Query 043261
Match_columns 233
No_of_seqs 243 out of 1099
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 03:07:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043261.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043261hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04770 ZF-HD_dimer: ZF-HD pr 100.0 4E-39 8.7E-44 231.5 3.4 58 44-101 2-60 (60)
2 TIGR01566 ZF_HD_prot_N ZF-HD h 100.0 3.3E-39 7.2E-44 225.3 2.7 52 47-98 1-53 (53)
3 TIGR01565 homeo_ZF_HD homeobox 99.9 3.7E-22 8.1E-27 143.5 6.6 58 170-227 1-58 (58)
4 KOG0484 Transcription factor P 99.7 2.9E-18 6.4E-23 137.0 -1.0 61 168-232 15-75 (125)
5 KOG0843 Transcription factor E 99.6 4.1E-17 8.9E-22 140.6 2.7 61 168-232 100-160 (197)
6 KOG2251 Homeobox transcription 99.6 1.8E-16 3.9E-21 139.9 4.1 63 166-232 33-95 (228)
7 KOG0485 Transcription factor N 99.6 5.5E-16 1.2E-20 137.3 3.9 62 167-232 101-162 (268)
8 KOG0494 Transcription factor C 99.6 4.1E-16 8.8E-21 141.1 3.0 60 169-232 140-199 (332)
9 KOG0489 Transcription factor z 99.6 2E-16 4.3E-21 142.1 0.4 61 168-232 157-217 (261)
10 KOG0488 Transcription factor B 99.6 7.6E-16 1.7E-20 141.8 2.5 62 167-232 169-230 (309)
11 PF00046 Homeobox: Homeobox do 99.6 4.8E-16 1.1E-20 107.9 0.0 57 171-231 1-57 (57)
12 KOG0850 Transcription factor D 99.5 2.1E-15 4.6E-20 134.0 2.6 62 166-231 118-179 (245)
13 KOG0493 Transcription factor E 99.5 2.5E-15 5.4E-20 136.2 2.4 58 171-232 247-304 (342)
14 KOG0842 Transcription factor t 99.5 1.3E-14 2.8E-19 133.7 6.3 62 167-232 150-211 (307)
15 KOG0844 Transcription factor E 99.5 1.2E-14 2.5E-19 134.2 3.3 61 168-232 179-239 (408)
16 KOG0487 Transcription factor A 99.4 5.5E-14 1.2E-18 129.6 3.6 61 168-232 233-293 (308)
17 KOG0492 Transcription factor M 99.4 7.9E-14 1.7E-18 122.9 3.4 59 169-231 143-201 (246)
18 smart00389 HOX Homeodomain. DN 99.4 1.9E-13 4E-18 93.9 3.3 56 171-230 1-56 (56)
19 KOG4577 Transcription factor L 99.4 1.9E-13 4.1E-18 125.4 2.8 60 168-231 165-224 (383)
20 cd00086 homeodomain Homeodomai 99.4 2.4E-13 5.2E-18 93.7 2.6 58 171-232 1-58 (59)
21 KOG0486 Transcription factor P 99.3 5.1E-13 1.1E-17 123.3 2.4 61 168-232 110-170 (351)
22 KOG3802 Transcription factor O 99.3 1.9E-12 4.1E-17 122.4 6.1 60 168-231 292-351 (398)
23 KOG0490 Transcription factor, 99.3 9.2E-13 2E-17 112.4 2.6 61 168-232 58-118 (235)
24 KOG0848 Transcription factor C 99.3 5.4E-13 1.2E-17 121.2 0.4 63 166-232 195-257 (317)
25 COG5576 Homeodomain-containing 99.2 4.5E-12 9.7E-17 107.1 3.5 61 168-232 49-109 (156)
26 KOG0483 Transcription factor H 99.2 5.9E-12 1.3E-16 110.0 2.8 56 174-233 54-109 (198)
27 KOG0847 Transcription factor, 99.2 5.6E-12 1.2E-16 112.3 0.5 62 168-233 165-226 (288)
28 KOG0491 Transcription factor B 99.1 5.6E-12 1.2E-16 108.0 -2.8 61 168-232 98-158 (194)
29 KOG0849 Transcription factor P 99.1 5.8E-11 1.2E-15 111.3 3.5 61 168-232 174-234 (354)
30 KOG1168 Transcription factor A 98.9 3.5E-10 7.5E-15 104.3 2.3 61 168-232 307-367 (385)
31 KOG0490 Transcription factor, 98.3 2.5E-07 5.5E-12 78.9 1.6 61 168-232 151-211 (235)
32 KOG1146 Homeobox protein [Gene 98.2 1.7E-06 3.7E-11 91.9 5.8 61 168-232 901-961 (1406)
33 KOG2252 CCAAT displacement pro 98.1 1.6E-06 3.4E-11 85.4 2.7 56 169-228 419-474 (558)
34 KOG0775 Transcription factor S 97.8 2.1E-05 4.5E-10 72.3 3.5 47 180-230 186-232 (304)
35 KOG0774 Transcription factor P 97.4 0.00011 2.4E-09 67.5 3.5 61 171-232 189-249 (334)
36 PF05920 Homeobox_KN: Homeobox 97.4 2.3E-05 5E-10 52.4 -1.2 35 194-228 6-40 (40)
37 PF04218 CENP-B_N: CENP-B N-te 95.1 0.024 5.3E-07 39.6 3.1 46 171-225 1-46 (53)
38 KOG0773 Transcription factor M 94.7 0.038 8.2E-07 51.1 4.2 61 169-231 238-299 (342)
39 PF11569 Homez: Homeodomain le 93.2 0.027 5.8E-07 40.7 0.2 42 182-227 10-51 (56)
40 KOG3623 Homeobox transcription 92.8 0.048 1E-06 56.4 1.4 49 177-230 564-612 (1007)
41 PF01527 HTH_Tnp_1: Transposas 89.6 0.12 2.6E-06 37.0 0.4 45 172-224 2-46 (76)
42 PF04967 HTH_10: HTH DNA bindi 79.1 1.9 4.2E-05 30.5 2.5 40 177-218 1-40 (53)
43 cd00569 HTH_Hin_like Helix-tur 73.6 4.1 8.9E-05 22.9 2.6 38 176-222 5-42 (42)
44 cd06171 Sigma70_r4 Sigma70, re 69.1 1.5 3.3E-05 27.8 -0.1 45 176-229 10-54 (55)
45 PRK03975 tfx putative transcri 63.5 2.1 4.5E-05 36.0 -0.3 47 175-231 5-51 (141)
46 COG2963 Transposase and inacti 63.4 8.6 0.00019 29.9 3.2 43 174-224 5-48 (116)
47 PF02796 HTH_7: Helix-turn-hel 62.7 3 6.4E-05 27.8 0.4 39 175-222 4-42 (45)
48 PHA02893 hypothetical protein; 59.8 3.5 7.7E-05 32.2 0.4 20 70-89 58-77 (88)
49 PF00196 GerE: Bacterial regul 56.6 2.2 4.7E-05 29.4 -1.1 45 176-230 3-47 (58)
50 KOG1146 Homeobox protein [Gene 56.0 9.5 0.00021 42.3 2.9 59 169-231 443-501 (1406)
51 PF08281 Sigma70_r4_2: Sigma-7 56.0 1.4 3E-05 29.7 -2.1 42 177-227 11-52 (54)
52 KOG3623 Homeobox transcription 55.3 10 0.00022 40.1 2.9 60 168-231 624-683 (1007)
53 PF13698 DUF4156: Domain of un 54.4 5.2 0.00011 31.0 0.5 18 49-66 51-68 (93)
54 PRK09413 IS2 repressor TnpA; R 52.2 16 0.00035 29.0 3.1 43 174-224 10-52 (121)
55 TIGR03879 near_KaiC_dom probab 51.1 3.2 6.9E-05 31.3 -1.1 28 199-226 30-57 (73)
56 COG3413 Predicted DNA binding 50.1 14 0.0003 32.0 2.6 41 176-218 155-195 (215)
57 PRK09646 RNA polymerase sigma 49.1 1.8 3.9E-05 36.3 -3.0 47 176-231 142-188 (194)
58 TIGR02989 Sig-70_gvs1 RNA poly 47.5 2.6 5.7E-05 33.5 -2.1 47 176-231 111-157 (159)
59 PRK10072 putative transcriptio 46.9 13 0.00029 29.1 1.8 41 176-227 32-72 (96)
60 PF13936 HTH_38: Helix-turn-he 46.9 4.4 9.4E-05 27.0 -0.8 39 175-222 3-41 (44)
61 PRK12519 RNA polymerase sigma 46.8 2.8 6.1E-05 34.8 -2.2 33 199-231 155-187 (194)
62 smart00421 HTH_LUXR helix_turn 46.6 9.3 0.0002 24.6 0.8 45 176-230 3-47 (58)
63 TIGR02939 RpoE_Sigma70 RNA pol 46.4 2.3 4.9E-05 34.9 -2.8 33 199-231 152-184 (190)
64 PRK06759 RNA polymerase factor 45.3 3 6.4E-05 33.1 -2.2 48 176-232 106-153 (154)
65 PRK12512 RNA polymerase sigma 44.5 2.1 4.5E-05 35.3 -3.3 47 176-231 131-177 (184)
66 PF09607 BrkDBD: Brinker DNA-b 44.5 14 0.0003 26.9 1.4 45 174-223 3-47 (58)
67 PRK10403 transcriptional regul 43.4 9 0.0002 30.5 0.4 48 175-232 152-199 (215)
68 PRK12526 RNA polymerase sigma 42.3 2.6 5.6E-05 35.9 -3.1 47 176-231 153-199 (206)
69 PRK09652 RNA polymerase sigma 42.2 2.7 5.8E-05 33.8 -2.9 47 176-231 128-174 (182)
70 PF12824 MRP-L20: Mitochondria 42.0 36 0.00077 29.2 3.8 42 173-220 82-123 (164)
71 PF06163 DUF977: Bacterial pro 41.7 9.7 0.00021 31.7 0.3 44 176-223 4-48 (127)
72 PRK04217 hypothetical protein; 40.6 7.4 0.00016 31.4 -0.5 45 176-229 42-86 (110)
73 PRK09644 RNA polymerase sigma 40.4 2.8 6.2E-05 33.9 -3.0 45 176-230 108-153 (165)
74 PRK02220 4-oxalocrotonate taut 40.4 55 0.0012 22.3 3.9 34 178-225 13-46 (61)
75 PRK12541 RNA polymerase sigma 39.8 3.8 8.1E-05 33.0 -2.4 48 176-232 112-159 (161)
76 PF04545 Sigma70_r4: Sigma-70, 39.6 4.7 0.0001 26.9 -1.6 44 176-228 4-47 (50)
77 COG2197 CitB Response regulato 38.4 20 0.00044 31.0 1.8 45 175-229 147-191 (211)
78 PRK12530 RNA polymerase sigma 38.1 3.2 6.9E-05 34.8 -3.2 47 176-231 134-180 (189)
79 PRK12546 RNA polymerase sigma 37.8 4.1 8.9E-05 34.4 -2.6 32 200-231 128-159 (188)
80 PRK10100 DNA-binding transcrip 37.4 16 0.00035 31.8 1.0 46 176-231 155-200 (216)
81 cd00029 C1 Protein kinase C co 37.4 14 0.0003 24.0 0.5 29 63-96 13-41 (50)
82 PRK12514 RNA polymerase sigma 37.2 3.8 8.2E-05 33.6 -2.8 30 202-231 146-175 (179)
83 PF01381 HTH_3: Helix-turn-hel 37.1 15 0.00033 24.3 0.6 22 205-226 13-34 (55)
84 KOG0705 GTPase-activating prot 36.8 14 0.0003 38.2 0.5 36 61-97 514-550 (749)
85 PRK12513 RNA polymerase sigma 36.8 4.4 9.6E-05 33.7 -2.5 34 198-231 152-185 (194)
86 cd04762 HTH_MerR-trunc Helix-T 36.8 12 0.00026 23.5 0.1 24 204-227 3-26 (49)
87 KOG1924 RhoA GTPase effector D 36.7 47 0.001 35.7 4.3 11 3-13 359-369 (1102)
88 PRK00118 putative DNA-binding 36.6 8.1 0.00017 30.9 -0.9 46 176-230 17-62 (104)
89 PRK12537 RNA polymerase sigma 36.5 4.5 9.7E-05 33.5 -2.5 30 202-231 150-179 (182)
90 PRK09648 RNA polymerase sigma 36.5 3.5 7.5E-05 34.2 -3.2 48 175-231 138-185 (189)
91 TIGR02937 sigma70-ECF RNA poly 36.4 5.5 0.00012 30.1 -1.8 47 176-231 110-156 (158)
92 PRK09726 antitoxin HipB; Provi 36.3 38 0.00082 25.3 2.8 22 204-225 28-49 (88)
93 PRK06424 transcription factor; 36.1 24 0.00052 29.6 1.8 24 204-227 100-123 (144)
94 PF10668 Phage_terminase: Phag 35.9 10 0.00022 27.7 -0.4 20 203-222 24-43 (60)
95 TIGR02947 SigH_actino RNA poly 35.7 5 0.00011 33.4 -2.3 35 197-231 143-177 (193)
96 TIGR02950 SigM_subfam RNA poly 35.7 8.9 0.00019 30.2 -0.8 35 197-231 117-151 (154)
97 TIGR02948 SigW_bacill RNA poly 35.2 4.9 0.00011 32.8 -2.4 47 176-231 136-182 (187)
98 TIGR03541 reg_near_HchA LuxR f 34.8 13 0.00029 32.5 0.1 49 174-232 169-217 (232)
99 PRK09649 RNA polymerase sigma 34.6 4.8 0.0001 33.6 -2.7 30 202-231 147-176 (185)
100 PRK09642 RNA polymerase sigma 34.3 3.9 8.4E-05 32.8 -3.1 29 203-231 124-152 (160)
101 PF13443 HTH_26: Cro/C1-type H 34.2 9.9 0.00021 26.1 -0.7 26 203-228 12-37 (63)
102 PF05077 DUF678: Protein of un 33.6 17 0.00037 27.7 0.5 10 80-89 56-65 (74)
103 TIGR02999 Sig-70_X6 RNA polyme 33.4 4.4 9.5E-05 33.2 -3.0 30 202-231 151-180 (183)
104 PRK10360 DNA-binding transcrip 33.1 21 0.00046 28.4 1.0 47 176-232 137-183 (196)
105 PRK05657 RNA polymerase sigma 33.1 12 0.00025 35.0 -0.6 51 176-231 262-312 (325)
106 PRK12539 RNA polymerase sigma 33.1 6 0.00013 32.7 -2.3 47 176-231 131-177 (184)
107 cd04761 HTH_MerR-SF Helix-Turn 33.0 12 0.00025 24.2 -0.4 23 204-226 3-25 (49)
108 TIGR02985 Sig70_bacteroi1 RNA 33.0 4.5 9.8E-05 31.7 -2.9 30 202-231 130-159 (161)
109 PF13518 HTH_28: Helix-turn-he 32.8 14 0.0003 24.2 -0.1 24 203-226 14-37 (52)
110 PF13551 HTH_29: Winged helix- 32.6 45 0.00097 24.8 2.7 20 171-190 52-71 (112)
111 TIGR00721 tfx DNA-binding prot 32.0 15 0.00032 30.7 -0.1 47 174-230 4-50 (137)
112 TIGR03070 couple_hipB transcri 32.0 35 0.00075 22.2 1.8 23 204-226 18-40 (58)
113 PRK06811 RNA polymerase factor 32.0 5.6 0.00012 33.2 -2.7 47 176-232 131-178 (189)
114 PRK09639 RNA polymerase sigma 31.1 5.8 0.00013 31.8 -2.6 45 176-230 112-156 (166)
115 TIGR02959 SigZ RNA polymerase 30.9 11 0.00025 30.8 -1.0 46 176-230 100-145 (170)
116 PRK11924 RNA polymerase sigma 30.8 5.6 0.00012 31.8 -2.8 30 201-230 141-170 (179)
117 PRK12516 RNA polymerase sigma 30.8 5.6 0.00012 33.4 -2.8 31 201-231 132-162 (187)
118 PF11516 DUF3220: Protein of u 30.7 8.5 0.00018 30.2 -1.6 9 217-225 32-40 (106)
119 TIGR00270 conserved hypothetic 30.6 58 0.0013 27.5 3.3 23 204-226 85-107 (154)
120 TIGR03020 EpsA transcriptional 30.6 17 0.00037 32.8 0.1 48 174-231 188-235 (247)
121 PRK09047 RNA polymerase factor 30.5 4.4 9.5E-05 32.3 -3.4 46 176-230 106-151 (161)
122 PRK12547 RNA polymerase sigma 30.3 5 0.00011 32.6 -3.1 30 201-230 128-157 (164)
123 cd06170 LuxR_C_like C-terminal 30.1 24 0.00052 22.8 0.7 42 178-229 2-43 (57)
124 PRK13558 bacterio-opsin activa 29.8 42 0.0009 33.2 2.6 40 175-218 606-647 (665)
125 PRK12524 RNA polymerase sigma 29.5 5.6 0.00012 33.3 -3.0 47 176-231 136-182 (196)
126 TIGR02983 SigE-fam_strep RNA p 29.2 6 0.00013 31.7 -2.8 29 203-231 128-156 (162)
127 PRK12545 RNA polymerase sigma 29.0 6.5 0.00014 33.3 -2.8 31 201-231 155-185 (201)
128 PRK02289 4-oxalocrotonate taut 28.8 1.1E+02 0.0025 21.1 4.1 33 178-224 13-45 (60)
129 PRK09638 RNA polymerase sigma 28.7 7 0.00015 31.7 -2.5 34 198-231 139-172 (176)
130 PRK08301 sporulation sigma fac 28.4 15 0.00032 31.8 -0.7 51 176-231 178-228 (234)
131 PRK12536 RNA polymerase sigma 28.2 5.2 0.00011 33.0 -3.4 32 200-231 144-175 (181)
132 PRK05602 RNA polymerase sigma 28.0 6.1 0.00013 32.6 -3.0 29 203-231 146-174 (186)
133 PRK12533 RNA polymerase sigma 27.8 7.4 0.00016 33.9 -2.7 32 200-231 149-180 (216)
134 smart00109 C1 Protein kinase C 27.7 34 0.00074 21.8 1.1 28 63-96 13-40 (49)
135 PRK12520 RNA polymerase sigma 27.6 6.3 0.00014 32.8 -3.1 30 202-231 148-177 (191)
136 PRK12532 RNA polymerase sigma 27.4 6.8 0.00015 32.7 -2.9 31 201-231 152-182 (195)
137 PRK12518 RNA polymerase sigma 27.4 5.7 0.00012 32.2 -3.3 35 197-231 132-166 (175)
138 KOG2767 Translation initiation 26.9 19 0.00042 34.9 -0.3 14 81-94 118-131 (400)
139 PRK13919 putative RNA polymera 26.7 6.6 0.00014 32.3 -3.1 47 176-231 135-181 (186)
140 PRK06986 fliA flagellar biosyn 26.5 8.5 0.00018 33.4 -2.6 33 199-231 198-230 (236)
141 PRK12515 RNA polymerase sigma 26.5 6.3 0.00014 32.7 -3.3 46 176-231 131-177 (189)
142 PRK12543 RNA polymerase sigma 26.3 6.9 0.00015 32.2 -3.0 30 202-231 134-163 (179)
143 PRK09637 RNA polymerase sigma 26.1 8.3 0.00018 32.2 -2.6 30 201-230 122-151 (181)
144 PRK15411 rcsA colanic acid cap 25.9 31 0.00068 29.6 0.9 45 176-230 137-181 (207)
145 PF13411 MerR_1: MerR HTH fami 25.8 18 0.00039 25.2 -0.6 21 204-224 3-23 (69)
146 PRK09645 RNA polymerase sigma 25.7 7.7 0.00017 31.5 -2.8 45 177-230 119-163 (173)
147 TIGR02952 Sig70_famx2 RNA poly 25.7 8.1 0.00018 30.9 -2.6 47 176-231 122-168 (170)
148 PRK09651 RNA polymerase sigma 25.2 10 0.00022 31.2 -2.2 31 198-228 132-162 (172)
149 PRK12538 RNA polymerase sigma 25.2 7.8 0.00017 34.1 -3.1 31 201-231 187-217 (233)
150 PRK10651 transcriptional regul 25.1 24 0.00052 28.1 0.0 46 176-231 155-200 (216)
151 PF06056 Terminase_5: Putative 25.1 13 0.00027 26.6 -1.5 25 204-230 16-40 (58)
152 COG2944 Predicted transcriptio 25.1 38 0.00082 27.3 1.1 40 177-227 44-83 (104)
153 PRK15479 transcriptional regul 25.1 55 0.0012 26.3 2.1 50 175-230 147-201 (221)
154 PRK12511 RNA polymerase sigma 24.8 8.5 0.00018 32.3 -2.8 30 201-230 127-156 (182)
155 PRK12522 RNA polymerase sigma 24.8 8.4 0.00018 31.4 -2.8 32 200-231 134-165 (173)
156 PF13384 HTH_23: Homeodomain-l 24.6 18 0.00038 23.8 -0.7 24 203-226 19-42 (50)
157 PRK12535 RNA polymerase sigma 24.6 9 0.0002 32.5 -2.7 29 202-230 150-178 (196)
158 PF12802 MarR_2: MarR family; 24.5 54 0.0012 22.0 1.7 36 177-218 3-38 (62)
159 PF06252 DUF1018: Protein of u 24.4 80 0.0017 25.0 2.9 24 175-198 20-43 (119)
160 PTZ00397 macrophage migration 24.2 1.5E+02 0.0031 23.1 4.3 35 178-226 70-104 (116)
161 PRK09390 fixJ response regulat 24.2 25 0.00054 27.4 -0.1 46 177-232 142-187 (202)
162 PRK15369 two component system 23.9 44 0.00095 26.1 1.3 46 175-230 148-193 (211)
163 PRK11923 algU RNA polymerase s 23.7 8.8 0.00019 31.8 -2.9 33 199-231 152-184 (193)
164 TIGR02607 antidote_HigA addict 23.1 48 0.001 23.5 1.3 16 199-214 45-60 (78)
165 cd00491 4Oxalocrotonate_Tautom 23.0 1.7E+02 0.0038 19.3 4.0 34 178-225 12-45 (58)
166 PRK10840 transcriptional regul 22.9 38 0.00083 28.2 0.8 44 176-229 150-193 (216)
167 PRK12529 RNA polymerase sigma 22.8 8.5 0.00018 31.8 -3.1 44 176-228 127-170 (178)
168 PRK12542 RNA polymerase sigma 22.7 8.4 0.00018 31.8 -3.2 29 202-230 139-167 (185)
169 cd01276 PKCI_related Protein K 22.5 1.4E+02 0.003 22.2 3.8 45 171-227 42-89 (104)
170 PRK10336 DNA-binding transcrip 22.5 59 0.0013 26.1 1.9 50 175-230 148-202 (219)
171 PRK09935 transcriptional regul 22.3 31 0.00068 27.5 0.2 46 175-230 148-193 (210)
172 PRK12540 RNA polymerase sigma 22.2 9.7 0.00021 31.9 -2.9 32 200-231 126-157 (182)
173 smart00661 RPOL9 RNA polymeras 22.1 56 0.0012 21.7 1.4 25 66-90 5-29 (52)
174 PRK06930 positive control sigm 22.0 20 0.00044 30.5 -1.0 47 176-231 114-160 (170)
175 PRK00745 4-oxalocrotonate taut 21.9 1.6E+02 0.0034 20.0 3.7 34 178-225 13-46 (62)
176 PRK13870 transcriptional regul 21.9 36 0.00077 30.1 0.5 48 173-230 170-217 (234)
177 PRK01964 4-oxalocrotonate taut 21.9 1.6E+02 0.0035 20.3 3.8 34 178-225 13-46 (64)
178 PF01873 eIF-5_eIF-2B: Domain 21.7 34 0.00073 28.1 0.3 13 79-91 112-124 (125)
179 TIGR00013 taut 4-oxalocrotonat 21.7 1.9E+02 0.004 19.7 4.0 34 178-225 13-46 (63)
180 PF01710 HTH_Tnp_IS630: Transp 21.7 55 0.0012 25.9 1.5 39 176-223 2-40 (119)
181 PF01361 Tautomerase: Tautomer 21.6 1.8E+02 0.0038 19.7 3.9 33 178-224 12-44 (60)
182 PRK07037 extracytoplasmic-func 21.5 21 0.00045 28.6 -1.0 28 203-230 127-154 (163)
183 PRK09641 RNA polymerase sigma 21.5 9.3 0.0002 31.1 -3.1 32 200-231 151-182 (187)
184 TIGR02954 Sig70_famx3 RNA poly 21.2 12 0.00027 30.2 -2.4 29 203-231 137-165 (169)
185 PLN03162 golden-2 like transcr 21.0 1E+02 0.0023 30.5 3.4 61 168-230 231-291 (526)
186 PRK12531 RNA polymerase sigma 21.0 10 0.00022 31.8 -3.1 29 203-231 159-187 (194)
187 PF08279 HTH_11: HTH domain; 20.7 46 0.00099 22.2 0.7 18 202-219 16-33 (55)
188 PRK11922 RNA polymerase sigma 20.6 14 0.00031 32.0 -2.3 35 197-231 161-195 (231)
189 PRK11511 DNA-binding transcrip 20.6 46 0.00099 26.5 0.8 40 180-224 9-48 (127)
190 PRK09483 response regulator; P 20.4 40 0.00086 27.2 0.4 46 175-230 147-192 (217)
191 PRK09640 RNA polymerase sigma 20.3 6.9 0.00015 32.5 -4.2 33 199-231 148-180 (188)
192 PRK12523 RNA polymerase sigma 20.2 12 0.00026 30.6 -2.8 29 201-229 135-163 (172)
193 PF12123 Amidase02_C: N-acetyl 20.2 1E+02 0.0022 21.3 2.3 20 176-195 23-42 (45)
194 PRK09480 slmA division inhibit 20.1 71 0.0015 25.8 1.9 30 196-226 26-55 (194)
195 PF01485 IBR: IBR domain; Int 20.1 77 0.0017 21.3 1.8 30 66-95 25-60 (64)
No 1
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=100.00 E-value=4e-39 Score=231.54 Aligned_cols=58 Identities=78% Similarity=1.452 Sum_probs=55.1
Q ss_pred CceehHHhhhhhhhccCCcccccccccccc-CCCCCcccccccccccccccccccccCC
Q 043261 44 KSIRYRECLKNHAVSIGGHAVDGCGEFMAA-GDEGTLESLKCAACNCHRNFHRKETDGA 101 (233)
Q Consensus 44 ~~~~y~eC~kNhaa~~g~~~~dgc~ef~~~-~~~~~~~~l~caac~chrnfhr~~~~~~ 101 (233)
..|+||||||||||+||||+||||+||||+ ++++|+++|+||||||||||||||++++
T Consensus 2 ~~v~Y~EC~kNHAa~~Gg~a~DGCgEFm~~~g~eg~~~al~CaACgCHRnFHRre~~~e 60 (60)
T PF04770_consen 2 KVVRYRECLKNHAASIGGHAVDGCGEFMPSPGEEGTPEALKCAACGCHRNFHRREVEGE 60 (60)
T ss_pred CceeHHHHHhhHhHhhCCcccccccccccCCCCCCCcccceecccCcchhcccCCcCCC
Confidence 468999999999999999999999999999 8899999999999999999999998763
No 2
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
Probab=100.00 E-value=3.3e-39 Score=225.27 Aligned_cols=52 Identities=77% Similarity=1.434 Sum_probs=50.1
Q ss_pred ehHHhhhhhhhccCCccccccccccc-cCCCCCcccccccccccccccccccc
Q 043261 47 RYRECLKNHAVSIGGHAVDGCGEFMA-AGDEGTLESLKCAACNCHRNFHRKET 98 (233)
Q Consensus 47 ~y~eC~kNhaa~~g~~~~dgc~ef~~-~~~~~~~~~l~caac~chrnfhr~~~ 98 (233)
+||||||||||+|||||||||+|||| +++++|+++|+||||||||||||||+
T Consensus 1 ~Y~EC~kNHAa~~Gg~a~DGCgEFmps~g~~~~~~al~CaACgCHRnFHRre~ 53 (53)
T TIGR01566 1 LYKECLKNHAASIGGHALDGCGEFMPSSGEEGDPESLTCAACGCHRNFHRKEP 53 (53)
T ss_pred CHHHHHHhhHHHhCCcccccccccccCCCCCCCCcceeeeecCcccccccCCC
Confidence 69999999999999999999999999 78899999999999999999999985
No 3
>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=99.86 E-value=3.7e-22 Score=143.45 Aligned_cols=58 Identities=64% Similarity=1.094 Sum_probs=56.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccccc
Q 043261 170 KKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKH 227 (233)
Q Consensus 170 kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRa 227 (233)
+||.||+||.+|++.|+.+|+++||+++.||..+|++||.+|||++.||||||||+|.
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k~ 58 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNKK 58 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCCC
Confidence 5899999999999999999999999999999999999999999999999999999984
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.68 E-value=2.9e-18 Score=137.01 Aligned_cols=61 Identities=20% Similarity=0.340 Sum_probs=58.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
++.||-||.||..||..|++.|. ..+|||+.+|++||.+|.|++..|||||||||+|+||+
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~----ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFA----ETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHH----hhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 56789999999999999999998 89999999999999999999999999999999999986
No 5
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.65 E-value=4.1e-17 Score=140.57 Aligned_cols=61 Identities=28% Similarity=0.265 Sum_probs=58.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
.+.||.||.||.+|+.+|+..|+ .++|....+|++||+.|+|++.+|||||||||.|.||.
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~----~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~ 160 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFE----GNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRM 160 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHh----cCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHH
Confidence 36799999999999999999999 99999999999999999999999999999999999875
No 6
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.62 E-value=1.8e-16 Score=139.92 Aligned_cols=63 Identities=21% Similarity=0.336 Sum_probs=59.9
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 166 SGGTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 166 ~~~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
..++.||-||.||..|++.|+.+|. +.+|||...|++||.+|+|++.+|||||.|||+|+|++
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~----kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFA----KTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHH----hhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 3467899999999999999999999 99999999999999999999999999999999999875
No 7
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.59 E-value=5.5e-16 Score=137.29 Aligned_cols=62 Identities=19% Similarity=0.285 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 167 GGTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 167 ~~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
..+|||.||.|+..|+.+||..|| .-.|.+..+|..||..|.|++.||||||||||+|||||
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe----~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFE----LKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHH----HHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 467899999999999999999999 89999999999999999999999999999999999986
No 8
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.59 E-value=4.1e-16 Score=141.06 Aligned_cols=60 Identities=22% Similarity=0.320 Sum_probs=56.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 169 TKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 169 ~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
++|++||.||..|++.|+..|. ..+|||...|+-|+.++.|++.+|+|||||||+||||+
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFk----eaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFK----EAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred ccccccchhhHHHHHHHHHHHh----hccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 4455699999999999999999 89999999999999999999999999999999999986
No 9
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.58 E-value=2e-16 Score=142.06 Aligned_cols=61 Identities=20% Similarity=0.251 Sum_probs=58.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
+..||.||.||..|+..||..|. .|+|+....|.+||..|.|+|++|||||||||+||||.
T Consensus 157 ~~~kR~RtayT~~QllELEkEFh----fN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~ 217 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFH----FNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKE 217 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhc----cccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHh
Confidence 45799999999999999999999 99999999999999999999999999999999999974
No 10
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.57 E-value=7.6e-16 Score=141.84 Aligned_cols=62 Identities=18% Similarity=0.287 Sum_probs=59.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 167 GGTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 167 ~~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
..++|+.||.||..|+..||.-|+ +..|+...+|.+||..|||+..|||+||||||+||||+
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~----~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq 230 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFE----KQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQ 230 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHH----HhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHH
Confidence 466788899999999999999999 89999999999999999999999999999999999985
No 11
>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=99.55 E-value=4.8e-16 Score=107.91 Aligned_cols=57 Identities=26% Similarity=0.430 Sum_probs=54.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 171 KRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 171 KR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
||.|+.||.+|+..|+.+|+ .++||+..+++.||.++||+..+|++||+|+|+++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~----~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQ----ENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHH----HSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHH----HhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 68999999999999999999 8999999999999999999999999999999999875
No 12
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.54 E-value=2.1e-15 Score=134.00 Aligned_cols=62 Identities=18% Similarity=0.323 Sum_probs=58.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 166 SGGTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 166 ~~~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+.+.|+.||.|+.-||..|.+-|+ +.+|+-..+|.+||..|||+..+|||||||||.|+||
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQ----kTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KK 179 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQ----QTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKK 179 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHh----hcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHH
Confidence 4456678899999999999999999 9999999999999999999999999999999999987
No 13
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.53 E-value=2.5e-15 Score=136.17 Aligned_cols=58 Identities=28% Similarity=0.465 Sum_probs=56.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 171 KRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 171 KR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
||.||.||.|||++|++.|. .|+|+.+..|++|+.+|+|.+.+|||||||+|+|.||-
T Consensus 247 KRPRTAFtaeQL~RLK~EF~----enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQ----ENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred cCccccccHHHHHHHHHHHh----hhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 78999999999999999999 99999999999999999999999999999999999984
No 14
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.52 E-value=1.3e-14 Score=133.75 Aligned_cols=62 Identities=13% Similarity=0.242 Sum_probs=58.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 167 GGTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 167 ~~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
..+|||.|-.||+.|..+||+-|. ..+|++..+|++||..|.|++.||||||||||.|-||+
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFr----qQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~ 211 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFR----QQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQ 211 (307)
T ss_pred cccccccccccchhHHHHHHHHHH----hhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhh
Confidence 356778889999999999999999 89999999999999999999999999999999999986
No 15
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.49 E-value=1.2e-14 Score=134.17 Aligned_cols=61 Identities=21% Similarity=0.270 Sum_probs=57.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
..-||+||.||.|||.+||..|- |-.|.+...|-+||..|+|++.+|||||||||.|.|||
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFy----rENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ 239 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFY----RENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ 239 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHH----HhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh
Confidence 34699999999999999999988 78999999999999999999999999999999999987
No 16
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.43 E-value=5.5e-14 Score=129.61 Aligned_cols=61 Identities=11% Similarity=0.128 Sum_probs=57.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
.+.|++|-.+|..|+.+||..|- -|.|+..+.|-+|++.|+|+++||||||||||.|.||-
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFl----fN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~ 293 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFL----FNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKV 293 (308)
T ss_pred cccccccCCchHHHHHHHHHHHH----HHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhh
Confidence 45577888999999999999998 89999999999999999999999999999999999983
No 17
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.42 E-value=7.9e-14 Score=122.87 Aligned_cols=59 Identities=19% Similarity=0.286 Sum_probs=55.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 169 TKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 169 ~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
..|+.||.||..||..|++-|. ..+|.++.+|.+|+..|.|++.+|||||||||+|-||
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfr----ekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKR 201 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFR----EKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKR 201 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHh----HhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHH
Confidence 3477899999999999999999 8999999999999999999999999999999999876
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.40 E-value=1.9e-13 Score=93.87 Aligned_cols=56 Identities=27% Similarity=0.429 Sum_probs=53.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 171 KRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 171 KR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
++.|+.||.+|+..|+..|+ .++||+..++++|+.++||+..+|+.||+|+|.+.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~----~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQ----KNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHH----hCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 46788999999999999999 999999999999999999999999999999998864
No 19
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.37 E-value=1.9e-13 Score=125.42 Aligned_cols=60 Identities=30% Similarity=0.423 Sum_probs=57.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
...||.||++|..||+.|+..|. ..++|-..+|++|+.++||.-+||||||||||+|.||
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn----~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKR 224 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYN----TSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKR 224 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhc----CCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHh
Confidence 45799999999999999999999 9999999999999999999999999999999999875
No 20
>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=99.37 E-value=2.4e-13 Score=93.65 Aligned_cols=58 Identities=28% Similarity=0.479 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 171 KRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 171 KR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
++.|+.|+.+|+..|+.+|+ .++||+..+++.||.++||+..+|++||+|+|.+.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~----~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFE----KNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHH----hCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 46788999999999999999 89999999999999999999999999999999998875
No 21
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.32 E-value=5.1e-13 Score=123.34 Aligned_cols=61 Identities=23% Similarity=0.411 Sum_probs=58.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
.++||-||.||..|++.||..|. +|.|||..+|++||.-++|++..|+|||.|||+||||+
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~----rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkr 170 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQ----RNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 170 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHh----hccCCccchhhHHHhhccccchhhhhhcccchhhhhhh
Confidence 35688999999999999999999 99999999999999999999999999999999999997
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.32 E-value=1.9e-12 Score=122.44 Aligned_cols=60 Identities=13% Similarity=0.317 Sum_probs=58.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+|||+||.|....+..|+.+|. +|++|+..++..||.+|+|.+.||+|||.|||+|.||
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~----~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR 351 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFL----KNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKR 351 (398)
T ss_pred ccccccccceeHHHHHHHHHHHH----hCCCCCHHHHHHHHHHhccccceEEEEeecccccccc
Confidence 57889999999999999999999 9999999999999999999999999999999999987
No 23
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.30 E-value=9.2e-13 Score=112.38 Aligned_cols=61 Identities=21% Similarity=0.205 Sum_probs=58.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
.++||.||.|+..|++.|+..|+ +++|||...++.|+..+.+++..|||||||+|+||+|+
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~----~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFE----KVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhc----CCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 56899999999999999999999 88999999999999999999999999999999999975
No 24
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.28 E-value=5.4e-13 Score=121.20 Aligned_cols=63 Identities=17% Similarity=0.249 Sum_probs=57.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 166 SGGTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 166 ~~~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
..+.|-+.|.++|..|.-+||..|. .++|+.+..+.+||.-|+|+|++|||||||||+|.||.
T Consensus 195 KtRTkDKYRvVYTDhQRLELEKEfh----~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~ 257 (317)
T KOG0848|consen 195 KTRTKDKYRVVYTDHQRLELEKEFH----TSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKD 257 (317)
T ss_pred eeecccceeEEecchhhhhhhhhhc----cccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHH
Confidence 3455667888999999999999999 99999999999999999999999999999999999873
No 25
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.24 E-value=4.5e-12 Score=107.07 Aligned_cols=61 Identities=16% Similarity=0.147 Sum_probs=57.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
+..++.|+.-|.+|+..|++.|+ .++||+..++..|+..|+|+++.|||||||+|++.|++
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~----i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~ 109 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFE----INPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109 (156)
T ss_pred CcCcccceechHHHHHHHHHHhc----cCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHh
Confidence 45677888889999999999999 99999999999999999999999999999999998875
No 26
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.21 E-value=5.9e-12 Score=110.04 Aligned_cols=56 Identities=20% Similarity=0.329 Sum_probs=52.3
Q ss_pred CCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCCC
Q 043261 174 RTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKKP 233 (233)
Q Consensus 174 RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK~ 233 (233)
.-+||.+|...|+.-|+ ...+.....+..||++|||.+++|+|||||||++||.|.
T Consensus 54 k~Rlt~eQ~~~LE~~F~----~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 54 KRRLTSEQVKFLEKSFE----SEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred cccccHHHHHHhHHhhc----cccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 33689999999999999 899999999999999999999999999999999999873
No 27
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.16 E-value=5.6e-12 Score=112.29 Aligned_cols=62 Identities=26% Similarity=0.364 Sum_probs=58.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKKP 233 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK~ 233 (233)
+++|-.|.+|+-.|+..|+.-|+ ..+|+-..++.++|..+|+++.+|||||||||+|||||.
T Consensus 165 G~rk~srPTf~g~qi~~le~~fe----qtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFE----QTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred ccccccCCCccchhhhhhhhhhh----hhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 56788899999999999999999 899999999999999999999999999999999999983
No 28
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.09 E-value=5.6e-12 Score=107.96 Aligned_cols=61 Identities=16% Similarity=0.268 Sum_probs=57.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
.++++.||.|+..|+..|+..|+ +..|.+..++.+|+..|+|++.+||.||||||.|.||.
T Consensus 98 ~~r~K~Rtvfs~~ql~~l~~rFe----~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~ 158 (194)
T KOG0491|consen 98 CRRRKARTVFSDPQLSGLEKRFE----RQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQ 158 (194)
T ss_pred HHhhhhcccccCccccccHHHHh----hhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999999 89999999999999999999999999999999998874
No 29
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.08 E-value=5.8e-11 Score=111.29 Aligned_cols=61 Identities=25% Similarity=0.404 Sum_probs=58.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
.+.+|.||+|+.+|++.|++.|+ +++||+...|++|+.+|++++..|+|||+|+|++++|.
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~----rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~ 234 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQ----RTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQ 234 (354)
T ss_pred ccccccccccccchHHHHHHHhc----CCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhc
Confidence 45678899999999999999999 99999999999999999999999999999999999885
No 30
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.93 E-value=3.5e-10 Score=104.26 Aligned_cols=61 Identities=21% Similarity=0.445 Sum_probs=57.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
+.|||+||.+-...+..||++|. ..++|+.+.+..+|.+|+|+..||+|||.|.|+|.||.
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFa----vQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFA----VQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred cccccccccccCcccccHHHHhc----cCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 56899999999999999999999 88899999999999999999999999999999999863
No 31
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.29 E-value=2.5e-07 Score=78.93 Aligned_cols=61 Identities=33% Similarity=0.498 Sum_probs=57.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
.+.++.||.|+..|+..|...|. ...+|+...+++|+..++++..+|+|||+|+|++.++.
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~ 211 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFR----ATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH 211 (235)
T ss_pred cccCCCccccccchhHhhhhccc----CCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence 56788999999999999999999 99999999999999999999999999999999998764
No 32
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=98.20 E-value=1.7e-06 Score=91.85 Aligned_cols=61 Identities=18% Similarity=0.235 Sum_probs=56.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
..+|+.||.|+..|+..|..+|+ ...++...+.+.|-..+++..++|+|||||.|+|-+|.
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~----~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~ 961 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYE----AQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKA 961 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHh----hccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhh
Confidence 44688999999999999999999 88899999999999999999999999999999998874
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.09 E-value=1.6e-06 Score=85.45 Aligned_cols=56 Identities=14% Similarity=0.202 Sum_probs=53.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccc
Q 043261 169 TKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHT 228 (233)
Q Consensus 169 ~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK 228 (233)
..||.|.+||+.|++.|..+|. .+++|+..+.+.|+.+|+|...+|..||.|-|.+
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFk----e~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR 474 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFK----ENKRPSREMQETISQQLNLELSTVINFFMNARRR 474 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHh----cCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence 4578899999999999999999 9999999999999999999999999999998876
No 34
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=97.75 E-value=2.1e-05 Score=72.34 Aligned_cols=47 Identities=9% Similarity=0.173 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 180 EQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 180 eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
.-...|+++|. +++||...+..+||+.+||+..||-.||+|||++.|
T Consensus 186 kSR~~LrewY~----~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 186 KSRSLLREWYL----QNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHHHHHHHHh----cCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 34567888999 999999999999999999999999999999999987
No 35
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=97.43 E-value=0.00011 Score=67.54 Aligned_cols=61 Identities=15% Similarity=0.258 Sum_probs=54.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 171 KRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 171 KR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
+|+|-.|+..--+.|.++|- -.-.++||++.+.++||++.+|+..+|--||-|.|-+++|.
T Consensus 189 rRKRRNFsK~aTeiLneyF~-~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFY-SHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHhhcccchhHHHHHHHHHH-HhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 67778899999999999775 23368899999999999999999999999999999999874
No 36
>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=97.37 E-value=2.3e-05 Score=52.44 Aligned_cols=35 Identities=17% Similarity=0.370 Sum_probs=29.2
Q ss_pred CccCCCCHHHHHHHHHHhCCCCCceeeeccccccc
Q 043261 194 WRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHT 228 (233)
Q Consensus 194 Wr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK 228 (233)
+.++||+..++++||.++|++..+|..||-|.|.+
T Consensus 6 ~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 6 LHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 46899999999999999999999999999998853
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=95.08 E-value=0.024 Score=39.63 Aligned_cols=46 Identities=28% Similarity=0.374 Sum_probs=35.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccc
Q 043261 171 KRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNN 225 (233)
Q Consensus 171 KR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNr 225 (233)
||.|..+|-+|+-.+...++ ... ....+|.+.||+..+|.-|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e----~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLE----EGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHH----CTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHH----cCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 68899999999999999999 332 57789999999999999999875
No 38
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=94.70 E-value=0.038 Score=51.05 Aligned_cols=61 Identities=20% Similarity=0.226 Sum_probs=50.8
Q ss_pred CCCCCCCCCCHHHHHHHHH-HHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 169 TKKRHRTKFTAEQKEKMLG-FAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 169 ~kKR~RT~FT~eQ~~~L~~-~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.++|.+..|..+....|+. +|+.+- .+||.+.....|+.++||+..+|..||-|.|-+..|
T Consensus 238 ~~~r~~~~lP~~a~~ilr~Wl~~h~~--~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 238 SKWRPQRGLPKEAVSILRAWLFEHLL--HPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHhcc--CCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 3677777999999999987 555322 469999999999999999999999999999987643
No 39
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=93.22 E-value=0.027 Score=40.67 Aligned_cols=42 Identities=7% Similarity=0.351 Sum_probs=30.5
Q ss_pred HHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccccc
Q 043261 182 KEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKH 227 (233)
Q Consensus 182 ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRa 227 (233)
++.|+++|. ..+.+.+...+.||.+.+|+..+|+.||--+..
T Consensus 10 ~~pL~~Yy~----~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYL----KHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHH----HT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHH----HcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 456999999 788899999999999999999999999976544
No 40
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=92.84 E-value=0.048 Score=56.44 Aligned_cols=49 Identities=12% Similarity=0.245 Sum_probs=43.4
Q ss_pred CCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 177 FTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 177 FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
|+.. ...|+.+|. .|..|...+...|+..+||+..+||+||+|.++...
T Consensus 564 ~~~p-~sllkayya----ln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~ 612 (1007)
T KOG3623|consen 564 FNHP-TSLLKAYYA----LNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEM 612 (1007)
T ss_pred cCCc-HHHHHHHHH----hcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhh
Confidence 4444 777888999 999999999999999999999999999999988754
No 41
>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=89.64 E-value=0.12 Score=37.01 Aligned_cols=45 Identities=22% Similarity=0.335 Sum_probs=31.6
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccc
Q 043261 172 RHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHN 224 (233)
Q Consensus 172 R~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQN 224 (233)
+.|..||.+++..+...+. .....+.++|.+.||++.+|.-|-.-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~--------~~g~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYL--------ESGESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp -SS----HHHHHHHHHHHH--------HHHCHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHH--------HCCCceEeeecccccccccccHHHHH
Confidence 4677999999999988773 12457889999999999999999753
No 42
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=79.08 E-value=1.9 Score=30.51 Aligned_cols=40 Identities=23% Similarity=0.364 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCce
Q 043261 177 FTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVL 218 (233)
Q Consensus 177 FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vV 218 (233)
+|+.|.+.|...++ .|+-. +|......+||.++||+..+|
T Consensus 1 LT~~Q~e~L~~A~~-~GYfd-~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYE-LGYFD-VPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHH-cCCCC-CCCcCCHHHHHHHhCCCHHHH
Confidence 58899999999998 33221 256667889999999998765
No 43
>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=73.65 E-value=4.1 Score=22.92 Aligned_cols=38 Identities=32% Similarity=0.385 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeec
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWM 222 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWF 222 (233)
.++.+++..+...++ .|| ...+++.+++++..+|..|+
T Consensus 5 ~~~~~~~~~i~~~~~-~~~--------s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLA-AGE--------SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHH-cCC--------CHHHHHHHHCCCHHHHHHhC
Confidence 467888877777766 121 45688999999998887764
No 44
>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=69.11 E-value=1.5 Score=27.78 Aligned_cols=45 Identities=20% Similarity=0.294 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccccccc
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTL 229 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~ 229 (233)
.++..+.+.+..+|. +.....++|.++|++..+|+.|.+.-+.+.
T Consensus 10 ~l~~~~~~~~~~~~~---------~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 10 KLPEREREVILLRFG---------EGLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred hCCHHHHHHHHHHHh---------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 467778777766653 222456889999999999999987665544
No 45
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=63.53 E-value=2.1 Score=36.00 Aligned_cols=47 Identities=15% Similarity=0.147 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 175 TKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 175 T~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
+.+|+.|++.|..+++ || ...++|..+|+++.+|+.|.++.+.++++
T Consensus 5 ~~Lt~rqreVL~lr~~--Gl--------Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 5 SFLTERQIEVLRLRER--GL--------TQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred cCCCHHHHHHHHHHHc--CC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5689999999877433 44 34689999999999999999887776653
No 46
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=63.38 E-value=8.6 Score=29.86 Aligned_cols=43 Identities=23% Similarity=0.332 Sum_probs=35.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCC-CCCceeeeccc
Q 043261 174 RTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGV-KRHVLKVWMHN 224 (233)
Q Consensus 174 RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl-~~~vVKVWFQN 224 (233)
|.+||.|.|..+-+++. ...+ .+..+|++.|| ...++..|...
T Consensus 5 ~r~~s~EfK~~iv~~~~----~~g~----sv~~vAr~~gv~~~~~l~~W~~~ 48 (116)
T COG2963 5 RKKYSPEFKLEAVALYL----RGGD----TVSEVAREFGIVSATQLYKWRIQ 48 (116)
T ss_pred cccCCHHHHHHHHHHHH----hcCc----cHHHHHHHhCCCChHHHHHHHHH
Confidence 78999999999888776 3322 67899999996 99999988763
No 47
>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=62.75 E-value=3 Score=27.82 Aligned_cols=39 Identities=21% Similarity=0.356 Sum_probs=27.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeec
Q 043261 175 TKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWM 222 (233)
Q Consensus 175 T~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWF 222 (233)
.+++.+|.+.+..++. .. ..+.++|.++||++.+|.=++
T Consensus 4 ~~~~~~~~~~i~~l~~------~G---~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYA------EG---MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHH------TT-----HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHH------CC---CCHHHHHHHHCcCHHHHHHHH
Confidence 3578878888888777 22 467899999999999876444
No 48
>PHA02893 hypothetical protein; Provisional
Probab=59.75 E-value=3.5 Score=32.21 Aligned_cols=20 Identities=25% Similarity=0.657 Sum_probs=12.5
Q ss_pred ccccCCCCCccccccccccc
Q 043261 70 FMAAGDEGTLESLKCAACNC 89 (233)
Q Consensus 70 f~~~~~~~~~~~l~caac~c 89 (233)
|.+.|..+....|.|+|||-
T Consensus 58 ~~~~Gk~~~~~tL~CaACGS 77 (88)
T PHA02893 58 YLNIGKAFSNSNIKCIACGS 77 (88)
T ss_pred HHhccccCCCCceeehhhch
Confidence 34444333346799999983
No 49
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=56.58 E-value=2.2 Score=29.44 Aligned_cols=45 Identities=22% Similarity=0.310 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
.||+.+++.|.-++. | ....++|.+++++..+|+.+..|=+.|++
T Consensus 3 ~LT~~E~~vl~~l~~--G--------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--G--------MSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHT--T--------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHh--c--------CCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 588999999988777 2 25678999999999999999887776654
No 50
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=56.04 E-value=9.5 Score=42.33 Aligned_cols=59 Identities=8% Similarity=-0.019 Sum_probs=51.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 169 TKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 169 ~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
..+-.|++++.-|...|..+|+ ...++.-.++..++.-|+|-.+++-+|++|++.++++
T Consensus 443 e~~~~s~r~~~~~t~~L~S~~k----t~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq 501 (1406)
T KOG1146|consen 443 EPLLESKRSLEGQTVVLHSFFK----TLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQ 501 (1406)
T ss_pred hhhhhhhcccccceeeeecccc----cccCCccchhhhhHHHhhhcccccccccchhHhHhcc
Confidence 3456799999999999999998 8999999999999999999999988888887777654
No 51
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=55.99 E-value=1.4 Score=29.68 Aligned_cols=42 Identities=14% Similarity=0.184 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccccc
Q 043261 177 FTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKH 227 (233)
Q Consensus 177 FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRa 227 (233)
+++.+.+.+.-. |.+.....++|..+|++...|++|.+.-|.
T Consensus 11 L~~~~r~i~~l~---------~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLR---------YFQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHH---------HTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHH---------HHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 455666666443 334556779999999999999999875543
No 52
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=55.33 E-value=10 Score=40.13 Aligned_cols=60 Identities=13% Similarity=0.173 Sum_probs=43.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
..+-+.|+.+..++-..|...++ .+..+.-..-...+.++...+.|+.||||||+.+-++
T Consensus 624 ~~p~kv~sp~k~~dq~ql~~a~e----lq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp 683 (1007)
T KOG3623|consen 624 ERPVKVRSPIKEEDQQQLKQAYE----LQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSP 683 (1007)
T ss_pred CCCccccCCCCccchhhhHhhhh----cccCccCcccchhhhhccCCCcchhhcccCCCCCCCC
Confidence 34566778888888888888888 4444444444444666778889999999999887554
No 53
>PF13698 DUF4156: Domain of unknown function (DUF4156)
Probab=54.44 E-value=5.2 Score=31.04 Aligned_cols=18 Identities=39% Similarity=0.553 Sum_probs=14.7
Q ss_pred HHhhhhhhhccCCccccc
Q 043261 49 RECLKNHAVSIGGHAVDG 66 (233)
Q Consensus 49 ~eC~kNhaa~~g~~~~dg 66 (233)
.-=|||.||.|||.+|-.
T Consensus 51 ~NdlrNeAa~lGgntV~~ 68 (93)
T PF13698_consen 51 RNDLRNEAAKLGGNTVVL 68 (93)
T ss_pred HHHHHHHHHHhCCCEEEE
Confidence 345899999999998853
No 54
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=52.21 E-value=16 Score=29.03 Aligned_cols=43 Identities=19% Similarity=0.275 Sum_probs=31.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccc
Q 043261 174 RTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHN 224 (233)
Q Consensus 174 RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQN 224 (233)
|..||.+++..+-...- . +...+.++|.++||+..+|--|.+-
T Consensus 10 rr~ys~EfK~~aV~~~~----~----~g~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSF----E----PGMTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHH----c----CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 45689998876655433 1 2235678899999999999999654
No 55
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=51.07 E-value=3.2 Score=31.35 Aligned_cols=28 Identities=7% Similarity=0.226 Sum_probs=22.9
Q ss_pred CCHHHHHHHHHHhCCCCCceeeeccccc
Q 043261 199 HDEASVEQFCAETGVKRHVLKVWMHNNK 226 (233)
Q Consensus 199 pd~~~re~La~eigl~~~vVKVWFQNrR 226 (233)
.......++|..+|+++.+|++|+.+..
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 3444677999999999999999998643
No 56
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=50.15 E-value=14 Score=31.98 Aligned_cols=41 Identities=20% Similarity=0.252 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCce
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVL 218 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vV 218 (233)
.+|+.|++.|...|+ +|+-. +|......+||.++||+..++
T Consensus 155 ~LTdrQ~~vL~~A~~-~GYFd-~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYK-MGYFD-YPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHH-cCCCC-CCccCCHHHHHHHhCCCHHHH
Confidence 799999999999998 34322 366667789999999998764
No 57
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=49.07 E-value=1.8 Score=36.26 Aligned_cols=47 Identities=15% Similarity=0.087 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.++..|++.+.-.| ......+++|..+|++..+|+++++.-|.++++
T Consensus 142 ~L~~~~r~vl~l~~---------~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 142 ALTDTQRESVTLAY---------YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred hCCHHHHHHHHHHH---------HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 46666666664322 223356789999999999999999887777654
No 58
>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=47.51 E-value=2.6 Score=33.48 Aligned_cols=47 Identities=13% Similarity=0.095 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+++.|.+.+...| .......++|..+|++..+|+++.+.-|.++++
T Consensus 111 ~L~~~~r~v~~l~~---------~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRY---------QRGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHH---------hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 46666666665522 223356789999999999999999877777664
No 59
>PRK10072 putative transcriptional regulator; Provisional
Probab=46.86 E-value=13 Score=29.13 Aligned_cols=41 Identities=17% Similarity=0.360 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccccc
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKH 227 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRa 227 (233)
..+...+..| .+++||+ ..+||..+||+..+|.-|.+.+|.
T Consensus 32 ~~~~~eik~L---R~~~glT--------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQL---RKGTGLK--------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHH---HHHcCCC--------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3455555554 4556665 568999999999999999987753
No 60
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=46.85 E-value=4.4 Score=27.03 Aligned_cols=39 Identities=18% Similarity=0.343 Sum_probs=19.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeec
Q 043261 175 TKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWM 222 (233)
Q Consensus 175 T~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWF 222 (233)
..+|.+|...++.+.+ .| ....++|..+|+++.+|.-|.
T Consensus 3 ~~Lt~~eR~~I~~l~~-~G--------~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLE-QG--------MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHC-S-----------HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHH-cC--------CCHHHHHHHHCcCcHHHHHHH
Confidence 5689999999988766 22 345689999999998876554
No 61
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=46.82 E-value=2.8 Score=34.80 Aligned_cols=33 Identities=12% Similarity=0.119 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 199 HDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 199 pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.......++|..+|++..+|++|++.-|.++++
T Consensus 155 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 155 YEGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 344566799999999999999999877766553
No 62
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=46.59 E-value=9.3 Score=24.59 Aligned_cols=45 Identities=22% Similarity=0.394 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
.++..+++.+..+++ |+ ...++|..+++++.+|..|.+.-+.|++
T Consensus 3 ~l~~~e~~i~~~~~~--g~--------s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVLRLLAE--GL--------TNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHHHHc--CC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 468888887655433 21 4578899999999999999876555543
No 63
>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=46.44 E-value=2.3 Score=34.91 Aligned_cols=33 Identities=6% Similarity=0.076 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 199 HDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 199 pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
......+++|..+|++..+|+++.+.-|.++|+
T Consensus 152 ~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 152 LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 334456799999999999999999877777654
No 64
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=45.27 E-value=3 Score=33.10 Aligned_cols=48 Identities=6% Similarity=0.026 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
.+++.|.+.+...| .+.....++|..+|++..+|++|.+.-|.++|+.
T Consensus 106 ~L~~~~r~ii~l~~---------~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 106 VLDEKEKYIIFERF---------FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred hCCHHHHHHHHHHH---------hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 44555555554322 2233567999999999999999998888777764
No 65
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=44.53 E-value=2.1 Score=35.31 Aligned_cols=47 Identities=15% Similarity=0.284 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+++.+++.+.-.|- .....+++|..+|++..+|+++++.-|.++++
T Consensus 131 ~L~~~~r~v~~l~~~---------~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 131 TLPPRQRDVVQSISV---------EGASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred hCCHHHHHHHHHHHH---------cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 455666666654332 23356799999999999999999888777654
No 66
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=44.51 E-value=14 Score=26.92 Aligned_cols=45 Identities=24% Similarity=0.369 Sum_probs=28.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecc
Q 043261 174 RTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMH 223 (233)
Q Consensus 174 RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQ 223 (233)
|-.||.+.+-...++|+ ....-....| ..+++.+|+++.|+-|.+
T Consensus 3 rrsy~~~FKL~Vv~~a~----~~~nc~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAE----KDNNCKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHH----H-TTTTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHH----HccchhhhHH-HHHHHhCccHHHHHHHHH
Confidence 55788888888888887 3333333333 459999999999999976
No 67
>PRK10403 transcriptional regulator NarP; Provisional
Probab=43.43 E-value=9 Score=30.45 Aligned_cols=48 Identities=17% Similarity=0.233 Sum_probs=38.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 175 TKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 175 T~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
..+|..+++.|..+++ . ..+.+++..+++++++|++..+|=+.|...+
T Consensus 152 ~~Lt~~e~~vl~~~~~----g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 152 SVLTERELDVLHELAQ----G------LSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred ccCCHHHHHHHHHHHC----C------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 3689999998886665 1 3467889999999999999999888777543
No 68
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=42.33 E-value=2.6 Score=35.91 Aligned_cols=47 Identities=21% Similarity=0.181 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.++..|.+.+... |......+++|..+|++..+|+++++.-|.++++
T Consensus 153 ~L~~~~r~vl~l~---------~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 153 KLPEAQQTVVKGV---------YFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred hCCHHHHHHHHHH---------HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3555666665532 2223356799999999999999999877766653
No 69
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=42.20 E-value=2.7 Score=33.77 Aligned_cols=47 Identities=11% Similarity=0.111 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+++.+++.+...|- ......++|..+|+++.+|+.|++.-|.++++
T Consensus 128 ~L~~~~r~vl~l~~~---------~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLREI---------EGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHHH---------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 466677776654332 22345689999999999999999876666554
No 70
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=41.98 E-value=36 Score=29.23 Aligned_cols=42 Identities=5% Similarity=0.151 Sum_probs=35.8
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceee
Q 043261 173 HRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKV 220 (233)
Q Consensus 173 ~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKV 220 (233)
....+|++++++|.++-. ..|....+..||++.|++..-|.+
T Consensus 82 k~y~Lt~e~i~Eir~LR~------~DP~~wTr~~LAkkF~~S~~fV~~ 123 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRA------EDPEKWTRKKLAKKFNCSPLFVSM 123 (164)
T ss_pred ccccCCHHHHHHHHHHHH------cCchHhhHHHHHHHhCCCHHHHHH
Confidence 346899999999999877 778889999999999998766543
No 71
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=41.73 E-value=9.7 Score=31.75 Aligned_cols=44 Identities=27% Similarity=0.576 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHH-HHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecc
Q 043261 176 KFTAEQKEKMLG-FAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMH 223 (233)
Q Consensus 176 ~FT~eQ~~~L~~-~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQ 223 (233)
.||++|.+.|.. .-| ..+.....+..++...+|+++.++++-|.
T Consensus 4 ~~T~eer~eLk~rIvE----lVRe~GRiTi~ql~~~TGasR~Tvk~~lr 48 (127)
T PF06163_consen 4 VFTPEEREELKARIVE----LVREHGRITIKQLVAKTGASRNTVKRYLR 48 (127)
T ss_pred cCCHHHHHHHHHHHHH----HHHHcCCccHHHHHHHHCCCHHHHHHHHH
Confidence 689999999987 334 33444455778899999999999887664
No 72
>PRK04217 hypothetical protein; Provisional
Probab=40.62 E-value=7.4 Score=31.38 Aligned_cols=45 Identities=16% Similarity=0.096 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccccccc
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTL 229 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~ 229 (233)
.++.+|++.+...+. .....+++|..+||++.+|+..++.-+.++
T Consensus 42 ~Lt~eereai~l~~~---------eGlS~~EIAk~LGIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 42 FMTYEEFEALRLVDY---------EGLTQEEAGKRMGVSRGTVWRALTSARKKV 86 (110)
T ss_pred cCCHHHHHHHHHHHH---------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 567888877765553 122667899999999999998887655554
No 73
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=40.36 E-value=2.8 Score=33.92 Aligned_cols=45 Identities=13% Similarity=0.146 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHH-HHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 176 KFTAEQKEKMLG-FAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 176 ~FT~eQ~~~L~~-~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
.+++.|.+.+.- +++ ....+++|..+|++..+|++|.+--|.+++
T Consensus 108 ~L~~~~r~v~~l~~~~----------g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr 153 (165)
T PRK09644 108 TLPVIEAQAILLCDVH----------ELTYEEAASVLDLKLNTYKSHLFRGRKRLK 153 (165)
T ss_pred hCCHHHHHHHHhHHHh----------cCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 456666666643 333 234569999999999999999987766654
No 74
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=40.35 E-value=55 Score=22.28 Aligned_cols=34 Identities=18% Similarity=0.206 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccc
Q 043261 178 TAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNN 225 (233)
Q Consensus 178 T~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNr 225 (233)
|.+||++|.+..- +.++..+|+++.-|.|.|...
T Consensus 13 s~eqk~~l~~~it--------------~~l~~~~~~p~~~v~V~i~e~ 46 (61)
T PRK02220 13 TEEQLKALVKDVT--------------AAVSKNTGAPAEHIHVIINEM 46 (61)
T ss_pred CHHHHHHHHHHHH--------------HHHHHHhCcChhhEEEEEEEe
Confidence 7999999865433 478999999888888877653
No 75
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=39.83 E-value=3.8 Score=33.00 Aligned_cols=48 Identities=15% Similarity=0.151 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
.++..|.+.+.-. +......+++|..+|++..+|+++.+.-|.++++.
T Consensus 112 ~L~~~~r~v~~l~---------~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 112 SLPLERRNVLLLR---------DYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HCCHHHHHHhhhH---------HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 3555555555432 22334567999999999999999998888877654
No 76
>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=39.55 E-value=4.7 Score=26.88 Aligned_cols=44 Identities=9% Similarity=0.184 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccc
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHT 228 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK 228 (233)
.+++.|.+.|...|- ......++|..+|+++..|+.+...-..|
T Consensus 4 ~L~~~er~vi~~~y~---------~~~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRYF---------EGLTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHHT---------ST-SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc---------CCCCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 467888888877663 22356789999999999988776544433
No 77
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=38.45 E-value=20 Score=30.99 Aligned_cols=45 Identities=20% Similarity=0.230 Sum_probs=36.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccccccc
Q 043261 175 TKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTL 229 (233)
Q Consensus 175 T~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~ 229 (233)
..+|+.|++.|.-+.+ ||.| .++|.++++++++||+--+|=-.|+
T Consensus 147 ~~LT~RE~eVL~lla~--G~sn--------keIA~~L~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLSN--------KEIAEELNLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCCH--------HHHHHHHCCCHhHHHHHHHHHHHHc
Confidence 4799999999998888 7665 4889999999999998776644443
No 78
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=38.07 E-value=3.2 Score=34.77 Aligned_cols=47 Identities=23% Similarity=0.258 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+++.|.+.+.-.|- .....+++|..+|+++.+|+++.+.-|.++|+
T Consensus 134 ~Lp~~~R~v~~L~~~---------~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 134 HLPAQQARVFMMREY---------LELSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred hCCHHHHHHHhHHHH---------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345555555544322 23356799999999999999999876666553
No 79
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=37.82 E-value=4.1 Score=34.45 Aligned_cols=32 Identities=19% Similarity=0.169 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 200 DEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 200 d~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.....+++|..+|++..+|+++++--|.++|+
T Consensus 128 ~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 128 SGFSYEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33456799999999999999999877766654
No 80
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=37.45 E-value=16 Score=31.83 Aligned_cols=46 Identities=13% Similarity=0.092 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+|+.|++.|.-.++ ||.+ .++|.++++++.+|+.+..|-..|+.-
T Consensus 155 ~Lt~rE~~Vl~l~~~--G~s~--------~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 155 LLTHREKEILNKLRI--GASN--------NEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCHHHHHHHHHHHc--CCCH--------HHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 489999999988877 5544 588999999999999999887766643
No 81
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=37.39 E-value=14 Score=24.01 Aligned_cols=29 Identities=24% Similarity=0.444 Sum_probs=20.8
Q ss_pred cccccccccccCCCCCcccccccccccccccccc
Q 043261 63 AVDGCGEFMAAGDEGTLESLKCAACNCHRNFHRK 96 (233)
Q Consensus 63 ~~dgc~ef~~~~~~~~~~~l~caac~chrnfhr~ 96 (233)
.=+-|.++|... ...+++|..| ..+.|++
T Consensus 13 ~C~~C~~~i~~~---~~~~~~C~~C--~~~~H~~ 41 (50)
T cd00029 13 FCDVCRKSIWGL---FKQGLRCSWC--KVKCHKK 41 (50)
T ss_pred Chhhcchhhhcc---ccceeEcCCC--CCchhhh
Confidence 356799999864 3578999987 5566654
No 82
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=37.16 E-value=3.8 Score=33.56 Aligned_cols=30 Identities=13% Similarity=0.356 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 202 ASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 202 ~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
...+++|..+|++...|+++++.-|.++|+
T Consensus 146 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 146 LSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 356789999999999999999877776654
No 83
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=37.10 E-value=15 Score=24.34 Aligned_cols=22 Identities=9% Similarity=0.332 Sum_probs=14.9
Q ss_pred HHHHHHhCCCCCceeeeccccc
Q 043261 205 EQFCAETGVKRHVLKVWMHNNK 226 (233)
Q Consensus 205 e~La~eigl~~~vVKVWFQNrR 226 (233)
.+||..+|+++.+|.-|..+++
T Consensus 13 ~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHhCCCcchhHHHhcCCC
Confidence 5777777777777777776643
No 84
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=36.81 E-value=14 Score=38.21 Aligned_cols=36 Identities=33% Similarity=0.537 Sum_probs=26.2
Q ss_pred CccccccccccccCCCCCccccccccc-cccccccccc
Q 043261 61 GHAVDGCGEFMAAGDEGTLESLKCAAC-NCHRNFHRKE 97 (233)
Q Consensus 61 ~~~~dgc~ef~~~~~~~~~~~l~caac-~chrnfhr~~ 97 (233)
+|++| |+---|.=..-.+.+|.|.-| |||||++...
T Consensus 514 ~~c~d-c~~~n~~wAslnlg~l~cieCsgihr~lgt~l 550 (749)
T KOG0705|consen 514 SHCVD-CGTPNPKWASLNLGVLMCIECSGIHRNLGTHL 550 (749)
T ss_pred ceeee-cCCCCcccccccCCeEEEEEchhhhhhhhhhh
Confidence 46676 776555433445689999999 8999999764
No 85
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=36.81 E-value=4.4 Score=33.68 Aligned_cols=34 Identities=21% Similarity=0.345 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 198 KHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 198 ~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
|......+++|.++|++..+|+++.+.-|.++|+
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 185 (194)
T PRK12513 152 EHGDLELEEIAELTGVPEETVKSRLRYALQKLRE 185 (194)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455567899999999999999999877776654
No 86
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=36.77 E-value=12 Score=23.50 Aligned_cols=24 Identities=21% Similarity=0.414 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCCCceeeecccccc
Q 043261 204 VEQFCAETGVKRHVLKVWMHNNKH 227 (233)
Q Consensus 204 re~La~eigl~~~vVKVWFQNrRa 227 (233)
..++|..+||++.+|.-|.++.+-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467899999999999999877653
No 87
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=36.75 E-value=47 Score=35.71 Aligned_cols=11 Identities=55% Similarity=1.111 Sum_probs=8.4
Q ss_pred CcchhhHHhhh
Q 043261 3 FEEHEEQEVEE 13 (233)
Q Consensus 3 ~~~~~~~~~~~ 13 (233)
||||-|+|-+|
T Consensus 359 fdE~~e~Dl~e 369 (1102)
T KOG1924|consen 359 FDEHKEDDLEE 369 (1102)
T ss_pred HhhhhhhhHHH
Confidence 78888877655
No 88
>PRK00118 putative DNA-binding protein; Validated
Probab=36.63 E-value=8.1 Score=30.87 Aligned_cols=46 Identities=20% Similarity=0.210 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
.++..|.+.+.-.|. ......++|..+|+++.+|+.|++.-|.+.+
T Consensus 17 ~L~ekqRevl~L~y~---------eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 17 LLTEKQRNYMELYYL---------DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred cCCHHHHHHHHHHHH---------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 356677777755444 2335668999999999999999876555443
No 89
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=36.52 E-value=4.5 Score=33.46 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 202 ASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 202 ~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
...+++|..+|++..+|++|.+.-|.++|+
T Consensus 150 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 150 CSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 356789999999999999999877766654
No 90
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=36.47 E-value=3.5 Score=34.17 Aligned_cols=48 Identities=17% Similarity=0.140 Sum_probs=34.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 175 TKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 175 T~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
..+++.|.+.+.-.|- .....+++|..+|++..+|+++.+.-|.++|+
T Consensus 138 ~~L~~~~r~i~~l~~~---------~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 138 DTLPEKQREILILRVV---------VGLSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred HhCCHHHHHHHHHHHH---------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3566667666654322 23456799999999999999999877766654
No 91
>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=36.44 E-value=5.5 Score=30.13 Aligned_cols=47 Identities=13% Similarity=0.179 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+++.|.+.+...+- ......++|.++|+++.+|+.|.+.-+.|.++
T Consensus 110 ~L~~~~~~ii~~~~~---------~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYL---------EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHh---------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 456666666654432 12245689999999999999998877776664
No 92
>PRK09726 antitoxin HipB; Provisional
Probab=36.26 E-value=38 Score=25.29 Aligned_cols=22 Identities=14% Similarity=0.351 Sum_probs=13.5
Q ss_pred HHHHHHHhCCCCCceeeecccc
Q 043261 204 VEQFCAETGVKRHVLKVWMHNN 225 (233)
Q Consensus 204 re~La~eigl~~~vVKVWFQNr 225 (233)
..+||..+||+...|.-|..++
T Consensus 28 q~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCC
Confidence 3466666666666666666543
No 93
>PRK06424 transcription factor; Provisional
Probab=36.05 E-value=24 Score=29.62 Aligned_cols=24 Identities=8% Similarity=0.066 Sum_probs=20.6
Q ss_pred HHHHHHHhCCCCCceeeecccccc
Q 043261 204 VEQFCAETGVKRHVLKVWMHNNKH 227 (233)
Q Consensus 204 re~La~eigl~~~vVKVWFQNrRa 227 (233)
.++||..+|++...|.-|..+++.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 569999999999999999977653
No 94
>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=35.91 E-value=10 Score=27.71 Aligned_cols=20 Identities=15% Similarity=0.539 Sum_probs=17.6
Q ss_pred HHHHHHHHhCCCCCceeeec
Q 043261 203 SVEQFCAETGVKRHVLKVWM 222 (233)
Q Consensus 203 ~re~La~eigl~~~vVKVWF 222 (233)
...+||.+|||++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45688999999999999994
No 95
>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=35.72 E-value=5 Score=33.42 Aligned_cols=35 Identities=11% Similarity=0.173 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 197 QKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 197 ~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.|.......++|..+|++..+|+++++--|.++++
T Consensus 143 ~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 177 (193)
T TIGR02947 143 ADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRK 177 (193)
T ss_pred hhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44455567899999999999999999877766653
No 96
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=35.66 E-value=8.9 Score=30.25 Aligned_cols=35 Identities=14% Similarity=0.153 Sum_probs=27.5
Q ss_pred CCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 197 QKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 197 ~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.|......+++|..+|+++.+|+++++--|.++++
T Consensus 117 ~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 117 REFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34455677899999999999999999866666543
No 97
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=35.21 E-value=4.9 Score=32.82 Aligned_cols=47 Identities=11% Similarity=0.160 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+++.+.+.+.-. |......+++|..+|+++.+|+++++.-|.++++
T Consensus 136 ~L~~~~r~v~~l~---------~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 136 ALPPKYRMVIVLK---------YMEDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCHHHhHHhhhH---------HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555565555432 2233466799999999999999999877766653
No 98
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=34.81 E-value=13 Score=32.48 Aligned_cols=49 Identities=14% Similarity=0.230 Sum_probs=39.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 174 RTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 174 RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
...+|+.|++.|.-.++ | ....++|..++|++++|+.+++|-+.|++-+
T Consensus 169 ~~~Lt~re~evl~~~a~--G--------~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~ 217 (232)
T TIGR03541 169 AGVLSEREREVLAWTAL--G--------RRQADIAAILGISERTVENHLRSARRKLGVA 217 (232)
T ss_pred hccCCHHHHHHHHHHHC--C--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence 45799999999977654 3 3456889999999999999999988887643
No 99
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=34.55 E-value=4.8 Score=33.61 Aligned_cols=30 Identities=13% Similarity=0.093 Sum_probs=24.5
Q ss_pred HHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 202 ASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 202 ~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
...+++|..+|++..+|+++.+--|.++++
T Consensus 147 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 147 LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 356799999999999999999876666553
No 100
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=34.34 E-value=3.9 Score=32.79 Aligned_cols=29 Identities=7% Similarity=0.170 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 203 SVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 203 ~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
..+++|..+|++..+|+++++.-|.++|+
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45689999999999999999877766553
No 101
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=34.20 E-value=9.9 Score=26.06 Aligned_cols=26 Identities=15% Similarity=0.350 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCCCCceeeeccccccc
Q 043261 203 SVEQFCAETGVKRHVLKVWMHNNKHT 228 (233)
Q Consensus 203 ~re~La~eigl~~~vVKVWFQNrRaK 228 (233)
...+||+.+||++.+|.-|+.++..+
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~ 37 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSN 37 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT---
T ss_pred CHHHHHHHHCcCHHHHHHHHhccccc
Confidence 56789999999999999999877433
No 102
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=33.65 E-value=17 Score=27.73 Aligned_cols=10 Identities=40% Similarity=1.115 Sum_probs=8.5
Q ss_pred cccccccccc
Q 043261 80 ESLKCAACNC 89 (233)
Q Consensus 80 ~~l~caac~c 89 (233)
..|.|+|||-
T Consensus 56 ~tLsCsACGS 65 (74)
T PF05077_consen 56 NTLSCSACGS 65 (74)
T ss_pred CeEeehhccc
Confidence 5799999983
No 103
>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=33.36 E-value=4.4 Score=33.15 Aligned_cols=30 Identities=17% Similarity=0.119 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 202 ASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 202 ~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
...+++|..+|++..+|++.++.-|.++++
T Consensus 151 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 151 LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 356689999999999999999877776654
No 104
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=33.12 E-value=21 Score=28.38 Aligned_cols=47 Identities=23% Similarity=0.343 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
.+|..+.+.|.-+++ | + .+++++.+++++.++|++..+|=|.|+.-+
T Consensus 137 ~Lt~~E~~il~~l~~--g----~----~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~ 183 (196)
T PRK10360 137 PLTKRERQVAEKLAQ--G----M----AVKEIAAELGLSPKTVHVHRANLMEKLGVS 183 (196)
T ss_pred CCCHHHHHHHHHHHC--C----C----CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 689999988887777 2 2 577899999999999999998877776543
No 105
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=33.12 E-value=12 Score=34.95 Aligned_cols=51 Identities=16% Similarity=0.217 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+++.|...|...|- ..+......+++|..+||+..+|+++.+.-+.++|+
T Consensus 262 ~L~~~~R~vl~lryg-----L~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~ 312 (325)
T PRK05657 262 ELNDKQREVLARRFG-----LLGYEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312 (325)
T ss_pred cCCHHHHHHHHHHhc-----cCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 566667777665552 234455677899999999999999999877776654
No 106
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=33.07 E-value=6 Score=32.74 Aligned_cols=47 Identities=17% Similarity=0.294 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+++.|.+.+.-. |......+++|..+|++..+|+.+.+.-|.++++
T Consensus 131 ~L~~~~r~v~~l~---------~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 131 RLPEKMRLAIQAV---------KLEGLSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred hCCHHHHHHHHHH---------HHcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3555555555432 2233456799999999999999999876666553
No 107
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=33.01 E-value=12 Score=24.22 Aligned_cols=23 Identities=17% Similarity=0.271 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCCCceeeeccccc
Q 043261 204 VEQFCAETGVKRHVLKVWMHNNK 226 (233)
Q Consensus 204 re~La~eigl~~~vVKVWFQNrR 226 (233)
..++|..+||+..+|+.|.++..
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 46889999999999999977654
No 108
>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=32.97 E-value=4.5 Score=31.67 Aligned_cols=30 Identities=17% Similarity=0.272 Sum_probs=24.7
Q ss_pred HHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 202 ASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 202 ~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
....++|..+|+++.+|+++.+.-|.++++
T Consensus 130 ~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 130 KSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 356689999999999999998877776654
No 109
>PF13518 HTH_28: Helix-turn-helix domain
Probab=32.81 E-value=14 Score=24.18 Aligned_cols=24 Identities=25% Similarity=0.569 Sum_probs=20.3
Q ss_pred HHHHHHHHhCCCCCceeeeccccc
Q 043261 203 SVEQFCAETGVKRHVLKVWMHNNK 226 (233)
Q Consensus 203 ~re~La~eigl~~~vVKVWFQNrR 226 (233)
...++|.++||+..+|.-|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 566799999999999999987543
No 110
>PF13551 HTH_29: Winged helix-turn helix
Probab=32.62 E-value=45 Score=24.76 Aligned_cols=20 Identities=20% Similarity=0.501 Sum_probs=16.3
Q ss_pred CCCCCCCCHHHHHHHHHHHH
Q 043261 171 KRHRTKFTAEQKEKMLGFAE 190 (233)
Q Consensus 171 KR~RT~FT~eQ~~~L~~~fe 190 (233)
.|.++.+++++.+.|.+++.
T Consensus 52 g~~~~~l~~~~~~~l~~~~~ 71 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLR 71 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHH
Confidence 34444599999999999998
No 111
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=32.04 E-value=15 Score=30.75 Aligned_cols=47 Identities=15% Similarity=0.104 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 174 RTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 174 RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
.+.+|..|++.+.-+++ || ..+++|..+|+++..|+.|-+.-+.|++
T Consensus 4 ~~~Lte~qr~VL~Lr~~--Gl--------Tq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 4 KTFLTERQIKVLELREK--GL--------SQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred cCCCCHHHHHHHHHHHc--CC--------CHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 46789999999876433 43 5578999999999999998877666655
No 112
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=32.00 E-value=35 Score=22.24 Aligned_cols=23 Identities=9% Similarity=0.098 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCCCceeeeccccc
Q 043261 204 VEQFCAETGVKRHVLKVWMHNNK 226 (233)
Q Consensus 204 re~La~eigl~~~vVKVWFQNrR 226 (233)
.++||..+|++...|.-|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46788888888888888876553
No 113
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=31.97 E-value=5.6 Score=33.18 Aligned_cols=47 Identities=13% Similarity=0.312 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHH-HHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 176 KFTAEQKEKMLG-FAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 176 ~FT~eQ~~~L~~-~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
.+++.|.+.+.- +++ ....+++|..+|++..+|++..+--|.+++++
T Consensus 131 ~L~~~~r~i~~l~~~~----------g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 131 DLEKLDREIFIRRYLL----------GEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred hCCHHHHHHHHHHHHc----------cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 456666666653 333 23567999999999999999988777777664
No 114
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=31.06 E-value=5.8 Score=31.80 Aligned_cols=45 Identities=16% Similarity=0.182 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
.++..|.+.|.-.+ ......++|..+|++..+|+.+.+.-|.++|
T Consensus 112 ~L~~~~r~il~l~~----------~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr 156 (166)
T PRK09639 112 KMTERDRTVLLLRF----------SGYSYKEIAEALGIKESSVGTTLARAKKKFR 156 (166)
T ss_pred cCCHHHHHHHHHHH----------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35555655554333 3335679999999999999999876666654
No 115
>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=30.86 E-value=11 Score=30.83 Aligned_cols=46 Identities=13% Similarity=0.146 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
.+++.|.+.+.-.|- .....+++|.++|++..+|+++.+--|.+++
T Consensus 100 ~L~~~~r~v~~l~~~---------~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 145 (170)
T TIGR02959 100 ELPDEYREAIRLTEL---------EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLK 145 (170)
T ss_pred hCCHHHHHHHHHHHH---------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 556666666654332 2235668999999999999999876665544
No 116
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=30.78 E-value=5.6 Score=31.82 Aligned_cols=30 Identities=17% Similarity=0.181 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 201 EASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 201 ~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
.....++|..+|+++.+|+.|.+--|.+++
T Consensus 141 ~~~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 141 GLSYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 335679999999999999999886666654
No 117
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=30.77 E-value=5.6 Score=33.44 Aligned_cols=31 Identities=13% Similarity=0.154 Sum_probs=24.7
Q ss_pred HHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 201 EASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 201 ~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.....++|..+|+++.+|+++++.-|.++++
T Consensus 132 g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~ 162 (187)
T PRK12516 132 GFAYEEAAEICGCAVGTIKSRVNRARQRLQE 162 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3355689999999999999999877666543
No 118
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=30.69 E-value=8.5 Score=30.19 Aligned_cols=9 Identities=56% Similarity=0.962 Sum_probs=6.8
Q ss_pred ceeeecccc
Q 043261 217 VLKVWMHNN 225 (233)
Q Consensus 217 vVKVWFQNr 225 (233)
-|||||||-
T Consensus 32 dvkvwmqnl 40 (106)
T PF11516_consen 32 DVKVWMQNL 40 (106)
T ss_dssp HHHHHHHHH
T ss_pred cHHHHHHHH
Confidence 478999884
No 119
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=30.62 E-value=58 Score=27.54 Aligned_cols=23 Identities=17% Similarity=0.147 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCCCceeeeccccc
Q 043261 204 VEQFCAETGVKRHVLKVWMHNNK 226 (233)
Q Consensus 204 re~La~eigl~~~vVKVWFQNrR 226 (233)
.++||..+|++...|.-|-.+.+
T Consensus 85 qeeLA~~lgvs~s~IsriE~G~~ 107 (154)
T TIGR00270 85 QEQLAKKIQEKESLIKKIENAEI 107 (154)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 56888888888888888876553
No 120
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=30.58 E-value=17 Score=32.84 Aligned_cols=48 Identities=19% Similarity=0.194 Sum_probs=38.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 174 RTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 174 RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
...+|+.+++.|.-.++ | ....++|..++|++.+||.+++|-+.|.+-
T Consensus 188 ~~~LT~RE~evl~l~a~--G--------~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVRD--G--------KTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHHC--C--------CCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 44789999999986655 2 244688999999999999999988877654
No 121
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=30.48 E-value=4.4 Score=32.27 Aligned_cols=46 Identities=24% Similarity=0.274 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
.++..|.+.+.-.|- ......++|..+|++..+|++..+.-|.++|
T Consensus 106 ~Lp~~~r~v~~l~~~---------~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 151 (161)
T PRK09047 106 KLPARQREAFLLRYW---------EDMDVAETAAAMGCSEGSVKTHCSRATHALA 151 (161)
T ss_pred hCCHHHHHHHHHHHH---------hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 455566655544221 2234578999999999999998876665554
No 122
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=30.26 E-value=5 Score=32.60 Aligned_cols=30 Identities=20% Similarity=0.160 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 201 EASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 201 ~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
....+++|..+|+++.+|+++.+.-|.+.+
T Consensus 128 g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 128 GFSYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 345679999999999999999886666554
No 123
>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=30.07 E-value=24 Score=22.83 Aligned_cols=42 Identities=21% Similarity=0.335 Sum_probs=28.0
Q ss_pred CHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccccccc
Q 043261 178 TAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTL 229 (233)
Q Consensus 178 T~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~ 229 (233)
+..|++.+..+++ | ....++|..+++++.+|+.|.+.-+.+.
T Consensus 2 ~~~e~~i~~~~~~--~--------~s~~eia~~l~~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 2 TPREREVLRLLAE--G--------KTNKEIADILGISEKTVKTHLRNIMRKL 43 (57)
T ss_pred CHHHHHHHHHHHc--C--------CCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 5566665544333 2 1457889999999999999986434433
No 124
>PRK13558 bacterio-opsin activator; Provisional
Probab=29.76 E-value=42 Score=33.21 Aligned_cols=40 Identities=13% Similarity=0.081 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCccCC--CCHHHHHHHHHHhCCCCCce
Q 043261 175 TKFTAEQKEKMLGFAEQLGWRIQK--HDEASVEQFCAETGVKRHVL 218 (233)
Q Consensus 175 T~FT~eQ~~~L~~~feklGWr~~~--pd~~~re~La~eigl~~~vV 218 (233)
..+|..|.+.|+..|+ .-.| |.....++||.++||+..+|
T Consensus 606 ~~lt~~q~e~l~~a~~----~gyf~~pr~~~~~e~a~~l~is~~t~ 647 (665)
T PRK13558 606 NDLTDRQLTALQKAYV----SGYFEWPRRVEGEELAESMGISRSTF 647 (665)
T ss_pred hhCCHHHHHHHHHHHH----cCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 4799999999999999 4454 67778899999999998875
No 125
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=29.54 E-value=5.6 Score=33.33 Aligned_cols=47 Identities=9% Similarity=0.082 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+++.|.+.+.-.| ......+++|..+|++..+|+++++--|.++++
T Consensus 136 ~L~~~~r~i~~L~~---------~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 136 ALPERQRQAVVLRH---------IEGLSNPEIAEVMEIGVEAVESLTARGKRALAA 182 (196)
T ss_pred hCCHHHHHHHHHHH---------HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45555555554322 223346689999999999999999866666543
No 126
>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=29.16 E-value=6 Score=31.68 Aligned_cols=29 Identities=17% Similarity=0.172 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 203 SVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 203 ~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
..+++|..+|++..+|+++.+.-|.++++
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45689999999999999999877777654
No 127
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=29.00 E-value=6.5 Score=33.30 Aligned_cols=31 Identities=13% Similarity=0.317 Sum_probs=24.7
Q ss_pred HHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 201 EASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 201 ~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.....++|..+|+++.+|++.++.-|.++|+
T Consensus 155 g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 185 (201)
T PRK12545 155 DFEIDDICTELTLTANHCSVLLYRARTRLRT 185 (201)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3456789999999999999998876666543
No 128
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=28.80 E-value=1.1e+02 Score=21.10 Aligned_cols=33 Identities=15% Similarity=0.259 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccc
Q 043261 178 TAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHN 224 (233)
Q Consensus 178 T~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQN 224 (233)
|.||+++|-+..- +.++..+++++..|.|.|..
T Consensus 13 s~EqK~~L~~~it--------------~a~~~~~~~p~~~v~V~i~e 45 (60)
T PRK02289 13 SQEQKNALAREVT--------------EVVSRIAKAPKEAIHVFIND 45 (60)
T ss_pred CHHHHHHHHHHHH--------------HHHHHHhCcCcceEEEEEEE
Confidence 7999999865333 37788999999999998864
No 129
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=28.73 E-value=7 Score=31.73 Aligned_cols=34 Identities=15% Similarity=0.142 Sum_probs=27.0
Q ss_pred CCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 198 KHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 198 ~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
|......+++|..+|++...|+++.+.-|.+.++
T Consensus 139 ~~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 139 HYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred hhcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 3445567799999999999999998877766654
No 130
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=28.37 E-value=15 Score=31.78 Aligned_cols=51 Identities=14% Similarity=0.130 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+++.|.+.+.-.|. ..+......+++|..+|++..+|+++.+.-|.++|+
T Consensus 178 ~Lp~~~R~v~~L~y~-----l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 178 KLSDREKQIMELRFG-----LNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred hCCHHHHHHHHHHhc-----cCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 455666666554331 011344467799999999999999998877766654
No 131
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=28.17 E-value=5.2 Score=33.03 Aligned_cols=32 Identities=25% Similarity=0.329 Sum_probs=26.4
Q ss_pred CHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 200 DEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 200 d~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.....+++|..+|+++.+|++.++.-|.++++
T Consensus 144 ~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 144 EGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34456799999999999999999887777664
No 132
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=28.00 E-value=6.1 Score=32.61 Aligned_cols=29 Identities=14% Similarity=0.135 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 203 SVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 203 ~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
..+++|..+|++..+|+++.+.-|.++++
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRA 174 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 55689999999999999999877776654
No 133
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=27.76 E-value=7.4 Score=33.92 Aligned_cols=32 Identities=13% Similarity=0.171 Sum_probs=25.7
Q ss_pred CHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 200 DEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 200 d~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
+....+++|..+|+++.+|+++.+.-|.++++
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~ 180 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARARRRLAA 180 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34456799999999999999999877766654
No 134
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=27.69 E-value=34 Score=21.82 Aligned_cols=28 Identities=21% Similarity=0.445 Sum_probs=19.4
Q ss_pred cccccccccccCCCCCcccccccccccccccccc
Q 043261 63 AVDGCGEFMAAGDEGTLESLKCAACNCHRNFHRK 96 (233)
Q Consensus 63 ~~dgc~ef~~~~~~~~~~~l~caac~chrnfhr~ 96 (233)
.=+-|.++|.... .+++|+.|+ ...|.+
T Consensus 13 ~C~~C~~~i~~~~----~~~~C~~C~--~~~H~~ 40 (49)
T smart00109 13 KCCVCRKSIWGSF----QGLRCSWCK--VKCHKK 40 (49)
T ss_pred CccccccccCcCC----CCcCCCCCC--chHHHH
Confidence 4578999998643 479999874 444443
No 135
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=27.56 E-value=6.3 Score=32.77 Aligned_cols=30 Identities=17% Similarity=0.246 Sum_probs=24.4
Q ss_pred HHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 202 ASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 202 ~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
...+++|..+|+++.+|++..+.-|.++++
T Consensus 148 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (191)
T PRK12520 148 LETEEICQELQITATNAWVLLYRARMRLRE 177 (191)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356799999999999999998877666543
No 136
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=27.41 E-value=6.8 Score=32.65 Aligned_cols=31 Identities=16% Similarity=0.258 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 201 EASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 201 ~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
....+++|..+|++..+|+++.+.-|.++|+
T Consensus 152 g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 182 (195)
T PRK12532 152 GFSSDEIQQMCGISTSNYHTIMHRARESLRQ 182 (195)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3356799999999999999998876665543
No 137
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=27.41 E-value=5.7 Score=32.22 Aligned_cols=35 Identities=9% Similarity=0.152 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 197 QKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 197 ~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.|......+++|..+|++..+|++.++.-|.+.++
T Consensus 132 ~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 132 HDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred hHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34455567899999999999999999877776653
No 138
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=26.91 E-value=19 Score=34.92 Aligned_cols=14 Identities=43% Similarity=0.918 Sum_probs=11.5
Q ss_pred cccccccccccccc
Q 043261 81 SLKCAACNCHRNFH 94 (233)
Q Consensus 81 ~l~caac~chrnfh 94 (233)
+++|+||||+-+--
T Consensus 118 ~~~CkACG~r~~~d 131 (400)
T KOG2767|consen 118 SLKCKACGFRSDMD 131 (400)
T ss_pred hhHHHHcCCccccc
Confidence 78999999986643
No 139
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=26.66 E-value=6.6 Score=32.26 Aligned_cols=47 Identities=11% Similarity=0.065 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.++..+.+.+.-.+ ......+++|..+|++..+|+++.+.-|.++++
T Consensus 135 ~L~~~~r~vl~l~~---------~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 135 ALSPEERRVIEVLY---------YQGYTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred hCCHHHHHHHHHHH---------HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35555555554322 223345689999999999999998876666543
No 140
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=26.53 E-value=8.5 Score=33.43 Aligned_cols=33 Identities=15% Similarity=0.172 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 199 HDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 199 pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.......++|..+|++..+|+.+++.-+.++|+
T Consensus 198 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 198 QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344466799999999999999999877776654
No 141
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=26.50 E-value=6.3 Score=32.71 Aligned_cols=46 Identities=22% Similarity=0.317 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHH-HHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLG-FAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~-~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+++.|.+.|.- +++ ....+++|..+|++..+|++-++.-|.++++
T Consensus 131 ~L~~~~r~vl~l~~~~----------~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 131 KLSPAHREIIDLVYYH----------EKSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred hCCHHHHHHHHHHHHc----------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 566777777644 333 2355689999999999999988877776654
No 142
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=26.33 E-value=6.9 Score=32.23 Aligned_cols=30 Identities=17% Similarity=0.137 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 202 ASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 202 ~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
....++|..+|++..+|++.++.-|.+.++
T Consensus 134 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 134 YSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356689999999999999998877776654
No 143
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=26.08 E-value=8.3 Score=32.18 Aligned_cols=30 Identities=13% Similarity=0.140 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 201 EASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 201 ~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
....+++|..+|++..+|+..++.-|.+++
T Consensus 122 g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr 151 (181)
T PRK09637 122 GLSQKEIAEKLGLSLSGAKSRVQRGRVKLK 151 (181)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 345678999999999999999886666554
No 144
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=25.86 E-value=31 Score=29.57 Aligned_cols=45 Identities=11% Similarity=0.138 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
.+|+.+++.|.-..+ |+.+ .++|.++++++++|+.-..|=..|++
T Consensus 137 ~LT~RE~eVL~lla~--G~sn--------keIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESSMLRMWMA--GQGT--------IQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHHHHHHHHc--CCCH--------HHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 499999999988887 5544 58899999999999877665554443
No 145
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=25.79 E-value=18 Score=25.16 Aligned_cols=21 Identities=14% Similarity=0.324 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCCCceeeeccc
Q 043261 204 VEQFCAETGVKRHVLKVWMHN 224 (233)
Q Consensus 204 re~La~eigl~~~vVKVWFQN 224 (233)
..++|+.+||+.++|+.|-..
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 458899999999999999654
No 146
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=25.74 E-value=7.7 Score=31.46 Aligned_cols=45 Identities=18% Similarity=0.233 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 177 FTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 177 FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
+++.|.+.|.-.| ......+++|..+|+++.+|++..+.-|.+++
T Consensus 119 L~~~~r~vl~L~~---------~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 163 (173)
T PRK09645 119 LSPEHRAVLVRSY---------YRGWSTAQIAADLGIPEGTVKSRLHYALRALR 163 (173)
T ss_pred CCHHHHHHHHHHH---------HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 5556666554422 12234679999999999999998876665554
No 147
>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=25.73 E-value=8.1 Score=30.92 Aligned_cols=47 Identities=11% Similarity=0.107 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+++.|.+.+.-.| .......++|..+|+++.+|++..+--|.++|+
T Consensus 122 ~L~~~~r~vl~l~~---------~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRF---------GQNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHH---------hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45555655555422 223355689999999999999988766666554
No 148
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=25.24 E-value=10 Score=31.15 Aligned_cols=31 Identities=13% Similarity=0.228 Sum_probs=23.4
Q ss_pred CCCHHHHHHHHHHhCCCCCceeeeccccccc
Q 043261 198 KHDEASVEQFCAETGVKRHVLKVWMHNNKHT 228 (233)
Q Consensus 198 ~pd~~~re~La~eigl~~~vVKVWFQNrRaK 228 (233)
|.......++|..+|++..+|+++++.-+.+
T Consensus 132 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 132 QLDGLTYSEIAHKLGVSVSSVKKYVAKATEH 162 (172)
T ss_pred hccCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 3344456799999999999999998654433
No 149
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=25.19 E-value=7.8 Score=34.12 Aligned_cols=31 Identities=6% Similarity=0.114 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 201 EASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 201 ~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
....+++|..+|++..+|+++.+.-|.++|+
T Consensus 187 g~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 187 NMSNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3456799999999999999999877776654
No 150
>PRK10651 transcriptional regulator NarL; Provisional
Probab=25.14 E-value=24 Score=28.08 Aligned_cols=46 Identities=9% Similarity=0.139 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+|..+.+.|.-+++ .+ ...+++++++++..+|++..+|=+.|+.-
T Consensus 155 ~Lt~rE~~vl~~l~~------g~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 155 QLTPRERDILKLIAQ------GL----PNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred cCCHHHHHHHHHHHc------CC----CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 499999998877665 11 34577999999999999998887777653
No 151
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=25.11 E-value=13 Score=26.61 Aligned_cols=25 Identities=20% Similarity=0.476 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCCCceeeeccccccccC
Q 043261 204 VEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 204 re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
..++|.+|||+..+|.-|-+ |.+|.
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~--r~~W~ 40 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD--RYKWD 40 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH--hhCcc
Confidence 45889999999999999975 44443
No 152
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=25.11 E-value=38 Score=27.30 Aligned_cols=40 Identities=15% Similarity=0.221 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccccc
Q 043261 177 FTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKH 227 (233)
Q Consensus 177 FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRa 227 (233)
++..++..|.+-+. - ....||+-+|++..+|+-|=|+|+.
T Consensus 44 ls~~eIk~iRe~~~----l-------SQ~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLG----L-------SQPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhC----C-------CHHHHHHHHCCCHHHHHHHHcCCcC
Confidence 88888888876555 1 3568999999999999999998864
No 153
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=25.08 E-value=55 Score=26.26 Aligned_cols=50 Identities=12% Similarity=0.208 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhC-----CCCCceeeeccccccccC
Q 043261 175 TKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETG-----VKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 175 T~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eig-----l~~~vVKVWFQNrRaK~k 230 (233)
-.+|+.+.+.|.-++. .......+++|+.++. ++.++|++...+=|.|+.
T Consensus 147 ~~Lt~~E~~il~~l~~------~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~ 201 (221)
T PRK15479 147 LALTPREQALLTVLMY------RRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ 201 (221)
T ss_pred EecCHHHHHHHHHHHh------CCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence 3689999999988888 3334445778887775 888999998887777764
No 154
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=24.81 E-value=8.5 Score=32.28 Aligned_cols=30 Identities=17% Similarity=0.133 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 201 EASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 201 ~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
....+++|..+|++..+|+++.+--|.+++
T Consensus 127 g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr 156 (182)
T PRK12511 127 GLSYQEAAAVLGIPIGTLMSRIGRARAALR 156 (182)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 335679999999999999999876655544
No 155
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=24.78 E-value=8.4 Score=31.41 Aligned_cols=32 Identities=9% Similarity=0.152 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 200 DEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 200 d~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
+....+++|..+|++..+|+++++.-|.++++
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 33456799999999999999998876666543
No 156
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.63 E-value=18 Score=23.80 Aligned_cols=24 Identities=21% Similarity=0.540 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCCCCceeeeccccc
Q 043261 203 SVEQFCAETGVKRHVLKVWMHNNK 226 (233)
Q Consensus 203 ~re~La~eigl~~~vVKVWFQNrR 226 (233)
...++|..+||++.+|.-|.+.-+
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT---
T ss_pred CHHHHHHHHCcCHHHHHHHHHHcc
Confidence 557899999999999999986533
No 157
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=24.63 E-value=9 Score=32.50 Aligned_cols=29 Identities=10% Similarity=0.084 Sum_probs=24.0
Q ss_pred HHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 202 ASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 202 ~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
...+++|..+|++..+|+++.+.-|.++|
T Consensus 150 ~s~~EIAe~lgis~~tV~~~l~Rar~~Lr 178 (196)
T PRK12535 150 YTYEEAAKIADVRVGTIRSRVARARADLI 178 (196)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 35679999999999999999887666554
No 158
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=24.53 E-value=54 Score=22.02 Aligned_cols=36 Identities=14% Similarity=0.334 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCce
Q 043261 177 FTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVL 218 (233)
Q Consensus 177 FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vV 218 (233)
||..|...|..++. .........+||..++++...|
T Consensus 3 lt~~q~~vL~~l~~------~~~~~~t~~~la~~l~~~~~~v 38 (62)
T PF12802_consen 3 LTPSQFRVLMALAR------HPGEELTQSELAERLGISKSTV 38 (62)
T ss_dssp STHHHHHHHHHHHH------STTSGEEHHHHHHHHTS-HHHH
T ss_pred cCHHHHHHHHHHHH------CCCCCcCHHHHHHHHCcCHHHH
Confidence 68889999988887 3332346778899999887654
No 159
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=24.35 E-value=80 Score=24.97 Aligned_cols=24 Identities=29% Similarity=0.447 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCccCC
Q 043261 175 TKFTAEQKEKMLGFAEQLGWRIQK 198 (233)
Q Consensus 175 T~FT~eQ~~~L~~~feklGWr~~~ 198 (233)
+..|..|+..+.+.|+++||+.++
T Consensus 20 k~lt~~el~~vl~~l~~~G~k~~~ 43 (119)
T PF06252_consen 20 KDLTEAELEKVLDELKRLGFKPPK 43 (119)
T ss_pred HHCCHHHHHHHHHHHHHccCcCcc
Confidence 468999999999999999997544
No 160
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=24.25 E-value=1.5e+02 Score=23.12 Aligned_cols=35 Identities=6% Similarity=0.074 Sum_probs=27.2
Q ss_pred CHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccc
Q 043261 178 TAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNK 226 (233)
Q Consensus 178 T~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrR 226 (233)
+.+|+++|-+. .-+.|...+|++...|-|-|++..
T Consensus 70 ~~e~k~~l~~~--------------i~~~l~~~lgi~~~rv~I~f~~~~ 104 (116)
T PTZ00397 70 SRSNNSSIAAA--------------ITKILASHLKVKSERVYIEFKDCS 104 (116)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCcCcccEEEEEEECC
Confidence 57888887542 234788999999999999998764
No 161
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=24.24 E-value=25 Score=27.40 Aligned_cols=46 Identities=13% Similarity=0.263 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCCC
Q 043261 177 FTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGKK 232 (233)
Q Consensus 177 FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kKK 232 (233)
+++.+.+.|..+++ | ..-.+++.+++++..+|+++.++=|.|+++.
T Consensus 142 l~~~e~~vl~~~~~--~--------~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~ 187 (202)
T PRK09390 142 LSERERQVMDGLVA--G--------LSNKVIARDLDISPRTVEVYRANVMTKMQAG 187 (202)
T ss_pred hhhhHHHHHHHHHc--c--------CchHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence 55556666654443 1 1245678999999999999998887776543
No 162
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=23.93 E-value=44 Score=26.11 Aligned_cols=46 Identities=9% Similarity=0.100 Sum_probs=35.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 175 TKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 175 T~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
..+|..+.+.|.-+.+ .+ ...++|..+++++.+|+.|.+|=+.|+.
T Consensus 148 ~~lt~~e~~vl~l~~~------g~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKLITE------GY----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHHHHC------CC----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3588888888876544 12 3568899999999999999998777664
No 163
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=23.72 E-value=8.8 Score=31.78 Aligned_cols=33 Identities=12% Similarity=0.178 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 199 HDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 199 pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
......+++|..+|++..+|++.++.-|.++|+
T Consensus 152 ~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 152 FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344456799999999999999998877666553
No 164
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=23.13 E-value=48 Score=23.46 Aligned_cols=16 Identities=6% Similarity=0.053 Sum_probs=7.8
Q ss_pred CCHHHHHHHHHHhCCC
Q 043261 199 HDEASVEQFCAETGVK 214 (233)
Q Consensus 199 pd~~~re~La~eigl~ 214 (233)
++......||..++++
T Consensus 45 ~~~~~~~~l~~~l~v~ 60 (78)
T TIGR02607 45 ITADMALRLAKALGTS 60 (78)
T ss_pred CCHHHHHHHHHHcCCC
Confidence 3444445555555544
No 165
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=23.00 E-value=1.7e+02 Score=19.33 Aligned_cols=34 Identities=21% Similarity=0.243 Sum_probs=25.9
Q ss_pred CHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccc
Q 043261 178 TAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNN 225 (233)
Q Consensus 178 T~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNr 225 (233)
|.+||++|-+.. .+.++..+|+++..|-|.|+..
T Consensus 12 t~eqk~~l~~~i--------------~~~l~~~~g~~~~~v~V~i~e~ 45 (58)
T cd00491 12 TDEQKRELIERV--------------TEAVSEILGAPEATIVVIIDEM 45 (58)
T ss_pred CHHHHHHHHHHH--------------HHHHHHHhCcCcccEEEEEEEe
Confidence 588888885432 2377888999999999988754
No 166
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=22.89 E-value=38 Score=28.17 Aligned_cols=44 Identities=14% Similarity=0.240 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccccccc
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTL 229 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~ 229 (233)
.+|+.+++.|.-+.+ |+++ .++|.++++++++|+.-..|=..|+
T Consensus 150 ~Lt~rE~evl~~~~~--G~s~--------~eIA~~l~iS~~TV~~h~~~i~~Kl 193 (216)
T PRK10840 150 RLSPKESEVLRLFAE--GFLV--------TEIAKKLNRSIKTISSQKKSAMMKL 193 (216)
T ss_pred cCCHHHHHHHHHHHC--CCCH--------HHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 599999999988887 5443 5889999999999987665544444
No 167
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=22.80 E-value=8.5 Score=31.82 Aligned_cols=44 Identities=14% Similarity=0.166 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccc
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHT 228 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK 228 (233)
.+++.|.+.+.-. +.+....+++|..+|+++.+|++.++.-+.+
T Consensus 127 ~Lp~~~R~v~~L~---------~~~g~s~~EIA~~lgis~~tVk~~l~rAl~~ 170 (178)
T PRK12529 127 TLRPRVKQAFLMA---------TLDGMKQKDIAQALDIALPTVKKYIHQAYVT 170 (178)
T ss_pred hCCHHHHHHHHHH---------HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4556666655432 2233356799999999999999988755443
No 168
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=22.74 E-value=8.4 Score=31.82 Aligned_cols=29 Identities=3% Similarity=0.180 Sum_probs=23.4
Q ss_pred HHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 202 ASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 202 ~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
...+++|..+|++..+|++..+.-|.+++
T Consensus 139 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr 167 (185)
T PRK12542 139 LTYQEISSVMGITEANVRKQFERARKRVQ 167 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35568999999999999998876666554
No 169
>cd01276 PKCI_related Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a hydrophobic residue) that is a signature for this family. No enzymatic activity has been reported however, for PKCI and its related members.
Probab=22.55 E-value=1.4e+02 Score=22.24 Aligned_cols=45 Identities=13% Similarity=0.279 Sum_probs=28.9
Q ss_pred CCCCCCCCH---HHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccccc
Q 043261 171 KRHRTKFTA---EQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKH 227 (233)
Q Consensus 171 KR~RT~FT~---eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRa 227 (233)
||..+.|.. +.+..|..+.. ....+++.++....-+.+||+|...
T Consensus 42 k~H~~~~~dl~~~~~~~l~~~~~------------~~~~~~~~~~~~~~~~n~~~~~g~~ 89 (104)
T cd01276 42 KKHIASLSDATEEDEELLGHLLS------------AAAKVAKDLGIAEDGYRLVINCGKD 89 (104)
T ss_pred cceeCChHHcccccHHHHHHHHH------------HHHHHHHHhCCCCCCEEEEEeCCCC
Confidence 445555444 56666666665 3456777776556778999988653
No 170
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=22.53 E-value=59 Score=26.10 Aligned_cols=50 Identities=10% Similarity=0.092 Sum_probs=38.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhC-----CCCCceeeeccccccccC
Q 043261 175 TKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETG-----VKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 175 T~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eig-----l~~~vVKVWFQNrRaK~k 230 (233)
..+|..+.+.|.-+++ .......+++++..+. ++.++|++...|=|.|+.
T Consensus 148 ~~Lt~~E~~il~~l~~------~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (219)
T PRK10336 148 LTLKPKEFALLELLMR------NAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG 202 (219)
T ss_pred EecCHHHHHHHHHHHh------CCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence 3599999999998887 3333345678888886 899999998887777764
No 171
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=22.35 E-value=31 Score=27.46 Aligned_cols=46 Identities=11% Similarity=0.072 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 175 TKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 175 T~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
..+|..+.+.|..+++ - ..+++++.+++++.++|+++..+=|.|+.
T Consensus 148 ~~lt~re~~vl~~l~~----g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 148 TVLSNREVTILRYLVS----G------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred ccCCHHHHHHHHHHHc----C------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 3588888888876666 1 46779999999999999999988877764
No 172
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=22.21 E-value=9.7 Score=31.85 Aligned_cols=32 Identities=19% Similarity=0.169 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 200 DEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 200 d~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.....+++|..+|+++.+|++.++--|.++++
T Consensus 126 ~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~ 157 (182)
T PRK12540 126 SGFSYEDAAAICGCAVGTIKSRVNRARSKLSA 157 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34456799999999999999998766665543
No 173
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.06 E-value=56 Score=21.68 Aligned_cols=25 Identities=16% Similarity=0.562 Sum_probs=15.7
Q ss_pred ccccccccCCCCCcccccccccccc
Q 043261 66 GCGEFMAAGDEGTLESLKCAACNCH 90 (233)
Q Consensus 66 gc~ef~~~~~~~~~~~l~caac~ch 90 (233)
-||..|...+.....-+.|..||-|
T Consensus 5 ~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 5 KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCccccccCCCCCEEECCcCCCe
Confidence 4777776543222236889999954
No 174
>PRK06930 positive control sigma-like factor; Validated
Probab=21.96 E-value=20 Score=30.47 Aligned_cols=47 Identities=13% Similarity=0.183 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.+++.+++.+.-.|. ......++|..+|++..+|+++++.-|.++++
T Consensus 114 ~L~~rer~V~~L~~~---------eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLMHRG---------YGLSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred hCCHHHHHHHHHHHH---------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 466666666654222 22355689999999999999999877776653
No 175
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=21.94 E-value=1.6e+02 Score=20.01 Aligned_cols=34 Identities=18% Similarity=0.201 Sum_probs=26.4
Q ss_pred CHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccc
Q 043261 178 TAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNN 225 (233)
Q Consensus 178 T~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNr 225 (233)
|.+|++.|-+..- +.++..+|++...|.|.|...
T Consensus 13 s~eqk~~l~~~it--------------~~l~~~~~~p~~~v~V~i~e~ 46 (62)
T PRK00745 13 TVEQKRKLVEEIT--------------RVTVETLGCPPESVDIIITDV 46 (62)
T ss_pred CHHHHHHHHHHHH--------------HHHHHHcCCChhHEEEEEEEc
Confidence 7899988865333 367899999999999988653
No 176
>PRK13870 transcriptional regulator TraR; Provisional
Probab=21.92 E-value=36 Score=30.12 Aligned_cols=48 Identities=13% Similarity=0.176 Sum_probs=37.3
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 173 HRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 173 ~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
.+..+|+-+++.|.=.++ ...-.+++..+||++++|+.-++|-+.|+.
T Consensus 170 ~~~~LT~RE~E~L~W~A~----------GKT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 170 DAAWLDPKEATYLRWIAV----------GKTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred ccCCCCHHHHHHHHHHHc----------CCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 345688888888875555 224458899999999999999999888874
No 177
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=21.91 E-value=1.6e+02 Score=20.30 Aligned_cols=34 Identities=15% Similarity=0.226 Sum_probs=26.2
Q ss_pred CHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccc
Q 043261 178 TAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNN 225 (233)
Q Consensus 178 T~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNr 225 (233)
|.+|+++|-+..- +.++..+|+++..|-|.|...
T Consensus 13 t~eqk~~l~~~it--------------~~l~~~lg~p~~~v~V~i~e~ 46 (64)
T PRK01964 13 PEEKIKNLIREVT--------------EAISATLDVPKERVRVIVNEV 46 (64)
T ss_pred CHHHHHHHHHHHH--------------HHHHHHhCcChhhEEEEEEEc
Confidence 7899988865332 377889999999998887654
No 178
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=21.72 E-value=34 Score=28.09 Aligned_cols=13 Identities=54% Similarity=0.925 Sum_probs=10.9
Q ss_pred ccccccccccccc
Q 043261 79 LESLKCAACNCHR 91 (233)
Q Consensus 79 ~~~l~caac~chr 91 (233)
.-.|+|.|||..|
T Consensus 112 ~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 112 LIFLKCKACGASR 124 (125)
T ss_dssp CCEEEETTTSCEE
T ss_pred EEEEEecccCCcC
Confidence 4589999999876
No 179
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=21.72 E-value=1.9e+02 Score=19.65 Aligned_cols=34 Identities=21% Similarity=0.261 Sum_probs=26.1
Q ss_pred CHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecccc
Q 043261 178 TAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNN 225 (233)
Q Consensus 178 T~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNr 225 (233)
|.+|++.|-+.. -+.|+..+|+++..+-|.+...
T Consensus 13 t~eqK~~l~~~i--------------t~~l~~~lg~~~~~v~V~i~e~ 46 (63)
T TIGR00013 13 TDEQKRQLIEGV--------------TEAMAETLGANLESIVVIIDEM 46 (63)
T ss_pred CHHHHHHHHHHH--------------HHHHHHHhCCCcccEEEEEEEc
Confidence 789998886532 2478899999999988877654
No 180
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.70 E-value=55 Score=25.92 Aligned_cols=39 Identities=18% Similarity=0.543 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeecc
Q 043261 176 KFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMH 223 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQ 223 (233)
.+|.+-.+++..+++ . .....++|...+|+.++|.-||+
T Consensus 2 aYS~DlR~rVl~~~~----~-----g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 2 AYSLDLRQRVLAYIE----K-----GKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CCCHHHHHHHHHHHH----c-----cchHHHHHHHhCcHHHHHHHHHH
Confidence 467777888888887 2 12456789999999999999998
No 181
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=21.64 E-value=1.8e+02 Score=19.75 Aligned_cols=33 Identities=21% Similarity=0.275 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccc
Q 043261 178 TAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHN 224 (233)
Q Consensus 178 T~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQN 224 (233)
|.+||++|-+..- +.+...+|+++..|.|.|+.
T Consensus 12 ~~e~K~~l~~~it--------------~~~~~~lg~~~~~i~V~i~E 44 (60)
T PF01361_consen 12 TAEQKRELAEAIT--------------DAVVEVLGIPPERISVVIEE 44 (60)
T ss_dssp -HHHHHHHHHHHH--------------HHHHHHHTS-GGGEEEEEEE
T ss_pred CHHHHHHHHHHHH--------------HHHHHHhCcCCCeEEEEEEE
Confidence 7889888865333 36788899999999998874
No 182
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=21.55 E-value=21 Score=28.56 Aligned_cols=28 Identities=11% Similarity=0.190 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCCCCceeeeccccccccC
Q 043261 203 SVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 203 ~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
..+++|..+|++..+|++.++--+.+.+
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr 154 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCR 154 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4568999999999999998765555443
No 183
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=21.54 E-value=9.3 Score=31.15 Aligned_cols=32 Identities=16% Similarity=0.300 Sum_probs=25.5
Q ss_pred CHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 200 DEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 200 d~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.....+++|..+|++..+|+++.+.-|.++++
T Consensus 151 ~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34456799999999999999998877776653
No 184
>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=21.20 E-value=12 Score=30.21 Aligned_cols=29 Identities=14% Similarity=0.303 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 203 SVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 203 ~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
..+++|..+|++..+|+++.+--|.++++
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45689999999999999988766665543
No 185
>PLN03162 golden-2 like transcription factor; Provisional
Probab=20.99 E-value=1e+02 Score=30.46 Aligned_cols=61 Identities=18% Similarity=0.296 Sum_probs=43.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 168 GTKKRHRTKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 168 ~~kKR~RT~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
..+|+.|-.+|++--++....-++|| ..+-....+-++-..-||++..|+.-.|.-|...|
T Consensus 231 ~g~KKpRLrWTpELH~rFVeAV~qLG--~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk 291 (526)
T PLN03162 231 PGKKKAKVDWTPELHRRFVHAVEQLG--VEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRR 291 (526)
T ss_pred CCCCCCcccCCHHHHHHHHHHHHHhC--cCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcc
Confidence 34677889999999999999889899 33444445556666668888888877776655444
No 186
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=20.98 E-value=10 Score=31.76 Aligned_cols=29 Identities=10% Similarity=0.038 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 203 SVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 203 ~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
..+++|..+|++..+|++.++.-|.++++
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 55689999999999999988876666543
No 187
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=20.69 E-value=46 Score=22.19 Aligned_cols=18 Identities=22% Similarity=0.545 Sum_probs=14.0
Q ss_pred HHHHHHHHHhCCCCCcee
Q 043261 202 ASVEQFCAETGVKRHVLK 219 (233)
Q Consensus 202 ~~re~La~eigl~~~vVK 219 (233)
-..++||.+++|++++|+
T Consensus 16 it~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIR 33 (55)
T ss_dssp BEHHHHHHHCTS-HHHHH
T ss_pred cCHHHHHHHhCCCHHHHH
Confidence 466789999999998875
No 188
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=20.65 E-value=14 Score=32.01 Aligned_cols=35 Identities=23% Similarity=0.359 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 197 QKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 197 ~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
.|......+++|..+|++..+|++..+.-|.++|+
T Consensus 161 ~~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~ 195 (231)
T PRK11922 161 RVVEELSVEETAQALGLPEETVKTRLHRARRLLRE 195 (231)
T ss_pred ehhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34445567799999999999999988766666654
No 189
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=20.61 E-value=46 Score=26.46 Aligned_cols=40 Identities=15% Similarity=0.238 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccc
Q 043261 180 EQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHN 224 (233)
Q Consensus 180 eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQN 224 (233)
.-+.++.++-+ . ++.+...+++||..+|++++.+.-+|+.
T Consensus 9 ~~i~~~~~~I~----~-~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 9 ITIHSILDWIE----D-NLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHHH----H-hcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 33455555555 2 3444567889999999999999988864
No 190
>PRK09483 response regulator; Provisional
Probab=20.39 E-value=40 Score=27.25 Aligned_cols=46 Identities=11% Similarity=0.208 Sum_probs=34.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCccCCCCHHHHHHHHHHhCCCCCceeeeccccccccC
Q 043261 175 TKFTAEQKEKMLGFAEQLGWRIQKHDEASVEQFCAETGVKRHVLKVWMHNNKHTLG 230 (233)
Q Consensus 175 T~FT~eQ~~~L~~~feklGWr~~~pd~~~re~La~eigl~~~vVKVWFQNrRaK~k 230 (233)
..+|+.+++.|.-+.+ |+. ..++|.++++++++|+.-.+|=+.|+.
T Consensus 147 ~~Lt~rE~~vl~~~~~--G~~--------~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIMLMITK--GQK--------VNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHHHHHHC--CCC--------HHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 4699999999976554 332 338899999999999887776666553
No 191
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=20.34 E-value=6.9 Score=32.52 Aligned_cols=33 Identities=9% Similarity=0.037 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHhCCCCCceeeeccccccccCC
Q 043261 199 HDEASVEQFCAETGVKRHVLKVWMHNNKHTLGK 231 (233)
Q Consensus 199 pd~~~re~La~eigl~~~vVKVWFQNrRaK~kK 231 (233)
......+++|..+|++..+|+++.+.-|.++|+
T Consensus 148 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 148 VAELEFQEIADIMHMGLSATKMRYKRALDKLRE 180 (188)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 334466799999999999999999876666553
No 192
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=20.22 E-value=12 Score=30.57 Aligned_cols=29 Identities=7% Similarity=0.143 Sum_probs=23.0
Q ss_pred HHHHHHHHHHhCCCCCceeeecccccccc
Q 043261 201 EASVEQFCAETGVKRHVLKVWMHNNKHTL 229 (233)
Q Consensus 201 ~~~re~La~eigl~~~vVKVWFQNrRaK~ 229 (233)
.....++|..+|++..+|+++.+.-+.+.
T Consensus 135 g~s~~EIA~~lgis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 135 GMGHAEIAERLGVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34567999999999999999987655443
No 193
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=20.18 E-value=1e+02 Score=21.29 Aligned_cols=20 Identities=15% Similarity=0.546 Sum_probs=14.1
Q ss_pred CCCHHHHHHHHHHHHhcCCc
Q 043261 176 KFTAEQKEKMLGFAEQLGWR 195 (233)
Q Consensus 176 ~FT~eQ~~~L~~~feklGWr 195 (233)
.++..|+++|.+.+++-||-
T Consensus 23 ~~s~~~L~k~~~wld~rgWw 42 (45)
T PF12123_consen 23 PLSDAELDKFTAWLDERGWW 42 (45)
T ss_dssp ---HHHHHHHHHHHHHTT--
T ss_pred CCCHHHHHHHHHHHHhcCcE
Confidence 35789999999999988884
No 194
>PRK09480 slmA division inhibitor protein; Provisional
Probab=20.13 E-value=71 Score=25.84 Aligned_cols=30 Identities=13% Similarity=0.195 Sum_probs=26.0
Q ss_pred cCCCCHHHHHHHHHHhCCCCCceeeeccccc
Q 043261 196 IQKHDEASVEQFCAETGVKRHVLKVWMHNNK 226 (233)
Q Consensus 196 ~~~pd~~~re~La~eigl~~~vVKVWFQNrR 226 (233)
... ....+.++|.+.||++.+|=-+|.|+.
T Consensus 26 ~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 26 PPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred cCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 345 778899999999999999999998864
No 195
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=20.09 E-value=77 Score=21.33 Aligned_cols=30 Identities=20% Similarity=0.618 Sum_probs=15.8
Q ss_pred ccccccccCCCCCcccccccccc------ccccccc
Q 043261 66 GCGEFMAAGDEGTLESLKCAACN------CHRNFHR 95 (233)
Q Consensus 66 gc~ef~~~~~~~~~~~l~caac~------chrnfhr 95 (233)
+|..++...........+|.+|+ |...+|.
T Consensus 25 ~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 25 DCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp ST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 68888886443322238899886 6666665
Done!