Query 023291
Match_columns 284
No_of_seqs 301 out of 1553
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 02:55:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023291.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023291hhsearch_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 7E-22 1.5E-26 176.1 9.4 103 62-164 50-152 (198)
2 KOG0842 Transcription factor t 99.7 2.6E-16 5.7E-21 148.2 9.3 67 62-128 151-219 (307)
3 KOG0487 Transcription factor A 99.6 4.7E-16 1E-20 146.5 8.9 64 61-124 234-297 (308)
4 KOG0489 Transcription factor z 99.6 5.8E-17 1.3E-21 150.0 2.8 63 62-124 159-221 (261)
5 KOG0484 Transcription factor P 99.6 1.6E-16 3.5E-21 128.2 3.3 57 65-121 20-76 (125)
6 PF00046 Homeobox: Homeobox do 99.6 7.9E-16 1.7E-20 110.0 4.3 57 63-119 1-57 (57)
7 KOG0488 Transcription factor B 99.6 1E-15 2.2E-20 145.0 6.3 53 69-121 179-231 (309)
8 KOG0843 Transcription factor E 99.6 1.9E-15 4E-20 132.3 5.0 62 63-124 103-164 (197)
9 KOG0494 Transcription factor C 99.6 5E-15 1.1E-19 136.0 6.6 56 69-124 148-203 (332)
10 KOG0492 Transcription factor M 99.5 1E-14 2.2E-19 130.3 6.5 63 67-130 149-211 (246)
11 KOG2251 Homeobox transcription 99.5 5.4E-15 1.2E-19 132.9 4.9 63 61-123 36-98 (228)
12 KOG0848 Transcription factor C 99.5 1.3E-14 2.9E-19 133.6 5.7 56 69-124 206-261 (317)
13 KOG0485 Transcription factor N 99.5 3.8E-14 8.3E-19 127.4 7.0 59 63-121 103-163 (268)
14 cd00086 homeodomain Homeodomai 99.5 4.5E-14 9.8E-19 100.5 4.5 57 64-120 2-58 (59)
15 KOG0850 Transcription factor D 99.5 4.3E-14 9.2E-19 127.8 5.0 54 68-121 128-181 (245)
16 smart00389 HOX Homeodomain. DN 99.4 6.2E-14 1.4E-18 99.2 4.0 55 64-118 2-56 (56)
17 KOG0493 Transcription factor E 99.4 2.6E-13 5.6E-18 124.9 7.9 68 68-135 252-319 (342)
18 COG5576 Homeodomain-containing 99.4 1.9E-13 4.1E-18 118.1 5.4 66 59-124 48-113 (156)
19 TIGR01565 homeo_ZF_HD homeobox 99.4 8.3E-13 1.8E-17 96.6 5.5 52 63-114 2-57 (58)
20 KOG0486 Transcription factor P 99.3 8.8E-13 1.9E-17 123.9 5.0 64 67-130 117-180 (351)
21 KOG4577 Transcription factor L 99.3 1.1E-12 2.3E-17 122.2 4.7 79 61-139 166-244 (383)
22 KOG3802 Transcription factor O 99.3 1.9E-12 4.1E-17 125.0 5.0 60 62-121 294-353 (398)
23 KOG0844 Transcription factor E 99.3 2.2E-12 4.8E-17 120.9 4.9 65 59-123 178-242 (408)
24 KOG0491 Transcription factor B 99.3 7.2E-13 1.6E-17 114.8 0.5 60 65-124 103-162 (194)
25 KOG0847 Transcription factor, 99.2 5.6E-12 1.2E-16 113.8 2.1 54 68-121 173-226 (288)
26 KOG0490 Transcription factor, 99.1 4.1E-11 8.9E-16 106.4 3.6 60 62-121 60-119 (235)
27 KOG0849 Transcription factor P 98.9 1.1E-09 2.4E-14 105.8 4.2 62 62-123 176-237 (354)
28 KOG1168 Transcription factor A 98.8 2E-09 4.3E-14 100.7 3.9 62 60-121 307-368 (385)
29 KOG0775 Transcription factor S 98.8 5.2E-09 1.1E-13 97.2 4.0 51 69-119 183-233 (304)
30 PF02183 HALZ: Homeobox associ 98.3 1.5E-06 3.4E-11 60.5 4.7 45 120-164 1-45 (45)
31 PF05920 Homeobox_KN: Homeobox 98.2 3.9E-07 8.4E-12 61.9 0.9 34 83-116 7-40 (40)
32 KOG0774 Transcription factor P 98.2 5.9E-07 1.3E-11 83.3 2.4 59 62-120 188-249 (334)
33 KOG2252 CCAAT displacement pro 97.8 2.4E-05 5.2E-10 78.9 4.6 55 63-117 421-475 (558)
34 KOG0490 Transcription factor, 97.8 2.5E-05 5.4E-10 69.3 4.2 59 64-122 155-213 (235)
35 KOG1146 Homeobox protein [Gene 96.9 0.00057 1.2E-08 74.9 2.9 61 62-122 903-963 (1406)
36 KOG0773 Transcription factor M 96.2 0.0043 9.4E-08 59.2 3.8 56 66-121 243-301 (342)
37 PF11569 Homez: Homeodomain le 96.0 0.0025 5.5E-08 46.5 0.8 42 74-115 10-51 (56)
38 KOG4005 Transcription factor X 94.4 0.48 1E-05 44.1 10.6 45 122-166 102-146 (292)
39 PRK09413 IS2 repressor TnpA; R 93.9 0.19 4.2E-06 41.2 6.5 43 64-111 8-51 (121)
40 KOG3623 Homeobox transcription 92.1 0.11 2.4E-06 54.8 2.9 52 69-121 564-615 (1007)
41 PF04218 CENP-B_N: CENP-B N-te 91.4 0.31 6.6E-06 34.7 3.8 47 63-114 1-47 (53)
42 smart00340 HALZ homeobox assoc 89.2 0.75 1.6E-05 31.8 3.9 32 121-159 2-33 (44)
43 PF06156 DUF972: Protein of un 89.1 2 4.3E-05 35.2 7.2 47 120-166 11-57 (107)
44 PF02183 HALZ: Homeobox associ 89.0 1.2 2.5E-05 31.1 4.9 36 129-164 3-38 (45)
45 PRK13169 DNA replication intia 79.6 8.3 0.00018 31.8 6.8 44 120-163 11-54 (110)
46 PF06005 DUF904: Protein of un 79.1 14 0.0003 28.2 7.4 41 121-161 22-62 (72)
47 PF10224 DUF2205: Predicted co 77.9 14 0.0003 28.9 7.2 49 116-164 15-63 (80)
48 KOG4196 bZIP transcription fac 77.5 22 0.00048 30.3 8.8 83 67-162 22-112 (135)
49 PF00170 bZIP_1: bZIP transcri 76.3 18 0.00038 26.2 7.1 37 124-160 26-62 (64)
50 PF01527 HTH_Tnp_1: Transposas 70.5 1.5 3.3E-05 32.1 0.2 43 64-111 2-45 (76)
51 PF04967 HTH_10: HTH DNA bindi 69.8 4.8 0.0001 28.9 2.7 37 69-105 1-39 (53)
52 KOG4403 Cell surface glycoprot 68.5 19 0.00042 36.5 7.4 63 108-170 230-327 (575)
53 COG4467 Regulator of replicati 68.2 15 0.00034 30.3 5.6 43 121-163 12-54 (114)
54 PF04545 Sigma70_r4: Sigma-70, 68.0 5.5 0.00012 27.2 2.6 40 68-112 4-43 (50)
55 smart00338 BRLZ basic region l 67.9 34 0.00073 24.8 7.0 37 125-161 27-63 (65)
56 cd06171 Sigma70_r4 Sigma70, re 67.6 4.9 0.00011 26.2 2.2 43 68-115 10-52 (55)
57 PF06005 DUF904: Protein of un 65.6 36 0.00078 25.9 6.8 41 121-161 15-55 (72)
58 PF13443 HTH_26: Cro/C1-type H 61.6 5.3 0.00011 28.2 1.6 41 91-131 12-52 (63)
59 PF00170 bZIP_1: bZIP transcri 60.9 37 0.0008 24.5 6.0 33 130-162 25-57 (64)
60 COG4026 Uncharacterized protei 59.7 44 0.00095 31.3 7.5 43 123-165 134-176 (290)
61 PF00424 REV: REV protein (ant 57.9 14 0.00031 29.6 3.5 34 74-121 14-47 (91)
62 cd00569 HTH_Hin_like Helix-tur 57.8 14 0.0003 21.3 2.8 39 67-110 4-42 (42)
63 KOG4571 Activating transcripti 57.6 45 0.00098 32.0 7.4 42 125-166 249-290 (294)
64 COG3413 Predicted DNA binding 57.1 12 0.00026 33.4 3.4 47 68-116 155-203 (215)
65 PF11731 Cdd1: Pathogenicity l 56.7 3.3 7.1E-05 33.2 -0.2 29 251-284 58-87 (93)
66 PF06156 DUF972: Protein of un 55.3 32 0.0007 28.1 5.4 41 119-159 17-57 (107)
67 PRK03975 tfx putative transcri 54.9 14 0.0003 31.7 3.3 48 66-119 4-51 (141)
68 PF05377 FlaC_arch: Flagella a 53.8 48 0.001 24.2 5.4 32 132-163 8-39 (55)
69 KOG3119 Basic region leucine z 53.6 37 0.00079 31.9 6.2 22 142-163 226-247 (269)
70 PF07407 Seadorna_VP6: Seadorn 53.2 18 0.00038 35.5 4.0 30 134-163 35-64 (420)
71 PRK00888 ftsB cell division pr 52.3 27 0.00059 28.3 4.5 25 135-159 38-62 (105)
72 PF05700 BCAS2: Breast carcino 51.8 60 0.0013 29.4 7.1 40 126-165 177-216 (221)
73 PRK13169 DNA replication intia 51.6 41 0.00088 27.8 5.4 41 119-159 17-57 (110)
74 PF12709 Kinetocho_Slk19: Cent 48.3 1.1E+02 0.0024 24.4 7.1 47 121-167 31-78 (87)
75 PRK10884 SH3 domain-containing 48.0 87 0.0019 28.4 7.5 38 126-163 127-164 (206)
76 KOG1146 Homeobox protein [Gene 47.4 22 0.00048 40.4 4.1 53 69-121 712-764 (1406)
77 PF13936 HTH_38: Helix-turn-he 47.3 7.4 0.00016 26.4 0.4 41 66-111 2-42 (44)
78 PF10668 Phage_terminase: Phag 47.3 6.6 0.00014 29.0 0.1 20 91-110 24-43 (60)
79 PRK15422 septal ring assembly 46.7 1E+02 0.0023 24.1 6.6 26 137-162 45-70 (79)
80 PF08281 Sigma70_r4_2: Sigma-7 46.7 15 0.00033 25.2 1.9 41 69-114 11-51 (54)
81 PF15035 Rootletin: Ciliary ro 45.1 98 0.0021 27.5 7.2 49 121-169 78-126 (182)
82 PF00196 GerE: Bacterial regul 43.7 20 0.00043 25.2 2.1 46 68-119 3-48 (58)
83 KOG0249 LAR-interacting protei 43.4 1.1E+02 0.0023 33.3 8.1 51 115-165 214-264 (916)
84 PRK10884 SH3 domain-containing 43.0 1.1E+02 0.0025 27.6 7.4 29 134-162 128-156 (206)
85 TIGR02449 conserved hypothetic 42.9 1.2E+02 0.0025 22.9 6.2 37 124-160 7-43 (65)
86 PF07334 IFP_35_N: Interferon- 42.6 43 0.00093 26.0 3.9 26 141-166 3-28 (76)
87 PF15058 Speriolin_N: Sperioli 41.8 43 0.00093 30.4 4.4 29 138-166 12-40 (200)
88 KOG4571 Activating transcripti 41.7 91 0.002 30.0 6.8 36 128-163 245-280 (294)
89 TIGR02937 sigma70-ECF RNA poly 41.6 29 0.00063 27.2 3.1 45 69-118 111-155 (158)
90 PRK09652 RNA polymerase sigma 41.2 29 0.00062 28.8 3.1 45 68-117 128-172 (182)
91 PRK09646 RNA polymerase sigma 40.6 34 0.00073 29.5 3.6 45 69-118 143-187 (194)
92 PRK06759 RNA polymerase factor 40.6 28 0.00061 28.4 2.9 46 68-118 106-151 (154)
93 PRK00888 ftsB cell division pr 40.0 76 0.0017 25.6 5.3 47 105-152 16-62 (105)
94 PF11932 DUF3450: Protein of u 39.9 1.6E+02 0.0035 26.9 8.1 44 122-165 47-90 (251)
95 KOG2391 Vacuolar sorting prote 39.2 1.5E+02 0.0032 29.4 7.8 48 113-160 221-268 (365)
96 PRK11924 RNA polymerase sigma 38.6 32 0.0007 28.4 3.0 46 69-119 126-171 (179)
97 PRK09642 RNA polymerase sigma 38.1 38 0.00083 27.9 3.4 46 69-119 107-152 (160)
98 smart00338 BRLZ basic region l 37.5 1.2E+02 0.0027 21.7 5.7 32 131-162 26-57 (65)
99 KOG4005 Transcription factor X 37.4 1E+02 0.0022 29.1 6.2 43 121-163 94-136 (292)
100 COG3074 Uncharacterized protei 36.7 1.3E+02 0.0029 23.2 5.7 12 125-136 26-37 (79)
101 PF08172 CASP_C: CASP C termin 36.6 1E+02 0.0022 28.8 6.2 42 114-162 90-131 (248)
102 PF11594 Med28: Mediator compl 36.2 46 0.00099 27.4 3.4 49 104-170 18-66 (106)
103 cd04779 HTH_MerR-like_sg4 Heli 36.1 2.1E+02 0.0046 24.0 7.6 35 66-113 35-69 (134)
104 KOG0709 CREB/ATF family transc 35.7 2.7E+02 0.0059 28.6 9.3 93 68-167 220-315 (472)
105 PF09607 BrkDBD: Brinker DNA-b 35.5 31 0.00067 25.4 2.1 44 66-111 3-47 (58)
106 PRK12526 RNA polymerase sigma 35.3 41 0.00089 29.5 3.3 45 69-118 154-198 (206)
107 cd04766 HTH_HspR Helix-Turn-He 35.0 48 0.001 25.5 3.3 70 92-162 4-89 (91)
108 PRK12512 RNA polymerase sigma 34.7 45 0.00098 28.2 3.4 46 69-119 132-177 (184)
109 PF14775 NYD-SP28_assoc: Sperm 34.0 1E+02 0.0022 22.6 4.6 28 135-162 30-57 (60)
110 PRK00118 putative DNA-binding 33.6 46 0.001 27.1 3.0 44 69-117 18-61 (104)
111 KOG3156 Uncharacterized membra 33.4 1.4E+02 0.0029 27.7 6.3 43 122-164 99-142 (220)
112 TIGR02985 Sig70_bacteroi1 RNA 33.3 46 0.00099 26.9 3.1 45 69-118 114-158 (161)
113 PRK14127 cell division protein 32.9 1.4E+02 0.0031 24.5 5.8 33 134-166 33-65 (109)
114 PF08826 DMPK_coil: DMPK coile 32.6 2.1E+02 0.0045 21.2 6.7 41 122-162 16-56 (61)
115 TIGR02894 DNA_bind_RsfA transc 32.6 1.4E+02 0.003 26.4 6.0 33 137-169 110-142 (161)
116 PRK12519 RNA polymerase sigma 32.2 41 0.00088 28.8 2.7 45 69-118 142-186 (194)
117 PF04297 UPF0122: Putative hel 32.2 89 0.0019 25.4 4.5 38 69-111 18-55 (101)
118 KOG3650 Predicted coiled-coil 32.1 1.7E+02 0.0037 24.0 6.0 39 125-163 64-102 (120)
119 PRK14872 rod shape-determining 32.1 73 0.0016 31.2 4.6 22 142-163 61-82 (337)
120 PRK12515 RNA polymerase sigma 31.6 54 0.0012 28.0 3.4 46 69-119 132-177 (189)
121 TIGR02989 Sig-70_gvs1 RNA poly 31.4 49 0.0011 27.0 3.0 42 69-115 112-153 (159)
122 PF07407 Seadorna_VP6: Seadorn 31.4 64 0.0014 31.8 4.0 22 142-163 36-57 (420)
123 PRK12514 RNA polymerase sigma 31.2 63 0.0014 27.2 3.7 45 69-118 130-174 (179)
124 PRK04217 hypothetical protein; 30.9 58 0.0013 26.7 3.3 44 68-116 42-85 (110)
125 PRK10072 putative transcriptio 30.8 33 0.00072 27.4 1.8 41 68-115 32-72 (96)
126 PF04977 DivIC: Septum formati 30.5 1.2E+02 0.0025 22.1 4.6 20 138-157 31-50 (80)
127 TIGR02948 SigW_bacill RNA poly 30.5 51 0.0011 27.7 3.0 46 68-118 136-181 (187)
128 TIGR03752 conj_TIGR03752 integ 30.4 1.4E+02 0.0031 30.5 6.5 27 68-97 41-67 (472)
129 KOG3119 Basic region leucine z 30.4 1.6E+02 0.0035 27.6 6.5 47 114-163 208-254 (269)
130 PRK09648 RNA polymerase sigma 30.2 56 0.0012 27.8 3.2 43 69-116 140-182 (189)
131 PF12325 TMF_TATA_bd: TATA ele 30.2 2.6E+02 0.0057 23.3 7.1 45 118-162 69-113 (120)
132 PF04899 MbeD_MobD: MbeD/MobD 30.2 2E+02 0.0042 21.9 5.7 36 127-162 24-59 (70)
133 cd04761 HTH_MerR-SF Helix-Turn 30.1 18 0.00039 23.9 0.1 23 92-114 3-25 (49)
134 PRK09644 RNA polymerase sigma 30.0 53 0.0012 27.3 3.0 45 69-118 109-153 (165)
135 TIGR02959 SigZ RNA polymerase 29.9 56 0.0012 27.6 3.1 40 68-112 100-139 (170)
136 PRK15422 septal ring assembly 29.7 1.9E+02 0.0042 22.6 5.7 12 149-160 50-61 (79)
137 TIGR02999 Sig-70_X6 RNA polyme 29.6 58 0.0013 27.4 3.2 45 69-118 135-179 (183)
138 PRK05602 RNA polymerase sigma 29.3 54 0.0012 27.9 2.9 45 69-118 129-173 (186)
139 PRK00409 recombination and DNA 29.3 2.2E+02 0.0047 30.9 8.1 19 89-107 487-505 (782)
140 COG2963 Transposase and inacti 29.3 71 0.0015 25.4 3.5 42 66-111 5-47 (116)
141 PRK12530 RNA polymerase sigma 29.1 72 0.0016 27.4 3.8 46 69-119 135-180 (189)
142 PRK09639 RNA polymerase sigma 29.1 57 0.0012 26.9 3.0 45 68-118 112-156 (166)
143 COG4026 Uncharacterized protei 29.1 2.1E+02 0.0045 26.9 6.8 47 119-165 144-190 (290)
144 PRK14760 hypothetical protein; 29.0 23 0.00051 22.0 0.4 8 275-282 18-25 (26)
145 KOG1962 B-cell receptor-associ 28.9 2E+02 0.0043 26.6 6.6 32 137-168 150-181 (216)
146 KOG0483 Transcription factor H 28.8 95 0.0021 28.1 4.5 38 130-167 111-148 (198)
147 smart00421 HTH_LUXR helix_turn 28.6 55 0.0012 21.5 2.4 40 68-113 3-42 (58)
148 PF03670 UPF0184: Uncharacteri 28.4 1.4E+02 0.003 23.6 4.8 37 123-159 25-61 (83)
149 TIGR03879 near_KaiC_dom probab 28.3 15 0.00033 28.1 -0.5 33 80-112 23-55 (73)
150 KOG1962 B-cell receptor-associ 27.4 1.4E+02 0.0031 27.5 5.4 39 122-160 163-201 (216)
151 PRK06811 RNA polymerase factor 27.3 63 0.0014 27.7 3.0 46 69-119 132-177 (189)
152 PF12999 PRKCSH-like: Glucosid 27.1 2.8E+02 0.0061 24.7 7.1 19 147-165 155-173 (176)
153 PF06056 Terminase_5: Putative 27.0 26 0.00056 25.4 0.5 27 91-119 15-41 (58)
154 PF12824 MRP-L20: Mitochondria 27.0 3.3E+02 0.0071 23.9 7.5 45 66-112 83-127 (164)
155 PRK12541 RNA polymerase sigma 27.0 58 0.0013 26.9 2.7 45 69-118 113-157 (161)
156 PRK12537 RNA polymerase sigma 26.9 80 0.0017 26.8 3.6 44 69-117 134-177 (182)
157 PRK13729 conjugal transfer pil 26.9 1.8E+02 0.0038 29.9 6.5 44 118-161 77-120 (475)
158 PF13518 HTH_28: Helix-turn-he 26.6 30 0.00066 23.1 0.7 22 91-112 14-35 (52)
159 PF08280 HTH_Mga: M protein tr 26.4 43 0.00093 23.9 1.5 33 71-107 5-37 (59)
160 TIGR02939 RpoE_Sigma70 RNA pol 26.4 54 0.0012 27.6 2.4 43 69-116 139-181 (190)
161 PF03954 Lectin_N: Hepatic lec 26.3 1.2E+02 0.0025 26.2 4.4 49 120-168 58-110 (138)
162 PRK12538 RNA polymerase sigma 26.1 78 0.0017 28.6 3.5 46 69-119 172-217 (233)
163 KOG0150 Spliceosomal protein F 26.1 1.5E+02 0.0033 28.9 5.5 14 106-119 16-29 (336)
164 PRK09047 RNA polymerase factor 26.0 78 0.0017 25.9 3.3 44 68-116 106-149 (161)
165 TIGR02954 Sig70_famx3 RNA poly 25.8 81 0.0017 26.3 3.4 45 69-118 120-164 (169)
166 KOG0977 Nuclear envelope prote 25.7 3.3E+02 0.0073 28.5 8.3 40 120-159 151-190 (546)
167 PRK14127 cell division protein 25.6 1.7E+02 0.0038 24.0 5.1 36 128-163 34-69 (109)
168 KOG0709 CREB/ATF family transc 25.6 1.8E+02 0.0039 29.8 6.2 73 87-160 221-301 (472)
169 PF11932 DUF3450: Protein of u 25.5 3.3E+02 0.0071 24.8 7.6 51 119-169 51-101 (251)
170 PF11544 Spc42p: Spindle pole 25.4 3.3E+02 0.0071 21.2 6.9 50 111-160 6-55 (76)
171 PF10883 DUF2681: Protein of u 25.3 1.8E+02 0.0039 23.1 5.0 18 143-160 35-52 (87)
172 PF02796 HTH_7: Helix-turn-hel 25.1 41 0.00089 22.7 1.2 38 68-110 5-42 (45)
173 PRK12543 RNA polymerase sigma 25.1 1.2E+02 0.0027 25.6 4.4 46 69-119 118-163 (179)
174 TIGR00219 mreC rod shape-deter 24.8 1.7E+02 0.0037 27.6 5.7 15 143-157 71-85 (283)
175 PRK06930 positive control sigm 24.8 93 0.002 27.1 3.6 47 68-119 114-160 (170)
176 PF04111 APG6: Autophagy prote 24.7 3E+02 0.0065 26.4 7.4 44 122-165 48-91 (314)
177 TIGR02983 SigE-fam_strep RNA p 24.6 79 0.0017 26.0 3.1 46 69-119 111-156 (162)
178 cd06170 LuxR_C_like C-terminal 24.5 78 0.0017 20.9 2.5 36 70-111 2-37 (57)
179 PTZ00454 26S protease regulato 24.5 2.2E+02 0.0048 28.2 6.7 40 123-162 21-60 (398)
180 cd04765 HTH_MlrA-like_sg2 Heli 24.2 1.1E+02 0.0024 24.2 3.7 36 65-112 35-70 (99)
181 PRK13922 rod shape-determining 24.2 1.7E+02 0.0037 27.0 5.5 19 142-160 73-91 (276)
182 PF08961 DUF1875: Domain of un 24.1 26 0.00056 32.5 0.0 33 125-157 130-162 (243)
183 KOG1853 LIS1-interacting prote 24.1 1.6E+02 0.0035 28.1 5.2 22 111-132 60-81 (333)
184 KOG3755 SATB1 matrix attachmen 23.9 23 0.00049 37.3 -0.4 44 78-121 708-758 (769)
185 KOG4343 bZIP transcription fac 23.9 1.6E+02 0.0034 31.0 5.5 30 136-165 307-336 (655)
186 PRK07037 extracytoplasmic-func 23.8 90 0.002 25.7 3.3 42 69-115 110-151 (163)
187 PRK09637 RNA polymerase sigma 23.7 83 0.0018 27.0 3.1 41 69-114 107-147 (181)
188 PHA02955 hypothetical protein; 23.7 1E+02 0.0022 28.3 3.8 42 71-112 60-102 (213)
189 TIGR01069 mutS2 MutS2 family p 23.7 4.2E+02 0.0091 28.7 9.0 20 88-107 481-500 (771)
190 PRK10403 transcriptional regul 23.6 53 0.0011 27.1 1.8 46 68-119 153-198 (215)
191 PF14197 Cep57_CLD_2: Centroso 23.5 3.2E+02 0.007 20.5 7.3 19 144-162 46-64 (69)
192 TIGR00219 mreC rod shape-deter 23.4 1.7E+02 0.0036 27.7 5.3 41 122-165 71-111 (283)
193 PF13384 HTH_23: Homeodomain-l 23.4 26 0.00057 23.5 -0.1 23 90-112 18-40 (50)
194 PF04880 NUDE_C: NUDE protein, 23.1 1E+02 0.0022 27.3 3.5 30 138-167 24-53 (166)
195 PF05377 FlaC_arch: Flagella a 23.1 2.8E+02 0.0061 20.2 5.2 37 121-157 4-40 (55)
196 cd01106 HTH_TipAL-Mta Helix-Tu 23.0 2.9E+02 0.0063 21.5 5.9 35 66-113 36-70 (103)
197 PRK12546 RNA polymerase sigma 22.9 59 0.0013 28.2 2.0 46 69-119 114-159 (188)
198 PRK06986 fliA flagellar biosyn 22.7 81 0.0018 28.2 3.0 46 69-119 185-230 (236)
199 PF06810 Phage_GP20: Phage min 22.7 4.9E+02 0.011 22.4 7.7 48 124-171 27-77 (155)
200 TIGR02952 Sig70_famx2 RNA poly 22.6 94 0.002 25.6 3.1 38 69-111 123-160 (170)
201 PRK12547 RNA polymerase sigma 22.6 94 0.002 25.9 3.2 45 69-118 113-157 (164)
202 TIGR03001 Sig-70_gmx1 RNA poly 22.3 1.1E+02 0.0023 28.1 3.7 57 69-130 162-218 (244)
203 PF05529 Bap31: B-cell recepto 22.1 3.8E+02 0.0083 23.3 7.1 28 143-170 152-179 (192)
204 PRK12536 RNA polymerase sigma 21.8 99 0.0021 26.2 3.2 46 69-119 130-175 (181)
205 PF13411 MerR_1: MerR HTH fami 21.7 30 0.00065 24.7 -0.1 20 92-111 3-22 (69)
206 KOG4343 bZIP transcription fac 21.4 2E+02 0.0043 30.2 5.6 35 125-159 303-337 (655)
207 cd04770 HTH_HMRTR Helix-Turn-H 21.3 4E+02 0.0086 21.3 6.6 36 66-114 36-71 (123)
208 PF07716 bZIP_2: Basic region 21.3 2.9E+02 0.0064 19.2 5.6 23 136-158 30-52 (54)
209 PRK12524 RNA polymerase sigma 21.3 95 0.0021 26.7 3.0 44 69-117 137-180 (196)
210 PRK13919 putative RNA polymera 21.2 1.1E+02 0.0024 25.7 3.4 42 69-115 136-177 (186)
211 PF09304 Cortex-I_coil: Cortex 21.1 4.8E+02 0.01 21.6 7.5 43 121-163 34-76 (107)
212 PF01166 TSC22: TSC-22/dip/bun 21.1 1.4E+02 0.0031 22.1 3.4 28 125-159 15-42 (59)
213 PF13815 Dzip-like_N: Iguana/D 21.0 3.3E+02 0.0071 22.1 6.0 28 134-161 83-110 (118)
214 TIGR03752 conj_TIGR03752 integ 21.0 2.5E+02 0.0054 28.9 6.2 26 136-161 107-132 (472)
215 COG3074 Uncharacterized protei 20.7 3.6E+02 0.0077 20.9 5.5 13 142-154 50-62 (79)
216 TIGR02479 FliA_WhiG RNA polyme 20.7 1E+02 0.0022 27.3 3.1 43 69-116 176-218 (224)
217 PF06785 UPF0242: Uncharacteri 20.6 3.4E+02 0.0073 27.0 6.7 36 133-168 129-164 (401)
218 PRK12532 RNA polymerase sigma 20.6 1.3E+02 0.0027 25.8 3.6 46 69-119 137-182 (195)
219 cd01392 HTH_LacI Helix-turn-he 20.3 51 0.0011 22.1 0.9 21 94-114 2-22 (52)
220 PRK13922 rod shape-determining 20.1 2.1E+02 0.0044 26.4 5.2 23 135-157 73-95 (276)
221 PRK10360 DNA-binding transcrip 20.1 73 0.0016 26.2 2.0 45 68-118 137-181 (196)
222 TIGR02894 DNA_bind_RsfA transc 20.1 3.1E+02 0.0066 24.3 5.8 8 146-153 105-112 (161)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.86 E-value=7e-22 Score=176.06 Aligned_cols=103 Identities=63% Similarity=0.910 Sum_probs=92.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHHHHHHHHHhHHHHhhhhh
Q 023291 62 LPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLERDYDLLKSSYDALLSSYD 141 (284)
Q Consensus 62 ~~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~~~Lk~~~~~l~s~~~ 141 (284)
...|++|||.+|+..||..|+...++.+.++..||++|||.+|||+|||||||||||.++++.+++.||..++.|...+.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~~ 129 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEND 129 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhh
Confidence 56778889999999999999999999999999999999999999999999999999999999999999999998888887
Q ss_pred HHHHhhHHHHHHHHHHHHHHHHH
Q 023291 142 SLVKENQKLKSEVVSLNEKIEAK 164 (284)
Q Consensus 142 sl~~en~~L~~E~~~L~e~l~~~ 164 (284)
.|..+++.|+.++..++..++..
T Consensus 130 ~Lq~e~~eL~~~~~~~~~~~~~~ 152 (198)
T KOG0483|consen 130 RLQSEVQELVAELSSLKREMQKS 152 (198)
T ss_pred HHHHHHHHHHHHHhhhhhhhccC
Confidence 77777777777776666665543
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.66 E-value=2.6e-16 Score=148.15 Aligned_cols=67 Identities=36% Similarity=0.590 Sum_probs=59.8
Q ss_pred CCCCCCC--CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHHHHHH
Q 023291 62 LPEKKRR--LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLERDYDL 128 (284)
Q Consensus 62 ~~rkRrR--fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~~~ 128 (284)
.+|||+| ||..|+.+||+.|++.+|++..+|+.||..|.|++.||+|||||||=|.||+++.+..+.
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 3444445 999999999999999999999999999999999999999999999999999987775443
No 3
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.64 E-value=4.7e-16 Score=146.51 Aligned_cols=64 Identities=34% Similarity=0.453 Sum_probs=57.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHH
Q 023291 61 QLPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLER 124 (284)
Q Consensus 61 ~~~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~ 124 (284)
..+|||.-+|..|+.+||+.|..|.|++.+.|.+|++.|+|++|||+|||||||+|.||..++.
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 3455555699999999999999999999999999999999999999999999999999987544
No 4
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.64 E-value=5.8e-17 Score=149.97 Aligned_cols=63 Identities=33% Similarity=0.595 Sum_probs=56.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHH
Q 023291 62 LPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLER 124 (284)
Q Consensus 62 ~~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~ 124 (284)
.+|.|+-||..|+.+||+.|..|+|++..+|.+||..|.|+++||+|||||||+||||..+..
T Consensus 159 ~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred CCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence 344455599999999999999999999999999999999999999999999999999875443
No 5
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.62 E-value=1.6e-16 Score=128.22 Aligned_cols=57 Identities=30% Similarity=0.550 Sum_probs=53.3
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHH
Q 023291 65 KKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121 (284)
Q Consensus 65 kRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq 121 (284)
-|+.||..||..||+.|...+||++..|++||.++.|++.+|||||||||||.||+.
T Consensus 20 IRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 20 IRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred hhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 334499999999999999999999999999999999999999999999999999864
No 6
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.60 E-value=7.9e-16 Score=109.98 Aligned_cols=57 Identities=44% Similarity=0.670 Sum_probs=54.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 63 PEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 63 ~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+++|++||..|+..|+..|..++||+..++..||..|||++.+|++||+|||+++|+
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 356778999999999999999999999999999999999999999999999999886
No 7
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.60 E-value=1e-15 Score=145.00 Aligned_cols=53 Identities=42% Similarity=0.708 Sum_probs=52.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq 121 (284)
||..||..||+.|++.+|++..+|.+||..|||+..||++||||||+||||..
T Consensus 179 FT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 179 FSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred hhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999965
No 8
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.57 E-value=1.9e-15 Score=132.32 Aligned_cols=62 Identities=39% Similarity=0.549 Sum_probs=56.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHH
Q 023291 63 PEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLER 124 (284)
Q Consensus 63 ~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~ 124 (284)
||.|+.||..|+..||..|+.++|....+|++||..|+|++.||+|||||||.|.||++.+.
T Consensus 103 kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 103 KRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 34444599999999999999999999999999999999999999999999999999987654
No 9
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.55 E-value=5e-15 Score=135.95 Aligned_cols=56 Identities=34% Similarity=0.577 Sum_probs=53.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLER 124 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~ 124 (284)
||..|+..||+.|+..+||+...|+.||.++.|++.+|+||||||||||||+...-
T Consensus 148 FT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 148 FTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred hhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 99999999999999999999999999999999999999999999999999976443
No 10
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.53 E-value=1e-14 Score=130.29 Aligned_cols=63 Identities=35% Similarity=0.561 Sum_probs=55.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHHHHHHHH
Q 023291 67 RRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLERDYDLLK 130 (284)
Q Consensus 67 rRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~~~Lk 130 (284)
+-||..||..||+.|...+|+++.+|.+++..|.|++.||+|||||||||.||.| +.+.+.+|
T Consensus 149 tPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ-eae~Ek~k 211 (246)
T KOG0492|consen 149 TPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ-EAELEKLK 211 (246)
T ss_pred CCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH-HHHHHHhh
Confidence 3499999999999999999999999999999999999999999999999999876 33344443
No 11
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.53 E-value=5.4e-15 Score=132.90 Aligned_cols=63 Identities=30% Similarity=0.484 Sum_probs=57.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHH
Q 023291 61 QLPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLE 123 (284)
Q Consensus 61 ~~~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~ 123 (284)
.++|-|++||..|+++||.+|.++.||+...|++||.+|+|++.+|+|||+|||||+|+++..
T Consensus 36 kqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 36 KQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred hcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 344556679999999999999999999999999999999999999999999999999987643
No 12
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.51 E-value=1.3e-14 Score=133.58 Aligned_cols=56 Identities=41% Similarity=0.620 Sum_probs=52.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLER 124 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~ 124 (284)
+|..|+.+||+.|..++|.++.++.+||..|||++|||+|||||||||+||.++++
T Consensus 206 YTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999875443
No 13
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.49 E-value=3.8e-14 Score=127.37 Aligned_cols=59 Identities=41% Similarity=0.686 Sum_probs=54.5
Q ss_pred CCCCCC--CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHH
Q 023291 63 PEKKRR--LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121 (284)
Q Consensus 63 ~rkRrR--fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq 121 (284)
+|||+| |+..|+..||..|+..+|++..+|.-||..|.|++.||+|||||||.||||+-
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 444444 99999999999999999999999999999999999999999999999999864
No 14
>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=99.47 E-value=4.5e-14 Score=100.48 Aligned_cols=57 Identities=49% Similarity=0.749 Sum_probs=53.4
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHH
Q 023291 64 EKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTK 120 (284)
Q Consensus 64 rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krk 120 (284)
+++.+|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||++.++.
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 456679999999999999999999999999999999999999999999999998764
No 15
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.46 E-value=4.3e-14 Score=127.83 Aligned_cols=54 Identities=33% Similarity=0.612 Sum_probs=51.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq 121 (284)
.++.-||..|.+.|+++.|+-..+|.+||..|||+..||+|||||||.|.||..
T Consensus 128 IYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 128 IYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred cccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 399999999999999999999999999999999999999999999999999854
No 16
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.45 E-value=6.2e-14 Score=99.22 Aligned_cols=55 Identities=51% Similarity=0.819 Sum_probs=51.3
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 64 EKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 64 rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
+.|.+|+..|+..|+..|..++||+..++..||..+||+..+|++||+|||++.|
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 4456699999999999999999999999999999999999999999999999754
No 17
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.43 E-value=2.6e-13 Score=124.87 Aligned_cols=68 Identities=32% Similarity=0.527 Sum_probs=59.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHHHHHHHHHhHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLERDYDLLKSSYDA 135 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~~~Lk~~~~~ 135 (284)
-||.+||+.|+..|..++|++..+|.+||.+|+|.+.||+|||||+|+|.||..-.+....|.-....
T Consensus 252 AFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~~lmaqg 319 (342)
T KOG0493|consen 252 AFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLALHLMAQG 319 (342)
T ss_pred cccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhhhhhccc
Confidence 39999999999999999999999999999999999999999999999999998766655555544333
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.41 E-value=1.9e-13 Score=118.11 Aligned_cols=66 Identities=33% Similarity=0.528 Sum_probs=60.1
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHH
Q 023291 59 DEQLPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLER 124 (284)
Q Consensus 59 ~~~~~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~ 124 (284)
....+++|+|.|..|+.+|++.|+.++||+...|..|+..|+|+++-|++||||||++.|+.....
T Consensus 48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred CCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence 345667788899999999999999999999999999999999999999999999999999876443
No 19
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.37 E-value=8.3e-13 Score=96.61 Aligned_cols=52 Identities=19% Similarity=0.367 Sum_probs=49.1
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHhCCCCcceeecchhhH
Q 023291 63 PEKKRRLTAEQVHLLEKSFEAENK----LEPERKGQLAKKLGLQPRQVAVWFQNRR 114 (284)
Q Consensus 63 ~rkRrRfT~~Ql~~LE~~F~~~~~----P~~~~r~eLA~~LgLs~rqVqvWFQNRR 114 (284)
+|.|+.||.+|+..|+..|+.++| |+...+.+||..|||++++|+|||||.+
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 566777999999999999999999 9999999999999999999999999964
No 20
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.34 E-value=8.8e-13 Score=123.88 Aligned_cols=64 Identities=28% Similarity=0.562 Sum_probs=57.0
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHHHHHHHH
Q 023291 67 RRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLERDYDLLK 130 (284)
Q Consensus 67 rRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~~~Lk 130 (284)
+.||..|++.||..|.++.||+...|++||..++|++.+|+|||.||||||||..+....+..|
T Consensus 117 thFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~~k 180 (351)
T KOG0486|consen 117 THFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELAK 180 (351)
T ss_pred hhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHhhh
Confidence 3399999999999999999999999999999999999999999999999999976555433333
No 21
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.32 E-value=1.1e-12 Score=122.22 Aligned_cols=79 Identities=27% Similarity=0.395 Sum_probs=69.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHHHHHHHHHhHHHHhhh
Q 023291 61 QLPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLERDYDLLKSSYDALLSS 139 (284)
Q Consensus 61 ~~~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~~~Lk~~~~~l~s~ 139 (284)
..+|-|+.+|+.||+.|+..|...++|....|++|+.++||.-|.|||||||||||.||.++..-..++-+.+.+++..
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK~s 244 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMKRS 244 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhhcc
Confidence 3444555699999999999999999999999999999999999999999999999999988777777887777777665
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.30 E-value=1.9e-12 Score=125.02 Aligned_cols=60 Identities=28% Similarity=0.378 Sum_probs=55.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHH
Q 023291 62 LPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121 (284)
Q Consensus 62 ~~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq 121 (284)
++|||+.|....+..||+.|..|++|+..++..||.+|+|....|+|||||||.|.||..
T Consensus 294 kRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 294 KRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred ccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 445555699999999999999999999999999999999999999999999999999854
No 23
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.29 E-value=2.2e-12 Score=120.94 Aligned_cols=65 Identities=38% Similarity=0.582 Sum_probs=58.5
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHH
Q 023291 59 DEQLPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLE 123 (284)
Q Consensus 59 ~~~~~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~ 123 (284)
+.+-+|-|+-||.+||..||+.|-+.+|-+..+|.+||..|+|++..|+|||||||+|.||+.+.
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 34455566679999999999999999999999999999999999999999999999999997654
No 24
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.27 E-value=7.2e-13 Score=114.83 Aligned_cols=60 Identities=35% Similarity=0.534 Sum_probs=55.2
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHH
Q 023291 65 KKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLER 124 (284)
Q Consensus 65 kRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~ 124 (284)
.|+.|+..|+..||+.|+..+|++..+|.+||..|+|++.||+.||||||+|.||.++..
T Consensus 103 ~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 103 ARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred hcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 344599999999999999999999999999999999999999999999999999877554
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.19 E-value=5.6e-12 Score=113.76 Aligned_cols=54 Identities=41% Similarity=0.748 Sum_probs=52.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq 121 (284)
.|+-.|+..||..|++.+||-...|.+||..+|+++.||+|||||||+||||+.
T Consensus 173 Tf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 173 TFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred CccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 399999999999999999999999999999999999999999999999999875
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.11 E-value=4.1e-11 Score=106.45 Aligned_cols=60 Identities=30% Similarity=0.326 Sum_probs=55.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHH
Q 023291 62 LPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121 (284)
Q Consensus 62 ~~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq 121 (284)
+++.|+.|+..|+..||+.|...+||+...|+.||..+++++..|+|||||||+||++..
T Consensus 60 ~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 60 KRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 344455699999999999999999999999999999999999999999999999999875
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.89 E-value=1.1e-09 Score=105.79 Aligned_cols=62 Identities=31% Similarity=0.567 Sum_probs=56.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHH
Q 023291 62 LPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLE 123 (284)
Q Consensus 62 ~~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~ 123 (284)
.+++|+.|+..|+..||+.|+.++||+...|+.||.++++++..|+|||+|||+|++|..+.
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 44455669999999999999999999999999999999999999999999999999987643
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.84 E-value=2e-09 Score=100.71 Aligned_cols=62 Identities=27% Similarity=0.431 Sum_probs=56.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHH
Q 023291 60 EQLPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121 (284)
Q Consensus 60 ~~~~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq 121 (284)
..+||||+.+-....+.||.+|...++|+.+.+..||.+|.|....|+|||+|.|+|.||..
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 44667777799999999999999999999999999999999999999999999999988854
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.76 E-value=5.2e-09 Score=97.15 Aligned_cols=51 Identities=31% Similarity=0.491 Sum_probs=48.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
|...-...|..+|..++||++.++.+||+.+||+..||-+||+|||+|.|.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 777889999999999999999999999999999999999999999999884
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=98.26 E-value=1.5e-06 Score=60.53 Aligned_cols=45 Identities=64% Similarity=0.933 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHH
Q 023291 120 KQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAK 164 (284)
Q Consensus 120 kq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~ 164 (284)
+|++++|+.|++.|++|.+.|++|.++|+.|++|+..|+++++.+
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl~~k 45 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEKLQMK 45 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 478999999999999999999999999999999999999998753
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=3.9e-07 Score=61.94 Aligned_cols=34 Identities=38% Similarity=0.598 Sum_probs=29.0
Q ss_pred hcCCCCHHHHHHHHHHhCCCCcceeecchhhHHH
Q 023291 83 AENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116 (284)
Q Consensus 83 ~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK 116 (284)
.++||+.+++..||..+||+..||..||-|.|.|
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 4799999999999999999999999999999875
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.21 E-value=5.9e-07 Score=83.30 Aligned_cols=59 Identities=29% Similarity=0.500 Sum_probs=53.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHH
Q 023291 62 LPEKKRRLTAEQVHLLEKSFE---AENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTK 120 (284)
Q Consensus 62 ~~rkRrRfT~~Ql~~LE~~F~---~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krk 120 (284)
.+||||.|+..-.++|..+|- .++||+.+.+++||++++++..||..||.|+|-+.||.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 456777899999999999995 47899999999999999999999999999999998874
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.77 E-value=2.4e-05 Score=78.89 Aligned_cols=55 Identities=22% Similarity=0.300 Sum_probs=49.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHH
Q 023291 63 PEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARW 117 (284)
Q Consensus 63 ~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~ 117 (284)
||-|..||..|.+.|-.+|+.+++|+.+..+.|+.+|+|..+.|.+||-|-|.|.
T Consensus 421 KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 421 KKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3334449999999999999999999999999999999999999999999988764
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.76 E-value=2.5e-05 Score=69.34 Aligned_cols=59 Identities=36% Similarity=0.634 Sum_probs=53.6
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHH
Q 023291 64 EKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQL 122 (284)
Q Consensus 64 rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~ 122 (284)
+.++.++..|+..|...|...++|+...+..|+..+|++++.|++||+|+|++.++...
T Consensus 155 ~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 155 RPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 33445999999999999999999999999999999999999999999999999988653
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.89 E-value=0.00057 Score=74.91 Aligned_cols=61 Identities=26% Similarity=0.439 Sum_probs=56.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHH
Q 023291 62 LPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQL 122 (284)
Q Consensus 62 ~~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~ 122 (284)
++.+|++++..||..|..+|....+|...+.+.|-..+++.++.|++||||-|+|.|+..+
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 5567778999999999999999999999999999999999999999999999999998765
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.21 E-value=0.0043 Score=59.24 Aligned_cols=56 Identities=32% Similarity=0.374 Sum_probs=47.3
Q ss_pred CCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHH
Q 023291 66 KRRLTAEQVHLLEKSFEA---ENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121 (284)
Q Consensus 66 RrRfT~~Ql~~LE~~F~~---~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq 121 (284)
++.|......+|+..... .+||+...+..||.++||+..||.+||-|.|.|..+-.
T Consensus 243 ~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 243 QRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence 335999999999977433 47999999999999999999999999999998866544
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.99 E-value=0.0025 Score=46.48 Aligned_cols=42 Identities=26% Similarity=0.436 Sum_probs=31.4
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHH
Q 023291 74 VHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRA 115 (284)
Q Consensus 74 l~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRa 115 (284)
++.|+++|...+.+.......|..+.+|+..||+.||--|+.
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 567999999999999999999999999999999999976543
No 38
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=94.43 E-value=0.48 Score=44.11 Aligned_cols=45 Identities=24% Similarity=0.434 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHhh
Q 023291 122 LERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKEE 166 (284)
Q Consensus 122 ~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~ee 166 (284)
+..+...|...++.|..-+.+|+.+|+.|++++..+++.|-+-..
T Consensus 102 L~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~~~~~ 146 (292)
T KOG4005|consen 102 LTEENEILQNENDSLRAINESLLAKNHELDSELELLRQELAELKQ 146 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhHH
Confidence 344466777778888888888888888888888888877765543
No 39
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=93.93 E-value=0.19 Score=41.25 Aligned_cols=43 Identities=28% Similarity=0.512 Sum_probs=30.2
Q ss_pred CCCCCCCHHHHH-HHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecch
Q 023291 64 EKKRRLTAEQVH-LLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQ 111 (284)
Q Consensus 64 rkRrRfT~~Ql~-~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQ 111 (284)
++|++||.++.. ++...+. +. ....++|.++|+++.+|..|.+
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~-~g----~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE-PG----MTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc-CC----CCHHHHHHHHCcCHHHHHHHHH
Confidence 456678887744 4444444 22 2467889999999999999964
No 40
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=92.07 E-value=0.11 Score=54.84 Aligned_cols=52 Identities=19% Similarity=0.349 Sum_probs=46.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq 121 (284)
|+.. +..|...|..|..|+.++...+|...||+.+.|+.||++++++....+
T Consensus 564 ~~~p-~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 564 FNHP-TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred cCCc-HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 4444 788999999999999999999999999999999999999999877655
No 41
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=91.39 E-value=0.31 Score=34.73 Aligned_cols=47 Identities=23% Similarity=0.392 Sum_probs=33.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhH
Q 023291 63 PEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRR 114 (284)
Q Consensus 63 ~rkRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRR 114 (284)
+++|+.+|-.+-..+-..++... ....||.++|++..+|..|..|+.
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 35667799988766666676554 588899999999999999998853
No 42
>smart00340 HALZ homeobox associated leucin zipper.
Probab=89.16 E-value=0.75 Score=31.84 Aligned_cols=32 Identities=44% Similarity=0.603 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHH
Q 023291 121 QLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNE 159 (284)
Q Consensus 121 q~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e 159 (284)
|.+-+++.||..++ +|..+|.+|+.|+.+|+.
T Consensus 2 QTEvdCe~LKrcce-------~LteeNrRL~ke~~eLra 33 (44)
T smart00340 2 QTEVDCELLKRCCE-------SLTEENRRLQKEVQELRA 33 (44)
T ss_pred chHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHh
Confidence 56777888886665 456788888888888874
No 43
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=89.06 E-value=2 Score=35.16 Aligned_cols=47 Identities=30% Similarity=0.436 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHhh
Q 023291 120 KQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKEE 166 (284)
Q Consensus 120 kq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~ee 166 (284)
.+++++...+-.....|+..-..+.+||..|+.|+..|++.|...+.
T Consensus 11 ~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 11 DQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35667777788888888888889999999999999999999987765
No 44
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=88.99 E-value=1.2 Score=31.08 Aligned_cols=36 Identities=42% Similarity=0.561 Sum_probs=30.6
Q ss_pred HHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHH
Q 023291 129 LKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAK 164 (284)
Q Consensus 129 Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~ 164 (284)
|-..|+.|++.|++|..+++.|..|+..|+..+..-
T Consensus 3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L 38 (45)
T PF02183_consen 3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQEL 38 (45)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445689999999999999999999999998877643
No 45
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=79.62 E-value=8.3 Score=31.82 Aligned_cols=44 Identities=30% Similarity=0.422 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHH
Q 023291 120 KQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 120 kq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~ 163 (284)
.+++++...+-.....|+..-..+.+||..|+.|+..|++.|..
T Consensus 11 ~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~ 54 (110)
T PRK13169 11 DDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEE 54 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35666777777778888888888999999999999999999884
No 46
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=79.12 E-value=14 Score=28.17 Aligned_cols=41 Identities=27% Similarity=0.382 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHH
Q 023291 121 QLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKI 161 (284)
Q Consensus 121 q~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l 161 (284)
.++.++..|+..+..+...+..|..+|++|+.+....+++|
T Consensus 22 ~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl 62 (72)
T PF06005_consen 22 LLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERL 62 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555666666666666666666666666666655554444
No 47
>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=77.88 E-value=14 Score=28.86 Aligned_cols=49 Identities=27% Similarity=0.285 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHH
Q 023291 116 RWKTKQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAK 164 (284)
Q Consensus 116 K~Krkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~ 164 (284)
+..+..+.++...|+.....|....+.++.++++|+.|+.-|...+..-
T Consensus 15 ~e~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nL 63 (80)
T PF10224_consen 15 KEEKEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNL 63 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566777888888888888889999999999999999988877643
No 48
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=77.53 E-value=22 Score=30.34 Aligned_cols=83 Identities=23% Similarity=0.298 Sum_probs=46.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHh-CCCCcceeecchhhHHHHH-------HHHHHHHHHHHHHhHHHHhh
Q 023291 67 RRLTAEQVHLLEKSFEAENKLEPERKGQLAKKL-GLQPRQVAVWFQNRRARWK-------TKQLERDYDLLKSSYDALLS 138 (284)
Q Consensus 67 rRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~L-gLs~rqVqvWFQNRRaK~K-------rkq~~~~~~~Lk~~~~~l~s 138 (284)
.+|+.++|..+ ...+|=+.| |++...|-.|=|.||+-.- |.++..+...|.+....|..
T Consensus 22 d~lsDd~Lvsm-------------SVReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~q 88 (135)
T KOG4196|consen 22 DRLSDDELVSM-------------SVRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQ 88 (135)
T ss_pred CCcCHHHHHHh-------------hHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46888777665 122333333 7777778888887775321 11222333444444444555
Q ss_pred hhhHHHHhhHHHHHHHHHHHHHHH
Q 023291 139 SYDSLVKENQKLKSEVVSLNEKIE 162 (284)
Q Consensus 139 ~~~sl~~en~~L~~E~~~L~e~l~ 162 (284)
.-+.|..+|.+++.|+.-++.+.+
T Consensus 89 qv~~L~~e~s~~~~E~da~k~k~e 112 (135)
T KOG4196|consen 89 QVEKLKEENSRLRRELDAYKSKYE 112 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 555666666666666666655544
No 49
>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=76.34 E-value=18 Score=26.25 Aligned_cols=37 Identities=30% Similarity=0.364 Sum_probs=23.5
Q ss_pred HHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHH
Q 023291 124 RDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEK 160 (284)
Q Consensus 124 ~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~ 160 (284)
..+..|......|...+..|..++..|..++..|+..
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 3455666666666666666666666666666666544
No 50
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=70.48 E-value=1.5 Score=32.13 Aligned_cols=43 Identities=23% Similarity=0.473 Sum_probs=27.8
Q ss_pred CCCCCCCHHHHHHHHHHH-hhcCCCCHHHHHHHHHHhCCCCcceeecch
Q 023291 64 EKKRRLTAEQVHLLEKSF-EAENKLEPERKGQLAKKLGLQPRQVAVWFQ 111 (284)
Q Consensus 64 rkRrRfT~~Ql~~LE~~F-~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQ 111 (284)
++|++||+++...+-..+ ... .....+|+++||++.++..|-+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHH
Confidence 456779998866665555 332 4788999999999999988874
No 51
>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=69.79 E-value=4.8 Score=28.92 Aligned_cols=37 Identities=24% Similarity=0.300 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHhCCCCcc
Q 023291 69 LTAEQVHLLEKSFEAENK--LEPERKGQLAKKLGLQPRQ 105 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~--P~~~~r~eLA~~LgLs~rq 105 (284)
+|..|..+|...|+.--| |-.....+||.+||+++.-
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st 39 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKST 39 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHH
Confidence 688999999999986543 6677888999999999875
No 52
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=68.50 E-value=19 Score=36.46 Aligned_cols=63 Identities=25% Similarity=0.398 Sum_probs=41.4
Q ss_pred ecc---hhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhHH--------------------------------HHhhHHHHH
Q 023291 108 VWF---QNRRARWKTKQLERDYDLLKSSYDALLSSYDSL--------------------------------VKENQKLKS 152 (284)
Q Consensus 108 vWF---QNRRaK~Krkq~~~~~~~Lk~~~~~l~s~~~sl--------------------------------~~en~~L~~ 152 (284)
+|| ||+.+|.+-.++.++.+.|+..-.+|......| -.+|+.+++
T Consensus 230 cw~ay~Qnk~akehv~km~kdle~Lq~aEqsl~dlQk~Lekar~e~rnvavek~~lerkl~ea~rl~elreg~e~e~~rk 309 (575)
T KOG4403|consen 230 CWFAYRQNKKAKEHVNKMMKDLEGLQRAEQSLEDLQKRLEKAREEQRNVAVEKLDLERKLDEAPRLSELREGVENETSRK 309 (575)
T ss_pred hhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhhhhhhHHHHHhhhhhhhhhhcchhHHHHHH
Confidence 587 888888887777777776665544443322222 135666777
Q ss_pred HHHHHHHHHHHHhhhhhh
Q 023291 153 EVVSLNEKIEAKEEESKE 170 (284)
Q Consensus 153 E~~~L~e~l~~~ee~~~~ 170 (284)
|++.|+.+|.+.|++-+.
T Consensus 310 elE~lR~~L~kAEkele~ 327 (575)
T KOG4403|consen 310 ELEQLRVALEKAEKELEA 327 (575)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 888888888888765543
No 53
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=68.17 E-value=15 Score=30.33 Aligned_cols=43 Identities=30% Similarity=0.404 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHH
Q 023291 121 QLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 121 q~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~ 163 (284)
.++..+..+-+....++..-.+++.||..|+.|+..|+++|..
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 4566666777777778888889999999999999999999876
No 54
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=68.03 E-value=5.5 Score=27.18 Aligned_cols=40 Identities=13% Similarity=0.249 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchh
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQN 112 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQN 112 (284)
.+++.+..+|...|-.. ..-.++|..+|++...|+.+...
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHH
Confidence 47889999999998322 35788999999999887766543
No 55
>smart00338 BRLZ basic region leucin zipper.
Probab=67.93 E-value=34 Score=24.79 Aligned_cols=37 Identities=22% Similarity=0.378 Sum_probs=21.1
Q ss_pred HHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHH
Q 023291 125 DYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKI 161 (284)
Q Consensus 125 ~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l 161 (284)
....|......|...+..|..+...|..|+..|+..+
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445555555555556666666666666666665543
No 56
>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=67.57 E-value=4.9 Score=26.19 Aligned_cols=43 Identities=14% Similarity=0.194 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRA 115 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRa 115 (284)
.+++.+..++...|... ....++|..+|++...|..|...-+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 37788888888777433 24677899999999999888865444
No 57
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=65.58 E-value=36 Score=25.91 Aligned_cols=41 Identities=27% Similarity=0.311 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHH
Q 023291 121 QLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKI 161 (284)
Q Consensus 121 q~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l 161 (284)
+.-..+..|+.....|+..+..+..+|..|+.++..|+...
T Consensus 15 ~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~ 55 (72)
T PF06005_consen 15 QAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQER 55 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 34445666666666666666666667777777777666443
No 58
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=61.58 E-value=5.3 Score=28.25 Aligned_cols=41 Identities=17% Similarity=0.236 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCCCcceeecchhhHHHHHHHHHHHHHHHHHH
Q 023291 91 RKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLERDYDLLKS 131 (284)
Q Consensus 91 ~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~~~Lk~ 131 (284)
....||+.+|++..+|..|+.++..+..-..+.+-...|.-
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 46789999999999999999988666666665555554443
No 59
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=60.92 E-value=37 Score=24.53 Aligned_cols=33 Identities=30% Similarity=0.437 Sum_probs=17.6
Q ss_pred HHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHH
Q 023291 130 KSSYDALLSSYDSLVKENQKLKSEVVSLNEKIE 162 (284)
Q Consensus 130 k~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~ 162 (284)
+.....|......|..+|..|..++..|+..+.
T Consensus 25 k~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~ 57 (64)
T PF00170_consen 25 KQYIEELEEKVEELESENEELKKELEQLKKEIQ 57 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444555555555555555555555555443
No 60
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=59.72 E-value=44 Score=31.30 Aligned_cols=43 Identities=28% Similarity=0.474 Sum_probs=24.0
Q ss_pred HHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHh
Q 023291 123 ERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKE 165 (284)
Q Consensus 123 ~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~e 165 (284)
+..+..+|...+-+..++..|.++++.|.+++..++++|+.-+
T Consensus 134 ke~~ee~kekl~E~~~EkeeL~~eleele~e~ee~~erlk~le 176 (290)
T COG4026 134 KEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLE 176 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455555555555566666666666666666666555433
No 61
>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=57.87 E-value=14 Score=29.56 Aligned_cols=34 Identities=32% Similarity=0.678 Sum_probs=19.2
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHH
Q 023291 74 VHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121 (284)
Q Consensus 74 l~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq 121 (284)
+....-.|..++||.+.--.. |. .|||.+||+.+
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-aR-------------RnRRRRWR~rq 47 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-AR-------------RNRRRRWRARQ 47 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-HH-------------HHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-cc-------------cchhhhHHHHH
Confidence 455566688999997542111 11 58999999865
No 62
>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=57.82 E-value=14 Score=21.32 Aligned_cols=39 Identities=21% Similarity=0.397 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecc
Q 023291 67 RRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWF 110 (284)
Q Consensus 67 rRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWF 110 (284)
+.++..+...+...|... . ...++|..+|++...|..|.
T Consensus 4 ~~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 346777776666666532 2 46688999999888777663
No 63
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=57.59 E-value=45 Score=32.01 Aligned_cols=42 Identities=17% Similarity=0.210 Sum_probs=24.5
Q ss_pred HHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHhh
Q 023291 125 DYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKEE 166 (284)
Q Consensus 125 ~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~ee 166 (284)
+.+.|-.....|...|+.|+.+-..|..|+..||..+.+.-+
T Consensus 249 e~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e~~~ 290 (294)
T KOG4571|consen 249 EKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILEVYK 290 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444445555556666666666666666666666655443
No 64
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=57.07 E-value=12 Score=33.42 Aligned_cols=47 Identities=26% Similarity=0.279 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHhCCCCcceeecchhhHHH
Q 023291 68 RLTAEQVHLLEKSFEAEN--KLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~--~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK 116 (284)
.||..|+++|...|..-= +|-.....+||+++|+++.- .+..=|||.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe 203 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAE 203 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHH
Confidence 599999999999998653 47777888999999999874 444445554
No 65
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=56.71 E-value=3.3 Score=33.24 Aligned_cols=29 Identities=31% Similarity=0.566 Sum_probs=19.5
Q ss_pred CCCCcccchhhhhcCCCcccccCCCC-CccccccC
Q 023291 251 SDDGRSYFSDVLVVAPDHVSNQQHEE-PLGWWVWS 284 (284)
Q Consensus 251 ~d~~~~~~~~~~~~~~~~~~~~~~~~-~~~~w~w~ 284 (284)
--|.| .+|||-.+- +.++++. .+.||.|.
T Consensus 58 ~~DpC--vldvfr~av---~~a~~~~~~~~WW~wt 87 (93)
T PF11731_consen 58 RHDPC--VLDVFRCAV---YFANGPEEKLKWWNWT 87 (93)
T ss_pred cCCcH--HHHHHHHHH---HHHcCCCCCCCCCcCh
Confidence 34567 789888653 2445554 89999994
No 66
>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=55.35 E-value=32 Score=28.11 Aligned_cols=41 Identities=27% Similarity=0.351 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHH
Q 023291 119 TKQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNE 159 (284)
Q Consensus 119 rkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e 159 (284)
-.++..+...||.....|..+|..|.-||++|+..+.++..
T Consensus 17 l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 17 LGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 44667788889999999999999999999999998888776
No 67
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=54.87 E-value=14 Score=31.69 Aligned_cols=48 Identities=19% Similarity=0.172 Sum_probs=36.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 66 KRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 66 RrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
...+|+.|..+|...+ .. ....+||..||++...|..|-++.+.+.|+
T Consensus 4 ~~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4569999999997742 22 246789999999999999999865555443
No 68
>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=53.78 E-value=48 Score=24.21 Aligned_cols=32 Identities=22% Similarity=0.386 Sum_probs=22.2
Q ss_pred hHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHH
Q 023291 132 SYDALLSSYDSLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 132 ~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~ 163 (284)
....+...-..++.+|+.|+.++.++++.+++
T Consensus 8 ~~~~~~~~i~tvk~en~~i~~~ve~i~envk~ 39 (55)
T PF05377_consen 8 ELPRIESSINTVKKENEEISESVEKIEENVKD 39 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444455667778888888888888887643
No 69
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=53.62 E-value=37 Score=31.92 Aligned_cols=22 Identities=32% Similarity=0.552 Sum_probs=11.9
Q ss_pred HHHHhhHHHHHHHHHHHHHHHH
Q 023291 142 SLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 142 sl~~en~~L~~E~~~L~e~l~~ 163 (284)
.|.+||+.|+.+|..|+..|.+
T Consensus 226 ~leken~~lr~~v~~l~~el~~ 247 (269)
T KOG3119|consen 226 ELEKENEALRTQVEQLKKELAT 247 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555556555555554443
No 70
>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=53.17 E-value=18 Score=35.53 Aligned_cols=30 Identities=40% Similarity=0.337 Sum_probs=22.0
Q ss_pred HHHhhhhhHHHHhhHHHHHHHHHHHHHHHH
Q 023291 134 DALLSSYDSLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 134 ~~l~s~~~sl~~en~~L~~E~~~L~e~l~~ 163 (284)
-+|+.++.+|++||..|+.|+.+|++...+
T Consensus 35 ~aLr~EN~~LKkEN~~Lk~eVerLE~e~l~ 64 (420)
T PF07407_consen 35 FALRMENHSLKKENNDLKIEVERLENEMLR 64 (420)
T ss_pred hhHHHHhHHHHHHHHHHHHHHHHHHHHhhh
Confidence 346667777888888888888888776664
No 71
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=52.33 E-value=27 Score=28.25 Aligned_cols=25 Identities=24% Similarity=0.240 Sum_probs=17.0
Q ss_pred HHhhhhhHHHHhhHHHHHHHHHHHH
Q 023291 135 ALLSSYDSLVKENQKLKSEVVSLNE 159 (284)
Q Consensus 135 ~l~s~~~sl~~en~~L~~E~~~L~e 159 (284)
.+...+..+.++|+.|+.|+..|+.
T Consensus 38 ~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 38 AQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3445555667778888888777765
No 72
>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=51.75 E-value=60 Score=29.43 Aligned_cols=40 Identities=18% Similarity=0.250 Sum_probs=25.7
Q ss_pred HHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHh
Q 023291 126 YDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKE 165 (284)
Q Consensus 126 ~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~e 165 (284)
...|......+...+-.+......|+.|+.+|+.+..+.+
T Consensus 177 L~~Le~~W~~~v~kn~eie~a~~~Le~ei~~l~~~~~~~~ 216 (221)
T PF05700_consen 177 LRYLEQRWKELVSKNLEIEVACEELEQEIEQLKRKAAELK 216 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4455555666666666667777777777777776655444
No 73
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=51.65 E-value=41 Score=27.76 Aligned_cols=41 Identities=27% Similarity=0.332 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHH
Q 023291 119 TKQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNE 159 (284)
Q Consensus 119 rkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e 159 (284)
-.++-++...||.....+..+|..|.-||++|+..+.+++.
T Consensus 17 l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~~ 57 (110)
T PRK13169 17 LGVLLKELGALKKQLAELLEENTALRLENDKLRERLEELEA 57 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34667788899999999999999999999999999888743
No 74
>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=48.26 E-value=1.1e+02 Score=24.37 Aligned_cols=47 Identities=36% Similarity=0.475 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhHHH-HhhhhhHHHHhhHHHHHHHHHHHHHHHHHhhh
Q 023291 121 QLERDYDLLKSSYDA-LLSSYDSLVKENQKLKSEVVSLNEKIEAKEEE 167 (284)
Q Consensus 121 q~~~~~~~Lk~~~~~-l~s~~~sl~~en~~L~~E~~~L~e~l~~~ee~ 167 (284)
+.+.....||.+|+. ....-..|..++..|..|+..|+.+|...-++
T Consensus 31 KHE~KV~~LKksYe~rwek~v~~L~~e~~~l~~E~e~L~~~l~~e~~E 78 (87)
T PF12709_consen 31 KHETKVKALKKSYEARWEKKVDELENENKALKRENEQLKKKLDTEREE 78 (87)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345567778877766 34456677778888888888888777655443
No 75
>PRK10884 SH3 domain-containing protein; Provisional
Probab=48.05 E-value=87 Score=28.42 Aligned_cols=38 Identities=13% Similarity=0.076 Sum_probs=18.1
Q ss_pred HHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHH
Q 023291 126 YDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 126 ~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~ 163 (284)
...+......|...+..|.++.+.++.++..|+.++..
T Consensus 127 ~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~ 164 (206)
T PRK10884 127 VAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQLDD 164 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444444455555555555555555544444433
No 76
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=47.38 E-value=22 Score=40.44 Aligned_cols=53 Identities=19% Similarity=0.300 Sum_probs=49.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq 121 (284)
+-..++..|-+.|-.+.-|+.+.+..|......+.+++.+||+|-|.|.++.+
T Consensus 712 ~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 712 ILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 44599999999999999999999999999999999999999999999998876
No 77
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=47.34 E-value=7.4 Score=26.39 Aligned_cols=41 Identities=24% Similarity=0.295 Sum_probs=20.4
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecch
Q 023291 66 KRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQ 111 (284)
Q Consensus 66 RrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQ 111 (284)
.++||..+...++..+... ....+||+.||.++..|..+.+
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ----------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 3468999999999887644 3567799999999888766553
No 78
>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=47.25 E-value=6.6 Score=29.05 Aligned_cols=20 Identities=25% Similarity=0.561 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCCcceeecc
Q 023291 91 RKGQLAKKLGLQPRQVAVWF 110 (284)
Q Consensus 91 ~r~eLA~~LgLs~rqVqvWF 110 (284)
.-.+||.+||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 46679999999999999885
No 79
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=46.67 E-value=1e+02 Score=24.07 Aligned_cols=26 Identities=23% Similarity=0.381 Sum_probs=15.1
Q ss_pred hhhhhHHHHhhHHHHHHHHHHHHHHH
Q 023291 137 LSSYDSLVKENQKLKSEVVSLNEKIE 162 (284)
Q Consensus 137 ~s~~~sl~~en~~L~~E~~~L~e~l~ 162 (284)
.+....|..+|++|+.|...-.++|.
T Consensus 45 ~~~r~~L~~en~qLk~E~~~WqerLr 70 (79)
T PRK15422 45 QHQREELERENNHLKEQQNGWQERLQ 70 (79)
T ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445566677777766655555543
No 80
>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=46.66 E-value=15 Score=25.17 Aligned_cols=41 Identities=17% Similarity=0.229 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRR 114 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRR 114 (284)
+++.+..++.-.|-.. ..-.++|..+|+++..|+.|.+.-|
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 6677777776665433 3578899999999999999986433
No 81
>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion
Probab=45.09 E-value=98 Score=27.52 Aligned_cols=49 Identities=24% Similarity=0.356 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHhhhhh
Q 023291 121 QLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKEEESK 169 (284)
Q Consensus 121 q~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~ee~~~ 169 (284)
.+..-+..|+...+.....|+.|..+.++|..+...+.+.|..++..--
T Consensus 78 ~L~qvN~lLReQLEq~~~~N~~L~~dl~klt~~~~~l~~eL~~ke~~~~ 126 (182)
T PF15035_consen 78 ELAQVNALLREQLEQARKANEALQEDLQKLTQDWERLRDELEQKEAEWR 126 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566777788888888999999999999999999998888875443
No 82
>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=43.72 E-value=20 Score=25.18 Aligned_cols=46 Identities=15% Similarity=0.229 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+||+.++.+|.-...-. ...++|..++++++.|..+..+=+.|..-
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 58899999988776533 47889999999999998888766665443
No 83
>KOG0249 consensus LAR-interacting protein and related proteins [General function prediction only]
Probab=43.43 E-value=1.1e+02 Score=33.28 Aligned_cols=51 Identities=22% Similarity=0.288 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHh
Q 023291 115 ARWKTKQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKE 165 (284)
Q Consensus 115 aK~Krkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~e 165 (284)
|+.++..+.++.+.+|..+..+.-..+.+...++.|+.|+..|++....++
T Consensus 214 Ale~kn~L~~e~~s~kk~l~~~~~~k~rl~~d~E~Lr~e~~qL~~~~~~~~ 264 (916)
T KOG0249|consen 214 ALEDKNRLEQELESVKKQLEEMRHDKDKLRTDIEDLRGELDQLRRSSLEKE 264 (916)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhhh
Confidence 456677788888888988998888899999999999999999987555444
No 84
>PRK10884 SH3 domain-containing protein; Provisional
Probab=43.00 E-value=1.1e+02 Score=27.64 Aligned_cols=29 Identities=31% Similarity=0.423 Sum_probs=15.0
Q ss_pred HHHhhhhhHHHHhhHHHHHHHHHHHHHHH
Q 023291 134 DALLSSYDSLVKENQKLKSEVVSLNEKIE 162 (284)
Q Consensus 134 ~~l~s~~~sl~~en~~L~~E~~~L~e~l~ 162 (284)
.........|.++|++|+.|+..++.++.
T Consensus 128 ~~~~~~~~~L~~~n~~L~~~l~~~~~~~~ 156 (206)
T PRK10884 128 AQSDSVINGLKEENQKLKNQLIVAQKKVD 156 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333444455666666666555555543
No 85
>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=42.87 E-value=1.2e+02 Score=22.87 Aligned_cols=37 Identities=22% Similarity=0.187 Sum_probs=16.3
Q ss_pred HHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHH
Q 023291 124 RDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEK 160 (284)
Q Consensus 124 ~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~ 160 (284)
..++.|-..+..|..+|..|.++...+..|...|.++
T Consensus 7 ~kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ek 43 (65)
T TIGR02449 7 AQVEHLLEYLERLKSENRLLRAQEKTWREERAQLLEK 43 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444444444444444444444444
No 86
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=42.63 E-value=43 Score=26.01 Aligned_cols=26 Identities=23% Similarity=0.495 Sum_probs=19.1
Q ss_pred hHHHHhhHHHHHHHHHHHHHHHHHhh
Q 023291 141 DSLVKENQKLKSEVVSLNEKIEAKEE 166 (284)
Q Consensus 141 ~sl~~en~~L~~E~~~L~e~l~~~ee 166 (284)
+.+.++|.+|+.++.+|+..|+....
T Consensus 3 ~ei~eEn~~Lk~eiqkle~ELq~~~~ 28 (76)
T PF07334_consen 3 HEIQEENARLKEEIQKLEAELQQNKR 28 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35678888888888888777775443
No 87
>PF15058 Speriolin_N: Speriolin N terminus
Probab=41.85 E-value=43 Score=30.43 Aligned_cols=29 Identities=34% Similarity=0.428 Sum_probs=18.8
Q ss_pred hhhhHHHHhhHHHHHHHHHHHHHHHHHhh
Q 023291 138 SSYDSLVKENQKLKSEVVSLNEKIEAKEE 166 (284)
Q Consensus 138 s~~~sl~~en~~L~~E~~~L~e~l~~~ee 166 (284)
...+.|+.||+.|+++|.-++|.+.-|--
T Consensus 12 hqierLv~ENeeLKKlVrLirEN~eLksa 40 (200)
T PF15058_consen 12 HQIERLVRENEELKKLVRLIRENHELKSA 40 (200)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHH
Confidence 33444567777777777777777665543
No 88
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=41.73 E-value=91 Score=30.01 Aligned_cols=36 Identities=28% Similarity=0.411 Sum_probs=25.2
Q ss_pred HHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHH
Q 023291 128 LLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 128 ~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~ 163 (284)
+-++..+++..+-..|.++|++|+.++.+|...++-
T Consensus 245 KkRae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~y 280 (294)
T KOG4571|consen 245 KKRAEKEALLGELEGLEKRNEELKDQASELEREIRY 280 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334556667777777888888888887777766553
No 89
>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=41.57 E-value=29 Score=27.17 Aligned_cols=45 Identities=16% Similarity=0.217 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
+++.+..++...|-. .....+||..+|+++..|+.+...-+.|.|
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 677777776555432 234668999999999999888765544443
No 90
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=41.22 E-value=29 Score=28.77 Aligned_cols=45 Identities=13% Similarity=0.012 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARW 117 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~ 117 (284)
++++.+..+|...|-.. ....+||..+|+++..|+.|...-|.+.
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~L 172 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREAL 172 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 38888888887765422 2466899999999999998887433333
No 91
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=40.63 E-value=34 Score=29.53 Aligned_cols=45 Identities=16% Similarity=0.178 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
+++.+..+|.-.|-.. ..-.+||..||++...|+++...-|.+.|
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence 7888888886655333 35778999999999999888865444444
No 92
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=40.59 E-value=28 Score=28.41 Aligned_cols=46 Identities=13% Similarity=0.177 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
++++.+..++...|-.. ....+||..+|+++..|+.|...-|.+.|
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 37788877776665433 34788999999999999988865444433
No 93
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=40.04 E-value=76 Score=25.64 Aligned_cols=47 Identities=19% Similarity=0.285 Sum_probs=26.1
Q ss_pred ceeecchhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHH
Q 023291 105 QVAVWFQNRRARWKTKQLERDYDLLKSSYDALLSSYDSLVKENQKLKS 152 (284)
Q Consensus 105 qVqvWFQNRRaK~Krkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~ 152 (284)
++..||.+.-- .+-.++++++..+++....+...+..|..+-++|+.
T Consensus 16 ~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 16 QYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 34578865421 112233455555666666666666666666666665
No 94
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=39.92 E-value=1.6e+02 Score=26.89 Aligned_cols=44 Identities=20% Similarity=0.302 Sum_probs=22.1
Q ss_pred HHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHh
Q 023291 122 LERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKE 165 (284)
Q Consensus 122 ~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~e 165 (284)
...+...|...+..+......+...|++|...+..++.++..-+
T Consensus 47 ~~~e~~~L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~ 90 (251)
T PF11932_consen 47 WDDEKQELLAEYRQLEREIENLEVYNEQLERQVASQEQELASLE 90 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444445555555555555555555555555555544444433
No 95
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=39.20 E-value=1.5e+02 Score=29.38 Aligned_cols=48 Identities=23% Similarity=0.320 Sum_probs=33.8
Q ss_pred hHHHHHHHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHH
Q 023291 113 RRARWKTKQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEK 160 (284)
Q Consensus 113 RRaK~Krkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~ 160 (284)
+|.+.+-.++..+.+.||..-+.|+.-...|..+.+.|+.++..|+..
T Consensus 221 ~r~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~~n 268 (365)
T KOG2391|consen 221 RRREEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQKN 268 (365)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHHhh
Confidence 344555556666777777777777777777777777777777777665
No 96
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=38.65 E-value=32 Score=28.40 Aligned_cols=46 Identities=15% Similarity=0.181 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+++.+..+|...|-.. ....+||..+|+++..|+.|...-|.+.|+
T Consensus 126 L~~~~r~i~~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 126 LPVKQREVFLLRYVEG-----LSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCHHHHHHhhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6666666666554322 346789999999999999988755555443
No 97
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=38.07 E-value=38 Score=27.92 Aligned_cols=46 Identities=13% Similarity=0.141 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+++.+..++.-.|-.. ..-.+||..+|+++..|++....-|.+.|+
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6677666666554333 245689999999999999888755555444
No 98
>smart00338 BRLZ basic region leucin zipper.
Probab=37.45 E-value=1.2e+02 Score=21.74 Aligned_cols=32 Identities=28% Similarity=0.458 Sum_probs=19.0
Q ss_pred HhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHH
Q 023291 131 SSYDALLSSYDSLVKENQKLKSEVVSLNEKIE 162 (284)
Q Consensus 131 ~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~ 162 (284)
.....|......|..+|..|..++..|+..+.
T Consensus 26 ~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~ 57 (65)
T smart00338 26 AEIEELERKVEQLEAENERLKKEIERLRRELE 57 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445555666666666666666666655544
No 99
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=37.38 E-value=1e+02 Score=29.09 Aligned_cols=43 Identities=23% Similarity=0.283 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHH
Q 023291 121 QLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 121 q~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~ 163 (284)
.++.++.-|-..+..|..+++.|...|+.|-.++.+|...|..
T Consensus 94 eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~ 136 (292)
T KOG4005|consen 94 EMEYEIKDLTEENEILQNENDSLRAINESLLAKNHELDSELEL 136 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence 3444455555556666666666666666666666666665553
No 100
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.66 E-value=1.3e+02 Score=23.17 Aligned_cols=12 Identities=25% Similarity=0.426 Sum_probs=4.9
Q ss_pred HHHHHHHhHHHH
Q 023291 125 DYDLLKSSYDAL 136 (284)
Q Consensus 125 ~~~~Lk~~~~~l 136 (284)
+++.||..+.+|
T Consensus 26 EieELKEknn~l 37 (79)
T COG3074 26 EIEELKEKNNSL 37 (79)
T ss_pred HHHHHHHHhhHh
Confidence 344444444433
No 101
>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=36.62 E-value=1e+02 Score=28.83 Aligned_cols=42 Identities=31% Similarity=0.432 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHH
Q 023291 114 RARWKTKQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIE 162 (284)
Q Consensus 114 RaK~Krkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~ 162 (284)
|-|.|...++++...++.. ...|..|.+.|++.+.+|-||+.
T Consensus 90 RFR~Rn~ELE~elr~~~~~-------~~~L~~Ev~~L~~DN~kLYEKiR 131 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQT-------ISSLRREVESLRADNVKLYEKIR 131 (248)
T ss_pred HHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455556655555543 34556677777777788888765
No 102
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=36.15 E-value=46 Score=27.42 Aligned_cols=49 Identities=24% Similarity=0.341 Sum_probs=29.3
Q ss_pred cceeecchhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHhhhhhh
Q 023291 104 RQVAVWFQNRRARWKTKQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKEEESKE 170 (284)
Q Consensus 104 rqVqvWFQNRRaK~Krkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~ee~~~~ 170 (284)
||...||-.+|.-..- ......++.+++.|+.|+ .++++|..|..+...
T Consensus 18 Rq~e~~FlqKr~~LS~-----------------~kpe~~lkEEi~eLK~El-qRKe~Ll~Kh~~kI~ 66 (106)
T PF11594_consen 18 RQMEAFFLQKRFELSA-----------------YKPEQVLKEEINELKEEL-QRKEQLLQKHYEKID 66 (106)
T ss_pred HHHHHHHHHHHHHHHh-----------------cCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence 4557999877764311 122335667778888775 555555555555544
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=36.05 E-value=2.1e+02 Score=23.99 Aligned_cols=35 Identities=11% Similarity=-0.021 Sum_probs=20.7
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhh
Q 023291 66 KRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNR 113 (284)
Q Consensus 66 RrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNR 113 (284)
.|.|+..++..|...- ..+.+|++-..|+.++.+.
T Consensus 35 ~R~Y~~~~l~~l~~I~-------------~lr~~G~sL~eI~~~l~~~ 69 (134)
T cd04779 35 YRYYDETALDRLQLIE-------------HLKGQRLSLAEIKDQLEEV 69 (134)
T ss_pred CeeECHHHHHHHHHHH-------------HHHHCCCCHHHHHHHHHhh
Confidence 4559999988885442 2244555555555555443
No 104
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=35.66 E-value=2.7e+02 Score=28.57 Aligned_cols=93 Identities=20% Similarity=0.210 Sum_probs=54.1
Q ss_pred CCCHHHHHHHHHH-Hhh-cCCCCHHHHHHHHHHhCCCCcceeecchhhHHH-HHHHHHHHHHHHHHHhHHHHhhhhhHHH
Q 023291 68 RLTAEQVHLLEKS-FEA-ENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR-WKTKQLERDYDLLKSSYDALLSSYDSLV 144 (284)
Q Consensus 68 RfT~~Ql~~LE~~-F~~-~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK-~Krkq~~~~~~~Lk~~~~~l~s~~~sl~ 144 (284)
++|.+....|.+. +.. ..+|-.+.-+++.++ |+.=.+|+|.+ .+|++++.-++-|-..+..-.+.+.+|.
T Consensus 220 ~LteeEkrLL~kEG~slPs~lPLTKaEEriLKr-------vRRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqeL~ 292 (472)
T KOG0709|consen 220 VLTEEEKRLLTKEGYSLPSKLPLTKAEERILKR-------VRRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQELQ 292 (472)
T ss_pred eccHHHHHHHHhccCcCcccCCchHHHHHHHHH-------HHHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHHHH
Confidence 4888888888766 322 234554444444443 34444555543 2233333334556666666666777777
Q ss_pred HhhHHHHHHHHHHHHHHHHHhhh
Q 023291 145 KENQKLKSEVVSLNEKIEAKEEE 167 (284)
Q Consensus 145 ~en~~L~~E~~~L~e~l~~~ee~ 167 (284)
+..++|..++..|-.+|++-+--
T Consensus 293 kkV~~Le~~N~sLl~qL~klQt~ 315 (472)
T KOG0709|consen 293 KKVEELELSNRSLLAQLKKLQTL 315 (472)
T ss_pred HHHHHHhhccHHHHHHHHHHHHH
Confidence 77777777777777777765533
No 105
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=35.54 E-value=31 Score=25.43 Aligned_cols=44 Identities=27% Similarity=0.445 Sum_probs=23.4
Q ss_pred CCCCCHHH-HHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecch
Q 023291 66 KRRLTAEQ-VHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQ 111 (284)
Q Consensus 66 RrRfT~~Q-l~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQ 111 (284)
|+.|+... |.+++..+.. ..--...|. -|+++|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~-~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKD-NNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH--TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHc-cchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 44576655 5566555543 322223344 49999999999998864
No 106
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=35.28 E-value=41 Score=29.45 Aligned_cols=45 Identities=22% Similarity=0.228 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
+++.+..+|...|-.. ....+||..+|+++..|+++..+-|.+.|
T Consensus 154 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 198 (206)
T PRK12526 154 LPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLK 198 (206)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6677777776544322 35778999999999998877754444433
No 107
>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=35.02 E-value=48 Score=25.51 Aligned_cols=70 Identities=17% Similarity=0.189 Sum_probs=38.9
Q ss_pred HHHHHHHhCCCCcceeecchhhHHHHHHH------HHHHH------HHHHHH-h---HHHHhhhhhHHHHhhHHHHHHHH
Q 023291 92 KGQLAKKLGLQPRQVAVWFQNRRARWKTK------QLERD------YDLLKS-S---YDALLSSYDSLVKENQKLKSEVV 155 (284)
Q Consensus 92 r~eLA~~LgLs~rqVqvWFQNRRaK~Krk------q~~~~------~~~Lk~-~---~~~l~s~~~sl~~en~~L~~E~~ 155 (284)
..++|+.+|++++.|+.|-+..--+-.+. -...+ ...|+. . ...+ ...-.+..+.+.|+.++.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i-~~~l~l~~~~~~l~~~l~ 82 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGV-KRILELEEELAELRAELD 82 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHH-HHHHHHHHHHHHHHHHHH
Confidence 56789999999999999975432221110 01111 222222 1 1111 123346777788888888
Q ss_pred HHHHHHH
Q 023291 156 SLNEKIE 162 (284)
Q Consensus 156 ~L~e~l~ 162 (284)
+|+++|.
T Consensus 83 ~l~~~~~ 89 (91)
T cd04766 83 ELRARLR 89 (91)
T ss_pred HHHHHhc
Confidence 8887765
No 108
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=34.68 E-value=45 Score=28.23 Aligned_cols=46 Identities=17% Similarity=0.119 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+++.+..+|.-.|-.. ..-.+||..+|++...|+.++..-|.+.|.
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 132 LPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 7777777777765433 246789999999999999988765555553
No 109
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=33.97 E-value=1e+02 Score=22.62 Aligned_cols=28 Identities=18% Similarity=0.325 Sum_probs=20.4
Q ss_pred HHhhhhhHHHHhhHHHHHHHHHHHHHHH
Q 023291 135 ALLSSYDSLVKENQKLKSEVVSLNEKIE 162 (284)
Q Consensus 135 ~l~s~~~sl~~en~~L~~E~~~L~e~l~ 162 (284)
.+......+.++++.|+.++.+|+.-|+
T Consensus 30 ~vL~~R~~l~~e~~~L~~qN~eLr~lLk 57 (60)
T PF14775_consen 30 KVLLDRAALIQEKESLEQQNEELRSLLK 57 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444556777888888888888887665
No 110
>PRK00118 putative DNA-binding protein; Validated
Probab=33.62 E-value=46 Score=27.08 Aligned_cols=44 Identities=16% Similarity=0.205 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARW 117 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~ 117 (284)
+++.|..++...|... ....+||..+|+++..|..|...-|.+.
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkL 61 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLL 61 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 6777777776665543 2467899999999999998886544433
No 111
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=33.42 E-value=1.4e+02 Score=27.68 Aligned_cols=43 Identities=23% Similarity=0.414 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhHHHH-hhhhhHHHHhhHHHHHHHHHHHHHHHHH
Q 023291 122 LERDYDLLKSSYDAL-LSSYDSLVKENQKLKSEVVSLNEKIEAK 164 (284)
Q Consensus 122 ~~~~~~~Lk~~~~~l-~s~~~sl~~en~~L~~E~~~L~e~l~~~ 164 (284)
.+.+...++....++ .++...+..||++|+.++++++..|...
T Consensus 99 Q~~~f~kiRsel~S~e~sEF~~lr~e~EklkndlEk~ks~lr~e 142 (220)
T KOG3156|consen 99 QKVDFAKIRSELVSIERSEFANLRAENEKLKNDLEKLKSSLRHE 142 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556666665554 4578888999999999999999888743
No 112
>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=33.26 E-value=46 Score=26.86 Aligned_cols=45 Identities=13% Similarity=0.149 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
++..+..+|.-.|-. .....+||..+|+++..|+.+...-|.|.|
T Consensus 114 L~~~~r~il~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 114 LPEQCRKIFILSRFE-----GKSYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 667777776664432 124677999999999998877764444433
No 113
>PRK14127 cell division protein GpsB; Provisional
Probab=32.88 E-value=1.4e+02 Score=24.54 Aligned_cols=33 Identities=21% Similarity=0.473 Sum_probs=21.5
Q ss_pred HHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHhh
Q 023291 134 DALLSSYDSLVKENQKLKSEVVSLNEKIEAKEE 166 (284)
Q Consensus 134 ~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~ee 166 (284)
+.+...+..+.+++..|+.++.+|+++|..-+.
T Consensus 33 d~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~ 65 (109)
T PRK14127 33 DDVIKDYEAFQKEIEELQQENARLKAQVDELTK 65 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455666667777777777777777665554
No 114
>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.
Probab=32.64 E-value=2.1e+02 Score=21.21 Aligned_cols=41 Identities=24% Similarity=0.357 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHH
Q 023291 122 LERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIE 162 (284)
Q Consensus 122 ~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~ 162 (284)
+..+....+..+-.+...-......|..|..++..|++.+.
T Consensus 16 ~~eEL~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~e 56 (61)
T PF08826_consen 16 IQEELTKVKSANLAFESKLQEAEKRNRELEQEIERLKKEME 56 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555555556667777777777777664
No 115
>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=32.63 E-value=1.4e+02 Score=26.39 Aligned_cols=33 Identities=27% Similarity=0.445 Sum_probs=15.5
Q ss_pred hhhhhHHHHhhHHHHHHHHHHHHHHHHHhhhhh
Q 023291 137 LSSYDSLVKENQKLKSEVVSLNEKIEAKEEESK 169 (284)
Q Consensus 137 ~s~~~sl~~en~~L~~E~~~L~e~l~~~ee~~~ 169 (284)
......|.++|+.|..|+..|..++..=+++..
T Consensus 110 ~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~ 142 (161)
T TIGR02894 110 KNQNESLQKRNEELEKELEKLRQRLSTIEEDYQ 142 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444455555555555554444444443
No 116
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=32.17 E-value=41 Score=28.77 Aligned_cols=45 Identities=22% Similarity=0.315 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
+++.+..+|...|- ......+||..+|++...|++|+..-|.+.|
T Consensus 142 L~~~~~~v~~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 142 LPESQRQVLELAYY-----EGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CCHHHhhhhhhhhh-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 56666666655432 2235778999999999999999865444444
No 117
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=32.16 E-value=89 Score=25.40 Aligned_cols=38 Identities=26% Similarity=0.376 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecch
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQ 111 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQ 111 (284)
+|..|...|+-.|... --..+||..+|++..-|--|.+
T Consensus 18 LT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ik 55 (101)
T PF04297_consen 18 LTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDSIK 55 (101)
T ss_dssp S-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 7889999998777644 3577899999999988888775
No 118
>KOG3650 consensus Predicted coiled-coil protein [General function prediction only]
Probab=32.15 E-value=1.7e+02 Score=24.04 Aligned_cols=39 Identities=36% Similarity=0.364 Sum_probs=29.2
Q ss_pred HHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHH
Q 023291 125 DYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 125 ~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~ 163 (284)
+.-.|+...+.|-...+++++||-+|++|+.-|-..++.
T Consensus 64 QVLELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeN 102 (120)
T KOG3650|consen 64 QVLELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIEN 102 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHH
Confidence 445566777777777888889999999998877666543
No 119
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=32.06 E-value=73 Score=31.20 Aligned_cols=22 Identities=32% Similarity=0.442 Sum_probs=10.8
Q ss_pred HHHHhhHHHHHHHHHHHHHHHH
Q 023291 142 SLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 142 sl~~en~~L~~E~~~L~e~l~~ 163 (284)
.+.+||++|+.|+.+|+.++..
T Consensus 61 ~L~~EN~~Lk~Ena~L~~~l~~ 82 (337)
T PRK14872 61 VLETENFLLKERIALLEERLKS 82 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555555444444
No 120
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=31.62 E-value=54 Score=27.98 Aligned_cols=46 Identities=11% Similarity=0.233 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+++.+..+|.-.|-.. ....+||..+|+++..|++-...-|.+.|+
T Consensus 132 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 132 LSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 7777777776655422 246789999999999998877655554443
No 121
>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=31.39 E-value=49 Score=27.02 Aligned_cols=42 Identities=24% Similarity=0.231 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRA 115 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRa 115 (284)
+++.+..++...|-. .....+||..+|++...|.++...-|.
T Consensus 112 L~~~~r~v~~l~~~~-----g~~~~eIA~~l~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 112 LPERQRELLQLRYQR-----GVSLTALAEQLGRTVNAVYKALSRLRV 153 (159)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 777777777664432 235778999999999999877654333
No 122
>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=31.39 E-value=64 Score=31.79 Aligned_cols=22 Identities=36% Similarity=0.407 Sum_probs=8.9
Q ss_pred HHHHhhHHHHHHHHHHHHHHHH
Q 023291 142 SLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 142 sl~~en~~L~~E~~~L~e~l~~ 163 (284)
.|++||.+|++|+.+|+.++..
T Consensus 36 aLr~EN~~LKkEN~~Lk~eVer 57 (420)
T PF07407_consen 36 ALRMENHSLKKENNDLKIEVER 57 (420)
T ss_pred hHHHHhHHHHHHHHHHHHHHHH
Confidence 3344444444444444443333
No 123
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=31.25 E-value=63 Score=27.18 Aligned_cols=45 Identities=9% Similarity=0.270 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
+++.+..++.-.|-. .....+||..+|+++..|+++...-|.+.|
T Consensus 130 L~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 130 LEKDRAAAVRRAYLE-----GLSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 666666666555422 224778999999999999888765444443
No 124
>PRK04217 hypothetical protein; Provisional
Probab=30.94 E-value=58 Score=26.75 Aligned_cols=44 Identities=16% Similarity=0.117 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK 116 (284)
.++.+|..++...|.... ...+||+.+|++...|...+..-|.+
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkk 85 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKK 85 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 589999888877765432 57789999999999888777544433
No 125
>PRK10072 putative transcriptional regulator; Provisional
Probab=30.80 E-value=33 Score=27.41 Aligned_cols=41 Identities=22% Similarity=0.307 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRA 115 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRa 115 (284)
+.+...+..|...-. . ...+||..+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~g----l---TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTG----L---KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcC----C---CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 346666766644322 1 3778999999999999999988764
No 126
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=30.54 E-value=1.2e+02 Score=22.15 Aligned_cols=20 Identities=40% Similarity=0.572 Sum_probs=10.8
Q ss_pred hhhhHHHHhhHHHHHHHHHH
Q 023291 138 SSYDSLVKENQKLKSEVVSL 157 (284)
Q Consensus 138 s~~~sl~~en~~L~~E~~~L 157 (284)
.....+.++|+.|+.++..|
T Consensus 31 ~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 31 KEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 34444455555566665555
No 127
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=30.47 E-value=51 Score=27.72 Aligned_cols=46 Identities=11% Similarity=0.116 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
++++.+..++...|-. ...-.++|..+|+++..|+++++.-|.+.|
T Consensus 136 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred hCCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3777777777664432 235678999999999999988865444443
No 128
>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=30.41 E-value=1.4e+02 Score=30.55 Aligned_cols=27 Identities=15% Similarity=0.195 Sum_probs=14.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAK 97 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~ 97 (284)
.+++++++.|.-. -..|....|..+|.
T Consensus 41 ~ltpee~kalGie---gDTP~DTlrTlva~ 67 (472)
T TIGR03752 41 ELSPEELKALGIE---GDTPADTLRTLVAE 67 (472)
T ss_pred cCCcchhHhcCCC---CCCccchHHHHHHH
Confidence 4777777666443 34455444544443
No 129
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=30.40 E-value=1.6e+02 Score=27.63 Aligned_cols=47 Identities=26% Similarity=0.284 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHH
Q 023291 114 RARWKTKQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 114 RaK~Krkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~ 163 (284)
|.|.++++.+ ..++....-|..++..|..+.+.|+.|+..|+..+..
T Consensus 208 kSR~~~k~~~---~e~~~r~~~leken~~lr~~v~~l~~el~~~~~~~~~ 254 (269)
T KOG3119|consen 208 KSRDKRKQKE---DEMAHRVAELEKENEALRTQVEQLKKELATLRRLFLQ 254 (269)
T ss_pred HhhhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444444433 3445555667778888888888888888888877554
No 130
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=30.21 E-value=56 Score=27.84 Aligned_cols=43 Identities=23% Similarity=0.185 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK 116 (284)
+++.|..++...|-.. ....+||..+|++...|+.+...-|.+
T Consensus 140 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 140 LPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALAR 182 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 7777877777765433 357889999999999988877543333
No 131
>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
Probab=30.16 E-value=2.6e+02 Score=23.26 Aligned_cols=45 Identities=24% Similarity=0.438 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHH
Q 023291 118 KTKQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIE 162 (284)
Q Consensus 118 Krkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~ 162 (284)
+...++.++..|...|+++...+..-..+.+.|+..+..|++-..
T Consensus 69 ~~~~L~~el~~l~~ry~t~LellGEK~E~veEL~~Dv~DlK~myr 113 (120)
T PF12325_consen 69 EVEELEQELEELQQRYQTLLELLGEKSEEVEELRADVQDLKEMYR 113 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHH
Confidence 333455556666666666666666666666666666666655443
No 132
>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids [].
Probab=30.16 E-value=2e+02 Score=21.90 Aligned_cols=36 Identities=25% Similarity=0.430 Sum_probs=20.9
Q ss_pred HHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHH
Q 023291 127 DLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIE 162 (284)
Q Consensus 127 ~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~ 162 (284)
..++..|..|..+.....+++..|.+.|..|..++.
T Consensus 24 ~~Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~ 59 (70)
T PF04899_consen 24 QEWQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQ 59 (70)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 345555555655555556666666666666655544
No 133
>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=30.10 E-value=18 Score=23.91 Aligned_cols=23 Identities=26% Similarity=0.352 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCCcceeecchhhH
Q 023291 92 KGQLAKKLGLQPRQVAVWFQNRR 114 (284)
Q Consensus 92 r~eLA~~LgLs~rqVqvWFQNRR 114 (284)
..++|+.+|++++.|+.|.++-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 46789999999999999976543
No 134
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=30.03 E-value=53 Score=27.31 Aligned_cols=45 Identities=18% Similarity=0.059 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
+++.+..++.-.|-.. ....+||..+|+++..|++|.+.-|.+.|
T Consensus 109 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr 153 (165)
T PRK09644 109 LPVIEAQAILLCDVHE-----LTYEEAASVLDLKLNTYKSHLFRGRKRLK 153 (165)
T ss_pred CCHHHHHHHHhHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6777777766543222 24678999999999999888865444443
No 135
>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=29.90 E-value=56 Score=27.58 Aligned_cols=40 Identities=20% Similarity=0.158 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchh
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQN 112 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQN 112 (284)
++++.+..+|.-.|-.. ....+||..+|+++..|+++...
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~R 139 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQR 139 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 37777777777665433 24678999999999988777643
No 136
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=29.72 E-value=1.9e+02 Score=22.60 Aligned_cols=12 Identities=33% Similarity=0.421 Sum_probs=5.6
Q ss_pred HHHHHHHHHHHH
Q 023291 149 KLKSEVVSLNEK 160 (284)
Q Consensus 149 ~L~~E~~~L~e~ 160 (284)
.|..++..|++.
T Consensus 50 ~L~~en~qLk~E 61 (79)
T PRK15422 50 ELERENNHLKEQ 61 (79)
T ss_pred HHHHHHHHHHHH
Confidence 344454444443
No 137
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=29.59 E-value=58 Score=27.37 Aligned_cols=45 Identities=24% Similarity=0.249 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
+++.+..++.-.|-.. ..-.+||..||+++..|++....-|.+.|
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLA 179 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 6666666665554332 24678999999999999988865554443
No 138
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=29.34 E-value=54 Score=27.88 Aligned_cols=45 Identities=9% Similarity=0.070 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
+++.+..+|...|-.. ..-.+||..+|++...|+.+...-|.+.|
T Consensus 129 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr 173 (186)
T PRK05602 129 LPERQREAIVLQYYQG-----LSNIEAAAVMDISVDALESLLARGRRALR 173 (186)
T ss_pred CCHHHHHHhhHHHhcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 6677766665544222 24678999999999999888764444443
No 139
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=29.33 E-value=2.2e+02 Score=30.87 Aligned_cols=19 Identities=26% Similarity=0.396 Sum_probs=13.7
Q ss_pred HHHHHHHHHHhCCCCccee
Q 023291 89 PERKGQLAKKLGLQPRQVA 107 (284)
Q Consensus 89 ~~~r~eLA~~LgLs~rqVq 107 (284)
...-..+|+.+||++..|.
T Consensus 487 ~S~a~~iA~~~Glp~~ii~ 505 (782)
T PRK00409 487 KSNAFEIAKRLGLPENIIE 505 (782)
T ss_pred CcHHHHHHHHhCcCHHHHH
Confidence 3345678899999888753
No 140
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.31 E-value=71 Score=25.37 Aligned_cols=42 Identities=12% Similarity=0.243 Sum_probs=31.3
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCC-CCcceeecch
Q 023291 66 KRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGL-QPRQVAVWFQ 111 (284)
Q Consensus 66 RrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgL-s~rqVqvWFQ 111 (284)
+++||.+....+-..+....+ ....||+++|+ ...++..|-+
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 667999887666555554443 57889999996 9988877764
No 141
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=29.15 E-value=72 Score=27.43 Aligned_cols=46 Identities=15% Similarity=0.182 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+++.+..++.-.|-.. ....+||..+|+++..|+++...-|.+.|+
T Consensus 135 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 135 LPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6777777766655332 246789999999999999988654444443
No 142
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=29.06 E-value=57 Score=26.92 Aligned_cols=45 Identities=16% Similarity=0.329 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
++++.+..+|.-.| .. ....+||..+|+++..|+.+...-|.+.|
T Consensus 112 ~L~~~~r~il~l~~-~g-----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr 156 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG-----YSYKEIAEALGIKESSVGTTLARAKKKFR 156 (166)
T ss_pred cCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 37777777777766 32 24678999999999998888754444333
No 143
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=29.06 E-value=2.1e+02 Score=26.94 Aligned_cols=47 Identities=17% Similarity=0.315 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHh
Q 023291 119 TKQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKE 165 (284)
Q Consensus 119 rkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~e 165 (284)
-....++...|......+.+.+..+..+-.+|+.|+.+|.+++.+-.
T Consensus 144 l~E~~~EkeeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~l~ 190 (290)
T COG4026 144 LEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKLP 190 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhch
Confidence 33445555666666666777777777777777778777777766555
No 144
>PRK14760 hypothetical protein; Provisional
Probab=28.98 E-value=23 Score=22.00 Aligned_cols=8 Identities=38% Similarity=1.503 Sum_probs=6.7
Q ss_pred CCCccccc
Q 023291 275 EEPLGWWV 282 (284)
Q Consensus 275 ~~~~~~w~ 282 (284)
+.+||||.
T Consensus 18 gt~~gww~ 25 (26)
T PRK14760 18 GTQFGWWX 25 (26)
T ss_pred cccccccc
Confidence 68899995
No 145
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=28.87 E-value=2e+02 Score=26.57 Aligned_cols=32 Identities=22% Similarity=0.309 Sum_probs=16.1
Q ss_pred hhhhhHHHHhhHHHHHHHHHHHHHHHHHhhhh
Q 023291 137 LSSYDSLVKENQKLKSEVVSLNEKIEAKEEES 168 (284)
Q Consensus 137 ~s~~~sl~~en~~L~~E~~~L~e~l~~~ee~~ 168 (284)
.+.++.+..+.+.|+.|+++...+|++.+++.
T Consensus 150 ~~~~~~~~~~~~kL~~el~~~~~~Le~~~~~~ 181 (216)
T KOG1962|consen 150 EEENDKLKADLEKLETELEKKQKKLEKAQKKV 181 (216)
T ss_pred hhhHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555555555555444433
No 146
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=28.76 E-value=95 Score=28.15 Aligned_cols=38 Identities=32% Similarity=0.500 Sum_probs=31.5
Q ss_pred HHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHhhh
Q 023291 130 KSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKEEE 167 (284)
Q Consensus 130 k~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~ee~ 167 (284)
-..|+.|+..++++..+|++|+.++.+|...+......
T Consensus 111 E~d~~~Lk~~~~~l~~~~~~Lq~e~~eL~~~~~~~~~~ 148 (198)
T KOG0483|consen 111 EKDYESLKRQLESLRSENDRLQSEVQELVAELSSLKRE 148 (198)
T ss_pred hhhHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhh
Confidence 33488899999999999999999999998887765543
No 147
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=28.59 E-value=55 Score=21.46 Aligned_cols=40 Identities=23% Similarity=0.334 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhh
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNR 113 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNR 113 (284)
.++..+...+...+. . ....++|..+|++...|..|.+.-
T Consensus 3 ~l~~~e~~i~~~~~~--g----~s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPREREVLRLLAE--G----LTNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 367888887765432 2 246889999999999988777643
No 148
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=28.41 E-value=1.4e+02 Score=23.58 Aligned_cols=37 Identities=32% Similarity=0.465 Sum_probs=30.9
Q ss_pred HHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHH
Q 023291 123 ERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNE 159 (284)
Q Consensus 123 ~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e 159 (284)
.++|..+-+..+.|.+.-+.|.+.|++|..++.+|-+
T Consensus 25 ~~E~~~ins~LD~Lns~LD~LE~rnD~l~~~L~~LLe 61 (83)
T PF03670_consen 25 EEEYAAINSMLDQLNSCLDHLEQRNDHLHAQLQELLE 61 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence 4578888888899999999999999999988777643
No 149
>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=28.26 E-value=15 Score=28.12 Aligned_cols=33 Identities=12% Similarity=0.185 Sum_probs=24.6
Q ss_pred HHhhcCCCCHHHHHHHHHHhCCCCcceeecchh
Q 023291 80 SFEAENKLEPERKGQLAKKLGLQPRQVAVWFQN 112 (284)
Q Consensus 80 ~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQN 112 (284)
.|.-..+.......+||..+|+++..|+.|+.+
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 344444444456889999999999999999864
No 150
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=27.42 E-value=1.4e+02 Score=27.51 Aligned_cols=39 Identities=23% Similarity=0.297 Sum_probs=17.3
Q ss_pred HHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHH
Q 023291 122 LERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEK 160 (284)
Q Consensus 122 ~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~ 160 (284)
++.+.+......+........++++-+.+..|..+|.|+
T Consensus 163 L~~el~~~~~~Le~~~~~~~al~Kq~e~~~~EydrLlee 201 (216)
T KOG1962|consen 163 LETELEKKQKKLEKAQKKVDALKKQSEGLQDEYDRLLEE 201 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHH
Confidence 333333333334444444444444444444444444443
No 151
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=27.32 E-value=63 Score=27.70 Aligned_cols=46 Identities=20% Similarity=0.315 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+++.+..++.-.|-.. ....+||..+|++...|++..+.-|.+.|+
T Consensus 132 L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 132 LEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 7777777776554322 246789999999999887776644444444
No 152
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=27.13 E-value=2.8e+02 Score=24.73 Aligned_cols=19 Identities=21% Similarity=0.457 Sum_probs=10.4
Q ss_pred hHHHHHHHHHHHHHHHHHh
Q 023291 147 NQKLKSEVVSLNEKIEAKE 165 (284)
Q Consensus 147 n~~L~~E~~~L~e~l~~~e 165 (284)
.+.++.++.+|+.+|+..+
T Consensus 155 ~~e~~~~l~~l~~ei~~~~ 173 (176)
T PF12999_consen 155 REELEKKLEELEKEIQAAK 173 (176)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 4455555556666555544
No 153
>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=27.05 E-value=26 Score=25.42 Aligned_cols=27 Identities=26% Similarity=0.603 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 91 RKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 91 ~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
...+||..||++.+.|..|-+ |-+|..
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 467899999999999999975 444443
No 154
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=27.02 E-value=3.3e+02 Score=23.87 Aligned_cols=45 Identities=24% Similarity=0.250 Sum_probs=35.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchh
Q 023291 66 KRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQN 112 (284)
Q Consensus 66 RrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQN 112 (284)
+..+|++++..+.+.-. .-|..-.+..||+++|+++.-|.+=..-
T Consensus 83 ~y~Lt~e~i~Eir~LR~--~DP~~wTr~~LAkkF~~S~~fV~~v~~~ 127 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRA--EDPEKWTRKKLAKKFNCSPLFVSMVAPA 127 (164)
T ss_pred cccCCHHHHHHHHHHHH--cCchHhhHHHHHHHhCCCHHHHHHhcCC
Confidence 34599999999988865 4466778999999999998877655543
No 155
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=26.96 E-value=58 Score=26.90 Aligned_cols=45 Identities=20% Similarity=0.105 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
+++.|..+|.-.|-.. ....+||..+|+++..|+.+...-|.+.|
T Consensus 113 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 113 LPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6777766666654322 24678999999999998887764444433
No 156
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=26.91 E-value=80 Score=26.80 Aligned_cols=44 Identities=14% Similarity=0.290 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARW 117 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~ 117 (284)
+++.+..++...|-.. ....+||..+|++...|+++...-|.+.
T Consensus 134 L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~L 177 (182)
T PRK12537 134 LEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSLKAL 177 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHHHHH
Confidence 6777776666655322 2467899999999999988876444433
No 157
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=26.88 E-value=1.8e+02 Score=29.93 Aligned_cols=44 Identities=18% Similarity=0.347 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHH
Q 023291 118 KTKQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKI 161 (284)
Q Consensus 118 Krkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l 161 (284)
|...++++++.|+...+-+......+...-+.|..|+..|+.++
T Consensus 77 kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql 120 (475)
T PRK13729 77 TAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQV 120 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 44455666666665555444444455555566777777777776
No 158
>PF13518 HTH_28: Helix-turn-helix domain
Probab=26.56 E-value=30 Score=23.10 Aligned_cols=22 Identities=18% Similarity=0.525 Sum_probs=19.1
Q ss_pred HHHHHHHHhCCCCcceeecchh
Q 023291 91 RKGQLAKKLGLQPRQVAVWFQN 112 (284)
Q Consensus 91 ~r~eLA~~LgLs~rqVqvWFQN 112 (284)
...++|.++|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 4667999999999999999864
No 159
>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=26.41 E-value=43 Score=23.88 Aligned_cols=33 Identities=30% Similarity=0.427 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCccee
Q 023291 71 AEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVA 107 (284)
Q Consensus 71 ~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVq 107 (284)
..|+..|+-.+. +...+ ..+||..+|++++.|+
T Consensus 5 ~rq~~Ll~~L~~-~~~~~---~~ela~~l~~S~rti~ 37 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWIT---LKELAKKLNISERTIK 37 (59)
T ss_dssp HHHHHHHHHHHH-HTSBB---HHHHHHHCTS-HHHHH
T ss_pred HHHHHHHHHHHc-CCCCc---HHHHHHHHCCCHHHHH
Confidence 357888888888 66664 4489999999987654
No 160
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=26.38 E-value=54 Score=27.63 Aligned_cols=43 Identities=14% Similarity=0.047 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK 116 (284)
+++.+..++.-.| .....-.+||..+|+++..|+++...-|.+
T Consensus 139 L~~~~r~v~~l~~-----~~~~s~~EIA~~lgis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 139 LPEDLRTAITLRE-----LEGLSYEDIARIMDCPVGTVRSRIFRAREA 181 (190)
T ss_pred CCHHHhhhhhhhh-----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 5555555554433 222356789999999999998887544433
No 161
>PF03954 Lectin_N: Hepatic lectin, N-terminal domain; InterPro: IPR005640 Animal lectins display a wide variety of architectures. They are classified according to the carbohydrate-recognition domain (CRD) of which there are two main types, S-type and C-type. C-type lectins display a wide range of specificities. They require Ca2+ for their activity They are found predominantly but not exclusively in vertebrates. This entry presents N-terminal domain, which is found in C-type lectins.; GO: 0005529 sugar binding, 0016020 membrane
Probab=26.26 E-value=1.2e+02 Score=26.18 Aligned_cols=49 Identities=29% Similarity=0.504 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHhHH----HHhhhhhHHHHhhHHHHHHHHHHHHHHHHHhhhh
Q 023291 120 KQLERDYDLLKSSYD----ALLSSYDSLVKENQKLKSEVVSLNEKIEAKEEES 168 (284)
Q Consensus 120 kq~~~~~~~Lk~~~~----~l~s~~~sl~~en~~L~~E~~~L~e~l~~~ee~~ 168 (284)
.+++++...|++.+. ...++..+|......+...+..|+.++++++.+-
T Consensus 58 ~qlq~dl~tLretfsNFssst~aEvqaL~S~G~sl~~kVtSLea~lEkqqQeL 110 (138)
T PF03954_consen 58 SQLQRDLRTLRETFSNFSSSTLAEVQALSSQGGSLQDKVTSLEAKLEKQQQEL 110 (138)
T ss_pred HHHHHHHHHHHHHHhcccHHHHHHHHHHHhccccHHhHcccHHHHHHHHHHHH
Confidence 456677788887776 4556666777777778888888888887776543
No 162
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=26.14 E-value=78 Score=28.63 Aligned_cols=46 Identities=15% Similarity=0.232 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
++..|..+|.-.|-.. ....+||..||+++..|++....-|.+.|+
T Consensus 172 Lp~~~R~v~~L~~~eg-----~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 172 LPEQQRIAVILSYHEN-----MSNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5666666655544322 246789999999999998888655554443
No 163
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=26.11 E-value=1.5e+02 Score=28.88 Aligned_cols=14 Identities=14% Similarity=0.503 Sum_probs=10.9
Q ss_pred eeecchhhHHHHHH
Q 023291 106 VAVWFQNRRARWKT 119 (284)
Q Consensus 106 VqvWFQNRRaK~Kr 119 (284)
+++||+|.|+-.+-
T Consensus 16 CKiWi~dN~~Sv~~ 29 (336)
T KOG0150|consen 16 CKIWIKDNPASVRF 29 (336)
T ss_pred hhhhhcCChHHHHh
Confidence 47999999886553
No 164
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=26.04 E-value=78 Score=25.87 Aligned_cols=44 Identities=14% Similarity=0.115 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK 116 (284)
++++.+..++.-.|-.. ..-.+||..||+++..|++....-|.+
T Consensus 106 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 106 KLPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRATHA 149 (161)
T ss_pred hCCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 37777777777655332 236789999999999988776543333
No 165
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=25.82 E-value=81 Score=26.25 Aligned_cols=45 Identities=9% Similarity=0.113 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
++..+..++...|-.. ....++|..||+++..|+++...-|.+.|
T Consensus 120 L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLK 164 (169)
T ss_pred CCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 7777777776655333 24678999999999998877654444433
No 166
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=25.72 E-value=3.3e+02 Score=28.49 Aligned_cols=40 Identities=28% Similarity=0.398 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHH
Q 023291 120 KQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNE 159 (284)
Q Consensus 120 kq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e 159 (284)
.+++.++..++..+..+..+...|+++|.+|..++..++.
T Consensus 151 ~~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~r~ 190 (546)
T KOG0977|consen 151 SELEAEINTLKRRIKALEDELKRLKAENSRLREELARARK 190 (546)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence 3455666667777777777777777777777766666653
No 167
>PRK14127 cell division protein GpsB; Provisional
Probab=25.57 E-value=1.7e+02 Score=24.04 Aligned_cols=36 Identities=25% Similarity=0.439 Sum_probs=27.1
Q ss_pred HHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHH
Q 023291 128 LLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 128 ~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~ 163 (284)
..-..|+.+..++..|..++.+|+.++.+++.++..
T Consensus 34 ~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~~ 69 (109)
T PRK14127 34 DVIKDYEAFQKEIEELQQENARLKAQVDELTKQVSV 69 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 344455666677788888999999999888887773
No 168
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=25.56 E-value=1.8e+02 Score=29.83 Aligned_cols=73 Identities=26% Similarity=0.283 Sum_probs=39.2
Q ss_pred CCHHHHHHHHHH-------hCCCCcceeecchhhHHHHHHHHHHHHHHHH-HHhHHHHhhhhhHHHHhhHHHHHHHHHHH
Q 023291 87 LEPERKGQLAKK-------LGLQPRQVAVWFQNRRARWKTKQLERDYDLL-KSSYDALLSSYDSLVKENQKLKSEVVSLN 158 (284)
Q Consensus 87 P~~~~r~eLA~~-------LgLs~rqVqvWFQNRRaK~Krkq~~~~~~~L-k~~~~~l~s~~~sl~~en~~L~~E~~~L~ 158 (284)
++.+++..|.++ |-|+.++=++-=+= |.|-|+|+..++-.+- |...+.|..-+..-.++|+.|++.|.+|+
T Consensus 221 LteeEkrLL~kEG~slPs~lPLTKaEEriLKrv-RRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqeL~kkV~~Le 299 (472)
T KOG0709|consen 221 LTEEEKRLLTKEGYSLPSKLPLTKAEERILKRV-RRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQELQKKVEELE 299 (472)
T ss_pred ccHHHHHHHHhccCcCcccCCchHHHHHHHHHH-HHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHHHHHHHHHHh
Confidence 455555555543 23444443333332 3344444444443333 33445566677777788888888877775
Q ss_pred HH
Q 023291 159 EK 160 (284)
Q Consensus 159 e~ 160 (284)
..
T Consensus 300 ~~ 301 (472)
T KOG0709|consen 300 LS 301 (472)
T ss_pred hc
Confidence 43
No 169
>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=25.55 E-value=3.3e+02 Score=24.85 Aligned_cols=51 Identities=24% Similarity=0.346 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHhhhhh
Q 023291 119 TKQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKEEESK 169 (284)
Q Consensus 119 rkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~ee~~~ 169 (284)
+..+..++..|....+.|..-+..+......++.++.+|+.++..-++...
T Consensus 51 ~~~L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~qi~~~~~~~~ 101 (251)
T PF11932_consen 51 KQELLAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQIEQIEETRQ 101 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555666666666666666666666666666666666666665554433
No 170
>PF11544 Spc42p: Spindle pole body component Spc42p; InterPro: IPR021611 Spc42p is a 42kDa component of the S.cerevisiae spindle body that localises to the electron dense central region of the SPB. Spc42p is a phosphoprotein which forms a polymeric layer at the periphery of the SPB central plaque. This functions during SPB duplication and also facilitates the attachment of the SPB to the nuclear membrane. ; PDB: 2Q6Q_B.
Probab=25.39 E-value=3.3e+02 Score=21.20 Aligned_cols=50 Identities=20% Similarity=0.266 Sum_probs=36.7
Q ss_pred hhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHH
Q 023291 111 QNRRARWKTKQLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEK 160 (284)
Q Consensus 111 QNRRaK~Krkq~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~ 160 (284)
||+--+.+-...+.+++.|.....+|...-.....-|.+|..+...++..
T Consensus 6 qNk~L~~kL~~K~eEI~rLn~lv~sLR~KLiKYt~LnkkLq~~~~~~~~~ 55 (76)
T PF11544_consen 6 QNKELKKKLNDKQEEIDRLNILVGSLRGKLIKYTELNKKLQDQLLNLQRS 55 (76)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 46655666666778888899888888877777777777787776666553
No 171
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=25.26 E-value=1.8e+02 Score=23.07 Aligned_cols=18 Identities=39% Similarity=0.503 Sum_probs=8.8
Q ss_pred HHHhhHHHHHHHHHHHHH
Q 023291 143 LVKENQKLKSEVVSLNEK 160 (284)
Q Consensus 143 l~~en~~L~~E~~~L~e~ 160 (284)
|.++|+.|+.|..-.+..
T Consensus 35 L~~en~qlk~Ek~~~~~q 52 (87)
T PF10883_consen 35 LQKENEQLKTEKAVAETQ 52 (87)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 445565555554433333
No 172
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=25.11 E-value=41 Score=22.65 Aligned_cols=38 Identities=18% Similarity=0.394 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecc
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWF 110 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWF 110 (284)
.++.+++..+...+... ....+||+.+|++...|..++
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 47777777777777655 247889999999988776554
No 173
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=25.11 E-value=1.2e+02 Score=25.56 Aligned_cols=46 Identities=9% Similarity=0.107 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+++.+..++.-.|-.. ....+||..||++...|++....-|++.|+
T Consensus 118 Lp~~~r~i~~l~~~e~-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 118 LPYKLRQVIILRYLHD-----YSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6666666665544322 246789999999999888777655554443
No 174
>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=24.80 E-value=1.7e+02 Score=27.62 Aligned_cols=15 Identities=40% Similarity=0.468 Sum_probs=6.7
Q ss_pred HHHhhHHHHHHHHHH
Q 023291 143 LVKENQKLKSEVVSL 157 (284)
Q Consensus 143 l~~en~~L~~E~~~L 157 (284)
+.+||++|+.|+.+|
T Consensus 71 l~~EN~~Lr~e~~~l 85 (283)
T TIGR00219 71 LEYENYKLRQELLKK 85 (283)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344444444444444
No 175
>PRK06930 positive control sigma-like factor; Validated
Probab=24.78 E-value=93 Score=27.12 Aligned_cols=47 Identities=11% Similarity=0.060 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
.+++.+..++.-.|-.. ..-.++|..+|+++..|+.+...-|.|.++
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 37888888777655333 246789999999999999998766555554
No 176
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=24.73 E-value=3e+02 Score=26.42 Aligned_cols=44 Identities=30% Similarity=0.496 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHh
Q 023291 122 LERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKE 165 (284)
Q Consensus 122 ~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~e 165 (284)
...+...|+.....+......+.++.+.|..|+..|++.+...+
T Consensus 48 ~~~el~~le~Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~ 91 (314)
T PF04111_consen 48 LEEELEKLEQEEEELLQELEELEKEREELDQELEELEEELEELD 91 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444445555555555555666666666666666655554444
No 177
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=24.61 E-value=79 Score=26.00 Aligned_cols=46 Identities=22% Similarity=0.274 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+++.+..+|...|-.. ..-.+||..+|++...|+++-..-|.+.|+
T Consensus 111 L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 111 LPARQRAVVVLRYYED-----LSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CCHHHHHHhhhHHHhc-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 6677777776655322 246789999999999999887655555443
No 178
>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=24.51 E-value=78 Score=20.89 Aligned_cols=36 Identities=19% Similarity=0.321 Sum_probs=25.5
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecch
Q 023291 70 TAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQ 111 (284)
Q Consensus 70 T~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQ 111 (284)
+..+...+...+ .. ....++|..+++++..|+.|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 456666665543 12 2567899999999999888875
No 179
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=24.51 E-value=2.2e+02 Score=28.15 Aligned_cols=40 Identities=18% Similarity=0.262 Sum_probs=19.5
Q ss_pred HHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHH
Q 023291 123 ERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIE 162 (284)
Q Consensus 123 ~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~ 162 (284)
...+..+......+......+..+..+++.|+.++++++.
T Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 (398)
T PTZ00454 21 YEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVK 60 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333334444444444455555555555555555555544
No 180
>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=24.19 E-value=1.1e+02 Score=24.17 Aligned_cols=36 Identities=17% Similarity=0.133 Sum_probs=22.7
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchh
Q 023291 65 KKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQN 112 (284)
Q Consensus 65 kRrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQN 112 (284)
.+|+||..++..|... ..|.+.+|++-..|+.+..+
T Consensus 35 g~R~Yt~~di~~l~~I------------~~llr~~G~~l~~i~~~l~~ 70 (99)
T cd04765 35 GRRYYRPKDVELLLLI------------KHLLYEKGYTIEGAKQALKE 70 (99)
T ss_pred CCeeeCHHHHHHHHHH------------HHHHHHCCCCHHHHHHHHHh
Confidence 3556999999888543 23445666666666555543
No 181
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=24.18 E-value=1.7e+02 Score=26.96 Aligned_cols=19 Identities=37% Similarity=0.641 Sum_probs=8.1
Q ss_pred HHHHhhHHHHHHHHHHHHH
Q 023291 142 SLVKENQKLKSEVVSLNEK 160 (284)
Q Consensus 142 sl~~en~~L~~E~~~L~e~ 160 (284)
.+.+||++|++|+.+|+..
T Consensus 73 ~l~~en~~L~~e~~~l~~~ 91 (276)
T PRK13922 73 DLREENEELKKELLELESR 91 (276)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444433
No 182
>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=24.11 E-value=26 Score=32.55 Aligned_cols=33 Identities=30% Similarity=0.388 Sum_probs=0.0
Q ss_pred HHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHH
Q 023291 125 DYDLLKSSYDALLSSYDSLVKENQKLKSEVVSL 157 (284)
Q Consensus 125 ~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L 157 (284)
.+.-|+...+.|.+.+..|.+||++|++|+.+|
T Consensus 130 ~I~dLrrlVe~L~aeNErLr~EnkqL~ae~arL 162 (243)
T PF08961_consen 130 KIADLRRLVEFLLAENERLRRENKQLKAENARL 162 (243)
T ss_dssp ---------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355666666666677777777777777776665
No 183
>KOG1853 consensus LIS1-interacting protein NUDE [Cytoskeleton]
Probab=24.07 E-value=1.6e+02 Score=28.14 Aligned_cols=22 Identities=18% Similarity=0.264 Sum_probs=10.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHHh
Q 023291 111 QNRRARWKTKQLERDYDLLKSS 132 (284)
Q Consensus 111 QNRRaK~Krkq~~~~~~~Lk~~ 132 (284)
+||-..-+.+++.-+...+|..
T Consensus 60 rnrdl~t~nqrl~~E~e~~Kek 81 (333)
T KOG1853|consen 60 RNRDLETRNQRLTTEQERNKEK 81 (333)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4554444444444444444443
No 184
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=23.88 E-value=23 Score=37.35 Aligned_cols=44 Identities=14% Similarity=0.113 Sum_probs=28.4
Q ss_pred HHHHhhcCCCCHHHHHHHHHHhC-------CCCcceeecchhhHHHHHHHH
Q 023291 78 EKSFEAENKLEPERKGQLAKKLG-------LQPRQVAVWFQNRRARWKTKQ 121 (284)
Q Consensus 78 E~~F~~~~~P~~~~r~eLA~~Lg-------Ls~rqVqvWFQNRRaK~Krkq 121 (284)
+..|-.++.+......+--.++. ...+-|+.||.|||+++|+.+
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 44456666666554444333332 346679999999999988754
No 185
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=23.86 E-value=1.6e+02 Score=30.97 Aligned_cols=30 Identities=27% Similarity=0.436 Sum_probs=19.2
Q ss_pred HhhhhhHHHHhhHHHHHHHHHHHHHHHHHh
Q 023291 136 LLSSYDSLVKENQKLKSEVVSLNEKIEAKE 165 (284)
Q Consensus 136 l~s~~~sl~~en~~L~~E~~~L~e~l~~~e 165 (284)
|.+.-..+.+||+.|++|+..|+.+|..-+
T Consensus 307 Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~ 336 (655)
T KOG4343|consen 307 LEARLQALLSENEQLKKENATLKRQLDELV 336 (655)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHh
Confidence 444445666777777777777777765433
No 186
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=23.76 E-value=90 Score=25.67 Aligned_cols=42 Identities=21% Similarity=0.260 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRA 115 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRa 115 (284)
+++.+..+|.-.|-.. ....++|..+|++...|+.....-|.
T Consensus 110 L~~~~r~v~~l~~~~~-----~s~~EIA~~lgis~~tV~~~l~ra~~ 151 (163)
T PRK07037 110 LPARTRYAFEMYRLHG-----ETQKDIARELGVSPTLVNFMIRDALV 151 (163)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6777777776554322 24678999999999999876543333
No 187
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=23.72 E-value=83 Score=26.95 Aligned_cols=41 Identities=22% Similarity=0.190 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRR 114 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRR 114 (284)
+++.+..+|...|-.. ....+||..+|+++..|+..+..-|
T Consensus 107 L~~~~r~i~~l~~~~g-----~~~~EIA~~lgis~~tV~~~l~Rar 147 (181)
T PRK09637 107 LPEKYAEALRLTELEG-----LSQKEIAEKLGLSLSGAKSRVQRGR 147 (181)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 6777766665554322 2467899999999998877775333
No 188
>PHA02955 hypothetical protein; Provisional
Probab=23.72 E-value=1e+02 Score=28.34 Aligned_cols=42 Identities=10% Similarity=0.207 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHhhc-CCCCHHHHHHHHHHhCCCCcceeecchh
Q 023291 71 AEQVHLLEKSFEAE-NKLEPERKGQLAKKLGLQPRQVAVWFQN 112 (284)
Q Consensus 71 ~~Ql~~LE~~F~~~-~~P~~~~r~eLA~~LgLs~rqVqvWFQN 112 (284)
..|+..|-+.|... ..+.+++|.++|++||+....|..||.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 45677777777665 6688899999999999999878888875
No 189
>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=23.72 E-value=4.2e+02 Score=28.72 Aligned_cols=20 Identities=10% Similarity=0.147 Sum_probs=14.4
Q ss_pred CHHHHHHHHHHhCCCCccee
Q 023291 88 EPERKGQLAKKLGLQPRQVA 107 (284)
Q Consensus 88 ~~~~r~eLA~~LgLs~rqVq 107 (284)
....-..+|+.+||++..|.
T Consensus 481 g~S~a~~iA~~~Glp~~ii~ 500 (771)
T TIGR01069 481 GESYAFEIAQRYGIPHFIIE 500 (771)
T ss_pred CCcHHHHHHHHhCcCHHHHH
Confidence 33455678999999988753
No 190
>PRK10403 transcriptional regulator NarP; Provisional
Probab=23.58 E-value=53 Score=27.06 Aligned_cols=46 Identities=20% Similarity=0.256 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
.+|..+..+|...... ..+.+||..++++++.|++..+|=|.|-..
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 3899999888766542 346789999999999998888876666443
No 191
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=23.51 E-value=3.2e+02 Score=20.48 Aligned_cols=19 Identities=42% Similarity=0.571 Sum_probs=9.9
Q ss_pred HHhhHHHHHHHHHHHHHHH
Q 023291 144 VKENQKLKSEVVSLNEKIE 162 (284)
Q Consensus 144 ~~en~~L~~E~~~L~e~l~ 162 (284)
-.++.+|+.|+..|+..|.
T Consensus 46 ~~e~~~Lk~E~e~L~~el~ 64 (69)
T PF14197_consen 46 YEENNKLKEENEALRKELE 64 (69)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3445555555555555544
No 192
>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=23.39 E-value=1.7e+02 Score=27.67 Aligned_cols=41 Identities=27% Similarity=0.175 Sum_probs=21.2
Q ss_pred HHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHh
Q 023291 122 LERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEAKE 165 (284)
Q Consensus 122 ~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~e 165 (284)
+.++++.|+.....+. ..+....+.|+.|+.+|++.|.-++
T Consensus 71 l~~EN~~Lr~e~~~l~---~~~~~~~~~l~~EN~rLr~LL~~~~ 111 (283)
T TIGR00219 71 LEYENYKLRQELLKKN---QQLEILTQNLKQENVRLRELLNSPL 111 (283)
T ss_pred HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHhcCcc
Confidence 4455555554443331 1222223347777777777766554
No 193
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=23.36 E-value=26 Score=23.52 Aligned_cols=23 Identities=26% Similarity=0.478 Sum_probs=17.4
Q ss_pred HHHHHHHHHhCCCCcceeecchh
Q 023291 90 ERKGQLAKKLGLQPRQVAVWFQN 112 (284)
Q Consensus 90 ~~r~eLA~~LgLs~rqVqvWFQN 112 (284)
....++|..+|++...|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 35788999999999999999753
No 194
>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=23.14 E-value=1e+02 Score=27.26 Aligned_cols=30 Identities=27% Similarity=0.392 Sum_probs=7.7
Q ss_pred hhhhHHHHhhHHHHHHHHHHHHHHHHHhhh
Q 023291 138 SSYDSLVKENQKLKSEVVSLNEKIEAKEEE 167 (284)
Q Consensus 138 s~~~sl~~en~~L~~E~~~L~e~l~~~ee~ 167 (284)
.+.+.|..++|+|+.|+..|+..|..+++.
T Consensus 24 dEKE~L~~~~QRLkDE~RDLKqEl~V~ek~ 53 (166)
T PF04880_consen 24 DEKENLREEVQRLKDELRDLKQELIVQEKL 53 (166)
T ss_dssp HHHHHHHHCH--------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456778889999999999998888555543
No 195
>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=23.09 E-value=2.8e+02 Score=20.23 Aligned_cols=37 Identities=19% Similarity=0.349 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHH
Q 023291 121 QLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSL 157 (284)
Q Consensus 121 q~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L 157 (284)
.++.+...+......++.++..+....+.|..-+.+|
T Consensus 4 elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~l 40 (55)
T PF05377_consen 4 ELENELPRIESSINTVKKENEEISESVEKIEENVKDL 40 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566677777777778888888877777777666544
No 196
>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=23.03 E-value=2.9e+02 Score=21.51 Aligned_cols=35 Identities=20% Similarity=0.324 Sum_probs=22.7
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhh
Q 023291 66 KRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNR 113 (284)
Q Consensus 66 RrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNR 113 (284)
++.|+..++..|..... .+.+|++..+|+.++...
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 45599999998865532 244566666666666543
No 197
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=22.87 E-value=59 Score=28.22 Aligned_cols=46 Identities=22% Similarity=0.070 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+++.+..+|.-.|-.. ....++|..||+++..|+++...-|.+.|+
T Consensus 114 Lp~~~r~v~~L~~~~g-----~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 114 LPDEQREALILVGASG-----FSYEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred CCHHHhHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6777766665554322 246789999999999999888755554443
No 198
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=22.74 E-value=81 Score=28.19 Aligned_cols=46 Identities=15% Similarity=0.231 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+++.+..+|...|-.. ....+||..+|++...|+.+...-|.+.|+
T Consensus 185 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 185 LPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6777777776666322 356889999999999999988766655554
No 199
>PF06810 Phage_GP20: Phage minor structural protein GP20; InterPro: IPR009636 This family consists of several phage minor structural protein Gp20 sequences and prophage sequences of around 180 residues in length. The function of this family is unknown.; GO: 0005198 structural molecule activity
Probab=22.70 E-value=4.9e+02 Score=22.37 Aligned_cols=48 Identities=25% Similarity=0.327 Sum_probs=26.2
Q ss_pred HHHHHHHHhHHHHhhhhhHHHH---hhHHHHHHHHHHHHHHHHHhhhhhhh
Q 023291 124 RDYDLLKSSYDALLSSYDSLVK---ENQKLKSEVVSLNEKIEAKEEESKEA 171 (284)
Q Consensus 124 ~~~~~Lk~~~~~l~s~~~sl~~---en~~L~~E~~~L~e~l~~~ee~~~~~ 171 (284)
.++..++.+.......-..|.. .|+.|+.++..|+.+.....++....
T Consensus 27 ~e~~~~k~ql~~~d~~i~~Lk~~~~d~eeLk~~i~~lq~~~~~~~~~~e~~ 77 (155)
T PF06810_consen 27 EERDNLKTQLKEADKQIKDLKKSAKDNEELKKQIEELQAKNKTAKEEYEAK 77 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444443333333333333 67777778777777776655555443
No 200
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=22.60 E-value=94 Score=25.58 Aligned_cols=38 Identities=24% Similarity=0.288 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecch
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQ 111 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQ 111 (284)
+++.+..+|.-.|-.. ..-.+||..||+++..|+....
T Consensus 123 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 123 LTPKQQHVIALRFGQN-----LPIAEVARILGKTEGAVKILQF 160 (170)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 6777777776654322 2467899999999998876664
No 201
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=22.55 E-value=94 Score=25.88 Aligned_cols=45 Identities=16% Similarity=0.040 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
+++.+..++.-.|-.. ..-.+||..+|+++..|+++...-|.+-|
T Consensus 113 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 113 LSADQREAIILIGASG-----FSYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 7777777776654322 24678999999999999888764444433
No 202
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=22.30 E-value=1.1e+02 Score=28.08 Aligned_cols=57 Identities=21% Similarity=0.303 Sum_probs=38.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHHHHHHHHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLERDYDLLK 130 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~~~Lk 130 (284)
+++.+..++.-.|-.. ....+||..+|++...|+++...-|.+.|+.-..+-..+++
T Consensus 162 Lp~~~R~v~~L~~~eg-----~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~~~~~ 218 (244)
T TIGR03001 162 LSERERHLLRLHFVDG-----LSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLAERLK 218 (244)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 6666666665554322 24678999999999999999987777666654333333333
No 203
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=22.13 E-value=3.8e+02 Score=23.28 Aligned_cols=28 Identities=39% Similarity=0.584 Sum_probs=20.9
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHhhhhhh
Q 023291 143 LVKENQKLKSEVVSLNEKIEAKEEESKE 170 (284)
Q Consensus 143 l~~en~~L~~E~~~L~e~l~~~ee~~~~ 170 (284)
..+++..+..|+..|+.+|.+++.+.+.
T Consensus 152 ~~~~~~~~~~ei~~lk~el~~~~~~~~~ 179 (192)
T PF05529_consen 152 LKEENKKLSEEIEKLKKELEKKEKEIEA 179 (192)
T ss_pred hhhhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 4466778888888888888887766553
No 204
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=21.84 E-value=99 Score=26.20 Aligned_cols=46 Identities=17% Similarity=0.031 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+++.+..++.-.|- ......++|..||+++..|++....-|.+.|+
T Consensus 130 L~~~~r~v~~l~~~-----~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 130 LPDRQRLPIVHVKL-----EGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55555554443332 22356789999999999998888655554443
No 205
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=21.68 E-value=30 Score=24.68 Aligned_cols=20 Identities=25% Similarity=0.428 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCCcceeecch
Q 023291 92 KGQLAKKLGLQPRQVAVWFQ 111 (284)
Q Consensus 92 r~eLA~~LgLs~rqVqvWFQ 111 (284)
..++|+.+|++++.|+.|=+
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46899999999999999954
No 206
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=21.36 E-value=2e+02 Score=30.23 Aligned_cols=35 Identities=34% Similarity=0.311 Sum_probs=29.5
Q ss_pred HHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHH
Q 023291 125 DYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNE 159 (284)
Q Consensus 125 ~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e 159 (284)
-..-|++....|..+++.|++||.-|+.++..|..
T Consensus 303 y~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~ 337 (655)
T KOG4343|consen 303 YMLGLEARLQALLSENEQLKKENATLKRQLDELVS 337 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Confidence 34568888888999999999999999999887755
No 207
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.34 E-value=4e+02 Score=21.31 Aligned_cols=36 Identities=17% Similarity=0.127 Sum_probs=24.7
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhH
Q 023291 66 KRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRR 114 (284)
Q Consensus 66 RrRfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRR 114 (284)
.|.|+..++..|. .....+.+|++-..|+..+.+..
T Consensus 36 yR~Y~~~~i~~l~-------------~I~~lr~~G~sl~eI~~~l~~~~ 71 (123)
T cd04770 36 YRLYGEADLARLR-------------FIRRAQALGFSLAEIRELLSLRD 71 (123)
T ss_pred CccCCHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHHhhh
Confidence 4559999999983 33345777777777777665443
No 208
>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=21.33 E-value=2.9e+02 Score=19.18 Aligned_cols=23 Identities=30% Similarity=0.498 Sum_probs=13.6
Q ss_pred HhhhhhHHHHhhHHHHHHHHHHH
Q 023291 136 LLSSYDSLVKENQKLKSEVVSLN 158 (284)
Q Consensus 136 l~s~~~sl~~en~~L~~E~~~L~ 158 (284)
+......|..+|..|..++..|+
T Consensus 30 le~~~~~L~~en~~L~~~i~~L~ 52 (54)
T PF07716_consen 30 LEQEVQELEEENEQLRQEIAQLE 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 33444555666666666666654
No 209
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=21.32 E-value=95 Score=26.72 Aligned_cols=44 Identities=9% Similarity=0.028 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARW 117 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~ 117 (284)
+++.+..++.-.|-.. ..-.+||..+|+++..|+++...-|.+.
T Consensus 137 L~~~~r~i~~L~~~~g-----~s~~eIA~~lgis~~tV~~~l~Ra~~~L 180 (196)
T PRK12524 137 LPERQRQAVVLRHIEG-----LSNPEIAEVMEIGVEAVESLTARGKRAL 180 (196)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 5666665555543321 2367899999999999998886444433
No 210
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=21.23 E-value=1.1e+02 Score=25.73 Aligned_cols=42 Identities=17% Similarity=0.186 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRA 115 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRa 115 (284)
++..+..+|.-.|-.. ..-.+||..+|+++..|+++...-|.
T Consensus 136 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~~V~~~l~ra~~ 177 (186)
T PRK13919 136 LSPEERRVIEVLYYQG-----YTHREAAQLLGLPLGTLKTRARRALS 177 (186)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6777777776554322 24678999999999988777654333
No 211
>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=21.14 E-value=4.8e+02 Score=21.56 Aligned_cols=43 Identities=16% Similarity=0.277 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHHHHHH
Q 023291 121 QLERDYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNEKIEA 163 (284)
Q Consensus 121 q~~~~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~ 163 (284)
.+.++.+.|++....|.....++.+....|++++.++...|..
T Consensus 34 eL~kqkd~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~le~ 76 (107)
T PF09304_consen 34 ELAKQKDQLRNALQSLQAQNASRNQRIAELQAKIDEARRNLED 76 (107)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555566666667677777777777777777777666555
No 212
>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=21.12 E-value=1.4e+02 Score=22.08 Aligned_cols=28 Identities=25% Similarity=0.369 Sum_probs=12.4
Q ss_pred HHHHHHHhHHHHhhhhhHHHHhhHHHHHHHHHHHH
Q 023291 125 DYDLLKSSYDALLSSYDSLVKENQKLKSEVVSLNE 159 (284)
Q Consensus 125 ~~~~Lk~~~~~l~s~~~sl~~en~~L~~E~~~L~e 159 (284)
+.+.||.....| ...|..|+.|+.-|+.
T Consensus 15 EVevLK~~I~eL-------~~~n~~Le~EN~~Lk~ 42 (59)
T PF01166_consen 15 EVEVLKEQIAEL-------EERNSQLEEENNLLKQ 42 (59)
T ss_dssp SHHHHHHHHHHH-------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH-------HHHHHHHHHHHHHHHh
Confidence 444555444433 3344444444444443
No 213
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=21.02 E-value=3.3e+02 Score=22.12 Aligned_cols=28 Identities=29% Similarity=0.374 Sum_probs=11.4
Q ss_pred HHHhhhhhHHHHhhHHHHHHHHHHHHHH
Q 023291 134 DALLSSYDSLVKENQKLKSEVVSLNEKI 161 (284)
Q Consensus 134 ~~l~s~~~sl~~en~~L~~E~~~L~e~l 161 (284)
..+......+.+++++|+..+.++++++
T Consensus 83 ~~l~~~~~~~~~~~~~l~~~~~~~~~~~ 110 (118)
T PF13815_consen 83 EQLEERLQELQQEIEKLKQKLKKQKEEI 110 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333334444444444444444433
No 214
>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=20.96 E-value=2.5e+02 Score=28.87 Aligned_cols=26 Identities=38% Similarity=0.367 Sum_probs=12.0
Q ss_pred HhhhhhHHHHhhHHHHHHHHHHHHHH
Q 023291 136 LLSSYDSLVKENQKLKSEVVSLNEKI 161 (284)
Q Consensus 136 l~s~~~sl~~en~~L~~E~~~L~e~l 161 (284)
+.+....+.++.++|+.+..+++..|
T Consensus 107 v~~~~~~~~~~~~ql~~~~~~~~~~l 132 (472)
T TIGR03752 107 VQSETQELTKEIEQLKSERQQLQGLI 132 (472)
T ss_pred HHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444445555555544444443
No 215
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.73 E-value=3.6e+02 Score=20.86 Aligned_cols=13 Identities=46% Similarity=0.667 Sum_probs=5.5
Q ss_pred HHHHhhHHHHHHH
Q 023291 142 SLVKENQKLKSEV 154 (284)
Q Consensus 142 sl~~en~~L~~E~ 154 (284)
.|..+|++|+.|.
T Consensus 50 aL~~eneqlk~e~ 62 (79)
T COG3074 50 ALERENEQLKEEQ 62 (79)
T ss_pred HHHHHHHHHHHHH
Confidence 3344444444443
No 216
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=20.69 E-value=1e+02 Score=27.30 Aligned_cols=43 Identities=16% Similarity=0.218 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK 116 (284)
+++.+..+|...|-.. ....+||..+|++...|+.+...-+.+
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~ 218 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKK 218 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 7888888888877433 246889999999999887776544443
No 217
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=20.63 E-value=3.4e+02 Score=27.00 Aligned_cols=36 Identities=33% Similarity=0.327 Sum_probs=23.7
Q ss_pred HHHHhhhhhHHHHhhHHHHHHHHHHHHHHHHHhhhh
Q 023291 133 YDALLSSYDSLVKENQKLKSEVVSLNEKIEAKEEES 168 (284)
Q Consensus 133 ~~~l~s~~~sl~~en~~L~~E~~~L~e~l~~~ee~~ 168 (284)
...|......+.+||++|+.++..+.....+|+|+.
T Consensus 129 ~q~LE~li~~~~EEn~~lqlqL~~l~~e~~Ekeees 164 (401)
T PF06785_consen 129 IQHLEGLIRHLREENQCLQLQLDALQQECGEKEEES 164 (401)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHhHhHHHH
Confidence 333444455667888888888888877766666544
No 218
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=20.57 E-value=1.3e+02 Score=25.82 Aligned_cols=46 Identities=7% Similarity=0.099 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHHH
Q 023291 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKT 119 (284)
Q Consensus 69 fT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~Kr 119 (284)
+++.+..++.-.|-.. ..-.+||..+|+++..|+.....-|.+.|+
T Consensus 137 L~~~~r~i~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 182 (195)
T PRK12532 137 LPENTARVFTLKEILG-----FSSDEIQQMCGISTSNYHTIMHRARESLRQ 182 (195)
T ss_pred CCHHHHHHhhhHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6666666666544322 246789999999999998888655554444
No 219
>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=20.31 E-value=51 Score=22.08 Aligned_cols=21 Identities=14% Similarity=0.290 Sum_probs=17.5
Q ss_pred HHHHHhCCCCcceeecchhhH
Q 023291 94 QLAKKLGLQPRQVAVWFQNRR 114 (284)
Q Consensus 94 eLA~~LgLs~rqVqvWFQNRR 114 (284)
+||..+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 578888999888888888874
No 220
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=20.10 E-value=2.1e+02 Score=26.41 Aligned_cols=23 Identities=30% Similarity=0.312 Sum_probs=10.8
Q ss_pred HHhhhhhHHHHhhHHHHHHHHHH
Q 023291 135 ALLSSYDSLVKENQKLKSEVVSL 157 (284)
Q Consensus 135 ~l~s~~~sl~~en~~L~~E~~~L 157 (284)
.+.+++..|++++..|+.++.++
T Consensus 73 ~l~~en~~L~~e~~~l~~~~~~~ 95 (276)
T PRK13922 73 DLREENEELKKELLELESRLQEL 95 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444455555554444444
No 221
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=20.10 E-value=73 Score=26.20 Aligned_cols=45 Identities=27% Similarity=0.310 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCCcceeecchhhHHHHH
Q 023291 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118 (284)
Q Consensus 68 RfT~~Ql~~LE~~F~~~~~P~~~~r~eLA~~LgLs~rqVqvWFQNRRaK~K 118 (284)
.+|+.+...|+-.... ..+.+||..++++++.|++..++=|.|-.
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4888888888776642 25788999999999998887776655543
No 222
>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=20.08 E-value=3.1e+02 Score=24.25 Aligned_cols=8 Identities=50% Similarity=0.900 Sum_probs=2.9
Q ss_pred hhHHHHHH
Q 023291 146 ENQKLKSE 153 (284)
Q Consensus 146 en~~L~~E 153 (284)
+|+.|+.|
T Consensus 105 e~~~l~~e 112 (161)
T TIGR02894 105 ENERLKNQ 112 (161)
T ss_pred HHHHHHHH
Confidence 33333333
Done!