Query psy17899
Match_columns 145
No_of_seqs 224 out of 642
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 16:57:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17899.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17899hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3802|consensus 100.0 1.2E-69 2.6E-74 461.5 9.4 133 8-144 214-346 (398)
2 KOG1168|consensus 100.0 4.2E-54 9.2E-59 355.5 6.4 137 8-144 225-361 (385)
3 PF00157 Pou: Pou domain - N-t 100.0 8.9E-39 1.9E-43 218.3 6.4 61 8-71 15-75 (75)
4 smart00352 POU Found in Pit-Oc 100.0 4.1E-30 8.9E-35 175.5 5.1 61 8-71 15-75 (75)
5 TIGR01565 homeo_ZF_HD homeobox 99.7 2.3E-18 4.9E-23 112.7 5.2 53 92-144 1-57 (58)
6 PF00046 Homeobox: Homeobox do 99.7 3.7E-18 8.1E-23 109.1 0.4 53 93-145 1-53 (57)
7 smart00389 HOX Homeodomain. DN 99.6 9.8E-17 2.1E-21 101.6 2.8 53 93-145 1-53 (56)
8 KOG0843|consensus 99.6 1.3E-16 2.9E-21 124.9 3.7 55 91-145 101-155 (197)
9 cd00086 homeodomain Homeodomai 99.6 1.9E-16 4.1E-21 100.8 2.1 53 93-145 1-53 (59)
10 KOG2251|consensus 99.6 1.1E-15 2.4E-20 122.8 4.5 57 89-145 34-90 (228)
11 KOG0484|consensus 99.6 1.7E-16 3.6E-21 115.1 -0.3 55 91-145 16-70 (125)
12 KOG0489|consensus 99.5 1.9E-15 4.2E-20 124.2 0.8 56 90-145 157-212 (261)
13 KOG0488|consensus 99.5 4.3E-15 9.4E-20 125.0 2.9 56 90-145 170-225 (309)
14 KOG0485|consensus 99.5 6E-15 1.3E-19 118.8 2.8 58 87-144 99-156 (268)
15 KOG0842|consensus 99.5 1.1E-14 2.3E-19 122.4 4.2 56 90-145 151-206 (307)
16 KOG0487|consensus 99.5 1.1E-14 2.3E-19 122.4 3.6 58 87-144 230-287 (308)
17 KOG4577|consensus 99.5 1.3E-14 2.8E-19 121.0 3.8 56 90-145 165-220 (383)
18 COG5576 Homeodomain-containing 99.5 4.5E-14 9.7E-19 108.7 5.3 55 91-145 50-104 (156)
19 KOG0492|consensus 99.5 3.5E-14 7.6E-19 113.7 3.3 54 92-145 144-197 (246)
20 KOG0850|consensus 99.4 5E-14 1.1E-18 113.9 3.3 55 91-145 121-175 (245)
21 KOG0494|consensus 99.4 7.2E-14 1.6E-18 115.1 2.9 54 92-145 140-194 (332)
22 KOG0493|consensus 99.4 3E-13 6.5E-18 111.6 2.5 54 92-145 246-299 (342)
23 KOG0844|consensus 99.3 8.7E-13 1.9E-17 110.9 1.4 53 92-144 181-233 (408)
24 KOG0848|consensus 99.3 6.2E-13 1.3E-17 109.8 0.5 54 92-145 199-252 (317)
25 KOG0486|consensus 99.2 5.8E-12 1.2E-16 105.9 2.6 56 90-145 110-165 (351)
26 KOG0490|consensus 99.2 8.2E-12 1.8E-16 98.3 3.0 56 90-145 58-113 (235)
27 KOG0491|consensus 99.2 1.5E-12 3.3E-17 101.1 -1.9 54 91-144 99-152 (194)
28 KOG0483|consensus 99.2 1.2E-11 2.7E-16 98.5 3.0 48 98-145 56-103 (198)
29 KOG0849|consensus 99.0 1.5E-10 3.2E-15 99.2 4.1 56 90-145 174-229 (354)
30 KOG0847|consensus 98.9 2.4E-10 5.1E-15 92.7 1.4 56 90-145 165-220 (288)
31 KOG2252|consensus 98.7 9.4E-09 2E-13 91.8 4.7 54 91-144 419-472 (558)
32 KOG0775|consensus 98.6 1.2E-07 2.6E-12 78.9 7.3 44 101-144 185-228 (304)
33 KOG0774|consensus 98.5 1.1E-07 2.3E-12 79.0 3.6 53 92-144 188-243 (334)
34 PF05920 Homeobox_KN: Homeobox 98.4 1.8E-08 3.9E-13 61.2 -1.5 32 113-144 7-38 (40)
35 KOG0490|consensus 98.4 1.6E-07 3.4E-12 73.9 3.2 56 90-145 151-206 (235)
36 KOG1146|consensus 97.8 7.9E-06 1.7E-10 79.2 2.4 55 91-145 902-956 (1406)
37 KOG3623|consensus 97.3 0.00011 2.3E-09 68.5 1.5 42 104-145 568-609 (1007)
38 PF13560 HTH_31: Helix-turn-he 96.4 0.0033 7.1E-08 40.6 2.7 34 9-51 6-39 (64)
39 KOG0773|consensus 96.3 0.0029 6.3E-08 53.4 2.9 53 92-144 239-294 (342)
40 COG3620 Predicted transcriptio 96.3 0.011 2.3E-07 46.6 5.5 61 1-72 1-62 (187)
41 PF11569 Homez: Homeodomain le 96.2 0.001 2.3E-08 43.2 -0.2 39 105-143 11-49 (56)
42 PF04218 CENP-B_N: CENP-B N-te 95.9 0.0063 1.4E-07 38.6 2.4 46 93-143 1-46 (53)
43 KOG3623|consensus 95.1 0.028 6.1E-07 52.9 4.5 82 60-144 597-678 (1007)
44 TIGR03070 couple_hipB transcri 95.0 0.052 1.1E-06 33.2 4.1 42 9-59 7-50 (58)
45 PF01381 HTH_3: Helix-turn-hel 94.5 0.1 2.2E-06 32.1 4.6 44 10-62 2-47 (55)
46 TIGR03830 CxxCG_CxxCG_HTH puta 94.4 0.12 2.6E-06 37.1 5.5 35 8-51 69-103 (127)
47 PHA01976 helix-turn-helix prot 93.7 0.16 3.4E-06 32.5 4.5 46 9-63 7-54 (67)
48 TIGR02612 mob_myst_A mobile my 93.3 0.12 2.5E-06 39.7 3.8 47 8-63 29-79 (150)
49 PHA00542 putative Cro-like pro 93.1 0.24 5.2E-06 33.8 4.9 46 10-64 24-72 (82)
50 PF12844 HTH_19: Helix-turn-he 93.0 0.11 2.4E-06 33.0 2.8 41 9-58 4-46 (64)
51 PRK10072 putative transcriptio 92.8 0.1 2.3E-06 37.1 2.7 36 7-51 36-71 (96)
52 TIGR00270 conserved hypothetic 92.8 0.15 3.4E-06 39.1 3.9 47 9-64 74-122 (154)
53 PF13744 HTH_37: Helix-turn-he 92.4 0.24 5.3E-06 33.5 4.1 31 11-50 25-55 (80)
54 PRK09726 antitoxin HipB; Provi 91.8 0.29 6.3E-06 33.5 3.9 32 9-49 17-48 (88)
55 PRK06424 transcription factor; 91.3 0.3 6.5E-06 37.2 3.9 41 10-59 90-132 (144)
56 PRK09706 transcriptional repre 91.1 0.2 4.4E-06 36.8 2.7 51 9-68 10-65 (135)
57 PRK09943 DNA-binding transcrip 89.6 0.61 1.3E-05 35.9 4.4 48 8-64 11-60 (185)
58 PF01527 HTH_Tnp_1: Transposas 88.3 0.12 2.6E-06 33.8 -0.4 43 94-140 2-44 (76)
59 PF04967 HTH_10: HTH DNA bindi 87.7 0.47 1E-05 30.3 2.1 38 99-136 1-40 (53)
60 TIGR02607 antidote_HigA addict 86.8 1.2 2.5E-05 29.1 3.8 47 9-64 9-58 (78)
61 COG1476 Predicted transcriptio 86.7 0.6 1.3E-05 31.5 2.3 34 6-48 3-36 (68)
62 PRK08359 transcription factor; 86.0 1.3 2.9E-05 34.8 4.3 49 12-69 93-143 (176)
63 PRK10856 cytoskeletal protein 83.9 3 6.5E-05 35.7 5.8 55 8-71 18-83 (331)
64 PF04545 Sigma70_r4: Sigma-70, 83.7 0.61 1.3E-05 28.4 1.1 37 98-139 4-40 (50)
65 PF01316 Arg_repressor: Argini 83.5 1.1 2.4E-05 30.2 2.4 25 17-45 19-43 (70)
66 cd00093 HTH_XRE Helix-turn-hel 83.4 3.5 7.6E-05 23.4 4.4 46 9-63 4-51 (58)
67 PRK04140 hypothetical protein; 83.4 1.9 4.2E-05 36.8 4.5 49 8-65 130-180 (317)
68 PRK13890 conjugal transfer pro 83.3 2.5 5.3E-05 30.9 4.5 45 11-64 12-58 (120)
69 PRK08154 anaerobic benzoate ca 82.6 1.6 3.5E-05 36.4 3.7 48 9-65 33-82 (309)
70 PF08281 Sigma70_r4_2: Sigma-7 81.1 1.3 2.9E-05 27.0 2.1 39 98-141 10-48 (54)
71 PF10668 Phage_terminase: Phag 80.1 0.51 1.1E-05 31.0 -0.2 33 105-140 11-43 (60)
72 PHA02591 hypothetical protein; 79.8 1.6 3.6E-05 30.3 2.3 24 14-46 56-79 (83)
73 smart00530 HTH_XRE Helix-turn- 79.5 5.7 0.00012 22.2 4.4 42 10-60 3-46 (56)
74 cd00569 HTH_Hin_like Helix-tur 79.4 2.6 5.6E-05 21.8 2.6 37 99-140 6-42 (42)
75 PF06056 Terminase_5: Putative 77.6 0.83 1.8E-05 29.5 0.3 22 119-140 13-34 (58)
76 PF13551 HTH_29: Winged helix- 75.2 8.1 0.00018 26.3 4.8 49 92-140 51-108 (112)
77 TIGR01321 TrpR trp operon repr 75.0 4.1 8.9E-05 29.1 3.3 38 16-69 54-92 (94)
78 TIGR03764 ICE_PFGI_1_parB inte 73.7 2.7 5.9E-05 35.1 2.4 30 16-49 135-164 (258)
79 TIGR01529 argR_whole arginine 73.5 3.8 8.2E-05 31.0 3.0 31 17-51 16-47 (146)
80 cd06171 Sigma70_r4 Sigma70, re 73.2 1.5 3.4E-05 25.3 0.6 40 98-142 10-49 (55)
81 COG3413 Predicted DNA binding 71.5 3.1 6.8E-05 32.8 2.2 39 98-136 155-195 (215)
82 PF13936 HTH_38: Helix-turn-he 70.2 2.8 6E-05 25.2 1.3 38 97-139 3-40 (44)
83 PF10691 DUF2497: Protein of u 69.8 3.1 6.7E-05 28.3 1.6 20 50-69 32-53 (73)
84 PF13613 HTH_Tnp_4: Helix-turn 69.7 3.1 6.8E-05 25.8 1.5 25 13-46 15-39 (53)
85 PF13411 MerR_1: MerR HTH fami 66.6 2 4.2E-05 27.4 0.1 19 122-140 3-21 (69)
86 cd00131 PAX Paired Box domain 66.5 49 0.0011 24.2 8.3 73 60-143 47-127 (128)
87 PRK03975 tfx putative transcri 63.1 11 0.00023 28.7 3.6 38 15-63 19-56 (141)
88 PRK05066 arginine repressor; P 62.9 6.8 0.00015 30.1 2.5 33 17-52 23-56 (156)
89 PF00376 MerR: MerR family reg 62.8 2 4.4E-05 25.3 -0.3 18 122-139 2-19 (38)
90 PRK13355 bifunctional HTH-doma 62.0 8.5 0.00018 34.2 3.2 57 9-69 8-69 (517)
91 PF08535 KorB: KorB domain; I 61.4 6.8 0.00015 26.9 2.1 25 17-50 3-27 (93)
92 PF09607 BrkDBD: Brinker DNA-b 60.8 6.1 0.00013 25.8 1.6 47 95-142 2-48 (58)
93 cd04761 HTH_MerR-SF Helix-Turn 60.6 2.3 5E-05 25.1 -0.4 20 122-141 3-22 (49)
94 PF13565 HTH_32: Homeodomain-l 60.6 42 0.00091 21.5 6.3 44 93-138 27-75 (77)
95 cd06170 LuxR_C_like C-terminal 58.2 5 0.00011 23.8 0.8 35 100-140 2-36 (57)
96 PRK10458 DNA cytosine methylas 57.1 11 0.00024 33.8 3.1 41 8-51 20-60 (467)
97 smart00421 HTH_LUXR helix_turn 56.6 9.4 0.0002 22.4 1.9 38 98-141 3-40 (58)
98 PRK04280 arginine repressor; P 55.8 9.9 0.00022 28.9 2.3 30 18-51 19-49 (148)
99 TIGR03879 near_KaiC_dom probab 54.5 1.6 3.5E-05 29.7 -2.0 25 118-142 31-55 (73)
100 COG3827 Uncharacterized protei 54.4 9.7 0.00021 31.2 2.1 17 53-69 190-208 (231)
101 PF13384 HTH_23: Homeodomain-l 53.8 3.4 7.4E-05 24.7 -0.5 24 119-142 17-40 (50)
102 PRK06759 RNA polymerase factor 53.0 13 0.00028 26.8 2.4 39 98-141 106-144 (154)
103 PF13518 HTH_28: Helix-turn-he 52.7 5.4 0.00012 23.7 0.3 22 121-142 14-35 (52)
104 COG1400 SEC65 Signal recogniti 50.7 15 0.00032 26.2 2.3 23 115-137 30-52 (93)
105 COG1438 ArgR Arginine represso 50.6 13 0.00027 28.7 2.1 24 18-45 21-44 (150)
106 COG2522 Predicted transcriptio 50.5 14 0.0003 27.4 2.3 23 15-46 20-42 (119)
107 cd04762 HTH_MerR-trunc Helix-T 50.0 4.1 8.9E-05 23.4 -0.5 21 122-142 3-23 (49)
108 TIGR00721 tfx DNA-binding prot 49.7 14 0.0003 27.9 2.2 26 16-50 20-45 (137)
109 PF13730 HTH_36: Helix-turn-he 49.6 23 0.00051 21.4 2.9 23 115-140 24-46 (55)
110 PRK09480 slmA division inhibit 49.5 12 0.00027 27.7 1.9 38 105-143 17-54 (194)
111 cd04764 HTH_MlrA-like_sg1 Heli 49.3 5.6 0.00012 25.4 -0.0 20 122-141 3-22 (67)
112 KOG1146|consensus 49.2 12 0.00026 37.8 2.3 55 91-145 704-758 (1406)
113 PRK09646 RNA polymerase sigma 48.1 12 0.00026 28.5 1.7 38 99-141 143-180 (194)
114 PRK10072 putative transcriptio 47.8 7.1 0.00015 27.7 0.3 23 122-144 49-71 (96)
115 PF05269 Phage_CII: Bacterioph 46.4 9.1 0.0002 27.1 0.7 44 17-71 23-66 (91)
116 cd01104 HTH_MlrA-CarA Helix-Tu 46.3 6.5 0.00014 24.8 -0.1 20 122-141 3-22 (68)
117 cd04763 HTH_MlrA-like Helix-Tu 46.1 6.6 0.00014 25.1 -0.0 20 122-141 3-22 (68)
118 TIGR02937 sigma70-ECF RNA poly 46.1 9.8 0.00021 26.3 0.9 39 98-141 110-148 (158)
119 PRK12537 RNA polymerase sigma 46.1 15 0.00032 27.6 1.9 37 99-140 134-170 (182)
120 PF07499 RuvA_C: RuvA, C-termi 46.0 16 0.00035 22.1 1.7 18 14-31 11-28 (47)
121 PF11774 Lsr2: Lsr2 ; InterPr 45.7 13 0.00029 26.9 1.5 24 48-71 32-55 (110)
122 PRK09413 IS2 repressor TnpA; R 45.2 22 0.00048 25.6 2.6 42 96-141 10-51 (121)
123 PHA03256 BDLF3; Provisional 45.0 50 0.0011 22.6 4.1 37 91-130 9-45 (77)
124 PRK03341 arginine repressor; P 43.0 22 0.00048 27.6 2.5 32 17-52 29-61 (168)
125 PF00196 GerE: Bacterial regul 42.5 6.1 0.00013 24.6 -0.6 38 98-141 3-40 (58)
126 PF13413 HTH_25: Helix-turn-he 42.2 23 0.00051 22.8 2.1 34 10-52 3-36 (62)
127 PF08280 HTH_Mga: M protein tr 41.8 16 0.00035 23.0 1.3 32 102-137 6-37 (59)
128 smart00351 PAX Paired Box doma 41.8 1.3E+02 0.0029 21.7 9.9 74 38-131 34-108 (125)
129 TIGR02959 SigZ RNA polymerase 41.7 15 0.00033 27.4 1.4 38 98-140 100-137 (170)
130 PRK11924 RNA polymerase sigma 41.7 16 0.00035 26.6 1.4 22 120-141 142-163 (179)
131 PRK09652 RNA polymerase sigma 41.2 14 0.00031 26.9 1.2 39 98-141 128-166 (182)
132 PF01922 SRP19: SRP19 protein; 41.1 22 0.00047 25.0 2.0 29 115-143 27-61 (95)
133 TIGR02989 Sig-70_gvs1 RNA poly 40.4 18 0.00038 26.2 1.5 38 98-140 111-148 (159)
134 cd01392 HTH_LacI Helix-turn-he 40.2 7.3 0.00016 23.3 -0.5 21 124-144 2-22 (52)
135 COG2963 Transposase and inacti 40.2 32 0.00068 24.2 2.8 41 96-140 5-46 (116)
136 PF03672 UPF0154: Uncharacteri 39.8 47 0.001 22.1 3.3 32 104-135 19-50 (64)
137 PF13701 DDE_Tnp_1_4: Transpos 38.4 59 0.0013 28.8 4.7 52 14-66 68-130 (448)
138 TIGR02983 SigE-fam_strep RNA p 38.3 16 0.00034 26.7 0.9 36 100-140 112-147 (162)
139 smart00422 HTH_MERR helix_turn 38.1 10 0.00023 23.9 -0.0 19 122-140 3-21 (70)
140 PRK04217 hypothetical protein; 37.2 27 0.0006 25.3 2.1 39 97-140 41-79 (110)
141 PF00325 Crp: Bacterial regula 37.2 12 0.00027 21.4 0.2 16 121-136 4-19 (32)
142 TIGR02939 RpoE_Sigma70 RNA pol 37.1 15 0.00032 27.4 0.7 22 119-140 154-175 (190)
143 PRK00118 putative DNA-binding 36.8 20 0.00044 25.8 1.3 38 99-141 18-55 (104)
144 PRK09648 RNA polymerase sigma 36.5 20 0.00044 26.9 1.3 39 97-140 138-176 (189)
145 TIGR02985 Sig70_bacteroi1 RNA 36.1 21 0.00046 25.4 1.4 37 99-140 114-150 (161)
146 TIGR00498 lexA SOS regulatory 36.0 41 0.0009 25.8 3.0 37 99-137 4-44 (199)
147 PRK15369 two component system 35.6 25 0.00055 25.2 1.7 40 97-142 148-187 (211)
148 PF13443 HTH_26: Cro/C1-type H 35.4 36 0.00077 21.0 2.1 30 107-136 27-57 (63)
149 PRK09644 RNA polymerase sigma 35.2 19 0.00041 26.5 1.0 38 99-141 109-146 (165)
150 PF08279 HTH_11: HTH domain; 34.9 15 0.00032 22.3 0.3 31 104-137 3-33 (55)
151 PRK12514 RNA polymerase sigma 34.9 22 0.00047 26.5 1.2 37 100-141 131-167 (179)
152 TIGR02948 SigW_bacill RNA poly 34.8 13 0.00029 27.6 0.1 39 98-141 136-174 (187)
153 PRK12526 RNA polymerase sigma 34.2 23 0.0005 27.4 1.3 37 100-141 155-191 (206)
154 PRK12519 RNA polymerase sigma 33.7 19 0.00041 27.2 0.7 22 120-141 158-179 (194)
155 PRK12528 RNA polymerase sigma 33.1 26 0.00055 25.6 1.4 38 98-140 113-150 (161)
156 PRK12539 RNA polymerase sigma 33.1 28 0.0006 26.2 1.6 38 98-140 131-168 (184)
157 COG1191 FliA DNA-directed RNA 33.1 34 0.00075 28.2 2.2 36 15-64 210-245 (247)
158 PRK15418 transcriptional regul 33.1 31 0.00066 29.2 2.0 20 17-45 29-48 (318)
159 PRK09642 RNA polymerase sigma 32.8 24 0.00051 25.7 1.2 20 121-140 124-143 (160)
160 COG4367 Uncharacterized protei 32.8 31 0.00068 24.6 1.7 35 98-136 2-40 (97)
161 PRK12515 RNA polymerase sigma 32.7 28 0.0006 26.2 1.5 38 98-140 131-168 (189)
162 PRK12512 RNA polymerase sigma 32.5 24 0.00052 26.3 1.2 37 100-141 133-169 (184)
163 PRK00523 hypothetical protein; 32.5 68 0.0015 21.8 3.2 32 104-135 27-58 (72)
164 TIGR02954 Sig70_famx3 RNA poly 32.5 28 0.00061 25.6 1.5 37 99-140 120-156 (169)
165 TIGR02999 Sig-70_X6 RNA polyme 32.3 29 0.00063 25.8 1.6 38 99-141 135-172 (183)
166 PF04297 UPF0122: Putative hel 31.8 40 0.00088 24.2 2.2 36 99-139 18-53 (101)
167 PRK12541 RNA polymerase sigma 31.7 24 0.00051 25.8 1.0 37 99-140 113-149 (161)
168 PRK09651 RNA polymerase sigma 31.3 23 0.0005 26.4 0.9 38 98-140 119-156 (172)
169 PRK12530 RNA polymerase sigma 31.2 27 0.00058 26.5 1.3 37 99-140 135-171 (189)
170 TIGR02952 Sig70_famx2 RNA poly 30.8 31 0.00067 25.1 1.5 36 99-139 123-158 (170)
171 PRK13919 putative RNA polymera 30.7 32 0.0007 25.6 1.6 37 99-140 136-172 (186)
172 PF13223 DUF4031: Protein of u 30.6 35 0.00077 23.7 1.6 21 118-142 22-42 (83)
173 PF01726 LexA_DNA_bind: LexA D 30.6 32 0.00069 22.5 1.3 38 98-137 3-44 (65)
174 PRK12534 RNA polymerase sigma 30.4 40 0.00088 25.2 2.1 34 100-138 139-172 (187)
175 cd08784 Death_DRs Death Domain 30.3 92 0.002 20.8 3.7 30 38-69 23-52 (79)
176 PRK01844 hypothetical protein; 30.2 79 0.0017 21.5 3.2 32 104-135 26-57 (72)
177 PRK00441 argR arginine repress 30.2 48 0.001 25.1 2.5 31 18-52 19-50 (149)
178 TIGR02885 spore_sigF RNA polym 30.0 30 0.00064 27.1 1.3 37 98-139 183-219 (231)
179 PRK12529 RNA polymerase sigma 30.0 34 0.00073 25.7 1.6 38 98-140 127-164 (178)
180 PRK09639 RNA polymerase sigma 29.7 31 0.00067 25.1 1.3 36 99-140 113-148 (166)
181 PF10945 DUF2629: Protein of u 29.5 56 0.0012 20.2 2.2 39 20-65 3-41 (44)
182 PRK05602 RNA polymerase sigma 29.4 29 0.00063 26.0 1.2 21 120-140 145-165 (186)
183 PRK09645 RNA polymerase sigma 29.4 39 0.00084 24.9 1.8 36 99-139 119-154 (173)
184 PRK06596 RNA polymerase factor 29.3 36 0.00079 28.0 1.8 38 98-138 230-267 (284)
185 PRK12524 RNA polymerase sigma 28.7 29 0.00064 26.4 1.1 37 99-140 137-173 (196)
186 PRK12547 RNA polymerase sigma 28.6 33 0.00072 25.2 1.4 21 120-140 129-149 (164)
187 PRK07037 extracytoplasmic-func 28.5 38 0.00081 24.6 1.6 36 99-139 110-145 (163)
188 PRK09047 RNA polymerase factor 28.2 36 0.00078 24.6 1.4 37 99-140 107-143 (161)
189 TIGR02980 SigBFG RNA polymeras 28.1 27 0.00059 27.2 0.8 38 98-140 178-215 (227)
190 PRK09643 RNA polymerase sigma 27.4 40 0.00086 25.7 1.6 19 120-138 151-169 (192)
191 PRK10403 transcriptional regul 27.3 26 0.00056 25.5 0.5 40 97-142 152-191 (215)
192 PF00872 Transposase_mut: Tran 27.2 23 0.0005 30.6 0.3 28 17-46 114-141 (381)
193 PRK12543 RNA polymerase sigma 27.1 39 0.00084 25.3 1.5 37 99-140 118-154 (179)
194 PRK12525 RNA polymerase sigma 26.6 38 0.00083 25.0 1.4 39 97-140 117-155 (168)
195 TIGR03209 P21_Cbot clostridium 26.4 55 0.0012 23.3 2.2 33 100-137 109-141 (142)
196 PF13743 Thioredoxin_5: Thiore 26.2 28 0.00061 26.7 0.6 39 103-141 85-125 (176)
197 PRK09637 RNA polymerase sigma 25.9 37 0.00081 25.7 1.2 22 120-141 123-144 (181)
198 PRK12511 RNA polymerase sigma 25.8 41 0.0009 25.5 1.5 38 98-140 111-148 (182)
199 PF13412 HTH_24: Winged helix- 25.8 53 0.0011 19.3 1.7 34 100-137 2-35 (48)
200 PRK01271 4-oxalocrotonate taut 25.7 94 0.002 21.0 3.0 32 100-141 14-45 (76)
201 PF12802 MarR_2: MarR family; 25.6 35 0.00075 20.8 0.8 36 99-136 3-38 (62)
202 TIGR01764 excise DNA binding d 25.5 22 0.00048 20.3 -0.1 21 122-142 4-24 (49)
203 PRK10840 transcriptional regul 25.4 39 0.00085 25.6 1.3 35 98-138 150-184 (216)
204 PF05263 DUF722: Protein of un 25.3 42 0.0009 25.2 1.3 39 100-141 83-121 (130)
205 PRK08583 RNA polymerase sigma 25.1 35 0.00075 27.3 0.9 38 98-140 205-242 (257)
206 PF02001 DUF134: Protein of un 24.8 55 0.0012 23.7 1.8 21 17-46 57-77 (106)
207 PRK10360 DNA-binding transcrip 24.7 31 0.00067 25.1 0.6 40 97-142 136-175 (196)
208 PRK12546 RNA polymerase sigma 24.7 31 0.00067 26.4 0.6 22 120-141 130-151 (188)
209 PF13542 HTH_Tnp_ISL3: Helix-t 24.7 23 0.00049 21.2 -0.2 20 121-140 29-48 (52)
210 PRK09649 RNA polymerase sigma 24.6 39 0.00085 25.5 1.1 20 121-140 148-167 (185)
211 TIGR02392 rpoH_proteo alternat 24.5 51 0.0011 26.8 1.8 38 98-138 218-255 (270)
212 PRK12531 RNA polymerase sigma 24.1 50 0.0011 25.0 1.6 21 120-140 158-178 (194)
213 PRK13558 bacterio-opsin activa 24.1 60 0.0013 29.3 2.3 40 97-136 606-647 (665)
214 PTZ00478 Sec superfamily; Prov 24.0 47 0.001 23.1 1.3 24 108-131 31-54 (81)
215 PRK00754 signal recognition pa 23.9 72 0.0016 22.6 2.3 29 115-143 33-67 (95)
216 PRK12516 RNA polymerase sigma 23.9 46 0.001 25.3 1.4 36 100-140 118-153 (187)
217 PRK12523 RNA polymerase sigma 23.9 48 0.001 24.5 1.5 37 99-140 120-156 (172)
218 PF04552 Sigma54_DBD: Sigma-54 23.9 26 0.00057 27.0 0.0 30 108-137 37-67 (160)
219 COG1983 PspC Putative stress-r 23.8 22 0.00049 24.0 -0.3 20 121-140 17-36 (70)
220 PF02796 HTH_7: Helix-turn-hel 23.7 33 0.00071 20.4 0.4 36 99-139 6-41 (45)
221 PHA02955 hypothetical protein; 23.7 94 0.002 25.3 3.2 41 102-142 61-102 (213)
222 smart00550 Zalpha Z-DNA-bindin 23.7 72 0.0016 20.6 2.1 31 106-137 10-40 (68)
223 smart00419 HTH_CRP helix_turn_ 23.2 59 0.0013 18.5 1.5 16 13-28 4-19 (48)
224 COG2944 Predicted transcriptio 23.2 31 0.00067 25.0 0.3 39 99-144 44-82 (104)
225 PRK12536 RNA polymerase sigma 23.1 52 0.0011 24.6 1.5 21 120-140 146-166 (181)
226 PRK06811 RNA polymerase factor 23.1 57 0.0012 24.6 1.7 38 98-140 131-168 (189)
227 PF01710 HTH_Tnp_IS630: Transp 22.7 22 0.00048 25.6 -0.6 38 99-141 3-40 (119)
228 TIGR02984 Sig-70_plancto1 RNA 22.7 44 0.00096 24.7 1.1 35 99-138 141-175 (189)
229 PRK05572 sporulation sigma fac 22.7 48 0.001 26.5 1.3 38 97-139 201-238 (252)
230 PF04355 SmpA_OmlA: SmpA / Oml 22.6 59 0.0013 20.8 1.5 19 11-29 9-27 (71)
231 PF13545 HTH_Crp_2: Crp-like h 22.5 44 0.00096 21.2 0.9 19 13-31 24-42 (76)
232 PRK09647 RNA polymerase sigma 22.4 52 0.0011 25.5 1.5 20 121-140 156-175 (203)
233 PRK06930 positive control sigm 22.4 49 0.0011 25.5 1.3 39 98-141 114-152 (170)
234 TIGR02941 Sigma_B RNA polymera 22.0 62 0.0013 25.8 1.9 38 98-140 205-242 (255)
235 PRK12545 RNA polymerase sigma 21.9 58 0.0013 25.0 1.6 37 99-140 140-176 (201)
236 TIGR02479 FliA_WhiG RNA polyme 21.8 66 0.0014 25.1 1.9 38 98-140 175-212 (224)
237 PRK08301 sporulation sigma fac 21.8 54 0.0012 25.7 1.5 41 99-140 179-219 (234)
238 PRK07921 RNA polymerase sigma 21.8 74 0.0016 27.0 2.4 38 98-137 262-300 (324)
239 COG0568 RpoD DNA-directed RNA 21.6 78 0.0017 27.5 2.5 39 99-138 280-318 (342)
240 PF13404 HTH_AsnC-type: AsnC-t 21.3 29 0.00063 20.7 -0.2 17 121-137 19-35 (42)
241 PRK12527 RNA polymerase sigma 21.2 61 0.0013 23.5 1.6 20 120-139 122-141 (159)
242 PRK12520 RNA polymerase sigma 21.2 58 0.0013 24.5 1.5 36 99-139 132-167 (191)
243 COG1905 NuoE NADH:ubiquinone o 21.2 1.1E+02 0.0023 23.9 2.9 35 102-136 26-60 (160)
244 PRK11475 DNA-binding transcrip 21.1 37 0.0008 26.7 0.4 36 97-138 133-168 (207)
245 PRK08215 sporulation sigma fac 21.0 54 0.0012 26.3 1.3 37 98-139 209-245 (258)
246 PRK06986 fliA flagellar biosyn 21.0 66 0.0014 25.3 1.8 38 99-141 185-222 (236)
247 KOG3755|consensus 20.8 47 0.001 31.4 1.0 54 92-145 647-704 (769)
248 COG1426 Predicted transcriptio 20.8 68 0.0015 26.8 1.9 48 7-55 6-67 (284)
249 PRK12535 RNA polymerase sigma 20.6 56 0.0012 25.1 1.3 21 120-140 150-170 (196)
250 TIGR02943 Sig70_famx1 RNA poly 20.6 57 0.0012 24.7 1.3 36 99-139 132-167 (188)
251 TIGR02997 Sig70-cyanoRpoD RNA 20.5 83 0.0018 26.0 2.4 40 99-139 250-289 (298)
252 PTZ00183 centrin; Provisional 20.3 3E+02 0.0064 19.3 5.0 38 94-131 6-48 (158)
253 PRK12533 RNA polymerase sigma 20.3 50 0.0011 26.0 1.0 36 100-140 136-171 (216)
254 cd02413 40S_S3_KH K homology R 20.2 67 0.0015 21.8 1.5 21 121-141 55-75 (81)
255 smart00354 HTH_LACI helix_turn 20.1 39 0.00085 21.8 0.3 23 122-144 3-25 (70)
256 PRK02220 4-oxalocrotonate taut 20.1 1.5E+02 0.0033 18.0 3.0 32 100-141 13-44 (61)
257 PRK11511 DNA-binding transcrip 20.1 51 0.0011 23.7 0.9 23 120-142 26-48 (127)
No 1
>KOG3802|consensus
Probab=100.00 E-value=1.2e-69 Score=461.53 Aligned_cols=133 Identities=43% Similarity=0.626 Sum_probs=123.4
Q ss_pred hhhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCCChHHHhhhhHHHHHHHHHHHHHhhcCCCCCCCCCCC
Q psy17899 8 DVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRRDPDAPSVL 87 (145)
Q Consensus 8 ~f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~LS~knm~klkPlL~kWL~eae~~~~~~~~~~~~~~~~ 87 (145)
.||+|||+|||||+|||+|||++| | ++||||||||||||||||||||||||||+|||+|||..+..+ ..++.+.+.
T Consensus 214 ~FKqRRIkLGfTQaDVGlALG~ly--G-n~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~-~~~~~e~i~ 289 (398)
T KOG3802|consen 214 TFKQRRIKLGFTQADVGLALGALY--G-NVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTG-SPNSIEKIG 289 (398)
T ss_pred HHHhheeccccchhHHHHHHHhhh--C-cccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccC-CCCCHHHhh
Confidence 599999999999999999999999 7 799999999999999999999999999999999999864333 234445566
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccC
Q psy17899 88 PAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 88 ~~~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
..+|||||||||+..++.+||++|++||||+++||.+||++|+|++|||||||+|||
T Consensus 290 a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRR 346 (398)
T KOG3802|consen 290 AQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRR 346 (398)
T ss_pred ccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccc
Confidence 677999999999999999999999999999999999999999999999999999998
No 2
>KOG1168|consensus
Probab=100.00 E-value=4.2e-54 Score=355.48 Aligned_cols=137 Identities=80% Similarity=1.082 Sum_probs=132.8
Q ss_pred hhhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCCChHHHhhhhHHHHHHHHHHHHHhhcCCCCCCCCCCC
Q psy17899 8 DVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRRDPDAPSVL 87 (145)
Q Consensus 8 ~f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~LS~knm~klkPlL~kWL~eae~~~~~~~~~~~~~~~~ 87 (145)
-||||||+||+||+|||.||+.|.+|||+.+||+||||||+|.||++||.+|||+|+.||||||....++...++..+++
T Consensus 225 rFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE~a~keK~~~pd~~~l~ 304 (385)
T KOG1168|consen 225 RFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAAMKEKDTKPDINELL 304 (385)
T ss_pred HHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHHHHHHHhhccCCchhhcc
Confidence 49999999999999999999999999999999999999999999999999999999999999999888777777778899
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccC
Q psy17899 88 PAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 88 ~~~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
+.+.||||||||...+++.||+||..+|+|+++.|..||++|+|.++||||||+|.|
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQR 361 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQR 361 (385)
T ss_pred CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccH
Confidence 999999999999999999999999999999999999999999999999999999987
No 3
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=100.00 E-value=8.9e-39 Score=218.29 Aligned_cols=61 Identities=57% Similarity=0.865 Sum_probs=57.3
Q ss_pred hhhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCCChHHHhhhhHHHHHHHHHHH
Q psy17899 8 DVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAE 71 (145)
Q Consensus 8 ~f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~LS~knm~klkPlL~kWL~eae 71 (145)
.||+|||+|||||+|||.|||.+| | +.||||||||||+|||||||||||+|+|++||+|||
T Consensus 15 ~fk~rRi~LG~TQ~dVg~al~~~~--G-~~~SQttI~RFE~L~LS~kn~~klkP~L~kWL~eaE 75 (75)
T PF00157_consen 15 EFKQRRIKLGYTQADVGAALGRLY--G-KEFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAE 75 (75)
T ss_dssp HHHHHHHHTT--HHHHHHHHHHHH--S-SGGSHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhhhhcccCHHHHhHHHHHhc--C-ccccchhhhhhHhcccCHHHHHHHHHHHHHHHHhcC
Confidence 699999999999999999999999 7 689999999999999999999999999999999997
No 4
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=99.96 E-value=4.1e-30 Score=175.55 Aligned_cols=61 Identities=57% Similarity=0.840 Sum_probs=58.5
Q ss_pred hhhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCCChHHHhhhhHHHHHHHHHHH
Q psy17899 8 DVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAE 71 (145)
Q Consensus 8 ~f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~LS~knm~klkPlL~kWL~eae 71 (145)
.||++|+++||||+|||.++|.+| | ..+||+||||||++||||||||||||+|++||+|||
T Consensus 15 ~lk~~R~~lGLTQ~dvA~~lg~~~--g-~i~SQstISR~Es~~ls~~n~~kl~p~l~~wl~~~e 75 (75)
T smart00352 15 TFKQRRIKLGFTQADVGLALGALY--G-PDFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAE 75 (75)
T ss_pred HHHHHHHHcCCCHHHHHHHhcccc--c-CcCCHHHHHHHHhcCccHHHHHHHHHHHHHHHHhcC
Confidence 689999999999999999999999 6 589999999999999999999999999999999986
No 5
>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=99.74 E-value=2.3e-18 Score=112.72 Aligned_cols=53 Identities=19% Similarity=0.333 Sum_probs=51.2
Q ss_pred CCCCCCCCCHHHHHHHHHhhhcCCC----CCHHHHHHHHhhcCCCCCccccccCccC
Q psy17899 92 KKRKRTSIAAPEKRSLEAYFAVQPR----PSGEKIAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 92 krR~RTs~s~~q~~~Le~~F~~np~----Ps~~e~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
+||.||.||++|+..||.+|+.++| |+..++.+||..|||++.||+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4789999999999999999999999 9999999999999999999999999975
No 6
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.69 E-value=3.7e-18 Score=109.12 Aligned_cols=53 Identities=34% Similarity=0.493 Sum_probs=51.4
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 93 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 93 rR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
||+|+.|+..|+..|+.+|..++||+.+++..||.++||+..+|++||+|+|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~ 53 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRR 53 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHH
Confidence 57899999999999999999999999999999999999999999999999984
No 7
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.64 E-value=9.8e-17 Score=101.59 Aligned_cols=53 Identities=36% Similarity=0.454 Sum_probs=50.9
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 93 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 93 rR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
++.|+.++..|+.+|+..|..|+||+.+++..||..+||+..+|++||+|+|+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~ 53 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRA 53 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhh
Confidence 46789999999999999999999999999999999999999999999999995
No 8
>KOG0843|consensus
Probab=99.63 E-value=1.3e-16 Score=124.89 Aligned_cols=55 Identities=24% Similarity=0.258 Sum_probs=53.4
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 91 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 91 rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
+.||.||.|+++|+..||.+|+.|.|-...||++||+.|+|++.+|+|||||||.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRt 155 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRT 155 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhH
Confidence 6789999999999999999999999999999999999999999999999999994
No 9
>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=99.61 E-value=1.9e-16 Score=100.77 Aligned_cols=53 Identities=32% Similarity=0.430 Sum_probs=50.7
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 93 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 93 rR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
+++|+.++..++.+||++|..||||+.+++..||.++||++.+|++||+|+|+
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~ 53 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRA 53 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 36789999999999999999999999999999999999999999999999985
No 10
>KOG2251|consensus
Probab=99.58 E-value=1.1e-15 Score=122.80 Aligned_cols=57 Identities=28% Similarity=0.306 Sum_probs=54.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 89 AGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 89 ~~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
+.+.||.||+|+..|+++||..|.+..||+...+++||.+|+|++.+|+|||.||||
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRA 90 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRA 90 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccc
Confidence 456788999999999999999999999999999999999999999999999999997
No 11
>KOG0484|consensus
Probab=99.58 E-value=1.7e-16 Score=115.09 Aligned_cols=55 Identities=29% Similarity=0.328 Sum_probs=53.0
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 91 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 91 rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
+.||-||.|+..|+..||..|....||+.-.+++||-+++|++..||||||||||
T Consensus 16 KQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRA 70 (125)
T KOG0484|consen 16 KQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRA 70 (125)
T ss_pred HhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHH
Confidence 4578899999999999999999999999999999999999999999999999997
No 12
>KOG0489|consensus
Probab=99.52 E-value=1.9e-15 Score=124.19 Aligned_cols=56 Identities=23% Similarity=0.289 Sum_probs=53.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 90 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 90 ~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
+..||.||.||..|+..||+.|..|.|.+...|.+||..|+|+|++|+|||||||+
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRM 212 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRM 212 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHH
Confidence 45788999999999999999999999999999999999999999999999999994
No 13
>KOG0488|consensus
Probab=99.52 E-value=4.3e-15 Score=125.01 Aligned_cols=56 Identities=21% Similarity=0.226 Sum_probs=53.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 90 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 90 ~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
.++||.||+||..|+..||+.|+++.|.+..+|.+||.+|||+..+|++||||||+
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRt 225 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRT 225 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhH
Confidence 45677799999999999999999999999999999999999999999999999995
No 14
>KOG0485|consensus
Probab=99.51 E-value=6e-15 Score=118.82 Aligned_cols=58 Identities=26% Similarity=0.295 Sum_probs=55.4
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccC
Q psy17899 87 LPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 87 ~~~~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
+...||||.||+|+..|...||..|+...|.+..||..||.+|+|+|.+|++||||||
T Consensus 99 ~g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRR 156 (268)
T KOG0485|consen 99 LGDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRR 156 (268)
T ss_pred ccccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhh
Confidence 3456999999999999999999999999999999999999999999999999999998
No 15
>KOG0842|consensus
Probab=99.51 E-value=1.1e-14 Score=122.37 Aligned_cols=56 Identities=21% Similarity=0.213 Sum_probs=53.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 90 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 90 ~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
.+|||+|--|+..|...||..|.++.|.|+.||++||..|+|++-+|+|||||||.
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRY 206 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRY 206 (307)
T ss_pred ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchh
Confidence 47788899999999999999999999999999999999999999999999999995
No 16
>KOG0487|consensus
Probab=99.50 E-value=1.1e-14 Score=122.38 Aligned_cols=58 Identities=21% Similarity=0.210 Sum_probs=55.0
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccC
Q psy17899 87 LPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 87 ~~~~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
+...+-||||.-+|..|...||++|..|-|.+.+.|.+||+.|+|++++|+|||||||
T Consensus 230 ~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRR 287 (308)
T KOG0487|consen 230 SSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRR 287 (308)
T ss_pred ccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhh
Confidence 3346789999999999999999999999999999999999999999999999999999
No 17
>KOG4577|consensus
Probab=99.50 E-value=1.3e-14 Score=121.00 Aligned_cols=56 Identities=25% Similarity=0.379 Sum_probs=54.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 90 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 90 ~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
+.-||+||+|++.|++.|..+|...|+|-...|++|+.++||+.+|||||||||||
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRA 220 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRA 220 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhH
Confidence 45688999999999999999999999999999999999999999999999999997
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.48 E-value=4.5e-14 Score=108.72 Aligned_cols=55 Identities=24% Similarity=0.255 Sum_probs=50.2
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 91 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 91 rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
..+++|+--+..|+.+|+..|+.||+|+..++..||..|+|+++.||+||||+||
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~ 104 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRA 104 (156)
T ss_pred cCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHH
Confidence 3455566667999999999999999999999999999999999999999999996
No 19
>KOG0492|consensus
Probab=99.45 E-value=3.5e-14 Score=113.66 Aligned_cols=54 Identities=22% Similarity=0.238 Sum_probs=52.6
Q ss_pred CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 92 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 92 krR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
.|+.||.|+..|+.+||+.|...+|.+..|+.+++.+|.|++.+|++|||||||
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRA 197 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRA 197 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhH
Confidence 488899999999999999999999999999999999999999999999999997
No 20
>KOG0850|consensus
Probab=99.44 E-value=5e-14 Score=113.91 Aligned_cols=55 Identities=18% Similarity=0.186 Sum_probs=52.3
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 91 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 91 rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
+-||.||.++.-|+.+|.+.|++++|.-..||.+||.+|||+-.+|+|||||||.
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRS 175 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRS 175 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHH
Confidence 3477799999999999999999999999999999999999999999999999993
No 21
>KOG0494|consensus
Probab=99.42 E-value=7.2e-14 Score=115.12 Aligned_cols=54 Identities=24% Similarity=0.273 Sum_probs=51.3
Q ss_pred CCCC-CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 92 KKRK-RTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 92 krR~-RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
|||. ||.|+..|+..||+.|..-.||+...++.||..+.|+++.|+||||||||
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRA 194 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRA 194 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhH
Confidence 3444 99999999999999999999999999999999999999999999999997
No 22
>KOG0493|consensus
Probab=99.35 E-value=3e-13 Score=111.61 Aligned_cols=54 Identities=24% Similarity=0.326 Sum_probs=52.2
Q ss_pred CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 92 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 92 krR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
-||+||.|+.+|+..|...|..|.|.+-+.|.+||.+|+|.+.+|++||||+||
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRA 299 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRA 299 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhh
Confidence 367899999999999999999999999999999999999999999999999997
No 23
>KOG0844|consensus
Probab=99.28 E-value=8.7e-13 Score=110.85 Aligned_cols=53 Identities=21% Similarity=0.237 Sum_probs=51.6
Q ss_pred CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccC
Q psy17899 92 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 92 krR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
=||-||.|+.+|+..||+.|-+..|-+...|.+||..|+|++.+|+|||||||
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRR 233 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRR 233 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhch
Confidence 47889999999999999999999999999999999999999999999999998
No 24
>KOG0848|consensus
Probab=99.28 E-value=6.2e-13 Score=109.84 Aligned_cols=54 Identities=20% Similarity=0.204 Sum_probs=51.7
Q ss_pred CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 92 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 92 krR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
|-|-|.++++.|+-.||++|..++|.+.+...+||.-|+|+|++|+||||||||
T Consensus 199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRA 252 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRA 252 (317)
T ss_pred ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhH
Confidence 455699999999999999999999999999999999999999999999999997
No 25
>KOG0486|consensus
Probab=99.20 E-value=5.8e-12 Score=105.92 Aligned_cols=56 Identities=27% Similarity=0.296 Sum_probs=54.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 90 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 90 ~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
.++||.||.|+..|+..||..|.+|.||+-..+++||--.+|++..|||||.||||
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrra 165 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRA 165 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchh
Confidence 47789999999999999999999999999999999999999999999999999997
No 26
>KOG0490|consensus
Probab=99.20 E-value=8.2e-12 Score=98.29 Aligned_cols=56 Identities=20% Similarity=0.051 Sum_probs=53.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 90 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 90 ~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
..+||.||.|+..|++.||..|+..+||+...++.+|..+++++..|+|||||+||
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrra 113 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRA 113 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcH
Confidence 46788999999999999999999999999999999999999999999999999996
No 27
>KOG0491|consensus
Probab=99.18 E-value=1.5e-12 Score=101.14 Aligned_cols=54 Identities=24% Similarity=0.318 Sum_probs=52.5
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccC
Q psy17899 91 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 91 rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
+++|.||+|+..|+.-||+.|+.+.|.+..++.+||..|+|++.+|+.||||||
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrR 152 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRR 152 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence 677889999999999999999999999999999999999999999999999998
No 28
>KOG0483|consensus
Probab=99.17 E-value=1.2e-11 Score=98.47 Aligned_cols=48 Identities=21% Similarity=0.259 Sum_probs=46.7
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
-++.+|...||..|..+.|..+++...||.+|||.+++|.||||||||
T Consensus 56 Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRA 103 (198)
T KOG0483|consen 56 RLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRA 103 (198)
T ss_pred cccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccc
Confidence 388999999999999999999999999999999999999999999998
No 29
>KOG0849|consensus
Probab=99.04 E-value=1.5e-10 Score=99.15 Aligned_cols=56 Identities=25% Similarity=0.290 Sum_probs=53.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 90 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 90 ~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
...+|.||+|+..|...||..|..++||+...+++||.++++++..|+|||+|+||
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra 229 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRA 229 (354)
T ss_pred ccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhh
Confidence 34577799999999999999999999999999999999999999999999999996
No 30
>KOG0847|consensus
Probab=98.94 E-value=2.4e-10 Score=92.65 Aligned_cols=56 Identities=21% Similarity=0.342 Sum_probs=53.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 90 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 90 ~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
+.++..|-+|+-.|+..||..|++..||-..++.++|..+||.+.+|.|||||||.
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRT 220 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRT 220 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchh
Confidence 56677799999999999999999999999999999999999999999999999994
No 31
>KOG2252|consensus
Probab=98.74 E-value=9.4e-09 Score=91.77 Aligned_cols=54 Identities=30% Similarity=0.405 Sum_probs=52.1
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccC
Q psy17899 91 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 91 rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
..||.|.+|+..|+..|...|..+++|+.+..+.|+.+|+|+..+|.+||-|-|
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaR 472 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNAR 472 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhh
Confidence 567889999999999999999999999999999999999999999999999977
No 32
>KOG0775|consensus
Probab=98.61 E-value=1.2e-07 Score=78.87 Aligned_cols=44 Identities=20% Similarity=0.265 Sum_probs=41.9
Q ss_pred HHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccC
Q psy17899 101 APEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 101 ~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
..-+..|...|.+||||+..+..+||+.+||+.-+|-+||.|||
T Consensus 185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRR 228 (304)
T KOG0775|consen 185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRR 228 (304)
T ss_pred HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhh
Confidence 56678999999999999999999999999999999999999998
No 33
>KOG0774|consensus
Probab=98.48 E-value=1.1e-07 Score=79.01 Aligned_cols=53 Identities=26% Similarity=0.429 Sum_probs=50.1
Q ss_pred CCCCCCCCCHHHHHHHHHhhh---cCCCCCHHHHHHHHhhcCCCCCccccccCccC
Q psy17899 92 KKRKRTSIAAPEKRSLEAYFA---VQPRPSGEKIAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 92 krR~RTs~s~~q~~~Le~~F~---~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
.||||..|+....++|..||. .|||||-++.++||.+.+++..+|-.||.|.|
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkr 243 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKR 243 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccce
Confidence 567888999999999999995 78999999999999999999999999999987
No 34
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.44 E-value=1.8e-08 Score=61.24 Aligned_cols=32 Identities=22% Similarity=0.291 Sum_probs=27.7
Q ss_pred cCCCCCHHHHHHHHhhcCCCCCccccccCccC
Q psy17899 113 VQPRPSGEKIAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 113 ~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
.|||||.+|..+||.++||+..+|..||-|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaR 38 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINAR 38 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhH
Confidence 57999999999999999999999999999987
No 35
>KOG0490|consensus
Probab=98.42 E-value=1.6e-07 Score=73.86 Aligned_cols=56 Identities=25% Similarity=0.421 Sum_probs=53.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 90 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 90 ~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
...++.||.+...|...++..|..+++|+...+..|+..+|+++.+|+|||||+|+
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~ 206 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRA 206 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHH
Confidence 46788899999999999999999999999999999999999999999999999874
No 36
>KOG1146|consensus
Probab=97.84 E-value=7.9e-06 Score=79.23 Aligned_cols=55 Identities=20% Similarity=0.308 Sum_probs=52.4
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 91 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 91 rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
-+|+.||.++..|+..+...|....+|.-++++.+...++++++||+|||||-|+
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~ 956 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARA 956 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhh
Confidence 3677899999999999999999999999999999999999999999999999885
No 37
>KOG3623|consensus
Probab=97.27 E-value=0.00011 Score=68.46 Aligned_cols=42 Identities=31% Similarity=0.439 Sum_probs=40.0
Q ss_pred HHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 104 KRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 104 ~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
...|..||..|+.|+.++...||++.|++.+||++||++++|
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a 609 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEA 609 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhh
Confidence 668999999999999999999999999999999999999875
No 38
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=96.35 E-value=0.0033 Score=40.57 Aligned_cols=34 Identities=29% Similarity=0.293 Sum_probs=27.0
Q ss_pred hhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCC
Q psy17899 9 VYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTL 51 (145)
Q Consensus 9 f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~L 51 (145)
.+..|...|+||++|+..+| +|++||+++|+=..
T Consensus 6 lr~~R~~~gls~~~lA~~~g---------~s~s~v~~iE~G~~ 39 (64)
T PF13560_consen 6 LRRLRERAGLSQAQLADRLG---------VSQSTVSRIERGRR 39 (64)
T ss_dssp HHHHHHCHTS-HHHHHHHHT---------S-HHHHHHHHTTSS
T ss_pred HHHHHHHcCCCHHHHHHHHC---------cCHHHHHHHHCCCC
Confidence 45667788999999999985 67899999998665
No 39
>KOG0773|consensus
Probab=96.33 E-value=0.0029 Score=53.40 Aligned_cols=53 Identities=21% Similarity=0.253 Sum_probs=45.4
Q ss_pred CCCCCCCCCHHHHHHHHHhhhc---CCCCCHHHHHHHHhhcCCCCCccccccCccC
Q psy17899 92 KKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 92 krR~RTs~s~~q~~~Le~~F~~---np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
+.|++..+......+|+..... .|||+-.+...||.++||+..+|-.||-|.|
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR 294 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINAR 294 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcc
Confidence 4566678888888888765543 5999999999999999999999999999987
No 40
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=96.27 E-value=0.011 Score=46.56 Aligned_cols=61 Identities=39% Similarity=0.575 Sum_probs=45.6
Q ss_pred CCCCCCc-hhhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCCChHHHhhhhHHHHHHHHHHHH
Q psy17899 1 MSLFPMP-DVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA 72 (145)
Q Consensus 1 ~~~~~~~-~f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~LS~knm~klkPlL~kWL~eae~ 72 (145)
|-.+|.| +-+++|-.||+||.|.+.- - | .||..|.|.|+=..-+ ..-+++-+|+. |+|+|.
T Consensus 1 m~~~P~pedlrk~Rk~LGitQ~dLA~~----a--G---VSQ~~IArlE~G~vdP-rlSt~k~Il~a-L~e~e~ 62 (187)
T COG3620 1 MMMLPTPEDLRKRRKELGITQKDLARR----A--G---VSQPYIARLEAGKVDP-RLSTVKRILEA-LEEAEK 62 (187)
T ss_pred CCcCCCHHHHHHHHHHcCCCHHHHHHH----c--C---ccHHHHHHHhcCCCCc-cHHHHHHHHHH-HHHhhc
Confidence 4566766 5788999999999997543 2 4 6899999999998866 45566666664 566664
No 41
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.24 E-value=0.001 Score=43.23 Aligned_cols=39 Identities=18% Similarity=0.301 Sum_probs=30.1
Q ss_pred HHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCcc
Q psy17899 105 RSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHT 143 (145)
Q Consensus 105 ~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNr 143 (145)
.-|+.||.....+.-.++..|.++.+|+-++|+.||--+
T Consensus 11 ~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~ 49 (56)
T PF11569_consen 11 QPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAER 49 (56)
T ss_dssp HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHh
Confidence 349999999999999999999999999999999999644
No 42
>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=95.93 E-value=0.0063 Score=38.64 Aligned_cols=46 Identities=24% Similarity=0.279 Sum_probs=36.2
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCcc
Q psy17899 93 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHT 143 (145)
Q Consensus 93 rR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNr 143 (145)
||+|+++|..++...-..++..+ -..+||.++|++..+|.-|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 57899999999998888888776 47889999999999999998875
No 43
>KOG3623|consensus
Probab=95.14 E-value=0.028 Score=52.86 Aligned_cols=82 Identities=23% Similarity=0.449 Sum_probs=64.1
Q ss_pred hHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 60 KPILQAWLEEAEAQAKNKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 60 kPlL~kWL~eae~~~~~~~~~~~~~~~~~~~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
.-+.++|.++.+..+......+..+ ...++-|.|+.+-..+-..|-.+++-+-.|+-.+...++..|...+.||.||
T Consensus 597 ~~vvk~wfE~~~a~e~sv~rsps~p---sg~~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~ 673 (1007)
T KOG3623|consen 597 FAVVKAWFEDEEAEEMSVERSPSQP---SGERPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVW 673 (1007)
T ss_pred HHHHHHHHHhhhhhhhhhccCccCC---CCCCCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhc
Confidence 3577899998876543222222222 2236667788888888899999999999999999999999999999999999
Q ss_pred cCccC
Q psy17899 140 NGHTR 144 (145)
Q Consensus 140 FqNrR 144 (145)
|++++
T Consensus 674 dhsrs 678 (1007)
T KOG3623|consen 674 DHSRS 678 (1007)
T ss_pred ccCCC
Confidence 99986
No 44
>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=94.97 E-value=0.052 Score=33.17 Aligned_cols=42 Identities=21% Similarity=0.237 Sum_probs=31.3
Q ss_pred hhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC--CChHHHhhh
Q psy17899 9 VYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT--LSHNNMIAL 59 (145)
Q Consensus 9 f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~--LS~knm~kl 59 (145)
.+..|...|+||.|++..+| .||+||++.|+=. .++.++.++
T Consensus 7 l~~~r~~~gltq~~lA~~~g---------vs~~~vs~~e~g~~~~~~~~~~~i 50 (58)
T TIGR03070 7 VRARRKALGLTQADLADLAG---------VGLRFIRDVENGKPTVRLDKVLRV 50 (58)
T ss_pred HHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHCCCCCCCHHHHHHH
Confidence 45667788999999998874 5789999999765 355444443
No 45
>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=94.52 E-value=0.1 Score=32.07 Aligned_cols=44 Identities=23% Similarity=0.257 Sum_probs=31.4
Q ss_pred hhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC--CChHHHhhhhHH
Q psy17899 10 YSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT--LSHNNMIALKPI 62 (145)
Q Consensus 10 ~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~--LS~knm~klkPl 62 (145)
|+-|...|+||.|++..+| .|++||.+.|.=. .+...+.++--+
T Consensus 2 k~~r~~~gls~~~la~~~g---------is~~~i~~~~~g~~~~~~~~~~~ia~~ 47 (55)
T PF01381_consen 2 KELRKEKGLSQKELAEKLG---------ISRSTISRIENGKRNPSLDTLKKIAKA 47 (55)
T ss_dssp HHHHHHTTS-HHHHHHHHT---------S-HHHHHHHHTTSSTSBHHHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHhC---------CCcchhHHHhcCCCCCCHHHHHHHHHH
Confidence 4557788999999999985 5689999999874 455555554433
No 46
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=94.42 E-value=0.12 Score=37.08 Aligned_cols=35 Identities=14% Similarity=0.193 Sum_probs=29.5
Q ss_pred hhhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCC
Q psy17899 8 DVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTL 51 (145)
Q Consensus 8 ~f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~L 51 (145)
..+.-|.++|+||.+++..+| +|+.||+|+|+=..
T Consensus 69 ~i~~~r~~~gltq~~lA~~lg---------~~~~tis~~e~g~~ 103 (127)
T TIGR03830 69 EIRRIRKKLGLSQREAAELLG---------GGVNAFSRYERGEV 103 (127)
T ss_pred HHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHCCCC
Confidence 567778899999999998874 46899999999776
No 47
>PHA01976 helix-turn-helix protein
Probab=93.72 E-value=0.16 Score=32.54 Aligned_cols=46 Identities=13% Similarity=0.166 Sum_probs=33.3
Q ss_pred hhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC--CChHHHhhhhHHH
Q psy17899 9 VYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT--LSHNNMIALKPIL 63 (145)
Q Consensus 9 f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~--LS~knm~klkPlL 63 (145)
.+..|...|+||.+++..+| .|++||+++|+=. .+..++.++--.|
T Consensus 7 l~~~R~~~glt~~~lA~~~g---------vs~~~v~~~e~g~~~p~~~~l~~ia~~l 54 (67)
T PHA01976 7 LIKARNARAWSAPELSRRAG---------VRHSLIYDFEADKRLPNLKTLLRLADAL 54 (67)
T ss_pred HHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 45668888999999999984 4689999999754 3555555544433
No 48
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=93.31 E-value=0.12 Score=39.69 Aligned_cols=47 Identities=15% Similarity=0.124 Sum_probs=35.8
Q ss_pred hhhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC----CChHHHhhhhHHH
Q psy17899 8 DVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT----LSHNNMIALKPIL 63 (145)
Q Consensus 8 ~f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~----LS~knm~klkPlL 63 (145)
-.+..|..+|+||.+++..+| .|+.||+++|.=. .|.+++.++-=.|
T Consensus 29 ~Ir~~R~~lGmTq~eLAerlG---------VS~~tIs~iE~G~~~~~psl~~L~kIA~aL 79 (150)
T TIGR02612 29 WVRAIRKALGMSGAQLAGRLG---------VTPQRVEALEKSELSGTVTLKTLRAAAEAL 79 (150)
T ss_pred HHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHcCCCCCCCCHHHHHHHHHHc
Confidence 467889999999999998874 4689999999964 4666655544333
No 49
>PHA00542 putative Cro-like protein
Probab=93.14 E-value=0.24 Score=33.82 Aligned_cols=46 Identities=24% Similarity=0.300 Sum_probs=34.3
Q ss_pred hhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC---CChHHHhhhhHHHH
Q psy17899 10 YSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT---LSHNNMIALKPILQ 64 (145)
Q Consensus 10 ~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~---LS~knm~klkPlL~ 64 (145)
...+..-|+||.+++..+| .||+||+|.|.-. .++..+.+|--++.
T Consensus 24 ~~~l~~~glTq~elA~~lg---------Is~~tIsr~e~g~~~~p~~~~l~ki~~~~~ 72 (82)
T PHA00542 24 VCALIRAGWSQEQIADATD---------VSQPTICRIYSGRHKDPRYSVVEKLRHLVL 72 (82)
T ss_pred HHHHHHCCCCHHHHHHHHC---------cCHHHHHHHHcCCCCCCCHHHHHHHHHHHH
Confidence 3445566999999999884 4689999999765 56777777665554
No 50
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=93.00 E-value=0.11 Score=32.98 Aligned_cols=41 Identities=27% Similarity=0.273 Sum_probs=27.9
Q ss_pred hhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC--CChHHHhh
Q psy17899 9 VYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT--LSHNNMIA 58 (145)
Q Consensus 9 f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~--LS~knm~k 58 (145)
.|+.|...|+||.+|+..+| .+.++|+++|+=+ .+...+.+
T Consensus 4 lk~~r~~~~lt~~~~a~~~~---------i~~~~i~~~e~g~~~~~~~~l~~ 46 (64)
T PF12844_consen 4 LKELREEKGLTQKDLAEKLG---------ISRSTISKIENGKRKPSVSTLKK 46 (64)
T ss_dssp HHHHHHHCT--HHHHHHHHT---------S-HHHHHHHHTTSS--BHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHC---------cCHHHHHHHHCCCcCCCHHHHHH
Confidence 57778899999999999875 4578999999653 44444433
No 51
>PRK10072 putative transcriptional regulator; Provisional
Probab=92.81 E-value=0.1 Score=37.11 Aligned_cols=36 Identities=19% Similarity=0.213 Sum_probs=30.3
Q ss_pred chhhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCC
Q psy17899 7 PDVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTL 51 (145)
Q Consensus 7 ~~f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~L 51 (145)
.+++.-|-.+|+||.+++..+| .|++||++.|.=.-
T Consensus 36 ~eik~LR~~~glTQ~elA~~lG---------vS~~TVs~WE~G~r 71 (96)
T PRK10072 36 TEFEQLRKGTGLKIDDFARVLG---------VSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHcCCC
Confidence 4678889999999999999885 46899999998654
No 52
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=92.81 E-value=0.15 Score=39.11 Aligned_cols=47 Identities=17% Similarity=0.178 Sum_probs=34.7
Q ss_pred hhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC--CChHHHhhhhHHHH
Q psy17899 9 VYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT--LSHNNMIALKPILQ 64 (145)
Q Consensus 9 f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~--LS~knm~klkPlL~ 64 (145)
.+..|...|+||.+++..+| .|+++|+++|+=+ -+...+.+|-=+|.
T Consensus 74 Ir~~Re~~glSqeeLA~~lg---------vs~s~IsriE~G~~~Ps~~~l~kLa~~Lg 122 (154)
T TIGR00270 74 IRREREKRGWSQEQLAKKIQ---------EKESLIKKIENAEIEPEPKVVEKLEKLLK 122 (154)
T ss_pred HHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHCCCCCCCHHHHHHHHHHhC
Confidence 35568899999999999874 5689999999755 45556555544443
No 53
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=92.41 E-value=0.24 Score=33.45 Aligned_cols=31 Identities=29% Similarity=0.358 Sum_probs=21.8
Q ss_pred hhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC
Q psy17899 11 SRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT 50 (145)
Q Consensus 11 ~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~ 50 (145)
..+-..|+||+|++..+| .||++|+|.|+-.
T Consensus 25 ~~~~~~~ltQ~e~A~~lg---------isq~~vS~l~~g~ 55 (80)
T PF13744_consen 25 ELREERGLTQAELAERLG---------ISQPRVSRLENGK 55 (80)
T ss_dssp HHHHCCT--HHHHHHHHT---------S-HHHHHHHHTT-
T ss_pred HHHHHcCCCHHHHHHHHC---------CChhHHHHHHcCc
Confidence 345567999999999985 5799999999643
No 54
>PRK09726 antitoxin HipB; Provisional
Probab=91.82 E-value=0.29 Score=33.55 Aligned_cols=32 Identities=28% Similarity=0.347 Sum_probs=26.1
Q ss_pred hhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhc
Q psy17899 9 VYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESL 49 (145)
Q Consensus 9 f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L 49 (145)
.+..|...|+||.+++..+| .||+||.+.|+=
T Consensus 17 lk~~R~~~gltq~elA~~~g---------vs~~tis~~e~g 48 (88)
T PRK09726 17 MKLVRQQNGWTQSELAKKIG---------IKQATISNFENN 48 (88)
T ss_pred HHHHHHHcCCCHHHHHHHHC---------cCHHHHHHHHCC
Confidence 34557788999999999874 568999999983
No 55
>PRK06424 transcription factor; Provisional
Probab=91.31 E-value=0.3 Score=37.19 Aligned_cols=41 Identities=17% Similarity=0.100 Sum_probs=31.0
Q ss_pred hhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCC--ChHHHhhh
Q psy17899 10 YSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTL--SHNNMIAL 59 (145)
Q Consensus 10 ~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~L--S~knm~kl 59 (145)
+..|-..|+||.+++..+| .|++||.+.|+=.. +...+.+|
T Consensus 90 r~lRe~~GLSQ~eLA~~iG---------vs~stIskiE~G~~~Ps~~~l~kL 132 (144)
T PRK06424 90 KNARERLSMSQADLAAKIF---------ERKNVIASIERGDLLPDIKTARKL 132 (144)
T ss_pred HHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHCCCCCCCHHHHHHH
Confidence 3457788999999999874 46899999999665 55554444
No 56
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=91.07 E-value=0.2 Score=36.80 Aligned_cols=51 Identities=27% Similarity=0.380 Sum_probs=36.1
Q ss_pred hhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC--CChHHHhhhhHHHH---HHHH
Q psy17899 9 VYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT--LSHNNMIALKPILQ---AWLE 68 (145)
Q Consensus 9 f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~--LS~knm~klkPlL~---kWL~ 68 (145)
.+..|...|+||.+++..+| .|++||++.|.=. .+..++.+|--+|. .||-
T Consensus 10 lk~~R~~~gltq~~lA~~~g---------vs~~~is~~E~g~~~p~~~~l~~la~~l~vs~~~l~ 65 (135)
T PRK09706 10 IRYRRKQLKLSQRSLAKAVK---------VSHVSISQWERDETEPTGKNLFALAKALQCSPTWLL 65 (135)
T ss_pred HHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHh
Confidence 45668899999999999885 4689999999765 34444555544443 4654
No 57
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=89.64 E-value=0.61 Score=35.86 Aligned_cols=48 Identities=15% Similarity=0.128 Sum_probs=35.7
Q ss_pred hhhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC--CChHHHhhhhHHHH
Q psy17899 8 DVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT--LSHNNMIALKPILQ 64 (145)
Q Consensus 8 ~f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~--LS~knm~klkPlL~ 64 (145)
..|..|...|+||.+++..+| .|++||++.|+-. .|..++.+|--.|.
T Consensus 11 ~l~~~R~~~glt~~elA~~~g---------is~~~is~~E~g~~~p~~~~l~~ia~~l~ 60 (185)
T PRK09943 11 RLSEIRQQQGLSQRRAAELSG---------LTHSAISTIEQDKVSPAISTLQKLLKVYG 60 (185)
T ss_pred HHHHHHHHcCCCHHHHHHHHC---------CCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Confidence 456778899999999998874 4689999999864 45566666554443
No 58
>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=88.26 E-value=0.12 Score=33.79 Aligned_cols=43 Identities=19% Similarity=0.237 Sum_probs=29.8
Q ss_pred CCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 94 RKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 94 R~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
++|+.|+++++..+-... ..+...+.++|.++|+++.++..|-
T Consensus 2 ~~r~~ys~e~K~~~v~~~----~~~g~sv~~va~~~gi~~~~l~~W~ 44 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREY----LESGESVSEVAREYGISPSTLYNWR 44 (76)
T ss_dssp -SS----HHHHHHHHHHH----HHHHCHHHHHHHHHTS-HHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHH----HHCCCceEeeecccccccccccHHH
Confidence 578899999997765555 2346889999999999999999994
No 59
>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=87.68 E-value=0.47 Score=30.33 Aligned_cols=38 Identities=21% Similarity=0.395 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHhhhcC--CCCCHHHHHHHHhhcCCCCCcc
Q psy17899 99 IAAPEKRSLEAYFAVQ--PRPSGEKIAAIAEKLDLKKNVV 136 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~n--p~Ps~~e~~~LA~~l~L~~~vV 136 (145)
+|+.|..+|...+..- ..|-.....+||+.||+++..|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 4788999999998866 5677888999999999998765
No 60
>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=86.85 E-value=1.2 Score=29.14 Aligned_cols=47 Identities=21% Similarity=0.241 Sum_probs=34.2
Q ss_pred hh-hhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC--CChHHHhhhhHHHH
Q psy17899 9 VY-SRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT--LSHNNMIALKPILQ 64 (145)
Q Consensus 9 f~-~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~--LS~knm~klkPlL~ 64 (145)
++ ..|-..|+||.|++..+| .|++||++.|+=. ++...+.++--.|.
T Consensus 9 i~~~~~~~~~~t~~~lA~~~g---------is~~tis~~~~g~~~~~~~~~~~l~~~l~ 58 (78)
T TIGR02607 9 LREEFLEPLGLSIRALAKALG---------VSRSTLSRIVNGRRGITADMALRLAKALG 58 (78)
T ss_pred HHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHcCCCCCCHHHHHHHHHHcC
Confidence 44 457788999999999985 4689999999754 46666666555443
No 61
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=86.72 E-value=0.6 Score=31.47 Aligned_cols=34 Identities=24% Similarity=0.214 Sum_probs=26.6
Q ss_pred CchhhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhh
Q psy17899 6 MPDVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFES 48 (145)
Q Consensus 6 ~~~f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~ 48 (145)
++..|.-|..+|+||++.+..+|. |=.||--.|+
T Consensus 3 knk~k~~R~~~~ltQ~elA~~vgV---------sRQTi~~iEk 36 (68)
T COG1476 3 KNKLKELRAELGLTQEELAKLVGV---------SRQTIIAIEK 36 (68)
T ss_pred hhHHHHHHHHhCcCHHHHHHHcCc---------CHHHHHHHHc
Confidence 457788899999999999999864 2357777665
No 62
>PRK08359 transcription factor; Validated
Probab=86.01 E-value=1.3 Score=34.83 Aligned_cols=49 Identities=14% Similarity=0.191 Sum_probs=36.8
Q ss_pred hhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCC--ChHHHhhhhHHHHHHHHH
Q psy17899 12 RVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTL--SHNNMIALKPILQAWLEE 69 (145)
Q Consensus 12 rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~L--S~knm~klkPlL~kWL~e 69 (145)
-|-..|+||.+++..+| .|++||.++|.=.. |++++.+|-=+|..=|.+
T Consensus 93 aRe~kglSQeeLA~~lg---------vs~stI~~iE~G~~~Ps~~~l~kLak~l~VsL~e 143 (176)
T PRK08359 93 AIQKSGLSYEELSHEVG---------LSVNDLRRIAHGEYEPTIKEAKKLERYFKIKLIE 143 (176)
T ss_pred HHHHcCCCHHHHHHHhC---------CCHHHHHHHHCCCcCCCHHHHHHHHHHhCCcccc
Confidence 36677999999998874 67999999987554 777777776666543433
No 63
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=83.90 E-value=3 Score=35.69 Aligned_cols=55 Identities=22% Similarity=0.104 Sum_probs=42.5
Q ss_pred hhhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCCC-----------hHHHhhhhHHHHHHHHHHH
Q psy17899 8 DVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTLS-----------HNNMIALKPILQAWLEEAE 71 (145)
Q Consensus 8 ~f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~LS-----------~knm~klkPlL~kWL~eae 71 (145)
..|+.|..+|+||.||+..|+ .++++|.+.|+=+.. .+++|++--+=..||...-
T Consensus 18 ~Lr~aRe~~GlSq~~vA~~l~---------l~~~~I~~iE~g~~~~~~~~tf~RGyir~yA~~lgv~~~~L~~~~ 83 (331)
T PRK10856 18 RLRQAREQLGLTQQAVAERLC---------LKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEELLPGL 83 (331)
T ss_pred HHHHHHHHcCCCHHHHHHHHC---------CCHHHHHHHHCCCCCCChhHHHHHHHHHHHHHHHCcCHHHHHHhh
Confidence 367789999999999999884 458999999987752 3567777777677776553
No 64
>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=83.66 E-value=0.61 Score=28.39 Aligned_cols=37 Identities=24% Similarity=0.477 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
.+++.++.+|...|. ......+||+.+|++...|+.+
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHH
Confidence 478899999999993 2355788999999999998764
No 65
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=83.48 E-value=1.1 Score=30.16 Aligned_cols=25 Identities=28% Similarity=0.403 Sum_probs=17.8
Q ss_pred ccchHHHHHHHhhccCCCCccchhhhhhh
Q psy17899 17 GVTQADVGKALANLKLPGVGALSQSTICR 45 (145)
Q Consensus 17 G~TQ~dVg~alg~l~~~g~~~fSQttIcR 45 (145)
=.||.++-..|... |+ ..+|+||+|
T Consensus 19 i~sQ~eL~~~L~~~---Gi-~vTQaTiSR 43 (70)
T PF01316_consen 19 ISSQEELVELLEEE---GI-EVTQATISR 43 (70)
T ss_dssp --SHHHHHHHHHHT---T--T--HHHHHH
T ss_pred cCCHHHHHHHHHHc---CC-CcchhHHHH
Confidence 35999999999873 76 599999998
No 66
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=83.40 E-value=3.5 Score=23.38 Aligned_cols=46 Identities=28% Similarity=0.286 Sum_probs=31.2
Q ss_pred hhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC--CChHHHhhhhHHH
Q psy17899 9 VYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT--LSHNNMIALKPIL 63 (145)
Q Consensus 9 f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~--LS~knm~klkPlL 63 (145)
.+..+...|+|+.+++.++| .|+.+|+++|+-. .+++...++-.+|
T Consensus 4 l~~~~~~~~~s~~~~a~~~~---------~~~~~v~~~~~g~~~~~~~~~~~i~~~~ 51 (58)
T cd00093 4 LKELRKEKGLTQEELAEKLG---------VSRSTISRIENGKRNPSLETLEKLAKAL 51 (58)
T ss_pred HHHHHHHcCCCHHHHHHHHC---------CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 34456667999999999875 4567888888764 5555555544433
No 67
>PRK04140 hypothetical protein; Provisional
Probab=83.39 E-value=1.9 Score=36.81 Aligned_cols=49 Identities=22% Similarity=0.319 Sum_probs=38.6
Q ss_pred hhhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhh--cCCChHHHhhhhHHHHH
Q psy17899 8 DVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFES--LTLSHNNMIALKPILQA 65 (145)
Q Consensus 8 ~f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~--L~LS~knm~klkPlL~k 65 (145)
..+..|-..|+||++++..+| .|++||++.|. -+.+..++.+|--+|..
T Consensus 130 rLk~lRe~~GlSq~eLA~~lG---------VSr~tIskyE~G~~~Ps~e~~~kLa~~Lgv 180 (317)
T PRK04140 130 VLREAREELGLSLGELASELG---------VSRRTISKYENGGMNASIEVAIKLEEILDV 180 (317)
T ss_pred HHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence 346678889999999999984 56899999998 45677787777666653
No 68
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=83.31 E-value=2.5 Score=30.90 Aligned_cols=45 Identities=16% Similarity=0.103 Sum_probs=34.5
Q ss_pred hhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhh--cCCChHHHhhhhHHHH
Q psy17899 11 SRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFES--LTLSHNNMIALKPILQ 64 (145)
Q Consensus 11 ~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~--L~LS~knm~klkPlL~ 64 (145)
.-+...|+||.+|+..+| .|++||.+.|. -+.|..++.+|--.|.
T Consensus 12 ~ll~~~Glsq~eLA~~~G---------is~~~is~iE~g~~~ps~~~l~kIa~aL~ 58 (120)
T PRK13890 12 RLLDERHMTKKELSERSG---------VSISFLSDLTTGKANPSLKVMEAIADALE 58 (120)
T ss_pred HHHHHcCCCHHHHHHHHC---------cCHHHHHHHHcCCCCCCHHHHHHHHHHHC
Confidence 334577999999998874 46899999997 4568888777766665
No 69
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=82.56 E-value=1.6 Score=36.45 Aligned_cols=48 Identities=17% Similarity=0.123 Sum_probs=36.6
Q ss_pred hhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC--CChHHHhhhhHHHHH
Q psy17899 9 VYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT--LSHNNMIALKPILQA 65 (145)
Q Consensus 9 f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~--LS~knm~klkPlL~k 65 (145)
.+..|...|+||.+++..+| .|++||+++|.=. .|+.++.+|-=.|.-
T Consensus 33 l~~~R~~~gltq~~lA~~~g---------vs~~~i~~~E~g~~~ps~~~l~~ia~~l~v 82 (309)
T PRK08154 33 VRTLRARRGMSRKVLAQASG---------VSERYLAQLESGQGNVSILLLRRVARALGC 82 (309)
T ss_pred HHHHHHHcCCCHHHHHHHHC---------cCHHHHHHHHCCCCCCCHHHHHHHHHHhCC
Confidence 35568888999999998874 5689999999865 577777776665543
No 70
>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=81.11 E-value=1.3 Score=27.02 Aligned_cols=39 Identities=15% Similarity=0.152 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
.+++.++.++.-+|..+ ....+||+.+|+++..|++|..
T Consensus 10 ~L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp CS-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHH
Confidence 35677788877766543 6778999999999999998865
No 71
>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=80.05 E-value=0.51 Score=31.01 Aligned_cols=33 Identities=27% Similarity=0.446 Sum_probs=22.6
Q ss_pred HHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 105 RSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 105 ~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+.|-|-..+-.- ...+||++||+++.+|+.|=
T Consensus 11 kA~e~y~~~~g~i---~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 11 KAFEIYKESNGKI---KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHHhCCCc---cHHHHHHHHCCCHHHHHHHh
Confidence 3444444434333 45678999999999999994
No 72
>PHA02591 hypothetical protein; Provisional
Probab=79.85 E-value=1.6 Score=30.31 Aligned_cols=24 Identities=21% Similarity=0.335 Sum_probs=19.1
Q ss_pred hhcccchHHHHHHHhhccCCCCccchhhhhhhh
Q psy17899 14 LFTGVTQADVGKALANLKLPGVGALSQSTICRF 46 (145)
Q Consensus 14 i~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRF 46 (145)
..+|+||.+|+..|| .||.|+.++
T Consensus 56 ~eqGlSqeqIA~~LG---------VsqetVrKY 79 (83)
T PHA02591 56 ARKGFTVEKIASLLG---------VSVRKVRRY 79 (83)
T ss_pred HHcCCCHHHHHHHhC---------CCHHHHHHH
Confidence 468999999999995 467777764
No 73
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=79.54 E-value=5.7 Score=22.24 Aligned_cols=42 Identities=26% Similarity=0.268 Sum_probs=28.7
Q ss_pred hhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCC--ChHHHhhhh
Q psy17899 10 YSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTL--SHNNMIALK 60 (145)
Q Consensus 10 ~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~L--S~knm~klk 60 (145)
+..+-..|+|+.+++.++| .|+.+|+++|.-.- +...+.++-
T Consensus 3 ~~~~~~~~~s~~~la~~~~---------i~~~~i~~~~~~~~~~~~~~~~~i~ 46 (56)
T smart00530 3 KELREEKGLTQEELAEKLG---------VSRSTLSRIENGKRKPSLETLKKLA 46 (56)
T ss_pred HHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHCCCCCCCHHHHHHHH
Confidence 3456667999999998874 45688998887653 444444433
No 74
>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=79.41 E-value=2.6 Score=21.77 Aligned_cols=37 Identities=14% Similarity=0.231 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
++.+....+...+.. .. ...++|+.+|++..+|..|.
T Consensus 6 ~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 566666666666653 22 56688999999999888773
No 75
>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=77.63 E-value=0.83 Score=29.51 Aligned_cols=22 Identities=32% Similarity=0.412 Sum_probs=18.8
Q ss_pred HHHHHHHHhhcCCCCCcccccc
Q psy17899 119 GEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 119 ~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+-.+.+||+.||++..+|..|-
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~ 34 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWK 34 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHH
Confidence 3456789999999999999984
No 76
>PF13551 HTH_29: Winged helix-turn helix
Probab=75.21 E-value=8.1 Score=26.33 Aligned_cols=49 Identities=22% Similarity=0.370 Sum_probs=34.2
Q ss_pred CCCCCCCCCHHHHHHHHHhhhcCC-----CCCHHHHHH-H-Hhhc--CCCCCcccccc
Q psy17899 92 KKRKRTSIAAPEKRSLEAYFAVQP-----RPSGEKIAA-I-AEKL--DLKKNVVRPIN 140 (145)
Q Consensus 92 krR~RTs~s~~q~~~Le~~F~~np-----~Ps~~e~~~-L-A~~l--~L~~~vVrVWF 140 (145)
..++++.+++++...|.+.+..+| ..+..++.+ | .+.. .++..+|+-|+
T Consensus 51 ~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L 108 (112)
T PF13551_consen 51 GGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRIL 108 (112)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHH
Confidence 344455599999999999999987 356666665 4 4443 45677777665
No 77
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=75.05 E-value=4.1 Score=29.05 Aligned_cols=38 Identities=21% Similarity=0.401 Sum_probs=29.2
Q ss_pred cccchHHHHHHHhhccCCCCccchhhhhhhhhhcCCChHHHhh-hhHHHHHHHHH
Q psy17899 16 TGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIA-LKPILQAWLEE 69 (145)
Q Consensus 16 LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~LS~knm~k-lkPlL~kWL~e 69 (145)
-|.||.+|...+| -|++||+|-|+ +.| .-|-...||+.
T Consensus 54 ~~~tQrEIa~~lG---------iS~atIsR~sn-------~lk~~~~~~~~~l~~ 92 (94)
T TIGR01321 54 GNMSQREIASKLG---------VSIATITRGSN-------NLKTMDPNFKQFLRK 92 (94)
T ss_pred CCCCHHHHHHHhC---------CChhhhhHHHh-------hcccCCHHHHHHHHh
Confidence 3799999999985 46899999774 444 56778888864
No 78
>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
Probab=73.67 E-value=2.7 Score=35.07 Aligned_cols=30 Identities=27% Similarity=0.421 Sum_probs=24.5
Q ss_pred cccchHHHHHHHhhccCCCCccchhhhhhhhhhc
Q psy17899 16 TGVTQADVGKALANLKLPGVGALSQSTICRFESL 49 (145)
Q Consensus 16 LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L 49 (145)
.|+||.+++..||.- |+ ..|++||+++..+
T Consensus 135 ~~ltq~ela~~lgk~---g~-~isrs~Isn~lrl 164 (258)
T TIGR03764 135 ESLSQRELARRLSAD---GY-PISQSHISRMGDT 164 (258)
T ss_pred CCCCHHHHHHHhccc---CC-CCCHHHHHHHHHH
Confidence 579999999999973 43 4899999988754
No 79
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=73.46 E-value=3.8 Score=30.99 Aligned_cols=31 Identities=26% Similarity=0.338 Sum_probs=25.2
Q ss_pred ccchHHHHHHHhhccCCCCccchhhhhhh-hhhcCC
Q psy17899 17 GVTQADVGKALANLKLPGVGALSQSTICR-FESLTL 51 (145)
Q Consensus 17 G~TQ~dVg~alg~l~~~g~~~fSQttIcR-FE~L~L 51 (145)
=.||.|+-..|... |+ ..||+||+| |+.|.+
T Consensus 16 i~tqeeL~~~L~~~---G~-~vsqaTIsRdL~elgl 47 (146)
T TIGR01529 16 ISTQEELVALLKAE---GI-EVTQATVSRDLRELGA 47 (146)
T ss_pred CCCHHHHHHHHHHh---CC-CcCHHHHHHHHHHcCC
Confidence 36999999999764 54 699999999 676776
No 80
>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=73.19 E-value=1.5 Score=25.33 Aligned_cols=40 Identities=20% Similarity=0.222 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGH 142 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqN 142 (145)
.+++.+..++...+... ....+||+.+|++..+|..|...
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 45677888888877533 35677899999999999887643
No 81
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=71.53 E-value=3.1 Score=32.82 Aligned_cols=39 Identities=13% Similarity=0.281 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHhhhcC--CCCCHHHHHHHHhhcCCCCCcc
Q psy17899 98 SIAAPEKRSLEAYFAVQ--PRPSGEKIAAIAEKLDLKKNVV 136 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~n--p~Ps~~e~~~LA~~l~L~~~vV 136 (145)
-+|+.|+.+|..+|..- -+|=.-...+||+++|+++.++
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 79999999999999876 7888899999999999998765
No 82
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=70.22 E-value=2.8 Score=25.23 Aligned_cols=38 Identities=24% Similarity=0.392 Sum_probs=19.2
Q ss_pred CCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 97 TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 97 Ts~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
..++..++..++.... ...-..+||+.||.++.+|.-+
T Consensus 3 ~~Lt~~eR~~I~~l~~-----~G~s~~~IA~~lg~s~sTV~re 40 (44)
T PF13936_consen 3 KHLTPEERNQIEALLE-----QGMSIREIAKRLGRSRSTVSRE 40 (44)
T ss_dssp ---------HHHHHHC-----S---HHHHHHHTT--HHHHHHH
T ss_pred cchhhhHHHHHHHHHH-----cCCCHHHHHHHHCcCcHHHHHH
Confidence 4578888888888765 3466778999999999988654
No 83
>PF10691 DUF2497: Protein of unknown function (DUF2497) ; InterPro: IPR019632 Members of this family belong to the Alphaproteobacteria. The function of the family is not known.
Probab=69.75 E-value=3.1 Score=28.31 Aligned_cols=20 Identities=30% Similarity=0.858 Sum_probs=15.4
Q ss_pred CCChHHHhh--hhHHHHHHHHH
Q psy17899 50 TLSHNNMIA--LKPILQAWLEE 69 (145)
Q Consensus 50 ~LS~knm~k--lkPlL~kWL~e 69 (145)
..|...+.+ |||.|+.||++
T Consensus 32 ~~TlE~lvremLRPmLkeWLD~ 53 (73)
T PF10691_consen 32 GRTLEDLVREMLRPMLKEWLDE 53 (73)
T ss_pred cccHHHHHHHHHHHHHHHHHHh
Confidence 345566666 99999999986
No 84
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=69.74 E-value=3.1 Score=25.83 Aligned_cols=25 Identities=36% Similarity=0.391 Sum_probs=19.2
Q ss_pred hhhcccchHHHHHHHhhccCCCCccchhhhhhhh
Q psy17899 13 VLFTGVTQADVGKALANLKLPGVGALSQSTICRF 46 (145)
Q Consensus 13 Ri~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRF 46 (145)
+++.|.|+.|+|.- | | .||+|+||.
T Consensus 15 ~LR~~~~~~~La~~----F--g---Is~stvsri 39 (53)
T PF13613_consen 15 YLRLNLTFQDLAYR----F--G---ISQSTVSRI 39 (53)
T ss_pred HHHcCCcHhHHhhh----e--e---ecHHHHHHH
Confidence 56779999987765 4 4 589999974
No 85
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=66.63 E-value=2 Score=27.41 Aligned_cols=19 Identities=21% Similarity=0.319 Sum_probs=17.1
Q ss_pred HHHHHhhcCCCCCcccccc
Q psy17899 122 IAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 122 ~~~LA~~l~L~~~vVrVWF 140 (145)
+.++|+.+|++.++||.|=
T Consensus 3 i~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 6789999999999999983
No 86
>cd00131 PAX Paired Box domain
Probab=66.51 E-value=49 Score=24.24 Aligned_cols=73 Identities=12% Similarity=0.118 Sum_probs=42.5
Q ss_pred hHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHH-HhhcCC-------
Q psy17899 60 KPILQAWLEEAEAQAKNKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAI-AEKLDL------- 131 (145)
Q Consensus 60 kPlL~kWL~eae~~~~~~~~~~~~~~~~~~~rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~L-A~~l~L------- 131 (145)
++-..+|+..-... |...+. +.+ .+++| ..++.+...++..-..||..+..|+.+. ++. |+
T Consensus 47 ~~tV~r~i~r~~e~---G~v~pk-----~~g-g~rpr-~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~-gv~~~~~~~ 115 (128)
T cd00131 47 HGCVSKILNRYYET---GSIRPG-----AIG-GSKPR-VATPEVVKKIEIYKQENPGMFAWEIRDRLLQE-GVCDKSNVP 115 (128)
T ss_pred HHHHHHHHHHHHHc---CCcCCC-----CCC-CCCCC-cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHc-CCcccCCCC
Confidence 45567788876654 221110 011 12233 4456666777777889999998888766 533 55
Q ss_pred CCCccccccCcc
Q psy17899 132 KKNVVRPINGHT 143 (145)
Q Consensus 132 ~~~vVrVWFqNr 143 (145)
+..+|--|++++
T Consensus 116 s~stI~R~L~~~ 127 (128)
T cd00131 116 SVSSINRILRNK 127 (128)
T ss_pred CHHHHHHHHHhc
Confidence 666666666553
No 87
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=63.15 E-value=11 Score=28.66 Aligned_cols=38 Identities=21% Similarity=0.343 Sum_probs=28.2
Q ss_pred hcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCCChHHHhhhhHHH
Q psy17899 15 FTGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPIL 63 (145)
Q Consensus 15 ~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~LS~knm~klkPlL 63 (145)
.-|+||.+|+..|| .|++||++.|+-- .+++-+.+.-|
T Consensus 19 ~~GlTq~EIAe~LG---------iS~~tVs~ie~ra--~kkLr~~~~tl 56 (141)
T PRK03975 19 ERGLTQQEIADILG---------TSRANVSSIEKRA--RENIEKARETL 56 (141)
T ss_pred HcCCCHHHHHHHHC---------CCHHHHHHHHHHH--HHHHHHHHHHH
Confidence 35999999999985 4789999999853 34555555554
No 88
>PRK05066 arginine repressor; Provisional
Probab=62.87 E-value=6.8 Score=30.12 Aligned_cols=33 Identities=21% Similarity=0.285 Sum_probs=25.8
Q ss_pred ccchHHHHHHHhhccCCCCccchhhhhhh-hhhcCCC
Q psy17899 17 GVTQADVGKALANLKLPGVGALSQSTICR-FESLTLS 52 (145)
Q Consensus 17 G~TQ~dVg~alg~l~~~g~~~fSQttIcR-FE~L~LS 52 (145)
=-||.|.-..|... |+.+.+|.|||| ...|++.
T Consensus 23 I~tQeeL~~~L~~~---Gi~~vTQATiSRDikeL~lv 56 (156)
T PRK05066 23 FGSQGEIVTALQEQ---GFDNINQSKVSRMLTKFGAV 56 (156)
T ss_pred CCCHHHHHHHHHHC---CCCeecHHHHHHHHHHcCCE
Confidence 35999999999863 763389999999 6667763
No 89
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=62.84 E-value=2 Score=25.28 Aligned_cols=18 Identities=22% Similarity=0.325 Sum_probs=15.5
Q ss_pred HHHHHhhcCCCCCccccc
Q psy17899 122 IAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 122 ~~~LA~~l~L~~~vVrVW 139 (145)
|.++|+.+|++.++||-|
T Consensus 2 i~e~A~~~gvs~~tlR~y 19 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYY 19 (38)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 678999999999999987
No 90
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=61.96 E-value=8.5 Score=34.16 Aligned_cols=57 Identities=25% Similarity=0.286 Sum_probs=39.3
Q ss_pred hhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcC--CChHHHhhhhHHHH---HHHHH
Q psy17899 9 VYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLT--LSHNNMIALKPILQ---AWLEE 69 (145)
Q Consensus 9 f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~--LS~knm~klkPlL~---kWL~e 69 (145)
-+..|...|+||.+++..++.. | ...|+++|++.|+=. .+..+..+|--.|. .||..
T Consensus 8 L~~~r~~~g~tq~~la~~~~~~---g-~~vs~~~is~~e~g~~~p~~~~l~~la~~l~v~~~~l~~ 69 (517)
T PRK13355 8 LKQAMKARGLKQEDLVHAAEAR---G-VKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDWLLG 69 (517)
T ss_pred HHHHHHHCCCCHHHHHHHHHhc---c-CCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHHHcc
Confidence 3556778899999999998753 4 248999999999765 34444444444443 58843
No 91
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=61.41 E-value=6.8 Score=26.93 Aligned_cols=25 Identities=32% Similarity=0.365 Sum_probs=17.3
Q ss_pred ccchHHHHHHHhhccCCCCccchhhhhhhhhhcC
Q psy17899 17 GVTQADVGKALANLKLPGVGALSQSTICRFESLT 50 (145)
Q Consensus 17 G~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~ 50 (145)
|+||.+|+..|| .|++.|+++-+|-
T Consensus 3 G~tq~eIA~~lG---------ks~s~Vs~~l~Ll 27 (93)
T PF08535_consen 3 GWTQEEIAKRLG---------KSRSWVSNHLALL 27 (93)
T ss_dssp T--HHHHHHHTT-----------HHHHHHHHGGG
T ss_pred CCCHHHHHHHHC---------CCHHHHHHHHHHH
Confidence 899999999985 4678888877663
No 92
>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=60.81 E-value=6.1 Score=25.83 Aligned_cols=47 Identities=26% Similarity=0.270 Sum_probs=27.9
Q ss_pred CCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCc
Q psy17899 95 KRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGH 142 (145)
Q Consensus 95 ~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqN 142 (145)
.|.+|+..-+-.--.+|.....--...|.. |.+.|+++..||-|-+-
T Consensus 2 ~rrsy~~~FKL~Vv~~a~~~~nc~~~~RAa-arkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 2 SRRSYTAEFKLKVVEYAEKDNNCKGNQRAA-ARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp ------HHHHHHHHHHHHH-TTTTT-HHHH-HHHTTS-HHHHHHHHTT
T ss_pred CccccChHHHHHHHHHHHHccchhhhHHHH-HHHhCccHHHHHHHHHH
Confidence 366888877766556665555555555655 99999999999999753
No 93
>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=60.63 E-value=2.3 Score=25.09 Aligned_cols=20 Identities=15% Similarity=0.208 Sum_probs=17.6
Q ss_pred HHHHHhhcCCCCCccccccC
Q psy17899 122 IAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 122 ~~~LA~~l~L~~~vVrVWFq 141 (145)
+.++|+.+|+++.+|+.|-+
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 57889999999999999954
No 94
>PF13565 HTH_32: Homeodomain-like domain
Probab=60.60 E-value=42 Score=21.50 Aligned_cols=44 Identities=20% Similarity=0.356 Sum_probs=30.8
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHH-HHhhcCC----CCCcccc
Q psy17899 93 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA-IAEKLDL----KKNVVRP 138 (145)
Q Consensus 93 rR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~-LA~~l~L----~~~vVrV 138 (145)
-|+|+ ++++...+.+....+|.-+..++.. |+++.|. +.++|.-
T Consensus 27 Grp~~--~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R 75 (77)
T PF13565_consen 27 GRPRK--DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYR 75 (77)
T ss_pred CCCCC--cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHH
Confidence 33455 7888899999999999888777654 5665553 5555543
No 95
>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=58.17 E-value=5 Score=23.81 Aligned_cols=35 Identities=20% Similarity=0.287 Sum_probs=25.1
Q ss_pred CHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 100 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 100 s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
++.+..++.-.+ + .....+||+.++++..+|+.|.
T Consensus 2 ~~~e~~i~~~~~--~----~~s~~eia~~l~~s~~tv~~~~ 36 (57)
T cd06170 2 TPREREVLRLLA--E----GKTNKEIADILGISEKTVKTHL 36 (57)
T ss_pred CHHHHHHHHHHH--c----CCCHHHHHHHHCCCHHHHHHHH
Confidence 456666665543 2 2366788999999999998874
No 96
>PRK10458 DNA cytosine methylase; Provisional
Probab=57.06 E-value=11 Score=33.84 Aligned_cols=41 Identities=12% Similarity=0.097 Sum_probs=33.8
Q ss_pred hhhhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCC
Q psy17899 8 DVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTL 51 (145)
Q Consensus 8 ~f~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~L 51 (145)
.+...+...+|||.++...|+.. |.+..|..||-|+|+=..
T Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~ 60 (467)
T PRK10458 20 QALLEKLLEIYDVKTLAAQLNGV---GENHWSRAILKRWLAGKS 60 (467)
T ss_pred HHHHHHHHHhcCHHHHHHHHhhc---ccCccCHHHHHHHHcCCC
Confidence 35667888899999999999875 336799999999998654
No 97
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=56.56 E-value=9.4 Score=22.37 Aligned_cols=38 Identities=24% Similarity=0.312 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
.+++.+..++...+. .....+||+.+|++..+|+.|..
T Consensus 3 ~l~~~e~~i~~~~~~------g~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRLLAE------GLTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHHHHc------CCCHHHHHHHHCCCHHHHHHHHH
Confidence 367778887766432 23568899999999999987743
No 98
>PRK04280 arginine repressor; Provisional
Probab=55.82 E-value=9.9 Score=28.89 Aligned_cols=30 Identities=30% Similarity=0.441 Sum_probs=24.5
Q ss_pred cchHHHHHHHhhccCCCCccchhhhhhh-hhhcCC
Q psy17899 18 VTQADVGKALANLKLPGVGALSQSTICR-FESLTL 51 (145)
Q Consensus 18 ~TQ~dVg~alg~l~~~g~~~fSQttIcR-FE~L~L 51 (145)
=||.|.-..|... |+ ..+|.|||| ...|.+
T Consensus 19 ~tQeeL~~~L~~~---Gi-~vTQATiSRDikeL~l 49 (148)
T PRK04280 19 ETQDELVDRLREE---GF-NVTQATVSRDIKELHL 49 (148)
T ss_pred CCHHHHHHHHHHc---CC-CeehHHHHHHHHHcCC
Confidence 3899999999874 76 599999999 666665
No 99
>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=54.51 E-value=1.6 Score=29.68 Aligned_cols=25 Identities=28% Similarity=0.320 Sum_probs=21.3
Q ss_pred CHHHHHHHHhhcCCCCCccccccCc
Q psy17899 118 SGEKIAAIAEKLDLKKNVVRPINGH 142 (145)
Q Consensus 118 s~~e~~~LA~~l~L~~~vVrVWFqN 142 (145)
......+||+.+|+++..|++|+.+
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 4456789999999999999999865
No 100
>COG3827 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.43 E-value=9.7 Score=31.18 Aligned_cols=17 Identities=47% Similarity=1.001 Sum_probs=12.8
Q ss_pred hHHHhh--hhHHHHHHHHH
Q psy17899 53 HNNMIA--LKPILQAWLEE 69 (145)
Q Consensus 53 ~knm~k--lkPlL~kWL~e 69 (145)
|..|.. |||.|+-||+.
T Consensus 190 leE~a~eMLRPmLqdWLDk 208 (231)
T COG3827 190 LEEMAAEMLRPMLQDWLDK 208 (231)
T ss_pred HHHHHHHHHHHHHHHHHHc
Confidence 334444 89999999985
No 101
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=53.78 E-value=3.4 Score=24.73 Aligned_cols=24 Identities=25% Similarity=0.298 Sum_probs=18.1
Q ss_pred HHHHHHHHhhcCCCCCccccccCc
Q psy17899 119 GEKIAAIAEKLDLKKNVVRPINGH 142 (145)
Q Consensus 119 ~~e~~~LA~~l~L~~~vVrVWFqN 142 (145)
.....+||+.+|++..+|.-|...
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 566789999999999999999764
No 102
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=53.01 E-value=13 Score=26.83 Aligned_cols=39 Identities=23% Similarity=0.185 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
.+++.++.++...|..+ ....+||+.+|++..+|++|..
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ 144 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYR 144 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 45667777776655443 4478999999999999998753
No 103
>PF13518 HTH_28: Helix-turn-helix domain
Probab=52.68 E-value=5.4 Score=23.73 Aligned_cols=22 Identities=14% Similarity=0.226 Sum_probs=18.5
Q ss_pred HHHHHHhhcCCCCCccccccCc
Q psy17899 121 KIAAIAEKLDLKKNVVRPINGH 142 (145)
Q Consensus 121 e~~~LA~~l~L~~~vVrVWFqN 142 (145)
...++|.++|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 4566999999999999999753
No 104
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=50.72 E-value=15 Score=26.20 Aligned_cols=23 Identities=43% Similarity=0.489 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHHhhcCCCCCccc
Q psy17899 115 PRPSGEKIAAIAEKLDLKKNVVR 137 (145)
Q Consensus 115 p~Ps~~e~~~LA~~l~L~~~vVr 137 (145)
+.|+.+++.+.|++||++..+++
T Consensus 30 ~~P~~~ei~~a~~~LGl~~~v~~ 52 (93)
T COG1400 30 ENPSLEEIAEALRELGLKPKVER 52 (93)
T ss_pred cCCCHHHHHHHHHHcCCCeeech
Confidence 58999999999999999987654
No 105
>COG1438 ArgR Arginine repressor [Transcription]
Probab=50.59 E-value=13 Score=28.72 Aligned_cols=24 Identities=29% Similarity=0.536 Sum_probs=20.8
Q ss_pred cchHHHHHHHhhccCCCCccchhhhhhh
Q psy17899 18 VTQADVGKALANLKLPGVGALSQSTICR 45 (145)
Q Consensus 18 ~TQ~dVg~alg~l~~~g~~~fSQttIcR 45 (145)
.||.++-..|.. + |+ ..+|+|++|
T Consensus 21 ~TQ~Elv~~L~~-~--Gi-~vTQaTvSR 44 (150)
T COG1438 21 STQEELVELLQE-E--GI-EVTQATVSR 44 (150)
T ss_pred CCHHHHHHHHHH-c--CC-eEehHHHHH
Confidence 599999999986 3 76 599999998
No 106
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=50.47 E-value=14 Score=27.38 Aligned_cols=23 Identities=26% Similarity=0.521 Sum_probs=16.1
Q ss_pred hcccchHHHHHHHhhccCCCCccchhhhhhhh
Q psy17899 15 FTGVTQADVGKALANLKLPGVGALSQSTICRF 46 (145)
Q Consensus 15 ~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRF 46 (145)
..||||.+|+.-|| .||+.++..
T Consensus 20 eeG~Sq~~iA~LLG---------ltqaAVS~Y 42 (119)
T COG2522 20 EEGLSQYRIAKLLG---------LTQAAVSQY 42 (119)
T ss_pred HcCCcHHHHHHHhC---------CCHHHHHHH
Confidence 34899999888875 456666554
No 107
>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=50.04 E-value=4.1 Score=23.38 Aligned_cols=21 Identities=19% Similarity=0.150 Sum_probs=17.6
Q ss_pred HHHHHhhcCCCCCccccccCc
Q psy17899 122 IAAIAEKLDLKKNVVRPINGH 142 (145)
Q Consensus 122 ~~~LA~~l~L~~~vVrVWFqN 142 (145)
+.++|+.+|+++.+|+-|-++
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 468899999999999999644
No 108
>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=49.66 E-value=14 Score=27.92 Aligned_cols=26 Identities=19% Similarity=0.442 Sum_probs=21.5
Q ss_pred cccchHHHHHHHhhccCCCCccchhhhhhhhhhcC
Q psy17899 16 TGVTQADVGKALANLKLPGVGALSQSTICRFESLT 50 (145)
Q Consensus 16 LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~ 50 (145)
=|+||.+++..|| .|++||++.|+--
T Consensus 20 ~GlTq~EIAe~Lg---------iS~stV~~~e~ra 45 (137)
T TIGR00721 20 KGLSQKEIAKELK---------TTRANVSAIEKRA 45 (137)
T ss_pred cCCCHHHHHHHHC---------cCHHHHHHHHHhH
Confidence 4999999999985 5688999887653
No 109
>PF13730 HTH_36: Helix-turn-helix domain
Probab=49.55 E-value=23 Score=21.38 Aligned_cols=23 Identities=22% Similarity=0.270 Sum_probs=17.9
Q ss_pred CCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 115 PRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 115 p~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+|| ++.||+.+|+++++|+-+.
T Consensus 24 ~~pS---~~~la~~~g~s~~Tv~~~i 46 (55)
T PF13730_consen 24 CFPS---QETLAKDLGVSRRTVQRAI 46 (55)
T ss_pred CCcC---HHHHHHHHCcCHHHHHHHH
Confidence 5564 7788999999999987543
No 110
>PRK09480 slmA division inhibitor protein; Provisional
Probab=49.47 E-value=12 Score=27.74 Aligned_cols=38 Identities=11% Similarity=0.146 Sum_probs=30.9
Q ss_pred HHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCcc
Q psy17899 105 RSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHT 143 (145)
Q Consensus 105 ~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNr 143 (145)
.+....|..++. +.-.+.+||++.|+++.++--+|.|+
T Consensus 17 ~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K 54 (194)
T PRK09480 17 QALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSK 54 (194)
T ss_pred HHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCH
Confidence 334445656666 89999999999999999999999886
No 111
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=49.34 E-value=5.6 Score=25.36 Aligned_cols=20 Identities=20% Similarity=0.340 Sum_probs=17.8
Q ss_pred HHHHHhhcCCCCCccccccC
Q psy17899 122 IAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 122 ~~~LA~~l~L~~~vVrVWFq 141 (145)
+.++|+.+|++..++|-|-+
T Consensus 3 i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 67899999999999999964
No 112
>KOG1146|consensus
Probab=49.22 E-value=12 Score=37.76 Aligned_cols=55 Identities=16% Similarity=0.066 Sum_probs=51.7
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccCC
Q psy17899 91 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 91 rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
+-+..|+.+-..+..+|-..|..+.-|+.+...-|........+++.+||+|.|+
T Consensus 704 ~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~ 758 (1406)
T KOG1146|consen 704 RDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRE 758 (1406)
T ss_pred ccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhh
Confidence 6678899999999999999999999999999999999999999999999999763
No 113
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=48.09 E-value=12 Score=28.52 Aligned_cols=38 Identities=13% Similarity=0.166 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
+++.++.+|.-.|..+ ....+||+.||++..+|+++..
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ 180 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMR 180 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHH
Confidence 5566666776654333 4567899999999999998753
No 114
>PRK10072 putative transcriptional regulator; Provisional
Probab=47.77 E-value=7.1 Score=27.69 Aligned_cols=23 Identities=17% Similarity=0.214 Sum_probs=21.0
Q ss_pred HHHHHhhcCCCCCccccccCccC
Q psy17899 122 IAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 122 ~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
..++|+.+|++..+|..|.+.+|
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 67889999999999999998876
No 115
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=46.39 E-value=9.1 Score=27.11 Aligned_cols=44 Identities=30% Similarity=0.408 Sum_probs=30.0
Q ss_pred ccchHHHHHHHhhccCCCCccchhhhhhhhhhcCCChHHHhhhhHHHHHHHHHHH
Q psy17899 17 GVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAE 71 (145)
Q Consensus 17 G~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~LS~knm~klkPlL~kWL~eae 71 (145)
..||..|+-++| .|.||||||-. + -+-.||.|--+|+-=+++.|
T Consensus 23 ~~gq~~vA~~~G---------v~eStISR~k~-~-~~~~~a~lLa~L~~~v~~~~ 66 (91)
T PF05269_consen 23 SVGQKKVAEAMG---------VDESTISRWKN-D-FIEKMAMLLAALELGVEDSE 66 (91)
T ss_dssp HHHHHHHHHHHT---------SSTTTHHHHHH-H-HHHHHHHHHHHTTTTHHHHH
T ss_pred HHhhHHHHHHhC---------CCHHHHHHHHh-h-HHHHHHHHHHHHHhcccccH
Confidence 788999999986 35689999842 1 23567777777764344444
No 116
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=46.28 E-value=6.5 Score=24.84 Aligned_cols=20 Identities=20% Similarity=0.300 Sum_probs=17.6
Q ss_pred HHHHHhhcCCCCCccccccC
Q psy17899 122 IAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 122 ~~~LA~~l~L~~~vVrVWFq 141 (145)
+.++|+.+|++..+++-|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56899999999999999965
No 117
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=46.12 E-value=6.6 Score=25.13 Aligned_cols=20 Identities=25% Similarity=0.315 Sum_probs=17.9
Q ss_pred HHHHHhhcCCCCCccccccC
Q psy17899 122 IAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 122 ~~~LA~~l~L~~~vVrVWFq 141 (145)
+.++|+.+|+++.+++-|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 67899999999999999965
No 118
>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=46.09 E-value=9.8 Score=26.34 Aligned_cols=39 Identities=21% Similarity=0.209 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
.+++.++.++..+|.. .....+||+.+|+++.+|+.+..
T Consensus 110 ~L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~ 148 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLK 148 (158)
T ss_pred hCCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHH
Confidence 4567777777666543 34566899999999999987654
No 119
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=46.06 E-value=15 Score=27.62 Aligned_cols=37 Identities=16% Similarity=0.212 Sum_probs=25.1
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+++.++.++.-.|.. .....+||+.+|++..+|+++-
T Consensus 134 L~~~~r~i~~l~~~~-----~~s~~eIA~~lgis~~tV~~~l 170 (182)
T PRK12537 134 LEPARRNCILHAYVD-----GCSHAEIAQRLGAPLGTVKAWI 170 (182)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCChhhHHHHH
Confidence 334555555554422 2456889999999999999864
No 120
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=45.95 E-value=16 Score=22.13 Aligned_cols=18 Identities=28% Similarity=0.420 Sum_probs=14.7
Q ss_pred hhcccchHHHHHHHhhcc
Q psy17899 14 LFTGVTQADVGKALANLK 31 (145)
Q Consensus 14 i~LG~TQ~dVg~alg~l~ 31 (145)
+.|||+..++-.++..+.
T Consensus 11 ~~LGy~~~e~~~av~~~~ 28 (47)
T PF07499_consen 11 ISLGYSKAEAQKAVSKLL 28 (47)
T ss_dssp HHTTS-HHHHHHHHHHHH
T ss_pred HHcCCCHHHHHHHHHHhh
Confidence 679999999999998765
No 121
>PF11774 Lsr2: Lsr2 ; InterPro: IPR024412 This entry represents Lsr2, which is a small, basic DNA-bridging protein present in Mycobacterium and related actinomycetes. It is a functional homologue of the H-NS-like proteins []. H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression [, ].; PDB: 4E1R_B 4E1P_B 2KNG_A.
Probab=45.67 E-value=13 Score=26.94 Aligned_cols=24 Identities=25% Similarity=0.421 Sum_probs=20.6
Q ss_pred hcCCChHHHhhhhHHHHHHHHHHH
Q psy17899 48 SLTLSHNNMIALKPILQAWLEEAE 71 (145)
Q Consensus 48 ~L~LS~knm~klkPlL~kWL~eae 71 (145)
.++||-+|+-+|+-.|+.|++.+-
T Consensus 32 eIDLs~~na~~lr~~l~~yi~~ar 55 (110)
T PF11774_consen 32 EIDLSAENAAKLRDALAPYIAAAR 55 (110)
T ss_dssp EEEE-HHHHHHHHHHHHHHHHHSE
T ss_pred EEECCHHHHHHHHHHHHHHHHHhe
Confidence 479999999999999999998764
No 122
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=45.20 E-value=22 Score=25.58 Aligned_cols=42 Identities=10% Similarity=-0.002 Sum_probs=29.2
Q ss_pred CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 96 RTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 96 RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
|..++.+.+...-.....+. ....++|..+|++..+|..|-.
T Consensus 10 rr~ys~EfK~~aV~~~~~~g----~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG----MTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHH
Confidence 44578887765444333333 3466789999999999999954
No 123
>PHA03256 BDLF3; Provisional
Probab=45.00 E-value=50 Score=22.61 Aligned_cols=37 Identities=19% Similarity=0.248 Sum_probs=31.9
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcC
Q psy17899 91 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLD 130 (145)
Q Consensus 91 rkrR~RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~ 130 (145)
++-|+|..++......+..+| ++|-+..+.+++..++
T Consensus 9 ~~sK~~~~IsE~df~~~~~ff---~rpLp~lVaevska~~ 45 (77)
T PHA03256 9 RQDKKRGTIGEREFGELLSWD---PTDLPRTVARVYVAVG 45 (77)
T ss_pred cccccCCccCHHHHHHHHHHc---CCcHHHHHHHHHHHhc
Confidence 556789999999999999999 7888888998888875
No 124
>PRK03341 arginine repressor; Provisional
Probab=42.97 E-value=22 Score=27.65 Aligned_cols=32 Identities=28% Similarity=0.449 Sum_probs=25.8
Q ss_pred ccchHHHHHHHhhccCCCCccchhhhhhh-hhhcCCC
Q psy17899 17 GVTQADVGKALANLKLPGVGALSQSTICR-FESLTLS 52 (145)
Q Consensus 17 G~TQ~dVg~alg~l~~~g~~~fSQttIcR-FE~L~LS 52 (145)
-.||.|+-..|... |+ ..||.||+| ...|.+.
T Consensus 29 i~tQ~eL~~~L~~~---Gi-~vTQaTiSRDl~eL~~~ 61 (168)
T PRK03341 29 VRSQAELAALLADE---GI-EVTQATLSRDLDELGAV 61 (168)
T ss_pred CccHHHHHHHHHHc---CC-cccHHHHHHHHHHhcCE
Confidence 56999999999763 76 599999999 6667653
No 125
>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=42.50 E-value=6.1 Score=24.59 Aligned_cols=38 Identities=24% Similarity=0.282 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
.+|+.+..+|.-.. .+....+||+.+|+++.+|..+..
T Consensus 3 ~LT~~E~~vl~~l~------~G~~~~eIA~~l~is~~tV~~~~~ 40 (58)
T PF00196_consen 3 SLTERELEVLRLLA------QGMSNKEIAEELGISEKTVKSHRR 40 (58)
T ss_dssp SS-HHHHHHHHHHH------TTS-HHHHHHHHTSHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHH------hcCCcchhHHhcCcchhhHHHHHH
Confidence 56777888777755 345678899999999999987543
No 126
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=42.20 E-value=23 Score=22.81 Aligned_cols=34 Identities=18% Similarity=0.137 Sum_probs=23.6
Q ss_pred hhhhhhcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCCC
Q psy17899 10 YSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTLS 52 (145)
Q Consensus 10 ~~rRi~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~LS 52 (145)
++.|...|+|..||...+. .+...|..+|+=+.+
T Consensus 3 r~~R~~~glsl~~va~~t~---------I~~~~l~aiE~~~~~ 36 (62)
T PF13413_consen 3 REAREAKGLSLEDVAEETK---------ISVSYLEAIENGDFD 36 (62)
T ss_dssp HHHHHCTT--HHHHHHHCS-----------HHHHHHHHCT-GC
T ss_pred HHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHCcChh
Confidence 6789999999999998864 446788888887763
No 127
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=41.83 E-value=16 Score=23.04 Aligned_cols=32 Identities=16% Similarity=0.288 Sum_probs=23.6
Q ss_pred HHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccc
Q psy17899 102 PEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 137 (145)
Q Consensus 102 ~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVr 137 (145)
.|...|+--+. ++..+.. +||+.+|+++.+|+
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~ 37 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIK 37 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHH
Confidence 46667777777 6666655 78999999998886
No 128
>smart00351 PAX Paired Box domain.
Probab=41.79 E-value=1.3e+02 Score=21.69 Aligned_cols=74 Identities=14% Similarity=0.092 Sum_probs=42.6
Q ss_pred chhhhhhhhhhcCCChHHHhhhhHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCC
Q psy17899 38 LSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRP 117 (145)
Q Consensus 38 fSQttIcRFE~L~LS~knm~klkPlL~kWL~eae~~~~~~~~~~~~~~~~~~~rkrR~RTs~s~~q~~~Le~~F~~np~P 117 (145)
.|+..||+ .+.+| ++-..+|+...... |.. .+.....+++-..+..+...++..-..+|..
T Consensus 34 ~s~~~iA~--~~gvs-------~~tV~kwi~r~~~~---G~~-------~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~ 94 (125)
T smart00351 34 VRPCDISR--QLCVS-------HGCVSKILGRYYET---GSI-------RPGAIGGSKPKVATPKVVKKIADYKQENPGI 94 (125)
T ss_pred CCHHHHHH--HHCcC-------HHHHHHHHHHHHHc---CCc-------CCcCCCCCCCCccCHHHHHHHHHHHHHCCCC
Confidence 45666653 33444 56678899887654 221 1111111233344556666777778899999
Q ss_pred CHHHHH-HHHhhcCC
Q psy17899 118 SGEKIA-AIAEKLDL 131 (145)
Q Consensus 118 s~~e~~-~LA~~l~L 131 (145)
+..++. .|+ .-|+
T Consensus 95 t~~el~~~L~-~~gv 108 (125)
T smart00351 95 FAWEIRDRLL-SEGV 108 (125)
T ss_pred CHHHHHHHHH-HcCC
Confidence 998884 555 3443
No 129
>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=41.73 E-value=15 Score=27.36 Aligned_cols=38 Identities=16% Similarity=0.062 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+++.++.++.-.|..+ ....+||+.+|+++.+|+++-
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l 137 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRV 137 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHH
Confidence 45566666766655443 456789999999999998753
No 130
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=41.67 E-value=16 Score=26.63 Aligned_cols=22 Identities=23% Similarity=0.123 Sum_probs=18.4
Q ss_pred HHHHHHHhhcCCCCCccccccC
Q psy17899 120 EKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 120 ~e~~~LA~~l~L~~~vVrVWFq 141 (145)
....+||+.+|+++.+|+.|..
T Consensus 142 ~~~~eIA~~lgis~~tv~~~~~ 163 (179)
T PRK11924 142 LSYREIAEILGVPVGTVKSRLR 163 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 4457999999999999998753
No 131
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=41.24 E-value=14 Score=26.94 Aligned_cols=39 Identities=18% Similarity=0.062 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
.+++.++.++.-.|.. .....+||+.+|++..+|+.|..
T Consensus 128 ~L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 128 SLPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHH
Confidence 3556667777665532 23456899999999999988754
No 132
>PF01922 SRP19: SRP19 protein; InterPro: IPR002778 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the SRP19 subunit. The SRP19 protein is unstructured but forms a compact core domain and two extended RNA-binding loops upon binding the signal recognition particle (SRP) RNA [].; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 3DLU_A 3DLV_B 2J37_B 1MFQ_B 3KTV_D 1RY1_B 1JID_A 1KVV_A 1KVN_A 3KTW_B ....
Probab=41.11 E-value=22 Score=25.05 Aligned_cols=29 Identities=31% Similarity=0.261 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHHhhcCCCCCcc------ccccCcc
Q psy17899 115 PRPSGEKIAAIAEKLDLKKNVV------RPINGHT 143 (145)
Q Consensus 115 p~Ps~~e~~~LA~~l~L~~~vV------rVWFqNr 143 (145)
..|+.+||.+.+++|||+-.+- +-||.|+
T Consensus 27 ~~P~~~EI~~a~~~Lgl~~~~E~~K~yPr~~~~~~ 61 (95)
T PF01922_consen 27 ENPTLEEIADACKKLGLPCVVEPDKRYPRDWWENP 61 (95)
T ss_dssp SS--HHHHHHHHHHTTSEEEEETTECTTCGSTSCT
T ss_pred CCCCHHHHHHHHHHcCCCEEEccccCcChhhcccC
Confidence 6899999999999999975543 4566554
No 133
>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=40.45 E-value=18 Score=26.18 Aligned_cols=38 Identities=21% Similarity=0.306 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+++.++.++...|. ......+||+.+|++..+|.++.
T Consensus 111 ~L~~~~r~v~~l~~~-----~g~~~~eIA~~l~is~~tv~~~l 148 (159)
T TIGR02989 111 KLPERQRELLQLRYQ-----RGVSLTALAEQLGRTVNAVYKAL 148 (159)
T ss_pred HCCHHHHHHHHHHHh-----cCCCHHHHHHHhCCCHHHHHHHH
Confidence 456666666666443 23557889999999999998764
No 134
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=40.20 E-value=7.3 Score=23.26 Aligned_cols=21 Identities=14% Similarity=0.090 Sum_probs=18.3
Q ss_pred HHHhhcCCCCCccccccCccC
Q psy17899 124 AIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 124 ~LA~~l~L~~~vVrVWFqNrR 144 (145)
+||+.+|++..+|..|+.|..
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999988863
No 135
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.16 E-value=32 Score=24.18 Aligned_cols=41 Identities=10% Similarity=0.113 Sum_probs=31.7
Q ss_pred CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCC-CCCcccccc
Q psy17899 96 RTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL-KKNVVRPIN 140 (145)
Q Consensus 96 RTs~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L-~~~vVrVWF 140 (145)
|..|+++.+..+-.......+ -+..+|+++|+ +..++..|-
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~ 46 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWR 46 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHH
Confidence 788999988766655544433 78899999996 998888774
No 136
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=39.77 E-value=47 Score=22.10 Aligned_cols=32 Identities=16% Similarity=0.227 Sum_probs=27.0
Q ss_pred HHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCc
Q psy17899 104 KRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNV 135 (145)
Q Consensus 104 ~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~v 135 (145)
+..+++++.+||..+.+.+..+..+.|-.++.
T Consensus 19 r~~~~k~l~~NPpine~mir~M~~QMG~kpSe 50 (64)
T PF03672_consen 19 RKYMEKQLKENPPINEKMIRAMMMQMGRKPSE 50 (64)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHhCCCccH
Confidence 45689999999999999999999999876543
No 137
>PF13701 DDE_Tnp_1_4: Transposase DDE domain group 1
Probab=38.38 E-value=59 Score=28.84 Aligned_cols=52 Identities=25% Similarity=0.352 Sum_probs=33.0
Q ss_pred hhcccchHH----------HHHHHhhccCCCCc-cchhhhhhhhhhcCCChHHHhhhhHHHHHH
Q psy17899 14 LFTGVTQAD----------VGKALANLKLPGVG-ALSQSTICRFESLTLSHNNMIALKPILQAW 66 (145)
Q Consensus 14 i~LG~TQ~d----------Vg~alg~l~~~g~~-~fSQttIcRFE~L~LS~knm~klkPlL~kW 66 (145)
|..||.-.+ ...++|.+-.+|-. .=||+||||||..- +..+..++...+..+
T Consensus 68 i~~Gyed~~d~~~LR~Dp~f~~~~g~~~~~~~~~Las~~t~sR~e~~~-~~~~~~~~~~~~~~~ 130 (448)
T PF13701_consen 68 IAAGYEDDNDADRLRHDPVFKLALGRLPEPGSDRLASQPTLSRLENRP-DERDLKRLRRALVDL 130 (448)
T ss_pred HHccCCChHHHHHhccCHHHHHHhccCCCCccccccchhhHHHHHccc-cHHHHHHHHHHHHHH
Confidence 344776554 45666665544522 47999999999665 355666666665553
No 138
>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=38.32 E-value=16 Score=26.69 Aligned_cols=36 Identities=17% Similarity=0.140 Sum_probs=24.3
Q ss_pred CHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 100 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 100 s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
++.++.++.-.|.. .....+||+.+|++..+|+++-
T Consensus 112 ~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l 147 (162)
T TIGR02983 112 PARQRAVVVLRYYE-----DLSEAQVAEALGISVGTVKSRL 147 (162)
T ss_pred CHHHHHHhhhHHHh-----cCCHHHHHHHhCCCHHHHHHHH
Confidence 34555555554422 3446789999999999998753
No 139
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=38.13 E-value=10 Score=23.86 Aligned_cols=19 Identities=16% Similarity=0.214 Sum_probs=16.5
Q ss_pred HHHHHhhcCCCCCcccccc
Q psy17899 122 IAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 122 ~~~LA~~l~L~~~vVrVWF 140 (145)
+.++|+.+|+++++|+-|-
T Consensus 3 ~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5688999999999999883
No 140
>PRK04217 hypothetical protein; Provisional
Probab=37.20 E-value=27 Score=25.35 Aligned_cols=39 Identities=8% Similarity=-0.033 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 97 TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 97 Ts~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
-.++.+++.++...|...- ...+||+.+|+++.+|....
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L 79 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRAL 79 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHH
Confidence 3467888888887775442 67789999999999987644
No 141
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=37.16 E-value=12 Score=21.42 Aligned_cols=16 Identities=31% Similarity=0.405 Sum_probs=12.3
Q ss_pred HHHHHHhhcCCCCCcc
Q psy17899 121 KIAAIAEKLDLKKNVV 136 (145)
Q Consensus 121 e~~~LA~~l~L~~~vV 136 (145)
.+.+||+-+|++.++|
T Consensus 4 tr~diA~~lG~t~ETV 19 (32)
T PF00325_consen 4 TRQDIADYLGLTRETV 19 (32)
T ss_dssp -HHHHHHHHTS-HHHH
T ss_pred CHHHHHHHhCCcHHHH
Confidence 3678999999998877
No 142
>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=37.08 E-value=15 Score=27.42 Aligned_cols=22 Identities=27% Similarity=0.229 Sum_probs=18.5
Q ss_pred HHHHHHHHhhcCCCCCcccccc
Q psy17899 119 GEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 119 ~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.....+||+.+|+++.+|+++.
T Consensus 154 ~~s~~EIA~~lgis~~tv~~~l 175 (190)
T TIGR02939 154 GLSYEDIARIMDCPVGTVRSRI 175 (190)
T ss_pred CCCHHHHHHHHCcCHHHHHHHH
Confidence 3456899999999999999875
No 143
>PRK00118 putative DNA-binding protein; Validated
Probab=36.78 E-value=20 Score=25.78 Aligned_cols=38 Identities=16% Similarity=0.319 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
+++.|+.++..+|..+ ....+||+.+|+++.+|..|..
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~ 55 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIK 55 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHH
Confidence 4567777777766553 4567899999999999988754
No 144
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=36.49 E-value=20 Score=26.94 Aligned_cols=39 Identities=18% Similarity=0.198 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 97 TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 97 Ts~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
..+++.++.++.-.|.. .....+||+.+|++..+|+++.
T Consensus 138 ~~L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l 176 (189)
T PRK09648 138 DTLPEKQREILILRVVV-----GLSAEETAEAVGSTPGAVRVAQ 176 (189)
T ss_pred HhCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHH
Confidence 34556677777765433 2457889999999999998764
No 145
>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=36.13 E-value=21 Score=25.38 Aligned_cols=37 Identities=16% Similarity=0.111 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+++.+..++.-.|.. .....+||+.+|+++..|+++.
T Consensus 114 L~~~~r~il~l~~~~-----~~~~~eIA~~lgis~~tv~~~~ 150 (161)
T TIGR02985 114 LPEQCRKIFILSRFE-----GKSYKEIAEELGISVKTVEYHI 150 (161)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHH
Confidence 445566666664432 2345678999999999998754
No 146
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=36.02 E-value=41 Score=25.81 Aligned_cols=37 Identities=19% Similarity=0.293 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHhh---hcCCCCCHHHHHHHHhhcCCC-CCccc
Q psy17899 99 IAAPEKRSLEAYF---AVQPRPSGEKIAAIAEKLDLK-KNVVR 137 (145)
Q Consensus 99 ~s~~q~~~Le~~F---~~np~Ps~~e~~~LA~~l~L~-~~vVr 137 (145)
+++.|..+|+... ..+.+|.. ..+||+.+|++ +.+|.
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~--~~ela~~~~~~s~~tv~ 44 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPS--IREIARAVGLRSPSAAE 44 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCc--HHHHHHHhCCCChHHHH
Confidence 5677777766655 55666633 77899999998 77765
No 147
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=35.55 E-value=25 Score=25.20 Aligned_cols=40 Identities=18% Similarity=0.173 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCc
Q psy17899 97 TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGH 142 (145)
Q Consensus 97 Ts~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqN 142 (145)
..+++.+..+|.- +..+ + ...+||+.+++++.+|+++.+|
T Consensus 148 ~~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~ 187 (211)
T PRK15369 148 PLLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLN 187 (211)
T ss_pred cCCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHH
Confidence 3488888888876 4443 2 2578899999999999987665
No 148
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=35.35 E-value=36 Score=21.00 Aligned_cols=30 Identities=20% Similarity=0.294 Sum_probs=17.1
Q ss_pred HHHhhhcC-CCCCHHHHHHHHhhcCCCCCcc
Q psy17899 107 LEAYFAVQ-PRPSGEKIAAIAEKLDLKKNVV 136 (145)
Q Consensus 107 Le~~F~~n-p~Ps~~e~~~LA~~l~L~~~vV 136 (145)
|...+... ..|+...+..||..||++.+.+
T Consensus 27 l~~~~~~~~~~~~~~~l~~ia~~l~~~~~el 57 (63)
T PF13443_consen 27 LSRILNGKPSNPSLDTLEKIAKALNCSPEEL 57 (63)
T ss_dssp HHHHHTTT-----HHHHHHHHHHHT--HHHC
T ss_pred HHHHHhcccccccHHHHHHHHHHcCCCHHHH
Confidence 44444444 5899999999999999876543
No 149
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=35.15 E-value=19 Score=26.46 Aligned_cols=38 Identities=18% Similarity=0.048 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
+++.++.++.-.|. ......+||+.+|++..+|++|.+
T Consensus 109 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~tv~~~l~ 146 (165)
T PRK09644 109 LPVIEAQAILLCDV-----HELTYEEAASVLDLKLNTYKSHLF 146 (165)
T ss_pred CCHHHHHHHHhHHH-----hcCCHHHHHHHHCCCHHHHHHHHH
Confidence 44555555554322 224567899999999999998754
No 150
>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=34.95 E-value=15 Score=22.30 Aligned_cols=31 Identities=19% Similarity=0.335 Sum_probs=18.9
Q ss_pred HHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccc
Q psy17899 104 KRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 137 (145)
Q Consensus 104 ~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVr 137 (145)
..+|.-....+.+ -...+||+.+++++.+|+
T Consensus 3 ~~il~~L~~~~~~---it~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 3 KQILKLLLESKEP---ITAKELAEELGVSRRTIR 33 (55)
T ss_dssp HHHHHHHHHTTTS---BEHHHHHHHCTS-HHHHH
T ss_pred HHHHHHHHHcCCC---cCHHHHHHHhCCCHHHHH
Confidence 3444443344433 445678999999998886
No 151
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=34.87 E-value=22 Score=26.49 Aligned_cols=37 Identities=16% Similarity=0.195 Sum_probs=24.9
Q ss_pred CHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 100 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 100 s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
++.++.++.-.|.. ....++||+.+|+++..|+++..
T Consensus 131 ~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 131 EKDRAAAVRRAYLE-----GLSYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred CHHHHHHHHHHHHc-----CCCHHHHHHHHCCChHHHHHHHH
Confidence 34555555544422 23467899999999999988754
No 152
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=34.79 E-value=13 Score=27.62 Aligned_cols=39 Identities=15% Similarity=0.175 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
.+++.++.++.-.|. ......+||+.+|+++.+|+++.+
T Consensus 136 ~L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~ 174 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-----EDLSLKEISEILDLPVGTVKTRIH 174 (187)
T ss_pred hCCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345555556555332 245578899999999999998764
No 153
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=34.19 E-value=23 Score=27.36 Aligned_cols=37 Identities=8% Similarity=0.152 Sum_probs=24.8
Q ss_pred CHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 100 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 100 s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
++.++.++.-.|. ......+||+.+|++..+|+++..
T Consensus 155 ~~~~r~vl~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~ 191 (206)
T PRK12526 155 PEAQQTVVKGVYF-----QELSQEQLAQQLNVPLGTVKSRLR 191 (206)
T ss_pred CHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3445555554332 224567899999999999988754
No 154
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=33.74 E-value=19 Score=27.20 Aligned_cols=22 Identities=18% Similarity=0.215 Sum_probs=18.8
Q ss_pred HHHHHHHhhcCCCCCccccccC
Q psy17899 120 EKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 120 ~e~~~LA~~l~L~~~vVrVWFq 141 (145)
....+||+.+|++..+|++|..
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~ 179 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARAR 179 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 4567899999999999998864
No 155
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=33.14 E-value=26 Score=25.61 Aligned_cols=38 Identities=16% Similarity=0.068 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+++.++.++.-.|... ....+||+.+|++..+|+++.
T Consensus 113 ~L~~~~r~v~~L~~~~g-----~s~~EIA~~l~is~~tV~~~l 150 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDG-----LGYGEIATELGISLATVKRYL 150 (161)
T ss_pred HCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHH
Confidence 34556666666554333 346789999999999998764
No 156
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=33.06 E-value=28 Score=26.19 Aligned_cols=38 Identities=13% Similarity=0.181 Sum_probs=27.0
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+++.++.++.-.|. ..-...+||+.+|++..+|+++.
T Consensus 131 ~L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l 168 (184)
T PRK12539 131 RLPEKMRLAIQAVKL-----EGLSVAEAATRSGMSESAVKVSV 168 (184)
T ss_pred hCCHHHHHHHHHHHH-----cCCcHHHHHHHHCcCHHHHHHHH
Confidence 455666666665443 23557889999999999998754
No 157
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=33.06 E-value=34 Score=28.21 Aligned_cols=36 Identities=22% Similarity=0.373 Sum_probs=26.3
Q ss_pred hcccchHHHHHHHhhccCCCCccchhhhhhhhhhcCCChHHHhhhhHHHH
Q psy17899 15 FTGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQ 64 (145)
Q Consensus 15 ~LG~TQ~dVg~alg~l~~~g~~~fSQttIcRFE~L~LS~knm~klkPlL~ 64 (145)
.-++||.+||.-|| -||++|||.++-- .-||+--|.
T Consensus 210 ~eelt~kEI~~~Lg---------ISes~VSql~kka-----i~kLr~~l~ 245 (247)
T COG1191 210 KEELTQKEIAEVLG---------ISESRVSRLHKKA-----IKKLRKELN 245 (247)
T ss_pred HhccCHHHHHHHhC---------ccHHHHHHHHHHH-----HHHHHHHhc
Confidence 34899999999884 5799999988743 445554444
No 158
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=33.06 E-value=31 Score=29.18 Aligned_cols=20 Identities=35% Similarity=0.752 Sum_probs=14.2
Q ss_pred ccchHHHHHHHhhccCCCCccchhhhhhh
Q psy17899 17 GVTQADVGKALANLKLPGVGALSQSTICR 45 (145)
Q Consensus 17 G~TQ~dVg~alg~l~~~g~~~fSQttIcR 45 (145)
|+||.+++..|| .|.++|+|
T Consensus 29 g~tQ~eIA~~lg---------iSR~~VsR 48 (318)
T PRK15418 29 GLTQSEIGERLG---------LTRLKVSR 48 (318)
T ss_pred CCCHHHHHHHhC---------CCHHHHHH
Confidence 788888887774 45567776
No 159
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=32.85 E-value=24 Score=25.69 Aligned_cols=20 Identities=15% Similarity=0.026 Sum_probs=16.7
Q ss_pred HHHHHHhhcCCCCCcccccc
Q psy17899 121 KIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 121 e~~~LA~~l~L~~~vVrVWF 140 (145)
...+||+.+|++..+|++..
T Consensus 124 s~~EIA~~lgis~~tV~~~l 143 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKL 143 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 35689999999999998764
No 160
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.82 E-value=31 Score=24.57 Aligned_cols=35 Identities=26% Similarity=0.343 Sum_probs=22.7
Q ss_pred CCCHHHHH----HHHHhhhcCCCCCHHHHHHHHhhcCCCCCcc
Q psy17899 98 SIAAPEKR----SLEAYFAVQPRPSGEKIAAIAEKLDLKKNVV 136 (145)
Q Consensus 98 s~s~~q~~----~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vV 136 (145)
|+++.|+. .|.+.|+.|+ =-+++||..|+.++.-|
T Consensus 2 SLn~eq~~~Tk~elqan~el~~----LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCP----LSDEEIATALNWTEVKL 40 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhcc----ccHHHHHHHhCCCHHHH
Confidence 45566655 4566665554 45678899999876543
No 161
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=32.67 E-value=28 Score=26.24 Aligned_cols=38 Identities=5% Similarity=0.260 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+++.++.+|.-.|... ....+||+.+|+++.+|++-.
T Consensus 131 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l 168 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRM 168 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 44556666665554332 346788999999999998643
No 162
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=32.51 E-value=24 Score=26.35 Aligned_cols=37 Identities=19% Similarity=0.250 Sum_probs=24.4
Q ss_pred CHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 100 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 100 s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
++.++.++.-.|.. .....+||+.+|++..+|+++..
T Consensus 133 ~~~~r~v~~l~~~~-----g~s~~eIA~~l~is~~tV~~~l~ 169 (184)
T PRK12512 133 PPRQRDVVQSISVE-----GASIKETAAKLSMSEGAVRVALH 169 (184)
T ss_pred CHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHH
Confidence 34444444444322 34567899999999999988654
No 163
>PRK00523 hypothetical protein; Provisional
Probab=32.50 E-value=68 Score=21.82 Aligned_cols=32 Identities=16% Similarity=0.179 Sum_probs=26.7
Q ss_pred HHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCc
Q psy17899 104 KRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNV 135 (145)
Q Consensus 104 ~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~v 135 (145)
+..+|+++.+||..+.+.+..+..+.|-.++.
T Consensus 27 rk~~~k~l~~NPpine~mir~M~~QMGqKPSe 58 (72)
T PRK00523 27 KKMFKKQIRENPPITENMIRAMYMQMGRKPSE 58 (72)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHHHHhCCCccH
Confidence 45689999999999999999999998876543
No 164
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=32.49 E-value=28 Score=25.61 Aligned_cols=37 Identities=14% Similarity=0.144 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+++.++.++...|... ....+||+.||++..+|+++.
T Consensus 120 L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l 156 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYL 156 (169)
T ss_pred CCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHH
Confidence 3455555665544332 456789999999999998753
No 165
>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=32.28 E-value=29 Score=25.76 Aligned_cols=38 Identities=18% Similarity=0.147 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
+++.++.++.-.|... -...+||+.||+++.+|++...
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~ 172 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWR 172 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHH
Confidence 4455555555444322 3467899999999999987543
No 166
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=31.77 E-value=40 Score=24.21 Aligned_cols=36 Identities=22% Similarity=0.428 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
+|..|+..|+-||..+ --..+||+.+|+++..|.-|
T Consensus 18 LT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ 53 (101)
T PF04297_consen 18 LTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDS 53 (101)
T ss_dssp S-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHH
T ss_pred CCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHH
Confidence 6789999999998655 45678999999998776543
No 167
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=31.75 E-value=24 Score=25.78 Aligned_cols=37 Identities=16% Similarity=-0.056 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+++.|+.++.-.|..+ -...+||+.+|++..+|+++.
T Consensus 113 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l 149 (161)
T PRK12541 113 LPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIEL 149 (161)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHH
Confidence 5555666655544333 346789999999999998764
No 168
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=31.29 E-value=23 Score=26.35 Aligned_cols=38 Identities=16% Similarity=0.155 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+++.++.++.-.+.. .....+||+.+|++..+|+++.
T Consensus 119 ~L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK09651 119 GLNGKTREAFLLSQLD-----GLTYSEIAHKLGVSVSSVKKYV 156 (172)
T ss_pred hCCHHHhHHhhhhhcc-----CCCHHHHHHHhCCCHHHHHHHH
Confidence 3455555555554322 2346889999999999998764
No 169
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=31.20 E-value=27 Score=26.54 Aligned_cols=37 Identities=11% Similarity=0.121 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+++.++.++.-.|... ....+||+.+|+++.+|+++.
T Consensus 135 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l 171 (189)
T PRK12530 135 LPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLL 171 (189)
T ss_pred CCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHH
Confidence 3455666655554332 346889999999999998764
No 170
>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=30.82 E-value=31 Score=25.09 Aligned_cols=36 Identities=17% Similarity=0.286 Sum_probs=23.2
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
+++.++.++.-.|. ......+||+.||+++.+|++.
T Consensus 123 L~~~~r~vl~l~~~-----~g~s~~eIA~~l~is~~tv~~~ 158 (170)
T TIGR02952 123 LTPKQQHVIALRFG-----QNLPIAEVARILGKTEGAVKIL 158 (170)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCCCHHHHHHH
Confidence 33444444444332 2345678999999999998864
No 171
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=30.73 E-value=32 Score=25.62 Aligned_cols=37 Identities=19% Similarity=0.302 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+++.++.++.-.|. ......+||+.+|++..+|+++.
T Consensus 136 L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~~V~~~l 172 (186)
T PRK13919 136 LSPEERRVIEVLYY-----QGYTHREAAQLLGLPLGTLKTRA 172 (186)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHH
Confidence 34444445543332 22445789999999999998764
No 172
>PF13223 DUF4031: Protein of unknown function (DUF4031)
Probab=30.65 E-value=35 Score=23.75 Aligned_cols=21 Identities=10% Similarity=0.213 Sum_probs=17.5
Q ss_pred CHHHHHHHHhhcCCCCCccccccCc
Q psy17899 118 SGEKIAAIAEKLDLKKNVVRPINGH 142 (145)
Q Consensus 118 s~~e~~~LA~~l~L~~~vVrVWFqN 142 (145)
+.+|.-..|+++|++++ |||.
T Consensus 22 t~~ELHafA~riGv~rr----~fq~ 42 (83)
T PF13223_consen 22 TLDELHAFAARIGVPRR----WFQR 42 (83)
T ss_pred CHHHHHHHHHHcCCCHH----HHcC
Confidence 36788899999999875 8887
No 173
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=30.60 E-value=32 Score=22.46 Aligned_cols=38 Identities=26% Similarity=0.455 Sum_probs=23.1
Q ss_pred CCCHHHHHH---HHHhhhcCCCCCHHHHHHHHhhcCCC-CCccc
Q psy17899 98 SIAAPEKRS---LEAYFAVQPRPSGEKIAAIAEKLDLK-KNVVR 137 (145)
Q Consensus 98 s~s~~q~~~---Le~~F~~np~Ps~~e~~~LA~~l~L~-~~vVr 137 (145)
.+|+.|..+ +..+...+.||. .+.+||+.+|+. ..+|+
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~ 44 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQ 44 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHH
Confidence 356666655 456777888885 677889999996 55553
No 174
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=30.43 E-value=40 Score=25.17 Aligned_cols=34 Identities=18% Similarity=0.302 Sum_probs=22.5
Q ss_pred CHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccc
Q psy17899 100 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRP 138 (145)
Q Consensus 100 s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrV 138 (145)
++.+..++...|. ......+||+.||+++.+|++
T Consensus 139 ~~~~r~i~~l~~~-----~g~s~~eIA~~lgis~~~v~~ 172 (187)
T PRK12534 139 EPPRSELIRTAFF-----EGITYEELAARTDTPIGTVKS 172 (187)
T ss_pred CHHHHHHHHHHHH-----cCCCHHHHHHHhCCChhHHHH
Confidence 3444444444432 334567899999999999875
No 175
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=30.27 E-value=92 Score=20.81 Aligned_cols=30 Identities=20% Similarity=0.186 Sum_probs=22.7
Q ss_pred chhhhhhhhhhcCCChHHHhhhhHHHHHHHHH
Q psy17899 38 LSQSTICRFESLTLSHNNMIALKPILQAWLEE 69 (145)
Q Consensus 38 fSQttIcRFE~L~LS~knm~klkPlL~kWL~e 69 (145)
||.+.|-++|..+-- -.-+...+|.+|.+.
T Consensus 23 ls~~~I~~ie~~~~~--~~eq~~~mL~~W~~k 52 (79)
T cd08784 23 LSDNEIKVAELDNPQ--HRDRVYELLRIWRNK 52 (79)
T ss_pred CCHHHHHHHHHcCCc--hHHHHHHHHHHHHhc
Confidence 778888888877643 345679999999874
No 176
>PRK01844 hypothetical protein; Provisional
Probab=30.23 E-value=79 Score=21.53 Aligned_cols=32 Identities=9% Similarity=0.245 Sum_probs=26.7
Q ss_pred HHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCc
Q psy17899 104 KRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNV 135 (145)
Q Consensus 104 ~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~v 135 (145)
+..+|+++.+||..+.+.+..+..+.|-.++.
T Consensus 26 rk~~~k~lk~NPpine~mir~Mm~QMGqkPSe 57 (72)
T PRK01844 26 RKYMMNYLQKNPPINEQMLKMMMMQMGQKPSQ 57 (72)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHhCCCccH
Confidence 45689999999999999999999998876543
No 177
>PRK00441 argR arginine repressor; Provisional
Probab=30.18 E-value=48 Score=25.14 Aligned_cols=31 Identities=29% Similarity=0.531 Sum_probs=24.7
Q ss_pred cchHHHHHHHhhccCCCCccchhhhhhh-hhhcCCC
Q psy17899 18 VTQADVGKALANLKLPGVGALSQSTICR-FESLTLS 52 (145)
Q Consensus 18 ~TQ~dVg~alg~l~~~g~~~fSQttIcR-FE~L~LS 52 (145)
.||.+....|... |+ ..||.||+| +..|.+.
T Consensus 19 ~~q~eL~~~L~~~---G~-~vSqaTisRDl~~L~lv 50 (149)
T PRK00441 19 ETQEELAEELKKM---GF-DVTQATVSRDIKELKLI 50 (149)
T ss_pred CcHHHHHHHHHhc---CC-CcCHHHHHHHHHHcCcE
Confidence 4899999999763 76 599999999 7777763
No 178
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=29.99 E-value=30 Score=27.14 Aligned_cols=37 Identities=11% Similarity=0.196 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
.+++.++.++..+|.. .....+||+.+|++...|+.+
T Consensus 183 ~L~~~e~~i~~~~~~~-----~~t~~eIA~~lgis~~~V~~~ 219 (231)
T TIGR02885 183 KLDERERQIIMLRYFK-----DKTQTEVANMLGISQVQVSRL 219 (231)
T ss_pred cCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHH
Confidence 5667777788777643 246889999999999998764
No 179
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=29.96 E-value=34 Score=25.68 Aligned_cols=38 Identities=18% Similarity=0.111 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+++.++.++.-.|..+ ....+||+.||+++.+|++..
T Consensus 127 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l 164 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYI 164 (178)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHH
Confidence 35567777776655332 346789999999999998754
No 180
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=29.66 E-value=31 Score=25.10 Aligned_cols=36 Identities=25% Similarity=0.309 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+++.++.+|.-+| . .....+||+.+|++..+|+++.
T Consensus 113 L~~~~r~il~l~~-~-----g~s~~eIA~~lgis~~tV~~~i 148 (166)
T PRK09639 113 MTERDRTVLLLRF-S-----GYSYKEIAEALGIKESSVGTTL 148 (166)
T ss_pred CCHHHHHHHHHHH-c-----CCCHHHHHHHHCCCHHHHHHHH
Confidence 5556666666665 2 2346789999999999998764
No 181
>PF10945 DUF2629: Protein of unknown function (DUF2629); InterPro: IPR024487 Some members in this family of proteins are annotated as YhjR however currently no function is known.
Probab=29.50 E-value=56 Score=20.20 Aligned_cols=39 Identities=26% Similarity=0.333 Sum_probs=28.3
Q ss_pred hHHHHHHHhhccCCCCccchhhhhhhhhhcCCChHHHhhhhHHHHH
Q psy17899 20 QADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQA 65 (145)
Q Consensus 20 Q~dVg~alg~l~~~g~~~fSQttIcRFE~L~LS~knm~klkPlL~k 65 (145)
|.|+. +|...| |...+.=.-|+|=|+|+ .|.+-.|||..
T Consensus 3 ~dDi~-~L~~~f--slp~~~Y~DIsr~e~l~----~~~~RWPLLaE 41 (44)
T PF10945_consen 3 QDDIA-ALSQAF--SLPDINYIDISREERLN----QALQRWPLLAE 41 (44)
T ss_pred hhHHH-HHHHHh--CCCCccHHHHHHHHHHH----HHHHHChhHHH
Confidence 55554 456656 55667678899999998 68888999863
No 182
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=29.45 E-value=29 Score=26.02 Aligned_cols=21 Identities=10% Similarity=0.113 Sum_probs=17.3
Q ss_pred HHHHHHHhhcCCCCCcccccc
Q psy17899 120 EKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 120 ~e~~~LA~~l~L~~~vVrVWF 140 (145)
....+||+.+|++..+|+++.
T Consensus 145 ~s~~EIA~~lgis~~tV~~~l 165 (186)
T PRK05602 145 LSNIEAAAVMDISVDALESLL 165 (186)
T ss_pred CCHHHHHHHhCcCHHHHHHHH
Confidence 345789999999999998764
No 183
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=29.40 E-value=39 Score=24.88 Aligned_cols=36 Identities=19% Similarity=0.267 Sum_probs=23.8
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
+++.++.+|.-.|.. .....+||+.||+++.+|++.
T Consensus 119 L~~~~r~vl~L~~~~-----g~s~~EIA~~lgis~~tV~~~ 154 (173)
T PRK09645 119 LSPEHRAVLVRSYYR-----GWSTAQIAADLGIPEGTVKSR 154 (173)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHH
Confidence 334555555554322 233678999999999999864
No 184
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=29.29 E-value=36 Score=28.02 Aligned_cols=38 Identities=13% Similarity=0.241 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRP 138 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrV 138 (145)
.+++.++.+|..+|... ......+||+.+|++.+.|+-
T Consensus 230 ~L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrq 267 (284)
T PRK06596 230 GLDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQ 267 (284)
T ss_pred cCCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHH
Confidence 46677888888888542 234477999999999988863
No 185
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=28.71 E-value=29 Score=26.37 Aligned_cols=37 Identities=14% Similarity=0.245 Sum_probs=24.1
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+++.++.++.-.|.. .-...+||+.+|++..+|+++.
T Consensus 137 L~~~~r~i~~L~~~~-----g~s~~eIA~~lgis~~tV~~~l 173 (196)
T PRK12524 137 LPERQRQAVVLRHIE-----GLSNPEIAEVMEIGVEAVESLT 173 (196)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHH
Confidence 344455454444332 2336789999999999998765
No 186
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=28.61 E-value=33 Score=25.22 Aligned_cols=21 Identities=5% Similarity=-0.129 Sum_probs=17.6
Q ss_pred HHHHHHHhhcCCCCCcccccc
Q psy17899 120 EKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 120 ~e~~~LA~~l~L~~~vVrVWF 140 (145)
....+||+.+|++..+|+++.
T Consensus 129 ~s~~eIA~~lgis~~tV~~~l 149 (164)
T PRK12547 129 FSYEDAAAICGCAVGTIKSRV 149 (164)
T ss_pred CCHHHHHHHhCCCHHHHHHHH
Confidence 446789999999999998764
No 187
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=28.50 E-value=38 Score=24.63 Aligned_cols=36 Identities=22% Similarity=0.289 Sum_probs=23.2
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
+++.++.++.-.|..+ ....+||+.+|++..+|++.
T Consensus 110 L~~~~r~v~~l~~~~~-----~s~~EIA~~lgis~~tV~~~ 145 (163)
T PRK07037 110 LPARTRYAFEMYRLHG-----ETQKDIARELGVSPTLVNFM 145 (163)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHH
Confidence 3444555554433222 23678999999999999864
No 188
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=28.21 E-value=36 Score=24.56 Aligned_cols=37 Identities=11% Similarity=0.154 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+++.++.++.-.|... -...+||+.||++..+|++..
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l 143 (161)
T PRK09047 107 LPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHC 143 (161)
T ss_pred CCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHH
Confidence 4556666666644322 236789999999999998753
No 189
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=28.14 E-value=27 Score=27.21 Aligned_cols=38 Identities=24% Similarity=0.293 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+++.++.++..+|.. .....+||+.+|++...|+.|.
T Consensus 178 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~ 215 (227)
T TIGR02980 178 ALPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLL 215 (227)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHH
Confidence 5677788888777643 2457889999999999998764
No 190
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=27.45 E-value=40 Score=25.67 Aligned_cols=19 Identities=21% Similarity=0.296 Sum_probs=15.4
Q ss_pred HHHHHHHhhcCCCCCcccc
Q psy17899 120 EKIAAIAEKLDLKKNVVRP 138 (145)
Q Consensus 120 ~e~~~LA~~l~L~~~vVrV 138 (145)
....+||+.+|++..+|++
T Consensus 151 ~s~~EIA~~lg~s~~tV~~ 169 (192)
T PRK09643 151 YSVADAARMLGVAEGTVKS 169 (192)
T ss_pred CCHHHHHHHHCcCHHHHHH
Confidence 3457899999999998864
No 191
>PRK10403 transcriptional regulator NarP; Provisional
Probab=27.30 E-value=26 Score=25.48 Aligned_cols=40 Identities=15% Similarity=0.095 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCc
Q psy17899 97 TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGH 142 (145)
Q Consensus 97 Ts~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqN 142 (145)
..++..+..+|+-.... -...+||+.+++++++|++...|
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~ 191 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRN 191 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHH
Confidence 45888999998865533 33568899999999999876544
No 192
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. 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
Probab=27.20 E-value=23 Score=30.56 Aligned_cols=28 Identities=43% Similarity=0.610 Sum_probs=24.0
Q ss_pred ccchHHHHHHHhhccCCCCccchhhhhhhh
Q psy17899 17 GVTQADVGKALANLKLPGVGALSQSTICRF 46 (145)
Q Consensus 17 G~TQ~dVg~alg~l~~~g~~~fSQttIcRF 46 (145)
|+|..||+.+|..+| |-..+|-+||+|+
T Consensus 114 G~Str~i~~~l~~l~--g~~~~S~s~vSri 141 (381)
T PF00872_consen 114 GVSTRDIEEALEELY--GEVAVSKSTVSRI 141 (381)
T ss_pred ccccccccchhhhhh--cccccCchhhhhh
Confidence 999999999999998 4125999999984
No 193
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=27.12 E-value=39 Score=25.25 Aligned_cols=37 Identities=11% Similarity=0.082 Sum_probs=24.0
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+++.++.++.-.|..+ ....+||+.+|++..+|++..
T Consensus 118 Lp~~~r~i~~l~~~e~-----~s~~EIA~~lgis~~tV~~~l 154 (179)
T PRK12543 118 LPYKLRQVIILRYLHD-----YSQEEIAQLLQIPIGTVKSRI 154 (179)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHH
Confidence 4455555555433222 346789999999999998743
No 194
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=26.57 E-value=38 Score=25.00 Aligned_cols=39 Identities=8% Similarity=0.072 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 97 TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 97 Ts~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
..+++.++.++.-.|..+ ....+||+.||+++.+|+.+-
T Consensus 117 ~~L~~~~r~v~~L~~~eg-----~s~~EIA~~l~is~~tV~~~l 155 (168)
T PRK12525 117 DGLSGKARAAFLMSQLEG-----LTYVEIGERLGVSLSRIHQYM 155 (168)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHH
Confidence 346667777776654333 346789999999999998764
No 195
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=26.41 E-value=55 Score=23.30 Aligned_cols=33 Identities=24% Similarity=0.261 Sum_probs=21.2
Q ss_pred CHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccc
Q psy17899 100 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 137 (145)
Q Consensus 100 s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVr 137 (145)
++.++.++.-.|... ....+||+.||+++.+|+
T Consensus 109 p~~~r~v~~l~~~~~-----~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 109 PNKQKKIIYMKFFED-----MKEIDIAKKLHISRQSVY 141 (142)
T ss_pred CHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHhhc
Confidence 445555544443222 345789999999998886
No 196
>PF13743 Thioredoxin_5: Thioredoxin; PDB: 3KZQ_C.
Probab=26.24 E-value=28 Score=26.66 Aligned_cols=39 Identities=23% Similarity=0.155 Sum_probs=24.6
Q ss_pred HHHHHHHhh-hcCCCCCH-HHHHHHHhhcCCCCCccccccC
Q psy17899 103 EKRSLEAYF-AVQPRPSG-EKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 103 q~~~Le~~F-~~np~Ps~-~e~~~LA~~l~L~~~vVrVWFq 141 (145)
-+..|...+ .....++. +...+||+++||+.+.....|+
T Consensus 85 fL~~lQ~a~~~~~~~~s~~~~l~~iA~~~gLD~~~F~~d~~ 125 (176)
T PF13743_consen 85 FLRALQEALFLEGKNYSDEELLLEIAEELGLDVEMFKEDLH 125 (176)
T ss_dssp HHHHHHHHHHTS---TTSHHHHHHHHHHTT--HHHHHHHHT
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHHhCCCHHHHHHHHh
Confidence 455665555 56666665 9999999999999887665543
No 197
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=25.92 E-value=37 Score=25.65 Aligned_cols=22 Identities=27% Similarity=0.146 Sum_probs=18.0
Q ss_pred HHHHHHHhhcCCCCCccccccC
Q psy17899 120 EKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 120 ~e~~~LA~~l~L~~~vVrVWFq 141 (145)
....+||+.+|+++.+|++.+.
T Consensus 123 ~~~~EIA~~lgis~~tV~~~l~ 144 (181)
T PRK09637 123 LSQKEIAEKLGLSLSGAKSRVQ 144 (181)
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 4568899999999999987653
No 198
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=25.84 E-value=41 Score=25.53 Aligned_cols=38 Identities=11% Similarity=0.072 Sum_probs=25.8
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+++.++.++.-.|.. .....+||+.+|++..+|+++.
T Consensus 111 ~Lp~~~R~v~~L~~~e-----g~s~~EIA~~lgis~~tV~~~l 148 (182)
T PRK12511 111 DLPEEQRAALHLVAIE-----GLSYQEAAAVLGIPIGTLMSRI 148 (182)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHhCcCHHHHHHHH
Confidence 3555666666554432 2346789999999999998753
No 199
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=25.80 E-value=53 Score=19.29 Aligned_cols=34 Identities=24% Similarity=0.398 Sum_probs=20.6
Q ss_pred CHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccc
Q psy17899 100 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 137 (145)
Q Consensus 100 s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVr 137 (145)
+..+..+|..... +|..| +.+||+.+|++...|.
T Consensus 2 ~~~~~~Il~~l~~-~~~~t---~~ela~~~~is~~tv~ 35 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPRIT---QKELAEKLGISRSTVN 35 (48)
T ss_dssp -HHHHHHHHHHHH-CTTS----HHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHHHHHH-cCCCC---HHHHHHHhCCCHHHHH
Confidence 3456667755444 55544 5667889999877664
No 200
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=25.70 E-value=94 Score=20.98 Aligned_cols=32 Identities=19% Similarity=0.167 Sum_probs=24.9
Q ss_pred CHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 100 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 100 s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
+.+|+..|-+.+ -..+++.||.++++|.|.|.
T Consensus 14 s~EqK~~La~~i----------T~a~~~~lg~~~e~v~V~I~ 45 (76)
T PRK01271 14 DEEQKAALAADI----------TDVIIRHLNSKDSSISIALQ 45 (76)
T ss_pred CHHHHHHHHHHH----------HHHHHHHhCcCcceEEEEEE
Confidence 577888777643 45678899999999999875
No 201
>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=25.63 E-value=35 Score=20.80 Aligned_cols=36 Identities=22% Similarity=0.242 Sum_probs=24.6
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVV 136 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vV 136 (145)
++..|..+|-......+. .-...+||+.+++++..|
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~v 38 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTV 38 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHH
Confidence 567777777776655543 236778899999987665
No 202
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=25.48 E-value=22 Score=20.30 Aligned_cols=21 Identities=24% Similarity=0.276 Sum_probs=16.6
Q ss_pred HHHHHhhcCCCCCccccccCc
Q psy17899 122 IAAIAEKLDLKKNVVRPINGH 142 (145)
Q Consensus 122 ~~~LA~~l~L~~~vVrVWFqN 142 (145)
+.++|+.||+++..|.-|-.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHc
Confidence 567888999999888887644
No 203
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=25.43 E-value=39 Score=25.64 Aligned_cols=35 Identities=20% Similarity=0.324 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRP 138 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrV 138 (145)
.+|+.++++|.-.. .+....+||+.|++++++|+.
T Consensus 150 ~Lt~rE~evl~~~~------~G~s~~eIA~~l~iS~~TV~~ 184 (216)
T PRK10840 150 RLSPKESEVLRLFA------EGFLVTEIAKKLNRSIKTISS 184 (216)
T ss_pred cCCHHHHHHHHHHH------CCCCHHHHHHHHCCCHHHHHH
Confidence 48999999988876 345567899999999999975
No 204
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=25.31 E-value=42 Score=25.19 Aligned_cols=39 Identities=23% Similarity=0.299 Sum_probs=29.4
Q ss_pred CHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 100 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 100 s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
..+.+.+++-+|..-+..|.. .||..+++++++++-|.+
T Consensus 83 ~de~k~Ii~lry~~r~~~TW~---~IA~~l~i~erta~r~~~ 121 (130)
T PF05263_consen 83 IDEEKRIIKLRYDRRSRRTWY---QIAQKLHISERTARRWRD 121 (130)
T ss_pred CHHHHHHHHHHHcccccchHH---HHHHHhCccHHHHHHHHH
Confidence 345677888888777666654 568899999999987754
No 205
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=25.07 E-value=35 Score=27.31 Aligned_cols=38 Identities=16% Similarity=0.229 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+++.++.+|.-+|... ....+||+.+|++..+|+.|.
T Consensus 205 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~ 242 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQ 242 (257)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHH
Confidence 46677777887766432 345889999999999998874
No 206
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=24.80 E-value=55 Score=23.73 Aligned_cols=21 Identities=24% Similarity=0.517 Sum_probs=16.4
Q ss_pred ccchHHHHHHHhhccCCCCccchhhhhhhh
Q psy17899 17 GVTQADVGKALANLKLPGVGALSQSTICRF 46 (145)
Q Consensus 17 G~TQ~dVg~alg~l~~~g~~~fSQttIcRF 46 (145)
|+||.+.+..+| -|++|+.|.
T Consensus 57 gl~QeeaA~~Mg---------VSR~T~~ri 77 (106)
T PF02001_consen 57 GLSQEEAAERMG---------VSRPTFQRI 77 (106)
T ss_pred CCCHHHHHHHcC---------CcHHHHHHH
Confidence 999999998874 467777764
No 207
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=24.71 E-value=31 Score=25.05 Aligned_cols=40 Identities=18% Similarity=0.200 Sum_probs=30.5
Q ss_pred CCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCc
Q psy17899 97 TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGH 142 (145)
Q Consensus 97 Ts~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqN 142 (145)
..+++.+...|+-.... ....+||+.+++++++|++..++
T Consensus 136 ~~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~ 175 (196)
T PRK10360 136 DPLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRAN 175 (196)
T ss_pred cCCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHH
Confidence 35888888888776543 36778899999999999876544
No 208
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=24.68 E-value=31 Score=26.43 Aligned_cols=22 Identities=14% Similarity=0.036 Sum_probs=17.9
Q ss_pred HHHHHHHhhcCCCCCccccccC
Q psy17899 120 EKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 120 ~e~~~LA~~l~L~~~vVrVWFq 141 (145)
....+||+.||++..+|+++..
T Consensus 130 ~s~~EIA~~LgiS~~tVk~~l~ 151 (188)
T PRK12546 130 FSYEEAAEMCGVAVGTVKSRAN 151 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 3457899999999999998754
No 209
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=24.65 E-value=23 Score=21.16 Aligned_cols=20 Identities=25% Similarity=0.318 Sum_probs=16.8
Q ss_pred HHHHHHhhcCCCCCcccccc
Q psy17899 121 KIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 121 e~~~LA~~l~L~~~vVrVWF 140 (145)
.+..+|+.+|++..+|+-+|
T Consensus 29 s~~~vA~~~~vs~~TV~ri~ 48 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIF 48 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 46788999999999988665
No 210
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=24.64 E-value=39 Score=25.51 Aligned_cols=20 Identities=15% Similarity=0.006 Sum_probs=16.6
Q ss_pred HHHHHHhhcCCCCCcccccc
Q psy17899 121 KIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 121 e~~~LA~~l~L~~~vVrVWF 140 (145)
...+||+.+|+++.+|++..
T Consensus 148 s~~EIA~~lgis~~tVk~~l 167 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRV 167 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 35789999999999998753
No 211
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. 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 RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=24.54 E-value=51 Score=26.78 Aligned_cols=38 Identities=18% Similarity=0.293 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRP 138 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrV 138 (145)
.+++.++.+|..+|... ......+||+.+|++...|+-
T Consensus 218 ~L~~rer~vl~l~y~~~---~~~t~~eIA~~lgvS~~~V~q 255 (270)
T TIGR02392 218 SLDARSRRIIEARWLDD---DKLTLQELAAEYGVSAERIRQ 255 (270)
T ss_pred cCCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHH
Confidence 46778888999888531 133567999999999988874
No 212
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=24.08 E-value=50 Score=25.01 Aligned_cols=21 Identities=19% Similarity=0.161 Sum_probs=17.0
Q ss_pred HHHHHHHhhcCCCCCcccccc
Q psy17899 120 EKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 120 ~e~~~LA~~l~L~~~vVrVWF 140 (145)
....+||+.+|++..+|++-.
T Consensus 158 ~s~~EIA~~lgis~~tVk~rl 178 (194)
T PRK12531 158 LPHQQVAEMFDIPLGTVKSRL 178 (194)
T ss_pred CCHHHHHHHhCcCHHHHHHHH
Confidence 346789999999999998643
No 213
>PRK13558 bacterio-opsin activator; Provisional
Probab=24.06 E-value=60 Score=29.31 Aligned_cols=40 Identities=10% Similarity=0.231 Sum_probs=33.5
Q ss_pred CCCCHHHHHHHHHhhhcC--CCCCHHHHHHHHhhcCCCCCcc
Q psy17899 97 TSIAAPEKRSLEAYFAVQ--PRPSGEKIAAIAEKLDLKKNVV 136 (145)
Q Consensus 97 Ts~s~~q~~~Le~~F~~n--p~Ps~~e~~~LA~~l~L~~~vV 136 (145)
..+|+.|.++|+..+..- -.|=....++||+.||++..++
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~ 647 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTF 647 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 469999999999999876 3566778899999999987665
No 214
>PTZ00478 Sec superfamily; Provisional
Probab=24.05 E-value=47 Score=23.12 Aligned_cols=24 Identities=13% Similarity=0.191 Sum_probs=19.7
Q ss_pred HHhhhcCCCCCHHHHHHHHhhcCC
Q psy17899 108 EAYFAVQPRPSGEKIAAIAEKLDL 131 (145)
Q Consensus 108 e~~F~~np~Ps~~e~~~LA~~l~L 131 (145)
...+.+|.+|+.+|-..+|...++
T Consensus 31 ~r~vkrctKPdrkEf~kiakat~i 54 (81)
T PTZ00478 31 RRLIRKCTKPDAKEYTNIAYACSV 54 (81)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHH
Confidence 345678999999999999987654
No 215
>PRK00754 signal recognition particle protein Srp19; Provisional
Probab=23.94 E-value=72 Score=22.60 Aligned_cols=29 Identities=34% Similarity=0.327 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHHhhcCCCCCcc------ccccCcc
Q psy17899 115 PRPSGEKIAAIAEKLDLKKNVV------RPINGHT 143 (145)
Q Consensus 115 p~Ps~~e~~~LA~~l~L~~~vV------rVWFqNr 143 (145)
..|+.+||.+.+++|||+..+- +-||.|.
T Consensus 33 ~~P~~~EI~~a~~~lgl~~~~e~~K~yPr~~~e~~ 67 (95)
T PRK00754 33 KEPRLEEIIEAAEKLGLNPEVEPDKAYPRSWWEVS 67 (95)
T ss_pred cCCCHHHHHHHHHHcCCCeEEeeCCCCCchHhcCC
Confidence 5899999999999999985443 3577543
No 216
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=23.93 E-value=46 Score=25.33 Aligned_cols=36 Identities=11% Similarity=0.011 Sum_probs=23.4
Q ss_pred CHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 100 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 100 s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
++.++.++.-.|.. .....+||+.||+++.+|++..
T Consensus 118 p~~~r~i~~L~~~~-----g~s~~EIA~~Lgis~~tVk~~l 153 (187)
T PRK12516 118 PDDQREAIILVGAS-----GFAYEEAAEICGCAVGTIKSRV 153 (187)
T ss_pred CHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHH
Confidence 34455555443322 2345689999999999998764
No 217
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=23.89 E-value=48 Score=24.50 Aligned_cols=37 Identities=19% Similarity=0.111 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+++.++.++.-.+... ....+||+.+|++..+|+++.
T Consensus 120 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK12523 120 LSSKARAAFLYNRLDG-----MGHAEIAERLGVSVSRVRQYL 156 (172)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHH
Confidence 4456666666544322 345789999999999998764
No 218
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=23.85 E-value=26 Score=26.99 Aligned_cols=30 Identities=20% Similarity=0.287 Sum_probs=0.0
Q ss_pred HHhhh-cCCCCCHHHHHHHHhhcCCCCCccc
Q psy17899 108 EAYFA-VQPRPSGEKIAAIAEKLDLKKNVVR 137 (145)
Q Consensus 108 e~~F~-~np~Ps~~e~~~LA~~l~L~~~vVr 137 (145)
..+|. ...++.+-.+.+||+.||+++.+|-
T Consensus 37 ~~ff~~g~~~l~PLt~~~iA~~lgl~~STVS 67 (160)
T PF04552_consen 37 KDFFLGGPGALKPLTMKDIADELGLHESTVS 67 (160)
T ss_dssp -------------------------------
T ss_pred HHHHhcCcccCcCCCHHHHHHHhCCCHhHHH
Confidence 34555 2457788899999999999999874
No 219
>COG1983 PspC Putative stress-responsive transcriptional regulator [Transcription / Signal transduction mechanisms]
Probab=23.80 E-value=22 Score=24.01 Aligned_cols=20 Identities=20% Similarity=0.293 Sum_probs=17.0
Q ss_pred HHHHHHhhcCCCCCcccccc
Q psy17899 121 KIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 121 e~~~LA~~l~L~~~vVrVWF 140 (145)
...-||+-+|+|...||+||
T Consensus 17 VcgGla~yf~id~tlVRll~ 36 (70)
T COG1983 17 VCGGLAEYFGIDPTLVRLLF 36 (70)
T ss_pred eehhHHHHhCCChHHHHHHH
Confidence 35678999999999999886
No 220
>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=23.71 E-value=33 Score=20.39 Aligned_cols=36 Identities=17% Similarity=0.307 Sum_probs=21.7
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
+++++.+..-..+..- ..+.+||+.+|++..+|.-+
T Consensus 6 ~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRY 41 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHH
T ss_pred CCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHH
Confidence 5554444444444332 56889999999999888644
No 221
>PHA02955 hypothetical protein; Provisional
Probab=23.71 E-value=94 Score=25.34 Aligned_cols=41 Identities=7% Similarity=-0.014 Sum_probs=30.5
Q ss_pred HHHHHHHHhhhcC-CCCCHHHHHHHHhhcCCCCCccccccCc
Q psy17899 102 PEKRSLEAYFAVQ-PRPSGEKIAAIAEKLDLKKNVVRPINGH 142 (145)
Q Consensus 102 ~q~~~Le~~F~~n-p~Ps~~e~~~LA~~l~L~~~vVrVWFqN 142 (145)
.+...|-+.|... -..+.+++.++|.+||++-++|--||.+
T Consensus 61 ~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 61 KNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 4445555555443 5677889999999999999888888875
No 222
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=23.70 E-value=72 Score=20.64 Aligned_cols=31 Identities=16% Similarity=0.220 Sum_probs=20.5
Q ss_pred HHHHhhhcCCCCCHHHHHHHHhhcCCCCCccc
Q psy17899 106 SLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 137 (145)
Q Consensus 106 ~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVr 137 (145)
.+-.++..++-| .-...+||++||+++..|+
T Consensus 10 ~IL~~L~~~g~~-~~ta~eLa~~lgl~~~~v~ 40 (68)
T smart00550 10 KILEFLENSGDE-TSTALQLAKNLGLPKKEVN 40 (68)
T ss_pred HHHHHHHHCCCC-CcCHHHHHHHHCCCHHHHH
Confidence 334444455443 3557889999999988774
No 223
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=23.24 E-value=59 Score=18.48 Aligned_cols=16 Identities=13% Similarity=0.212 Sum_probs=11.7
Q ss_pred hhhcccchHHHHHHHh
Q psy17899 13 VLFTGVTQADVGKALA 28 (145)
Q Consensus 13 Ri~LG~TQ~dVg~alg 28 (145)
+|.+..|+.|++..+|
T Consensus 4 ~~~~~~s~~~la~~l~ 19 (48)
T smart00419 4 RVRLPLTRQEIAELLG 19 (48)
T ss_pred eEEeccCHHHHHHHHC
Confidence 4566778888888775
No 224
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=23.17 E-value=31 Score=25.04 Aligned_cols=39 Identities=13% Similarity=0.235 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccCccC
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
+++.+...+...+... ....|..||++..+|+.|=|+|+
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~ 82 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRK 82 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCc
Confidence 6666666666655332 34678889999999999999886
No 225
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=23.13 E-value=52 Score=24.61 Aligned_cols=21 Identities=19% Similarity=0.102 Sum_probs=17.4
Q ss_pred HHHHHHHhhcCCCCCcccccc
Q psy17899 120 EKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 120 ~e~~~LA~~l~L~~~vVrVWF 140 (145)
....+||+.+|+++.+|++..
T Consensus 146 ~s~~EIA~~l~is~~tV~~~l 166 (181)
T PRK12536 146 LSVAETAQLTGLSESAVKVGI 166 (181)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 456789999999999998754
No 226
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=23.08 E-value=57 Score=24.62 Aligned_cols=38 Identities=24% Similarity=0.385 Sum_probs=26.0
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+++.++.++.-.|.. .-...+||+.+|++..+|++..
T Consensus 131 ~L~~~~r~i~~l~~~~-----g~s~~EIAe~lgis~~~V~~~l 168 (189)
T PRK06811 131 DLEKLDREIFIRRYLL-----GEKIEEIAKKLGLTRSAIDNRL 168 (189)
T ss_pred hCCHHHHHHHHHHHHc-----cCCHHHHHHHHCCCHHHHHHHH
Confidence 3456666666654432 2446789999999999998753
No 227
>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=22.73 E-value=22 Score=25.56 Aligned_cols=38 Identities=16% Similarity=0.201 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
+|-+-+...-.++... .-+.++|..++++..+|..|++
T Consensus 3 YS~DlR~rVl~~~~~g-----~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 3 YSLDLRQRVLAYIEKG-----KSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CCHHHHHHHHHHHHcc-----chHHHHHHHhCcHHHHHHHHHH
Confidence 3444444444566542 3567789999999999999998
No 228
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=22.68 E-value=44 Score=24.71 Aligned_cols=35 Identities=17% Similarity=0.237 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRP 138 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrV 138 (145)
+++.++.++...|. ......+||+.||++..+|++
T Consensus 141 L~~~~r~vi~l~~~-----~g~s~~eIA~~lgis~~~v~~ 175 (189)
T TIGR02984 141 LPEDYREVILLRHL-----EGLSFAEVAERMDRSEGAVSM 175 (189)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHH
Confidence 45666666666442 344567899999999988864
No 229
>PRK05572 sporulation sigma factor SigF; Validated
Probab=22.67 E-value=48 Score=26.49 Aligned_cols=38 Identities=11% Similarity=0.186 Sum_probs=29.6
Q ss_pred CCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 97 TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 97 Ts~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
..+++.++.++..+|.. .....+||+.+|++...|+.+
T Consensus 201 ~~L~~~~~~v~~l~~~~-----~~s~~eIA~~lgis~~~V~~~ 238 (252)
T PRK05572 201 RELDERERLIVYLRYFK-----DKTQSEVAKRLGISQVQVSRL 238 (252)
T ss_pred HcCCHHHHHHHHHHHhC-----CCCHHHHHHHHCcCHHHHHHH
Confidence 35677888888888753 356789999999999988765
No 230
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=22.57 E-value=59 Score=20.82 Aligned_cols=19 Identities=21% Similarity=0.254 Sum_probs=15.6
Q ss_pred hhhhhcccchHHHHHHHhh
Q psy17899 11 SRVLFTGVTQADVGKALAN 29 (145)
Q Consensus 11 ~rRi~LG~TQ~dVg~alg~ 29 (145)
-.+|+.|.|++||=..||.
T Consensus 9 ~~~i~~GmTk~qV~~lLG~ 27 (71)
T PF04355_consen 9 LAQIKPGMTKDQVRALLGS 27 (71)
T ss_dssp HTTT-TTSBHHHHHHHHTS
T ss_pred HHhhcCCCCHHHHHHhcCC
Confidence 4578999999999999984
No 231
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=22.50 E-value=44 Score=21.22 Aligned_cols=19 Identities=16% Similarity=0.179 Sum_probs=15.1
Q ss_pred hhhcccchHHHHHHHhhcc
Q psy17899 13 VLFTGVTQADVGKALANLK 31 (145)
Q Consensus 13 Ri~LG~TQ~dVg~alg~l~ 31 (145)
.+.+.+||.+++..+|...
T Consensus 24 ~~~~~lt~~~iA~~~g~sr 42 (76)
T PF13545_consen 24 RIPLPLTQEEIADMLGVSR 42 (76)
T ss_dssp EEEEESSHHHHHHHHTSCH
T ss_pred eEEecCCHHHHHHHHCCCH
Confidence 5678899999999987543
No 232
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=22.39 E-value=52 Score=25.52 Aligned_cols=20 Identities=30% Similarity=0.278 Sum_probs=17.0
Q ss_pred HHHHHHhhcCCCCCcccccc
Q psy17899 121 KIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 121 e~~~LA~~l~L~~~vVrVWF 140 (145)
...+||+.||+++.+|+++.
T Consensus 156 s~~EIA~~Lgis~~tV~~~l 175 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRI 175 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 45789999999999998764
No 233
>PRK06930 positive control sigma-like factor; Validated
Probab=22.36 E-value=49 Score=25.47 Aligned_cols=39 Identities=21% Similarity=0.193 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
.+++.++.++.-+|..+ ....+||+.+|++..+|+++..
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~ 152 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIE 152 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHH
Confidence 46677777777654333 3467899999999999998754
No 234
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=22.00 E-value=62 Score=25.79 Aligned_cols=38 Identities=16% Similarity=0.220 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+++.++.++.-+|... ....+||+.+|++...|+.+.
T Consensus 205 ~L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~ 242 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQ 242 (255)
T ss_pred cCCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 45677788887776443 345799999999999998765
No 235
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=21.88 E-value=58 Score=24.96 Aligned_cols=37 Identities=16% Similarity=0.096 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+++.++.++.-.|... ....+||+.+|++..+|++..
T Consensus 140 Lp~~~r~v~~L~~~eg-----~s~~EIA~~lgis~~tVk~~l 176 (201)
T PRK12545 140 LPEQIGRVFMMREFLD-----FEIDDICTELTLTANHCSVLL 176 (201)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 3344455544433222 346789999999999998753
No 236
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=21.77 E-value=66 Score=25.06 Aligned_cols=38 Identities=26% Similarity=0.386 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
.+++.++.+|...|... ....+||+.+|++...|+.+.
T Consensus 175 ~L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~ 212 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIH 212 (224)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHH
Confidence 35677888888876433 346889999999999998764
No 237
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=21.77 E-value=54 Score=25.67 Aligned_cols=41 Identities=15% Similarity=0.307 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
+++.++.++.-+|.- .+-......+||+.+|++..+|+++.
T Consensus 179 Lp~~~R~v~~L~y~l-~~~eg~s~~EIA~~lgis~~tVk~~~ 219 (234)
T PRK08301 179 LSDREKQIMELRFGL-NGGEEKTQKEVADMLGISQSYISRLE 219 (234)
T ss_pred CCHHHHHHHHHHhcc-CCCCCCCHHHHHHHHCCCHHHHHHHH
Confidence 456666666665511 01223447789999999999998764
No 238
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=21.76 E-value=74 Score=26.99 Aligned_cols=38 Identities=18% Similarity=0.430 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHhhhcC-CCCCHHHHHHHHhhcCCCCCccc
Q psy17899 98 SIAAPEKRSLEAYFAVQ-PRPSGEKIAAIAEKLDLKKNVVR 137 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~n-p~Ps~~e~~~LA~~l~L~~~vVr 137 (145)
.+++.++.+|..+|..+ ..| ....+||+.+|++++.|+
T Consensus 262 ~L~eREr~Vl~~rygl~~~~~--~Tl~eIa~~lgvS~eRVr 300 (324)
T PRK07921 262 TLDEREQQVIRLRFGLDDGQP--RTLDQIGKLFGLSRERVR 300 (324)
T ss_pred hCCHHHHHHHHHHHhcCCCCC--cCHHHHHHHHCCCHHHHH
Confidence 47788889999999643 222 357899999999998886
No 239
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=21.61 E-value=78 Score=27.50 Aligned_cols=39 Identities=15% Similarity=0.397 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRP 138 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrV 138 (145)
+++.+..++...|... -......++||+.+|++++.||-
T Consensus 280 Lt~rE~~Vi~~R~gl~-~~~~~TLeevg~~~~isrERvRQ 318 (342)
T COG0568 280 LTERERRVIRLRFGLD-DGEPKTLEELGEEFGISRERVRQ 318 (342)
T ss_pred CCHHHHHHHHHHhccC-CCCcchHHHHHHHhCCcHHHHHH
Confidence 8999999999999986 33467889999999999998874
No 240
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=21.29 E-value=29 Score=20.67 Aligned_cols=17 Identities=41% Similarity=0.593 Sum_probs=12.0
Q ss_pred HHHHHHhhcCCCCCccc
Q psy17899 121 KIAAIAEKLDLKKNVVR 137 (145)
Q Consensus 121 e~~~LA~~l~L~~~vVr 137 (145)
-..+||+.+|+++..|.
T Consensus 19 s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 19 SYAELAEELGLSESTVR 35 (42)
T ss_dssp -HHHHHHHHTS-HHHHH
T ss_pred cHHHHHHHHCcCHHHHH
Confidence 34578999999988774
No 241
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=21.20 E-value=61 Score=23.48 Aligned_cols=20 Identities=25% Similarity=0.313 Sum_probs=16.2
Q ss_pred HHHHHHHhhcCCCCCccccc
Q psy17899 120 EKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 120 ~e~~~LA~~l~L~~~vVrVW 139 (145)
....+||+.+|+++.+|++.
T Consensus 122 ~s~~eIA~~lgis~~tv~~~ 141 (159)
T PRK12527 122 LSHQQIAEHLGISRSLVEKH 141 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHH
Confidence 34678999999999998764
No 242
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=21.18 E-value=58 Score=24.48 Aligned_cols=36 Identities=8% Similarity=0.085 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
+++.++.++.-.|... ....+||+.+|+++.+|++.
T Consensus 132 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~ 167 (191)
T PRK12520 132 LPPRTGRVFMMREWLE-----LETEEICQELQITATNAWVL 167 (191)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHH
Confidence 4455666665554332 34678999999999999875
No 243
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=21.17 E-value=1.1e+02 Score=23.88 Aligned_cols=35 Identities=20% Similarity=0.054 Sum_probs=30.0
Q ss_pred HHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcc
Q psy17899 102 PEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVV 136 (145)
Q Consensus 102 ~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vV 136 (145)
.-...|...+.+.-|-+...+..||+.||++...|
T Consensus 26 Alip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 26 ALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 35667888888888999999999999999997655
No 244
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=21.15 E-value=37 Score=26.73 Aligned_cols=36 Identities=22% Similarity=0.337 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccc
Q psy17899 97 TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRP 138 (145)
Q Consensus 97 Ts~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrV 138 (145)
..+|+.++++|+-.-. +..-.+||++|++++.+|+.
T Consensus 133 ~~LT~RE~eVL~ll~~------G~snkeIA~~L~iS~~TV~~ 168 (207)
T PRK11475 133 RMLSPTEREILRFMSR------GYSMPQIAEQLERNIKTIRA 168 (207)
T ss_pred CCCCHHHHHHHHHHHC------CCCHHHHHHHHCCCHHHHHH
Confidence 4589999999988663 44567899999999999875
No 245
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=21.00 E-value=54 Score=26.28 Aligned_cols=37 Identities=19% Similarity=0.253 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 98 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 98 s~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
.+++.++.+++..|..+ ....+||+.+|++..+|+..
T Consensus 209 ~L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~V~~~ 245 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQVSRL 245 (258)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHH
Confidence 57788888998888532 34788999999999988764
No 246
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=20.98 E-value=66 Score=25.32 Aligned_cols=38 Identities=18% Similarity=0.309 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
+++.++.++...|.. .....+||+.+|++..+|+++..
T Consensus 185 L~~~~r~vl~l~~~~-----g~s~~EIA~~lgis~~tV~~~~~ 222 (236)
T PRK06986 185 LPEREQLVLSLYYQE-----ELNLKEIGAVLGVSESRVSQIHS 222 (236)
T ss_pred CCHHHHHHHHhHhcc-----CCCHHHHHHHHCCCHHHHHHHHH
Confidence 456666666666533 23578899999999999998754
No 247
>KOG3755|consensus
Probab=20.83 E-value=47 Score=31.36 Aligned_cols=54 Identities=30% Similarity=0.411 Sum_probs=46.6
Q ss_pred CCCCCCCCCHHHHHHHHHhhh-cCCCCCHHH---HHHHHhhcCCCCCccccccCccCC
Q psy17899 92 KKRKRTSIAAPEKRSLEAYFA-VQPRPSGEK---IAAIAEKLDLKKNVVRPINGHTRA 145 (145)
Q Consensus 92 krR~RTs~s~~q~~~Le~~F~-~np~Ps~~e---~~~LA~~l~L~~~vVrVWFqNrRa 145 (145)
+.++||-|+-+-..+|...-. .--||+... +..|+.++++++..+---|||.|.
T Consensus 647 ~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ 704 (769)
T KOG3755|consen 647 KPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRY 704 (769)
T ss_pred CccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhccee
Confidence 678899999999999887654 447899888 999999999999999999999873
No 248
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=20.82 E-value=68 Score=26.85 Aligned_cols=48 Identities=21% Similarity=0.234 Sum_probs=34.5
Q ss_pred chhhhhhhhcccchHHHHHHHhhc-------------cCCCCccchhhhhhhh-hhcCCChHH
Q psy17899 7 PDVYSRVLFTGVTQADVGKALANL-------------KLPGVGALSQSTICRF-ESLTLSHNN 55 (145)
Q Consensus 7 ~~f~~rRi~LG~TQ~dVg~alg~l-------------~~~g~~~fSQttIcRF-E~L~LS~kn 55 (145)
-.||+.|..+|+|+.||...++.- -+|| ..|.|..|-.+ |.|+|-...
T Consensus 6 e~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~-~~y~rG~ir~YA~~l~ld~~~ 67 (284)
T COG1426 6 ERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPG-PVYIRGYIRSYAKFLGLDEDE 67 (284)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCccHHHHHHHhcCccccccc-hHHHHHHHHHHHHHhCCCHHH
Confidence 358999999999999999887431 1456 67888877754 447765533
No 249
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=20.59 E-value=56 Score=25.09 Aligned_cols=21 Identities=14% Similarity=0.124 Sum_probs=17.5
Q ss_pred HHHHHHHhhcCCCCCcccccc
Q psy17899 120 EKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 120 ~e~~~LA~~l~L~~~vVrVWF 140 (145)
....+||+.+|++..+|+++.
T Consensus 150 ~s~~EIAe~lgis~~tV~~~l 170 (196)
T PRK12535 150 YTYEEAAKIADVRVGTIRSRV 170 (196)
T ss_pred CCHHHHHHHhCCCHHHHHHHH
Confidence 346789999999999998864
No 250
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=20.58 E-value=57 Score=24.73 Aligned_cols=36 Identities=11% Similarity=0.195 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
+++.++.++.-.|.. .....+||+.+|++...|++.
T Consensus 132 L~~~~r~v~~l~~~~-----g~s~~EIA~~lgis~~tvk~r 167 (188)
T TIGR02943 132 LPEQTARVFMMREVL-----GFESDEICQELEISTSNCHVL 167 (188)
T ss_pred CCHHHHHHHHHHHHh-----CCCHHHHHHHhCCCHHHHHHH
Confidence 344555555554432 245688999999999998764
No 251
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=20.49 E-value=83 Score=25.95 Aligned_cols=40 Identities=25% Similarity=0.427 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccc
Q psy17899 99 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPI 139 (145)
Q Consensus 99 ~s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVW 139 (145)
+++.++.+|...|...-. ......+||+.+|++++.|+..
T Consensus 250 L~~rer~Vi~lr~gl~~~-~~~Tl~EIa~~lgiS~erVrq~ 289 (298)
T TIGR02997 250 LTPRERQVLRLRFGLDGG-EPLTLAEIGRRLNLSRERVRQI 289 (298)
T ss_pred CCHHHHHHHHHHhccCCC-CCcCHHHHHHHHCcCHHHHHHH
Confidence 677888888888853211 1245889999999999999853
No 252
>PTZ00183 centrin; Provisional
Probab=20.29 E-value=3e+02 Score=19.32 Aligned_cols=38 Identities=11% Similarity=0.273 Sum_probs=29.7
Q ss_pred CCCCCCCHHHHHHHHHhhhc-----CCCCCHHHHHHHHhhcCC
Q psy17899 94 RKRTSIAAPEKRSLEAYFAV-----QPRPSGEKIAAIAEKLDL 131 (145)
Q Consensus 94 R~RTs~s~~q~~~Le~~F~~-----np~Ps~~e~~~LA~~l~L 131 (145)
--++.++..+...++..|.. +.+.+..+...+-..+|+
T Consensus 6 ~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 6 SERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred cccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 34788999999999999863 566788888887777775
No 253
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=20.28 E-value=50 Score=26.05 Aligned_cols=36 Identities=14% Similarity=-0.065 Sum_probs=23.7
Q ss_pred CHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCcccccc
Q psy17899 100 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPIN 140 (145)
Q Consensus 100 s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWF 140 (145)
++.++.++.-+|.. .....+||+.||+++.+|+++.
T Consensus 136 p~~~R~v~~L~y~e-----g~s~~EIAe~LgiS~~tVk~~L 171 (216)
T PRK12533 136 PVEYREVLVLRELE-----DMSYREIAAIADVPVGTVMSRL 171 (216)
T ss_pred CHHHHhHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHH
Confidence 34455555554432 2345789999999999998753
No 254
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=20.20 E-value=67 Score=21.82 Aligned_cols=21 Identities=5% Similarity=0.159 Sum_probs=16.2
Q ss_pred HHHHHHhhcCCCCCccccccC
Q psy17899 121 KIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 121 e~~~LA~~l~L~~~vVrVWFq 141 (145)
-...|...++|+..+|.||+.
T Consensus 55 L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 55 LTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHHhCCCCCeEEEEEE
Confidence 345567777999999999975
No 255
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=20.14 E-value=39 Score=21.82 Aligned_cols=23 Identities=17% Similarity=0.172 Sum_probs=18.2
Q ss_pred HHHHHhhcCCCCCccccccCccC
Q psy17899 122 IAAIAEKLDLKKNVVRPINGHTR 144 (145)
Q Consensus 122 ~~~LA~~l~L~~~vVrVWFqNrR 144 (145)
+.+||+.+|++..+|--.+.+++
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln~~~ 25 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLNGNG 25 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCC
Confidence 56899999999988877776653
No 256
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=20.12 E-value=1.5e+02 Score=18.02 Aligned_cols=32 Identities=13% Similarity=0.126 Sum_probs=24.7
Q ss_pred CHHHHHHHHHhhhcCCCCCHHHHHHHHhhcCCCCCccccccC
Q psy17899 100 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPING 141 (145)
Q Consensus 100 s~~q~~~Le~~F~~np~Ps~~e~~~LA~~l~L~~~vVrVWFq 141 (145)
|.+|+..|-+.+ -..+++.+|++++.|.|.|.
T Consensus 13 s~eqk~~l~~~i----------t~~l~~~~~~p~~~v~V~i~ 44 (61)
T PRK02220 13 TEEQLKALVKDV----------TAAVSKNTGAPAEHIHVIIN 44 (61)
T ss_pred CHHHHHHHHHHH----------HHHHHHHhCcChhhEEEEEE
Confidence 678888877644 45688899999888888764
No 257
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=20.11 E-value=51 Score=23.70 Aligned_cols=23 Identities=9% Similarity=0.107 Sum_probs=19.1
Q ss_pred HHHHHHHhhcCCCCCccccccCc
Q psy17899 120 EKIAAIAEKLDLKKNVVRPINGH 142 (145)
Q Consensus 120 ~e~~~LA~~l~L~~~vVrVWFqN 142 (145)
-.+++||+.+|+++..++-+|+.
T Consensus 26 ~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 26 LSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 55688899999999999888763
Done!