Query psy8488
Match_columns 150
No_of_seqs 106 out of 292
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 20:09:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8488.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8488hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3806|consensus 100.0 5.6E-42 1.2E-46 272.7 11.6 104 35-139 61-165 (177)
2 smart00413 ETS erythroblast tr 100.0 9.8E-42 2.1E-46 244.9 9.9 85 42-126 1-86 (87)
3 PF00178 Ets: Ets-domain; Int 100.0 1.2E-39 2.7E-44 233.0 8.0 84 42-125 1-85 (85)
4 KOG3805|consensus 100.0 4.5E-31 9.8E-36 225.4 8.8 100 19-124 255-357 (361)
5 KOG3804|consensus 100.0 1.2E-28 2.6E-33 216.1 9.1 88 43-130 294-383 (390)
6 KOG3804|consensus 98.8 9.3E-10 2E-14 97.3 2.0 84 40-123 169-256 (390)
7 PF00447 HSF_DNA-bind: HSF-typ 97.2 0.0014 3E-08 47.3 6.1 64 47-114 4-67 (103)
8 smart00415 HSF heat shock fact 96.9 0.0035 7.7E-08 45.7 6.2 63 46-109 6-68 (105)
9 COG5169 HSF1 Heat shock transc 94.7 0.028 6E-07 48.3 3.0 56 48-104 16-71 (282)
10 KOG0627|consensus 87.9 0.54 1.2E-05 39.7 3.2 40 45-84 15-54 (304)
11 cd04777 HTH_MerR-like_sg1 Heli 81.0 1.3 2.9E-05 31.8 2.3 46 98-144 14-68 (107)
12 PRK15002 redox-sensitivie tran 77.2 2.6 5.6E-05 33.0 3.0 46 99-144 26-80 (154)
13 PF00605 IRF: Interferon regul 76.4 7.5 0.00016 29.0 5.1 63 43-106 2-82 (109)
14 PRK10227 DNA-binding transcrip 75.2 2.9 6.4E-05 31.8 2.8 48 98-145 14-71 (135)
15 cd04784 HTH_CadR-PbrR Helix-Tu 74.2 3.6 7.8E-05 30.4 3.0 47 98-144 14-70 (127)
16 cd04787 HTH_HMRTR_unk Helix-Tu 72.4 4.8 0.0001 30.1 3.3 47 99-145 15-71 (133)
17 cd04785 HTH_CadR-PbrR-like Hel 72.0 4 8.7E-05 30.3 2.8 48 98-145 14-71 (126)
18 PRK13749 transcriptional regul 71.0 3.9 8.4E-05 30.9 2.5 49 99-147 18-76 (121)
19 TIGR02044 CueR Cu(I)-responsiv 70.3 4.7 0.0001 29.9 2.8 47 98-144 14-70 (127)
20 cd04770 HTH_HMRTR Helix-Turn-H 70.2 4.2 9.1E-05 29.7 2.5 47 99-145 15-71 (123)
21 cd04788 HTH_NolA-AlbR Helix-Tu 68.9 5.9 0.00013 28.1 3.0 57 77-144 4-70 (96)
22 smart00348 IRF interferon regu 67.1 8.5 0.00018 28.5 3.6 44 45-89 2-58 (107)
23 PRK13752 putative transcriptio 63.8 7.7 0.00017 29.8 2.9 46 99-144 22-77 (144)
24 PRK09514 zntR zinc-responsive 62.5 8.1 0.00017 29.4 2.8 47 98-144 15-71 (140)
25 cd04767 HTH_HspR-like_MBC Heli 61.9 5.5 0.00012 30.2 1.8 58 76-146 4-72 (120)
26 PF01978 TrmB: Sugar-specific 61.5 14 0.0003 24.1 3.5 33 91-123 33-65 (68)
27 cd04768 HTH_BmrR-like Helix-Tu 61.3 8.9 0.00019 27.1 2.7 46 99-144 15-70 (96)
28 cd00103 IRF Interferon Regulat 60.0 13 0.00027 27.6 3.4 46 43-89 2-59 (107)
29 cd04782 HTH_BltR Helix-Turn-He 59.6 7.5 0.00016 27.6 2.1 45 99-143 15-69 (97)
30 cd01110 HTH_SoxR Helix-Turn-He 59.0 9.4 0.0002 29.0 2.6 44 99-143 16-69 (139)
31 TIGR02047 CadR-PbrR Cd(II)/Pb( 58.7 8.7 0.00019 28.6 2.4 46 99-144 15-70 (127)
32 TIGR01950 SoxR redox-sensitive 58.4 13 0.00028 28.5 3.3 46 98-143 15-69 (142)
33 cd01108 HTH_CueR Helix-Turn-He 57.9 10 0.00023 28.1 2.7 46 99-144 15-70 (127)
34 cd04783 HTH_MerR1 Helix-Turn-H 57.8 9.8 0.00021 28.1 2.5 47 99-145 15-71 (126)
35 TIGR02054 MerD mercuric resist 57.7 11 0.00024 28.3 2.8 48 99-146 18-75 (120)
36 smart00422 HTH_MERR helix_turn 57.4 12 0.00026 24.0 2.6 46 99-144 15-70 (70)
37 TIGR02051 MerR Hg(II)-responsi 57.1 9.3 0.0002 28.3 2.3 46 99-144 14-69 (124)
38 TIGR02043 ZntR Zn(II)-responsi 57.1 10 0.00022 28.4 2.6 46 99-144 16-71 (131)
39 cd01282 HTH_MerR-like_sg3 Heli 56.2 11 0.00023 27.5 2.4 46 99-145 15-70 (112)
40 cd04769 HTH_MerR2 Helix-Turn-H 54.6 16 0.00034 26.6 3.1 46 99-145 15-70 (116)
41 cd04786 HTH_MerR-like_sg7 Heli 54.1 17 0.00037 27.4 3.3 47 98-144 14-70 (131)
42 PF13411 MerR_1: MerR HTH fami 53.4 8.3 0.00018 24.8 1.3 45 99-143 15-68 (69)
43 cd04781 HTH_MerR-like_sg6 Heli 52.9 14 0.00031 27.0 2.7 45 99-144 15-69 (120)
44 cd01109 HTH_YyaN Helix-Turn-He 51.8 13 0.00029 26.8 2.3 46 99-144 15-70 (113)
45 cd01105 HTH_GlnR-like Helix-Tu 51.2 17 0.00037 25.3 2.7 58 75-143 3-70 (88)
46 cd04776 HTH_GnyR Helix-Turn-He 51.1 15 0.00034 27.0 2.6 47 98-146 14-70 (118)
47 COG0789 SoxR Predicted transcr 47.8 21 0.00046 25.5 2.9 49 98-146 14-72 (124)
48 cd04789 HTH_Cfa Helix-Turn-Hel 47.5 18 0.0004 25.8 2.5 56 76-142 4-68 (102)
49 cd04790 HTH_Cfa-like_unk Helix 46.3 16 0.00034 28.8 2.2 46 99-144 16-71 (172)
50 cd01107 HTH_BmrR Helix-Turn-He 45.0 24 0.00052 25.4 2.8 48 98-145 14-72 (108)
51 cd00592 HTH_MerR-like Helix-Tu 43.7 15 0.00033 25.5 1.5 47 99-146 15-71 (100)
52 cd04775 HTH_Cfa-like Helix-Tur 42.8 28 0.00061 24.8 2.8 44 99-143 16-69 (102)
53 cd01111 HTH_MerD Helix-Turn-He 42.4 24 0.00051 25.7 2.4 47 99-145 15-71 (107)
54 cd04774 HTH_YfmP Helix-Turn-He 42.2 37 0.0008 24.1 3.4 49 98-146 14-72 (96)
55 cd04779 HTH_MerR-like_sg4 Heli 38.7 33 0.00072 26.1 2.8 46 99-145 15-70 (134)
56 cd04761 HTH_MerR-SF Helix-Turn 38.4 37 0.00079 20.1 2.5 24 99-122 15-38 (49)
57 PF13835 DUF4194: Domain of un 38.3 71 0.0015 24.4 4.7 68 68-137 95-165 (166)
58 cd01106 HTH_TipAL-Mta Helix-Tu 38.3 35 0.00075 24.2 2.7 46 99-144 15-70 (103)
59 cd04773 HTH_TioE_rpt2 Second H 38.2 32 0.00068 24.9 2.5 46 99-144 15-70 (108)
60 cd04763 HTH_MlrA-like Helix-Tu 37.7 31 0.00067 22.4 2.2 55 76-141 3-67 (68)
61 PF02082 Rrf2: Transcriptional 37.6 54 0.0012 22.2 3.5 37 92-128 37-73 (83)
62 cd04766 HTH_HspR Helix-Turn-He 37.1 36 0.00078 23.6 2.6 45 99-143 16-70 (91)
63 cd04765 HTH_MlrA-like_sg2 Heli 34.0 50 0.0011 23.6 3.0 49 99-147 15-74 (99)
64 PRK13182 racA polar chromosome 33.9 40 0.00087 27.0 2.7 53 76-139 3-64 (175)
65 cd01279 HTH_HspR-like Helix-Tu 33.8 43 0.00094 23.8 2.6 46 99-144 16-71 (98)
66 PF14475 Mso1_Sec1_bdg: Sec1-b 31.7 28 0.00061 21.9 1.2 14 95-108 20-33 (41)
67 cd06404 PB1_aPKC PB1 domain is 30.9 86 0.0019 22.5 3.7 55 90-149 18-73 (83)
68 cd05992 PB1 The PB1 domain is 28.1 98 0.0021 20.2 3.5 51 90-146 19-70 (81)
69 smart00418 HTH_ARSR helix_turn 27.8 1.2E+02 0.0027 17.9 3.7 32 92-123 22-54 (66)
70 PF00564 PB1: PB1 domain; Int 27.5 85 0.0018 20.7 3.1 50 89-144 19-69 (84)
71 PF02918 Pertussis_S2S3: Pertu 26.2 85 0.0018 23.7 3.1 30 88-117 51-80 (109)
72 cd04764 HTH_MlrA-like_sg1 Heli 26.2 79 0.0017 20.3 2.7 54 76-141 3-66 (67)
73 PRK09391 fixK transcriptional 25.9 1E+02 0.0022 24.5 3.7 46 75-130 181-226 (230)
74 cd04780 HTH_MerR-like_sg5 Heli 24.1 83 0.0018 22.3 2.7 45 99-143 15-70 (95)
75 cd07321 Extradiol_Dioxygenase_ 24.1 34 0.00075 23.7 0.6 22 121-142 21-45 (77)
76 PF01698 FLO_LFY: Floricaula / 24.0 26 0.00056 31.7 0.0 18 125-142 74-91 (386)
77 cd01104 HTH_MlrA-CarA Helix-Tu 23.3 84 0.0018 19.9 2.4 56 76-142 3-68 (68)
78 PF00325 Crp: Bacterial regula 23.3 33 0.00073 20.3 0.4 13 131-143 2-14 (32)
79 COG3682 Predicted transcriptio 21.7 1.2E+02 0.0025 23.3 3.2 53 90-142 34-88 (123)
80 cd03271 ABC_UvrA_II The excisi 21.7 1.2E+02 0.0025 25.5 3.5 98 38-143 30-142 (261)
81 cd07153 Fur_like Ferric uptake 21.3 1.6E+02 0.0034 20.6 3.7 43 88-130 29-74 (116)
82 PF13545 HTH_Crp_2: Crp-like h 20.6 1.3E+02 0.0029 19.3 3.0 35 74-115 29-63 (76)
No 1
>KOG3806|consensus
Probab=100.00 E-value=5.6e-42 Score=272.68 Aligned_cols=104 Identities=63% Similarity=1.107 Sum_probs=95.3
Q ss_pred CCcCCCCceehHHHHHHhhCCCCCCCceEEecC-CceEEecCHHHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEec
Q psy8488 35 PCFTGSGPIQLWQFLLELLTDKTCQAFISWTGD-GWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKT 113 (150)
Q Consensus 35 ~~~~~~g~~~LW~FLl~LL~d~~~~~~I~Wt~~-~~eFri~dp~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv 113 (150)
....++|+++|||||++||+|+++++||+||++ ++||+++||++|||+||.+||||+||||||||||||||+++||+||
T Consensus 61 ~s~~~sg~iqLwqFLleLl~d~~~~~~I~Wtg~~g~EFkl~dp~eVArlWG~rK~kp~MNYdKLSRaLRyyY~kni~~Kv 140 (177)
T KOG3806|consen 61 ESTSGSGQIQLWQFLLELLQDESNAHIIAWTGKDGLEFKLVDPDEVARLWGARKNKPNMNYDKLSRALRYYYDKNILKKV 140 (177)
T ss_pred ccCCCCchhhHHHHHHHHHhCcccCCeeEEeCCCCceEEecCHHHHHHHHhhhhCCCCCCHHHHHHHHHHHHhcCceeec
Confidence 345788999999999999999999999999996 6799999999999999999999999999999999999999999999
Q ss_pred ccceeEEEeccchhhhhcCCHHHHHH
Q psy8488 114 AGKRYVYRFVCDLQTLLGYSPEELHA 139 (150)
Q Consensus 114 ~g~rl~Y~F~~ep~~~~~mt~eel~~ 139 (150)
+|+|++|+|++++.+. .+.++....
T Consensus 141 ~Gkr~~YkF~~~~~~~-~~~~~~~~~ 165 (177)
T KOG3806|consen 141 PGKRFVYKFVFDPLNL-ALYPHTLKN 165 (177)
T ss_pred CCceEEEEEecCHHHh-ccCcccccc
Confidence 9999999999999988 555544433
No 2
>smart00413 ETS erythroblast transformation specific domain. variation of the helix-turn-helix motif
Probab=100.00 E-value=9.8e-42 Score=244.95 Aligned_cols=85 Identities=66% Similarity=1.112 Sum_probs=82.4
Q ss_pred ceehHHHHHHhhCCCCCCCceEEecC-CceEEecCHHHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEecccceeEE
Q psy8488 42 PIQLWQFLLELLTDKTCQAFISWTGD-GWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVY 120 (150)
Q Consensus 42 ~~~LW~FLl~LL~d~~~~~~I~Wt~~-~~eFri~dp~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y 120 (150)
+++||+||++||.|+++++||+|||+ ++||+|+||++||+|||.+||+++||||||||||||||++|||+||+|++++|
T Consensus 1 ~~~Lw~FL~~LL~d~~~~~~I~W~~k~~g~Fkl~~~~~vA~lWG~~Knk~~M~YeklSRaLRyyy~~~il~Kv~g~rl~Y 80 (87)
T smart00413 1 QIQLWQFLLDLLLDPENGDIIRWTDRDGGEFKLVDPEEVARLWGQRKNKPNMNYEKLSRALRYYYKKNILRKVPGKRLVY 80 (87)
T ss_pred CccHHHHHHHHHcCccCCCeEEeeCCCCCEEEecCHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHhcCcEEecCCceEEE
Confidence 36899999999999999999999997 89999999999999999999999999999999999999999999999999999
Q ss_pred Eeccch
Q psy8488 121 RFVCDL 126 (150)
Q Consensus 121 ~F~~ep 126 (150)
+|+++|
T Consensus 81 ~F~~~~ 86 (87)
T smart00413 81 KFVKNP 86 (87)
T ss_pred ecCCCC
Confidence 999876
No 3
>PF00178 Ets: Ets-domain; InterPro: IPR000418 Transcription factors are protein molecules that bind to specific DNA sequences in the genome, resulting in the induction or inhibition of gene transcription []. The ets oncogene is such a factor, possessing a region of 85-90 amino acids known as the ETS (erythroblast transformation specific) domain [, , ]. This domain is rich in positively-charged and aromatic residues, and binds to purine-rich segments of DNA. The ETS domain has been identified in other transcription factors such as PU.1, human erg, human elf-1, human elk-1, GA binding protein, and a number of others [, , ]. It is generally localized at the C terminus of the protein, with the exception of ELF-1, ELK-1, ELK-3, ELK-4 and ERF where it is found at the N terminus. NMR-analysis of the structure of the Ets domains revealed that it contains three alpha-helixes (1-3) and four-stranded beta-sheets (1-4) arranged in the order alpha1-beta1-beta2-alpha2-alpha3-beta3-beta4 forming a winged helix-turn-helix (wHTH) topology []. The third alpha-helix is responsive to contact to the major groove of the DNA. Different members of the Ets family proteins display distinct DNA binding specificities. The Ets domains and the flanking amino acid sequences of the proteins influence the binding affinity, and the alteration of a single amino acid in the Ets domain can change its DNA binding specificities. Avian leukemia virus E26 is a replication defective retrovirus that induces a mixed erythroid/myeloid leukemia in chickens.This virus carries two distinct oncogenes: v-myb and v-ets. The ets portion of this oncogene is required for the induction of erythroblastosis. V-ets and c-ets-1, its cellular progenitor, have been shown [] to be nuclear DNA-binding proteins. Ets-1 differs slightly from v-ets at its carboxy-terminal region. In most species where it has been sequenced, c-ets-1 exists in various isoforms generated by alternative splicing and differential phosphorylation.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1DUX_F 4AVP_B 1HBX_G 1BC7_C 1K6O_A 1BC8_C 1PUE_E 1FLI_A 2DAO_A 1WWX_A ....
Probab=100.00 E-value=1.2e-39 Score=232.98 Aligned_cols=84 Identities=63% Similarity=1.130 Sum_probs=79.1
Q ss_pred ceehHHHHHHhhCCCCCCCceEEec-CCceEEecCHHHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEecccceeEE
Q psy8488 42 PIQLWQFLLELLTDKTCQAFISWTG-DGWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVY 120 (150)
Q Consensus 42 ~~~LW~FLl~LL~d~~~~~~I~Wt~-~~~eFri~dp~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y 120 (150)
+++||+||++||+|++++++|+||| +++||+|+||++||+|||.+||+++|+||+|||+||+||++|||.||+|++++|
T Consensus 1 ~~~Lw~FLl~LL~d~~~~~~I~Wt~~~~~eFki~d~~~vA~lWG~~k~~~~m~yeklsR~LR~yy~k~il~kv~g~r~~Y 80 (85)
T PF00178_consen 1 QIQLWQFLLELLEDPSNSDIIAWTGKRGGEFKIVDPEAVARLWGKHKNRPNMNYEKLSRALRYYYKKGILEKVKGQRLVY 80 (85)
T ss_dssp S-SHHHHHHHHHHSGGGTTTEEEEETSTTEEEESSHHHHHHHHHHHTTSTT-SHHHHHHHHHHHHHTTSEEEETTSTTEE
T ss_pred CccHHHHHHHHhcCccCCCeeEeeccCCCeEEecCHHHHHHHHHHHcCCccccHHHHHHHHHHHhhCCeEEecCCcEEEE
Confidence 4689999999999999999999999 589999999999999999999999999999999999999999999999999999
Q ss_pred Eeccc
Q psy8488 121 RFVCD 125 (150)
Q Consensus 121 ~F~~e 125 (150)
+|+++
T Consensus 81 ~F~~~ 85 (85)
T PF00178_consen 81 RFVEN 85 (85)
T ss_dssp EESS-
T ss_pred ecCcC
Confidence 99974
No 4
>KOG3805|consensus
Probab=99.97 E-value=4.5e-31 Score=225.38 Aligned_cols=100 Identities=43% Similarity=0.691 Sum_probs=88.1
Q ss_pred CCCCchhhhcCCCCCCCCcCCCCceehHHHHHHhhCCCC-CCCceEEecC-CceEEecCHHHHHHHhhcccCCCCccHHH
Q psy8488 19 PYVQPASMLAGYSGSGPCFTGSGPIQLWQFLLELLTDKT-CQAFISWTGD-GWEFKLTDPDEVARRWGIRKNKPKMNYEK 96 (150)
Q Consensus 19 ~p~~p~~~~~~~~~~~~~~~~~g~~~LW~FLl~LL~d~~-~~~~I~Wt~~-~~eFri~dp~~vA~lWG~~Knk~~M~Ydk 96 (150)
++..|.++.++. .++..+++|||||++||..|. ++.||+|+|+ +|.|+|.+.+.||++||+||||+.|||||
T Consensus 255 ~~P~~~~~nG~t------g~~kk~IhLwQFLkELL~sP~~~~~~IrWVDkdKGiFkiess~~lArlWG~RKNR~~MnYdK 328 (361)
T KOG3805|consen 255 LEPQPTLLNGKT------GKGKKKIHLWQFLKELLYSPEQMGSCIRWVDKDKGIFKIESSEKLARLWGIRKNRKAMNYDK 328 (361)
T ss_pred CCCCccccCCCC------CCCcceeeHHHHHHHHHhChhhhchheEeeccCCceEEeecHHHHHHHhhhhcccccccHHH
Confidence 355566555332 244569999999999999987 9999999998 89999999999999999999999999999
Q ss_pred HHHHHHhhhhcceeEeccc-ceeEEEecc
Q psy8488 97 LSRGLRYYYDKNIIHKTAG-KRYVYRFVC 124 (150)
Q Consensus 97 lsRsLR~yY~kgIl~Kv~g-~rl~Y~F~~ 124 (150)
||||||.||++|||.|+.. +|++|+|..
T Consensus 329 lsRslRqYyKkGiikK~ekkqrLvyqf~p 357 (361)
T KOG3805|consen 329 LSRSLRQYYKKGIIKKPEKKQRLVYQFQP 357 (361)
T ss_pred HHHHHHHHhhcCccccchhhhheeeeecC
Confidence 9999999999999999984 699999985
No 5
>KOG3804|consensus
Probab=99.95 E-value=1.2e-28 Score=216.15 Aligned_cols=88 Identities=42% Similarity=0.842 Sum_probs=82.2
Q ss_pred eehHHHHHHhhCCCCC-CCceEEecC-CceEEecCHHHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEecccceeEE
Q psy8488 43 IQLWQFLLELLTDKTC-QAFISWTGD-GWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVY 120 (150)
Q Consensus 43 ~~LW~FLl~LL~d~~~-~~~I~Wt~~-~~eFri~dp~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y 120 (150)
..||+||++||.|+++ ..+|.|+++ .|+|||||+++||||||.|||+.+|||+||+|||||||+++||+||.|+|++|
T Consensus 294 t~LWefl~~lL~d~~~~p~~IkWedr~~GVFrvVds~a~arlWG~~Kn~~~MtYekmsRAlRyYYk~~IL~kv~GqrLvy 373 (390)
T KOG3804|consen 294 TGLWEFLRQLLLDPNYNPGFIKWEDREKGVFRVVDSEALARLWGMHKNNSSMTYEKMSRALRYYYKREILRKVDGQRLVY 373 (390)
T ss_pred chHHHHHHHHhcCCCcCCccccccccCCCeeEEecccHHHHHhcCcCCCCCcCHHHHhHHhhhhhhcceeecCCCceeeE
Confidence 3799999999999875 459999998 79999999999999999999999999999999999999999999999999999
Q ss_pred Eeccchhhhh
Q psy8488 121 RFVCDLQTLL 130 (150)
Q Consensus 121 ~F~~ep~~~~ 130 (150)
+|+..|....
T Consensus 374 qF~k~~~~~~ 383 (390)
T KOG3804|consen 374 QFVKNPSGWA 383 (390)
T ss_pred EeccCccccc
Confidence 9999876544
No 6
>KOG3804|consensus
Probab=98.85 E-value=9.3e-10 Score=97.34 Aligned_cols=84 Identities=42% Similarity=0.736 Sum_probs=77.5
Q ss_pred CCceehHHHHHHhhCCC-CCCCceEEecC-CceEEecCHHHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEecc--c
Q psy8488 40 SGPIQLWQFLLELLTDK-TCQAFISWTGD-GWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKTA--G 115 (150)
Q Consensus 40 ~g~~~LW~FLl~LL~d~-~~~~~I~Wt~~-~~eFri~dp~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv~--g 115 (150)
.....+|+|++.+|.|. ++...|.|+.+ ++.|+.++...++.+||+++|++.|+|+.|.|++|+||.++|+.||. +
T Consensus 169 ~~tp~~~~~l~~~~q~~~~~p~~~~~~~~~~~~~~~~~s~~~s~~~~a~sn~~~m~~~~m~~a~~~~~q~~il~~~~~~~ 248 (390)
T KOG3804|consen 169 GNTPYLWEFLLDLLQDSATCPKPIKWTQREKGCFKLVDSKAVSKLWGAHSNKPDMNYETMGRALRYYPQRGILAKVEGVL 248 (390)
T ss_pred CCCcchHHHHhhhhhcccCCCcccccccccccccccccCccccccchhhccCccccccccccccccccCCccccccchhh
Confidence 34678999999999996 78999999996 78999999999999999999999999999999999999999999999 7
Q ss_pred ceeEEEec
Q psy8488 116 KRYVYRFV 123 (150)
Q Consensus 116 ~rl~Y~F~ 123 (150)
++..+++.
T Consensus 249 ~~~~~q~~ 256 (390)
T KOG3804|consen 249 QRSCHQNK 256 (390)
T ss_pred hhhcccCC
Confidence 77777775
No 7
>PF00447 HSF_DNA-bind: HSF-type DNA-binding; InterPro: IPR000232 Heat shock factor (HSF) is a transcriptional activator of heat shock genes []: it binds specifically to heat shock promoter elements, which are palindromic sequences rich with repetitive purine and pyrimidine motifs []. Under normal conditions, HSF is a homo-trimeric cytoplasmic protein, but heat shock activation results in relocalisation to the nucleus []. Each HSF monomer contains one C-terminal and three N-terminal leucine zipper repeats []. Point mutations in these regions result in disruption of cellular localisation, rendering the protein constitutively nuclear []. Two sequences flanking the N-terminal zippers fit the consensus of a bi- partite nuclear localisation signal (NLS). Interaction between the N- and C-terminal zippers may result in a structure that masks the NLS sequences: following activation of HSF, these may then be unmasked, resulting in relocalisation of the protein to the nucleus []. The DNA-binding component of HSF lies to the N terminus of the first NLS region, and is referred to as the HSF domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1FBQ_B 1FYL_B 1FBS_A 1FYM_B 3HTS_B 2HTS_A 3HSF_A 1FBU_B 1FYK_A 2LDU_A ....
Probab=97.16 E-value=0.0014 Score=47.32 Aligned_cols=64 Identities=25% Similarity=0.421 Sum_probs=45.0
Q ss_pred HHHHHhhCCCCCCCceEEecCCceEEecCHHHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEecc
Q psy8488 47 QFLLELLTDKTCQAFISWTGDGWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKTA 114 (150)
Q Consensus 47 ~FLl~LL~d~~~~~~I~Wt~~~~eFri~dp~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv~ 114 (150)
.=|.++|+|+.+.++|+|...|..|.|.|++++++--=.+- -..-+|.++.|-|-.| |......
T Consensus 4 ~kL~~~l~~~~~~~~I~W~~~G~~fiI~d~~~f~~~vLp~~-F~~~~~~SF~RQLn~y---GF~k~~~ 67 (103)
T PF00447_consen 4 SKLYEMLEDPENSDIIRWSPDGDSFIIHDPEEFEKEVLPKY-FKHSNFSSFVRQLNMY---GFKKVSS 67 (103)
T ss_dssp HHHHHHHCTTTTTTTCEECTTSSEEEES-HHHHHHHTHHHH-SST--HHHHHHHHHHT---TEEECC-
T ss_pred HHHHHHHcCCCCCCEEEEeCCCCEEEEeecHHHhhhccccc-cCccccceeeeEeeee---eeEEEec
Confidence 34677889999999999999999999999998887322211 1123689999999887 5544443
No 8
>smart00415 HSF heat shock factor.
Probab=96.88 E-value=0.0035 Score=45.68 Aligned_cols=63 Identities=27% Similarity=0.401 Sum_probs=46.8
Q ss_pred HHHHHHhhCCCCCCCceEEecCCceEEecCHHHHHHHhhcccCCCCccHHHHHHHHHhhhhcce
Q psy8488 46 WQFLLELLTDKTCQAFISWTGDGWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNI 109 (150)
Q Consensus 46 W~FLl~LL~d~~~~~~I~Wt~~~~eFri~dp~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgI 109 (150)
-.=|.++|+|++..++|+|+..+..|.|.|++++++---.+- -..-+|.++-|-|-.|.=+.+
T Consensus 6 ~~kL~~~l~~~~~~~iI~W~~~G~~f~I~d~~~f~~~vLp~~-Fk~~~~~SF~RqLn~yGF~k~ 68 (105)
T smart00415 6 LTKLYLLVEDPSTDKIISWSPSGKSFVIWDPEEFAKNLLPRY-FKHNNFSSFVRQLNMYGFRKV 68 (105)
T ss_pred HHHHHHHHhCCCCCCEEEECCCCCEEEEcCHHHHHHHHHHHh-cCCCCHHHHHHHHHhcCCEEe
Confidence 345678889999999999999999999999988776322221 123369999999988754333
No 9
>COG5169 HSF1 Heat shock transcription factor [Transcription]
Probab=94.67 E-value=0.028 Score=48.35 Aligned_cols=56 Identities=29% Similarity=0.478 Sum_probs=40.0
Q ss_pred HHHHhhCCCCCCCceEEecCCceEEecCHHHHHHHhhcccCCCCccHHHHHHHHHhh
Q psy8488 48 FLLELLTDKTCQAFISWTGDGWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRYY 104 (150)
Q Consensus 48 FLl~LL~d~~~~~~I~Wt~~~~eFri~dp~~vA~lWG~~Knk~~M~YdklsRsLR~y 104 (150)
=|.++|+|+++.++|+|+..|.-|.|.|++.+++.=..+--+ --++.++-|-|--|
T Consensus 16 KLy~iLe~~e~~k~I~Ws~~G~sfvI~~~~~F~~~iLpr~FK-h~NfaSFVRQLN~Y 71 (282)
T COG5169 16 KLYQILEEPEYYKLIQWSPDGRSFVILDPEEFTKVILPRYFK-HGNFASFVRQLNKY 71 (282)
T ss_pred HHHHHhcCcccCCceEECCCCCEEEEeCcchhhhhhhhhhhc-ccCHHHHHHHHHhc
Confidence 355678999999999999999999999998777644433211 11456666666444
No 10
>KOG0627|consensus
Probab=87.87 E-value=0.54 Score=39.72 Aligned_cols=40 Identities=28% Similarity=0.514 Sum_probs=33.0
Q ss_pred hHHHHHHhhCCCCCCCceEEecCCceEEecCHHHHHHHhh
Q psy8488 45 LWQFLLELLTDKTCQAFISWTGDGWEFKLTDPDEVARRWG 84 (150)
Q Consensus 45 LW~FLl~LL~d~~~~~~I~Wt~~~~eFri~dp~~vA~lWG 84 (150)
+..=|.++++|++..++|+|+..+.-|.|.|+.++|+.=-
T Consensus 15 Fl~K~y~~v~Dps~~~iisWs~~g~sFvv~d~~~F~~~~L 54 (304)
T KOG0627|consen 15 FLEKLYEMVEDPSTDEIISWSPSGNSFVIWNPEEFAKVLL 54 (304)
T ss_pred HHHHHHHHhcCCCCCCceEECCCCCccccCCHHHHHHHHh
Confidence 3344556788999999999999989999999999997443
No 11
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=80.97 E-value=1.3 Score=31.78 Aligned_cols=46 Identities=26% Similarity=0.291 Sum_probs=32.8
Q ss_pred HHHHHhhhhcceeEecccceeEEEeccchhhh---------hcCCHHHHHHhcccC
Q psy8488 98 SRGLRYYYDKNIIHKTAGKRYVYRFVCDLQTL---------LGYSPEELHAMVDLK 144 (150)
Q Consensus 98 sRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~~---------~~mt~eel~~~i~~~ 144 (150)
.++||||=+.|+|.+.. ....|.|..+-... +|||-+|+.++++..
T Consensus 14 ~~tlRyYe~~GLl~p~~-~~g~r~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~ 68 (107)
T cd04777 14 IDTVRHYIDLGLLIPEK-KGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSYK 68 (107)
T ss_pred HHHHHHHHHCCCcCCcc-CCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhc
Confidence 36789999999998753 34455665432221 389999999999874
No 12
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=77.19 E-value=2.6 Score=32.99 Aligned_cols=46 Identities=15% Similarity=0.272 Sum_probs=31.7
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchhhh---------hcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQTL---------LGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~~---------~~mt~eel~~~i~~~ 144 (150)
++||||-+.|+|.++........|..+--.. +|||-+|+.++++..
T Consensus 26 ~TlRyYE~~GLi~~~r~~~g~R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~~~ 80 (154)
T PRK15002 26 SALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVL 80 (154)
T ss_pred HHHHHHHHCCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 5679999999998765433334454322111 389999999999864
No 13
>PF00605 IRF: Interferon regulatory factor transcription factor; InterPro: IPR001346 Viral infections induce the expression of type I interferons (IFN-alpha and IFN-beta) genes. The induction is due to the transcriptional activation of the IFN genes. Interferon regulatory factor I (IRF-1) is one of the transcription factors responsible for that activation. IRF-1 binds to an upstream regulatory cis element, known as the interferon consensus sequence (ICS), which is found in the promoters of type I IFN and IFN-inducible MHC class I genes. Interferon regulatory factor 2 (IRF-2) is a protein that also interacts with the ICS, but that does not function as an activator; rather, it suppresses the function of IRF-1 under certain circumstances []. These proteins share a highly conserved N-terminal domain of about 100 amino acid residues which is involved in DNA-binding and which contain five conserved tryptophans. This domain is known as a 'tryptophan pentad repeat' or a 'tryptophan cluster' and is also present in: Interferon consensus sequence binding protein (ICSBP) [], a transcription factor expressed predominantly in lymphoid tissues and induced by IFN-gamma that also binds to the ICS. Transcriptional regulator ISGF3 gamma subunit []. ISGF3 is responsible for the initial stimulation of interferon-alpha-responsive genes. It recognises and binds to the interferon-stimulated response element (ISRE) within the regulatory sequences of target genes. Interferon regulatory factor 3 (IRF-3). Interferon regulatory factor 4 (IRF-4) which binds to the interferon- stimulated response element (ISRE) of the MHC class I promoter. Interferon regulatory factor 5 (IRF-5). Interferon regulatory factor 6 (IRF-6). Interferon regulatory factor 7 (IRF-7). Gamma Herpesviruses vIRF-1, -2 and -3, proteins with homology to the cellular transcription factors of the IRF family []. Neither vIRF-1 nor vIRF-2 bind to DNA with the same specificity as cellular IRFs, indicating that if vIRFs are DNA-binding proteins, their binding has a pattern distinct from that of the cellular IRFs. Whether vIRF-3 can bind DNA with the same specificity as cellular IRFs is not known. The IRF tryptophan pentad repeat DNA-binding domain has an alpha/beta architecture comprising a cluster of three alpha-helices (alpha1-alpha3) flanked on one side by a mixed four-stranded beta-sheet (beta1-beta4). It forms a helix-turn-helix motif that binds to ISRE consensus sequences found in target promoters. Three of the tryptophan residues contact DNA by recognising a GAAA sequence []. This entry represents the IRF tryptophan pentad repeat DNA-binding domain.; GO: 0000975 regulatory region DNA binding; PDB: 2IRF_H 1IRF_A 1IRG_A 2DLL_A 3QU3_C 2PI0_D 2O6G_G 1T2K_A 2O61_A 3QU6_C ....
Probab=76.38 E-value=7.5 Score=28.96 Aligned_cols=63 Identities=14% Similarity=0.410 Sum_probs=45.2
Q ss_pred eehHHHHHHhhCCCCCCCceEEecC-CceEEec------------CHHHHHHHhhcccCCC-----CccHHHHHHHHHhh
Q psy8488 43 IQLWQFLLELLTDKTCQAFISWTGD-GWEFKLT------------DPDEVARRWGIRKNKP-----KMNYEKLSRGLRYY 104 (150)
Q Consensus 43 ~~LW~FLl~LL~d~~~~~~I~Wt~~-~~eFri~------------dp~~vA~lWG~~Knk~-----~M~YdklsRsLR~y 104 (150)
++|-.+|++.+++..+.++ .|+|+ ...|+|- +..++=+.|+.++++. ..+..+....+|.=
T Consensus 2 ~rlr~WL~~~i~sg~ypGL-~W~d~~kt~FrIPWkH~~r~~~~~~~D~~iFkaWA~~~Gk~~~g~~~~dp~~wKtnfRcA 80 (109)
T PF00605_consen 2 LRLRPWLIEQIDSGRYPGL-EWLDEEKTIFRIPWKHAGRQDWDQEEDAKIFKAWAVHRGKYRPGIDKPDPSTWKTNFRCA 80 (109)
T ss_dssp --HHHHHHHHHHHTCSTTS-EESSTTSSEEEEETTSTTSTTSSHCGGGHHHHHHHHHTTSS-CTTCSSHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHhcCCCCCc-EEEcCCCCEEEeeCccCCCCCccccchHHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHH
Confidence 5788999999999999665 99997 6799983 2357789999988762 34666655555544
Q ss_pred hh
Q psy8488 105 YD 106 (150)
Q Consensus 105 Y~ 106 (150)
-.
T Consensus 81 Ln 82 (109)
T PF00605_consen 81 LN 82 (109)
T ss_dssp HH
T ss_pred Hh
Confidence 43
No 14
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=75.19 E-value=2.9 Score=31.76 Aligned_cols=48 Identities=23% Similarity=0.410 Sum_probs=34.5
Q ss_pred HHHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccCC
Q psy8488 98 SRGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLKP 145 (150)
Q Consensus 98 sRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~~ 145 (150)
.++||||-+.|++.++.....-|+.-.+-.. -+||+-+|+.++++...
T Consensus 14 ~~tlRyYE~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~~~ 71 (135)
T PRK10227 14 SKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFN 71 (135)
T ss_pred HHHHHHHHHCCCCCCcccCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhc
Confidence 3678999999999887543456776643211 23899999999998643
No 15
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=74.17 E-value=3.6 Score=30.42 Aligned_cols=47 Identities=21% Similarity=0.393 Sum_probs=33.5
Q ss_pred HHHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccC
Q psy8488 98 SRGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLK 144 (150)
Q Consensus 98 sRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~ 144 (150)
.++||||=+.|+|.+.......|++-.+-.. -+|||-+|+.++++..
T Consensus 14 ~~tLRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (127)
T cd04784 14 VETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQ 70 (127)
T ss_pred HHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhh
Confidence 3678999999999865322356776654332 1399999999999764
No 16
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=72.37 E-value=4.8 Score=30.14 Aligned_cols=47 Identities=17% Similarity=0.364 Sum_probs=33.6
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccCC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLKP 145 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~~ 145 (150)
++||||=+.|+|.+.......||+-.+-.. -+|||-+|+.++++...
T Consensus 15 ~TLRyYE~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~ 71 (133)
T cd04787 15 DTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHAD 71 (133)
T ss_pred HHHHHHHHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhhc
Confidence 678999999999986544356666543221 13899999999997643
No 17
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=71.97 E-value=4 Score=30.31 Aligned_cols=48 Identities=27% Similarity=0.418 Sum_probs=32.3
Q ss_pred HHHHHhhhhcceeEecccceeEEEeccchh----------hhhcCCHHHHHHhcccCC
Q psy8488 98 SRGLRYYYDKNIIHKTAGKRYVYRFVCDLQ----------TLLGYSPEELHAMVDLKP 145 (150)
Q Consensus 98 sRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~----------~~~~mt~eel~~~i~~~~ 145 (150)
.++||||-+.|++.++......|++-.+-. .-+||+-+|+.++++...
T Consensus 14 ~~tlR~Ye~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~ 71 (126)
T cd04785 14 VETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALSD 71 (126)
T ss_pred HHHHHHHHHCCCCCCCCcCCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHhhhh
Confidence 367899999999986533234555554221 123899999999998643
No 18
>PRK13749 transcriptional regulator MerD; Provisional
Probab=71.05 E-value=3.9 Score=30.91 Aligned_cols=49 Identities=14% Similarity=0.112 Sum_probs=36.7
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccCCCC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLKPDK 147 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~~~~ 147 (150)
++||||=+.|+|..+......|++-.+-.. -+||+-+|+.++++..+..
T Consensus 18 ~tiR~YE~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l~~~~ 76 (121)
T PRK13749 18 HIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAA 76 (121)
T ss_pred HHHHHHHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhhcCC
Confidence 578999999999887543467777654321 3499999999999987543
No 19
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=70.27 E-value=4.7 Score=29.89 Aligned_cols=47 Identities=28% Similarity=0.417 Sum_probs=31.7
Q ss_pred HHHHHhhhhcceeEecccceeEEEeccchh----------hhhcCCHHHHHHhcccC
Q psy8488 98 SRGLRYYYDKNIIHKTAGKRYVYRFVCDLQ----------TLLGYSPEELHAMVDLK 144 (150)
Q Consensus 98 sRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~----------~~~~mt~eel~~~i~~~ 144 (150)
.++||||-+.|++.++......|+.-.+-. --+||+-+|+.+++...
T Consensus 14 ~~tlRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (127)
T TIGR02044 14 SKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLW 70 (127)
T ss_pred HHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 367899999999987643234455543221 12489999999998753
No 20
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=70.20 E-value=4.2 Score=29.72 Aligned_cols=47 Identities=21% Similarity=0.431 Sum_probs=32.6
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccCC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLKP 145 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~~ 145 (150)
++||||=+.|++.++......|++-.+-.+ -+||+-+|+..+++...
T Consensus 15 ~tLRyYe~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~~~ 71 (123)
T cd04770 15 DTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRD 71 (123)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhh
Confidence 678999999999865432356666543222 13899999999987643
No 21
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=68.89 E-value=5.9 Score=28.08 Aligned_cols=57 Identities=25% Similarity=0.282 Sum_probs=36.2
Q ss_pred HHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccC
Q psy8488 77 DEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLK 144 (150)
Q Consensus 77 ~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~ 144 (150)
.+||++.|.. .++||||-+.|++.++......|+.-.+-.. -+||+-+|+..+++..
T Consensus 4 ~eva~~~gvs-----------~~tlR~ye~~Gll~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~ 70 (96)
T cd04788 4 GELARRTGLS-----------VRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGP 70 (96)
T ss_pred HHHHHHHCcC-----------HHHHHHHHHCCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhCC
Confidence 4566665542 3678999999999875322234554421111 1389999999998754
No 22
>smart00348 IRF interferon regulatory factor. interferon regulatory factor, also known as trytophan pentad repeat
Probab=67.14 E-value=8.5 Score=28.53 Aligned_cols=44 Identities=14% Similarity=0.368 Sum_probs=35.5
Q ss_pred hHHHHHHhhCCCCCCCceEEecC-CceEEecC-----------H-HHHHHHhhcccCC
Q psy8488 45 LWQFLLELLTDKTCQAFISWTGD-GWEFKLTD-----------P-DEVARRWGIRKNK 89 (150)
Q Consensus 45 LW~FLl~LL~d~~~~~~I~Wt~~-~~eFri~d-----------p-~~vA~lWG~~Knk 89 (150)
|-.+|.+.++..++.+ +.|.|+ ...|+|-= . ..+=+.|..++++
T Consensus 2 lr~WL~~~i~sg~ypG-L~W~d~ekt~FrIPWkh~~~~~~~~e~D~~iFkaWa~~~Gk 58 (107)
T smart00348 2 LRPWLVEQVESGQYPG-LCWEDEEKTRFRIPWKHAGRSGFDEERDAEIFKAYCVARGI 58 (107)
T ss_pred hHHHHHHHhccCCCCC-ceEecCCCCEEEeccccCCcCCCCchhccHHHHHHHHHhCC
Confidence 5678999999999999 999997 67999832 1 2477889988764
No 23
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=63.79 E-value=7.7 Score=29.82 Aligned_cols=46 Identities=20% Similarity=0.361 Sum_probs=33.1
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~ 144 (150)
++||||=+.|++.+......-||+-.+-.. -+||+-+|+.++++..
T Consensus 22 ~TLRyYE~~GLl~p~~r~~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll~~~ 77 (144)
T PRK13752 22 ETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRLE 77 (144)
T ss_pred HHHHHHHHCCCCCCCccCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 678999999999865433355777653322 2489999999999754
No 24
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=62.48 E-value=8.1 Score=29.38 Aligned_cols=47 Identities=19% Similarity=0.477 Sum_probs=31.8
Q ss_pred HHHHHhhhhcceeEecccceeEEEeccchh----------hhhcCCHHHHHHhcccC
Q psy8488 98 SRGLRYYYDKNIIHKTAGKRYVYRFVCDLQ----------TLLGYSPEELHAMVDLK 144 (150)
Q Consensus 98 sRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~----------~~~~mt~eel~~~i~~~ 144 (150)
.++||||-+.|+|.++.....-|++-.+-. --+||+-+|+.++++..
T Consensus 15 ~~tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 71 (140)
T PRK09514 15 PDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIR 71 (140)
T ss_pred HHHHHHHHHCCCCCCcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 367899999999987642234455543221 12389999999999754
No 25
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=61.93 E-value=5.5 Score=30.18 Aligned_cols=58 Identities=17% Similarity=0.197 Sum_probs=38.7
Q ss_pred HHHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEecccceeEEEecc-----------chhhhhcCCHHHHHHhcccC
Q psy8488 76 PDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVC-----------DLQTLLGYSPEELHAMVDLK 144 (150)
Q Consensus 76 p~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~-----------ep~~~~~mt~eel~~~i~~~ 144 (150)
-.+||++-|. +. +.||+|-++|++.+.. + ..|++-. ....-.||+.+++..++++.
T Consensus 4 I~eVA~~~GV-------s~----~TLR~wE~~GLl~p~r-~-~G~R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L~l~ 70 (120)
T cd04767 4 IGVVAELLNI-------HP----ETLRIWERHGLIKPAR-R-NGQRLYSNNDLKRLRFIKKLINEKGLNIAGVKQILSMY 70 (120)
T ss_pred HHHHHHHHCc-------CH----HHHHHHHHCCCCCCcC-C-CCcEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence 3567776663 22 4569999999998764 2 3334332 22233789999999999887
Q ss_pred CC
Q psy8488 145 PD 146 (150)
Q Consensus 145 ~~ 146 (150)
|.
T Consensus 71 ~~ 72 (120)
T cd04767 71 PC 72 (120)
T ss_pred cc
Confidence 64
No 26
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=61.52 E-value=14 Score=24.08 Aligned_cols=33 Identities=24% Similarity=0.471 Sum_probs=27.7
Q ss_pred CccHHHHHHHHHhhhhcceeEecccceeEEEec
Q psy8488 91 KMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFV 123 (150)
Q Consensus 91 ~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y~F~ 123 (150)
++...++.++|+...++|++.+..++..+|+=+
T Consensus 33 ~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 33 GISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 456788999999999999999999887777643
No 27
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=61.32 E-value=8.9 Score=27.14 Aligned_cols=46 Identities=28% Similarity=0.406 Sum_probs=31.5
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~ 144 (150)
++||||=+.|++.++......|+.-.+-.. -+||+-+++.++++..
T Consensus 15 ~tLRyye~~Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~ 70 (96)
T cd04768 15 RTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTE 70 (96)
T ss_pred HHHHHHHHCCCCCCCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 567999999999887532345665532211 1489999999988753
No 28
>cd00103 IRF Interferon Regulatory Factor (IRF); also known as tryptophan pentad repeat. The family of IRF transcription factors is important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. The IRF family is characterized by a unique 'tryptophan cluster' DNA-binding region. Viral IRFs bind to cellular IRFs; block type I and II interferons and host IRF-mediated transcriptional activation.
Probab=60.05 E-value=13 Score=27.59 Aligned_cols=46 Identities=15% Similarity=0.473 Sum_probs=37.2
Q ss_pred eehHHHHHHhhCCCCCCCceEEecC-CceEEec-----------CHHHHHHHhhcccCC
Q psy8488 43 IQLWQFLLELLTDKTCQAFISWTGD-GWEFKLT-----------DPDEVARRWGIRKNK 89 (150)
Q Consensus 43 ~~LW~FLl~LL~d~~~~~~I~Wt~~-~~eFri~-----------dp~~vA~lWG~~Knk 89 (150)
.+|-.+|.+.+++.++.+ +.|.|+ ...|+|= +...+=+.|..++++
T Consensus 2 ~~lr~WL~~~i~sg~ypG-L~W~d~ek~~FrIPWkh~~~~~~~e~d~~iFkawa~~~Gk 59 (107)
T cd00103 2 MRLRPWLVEQVDSGTYPG-LIWLDEEKTIFRIPWKHAARHDVQEADAKIFKAWAVERGI 59 (107)
T ss_pred cchHHHHHHHhccCCCCC-CeEecCCCCEEECCCccCcccCcchhhhHHHHHHHHHhCC
Confidence 468899999999999996 899997 6799983 235677889988865
No 29
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=59.64 E-value=7.5 Score=27.59 Aligned_cols=45 Identities=24% Similarity=0.234 Sum_probs=29.8
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchh--h--------hhcCCHHHHHHhccc
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQ--T--------LLGYSPEELHAMVDL 143 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~--~--------~~~mt~eel~~~i~~ 143 (150)
++||||-+.|++.++......|++-.+-. . -+||+-+|+..+++.
T Consensus 15 ~tlR~ye~~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~ 69 (97)
T cd04782 15 QTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN 69 (97)
T ss_pred HHHHHHHHCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 57799999999987642224455443221 1 138999999998865
No 30
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=58.99 E-value=9.4 Score=29.02 Aligned_cols=44 Identities=20% Similarity=0.215 Sum_probs=29.9
Q ss_pred HHHHhhhhcceeEecccceeEEEeccc-hh---------hhhcCCHHHHHHhccc
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCD-LQ---------TLLGYSPEELHAMVDL 143 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~e-p~---------~~~~mt~eel~~~i~~ 143 (150)
++||||=+.|+|.+...... |++-.+ -- --+|||-+|+.+++..
T Consensus 16 ~tLRyYE~~GLl~p~r~~~g-~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (139)
T cd01110 16 SALHFYEQKGLIASWRNAGN-QRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALAT 69 (139)
T ss_pred HHHHHHHHCCCCCCCcCCCC-CeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 56799999999987654433 444322 11 1248999999998863
No 31
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=58.69 E-value=8.7 Score=28.62 Aligned_cols=46 Identities=17% Similarity=0.297 Sum_probs=31.2
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchh----------hhhcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQ----------TLLGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~----------~~~~mt~eel~~~i~~~ 144 (150)
++||||-+.|++.........|+.-.+-. --+|||-+|+.+++...
T Consensus 15 ~tlR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~~ 70 (127)
T TIGR02047 15 ETIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRYQ 70 (127)
T ss_pred HHHHHHHHCCCCCCCCcCCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhh
Confidence 57799999999976533234455543221 12499999999998754
No 32
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=58.44 E-value=13 Score=28.52 Aligned_cols=46 Identities=15% Similarity=0.266 Sum_probs=30.6
Q ss_pred HHHHHhhhhcceeEecccceeEEEeccchhh---------hhcCCHHHHHHhccc
Q psy8488 98 SRGLRYYYDKNIIHKTAGKRYVYRFVCDLQT---------LLGYSPEELHAMVDL 143 (150)
Q Consensus 98 sRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~---------~~~mt~eel~~~i~~ 143 (150)
.++||||=+.|+|.+.........|..+--. -+|||-+++.+++..
T Consensus 15 ~~tLRyYE~~GLl~~~r~~~g~R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (142)
T TIGR01950 15 VSALHFYESKGLITSIRNSGNQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALAV 69 (142)
T ss_pred HHHHHHHHHCCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 3567999999999876543333344432111 148999999999864
No 33
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=57.92 E-value=10 Score=28.09 Aligned_cols=46 Identities=26% Similarity=0.407 Sum_probs=30.4
Q ss_pred HHHHhhhhcceeEecccceeEEEeccch----------hhhhcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDL----------QTLLGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep----------~~~~~mt~eel~~~i~~~ 144 (150)
++||||=+.|++.++......|++-.+- ---+||+-+|+.++++..
T Consensus 15 ~tlRyYe~~GLl~~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (127)
T cd01108 15 KMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALW 70 (127)
T ss_pred HHHHHHHHCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 5779999999998543222345544321 112489999999998753
No 34
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=57.83 E-value=9.8 Score=28.08 Aligned_cols=47 Identities=19% Similarity=0.410 Sum_probs=32.0
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccCC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLKP 145 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~~ 145 (150)
++||||=+.|++.++......|++-.+-.. -+||+-+|+.++++...
T Consensus 15 ~tlR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~ 71 (126)
T cd04783 15 ETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDD 71 (126)
T ss_pred HHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccc
Confidence 567999999999854333345666543211 13899999999987643
No 35
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=57.71 E-value=11 Score=28.29 Aligned_cols=48 Identities=17% Similarity=0.153 Sum_probs=33.9
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchh----------hhhcCCHHHHHHhcccCCC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQ----------TLLGYSPEELHAMVDLKPD 146 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~----------~~~~mt~eel~~~i~~~~~ 146 (150)
++||||-+.|+|.++......|+.-.+-. --+||+-+++..+++....
T Consensus 18 ~tlR~Ye~~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll~~~~~ 75 (120)
T TIGR02054 18 HVVRDYLLRGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCRALDA 75 (120)
T ss_pred HHHHHHHHCCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhcc
Confidence 57899999999998753345666554321 1248999999999876543
No 36
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=57.36 E-value=12 Score=23.99 Aligned_cols=46 Identities=30% Similarity=0.487 Sum_probs=28.9
Q ss_pred HHHHhhhhcceeEec-ccceeEEEecc-chhhh--------hcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKT-AGKRYVYRFVC-DLQTL--------LGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv-~g~rl~Y~F~~-ep~~~--------~~mt~eel~~~i~~~ 144 (150)
+.||+|-+.|++..+ ........|.. |...+ .|++.+++..+++++
T Consensus 15 ~tlr~~~~~gli~~~~~~~~g~r~y~~~dl~~l~~i~~lr~~g~~~~~i~~~l~l~ 70 (70)
T smart00422 15 RTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70 (70)
T ss_pred HHHHHHHHCCCCCCCccCCCCCEecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 456999899998765 33333344543 22111 478888888888753
No 37
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=57.14 E-value=9.3 Score=28.29 Aligned_cols=46 Identities=26% Similarity=0.390 Sum_probs=30.4
Q ss_pred HHHHhhhhcceeEecccceeEEEeccch----------hhhhcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDL----------QTLLGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep----------~~~~~mt~eel~~~i~~~ 144 (150)
++||||-+.|++.+.......|++-.+- -.-+||+-+|+..+++..
T Consensus 14 ~tlR~Ye~~GLl~~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~~~ 69 (124)
T TIGR02051 14 ETIRYYERKGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGLV 69 (124)
T ss_pred HHHHHHHHCCCCCCCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHhcc
Confidence 4679999999998543223445544321 112489999999998754
No 38
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=57.10 E-value=10 Score=28.36 Aligned_cols=46 Identities=24% Similarity=0.508 Sum_probs=30.7
Q ss_pred HHHHhhhhcceeEecccceeEEEeccch--h--------hhhcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDL--Q--------TLLGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep--~--------~~~~mt~eel~~~i~~~ 144 (150)
++||||-+.|++.++......|++-.+- . --+||+-+|+.+++...
T Consensus 16 ~tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~~ 71 (131)
T TIGR02043 16 DTLRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSIK 71 (131)
T ss_pred HHHHHHHHCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhh
Confidence 5789999999998753223344444321 1 11489999999999754
No 39
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=56.25 E-value=11 Score=27.50 Aligned_cols=46 Identities=22% Similarity=0.364 Sum_probs=31.7
Q ss_pred HHHHhhhhcceeEecccceeEEEeccch--hhh--------hcCCHHHHHHhcccCC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDL--QTL--------LGYSPEELHAMVDLKP 145 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep--~~~--------~~mt~eel~~~i~~~~ 145 (150)
++||||=+.|++.+.... ..|++-.+- ..+ +||+-+|+.+++....
T Consensus 15 ~tlR~Ye~~GLl~p~r~~-~g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~~~ 70 (112)
T cd01282 15 RSLRYYEEQGLLVPERSA-NGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCLR 70 (112)
T ss_pred HHHHHHHHCCCCCCCcCC-CCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 567999999999875543 445554322 111 4899999999988644
No 40
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=54.58 E-value=16 Score=26.64 Aligned_cols=46 Identities=22% Similarity=0.376 Sum_probs=31.7
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchh-h---------hhcCCHHHHHHhcccCC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQ-T---------LLGYSPEELHAMVDLKP 145 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~-~---------~~~mt~eel~~~i~~~~ 145 (150)
+.||||=+.|+|.++.... -|+.-.+-. . -+|++-+|+.++++...
T Consensus 15 ~tLryYe~~GLi~p~~~~~-~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~~~ 70 (116)
T cd04769 15 KAIRLYEEKGLLPSPKRSG-NYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHE 70 (116)
T ss_pred HHHHHHHHCCCCCCCCCCC-CceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccc
Confidence 5789999999998765333 555433211 1 24899999999987654
No 41
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=54.06 E-value=17 Score=27.42 Aligned_cols=47 Identities=15% Similarity=0.285 Sum_probs=32.1
Q ss_pred HHHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccC
Q psy8488 98 SRGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLK 144 (150)
Q Consensus 98 sRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~ 144 (150)
.++||||=+.|++.+......-|++-.+-.. -+|++-+|+.+++...
T Consensus 14 ~~tLRyYE~~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~~ 70 (131)
T cd04786 14 ASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPAD 70 (131)
T ss_pred HHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 3678999999999875432345555542211 1489999999999764
No 42
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=53.37 E-value=8.3 Score=24.85 Aligned_cols=45 Identities=20% Similarity=0.310 Sum_probs=27.7
Q ss_pred HHHHhhhhcceeEecccceeEEEeccch-hhh--------hcCCHHHHHHhccc
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDL-QTL--------LGYSPEELHAMVDL 143 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep-~~~--------~~mt~eel~~~i~~ 143 (150)
+.||+|-++|++......+....|..+- ..+ .|+|.+++.+++..
T Consensus 15 ~tlr~y~~~gll~~~~~~~g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 15 STLRYYEREGLLPPPRDENGYRYYSEEDVERLREIKELRKQGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHHHHTTSSTTBESTTSSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH--
T ss_pred HHHHHHHHhcCcccccccCceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHHcc
Confidence 5679999999987666443434454322 111 37888888888764
No 43
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=52.86 E-value=14 Score=27.04 Aligned_cols=45 Identities=27% Similarity=0.372 Sum_probs=32.3
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~ 144 (150)
++||||-+.|++.++... ..|+.-.+-.+ -+|++-+|+.++++..
T Consensus 15 ~tlRyYe~~GLl~p~~~~-~gyR~Y~~~~l~~l~~I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 15 STLRYYEEKGLIASIGRR-GLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred HHHHHHHHCCCCCCCcCC-CCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 567999999999987643 36666543211 1389999999998764
No 44
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=51.83 E-value=13 Score=26.81 Aligned_cols=46 Identities=22% Similarity=0.366 Sum_probs=29.8
Q ss_pred HHHHhhhhcceeEecccceeEEEeccc--hhhh--------hcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCD--LQTL--------LGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~e--p~~~--------~~mt~eel~~~i~~~ 144 (150)
++||||-+.|++.++.....-|++-.+ ...+ +|++-+|+.+++...
T Consensus 15 ~tlr~ye~~gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (113)
T cd01109 15 DTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELR 70 (113)
T ss_pred HHHHHHHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 678999999999654322234444331 1111 589999999988753
No 45
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=51.17 E-value=17 Score=25.30 Aligned_cols=58 Identities=21% Similarity=0.295 Sum_probs=35.8
Q ss_pred CHHHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEecccceeEEE-ecc-chhh--------hhcCCHHHHHHhccc
Q psy8488 75 DPDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYR-FVC-DLQT--------LLGYSPEELHAMVDL 143 (150)
Q Consensus 75 dp~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y~-F~~-ep~~--------~~~mt~eel~~~i~~ 143 (150)
...+||++.|.. .+.||+|-++|++.++......|+ |.. |... -.||+.+++.+++..
T Consensus 3 ti~evA~~~gvs-----------~~tLR~ye~~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~ 70 (88)
T cd01105 3 GIGEVSKLTGVS-----------PRQLRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRR 70 (88)
T ss_pred CHHHHHHHHCcC-----------HHHHHHHHHCCCCCCCccCCCCceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 346677776653 356799999999886654331232 322 1111 138999999888863
No 46
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=51.06 E-value=15 Score=27.02 Aligned_cols=47 Identities=30% Similarity=0.466 Sum_probs=33.1
Q ss_pred HHHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccCCC
Q psy8488 98 SRGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLKPD 146 (150)
Q Consensus 98 sRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~~~ 146 (150)
.+.||||=+.|++.+.... -|++-.+-.. -+|||-+++.++++....
T Consensus 14 ~~tlRyYe~~GLl~p~r~~--gyR~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~~~~ 70 (118)
T cd04776 14 PRTLRFYEDKGLLSPERRG--QTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDP 70 (118)
T ss_pred HHHHHHHHHCCCCCCcCCC--CccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhcc
Confidence 3678999999999876432 6776643211 138999999999986543
No 47
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=47.81 E-value=21 Score=25.50 Aligned_cols=49 Identities=27% Similarity=0.441 Sum_probs=34.0
Q ss_pred HHHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccCCC
Q psy8488 98 SRGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLKPD 146 (150)
Q Consensus 98 sRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~~~ 146 (150)
.|.||||=+.|.|.+.......||.-.+-.. -+|++-+++.++++....
T Consensus 14 ~~tLRyYE~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I~~~l~~~~~ 72 (124)
T COG0789 14 VRTLRFYERKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEIKELLDLLSA 72 (124)
T ss_pred HHHHHHHHHcCCCCCcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcccc
Confidence 3678999999999888543345555442211 148999999999987654
No 48
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=47.54 E-value=18 Score=25.82 Aligned_cols=56 Identities=23% Similarity=0.166 Sum_probs=35.5
Q ss_pred HHHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEecccceeEEEeccchhh---------hhcCCHHHHHHhcc
Q psy8488 76 PDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQT---------LLGYSPEELHAMVD 142 (150)
Q Consensus 76 p~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~---------~~~mt~eel~~~i~ 142 (150)
..+||++.|.. .++||+|=+.|++.+.........|..+--. -+||+-+|+.+++.
T Consensus 4 i~eva~~~gvs-----------~~tlR~ye~~Gll~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l~ 68 (102)
T cd04789 4 ISELAEKAGIS-----------RSTLLYYEKLGLITGTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQ 68 (102)
T ss_pred HHHHHHHHCcC-----------HHHHHHHHHCCCCCCCcCCCCCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHHc
Confidence 45677766653 3577999999999876544333334332211 12889888888775
No 49
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=46.28 E-value=16 Score=28.76 Aligned_cols=46 Identities=20% Similarity=0.314 Sum_probs=32.6
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~ 144 (150)
++||||-+.|++.+......-|++-.+-.. -+|++-+|+..+++..
T Consensus 16 ~tLRyYe~~GLl~p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~ 71 (172)
T cd04790 16 STLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQP 71 (172)
T ss_pred HHHHHHHHCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 568999999999876433456776653311 1489999999988754
No 50
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=44.95 E-value=24 Score=25.38 Aligned_cols=48 Identities=25% Similarity=0.418 Sum_probs=30.8
Q ss_pred HHHHHhhhhcceeEeccc-ceeEEEeccchh--h--------hhcCCHHHHHHhcccCC
Q psy8488 98 SRGLRYYYDKNIIHKTAG-KRYVYRFVCDLQ--T--------LLGYSPEELHAMVDLKP 145 (150)
Q Consensus 98 sRsLR~yY~kgIl~Kv~g-~rl~Y~F~~ep~--~--------~~~mt~eel~~~i~~~~ 145 (150)
.++||+|-++|++.+..- ....|+.-.+-. . -+||+-.++.++++...
T Consensus 14 ~~tlR~ye~~GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~ 72 (108)
T cd01107 14 IKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADN 72 (108)
T ss_pred HHHHHHHHHcCCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCC
Confidence 367799999999987542 223444433211 1 13889999988887644
No 51
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=43.67 E-value=15 Score=25.55 Aligned_cols=47 Identities=28% Similarity=0.521 Sum_probs=30.1
Q ss_pred HHHHhhhhcceeEeccc--ceeEEEe--------ccchhhhhcCCHHHHHHhcccCCC
Q psy8488 99 RGLRYYYDKNIIHKTAG--KRYVYRF--------VCDLQTLLGYSPEELHAMVDLKPD 146 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g--~rl~Y~F--------~~ep~~~~~mt~eel~~~i~~~~~ 146 (150)
+.||+|-+.|++..+.. .+..|.+ +..... .|++.+++..++.....
T Consensus 15 ~tlr~~~~~Gll~~~~~~~g~r~y~~~dv~~l~~i~~l~~-~g~~~~~i~~~l~~~~~ 71 (100)
T cd00592 15 RTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRE-LGLSLKEIRELLDARDE 71 (100)
T ss_pred HHHHHHHHCCCcCCCcCCCCCcccCHHHHHHHHHHHHHHH-cCCCHHHHHHHHhcccc
Confidence 46799999999864432 2333422 222223 69999999999876543
No 52
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=42.75 E-value=28 Score=24.83 Aligned_cols=44 Identities=20% Similarity=0.258 Sum_probs=28.0
Q ss_pred HHHHhhhhcceeEecccceeEEE-eccchhh---------hhcCCHHHHHHhccc
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYR-FVCDLQT---------LLGYSPEELHAMVDL 143 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~-F~~ep~~---------~~~mt~eel~~~i~~ 143 (150)
++||+|=+.|++.+..... -|+ |..+--. -.||+-+++..++..
T Consensus 16 ~tLR~ye~~Gll~~~r~~~-g~R~Y~~~dl~~l~~I~~l~~~G~~l~ei~~~~~~ 69 (102)
T cd04775 16 STLLYYESIGLIPSARSEA-NYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQ 69 (102)
T ss_pred HHHHHHHHCCCCCCCCCCC-CCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHcC
Confidence 5679999999995444333 444 4332111 138999999888764
No 53
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=42.44 E-value=24 Score=25.67 Aligned_cols=47 Identities=19% Similarity=0.194 Sum_probs=31.5
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccCC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLKP 145 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~~ 145 (150)
+.||+|=+.|+|.++.....-|+...+-.. -+||+-+++.+++....
T Consensus 15 ~tlR~ye~~GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~~ 71 (107)
T cd01111 15 HIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRALD 71 (107)
T ss_pred HHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 567999999999886432244554432211 13899999999987653
No 54
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=42.21 E-value=37 Score=24.12 Aligned_cols=49 Identities=18% Similarity=0.380 Sum_probs=32.4
Q ss_pred HHHHHhhhhcceeEecccceeEEEecc----------chhhhhcCCHHHHHHhcccCCC
Q psy8488 98 SRGLRYYYDKNIIHKTAGKRYVYRFVC----------DLQTLLGYSPEELHAMVDLKPD 146 (150)
Q Consensus 98 sRsLR~yY~kgIl~Kv~g~rl~Y~F~~----------ep~~~~~mt~eel~~~i~~~~~ 146 (150)
.+.||+|-+.|++.++........|.. ....-+||+.+++.+++.....
T Consensus 14 ~~tLR~ye~~Gll~p~r~~~g~R~Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l~~~~~ 72 (96)
T cd04774 14 KRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERILRLREVLGFSLQEVTHFLERPLE 72 (96)
T ss_pred HHHHHHHHHCCCCCCCcCCCCCEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHhcccc
Confidence 356799999999986554333323432 2233368999999999987553
No 55
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=38.75 E-value=33 Score=26.09 Aligned_cols=46 Identities=15% Similarity=0.239 Sum_probs=31.3
Q ss_pred HHHHhhhhcceeEecccceeEEEeccchhh----------hhcCCHHHHHHhcccCC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCDLQT----------LLGYSPEELHAMVDLKP 145 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~----------~~~mt~eel~~~i~~~~ 145 (150)
++||||-+.|+|.+.... ..|++-.+... -.|+|-+|+.++++...
T Consensus 15 ~TLR~Ye~~GLl~p~r~~-~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~ 70 (134)
T cd04779 15 RTIDYYTNLGLLTPERSD-SNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEVQ 70 (134)
T ss_pred HHHHHHHHCCCCCCccCC-CCCeeECHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhc
Confidence 577999999999865433 35664433221 24899999999987543
No 56
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=38.43 E-value=37 Score=20.11 Aligned_cols=24 Identities=17% Similarity=0.254 Sum_probs=15.4
Q ss_pred HHHHhhhhcceeEecccceeEEEe
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRF 122 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F 122 (150)
+.||+|-++|.+..+......+.|
T Consensus 15 ~tlr~~~~~g~l~~~~~~~~~~~y 38 (49)
T cd04761 15 STLRYYERIGLLSPARTEGGYRLY 38 (49)
T ss_pred HHHHHHHHCCCCCCCcCCCCCEEe
Confidence 457999999988744333344455
No 57
>PF13835 DUF4194: Domain of unknown function (DUF4194)
Probab=38.35 E-value=71 Score=24.43 Aligned_cols=68 Identities=15% Similarity=0.099 Sum_probs=53.2
Q ss_pred CceEEecCHHHHHHHhhccc---CCCCccHHHHHHHHHhhhhcceeEecccceeEEEeccchhhhhcCCHHHH
Q psy8488 68 GWEFKLTDPDEVARRWGIRK---NKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQTLLGYSPEEL 137 (150)
Q Consensus 68 ~~eFri~dp~~vA~lWG~~K---nk~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~~~~mt~eel 137 (150)
+.+.-+++.+++...+.... .+....=..+.++|+..-+.|++.++.+..-. |..-|.+.+-++.|+|
T Consensus 95 ~~~~~~v~~~ei~e~~~~~~~~~~d~~~~~~~~~~~l~~l~~~~ll~~~~~de~r--~~I~P~I~~~v~~~~l 165 (166)
T PF13835_consen 95 GSERVVVTREEIVEKLESFLPESRDEAPFKKRLDAALRRLKRYGLLRRLDGDEDR--YEIRPIIKLVVSADWL 165 (166)
T ss_pred CCCcEEEeHHHHHHHHHHHccccccccchHHHHHHHHHHHHHCCCeeccCCCCCE--EEEEecHHHhcCHHHc
Confidence 45677889999999888754 34566778899999999999999999872222 6667888888888876
No 58
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=38.27 E-value=35 Score=24.17 Aligned_cols=46 Identities=24% Similarity=0.439 Sum_probs=28.7
Q ss_pred HHHHhhhhcceeEecc-cceeEEEecc-chhhh--------hcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKTA-GKRYVYRFVC-DLQTL--------LGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~-g~rl~Y~F~~-ep~~~--------~~mt~eel~~~i~~~ 144 (150)
+.||+|-+.|++..+. +......|.. |...+ .||+-+++.++++..
T Consensus 15 ~tlR~ye~~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~~ 70 (103)
T cd01106 15 RTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDP 70 (103)
T ss_pred HHHHHHHHCCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 5679998999986532 2222233443 22221 489999999988764
No 59
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=38.17 E-value=32 Score=24.86 Aligned_cols=46 Identities=17% Similarity=0.208 Sum_probs=30.4
Q ss_pred HHHHhhhhcceeEecccceeEEE-eccchhh---------hhcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYR-FVCDLQT---------LLGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~-F~~ep~~---------~~~mt~eel~~~i~~~ 144 (150)
+.||+|-+.|++.++......|+ |..+--. -.||+-+++.++++..
T Consensus 15 ~tlR~ye~~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~~ 70 (108)
T cd04773 15 STLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQL 70 (108)
T ss_pred HHHHHHHHCCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHh
Confidence 56799999999987654334444 4332111 1389999999988753
No 60
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=37.66 E-value=31 Score=22.38 Aligned_cols=55 Identities=16% Similarity=0.187 Sum_probs=30.3
Q ss_pred HHHHHHHhhcccCCCCccHHHHHHHHHhhhhc-ceeEecccceeEEEeccc-hhhh--------hcCCHHHHHHhc
Q psy8488 76 PDEVARRWGIRKNKPKMNYEKLSRGLRYYYDK-NIIHKTAGKRYVYRFVCD-LQTL--------LGYSPEELHAMV 141 (150)
Q Consensus 76 p~~vA~lWG~~Knk~~M~YdklsRsLR~yY~k-gIl~Kv~g~rl~Y~F~~e-p~~~--------~~mt~eel~~~i 141 (150)
..+||++.|.. .+.||+|.++ |++.........-.|..+ ...+ .|||-+++.+++
T Consensus 3 i~e~A~~~gVs-----------~~tlr~ye~~~gl~~~~r~~~g~R~yt~~di~~l~~i~~l~~~g~~l~~i~~~l 67 (68)
T cd04763 3 IGEVALLTGIK-----------PHVLRAWEREFGLLKPQRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred HHHHHHHHCcC-----------HHHHHHHHHhcCCCCCCcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence 35677766653 3467988876 877544332222234321 1111 478888877765
No 61
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=37.60 E-value=54 Score=22.21 Aligned_cols=37 Identities=16% Similarity=0.204 Sum_probs=29.9
Q ss_pred ccHHHHHHHHHhhhhcceeEecccceeEEEeccchhh
Q psy8488 92 MNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQT 128 (150)
Q Consensus 92 M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~ 128 (150)
++...+.+-++..-+.|++....|+...|....+|..
T Consensus 37 i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~~~ 73 (83)
T PF02082_consen 37 ISPSYLRKILQKLKKAGLIESSRGRGGGYRLARPPEE 73 (83)
T ss_dssp S-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-CCG
T ss_pred cCHHHHHHHHHHHhhCCeeEecCCCCCceeecCCHHH
Confidence 4566777788888889999999999999999988754
No 62
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=37.12 E-value=36 Score=23.58 Aligned_cols=45 Identities=16% Similarity=0.269 Sum_probs=29.1
Q ss_pred HHHHhhhhcceeEecccceeEEEeccc-h---------hhhhcCCHHHHHHhccc
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVCD-L---------QTLLGYSPEELHAMVDL 143 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~e-p---------~~~~~mt~eel~~~i~~ 143 (150)
+.||+|-+.|++.+.........|..+ . ..-.|++.+++..++++
T Consensus 16 ~tLr~ye~~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~l 70 (91)
T cd04766 16 QTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILEL 70 (91)
T ss_pred HHHHHHHHCCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 567999999999875543343445431 1 12257888888877764
No 63
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=34.00 E-value=50 Score=23.59 Aligned_cols=49 Identities=14% Similarity=0.156 Sum_probs=30.0
Q ss_pred HHHHhhhhc-ceeEecccceeEEEeccc-------hhhh---hcCCHHHHHHhcccCCCC
Q psy8488 99 RGLRYYYDK-NIIHKTAGKRYVYRFVCD-------LQTL---LGYSPEELHAMVDLKPDK 147 (150)
Q Consensus 99 RsLR~yY~k-gIl~Kv~g~rl~Y~F~~e-------p~~~---~~mt~eel~~~i~~~~~~ 147 (150)
+.||+|.+. |++.+..+......|..+ ...+ .||+-+++..++....+.
T Consensus 15 ~tLR~ye~~~gli~p~r~~~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~~~ 74 (99)
T cd04765 15 HVLRYWETEFPQLKPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDGAA 74 (99)
T ss_pred HHHHHHHHHcCCCCCcCCCCCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhcccc
Confidence 567999887 777654433333334321 1222 489999999998865543
No 64
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=33.89 E-value=40 Score=26.99 Aligned_cols=53 Identities=15% Similarity=0.204 Sum_probs=34.3
Q ss_pred HHHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEecccceeEEEeccchhhhh---------cCCHHHHHH
Q psy8488 76 PDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQTLL---------GYSPEELHA 139 (150)
Q Consensus 76 p~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~~~---------~mt~eel~~ 139 (150)
..+||++.|.. ...||+|+++|.+.........+.|..+--..| ||+-+++..
T Consensus 3 i~evA~~lGVS-----------~~TLRrw~k~g~L~~~R~~~G~R~y~~~dl~~L~~I~~l~~~Gm~i~~i~~ 64 (175)
T PRK13182 3 TPFVAKKLGVS-----------PKTVQRWVKQLNLPCEKNEYGHYIFTEEDLQLLEYVKSQIEEGQNMQDTQK 64 (175)
T ss_pred HHHHHHHHCcC-----------HHHHHHHHHcCCCCCCcCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 35566665542 245799999998854444456777865433332 789888866
No 65
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=33.75 E-value=43 Score=23.75 Aligned_cols=46 Identities=15% Similarity=0.236 Sum_probs=29.5
Q ss_pred HHHHhhhhcceeEecccceeEEEecc----------chhhhhcCCHHHHHHhcccC
Q psy8488 99 RGLRYYYDKNIIHKTAGKRYVYRFVC----------DLQTLLGYSPEELHAMVDLK 144 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g~rl~Y~F~~----------ep~~~~~mt~eel~~~i~~~ 144 (150)
+.||+|-+.|++.++........|.. ....-.||+.+++..+++..
T Consensus 16 ~tLR~ye~~Gli~p~r~~~g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l~l~ 71 (98)
T cd01279 16 QTLRVYDRLGLVSPARTNGGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIELY 71 (98)
T ss_pred HHHHHHHHCCCCCCCcCCCCCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 56799999999987543322333432 12223588989888888764
No 66
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=31.70 E-value=28 Score=21.95 Aligned_cols=14 Identities=36% Similarity=0.660 Sum_probs=11.4
Q ss_pred HHHHHHHHhhhhcc
Q psy8488 95 EKLSRGLRYYYDKN 108 (150)
Q Consensus 95 dklsRsLR~yY~kg 108 (150)
.-++|+||.||...
T Consensus 20 T~v~r~l~~yY~~k 33 (41)
T PF14475_consen 20 THVHRVLRKYYTEK 33 (41)
T ss_pred hHHHHHHHHHHHHc
Confidence 44899999999854
No 67
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=30.92 E-value=86 Score=22.55 Aligned_cols=55 Identities=18% Similarity=0.225 Sum_probs=43.5
Q ss_pred CCccHHHHHHHHHhhhhcceeEecccceeEEEeccchhhhhcC-CHHHHHHhcccCCCCCC
Q psy8488 90 PKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQTLLGY-SPEELHAMVDLKPDKKD 149 (150)
Q Consensus 90 ~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~~~~m-t~eel~~~i~~~~~~~~ 149 (150)
+..+|+.|+.-+|.-+.- ..++-++-+++.|--..+-. |.+||+.=+++-+.+.|
T Consensus 18 ~~~s~e~L~~~v~~~c~~-----~~~q~ft~kw~DEEGDp~tiSS~~EL~EA~rl~~~n~~ 73 (83)
T cd06404 18 PSISLEELCNEVRDMCRF-----HNDQPFTLKWIDEEGDPCTISSQMELEEAFRLYELNKD 73 (83)
T ss_pred CCcCHHHHHHHHHHHhCC-----CCCCcEEEEEECCCCCceeecCHHHHHHHHHHHHhcCc
Confidence 478999999999987773 44567888899877777766 78899998888776655
No 68
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=28.06 E-value=98 Score=20.25 Aligned_cols=51 Identities=12% Similarity=0.231 Sum_probs=39.1
Q ss_pred CCccHHHHHHHHHhhhhcceeEecccceeEEEeccchhhhhcC-CHHHHHHhcccCCC
Q psy8488 90 PKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQTLLGY-SPEELHAMVDLKPD 146 (150)
Q Consensus 90 ~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~~~~m-t~eel~~~i~~~~~ 146 (150)
..++|+.|.-.++.-+.... ..+.+++..+...++.+ +.++|..++.+...
T Consensus 19 ~~~s~~~L~~~i~~~~~~~~------~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~~ 70 (81)
T cd05992 19 RSISFEDLRSKIAEKFGLDA------VSFKLKYPDEDGDLVTISSDEDLEEAIEEARR 70 (81)
T ss_pred CCCCHHHHHHHHHHHhCCCC------CcEEEEeeCCCCCEEEeCCHHHHHHHHHHHhh
Confidence 57899999999988887443 46777777777677776 56899999987653
No 69
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=27.81 E-value=1.2e+02 Score=17.85 Aligned_cols=32 Identities=19% Similarity=0.402 Sum_probs=23.8
Q ss_pred ccHHHHHHHHHhhhhcceeEecc-cceeEEEec
Q psy8488 92 MNYEKLSRGLRYYYDKNIIHKTA-GKRYVYRFV 123 (150)
Q Consensus 92 M~YdklsRsLR~yY~kgIl~Kv~-g~rl~Y~F~ 123 (150)
++.-.+++.|+...++|++.... ++...|.+.
T Consensus 22 is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~ 54 (66)
T smart00418 22 LSQSTVSHHLKKLREAGLVESRREGKRVYYSLT 54 (66)
T ss_pred CCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEc
Confidence 45678999999999999999776 444445443
No 70
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=27.48 E-value=85 Score=20.73 Aligned_cols=50 Identities=12% Similarity=0.280 Sum_probs=39.1
Q ss_pred CCCccHHHHHHHHHhhhhcceeEecccceeEEEeccchhhhhcC-CHHHHHHhcccC
Q psy8488 89 KPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQTLLGY-SPEELHAMVDLK 144 (150)
Q Consensus 89 k~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~~~~m-t~eel~~~i~~~ 144 (150)
..+++|+.|...++..+... +..+.++|..+-...+.+ +.++|...+.+.
T Consensus 19 ~~~~s~~~L~~~i~~~~~~~------~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~ 69 (84)
T PF00564_consen 19 PSDVSFDDLRSKIREKFGLL------DEDFQLKYKDEDGDLVTISSDEDLQEAIEQA 69 (84)
T ss_dssp CSTSHHHHHHHHHHHHHTTS------TSSEEEEEEETTSSEEEESSHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHhCCC------CccEEEEeeCCCCCEEEeCCHHHHHHHHHHH
Confidence 35679999999999988855 456888888877777777 577888887664
No 71
>PF02918 Pertussis_S2S3: Pertussis toxin, subunit 2 and 3, C-terminal domain; InterPro: IPR020063 A large group of bacterial exotoxins are referred to as "A/B toxins", essentially because they are formed from two subunits []. The "A" subunit possesses enzyme activity, and is transferred to the host cell following a conformational change in the membrane-bound transport "B" subunit []. Bordetella pertussis is the causative agent of whooping cough, and is a Gram-negative aerobic coccus. Its major virulence factor is the pertussis toxin, an A/B exotoxin that mediates both colonisation and toxaemic stages of the the disease [, ]. Recombinant, inactive forms of the 5 subunits that make up the toxin have proven to be good vaccines. The S2 and S3 subunits of the toxin form part of the "B" moiety. They are responsible for binding the whole toxin to host cells prior to invasion, and are classed as adhesins []. S2 attaches to a host receptor called lactosylceramide. It has also been speculated that the S3 unit may preferentially bind phagocytes. The crystal structure of pertussis toxin has been determined to 2.9A resolution []. The catalytic A-subunit (S1) shares structural similarity with other ADP-ribosylating bacterial toxins, although differences in the C-terminal portion explain its unique activation mechanism. Despite its heterogeneous subunit composition, the structure of the cell-binding B-oligomer (S2, S3, two copies of S4, and S5) resembles the symmetrical B-pentamers of the cholera and shiga toxin families, but it interacts differently with the A-subunit and there is virtually no sequence similarity between B-subunits of the different toxins. Two peripheral domains that are unique to the pertussis toxin B-oligomer share structural similarity with a calcium-dependent eukaryotic lectin, and reveal possible receptor-binding sites.; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1BCP_H 1PRT_H 1PTO_B.
Probab=26.21 E-value=85 Score=23.70 Aligned_cols=30 Identities=20% Similarity=0.413 Sum_probs=23.2
Q ss_pred CCCCccHHHHHHHHHhhhhcceeEecccce
Q psy8488 88 NKPKMNYEKLSRGLRYYYDKNIIHKTAGKR 117 (150)
Q Consensus 88 nk~~M~YdklsRsLR~yY~kgIl~Kv~g~r 117 (150)
++-.-.|+.|.|.++++|..|+-..|+-++
T Consensus 51 g~~~~~y~~L~~~~~~~y~tGl~VRVhV~k 80 (109)
T PF02918_consen 51 GKYRPSYSALRDQLYYFYSTGLAVRVHVSK 80 (109)
T ss_dssp STTCCCHHHHHHHHHHHHHCT-EEEEEEEE
T ss_pred cchhHHHHHHHHHHHHHHHcCcEEEEEEec
Confidence 344447999999999999999988887543
No 72
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=26.16 E-value=79 Score=20.26 Aligned_cols=54 Identities=20% Similarity=0.258 Sum_probs=27.7
Q ss_pred HHHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEecccceeEEEecc----------chhhhhcCCHHHHHHhc
Q psy8488 76 PDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVC----------DLQTLLGYSPEELHAMV 141 (150)
Q Consensus 76 p~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~----------ep~~~~~mt~eel~~~i 141 (150)
..+||++.|.. .+.||+|-++|.+.........-.|.. .... .||+-+|+.+++
T Consensus 3 i~evA~~~gvs-----------~~tlR~~~~~g~l~~~~~~~g~R~y~~~~l~~l~~i~~l~~-~g~~l~~i~~~l 66 (67)
T cd04764 3 IKEVSEIIGVK-----------PHTLRYYEKEFNLYIPRTENGRRYYTDEDIELLKKIKTLLE-KGLSIKEIKEIL 66 (67)
T ss_pred HHHHHHHHCcC-----------HHHHHHHHHhcCCCCCCCCCCceeeCHHHHHHHHHHHHHHH-CCCCHHHHHHHh
Confidence 35666666543 246798887654432222212222422 1112 477877777765
No 73
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=25.90 E-value=1e+02 Score=24.53 Aligned_cols=46 Identities=22% Similarity=0.343 Sum_probs=31.1
Q ss_pred CHHHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEecccceeEEEeccchhhhh
Q psy8488 75 DPDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQTLL 130 (150)
Q Consensus 75 dp~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~ep~~~~ 130 (150)
..+.+|.+=| ++-+++||.|+..-++|+|....+++.+ +.|+..+.
T Consensus 181 t~~~IA~~lG-------isretlsR~L~~L~~~GlI~~~~~~~i~---I~D~~~L~ 226 (230)
T PRK09391 181 SRRDIADYLG-------LTIETVSRALSQLQDRGLIGLSGARQIE---LRNRQALR 226 (230)
T ss_pred CHHHHHHHHC-------CCHHHHHHHHHHHHHCCcEEecCCceEE---EcCHHHHH
Confidence 4466666544 5789999999999999999766433332 34555543
No 74
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.10 E-value=83 Score=22.28 Aligned_cols=45 Identities=9% Similarity=0.210 Sum_probs=29.9
Q ss_pred HHHHhhhhcceeEeccc-ceeEEEeccch-------hh---hhcCCHHHHHHhccc
Q psy8488 99 RGLRYYYDKNIIHKTAG-KRYVYRFVCDL-------QT---LLGYSPEELHAMVDL 143 (150)
Q Consensus 99 RsLR~yY~kgIl~Kv~g-~rl~Y~F~~ep-------~~---~~~mt~eel~~~i~~ 143 (150)
+.||+|-+.|++.+... ....+.|..+- .. -+|++-+++..+++.
T Consensus 15 ~tlR~Ye~~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 15 ATIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHHHCCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 57899999999987542 22233454321 11 158899999998876
No 75
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=24.09 E-value=34 Score=23.68 Aligned_cols=22 Identities=41% Similarity=0.723 Sum_probs=18.5
Q ss_pred Eeccchhhhh---cCCHHHHHHhcc
Q psy8488 121 RFVCDLQTLL---GYSPEELHAMVD 142 (150)
Q Consensus 121 ~F~~ep~~~~---~mt~eel~~~i~ 142 (150)
+|..||.+++ ++|+||.+.+.+
T Consensus 21 ~f~~dp~a~~~~~~Lt~eE~~al~~ 45 (77)
T cd07321 21 RFKADPEAVLAEYGLTPEEKAALLA 45 (77)
T ss_pred HHHhCHHHHHHHcCCCHHHHHHHHc
Confidence 5889999988 799999887764
No 76
>PF01698 FLO_LFY: Floricaula / Leafy protein; InterPro: IPR002910 This family consists of various plant development proteins which are homologues of Floricaula (FLO) and leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2VY1_A 2VY2_A.
Probab=24.03 E-value=26 Score=31.73 Aligned_cols=18 Identities=39% Similarity=0.610 Sum_probs=0.0
Q ss_pred chhhhhcCCHHHHHHhcc
Q psy8488 125 DLQTLLGYSPEELHAMVD 142 (150)
Q Consensus 125 ep~~~~~mt~eel~~~i~ 142 (150)
-.+.||+||.||||+|+.
T Consensus 74 TvsTLl~M~deELDdmM~ 91 (386)
T PF01698_consen 74 TVSTLLNMTDEELDDMMN 91 (386)
T ss_dssp ------------------
T ss_pred cHHHHhcccHHHHHHHHH
Confidence 368999999999999875
No 77
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=23.33 E-value=84 Score=19.91 Aligned_cols=56 Identities=18% Similarity=0.103 Sum_probs=28.8
Q ss_pred HHHHHHHhhcccCCCCccHHHHHHHHHhhhhc-ceeEecccceeEEEecc-chh--------hhhcCCHHHHHHhcc
Q psy8488 76 PDEVARRWGIRKNKPKMNYEKLSRGLRYYYDK-NIIHKTAGKRYVYRFVC-DLQ--------TLLGYSPEELHAMVD 142 (150)
Q Consensus 76 p~~vA~lWG~~Knk~~M~YdklsRsLR~yY~k-gIl~Kv~g~rl~Y~F~~-ep~--------~~~~mt~eel~~~i~ 142 (150)
..+||++.|.. .+.||+|.++ |++...........|.. |.. .-.|||.+++.++++
T Consensus 3 ~~eva~~~gvs-----------~~tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~~ 68 (68)
T cd01104 3 IGAVARLTGVS-----------PDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALAL 68 (68)
T ss_pred HHHHHHHHCcC-----------HHHHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHhC
Confidence 35677766642 2456888775 66554332222222322 111 113788888877753
No 78
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=23.26 E-value=33 Score=20.26 Aligned_cols=13 Identities=8% Similarity=0.273 Sum_probs=5.3
Q ss_pred cCCHHHHHHhccc
Q psy8488 131 GYSPEELHAMVDL 143 (150)
Q Consensus 131 ~mt~eel~~~i~~ 143 (150)
.||++||.+++..
T Consensus 2 ~mtr~diA~~lG~ 14 (32)
T PF00325_consen 2 PMTRQDIADYLGL 14 (32)
T ss_dssp E--HHHHHHHHTS
T ss_pred CcCHHHHHHHhCC
Confidence 3455555555443
No 79
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=21.68 E-value=1.2e+02 Score=23.33 Aligned_cols=53 Identities=17% Similarity=0.330 Sum_probs=39.6
Q ss_pred CCccHHHHHHHHHhhhhcceeEec-ccceeEEEeccchhhhh-cCCHHHHHHhcc
Q psy8488 90 PKMNYEKLSRGLRYYYDKNIIHKT-AGKRYVYRFVCDLQTLL-GYSPEELHAMVD 142 (150)
Q Consensus 90 ~~M~YdklsRsLR~yY~kgIl~Kv-~g~rl~Y~F~~ep~~~~-~mt~eel~~~i~ 142 (150)
..-.|-++.--|+..++||.+... .|+++.|+-+-+-..+. +.+...|+.+.+
T Consensus 34 ~ews~sTV~TLl~RL~KKg~l~~~kdgr~~~y~pL~~~~~~~~~~~~~~l~k~~d 88 (123)
T COG3682 34 REWSYSTVKTLLNRLVKKGLLTRKKDGRAFRYSPLLTRDQYVAGESQDLLDKICD 88 (123)
T ss_pred ccccHHHHHHHHHHHHhccchhhhhcCCeeeeecccCHHHHHHHHHHHHHHHHHc
Confidence 556888999999999999987654 48899999887665555 445666666554
No 80
>cd03271 ABC_UvrA_II The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins and UvrB having one ATP binding site that is structurally related to that of helicases.
Probab=21.66 E-value=1.2e+02 Score=25.47 Aligned_cols=98 Identities=18% Similarity=0.185 Sum_probs=55.8
Q ss_pred CCCCceehHH-HHHHh----hCC----CCCCCceEEecCCceEEecCHHHHHHHhhcccCCCCccHHHHHHHHHhhhhcc
Q psy8488 38 TGSGPIQLWQ-FLLEL----LTD----KTCQAFISWTGDGWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKN 108 (150)
Q Consensus 38 ~~~g~~~LW~-FLl~L----L~d----~~~~~~I~Wt~~~~eFri~dp~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kg 108 (150)
.|+||.+|-. .|... +.+ +...+.|.+...-.+...+|..-+. ........||-.+--.+|..|
T Consensus 30 SGsGKStL~~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~vdq~pi~----~~~rs~~~ty~~~~~~ir~~f--- 102 (261)
T cd03271 30 SGSGKSSLINDTLYPALARRLHLKKEQPGNHDRIEGLEHIDKVIVIDQSPIG----RTPRSNPATYTGVFDEIRELF--- 102 (261)
T ss_pred CCCchHHHHHHHHHHHHHHHhcccccCCCcccccccccccCceEEecCCcCC----CCCCCcHHHHHHHHHHHHHhc---
Confidence 6788888864 33222 222 2112334433332345666665542 233334579999999999987
Q ss_pred eeEecccceeE-----EEec-cchhhhhcCCHHHHHHhccc
Q psy8488 109 IIHKTAGKRYV-----YRFV-CDLQTLLGYSPEELHAMVDL 143 (150)
Q Consensus 109 Il~Kv~g~rl~-----Y~F~-~ep~~~~~mt~eel~~~i~~ 143 (150)
-..-.|+|+. ++|. .++..++.||.+|.-+|...
T Consensus 103 -C~~C~G~r~~~~~l~~~~~g~~i~~v~~ltv~e~~~~~~~ 142 (261)
T cd03271 103 -CEVCKGKRYNRETLEVRYKGKSIADVLDMTVEEALEFFEN 142 (261)
T ss_pred -CccccccccCHHHHhcCcCCCCHHHHhcCCHHHHHHHHHh
Confidence 2333354432 2232 36778899999988776543
No 81
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=21.29 E-value=1.6e+02 Score=20.63 Aligned_cols=43 Identities=12% Similarity=0.236 Sum_probs=31.4
Q ss_pred CCCCccHHHHHHHHHhhhhcceeEeccc--ceeEEEecc-chhhhh
Q psy8488 88 NKPKMNYEKLSRGLRYYYDKNIIHKTAG--KRYVYRFVC-DLQTLL 130 (150)
Q Consensus 88 nk~~M~YdklsRsLR~yY~kgIl~Kv~g--~rl~Y~F~~-ep~~~~ 130 (150)
..+.++--++-|+|...-+.|++.++.. ....|.... ++-.|+
T Consensus 29 ~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~~~~~~h~H~ 74 (116)
T cd07153 29 KGPSISLATVYRTLELLEEAGLVREIELGDGKARYELNTDEHHHHL 74 (116)
T ss_pred cCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEeCCCCCCCce
Confidence 3467889999999999999999999863 335665544 344444
No 82
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=20.57 E-value=1.3e+02 Score=19.26 Aligned_cols=35 Identities=31% Similarity=0.427 Sum_probs=29.7
Q ss_pred cCHHHHHHHhhcccCCCCccHHHHHHHHHhhhhcceeEeccc
Q psy8488 74 TDPDEVARRWGIRKNKPKMNYEKLSRGLRYYYDKNIIHKTAG 115 (150)
Q Consensus 74 ~dp~~vA~lWG~~Knk~~M~YdklsRsLR~yY~kgIl~Kv~g 115 (150)
+..+.+|.+=| ++.+.++|.|+..-++|+|..-.+
T Consensus 29 lt~~~iA~~~g-------~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 29 LTQEEIADMLG-------VSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp SSHHHHHHHHT-------SCHHHHHHHHHHHHHTTSEEEETT
T ss_pred CCHHHHHHHHC-------CCHHHHHHHHHHHHHCCCEEEcCC
Confidence 47889998766 478999999999999999997654
Done!