Query 029280
Match_columns 196
No_of_seqs 216 out of 1414
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 10:22:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029280.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029280hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.9 3.9E-22 8.3E-27 166.9 7.8 111 24-136 52-162 (198)
2 KOG0488 Transcription factor B 99.7 5.8E-18 1.3E-22 150.3 5.1 67 15-82 165-231 (309)
3 KOG0843 Transcription factor E 99.7 4.2E-17 9E-22 134.0 4.7 64 21-85 101-164 (197)
4 KOG0842 Transcription factor t 99.7 5.8E-17 1.3E-21 143.2 5.4 70 19-89 150-219 (307)
5 KOG0489 Transcription factor z 99.7 2.9E-17 6.2E-22 142.7 2.2 60 21-81 158-217 (261)
6 KOG0850 Transcription factor D 99.7 8.3E-17 1.8E-21 136.5 4.8 63 17-80 117-179 (245)
7 KOG0492 Transcription factor M 99.6 3.3E-16 7.1E-21 131.4 6.4 64 17-81 139-202 (246)
8 KOG0487 Transcription factor A 99.6 2.5E-16 5.4E-21 139.3 5.2 64 20-84 233-296 (308)
9 KOG0494 Transcription factor C 99.6 2E-16 4.3E-21 136.5 4.2 80 16-96 135-214 (332)
10 KOG0485 Transcription factor N 99.6 5.5E-16 1.2E-20 130.9 5.1 62 19-81 101-162 (268)
11 PF00046 Homeobox: Homeobox do 99.6 5.5E-16 1.2E-20 104.2 3.6 57 23-80 1-57 (57)
12 KOG0484 Transcription factor P 99.6 2.7E-16 5.8E-21 119.4 1.6 61 19-80 14-74 (125)
13 KOG0493 Transcription factor E 99.6 1.3E-15 2.7E-20 131.7 4.6 76 5-81 223-304 (342)
14 KOG2251 Homeobox transcription 99.5 6.3E-15 1.4E-19 124.4 5.0 66 19-85 34-99 (228)
15 KOG4577 Transcription factor L 99.5 3.4E-14 7.4E-19 124.3 6.3 98 21-121 166-263 (383)
16 KOG0848 Transcription factor C 99.5 1E-14 2.2E-19 126.3 1.5 58 23-81 200-257 (317)
17 smart00389 HOX Homeodomain. DN 99.5 4.4E-14 9.4E-19 94.1 3.7 55 24-79 2-56 (56)
18 cd00086 homeodomain Homeodomai 99.5 6.4E-14 1.4E-18 93.8 4.2 57 24-81 2-58 (59)
19 TIGR01565 homeo_ZF_HD homeobox 99.4 2.5E-13 5.5E-18 93.3 5.9 52 23-75 2-57 (58)
20 COG5576 Homeodomain-containing 99.4 2.4E-13 5.2E-18 110.3 5.2 63 21-84 50-112 (156)
21 KOG3802 Transcription factor O 99.3 1.4E-12 3E-17 118.2 6.3 77 6-83 278-354 (398)
22 KOG0486 Transcription factor P 99.3 8.4E-13 1.8E-17 116.6 4.6 75 11-86 99-175 (351)
23 KOG0491 Transcription factor B 99.3 3.3E-13 7.1E-18 109.9 -0.1 62 22-84 100-161 (194)
24 KOG0844 Transcription factor E 99.3 1.3E-12 2.8E-17 115.2 2.6 63 21-84 180-242 (408)
25 KOG0847 Transcription factor, 99.3 1.3E-12 2.8E-17 110.8 1.9 63 18-81 163-225 (288)
26 KOG0490 Transcription factor, 99.1 4.2E-11 9.1E-16 99.9 3.4 63 19-82 57-119 (235)
27 KOG0849 Transcription factor P 98.9 1.5E-09 3.2E-14 98.3 3.8 63 19-82 173-235 (354)
28 KOG1168 Transcription factor A 98.7 1.3E-08 2.9E-13 89.6 3.5 60 22-82 309-368 (385)
29 KOG0775 Transcription factor S 98.6 3E-08 6.5E-13 86.6 3.8 50 29-79 183-232 (304)
30 KOG0774 Transcription factor P 98.3 4.3E-07 9.4E-12 79.1 3.3 58 23-80 189-248 (334)
31 PF05920 Homeobox_KN: Homeobox 98.2 4.5E-07 9.7E-12 57.8 0.4 33 45-77 8-40 (40)
32 PF02183 HALZ: Homeobox associ 97.9 2.4E-05 5.2E-10 51.1 5.3 44 81-125 1-44 (45)
33 KOG0490 Transcription factor, 97.9 9.2E-06 2E-10 67.6 3.4 63 20-83 151-213 (235)
34 KOG2252 CCAAT displacement pro 97.9 9.1E-06 2E-10 76.8 3.5 57 21-78 419-475 (558)
35 KOG0773 Transcription factor M 96.8 0.001 2.3E-08 59.4 3.4 60 22-81 239-300 (342)
36 KOG1146 Homeobox protein [Gene 96.8 0.00084 1.8E-08 69.1 2.7 60 23-83 904-963 (1406)
37 PF11569 Homez: Homeodomain le 95.8 0.0026 5.7E-08 43.4 0.3 42 33-75 9-50 (56)
38 PF02183 HALZ: Homeobox associ 93.1 0.2 4.3E-06 32.7 4.1 37 90-127 3-39 (45)
39 PF04218 CENP-B_N: CENP-B N-te 92.2 0.15 3.3E-06 33.9 2.7 47 23-75 1-47 (53)
40 KOG3623 Homeobox transcription 90.9 0.16 3.5E-06 50.4 2.5 48 34-82 568-615 (1007)
41 PRK09413 IS2 repressor TnpA; R 89.9 0.48 1E-05 36.4 3.9 42 26-73 10-52 (121)
42 smart00340 HALZ homeobox assoc 89.5 0.72 1.6E-05 29.8 3.8 38 81-126 1-38 (44)
43 smart00340 HALZ homeobox assoc 87.4 1.3 2.8E-05 28.7 4.0 21 104-125 10-30 (44)
44 PF00170 bZIP_1: bZIP transcri 81.0 9.1 0.0002 25.9 6.4 38 85-123 26-63 (64)
45 KOG0709 CREB/ATF family transc 79.3 11 0.00023 35.9 8.2 94 26-127 218-320 (472)
46 PF06156 DUF972: Protein of un 78.0 7.6 0.00016 29.7 5.7 46 81-127 11-56 (107)
47 PF01527 HTH_Tnp_1: Transposas 74.9 2.1 4.5E-05 29.4 1.7 43 24-72 2-45 (76)
48 PRK13169 DNA replication intia 73.5 14 0.0003 28.4 6.1 45 81-126 11-55 (110)
49 KOG4571 Activating transcripti 69.4 17 0.00036 32.7 6.5 42 82-124 245-286 (294)
50 KOG3119 Basic region leucine z 68.4 16 0.00034 32.1 6.1 49 74-126 207-255 (269)
51 PF10224 DUF2205: Predicted co 67.3 32 0.0007 25.0 6.6 45 80-125 18-62 (80)
52 smart00338 BRLZ basic region l 67.0 36 0.00078 22.9 6.6 39 85-124 26-64 (65)
53 PF06005 DUF904: Protein of un 66.8 31 0.00066 24.5 6.3 33 88-121 21-53 (72)
54 cd06171 Sigma70_r4 Sigma70, re 64.9 3.9 8.4E-05 24.9 1.2 42 28-75 10-51 (55)
55 PF14775 NYD-SP28_assoc: Sperm 62.0 17 0.00037 24.9 4.1 31 94-125 28-58 (60)
56 PF04545 Sigma70_r4: Sigma-70, 61.6 7.4 0.00016 24.7 2.1 38 28-71 4-41 (50)
57 KOG4005 Transcription factor X 60.7 28 0.0006 30.7 6.1 33 90-123 102-134 (292)
58 KOG0483 Transcription factor H 60.4 11 0.00023 32.0 3.4 43 85-128 105-147 (198)
59 COG4467 Regulator of replicati 59.3 33 0.00071 26.6 5.6 45 82-127 12-56 (114)
60 PRK00118 putative DNA-binding 55.5 33 0.00073 26.0 5.1 46 28-79 17-62 (104)
61 PF04967 HTH_10: HTH DNA bindi 54.4 15 0.00033 24.6 2.7 38 29-67 1-40 (53)
62 PF00170 bZIP_1: bZIP transcri 53.3 61 0.0013 21.8 5.7 31 83-113 31-61 (64)
63 cd00569 HTH_Hin_like Helix-tur 53.0 17 0.00037 19.5 2.5 38 27-70 4-41 (42)
64 PF08281 Sigma70_r4_2: Sigma-7 52.8 9.7 0.00021 24.4 1.6 40 28-73 10-49 (54)
65 PRK00888 ftsB cell division pr 49.2 36 0.00077 25.7 4.4 45 66-111 16-60 (105)
66 PRK13922 rod shape-determining 49.0 42 0.00091 28.9 5.4 41 86-127 70-113 (276)
67 PRK03975 tfx putative transcri 47.3 18 0.00039 29.0 2.6 48 26-80 4-51 (141)
68 PF10668 Phage_terminase: Phag 46.6 5.9 0.00013 27.3 -0.2 20 52-71 24-43 (60)
69 KOG4005 Transcription factor X 46.3 51 0.0011 29.1 5.4 44 82-126 101-144 (292)
70 PF06005 DUF904: Protein of un 44.5 1E+02 0.0022 21.9 5.8 32 82-113 22-53 (72)
71 PF07407 Seadorna_VP6: Seadorn 43.9 28 0.0006 32.1 3.5 21 98-119 38-58 (420)
72 PRK10072 putative transcriptio 42.8 17 0.00036 27.2 1.7 41 28-76 32-72 (96)
73 COG4026 Uncharacterized protei 42.2 65 0.0014 28.3 5.4 44 83-127 147-190 (290)
74 PF00196 GerE: Bacterial regul 42.1 17 0.00037 23.8 1.5 45 27-78 2-46 (58)
75 PF00424 REV: REV protein (ant 41.9 31 0.00067 25.8 3.0 39 34-87 14-52 (91)
76 PRK00888 ftsB cell division pr 41.7 44 0.00095 25.2 3.9 34 87-121 29-62 (105)
77 PF13936 HTH_38: Helix-turn-he 41.6 14 0.00031 23.2 1.0 39 26-70 2-40 (44)
78 PRK09642 RNA polymerase sigma 40.8 23 0.00051 27.3 2.4 27 53-79 125-151 (160)
79 PF06156 DUF972: Protein of un 40.4 85 0.0018 23.9 5.3 40 81-121 18-57 (107)
80 PF15058 Speriolin_N: Sperioli 40.3 53 0.0011 27.9 4.5 40 85-126 5-44 (200)
81 TIGR03752 conj_TIGR03752 integ 39.9 71 0.0015 30.6 5.7 10 28-37 41-50 (472)
82 COG3413 Predicted DNA binding 39.8 34 0.00075 28.4 3.4 39 28-67 155-195 (215)
83 TIGR02937 sigma70-ECF RNA poly 39.2 23 0.00049 26.0 2.0 43 29-77 111-153 (158)
84 TIGR00219 mreC rod shape-deter 39.2 72 0.0016 28.1 5.4 16 111-127 96-111 (283)
85 PF13443 HTH_26: Cro/C1-type H 38.8 19 0.00041 23.6 1.4 29 52-80 12-40 (63)
86 PRK06759 RNA polymerase factor 38.5 23 0.0005 27.0 2.0 42 28-75 106-147 (154)
87 PF12824 MRP-L20: Mitochondria 38.1 89 0.0019 25.6 5.4 47 25-74 82-128 (164)
88 PRK11924 RNA polymerase sigma 37.9 25 0.00055 27.1 2.1 28 52-79 143-170 (179)
89 PRK09652 RNA polymerase sigma 37.5 26 0.00057 27.1 2.2 39 28-72 128-166 (182)
90 PRK09646 RNA polymerase sigma 37.3 30 0.00065 27.8 2.6 26 52-77 160-185 (194)
91 TIGR02894 DNA_bind_RsfA transc 37.2 1E+02 0.0022 25.4 5.5 28 86-113 105-132 (161)
92 KOG4343 bZIP transcription fac 36.7 81 0.0018 30.9 5.6 33 88-121 305-337 (655)
93 PF09607 BrkDBD: Brinker DNA-b 35.6 29 0.00062 23.9 1.8 44 26-72 3-47 (58)
94 PRK12526 RNA polymerase sigma 35.5 30 0.00064 28.3 2.3 27 52-78 171-197 (206)
95 KOG4403 Cell surface glycoprot 35.3 1E+02 0.0022 29.6 5.9 26 67-92 228-256 (575)
96 KOG4196 bZIP transcription fac 35.3 2.3E+02 0.005 22.6 9.2 82 26-122 21-117 (135)
97 PRK13169 DNA replication intia 35.1 1.1E+02 0.0024 23.4 5.2 40 81-121 18-57 (110)
98 PRK12512 RNA polymerase sigma 34.7 34 0.00074 27.1 2.5 45 29-79 132-176 (184)
99 PF07716 bZIP_2: Basic region 34.7 1.3E+02 0.0028 19.5 5.2 26 94-120 27-52 (54)
100 smart00338 BRLZ basic region l 34.5 1.4E+02 0.0031 19.9 5.5 32 91-123 25-56 (65)
101 PRK09644 RNA polymerase sigma 33.9 39 0.00084 26.3 2.6 28 52-79 126-153 (165)
102 TIGR02989 Sig-70_gvs1 RNA poly 33.4 33 0.00071 26.2 2.1 21 52-72 129-149 (159)
103 PRK12514 RNA polymerase sigma 33.4 42 0.00091 26.4 2.8 27 53-79 148-174 (179)
104 PF04977 DivIC: Septum formati 32.5 1.2E+02 0.0026 20.5 4.7 29 83-111 22-50 (80)
105 TIGR02985 Sig70_bacteroi1 RNA 32.0 37 0.0008 25.6 2.2 22 52-73 131-152 (161)
106 KOG1962 B-cell receptor-associ 31.7 1.5E+02 0.0033 25.5 6.0 40 87-127 174-213 (216)
107 COG3074 Uncharacterized protei 31.6 1.9E+02 0.0042 20.7 5.5 14 100-113 47-60 (79)
108 TIGR02959 SigZ RNA polymerase 31.3 38 0.00083 26.7 2.2 38 28-71 100-137 (170)
109 PRK12519 RNA polymerase sigma 31.2 32 0.00069 27.5 1.8 28 52-79 159-186 (194)
110 PRK09639 RNA polymerase sigma 30.2 40 0.00086 26.0 2.1 38 29-73 113-150 (166)
111 COG2944 Predicted transcriptio 29.8 39 0.00085 25.8 1.9 42 27-76 42-83 (104)
112 PRK14127 cell division protein 29.7 1.6E+02 0.0035 22.5 5.3 37 89-126 34-70 (109)
113 PRK09648 RNA polymerase sigma 29.6 44 0.00095 26.6 2.3 21 52-72 157-177 (189)
114 smart00421 HTH_LUXR helix_turn 29.5 52 0.0011 20.1 2.2 38 28-72 3-40 (58)
115 PRK12515 RNA polymerase sigma 29.5 51 0.0011 26.3 2.7 25 53-77 150-174 (189)
116 PRK09047 RNA polymerase factor 29.4 47 0.001 25.4 2.4 38 29-72 107-144 (161)
117 PF02796 HTH_7: Helix-turn-hel 29.0 27 0.00059 21.9 0.8 38 27-70 4-41 (45)
118 PRK12543 RNA polymerase sigma 28.6 81 0.0018 24.9 3.7 27 53-79 136-162 (179)
119 PRK05602 RNA polymerase sigma 28.5 43 0.00093 26.6 2.1 25 52-76 146-170 (186)
120 cd04761 HTH_MerR-SF Helix-Turn 28.3 18 0.00038 22.3 -0.2 22 53-74 3-24 (49)
121 PF07407 Seadorna_VP6: Seadorn 28.2 94 0.002 28.7 4.3 26 88-113 35-60 (420)
122 PRK12537 RNA polymerase sigma 28.0 57 0.0012 25.9 2.7 24 52-75 151-174 (182)
123 TIGR02948 SigW_bacill RNA poly 28.0 43 0.00093 26.3 2.0 26 52-77 154-179 (187)
124 PF13518 HTH_28: Helix-turn-he 27.9 22 0.00048 22.2 0.2 22 52-73 14-35 (52)
125 TIGR02999 Sig-70_X6 RNA polyme 27.8 49 0.0011 26.0 2.3 24 53-76 153-176 (183)
126 KOG1146 Homeobox protein [Gene 27.5 59 0.0013 34.9 3.3 59 23-82 706-764 (1406)
127 KOG2391 Vacuolar sorting prote 27.2 2.1E+02 0.0046 26.4 6.4 39 82-121 229-267 (365)
128 PF04899 MbeD_MobD: MbeD/MobD 27.2 2.3E+02 0.005 20.0 5.4 36 88-124 24-59 (70)
129 PRK12541 RNA polymerase sigma 27.0 43 0.00094 25.8 1.8 24 53-76 131-154 (161)
130 PF12325 TMF_TATA_bd: TATA ele 26.9 2.6E+02 0.0056 21.7 6.1 45 80-125 70-114 (120)
131 PRK15422 septal ring assembly 26.9 2.5E+02 0.0055 20.4 6.2 14 100-113 47-60 (79)
132 PRK12530 RNA polymerase sigma 26.9 68 0.0015 25.7 3.0 28 52-79 152-179 (189)
133 COG4026 Uncharacterized protei 26.4 2.5E+02 0.0055 24.7 6.5 32 91-123 141-172 (290)
134 PRK04217 hypothetical protein; 26.4 59 0.0013 24.9 2.4 42 26-73 40-81 (110)
135 TIGR02939 RpoE_Sigma70 RNA pol 25.8 42 0.00091 26.4 1.6 21 52-72 156-176 (190)
136 PRK12546 RNA polymerase sigma 25.6 51 0.0011 26.7 2.1 28 52-79 131-158 (188)
137 PRK15422 septal ring assembly 25.4 2.3E+02 0.005 20.6 5.1 31 91-122 24-61 (79)
138 cd01106 HTH_TipAL-Mta Helix-Tu 24.9 2.7E+02 0.006 20.2 6.1 35 25-73 35-69 (103)
139 PRK10884 SH3 domain-containing 24.8 2.6E+02 0.0057 23.6 6.3 31 90-121 137-167 (206)
140 PF15397 DUF4618: Domain of un 24.7 2.3E+02 0.0049 25.1 6.0 52 85-137 186-244 (258)
141 KOG3156 Uncharacterized membra 24.3 2.3E+02 0.0051 24.4 5.8 41 83-124 99-140 (220)
142 PRK09637 RNA polymerase sigma 24.0 61 0.0013 25.9 2.2 21 52-72 124-144 (181)
143 KOG0150 Spliceosomal protein F 24.0 3.2E+02 0.007 25.0 6.9 14 67-80 16-29 (336)
144 PRK07037 extracytoplasmic-func 23.5 66 0.0014 24.7 2.3 20 53-72 128-147 (163)
145 PRK06930 positive control sigm 23.2 67 0.0014 26.1 2.3 46 28-79 114-159 (170)
146 KOG3119 Basic region leucine z 23.0 2.2E+02 0.0048 24.9 5.7 27 98-125 221-247 (269)
147 TIGR02954 Sig70_famx3 RNA poly 22.7 71 0.0015 24.8 2.3 21 52-72 137-157 (169)
148 PF06056 Terminase_5: Putative 22.5 15 0.00033 24.8 -1.4 26 52-79 15-40 (58)
149 COG4367 Uncharacterized protei 22.3 1.1E+02 0.0025 22.9 3.1 37 28-65 2-38 (97)
150 PRK12547 RNA polymerase sigma 22.2 69 0.0015 24.9 2.1 22 52-73 130-151 (164)
151 PRK12524 RNA polymerase sigma 22.1 68 0.0015 25.8 2.2 21 53-73 155-175 (196)
152 TIGR02983 SigE-fam_strep RNA p 22.1 69 0.0015 24.6 2.1 28 52-79 128-155 (162)
153 PRK06811 RNA polymerase factor 21.9 70 0.0015 25.6 2.1 20 53-72 150-169 (189)
154 PRK14127 cell division protein 21.7 2.2E+02 0.0047 21.9 4.7 40 88-128 26-65 (109)
155 PF13411 MerR_1: MerR HTH fami 21.7 24 0.00052 23.5 -0.5 20 53-72 3-22 (69)
156 KOG4343 bZIP transcription fac 21.7 1.2E+02 0.0026 29.8 3.9 33 92-125 302-334 (655)
157 PRK12538 RNA polymerase sigma 21.5 77 0.0017 26.7 2.4 28 52-79 189-216 (233)
158 TIGR02952 Sig70_famx2 RNA poly 21.3 77 0.0017 24.3 2.3 19 53-71 141-159 (170)
159 PHA02955 hypothetical protein; 21.2 1.2E+02 0.0026 26.1 3.5 42 32-73 61-102 (213)
160 PF11932 DUF3450: Protein of u 21.2 3.9E+02 0.0084 22.7 6.7 28 86-113 50-77 (251)
161 PRK10884 SH3 domain-containing 21.1 3.3E+02 0.0072 23.0 6.2 35 89-124 129-163 (206)
162 PF08961 DUF1875: Domain of un 20.9 32 0.0007 29.8 0.0 31 88-119 132-162 (243)
163 PRK13919 putative RNA polymera 20.9 87 0.0019 24.7 2.5 20 53-72 154-173 (186)
164 PF15058 Speriolin_N: Sperioli 20.9 1.3E+02 0.0027 25.7 3.5 32 92-124 5-36 (200)
165 PF14197 Cep57_CLD_2: Centroso 20.8 3E+02 0.0066 19.2 6.2 40 84-124 25-64 (69)
166 PF13384 HTH_23: Homeodomain-l 20.7 26 0.00057 21.9 -0.5 22 52-73 19-40 (50)
167 PF08280 HTH_Mga: M protein tr 20.7 67 0.0014 21.3 1.5 32 32-68 6-37 (59)
168 PF04880 NUDE_C: NUDE protein, 20.6 1.2E+02 0.0027 24.9 3.3 23 100-123 25-47 (166)
169 cd04766 HTH_HspR Helix-Turn-He 20.5 1.9E+02 0.0042 20.5 4.0 21 53-73 4-24 (91)
170 PRK12532 RNA polymerase sigma 20.4 76 0.0016 25.4 2.1 28 52-79 154-181 (195)
171 KOG4797 Transcriptional regula 20.1 4E+02 0.0087 20.7 5.8 42 83-124 65-110 (123)
172 TIGR03879 near_KaiC_dom probab 20.1 24 0.00051 25.3 -0.9 32 41-73 24-55 (73)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.86 E-value=3.9e-22 Score=166.90 Aligned_cols=111 Identities=47% Similarity=0.758 Sum_probs=101.3
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhhHHHHHHHHHhhHHhhhhhHh
Q 029280 24 KNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDYAQLRANYDSLASGFES 103 (196)
Q Consensus 24 r~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~~~e~~~lk~~~~~L~~~~~s 103 (196)
+++.+|+.+|+..||..|+.. .++.+..+..||++|||+++||+|||||||||||.++++.++..|+.+|+.|..++..
T Consensus 52 ~kk~Rlt~eQ~~~LE~~F~~~-~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~~~ 130 (198)
T KOG0483|consen 52 GKKRRLTSEQVKFLEKSFESE-KKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSENDR 130 (198)
T ss_pred cccccccHHHHHHhHHhhccc-cccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhhH
Confidence 446799999999999999999 9999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhHHHHHHHHHHhcccCCcCCCCCCC
Q 029280 104 LIKEKESLLLEQLQMLNEQLGKSDYEINGVGKD 136 (196)
Q Consensus 104 l~~e~~~L~~~e~~~L~~~~~~~~~~~~~~c~~ 136 (196)
|..++..|.. ++..++..++.........|..
T Consensus 131 Lq~e~~eL~~-~~~~~~~~~~~~~~~~~~~~~~ 162 (198)
T KOG0483|consen 131 LQSEVQELVA-ELSSLKREMQKSPENTLTMCPN 162 (198)
T ss_pred HHHHHHHHHH-HHhhhhhhhccCcccccccCcc
Confidence 9999999999 8888888888755554456643
No 2
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.71 E-value=5.8e-18 Score=150.28 Aligned_cols=67 Identities=36% Similarity=0.654 Sum_probs=61.7
Q ss_pred hhhccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHh
Q 029280 15 AKRKKKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82 (196)
Q Consensus 15 ~~~~~kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq 82 (196)
.+...||.|+.|+.||..|+..||+.|+.. .|++..+|.+||..|||+..||++||||||+|||+..
T Consensus 165 ~~~~pkK~RksRTaFT~~Ql~~LEkrF~~Q-KYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 165 QRSTPKKRRKSRTAFSDHQLFELEKRFEKQ-KYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred ccCCCcccccchhhhhHHHHHHHHHHHHHh-hcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 344457778899999999999999999999 9999999999999999999999999999999999843
No 3
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.67 E-value=4.2e-17 Score=134.03 Aligned_cols=64 Identities=33% Similarity=0.504 Sum_probs=60.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhhHH
Q 029280 21 SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEH 85 (196)
Q Consensus 21 k~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~~~ 85 (196)
+.+|.||.||++|+..||..|+.+ +|....+|.+||..|+|++.||+|||||||+|.||++.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~-~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGN-QYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcC-CeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 567889999999999999999999 9999999999999999999999999999999999976664
No 4
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.66 E-value=5.8e-17 Score=143.23 Aligned_cols=70 Identities=34% Similarity=0.522 Sum_probs=63.6
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhhHHHHHH
Q 029280 19 KKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDYAQ 89 (196)
Q Consensus 19 ~kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~~~e~~~ 89 (196)
+.++||.|.-||..|+..||+.|... .|++..+|+.||..|.|++.||||||||||-|.||+++......
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQ-RYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQ-RYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhh-hccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 44556778999999999999999999 99999999999999999999999999999999999877776543
No 5
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.65 E-value=2.9e-17 Score=142.66 Aligned_cols=60 Identities=32% Similarity=0.632 Sum_probs=57.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhH
Q 029280 21 SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (196)
Q Consensus 21 k~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krk 81 (196)
+.||.|+.||..|+..||+.|..+ .|+++..|.+||..|.|+++||+|||||||+||||.
T Consensus 158 ~~kR~RtayT~~QllELEkEFhfN-~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~ 217 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHFN-KYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKE 217 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhccc-cccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHh
Confidence 457889999999999999999999 999999999999999999999999999999999983
No 6
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.65 E-value=8.3e-17 Score=136.54 Aligned_cols=63 Identities=33% Similarity=0.549 Sum_probs=60.4
Q ss_pred hccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHh
Q 029280 17 RKKKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (196)
Q Consensus 17 ~~~kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Kr 80 (196)
+|.||.|++||.|+.-||..|.+.|+.+ +|+--.+|.+||..|||+..||+|||||||.|.||
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQkT-QYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KK 179 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQT-QYLALPERAELAASLGLTQTQVKIWFQNRRSKFKK 179 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhhc-chhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHH
Confidence 4667788999999999999999999999 99999999999999999999999999999999997
No 7
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.63 E-value=3.3e-16 Score=131.41 Aligned_cols=64 Identities=34% Similarity=0.531 Sum_probs=60.9
Q ss_pred hccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhH
Q 029280 17 RKKKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (196)
Q Consensus 17 ~~~kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krk 81 (196)
+|.+.+|++|+.||..|+..||+.|... +|+++.+|.+++..|.|++.||+|||||||+|.||-
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfrek-qYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFREK-QYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhHh-hhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 5667788999999999999999999999 999999999999999999999999999999999983
No 8
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.63 E-value=2.5e-16 Score=139.29 Aligned_cols=64 Identities=30% Similarity=0.452 Sum_probs=59.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhhH
Q 029280 20 KSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIE 84 (196)
Q Consensus 20 kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~~ 84 (196)
+..||+|..+|..|+..||+.|..+ .|++...|.+|++.|+|+++||+|||||||.|.||...+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN-~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFN-MYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHH-HHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 4456778999999999999999999 999999999999999999999999999999999986543
No 9
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.62 E-value=2e-16 Score=136.48 Aligned_cols=80 Identities=24% Similarity=0.446 Sum_probs=71.5
Q ss_pred hhccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhhHHHHHHHHHhhH
Q 029280 16 KRKKKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDYAQLRANYD 95 (196)
Q Consensus 16 ~~~~kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~~~e~~~lk~~~~ 95 (196)
.++++|+|+-||.||..|+..||..|+.. +||+...|+-||..+.|++.+|+|||||||+||||+..+....+..++|-
T Consensus 135 ~kkk~kRRh~RTiFT~~Qle~LEkaFkea-HYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~maeyg 213 (332)
T KOG0494|consen 135 AKKKKKRRHFRTIFTSYQLEELEKAFKEA-HYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMAEYG 213 (332)
T ss_pred cccccccccccchhhHHHHHHHHHHHhhc-cCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhhhhc
Confidence 34444444459999999999999999999 99999999999999999999999999999999999999999888888875
Q ss_pred H
Q 029280 96 S 96 (196)
Q Consensus 96 ~ 96 (196)
-
T Consensus 214 l 214 (332)
T KOG0494|consen 214 L 214 (332)
T ss_pred c
Confidence 4
No 10
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.61 E-value=5.5e-16 Score=130.91 Aligned_cols=62 Identities=39% Similarity=0.628 Sum_probs=58.2
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhH
Q 029280 19 KKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (196)
Q Consensus 19 ~kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krk 81 (196)
..++||+|++|+..|+..||..|+.. .|++..+|.-||.+|.|++.||+|||||||.||||+
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~k-rYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELK-RYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHH-hhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 33567789999999999999999999 999999999999999999999999999999999983
No 11
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.60 E-value=5.5e-16 Score=104.24 Aligned_cols=57 Identities=37% Similarity=0.666 Sum_probs=54.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHh
Q 029280 23 MKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (196)
Q Consensus 23 rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Kr 80 (196)
|++|+.||.+|+.+|+..|..+ +||+...+..||..|||++.+|.+||+|||++.|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~-~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQEN-PYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHS-SSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHh-ccccccccccccccccccccccccCHHHhHHHhCc
Confidence 4678999999999999999999 99999999999999999999999999999999985
No 12
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.59 E-value=2.7e-16 Score=119.38 Aligned_cols=61 Identities=25% Similarity=0.556 Sum_probs=57.6
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHh
Q 029280 19 KKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (196)
Q Consensus 19 ~kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Kr 80 (196)
++|.||-|+.||..|+..||+.|... +||++..|++||..+.|++..|+|||||||+|.++
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ET-HYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRK 74 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAET-HYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRK 74 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhh-cCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHH
Confidence 44556789999999999999999999 99999999999999999999999999999999997
No 13
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.58 E-value=1.3e-15 Score=131.70 Aligned_cols=76 Identities=34% Similarity=0.625 Sum_probs=63.8
Q ss_pred CCCCCCCCchhhhccCCC------CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHH
Q 029280 5 RKDDSAASPEAKRKKKSK------MKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARW 78 (196)
Q Consensus 5 ~~~~s~~s~~~~~~~kk~------rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~ 78 (196)
+++-..+.|..++.++|+ +|+|+-||.+||..|...|+.+ .|++...|.+||.+|||.+.||+|||||+|+|.
T Consensus 223 YSDRPSsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~en-RYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKi 301 (342)
T KOG0493|consen 223 YSDRPSSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQEN-RYLTEQRRQELAQELGLNESQIKIWFQNKRAKI 301 (342)
T ss_pred ccCCCCCCcccccccccCCccchhcCccccccHHHHHHHHHHHhhh-hhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhh
Confidence 444444444444434433 5889999999999999999999 999999999999999999999999999999999
Q ss_pred HhH
Q 029280 79 KSK 81 (196)
Q Consensus 79 Krk 81 (196)
||.
T Consensus 302 KKs 304 (342)
T KOG0493|consen 302 KKS 304 (342)
T ss_pred hhc
Confidence 984
No 14
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.53 E-value=6.3e-15 Score=124.45 Aligned_cols=66 Identities=23% Similarity=0.520 Sum_probs=61.2
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhhHH
Q 029280 19 KKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEH 85 (196)
Q Consensus 19 ~kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~~~ 85 (196)
.+|.||.||+|+-.|+.+||..|.+. +||+...+++||.+|+|++.+|+|||.|||+|+|+.+...
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kT-qYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKT-QYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhh-cCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 45668899999999999999999999 9999999999999999999999999999999999865544
No 15
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.49 E-value=3.4e-14 Score=124.33 Aligned_cols=98 Identities=24% Similarity=0.387 Sum_probs=84.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhhHHHHHHHHHhhHHhhhh
Q 029280 21 SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDYAQLRANYDSLASG 100 (196)
Q Consensus 21 k~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~~~e~~~lk~~~~~L~~~ 100 (196)
..+|+||++|+.|++.|...|... ++|.+..|++|+.++||..+.|+|||||||||+||-+...++..+.+.|...+..
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~S-pKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK~s 244 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTS-PKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMKRS 244 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCC-CchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhhcc
Confidence 457889999999999999999999 9999999999999999999999999999999999999999999999999888777
Q ss_pred hHhHHHHHHHHhHHHHHHHHH
Q 029280 101 FESLIKEKESLLLEQLQMLNE 121 (196)
Q Consensus 101 ~~sl~~e~~~L~~~e~~~L~~ 121 (196)
.+.+.|+.+=.. |+.-..+
T Consensus 245 -gs~r~ekdsd~s-el~~~~d 263 (383)
T KOG4577|consen 245 -GSSRAEKDSDDS-ELSFIND 263 (383)
T ss_pred -CCcccccccccC-ccccccc
Confidence 666666666333 4444444
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.47 E-value=1e-14 Score=126.27 Aligned_cols=58 Identities=38% Similarity=0.575 Sum_probs=54.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhH
Q 029280 23 MKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (196)
Q Consensus 23 rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krk 81 (196)
-|-|.++|..|...||+.|... +|+++..+.+||.-|||++|||+|||||||+|+||.
T Consensus 200 DKYRvVYTDhQRLELEKEfh~S-ryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~ 257 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEFHTS-RYITIRRKSELAATLGLSERQVKIWFQNRRAKERKD 257 (317)
T ss_pred cceeEEecchhhhhhhhhhccc-cceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHH
Confidence 3457899999999999999999 999999999999999999999999999999999983
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.46 E-value=4.4e-14 Score=94.10 Aligned_cols=55 Identities=38% Similarity=0.760 Sum_probs=51.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 24 KNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 24 r~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
+.|++|+.+|+.+|+..|..+ +||+...+..||..+||+..+|++||+|||++.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~-~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKN-PYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 456789999999999999999 9999999999999999999999999999998754
No 18
>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=99.45 E-value=6.4e-14 Score=93.79 Aligned_cols=57 Identities=42% Similarity=0.701 Sum_probs=53.8
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhH
Q 029280 24 KNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (196)
Q Consensus 24 r~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krk 81 (196)
+.+..++..++.+|+..|..+ +||+...+..||..+||+..+|++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~-~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKN-PYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 457899999999999999999 999999999999999999999999999999998863
No 19
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.43 E-value=2.5e-13 Score=93.28 Aligned_cols=52 Identities=15% Similarity=0.362 Sum_probs=49.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCC----CCHHHHHHHHHHhCCCCcceeeeccchh
Q 029280 23 MKNKRRFSDEQIRLLESIFESESTK----LEPRKKMQVATELGLQPRQVAIWFQNKR 75 (196)
Q Consensus 23 rr~Rtr~t~eQl~~LE~~F~~~~~~----p~~~~r~eLA~~LgL~~rQVkvWFQNRR 75 (196)
+|.||.||++|+..|+..|+.. +| |+...+.+||..|||++++|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~-~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKL-GWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHc-CCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 6789999999999999999999 99 9999999999999999999999999964
No 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.41 E-value=2.4e-13 Score=110.26 Aligned_cols=63 Identities=35% Similarity=0.556 Sum_probs=58.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhhH
Q 029280 21 SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIE 84 (196)
Q Consensus 21 k~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~~ 84 (196)
..+++|++.|..|+.+|+..|..+ +||+...|..|+..|+|+++-|+|||||||++.|+....
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i~-p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEIN-PYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cCcccceechHHHHHHHHHHhccC-CCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 345678999999999999999999 999999999999999999999999999999999985544
No 21
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.34 E-value=1.4e-12 Score=118.21 Aligned_cols=77 Identities=23% Similarity=0.271 Sum_probs=68.9
Q ss_pred CCCCCCCchhhhccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhh
Q 029280 6 KDDSAASPEAKRKKKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQI 83 (196)
Q Consensus 6 ~~~s~~s~~~~~~~kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~ 83 (196)
++++..+.+......|+||+||.|.......||.+|..| ++|+..++..||.+|+|....|+|||+|||.|.||...
T Consensus 278 ~~~~~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~n-pKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 278 STGSPNSIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKN-PKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccCCCCCHHHhhccccccccccceeHHHHHHHHHHHHhC-CCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 456666667766666788899999999999999999999 99999999999999999999999999999999998543
No 22
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.34 E-value=8.4e-13 Score=116.57 Aligned_cols=75 Identities=24% Similarity=0.533 Sum_probs=65.5
Q ss_pred CCchhhhccC--CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhhHHH
Q 029280 11 ASPEAKRKKK--SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHD 86 (196)
Q Consensus 11 ~s~~~~~~~k--k~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~~~e 86 (196)
.+.+...++| |+||-|+.||..|+..||..|+++ .||+...|++||..++|++..|+|||.|||+||+++.....
T Consensus 99 ~gn~~~~~kki~KqrrQrthFtSqqlqele~tF~rN-rypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 99 MGNEDPNKKKISKQRRQRTHFTSQQLQELEATFQRN-RYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred cCCCCcccchhhhhhhhhhhhHHHHHHHHHHHHhhc-cCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 3344444444 788889999999999999999999 99999999999999999999999999999999998665554
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.30 E-value=3.3e-13 Score=109.93 Aligned_cols=62 Identities=35% Similarity=0.548 Sum_probs=57.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhhH
Q 029280 22 KMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIE 84 (196)
Q Consensus 22 ~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~~ 84 (196)
+++.|++|+..|+..|+..|+.. .|++..++.+||..|+|++.||+.||||||+|.||.+..
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~Q-rYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~ 161 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQ-RYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN 161 (194)
T ss_pred hhhhcccccCccccccHHHHhhh-hhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 35669999999999999999999 999999999999999999999999999999999985543
No 24
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.28 E-value=1.3e-12 Score=115.23 Aligned_cols=63 Identities=27% Similarity=0.489 Sum_probs=58.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhhH
Q 029280 21 SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIE 84 (196)
Q Consensus 21 k~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~~ 84 (196)
..||-||-||.+||..||+.|-+. .|.++..|.+||..|+|++..|+|||||||+|.||+.+.
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrE-NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRE-NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHh-ccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 456779999999999999999999 999999999999999999999999999999999986543
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.27 E-value=1.3e-12 Score=110.81 Aligned_cols=63 Identities=33% Similarity=0.625 Sum_probs=58.6
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhH
Q 029280 18 KKKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (196)
Q Consensus 18 ~~kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krk 81 (196)
+..+++..|.+|+..||..|+..|+.. +|+-...+.+||..+|+++.||+|||||||+||||+
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqt-kylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKk 225 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQT-KYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKK 225 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhh-hcccchhHHHhhccccccHHHHHHHHhcchhhhhhh
Confidence 445556778999999999999999999 999999999999999999999999999999999984
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.11 E-value=4.2e-11 Score=99.86 Aligned_cols=63 Identities=29% Similarity=0.288 Sum_probs=59.3
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHh
Q 029280 19 KKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82 (196)
Q Consensus 19 ~kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq 82 (196)
+.++++.|+.|+..|+..|++.|+.. +||+...++.||..+++++..|+|||||||++|++..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 45667889999999999999999999 9999999999999999999999999999999999854
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.86 E-value=1.5e-09 Score=98.30 Aligned_cols=63 Identities=30% Similarity=0.612 Sum_probs=58.1
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHh
Q 029280 19 KKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82 (196)
Q Consensus 19 ~kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq 82 (196)
+++.+++|++|+..|+..|+..|+.+ +||....|++||.++++++..|+|||+|||+++++..
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt-~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRT-PYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccccchHHHHHHHhcCC-CCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 34456779999999999999999999 9999999999999999999999999999999999843
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.67 E-value=1.3e-08 Score=89.58 Aligned_cols=60 Identities=25% Similarity=0.437 Sum_probs=55.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHh
Q 029280 22 KMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82 (196)
Q Consensus 22 ~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq 82 (196)
++|+||.+.+...+.||.+|... +.|+.+.+..||.+|+|....|+|||+|.|.|.||+.
T Consensus 309 kKRKRTSIAAPEKRsLEayFavQ-PRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAVQ-PRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred cccccccccCcccccHHHHhccC-CCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 35678999999999999999999 9999999999999999999999999999999988843
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.61 E-value=3e-08 Score=86.57 Aligned_cols=50 Identities=32% Similarity=0.549 Sum_probs=46.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 29 ~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
|...-..+|...|..+ +||++.++.+||+.+||+..||-.||.|||.|+|
T Consensus 183 FKekSR~~LrewY~~~-~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQN-PYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhcC-CCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 4445567999999999 9999999999999999999999999999999988
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.30 E-value=4.3e-07 Score=79.13 Aligned_cols=58 Identities=29% Similarity=0.501 Sum_probs=53.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhc--CCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHh
Q 029280 23 MKNKRRFSDEQIRLLESIFESE--STKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (196)
Q Consensus 23 rr~Rtr~t~eQl~~LE~~F~~~--~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Kr 80 (196)
+|+|+.|+..-..+|..+|-.+ ++||+...+++||++++++..||-.||.|+|-+.||
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK 248 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKK 248 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhh
Confidence 5668899999999999999754 699999999999999999999999999999999987
No 31
>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=98.17 E-value=4.5e-07 Score=57.79 Aligned_cols=33 Identities=30% Similarity=0.542 Sum_probs=28.2
Q ss_pred CCCCCHHHHHHHHHHhCCCCcceeeeccchhhH
Q 029280 45 STKLEPRKKMQVATELGLQPRQVAIWFQNKRAR 77 (196)
Q Consensus 45 ~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak 77 (196)
++||+..++..||..+||+..||..||-|.|.|
T Consensus 8 nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 8 NPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp SGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 399999999999999999999999999999875
No 32
>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=97.95 E-value=2.4e-05 Score=51.14 Aligned_cols=44 Identities=48% Similarity=0.705 Sum_probs=41.4
Q ss_pred HhhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhcc
Q 029280 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGK 125 (196)
Q Consensus 81 kq~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~ 125 (196)
+|++.++..|+..|+.|.+++.+|..|++.|.+ ++..|+..++.
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~a-ev~~L~~kl~~ 44 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRA-EVQELKEKLQM 44 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHhhcC
Confidence 478999999999999999999999999999999 99999998864
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.89 E-value=9.2e-06 Score=67.65 Aligned_cols=63 Identities=30% Similarity=0.641 Sum_probs=58.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhh
Q 029280 20 KSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQI 83 (196)
Q Consensus 20 kk~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~ 83 (196)
.+.++.++.++..|+..+...|... ++|....+..|+..+|++++.|++||||+|++.++...
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRAT-PKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccCCCccccccchhHhhhhcccCC-CCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 4556778999999999999999999 99999999999999999999999999999999998654
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.88 E-value=9.1e-06 Score=76.83 Aligned_cols=57 Identities=26% Similarity=0.378 Sum_probs=53.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHH
Q 029280 21 SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARW 78 (196)
Q Consensus 21 k~rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~ 78 (196)
+.+|+|.+||..|...|..+|+.+ ++|+.+..+.|+.+|+|....|.+||-|-|.|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~-~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKEN-KRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcC-CCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 445679999999999999999999 999999999999999999999999999988876
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.80 E-value=0.001 Score=59.44 Aligned_cols=60 Identities=25% Similarity=0.391 Sum_probs=50.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhc--CCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhH
Q 029280 22 KMKNKRRFSDEQIRLLESIFESE--STKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (196)
Q Consensus 22 ~rr~Rtr~t~eQl~~LE~~F~~~--~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krk 81 (196)
..+++..++...+.+|+.....+ ++||+...+..||.++||+..||.+||-|.|-|..+-
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 45566789999999999774442 4799999999999999999999999999999887763
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.75 E-value=0.00084 Score=69.15 Aligned_cols=60 Identities=23% Similarity=0.460 Sum_probs=56.1
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhh
Q 029280 23 MKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQI 83 (196)
Q Consensus 23 rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~ 83 (196)
+..|++++..|+..|..+|... .+|...+.+.|...+++.++.|.+||||-|++.|+...
T Consensus 904 ~a~~~~~~d~qlk~i~~~~~~q-~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 904 RAYRTQESDLQLKIIKACYEAQ-RTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhccchhHHHHHHHHHHHhhc-cCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 4568999999999999999999 99999999999999999999999999999999998554
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.85 E-value=0.0026 Score=43.43 Aligned_cols=42 Identities=19% Similarity=0.358 Sum_probs=31.1
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchh
Q 029280 33 QIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKR 75 (196)
Q Consensus 33 Ql~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRR 75 (196)
-+..|+.+|... +.+.......|+.+.+|+..||+.||-.|+
T Consensus 9 d~~pL~~Yy~~h-~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 9 DIQPLEDYYLKH-KQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp --HHHHHHHHHT-----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred chHHHHHHHHHc-CCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 356799999999 999999999999999999999999996554
No 38
>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=93.09 E-value=0.2 Score=32.65 Aligned_cols=37 Identities=27% Similarity=0.432 Sum_probs=32.3
Q ss_pred HHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhcccC
Q 029280 90 LRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKSD 127 (196)
Q Consensus 90 lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~~ 127 (196)
+...|+.|++.+++|+.+.++|.. |++.|+.++....
T Consensus 3 lE~Dy~~LK~~yd~Lk~~~~~L~~-E~~~L~aev~~L~ 39 (45)
T PF02183_consen 3 LERDYDALKASYDSLKAEYDSLKK-ENEKLRAEVQELK 39 (45)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Confidence 567899999999999999999999 9999999887654
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=92.20 E-value=0.15 Score=33.95 Aligned_cols=47 Identities=19% Similarity=0.292 Sum_probs=35.1
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchh
Q 029280 23 MKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKR 75 (196)
Q Consensus 23 rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRR 75 (196)
+++|..+|.++-..+-..++.. . ....||..+|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g-~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG-E-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT-T------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcC-C-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 3568899999888888888877 3 577899999999999999998853
No 40
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=90.90 E-value=0.16 Score=50.39 Aligned_cols=48 Identities=21% Similarity=0.336 Sum_probs=44.5
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHh
Q 029280 34 IRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82 (196)
Q Consensus 34 l~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq 82 (196)
+.+|..+|..+ ..|...+...+|.+.||+.+.|+.||+++++.....+
T Consensus 568 ~sllkayyaln-~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALN-GLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhc-CCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 78899999999 9999999999999999999999999999999877644
No 41
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=89.87 E-value=0.48 Score=36.38 Aligned_cols=42 Identities=21% Similarity=0.396 Sum_probs=29.2
Q ss_pred CCCCCHHHHH-HHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccc
Q 029280 26 KRRFSDEQIR-LLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQN 73 (196)
Q Consensus 26 Rtr~t~eQl~-~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQN 73 (196)
|++||.++.. ++...+... ....++|..+||++.+|..|.+.
T Consensus 10 rr~ys~EfK~~aV~~~~~~g------~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG------MTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC------CCHHHHHHHHCcCHHHHHHHHHH
Confidence 5678887654 334444433 24567899999999999999654
No 42
>smart00340 HALZ homeobox associated leucin zipper.
Probab=89.51 E-value=0.72 Score=29.80 Aligned_cols=38 Identities=32% Similarity=0.256 Sum_probs=25.1
Q ss_pred HhhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhccc
Q 029280 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKS 126 (196)
Q Consensus 81 kq~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~ 126 (196)
+|++.+++-|+. ..++|..||.+|.. |+++|+.+...+
T Consensus 1 KQTEvdCe~LKr-------cce~LteeNrRL~k-e~~eLralk~~~ 38 (44)
T smart00340 1 KQTEVDCELLKR-------CCESLTEENRRLQK-EVQELRALKLSP 38 (44)
T ss_pred CchHHHHHHHHH-------HHHHHHHHHHHHHH-HHHHHHhcccCC
Confidence 366777766555 45556667777777 788888765544
No 43
>smart00340 HALZ homeobox associated leucin zipper.
Probab=87.40 E-value=1.3 Score=28.65 Aligned_cols=21 Identities=24% Similarity=0.202 Sum_probs=10.7
Q ss_pred HHHHHHHHhHHHHHHHHHHhcc
Q 029280 104 LIKEKESLLLEQLQMLNEQLGK 125 (196)
Q Consensus 104 l~~e~~~L~~~e~~~L~~~~~~ 125 (196)
|+.=-++|.. |+.+|+..++.
T Consensus 10 LKrcce~Lte-eNrRL~ke~~e 30 (44)
T smart00340 10 LKRCCESLTE-ENRRLQKEVQE 30 (44)
T ss_pred HHHHHHHHHH-HHHHHHHHHHH
Confidence 4444445555 55555555543
No 44
>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=80.99 E-value=9.1 Score=25.92 Aligned_cols=38 Identities=29% Similarity=0.284 Sum_probs=24.9
Q ss_pred HHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHh
Q 029280 85 HDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQL 123 (196)
Q Consensus 85 ~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~ 123 (196)
.....|...+..|..++..|..+...|.. ++..|...+
T Consensus 26 ~~~~~Le~~~~~L~~en~~L~~~~~~L~~-~~~~L~~e~ 63 (64)
T PF00170_consen 26 QYIEELEEKVEELESENEELKKELEQLKK-EIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhhc
Confidence 34455666667777777777777777777 676666543
No 45
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=79.25 E-value=11 Score=35.87 Aligned_cols=94 Identities=20% Similarity=0.225 Sum_probs=54.0
Q ss_pred CCCCCHHHHHHHHHH-HhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhhHHH--------HHHHHHhhHH
Q 029280 26 KRRFSDEQIRLLESI-FESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHD--------YAQLRANYDS 96 (196)
Q Consensus 26 Rtr~t~eQl~~LE~~-F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~~~e--------~~~lk~~~~~ 96 (196)
--++|.+....|.+. |.....+|-...-+++.++.. .=..|+|.+.-.+.+..+ +...-+++..
T Consensus 218 ~L~LteeEkrLL~kEG~slPs~lPLTKaEEriLKrvR-------RKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqe 290 (472)
T KOG0709|consen 218 PLVLTEEEKRLLTKEGYSLPSKLPLTKAEERILKRVR-------RKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQE 290 (472)
T ss_pred ceeccHHHHHHHHhccCcCcccCCchHHHHHHHHHHH-------HHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHH
Confidence 457788888877665 444445555554455554441 112344433222222222 2223445566
Q ss_pred hhhhhHhHHHHHHHHhHHHHHHHHHHhcccC
Q 029280 97 LASGFESLIKEKESLLLEQLQMLNEQLGKSD 127 (196)
Q Consensus 97 L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~~ 127 (196)
|......|..+|.+|.. ++.+|+.++....
T Consensus 291 L~kkV~~Le~~N~sLl~-qL~klQt~v~q~a 320 (472)
T KOG0709|consen 291 LQKKVEELELSNRSLLA-QLKKLQTLVIQVA 320 (472)
T ss_pred HHHHHHHHhhccHHHHH-HHHHHHHHHhhcc
Confidence 66667777778889999 9999998875543
No 46
>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=78.03 E-value=7.6 Score=29.66 Aligned_cols=46 Identities=24% Similarity=0.417 Sum_probs=36.9
Q ss_pred HhhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhcccC
Q 029280 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKSD 127 (196)
Q Consensus 81 kq~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~~ 127 (196)
.+.+.....+-.+...|+.....|.+||..|.. |+..|+..|....
T Consensus 11 ~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~-EN~~Lr~~l~~~~ 56 (107)
T PF06156_consen 11 DQLEQQLGQLLEELEELKKQLQELLEENARLRI-ENEHLRERLEELE 56 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHh
Confidence 355666677777888888888888899999999 9999999887654
No 47
>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=74.89 E-value=2.1 Score=29.38 Aligned_cols=43 Identities=28% Similarity=0.435 Sum_probs=28.3
Q ss_pred CCCCCCCHHHHHHHHHHH-hhcCCCCCHHHHHHHHHHhCCCCcceeeecc
Q 029280 24 KNKRRFSDEQIRLLESIF-ESESTKLEPRKKMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 24 r~Rtr~t~eQl~~LE~~F-~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQ 72 (196)
+.|++||+++...+-..+ ... .....+|..+||++.++..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g------~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG------ESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH------CHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC------CceEeeecccccccccccHHHH
Confidence 346889998877766666 433 4678899999999999888864
No 48
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=73.49 E-value=14 Score=28.44 Aligned_cols=45 Identities=22% Similarity=0.355 Sum_probs=35.6
Q ss_pred HhhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhccc
Q 029280 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKS 126 (196)
Q Consensus 81 kq~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~ 126 (196)
.+.+.....+-.+...|+.....+.+||..|.. |+..|+..|...
T Consensus 11 ~~le~~l~~l~~el~~LK~~~~el~EEN~~L~i-EN~~Lr~~l~~~ 55 (110)
T PRK13169 11 DDLEQNLGVLLKELGALKKQLAELLEENTALRL-ENDKLRERLEEL 55 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHh
Confidence 345666667777778888888888889999988 999999888764
No 49
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=69.37 E-value=17 Score=32.66 Aligned_cols=42 Identities=14% Similarity=0.174 Sum_probs=36.0
Q ss_pred hhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhc
Q 029280 82 QIEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLG 124 (196)
Q Consensus 82 q~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~ 124 (196)
+.+.+.+.+..+...|...|+.|+....+|.. |++.|+.++-
T Consensus 245 KkRae~E~l~ge~~~Le~rN~~LK~qa~~ler-EI~ylKqli~ 286 (294)
T KOG4571|consen 245 KKRAEKEALLGELEGLEKRNEELKDQASELER-EIRYLKQLIL 286 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Confidence 44567788888899999999999999999999 9999998764
No 50
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=68.39 E-value=16 Score=32.14 Aligned_cols=49 Identities=24% Similarity=0.230 Sum_probs=33.8
Q ss_pred hhhHHHhHhhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhccc
Q 029280 74 KRARWKSKQIEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKS 126 (196)
Q Consensus 74 RRak~Krkq~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~ 126 (196)
||.|.++++.. ..+......|..++..|+.++..|.. |+..|+..+...
T Consensus 207 ~kSR~~~k~~~---~e~~~r~~~leken~~lr~~v~~l~~-el~~~~~~~~~~ 255 (269)
T KOG3119|consen 207 RKSRDKRKQKE---DEMAHRVAELEKENEALRTQVEQLKK-ELATLRRLFLQL 255 (269)
T ss_pred HHhhhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHhh
Confidence 34555555444 33344456677788888888888888 888888887663
No 51
>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=67.34 E-value=32 Score=25.03 Aligned_cols=45 Identities=18% Similarity=0.360 Sum_probs=35.0
Q ss_pred hHhhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhcc
Q 029280 80 SKQIEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGK 125 (196)
Q Consensus 80 rkq~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~ 125 (196)
+.....+...|+.....|....+..+.|+..|.. +++-|+..+..
T Consensus 18 k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~-EN~~Lq~YI~n 62 (80)
T PF10224_consen 18 KEELIQEILELQDSLEALSDRVEEVKEENEKLES-ENEYLQQYIGN 62 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 3345556667788888888888888999999999 99988887644
No 52
>smart00338 BRLZ basic region leucin zipper.
Probab=66.99 E-value=36 Score=22.94 Aligned_cols=39 Identities=28% Similarity=0.338 Sum_probs=26.5
Q ss_pred HHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhc
Q 029280 85 HDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLG 124 (196)
Q Consensus 85 ~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~ 124 (196)
.....|......|...+..|..+...|.. ++..|+..+.
T Consensus 26 ~~~~~Le~~~~~L~~en~~L~~~~~~l~~-e~~~lk~~~~ 64 (65)
T smart00338 26 AEIEELERKVEQLEAENERLKKEIERLRR-ELEKLKSELE 64 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhc
Confidence 34455666667777777777777777777 7777776653
No 53
>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=66.82 E-value=31 Score=24.51 Aligned_cols=33 Identities=24% Similarity=0.254 Sum_probs=17.7
Q ss_pred HHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHH
Q 029280 88 AQLRANYDSLASGFESLIKEKESLLLEQLQMLNE 121 (196)
Q Consensus 88 ~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~ 121 (196)
..|+.+++.|+..+..+..++..|.. ++.+|+.
T Consensus 21 ~~Lq~e~eeLke~n~~L~~e~~~L~~-en~~L~~ 53 (72)
T PF06005_consen 21 ALLQMENEELKEKNNELKEENEELKE-ENEQLKQ 53 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHH-HHHHHHH
Confidence 44455555555555555555555555 5555554
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=64.86 E-value=3.9 Score=24.92 Aligned_cols=42 Identities=12% Similarity=0.174 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchh
Q 029280 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKR 75 (196)
Q Consensus 28 r~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRR 75 (196)
.+++.+..++...|... ..-.++|..+|++...|..|...-+
T Consensus 10 ~l~~~~~~~~~~~~~~~------~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 10 KLPEREREVILLRFGEG------LSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred hCCHHHHHHHHHHHhcC------CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46777888888777544 2356789999999999987775433
No 55
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=62.03 E-value=17 Score=24.90 Aligned_cols=31 Identities=35% Similarity=0.378 Sum_probs=24.8
Q ss_pred hHHhhhhhHhHHHHHHHHhHHHHHHHHHHhcc
Q 029280 94 YDSLASGFESLIKEKESLLLEQLQMLNEQLGK 125 (196)
Q Consensus 94 ~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~ 125 (196)
|..+..+...+..|+.+|.. |+.+|+.+|..
T Consensus 28 Y~~vL~~R~~l~~e~~~L~~-qN~eLr~lLkq 58 (60)
T PF14775_consen 28 YNKVLLDRAALIQEKESLEQ-QNEELRSLLKQ 58 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHh
Confidence 44555667788899999999 99999998753
No 56
>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=61.58 E-value=7.4 Score=24.75 Aligned_cols=38 Identities=11% Similarity=0.167 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeec
Q 029280 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWF 71 (196)
Q Consensus 28 r~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWF 71 (196)
.+++.+..+|...|-.. ..-.++|..+|++...|..+.
T Consensus 4 ~L~~~er~vi~~~y~~~------~t~~eIa~~lg~s~~~V~~~~ 41 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG------LTLEEIAERLGISRSTVRRIL 41 (50)
T ss_dssp TS-HHHHHHHHHHHTST-------SHHHHHHHHTSCHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC------CCHHHHHHHHCCcHHHHHHHH
Confidence 57888999999998555 346789999999998876543
No 57
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=60.72 E-value=28 Score=30.67 Aligned_cols=33 Identities=30% Similarity=0.321 Sum_probs=15.5
Q ss_pred HHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHh
Q 029280 90 LRANYDSLASGFESLIKEKESLLLEQLQMLNEQL 123 (196)
Q Consensus 90 lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~ 123 (196)
|-.++..|..++++|+.-++.|+. ++.+|...|
T Consensus 102 L~een~~L~~en~~Lr~~n~~L~~-~n~el~~~l 134 (292)
T KOG4005|consen 102 LTEENEILQNENDSLRAINESLLA-KNHELDSEL 134 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh-hhHHHHHHH
Confidence 344444455555555554444444 444444433
No 58
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=60.36 E-value=11 Score=32.00 Aligned_cols=43 Identities=30% Similarity=0.365 Sum_probs=36.9
Q ss_pred HHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhcccCC
Q 029280 85 HDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKSDY 128 (196)
Q Consensus 85 ~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~~~ 128 (196)
.....+...|+.|+..++++..++.+|.. ++..|+.++.....
T Consensus 105 wK~kqlE~d~~~Lk~~~~~l~~~~~~Lq~-e~~eL~~~~~~~~~ 147 (198)
T KOG0483|consen 105 WKTKQLEKDYESLKRQLESLRSENDRLQS-EVQELVAELSSLKR 147 (198)
T ss_pred ccchhhhhhHHHHHHHHHHHhhhhhHHHH-HHHHHHHHHhhhhh
Confidence 34455678899999999999999999999 99999999987653
No 59
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=59.33 E-value=33 Score=26.56 Aligned_cols=45 Identities=29% Similarity=0.437 Sum_probs=37.0
Q ss_pred hhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhcccC
Q 029280 82 QIEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKSD 127 (196)
Q Consensus 82 q~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~~ 127 (196)
..+.....+-++...|+....++..||..|.. |+.+|+..|..|.
T Consensus 12 ~le~~l~~l~~el~~lK~~l~~lvEEN~~L~l-ENe~LR~RL~~~~ 56 (114)
T COG4467 12 NLEEQLGVLLAELGGLKQHLGSLVEENTALRL-ENEKLRERLGEPT 56 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHh-hHHHHHHHhCCcc
Confidence 44555666777788888888999999999999 9999999998743
No 60
>PRK00118 putative DNA-binding protein; Validated
Probab=55.49 E-value=33 Score=26.01 Aligned_cols=46 Identities=11% Similarity=0.133 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 28 r~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
.+++.|..++...|... ....+||..+|+++..|..+...-|.+.+
T Consensus 17 ~L~ekqRevl~L~y~eg------~S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD------YSLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred cCCHHHHHHHHHHHHcC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 45677777777666655 24567999999999999888765444444
No 61
>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=54.36 E-value=15 Score=24.58 Aligned_cols=38 Identities=24% Similarity=0.270 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCC--HHHHHHHHHHhCCCCcce
Q 029280 29 FSDEQIRLLESIFESESTKLE--PRKKMQVATELGLQPRQV 67 (196)
Q Consensus 29 ~t~eQl~~LE~~F~~~~~~p~--~~~r~eLA~~LgL~~rQV 67 (196)
+|+.|..+|...|... -|-. .....+||..||+++.-|
T Consensus 1 LT~~Q~e~L~~A~~~G-Yfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELG-YFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcC-CCCCCCcCCHHHHHHHhCCCHHHH
Confidence 5789999999999877 4433 345578999999998654
No 62
>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=53.25 E-value=61 Score=21.77 Aligned_cols=31 Identities=29% Similarity=0.375 Sum_probs=14.6
Q ss_pred hHHHHHHHHHhhHHhhhhhHhHHHHHHHHhH
Q 029280 83 IEHDYAQLRANYDSLASGFESLIKEKESLLL 113 (196)
Q Consensus 83 ~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~ 113 (196)
.+.....|...++.|...+..|..+...|..
T Consensus 31 Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~ 61 (64)
T PF00170_consen 31 LEEKVEELESENEELKKELEQLKKEIQSLKS 61 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3333444444445555555555555444444
No 63
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=53.03 E-value=17 Score=19.49 Aligned_cols=38 Identities=16% Similarity=0.303 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeee
Q 029280 27 RRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIW 70 (196)
Q Consensus 27 tr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvW 70 (196)
..++.++...+...|... . ....+|..+|++...|..|
T Consensus 4 ~~~~~~~~~~i~~~~~~~-~-----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 4 PKLTPEQIEEARRLLAAG-E-----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CcCCHHHHHHHHHHHHcC-C-----CHHHHHHHHCCCHHHHHHh
Confidence 345666666666666544 2 4567899999988776655
No 64
>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=52.81 E-value=9.7 Score=24.38 Aligned_cols=40 Identities=13% Similarity=0.181 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccc
Q 029280 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQN 73 (196)
Q Consensus 28 r~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQN 73 (196)
.+++.+..++...|-.. -.-.++|..+|+++..|+.|...
T Consensus 10 ~L~~~~r~i~~l~~~~g------~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG------MSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp CS-HHHHHHHHHHHTS---------HHHHHHHCTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC------cCHHHHHHHHCcCHHHHHHHHHH
Confidence 35667777777766655 45678999999999999988753
No 65
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=49.23 E-value=36 Score=25.71 Aligned_cols=45 Identities=18% Similarity=0.322 Sum_probs=20.0
Q ss_pred ceeeeccchhhHHHhHhhHHHHHHHHHhhHHhhhhhHhHHHHHHHH
Q 029280 66 QVAIWFQNKRARWKSKQIEHDYAQLRANYDSLASGFESLIKEKESL 111 (196)
Q Consensus 66 QVkvWFQNRRak~Krkq~~~e~~~lk~~~~~L~~~~~sl~~e~~~L 111 (196)
++..||++.-- .+-.+.+.+...++.+++.+..++..|..+...|
T Consensus 16 ~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L 60 (105)
T PRK00888 16 QYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDL 60 (105)
T ss_pred HHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44567765321 1112333444444454444444444444444444
No 66
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=48.97 E-value=42 Score=28.93 Aligned_cols=41 Identities=20% Similarity=0.183 Sum_probs=26.0
Q ss_pred HHHHHHHhhHHhhhhhHhHHHHHH---HHhHHHHHHHHHHhcccC
Q 029280 86 DYAQLRANYDSLASGFESLIKEKE---SLLLEQLQMLNEQLGKSD 127 (196)
Q Consensus 86 e~~~lk~~~~~L~~~~~sl~~e~~---~L~~~e~~~L~~~~~~~~ 127 (196)
.+..+.+++..|+.++..|+.+.. .|.. |+.+|+.+|.-..
T Consensus 70 ~~~~l~~en~~L~~e~~~l~~~~~~~~~l~~-en~~L~~lL~~~~ 113 (276)
T PRK13922 70 SLFDLREENEELKKELLELESRLQELEQLEA-ENARLRELLNLKE 113 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhcCcc
Confidence 344555556666666666655554 5566 8888898876543
No 67
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=47.27 E-value=18 Score=29.00 Aligned_cols=48 Identities=19% Similarity=0.212 Sum_probs=36.2
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHh
Q 029280 26 KRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (196)
Q Consensus 26 Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Kr 80 (196)
...+|+.|..+|... ... ....++|..||++...|..|..+.+.+.++
T Consensus 4 ~~~Lt~rqreVL~lr-~~G------lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ERG------LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHH-HcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 467899999999884 333 246689999999999999888765554443
No 68
>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=46.61 E-value=5.9 Score=27.35 Aligned_cols=20 Identities=25% Similarity=0.507 Sum_probs=17.0
Q ss_pred HHHHHHHHhCCCCcceeeec
Q 029280 52 KKMQVATELGLQPRQVAIWF 71 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWF 71 (196)
.-.+||.+||+++.+|..|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45679999999999998874
No 69
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=46.28 E-value=51 Score=29.07 Aligned_cols=44 Identities=25% Similarity=0.351 Sum_probs=36.3
Q ss_pred hhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhccc
Q 029280 82 QIEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKS 126 (196)
Q Consensus 82 q~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~ 126 (196)
-...+...|..+++.|.+.+++|..+++.|.. ++..|+..|...
T Consensus 101 dL~een~~L~~en~~Lr~~n~~L~~~n~el~~-~le~~~~~l~~~ 144 (292)
T KOG4005|consen 101 DLTEENEILQNENDSLRAINESLLAKNHELDS-ELELLRQELAEL 144 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH-HHHHHHHHHHhh
Confidence 35567788999999999999999999999988 888888776654
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=44.46 E-value=1e+02 Score=21.85 Aligned_cols=32 Identities=22% Similarity=0.297 Sum_probs=22.5
Q ss_pred hhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhH
Q 029280 82 QIEHDYAQLRANYDSLASGFESLIKEKESLLL 113 (196)
Q Consensus 82 q~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~ 113 (196)
..+.+...|+..+..|...+..|..++..|..
T Consensus 22 ~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~ 53 (72)
T PF06005_consen 22 LLQMENEELKEKNNELKEENEELKEENEQLKQ 53 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 44556667777777777777777777777776
No 71
>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=43.90 E-value=28 Score=32.07 Aligned_cols=21 Identities=29% Similarity=0.316 Sum_probs=8.3
Q ss_pred hhhhHhHHHHHHHHhHHHHHHH
Q 029280 98 ASGFESLIKEKESLLLEQLQML 119 (196)
Q Consensus 98 ~~~~~sl~~e~~~L~~~e~~~L 119 (196)
+.+|.+|++|+..|.. ++.+|
T Consensus 38 r~EN~~LKkEN~~Lk~-eVerL 58 (420)
T PF07407_consen 38 RMENHSLKKENNDLKI-EVERL 58 (420)
T ss_pred HHHhHHHHHHHHHHHH-HHHHH
Confidence 3333333444444444 44443
No 72
>PRK10072 putative transcriptional regulator; Provisional
Probab=42.79 E-value=17 Score=27.22 Aligned_cols=41 Identities=17% Similarity=0.080 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhh
Q 029280 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRA 76 (196)
Q Consensus 28 r~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRa 76 (196)
+.+...+..|...-... ..+||..+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~glT--------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGLK--------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 44666677665433333 678999999999999999987764
No 73
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=42.18 E-value=65 Score=28.26 Aligned_cols=44 Identities=18% Similarity=0.283 Sum_probs=24.0
Q ss_pred hHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhcccC
Q 029280 83 IEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKSD 127 (196)
Q Consensus 83 ~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~~ 127 (196)
...+...|...+..|.++.+.+.....+|.. ++.+|.+++-+..
T Consensus 147 ~~~EkeeL~~eleele~e~ee~~erlk~le~-E~s~LeE~~~~l~ 190 (290)
T COG4026 147 LQKEKEELLKELEELEAEYEEVQERLKRLEV-ENSRLEEMLKKLP 190 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHhch
Confidence 3344445555555555555555555555555 6666666555443
No 74
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=42.07 E-value=17 Score=23.75 Aligned_cols=45 Identities=13% Similarity=0.282 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHH
Q 029280 27 RRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARW 78 (196)
Q Consensus 27 tr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~ 78 (196)
..||+.++.+|.....-. ...++|..+|+++..|.....+=+.|.
T Consensus 2 ~~LT~~E~~vl~~l~~G~-------~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 2 PSLTERELEVLRLLAQGM-------SNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp GSS-HHHHHHHHHHHTTS--------HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred CccCHHHHHHHHHHHhcC-------CcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 368888999887777655 567899999999999887665544443
No 75
>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=41.90 E-value=31 Score=25.81 Aligned_cols=39 Identities=26% Similarity=0.568 Sum_probs=21.8
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHhhHHHH
Q 029280 34 IRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDY 87 (196)
Q Consensus 34 l~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq~~~e~ 87 (196)
+.+..-.|+.+ +||.+.--.. |+ .|||.+|++.+.....
T Consensus 14 vRiIk~Lyqsn-PyP~~~GTr~-aR-------------RnRRRRWR~rq~QI~~ 52 (91)
T PF00424_consen 14 VRIIKILYQSN-PYPSPEGTRQ-AR-------------RNRRRRWRARQRQIRA 52 (91)
T ss_dssp HHHHHHHHHTS--S--S-S-HH-HH-------------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccc-cCCCCCCccc-cc-------------cchhhhHHHHHHHHHH
Confidence 44556669999 9998542111 10 5899999987665544
No 76
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=41.74 E-value=44 Score=25.22 Aligned_cols=34 Identities=12% Similarity=0.188 Sum_probs=17.5
Q ss_pred HHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHH
Q 029280 87 YAQLRANYDSLASGFESLIKEKESLLLEQLQMLNE 121 (196)
Q Consensus 87 ~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~ 121 (196)
+..++++...+..++..++.++..|.. ++..|++
T Consensus 29 ~~~l~~q~~~~~~e~~~l~~~n~~L~~-eI~~L~~ 62 (105)
T PRK00888 29 YWRVNDQVAAQQQTNAKLKARNDQLFA-EIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhhC
Confidence 344455555555555555555555555 5555543
No 77
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=41.59 E-value=14 Score=23.25 Aligned_cols=39 Identities=18% Similarity=0.245 Sum_probs=18.7
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeee
Q 029280 26 KRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIW 70 (196)
Q Consensus 26 Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvW 70 (196)
.+.+|.++...++..+... ....+||..||.++..|..+
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G------~s~~~IA~~lg~s~sTV~re 40 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG------MSIREIAKRLGRSRSTVSRE 40 (44)
T ss_dssp ----------HHHHHHCS---------HHHHHHHTT--HHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC------CCHHHHHHHHCcCcHHHHHH
Confidence 3578888999998887766 34567999999988776543
No 78
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=40.79 E-value=23 Score=27.27 Aligned_cols=27 Identities=15% Similarity=0.159 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 53 KMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
-.++|..+|+++..|++....-|.+.|
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr 151 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIK 151 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 358999999999999887654444443
No 79
>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=40.44 E-value=85 Score=23.90 Aligned_cols=40 Identities=23% Similarity=0.264 Sum_probs=34.3
Q ss_pred HhhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHH
Q 029280 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNE 121 (196)
Q Consensus 81 kq~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~ 121 (196)
..+-.+...|+.....|..+|..|+.|++.|.. .+.++..
T Consensus 18 ~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~-~l~~~~~ 57 (107)
T PF06156_consen 18 GQLLEELEELKKQLQELLEENARLRIENEHLRE-RLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhc
Confidence 456778889999999999999999999999998 7777665
No 80
>PF15058 Speriolin_N: Speriolin N terminus
Probab=40.26 E-value=53 Score=27.89 Aligned_cols=40 Identities=25% Similarity=0.318 Sum_probs=29.9
Q ss_pred HHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhccc
Q 029280 85 HDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKS 126 (196)
Q Consensus 85 ~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~ 126 (196)
..|+.++.+++.|..+|+.||+...-+ . |+++|+..|...
T Consensus 5 ~~yeGlrhqierLv~ENeeLKKlVrLi-r-EN~eLksaL~ea 44 (200)
T PF15058_consen 5 TNYEGLRHQIERLVRENEELKKLVRLI-R-ENHELKSALGEA 44 (200)
T ss_pred cchHHHHHHHHHHHhhhHHHHHHHHHH-H-HHHHHHHHHHHh
Confidence 356777888888888888888876544 4 588888886554
No 81
>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=39.90 E-value=71 Score=30.57 Aligned_cols=10 Identities=30% Similarity=0.584 Sum_probs=6.1
Q ss_pred CCCHHHHHHH
Q 029280 28 RFSDEQIRLL 37 (196)
Q Consensus 28 r~t~eQl~~L 37 (196)
.++++++..|
T Consensus 41 ~ltpee~kal 50 (472)
T TIGR03752 41 ELSPEELKAL 50 (472)
T ss_pred cCCcchhHhc
Confidence 5666666554
No 82
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=39.82 E-value=34 Score=28.43 Aligned_cols=39 Identities=18% Similarity=0.272 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHhhcCCC--CCHHHHHHHHHHhCCCCcce
Q 029280 28 RFSDEQIRLLESIFESESTK--LEPRKKMQVATELGLQPRQV 67 (196)
Q Consensus 28 r~t~eQl~~LE~~F~~~~~~--p~~~~r~eLA~~LgL~~rQV 67 (196)
-+|+.|+.+|...|... -| |-.....+||+++|+++.-+
T Consensus 155 ~LTdrQ~~vL~~A~~~G-YFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMG-YFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcC-CCCCCccCCHHHHHHHhCCCHHHH
Confidence 69999999999999977 33 33334578999999998653
No 83
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=39.19 E-value=23 Score=25.96 Aligned_cols=43 Identities=14% Similarity=0.198 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhH
Q 029280 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRAR 77 (196)
Q Consensus 29 ~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak 77 (196)
+++.+..++...|-.. ....++|..+|+++..|..+...-+.+
T Consensus 111 L~~~~~~ii~~~~~~g------~s~~eIA~~l~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 111 LPEREREVLVLRYLEG------LSYKEIAEILGISVGTVKRRLKRARKK 153 (158)
T ss_pred CCHHHHHHHhhHHhcC------CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4455555554443322 245689999999999887766543333
No 84
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=39.17 E-value=72 Score=28.10 Aligned_cols=16 Identities=25% Similarity=0.065 Sum_probs=12.8
Q ss_pred HhHHHHHHHHHHhcccC
Q 029280 111 LLLEQLQMLNEQLGKSD 127 (196)
Q Consensus 111 L~~~e~~~L~~~~~~~~ 127 (196)
|.. |+.+|+.+|.-..
T Consensus 96 l~~-EN~rLr~LL~~~~ 111 (283)
T TIGR00219 96 LKQ-ENVRLRELLNSPL 111 (283)
T ss_pred HHH-HHHHHHHHhcCcc
Confidence 666 8999999987754
No 85
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=38.82 E-value=19 Score=23.57 Aligned_cols=29 Identities=10% Similarity=0.140 Sum_probs=17.6
Q ss_pred HHHHHHHHhCCCCcceeeeccchhhHHHh
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRak~Kr 80 (196)
....||+.+|++...|..|+.++.....-
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~ 40 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSL 40 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----H
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccH
Confidence 35678999999999999999876444443
No 86
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=38.45 E-value=23 Score=26.97 Aligned_cols=42 Identities=12% Similarity=0.104 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchh
Q 029280 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKR 75 (196)
Q Consensus 28 r~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRR 75 (196)
.+++.+..++...|-.. ..-.++|..+|++...|+.+...-+
T Consensus 106 ~L~~~~r~ii~l~~~~~------~s~~EIA~~l~is~~tV~~~~~ra~ 147 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG------KTMGEIALETEMTYYQVRWIYRQAL 147 (154)
T ss_pred hCCHHHHHHHHHHHhcC------CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34445555554444333 2356899999999999988765433
No 87
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=38.11 E-value=89 Score=25.58 Aligned_cols=47 Identities=15% Similarity=0.220 Sum_probs=39.5
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccch
Q 029280 25 NKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNK 74 (196)
Q Consensus 25 ~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNR 74 (196)
+...+|++++..+...-..+ |..-.+..||+++|+++.-|.+-..--
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D---P~~wTr~~LAkkF~~S~~fV~~v~~~~ 128 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED---PEKWTRKKLAKKFNCSPLFVSMVAPAP 128 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC---chHhhHHHHHHHhCCCHHHHHHhcCCC
Confidence 35789999999999988877 888899999999999988777655433
No 88
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=37.86 E-value=25 Score=27.09 Aligned_cols=28 Identities=18% Similarity=0.209 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
.-.++|..+|+++..|..+...-|.+.|
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3468999999999999887764444433
No 89
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=37.54 E-value=26 Score=27.09 Aligned_cols=39 Identities=10% Similarity=-0.047 Sum_probs=26.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeecc
Q 029280 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 28 r~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQ 72 (196)
.+++.+..+|...|-.. ..-.++|..+|+++..|..+..
T Consensus 128 ~L~~~~r~vl~l~~~~~------~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 128 SLPEELRTAITLREIEG------LSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHH
Confidence 45555656665554333 2345889999999999987765
No 90
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=37.34 E-value=30 Score=27.85 Aligned_cols=26 Identities=19% Similarity=0.176 Sum_probs=19.1
Q ss_pred HHHHHHHHhCCCCcceeeeccchhhH
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRAR 77 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRak 77 (196)
.-.++|..||++...|+++...-|.+
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~ 185 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIR 185 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHH
Confidence 34689999999999997766443333
No 91
>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=37.16 E-value=1e+02 Score=25.40 Aligned_cols=28 Identities=32% Similarity=0.322 Sum_probs=12.4
Q ss_pred HHHHHHHhhHHhhhhhHhHHHHHHHHhH
Q 029280 86 DYAQLRANYDSLASGFESLIKEKESLLL 113 (196)
Q Consensus 86 e~~~lk~~~~~L~~~~~sl~~e~~~L~~ 113 (196)
+...++.+...|...++.|..|+..|..
T Consensus 105 e~~~l~~e~~~l~~~~e~Le~e~~~L~~ 132 (161)
T TIGR02894 105 ENERLKNQNESLQKRNEELEKELEKLRQ 132 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444444444444444
No 92
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=36.69 E-value=81 Score=30.92 Aligned_cols=33 Identities=36% Similarity=0.306 Sum_probs=21.6
Q ss_pred HHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHH
Q 029280 88 AQLRANYDSLASGFESLIKEKESLLLEQLQMLNE 121 (196)
Q Consensus 88 ~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~ 121 (196)
..|.+....|..+++.|+.|+..|+. ++..|-.
T Consensus 305 ~~Le~rLq~ll~Ene~Lk~ENatLk~-qL~~l~~ 337 (655)
T KOG4343|consen 305 LGLEARLQALLSENEQLKKENATLKR-QLDELVS 337 (655)
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHH-HHHHHhh
Confidence 45666677777777777777777766 5544443
No 93
>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=35.58 E-value=29 Score=23.88 Aligned_cols=44 Identities=18% Similarity=0.406 Sum_probs=22.1
Q ss_pred CCCCCHHH-HHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeecc
Q 029280 26 KRRFSDEQ-IRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 26 Rtr~t~eQ-l~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQ 72 (196)
|..|+... +.+++.++..+ .--...|. -|+++|++.++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~--nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDN--NCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-T--TTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHcc--chhhhHHH-HHHHhCccHHHHHHHHH
Confidence 45666644 44555544433 22222333 49999999999988864
No 94
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=35.52 E-value=30 Score=28.33 Aligned_cols=27 Identities=19% Similarity=0.160 Sum_probs=19.3
Q ss_pred HHHHHHHHhCCCCcceeeeccchhhHH
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRARW 78 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRak~ 78 (196)
.-.++|..+|+++..|+++...-+.+.
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~L 197 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKL 197 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 346899999999999877664433333
No 95
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=35.30 E-value=1e+02 Score=29.57 Aligned_cols=26 Identities=31% Similarity=0.541 Sum_probs=18.4
Q ss_pred eeeec---cchhhHHHhHhhHHHHHHHHH
Q 029280 67 VAIWF---QNKRARWKSKQIEHDYAQLRA 92 (196)
Q Consensus 67 VkvWF---QNRRak~Krkq~~~e~~~lk~ 92 (196)
.-+|| ||+.+|.+-...-.+.+.|+.
T Consensus 228 ~gcw~ay~Qnk~akehv~km~kdle~Lq~ 256 (575)
T KOG4403|consen 228 GGCWFAYRQNKKAKEHVNKMMKDLEGLQR 256 (575)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence 34788 899888887766666666543
No 96
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=35.27 E-value=2.3e+02 Score=22.62 Aligned_cols=82 Identities=21% Similarity=0.266 Sum_probs=45.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHH-HHhCCCCcceeeeccchhhH----------HHhHh----hHHHHHHH
Q 029280 26 KRRFSDEQIRLLESIFESESTKLEPRKKMQVA-TELGLQPRQVAIWFQNKRAR----------WKSKQ----IEHDYAQL 90 (196)
Q Consensus 26 Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA-~~LgL~~rQVkvWFQNRRak----------~Krkq----~~~e~~~l 90 (196)
-.+|+.+++..|- -.+|- .--|++...|-.|=|.||+- .|+.+ .+.+...|
T Consensus 21 ~d~lsDd~LvsmS--------------VReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L 86 (135)
T KOG4196|consen 21 GDRLSDDELVSMS--------------VRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAEL 86 (135)
T ss_pred CCCcCHHHHHHhh--------------HHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789998887651 11222 23367777777777777753 33332 33334445
Q ss_pred HHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHH
Q 029280 91 RANYDSLASGFESLIKEKESLLLEQLQMLNEQ 122 (196)
Q Consensus 91 k~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~ 122 (196)
.++.+.|+.++..+..|.+.+.. -...|..-
T Consensus 87 ~qqv~~L~~e~s~~~~E~da~k~-k~e~l~~~ 117 (135)
T KOG4196|consen 87 QQQVEKLKEENSRLRRELDAYKS-KYEALQNS 117 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhh
Confidence 55556666666666666555555 44444443
No 97
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=35.13 E-value=1.1e+02 Score=23.45 Aligned_cols=40 Identities=18% Similarity=0.200 Sum_probs=34.0
Q ss_pred HhhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHH
Q 029280 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNE 121 (196)
Q Consensus 81 kq~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~ 121 (196)
..+-.+...|+.....|..+|..|+.||+.|.. .+.++..
T Consensus 18 ~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~-~l~~~~~ 57 (110)
T PRK13169 18 GVLLKELGALKKQLAELLEENTALRLENDKLRE-RLEELEA 57 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhhc
Confidence 356678889999999999999999999999999 7777633
No 98
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=34.73 E-value=34 Score=27.06 Aligned_cols=45 Identities=16% Similarity=0.144 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 29 ~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
+++.+..++...|-.. ..-.+||..+|++...|+..+..-|.+.|
T Consensus 132 L~~~~r~v~~l~~~~g------~s~~eIA~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 132 LPPRQRDVVQSISVEG------ASIKETAAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4444444554444333 24568999999999999887765444444
No 99
>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=34.67 E-value=1.3e+02 Score=19.53 Aligned_cols=26 Identities=23% Similarity=0.318 Sum_probs=14.4
Q ss_pred hHHhhhhhHhHHHHHHHHhHHHHHHHH
Q 029280 94 YDSLASGFESLIKEKESLLLEQLQMLN 120 (196)
Q Consensus 94 ~~~L~~~~~sl~~e~~~L~~~e~~~L~ 120 (196)
...|......|..++..|.. ++..|.
T Consensus 27 ~~~le~~~~~L~~en~~L~~-~i~~L~ 52 (54)
T PF07716_consen 27 EEELEQEVQELEEENEQLRQ-EIAQLE 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHH-HHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHh
Confidence 34444455555666666666 665554
No 100
>smart00338 BRLZ basic region leucin zipper.
Probab=34.46 E-value=1.4e+02 Score=19.92 Aligned_cols=32 Identities=28% Similarity=0.399 Sum_probs=16.6
Q ss_pred HHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHh
Q 029280 91 RANYDSLASGFESLIKEKESLLLEQLQMLNEQL 123 (196)
Q Consensus 91 k~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~ 123 (196)
+.....|......|..++..|.. ++..|...+
T Consensus 25 k~~~~~Le~~~~~L~~en~~L~~-~~~~l~~e~ 56 (65)
T smart00338 25 KAEIEELERKVEQLEAENERLKK-EIERLRREL 56 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHH
Confidence 34444555555555555555555 555555444
No 101
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=33.92 E-value=39 Score=26.26 Aligned_cols=28 Identities=21% Similarity=0.162 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
.-.++|..+|+++..|+++...-|.+.|
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr 153 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLK 153 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3468999999999999887764444443
No 102
>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=33.40 E-value=33 Score=26.21 Aligned_cols=21 Identities=19% Similarity=0.120 Sum_probs=16.9
Q ss_pred HHHHHHHHhCCCCcceeeecc
Q 029280 52 KKMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQ 72 (196)
.-.++|..+|+++..|.++..
T Consensus 129 ~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 129 SLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 456899999999999886553
No 103
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=33.37 E-value=42 Score=26.40 Aligned_cols=27 Identities=7% Similarity=0.252 Sum_probs=20.1
Q ss_pred HHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 53 KMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
-.++|..+|+++..|++....-|.+.|
T Consensus 148 ~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 148 YKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred HHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 468999999999999877654444433
No 104
>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=32.48 E-value=1.2e+02 Score=20.50 Aligned_cols=29 Identities=28% Similarity=0.401 Sum_probs=14.4
Q ss_pred hHHHHHHHHHhhHHhhhhhHhHHHHHHHH
Q 029280 83 IEHDYAQLRANYDSLASGFESLIKEKESL 111 (196)
Q Consensus 83 ~~~e~~~lk~~~~~L~~~~~sl~~e~~~L 111 (196)
...+...+...++.+..++..|+.+...|
T Consensus 22 ~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 22 LNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34444455555555555555555444444
No 105
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=32.02 E-value=37 Score=25.58 Aligned_cols=22 Identities=23% Similarity=0.391 Sum_probs=16.9
Q ss_pred HHHHHHHHhCCCCcceeeeccc
Q 029280 52 KKMQVATELGLQPRQVAIWFQN 73 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQN 73 (196)
...++|..+|+++..|+.....
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~r 152 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISK 152 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 3457899999999988765543
No 106
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=31.74 E-value=1.5e+02 Score=25.47 Aligned_cols=40 Identities=25% Similarity=0.307 Sum_probs=25.0
Q ss_pred HHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhcccC
Q 029280 87 YAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKSD 127 (196)
Q Consensus 87 ~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~~ 127 (196)
.+......+.|....+.+..|-++|+. +.++|++.+....
T Consensus 174 Le~~~~~~~al~Kq~e~~~~EydrLle-e~~~Lq~~i~~~~ 213 (216)
T KOG1962|consen 174 LEKAQKKVDALKKQSEGLQDEYDRLLE-EYSKLQEQIESGG 213 (216)
T ss_pred HHHHHHHHHHHHHHHHHcccHHHHHHH-HHHHHHHHHhccC
Confidence 334444555555555666667777777 7778887776543
No 107
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.61 E-value=1.9e+02 Score=20.75 Aligned_cols=14 Identities=36% Similarity=0.283 Sum_probs=5.8
Q ss_pred hhHhHHHHHHHHhH
Q 029280 100 GFESLIKEKESLLL 113 (196)
Q Consensus 100 ~~~sl~~e~~~L~~ 113 (196)
.++.|..|++.|+.
T Consensus 47 ~reaL~~eneqlk~ 60 (79)
T COG3074 47 QREALERENEQLKE 60 (79)
T ss_pred HHHHHHHHHHHHHH
Confidence 33344444444444
No 108
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=31.32 E-value=38 Score=26.66 Aligned_cols=38 Identities=16% Similarity=0.123 Sum_probs=23.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeec
Q 029280 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWF 71 (196)
Q Consensus 28 r~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWF 71 (196)
.+++.+..+|...|-.. ..-.++|..+|+++..|++..
T Consensus 100 ~L~~~~r~v~~l~~~~g------~s~~eIA~~lgis~~tV~~~l 137 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG------LSQQEIAEKLGLSLSGAKSRV 137 (170)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHH
Confidence 34455555555444333 234678999999988876644
No 109
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=31.17 E-value=32 Score=27.46 Aligned_cols=28 Identities=14% Similarity=0.222 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
...++|..+|++...|+.++..-|.+.+
T Consensus 159 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 159 SQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4568999999999999988854444333
No 110
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=30.23 E-value=40 Score=26.01 Aligned_cols=38 Identities=18% Similarity=0.261 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccc
Q 029280 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQN 73 (196)
Q Consensus 29 ~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQN 73 (196)
+++.+..+|...| .. ..-.+||..+|+++..|+.....
T Consensus 113 L~~~~r~il~l~~-~g------~s~~eIA~~lgis~~tV~~~i~r 150 (166)
T PRK09639 113 MTERDRTVLLLRF-SG------YSYKEIAEALGIKESSVGTTLAR 150 (166)
T ss_pred CCHHHHHHHHHHH-cC------CCHHHHHHHHCCCHHHHHHHHHH
Confidence 4444445554444 33 23457899999999988876643
No 111
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=29.76 E-value=39 Score=25.83 Aligned_cols=42 Identities=19% Similarity=0.324 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhh
Q 029280 27 RRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRA 76 (196)
Q Consensus 27 tr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRa 76 (196)
..+++..+..+...+... ....|.-||++..-|+.|=|+|+.
T Consensus 42 ~~ls~~eIk~iRe~~~lS--------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 42 KTLSPTEIKAIREKLGLS--------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCCHHHHHHHHHHhCCC--------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 458999999998888777 567899999999999999998764
No 112
>PRK14127 cell division protein GpsB; Provisional
Probab=29.69 E-value=1.6e+02 Score=22.54 Aligned_cols=37 Identities=22% Similarity=0.369 Sum_probs=24.3
Q ss_pred HHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhccc
Q 029280 89 QLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKS 126 (196)
Q Consensus 89 ~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~ 126 (196)
.+-..|+.|..++..|+.++..|.. ++..++..+..+
T Consensus 34 ~V~~dye~l~~e~~~Lk~e~~~l~~-~l~e~~~~~~~~ 70 (109)
T PRK14127 34 DVIKDYEAFQKEIEELQQENARLKA-QVDELTKQVSVG 70 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHhhccc
Confidence 3445566666667777777777777 777777766544
No 113
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=29.63 E-value=44 Score=26.58 Aligned_cols=21 Identities=19% Similarity=0.245 Sum_probs=16.8
Q ss_pred HHHHHHHHhCCCCcceeeecc
Q 029280 52 KKMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQ 72 (196)
.-.+||..+|++...|+....
T Consensus 157 s~~EIA~~lgis~~tV~~~l~ 177 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQH 177 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356899999999998887653
No 114
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=29.54 E-value=52 Score=20.10 Aligned_cols=38 Identities=13% Similarity=0.274 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeecc
Q 029280 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 28 r~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQ 72 (196)
.+++.+..++...+ .. ....++|..+|++...|..+..
T Consensus 3 ~l~~~e~~i~~~~~-~g------~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRLLA-EG------LTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHHHH-cC------CCHHHHHHHHCCCHHHHHHHHH
Confidence 46777887775533 23 1457899999999998876554
No 115
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=29.51 E-value=51 Score=26.26 Aligned_cols=25 Identities=16% Similarity=0.194 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCCcceeeeccchhhH
Q 029280 53 KMQVATELGLQPRQVAIWFQNKRAR 77 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWFQNRRak 77 (196)
-.++|..+|+++..|++-...-|.+
T Consensus 150 ~~eIA~~lgis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 150 VEEVGEIVGIPESTVKTRMFYARKK 174 (189)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 4588999999999988755433333
No 116
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=29.41 E-value=47 Score=25.36 Aligned_cols=38 Identities=11% Similarity=0.084 Sum_probs=23.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeecc
Q 029280 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 29 ~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQ 72 (196)
+++.+..++...|-.. ..-.++|..||+++..|++...
T Consensus 107 Lp~~~r~v~~l~~~~g------~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 107 LPARQREAFLLRYWED------MDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred CCHHHHHHHHHHHHhc------CCHHHHHHHHCCCHHHHHHHHH
Confidence 4444444444433333 2346899999999999876554
No 117
>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=29.03 E-value=27 Score=21.91 Aligned_cols=38 Identities=18% Similarity=0.378 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeee
Q 029280 27 RRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIW 70 (196)
Q Consensus 27 tr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvW 70 (196)
..++.+++..+...+... ....+||+.+|++...|.-+
T Consensus 4 ~~~~~~~~~~i~~l~~~G------~si~~IA~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEG------MSIAEIAKQFGVSRSTVYRY 41 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT--------HHHHHHHTTS-HHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHH
Confidence 346666667777777665 35778999999998776543
No 118
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=28.65 E-value=81 Score=24.88 Aligned_cols=27 Identities=11% Similarity=0.115 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 53 KMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
-.++|..+|++...|++-...-|.+.|
T Consensus 136 ~~EIA~~lgis~~tV~~~l~ra~~~Lr 162 (179)
T PRK12543 136 QEEIAQLLQIPIGTVKSRIHAALKKLR 162 (179)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 457899999998888765544333333
No 119
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=28.46 E-value=43 Score=26.57 Aligned_cols=25 Identities=8% Similarity=0.193 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCCCcceeeeccchhh
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRA 76 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRa 76 (196)
.-.++|..+|++...|+.....-|.
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~ 170 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRR 170 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 3468999999999999876643333
No 120
>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=28.31 E-value=18 Score=22.32 Aligned_cols=22 Identities=14% Similarity=0.162 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCCcceeeeccch
Q 029280 53 KMQVATELGLQPRQVAIWFQNK 74 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWFQNR 74 (196)
..++|+.+|+++..|+.|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3578999999999999997554
No 121
>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=28.17 E-value=94 Score=28.71 Aligned_cols=26 Identities=31% Similarity=0.157 Sum_probs=13.6
Q ss_pred HHHHHhhHHhhhhhHhHHHHHHHHhH
Q 029280 88 AQLRANYDSLASGFESLIKEKESLLL 113 (196)
Q Consensus 88 ~~lk~~~~~L~~~~~sl~~e~~~L~~ 113 (196)
..|+.++..|+.++..|+.+.++|..
T Consensus 35 ~aLr~EN~~LKkEN~~Lk~eVerLE~ 60 (420)
T PF07407_consen 35 FALRMENHSLKKENNDLKIEVERLEN 60 (420)
T ss_pred hhHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555555555555543
No 122
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.04 E-value=57 Score=25.86 Aligned_cols=24 Identities=21% Similarity=0.426 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCCCcceeeeccchh
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKR 75 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRR 75 (196)
.-.++|..+|++...|+++...-|
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~ 174 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSL 174 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHH
Confidence 346889999999999987665333
No 123
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=28.01 E-value=43 Score=26.30 Aligned_cols=26 Identities=15% Similarity=0.144 Sum_probs=19.4
Q ss_pred HHHHHHHHhCCCCcceeeeccchhhH
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRAR 77 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRak 77 (196)
.-.++|..+|+++..|++.+..-|.+
T Consensus 154 s~~eIA~~lgis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 154 SLKEISEILDLPVGTVKTRIHRGREA 179 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45689999999999988777544433
No 124
>PF13518 HTH_28: Helix-turn-helix domain
Probab=27.90 E-value=22 Score=22.18 Aligned_cols=22 Identities=23% Similarity=0.510 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCCCcceeeeccc
Q 029280 52 KKMQVATELGLQPRQVAIWFQN 73 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQN 73 (196)
...++|..+||+..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3567999999999999999864
No 125
>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=27.82 E-value=49 Score=26.00 Aligned_cols=24 Identities=29% Similarity=0.288 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCCcceeeeccchhh
Q 029280 53 KMQVATELGLQPRQVAIWFQNKRA 76 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWFQNRRa 76 (196)
-.++|..+|+++..|++....-|.
T Consensus 153 ~~EIA~~lgis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 153 VEEIAELLGVSVRTVERDWRFARA 176 (183)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHH
Confidence 458999999999999876654333
No 126
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=27.54 E-value=59 Score=34.94 Aligned_cols=59 Identities=15% Similarity=0.191 Sum_probs=53.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHHhHh
Q 029280 23 MKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82 (196)
Q Consensus 23 rr~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~Krkq 82 (196)
+.-+..+-+++...|-..|-.+ .-|+...+..|....+.+.+++.+||+|-|.|.++-+
T Consensus 706 ~~~~~~~~~~aa~~l~~a~~~~-~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 706 KLLRLTILPEAAMILGRAYMQD-NSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccCcccccHHHHhhhhhcccCC-CCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 4457778889999999999999 8899999999999999999999999999999998855
No 127
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.24 E-value=2.1e+02 Score=26.42 Aligned_cols=39 Identities=28% Similarity=0.400 Sum_probs=20.1
Q ss_pred hhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHH
Q 029280 82 QIEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNE 121 (196)
Q Consensus 82 q~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~ 121 (196)
+...+.+.++..-+.|..-...|+.+++.|.. +++.|+.
T Consensus 229 ~~~aeq~slkRt~EeL~~G~~kL~~~~etLEq-q~~~L~~ 267 (365)
T KOG2391|consen 229 RLQAEQESLKRTEEELNIGKQKLVAMKETLEQ-QLQSLQK 267 (365)
T ss_pred HHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHH-HHHHHHh
Confidence 33444444555555555555555555555555 5555544
No 128
>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=27.24 E-value=2.3e+02 Score=20.02 Aligned_cols=36 Identities=25% Similarity=0.365 Sum_probs=20.9
Q ss_pred HHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhc
Q 029280 88 AQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLG 124 (196)
Q Consensus 88 ~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~ 124 (196)
..+...|..|..++.....++..|.. +|..|...+.
T Consensus 24 ~~Wq~sy~~Lq~~~~~t~~~~a~L~~-qv~~Ls~qv~ 59 (70)
T PF04899_consen 24 QEWQSSYADLQHMFEQTSQENAALSE-QVNNLSQQVQ 59 (70)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHH-HHHHHHHHHH
Confidence 34555666666666666666666655 5555555443
No 129
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=27.00 E-value=43 Score=25.82 Aligned_cols=24 Identities=25% Similarity=0.267 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCCcceeeeccchhh
Q 029280 53 KMQVATELGLQPRQVAIWFQNKRA 76 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWFQNRRa 76 (196)
-.++|..+|+++..|++....-|.
T Consensus 131 ~~eIA~~lgis~~tv~~~l~Rar~ 154 (161)
T PRK12541 131 YKEIAEMTGLSLAKVKIELHRGRK 154 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHH
Confidence 468899999999888776653333
No 130
>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
Probab=26.93 E-value=2.6e+02 Score=21.70 Aligned_cols=45 Identities=22% Similarity=0.322 Sum_probs=30.4
Q ss_pred hHhhHHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhcc
Q 029280 80 SKQIEHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGK 125 (196)
Q Consensus 80 rkq~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~ 125 (196)
....+.+...+...|+.+....+.-.++++.|.. .+..|++++..
T Consensus 70 ~~~L~~el~~l~~ry~t~LellGEK~E~veEL~~-Dv~DlK~myr~ 114 (120)
T PF12325_consen 70 VEELEQELEELQQRYQTLLELLGEKSEEVEELRA-DVQDLKEMYRE 114 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHH-HHHHHHHHHHH
Confidence 3445556666666666666666666667777877 78777777643
No 131
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=26.93 E-value=2.5e+02 Score=20.44 Aligned_cols=14 Identities=29% Similarity=0.188 Sum_probs=6.2
Q ss_pred hhHhHHHHHHHHhH
Q 029280 100 GFESLIKEKESLLL 113 (196)
Q Consensus 100 ~~~sl~~e~~~L~~ 113 (196)
....|..++..|+.
T Consensus 47 ~r~~L~~en~qLk~ 60 (79)
T PRK15422 47 QREELERENNHLKE 60 (79)
T ss_pred hHHHHHHHHHHHHH
Confidence 33334444444444
No 132
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=26.85 E-value=68 Score=25.72 Aligned_cols=28 Identities=11% Similarity=0.236 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
.-.++|..+|+++..|+++...-|.+-|
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr 179 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQ 179 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3568999999999999987754333333
No 133
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=26.43 E-value=2.5e+02 Score=24.67 Aligned_cols=32 Identities=28% Similarity=0.400 Sum_probs=13.0
Q ss_pred HHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHh
Q 029280 91 RANYDSLASGFESLIKEKESLLLEQLQMLNEQL 123 (196)
Q Consensus 91 k~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~ 123 (196)
+..++.+..++..|..++..|.+ ++..+++.+
T Consensus 141 kekl~E~~~EkeeL~~eleele~-e~ee~~erl 172 (290)
T COG4026 141 KEKLEELQKEKEELLKELEELEA-EYEEVQERL 172 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHH
Confidence 33333333344444444444444 444444433
No 134
>PRK04217 hypothetical protein; Provisional
Probab=26.40 E-value=59 Score=24.93 Aligned_cols=42 Identities=10% Similarity=0.031 Sum_probs=31.9
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccc
Q 029280 26 KRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQN 73 (196)
Q Consensus 26 Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQN 73 (196)
-..++.++..++...|... ....+||+.+|++...|...+..
T Consensus 40 ~~~Lt~eereai~l~~~eG------lS~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEG------LTQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred cccCCHHHHHHHHHHHHcC------CCHHHHHHHHCcCHHHHHHHHHH
Confidence 4567889988887777655 25678999999999888765543
No 135
>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=25.83 E-value=42 Score=26.42 Aligned_cols=21 Identities=10% Similarity=-0.065 Sum_probs=17.0
Q ss_pred HHHHHHHHhCCCCcceeeecc
Q 029280 52 KKMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQ 72 (196)
.-.++|..+|+++..|+++..
T Consensus 156 s~~EIA~~lgis~~tv~~~l~ 176 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIF 176 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 346899999999999877664
No 136
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=25.61 E-value=51 Score=26.70 Aligned_cols=28 Identities=21% Similarity=0.128 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
.-.++|..+|+++..|++....-|.+.|
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr 158 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLA 158 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3468999999999999887754443333
No 137
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=25.44 E-value=2.3e+02 Score=20.65 Aligned_cols=31 Identities=29% Similarity=0.309 Sum_probs=15.9
Q ss_pred HHhhHHhhhhhHhHHHH-------HHHHhHHHHHHHHHH
Q 029280 91 RANYDSLASGFESLIKE-------KESLLLEQLQMLNEQ 122 (196)
Q Consensus 91 k~~~~~L~~~~~sl~~e-------~~~L~~~e~~~L~~~ 122 (196)
+-+.+.|+..+..|..+ +..|.. ++++|+..
T Consensus 24 qmEieELKekn~~L~~e~~~~~~~r~~L~~-en~qLk~E 61 (79)
T PRK15422 24 QMEIEELKEKNNSLSQEVQNAQHQREELER-ENNHLKEQ 61 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHH-HHHHHHHH
Confidence 44444444444444444 444666 77766654
No 138
>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=24.90 E-value=2.7e+02 Score=20.15 Aligned_cols=35 Identities=20% Similarity=0.439 Sum_probs=22.1
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccc
Q 029280 25 NKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQN 73 (196)
Q Consensus 25 ~Rtr~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQN 73 (196)
.++.|+..++..|..... .+.+|++..+|+-.+..
T Consensus 35 g~R~y~~~di~~l~~i~~--------------lr~~g~~l~~i~~~~~~ 69 (103)
T cd01106 35 GYRLYTEEDLERLQQILF--------------LKELGFSLKEIKELLKD 69 (103)
T ss_pred CceeeCHHHHHHHHHHHH--------------HHHcCCCHHHHHHHHHc
Confidence 467899999988865532 23456666666555543
No 139
>PRK10884 SH3 domain-containing protein; Provisional
Probab=24.83 E-value=2.6e+02 Score=23.58 Aligned_cols=31 Identities=19% Similarity=0.172 Sum_probs=15.7
Q ss_pred HHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHH
Q 029280 90 LRANYDSLASGFESLIKEKESLLLEQLQMLNE 121 (196)
Q Consensus 90 lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~ 121 (196)
|+.++..|..+...++.+++.|.. ++..++.
T Consensus 137 L~~~n~~L~~~l~~~~~~~~~l~~-~~~~~~~ 167 (206)
T PRK10884 137 LKEENQKLKNQLIVAQKKVDAANL-QLDDKQR 167 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH
Confidence 455555555555555555555555 4544443
No 140
>PF15397 DUF4618: Domain of unknown function (DUF4618)
Probab=24.71 E-value=2.3e+02 Score=25.06 Aligned_cols=52 Identities=12% Similarity=0.053 Sum_probs=33.7
Q ss_pred HHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhcccCCcC-------CCCCCCC
Q 029280 85 HDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKSDYEI-------NGVGKDL 137 (196)
Q Consensus 85 ~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~~~~~-------~~~c~~~ 137 (196)
.++..+..+..........++.+.+.|.+ +|+.|+.....+.... ..-|.++
T Consensus 186 ~~N~~m~kei~~~re~i~el~e~I~~L~~-eV~~L~~~~~~~Re~iF~dvll~rpKCTPD 244 (258)
T PF15397_consen 186 LENQVMQKEIVQFREEIDELEEEIPQLRA-EVEQLQAQAQDPREVIFADVLLRRPKCTPD 244 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHhhcchHHHhhHHHhcCCCCCCCC
Confidence 44455555556666666677778888888 8888877776554322 4667764
No 141
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=24.30 E-value=2.3e+02 Score=24.43 Aligned_cols=41 Identities=32% Similarity=0.431 Sum_probs=23.0
Q ss_pred hHHHHHHHHHhhHHh-hhhhHhHHHHHHHHhHHHHHHHHHHhc
Q 029280 83 IEHDYAQLRANYDSL-ASGFESLIKEKESLLLEQLQMLNEQLG 124 (196)
Q Consensus 83 ~~~e~~~lk~~~~~L-~~~~~sl~~e~~~L~~~e~~~L~~~~~ 124 (196)
...+...++.+...+ ..+|..+..|++.|.. ++.+|+..+-
T Consensus 99 Q~~~f~kiRsel~S~e~sEF~~lr~e~Eklkn-dlEk~ks~lr 140 (220)
T KOG3156|consen 99 QKVDFAKIRSELVSIERSEFANLRAENEKLKN-DLEKLKSSLR 140 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Confidence 344444444444333 3456666667777777 7776666553
No 142
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=24.05 E-value=61 Score=25.92 Aligned_cols=21 Identities=24% Similarity=0.302 Sum_probs=15.3
Q ss_pred HHHHHHHHhCCCCcceeeecc
Q 029280 52 KKMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQ 72 (196)
...++|..+|+++..|+..+.
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~ 144 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQ 144 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 345788889998887766553
No 143
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=24.00 E-value=3.2e+02 Score=24.97 Aligned_cols=14 Identities=21% Similarity=0.522 Sum_probs=11.1
Q ss_pred eeeeccchhhHHHh
Q 029280 67 VAIWFQNKRARWKS 80 (196)
Q Consensus 67 VkvWFQNRRak~Kr 80 (196)
++|||+|.|+-.+-
T Consensus 16 CKiWi~dN~~Sv~~ 29 (336)
T KOG0150|consen 16 CKIWIKDNPASVRF 29 (336)
T ss_pred hhhhhcCChHHHHh
Confidence 47999999887653
No 144
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=23.51 E-value=66 Score=24.70 Aligned_cols=20 Identities=30% Similarity=0.566 Sum_probs=16.1
Q ss_pred HHHHHHHhCCCCcceeeecc
Q 029280 53 KMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWFQ 72 (196)
..++|..+|++...|+....
T Consensus 128 ~~EIA~~lgis~~tV~~~l~ 147 (163)
T PRK07037 128 QKDIARELGVSPTLVNFMIR 147 (163)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 46899999999999886543
No 145
>PRK06930 positive control sigma-like factor; Validated
Probab=23.21 E-value=67 Score=26.13 Aligned_cols=46 Identities=7% Similarity=0.029 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 28 r~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
.+++.+..++...|... ..-.++|..+|+++..|+.+...-+.+.+
T Consensus 114 ~L~~rer~V~~L~~~eg------~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr 159 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG------LSYSEIADYLNIKKSTVQSMIERAEKKIA 159 (170)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 46666666666655434 24568899999999999887765444444
No 146
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=23.01 E-value=2.2e+02 Score=24.91 Aligned_cols=27 Identities=33% Similarity=0.410 Sum_probs=12.3
Q ss_pred hhhhHhHHHHHHHHhHHHHHHHHHHhcc
Q 029280 98 ASGFESLIKEKESLLLEQLQMLNEQLGK 125 (196)
Q Consensus 98 ~~~~~sl~~e~~~L~~~e~~~L~~~~~~ 125 (196)
......|.+|+..|.. +|.+|+..+.+
T Consensus 221 ~~r~~~leken~~lr~-~v~~l~~el~~ 247 (269)
T KOG3119|consen 221 AHRVAELEKENEALRT-QVEQLKKELAT 247 (269)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 3333444444444444 44444444443
No 147
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=22.69 E-value=71 Score=24.80 Aligned_cols=21 Identities=10% Similarity=0.175 Sum_probs=16.5
Q ss_pred HHHHHHHHhCCCCcceeeecc
Q 029280 52 KKMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQ 72 (196)
.-.++|..+|+++..|++...
T Consensus 137 s~~eiA~~lgis~~tv~~~l~ 157 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLH 157 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 456899999999998876543
No 148
>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=22.49 E-value=15 Score=24.82 Aligned_cols=26 Identities=31% Similarity=0.635 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
...+||..||++.+.|..|-+ |-+|.
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~ 40 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWD 40 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCcc
Confidence 456899999999999999974 44444
No 149
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.28 E-value=1.1e+02 Score=22.87 Aligned_cols=37 Identities=19% Similarity=0.214 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCc
Q 029280 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPR 65 (196)
Q Consensus 28 r~t~eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~r 65 (196)
.+.++|...-...|+.+ --+++...+++|..|++++-
T Consensus 2 SLn~eq~~~Tk~elqan-~el~~LS~~~iA~~Ln~t~~ 38 (97)
T COG4367 2 SLNPEQKQRTKQELQAN-FELCPLSDEEIATALNWTEV 38 (97)
T ss_pred CCCHHHHHHHHHHHHHh-hhhccccHHHHHHHhCCCHH
Confidence 35677877777777777 66667778899999998874
No 150
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=22.24 E-value=69 Score=24.91 Aligned_cols=22 Identities=9% Similarity=-0.031 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCCCcceeeeccc
Q 029280 52 KKMQVATELGLQPRQVAIWFQN 73 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQN 73 (196)
.-.++|..+|+++..|++....
T Consensus 130 s~~eIA~~lgis~~tV~~~l~R 151 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSR 151 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHH
Confidence 3568999999999998876643
No 151
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=22.15 E-value=68 Score=25.79 Aligned_cols=21 Identities=10% Similarity=0.075 Sum_probs=17.0
Q ss_pred HHHHHHHhCCCCcceeeeccc
Q 029280 53 KMQVATELGLQPRQVAIWFQN 73 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWFQN 73 (196)
-.+||..+|+++..|+.++..
T Consensus 155 ~~eIA~~lgis~~tV~~~l~R 175 (196)
T PRK12524 155 NPEIAEVMEIGVEAVESLTAR 175 (196)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 458899999999998877653
No 152
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=22.06 E-value=69 Score=24.58 Aligned_cols=28 Identities=29% Similarity=0.340 Sum_probs=19.6
Q ss_pred HHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
.-.++|..+|++...|+.+...-|.+-+
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr 155 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLR 155 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3468899999999998876654444333
No 153
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=21.85 E-value=70 Score=25.57 Aligned_cols=20 Identities=20% Similarity=0.307 Sum_probs=15.3
Q ss_pred HHHHHHHhCCCCcceeeecc
Q 029280 53 KMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWFQ 72 (196)
..++|..+|++...|+...+
T Consensus 150 ~~EIAe~lgis~~~V~~~l~ 169 (189)
T PRK06811 150 IEEIAKKLGLTRSAIDNRLS 169 (189)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 46889999999988766443
No 154
>PRK14127 cell division protein GpsB; Provisional
Probab=21.73 E-value=2.2e+02 Score=21.87 Aligned_cols=40 Identities=20% Similarity=0.237 Sum_probs=29.7
Q ss_pred HHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhcccCC
Q 029280 88 AQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLGKSDY 128 (196)
Q Consensus 88 ~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~~~~ 128 (196)
.......+.+....+.+..|+..|.. ++..|+..+..-..
T Consensus 26 ~EVD~FLd~V~~dye~l~~e~~~Lk~-e~~~l~~~l~e~~~ 65 (109)
T PRK14127 26 DEVDKFLDDVIKDYEAFQKEIEELQQ-ENARLKAQVDELTK 65 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
Confidence 44566777778888888888888888 88888887765443
No 155
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=21.73 E-value=24 Score=23.47 Aligned_cols=20 Identities=25% Similarity=0.393 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCCcceeeecc
Q 029280 53 KMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWFQ 72 (196)
..++|+.+|++++.|+.|=.
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999954
No 156
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=21.68 E-value=1.2e+02 Score=29.79 Aligned_cols=33 Identities=24% Similarity=0.302 Sum_probs=20.6
Q ss_pred HhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhcc
Q 029280 92 ANYDSLASGFESLIKEKESLLLEQLQMLNEQLGK 125 (196)
Q Consensus 92 ~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~~ 125 (196)
.....|.+....+..|++.|+. |+..|+..|..
T Consensus 302 Ey~~~Le~rLq~ll~Ene~Lk~-ENatLk~qL~~ 334 (655)
T KOG4343|consen 302 EYMLGLEARLQALLSENEQLKK-ENATLKRQLDE 334 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh-hhHHHHHHHHH
Confidence 3334555666666667777777 77777666544
No 157
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=21.51 E-value=77 Score=26.73 Aligned_cols=28 Identities=11% Similarity=0.159 Sum_probs=19.9
Q ss_pred HHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
.-.+||..+|++...|++....-|.+.|
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3468999999999999876654444333
No 158
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=21.34 E-value=77 Score=24.32 Aligned_cols=19 Identities=32% Similarity=0.218 Sum_probs=14.7
Q ss_pred HHHHHHHhCCCCcceeeec
Q 029280 53 KMQVATELGLQPRQVAIWF 71 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWF 71 (196)
-.++|..+|+++..|+...
T Consensus 141 ~~eIA~~l~is~~tv~~~l 159 (170)
T TIGR02952 141 IAEVARILGKTEGAVKILQ 159 (170)
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 4588999999998876543
No 159
>PHA02955 hypothetical protein; Provisional
Probab=21.21 E-value=1.2e+02 Score=26.10 Aligned_cols=42 Identities=10% Similarity=0.210 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCcceeeeccc
Q 029280 32 EQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQN 73 (196)
Q Consensus 32 eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQN 73 (196)
.++..|-..|...-..+++++|.++|++||+....|..||.+
T Consensus 61 ~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 61 KNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 455555555544436688899999999999999877888875
No 160
>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=21.19 E-value=3.9e+02 Score=22.71 Aligned_cols=28 Identities=29% Similarity=0.286 Sum_probs=11.5
Q ss_pred HHHHHHHhhHHhhhhhHhHHHHHHHHhH
Q 029280 86 DYAQLRANYDSLASGFESLIKEKESLLL 113 (196)
Q Consensus 86 e~~~lk~~~~~L~~~~~sl~~e~~~L~~ 113 (196)
+...+...|..|..+.+.+..++..|..
T Consensus 50 e~~~L~~e~~~l~~e~e~L~~~~~~l~~ 77 (251)
T PF11932_consen 50 EKQELLAEYRQLEREIENLEVYNEQLER 77 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444444443333333
No 161
>PRK10884 SH3 domain-containing protein; Provisional
Probab=21.14 E-value=3.3e+02 Score=22.98 Aligned_cols=35 Identities=17% Similarity=0.065 Sum_probs=18.8
Q ss_pred HHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhc
Q 029280 89 QLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLG 124 (196)
Q Consensus 89 ~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~ 124 (196)
.....+..|..++..|+.+...+.. ++..|+.++.
T Consensus 129 ~~~~~~~~L~~~n~~L~~~l~~~~~-~~~~l~~~~~ 163 (206)
T PRK10884 129 QSDSVINGLKEENQKLKNQLIVAQK-KVDAANLQLD 163 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Confidence 3444455555555555555555555 5555554443
No 162
>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=20.94 E-value=32 Score=29.84 Aligned_cols=31 Identities=29% Similarity=0.240 Sum_probs=0.0
Q ss_pred HHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHH
Q 029280 88 AQLRANYDSLASGFESLIKEKESLLLEQLQML 119 (196)
Q Consensus 88 ~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L 119 (196)
.-|+...+.|.++|+.|+.||.+|.+ ++.+|
T Consensus 132 ~dLrrlVe~L~aeNErLr~EnkqL~a-e~arL 162 (243)
T PF08961_consen 132 ADLRRLVEFLLAENERLRRENKQLKA-ENARL 162 (243)
T ss_dssp --------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHH
Confidence 33455555666666666666666666 55444
No 163
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=20.90 E-value=87 Score=24.65 Aligned_cols=20 Identities=20% Similarity=0.165 Sum_probs=15.7
Q ss_pred HHHHHHHhCCCCcceeeecc
Q 029280 53 KMQVATELGLQPRQVAIWFQ 72 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWFQ 72 (196)
-.++|..+|+++..|+.+..
T Consensus 154 ~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 154 HREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35889999999988876554
No 164
>PF15058 Speriolin_N: Speriolin N terminus
Probab=20.87 E-value=1.3e+02 Score=25.67 Aligned_cols=32 Identities=28% Similarity=0.510 Sum_probs=20.0
Q ss_pred HhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhc
Q 029280 92 ANYDSLASGFESLIKEKESLLLEQLQMLNEQLG 124 (196)
Q Consensus 92 ~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~ 124 (196)
..|+-|.+..+.|..||+.|+. +|.-|++...
T Consensus 5 ~~yeGlrhqierLv~ENeeLKK-lVrLirEN~e 36 (200)
T PF15058_consen 5 TNYEGLRHQIERLVRENEELKK-LVRLIRENHE 36 (200)
T ss_pred cchHHHHHHHHHHHhhhHHHHH-HHHHHHHHHH
Confidence 4566666666666666666666 6666665443
No 165
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=20.81 E-value=3e+02 Score=19.17 Aligned_cols=40 Identities=23% Similarity=0.261 Sum_probs=22.2
Q ss_pred HHHHHHHHHhhHHhhhhhHhHHHHHHHHhHHHHHHHHHHhc
Q 029280 84 EHDYAQLRANYDSLASGFESLIKEKESLLLEQLQMLNEQLG 124 (196)
Q Consensus 84 ~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~~e~~~L~~~~~ 124 (196)
......|..+.+.....-.....++..|+. ++..|+..+.
T Consensus 25 ~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~-E~e~L~~el~ 64 (69)
T PF14197_consen 25 EIENKRLRRERDSAERQLGDAYEENNKLKE-ENEALRKELE 64 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Confidence 344455555555555555555556666666 6666655543
No 166
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=20.71 E-value=26 Score=21.90 Aligned_cols=22 Identities=23% Similarity=0.475 Sum_probs=16.9
Q ss_pred HHHHHHHHhCCCCcceeeeccc
Q 029280 52 KKMQVATELGLQPRQVAIWFQN 73 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQN 73 (196)
...++|..+|++...|..|...
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT-
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4678999999999999999753
No 167
>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=20.70 E-value=67 Score=21.28 Aligned_cols=32 Identities=22% Similarity=0.482 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCccee
Q 029280 32 EQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVA 68 (196)
Q Consensus 32 eQl~~LE~~F~~~~~~p~~~~r~eLA~~LgL~~rQVk 68 (196)
.|+..|+-.|. . ...+.. +||..+|++.+.|+
T Consensus 6 rq~~Ll~~L~~-~-~~~~~~---ela~~l~~S~rti~ 37 (59)
T PF08280_consen 6 RQLKLLELLLK-N-KWITLK---ELAKKLNISERTIK 37 (59)
T ss_dssp HHHHHHHHHHH-H-TSBBHH---HHHHHCTS-HHHHH
T ss_pred HHHHHHHHHHc-C-CCCcHH---HHHHHHCCCHHHHH
Confidence 47788888888 5 445443 89999999987654
No 168
>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=20.61 E-value=1.2e+02 Score=24.93 Aligned_cols=23 Identities=30% Similarity=0.304 Sum_probs=4.2
Q ss_pred hhHhHHHHHHHHhHHHHHHHHHHh
Q 029280 100 GFESLIKEKESLLLEQLQMLNEQL 123 (196)
Q Consensus 100 ~~~sl~~e~~~L~~~e~~~L~~~~ 123 (196)
+.+.|+.++++|+. |+..|+..+
T Consensus 25 EKE~L~~~~QRLkD-E~RDLKqEl 47 (166)
T PF04880_consen 25 EKENLREEVQRLKD-ELRDLKQEL 47 (166)
T ss_dssp HHHHHHHCH---------------
T ss_pred HHHHHHHHHHHHHH-HHHHHHHHH
Confidence 34444455555555 554444444
No 169
>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=20.48 E-value=1.9e+02 Score=20.54 Aligned_cols=21 Identities=14% Similarity=0.238 Sum_probs=16.8
Q ss_pred HHHHHHHhCCCCcceeeeccc
Q 029280 53 KMQVATELGLQPRQVAIWFQN 73 (196)
Q Consensus 53 r~eLA~~LgL~~rQVkvWFQN 73 (196)
..++|..+|++++.|..|.+.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 346889999999999988753
No 170
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=20.44 E-value=76 Score=25.37 Aligned_cols=28 Identities=7% Similarity=0.162 Sum_probs=20.1
Q ss_pred HHHHHHHHhCCCCcceeeeccchhhHHH
Q 029280 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (196)
Q Consensus 52 ~r~eLA~~LgL~~rQVkvWFQNRRak~K 79 (196)
.-.++|..+|+++..|+.....-|.+.|
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr 181 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLR 181 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3468999999999999876654443333
No 171
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=20.12 E-value=4e+02 Score=20.72 Aligned_cols=42 Identities=26% Similarity=0.306 Sum_probs=29.9
Q ss_pred hHHHHHHHHHhhHHhhhhhHhHHHHHHHHhH----HHHHHHHHHhc
Q 029280 83 IEHDYAQLRANYDSLASGFESLIKEKESLLL----EQLQMLNEQLG 124 (196)
Q Consensus 83 ~~~e~~~lk~~~~~L~~~~~sl~~e~~~L~~----~e~~~L~~~~~ 124 (196)
-+.+-+.|+..+..|...+..|..||.-|+. |++.+|...+.
T Consensus 65 VREEVe~Lk~qI~eL~er~~~Le~EN~lLk~~~spe~L~ql~~~~~ 110 (123)
T KOG4797|consen 65 VREEVEVLKEQIRELEERNSALERENSLLKTLASPEQLAQLPAQLS 110 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhcc
Confidence 3556677888888888888888888776654 45666666655
No 172
>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=20.06 E-value=24 Score=25.28 Aligned_cols=32 Identities=16% Similarity=0.173 Sum_probs=23.1
Q ss_pred HhhcCCCCCHHHHHHHHHHhCCCCcceeeeccc
Q 029280 41 FESESTKLEPRKKMQVATELGLQPRQVAIWFQN 73 (196)
Q Consensus 41 F~~~~~~p~~~~r~eLA~~LgL~~rQVkvWFQN 73 (196)
|... .+...-...+||..+|+++..|+.|+.+
T Consensus 24 f~L~-R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 24 AALA-REEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHH-HHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 4433 3333345779999999999999988754
Done!