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=37.94 E-value=25 Score=29.87 Aligned_cols=48 Identities=8% Similarity=0.149 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRR 101 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk 101 (282)
.++++|.++|+..|-.+. +. .+||+.| |+++..|++....=|.+.|+.
T Consensus 131 ~L~~~~r~vl~l~~~~~~---s~---~eIA~~l----gis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYYHEK---SV---EEVGEIV----GIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHHcCC---CH---HHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 456666677766655542 11 2345555 899999998775555555543
No 88
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=37.20 E-value=12 Score=24.67 Aligned_cols=38 Identities=16% Similarity=0.276 Sum_probs=25.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQ 92 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQ 92 (282)
.+++++.++++.++ .+. + ..+|++.| +++...|..|.+
T Consensus 3 ~l~~~e~~i~~~~~-~g~---s---~~eia~~l----~is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRLLA-EGL---T---NKEIAERL----GISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHHHH-cCC---C---HHHHHHHH----CCCHHHHHHHHH
Confidence 36788999887744 432 1 23455555 899999987766
No 89
>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=37.17 E-value=9.9 Score=26.93 Aligned_cols=45 Identities=9% Similarity=0.049 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSR 99 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~K 99 (282)
.+|+.++++|+-...-.. ..+|+++| +++++.|+.+..|=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G~~-------~~eIA~~l----~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMS-------NKEIAEEL----GISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS--------HHHHHHHH----TSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcCC-------cchhHHhc----CcchhhHHHHHHHHHHHhC
Confidence 589999999998887742 24577777 7999999988766555543
No 90
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=36.63 E-value=24 Score=31.97 Aligned_cols=31 Identities=16% Similarity=0.059 Sum_probs=22.0
Q ss_pred HHHhcCCCCCCceeecccccchhhHHHHHHH
Q 047211 75 LLEKFGSVGDANVFYWFQNRRSRSRRRQRQL 105 (282)
Q Consensus 75 eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~ 105 (282)
++++.+|+++..|+++.+.=|.|.|+.....
T Consensus 192 EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~~ 222 (233)
T PRK12538 192 EIAEVMDTTVAAVESLLKRGRQQLRDLLRRH 222 (233)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 4444458999999998877777776655433
No 91
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=35.96 E-value=25 Score=29.74 Aligned_cols=47 Identities=9% Similarity=0.004 Sum_probs=27.0
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHH
Q 047211 46 KPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQ 102 (282)
Q Consensus 46 T~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~ 102 (282)
++.+.++|+..|-.+. + . +++++.+|++...|+.+...=|.+.|+..
T Consensus 130 ~~~~r~i~~l~~~~g~--s-~-------~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 130 PERQREAIVLQYYQGL--S-N-------IEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CHHHHHHhhHHHhcCC--C-H-------HHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 4555555555444432 1 1 24444458999999988755554444433
No 92
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=35.79 E-value=30 Score=29.01 Aligned_cols=47 Identities=9% Similarity=0.152 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRR 101 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk 101 (282)
.++++.++|...|-.+. + ..+||+.| |+++..|+++.+.=|.+.|+.
T Consensus 130 L~~~~r~i~~l~~~~g~--s----~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 130 LEKDRAAAVRRAYLEGL--S----YKELAERH----DVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CCHHHHHHHHHHHHcCC--C----HHHHHHHH----CCChHHHHHHHHHHHHHHHHH
Confidence 34455555555554432 1 12345555 899999988876655555543
No 93
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=35.46 E-value=41 Score=28.35 Aligned_cols=36 Identities=8% Similarity=0.043 Sum_probs=27.2
Q ss_pred HHHhcCCCCCCceeecccccchhhHHHHHHHHHhhh
Q 047211 75 LLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQASLA 110 (282)
Q Consensus 75 eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~~~ 110 (282)
++++.+|+++..|++....=|.+.|+...+......
T Consensus 138 EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~~~~ 173 (179)
T PRK12543 138 EIAQLLQIPIGTVKSRIHAALKKLRQKEQIEEIFLG 173 (179)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445555899999999988888888887777665543
No 94
>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=35.08 E-value=23 Score=28.76 Aligned_cols=39 Identities=13% Similarity=0.135 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQ 92 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQ 92 (282)
.+++.|.+++...|-.+. + ..+|++.| ||+...|+++..
T Consensus 111 ~L~~~~r~v~~l~~~~g~--~----~~eIA~~l----~is~~tv~~~l~ 149 (159)
T TIGR02989 111 KLPERQRELLQLRYQRGV--S----LTALAEQL----GRTVNAVYKALS 149 (159)
T ss_pred HCCHHHHHHHHHHHhcCC--C----HHHHHHHh----CCCHHHHHHHHH
Confidence 467777777777665553 2 12345555 899999997644
No 95
>PRK10072 putative transcriptional regulator; Provisional
Probab=34.78 E-value=19 Score=29.25 Aligned_cols=41 Identities=17% Similarity=0.007 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccch
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRS 96 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRA 96 (282)
..++..|+.|-..-.-. . .+|++.+|++...|..|.+.||.
T Consensus 32 ~~~~~eik~LR~~~glT--------Q----~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGLK--------I----DDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCCC--------H----HHHHHHhCCCHHHHHHHHcCCCC
Confidence 45777788875433332 1 45666668999999999999875
No 96
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=34.72 E-value=27 Score=28.92 Aligned_cols=51 Identities=8% Similarity=-0.090 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQ 104 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~ 104 (282)
.++++|.++|...|-.+. + ..+||+.| |+++..|+.|.+-=|.|.|+.-++
T Consensus 108 ~L~~~~r~v~~l~~~~g~--s----~~eIA~~l----gis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 108 TLPVIEAQAILLCDVHEL--T----YEEAASVL----DLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred hCCHHHHHHHHhHHHhcC--C----HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHh
Confidence 345555555554443332 1 12345555 899999988877666666555443
No 97
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=34.46 E-value=18 Score=30.20 Aligned_cols=40 Identities=18% Similarity=0.315 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccch
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRS 96 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRA 96 (282)
+++.+|.++.+-++-.+ .++++.+|++...|+.|=|+|+.
T Consensus 44 ls~~eIk~iRe~~~lSQ------------~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLGLSQ------------PVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhCCCH------------HHHHHHHCCCHHHHHHHHcCCcC
Confidence 77888888887777653 36677779999999999999975
No 98
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=34.22 E-value=29 Score=29.69 Aligned_cols=39 Identities=10% Similarity=-0.070 Sum_probs=24.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQ 92 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQ 92 (282)
.++++|.++|...|-.+. + .++++..+|+++..|+.++.
T Consensus 106 ~L~~~~r~i~~l~~~~g~--~--------~~EIA~~lgis~~tV~~~l~ 144 (181)
T PRK09637 106 ALPEKYAEALRLTELEGL--S--------QKEIAEKLGLSLSGAKSRVQ 144 (181)
T ss_pred hCCHHHHHHHHHHHhcCC--C--------HHHHHHHhCCCHHHHHHHHH
Confidence 455666666666555542 2 13445555899999988875
No 99
>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=34.13 E-value=19 Score=23.96 Aligned_cols=37 Identities=16% Similarity=0.283 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQ 92 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQ 92 (282)
+++.|.++++.++ .+. + ..+|++.| +++...|+.|..
T Consensus 1 l~~~e~~i~~~~~-~~~---s---~~eia~~l----~~s~~tv~~~~~ 37 (57)
T cd06170 1 LTPREREVLRLLA-EGK---T---NKEIADIL----GISEKTVKTHLR 37 (57)
T ss_pred CCHHHHHHHHHHH-cCC---C---HHHHHHHH----CCCHHHHHHHHH
Confidence 3567788887654 332 2 23455555 899999988874
No 100
>PRK06930 positive control sigma-like factor; Validated
Probab=33.79 E-value=31 Score=30.25 Aligned_cols=51 Identities=10% Similarity=0.094 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQ 104 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~ 104 (282)
.+++.+.++|...|..+. . ..+||+.| |+++..|+.|...-|.|.++...+
T Consensus 114 ~L~~rer~V~~L~~~eg~--s----~~EIA~~l----giS~~tVk~~l~Ra~~kLr~~l~~ 164 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGL--S----YSEIADYL----NIKKSTVQSMIERAEKKIARQINE 164 (170)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHHH
Confidence 577777787777665553 2 13455555 899999999988777777765544
No 101
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=33.49 E-value=47 Score=30.34 Aligned_cols=58 Identities=12% Similarity=0.024 Sum_probs=42.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHH
Q 047211 38 PVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQ 106 (282)
Q Consensus 38 ~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q 106 (282)
|.=+|-.||+|.-++|-+....- =+ .-..||+.|- |=++..||++. .++.||+.++..
T Consensus 58 P~ikrg~fT~eEe~~Ii~lH~~~---GN--rWs~IA~~LP---GRTDNeIKN~W---nt~lkkkl~~~~ 115 (238)
T KOG0048|consen 58 PDLKRGNFSDEEEDLIIKLHALL---GN--RWSLIAGRLP---GRTDNEVKNHW---NTHLKKKLLKMG 115 (238)
T ss_pred CCccCCCCCHHHHHHHHHHHHHH---Cc--HHHHHHhhCC---CcCHHHHHHHH---HHHHHHHHHHcC
Confidence 44457789999988888887772 22 2567899987 78888899442 777777777665
No 102
>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=33.47 E-value=27 Score=29.18 Aligned_cols=46 Identities=24% Similarity=0.232 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
+.+.|..+++..|-.+. . ..+||+.| |+++..|++....=|.+.|+
T Consensus 135 Lp~~~r~v~~l~~~~g~--s----~~EIA~~l----gis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGL--T----VEEIAELL----GVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcCC--C----HHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 55666666666665553 1 12455555 89999999888765555554
No 103
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=33.14 E-value=21 Score=30.53 Aligned_cols=26 Identities=4% Similarity=-0.115 Sum_probs=15.3
Q ss_pred HHHhcCCCCCCceeecccccchhhHH
Q 047211 75 LLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 75 eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
+++..+|+++..|++....-|.|.|+
T Consensus 175 EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 175 EIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34444489999998644443333333
No 104
>PRK04217 hypothetical protein; Provisional
Probab=32.79 E-value=34 Score=28.49 Aligned_cols=48 Identities=15% Similarity=0.135 Sum_probs=33.6
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 43 WTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 43 t~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
-.++++|+++++..|..+. + ..+||+.| +++...|+..+..-|.+.|.
T Consensus 41 ~~Lt~eereai~l~~~eGl---S---~~EIAk~L----GIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL---T---QEEAGKRM----GVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC---C---HHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 3578999999998887753 2 23455555 89999999777655444443
No 105
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=31.84 E-value=19 Score=24.70 Aligned_cols=39 Identities=23% Similarity=0.391 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecc
Q 047211 43 WTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWF 91 (282)
Q Consensus 43 t~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWF 91 (282)
..++++|++.+-+.+..+. + +.+||+++ ||+...|.-|+
T Consensus 4 ~~~~~~~~~~i~~l~~~G~--s----i~~IA~~~----gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEGM--S----IAEIAKQF----GVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT--------HHHHHHHT----TS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCCC--C----HHHHHHHH----CcCHHHHHHHH
Confidence 3478889999999999983 2 33455555 89988876543
No 106
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=31.77 E-value=37 Score=28.56 Aligned_cols=47 Identities=13% Similarity=0.038 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
.+++.+..+|+-.|-.+. +- .+||++| |+++..|+.+-+-=|.+.|+
T Consensus 100 ~L~~~~r~v~~l~~~~g~--s~----~eIA~~l----gis~~tV~~~l~Rar~~Lr~ 146 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGL--SQ----QEIAEKL----GLSLSGAKSRVQRGRKKLKE 146 (170)
T ss_pred hCCHHHHHHHHHHHHcCC--CH----HHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 567777777777766653 21 2455555 89999999877544444433
No 107
>COG4276 Uncharacterized conserved protein [Function unknown]
Probab=31.61 E-value=23 Score=31.34 Aligned_cols=18 Identities=39% Similarity=0.554 Sum_probs=16.1
Q ss_pred eceEEEEECCeeeeecCc
Q 047211 218 TGFITVFINGAPTEIPRG 235 (282)
Q Consensus 218 ~g~~tVfINgv~~EV~~G 235 (282)
.|-=||.||.|.+|+|.|
T Consensus 103 egg~TvliD~Vsye~p~g 120 (153)
T COG4276 103 EGGGTVLIDSVSYELPAG 120 (153)
T ss_pred CCCcEEEEeeEEeeccCc
Confidence 456789999999999999
No 108
>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=31.36 E-value=26 Score=29.32 Aligned_cols=29 Identities=10% Similarity=-0.059 Sum_probs=19.1
Q ss_pred HHHHhcCCCCCCceeecccccchhhHHHH
Q 047211 74 KLLEKFGSVGDANVFYWFQNRRSRSRRRQ 102 (282)
Q Consensus 74 ~eLa~~~~Lse~qVkvWFQNRRAK~KRk~ 102 (282)
+++++.+|+++..|++|...=|.|.|+..
T Consensus 158 ~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 158 EDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34555558999999988755555555443
No 109
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=30.36 E-value=39 Score=27.45 Aligned_cols=46 Identities=7% Similarity=-0.043 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
+++.|.+++.-.|-.+. +. .+||+.| |+++..|+++..-=|.+.|+
T Consensus 107 Lp~~~r~v~~l~~~~g~--s~----~EIA~~l----gis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 107 LPARQREAFLLRYWEDM--DV----AETAAAM----GCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred CCHHHHHHHHHHHHhcC--CH----HHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 44555555555444432 21 2344554 89999998776544444443
No 110
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=30.34 E-value=40 Score=28.91 Aligned_cols=48 Identities=8% Similarity=0.010 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQ 102 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~ 102 (282)
+++.|.++|.-.|-.+. . ..+||+.| |+++..|++|..-=|.+.|+..
T Consensus 135 Lp~~~R~v~~L~~~~g~--s----~~EIA~~l----gis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 135 LPAQQARVFMMREYLEL--S----SEQICQEC----DISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred CCHHHHHHHhHHHHcCC--C----HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 45556666666655542 1 12345555 8999999998765555555443
No 111
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=30.31 E-value=39 Score=28.83 Aligned_cols=49 Identities=8% Similarity=0.089 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
+++.|.++++-.|-.+. . - +++++.+|++...|+.+...-|.+.|+...
T Consensus 137 L~~~~r~i~~L~~~~g~--s----~----~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 137 LPENTARVFTLKEILGF--S----S----DEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred CCHHHHHHhhhHHHhCC--C----H----HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 44555566655444432 1 1 344444589999999888766666666543
No 112
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=30.29 E-value=41 Score=28.44 Aligned_cols=45 Identities=16% Similarity=0.205 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSR 99 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~K 99 (282)
+++.|.+++...|-.+. + ..+||+.| |+++..|++|-..=|.+.|
T Consensus 134 L~~~~r~i~~l~~~~~~--s----~~eIA~~l----gis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 134 LEPARRNCILHAYVDGC--S----HAEIAQRL----GAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred CCHHHHHHHHHHHHcCC--C----HHHHHHHH----CCChhhHHHHHHHHHHHHH
Confidence 45566666666665543 2 13455565 8999999987654444443
No 113
>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=30.25 E-value=32 Score=28.18 Aligned_cols=46 Identities=11% Similarity=0.127 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
+++++.++|+..|-.+. +. .+||+.| |+++..|+.|-..-|.+.|+
T Consensus 111 L~~~~r~i~~l~~~~g~--s~----~eIA~~l----gis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 111 LPARQRAVVVLRYYEDL--SE----AQVAEAL----GISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CCHHHHHHhhhHHHhcC--CH----HHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 35666666666665542 21 2345555 89999999876655555554
No 114
>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=29.94 E-value=34 Score=27.36 Aligned_cols=45 Identities=13% Similarity=-0.048 Sum_probs=25.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSR 99 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~K 99 (282)
+++.+.++|...|-.+. +. +++++.+|+++..|+.+...=|.|.|
T Consensus 114 L~~~~r~il~l~~~~~~--~~--------~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 114 LPEQCRKIFILSRFEGK--SY--------KEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CCHHHHHHHHHHHHcCC--CH--------HHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45566666666444432 21 23444458999999877655444444
No 115
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=29.58 E-value=28 Score=28.62 Aligned_cols=47 Identities=15% Similarity=0.051 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
.+++.|..+|+-.|-.+. +. .+||+.| |+++..|+.+...=|.|.|+
T Consensus 112 ~L~~~~r~v~~l~~~~~~--s~----~eIA~~l----gis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYYGF--SY----KEIAEMT----GLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhcCC--CH----HHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 466777777777665552 22 2355555 89999999887655555554
No 116
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=29.30 E-value=33 Score=28.35 Aligned_cols=53 Identities=26% Similarity=0.460 Sum_probs=29.3
Q ss_pred EEEECCeeeeecCcccchhhccCC---ceE----EEec--CCCccccCCccccccccCCcceEEEeecC
Q 047211 222 TVFINGAPTEIPRGPIDMKALFGQ---DVV----LVHS--SGVPIPTNEFGFLMQSLQHGESYFLVSRP 281 (282)
Q Consensus 222 tVfINgv~~EV~~Gp~dvr~~FG~---dav----LvhS--sG~pvptne~Gvt~~sLq~G~~Y~Lv~~~ 281 (282)
.|..||...|. ..|+-+.++-.+ -+| ..+. .-.+|+-|| -|+-|..||||+..
T Consensus 20 vv~~~G~v~~~-~~pv~a~evm~~~P~h~v~~~~~~~~~~~~~~l~~d~------~L~~G~~Y~llP~~ 81 (181)
T PF14009_consen 20 VVHPDGKVEEF-KRPVTAAEVMLENPGHFVCDSDSFRFGRRIKPLPPDE------ELQPGQIYFLLPMS 81 (181)
T ss_pred EEcCCCcEEEe-CCCcCHHHHHHHCCCCEEeccccccCCCcccCCCccC------eecCCCEEEEEEcc
Confidence 35567777776 456665543222 111 1111 122344443 58999999999864
No 117
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=29.17 E-value=36 Score=28.87 Aligned_cols=46 Identities=17% Similarity=0.023 Sum_probs=27.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSR 99 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~K 99 (282)
.+.+.|.++++..|-.+. . ..+||+.| |++...|+.+...=|.|.|
T Consensus 139 ~L~~~~r~i~~l~~~~g~--s----~~EIA~~l----gis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 139 TLPEKQREILILRVVVGL--S----AEETAEAV----GSTPGAVRVAQHRALARLR 184 (189)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 455666666666555542 1 12345555 8999999987744333333
No 118
>PHA02955 hypothetical protein; Provisional
Probab=28.68 E-value=70 Score=29.90 Aligned_cols=44 Identities=11% Similarity=0.051 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccc
Q 047211 47 PEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNR 94 (282)
Q Consensus 47 ~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNR 94 (282)
..|+..|-+.|.+---..++++|.+++++| |+....|..||++.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~l----gI~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADI----GINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHh----CCChhhccCcccch
Confidence 456666655555531126677888888887 68776688999873
No 119
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=28.58 E-value=50 Score=25.50 Aligned_cols=48 Identities=21% Similarity=0.234 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHHHHHhcCCCC-CCHHHHHHHHHHHHhcCCCCCCceeecc
Q 047211 43 WTPKPEQILILESIFNSGMVN-PPKDETVRIRKLLEKFGSVGDANVFYWF 91 (282)
Q Consensus 43 t~fT~eQL~~LE~~F~~~~~y-P~~~eR~~Ia~eLa~~~~Lse~qVkvWF 91 (282)
|-+|.+|+..|..+|...-.. -+.-...++++-|.. .++++..|.-+|
T Consensus 2 ~~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~-~~~~~~ev~~i~ 50 (96)
T smart00027 2 WAISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLK-SGLPQTLLAKIW 50 (96)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHH-cCCCHHHHHHHH
Confidence 778999999999999883211 122223344555543 356555544443
No 120
>PRK00118 putative DNA-binding protein; Validated
Probab=27.69 E-value=51 Score=27.21 Aligned_cols=49 Identities=10% Similarity=0.046 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
.++.|.+++...|..+. . ..+|++.+ |+++..|+.|...-|.+.|....
T Consensus 18 L~ekqRevl~L~y~eg~--S----~~EIAe~l----GIS~~TV~r~L~RArkkLr~~~~ 66 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY--S----LGEIAEEF----NVSRQAVYDNIKRTEKLLEDYEE 66 (104)
T ss_pred CCHHHHHHHHHHHHcCC--C----HHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 46788888888888764 2 23455555 89999999988766655555443
No 121
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=27.04 E-value=37 Score=30.26 Aligned_cols=48 Identities=17% Similarity=0.154 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQ 102 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~ 102 (282)
+.+.|.++|...|..++ + . +++++.+|++...|+.|...=|.|.|+..
T Consensus 185 L~~~~r~vl~l~~~~g~---s---~----~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 185 LPEREQLVLSLYYQEEL---N---L----KEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CCHHHHHHHHhHhccCC---C---H----HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34555566666555442 1 1 34444458999999999887777777654
No 122
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=26.88 E-value=45 Score=27.31 Aligned_cols=38 Identities=16% Similarity=0.087 Sum_probs=21.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQ 92 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQ 92 (282)
+++++.++|+..|-.+. + ..+||++| |++...|+.+..
T Consensus 110 L~~~~r~v~~l~~~~~~--s----~~EIA~~l----gis~~tV~~~l~ 147 (163)
T PRK07037 110 LPARTRYAFEMYRLHGE--T----QKDIAREL----GVSPTLVNFMIR 147 (163)
T ss_pred CCHHHHHHHHHHHHcCC--C----HHHHHHHH----CCCHHHHHHHHH
Confidence 44555555555444432 1 12345555 899999997643
No 123
>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=26.72 E-value=38 Score=28.06 Aligned_cols=47 Identities=6% Similarity=0.113 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
.+++.+.+++...|-.+. + .++||+.| |+++..|+++..-=|.+.|+
T Consensus 119 ~L~~~~r~i~~l~~~~g~--s----~~eiA~~l----gis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHDL--T----IKEIAEVM----NKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred hCCHHHhHHHHHHHHcCC--C----HHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 466777777777766653 2 12455555 89999998766544444443
No 124
>PTZ00305 NADH:ubiquinone oxidoreductase; Provisional
Probab=26.70 E-value=49 Score=32.24 Aligned_cols=22 Identities=27% Similarity=0.564 Sum_probs=17.9
Q ss_pred eEEEEECCeeeee-cCcc--cchhh
Q 047211 220 FITVFINGAPTEI-PRGP--IDMKA 241 (282)
Q Consensus 220 ~~tVfINgv~~EV-~~Gp--~dvr~ 241 (282)
+..|+|||+++|| |.|- +|+..
T Consensus 68 ~~~I~IDGk~VeV~~~G~TILeAAr 92 (297)
T PTZ00305 68 RAIMFVNKRPVEIIPQEENLLEVLE 92 (297)
T ss_pred ceEEEECCEEEEecCCCChHHHHHH
Confidence 6889999999999 8885 55544
No 125
>cd01616 TGS The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=26.70 E-value=99 Score=20.11 Aligned_cols=46 Identities=22% Similarity=0.441 Sum_probs=30.0
Q ss_pred EEEECCeeeeecCc--ccchhhcc----CCceEEEecCCCccccCCccccccccCCcc
Q 047211 222 TVFINGAPTEIPRG--PIDMKALF----GQDVVLVHSSGVPIPTNEFGFLMQSLQHGE 273 (282)
Q Consensus 222 tVfINgv~~EV~~G--p~dvr~~F----G~davLvhSsG~pvptne~Gvt~~sLq~G~ 273 (282)
.+++||..+++|.| +.|+...+ ..+++.+.-.|+++..+ ++|+.|.
T Consensus 3 ~~~~~~~~~~~~~g~t~~~~~~~~~~~~~~~~~~~~vn~~~~~l~------~~l~~~~ 54 (60)
T cd01616 3 IFTPDGSAVELPKGATAMDFALKIHTDLGKGFIGALVNGQLVDLS------YTLQDGD 54 (60)
T ss_pred EECCCCCEEEcCCCCCHHHHHHHHHHHHHhheEEEEECCEECCCC------cCcCCCC
Confidence 46678999999987 36665554 33556666677776654 5555554
No 126
>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=26.63 E-value=51 Score=22.59 Aligned_cols=13 Identities=23% Similarity=0.227 Sum_probs=11.5
Q ss_pred CCCHHHHHHHHHH
Q 047211 44 TPKPEQILILESI 56 (282)
Q Consensus 44 ~fT~eQL~~LE~~ 56 (282)
.||++|+..||.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 5999999999974
No 127
>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=26.57 E-value=29 Score=23.76 Aligned_cols=23 Identities=30% Similarity=0.263 Sum_probs=19.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCC
Q 047211 39 VRSRWTPKPEQILILESIFNSGM 61 (282)
Q Consensus 39 kR~Rt~fT~eQL~~LE~~F~~~~ 61 (282)
.+-|..||++|.+.|+..|..++
T Consensus 5 ~k~rl~Pt~~Q~~~L~~~~~~~R 27 (46)
T PF12323_consen 5 YKYRLYPTKEQEEKLERWFGACR 27 (46)
T ss_pred eEEEEecCHHHHHHHHHHHHHHH
Confidence 45688999999999999998875
No 128
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=26.47 E-value=42 Score=28.36 Aligned_cols=27 Identities=4% Similarity=-0.027 Sum_probs=18.8
Q ss_pred HHHhcCCCCCCceeecccccchhhHHH
Q 047211 75 LLEKFGSVGDANVFYWFQNRRSRSRRR 101 (282)
Q Consensus 75 eLa~~~~Lse~qVkvWFQNRRAK~KRk 101 (282)
++++.+|+++..|+++...-|.|.|+.
T Consensus 150 EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 150 ETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 444445899999999886655555553
No 129
>PRK15198 outer membrane usher protein FimD; Provisional
Probab=25.94 E-value=76 Score=34.58 Aligned_cols=38 Identities=24% Similarity=0.351 Sum_probs=27.3
Q ss_pred eceEEEEECCee---eeecCcccchhhc-----cCC-ceEEEecCCC
Q 047211 218 TGFITVFINGAP---TEIPRGPIDMKAL-----FGQ-DVVLVHSSGV 255 (282)
Q Consensus 218 ~g~~tVfINgv~---~EV~~Gp~dvr~~-----FG~-davLvhSsG~ 255 (282)
..++||+.||.. +.||.|||-+... -|| ++++....|.
T Consensus 287 ~A~V~V~QnG~~iYst~VppGPF~I~Dl~~~~~~GdL~VtV~EadG~ 333 (860)
T PRK15198 287 AAKLTIRQNGYVIYQSYVSPGAFAITDLNPTSSSGDLDVTVDEKDGN 333 (860)
T ss_pred CcEEEEEECCEEEEEeEeCCCCeEeccccCCCCCccEEEEEEECCCC
Confidence 469999999986 5899999877544 244 3444556777
No 130
>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=25.77 E-value=36 Score=25.48 Aligned_cols=41 Identities=12% Similarity=0.112 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeec
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYW 90 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvW 90 (282)
+|++|+..|+.+|.. ++ +.|.++-.+.-+.|-|+..+=..|
T Consensus 1 lT~~Qk~el~~l~~q-m~----e~kK~~idk~Ve~G~iTqeqAd~i 41 (59)
T PF10925_consen 1 LTDQQKKELKALYKQ-ML----ELKKQIIDKYVEAGVITQEQADAI 41 (59)
T ss_pred CCHHHHHHHHHHHHH-HH----HHHHHHHHHHHHcCCCCHHHHHHH
Confidence 589999999999988 32 456677788888888988875555
No 131
>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=25.75 E-value=21 Score=27.00 Aligned_cols=17 Identities=24% Similarity=0.491 Sum_probs=14.0
Q ss_pred HHHHHHHHhcCCCCCCceeec
Q 047211 70 VRIRKLLEKFGSVGDANVFYW 90 (282)
Q Consensus 70 ~~Ia~eLa~~~~Lse~qVkvW 90 (282)
.+||++| |+++.+|..|
T Consensus 26 kdIA~~L----gvs~~tIr~W 42 (60)
T PF10668_consen 26 KDIAEKL----GVSESTIRKW 42 (60)
T ss_pred HHHHHHH----CCCHHHHHHH
Confidence 3567777 7999999988
No 132
>PRK15248 fimbrial outer membrane usher protein StbC; Provisional
Probab=25.42 E-value=53 Score=35.74 Aligned_cols=38 Identities=29% Similarity=0.523 Sum_probs=27.8
Q ss_pred eceEEEEECCee---eeecCcccchhhc-----cCC-ceEEEecCCC
Q 047211 218 TGFITVFINGAP---TEIPRGPIDMKAL-----FGQ-DVVLVHSSGV 255 (282)
Q Consensus 218 ~g~~tVfINgv~---~EV~~Gp~dvr~~-----FG~-davLvhSsG~ 255 (282)
+.++||+.||.. ..||.|||.+... -|| ++++....|.
T Consensus 285 ~A~V~V~QnG~~iY~t~VppGPF~I~dl~~~~~~GdL~VtV~EadG~ 331 (853)
T PRK15248 285 SAHVVVKQLGKVIYETNVPPGPFYIDDLYNTRYQGDLEVEVIEASGK 331 (853)
T ss_pred ccEEEEEECCEEEEEeEcCCCCeEeccCcCCCCCceEEEEEEECCCC
Confidence 468999999985 6899999977554 243 3456666776
No 133
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=25.14 E-value=51 Score=27.95 Aligned_cols=47 Identities=6% Similarity=0.009 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
.+++.|.++|+-.|-.+. + ..+||+.| |++...|+.+...-|.+.|+
T Consensus 131 ~L~~~~r~v~~l~~~~g~---s---~~eIA~~l----gis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEGL---S---VAEAATRS----GMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred hCCHHHHHHHHHHHHcCC---c---HHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 456666667766554442 1 12345555 89999999887544444444
No 134
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=24.90 E-value=45 Score=28.01 Aligned_cols=47 Identities=17% Similarity=0.227 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
.+++.+.++|...|-.+. + -.+||+.| |+++..|+.+...=|.|.|.
T Consensus 135 ~L~~~~r~vl~l~~~~~~---s---~~eIA~~l----gis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 135 ALSPEERRVIEVLYYQGY---T---HREAAQLL----GLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred hCCHHHHHHHHHHHHcCC---C---HHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 345555556655444432 1 12345554 89999998876544444443
No 135
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=24.89 E-value=59 Score=27.62 Aligned_cols=50 Identities=14% Similarity=0.044 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQ 104 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~ 104 (282)
+++.|.+++.-.|-.+. +. .+||+.| |+++..|+++...=|.|.|+....
T Consensus 132 Lp~~~r~v~~l~~~~g~--s~----~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~~ 181 (191)
T PRK12520 132 LPPRTGRVFMMREWLEL--ET----EEICQEL----QITATNAWVLLYRARMRLRECLDL 181 (191)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 55666666666655542 21 2345555 899999998776555555544433
No 136
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=24.69 E-value=44 Score=28.99 Aligned_cols=31 Identities=13% Similarity=-0.004 Sum_probs=22.0
Q ss_pred HHHHhcCCCCCCceeecccccchhhHHHHHH
Q 047211 74 KLLEKFGSVGDANVFYWFQNRRSRSRRRQRQ 104 (282)
Q Consensus 74 ~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~ 104 (282)
+++++.+|+++..|+++.+-=|.+.|+....
T Consensus 133 ~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 133 EEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 3445555899999999988777666665543
No 137
>TIGR03142 cytochro_ccmI cytochrome c-type biogenesis protein CcmI. This TPR repeat-containing protein is the CcmI protein (also called CycH) of c-type cytochrome biogenesis. CcmI is thought to act as an apo-cytochrome c chaperone. This model describes the N-terminal region of the protein, Members of this protein family
Probab=24.65 E-value=1.1e+02 Score=25.00 Aligned_cols=34 Identities=18% Similarity=0.142 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcC
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFG 80 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~ 80 (282)
+=.+||.+||+.-..+. .+.++-.+.+.||.+.+
T Consensus 40 iyr~qL~ELe~d~~~G~--l~~~e~~~~~~El~rrL 73 (117)
T TIGR03142 40 VYRDRLAELERDLAEGL--LDEAEAEAARAELQRRL 73 (117)
T ss_pred HHHHHHHHHHHHHHcCC--CCHHHHHHHHHHHHHHH
Confidence 44789999999999985 78887777888886554
No 138
>cd03113 CTGs CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent ammonia to the acceptor substrate at the synthetase domain to form an aminated product. Glutaminase domains have evolved from the same ancestor, whereas the synthetase domains are evolutionarily unrelated and have different functions. This protein family is classified based on the N-terminal synthetase domain.
Probab=24.64 E-value=34 Score=32.66 Aligned_cols=13 Identities=38% Similarity=0.652 Sum_probs=12.0
Q ss_pred cccccCCcceEEE
Q 047211 265 LMQSLQHGESYFL 277 (282)
Q Consensus 265 t~~sLq~G~~Y~L 277 (282)
||.|.||||.|.+
T Consensus 48 tmsP~~HGEvfVt 60 (255)
T cd03113 48 TMSPYQHGEVFVT 60 (255)
T ss_pred CCCCccceeEEEc
Confidence 8999999999976
No 139
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=24.51 E-value=51 Score=27.94 Aligned_cols=31 Identities=6% Similarity=-0.081 Sum_probs=22.9
Q ss_pred HHHHhcCCCCCCceeecccccchhhHHHHHH
Q 047211 74 KLLEKFGSVGDANVFYWFQNRRSRSRRRQRQ 104 (282)
Q Consensus 74 ~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~ 104 (282)
+++++.+|+++..|+++.+.=|.+.|+.-+.
T Consensus 158 ~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 188 (193)
T PRK11923 158 EDIASVMQCPVGTVRSRIFRAREAIDKALQP 188 (193)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666999999998887777777666554
No 140
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=24.34 E-value=58 Score=29.78 Aligned_cols=52 Identities=13% Similarity=0.156 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQL 105 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~ 105 (282)
.+++.+.++|+..|..+. + ..+||+.| |++...|+.+...=+.|.|+...+.
T Consensus 212 ~L~~~~r~vl~l~~~~~~---s---~~eIA~~l----gis~~tV~~~~~ra~~~Lr~~l~~~ 263 (268)
T PRK06288 212 TLPEREKKVLILYYYEDL---T---LKEIGKVL----GVTESRISQLHTKAVLQLRAKLAEI 263 (268)
T ss_pred hCCHHHHHHHHHHHHcCC---C---HHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666677777665543 1 12345554 8999999877766666666665443
No 141
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=23.97 E-value=65 Score=27.97 Aligned_cols=49 Identities=10% Similarity=-0.080 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
+++.|.++|.-.|-.+. + -.+||+.| |+++..|++....=|.+.|+.-.
T Consensus 140 Lp~~~r~v~~L~~~eg~--s----~~EIA~~l----gis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 140 LPEQIGRVFMMREFLDF--E----IDDICTEL----TLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred CCHHHHHHHHHHHHcCC--C----HHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 44455555555544432 1 12345555 89999999887765555555443
No 142
>PRK15294 putative fimbrial outer membrane usher protein SthC; Provisional
Probab=23.74 E-value=88 Score=33.95 Aligned_cols=38 Identities=34% Similarity=0.539 Sum_probs=27.8
Q ss_pred eceEEEEECCee---eeecCcccchhhc-----cCC-ceEEEecCCC
Q 047211 218 TGFITVFINGAP---TEIPRGPIDMKAL-----FGQ-DVVLVHSSGV 255 (282)
Q Consensus 218 ~g~~tVfINgv~---~EV~~Gp~dvr~~-----FG~-davLvhSsG~ 255 (282)
..++||+.||.. +.||.|||.+... -|| ++++....|.
T Consensus 289 nA~V~V~QnG~~iY~t~VppGPF~I~Dl~~~~~~GdL~VtV~EadG~ 335 (845)
T PRK15294 289 SAQVTVEQNGYTIYKTNVPAGPFAINDLYPTGGSGDLYVTIKESDGS 335 (845)
T ss_pred CcEEEEEECCEEEEEeEeCCCCeEeccccCCCCCceEEEEEEeCCCC
Confidence 468999999986 5899999977544 244 4555566776
No 143
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=23.62 E-value=55 Score=27.22 Aligned_cols=47 Identities=13% Similarity=0.033 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
.+++.+.++|.-.|-.+. . ..+||+.| |+++..|+.+..-=|.+.|.
T Consensus 112 ~L~~~~r~v~~l~~~~g~--s----~~eIA~~l----gis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 112 LLSADQREAIILIGASGF--S----YEDAAAIC----GCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 345566666666555542 1 12345555 89999999877654444443
No 144
>PRK15217 fimbrial outer membrane usher protein; Provisional
Probab=23.58 E-value=62 Score=35.04 Aligned_cols=38 Identities=29% Similarity=0.504 Sum_probs=27.5
Q ss_pred eceEEEEECCee---eeecCcccchhhc----c-CC-ceEEEecCCC
Q 047211 218 TGFITVFINGAP---TEIPRGPIDMKAL----F-GQ-DVVLVHSSGV 255 (282)
Q Consensus 218 ~g~~tVfINgv~---~EV~~Gp~dvr~~----F-G~-davLvhSsG~ 255 (282)
+.++||+.||.. +.||.|||.+... - || ++++....|.
T Consensus 272 nA~V~V~QnG~~iy~t~VppGPF~I~dl~~~~~~GdL~V~V~EadG~ 318 (826)
T PRK15217 272 NALVTIEQNGFVVYQKEVPPGPFAIADLQLAGGGADLDVSVKEADGS 318 (826)
T ss_pred CcEEEEEECCEEEEEEEeCCCCeEeccccCCCCCceEEEEEEECCCC
Confidence 469999999986 5799999977544 2 23 4555566776
No 145
>PRK15213 fimbrial outer membrane usher protein PefC; Provisional
Probab=23.22 E-value=64 Score=34.68 Aligned_cols=39 Identities=23% Similarity=0.422 Sum_probs=26.5
Q ss_pred eceEEEEECCee---eeecCcccchhh---cc-CC-ceEEEecCCCc
Q 047211 218 TGFITVFINGAP---TEIPRGPIDMKA---LF-GQ-DVVLVHSSGVP 256 (282)
Q Consensus 218 ~g~~tVfINgv~---~EV~~Gp~dvr~---~F-G~-davLvhSsG~p 256 (282)
+.+++|++||.. ..||.|||.+.. +. || ++++....|..
T Consensus 273 ~A~V~V~QnG~~iy~t~VppGpF~I~dlp~~~~Gdl~V~V~EadG~~ 319 (797)
T PRK15213 273 PSRVTISQNGYTLYSEVVPAGPFQLDDVPLVGSGDLTVTVEEEDGHK 319 (797)
T ss_pred CcEEEEEECCEEEEEEEeCCCCeEeccCCCCCCceEEEEEEECCCcE
Confidence 468999999986 579999986632 22 32 34445567763
No 146
>PRK11840 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional
Probab=23.22 E-value=97 Score=30.60 Aligned_cols=58 Identities=26% Similarity=0.462 Sum_probs=41.5
Q ss_pred EEEEECCeeeeecCc--ccchhhccCCc--eEEEecCCCccccCCccccccccCCcceEEEeec
Q 047211 221 ITVFINGAPTEIPRG--PIDMKALFGQD--VVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSR 280 (282)
Q Consensus 221 ~tVfINgv~~EV~~G--p~dvr~~FG~d--avLvhSsG~pvptne~Gvt~~sLq~G~~Y~Lv~~ 280 (282)
|+|.|||..++++.| --||-..+|-+ .|-|-=.|++||-++|.-+. |+-|...-||+.
T Consensus 1 M~I~VNGk~~el~e~~TL~dLL~~L~i~~~~VAVeVNgeIVpr~~w~~t~--LkeGD~IEII~~ 62 (326)
T PRK11840 1 MRIRLNGEPRQVPAGLTIAALLAELGLAPKKVAVERNLEIVPRSEYGQVA--LEEGDELEIVHF 62 (326)
T ss_pred CEEEECCEEEecCCCCcHHHHHHHcCCCCCeEEEEECCEECCHHHcCccc--cCCCCEEEEEEE
Confidence 579999999999876 34444556544 33344589999999997654 888877776653
No 147
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=23.06 E-value=65 Score=26.71 Aligned_cols=46 Identities=17% Similarity=0.182 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRR 100 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KR 100 (282)
+++.+.++|+-.|-.+. +. .+||+.| |+++..|+.+..--|.+.|+
T Consensus 119 L~~~~r~vl~L~~~~g~--s~----~EIA~~l----gis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 119 LSPEHRAVLVRSYYRGW--ST----AQIAADL----GIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 44566666666555542 21 2345555 89999999776544444443
No 148
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=23.00 E-value=30 Score=29.48 Aligned_cols=27 Identities=19% Similarity=0.159 Sum_probs=18.1
Q ss_pred HHHHHHHhcCCCCCCceeecccccchhhHHH
Q 047211 71 RIRKLLEKFGSVGDANVFYWFQNRRSRSRRR 101 (282)
Q Consensus 71 ~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk 101 (282)
+||++| |++...|+.+...=|.+.|+.
T Consensus 160 EIA~~l----gis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 160 EIAELT----GVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred HHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 455665 899999987665555555543
No 149
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=22.96 E-value=69 Score=27.49 Aligned_cols=49 Identities=12% Similarity=0.034 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
+++.|.++|...|-.++ + .++||+.| |++...|+.+..-=|.|.|+...
T Consensus 132 L~~~~r~v~~l~~~~g~--s----~~EIA~~l----gis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 132 LPEQTARVFMMREVLGF--E----SDEICQEL----EISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred CCHHHHHHHHHHHHhCC--C----HHHHHHHh----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 44556666666555543 1 13445555 89999998776655555555443
No 150
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=22.90 E-value=69 Score=26.17 Aligned_cols=41 Identities=22% Similarity=0.482 Sum_probs=26.3
Q ss_pred CCCCCHHH-HHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 047211 42 RWTPKPEQ-ILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQ 92 (282)
Q Consensus 42 Rt~fT~eQ-L~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQ 92 (282)
|..||.|. ++++..++..+. + ..+|++++ ||++..|..|-+
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~--s----v~evA~e~----gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM--T----VSLVARQH----GVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC--C----HHHHHHHH----CcCHHHHHHHHH
Confidence 44566776 456666666653 2 12355555 899999999943
No 151
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=22.84 E-value=66 Score=27.75 Aligned_cols=49 Identities=10% Similarity=0.011 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQR 103 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r 103 (282)
+++.|.+++.-.|-.+. +. .+||+.| |+++..|+++...=|.+.|+...
T Consensus 117 Lp~~~r~i~~L~~~~g~--s~----~EIA~~L----gis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 117 LPDDQREAIILVGASGF--AY----EEAAEIC----GCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 45566666666555542 22 2345555 89999999887666655555443
No 152
>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=22.75 E-value=67 Score=29.41 Aligned_cols=31 Identities=23% Similarity=0.302 Sum_probs=22.8
Q ss_pred HHHhcCCCCCCceeecccccchhhHHHHHHH
Q 047211 75 LLEKFGSVGDANVFYWFQNRRSRSRRRQRQL 105 (282)
Q Consensus 75 eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~ 105 (282)
++|..+|+++..|+.+...=|.+.|+..+..
T Consensus 182 EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~ 212 (244)
T TIGR03001 182 RIGAMYQVHRSTVSRWVAQARERLLERTRRR 212 (244)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444448999999999987777777765443
No 153
>PRK15207 long polar fimbrial outer membrane usher protein LpfC; Provisional
Probab=22.60 E-value=67 Score=34.96 Aligned_cols=38 Identities=21% Similarity=0.380 Sum_probs=27.7
Q ss_pred eceEEEEECCee---eeecCcccchhhc----c-CC-ceEEEecCCC
Q 047211 218 TGFITVFINGAP---TEIPRGPIDMKAL----F-GQ-DVVLVHSSGV 255 (282)
Q Consensus 218 ~g~~tVfINgv~---~EV~~Gp~dvr~~----F-G~-davLvhSsG~ 255 (282)
+.++||+.||.. +.||.|||.+... . || ++++....|.
T Consensus 302 ~A~V~V~QnG~~iY~t~VppGPF~I~dl~~~~~~GdL~VtV~EadG~ 348 (842)
T PRK15207 302 NAEVSIEQNGYVIYRTFVQPGAFEINDLYPTSNSGDLTVIIKEADGS 348 (842)
T ss_pred CcEEEEEECCEEEEEEEeCCCCeEeccccCCCCCceEEEEEEeCCCC
Confidence 468999999986 5799999977654 2 32 3445577777
No 154
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=22.60 E-value=45 Score=28.85 Aligned_cols=28 Identities=14% Similarity=0.159 Sum_probs=20.2
Q ss_pred HHHHhcCCCCCCceeecccccchhhHHH
Q 047211 74 KLLEKFGSVGDANVFYWFQNRRSRSRRR 101 (282)
Q Consensus 74 ~eLa~~~~Lse~qVkvWFQNRRAK~KRk 101 (282)
+|+++.+||+++.|+..++.=|++.+++
T Consensus 155 ~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 155 EEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3566666999999998777666655554
No 155
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.54 E-value=37 Score=30.45 Aligned_cols=50 Identities=14% Similarity=0.069 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQ 104 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~ 104 (282)
.+|+.|+++|+-+.+- . .+ ++||++| +++++.|+.+..|=..|..-+-|-
T Consensus 155 ~Lt~rE~~Vl~l~~~G-~--s~----~eIA~~L----~iS~~TVk~~~~~i~~Kl~v~nr~ 204 (216)
T PRK10100 155 LLTHREKEILNKLRIG-A--SN----NEIARSL----FISENTVKTHLYNLFKKIAVKNRT 204 (216)
T ss_pred CCCHHHHHHHHHHHcC-C--CH----HHHHHHh----CCCHHHHHHHHHHHHHHhCCCCHH
Confidence 4899999999999884 2 32 3567776 899999999988877766554443
No 156
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=22.16 E-value=65 Score=27.60 Aligned_cols=37 Identities=11% Similarity=0.206 Sum_probs=22.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecc
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWF 91 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWF 91 (282)
+++++.++|.-.|-.+. +. .+||+.| |++...|++..
T Consensus 142 Lp~~~r~v~~l~~~eg~--s~----~EIA~~l----gis~~tVk~rl 178 (194)
T PRK12531 142 LPKAQRDVLQAVYLEEL--PH----QQVAEMF----DIPLGTVKSRL 178 (194)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHh----CcCHHHHHHHH
Confidence 45566666666554442 21 2455555 89999996554
No 157
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=22.10 E-value=45 Score=29.84 Aligned_cols=48 Identities=17% Similarity=-0.024 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHH
Q 047211 45 PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQ 102 (282)
Q Consensus 45 fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~ 102 (282)
+++.+.++|...|-.+. +. .+|++.| ||++..|+.+-..=|.|.|+..
T Consensus 135 Lp~~~R~v~~L~y~eg~--s~----~EIAe~L----giS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 135 LPVEYREVLVLRELEDM--SY----REIAAIA----DVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CCHHHHhHhhhHHhcCC--CH----HHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 44556666666555542 22 2345555 8999999887764444444443
No 158
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=22.09 E-value=54 Score=27.99 Aligned_cols=48 Identities=8% Similarity=-0.007 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRR 101 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk 101 (282)
.+++++..+|.-.|-.+. +- +++++.+|++...|+.+.+-=|.+.|+.
T Consensus 131 ~L~~~~r~i~~l~~~~g~--s~--------~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 131 DLEKLDREIFIRRYLLGE--KI--------EEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred hCCHHHHHHHHHHHHccC--CH--------HHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 345555566655444432 11 3444445899999987665444444443
No 159
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=21.90 E-value=46 Score=29.00 Aligned_cols=53 Identities=15% Similarity=-0.016 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQ 106 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q 106 (282)
.+++.+.+++...|-.+. . -.+||+.| |+++..|+++...=|.+.|+...+.+
T Consensus 133 ~Lp~~~r~v~~l~~~~g~--s----~~EIAe~l----gis~~tV~~~l~Rar~~Lr~~l~~~~ 185 (196)
T PRK12535 133 ALPPERREALILTQVLGY--T----YEEAAKIA----DVRVGTIRSRVARARADLIAATATGQ 185 (196)
T ss_pred cCCHHHHHHhhhHHHhCC--C----HHHHHHHh----CCCHHHHHHHHHHHHHHHHHHhcccc
Confidence 355556666665555442 1 12345555 89999999888655555554444433
No 160
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=21.80 E-value=80 Score=26.30 Aligned_cols=28 Identities=11% Similarity=0.140 Sum_probs=19.0
Q ss_pred HHHhcCCCCCCceeecccccchhhHHHH
Q 047211 75 LLEKFGSVGDANVFYWFQNRRSRSRRRQ 102 (282)
Q Consensus 75 eLa~~~~Lse~qVkvWFQNRRAK~KRk~ 102 (282)
++|+.+|+++..|+.+...=|.+.|+..
T Consensus 140 EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 140 EMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred HHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4555558999999987765555555443
No 161
>PRK15304 putative fimbrial outer membrane usher protein; Provisional
Probab=21.77 E-value=1e+02 Score=33.28 Aligned_cols=37 Identities=19% Similarity=0.354 Sum_probs=27.5
Q ss_pred ceEEEEECCee---eeecCcccchhhc----c-CC-ceEEEecCCC
Q 047211 219 GFITVFINGAP---TEIPRGPIDMKAL----F-GQ-DVVLVHSSGV 255 (282)
Q Consensus 219 g~~tVfINgv~---~EV~~Gp~dvr~~----F-G~-davLvhSsG~ 255 (282)
.++||+.||.. ..||.|||.+... . || ++++..+.|.
T Consensus 271 A~V~V~QnG~~iY~t~VppGPF~I~Dl~~~~~~GdL~V~V~EadG~ 316 (801)
T PRK15304 271 ARVEIRQSGQLIYSTLVPAGAFTLDDVPVINGNTDLNVTVVETDGS 316 (801)
T ss_pred cEEEEEECCEEEEEeEcCCCCeEeccccCCCCCccEEEEEEEcCCC
Confidence 58999999986 5799999977554 2 33 4555566887
No 162
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=21.61 E-value=51 Score=35.41 Aligned_cols=66 Identities=21% Similarity=0.193 Sum_probs=44.4
Q ss_pred CCCCCCCCCCCCCCCCCH-HHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCC----CceeecccccchhhHHHHHH
Q 047211 30 GSAERSTEPVRSRWTPKP-EQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGD----ANVFYWFQNRRSRSRRRQRQ 104 (282)
Q Consensus 30 ~~~~~~~~~kR~Rt~fT~-eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse----~qVkvWFQNRRAK~KRk~r~ 104 (282)
++|+.- +|+-+|+.|.| .|+-.|...|... -+++++.+|.+. +.++ +.-.+||||-|+--+|++.+
T Consensus 347 ~~~~~H-~Pp~pRa~~~P~~ql~~lq~~fs~~-------~~qQv~d~~~rl-~~sqav~gr~~~N~~q~~~s~~~raE~~ 417 (769)
T KOG3755|consen 347 QQGLNH-PPPYPRAQLKPGFQLNLLQSEFSEP-------IYQQVRDELKRL-DESQAVFGRVAFNRTQGLLSEILRAEED 417 (769)
T ss_pred ccccCC-CCCCchhhcCccccchhhhhhhccH-------HHHHHHHHHHHh-hhhhhhhhhhhhhhhhhhhccccchhcc
Confidence 444444 45567999888 6999999999882 235666666432 3332 33468999999988887654
No 163
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=21.56 E-value=72 Score=22.06 Aligned_cols=28 Identities=7% Similarity=0.122 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHhcCCCCCCceeeccccc
Q 047211 67 DETVRIRKLLEKFGSVGDANVFYWFQNR 94 (282)
Q Consensus 67 ~eR~~Ia~eLa~~~~Lse~qVkvWFQNR 94 (282)
....+|+++|++..+++...++.||..+
T Consensus 18 ~ti~~lK~~i~~~~~~~~~~~~l~~~g~ 45 (69)
T cd01769 18 DTVAELKAKIAAKEGVPPEQQRLIYAGK 45 (69)
T ss_pred ChHHHHHHHHHHHHCcChHHEEEEECCc
Confidence 3466788889888899999999999774
No 164
>PF06418 CTP_synth_N: CTP synthase N-terminus; InterPro: IPR017456 CTP synthase is involved in pyrimidine ribonucleotide/ribonucleoside metabolism, catalysing the synthesis of CTP from UTP by amination of the pyrimidine ring at the 4-position []. The enzyme exists as a dimer of identical chains that aggregates as a tetramer. This gene has been found roughly 500 bp upstream of enolase in both beta (Nitrosomonas europaea) and gamma (Escherichia coli) subdivisions of Proteobacterium [].; GO: 0003883 CTP synthase activity, 0006221 pyrimidine nucleotide biosynthetic process; PDB: 2VO1_A 3NVA_B 1VCN_A 1VCO_A 1VCM_A 3IHL_B 2AD5_A 1S1M_B.
Probab=21.44 E-value=46 Score=32.16 Aligned_cols=13 Identities=38% Similarity=0.652 Sum_probs=9.3
Q ss_pred cccccCCcceEEE
Q 047211 265 LMQSLQHGESYFL 277 (282)
Q Consensus 265 t~~sLq~G~~Y~L 277 (282)
||.|.||||.|.+
T Consensus 49 tmsP~qHGEVfVt 61 (276)
T PF06418_consen 49 TMSPYQHGEVFVT 61 (276)
T ss_dssp CS-CCTCS-EEE-
T ss_pred CCCCcCccceeEe
Confidence 8999999999975
No 165
>PRK10651 transcriptional regulator NarL; Provisional
Probab=21.32 E-value=35 Score=27.76 Aligned_cols=51 Identities=18% Similarity=0.225 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHH
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQL 105 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~ 105 (282)
.+|+.+.++|+-+.+. . ++ ++|+++| +++++.|++..+|=|.|..-+-+..
T Consensus 155 ~Lt~rE~~vl~~l~~g-~--~~----~~ia~~l----~is~~tV~~~~~~l~~Kl~~~~~~~ 205 (216)
T PRK10651 155 QLTPRERDILKLIAQG-L--PN----KMIARRL----DITESTVKVHVKHMLKKMKLKSRVE 205 (216)
T ss_pred cCCHHHHHHHHHHHcC-C--CH----HHHHHHc----CCCHHHHHHHHHHHHHHcCCCCHHH
Confidence 4999999999986643 1 32 3455555 8999999998888777775444433
No 166
>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=21.27 E-value=61 Score=26.49 Aligned_cols=38 Identities=13% Similarity=0.148 Sum_probs=21.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecc
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWF 91 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWF 91 (282)
.+++.|.++|.-.|-.+. +. +++++.+|+++..|+...
T Consensus 122 ~L~~~~r~vl~l~~~~g~--s~--------~eIA~~l~is~~tv~~~l 159 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQNL--PI--------AEVARILGKTEGAVKILQ 159 (170)
T ss_pred hCCHHHHHHHHHHHhcCC--CH--------HHHHHHHCCCHHHHHHHH
Confidence 345555555555444432 11 344444589999998654
No 167
>cd00131 PAX Paired Box domain
Probab=21.10 E-value=1e+02 Score=25.72 Aligned_cols=46 Identities=20% Similarity=0.182 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCC-------CCCceeeccccc
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSV-------GDANVFYWFQNR 94 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~L-------se~qVkvWFQNR 94 (282)
..++++...|+.+-..+ |+.. -.+|+++|... ++ +...|..||+++
T Consensus 75 ~~~~~~~~~i~~~v~~~---p~~T-l~El~~~L~~~-gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQEN---PGMF-AWEIRDRLLQE-GVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHHC---CCCC-HHHHHHHHHHc-CCcccCCCCCHHHHHHHHHhc
Confidence 34677777787766664 5543 24678887654 34 777787777654
No 168
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=21.07 E-value=45 Score=28.41 Aligned_cols=30 Identities=10% Similarity=0.103 Sum_probs=21.1
Q ss_pred HHHhcCCCCCCceeecccccchhhHHHHHH
Q 047211 75 LLEKFGSVGDANVFYWFQNRRSRSRRRQRQ 104 (282)
Q Consensus 75 eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~ 104 (282)
++++.+|+++..|+++..-=|.+.|+....
T Consensus 152 EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 152 EIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 344444899999999987666666665543
No 169
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=20.98 E-value=36 Score=35.59 Aligned_cols=44 Identities=25% Similarity=0.265 Sum_probs=33.4
Q ss_pred HHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHHhhhccc
Q 047211 69 TVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQASLAGEQ 113 (282)
Q Consensus 69 R~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~~~~~~ 113 (282)
.++||+.|.+.+ ..|++.++-.|-|=-|+||-+++.|++...+.
T Consensus 540 erelreslekql-~~ErklR~~~qkr~kkEkk~k~k~qe~L~~~s 583 (641)
T KOG3915|consen 540 ERELRESLEKQL-AMERKLRAIVQKRLKKEKKAKRKLQEALEFES 583 (641)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 346777777665 45777888889998999999999998865433
No 170
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=20.84 E-value=71 Score=25.68 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=20.0
Q ss_pred HHHHHHHhcCCCCCCceeecccccc
Q 047211 71 RIRKLLEKFGSVGDANVFYWFQNRR 95 (282)
Q Consensus 71 ~Ia~eLa~~~~Lse~qVkvWFQNRR 95 (282)
+|.+.|.+.+|+++.+|.+.|++=.
T Consensus 80 ~i~~~l~~~lgi~~~rv~I~f~~~~ 104 (116)
T PTZ00397 80 AITKILASHLKVKSERVYIEFKDCS 104 (116)
T ss_pred HHHHHHHHHhCcCcccEEEEEEECC
Confidence 4566777778999999999998643
No 171
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=20.35 E-value=30 Score=28.73 Aligned_cols=28 Identities=11% Similarity=-0.012 Sum_probs=19.1
Q ss_pred HHHhcCCCCCCceeecccccchhhHHHH
Q 047211 75 LLEKFGSVGDANVFYWFQNRRSRSRRRQ 102 (282)
Q Consensus 75 eLa~~~~Lse~qVkvWFQNRRAK~KRk~ 102 (282)
++++.+|+++..|+.++..=|.|.|+..
T Consensus 141 eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 141 EIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4444458999999988865555555543
No 172
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=20.31 E-value=65 Score=27.29 Aligned_cols=45 Identities=16% Similarity=0.118 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhh
Q 047211 44 TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRS 98 (282)
Q Consensus 44 ~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~ 98 (282)
.+.++|..+++-.|-.+. . .++||+.| |+++..|+.+...-+.+.
T Consensus 127 ~Lp~~~R~v~~L~~~~g~--s----~~EIA~~l----gis~~tVk~~l~rAl~~~ 171 (178)
T PRK12529 127 TLRPRVKQAFLMATLDGM--K----QKDIAQAL----DIALPTVKKYIHQAYVTC 171 (178)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHH----CCCHHHHHHHHHHHHHHH
Confidence 355666666666555542 1 12345555 899999998876444444
No 173
>PRK13558 bacterio-opsin activator; Provisional
Probab=20.31 E-value=1.1e+02 Score=31.05 Aligned_cols=42 Identities=14% Similarity=0.125 Sum_probs=30.9
Q ss_pred CCCCCHHHHHHHHHHHhcCCCC--CCHHHHHHHHHHHHhcCCCCCCcee
Q 047211 42 RWTPKPEQILILESIFNSGMVN--PPKDETVRIRKLLEKFGSVGDANVF 88 (282)
Q Consensus 42 Rt~fT~eQL~~LE~~F~~~~~y--P~~~eR~~Ia~eLa~~~~Lse~qVk 88 (282)
+..+|+.|.+.|+..|..+ || |-.. -.++|+..++|+...+.
T Consensus 605 ~~~lt~~q~e~l~~a~~~g-yf~~pr~~----~~~e~a~~l~is~~t~~ 648 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVSG-YFEWPRRV----EGEELAESMGISRSTFH 648 (665)
T ss_pred hhhCCHHHHHHHHHHHHcC-CCCCCccC----CHHHHHHHhCCCHHHHH
Confidence 4579999999999999998 44 4332 34666666689877654
No 174
>COG2132 SufI Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.22 E-value=1.6e+02 Score=29.14 Aligned_cols=35 Identities=23% Similarity=0.398 Sum_probs=29.6
Q ss_pred CCceEEEecCCCccccCCccccccccCCcceEEEeec
Q 047211 244 GQDVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSR 280 (282)
Q Consensus 244 G~davLvhSsG~pvptne~Gvt~~sLq~G~~Y~Lv~~ 280 (282)
|....+|++.|.+|+- .-+.--.|..||-|+|+-.
T Consensus 228 ~~~~~Vi~~DG~~v~~--~~~d~~~l~p~er~~v~v~ 262 (451)
T COG2132 228 GGPLTVIAVDGGPLPP--VSVDELYLAPGERYEVLVD 262 (451)
T ss_pred CceEEEEEeCCcCcCc--eeeeeEEecCcceEEEEEE
Confidence 8899999999999987 6677778889999998743
No 175
>cd04759 Rib_hydrolase ADP-ribosyl cyclase (also known as cyclic ADP-ribose hydrolase or CD38) synthesizes the second messenger cyclic-ADP ribose (cADPR), which in turn releases calcium from internal stores. Mammals possess two membrane proteins, CD38 and BST-1/CD157, which exhibit ADP-ribosyl cyclase function, as well as intracellular soluble ADP-ribose cyclases. CD38 is involved in differentiation, adhesion, and cell proliferation, as well as diseases such as AIDS, diabetes, and B-cell chronic lymphocytic leukemia. The extramembrane domain of CD38 acts as a multifunctional enzyme and can synthesize cADPR from NAD+, hydrolyze NAD+, and cADPR to ADPR, as well as catalyze the exchange of the nicotinamide group of NADP+ with nicotinic acid under acidic conditions to yield NAADP+ (nicotinic acid-adenine dinucleotide phosphate), a metabolite involved in Ca2+ mobilization from acidic stores.
Probab=20.18 E-value=99 Score=29.38 Aligned_cols=36 Identities=25% Similarity=0.521 Sum_probs=29.5
Q ss_pred eceEEEEECCeeeeecCcccchhhccCC--------------ceEEEecCCCc
Q 047211 218 TGFITVFINGAPTEIPRGPIDMKALFGQ--------------DVVLVHSSGVP 256 (282)
Q Consensus 218 ~g~~tVfINgv~~EV~~Gp~dvr~~FG~--------------davLvhSsG~p 256 (282)
.|.+.|+.||- .+.|||+-...||. .+.|||.-|.+
T Consensus 146 ~G~V~VmLNGS---~~~~af~~~S~Fg~vElp~L~p~kV~~v~i~vvh~l~~~ 195 (242)
T cd04759 146 CGVVHVMLNGS---ASGGAFRNNSTFGSVEIPNLNPDKVSQVIIWVIHDLEGP 195 (242)
T ss_pred CCeEEEEEcCC---CCCCCcCCCCceeeEEcccCCccceeeEEEEEEcCCCCC
Confidence 47899999995 46779999999997 47789986654
No 176
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=20.04 E-value=85 Score=27.61 Aligned_cols=28 Identities=14% Similarity=-0.032 Sum_probs=19.0
Q ss_pred HHHhcCCCCCCceeecccccchhhHHHH
Q 047211 75 LLEKFGSVGDANVFYWFQNRRSRSRRRQ 102 (282)
Q Consensus 75 eLa~~~~Lse~qVkvWFQNRRAK~KRk~ 102 (282)
++++.+|+++..|+.+..-=|.|.|+..
T Consensus 159 EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 159 EIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4455558999999988765555555443
Done!