Query 038544
Match_columns 69
No_of_seqs 117 out of 365
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 12:10:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038544.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038544hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03162 golden-2 like transcr 99.9 2.9E-27 6.3E-32 181.2 6.1 55 14-69 232-286 (526)
2 TIGR01557 myb_SHAQKYF myb-like 99.9 5.4E-27 1.2E-31 137.5 5.5 53 17-69 1-53 (57)
3 PF00249 Myb_DNA-binding: Myb- 98.7 1.6E-08 3.4E-13 55.8 4.0 47 19-69 1-47 (48)
4 smart00717 SANT SANT SWI3, AD 97.2 0.0018 4E-08 33.4 5.1 43 20-67 2-44 (49)
5 cd00167 SANT 'SWI3, ADA2, N-Co 97.1 0.0019 4E-08 33.0 4.9 43 21-68 1-43 (45)
6 smart00426 TEA TEA domain. 97.0 0.0017 3.7E-08 39.6 4.5 48 20-68 4-67 (68)
7 PF13921 Myb_DNA-bind_6: Myb-l 95.0 0.097 2.1E-06 29.2 4.9 40 22-67 1-40 (60)
8 PF01285 TEA: TEA/ATTS domain 94.4 0.031 6.8E-07 43.5 2.4 52 16-68 46-111 (431)
9 KOG0457 Histone acetyltransfer 91.9 0.25 5.5E-06 39.0 4.0 48 16-68 69-116 (438)
10 PF12776 Myb_DNA-bind_3: Myb/S 91.6 0.32 7E-06 29.0 3.5 47 21-67 1-59 (96)
11 PLN03212 Transcription repress 90.1 0.69 1.5E-05 34.2 4.7 46 15-64 21-66 (249)
12 KOG3841 TEF-1 and related tran 88.3 0.66 1.4E-05 36.7 3.6 52 17-68 74-140 (455)
13 PLN03091 hypothetical protein; 86.8 1.6 3.5E-05 34.8 5.0 46 14-63 9-54 (459)
14 PLN03212 Transcription repress 83.9 2.7 5.8E-05 31.1 4.8 48 12-65 71-118 (249)
15 PLN03091 hypothetical protein; 82.6 4.5 9.7E-05 32.4 5.8 47 13-65 61-107 (459)
16 smart00501 BRIGHT BRIGHT, ARID 80.0 2.7 5.8E-05 25.5 3.1 43 25-68 33-82 (93)
17 PF13837 Myb_DNA-bind_4: Myb/S 78.0 2.2 4.8E-05 24.9 2.2 47 19-65 1-59 (90)
18 COG5114 Histone acetyltransfer 77.6 2.6 5.6E-05 33.0 3.0 45 19-68 63-107 (432)
19 KOG0724 Zuotin and related mol 76.3 1.6 3.4E-05 31.9 1.4 45 19-69 53-97 (335)
20 KOG0048 Transcription factor, 72.6 16 0.00034 25.9 5.7 48 12-65 55-102 (238)
21 PF07384 DUF1497: Protein of u 69.6 5.4 0.00012 23.4 2.4 21 21-41 37-57 (59)
22 PF00690 Cation_ATPase_N: Cati 65.3 5.1 0.00011 22.8 1.7 26 44-69 5-33 (69)
23 PRK11923 algU RNA polymerase s 64.9 13 0.00029 24.3 3.8 39 26-67 128-176 (193)
24 PF08127 Propeptide_C1: Peptid 64.7 6.2 0.00014 21.4 1.9 34 26-66 1-34 (41)
25 KOG0049 Transcription factor, 63.0 15 0.00032 31.4 4.5 44 15-63 356-399 (939)
26 PF13601 HTH_34: Winged helix 60.4 5.3 0.00011 24.0 1.2 26 40-68 12-37 (80)
27 PRK09640 RNA polymerase sigma 56.5 31 0.00068 22.6 4.5 45 20-67 118-172 (188)
28 KOG2983 Uncharacterized conser 55.9 9.6 0.00021 29.2 2.1 17 24-40 85-101 (334)
29 cd08783 Death_MALT1 Death doma 55.1 22 0.00048 23.0 3.5 47 18-68 36-83 (97)
30 TIGR02894 DNA_bind_RsfA transc 53.9 20 0.00043 25.0 3.3 48 16-69 45-92 (161)
31 PRK12530 RNA polymerase sigma 53.7 31 0.00066 22.8 4.1 38 27-67 125-172 (189)
32 PF07638 Sigma70_ECF: ECF sigm 53.5 29 0.00062 23.2 4.0 44 23-67 119-162 (185)
33 PF00046 Homeobox: Homeobox do 52.4 34 0.00075 18.2 3.6 46 16-64 1-46 (57)
34 TIGR02989 Sig-70_gvs1 RNA poly 52.0 34 0.00073 21.4 4.0 41 24-67 99-149 (159)
35 PF01325 Fe_dep_repress: Iron 51.3 14 0.00031 21.0 1.9 34 28-61 7-41 (60)
36 PF08281 Sigma70_r4_2: Sigma-7 50.6 38 0.00082 17.9 3.6 23 43-68 27-49 (54)
37 PF14075 UBN_AB: Ubinuclein co 49.6 23 0.00049 25.3 3.1 23 12-34 145-167 (214)
38 PRK12522 RNA polymerase sigma 49.6 25 0.00055 22.6 3.2 43 22-67 105-157 (173)
39 PRK12541 RNA polymerase sigma 49.2 36 0.00078 21.5 3.8 37 28-67 104-150 (161)
40 TIGR02985 Sig70_bacteroi1 RNA 48.1 45 0.00097 20.4 4.0 41 24-67 101-151 (161)
41 PRK09642 RNA polymerase sigma 47.2 48 0.001 20.9 4.1 36 29-67 99-144 (160)
42 PRK12536 RNA polymerase sigma 46.9 47 0.001 21.6 4.2 39 25-66 118-166 (181)
43 PRK13919 putative RNA polymera 44.8 49 0.0011 21.4 4.0 35 30-67 129-173 (186)
44 KOG1279 Chromatin remodeling f 44.5 52 0.0011 26.6 4.7 44 17-66 251-294 (506)
45 PRK09646 RNA polymerase sigma 43.7 47 0.001 21.9 3.8 39 25-66 131-179 (194)
46 PF07065 D123: D123; InterPro 42.6 16 0.00035 27.1 1.6 17 24-40 71-87 (299)
47 cd02185 AroH Chorismate mutase 42.1 5.8 0.00012 26.4 -0.8 36 20-56 45-81 (117)
48 cd06171 Sigma70_r4 Sigma70, re 41.5 46 0.00099 16.3 3.7 22 43-67 27-48 (55)
49 PF04539 Sigma70_r3: Sigma-70 41.2 67 0.0015 18.1 4.5 37 25-66 1-41 (78)
50 COG1595 RpoE DNA-directed RNA 41.1 61 0.0013 21.1 4.0 40 25-67 116-165 (182)
51 TIGR02960 SigX5 RNA polymerase 40.8 51 0.0011 23.4 3.8 39 26-67 132-180 (324)
52 PF02201 SWIB: SWIB/MDM2 domai 40.5 14 0.00031 21.8 0.9 25 45-69 8-32 (76)
53 TIGR02948 SigW_bacill RNA poly 39.9 62 0.0013 20.7 3.8 22 43-67 153-174 (187)
54 TIGR02983 SigE-fam_strep RNA p 39.5 61 0.0013 20.3 3.7 22 43-67 127-148 (162)
55 COG4672 gp18 Phage-related pro 39.4 23 0.00049 26.1 1.8 24 27-50 108-131 (231)
56 PRK09415 RNA polymerase factor 39.4 63 0.0014 21.0 3.9 38 27-67 118-165 (179)
57 PRK09644 RNA polymerase sigma 39.0 46 0.001 21.2 3.1 39 25-67 97-135 (165)
58 TIGR02947 SigH_actino RNA poly 38.9 55 0.0012 21.4 3.5 37 28-67 123-169 (193)
59 PF09535 Gmx_para_CXXCG: Prote 38.8 22 0.00048 26.2 1.7 13 28-40 215-227 (237)
60 PHA02943 hypothetical protein; 38.0 96 0.0021 21.8 4.7 41 23-67 6-46 (165)
61 PF07750 GcrA: GcrA cell cycle 37.5 47 0.001 22.6 3.1 37 20-63 1-37 (162)
62 KOG0048 Transcription factor, 37.0 45 0.00098 23.5 3.1 30 19-48 9-39 (238)
63 PRK12544 RNA polymerase sigma 37.0 70 0.0015 21.7 3.9 36 29-67 141-186 (206)
64 PRK09636 RNA polymerase sigma 36.8 69 0.0015 22.7 4.0 38 27-67 106-153 (293)
65 TIGR03001 Sig-70_gmx1 RNA poly 36.5 56 0.0012 23.1 3.5 39 26-67 151-199 (244)
66 PF08671 SinI: Anti-repressor 36.1 22 0.00048 18.2 1.0 13 55-67 15-27 (30)
67 PRK09643 RNA polymerase sigma 35.9 93 0.002 20.5 4.3 21 43-66 151-171 (192)
68 TIGR02943 Sig70_famx1 RNA poly 35.8 72 0.0016 21.1 3.7 21 44-67 149-169 (188)
69 PF13412 HTH_24: Winged helix- 35.2 70 0.0015 16.6 4.1 37 26-68 4-40 (48)
70 TIGR03830 CxxCG_CxxCG_HTH puta 34.7 1E+02 0.0022 18.8 4.1 48 20-67 40-89 (127)
71 PRK05803 sporulation sigma fac 34.3 92 0.002 21.3 4.2 22 42-66 195-216 (233)
72 PRK12545 RNA polymerase sigma 34.2 76 0.0016 21.2 3.7 36 29-67 132-177 (201)
73 TIGR02952 Sig70_famx2 RNA poly 34.2 75 0.0016 19.9 3.5 36 28-67 114-149 (170)
74 PRK12515 RNA polymerase sigma 33.9 80 0.0017 20.6 3.7 38 27-67 122-169 (189)
75 PRK05602 RNA polymerase sigma 33.9 94 0.002 20.1 4.0 37 28-67 120-166 (186)
76 smart00831 Cation_ATPase_N Cat 33.8 23 0.00051 19.4 1.0 15 55-69 9-23 (64)
77 TIGR01517 ATPase-IIB_Ca plasma 33.6 60 0.0013 27.4 3.7 33 32-69 36-73 (941)
78 smart00344 HTH_ASNC helix_turn 33.5 1.1E+02 0.0023 18.2 4.1 38 24-67 2-39 (108)
79 PF14383 VARLMGL: DUF761-assoc 32.7 20 0.00042 19.2 0.5 21 41-61 11-31 (34)
80 COG4401 AroH Chorismate mutase 32.3 11 0.00025 25.3 -0.6 36 20-56 47-83 (125)
81 PF10309 DUF2414: Protein of u 31.8 29 0.00062 20.5 1.1 18 51-68 10-27 (62)
82 PRK09649 RNA polymerase sigma 31.7 1.1E+02 0.0023 20.1 4.0 38 27-67 121-168 (185)
83 PRK10507 bifunctional glutathi 31.5 47 0.001 27.4 2.7 37 22-63 266-302 (619)
84 PF12840 HTH_20: Helix-turn-he 31.0 67 0.0015 17.6 2.6 25 41-68 23-47 (61)
85 PF13932 GIDA_assoc_3: GidA as 30.8 23 0.0005 21.1 0.6 29 32-63 40-68 (72)
86 PRK08241 RNA polymerase factor 30.4 91 0.002 22.4 3.8 37 28-67 145-191 (339)
87 PRK12531 RNA polymerase sigma 30.1 1.1E+02 0.0024 20.1 4.0 38 27-67 132-179 (194)
88 PRK12538 RNA polymerase sigma 29.7 1E+02 0.0022 21.5 3.8 22 43-67 188-209 (233)
89 PF12170 DNA_pol3_tau_5: DNA p 29.5 54 0.0012 21.9 2.3 32 23-60 8-40 (142)
90 PF08593 MUG2_C: Meiotically u 29.4 30 0.00064 20.1 0.9 21 47-67 37-57 (58)
91 TIGR02937 sigma70-ECF RNA poly 29.0 1.1E+02 0.0025 17.9 3.5 10 45-54 129-138 (158)
92 PF00570 HRDC: HRDC domain Blo 28.7 28 0.0006 19.3 0.7 24 43-66 38-61 (68)
93 PHA02117 glutathionylspermidin 28.1 42 0.00092 26.1 1.8 17 22-38 55-71 (397)
94 PF00196 GerE: Bacterial regul 27.9 45 0.00097 18.1 1.5 22 43-67 19-40 (58)
95 PRK06811 RNA polymerase factor 27.9 52 0.0011 21.6 2.0 21 44-67 149-169 (189)
96 PF03982 DAGAT: Diacylglycerol 27.5 54 0.0012 24.3 2.2 14 24-37 265-278 (297)
97 PRK12525 RNA polymerase sigma 27.3 88 0.0019 20.0 3.0 35 28-66 110-144 (168)
98 smart00389 HOX Homeodomain. DN 27.1 1E+02 0.0022 16.0 4.2 45 17-64 2-46 (56)
99 PF02954 HTH_8: Bacterial regu 27.1 1E+02 0.0022 15.9 3.7 33 30-69 10-42 (42)
100 PRK12514 RNA polymerase sigma 26.9 60 0.0013 20.9 2.2 21 44-67 147-167 (179)
101 PRK09652 RNA polymerase sigma 26.9 1.1E+02 0.0024 19.1 3.3 39 26-67 118-166 (182)
102 COG0754 Gsp Glutathionylspermi 26.8 59 0.0013 25.7 2.4 17 23-39 53-69 (387)
103 TIGR02959 SigZ RNA polymerase 26.7 1.5E+02 0.0032 19.1 4.0 39 26-67 90-138 (170)
104 PRK12518 RNA polymerase sigma 26.2 1.4E+02 0.0031 18.9 3.8 36 29-67 113-158 (175)
105 COG3623 SgaU Putative L-xylulo 26.2 68 0.0015 24.3 2.6 24 16-39 45-68 (287)
106 PF05534 HicB: HicB family; I 25.9 1.3E+02 0.0028 16.6 4.0 26 15-40 17-42 (51)
107 TIGR03879 near_KaiC_dom probab 25.8 1.6E+02 0.0035 17.8 4.5 43 18-67 11-54 (73)
108 PF14338 Mrr_N: Mrr N-terminal 25.8 1.5E+02 0.0034 17.6 3.9 36 25-62 4-40 (92)
109 smart00351 PAX Paired Box doma 25.4 1.9E+02 0.004 18.4 5.2 30 21-55 17-46 (125)
110 TIGR02393 RpoD_Cterm RNA polym 25.1 1.4E+02 0.0031 20.5 3.9 39 25-66 165-217 (238)
111 KOG4411 Phytoene/squalene synt 24.7 47 0.001 25.1 1.4 19 50-68 148-166 (292)
112 smart00421 HTH_LUXR helix_turn 24.6 94 0.002 15.5 2.3 22 43-67 19-40 (58)
113 PF11767 SET_assoc: Histone ly 24.2 65 0.0014 19.0 1.8 17 53-69 8-24 (66)
114 cd00086 homeodomain Homeodomai 24.1 1.2E+02 0.0026 15.7 4.5 47 17-66 2-48 (59)
115 PF04255 DUF433: Protein of un 24.0 1.1E+02 0.0024 16.9 2.6 22 43-66 32-53 (56)
116 PF02134 UBACT: Repeat in ubiq 23.8 1.5E+02 0.0032 17.1 3.3 38 23-61 5-49 (67)
117 PRK12519 RNA polymerase sigma 23.8 71 0.0015 20.8 2.1 21 44-67 159-179 (194)
118 PRK09647 RNA polymerase sigma 23.7 1.3E+02 0.0027 20.4 3.3 35 28-66 130-164 (203)
119 PF06056 Terminase_5: Putative 23.3 86 0.0019 17.8 2.1 13 43-55 14-26 (58)
120 PRK12524 RNA polymerase sigma 23.1 1.8E+02 0.0039 19.1 3.9 38 27-67 127-174 (196)
121 PF09712 PHA_synth_III_E: Poly 23.1 78 0.0017 23.4 2.4 36 27-64 241-276 (293)
122 PRK12527 RNA polymerase sigma 23.1 1.3E+02 0.0029 18.8 3.2 35 29-67 98-132 (159)
123 smart00526 H15 Domain in histo 22.7 1.5E+02 0.0034 16.5 3.3 25 29-53 10-34 (66)
124 COG1460 Uncharacterized protei 22.5 2E+02 0.0044 19.0 4.0 44 21-67 47-90 (114)
125 PF14549 P22_Cro: DNA-binding 22.4 1.4E+02 0.0031 17.2 3.0 18 32-54 4-21 (60)
126 PRK06759 RNA polymerase factor 22.1 1.6E+02 0.0035 18.1 3.4 40 25-67 95-144 (154)
127 PRK12542 RNA polymerase sigma 22.1 1.9E+02 0.0042 18.7 3.9 22 43-67 139-160 (185)
128 PRK12539 RNA polymerase sigma 21.7 2.2E+02 0.0047 18.4 4.1 39 25-66 120-168 (184)
129 PHA01976 helix-turn-helix prot 21.5 82 0.0018 17.1 1.8 20 46-65 5-24 (67)
130 PF00633 HHH: Helix-hairpin-he 21.4 39 0.00085 16.9 0.4 17 44-60 6-22 (30)
131 KOG4468 Polycomb-group transcr 21.4 1.1E+02 0.0024 26.0 3.1 47 19-65 88-138 (782)
132 TIGR02264 gmx_para_CXXCG Myxoc 21.3 69 0.0015 23.7 1.8 12 28-39 215-226 (237)
133 TIGR02950 SigM_subfam RNA poly 21.0 88 0.0019 19.3 2.0 11 28-38 97-107 (154)
134 PF06971 Put_DNA-bind_N: Putat 20.6 1.7E+02 0.0038 16.3 3.4 31 29-63 16-46 (50)
135 PRK12533 RNA polymerase sigma 20.5 1.4E+02 0.003 20.6 3.1 40 25-67 123-172 (216)
136 PRK09639 RNA polymerase sigma 20.2 2.2E+02 0.0049 17.7 3.8 20 44-66 129-148 (166)
137 COG1321 TroR Mn-dependent tran 20.2 1.7E+02 0.0036 19.6 3.4 40 28-67 9-49 (154)
No 1
>PLN03162 golden-2 like transcription factor; Provisional
Probab=99.94 E-value=2.9e-27 Score=181.23 Aligned_cols=55 Identities=47% Similarity=0.720 Sum_probs=53.1
Q ss_pred CCCCCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhccC
Q 038544 14 KSELPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQVN 69 (69)
Q Consensus 14 ~~kk~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQKy 69 (69)
..||+|++||+|||++||+||++||. ++|+||+||++|+|+|||++|||||||||
T Consensus 232 g~KKpRLrWTpELH~rFVeAV~qLG~-dKATPK~ILelMnV~GLTRenVKSHLQKY 286 (526)
T PLN03162 232 GKKKAKVDWTPELHRRFVHAVEQLGV-EKAFPSRILELMGVQCLTRHNIASHLQKY 286 (526)
T ss_pred CCCCCcccCCHHHHHHHHHHHHHhCc-CccchHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 47899999999999999999999995 89999999999999999999999999998
No 2
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=99.94 E-value=5.4e-27 Score=137.47 Aligned_cols=53 Identities=51% Similarity=0.814 Sum_probs=51.2
Q ss_pred CCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhccC
Q 038544 17 LPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQVN 69 (69)
Q Consensus 17 k~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQKy 69 (69)
|+|+.||+|+|.+|++||+.||+.+.|+|+.|+++|++++||+.||+||||||
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy 53 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKY 53 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 68999999999999999999998679999999999999999999999999998
No 3
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=98.75 E-value=1.6e-08 Score=55.84 Aligned_cols=47 Identities=28% Similarity=0.343 Sum_probs=40.7
Q ss_pred cccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhccC
Q 038544 19 RLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQVN 69 (69)
Q Consensus 19 R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQKy 69 (69)
|..||+|.+..|++||..+|.. .++.|.+.|+ .+-|..+|++|.++|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~---~W~~Ia~~~~-~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKD---NWKKIAKRMP-GGRTAKQCRSRYQNL 47 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTT---HHHHHHHHHS-SSSTHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhCCc---HHHHHHHHcC-CCCCHHHHHHHHHhh
Confidence 5689999999999999999963 6999999999 788999999999875
No 4
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=97.17 E-value=0.0018 Score=33.40 Aligned_cols=43 Identities=16% Similarity=0.282 Sum_probs=36.3
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 20 LRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 20 ~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
-.||++....|+.++.++|- ..+..|.+.|+ +-|..+|+.+..
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~---~~w~~Ia~~~~--~rt~~~~~~~~~ 44 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGK---NNWEKIAKELP--GRTAEQCRERWN 44 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCc---CCHHHHHHHcC--CCCHHHHHHHHH
Confidence 46999999999999999992 23899999886 679999988754
No 5
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=97.14 E-value=0.0019 Score=33.02 Aligned_cols=43 Identities=16% Similarity=0.234 Sum_probs=36.4
Q ss_pred cCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhcc
Q 038544 21 RWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQV 68 (69)
Q Consensus 21 ~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQK 68 (69)
.||+|....|+.++..+|. ..+..|.+.|+- -|..+|+++.+.
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~---~~w~~Ia~~~~~--rs~~~~~~~~~~ 43 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK---NNWEKIAKELPG--RTPKQCRERWRN 43 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc---CCHHHHHhHcCC--CCHHHHHHHHHH
Confidence 4999999999999999993 248999999854 699999988754
No 6
>smart00426 TEA TEA domain.
Probab=97.01 E-value=0.0017 Score=39.62 Aligned_cols=48 Identities=21% Similarity=0.301 Sum_probs=31.0
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCcc----------------ChHHHHHHcCCCCCCHHHHHhhhcc
Q 038544 20 LRWTPELHKHFSQAVERLGGKYKA----------------SPKRILHMMNVKGLKLSHIKSHLQV 68 (69)
Q Consensus 20 ~~WT~eLH~~Fv~Av~~LGg~~~A----------------~Pk~Il~~M~v~gLT~~~VkSHLQK 68 (69)
-+|.++|...|++|+..+--.... ....|...-| .--|+.||.||+|.
T Consensus 4 ~vWp~~lE~Af~~aL~~~~~~g~~kik~~~r~k~~gRNelIs~YI~~~tG-k~Rt~KQVsShIQv 67 (68)
T smart00426 4 GVWSPDIEQAFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTG-KTRTRKQVSSHIQV 67 (68)
T ss_pred CcCcHHHHHHHHHHHHHcCccCcccchhhhcCcccchhHHHHHHHHHHhC-Cccchhhhcchhee
Confidence 379999999999999876421000 0112232223 22599999999995
No 7
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=95.00 E-value=0.097 Score=29.17 Aligned_cols=40 Identities=18% Similarity=0.326 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 22 WTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 22 WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
||+|.-...+.+|...|. .++.|.+.|+ .-|..+|+.+..
T Consensus 1 WT~eEd~~L~~~~~~~g~----~W~~Ia~~l~--~Rt~~~~~~r~~ 40 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN----DWKKIAEHLG--NRTPKQCRNRWR 40 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-----HHHHHHHST--TS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc----CHHHHHHHHC--cCCHHHHHHHHH
Confidence 999999999999999985 4999999996 568999887754
No 8
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=94.39 E-value=0.031 Score=43.52 Aligned_cols=52 Identities=19% Similarity=0.262 Sum_probs=28.9
Q ss_pred CCCcccCCHHHHHHHHHHHHHhC---CC-----------CccChHHHHHHcCCCCCCHHHHHhhhcc
Q 038544 16 ELPRLRWTPELHKHFSQAVERLG---GK-----------YKASPKRILHMMNVKGLKLSHIKSHLQV 68 (69)
Q Consensus 16 kk~R~~WT~eLH~~Fv~Av~~LG---g~-----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQK 68 (69)
....-+|++++...|++|+..+- .. ..-.-..|...-| .--|+.||.||+|.
T Consensus 46 ~~~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg-~~rt~kqvsshiqv 111 (431)
T PF01285_consen 46 GDGEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTG-KTRTRKQVSSHIQV 111 (431)
T ss_dssp GGGS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS-----SHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhC-cccchhHHHHHHHH
Confidence 46788999999999999997663 11 1111123332333 23699999999993
No 9
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=91.90 E-value=0.25 Score=39.03 Aligned_cols=48 Identities=19% Similarity=0.200 Sum_probs=40.8
Q ss_pred CCCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhcc
Q 038544 16 ELPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQV 68 (69)
Q Consensus 16 kk~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQK 68 (69)
+--...||.+.-..|++|++.+|. -.|..|.+.||.. |.++++.|--|
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~---GNW~dIA~hIGtK--tkeeck~hy~k 116 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGF---GNWQDIADHIGTK--TKEECKEHYLK 116 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCC---CcHHHHHHHHccc--chHHHHHHHHH
Confidence 344678999999999999999995 3599999999954 99999999644
No 10
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=91.59 E-value=0.32 Score=28.98 Aligned_cols=47 Identities=19% Similarity=0.343 Sum_probs=33.5
Q ss_pred cCCHHHHHHHHHHHHHh---CCC------CccChHHHHHHcCC---CCCCHHHHHhhhc
Q 038544 21 RWTPELHKHFSQAVERL---GGK------YKASPKRILHMMNV---KGLKLSHIKSHLQ 67 (69)
Q Consensus 21 ~WT~eLH~~Fv~Av~~L---Gg~------~~A~Pk~Il~~M~v---~gLT~~~VkSHLQ 67 (69)
.||++..+.||+.+-+. |.. .+.....|.+.++- -.+|..||++|+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~ 59 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWK 59 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHH
Confidence 59999999999988433 432 12345677777763 4478999999975
No 11
>PLN03212 Transcription repressor MYB5; Provisional
Probab=90.15 E-value=0.69 Score=34.19 Aligned_cols=46 Identities=11% Similarity=0.030 Sum_probs=35.6
Q ss_pred CCCCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHh
Q 038544 15 SELPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKS 64 (69)
Q Consensus 15 ~kk~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkS 64 (69)
....|-.||+|.-..-+++|+.+|. ..++.|.+.|+ ++-|..|++-
T Consensus 21 ~glKRg~WT~EEDe~L~~lV~kyG~---~nW~~IAk~~g-~gRT~KQCRe 66 (249)
T PLN03212 21 MGMKRGPWTVEEDEILVSFIKKEGE---GRWRSLPKRAG-LLRCGKSCRL 66 (249)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCc---ccHHHHHHhhh-cCCCcchHHH
Confidence 3456788999999999999999995 35889988876 4556666554
No 12
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=88.31 E-value=0.66 Score=36.68 Aligned_cols=52 Identities=21% Similarity=0.413 Sum_probs=33.4
Q ss_pred CCcccCCHHHHHHHHHHHHHh---CCC-----Cc----cChHHHHHHcCC---CCCCHHHHHhhhcc
Q 038544 17 LPRLRWTPELHKHFSQAVERL---GGK-----YK----ASPKRILHMMNV---KGLKLSHIKSHLQV 68 (69)
Q Consensus 17 k~R~~WT~eLH~~Fv~Av~~L---Gg~-----~~----A~Pk~Il~~M~v---~gLT~~~VkSHLQK 68 (69)
-.--+|+++..+.|.||+..+ |.. |. ..-.-|...++. .--|+.||.||.|.
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQV 140 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQV 140 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHH
Confidence 456799999999999999775 211 00 011222222222 34699999999984
No 13
>PLN03091 hypothetical protein; Provisional
Probab=86.77 E-value=1.6 Score=34.76 Aligned_cols=46 Identities=13% Similarity=0.192 Sum_probs=34.9
Q ss_pred CCCCCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHH
Q 038544 14 KSELPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIK 63 (69)
Q Consensus 14 ~~kk~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~Vk 63 (69)
+.+..+..||+|.-++.+++|..+|. ..|+.|...|+ ++-|..|++
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~---~nWs~IAk~~g-~gRT~KQCR 54 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGH---GCWSSVPKQAG-LQRCGKSCR 54 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCc---CCHHHHhhhhc-cCcCcchHh
Confidence 34566778999999999999999995 36888888876 344554444
No 14
>PLN03212 Transcription repressor MYB5; Provisional
Probab=83.92 E-value=2.7 Score=31.13 Aligned_cols=48 Identities=19% Similarity=0.140 Sum_probs=38.8
Q ss_pred ccCCCCCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhh
Q 038544 12 YNKSELPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSH 65 (69)
Q Consensus 12 ~~~~kk~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSH 65 (69)
+-.+.-.+-.||+|.-..-++++..+|.. +..|...| ||-|-.+||.+
T Consensus 71 ~L~P~I~kgpWT~EED~lLlel~~~~GnK----Ws~IAk~L--pGRTDnqIKNR 118 (249)
T PLN03212 71 YLRPSVKRGGITSDEEDLILRLHRLLGNR----WSLIAGRI--PGRTDNEIKNY 118 (249)
T ss_pred hhchhcccCCCChHHHHHHHHHHHhcccc----HHHHHhhc--CCCCHHHHHHH
Confidence 33455667789999999999999999963 88898866 88899999865
No 15
>PLN03091 hypothetical protein; Provisional
Probab=82.63 E-value=4.5 Score=32.35 Aligned_cols=47 Identities=17% Similarity=0.170 Sum_probs=39.2
Q ss_pred cCCCCCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhh
Q 038544 13 NKSELPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSH 65 (69)
Q Consensus 13 ~~~kk~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSH 65 (69)
-.+.-.+-.||+|.-...++.+..+|. .+..|.+.| ||-|-.+||.+
T Consensus 61 LdP~IkKgpWT~EED~lLLeL~k~~Gn----KWskIAk~L--PGRTDnqIKNR 107 (459)
T PLN03091 61 LRPDLKRGTFSQQEENLIIELHAVLGN----RWSQIAAQL--PGRTDNEIKNL 107 (459)
T ss_pred cCCcccCCCCCHHHHHHHHHHHHHhCc----chHHHHHhc--CCCCHHHHHHH
Confidence 345555678999999999999999995 489999876 88999999865
No 16
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=79.95 E-value=2.7 Score=25.45 Aligned_cols=43 Identities=19% Similarity=0.296 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHhCCCCc----cChHHHHHHcCCCCC---CHHHHHhhhcc
Q 038544 25 ELHKHFSQAVERLGGKYK----ASPKRILHMMNVKGL---KLSHIKSHLQV 68 (69)
Q Consensus 25 eLH~~Fv~Av~~LGg~~~----A~Pk~Il~~M~v~gL---T~~~VkSHLQK 68 (69)
+|++.|. +|..+||.+. ..|..|.+.||++.- ...++++|-++
T Consensus 33 dL~~Ly~-~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k 82 (93)
T smart00501 33 DLYRLYR-LVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYER 82 (93)
T ss_pred cHHHHHH-HHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHH
Confidence 7888898 5888898542 469999999999742 13345555443
No 17
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=77.98 E-value=2.2 Score=24.89 Aligned_cols=47 Identities=26% Similarity=0.344 Sum_probs=29.1
Q ss_pred cccCCHHHHHHHHHHHHH------h--CCCC--ccChHHHHHHcCCCCC--CHHHHHhh
Q 038544 19 RLRWTPELHKHFSQAVER------L--GGKY--KASPKRILHMMNVKGL--KLSHIKSH 65 (69)
Q Consensus 19 R~~WT~eLH~~Fv~Av~~------L--Gg~~--~A~Pk~Il~~M~v~gL--T~~~VkSH 65 (69)
|-.||++.-..|++++.. + |+.. ...++.|.+.|..-|. |..|++..
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~K 59 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNK 59 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence 457999999999999866 2 1111 2367888888875554 77777653
No 18
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=77.57 E-value=2.6 Score=33.02 Aligned_cols=45 Identities=18% Similarity=0.220 Sum_probs=38.6
Q ss_pred cccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhcc
Q 038544 19 RLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQV 68 (69)
Q Consensus 19 R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQK 68 (69)
.--|+.+....|+++.+.||. ..|..|.+..|. -+.+.|+||-=|
T Consensus 63 ~e~WgadEEllli~~~~TlGl---GNW~dIadyiGs--r~kee~k~HylK 107 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGL---GNWEDIADYIGS--RAKEEIKSHYLK 107 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCC---CcHHHHHHHHhh--hhhHHHHHHHHH
Confidence 446999999999999999996 369999999994 589999999654
No 19
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=76.30 E-value=1.6 Score=31.87 Aligned_cols=45 Identities=20% Similarity=0.203 Sum_probs=29.5
Q ss_pred cccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhccC
Q 038544 19 RLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQVN 69 (69)
Q Consensus 19 R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQKy 69 (69)
.-+||++.|.+|.+++-.. +..|..|-+.-+. .+.-++.+|-|+|
T Consensus 53 ~~~~t~~~~~~~~~~l~~~----~~~~~~~~~~~~~--~~~v~~~~~~~~~ 97 (335)
T KOG0724|consen 53 EPRRTPDSWDKFAEALPLE----KRLEDKIEEYIGL--VFDVNIRESGQKP 97 (335)
T ss_pred ccccchhhhhHHHhcCccc----cccchhHHhhhhh--HHHHhhhhccCCC
Confidence 3458888888887776543 2356777666554 3666777776664
No 20
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=72.61 E-value=16 Score=25.85 Aligned_cols=48 Identities=21% Similarity=0.256 Sum_probs=40.0
Q ss_pred ccCCCCCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhh
Q 038544 12 YNKSELPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSH 65 (69)
Q Consensus 12 ~~~~kk~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSH 65 (69)
|-++.-.|-.||+|.-+.-+++-..+|-. +..|... +||-|-..||.|
T Consensus 55 yLrP~ikrg~fT~eEe~~Ii~lH~~~GNr----Ws~IA~~--LPGRTDNeIKN~ 102 (238)
T KOG0048|consen 55 YLRPDLKRGNFSDEEEDLIIKLHALLGNR----WSLIAGR--LPGRTDNEVKNH 102 (238)
T ss_pred ccCCCccCCCCCHHHHHHHHHHHHHHCcH----HHHHHhh--CCCcCHHHHHHH
Confidence 55666678889999999999999999974 8888655 688999999876
No 21
>PF07384 DUF1497: Protein of unknown function (DUF1497); InterPro: IPR009972 This entry is represented by Bacteriophage r1t, Orf17. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins of around 59 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this organism. The function of this family is unknown.
Probab=69.61 E-value=5.4 Score=23.42 Aligned_cols=21 Identities=29% Similarity=0.763 Sum_probs=18.5
Q ss_pred cCCHHHHHHHHHHHHHhCCCC
Q 038544 21 RWTPELHKHFSQAVERLGGKY 41 (69)
Q Consensus 21 ~WT~eLH~~Fv~Av~~LGg~~ 41 (69)
.+..|+|..|-+-|+.|||..
T Consensus 37 kfnqem~aefheri~klggk~ 57 (59)
T PF07384_consen 37 KFNQEMQAEFHERIKKLGGKN 57 (59)
T ss_pred HhhHHHHHHHHHHHHHhcccc
Confidence 467899999999999999953
No 22
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=65.30 E-value=5.1 Score=22.80 Aligned_cols=26 Identities=19% Similarity=0.330 Sum_probs=21.2
Q ss_pred ChHHHHHHcC---CCCCCHHHHHhhhccC
Q 038544 44 SPKRILHMMN---VKGLKLSHIKSHLQVN 69 (69)
Q Consensus 44 ~Pk~Il~~M~---v~gLT~~~VkSHLQKy 69 (69)
++..+++.++ ..|||.++|...+++|
T Consensus 5 ~~~~v~~~l~t~~~~GLs~~ev~~r~~~~ 33 (69)
T PF00690_consen 5 SVEEVLKRLNTSSSQGLSSEEVEERRKKY 33 (69)
T ss_dssp SHHHHHHHHTTBTSSBBTHHHHHHHHHHH
T ss_pred CHHHHHHHHCcCCCCCCCHHHHHHHHHhc
Confidence 4667788887 4899999999998875
No 23
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=64.88 E-value=13 Score=24.29 Aligned_cols=39 Identities=13% Similarity=0.227 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 26 LHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 26 LH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
.+..+.+|++.|... +.-+++.|.+.||+ |...|+++++
T Consensus 128 ~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgi---s~~tv~~~l~ 176 (193)
T PRK11923 128 IEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQC---PVGTVRSRIF 176 (193)
T ss_pred HHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 456677888777632 12234555555554 4555555554
No 24
>PF08127 Propeptide_C1: Peptidase family C1 propeptide; InterPro: IPR012599 This domain is found at the N-terminal of cathepsin B and cathepsin B-like peptidases that belong to MEROPS peptidase subfamily C1A. Cathepsin B are lysosomal cysteine proteinases belonging to the papain superfamily and are unique in their ability to act as both an endo- and an exopeptidases. They are synthesized as inactive zymogens. Activation of the peptidases occurs with the removal of the propeptide [, ]. ; GO: 0004197 cysteine-type endopeptidase activity, 0050790 regulation of catalytic activity; PDB: 1MIR_A 1PBH_A 2PBH_A 3PBH_A.
Probab=64.71 E-value=6.2 Score=21.43 Aligned_cols=34 Identities=21% Similarity=0.297 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhh
Q 038544 26 LHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 26 LH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
|-+.|++-|+...-.++|-.. .++.|.++|++.|
T Consensus 1 Lsde~I~~IN~~~~tWkAG~N-------F~~~~~~~ik~Ll 34 (41)
T PF08127_consen 1 LSDEFIDYINSKNTTWKAGRN-------FENTSIEYIKRLL 34 (41)
T ss_dssp S-HHHHHHHHHCT-SEEE-----------SSB-HHHHHHCS
T ss_pred CCHHHHHHHHcCCCcccCCCC-------CCCCCHHHHHHHc
Confidence 346799999998755555432 3666666666654
No 25
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=62.97 E-value=15 Score=31.44 Aligned_cols=44 Identities=25% Similarity=0.259 Sum_probs=34.5
Q ss_pred CCCCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHH
Q 038544 15 SELPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIK 63 (69)
Q Consensus 15 ~kk~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~Vk 63 (69)
+.-+.-.||++.-...+.||+.+|+.+-+.|... |||-+..|+.
T Consensus 356 Psikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~-----vPnRSdsQcR 399 (939)
T KOG0049|consen 356 PSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQA-----VPNRSDSQCR 399 (939)
T ss_pred ccccCCCCCCHHHHHHHHHHHHhCccchhhHHHh-----cCCccHHHHH
Confidence 3456778999999999999999999876666653 6777766654
No 26
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=60.36 E-value=5.3 Score=23.96 Aligned_cols=26 Identities=12% Similarity=0.188 Sum_probs=20.3
Q ss_pred CCccChHHHHHHcCCCCCCHHHHHhhhcc
Q 038544 40 KYKASPKRILHMMNVKGLKLSHIKSHLQV 68 (69)
Q Consensus 40 ~~~A~Pk~Il~~M~v~gLT~~~VkSHLQK 68 (69)
.+.++.+.|.+..++ |..++.+||++
T Consensus 12 ~~~~~f~~L~~~l~l---t~g~Ls~hL~~ 37 (80)
T PF13601_consen 12 NEEATFSELKEELGL---TDGNLSKHLKK 37 (80)
T ss_dssp HSEEEHHHHHHHTT-----HHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCc---CHHHHHHHHHH
Confidence 357889999998887 89999999974
No 27
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=56.49 E-value=31 Score=22.59 Aligned_cols=45 Identities=16% Similarity=0.112 Sum_probs=30.9
Q ss_pred ccCCHHHHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 20 LRWTPELHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 20 ~~WT~eLH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
..+.+++.....++++.|... +.-+.+.|.+.||+ |...|+++|.
T Consensus 118 ~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgi---s~~tV~~~l~ 172 (188)
T PRK09640 118 KAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHM---GLSATKMRYK 172 (188)
T ss_pred ccccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 345677778888888888733 23456777777776 5677777764
No 28
>KOG2983 consensus Uncharacterized conserved protein [Function unknown]
Probab=55.87 E-value=9.6 Score=29.21 Aligned_cols=17 Identities=41% Similarity=0.858 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHhCCC
Q 038544 24 PELHKHFSQAVERLGGK 40 (69)
Q Consensus 24 ~eLH~~Fv~Av~~LGg~ 40 (69)
||||++--+||+.|||.
T Consensus 85 ~El~qki~eaineLGga 101 (334)
T KOG2983|consen 85 PELEQKIREAINELGGA 101 (334)
T ss_pred HHHHHHHHHHHHHccce
Confidence 38999999999999984
No 29
>cd08783 Death_MALT1 Death domain similar to that found in Mucosa-associated lymphoid tissue-lymphoma-translocation gene 1. Death domain (DD) similar to that found in Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1). Malt1, together with Bcl10 (B-cell lymphoma 10), are the integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins
Probab=55.08 E-value=22 Score=22.98 Aligned_cols=47 Identities=19% Similarity=0.401 Sum_probs=36.9
Q ss_pred CcccCCH-HHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhcc
Q 038544 18 PRLRWTP-ELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQV 68 (69)
Q Consensus 18 ~R~~WT~-eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQK 68 (69)
+||+-++ ||+++-+..++.-|- ..+..|..|++.|-|..+.-.-||.
T Consensus 36 ~~fr~S~~el~~cslkvl~p~gS----Psk~LL~~~~~rg~Tv~~Ll~~L~~ 83 (97)
T cd08783 36 GRFRLSCLDLEQCSLKVLEPEGS----PSRSLLKLLGERGCTVTELSEFLQA 83 (97)
T ss_pred CccccCHHHHHHHHHHHhcCCCC----chHHHHHHHHHcCCcHHHHHHHHHH
Confidence 3788888 787777777766553 3688999999999999998887764
No 30
>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=53.90 E-value=20 Score=25.04 Aligned_cols=48 Identities=25% Similarity=0.355 Sum_probs=33.5
Q ss_pred CCCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhccC
Q 038544 16 ELPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQVN 69 (69)
Q Consensus 16 kk~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQKy 69 (69)
-...|+|+..+-..+.+||+.--- ..-.++. ....||.++|-+-||.|
T Consensus 45 AACGFRWNs~VRkqY~~~i~~AKk-qRk~~~~-----~~~~ltl~~vI~fLq~l 92 (161)
T TIGR02894 45 AACGFRWNAYVRKQYEEAIELAKK-QRKELKR-----EAGSLTLQDVISFLQNL 92 (161)
T ss_pred HHhcchHHHHHHHHHHHHHHHHHH-HHhcccc-----CcccCCHHHHHHHHHHH
Confidence 457899999999999999986432 1111111 12568999999988864
No 31
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=53.74 E-value=31 Score=22.82 Aligned_cols=38 Identities=16% Similarity=0.234 Sum_probs=21.9
Q ss_pred HHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 27 HKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 27 H~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
...+..|+++|... +.-+-+.|.+.||+ |...|+|||.
T Consensus 125 ~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgi---s~~tVk~~l~ 172 (189)
T PRK12530 125 WLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDI---STSNLHVLLY 172 (189)
T ss_pred HHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 34566788887632 12334555555554 5667777764
No 32
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=53.52 E-value=29 Score=23.18 Aligned_cols=44 Identities=25% Similarity=0.423 Sum_probs=31.6
Q ss_pred CHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 23 TPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 23 T~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
+++.=..+-++++.|-. ....-.++++++-+.|+|.++|+..|.
T Consensus 119 ~~~~~~~l~e~l~~L~~-l~~~~~~~v~l~~~~Gls~~EIA~~lg 162 (185)
T PF07638_consen 119 SPEELLELEEALERLLA-LDPRQRRVVELRFFEGLSVEEIAERLG 162 (185)
T ss_pred CHHHHHHHHHHHHHHHc-cCHHHHHHHHHHHHCCCCHHHHHHHHC
Confidence 34444556777777764 334557888888899999999998774
No 33
>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=52.45 E-value=34 Score=18.23 Aligned_cols=46 Identities=17% Similarity=0.120 Sum_probs=29.6
Q ss_pred CCCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHh
Q 038544 16 ELPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKS 64 (69)
Q Consensus 16 kk~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkS 64 (69)
|++|..+|++- ...|+++...+. ..+...+.++...=|||..+|..
T Consensus 1 kr~r~~~t~~q-~~~L~~~f~~~~--~p~~~~~~~la~~l~l~~~~V~~ 46 (57)
T PF00046_consen 1 KRKRTRFTKEQ-LKVLEEYFQENP--YPSKEEREELAKELGLTERQVKN 46 (57)
T ss_dssp SSSSSSSSHHH-HHHHHHHHHHSS--SCHHHHHHHHHHHHTSSHHHHHH
T ss_pred CcCCCCCCHHH-HHHHHHHHHHhc--ccccccccccccccccccccccc
Confidence 46778888664 456666666543 35555666655555778888865
No 34
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=51.97 E-value=34 Score=21.36 Aligned_cols=41 Identities=10% Similarity=0.145 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 24 PELHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 24 ~eLH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
.+++..+.++++.|.-. +.-+.+.|.+.||+ |...|++++.
T Consensus 99 ~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~i---s~~tv~~~l~ 149 (159)
T TIGR02989 99 EDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGR---TVNAVYKALS 149 (159)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCC---CHHHHHHHHH
Confidence 44455566777666521 22346666666665 5666766653
No 35
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=51.29 E-value=14 Score=21.01 Aligned_cols=34 Identities=15% Similarity=0.180 Sum_probs=23.9
Q ss_pred HHHHHHHHHhC-CCCccChHHHHHHcCCCCCCHHH
Q 038544 28 KHFSQAVERLG-GKYKASPKRILHMMNVKGLKLSH 61 (69)
Q Consensus 28 ~~Fv~Av~~LG-g~~~A~Pk~Il~~M~v~gLT~~~ 61 (69)
..|+.+|..|+ ....++++.|.+.|||.-=|...
T Consensus 7 e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ 41 (60)
T PF01325_consen 7 EDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTE 41 (60)
T ss_dssp HHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHH
Confidence 46889998876 22468999999999994334333
No 36
>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=50.60 E-value=38 Score=17.92 Aligned_cols=23 Identities=22% Similarity=0.288 Sum_probs=15.3
Q ss_pred cChHHHHHHcCCCCCCHHHHHhhhcc
Q 038544 43 ASPKRILHMMNVKGLKLSHIKSHLQV 68 (69)
Q Consensus 43 A~Pk~Il~~M~v~gLT~~~VkSHLQK 68 (69)
-+.+.|.+.||+ |...|++++++
T Consensus 27 ~s~~eIa~~l~~---s~~~v~~~l~r 49 (54)
T PF08281_consen 27 MSYAEIAEILGI---SESTVKRRLRR 49 (54)
T ss_dssp --HHHHHHHCTS----HHHHHHHHHH
T ss_pred cCHHHHHHHHCc---CHHHHHHHHHH
Confidence 357788888865 78888888753
No 37
>PF14075 UBN_AB: Ubinuclein conserved middle domain
Probab=49.59 E-value=23 Score=25.28 Aligned_cols=23 Identities=22% Similarity=0.443 Sum_probs=18.8
Q ss_pred ccCCCCCcccCCHHHHHHHHHHH
Q 038544 12 YNKSELPRLRWTPELHKHFSQAV 34 (69)
Q Consensus 12 ~~~~kk~R~~WT~eLH~~Fv~Av 34 (69)
.....+.+|.||+++-..+.+.|
T Consensus 145 ~~~~PrKkF~Wtde~R~lL~~lv 167 (214)
T PF14075_consen 145 KVKGPRKKFQWTDEIRELLCELV 167 (214)
T ss_pred CCCCCCcCCCCCHHHHHHHHHHH
Confidence 44566789999999999987776
No 38
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=49.56 E-value=25 Score=22.58 Aligned_cols=43 Identities=16% Similarity=0.221 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 22 WTPELHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 22 WT~eLH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
|..+.-.....+++.|... +.-+.+.|.+.||+ +...|++||.
T Consensus 105 ~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~lgi---s~~tV~~~l~ 157 (173)
T PRK12522 105 IQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNI---PIGTVKYRLN 157 (173)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCC---CHHHHHHHHH
Confidence 3333334455566555531 23456777777776 5778888875
No 39
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=49.25 E-value=36 Score=21.54 Aligned_cols=37 Identities=24% Similarity=0.326 Sum_probs=21.6
Q ss_pred HHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 28 KHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 28 ~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
..++.|+..|... +.-+.+.|.+.||+ |...|++||.
T Consensus 104 ~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgi---s~~tv~~~l~ 150 (161)
T PRK12541 104 ASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGL---SLAKVKIELH 150 (161)
T ss_pred HHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 4566777666632 22345566666665 5666777664
No 40
>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=48.11 E-value=45 Score=20.44 Aligned_cols=41 Identities=22% Similarity=0.314 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 24 PELHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 24 ~eLH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
.|+...+.+++..|... +.-+++.|.+.||+ |...|++++.
T Consensus 101 ~e~~~~l~~~l~~L~~~~r~il~l~~~~~~~~~eIA~~lgi---s~~tv~~~~~ 151 (161)
T TIGR02985 101 KELQLIIYKAIEKLPEQCRKIFILSRFEGKSYKEIAEELGI---SVKTVEYHIS 151 (161)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 34555566666655421 22345666666655 5666666553
No 41
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=47.15 E-value=48 Score=20.86 Aligned_cols=36 Identities=14% Similarity=0.159 Sum_probs=19.9
Q ss_pred HHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 29 HFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 29 ~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
.+..+++.|... +.-+.+.|.+.||+ +...|++||.
T Consensus 99 ~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgi---s~~tV~~~l~ 144 (160)
T PRK09642 99 LIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKI---EVKTVEMKLY 144 (160)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 455666666522 22345556666655 5666777664
No 42
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=46.94 E-value=47 Score=21.60 Aligned_cols=39 Identities=15% Similarity=0.220 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhh
Q 038544 25 ELHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 25 eLH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
++...+.++++.|... +.-+++.|.+.||+ +...|+++|
T Consensus 118 ~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~i---s~~tV~~~l 166 (181)
T PRK12536 118 EARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGL---SESAVKVGI 166 (181)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCC---CHHHHHHHH
Confidence 4556677777776532 22346666666665 566666665
No 43
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=44.80 E-value=49 Score=21.38 Aligned_cols=35 Identities=11% Similarity=0.288 Sum_probs=22.2
Q ss_pred HHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 30 FSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 30 Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
..+|+..|... +.-+++.|.+.||+ |...|+++|+
T Consensus 129 l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgi---s~~~V~~~l~ 173 (186)
T PRK13919 129 LGRALKALSPEERRVIEVLYYQGYTHREAAQLLGL---PLGTLKTRAR 173 (186)
T ss_pred HHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHH
Confidence 45666666522 33457777777776 5677777765
No 44
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=44.50 E-value=52 Score=26.62 Aligned_cols=44 Identities=16% Similarity=0.228 Sum_probs=36.5
Q ss_pred CCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhh
Q 038544 17 LPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 17 k~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
..+-.||++.=...++||+.+|-. |.+|....|.+ |.++.-+|.
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~dd----W~kVa~hVg~k--s~eqCI~kF 294 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGDD----WNKVADHVGTK--SQEQCILKF 294 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhccc----HHHHHhccCCC--CHHHHHHHH
Confidence 456789999999999999999963 99999988865 888877663
No 45
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=43.73 E-value=47 Score=21.88 Aligned_cols=39 Identities=10% Similarity=0.186 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhh
Q 038544 25 ELHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 25 eLH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
++...+.+|++.|... +.-+.+.|.+.||+ +...|+++|
T Consensus 131 ~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~Lgi---s~~tVk~~l 179 (194)
T PRK09646 131 LERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAV---PLGTVKTRM 179 (194)
T ss_pred hHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCC---ChHhHHHHH
Confidence 3445677788777632 22344555555555 555566654
No 46
>PF07065 D123: D123; InterPro: IPR009772 This family contains a number of eukaryotic D123 proteins approximately 330 residues long. It has been shown that mutated variants of D123 exhibit temperature-dependent differences in their degradation rate [].
Probab=42.61 E-value=16 Score=27.12 Aligned_cols=17 Identities=53% Similarity=1.027 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHhCCC
Q 038544 24 PELHKHFSQAVERLGGK 40 (69)
Q Consensus 24 ~eLH~~Fv~Av~~LGg~ 40 (69)
++||+..-+||+.|||.
T Consensus 71 p~l~~~I~~aI~~lgg~ 87 (299)
T PF07065_consen 71 PELHQEIREAIEELGGS 87 (299)
T ss_pred HHHHHHHHHHHHHcCCe
Confidence 78999999999999984
No 47
>cd02185 AroH Chorismate mutase (AroH) is one of at least five chorismate-utilizing enzymes present in microorganisms that catalyze the rearrangement of chorismate to prephenic acid, the first committed step in the biosynthesis of aromatic amino acids. In prokaryotes, chorismate mutase may be fused to prephenate dehydratase, prephenate dehydrogenase, or 3-deoxy-D-arabino-heptulosonat-7-phosphate (DAHP) as part of a bifunctional enzyme. The AroH domain forms a homotrimer with three-fold symmetry.
Probab=42.06 E-value=5.8 Score=26.37 Aligned_cols=36 Identities=36% Similarity=0.612 Sum_probs=24.5
Q ss_pred ccCCHHHHHHH-HHHHHHhCCCCccChHHHHHHcCCCC
Q 038544 20 LRWTPELHKHF-SQAVERLGGKYKASPKRILHMMNVKG 56 (69)
Q Consensus 20 ~~WT~eLH~~F-v~Av~~LGg~~~A~Pk~Il~~M~v~g 56 (69)
|.=|++|+..| -.|..++|| ++.+|--=.+-|.|||
T Consensus 45 FT~T~DL~a~FPA~aaR~~~~-~~~Vplmc~qE~~V~g 81 (117)
T cd02185 45 FTVTPDLDAAFPAKAARELGG-WKYVPLMCAQEMDVPG 81 (117)
T ss_pred EEeCCcccccChHHHHHhcCC-CCCcceeecCcCCCCC
Confidence 45588999999 455677776 5667765555666655
No 48
>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=41.53 E-value=46 Score=16.29 Aligned_cols=22 Identities=18% Similarity=0.351 Sum_probs=16.3
Q ss_pred cChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 43 ASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 43 A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
-+++.|.+.||+ +...|.++++
T Consensus 27 ~~~~~ia~~~~~---s~~~i~~~~~ 48 (55)
T cd06171 27 LSYEEIAEILGI---SRSTVRQRLH 48 (55)
T ss_pred CCHHHHHHHHCc---CHHHHHHHHH
Confidence 368899998886 6677776654
No 49
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=41.22 E-value=67 Score=18.12 Aligned_cols=37 Identities=16% Similarity=0.347 Sum_probs=22.7
Q ss_pred HHHHHHHHHHH----HhCCCCccChHHHHHHcCCCCCCHHHHHhhh
Q 038544 25 ELHKHFSQAVE----RLGGKYKASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 25 eLH~~Fv~Av~----~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
|+..+...|+. .+|. .+++..|.+.||+ +.+.|..-|
T Consensus 1 E~l~~i~~a~~~L~~~lgr--~Pt~eEiA~~lgi---s~~~v~~~l 41 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGR--EPTDEEIAEELGI---SVEEVRELL 41 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS----BHHHHHHHHTS----HHHHHHHH
T ss_pred ChHHHHHHHHHHHHHHhCC--CCCHHHHHHHHcc---cHHHHHHHH
Confidence 34455666664 4565 5899999999987 566665433
No 50
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=41.12 E-value=61 Score=21.12 Aligned_cols=40 Identities=23% Similarity=0.338 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 25 ELHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 25 eLH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
+....+.+|+..|--. +.=++..|.+.||+ +...|+|++.
T Consensus 116 ~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i---~~~tVks~l~ 165 (182)
T COG1595 116 EELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGI---SVGTVKSRLH 165 (182)
T ss_pred HHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 4445666777665421 22356677777766 4666777764
No 51
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=40.82 E-value=51 Score=23.36 Aligned_cols=39 Identities=15% Similarity=0.223 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 26 LHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 26 LH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
+...+.+++++|... +.-+-+.|.+.||+ +...|++||+
T Consensus 132 ~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgi---s~~tV~~~l~ 180 (324)
T TIGR02960 132 VRLAFVAAIQYLPPRQRAVLLLRDVLGWRAAETAELLGT---STASVNSALQ 180 (324)
T ss_pred HHHHHHHHHHhCCHHHhhHhhhHHHhCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 345577788877632 12234555555555 5666777765
No 52
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=40.48 E-value=14 Score=21.77 Aligned_cols=25 Identities=12% Similarity=0.133 Sum_probs=19.4
Q ss_pred hHHHHHHcCCCCCCHHHHHhhhccC
Q 038544 45 PKRILHMMNVKGLKLSHIKSHLQVN 69 (69)
Q Consensus 45 Pk~Il~~M~v~gLT~~~VkSHLQKy 69 (69)
+....+.||.+.+|+.+|-+++-+|
T Consensus 8 s~~L~~~lg~~~~sr~~v~~~lw~Y 32 (76)
T PF02201_consen 8 SPELAEFLGEDELSRSEVVKRLWQY 32 (76)
T ss_dssp HHHHHHHTT-SCEEHHHHHHHHHHH
T ss_pred CHHHHHHhCCCCCCHHHHHHHHHHH
Confidence 4567888999889999998887655
No 53
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=39.85 E-value=62 Score=20.73 Aligned_cols=22 Identities=18% Similarity=0.419 Sum_probs=14.1
Q ss_pred cChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 43 ASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 43 A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
-+.+.|.+.||+ |...|+++|+
T Consensus 153 ~s~~eIA~~lgi---s~~~v~~~l~ 174 (187)
T TIGR02948 153 LSLKEISEILDL---PVGTVKTRIH 174 (187)
T ss_pred CCHHHHHHHHCC---CHHHHHHHHH
Confidence 456666666666 5666776664
No 54
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=39.46 E-value=61 Score=20.34 Aligned_cols=22 Identities=18% Similarity=0.377 Sum_probs=15.4
Q ss_pred cChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 43 ASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 43 A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
-+.+.|.+.||+ +...|++|+.
T Consensus 127 ~s~~eIA~~lgi---s~~tV~~~l~ 148 (162)
T TIGR02983 127 LSEAQVAEALGI---SVGTVKSRLS 148 (162)
T ss_pred CCHHHHHHHhCC---CHHHHHHHHH
Confidence 456777777776 5777887764
No 55
>COG4672 gp18 Phage-related protein [Function unknown]
Probab=39.44 E-value=23 Score=26.09 Aligned_cols=24 Identities=29% Similarity=0.385 Sum_probs=20.4
Q ss_pred HHHHHHHHHHhCCCCccChHHHHH
Q 038544 27 HKHFSQAVERLGGKYKASPKRILH 50 (69)
Q Consensus 27 H~~Fv~Av~~LGg~~~A~Pk~Il~ 50 (69)
-.+|++||+.-.|.-.|.|.+.+-
T Consensus 108 yarfLDAvNF~~GNp~ADPeQe~~ 131 (231)
T COG4672 108 YARFLDAVNFVAGNPEADPEQELV 131 (231)
T ss_pred HHhhhhhhcccCCCCCCChhHHHH
Confidence 468999999998877899998763
No 56
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=39.39 E-value=63 Score=21.01 Aligned_cols=38 Identities=26% Similarity=0.275 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 27 HKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 27 H~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
......+++.|... +.-+.+.|.+.||+ +...|++||.
T Consensus 118 ~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~i---s~~tv~~~l~ 165 (179)
T PRK09415 118 DERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGV---NENTVKTRLK 165 (179)
T ss_pred HHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 34456666666532 22345666666665 5666777764
No 57
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=39.02 E-value=46 Score=21.17 Aligned_cols=39 Identities=15% Similarity=0.153 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 25 ELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 25 eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
++...+..++..|.. .-+.|+.+.-+.|++.++|+..|.
T Consensus 97 ~~~~~l~~~l~~L~~----~~r~v~~l~~~~g~s~~eIA~~lg 135 (165)
T PRK09644 97 NSYEKLIQIIHTLPV----IEAQAILLCDVHELTYEEAASVLD 135 (165)
T ss_pred HHHHHHHHHHHhCCH----HHHHHHHhHHHhcCCHHHHHHHHC
Confidence 344555666666653 245555555567777777666554
No 58
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=38.87 E-value=55 Score=21.43 Aligned_cols=37 Identities=19% Similarity=0.267 Sum_probs=21.6
Q ss_pred HHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 28 KHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 28 ~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
.....|++.|... +.-+.+.|.+.||+ |...|++||.
T Consensus 123 ~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lgi---s~~tVk~~l~ 169 (193)
T TIGR02947 123 QDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGT---PIGTVMSRLH 169 (193)
T ss_pred HHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 4455667666521 23445666666665 5667777764
No 59
>PF09535 Gmx_para_CXXCG: Protein of unknown function (Gmx_para_CXXCG); InterPro: IPR011750 This entry consists of at least 10 paralogous proteins from Myxococcus xanthus that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment.
Probab=38.75 E-value=22 Score=26.25 Aligned_cols=13 Identities=46% Similarity=0.728 Sum_probs=11.2
Q ss_pred HHHHHHHHHhCCC
Q 038544 28 KHFSQAVERLGGK 40 (69)
Q Consensus 28 ~~Fv~Av~~LGg~ 40 (69)
.+||+||++||..
T Consensus 215 ERFVeAv~rL~l~ 227 (237)
T PF09535_consen 215 ERFVEAVQRLGLD 227 (237)
T ss_pred HHHHHHHHhcCCC
Confidence 5799999999963
No 60
>PHA02943 hypothetical protein; Provisional
Probab=37.97 E-value=96 Score=21.83 Aligned_cols=41 Identities=17% Similarity=0.225 Sum_probs=31.6
Q ss_pred CHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 23 TPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 23 T~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
|+.+|.+-.+.++.|.. ..++...|.+.+|+ +-.+|.-||.
T Consensus 6 sd~v~~R~~eILE~Lk~-G~~TtseIAkaLGl---S~~qa~~~Ly 46 (165)
T PHA02943 6 SDTVHTRMIKTLRLLAD-GCKTTSRIANKLGV---SHSMARNALY 46 (165)
T ss_pred hHHHHHHHHHHHHHHhc-CCccHHHHHHHHCC---CHHHHHHHHH
Confidence 67888888888888832 34778899998887 6778777763
No 61
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=37.48 E-value=47 Score=22.56 Aligned_cols=37 Identities=19% Similarity=0.340 Sum_probs=22.8
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHH
Q 038544 20 LRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIK 63 (69)
Q Consensus 20 ~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~Vk 63 (69)
|.||+|- ++.+.+|=. +..+=.+|.+.|| ++|+.-|-
T Consensus 1 M~Wtde~----~~~L~~lw~-~G~SasqIA~~lg--~vsRnAVi 37 (162)
T PF07750_consen 1 MSWTDER----VERLRKLWA-EGLSASQIARQLG--GVSRNAVI 37 (162)
T ss_pred CCCCHHH----HHHHHHHHH-cCCCHHHHHHHhC--Ccchhhhh
Confidence 5799986 445554432 3355678888887 45665553
No 62
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=37.02 E-value=45 Score=23.50 Aligned_cols=30 Identities=23% Similarity=0.307 Sum_probs=23.4
Q ss_pred cccCCHHHHHHHHHHHHHhCC-CCccChHHH
Q 038544 19 RLRWTPELHKHFSQAVERLGG-KYKASPKRI 48 (69)
Q Consensus 19 R~~WT~eLH~~Fv~Av~~LGg-~~~A~Pk~I 48 (69)
+..||+|.-.+.++-|...|- .+.+.|+.+
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~ 39 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLA 39 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhc
Confidence 689999999999999999993 244455443
No 63
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=36.96 E-value=70 Score=21.69 Aligned_cols=36 Identities=19% Similarity=0.348 Sum_probs=22.5
Q ss_pred HHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 29 HFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 29 ~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
.+..++..|.-. +.-+-+.|.+.||+ |...|++||+
T Consensus 141 ~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIAe~lgi---s~~tV~~~l~ 186 (206)
T PRK12544 141 IFEACLDGLPAKYARVFMMREFIELETNEICHAVDL---SVSNLNVLLY 186 (206)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHH
Confidence 466667666521 22345667777766 6788888875
No 64
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=36.84 E-value=69 Score=22.73 Aligned_cols=38 Identities=13% Similarity=0.098 Sum_probs=23.3
Q ss_pred HHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 27 HKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 27 H~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
...+..+++.|... +.-+.+.|.+.||+ |...|+|+|+
T Consensus 106 ~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~---s~~tVk~~l~ 153 (293)
T PRK09636 106 SLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGR---SPAACRQLAS 153 (293)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 34577778777632 22345666666655 6777777765
No 65
>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=36.48 E-value=56 Score=23.08 Aligned_cols=39 Identities=21% Similarity=0.238 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 26 LHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 26 LH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
+.....+|+++|... +.-+-+.|.+.||+ +...|+|||.
T Consensus 151 ~~~~l~~aL~~Lp~~~R~v~~L~~~eg~S~~EIA~~Lgi---s~~TVk~rl~ 199 (244)
T TIGR03001 151 FRQALREALAALSERERHLLRLHFVDGLSMDRIGAMYQV---HRSTVSRWVA 199 (244)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHH
Confidence 334456677776532 22334555555554 5566666654
No 66
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=36.08 E-value=22 Score=18.24 Aligned_cols=13 Identities=31% Similarity=0.560 Sum_probs=9.1
Q ss_pred CCCCHHHHHhhhc
Q 038544 55 KGLKLSHIKSHLQ 67 (69)
Q Consensus 55 ~gLT~~~VkSHLQ 67 (69)
-|||.++|+..|+
T Consensus 15 ~Gls~eeir~FL~ 27 (30)
T PF08671_consen 15 SGLSKEEIREFLE 27 (30)
T ss_dssp TT--HHHHHHHHH
T ss_pred cCCCHHHHHHHHH
Confidence 4789999998875
No 67
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=35.90 E-value=93 Score=20.54 Aligned_cols=21 Identities=24% Similarity=0.184 Sum_probs=14.3
Q ss_pred cChHHHHHHcCCCCCCHHHHHhhh
Q 038544 43 ASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 43 A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
-+++.|.+.||+ |...|+++|
T Consensus 151 ~s~~EIA~~lg~---s~~tV~~rl 171 (192)
T PRK09643 151 YSVADAARMLGV---AEGTVKSRC 171 (192)
T ss_pred CCHHHHHHHHCc---CHHHHHHHH
Confidence 456777777776 567777776
No 68
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=35.82 E-value=72 Score=21.07 Aligned_cols=21 Identities=14% Similarity=0.178 Sum_probs=12.2
Q ss_pred ChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 44 SPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 44 ~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
+.+.|.+.||+ |...|+++|.
T Consensus 149 s~~EIA~~lgi---s~~tvk~rl~ 169 (188)
T TIGR02943 149 ESDEICQELEI---STSNCHVLLY 169 (188)
T ss_pred CHHHHHHHhCC---CHHHHHHHHH
Confidence 44555555554 5666777654
No 69
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=35.25 E-value=70 Score=16.56 Aligned_cols=37 Identities=8% Similarity=0.159 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhcc
Q 038544 26 LHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQV 68 (69)
Q Consensus 26 LH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQK 68 (69)
-..+-+.++..-| .++.+.|.+.+|+ |..-|..||++
T Consensus 4 ~~~~Il~~l~~~~---~~t~~ela~~~~i---s~~tv~~~l~~ 40 (48)
T PF13412_consen 4 TQRKILNYLRENP---RITQKELAEKLGI---SRSTVNRYLKK 40 (48)
T ss_dssp HHHHHHHHHHHCT---TS-HHHHHHHHTS----HHHHHHHHHH
T ss_pred HHHHHHHHHHHcC---CCCHHHHHHHhCC---CHHHHHHHHHH
Confidence 3455567777744 3788899988886 78888888764
No 70
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=34.74 E-value=1e+02 Score=18.83 Aligned_cols=48 Identities=21% Similarity=0.110 Sum_probs=33.9
Q ss_pred ccCCHHHHHHHHHHHHHhC--CCCccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 20 LRWTPELHKHFSQAVERLG--GKYKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 20 ~~WT~eLH~~Fv~Av~~LG--g~~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
..+++++.....+++..+= ....-+|..|..++.-.|+|..+++..|.
T Consensus 40 ~~~~~e~~~~~~~~i~~~~~~~~~~~~~~~i~~~r~~~gltq~~lA~~lg 89 (127)
T TIGR03830 40 ELLDPEESKRNSAALADFYRKVDGLLTPPEIRRIRKKLGLSQREAAELLG 89 (127)
T ss_pred EEEcHHHHHHHHHHHHHHHHHccCCcCHHHHHHHHHHcCCCHHHHHHHhC
Confidence 3567777777777775541 11246788898888888999998887663
No 71
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=34.26 E-value=92 Score=21.32 Aligned_cols=22 Identities=9% Similarity=0.155 Sum_probs=15.2
Q ss_pred ccChHHHHHHcCCCCCCHHHHHhhh
Q 038544 42 KASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 42 ~A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
.-+.+.|.+.||+ |...|++++
T Consensus 195 ~~S~~EIA~~lgi---s~~tV~~~~ 216 (233)
T PRK05803 195 EKTQREIAKALGI---SRSYVSRIE 216 (233)
T ss_pred CcCHHHHHHHHCc---CHHHHHHHH
Confidence 4567777777776 577777765
No 72
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=34.24 E-value=76 Score=21.18 Aligned_cols=36 Identities=14% Similarity=0.182 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 29 HFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 29 ~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
.+.+++..|... +.-+-+.|.+.||+ +...|+++|.
T Consensus 132 ~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgi---s~~tVk~~l~ 177 (201)
T PRK12545 132 LFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTL---TANHCSVLLY 177 (201)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHH
Confidence 455677766521 22345566666655 5677777764
No 73
>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=34.18 E-value=75 Score=19.92 Aligned_cols=36 Identities=14% Similarity=0.236 Sum_probs=19.9
Q ss_pred HHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 28 KHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 28 ~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
..+.+|+++|... -+.|+.+.-+.|++.++|+..|.
T Consensus 114 ~~l~~~l~~L~~~----~r~vl~l~~~~g~s~~eIA~~l~ 149 (170)
T TIGR02952 114 EKLLKALKILTPK----QQHVIALRFGQNLPIAEVARILG 149 (170)
T ss_pred HHHHHHHHhCCHH----HHHHHHHHHhcCCCHHHHHHHHC
Confidence 3456666666521 34555555556666666665543
No 74
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=33.92 E-value=80 Score=20.57 Aligned_cols=38 Identities=11% Similarity=0.195 Sum_probs=19.6
Q ss_pred HHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 27 HKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 27 H~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
...+.+++..|.-. +.-+.+.|.+.||+ |...|+++|.
T Consensus 122 ~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgi---s~~tV~~~l~ 169 (189)
T PRK12515 122 SAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGI---PESTVKTRMF 169 (189)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHH
Confidence 34455666655421 22345555555555 5566666553
No 75
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=33.85 E-value=94 Score=20.13 Aligned_cols=37 Identities=19% Similarity=0.253 Sum_probs=19.8
Q ss_pred HHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 28 KHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 28 ~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
.....+++.|.-. +.-+.+.|.+.||+ |...|++++.
T Consensus 120 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgi---s~~tV~~~l~ 166 (186)
T PRK05602 120 RRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDI---SVDALESLLA 166 (186)
T ss_pred HHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHhCc---CHHHHHHHHH
Confidence 4456666666521 22345555555554 5666666653
No 76
>smart00831 Cation_ATPase_N Cation transporter/ATPase, N-terminus. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+, Na+, Ca2+, Na+/K+, and H+/K+. In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases PUBMED:12480547, PUBMED:12529322.
Probab=33.79 E-value=23 Score=19.43 Aligned_cols=15 Identities=20% Similarity=0.242 Sum_probs=13.1
Q ss_pred CCCCHHHHHhhhccC
Q 038544 55 KGLKLSHIKSHLQVN 69 (69)
Q Consensus 55 ~gLT~~~VkSHLQKy 69 (69)
.|||.++|...+++|
T Consensus 9 ~GLs~~~v~~r~~~~ 23 (64)
T smart00831 9 SGLSSEEAARRLERY 23 (64)
T ss_pred cCCCHHHHHHHHHHh
Confidence 399999999998876
No 77
>TIGR01517 ATPase-IIB_Ca plasma-membrane calcium-translocating P-type ATPase. The calcium P-type ATPases have been characterized as Type IIB based on a phylogenetic analysis which distinguishes this group from the Type IIA SERCA calcium pump. A separate analysis divides Type IIA into sub-types (SERCA and PMR1), which are modelled by the corresponding TIGR01116 and TIGR01522. This model is well separated from the two others.
Probab=33.59 E-value=60 Score=27.35 Aligned_cols=33 Identities=24% Similarity=0.436 Sum_probs=26.6
Q ss_pred HHHHHhCCCCccChHHHHHHcCCC---CCC--HHHHHhhhccC
Q 038544 32 QAVERLGGKYKASPKRILHMMNVK---GLK--LSHIKSHLQVN 69 (69)
Q Consensus 32 ~Av~~LGg~~~A~Pk~Il~~M~v~---gLT--~~~VkSHLQKy 69 (69)
+.++.+|| +..+++.++.. ||| .++|+..+++|
T Consensus 36 ~~~~~~~~-----~~~~~~~l~t~~~~GLs~~~~ev~~r~~~y 73 (941)
T TIGR01517 36 PIYEKLGG-----AEGIATKLKTDLNEGVRLSSSTLERREKVY 73 (941)
T ss_pred HHHHHhCC-----HHHHHHHhCcCcccCCCCCHHHHHHHHHHh
Confidence 34567887 67788888873 999 99999999887
No 78
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=33.50 E-value=1.1e+02 Score=18.21 Aligned_cols=38 Identities=8% Similarity=0.241 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 24 PELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 24 ~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
+++..+.+.++.+-| .++...|.+.+|+ +...|..+++
T Consensus 2 d~~D~~il~~L~~~~---~~~~~~la~~l~~---s~~tv~~~l~ 39 (108)
T smart00344 2 DEIDRKILEELQKDA---RISLAELAKKVGL---SPSTVHNRVK 39 (108)
T ss_pred CHHHHHHHHHHHHhC---CCCHHHHHHHHCc---CHHHHHHHHH
Confidence 356778888888765 3678888888866 5666666654
No 79
>PF14383 VARLMGL: DUF761-associated sequence motif
Probab=32.71 E-value=20 Score=19.21 Aligned_cols=21 Identities=19% Similarity=0.265 Sum_probs=16.6
Q ss_pred CccChHHHHHHcCCCCCCHHH
Q 038544 41 YKASPKRILHMMNVKGLKLSH 61 (69)
Q Consensus 41 ~~A~Pk~Il~~M~v~gLT~~~ 61 (69)
...+|--|..+||.+.|...+
T Consensus 11 ~~r~P~vvarLMGld~lP~~~ 31 (34)
T PF14383_consen 11 GTRAPGVVARLMGLDSLPDSQ 31 (34)
T ss_pred cccChhHHHHHhccccCCccc
Confidence 457899999999998776543
No 80
>COG4401 AroH Chorismate mutase [Amino acid transport and metabolism]
Probab=32.31 E-value=11 Score=25.26 Aligned_cols=36 Identities=33% Similarity=0.484 Sum_probs=26.1
Q ss_pred ccCCHHHHHHHH-HHHHHhCCCCccChHHHHHHcCCCC
Q 038544 20 LRWTPELHKHFS-QAVERLGGKYKASPKRILHMMNVKG 56 (69)
Q Consensus 20 ~~WT~eLH~~Fv-~Av~~LGg~~~A~Pk~Il~~M~v~g 56 (69)
+.=|++|+..|= .|+.++-| +.-+|--=++-|.|||
T Consensus 47 ~svT~Dl~A~FPAka~R~~~g-w~~Vpv~~~Qem~V~g 83 (125)
T COG4401 47 LSVTEDLDAIFPAKAVRELPG-WEYVPVMCMQEMPVPG 83 (125)
T ss_pred EEeccchhhhCcHHHhccCCC-CcccceeeeeeccCCC
Confidence 456899999994 55677777 6777776666677765
No 81
>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function.
Probab=31.78 E-value=29 Score=20.47 Aligned_cols=18 Identities=22% Similarity=0.268 Sum_probs=14.6
Q ss_pred HcCCCCCCHHHHHhhhcc
Q 038544 51 MMNVKGLKLSHIKSHLQV 68 (69)
Q Consensus 51 ~M~v~gLT~~~VkSHLQK 68 (69)
+-||+.|++++|+....-
T Consensus 10 irGvd~lsT~dI~~y~~~ 27 (62)
T PF10309_consen 10 IRGVDELSTDDIKAYFSE 27 (62)
T ss_pred EEcCCCCCHHHHHHHHHH
Confidence 568899999999987653
No 82
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=31.70 E-value=1.1e+02 Score=20.12 Aligned_cols=38 Identities=11% Similarity=0.086 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 27 HKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 27 H~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
.....+++++|... +.-+-+.|.+.||+ +...|+|+|.
T Consensus 121 ~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgi---s~~tVk~~l~ 168 (185)
T PRK09649 121 LVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGC---PVGTIRSRVA 168 (185)
T ss_pred HHHHHHHHHhCCHHHhHHhhhHHHcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 34456677666522 22345566666665 5666777664
No 83
>PRK10507 bifunctional glutathionylspermidine amidase/glutathionylspermidine synthetase; Provisional
Probab=31.53 E-value=47 Score=27.39 Aligned_cols=37 Identities=16% Similarity=0.336 Sum_probs=24.1
Q ss_pred CCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHH
Q 038544 22 WTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIK 63 (69)
Q Consensus 22 WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~Vk 63 (69)
-|.|||+.|++|++.+=. ...+++.+++|....+-|+
T Consensus 266 At~eLh~m~l~a~~~vl~-----dd~ll~~fgIP~~l~~lIr 302 (619)
T PRK10507 266 ATNELHLMYLHATDKVLK-----DDNLLALFDIPKILWPRLR 302 (619)
T ss_pred HHHHHHHHHHHHHHHHHc-----CHHHHHHcCcCHHHHHHHH
Confidence 478999999999987543 2245666666654444443
No 84
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=31.02 E-value=67 Score=17.61 Aligned_cols=25 Identities=12% Similarity=0.171 Sum_probs=18.6
Q ss_pred CccChHHHHHHcCCCCCCHHHHHhhhcc
Q 038544 41 YKASPKRILHMMNVKGLKLSHIKSHLQV 68 (69)
Q Consensus 41 ~~A~Pk~Il~~M~v~gLT~~~VkSHLQK 68 (69)
+..+...|.+.+|+ +...|.-||++
T Consensus 23 ~~~t~~ela~~l~~---~~~t~s~hL~~ 47 (61)
T PF12840_consen 23 GPMTVSELAEELGI---SQSTVSYHLKK 47 (61)
T ss_dssp STBEHHHHHHHHTS----HHHHHHHHHH
T ss_pred CCCCHHHHHHHHCC---CHHHHHHHHHH
Confidence 35788888888864 78888888864
No 85
>PF13932 GIDA_assoc_3: GidA associated domain 3; PDB: 3CES_C 3CP2_A 3G05_A 3CP8_A 2ZXI_B 2ZXH_A.
Probab=30.83 E-value=23 Score=21.06 Aligned_cols=29 Identities=28% Similarity=0.415 Sum_probs=19.3
Q ss_pred HHHHHhCCCCccChHHHHHHcCCCCCCHHHHH
Q 038544 32 QAVERLGGKYKASPKRILHMMNVKGLKLSHIK 63 (69)
Q Consensus 32 ~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~Vk 63 (69)
|+.+.|- ++.|..|-+..-++|+|...|.
T Consensus 40 E~~ekL~---~~rP~Ti~~A~rI~GvtPa~i~ 68 (72)
T PF13932_consen 40 EAREKLE---KIRPRTIGQASRIPGVTPAAIS 68 (72)
T ss_dssp HHHHHHH---HH--SCHHHHTTSTTS-HHHHH
T ss_pred HHHHHHH---hcCCCCHHHHHhCCCCCHHHHH
Confidence 4445543 4679999999999999988764
No 86
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=30.44 E-value=91 Score=22.39 Aligned_cols=37 Identities=19% Similarity=0.317 Sum_probs=22.0
Q ss_pred HHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 28 KHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 28 ~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
..+..++++|... +.-+.+.|.+.||+ |...|++||.
T Consensus 145 ~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgi---s~~tVk~~l~ 191 (339)
T PRK08241 145 LAFVAALQHLPPRQRAVLILRDVLGWSAAEVAELLDT---SVAAVNSALQ 191 (339)
T ss_pred HHHHHHHHhCCHHHhhhhhhHHhhCCCHHHHHHHhCC---CHHHHHHHHH
Confidence 3467788777632 22345566666665 5666777764
No 87
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=30.12 E-value=1.1e+02 Score=20.07 Aligned_cols=38 Identities=18% Similarity=0.371 Sum_probs=20.2
Q ss_pred HHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 27 HKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 27 H~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
.....+++.+|.-. +.-+.+.|.+.||+ |...|+++|.
T Consensus 132 ~~~l~~~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~lgi---s~~tVk~rl~ 179 (194)
T PRK12531 132 KEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDI---PLGTVKSRLR 179 (194)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCc---CHHHHHHHHH
Confidence 34455666665521 22345666666655 4566666653
No 88
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=29.66 E-value=1e+02 Score=21.50 Aligned_cols=22 Identities=23% Similarity=0.357 Sum_probs=13.2
Q ss_pred cChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 43 ASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 43 A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
-+.+.|.+.||+ +...|+++|+
T Consensus 188 ~s~~EIA~~Lgi---s~~tVk~~l~ 209 (233)
T PRK12538 188 MSNGEIAEVMDT---TVAAVESLLK 209 (233)
T ss_pred CCHHHHHHHHCc---CHHHHHHHHH
Confidence 345666666665 5666777664
No 89
>PF12170 DNA_pol3_tau_5: DNA polymerase III tau subunit V interacting with alpha; InterPro: IPR021029 This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found in association with PF00004 from PFAM. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. The extreme C-terminal region of this domain 5 is the part which interacts with the alpha subunit of the DNA polymerase III holoenzyme [, ]. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 2AYA_A.
Probab=29.47 E-value=54 Score=21.86 Aligned_cols=32 Identities=22% Similarity=0.360 Sum_probs=22.8
Q ss_pred CHHHHHHHHH-HHHHhCCCCccChHHHHHHcCCCCCCHH
Q 038544 23 TPELHKHFSQ-AVERLGGKYKASPKRILHMMNVKGLKLS 60 (69)
Q Consensus 23 T~eLH~~Fv~-Av~~LGg~~~A~Pk~Il~~M~v~gLT~~ 60 (69)
||||-.+.+. |++. -.|-.+..-|+++|+++.
T Consensus 8 tpel~~k~~~~a~~~------D~W~~~i~~L~l~gl~rq 40 (142)
T PF12170_consen 8 TPELAAKLIAEAIQQ------DPWAALIEQLPLGGLVRQ 40 (142)
T ss_dssp SHHHHHHHHHHHHHH-------HHHHHHHHHT--SHHHH
T ss_pred CHHHHHHHHHHHhcc------CHHHHHHHHCCCchHHHH
Confidence 8999888865 4443 248999999999998864
No 90
>PF08593 MUG2_C: Meiotically up-regulated glycoproteins C-terminal; InterPro: IPR013902 This entry represents a conserved domain found in certain meiotically up-regulated gene products (MUG) from fungi []. The actual function is not yet known. The proteins are likely to be cell-surface glycoproteins and may be situated close to telomeres, hence their being expressed during meiosis [].
Probab=29.40 E-value=30 Score=20.12 Aligned_cols=21 Identities=14% Similarity=0.213 Sum_probs=16.9
Q ss_pred HHHHHcCCCCCCHHHHHhhhc
Q 038544 47 RILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 47 ~Il~~M~v~gLT~~~VkSHLQ 67 (69)
.|-++|+++.||++|+.-.|+
T Consensus 37 ~~~~I~did~LS~~Q~s~fL~ 57 (58)
T PF08593_consen 37 PIGSILDIDNLSKEQCSFFLP 57 (58)
T ss_pred CchhhhchhhhCHHHHHHhcC
Confidence 466789999999999976654
No 91
>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=28.95 E-value=1.1e+02 Score=17.87 Aligned_cols=10 Identities=20% Similarity=0.418 Sum_probs=4.7
Q ss_pred hHHHHHHcCC
Q 038544 45 PKRILHMMNV 54 (69)
Q Consensus 45 Pk~Il~~M~v 54 (69)
+..|.+.||+
T Consensus 129 ~~eIA~~l~~ 138 (158)
T TIGR02937 129 YKEIAEILGI 138 (158)
T ss_pred HHHHHHHHCC
Confidence 4444444444
No 92
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=28.71 E-value=28 Score=19.26 Aligned_cols=24 Identities=13% Similarity=0.295 Sum_probs=18.7
Q ss_pred cChHHHHHHcCCCCCCHHHHHhhh
Q 038544 43 ASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 43 A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
..|..+-++..++|++...|+.|-
T Consensus 38 ~~P~s~~~L~~i~g~~~~~~~~~g 61 (68)
T PF00570_consen 38 RLPTSIEELLQIPGMGKRKVRKYG 61 (68)
T ss_dssp H--SSHHHHHTSTTCGHHHHHHCH
T ss_pred hCCCCHHHHHHccCCCHHHHHHHH
Confidence 358888889999999999998764
No 93
>PHA02117 glutathionylspermidine synthase domain-containing protein
Probab=28.14 E-value=42 Score=26.06 Aligned_cols=17 Identities=24% Similarity=0.231 Sum_probs=14.5
Q ss_pred CCHHHHHHHHHHHHHhC
Q 038544 22 WTPELHKHFSQAVERLG 38 (69)
Q Consensus 22 WT~eLH~~Fv~Av~~LG 38 (69)
-|.|||+.|++|++.+=
T Consensus 55 at~eLh~m~~~a~~~v~ 71 (397)
T PHA02117 55 AANELHAMCGHALDWMF 71 (397)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 47899999999998764
No 94
>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=27.93 E-value=45 Score=18.09 Aligned_cols=22 Identities=27% Similarity=0.344 Sum_probs=15.9
Q ss_pred cChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 43 ASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 43 A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
-+++.|.+.|++ +..-|++|+.
T Consensus 19 ~~~~eIA~~l~i---s~~tV~~~~~ 40 (58)
T PF00196_consen 19 MSNKEIAEELGI---SEKTVKSHRR 40 (58)
T ss_dssp S-HHHHHHHHTS---HHHHHHHHHH
T ss_pred CCcchhHHhcCc---chhhHHHHHH
Confidence 468999999987 5666777653
No 95
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=27.92 E-value=52 Score=21.58 Aligned_cols=21 Identities=19% Similarity=0.249 Sum_probs=14.7
Q ss_pred ChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 44 SPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 44 ~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
+.+.|.+.||+ |...|+++|+
T Consensus 149 s~~EIAe~lgi---s~~~V~~~l~ 169 (189)
T PRK06811 149 KIEEIAKKLGL---TRSAIDNRLS 169 (189)
T ss_pred CHHHHHHHHCC---CHHHHHHHHH
Confidence 45666666666 6777888775
No 96
>PF03982 DAGAT: Diacylglycerol acyltransferase ; InterPro: IPR007130 The terminal step of triacylglycerol (TAG) formation is catalysed by the enzyme diacylglycerol acyltransferase (DAGAT) [, ].; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups
Probab=27.48 E-value=54 Score=24.27 Aligned_cols=14 Identities=29% Similarity=0.589 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHh
Q 038544 24 PELHKHFSQAVERL 37 (69)
Q Consensus 24 ~eLH~~Fv~Av~~L 37 (69)
+++|++|++|+.+|
T Consensus 265 d~~H~~Y~~~L~~L 278 (297)
T PF03982_consen 265 DKLHARYIEALREL 278 (297)
T ss_pred HHHHHHHHHHHHHH
Confidence 46999999999876
No 97
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=27.29 E-value=88 Score=20.04 Aligned_cols=35 Identities=23% Similarity=0.408 Sum_probs=17.7
Q ss_pred HHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhh
Q 038544 28 KHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 28 ~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
.....++..|... -+.|+.+--+.|+|.++|+..|
T Consensus 110 ~~l~~~l~~L~~~----~r~v~~L~~~eg~s~~EIA~~l 144 (168)
T PRK12525 110 LAIDRLLDGLSGK----ARAAFLMSQLEGLTYVEIGERL 144 (168)
T ss_pred HHHHHHHHhCCHH----HHHHHHHHHHcCCCHHHHHHHH
Confidence 3345555555532 3444444445566666555544
No 98
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=27.13 E-value=1e+02 Score=15.99 Aligned_cols=45 Identities=18% Similarity=0.081 Sum_probs=30.8
Q ss_pred CCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHh
Q 038544 17 LPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKS 64 (69)
Q Consensus 17 k~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkS 64 (69)
++|..+|++- ...++++..-.- ..++..|.++...-|||..+|..
T Consensus 2 k~r~~~~~~~-~~~L~~~f~~~~--~P~~~~~~~la~~~~l~~~qV~~ 46 (56)
T smart00389 2 RKRTSFTPEQ-LEELEKEFQKNP--YPSREEREELAAKLGLSERQVKV 46 (56)
T ss_pred CCCCcCCHHH-HHHHHHHHHhCC--CCCHHHHHHHHHHHCcCHHHHHH
Confidence 4556677654 445566655553 46777888888877889999875
No 99
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=27.07 E-value=1e+02 Score=15.94 Aligned_cols=33 Identities=21% Similarity=0.386 Sum_probs=22.7
Q ss_pred HHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhccC
Q 038544 30 FSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQVN 69 (69)
Q Consensus 30 Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQKy 69 (69)
..+|++..||. .....+.+|+ ++..+..-|+||
T Consensus 10 i~~aL~~~~gn----~~~aA~~Lgi---sr~tL~~klkk~ 42 (42)
T PF02954_consen 10 IRQALERCGGN----VSKAARLLGI---SRRTLYRKLKKY 42 (42)
T ss_dssp HHHHHHHTTT-----HHHHHHHHTS----HHHHHHHHHHC
T ss_pred HHHHHHHhCCC----HHHHHHHHCC---CHHHHHHHHHhC
Confidence 35677888874 5566667766 788888888776
No 100
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=26.94 E-value=60 Score=20.87 Aligned_cols=21 Identities=24% Similarity=0.362 Sum_probs=11.4
Q ss_pred ChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 44 SPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 44 ~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
+.+.|.+.||+ |...|+++|+
T Consensus 147 s~~eIA~~lgi---s~~tV~~~l~ 167 (179)
T PRK12514 147 SYKELAERHDV---PLNTMRTWLR 167 (179)
T ss_pred CHHHHHHHHCC---ChHHHHHHHH
Confidence 45555555554 4555666554
No 101
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=26.86 E-value=1.1e+02 Score=19.14 Aligned_cols=39 Identities=21% Similarity=0.302 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 26 LHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 26 LH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
....+..++..|... +.-+++.|.+.||+ |...|+++++
T Consensus 118 ~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgi---s~~tV~~~l~ 166 (182)
T PRK09652 118 LEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGC---PIGTVRSRIF 166 (182)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 345566666665521 22345566666555 4555555543
No 102
>COG0754 Gsp Glutathionylspermidine synthase [Amino acid transport and metabolism]
Probab=26.79 E-value=59 Score=25.67 Aligned_cols=17 Identities=35% Similarity=0.317 Sum_probs=14.3
Q ss_pred CHHHHHHHHHHHHHhCC
Q 038544 23 TPELHKHFSQAVERLGG 39 (69)
Q Consensus 23 T~eLH~~Fv~Av~~LGg 39 (69)
|.|||+.|+++++..=-
T Consensus 53 t~eLh~Mcle~~e~~i~ 69 (387)
T COG0754 53 TNELHDMCLELVEDVVK 69 (387)
T ss_pred HHHHHHHHHHHHHHHHc
Confidence 78999999999987643
No 103
>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=26.65 E-value=1.5e+02 Score=19.07 Aligned_cols=39 Identities=23% Similarity=0.285 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 26 LHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 26 LH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
+...+..+++.|... +.-+.+.|.+.||+ |...|+++|+
T Consensus 90 ~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgi---s~~tV~~~l~ 138 (170)
T TIGR02959 90 LSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGL---SLSGAKSRVQ 138 (170)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 334455566655421 12334555555554 4555666554
No 104
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=26.19 E-value=1.4e+02 Score=18.88 Aligned_cols=36 Identities=22% Similarity=0.314 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 29 HFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 29 ~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
...++++.|... +.-+.+.|.+.||+ |...|++++.
T Consensus 113 ~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~lg~---s~~tv~~~l~ 158 (175)
T PRK12518 113 LVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNI---PVGTVKSRLF 158 (175)
T ss_pred HHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 345566666522 23456777777776 4566666653
No 105
>COG3623 SgaU Putative L-xylulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism]
Probab=26.18 E-value=68 Score=24.29 Aligned_cols=24 Identities=29% Similarity=0.529 Sum_probs=20.8
Q ss_pred CCCcccCCHHHHHHHHHHHHHhCC
Q 038544 16 ELPRLRWTPELHKHFSQAVERLGG 39 (69)
Q Consensus 16 kk~R~~WT~eLH~~Fv~Av~~LGg 39 (69)
+-.||.||.+.-...+.|+.+-|.
T Consensus 45 RLaRLDWs~~er~~l~~ai~etgv 68 (287)
T COG3623 45 RLARLDWSKEERLALVNAIQETGV 68 (287)
T ss_pred HHHhcCCCHHHHHHHHHHHHHhCC
Confidence 567999999999999999988774
No 106
>PF05534 HicB: HicB family; InterPro: IPR008651 This family consists of several bacterial HicB related proteins. The function of HicB is unknown although it is thought to be involved in pilus formation. It has been speculated that HicB performs a function antagonistic to that of pili and yet is necessary for invasion of certain niches [].
Probab=25.85 E-value=1.3e+02 Score=16.65 Aligned_cols=26 Identities=35% Similarity=0.427 Sum_probs=21.6
Q ss_pred CCCCcccCCHHHHHHHHHHHHHhCCC
Q 038544 15 SELPRLRWTPELHKHFSQAVERLGGK 40 (69)
Q Consensus 15 ~kk~R~~WT~eLH~~Fv~Av~~LGg~ 40 (69)
+++=-+|=+++||++...+-..-|..
T Consensus 17 sg~~~lRi~~~Lh~~l~~~A~~~gvS 42 (51)
T PF05534_consen 17 SGKFNLRIPPELHRALAEAAAAEGVS 42 (51)
T ss_pred CCceeeeCCHHHHHHHHHHHHHhCCC
Confidence 46667899999999999998888853
No 107
>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=25.85 E-value=1.6e+02 Score=17.78 Aligned_cols=43 Identities=21% Similarity=0.387 Sum_probs=26.1
Q ss_pred CcccCCHHHHHH-HHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 18 PRLRWTPELHKH-FSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 18 ~R~~WT~eLH~~-Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
.|+.|=|++-+. |.=. ..+.| -+-+.|.+.||+ |...|++|+-
T Consensus 11 ~~l~~l~~~~r~af~L~-R~~eG---lS~kEIAe~LGI---S~~TVk~~l~ 54 (73)
T TIGR03879 11 ERLTWVDSLAEAAAALA-REEAG---KTASEIAEELGR---TEQTVRNHLK 54 (73)
T ss_pred HHHhcCCHHHHHHHHHH-HHHcC---CCHHHHHHHHCc---CHHHHHHHHh
Confidence 466676665332 2222 23333 367888888887 6777887764
No 108
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=25.75 E-value=1.5e+02 Score=17.57 Aligned_cols=36 Identities=33% Similarity=0.359 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHhCCCCccChHHHHHHcCC-CCCCHHHH
Q 038544 25 ELHKHFSQAVERLGGKYKASPKRILHMMNV-KGLKLSHI 62 (69)
Q Consensus 25 eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v-~gLT~~~V 62 (69)
++-.-+++++..+|| .++.+.|.+.+-. -+||.++.
T Consensus 4 ~~~~piL~~L~~~g~--~~~~~ei~~~v~~~~~ls~e~~ 40 (92)
T PF14338_consen 4 ELMPPILEALKDLGG--SASRKEIYERVAERFGLSDEER 40 (92)
T ss_pred HHHHHHHHHHHHcCC--CcCHHHHHHHHHHHhCCCHHHH
Confidence 455667899999998 4788888776542 45666553
No 109
>smart00351 PAX Paired Box domain.
Probab=25.42 E-value=1.9e+02 Score=18.39 Aligned_cols=30 Identities=17% Similarity=0.235 Sum_probs=23.7
Q ss_pred cCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCC
Q 038544 21 RWTPELHKHFSQAVERLGGKYKASPKRILHMMNVK 55 (69)
Q Consensus 21 ~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~ 55 (69)
.++.|+-.+|+.++. +| .+...|.+.+||.
T Consensus 17 ~~s~~~R~riv~~~~--~G---~s~~~iA~~~gvs 46 (125)
T smart00351 17 PLPDEERQRIVELAQ--NG---VRPCDISRQLCVS 46 (125)
T ss_pred CCCHHHHHHHHHHHH--cC---CCHHHHHHHHCcC
Confidence 389999999999886 33 3578888888873
No 110
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=25.07 E-value=1.4e+02 Score=20.46 Aligned_cols=39 Identities=15% Similarity=0.164 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHhCC--------------CCccChHHHHHHcCCCCCCHHHHHhhh
Q 038544 25 ELHKHFSQAVERLGG--------------KYKASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 25 eLH~~Fv~Av~~LGg--------------~~~A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
++...+..|+..|.- .+..+-+.|.+.||+ |.+.|+..+
T Consensus 165 ~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgi---s~~~V~q~~ 217 (238)
T TIGR02393 165 LLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNV---TRERIRQIE 217 (238)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCC---CHHHHHHHH
Confidence 455556666665531 133455566666555 455555443
No 111
>KOG4411 consensus Phytoene/squalene synthetase [Lipid transport and metabolism]
Probab=24.65 E-value=47 Score=25.13 Aligned_cols=19 Identities=21% Similarity=-0.020 Sum_probs=15.1
Q ss_pred HHcCCCCCCHHHHHhhhcc
Q 038544 50 HMMNVKGLKLSHIKSHLQV 68 (69)
Q Consensus 50 ~~M~v~gLT~~~VkSHLQK 68 (69)
+.-|+...+.+|++|||-|
T Consensus 148 ~agg~~~~~AdhaAshlGk 166 (292)
T KOG4411|consen 148 DAGGKVLPMADHAASHLGK 166 (292)
T ss_pred HhcCccccchHHHHHHHhH
Confidence 3446677899999999976
No 112
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=24.61 E-value=94 Score=15.50 Aligned_cols=22 Identities=23% Similarity=0.394 Sum_probs=17.0
Q ss_pred cChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 43 ASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 43 A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
-+.+.|.+.+++ +...|.+|++
T Consensus 19 ~s~~eia~~l~i---s~~tv~~~~~ 40 (58)
T smart00421 19 LTNKEIAERLGI---SEKTVKTHLS 40 (58)
T ss_pred CCHHHHHHHHCC---CHHHHHHHHH
Confidence 368889988887 7788887765
No 113
>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes. This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].
Probab=24.24 E-value=65 Score=19.03 Aligned_cols=17 Identities=24% Similarity=0.419 Sum_probs=14.6
Q ss_pred CCCCCCHHHHHhhhccC
Q 038544 53 NVKGLKLSHIKSHLQVN 69 (69)
Q Consensus 53 ~v~gLT~~~VkSHLQKy 69 (69)
.+.++|.+++|..|-+|
T Consensus 8 p~~~~~v~d~K~~Lr~y 24 (66)
T PF11767_consen 8 PVHGVTVEDFKKRLRKY 24 (66)
T ss_pred CCCCccHHHHHHHHhcC
Confidence 46778999999999887
No 114
>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=24.10 E-value=1.2e+02 Score=15.73 Aligned_cols=47 Identities=19% Similarity=0.114 Sum_probs=33.2
Q ss_pred CCcccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhh
Q 038544 17 LPRLRWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 17 k~R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
+.+..++++- ...++++..... ..++..|.++...-|||..+|..-.
T Consensus 2 ~~r~~~~~~~-~~~Le~~f~~~~--~P~~~~~~~la~~~~l~~~qV~~WF 48 (59)
T cd00086 2 RKRTRFTPEQ-LEELEKEFEKNP--YPSREEREELAKELGLTERQVKIWF 48 (59)
T ss_pred CCCCcCCHHH-HHHHHHHHHhCC--CCCHHHHHHHHHHHCcCHHHHHHHH
Confidence 4455666654 556677666643 5677888888888889999998644
No 115
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=23.95 E-value=1.1e+02 Score=16.92 Aligned_cols=22 Identities=32% Similarity=0.455 Sum_probs=15.1
Q ss_pred cChHHHHHHcCCCCCCHHHHHhhh
Q 038544 43 ASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 43 A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
.+|..|++- -|+||.++|.+-|
T Consensus 32 ~s~eeI~~~--yp~Lt~~~i~aAl 53 (56)
T PF04255_consen 32 ESPEEIAED--YPSLTLEDIRAAL 53 (56)
T ss_dssp --HHHHHHH--STT--HHHHHHHH
T ss_pred CCHHHHHHH--CCCCCHHHHHHHH
Confidence 579999887 6789999998765
No 116
>PF02134 UBACT: Repeat in ubiquitin-activating (UBA) protein; InterPro: IPR000127 The post-translational attachment of ubiquitin (IPR000626 from INTERPRO) to proteins (ubiquitinylation) alters the function, location or trafficking of a protein, or targets it to the 26S proteasome for degradation [, , ]. Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade []. The E1 enzyme is responsible for activating ubiquitin, the first step in ubiquitinylation. The E1 enzyme hydrolyses ATP and adenylates the C-terminal glycine residue of ubiquitin, and then links this residue to the active site cysteine of E1, yielding a ubiquitin-thioester and free AMP. To be fully active, E1 must non-covalently bind to and adenylate a second ubiquitin molecule. The E1 enzyme can then transfer the thioester-linked ubiquitin molecule to a cysteine residue on the ubiquitin-conjugating enzyme, E2, in an ATP-dependent reaction. This domain is found 2 times in each member of the ubiquitin activating enzymes and is located downstream of the active site cysteine [].; GO: 0005524 ATP binding, 0008641 small protein activating enzyme activity, 0006464 protein modification process; PDB: 1Z7L_A 3CMM_A 3GZN_D 3DBL_F 1R4N_H 1R4M_D 2NVU_B 1TT5_D 3DBR_D 3DBH_H ....
Probab=23.77 E-value=1.5e+02 Score=17.05 Aligned_cols=38 Identities=16% Similarity=0.230 Sum_probs=23.0
Q ss_pred CHHHHHHHHHHHH-----HhCCCCccChHHHHHHcC--CCCCCHHH
Q 038544 23 TPELHKHFSQAVE-----RLGGKYKASPKRILHMMN--VKGLKLSH 61 (69)
Q Consensus 23 T~eLH~~Fv~Av~-----~LGg~~~A~Pk~Il~~M~--v~gLT~~~ 61 (69)
.+++|..|+-|.. .+|.. ..++..+.++.+ ||.++..+
T Consensus 5 dd~~h~~fI~a~anLrA~~f~I~-~~~~~~~~~i~~~iIP~~~~t~ 49 (67)
T PF02134_consen 5 DDPLHLDFIYAAANLRAQNFGIP-PLDREEIKKIAGNIIPAFAPTN 49 (67)
T ss_dssp TSHHHHHHHHHHHHHHHHHTT----S-HHHHHHHHTTEE-B-HHHH
T ss_pred CcHHHHHHHHHHHHHHHHHhCCC-cccHHHHHHHhcCcCCCcCCch
Confidence 4689999999884 45775 577777777766 47765544
No 117
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=23.75 E-value=71 Score=20.81 Aligned_cols=21 Identities=19% Similarity=0.355 Sum_probs=12.2
Q ss_pred ChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 44 SPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 44 ~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
+.+.|.+.||+ |...|+++++
T Consensus 159 s~~EIA~~lgi---s~~tV~~~l~ 179 (194)
T PRK12519 159 SQSEIAKRLGI---PLGTVKARAR 179 (194)
T ss_pred CHHHHHHHhCC---CHHHHHHHHH
Confidence 45555555555 5666666654
No 118
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=23.65 E-value=1.3e+02 Score=20.40 Aligned_cols=35 Identities=17% Similarity=0.343 Sum_probs=15.6
Q ss_pred HHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhh
Q 038544 28 KHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 28 ~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
..+..+++.|... =+.|+.+.-+.|++.++|+..|
T Consensus 130 ~~l~~~L~~L~~~----~r~v~~L~~~~g~s~~EIA~~L 164 (203)
T PRK09647 130 PDLQAALDSLPPE----FRAAVVLCDIEGLSYEEIAATL 164 (203)
T ss_pred HHHHHHHHhCCHH----HHHHHHHHHHcCCCHHHHHHHH
Confidence 3455566655521 2233334344444444444443
No 119
>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=23.34 E-value=86 Score=17.82 Aligned_cols=13 Identities=31% Similarity=0.176 Sum_probs=11.5
Q ss_pred cChHHHHHHcCCC
Q 038544 43 ASPKRILHMMNVK 55 (69)
Q Consensus 43 A~Pk~Il~~M~v~ 55 (69)
-+|+.|.+.+|++
T Consensus 14 ~~~~eIA~~Lg~~ 26 (58)
T PF06056_consen 14 WSIKEIAEELGVP 26 (58)
T ss_pred CCHHHHHHHHCCC
Confidence 4699999999997
No 120
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=23.14 E-value=1.8e+02 Score=19.12 Aligned_cols=38 Identities=16% Similarity=0.205 Sum_probs=21.0
Q ss_pred HHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 27 HKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 27 H~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
......+++.|... +.-+.+.|.+.||+ +...|+++|.
T Consensus 127 ~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~eIA~~lgi---s~~tV~~~l~ 174 (196)
T PRK12524 127 MRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEI---GVEAVESLTA 174 (196)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHH
Confidence 34455566655421 22346666666666 5666776664
No 121
>PF09712 PHA_synth_III_E: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
Probab=23.12 E-value=78 Score=23.39 Aligned_cols=36 Identities=14% Similarity=0.170 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHh
Q 038544 27 HKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKS 64 (69)
Q Consensus 27 H~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkS 64 (69)
+-.|++|.-.|-......=..+|+.||+| |+.+|.+
T Consensus 241 ~g~~~~a~m~~r~~~~~~~e~~L~~l~lP--Tr~evd~ 276 (293)
T PF09712_consen 241 YGQLVNALMDLRKQQQEVVEEYLRSLNLP--TRSEVDE 276 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCC--CHHHHHH
Confidence 33444554444322223455788899999 8888764
No 122
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=23.11 E-value=1.3e+02 Score=18.79 Aligned_cols=35 Identities=20% Similarity=0.309 Sum_probs=19.3
Q ss_pred HHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 29 HFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 29 ~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
....|+..|... =+.|+.+--+.|+|.++|+..|.
T Consensus 98 ~l~~~l~~L~~~----~r~v~~l~~~~~~s~~eIA~~lg 132 (159)
T PRK12527 98 LLQRALAELPPA----CRDSFLLRKLEGLSHQQIAEHLG 132 (159)
T ss_pred HHHHHHHhCCHH----HHHHHHHHHHcCCCHHHHHHHhC
Confidence 455666666532 23455554456666666665553
No 123
>smart00526 H15 Domain in histone families 1 and 5.
Probab=22.67 E-value=1.5e+02 Score=16.49 Aligned_cols=25 Identities=16% Similarity=0.231 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCCCccChHHHHHHcC
Q 038544 29 HFSQAVERLGGKYKASPKRILHMMN 53 (69)
Q Consensus 29 ~Fv~Av~~LGg~~~A~Pk~Il~~M~ 53 (69)
.-++||..|.....++...|...+.
T Consensus 10 mI~eAI~~l~er~GsS~~aI~kyi~ 34 (66)
T smart00526 10 MITEAISALKERKGSSLQAIKKYIE 34 (66)
T ss_pred HHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 4688999998665677777776664
No 124
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.48 E-value=2e+02 Score=18.98 Aligned_cols=44 Identities=14% Similarity=0.194 Sum_probs=30.6
Q ss_pred cCCHHHHHHHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 21 RWTPELHKHFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 21 ~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
.|.+|--+.+++-+-.+++.....--+|+++|.. |.+.++|=|-
T Consensus 47 kldpe~a~e~veEL~~i~~~~e~~avkIadI~P~---t~~ElRsIla 90 (114)
T COG1460 47 KLDPEKARELVEELLSIVKMSEKIAVKIADIMPR---TPDELRSILA 90 (114)
T ss_pred cCCHHHHHHHHHHHHhhccccHHHHHHHHHhCCC---CHHHHHHHHH
Confidence 5778888888887777776334555678888876 6777766543
No 125
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=22.37 E-value=1.4e+02 Score=17.15 Aligned_cols=18 Identities=22% Similarity=0.588 Sum_probs=13.1
Q ss_pred HHHHHhCCCCccChHHHHHHcCC
Q 038544 32 QAVERLGGKYKASPKRILHMMNV 54 (69)
Q Consensus 32 ~Av~~LGg~~~A~Pk~Il~~M~v 54 (69)
+||..+|+ ..++.+.+||
T Consensus 4 ~aI~~~G~-----~~~lAkalGV 21 (60)
T PF14549_consen 4 DAIKYFGG-----QSKLAKALGV 21 (60)
T ss_dssp HHHHHHSS-----HHHHHHHHTS
T ss_pred HHHHHHCC-----HHHHHHHHCC
Confidence 67888887 5566667776
No 126
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=22.14 E-value=1.6e+02 Score=18.14 Aligned_cols=40 Identities=8% Similarity=0.061 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 25 ELHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 25 eLH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
+......+|+.+|... +.-+.+.|.+.||+ +...|++++.
T Consensus 95 ~~~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l~i---s~~tV~~~~~ 144 (154)
T PRK06759 95 DVEMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALETEM---TYYQVRWIYR 144 (154)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 4455566777777632 22344555555544 4555555543
No 127
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=22.12 E-value=1.9e+02 Score=18.66 Aligned_cols=22 Identities=9% Similarity=0.314 Sum_probs=14.6
Q ss_pred cChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 43 ASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 43 A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
-+.+.|.+.||+ |...|+|+|.
T Consensus 139 ~s~~EIA~~lgi---s~~tVk~~l~ 160 (185)
T PRK12542 139 LTYQEISSVMGI---TEANVRKQFE 160 (185)
T ss_pred CCHHHHHHHHCC---CHHHHHHHHH
Confidence 346666666665 6777888764
No 128
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=21.70 E-value=2.2e+02 Score=18.43 Aligned_cols=39 Identities=18% Similarity=0.097 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhh
Q 038544 25 ELHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 25 eLH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
+......+++..|.-. +.-+.+.|.+.||+ +...|+|+|
T Consensus 120 e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgi---s~~tV~~~l 168 (184)
T PRK12539 120 ESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGM---SESAVKVSV 168 (184)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHcCCcHHHHHHHHCc---CHHHHHHHH
Confidence 3344566666665421 12334555555555 566666665
No 129
>PHA01976 helix-turn-helix protein
Probab=21.49 E-value=82 Score=17.15 Aligned_cols=20 Identities=5% Similarity=0.212 Sum_probs=9.5
Q ss_pred HHHHHHcCCCCCCHHHHHhh
Q 038544 46 KRILHMMNVKGLKLSHIKSH 65 (69)
Q Consensus 46 k~Il~~M~v~gLT~~~VkSH 65 (69)
..|..++...|+|..+++..
T Consensus 5 ~rl~~~R~~~glt~~~lA~~ 24 (67)
T PHA01976 5 IQLIKARNARAWSAPELSRR 24 (67)
T ss_pred HHHHHHHHHcCCCHHHHHHH
Confidence 34444444455555554443
No 130
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=21.41 E-value=39 Score=16.94 Aligned_cols=17 Identities=24% Similarity=0.432 Sum_probs=11.8
Q ss_pred ChHHHHHHcCCCCCCHH
Q 038544 44 SPKRILHMMNVKGLKLS 60 (69)
Q Consensus 44 ~Pk~Il~~M~v~gLT~~ 60 (69)
.|..+-|+|.+||+-..
T Consensus 6 ~pas~eeL~~lpGIG~~ 22 (30)
T PF00633_consen 6 IPASIEELMKLPGIGPK 22 (30)
T ss_dssp HTSSHHHHHTSTT-SHH
T ss_pred CCCCHHHHHhCCCcCHH
Confidence 46677788999998553
No 131
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=21.37 E-value=1.1e+02 Score=26.04 Aligned_cols=47 Identities=17% Similarity=0.338 Sum_probs=30.9
Q ss_pred cccCCHHHHHHHHHHHHHhCCCCccChHHHHHHcC----CCCCCHHHHHhh
Q 038544 19 RLRWTPELHKHFSQAVERLGGKYKASPKRILHMMN----VKGLKLSHIKSH 65 (69)
Q Consensus 19 R~~WT~eLH~~Fv~Av~~LGg~~~A~Pk~Il~~M~----v~gLT~~~VkSH 65 (69)
+-.||...-..|-+|+++.|-...++=+.-+..-+ +..-|.+||.-|
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~ 138 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHY 138 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHH
Confidence 67899999999999999999654444332233222 233466666544
No 132
>TIGR02264 gmx_para_CXXCG Myxococcus xanthus double-CXXCG motif paralogous family. This family consists of at least 10 paralogous proteins from Myxococcus xanthus that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment.
Probab=21.35 E-value=69 Score=23.72 Aligned_cols=12 Identities=42% Similarity=0.556 Sum_probs=10.6
Q ss_pred HHHHHHHHHhCC
Q 038544 28 KHFSQAVERLGG 39 (69)
Q Consensus 28 ~~Fv~Av~~LGg 39 (69)
.+||+||++|..
T Consensus 215 eRfveav~rLeL 226 (237)
T TIGR02264 215 ERFVEAVKRLEL 226 (237)
T ss_pred HHHHHHHHhccc
Confidence 579999999986
No 133
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=20.98 E-value=88 Score=19.32 Aligned_cols=11 Identities=18% Similarity=0.413 Sum_probs=7.3
Q ss_pred HHHHHHHHHhC
Q 038544 28 KHFSQAVERLG 38 (69)
Q Consensus 28 ~~Fv~Av~~LG 38 (69)
..+..+++.|.
T Consensus 97 ~~l~~~l~~L~ 107 (154)
T TIGR02950 97 EEITHHLSRLP 107 (154)
T ss_pred HHHHHHHHhCC
Confidence 45667777765
No 134
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=20.61 E-value=1.7e+02 Score=16.28 Aligned_cols=31 Identities=6% Similarity=0.293 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCCccChHHHHHHcCCCCCCHHHHH
Q 038544 29 HFSQAVERLGGKYKASPKRILHMMNVKGLKLSHIK 63 (69)
Q Consensus 29 ~Fv~Av~~LGg~~~A~Pk~Il~~M~v~gLT~~~Vk 63 (69)
++++.+..-|. +......|.+.+|+ +..||.
T Consensus 16 r~L~~l~~~G~-~~vSS~~La~~~gi---~~~qVR 46 (50)
T PF06971_consen 16 RYLEQLKEEGV-ERVSSQELAEALGI---TPAQVR 46 (50)
T ss_dssp HHHHHHHHTT--SEE-HHHHHHHHTS----HHHHH
T ss_pred HHHHHHHHcCC-eeECHHHHHHHHCC---CHHHhc
Confidence 45556666665 67889999999988 566664
No 135
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=20.49 E-value=1.4e+02 Score=20.60 Aligned_cols=40 Identities=20% Similarity=0.208 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHhCCC----------CccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 25 ELHKHFSQAVERLGGK----------YKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 25 eLH~~Fv~Av~~LGg~----------~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
|....+..|++.|... +.-+-+.|.+.||+ |...|++||.
T Consensus 123 e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~Lgi---S~~tVk~~L~ 172 (216)
T PRK12533 123 EDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADV---PVGTVMSRLA 172 (216)
T ss_pred HHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 3445677888877742 22334455555544 5666666653
No 136
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=20.19 E-value=2.2e+02 Score=17.73 Aligned_cols=20 Identities=30% Similarity=0.353 Sum_probs=10.2
Q ss_pred ChHHHHHHcCCCCCCHHHHHhhh
Q 038544 44 SPKRILHMMNVKGLKLSHIKSHL 66 (69)
Q Consensus 44 ~Pk~Il~~M~v~gLT~~~VkSHL 66 (69)
+.+.|.+.||+ |...|++++
T Consensus 129 s~~eIA~~lgi---s~~tV~~~i 148 (166)
T PRK09639 129 SYKEIAEALGI---KESSVGTTL 148 (166)
T ss_pred CHHHHHHHHCC---CHHHHHHHH
Confidence 34555555554 445555554
No 137
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=20.17 E-value=1.7e+02 Score=19.63 Aligned_cols=40 Identities=18% Similarity=0.193 Sum_probs=28.9
Q ss_pred HHHHHHHHHhCC-CCccChHHHHHHcCCCCCCHHHHHhhhc
Q 038544 28 KHFSQAVERLGG-KYKASPKRILHMMNVKGLKLSHIKSHLQ 67 (69)
Q Consensus 28 ~~Fv~Av~~LGg-~~~A~Pk~Il~~M~v~gLT~~~VkSHLQ 67 (69)
..++.+|..+.. ...|..+.|.+.|+|.-=|..+.-.+|+
T Consensus 9 edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~ 49 (154)
T COG1321 9 EDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLE 49 (154)
T ss_pred HHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHH
Confidence 457888886653 3458999999999996556666555554
Done!