Query 029338
Match_columns 195
No_of_seqs 237 out of 1333
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 11:19:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029338.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029338hhsearch_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 1.3E-22 2.8E-27 168.6 10.2 111 23-134 51-161 (198)
2 KOG0488 Transcription factor B 99.7 6.6E-18 1.4E-22 149.1 7.7 68 16-84 166-233 (309)
3 KOG0489 Transcription factor z 99.7 1.1E-17 2.4E-22 144.5 5.4 60 21-81 158-217 (261)
4 KOG0842 Transcription factor t 99.7 1.3E-17 2.7E-22 146.4 3.5 71 19-90 150-220 (307)
5 KOG0850 Transcription factor D 99.7 5.6E-17 1.2E-21 136.4 5.9 64 17-81 117-180 (245)
6 KOG0843 Transcription factor E 99.7 7.2E-17 1.6E-21 131.5 6.1 64 21-85 101-164 (197)
7 KOG0485 Transcription factor N 99.7 1.5E-16 3.3E-21 133.1 7.0 60 21-81 103-162 (268)
8 PF00046 Homeobox: Homeobox do 99.7 3.3E-16 7.1E-21 104.8 7.2 57 23-80 1-57 (57)
9 KOG0487 Transcription factor A 99.6 5.9E-17 1.3E-21 142.3 3.3 65 20-85 233-297 (308)
10 KOG0494 Transcription factor C 99.6 3.1E-16 6.7E-21 134.2 5.9 85 11-96 130-214 (332)
11 KOG0492 Transcription factor M 99.6 5.5E-16 1.2E-20 128.9 6.6 66 17-83 139-204 (246)
12 KOG0484 Transcription factor P 99.6 5.5E-16 1.2E-20 116.5 5.6 62 19-81 14-75 (125)
13 KOG0493 Transcription factor E 99.6 1.3E-15 2.8E-20 130.5 6.6 78 4-82 222-305 (342)
14 smart00389 HOX Homeodomain. DN 99.5 2.3E-14 5E-19 95.0 6.6 55 24-79 2-56 (56)
15 KOG0848 Transcription factor C 99.5 3.9E-15 8.5E-20 127.8 3.4 57 24-81 201-257 (317)
16 cd00086 homeodomain Homeodomai 99.5 3.8E-14 8.2E-19 94.6 7.4 57 24-81 2-58 (59)
17 KOG4577 Transcription factor L 99.5 3.1E-14 6.7E-19 123.5 7.0 93 21-115 166-258 (383)
18 KOG2251 Homeobox transcription 99.5 1.8E-14 3.9E-19 120.7 5.3 68 17-85 32-99 (228)
19 TIGR01565 homeo_ZF_HD homeobox 99.4 1E-13 2.2E-18 94.5 4.2 52 23-75 2-57 (58)
20 KOG0491 Transcription factor B 99.4 7.1E-14 1.5E-18 112.7 3.1 64 21-85 99-162 (194)
21 COG5576 Homeodomain-containing 99.4 2.5E-13 5.4E-18 109.5 5.9 64 20-84 49-112 (156)
22 KOG3802 Transcription factor O 99.3 9E-13 1.9E-17 118.6 2.8 73 8-81 280-352 (398)
23 KOG0486 Transcription factor P 99.3 3E-12 6.5E-17 112.2 4.6 75 20-95 110-184 (351)
24 KOG0847 Transcription factor, 99.3 2.8E-12 6.1E-17 107.8 4.0 62 19-81 164-225 (288)
25 KOG0844 Transcription factor E 99.3 1.4E-12 3E-17 114.1 1.8 63 21-84 180-242 (408)
26 KOG0490 Transcription factor, 99.0 9.9E-11 2.2E-15 97.4 2.4 63 19-82 57-119 (235)
27 KOG0775 Transcription factor S 98.9 1.9E-09 4.1E-14 93.2 5.6 74 6-80 151-233 (304)
28 KOG0849 Transcription factor P 98.8 3.7E-09 8E-14 95.3 5.8 64 18-82 172-235 (354)
29 KOG1168 Transcription factor A 98.6 6.1E-09 1.3E-13 90.9 0.2 60 22-82 309-368 (385)
30 PF05920 Homeobox_KN: Homeobox 98.5 1.1E-07 2.4E-12 60.0 3.9 33 45-77 8-40 (40)
31 KOG0774 Transcription factor P 98.3 2.6E-07 5.6E-12 79.8 2.7 58 23-80 189-248 (334)
32 KOG2252 CCAAT displacement pro 98.2 2.9E-06 6.2E-11 79.6 6.3 58 21-79 419-476 (558)
33 PF02183 HALZ: Homeobox associ 98.2 6E-06 1.3E-10 53.5 5.6 44 81-124 1-44 (45)
34 KOG0490 Transcription factor, 97.8 2E-05 4.3E-10 65.5 4.2 63 20-83 151-213 (235)
35 KOG1146 Homeobox protein [Gene 96.9 0.0007 1.5E-08 69.3 3.8 61 22-83 903-963 (1406)
36 PF11569 Homez: Homeodomain le 96.9 0.0011 2.4E-08 44.8 3.4 42 33-75 9-50 (56)
37 KOG0773 Transcription factor M 96.7 0.00096 2.1E-08 59.4 2.6 60 22-81 239-300 (342)
38 PF02183 HALZ: Homeobox associ 95.4 0.034 7.3E-07 35.9 4.3 38 90-127 3-40 (45)
39 KOG3623 Homeobox transcription 94.0 0.11 2.4E-06 51.1 5.7 48 34-82 568-615 (1007)
40 PRK09413 IS2 repressor TnpA; R 93.7 0.57 1.2E-05 35.7 8.3 91 26-122 10-101 (121)
41 PF04218 CENP-B_N: CENP-B N-te 93.3 0.24 5.1E-06 32.7 4.8 47 23-75 1-47 (53)
42 smart00340 HALZ homeobox assoc 92.1 0.34 7.3E-06 30.9 4.0 31 95-125 8-38 (44)
43 PF06156 DUF972: Protein of un 88.3 1.8 3.8E-05 32.9 6.0 47 81-127 11-57 (107)
44 PF00170 bZIP_1: bZIP transcri 86.5 6.4 0.00014 26.5 7.4 39 84-122 25-63 (64)
45 PRK13169 DNA replication intia 86.1 2.7 5.8E-05 32.2 5.9 45 81-125 11-55 (110)
46 smart00340 HALZ homeobox assoc 85.8 1.8 4E-05 27.6 4.0 34 81-114 1-34 (44)
47 KOG0709 CREB/ATF family transc 84.2 6.5 0.00014 37.0 8.5 93 26-125 218-319 (472)
48 PF06005 DUF904: Protein of un 83.5 6.7 0.00014 27.7 6.5 40 82-121 15-54 (72)
49 PF10224 DUF2205: Predicted co 82.7 7.9 0.00017 28.0 6.8 45 80-124 18-62 (80)
50 PF01527 HTH_Tnp_1: Transposas 82.6 2.8 6.1E-05 28.5 4.4 43 24-72 2-45 (76)
51 KOG4571 Activating transcripti 82.5 5.7 0.00012 35.3 7.1 44 81-124 244-287 (294)
52 cd06171 Sigma70_r4 Sigma70, re 81.9 3.6 7.7E-05 25.0 4.3 44 28-77 10-53 (55)
53 KOG4196 bZIP transcription fac 81.3 15 0.00034 28.9 8.4 87 26-126 21-115 (135)
54 PF04545 Sigma70_r4: Sigma-70, 80.0 7.6 0.00016 24.5 5.4 42 28-75 4-45 (50)
55 COG4467 Regulator of replicati 78.5 8.2 0.00018 29.5 5.9 45 82-126 12-56 (114)
56 KOG4005 Transcription factor X 76.9 12 0.00027 32.5 7.2 55 71-125 81-144 (292)
57 PF08281 Sigma70_r4_2: Sigma-7 76.0 10 0.00022 24.1 5.2 43 28-76 10-52 (54)
58 PRK00118 putative DNA-binding 75.0 31 0.00066 26.0 8.2 47 28-80 17-63 (104)
59 KOG3119 Basic region leucine z 74.5 10 0.00022 33.1 6.3 49 75-126 208-256 (269)
60 PF00170 bZIP_1: bZIP transcri 73.8 18 0.0004 24.2 6.2 34 82-115 30-63 (64)
61 PF14775 NYD-SP28_assoc: Sperm 73.5 7.9 0.00017 26.3 4.3 30 95-124 29-58 (60)
62 KOG0483 Transcription factor H 72.9 5.4 0.00012 33.5 4.0 43 86-128 106-148 (198)
63 smart00338 BRLZ basic region l 71.7 27 0.00059 23.4 8.5 40 84-123 25-64 (65)
64 PRK00888 ftsB cell division pr 69.0 11 0.00024 28.3 4.6 49 64-120 14-62 (105)
65 PF07716 bZIP_2: Basic region 66.8 27 0.00059 22.7 5.7 28 93-120 26-53 (54)
66 PRK03975 tfx putative transcri 66.4 19 0.00042 28.6 5.8 48 26-80 4-51 (141)
67 PF13936 HTH_38: Helix-turn-he 65.6 11 0.00023 23.6 3.4 41 26-72 2-42 (44)
68 PF06005 DUF904: Protein of un 65.0 33 0.00071 24.1 6.1 42 81-122 21-62 (72)
69 PF10668 Phage_terminase: Phag 65.0 6.2 0.00013 27.0 2.3 20 52-71 24-43 (60)
70 PF04967 HTH_10: HTH DNA bindi 64.8 18 0.00039 24.0 4.5 40 29-69 1-42 (53)
71 PRK13922 rod shape-determining 64.6 18 0.00038 31.2 5.7 41 86-126 70-113 (276)
72 PRK09642 RNA polymerase sigma 64.4 19 0.00041 27.7 5.4 29 53-81 125-153 (160)
73 KOG4005 Transcription factor X 63.8 16 0.00034 31.9 5.1 42 81-122 107-148 (292)
74 PF07407 Seadorna_VP6: Seadorn 61.5 11 0.00024 34.3 3.9 29 95-123 35-63 (420)
75 PF00196 GerE: Bacterial regul 60.6 31 0.00067 22.3 5.1 45 28-79 3-47 (58)
76 cd00569 HTH_Hin_like Helix-tur 59.3 26 0.00056 18.6 4.6 38 28-71 5-42 (42)
77 KOG4403 Cell surface glycoprot 59.0 30 0.00065 32.7 6.3 69 66-134 227-331 (575)
78 smart00338 BRLZ basic region l 58.4 48 0.001 22.1 5.9 32 91-122 25-56 (65)
79 cd04766 HTH_HspR Helix-Turn-He 58.1 65 0.0014 22.9 7.0 71 53-124 4-90 (91)
80 PF09607 BrkDBD: Brinker DNA-b 57.3 31 0.00067 23.5 4.6 44 26-72 3-47 (58)
81 PF13518 HTH_28: Helix-turn-he 57.1 14 0.0003 23.0 2.9 22 52-73 14-35 (52)
82 TIGR00219 mreC rod shape-deter 57.1 28 0.00061 30.5 5.7 38 90-127 71-112 (283)
83 PRK06759 RNA polymerase factor 56.8 27 0.00058 26.5 5.0 46 28-79 106-151 (154)
84 TIGR02937 sigma70-ECF RNA poly 56.7 29 0.00063 25.3 5.0 45 29-79 111-155 (158)
85 PRK09652 RNA polymerase sigma 56.5 29 0.00062 26.8 5.2 47 28-80 128-174 (182)
86 PRK11924 RNA polymerase sigma 55.8 28 0.00061 26.8 5.0 29 52-80 143-171 (179)
87 PF15058 Speriolin_N: Sperioli 55.6 23 0.00051 29.7 4.6 41 85-126 5-45 (200)
88 PRK09644 RNA polymerase sigma 55.3 39 0.00085 26.1 5.8 29 52-80 126-154 (165)
89 PRK09646 RNA polymerase sigma 54.8 32 0.00069 27.6 5.3 29 52-80 160-188 (194)
90 PRK12526 RNA polymerase sigma 54.7 29 0.00063 28.3 5.1 29 52-80 171-199 (206)
91 cd04761 HTH_MerR-SF Helix-Turn 54.6 15 0.00034 22.4 2.7 22 53-74 3-24 (49)
92 PF13443 HTH_26: Cro/C1-type H 54.4 25 0.00055 22.8 3.9 29 52-80 12-40 (63)
93 PRK14127 cell division protein 54.4 40 0.00087 25.7 5.4 37 90-126 35-71 (109)
94 PRK10072 putative transcriptio 54.4 23 0.0005 26.2 4.0 42 28-77 32-73 (96)
95 PF04899 MbeD_MobD: MbeD/MobD 53.5 55 0.0012 23.0 5.6 37 88-124 24-60 (70)
96 TIGR03752 conj_TIGR03752 integ 53.2 40 0.00087 32.0 6.3 11 28-38 41-51 (472)
97 COG4026 Uncharacterized protei 53.0 42 0.00092 29.1 5.8 45 82-126 146-190 (290)
98 PF06156 DUF972: Protein of un 52.8 47 0.001 25.1 5.5 40 81-120 18-57 (107)
99 PRK12512 RNA polymerase sigma 52.6 37 0.0008 26.7 5.3 46 29-80 132-177 (184)
100 PRK00888 ftsB cell division pr 52.6 50 0.0011 24.7 5.7 34 72-105 28-61 (105)
101 PF04977 DivIC: Septum formati 52.3 43 0.00092 22.7 4.9 28 91-118 23-50 (80)
102 PRK12515 RNA polymerase sigma 52.0 44 0.00094 26.5 5.6 46 29-80 132-177 (189)
103 TIGR02989 Sig-70_gvs1 RNA poly 51.9 37 0.0008 25.8 5.1 28 52-79 129-156 (159)
104 TIGR02985 Sig70_bacteroi1 RNA 51.7 40 0.00087 25.3 5.2 28 52-79 131-158 (161)
105 smart00421 HTH_LUXR helix_turn 50.4 56 0.0012 19.8 5.4 40 28-74 3-42 (58)
106 PRK15422 septal ring assembly 50.3 89 0.0019 22.6 6.3 11 104-114 51-61 (79)
107 PRK12530 RNA polymerase sigma 50.0 56 0.0012 26.1 6.0 46 29-80 135-180 (189)
108 KOG1962 B-cell receptor-associ 49.8 61 0.0013 27.7 6.3 40 86-125 173-212 (216)
109 PRK12514 RNA polymerase sigma 49.6 45 0.00098 26.1 5.3 28 53-80 148-175 (179)
110 TIGR02959 SigZ RNA polymerase 49.6 44 0.00094 26.2 5.2 45 28-78 100-144 (170)
111 PRK09648 RNA polymerase sigma 49.6 44 0.00096 26.4 5.3 45 29-79 140-184 (189)
112 COG3413 Predicted DNA binding 48.7 40 0.00086 27.9 5.1 49 28-79 155-205 (215)
113 PF02796 HTH_7: Helix-turn-hel 48.7 37 0.0008 21.1 3.8 38 28-71 5-42 (45)
114 KOG4343 bZIP transcription fac 48.5 76 0.0016 30.8 7.3 33 88-120 305-337 (655)
115 PRK12519 RNA polymerase sigma 48.4 36 0.00077 27.1 4.6 29 52-80 159-187 (194)
116 PRK12541 RNA polymerase sigma 47.8 42 0.0009 25.8 4.8 29 52-80 130-158 (161)
117 PRK05602 RNA polymerase sigma 47.5 44 0.00096 26.4 5.0 29 52-80 146-174 (186)
118 PF07989 Microtub_assoc: Micro 47.5 97 0.0021 21.9 6.1 48 67-124 21-68 (75)
119 PRK13169 DNA replication intia 47.3 63 0.0014 24.6 5.5 40 81-120 18-57 (110)
120 PRK09047 RNA polymerase factor 47.1 56 0.0012 24.8 5.4 47 28-80 106-152 (161)
121 TIGR02948 SigW_bacill RNA poly 47.0 43 0.00092 26.2 4.8 47 28-80 136-182 (187)
122 TIGR02894 DNA_bind_RsfA transc 46.8 70 0.0015 26.1 6.0 31 87-117 106-136 (161)
123 PRK09639 RNA polymerase sigma 46.7 66 0.0014 24.6 5.8 45 29-80 113-157 (166)
124 PF14197 Cep57_CLD_2: Centroso 46.3 99 0.0021 21.5 6.9 40 84-123 25-64 (69)
125 PF05377 FlaC_arch: Flagella a 46.2 67 0.0015 21.6 4.8 29 93-121 8-36 (55)
126 TIGR02939 RpoE_Sigma70 RNA pol 45.7 41 0.0009 26.4 4.6 29 52-80 156-184 (190)
127 PRK04217 hypothetical protein; 45.5 66 0.0014 24.4 5.4 48 26-79 40-87 (110)
128 TIGR02999 Sig-70_X6 RNA polyme 45.2 58 0.0013 25.4 5.3 29 52-80 152-180 (183)
129 PRK10884 SH3 domain-containing 45.2 1.1E+02 0.0024 25.7 7.2 34 88-121 135-168 (206)
130 PF08172 CASP_C: CASP C termin 43.8 97 0.0021 26.8 6.8 46 75-120 90-135 (248)
131 PF13411 MerR_1: MerR HTH fami 43.2 25 0.00055 23.2 2.5 20 54-73 4-23 (69)
132 PF13384 HTH_23: Homeodomain-l 43.2 26 0.00056 21.8 2.4 21 52-72 19-39 (50)
133 KOG3650 Predicted coiled-coil 43.0 84 0.0018 23.8 5.4 37 88-124 66-102 (120)
134 KOG4286 Dystrophin-like protei 42.8 90 0.002 31.6 7.0 57 86-142 842-898 (966)
135 PF12824 MRP-L20: Mitochondria 42.6 1.4E+02 0.003 24.3 7.1 46 25-73 82-127 (164)
136 PRK12546 RNA polymerase sigma 42.4 58 0.0012 26.2 5.0 29 52-80 131-159 (188)
137 PF04297 UPF0122: Putative hel 42.2 1.5E+02 0.0032 22.3 8.0 40 28-73 17-56 (101)
138 PF00424 REV: REV protein (ant 42.2 40 0.00088 25.0 3.6 37 34-85 14-50 (91)
139 PF07407 Seadorna_VP6: Seadorn 42.0 47 0.001 30.4 4.7 30 87-116 34-63 (420)
140 PRK12537 RNA polymerase sigma 41.7 67 0.0015 25.3 5.2 28 52-79 151-178 (182)
141 PRK09637 RNA polymerase sigma 41.5 63 0.0014 25.7 5.1 23 53-75 125-147 (181)
142 PF11932 DUF3450: Protein of u 41.0 1.3E+02 0.0028 25.5 7.2 8 176-183 205-212 (251)
143 cd04765 HTH_MlrA-like_sg2 Heli 40.5 88 0.0019 22.9 5.3 20 54-73 4-23 (99)
144 PRK12543 RNA polymerase sigma 40.2 1.2E+02 0.0027 23.7 6.5 29 52-80 135-163 (179)
145 PRK12538 RNA polymerase sigma 40.2 81 0.0018 26.5 5.7 29 52-80 189-217 (233)
146 KOG4343 bZIP transcription fac 40.2 71 0.0015 31.0 5.7 37 88-124 298-334 (655)
147 PF06056 Terminase_5: Putative 40.2 30 0.00066 23.1 2.5 27 52-80 15-41 (58)
148 PRK12547 RNA polymerase sigma 40.0 78 0.0017 24.5 5.3 28 52-79 130-157 (164)
149 PRK07037 extracytoplasmic-func 40.0 83 0.0018 24.0 5.4 27 53-79 128-154 (163)
150 PRK12524 RNA polymerase sigma 39.8 71 0.0015 25.6 5.2 28 53-80 155-182 (196)
151 PRK06930 positive control sigm 39.8 92 0.002 25.2 5.8 47 28-80 114-160 (170)
152 TIGR02952 Sig70_famx2 RNA poly 39.8 79 0.0017 24.2 5.3 28 52-79 140-167 (170)
153 cd04764 HTH_MlrA-like_sg1 Heli 39.6 36 0.00077 22.6 2.8 21 53-73 3-23 (67)
154 TIGR02983 SigE-fam_strep RNA p 39.5 76 0.0017 24.2 5.1 28 53-80 129-156 (162)
155 cd04762 HTH_MerR-trunc Helix-T 39.5 39 0.00083 20.1 2.8 24 53-76 3-26 (49)
156 TIGR02954 Sig70_famx3 RNA poly 38.7 76 0.0017 24.5 5.0 29 52-80 137-165 (169)
157 COG4026 Uncharacterized protei 38.5 1.3E+02 0.0028 26.2 6.5 7 91-97 162-168 (290)
158 PF13551 HTH_29: Winged helix- 38.2 1.4E+02 0.0031 21.0 6.5 48 24-72 53-109 (112)
159 TIGR00721 tfx DNA-binding prot 38.0 2E+02 0.0043 22.7 7.2 48 26-80 4-51 (137)
160 COG3074 Uncharacterized protei 37.9 1.5E+02 0.0032 21.1 6.0 20 89-108 43-62 (79)
161 PF08280 HTH_Mga: M protein tr 37.9 75 0.0016 20.9 4.2 35 32-71 6-40 (59)
162 KOG3119 Basic region leucine z 37.6 1E+02 0.0022 26.9 6.0 31 95-125 218-248 (269)
163 TIGR03879 near_KaiC_dom probab 37.6 22 0.00049 25.2 1.6 23 51-73 33-55 (73)
164 cd04763 HTH_MlrA-like Helix-Tu 37.6 38 0.00083 22.5 2.8 21 53-73 3-23 (68)
165 PRK06811 RNA polymerase factor 37.4 77 0.0017 25.2 5.0 28 53-80 150-177 (189)
166 PRK12536 RNA polymerase sigma 36.8 94 0.002 24.4 5.3 29 52-80 147-175 (181)
167 PRK12532 RNA polymerase sigma 36.7 1.1E+02 0.0023 24.4 5.7 29 52-80 154-182 (195)
168 PF08961 DUF1875: Domain of un 36.7 12 0.00025 32.3 0.0 33 86-118 130-162 (243)
169 COG2919 Septum formation initi 36.6 1.8E+02 0.0039 22.0 6.6 25 96-120 61-85 (117)
170 PRK10884 SH3 domain-containing 36.6 1.4E+02 0.003 25.1 6.5 41 85-125 125-165 (206)
171 PF00376 MerR: MerR family reg 36.1 42 0.0009 20.4 2.5 18 54-71 3-20 (38)
172 COG4367 Uncharacterized protei 35.5 70 0.0015 23.8 3.9 39 29-68 3-41 (97)
173 KOG4571 Activating transcripti 35.5 1.5E+02 0.0032 26.6 6.6 31 83-113 253-283 (294)
174 PF04880 NUDE_C: NUDE protein, 35.4 52 0.0011 26.9 3.6 19 102-120 27-45 (166)
175 PRK13919 putative RNA polymera 35.0 1E+02 0.0022 24.1 5.3 27 53-79 154-180 (186)
176 TIGR02943 Sig70_famx1 RNA poly 34.8 1.4E+02 0.0029 23.9 6.0 47 28-80 131-177 (188)
177 PRK14127 cell division protein 34.8 1E+02 0.0022 23.5 4.9 38 90-127 28-65 (109)
178 TIGR02209 ftsL_broad cell divi 34.7 1.1E+02 0.0024 21.2 4.9 14 105-118 44-57 (85)
179 PF15058 Speriolin_N: Sperioli 34.7 55 0.0012 27.6 3.7 29 92-120 5-33 (200)
180 PRK09649 RNA polymerase sigma 34.6 93 0.002 24.7 5.0 27 53-79 149-175 (185)
181 TIGR03752 conj_TIGR03752 integ 34.6 1.7E+02 0.0037 27.9 7.3 17 106-122 116-132 (472)
182 PRK09645 RNA polymerase sigma 34.5 87 0.0019 24.2 4.7 28 53-80 137-164 (173)
183 PF12325 TMF_TATA_bd: TATA ele 34.0 2E+02 0.0044 22.1 6.6 45 80-124 70-114 (120)
184 PF09304 Cortex-I_coil: Cortex 33.9 1.8E+02 0.0038 22.2 6.0 29 90-118 21-49 (107)
185 PRK06986 fliA flagellar biosyn 33.9 92 0.002 25.8 5.1 46 29-80 185-230 (236)
186 PRK12542 RNA polymerase sigma 33.9 1.3E+02 0.0029 23.6 5.8 29 52-80 140-168 (185)
187 PRK09651 RNA polymerase sigma 33.8 99 0.0021 24.1 5.0 28 52-79 137-164 (172)
188 PRK12544 RNA polymerase sigma 33.7 1.4E+02 0.0031 24.3 6.1 47 28-80 148-194 (206)
189 PRK12545 RNA polymerase sigma 33.7 1.2E+02 0.0026 24.5 5.6 29 52-80 157-185 (201)
190 PRK11923 algU RNA polymerase s 33.6 91 0.002 24.6 4.8 28 53-80 157-184 (193)
191 PRK12539 RNA polymerase sigma 33.4 1.1E+02 0.0024 24.1 5.2 29 52-80 149-177 (184)
192 PRK12529 RNA polymerase sigma 33.0 1.2E+02 0.0026 23.9 5.4 46 28-79 127-172 (178)
193 cd01104 HTH_MlrA-CarA Helix-Tu 33.0 52 0.0011 21.6 2.8 20 53-72 3-22 (68)
194 TIGR02980 SigBFG RNA polymeras 33.0 1.1E+02 0.0024 25.1 5.3 46 28-79 178-223 (227)
195 PF01166 TSC22: TSC-22/dip/bun 32.9 66 0.0014 21.9 3.2 34 91-124 13-46 (59)
196 PRK12531 RNA polymerase sigma 32.9 1.2E+02 0.0026 24.2 5.4 29 52-80 159-187 (194)
197 COG2944 Predicted transcriptio 32.6 93 0.002 23.6 4.3 42 27-76 42-83 (104)
198 PRK08583 RNA polymerase sigma 32.4 1E+02 0.0022 25.9 5.2 46 28-79 205-250 (257)
199 PF00038 Filament: Intermediat 32.4 3E+02 0.0065 23.7 8.2 57 64-120 186-251 (312)
200 TIGR02449 conserved hypothetic 32.3 1.7E+02 0.0037 20.2 6.2 33 89-121 11-43 (65)
201 TIGR02957 SigX4 RNA polymerase 32.2 1.8E+02 0.0039 24.9 6.7 29 53-81 127-155 (281)
202 cd01106 HTH_TipAL-Mta Helix-Tu 32.1 2E+02 0.0043 20.8 8.9 36 25-74 35-70 (103)
203 PRK09641 RNA polymerase sigma 32.0 1.1E+02 0.0024 23.8 5.0 29 52-80 154-182 (187)
204 KOG3156 Uncharacterized membra 31.6 1.6E+02 0.0035 25.2 6.1 42 83-124 99-141 (220)
205 PF04568 IATP: Mitochondrial A 31.6 2.2E+02 0.0048 21.3 6.6 44 79-122 56-99 (100)
206 cd06170 LuxR_C_like C-terminal 31.6 1.2E+02 0.0027 18.3 5.0 36 30-72 2-37 (57)
207 PF07334 IFP_35_N: Interferon- 31.5 63 0.0014 23.2 3.1 22 104-125 5-26 (76)
208 smart00027 EH Eps15 homology d 31.4 1.7E+02 0.0037 20.7 5.5 45 28-72 3-51 (96)
209 PRK12520 RNA polymerase sigma 31.4 1.5E+02 0.0032 23.4 5.8 46 29-80 132-177 (191)
210 TIGR02479 FliA_WhiG RNA polyme 31.2 1.2E+02 0.0025 24.9 5.2 46 28-79 175-220 (224)
211 PRK12516 RNA polymerase sigma 31.2 1.3E+02 0.0027 24.1 5.3 28 53-80 135-162 (187)
212 PF04728 LPP: Lipoprotein leuc 31.2 1.7E+02 0.0036 19.7 6.6 46 79-124 4-49 (56)
213 PRK12523 RNA polymerase sigma 31.1 1.4E+02 0.003 23.2 5.5 28 52-79 137-164 (172)
214 KOG4196 bZIP transcription fac 31.1 2E+02 0.0043 22.8 6.0 52 72-123 66-119 (135)
215 PF04899 MbeD_MobD: MbeD/MobD 30.9 1.9E+02 0.0041 20.3 6.1 42 83-124 26-67 (70)
216 PF03670 UPF0184: Uncharacteri 30.9 1.4E+02 0.0031 21.7 4.9 34 85-118 26-59 (83)
217 PRK00409 recombination and DNA 30.8 2.8E+02 0.006 28.0 8.5 21 48-68 485-505 (782)
218 PRK13729 conjugal transfer pil 30.2 1.8E+02 0.0038 27.8 6.7 43 81-123 79-121 (475)
219 PRK08295 RNA polymerase factor 30.1 1.6E+02 0.0035 23.4 5.8 29 52-80 172-200 (208)
220 PF01381 HTH_3: Helix-turn-hel 30.0 46 0.001 20.8 2.1 23 53-75 12-34 (55)
221 PRK09636 RNA polymerase sigma 30.0 2E+02 0.0044 24.6 6.7 29 53-81 134-162 (293)
222 PTZ00454 26S protease regulato 29.8 1.6E+02 0.0034 27.1 6.2 33 92-124 29-61 (398)
223 TIGR01069 mutS2 MutS2 family p 29.7 3.1E+02 0.0067 27.6 8.7 21 48-68 480-500 (771)
224 TIGR02894 DNA_bind_RsfA transc 29.6 2.4E+02 0.0053 23.0 6.5 44 82-125 108-151 (161)
225 cd00093 HTH_XRE Helix-turn-hel 29.6 53 0.0011 19.2 2.2 23 53-75 15-37 (58)
226 PRK09647 RNA polymerase sigma 29.5 1.4E+02 0.003 24.3 5.4 27 53-79 157-183 (203)
227 PRK12533 RNA polymerase sigma 29.5 1.2E+02 0.0026 25.1 5.0 28 52-79 152-179 (216)
228 PRK12511 RNA polymerase sigma 29.4 1.3E+02 0.0028 24.0 5.1 27 53-79 130-156 (182)
229 COG2963 Transposase and inacti 29.4 1.5E+02 0.0032 21.8 5.0 42 26-72 5-47 (116)
230 KOG1146 Homeobox protein [Gene 29.3 92 0.002 33.3 5.0 59 23-82 706-764 (1406)
231 cd01392 HTH_LacI Helix-turn-he 29.1 40 0.00086 20.9 1.6 21 55-75 2-22 (52)
232 PF04999 FtsL: Cell division p 28.9 1.3E+02 0.0027 21.6 4.5 26 94-119 44-69 (97)
233 PF10226 DUF2216: Uncharacteri 28.8 2.8E+02 0.0061 23.3 6.9 24 99-122 55-78 (195)
234 PF06971 Put_DNA-bind_N: Putat 28.6 49 0.0011 21.6 2.0 17 53-69 31-47 (50)
235 PRK13922 rod shape-determining 28.4 1.4E+02 0.003 25.6 5.3 35 82-116 73-110 (276)
236 KOG2391 Vacuolar sorting prote 28.4 2.4E+02 0.0051 25.9 6.8 13 105-117 252-264 (365)
237 PRK12513 RNA polymerase sigma 28.3 77 0.0017 25.1 3.6 29 52-80 157-185 (194)
238 PF07638 Sigma70_ECF: ECF sigm 28.3 1.5E+02 0.0032 23.8 5.2 28 52-79 153-180 (185)
239 PRK05657 RNA polymerase sigma 28.2 1.4E+02 0.003 26.6 5.4 51 28-80 262-312 (325)
240 TIGR02947 SigH_actino RNA poly 28.2 70 0.0015 25.4 3.3 29 52-80 149-177 (193)
241 PRK11546 zraP zinc resistance 28.1 3E+02 0.0066 21.9 6.8 17 102-118 92-108 (143)
242 COG3074 Uncharacterized protei 28.0 2.2E+02 0.0049 20.2 5.5 22 94-115 41-62 (79)
243 PRK12522 RNA polymerase sigma 27.9 1.4E+02 0.0031 23.1 5.0 28 52-79 137-164 (173)
244 PRK07408 RNA polymerase sigma 27.7 1.2E+02 0.0026 25.7 4.8 46 29-80 204-249 (256)
245 PRK07670 RNA polymerase sigma 27.5 1.5E+02 0.0032 24.9 5.3 46 29-80 202-247 (251)
246 TIGR03001 Sig-70_gmx1 RNA poly 27.4 1.9E+02 0.004 24.5 5.9 31 52-82 179-209 (244)
247 PF07334 IFP_35_N: Interferon- 27.4 1.2E+02 0.0027 21.7 4.0 30 95-124 3-32 (76)
248 TIGR02941 Sigma_B RNA polymera 27.4 1.4E+02 0.003 25.1 5.1 47 28-80 205-251 (255)
249 PRK12528 RNA polymerase sigma 27.2 1.6E+02 0.0035 22.5 5.1 40 29-74 114-153 (161)
250 PF14645 Chibby: Chibby family 26.9 1.8E+02 0.004 22.2 5.2 27 97-123 76-102 (116)
251 TIGR02960 SigX5 RNA polymerase 26.8 2.7E+02 0.0058 23.9 7.0 29 53-81 161-189 (324)
252 PRK12518 RNA polymerase sigma 26.8 94 0.002 24.0 3.7 29 52-80 138-166 (175)
253 PF05700 BCAS2: Breast carcino 26.7 2.9E+02 0.0062 23.1 6.9 41 86-126 176-216 (221)
254 PRK15422 septal ring assembly 26.5 2.5E+02 0.0054 20.3 6.1 36 87-122 20-62 (79)
255 PRK12535 RNA polymerase sigma 26.4 1.6E+02 0.0034 23.8 5.1 27 53-79 152-178 (196)
256 PRK09415 RNA polymerase factor 26.4 1.4E+02 0.003 23.5 4.7 28 52-79 145-172 (179)
257 PF15035 Rootletin: Ciliary ro 26.3 2.8E+02 0.0061 22.8 6.6 40 84-123 80-119 (182)
258 TIGR02859 spore_sigH RNA polym 26.2 1.9E+02 0.0041 22.7 5.5 28 52-79 167-194 (198)
259 KOG0773 Transcription factor M 26.1 90 0.0019 27.6 3.9 35 46-80 120-154 (342)
260 PRK12517 RNA polymerase sigma 25.7 2.4E+02 0.0052 22.4 6.0 29 52-80 146-174 (188)
261 KOG0977 Nuclear envelope prote 25.5 4.7E+02 0.01 25.5 8.7 39 88-126 151-189 (546)
262 PF11418 Scaffolding_pro: Phi2 25.2 2.9E+02 0.0062 20.4 5.7 44 82-125 30-73 (97)
263 PRK12540 RNA polymerase sigma 25.0 1.8E+02 0.004 23.0 5.2 23 53-75 130-152 (182)
264 TIGR02950 SigM_subfam RNA poly 25.0 1.1E+02 0.0024 23.0 3.7 30 50-79 121-150 (154)
265 COG1905 NuoE NADH:ubiquinone o 24.9 1.4E+02 0.003 24.3 4.4 37 30-67 24-60 (160)
266 PRK06288 RNA polymerase sigma 24.9 2.3E+02 0.0049 24.1 6.0 47 28-80 212-258 (268)
267 PRK08301 sporulation sigma fac 24.7 1.9E+02 0.0042 23.7 5.5 50 29-80 179-228 (234)
268 smart00422 HTH_MERR helix_turn 24.5 77 0.0017 20.7 2.5 20 53-72 3-22 (70)
269 PRK12525 RNA polymerase sigma 24.5 1.9E+02 0.0042 22.3 5.1 44 29-78 119-162 (168)
270 TIGR03830 CxxCG_CxxCG_HTH puta 24.2 1.3E+02 0.0029 22.1 4.0 41 27-75 63-103 (127)
271 PF07219 HemY_N: HemY protein 24.1 1.5E+02 0.0032 21.8 4.2 31 62-92 42-72 (108)
272 TIGR03070 couple_hipB transcri 24.0 68 0.0015 19.8 2.0 23 53-75 18-40 (58)
273 PF04977 DivIC: Septum formati 23.8 1.6E+02 0.0035 19.7 4.1 30 82-111 21-50 (80)
274 KOG0249 LAR-interacting protei 23.5 4.1E+02 0.0089 27.1 7.9 47 76-122 214-260 (916)
275 TIGR01764 excise DNA binding d 23.4 89 0.0019 18.5 2.4 23 53-75 4-26 (49)
276 PF14662 CCDC155: Coiled-coil 23.4 2.3E+02 0.0049 23.8 5.5 31 90-120 20-50 (193)
277 TIGR02984 Sig-70_plancto1 RNA 23.2 2.1E+02 0.0046 22.1 5.2 45 29-79 141-185 (189)
278 PRK12534 RNA polymerase sigma 23.0 2.2E+02 0.0048 22.3 5.3 25 53-77 156-180 (187)
279 PF11559 ADIP: Afadin- and alp 22.9 3.6E+02 0.0078 20.8 7.2 26 94-119 96-121 (151)
280 PRK09643 RNA polymerase sigma 22.8 2.2E+02 0.0048 22.6 5.3 19 53-71 153-171 (192)
281 PF10482 CtIP_N: Tumour-suppre 22.8 2.2E+02 0.0048 22.0 4.9 20 96-115 100-119 (120)
282 COG1792 MreC Cell shape-determ 22.6 2.3E+02 0.005 24.8 5.7 25 104-128 88-112 (284)
283 PRK11511 DNA-binding transcrip 22.6 1.7E+02 0.0036 22.1 4.3 24 50-73 25-48 (127)
284 PF08826 DMPK_coil: DMPK coile 22.5 2.6E+02 0.0056 19.0 6.5 41 83-123 16-56 (61)
285 PRK05988 formate dehydrogenase 22.4 1.8E+02 0.0039 23.2 4.6 36 32-68 24-59 (156)
286 TIGR02885 spore_sigF RNA polym 22.4 2.1E+02 0.0045 23.5 5.2 39 28-72 183-221 (231)
287 PRK08241 RNA polymerase factor 22.3 2.7E+02 0.0059 24.2 6.2 29 52-80 171-199 (339)
288 KOG0150 Spliceosomal protein F 22.0 4.6E+02 0.0099 23.8 7.4 53 67-119 16-69 (336)
289 PRK14872 rod shape-determining 22.0 1.4E+02 0.0031 27.1 4.3 37 87-123 59-98 (337)
290 PF03980 Nnf1: Nnf1 ; InterPr 22.0 1.9E+02 0.0042 21.1 4.5 29 91-119 79-107 (109)
291 PF11932 DUF3450: Protein of u 22.0 3.1E+02 0.0068 23.2 6.3 30 88-117 52-81 (251)
292 PRK10651 transcriptional regul 21.8 2.1E+02 0.0045 21.8 4.8 46 28-80 155-200 (216)
293 PRK05803 sporulation sigma fac 21.6 2.7E+02 0.0059 22.9 5.8 43 28-72 175-217 (233)
294 PRK12527 RNA polymerase sigma 21.5 2.6E+02 0.0055 21.2 5.3 24 53-76 124-147 (159)
295 PF14662 CCDC155: Coiled-coil 21.5 4.3E+02 0.0093 22.2 6.7 29 96-124 85-113 (193)
296 PRK10403 transcriptional regul 21.5 2.1E+02 0.0046 21.7 4.8 46 28-80 153-198 (215)
297 PF01257 2Fe-2S_thioredx: Thio 21.4 1.8E+02 0.0038 22.7 4.3 34 34-68 16-49 (145)
298 TIGR02393 RpoD_Cterm RNA polym 21.2 3.7E+02 0.008 22.3 6.5 51 28-80 176-226 (238)
299 KOG3335 Predicted coiled-coil 21.1 3.1E+02 0.0066 22.8 5.7 55 66-127 87-141 (181)
300 cd04774 HTH_YfmP Helix-Turn-He 20.9 1.1E+02 0.0023 22.3 2.8 22 53-74 3-24 (96)
301 PF08671 SinI: Anti-repressor 20.9 1.4E+02 0.0031 17.4 2.8 20 53-72 8-27 (30)
302 cd04781 HTH_MerR-like_sg6 Heli 20.8 3.6E+02 0.0078 20.0 9.4 36 25-74 34-69 (120)
303 PF06210 DUF1003: Protein of u 20.8 3.7E+02 0.0079 20.3 5.8 17 72-88 57-73 (108)
304 PRK07122 RNA polymerase sigma 20.7 2.1E+02 0.0046 24.4 5.0 47 28-80 215-261 (264)
305 KOG0977 Nuclear envelope prote 20.7 2.3E+02 0.0051 27.5 5.7 43 82-124 152-194 (546)
306 cd01105 HTH_GlnR-like Helix-Tu 20.6 96 0.0021 22.0 2.5 20 53-72 4-23 (88)
307 PF10205 KLRAQ: Predicted coil 20.5 3.8E+02 0.0083 20.2 6.7 40 86-125 34-73 (102)
308 PF15397 DUF4618: Domain of un 20.5 3E+02 0.0066 24.1 5.9 40 88-127 189-228 (258)
309 PRK14872 rod shape-determining 20.3 1.1E+02 0.0024 27.8 3.3 26 92-117 57-82 (337)
310 PHA00489 scaffolding protein 20.2 2.5E+02 0.0053 20.9 4.5 42 82-123 31-72 (101)
311 PHA01976 helix-turn-helix prot 20.2 94 0.002 20.2 2.2 23 53-75 18-40 (67)
312 smart00595 MADF subfamily of S 20.1 2.8E+02 0.0061 19.0 4.8 32 54-85 31-62 (89)
313 PRK07539 NADH dehydrogenase su 20.0 2.1E+02 0.0046 22.5 4.6 35 33-68 24-58 (154)
314 TIGR01958 nuoE_fam NADH-quinon 20.0 2.2E+02 0.0047 22.3 4.6 34 33-67 18-51 (148)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.88 E-value=1.3e-22 Score=168.60 Aligned_cols=111 Identities=48% Similarity=0.753 Sum_probs=100.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhHHHHHHHHHhhHHHhhhhH
Q 029338 23 MKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDYAQLRANYDSLASGFE 102 (195)
Q Consensus 23 rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~~e~~~l~~~~~~L~~~~~ 102 (195)
..++.+|+.+|+..||..|+.. .++.+.++..||.+|||.+|||+|||||||||||.++.+.++..|+.+|+.|..++.
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~-~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~~ 129 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESE-KKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEND 129 (198)
T ss_pred ccccccccHHHHHHhHHhhccc-cccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhh
Confidence 3446789999999999999999 999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHHhcccccccCCccc
Q 029338 103 SLIKEKESLLLELQMLNEQLGKSDYEINGVGK 134 (195)
Q Consensus 103 ~l~~e~~~L~~e~~~l~~~l~~~~~~~~~~c~ 134 (195)
.|..++..|..++..+...++.......+.|.
T Consensus 130 ~Lq~e~~eL~~~~~~~~~~~~~~~~~~~~~~~ 161 (198)
T KOG0483|consen 130 RLQSEVQELVAELSSLKREMQKSPENTLTMCP 161 (198)
T ss_pred HHHHHHHHHHHHHhhhhhhhccCcccccccCc
Confidence 99999999999999998888885444445554
No 2
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=6.6e-18 Score=149.12 Aligned_cols=68 Identities=37% Similarity=0.659 Sum_probs=62.5
Q ss_pred hhccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhH
Q 029338 16 KRKKKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIE 84 (195)
Q Consensus 16 ~~~~kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~ 84 (195)
....||+|+.|+.||..|+..||+.|+.. +|++..+|++||..|||+..||++||||||+||||...+
T Consensus 166 ~~~pkK~RksRTaFT~~Ql~~LEkrF~~Q-KYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 166 RSTPKKRRKSRTAFSDHQLFELEKRFEKQ-KYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cCCCcccccchhhhhHHHHHHHHHHHHHh-hcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 34457788999999999999999999999 999999999999999999999999999999999985444
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.70 E-value=1.1e-17 Score=144.50 Aligned_cols=60 Identities=32% Similarity=0.632 Sum_probs=57.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHH
Q 029338 21 SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (195)
Q Consensus 21 k~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krk 81 (195)
+.||.|+.||..|+..||+.|..+ +|++..+|++||..|.|+++||+|||||||+||||.
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 467889999999999999999999 999999999999999999999999999999999984
No 4
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.68 E-value=1.3e-17 Score=146.42 Aligned_cols=71 Identities=35% Similarity=0.534 Sum_probs=64.5
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhHHHHHHH
Q 029338 19 KKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDYAQL 90 (195)
Q Consensus 19 ~kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~~e~~~l 90 (195)
+.++||.|..|+..|+..||+.|... +|++..+|+.||..|.||+.||||||||||-|.||++++..+..+
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQ-RYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQ-RYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhh-hccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 44567778899999999999999999 999999999999999999999999999999999998887766544
No 5
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.67 E-value=5.6e-17 Score=136.45 Aligned_cols=64 Identities=33% Similarity=0.529 Sum_probs=60.6
Q ss_pred hccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHH
Q 029338 17 RKKKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (195)
Q Consensus 17 ~~~kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krk 81 (195)
.+.||.||.||.|+.-|+..|.+.|+.+ .|+.-.+|.+||..|||+..||+|||||||.|.||.
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQkT-QYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQT-QYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhhc-chhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 4567788999999999999999999999 999999999999999999999999999999999983
No 6
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.67 E-value=7.2e-17 Score=131.50 Aligned_cols=64 Identities=33% Similarity=0.504 Sum_probs=60.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhHH
Q 029338 21 SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEH 85 (195)
Q Consensus 21 k~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~~ 85 (195)
+.+|.||.||++|+..||..|+.+ .|....+|..||..|+|++.||+|||||||+|.||++.+.
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 9999999999999999999999999999999999976654
No 7
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.66 E-value=1.5e-16 Score=133.07 Aligned_cols=60 Identities=40% Similarity=0.643 Sum_probs=57.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHH
Q 029338 21 SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (195)
Q Consensus 21 k~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krk 81 (195)
++||.|++|+..|+..||..|+.. +|++..+|..||.+|.|++.||+|||||||.||||+
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~k-rYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELK-RYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHH-hhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 567889999999999999999999 999999999999999999999999999999999984
No 8
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.66 E-value=3.3e-16 Score=104.82 Aligned_cols=57 Identities=37% Similarity=0.666 Sum_probs=54.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 23 MKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 23 rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
+++|+.||.+|+.+|+..|..+ +||+..++..||..|||+..+|.+||+|||++.|+
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 9
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.65 E-value=5.9e-17 Score=142.26 Aligned_cols=65 Identities=29% Similarity=0.451 Sum_probs=59.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhHH
Q 029338 20 KSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEH 85 (195)
Q Consensus 20 kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~~ 85 (195)
+..||+|.-+|..|+..||+.|..| .|++.+.|.+|++.|+|++|||+|||||||+|.||...+.
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN-~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFN-MYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHH-HHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 4456778899999999999999999 9999999999999999999999999999999999966433
No 10
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.63 E-value=3.1e-16 Score=134.17 Aligned_cols=85 Identities=25% Similarity=0.469 Sum_probs=74.0
Q ss_pred CCchhhhccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhHHHHHHH
Q 029338 11 ASPEAKRKKKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDYAQL 90 (195)
Q Consensus 11 ~sp~~~~~~kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~~e~~~l 90 (195)
.++...++++++|+.||.||..|+..||+.|+.. +||+...|+.||..+.|.+..|+|||||||+||||+.........
T Consensus 130 ~s~~~~kkk~kRRh~RTiFT~~Qle~LEkaFkea-HYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~ 208 (332)
T KOG0494|consen 130 GSPDNAKKKKKRRHFRTIFTSYQLEELEKAFKEA-HYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTI 208 (332)
T ss_pred CCCcccccccccccccchhhHHHHHHHHHHHhhc-cCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchh
Confidence 3444445555555669999999999999999999 999999999999999999999999999999999999988888888
Q ss_pred HHhhHH
Q 029338 91 RANYDS 96 (195)
Q Consensus 91 ~~~~~~ 96 (195)
.++|--
T Consensus 209 maeygl 214 (332)
T KOG0494|consen 209 MAEYGL 214 (332)
T ss_pred hhhhcc
Confidence 777754
No 11
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.62 E-value=5.5e-16 Score=128.92 Aligned_cols=66 Identities=35% Similarity=0.515 Sum_probs=61.1
Q ss_pred hccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHh
Q 029338 17 RKKKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQI 83 (195)
Q Consensus 17 ~~~kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~ 83 (195)
++.|..|++|+.||..|+..||+.|... .|+++.++.+++..|.||+.||+|||||||+|.||-|.
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfrek-qYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFREK-QYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhHh-hhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 4556678899999999999999999999 99999999999999999999999999999999998543
No 12
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.62 E-value=5.5e-16 Score=116.47 Aligned_cols=62 Identities=24% Similarity=0.556 Sum_probs=58.2
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHH
Q 029338 19 KKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (195)
Q Consensus 19 ~kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krk 81 (195)
++|.+|-|+.||..|+..||+.|... +||++-.+++||..+.|++..|+|||||||+|.+++
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ET-HYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAET-HYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhh-cCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 44567889999999999999999999 999999999999999999999999999999999984
No 13
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.60 E-value=1.3e-15 Score=130.55 Aligned_cols=78 Identities=35% Similarity=0.629 Sum_probs=66.4
Q ss_pred CCCCCCCCCchhhhccCCC------CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHH
Q 029338 4 RRKDDSAASPEAKRKKKSK------MKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRAR 77 (195)
Q Consensus 4 ~~~~~s~~sp~~~~~~kk~------rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak 77 (195)
+++|+....|..++.+|++ +|+|+.||.+|+..|...|..+ +|++...|++||.+|||.+.||+|||||+|+|
T Consensus 222 RYSDRPSsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~en-RYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAK 300 (342)
T KOG0493|consen 222 RYSDRPSSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQEN-RYLTEQRRQELAQELGLNESQIKIWFQNKRAK 300 (342)
T ss_pred cccCCCCCCcccccccccCCccchhcCccccccHHHHHHHHHHHhhh-hhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhh
Confidence 4455555555555444444 6889999999999999999999 99999999999999999999999999999999
Q ss_pred HHHHH
Q 029338 78 WKSKQ 82 (195)
Q Consensus 78 ~Krkq 82 (195)
.||-.
T Consensus 301 iKKsT 305 (342)
T KOG0493|consen 301 IKKST 305 (342)
T ss_pred hhhcc
Confidence 99843
No 14
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.53 E-value=2.3e-14 Score=95.00 Aligned_cols=55 Identities=38% Similarity=0.760 Sum_probs=51.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 24 KNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 24 r~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
+.|+.|+.+|+.+|+..|..+ +||+..++..||..+||+..||++||+|||++.+
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 15
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.53 E-value=3.9e-15 Score=127.81 Aligned_cols=57 Identities=39% Similarity=0.602 Sum_probs=54.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHH
Q 029338 24 KNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (195)
Q Consensus 24 r~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krk 81 (195)
|-|.++|..|...||+.|... +|.++.++.+||.-|||++|||+|||||||+|+||.
T Consensus 201 KYRvVYTDhQRLELEKEfh~S-ryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~ 257 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTS-RYITIRRKSELAATLGLSERQVKIWFQNRRAKERKD 257 (317)
T ss_pred ceeEEecchhhhhhhhhhccc-cceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHH
Confidence 446789999999999999999 999999999999999999999999999999999984
No 16
>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=99.53 E-value=3.8e-14 Score=94.55 Aligned_cols=57 Identities=42% Similarity=0.701 Sum_probs=53.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHH
Q 029338 24 KNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (195)
Q Consensus 24 r~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krk 81 (195)
+.+..|+..++.+|+..|..+ +||+..++..||..+||+..||++||+|||++.++.
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 457789999999999999999 999999999999999999999999999999998863
No 17
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.50 E-value=3.1e-14 Score=123.55 Aligned_cols=93 Identities=26% Similarity=0.375 Sum_probs=83.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhHHHHHHHHHhhHHHhhh
Q 029338 21 SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDYAQLRANYDSLASG 100 (195)
Q Consensus 21 k~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~~e~~~l~~~~~~L~~~ 100 (195)
..+|+|+.+|+.|+..|...|... ++|....|++|+.++||..|.|+|||||||||.||-++..+...+.+.|..++..
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 347889999999999999999999 9999999999999999999999999999999999999999999999999999887
Q ss_pred hHhHHHHHHHHHHHH
Q 029338 101 FESLIKEKESLLLEL 115 (195)
Q Consensus 101 ~~~l~~e~~~L~~e~ 115 (195)
.+.+.|+.+=..|+
T Consensus 245 -gs~r~ekdsd~sel 258 (383)
T KOG4577|consen 245 -GSSRAEKDSDDSEL 258 (383)
T ss_pred -CCcccccccccCcc
Confidence 66666666533333
No 18
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.50 E-value=1.8e-14 Score=120.72 Aligned_cols=68 Identities=22% Similarity=0.499 Sum_probs=62.4
Q ss_pred hccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhHH
Q 029338 17 RKKKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEH 85 (195)
Q Consensus 17 ~~~kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~~ 85 (195)
...+|.+|.||.|+-.|+.+||..|.+. .||+...+++||.+|+|.+-+|+|||.|||+|+|+.+...
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kT-qYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKT-QYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhh-cCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 3455678999999999999999999999 9999999999999999999999999999999999865544
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=99.44 E-value=1e-13 Score=94.47 Aligned_cols=52 Identities=15% Similarity=0.362 Sum_probs=49.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCC----CCHHHHHHHHHHhCCChhHHHHHHHhhH
Q 029338 23 MKNKRRFSDEQIRLLESIFESESTK----LEPRKKMQVATELGLQPRQVAIWFQNKR 75 (195)
Q Consensus 23 rr~R~~ft~eQ~~~Le~~F~~~~~~----ps~~~r~~LA~~LgLt~rQVkvWFQNRR 75 (195)
+|.||.||++|+..|+.+|+.. +| |+...+.+||..|||++++|+|||||.+
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
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.42 E-value=7.1e-14 Score=112.73 Aligned_cols=64 Identities=34% Similarity=0.536 Sum_probs=58.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhHH
Q 029338 21 SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEH 85 (195)
Q Consensus 21 k~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~~ 85 (195)
+++|.|++|+..|+..|++.|+.. +|++..++.+||..|+|++.||+.||||||+|.||.+...
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Q-rYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQ-RYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred HhhhhcccccCccccccHHHHhhh-hhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 346779999999999999999999 9999999999999999999999999999999999865443
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.42 E-value=2.5e-13 Score=109.46 Aligned_cols=64 Identities=34% Similarity=0.548 Sum_probs=58.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhH
Q 029338 20 KSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIE 84 (195)
Q Consensus 20 kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~ 84 (195)
...+++|++.|.+|+.+|+..|+.+ +||+...+..|+..|+|+++-|+|||||||++.|++...
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~-p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEIN-PYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccC-CCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 4456778899999999999999999 999999999999999999999999999999999986544
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.30 E-value=9e-13 Score=118.59 Aligned_cols=73 Identities=25% Similarity=0.297 Sum_probs=63.5
Q ss_pred CCCCCchhhhccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHH
Q 029338 8 DSAASPEAKRKKKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (195)
Q Consensus 8 ~s~~sp~~~~~~kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krk 81 (195)
.+....+.-....|+||+||.|.......||.+|..| ++|+..++..||.+|+|....|+|||+|||.|.||.
T Consensus 280 ~~~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~n-pKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~ 352 (398)
T KOG3802|consen 280 GSPNSIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKN-PKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRI 352 (398)
T ss_pred CCCCCHHHhhccccccccccceeHHHHHHHHHHHHhC-CCCCHHHHHHHHHHhccccceEEEEeeccccccccC
Confidence 3344444444444678889999999999999999999 999999999999999999999999999999999994
No 23
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.28 E-value=3e-12 Score=112.19 Aligned_cols=75 Identities=19% Similarity=0.500 Sum_probs=65.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhHHHHHHHHHhhH
Q 029338 20 KSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDYAQLRANYD 95 (195)
Q Consensus 20 kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~~e~~~l~~~~~ 95 (195)
+|+||.|+.||..|+..||..|.++ +||+...+++||.-++|++..|+|||.|||+||+++..-...+..+..+-
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rN-rypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~~k~~f~ 184 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRN-RYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELAKGGFG 184 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhc-cCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHhhhcCCc
Confidence 3788899999999999999999999 99999999999999999999999999999999998655554333344443
No 24
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.27 E-value=2.8e-12 Score=107.80 Aligned_cols=62 Identities=34% Similarity=0.647 Sum_probs=57.2
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHH
Q 029338 19 KKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (195)
Q Consensus 19 ~kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krk 81 (195)
..+++..|..|+..||..|+..|+.. +|+-..++.+||..+|+++.||+|||||||+||||+
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqt-kylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKk 225 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQT-KYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKK 225 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhh-hcccchhHHHhhccccccHHHHHHHHhcchhhhhhh
Confidence 34455667889999999999999999 999999999999999999999999999999999985
No 25
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.26 E-value=1.4e-12 Score=114.11 Aligned_cols=63 Identities=27% Similarity=0.489 Sum_probs=58.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhH
Q 029338 21 SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIE 84 (195)
Q Consensus 21 k~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~ 84 (195)
..||-|+.||.+||..||+.|-+. .|.+...|.+||..|+|.+..|+|||||||+|+||+.+.
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrE-NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRE-NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHh-ccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 346779999999999999999999 999999999999999999999999999999999997665
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.03 E-value=9.9e-11 Score=97.39 Aligned_cols=63 Identities=29% Similarity=0.288 Sum_probs=59.3
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHH
Q 029338 19 KKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82 (195)
Q Consensus 19 ~kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq 82 (195)
+.++++.|+.|+..|+..|++.|+.. +||+...++.||..+++++..|+|||||||++|++..
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 45668889999999999999999999 9999999999999999999999999999999999854
No 27
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.90 E-value=1.9e-09 Score=93.21 Aligned_cols=74 Identities=23% Similarity=0.377 Sum_probs=63.5
Q ss_pred CCCCCCCchhhhccCCCCCCCCCCCHHH---------HHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHH
Q 029338 6 KDDSAASPEAKRKKKSKMKNKRRFSDEQ---------IRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRA 76 (195)
Q Consensus 6 ~~~s~~sp~~~~~~kk~rr~R~~ft~eQ---------~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRa 76 (195)
.+++.+..+..+-.||..-+||....|+ ..+|..+|..+ +||++.++.+||+.+||+..||-.||.|||.
T Consensus 151 RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~-~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQ 229 (304)
T KOG0775|consen 151 RGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQN-PYPSPREKRELAEATGLTITQVSNWFKNRRQ 229 (304)
T ss_pred cCCcCCccccceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcC-CCCChHHHHHHHHHhCCchhhhhhhhhhhhh
Confidence 4566677777777777777888765555 67999999999 9999999999999999999999999999999
Q ss_pred HHHH
Q 029338 77 RWKS 80 (195)
Q Consensus 77 k~Kr 80 (195)
|+|-
T Consensus 230 RDRa 233 (304)
T KOG0775|consen 230 RDRA 233 (304)
T ss_pred hhhh
Confidence 9983
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.85 E-value=3.7e-09 Score=95.25 Aligned_cols=64 Identities=30% Similarity=0.591 Sum_probs=59.1
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHH
Q 029338 18 KKKSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82 (195)
Q Consensus 18 ~~kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq 82 (195)
.+++.++.|+.|+..|+..|+..|+.+ +||....+..||.++++++..|+|||+|||++++|..
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt-~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRT-PYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCC-CCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 445567779999999999999999999 9999999999999999999999999999999999854
No 29
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.63 E-value=6.1e-09 Score=90.94 Aligned_cols=60 Identities=25% Similarity=0.437 Sum_probs=55.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHH
Q 029338 22 KMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82 (195)
Q Consensus 22 ~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq 82 (195)
++|+|+.+.....+.||.+|... +.|+.+.+..||.+|.|....|+|||+|.|.|.||..
T Consensus 309 kKRKRTSIAAPEKRsLEayFavQ-PRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAVQ-PRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred cccccccccCcccccHHHHhccC-CCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 35678999999999999999999 9999999999999999999999999999999999843
No 30
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.53 E-value=1.1e-07 Score=60.04 Aligned_cols=33 Identities=30% Similarity=0.542 Sum_probs=28.3
Q ss_pred CCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHH
Q 029338 45 STKLEPRKKMQVATELGLQPRQVAIWFQNKRAR 77 (195)
Q Consensus 45 ~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak 77 (195)
++||+.+++..||.++||+..||..||-|.|.|
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 389999999999999999999999999999875
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.34 E-value=2.6e-07 Score=79.85 Aligned_cols=58 Identities=29% Similarity=0.501 Sum_probs=53.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhc--CCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 23 MKNKRRFSDEQIRLLESIFESE--STKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 23 rr~R~~ft~eQ~~~Le~~F~~~--~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
+|+|+.|+.....+|..+|..+ ++||+.+.+++||++++++..||-.||-|+|-+.||
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK 248 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKK 248 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhh
Confidence 5667899999999999999765 699999999999999999999999999999999987
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.19 E-value=2.9e-06 Score=79.60 Aligned_cols=58 Identities=26% Similarity=0.359 Sum_probs=54.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 21 SKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 21 k~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
..+|+|.+||..|...|..+|+.+ ++|+.+..+.|+.+|+|...-|..||.|-|.|.+
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~-~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKEN-KRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcC-CCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 446779999999999999999999 9999999999999999999999999999988863
No 33
>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=98.16 E-value=6e-06 Score=53.47 Aligned_cols=44 Identities=50% Similarity=0.719 Sum_probs=41.4
Q ss_pred HHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 81 kq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
||++.+|..|+..|+.|.+.+++|+.|++.|++++..|+..++.
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl~~ 44 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEKLQM 44 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 57899999999999999999999999999999999999998863
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.82 E-value=2e-05 Score=65.48 Aligned_cols=63 Identities=30% Similarity=0.641 Sum_probs=57.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHh
Q 029338 20 KSKMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQI 83 (195)
Q Consensus 20 kk~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~ 83 (195)
.+.++.++.+...|+..+...|... ++|....+..|+..+|++.+.|++||+|+|++.++...
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRAT-PKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccCCCccccccchhHhhhhcccCC-CCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 4556778899999999999999999 99999999999999999999999999999999998544
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.95 E-value=0.0007 Score=69.25 Aligned_cols=61 Identities=23% Similarity=0.468 Sum_probs=56.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHh
Q 029338 22 KMKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQI 83 (195)
Q Consensus 22 ~rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~ 83 (195)
++..|++++..|+..|..+|... .+|...+.+.|...+++.++.|.+||||-|++.++...
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q-~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQ-RTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhc-cCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 35678999999999999999999 99999999999999999999999999999999998544
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.91 E-value=0.0011 Score=44.82 Aligned_cols=42 Identities=19% Similarity=0.358 Sum_probs=31.3
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhH
Q 029338 33 QIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKR 75 (195)
Q Consensus 33 Q~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRR 75 (195)
.+..|+.+|... +.+.......|..+.+|+..||+.||-.|+
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 456799999999 999999999999999999999999997654
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.72 E-value=0.00096 Score=59.42 Aligned_cols=60 Identities=25% Similarity=0.391 Sum_probs=50.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhc--CCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHH
Q 029338 22 KMKNKRRFSDEQIRLLESIFESE--STKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81 (195)
Q Consensus 22 ~rr~R~~ft~eQ~~~Le~~F~~~--~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krk 81 (195)
..+++..+....+.+|+.....+ ++||+..++..||.++||+..||.+||-|.|-|..+-
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 34556689999999999875443 4799999999999999999999999999999887763
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=95.42 E-value=0.034 Score=35.93 Aligned_cols=38 Identities=29% Similarity=0.413 Sum_probs=34.0
Q ss_pred HHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhccccc
Q 029338 90 LRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSDY 127 (195)
Q Consensus 90 l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~~ 127 (195)
+...|+.|++.+++|+.++++|..|++.|+.++.....
T Consensus 3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~ 40 (45)
T PF02183_consen 3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKE 40 (45)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999999999999999999887654
No 39
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.97 E-value=0.11 Score=51.12 Aligned_cols=48 Identities=21% Similarity=0.336 Sum_probs=44.6
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHH
Q 029338 34 IRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82 (195)
Q Consensus 34 ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq 82 (195)
+.+|..+|..| ..|+..+...+|.++||..+.|+.||+++++....-+
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 9999999999999999999999999999999887644
No 40
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=93.73 E-value=0.57 Score=35.75 Aligned_cols=91 Identities=14% Similarity=0.196 Sum_probs=49.0
Q ss_pred CCCCCHHHHH-HHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhHHHHHHHHHhhHHHhhhhHhH
Q 029338 26 KRRFSDEQIR-LLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDYAQLRANYDSLASGFESL 104 (195)
Q Consensus 26 R~~ft~eQ~~-~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~~e~~~l~~~~~~L~~~~~~l 104 (195)
+++|+.++.. ++...+... ....++|.++|+++.+|..|.+.=+....-.-..............+..++..|
T Consensus 10 rr~ys~EfK~~aV~~~~~~g------~sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~L 83 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG------MTVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKEL 83 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC------CCHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHHH
Confidence 5568887654 444444333 235678999999999999996432211000000000000011112344556667
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 029338 105 IKEKESLLLELQMLNEQL 122 (195)
Q Consensus 105 ~~e~~~L~~e~~~l~~~l 122 (195)
++++..|..|+.-|+..+
T Consensus 84 ~~el~~L~~E~diLKKa~ 101 (121)
T PRK09413 84 QRLLGKKTMENELLKEAV 101 (121)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 777777777777777655
No 41
>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=93.28 E-value=0.24 Score=32.73 Aligned_cols=47 Identities=19% Similarity=0.292 Sum_probs=35.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhH
Q 029338 23 MKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKR 75 (195)
Q Consensus 23 rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRR 75 (195)
+++|..+|.++-..+-..++.. . ....||.++|++..+|..|..|+.
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 3567889999888888888777 3 577899999999999999998853
No 42
>smart00340 HALZ homeobox associated leucin zipper.
Probab=92.06 E-value=0.34 Score=30.93 Aligned_cols=31 Identities=29% Similarity=0.209 Sum_probs=24.7
Q ss_pred HHHhhhhHhHHHHHHHHHHHHHHHHHHhccc
Q 029338 95 DSLASGFESLIKEKESLLLELQMLNEQLGKS 125 (195)
Q Consensus 95 ~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~ 125 (195)
+.|+..+++|.+||.+|+.|++.|+..-..+
T Consensus 8 e~LKrcce~LteeNrRL~ke~~eLralk~~~ 38 (44)
T smart00340 8 ELLKRCCESLTEENRRLQKEVQELRALKLSP 38 (44)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcccCC
Confidence 4556677888899999999999999765544
No 43
>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=88.31 E-value=1.8 Score=32.91 Aligned_cols=47 Identities=26% Similarity=0.410 Sum_probs=38.7
Q ss_pred HHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhccccc
Q 029338 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSDY 127 (195)
Q Consensus 81 kq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~~ 127 (195)
.+.+.....+-.+...|+.....+.+||..|..|++.|+..|.....
T Consensus 11 ~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 11 DQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34566677778888888888888999999999999999999987544
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=86.51 E-value=6.4 Score=26.52 Aligned_cols=39 Identities=31% Similarity=0.303 Sum_probs=26.0
Q ss_pred HHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHh
Q 029338 84 EHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQL 122 (195)
Q Consensus 84 ~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l 122 (195)
......|...+..|..++..|..++..|..++..|...+
T Consensus 25 k~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 25 KQYIEELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 344555666667777777777777777777777776543
No 45
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=86.11 E-value=2.7 Score=32.17 Aligned_cols=45 Identities=24% Similarity=0.369 Sum_probs=37.4
Q ss_pred HHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhccc
Q 029338 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKS 125 (195)
Q Consensus 81 kq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~ 125 (195)
.+.+.....+-.+...|+.....+.+||..|..||+.|+..|...
T Consensus 11 ~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~ 55 (110)
T PRK13169 11 DDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEEL 55 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345666677777888888888889999999999999999999875
No 46
>smart00340 HALZ homeobox associated leucin zipper.
Probab=85.82 E-value=1.8 Score=27.61 Aligned_cols=34 Identities=32% Similarity=0.259 Sum_probs=30.3
Q ss_pred HHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHH
Q 029338 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLE 114 (195)
Q Consensus 81 kq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e 114 (195)
||.+.+++.|+.-.+.|..+|..|++|.+.|++-
T Consensus 1 KQTEvdCe~LKrcce~LteeNrRL~ke~~eLral 34 (44)
T smart00340 1 KQTEVDCELLKRCCESLTEENRRLQKEVQELRAL 34 (44)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4788999999999999999999999999988753
No 47
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=84.15 E-value=6.5 Score=37.02 Aligned_cols=93 Identities=22% Similarity=0.272 Sum_probs=53.1
Q ss_pred CCCCCHHHHHHHHHH-HhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhHHHH-H-------HHHHhhHH
Q 029338 26 KRRFSDEQIRLLESI-FESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDY-A-------QLRANYDS 96 (195)
Q Consensus 26 R~~ft~eQ~~~Le~~-F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~~e~-~-------~l~~~~~~ 96 (195)
--++|.+....|.+. |.....+|....-+++. .+|+.=.+|+|...-.+.+..+| . ...+++..
T Consensus 218 ~L~LteeEkrLL~kEG~slPs~lPLTKaEEriL-------KrvRRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqe 290 (472)
T KOG0709|consen 218 PLVLTEEEKRLLTKEGYSLPSKLPLTKAEERIL-------KRVRRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQE 290 (472)
T ss_pred ceeccHHHHHHHHhccCcCcccCCchHHHHHHH-------HHHHHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHH
Confidence 346777777777654 43343444433333332 34555556666544333333332 3 33445566
Q ss_pred HhhhhHhHHHHHHHHHHHHHHHHHHhccc
Q 029338 97 LASGFESLIKEKESLLLELQMLNEQLGKS 125 (195)
Q Consensus 97 L~~~~~~l~~e~~~L~~e~~~l~~~l~~~ 125 (195)
|......|..+|.+|.+++.+|+.++...
T Consensus 291 L~kkV~~Le~~N~sLl~qL~klQt~v~q~ 319 (472)
T KOG0709|consen 291 LQKKVEELELSNRSLLAQLKKLQTLVIQV 319 (472)
T ss_pred HHHHHHHHhhccHHHHHHHHHHHHHHhhc
Confidence 66666667778888888888888877543
No 48
>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=83.46 E-value=6.7 Score=27.67 Aligned_cols=40 Identities=25% Similarity=0.238 Sum_probs=24.9
Q ss_pred HhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHH
Q 029338 82 QIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQ 121 (195)
Q Consensus 82 q~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~ 121 (195)
+.-..+..|+..++.|+..+..+..++..|..++++|+..
T Consensus 15 ~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e 54 (72)
T PF06005_consen 15 QAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQE 54 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 3344455566666666666666666666666666666643
No 49
>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=82.74 E-value=7.9 Score=27.97 Aligned_cols=45 Identities=20% Similarity=0.374 Sum_probs=36.6
Q ss_pred HHHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 80 SKQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 80 rkq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
+.....+...|+.....|....+..+.|+..|..|++.|+.-+.+
T Consensus 18 k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~n 62 (80)
T PF10224_consen 18 KEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGN 62 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566777788888889999999999999999999999876554
No 50
>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=82.56 E-value=2.8 Score=28.50 Aligned_cols=43 Identities=28% Similarity=0.435 Sum_probs=28.4
Q ss_pred CCCCCCCHHHHHHHHHHH-hhcCCCCCHHHHHHHHHHhCCChhHHHHHHH
Q 029338 24 KNKRRFSDEQIRLLESIF-ESESTKLEPRKKMQVATELGLQPRQVAIWFQ 72 (195)
Q Consensus 24 r~R~~ft~eQ~~~Le~~F-~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQ 72 (195)
+.|+.||+++...+-..+ ... .....+|.++||++.+|..|-.
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 346789998877666655 333 4678899999999999999964
No 51
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=82.55 E-value=5.7 Score=35.29 Aligned_cols=44 Identities=16% Similarity=0.201 Sum_probs=37.1
Q ss_pred HHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 81 kq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
++++.+.+.+-.+...|..+|+.|+....+|..|++.|+..+..
T Consensus 244 qKkRae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e 287 (294)
T KOG4571|consen 244 QKKRAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILE 287 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456677788889999999999999999999999999987754
No 52
>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=81.92 E-value=3.6 Score=24.98 Aligned_cols=44 Identities=11% Similarity=0.184 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRAR 77 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak 77 (195)
.+++.+..++...|... .....+|..+|++...|..|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~------~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG------LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC------CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46777888888777444 235667999999999999998665443
No 53
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=81.34 E-value=15 Score=28.92 Aligned_cols=87 Identities=18% Similarity=0.189 Sum_probs=53.4
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHH-HHhCCChhHHHHHHHhhHHHHH-------HHHhHHHHHHHHHhhHHH
Q 029338 26 KRRFSDEQIRLLESIFESESTKLEPRKKMQVA-TELGLQPRQVAIWFQNKRARWK-------SKQIEHDYAQLRANYDSL 97 (195)
Q Consensus 26 R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA-~~LgLt~rQVkvWFQNRRak~K-------rkq~~~e~~~l~~~~~~L 97 (195)
-.+|+.+++..|- ..+|- +.-|++...|-.|=|.||+-.- |-+.-.+...|..+...|
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 3688888877651 12232 3348899999999998886322 112223333445555566
Q ss_pred hhhhHhHHHHHHHHHHHHHHHHHHhcccc
Q 029338 98 ASGFESLIKEKESLLLELQMLNEQLGKSD 126 (195)
Q Consensus 98 ~~~~~~l~~e~~~L~~e~~~l~~~l~~~~ 126 (195)
..+.+.|+.|+.++..|+.-++..+.+..
T Consensus 87 ~qqv~~L~~e~s~~~~E~da~k~k~e~l~ 115 (135)
T KOG4196|consen 87 QQQVEKLKEENSRLRRELDAYKSKYEALQ 115 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66667777777777777777776665543
No 54
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=80.00 E-value=7.6 Score=24.52 Aligned_cols=42 Identities=10% Similarity=0.145 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKR 75 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRR 75 (195)
.+++.+..+|...|... ..-.++|..+|++...|..+...-.
T Consensus 4 ~L~~~er~vi~~~y~~~------~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG------LTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp TS-HHHHHHHHHHHTST-------SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC------CCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 47888999999998554 3466789999999999988765433
No 55
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=78.45 E-value=8.2 Score=29.53 Aligned_cols=45 Identities=31% Similarity=0.451 Sum_probs=37.8
Q ss_pred HhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcccc
Q 029338 82 QIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSD 126 (195)
Q Consensus 82 q~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~ 126 (195)
..+.....+-++...|+....++.+||..|+.|+..|+..|..+.
T Consensus 12 ~le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~~~~ 56 (114)
T COG4467 12 NLEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKLRERLGEPT 56 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhCCcc
Confidence 455666677778888888889999999999999999999998843
No 56
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=76.87 E-value=12 Score=32.52 Aligned_cols=55 Identities=25% Similarity=0.294 Sum_probs=25.5
Q ss_pred HHhhHHHHHHHHhH--HHHHHHHHhhHHHhhhhHhHHH-------HHHHHHHHHHHHHHHhccc
Q 029338 71 FQNKRARWKSKQIE--HDYAQLRANYDSLASGFESLIK-------EKESLLLELQMLNEQLGKS 125 (195)
Q Consensus 71 FQNRRak~Krkq~~--~e~~~l~~~~~~L~~~~~~l~~-------e~~~L~~e~~~l~~~l~~~ 125 (195)
-|+-|-|.|-+..+ .+...|..++..|..++++|.. +++.|..++..|+..|...
T Consensus 81 AQtaRDrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~~~ 144 (292)
T KOG4005|consen 81 AQTARDRKKARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNHELDSELELLRQELAEL 144 (292)
T ss_pred HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhh
Confidence 35555555543322 2223334444455555544444 5555555555455444443
No 57
>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=75.97 E-value=10 Score=24.13 Aligned_cols=43 Identities=14% Similarity=0.199 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRA 76 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRa 76 (195)
.+++.+..++.-.|-.. ..-.++|..+|+++..|+.|...-|.
T Consensus 10 ~L~~~~r~i~~l~~~~g------~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG------MSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp CS-HHHHHHHHHHHTS---------HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC------cCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 35667777777766555 45678899999999999999875443
No 58
>PRK00118 putative DNA-binding protein; Validated
Probab=75.03 E-value=31 Score=26.01 Aligned_cols=47 Identities=11% Similarity=0.134 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+++.|..++...|... ....++|..+|+++..|..+...-|.+.+.
T Consensus 17 ~L~ekqRevl~L~y~eg------~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD------YSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHcC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45677777776666555 235668999999999999998766655554
No 59
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=74.49 E-value=10 Score=33.10 Aligned_cols=49 Identities=27% Similarity=0.211 Sum_probs=32.1
Q ss_pred HHHHHHHHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcccc
Q 029338 75 RARWKSKQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSD 126 (195)
Q Consensus 75 Rak~Krkq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~ 126 (195)
|.|.++++...+. ......|..+++.|..+++.|..|+..|+..+....
T Consensus 208 kSR~~~k~~~~e~---~~r~~~leken~~lr~~v~~l~~el~~~~~~~~~~~ 256 (269)
T KOG3119|consen 208 KSRDKRKQKEDEM---AHRVAELEKENEALRTQVEQLKKELATLRRLFLQLP 256 (269)
T ss_pred HhhhhHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 5566665555333 333445666777778888888888888887776643
No 60
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=73.82 E-value=18 Score=24.20 Aligned_cols=34 Identities=29% Similarity=0.365 Sum_probs=21.3
Q ss_pred HhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHH
Q 029338 82 QIEHDYAQLRANYDSLASGFESLIKEKESLLLEL 115 (195)
Q Consensus 82 q~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~ 115 (195)
..+.....|...++.|...+..|..+...|..++
T Consensus 30 ~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 30 ELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3455556666666666666666666666666654
No 61
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=73.48 E-value=7.9 Score=26.30 Aligned_cols=30 Identities=30% Similarity=0.293 Sum_probs=23.7
Q ss_pred HHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 95 DSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 95 ~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
..+......+..|+.+|..||.+|+..|..
T Consensus 29 ~~vL~~R~~l~~e~~~L~~qN~eLr~lLkq 58 (60)
T PF14775_consen 29 NKVLLDRAALIQEKESLEQQNEELRSLLKQ 58 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 334445677889999999999999998864
No 62
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=72.93 E-value=5.4 Score=33.51 Aligned_cols=43 Identities=35% Similarity=0.414 Sum_probs=37.2
Q ss_pred HHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcccccc
Q 029338 86 DYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSDYE 128 (195)
Q Consensus 86 e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~~~ 128 (195)
-...+...|+.|+..++++..++++|+.+++.|+.++......
T Consensus 106 K~kqlE~d~~~Lk~~~~~l~~~~~~Lq~e~~eL~~~~~~~~~~ 148 (198)
T KOG0483|consen 106 KTKQLEKDYESLKRQLESLRSENDRLQSEVQELVAELSSLKRE 148 (198)
T ss_pred cchhhhhhHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhh
Confidence 3355677899999999999999999999999999999876543
No 63
>smart00338 BRLZ basic region leucin zipper.
Probab=71.66 E-value=27 Score=23.37 Aligned_cols=40 Identities=30% Similarity=0.355 Sum_probs=27.6
Q ss_pred HHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhc
Q 029338 84 EHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLG 123 (195)
Q Consensus 84 ~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~ 123 (195)
......|......|..++..|..+...|..++..|...+.
T Consensus 25 k~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~~ 64 (65)
T smart00338 25 KAEIEELERKVEQLEAENERLKKEIERLRRELEKLKSELE 64 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3444556666777777777777777777777777776653
No 64
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=69.03 E-value=11 Score=28.31 Aligned_cols=49 Identities=18% Similarity=0.287 Sum_probs=24.3
Q ss_pred hhHHHHHHHhhHHHHHHHHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHH
Q 029338 64 PRQVAIWFQNKRARWKSKQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNE 120 (195)
Q Consensus 64 ~rQVkvWFQNRRak~Krkq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~ 120 (195)
.-++..||.+.-- ..+..++++...++.++..++.+|..|..++..|++
T Consensus 14 ~l~y~l~~g~~G~--------~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 14 WLQYSLWFGKNGI--------LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHhccCCcH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3466788865311 112223444444444555555555555555555543
No 65
>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=66.80 E-value=27 Score=22.67 Aligned_cols=28 Identities=25% Similarity=0.326 Sum_probs=17.1
Q ss_pred hhHHHhhhhHhHHHHHHHHHHHHHHHHH
Q 029338 93 NYDSLASGFESLIKEKESLLLELQMLNE 120 (195)
Q Consensus 93 ~~~~L~~~~~~l~~e~~~L~~e~~~l~~ 120 (195)
....|......|..++..|..++..|..
T Consensus 26 ~~~~le~~~~~L~~en~~L~~~i~~L~~ 53 (54)
T PF07716_consen 26 REEELEQEVQELEEENEQLRQEIAQLER 53 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3444555556666777777777776653
No 66
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=66.41 E-value=19 Score=28.56 Aligned_cols=48 Identities=17% Similarity=0.160 Sum_probs=36.9
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 26 KRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 26 R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...+++.|..+|...+ .. ....++|..||++...|..|-.+.+.+.++
T Consensus 4 ~~~Lt~rqreVL~lr~-~G------lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-RG------LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHHH-cC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4578999999998843 33 245678999999999999999866655554
No 67
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=65.56 E-value=11 Score=23.65 Aligned_cols=41 Identities=17% Similarity=0.262 Sum_probs=21.2
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHH
Q 029338 26 KRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQ 72 (195)
Q Consensus 26 R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQ 72 (195)
.+.+|.++...++..+... ....+||..||.++.-|..+..
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G------~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG------MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ----------HHHHHHCS---------HHHHHHHTT--HHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC------CCHHHHHHHHCcCcHHHHHHHh
Confidence 3568889999999888665 3456789999999998887764
No 68
>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=65.02 E-value=33 Score=24.14 Aligned_cols=42 Identities=24% Similarity=0.307 Sum_probs=26.3
Q ss_pred HHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHh
Q 029338 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQL 122 (195)
Q Consensus 81 kq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l 122 (195)
...+.+...|+..+..|..++..|+.++..|+.+-......+
T Consensus 21 ~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl 62 (72)
T PF06005_consen 21 ALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERL 62 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556666666666676777777777777766655544443
No 69
>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=65.00 E-value=6.2 Score=26.99 Aligned_cols=20 Identities=25% Similarity=0.507 Sum_probs=17.3
Q ss_pred HHHHHHHHhCCChhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWF 71 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWF 71 (195)
....||.+||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45678999999999999993
No 70
>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=64.83 E-value=18 Score=23.95 Aligned_cols=40 Identities=23% Similarity=0.277 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhcCCC--CCHHHHHHHHHHhCCChhHHHH
Q 029338 29 FSDEQIRLLESIFESESTK--LEPRKKMQVATELGLQPRQVAI 69 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~--ps~~~r~~LA~~LgLt~rQVkv 69 (195)
+|+.|..+|...|+.. -| |-.....+||.+||+++.-|-.
T Consensus 1 LT~~Q~e~L~~A~~~G-Yfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELG-YFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcC-CCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 5788999999999887 44 4445667899999999876543
No 71
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=64.61 E-value=18 Score=31.16 Aligned_cols=41 Identities=22% Similarity=0.199 Sum_probs=27.5
Q ss_pred HHHHHHHhhHHHhhhhHhHHHHHH---HHHHHHHHHHHHhcccc
Q 029338 86 DYAQLRANYDSLASGFESLIKEKE---SLLLELQMLNEQLGKSD 126 (195)
Q Consensus 86 e~~~l~~~~~~L~~~~~~l~~e~~---~L~~e~~~l~~~l~~~~ 126 (195)
.+..+..+++.|+.++..++.+.. .|+.|+++|+.+|.-..
T Consensus 70 ~~~~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL~~~~ 113 (276)
T PRK13922 70 SLFDLREENEELKKELLELESRLQELEQLEAENARLRELLNLKE 113 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcc
Confidence 344556666666666666665555 77888999998886544
No 72
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=64.41 E-value=19 Score=27.67 Aligned_cols=29 Identities=14% Similarity=0.156 Sum_probs=23.3
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWKSK 81 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~Krk 81 (195)
-.++|..+|+++..|++....-|.+.|+.
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999988666666653
No 73
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=63.80 E-value=16 Score=31.87 Aligned_cols=42 Identities=31% Similarity=0.278 Sum_probs=30.9
Q ss_pred HHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHh
Q 029338 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQL 122 (195)
Q Consensus 81 kq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l 122 (195)
.....++..|+..+..|..++..+..+.+-|..++..|+...
T Consensus 107 ~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~~~~~~~ 148 (292)
T KOG4005|consen 107 EILQNENDSLRAINESLLAKNHELDSELELLRQELAELKQQQ 148 (292)
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhHHHH
Confidence 345556677777778888888888888888888777777643
No 74
>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=61.47 E-value=11 Score=34.27 Aligned_cols=29 Identities=28% Similarity=0.280 Sum_probs=14.5
Q ss_pred HHHhhhhHhHHHHHHHHHHHHHHHHHHhc
Q 029338 95 DSLASGFESLIKEKESLLLELQMLNEQLG 123 (195)
Q Consensus 95 ~~L~~~~~~l~~e~~~L~~e~~~l~~~l~ 123 (195)
-+|+.++.+|++|+..|..++.+|.+.+.
T Consensus 35 ~aLr~EN~~LKkEN~~Lk~eVerLE~e~l 63 (420)
T PF07407_consen 35 FALRMENHSLKKENNDLKIEVERLENEML 63 (420)
T ss_pred hhHHHHhHHHHHHHHHHHHHHHHHHHHhh
Confidence 34444555555555555555555544443
No 75
>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=60.62 E-value=31 Score=22.33 Aligned_cols=45 Identities=13% Similarity=0.281 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
.||+.+..+|.-...-. ...++|..+|+++..|.....+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G~-------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM-------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS--------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcC-------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 57888888887776555 4677899999999999998876665544
No 76
>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=59.28 E-value=26 Score=18.61 Aligned_cols=38 Identities=16% Similarity=0.340 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWF 71 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWF 71 (195)
.++.++...+...|... . ....+|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~--~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG--E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC--C----CHHHHHHHHCCCHHHHHHhC
Confidence 45666666666666543 2 35578899999998887773
No 77
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=59.00 E-value=30 Score=32.73 Aligned_cols=69 Identities=26% Similarity=0.350 Sum_probs=41.2
Q ss_pred HHHHHH---HhhHHHHHHHHhHHHHHHHHH---hhHHHhhhhHhHH-----------------------------HHHHH
Q 029338 66 QVAIWF---QNKRARWKSKQIEHDYAQLRA---NYDSLASGFESLI-----------------------------KEKES 110 (195)
Q Consensus 66 QVkvWF---QNRRak~Krkq~~~e~~~l~~---~~~~L~~~~~~l~-----------------------------~e~~~ 110 (195)
..-+|| ||+.+|.+-...-.+.+.|+. .+..|+.+.+... .|++.
T Consensus 227 v~gcw~ay~Qnk~akehv~km~kdle~Lq~aEqsl~dlQk~Lekar~e~rnvavek~~lerkl~ea~rl~elreg~e~e~ 306 (575)
T KOG4403|consen 227 VGGCWFAYRQNKKAKEHVNKMMKDLEGLQRAEQSLEDLQKRLEKAREEQRNVAVEKLDLERKLDEAPRLSELREGVENET 306 (575)
T ss_pred hhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhhhhhhHHHHHhhhhhhhhhhcchhHHH
Confidence 345788 888888877666666655532 2222222211111 16677
Q ss_pred HHHHHHHHHHHhccccccc-CCccc
Q 029338 111 LLLELQMLNEQLGKSDYEI-NGVGK 134 (195)
Q Consensus 111 L~~e~~~l~~~l~~~~~~~-~~~c~ 134 (195)
+..|+.+|+..|.++.... .++|-
T Consensus 307 ~rkelE~lR~~L~kAEkele~nS~w 331 (575)
T KOG4403|consen 307 SRKELEQLRVALEKAEKELEANSSW 331 (575)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccCC
Confidence 7788888888888876655 34443
No 78
>smart00338 BRLZ basic region leucin zipper.
Probab=58.41 E-value=48 Score=22.15 Aligned_cols=32 Identities=31% Similarity=0.419 Sum_probs=15.6
Q ss_pred HHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHh
Q 029338 91 RANYDSLASGFESLIKEKESLLLELQMLNEQL 122 (195)
Q Consensus 91 ~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l 122 (195)
+.....|......|..++..|..++..|...+
T Consensus 25 k~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~ 56 (65)
T smart00338 25 KAEIEELERKVEQLEAENERLKKEIERLRREL 56 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444455555555555555555554443
No 79
>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=58.13 E-value=65 Score=22.90 Aligned_cols=71 Identities=20% Similarity=0.177 Sum_probs=40.2
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHHHH------HhHHHHHHHHHhh----------HHHhhhhHhHHHHHHHHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWKSK------QIEHDYAQLRANY----------DSLASGFESLIKEKESLLLELQ 116 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~Krk------q~~~e~~~l~~~~----------~~L~~~~~~l~~e~~~L~~e~~ 116 (195)
..++|..+|+++..|+.|-+..--.-.+. =...+...+..-. +.+ ...-.+..+.+.|+.++.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i-~~~l~l~~~~~~l~~~l~ 82 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGV-KRILELEEELAELRAELD 82 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHH-HHHHHHHHHHHHHHHHHH
Confidence 35689999999999999986542221110 0111222221111 111 122236678888888888
Q ss_pred HHHHHhcc
Q 029338 117 MLNEQLGK 124 (195)
Q Consensus 117 ~l~~~l~~ 124 (195)
.|+..+.+
T Consensus 83 ~l~~~~~~ 90 (91)
T cd04766 83 ELRARLRR 90 (91)
T ss_pred HHHHHhcc
Confidence 88887754
No 80
>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=57.32 E-value=31 Score=23.48 Aligned_cols=44 Identities=18% Similarity=0.408 Sum_probs=22.4
Q ss_pred CCCCCHHH-HHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHH
Q 029338 26 KRRFSDEQ-IRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQ 72 (195)
Q Consensus 26 R~~ft~eQ-~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQ 72 (195)
|..|+... +.+++.++..+ . --...| ..|+++|++.++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~-n-c~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDN-N-CKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-T-T-TTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHcc-c-hhhhHH-HHHHHhCccHHHHHHHHH
Confidence 44566544 45555554443 1 111223 349999999999999964
No 81
>PF13518 HTH_28: Helix-turn-helix domain
Probab=57.13 E-value=14 Score=22.97 Aligned_cols=22 Identities=23% Similarity=0.510 Sum_probs=18.5
Q ss_pred HHHHHHHHhCCChhHHHHHHHh
Q 029338 52 KKMQVATELGLQPRQVAIWFQN 73 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQN 73 (195)
...++|.++|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3556899999999999999753
No 82
>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=57.07 E-value=28 Score=30.52 Aligned_cols=38 Identities=18% Similarity=-0.024 Sum_probs=22.2
Q ss_pred HHHhhHHHhhhhHhHH----HHHHHHHHHHHHHHHHhccccc
Q 029338 90 LRANYDSLASGFESLI----KEKESLLLELQMLNEQLGKSDY 127 (195)
Q Consensus 90 l~~~~~~L~~~~~~l~----~e~~~L~~e~~~l~~~l~~~~~ 127 (195)
+.++++.|+.+...+. ...+.|+.|+++|+.+|.-...
T Consensus 71 l~~EN~~Lr~e~~~l~~~~~~~~~~l~~EN~rLr~LL~~~~~ 112 (283)
T TIGR00219 71 LEYENYKLRQELLKKNQQLEILTQNLKQENVRLRELLNSPLS 112 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccc
Confidence 3444444444443332 2333488999999998877543
No 83
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=56.78 E-value=27 Score=26.51 Aligned_cols=46 Identities=11% Similarity=0.127 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
.+++.+..++...|-.. ....++|..+|++...|+.+...-+.+-|
T Consensus 106 ~L~~~~r~ii~l~~~~~------~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG------KTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 34555555555544333 23567899999999999999875555444
No 84
>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=56.71 E-value=29 Score=25.31 Aligned_cols=45 Identities=13% Similarity=0.204 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
+++.+..++...|-.. ....++|..+|+++..|..+...-+.+.|
T Consensus 111 L~~~~~~ii~~~~~~g------~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 111 LPEREREVLVLRYLEG------LSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCHHHHHHHhhHHhcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4555555554443222 24567899999999999988876555544
No 85
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=56.55 E-value=29 Score=26.77 Aligned_cols=47 Identities=11% Similarity=0.012 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+++.+..+|...|-.. ....++|..+|+++..|..+...-+.+.++
T Consensus 128 ~L~~~~r~vl~l~~~~~------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLREIEG------LSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45666666666554333 134578999999999999998754444443
No 86
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=55.82 E-value=28 Score=26.75 Aligned_cols=29 Identities=17% Similarity=0.204 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..+|+++..|..+...-|.+.|+
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34678999999999999998766655554
No 87
>PF15058 Speriolin_N: Speriolin N terminus
Probab=55.64 E-value=23 Score=29.74 Aligned_cols=41 Identities=29% Similarity=0.349 Sum_probs=29.6
Q ss_pred HHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcccc
Q 029338 85 HDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSD 126 (195)
Q Consensus 85 ~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~ 126 (195)
..|+.++...+.|.++|+.||+.+. |..|+++|+..|....
T Consensus 5 ~~yeGlrhqierLv~ENeeLKKlVr-LirEN~eLksaL~ea~ 45 (200)
T PF15058_consen 5 TNYEGLRHQIERLVRENEELKKLVR-LIRENHELKSALGEAC 45 (200)
T ss_pred cchHHHHHHHHHHHhhhHHHHHHHH-HHHHHHHHHHHHHHhh
Confidence 3567777778888888888887764 6677888887765543
No 88
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=55.33 E-value=39 Score=26.12 Aligned_cols=29 Identities=21% Similarity=0.169 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..+|++...|+++...-|.+-++
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999998766655554
No 89
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=54.82 E-value=32 Score=27.59 Aligned_cols=29 Identities=17% Similarity=0.187 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.-.++|..||++...|+++...-|.+-|+
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 35678999999999999888655555544
No 90
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=54.71 E-value=29 Score=28.25 Aligned_cols=29 Identities=21% Similarity=0.175 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..+|++...|+++..+-+.+.++
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35678999999999998888665555554
No 91
>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=54.59 E-value=15 Score=22.45 Aligned_cols=22 Identities=14% Similarity=0.162 Sum_probs=18.7
Q ss_pred HHHHHHHhCCChhHHHHHHHhh
Q 029338 53 KMQVATELGLQPRQVAIWFQNK 74 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNR 74 (195)
..++|+.+|+++..|+.|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3578999999999999997654
No 92
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=54.44 E-value=25 Score=22.80 Aligned_cols=29 Identities=10% Similarity=0.140 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
....||+.+|++...|..|+.++.....-
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 45678999999999999999877544443
No 93
>PRK14127 cell division protein GpsB; Provisional
Probab=54.44 E-value=40 Score=25.69 Aligned_cols=37 Identities=19% Similarity=0.349 Sum_probs=27.1
Q ss_pred HHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcccc
Q 029338 90 LRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSD 126 (195)
Q Consensus 90 l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~ 126 (195)
+...|+.|..++..|+.++..|..++..++..+..+.
T Consensus 35 V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~~~~ 71 (109)
T PRK14127 35 VIKDYEAFQKEIEELQQENARLKAQVDELTKQVSVGA 71 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 4556677777777778888888888888887776543
No 94
>PRK10072 putative transcriptional regulator; Provisional
Probab=54.35 E-value=23 Score=26.21 Aligned_cols=42 Identities=17% Similarity=0.071 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRAR 77 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak 77 (195)
+.+...+..|....... ..+||..+|++...|..|.+.+|.-
T Consensus 32 ~~~~~eik~LR~~~glT--------Q~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 32 TTSFTEFEQLRKGTGLK--------IDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred cCChHHHHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 44677777774433222 6789999999999999999877643
No 95
>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=53.48 E-value=55 Score=22.97 Aligned_cols=37 Identities=22% Similarity=0.371 Sum_probs=22.4
Q ss_pred HHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 88 AQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 88 ~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
..+...|..|..++.....++..|.++|..|...+..
T Consensus 24 ~~Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~ 60 (70)
T PF04899_consen 24 QEWQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQR 60 (70)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 3455566666666666666666666666666655544
No 96
>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=53.22 E-value=40 Score=31.98 Aligned_cols=11 Identities=27% Similarity=0.507 Sum_probs=6.9
Q ss_pred CCCHHHHHHHH
Q 029338 28 RFSDEQIRLLE 38 (195)
Q Consensus 28 ~ft~eQ~~~Le 38 (195)
.++++++..|.
T Consensus 41 ~ltpee~kalG 51 (472)
T TIGR03752 41 ELSPEELKALG 51 (472)
T ss_pred cCCcchhHhcC
Confidence 56777766653
No 97
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=53.02 E-value=42 Score=29.11 Aligned_cols=45 Identities=20% Similarity=0.304 Sum_probs=28.2
Q ss_pred HhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcccc
Q 029338 82 QIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSD 126 (195)
Q Consensus 82 q~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~ 126 (195)
....+...|...+..|.++++.+...-.+|..++.+|.+++.+..
T Consensus 146 E~~~EkeeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~l~ 190 (290)
T COG4026 146 ELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKLP 190 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhch
Confidence 344455555666666666666666666667777777777666554
No 98
>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=52.75 E-value=47 Score=25.11 Aligned_cols=40 Identities=23% Similarity=0.255 Sum_probs=33.5
Q ss_pred HHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHH
Q 029338 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNE 120 (195)
Q Consensus 81 kq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~ 120 (195)
...-.+...|+.....|..++..|+-||+.|+..+.++..
T Consensus 18 ~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 18 GQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4566677888888888999999999999999998888876
No 99
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=52.64 E-value=37 Score=26.73 Aligned_cols=46 Identities=15% Similarity=0.148 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
+++.+..++...|-.. ....+||..+|++...|+..+..-|.+-+.
T Consensus 132 L~~~~r~v~~l~~~~g------~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 132 LPPRQRDVVQSISVEG------ASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4444445554444333 245678999999999999998776666654
No 100
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=52.59 E-value=50 Score=24.71 Aligned_cols=34 Identities=21% Similarity=0.201 Sum_probs=15.3
Q ss_pred HhhHHHHHHHHhHHHHHHHHHhhHHHhhhhHhHH
Q 029338 72 QNKRARWKSKQIEHDYAQLRANYDSLASGFESLI 105 (195)
Q Consensus 72 QNRRak~Krkq~~~e~~~l~~~~~~L~~~~~~l~ 105 (195)
..+..+......+.+...+++.+..|..+...|+
T Consensus 28 ~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~ 61 (105)
T PRK00888 28 DYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLK 61 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3333333444444444445555544444444443
No 101
>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=52.26 E-value=43 Score=22.73 Aligned_cols=28 Identities=32% Similarity=0.369 Sum_probs=14.5
Q ss_pred HHhhHHHhhhhHhHHHHHHHHHHHHHHH
Q 029338 91 RANYDSLASGFESLIKEKESLLLELQML 118 (195)
Q Consensus 91 ~~~~~~L~~~~~~l~~e~~~L~~e~~~l 118 (195)
+.+...|......++.++..|..+++.|
T Consensus 23 ~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 23 NQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3344444444455555555555555555
No 102
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=52.02 E-value=44 Score=26.54 Aligned_cols=46 Identities=13% Similarity=0.249 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
+++.+..+|...|-.. ....++|..+|+++..|++-...-|.+.++
T Consensus 132 L~~~~r~vl~l~~~~~------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 132 LSPAHREIIDLVYYHE------KSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4444444444433332 234678999999999999888766665555
No 103
>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=51.93 E-value=37 Score=25.81 Aligned_cols=28 Identities=21% Similarity=0.205 Sum_probs=20.7
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
...++|..+|++...|.++...-|.+.+
T Consensus 129 ~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 129 SLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4567899999999999988765444433
No 104
>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=51.66 E-value=40 Score=25.30 Aligned_cols=28 Identities=18% Similarity=0.300 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
...++|..+|+++..|+.+...-|.+.|
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3556899999999999988765555544
No 105
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=50.41 E-value=56 Score=19.84 Aligned_cols=40 Identities=15% Similarity=0.276 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhh
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNK 74 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNR 74 (195)
.+++.+..++...+ .. + ...++|..+|++...|..+...-
T Consensus 3 ~l~~~e~~i~~~~~-~g--~----s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPREREVLRLLA-EG--L----TNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHHHH-cC--C----CHHHHHHHHCCCHHHHHHHHHHH
Confidence 46777887775533 22 1 35678999999999999887643
No 106
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=50.31 E-value=89 Score=22.56 Aligned_cols=11 Identities=27% Similarity=0.302 Sum_probs=4.4
Q ss_pred HHHHHHHHHHH
Q 029338 104 LIKEKESLLLE 114 (195)
Q Consensus 104 l~~e~~~L~~e 114 (195)
|..+++.|+.+
T Consensus 51 L~~en~qLk~E 61 (79)
T PRK15422 51 LERENNHLKEQ 61 (79)
T ss_pred HHHHHHHHHHH
Confidence 33344444433
No 107
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=49.99 E-value=56 Score=26.08 Aligned_cols=46 Identities=13% Similarity=0.161 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
+++.+..++.-.|-.. ....++|..+|+++..|+++...-|.+-|+
T Consensus 135 Lp~~~R~v~~L~~~~g------~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 135 LPAQQARVFMMREYLE------LSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CCHHHHHHHhHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3444444444444333 235678999999999999998766655554
No 108
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=49.80 E-value=61 Score=27.66 Aligned_cols=40 Identities=28% Similarity=0.326 Sum_probs=24.9
Q ss_pred HHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhccc
Q 029338 86 DYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKS 125 (195)
Q Consensus 86 e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~ 125 (195)
+.+.....+++|+-..+.+..|-.+|.++.++|++++...
T Consensus 173 ~Le~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~~~ 212 (216)
T KOG1962|consen 173 KLEKAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQIESG 212 (216)
T ss_pred HHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHhcc
Confidence 3344445555555555556667777777777777777654
No 109
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=49.61 E-value=45 Score=26.09 Aligned_cols=28 Identities=7% Similarity=0.246 Sum_probs=22.3
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
..++|..+|+++..|++....-|.+.|+
T Consensus 148 ~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 148 YKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred HHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 5678999999999999988766655554
No 110
>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=49.59 E-value=44 Score=26.21 Aligned_cols=45 Identities=18% Similarity=0.165 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARW 78 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~ 78 (195)
.+++.+..+|.-.|-.. ....++|..+|+++..|++....-|.+.
T Consensus 100 ~L~~~~r~v~~l~~~~g------~s~~eIA~~lgis~~tV~~~l~Rar~~L 144 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG------LSQQEIAEKLGLSLSGAKSRVQRGRKKL 144 (170)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34555555555544333 2356678899999988887765433333
No 111
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=49.57 E-value=44 Score=26.44 Aligned_cols=45 Identities=18% Similarity=0.172 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
+++.+..++...|-.. ....++|..+|++...|+.....-|.+-|
T Consensus 140 L~~~~r~i~~l~~~~g------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 140 LPEKQREILILRVVVG------LSAEETAEAVGSTPGAVRVAQHRALARLR 184 (189)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4444444554443333 24567899999999999988765444444
No 112
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=48.75 E-value=40 Score=27.89 Aligned_cols=49 Identities=20% Similarity=0.243 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHhhcCCC--CCHHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTK--LEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~--ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
-+|+.|+.+|...|... -| |-......||++||+++.- ++..=||+..|
T Consensus 155 ~LTdrQ~~vL~~A~~~G-YFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMG-YFDYPRRVSLKDLAKELGISKST--LSEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcC-CCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHH
Confidence 69999999999999887 43 4445567899999999865 34444455444
No 113
>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=48.66 E-value=37 Score=21.12 Aligned_cols=38 Identities=18% Similarity=0.403 Sum_probs=26.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWF 71 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWF 71 (195)
.++.+++..+...+... ....++|+.+|++...|..++
T Consensus 5 ~~~~~~~~~i~~l~~~G------~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG------MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT--------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHH
Confidence 46666666666666655 357789999999999887665
No 114
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=48.46 E-value=76 Score=30.85 Aligned_cols=33 Identities=33% Similarity=0.296 Sum_probs=18.9
Q ss_pred HHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHH
Q 029338 88 AQLRANYDSLASGFESLIKEKESLLLELQMLNE 120 (195)
Q Consensus 88 ~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~ 120 (195)
..|.+...+|..+++.|+.||..|+.++..|-.
T Consensus 305 ~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~ 337 (655)
T KOG4343|consen 305 LGLEARLQALLSENEQLKKENATLKRQLDELVS 337 (655)
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Confidence 445555556666666666666666555555544
No 115
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=48.43 E-value=36 Score=27.08 Aligned_cols=29 Identities=14% Similarity=0.217 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..+|++...|+.++..-|.+-++
T Consensus 159 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 159 SQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999765555554
No 116
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=47.76 E-value=42 Score=25.80 Aligned_cols=29 Identities=28% Similarity=0.249 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..+|++...|+.....-|.+-++
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 34678999999999999888755555543
No 117
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=47.54 E-value=44 Score=26.39 Aligned_cols=29 Identities=7% Similarity=0.195 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..+|++...|+.....-|.+-++
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRA 174 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 34678999999999999988655555554
No 118
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=47.48 E-value=97 Score=21.86 Aligned_cols=48 Identities=27% Similarity=0.210 Sum_probs=23.6
Q ss_pred HHHHHHhhHHHHHHHHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 67 VAIWFQNKRARWKSKQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 67 VkvWFQNRRak~Krkq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
++|.|-..|... .... ....+..++-.|+.+...|..+++.++..|..
T Consensus 21 LrI~fLee~l~~---~~~~-------~~~~~~keNieLKve~~~L~~el~~~~~~l~~ 68 (75)
T PF07989_consen 21 LRIYFLEERLQK---LGPE-------SIEELLKENIELKVEVESLKRELQEKKKLLKE 68 (75)
T ss_pred HHHHHHHHHHHh---cccc-------cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567776655541 1122 22333334444555555555555555555543
No 119
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=47.25 E-value=63 Score=24.63 Aligned_cols=40 Identities=18% Similarity=0.191 Sum_probs=33.3
Q ss_pred HHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHH
Q 029338 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNE 120 (195)
Q Consensus 81 kq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~ 120 (195)
...-.+...|+.....|..+|..|+-||+.|+..+.++..
T Consensus 18 ~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~~ 57 (110)
T PRK13169 18 GVLLKELGALKKQLAELLEENTALRLENDKLRERLEELEA 57 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3556677888888999999999999999999999988743
No 120
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=47.07 E-value=56 Score=24.84 Aligned_cols=47 Identities=9% Similarity=0.068 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+++.+..++.-.|-.. ....++|..||++...|++....-|.+.|.
T Consensus 106 ~Lp~~~r~v~~l~~~~g------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 106 KLPARQREAFLLRYWED------MDVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred hCCHHHHHHHHHHHHhc------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34455555555544333 135678999999999999887655544443
No 121
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=47.00 E-value=43 Score=26.21 Aligned_cols=47 Identities=9% Similarity=0.087 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+++.+..++...|-.. ..-.++|..+|+++..|++.+..-|.+-+.
T Consensus 136 ~L~~~~r~v~~l~~~~g------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMED------LSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCHHHhHHhhhHHhcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34444444544433222 245678999999999999998765555543
No 122
>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=46.83 E-value=70 Score=26.10 Aligned_cols=31 Identities=32% Similarity=0.305 Sum_probs=12.4
Q ss_pred HHHHHHhhHHHhhhhHhHHHHHHHHHHHHHH
Q 029338 87 YAQLRANYDSLASGFESLIKEKESLLLELQM 117 (195)
Q Consensus 87 ~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~ 117 (195)
...++.+...|...++.|..++..|..+...
T Consensus 106 ~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~ 136 (161)
T TIGR02894 106 NERLKNQNESLQKRNEELEKELEKLRQRLST 136 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333334444444444444444333333
No 123
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=46.69 E-value=66 Score=24.62 Aligned_cols=45 Identities=16% Similarity=0.302 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
+++.+..+|.-.| .. ....+||..+|+++..|+.....-|.+.|.
T Consensus 113 L~~~~r~il~l~~-~g------~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 113 MTERDRTVLLLRF-SG------YSYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred CCHHHHHHHHHHH-cC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444455555445 33 234568999999999999888655554443
No 124
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=46.26 E-value=99 Score=21.48 Aligned_cols=40 Identities=25% Similarity=0.277 Sum_probs=21.2
Q ss_pred HHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhc
Q 029338 84 EHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLG 123 (195)
Q Consensus 84 ~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~ 123 (195)
...+..|..+.+...........++..|+.++..|+..+.
T Consensus 25 ~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~ 64 (69)
T PF14197_consen 25 EIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELE 64 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455555555555555555555556666655555543
No 125
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=46.24 E-value=67 Score=21.60 Aligned_cols=29 Identities=17% Similarity=0.324 Sum_probs=14.6
Q ss_pred hhHHHhhhhHhHHHHHHHHHHHHHHHHHH
Q 029338 93 NYDSLASGFESLIKEKESLLLELQMLNEQ 121 (195)
Q Consensus 93 ~~~~L~~~~~~l~~e~~~L~~e~~~l~~~ 121 (195)
....+......++.|++.|..+++++.+-
T Consensus 8 ~~~~~~~~i~tvk~en~~i~~~ve~i~en 36 (55)
T PF05377_consen 8 ELPRIESSINTVKKENEEISESVEKIEEN 36 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444555555555555555555443
No 126
>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=45.66 E-value=41 Score=26.36 Aligned_cols=29 Identities=10% Similarity=-0.047 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.-.++|..+|+++..|+++...-|.+-|+
T Consensus 156 s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988655554443
No 127
>PRK04217 hypothetical protein; Provisional
Probab=45.54 E-value=66 Score=24.45 Aligned_cols=48 Identities=10% Similarity=0.059 Sum_probs=35.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 26 KRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 26 R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
-..++.++..++...|... - ...+||..+|++...|...+..-+.+.+
T Consensus 40 ~~~Lt~eereai~l~~~eG-l-----S~~EIAk~LGIS~sTV~r~L~RArkkLr 87 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEG-L-----TQEEAGKRMGVSRGTVWRALTSARKKVA 87 (110)
T ss_pred cccCCHHHHHHHHHHHHcC-C-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3468889988887777555 2 4667899999999999888765444443
No 128
>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=45.23 E-value=58 Score=25.44 Aligned_cols=29 Identities=24% Similarity=0.215 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.-.++|..||+++..|++....-|.+-++
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 34678999999999999988765555543
No 129
>PRK10884 SH3 domain-containing protein; Provisional
Probab=45.21 E-value=1.1e+02 Score=25.70 Aligned_cols=34 Identities=15% Similarity=0.134 Sum_probs=18.6
Q ss_pred HHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHH
Q 029338 88 AQLRANYDSLASGFESLIKEKESLLLELQMLNEQ 121 (195)
Q Consensus 88 ~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~ 121 (195)
..|+.++..|..+...++.+++.|..++..++..
T Consensus 135 ~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~~~ 168 (206)
T PRK10884 135 NGLKEENQKLKNQLIVAQKKVDAANLQLDDKQRT 168 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3355555555555555555555555555555543
No 130
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=43.76 E-value=97 Score=26.80 Aligned_cols=46 Identities=22% Similarity=0.324 Sum_probs=29.7
Q ss_pred HHHHHHHHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHH
Q 029338 75 RARWKSKQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNE 120 (195)
Q Consensus 75 Rak~Krkq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~ 120 (195)
|-|.|-...+.+.....+....|+.+.++|+.+|-.|=+-+.-|+.
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylqS 135 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQS 135 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 5555555666666667777777777766666666666665555544
No 131
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=43.24 E-value=25 Score=23.22 Aligned_cols=20 Identities=25% Similarity=0.443 Sum_probs=17.4
Q ss_pred HHHHHHhCCChhHHHHHHHh
Q 029338 54 MQVATELGLQPRQVAIWFQN 73 (195)
Q Consensus 54 ~~LA~~LgLt~rQVkvWFQN 73 (195)
.++|+.+|+++..|+.|=..
T Consensus 4 ~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999654
No 132
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=43.23 E-value=26 Score=21.77 Aligned_cols=21 Identities=24% Similarity=0.493 Sum_probs=16.9
Q ss_pred HHHHHHHHhCCChhHHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQ 72 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQ 72 (195)
...++|..+|++...|..|..
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 466789999999999999974
No 133
>KOG3650 consensus Predicted coiled-coil protein [General function prediction only]
Probab=42.95 E-value=84 Score=23.83 Aligned_cols=37 Identities=24% Similarity=0.318 Sum_probs=29.8
Q ss_pred HHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 88 AQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 88 ~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
-.|..-.+.|....++.|+|+-.|+.|+|-|-.-+++
T Consensus 66 LELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeN 102 (120)
T KOG3650|consen 66 LELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIEN 102 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHH
Confidence 3456677888889999999999999999988765554
No 134
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=42.83 E-value=90 Score=31.63 Aligned_cols=57 Identities=19% Similarity=0.207 Sum_probs=44.0
Q ss_pred HHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcccccccCCcccCCCcCCCC
Q 029338 86 DYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSDYEINGVGKDLKRSDWS 142 (195)
Q Consensus 86 e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~~~~~~~c~~~~~~~~~ 142 (195)
+...+++.--.|.+....+.+.|.+|..++++|+..+..+..+....-+++++-+-.
T Consensus 842 EAkaLRqHK~RLE~R~rILEdhNKQLESQLqRLr~LLrQP~s~~r~~gGS~ssp~~s 898 (966)
T KOG4286|consen 842 EAKALRQHKGRLEARMQILEDHNKQLESQLHRLRQLLRQPQAEAKVNGGSVSSPSTS 898 (966)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHhHHHHHHHHHHHHHHhCCCCccCCCCCCCCCCCcc
Confidence 445667788888899999999999999999999999988877664444444554444
No 135
>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=42.56 E-value=1.4e+02 Score=24.28 Aligned_cols=46 Identities=15% Similarity=0.229 Sum_probs=38.2
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHh
Q 029338 25 NKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQN 73 (195)
Q Consensus 25 ~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQN 73 (195)
+...+|++++..+...-..+ |..-.+..||+++|+++.-|.+=..-
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D---P~~wTr~~LAkkF~~S~~fV~~v~~~ 127 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED---PEKWTRKKLAKKFNCSPLFVSMVAPA 127 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC---chHhhHHHHHHHhCCCHHHHHHhcCC
Confidence 34689999999999988877 77888999999999998877665543
No 136
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=42.37 E-value=58 Score=26.25 Aligned_cols=29 Identities=21% Similarity=0.126 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..||++...|++.+..-|.+.|+
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34678999999999999998765555554
No 137
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=42.23 E-value=1.5e+02 Score=22.30 Aligned_cols=40 Identities=23% Similarity=0.344 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHh
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQN 73 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQN 73 (195)
.+|..|..+|+-+|..+ --..++|..+|++..-|--+.+.
T Consensus 17 LLT~kQ~~~l~lyy~eD------lSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 17 LLTEKQREILELYYEED------LSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp GS-HHHHHHHHHHCTS---------HHHHHHHCTS-HHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccC------CCHHHHHHHHCCCHHHHHHHHHH
Confidence 47888999998888766 45667899999999999988853
No 138
>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=42.16 E-value=40 Score=24.95 Aligned_cols=37 Identities=24% Similarity=0.540 Sum_probs=20.1
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHHhHH
Q 029338 34 IRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEH 85 (195)
Q Consensus 34 ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~~ 85 (195)
+.+..-.|+.+ +||.+.--.. ==.|||.+|++.+...
T Consensus 14 vRiIk~Lyqsn-PyP~~~GTr~--------------aRRnRRRRWR~rq~QI 50 (91)
T PF00424_consen 14 VRIIKILYQSN-PYPSPEGTRQ--------------ARRNRRRRWRARQRQI 50 (91)
T ss_dssp HHHHHHHHHTS--S--S-S-HH--------------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccc-cCCCCCCccc--------------cccchhhhHHHHHHHH
Confidence 44556668888 9997441111 1168999999865543
No 139
>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=42.00 E-value=47 Score=30.35 Aligned_cols=30 Identities=30% Similarity=0.174 Sum_probs=18.6
Q ss_pred HHHHHHhhHHHhhhhHhHHHHHHHHHHHHH
Q 029338 87 YAQLRANYDSLASGFESLIKEKESLLLELQ 116 (195)
Q Consensus 87 ~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~ 116 (195)
...|+.++++|+.+++.|+.+.++|..++.
T Consensus 34 ~~aLr~EN~~LKkEN~~Lk~eVerLE~e~l 63 (420)
T PF07407_consen 34 NFALRMENHSLKKENNDLKIEVERLENEML 63 (420)
T ss_pred hhhHHHHhHHHHHHHHHHHHHHHHHHHHhh
Confidence 345666666666666666666666644444
No 140
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=41.74 E-value=67 Score=25.31 Aligned_cols=28 Identities=18% Similarity=0.378 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
...++|..+|++...|+++...-|.+.|
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 3467899999999999988875554444
No 141
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=41.47 E-value=63 Score=25.70 Aligned_cols=23 Identities=26% Similarity=0.330 Sum_probs=16.2
Q ss_pred HHHHHHHhCCChhHHHHHHHhhH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKR 75 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRR 75 (195)
..++|..+|+++..|+..+..-|
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar 147 (181)
T PRK09637 125 QKEIAEKLGLSLSGAKSRVQRGR 147 (181)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHH
Confidence 45678888888887777765333
No 142
>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=41.03 E-value=1.3e+02 Score=25.49 Aligned_cols=8 Identities=50% Similarity=0.999 Sum_probs=3.7
Q ss_pred CCCCCCCC
Q 029338 176 GLLDPSTS 183 (195)
Q Consensus 176 ~~~~~~~~ 183 (195)
|++|+..-
T Consensus 205 g~~~~~~~ 212 (251)
T PF11932_consen 205 GVWDPATG 212 (251)
T ss_pred eeecCCCC
Confidence 35555443
No 143
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=40.51 E-value=88 Score=22.89 Aligned_cols=20 Identities=35% Similarity=0.567 Sum_probs=15.9
Q ss_pred HHHHHHhCCChhHHHHHHHh
Q 029338 54 MQVATELGLQPRQVAIWFQN 73 (195)
Q Consensus 54 ~~LA~~LgLt~rQVkvWFQN 73 (195)
.++|+.+|+++..++.|-++
T Consensus 4 ~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 4 GEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred HHHHHHHCcCHHHHHHHHHH
Confidence 46788888888888888655
No 144
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=40.25 E-value=1.2e+02 Score=23.72 Aligned_cols=29 Identities=10% Similarity=0.110 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..+|++...|++-...-|.+.|+
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34667889999999888887766666554
No 145
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=40.24 E-value=81 Score=26.46 Aligned_cols=29 Identities=10% Similarity=0.160 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.-.++|..||++...|++....-|.+-|+
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34678999999999999988766665554
No 146
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=40.20 E-value=71 Score=31.04 Aligned_cols=37 Identities=24% Similarity=0.302 Sum_probs=27.0
Q ss_pred HHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 88 AQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 88 ~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
..-+.+-..|.+....+.+|++.|+.|+..|+.+|..
T Consensus 298 kKKKEy~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~ 334 (655)
T KOG4343|consen 298 KKKKEYMLGLEARLQALLSENEQLKKENATLKRQLDE 334 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence 3344555667777778888888888888888877765
No 147
>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=40.16 E-value=30 Score=23.14 Aligned_cols=27 Identities=30% Similarity=0.614 Sum_probs=20.7
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..||++...|..|-+ |-+|..
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 356789999999999999964 444443
No 148
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=40.04 E-value=78 Score=24.47 Aligned_cols=28 Identities=14% Similarity=0.089 Sum_probs=21.6
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
...++|..+|+++..|+.....-|.+-|
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3567899999999999998875555544
No 149
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=40.01 E-value=83 Score=24.02 Aligned_cols=27 Identities=22% Similarity=0.444 Sum_probs=20.0
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
..++|..+|++...|+.....-+.+.+
T Consensus 128 ~~EIA~~lgis~~tV~~~l~ra~~~lr 154 (163)
T PRK07037 128 QKDIARELGVSPTLVNFMIRDALVHCR 154 (163)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 567899999999999987654444444
No 150
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=39.82 E-value=71 Score=25.55 Aligned_cols=28 Identities=7% Similarity=0.062 Sum_probs=21.2
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
-.++|..+|++...|+.++..-|.+-|+
T Consensus 155 ~~eIA~~lgis~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 155 NPEIAEVMEIGVEAVESLTARGKRALAA 182 (196)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4678999999999999988755544443
No 151
>PRK06930 positive control sigma-like factor; Validated
Probab=39.79 E-value=92 Score=25.15 Aligned_cols=47 Identities=6% Similarity=0.027 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+++.+..++.-.|... ..-.++|..+|+++..|+.+...-+.+.++
T Consensus 114 ~L~~rer~V~~L~~~eg------~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG------LSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46666666666654333 235678999999999999998766666554
No 152
>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=39.79 E-value=79 Score=24.17 Aligned_cols=28 Identities=21% Similarity=0.095 Sum_probs=19.1
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
...++|..||++...|+.....-|.+-|
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3467788899999888877654444333
No 153
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=39.60 E-value=36 Score=22.57 Aligned_cols=21 Identities=14% Similarity=0.381 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChhHHHHHHHh
Q 029338 53 KMQVATELGLQPRQVAIWFQN 73 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQN 73 (195)
..++|+.+|+++..|+.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999865
No 154
>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=39.48 E-value=76 Score=24.21 Aligned_cols=28 Identities=29% Similarity=0.341 Sum_probs=21.6
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
-.++|..+|++...|+.+-..-|.+-++
T Consensus 129 ~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 129 EAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4568999999999999888766555554
No 155
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=39.46 E-value=39 Score=20.05 Aligned_cols=24 Identities=21% Similarity=0.499 Sum_probs=20.0
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRA 76 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRa 76 (195)
..++|..+|+++..|..|.++...
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 357899999999999999876543
No 156
>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=38.74 E-value=76 Score=24.52 Aligned_cols=29 Identities=10% Similarity=0.157 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..||+++..|++....-|.+-++
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999998887655554443
No 157
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=38.52 E-value=1.3e+02 Score=26.24 Aligned_cols=7 Identities=29% Similarity=0.771 Sum_probs=2.5
Q ss_pred HHhhHHH
Q 029338 91 RANYDSL 97 (195)
Q Consensus 91 ~~~~~~L 97 (195)
.+.|+.+
T Consensus 162 e~e~ee~ 168 (290)
T COG4026 162 EAEYEEV 168 (290)
T ss_pred HHHHHHH
Confidence 3333333
No 158
>PF13551 HTH_29: Winged helix-turn helix
Probab=38.21 E-value=1.4e+02 Score=21.03 Aligned_cols=48 Identities=15% Similarity=0.306 Sum_probs=31.2
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCC-----CCHHHHHH-H-HHHh--CCChhHHHHHHH
Q 029338 24 KNKRRFSDEQIRLLESIFESESTK-----LEPRKKMQ-V-ATEL--GLQPRQVAIWFQ 72 (195)
Q Consensus 24 r~R~~ft~eQ~~~Le~~F~~~~~~-----ps~~~r~~-L-A~~L--gLt~rQVkvWFQ 72 (195)
+++..+++++...|...+... +. .+...... | .... .+++..|..|+.
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~-p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLREN-PPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHC-CCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 334449999999999999887 52 33444433 3 3333 467778887774
No 159
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=37.99 E-value=2e+02 Score=22.70 Aligned_cols=48 Identities=19% Similarity=0.164 Sum_probs=35.0
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 26 KRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 26 R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+.+++.|..+|.-.+ .. ....++|..+|++...|..+-..-+.+-++
T Consensus 4 ~~~Lte~qr~VL~Lr~-~G------lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-KG------LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH-cC------CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4578999999998743 33 146678999999999998887655544443
No 160
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.93 E-value=1.5e+02 Score=21.11 Aligned_cols=20 Identities=20% Similarity=0.248 Sum_probs=8.1
Q ss_pred HHHHhhHHHhhhhHhHHHHH
Q 029338 89 QLRANYDSLASGFESLIKEK 108 (195)
Q Consensus 89 ~l~~~~~~L~~~~~~l~~e~ 108 (195)
.+....++|..+++.++.|.
T Consensus 43 ~~q~~reaL~~eneqlk~e~ 62 (79)
T COG3074 43 NAQHQREALERENEQLKEEQ 62 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33333444444444444433
No 161
>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=37.91 E-value=75 Score=20.86 Aligned_cols=35 Identities=20% Similarity=0.375 Sum_probs=25.8
Q ss_pred HHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHH
Q 029338 32 EQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWF 71 (195)
Q Consensus 32 eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWF 71 (195)
.|+..|+-.+. . ...+.. +||..+|++.+.|+.-.
T Consensus 6 rq~~Ll~~L~~-~-~~~~~~---ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLK-N-KWITLK---ELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHH-H-TSBBHH---HHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHc-C-CCCcHH---HHHHHHCCCHHHHHHHH
Confidence 46788888888 6 666544 78999999998877544
No 162
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=37.65 E-value=1e+02 Score=26.91 Aligned_cols=31 Identities=29% Similarity=0.407 Sum_probs=18.1
Q ss_pred HHHhhhhHhHHHHHHHHHHHHHHHHHHhccc
Q 029338 95 DSLASGFESLIKEKESLLLELQMLNEQLGKS 125 (195)
Q Consensus 95 ~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~ 125 (195)
+.+......|.+||+.|+.+|.+|+..+.+-
T Consensus 218 ~e~~~r~~~leken~~lr~~v~~l~~el~~~ 248 (269)
T KOG3119|consen 218 DEMAHRVAELEKENEALRTQVEQLKKELATL 248 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555556666666666666666655543
No 163
>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=37.56 E-value=22 Score=25.15 Aligned_cols=23 Identities=22% Similarity=0.352 Sum_probs=19.8
Q ss_pred HHHHHHHHHhCCChhHHHHHHHh
Q 029338 51 RKKMQVATELGLQPRQVAIWFQN 73 (195)
Q Consensus 51 ~~r~~LA~~LgLt~rQVkvWFQN 73 (195)
....+||..+|+++..|+.|+.+
T Consensus 33 lS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 33 KTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred CCHHHHHHHHCcCHHHHHHHHhc
Confidence 35678999999999999999864
No 164
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=37.55 E-value=38 Score=22.53 Aligned_cols=21 Identities=24% Similarity=0.433 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChhHHHHHHHh
Q 029338 53 KMQVATELGLQPRQVAIWFQN 73 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQN 73 (195)
..++|+.+|+++..++.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999864
No 165
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=37.42 E-value=77 Score=25.21 Aligned_cols=28 Identities=18% Similarity=0.304 Sum_probs=19.7
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
..++|..+|++...|+...+.-|.+-++
T Consensus 150 ~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 150 IEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4567888999998888776655444443
No 166
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=36.76 E-value=94 Score=24.44 Aligned_cols=29 Identities=14% Similarity=0.093 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..+|+++..|++....-|.+.|+
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35678999999999999888766655554
No 167
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=36.75 E-value=1.1e+02 Score=24.38 Aligned_cols=29 Identities=7% Similarity=0.158 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..+|+++..|+.....-|.+.|+
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 182 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQ 182 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34678999999999999998766666655
No 168
>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=36.71 E-value=12 Score=32.26 Aligned_cols=33 Identities=30% Similarity=0.243 Sum_probs=0.0
Q ss_pred HHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHH
Q 029338 86 DYAQLRANYDSLASGFESLIKEKESLLLELQML 118 (195)
Q Consensus 86 e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l 118 (195)
.++-|+...+-|.++++.|.+||.+|.+++.+|
T Consensus 130 ~I~dLrrlVe~L~aeNErLr~EnkqL~ae~arL 162 (243)
T PF08961_consen 130 KIADLRRLVEFLLAENERLRRENKQLKAENARL 162 (243)
T ss_dssp ---------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556666666666666666666666666666
No 169
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=36.61 E-value=1.8e+02 Score=21.99 Aligned_cols=25 Identities=20% Similarity=0.291 Sum_probs=11.0
Q ss_pred HHhhhhHhHHHHHHHHHHHHHHHHH
Q 029338 96 SLASGFESLIKEKESLLLELQMLNE 120 (195)
Q Consensus 96 ~L~~~~~~l~~e~~~L~~e~~~l~~ 120 (195)
.+.++++.|..++..|..++..|++
T Consensus 61 ~~~~e~~~L~~~~~~l~~ei~~L~d 85 (117)
T COG2919 61 AQQAELEKLSARNTALEAEIKDLKD 85 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3334444444444444444444443
No 170
>PRK10884 SH3 domain-containing protein; Provisional
Probab=36.58 E-value=1.4e+02 Score=25.07 Aligned_cols=41 Identities=17% Similarity=0.083 Sum_probs=24.9
Q ss_pred HHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhccc
Q 029338 85 HDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKS 125 (195)
Q Consensus 85 ~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~ 125 (195)
............|..++..|+++...++.++..|+.++...
T Consensus 125 ~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~ 165 (206)
T PRK10884 125 QKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQLDDK 165 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444555556666666666666666666666666655443
No 171
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=36.06 E-value=42 Score=20.43 Aligned_cols=18 Identities=33% Similarity=0.499 Sum_probs=14.9
Q ss_pred HHHHHHhCCChhHHHHHH
Q 029338 54 MQVATELGLQPRQVAIWF 71 (195)
Q Consensus 54 ~~LA~~LgLt~rQVkvWF 71 (195)
-++|+.+|++++.|+.|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 468999999999999984
No 172
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.52 E-value=70 Score=23.76 Aligned_cols=39 Identities=18% Similarity=0.233 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVA 68 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVk 68 (195)
+.++|...-...|..+ .-.++....++|..|++++--|.
T Consensus 3 Ln~eq~~~Tk~elqan-~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQAN-FELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHHh-hhhccccHHHHHHHhCCCHHHHH
Confidence 5677777766666666 66666778889999999986543
No 173
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=35.51 E-value=1.5e+02 Score=26.56 Aligned_cols=31 Identities=16% Similarity=0.127 Sum_probs=15.2
Q ss_pred hHHHHHHHHHhhHHHhhhhHhHHHHHHHHHH
Q 029338 83 IEHDYAQLRANYDSLASGFESLIKEKESLLL 113 (195)
Q Consensus 83 ~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~ 113 (195)
...+...|...++.|+....++..|.+-|+.
T Consensus 253 l~ge~~~Le~rN~~LK~qa~~lerEI~ylKq 283 (294)
T KOG4571|consen 253 LLGELEGLEKRNEELKDQASELEREIRYLKQ 283 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444555555555555555555444443
No 174
>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=35.44 E-value=52 Score=26.91 Aligned_cols=19 Identities=37% Similarity=0.373 Sum_probs=2.8
Q ss_pred HhHHHHHHHHHHHHHHHHH
Q 029338 102 ESLIKEKESLLLELQMLNE 120 (195)
Q Consensus 102 ~~l~~e~~~L~~e~~~l~~ 120 (195)
+.|..++|+|+.|+..|+.
T Consensus 27 E~L~~~~QRLkDE~RDLKq 45 (166)
T PF04880_consen 27 ENLREEVQRLKDELRDLKQ 45 (166)
T ss_dssp HHHHHCH------------
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444443
No 175
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=34.96 E-value=1e+02 Score=24.10 Aligned_cols=27 Identities=22% Similarity=0.197 Sum_probs=19.5
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
-.++|..+|++...|+.+...-|.+-+
T Consensus 154 ~~eIA~~lgis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 154 HREAAQLLGLPLGTLKTRARRALSRLK 180 (186)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 456788999999988887765444444
No 176
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=34.80 E-value=1.4e+02 Score=23.86 Aligned_cols=47 Identities=9% Similarity=0.141 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+++.+..++...|-.. ....+||..+|++..-|+.....-|.+-++
T Consensus 131 ~L~~~~r~v~~l~~~~g------~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~ 177 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG------FESDEICQELEISTSNCHVLLYRARLSLRA 177 (188)
T ss_pred hCCHHHHHHHHHHHHhC------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 34455555555544333 245678999999999998887655555554
No 177
>PRK14127 cell division protein GpsB; Provisional
Probab=34.79 E-value=1e+02 Score=23.46 Aligned_cols=38 Identities=24% Similarity=0.253 Sum_probs=24.2
Q ss_pred HHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhccccc
Q 029338 90 LRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSDY 127 (195)
Q Consensus 90 l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~~ 127 (195)
.....+.+...++.+..|+..|..++..|+..+.....
T Consensus 28 VD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~ 65 (109)
T PRK14127 28 VDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTK 65 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666666666667777777777777766665544
No 178
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=34.71 E-value=1.1e+02 Score=21.18 Aligned_cols=14 Identities=43% Similarity=0.380 Sum_probs=5.8
Q ss_pred HHHHHHHHHHHHHH
Q 029338 105 IKEKESLLLELQML 118 (195)
Q Consensus 105 ~~e~~~L~~e~~~l 118 (195)
+.++..|+.|...|
T Consensus 44 ~~en~~L~~ei~~l 57 (85)
T TIGR02209 44 QKEWRDLQLEVAEL 57 (85)
T ss_pred HHHHHHHHHHHHHH
Confidence 33444444444443
No 179
>PF15058 Speriolin_N: Speriolin N terminus
Probab=34.67 E-value=55 Score=27.58 Aligned_cols=29 Identities=31% Similarity=0.572 Sum_probs=22.2
Q ss_pred HhhHHHhhhhHhHHHHHHHHHHHHHHHHH
Q 029338 92 ANYDSLASGFESLIKEKESLLLELQMLNE 120 (195)
Q Consensus 92 ~~~~~L~~~~~~l~~e~~~L~~e~~~l~~ 120 (195)
..|+-|.+.++.+..||+.|+.+|.-+++
T Consensus 5 ~~yeGlrhqierLv~ENeeLKKlVrLirE 33 (200)
T PF15058_consen 5 TNYEGLRHQIERLVRENEELKKLVRLIRE 33 (200)
T ss_pred cchHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence 46777777888888888888887777765
No 180
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=34.59 E-value=93 Score=24.70 Aligned_cols=27 Identities=11% Similarity=0.000 Sum_probs=20.4
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
..+||..+|+++..|++....-|.+-|
T Consensus 149 ~~EIA~~lgis~~tVk~~l~Rar~~Lr 175 (185)
T PRK09649 149 YADAAAVCGCPVGTIRSRVARARDALL 175 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 467899999999999988865444444
No 181
>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=34.58 E-value=1.7e+02 Score=27.88 Aligned_cols=17 Identities=41% Similarity=0.325 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHHHHHh
Q 029338 106 KEKESLLLELQMLNEQL 122 (195)
Q Consensus 106 ~e~~~L~~e~~~l~~~l 122 (195)
++.+.|..+.++|+..|
T Consensus 116 ~~~~ql~~~~~~~~~~l 132 (472)
T TIGR03752 116 KEIEQLKSERQQLQGLI 132 (472)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34444444444444443
No 182
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=34.49 E-value=87 Score=24.24 Aligned_cols=28 Identities=18% Similarity=0.241 Sum_probs=20.8
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
..++|..||+++..|+.....-|.+-|+
T Consensus 137 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 137 TAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5678999999999998887655544443
No 183
>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=34.04 E-value=2e+02 Score=22.11 Aligned_cols=45 Identities=22% Similarity=0.336 Sum_probs=29.6
Q ss_pred HHHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 80 SKQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 80 rkq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
....+.+...+...|+.+...++.-.++++.|+..++.|++++..
T Consensus 70 ~~~L~~el~~l~~ry~t~LellGEK~E~veEL~~Dv~DlK~myr~ 114 (120)
T PF12325_consen 70 VEELEQELEELQQRYQTLLELLGEKSEEVEELRADVQDLKEMYRE 114 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHH
Confidence 334555566666666666666666666777888888887777653
No 184
>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold). The domain has a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and is a prerequisite for the assembly of Cortexillin I []. ; PDB: 1D7M_A.
Probab=33.94 E-value=1.8e+02 Score=22.24 Aligned_cols=29 Identities=28% Similarity=0.297 Sum_probs=10.9
Q ss_pred HHHhhHHHhhhhHhHHHHHHHHHHHHHHH
Q 029338 90 LRANYDSLASGFESLIKEKESLLLELQML 118 (195)
Q Consensus 90 l~~~~~~L~~~~~~l~~e~~~L~~e~~~l 118 (195)
|....+..+.+.+.|.++++.|...++.|
T Consensus 21 Le~slE~~K~S~~eL~kqkd~L~~~l~~L 49 (107)
T PF09304_consen 21 LERSLEDEKTSQGELAKQKDQLRNALQSL 49 (107)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhhHHHHHHhHHHHHHHHHHH
Confidence 33333333333333333333333333333
No 185
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=33.94 E-value=92 Score=25.83 Aligned_cols=46 Identities=13% Similarity=0.260 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
+++.+..++...|... ....++|..+|++...|+.+...-+.+.|+
T Consensus 185 L~~~~r~vl~l~~~~g------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 185 LPEREQLVLSLYYQEE------LNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CCHHHHHHHHhHhccC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455555555544333 245778999999999999998776666654
No 186
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=33.93 E-value=1.3e+02 Score=23.60 Aligned_cols=29 Identities=17% Similarity=0.343 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.-.++|..+|+++..|++....-|.+-++
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34678999999999999987655555544
No 187
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=33.76 E-value=99 Score=24.14 Aligned_cols=28 Identities=14% Similarity=0.217 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
...++|..+|++...|++....-+.+.+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4567899999999999988865444444
No 188
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=33.71 E-value=1.4e+02 Score=24.33 Aligned_cols=47 Identities=11% Similarity=0.128 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+++.+..++.-.|-.. ....++|..+|++...|++....-|.+-|+
T Consensus 148 ~L~~~~r~v~~L~~~~g------~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~ 194 (206)
T PRK12544 148 GLPAKYARVFMMREFIE------LETNEICHAVDLSVSNLNVLLYRARLRLRE 194 (206)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34455555555544333 234678999999999999988766666555
No 189
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=33.67 E-value=1.2e+02 Score=24.45 Aligned_cols=29 Identities=21% Similarity=0.376 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.-.++|..+|+++..|++....-|.+-|+
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 185 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRT 185 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35678999999999999888765555554
No 190
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=33.64 E-value=91 Score=24.64 Aligned_cols=28 Identities=11% Similarity=0.000 Sum_probs=21.0
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
..++|..+|+++..|++....-|.+-|+
T Consensus 157 ~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 157 YEDIASVMQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4678999999999998887655554443
No 191
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=33.41 E-value=1.1e+02 Score=24.11 Aligned_cols=29 Identities=14% Similarity=0.134 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..+|++...|+.....-|.+.|+
T Consensus 149 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 149 SVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999888655555543
No 192
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=33.00 E-value=1.2e+02 Score=23.89 Aligned_cols=46 Identities=9% Similarity=0.029 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
.+++.|..++.-.|-.. ....++|..||+++..|+....+-+.+.+
T Consensus 127 ~Lp~~~R~v~~L~~~~g------~s~~EIA~~lgis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG------MKQKDIAQALDIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35555555555544333 13567899999999999988875554443
No 193
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=33.00 E-value=52 Score=21.57 Aligned_cols=20 Identities=25% Similarity=0.398 Sum_probs=17.6
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQ 72 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQ 72 (195)
..++|+.+|+++..|+.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999985
No 194
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=32.96 E-value=1.1e+02 Score=25.07 Aligned_cols=46 Identities=15% Similarity=0.325 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
.+++.+..++...|... ....++|..+|+++..|..+...-+.+.+
T Consensus 178 ~L~~~~r~vl~l~y~~~------~s~~eIA~~lgis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 178 ALPERERRILLLRFFED------KTQSEIAERLGISQMHVSRLLRRALKKLR 223 (227)
T ss_pred cCCHHHHHHHHHHHhcC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 46666666666665433 24567899999999999988764444433
No 195
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=32.93 E-value=66 Score=21.94 Aligned_cols=34 Identities=18% Similarity=0.223 Sum_probs=24.9
Q ss_pred HHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 91 RANYDSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 91 ~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
+.+.+.|+.....|...+..|..|+..|+.....
T Consensus 13 rEEVevLK~~I~eL~~~n~~Le~EN~~Lk~~~~p 46 (59)
T PF01166_consen 13 REEVEVLKEQIAELEERNSQLEEENNLLKQNASP 46 (59)
T ss_dssp TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCH
Confidence 4455667777777778888888888888876543
No 196
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=32.93 E-value=1.2e+02 Score=24.17 Aligned_cols=29 Identities=14% Similarity=0.106 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.-.++|..+|++...|++-...-|.+-|+
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 34678999999999998776554444443
No 197
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=32.57 E-value=93 Score=23.55 Aligned_cols=42 Identities=19% Similarity=0.324 Sum_probs=34.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHH
Q 029338 27 RRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRA 76 (195)
Q Consensus 27 ~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRa 76 (195)
..+++..+..+...+... ....|+.||++..-|+.|=|+|+.
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 358899999998887666 456899999999999999988753
No 198
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=32.42 E-value=1e+02 Score=25.88 Aligned_cols=46 Identities=13% Similarity=0.254 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
.+++.+..+|...|-.. ....++|..+|+++..|+.+...-+.+-|
T Consensus 205 ~L~~~~r~vl~l~~~~g------~s~~eIA~~l~is~~tV~~~~~ra~~kLr 250 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN------LSQKETGERLGISQMHVSRLQRQAIKKLR 250 (257)
T ss_pred hCCHHHHHHHHHHHhCC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45666666776665443 13467899999999999988765554444
No 199
>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....
Probab=32.35 E-value=3e+02 Score=23.69 Aligned_cols=57 Identities=25% Similarity=0.424 Sum_probs=28.1
Q ss_pred hhHHHHHHHhhHHHHHH---------HHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHH
Q 029338 64 PRQVAIWFQNKRARWKS---------KQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNE 120 (195)
Q Consensus 64 ~rQVkvWFQNRRak~Kr---------kq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~ 120 (195)
...+..||+.+=...+. .....+...++.....|..+..+++..+..|...+..|..
T Consensus 186 ~~e~e~~y~~k~~~l~~~~~~~~~~~~~~~~E~~~~r~~~~~l~~el~~l~~~~~~Le~~l~~le~ 251 (312)
T PF00038_consen 186 REELEEWYQSKLEELRQQSEKSSEELESAKEELKELRRQIQSLQAELESLRAKNASLERQLRELEQ 251 (312)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhhhcccccccccccccccccccchhHhHHHHHHhhhhHhhhhhhccccchhhhhhhHHHHHH
Confidence 45788999887433332 1223333334444444444444444444444444444443
No 200
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=32.29 E-value=1.7e+02 Score=20.22 Aligned_cols=33 Identities=21% Similarity=0.120 Sum_probs=14.5
Q ss_pred HHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHH
Q 029338 89 QLRANYDSLASGFESLIKEKESLLLELQMLNEQ 121 (195)
Q Consensus 89 ~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~ 121 (195)
.|-..|..|..+|..|..+...+..|...|.+.
T Consensus 11 ~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ek 43 (65)
T TIGR02449 11 HLLEYLERLKSENRLLRAQEKTWREERAQLLEK 43 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333344444444444444444444444444443
No 201
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=32.15 E-value=1.8e+02 Score=24.93 Aligned_cols=29 Identities=10% Similarity=0.155 Sum_probs=23.5
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWKSK 81 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~Krk 81 (195)
-.++|..+|+++..|+..+..-|.+-+..
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 45689999999999999998777766653
No 202
>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=32.11 E-value=2e+02 Score=20.81 Aligned_cols=36 Identities=19% Similarity=0.458 Sum_probs=25.7
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhh
Q 029338 25 NKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNK 74 (195)
Q Consensus 25 ~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNR 74 (195)
.++.|+..++..|.... ..+.+|++..+|+..+...
T Consensus 35 g~R~y~~~di~~l~~i~--------------~lr~~g~~l~~i~~~~~~~ 70 (103)
T cd01106 35 GYRLYTEEDLERLQQIL--------------FLKELGFSLKEIKELLKDP 70 (103)
T ss_pred CceeeCHHHHHHHHHHH--------------HHHHcCCCHHHHHHHHHcC
Confidence 45679999888885543 2456788888888888654
No 203
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=32.04 E-value=1.1e+02 Score=23.82 Aligned_cols=29 Identities=14% Similarity=0.154 Sum_probs=21.6
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.-.++|..+|++...|......-|.+.++
T Consensus 154 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 154 SLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999998887655555443
No 204
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=31.62 E-value=1.6e+02 Score=25.16 Aligned_cols=42 Identities=31% Similarity=0.396 Sum_probs=25.2
Q ss_pred hHHHHHHHHHhhHH-HhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 83 IEHDYAQLRANYDS-LASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 83 ~~~e~~~l~~~~~~-L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
...+...++.+... ...+|..+..|+++|..++.+++..+..
T Consensus 99 Q~~~f~kiRsel~S~e~sEF~~lr~e~EklkndlEk~ks~lr~ 141 (220)
T KOG3156|consen 99 QKVDFAKIRSELVSIERSEFANLRAENEKLKNDLEKLKSSLRH 141 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444443332 3456666777888888888877776653
No 205
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=31.61 E-value=2.2e+02 Score=21.29 Aligned_cols=44 Identities=18% Similarity=0.155 Sum_probs=29.9
Q ss_pred HHHHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHh
Q 029338 79 KSKQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQL 122 (195)
Q Consensus 79 Krkq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l 122 (195)
|+....++....+.+.+.|..-.+.+++|....+.+++.|...+
T Consensus 56 krE~A~E~~Y~r~~EkEqL~~Lk~kl~~e~~~~~k~i~~le~~I 99 (100)
T PF04568_consen 56 KREAAQEEQYFRKKEKEQLKKLKEKLKEEIEHHRKEIDELEKHI 99 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34444555556666667777777777777777788888777654
No 206
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=31.59 E-value=1.2e+02 Score=18.34 Aligned_cols=36 Identities=19% Similarity=0.336 Sum_probs=24.4
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHH
Q 029338 30 SDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQ 72 (195)
Q Consensus 30 t~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQ 72 (195)
++.+..++...+ . .+ ...++|..+|++...|..+..
T Consensus 2 ~~~e~~i~~~~~--~-~~----s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--E-GK----TNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--c-CC----CHHHHHHHHCCCHHHHHHHHH
Confidence 445555654433 2 21 456789999999999998875
No 207
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=31.46 E-value=63 Score=23.16 Aligned_cols=22 Identities=27% Similarity=0.382 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHHHHhccc
Q 029338 104 LIKEKESLLLELQMLNEQLGKS 125 (195)
Q Consensus 104 l~~e~~~L~~e~~~l~~~l~~~ 125 (195)
+.+|+..|+.++++|.+.|+..
T Consensus 5 i~eEn~~Lk~eiqkle~ELq~~ 26 (76)
T PF07334_consen 5 IQEENARLKEEIQKLEAELQQN 26 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4455666666666555555543
No 208
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=31.44 E-value=1.7e+02 Score=20.68 Aligned_cols=45 Identities=20% Similarity=0.205 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHhhc----CCCCCHHHHHHHHHHhCCChhHHHHHHH
Q 029338 28 RFSDEQIRLLESIFESE----STKLEPRKKMQVATELGLQPRQVAIWFQ 72 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~----~~~ps~~~r~~LA~~LgLt~rQVkvWFQ 72 (195)
.++.+|+..|...|... ..+.+..+...+...+|++...|...|.
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 46788999999998774 2357777777777778888877777764
No 209
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=31.41 E-value=1.5e+02 Score=23.43 Aligned_cols=46 Identities=13% Similarity=0.120 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
+++.+..++.-.|-.. ..-.++|..+|++..-|++....-|.+-++
T Consensus 132 Lp~~~r~v~~l~~~~g------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (191)
T PRK12520 132 LPPRTGRVFMMREWLE------LETEEICQELQITATNAWVLLYRARMRLRE 177 (191)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455555554444333 235678999999999999988766666554
No 210
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=31.24 E-value=1.2e+02 Score=24.94 Aligned_cols=46 Identities=15% Similarity=0.228 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
.+++.+..+|...|-.. ....++|..+|++...|+.+...-+.+-|
T Consensus 175 ~L~~~~r~il~l~y~~~------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE------LNLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred hCCHHHHHHHHHHHhCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 45666677776666444 23567899999999999888765554444
No 211
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=31.24 E-value=1.3e+02 Score=24.12 Aligned_cols=28 Identities=14% Similarity=0.099 Sum_probs=20.2
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
-.++|..||+++..|++....-|.+.++
T Consensus 135 ~~EIA~~Lgis~~tVk~~l~Rar~~Lr~ 162 (187)
T PRK12516 135 YEEAAEICGCAVGTIKSRVNRARQRLQE 162 (187)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4567889999999888887655544443
No 212
>PF04728 LPP: Lipoprotein leucine-zipper; InterPro: IPR006817 This repeating sequence, NAKVDQLSNDV, is found in the enterobacterial outer membrane lipoprotein LPP. The outer membrane lipoprotein is the most abundant protein in an Escherichia coli cell. The messenger RNA for the lipoprotein of the E. coli outer membrane codes for a putative precursor, prolipoprotein, which has 20 additional amino acid residues extending from the amino terminus of the lipoprotein.; GO: 0019867 outer membrane; PDB: 1JCC_A 2GUV_C 2GUS_A 1JCD_A 1KFM_A 1T8Z_D 1KFN_A 1EQ7_A.
Probab=31.22 E-value=1.7e+02 Score=19.75 Aligned_cols=46 Identities=24% Similarity=0.294 Sum_probs=34.4
Q ss_pred HHHHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 79 KSKQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 79 Krkq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
|-.++..+...|....+.|......++.+....+.|..+.+..|.+
T Consensus 4 kid~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~RlDN 49 (56)
T PF04728_consen 4 KIDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRLDN 49 (56)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445666777788888888888888888888888888777776654
No 213
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=31.15 E-value=1.4e+02 Score=23.17 Aligned_cols=28 Identities=14% Similarity=0.245 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
.-.++|..+|++...|++...+-+.+.+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3567899999999999998866555544
No 214
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=31.11 E-value=2e+02 Score=22.82 Aligned_cols=52 Identities=17% Similarity=0.230 Sum_probs=39.7
Q ss_pred HhhHHHHH--HHHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhc
Q 029338 72 QNKRARWK--SKQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLG 123 (195)
Q Consensus 72 QNRRak~K--rkq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~ 123 (195)
+|-|.|.- +...+.+...|.++.+.|+.++..+..|.+.+..-...|..-..
T Consensus 66 ~sCR~KRv~Qk~eLE~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l~~~~~ 119 (135)
T KOG4196|consen 66 QSCRVKRVQQKHELEKEKAELQQQVEKLKEENSRLRRELDAYKSKYEALQNSAV 119 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 44444432 34567777888999999999999999999999988888887654
No 215
>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=30.94 E-value=1.9e+02 Score=20.25 Aligned_cols=42 Identities=24% Similarity=0.367 Sum_probs=32.6
Q ss_pred hHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 83 IEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 83 ~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
-+..|..|+..+.....++..|...+..|-.+|..|...+.+
T Consensus 26 Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~Ls~ql~r 67 (70)
T PF04899_consen 26 WQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQRLSEQLER 67 (70)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 355777788888877777788888888888888888877765
No 216
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=30.91 E-value=1.4e+02 Score=21.68 Aligned_cols=34 Identities=29% Similarity=0.454 Sum_probs=18.2
Q ss_pred HHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHH
Q 029338 85 HDYAQLRANYDSLASGFESLIKEKESLLLELQML 118 (195)
Q Consensus 85 ~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l 118 (195)
.+|+.+....+.|-.....|.+-+.+|..+++.|
T Consensus 26 ~E~~~ins~LD~Lns~LD~LE~rnD~l~~~L~~L 59 (83)
T PF03670_consen 26 EEYAAINSMLDQLNSCLDHLEQRNDHLHAQLQEL 59 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence 4555565555555555555555555555444443
No 217
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=30.79 E-value=2.8e+02 Score=27.97 Aligned_cols=21 Identities=19% Similarity=0.338 Sum_probs=14.3
Q ss_pred CCHHHHHHHHHHhCCChhHHH
Q 029338 48 LEPRKKMQVATELGLQPRQVA 68 (195)
Q Consensus 48 ps~~~r~~LA~~LgLt~rQVk 68 (195)
|....-..+|+.+|+++.-|.
T Consensus 485 ~g~S~a~~iA~~~Glp~~ii~ 505 (782)
T PRK00409 485 PGKSNAFEIAKRLGLPENIIE 505 (782)
T ss_pred CCCcHHHHHHHHhCcCHHHHH
Confidence 444456677888888877654
No 218
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=30.21 E-value=1.8e+02 Score=27.79 Aligned_cols=43 Identities=23% Similarity=0.270 Sum_probs=22.5
Q ss_pred HHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhc
Q 029338 81 KQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLG 123 (195)
Q Consensus 81 kq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~ 123 (195)
...+..++.++++.+.+......+......|..+++.|+.++.
T Consensus 79 sELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~ 121 (475)
T PRK13729 79 AQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVK 121 (475)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 3344444445544444444444455555566666666666653
No 219
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=30.07 E-value=1.6e+02 Score=23.39 Aligned_cols=29 Identities=14% Similarity=0.201 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.-.++|..+|+++..|++-+..-|.+.++
T Consensus 172 s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 172 SYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34568999999999998776655554444
No 220
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=29.99 E-value=46 Score=20.82 Aligned_cols=23 Identities=22% Similarity=0.359 Sum_probs=18.9
Q ss_pred HHHHHHHhCCChhHHHHHHHhhH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKR 75 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRR 75 (195)
..+||..+|+++..|..|..+++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 46799999999999999998744
No 221
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=29.97 E-value=2e+02 Score=24.64 Aligned_cols=29 Identities=17% Similarity=0.209 Sum_probs=23.5
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWKSK 81 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~Krk 81 (195)
-.++|..+|+++.-|+...+.-|.+-+..
T Consensus 134 ~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 134 FDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 46789999999999999998766666653
No 222
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=29.80 E-value=1.6e+02 Score=27.11 Aligned_cols=33 Identities=21% Similarity=0.206 Sum_probs=14.8
Q ss_pred HhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 92 ANYDSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 92 ~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
..+..|...+..+..+..++..++.+++..+.+
T Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (398)
T PTZ00454 29 KELEFLDIQEEYIKEEQKNLKRELIRAKEEVKR 61 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444444444444444444444433
No 223
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=29.71 E-value=3.1e+02 Score=27.60 Aligned_cols=21 Identities=10% Similarity=0.145 Sum_probs=13.6
Q ss_pred CCHHHHHHHHHHhCCChhHHH
Q 029338 48 LEPRKKMQVATELGLQPRQVA 68 (195)
Q Consensus 48 ps~~~r~~LA~~LgLt~rQVk 68 (195)
|....-..+|+.+|+++.-|.
T Consensus 480 ~g~S~a~~iA~~~Glp~~ii~ 500 (771)
T TIGR01069 480 PGESYAFEIAQRYGIPHFIIE 500 (771)
T ss_pred CCCcHHHHHHHHhCcCHHHHH
Confidence 444455667888888776554
No 224
>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=29.65 E-value=2.4e+02 Score=23.00 Aligned_cols=44 Identities=14% Similarity=0.275 Sum_probs=23.3
Q ss_pred HhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhccc
Q 029338 82 QIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKS 125 (195)
Q Consensus 82 q~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~ 125 (195)
..+.+...|+..++.|..++..|.++...+...-..|-..|.+.
T Consensus 108 ~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L~~Im~RA 151 (161)
T TIGR02894 108 RLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLIDIMDRA 151 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555555555555555555555554444443
No 225
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=29.56 E-value=53 Score=19.15 Aligned_cols=23 Identities=22% Similarity=0.336 Sum_probs=19.3
Q ss_pred HHHHHHHhCCChhHHHHHHHhhH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKR 75 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRR 75 (195)
...+|..+|+++..|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 35789999999999999987753
No 226
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=29.52 E-value=1.4e+02 Score=24.32 Aligned_cols=27 Identities=19% Similarity=0.286 Sum_probs=20.4
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
..++|..||+++..|+++...-|.+-+
T Consensus 157 ~~EIA~~Lgis~~tV~~~l~RArk~Lr 183 (203)
T PRK09647 157 YEEIAATLGVKLGTVRSRIHRGRQQLR 183 (203)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 456899999999999988865444444
No 227
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=29.46 E-value=1.2e+02 Score=25.14 Aligned_cols=28 Identities=14% Similarity=0.095 Sum_probs=20.0
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
.-.++|..||+++..|++....-|.+-+
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr 179 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLA 179 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3467899999999999887764444443
No 228
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=29.41 E-value=1.3e+02 Score=23.95 Aligned_cols=27 Identities=19% Similarity=0.193 Sum_probs=19.3
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
-.++|..+|+++..|++....-|.+-+
T Consensus 130 ~~EIA~~lgis~~tV~~~l~Rar~~Lr 156 (182)
T PRK12511 130 YQEAAAVLGIPIGTLMSRIGRARAALR 156 (182)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 566889999999988888754444433
No 229
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.36 E-value=1.5e+02 Score=21.78 Aligned_cols=42 Identities=19% Similarity=0.311 Sum_probs=31.2
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCC-ChhHHHHHHH
Q 029338 26 KRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGL-QPRQVAIWFQ 72 (195)
Q Consensus 26 R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgL-t~rQVkvWFQ 72 (195)
+.+|+.+....+-..+... .+ ....+|+.+|+ .+.++..|-.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~-g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRG-GD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhc-Cc----cHHHHHHHhCCCChHHHHHHHH
Confidence 6789998776665555544 22 57789999996 9999998864
No 230
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=29.31 E-value=92 Score=33.32 Aligned_cols=59 Identities=15% Similarity=0.191 Sum_probs=52.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHHHH
Q 029338 23 MKNKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82 (195)
Q Consensus 23 rr~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq 82 (195)
+.-+..+-+++..+|-..|-.+ .-|+.....-|....+.+.+++.+||+|-|.|.++.+
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 4456677789999999999999 8899999999999999999999999999999999866
No 231
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=29.12 E-value=40 Score=20.92 Aligned_cols=21 Identities=19% Similarity=0.257 Sum_probs=19.0
Q ss_pred HHHHHhCCChhHHHHHHHhhH
Q 029338 55 QVATELGLQPRQVAIWFQNKR 75 (195)
Q Consensus 55 ~LA~~LgLt~rQVkvWFQNRR 75 (195)
+||..+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999874
No 232
>PF04999 FtsL: Cell division protein FtsL; InterPro: IPR007082 In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein IPR007060 from INTERPRO [], however this interaction may be indirect [].; GO: 0007049 cell cycle, 0016021 integral to membrane
Probab=28.88 E-value=1.3e+02 Score=21.58 Aligned_cols=26 Identities=31% Similarity=0.459 Sum_probs=13.2
Q ss_pred hHHHhhhhHhHHHHHHHHHHHHHHHH
Q 029338 94 YDSLASGFESLIKEKESLLLELQMLN 119 (195)
Q Consensus 94 ~~~L~~~~~~l~~e~~~L~~e~~~l~ 119 (195)
.+.+..+...+..|+..|..|...|.
T Consensus 44 l~~l~~~~~~l~~e~~~L~lE~~~l~ 69 (97)
T PF04999_consen 44 LQQLEKEIDQLQEENERLRLEIATLS 69 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 33444444445555555555555554
No 233
>PF10226 DUF2216: Uncharacterized conserved proteins (DUF2216); InterPro: IPR019359 Proteins in this entry are found in Metazoa and contain a coiled-coil domain. Some annotation suggests it might be PKR, the Hepatitis delta antigen-interacting protein A, but this could not be confirmed.
Probab=28.78 E-value=2.8e+02 Score=23.30 Aligned_cols=24 Identities=17% Similarity=0.135 Sum_probs=17.4
Q ss_pred hhhHhHHHHHHHHHHHHHHHHHHh
Q 029338 99 SGFESLIKEKESLLLELQMLNEQL 122 (195)
Q Consensus 99 ~~~~~l~~e~~~L~~e~~~l~~~l 122 (195)
.++..|+..|++|+.++++|++..
T Consensus 55 ~EIR~LKe~NqkLqedNqELRdLC 78 (195)
T PF10226_consen 55 NEIRGLKEVNQKLQEDNQELRDLC 78 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455667778888888888877654
No 234
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=28.56 E-value=49 Score=21.63 Aligned_cols=17 Identities=35% Similarity=0.563 Sum_probs=13.3
Q ss_pred HHHHHHHhCCChhHHHH
Q 029338 53 KMQVATELGLQPRQVAI 69 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkv 69 (195)
-.+||..+|+++.||+-
T Consensus 31 S~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 31 SQELAEALGITPAQVRK 47 (50)
T ss_dssp HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHCCCHHHhcc
Confidence 45789999999999973
No 235
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=28.41 E-value=1.4e+02 Score=25.59 Aligned_cols=35 Identities=20% Similarity=0.249 Sum_probs=19.4
Q ss_pred HhHHHHHHHHHhhHHHhhhhH---hHHHHHHHHHHHHH
Q 029338 82 QIEHDYAQLRANYDSLASGFE---SLIKEKESLLLELQ 116 (195)
Q Consensus 82 q~~~e~~~l~~~~~~L~~~~~---~l~~e~~~L~~e~~ 116 (195)
....++..|+.++..|..+.. .+++|+++|+..+.
T Consensus 73 ~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL~ 110 (276)
T PRK13922 73 DLREENEELKKELLELESRLQELEQLEAENARLRELLN 110 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 445555555555555555444 45566666666443
No 236
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=28.40 E-value=2.4e+02 Score=25.94 Aligned_cols=13 Identities=38% Similarity=0.401 Sum_probs=4.8
Q ss_pred HHHHHHHHHHHHH
Q 029338 105 IKEKESLLLELQM 117 (195)
Q Consensus 105 ~~e~~~L~~e~~~ 117 (195)
+.+++.|..+++.
T Consensus 252 ~~~~etLEqq~~~ 264 (365)
T KOG2391|consen 252 VAMKETLEQQLQS 264 (365)
T ss_pred HHHHHHHHHHHHH
Confidence 3333333333333
No 237
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=28.35 E-value=77 Score=25.14 Aligned_cols=29 Identities=10% Similarity=0.140 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..+|++...|+.....-|.+.|.
T Consensus 157 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 185 (194)
T PRK12513 157 ELEEIAELTGVPEETVKSRLRYALQKLRE 185 (194)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45778999999999999887766665554
No 238
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=28.34 E-value=1.5e+02 Score=23.79 Aligned_cols=28 Identities=25% Similarity=0.375 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
...++|..||++++.|+..++.=|++.+
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~ 180 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLR 180 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4567899999999999988876664443
No 239
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=28.23 E-value=1.4e+02 Score=26.59 Aligned_cols=51 Identities=24% Similarity=0.242 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+++.+..+|...|.-. +.......+||..+|++...|+.....-+.+-|+
T Consensus 262 ~L~~~~R~vl~lrygL~--~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~ 312 (325)
T PRK05657 262 ELNDKQREVLARRFGLL--GYEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312 (325)
T ss_pred cCCHHHHHHHHHHhccC--CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56777777777666322 2233456788999999999999998766666554
No 240
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=28.22 E-value=70 Score=25.43 Aligned_cols=29 Identities=14% Similarity=0.168 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.-.++|..||+++..|++....-|.+.|+
T Consensus 149 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 177 (193)
T TIGR02947 149 AYKEIAEIMGTPIGTVMSRLHRGRKQLRK 177 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45778999999999999998766655554
No 241
>PRK11546 zraP zinc resistance protein; Provisional
Probab=28.12 E-value=3e+02 Score=21.92 Aligned_cols=17 Identities=35% Similarity=0.397 Sum_probs=8.5
Q ss_pred HhHHHHHHHHHHHHHHH
Q 029338 102 ESLIKEKESLLLELQML 118 (195)
Q Consensus 102 ~~l~~e~~~L~~e~~~l 118 (195)
..+.+|...|+.++..+
T Consensus 92 ~aL~kEI~~Lr~kL~e~ 108 (143)
T PRK11546 92 NAVAKEMENLRQSLDEL 108 (143)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34445555555555533
No 242
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.02 E-value=2.2e+02 Score=20.19 Aligned_cols=22 Identities=27% Similarity=0.197 Sum_probs=9.7
Q ss_pred hHHHhhhhHhHHHHHHHHHHHH
Q 029338 94 YDSLASGFESLIKEKESLLLEL 115 (195)
Q Consensus 94 ~~~L~~~~~~l~~e~~~L~~e~ 115 (195)
...+....+.|..++++|+.+-
T Consensus 41 ~q~~q~~reaL~~eneqlk~e~ 62 (79)
T COG3074 41 VQNAQHQREALERENEQLKEEQ 62 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444444444444444443
No 243
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=27.89 E-value=1.4e+02 Score=23.07 Aligned_cols=28 Identities=7% Similarity=0.106 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
.-.++|..+|++...|++....-|.+-+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 164 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMR 164 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3467889999999999888764444443
No 244
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=27.73 E-value=1.2e+02 Score=25.72 Aligned_cols=46 Identities=20% Similarity=0.326 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
+++.+..+|...|-.. ....++|..+|++...|+.+...-+.+.|.
T Consensus 204 L~~~~r~vl~l~y~~~------~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~ 249 (256)
T PRK07408 204 LEERTREVLEFVFLHD------LTQKEAAERLGISPVTVSRRVKKGLDQLKK 249 (256)
T ss_pred CCHHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4555555555555333 245678999999999999887655555544
No 245
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=27.47 E-value=1.5e+02 Score=24.94 Aligned_cols=46 Identities=11% Similarity=0.218 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
+++.+..++...|... ....++|..+|++...|+..+..-|.+-|.
T Consensus 202 L~~~~r~vl~l~~~~~------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 202 LSEKEQLVISLFYKEE------LTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCHHHHHHHHHHHhcC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4555666666555333 235678999999999999888655555443
No 246
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=27.42 E-value=1.9e+02 Score=24.54 Aligned_cols=31 Identities=13% Similarity=0.284 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Krkq 82 (195)
...++|..+|++...|+++...-|.+-++.-
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999987777766643
No 247
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=27.37 E-value=1.2e+02 Score=21.66 Aligned_cols=30 Identities=20% Similarity=0.155 Sum_probs=23.3
Q ss_pred HHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 95 DSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 95 ~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
+.|..++..|+.+.+.|.+++++++...+=
T Consensus 3 ~ei~eEn~~Lk~eiqkle~ELq~~~~~~qI 32 (76)
T PF07334_consen 3 HEIQEENARLKEEIQKLEAELQQNKREFQI 32 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 356677788889999999999998877443
No 248
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=27.35 E-value=1.4e+02 Score=25.06 Aligned_cols=47 Identities=15% Similarity=0.282 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+++.+..++...|... ....++|..+|+++..|+.+...-+.+-|.
T Consensus 205 ~L~~~~r~ii~l~~~~g------~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN------LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHcCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45666666666665444 134678999999999998887655554443
No 249
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=27.23 E-value=1.6e+02 Score=22.46 Aligned_cols=40 Identities=18% Similarity=0.112 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhh
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNK 74 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNR 74 (195)
+++.+..++.-.|-.. ..-.++|..+|++...|++....-
T Consensus 114 L~~~~r~v~~L~~~~g------~s~~EIA~~l~is~~tV~~~l~ra 153 (161)
T PRK12528 114 LPPLVKRAFLLAQVDG------LGYGEIATELGISLATVKRYLNKA 153 (161)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4444444544444333 134568999999999998887543
No 250
>PF14645 Chibby: Chibby family
Probab=26.93 E-value=1.8e+02 Score=22.16 Aligned_cols=27 Identities=26% Similarity=0.337 Sum_probs=11.9
Q ss_pred HhhhhHhHHHHHHHHHHHHHHHHHHhc
Q 029338 97 LASGFESLIKEKESLLLELQMLNEQLG 123 (195)
Q Consensus 97 L~~~~~~l~~e~~~L~~e~~~l~~~l~ 123 (195)
++.++..|.+||--|+-+++-|-+||.
T Consensus 76 l~~~n~~L~EENN~Lklk~elLlDMLt 102 (116)
T PF14645_consen 76 LRKENQQLEEENNLLKLKIELLLDMLT 102 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333344444444444444444444443
No 251
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=26.83 E-value=2.7e+02 Score=23.95 Aligned_cols=29 Identities=24% Similarity=0.195 Sum_probs=23.2
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWKSK 81 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~Krk 81 (195)
-.++|..||+++..|+.....-|.+-|+.
T Consensus 161 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 189 (324)
T TIGR02960 161 AAETAELLGTSTASVNSALQRARATLDEV 189 (324)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 46789999999999999987666666553
No 252
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=26.76 E-value=94 Score=24.02 Aligned_cols=29 Identities=14% Similarity=0.152 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.-.++|..+|+++..|++.+..-|.+.++
T Consensus 138 s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 138 PQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46788999999999999998766666665
No 253
>PF05700 BCAS2: Breast carcinoma amplified sequence 2 (BCAS2); InterPro: IPR008409 This family consists of several eukaryotic sequences of unknown function. The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins []. BCAS2 is a putative spliceosome associated protein [].
Probab=26.69 E-value=2.9e+02 Score=23.15 Aligned_cols=41 Identities=17% Similarity=0.172 Sum_probs=27.4
Q ss_pred HHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcccc
Q 029338 86 DYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSD 126 (195)
Q Consensus 86 e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~ 126 (195)
....|......+...+-.+..+...|..|+.+|+.......
T Consensus 176 ~L~~Le~~W~~~v~kn~eie~a~~~Le~ei~~l~~~~~~~~ 216 (221)
T PF05700_consen 176 ELRYLEQRWKELVSKNLEIEVACEELEQEIEQLKRKAAELK 216 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 33455566666666666677788888888888877665443
No 254
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=26.55 E-value=2.5e+02 Score=20.26 Aligned_cols=36 Identities=31% Similarity=0.290 Sum_probs=18.3
Q ss_pred HHHHHHhhHHHhhhhHhHHHH-------HHHHHHHHHHHHHHh
Q 029338 87 YAQLRANYDSLASGFESLIKE-------KESLLLELQMLNEQL 122 (195)
Q Consensus 87 ~~~l~~~~~~L~~~~~~l~~e-------~~~L~~e~~~l~~~l 122 (195)
...|+-+.+.|+..+..+..+ ...|..++++|+...
T Consensus 20 I~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E~ 62 (79)
T PRK15422 20 ITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQ 62 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 334444444444444444444 444777777776543
No 255
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=26.42 E-value=1.6e+02 Score=23.81 Aligned_cols=27 Identities=11% Similarity=0.000 Sum_probs=18.9
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
-.++|..+|+++..|+++...-|.+-|
T Consensus 152 ~~EIAe~lgis~~tV~~~l~Rar~~Lr 178 (196)
T PRK12535 152 YEEAAKIADVRVGTIRSRVARARADLI 178 (196)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 456788888888888887755444444
No 256
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=26.37 E-value=1.4e+02 Score=23.47 Aligned_cols=28 Identities=14% Similarity=0.205 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
...++|..+|++...|+.....-|.+.+
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr 172 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLK 172 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3467899999999999888765444444
No 257
>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion
Probab=26.34 E-value=2.8e+02 Score=22.76 Aligned_cols=40 Identities=20% Similarity=0.261 Sum_probs=22.9
Q ss_pred HHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhc
Q 029338 84 EHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLG 123 (195)
Q Consensus 84 ~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~ 123 (195)
..-+..|+.+.+.....|+.|..+...|..+...+++.|.
T Consensus 80 ~qvN~lLReQLEq~~~~N~~L~~dl~klt~~~~~l~~eL~ 119 (182)
T PF15035_consen 80 AQVNALLREQLEQARKANEALQEDLQKLTQDWERLRDELE 119 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555566666666666666666666555554
No 258
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=26.16 E-value=1.9e+02 Score=22.75 Aligned_cols=28 Identities=11% Similarity=0.191 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
...++|..+|++...|++.+..-|.+-|
T Consensus 167 s~~eIA~~l~~s~~tV~~~l~r~r~~L~ 194 (198)
T TIGR02859 167 SYQEIACDLNRHVKSIDNALQRVKRKLE 194 (198)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567899999999999987765554444
No 259
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=26.11 E-value=90 Score=27.63 Aligned_cols=35 Identities=31% Similarity=0.396 Sum_probs=32.0
Q ss_pred CCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 46 TKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 46 ~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
+||+......|+....++..+|..||-|-|.+.+.
T Consensus 120 ~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~ 154 (342)
T KOG0773|consen 120 PYPSKLEKILLAVITKLTLTQVSTWFANARRRLKK 154 (342)
T ss_pred cCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence 89999999999999999999999999998877665
No 260
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=25.70 E-value=2.4e+02 Score=22.45 Aligned_cols=29 Identities=21% Similarity=0.212 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..||+++.-|++....-|.+.++
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKE 174 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35678999999999998887655555544
No 261
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=25.46 E-value=4.7e+02 Score=25.47 Aligned_cols=39 Identities=26% Similarity=0.351 Sum_probs=19.8
Q ss_pred HHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcccc
Q 029338 88 AQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSD 126 (195)
Q Consensus 88 ~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~ 126 (195)
..+.+++..+++.+..+..++..|+.|+.+|...|....
T Consensus 151 ~~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~r 189 (546)
T KOG0977|consen 151 SELEAEINTLKRRIKALEDELKRLKAENSRLREELARAR 189 (546)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Confidence 334445555555555555555555555555555554443
No 262
>PF11418 Scaffolding_pro: Phi29 scaffolding protein; InterPro: IPR024374 This protein is also referred to as Gp7. The protein contains a DNA-binding function and may have a role in mediating the structural transition from prohead to mature virus and also scaffold release [].Gp7 is arranged within the capsid as a series of concentric shells [].; PDB: 1NOH_C 1NO4_C 3MTU_E 3OA7_A.
Probab=25.21 E-value=2.9e+02 Score=20.44 Aligned_cols=44 Identities=30% Similarity=0.520 Sum_probs=33.5
Q ss_pred HhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhccc
Q 029338 82 QIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKS 125 (195)
Q Consensus 82 q~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~ 125 (195)
+.+..+-..-.+|+.|....+.+.+++..|..-+.+|=.++.-+
T Consensus 30 qlr~~~~sf~sEy~dlT~~~eKl~aek~DL~vsNskLFrQ~~lt 73 (97)
T PF11418_consen 30 QLRESYTSFHSEYEDLTEALEKLTAEKEDLIVSNSKLFRQHGLT 73 (97)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHhCCC
Confidence 44566777788888888888888889988888888876555433
No 263
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=25.02 E-value=1.8e+02 Score=23.05 Aligned_cols=23 Identities=13% Similarity=0.039 Sum_probs=15.7
Q ss_pred HHHHHHHhCCChhHHHHHHHhhH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKR 75 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRR 75 (195)
-.++|..||++...|+.....-|
T Consensus 130 ~~EIA~~Lgis~~tV~~~l~RAr 152 (182)
T PRK12540 130 YEDAAAICGCAVGTIKSRVNRAR 152 (182)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHH
Confidence 45678888888877777665333
No 264
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=24.99 E-value=1.1e+02 Score=23.01 Aligned_cols=30 Identities=20% Similarity=0.097 Sum_probs=22.9
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 50 PRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 50 ~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
.....++|..+|+++..|++....-|.+-+
T Consensus 121 g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr 150 (154)
T TIGR02950 121 EFSYKEIAELLNLSLAKVKSNLFRARKELK 150 (154)
T ss_pred cCcHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 345678899999999999998875555544
No 265
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=24.92 E-value=1.4e+02 Score=24.34 Aligned_cols=37 Identities=27% Similarity=0.264 Sum_probs=32.2
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHH
Q 029338 30 SDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQV 67 (195)
Q Consensus 30 t~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQV 67 (195)
...-+..|...+... .|.+......+|..||++...|
T Consensus 24 rsAlip~L~~aQ~~~-G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 24 RSALIPLLHIAQEQF-GWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hhHHHHHHHHHHHHh-CCCCHHHHHHHHHHhCCCHHHh
Confidence 355688899999999 8999999999999999998764
No 266
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=24.86 E-value=2.3e+02 Score=24.07 Aligned_cols=47 Identities=6% Similarity=0.198 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+++.+..+|...|... ....++|..+|++...|+.....-+.+-|+
T Consensus 212 ~L~~~~r~vl~l~~~~~------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 258 (268)
T PRK06288 212 TLPEREKKVLILYYYED------LTLKEIGKVLGVTESRISQLHTKAVLQLRA 258 (268)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45666666666655443 235678999999999998776554444443
No 267
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=24.70 E-value=1.9e+02 Score=23.73 Aligned_cols=50 Identities=22% Similarity=0.262 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
+++.+..++.-.|... +.....-.++|..+|++...|+.+...-|.+-|+
T Consensus 179 Lp~~~R~v~~L~y~l~--~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 179 LSDREKQIMELRFGLN--GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CCHHHHHHHHHHhccC--CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555555555544100 0112235678999999999998887655544443
No 268
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=24.53 E-value=77 Score=20.74 Aligned_cols=20 Identities=20% Similarity=0.197 Sum_probs=17.1
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQ 72 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQ 72 (195)
..++|+.+|+++..|+.|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35689999999999999964
No 269
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=24.47 E-value=1.9e+02 Score=22.32 Aligned_cols=44 Identities=7% Similarity=0.033 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARW 78 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~ 78 (195)
+++.+..++.-.|-.. ..-.++|..||++...|+....+-+...
T Consensus 119 L~~~~r~v~~L~~~eg------~s~~EIA~~l~is~~tV~~~l~ra~~~~ 162 (168)
T PRK12525 119 LSGKARAAFLMSQLEG------LTYVEIGERLGVSLSRIHQYMVEAFKCC 162 (168)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4455555554444333 2346789999999999887775444433
No 270
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=24.22 E-value=1.3e+02 Score=22.08 Aligned_cols=41 Identities=12% Similarity=0.104 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhH
Q 029338 27 RRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKR 75 (195)
Q Consensus 27 ~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRR 75 (195)
..+++.++..+...+..+ ..+||..+|+++..|.-|-..+.
T Consensus 63 ~~~~~~~i~~~r~~~glt--------q~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 63 GLLTPPEIRRIRKKLGLS--------QREAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred CCcCHHHHHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHCCCC
Confidence 455566665554444333 34688999999999988876544
No 271
>PF07219 HemY_N: HemY protein N-terminus; InterPro: IPR010817 This entry represents the N terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. These are membrane protein involved in a late step of protoheme IX synthesis [].
Probab=24.09 E-value=1.5e+02 Score=21.81 Aligned_cols=31 Identities=19% Similarity=0.376 Sum_probs=24.0
Q ss_pred CChhHHHHHHHhhHHHHHHHHhHHHHHHHHH
Q 029338 62 LQPRQVAIWFQNKRARWKSKQIEHDYAQLRA 92 (195)
Q Consensus 62 Lt~rQVkvWFQNRRak~Krkq~~~e~~~l~~ 92 (195)
=.|..+..||.+||.+.-.+........+-.
T Consensus 42 ~~p~~~~~~~~~rr~~ka~~al~~Gl~al~~ 72 (108)
T PF07219_consen 42 SLPSRVRRWRRRRRRRKAQRALSRGLIALAE 72 (108)
T ss_pred hChHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 3477899999999998888777777766643
No 272
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=24.00 E-value=68 Score=19.79 Aligned_cols=23 Identities=17% Similarity=0.071 Sum_probs=19.7
Q ss_pred HHHHHHHhCCChhHHHHHHHhhH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKR 75 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRR 75 (195)
..+||..+|+++..|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46789999999999999987654
No 273
>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=23.84 E-value=1.6e+02 Score=19.75 Aligned_cols=30 Identities=30% Similarity=0.418 Sum_probs=21.2
Q ss_pred HhHHHHHHHHHhhHHHhhhhHhHHHHHHHH
Q 029338 82 QIEHDYAQLRANYDSLASGFESLIKEKESL 111 (195)
Q Consensus 82 q~~~e~~~l~~~~~~L~~~~~~l~~e~~~L 111 (195)
+...+...+....+.+..++..|+.+...|
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445566677777777777777777777777
No 274
>KOG0249 consensus LAR-interacting protein and related proteins [General function prediction only]
Probab=23.46 E-value=4.1e+02 Score=27.06 Aligned_cols=47 Identities=17% Similarity=0.234 Sum_probs=33.7
Q ss_pred HHHHHHHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHh
Q 029338 76 ARWKSKQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQL 122 (195)
Q Consensus 76 ak~Krkq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l 122 (195)
+..++-...++...++..++.+....+.+..+++.|+.++.+|+...
T Consensus 214 Ale~kn~L~~e~~s~kk~l~~~~~~k~rl~~d~E~Lr~e~~qL~~~~ 260 (916)
T KOG0249|consen 214 ALEDKNRLEQELESVKKQLEEMRHDKDKLRTDIEDLRGELDQLRRSS 260 (916)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence 34445556666667777777777777778888888888888888533
No 275
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=23.42 E-value=89 Score=18.53 Aligned_cols=23 Identities=17% Similarity=0.146 Sum_probs=19.0
Q ss_pred HHHHHHHhCCChhHHHHHHHhhH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKR 75 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRR 75 (195)
..++|..||++...|..|.++.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 35689999999999999986654
No 276
>PF14662 CCDC155: Coiled-coil region of CCDC155
Probab=23.41 E-value=2.3e+02 Score=23.84 Aligned_cols=31 Identities=19% Similarity=0.195 Sum_probs=12.6
Q ss_pred HHHhhHHHhhhhHhHHHHHHHHHHHHHHHHH
Q 029338 90 LRANYDSLASGFESLIKEKESLLLELQMLNE 120 (195)
Q Consensus 90 l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~ 120 (195)
|..++..|++..+.+...+..|..++..|+.
T Consensus 20 L~~en~kL~~~ve~~ee~na~L~~e~~~L~~ 50 (193)
T PF14662_consen 20 LADENAKLQRSVETAEEGNAQLAEEITDLRK 50 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444444444444433333
No 277
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=23.24 E-value=2.1e+02 Score=22.11 Aligned_cols=45 Identities=11% Similarity=0.101 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHH
Q 029338 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79 (195)
Q Consensus 29 ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~K 79 (195)
+++.+..++...|-.. ....++|..||++...|+.=...-|.+.|
T Consensus 141 L~~~~r~vi~l~~~~g------~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr 185 (189)
T TIGR02984 141 LPEDYREVILLRHLEG------LSFAEVAERMDRSEGAVSMLWVRGLARLR 185 (189)
T ss_pred CCHHHHHHHHHHHhcC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4445555554433222 24567889999999888766554444443
No 278
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=22.98 E-value=2.2e+02 Score=22.27 Aligned_cols=25 Identities=16% Similarity=0.222 Sum_probs=17.0
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRAR 77 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRak 77 (195)
-.++|..||+++..|++-...-|.+
T Consensus 156 ~~eIA~~lgis~~~v~~~l~Rar~~ 180 (187)
T PRK12534 156 YEELAARTDTPIGTVKSWIRRGLAK 180 (187)
T ss_pred HHHHHHHhCCChhHHHHHHHHHHHH
Confidence 4567888899888877665443333
No 279
>PF11559 ADIP: Afadin- and alpha -actinin-Binding; InterPro: IPR021622 This family is found in mammals where it is localised at cell-cell adherens junctions [], and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.
Probab=22.94 E-value=3.6e+02 Score=20.81 Aligned_cols=26 Identities=27% Similarity=0.167 Sum_probs=9.8
Q ss_pred hHHHhhhhHhHHHHHHHHHHHHHHHH
Q 029338 94 YDSLASGFESLIKEKESLLLELQMLN 119 (195)
Q Consensus 94 ~~~L~~~~~~l~~e~~~L~~e~~~l~ 119 (195)
...+...+..+..-...+..++++++
T Consensus 96 ~~~l~~~~~~~~~~~k~~kee~~klk 121 (151)
T PF11559_consen 96 ERQLQKQLKSLEAKLKQEKEELQKLK 121 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333333333333333333444433
No 280
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=22.81 E-value=2.2e+02 Score=22.63 Aligned_cols=19 Identities=21% Similarity=0.148 Sum_probs=13.0
Q ss_pred HHHHHHHhCCChhHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWF 71 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWF 71 (195)
-.+||..+|++...|++=.
T Consensus 153 ~~EIA~~lg~s~~tV~~rl 171 (192)
T PRK09643 153 VADAARMLGVAEGTVKSRC 171 (192)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4567888888887775443
No 281
>PF10482 CtIP_N: Tumour-suppressor protein CtIP N-terminal domain; InterPro: IPR019518 CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control []. This N-terminal domain carries a coiled-coil region and is essential for homodimerisation of the protein []. The C-terminal domain is family CtIP_C and carries functionally important CxxC and RHR motifs, absence of which lead cells to grow slowly and show hypersensitivity to genotoxins [].
Probab=22.81 E-value=2.2e+02 Score=22.04 Aligned_cols=20 Identities=30% Similarity=0.408 Sum_probs=9.4
Q ss_pred HHhhhhHhHHHHHHHHHHHH
Q 029338 96 SLASGFESLIKEKESLLLEL 115 (195)
Q Consensus 96 ~L~~~~~~l~~e~~~L~~e~ 115 (195)
.|..+...|++||..|..|+
T Consensus 100 ~L~nE~n~L~eEN~~L~eEl 119 (120)
T PF10482_consen 100 ELTNEMNTLKEENKKLKEEL 119 (120)
T ss_pred HHHHHHHhHHHHHHHHHHHh
Confidence 34444444555555554443
No 282
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=22.65 E-value=2.3e+02 Score=24.82 Aligned_cols=25 Identities=36% Similarity=0.311 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHhcccccc
Q 029338 104 LIKEKESLLLELQMLNEQLGKSDYE 128 (195)
Q Consensus 104 l~~e~~~L~~e~~~l~~~l~~~~~~ 128 (195)
+..+...|..|+++|+.+|.-....
T Consensus 88 ~~~~~~~l~~EN~~Lr~lL~~~~~~ 112 (284)
T COG1792 88 LLEEVESLEEENKRLKELLDFKESS 112 (284)
T ss_pred HHHHHHHHHHHHHHHHHHhCCcccc
Confidence 4457888899999999988766554
No 283
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=22.55 E-value=1.7e+02 Score=22.07 Aligned_cols=24 Identities=17% Similarity=0.264 Sum_probs=20.4
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHh
Q 029338 50 PRKKMQVATELGLQPRQVAIWFQN 73 (195)
Q Consensus 50 ~~~r~~LA~~LgLt~rQVkvWFQN 73 (195)
......||..+|++++.+..+|+.
T Consensus 25 ~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 356788999999999999999964
No 284
>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.
Probab=22.54 E-value=2.6e+02 Score=19.03 Aligned_cols=41 Identities=15% Similarity=0.292 Sum_probs=25.0
Q ss_pred hHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhc
Q 029338 83 IEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLG 123 (195)
Q Consensus 83 ~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~ 123 (195)
...+....+..+-.+..........+..|..++..|+..|.
T Consensus 16 ~~eEL~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~e 56 (61)
T PF08826_consen 16 IQEELTKVKSANLAFESKLQEAEKRNRELEQEIERLKKEME 56 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44445555655655555555556667777777777766653
No 285
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=22.38 E-value=1.8e+02 Score=23.22 Aligned_cols=36 Identities=17% Similarity=0.160 Sum_probs=28.1
Q ss_pred HHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHH
Q 029338 32 EQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVA 68 (195)
Q Consensus 32 eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVk 68 (195)
.-+.+|...=+.. .|.+.+....+|..||+++.+|.
T Consensus 24 ~li~~L~~vQ~~~-G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 24 ALLPILHAIQDEF-GYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHH
Confidence 3455665555666 89999999999999999997753
No 286
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=22.37 E-value=2.1e+02 Score=23.48 Aligned_cols=39 Identities=15% Similarity=0.301 Sum_probs=25.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQ 72 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQ 72 (195)
.+++.+..++...|... ....++|..+|+++..|..+-.
T Consensus 183 ~L~~~e~~i~~~~~~~~------~t~~eIA~~lgis~~~V~~~~~ 221 (231)
T TIGR02885 183 KLDERERQIIMLRYFKD------KTQTEVANMLGISQVQVSRLEK 221 (231)
T ss_pred cCCHHHHHHHHHHHHcC------CCHHHHHHHHCcCHHHHHHHHH
Confidence 45556666666555333 2467789999999988876643
No 287
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=22.31 E-value=2.7e+02 Score=24.24 Aligned_cols=29 Identities=24% Similarity=0.144 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 52 KKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 52 ~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
...++|..||+++..|+.-...-|.+.|+
T Consensus 171 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 171 SAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 35678999999999999988766665555
No 288
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=22.03 E-value=4.6e+02 Score=23.83 Aligned_cols=53 Identities=15% Similarity=0.198 Sum_probs=26.5
Q ss_pred HHHHHHhhHHHHHHH-HhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHH
Q 029338 67 VAIWFQNKRARWKSK-QIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLN 119 (195)
Q Consensus 67 VkvWFQNRRak~Krk-q~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~ 119 (195)
.+|||+|.|+-.+-. +.....+.+..-...+......-.++-..|-.+++++-
T Consensus 16 CKiWi~dN~~Sv~~He~GkrHke~V~Kritdi~rks~~kekeekKls~~la~mE 69 (336)
T KOG0150|consen 16 CKIWIKDNPASVRFHERGKRHKENVAKRITDIHRKSLKKEKEEKKLSKELAAME 69 (336)
T ss_pred hhhhhcCChHHHHhHhhhhHHHHHHHHHHHHHHHhhHHHHHHHHhhhhHHHHHH
Confidence 589999988766542 22333344444444444332222234444444554443
No 289
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=22.00 E-value=1.4e+02 Score=27.12 Aligned_cols=37 Identities=16% Similarity=0.027 Sum_probs=16.1
Q ss_pred HHHHHHhhHHHhhhhHhHHHHH---HHHHHHHHHHHHHhc
Q 029338 87 YAQLRANYDSLASGFESLIKEK---ESLLLELQMLNEQLG 123 (195)
Q Consensus 87 ~~~l~~~~~~L~~~~~~l~~e~---~~L~~e~~~l~~~l~ 123 (195)
+-.+..+++.|+.++..|..+. +.+..++..|+..+.
T Consensus 59 y~~L~~EN~~Lk~Ena~L~~~l~~~e~l~~En~~Lr~ll~ 98 (337)
T PRK14872 59 ALVLETENFLLKERIALLEERLKSYEEANQTPPLFSEILS 98 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3444444444444444443322 233455555554443
No 290
>PF03980 Nnf1: Nnf1 ; InterPro: IPR007128 NNF1 is an essential yeast gene required for proper spindle orientation, nucleolar and nuclear envelope structure and mRNA export [].
Probab=21.99 E-value=1.9e+02 Score=21.15 Aligned_cols=29 Identities=24% Similarity=0.339 Sum_probs=17.1
Q ss_pred HHhhHHHhhhhHhHHHHHHHHHHHHHHHH
Q 029338 91 RANYDSLASGFESLIKEKESLLLELQMLN 119 (195)
Q Consensus 91 ~~~~~~L~~~~~~l~~e~~~L~~e~~~l~ 119 (195)
....+.|......+..+|..|..+++.++
T Consensus 79 ~~~~~~L~~~l~~l~~eN~~L~~~i~~~r 107 (109)
T PF03980_consen 79 KKEREQLNARLQELEEENEALAEEIQEQR 107 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44445555555666666666666666554
No 291
>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=21.98 E-value=3.1e+02 Score=23.15 Aligned_cols=30 Identities=27% Similarity=0.282 Sum_probs=11.8
Q ss_pred HHHHHhhHHHhhhhHhHHHHHHHHHHHHHH
Q 029338 88 AQLRANYDSLASGFESLIKEKESLLLELQM 117 (195)
Q Consensus 88 ~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~ 117 (195)
..+...|..|..+.+.+..++..|...+..
T Consensus 52 ~~L~~e~~~l~~e~e~L~~~~~~l~~~v~~ 81 (251)
T PF11932_consen 52 QELLAEYRQLEREIENLEVYNEQLERQVAS 81 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444444333333333333
No 292
>PRK10651 transcriptional regulator NarL; Provisional
Probab=21.83 E-value=2.1e+02 Score=21.85 Aligned_cols=46 Identities=13% Similarity=0.199 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+|+.+..+|+-....- .-.++|++++++.+.|++..+|=|.|-.-
T Consensus 155 ~Lt~rE~~vl~~l~~g~-------~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 155 QLTPRERDILKLIAQGL-------PNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred cCCHHHHHHHHHHHcCC-------CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 48999998887655322 24567999999999999998887766653
No 293
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=21.63 E-value=2.7e+02 Score=22.95 Aligned_cols=43 Identities=12% Similarity=0.191 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQ 72 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQ 72 (195)
.+++.+..++...|-.. . .......++|..+|++...|..+-.
T Consensus 175 ~Lp~~~R~i~~l~y~~~-~-~e~~S~~EIA~~lgis~~tV~~~~~ 217 (233)
T PRK05803 175 ILDEREKEVIEMRYGLG-N-GKEKTQREIAKALGISRSYVSRIEK 217 (233)
T ss_pred hCCHHHHHHHHHHhCCC-C-CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 34555555555544111 0 1123466789999999999977743
No 294
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=21.53 E-value=2.6e+02 Score=21.23 Aligned_cols=24 Identities=25% Similarity=0.284 Sum_probs=16.0
Q ss_pred HHHHHHHhCCChhHHHHHHHhhHH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKRA 76 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRRa 76 (195)
..++|..+|++..-|+.-...-+.
T Consensus 124 ~~eIA~~lgis~~tv~~~l~ra~~ 147 (159)
T PRK12527 124 HQQIAEHLGISRSLVEKHIVNAMK 147 (159)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHH
Confidence 456778888888777766653333
No 295
>PF14662 CCDC155: Coiled-coil region of CCDC155
Probab=21.52 E-value=4.3e+02 Score=22.22 Aligned_cols=29 Identities=41% Similarity=0.527 Sum_probs=13.4
Q ss_pred HHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 96 SLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 96 ~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
.|.+....+.+|+++|.++++.|++...+
T Consensus 85 ~L~aq~rqlEkE~q~L~~~i~~Lqeen~k 113 (193)
T PF14662_consen 85 SLLAQARQLEKEQQSLVAEIETLQEENGK 113 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 33333334444555555555555544433
No 296
>PRK10403 transcriptional regulator NarP; Provisional
Probab=21.51 E-value=2.1e+02 Score=21.71 Aligned_cols=46 Identities=13% Similarity=0.286 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+|+.+..+|.-..... ...+||..++++++.|++...|=|.|-..
T Consensus 153 ~Lt~~e~~vl~~~~~g~-------s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 153 VLTERELDVLHELAQGL-------SNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred cCCHHHHHHHHHHHCCC-------CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 57888888887654322 34678999999999999998876666543
No 297
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=21.36 E-value=1.8e+02 Score=22.71 Aligned_cols=34 Identities=21% Similarity=0.350 Sum_probs=24.5
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHH
Q 029338 34 IRLLESIFESESTKLEPRKKMQVATELGLQPRQVA 68 (195)
Q Consensus 34 ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVk 68 (195)
+.+|...=+.. .|.+.+....+|..||+++.+|.
T Consensus 16 l~~L~~~Q~~~-g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 16 LPILHEVQEEY-GYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHH-SS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHc-CCCCHHHHHHHHHHHCCCHHHHH
Confidence 55665555556 89999999999999999998754
No 298
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=21.21 E-value=3.7e+02 Score=22.26 Aligned_cols=51 Identities=8% Similarity=0.147 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+++.+..+|...|... . .......++|..+|++...|+.....-..|.|.
T Consensus 176 ~L~~~er~vl~l~ygl~-~-~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~ 226 (238)
T TIGR02393 176 TLTERERKVLRMRYGLL-D-GRPHTLEEVGKEFNVTRERIRQIESKALRKLRH 226 (238)
T ss_pred hCCHHHHHHHHHHhCCC-C-CCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 46677777777777322 1 122346788999999999999887765555554
No 299
>KOG3335 consensus Predicted coiled-coil protein [General function prediction only]
Probab=21.09 E-value=3.1e+02 Score=22.84 Aligned_cols=55 Identities=20% Similarity=0.250 Sum_probs=35.3
Q ss_pred HHHHHHHhhHHHHHHHHhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhccccc
Q 029338 66 QVAIWFQNKRARWKSKQIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSDY 127 (195)
Q Consensus 66 QVkvWFQNRRak~Krkq~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~~ 127 (195)
...+|.+-|-.+.|..+...+. ..|....+.|..+.+.+...+..|...+..+..
T Consensus 87 v~Ey~R~~~~e~~kee~~~~e~-------~elr~~~~~l~~~i~~~~~~~~~L~~~l~~~~~ 141 (181)
T KOG3335|consen 87 VFEYWRQARKERKKEEKRKQEI-------MELRLKVEKLENAIAELTKFFSQLHSKLNKPES 141 (181)
T ss_pred eehhHHhhhcchhhHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCccc
Confidence 3466766655555544444444 445555666677888888888888877777653
No 300
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.92 E-value=1.1e+02 Score=22.29 Aligned_cols=22 Identities=27% Similarity=0.315 Sum_probs=18.7
Q ss_pred HHHHHHHhCCChhHHHHHHHhh
Q 029338 53 KMQVATELGLQPRQVAIWFQNK 74 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNR 74 (195)
..++|+.+|+++..|+.|.+..
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~G 24 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEIG 24 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3578999999999999998654
No 301
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=20.89 E-value=1.4e+02 Score=17.45 Aligned_cols=20 Identities=20% Similarity=0.391 Sum_probs=14.4
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQ 72 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQ 72 (195)
...-|...||+..+|+..+.
T Consensus 8 Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 8 LIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 34569999999999998774
No 302
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=20.84 E-value=3.6e+02 Score=20.04 Aligned_cols=36 Identities=8% Similarity=0.273 Sum_probs=27.8
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhh
Q 029338 25 NKRRFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNK 74 (195)
Q Consensus 25 ~R~~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNR 74 (195)
..+.|+..++..|. .....+.+|++-..|+..+.+.
T Consensus 34 gyR~Y~~~~l~~l~--------------~I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 34 LRRQYDPQVLDRLA--------------LIALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred CceecCHHHHHHHH--------------HHHHHHHcCCCHHHHHHHHhcc
Confidence 56789998888873 3345788899999999888764
No 303
>PF06210 DUF1003: Protein of unknown function (DUF1003); InterPro: IPR010406 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.83 E-value=3.7e+02 Score=20.26 Aligned_cols=17 Identities=35% Similarity=0.468 Sum_probs=9.0
Q ss_pred HhhHHHHHHHHhHHHHH
Q 029338 72 QNKRARWKSKQIEHDYA 88 (195)
Q Consensus 72 QNRRak~Krkq~~~e~~ 88 (195)
|||-++.-+.+.+.++.
T Consensus 57 QNRq~~~dr~ra~~D~~ 73 (108)
T PF06210_consen 57 QNRQAARDRLRAELDYQ 73 (108)
T ss_pred hhHhHHHHHHHHHHHHH
Confidence 67655544444444443
No 304
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=20.74 E-value=2.1e+02 Score=24.44 Aligned_cols=47 Identities=17% Similarity=0.263 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHHHHHHhhHHHHHH
Q 029338 28 RFSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80 (195)
Q Consensus 28 ~ft~eQ~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVkvWFQNRRak~Kr 80 (195)
.+++.+..+|...|... ....++|..+|++...|+.+...-+.+.|.
T Consensus 215 ~L~~rer~vl~l~y~~~------~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 215 ALPERERTVLVLRFFES------MTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred cCCHHHHHHHHHHhcCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35556666666665333 235778999999999999887655554443
No 305
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=20.72 E-value=2.3e+02 Score=27.50 Aligned_cols=43 Identities=23% Similarity=0.321 Sum_probs=32.7
Q ss_pred HhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhcc
Q 029338 82 QIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGK 124 (195)
Q Consensus 82 q~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~ 124 (195)
..+.++..++..+..|..+...|+.|+.+|..+++.++.++..
T Consensus 152 ~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~r~~ld~ 194 (546)
T KOG0977|consen 152 ELEAEINTLKRRIKALEDELKRLKAENSRLREELARARKQLDD 194 (546)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence 4567777778888888888888888888888888887765543
No 306
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. 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 two 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=20.63 E-value=96 Score=22.01 Aligned_cols=20 Identities=30% Similarity=0.546 Sum_probs=17.1
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q 029338 53 KMQVATELGLQPRQVAIWFQ 72 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQ 72 (195)
..++|+.+|+++..++.|-.
T Consensus 4 i~evA~~~gvs~~tLR~ye~ 23 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWEE 23 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999943
No 307
>PF10205 KLRAQ: Predicted coiled-coil domain-containing protein; InterPro: IPR019343 This entry represents a N-terminal 100 residues long domain, which contains a conserved KLRAQ motif. This domain is found in a family of coiled-coil domain-containing proteins that are conserved from nematodes to humans. These proteins also contain a C-terminal TTKRSYEDQ motif domain (IPR019348 from INTERPRO). The function of these proteins is not known.
Probab=20.52 E-value=3.8e+02 Score=20.20 Aligned_cols=40 Identities=20% Similarity=0.259 Sum_probs=28.2
Q ss_pred HHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhccc
Q 029338 86 DYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKS 125 (195)
Q Consensus 86 e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~ 125 (195)
+...-.+..-.+..++++|..-|++|...+..|+..+...
T Consensus 34 ~Lk~ke~~LRk~eqE~dSL~FrN~QL~kRV~~LQ~El~~~ 73 (102)
T PF10205_consen 34 QLKEKEQALRKLEQENDSLTFRNQQLTKRVEVLQEELEES 73 (102)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3333344555666777888888888888888888888743
No 308
>PF15397 DUF4618: Domain of unknown function (DUF4618)
Probab=20.47 E-value=3e+02 Score=24.09 Aligned_cols=40 Identities=15% Similarity=0.151 Sum_probs=26.0
Q ss_pred HHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhccccc
Q 029338 88 AQLRANYDSLASGFESLIKEKESLLLELQMLNEQLGKSDY 127 (195)
Q Consensus 88 ~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~~~~~ 127 (195)
..+..+...-+...+.++.+.+.|+++|+.|+.....++.
T Consensus 189 ~~m~kei~~~re~i~el~e~I~~L~~eV~~L~~~~~~~Re 228 (258)
T PF15397_consen 189 QVMQKEIVQFREEIDELEEEIPQLRAEVEQLQAQAQDPRE 228 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHH
Confidence 3334444444555566777888888888888877775543
No 309
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=20.33 E-value=1.1e+02 Score=27.81 Aligned_cols=26 Identities=15% Similarity=-0.088 Sum_probs=11.2
Q ss_pred HhhHHHhhhhHhHHHHHHHHHHHHHH
Q 029338 92 ANYDSLASGFESLIKEKESLLLELQM 117 (195)
Q Consensus 92 ~~~~~L~~~~~~l~~e~~~L~~e~~~ 117 (195)
..|-.|..+|+.|++|+..|..++..
T Consensus 57 ~~y~~L~~EN~~Lk~Ena~L~~~l~~ 82 (337)
T PRK14872 57 SHALVLETENFLLKERIALLEERLKS 82 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444444333
No 310
>PHA00489 scaffolding protein
Probab=20.25 E-value=2.5e+02 Score=20.91 Aligned_cols=42 Identities=33% Similarity=0.593 Sum_probs=31.6
Q ss_pred HhHHHHHHHHHhhHHHhhhhHhHHHHHHHHHHHHHHHHHHhc
Q 029338 82 QIEHDYAQLRANYDSLASGFESLIKEKESLLLELQMLNEQLG 123 (195)
Q Consensus 82 q~~~e~~~l~~~~~~L~~~~~~l~~e~~~L~~e~~~l~~~l~ 123 (195)
+.+..+...-.+|+.|....+.+.+++..|..-+.+|=..+.
T Consensus 31 qlr~~ygSf~sEy~elT~a~eKl~aek~DLivsNskLFrqlg 72 (101)
T PHA00489 31 QLRESYGSFHSEYEELTEALEKLTAEKEDLIVSNSKLFRQLG 72 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHcC
Confidence 456667777778888888888888888888888877765554
No 311
>PHA01976 helix-turn-helix protein
Probab=20.19 E-value=94 Score=20.25 Aligned_cols=23 Identities=13% Similarity=0.212 Sum_probs=19.3
Q ss_pred HHHHHHHhCCChhHHHHHHHhhH
Q 029338 53 KMQVATELGLQPRQVAIWFQNKR 75 (195)
Q Consensus 53 r~~LA~~LgLt~rQVkvWFQNRR 75 (195)
..+||..+|+++..|..|...++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46789999999999999986543
No 312
>smart00595 MADF subfamily of SANT domain.
Probab=20.12 E-value=2.8e+02 Score=19.03 Aligned_cols=32 Identities=25% Similarity=0.399 Sum_probs=26.0
Q ss_pred HHHHHHhCCChhHHHHHHHhhHHHHHHHHhHH
Q 029338 54 MQVATELGLQPRQVAIWFQNKRARWKSKQIEH 85 (195)
Q Consensus 54 ~~LA~~LgLt~rQVkvWFQNRRak~Krkq~~~ 85 (195)
..||.++|.+...|+.-+.|=|.+.++.....
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~ 62 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELKRL 62 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999888888754443
No 313
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=20.04 E-value=2.1e+02 Score=22.52 Aligned_cols=35 Identities=23% Similarity=0.180 Sum_probs=27.1
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHHH
Q 029338 33 QIRLLESIFESESTKLEPRKKMQVATELGLQPRQVA 68 (195)
Q Consensus 33 Q~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQVk 68 (195)
-+.+|...=... .|.+......+|..+|+++.+|.
T Consensus 24 ll~~L~~vQ~~~-g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 24 VIPALKIVQEQR-GWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHh-CCCCHHHHHHHHHHhCcCHHHHH
Confidence 345555555555 89999999999999999998753
No 314
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=20.01 E-value=2.2e+02 Score=22.28 Aligned_cols=34 Identities=26% Similarity=0.249 Sum_probs=26.1
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhHH
Q 029338 33 QIRLLESIFESESTKLEPRKKMQVATELGLQPRQV 67 (195)
Q Consensus 33 Q~~~Le~~F~~~~~~ps~~~r~~LA~~LgLt~rQV 67 (195)
-+.+|...=... .|.+.+....+|..||+++.+|
T Consensus 18 li~~L~~vQ~~~-G~i~~~~~~~iA~~l~~~~~~v 51 (148)
T TIGR01958 18 IMPALMIAQEQK-GWVTPEAIAAVAEMLGIPPVWV 51 (148)
T ss_pred HHHHHHHHHHHh-CCCCHHHHHHHHHHhCcCHHHH
Confidence 345555544555 7999999999999999998764
Done!