Query 035661
Match_columns 211
No_of_seqs 215 out of 1524
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 05:08:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035661.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035661hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.8 8.9E-21 1.9E-25 157.7 8.5 102 17-118 50-151 (198)
2 KOG0489 Transcription factor z 99.8 4.1E-19 8.8E-24 154.1 4.9 64 13-76 155-218 (261)
3 KOG0488 Transcription factor B 99.7 7E-18 1.5E-22 149.4 5.9 69 10-78 165-233 (309)
4 KOG0843 Transcription factor E 99.7 1.2E-17 2.7E-22 135.3 5.3 64 16-79 101-164 (197)
5 KOG0842 Transcription factor t 99.7 1.1E-17 2.4E-22 146.8 4.4 71 13-83 149-219 (307)
6 KOG2251 Homeobox transcription 99.7 3.4E-17 7.4E-22 136.6 5.8 69 10-78 30-98 (228)
7 KOG4577 Transcription factor L 99.7 8.7E-17 1.9E-21 138.8 8.0 78 17-94 167-244 (383)
8 KOG0487 Transcription factor A 99.7 2E-17 4.2E-22 145.3 3.7 66 14-79 232-297 (308)
9 KOG0484 Transcription factor P 99.7 2.4E-17 5.1E-22 122.9 3.5 67 10-76 10-76 (125)
10 PF00046 Homeobox: Homeobox do 99.7 1.2E-16 2.5E-21 107.4 5.3 57 18-74 1-57 (57)
11 KOG0494 Transcription factor C 99.6 1.5E-16 3.3E-21 135.5 5.0 74 16-89 140-213 (332)
12 KOG0850 Transcription factor D 99.6 3E-16 6.4E-21 131.7 5.3 65 13-77 118-182 (245)
13 KOG0485 Transcription factor N 99.6 5.4E-16 1.2E-20 129.2 3.7 61 16-76 103-163 (268)
14 KOG0848 Transcription factor C 99.6 6.3E-16 1.4E-20 132.2 3.6 61 18-78 200-260 (317)
15 KOG0492 Transcription factor M 99.6 2E-15 4.3E-20 125.0 5.4 60 17-76 144-203 (246)
16 TIGR01565 homeo_ZF_HD homeobox 99.6 2.2E-15 4.9E-20 102.1 4.7 53 17-69 1-57 (58)
17 KOG0493 Transcription factor E 99.6 1.8E-15 3.9E-20 129.1 4.9 59 18-76 247-305 (342)
18 smart00389 HOX Homeodomain. DN 99.5 7.8E-15 1.7E-19 97.7 5.2 55 19-73 2-56 (56)
19 cd00086 homeodomain Homeodomai 99.5 1.2E-14 2.7E-19 97.4 5.8 57 19-75 2-58 (59)
20 KOG3802 Transcription factor O 99.5 6E-15 1.3E-19 132.4 3.0 61 16-76 293-353 (398)
21 COG5576 Homeodomain-containing 99.5 5.5E-14 1.2E-18 113.3 5.7 66 13-78 47-112 (156)
22 KOG0844 Transcription factor E 99.4 4.2E-14 9.1E-19 123.1 2.0 63 16-78 180-242 (408)
23 KOG0491 Transcription factor B 99.4 5.6E-14 1.2E-18 112.7 1.2 65 14-78 97-161 (194)
24 KOG0847 Transcription factor, 99.3 2.9E-12 6.3E-17 107.2 3.4 62 15-76 165-226 (288)
25 KOG0486 Transcription factor P 99.2 6.4E-12 1.4E-16 109.9 2.9 61 16-76 111-171 (351)
26 KOG0490 Transcription factor, 99.2 1.8E-11 3.9E-16 102.9 3.7 63 14-76 57-119 (235)
27 KOG0849 Transcription factor P 99.0 1.8E-10 3.9E-15 104.1 5.0 68 9-76 168-235 (354)
28 KOG1168 Transcription factor A 99.0 8.9E-11 1.9E-15 101.9 2.7 64 13-76 305-368 (385)
29 KOG0775 Transcription factor S 98.8 2.4E-09 5.2E-14 92.3 4.4 52 23-74 182-233 (304)
30 PF05920 Homeobox_KN: Homeobox 98.4 1.8E-07 3.9E-12 58.8 2.5 34 38-71 7-40 (40)
31 KOG2252 CCAAT displacement pro 98.4 4.3E-07 9.2E-12 85.0 5.7 61 14-74 417-477 (558)
32 KOG0774 Transcription factor P 98.2 5.9E-07 1.3E-11 77.3 2.9 58 18-75 189-249 (334)
33 KOG0490 Transcription factor, 98.1 2.7E-06 5.8E-11 71.4 4.3 63 14-76 150-212 (235)
34 KOG1146 Homeobox protein [Gene 97.4 0.0001 2.2E-09 75.2 3.5 65 14-78 900-964 (1406)
35 KOG0773 Transcription factor M 96.7 0.002 4.3E-08 57.9 4.3 62 15-76 237-301 (342)
36 PF11569 Homez: Homeodomain le 96.5 0.0013 2.8E-08 44.2 1.6 41 29-69 10-50 (56)
37 PF02183 HALZ: Homeobox associ 95.8 0.039 8.5E-07 35.4 5.5 42 76-117 2-43 (45)
38 PRK09413 IS2 repressor TnpA; R 94.8 0.16 3.4E-06 39.0 7.1 94 20-117 9-102 (121)
39 PF04218 CENP-B_N: CENP-B N-te 94.7 0.069 1.5E-06 35.2 4.4 46 18-68 1-46 (53)
40 KOG3623 Homeobox transcription 94.3 0.05 1.1E-06 53.3 4.1 48 29-76 568-615 (1007)
41 smart00340 HALZ homeobox assoc 92.4 0.34 7.4E-06 30.6 4.3 32 76-107 2-33 (44)
42 smart00338 BRLZ basic region l 88.2 3.4 7.3E-05 28.0 6.9 39 78-116 25-63 (65)
43 PF00170 bZIP_1: bZIP transcri 87.3 4.8 0.0001 27.1 7.2 44 69-115 19-62 (64)
44 KOG4571 Activating transcripti 86.6 2.9 6.3E-05 37.1 7.1 44 76-119 245-288 (294)
45 PF01527 HTH_Tnp_1: Transposas 83.6 0.42 9.2E-06 32.9 0.5 47 19-69 2-48 (76)
46 PF02183 HALZ: Homeobox associ 82.5 3.9 8.4E-05 26.1 4.6 32 78-109 11-42 (45)
47 KOG3119 Basic region leucine z 82.1 6.9 0.00015 34.3 7.6 49 69-120 208-256 (269)
48 PRK00888 ftsB cell division pr 81.4 14 0.0003 27.7 8.0 54 60-114 16-69 (105)
49 KOG4196 bZIP transcription fac 80.5 26 0.00057 27.5 10.9 38 22-71 22-59 (135)
50 PF10224 DUF2205: Predicted co 78.9 18 0.00038 26.1 7.5 50 71-120 15-64 (80)
51 PF07716 bZIP_2: Basic region 78.9 9.8 0.00021 24.8 5.8 36 69-107 18-53 (54)
52 PF04545 Sigma70_r4: Sigma-70, 77.5 4.4 9.6E-05 25.6 3.7 41 23-68 4-44 (50)
53 PF10226 DUF2216: Uncharacteri 74.0 28 0.00062 29.1 8.4 29 85-113 114-142 (195)
54 cd06171 Sigma70_r4 Sigma70, re 73.6 3.4 7.4E-05 25.2 2.4 43 23-70 10-52 (55)
55 KOG0709 CREB/ATF family transc 71.5 16 0.00035 34.5 7.1 93 21-120 218-313 (472)
56 PF04967 HTH_10: HTH DNA bindi 69.0 6.1 0.00013 26.1 2.8 39 24-62 1-41 (53)
57 KOG1146 Homeobox protein [Gene 65.1 8.2 0.00018 40.8 4.2 67 10-76 698-764 (1406)
58 PF08172 CASP_C: CASP C termin 61.8 51 0.0011 28.6 8.0 45 69-113 90-134 (248)
59 cd00569 HTH_Hin_like Helix-tur 61.2 16 0.00035 19.6 3.4 38 23-65 5-42 (42)
60 PF00170 bZIP_1: bZIP transcri 60.6 48 0.001 22.1 6.5 41 69-109 23-63 (64)
61 PF15058 Speriolin_N: Sperioli 59.7 26 0.00056 29.4 5.5 38 80-118 6-43 (200)
62 PRK03975 tfx putative transcri 59.5 26 0.00056 27.8 5.3 48 21-74 4-51 (141)
63 PF14645 Chibby: Chibby family 58.3 25 0.00054 26.9 4.9 28 90-117 75-102 (116)
64 PF10668 Phage_terminase: Phag 58.2 5.7 0.00012 27.0 1.2 21 46-66 24-44 (60)
65 PF08281 Sigma70_r4_2: Sigma-7 57.4 23 0.00049 22.4 4.0 42 23-69 10-51 (54)
66 KOG4343 bZIP transcription fac 56.4 24 0.00053 34.0 5.4 38 78-115 301-338 (655)
67 PF13936 HTH_38: Helix-turn-he 55.7 12 0.00026 23.3 2.3 41 21-66 2-42 (44)
68 COG3416 Uncharacterized protei 55.4 1.3E+02 0.0029 25.6 9.9 18 24-41 1-18 (233)
69 PRK04217 hypothetical protein; 55.2 43 0.00094 25.4 5.7 47 19-70 38-84 (110)
70 PF06005 DUF904: Protein of un 55.2 70 0.0015 22.4 7.1 30 82-111 28-57 (72)
71 PF06156 DUF972: Protein of un 54.9 44 0.00095 25.2 5.7 33 80-112 23-55 (107)
72 PF09607 BrkDBD: Brinker DNA-b 51.1 21 0.00046 24.1 3.0 44 21-66 3-47 (58)
73 COG3413 Predicted DNA binding 51.1 23 0.0005 29.5 4.0 49 23-73 155-205 (215)
74 cd04765 HTH_MlrA-like_sg2 Heli 49.8 60 0.0013 23.8 5.7 38 18-67 33-70 (99)
75 PRK13169 DNA replication intia 49.5 59 0.0013 24.7 5.6 32 80-111 23-54 (110)
76 PF00424 REV: REV protein (ant 48.7 23 0.0005 26.1 3.1 33 30-76 15-47 (91)
77 KOG4005 Transcription factor X 48.7 84 0.0018 27.4 7.0 9 66-74 82-90 (292)
78 PF00196 GerE: Bacterial regul 48.3 31 0.00066 22.4 3.5 46 22-73 2-47 (58)
79 TIGR03752 conj_TIGR03752 integ 47.6 56 0.0012 31.1 6.3 92 23-117 41-133 (472)
80 cd01106 HTH_TipAL-Mta Helix-Tu 46.8 1.1E+02 0.0024 22.2 8.1 37 19-68 34-70 (103)
81 PRK00118 putative DNA-binding 46.3 1.1E+02 0.0024 22.9 6.6 47 23-74 17-63 (104)
82 cd01109 HTH_YyaN Helix-Turn-He 46.0 1.2E+02 0.0026 22.4 9.0 38 18-68 33-70 (113)
83 TIGR02051 MerR Hg(II)-responsi 45.8 1.3E+02 0.0028 22.8 8.3 40 16-68 30-69 (124)
84 PF06156 DUF972: Protein of un 44.7 1.3E+02 0.0029 22.6 7.0 45 76-120 12-56 (107)
85 PF13443 HTH_26: Cro/C1-type H 44.7 19 0.00041 23.5 2.1 28 46-73 12-39 (63)
86 PF07334 IFP_35_N: Interferon- 44.5 57 0.0012 23.3 4.5 27 89-115 3-29 (76)
87 cd04766 HTH_HspR Helix-Turn-He 44.2 1.1E+02 0.0025 21.6 6.4 34 20-65 35-68 (91)
88 PRK00888 ftsB cell division pr 43.7 69 0.0015 23.9 5.2 38 64-101 26-63 (105)
89 PF13518 HTH_28: Helix-turn-he 42.2 18 0.0004 22.4 1.6 23 46-68 14-36 (52)
90 PRK14127 cell division protein 41.8 88 0.0019 23.8 5.5 35 84-118 35-69 (109)
91 smart00421 HTH_LUXR helix_turn 41.7 60 0.0013 19.8 4.1 39 23-67 3-41 (58)
92 KOG4005 Transcription factor X 41.6 1.6E+02 0.0035 25.7 7.6 36 78-113 110-145 (292)
93 PF13551 HTH_29: Winged helix- 41.2 75 0.0016 22.7 5.0 48 19-66 53-109 (112)
94 KOG4571 Activating transcripti 41.2 1.2E+02 0.0026 27.0 7.0 33 85-117 247-279 (294)
95 cd04783 HTH_MerR1 Helix-Turn-H 41.2 1.6E+02 0.0034 22.3 8.5 41 15-68 30-70 (126)
96 cd04770 HTH_HMRTR Helix-Turn-H 40.7 1.5E+02 0.0033 22.1 9.1 38 18-68 33-70 (123)
97 KOG3335 Predicted coiled-coil 39.7 64 0.0014 26.7 4.7 54 58-118 85-138 (181)
98 COG2963 Transposase and inacti 39.5 1.5E+02 0.0033 21.8 7.1 43 21-67 5-48 (116)
99 cd04779 HTH_MerR-like_sg4 Heli 39.4 1.8E+02 0.0039 22.6 8.9 38 19-69 33-70 (134)
100 KOG4403 Cell surface glycoprot 39.3 1.6E+02 0.0035 27.9 7.8 32 94-125 303-334 (575)
101 PRK06759 RNA polymerase factor 39.2 59 0.0013 24.8 4.4 28 46-73 124-151 (154)
102 cd04781 HTH_MerR-like_sg6 Heli 38.7 1.7E+02 0.0036 22.0 8.2 38 18-68 32-69 (120)
103 cd00131 PAX Paired Box domain 38.2 1E+02 0.0022 23.7 5.6 47 21-67 73-126 (128)
104 cd04769 HTH_MerR2 Helix-Turn-H 37.3 1.7E+02 0.0037 21.7 8.3 38 20-70 34-71 (116)
105 PRK09652 RNA polymerase sigma 37.3 36 0.00077 26.5 2.9 43 24-71 129-171 (182)
106 smart00338 BRLZ basic region l 37.2 1.2E+02 0.0027 20.1 6.0 29 79-107 33-61 (65)
107 PF07407 Seadorna_VP6: Seadorn 36.9 53 0.0011 29.9 4.1 29 81-109 34-62 (420)
108 PF07407 Seadorna_VP6: Seadorn 36.6 59 0.0013 29.7 4.4 26 77-102 37-62 (420)
109 PRK12514 RNA polymerase sigma 36.5 41 0.00088 26.5 3.2 29 46-74 147-175 (179)
110 PF04880 NUDE_C: NUDE protein, 36.4 27 0.00059 28.5 2.1 20 90-109 28-47 (166)
111 cd04761 HTH_MerR-SF Helix-Turn 36.4 23 0.00051 21.6 1.4 23 47-69 3-25 (49)
112 PF11594 Med28: Mediator compl 36.3 1.9E+02 0.0041 21.9 6.8 56 59-117 18-73 (106)
113 PRK11924 RNA polymerase sigma 36.2 38 0.00081 26.3 2.9 28 46-73 143-170 (179)
114 PF06005 DUF904: Protein of un 35.9 1.5E+02 0.0033 20.7 7.7 42 76-117 15-56 (72)
115 cd04787 HTH_HMRTR_unk Helix-Tu 35.8 2E+02 0.0043 22.0 8.8 37 19-68 34-70 (133)
116 TIGR03879 near_KaiC_dom probab 35.7 11 0.00023 26.7 -0.3 35 33-67 21-55 (73)
117 PRK09646 RNA polymerase sigma 35.7 56 0.0012 26.3 3.9 29 46-74 160-188 (194)
118 PRK13922 rod shape-determining 35.2 1.1E+02 0.0024 26.3 5.9 40 80-119 70-112 (276)
119 PF04977 DivIC: Septum formati 34.6 1.4E+02 0.0031 20.1 5.4 38 76-113 21-58 (80)
120 TIGR02937 sigma70-ECF RNA poly 34.5 47 0.001 24.4 3.1 44 24-72 111-154 (158)
121 KOG0977 Nuclear envelope prote 34.2 1.9E+02 0.004 28.2 7.6 43 75-117 151-193 (546)
122 PRK13169 DNA replication intia 34.0 2.1E+02 0.0045 21.7 7.0 45 76-120 12-56 (110)
123 TIGR02044 CueR Cu(I)-responsiv 33.6 2.1E+02 0.0046 21.6 8.8 38 16-66 31-68 (127)
124 PF08280 HTH_Mga: M protein tr 33.4 38 0.00081 22.3 2.1 35 27-65 6-40 (59)
125 PRK09644 RNA polymerase sigma 33.3 94 0.002 24.1 4.8 28 47-74 127-154 (165)
126 KOG4343 bZIP transcription fac 33.1 62 0.0014 31.4 4.2 41 72-112 302-342 (655)
127 PRK10072 putative transcriptio 32.8 58 0.0013 24.1 3.2 41 23-70 32-72 (96)
128 KOG4196 bZIP transcription fac 32.7 2.5E+02 0.0054 22.2 7.2 31 81-111 83-113 (135)
129 PF06056 Terminase_5: Putative 31.4 29 0.00063 23.2 1.3 27 46-74 15-41 (58)
130 PRK12526 RNA polymerase sigma 30.9 54 0.0012 26.8 3.1 29 46-74 171-199 (206)
131 cd04775 HTH_Cfa-like Helix-Tur 30.7 2.1E+02 0.0046 20.8 8.0 41 14-67 29-69 (102)
132 PF01166 TSC22: TSC-22/dip/bun 30.7 1.2E+02 0.0027 20.5 4.2 30 85-114 13-42 (59)
133 TIGR00721 tfx DNA-binding prot 30.5 2E+02 0.0044 22.6 6.2 47 21-73 4-50 (137)
134 PRK09642 RNA polymerase sigma 30.5 98 0.0021 23.8 4.4 28 47-74 125-152 (160)
135 PF04977 DivIC: Septum formati 30.1 1.7E+02 0.0037 19.7 5.2 33 80-112 18-50 (80)
136 COG4367 Uncharacterized protei 30.1 52 0.0011 24.3 2.5 39 23-61 2-40 (97)
137 PF13384 HTH_23: Homeodomain-l 29.8 32 0.0007 21.3 1.3 23 45-67 18-40 (50)
138 PF02777 Sod_Fe_C: Iron/mangan 29.6 18 0.0004 26.7 0.1 22 181-203 17-38 (106)
139 cd06170 LuxR_C_like C-terminal 29.3 1.1E+02 0.0023 18.7 3.7 36 25-66 2-37 (57)
140 TIGR02985 Sig70_bacteroi1 RNA 29.2 60 0.0013 24.5 3.0 26 46-71 131-156 (161)
141 PF13411 MerR_1: MerR HTH fami 28.8 34 0.00074 22.6 1.3 23 47-69 3-25 (69)
142 PRK12519 RNA polymerase sigma 28.7 54 0.0012 26.2 2.7 30 44-73 157-186 (194)
143 PRK11546 zraP zinc resistance 28.6 1.7E+02 0.0038 23.3 5.5 18 21-38 41-58 (143)
144 TIGR02989 Sig-70_gvs1 RNA poly 28.0 1.2E+02 0.0025 23.2 4.4 26 45-70 128-153 (159)
145 PRK10884 SH3 domain-containing 27.9 3.2E+02 0.0069 23.0 7.3 30 84-113 137-166 (206)
146 PF14775 NYD-SP28_assoc: Sperm 26.9 2E+02 0.0044 19.3 5.2 28 91-118 31-58 (60)
147 TIGR02948 SigW_bacill RNA poly 26.5 1.2E+02 0.0025 23.8 4.3 30 44-73 152-181 (187)
148 PRK05602 RNA polymerase sigma 26.2 68 0.0015 25.5 2.9 28 47-74 147-174 (186)
149 PF02796 HTH_7: Helix-turn-hel 26.2 73 0.0016 19.7 2.4 39 22-65 4-42 (45)
150 cd04784 HTH_CadR-PbrR Helix-Tu 26.1 2.9E+02 0.0062 20.8 8.7 37 18-67 33-69 (127)
151 PRK12541 RNA polymerase sigma 26.0 63 0.0014 24.9 2.6 27 47-73 131-157 (161)
152 PRK09648 RNA polymerase sigma 26.0 95 0.0021 24.7 3.7 25 46-70 157-181 (189)
153 KOG0709 CREB/ATF family transc 25.4 1.9E+02 0.0042 27.5 6.0 53 68-120 268-320 (472)
154 cd01282 HTH_MerR-like_sg3 Heli 25.4 2.8E+02 0.0061 20.5 7.8 39 16-67 30-68 (112)
155 TIGR02894 DNA_bind_RsfA transc 25.0 3.8E+02 0.0082 21.8 7.2 28 83-110 115-142 (161)
156 TIGR02209 ftsL_broad cell divi 25.0 1.9E+02 0.0041 19.9 4.7 38 76-114 28-65 (85)
157 PRK10403 transcriptional regul 24.8 84 0.0018 24.3 3.1 46 22-73 152-197 (215)
158 smart00027 EH Eps15 homology d 24.6 1.2E+02 0.0026 21.6 3.7 44 23-66 3-51 (96)
159 PF07795 DUF1635: Protein of u 24.5 4.4E+02 0.0096 22.4 8.0 15 92-106 46-60 (214)
160 TIGR02479 FliA_WhiG RNA polyme 24.5 86 0.0019 25.9 3.3 44 24-72 176-219 (224)
161 PRK12512 RNA polymerase sigma 24.5 89 0.0019 24.7 3.3 29 46-74 149-177 (184)
162 cd04762 HTH_MerR-trunc Helix-T 24.5 51 0.0011 19.5 1.5 24 47-70 3-26 (49)
163 PRK12515 RNA polymerase sigma 24.4 1.5E+02 0.0033 23.5 4.6 28 47-74 150-177 (189)
164 cd04764 HTH_MlrA-like_sg1 Heli 24.3 43 0.00093 22.2 1.2 21 47-67 3-23 (67)
165 PRK09480 slmA division inhibit 24.2 74 0.0016 25.0 2.7 40 30-70 17-56 (194)
166 TIGR02939 RpoE_Sigma70 RNA pol 24.0 71 0.0015 25.2 2.6 30 44-73 154-183 (190)
167 PRK09639 RNA polymerase sigma 23.9 1.7E+02 0.0037 22.4 4.8 27 47-73 130-156 (166)
168 cd04763 HTH_MlrA-like Helix-Tu 23.8 43 0.00094 22.3 1.1 21 47-67 3-23 (68)
169 PF04899 MbeD_MobD: MbeD/MobD 23.4 2.6E+02 0.0057 19.4 6.5 42 76-117 25-66 (70)
170 PHA02955 hypothetical protein; 23.4 91 0.002 26.6 3.1 42 27-68 61-103 (213)
171 COG5414 TATA-binding protein-a 23.2 3.7E+02 0.0079 24.3 7.0 67 29-99 152-220 (392)
172 KOG0150 Spliceosomal protein F 23.0 3E+02 0.0066 24.9 6.4 50 61-110 16-66 (336)
173 PF09726 Macoilin: Transmembra 22.8 4.2E+02 0.0092 26.5 8.1 6 112-117 507-512 (697)
174 PF00376 MerR: MerR family reg 22.7 43 0.00094 20.3 0.8 19 48-66 3-21 (38)
175 PRK09047 RNA polymerase factor 22.7 1.8E+02 0.004 22.1 4.7 25 47-71 125-149 (161)
176 PRK06811 RNA polymerase factor 22.6 1.1E+02 0.0024 24.4 3.5 28 47-74 150-177 (189)
177 TIGR02959 SigZ RNA polymerase 22.6 1.5E+02 0.0032 23.3 4.2 20 47-66 119-138 (170)
178 PF11932 DUF3450: Protein of u 22.4 4.6E+02 0.01 22.2 7.5 38 78-115 55-92 (251)
179 TIGR02894 DNA_bind_RsfA transc 22.3 3.7E+02 0.0081 21.9 6.4 32 82-113 107-138 (161)
180 PRK06986 fliA flagellar biosyn 22.2 99 0.0022 25.8 3.3 29 46-74 202-230 (236)
181 PRK08583 RNA polymerase sigma 22.0 1E+02 0.0022 26.1 3.3 46 23-73 205-250 (257)
182 cd04785 HTH_CadR-PbrR-like Hel 22.0 3.5E+02 0.0077 20.4 8.8 37 18-67 33-69 (126)
183 KOG2391 Vacuolar sorting prote 22.0 3.7E+02 0.008 24.7 6.8 34 80-113 233-266 (365)
184 TIGR02047 CadR-PbrR Cd(II)/Pb( 21.9 3.6E+02 0.0078 20.4 9.1 38 16-66 31-68 (127)
185 PRK10360 DNA-binding transcrip 21.9 1.1E+02 0.0024 23.6 3.3 43 23-71 137-179 (196)
186 TIGR02449 conserved hypothetic 21.6 2.8E+02 0.0061 19.1 6.8 40 80-119 15-54 (65)
187 PRK13919 putative RNA polymera 21.5 1.1E+02 0.0023 24.2 3.2 23 47-69 154-176 (186)
188 PF10482 CtIP_N: Tumour-suppre 21.4 3.1E+02 0.0067 21.2 5.3 22 88-109 98-119 (120)
189 PF08961 DUF1875: Domain of un 21.3 31 0.00068 29.6 0.0 34 79-112 129-162 (243)
190 PRK12546 RNA polymerase sigma 21.2 1.8E+02 0.0038 23.5 4.4 28 46-73 131-158 (188)
191 PRK14127 cell division protein 21.1 3.7E+02 0.0081 20.3 6.0 39 82-120 26-64 (109)
192 PRK13922 rod shape-determining 21.0 3.2E+02 0.0068 23.5 6.2 24 88-111 71-94 (276)
193 PRK13729 conjugal transfer pil 21.0 3.3E+02 0.0071 26.1 6.6 38 79-116 83-120 (475)
194 COG4026 Uncharacterized protei 20.8 3.8E+02 0.0082 23.3 6.3 15 97-111 174-188 (290)
195 TIGR03629 arch_S13P archaeal r 20.6 85 0.0018 25.0 2.3 32 22-71 50-81 (144)
196 PHA02535 P terminase ATPase su 20.5 2.1E+02 0.0045 28.1 5.3 85 23-114 2-90 (581)
197 TIGR02999 Sig-70_X6 RNA polyme 20.5 1.8E+02 0.0039 22.8 4.3 26 47-72 153-178 (183)
198 cd00093 HTH_XRE Helix-turn-hel 20.4 57 0.0012 19.1 1.1 22 47-68 15-36 (58)
199 COG4985 ABC-type phosphate tra 20.4 2.8E+02 0.0061 24.2 5.5 31 89-119 217-247 (289)
200 PRK05657 RNA polymerase sigma 20.4 1.5E+02 0.0032 26.5 4.1 51 23-74 262-312 (325)
201 PF01381 HTH_3: Helix-turn-hel 20.2 53 0.0011 20.6 0.9 23 47-69 12-34 (55)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.83 E-value=8.9e-21 Score=157.67 Aligned_cols=102 Identities=45% Similarity=0.720 Sum_probs=95.3
Q ss_pred CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhhhhHHHHHHhHHHHHHHH
Q 035661 17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKR 96 (211)
Q Consensus 17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~~~~~~~~~~l~~e~~ 96 (211)
.++++.+||.+|+..||+.|+...++.+.++..||++|||.+|||+|||||||+|||.++.+.++..++..++.+..++.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~~ 129 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEND 129 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhh
Confidence 34566789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 035661 97 RLEKDVKLLKEELRQAQEILFA 118 (211)
Q Consensus 97 ~l~~e~~~l~~e~~~~~~~l~~ 118 (211)
+|++++..|..++......++.
T Consensus 130 ~Lq~e~~eL~~~~~~~~~~~~~ 151 (198)
T KOG0483|consen 130 RLQSEVQELVAELSSLKREMQK 151 (198)
T ss_pred HHHHHHHHHHHHHhhhhhhhcc
Confidence 9999999999998877665554
No 2
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.76 E-value=4.1e-19 Score=154.13 Aligned_cols=64 Identities=25% Similarity=0.542 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
...+.||.||.||..|+.+||+.|+.++|+++.+|.+||..|+|++|||||||||||+||||..
T Consensus 155 ~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 155 TGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred ccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhh
Confidence 4456789999999999999999999999999999999999999999999999999999999865
No 3
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.71 E-value=7e-18 Score=149.38 Aligned_cols=69 Identities=32% Similarity=0.625 Sum_probs=64.2
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661 10 QKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78 (211)
Q Consensus 10 ~~~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~ 78 (211)
....++|+||.||.||..|+..||+.|++.+|++..+|.+||..|||+..||++||||||+|||+...+
T Consensus 165 ~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 165 QRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred ccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 445668888899999999999999999999999999999999999999999999999999999997744
No 4
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.70 E-value=1.2e-17 Score=135.35 Aligned_cols=64 Identities=28% Similarity=0.427 Sum_probs=61.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhh
Q 035661 16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLEL 79 (211)
Q Consensus 16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~ 79 (211)
+.||.||.||.+|+..||..|+.|.|....+|++||..|+|++.||+|||||||.|.||++.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 7788999999999999999999999999999999999999999999999999999999987553
No 5
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.69 E-value=1.1e-17 Score=146.83 Aligned_cols=71 Identities=28% Similarity=0.397 Sum_probs=64.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhhhhHH
Q 035661 13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNT 83 (211)
Q Consensus 13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~~~ 83 (211)
.+++|||.|..|+..|+.+||+.|+..+|++..+|+.||..|.|+++||||||||||-|.||+..+.....
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 46677788899999999999999999999999999999999999999999999999999999886655443
No 6
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.68 E-value=3.4e-17 Score=136.63 Aligned_cols=69 Identities=26% Similarity=0.483 Sum_probs=64.5
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661 10 QKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78 (211)
Q Consensus 10 ~~~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~ 78 (211)
=...++|.||.||+||..|+++||..|.+..||+...|++||.+|+|.+.+|+|||+|||+|+|+++..
T Consensus 30 ~~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 30 YSSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred cCccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 345788999999999999999999999999999999999999999999999999999999999987743
No 7
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.68 E-value=8.7e-17 Score=138.76 Aligned_cols=78 Identities=19% Similarity=0.336 Sum_probs=73.9
Q ss_pred CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhhhhHHHHHHhHHHHHH
Q 035661 17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALAD 94 (211)
Q Consensus 17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~~~~~~~~~~l~~e 94 (211)
.||+||+||..|++.|+..|+..++|.+..|++|+.++||..|+|+|||||||+|+|+.++......|.+.+..+...
T Consensus 167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK~s 244 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMKRS 244 (383)
T ss_pred cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhhcc
Confidence 468999999999999999999999999999999999999999999999999999999999999999999999887553
No 8
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.67 E-value=2e-17 Score=145.34 Aligned_cols=66 Identities=26% Similarity=0.385 Sum_probs=61.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhh
Q 035661 14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLEL 79 (211)
Q Consensus 14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~ 79 (211)
.++.||||.-||..|+..||+.|-.|.|++...|.+|++.|+|++|||||||||||.|+||...+.
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 466778899999999999999999999999999999999999999999999999999999987543
No 9
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.67 E-value=2.4e-17 Score=122.88 Aligned_cols=67 Identities=24% Similarity=0.446 Sum_probs=62.8
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 10 QKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 10 ~~~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
+...++|.||-||+||..|+..||++|.+.+||++..|++||.++.|++..|+|||||||++-|++.
T Consensus 10 ~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 10 GLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred ChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 4456788899999999999999999999999999999999999999999999999999999998754
No 10
>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=99.66 E-value=1.2e-16 Score=107.36 Aligned_cols=57 Identities=35% Similarity=0.568 Sum_probs=55.1
Q ss_pred CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
||+|+.||.+|+..|+.+|..++||+..++..||.++||++.+|++||+|+|.++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999885
No 11
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.64 E-value=1.5e-16 Score=135.48 Aligned_cols=74 Identities=23% Similarity=0.458 Sum_probs=66.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhhhhHHHHHHhH
Q 035661 16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLE 89 (211)
Q Consensus 16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~~~~~~~~~ 89 (211)
|+|+-||.||..|++.||+.|++.+||+..-|+-||.++.|.+.+|+|||||||+||||..++....++.+++.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~maeyg 213 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMAEYG 213 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhhhhc
Confidence 33344899999999999999999999999999999999999999999999999999999998887777776653
No 12
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.63 E-value=3e-16 Score=131.68 Aligned_cols=65 Identities=25% Similarity=0.423 Sum_probs=61.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661 13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL 77 (211)
Q Consensus 13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~ 77 (211)
+.+|.||.||.|+.-||..|.+.|+++.|+.-.+|.+||..|||+.+|||+||||||.|-||..+
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 56677778999999999999999999999999999999999999999999999999999998764
No 13
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.59 E-value=5.4e-16 Score=129.21 Aligned_cols=61 Identities=33% Similarity=0.566 Sum_probs=58.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
+|||.||+|+..|+-.||..|+...|++..+|..||.+|.|+++|||+||||||.|||++.
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 6678999999999999999999999999999999999999999999999999999999864
No 14
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.59 E-value=6.3e-16 Score=132.18 Aligned_cols=61 Identities=30% Similarity=0.475 Sum_probs=56.6
Q ss_pred CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661 18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78 (211)
Q Consensus 18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~ 78 (211)
-|-|.+||..|..+||+.|...+|.++.++.+||.-|||+|||||+||||||+|+||..++
T Consensus 200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK 260 (317)
T ss_pred cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence 3457899999999999999999999999999999999999999999999999999987643
No 15
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.58 E-value=2e-15 Score=125.05 Aligned_cols=60 Identities=27% Similarity=0.473 Sum_probs=57.1
Q ss_pred CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
.|+.||-||..|+..||+.|.+.+|+++.+|.+++..|.|+++|||+||||||+|.||.+
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 356799999999999999999999999999999999999999999999999999999866
No 16
>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=99.57 E-value=2.2e-15 Score=102.11 Aligned_cols=53 Identities=17% Similarity=0.259 Sum_probs=50.7
Q ss_pred CCCCCCCCCHHHHHHHHHHhccCCC----CCHHHHHHHHHHhCCCccchhhhhhhhH
Q 035661 17 KLNIKKRLNQEQVRVLERSFTTKKK----LDTELKLKLANQLGVPARQVAVWYQNKR 69 (211)
Q Consensus 17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~----p~~~~r~~La~~lgL~~rqVkvWFqNRR 69 (211)
+||.||.||.+|++.||.+|..++| |+...+.+||.++||++++|+|||||-+
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 9999999999999999999999999964
No 17
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.57 E-value=1.8e-15 Score=129.08 Aligned_cols=59 Identities=29% Similarity=0.549 Sum_probs=56.8
Q ss_pred CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
||.||.||.+||..|+..|+.+.|++..+|++||.+|||.+.||++||||+|+|.||-.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 67899999999999999999999999999999999999999999999999999999864
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.54 E-value=7.8e-15 Score=97.71 Aligned_cols=55 Identities=38% Similarity=0.698 Sum_probs=52.2
Q ss_pred CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
+.|+.|+.+|+..|+..|..++||+..++.+||..+||+.++|+.||+|||.+.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 5678899999999999999999999999999999999999999999999998764
No 19
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.54 E-value=1.2e-14 Score=97.43 Aligned_cols=57 Identities=35% Similarity=0.619 Sum_probs=54.3
Q ss_pred CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661 19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75 (211)
Q Consensus 19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~ 75 (211)
+.+..|+.+|+..||.+|..++||+..++..||.++||++++|++||+|||.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 567899999999999999999999999999999999999999999999999998763
No 20
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.51 E-value=6e-15 Score=132.44 Aligned_cols=61 Identities=21% Similarity=0.330 Sum_probs=59.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
||||+||.|+...+..||++|.+|++|+..+...||.+|+|++.+|+|||||||.|+||..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 7788999999999999999999999999999999999999999999999999999999876
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.47 E-value=5.5e-14 Score=113.29 Aligned_cols=66 Identities=30% Similarity=0.483 Sum_probs=60.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661 13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78 (211)
Q Consensus 13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~ 78 (211)
..+..+++|++.|.+|+.+|++.|..|+||+...|..|+..|+|+++-|++||||||++.|+....
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 345566788999999999999999999999999999999999999999999999999999987643
No 22
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.42 E-value=4.2e-14 Score=123.05 Aligned_cols=63 Identities=27% Similarity=0.487 Sum_probs=58.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661 16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78 (211)
Q Consensus 16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~ 78 (211)
.-||-||.||.+|+..||+.|-+..|-++.+|.+||..|+|.++-|||||||||.|+||+...
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 346789999999999999999999999999999999999999999999999999999997654
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.40 E-value=5.6e-14 Score=112.70 Aligned_cols=65 Identities=28% Similarity=0.452 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661 14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78 (211)
Q Consensus 14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~ 78 (211)
..+++|-|++|...|+..||+.|+..+|++..+|.+||..|+|+++||+.||||||.|.||.++.
T Consensus 97 ~~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~ 161 (194)
T KOG0491|consen 97 HCRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN 161 (194)
T ss_pred HHHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 45677889999999999999999999999999999999999999999999999999999987633
No 24
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.26 E-value=2.9e-12 Score=107.21 Aligned_cols=62 Identities=29% Similarity=0.568 Sum_probs=58.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 15 PNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 15 ~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
.++|..|.+|+..|+..||+.|...+|+-...|.+||..+|+++.||+|||||||.|||++.
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 45566788999999999999999999999999999999999999999999999999999865
No 25
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.20 E-value=6.4e-12 Score=109.85 Aligned_cols=61 Identities=21% Similarity=0.510 Sum_probs=58.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
|+||.|+-||..|+..||..|.++.||+-..|++||--.+|++..|+|||.|||++||++.
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 6678899999999999999999999999999999999999999999999999999999876
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.16 E-value=1.8e-11 Score=102.95 Aligned_cols=63 Identities=25% Similarity=0.261 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
+.++||.|+.|+..|++.||+.|...+||+...|+.||..+++++..|++||||||++|++..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 677889999999999999999999999999999999999999999999999999999999865
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.05 E-value=1.8e-10 Score=104.12 Aligned_cols=68 Identities=26% Similarity=0.457 Sum_probs=63.2
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 9 NQKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 9 ~~~~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
.....+++.+|.|++|+..|++.||+.|+.++||+...|++||.++++.+..|+|||+|||+++++..
T Consensus 168 p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 168 PGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 34556778888899999999999999999999999999999999999999999999999999999865
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.04 E-value=8.9e-11 Score=101.85 Aligned_cols=64 Identities=23% Similarity=0.367 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
+...|||+||.+-....+.||.+|...++|+.+....||.+|+|.+.+|+|||+|.|.|.||++
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 3456789999999999999999999999999999999999999999999999999999999865
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.85 E-value=2.4e-09 Score=92.32 Aligned_cols=52 Identities=21% Similarity=0.371 Sum_probs=48.5
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
.|...-..+|..+|..++||++.++.+||+.+||+..||-.||.|||.|+|.
T Consensus 182 CFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 182 CFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred ehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 4666778899999999999999999999999999999999999999999994
No 30
>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=98.40 E-value=1.8e-07 Score=58.84 Aligned_cols=34 Identities=32% Similarity=0.514 Sum_probs=29.0
Q ss_pred cCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q 035661 38 TKKKLDTELKLKLANQLGVPARQVAVWYQNKRAR 71 (211)
Q Consensus 38 ~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r 71 (211)
.+|||+..++..||.++||+.+||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4699999999999999999999999999999875
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.39 E-value=4.3e-07 Score=85.02 Aligned_cols=61 Identities=20% Similarity=0.242 Sum_probs=56.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
..+.||.|.+||..|++.|..+|+.+++|+..+.+.|+.+|||..+-|.+||-|-|.|.+-
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl~ 477 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSLD 477 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhccc
Confidence 3455678999999999999999999999999999999999999999999999999888643
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.25 E-value=5.9e-07 Score=77.34 Aligned_cols=58 Identities=26% Similarity=0.462 Sum_probs=53.9
Q ss_pred CCCCCCCCHHHHHHHHHHhc---cCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661 18 LNIKKRLNQEQVRVLERSFT---TKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75 (211)
Q Consensus 18 kr~Rt~~t~~Ql~~Le~~F~---~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~ 75 (211)
||+|+.|+..-.++|..+|. .+|||+...+++||+++|++..||-.||.|+|.|.|+.
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 57889999999999999995 57999999999999999999999999999999999874
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.12 E-value=2.7e-06 Score=71.43 Aligned_cols=63 Identities=27% Similarity=0.517 Sum_probs=59.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
..+.++.|+.++..|+..|+..|...++|+...+.+|+..+|+.++.|++||+|+|.+.++..
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 456677899999999999999999999999999999999999999999999999999999865
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.43 E-value=0.0001 Score=75.21 Aligned_cols=65 Identities=20% Similarity=0.419 Sum_probs=59.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661 14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78 (211)
Q Consensus 14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~ 78 (211)
..-+|+.|+.++..||..+..+|....+|...+.+.|...+++..++|.|||||-|.+.|+..+.
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n 964 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLN 964 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhc
Confidence 34467789999999999999999999999999999999999999999999999999999988763
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.68 E-value=0.002 Score=57.86 Aligned_cols=62 Identities=27% Similarity=0.356 Sum_probs=52.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhcc---CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 15 PNKLNIKKRLNQEQVRVLERSFTT---KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 15 ~~~kr~Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
..++|++..+....+.+|+.+... .+||+...+..||+++||+..||..||-|.|-|..+--
T Consensus 237 ~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 237 QSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred cCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence 335566778999999999987433 47999999999999999999999999999988876544
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.54 E-value=0.0013 Score=44.20 Aligned_cols=41 Identities=22% Similarity=0.383 Sum_probs=31.3
Q ss_pred HHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhH
Q 035661 29 VRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKR 69 (211)
Q Consensus 29 l~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR 69 (211)
+..|++.|...+++.......|+.+.+|+..||+.||-.|+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 46699999999999999999999999999999999997653
No 37
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=95.76 E-value=0.039 Score=35.45 Aligned_cols=42 Identities=26% Similarity=0.435 Sum_probs=36.9
Q ss_pred hhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 76 SLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILF 117 (211)
Q Consensus 76 ~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~ 117 (211)
+.+.++..++..++.+..++++|..|+..|..++..+...++
T Consensus 2 QlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl~ 43 (45)
T PF02183_consen 2 QLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEKLQ 43 (45)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 567899999999999999999999999999999988776543
No 38
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=94.75 E-value=0.16 Score=39.00 Aligned_cols=94 Identities=15% Similarity=0.087 Sum_probs=51.8
Q ss_pred CCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhhhhHHHHHHhHHHHHHHHHHH
Q 035661 20 IKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLE 99 (211)
Q Consensus 20 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~ 99 (211)
+|++||.++....-..+..+.. ...++|+++|+++..|..|.+--+.....................+.+++.+|+
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~L~ 84 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKELQ 84 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHHHH
Confidence 4566888775443333333332 356789999999999999975432211000000000001112223456677788
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 035661 100 KDVKLLKEELRQAQEILF 117 (211)
Q Consensus 100 ~e~~~l~~e~~~~~~~l~ 117 (211)
+++.+|..|+..+...+.
T Consensus 85 ~el~~L~~E~diLKKa~~ 102 (121)
T PRK09413 85 RLLGKKTMENELLKEAVE 102 (121)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 888888887776665443
No 39
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=94.72 E-value=0.069 Score=35.24 Aligned_cols=46 Identities=22% Similarity=0.278 Sum_probs=34.9
Q ss_pred CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhh
Q 035661 18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNK 68 (211)
Q Consensus 18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNR 68 (211)
||+|+.+|-++...+=..++... ....||+++|+...+|..|..|+
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 57889999998887777777666 57889999999999999999885
No 40
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.28 E-value=0.05 Score=53.35 Aligned_cols=48 Identities=21% Similarity=0.358 Sum_probs=45.0
Q ss_pred HHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 29 VRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 29 l~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
+.+|...|..|..|+..+...+|.+.||..+.|+.||+++++......
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 788999999999999999999999999999999999999998877655
No 41
>smart00340 HALZ homeobox associated leucin zipper.
Probab=92.43 E-value=0.34 Score=30.59 Aligned_cols=32 Identities=28% Similarity=0.432 Sum_probs=27.1
Q ss_pred hhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 035661 76 SLELDYNTIQVKLENALADKRRLEKDVKLLKE 107 (211)
Q Consensus 76 ~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~ 107 (211)
+.+.+..-++..++.+.+||++|++|+..|+.
T Consensus 2 QTEvdCe~LKrcce~LteeNrRL~ke~~eLra 33 (44)
T smart00340 2 QTEVDCELLKRCCESLTEENRRLQKEVQELRA 33 (44)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45667888999999999999999999988764
No 42
>smart00338 BRLZ basic region leucin zipper.
Probab=88.22 E-value=3.4 Score=27.96 Aligned_cols=39 Identities=26% Similarity=0.456 Sum_probs=30.5
Q ss_pred hhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 78 ELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEIL 116 (211)
Q Consensus 78 ~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l 116 (211)
......+..+...+..+|..|..++..|..++..+...+
T Consensus 25 k~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 25 KAEIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 335667777888888889999999988888888776644
No 43
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=87.26 E-value=4.8 Score=27.14 Aligned_cols=44 Identities=20% Similarity=0.379 Sum_probs=28.9
Q ss_pred HHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 69 RARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEI 115 (211)
Q Consensus 69 R~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~ 115 (211)
++|.|++. ....+...+..+..++..|..++..|..++..+...
T Consensus 19 ~~R~RKk~---~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e 62 (64)
T PF00170_consen 19 RSRQRKKQ---YIEELEEKVEELESENEELKKELEQLKKEIQSLKSE 62 (64)
T ss_dssp HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHh---hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44444443 555666677777777777777777777777766543
No 44
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=86.63 E-value=2.9 Score=37.06 Aligned_cols=44 Identities=14% Similarity=0.231 Sum_probs=36.2
Q ss_pred hhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 035661 76 SLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAK 119 (211)
Q Consensus 76 ~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~~ 119 (211)
+++.+...+--+++.|...|++|+.++++|..|+.++.+.+...
T Consensus 245 KkRae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e~ 288 (294)
T KOG4571|consen 245 KKRAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILEV 288 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33446667777888899999999999999999999999877643
No 45
>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=83.63 E-value=0.42 Score=32.87 Aligned_cols=47 Identities=17% Similarity=0.281 Sum_probs=31.2
Q ss_pred CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhH
Q 035661 19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKR 69 (211)
Q Consensus 19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR 69 (211)
++|++||+++...+-..+.. ......++|+++||++..|..|-.--+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHHHHh
Confidence 46789999988777666622 235678899999999999999986444
No 46
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=82.48 E-value=3.9 Score=26.14 Aligned_cols=32 Identities=22% Similarity=0.510 Sum_probs=21.2
Q ss_pred hhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 035661 78 ELDYNTIQVKLENALADKRRLEKDVKLLKEEL 109 (211)
Q Consensus 78 ~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~ 109 (211)
+..+..+..+++.+..|+..|..++..|...+
T Consensus 11 K~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl 42 (45)
T PF02183_consen 11 KASYDSLKAEYDSLKKENEKLRAEVQELKEKL 42 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44566667777777777777777776666544
No 47
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=82.14 E-value=6.9 Score=34.27 Aligned_cols=49 Identities=18% Similarity=0.293 Sum_probs=37.3
Q ss_pred HHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 035661 69 RARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKL 120 (211)
Q Consensus 69 R~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~~~ 120 (211)
|.|.+++... ..+..+...|..||..|..++.+|+.++..+...+..+.
T Consensus 208 kSR~~~k~~~---~e~~~r~~~leken~~lr~~v~~l~~el~~~~~~~~~~~ 256 (269)
T KOG3119|consen 208 KSRDKRKQKE---DEMAHRVAELEKENEALRTQVEQLKKELATLRRLFLQLP 256 (269)
T ss_pred HhhhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 5555555544 455566677888999999999999999999988777654
No 48
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=81.37 E-value=14 Score=27.75 Aligned_cols=54 Identities=15% Similarity=0.157 Sum_probs=34.8
Q ss_pred chhhhhhhhHHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 60 QVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQE 114 (211)
Q Consensus 60 qVkvWFqNRR~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~ 114 (211)
++..||.+.-. .+-...+.+...++.+++.+..+|..|+.++..|+....++..
T Consensus 16 ~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~dyiEe 69 (105)
T PRK00888 16 QYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQEAIEE 69 (105)
T ss_pred HHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcHHHHHH
Confidence 45678865422 1223344566677788888888888888888888774444443
No 49
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=80.48 E-value=26 Score=27.54 Aligned_cols=38 Identities=16% Similarity=0.251 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q 035661 22 KRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRAR 71 (211)
Q Consensus 22 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r 71 (211)
..|+.+++..| ..|+.--+.-|++...|-.|=|.||.-
T Consensus 22 d~lsDd~Lvsm------------SVReLNr~LrG~~reEVvrlKQrRRTL 59 (135)
T KOG4196|consen 22 DRLSDDELVSM------------SVRELNRHLRGLSREEVVRLKQRRRTL 59 (135)
T ss_pred CCcCHHHHHHh------------hHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 67888877766 333332333489999999999988743
No 50
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=78.88 E-value=18 Score=26.05 Aligned_cols=50 Identities=14% Similarity=0.098 Sum_probs=39.3
Q ss_pred HHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 035661 71 RWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKL 120 (211)
Q Consensus 71 r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~~~ 120 (211)
+..+.....+...++..+..|...-+..+.|+..|..|++.++..|.+..
T Consensus 15 ~e~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nLm 64 (80)
T PF10224_consen 15 KEEKEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNLM 64 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344555566778888888888888999999999999999998887764
No 51
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=78.87 E-value=9.8 Score=24.81 Aligned_cols=36 Identities=11% Similarity=0.329 Sum_probs=18.8
Q ss_pred HHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 035661 69 RARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKE 107 (211)
Q Consensus 69 R~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~ 107 (211)
|+|.|++. ....+...+..|..+|..|..++..|..
T Consensus 18 r~R~rkk~---~~~~le~~~~~L~~en~~L~~~i~~L~~ 53 (54)
T PF07716_consen 18 RSRQRKKQ---REEELEQEVQELEEENEQLRQEIAQLER 53 (54)
T ss_dssp HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 44444433 3344555555555666666666555543
No 52
>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=77.53 E-value=4.4 Score=25.63 Aligned_cols=41 Identities=15% Similarity=0.256 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhh
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNK 68 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNR 68 (211)
.+++.+..+|...| .....-.++|..+|++...|+.+...-
T Consensus 4 ~L~~~er~vi~~~y-----~~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 4 QLPPREREVIRLRY-----FEGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TS-HHHHHHHHHHH-----TST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh-----cCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 57889999999999 233446788999999999988776543
No 53
>PF10226 DUF2216: Uncharacterized conserved proteins (DUF2216); InterPro: IPR019359 Proteins in this entry are found in Metazoa and contain a coiled-coil domain. Some annotation suggests it might be PKR, the Hepatitis delta antigen-interacting protein A, but this could not be confirmed.
Probab=74.02 E-value=28 Score=29.07 Aligned_cols=29 Identities=24% Similarity=0.127 Sum_probs=13.3
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 85 QVKLENALADKRRLEKDVKLLKEELRQAQ 113 (211)
Q Consensus 85 ~~~~~~l~~e~~~l~~e~~~l~~e~~~~~ 113 (211)
.+++..+-...+.|..|+..|++-.-++.
T Consensus 114 ~~KL~eLE~kq~~L~rEN~eLKElcl~LD 142 (195)
T PF10226_consen 114 QQKLKELEDKQEELIRENLELKELCLYLD 142 (195)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence 33333333344455555555555443333
No 54
>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=73.58 E-value=3.4 Score=25.22 Aligned_cols=43 Identities=16% Similarity=0.163 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHH
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRA 70 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~ 70 (211)
.+++.+...+...|-.. ..-.++|..+|++...|..|....+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46788888888887422 23567899999999999999865443
No 55
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=71.50 E-value=16 Score=34.48 Aligned_cols=93 Identities=17% Similarity=0.165 Sum_probs=59.3
Q ss_pred CCCCCHHHHHHHHHH-hccCC-CCCHHHHHHHHHHhCCCccchhhhhhhhHH-HHhhhhhhhhhHHHHHHhHHHHHHHHH
Q 035661 21 KKRLNQEQVRVLERS-FTTKK-KLDTELKLKLANQLGVPARQVAVWYQNKRA-RWKTQSLELDYNTIQVKLENALADKRR 97 (211)
Q Consensus 21 Rt~~t~~Ql~~Le~~-F~~~~-~p~~~~r~~La~~lgL~~rqVkvWFqNRR~-r~k~~~~~~~~~~~~~~~~~l~~e~~~ 97 (211)
--++|.+....|.+. |-... +|-...-+++.+ +|+.=.+|+|. .++|++++.-...+..+...-..+|.+
T Consensus 218 ~L~LteeEkrLL~kEG~slPs~lPLTKaEEriLK-------rvRRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqe 290 (472)
T KOG0709|consen 218 PLVLTEEEKRLLTKEGYSLPSKLPLTKAEERILK-------RVRRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQE 290 (472)
T ss_pred ceeccHHHHHHHHhccCcCcccCCchHHHHHHHH-------HHHHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHH
Confidence 346788888888776 33332 455554444443 34444455553 344444444455666666667889999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhh
Q 035661 98 LEKDVKLLKEELRQAQEILFAKL 120 (211)
Q Consensus 98 l~~e~~~l~~e~~~~~~~l~~~~ 120 (211)
|++++.+|..++..+.++|....
T Consensus 291 L~kkV~~Le~~N~sLl~qL~klQ 313 (472)
T KOG0709|consen 291 LQKKVEELELSNRSLLAQLKKLQ 313 (472)
T ss_pred HHHHHHHHhhccHHHHHHHHHHH
Confidence 99999999888888877776643
No 56
>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=68.98 E-value=6.1 Score=26.11 Aligned_cols=39 Identities=21% Similarity=0.253 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHhccCCC--CCHHHHHHHHHHhCCCccchh
Q 035661 24 LNQEQVRVLERSFTTKKK--LDTELKLKLANQLGVPARQVA 62 (211)
Q Consensus 24 ~t~~Ql~~Le~~F~~~~~--p~~~~r~~La~~lgL~~rqVk 62 (211)
+|+.|.++|...|..-=| |-.....+||.++|+++.-|-
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 588999999999877643 666778899999999886544
No 57
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=65.13 E-value=8.2 Score=40.76 Aligned_cols=67 Identities=13% Similarity=0.242 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 10 QKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 10 ~~~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
+.+...+.++.+..+-.++...|-++|-.+.-|+.+.+.-|......+.+++.+||+|-|.|.++..
T Consensus 698 ~~~~~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 698 GESLSPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CCCCCcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 3445666778889999999999999999999999999999999999999999999999999998876
No 58
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=61.81 E-value=51 Score=28.59 Aligned_cols=45 Identities=24% Similarity=0.244 Sum_probs=28.2
Q ss_pred HHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 69 RARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQ 113 (211)
Q Consensus 69 R~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~ 113 (211)
|-|.|-..++.+..........+..|.+.|+.++-.|-+...+++
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylq 134 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQ 134 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 444555555666666666666666677777777766666666644
No 59
>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=61.20 E-value=16 Score=19.64 Aligned_cols=38 Identities=21% Similarity=0.339 Sum_probs=26.1
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhh
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWY 65 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWF 65 (211)
.++.++...+...|... . ...++|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 35666666666666532 2 45678899999988887773
No 60
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=60.56 E-value=48 Score=22.12 Aligned_cols=41 Identities=22% Similarity=0.287 Sum_probs=22.2
Q ss_pred HHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 035661 69 RARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEEL 109 (211)
Q Consensus 69 R~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~ 109 (211)
|-+......+.....+..+++.|..++..|..++..|..++
T Consensus 23 RKk~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 23 RKKQYIEELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 33444445555555555555555555555555555555543
No 61
>PF15058 Speriolin_N: Speriolin N terminus
Probab=59.71 E-value=26 Score=29.38 Aligned_cols=38 Identities=21% Similarity=0.405 Sum_probs=27.2
Q ss_pred hhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 035661 80 DYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFA 118 (211)
Q Consensus 80 ~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~ 118 (211)
.|..++..++.++.||.+|+|++.-++ |+..++..+..
T Consensus 6 ~yeGlrhqierLv~ENeeLKKlVrLir-EN~eLksaL~e 43 (200)
T PF15058_consen 6 NYEGLRHQIERLVRENEELKKLVRLIR-ENHELKSALGE 43 (200)
T ss_pred chHHHHHHHHHHHhhhHHHHHHHHHHH-HHHHHHHHHHH
Confidence 456677788889999999999995554 45555554443
No 62
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=59.52 E-value=26 Score=27.83 Aligned_cols=48 Identities=19% Similarity=0.223 Sum_probs=36.4
Q ss_pred CCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 21 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
...+|+.|.++|...+ . .....++|..+|++...|..|..+.+.+.++
T Consensus 4 ~~~Lt~rqreVL~lr~--~----GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLRE--R----GLTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHHH--c----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4678999999998843 2 2345689999999999999999765554444
No 63
>PF14645 Chibby: Chibby family
Probab=58.30 E-value=25 Score=26.95 Aligned_cols=28 Identities=21% Similarity=0.341 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 90 NALADKRRLEKDVKLLKEELRQAQEILF 117 (211)
Q Consensus 90 ~l~~e~~~l~~e~~~l~~e~~~~~~~l~ 117 (211)
.+..+++.|+.|+-.|+-+++-+-+++.
T Consensus 75 ~l~~~n~~L~EENN~Lklk~elLlDMLt 102 (116)
T PF14645_consen 75 RLRKENQQLEEENNLLKLKIELLLDMLT 102 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555555555555444444
No 64
>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=58.19 E-value=5.7 Score=27.05 Aligned_cols=21 Identities=24% Similarity=0.463 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCCccchhhhhh
Q 035661 46 LKLKLANQLGVPARQVAVWYQ 66 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFq 66 (211)
.-.+||.+||+++.+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 456889999999999999964
No 65
>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=57.38 E-value=23 Score=22.44 Aligned_cols=42 Identities=17% Similarity=0.256 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhH
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKR 69 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR 69 (211)
.+++.+..++...| .....-.++|..+|+++..|+.|...-|
T Consensus 10 ~L~~~~r~i~~l~~-----~~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 10 QLPERQREIFLLRY-----FQGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp CS-HHHHHHHHHHH-----TS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHH-----HHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35666667776655 3345578899999999999999997433
No 66
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=56.44 E-value=24 Score=34.04 Aligned_cols=38 Identities=18% Similarity=0.265 Sum_probs=28.6
Q ss_pred hhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 78 ELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEI 115 (211)
Q Consensus 78 ~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~ 115 (211)
++-...+..++.+++.||+.|++|+..|+.++..+..+
T Consensus 301 KEy~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~E 338 (655)
T KOG4343|consen 301 KEYMLGLEARLQALLSENEQLKKENATLKRQLDELVSE 338 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhc
Confidence 34456677788888888888888888888887766543
No 67
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=55.73 E-value=12 Score=23.34 Aligned_cols=41 Identities=20% Similarity=0.171 Sum_probs=20.4
Q ss_pred CCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhh
Q 035661 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQ 66 (211)
Q Consensus 21 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFq 66 (211)
++.+|.++...++..+... ....+||+.+|.++.-|..+..
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ----------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 4678899999999887633 4456799999999888877653
No 68
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.43 E-value=1.3e+02 Score=25.65 Aligned_cols=18 Identities=33% Similarity=0.493 Sum_probs=14.6
Q ss_pred CCHHHHHHHHHHhccCCC
Q 035661 24 LNQEQVRVLERSFTTKKK 41 (211)
Q Consensus 24 ~t~~Ql~~Le~~F~~~~~ 41 (211)
.|++....||.+|.+-+.
T Consensus 1 MtpeE~qlle~lf~rlk~ 18 (233)
T COG3416 1 MTPEEKQLLENLFHRLKK 18 (233)
T ss_pred CCHHHHHHHHHHHHHHhh
Confidence 478889999999987654
No 69
>PRK04217 hypothetical protein; Provisional
Probab=55.18 E-value=43 Score=25.41 Aligned_cols=47 Identities=13% Similarity=0.017 Sum_probs=35.0
Q ss_pred CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHH
Q 035661 19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRA 70 (211)
Q Consensus 19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~ 70 (211)
..-..++.+|.+++...|...- ...+||+.+|++..-|...+..-+.
T Consensus 38 ~p~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArk 84 (110)
T PRK04217 38 KPPIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARK 84 (110)
T ss_pred CCcccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3456789999988887764332 4678999999999998887754333
No 70
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=55.17 E-value=70 Score=22.38 Aligned_cols=30 Identities=17% Similarity=0.258 Sum_probs=12.6
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 82 NTIQVKLENALADKRRLEKDVKLLKEELRQ 111 (211)
Q Consensus 82 ~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~ 111 (211)
..++.++..+.+++..|..++.+|+.+...
T Consensus 28 eeLke~n~~L~~e~~~L~~en~~L~~e~~~ 57 (72)
T PF06005_consen 28 EELKEKNNELKEENEELKEENEQLKQERNA 57 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence 333333333334444444444444444333
No 71
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=54.91 E-value=44 Score=25.24 Aligned_cols=33 Identities=21% Similarity=0.428 Sum_probs=16.4
Q ss_pred hhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 80 DYNTIQVKLENALADKRRLEKDVKLLKEELRQA 112 (211)
Q Consensus 80 ~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~ 112 (211)
+...++.....+.+||.+|+-|+..|...+...
T Consensus 23 ~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~ 55 (107)
T PF06156_consen 23 ELEELKKQLQELLEENARLRIENEHLRERLEEL 55 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444445555555555555555555444443
No 72
>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=51.14 E-value=21 Score=24.12 Aligned_cols=44 Identities=20% Similarity=0.354 Sum_probs=22.2
Q ss_pred CCCCCHHH-HHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhh
Q 035661 21 KKRLNQEQ-VRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQ 66 (211)
Q Consensus 21 Rt~~t~~Q-l~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFq 66 (211)
|..|+... +.+++.++.. ..-....|. -|++.|+.+++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~-~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKD-NNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH--TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHc-cchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 34555543 4455544432 222223333 49999999999999975
No 73
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=51.08 E-value=23 Score=29.49 Aligned_cols=49 Identities=22% Similarity=0.234 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHhccCC--CCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 23 RLNQEQVRVLERSFTTKK--KLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~--~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
-+|+.|+++|...|+.-= +|-.....+||+++|+++.- +|..=||+..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHH
Confidence 699999999999998754 47777788999999999854 34443444433
No 74
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), 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. 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.
Probab=49.76 E-value=60 Score=23.79 Aligned_cols=38 Identities=11% Similarity=0.038 Sum_probs=27.6
Q ss_pred CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhh
Q 035661 18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQN 67 (211)
Q Consensus 18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqN 67 (211)
...+..||.+++..|... ..|.+.+|++-..|+.++.+
T Consensus 33 ~~g~R~Yt~~di~~l~~I------------~~llr~~G~~l~~i~~~l~~ 70 (99)
T cd04765 33 AGGRRYYRPKDVELLLLI------------KHLLYEKGYTIEGAKQALKE 70 (99)
T ss_pred CCCCeeeCHHHHHHHHHH------------HHHHHHCCCCHHHHHHHHHh
Confidence 345778999999988443 34567788888888877754
No 75
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=49.47 E-value=59 Score=24.75 Aligned_cols=32 Identities=19% Similarity=0.378 Sum_probs=18.3
Q ss_pred hhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 80 DYNTIQVKLENALADKRRLEKDVKLLKEELRQ 111 (211)
Q Consensus 80 ~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~ 111 (211)
+...++.....+.+||.+|+-|+..|+..+..
T Consensus 23 el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~ 54 (110)
T PRK13169 23 ELGALKKQLAELLEENTALRLENDKLRERLEE 54 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555555566666666666666555554
No 76
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=48.71 E-value=23 Score=26.14 Aligned_cols=33 Identities=21% Similarity=0.461 Sum_probs=18.2
Q ss_pred HHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661 30 RVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76 (211)
Q Consensus 30 ~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~ 76 (211)
....-.|+.+|||.+.-..+ | -.|||.||++++
T Consensus 15 RiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq 47 (91)
T PF00424_consen 15 RIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQ 47 (91)
T ss_dssp HHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHH
T ss_pred HHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHH
Confidence 34455589999998542211 1 158999999876
No 77
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=48.67 E-value=84 Score=27.38 Aligned_cols=9 Identities=44% Similarity=0.453 Sum_probs=3.8
Q ss_pred hhhHHHHhh
Q 035661 66 QNKRARWKT 74 (211)
Q Consensus 66 qNRR~r~k~ 74 (211)
|+-|.|.|-
T Consensus 82 QtaRDrKKa 90 (292)
T KOG4005|consen 82 QTARDRKKA 90 (292)
T ss_pred hhhhhHHHH
Confidence 344444443
No 78
>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=48.31 E-value=31 Score=22.36 Aligned_cols=46 Identities=15% Similarity=0.210 Sum_probs=33.6
Q ss_pred CCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 22 KRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 22 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
..||+.++++|.....-. ...++|..+|++++-|..+..+=+.|..
T Consensus 2 ~~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 2 PSLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp GSS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred CccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 368888888887775433 3678999999999999988876554443
No 79
>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=47.63 E-value=56 Score=31.08 Aligned_cols=92 Identities=18% Similarity=0.276 Sum_probs=44.5
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhhhhHHHHHHhHHHH-HHHHHHHHH
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENAL-ADKRRLEKD 101 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~~~~~~~~~~l~-~e~~~l~~e 101 (211)
.+++++++.|.-. --.|....|.-+++.-.+..+.-.+=-+|++.+.....++.+...+.......+ .+..++.++
T Consensus 41 ~ltpee~kalGie---gDTP~DTlrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~ 117 (472)
T TIGR03752 41 ELSPEELKALGIE---GDTPADTLRTLVAEVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKE 117 (472)
T ss_pred cCCcchhHhcCCC---CCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHH
Confidence 6888887777543 234555555555544433333333334555555444444443333333332222 234445555
Q ss_pred HHHHHHHHHHHHHHHH
Q 035661 102 VKLLKEELRQAQEILF 117 (211)
Q Consensus 102 ~~~l~~e~~~~~~~l~ 117 (211)
..+|+.+...+...+.
T Consensus 118 ~~ql~~~~~~~~~~l~ 133 (472)
T TIGR03752 118 IEQLKSERQQLQGLID 133 (472)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5555555555444433
No 80
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=46.81 E-value=1.1e+02 Score=22.21 Aligned_cols=37 Identities=14% Similarity=0.297 Sum_probs=27.3
Q ss_pred CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhh
Q 035661 19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNK 68 (211)
Q Consensus 19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNR 68 (211)
..+..|+.+++..|.... ..+.+|++...|+.++...
T Consensus 34 ~g~R~y~~~di~~l~~i~-------------~lr~~g~~l~~i~~~~~~~ 70 (103)
T cd01106 34 NGYRLYTEEDLERLQQIL-------------FLKELGFSLKEIKELLKDP 70 (103)
T ss_pred CCceeeCHHHHHHHHHHH-------------HHHHcCCCHHHHHHHHHcC
Confidence 356789999999986553 2456788888888888654
No 81
>PRK00118 putative DNA-binding protein; Validated
Probab=46.30 E-value=1.1e+02 Score=22.94 Aligned_cols=47 Identities=13% Similarity=0.077 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
.+++.|..++...|... ....++|..+|+++.-|..|...-|.+.+.
T Consensus 17 ~L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45677777776655443 235678999999999999998755544444
No 82
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=46.04 E-value=1.2e+02 Score=22.42 Aligned_cols=38 Identities=16% Similarity=0.207 Sum_probs=28.2
Q ss_pred CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhh
Q 035661 18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNK 68 (211)
Q Consensus 18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNR 68 (211)
...+..|+.+++..|... ...+.+|++-..|+..+...
T Consensus 33 ~~gyR~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~~ 70 (113)
T cd01109 33 ENGIRDFTEEDLEWLEFI-------------KCLRNTGMSIKDIKEYAELR 70 (113)
T ss_pred CCCCccCCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHHHH
Confidence 345678999999888433 34677899999999888643
No 83
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=45.76 E-value=1.3e+02 Score=22.76 Aligned_cols=40 Identities=20% Similarity=0.187 Sum_probs=29.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhh
Q 035661 16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNK 68 (211)
Q Consensus 16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNR 68 (211)
+....+..|+.+++..|+ ....++.+|++-..|+..|...
T Consensus 30 r~~~g~R~Y~~~~l~~l~-------------~I~~l~~~G~sl~eI~~~l~~~ 69 (124)
T TIGR02051 30 RPEGGYRRYPEETVKRLR-------------FIKRAQELGFSLEEIGGLLGLV 69 (124)
T ss_pred cCCCCCEeECHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHhcc
Confidence 334567889999998883 3344788899999999888643
No 84
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=44.71 E-value=1.3e+02 Score=22.58 Aligned_cols=45 Identities=20% Similarity=0.126 Sum_probs=37.3
Q ss_pred hhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 035661 76 SLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKL 120 (211)
Q Consensus 76 ~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~~~ 120 (211)
..+.....+..++..+...-..|..|+..|..|+..++..+....
T Consensus 12 ~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~ 56 (107)
T PF06156_consen 12 QLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELE 56 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445566777788888888888899999999999999999888765
No 85
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=44.65 E-value=19 Score=23.47 Aligned_cols=28 Identities=14% Similarity=0.166 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 46 LKLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
....||+.+|+++..|..|+.++.....
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~ 39 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPS 39 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----
T ss_pred CHHHHHHHHCcCHHHHHHHHhccccccc
Confidence 4678899999999999999987643333
No 86
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=44.46 E-value=57 Score=23.27 Aligned_cols=27 Identities=22% Similarity=0.421 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 89 ENALADKRRLEKDVKLLKEELRQAQEI 115 (211)
Q Consensus 89 ~~l~~e~~~l~~e~~~l~~e~~~~~~~ 115 (211)
..+.++|.+|+.+...|..+++.....
T Consensus 3 ~ei~eEn~~Lk~eiqkle~ELq~~~~~ 29 (76)
T PF07334_consen 3 HEIQEENARLKEEIQKLEAELQQNKRE 29 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 356777888888888888777776654
No 87
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=44.23 E-value=1.1e+02 Score=21.63 Aligned_cols=34 Identities=24% Similarity=0.328 Sum_probs=22.8
Q ss_pred CCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhh
Q 035661 20 IKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWY 65 (211)
Q Consensus 20 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWF 65 (211)
.+..|+..++..|... ..|...+|++...|+.-+
T Consensus 35 g~R~y~~~dv~~l~~i------------~~L~~d~g~~l~~i~~~l 68 (91)
T cd04766 35 GTRRYSERDIERLRRI------------QRLTQELGVNLAGVKRIL 68 (91)
T ss_pred CCeeECHHHHHHHHHH------------HHHHHHcCCCHHHHHHHH
Confidence 4567888888888443 455556787776665544
No 88
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=43.66 E-value=69 Score=23.93 Aligned_cols=38 Identities=8% Similarity=0.075 Sum_probs=21.7
Q ss_pred hhhhhHHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHH
Q 035661 64 WYQNKRARWKTQSLELDYNTIQVKLENALADKRRLEKD 101 (211)
Q Consensus 64 WFqNRR~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e 101 (211)
|+..+..+.+....+.+...++.+++.|..+...|+..
T Consensus 26 ~~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~ 63 (105)
T PRK00888 26 ILDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGG 63 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCc
Confidence 34444444455555556666666666666666666653
No 89
>PF13518 HTH_28: Helix-turn-helix domain
Probab=42.23 E-value=18 Score=22.44 Aligned_cols=23 Identities=17% Similarity=0.380 Sum_probs=19.2
Q ss_pred HHHHHHHHhCCCccchhhhhhhh
Q 035661 46 LKLKLANQLGVPARQVAVWYQNK 68 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFqNR 68 (211)
...++|.++|++..+|..|.+.-
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHH
Confidence 35568999999999999999643
No 90
>PRK14127 cell division protein GpsB; Provisional
Probab=41.79 E-value=88 Score=23.77 Aligned_cols=35 Identities=11% Similarity=0.143 Sum_probs=23.0
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 035661 84 IQVKLENALADKRRLEKDVKLLKEELRQAQEILFA 118 (211)
Q Consensus 84 ~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~ 118 (211)
+-..++.+..++.+|+.++.+|+.++......+..
T Consensus 35 V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~~ 69 (109)
T PRK14127 35 VIKDYEAFQKEIEELQQENARLKAQVDELTKQVSV 69 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 34455566667777777777777777776665553
No 91
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=41.74 E-value=60 Score=19.77 Aligned_cols=39 Identities=21% Similarity=0.267 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhh
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQN 67 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqN 67 (211)
.+++.+...+...+.. ....++|..+|+++..|..|...
T Consensus 3 ~l~~~e~~i~~~~~~g------~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLAEG------LTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHH
Confidence 4678888888664422 24578899999999999988763
No 92
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=41.58 E-value=1.6e+02 Score=25.71 Aligned_cols=36 Identities=22% Similarity=0.454 Sum_probs=18.3
Q ss_pred hhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 78 ELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQ 113 (211)
Q Consensus 78 ~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~ 113 (211)
..++..++..++.|+.+|.+|..+...+..++-.+.
T Consensus 110 ~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~~~~ 145 (292)
T KOG4005|consen 110 QNENDSLRAINESLLAKNHELDSELELLRQELAELK 145 (292)
T ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhH
Confidence 334444555555555555555555555555544443
No 93
>PF13551 HTH_29: Winged helix-turn helix
Probab=41.24 E-value=75 Score=22.70 Aligned_cols=48 Identities=19% Similarity=0.193 Sum_probs=30.3
Q ss_pred CCCCCCCHHHHHHHHHHhccCCC-----CCHHHHHH-H-HHHh--CCCccchhhhhh
Q 035661 19 NIKKRLNQEQVRVLERSFTTKKK-----LDTELKLK-L-ANQL--GVPARQVAVWYQ 66 (211)
Q Consensus 19 r~Rt~~t~~Ql~~Le~~F~~~~~-----p~~~~r~~-L-a~~l--gL~~rqVkvWFq 66 (211)
+.+..+++++...|.+.+...+. .+.....+ | .... .+++..|..|+.
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 44444999999999999988763 33343333 3 2232 356666666664
No 94
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=41.23 E-value=1.2e+02 Score=27.02 Aligned_cols=33 Identities=21% Similarity=0.241 Sum_probs=18.2
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 85 QVKLENALADKRRLEKDVKLLKEELRQAQEILF 117 (211)
Q Consensus 85 ~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~ 117 (211)
+.+-++++.+...|++.+.+|+++...+..+|.
T Consensus 247 Rae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ 279 (294)
T KOG4571|consen 247 RAEKEALLGELEGLEKRNEELKDQASELEREIR 279 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455555555566666666665555555544
No 95
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.18 E-value=1.6e+02 Score=22.31 Aligned_cols=41 Identities=24% Similarity=0.279 Sum_probs=31.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhh
Q 035661 15 PNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNK 68 (211)
Q Consensus 15 ~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNR 68 (211)
.+....+..|+.+++..|. .....+.+|++-..|+-+|...
T Consensus 30 ~r~~~gyR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04783 30 PRPEGGYRRYPEETVTRLR-------------FIKRAQELGFTLDEIAELLELD 70 (126)
T ss_pred CcCCCCCeecCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhcc
Confidence 3334467889999999984 3445788999999999988654
No 96
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=40.73 E-value=1.5e+02 Score=22.09 Aligned_cols=38 Identities=13% Similarity=0.096 Sum_probs=29.0
Q ss_pred CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhh
Q 035661 18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNK 68 (211)
Q Consensus 18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNR 68 (211)
...+..|+.+++..|+.. ...+.+|++-..|+..+...
T Consensus 33 ~~gyR~Y~~~~i~~l~~I-------------~~lr~~G~sl~eI~~~l~~~ 70 (123)
T cd04770 33 ENGYRLYGEADLARLRFI-------------RRAQALGFSLAEIRELLSLR 70 (123)
T ss_pred CCCCccCCHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHHhh
Confidence 446788999999999433 34688899999998888654
No 97
>KOG3335 consensus Predicted coiled-coil protein [General function prediction only]
Probab=39.73 E-value=64 Score=26.71 Aligned_cols=54 Identities=20% Similarity=0.302 Sum_probs=27.6
Q ss_pred ccchhhhhhhhHHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 035661 58 ARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFA 118 (211)
Q Consensus 58 ~rqVkvWFqNRR~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~ 118 (211)
--...+|.+-|..+.|..+.+.+...++...+ .|+.++++++..+..+...+..
T Consensus 85 ~lv~Ey~R~~~~e~~kee~~~~e~~elr~~~~-------~l~~~i~~~~~~~~~L~~~l~~ 138 (181)
T KOG3335|consen 85 VLVFEYWRQARKERKKEEKRKQEIMELRLKVE-------KLENAIAELTKFFSQLHSKLNK 138 (181)
T ss_pred eeeehhHHhhhcchhhHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHcC
Confidence 33445677766555554444444444444444 4445555555555555544443
No 98
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.50 E-value=1.5e+02 Score=21.75 Aligned_cols=43 Identities=16% Similarity=0.227 Sum_probs=34.5
Q ss_pred CCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCC-Cccchhhhhhh
Q 035661 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGV-PARQVAVWYQN 67 (211)
Q Consensus 21 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL-~~rqVkvWFqN 67 (211)
|.+|+.+....+-+.+....+ ....+|+++|+ ...++..|-..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~ 48 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQ 48 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHH
Confidence 788999988777777766554 57789999996 99999988753
No 99
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=39.40 E-value=1.8e+02 Score=22.59 Aligned_cols=38 Identities=3% Similarity=-0.023 Sum_probs=26.4
Q ss_pred CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhH
Q 035661 19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKR 69 (211)
Q Consensus 19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR 69 (211)
..+..|+..++..|... .. .+.+|++-..|+.++.+..
T Consensus 33 ~g~R~Y~~~~l~~l~~I------------~~-lr~~G~sL~eI~~~l~~~~ 70 (134)
T cd04779 33 SNYRYYDETALDRLQLI------------EH-LKGQRLSLAEIKDQLEEVQ 70 (134)
T ss_pred CCCeeECHHHHHHHHHH------------HH-HHHCCCCHHHHHHHHHhhc
Confidence 46778999999888544 22 3667777777777776543
No 100
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=39.29 E-value=1.6e+02 Score=27.93 Aligned_cols=32 Identities=22% Similarity=0.209 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 035661 94 DKRRLEKDVKLLKEELRQAQEILFAKLMTSNN 125 (211)
Q Consensus 94 e~~~l~~e~~~l~~e~~~~~~~l~~~~~~~~~ 125 (211)
++....+|...|..++.++...+-.-++|+..
T Consensus 303 e~e~~rkelE~lR~~L~kAEkele~nS~wsaP 334 (575)
T KOG4403|consen 303 ENETSRKELEQLRVALEKAEKELEANSSWSAP 334 (575)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhccCCCCc
Confidence 34445567777777777777766655555543
No 101
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=39.21 E-value=59 Score=24.76 Aligned_cols=28 Identities=14% Similarity=0.080 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 46 LKLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
...++|..+|+++..|+.|...-+.+.|
T Consensus 124 s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 124 TMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 3568899999999999998865444433
No 102
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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, an
Probab=38.68 E-value=1.7e+02 Score=21.96 Aligned_cols=38 Identities=8% Similarity=0.251 Sum_probs=29.5
Q ss_pred CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhh
Q 035661 18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNK 68 (211)
Q Consensus 18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNR 68 (211)
...+..|+..++..|+. ....+.+|++-..|+..+.+.
T Consensus 32 ~~gyR~Y~~~~l~~l~~-------------I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 32 RGLRRQYDPQVLDRLAL-------------IALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred CCCceecCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhcc
Confidence 34788999999999843 355788899988898888653
No 103
>cd00131 PAX Paired Box domain
Probab=38.22 E-value=1e+02 Score=23.67 Aligned_cols=47 Identities=15% Similarity=0.001 Sum_probs=29.8
Q ss_pred CCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCC-------Cccchhhhhhh
Q 035661 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGV-------PARQVAVWYQN 67 (211)
Q Consensus 21 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL-------~~rqVkvWFqN 67 (211)
+...+..+...++.....++..+-.+..++...-|+ +...|-.||++
T Consensus 73 pr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 73 PRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred CCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 334567777778777777777765555444224455 67777777654
No 104
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=37.34 E-value=1.7e+02 Score=21.73 Aligned_cols=38 Identities=18% Similarity=0.238 Sum_probs=27.9
Q ss_pred CCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHH
Q 035661 20 IKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRA 70 (211)
Q Consensus 20 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~ 70 (211)
.+..|+..++..|... ...+.+|++-..|+..+.....
T Consensus 34 ~yR~Y~~~d~~~l~~I-------------~~lr~~G~sl~eI~~~l~~~~~ 71 (116)
T cd04769 34 NYRVYDAQHVECLRFI-------------KEARQLGFTLAELKAIFAGHEG 71 (116)
T ss_pred CceeeCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHhcccc
Confidence 5678999888888433 3367889999999988865443
No 105
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=37.27 E-value=36 Score=26.47 Aligned_cols=43 Identities=16% Similarity=0.109 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q 035661 24 LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRAR 71 (211)
Q Consensus 24 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r 71 (211)
+++.+..++...|- ....-.++|..+|+++..|+.|...-+.+
T Consensus 129 L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 129 LPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFRAREA 171 (182)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 44555555544432 22234578999999999999888643333
No 106
>smart00338 BRLZ basic region leucin zipper.
Probab=37.16 E-value=1.2e+02 Score=20.05 Aligned_cols=29 Identities=17% Similarity=0.288 Sum_probs=12.9
Q ss_pred hhhHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 035661 79 LDYNTIQVKLENALADKRRLEKDVKLLKE 107 (211)
Q Consensus 79 ~~~~~~~~~~~~l~~e~~~l~~e~~~l~~ 107 (211)
.....+..++..|..+...|..++..|..
T Consensus 33 ~~~~~L~~en~~L~~~~~~l~~e~~~lk~ 61 (65)
T smart00338 33 RKVEQLEAENERLKKEIERLRRELEKLKS 61 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444444444444444444444443
No 107
>PF07407 Seadorna_VP6: Seadornavirus VP6 protein; InterPro: IPR009982 This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Probab=36.88 E-value=53 Score=29.95 Aligned_cols=29 Identities=14% Similarity=0.255 Sum_probs=16.1
Q ss_pred hHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 035661 81 YNTIQVKLENALADKRRLEKDVKLLKEEL 109 (211)
Q Consensus 81 ~~~~~~~~~~l~~e~~~l~~e~~~l~~e~ 109 (211)
...|+.+++.|..||..|+.++.+|+.+.
T Consensus 34 ~~aLr~EN~~LKkEN~~Lk~eVerLE~e~ 62 (420)
T PF07407_consen 34 NFALRMENHSLKKENNDLKIEVERLENEM 62 (420)
T ss_pred hhhHHHHhHHHHHHHHHHHHHHHHHHHHh
Confidence 34555555556666666665555554443
No 108
>PF07407 Seadorna_VP6: Seadornavirus VP6 protein; InterPro: IPR009982 This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Probab=36.64 E-value=59 Score=29.67 Aligned_cols=26 Identities=15% Similarity=0.383 Sum_probs=13.2
Q ss_pred hhhhhHHHHHHhHHHHHHHHHHHHHH
Q 035661 77 LELDYNTIQVKLENALADKRRLEKDV 102 (211)
Q Consensus 77 ~~~~~~~~~~~~~~l~~e~~~l~~e~ 102 (211)
++.++..|+++++.|..+-.+|+.+.
T Consensus 37 Lr~EN~~LKkEN~~Lk~eVerLE~e~ 62 (420)
T PF07407_consen 37 LRMENHSLKKENNDLKIEVERLENEM 62 (420)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHh
Confidence 34455555555555555555554433
No 109
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=36.50 E-value=41 Score=26.55 Aligned_cols=29 Identities=17% Similarity=0.350 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 46 LKLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
...++|..+|+++..|+++...-|.+-|+
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 34588999999999999888654444443
No 110
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=36.44 E-value=27 Score=28.53 Aligned_cols=20 Identities=35% Similarity=0.551 Sum_probs=2.6
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 035661 90 NALADKRRLEKDVKLLKEEL 109 (211)
Q Consensus 90 ~l~~e~~~l~~e~~~l~~e~ 109 (211)
.|..+.++|++|...|+.|+
T Consensus 28 ~L~~~~QRLkDE~RDLKqEl 47 (166)
T PF04880_consen 28 NLREEVQRLKDELRDLKQEL 47 (166)
T ss_dssp HHHHCH--------------
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444455555555555554
No 111
>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=36.38 E-value=23 Score=21.64 Aligned_cols=23 Identities=17% Similarity=0.095 Sum_probs=19.3
Q ss_pred HHHHHHHhCCCccchhhhhhhhH
Q 035661 47 KLKLANQLGVPARQVAVWYQNKR 69 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR 69 (211)
..++|+.+|++++.|+.|.++..
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 35789999999999999986654
No 112
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=36.33 E-value=1.9e+02 Score=21.92 Aligned_cols=56 Identities=14% Similarity=0.213 Sum_probs=27.2
Q ss_pred cchhhhhhhhHHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 59 RQVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILF 117 (211)
Q Consensus 59 rqVkvWFqNRR~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~ 117 (211)
||...||-.+|.--.-.+ ....++.+.+.+..|-.+-+.=...+...+.+-...+.
T Consensus 18 Rq~e~~FlqKr~~LS~~k---pe~~lkEEi~eLK~ElqRKe~Ll~Kh~~kI~~w~~lL~ 73 (106)
T PF11594_consen 18 RQMEAFFLQKRFELSAYK---PEQVLKEEINELKEELQRKEQLLQKHYEKIDYWEKLLS 73 (106)
T ss_pred HHHHHHHHHHHHHHHhcC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 677899988877663322 23344444444443333333323333333344343333
No 113
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=36.20 E-value=38 Score=26.25 Aligned_cols=28 Identities=25% Similarity=0.309 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 46 LKLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
.-.++|..+|+++..|..|...-|.+.|
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4568999999999999998875444444
No 114
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=35.86 E-value=1.5e+02 Score=20.67 Aligned_cols=42 Identities=19% Similarity=0.116 Sum_probs=29.0
Q ss_pred hhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 76 SLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILF 117 (211)
Q Consensus 76 ~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~ 117 (211)
..-.....++.+++.+..+|..|..++..|..++..+++.-.
T Consensus 15 ~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~ 56 (72)
T PF06005_consen 15 QAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERN 56 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 334455667777777777777777778888877777765433
No 115
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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. This subgroup lacks one of the c
Probab=35.78 E-value=2e+02 Score=21.99 Aligned_cols=37 Identities=16% Similarity=0.187 Sum_probs=28.6
Q ss_pred CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhh
Q 035661 19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNK 68 (211)
Q Consensus 19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNR 68 (211)
..+..|+.+++..|. .....+.+|++-..|+.+|...
T Consensus 34 ~gyR~Y~~~~~~~l~-------------~I~~lr~~G~sL~eI~~~l~~~ 70 (133)
T cd04787 34 NGYRLYSEKDLSRLR-------------FILSARQLGFSLKDIKEILSHA 70 (133)
T ss_pred CCeeeCCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhhh
Confidence 456789999999883 3344788999999999988753
No 116
>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=35.68 E-value=11 Score=26.69 Aligned_cols=35 Identities=14% Similarity=0.180 Sum_probs=25.9
Q ss_pred HHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhh
Q 035661 33 ERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQN 67 (211)
Q Consensus 33 e~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqN 67 (211)
+..|..+.+-......+||..+|+++.-|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 34454444445556789999999999999999864
No 117
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=35.67 E-value=56 Score=26.31 Aligned_cols=29 Identities=21% Similarity=0.266 Sum_probs=20.9
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 46 LKLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
.-.++|..||++...|+++...-|.+.|+
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 34578899999999998888654444443
No 118
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=35.18 E-value=1.1e+02 Score=26.35 Aligned_cols=40 Identities=20% Similarity=0.194 Sum_probs=22.9
Q ss_pred hhHHHHHHhHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhh
Q 035661 80 DYNTIQVKLENALADKRRLEKDVK---LLKEELRQAQEILFAK 119 (211)
Q Consensus 80 ~~~~~~~~~~~l~~e~~~l~~e~~---~l~~e~~~~~~~l~~~ 119 (211)
.+..+..+++.|.+++..|+.+.. .+..|+.+++..+...
T Consensus 70 ~~~~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL~~~ 112 (276)
T PRK13922 70 SLFDLREENEELKKELLELESRLQELEQLEAENARLRELLNLK 112 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 344555556666666666665554 5566666666655443
No 119
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=34.59 E-value=1.4e+02 Score=20.06 Aligned_cols=38 Identities=16% Similarity=0.323 Sum_probs=25.8
Q ss_pred hhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 76 SLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQ 113 (211)
Q Consensus 76 ~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~ 113 (211)
....+...++.+++.+..+++.|+.+...|+....++.
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~ie 58 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIERLKNDPDYIE 58 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHH
Confidence 34456677777888888888888888888833334433
No 120
>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=34.50 E-value=47 Score=24.41 Aligned_cols=44 Identities=18% Similarity=0.232 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHH
Q 035661 24 LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARW 72 (211)
Q Consensus 24 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~ 72 (211)
+++.+...+...|- ......++|..+|+++..|..+...-+.+.
T Consensus 111 L~~~~~~ii~~~~~-----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 111 LPEREREVLVLRYL-----EGLSYKEIAEILGISVGTVKRRLKRARKKL 154 (158)
T ss_pred CCHHHHHHHhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 44555555544332 123455889999999999998886544443
No 121
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=34.18 E-value=1.9e+02 Score=28.18 Aligned_cols=43 Identities=28% Similarity=0.406 Sum_probs=32.9
Q ss_pred hhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 75 QSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILF 117 (211)
Q Consensus 75 ~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~ 117 (211)
...+.+...++.....+.++..+|++|+.+|..++..+...+.
T Consensus 151 ~~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~r~~ld 193 (546)
T KOG0977|consen 151 SELEAEINTLKRRIKALEDELKRLKAENSRLREELARARKQLD 193 (546)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence 3455667777777788888888888888888888888876544
No 122
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=34.04 E-value=2.1e+02 Score=21.73 Aligned_cols=45 Identities=18% Similarity=0.090 Sum_probs=36.1
Q ss_pred hhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 035661 76 SLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKL 120 (211)
Q Consensus 76 ~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~~~ 120 (211)
..+.....+..++..+...-..+..|+..|..|+..++..+....
T Consensus 12 ~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~ 56 (110)
T PRK13169 12 DLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEELE 56 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 445556677777888888888888999999999999998888653
No 123
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=33.56 E-value=2.1e+02 Score=21.62 Aligned_cols=38 Identities=13% Similarity=0.097 Sum_probs=28.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhh
Q 035661 16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQ 66 (211)
Q Consensus 16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFq 66 (211)
+....+..|+.+++..|... ..++.+|++-..|+..|.
T Consensus 31 r~~~gyR~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 31 RSEGGYRTYTQQHLDELRLI-------------SRARQVGFSLEECKELLN 68 (127)
T ss_pred cCCCCCeecCHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHH
Confidence 33456889999999988433 347788999888888775
No 124
>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=33.40 E-value=38 Score=22.32 Aligned_cols=35 Identities=23% Similarity=0.336 Sum_probs=26.5
Q ss_pred HHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhh
Q 035661 27 EQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWY 65 (211)
Q Consensus 27 ~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWF 65 (211)
.|+..|+-.|. .+..+.. +||..+|++++.|+.-.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHH
Confidence 57888888888 6666554 89999999998887544
No 125
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=33.29 E-value=94 Score=24.09 Aligned_cols=28 Identities=18% Similarity=0.082 Sum_probs=20.8
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 47 KLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
..++|..+|+++..|++|...-|.+.|+
T Consensus 127 ~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 127 YEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4578889999999999888754444443
No 126
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=33.09 E-value=62 Score=31.36 Aligned_cols=41 Identities=15% Similarity=0.117 Sum_probs=32.5
Q ss_pred HhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 72 WKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQA 112 (211)
Q Consensus 72 ~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~ 112 (211)
+.-...+...+++-++++.|..||..|+.+...|..|+..+
T Consensus 302 Ey~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~En~~~ 342 (655)
T KOG4343|consen 302 EYMLGLEARLQALLSENEQLKKENATLKRQLDELVSENQRL 342 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCccc
Confidence 33346677888888899999999999998888888877654
No 127
>PRK10072 putative transcriptional regulator; Provisional
Probab=32.84 E-value=58 Score=24.05 Aligned_cols=41 Identities=17% Similarity=0.182 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHH
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRA 70 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~ 70 (211)
..+...+..|...-.. ...+||+.+|++..-|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3455556666443222 2578999999999999999987654
No 128
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=32.70 E-value=2.5e+02 Score=22.16 Aligned_cols=31 Identities=16% Similarity=0.320 Sum_probs=14.5
Q ss_pred hHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 81 YNTIQVKLENALADKRRLEKDVKLLKEELRQ 111 (211)
Q Consensus 81 ~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~ 111 (211)
...+.++++.|..|+.++.-|.+.++..+..
T Consensus 83 k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~ 113 (135)
T KOG4196|consen 83 KAELQQQVEKLKEENSRLRRELDAYKSKYEA 113 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444555555444444444443
No 129
>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=31.37 E-value=29 Score=23.15 Aligned_cols=27 Identities=33% Similarity=0.698 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 46 LKLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
...++|..||++.+.|..|-+ |-+|..
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 356789999999999999985 445444
No 130
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=30.88 E-value=54 Score=26.80 Aligned_cols=29 Identities=31% Similarity=0.289 Sum_probs=20.9
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 46 LKLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
...++|..+|+++..|+++...-+.+.++
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34578999999999998887654444443
No 131
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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 dissimil
Probab=30.71 E-value=2.1e+02 Score=20.77 Aligned_cols=41 Identities=12% Similarity=0.142 Sum_probs=28.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhh
Q 035661 14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQN 67 (211)
Q Consensus 14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqN 67 (211)
+.+....+..|+.+++..|... .. .+++|++-..|+..+..
T Consensus 29 ~~r~~~g~R~Y~~~dl~~l~~I------------~~-l~~~G~~l~ei~~~~~~ 69 (102)
T cd04775 29 SARSEANYRLYSEADLSRLEKI------------VF-LQAGGLPLEEIAGCLAQ 69 (102)
T ss_pred CCCCCCCCeeeCHHHHHHHHHH------------HH-HHHCCCCHHHHHHHHcC
Confidence 3333446778999999988544 22 47778888888876654
No 132
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=30.71 E-value=1.2e+02 Score=20.46 Aligned_cols=30 Identities=20% Similarity=0.160 Sum_probs=17.6
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 85 QVKLENALADKRRLEKDVKLLKEELRQAQE 114 (211)
Q Consensus 85 ~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~ 114 (211)
+.+.+.+.+....|+.++..|..|+..+.+
T Consensus 13 rEEVevLK~~I~eL~~~n~~Le~EN~~Lk~ 42 (59)
T PF01166_consen 13 REEVEVLKEQIAELEERNSQLEEENNLLKQ 42 (59)
T ss_dssp TTSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 334455555556666666666666666554
No 133
>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=30.54 E-value=2e+02 Score=22.60 Aligned_cols=47 Identities=21% Similarity=0.196 Sum_probs=34.6
Q ss_pred CCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 21 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
.+.+|+.|..+|...+ .. ....++|..+|+++.-|..+-..-+.+-+
T Consensus 4 ~~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred cCCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 4678999999998843 22 24678999999999998887764444443
No 134
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=30.50 E-value=98 Score=23.76 Aligned_cols=28 Identities=18% Similarity=0.095 Sum_probs=20.5
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 47 KLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
-.++|..+|+++..|++.+..-|.+.|+
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3478899999999999888655544443
No 135
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=30.12 E-value=1.7e+02 Score=19.67 Aligned_cols=33 Identities=21% Similarity=0.369 Sum_probs=19.1
Q ss_pred hhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 80 DYNTIQVKLENALADKRRLEKDVKLLKEELRQA 112 (211)
Q Consensus 80 ~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~ 112 (211)
....++.+...+..+...++.++..|..++..+
T Consensus 18 ~~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 18 RYYQLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344555555555666666666666666655554
No 136
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.05 E-value=52 Score=24.26 Aligned_cols=39 Identities=18% Similarity=0.156 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccch
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQV 61 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqV 61 (211)
++.++|...-...|+.+--.++...+++|..||+++--|
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 467788877777777777777788899999999887443
No 137
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=29.83 E-value=32 Score=21.33 Aligned_cols=23 Identities=26% Similarity=0.380 Sum_probs=17.3
Q ss_pred HHHHHHHHHhCCCccchhhhhhh
Q 035661 45 ELKLKLANQLGVPARQVAVWYQN 67 (211)
Q Consensus 45 ~~r~~La~~lgL~~rqVkvWFqN 67 (211)
....++|+.+|++...|..|...
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 45678999999999999999853
No 138
>PF02777 Sod_Fe_C: Iron/manganese superoxide dismutases, C-terminal domain Note: SCOP classifies the two domains separately.; InterPro: IPR019832 Superoxide dismutases (SODs) (1.15.1.1 from EC) catalyse the conversion of superoxide radicals to molecular oxygen. Their function is to destroy the radicals that are normally produced within cells and are toxic to biological systems. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one [, , ]. This family includes both single metal-binding SODs and cambialistic SOD, which can bind either Mn or Fe. Fe/MnSODs are ubiquitous enzymes that are responsible for the majority of SOD activity in prokaryotes, fungi, blue-green algae and mitochondria. Fe/MnSODs are found as homodimers or homotetramers. The structure of Fe/MnSODs can be divided into two domains, an alpha N-terminal domain and an alpha/beta C-terminal domain, connected by a loop. The structure of the N-terminal domain consists of a two helices in an antiparallel hairpin, with a left-handed twist []. The structure of the C-terminal domain is of the alpha/beta type, and consists of a three-stranded antiparallel beta-sheet in the order 213, along with four helices in the arrangement alpha/beta(2)/alpha/beta/alpha(2) []. This entry represents the C-terminal domain of Manganese/iron superoxide dismutase. ; GO: 0004784 superoxide dismutase activity, 0046872 metal ion binding, 0006801 superoxide metabolic process, 0055114 oxidation-reduction process; PDB: 1KKC_Y 2GOJ_B 1UES_C 1UER_C 1QNN_A 1MY6_A 1MA1_F 1P7G_Q 3EVK_D 2GPC_A ....
Probab=29.56 E-value=18 Score=26.74 Aligned_cols=22 Identities=23% Similarity=0.302 Sum_probs=19.1
Q ss_pred cchHHHHHHHHhccCCCCCchhh
Q 035661 181 QIDHELFACLIGNGGHSNSSGWE 203 (211)
Q Consensus 181 ~i~~e~~~~~~~~~~~~~~~~~~ 203 (211)
+++ .+-++|+..|++.-||+|+
T Consensus 17 S~d-~fk~~f~~~a~~~~GsGW~ 38 (106)
T PF02777_consen 17 SFD-NFKAEFTAAALSVFGSGWV 38 (106)
T ss_dssp SHH-HHHHHHHHHHHHSSSSEEE
T ss_pred CHH-HHHHHHHHHHhcCCCCCee
Confidence 345 8899999999999999997
No 139
>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=29.27 E-value=1.1e+02 Score=18.73 Aligned_cols=36 Identities=17% Similarity=0.248 Sum_probs=25.8
Q ss_pred CHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhh
Q 035661 25 NQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQ 66 (211)
Q Consensus 25 t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFq 66 (211)
++.+...+...+. . ....++|..+++++..|..|..
T Consensus 2 ~~~e~~i~~~~~~--~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLAE--G----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHH
Confidence 4556666655442 2 2567889999999999998885
No 140
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=29.23 E-value=60 Score=24.52 Aligned_cols=26 Identities=15% Similarity=0.243 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHH
Q 035661 46 LKLKLANQLGVPARQVAVWYQNKRAR 71 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFqNRR~r 71 (211)
...++|..+|+++..|+.+...-|.+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKE 156 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 34578899999999998877543333
No 141
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=28.85 E-value=34 Score=22.63 Aligned_cols=23 Identities=17% Similarity=0.226 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCccchhhhhhhhH
Q 035661 47 KLKLANQLGVPARQVAVWYQNKR 69 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR 69 (211)
..++|+.+|+++..|+.|-....
T Consensus 3 i~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTTS
T ss_pred HHHHHHHHCcCHHHHHHHHHhcC
Confidence 35789999999999999976543
No 142
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=28.71 E-value=54 Score=26.20 Aligned_cols=30 Identities=17% Similarity=0.256 Sum_probs=21.8
Q ss_pred HHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 44 TELKLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 44 ~~~r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
.....++|..+|+++..|++|+..-|.+-|
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 344568899999999999999864444333
No 143
>PRK11546 zraP zinc resistance protein; Provisional
Probab=28.57 E-value=1.7e+02 Score=23.27 Aligned_cols=18 Identities=17% Similarity=0.176 Sum_probs=12.7
Q ss_pred CCCCCHHHHHHHHHHhcc
Q 035661 21 KKRLNQEQVRVLERSFTT 38 (211)
Q Consensus 21 Rt~~t~~Ql~~Le~~F~~ 38 (211)
...+|+||...++.++++
T Consensus 41 ~~~LT~EQQa~~q~I~~~ 58 (143)
T PRK11546 41 AAPLTTEQQAAWQKIHND 58 (143)
T ss_pred cccCCHHHHHHHHHHHHH
Confidence 345888888888777544
No 144
>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=28.03 E-value=1.2e+02 Score=23.16 Aligned_cols=26 Identities=27% Similarity=0.133 Sum_probs=19.0
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHH
Q 035661 45 ELKLKLANQLGVPARQVAVWYQNKRA 70 (211)
Q Consensus 45 ~~r~~La~~lgL~~rqVkvWFqNRR~ 70 (211)
..-.++|..+|++...|+++...-|.
T Consensus 128 ~~~~eIA~~l~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 128 VSLTALAEQLGRTVNAVYKALSRLRV 153 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34567899999999999987653333
No 145
>PRK10884 SH3 domain-containing protein; Provisional
Probab=27.90 E-value=3.2e+02 Score=22.97 Aligned_cols=30 Identities=13% Similarity=0.071 Sum_probs=13.1
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 84 IQVKLENALADKRRLEKDVKLLKEELRQAQ 113 (211)
Q Consensus 84 ~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~ 113 (211)
++.++..+..+...++.++..|..++...+
T Consensus 137 L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~ 166 (206)
T PRK10884 137 LKEENQKLKNQLIVAQKKVDAANLQLDDKQ 166 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444444444444443
No 146
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=26.89 E-value=2e+02 Score=19.27 Aligned_cols=28 Identities=18% Similarity=0.281 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 035661 91 ALADKRRLEKDVKLLKEELRQAQEILFA 118 (211)
Q Consensus 91 l~~e~~~l~~e~~~l~~e~~~~~~~l~~ 118 (211)
++.+...+..|+..|..++..++..+.+
T Consensus 31 vL~~R~~l~~e~~~L~~qN~eLr~lLkq 58 (60)
T PF14775_consen 31 VLLDRAALIQEKESLEQQNEELRSLLKQ 58 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444555556666666666666655544
No 147
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=26.46 E-value=1.2e+02 Score=23.84 Aligned_cols=30 Identities=13% Similarity=0.167 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 44 TELKLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 44 ~~~r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
...-.++|..+|+++..|++++..-|.+-+
T Consensus 152 g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 152 DLSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 344568899999999999988864444433
No 148
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=26.22 E-value=68 Score=25.47 Aligned_cols=28 Identities=7% Similarity=0.185 Sum_probs=20.4
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 47 KLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
-.++|..+|++...|+.+...-|.+.|+
T Consensus 147 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 147 NIEAAAVMDISVDALESLLARGRRALRA 174 (186)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 4578999999999999887644444443
No 149
>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=26.16 E-value=73 Score=19.67 Aligned_cols=39 Identities=21% Similarity=0.348 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhh
Q 035661 22 KRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWY 65 (211)
Q Consensus 22 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWF 65 (211)
..++.+|++.+.+.|..- ....++|+.+|++...|..++
T Consensus 4 ~~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 346666666666666544 346789999999988887655
No 150
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=26.11 E-value=2.9e+02 Score=20.79 Aligned_cols=37 Identities=14% Similarity=0.116 Sum_probs=28.1
Q ss_pred CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhh
Q 035661 18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQN 67 (211)
Q Consensus 18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqN 67 (211)
...+..|+.+++..|... ...+.+|++-..|+..+..
T Consensus 33 ~~gyR~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd04784 33 ANNYRLYDEEHLERLLFI-------------RRCRSLDMSLDEIRTLLQL 69 (127)
T ss_pred CCCCeecCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHHh
Confidence 356788999999888433 4477889999999887764
No 151
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=26.02 E-value=63 Score=24.94 Aligned_cols=27 Identities=19% Similarity=0.198 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 47 KLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
-.++|..+|+++..|+.+...-|.+-+
T Consensus 131 ~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 131 YKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 457788888888888877764444433
No 152
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=26.00 E-value=95 Score=24.68 Aligned_cols=25 Identities=20% Similarity=0.089 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHH
Q 035661 46 LKLKLANQLGVPARQVAVWYQNKRA 70 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFqNRR~ 70 (211)
.-.++|..+|++...|+.+...-|.
T Consensus 157 s~~EIA~~lgis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHRALA 181 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4568899999999998887754333
No 153
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=25.43 E-value=1.9e+02 Score=27.46 Aligned_cols=53 Identities=13% Similarity=0.166 Sum_probs=36.6
Q ss_pred hHHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 035661 68 KRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKL 120 (211)
Q Consensus 68 RR~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~~~ 120 (211)
||.++.....+.++...-.++..|...-.+|+.++..|-+++...+..+.+..
T Consensus 268 rkKkeYid~LE~rv~~~taeNqeL~kkV~~Le~~N~sLl~qL~klQt~v~q~a 320 (472)
T KOG0709|consen 268 RKKKEYIDGLESRVSAFTAENQELQKKVEELELSNRSLLAQLKKLQTLVIQVA 320 (472)
T ss_pred HhHhhHHHHHhhhhhhcccCcHHHHHHHHHHhhccHHHHHHHHHHHHHHhhcc
Confidence 55566666777777666666777777777777777777777777776665543
No 154
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=25.38 E-value=2.8e+02 Score=20.47 Aligned_cols=39 Identities=8% Similarity=0.105 Sum_probs=27.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhh
Q 035661 16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQN 67 (211)
Q Consensus 16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqN 67 (211)
+....+..|+.+++..|... ...+.+|++-..|+..+..
T Consensus 30 r~~~g~R~Y~~~~~~~l~~I-------------~~lr~~G~sl~eI~~~l~~ 68 (112)
T cd01282 30 RSANGYRDYDEAAVDRVRQI-------------RRLLAAGLTLEEIREFLPC 68 (112)
T ss_pred cCCCCCeecCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHHH
Confidence 33456788999999988443 3356788888888876643
No 155
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=25.02 E-value=3.8e+02 Score=21.83 Aligned_cols=28 Identities=14% Similarity=0.321 Sum_probs=11.2
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 035661 83 TIQVKLENALADKRRLEKDVKLLKEELR 110 (211)
Q Consensus 83 ~~~~~~~~l~~e~~~l~~e~~~l~~e~~ 110 (211)
.++.+++.|..++..|.++...+.+++.
T Consensus 115 ~l~~~~e~Le~e~~~L~~~~~~~~eDY~ 142 (161)
T TIGR02894 115 SLQKRNEELEKELEKLRQRLSTIEEDYQ 142 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333334444444444443333343333
No 156
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=25.01 E-value=1.9e+02 Score=19.94 Aligned_cols=38 Identities=16% Similarity=0.299 Sum_probs=25.2
Q ss_pred hhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 76 SLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQE 114 (211)
Q Consensus 76 ~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~ 114 (211)
....+...++.+.+.+..++.+|+.|...|.. ..++..
T Consensus 28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~-~~rIe~ 65 (85)
T TIGR02209 28 QLNNELQKLQLEIDKLQKEWRDLQLEVAELSR-HERIEK 65 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-HHHHHH
Confidence 34445566777777777888888888877765 344443
No 157
>PRK10403 transcriptional regulator NarP; Provisional
Probab=24.77 E-value=84 Score=24.32 Aligned_cols=46 Identities=17% Similarity=0.205 Sum_probs=35.0
Q ss_pred CCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 22 KRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 22 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
..+|+.+.++|+..... ..+.++|+.++++++-|++...+=+.|-.
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 35899999999876543 34678899999999999998876555543
No 158
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=24.65 E-value=1.2e+02 Score=21.59 Aligned_cols=44 Identities=14% Similarity=0.194 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHhccC-----CCCCHHHHHHHHHHhCCCccchhhhhh
Q 035661 23 RLNQEQVRVLERSFTTK-----KKLDTELKLKLANQLGVPARQVAVWYQ 66 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~-----~~p~~~~r~~La~~lgL~~rqVkvWFq 66 (211)
-++.+|+..|...|... .+.+..+...+.+.+|+++..|..+|.
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 46889999999998753 356777777766667777766666553
No 159
>PF07795 DUF1635: Protein of unknown function (DUF1635); InterPro: IPR012862 The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids long.
Probab=24.52 E-value=4.4e+02 Score=22.44 Aligned_cols=15 Identities=7% Similarity=0.217 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHHHHH
Q 035661 92 LADKRRLEKDVKLLK 106 (211)
Q Consensus 92 ~~e~~~l~~e~~~l~ 106 (211)
..|.++.+.+..+|-
T Consensus 46 ~~ERDEAr~qlq~Ll 60 (214)
T PF07795_consen 46 YQERDEAREQLQKLL 60 (214)
T ss_pred HHHHHHHHHHHHHHH
Confidence 334444444444443
No 160
>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=24.49 E-value=86 Score=25.89 Aligned_cols=44 Identities=14% Similarity=0.139 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHH
Q 035661 24 LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARW 72 (211)
Q Consensus 24 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~ 72 (211)
+++.+..+|...|-. .....++|..+|++...|+.+...-+.+.
T Consensus 176 L~~~~r~il~l~y~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~~L 219 (224)
T TIGR02479 176 LSEREQLVLSLYYYE-----ELNLKEIGEVLGLTESRVSQIHSQALKKL 219 (224)
T ss_pred CCHHHHHHHHHHHhC-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 455555555555522 22357889999999999888775444333
No 161
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=24.49 E-value=89 Score=24.65 Aligned_cols=29 Identities=17% Similarity=0.054 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 46 LKLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
.-.++|..+|++...|+.++..-|.+-|.
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 34588999999999999888655554443
No 162
>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=24.46 E-value=51 Score=19.54 Aligned_cols=24 Identities=21% Similarity=0.408 Sum_probs=20.1
Q ss_pred HHHHHHHhCCCccchhhhhhhhHH
Q 035661 47 KLKLANQLGVPARQVAVWYQNKRA 70 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR~ 70 (211)
..++|+.+|++++-|..|.++...
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467899999999999999876554
No 163
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.38 E-value=1.5e+02 Score=23.51 Aligned_cols=28 Identities=14% Similarity=0.234 Sum_probs=19.8
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 47 KLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
-.++|..+|+++..|++-...-|.+.++
T Consensus 150 ~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 150 VEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4578889999999998877544444443
No 164
>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=24.25 E-value=43 Score=22.20 Aligned_cols=21 Identities=10% Similarity=0.254 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCccchhhhhhh
Q 035661 47 KLKLANQLGVPARQVAVWYQN 67 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqN 67 (211)
..++|+.+|++++.++.|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999865
No 165
>PRK09480 slmA division inhibitor protein; Provisional
Probab=24.20 E-value=74 Score=25.01 Aligned_cols=40 Identities=18% Similarity=0.260 Sum_probs=31.2
Q ss_pred HHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHH
Q 035661 30 RVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRA 70 (211)
Q Consensus 30 ~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~ 70 (211)
+.....|...+. ......+||++.|+++.-+-.+|.|+-.
T Consensus 17 ~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 17 QALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 333444555555 7888999999999999999999998654
No 166
>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=24.04 E-value=71 Score=25.21 Aligned_cols=30 Identities=13% Similarity=0.019 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 44 TELKLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 44 ~~~r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
...-.++|..+|+++..|+++...-|.+-|
T Consensus 154 ~~s~~EIA~~lgis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 154 GLSYEDIARIMDCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 334568899999999999988864443333
No 167
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=23.86 E-value=1.7e+02 Score=22.38 Aligned_cols=27 Identities=15% Similarity=0.340 Sum_probs=18.7
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 47 KLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
-.++|..+|+++..|+.+...-|.+.|
T Consensus 130 ~~eIA~~lgis~~tV~~~i~ra~~~Lr 156 (166)
T PRK09639 130 YKEIAEALGIKESSVGTTLARAKKKFR 156 (166)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 456788888888888887754444433
No 168
>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=23.77 E-value=43 Score=22.30 Aligned_cols=21 Identities=14% Similarity=0.267 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCccchhhhhhh
Q 035661 47 KLKLANQLGVPARQVAVWYQN 67 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqN 67 (211)
..++|+.+|++++.++.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999864
No 169
>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids [].
Probab=23.43 E-value=2.6e+02 Score=19.44 Aligned_cols=42 Identities=19% Similarity=0.293 Sum_probs=29.8
Q ss_pred hhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 76 SLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILF 117 (211)
Q Consensus 76 ~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~ 117 (211)
..+..+..++..++....++..|..++..|...+..+...+.
T Consensus 25 ~Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~Ls~ql~ 66 (70)
T PF04899_consen 25 EWQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQRLSEQLE 66 (70)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344567777777777777777888888888777777665543
No 170
>PHA02955 hypothetical protein; Provisional
Probab=23.37 E-value=91 Score=26.56 Aligned_cols=42 Identities=7% Similarity=0.192 Sum_probs=32.5
Q ss_pred HHHHHHHHHhccC-CCCCHHHHHHHHHHhCCCccchhhhhhhh
Q 035661 27 EQVRVLERSFTTK-KKLDTELKLKLANQLGVPARQVAVWYQNK 68 (211)
Q Consensus 27 ~Ql~~Le~~F~~~-~~p~~~~r~~La~~lgL~~rqVkvWFqNR 68 (211)
.|+..|-+.|.+. ....+.+|.++++++|+....|..||.+.
T Consensus 61 ~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 61 KNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 4556665666554 56788999999999999998888898763
No 171
>COG5414 TATA-binding protein-associated factor [Transcription]
Probab=23.22 E-value=3.7e+02 Score=24.33 Aligned_cols=67 Identities=19% Similarity=0.304 Sum_probs=39.3
Q ss_pred HHHHHHHhccCCCCCHHHHHH--HHHHhCCCccchhhhhhhhHHHHhhhhhhhhhHHHHHHhHHHHHHHHHHH
Q 035661 29 VRVLERSFTTKKKLDTELKLK--LANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLE 99 (211)
Q Consensus 29 l~~Le~~F~~~~~p~~~~r~~--La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~ 99 (211)
+.+||++|+.+.+.+..-++. .-..-||++ --.|.++||-|.|--... ...+....+.|++...+.+
T Consensus 152 lvA~E~v~hensflN~~lk~~~~y~y~hGlsp--Pl~~Vr~rRFRkk~s~~e--Ie~VEk~Vd~LL~~D~~Ae 220 (392)
T COG5414 152 LVALEAVYHENSFLNKHLKKEREYYYLHGLSP--PLKYVRARRFRKKSSKIE--IEEVEKKVDDLLEKDMKAE 220 (392)
T ss_pred HHHHhhhcccchhhHHHHHHHhhhhccccCCc--hhHHHHHHHHHhhcCcch--HHHHHHHHHHHHHHhhhhh
Confidence 456999999998875433322 112226665 457999999886654433 4445555555555443333
No 172
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=23.01 E-value=3e+02 Score=24.88 Aligned_cols=50 Identities=16% Similarity=0.276 Sum_probs=26.0
Q ss_pred hhhhhhhhHHHHhhhh-hhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 035661 61 VAVWYQNKRARWKTQS-LELDYNTIQVKLENALADKRRLEKDVKLLKEELR 110 (211)
Q Consensus 61 VkvWFqNRR~r~k~~~-~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~ 110 (211)
+++||+|.|+-.+--. -..+...+...+..++.....-+++...|..++.
T Consensus 16 CKiWi~dN~~Sv~~He~GkrHke~V~Kritdi~rks~~kekeekKls~~la 66 (336)
T KOG0150|consen 16 CKIWIKDNPASVRFHERGKRHKENVAKRITDIHRKSLKKEKEEKKLSKELA 66 (336)
T ss_pred hhhhhcCChHHHHhHhhhhHHHHHHHHHHHHHHHhhHHHHHHHHhhhhHHH
Confidence 6899998877654322 2233445566666665443333333333333333
No 173
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=22.78 E-value=4.2e+02 Score=26.53 Aligned_cols=6 Identities=17% Similarity=0.069 Sum_probs=2.3
Q ss_pred HHHHHH
Q 035661 112 AQEILF 117 (211)
Q Consensus 112 ~~~~l~ 117 (211)
+.++|.
T Consensus 507 lEkQL~ 512 (697)
T PF09726_consen 507 LEKQLQ 512 (697)
T ss_pred HHHHHH
Confidence 333343
No 174
>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=22.67 E-value=43 Score=20.25 Aligned_cols=19 Identities=26% Similarity=0.398 Sum_probs=15.1
Q ss_pred HHHHHHhCCCccchhhhhh
Q 035661 48 LKLANQLGVPARQVAVWYQ 66 (211)
Q Consensus 48 ~~La~~lgL~~rqVkvWFq 66 (211)
-++|+.+|++.+.|+.|=.
T Consensus 3 ~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 4679999999999998864
No 175
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=22.67 E-value=1.8e+02 Score=22.05 Aligned_cols=25 Identities=12% Similarity=0.110 Sum_probs=18.5
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHH
Q 035661 47 KLKLANQLGVPARQVAVWYQNKRAR 71 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR~r 71 (211)
-.++|..+|+++..|++....-|.+
T Consensus 125 ~~EIA~~lgis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 125 VAETAAAMGCSEGSVKTHCSRATHA 149 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4588999999999998877543333
No 176
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=22.65 E-value=1.1e+02 Score=24.43 Aligned_cols=28 Identities=14% Similarity=0.259 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 47 KLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
..++|..+|++...|+...+.-|.+-|+
T Consensus 150 ~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 150 IEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4578888888888888766544444444
No 177
>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=22.64 E-value=1.5e+02 Score=23.28 Aligned_cols=20 Identities=20% Similarity=0.298 Sum_probs=13.8
Q ss_pred HHHHHHHhCCCccchhhhhh
Q 035661 47 KLKLANQLGVPARQVAVWYQ 66 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFq 66 (211)
..++|..+|+++..|+++..
T Consensus 119 ~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 119 QQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 34677777777777776654
No 178
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=22.41 E-value=4.6e+02 Score=22.19 Aligned_cols=38 Identities=21% Similarity=0.331 Sum_probs=18.3
Q ss_pred hhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 78 ELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEI 115 (211)
Q Consensus 78 ~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~ 115 (211)
..++..+..+.+.+...++.+++.+..+..++..+...
T Consensus 55 ~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~q 92 (251)
T PF11932_consen 55 LAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQ 92 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444555555555555555554444444444444333
No 179
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=22.26 E-value=3.7e+02 Score=21.87 Aligned_cols=32 Identities=19% Similarity=0.333 Sum_probs=13.9
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 82 NTIQVKLENALADKRRLEKDVKLLKEELRQAQ 113 (211)
Q Consensus 82 ~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~ 113 (211)
..++.++..+...+..|++++..|..++..+.
T Consensus 107 ~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~ 138 (161)
T TIGR02894 107 ERLKNQNESLQKRNEELEKELEKLRQRLSTIE 138 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444444444444444444444444333
No 180
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=22.23 E-value=99 Score=25.79 Aligned_cols=29 Identities=17% Similarity=0.177 Sum_probs=22.5
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 46 LKLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
.-.++|..+|++...|+.+...-+.+.|+
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45688999999999999988765555544
No 181
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=22.04 E-value=1e+02 Score=26.13 Aligned_cols=46 Identities=11% Similarity=0.255 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
.+++.+..+|...|- ....-.++|..+|+++..|+.|...-+.+.|
T Consensus 205 ~L~~~~r~vl~l~~~-----~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr 250 (257)
T PRK08583 205 VLSDREKSIIQCTFI-----ENLSQKETGERLGISQMHVSRLQRQAIKKLR 250 (257)
T ss_pred hCCHHHHHHHHHHHh-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 355566666665542 2223578999999999999988764444443
No 182
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.97 E-value=3.5e+02 Score=20.36 Aligned_cols=37 Identities=14% Similarity=0.097 Sum_probs=28.0
Q ss_pred CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhh
Q 035661 18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQN 67 (211)
Q Consensus 18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqN 67 (211)
...+..|+.+++..|... ..++.+|++-..|+.+|.-
T Consensus 33 ~~g~R~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~ 69 (126)
T cd04785 33 AGGYRLYGAAHVERLRFI-------------RRARDLGFSLEEIRALLAL 69 (126)
T ss_pred CCCccccCHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHhh
Confidence 346778999999988543 3367889998888888853
No 183
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.97 E-value=3.7e+02 Score=24.68 Aligned_cols=34 Identities=18% Similarity=0.224 Sum_probs=16.2
Q ss_pred hhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 80 DYNTIQVKLENALADKRRLEKDVKLLKEELRQAQ 113 (211)
Q Consensus 80 ~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~ 113 (211)
....++..-+.+.....+|+.+..+|+.+...++
T Consensus 233 eq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~ 266 (365)
T KOG2391|consen 233 EQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQ 266 (365)
T ss_pred HHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 3344444445554455555555555554444433
No 184
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=21.92 E-value=3.6e+02 Score=20.42 Aligned_cols=38 Identities=11% Similarity=0.042 Sum_probs=28.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhh
Q 035661 16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQ 66 (211)
Q Consensus 16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFq 66 (211)
+....+..|+.+++..|..+ ..++.+|++-..|+..+.
T Consensus 31 r~~~gyR~Y~~~~l~~l~~I-------------~~lr~lG~sL~eI~~~l~ 68 (127)
T TIGR02047 31 RTDNNYRVYTVGHVERLAFI-------------RNCRTLDMSLAEIRQLLR 68 (127)
T ss_pred cCCCCCCcCCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHH
Confidence 33457788999999888433 346888999999998875
No 185
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=21.88 E-value=1.1e+02 Score=23.55 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRAR 71 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r 71 (211)
.+|+.+.+.|+....- ..+.++|..++++++.|++..++=|.|
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEK 179 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 5888888888776643 257788999999999998877655444
No 186
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=21.55 E-value=2.8e+02 Score=19.07 Aligned_cols=40 Identities=15% Similarity=0.079 Sum_probs=21.6
Q ss_pred hhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 035661 80 DYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAK 119 (211)
Q Consensus 80 ~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~~ 119 (211)
.+..++.++..+..+...+..|...|.+.+..+...+-.+
T Consensus 15 ~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar~rvEam 54 (65)
T TIGR02449 15 YLERLKSENRLLRAQEKTWREERAQLLEKNEQARQKVEAM 54 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455555555555555566666666666555554443
No 187
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=21.46 E-value=1.1e+02 Score=24.20 Aligned_cols=23 Identities=17% Similarity=0.212 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCccchhhhhhhhH
Q 035661 47 KLKLANQLGVPARQVAVWYQNKR 69 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR 69 (211)
-.++|..+|+++..|+++...-|
T Consensus 154 ~~eIA~~lgis~~~V~~~l~ra~ 176 (186)
T PRK13919 154 HREAAQLLGLPLGTLKTRARRAL 176 (186)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHH
Confidence 34778888999888887765333
No 188
>PF10482 CtIP_N: Tumour-suppressor protein CtIP N-terminal domain; InterPro: IPR019518 CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control []. This N-terminal domain carries a coiled-coil region and is essential for homodimerisation of the protein []. The C-terminal domain is family CtIP_C and carries functionally important CxxC and RHR motifs, absence of which lead cells to grow slowly and show hypersensitivity to genotoxins [].
Probab=21.38 E-value=3.1e+02 Score=21.18 Aligned_cols=22 Identities=32% Similarity=0.377 Sum_probs=14.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH
Q 035661 88 LENALADKRRLEKDVKLLKEEL 109 (211)
Q Consensus 88 ~~~l~~e~~~l~~e~~~l~~e~ 109 (211)
+..++.|...|++|+..|.+|+
T Consensus 98 i~~L~nE~n~L~eEN~~L~eEl 119 (120)
T PF10482_consen 98 IFELTNEMNTLKEENKKLKEEL 119 (120)
T ss_pred HHHHHHHHHhHHHHHHHHHHHh
Confidence 3345667777777777776654
No 189
>PF08961 DUF1875: Domain of unknown function (DUF1875); InterPro: IPR015056 MIT can be found in the Nuclear receptor-binding factor 2, it has no known function. ; PDB: 2CRB_A.
Probab=21.30 E-value=31 Score=29.56 Aligned_cols=34 Identities=26% Similarity=0.307 Sum_probs=0.0
Q ss_pred hhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 79 LDYNTIQVKLENALADKRRLEKDVKLLKEELRQA 112 (211)
Q Consensus 79 ~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~ 112 (211)
.....++...+.++++|++|++|+.+|..++.++
T Consensus 129 T~I~dLrrlVe~L~aeNErLr~EnkqL~ae~arL 162 (243)
T PF08961_consen 129 TKIADLRRLVEFLLAENERLRRENKQLKAENARL 162 (243)
T ss_dssp ----------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566666777889999999999988888876
No 190
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=21.15 E-value=1.8e+02 Score=23.48 Aligned_cols=28 Identities=25% Similarity=0.153 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661 46 LKLKLANQLGVPARQVAVWYQNKRARWK 73 (211)
Q Consensus 46 ~r~~La~~lgL~~rqVkvWFqNRR~r~k 73 (211)
...++|..+|+++..|++++..-|.+-|
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr 158 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLA 158 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3468899999999999988875444444
No 191
>PRK14127 cell division protein GpsB; Provisional
Probab=21.11 E-value=3.7e+02 Score=20.33 Aligned_cols=39 Identities=13% Similarity=0.233 Sum_probs=29.2
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 035661 82 NTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKL 120 (211)
Q Consensus 82 ~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~~~ 120 (211)
..+..-++.+..+...+.+++..|+.++..+...+....
T Consensus 26 ~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~ 64 (109)
T PRK14127 26 DEVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELT 64 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556677777888888888888888888887777665
No 192
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=21.01 E-value=3.2e+02 Score=23.46 Aligned_cols=24 Identities=21% Similarity=0.338 Sum_probs=13.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 88 LENALADKRRLEKDVKLLKEELRQ 111 (211)
Q Consensus 88 ~~~l~~e~~~l~~e~~~l~~e~~~ 111 (211)
+..+.+||++|++|+..|+.++..
T Consensus 71 ~~~l~~en~~L~~e~~~l~~~~~~ 94 (276)
T PRK13922 71 LFDLREENEELKKELLELESRLQE 94 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555666666666666555553
No 193
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=20.96 E-value=3.3e+02 Score=26.06 Aligned_cols=38 Identities=13% Similarity=0.197 Sum_probs=20.0
Q ss_pred hhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661 79 LDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEIL 116 (211)
Q Consensus 79 ~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l 116 (211)
.+...++.+.+.+......++..+..+..++..++.++
T Consensus 83 KqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql 120 (475)
T PRK13729 83 KQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQV 120 (475)
T ss_pred HHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 33344444444333444555566666666666666555
No 194
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=20.77 E-value=3.8e+02 Score=23.31 Aligned_cols=15 Identities=40% Similarity=0.534 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHHHHH
Q 035661 97 RLEKDVKLLKEELRQ 111 (211)
Q Consensus 97 ~l~~e~~~l~~e~~~ 111 (211)
+++.++++|.+.+..
T Consensus 174 ~le~E~s~LeE~~~~ 188 (290)
T COG4026 174 RLEVENSRLEEMLKK 188 (290)
T ss_pred HHHHHHHHHHHHHHh
Confidence 334444444444333
No 195
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=20.57 E-value=85 Score=24.98 Aligned_cols=32 Identities=22% Similarity=0.443 Sum_probs=19.1
Q ss_pred CCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q 035661 22 KRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRAR 71 (211)
Q Consensus 22 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r 71 (211)
.-+|.+|+..|+.+.....+ .|..||-||+.=
T Consensus 50 ~~Lt~~qi~~l~~~i~~~~~------------------~iP~w~~Nr~~d 81 (144)
T TIGR03629 50 GYLDDEEIEKLEEAVENYEY------------------GIPSWLLNRRKD 81 (144)
T ss_pred ccCCHHHHHHHHHHHHhccc------------------cCCHHHhhcccc
Confidence 34667777777665543222 256799996543
No 196
>PHA02535 P terminase ATPase subunit; Provisional
Probab=20.47 E-value=2.1e+02 Score=28.11 Aligned_cols=85 Identities=16% Similarity=0.286 Sum_probs=51.1
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhhhh-HHHHHHhHHHHHHH---HHH
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDY-NTIQVKLENALADK---RRL 98 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~-~~~~~~~~~l~~e~---~~l 98 (211)
+||++..+.-...|-. .+ ...++|++||+.++.|..|-. |-+|......... ..+..++..|.... ..-
T Consensus 2 ~yt~EfK~~Av~Ly~~-G~----sv~eIA~~LGv~~~Tl~~W~k--r~~w~~~~~~~~v~~~~~~r~~~l~~k~~k~~~d 74 (581)
T PHA02535 2 AYDDDVRRAAKFLYWQ-GW----TVAEIAEELGLKSRTIYSWKE--RDGWRDLLPEERIEESIEARLIQLIEKENKTGGD 74 (581)
T ss_pred CCCHHHHHHHHHHHHc-CC----CHHHHHHHhCCChhHHHHHhc--cccccccCCcccHHHHHHHHHHHHHccCCCChhh
Confidence 4677665555555644 33 345789999999999999964 5666655433332 33355555553321 112
Q ss_pred HHHHHHHHHHHHHHHH
Q 035661 99 EKDVKLLKEELRQAQE 114 (211)
Q Consensus 99 ~~e~~~l~~e~~~~~~ 114 (211)
-+|.+.|..++.++..
T Consensus 75 ~keid~l~~~~~r~~r 90 (581)
T PHA02535 75 YKEIDLLIRQHERLAR 90 (581)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 2667777777666543
No 197
>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=20.47 E-value=1.8e+02 Score=22.76 Aligned_cols=26 Identities=31% Similarity=0.303 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHHH
Q 035661 47 KLKLANQLGVPARQVAVWYQNKRARW 72 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR~r~ 72 (211)
-.++|..+|+++..|++....-|.+-
T Consensus 153 ~~EIA~~lgis~~tVk~~l~Rar~~L 178 (183)
T TIGR02999 153 VEEIAELLGVSVRTVERDWRFARAWL 178 (183)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 34788899999999998776444433
No 198
>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=20.44 E-value=57 Score=19.13 Aligned_cols=22 Identities=27% Similarity=0.370 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCccchhhhhhhh
Q 035661 47 KLKLANQLGVPARQVAVWYQNK 68 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNR 68 (211)
..++|+.+|+++..|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 3578999999999999998765
No 199
>COG4985 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]
Probab=20.41 E-value=2.8e+02 Score=24.21 Aligned_cols=31 Identities=26% Similarity=0.329 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 035661 89 ENALADKRRLEKDVKLLKEELRQAQEILFAK 119 (211)
Q Consensus 89 ~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~~ 119 (211)
+.+..|..+|+++.+.|..++..+++++...
T Consensus 217 ~~~~ae~seLq~r~~~l~~~L~~L~~e~~r~ 247 (289)
T COG4985 217 QHYVAEKSELQKRLAQLQTELDALRAELERQ 247 (289)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Confidence 4456678888888888888888888777654
No 200
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=20.35 E-value=1.5e+02 Score=26.51 Aligned_cols=51 Identities=22% Similarity=0.274 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT 74 (211)
Q Consensus 23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~ 74 (211)
.+++.|..+|...|-.. +.......++|..+|++...|+.+...-+.+-|+
T Consensus 262 ~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~ 312 (325)
T PRK05657 262 ELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312 (325)
T ss_pred cCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56677777777666322 2234556889999999999999988755555544
No 201
>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=20.24 E-value=53 Score=20.57 Aligned_cols=23 Identities=26% Similarity=0.427 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCccchhhhhhhhH
Q 035661 47 KLKLANQLGVPARQVAVWYQNKR 69 (211)
Q Consensus 47 r~~La~~lgL~~rqVkvWFqNRR 69 (211)
..+||+.+|+++..|..|..+++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 47899999999999999998743
Done!