Query 023725
Match_columns 278
No_of_seqs 226 out of 1446
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 06:11:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023725.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023725hhsearch_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 6.4E-22 1.4E-26 175.8 9.1 103 36-138 48-150 (198)
2 KOG0842 Transcription factor t 99.7 6.7E-17 1.4E-21 151.7 4.9 59 45-103 160-218 (307)
3 KOG0489 Transcription factor z 99.6 1E-16 2.2E-21 147.9 4.6 61 37-97 158-218 (261)
4 KOG0843 Transcription factor E 99.6 1.2E-15 2.6E-20 133.2 5.8 64 37-100 101-164 (197)
5 PF00046 Homeobox: Homeobox do 99.6 3.8E-15 8.3E-20 106.1 6.3 57 39-95 1-57 (57)
6 KOG0488 Transcription factor B 99.6 2.5E-15 5.3E-20 141.9 6.0 57 41-97 175-231 (309)
7 KOG0487 Transcription factor A 99.6 1.7E-15 3.8E-20 142.3 3.9 61 38-98 235-295 (308)
8 KOG0485 Transcription factor N 99.5 1.4E-14 3E-19 129.9 6.3 61 37-97 103-163 (268)
9 KOG0484 Transcription factor P 99.5 1.6E-14 3.5E-19 116.5 3.5 63 34-96 13-75 (125)
10 KOG0848 Transcription factor C 99.5 2.9E-14 6.3E-19 131.0 4.2 54 44-97 205-258 (317)
11 cd00086 homeodomain Homeodomai 99.5 1.3E-13 2.8E-18 97.8 6.5 57 40-96 2-58 (59)
12 KOG0850 Transcription factor D 99.5 8.5E-14 1.8E-18 125.6 6.7 57 40-96 124-180 (245)
13 smart00389 HOX Homeodomain. DN 99.4 1.5E-13 3.1E-18 97.0 5.9 55 40-94 2-56 (56)
14 KOG0493 Transcription factor E 99.4 9.4E-14 2E-18 127.4 5.7 75 39-113 247-321 (342)
15 KOG0492 Transcription factor M 99.4 2.4E-13 5.1E-18 121.3 6.4 58 40-97 146-203 (246)
16 KOG2251 Homeobox transcription 99.4 2.2E-13 4.9E-18 122.2 5.2 63 35-97 34-96 (228)
17 KOG4577 Transcription factor L 99.4 1.5E-13 3.3E-18 127.6 3.7 92 33-125 162-253 (383)
18 COG5576 Homeodomain-containing 99.4 4.7E-13 1E-17 115.3 6.0 66 34-99 47-112 (156)
19 KOG0494 Transcription factor C 99.4 5.4E-13 1.2E-17 122.4 5.6 57 42-98 145-201 (332)
20 TIGR01565 homeo_ZF_HD homeobox 99.3 1.5E-12 3.2E-17 95.0 4.9 52 39-90 2-57 (58)
21 KOG3802 Transcription factor O 99.3 6.7E-13 1.5E-17 127.7 3.2 61 37-97 293-353 (398)
22 KOG0844 Transcription factor E 99.2 4.7E-12 1E-16 118.5 4.3 61 39-99 182-242 (408)
23 KOG0491 Transcription factor B 99.2 6.7E-12 1.4E-16 108.6 2.4 60 38-97 100-159 (194)
24 KOG0486 Transcription factor P 99.1 1.1E-10 2.3E-15 109.8 5.8 60 37-96 111-170 (351)
25 KOG0847 Transcription factor, 99.1 6.7E-11 1.5E-15 106.6 3.5 61 37-97 166-226 (288)
26 KOG0490 Transcription factor, 99.0 6E-10 1.3E-14 98.6 4.5 63 35-97 57-119 (235)
27 KOG1168 Transcription factor A 98.7 3.1E-09 6.8E-14 99.2 1.9 65 32-96 303-367 (385)
28 KOG0849 Transcription factor P 98.7 1.5E-08 3.2E-13 97.6 4.9 61 37-97 175-235 (354)
29 KOG0775 Transcription factor S 98.6 3.2E-08 6.9E-13 91.8 4.6 51 45-95 183-233 (304)
30 PF02183 HALZ: Homeobox associ 98.2 2.1E-06 4.5E-11 59.8 5.0 44 96-139 1-44 (45)
31 PF05920 Homeobox_KN: Homeobox 98.2 1.1E-06 2.3E-11 59.7 3.1 34 59-92 7-40 (40)
32 KOG0774 Transcription factor P 98.1 1.2E-06 2.6E-11 81.1 2.8 59 38-96 188-249 (334)
33 KOG2252 CCAAT displacement pro 97.9 2.4E-05 5.3E-10 78.6 6.2 60 36-95 418-477 (558)
34 KOG0490 Transcription factor, 97.6 7.2E-05 1.6E-09 66.2 4.7 60 38-97 153-212 (235)
35 KOG1146 Homeobox protein [Gene 96.8 0.0018 3.8E-08 71.0 5.6 64 35-98 900-963 (1406)
36 KOG0773 Transcription factor M 96.3 0.0043 9.4E-08 59.0 4.1 61 39-99 240-303 (342)
37 PF11569 Homez: Homeodomain le 96.2 0.004 8.8E-08 45.3 2.7 42 50-91 10-51 (56)
38 PRK09413 IS2 repressor TnpA; R 93.5 0.41 8.9E-06 39.2 7.7 97 40-141 8-105 (121)
39 PF02183 HALZ: Homeobox associ 92.8 0.3 6.6E-06 33.9 4.9 34 105-138 3-36 (45)
40 PF04218 CENP-B_N: CENP-B N-te 91.9 0.38 8.2E-06 34.1 4.7 47 39-90 1-47 (53)
41 smart00340 HALZ homeobox assoc 91.6 0.37 8.1E-06 33.2 4.1 31 97-134 2-32 (44)
42 KOG3623 Homeobox transcription 91.4 0.28 6E-06 51.8 5.0 47 50-96 568-614 (1007)
43 KOG4005 Transcription factor X 86.3 7.6 0.00016 36.3 9.9 44 99-142 103-146 (292)
44 PF00170 bZIP_1: bZIP transcri 81.2 12 0.00026 27.1 7.5 37 100-136 26-62 (64)
45 PRK00888 ftsB cell division pr 79.3 4.2 9.1E-05 32.9 4.9 48 80-135 15-62 (105)
46 KOG4196 bZIP transcription fac 77.4 25 0.00053 30.0 9.0 80 43-138 22-112 (135)
47 PF06156 DUF972: Protein of un 76.5 13 0.00027 30.4 6.9 46 97-142 12-57 (107)
48 PF06005 DUF904: Protein of un 75.5 16 0.00035 27.7 6.9 34 101-134 19-52 (72)
49 PRK13169 DNA replication intia 72.7 15 0.00034 30.1 6.6 43 97-139 12-54 (110)
50 PF13443 HTH_26: Cro/C1-type H 72.1 6.1 0.00013 27.8 3.7 41 67-107 12-52 (63)
51 cd06171 Sigma70_r4 Sigma70, re 71.3 6 0.00013 25.6 3.3 43 44-91 10-52 (55)
52 KOG3119 Basic region leucine z 71.2 12 0.00026 35.0 6.4 50 89-141 207-256 (269)
53 PF06005 DUF904: Protein of un 70.6 31 0.00068 26.2 7.4 46 93-138 18-63 (72)
54 KOG4343 bZIP transcription fac 70.3 12 0.00026 38.7 6.4 49 84-138 285-333 (655)
55 smart00338 BRLZ basic region l 69.6 39 0.00085 24.4 7.7 37 101-137 27-63 (65)
56 PF01527 HTH_Tnp_1: Transposas 69.4 3.4 7.5E-05 30.1 1.9 44 40-87 2-45 (76)
57 PF14775 NYD-SP28_assoc: Sperm 68.7 27 0.00058 25.6 6.5 31 108-138 27-57 (60)
58 PF04545 Sigma70_r4: Sigma-70, 66.7 16 0.00034 24.8 4.7 39 44-87 4-42 (50)
59 KOG4571 Activating transcripti 66.7 27 0.00058 33.4 7.7 45 99-143 247-291 (294)
60 PF00170 bZIP_1: bZIP transcri 63.5 36 0.00078 24.5 6.3 34 97-130 30-63 (64)
61 TIGR02449 conserved hypothetic 62.8 40 0.00087 25.3 6.5 44 98-141 5-48 (65)
62 PF10224 DUF2205: Predicted co 62.4 40 0.00086 26.3 6.6 39 97-135 20-58 (80)
63 cd04766 HTH_HspR Helix-Turn-He 62.2 56 0.0012 25.0 7.6 70 68-138 4-89 (91)
64 cd00569 HTH_Hin_like Helix-tur 58.1 30 0.00065 19.7 4.4 38 44-86 5-42 (42)
65 COG4467 Regulator of replicati 57.4 40 0.00087 27.9 6.1 43 97-139 12-54 (114)
66 PF10668 Phage_terminase: Phag 56.5 8.2 0.00018 28.5 1.8 19 67-85 24-42 (60)
67 PF04967 HTH_10: HTH DNA bindi 55.2 22 0.00048 25.4 3.9 40 45-84 1-42 (53)
68 PF13936 HTH_38: Helix-turn-he 52.5 17 0.00037 24.5 2.8 41 42-87 2-42 (44)
69 PF07407 Seadorna_VP6: Seadorn 51.6 21 0.00046 34.9 4.2 25 111-135 36-60 (420)
70 COG3413 Predicted DNA binding 51.4 25 0.00055 31.2 4.5 50 44-95 155-206 (215)
71 PRK14127 cell division protein 51.3 48 0.001 27.3 5.7 31 112-142 35-65 (109)
72 PF04899 MbeD_MobD: MbeD/MobD 49.5 64 0.0014 24.5 5.8 39 101-139 22-60 (70)
73 PF08281 Sigma70_r4_2: Sigma-7 48.8 42 0.00092 22.8 4.5 40 45-89 11-50 (54)
74 KOG2391 Vacuolar sorting prote 47.9 60 0.0013 31.9 6.7 50 89-138 221-270 (365)
75 PRK03975 tfx putative transcri 47.0 50 0.0011 28.2 5.5 47 42-94 4-50 (141)
76 PF06156 DUF972: Protein of un 46.8 60 0.0013 26.4 5.7 40 96-135 18-57 (107)
77 cd04765 HTH_MlrA-like_sg2 Heli 46.8 79 0.0017 24.9 6.3 64 41-136 35-98 (99)
78 cd04761 HTH_MerR-SF Helix-Turn 46.3 18 0.00038 23.9 2.1 23 68-90 3-25 (49)
79 smart00338 BRLZ basic region l 45.5 81 0.0018 22.7 5.7 28 109-136 28-55 (65)
80 PF15058 Speriolin_N: Sperioli 45.0 36 0.00079 30.8 4.4 33 109-141 7-39 (200)
81 KOG0709 CREB/ATF family transc 44.4 38 0.00083 34.4 4.9 88 44-138 220-310 (472)
82 COG4026 Uncharacterized protei 42.9 65 0.0014 30.1 5.8 36 102-137 137-172 (290)
83 PF12709 Kinetocho_Slk19: Cent 42.5 1.7E+02 0.0037 23.2 8.4 37 102-138 36-73 (87)
84 PF09607 BrkDBD: Brinker DNA-b 41.8 55 0.0012 24.1 4.2 44 42-87 3-47 (58)
85 KOG1146 Homeobox protein [Gene 41.4 52 0.0011 37.5 5.8 81 15-97 684-764 (1406)
86 PRK14127 cell division protein 41.1 68 0.0015 26.4 5.1 40 99-138 29-68 (109)
87 KOG4403 Cell surface glycoprot 40.7 1.2E+02 0.0026 31.0 7.6 26 82-107 228-256 (575)
88 PRK13169 DNA replication intia 40.2 79 0.0017 26.0 5.4 39 97-135 19-57 (110)
89 TIGR03879 near_KaiC_dom probab 39.5 15 0.00033 28.1 1.0 36 53-88 20-55 (73)
90 KOG3156 Uncharacterized membra 39.4 1.1E+02 0.0024 28.2 6.7 30 111-140 113-142 (220)
91 PF13518 HTH_28: Helix-turn-he 39.3 32 0.00068 22.9 2.5 22 67-88 14-35 (52)
92 PF13411 MerR_1: MerR HTH fami 38.9 24 0.00053 25.1 2.0 21 68-88 3-23 (69)
93 PRK10884 SH3 domain-containing 38.8 1.5E+02 0.0032 26.8 7.5 30 105-134 137-166 (206)
94 PF07334 IFP_35_N: Interferon- 38.4 61 0.0013 25.1 4.2 27 112-138 5-31 (76)
95 PF04977 DivIC: Septum formati 37.9 83 0.0018 22.9 4.9 27 107-133 24-50 (80)
96 KOG0483 Transcription factor H 37.8 54 0.0012 29.6 4.4 40 105-144 110-149 (198)
97 PF05700 BCAS2: Breast carcino 37.6 1.5E+02 0.0032 26.8 7.4 48 95-142 170-217 (221)
98 PF00196 GerE: Bacterial regul 36.6 88 0.0019 21.7 4.6 45 44-94 3-47 (58)
99 PRK15422 septal ring assembly 36.4 1.9E+02 0.004 22.7 6.6 20 116-135 48-67 (79)
100 cd01106 HTH_TipAL-Mta Helix-Tu 36.3 2.1E+02 0.0045 22.3 7.9 35 42-89 36-70 (103)
101 PRK15422 septal ring assembly 35.1 2E+02 0.0044 22.4 6.6 37 103-139 21-64 (79)
102 COG2919 Septum formation initi 35.0 1.4E+02 0.003 24.4 6.1 35 102-136 52-86 (117)
103 cd04779 HTH_MerR-like_sg4 Heli 34.5 2.8E+02 0.006 23.2 9.6 37 41-90 34-70 (134)
104 PRK10884 SH3 domain-containing 33.8 1.9E+02 0.004 26.2 7.3 35 104-138 129-163 (206)
105 PF13384 HTH_23: Homeodomain-l 33.4 35 0.00077 22.8 2.0 23 65-87 17-39 (50)
106 PF00376 MerR: MerR family reg 33.1 36 0.00078 22.4 1.9 19 68-86 2-20 (38)
107 smart00421 HTH_LUXR helix_turn 33.1 1.2E+02 0.0026 19.6 4.7 39 44-88 3-41 (58)
108 PRK13922 rod shape-determining 32.9 1E+02 0.0022 28.4 5.6 21 111-131 73-93 (276)
109 PRK06759 RNA polymerase factor 32.8 1.1E+02 0.0023 24.8 5.2 42 44-90 106-147 (154)
110 PRK10072 putative transcriptio 32.7 31 0.00068 27.5 1.9 42 44-92 32-73 (96)
111 PF07716 bZIP_2: Basic region 32.2 1.8E+02 0.0038 20.3 5.7 24 111-134 29-52 (54)
112 cd00093 HTH_XRE Helix-turn-hel 32.2 58 0.0013 20.4 2.9 23 68-90 15-37 (58)
113 PF06056 Terminase_5: Putative 32.2 38 0.00082 24.5 2.1 27 67-95 15-41 (58)
114 cd04764 HTH_MlrA-like_sg1 Heli 32.0 39 0.00086 24.1 2.2 21 68-88 3-23 (67)
115 TIGR02937 sigma70-ECF RNA poly 31.5 75 0.0016 24.6 4.0 43 45-92 111-153 (158)
116 PRK14086 dnaA chromosomal repl 31.5 2.9E+02 0.0062 29.3 9.1 77 62-138 523-615 (617)
117 PF08280 HTH_Mga: M protein tr 31.3 59 0.0013 23.1 3.0 35 48-86 6-40 (59)
118 cd04762 HTH_MerR-trunc Helix-T 31.2 44 0.00096 21.3 2.2 24 68-91 3-26 (49)
119 PRK12514 RNA polymerase sigma 31.0 69 0.0015 26.8 3.9 45 45-94 130-174 (179)
120 cd04763 HTH_MlrA-like Helix-Tu 30.4 42 0.00091 24.1 2.1 21 68-88 3-23 (68)
121 PRK11924 RNA polymerase sigma 30.4 71 0.0015 26.2 3.8 45 45-94 126-170 (179)
122 KOG1853 LIS1-interacting prote 30.3 2.2E+02 0.0048 27.2 7.3 29 117-145 160-188 (333)
123 KOG1962 B-cell receptor-associ 30.2 1.1E+02 0.0023 28.2 5.1 16 118-133 183-198 (216)
124 PRK13729 conjugal transfer pil 30.0 1.5E+02 0.0032 30.4 6.5 44 94-137 77-120 (475)
125 PF13551 HTH_29: Winged helix- 29.9 1.2E+02 0.0027 23.0 4.9 47 41-87 54-109 (112)
126 COG3074 Uncharacterized protei 29.8 2.6E+02 0.0057 21.5 6.5 25 111-135 43-67 (79)
127 PRK14872 rod shape-determining 29.7 74 0.0016 31.1 4.2 27 108-134 58-84 (337)
128 PF11594 Med28: Mediator compl 29.6 3E+02 0.0065 22.6 7.1 15 79-93 17-31 (106)
129 PRK04217 hypothetical protein; 29.4 1.4E+02 0.003 24.5 5.2 41 43-88 41-81 (110)
130 PRK09646 RNA polymerase sigma 29.4 1E+02 0.0022 26.5 4.7 45 45-94 143-187 (194)
131 TIGR03752 conj_TIGR03752 integ 28.6 2.2E+02 0.0048 29.1 7.5 92 44-138 41-133 (472)
132 PF08961 DUF1875: Domain of un 28.6 19 0.00041 33.3 0.0 29 105-133 134-162 (243)
133 cd04769 HTH_MerR2 Helix-Turn-H 28.5 3E+02 0.0064 22.0 7.0 38 42-92 35-72 (116)
134 PF12844 HTH_19: Helix-turn-he 28.5 72 0.0016 22.2 3.1 38 68-106 15-52 (64)
135 PRK09652 RNA polymerase sigma 28.5 81 0.0018 25.9 3.8 39 45-88 129-167 (182)
136 PF01166 TSC22: TSC-22/dip/bun 28.4 87 0.0019 23.1 3.4 20 117-136 24-43 (59)
137 PF03670 UPF0184: Uncharacteri 28.3 1.4E+02 0.0031 23.5 4.8 36 99-134 25-60 (83)
138 COG4367 Uncharacterized protei 28.1 75 0.0016 25.5 3.3 38 45-82 3-40 (97)
139 cd01392 HTH_LacI Helix-turn-he 28.1 58 0.0013 21.7 2.4 21 70-90 2-22 (52)
140 PF01381 HTH_3: Helix-turn-hel 27.9 45 0.00097 22.5 1.8 23 68-90 12-34 (55)
141 PF02344 Myc-LZ: Myc leucine z 27.6 1.6E+02 0.0034 19.2 4.0 22 117-138 4-25 (32)
142 KOG0249 LAR-interacting protei 27.6 4.5E+02 0.0097 28.7 9.6 50 91-140 214-263 (916)
143 TIGR01069 mutS2 MutS2 family p 27.4 3E+02 0.0066 29.7 8.7 22 63-84 480-501 (771)
144 PRK00888 ftsB cell division pr 27.3 1.3E+02 0.0027 24.3 4.6 28 101-128 35-62 (105)
145 PF04899 MbeD_MobD: MbeD/MobD 27.3 2.7E+02 0.0059 21.0 6.1 40 99-138 27-66 (70)
146 COG4026 Uncharacterized protei 27.2 1.7E+02 0.0037 27.4 5.9 31 104-134 132-162 (290)
147 PF07334 IFP_35_N: Interferon- 27.1 1.1E+02 0.0024 23.7 4.0 27 117-143 3-29 (76)
148 PRK13890 conjugal transfer pro 27.0 79 0.0017 25.9 3.4 41 68-109 21-61 (120)
149 PRK09642 RNA polymerase sigma 26.9 1.5E+02 0.0033 24.1 5.2 45 45-94 107-151 (160)
150 TIGR03752 conj_TIGR03752 integ 26.8 1.6E+02 0.0035 30.1 6.1 7 72-78 47-53 (472)
151 cd01104 HTH_MlrA-CarA Helix-Tu 26.6 55 0.0012 23.1 2.2 20 68-87 3-22 (68)
152 PF12709 Kinetocho_Slk19: Cent 26.6 2.5E+02 0.0054 22.3 6.0 32 103-134 45-76 (87)
153 TIGR00219 mreC rod shape-deter 26.6 1.3E+02 0.0028 28.3 5.2 17 125-141 95-111 (283)
154 PRK12526 RNA polymerase sigma 25.8 1.5E+02 0.0032 25.8 5.2 44 45-93 154-197 (206)
155 cd06170 LuxR_C_like C-terminal 25.8 1.2E+02 0.0026 19.9 3.6 36 46-87 2-37 (57)
156 COG2963 Transposase and inacti 25.6 3.3E+02 0.0072 21.4 7.1 42 42-87 5-47 (116)
157 TIGR02985 Sig70_bacteroi1 RNA 25.5 98 0.0021 24.8 3.7 41 45-90 114-154 (161)
158 PF07407 Seadorna_VP6: Seadorn 25.3 1.4E+02 0.003 29.4 5.2 31 102-132 34-64 (420)
159 TIGR02989 Sig-70_gvs1 RNA poly 25.1 1E+02 0.0022 25.0 3.8 39 45-88 112-150 (159)
160 PF04880 NUDE_C: NUDE protein, 25.0 63 0.0014 28.5 2.6 29 115-143 25-53 (166)
161 PRK00409 recombination and DNA 24.9 3.4E+02 0.0074 29.3 8.6 22 63-84 485-506 (782)
162 PRK12530 RNA polymerase sigma 24.7 2.1E+02 0.0045 24.4 5.8 46 45-95 135-180 (189)
163 TIGR02449 conserved hypothetic 24.2 3.1E+02 0.0067 20.5 6.4 41 97-137 11-51 (65)
164 PF07989 Microtub_assoc: Micro 24.2 2.9E+02 0.0062 21.0 5.8 32 111-142 40-71 (75)
165 PRK12512 RNA polymerase sigma 23.9 1.8E+02 0.0038 24.5 5.2 45 45-94 132-176 (184)
166 PF08172 CASP_C: CASP C termin 23.8 1.7E+02 0.0036 27.3 5.3 29 110-138 103-131 (248)
167 PF15035 Rootletin: Ciliary ro 23.7 3.5E+02 0.0076 24.0 7.1 41 102-142 83-123 (182)
168 PF10224 DUF2205: Predicted co 23.6 3.6E+02 0.0077 21.0 6.8 42 94-135 24-65 (80)
169 PF09304 Cortex-I_coil: Cortex 23.5 3.7E+02 0.008 22.2 6.6 41 98-138 35-75 (107)
170 PF14197 Cep57_CLD_2: Centroso 23.4 3.2E+02 0.007 20.4 6.1 18 119-136 45-62 (69)
171 PF04999 FtsL: Cell division p 23.4 1.9E+02 0.004 22.3 4.8 30 109-138 44-73 (97)
172 PRK13922 rod shape-determining 23.3 3.6E+02 0.0078 24.7 7.5 39 103-141 72-113 (276)
173 PRK00118 putative DNA-binding 23.2 2.1E+02 0.0045 23.2 5.1 45 45-94 18-62 (104)
174 PRK12519 RNA polymerase sigma 23.1 1E+02 0.0022 26.2 3.5 45 45-94 142-186 (194)
175 PF14197 Cep57_CLD_2: Centroso 23.1 3.3E+02 0.0071 20.4 7.4 27 108-134 41-67 (69)
176 PF11559 ADIP: Afadin- and alp 23.1 4.4E+02 0.0096 21.9 7.5 49 90-138 77-125 (151)
177 TIGR02209 ftsL_broad cell divi 22.8 2.3E+02 0.005 21.0 5.1 25 111-135 35-59 (85)
178 cd01279 HTH_HspR-like Helix-Tu 22.7 3.4E+02 0.0073 21.1 6.2 22 68-89 4-25 (98)
179 TIGR02948 SigW_bacill RNA poly 22.6 1.2E+02 0.0026 25.3 3.8 44 45-93 137-180 (187)
180 PRK14872 rod shape-determining 22.6 1.6E+02 0.0034 28.9 5.0 19 102-120 59-77 (337)
181 PF11932 DUF3450: Protein of u 22.6 3.5E+02 0.0077 24.5 7.2 31 105-135 61-91 (251)
182 KOG0977 Nuclear envelope prote 22.6 2.4E+02 0.0052 29.4 6.6 35 104-138 152-186 (546)
183 PF05377 FlaC_arch: Flagella a 22.6 3.1E+02 0.0066 20.0 5.3 31 107-137 7-37 (55)
184 TIGR02894 DNA_bind_RsfA transc 22.3 2.4E+02 0.0052 24.8 5.6 22 113-134 110-131 (161)
185 PF00038 Filament: Intermediat 22.2 4.6E+02 0.01 24.2 8.0 56 79-134 186-250 (312)
186 PRK05602 RNA polymerase sigma 22.1 1.2E+02 0.0025 25.7 3.7 41 45-90 129-169 (186)
187 PF12999 PRKCSH-like: Glucosid 22.1 4.8E+02 0.01 23.2 7.6 23 120-142 152-174 (176)
188 PRK09644 RNA polymerase sigma 22.0 1.6E+02 0.0035 24.3 4.4 45 45-94 109-153 (165)
189 TIGR00219 mreC rod shape-deter 21.9 1.6E+02 0.0036 27.6 4.9 17 117-133 69-85 (283)
190 KOG0150 Spliceosomal protein F 21.9 4.3E+02 0.0094 25.8 7.7 58 82-139 16-74 (336)
191 PF08614 ATG16: Autophagy prot 21.8 5.3E+02 0.012 22.5 7.9 44 99-142 143-186 (194)
192 KOG3119 Basic region leucine z 21.8 2.8E+02 0.006 26.0 6.4 33 106-138 214-246 (269)
193 TIGR02959 SigZ RNA polymerase 21.7 2E+02 0.0044 24.0 5.1 38 45-87 101-138 (170)
194 TIGR02607 antidote_HigA addict 21.6 2.1E+02 0.0045 20.6 4.5 23 68-90 21-43 (78)
195 KOG4187 Proprotein convertase 21.5 1.4E+02 0.003 27.1 4.1 24 246-271 103-128 (228)
196 KOG1029 Endocytic adaptor prot 21.4 4.6E+02 0.0099 29.0 8.4 13 83-95 411-423 (1118)
197 PRK09047 RNA polymerase factor 21.4 2.6E+02 0.0057 22.6 5.6 39 45-88 107-145 (161)
198 smart00530 HTH_XRE Helix-turn- 21.3 1.1E+02 0.0023 18.9 2.6 23 68-90 13-35 (56)
199 PRK09648 RNA polymerase sigma 21.1 2.1E+02 0.0046 24.1 5.2 38 45-87 140-177 (189)
200 PF10482 CtIP_N: Tumour-suppre 21.0 2.6E+02 0.0056 23.4 5.3 18 51-68 35-52 (120)
201 COG3074 Uncharacterized protei 20.8 4E+02 0.0087 20.5 6.7 42 98-139 23-64 (79)
202 cd01111 HTH_MerD Helix-Turn-He 20.8 4.4E+02 0.0094 21.0 7.5 18 69-86 4-21 (107)
203 TIGR03070 couple_hipB transcri 20.7 75 0.0016 21.1 1.8 23 68-90 18-40 (58)
204 PF07716 bZIP_2: Basic region 20.7 3E+02 0.0065 19.1 6.8 27 103-129 28-54 (54)
205 PRK10403 transcriptional regul 20.4 1.4E+02 0.0029 24.4 3.7 45 44-94 153-197 (215)
206 PF10473 CENP-F_leu_zip: Leuci 20.3 4.8E+02 0.01 22.3 7.0 48 91-138 50-97 (140)
207 PRK09639 RNA polymerase sigma 20.2 2.3E+02 0.0051 23.1 5.1 42 45-92 113-154 (166)
208 cd00131 PAX Paired Box domain 20.1 4.4E+02 0.0095 21.7 6.6 46 44-89 75-127 (128)
209 KOG3650 Predicted coiled-coil 20.1 2.7E+02 0.0058 22.9 5.0 30 104-133 67-96 (120)
210 PF00424 REV: REV protein (ant 20.0 1.3E+02 0.0029 24.0 3.3 34 50-97 14-47 (91)
211 TIGR00721 tfx DNA-binding prot 20.0 4.3E+02 0.0093 22.4 6.6 47 42-94 4-50 (137)
212 KOG3755 SATB1 matrix attachmen 20.0 44 0.00095 35.2 0.7 60 38-97 691-758 (769)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.86 E-value=6.4e-22 Score=175.81 Aligned_cols=103 Identities=62% Similarity=0.928 Sum_probs=92.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHHHHHHHHHhhhhhhHHHh
Q 023725 36 FHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKAD 115 (278)
Q Consensus 36 ~~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~k~~~~l~~~~~~Lk~~ 115 (278)
....+|++||+.+|+..||+.|+.+.++.+.+|..||++|||.+|||+|||||||||||+++++.+|+.|+..++.|+.+
T Consensus 48 ~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~ 127 (198)
T KOG0483|consen 48 SKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSE 127 (198)
T ss_pred cccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhh
Confidence 34567888999999999999999999999999999999999999999999999999999999999999999988888888
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHh
Q 023725 116 YDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 116 ~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
+..|..++..|++++..++...+
T Consensus 128 ~~~Lq~e~~eL~~~~~~~~~~~~ 150 (198)
T KOG0483|consen 128 NDRLQSEVQELVAELSSLKREMQ 150 (198)
T ss_pred hhHHHHHHHHHHHHHhhhhhhhc
Confidence 88888888888888776655444
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.65 E-value=6.7e-17 Score=151.73 Aligned_cols=59 Identities=39% Similarity=0.579 Sum_probs=56.5
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHHHHHHH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYD 103 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~k~~~ 103 (278)
|+..|+..||+.|...+|++..+|+.||..|+|+++||||||||||-|+||+++++..+
T Consensus 160 FSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~ 218 (307)
T KOG0842|consen 160 FSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALE 218 (307)
T ss_pred cchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhh
Confidence 99999999999999999999999999999999999999999999999999998777654
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.64 E-value=1e-16 Score=147.89 Aligned_cols=61 Identities=38% Similarity=0.679 Sum_probs=57.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHH
Q 023725 37 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 37 ~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~ 97 (278)
..+|.|+.||..|+..||+.|+.|+|+++.+|.+||..|.|++|||+|||||||+|||+..
T Consensus 158 ~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhh
Confidence 4567777899999999999999999999999999999999999999999999999999854
No 4
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.59 E-value=1.2e-15 Score=133.17 Aligned_cols=64 Identities=34% Similarity=0.494 Sum_probs=59.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHHHH
Q 023725 37 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEK 100 (278)
Q Consensus 37 ~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~k 100 (278)
+.+|.|+.||.+|+..||..|+.++|....+|.+||..|+|++.||+|||||||+|.|+.+.+.
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 4566777899999999999999999999999999999999999999999999999999987653
No 5
>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=99.58 E-value=3.8e-15 Score=106.11 Aligned_cols=57 Identities=42% Similarity=0.636 Sum_probs=54.5
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHH
Q 023725 39 PEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 95 (278)
Q Consensus 39 ~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~ 95 (278)
+++|++||.+|+..|+..|..++||+..++..||.+|||+..+|++||+|||+++|+
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 467888999999999999999999999999999999999999999999999999885
No 6
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.57 E-value=2.5e-15 Score=141.95 Aligned_cols=57 Identities=40% Similarity=0.675 Sum_probs=53.9
Q ss_pred CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHH
Q 023725 41 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 41 kR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~ 97 (278)
.|+.||..|+..||+.|++.+|++...|++||..|||+..||++||||||+|||+..
T Consensus 175 sRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 175 SRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred chhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 345599999999999999999999999999999999999999999999999999964
No 7
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.56 E-value=1.7e-15 Score=142.29 Aligned_cols=61 Identities=36% Similarity=0.509 Sum_probs=56.4
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHH
Q 023725 38 QPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQL 98 (278)
Q Consensus 38 ~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~ 98 (278)
.||||..+|..|+..||+.|..|.|++.+.|.+|++.|+|++|||+|||||||+|.|+...
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 4455667999999999999999999999999999999999999999999999999998754
No 8
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.52 E-value=1.4e-14 Score=129.86 Aligned_cols=61 Identities=36% Similarity=0.609 Sum_probs=56.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHH
Q 023725 37 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 37 ~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~ 97 (278)
+++|.|+.|+..|+..||..|+..+|++..+|..||++|.|++.||+|||||||.|||++-
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 3445566799999999999999999999999999999999999999999999999999964
No 9
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.48 E-value=1.6e-14 Score=116.46 Aligned_cols=63 Identities=27% Similarity=0.445 Sum_probs=58.2
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHH
Q 023725 34 EYFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 96 (278)
Q Consensus 34 ~~~~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k 96 (278)
..++++|-|+.||..|+..||+.|...+||++..|++||..+.|++..|+|||||||+|.+++
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 345677778889999999999999999999999999999999999999999999999999874
No 10
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.47 E-value=2.9e-14 Score=131.03 Aligned_cols=54 Identities=44% Similarity=0.586 Sum_probs=51.8
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHH
Q 023725 44 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 44 rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~ 97 (278)
.+|..|+..||+.|...+|.++.+|.+||..|||++|||+|||||||+|+|+..
T Consensus 205 VYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 205 VYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred EecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 399999999999999999999999999999999999999999999999999754
No 11
>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=99.46 E-value=1.3e-13 Score=97.80 Aligned_cols=57 Identities=49% Similarity=0.728 Sum_probs=53.6
Q ss_pred CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHH
Q 023725 40 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 96 (278)
Q Consensus 40 rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k 96 (278)
+++..++..|+.+|+.+|..++||+..++..||.++||+..||+.||+|||.+.++.
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 456789999999999999999999999999999999999999999999999998763
No 12
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.46 E-value=8.5e-14 Score=125.60 Aligned_cols=57 Identities=35% Similarity=0.565 Sum_probs=53.5
Q ss_pred CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHH
Q 023725 40 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 96 (278)
Q Consensus 40 rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k 96 (278)
+.|+.++.-||..|.+.|++++|+--.+|.+||..|||+..||+|||||||.|.|+.
T Consensus 124 KPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 124 KPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred CCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 345669999999999999999999999999999999999999999999999999974
No 13
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.45 E-value=1.5e-13 Score=97.02 Aligned_cols=55 Identities=45% Similarity=0.764 Sum_probs=51.5
Q ss_pred CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 40 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 40 rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
+.|.+|+.+|+.+|+..|..++||+..++..||..+||+..||+.||+|||++.+
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 4566799999999999999999999999999999999999999999999998764
No 14
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.44 E-value=9.4e-14 Score=127.44 Aligned_cols=75 Identities=32% Similarity=0.486 Sum_probs=64.3
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHHHHHHHHHhhhhhhHH
Q 023725 39 PEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLK 113 (278)
Q Consensus 39 ~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~k~~~~l~~~~~~Lk 113 (278)
+|.|+.||.+||.+|...|+.++|++..+|.+||.+|||.+.||+|||||+|+|.|+..-.+....|......|.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~~lmaqgly 321 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLALHLMAQGLY 321 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhhhhhccccc
Confidence 455667999999999999999999999999999999999999999999999999998776666655555443333
No 15
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.42 E-value=2.4e-13 Score=121.28 Aligned_cols=58 Identities=34% Similarity=0.527 Sum_probs=54.3
Q ss_pred CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHH
Q 023725 40 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 40 rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~ 97 (278)
+.|+.||.+|+..||+.|...+|+++.+|.+++..|.|++.||+|||||||+|.||.+
T Consensus 146 kPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 146 KPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 3455699999999999999999999999999999999999999999999999999854
No 16
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.40 E-value=2.2e-13 Score=122.22 Aligned_cols=63 Identities=29% Similarity=0.423 Sum_probs=59.1
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHH
Q 023725 35 YFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 35 ~~~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~ 97 (278)
.++++|.|++|+..|+.+||..|.+.+||+...|++||.+|+|.+-+|+|||.|||+|+|+.+
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq 96 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQ 96 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhh
Confidence 456778888999999999999999999999999999999999999999999999999999864
No 17
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.39 E-value=1.5e-13 Score=127.59 Aligned_cols=92 Identities=24% Similarity=0.365 Sum_probs=78.0
Q ss_pred cccCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHHHHHHHHHhhhhhhH
Q 023725 33 DEYFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSL 112 (278)
Q Consensus 33 d~~~~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~k~~~~l~~~~~~L 112 (278)
+.....+|.|+.+|+.|++.|...|+..++|.+..|++|+.++||..|.|+|||||||+|+|+.+...-...|.+.+...
T Consensus 162 ~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsm 241 (383)
T KOG4577|consen 162 EGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSM 241 (383)
T ss_pred ccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHh
Confidence 34445577788899999999999999999999999999999999999999999999999999988888888888887777
Q ss_pred HHhhHHHHHHHHH
Q 023725 113 KADYDNLFKEKEK 125 (278)
Q Consensus 113 k~~~~~l~~ene~ 125 (278)
|.. ..-++|++.
T Consensus 242 K~s-gs~r~ekds 253 (383)
T KOG4577|consen 242 KRS-GSSRAEKDS 253 (383)
T ss_pred hcc-CCccccccc
Confidence 666 444444443
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.38 E-value=4.7e-13 Score=115.33 Aligned_cols=66 Identities=35% Similarity=0.522 Sum_probs=60.5
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHHH
Q 023725 34 EYFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 99 (278)
Q Consensus 34 ~~~~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~ 99 (278)
.....+++|+|.|..|+.+|+..|..++||+...|..|+..|||+++-|+|||||||++.|+....
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 344677889999999999999999999999999999999999999999999999999999986544
No 19
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.37 E-value=5.4e-13 Score=122.41 Aligned_cols=57 Identities=30% Similarity=0.524 Sum_probs=53.5
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHH
Q 023725 42 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQL 98 (278)
Q Consensus 42 R~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~ 98 (278)
|+.||..|+..||+.|+..+||+...|+-||-.+.|.+..|+|||||||+|||++..
T Consensus 145 RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred cchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 445999999999999999999999999999999999999999999999999998643
No 20
>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=99.33 E-value=1.5e-12 Score=95.03 Aligned_cols=52 Identities=13% Similarity=0.338 Sum_probs=49.7
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHhCCCchhhhhHhhhhh
Q 023725 39 PEKKRRLTVDQVQFLEKSFEVENK----LEPERKIQLAKDLGLQPRQVAIWFQNRR 90 (278)
Q Consensus 39 ~rkR~rft~eQl~~LE~~F~~~~~----P~~~~r~eLA~~LgLs~rQVqvWFQNRR 90 (278)
+|.|+.||.+|+..||..|+.++| |+...+.+||..|||++++|+|||||-+
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 678889999999999999999999 9999999999999999999999999964
No 21
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.32 E-value=6.7e-13 Score=127.73 Aligned_cols=61 Identities=28% Similarity=0.412 Sum_probs=56.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHH
Q 023725 37 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 37 ~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~ 97 (278)
++||||+.|....+..||+.|.+|++|+.+++..||.+|+|.+.+|+|||||||.|.||..
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 5666777799999999999999999999999999999999999999999999999999853
No 22
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.24 E-value=4.7e-12 Score=118.49 Aligned_cols=61 Identities=34% Similarity=0.531 Sum_probs=57.1
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHHH
Q 023725 39 PEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 99 (278)
Q Consensus 39 ~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~ 99 (278)
+|=|+-||.+|+.+||+.|-+.+|.++.+|.+||..|+|++..|+|||||||+|.|++.+.
T Consensus 182 RRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 182 RRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 4556679999999999999999999999999999999999999999999999999998765
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.19 E-value=6.7e-12 Score=108.60 Aligned_cols=60 Identities=35% Similarity=0.516 Sum_probs=55.8
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHH
Q 023725 38 QPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 38 ~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~ 97 (278)
+++-|+.|+..|+..||+.|+..+|++-.+|.+||..|+|++.||+.||||||+|.|+.+
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 445567799999999999999999999999999999999999999999999999999864
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.09 E-value=1.1e-10 Score=109.75 Aligned_cols=60 Identities=28% Similarity=0.544 Sum_probs=56.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHH
Q 023725 37 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 96 (278)
Q Consensus 37 ~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k 96 (278)
+++|.|+.||..|+..||..|.++.||+...|++||.-++|++..|+|||.|||+||++.
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkr 170 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 170 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhh
Confidence 566667779999999999999999999999999999999999999999999999999975
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.08 E-value=6.7e-11 Score=106.58 Aligned_cols=61 Identities=34% Similarity=0.662 Sum_probs=55.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHH
Q 023725 37 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 37 ~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~ 97 (278)
+++..|..|+-.|+..||+.|+..+||-...|.+||-.+|+++.||+|||||||+||+++.
T Consensus 166 ~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred cccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 3344455699999999999999999999999999999999999999999999999999863
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.95 E-value=6e-10 Score=98.62 Aligned_cols=63 Identities=29% Similarity=0.345 Sum_probs=57.8
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHH
Q 023725 35 YFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 35 ~~~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~ 97 (278)
...+++.|+.|+..|+..||+.|+..+||+...++.||..+++++..|++||||||++|++..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 345667777899999999999999999999999999999999999999999999999999753
No 27
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.74 E-value=3.1e-09 Score=99.17 Aligned_cols=65 Identities=23% Similarity=0.342 Sum_probs=59.5
Q ss_pred CcccCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHH
Q 023725 32 FDEYFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 96 (278)
Q Consensus 32 ~d~~~~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k 96 (278)
.-.++.++|||+.+.+...+.||.+|...++|+.+.+..||.+|.|.+..|+|||||.|.|-||.
T Consensus 303 l~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 303 LLPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred ccCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 33455678899999999999999999999999999999999999999999999999999999884
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.69 E-value=1.5e-08 Score=97.64 Aligned_cols=61 Identities=30% Similarity=0.564 Sum_probs=56.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHH
Q 023725 37 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 37 ~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~ 97 (278)
.++|+|+.|+..|+..||+.|+.++||+...|++||+++|+++-.|++||+|||+++++..
T Consensus 175 ~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 175 GGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 4556677899999999999999999999999999999999999999999999999999853
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.62 E-value=3.2e-08 Score=91.79 Aligned_cols=51 Identities=29% Similarity=0.443 Sum_probs=47.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 95 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~ 95 (278)
|...-+..|..+|..++||++.+|.+||+.+||+..||-.||.|||.|+|.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 666667899999999999999999999999999999999999999999984
No 30
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=98.24 E-value=2.1e-06 Score=59.76 Aligned_cols=44 Identities=66% Similarity=0.968 Sum_probs=41.6
Q ss_pred HHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 023725 96 KQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 139 (278)
Q Consensus 96 k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~ 139 (278)
++++++|+.|+..|+.|+++|++|..||+.|++|+..|+++++.
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl~~ 44 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEKLQM 44 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 47899999999999999999999999999999999999998864
No 31
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.22 E-value=1.1e-06 Score=59.67 Aligned_cols=34 Identities=38% Similarity=0.556 Sum_probs=29.0
Q ss_pred hcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhH
Q 023725 59 VENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 92 (278)
Q Consensus 59 ~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak 92 (278)
.++||+.+++..||+++||+..||..||-|.|.|
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 4789999999999999999999999999999875
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.14 E-value=1.2e-06 Score=81.10 Aligned_cols=59 Identities=29% Similarity=0.461 Sum_probs=54.8
Q ss_pred CCCCCCCCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHH
Q 023725 38 QPEKKRRLTVDQVQFLEKSFE---VENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 96 (278)
Q Consensus 38 ~~rkR~rft~eQl~~LE~~F~---~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k 96 (278)
.+|||+.|+..-..+|..+|. .++||+.+.+++||+++|++..||..||.|+|-+.|+.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 578888899999999999996 57899999999999999999999999999999999874
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.85 E-value=2.4e-05 Score=78.63 Aligned_cols=60 Identities=20% Similarity=0.233 Sum_probs=54.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHH
Q 023725 36 FHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 95 (278)
Q Consensus 36 ~~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~ 95 (278)
...+|.|..||..|.+.|..+|+.+++|+.+..+.|+.+|||..+.|.+||.|-|.|.+.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl~ 477 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSLD 477 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhccc
Confidence 345566778999999999999999999999999999999999999999999998887643
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.61 E-value=7.2e-05 Score=66.16 Aligned_cols=60 Identities=32% Similarity=0.607 Sum_probs=54.6
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHH
Q 023725 38 QPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 38 ~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~ 97 (278)
.++.++.++..|+..+...|...++|+...+.+|+..+|++.+.|++||+|+|++.++..
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred cCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 344556699999999999999999999999999999999999999999999999998754
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.79 E-value=0.0018 Score=71.02 Aligned_cols=64 Identities=22% Similarity=0.369 Sum_probs=58.6
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHH
Q 023725 35 YFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQL 98 (278)
Q Consensus 35 ~~~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~ 98 (278)
...++++|++++..|+..|..+|....+|...+.+-|...+++.+|.|.+||||-|++.|+...
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 3356778899999999999999999999999999999999999999999999999999987654
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.26 E-value=0.0043 Score=59.03 Aligned_cols=61 Identities=30% Similarity=0.353 Sum_probs=49.8
Q ss_pred CCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHHH
Q 023725 39 PEKKRRLTVDQVQFLEKSFEV---ENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 99 (278)
Q Consensus 39 ~rkR~rft~eQl~~LE~~F~~---~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~ 99 (278)
.|.++.+....+.+|+.+... .+||+...+..||+++||+..||.+||-|.|-|..+...+
T Consensus 240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~ 303 (342)
T KOG0773|consen 240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIE 303 (342)
T ss_pred CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHH
Confidence 344446999999999988433 5799999999999999999999999999988877654433
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.21 E-value=0.004 Score=45.30 Aligned_cols=42 Identities=26% Similarity=0.366 Sum_probs=31.4
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhh
Q 023725 50 VQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRA 91 (278)
Q Consensus 50 l~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRa 91 (278)
+..|+++|...+.+.......|..+.||+..||+.||-.|+.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 456999999999999999999999999999999999976543
No 38
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=93.50 E-value=0.41 Score=39.16 Aligned_cols=97 Identities=19% Similarity=0.196 Sum_probs=49.8
Q ss_pred CCCCCCCHHHHH-HHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHHHHHHHHHhhhhhhHHHhhHH
Q 023725 40 EKKRRLTVDQVQ-FLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDN 118 (278)
Q Consensus 40 rkR~rft~eQl~-~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~k~~~~l~~~~~~Lk~~~~~ 118 (278)
++|++++.+... ++...+. +. ....++|+++|+++.+|..|.+.-+.....................+..+...
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~-~g----~sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~ 82 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE-PG----MTVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKE 82 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc-CC----CCHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHH
Confidence 456678887644 3333333 22 24567899999999999999643221110000000000000001123444556
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhh
Q 023725 119 LFKEKEKLKAEVLKLTDKLQVKE 141 (278)
Q Consensus 119 l~~ene~L~~E~~~L~~~l~~~~ 141 (278)
|.+++.+|+.|+.=|+..+..-.
T Consensus 83 L~~el~~L~~E~diLKKa~~~~~ 105 (121)
T PRK09413 83 LQRLLGKKTMENELLKEAVEYGR 105 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 66666666666666666555433
No 39
>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=92.78 E-value=0.3 Score=33.93 Aligned_cols=34 Identities=44% Similarity=0.623 Sum_probs=30.2
Q ss_pred HhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 105 LQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 105 l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
|..-|+.|++.|+.|..++++|+.|+..|+..+.
T Consensus 3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~ 36 (45)
T PF02183_consen 3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQ 36 (45)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999999999999988776
No 40
>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=91.93 E-value=0.38 Score=34.15 Aligned_cols=47 Identities=21% Similarity=0.384 Sum_probs=33.7
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhh
Q 023725 39 PEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 90 (278)
Q Consensus 39 ~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRR 90 (278)
+|+|+.+|.++-..+=..++... ....||+++|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 46777899988777666676555 578899999999999999998753
No 41
>smart00340 HALZ homeobox associated leucin zipper.
Probab=91.63 E-value=0.37 Score=33.22 Aligned_cols=31 Identities=35% Similarity=0.438 Sum_probs=24.3
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 023725 97 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 134 (278)
Q Consensus 97 ~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~ 134 (278)
+++.+++ .|+...++|..||.+|+.|+++|+
T Consensus 2 QTEvdCe-------~LKrcce~LteeNrRL~ke~~eLr 32 (44)
T smart00340 2 QTEVDCE-------LLKRCCESLTEENRRLQKEVQELR 32 (44)
T ss_pred chHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556665 466678888999999999999886
No 42
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=91.43 E-value=0.28 Score=51.82 Aligned_cols=47 Identities=19% Similarity=0.350 Sum_probs=43.6
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHH
Q 023725 50 VQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 96 (278)
Q Consensus 50 l~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k 96 (278)
+..|...|..|..|..++...+|.+.||+.+.|+.||+++++....-
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv 614 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSV 614 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhh
Confidence 67899999999999999999999999999999999999999877653
No 43
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=86.32 E-value=7.6 Score=36.31 Aligned_cols=44 Identities=25% Similarity=0.404 Sum_probs=27.8
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 023725 99 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 142 (278)
Q Consensus 99 ~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~~~~ 142 (278)
..+.+.|+..++.|++-+..|..+|..|..++..+++.|..-..
T Consensus 103 ~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~~~~~ 146 (292)
T KOG4005|consen 103 TEENEILQNENDSLRAINESLLAKNHELDSELELLRQELAELKQ 146 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhHH
Confidence 33445566666666666677777777777777666666664443
No 44
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=81.17 E-value=12 Score=27.05 Aligned_cols=37 Identities=27% Similarity=0.407 Sum_probs=26.0
Q ss_pred HHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 023725 100 KDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 136 (278)
Q Consensus 100 k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~ 136 (278)
.....|...+..|...+..|..++..|+.++..|+..
T Consensus 26 ~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e 62 (64)
T PF00170_consen 26 QYIEELEEKVEELESENEELKKELEQLKKEIQSLKSE 62 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3445666777777777777777777777777777654
No 45
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=79.29 E-value=4.2 Score=32.89 Aligned_cols=48 Identities=21% Similarity=0.318 Sum_probs=30.8
Q ss_pred hhhhhHhhhhhhHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 023725 80 RQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 135 (278)
Q Consensus 80 rQVqvWFQNRRak~K~k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~ 135 (278)
-++..||++.-- ..+..+++....++..+..+.++|+.|+.|+..|+.
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 356678865311 122334445556677777888888888888888876
No 46
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=77.43 E-value=25 Score=29.98 Aligned_cols=80 Identities=24% Similarity=0.294 Sum_probs=48.5
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHH-hCCCchhhhhHhhhhhhH----------HHHHHHHHHHHHHhhhhhh
Q 023725 43 RRLTVDQVQFLEKSFEVENKLEPERKIQLAKD-LGLQPRQVAIWFQNRRAR----------WKTKQLEKDYDVLQNSYNS 111 (278)
Q Consensus 43 ~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~-LgLs~rQVqvWFQNRRak----------~K~k~~~k~~~~l~~~~~~ 111 (278)
.+|+.+++..| .. .+|=+. -|++...|-.|=|.||+- .|+-+.. ..|......
T Consensus 22 d~lsDd~Lvsm------------SV-ReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk---~eLE~~k~~ 85 (135)
T KOG4196|consen 22 DRLSDDELVSM------------SV-RELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQK---HELEKEKAE 85 (135)
T ss_pred CCcCHHHHHHh------------hH-HHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH---HHHHHHHHH
Confidence 57888887655 11 233333 489999999999988853 2332222 234444555
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 112 LKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 112 Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
|..+.+.|..|+.+++.|+..++.+..
T Consensus 86 L~qqv~~L~~e~s~~~~E~da~k~k~e 112 (135)
T KOG4196|consen 86 LQQQVEKLKEENSRLRRELDAYKSKYE 112 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666666666666666666666655544
No 47
>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=76.46 E-value=13 Score=30.41 Aligned_cols=46 Identities=28% Similarity=0.442 Sum_probs=36.1
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 023725 97 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 142 (278)
Q Consensus 97 ~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~~~~ 142 (278)
..+.....+......|+..-..|..||.+|+-|+..|++.|....+
T Consensus 12 ~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 12 QLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4555566666777788888888999999999999999988875544
No 48
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=75.51 E-value=16 Score=27.72 Aligned_cols=34 Identities=32% Similarity=0.365 Sum_probs=17.7
Q ss_pred HHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 023725 101 DYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 134 (278)
Q Consensus 101 ~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~ 134 (278)
-+..|+..+..|+..+..+..+++.|+.++.+|+
T Consensus 19 ti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~ 52 (72)
T PF06005_consen 19 TIALLQMENEELKEKNNELKEENEELKEENEQLK 52 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 3444555555555555555555555555555554
No 49
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=72.70 E-value=15 Score=30.14 Aligned_cols=43 Identities=30% Similarity=0.459 Sum_probs=33.6
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 023725 97 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 139 (278)
Q Consensus 97 ~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~ 139 (278)
+++.....+......|+..-..+..||..|+-|+..|+..|..
T Consensus 12 ~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~ 54 (110)
T PRK13169 12 DLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEE 54 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455556666677788888888888999999998888888874
No 50
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=72.14 E-value=6.1 Score=27.81 Aligned_cols=41 Identities=17% Similarity=0.201 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCchhhhhHhhhhhhHHHHHHHHHHHHHHhh
Q 023725 67 RKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQN 107 (278)
Q Consensus 67 ~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~k~~~~l~~ 107 (278)
....||+.+|++...|..|+.++........+.+-+..|.-
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~ 52 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALNC 52 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcCC
Confidence 46789999999999999999988666666666655554443
No 51
>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=71.33 E-value=6 Score=25.65 Aligned_cols=43 Identities=14% Similarity=0.125 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhh
Q 023725 44 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRA 91 (278)
Q Consensus 44 rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRa 91 (278)
.++..+..++...|... ....++|..+|++...|..|...-+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 36777778887777422 34567899999999999999865443
No 52
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=71.21 E-value=12 Score=35.00 Aligned_cols=50 Identities=28% Similarity=0.314 Sum_probs=33.8
Q ss_pred hhhHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023725 89 RRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 141 (278)
Q Consensus 89 RRak~K~k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~~~ 141 (278)
||.|.++++.. ..++.....|..+++.|+.+++.|+.|+..|+.-+....
T Consensus 207 ~kSR~~~k~~~---~e~~~r~~~leken~~lr~~v~~l~~el~~~~~~~~~~~ 256 (269)
T KOG3119|consen 207 RKSRDKRKQKE---DEMAHRVAELEKENEALRTQVEQLKKELATLRRLFLQLP 256 (269)
T ss_pred HHhhhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34555555444 345556677888888888888888888888876665433
No 53
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=70.58 E-value=31 Score=26.17 Aligned_cols=46 Identities=26% Similarity=0.346 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 93 WKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 93 ~K~k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
.....+..+.+.|+..+..|...+..|..+|++|+.+....+.++.
T Consensus 18 eti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl~ 63 (72)
T PF06005_consen 18 ETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERLR 63 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445667777888888888888889999999999888777665553
No 54
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=70.29 E-value=12 Score=38.73 Aligned_cols=49 Identities=29% Similarity=0.428 Sum_probs=23.7
Q ss_pred hHhhhhhhHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 84 IWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 84 vWFQNRRak~K~k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
....||-..+-..+.+|+|. -.|.+.-.+|.+||+.|++|++.|+.+|.
T Consensus 285 RmIKNResA~~SRkKKKEy~------~~Le~rLq~ll~Ene~Lk~ENatLk~qL~ 333 (655)
T KOG4343|consen 285 RMIKNRESACQSRKKKKEYM------LGLEARLQALLSENEQLKKENATLKRQLD 333 (655)
T ss_pred HHHhhHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence 34456654444333344442 13444445555555555555555555544
No 55
>smart00338 BRLZ basic region leucin zipper.
Probab=69.63 E-value=39 Score=24.35 Aligned_cols=37 Identities=32% Similarity=0.489 Sum_probs=26.6
Q ss_pred HHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 023725 101 DYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 137 (278)
Q Consensus 101 ~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l 137 (278)
....|......|...+..|..+...|..|+..|+..+
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455666677777777778888888888877777654
No 56
>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=69.36 E-value=3.4 Score=30.12 Aligned_cols=44 Identities=18% Similarity=0.342 Sum_probs=27.9
Q ss_pred CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhh
Q 023725 40 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 87 (278)
Q Consensus 40 rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQ 87 (278)
++|++||.++...+-..+. ........+|+++||++.++..|-.
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 4567799988775544442 1235678899999999999999964
No 57
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=68.69 E-value=27 Score=25.58 Aligned_cols=31 Identities=32% Similarity=0.430 Sum_probs=25.0
Q ss_pred hhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 108 SYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 108 ~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
.|..+..+..++..|++.|++|+.+|+.-|.
T Consensus 27 rY~~vL~~R~~l~~e~~~L~~qN~eLr~lLk 57 (60)
T PF14775_consen 27 RYNKVLLDRAALIQEKESLEQQNEELRSLLK 57 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566677788899999999999999987654
No 58
>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=66.72 E-value=16 Score=24.79 Aligned_cols=39 Identities=15% Similarity=0.255 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhh
Q 023725 44 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 87 (278)
Q Consensus 44 rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQ 87 (278)
.+++.+..+|...| .....-.++|..+|++...|+.+..
T Consensus 4 ~L~~~er~vi~~~y-----~~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRY-----FEGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHH-----TST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh-----cCCCCHHHHHHHHCCcHHHHHHHHH
Confidence 47888889999988 3334577899999999999988754
No 59
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=66.71 E-value=27 Score=33.45 Aligned_cols=45 Identities=16% Similarity=0.206 Sum_probs=35.6
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 023725 99 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKE 143 (278)
Q Consensus 99 ~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~~~~~ 143 (278)
+.+.+.+-.....|-..|+.|+....+|..|++.||..+...-+.
T Consensus 247 Rae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e~~~~ 291 (294)
T KOG4571|consen 247 RAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILEVYKK 291 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345566667777888889999999999999999999888866553
No 60
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=63.53 E-value=36 Score=24.54 Aligned_cols=34 Identities=32% Similarity=0.462 Sum_probs=16.1
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHH
Q 023725 97 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEV 130 (278)
Q Consensus 97 ~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~ 130 (278)
.++.....|...+..|+..+..|..+...|+.++
T Consensus 30 ~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 30 ELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3444444444444444444444444444444443
No 61
>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=62.82 E-value=40 Score=25.28 Aligned_cols=44 Identities=18% Similarity=0.205 Sum_probs=31.2
Q ss_pred HHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023725 98 LEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 141 (278)
Q Consensus 98 ~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~~~ 141 (278)
++...+.|-..+..|+.+|..|.++...+..|...|.++....-
T Consensus 5 Le~kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar 48 (65)
T TIGR02449 5 LAAQVEHLLEYLERLKSENRLLRAQEKTWREERAQLLEKNEQAR 48 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555666667777778888888888888888777777766443
No 62
>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=62.39 E-value=40 Score=26.27 Aligned_cols=39 Identities=28% Similarity=0.329 Sum_probs=24.0
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 023725 97 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 135 (278)
Q Consensus 97 ~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~ 135 (278)
.+.++...|+.....|....+....|+++|+.|+.-|..
T Consensus 20 ~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~ 58 (80)
T PF10224_consen 20 ELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQ 58 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445556666666666666666677777766665543
No 63
>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=62.24 E-value=56 Score=25.01 Aligned_cols=70 Identities=20% Similarity=0.216 Sum_probs=39.6
Q ss_pred HHHHHHHhCCCchhhhhHhhhhhhHHHHH------HHHHHHHH------Hhh----hhhhHHHhhHHHHHHHHHHHHHHH
Q 023725 68 KIQLAKDLGLQPRQVAIWFQNRRARWKTK------QLEKDYDV------LQN----SYNSLKADYDNLFKEKEKLKAEVL 131 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQNRRak~K~k------~~~k~~~~------l~~----~~~~Lk~~~~~l~~ene~L~~E~~ 131 (278)
..++|+.+|++++.|+.|.+...-.-.+. =...+... |+. ....++ ..-.|..+.+.|++++.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~-~~l~l~~~~~~l~~~l~ 82 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVK-RILELEEELAELRAELD 82 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHH-HHHHHHHHHHHHHHHHH
Confidence 46789999999999999975432221110 00111111 111 111111 22347778888888888
Q ss_pred HHHHHHh
Q 023725 132 KLTDKLQ 138 (278)
Q Consensus 132 ~L~~~l~ 138 (278)
+|+.++.
T Consensus 83 ~l~~~~~ 89 (91)
T cd04766 83 ELRARLR 89 (91)
T ss_pred HHHHHhc
Confidence 8887764
No 64
>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=58.09 E-value=30 Score=19.69 Aligned_cols=38 Identities=16% Similarity=0.329 Sum_probs=26.0
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHh
Q 023725 44 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWF 86 (278)
Q Consensus 44 rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWF 86 (278)
.++..+...+...|... . ...++|+.+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 36666666665566532 2 56678999999988887773
No 65
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=57.45 E-value=40 Score=27.86 Aligned_cols=43 Identities=30% Similarity=0.406 Sum_probs=34.4
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 023725 97 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 139 (278)
Q Consensus 97 ~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~ 139 (278)
.++....++-+....|+..-..+..||-.|+-|+..|+++|..
T Consensus 12 ~le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~~ 54 (114)
T COG4467 12 NLEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKLRERLGE 54 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhCC
Confidence 3444555666677788888899999999999999999998875
No 66
>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=56.48 E-value=8.2 Score=28.49 Aligned_cols=19 Identities=21% Similarity=0.576 Sum_probs=16.8
Q ss_pred HHHHHHHHhCCCchhhhhH
Q 023725 67 RKIQLAKDLGLQPRQVAIW 85 (278)
Q Consensus 67 ~r~eLA~~LgLs~rQVqvW 85 (278)
.-.+||.+||+++.+|+.|
T Consensus 24 ~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 3457899999999999999
No 67
>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=55.15 E-value=22 Score=25.42 Aligned_cols=40 Identities=25% Similarity=0.282 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHhCCCchhhhh
Q 023725 45 LTVDQVQFLEKSFEVENK--LEPERKIQLAKDLGLQPRQVAI 84 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~--P~~~~r~eLA~~LgLs~rQVqv 84 (278)
+|..|..+|...|+..=| |-.....+||.+||+++.-+..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 578999999999987654 6677788999999999866543
No 68
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=52.46 E-value=17 Score=24.49 Aligned_cols=41 Identities=22% Similarity=0.203 Sum_probs=20.7
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhh
Q 023725 42 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 87 (278)
Q Consensus 42 R~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQ 87 (278)
.++||.++...++..+.. ..-..+||+.||.++.-|..+..
T Consensus 2 ~~~Lt~~eR~~I~~l~~~-----G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQ-----GMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ----------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHc-----CCCHHHHHHHHCcCcHHHHHHHh
Confidence 356888888888888653 34567799999999998887753
No 69
>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=51.59 E-value=21 Score=34.93 Aligned_cols=25 Identities=36% Similarity=0.518 Sum_probs=12.8
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHH
Q 023725 111 SLKADYDNLFKEKEKLKAEVLKLTD 135 (278)
Q Consensus 111 ~Lk~~~~~l~~ene~L~~E~~~L~~ 135 (278)
+|+.+|.+|++||+.|+.++.+|.+
T Consensus 36 aLr~EN~~LKkEN~~Lk~eVerLE~ 60 (420)
T PF07407_consen 36 ALRMENHSLKKENNDLKIEVERLEN 60 (420)
T ss_pred hHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 4445555555555555555555543
No 70
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=51.36 E-value=25 Score=31.22 Aligned_cols=50 Identities=26% Similarity=0.265 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHhhhcC--CCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHH
Q 023725 44 RLTVDQVQFLEKSFEVEN--KLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 95 (278)
Q Consensus 44 rft~eQl~~LE~~F~~~~--~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~ 95 (278)
.||..|+.+|...|...= +|-.....+||++||+++.- ++..=||+..|.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~Kl 206 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAERKL 206 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHHH
Confidence 599999999999998764 47777888999999999854 444555665553
No 71
>PRK14127 cell division protein GpsB; Provisional
Probab=51.29 E-value=48 Score=27.26 Aligned_cols=31 Identities=29% Similarity=0.414 Sum_probs=17.6
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 023725 112 LKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 142 (278)
Q Consensus 112 Lk~~~~~l~~ene~L~~E~~~L~~~l~~~~~ 142 (278)
+..+++.+..|+..|+.++.+|+.++..-..
T Consensus 35 V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~ 65 (109)
T PRK14127 35 VIKDYEAFQKEIEELQQENARLKAQVDELTK 65 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555566666666666666666554443
No 72
>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=49.55 E-value=64 Score=24.45 Aligned_cols=39 Identities=23% Similarity=0.346 Sum_probs=29.1
Q ss_pred HHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 023725 101 DYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 139 (278)
Q Consensus 101 ~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~ 139 (278)
....|+..|..|...+..-.+++..|.+.|..|..++..
T Consensus 22 q~~~Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~ 60 (70)
T PF04899_consen 22 QQQEWQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQR 60 (70)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 345677778888888888888888888888887776653
No 73
>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=48.83 E-value=42 Score=22.77 Aligned_cols=40 Identities=15% Similarity=0.199 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhh
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNR 89 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNR 89 (278)
+++.+..++...| .....-.++|..+|+++..|+.|.+.=
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 5566666666555 344567889999999999999998643
No 74
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=47.87 E-value=60 Score=31.87 Aligned_cols=50 Identities=20% Similarity=0.336 Sum_probs=36.8
Q ss_pred hhhHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 89 RRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 89 RRak~K~k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
+|.+.+-.++..+.+.|+..-+.|+.-...|..++++|+.++..|+...-
T Consensus 221 ~r~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~~niD 270 (365)
T KOG2391|consen 221 RRREEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQKNID 270 (365)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHHhhhH
Confidence 45666666667777777777778888888888888888888877765443
No 75
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=47.03 E-value=50 Score=28.21 Aligned_cols=47 Identities=19% Similarity=0.131 Sum_probs=34.7
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 42 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 42 R~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
...+++.|..+|...+ ......++|..||++...|..|-.+.+.+.+
T Consensus 4 ~~~Lt~rqreVL~lr~------~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 4 ESFLTERQIEVLRLRE------RGLTQQEIADILGTSRANVSSIEKRARENIE 50 (141)
T ss_pred ccCCCHHHHHHHHHHH------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4568999999987732 2234568999999999999999875444433
No 76
>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=46.80 E-value=60 Score=26.44 Aligned_cols=40 Identities=23% Similarity=0.314 Sum_probs=34.3
Q ss_pred HHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 023725 96 KQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 135 (278)
Q Consensus 96 k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~ 135 (278)
..+-.+...|+.....|-.+|..|.-||+.|+..+.++..
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 3556677888889999999999999999999999888876
No 77
>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=46.76 E-value=79 Score=24.95 Aligned_cols=64 Identities=17% Similarity=0.146 Sum_probs=40.3
Q ss_pred CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHHHHHHHHHhhhhhhHHHhhHHHH
Q 023725 41 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLF 120 (278)
Q Consensus 41 kR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~k~~~~l~~~~~~Lk~~~~~l~ 120 (278)
.+++|+.+++..|.. ...|.+.+|++-..|+.+..+.....- ....+.
T Consensus 35 g~R~Yt~~di~~l~~------------I~~llr~~G~~l~~i~~~l~~~~~~~~--------------------~~~~~~ 82 (99)
T cd04765 35 GRRYYRPKDVELLLL------------IKHLLYEKGYTIEGAKQALKEDGAAAI--------------------REEEAE 82 (99)
T ss_pred CCeeeCHHHHHHHHH------------HHHHHHHCCCCHHHHHHHHHhcccccc--------------------chhhHH
Confidence 355699999988844 334567889999888888764333211 112345
Q ss_pred HHHHHHHHHHHHHHHH
Q 023725 121 KEKEKLKAEVLKLTDK 136 (278)
Q Consensus 121 ~ene~L~~E~~~L~~~ 136 (278)
.+...+++|+..|+..
T Consensus 83 ~~~~~~~~~~~~l~~~ 98 (99)
T cd04765 83 ERLPSIRAELLDLRDQ 98 (99)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 5566677777666653
No 78
>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=46.28 E-value=18 Score=23.88 Aligned_cols=23 Identities=22% Similarity=0.170 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCchhhhhHhhhhh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQNRR 90 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQNRR 90 (278)
..++|+.+|++++.|+.|.++-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 46789999999999999976543
No 79
>smart00338 BRLZ basic region leucin zipper.
Probab=45.52 E-value=81 Score=22.68 Aligned_cols=28 Identities=29% Similarity=0.433 Sum_probs=13.3
Q ss_pred hhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 023725 109 YNSLKADYDNLFKEKEKLKAEVLKLTDK 136 (278)
Q Consensus 109 ~~~Lk~~~~~l~~ene~L~~E~~~L~~~ 136 (278)
...|-.....|..+|..|+.++..|...
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e 55 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRE 55 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444555555555555444433
No 80
>PF15058 Speriolin_N: Speriolin N terminus
Probab=45.00 E-value=36 Score=30.80 Aligned_cols=33 Identities=27% Similarity=0.490 Sum_probs=22.3
Q ss_pred hhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023725 109 YNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 141 (278)
Q Consensus 109 ~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~~~ 141 (278)
|..+++....|..||+.||++|.-|++....|.
T Consensus 7 yeGlrhqierLv~ENeeLKKlVrLirEN~eLks 39 (200)
T PF15058_consen 7 YEGLRHQIERLVRENEELKKLVRLIRENHELKS 39 (200)
T ss_pred hHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence 555666667777788888877777766655444
No 81
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=44.35 E-value=38 Score=34.39 Aligned_cols=88 Identities=18% Similarity=0.256 Sum_probs=54.2
Q ss_pred CCCHHHHHHHHHH-hhhcC-CCCHHHHHHHHHHhCCCchhhhhHhhhhhh-HHHHHHHHHHHHHHhhhhhhHHHhhHHHH
Q 023725 44 RLTVDQVQFLEKS-FEVEN-KLEPERKIQLAKDLGLQPRQVAIWFQNRRA-RWKTKQLEKDYDVLQNSYNSLKADYDNLF 120 (278)
Q Consensus 44 rft~eQl~~LE~~-F~~~~-~P~~~~r~eLA~~LgLs~rQVqvWFQNRRa-k~K~k~~~k~~~~l~~~~~~Lk~~~~~l~ 120 (278)
++|.+..+.|.+. +-... +|-...-+++. .+|+.=.+|+|. +.+|++.+.-.+.|..++..+.++|..|.
T Consensus 220 ~LteeEkrLL~kEG~slPs~lPLTKaEEriL-------KrvRRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqeL~ 292 (472)
T KOG0709|consen 220 VLTEEEKRLLTKEGYSLPSKLPLTKAEERIL-------KRVRRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQELQ 292 (472)
T ss_pred eccHHHHHHHHhccCcCcccCCchHHHHHHH-------HHHHHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHHHH
Confidence 4666666666554 22222 23333333332 245555667664 44444444444777788888888888888
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 023725 121 KEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 121 ~ene~L~~E~~~L~~~l~ 138 (278)
+..++|..++..|-.+|.
T Consensus 293 kkV~~Le~~N~sLl~qL~ 310 (472)
T KOG0709|consen 293 KKVEELELSNRSLLAQLK 310 (472)
T ss_pred HHHHHHhhccHHHHHHHH
Confidence 888888888877777665
No 82
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=42.89 E-value=65 Score=30.10 Aligned_cols=36 Identities=31% Similarity=0.563 Sum_probs=16.3
Q ss_pred HHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 023725 102 YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 137 (278)
Q Consensus 102 ~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l 137 (278)
++.++.....+..++..|..+++.|++++..++++|
T Consensus 137 ~ee~kekl~E~~~EkeeL~~eleele~e~ee~~erl 172 (290)
T COG4026 137 YEELKEKLEELQKEKEELLKELEELEAEYEEVQERL 172 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333333444444445555555555554444443
No 83
>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=42.47 E-value=1.7e+02 Score=23.19 Aligned_cols=37 Identities=32% Similarity=0.425 Sum_probs=17.5
Q ss_pred HHHHhhhhh-hHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 102 YDVLQNSYN-SLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 102 ~~~l~~~~~-~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
...|+.+|. ......+.|..++..|..|+.+|+.++.
T Consensus 36 V~~LKksYe~rwek~v~~L~~e~~~l~~E~e~L~~~l~ 73 (87)
T PF12709_consen 36 VKALKKSYEARWEKKVDELENENKALKRENEQLKKKLD 73 (87)
T ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444333 2333344455555555555555555544
No 84
>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=41.81 E-value=55 Score=24.10 Aligned_cols=44 Identities=20% Similarity=0.404 Sum_probs=22.1
Q ss_pred CCCCCHHH-HHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhh
Q 023725 42 KRRLTVDQ-VQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 87 (278)
Q Consensus 42 R~rft~eQ-l~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQ 87 (278)
|+.|+..- +.+++..+. ...--..+|. .|+++|++.++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~-~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEK-DNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH--TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHH-ccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 34466543 444544443 3222223333 49999999999999953
No 85
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=41.35 E-value=52 Score=37.51 Aligned_cols=81 Identities=19% Similarity=0.306 Sum_probs=59.9
Q ss_pred CCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 15 NRPFFRPFDRDENGDEDFDEYFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 15 ~~p~~~~~~~~e~~~e~~d~~~~~~rkR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
..+|..+..++-++.+..+. +.+.-+..+-.++...|-++|-.+.-|+.+.+..|....+.+.+++.+||+|-|.|.+
T Consensus 684 ~~~~~aPt~s~~g~~~~~~~--~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ 761 (1406)
T KOG1146|consen 684 ADPFLAPTGSEVGGGESLSP--RDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSR 761 (1406)
T ss_pred CCcccCCCCCCCCCCCCCCc--ccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhh
Confidence 34455544444444222221 1223344466699999999999999999999999999999999999999999999988
Q ss_pred HHH
Q 023725 95 TKQ 97 (278)
Q Consensus 95 ~k~ 97 (278)
+..
T Consensus 762 ke~ 764 (1406)
T KOG1146|consen 762 KEQ 764 (1406)
T ss_pred hhc
Confidence 765
No 86
>PRK14127 cell division protein GpsB; Provisional
Probab=41.07 E-value=68 Score=26.36 Aligned_cols=40 Identities=28% Similarity=0.462 Sum_probs=31.1
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 99 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 99 ~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
..+.+.+-..|..|..++..|..++.+|+.++.+++.++.
T Consensus 29 D~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~ 68 (109)
T PRK14127 29 DKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTKQVS 68 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3344455556667788888999999999999999988877
No 87
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=40.69 E-value=1.2e+02 Score=31.01 Aligned_cols=26 Identities=35% Similarity=0.616 Sum_probs=19.2
Q ss_pred hhhHh---hhhhhHHHHHHHHHHHHHHhh
Q 023725 82 VAIWF---QNRRARWKTKQLEKDYDVLQN 107 (278)
Q Consensus 82 VqvWF---QNRRak~K~k~~~k~~~~l~~ 107 (278)
.-+|| ||+.+|.+-.+.-++.+.|+.
T Consensus 228 ~gcw~ay~Qnk~akehv~km~kdle~Lq~ 256 (575)
T KOG4403|consen 228 GGCWFAYRQNKKAKEHVNKMMKDLEGLQR 256 (575)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence 35788 899998887777777666653
No 88
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=40.22 E-value=79 Score=25.99 Aligned_cols=39 Identities=23% Similarity=0.301 Sum_probs=33.5
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 023725 97 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 135 (278)
Q Consensus 97 ~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~ 135 (278)
.+-.+...|+.....|-.+|..|..||+.|+..+.++..
T Consensus 19 ~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~~ 57 (110)
T PRK13169 19 VLLKELGALKKQLAELLEENTALRLENDKLRERLEELEA 57 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 456677788889999999999999999999999988743
No 89
>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=39.55 E-value=15 Score=28.07 Aligned_cols=36 Identities=14% Similarity=0.204 Sum_probs=27.9
Q ss_pred HHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhh
Q 023725 53 LEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQN 88 (278)
Q Consensus 53 LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQN 88 (278)
.+..|..+.+-......+||..+|+++..|+.|+.+
T Consensus 20 ~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 20 AEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 345566555556667889999999999999999864
No 90
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=39.40 E-value=1.1e+02 Score=28.19 Aligned_cols=30 Identities=33% Similarity=0.482 Sum_probs=24.7
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 023725 111 SLKADYDNLFKEKEKLKAEVLKLTDKLQVK 140 (278)
Q Consensus 111 ~Lk~~~~~l~~ene~L~~E~~~L~~~l~~~ 140 (278)
..+.++..|..|||+|+.++.+++..|...
T Consensus 113 ~e~sEF~~lr~e~EklkndlEk~ks~lr~e 142 (220)
T KOG3156|consen 113 IERSEFANLRAENEKLKNDLEKLKSSLRHE 142 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456778889999999999999998888743
No 91
>PF13518 HTH_28: Helix-turn-helix domain
Probab=39.30 E-value=32 Score=22.94 Aligned_cols=22 Identities=18% Similarity=0.520 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCCchhhhhHhhh
Q 023725 67 RKIQLAKDLGLQPRQVAIWFQN 88 (278)
Q Consensus 67 ~r~eLA~~LgLs~rQVqvWFQN 88 (278)
...++|+++|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 4566999999999999999754
No 92
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=38.90 E-value=24 Score=25.07 Aligned_cols=21 Identities=24% Similarity=0.382 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCchhhhhHhhh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQN 88 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQN 88 (278)
..++|+.+|++++.|+.|-+.
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 467999999999999999543
No 93
>PRK10884 SH3 domain-containing protein; Provisional
Probab=38.76 E-value=1.5e+02 Score=26.83 Aligned_cols=30 Identities=13% Similarity=0.061 Sum_probs=11.9
Q ss_pred HhhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 023725 105 LQNSYNSLKADYDNLFKEKEKLKAEVLKLT 134 (278)
Q Consensus 105 l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~ 134 (278)
|+..+..|+.....+..+++.|++++..++
T Consensus 137 L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~ 166 (206)
T PRK10884 137 LKEENQKLKNQLIVAQKKVDAANLQLDDKQ 166 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333333333344444444444443333
No 94
>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=38.37 E-value=61 Score=25.09 Aligned_cols=27 Identities=26% Similarity=0.366 Sum_probs=12.2
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 112 LKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 112 Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
+..++..|..+.++|++|+++++...+
T Consensus 5 i~eEn~~Lk~eiqkle~ELq~~~~~~q 31 (76)
T PF07334_consen 5 IQEENARLKEEIQKLEAELQQNKREFQ 31 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 333444444444444444444444333
No 95
>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=37.93 E-value=83 Score=22.87 Aligned_cols=27 Identities=33% Similarity=0.516 Sum_probs=16.4
Q ss_pred hhhhhHHHhhHHHHHHHHHHHHHHHHH
Q 023725 107 NSYNSLKADYDNLFKEKEKLKAEVLKL 133 (278)
Q Consensus 107 ~~~~~Lk~~~~~l~~ene~L~~E~~~L 133 (278)
..+..+......+.++++.|+.++..|
T Consensus 24 ~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 24 QEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 334455555666666666666666666
No 96
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=37.79 E-value=54 Score=29.65 Aligned_cols=40 Identities=33% Similarity=0.542 Sum_probs=32.5
Q ss_pred HhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 023725 105 LQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKES 144 (278)
Q Consensus 105 l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~~~~~~ 144 (278)
+...|+.|+..++.|..++++|+.|+..|...+.......
T Consensus 110 lE~d~~~Lk~~~~~l~~~~~~Lq~e~~eL~~~~~~~~~~~ 149 (198)
T KOG0483|consen 110 LEKDYESLKRQLESLRSENDRLQSEVQELVAELSSLKREM 149 (198)
T ss_pred hhhhHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhh
Confidence 3445889999999999999999999999987777544433
No 97
>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=37.63 E-value=1.5e+02 Score=26.75 Aligned_cols=48 Identities=15% Similarity=0.194 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 023725 95 TKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 142 (278)
Q Consensus 95 ~k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~~~~ 142 (278)
..........|......+...+-.+..+...|+.|+.+|+.+....++
T Consensus 170 Q~~~~~~L~~Le~~W~~~v~kn~eie~a~~~Le~ei~~l~~~~~~~~~ 217 (221)
T PF05700_consen 170 QEEAGEELRYLEQRWKELVSKNLEIEVACEELEQEIEQLKRKAAELKE 217 (221)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 333444445566666677777788888888888888888877665443
No 98
>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=36.65 E-value=88 Score=21.69 Aligned_cols=45 Identities=16% Similarity=0.181 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 44 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 44 rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
+||..++.+|.....- ....++|..+|++++.|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 4788888888766543 33678999999999999998766555544
No 99
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=36.42 E-value=1.9e+02 Score=22.65 Aligned_cols=20 Identities=20% Similarity=0.265 Sum_probs=9.4
Q ss_pred hHHHHHHHHHHHHHHHHHHH
Q 023725 116 YDNLFKEKEKLKAEVLKLTD 135 (278)
Q Consensus 116 ~~~l~~ene~L~~E~~~L~~ 135 (278)
...|..+|++|+.|...-.+
T Consensus 48 r~~L~~en~qLk~E~~~Wqe 67 (79)
T PRK15422 48 REELERENNHLKEQQNGWQE 67 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33455555555555444333
No 100
>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=36.33 E-value=2.1e+02 Score=22.31 Aligned_cols=35 Identities=17% Similarity=0.307 Sum_probs=26.4
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhh
Q 023725 42 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNR 89 (278)
Q Consensus 42 R~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNR 89 (278)
++.|+..++..|..... .+.+|++..+|+-++...
T Consensus 36 ~R~y~~~di~~l~~i~~-------------lr~~g~~l~~i~~~~~~~ 70 (103)
T cd01106 36 YRLYTEEDLERLQQILF-------------LKELGFSLKEIKELLKDP 70 (103)
T ss_pred ceeeCHHHHHHHHHHHH-------------HHHcCCCHHHHHHHHHcC
Confidence 45699999988865432 456899999999988654
No 101
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=35.05 E-value=2e+02 Score=22.45 Aligned_cols=37 Identities=27% Similarity=0.342 Sum_probs=20.4
Q ss_pred HHHhhhhhhHHHhhHHHHHH-------HHHHHHHHHHHHHHHhh
Q 023725 103 DVLQNSYNSLKADYDNLFKE-------KEKLKAEVLKLTDKLQV 139 (278)
Q Consensus 103 ~~l~~~~~~Lk~~~~~l~~e-------ne~L~~E~~~L~~~l~~ 139 (278)
..|+-.+.-||..+..|.++ ++.|..++.+|+.....
T Consensus 21 ~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E~~~ 64 (79)
T PRK15422 21 TLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNG 64 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 33444444444444444444 45577777777766543
No 102
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=35.01 E-value=1.4e+02 Score=24.43 Aligned_cols=35 Identities=26% Similarity=0.298 Sum_probs=22.1
Q ss_pred HHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 023725 102 YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 136 (278)
Q Consensus 102 ~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~ 136 (278)
+..+........+.++.|.+++..|++|+..|+..
T Consensus 52 ~~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 52 VLQLQRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 33344444466666777777777777777777655
No 103
>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=34.45 E-value=2.8e+02 Score=23.23 Aligned_cols=37 Identities=11% Similarity=0.021 Sum_probs=26.0
Q ss_pred CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhh
Q 023725 41 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 90 (278)
Q Consensus 41 kR~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRR 90 (278)
.++.|+..++..|... .. .+.+|++-..|+-++.+..
T Consensus 34 g~R~Y~~~~l~~l~~I------------~~-lr~~G~sL~eI~~~l~~~~ 70 (134)
T cd04779 34 NYRYYDETALDRLQLI------------EH-LKGQRLSLAEIKDQLEEVQ 70 (134)
T ss_pred CCeeECHHHHHHHHHH------------HH-HHHCCCCHHHHHHHHHhhc
Confidence 3456999998888543 22 4678888888888876654
No 104
>PRK10884 SH3 domain-containing protein; Provisional
Probab=33.80 E-value=1.9e+02 Score=26.21 Aligned_cols=35 Identities=17% Similarity=0.092 Sum_probs=19.3
Q ss_pred HHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 104 VLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 104 ~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
.....+..|+.+|..|.++.+.+++++..|+.++.
T Consensus 129 ~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~ 163 (206)
T PRK10884 129 QSDSVINGLKEENQKLKNQLIVAQKKVDAANLQLD 163 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444555666666666666666666555544443
No 105
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=33.36 E-value=35 Score=22.77 Aligned_cols=23 Identities=26% Similarity=0.381 Sum_probs=17.6
Q ss_pred HHHHHHHHHHhCCCchhhhhHhh
Q 023725 65 PERKIQLAKDLGLQPRQVAIWFQ 87 (278)
Q Consensus 65 ~~~r~eLA~~LgLs~rQVqvWFQ 87 (278)
.....++|+.||++...|..|..
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 34567899999999999999965
No 106
>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=33.11 E-value=36 Score=22.43 Aligned_cols=19 Identities=32% Similarity=0.424 Sum_probs=15.7
Q ss_pred HHHHHHHhCCCchhhhhHh
Q 023725 68 KIQLAKDLGLQPRQVAIWF 86 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWF 86 (278)
+.++|+.+|++.+.|+.|=
T Consensus 2 i~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 4578999999999999994
No 107
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=33.07 E-value=1.2e+02 Score=19.65 Aligned_cols=39 Identities=23% Similarity=0.296 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhh
Q 023725 44 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQN 88 (278)
Q Consensus 44 rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQN 88 (278)
.++..+..++...+. . ....++|..+|++...|..|.+.
T Consensus 3 ~l~~~e~~i~~~~~~--g----~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLAE--G----LTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 367777777765432 1 25578999999999999998763
No 108
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=32.89 E-value=1e+02 Score=28.39 Aligned_cols=21 Identities=24% Similarity=0.363 Sum_probs=9.2
Q ss_pred hHHHhhHHHHHHHHHHHHHHH
Q 023725 111 SLKADYDNLFKEKEKLKAEVL 131 (278)
Q Consensus 111 ~Lk~~~~~l~~ene~L~~E~~ 131 (278)
.+.++|..|++|+..|+.++.
T Consensus 73 ~l~~en~~L~~e~~~l~~~~~ 93 (276)
T PRK13922 73 DLREENEELKKELLELESRLQ 93 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444443
No 109
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=32.80 E-value=1.1e+02 Score=24.83 Aligned_cols=42 Identities=14% Similarity=0.078 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhh
Q 023725 44 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 90 (278)
Q Consensus 44 rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRR 90 (278)
.+++.+..++...|-. .....++|..+|++...|+.|...=|
T Consensus 106 ~L~~~~r~ii~l~~~~-----~~s~~EIA~~l~is~~tV~~~~~ra~ 147 (154)
T PRK06759 106 VLDEKEKYIIFERFFV-----GKTMGEIALETEMTYYQVRWIYRQAL 147 (154)
T ss_pred hCCHHHHHHHHHHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3666676666655533 23477899999999999999875433
No 110
>PRK10072 putative transcriptional regulator; Provisional
Probab=32.70 E-value=31 Score=27.49 Aligned_cols=42 Identities=19% Similarity=0.251 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhH
Q 023725 44 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 92 (278)
Q Consensus 44 rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak 92 (278)
+.+...+..|...-.. ...+||+.+|++...|..|.+.+|.-
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 3466666666443322 26789999999999999999887653
No 111
>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=32.24 E-value=1.8e+02 Score=20.28 Aligned_cols=24 Identities=29% Similarity=0.512 Sum_probs=14.0
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHH
Q 023725 111 SLKADYDNLFKEKEKLKAEVLKLT 134 (278)
Q Consensus 111 ~Lk~~~~~l~~ene~L~~E~~~L~ 134 (278)
.+......|..+|..|+.++..|+
T Consensus 29 ~le~~~~~L~~en~~L~~~i~~L~ 52 (54)
T PF07716_consen 29 ELEQEVQELEEENEQLRQEIAQLE 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 444555556666666666666554
No 112
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=32.22 E-value=58 Score=20.38 Aligned_cols=23 Identities=22% Similarity=0.359 Sum_probs=19.3
Q ss_pred HHHHHHHhCCCchhhhhHhhhhh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQNRR 90 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQNRR 90 (278)
..++|+.+|+++..|..|..+++
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 35789999999999999987764
No 113
>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=32.17 E-value=38 Score=24.50 Aligned_cols=27 Identities=26% Similarity=0.599 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCchhhhhHhhhhhhHHHH
Q 023725 67 RKIQLAKDLGLQPRQVAIWFQNRRARWKT 95 (278)
Q Consensus 67 ~r~eLA~~LgLs~rQVqvWFQNRRak~K~ 95 (278)
...++|..||++.+.|..|-+ |.+|..
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 456899999999999999953 555544
No 114
>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=31.96 E-value=39 Score=24.08 Aligned_cols=21 Identities=10% Similarity=0.347 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCchhhhhHhhh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQN 88 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQN 88 (278)
..++|+.+|++++.++.|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999764
No 115
>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=31.49 E-value=75 Score=24.64 Aligned_cols=43 Identities=19% Similarity=0.193 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 92 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak 92 (278)
++..+..++...|- ......++|+.+|+++..|..+...-+.+
T Consensus 111 L~~~~~~ii~~~~~-----~g~s~~eIA~~l~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 111 LPEREREVLVLRYL-----EGLSYKEIAEILGISVGTVKRRLKRARKK 153 (158)
T ss_pred CCHHHHHHHhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 55566555544432 23355689999999999999987644333
No 116
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=31.47 E-value=2.9e+02 Score=29.26 Aligned_cols=77 Identities=14% Similarity=0.290 Sum_probs=45.1
Q ss_pred CCCHHHHHH-HHHHhCCC---------------chhhhhHhhhhhhHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHH
Q 023725 62 KLEPERKIQ-LAKDLGLQ---------------PRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEK 125 (278)
Q Consensus 62 ~P~~~~r~e-LA~~LgLs---------------~rQVqvWFQNRRak~K~k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~ 125 (278)
.++...+.. +|+.+|++ .|||.+|.+.+-....-..+.+.+..=......-...-.....++..
T Consensus 523 ~it~d~I~~~Va~~f~v~~~dl~s~~R~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~d~~ 602 (617)
T PRK14086 523 EITAAAIMAATADYFGLTVEDLCGTSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMAERRS 602 (617)
T ss_pred cCCHHHHHHHHHHHhCCCHHHHhCCCCCcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHhCHH
Confidence 356665555 46666644 56777887766666555555544431111122222233445667788
Q ss_pred HHHHHHHHHHHHh
Q 023725 126 LKAEVLKLTDKLQ 138 (278)
Q Consensus 126 L~~E~~~L~~~l~ 138 (278)
|+.++..|+.+|.
T Consensus 603 l~~~V~~L~~~i~ 615 (617)
T PRK14086 603 IYNQVTELTNRIK 615 (617)
T ss_pred HHHHHHHHHHHHh
Confidence 8899988888774
No 117
>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=31.32 E-value=59 Score=23.07 Aligned_cols=35 Identities=23% Similarity=0.318 Sum_probs=26.4
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHh
Q 023725 48 DQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWF 86 (278)
Q Consensus 48 eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWF 86 (278)
.|+..|+-.+. +...+.. +||..||++.+.|+.-.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHH
Confidence 56778888888 6666554 89999999998887654
No 118
>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=31.15 E-value=44 Score=21.31 Aligned_cols=24 Identities=21% Similarity=0.475 Sum_probs=20.1
Q ss_pred HHHHHHHhCCCchhhhhHhhhhhh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQNRRA 91 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQNRRa 91 (278)
..++|+.||++.+.|..|.++.+-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467899999999999999876543
No 119
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=31.01 E-value=69 Score=26.83 Aligned_cols=45 Identities=16% Similarity=0.314 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
+++.+..++...| .......++|..||++...|+.+...-|.+.|
T Consensus 130 L~~~~r~i~~l~~-----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 130 LEKDRAAAVRRAY-----LEGLSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 4555544444444 22334678999999999999998764444433
No 120
>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=30.39 E-value=42 Score=24.06 Aligned_cols=21 Identities=19% Similarity=0.360 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCchhhhhHhhh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQN 88 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQN 88 (278)
..++|+.+|++++.++.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 467899999999999999764
No 121
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=30.38 E-value=71 Score=26.18 Aligned_cols=45 Identities=20% Similarity=0.194 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
+++.+..++...|- ....-.++|..+|+++..|+.|...=|.+.|
T Consensus 126 L~~~~r~i~~l~~~-----~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 126 LPVKQREVFLLRYV-----EGLSYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CCHHHHHHhhHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 55555555544442 2334578999999999999999764444333
No 122
>KOG1853 consensus LIS1-interacting protein NUDE [Cytoskeleton]
Probab=30.32 E-value=2.2e+02 Score=27.16 Aligned_cols=29 Identities=28% Similarity=0.493 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhcc
Q 023725 117 DNLFKEKEKLKAEVLKLTDKLQVKEKESK 145 (278)
Q Consensus 117 ~~l~~ene~L~~E~~~L~~~l~~~~~~~~ 145 (278)
+.+.....+|+.|-..|+..|+.+.++..
T Consensus 160 e~llesvqRLkdEardlrqelavr~kq~E 188 (333)
T KOG1853|consen 160 EVLLESVQRLKDEARDLRQELAVRTKQTE 188 (333)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 44555666777777777777887776643
No 123
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=30.19 E-value=1.1e+02 Score=28.18 Aligned_cols=16 Identities=38% Similarity=0.382 Sum_probs=5.8
Q ss_pred HHHHHHHHHHHHHHHH
Q 023725 118 NLFKEKEKLKAEVLKL 133 (278)
Q Consensus 118 ~l~~ene~L~~E~~~L 133 (278)
+|...-+.+..|..+|
T Consensus 183 al~Kq~e~~~~EydrL 198 (216)
T KOG1962|consen 183 ALKKQSEGLQDEYDRL 198 (216)
T ss_pred HHHHHHHHcccHHHHH
Confidence 3333333333333333
No 124
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=30.04 E-value=1.5e+02 Score=30.41 Aligned_cols=44 Identities=18% Similarity=0.345 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 023725 94 KTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 137 (278)
Q Consensus 94 K~k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l 137 (278)
|...+++.++.+++...-+.+....+....+.|+.|+.+|+.++
T Consensus 77 kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql 120 (475)
T PRK13729 77 TAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQV 120 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 34455566666665555455666667777778888888888887
No 125
>PF13551 HTH_29: Winged helix-turn helix
Probab=29.87 E-value=1.2e+02 Score=22.99 Aligned_cols=47 Identities=15% Similarity=0.249 Sum_probs=30.3
Q ss_pred CCCCCCHHHHHHHHHHhhhcCC-----CCHHHHHH-H-HHHh--CCCchhhhhHhh
Q 023725 41 KKRRLTVDQVQFLEKSFEVENK-----LEPERKIQ-L-AKDL--GLQPRQVAIWFQ 87 (278)
Q Consensus 41 kR~rft~eQl~~LE~~F~~~~~-----P~~~~r~e-L-A~~L--gLs~rQVqvWFQ 87 (278)
.+.+++.++...|...+...+. .+.....+ | .... .+++..|..|+.
T Consensus 54 ~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 54 PRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 3334999999999999998763 33444443 4 3333 356777777764
No 126
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.78 E-value=2.6e+02 Score=21.53 Aligned_cols=25 Identities=24% Similarity=0.287 Sum_probs=11.9
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHH
Q 023725 111 SLKADYDNLFKEKEKLKAEVLKLTD 135 (278)
Q Consensus 111 ~Lk~~~~~l~~ene~L~~E~~~L~~ 135 (278)
.+....++|..+|+.|+.|-..-.+
T Consensus 43 ~~q~~reaL~~eneqlk~e~~~WQe 67 (79)
T COG3074 43 NAQHQREALERENEQLKEEQNGWQE 67 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344445555555555555443333
No 127
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=29.69 E-value=74 Score=31.08 Aligned_cols=27 Identities=11% Similarity=-0.039 Sum_probs=14.9
Q ss_pred hhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 023725 108 SYNSLKADYDNLFKEKEKLKAEVLKLT 134 (278)
Q Consensus 108 ~~~~Lk~~~~~l~~ene~L~~E~~~L~ 134 (278)
.|-.|+.+|+.|++|+..|++++.++.
T Consensus 58 ~y~~L~~EN~~Lk~Ena~L~~~l~~~e 84 (337)
T PRK14872 58 HALVLETENFLLKERIALLEERLKSYE 84 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555556666666666655555543
No 128
>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=29.62 E-value=3e+02 Score=22.62 Aligned_cols=15 Identities=27% Similarity=0.512 Sum_probs=12.2
Q ss_pred chhhhhHhhhhhhHH
Q 023725 79 PRQVAIWFQNRRARW 93 (278)
Q Consensus 79 ~rQVqvWFQNRRak~ 93 (278)
-||...||-.+|.-.
T Consensus 17 aRq~e~~FlqKr~~L 31 (106)
T PF11594_consen 17 ARQMEAFFLQKRFEL 31 (106)
T ss_pred HHHHHHHHHHHHHHH
Confidence 367899999888866
No 129
>PRK04217 hypothetical protein; Provisional
Probab=29.43 E-value=1.4e+02 Score=24.48 Aligned_cols=41 Identities=12% Similarity=-0.001 Sum_probs=31.5
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhh
Q 023725 43 RRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQN 88 (278)
Q Consensus 43 ~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQN 88 (278)
..++.++..++...|...- ...+||+.+|++...|...+..
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHH
Confidence 3588999888877764332 5677999999999999887654
No 130
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=29.37 E-value=1e+02 Score=26.46 Aligned_cols=45 Identities=16% Similarity=0.112 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
++..+..+|...|- ....-.++|+.||++...|+.+...-|.+.|
T Consensus 143 L~~~~r~vl~l~~~-----~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 143 LTDTQRESVTLAYY-----GGLTYREVAERLAVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence 66667666665542 2244678999999999999998754444333
No 131
>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=28.61 E-value=2.2e+02 Score=29.12 Aligned_cols=92 Identities=17% Similarity=0.234 Sum_probs=43.4
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHHHHHHHHHHhhhhh-hHHHhhHHHHHH
Q 023725 44 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYN-SLKADYDNLFKE 122 (278)
Q Consensus 44 rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~k~~~~l~~~~~-~Lk~~~~~l~~e 122 (278)
.++++++..|.- .---|...-|..+|+--.+..++-.+==+|++-+....++.+....+..++. .+......+.++
T Consensus 41 ~ltpee~kalGi---egDTP~DTlrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~ 117 (472)
T TIGR03752 41 ELSPEELKALGI---EGDTPADTLRTLVAEVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKE 117 (472)
T ss_pred cCCcchhHhcCC---CCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHH
Confidence 355665544422 1123444444444443333333333334555555555444443333333322 444555556666
Q ss_pred HHHHHHHHHHHHHHHh
Q 023725 123 KEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 123 ne~L~~E~~~L~~~l~ 138 (278)
.+.|+.++++++..|.
T Consensus 118 ~~ql~~~~~~~~~~l~ 133 (472)
T TIGR03752 118 IEQLKSERQQLQGLID 133 (472)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 6666666666655554
No 132
>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=28.57 E-value=19 Score=33.30 Aligned_cols=29 Identities=34% Similarity=0.419 Sum_probs=0.0
Q ss_pred HhhhhhhHHHhhHHHHHHHHHHHHHHHHH
Q 023725 105 LQNSYNSLKADYDNLFKEKEKLKAEVLKL 133 (278)
Q Consensus 105 l~~~~~~Lk~~~~~l~~ene~L~~E~~~L 133 (278)
|+.....|-++|+.|..||++|++|+.+|
T Consensus 134 LrrlVe~L~aeNErLr~EnkqL~ae~arL 162 (243)
T PF08961_consen 134 LRRLVEFLLAENERLRRENKQLKAENARL 162 (243)
T ss_dssp -----------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444455555555555555555555555
No 133
>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=28.55 E-value=3e+02 Score=21.99 Aligned_cols=38 Identities=21% Similarity=0.306 Sum_probs=27.6
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhH
Q 023725 42 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 92 (278)
Q Consensus 42 R~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak 92 (278)
.+.|+..++..|... ...+.+|++-..|+..+......
T Consensus 35 yR~Y~~~d~~~l~~I-------------~~lr~~G~sl~eI~~~l~~~~~~ 72 (116)
T cd04769 35 YRVYDAQHVECLRFI-------------KEARQLGFTLAELKAIFAGHEGR 72 (116)
T ss_pred ceeeCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHhccccC
Confidence 455888888877442 33688999999999988765543
No 134
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=28.53 E-value=72 Score=22.24 Aligned_cols=38 Identities=21% Similarity=0.281 Sum_probs=24.7
Q ss_pred HHHHHHHhCCCchhhhhHhhhhhhHHHHHHHHHHHHHHh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQ 106 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~k~~~~l~ 106 (278)
...+|..+|++..+|..|-.+++ .-....+.+-++.+.
T Consensus 15 ~~~~a~~~~i~~~~i~~~e~g~~-~~~~~~l~~i~~~~~ 52 (64)
T PF12844_consen 15 QKDLAEKLGISRSTISKIENGKR-KPSVSTLKKIAEALG 52 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS---BHHHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHCCCc-CCCHHHHHHHHHHhC
Confidence 56789999999999999998877 444444444444433
No 135
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=28.45 E-value=81 Score=25.92 Aligned_cols=39 Identities=13% Similarity=-0.053 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhh
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQN 88 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQN 88 (278)
+++.+..+|...|- ......++|..||++...|+.|...
T Consensus 129 L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~r 167 (182)
T PRK09652 129 LPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFR 167 (182)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 67777777766543 2234567899999999999998763
No 136
>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=28.35 E-value=87 Score=23.15 Aligned_cols=20 Identities=20% Similarity=0.204 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 023725 117 DNLFKEKEKLKAEVLKLTDK 136 (278)
Q Consensus 117 ~~l~~ene~L~~E~~~L~~~ 136 (278)
..|...|..|+.|+.-|+..
T Consensus 24 ~eL~~~n~~Le~EN~~Lk~~ 43 (59)
T PF01166_consen 24 AELEERNSQLEEENNLLKQN 43 (59)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhc
Confidence 34455555555555555543
No 137
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=28.26 E-value=1.4e+02 Score=23.47 Aligned_cols=36 Identities=22% Similarity=0.445 Sum_probs=26.6
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 023725 99 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 134 (278)
Q Consensus 99 ~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~ 134 (278)
..+|..+-...+.|-..-+.|.+.++.|..++.+|-
T Consensus 25 ~~E~~~ins~LD~Lns~LD~LE~rnD~l~~~L~~LL 60 (83)
T PF03670_consen 25 EEEYAAINSMLDQLNSCLDHLEQRNDHLHAQLQELL 60 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 346777777777777777888888888887776653
No 138
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.09 E-value=75 Score=25.48 Aligned_cols=38 Identities=18% Similarity=0.220 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhh
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQV 82 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQV 82 (278)
+.++|.+.-...|+.+--++.-..+++|..||+++--|
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 56788887777777777777788899999999988544
No 139
>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=28.05 E-value=58 Score=21.70 Aligned_cols=21 Identities=14% Similarity=0.286 Sum_probs=18.7
Q ss_pred HHHHHhCCCchhhhhHhhhhh
Q 023725 70 QLAKDLGLQPRQVAIWFQNRR 90 (278)
Q Consensus 70 eLA~~LgLs~rQVqvWFQNRR 90 (278)
+||+.+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998874
No 140
>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=27.88 E-value=45 Score=22.52 Aligned_cols=23 Identities=22% Similarity=0.382 Sum_probs=19.2
Q ss_pred HHHHHHHhCCCchhhhhHhhhhh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQNRR 90 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQNRR 90 (278)
..+||+.+|+++..|..|..+++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 36899999999999999998854
No 141
>PF02344 Myc-LZ: Myc leucine zipper domain; InterPro: IPR003327 This family consists of the leucine zipper dimerisation domain found in both cellular c-Myc proto-oncogenes and viral v-Myc oncogenes. Dimerisation via the leucine zipper motif with other basic helix-loop-helix-leucine zipper (b/HLH/lz) proteins is required for efficient DNA binding []. The Myc-Max dimer is a transactivating complex activating expression of growth related genes promoting cell proliferation. The dimerisation is facilitated via interdigitating leucine residues every 7th position of the alpha helix. Like charge repulsion of adjacent residues in this region preturbs the formation of homodimers with heterodimers being promoted by opposing charge attractions. It has been demonstrated that in transgenic mice the balance between oncogene-induced proliferation and apoptosis in a given tissue can be a critical determinant in the initiation and maintenance of the tumor [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1NKP_D 1A93_A 2A93_A.
Probab=27.57 E-value=1.6e+02 Score=19.24 Aligned_cols=22 Identities=36% Similarity=0.536 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 023725 117 DNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 117 ~~l~~ene~L~~E~~~L~~~l~ 138 (278)
..|..|++.|+....+|+.+|.
T Consensus 4 qkL~sekeqLrrr~eqLK~kLe 25 (32)
T PF02344_consen 4 QKLISEKEQLRRRREQLKHKLE 25 (32)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3455666666666666665554
No 142
>KOG0249 consensus LAR-interacting protein and related proteins [General function prediction only]
Probab=27.56 E-value=4.5e+02 Score=28.73 Aligned_cols=50 Identities=22% Similarity=0.318 Sum_probs=36.3
Q ss_pred hHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 023725 91 ARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVK 140 (278)
Q Consensus 91 ak~K~k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~~ 140 (278)
+..++-.+..+.+.++..+..+...-+.|...++.|+.|+.+|....+..
T Consensus 214 Ale~kn~L~~e~~s~kk~l~~~~~~k~rl~~d~E~Lr~e~~qL~~~~~~~ 263 (916)
T KOG0249|consen 214 ALEDKNRLEQELESVKKQLEEMRHDKDKLRTDIEDLRGELDQLRRSSLEK 263 (916)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhh
Confidence 34455556666677777777777788888888889999998888644433
No 143
>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=27.39 E-value=3e+02 Score=29.67 Aligned_cols=22 Identities=9% Similarity=0.119 Sum_probs=15.6
Q ss_pred CCHHHHHHHHHHhCCCchhhhh
Q 023725 63 LEPERKIQLAKDLGLQPRQVAI 84 (278)
Q Consensus 63 P~~~~r~eLA~~LgLs~rQVqv 84 (278)
|....-..+|+.+|+++..|..
T Consensus 480 ~g~S~a~~iA~~~Glp~~ii~~ 501 (771)
T TIGR01069 480 PGESYAFEIAQRYGIPHFIIEQ 501 (771)
T ss_pred CCCcHHHHHHHHhCcCHHHHHH
Confidence 4445566788888988877753
No 144
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=27.34 E-value=1.3e+02 Score=24.29 Aligned_cols=28 Identities=36% Similarity=0.449 Sum_probs=17.6
Q ss_pred HHHHHhhhhhhHHHhhHHHHHHHHHHHH
Q 023725 101 DYDVLQNSYNSLKADYDNLFKEKEKLKA 128 (278)
Q Consensus 101 ~~~~l~~~~~~Lk~~~~~l~~ene~L~~ 128 (278)
+.+.++..+..++..+..|..+.+.|+.
T Consensus 35 q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 35 QVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3444555556666677777777777765
No 145
>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids [].
Probab=27.25 E-value=2.7e+02 Score=21.04 Aligned_cols=40 Identities=20% Similarity=0.405 Sum_probs=29.5
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 99 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 99 ~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
+..|..|+.....-...+..|.+.+..|-.++..|.+++.
T Consensus 27 q~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~Ls~ql~ 66 (70)
T PF04899_consen 27 QSSYADLQHMFEQTSQENAALSEQVNNLSQQVQRLSEQLE 66 (70)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566777777777777777888888888888887777664
No 146
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=27.19 E-value=1.7e+02 Score=27.42 Aligned_cols=31 Identities=39% Similarity=0.534 Sum_probs=12.1
Q ss_pred HHhhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 023725 104 VLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 134 (278)
Q Consensus 104 ~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~ 134 (278)
-++..+..++...+.+.+||+.|..++.+|.
T Consensus 132 d~ke~~ee~kekl~E~~~EkeeL~~eleele 162 (290)
T COG4026 132 DLKEDYEELKEKLEELQKEKEELLKELEELE 162 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333333333333444444444433333
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=27.10 E-value=1.1e+02 Score=23.69 Aligned_cols=27 Identities=33% Similarity=0.539 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 023725 117 DNLFKEKEKLKAEVLKLTDKLQVKEKE 143 (278)
Q Consensus 117 ~~l~~ene~L~~E~~~L~~~l~~~~~~ 143 (278)
..+.+||.+|+.++++|...|+...+.
T Consensus 3 ~ei~eEn~~Lk~eiqkle~ELq~~~~~ 29 (76)
T PF07334_consen 3 HEIQEENARLKEEIQKLEAELQQNKRE 29 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 468899999999999998888865544
No 148
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=26.97 E-value=79 Score=25.87 Aligned_cols=41 Identities=17% Similarity=0.126 Sum_probs=28.2
Q ss_pred HHHHHHHhCCCchhhhhHhhhhhhHHHHHHHHHHHHHHhhhh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSY 109 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQNRRak~K~k~~~k~~~~l~~~~ 109 (278)
+.+||..+|++...|..|.++++. -....+.+-...|.-..
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~~-ps~~~l~kIa~aL~v~~ 61 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKAN-PSLKVMEAIADALETPL 61 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCCC-CCHHHHHHHHHHHCCCH
Confidence 567999999999999999988763 34444454444444433
No 149
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=26.91 E-value=1.5e+02 Score=24.14 Aligned_cols=45 Identities=11% Similarity=0.082 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
+++.+..++...|-. ...-.++|..||+++..|+.....-|.+.|
T Consensus 107 Lp~~~r~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr 151 (160)
T PRK09642 107 LPENYRDVVLAHYLE-----EKSYQEIALQEKIEVKTVEMKLYRARKWIK 151 (160)
T ss_pred CCHHHHHHHHHHHHh-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 555555555444322 223568899999999999998764444443
No 150
>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=26.83 E-value=1.6e+02 Score=30.15 Aligned_cols=7 Identities=43% Similarity=0.800 Sum_probs=3.6
Q ss_pred HHHhCCC
Q 023725 72 AKDLGLQ 78 (278)
Q Consensus 72 A~~LgLs 78 (278)
++.||+.
T Consensus 47 ~kalGie 53 (472)
T TIGR03752 47 LKALGIE 53 (472)
T ss_pred hHhcCCC
Confidence 3555553
No 151
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=26.63 E-value=55 Score=23.12 Aligned_cols=20 Identities=20% Similarity=0.383 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhhhhHhh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQ 87 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQ 87 (278)
..++|+.+|++++.++.|.+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999975
No 152
>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=26.58 E-value=2.5e+02 Score=22.28 Aligned_cols=32 Identities=19% Similarity=0.242 Sum_probs=24.4
Q ss_pred HHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 023725 103 DVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 134 (278)
Q Consensus 103 ~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~ 134 (278)
..+....+.|...+..+..|++.|+.++...+
T Consensus 45 ~rwek~v~~L~~e~~~l~~E~e~L~~~l~~e~ 76 (87)
T PF12709_consen 45 ARWEKKVDELENENKALKRENEQLKKKLDTER 76 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34667777888888888888888888775543
No 153
>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=26.55 E-value=1.3e+02 Score=28.29 Aligned_cols=17 Identities=29% Similarity=0.362 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHhhhh
Q 023725 125 KLKAEVLKLTDKLQVKE 141 (278)
Q Consensus 125 ~L~~E~~~L~~~l~~~~ 141 (278)
.|++|+.+|++-|..++
T Consensus 95 ~l~~EN~rLr~LL~~~~ 111 (283)
T TIGR00219 95 NLKQENVRLRELLNSPL 111 (283)
T ss_pred HHHHHHHHHHHHhcCcc
Confidence 36777777777665544
No 154
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=25.82 E-value=1.5e+02 Score=25.81 Aligned_cols=44 Identities=18% Similarity=0.185 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARW 93 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~ 93 (278)
++..+..+|...| .......++|..+|++...|+.+...-|.+.
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 2233467889999999999988875444433
No 155
>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=25.79 E-value=1.2e+02 Score=19.90 Aligned_cols=36 Identities=19% Similarity=0.242 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhh
Q 023725 46 TVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 87 (278)
Q Consensus 46 t~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQ 87 (278)
+..+...+...+ . .....++|+.+|++...|..|..
T Consensus 2 ~~~e~~i~~~~~--~----~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--E----GKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--c----CCCHHHHHHHHCCCHHHHHHHHH
Confidence 445555554433 1 23567889999999999999875
No 156
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.62 E-value=3.3e+02 Score=21.36 Aligned_cols=42 Identities=10% Similarity=0.193 Sum_probs=31.4
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCC-CchhhhhHhh
Q 023725 42 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGL-QPRQVAIWFQ 87 (278)
Q Consensus 42 R~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgL-s~rQVqvWFQ 87 (278)
+++|+.+....+=..+....+ ....+|+++|+ ...++..|-+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 677998877655555544443 67889999996 9999999964
No 157
>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=25.51 E-value=98 Score=24.78 Aligned_cols=41 Identities=17% Similarity=0.154 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhh
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 90 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRR 90 (278)
++..+..+|...|- ......++|..+|+++..|+.+...-|
T Consensus 114 L~~~~r~il~l~~~-----~~~~~~eIA~~lgis~~tv~~~~~ra~ 154 (161)
T TIGR02985 114 LPEQCRKIFILSRF-----EGKSYKEIAEELGISVKTVEYHISKAL 154 (161)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45555555554332 223456789999999999998765433
No 158
>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=25.27 E-value=1.4e+02 Score=29.42 Aligned_cols=31 Identities=32% Similarity=0.386 Sum_probs=21.5
Q ss_pred HHHHhhhhhhHHHhhHHHHHHHHHHHHHHHH
Q 023725 102 YDVLQNSYNSLKADYDNLFKEKEKLKAEVLK 132 (278)
Q Consensus 102 ~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~ 132 (278)
...|+..+.+||+++..|..+.++|++++.+
T Consensus 34 ~~aLr~EN~~LKkEN~~Lk~eVerLE~e~l~ 64 (420)
T PF07407_consen 34 NFALRMENHSLKKENNDLKIEVERLENEMLR 64 (420)
T ss_pred hhhHHHHhHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3456667777777777777777777666543
No 159
>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=25.09 E-value=1e+02 Score=25.01 Aligned_cols=39 Identities=21% Similarity=0.175 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhh
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQN 88 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQN 88 (278)
+++.+..++...| .......++|..+|++...|+.+...
T Consensus 112 L~~~~r~v~~l~~-----~~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 112 LPERQRELLQLRY-----QRGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred CCHHHHHHHHHHH-----hcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5666655555533 23345678999999999999987643
No 160
>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=24.99 E-value=63 Score=28.47 Aligned_cols=29 Identities=38% Similarity=0.497 Sum_probs=5.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 023725 115 DYDNLFKEKEKLKAEVLKLTDKLQVKEKE 143 (278)
Q Consensus 115 ~~~~l~~ene~L~~E~~~L~~~l~~~~~~ 143 (278)
+.+.|+.++++|+.|+..|+..|..+++.
T Consensus 25 EKE~L~~~~QRLkDE~RDLKqEl~V~ek~ 53 (166)
T PF04880_consen 25 EKENLREEVQRLKDELRDLKQELIVQEKL 53 (166)
T ss_dssp HHHHHHHCH--------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45566667777777777777776555553
No 161
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=24.87 E-value=3.4e+02 Score=29.31 Aligned_cols=22 Identities=23% Similarity=0.303 Sum_probs=15.9
Q ss_pred CCHHHHHHHHHHhCCCchhhhh
Q 023725 63 LEPERKIQLAKDLGLQPRQVAI 84 (278)
Q Consensus 63 P~~~~r~eLA~~LgLs~rQVqv 84 (278)
|....-..+|+.+|+++..|..
T Consensus 485 ~g~S~a~~iA~~~Glp~~ii~~ 506 (782)
T PRK00409 485 PGKSNAFEIAKRLGLPENIIEE 506 (782)
T ss_pred CCCcHHHHHHHHhCcCHHHHHH
Confidence 4445666788899998887754
No 162
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=24.68 E-value=2.1e+02 Score=24.42 Aligned_cols=46 Identities=9% Similarity=0.141 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 95 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~ 95 (278)
+++.+..++...|-. ...-.++|..||+++..|+.+...-|.+.|.
T Consensus 135 Lp~~~R~v~~L~~~~-----g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 135 LPAQQARVFMMREYL-----ELSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CCHHHHHHHhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 555555555554422 2346789999999999999987644444443
No 163
>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=24.22 E-value=3.1e+02 Score=20.53 Aligned_cols=41 Identities=17% Similarity=0.184 Sum_probs=21.2
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 023725 97 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 137 (278)
Q Consensus 97 ~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l 137 (278)
++-.-|+.|+..+..|+.....+..|...|...+...+.++
T Consensus 11 ~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar~rv 51 (65)
T TIGR02449 11 HLLEYLERLKSENRLLRAQEKTWREERAQLLEKNEQARQKV 51 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444555555555555555555555555555554444433
No 164
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=24.19 E-value=2.9e+02 Score=21.02 Aligned_cols=32 Identities=31% Similarity=0.238 Sum_probs=20.0
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 023725 111 SLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 142 (278)
Q Consensus 111 ~Lk~~~~~l~~ene~L~~E~~~L~~~l~~~~~ 142 (278)
.+...+..|..+++.|+.|+.+++..|...++
T Consensus 40 ~~~keNieLKve~~~L~~el~~~~~~l~~a~~ 71 (75)
T PF07989_consen 40 ELLKENIELKVEVESLKRELQEKKKLLKEAEK 71 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555666677777777777776666654443
No 165
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=23.94 E-value=1.8e+02 Score=24.46 Aligned_cols=45 Identities=13% Similarity=0.038 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
++..+..+|...|-. ...-.++|..||++...|+.++..-|.+.+
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 666666666655432 334678899999999999998765444444
No 166
>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=23.76 E-value=1.7e+02 Score=27.29 Aligned_cols=29 Identities=28% Similarity=0.424 Sum_probs=19.8
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 110 NSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 110 ~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
..+......|..|.+.|++.+.+|=+|+.
T Consensus 103 r~~~~~~~~L~~Ev~~L~~DN~kLYEKiR 131 (248)
T PF08172_consen 103 RKQQQTISSLRREVESLRADNVKLYEKIR 131 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455566677777777777777777665
No 167
>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion
Probab=23.71 E-value=3.5e+02 Score=23.96 Aligned_cols=41 Identities=22% Similarity=0.342 Sum_probs=31.3
Q ss_pred HHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 023725 102 YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 142 (278)
Q Consensus 102 ~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~~~~ 142 (278)
...|+...+..+..|+.|..+..+|..++..+.+.|..++.
T Consensus 83 N~lLReQLEq~~~~N~~L~~dl~klt~~~~~l~~eL~~ke~ 123 (182)
T PF15035_consen 83 NALLREQLEQARKANEALQEDLQKLTQDWERLRDELEQKEA 123 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34466666667788888888888888888888888887764
No 168
>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=23.59 E-value=3.6e+02 Score=20.98 Aligned_cols=42 Identities=19% Similarity=0.302 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 023725 94 KTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 135 (278)
Q Consensus 94 K~k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~ 135 (278)
....+......|-..++..+.+++.|..||+-|+.=+..|..
T Consensus 24 ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nLm~ 65 (80)
T PF10224_consen 24 EILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNLMS 65 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566677788888999999999999999999998888743
No 169
>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold). The domain has a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and is a prerequisite for the assembly of Cortexillin I []. ; PDB: 1D7M_A.
Probab=23.54 E-value=3.7e+02 Score=22.17 Aligned_cols=41 Identities=27% Similarity=0.330 Sum_probs=23.1
Q ss_pred HHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 98 LEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 98 ~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
+.++.+.|++....|.+.+....+....|++++..+...+-
T Consensus 35 L~kqkd~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~le 75 (107)
T PF09304_consen 35 LAKQKDQLRNALQSLQAQNASRNQRIAELQAKIDEARRNLE 75 (107)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444455566666666666666666666666655544443
No 170
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=23.37 E-value=3.2e+02 Score=20.43 Aligned_cols=18 Identities=33% Similarity=0.455 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 023725 119 LFKEKEKLKAEVLKLTDK 136 (278)
Q Consensus 119 l~~ene~L~~E~~~L~~~ 136 (278)
...++.+|+.|+..|+..
T Consensus 45 a~~e~~~Lk~E~e~L~~e 62 (69)
T PF14197_consen 45 AYEENNKLKEENEALRKE 62 (69)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 333444444444444443
No 171
>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=23.37 E-value=1.9e+02 Score=22.31 Aligned_cols=30 Identities=27% Similarity=0.471 Sum_probs=20.8
Q ss_pred hhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 109 YNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 109 ~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
...+..+...+..|+++|+-|...|+.--.
T Consensus 44 l~~l~~~~~~l~~e~~~L~lE~~~l~~~~r 73 (97)
T PF04999_consen 44 LQQLEKEIDQLQEENERLRLEIATLSSPSR 73 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhCHHH
Confidence 445666677788888888888877765333
No 172
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=23.34 E-value=3.6e+02 Score=24.68 Aligned_cols=39 Identities=28% Similarity=0.302 Sum_probs=22.5
Q ss_pred HHHhhhhhhHHHhhHHHHHHHH---HHHHHHHHHHHHHhhhh
Q 023725 103 DVLQNSYNSLKADYDNLFKEKE---KLKAEVLKLTDKLQVKE 141 (278)
Q Consensus 103 ~~l~~~~~~Lk~~~~~l~~ene---~L~~E~~~L~~~l~~~~ 141 (278)
..+.+.+..|++++..|..++. .+++|+.+|++.|..+.
T Consensus 72 ~~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL~~~~ 113 (276)
T PRK13922 72 FDLREENEELKKELLELESRLQELEQLEAENARLRELLNLKE 113 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcc
Confidence 3445555556666655555554 55677777766555443
No 173
>PRK00118 putative DNA-binding protein; Validated
Probab=23.22 E-value=2.1e+02 Score=23.22 Aligned_cols=45 Identities=13% Similarity=0.127 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
++..|..++...|... ....++|..+|+++..|..|...-|.+.+
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 5666777776655432 34567999999999999999864444333
No 174
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=23.14 E-value=1e+02 Score=26.20 Aligned_cols=45 Identities=24% Similarity=0.276 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
+++.+..+|...| .......++|..+|++...|+.|...-|.+.+
T Consensus 142 L~~~~~~v~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 142 LPESQRQVLELAY-----YEGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CCHHHhhhhhhhh-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4444444444433 33445678999999999999999864444333
No 175
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=23.12 E-value=3.3e+02 Score=20.40 Aligned_cols=27 Identities=22% Similarity=0.316 Sum_probs=17.1
Q ss_pred hhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 023725 108 SYNSLKADYDNLFKEKEKLKAEVLKLT 134 (278)
Q Consensus 108 ~~~~Lk~~~~~l~~ene~L~~E~~~L~ 134 (278)
........+..|..|++.|+.|+..+.
T Consensus 41 ~l~~a~~e~~~Lk~E~e~L~~el~~~r 67 (69)
T PF14197_consen 41 QLGDAYEENNKLKEENEALRKELEELR 67 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 334455666777777777777765543
No 176
>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=23.08 E-value=4.4e+02 Score=21.88 Aligned_cols=49 Identities=22% Similarity=0.320 Sum_probs=25.6
Q ss_pred hhHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 90 RARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 90 Rak~K~k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
|.+.+....+++...++.....+......+...+...+.|+.+++..+.
T Consensus 77 rL~~~~~~~ere~~~~~~~~~~l~~~~~~~~~~~k~~kee~~klk~~~~ 125 (151)
T PF11559_consen 77 RLKEQLEELERELASAEEKERQLQKQLKSLEAKLKQEKEELQKLKNQLQ 125 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444444444445555555555555555555555555555555444
No 177
>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=22.75 E-value=2.3e+02 Score=21.03 Aligned_cols=25 Identities=36% Similarity=0.454 Sum_probs=14.9
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHH
Q 023725 111 SLKADYDNLFKEKEKLKAEVLKLTD 135 (278)
Q Consensus 111 ~Lk~~~~~l~~ene~L~~E~~~L~~ 135 (278)
.+......+..++++|+.|+..|..
T Consensus 35 ~~~~~~~~l~~en~~L~~ei~~l~~ 59 (85)
T TIGR02209 35 KLQLEIDKLQKEWRDLQLEVAELSR 59 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 3444455566666666666666654
No 178
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, 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 two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.73 E-value=3.4e+02 Score=21.12 Aligned_cols=22 Identities=18% Similarity=0.276 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCchhhhhHhhhh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQNR 89 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQNR 89 (278)
..++|+.+|++.+.++.|.+..
T Consensus 4 i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4678999999999999996543
No 179
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=22.64 E-value=1.2e+02 Score=25.34 Aligned_cols=44 Identities=14% Similarity=0.076 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARW 93 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~ 93 (278)
+++.+..++...|- ....-.++|..||+++..|+.+.+.-|.+.
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 55555555555332 344567889999999999999876444433
No 180
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=22.63 E-value=1.6e+02 Score=28.88 Aligned_cols=19 Identities=26% Similarity=0.003 Sum_probs=8.4
Q ss_pred HHHHhhhhhhHHHhhHHHH
Q 023725 102 YDVLQNSYNSLKADYDNLF 120 (278)
Q Consensus 102 ~~~l~~~~~~Lk~~~~~l~ 120 (278)
|..++..+..|+.++..|.
T Consensus 59 y~~L~~EN~~Lk~Ena~L~ 77 (337)
T PRK14872 59 ALVLETENFLLKERIALLE 77 (337)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444443
No 181
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=22.63 E-value=3.5e+02 Score=24.54 Aligned_cols=31 Identities=16% Similarity=0.251 Sum_probs=11.4
Q ss_pred HhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 023725 105 LQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 135 (278)
Q Consensus 105 l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~ 135 (278)
+......|..-+..+......++.++.+|+.
T Consensus 61 l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~ 91 (251)
T PF11932_consen 61 LEREIENLEVYNEQLERQVASQEQELASLEQ 91 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333333333333333333333333333
No 182
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=22.58 E-value=2.4e+02 Score=29.44 Aligned_cols=35 Identities=34% Similarity=0.413 Sum_probs=18.9
Q ss_pred HHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 104 VLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 104 ~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
.+.+.++.+++....+..++.+|++|+.+|...|.
T Consensus 152 ~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~ 186 (546)
T KOG0977|consen 152 ELEAEINTLKRRIKALEDELKRLKAENSRLREELA 186 (546)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHH
Confidence 34444555555555555555555555555555444
No 183
>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=22.55 E-value=3.1e+02 Score=19.98 Aligned_cols=31 Identities=19% Similarity=0.392 Sum_probs=17.2
Q ss_pred hhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 023725 107 NSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 137 (278)
Q Consensus 107 ~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l 137 (278)
+...++...-.+++.|++.|+.++..+.+.+
T Consensus 7 n~~~~~~~~i~tvk~en~~i~~~ve~i~env 37 (55)
T PF05377_consen 7 NELPRIESSINTVKKENEEISESVEKIEENV 37 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344455555556666666666666655543
No 184
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=22.28 E-value=2.4e+02 Score=24.82 Aligned_cols=22 Identities=36% Similarity=0.471 Sum_probs=8.8
Q ss_pred HHhhHHHHHHHHHHHHHHHHHH
Q 023725 113 KADYDNLFKEKEKLKAEVLKLT 134 (278)
Q Consensus 113 k~~~~~l~~ene~L~~E~~~L~ 134 (278)
+.....|..+++.|..|+..|.
T Consensus 110 ~~e~~~l~~~~e~Le~e~~~L~ 131 (161)
T TIGR02894 110 KNQNESLQKRNEELEKELEKLR 131 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333444444444444443
No 185
>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=22.25 E-value=4.6e+02 Score=24.17 Aligned_cols=56 Identities=16% Similarity=0.395 Sum_probs=26.7
Q ss_pred chhhhhHhhhhhhHHHHH---------HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 023725 79 PRQVAIWFQNRRARWKTK---------QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 134 (278)
Q Consensus 79 ~rQVqvWFQNRRak~K~k---------~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~ 134 (278)
...+..||+.+-...+.. ....+...++..+..|......+...|..|...+..|.
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 457888998775443322 12222333333344444444444444444444444443
No 186
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=22.06 E-value=1.2e+02 Score=25.66 Aligned_cols=41 Identities=12% Similarity=0.135 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhh
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 90 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRR 90 (278)
+++.+..++...| .....-.++|..||++...|+.+...-|
T Consensus 129 L~~~~r~i~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Rar 169 (186)
T PRK05602 129 LPERQREAIVLQY-----YQGLSNIEAAAVMDISVDALESLLARGR 169 (186)
T ss_pred CCHHHHHHhhHHH-----hcCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 4555555554443 2233457889999999999999865333
No 187
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=22.05 E-value=4.8e+02 Score=23.21 Aligned_cols=23 Identities=22% Similarity=0.411 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhh
Q 023725 120 FKEKEKLKAEVLKLTDKLQVKEK 142 (278)
Q Consensus 120 ~~ene~L~~E~~~L~~~l~~~~~ 142 (278)
....+.++.++.+|+..+...++
T Consensus 152 ~~~~~e~~~~l~~l~~ei~~~~~ 174 (176)
T PF12999_consen 152 KKKREELEKKLEELEKEIQAAKQ 174 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 34456666666667766665443
No 188
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=21.97 E-value=1.6e+02 Score=24.30 Aligned_cols=45 Identities=20% Similarity=0.055 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
+++.+..++...| .......++|..||++...|+.|.+.-|.+.+
T Consensus 109 L~~~~r~v~~l~~-----~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr 153 (165)
T PRK09644 109 LPVIEAQAILLCD-----VHELTYEEAASVLDLKLNTYKSHLFRGRKRLK 153 (165)
T ss_pred CCHHHHHHHHhHH-----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4444444444332 22334678899999999999998764444433
No 189
>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=21.89 E-value=1.6e+02 Score=27.63 Aligned_cols=17 Identities=47% Similarity=0.509 Sum_probs=8.8
Q ss_pred HHHHHHHHHHHHHHHHH
Q 023725 117 DNLFKEKEKLKAEVLKL 133 (278)
Q Consensus 117 ~~l~~ene~L~~E~~~L 133 (278)
..+.+||++|++|+.+|
T Consensus 69 ~~l~~EN~~Lr~e~~~l 85 (283)
T TIGR00219 69 NNLEYENYKLRQELLKK 85 (283)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34455555555555544
No 190
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=21.86 E-value=4.3e+02 Score=25.79 Aligned_cols=58 Identities=14% Similarity=0.224 Sum_probs=38.7
Q ss_pred hhhHhhhhhhHHHH-HHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 023725 82 VAIWFQNRRARWKT-KQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 139 (278)
Q Consensus 82 VqvWFQNRRak~K~-k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~ 139 (278)
++|||+|-|+-.+- -+..+..+.+...+..++.....-..+-.+|-.+++.|..+...
T Consensus 16 CKiWi~dN~~Sv~~He~GkrHke~V~Kritdi~rks~~kekeekKls~~la~mEaaA~~ 74 (336)
T KOG0150|consen 16 CKIWIKDNPASVRFHERGKRHKENVAKRITDIHRKSLKKEKEEKKLSKELAAMEAAASA 74 (336)
T ss_pred hhhhhcCChHHHHhHhhhhHHHHHHHHHHHHHHHhhHHHHHHHHhhhhHHHHHHHHHHH
Confidence 68999887765543 33344455666777777777766666777777777777655543
No 191
>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=21.82 E-value=5.3e+02 Score=22.51 Aligned_cols=44 Identities=20% Similarity=0.332 Sum_probs=31.6
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 023725 99 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 142 (278)
Q Consensus 99 ~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~~~~ 142 (278)
.+..+.++-.+..|...+..+.....+|+.|+..|-++.+.+..
T Consensus 143 ~k~~e~l~DE~~~L~l~~~~~e~k~~~l~~En~~Lv~Rwm~~k~ 186 (194)
T PF08614_consen 143 NKANEILQDELQALQLQLNMLEEKLRKLEEENRELVERWMQRKA 186 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445666666777777777888888888888888887775543
No 192
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=21.77 E-value=2.8e+02 Score=25.96 Aligned_cols=33 Identities=24% Similarity=0.349 Sum_probs=25.0
Q ss_pred hhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 106 QNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 106 ~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
+...+.....-.-|..||+.|+.++.+|+..+.
T Consensus 214 k~~~~e~~~r~~~leken~~lr~~v~~l~~el~ 246 (269)
T KOG3119|consen 214 KQKEDEMAHRVAELEKENEALRTQVEQLKKELA 246 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344456666667788999999999999987776
No 193
>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=21.66 E-value=2e+02 Score=24.02 Aligned_cols=38 Identities=18% Similarity=0.117 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhh
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 87 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQ 87 (278)
+++.+..+|...|- ......++|..+|+++..|+.+..
T Consensus 101 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 101 LPDEYREAIRLTEL-----EGLSQQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 56666666655442 223456789999999988888754
No 194
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=21.62 E-value=2.1e+02 Score=20.57 Aligned_cols=23 Identities=30% Similarity=0.369 Sum_probs=18.7
Q ss_pred HHHHHHHhCCCchhhhhHhhhhh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQNRR 90 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQNRR 90 (278)
..+||+.+|++...|..|...++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 35789999999999999987664
No 195
>KOG4187 consensus Proprotein convertase (PC) 2 chaperone involved in secretion (neuroendocrine protein 7B2) [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.49 E-value=1.4e+02 Score=27.14 Aligned_cols=24 Identities=42% Similarity=0.645 Sum_probs=17.3
Q ss_pred Cccc--ccccCCCCCCCCcccccccCCc
Q 023725 246 FPKL--EETEYSDPPTNSCNFGFPIEDH 271 (278)
Q Consensus 246 ~~k~--e~~~y~~~~~~scn~~f~~edq 271 (278)
.+|. |..-|++|| |-|=-||.+| |
T Consensus 103 ivK~d~~lpaYc~PP-NPCPvG~t~e-q 128 (228)
T KOG4187|consen 103 IVKDDSELPAYCDPP-NPCPVGKTDE-Q 128 (228)
T ss_pred ccccccCCcCcCCCC-CCCCCCcccc-c
Confidence 4555 334599988 7999999966 5
No 196
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.42 E-value=4.6e+02 Score=29.01 Aligned_cols=13 Identities=23% Similarity=0.376 Sum_probs=8.4
Q ss_pred hhHhhhhhhHHHH
Q 023725 83 AIWFQNRRARWKT 95 (278)
Q Consensus 83 qvWFQNRRak~K~ 95 (278)
.-|=++||...-.
T Consensus 411 lewErar~qem~~ 423 (1118)
T KOG1029|consen 411 LEWERARRQEMLN 423 (1118)
T ss_pred HHHHHHHHHHHHh
Confidence 3488888765543
No 197
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=21.41 E-value=2.6e+02 Score=22.57 Aligned_cols=39 Identities=13% Similarity=0.041 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhh
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQN 88 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQN 88 (278)
++..+..++...|-. ...-.++|..||++...|++....
T Consensus 107 Lp~~~r~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~r 145 (161)
T PRK09047 107 LPARQREAFLLRYWE-----DMDVAETAAAMGCSEGSVKTHCSR 145 (161)
T ss_pred CCHHHHHHHHHHHHh-----cCCHHHHHHHHCCCHHHHHHHHHH
Confidence 566666655554422 223578899999999999987653
No 198
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=21.26 E-value=1.1e+02 Score=18.93 Aligned_cols=23 Identities=22% Similarity=0.341 Sum_probs=18.6
Q ss_pred HHHHHHHhCCCchhhhhHhhhhh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQNRR 90 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQNRR 90 (278)
...+|+.+|++...|..|-.+++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 45789999999999999976654
No 199
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=21.13 E-value=2.1e+02 Score=24.09 Aligned_cols=38 Identities=21% Similarity=0.145 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhh
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 87 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQ 87 (278)
+++.+..++...|-. .....++|..||++...|+.+..
T Consensus 140 L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~ 177 (189)
T PRK09648 140 LPEKQREILILRVVV-----GLSAEETAEAVGSTPGAVRVAQH 177 (189)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHH
Confidence 666666666665433 24467899999999999999764
No 200
>PF10482 CtIP_N: Tumour-suppressor protein CtIP N-terminal domain; InterPro: IPR019518 CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control []. This N-terminal domain carries a coiled-coil region and is essential for homodimerisation of the protein []. The C-terminal domain is family CtIP_C and carries functionally important CxxC and RHR motifs, absence of which lead cells to grow slowly and show hypersensitivity to genotoxins [].
Probab=21.05 E-value=2.6e+02 Score=23.42 Aligned_cols=18 Identities=33% Similarity=0.466 Sum_probs=11.0
Q ss_pred HHHHHHhhhcCCCCHHHH
Q 023725 51 QFLEKSFEVENKLEPERK 68 (278)
Q Consensus 51 ~~LE~~F~~~~~P~~~~r 68 (278)
..||.+|.+++.+-..++
T Consensus 35 qrleel~~knqqLreQqk 52 (120)
T PF10482_consen 35 QRLEELFSKNQQLREQQK 52 (120)
T ss_pred HHHHHHHcccHHHHHHHH
Confidence 356788877775544433
No 201
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.82 E-value=4e+02 Score=20.54 Aligned_cols=42 Identities=24% Similarity=0.329 Sum_probs=25.9
Q ss_pred HHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 023725 98 LEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 139 (278)
Q Consensus 98 ~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~~ 139 (278)
+..+.+.|+..++.|..+...+....+.|..++.+|++....
T Consensus 23 LQmEieELKEknn~l~~e~q~~q~~reaL~~eneqlk~e~~~ 64 (79)
T COG3074 23 LQMEIEELKEKNNSLSQEVQNAQHQREALERENEQLKEEQNG 64 (79)
T ss_pred HHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555555666666666666677777777777665543
No 202
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=20.81 E-value=4.4e+02 Score=20.97 Aligned_cols=18 Identities=33% Similarity=0.359 Sum_probs=12.3
Q ss_pred HHHHHHhCCCchhhhhHh
Q 023725 69 IQLAKDLGLQPRQVAIWF 86 (278)
Q Consensus 69 ~eLA~~LgLs~rQVqvWF 86 (278)
.++|+.+|++.+.|+.|-
T Consensus 4 ge~A~~~gvs~~tlR~ye 21 (107)
T cd01111 4 SQLALDAGVSVHIVRDYL 21 (107)
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 456777777777777773
No 203
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=20.73 E-value=75 Score=21.13 Aligned_cols=23 Identities=17% Similarity=0.084 Sum_probs=20.1
Q ss_pred HHHHHHHhCCCchhhhhHhhhhh
Q 023725 68 KIQLAKDLGLQPRQVAIWFQNRR 90 (278)
Q Consensus 68 r~eLA~~LgLs~rQVqvWFQNRR 90 (278)
..+||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46789999999999999987765
No 204
>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=20.67 E-value=3e+02 Score=19.06 Aligned_cols=27 Identities=22% Similarity=0.379 Sum_probs=15.7
Q ss_pred HHHhhhhhhHHHhhHHHHHHHHHHHHH
Q 023725 103 DVLQNSYNSLKADYDNLFKEKEKLKAE 129 (278)
Q Consensus 103 ~~l~~~~~~Lk~~~~~l~~ene~L~~E 129 (278)
..+......|...+..|..++..|+.|
T Consensus 28 ~~le~~~~~L~~en~~L~~~i~~L~~E 54 (54)
T PF07716_consen 28 EELEQEVQELEEENEQLRQEIAQLERE 54 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 344555556666666666666666543
No 205
>PRK10403 transcriptional regulator NarP; Provisional
Probab=20.41 E-value=1.4e+02 Score=24.45 Aligned_cols=45 Identities=18% Similarity=0.187 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 44 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 44 rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
.+|..+..+|...... ....+||+.+|++++.|+...+|=|.|-.
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 4888888888765432 34578899999999999998876655543
No 206
>PF10473 CENP-F_leu_zip: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; InterPro: IPR019513 Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [, ]. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding
Probab=20.32 E-value=4.8e+02 Score=22.31 Aligned_cols=48 Identities=29% Similarity=0.448 Sum_probs=33.1
Q ss_pred hHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 023725 91 ARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 138 (278)
Q Consensus 91 ak~K~k~~~k~~~~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L~~~l~ 138 (278)
++.-...+......+....+.|..+-.++..+++.|..++..+++++.
T Consensus 50 ~k~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~q~kv~ 97 (140)
T PF10473_consen 50 SKAEIETLEEELEELTSELNQLELELDTLRSEKENLDKELQKKQEKVS 97 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333344455666666677777777778888888888888777777665
No 207
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=20.24 E-value=2.3e+02 Score=23.06 Aligned_cols=42 Identities=17% Similarity=0.215 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhH
Q 023725 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 92 (278)
Q Consensus 45 ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak 92 (278)
++..+..+|...| . ...-.++|..+|++...|+.+...-|.+
T Consensus 113 L~~~~r~il~l~~-~-----g~s~~eIA~~lgis~~tV~~~i~ra~~~ 154 (166)
T PRK09639 113 MTERDRTVLLLRF-S-----GYSYKEIAEALGIKESSVGTTLARAKKK 154 (166)
T ss_pred CCHHHHHHHHHHH-c-----CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 5565655555555 2 2245678999999999999887543333
No 208
>cd00131 PAX Paired Box domain
Probab=20.05 E-value=4.4e+02 Score=21.67 Aligned_cols=46 Identities=11% Similarity=-0.013 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCC-------CchhhhhHhhhh
Q 023725 44 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGL-------QPRQVAIWFQNR 89 (278)
Q Consensus 44 rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgL-------s~rQVqvWFQNR 89 (278)
..+..+...++.....++..+..+..++...-|+ +...|-.|++++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 3566777777777778888877776665334466 777787777653
No 209
>KOG3650 consensus Predicted coiled-coil protein [General function prediction only]
Probab=20.05 E-value=2.7e+02 Score=22.89 Aligned_cols=30 Identities=33% Similarity=0.393 Sum_probs=22.6
Q ss_pred HHhhhhhhHHHhhHHHHHHHHHHHHHHHHH
Q 023725 104 VLQNSYNSLKADYDNLFKEKEKLKAEVLKL 133 (278)
Q Consensus 104 ~l~~~~~~Lk~~~~~l~~ene~L~~E~~~L 133 (278)
.|+...+.|-+..+++.+||-+|+.|++-|
T Consensus 67 ELQnTLdDLSqRVdsVKEEnLKLrSENQVL 96 (120)
T KOG3650|consen 67 ELQNTLDDLSQRVDSVKEENLKLRSENQVL 96 (120)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhhhHHH
Confidence 366667777778888888888888887655
No 210
>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=20.04 E-value=1.3e+02 Score=24.02 Aligned_cols=34 Identities=32% Similarity=0.577 Sum_probs=18.1
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHHHHH
Q 023725 50 VQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 50 l~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K~k~ 97 (278)
+.+..-.|+.++||.+.--.. | =+|||.+|+..+
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq 47 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQ 47 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHH
Confidence 345556689999987542111 1 158899998754
No 211
>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=20.02 E-value=4.3e+02 Score=22.42 Aligned_cols=47 Identities=21% Similarity=0.142 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCchhhhhHhhhhhhHHH
Q 023725 42 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94 (278)
Q Consensus 42 R~rft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rQVqvWFQNRRak~K 94 (278)
..-++..|..+|...+ ......++|..||++...|..+-..-+.+.+
T Consensus 4 ~~~Lte~qr~VL~Lr~------~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 4 KTFLTERQIKVLELRE------KGLSQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred cCCCCHHHHHHHHHHH------cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 3458888988887742 1225678999999999999988654444333
No 212
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=20.01 E-value=44 Score=35.24 Aligned_cols=60 Identities=13% Similarity=0.115 Sum_probs=0.0
Q ss_pred CCCCCCC-CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCc-------hhhhhHhhhhhhHHHHHH
Q 023725 38 QPEKKRR-LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQP-------RQVAIWFQNRRARWKTKQ 97 (278)
Q Consensus 38 ~~rkR~r-ft~eQl~~LE~~F~~~~~P~~~~r~eLA~~LgLs~-------rQVqvWFQNRRak~K~k~ 97 (278)
.++++.+ |-..-..+-+.+|.+++.+......+--.++.+.+ .-|+.||.+||.++|+-+
T Consensus 691 pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 691 PKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Done!