Query 022702
Match_columns 293
No_of_seqs 321 out of 1689
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 05:31:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022702.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022702hhsearch_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 2.1E-24 4.6E-29 192.1 14.2 105 74-178 47-151 (198)
2 KOG0842 Transcription factor t 99.8 1.9E-19 4E-24 169.2 6.5 58 84-141 160-217 (307)
3 KOG0489 Transcription factor z 99.8 2.2E-19 4.9E-24 166.5 4.8 63 75-137 157-219 (261)
4 KOG0488 Transcription factor B 99.7 1.9E-18 4E-23 163.8 7.6 57 81-137 176-232 (309)
5 KOG0487 Transcription factor A 99.7 1.6E-17 3.5E-22 156.3 8.5 64 76-139 234-297 (308)
6 KOG0843 Transcription factor E 99.7 1.3E-17 2.9E-22 145.1 5.8 64 76-139 101-164 (197)
7 KOG0485 Transcription factor N 99.7 5.4E-17 1.2E-21 145.0 7.9 59 78-136 105-163 (268)
8 KOG0484 Transcription factor P 99.7 2.8E-17 6.1E-22 131.7 4.7 62 76-137 16-77 (125)
9 KOG0850 Transcription factor D 99.7 3.6E-16 7.9E-21 140.7 11.2 65 72-136 117-181 (245)
10 KOG0492 Transcription factor M 99.7 2.3E-16 5E-21 140.1 9.4 61 77-137 144-204 (246)
11 PF00046 Homeobox: Homeobox do 99.6 2.6E-16 5.6E-21 112.7 6.2 57 78-134 1-57 (57)
12 KOG0848 Transcription factor C 99.6 4.4E-16 9.5E-21 142.8 8.8 55 83-137 205-259 (317)
13 KOG0494 Transcription factor C 99.6 3.6E-16 7.8E-21 142.8 7.3 57 83-139 147-203 (332)
14 KOG2251 Homeobox transcription 99.6 1.8E-16 3.8E-21 142.0 5.1 63 75-137 35-97 (228)
15 KOG0844 Transcription factor E 99.6 3.6E-16 7.7E-21 145.6 4.6 65 75-139 179-243 (408)
16 KOG4577 Transcription factor L 99.6 6.6E-15 1.4E-19 136.3 9.5 80 75-154 165-244 (383)
17 KOG0493 Transcription factor E 99.5 1.1E-14 2.5E-19 133.2 4.9 59 78-136 247-305 (342)
18 cd00086 homeodomain Homeodomai 99.5 3.4E-14 7.4E-19 101.5 6.1 57 79-135 2-58 (59)
19 smart00389 HOX Homeodomain. DN 99.5 2.8E-14 6E-19 101.3 5.1 55 79-133 2-56 (56)
20 COG5576 Homeodomain-containing 99.5 5E-14 1.1E-18 121.7 6.2 66 73-138 47-112 (156)
21 TIGR01565 homeo_ZF_HD homeobox 99.4 9.1E-14 2E-18 101.3 4.6 52 78-129 2-57 (58)
22 KOG0491 Transcription factor B 99.4 2.3E-14 5E-19 123.4 1.4 57 80-136 103-159 (194)
23 KOG0847 Transcription factor, 99.4 2.2E-13 4.8E-18 122.2 3.3 58 80-137 170-227 (288)
24 KOG0486 Transcription factor P 99.4 3.3E-13 7.2E-18 126.3 4.2 56 83-138 118-173 (351)
25 KOG3802 Transcription factor O 99.3 8E-13 1.7E-17 127.4 3.3 61 76-136 293-353 (398)
26 KOG0490 Transcription factor, 99.2 1.2E-11 2.5E-16 110.7 3.2 62 75-136 58-119 (235)
27 KOG0849 Transcription factor P 99.0 4.6E-10 1E-14 108.6 5.7 62 76-137 175-236 (354)
28 KOG1168 Transcription factor A 98.8 1.5E-09 3.2E-14 101.1 2.4 64 73-136 305-368 (385)
29 KOG0775 Transcription factor S 98.7 9.3E-09 2E-13 95.2 4.6 51 84-134 183-233 (304)
30 PF05920 Homeobox_KN: Homeobox 98.3 6.2E-07 1.4E-11 60.7 2.8 34 98-131 7-40 (40)
31 KOG0774 Transcription factor P 98.2 8.9E-07 1.9E-11 81.8 2.4 59 77-135 188-249 (334)
32 KOG0490 Transcription factor, 98.0 5.5E-06 1.2E-10 74.1 4.8 62 75-136 151-212 (235)
33 PF02183 HALZ: Homeobox associ 98.0 1.9E-05 4.1E-10 54.8 5.5 42 135-176 1-42 (45)
34 KOG2252 CCAAT displacement pro 97.8 2.9E-05 6.3E-10 78.2 6.0 60 73-132 416-475 (558)
35 KOG1146 Homeobox protein [Gene 97.6 0.0001 2.2E-09 80.5 5.9 64 74-137 900-963 (1406)
36 PF11569 Homez: Homeodomain le 96.3 0.0024 5.2E-08 46.3 2.1 41 89-129 10-50 (56)
37 KOG0773 Transcription factor M 96.3 0.0032 6.9E-08 60.4 3.5 59 78-136 240-301 (342)
38 smart00340 HALZ homeobox assoc 95.2 0.045 9.8E-07 37.4 4.6 33 135-167 1-33 (44)
39 KOG4005 Transcription factor X 95.0 0.21 4.5E-06 46.3 9.7 45 126-170 82-128 (292)
40 KOG3623 Homeobox transcription 94.7 0.034 7.4E-07 58.3 4.4 48 89-136 568-615 (1007)
41 PF04218 CENP-B_N: CENP-B N-te 93.8 0.19 4E-06 35.7 5.3 46 78-128 1-46 (53)
42 PRK09413 IS2 repressor TnpA; R 92.8 1.2 2.7E-05 36.5 9.6 43 79-126 8-51 (121)
43 KOG4196 bZIP transcription fac 90.9 6.5 0.00014 33.3 11.7 79 82-172 22-114 (135)
44 PF02183 HALZ: Homeobox associ 90.3 0.96 2.1E-05 31.3 5.3 32 138-169 11-42 (45)
45 PF00170 bZIP_1: bZIP transcri 88.0 4 8.8E-05 29.6 7.6 35 140-174 27-61 (64)
46 PF06005 DUF904: Protein of un 87.8 2.8 6.1E-05 31.9 6.8 37 137-173 23-59 (72)
47 KOG3119 Basic region leucine z 87.7 2 4.4E-05 40.3 7.3 49 128-179 207-255 (269)
48 smart00338 BRLZ basic region l 85.6 5.9 0.00013 28.8 7.4 36 140-175 27-62 (65)
49 PF06005 DUF904: Protein of un 84.8 5.8 0.00013 30.1 7.1 43 133-175 12-54 (72)
50 PF00170 bZIP_1: bZIP transcri 84.3 6.7 0.00015 28.5 7.2 39 131-169 25-63 (64)
51 PRK00888 ftsB cell division pr 82.5 3.5 7.5E-05 33.4 5.5 48 119-167 15-62 (105)
52 PRK00888 ftsB cell division pr 82.5 4 8.6E-05 33.1 5.8 35 140-174 28-62 (105)
53 KOG4571 Activating transcripti 79.5 6.9 0.00015 37.3 7.1 39 138-176 247-285 (294)
54 PF06156 DUF972: Protein of un 76.8 9 0.0002 31.3 6.2 40 135-174 18-57 (107)
55 PRK13169 DNA replication intia 76.0 9.8 0.00021 31.3 6.2 37 136-172 19-55 (110)
56 smart00338 BRLZ basic region l 73.7 18 0.0004 26.2 6.7 37 133-169 27-63 (65)
57 PF07716 bZIP_2: Basic region 73.5 20 0.00044 25.1 6.6 28 141-168 27-54 (54)
58 PF01527 HTH_Tnp_1: Transposas 72.8 0.89 1.9E-05 33.5 -0.6 44 79-126 2-45 (76)
59 PF04545 Sigma70_r4: Sigma-70, 71.0 8.7 0.00019 26.1 4.2 40 83-127 4-43 (50)
60 PRK10884 SH3 domain-containing 70.8 35 0.00076 30.9 9.1 37 139-175 132-168 (206)
61 PF10224 DUF2205: Predicted co 70.2 28 0.00062 27.0 7.2 40 133-172 24-63 (80)
62 cd01109 HTH_YyaN Helix-Turn-He 69.8 51 0.0011 26.4 9.1 73 80-167 35-107 (113)
63 PF13443 HTH_26: Cro/C1-type H 69.5 5.3 0.00012 28.2 2.9 40 106-145 12-51 (63)
64 TIGR02449 conserved hypothetic 69.0 23 0.00049 26.5 6.2 25 140-164 22-46 (65)
65 cd01106 HTH_TipAL-Mta Helix-Tu 68.8 42 0.0009 26.4 8.2 37 80-129 35-71 (103)
66 PF10224 DUF2205: Predicted co 68.1 35 0.00075 26.5 7.3 48 129-176 13-60 (80)
67 PF06156 DUF972: Protein of un 67.4 23 0.00049 28.9 6.5 47 133-179 9-55 (107)
68 PRK10722 hypothetical protein; 67.2 1.1E+02 0.0024 28.6 13.4 81 98-178 116-208 (247)
69 PF04977 DivIC: Septum formati 66.8 17 0.00038 26.7 5.4 29 137-165 22-50 (80)
70 cd04770 HTH_HMRTR Helix-Turn-H 66.8 58 0.0013 26.3 8.9 72 80-166 35-106 (123)
71 cd04779 HTH_MerR-like_sg4 Heli 66.8 63 0.0014 27.2 9.3 73 80-165 34-107 (134)
72 TIGR02051 MerR Hg(II)-responsi 66.6 51 0.0011 27.0 8.6 70 80-166 34-103 (124)
73 PRK15422 septal ring assembly 65.6 30 0.00066 26.8 6.4 12 158-169 51-62 (79)
74 cd06171 Sigma70_r4 Sigma70, re 64.8 6.7 0.00014 25.6 2.5 43 83-130 10-52 (55)
75 cd04783 HTH_MerR1 Helix-Turn-H 63.1 70 0.0015 26.1 8.8 72 80-168 35-106 (126)
76 PF07795 DUF1635: Protein of u 61.8 80 0.0017 29.0 9.5 46 129-174 23-68 (214)
77 KOG3335 Predicted coiled-coil 61.3 42 0.00091 29.9 7.4 50 117-166 84-133 (181)
78 KOG1962 B-cell receptor-associ 61.2 21 0.00046 32.7 5.8 39 135-173 161-199 (216)
79 PF08172 CASP_C: CASP C termin 61.1 35 0.00075 31.8 7.3 43 129-171 90-132 (248)
80 KOG4343 bZIP transcription fac 60.9 14 0.00031 38.1 5.0 32 142-173 305-336 (655)
81 KOG3755 SATB1 matrix attachmen 60.9 3.6 7.8E-05 42.9 0.8 48 89-136 704-758 (769)
82 KOG1146 Homeobox protein [Gene 60.8 8.1 0.00018 43.7 3.5 57 81-137 448-504 (1406)
83 cd00569 HTH_Hin_like Helix-tur 60.7 19 0.00042 20.7 3.9 39 82-125 4-42 (42)
84 COG3074 Uncharacterized protei 60.6 43 0.00094 25.5 6.3 17 145-161 45-61 (79)
85 PRK10884 SH3 domain-containing 60.5 32 0.0007 31.1 6.8 32 141-172 127-158 (206)
86 PRK13169 DNA replication intia 59.3 39 0.00085 27.8 6.5 45 134-178 10-54 (110)
87 KOG0249 LAR-interacting protei 59.1 36 0.00079 36.5 7.7 45 130-174 214-258 (916)
88 PF07407 Seadorna_VP6: Seadorn 59.1 12 0.00025 36.6 3.8 23 143-165 36-58 (420)
89 PF05377 FlaC_arch: Flagella a 58.3 43 0.00093 24.3 5.7 37 135-171 3-39 (55)
90 COG2919 Septum formation initi 58.0 54 0.0012 26.8 7.2 29 140-168 58-86 (117)
91 cd04765 HTH_MlrA-like_sg2 Heli 57.8 34 0.00075 27.1 5.8 39 80-130 35-73 (99)
92 KOG3863 bZIP transcription fac 57.6 1.7E+02 0.0037 30.9 12.1 53 123-175 500-554 (604)
93 PRK03975 tfx putative transcri 57.1 31 0.00067 29.5 5.7 48 81-134 4-51 (141)
94 COG4026 Uncharacterized protei 56.7 41 0.00089 31.3 6.7 30 139-168 149-178 (290)
95 KOG4196 bZIP transcription fac 56.1 52 0.0011 28.0 6.8 34 135-168 84-117 (135)
96 PF04880 NUDE_C: NUDE protein, 56.0 14 0.00031 32.5 3.6 24 153-176 24-47 (166)
97 PF01166 TSC22: TSC-22/dip/bun 55.9 19 0.00041 26.4 3.6 28 139-166 14-41 (59)
98 TIGR02209 ftsL_broad cell divi 55.8 43 0.00093 25.2 5.9 29 138-166 30-58 (85)
99 PF08172 CASP_C: CASP C termin 55.0 84 0.0018 29.3 8.7 48 134-181 88-135 (248)
100 PRK13922 rod shape-determining 54.9 28 0.00062 32.2 5.7 34 142-175 72-108 (276)
101 cd04787 HTH_HMRTR_unk Helix-Tu 54.4 1.2E+02 0.0026 25.0 8.9 76 80-170 35-110 (133)
102 PF04967 HTH_10: HTH DNA bindi 54.0 16 0.00034 26.1 2.9 39 84-122 1-41 (53)
103 PF10668 Phage_terminase: Phag 53.5 8.1 0.00018 28.4 1.4 18 107-124 25-42 (60)
104 PF04977 DivIC: Septum formati 53.0 46 0.001 24.4 5.6 33 140-172 18-50 (80)
105 cd04769 HTH_MerR2 Helix-Turn-H 52.7 89 0.0019 25.2 7.6 78 80-171 34-111 (116)
106 TIGR02894 DNA_bind_RsfA transc 52.2 48 0.001 29.1 6.2 28 141-168 106-133 (161)
107 TIGR03752 conj_TIGR03752 integ 52.1 41 0.00088 34.3 6.5 53 83-138 41-93 (472)
108 COG3074 Uncharacterized protei 52.1 70 0.0015 24.4 6.2 36 140-175 26-61 (79)
109 TIGR02209 ftsL_broad cell divi 51.9 54 0.0012 24.6 5.9 39 121-159 20-58 (85)
110 PRK13729 conjugal transfer pil 51.0 41 0.00088 34.4 6.4 43 133-175 77-119 (475)
111 PF04899 MbeD_MobD: MbeD/MobD 50.9 74 0.0016 24.1 6.3 42 135-176 24-65 (70)
112 PF15058 Speriolin_N: Sperioli 50.6 29 0.00063 31.4 4.7 36 139-175 5-40 (200)
113 PF07888 CALCOCO1: Calcium bin 50.5 2.6E+02 0.0057 29.2 12.1 34 143-176 421-454 (546)
114 PF13942 Lipoprotein_20: YfhG 50.2 1.2E+02 0.0026 27.0 8.4 75 97-176 69-160 (179)
115 PF05529 Bap31: B-cell recepto 50.1 38 0.00082 29.7 5.5 29 139-167 161-189 (192)
116 COG4467 Regulator of replicati 49.9 44 0.00094 27.6 5.2 30 140-169 23-52 (114)
117 PF08281 Sigma70_r4_2: Sigma-7 49.7 34 0.00073 23.3 4.1 40 84-128 11-50 (54)
118 PF08961 DUF1875: Domain of un 49.1 5.7 0.00012 36.6 0.0 38 135-172 125-162 (243)
119 PF04728 LPP: Lipoprotein leuc 48.1 1.1E+02 0.0023 22.4 6.5 44 133-176 4-47 (56)
120 cd04781 HTH_MerR-like_sg6 Heli 47.8 1.5E+02 0.0032 24.0 8.7 36 80-128 34-69 (120)
121 PHA03308 transcriptional regul 47.6 31 0.00068 37.2 5.0 18 74-91 1291-1308(1463)
122 PF00196 GerE: Bacterial regul 47.5 32 0.0007 24.0 3.7 47 83-135 3-49 (58)
123 TIGR02894 DNA_bind_RsfA transc 47.2 95 0.0021 27.3 7.2 36 136-171 108-143 (161)
124 PF11594 Med28: Mediator compl 46.9 81 0.0018 25.9 6.3 36 119-157 18-53 (106)
125 PF09744 Jnk-SapK_ap_N: JNK_SA 46.2 1.6E+02 0.0034 25.6 8.5 75 88-172 34-108 (158)
126 KOG4005 Transcription factor X 46.1 39 0.00084 31.7 4.9 39 138-176 110-148 (292)
127 TIGR01069 mutS2 MutS2 family p 45.0 78 0.0017 34.2 7.8 18 105-122 483-500 (771)
128 PF11932 DUF3450: Protein of u 44.9 73 0.0016 29.2 6.7 41 135-175 52-92 (251)
129 PRK13922 rod shape-determining 44.8 55 0.0012 30.3 5.9 37 134-170 71-110 (276)
130 PF00038 Filament: Intermediat 44.6 1.1E+02 0.0023 28.7 7.8 56 118-173 186-250 (312)
131 COG4467 Regulator of replicati 43.7 96 0.0021 25.6 6.3 44 135-178 11-54 (114)
132 TIGR00219 mreC rod shape-deter 43.5 85 0.0018 29.6 7.0 34 136-169 70-107 (283)
133 TIGR02047 CadR-PbrR Cd(II)/Pb( 43.4 1.8E+02 0.004 23.8 8.5 72 80-166 35-106 (127)
134 TIGR02449 conserved hypothetic 43.3 1.3E+02 0.0028 22.5 6.5 38 137-174 5-42 (65)
135 KOG2391 Vacuolar sorting prote 43.2 88 0.0019 30.8 7.0 44 129-172 222-265 (365)
136 KOG1962 B-cell receptor-associ 43.0 66 0.0014 29.6 5.9 32 138-169 178-209 (216)
137 cd04784 HTH_CadR-PbrR Helix-Tu 42.8 1.8E+02 0.004 23.6 8.3 73 80-167 35-107 (127)
138 cd04785 HTH_CadR-PbrR-like Hel 42.8 1.9E+02 0.004 23.7 8.4 73 80-167 35-107 (126)
139 PRK14127 cell division protein 42.6 66 0.0014 26.4 5.3 33 144-176 35-67 (109)
140 PF11544 Spc42p: Spindle pole 42.6 1.6E+02 0.0034 22.8 7.6 49 126-174 6-54 (76)
141 KOG3119 Basic region leucine z 42.6 84 0.0018 29.5 6.7 38 135-172 218-255 (269)
142 PF13936 HTH_38: Helix-turn-he 42.4 25 0.00054 23.7 2.4 40 81-125 2-41 (44)
143 PF07407 Seadorna_VP6: Seadorn 42.3 42 0.00092 32.8 4.7 20 139-158 39-58 (420)
144 PF09607 BrkDBD: Brinker DNA-b 42.2 40 0.00087 24.7 3.5 44 81-126 3-47 (58)
145 PF03234 CDC37_N: Cdc37 N term 41.9 1E+02 0.0022 27.4 6.8 45 131-175 31-75 (177)
146 PRK00409 recombination and DNA 41.8 94 0.002 33.7 7.8 17 106-122 489-505 (782)
147 PF07334 IFP_35_N: Interferon- 41.8 48 0.001 25.6 4.1 26 150-175 4-29 (76)
148 cd04777 HTH_MerR-like_sg1 Heli 41.6 1.3E+02 0.0028 23.8 6.8 35 81-128 34-68 (107)
149 PF10883 DUF2681: Protein of u 40.9 1.2E+02 0.0025 24.0 6.2 12 122-133 20-31 (87)
150 KOG0709 CREB/ATF family transc 40.9 4.1E+02 0.0089 27.2 11.5 30 83-112 220-251 (472)
151 TIGR00219 mreC rod shape-deter 40.6 64 0.0014 30.5 5.7 38 140-177 67-108 (283)
152 PF07716 bZIP_2: Basic region 40.4 1.1E+02 0.0024 21.3 5.6 30 144-173 23-52 (54)
153 KOG4571 Activating transcripti 40.2 1.1E+02 0.0023 29.5 7.0 40 133-172 249-288 (294)
154 KOG0150 Spliceosomal protein F 40.0 77 0.0017 30.7 6.0 54 121-174 16-70 (336)
155 cd04766 HTH_HspR Helix-Turn-He 39.9 1E+02 0.0022 23.7 5.8 20 108-127 5-24 (91)
156 PF04999 FtsL: Cell division p 39.5 86 0.0019 24.3 5.4 21 142-162 45-65 (97)
157 PRK15422 septal ring assembly 39.4 1.4E+02 0.0031 23.2 6.3 42 134-175 13-61 (79)
158 TIGR03752 conj_TIGR03752 integ 39.2 1.1E+02 0.0023 31.4 7.2 49 126-174 88-137 (472)
159 PF11932 DUF3450: Protein of u 39.0 1.2E+02 0.0027 27.7 7.2 51 120-170 43-94 (251)
160 PF00424 REV: REV protein (ant 38.9 44 0.00096 26.6 3.6 35 89-137 14-48 (91)
161 PF07989 Microtub_assoc: Micro 38.8 1E+02 0.0023 23.4 5.6 49 121-172 21-69 (75)
162 PF15035 Rootletin: Ciliary ro 38.5 1.1E+02 0.0023 27.3 6.4 40 135-174 77-116 (182)
163 PRK14127 cell division protein 38.2 91 0.002 25.6 5.5 50 115-173 22-71 (109)
164 PF10883 DUF2681: Protein of u 38.2 1.3E+02 0.0028 23.8 6.1 32 129-160 20-51 (87)
165 KOG4403 Cell surface glycoprot 37.9 77 0.0017 32.2 5.9 24 122-145 229-255 (575)
166 PF10481 CENP-F_N: Cenp-F N-te 37.8 1.8E+02 0.0039 27.9 8.0 88 86-176 38-125 (307)
167 PRK04217 hypothetical protein; 37.7 71 0.0015 26.2 4.8 40 83-127 42-81 (110)
168 COG2919 Septum formation initi 37.6 1.2E+02 0.0026 24.8 6.1 53 121-175 34-86 (117)
169 KOG3156 Uncharacterized membra 37.1 77 0.0017 29.1 5.3 41 139-179 101-142 (220)
170 PRK13729 conjugal transfer pil 36.5 1.1E+02 0.0024 31.3 6.9 36 141-176 92-127 (475)
171 PF12325 TMF_TATA_bd: TATA ele 36.4 1.9E+02 0.0041 24.0 7.2 13 102-114 13-25 (120)
172 TIGR02937 sigma70-ECF RNA poly 36.3 69 0.0015 25.1 4.6 44 84-132 111-154 (158)
173 KOG4343 bZIP transcription fac 36.0 1E+02 0.0022 32.1 6.5 39 137-175 307-345 (655)
174 cd04761 HTH_MerR-SF Helix-Turn 35.9 24 0.00052 23.3 1.5 21 108-128 4-24 (49)
175 PRK10072 putative transcriptio 35.9 46 0.00099 26.6 3.3 41 83-130 32-72 (96)
176 PF14662 CCDC155: Coiled-coil 35.8 1.4E+02 0.003 27.0 6.7 40 127-166 83-122 (193)
177 PRK06759 RNA polymerase factor 35.3 82 0.0018 25.7 5.0 43 84-131 107-149 (154)
178 PTZ00454 26S protease regulato 35.2 1.4E+02 0.003 29.6 7.3 43 136-178 26-68 (398)
179 PF14645 Chibby: Chibby family 34.9 1.5E+02 0.0033 24.4 6.3 24 142-165 74-97 (116)
180 PF14197 Cep57_CLD_2: Centroso 34.8 1.7E+02 0.0038 21.8 6.1 24 147-170 41-64 (69)
181 PF05700 BCAS2: Breast carcino 34.4 1.6E+02 0.0036 26.6 7.2 40 137-176 173-212 (221)
182 cd01108 HTH_CueR Helix-Turn-He 34.2 2.6E+02 0.0056 22.8 8.5 74 80-168 35-108 (127)
183 KOG4797 Transcriptional regula 34.0 95 0.0021 25.7 4.9 29 138-166 66-94 (123)
184 cd04786 HTH_MerR-like_sg7 Heli 34.0 2.7E+02 0.006 23.1 9.1 77 80-172 35-111 (131)
185 PRK09646 RNA polymerase sigma 33.8 69 0.0015 27.7 4.4 43 84-131 143-185 (194)
186 KOG0977 Nuclear envelope prote 33.8 1.4E+02 0.003 31.2 7.2 40 136-175 152-191 (546)
187 COG2433 Uncharacterized conser 33.8 1.2E+02 0.0025 32.1 6.6 34 141-174 431-464 (652)
188 PTZ00361 26 proteosome regulat 33.2 1.3E+02 0.0028 30.4 6.8 53 126-178 52-106 (438)
189 COG4026 Uncharacterized protei 33.0 1.7E+02 0.0036 27.4 6.8 31 141-171 137-167 (290)
190 smart00340 HALZ homeobox assoc 32.8 1.1E+02 0.0025 21.0 4.3 29 147-175 6-34 (44)
191 TIGR03879 near_KaiC_dom probab 32.5 16 0.00034 27.9 0.1 34 94-127 22-55 (73)
192 cd01107 HTH_BmrR Helix-Turn-He 32.3 2.5E+02 0.0055 22.2 8.9 67 80-166 36-102 (108)
193 PF05377 FlaC_arch: Flagella a 32.3 1.5E+02 0.0032 21.5 5.1 33 143-175 4-36 (55)
194 PF13815 Dzip-like_N: Iguana/D 32.1 1.8E+02 0.0039 23.6 6.4 38 137-174 78-115 (118)
195 PRK12514 RNA polymerase sigma 32.0 58 0.0013 27.5 3.6 44 84-132 130-173 (179)
196 PRK09652 RNA polymerase sigma 31.8 56 0.0012 27.1 3.5 40 83-127 128-167 (182)
197 cd04775 HTH_Cfa-like Helix-Tur 31.8 2.5E+02 0.0055 22.0 7.9 36 80-128 35-70 (102)
198 PRK11924 RNA polymerase sigma 31.5 82 0.0018 26.0 4.4 44 84-132 126-169 (179)
199 PF06210 DUF1003: Protein of u 31.4 2.5E+02 0.0054 22.9 7.0 17 126-142 57-73 (108)
200 PF13518 HTH_28: Helix-turn-he 31.3 35 0.00075 22.8 1.7 20 107-126 15-34 (52)
201 KOG0288 WD40 repeat protein Ti 31.0 1.6E+02 0.0035 29.7 6.8 13 153-165 55-67 (459)
202 PF03670 UPF0184: Uncharacteri 31.0 1.6E+02 0.0034 23.2 5.4 18 144-161 38-55 (83)
203 KOG1924 RhoA GTPase effector D 30.7 5.2E+02 0.011 28.6 10.8 30 137-166 472-501 (1102)
204 smart00421 HTH_LUXR helix_turn 30.7 99 0.0021 20.2 4.0 39 83-127 3-41 (58)
205 PF10226 DUF2216: Uncharacteri 30.5 3.7E+02 0.008 24.4 8.4 20 140-159 56-75 (195)
206 cd00592 HTH_MerR-like Helix-Tu 30.5 2.5E+02 0.0054 21.5 7.3 38 80-130 34-71 (100)
207 cd04776 HTH_GnyR Helix-Turn-He 30.3 3E+02 0.0064 22.3 9.1 80 80-172 33-113 (118)
208 TIGR02044 CueR Cu(I)-responsiv 30.0 3E+02 0.0066 22.4 9.7 35 79-126 34-68 (127)
209 COG3413 Predicted DNA binding 29.6 79 0.0017 28.2 4.2 38 83-120 155-194 (215)
210 cd07429 Cby_like Chibby, a nuc 29.6 1.6E+02 0.0035 24.2 5.6 21 131-151 78-98 (108)
211 PF12709 Kinetocho_Slk19: Cent 29.5 2.2E+02 0.0049 22.5 6.1 19 144-162 54-72 (87)
212 PF11559 ADIP: Afadin- and alp 29.1 2.9E+02 0.0062 23.1 7.4 20 151-170 99-118 (151)
213 TIGR02985 Sig70_bacteroi1 RNA 28.9 67 0.0014 26.0 3.4 43 84-131 114-156 (161)
214 PF05308 Mito_fiss_reg: Mitoch 28.9 3E+02 0.0065 25.8 8.0 15 158-172 127-141 (253)
215 PF04859 DUF641: Plant protein 28.8 3.6E+02 0.0078 22.8 8.0 34 140-173 95-128 (131)
216 PRK00247 putative inner membra 28.8 4.2E+02 0.0092 26.8 9.5 8 124-131 326-333 (429)
217 PF08614 ATG16: Autophagy prot 28.7 2.9E+02 0.0063 24.3 7.6 35 141-175 153-187 (194)
218 cd04765 HTH_MlrA-like_sg2 Heli 28.7 81 0.0018 24.9 3.7 20 108-127 4-23 (99)
219 PF04420 CHD5: CHD5-like prote 28.6 1.4E+02 0.003 25.8 5.4 18 158-175 71-88 (161)
220 PRK12519 RNA polymerase sigma 28.5 60 0.0013 27.8 3.2 44 84-132 142-185 (194)
221 cd04782 HTH_BltR Helix-Turn-He 28.3 2.8E+02 0.0062 21.5 7.9 36 80-128 35-70 (97)
222 PRK12526 RNA polymerase sigma 28.2 68 0.0015 28.1 3.5 44 84-132 154-197 (206)
223 PRK10869 recombination and rep 27.8 5.4E+02 0.012 26.6 10.4 51 108-158 309-360 (553)
224 cd04766 HTH_HspR Helix-Turn-He 27.8 2.6E+02 0.0057 21.3 6.4 34 80-125 35-68 (91)
225 PF06056 Terminase_5: Putative 27.0 42 0.00091 24.2 1.6 28 106-135 15-42 (58)
226 KOG0773 Transcription factor M 26.8 66 0.0014 30.8 3.4 39 96-134 116-154 (342)
227 PF13411 MerR_1: MerR HTH fami 26.7 36 0.00079 24.2 1.2 20 108-127 4-23 (69)
228 PTZ00454 26S protease regulato 26.7 1.8E+02 0.0039 28.9 6.4 37 139-175 22-58 (398)
229 PF07058 Myosin_HC-like: Myosi 26.6 6.1E+02 0.013 24.8 11.4 55 120-180 109-163 (351)
230 COG2433 Uncharacterized conser 26.6 1.2E+02 0.0027 32.0 5.4 34 142-175 425-458 (652)
231 cd01392 HTH_LacI Helix-turn-he 26.4 66 0.0014 21.5 2.4 21 109-129 2-22 (52)
232 PHA02955 hypothetical protein; 26.3 72 0.0016 29.3 3.3 42 86-127 60-102 (213)
233 PF06305 DUF1049: Protein of u 26.2 83 0.0018 22.5 3.1 20 122-141 38-57 (68)
234 PF05266 DUF724: Protein of un 26.2 4.7E+02 0.01 23.3 9.4 25 96-120 81-105 (190)
235 TIGR00721 tfx DNA-binding prot 25.9 2.9E+02 0.0062 23.5 6.7 47 81-133 4-50 (137)
236 PF07106 TBPIP: Tat binding pr 25.9 1.6E+02 0.0035 25.2 5.3 7 122-128 57-63 (169)
237 PRK15369 two component system 25.7 1.7E+02 0.0037 23.8 5.3 46 83-134 149-194 (211)
238 PF09726 Macoilin: Transmembra 25.5 2.7E+02 0.0059 29.9 7.9 37 130-166 543-579 (697)
239 PRK10403 transcriptional regul 25.5 79 0.0017 26.2 3.3 47 83-135 153-199 (215)
240 PF03980 Nnf1: Nnf1 ; InterPr 25.4 1.8E+02 0.0039 23.0 5.2 32 142-173 76-107 (109)
241 PF08280 HTH_Mga: M protein tr 25.4 60 0.0013 23.0 2.2 34 87-124 6-39 (59)
242 PRK09642 RNA polymerase sigma 25.2 72 0.0016 26.3 3.0 45 84-133 107-151 (160)
243 PF14197 Cep57_CLD_2: Centroso 25.0 3E+02 0.0065 20.6 7.2 15 160-174 47-61 (69)
244 PRK09413 IS2 repressor TnpA; R 24.9 1.5E+02 0.0032 24.1 4.7 25 151-175 76-100 (121)
245 PF03980 Nnf1: Nnf1 ; InterPr 24.7 1.3E+02 0.0028 23.9 4.2 31 138-168 79-109 (109)
246 PF09738 DUF2051: Double stran 24.7 2.7E+02 0.0059 26.8 7.1 62 136-197 130-192 (302)
247 PF08826 DMPK_coil: DMPK coile 24.6 2.9E+02 0.0063 20.3 6.4 30 144-173 30-59 (61)
248 PRK09648 RNA polymerase sigma 24.5 1.2E+02 0.0026 25.9 4.3 39 84-127 140-178 (189)
249 PF13863 DUF4200: Domain of un 24.4 3.7E+02 0.008 21.5 7.3 31 142-172 77-107 (126)
250 PRK12512 RNA polymerase sigma 24.4 1E+02 0.0022 26.1 3.8 45 84-133 132-176 (184)
251 PF01166 TSC22: TSC-22/dip/bun 24.2 1E+02 0.0022 22.6 3.1 37 144-180 12-48 (59)
252 PF04999 FtsL: Cell division p 24.2 3.4E+02 0.0073 20.9 6.5 35 125-159 35-69 (97)
253 PRK05657 RNA polymerase sigma 24.0 1.2E+02 0.0026 29.1 4.5 49 83-132 262-310 (325)
254 TIGR02989 Sig-70_gvs1 RNA poly 23.8 95 0.0021 25.4 3.4 38 84-126 112-149 (159)
255 PF14775 NYD-SP28_assoc: Sperm 23.5 2.8E+02 0.0061 20.1 5.4 19 150-168 37-55 (60)
256 PRK10698 phage shock protein P 23.5 3.4E+02 0.0073 24.7 7.2 44 132-175 92-135 (222)
257 PF08826 DMPK_coil: DMPK coile 23.4 3.1E+02 0.0067 20.2 6.5 39 137-175 16-54 (61)
258 PRK05602 RNA polymerase sigma 23.4 90 0.002 26.5 3.3 42 84-130 129-170 (186)
259 PRK12515 RNA polymerase sigma 23.3 92 0.002 26.6 3.4 45 84-133 132-176 (189)
260 TIGR02043 ZntR Zn(II)-responsi 23.3 4.2E+02 0.0092 21.7 9.3 36 80-128 36-71 (131)
261 PF12325 TMF_TATA_bd: TATA ele 23.2 3.1E+02 0.0067 22.8 6.3 40 136-175 72-111 (120)
262 PF07047 OPA3: Optic atrophy 3 23.0 1.6E+02 0.0034 24.7 4.6 13 122-134 91-103 (134)
263 cd04790 HTH_Cfa-like_unk Helix 22.9 5E+02 0.011 22.5 9.8 69 79-168 35-103 (172)
264 PF13384 HTH_23: Homeodomain-l 22.9 57 0.0012 21.8 1.5 22 105-126 18-39 (50)
265 PF05384 DegS: Sensor protein 22.8 2E+02 0.0043 25.1 5.3 47 138-184 26-72 (159)
266 KOG4752 Ribosomal protein L41 22.8 1.5E+02 0.0031 18.0 3.0 9 129-137 2-10 (26)
267 PF04728 LPP: Lipoprotein leuc 22.4 3.1E+02 0.0068 19.9 5.4 35 141-175 5-39 (56)
268 COG3416 Uncharacterized protei 22.4 3.3E+02 0.0071 25.2 6.7 30 84-113 1-30 (233)
269 PF12808 Mto2_bdg: Micro-tubul 22.4 2.8E+02 0.006 19.8 5.0 18 154-171 30-47 (52)
270 PRK14872 rod shape-determining 22.3 1.3E+02 0.0029 29.4 4.5 19 141-159 59-77 (337)
271 KOG0995 Centromere-associated 22.3 2.4E+02 0.0052 29.6 6.4 30 138-167 293-322 (581)
272 PRK00118 putative DNA-binding 22.2 4.3E+02 0.0092 21.4 7.2 49 84-139 18-66 (104)
273 KOG2264 Exostosin EXT1L [Signa 22.1 2E+02 0.0044 30.5 5.8 38 133-170 101-138 (907)
274 cd04762 HTH_MerR-trunc Helix-T 22.0 65 0.0014 20.5 1.7 24 107-130 3-26 (49)
275 PRK12518 RNA polymerase sigma 22.0 87 0.0019 26.2 2.9 29 105-133 137-165 (175)
276 PF12709 Kinetocho_Slk19: Cent 21.9 4.1E+02 0.0088 21.0 6.4 23 148-170 51-73 (87)
277 PF02796 HTH_7: Helix-turn-hel 21.8 1.1E+02 0.0024 20.4 2.8 38 83-125 5-42 (45)
278 TIGR01242 26Sp45 26S proteasom 21.8 2.3E+02 0.0049 27.2 6.1 38 139-176 6-43 (364)
279 PRK10360 DNA-binding transcrip 21.8 1.1E+02 0.0023 25.3 3.4 45 83-133 137-181 (196)
280 cd04763 HTH_MlrA-like Helix-Tu 21.6 55 0.0012 23.5 1.4 20 108-127 4-23 (68)
281 PRK09639 RNA polymerase sigma 21.5 1.7E+02 0.0037 24.0 4.6 41 84-130 113-153 (166)
282 KOG3650 Predicted coiled-coil 21.5 3.7E+02 0.008 22.0 6.1 38 137-174 68-105 (120)
283 PF11382 DUF3186: Protein of u 21.5 1.6E+02 0.0035 28.1 4.9 22 141-162 41-62 (308)
284 cd04764 HTH_MlrA-like_sg1 Heli 21.5 57 0.0012 23.3 1.4 20 108-127 4-23 (67)
285 TIGR03629 arch_S13P archaeal r 21.4 2E+02 0.0044 24.6 5.0 32 83-132 51-82 (144)
286 PRK06811 RNA polymerase factor 21.4 1.3E+02 0.0028 25.8 3.9 46 84-134 132-177 (189)
287 KOG3584 cAMP response element 21.4 2.1E+02 0.0045 27.7 5.4 29 147-175 313-341 (348)
288 cd01282 HTH_MerR-like_sg3 Heli 21.2 4.3E+02 0.0093 21.0 8.4 35 80-127 34-68 (112)
289 TIGR02977 phageshock_pspA phag 21.2 4E+02 0.0087 23.9 7.2 44 132-175 92-135 (219)
290 PF12824 MRP-L20: Mitochondria 21.1 5.6E+02 0.012 22.4 9.1 48 80-129 82-129 (164)
291 PF04111 APG6: Autophagy prote 21.0 3.2E+02 0.0069 26.2 6.8 37 137-173 55-91 (314)
292 cd06170 LuxR_C_like C-terminal 21.0 1.9E+02 0.0041 18.9 3.9 36 85-126 2-37 (57)
293 PRK03992 proteasome-activating 20.8 3.2E+02 0.0069 26.8 6.9 40 136-175 12-51 (389)
294 PRK09935 transcriptional regul 20.7 1.2E+02 0.0025 25.2 3.4 45 83-133 149-193 (210)
295 TIGR02948 SigW_bacill RNA poly 20.5 96 0.0021 26.1 2.9 44 84-132 137-180 (187)
296 PF09766 FimP: Fms-interacting 20.4 3.2E+02 0.0068 26.7 6.7 49 127-175 7-55 (355)
297 PF08898 DUF1843: Domain of un 20.4 2.8E+02 0.006 20.0 4.6 30 144-173 22-51 (53)
298 KOG3584 cAMP response element 20.4 2E+02 0.0043 27.9 5.1 26 134-159 314-339 (348)
299 PRK09047 RNA polymerase factor 20.4 2.6E+02 0.0056 22.8 5.4 38 84-126 107-144 (161)
300 PF12718 Tropomyosin_1: Tropom 20.3 4.2E+02 0.0092 22.4 6.7 43 133-175 22-64 (143)
301 PF01381 HTH_3: Helix-turn-hel 20.3 59 0.0013 22.0 1.2 22 108-129 13-34 (55)
302 TIGR02939 RpoE_Sigma70 RNA pol 20.2 94 0.002 26.2 2.8 21 106-126 156-176 (190)
303 PF00376 MerR: MerR family reg 20.2 59 0.0013 21.3 1.1 18 108-125 3-20 (38)
304 PRK10100 DNA-binding transcrip 20.1 2.2E+02 0.0048 25.4 5.3 48 83-136 155-202 (216)
305 cd04768 HTH_BmrR-like Helix-Tu 20.0 4.2E+02 0.0091 20.5 7.5 36 80-128 35-70 (96)
306 TIGR02959 SigZ RNA polymerase 20.0 1.2E+02 0.0026 25.5 3.4 39 83-126 100-138 (170)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.92 E-value=2.1e-24 Score=192.11 Aligned_cols=105 Identities=62% Similarity=0.916 Sum_probs=98.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 74 GSQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKA 153 (293)
Q Consensus 74 ~~~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~ 153 (293)
+...++||+||+.+|+..||..|+...|+.+.+|..||+.|||.+|||+|||||||||||.++++.+|+.||.+++.++.
T Consensus 47 ~~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~ 126 (198)
T KOG0483|consen 47 GSKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRS 126 (198)
T ss_pred ccccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhh
Confidence 34456788899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcccc
Q 022702 154 DREALQAQNQKLHAEIMALKSREVT 178 (293)
Q Consensus 154 e~~~l~~e~~~l~~e~~~lk~~~~~ 178 (293)
+++.|+.+++.|.+++..++.....
T Consensus 127 ~~~~Lq~e~~eL~~~~~~~~~~~~~ 151 (198)
T KOG0483|consen 127 ENDRLQSEVQELVAELSSLKREMQK 151 (198)
T ss_pred hhhHHHHHHHHHHHHHhhhhhhhcc
Confidence 9999999999999999887766543
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.78 E-value=1.9e-19 Score=169.25 Aligned_cols=58 Identities=40% Similarity=0.586 Sum_probs=55.5
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDY 141 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~ 141 (293)
|+..|+.+||+.|..++|++..+|+.||..|+|+++||||||||||.|.||+++++.+
T Consensus 160 FSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 160 FSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred cchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhh
Confidence 9999999999999999999999999999999999999999999999999998876643
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.77 E-value=2.2e-19 Score=166.50 Aligned_cols=63 Identities=35% Similarity=0.682 Sum_probs=58.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHH
Q 022702 75 SQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQL 137 (293)
Q Consensus 75 ~~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~ 137 (293)
++.||.|+.||..||.+||+.|..++|+++.+|.+||..|.|+++||||||||||+||||.+.
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence 345667777999999999999999999999999999999999999999999999999998653
No 4
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.75 E-value=1.9e-18 Score=163.82 Aligned_cols=57 Identities=39% Similarity=0.660 Sum_probs=54.0
Q ss_pred CCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHH
Q 022702 81 KRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQL 137 (293)
Q Consensus 81 r~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~ 137 (293)
|+.||..||..||+.|++.+|++..+|++||+.|||+..|||+||||||+||||+..
T Consensus 176 RTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 176 RTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred hhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 444999999999999999999999999999999999999999999999999999764
No 5
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.71 E-value=1.6e-17 Score=156.32 Aligned_cols=64 Identities=36% Similarity=0.556 Sum_probs=58.1
Q ss_pred CCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHH
Q 022702 76 QAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEK 139 (293)
Q Consensus 76 ~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~ 139 (293)
..||||.-+|..|+.+||+.|-.+.|++.+.|.+|++.|+|++|||||||||||+|.||..+|.
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 3455555699999999999999999999999999999999999999999999999999987544
No 6
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.70 E-value=1.3e-17 Score=145.14 Aligned_cols=64 Identities=34% Similarity=0.496 Sum_probs=59.1
Q ss_pred CCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHH
Q 022702 76 QAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEK 139 (293)
Q Consensus 76 ~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~ 139 (293)
+.||.|+.||.+||..||..|+.+.|....+|++||+.|+|++.||||||||||+|.||++.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 4466677799999999999999999999999999999999999999999999999999987553
No 7
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.69 E-value=5.4e-17 Score=144.96 Aligned_cols=59 Identities=39% Similarity=0.622 Sum_probs=54.9
Q ss_pred CCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHH
Q 022702 78 GEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136 (293)
Q Consensus 78 krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~ 136 (293)
||.|+.|+..|+..||..|+..+|++..+|..||++|.|++.||||||||||.||||+-
T Consensus 105 KktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 105 KKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 44455599999999999999999999999999999999999999999999999999965
No 8
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.68 E-value=2.8e-17 Score=131.70 Aligned_cols=62 Identities=24% Similarity=0.447 Sum_probs=57.1
Q ss_pred CCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHH
Q 022702 76 QAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQL 137 (293)
Q Consensus 76 ~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~ 137 (293)
+.+|-|++||..||..||+.|...+||++..|++||.++.|++..|+|||||||||.|++..
T Consensus 16 KQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 16 KQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 44566677999999999999999999999999999999999999999999999999998653
No 9
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.67 E-value=3.6e-16 Score=140.71 Aligned_cols=65 Identities=31% Similarity=0.553 Sum_probs=58.5
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHH
Q 022702 72 DDGSQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136 (293)
Q Consensus 72 ~~~~~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~ 136 (293)
..+.+.|+.|+.|+.-||..|.+.|+++.|+--.+|.+||+.|||+.+||||||||||.|.||..
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 44455566677799999999999999999999999999999999999999999999999999843
No 10
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.67 E-value=2.3e-16 Score=140.10 Aligned_cols=61 Identities=31% Similarity=0.471 Sum_probs=56.5
Q ss_pred CCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHH
Q 022702 77 AGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQL 137 (293)
Q Consensus 77 ~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~ 137 (293)
.|+.|+-||..||..||+.|...+|+++.+|.+++..|.|+++||||||||||||.||.+.
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 3455667999999999999999999999999999999999999999999999999999763
No 11
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.65 E-value=2.6e-16 Score=112.74 Aligned_cols=57 Identities=42% Similarity=0.617 Sum_probs=54.8
Q ss_pred CCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHH
Q 022702 78 GEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKT 134 (293)
Q Consensus 78 krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Kr 134 (293)
|++|++||.+|+..||..|..++||+..++..||..|||+..+|++||+|||+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 467888999999999999999999999999999999999999999999999999986
No 12
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.64 E-value=4.4e-16 Score=142.78 Aligned_cols=55 Identities=42% Similarity=0.573 Sum_probs=52.8
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQL 137 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~ 137 (293)
.+|..|+.+||+.|...+|+.+.+|.+||.-|||++|||||||||||||+||.+.
T Consensus 205 VYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 205 VYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred EecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 4999999999999999999999999999999999999999999999999998763
No 13
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.63 E-value=3.6e-16 Score=142.83 Aligned_cols=57 Identities=28% Similarity=0.481 Sum_probs=53.9
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEK 139 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~ 139 (293)
.||..|+..||+.|+..+||+...|+.||.++.|.+.+|+||||||||||||++..-
T Consensus 147 iFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 147 IFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred hhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 399999999999999999999999999999999999999999999999999976543
No 14
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.63 E-value=1.8e-16 Score=142.05 Aligned_cols=63 Identities=25% Similarity=0.413 Sum_probs=59.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHH
Q 022702 75 SQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQL 137 (293)
Q Consensus 75 ~~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~ 137 (293)
++.+|.|++||.+|+++||..|.+..||+...|++||.+|+|.+.+|+|||+|||||+|+++.
T Consensus 35 RkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 35 RKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred hhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence 455777889999999999999999999999999999999999999999999999999999764
No 15
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.61 E-value=3.6e-16 Score=145.58 Aligned_cols=65 Identities=34% Similarity=0.508 Sum_probs=59.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHH
Q 022702 75 SQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEK 139 (293)
Q Consensus 75 ~~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~ 139 (293)
.+.||-|+.||.+||..||+.|-+.+|.++.+|++||..|+|++..|||||||||+|+||+.+-.
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlam 243 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAM 243 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhc
Confidence 34567777899999999999999999999999999999999999999999999999999987653
No 16
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.58 E-value=6.6e-15 Score=136.31 Aligned_cols=80 Identities=24% Similarity=0.395 Sum_probs=74.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 75 SQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKAD 154 (293)
Q Consensus 75 ~~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e 154 (293)
...||.|+++|..||+.|+..|...++|.+..|++|+.++||..|.|||||||||||+||.+.+.....+.+.+..+|..
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK~s 244 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMKRS 244 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhhcc
Confidence 34578899999999999999999999999999999999999999999999999999999999888888888888888755
No 17
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.51 E-value=1.1e-14 Score=133.20 Aligned_cols=59 Identities=34% Similarity=0.616 Sum_probs=54.6
Q ss_pred CCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHH
Q 022702 78 GEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136 (293)
Q Consensus 78 krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~ 136 (293)
||.|+.||.+||..|+..|..++|+...+|.+||.+|||.+.||||||||+|+|.||..
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 34455699999999999999999999999999999999999999999999999999854
No 18
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.50 E-value=3.4e-14 Score=101.45 Aligned_cols=57 Identities=47% Similarity=0.721 Sum_probs=53.8
Q ss_pred CCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHH
Q 022702 79 EKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTK 135 (293)
Q Consensus 79 rkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk 135 (293)
+++..|+.+|+..||..|..++||+..++..||..+||+.++|++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 456789999999999999999999999999999999999999999999999998863
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.50 E-value=2.8e-14 Score=101.31 Aligned_cols=55 Identities=45% Similarity=0.770 Sum_probs=51.6
Q ss_pred CCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHH
Q 022702 79 EKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133 (293)
Q Consensus 79 rkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~K 133 (293)
+.|.+|+.+|+..||..|..++||+..++..||..+||+..+|++||+|||++.|
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 4566799999999999999999999999999999999999999999999999753
No 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.48 E-value=5e-14 Score=121.66 Aligned_cols=66 Identities=35% Similarity=0.564 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHH
Q 022702 73 DGSQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLE 138 (293)
Q Consensus 73 ~~~~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~ 138 (293)
..+..+++|+|.|.+|+.+|++.|+.++||+...|..|+..|+|+++-|+|||||||++.|++...
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 334567888999999999999999999999999999999999999999999999999999987643
No 21
>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=9.1e-14 Score=101.27 Aligned_cols=52 Identities=13% Similarity=0.309 Sum_probs=49.6
Q ss_pred CCCCCCCCHHHHHHHHHhHhhCCC----CCHHHHHHHHHHhCCCcchhhhhhhhhH
Q 022702 78 GEKKRRLNMEQVKTLEKNFELGNK----LEPERKMQLARALGLQPRQVAIWFQNRR 129 (293)
Q Consensus 78 krkr~rft~~Ql~~LE~~F~~~~~----p~~~~r~~LA~~lgL~~~qVkvWFQNRR 129 (293)
+|.|+.||.+|+..||..|+...| |+..+|.+||..|||++++|||||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 677888999999999999999999 9999999999999999999999999964
No 22
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.44 E-value=2.3e-14 Score=123.41 Aligned_cols=57 Identities=39% Similarity=0.557 Sum_probs=53.8
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~ 136 (293)
-|+.|+..|+..||+.|+.++|++-.+|.+||..|+|+++|||.||||||+|.||.+
T Consensus 103 ~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 103 ARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred hcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 345599999999999999999999999999999999999999999999999999865
No 23
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.37 E-value=2.2e-13 Score=122.18 Aligned_cols=58 Identities=34% Similarity=0.650 Sum_probs=54.3
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQL 137 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~ 137 (293)
.|.+|+..||..||+.|+..+|+-..+|.+||..+|+++.||+|||||||+||||+..
T Consensus 170 srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 170 SRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred cCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 3445999999999999999999999999999999999999999999999999999763
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.37 E-value=3.3e-13 Score=126.35 Aligned_cols=56 Identities=25% Similarity=0.552 Sum_probs=53.4
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLE 138 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~ 138 (293)
-||..||..||..|.+++||+...|++||..++|++.+|+|||.|||+|||+++.-
T Consensus 118 hFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN 173 (351)
T KOG0486|consen 118 HFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERN 173 (351)
T ss_pred hhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhh
Confidence 49999999999999999999999999999999999999999999999999997643
No 25
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.31 E-value=8e-13 Score=127.40 Aligned_cols=61 Identities=26% Similarity=0.412 Sum_probs=56.1
Q ss_pred CCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHH
Q 022702 76 QAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136 (293)
Q Consensus 76 ~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~ 136 (293)
++||||+.|....+..||++|.+|++|+..+...||.+|+|...+|+|||+|||.|.||..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 4455666699999999999999999999999999999999999999999999999999854
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.17 E-value=1.2e-11 Score=110.74 Aligned_cols=62 Identities=26% Similarity=0.305 Sum_probs=57.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHH
Q 022702 75 SQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136 (293)
Q Consensus 75 ~~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~ 136 (293)
...++.|+.|+..|+.+||+.|...+||+...|+.||..++|++..|+|||||||+||+++.
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 34466677799999999999999999999999999999999999999999999999999865
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.99 E-value=4.6e-10 Score=108.61 Aligned_cols=62 Identities=27% Similarity=0.528 Sum_probs=57.2
Q ss_pred CCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHH
Q 022702 76 QAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQL 137 (293)
Q Consensus 76 ~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~ 137 (293)
..+|+|++|+..|+..||+.|++++||+...|+.||.+++|++..|+|||+|||+||+|...
T Consensus 175 ~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 175 GGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 34555678999999999999999999999999999999999999999999999999999764
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.82 E-value=1.5e-09 Score=101.14 Aligned_cols=64 Identities=23% Similarity=0.436 Sum_probs=58.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHH
Q 022702 73 DGSQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136 (293)
Q Consensus 73 ~~~~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~ 136 (293)
.++.+||||+.+-.-....||.+|..++.|+.+....||++|.|....|+|||+|.|.|.||.+
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 4556788888899999999999999999999999999999999999999999999999998854
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.73 E-value=9.3e-09 Score=95.23 Aligned_cols=51 Identities=31% Similarity=0.440 Sum_probs=48.2
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKT 134 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Kr 134 (293)
|...-...|..+|..++||++.+|.+||+++||+..||-.||+|||.|+|.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 667778999999999999999999999999999999999999999999884
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=98.27 E-value=6.2e-07 Score=60.65 Aligned_cols=34 Identities=35% Similarity=0.543 Sum_probs=28.9
Q ss_pred hCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHH
Q 022702 98 LGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR 131 (293)
Q Consensus 98 ~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK 131 (293)
.++||+..++.+||+.+||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4689999999999999999999999999999875
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.16 E-value=8.9e-07 Score=81.83 Aligned_cols=59 Identities=29% Similarity=0.455 Sum_probs=54.2
Q ss_pred CCCCCCCCCHHHHHHHHHhHhh---CCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHH
Q 022702 77 AGEKKRRLNMEQVKTLEKNFEL---GNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTK 135 (293)
Q Consensus 77 ~krkr~rft~~Ql~~LE~~F~~---~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk 135 (293)
.+||||-|+..-.++|..+|.. ++||+.+.+++||+++|++..||-.||.|+|-++||-
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 4678888999999999999964 6799999999999999999999999999999999874
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.03 E-value=5.5e-06 Score=74.07 Aligned_cols=62 Identities=29% Similarity=0.543 Sum_probs=56.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHH
Q 022702 75 SQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136 (293)
Q Consensus 75 ~~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~ 136 (293)
.+.++.++.++..|+..|+..|....+|+...+.+|+..+|+.++.|+|||||+|++.++..
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 34456667799999999999999999999999999999999999999999999999999865
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=97.97 E-value=1.9e-05 Score=54.81 Aligned_cols=42 Identities=48% Similarity=0.779 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 022702 135 KQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSRE 176 (293)
Q Consensus 135 k~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 176 (293)
+++|.+|+.|++.|+.|++++++|+.+++.|++++..|+...
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl 42 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEKL 42 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 478999999999999999999999999999999999998764
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.82 E-value=2.9e-05 Score=78.19 Aligned_cols=60 Identities=22% Similarity=0.226 Sum_probs=54.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHH
Q 022702 73 DGSQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARW 132 (293)
Q Consensus 73 ~~~~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~ 132 (293)
...+.||.|..||..|...|...|+.+++|+.+..+.|+.+|||..+.|..||-|-|.|.
T Consensus 416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 344556677779999999999999999999999999999999999999999999988764
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.56 E-value=0.0001 Score=80.47 Aligned_cols=64 Identities=25% Similarity=0.377 Sum_probs=58.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHH
Q 022702 74 GSQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQL 137 (293)
Q Consensus 74 ~~~~krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~ 137 (293)
+-.++++|++++..||+.|...|....|+...+.+.|...++|..+.|+|||||-|+|.|+..+
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 3345667888999999999999999999999999999999999999999999999999998765
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.33 E-value=0.0024 Score=46.28 Aligned_cols=41 Identities=24% Similarity=0.378 Sum_probs=31.2
Q ss_pred HHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhH
Q 022702 89 VKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRR 129 (293)
Q Consensus 89 l~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRR 129 (293)
+..|+.+|...+++.......|..+.+|+..||+.||--|+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 46799999999999999999999999999999999997554
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.32 E-value=0.0032 Score=60.42 Aligned_cols=59 Identities=29% Similarity=0.300 Sum_probs=48.5
Q ss_pred CCCCCCCCHHHHHHHHHhHhh---CCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHH
Q 022702 78 GEKKRRLNMEQVKTLEKNFEL---GNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136 (293)
Q Consensus 78 krkr~rft~~Ql~~LE~~F~~---~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~ 136 (293)
.|+++.|....+.+|+.+... .+||+..++..||+++||+..||..||-|.|-|..+--
T Consensus 240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence 344456999999999988433 46999999999999999999999999999888766543
No 38
>smart00340 HALZ homeobox associated leucin zipper.
Probab=95.22 E-value=0.045 Score=37.38 Aligned_cols=33 Identities=42% Similarity=0.531 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 135 KQLEKDYDLLKRQYEAVKADREALQAQNQKLHA 167 (293)
Q Consensus 135 k~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~ 167 (293)
++.+.+.+.||+..+.|.+||..|+.|.+.|++
T Consensus 1 KQTEvdCe~LKrcce~LteeNrRL~ke~~eLra 33 (44)
T smart00340 1 KQTEVDCELLKRCCESLTEENRRLQKEVQELRA 33 (44)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 467889999999999999999999988876653
No 39
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=95.01 E-value=0.21 Score=46.26 Aligned_cols=45 Identities=27% Similarity=0.370 Sum_probs=21.9
Q ss_pred hhhHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 126 QNRRARWKTK--QLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIM 170 (293)
Q Consensus 126 QNRRaK~Krk--~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~ 170 (293)
||-|.|.|-+ +.+.+...|..+++.|..||+.|+..+..|..+..
T Consensus 82 QtaRDrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~ 128 (292)
T KOG4005|consen 82 QTARDRKKARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNH 128 (292)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Confidence 5555544432 23333444555555555555555554444444433
No 40
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.74 E-value=0.034 Score=58.31 Aligned_cols=48 Identities=21% Similarity=0.341 Sum_probs=45.3
Q ss_pred HHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHH
Q 022702 89 VKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136 (293)
Q Consensus 89 l~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~ 136 (293)
+..|..+|..+..|+..+...+|..+||..+.|++||++++++...-+
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 788999999999999999999999999999999999999999887755
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=93.75 E-value=0.19 Score=35.74 Aligned_cols=46 Identities=26% Similarity=0.465 Sum_probs=34.3
Q ss_pred CCCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhh
Q 022702 78 GEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNR 128 (293)
Q Consensus 78 krkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNR 128 (293)
||+|+.+|-++-..+=..++.+. ....||+.+|+...+|..|..||
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 46778899998777777777776 46789999999999999999884
No 42
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=92.83 E-value=1.2 Score=36.45 Aligned_cols=43 Identities=26% Similarity=0.439 Sum_probs=28.4
Q ss_pred CCCCCCCHHHHH-HHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhh
Q 022702 79 EKKRRLNMEQVK-TLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQ 126 (293)
Q Consensus 79 rkr~rft~~Ql~-~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQ 126 (293)
++|++|+.++.. ++...+.. .+ ...++|+++|+++.+|..|.+
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~-g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEP-GM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcC-CC----CHHHHHHHHCcCHHHHHHHHH
Confidence 345678888644 33333332 22 245789999999999999954
No 43
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=90.86 E-value=6.5 Score=33.29 Aligned_cols=79 Identities=27% Similarity=0.308 Sum_probs=47.0
Q ss_pred CCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHH----------HHHHHH----HHHHHHHHHHH
Q 022702 82 RRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRA----------RWKTKQ----LEKDYDLLKRQ 147 (293)
Q Consensus 82 ~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRa----------K~Krk~----~~~~~~~lk~~ 147 (293)
.+|+.++|..+ ..|+.=-..-|++...|--|=|-||+ |.||-+ +|.+...|.++
T Consensus 22 d~lsDd~Lvsm------------SVReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~qq 89 (135)
T KOG4196|consen 22 DRLSDDELVSM------------SVRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQQ 89 (135)
T ss_pred CCcCHHHHHHh------------hHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57888888776 33322223348888888888888875 334333 33444555555
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 022702 148 YEAVKADREALQAQNQKLHAEIMAL 172 (293)
Q Consensus 148 ~~~l~~e~~~l~~e~~~l~~e~~~l 172 (293)
.+.|++|+..++.|.+.+.....+|
T Consensus 90 v~~L~~e~s~~~~E~da~k~k~e~l 114 (135)
T KOG4196|consen 90 VEKLKEENSRLRRELDAYKSKYEAL 114 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6666666666665555555555444
No 44
>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=90.26 E-value=0.96 Score=31.32 Aligned_cols=32 Identities=34% Similarity=0.649 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 138 EKDYDLLKRQYEAVKADREALQAQNQKLHAEI 169 (293)
Q Consensus 138 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~ 169 (293)
...|+.|+..|++|..|++.|+.+...|...+
T Consensus 11 K~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl 42 (45)
T PF02183_consen 11 KASYDSLKAEYDSLKKENEKLRAEVQELKEKL 42 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34566666666666666666666666665543
No 45
>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=88.03 E-value=4 Score=29.64 Aligned_cols=35 Identities=29% Similarity=0.430 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022702 140 DYDLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174 (293)
Q Consensus 140 ~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 174 (293)
....|...+..|..++..|..++..|..++..|+.
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~ 61 (64)
T PF00170_consen 27 YIEELEEKVEELESENEELKKELEQLKKEIQSLKS 61 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44556677777777777777777777777766654
No 46
>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=87.77 E-value=2.8 Score=31.86 Aligned_cols=37 Identities=27% Similarity=0.420 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022702 137 LEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALK 173 (293)
Q Consensus 137 ~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 173 (293)
++.+++.|+.++..+..++..|+.+|++|+.+.....
T Consensus 23 Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~ 59 (72)
T PF06005_consen 23 LQMENEELKEKNNELKEENEELKEENEQLKQERNAWQ 59 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444555555555555555544433
No 47
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=87.67 E-value=2 Score=40.35 Aligned_cols=49 Identities=29% Similarity=0.375 Sum_probs=34.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccc
Q 022702 128 RRARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSREVTE 179 (293)
Q Consensus 128 RRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~~~ 179 (293)
||.|.|+++.+ .....+...|..||+.|+.+++.|++|+..++......
T Consensus 207 ~kSR~~~k~~~---~e~~~r~~~leken~~lr~~v~~l~~el~~~~~~~~~~ 255 (269)
T KOG3119|consen 207 RKSRDKRKQKE---DEMAHRVAELEKENEALRTQVEQLKKELATLRRLFLQL 255 (269)
T ss_pred HHhhhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 35566665554 34556677788888888888888888888887765443
No 48
>smart00338 BRLZ basic region leucin zipper.
Probab=85.61 E-value=5.9 Score=28.80 Aligned_cols=36 Identities=31% Similarity=0.493 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 140 DYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 140 ~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
....|..+...|..+|..|..++..|..++..|+..
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~ 62 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKSE 62 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455677778888888888888888888888777653
No 49
>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=84.75 E-value=5.8 Score=30.14 Aligned_cols=43 Identities=28% Similarity=0.367 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 133 KTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 133 Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
|-.++-..+..|+.+++.|+++|..|..++..|..++..++..
T Consensus 12 ki~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e 54 (72)
T PF06005_consen 12 KIQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQE 54 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 4455666788888888888888888888888888888888754
No 50
>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=84.35 E-value=6.7 Score=28.47 Aligned_cols=39 Identities=26% Similarity=0.335 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 131 RWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEI 169 (293)
Q Consensus 131 K~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~ 169 (293)
+.....++..+..|..+++.|+.++..|..+++.|..++
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 334455667788888888889999999998888888876
No 51
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=82.55 E-value=3.5 Score=33.43 Aligned_cols=48 Identities=17% Similarity=0.272 Sum_probs=21.9
Q ss_pred chhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 119 RQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHA 167 (293)
Q Consensus 119 ~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~ 167 (293)
-++..||++.=- .+-.+.+++...++++++.++++|+.|+.+.+.|+.
T Consensus 15 l~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 15 LQYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 356788865411 111222333444444444455554444444444443
No 52
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=82.51 E-value=4 Score=33.07 Aligned_cols=35 Identities=37% Similarity=0.429 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022702 140 DYDLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174 (293)
Q Consensus 140 ~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 174 (293)
.+..++++...++++++.++.+|+.|..|+..|+.
T Consensus 28 ~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 28 DYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 34445555555555555555555555555555544
No 53
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=79.47 E-value=6.9 Score=37.33 Aligned_cols=39 Identities=26% Similarity=0.292 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 022702 138 EKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSRE 176 (293)
Q Consensus 138 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 176 (293)
+.+.+.|-.+.+.|...|+.|+.+.+.|..|+..||...
T Consensus 247 Rae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli 285 (294)
T KOG4571|consen 247 RAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLI 285 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566777888888889999998889999988888764
No 54
>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=76.79 E-value=9 Score=31.26 Aligned_cols=40 Identities=23% Similarity=0.390 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022702 135 KQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174 (293)
Q Consensus 135 k~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 174 (293)
..+-.+...||.+...+-+||..|+.||++|+..+..+..
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 3444556667777777777777777777777766655433
No 55
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=75.96 E-value=9.8 Score=31.29 Aligned_cols=37 Identities=30% Similarity=0.414 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022702 136 QLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMAL 172 (293)
Q Consensus 136 ~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 172 (293)
..-.+...||.....+-+||..|+.||++|+..+..+
T Consensus 19 ~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~ 55 (110)
T PRK13169 19 VLLKELGALKKQLAELLEENTALRLENDKLRERLEEL 55 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4445667777777777788888888888887777654
No 56
>smart00338 BRLZ basic region leucin zipper.
Probab=73.68 E-value=18 Score=26.15 Aligned_cols=37 Identities=27% Similarity=0.458 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 133 KTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEI 169 (293)
Q Consensus 133 Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~ 169 (293)
....++.....|..++..|..+...|..++..|..++
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445666677888888888888888888888877765
No 57
>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=73.49 E-value=20 Score=25.14 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 141 YDLLKRQYEAVKADREALQAQNQKLHAE 168 (293)
Q Consensus 141 ~~~lk~~~~~l~~e~~~l~~e~~~l~~e 168 (293)
...|...+..|..+|..|+.++..|+.|
T Consensus 27 ~~~le~~~~~L~~en~~L~~~i~~L~~E 54 (54)
T PF07716_consen 27 EEELEQEVQELEEENEQLRQEIAQLERE 54 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3445566666666666666666665543
No 58
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=72.79 E-value=0.89 Score=33.49 Aligned_cols=44 Identities=23% Similarity=0.359 Sum_probs=27.2
Q ss_pred CCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhh
Q 022702 79 EKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQ 126 (293)
Q Consensus 79 rkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQ 126 (293)
++|++||.++...+=..+. .......++|+.+||++.+|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHH
Confidence 4567899997666655541 2234567899999999999999953
No 59
>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=71.03 E-value=8.7 Score=26.14 Aligned_cols=40 Identities=15% Similarity=0.190 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhh
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQN 127 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQN 127 (293)
.++..+..+|...|. ....-.++|..+|++...|+.+...
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 477888999999882 2233568999999999999877643
No 60
>PRK10884 SH3 domain-containing protein; Provisional
Probab=70.76 E-value=35 Score=30.93 Aligned_cols=37 Identities=11% Similarity=0.040 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 139 KDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 139 ~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
.....|+.++..|+.+...++.+++.|.+++..++..
T Consensus 132 ~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~~~ 168 (206)
T PRK10884 132 SVINGLKEENQKLKNQLIVAQKKVDAANLQLDDKQRT 168 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344455666666666666666666666666555543
No 61
>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=70.21 E-value=28 Score=27.02 Aligned_cols=40 Identities=28% Similarity=0.396 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022702 133 KTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMAL 172 (293)
Q Consensus 133 Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 172 (293)
..+.++..+..|...++.++.|++.|..+|+-|+.=+..|
T Consensus 24 ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nL 63 (80)
T PF10224_consen 24 EILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNL 63 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345566677777778888888888888888887776655
No 62
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=69.82 E-value=51 Score=26.37 Aligned_cols=73 Identities=19% Similarity=0.241 Sum_probs=43.6
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
..|.|+.+++..|.. ....+.+|++-.+|+..+........ ........|..+...+..+...|+
T Consensus 35 gyR~Y~~~~l~~l~~-------------I~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~l~ 99 (113)
T cd01109 35 GIRDFTEEDLEWLEF-------------IKCLRNTGMSIKDIKEYAELRREGDS--TIPERLELLEEHREELEEQIAELQ 99 (113)
T ss_pred CCccCCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHHHHccCCc--cHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356799999988843 33467789999999988875432111 112234455555555555555555
Q ss_pred HHHHHHHH
Q 022702 160 AQNQKLHA 167 (293)
Q Consensus 160 ~e~~~l~~ 167 (293)
...+.|..
T Consensus 100 ~~~~~l~~ 107 (113)
T cd01109 100 ETLAYLDY 107 (113)
T ss_pred HHHHHHHH
Confidence 44444443
No 63
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=69.53 E-value=5.3 Score=28.23 Aligned_cols=40 Identities=20% Similarity=0.226 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHH
Q 022702 106 RKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLK 145 (293)
Q Consensus 106 ~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk 145 (293)
...+||+.+|++...|.-|+.++..+..-.....-...|.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~ 51 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALN 51 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcC
Confidence 3568999999999999999998866766665555444443
No 64
>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=68.99 E-value=23 Score=26.53 Aligned_cols=25 Identities=24% Similarity=0.416 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 140 DYDLLKRQYEAVKADREALQAQNQK 164 (293)
Q Consensus 140 ~~~~lk~~~~~l~~e~~~l~~e~~~ 164 (293)
++..|+.+...+..|+..|...++.
T Consensus 22 EN~~Lr~q~~~~~~ER~~L~ekne~ 46 (65)
T TIGR02449 22 ENRLLRAQEKTWREERAQLLEKNEQ 46 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444444443333
No 65
>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=68.82 E-value=42 Score=26.42 Aligned_cols=37 Identities=14% Similarity=0.306 Sum_probs=27.5
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRR 129 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRR 129 (293)
.++.|+.+++..|.... ..+.+|++..+|+-++....
T Consensus 35 g~R~y~~~di~~l~~i~-------------~lr~~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 35 GYRLYTEEDLERLQQIL-------------FLKELGFSLKEIKELLKDPS 71 (103)
T ss_pred CceeeCHHHHHHHHHHH-------------HHHHcCCCHHHHHHHHHcCc
Confidence 35679999999986543 23567999999998887654
No 66
>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=68.13 E-value=35 Score=26.53 Aligned_cols=48 Identities=21% Similarity=0.208 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 022702 129 RARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSRE 176 (293)
Q Consensus 129 RaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 176 (293)
..+..+..+.++...|+..+..|....+.++.++++|..|+.-|..-.
T Consensus 13 ~~~e~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI 60 (80)
T PF10224_consen 13 LEKEEKEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYI 60 (80)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556677778888888888888888899999999999888776554
No 67
>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=67.38 E-value=23 Score=28.94 Aligned_cols=47 Identities=26% Similarity=0.299 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccc
Q 022702 133 KTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSREVTE 179 (293)
Q Consensus 133 Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~~~ 179 (293)
+-.+.++....+-.+++.||.....|..||..|+-|+..|+.+....
T Consensus 9 ~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~ 55 (107)
T PF06156_consen 9 RLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEEL 55 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567788899999999999999999999999999999999987543
No 68
>PRK10722 hypothetical protein; Provisional
Probab=67.20 E-value=1.1e+02 Score=28.64 Aligned_cols=81 Identities=17% Similarity=0.276 Sum_probs=44.3
Q ss_pred hCCCCCHHHHHHHHHHhCCCcch--------hhhhhhhhHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHH
Q 022702 98 LGNKLEPERKMQLARALGLQPRQ--------VAIWFQNRRARWKTKQLEKDYDLL----KRQYEAVKADREALQAQNQKL 165 (293)
Q Consensus 98 ~~~~p~~~~r~~LA~~lgL~~~q--------VkvWFQNRRaK~Krk~~~~~~~~l----k~~~~~l~~e~~~l~~e~~~l 165 (293)
.+..+...+|..+...|.-...+ +++|-.+.-...--...+..|..| ..++++++..+..|+.+.+..
T Consensus 116 ~~a~~t~~err~~l~rl~~~~~~~p~~lrPL~qlwr~~Q~l~l~LaeEr~Ry~rLQq~sD~qlD~lrqq~~~Lq~~L~~t 195 (247)
T PRK10722 116 ADAKITPAERRQIVERLNAYSLQIPAQVRPLYQLWRDGQALQLALAEERQRYQKLQQSSDSELDALRQQQQRLQYQLELT 195 (247)
T ss_pred cCCCCChHHHHHHHHHHhhcccccchhhhHHHHHHHHhhHHHHhHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHH
Confidence 34456677777766666433333 467754421111111111223333 456677777777777777777
Q ss_pred HHHHHHhhhcccc
Q 022702 166 HAEIMALKSREVT 178 (293)
Q Consensus 166 ~~e~~~lk~~~~~ 178 (293)
...++.|+.-+..
T Consensus 196 ~rKLEnLTdIERq 208 (247)
T PRK10722 196 TRKLENLTDIERQ 208 (247)
T ss_pred HHHHHHHHHHHHH
Confidence 7777777665543
No 69
>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=66.83 E-value=17 Score=26.70 Aligned_cols=29 Identities=24% Similarity=0.485 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 137 LEKDYDLLKRQYEAVKADREALQAQNQKL 165 (293)
Q Consensus 137 ~~~~~~~lk~~~~~l~~e~~~l~~e~~~l 165 (293)
...++..|+.+++.++.+++.|+.+.+.|
T Consensus 22 ~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 22 LNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34445566666666666666666665555
No 70
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=66.82 E-value=58 Score=26.30 Aligned_cols=72 Identities=21% Similarity=0.190 Sum_probs=43.1
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
..|.|+.+++..|+ .....+.+|++-..|+..+.+..... .....-...|..+.+.+.++...|+
T Consensus 35 gyR~Y~~~~i~~l~-------------~I~~lr~~G~sl~eI~~~l~~~~~~~--~~~~~~~~~l~~~~~~l~~~i~~l~ 99 (123)
T cd04770 35 GYRLYGEADLARLR-------------FIRRAQALGFSLAEIRELLSLRDDGA--APCAEVRALLEEKLAEVEAKIAELQ 99 (123)
T ss_pred CCccCCHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHHhhhcCC--CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46679999999983 33446889999999998887654310 0112223445555555555555554
Q ss_pred HHHHHHH
Q 022702 160 AQNQKLH 166 (293)
Q Consensus 160 ~e~~~l~ 166 (293)
.-.+.|.
T Consensus 100 ~~~~~l~ 106 (123)
T cd04770 100 ALRAELA 106 (123)
T ss_pred HHHHHHH
Confidence 4444443
No 71
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=66.80 E-value=63 Score=27.19 Aligned_cols=73 Identities=8% Similarity=0.120 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRA-RWKTKQLEKDYDLLKRQYEAVKADREAL 158 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRa-K~Krk~~~~~~~~lk~~~~~l~~e~~~l 158 (293)
.+|.|+..++..|... .. .+.+|++-..|+-++.+... ........+..+.+..+.+.+.+....+
T Consensus 34 g~R~Y~~~~l~~l~~I------------~~-lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~i~~Le~~l~~L 100 (134)
T cd04779 34 NYRYYDETALDRLQLI------------EH-LKGQRLSLAEIKDQLEEVQRSDKEQREVAQEVQLVCDQIDGLEHRLKQL 100 (134)
T ss_pred CCeeECHHHHHHHHHH------------HH-HHHCCCCHHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667999999888442 22 36678887788777766543 1223334444555555555555555544
Q ss_pred HHHHHHH
Q 022702 159 QAQNQKL 165 (293)
Q Consensus 159 ~~e~~~l 165 (293)
+.-.+.+
T Consensus 101 ~~~~~~l 107 (134)
T cd04779 101 KPIASQT 107 (134)
T ss_pred HHHHHHH
Confidence 4433333
No 72
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=66.59 E-value=51 Score=26.97 Aligned_cols=70 Identities=23% Similarity=0.278 Sum_probs=41.6
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
..|.|+..++..|+ ....++.+|++-..|+..+..... .........+..+.+.++++...|+
T Consensus 34 g~R~Y~~~~l~~l~-------------~I~~l~~~G~sl~eI~~~l~~~~~----~~~~~~~~~l~~~~~~l~~~i~~L~ 96 (124)
T TIGR02051 34 GYRRYPEETVKRLR-------------FIKRAQELGFSLEEIGGLLGLVDG----THCREMYELASRKLKSVQAKMADLL 96 (124)
T ss_pred CCEeECHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHhcccC----CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46679999999882 334578899999999998865432 1111223344445555555555544
Q ss_pred HHHHHHH
Q 022702 160 AQNQKLH 166 (293)
Q Consensus 160 ~e~~~l~ 166 (293)
.-...|.
T Consensus 97 ~~~~~L~ 103 (124)
T TIGR02051 97 RIERLLE 103 (124)
T ss_pred HHHHHHH
Confidence 4333333
No 73
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=65.63 E-value=30 Score=26.85 Aligned_cols=12 Identities=25% Similarity=0.454 Sum_probs=5.2
Q ss_pred HHHHHHHHHHHH
Q 022702 158 LQAQNQKLHAEI 169 (293)
Q Consensus 158 l~~e~~~l~~e~ 169 (293)
|..+|++|+.|.
T Consensus 51 L~~en~qLk~E~ 62 (79)
T PRK15422 51 LERENNHLKEQQ 62 (79)
T ss_pred HHHHHHHHHHHH
Confidence 444444444443
No 74
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=64.76 E-value=6.7 Score=25.58 Aligned_cols=43 Identities=16% Similarity=0.194 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRA 130 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRa 130 (293)
.++..+...++..|... ..-.++|..+|++...|..|...-|.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 36777888887776422 23457899999999999999865443
No 75
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=63.06 E-value=70 Score=26.12 Aligned_cols=72 Identities=19% Similarity=0.229 Sum_probs=43.9
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
..|.|+.+++..|. .....+.+|++-..|+-++...... ........+..+.+.+.++...|+
T Consensus 35 gyR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~~~~~----~~~~~~~~l~~~~~~l~~~i~~L~ 97 (126)
T cd04783 35 GYRRYPEETVTRLR-------------FIKRAQELGFTLDEIAELLELDDGT----DCSEARELAEQKLAEVDEKIADLQ 97 (126)
T ss_pred CCeecCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhcccCC----CHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45679999999984 3455788999999999999765421 111223334455555555555554
Q ss_pred HHHHHHHHH
Q 022702 160 AQNQKLHAE 168 (293)
Q Consensus 160 ~e~~~l~~e 168 (293)
.-...|..-
T Consensus 98 ~~~~~l~~~ 106 (126)
T cd04783 98 RMRASLQEL 106 (126)
T ss_pred HHHHHHHHH
Confidence 444444433
No 76
>PF07795 DUF1635: Protein of unknown function (DUF1635); InterPro: IPR012862 The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids long.
Probab=61.78 E-value=80 Score=28.99 Aligned_cols=46 Identities=24% Similarity=0.258 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022702 129 RARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174 (293)
Q Consensus 129 RaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 174 (293)
+|++..++.+++...|+.-......|.+..+.+.++|..+...+..
T Consensus 23 ~A~EElRk~eeqi~~L~~Ll~~a~~ERDEAr~qlq~Ll~~~~~l~~ 68 (214)
T PF07795_consen 23 EANEELRKREEQIAHLKDLLKKAYQERDEAREQLQKLLLEKLSLQQ 68 (214)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Confidence 4666666777788888888888999999999999998866644443
No 77
>KOG3335 consensus Predicted coiled-coil protein [General function prediction only]
Probab=61.28 E-value=42 Score=29.94 Aligned_cols=50 Identities=20% Similarity=0.236 Sum_probs=34.9
Q ss_pred CcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 117 QPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLH 166 (293)
Q Consensus 117 ~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~ 166 (293)
..-...+|.+-|-.+.|..+.+.+...|+.+.+.+..+.+.++...+.|.
T Consensus 84 g~lv~Ey~R~~~~e~~kee~~~~e~~elr~~~~~l~~~i~~~~~~~~~L~ 133 (181)
T KOG3335|consen 84 GVLVFEYWRQARKERKKEEKRKQEIMELRLKVEKLENAIAELTKFFSQLH 133 (181)
T ss_pred eeeeehhHHhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33345688887777777777777777777777777776666666665555
No 78
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=61.18 E-value=21 Score=32.71 Aligned_cols=39 Identities=23% Similarity=0.349 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022702 135 KQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALK 173 (293)
Q Consensus 135 k~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 173 (293)
..++.+.+....+++.+..+.+.|+.+.+.++.|..+|.
T Consensus 161 ~kL~~el~~~~~~Le~~~~~~~al~Kq~e~~~~EydrLl 199 (216)
T KOG1962|consen 161 EKLETELEKKQKKLEKAQKKVDALKKQSEGLQDEYDRLL 199 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHH
Confidence 333333333344444444444444444444444444443
No 79
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=61.09 E-value=35 Score=31.84 Aligned_cols=43 Identities=26% Similarity=0.363 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 129 RARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMA 171 (293)
Q Consensus 129 RaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~ 171 (293)
|-|.|..++|+++..++.++..|+.|.+.|+++|.+|=..+.-
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRy 132 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRY 132 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555666677777777777777777777777777666655543
No 80
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=60.88 E-value=14 Score=38.11 Aligned_cols=32 Identities=22% Similarity=0.286 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022702 142 DLLKRQYEAVKADREALQAQNQKLHAEIMALK 173 (293)
Q Consensus 142 ~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 173 (293)
.-|+..+.++..|++.|+.||..|+.++..+-
T Consensus 305 ~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~ 336 (655)
T KOG4343|consen 305 LGLEARLQALLSENEQLKKENATLKRQLDELV 336 (655)
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHh
Confidence 34555555555566666666655555555443
No 81
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=60.87 E-value=3.6 Score=42.91 Aligned_cols=48 Identities=15% Similarity=0.067 Sum_probs=32.8
Q ss_pred HHHHHHhHhhCCCCCHHHHHHHHHHhCC-------CcchhhhhhhhhHHHHHHHH
Q 022702 89 VKTLEKNFELGNKLEPERKMQLARALGL-------QPRQVAIWFQNRRARWKTKQ 136 (293)
Q Consensus 89 l~~LE~~F~~~~~p~~~~r~~LA~~lgL-------~~~qVkvWFQNRRaK~Krk~ 136 (293)
.++-+.+|.+++.+......+--+.+.| ..+-|+.||.|||+++|+.+
T Consensus 704 ~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 704 YEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred eecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 3444666777777776665554444433 44569999999999998854
No 82
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=60.80 E-value=8.1 Score=43.67 Aligned_cols=57 Identities=18% Similarity=0.068 Sum_probs=50.4
Q ss_pred CCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHH
Q 022702 81 KRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQL 137 (293)
Q Consensus 81 r~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~ 137 (293)
++|++.-|+..|-.+|+...+|.-.++..++..|++..|.+-.||++++.+|..-..
T Consensus 448 s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~ 504 (1406)
T KOG1146|consen 448 SKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHP 504 (1406)
T ss_pred hhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccc
Confidence 556888899999999999999999999999999999999999999998888875443
No 83
>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=60.66 E-value=19 Score=20.71 Aligned_cols=39 Identities=21% Similarity=0.384 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhh
Q 022702 82 RRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWF 125 (293)
Q Consensus 82 ~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWF 125 (293)
..++.++...+...|.... ...++|..+|++...|..|.
T Consensus 4 ~~~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHhC
Confidence 3466777666666665332 34578999999988887773
No 84
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.56 E-value=43 Score=25.55 Aligned_cols=17 Identities=29% Similarity=0.491 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHHHHHH
Q 022702 145 KRQYEAVKADREALQAQ 161 (293)
Q Consensus 145 k~~~~~l~~e~~~l~~e 161 (293)
....++|..+|+.|+.+
T Consensus 45 q~~reaL~~eneqlk~e 61 (79)
T COG3074 45 QHQREALERENEQLKEE 61 (79)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33333333333333333
No 85
>PRK10884 SH3 domain-containing protein; Provisional
Probab=60.55 E-value=32 Score=31.14 Aligned_cols=32 Identities=13% Similarity=0.076 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022702 141 YDLLKRQYEAVKADREALQAQNQKLHAEIMAL 172 (293)
Q Consensus 141 ~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 172 (293)
++.++..+..|+++|..|+.+.+.++.++..+
T Consensus 127 ~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l 158 (206)
T PRK10884 127 VAQSDSVINGLKEENQKLKNQLIVAQKKVDAA 158 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444445555555555555555554443
No 86
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=59.33 E-value=39 Score=27.76 Aligned_cols=45 Identities=24% Similarity=0.295 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccc
Q 022702 134 TKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSREVT 178 (293)
Q Consensus 134 rk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~~ 178 (293)
-.+.++....+-.++..||.....|..||..|+.|+..|+.+...
T Consensus 10 l~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~ 54 (110)
T PRK13169 10 LDDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEE 54 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456778888899999999999999999999999999999998754
No 87
>KOG0249 consensus LAR-interacting protein and related proteins [General function prediction only]
Probab=59.12 E-value=36 Score=36.50 Aligned_cols=45 Identities=24% Similarity=0.443 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022702 130 ARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174 (293)
Q Consensus 130 aK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 174 (293)
|+.++..+.++.+.+|++++.+..+.+.|...++.|+.++..|+.
T Consensus 214 Ale~kn~L~~e~~s~kk~l~~~~~~k~rl~~d~E~Lr~e~~qL~~ 258 (916)
T KOG0249|consen 214 ALEDKNRLEQELESVKKQLEEMRHDKDKLRTDIEDLRGELDQLRR 258 (916)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence 556677777888888899999998999999889999988888874
No 88
>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=59.08 E-value=12 Score=36.57 Aligned_cols=23 Identities=17% Similarity=0.384 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 022702 143 LLKRQYEAVKADREALQAQNQKL 165 (293)
Q Consensus 143 ~lk~~~~~l~~e~~~l~~e~~~l 165 (293)
.|+.++.+||.||..|+.+.++|
T Consensus 36 aLr~EN~~LKkEN~~Lk~eVerL 58 (420)
T PF07407_consen 36 ALRMENHSLKKENNDLKIEVERL 58 (420)
T ss_pred hHHHHhHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444444
No 89
>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=58.30 E-value=43 Score=24.28 Aligned_cols=37 Identities=16% Similarity=0.356 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 135 KQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMA 171 (293)
Q Consensus 135 k~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~ 171 (293)
..++.+...+......++.+++.+....+.+..-+..
T Consensus 3 ~elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~ 39 (55)
T PF05377_consen 3 DELENELPRIESSINTVKKENEEISESVEKIEENVKD 39 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666777777777777777777777777665543
No 90
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=58.04 E-value=54 Score=26.85 Aligned_cols=29 Identities=21% Similarity=0.255 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 140 DYDLLKRQYEAVKADREALQAQNQKLHAE 168 (293)
Q Consensus 140 ~~~~lk~~~~~l~~e~~~l~~e~~~l~~e 168 (293)
+...++++++.+++++..|.+++..|+.+
T Consensus 58 qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 58 QIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 33344444444444444444444444444
No 91
>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=57.83 E-value=34 Score=27.07 Aligned_cols=39 Identities=15% Similarity=0.053 Sum_probs=28.1
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRA 130 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRa 130 (293)
.+|+|+.+++..|... ..|.+.+|++-..|+-+..+...
T Consensus 35 g~R~Yt~~di~~l~~I------------~~llr~~G~~l~~i~~~l~~~~~ 73 (99)
T cd04765 35 GRRYYRPKDVELLLLI------------KHLLYEKGYTIEGAKQALKEDGA 73 (99)
T ss_pred CCeeeCHHHHHHHHHH------------HHHHHHCCCCHHHHHHHHHhccc
Confidence 4667999999988442 23567788888888888765443
No 92
>KOG3863 consensus bZIP transcription factor NRF1 [Transcription]
Probab=57.63 E-value=1.7e+02 Score=30.89 Aligned_cols=53 Identities=21% Similarity=0.255 Sum_probs=28.6
Q ss_pred hhhhhhHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 123 IWFQNRRAR--WKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 123 vWFQNRRaK--~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
|=-||+|-| .+..+++.+.+.|+.+-+.|..|...+......++.++..|--.
T Consensus 500 vAAQnCRKRKLd~I~nLE~ev~~l~~eKeqLl~Er~~~d~~L~~~kqqls~L~~~ 554 (604)
T KOG3863|consen 500 VAAQNCRKRKLDCILNLEDEVEKLQKEKEQLLRERDELDSTLGVMKQQLSELYQE 554 (604)
T ss_pred hhccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445565543 23345555566666666666666666555555555555544433
No 93
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=57.10 E-value=31 Score=29.54 Aligned_cols=48 Identities=19% Similarity=0.179 Sum_probs=35.4
Q ss_pred CCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHH
Q 022702 81 KRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKT 134 (293)
Q Consensus 81 r~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Kr 134 (293)
...++..|..+|...+ .+ ....++|..||++...|+.|-.+.|.|.|+
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 4568999999997732 11 234589999999999999998765555443
No 94
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=56.65 E-value=41 Score=31.32 Aligned_cols=30 Identities=27% Similarity=0.432 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 139 KDYDLLKRQYEAVKADREALQAQNQKLHAE 168 (293)
Q Consensus 139 ~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e 168 (293)
++...|..+++.+.++.+.++.....|..|
T Consensus 149 ~EkeeL~~eleele~e~ee~~erlk~le~E 178 (290)
T COG4026 149 KEKEELLKELEELEAEYEEVQERLKRLEVE 178 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444444444333333333
No 95
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=56.10 E-value=52 Score=27.96 Aligned_cols=34 Identities=15% Similarity=0.345 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 135 KQLEKDYDLLKRQYEAVKADREALQAQNQKLHAE 168 (293)
Q Consensus 135 k~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e 168 (293)
..+..+.+.|+.++..+..|.+.++.--++|..-
T Consensus 84 ~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l~~~ 117 (135)
T KOG4196|consen 84 AELQQQVEKLKEENSRLRRELDAYKSKYEALQNS 117 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3455566666666666666666666655555544
No 96
>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=55.98 E-value=14 Score=32.48 Aligned_cols=24 Identities=29% Similarity=0.452 Sum_probs=6.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcc
Q 022702 153 ADREALQAQNQKLHAEIMALKSRE 176 (293)
Q Consensus 153 ~e~~~l~~e~~~l~~e~~~lk~~~ 176 (293)
.|.+.|+.++|+|++|+..||...
T Consensus 24 dEKE~L~~~~QRLkDE~RDLKqEl 47 (166)
T PF04880_consen 24 DEKENLREEVQRLKDELRDLKQEL 47 (166)
T ss_dssp HHHHHHHHCH--------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556666667777777776666665
No 97
>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=55.92 E-value=19 Score=26.41 Aligned_cols=28 Identities=21% Similarity=0.410 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 139 KDYDLLKRQYEAVKADREALQAQNQKLH 166 (293)
Q Consensus 139 ~~~~~lk~~~~~l~~e~~~l~~e~~~l~ 166 (293)
++.+.||.++..|.+.+..|+.||.-|+
T Consensus 14 EEVevLK~~I~eL~~~n~~Le~EN~~Lk 41 (59)
T PF01166_consen 14 EEVEVLKEQIAELEERNSQLEEENNLLK 41 (59)
T ss_dssp TSHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666666666666666666655544
No 98
>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=55.82 E-value=43 Score=25.18 Aligned_cols=29 Identities=14% Similarity=0.274 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 138 EKDYDLLKRQYEAVKADREALQAQNQKLH 166 (293)
Q Consensus 138 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~ 166 (293)
..+...++++.+.++.+++.|+.|...|.
T Consensus 30 ~~~~~~~~~~~~~l~~en~~L~~ei~~l~ 58 (85)
T TIGR02209 30 NNELQKLQLEIDKLQKEWRDLQLEVAELS 58 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 33444455555555555555555444443
No 99
>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=54.98 E-value=84 Score=29.31 Aligned_cols=48 Identities=10% Similarity=0.106 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccc
Q 022702 134 TKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSREVTESI 181 (293)
Q Consensus 134 rk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~~~~~ 181 (293)
|..-+..+..|..+...+..+...|+.|.++|++++..|-++......
T Consensus 88 RDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylqS 135 (248)
T PF08172_consen 88 RDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQS 135 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 444455667777888888888999999999999999999888755543
No 100
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=54.87 E-value=28 Score=32.21 Aligned_cols=34 Identities=26% Similarity=0.250 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHhhhc
Q 022702 142 DLLKRQYEAVKADREALQAQNQ---KLHAEIMALKSR 175 (293)
Q Consensus 142 ~~lk~~~~~l~~e~~~l~~e~~---~l~~e~~~lk~~ 175 (293)
..++++++.|++|+..|+.+.. .+++|+.+|+.-
T Consensus 72 ~~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~l 108 (276)
T PRK13922 72 FDLREENEELKKELLELESRLQELEQLEAENARLREL 108 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444444333 344555555443
No 101
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=54.43 E-value=1.2e+02 Score=25.00 Aligned_cols=76 Identities=11% Similarity=0.132 Sum_probs=45.8
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
..|.|+.+++..|. .....+.+|++-.+|+-++........ ........|..+...+.++...++
T Consensus 35 gyR~Y~~~~~~~l~-------------~I~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~l~ 99 (133)
T cd04787 35 GYRLYSEKDLSRLR-------------FILSARQLGFSLKDIKEILSHADQGES--PCPMVRRLIEQRLAETERRIKELL 99 (133)
T ss_pred CeeeCCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhhhccCCC--cHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35679999999882 334578899999999999975432110 011223445555566666666655
Q ss_pred HHHHHHHHHHH
Q 022702 160 AQNQKLHAEIM 170 (293)
Q Consensus 160 ~e~~~l~~e~~ 170 (293)
.-.+.|...+.
T Consensus 100 ~~~~~l~~~~~ 110 (133)
T cd04787 100 KLRDRMQQAVS 110 (133)
T ss_pred HHHHHHHHHHH
Confidence 55555544443
No 102
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=54.03 E-value=16 Score=26.12 Aligned_cols=39 Identities=28% Similarity=0.295 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHhHhhCCCCC--HHHHHHHHHHhCCCcchhh
Q 022702 84 LNMEQVKTLEKNFELGNKLE--PERKMQLARALGLQPRQVA 122 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~--~~~r~~LA~~lgL~~~qVk 122 (293)
+|..|.+.|...|+..-|-. ...-.+||+.||++..-|-
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 58899999999998877543 3344789999999986643
No 103
>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=53.51 E-value=8.1 Score=28.43 Aligned_cols=18 Identities=22% Similarity=0.540 Sum_probs=16.3
Q ss_pred HHHHHHHhCCCcchhhhh
Q 022702 107 KMQLARALGLQPRQVAIW 124 (293)
Q Consensus 107 r~~LA~~lgL~~~qVkvW 124 (293)
-.+||.+||+++.+|+.|
T Consensus 25 lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKW 42 (60)
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 357899999999999999
No 104
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=53.00 E-value=46 Score=24.37 Aligned_cols=33 Identities=27% Similarity=0.449 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022702 140 DYDLLKRQYEAVKADREALQAQNQKLHAEIMAL 172 (293)
Q Consensus 140 ~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 172 (293)
.+..++.++..+..+.+.++.+++.|+.++..+
T Consensus 18 ~~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 18 RYYQLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456677777777777777777777777777777
No 105
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=52.67 E-value=89 Score=25.15 Aligned_cols=78 Identities=19% Similarity=0.206 Sum_probs=44.8
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
..|.|+..++..|.. ....+.+|++-..|+..+....... ......-...|..+.+.+.++...++
T Consensus 34 ~yR~Y~~~d~~~l~~-------------I~~lr~~G~sl~eI~~~l~~~~~~~-~~~~~~~~~~l~~~~~~l~~~i~~l~ 99 (116)
T cd04769 34 NYRVYDAQHVECLRF-------------IKEARQLGFTLAELKAIFAGHEGRA-VLPWPHLQQALEDKKQEIRAQITELQ 99 (116)
T ss_pred CceeeCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhccccCC-cCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456799999888743 2346788999999998887665432 01111223444455555555555555
Q ss_pred HHHHHHHHHHHH
Q 022702 160 AQNQKLHAEIMA 171 (293)
Q Consensus 160 ~e~~~l~~e~~~ 171 (293)
...+.|..-+..
T Consensus 100 ~~~~~l~~~~~~ 111 (116)
T cd04769 100 QLLARLDAFEAS 111 (116)
T ss_pred HHHHHHHHHHHH
Confidence 444444444433
No 106
>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=52.21 E-value=48 Score=29.11 Aligned_cols=28 Identities=29% Similarity=0.392 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 141 YDLLKRQYEAVKADREALQAQNQKLHAE 168 (293)
Q Consensus 141 ~~~lk~~~~~l~~e~~~l~~e~~~l~~e 168 (293)
+..|+.++..|+..+..|+.+++.|..+
T Consensus 106 ~~~l~~e~~~l~~~~e~Le~e~~~L~~~ 133 (161)
T TIGR02894 106 NERLKNQNESLQKRNEELEKELEKLRQR 133 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333333333334444333333333
No 107
>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=52.15 E-value=41 Score=34.33 Aligned_cols=53 Identities=19% Similarity=0.236 Sum_probs=22.5
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLE 138 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~ 138 (293)
.+++++++.|.- ...-|..-.|..+|+.-.|..+.-++==+|++-|...++++
T Consensus 41 ~ltpee~kalGi---egDTP~DTlrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~ 93 (472)
T TIGR03752 41 ELSPEELKALGI---EGDTPADTLRTLVAEVKELRKRLAKLISENEALKAENERLQ 93 (472)
T ss_pred cCCcchhHhcCC---CCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355555554432 23344444454444433333333333334555444444433
No 108
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.12 E-value=70 Score=24.44 Aligned_cols=36 Identities=22% Similarity=0.285 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 140 DYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 140 ~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
+.+.||.++..|..|...++...+.|..+...+|..
T Consensus 26 EieELKEknn~l~~e~q~~q~~reaL~~eneqlk~e 61 (79)
T COG3074 26 EIEELKEKNNSLSQEVQNAQHQREALERENEQLKEE 61 (79)
T ss_pred HHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444333333444444555555555543
No 109
>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=51.86 E-value=54 Score=24.62 Aligned_cols=39 Identities=18% Similarity=0.326 Sum_probs=18.4
Q ss_pred hhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 121 VAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 121 VkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
|..+++.|.........+.+.+.++.+++.|+.|...|.
T Consensus 20 v~~~~~~~~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~ 58 (85)
T TIGR02209 20 VSAQHQTRQLNNELQKLQLEIDKLQKEWRDLQLEVAELS 58 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 334444444444444444445555555555555544443
No 110
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=51.04 E-value=41 Score=34.37 Aligned_cols=43 Identities=23% Similarity=0.402 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 133 KTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 133 Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
|..+++++++.|+.+.+.+.+....++...++|..|+.+|+..
T Consensus 77 kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Q 119 (475)
T PRK13729 77 TAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQ 119 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHH
Confidence 3444555555666555544444444454445555555555444
No 111
>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=50.89 E-value=74 Score=24.07 Aligned_cols=42 Identities=19% Similarity=0.344 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 022702 135 KQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSRE 176 (293)
Q Consensus 135 k~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 176 (293)
+..+..|..|+.+++..+.++..|..++..|...+..|.+..
T Consensus 24 ~~Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~Ls~ql 65 (70)
T PF04899_consen 24 QEWQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQRLSEQL 65 (70)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344567889999999999999999999998888888776543
No 112
>PF15058 Speriolin_N: Speriolin N terminus
Probab=50.61 E-value=29 Score=31.36 Aligned_cols=36 Identities=28% Similarity=0.353 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 139 KDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 139 ~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
..|+-|+++++++-.||+.|++++.-+ +|+.+||..
T Consensus 5 ~~yeGlrhqierLv~ENeeLKKlVrLi-rEN~eLksa 40 (200)
T PF15058_consen 5 TNYEGLRHQIERLVRENEELKKLVRLI-RENHELKSA 40 (200)
T ss_pred cchHHHHHHHHHHHhhhHHHHHHHHHH-HHHHHHHHH
Confidence 357788899999999999999887544 455677777
No 113
>PF07888 CALCOCO1: Calcium binding and coiled-coil domain (CALCOCO1) like; InterPro: IPR012852 Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein expressed by Mus musculus (CoCoA, Q8CGU1 from SWISSPROT). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (Q61026 from SWISSPROT), and thus enhances transcriptional activation by a number of nuclear receptors. CoCoA has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region [].
Probab=50.48 E-value=2.6e+02 Score=29.19 Aligned_cols=34 Identities=29% Similarity=0.355 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 022702 143 LLKRQYEAVKADREALQAQNQKLHAEIMALKSRE 176 (293)
Q Consensus 143 ~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 176 (293)
.|+..+..+..|.+.|+.+++.|...+..|..+.
T Consensus 421 Elks~lrv~qkEKEql~~EkQeL~~yi~~Le~r~ 454 (546)
T PF07888_consen 421 ELKSSLRVAQKEKEQLQEEKQELLEYIERLEQRL 454 (546)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444445555555555555555555555555443
No 114
>PF13942 Lipoprotein_20: YfhG lipoprotein
Probab=50.22 E-value=1.2e+02 Score=27.05 Aligned_cols=75 Identities=20% Similarity=0.326 Sum_probs=41.7
Q ss_pred hhCCCCCHHHHHHHHHHhCCCcc----h----hhhhhhhh---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 97 ELGNKLEPERKMQLARALGLQPR----Q----VAIWFQNR---------RARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 97 ~~~~~p~~~~r~~LA~~lgL~~~----q----VkvWFQNR---------RaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
-.+..|++.+|..+...|+---. + +++|-.+. |+|++|-+...+ .++++|+..+..|+
T Consensus 69 L~~A~~T~~ERR~~~~~l~~y~~~~P~~vRPL~QlWRe~Q~lql~L~eEr~Ry~rLQqssD-----~~lD~Lr~qq~~Lq 143 (179)
T PF13942_consen 69 LANAEPTPAERRQMVDRLNSYSLQFPASVRPLLQLWREQQVLQLQLSEERARYQRLQQSSD-----SELDALRQQQQRLQ 143 (179)
T ss_pred hcCCCCCHHHHHHHHHHHHHhhhhcCHHHhHHHHHHHHhHHHHHHHHHHHHHHHHHHHhhH-----HHHHHHHHHHHHHH
Confidence 34557888888877666642221 2 57787654 445444443332 34555566666666
Q ss_pred HHHHHHHHHHHHhhhcc
Q 022702 160 AQNQKLHAEIMALKSRE 176 (293)
Q Consensus 160 ~e~~~l~~e~~~lk~~~ 176 (293)
.+.+.-...++.|..-+
T Consensus 144 ~qL~~T~RKLEnLTDIE 160 (179)
T PF13942_consen 144 YQLDTTTRKLENLTDIE 160 (179)
T ss_pred HHHHHHHHHHhhhhHHH
Confidence 65555555555554443
No 115
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=50.13 E-value=38 Score=29.72 Aligned_cols=29 Identities=28% Similarity=0.439 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 139 KDYDLLKRQYEAVKADREALQAQNQKLHA 167 (293)
Q Consensus 139 ~~~~~lk~~~~~l~~e~~~l~~e~~~l~~ 167 (293)
++++.|+.+.+....|.+.|+.|.+.+++
T Consensus 161 ~ei~~lk~el~~~~~~~~~LkkQ~~~l~~ 189 (192)
T PF05529_consen 161 EEIEKLKKELEKKEKEIEALKKQSEGLQK 189 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 33444444444444444444444444443
No 116
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=49.88 E-value=44 Score=27.57 Aligned_cols=30 Identities=23% Similarity=0.407 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 140 DYDLLKRQYEAVKADREALQAQNQKLHAEI 169 (293)
Q Consensus 140 ~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~ 169 (293)
+...||+....+-+||..|+.||++|+..+
T Consensus 23 el~~lK~~l~~lvEEN~~L~lENe~LR~RL 52 (114)
T COG4467 23 ELGGLKQHLGSLVEENTALRLENEKLRERL 52 (114)
T ss_pred HHHHHHHHHHHHHHhhHHHHhhHHHHHHHh
Confidence 344455555555555555555555555444
No 117
>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=49.67 E-value=34 Score=23.32 Aligned_cols=40 Identities=15% Similarity=0.202 Sum_probs=25.8
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhh
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNR 128 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNR 128 (293)
++..+...+.-.| .....-.++|..+|+++..|+.|...-
T Consensus 11 L~~~~r~i~~l~~-----~~g~s~~eIa~~l~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 11 LPERQREIFLLRY-----FQGMSYAEIAEILGISESTVKRRLRRA 50 (54)
T ss_dssp S-HHHHHHHHHHH-----TS---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH-----HHCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4555666665544 344456789999999999999998643
No 118
>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=49.05 E-value=5.7 Score=36.58 Aligned_cols=38 Identities=29% Similarity=0.343 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022702 135 KQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMAL 172 (293)
Q Consensus 135 k~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 172 (293)
.+....+..|++-.+.|-++|+.|+.+|+.|.+|..+|
T Consensus 125 EEQ~T~I~dLrrlVe~L~aeNErLr~EnkqL~ae~arL 162 (243)
T PF08961_consen 125 EEQATKIADLRRLVEFLLAENERLRRENKQLKAENARL 162 (243)
T ss_dssp --------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444477888889999999999999999999998887
No 119
>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=48.08 E-value=1.1e+02 Score=22.35 Aligned_cols=44 Identities=27% Similarity=0.314 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 022702 133 KTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSRE 176 (293)
Q Consensus 133 Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 176 (293)
|-.++..+...|+.+.+.|..+...++.+.+..+.|-.+...++
T Consensus 4 kid~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~Rl 47 (56)
T PF04728_consen 4 KIDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRL 47 (56)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566777777888888888888888777777777665554443
No 120
>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=47.76 E-value=1.5e+02 Score=23.97 Aligned_cols=36 Identities=17% Similarity=0.331 Sum_probs=28.7
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhh
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNR 128 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNR 128 (293)
.+|.|+.+++..|+. ....+.+|++-..|+..+.+.
T Consensus 34 gyR~Y~~~~l~~l~~-------------I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 34 LRRQYDPQVLDRLAL-------------IALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred CceecCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhcc
Confidence 466799999998842 356788899999999998765
No 121
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=47.63 E-value=31 Score=37.19 Aligned_cols=18 Identities=17% Similarity=0.263 Sum_probs=12.1
Q ss_pred CCCCCCCCCCCCHHHHHH
Q 022702 74 GSQAGEKKRRLNMEQVKT 91 (293)
Q Consensus 74 ~~~~krkr~rft~~Ql~~ 91 (293)
++.+||.|+++..+|...
T Consensus 1291 g~~KKRGRK~LPpe~Ka~ 1308 (1463)
T PHA03308 1291 GGGKRRGRQRLPIRDRVY 1308 (1463)
T ss_pred CCccccCCCCCChHHhhh
Confidence 444566677788887655
No 122
>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=47.46 E-value=32 Score=24.03 Aligned_cols=47 Identities=15% Similarity=0.145 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTK 135 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk 135 (293)
+||..++.+|.....-.. ..++|..+|++++.|+.+..+=+.|..-.
T Consensus 3 ~LT~~E~~vl~~l~~G~~------~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMS------NKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred ccCHHHHHHHHHHHhcCC------cchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 578888888877654433 56899999999999999887766665443
No 123
>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=47.21 E-value=95 Score=27.28 Aligned_cols=36 Identities=14% Similarity=0.323 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 136 QLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMA 171 (293)
Q Consensus 136 ~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~ 171 (293)
.++.+...|+.+++.|..++..|..+...++.+...
T Consensus 108 ~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~ 143 (161)
T TIGR02894 108 RLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQT 143 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444555555555555555555555554444433
No 124
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=46.87 E-value=81 Score=25.86 Aligned_cols=36 Identities=22% Similarity=0.350 Sum_probs=22.8
Q ss_pred chhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 119 RQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREA 157 (293)
Q Consensus 119 ~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~ 157 (293)
||.+.||-.+|.-. ...+....++.+++.+++|-..
T Consensus 18 Rq~e~~FlqKr~~L---S~~kpe~~lkEEi~eLK~ElqR 53 (106)
T PF11594_consen 18 RQMEAFFLQKRFEL---SAYKPEQVLKEEINELKEELQR 53 (106)
T ss_pred HHHHHHHHHHHHHH---HhcCHHHHHHHHHHHHHHHHHH
Confidence 57789999988866 2333445566666666655433
No 125
>PF09744 Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; InterPro: IPR019143 This entry represents the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have a RhoGEF domain (IPR000219 from INTERPRO) at their C-terminal end.
Probab=46.15 E-value=1.6e+02 Score=25.65 Aligned_cols=75 Identities=24% Similarity=0.208 Sum_probs=34.6
Q ss_pred HHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHA 167 (293)
Q Consensus 88 Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~ 167 (293)
-|+.||.++..+.-...... +. ....-+.=.|.+|-|..+++.+..+..+. +.++.+...|+.+.+.|+.
T Consensus 34 vLE~Le~~~~~n~~~~~e~~--~L-----~~d~e~L~~q~~~ek~~r~~~e~~l~~~E---d~~~~e~k~L~~~v~~Le~ 103 (158)
T PF09744_consen 34 VLELLESLASRNQEHEVELE--LL-----REDNEQLETQYEREKELRKQAEEELLELE---DQWRQERKDLQSQVEQLEE 103 (158)
T ss_pred HHHHHHHHHHhhhhhhhHHH--HH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH
Confidence 46667777776663322211 11 11222333455677766666665544221 3333444444444444444
Q ss_pred HHHHh
Q 022702 168 EIMAL 172 (293)
Q Consensus 168 e~~~l 172 (293)
++..|
T Consensus 104 e~r~L 108 (158)
T PF09744_consen 104 ENRQL 108 (158)
T ss_pred HHHHH
Confidence 44433
No 126
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=46.08 E-value=39 Score=31.66 Aligned_cols=39 Identities=23% Similarity=0.362 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 022702 138 EKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSRE 176 (293)
Q Consensus 138 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 176 (293)
+.+++.|++.++.|-++|..|..+.+.+..++..+|...
T Consensus 110 ~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~~~~~~~ 148 (292)
T KOG4005|consen 110 QNENDSLRAINESLLAKNHELDSELELLRQELAELKQQQ 148 (292)
T ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhHHHH
Confidence 334444444444444555555555555555555555543
No 127
>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=45.01 E-value=78 Score=34.23 Aligned_cols=18 Identities=11% Similarity=0.252 Sum_probs=13.7
Q ss_pred HHHHHHHHHhCCCcchhh
Q 022702 105 ERKMQLARALGLQPRQVA 122 (293)
Q Consensus 105 ~~r~~LA~~lgL~~~qVk 122 (293)
..=.++|+.+||++..|.
T Consensus 483 S~a~~iA~~~Glp~~ii~ 500 (771)
T TIGR01069 483 SYAFEIAQRYGIPHFIIE 500 (771)
T ss_pred cHHHHHHHHhCcCHHHHH
Confidence 344578999999998875
No 128
>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=44.94 E-value=73 Score=29.21 Aligned_cols=41 Identities=24% Similarity=0.396 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 135 KQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 135 k~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
..+..++..|+.+.+.++..++.++.....++.++..|+..
T Consensus 52 ~~L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~q 92 (251)
T PF11932_consen 52 QELLAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQ 92 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445566666666666666666666655555555555444
No 129
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=44.79 E-value=55 Score=30.31 Aligned_cols=37 Identities=19% Similarity=0.303 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHH
Q 022702 134 TKQLEKDYDLLKRQYEAVKADRE---ALQAQNQKLHAEIM 170 (293)
Q Consensus 134 rk~~~~~~~~lk~~~~~l~~e~~---~l~~e~~~l~~e~~ 170 (293)
..+..++++.|++++..++.+.. .++.|+++|++-+.
T Consensus 71 ~~~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL~ 110 (276)
T PRK13922 71 LFDLREENEELKKELLELESRLQELEQLEAENARLRELLN 110 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34566777888888888777666 66788888887653
No 130
>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=44.61 E-value=1.1e+02 Score=28.69 Aligned_cols=56 Identities=21% Similarity=0.476 Sum_probs=31.2
Q ss_pred cchhhhhhhhhHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022702 118 PRQVAIWFQNRRARWK---------TKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALK 173 (293)
Q Consensus 118 ~~qVkvWFQNRRaK~K---------rk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 173 (293)
...+..||+.+=...+ ......++..++..+..+..+...|+..+..|...+..+.
T Consensus 186 ~~e~e~~y~~k~~~l~~~~~~~~~~~~~~~~E~~~~r~~~~~l~~el~~l~~~~~~Le~~l~~le 250 (312)
T PF00038_consen 186 REELEEWYQSKLEELRQQSEKSSEELESAKEELKELRRQIQSLQAELESLRAKNASLERQLRELE 250 (312)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhhhcccccccccccccccccccchhHhHHHHHHhhhhHhhhhhhccccchhhhhhhHHHHH
Confidence 4567889988733222 2223344555555555566666666665655555555444
No 131
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=43.72 E-value=96 Score=25.61 Aligned_cols=44 Identities=23% Similarity=0.256 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccc
Q 022702 135 KQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSREVT 178 (293)
Q Consensus 135 k~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~~ 178 (293)
...++.+..+-++.+.+|....++..||..|+-|+..|+.++..
T Consensus 11 ~~le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~~ 54 (114)
T COG4467 11 DNLEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKLRERLGE 54 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhCC
Confidence 45677788889999999999999999999999999999999744
No 132
>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=43.52 E-value=85 Score=29.65 Aligned_cols=34 Identities=21% Similarity=0.264 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHH
Q 022702 136 QLEKDYDLLKRQYEAVKADRE----ALQAQNQKLHAEI 169 (293)
Q Consensus 136 ~~~~~~~~lk~~~~~l~~e~~----~l~~e~~~l~~e~ 169 (293)
+..+|++.||+++..++++.. .++.||++|++.+
T Consensus 70 ~l~~EN~~Lr~e~~~l~~~~~~~~~~l~~EN~rLr~LL 107 (283)
T TIGR00219 70 NLEYENYKLRQELLKKNQQLEILTQNLKQENVRLRELL 107 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345556666666554433222 2455555555543
No 133
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=43.39 E-value=1.8e+02 Score=23.79 Aligned_cols=72 Identities=19% Similarity=0.181 Sum_probs=42.0
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
..|.|+.+++..|.. ...++.+|++-.+|+-.+.....-. .........|..+.+.+.++...|+
T Consensus 35 gyR~Y~~~~l~~l~~-------------I~~lr~lG~sL~eI~~~l~~~~~~~--~~~~~~~~~l~~~~~~l~~~i~~L~ 99 (127)
T TIGR02047 35 NYRVYTVGHVERLAF-------------IRNCRTLDMSLAEIRQLLRYQDKPE--KSCSDVNALLDEHISHVRARIIKLQ 99 (127)
T ss_pred CCCcCCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHHhhhCCC--CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466799999888843 3346789999999998875322110 0112223445555555555555555
Q ss_pred HHHHHHH
Q 022702 160 AQNQKLH 166 (293)
Q Consensus 160 ~e~~~l~ 166 (293)
.....|.
T Consensus 100 ~~~~~L~ 106 (127)
T TIGR02047 100 ALIEQLV 106 (127)
T ss_pred HHHHHHH
Confidence 4444444
No 134
>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=43.31 E-value=1.3e+02 Score=22.50 Aligned_cols=38 Identities=24% Similarity=0.278 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022702 137 LEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174 (293)
Q Consensus 137 ~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 174 (293)
++...+.|-..++.+++||..|+.+...+..|...|..
T Consensus 5 Le~kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~e 42 (65)
T TIGR02449 5 LAAQVEHLLEYLERLKSENRLLRAQEKTWREERAQLLE 42 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444555555566666666666666655555555443
No 135
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=43.20 E-value=88 Score=30.75 Aligned_cols=44 Identities=23% Similarity=0.368 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022702 129 RARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMAL 172 (293)
Q Consensus 129 RaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 172 (293)
|.+++-.+...+.+.||+.-+.++.....|+.+.+.|..++..+
T Consensus 222 r~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L 265 (365)
T KOG2391|consen 222 RREEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSL 265 (365)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence 34444444444455555555555544444444444444444433
No 136
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=42.97 E-value=66 Score=29.57 Aligned_cols=32 Identities=31% Similarity=0.476 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 138 EKDYDLLKRQYEAVKADREALQAQNQKLHAEI 169 (293)
Q Consensus 138 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~ 169 (293)
+++...|+.+.+.+..|++.|..++++|+.++
T Consensus 178 ~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i 209 (216)
T KOG1962|consen 178 QKKVDALKKQSEGLQDEYDRLLEEYSKLQEQI 209 (216)
T ss_pred HHHHHHHHHHHHHcccHHHHHHHHHHHHHHHH
Confidence 34455555555555555555555555555554
No 137
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=42.85 E-value=1.8e+02 Score=23.60 Aligned_cols=73 Identities=19% Similarity=0.219 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
..|.|+.+++..|.. ...++.+|++-..|+-.+....... .....-...|..+.+.+.++...|+
T Consensus 35 gyR~Y~~~~l~~l~~-------------I~~lr~~G~sL~eI~~~l~~~~~~~--~~~~~~~~~l~~~~~~l~~~i~~L~ 99 (127)
T cd04784 35 NYRLYDEEHLERLLF-------------IRRCRSLDMSLDEIRTLLQLQDDPE--ASCAEVNALIDEHLAHVRARIAELQ 99 (127)
T ss_pred CCeecCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHHhhhcCC--CcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466799999988743 3457788999999998886533210 0112223445555555555555555
Q ss_pred HHHHHHHH
Q 022702 160 AQNQKLHA 167 (293)
Q Consensus 160 ~e~~~l~~ 167 (293)
.....|..
T Consensus 100 ~~~~~L~~ 107 (127)
T cd04784 100 ALEKQLQA 107 (127)
T ss_pred HHHHHHHH
Confidence 44444433
No 138
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=42.80 E-value=1.9e+02 Score=23.66 Aligned_cols=73 Identities=15% Similarity=0.175 Sum_probs=40.4
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
..|.|+.+++..|.. ...++.+|++-..|+-++.-.+... .........+..+.+.+.++...|+
T Consensus 35 g~R~Y~~~~l~~l~~-------------I~~lr~~G~sL~eI~~~l~~~~~~~--~~~~~~~~~l~~~~~~l~~~i~~L~ 99 (126)
T cd04785 35 GYRLYGAAHVERLRF-------------IRRARDLGFSLEEIRALLALSDRPD--RSCAEADAIARAHLADVRARIADLR 99 (126)
T ss_pred CccccCHHHHHHHHH-------------HHHHHHCCCCHHHHHHHHhhhhcCC--CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456799999998843 2346788888888888886432210 0111123334444455555544444
Q ss_pred HHHHHHHH
Q 022702 160 AQNQKLHA 167 (293)
Q Consensus 160 ~e~~~l~~ 167 (293)
.-...|..
T Consensus 100 ~~~~~L~~ 107 (126)
T cd04785 100 RLEAELKR 107 (126)
T ss_pred HHHHHHHH
Confidence 44444433
No 139
>PRK14127 cell division protein GpsB; Provisional
Probab=42.60 E-value=66 Score=26.41 Aligned_cols=33 Identities=30% Similarity=0.499 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 022702 144 LKRQYEAVKADREALQAQNQKLHAEIMALKSRE 176 (293)
Q Consensus 144 lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 176 (293)
.-..|+.+..++..|+.++..|+.++.+++...
T Consensus 35 V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~ 67 (109)
T PRK14127 35 VIKDYEAFQKEIEELQQENARLKAQVDELTKQV 67 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 344555555666666666666666666555543
No 140
>PF11544 Spc42p: Spindle pole body component Spc42p; InterPro: IPR021611 Spc42p is a 42kDa component of the S.cerevisiae spindle body that localises to the electron dense central region of the SPB. Spc42p is a phosphoprotein which forms a polymeric layer at the periphery of the SPB central plaque. This functions during SPB duplication and also facilitates the attachment of the SPB to the nuclear membrane. ; PDB: 2Q6Q_B.
Probab=42.56 E-value=1.6e+02 Score=22.78 Aligned_cols=49 Identities=18% Similarity=0.279 Sum_probs=37.8
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022702 126 QNRRARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174 (293)
Q Consensus 126 QNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 174 (293)
||+--+.+-...+++++.|+...+.++..-...-.-+.+|+++...+..
T Consensus 6 qNk~L~~kL~~K~eEI~rLn~lv~sLR~KLiKYt~LnkkLq~~~~~~~~ 54 (76)
T PF11544_consen 6 QNKELKKKLNDKQEEIDRLNILVGSLRGKLIKYTELNKKLQDQLLNLQR 54 (76)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 6777777777788889999999988888877777777777777665544
No 141
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=42.56 E-value=84 Score=29.53 Aligned_cols=38 Identities=18% Similarity=0.310 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022702 135 KQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMAL 172 (293)
Q Consensus 135 k~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 172 (293)
.+.......|.+++++|+.+.+.|+.++.+|+.-+...
T Consensus 218 ~e~~~r~~~leken~~lr~~v~~l~~el~~~~~~~~~~ 255 (269)
T KOG3119|consen 218 DEMAHRVAELEKENEALRTQVEQLKKELATLRRLFLQL 255 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45555566777778888888888888888877766543
No 142
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=42.40 E-value=25 Score=23.66 Aligned_cols=40 Identities=23% Similarity=0.263 Sum_probs=19.7
Q ss_pred CCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhh
Q 022702 81 KRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWF 125 (293)
Q Consensus 81 r~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWF 125 (293)
.+.||.++...++..+... .-..+||+.||.+...|..+.
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ----------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHH
Confidence 3568889999998887533 334579999999998887664
No 143
>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=42.30 E-value=42 Score=32.84 Aligned_cols=20 Identities=25% Similarity=0.350 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 022702 139 KDYDLLKRQYEAVKADREAL 158 (293)
Q Consensus 139 ~~~~~lk~~~~~l~~e~~~l 158 (293)
+|+..||++++.|+.+.++|
T Consensus 39 ~EN~~LKkEN~~Lk~eVerL 58 (420)
T PF07407_consen 39 MENHSLKKENNDLKIEVERL 58 (420)
T ss_pred HHhHHHHHHHHHHHHHHHHH
Confidence 33444444444444444443
No 144
>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=42.24 E-value=40 Score=24.70 Aligned_cols=44 Identities=25% Similarity=0.360 Sum_probs=22.6
Q ss_pred CCCCCHHH-HHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhh
Q 022702 81 KRRLNMEQ-VKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQ 126 (293)
Q Consensus 81 r~rft~~Q-l~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQ 126 (293)
|+.|+..- |.+++..+ ....--...| ..|+++|+.+++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~-~~~nc~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAE-KDNNCKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHH-H-TTTTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHH-HccchhhhHH-HHHHHhCccHHHHHHHHH
Confidence 44566663 45555444 3332332333 349999999999999954
No 145
>PF03234 CDC37_N: Cdc37 N terminal kinase binding; InterPro: IPR013855 In Saccharomyces cerevisiae (Baker's yeast), cell division control protein Cdc37 is required for the productive formation of Cdc28-cyclin complexes. Cdc37 may be a kinase targeting subunit of Hsp90 [].
Probab=41.89 E-value=1e+02 Score=27.43 Aligned_cols=45 Identities=20% Similarity=0.338 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 131 RWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 131 K~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
|||++++.+..+..+++.+.++.+.......+..++.-+..++..
T Consensus 31 rwk~~~~~e~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~ 75 (177)
T PF03234_consen 31 RWKHQARHERREERKQEIEELKYERKINEKLLKRIQKLLSALDKE 75 (177)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 456666666666677777777766665555555555555555444
No 146
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=41.82 E-value=94 Score=33.68 Aligned_cols=17 Identities=24% Similarity=0.509 Sum_probs=13.4
Q ss_pred HHHHHHHHhCCCcchhh
Q 022702 106 RKMQLARALGLQPRQVA 122 (293)
Q Consensus 106 ~r~~LA~~lgL~~~qVk 122 (293)
.=.++|+.+||++..|.
T Consensus 489 ~a~~iA~~~Glp~~ii~ 505 (782)
T PRK00409 489 NAFEIAKRLGLPENIIE 505 (782)
T ss_pred HHHHHHHHhCcCHHHHH
Confidence 44578999999998875
No 147
>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=41.81 E-value=48 Score=25.58 Aligned_cols=26 Identities=27% Similarity=0.382 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 150 AVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 150 ~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
.+..||..|+.+.++|.+|+..++..
T Consensus 4 ei~eEn~~Lk~eiqkle~ELq~~~~~ 29 (76)
T PF07334_consen 4 EIQEENARLKEEIQKLEAELQQNKRE 29 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45566666666667666666655443
No 148
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=41.61 E-value=1.3e+02 Score=23.76 Aligned_cols=35 Identities=14% Similarity=0.175 Sum_probs=27.3
Q ss_pred CCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhh
Q 022702 81 KRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNR 128 (293)
Q Consensus 81 r~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNR 128 (293)
.++|+.+.+..|. ....++.+|++-..|+-+|...
T Consensus 34 ~r~Y~~~~~~~l~-------------~I~~lr~~G~sL~eI~~~l~~~ 68 (107)
T cd04777 34 QYFFDEKCQDDLE-------------FILELKGLGFSLIEIQKIFSYK 68 (107)
T ss_pred ccccCHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHHhc
Confidence 4468988887764 3456888999999999999764
No 149
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=40.95 E-value=1.2e+02 Score=24.04 Aligned_cols=12 Identities=17% Similarity=0.728 Sum_probs=6.3
Q ss_pred hhhhhhhHHHHH
Q 022702 122 AIWFQNRRARWK 133 (293)
Q Consensus 122 kvWFQNRRaK~K 133 (293)
-+|||=++++.+
T Consensus 20 y~~~k~~ka~~~ 31 (87)
T PF10883_consen 20 YLWWKVKKAKKQ 31 (87)
T ss_pred HHHHHHHHHHHH
Confidence 356665555433
No 150
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=40.87 E-value=4.1e+02 Score=27.24 Aligned_cols=30 Identities=17% Similarity=0.252 Sum_probs=16.2
Q ss_pred CCCHHHHHHHHHh-Hhh-CCCCCHHHHHHHHH
Q 022702 83 RLNMEQVKTLEKN-FEL-GNKLEPERKMQLAR 112 (293)
Q Consensus 83 rft~~Ql~~LE~~-F~~-~~~p~~~~r~~LA~ 112 (293)
++|.+....|.+. +-. ..+|--+.-+++.+
T Consensus 220 ~LteeEkrLL~kEG~slPs~lPLTKaEEriLK 251 (472)
T KOG0709|consen 220 VLTEEEKRLLTKEGYSLPSKLPLTKAEERILK 251 (472)
T ss_pred eccHHHHHHHHhccCcCcccCCchHHHHHHHH
Confidence 5788888877765 222 22444443344433
No 151
>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=40.62 E-value=64 Score=30.48 Aligned_cols=38 Identities=16% Similarity=0.103 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhhhccc
Q 022702 140 DYDLLKRQYEAVKADREALQAQNQ----KLHAEIMALKSREV 177 (293)
Q Consensus 140 ~~~~lk~~~~~l~~e~~~l~~e~~----~l~~e~~~lk~~~~ 177 (293)
.+..++++++.|++++..+..+.+ .+++|+.+|+.-+.
T Consensus 67 ~~~~l~~EN~~Lr~e~~~l~~~~~~~~~~l~~EN~rLr~LL~ 108 (283)
T TIGR00219 67 DVNNLEYENYKLRQELLKKNQQLEILTQNLKQENVRLRELLN 108 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 456677888888888766643333 37888888887653
No 152
>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=40.39 E-value=1.1e+02 Score=21.34 Aligned_cols=30 Identities=27% Similarity=0.456 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022702 144 LKRQYEAVKADREALQAQNQKLHAEIMALK 173 (293)
Q Consensus 144 lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 173 (293)
-+.....+..+...|..+|..|..++..|+
T Consensus 23 kk~~~~~le~~~~~L~~en~~L~~~i~~L~ 52 (54)
T PF07716_consen 23 KKQREEELEQEVQELEEENEQLRQEIAQLE 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 356677777778888888888888877664
No 153
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=40.24 E-value=1.1e+02 Score=29.50 Aligned_cols=40 Identities=18% Similarity=0.283 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022702 133 KTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMAL 172 (293)
Q Consensus 133 Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 172 (293)
+++.++.+++.|.+.++.||.....|..|.+.|++=+.+.
T Consensus 249 e~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e~ 288 (294)
T KOG4571|consen 249 EKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILEV 288 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455667788999999999999999999998888766544
No 154
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=39.99 E-value=77 Score=30.72 Aligned_cols=54 Identities=13% Similarity=0.308 Sum_probs=31.0
Q ss_pred hhhhhhhhHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022702 121 VAIWFQNRRARWKTKQ-LEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174 (293)
Q Consensus 121 VkvWFQNRRaK~Krk~-~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 174 (293)
.||||+|.|+-.+-.. -....+.+.+.+..++..+..-+.+.++|..++.++..
T Consensus 16 CKiWi~dN~~Sv~~He~GkrHke~V~Kritdi~rks~~kekeekKls~~la~mEa 70 (336)
T KOG0150|consen 16 CKIWIKDNPASVRFHERGKRHKENVAKRITDIHRKSLKKEKEEKKLSKELAAMEA 70 (336)
T ss_pred hhhhhcCChHHHHhHhhhhHHHHHHHHHHHHHHHhhHHHHHHHHhhhhHHHHHHH
Confidence 5899999887655322 22334455555555555555555555566666555443
No 155
>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=39.86 E-value=1e+02 Score=23.65 Aligned_cols=20 Identities=15% Similarity=0.298 Sum_probs=16.9
Q ss_pred HHHHHHhCCCcchhhhhhhh
Q 022702 108 MQLARALGLQPRQVAIWFQN 127 (293)
Q Consensus 108 ~~LA~~lgL~~~qVkvWFQN 127 (293)
.++|+.+|++++.|+.|-+.
T Consensus 5 ~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 5 SVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 47899999999999999754
No 156
>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=39.51 E-value=86 Score=24.28 Aligned_cols=21 Identities=14% Similarity=0.370 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 022702 142 DLLKRQYEAVKADREALQAQN 162 (293)
Q Consensus 142 ~~lk~~~~~l~~e~~~l~~e~ 162 (293)
..++.+.+.++.|+..|+.|.
T Consensus 45 ~~l~~~~~~l~~e~~~L~lE~ 65 (97)
T PF04999_consen 45 QQLEKEIDQLQEENERLRLEI 65 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 333344444444444444333
No 157
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=39.39 E-value=1.4e+02 Score=23.19 Aligned_cols=42 Identities=26% Similarity=0.305 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHhhhc
Q 022702 134 TKQLEKDYDLLKRQYEAVKADREALQAQNQ-------KLHAEIMALKSR 175 (293)
Q Consensus 134 rk~~~~~~~~lk~~~~~l~~e~~~l~~e~~-------~l~~e~~~lk~~ 175 (293)
.++.-..+..|+-+++.+|+.|..|..+++ .|..++..+|..
T Consensus 13 IqqAvdtI~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E 61 (79)
T PRK15422 13 VQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQ 61 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 334444455555555555555555555444 366666666654
No 158
>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=39.16 E-value=1.1e+02 Score=31.43 Aligned_cols=49 Identities=16% Similarity=0.343 Sum_probs=20.8
Q ss_pred hhhHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022702 126 QNRRARWKTKQLEKDY-DLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174 (293)
Q Consensus 126 QNRRaK~Krk~~~~~~-~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 174 (293)
+|.|-|.|........ .++......+..+.+.|+.+.++++..+..|..
T Consensus 88 eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~~~~~~~~l~~l~~ 137 (472)
T TIGR03752 88 ENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQLQGLIDQLQR 137 (472)
T ss_pred HHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555554444433332 223333333444444444444444444444433
No 159
>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=39.04 E-value=1.2e+02 Score=27.70 Aligned_cols=51 Identities=16% Similarity=0.257 Sum_probs=20.9
Q ss_pred hhhhhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 120 QVAIWFQNR-RARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIM 170 (293)
Q Consensus 120 qVkvWFQNR-RaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~ 170 (293)
.|.-|...+ ....+-++...+.+.|+.+++.+......++.+...|+.++.
T Consensus 43 ~id~~~~e~~~L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~qi~ 94 (251)
T PF11932_consen 43 RIDQWDDEKQELLAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQIE 94 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455333 222233334444444444444444444444444444443333
No 160
>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=38.92 E-value=44 Score=26.64 Aligned_cols=35 Identities=31% Similarity=0.519 Sum_probs=19.8
Q ss_pred HHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHH
Q 022702 89 VKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQL 137 (293)
Q Consensus 89 l~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~ 137 (293)
+....-.|+.++||...--.. | =.|||.+||+.+.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~ 48 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQR 48 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHH
Confidence 445566688999997542111 1 1589999998764
No 161
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=38.81 E-value=1e+02 Score=23.43 Aligned_cols=49 Identities=18% Similarity=0.235 Sum_probs=26.6
Q ss_pred hhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022702 121 VAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMAL 172 (293)
Q Consensus 121 VkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 172 (293)
++|.|-..|.. +........+-.++-.++.+...|+.+++.++..+..+
T Consensus 21 LrI~fLee~l~---~~~~~~~~~~~keNieLKve~~~L~~el~~~~~~l~~a 69 (75)
T PF07989_consen 21 LRIYFLEERLQ---KLGPESIEELLKENIELKVEVESLKRELQEKKKLLKEA 69 (75)
T ss_pred HHHHHHHHHHH---hcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36777655554 11223333444455556666666666666666665544
No 162
>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion
Probab=38.47 E-value=1.1e+02 Score=27.27 Aligned_cols=40 Identities=33% Similarity=0.409 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022702 135 KQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174 (293)
Q Consensus 135 k~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 174 (293)
..+...+..|+.+.+..+..|+.|..++++|..+...+..
T Consensus 77 ~~L~qvN~lLReQLEq~~~~N~~L~~dl~klt~~~~~l~~ 116 (182)
T PF15035_consen 77 EELAQVNALLREQLEQARKANEALQEDLQKLTQDWERLRD 116 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444567778888888888888888888887777665433
No 163
>PRK14127 cell division protein GpsB; Provisional
Probab=38.24 E-value=91 Score=25.59 Aligned_cols=50 Identities=20% Similarity=0.416 Sum_probs=34.4
Q ss_pred CCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022702 115 GLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALK 173 (293)
Q Consensus 115 gL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 173 (293)
|..+.+|.-+.. +...+|+.+..++..|++++..|+.+...++.++....
T Consensus 22 GYd~~EVD~FLd---------~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~~~~ 71 (109)
T PRK14127 22 GYDQDEVDKFLD---------DVIKDYEAFQKEIEELQQENARLKAQVDELTKQVSVGA 71 (109)
T ss_pred CCCHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 555555555542 34457777788888888888888888888887776553
No 164
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=38.15 E-value=1.3e+02 Score=23.79 Aligned_cols=32 Identities=22% Similarity=0.438 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 129 RARWKTKQLEKDYDLLKRQYEAVKADREALQA 160 (293)
Q Consensus 129 RaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~ 160 (293)
...||-++.+++.+.|..+++.++.|......
T Consensus 20 y~~~k~~ka~~~~~kL~~en~qlk~Ek~~~~~ 51 (87)
T PF10883_consen 20 YLWWKVKKAKKQNAKLQKENEQLKTEKAVAET 51 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667666665555555544444444444443
No 165
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=37.86 E-value=77 Score=32.22 Aligned_cols=24 Identities=33% Similarity=0.677 Sum_probs=16.5
Q ss_pred hhhh---hhhHHHHHHHHHHHHHHHHH
Q 022702 122 AIWF---QNRRARWKTKQLEKDYDLLK 145 (293)
Q Consensus 122 kvWF---QNRRaK~Krk~~~~~~~~lk 145 (293)
-+|| ||+.+|.+-.+..++++.|+
T Consensus 229 gcw~ay~Qnk~akehv~km~kdle~Lq 255 (575)
T KOG4403|consen 229 GCWFAYRQNKKAKEHVNKMMKDLEGLQ 255 (575)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHHHHHH
Confidence 5788 89999888766655544443
No 166
>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []. Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].
Probab=37.76 E-value=1.8e+02 Score=27.91 Aligned_cols=88 Identities=16% Similarity=0.129 Sum_probs=40.9
Q ss_pred HHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 86 MEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKL 165 (293)
Q Consensus 86 ~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l 165 (293)
.-||..||..+++.+.-...++.+.+..-.-.-+-+-+ +++ .-..|+++..++.....+..-+.......+.+.++|
T Consensus 38 QfQleSlEAaLqKQKqK~e~ek~e~s~LkREnq~l~e~--c~~-lek~rqKlshdlq~Ke~qv~~lEgQl~s~Kkqie~L 114 (307)
T PF10481_consen 38 QFQLESLEAALQKQKQKVEEEKNEYSALKRENQSLMES--CEN-LEKTRQKLSHDLQVKESQVNFLEGQLNSCKKQIEKL 114 (307)
T ss_pred HHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHH--HHH-HHHHHHHhhHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 34788888888777654444444433211100000000 111 111233344444444444444555555555555566
Q ss_pred HHHHHHhhhcc
Q 022702 166 HAEIMALKSRE 176 (293)
Q Consensus 166 ~~e~~~lk~~~ 176 (293)
..|+..+|..+
T Consensus 115 eqelkr~KsEL 125 (307)
T PF10481_consen 115 EQELKRCKSEL 125 (307)
T ss_pred HHHHHHHHHHH
Confidence 66666555554
No 167
>PRK04217 hypothetical protein; Provisional
Probab=37.69 E-value=71 Score=26.16 Aligned_cols=40 Identities=13% Similarity=0.081 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhh
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQN 127 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQN 127 (293)
.++.+|..++...|...- ...+||+.+|++...|+..+..
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHH
Confidence 478888888877764433 4567999999999999877754
No 168
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=37.56 E-value=1.2e+02 Score=24.84 Aligned_cols=53 Identities=38% Similarity=0.404 Sum_probs=39.8
Q ss_pred hhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 121 VAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 121 VkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
+.+||+- ..|.-+..-.++..+..+...+.++++.|.+++..|.+++..|+..
T Consensus 34 ~l~~f~~--~~~~g~~~~~~~~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 34 LLALFQY--LAWFGKNGAADVLQLQRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHH--HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 4456653 3344455556677888888888999999999999999999888776
No 169
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=37.11 E-value=77 Score=29.12 Aligned_cols=41 Identities=24% Similarity=0.379 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhhhccccc
Q 022702 139 KDYDLLKRQYEA-VKADREALQAQNQKLHAEIMALKSREVTE 179 (293)
Q Consensus 139 ~~~~~lk~~~~~-l~~e~~~l~~e~~~l~~e~~~lk~~~~~~ 179 (293)
.+...++.+... .+.|...|+.|+++|..+++++|.....+
T Consensus 101 ~~f~kiRsel~S~e~sEF~~lr~e~EklkndlEk~ks~lr~e 142 (220)
T KOG3156|consen 101 VDFAKIRSELVSIERSEFANLRAENEKLKNDLEKLKSSLRHE 142 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555555544 34677888888888888888888776544
No 170
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=36.45 E-value=1.1e+02 Score=31.32 Aligned_cols=36 Identities=25% Similarity=0.298 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 022702 141 YDLLKRQYEAVKADREALQAQNQKLHAEIMALKSRE 176 (293)
Q Consensus 141 ~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 176 (293)
.+.+.++.+.+.+..+.++.+++.|++++.+++...
T Consensus 92 lq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~~~~~ 127 (475)
T PRK13729 92 LDVLNKQRGDDQRRIEKLGQDNAALAEQVKALGANP 127 (475)
T ss_pred HHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcCC
Confidence 344446666677777777777777777776665553
No 171
>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=36.36 E-value=1.9e+02 Score=24.04 Aligned_cols=13 Identities=15% Similarity=0.023 Sum_probs=5.4
Q ss_pred CCHHHHHHHHHHh
Q 022702 102 LEPERKMQLARAL 114 (293)
Q Consensus 102 p~~~~r~~LA~~l 114 (293)
++...-..|...+
T Consensus 13 ~~~~~ve~L~s~l 25 (120)
T PF12325_consen 13 PSVQLVERLQSQL 25 (120)
T ss_pred chHHHHHHHHHHH
Confidence 3333334444444
No 172
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=36.31 E-value=69 Score=25.09 Aligned_cols=44 Identities=16% Similarity=0.153 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARW 132 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~ 132 (293)
++..+...+...|-. ...-.++|..+|+++..|..+...-+.|.
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKL 154 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 566666666544322 22345899999999999998876544443
No 173
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=35.98 E-value=1e+02 Score=32.13 Aligned_cols=39 Identities=28% Similarity=0.296 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 137 LEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 137 ~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
++..+.+|-++++.|++||..|+.+...|..|...+|-.
T Consensus 307 Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~En~~~kvp 345 (655)
T KOG4343|consen 307 LEARLQALLSENEQLKKENATLKRQLDELVSENQRLKVP 345 (655)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCcccccC
Confidence 455666677777777777777777777777776655443
No 174
>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=35.89 E-value=24 Score=23.29 Aligned_cols=21 Identities=19% Similarity=0.306 Sum_probs=18.2
Q ss_pred HHHHHHhCCCcchhhhhhhhh
Q 022702 108 MQLARALGLQPRQVAIWFQNR 128 (293)
Q Consensus 108 ~~LA~~lgL~~~qVkvWFQNR 128 (293)
.++|+.+|+++..|+.|.++-
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHCC
Confidence 578999999999999997654
No 175
>PRK10072 putative transcriptional regulator; Provisional
Probab=35.87 E-value=46 Score=26.56 Aligned_cols=41 Identities=24% Similarity=0.322 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRA 130 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRa 130 (293)
+.+...+..|...-... ..+||+.+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 44666677764433222 568999999999999999988764
No 176
>PF14662 CCDC155: Coiled-coil region of CCDC155
Probab=35.80 E-value=1.4e+02 Score=26.99 Aligned_cols=40 Identities=28% Similarity=0.356 Sum_probs=16.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 127 NRRARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLH 166 (293)
Q Consensus 127 NRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~ 166 (293)
||+--...++.+++...|-.+++.|..+|..+..+.+.++
T Consensus 83 ~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl~~e~~~lk 122 (193)
T PF14662_consen 83 NRSLLAQARQLEKEQQSLVAEIETLQEENGKLLAERDGLK 122 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhHH
Confidence 3333333344444444444444444444444443333333
No 177
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=35.31 E-value=82 Score=25.68 Aligned_cols=43 Identities=14% Similarity=0.159 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR 131 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK 131 (293)
++..+..++...|-.+ ..-.++|..+|++...|+.|...-|.|
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEK 149 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 6666666666555332 235689999999999999997644433
No 178
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=35.20 E-value=1.4e+02 Score=29.63 Aligned_cols=43 Identities=23% Similarity=0.382 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccc
Q 022702 136 QLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSREVT 178 (293)
Q Consensus 136 ~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~~ 178 (293)
.++.++..|+.+.+.+..+...++.+..+++.|+.+++.....
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 (398)
T PTZ00454 26 ELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQSVPLV 68 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCce
Confidence 3445667777888888888888888888899998888776543
No 179
>PF14645 Chibby: Chibby family
Probab=34.88 E-value=1.5e+02 Score=24.43 Aligned_cols=24 Identities=13% Similarity=0.310 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 142 DLLKRQYEAVKADREALQAQNQKL 165 (293)
Q Consensus 142 ~~lk~~~~~l~~e~~~l~~e~~~l 165 (293)
..+++++..|.+||..|+.+++-|
T Consensus 74 ~~l~~~n~~L~EENN~Lklk~elL 97 (116)
T PF14645_consen 74 QRLRKENQQLEEENNLLKLKIELL 97 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444444444444433
No 180
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=34.83 E-value=1.7e+02 Score=21.84 Aligned_cols=24 Identities=21% Similarity=0.335 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 147 QYEAVKADREALQAQNQKLHAEIM 170 (293)
Q Consensus 147 ~~~~l~~e~~~l~~e~~~l~~e~~ 170 (293)
+....-.++..|+.+++.|+.|+.
T Consensus 41 ~l~~a~~e~~~Lk~E~e~L~~el~ 64 (69)
T PF14197_consen 41 QLGDAYEENNKLKEENEALRKELE 64 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444455555555555555544
No 181
>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=34.43 E-value=1.6e+02 Score=26.57 Aligned_cols=40 Identities=15% Similarity=0.327 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 022702 137 LEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSRE 176 (293)
Q Consensus 137 ~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 176 (293)
.-.++..|......+...|-.+......|.+|+.+++...
T Consensus 173 ~~~~L~~Le~~W~~~v~kn~eie~a~~~Le~ei~~l~~~~ 212 (221)
T PF05700_consen 173 AGEELRYLEQRWKELVSKNLEIEVACEELEQEIEQLKRKA 212 (221)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344556666666677777777777778888887776653
No 182
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=34.25 E-value=2.6e+02 Score=22.83 Aligned_cols=74 Identities=18% Similarity=0.166 Sum_probs=42.6
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
..|.|+.+++..|.. ....+.+|++-.+|+.++....... .........|+.+.+.+.++...|+
T Consensus 35 g~R~Y~~~~~~~l~~-------------I~~lr~~G~sL~eI~~~l~~~~~~~--~~~~~~~~~l~~~~~~l~~~i~~L~ 99 (127)
T cd01108 35 GYRVYNQRDIEELRF-------------IRRARDLGFSLEEIRELLALWRDPS--RASADVKALALEHIAELERKIAELQ 99 (127)
T ss_pred CceecCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHHHHhCCC--CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466799999888843 2346788999999998886322110 0111223445555555555555555
Q ss_pred HHHHHHHHH
Q 022702 160 AQNQKLHAE 168 (293)
Q Consensus 160 ~e~~~l~~e 168 (293)
...+.|..-
T Consensus 100 ~~~~~l~~~ 108 (127)
T cd01108 100 AMRRTLQQL 108 (127)
T ss_pred HHHHHHHHH
Confidence 444444433
No 183
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=34.05 E-value=95 Score=25.67 Aligned_cols=29 Identities=24% Similarity=0.422 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 138 EKDYDLLKRQYEAVKADREALQAQNQKLH 166 (293)
Q Consensus 138 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~ 166 (293)
+++.+.||.++..|.+.+..|+.||.-|+
T Consensus 66 REEVe~Lk~qI~eL~er~~~Le~EN~lLk 94 (123)
T KOG4797|consen 66 REEVEVLKEQIRELEERNSALERENSLLK 94 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566677777777777777666665544
No 184
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine 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, and organic su
Probab=33.97 E-value=2.7e+02 Score=23.06 Aligned_cols=77 Identities=19% Similarity=0.236 Sum_probs=43.9
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
..|.|+..++..|+. ...++.+|++-.+|+-.+...+... ..+.-...|..+.+.+.++...|+
T Consensus 35 gyR~Y~~~~v~~l~~-------------I~~lr~~GfsL~eI~~ll~~~~~~~---~~~~~~~~l~~k~~~i~~~i~~L~ 98 (131)
T cd04786 35 GYRDYPPETVWVLEI-------------ISSAQQAGFSLDEIRQLLPADASNW---QHDELLAALERKVADIEALEARLA 98 (131)
T ss_pred CCeecCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhcccCCC---CHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456799999888844 2346778888888888886432111 112223445555555555555555
Q ss_pred HHHHHHHHHHHHh
Q 022702 160 AQNQKLHAEIMAL 172 (293)
Q Consensus 160 ~e~~~l~~e~~~l 172 (293)
.-...|..-+..+
T Consensus 99 ~~~~~L~~~i~~~ 111 (131)
T cd04786 99 QNKAQLLVLIDLI 111 (131)
T ss_pred HHHHHHHHHHHHH
Confidence 4444444444333
No 185
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=33.81 E-value=69 Score=27.65 Aligned_cols=43 Identities=16% Similarity=0.136 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR 131 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK 131 (293)
++..+..+|...|-.+ ..-.++|+.||++...|+++...-|.+
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~ 185 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIR 185 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHH
Confidence 6667777766554222 234589999999999999988544443
No 186
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=33.78 E-value=1.4e+02 Score=31.15 Aligned_cols=40 Identities=28% Similarity=0.509 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 136 QLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 136 ~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
.++.++..+++.+..+..+...|+.++..|..++.+++..
T Consensus 152 ~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~r~~ 191 (546)
T KOG0977|consen 152 ELEAEINTLKRRIKALEDELKRLKAENSRLREELARARKQ 191 (546)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 4455566666666666666666666666666666666553
No 187
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=33.75 E-value=1.2e+02 Score=32.14 Aligned_cols=34 Identities=21% Similarity=0.359 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022702 141 YDLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174 (293)
Q Consensus 141 ~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 174 (293)
.+.|+.++..|+++.+.++.++++|..++..++.
T Consensus 431 ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~r 464 (652)
T COG2433 431 VERLEEENSELKRELEELKREIEKLESELERFRR 464 (652)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444555555555555555555555444433
No 188
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=33.21 E-value=1.3e+02 Score=30.37 Aligned_cols=53 Identities=19% Similarity=0.245 Sum_probs=41.1
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHhhhcccc
Q 022702 126 QNRRARWKTKQLEKDYDLLKRQYEAVKADRE--ALQAQNQKLHAEIMALKSREVT 178 (293)
Q Consensus 126 QNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~--~l~~e~~~l~~e~~~lk~~~~~ 178 (293)
-+++++.|.+++++.++.|..+.+-++.+.. .++.++..++.++.+++.....
T Consensus 52 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 106 (438)
T PTZ00361 52 PNTKCRLRLLKLERIKDYLLLEEEFITNQEAQKPAQEKNEAELKKVDDLRGSPLS 106 (438)
T ss_pred CchhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhCCCcE
Confidence 3667777777787888888877777777764 6788888999999998877543
No 189
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=33.00 E-value=1.7e+02 Score=27.42 Aligned_cols=31 Identities=29% Similarity=0.470 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 141 YDLLKRQYEAVKADREALQAQNQKLHAEIMA 171 (293)
Q Consensus 141 ~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~ 171 (293)
|..+|.+++.+.+|+..|..+++.|++++.+
T Consensus 137 ~ee~kekl~E~~~EkeeL~~eleele~e~ee 167 (290)
T COG4026 137 YEELKEKLEELQKEKEELLKELEELEAEYEE 167 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444444444444444433
No 190
>smart00340 HALZ homeobox associated leucin zipper.
Probab=32.83 E-value=1.1e+02 Score=21.04 Aligned_cols=29 Identities=28% Similarity=0.418 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 147 QYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 147 ~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
..+-||.=-+.|-.+|.+|+.|+.+|+.-
T Consensus 6 dCe~LKrcce~LteeNrRL~ke~~eLral 34 (44)
T smart00340 6 DCELLKRCCESLTEENRRLQKEVQELRAL 34 (44)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45667788888999999999999888754
No 191
>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=32.49 E-value=16 Score=27.95 Aligned_cols=34 Identities=15% Similarity=0.175 Sum_probs=25.6
Q ss_pred HhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhh
Q 022702 94 KNFELGNKLEPERKMQLARALGLQPRQVAIWFQN 127 (293)
Q Consensus 94 ~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQN 127 (293)
..|...+|.......+||..+|+++..|+.|+.+
T Consensus 22 ~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 22 AAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 3455555545555678999999999999999864
No 192
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=32.34 E-value=2.5e+02 Score=22.18 Aligned_cols=67 Identities=21% Similarity=0.310 Sum_probs=41.0
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
..|.|+...+..|.. ....+.+|++-..|+-.+..... ..-...++.+.+.+.++...++
T Consensus 36 gyR~Y~~~~i~~l~~-------------I~~lr~~G~sl~~i~~l~~~~~~-------~~~~~~l~~~~~~l~~~i~~l~ 95 (108)
T cd01107 36 GYRYYSAEQLERLNR-------------IKYLRDLGFPLEEIKEILDADND-------DELRKLLREKLAELEAEIEELQ 95 (108)
T ss_pred CccccCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhcCCH-------HHHHHHHHHHHHHHHHHHHHHH
Confidence 456799999888843 23457789999999988876554 2223344455555555555544
Q ss_pred HHHHHHH
Q 022702 160 AQNQKLH 166 (293)
Q Consensus 160 ~e~~~l~ 166 (293)
...+.|.
T Consensus 96 ~~~~~l~ 102 (108)
T cd01107 96 RILRLLE 102 (108)
T ss_pred HHHHHHH
Confidence 4443333
No 193
>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=32.28 E-value=1.5e+02 Score=21.49 Aligned_cols=33 Identities=6% Similarity=0.280 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 143 LLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 143 ~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
.+..+..++......++.|++.+..++..++..
T Consensus 4 elEn~~~~~~~~i~tvk~en~~i~~~ve~i~en 36 (55)
T PF05377_consen 4 ELENELPRIESSINTVKKENEEISESVEKIEEN 36 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555556666666666666666555543
No 194
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=32.11 E-value=1.8e+02 Score=23.65 Aligned_cols=38 Identities=24% Similarity=0.372 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022702 137 LEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174 (293)
Q Consensus 137 ~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 174 (293)
+......++..+..+..+.+.++....++.+++..+|.
T Consensus 78 L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~ 115 (118)
T PF13815_consen 78 LSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKK 115 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445555666666666666666666666666666554
No 195
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=32.01 E-value=58 Score=27.51 Aligned_cols=44 Identities=11% Similarity=0.251 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARW 132 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~ 132 (293)
++..+..++...|- ......++|..+|+++..|+++...-|.+.
T Consensus 130 L~~~~r~i~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~Rar~~L 173 (179)
T PRK12514 130 LEKDRAAAVRRAYL-----EGLSYKELAERHDVPLNTMRTWLRRSLLKL 173 (179)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCChHHHHHHHHHHHHHH
Confidence 55555555555542 222356899999999999999886444443
No 196
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=31.83 E-value=56 Score=27.13 Aligned_cols=40 Identities=15% Similarity=0.013 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhh
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQN 127 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQN 127 (293)
.++..+..+|...|-.+ ..-.++|..+|++...|+.|...
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~r 167 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFR 167 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 37777777777654322 22457899999999999999863
No 197
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=31.76 E-value=2.5e+02 Score=21.98 Aligned_cols=36 Identities=22% Similarity=0.199 Sum_probs=26.0
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhh
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNR 128 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNR 128 (293)
..+.|+.+++..|... ...+.+|++-..|+..+...
T Consensus 35 g~R~Y~~~dl~~l~~I-------------~~l~~~G~~l~ei~~~~~~~ 70 (102)
T cd04775 35 NYRLYSEADLSRLEKI-------------VFLQAGGLPLEEIAGCLAQP 70 (102)
T ss_pred CCeeeCHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHcCC
Confidence 4567999999988542 23477888888888777653
No 198
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=31.52 E-value=82 Score=26.03 Aligned_cols=44 Identities=16% Similarity=0.135 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARW 132 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~ 132 (293)
++..+..++...|.. ...-.+||..+|+++..|+.|..--|.|.
T Consensus 126 L~~~~r~i~~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~l 169 (179)
T PRK11924 126 LPVKQREVFLLRYVE-----GLSYREIAEILGVPVGTVKSRLRRARQLL 169 (179)
T ss_pred CCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 555555555544422 22346899999999999999986434333
No 199
>PF06210 DUF1003: Protein of unknown function (DUF1003); InterPro: IPR010406 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=31.37 E-value=2.5e+02 Score=22.86 Aligned_cols=17 Identities=41% Similarity=0.517 Sum_probs=10.0
Q ss_pred hhhHHHHHHHHHHHHHH
Q 022702 126 QNRRARWKTKQLEKDYD 142 (293)
Q Consensus 126 QNRRaK~Krk~~~~~~~ 142 (293)
|||-++.-+.+.+.+++
T Consensus 57 QNRq~~~dr~ra~~D~~ 73 (108)
T PF06210_consen 57 QNRQAARDRLRAELDYQ 73 (108)
T ss_pred hhHhHHHHHHHHHHHHH
Confidence 78766555555555543
No 200
>PF13518 HTH_28: Helix-turn-helix domain
Probab=31.29 E-value=35 Score=22.80 Aligned_cols=20 Identities=25% Similarity=0.571 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCcchhhhhhh
Q 022702 107 KMQLARALGLQPRQVAIWFQ 126 (293)
Q Consensus 107 r~~LA~~lgL~~~qVkvWFQ 126 (293)
..++|..+|++..+|..|.+
T Consensus 15 ~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIK 34 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHH
Confidence 45689999999999999975
No 201
>KOG0288 consensus WD40 repeat protein TipD [General function prediction only]
Probab=31.02 E-value=1.6e+02 Score=29.72 Aligned_cols=13 Identities=31% Similarity=0.445 Sum_probs=4.8
Q ss_pred HHHHHHHHHHHHH
Q 022702 153 ADREALQAQNQKL 165 (293)
Q Consensus 153 ~e~~~l~~e~~~l 165 (293)
.+...|+.|+..|
T Consensus 55 ~~l~~Lq~e~~~l 67 (459)
T KOG0288|consen 55 LELNRLQEENTQL 67 (459)
T ss_pred HHHHHHHHHHHHH
Confidence 3333333333333
No 202
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=30.98 E-value=1.6e+02 Score=23.16 Aligned_cols=18 Identities=22% Similarity=0.355 Sum_probs=6.8
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 022702 144 LKRQYEAVKADREALQAQ 161 (293)
Q Consensus 144 lk~~~~~l~~e~~~l~~e 161 (293)
|....+.|...++.|..+
T Consensus 38 Lns~LD~LE~rnD~l~~~ 55 (83)
T PF03670_consen 38 LNSCLDHLEQRNDHLHAQ 55 (83)
T ss_pred HHHHHHHHHHhhhHHHHH
Confidence 333333333333333333
No 203
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=30.74 E-value=5.2e+02 Score=28.62 Aligned_cols=30 Identities=23% Similarity=0.276 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 137 LEKDYDLLKRQYEAVKADREALQAQNQKLH 166 (293)
Q Consensus 137 ~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~ 166 (293)
-++....+..+++..--+.+..+++.++..
T Consensus 472 seqkA~e~~kk~~ke~ta~qe~qael~k~e 501 (1102)
T KOG1924|consen 472 SEQKAAELEKKFDKELTARQEAQAELQKHE 501 (1102)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHhh
Confidence 333344445555555444444444444443
No 204
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=30.65 E-value=99 Score=20.21 Aligned_cols=39 Identities=21% Similarity=0.262 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhh
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQN 127 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQN 127 (293)
.++..+...+...+ .. ....++|..+|++...|..|...
T Consensus 3 ~l~~~e~~i~~~~~-~g-----~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLA-EG-----LTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 36777777776543 22 13468999999999999888763
No 205
>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=30.54 E-value=3.7e+02 Score=24.36 Aligned_cols=20 Identities=20% Similarity=0.315 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 022702 140 DYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 140 ~~~~lk~~~~~l~~e~~~l~ 159 (293)
++..||.-+.+|.+||..|+
T Consensus 56 EIR~LKe~NqkLqedNqELR 75 (195)
T PF10226_consen 56 EIRGLKEVNQKLQEDNQELR 75 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444
No 206
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, 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=30.45 E-value=2.5e+02 Score=21.49 Aligned_cols=38 Identities=24% Similarity=0.309 Sum_probs=27.0
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRA 130 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRa 130 (293)
.+++|+...+..|+..+ .| ..+|++..+|+..+.....
T Consensus 34 g~r~y~~~dv~~l~~i~------------~l-~~~g~~~~~i~~~l~~~~~ 71 (100)
T cd00592 34 GYRLYSEEDLERLRLIR------------RL-RELGLSLKEIRELLDARDE 71 (100)
T ss_pred CCcccCHHHHHHHHHHH------------HH-HHcCCCHHHHHHHHhcccc
Confidence 45579999999987765 22 3378888888877765443
No 207
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. 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=30.30 E-value=3e+02 Score=22.31 Aligned_cols=80 Identities=16% Similarity=0.168 Sum_probs=41.2
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR-WKTKQLEKDYDLLKRQYEAVKADREAL 158 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK-~Krk~~~~~~~~lk~~~~~l~~e~~~l 158 (293)
..|.|+.+++..|... ..++.+|++-.+|+--+.....- ......++....+..+...+..+...+
T Consensus 33 gyR~Y~~~~l~~l~~I-------------~~lr~~G~~L~~I~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l 99 (118)
T cd04776 33 QTRVYSRRDRARLKLI-------------LRGKRLGFSLEEIRELLDLYDPPGGNRKQLEKMLEKIEKRRAELEQQRRDI 99 (118)
T ss_pred CccccCHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHHhhccCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567999999888532 23556677776666555432110 001111222344555555555555555
Q ss_pred HHHHHHHHHHHHHh
Q 022702 159 QAQNQKLHAEIMAL 172 (293)
Q Consensus 159 ~~e~~~l~~e~~~l 172 (293)
+...+.|...+...
T Consensus 100 ~~~~~~L~~~~~~~ 113 (118)
T cd04776 100 DAALAELDAAEERC 113 (118)
T ss_pred HHHHHHHHHHHHHH
Confidence 55555555544443
No 208
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=29.99 E-value=3e+02 Score=22.35 Aligned_cols=35 Identities=14% Similarity=0.231 Sum_probs=26.5
Q ss_pred CCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhh
Q 022702 79 EKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQ 126 (293)
Q Consensus 79 rkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQ 126 (293)
..+|.|+.+++..|.. ...++.+|++-.+|+..|.
T Consensus 34 ~gyR~Y~~~~l~~l~~-------------I~~lr~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 34 GGYRTYTQQHLDELRL-------------ISRARQVGFSLEECKELLN 68 (127)
T ss_pred CCCeecCHHHHHHHHH-------------HHHHHHCCCCHHHHHHHHH
Confidence 3466799999988843 3447788999999888775
No 209
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=29.63 E-value=79 Score=28.20 Aligned_cols=38 Identities=21% Similarity=0.306 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHhHhhCCC--CCHHHHHHHHHHhCCCcch
Q 022702 83 RLNMEQVKTLEKNFELGNK--LEPERKMQLARALGLQPRQ 120 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~--p~~~~r~~LA~~lgL~~~q 120 (293)
.+|..|++.|...|...-| |-...-.+||++||+++.-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst 194 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST 194 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 5999999999999988764 3333447899999999865
No 210
>cd07429 Cby_like Chibby, a nuclear inhibitor of Wnt/beta-catenin mediated transcription, and similar proteins. Chibby(Cby) is a well-conserved nuclear protein that functions as part of the Wnt/beta-catenin signaling pathway. Specifically, Cby binds directly to beta-catenin by interacting with its central region, which harbors armadillo repeats. Cby-beta-catenin interactions may also involve 14-3-3 proteins. By competing with other binding partners of beta-catenin, the Tcf/Lef transcription factors, Cby inhibits transcriptional activation. Cby has been shown to play a role in adipocyte differentiation. The C-terminal region of Cby appears to contain an alpha-helical coiled-coil motif.
Probab=29.59 E-value=1.6e+02 Score=24.18 Aligned_cols=21 Identities=38% Similarity=0.552 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 022702 131 RWKTKQLEKDYDLLKRQYEAV 151 (293)
Q Consensus 131 K~Krk~~~~~~~~lk~~~~~l 151 (293)
|.|.+++++|+..||-+++.|
T Consensus 78 kkk~~~LeEENNlLklKievL 98 (108)
T cd07429 78 KKKNQQLEEENNLLKLKIEVL 98 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444444444433
No 211
>PF12709 Kinetocho_Slk19: Central kinetochore-associated; InterPro: IPR024312 This is a family of proteins integrally involved in the central kinetochore. Slk19 is a yeast member and it may play an important role in the timing of nuclear migration. It may also participate, directly or indirectly, in the maintenance of centromeric tensile strength during mitotic stagnation, for instance during activation of checkpoint controls, when cells need to preserve nuclear integrity until cell cycle progression can be resumed [].
Probab=29.49 E-value=2.2e+02 Score=22.49 Aligned_cols=19 Identities=26% Similarity=0.419 Sum_probs=7.4
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 022702 144 LKRQYEAVKADREALQAQN 162 (293)
Q Consensus 144 lk~~~~~l~~e~~~l~~e~ 162 (293)
|..++..+..|++.|+.+.
T Consensus 54 L~~e~~~l~~E~e~L~~~l 72 (87)
T PF12709_consen 54 LENENKALKRENEQLKKKL 72 (87)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3333333444444443333
No 212
>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=29.06 E-value=2.9e+02 Score=23.13 Aligned_cols=20 Identities=15% Similarity=0.280 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 022702 151 VKADREALQAQNQKLHAEIM 170 (293)
Q Consensus 151 l~~e~~~l~~e~~~l~~e~~ 170 (293)
+..+...+...+..++.|+.
T Consensus 99 l~~~~~~~~~~~k~~kee~~ 118 (151)
T PF11559_consen 99 LQKQLKSLEAKLKQEKEELQ 118 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33333333333333333333
No 213
>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=28.91 E-value=67 Score=26.00 Aligned_cols=43 Identities=16% Similarity=0.114 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR 131 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK 131 (293)
++..+...|...|- ......++|..+|+++..|+.+...-|.|
T Consensus 114 L~~~~r~il~l~~~-----~~~~~~eIA~~lgis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 114 LPEQCRKIFILSRF-----EGKSYKEIAEELGISVKTVEYHISKALKE 156 (161)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45555555555442 12234578999999999999887543333
No 214
>PF05308 Mito_fiss_reg: Mitochondrial fission regulator; InterPro: IPR007972 This family consists of several uncharacterised eukaryotic proteins of unknown function.
Probab=28.91 E-value=3e+02 Score=25.80 Aligned_cols=15 Identities=27% Similarity=0.476 Sum_probs=7.0
Q ss_pred HHHHHHHHHHHHHHh
Q 022702 158 LQAQNQKLHAEIMAL 172 (293)
Q Consensus 158 l~~e~~~l~~e~~~l 172 (293)
|+.|...|++++.++
T Consensus 127 LEdELs~LRaQIA~I 141 (253)
T PF05308_consen 127 LEDELSRLRAQIAKI 141 (253)
T ss_pred HHHHHHHHHHHHHHH
Confidence 444444445554443
No 215
>PF04859 DUF641: Plant protein of unknown function (DUF641); InterPro: IPR006943 This conserved region is found in a number of plant proteins of unknown function.
Probab=28.83 E-value=3.6e+02 Score=22.82 Aligned_cols=34 Identities=15% Similarity=0.184 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022702 140 DYDLLKRQYEAVKADREALQAQNQKLHAEIMALK 173 (293)
Q Consensus 140 ~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 173 (293)
-.+.|+.+...-..|...|+.+.+.+...+..|.
T Consensus 95 ~~~kLe~e~~~Kdsei~~Lr~~L~~~~~~n~~Le 128 (131)
T PF04859_consen 95 VVKKLEAELRAKDSEIDRLREKLDELNRANKSLE 128 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3445555555555666666665555555554443
No 216
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=28.78 E-value=4.2e+02 Score=26.83 Aligned_cols=8 Identities=13% Similarity=0.173 Sum_probs=3.1
Q ss_pred hhhhhHHH
Q 022702 124 WFQNRRAR 131 (293)
Q Consensus 124 WFQNRRaK 131 (293)
|-+|+.-|
T Consensus 326 ~~~~~~~~ 333 (429)
T PRK00247 326 HAENAEIK 333 (429)
T ss_pred HHHHHHHH
Confidence 33443333
No 217
>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.
Probab=28.72 E-value=2.9e+02 Score=24.27 Aligned_cols=35 Identities=20% Similarity=0.282 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 141 YDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 141 ~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
+..|.-++..+......|+.||..|-...++.|..
T Consensus 153 ~~~L~l~~~~~e~k~~~l~~En~~Lv~Rwm~~k~~ 187 (194)
T PF08614_consen 153 LQALQLQLNMLEEKLRKLEEENRELVERWMQRKAQ 187 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444555555555555444443
No 218
>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=28.70 E-value=81 Score=24.92 Aligned_cols=20 Identities=30% Similarity=0.581 Sum_probs=16.9
Q ss_pred HHHHHHhCCCcchhhhhhhh
Q 022702 108 MQLARALGLQPRQVAIWFQN 127 (293)
Q Consensus 108 ~~LA~~lgL~~~qVkvWFQN 127 (293)
.++|+.+|++++.++.|-++
T Consensus 4 ~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 4 GEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred HHHHHHHCcCHHHHHHHHHH
Confidence 47899999999999999654
No 219
>PF04420 CHD5: CHD5-like protein; InterPro: IPR007514 Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. The exact molecular function of these eukaryotic proteins is unknown.; PDB: 3SJA_H 3SJC_D 3SJB_D 3ZS8_D 3VLC_E.
Probab=28.63 E-value=1.4e+02 Score=25.77 Aligned_cols=18 Identities=28% Similarity=0.368 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHHHhhhc
Q 022702 158 LQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 158 l~~e~~~l~~e~~~lk~~ 175 (293)
++.+.+++.+|+.+++..
T Consensus 71 l~Rk~~kl~~el~~~~~~ 88 (161)
T PF04420_consen 71 LNRKLDKLEEELEKLNKS 88 (161)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 445555555555554444
No 220
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=28.54 E-value=60 Score=27.79 Aligned_cols=44 Identities=20% Similarity=0.228 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARW 132 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~ 132 (293)
++..+..++...| .....-.++|..+|++...|++|+..-|.+.
T Consensus 142 L~~~~~~v~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 185 (194)
T PRK12519 142 LPESQRQVLELAY-----YEGLSQSEIAKRLGIPLGTVKARARQGLLKL 185 (194)
T ss_pred CCHHHhhhhhhhh-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4445544444433 2223345899999999999999986444433
No 221
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are 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 C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=28.28 E-value=2.8e+02 Score=21.47 Aligned_cols=36 Identities=25% Similarity=0.431 Sum_probs=25.3
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhh
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNR 128 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNR 128 (293)
.+|.|+.+++..|... ...+.+|++-..|+.-+.+.
T Consensus 35 gyR~Y~~~~~~~l~~I-------------~~lr~~G~~l~eI~~~l~~~ 70 (97)
T cd04782 35 GYRYYTLEQFEQLDII-------------LLLKELGISLKEIKDYLDNR 70 (97)
T ss_pred CCccCCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHhcC
Confidence 4667999998888542 33567788888877766653
No 222
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=28.23 E-value=68 Score=28.11 Aligned_cols=44 Identities=18% Similarity=0.166 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARW 132 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~ 132 (293)
++..+..+|...| .....-.++|..+|++...|+++...-|.+.
T Consensus 154 L~~~~r~vl~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 197 (206)
T PRK12526 154 LPEAQQTVVKGVY-----FQELSQEQLAQQLNVPLGTVKSRLRLALAKL 197 (206)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 5555555555433 2222345899999999999988875444433
No 223
>PRK10869 recombination and repair protein; Provisional
Probab=27.84 E-value=5.4e+02 Score=26.64 Aligned_cols=51 Identities=18% Similarity=0.180 Sum_probs=33.3
Q ss_pred HHHHHHhCCCcchhhhhhhhhHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 108 MQLARALGLQPRQVAIWFQNRRARWKT-KQLEKDYDLLKRQYEAVKADREAL 158 (293)
Q Consensus 108 ~~LA~~lgL~~~qVkvWFQNRRaK~Kr-k~~~~~~~~lk~~~~~l~~e~~~l 158 (293)
..|.++.|.+...|-.|++.-+.+... ...+...+.|..+.+.++.+...+
T Consensus 309 ~~L~rKyg~~~~~~~~~~~~l~~eL~~L~~~e~~l~~Le~e~~~l~~~l~~~ 360 (553)
T PRK10869 309 ISLARKHHVSPEELPQHHQQLLEEQQQLDDQEDDLETLALAVEKHHQQALET 360 (553)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHH
Confidence 357888899999999998877666554 333344555555555555444443
No 224
>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=27.82 E-value=2.6e+02 Score=21.28 Aligned_cols=34 Identities=21% Similarity=0.338 Sum_probs=24.0
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhh
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWF 125 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWF 125 (293)
..++|+..++..|.. ...|...+|++...|+.-+
T Consensus 35 g~R~y~~~dv~~l~~------------i~~L~~d~g~~l~~i~~~l 68 (91)
T cd04766 35 GTRRYSERDIERLRR------------IQRLTQELGVNLAGVKRIL 68 (91)
T ss_pred CCeeECHHHHHHHHH------------HHHHHHHcCCCHHHHHHHH
Confidence 355699999999854 3355556888887776555
No 225
>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=26.96 E-value=42 Score=24.23 Aligned_cols=28 Identities=25% Similarity=0.520 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCCcchhhhhhhhhHHHHHHH
Q 022702 106 RKMQLARALGLQPRQVAIWFQNRRARWKTK 135 (293)
Q Consensus 106 ~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk 135 (293)
...+||+.||++.+.|..|-+ |.+|...
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~~~ 42 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWDEL 42 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCcccc
Confidence 345899999999999999964 6666553
No 226
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=26.78 E-value=66 Score=30.76 Aligned_cols=39 Identities=33% Similarity=0.391 Sum_probs=34.0
Q ss_pred HhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHH
Q 022702 96 FELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKT 134 (293)
Q Consensus 96 F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Kr 134 (293)
=..+.|+...+...|+...+|+-.+|.+||-|.|.+.+.
T Consensus 116 ~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~ 154 (342)
T KOG0773|consen 116 HRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKK 154 (342)
T ss_pred hhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence 345789999999999999999999999999998877655
No 227
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=26.68 E-value=36 Score=24.23 Aligned_cols=20 Identities=20% Similarity=0.486 Sum_probs=17.3
Q ss_pred HHHHHHhCCCcchhhhhhhh
Q 022702 108 MQLARALGLQPRQVAIWFQN 127 (293)
Q Consensus 108 ~~LA~~lgL~~~qVkvWFQN 127 (293)
.++|+.+|++.+.|+.|=+.
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 47899999999999999543
No 228
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=26.67 E-value=1.8e+02 Score=28.87 Aligned_cols=37 Identities=16% Similarity=0.347 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 139 KDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 139 ~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
+.+..++.++..+..++..+..+...++.++..++..
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 (398)
T PTZ00454 22 EKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEE 58 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333344444444444444444444444444444443
No 229
>PF07058 Myosin_HC-like: Myosin II heavy chain-like; InterPro: IPR009768 This family represents a conserved region within a number of myosin II heavy chain-like proteins that seem to be specific to Arabidopsis thaliana.
Probab=26.62 E-value=6.1e+02 Score=24.78 Aligned_cols=55 Identities=20% Similarity=0.313 Sum_probs=31.6
Q ss_pred hhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccc
Q 022702 120 QVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSREVTES 180 (293)
Q Consensus 120 qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~~~~ 180 (293)
.|+.|.-.||- ++.+.+.|+..+.....--...-+-+++|+-.+..|.+.+-..+
T Consensus 109 PVKqWLEERR~------lQgEmQ~LrDKLAiaERtAkaEaQLkeK~klRLK~LEe~Lk~~~ 163 (351)
T PF07058_consen 109 PVKQWLEERRF------LQGEMQQLRDKLAIAERTAKAEAQLKEKLKLRLKVLEEGLKGSS 163 (351)
T ss_pred cHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCC
Confidence 47779987775 44555566655554443333333445667766666666554433
No 230
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=26.60 E-value=1.2e+02 Score=32.00 Aligned_cols=34 Identities=24% Similarity=0.350 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 142 DLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 142 ~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
..+....+.+..+|..|+.+++.+++++..|+..
T Consensus 425 ~~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~ 458 (652)
T COG2433 425 KKLEETVERLEEENSELKRELEELKREIEKLESE 458 (652)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444444444444444444444444444443
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=26.39 E-value=66 Score=21.48 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=18.6
Q ss_pred HHHHHhCCCcchhhhhhhhhH
Q 022702 109 QLARALGLQPRQVAIWFQNRR 129 (293)
Q Consensus 109 ~LA~~lgL~~~qVkvWFQNRR 129 (293)
+||+.+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998874
No 232
>PHA02955 hypothetical protein; Provisional
Probab=26.28 E-value=72 Score=29.25 Aligned_cols=42 Identities=7% Similarity=0.093 Sum_probs=32.9
Q ss_pred HHHHHHHHHhHhhC-CCCCHHHHHHHHHHhCCCcchhhhhhhh
Q 022702 86 MEQVKTLEKNFELG-NKLEPERKMQLARALGLQPRQVAIWFQN 127 (293)
Q Consensus 86 ~~Ql~~LE~~F~~~-~~p~~~~r~~LA~~lgL~~~qVkvWFQN 127 (293)
..++..|-+.|... ..+..++|.++|++||+....|..||.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 34566555555554 6788999999999999999888999976
No 233
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=26.23 E-value=83 Score=22.54 Aligned_cols=20 Identities=20% Similarity=0.235 Sum_probs=8.3
Q ss_pred hhhhhhhHHHHHHHHHHHHH
Q 022702 122 AIWFQNRRARWKTKQLEKDY 141 (293)
Q Consensus 122 kvWFQNRRaK~Krk~~~~~~ 141 (293)
-.|+.-.|.|++.++.+++.
T Consensus 38 ~~~~~~~~~r~~~~~~~k~l 57 (68)
T PF06305_consen 38 LSLPSRLRLRRRIRRLRKEL 57 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444433333
No 234
>PF05266 DUF724: Protein of unknown function (DUF724); InterPro: IPR007930 This family contains several uncharacterised proteins found exclusively in Arabidopsis thaliana.
Probab=26.16 E-value=4.7e+02 Score=23.31 Aligned_cols=25 Identities=20% Similarity=0.089 Sum_probs=13.4
Q ss_pred HhhCCCCCHHHHHHHHHHhCCCcch
Q 022702 96 FELGNKLEPERKMQLARALGLQPRQ 120 (293)
Q Consensus 96 F~~~~~p~~~~r~~LA~~lgL~~~q 120 (293)
|+.+-|--..-+.+|-+.|.+..++
T Consensus 81 LE~~GFnV~~l~~RL~kLL~lk~~~ 105 (190)
T PF05266_consen 81 LEEHGFNVKFLRSRLNKLLSLKDDQ 105 (190)
T ss_pred HHHcCCccHHHHHHHHHHHHHHHhH
Confidence 3445555555666666655544443
No 235
>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=25.95 E-value=2.9e+02 Score=23.50 Aligned_cols=47 Identities=21% Similarity=0.164 Sum_probs=33.0
Q ss_pred CCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHH
Q 022702 81 KRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133 (293)
Q Consensus 81 r~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~K 133 (293)
..-++..|..+|+-.+ .+ ....++|..+|++...|+.+-..-|.|.|
T Consensus 4 ~~~Lte~qr~VL~Lr~-~G-----lTq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-KG-----LSQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred cCCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 3458889999987742 11 24568999999999999888654444443
No 236
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=25.94 E-value=1.6e+02 Score=25.22 Aligned_cols=7 Identities=43% Similarity=0.942 Sum_probs=3.7
Q ss_pred hhhhhhh
Q 022702 122 AIWFQNR 128 (293)
Q Consensus 122 kvWFQNR 128 (293)
+|||-|.
T Consensus 57 kiY~~~Q 63 (169)
T PF07106_consen 57 KIYFANQ 63 (169)
T ss_pred EEEeeCc
Confidence 4565553
No 237
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=25.71 E-value=1.7e+02 Score=23.83 Aligned_cols=46 Identities=15% Similarity=0.138 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKT 134 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Kr 134 (293)
.+|..+..+|+- +..+ + ...++|+.++++++.|+.+.+|=|.|..-
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 488888888876 3332 2 25689999999999999998876655543
No 238
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=25.52 E-value=2.7e+02 Score=29.92 Aligned_cols=37 Identities=24% Similarity=0.413 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 130 ARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLH 166 (293)
Q Consensus 130 aK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~ 166 (293)
.|.|++++|.|+..|+.++....+....++.+.+.|+
T Consensus 543 ~r~r~~~lE~E~~~lr~elk~kee~~~~~e~~~~~lr 579 (697)
T PF09726_consen 543 CRQRRRQLESELKKLRRELKQKEEQIRELESELQELR 579 (697)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556777788888887777766666666655554333
No 239
>PRK10403 transcriptional regulator NarP; Provisional
Probab=25.48 E-value=79 Score=26.16 Aligned_cols=47 Identities=15% Similarity=0.195 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTK 135 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk 135 (293)
.+|..+...|+..... ..+.+||+.++++++.|++...|=|.|-...
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 4888888888765433 3356889999999999999988766665443
No 240
>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=25.44 E-value=1.8e+02 Score=23.04 Aligned_cols=32 Identities=25% Similarity=0.356 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022702 142 DLLKRQYEAVKADREALQAQNQKLHAEIMALK 173 (293)
Q Consensus 142 ~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 173 (293)
..++...+.|.+....++.+|..|..++.+++
T Consensus 76 ~~~~~~~~~L~~~l~~l~~eN~~L~~~i~~~r 107 (109)
T PF03980_consen 76 PYKKKEREQLNARLQELEEENEALAEEIQEQR 107 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 33444555556666666666666666665543
No 241
>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=25.44 E-value=60 Score=23.03 Aligned_cols=34 Identities=24% Similarity=0.281 Sum_probs=25.2
Q ss_pred HHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhh
Q 022702 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIW 124 (293)
Q Consensus 87 ~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvW 124 (293)
.|+..|+-.+. ....... +||..+|++++.|+.-
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~ 39 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKND 39 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHH
Confidence 47888888888 6555555 8999999999887643
No 242
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=25.22 E-value=72 Score=26.31 Aligned_cols=45 Identities=11% Similarity=0.059 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~K 133 (293)
++..+..++.-.|-.+ ..-.++|..+|+++..|++....-|.+.|
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr 151 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIK 151 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4555555554443222 12348999999999999998864444433
No 243
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=24.95 E-value=3e+02 Score=20.58 Aligned_cols=15 Identities=40% Similarity=0.490 Sum_probs=7.0
Q ss_pred HHHHHHHHHHHHhhh
Q 022702 160 AQNQKLHAEIMALKS 174 (293)
Q Consensus 160 ~e~~~l~~e~~~lk~ 174 (293)
.++.+|++|+.+++.
T Consensus 47 ~e~~~Lk~E~e~L~~ 61 (69)
T PF14197_consen 47 EENNKLKEENEALRK 61 (69)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344445555544443
No 244
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=24.88 E-value=1.5e+02 Score=24.08 Aligned_cols=25 Identities=24% Similarity=0.042 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 151 VKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 151 l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
+.+++..|+.++..|+.|+.-||.+
T Consensus 76 ~~~ei~~L~~el~~L~~E~diLKKa 100 (121)
T PRK09413 76 AMKQIKELQRLLGKKTMENELLKEA 100 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444445555555555555555444
No 245
>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=24.72 E-value=1.3e+02 Score=23.90 Aligned_cols=31 Identities=23% Similarity=0.373 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 138 EKDYDLLKRQYEAVKADREALQAQNQKLHAE 168 (293)
Q Consensus 138 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e 168 (293)
....+.|+..+..+..+|..|..+.+.+++|
T Consensus 79 ~~~~~~L~~~l~~l~~eN~~L~~~i~~~r~e 109 (109)
T PF03980_consen 79 KKEREQLNARLQELEEENEALAEEIQEQRKE 109 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 3456678888888999999988888776653
No 246
>PF09738 DUF2051: Double stranded RNA binding protein (DUF2051); InterPro: IPR019139 This entry represents transcriptional repressors which preferentially bind to the GC-rich consensus sequence (5'-AGCCCCCGGCG-3') and may regulate expression of TNF, EGFR and PDGFA. They may control smooth muscle cell proliferation following artery injury through PDGFA repression and may also bind double-stranded RNA. They interact with the leucine-rich repeat domain of human flightless-I (FliI) protein.
Probab=24.67 E-value=2.7e+02 Score=26.76 Aligned_cols=62 Identities=21% Similarity=0.308 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccccCC-CCCCCCCCCCCC
Q 022702 136 QLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSREVTESINLNK-ETEGSCSNRSEN 197 (293)
Q Consensus 136 ~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~~~~~~~~~-~t~~s~s~~s~n 197 (293)
+..+++....+.++.+|...+.|+.+...|+.++...+.-.....+.+.. .+.|-.+....+
T Consensus 130 ~~~re~~eK~~elEr~K~~~d~L~~e~~~Lre~L~~rdeli~khGlVlv~~~~ngd~~~~~~~ 192 (302)
T PF09738_consen 130 QLQREYREKIRELERQKRAHDSLREELDELREQLKQRDELIEKHGLVLVPDATNGDTSDEPNN 192 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCeeeCCCCCCCccccCccc
No 247
>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=24.65 E-value=2.9e+02 Score=20.32 Aligned_cols=30 Identities=13% Similarity=0.349 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022702 144 LKRQYEAVKADREALQAQNQKLHAEIMALK 173 (293)
Q Consensus 144 lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 173 (293)
+..........|..|..+...|..++..++
T Consensus 30 ~e~kLqeaE~rn~eL~~ei~~L~~e~ee~r 59 (61)
T PF08826_consen 30 FESKLQEAEKRNRELEQEIERLKKEMEELR 59 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 334444444555556666666666655544
No 248
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=24.50 E-value=1.2e+02 Score=25.87 Aligned_cols=39 Identities=23% Similarity=0.205 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhh
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQN 127 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQN 127 (293)
++..|..++...|-.+ ..-.++|..+|++...|+.+...
T Consensus 140 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~R 178 (189)
T PRK09648 140 LPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHR 178 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 6666766666654332 23568999999999999988743
No 249
>PF13863 DUF4200: Domain of unknown function (DUF4200)
Probab=24.37 E-value=3.7e+02 Score=21.46 Aligned_cols=31 Identities=19% Similarity=0.292 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022702 142 DLLKRQYEAVKADREALQAQNQKLHAEIMAL 172 (293)
Q Consensus 142 ~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 172 (293)
.....++..+..+...|+.+..++...+..+
T Consensus 77 ~~k~~ei~~l~~~l~~l~~~~~k~e~~l~~~ 107 (126)
T PF13863_consen 77 EEKEAEIKKLKAELEELKSEISKLEEKLEEY 107 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334445555555555555555555555443
No 250
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=24.37 E-value=1e+02 Score=26.09 Aligned_cols=45 Identities=13% Similarity=0.011 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~K 133 (293)
++..+..+|.-.|-. ...-.+||..||++...|+.++..-|.+.|
T Consensus 132 L~~~~r~v~~l~~~~-----g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 132 LPPRQRDVVQSISVE-----GASIKETAAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 566666666655433 223458999999999999999875555444
No 251
>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=24.20 E-value=1e+02 Score=22.64 Aligned_cols=37 Identities=24% Similarity=0.342 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccc
Q 022702 144 LKRQYEAVKADREALQAQNQKLHAEIMALKSREVTES 180 (293)
Q Consensus 144 lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~~~~ 180 (293)
.+.+.+.||.....|...+..|+.|+.-||.....+.
T Consensus 12 VrEEVevLK~~I~eL~~~n~~Le~EN~~Lk~~~~pe~ 48 (59)
T PF01166_consen 12 VREEVEVLKEQIAELEERNSQLEEENNLLKQNASPEQ 48 (59)
T ss_dssp -TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSSS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHH
Confidence 4567788999999999999999999999988765553
No 252
>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=24.18 E-value=3.4e+02 Score=20.90 Aligned_cols=35 Identities=29% Similarity=0.449 Sum_probs=17.0
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 125 FQNRRARWKTKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 125 FQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
|+.|+.-....+.+.+...|+.+++.|+.|...+.
T Consensus 35 ~~~~~~~~~l~~l~~~~~~l~~e~~~L~lE~~~l~ 69 (97)
T PF04999_consen 35 HQSRQLFYELQQLEKEIDQLQEENERLRLEIATLS 69 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34455444444444455555555555554444443
No 253
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=23.98 E-value=1.2e+02 Score=29.13 Aligned_cols=49 Identities=27% Similarity=0.286 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARW 132 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~ 132 (293)
+++..|..+|+..|.... .......+||..+|++...|+.+...-|.|.
T Consensus 262 ~L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kL 310 (325)
T PRK05657 262 ELNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRL 310 (325)
T ss_pred cCCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 488899999988774332 3344457899999999999999876444433
No 254
>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=23.76 E-value=95 Score=25.38 Aligned_cols=38 Identities=21% Similarity=0.156 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhh
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQ 126 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQ 126 (293)
++..+..++...|- ....-.++|..+|++...|+++..
T Consensus 112 L~~~~r~v~~l~~~-----~g~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 112 LPERQRELLQLRYQ-----RGVSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 66666666665432 223356899999999999998864
No 255
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=23.50 E-value=2.8e+02 Score=20.12 Aligned_cols=19 Identities=32% Similarity=0.524 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 022702 150 AVKADREALQAQNQKLHAE 168 (293)
Q Consensus 150 ~l~~e~~~l~~e~~~l~~e 168 (293)
++..|.+.|++||..|+.-
T Consensus 37 ~l~~e~~~L~~qN~eLr~l 55 (60)
T PF14775_consen 37 ALIQEKESLEQQNEELRSL 55 (60)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3445555555555555443
No 256
>PRK10698 phage shock protein PspA; Provisional
Probab=23.48 E-value=3.4e+02 Score=24.67 Aligned_cols=44 Identities=11% Similarity=0.182 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 132 WKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 132 ~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
.+++........|+.+++......+.|+.+...|+..+..++..
T Consensus 92 ~~K~~~~~~~~~l~~~~~~~~~~~~~L~~~l~~L~~ki~eak~k 135 (222)
T PRK10698 92 IEKQKLTDLIATLEHEVTLVDETLARMKKEIGELENKLSETRAR 135 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555566666666666666666666666666666655544
No 257
>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=23.37 E-value=3.1e+02 Score=20.17 Aligned_cols=39 Identities=21% Similarity=0.314 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 137 LEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 137 ~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
+.+++...+..+-.....-......+..|..++..|+..
T Consensus 16 ~~eEL~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e 54 (61)
T PF08826_consen 16 IQEELTKVKSANLAFESKLQEAEKRNRELEQEIERLKKE 54 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445555555555555555556666666666666543
No 258
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=23.36 E-value=90 Score=26.54 Aligned_cols=42 Identities=10% Similarity=0.135 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRA 130 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRa 130 (293)
++..+..++...|- ....-.++|..+|++...|+.+...-|.
T Consensus 129 L~~~~r~i~~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~Rar~ 170 (186)
T PRK05602 129 LPERQREAIVLQYY-----QGLSNIEAAAVMDISVDALESLLARGRR 170 (186)
T ss_pred CCHHHHHHhhHHHh-----cCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 45555555544432 2223458999999999999988753333
No 259
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=23.33 E-value=92 Score=26.61 Aligned_cols=45 Identities=9% Similarity=0.138 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~K 133 (293)
++..+..+|+-.|-. ...-.++|..+|+++..|++-...-|.+.|
T Consensus 132 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 176 (189)
T PRK12515 132 LSPAHREIIDLVYYH-----EKSVEEVGEIVGIPESTVKTRMFYARKKLA 176 (189)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 666666666655422 223458899999999999987754444443
No 260
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=23.27 E-value=4.2e+02 Score=21.74 Aligned_cols=36 Identities=19% Similarity=0.195 Sum_probs=27.2
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhh
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNR 128 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNR 128 (293)
..|.|+.+++..|.. ....+.+|++-.+|+.++.++
T Consensus 36 gyR~Y~~~~l~~l~~-------------I~~lr~~G~sl~eI~~~l~~~ 71 (131)
T TIGR02043 36 GYRLYTDEDQKRLRF-------------ILKAKELGFTLDEIKELLSIK 71 (131)
T ss_pred CceecCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHHhh
Confidence 456799999988843 233677899999999888753
No 261
>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=23.24 E-value=3.1e+02 Score=22.76 Aligned_cols=40 Identities=20% Similarity=0.355 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 136 QLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 136 ~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
.++.++..|...|+++-.=...-..+++.|++.+..+|.-
T Consensus 72 ~L~~el~~l~~ry~t~LellGEK~E~veEL~~Dv~DlK~m 111 (120)
T PF12325_consen 72 ELEQELEELQQRYQTLLELLGEKSEEVEELRADVQDLKEM 111 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHH
Confidence 3344444444444444433333344666777777666653
No 262
>PF07047 OPA3: Optic atrophy 3 protein (OPA3); InterPro: IPR010754 OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity []. This family consists of several optic atrophy 3 (OPA3) proteins and related proteins from other eukaryotic species, the function is unknown.
Probab=22.98 E-value=1.6e+02 Score=24.68 Aligned_cols=13 Identities=23% Similarity=0.297 Sum_probs=7.1
Q ss_pred hhhhhhhHHHHHH
Q 022702 122 AIWFQNRRARWKT 134 (293)
Q Consensus 122 kvWFQNRRaK~Kr 134 (293)
-++|-..|...|.
T Consensus 91 li~~E~~Rs~~ke 103 (134)
T PF07047_consen 91 LIIYEYWRSARKE 103 (134)
T ss_pred HHHHHHHHHHhhH
Confidence 3566665655443
No 263
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=22.86 E-value=5e+02 Score=22.46 Aligned_cols=69 Identities=16% Similarity=0.267 Sum_probs=41.7
Q ss_pred CCCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 79 EKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDYDLLKRQYEAVKADREAL 158 (293)
Q Consensus 79 rkr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l 158 (293)
...|.|+.+++..|.. ....+.+|++-..|+.-+...... ....|..+...+.++...|
T Consensus 35 ~gyR~Y~~~dl~rL~~-------------I~~lr~~G~sL~eI~~ll~~~~~~--------~~~~L~~~~~~l~~ei~~L 93 (172)
T cd04790 35 SNYRLYGERDLERLEQ-------------ICAYRSAGVSLEDIRSLLQQPGDD--------ATDVLRRRLAELNREIQRL 93 (172)
T ss_pred CCCccCCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhcCChh--------HHHHHHHHHHHHHHHHHHH
Confidence 3466799999988843 233577888888888777654431 1234455555555555555
Q ss_pred HHHHHHHHHH
Q 022702 159 QAQNQKLHAE 168 (293)
Q Consensus 159 ~~e~~~l~~e 168 (293)
+.....|..-
T Consensus 94 ~~~~~~l~~l 103 (172)
T cd04790 94 RQQQRAIATL 103 (172)
T ss_pred HHHHHHHHHH
Confidence 5544444443
No 264
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=22.86 E-value=57 Score=21.79 Aligned_cols=22 Identities=23% Similarity=0.421 Sum_probs=16.8
Q ss_pred HHHHHHHHHhCCCcchhhhhhh
Q 022702 105 ERKMQLARALGLQPRQVAIWFQ 126 (293)
Q Consensus 105 ~~r~~LA~~lgL~~~qVkvWFQ 126 (293)
....++|+.+|++...|..|.+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3456899999999999999964
No 265
>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction
Probab=22.82 E-value=2e+02 Score=25.11 Aligned_cols=47 Identities=21% Similarity=0.341 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccccC
Q 022702 138 EKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSREVTESINLN 184 (293)
Q Consensus 138 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~~~~~~~~ 184 (293)
+.+++.++++++.++.+....-.++++|.......+.++..++.+..
T Consensus 26 R~E~~~l~~EL~evk~~v~~~I~evD~Le~~er~aR~rL~eVS~~f~ 72 (159)
T PF05384_consen 26 RQEYERLRKELEEVKEEVSEVIEEVDKLEKRERQARQRLAEVSRNFD 72 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 34555566666666666666666666666665555555554444443
No 266
>KOG4752 consensus Ribosomal protein L41 [Translation, ribosomal structure and biogenesis]
Probab=22.75 E-value=1.5e+02 Score=17.95 Aligned_cols=9 Identities=44% Similarity=1.269 Sum_probs=5.7
Q ss_pred HHHHHHHHH
Q 022702 129 RARWKTKQL 137 (293)
Q Consensus 129 RaK~Krk~~ 137 (293)
|+||+++..
T Consensus 2 r~kwrkkrm 10 (26)
T KOG4752|consen 2 RAKWRKKRM 10 (26)
T ss_pred chHHHHHHH
Confidence 567776553
No 267
>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=22.45 E-value=3.1e+02 Score=19.92 Aligned_cols=35 Identities=20% Similarity=0.327 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 141 YDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 141 ~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
.+.|-.+...|....+.|..+...++.++...|+.
T Consensus 5 id~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~E 39 (56)
T PF04728_consen 5 IDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEE 39 (56)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555666666666666666666666666655543
No 268
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.43 E-value=3.3e+02 Score=25.16 Aligned_cols=30 Identities=27% Similarity=0.246 Sum_probs=21.0
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARA 113 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~ 113 (293)
.|.+....||.+|.+-+.-...+|..-|+.
T Consensus 1 MtpeE~qlle~lf~rlk~a~~~~rD~~Ae~ 30 (233)
T COG3416 1 MTPEEKQLLENLFHRLKKAEANERDPQAEA 30 (233)
T ss_pred CCHHHHHHHHHHHHHHhhcccCCCChHHHH
Confidence 378889999999988876555555443333
No 269
>PF12808 Mto2_bdg: Micro-tubular organiser Mto1 C-term Mto2-binding region; InterPro: IPR024545 This domain occurs at the C terminus of microtubule organising proteins in both budding and fission fungi. In Schizosaccharomyces pombe it has been shown to interact with the Mto2p protein, an interaction which is critical for anchoring the cytokinetic actin ring to the medial region of the cell and for proper coordination of mitosis with cytokinesis [, ].
Probab=22.42 E-value=2.8e+02 Score=19.83 Aligned_cols=18 Identities=28% Similarity=0.357 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 022702 154 DREALQAQNQKLHAEIMA 171 (293)
Q Consensus 154 e~~~l~~e~~~l~~e~~~ 171 (293)
+...|..+|..|++++..
T Consensus 30 rl~~l~~EN~~Lr~eL~~ 47 (52)
T PF12808_consen 30 RLSKLEGENRLLRAELER 47 (52)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 333344444444444443
No 270
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=22.34 E-value=1.3e+02 Score=29.42 Aligned_cols=19 Identities=16% Similarity=0.048 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 022702 141 YDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 141 ~~~lk~~~~~l~~e~~~l~ 159 (293)
|..|+++++.|++|+..|+
T Consensus 59 y~~L~~EN~~Lk~Ena~L~ 77 (337)
T PRK14872 59 ALVLETENFLLKERIALLE 77 (337)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444443
No 271
>KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]
Probab=22.27 E-value=2.4e+02 Score=29.64 Aligned_cols=30 Identities=33% Similarity=0.506 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 138 EKDYDLLKRQYEAVKADREALQAQNQKLHA 167 (293)
Q Consensus 138 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~ 167 (293)
+...+.|+.+++....|.+.|+++++.|+.
T Consensus 293 ~~~l~~l~~Eie~kEeE~e~lq~~~d~Lk~ 322 (581)
T KOG0995|consen 293 EKKLEMLKSEIEEKEEEIEKLQKENDELKK 322 (581)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444444444444444333
No 272
>PRK00118 putative DNA-binding protein; Validated
Probab=22.16 E-value=4.3e+02 Score=21.37 Aligned_cols=49 Identities=12% Similarity=0.051 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEK 139 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~~~~ 139 (293)
++..|..++...|..+. .-.+||..+|+++..|..|... ++.+-++..+
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~R--ArkkLr~~~~ 66 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKR--TEKLLEDYEE 66 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHH--HHHHHHHHHH
Confidence 45666666655544322 2457999999999999999864 4434333333
No 273
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=22.06 E-value=2e+02 Score=30.48 Aligned_cols=38 Identities=21% Similarity=0.237 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 133 KTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIM 170 (293)
Q Consensus 133 Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~ 170 (293)
||+++..+++.++..++.+|.+....+.+...|+.+++
T Consensus 101 krqel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ie 138 (907)
T KOG2264|consen 101 KRQELNSEIEEINTKIEELKRLIPQKQLELSALKGEIE 138 (907)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHH
Confidence 56677777777777777777766666666555555544
No 274
>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=22.03 E-value=65 Score=20.55 Aligned_cols=24 Identities=21% Similarity=0.512 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCcchhhhhhhhhHH
Q 022702 107 KMQLARALGLQPRQVAIWFQNRRA 130 (293)
Q Consensus 107 r~~LA~~lgL~~~qVkvWFQNRRa 130 (293)
..++|+.||++.+.|..|.++.+-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 357899999999999999876543
No 275
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=22.01 E-value=87 Score=26.19 Aligned_cols=29 Identities=14% Similarity=0.137 Sum_probs=21.8
Q ss_pred HHHHHHHHHhCCCcchhhhhhhhhHHHHH
Q 022702 105 ERKMQLARALGLQPRQVAIWFQNRRARWK 133 (293)
Q Consensus 105 ~~r~~LA~~lgL~~~qVkvWFQNRRaK~K 133 (293)
..-.++|..+|+++..|++.+..-|.+.|
T Consensus 137 ~s~~eIA~~lg~s~~tv~~~l~Rar~~L~ 165 (175)
T PRK12518 137 LPQKEIAEILNIPVGTVKSRLFYARRQLR 165 (175)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34568999999999999998864444433
No 276
>PF12709 Kinetocho_Slk19: Central kinetochore-associated; InterPro: IPR024312 This is a family of proteins integrally involved in the central kinetochore. Slk19 is a yeast member and it may play an important role in the timing of nuclear migration. It may also participate, directly or indirectly, in the maintenance of centromeric tensile strength during mitotic stagnation, for instance during activation of checkpoint controls, when cells need to preserve nuclear integrity until cell cycle progression can be resumed [].
Probab=21.89 E-value=4.1e+02 Score=21.04 Aligned_cols=23 Identities=17% Similarity=0.432 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 022702 148 YEAVKADREALQAQNQKLHAEIM 170 (293)
Q Consensus 148 ~~~l~~e~~~l~~e~~~l~~e~~ 170 (293)
.+.|..++..+..+++.|+.++.
T Consensus 51 v~~L~~e~~~l~~E~e~L~~~l~ 73 (87)
T PF12709_consen 51 VDELENENKALKRENEQLKKKLD 73 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444455555555555544443
No 277
>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=21.83 E-value=1.1e+02 Score=20.39 Aligned_cols=38 Identities=18% Similarity=0.410 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhh
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWF 125 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWF 125 (293)
.++.+++..+-..+... ....+||+.+|++...|.-++
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 46676666666666655 235689999999998887554
No 278
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=21.80 E-value=2.3e+02 Score=27.23 Aligned_cols=38 Identities=18% Similarity=0.282 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 022702 139 KDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSRE 176 (293)
Q Consensus 139 ~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 176 (293)
..++.|+.+...+..+.+.++.+..+++.++..++...
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 43 (364)
T TIGR01242 6 VRIRKLEDEKRSLEKEKIRLERELERLRSEIERLRSPP 43 (364)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 34566777777777787788888888888887776654
No 279
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=21.78 E-value=1.1e+02 Score=25.32 Aligned_cols=45 Identities=22% Similarity=0.220 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~K 133 (293)
.+|..+...|+-...- ..+.+||..++++++.|++..++=|.|..
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4888888888776543 25778999999999999988876555543
No 280
>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=21.58 E-value=55 Score=23.49 Aligned_cols=20 Identities=20% Similarity=0.474 Sum_probs=17.8
Q ss_pred HHHHHHhCCCcchhhhhhhh
Q 022702 108 MQLARALGLQPRQVAIWFQN 127 (293)
Q Consensus 108 ~~LA~~lgL~~~qVkvWFQN 127 (293)
.++|+.+|+++..|+.|.+.
T Consensus 4 ~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 4 GEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999864
No 281
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=21.53 E-value=1.7e+02 Score=24.04 Aligned_cols=41 Identities=20% Similarity=0.269 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRA 130 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRa 130 (293)
++..+...|.-.| .+ ..-.+||..+|++...|+.+...-|.
T Consensus 113 L~~~~r~il~l~~-~g-----~s~~eIA~~lgis~~tV~~~i~ra~~ 153 (166)
T PRK09639 113 MTERDRTVLLLRF-SG-----YSYKEIAEALGIKESSVGTTLARAKK 153 (166)
T ss_pred CCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6666666666655 22 23457899999999999988853333
No 282
>KOG3650 consensus Predicted coiled-coil protein [General function prediction only]
Probab=21.52 E-value=3.7e+02 Score=21.96 Aligned_cols=38 Identities=32% Similarity=0.376 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022702 137 LEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174 (293)
Q Consensus 137 ~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 174 (293)
++.-++.|-+..+.+|+||-.|+.||+-|-.=+..|-.
T Consensus 68 LQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeNLMS 105 (120)
T KOG3650|consen 68 LQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIENLMS 105 (120)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHh
Confidence 44456777788888888888888888887776665543
No 283
>PF11382 DUF3186: Protein of unknown function (DUF3186); InterPro: IPR021522 This bacterial family of proteins has no known function.
Probab=21.50 E-value=1.6e+02 Score=28.06 Aligned_cols=22 Identities=36% Similarity=0.593 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 022702 141 YDLLKRQYEAVKADREALQAQN 162 (293)
Q Consensus 141 ~~~lk~~~~~l~~e~~~l~~e~ 162 (293)
...|+++++.++.+.+.++.++
T Consensus 41 ~~~lr~e~~~l~~~~~~~~~~~ 62 (308)
T PF11382_consen 41 FDSLREENDELRAELDALQAQL 62 (308)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444444433
No 284
>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=21.48 E-value=57 Score=23.28 Aligned_cols=20 Identities=10% Similarity=0.448 Sum_probs=17.8
Q ss_pred HHHHHHhCCCcchhhhhhhh
Q 022702 108 MQLARALGLQPRQVAIWFQN 127 (293)
Q Consensus 108 ~~LA~~lgL~~~qVkvWFQN 127 (293)
.++|+.+|++++.|+.|-++
T Consensus 4 ~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999765
No 285
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=21.44 E-value=2e+02 Score=24.58 Aligned_cols=32 Identities=28% Similarity=0.454 Sum_probs=21.5
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARW 132 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~ 132 (293)
-+|.+|+..|+...+...|. |-.||-|||.-.
T Consensus 51 ~Lt~~qi~~l~~~i~~~~~~------------------iP~w~~Nr~~d~ 82 (144)
T TIGR03629 51 YLDDEEIEKLEEAVENYEYG------------------IPSWLLNRRKDY 82 (144)
T ss_pred cCCHHHHHHHHHHHHhcccc------------------CCHHHhhccccc
Confidence 48888888887766542222 456999977443
No 286
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=21.43 E-value=1.3e+02 Score=25.77 Aligned_cols=46 Identities=17% Similarity=0.289 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKT 134 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Kr 134 (293)
++..+..++.-.|-. .....++|+.+|++...|++..+.-|.+.|+
T Consensus 132 L~~~~r~i~~l~~~~-----g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 132 LEKLDREIFIRRYLL-----GEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred CCHHHHHHHHHHHHc-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 666666666654422 2234589999999999998876644444333
No 287
>KOG3584 consensus cAMP response element binding protein and related transcription factors [Transcription]
Probab=21.38 E-value=2.1e+02 Score=27.69 Aligned_cols=29 Identities=24% Similarity=0.289 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 147 QYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 147 ~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
..+.|.....-|..+|..|-.||..||+-
T Consensus 313 YVKCLENRVAVLENQNKaLIEELKtLKeL 341 (348)
T KOG3584|consen 313 YVKCLENRVAVLENQNKALIEELKTLKEL 341 (348)
T ss_pred HHHHHHhHHHHHhcccHHHHHHHHHHHHH
Confidence 34445555555666777777777777764
No 288
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.23 E-value=4.3e+02 Score=21.04 Aligned_cols=35 Identities=14% Similarity=0.211 Sum_probs=25.0
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhh
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQN 127 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQN 127 (293)
..|.|+..++..|.. ....+.+|++...|+-.+..
T Consensus 34 g~R~Y~~~~~~~l~~-------------I~~lr~~G~sl~eI~~~l~~ 68 (112)
T cd01282 34 GYRDYDEAAVDRVRQ-------------IRRLLAAGLTLEEIREFLPC 68 (112)
T ss_pred CCeecCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHHH
Confidence 456799999988843 23356788888888877654
No 289
>TIGR02977 phageshock_pspA phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.
Probab=21.20 E-value=4e+02 Score=23.89 Aligned_cols=44 Identities=23% Similarity=0.316 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 132 WKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 132 ~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
.+++..+.....|+.+++.++...+.|+.....|+.++..++..
T Consensus 92 ~~k~~~~~~~~~l~~~~~~~~~~v~~l~~~l~~L~~ki~~~k~k 135 (219)
T TIGR02977 92 IEKQKAQELAEALERELAAVEETLAKLQEDIAKLQAKLAEARAR 135 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555566666666666666666666666666666655544
No 290
>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=21.09 E-value=5.6e+02 Score=22.35 Aligned_cols=48 Identities=19% Similarity=0.198 Sum_probs=36.9
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhH
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRR 129 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRR 129 (293)
++..+|.+++..+...-..+ |..-.+..||+++|++..-|.+-..--.
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~~ 129 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAPK 129 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCCH
Confidence 44569999999998876655 4566788999999999988887664433
No 291
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=21.01 E-value=3.2e+02 Score=26.21 Aligned_cols=37 Identities=27% Similarity=0.460 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022702 137 LEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALK 173 (293)
Q Consensus 137 ~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 173 (293)
++++...+..+++.+..+.+.+.++...|+.+..+++
T Consensus 55 le~Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~ 91 (314)
T PF04111_consen 55 LEQEEEELLQELEELEKEREELDQELEELEEELEELD 91 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444455555555555555555555554444443
No 292
>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=21.00 E-value=1.9e+02 Score=18.93 Aligned_cols=36 Identities=14% Similarity=0.216 Sum_probs=24.6
Q ss_pred CHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhh
Q 022702 85 NMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQ 126 (293)
Q Consensus 85 t~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQ 126 (293)
+..+...+...+ .. ....++|..+|++...|+.|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 445556665433 11 2446889999999999998875
No 293
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=20.75 E-value=3.2e+02 Score=26.76 Aligned_cols=40 Identities=28% Similarity=0.429 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 136 QLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 136 ~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
..+..++.|+..++.+..+...++.+..+++.++..++..
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 (389)
T PRK03992 12 ELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKSP 51 (389)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 3455677778888888888888888888888888777654
No 294
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=20.69 E-value=1.2e+02 Score=25.24 Aligned_cols=45 Identities=18% Similarity=0.077 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~K 133 (293)
.+|..+...|....+. ..+.+||..|+++.+.|+++..+=|.|..
T Consensus 149 ~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 4788888888654433 45778999999999999999876665543
No 295
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=20.52 E-value=96 Score=26.12 Aligned_cols=44 Identities=14% Similarity=0.092 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHH
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARW 132 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~ 132 (293)
++..+..+++..|- ....-.++|..+|+++..|+++...-|.+.
T Consensus 137 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~L 180 (187)
T TIGR02948 137 LPPKYRMVIVLKYM-----EDLSLKEISEILDLPVGTVKTRIHRGREAL 180 (187)
T ss_pred CCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 56666666555432 223346899999999999999986444433
No 296
>PF09766 FimP: Fms-interacting protein; InterPro: IPR019163 This entry represents Thoc5 which is one of the subunits of the THO complex, which additionally contains: HPR1, Thoc2, Thoc6 and Thoc7. The evolutionarily conserved multisubunit THO complex, which is recruited to actively transcribed genes is required for the efficient expression of genes that have internal tandem repeats. It is suggested that the THO complex functions to rectify aberrant structures that arise during transcription [, ] and is required for cell proliferation and for proper export of heat-shock mRNAs under heat stress []. This entry also identifies the crucial 144 N-terminal residues of the FmiP protein, which is essential for the binding of the protein to the cytoplasmic domain of activated Fms-molecules in M-CSF induced haematopoietic differentiation of macrophages. The C terminus contains a putative nuclear localisation sequence and a leucine zipper which suggest further, as yet unknown, nuclear functions. The level of FMIP expression might form a threshold that determines whether cells differentiate into macrophages or into granulocytes [].
Probab=20.44 E-value=3.2e+02 Score=26.70 Aligned_cols=49 Identities=20% Similarity=0.265 Sum_probs=36.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 127 NRRARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 127 NRRaK~Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
||.+..+.+..+......|...+.+.-..+.|.=|...|+.|+.+..+-
T Consensus 7 nR~~~~~~~~~k~~t~e~k~~vD~~~LqLqNl~YE~~hL~kEI~~C~~F 55 (355)
T PF09766_consen 7 NRAAQFRIKKAKDETAEAKQEVDALHLQLQNLLYEKSHLQKEIKKCLDF 55 (355)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhHHHHHHhHHHHHHHHHHHHHHHHhcc
Confidence 7777777777777777777777777777777777888888888766554
No 297
>PF08898 DUF1843: Domain of unknown function (DUF1843); InterPro: IPR014994 This domain is found in functionally uncharacterised proteins. It can be found independently or at the C terminus of the protein.
Probab=20.43 E-value=2.8e+02 Score=20.02 Aligned_cols=30 Identities=37% Similarity=0.358 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022702 144 LKRQYEAVKADREALQAQNQKLHAEIMALK 173 (293)
Q Consensus 144 lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 173 (293)
|-.+-+...++...+....+.|+.|+.++.
T Consensus 22 l~~~aeq~L~~~~~i~~al~~Lk~EIaklE 51 (53)
T PF08898_consen 22 LAAQAEQQLAEAGDIAAALEKLKAEIAKLE 51 (53)
T ss_pred HHHHHHHHHccchHHHHHHHHHHHHHHHHh
Confidence 344455556667777777778888877664
No 298
>KOG3584 consensus cAMP response element binding protein and related transcription factors [Transcription]
Probab=20.40 E-value=2e+02 Score=27.85 Aligned_cols=26 Identities=27% Similarity=0.350 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022702 134 TKQLEKDYDLLKRQYEAVKADREALQ 159 (293)
Q Consensus 134 rk~~~~~~~~lk~~~~~l~~e~~~l~ 159 (293)
.|.+|.....|..++++|.+|...|+
T Consensus 314 VKCLENRVAVLENQNKaLIEELKtLK 339 (348)
T KOG3584|consen 314 VKCLENRVAVLENQNKALIEELKTLK 339 (348)
T ss_pred HHHHHhHHHHHhcccHHHHHHHHHHH
Confidence 34455555555555555555544443
No 299
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=20.38 E-value=2.6e+02 Score=22.79 Aligned_cols=38 Identities=16% Similarity=0.077 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhh
Q 022702 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQ 126 (293)
Q Consensus 84 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQ 126 (293)
++..+..++.-.|-.. ..-.++|..||++...|++...
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 107 LPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred CCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 6666666665544222 1245899999999999998765
No 300
>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].
Probab=20.31 E-value=4.2e+02 Score=22.39 Aligned_cols=43 Identities=21% Similarity=0.383 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022702 133 KTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSR 175 (293)
Q Consensus 133 Krk~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 175 (293)
+.+.++.+...+..++..|...+..|..+.+++...+..++..
T Consensus 22 ~~K~le~~~~~~E~EI~sL~~K~~~lE~eld~~~~~l~~~k~~ 64 (143)
T PF12718_consen 22 KVKQLEQENEQKEQEITSLQKKNQQLEEELDKLEEQLKEAKEK 64 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444455555555555555555555555444443
No 301
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=20.31 E-value=59 Score=21.96 Aligned_cols=22 Identities=23% Similarity=0.362 Sum_probs=18.7
Q ss_pred HHHHHHhCCCcchhhhhhhhhH
Q 022702 108 MQLARALGLQPRQVAIWFQNRR 129 (293)
Q Consensus 108 ~~LA~~lgL~~~qVkvWFQNRR 129 (293)
.+||+.+|++...|.-|..++|
T Consensus 13 ~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHhCCCcchhHHHhcCCC
Confidence 6899999999999999998854
No 302
>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=20.21 E-value=94 Score=26.24 Aligned_cols=21 Identities=14% Similarity=0.033 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCCcchhhhhhh
Q 022702 106 RKMQLARALGLQPRQVAIWFQ 126 (293)
Q Consensus 106 ~r~~LA~~lgL~~~qVkvWFQ 126 (293)
.-.++|..+|+++..|+++..
T Consensus 156 s~~EIA~~lgis~~tv~~~l~ 176 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIF 176 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 346899999999999998875
No 303
>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=20.16 E-value=59 Score=21.32 Aligned_cols=18 Identities=28% Similarity=0.547 Sum_probs=14.6
Q ss_pred HHHHHHhCCCcchhhhhh
Q 022702 108 MQLARALGLQPRQVAIWF 125 (293)
Q Consensus 108 ~~LA~~lgL~~~qVkvWF 125 (293)
-++|+.+|++.+.|+.|=
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 478999999999999883
No 304
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=20.15 E-value=2.2e+02 Score=25.44 Aligned_cols=48 Identities=19% Similarity=0.098 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHHHHHH
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNRRaK~Krk~ 136 (293)
.+|..++++|+-...- ....++|+.|+++++.|+.+..+-..|..-+.
T Consensus 155 ~Lt~rE~~Vl~l~~~G------~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~n 202 (216)
T PRK10100 155 LLTHREKEILNKLRIG------ASNNEIARSLFISENTVKTHLYNLFKKIAVKN 202 (216)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 4888888888776652 22457899999999999999988777666544
No 305
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.04 E-value=4.2e+02 Score=20.46 Aligned_cols=36 Identities=17% Similarity=0.245 Sum_probs=27.3
Q ss_pred CCCCCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhh
Q 022702 80 KKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNR 128 (293)
Q Consensus 80 kr~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQNR 128 (293)
..|.|+.+++..|.. ....+.+|++-.+|+-.+.+.
T Consensus 35 gyR~Y~~~~l~~l~~-------------I~~lr~~G~~l~~I~~~l~~~ 70 (96)
T cd04768 35 GYRYYSYAQLYQLQF-------------ILFLRELGFSLAEIKELLDTE 70 (96)
T ss_pred CeeeCCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhcC
Confidence 456799999988843 234677899999998888763
No 306
>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=20.01 E-value=1.2e+02 Score=25.53 Aligned_cols=39 Identities=21% Similarity=0.136 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHhCCCcchhhhhhh
Q 022702 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQ 126 (293)
Q Consensus 83 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~lgL~~~qVkvWFQ 126 (293)
.++..+..+|.-.|-.. ..-.++|..+|+++..|+++-.
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 36666666666554222 2345889999999999998764
Done!