Query psy18222
Match_columns 130
No_of_seqs 111 out of 294
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 16:50:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy18222.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/18222hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3806|consensus 100.0 3.1E-45 6.8E-50 283.1 10.8 114 1-114 50-165 (177)
2 smart00413 ETS erythroblast tr 100.0 1.4E-42 2.9E-47 242.5 9.8 85 18-102 1-86 (87)
3 PF00178 Ets: Ets-domain; Int 100.0 2E-40 4.4E-45 230.6 7.6 83 18-100 1-84 (85)
4 KOG3805|consensus 100.0 8.6E-32 1.9E-36 223.3 8.1 85 16-100 270-357 (361)
5 KOG3804|consensus 100.0 1.9E-28 4E-33 208.9 8.9 82 19-100 294-377 (390)
6 KOG3804|consensus 98.9 3.6E-10 7.7E-15 97.1 0.3 85 15-99 168-256 (390)
7 PF00447 HSF_DNA-bind: HSF-typ 97.2 0.0012 2.6E-08 46.3 6.0 65 24-92 5-69 (103)
8 smart00415 HSF heat shock fact 97.0 0.0029 6.2E-08 44.9 6.1 58 23-81 7-64 (105)
9 COG5169 HSF1 Heat shock transc 94.7 0.033 7.1E-07 46.5 3.3 51 25-80 17-71 (282)
10 KOG0627|consensus 90.2 0.28 6.1E-06 40.2 3.1 36 25-60 19-54 (304)
11 PF00605 IRF: Interferon regul 84.7 3 6.5E-05 30.2 5.3 62 19-81 2-81 (109)
12 smart00348 IRF interferon regu 68.8 7.8 0.00017 27.9 3.6 44 21-65 2-58 (107)
13 PF01978 TrmB: Sugar-specific 67.2 10 0.00023 23.9 3.6 31 67-97 33-63 (68)
14 cd00103 IRF Interferon Regulat 61.7 11 0.00024 27.0 3.3 61 19-80 2-78 (107)
15 cd04761 HTH_MerR-SF Helix-Turn 50.9 10 0.00022 22.0 1.3 44 52-106 3-46 (49)
16 cd01105 HTH_GlnR-like Helix-Tu 50.0 14 0.00031 24.9 2.2 43 51-104 3-46 (88)
17 cd04777 HTH_MerR-like_sg1 Heli 48.7 9 0.0002 26.6 1.0 28 75-103 15-42 (107)
18 PF02918 Pertussis_S2S3: Pertu 42.5 36 0.00077 24.9 3.3 40 65-104 52-92 (109)
19 PRK15002 redox-sensitivie tran 38.5 19 0.00042 27.2 1.5 30 75-104 26-55 (154)
20 cd04766 HTH_HspR Helix-Turn-He 37.9 23 0.00049 23.9 1.6 32 75-106 16-47 (91)
21 cd04788 HTH_NolA-AlbR Helix-Tu 37.7 18 0.00039 24.8 1.1 41 53-104 4-45 (96)
22 PF14475 Mso1_Sec1_bdg: Sec1-b 36.6 22 0.00048 21.7 1.2 16 69-84 18-33 (41)
23 TIGR01950 SoxR redox-sensitive 35.2 24 0.00052 26.2 1.5 30 75-104 16-45 (142)
24 cd04769 HTH_MerR2 Helix-Turn-H 33.1 22 0.00049 25.1 1.0 29 75-104 15-44 (116)
25 cd04763 HTH_MlrA-like Helix-Tu 32.3 33 0.00072 21.5 1.7 42 52-104 3-45 (68)
26 cd04784 HTH_CadR-PbrR Helix-Tu 31.8 22 0.00048 25.4 0.8 29 75-103 15-44 (127)
27 PF13545 HTH_Crp_2: Crp-like h 30.6 85 0.0018 19.6 3.4 35 50-91 29-63 (76)
28 cd04787 HTH_HMRTR_unk Helix-Tu 30.4 27 0.00059 25.3 1.1 30 75-104 15-45 (133)
29 cd04781 HTH_MerR-like_sg6 Heli 30.3 29 0.00062 24.7 1.2 29 75-104 15-44 (120)
30 cd01107 HTH_BmrR Helix-Turn-He 30.3 25 0.00055 24.5 0.9 30 75-104 15-46 (108)
31 cd01110 HTH_SoxR Helix-Turn-He 29.9 30 0.00066 25.4 1.3 29 75-103 16-44 (139)
32 TIGR02044 CueR Cu(I)-responsiv 29.2 26 0.00057 25.1 0.8 29 75-103 15-44 (127)
33 cd04764 HTH_MlrA-like_sg1 Heli 29.1 56 0.0012 20.4 2.3 44 52-106 3-46 (67)
34 cd04773 HTH_TioE_rpt2 Second H 29.0 28 0.00061 24.4 1.0 30 75-104 15-45 (108)
35 cd04768 HTH_BmrR-like Helix-Tu 28.8 30 0.00066 23.6 1.1 29 75-103 15-44 (96)
36 PF13411 MerR_1: MerR HTH fami 28.2 23 0.00049 22.1 0.3 31 75-105 15-45 (69)
37 PF05732 RepL: Firmicute plasm 27.8 88 0.0019 23.9 3.6 45 51-104 77-121 (165)
38 smart00422 HTH_MERR helix_turn 27.1 35 0.00075 21.1 1.1 43 52-105 3-46 (70)
39 PRK09514 zntR zinc-responsive 27.0 29 0.00063 25.5 0.8 41 53-104 5-46 (140)
40 cd04789 HTH_Cfa Helix-Turn-Hel 26.9 32 0.0007 23.8 0.9 42 52-104 4-45 (102)
41 cd01282 HTH_MerR-like_sg3 Heli 26.4 37 0.00079 23.9 1.2 29 75-103 15-43 (112)
42 PF01475 FUR: Ferric uptake re 26.3 88 0.0019 21.7 3.1 37 63-99 35-73 (120)
43 PRK13918 CRP/FNR family transc 26.2 1.2E+02 0.0025 22.4 3.9 76 18-107 122-198 (202)
44 PRK09391 fixK transcriptional 26.0 99 0.0021 23.8 3.6 47 51-105 181-227 (230)
45 TIGR02043 ZntR Zn(II)-responsi 25.8 33 0.00072 24.8 0.9 16 75-90 16-31 (131)
46 smart00419 HTH_CRP helix_turn_ 24.5 1.4E+02 0.003 16.7 3.3 33 52-91 11-43 (48)
47 TIGR03697 NtcA_cyano global ni 24.4 1E+02 0.0022 22.4 3.3 35 51-92 145-179 (193)
48 smart00418 HTH_ARSR helix_turn 24.4 1.5E+02 0.0032 16.9 4.1 33 68-100 22-55 (66)
49 cd04782 HTH_BltR Helix-Turn-He 24.3 30 0.00066 23.7 0.4 16 75-90 15-30 (97)
50 cd01460 vWA_midasin VWA_Midasi 24.1 52 0.0011 27.1 1.8 64 49-112 12-79 (266)
51 cd04770 HTH_HMRTR Helix-Turn-H 24.0 31 0.00068 24.3 0.4 24 75-98 15-38 (123)
52 cd04775 HTH_Cfa-like Helix-Tur 23.8 50 0.0011 22.8 1.4 29 75-104 16-45 (102)
53 cd04774 HTH_YfmP Helix-Turn-He 23.8 52 0.0011 22.6 1.5 41 53-104 4-44 (96)
54 cd04780 HTH_MerR-like_sg5 Heli 23.0 49 0.0011 22.8 1.3 31 75-105 15-46 (95)
55 cd07153 Fur_like Ferric uptake 22.6 1.6E+02 0.0035 20.0 3.9 34 65-98 30-65 (116)
56 cd01279 HTH_HspR-like Helix-Tu 21.4 58 0.0013 22.4 1.4 30 75-104 16-45 (98)
57 smart00345 HTH_GNTR helix_turn 20.4 1.9E+02 0.0041 16.6 3.6 35 51-92 22-56 (60)
58 PF06970 RepA_N: Replication i 20.0 1.4E+02 0.003 20.0 3.0 42 19-63 24-66 (76)
No 1
>KOG3806|consensus
Probab=100.00 E-value=3.1e-45 Score=283.14 Aligned_cols=114 Identities=58% Similarity=0.993 Sum_probs=107.3
Q ss_pred CcccccCC-CcCcCCCCCceehHHHHHHhhCCCCCCCCeeEecC-CCeEEEeChHHHHHHhhcccCCCCCcHHHHHHHHH
Q psy18222 1 PYELACAV-SRGLSGSGGQVQLWQFLLELLGEPSNGGVIVWEGS-QGEFRLVDPDEVARRWGLRKSKPNMNYDKLSRALR 78 (130)
Q Consensus 1 ~~~~~~p~-~r~~~~~~g~~~LW~FLl~LL~d~~~~~~I~Wt~~-~~eFri~d~~~vArlWG~~Knk~~M~YeklsRsLR 78 (130)
||++.+|+ ...+..++|+++|||||++||+|+++++||+|||. ++||+++||++||||||.+||+|+|||||||||||
T Consensus 50 ~~~~~~~~~~~~s~~~sg~iqLwqFLleLl~d~~~~~~I~Wtg~~g~EFkl~dp~eVArlWG~rK~kp~MNYdKLSRaLR 129 (177)
T KOG3806|consen 50 PYQPENPLSKNESTSGSGQIQLWQFLLELLQDESNAHIIAWTGKDGLEFKLVDPDEVARLWGARKNKPNMNYDKLSRALR 129 (177)
T ss_pred cccccccccccccCCCCchhhHHHHHHHHHhCcccCCeeEEeCCCCceEEecCHHHHHHHHhhhhCCCCCCHHHHHHHHH
Confidence 57888888 55677799999999999999999999999999995 67999999999999999999999999999999999
Q ss_pred HhhhcccEEecCceeeEEEecccchhhhhccCCCCh
Q psy18222 79 YYYDKNIMTKVHGKRYAYRFDFQGLMLACQASNTSD 114 (130)
Q Consensus 79 ~yY~kgIl~Kv~g~rl~Y~F~~~~~~~~~~~~~~~~ 114 (130)
|||+++||+||+|+|++|+|+.+....+++|++..+
T Consensus 130 yyY~kni~~Kv~Gkr~~YkF~~~~~~~~~~~~~~~~ 165 (177)
T KOG3806|consen 130 YYYDKNILKKVPGKRFVYKFVFDPLNLALYPHTLKN 165 (177)
T ss_pred HHHhcCceeecCCceEEEEEecCHHHhccCcccccc
Confidence 999999999999999999999999999999998866
No 2
>smart00413 ETS erythroblast transformation specific domain. variation of the helix-turn-helix motif
Probab=100.00 E-value=1.4e-42 Score=242.47 Aligned_cols=85 Identities=66% Similarity=1.171 Sum_probs=81.2
Q ss_pred ceehHHHHHHhhCCCCCCCCeeEec-CCCeEEEeChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCceeeEE
Q psy18222 18 QVQLWQFLLELLGEPSNGGVIVWEG-SQGEFRLVDPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAY 96 (130)
Q Consensus 18 ~~~LW~FLl~LL~d~~~~~~I~Wt~-~~~eFri~d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~rl~Y 96 (130)
+++||+||++||.||+++++|+||| .+|||+|+||++||+|||.+||+++||||||||||||||++|||+||+|++++|
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 3689999999999999999999999 589999999999999999999999999999999999999999999999999999
Q ss_pred Eecccc
Q psy18222 97 RFDFQG 102 (130)
Q Consensus 97 ~F~~~~ 102 (130)
+|..++
T Consensus 81 ~F~~~~ 86 (87)
T smart00413 81 KFVKNP 86 (87)
T ss_pred ecCCCC
Confidence 997653
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=2e-40 Score=230.57 Aligned_cols=83 Identities=64% Similarity=1.189 Sum_probs=78.8
Q ss_pred ceehHHHHHHhhCCCCCCCCeeEec-CCCeEEEeChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCceeeEE
Q psy18222 18 QVQLWQFLLELLGEPSNGGVIVWEG-SQGEFRLVDPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAY 96 (130)
Q Consensus 18 ~~~LW~FLl~LL~d~~~~~~I~Wt~-~~~eFri~d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~rl~Y 96 (130)
+++||+||++||+|++++++|+||| +++||+|+||++||+|||.+||+++||||||||+||+||++|||+||+|++++|
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 4789999999999999999999999 789999999999999999999999999999999999999999999999999999
Q ss_pred Eecc
Q psy18222 97 RFDF 100 (130)
Q Consensus 97 ~F~~ 100 (130)
+|..
T Consensus 81 ~F~~ 84 (85)
T PF00178_consen 81 RFVE 84 (85)
T ss_dssp EESS
T ss_pred ecCc
Confidence 9964
No 4
>KOG3805|consensus
Probab=99.97 E-value=8.6e-32 Score=223.30 Aligned_cols=85 Identities=45% Similarity=0.862 Sum_probs=79.9
Q ss_pred CCceehHHHHHHhhCCCC-CCCCeeEec-CCCeEEEeChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecC-ce
Q psy18222 16 GGQVQLWQFLLELLGEPS-NGGVIVWEG-SQGEFRLVDPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVH-GK 92 (130)
Q Consensus 16 ~g~~~LW~FLl~LL~d~~-~~~~I~Wt~-~~~eFri~d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~-g~ 92 (130)
..+++|||||++||..|. +++||+|+| .+|+|+|.+++.||++||++|||+.|||||||||||.|||+|||.|++ .+
T Consensus 270 kk~IhLwQFLkELL~sP~~~~~~IrWVDkdKGiFkiess~~lArlWG~RKNR~~MnYdKlsRslRqYyKkGiikK~ekkq 349 (361)
T KOG3805|consen 270 KKKIHLWQFLKELLYSPEQMGSCIRWVDKDKGIFKIESSEKLARLWGIRKNRKAMNYDKLSRSLRQYYKKGIIKKPEKKQ 349 (361)
T ss_pred cceeeHHHHHHHHHhChhhhchheEeeccCCceEEeecHHHHHHHhhhhcccccccHHHHHHHHHHHhhcCccccchhhh
Confidence 337999999999999998 999999999 589999999999999999999999999999999999999999999997 55
Q ss_pred eeEEEecc
Q psy18222 93 RYAYRFDF 100 (130)
Q Consensus 93 rl~Y~F~~ 100 (130)
||+|+|.+
T Consensus 350 rLvyqf~p 357 (361)
T KOG3805|consen 350 RLVYQFQP 357 (361)
T ss_pred heeeeecC
Confidence 89999954
No 5
>KOG3804|consensus
Probab=99.95 E-value=1.9e-28 Score=208.87 Aligned_cols=82 Identities=48% Similarity=0.982 Sum_probs=77.6
Q ss_pred eehHHHHHHhhCCCCCC-CCeeEec-CCCeEEEeChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCceeeEE
Q psy18222 19 VQLWQFLLELLGEPSNG-GVIVWEG-SQGEFRLVDPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAY 96 (130)
Q Consensus 19 ~~LW~FLl~LL~d~~~~-~~I~Wt~-~~~eFri~d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~rl~Y 96 (130)
..||+||++||.|++.. ..|.|++ ..|+|||||+++||||||.+||+.+||||||+|+|||||+++||+||.|+|++|
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 48999999999999864 5999999 579999999999999999999999999999999999999999999999999999
Q ss_pred Eecc
Q psy18222 97 RFDF 100 (130)
Q Consensus 97 ~F~~ 100 (130)
+|.-
T Consensus 374 qF~k 377 (390)
T KOG3804|consen 374 QFVK 377 (390)
T ss_pred Eecc
Confidence 9943
No 6
>KOG3804|consensus
Probab=98.88 E-value=3.6e-10 Score=97.12 Aligned_cols=85 Identities=39% Similarity=0.763 Sum_probs=77.1
Q ss_pred CCCceehHHHHHHhhCCCC-CCCCeeEec-CCCeEEEeChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecC--
Q psy18222 15 SGGQVQLWQFLLELLGEPS-NGGVIVWEG-SQGEFRLVDPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVH-- 90 (130)
Q Consensus 15 ~~g~~~LW~FLl~LL~d~~-~~~~I~Wt~-~~~eFri~d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~-- 90 (130)
..+...+|+|++.+|.|.. ....|.|+. .++.|+.+|...++.+||+++|++.|+|+.|.|++|+||..||+.||.
T Consensus 168 p~~tp~~~~~l~~~~q~~~~~p~~~~~~~~~~~~~~~~~s~~~s~~~~a~sn~~~m~~~~m~~a~~~~~q~~il~~~~~~ 247 (390)
T KOG3804|consen 168 PGNTPYLWEFLLDLLQDSATCPKPIKWTQREKGCFKLVDSKAVSKLWGAHSNKPDMNYETMGRALRYYPQRGILAKVEGV 247 (390)
T ss_pred CCCCcchHHHHhhhhhcccCCCcccccccccccccccccCccccccchhhccCccccccccccccccccCCccccccchh
Confidence 3446789999999999986 478999999 689999999999999999999999999999999999999999999999
Q ss_pred ceeeEEEec
Q psy18222 91 GKRYAYRFD 99 (130)
Q Consensus 91 g~rl~Y~F~ 99 (130)
+++..+++.
T Consensus 248 ~~~~~~q~~ 256 (390)
T KOG3804|consen 248 LQRSCHQNK 256 (390)
T ss_pred hhhhcccCC
Confidence 777777774
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=97.21 E-value=0.0012 Score=46.35 Aligned_cols=65 Identities=23% Similarity=0.420 Sum_probs=46.2
Q ss_pred HHHHhhCCCCCCCCeeEecCCCeEEEeChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCce
Q psy18222 24 FLLELLGEPSNGGVIVWEGSQGEFRLVDPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGK 92 (130)
Q Consensus 24 FLl~LL~d~~~~~~I~Wt~~~~eFri~d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~ 92 (130)
=|.++|+|++..++|+|.+.+..|.|.|++++++.-=.. --..-+|.++.|-|-.| |.-....+.
T Consensus 5 kL~~~l~~~~~~~~I~W~~~G~~fiI~d~~~f~~~vLp~-~F~~~~~~SF~RQLn~y---GF~k~~~~~ 69 (103)
T PF00447_consen 5 KLYEMLEDPENSDIIRWSPDGDSFIIHDPEEFEKEVLPK-YFKHSNFSSFVRQLNMY---GFKKVSSDS 69 (103)
T ss_dssp HHHHHHCTTTTTTTCEECTTSSEEEES-HHHHHHHTHHH-HSST--HHHHHHHHHHT---TEEECC-SS
T ss_pred HHHHHHcCCCCCCEEEEeCCCCEEEEeecHHHhhhcccc-ccCccccceeeeEeeee---eeEEEecCc
Confidence 467899999999999999999999999998887632211 11234799999999888 655555443
No 8
>smart00415 HSF heat shock factor.
Probab=96.96 E-value=0.0029 Score=44.86 Aligned_cols=58 Identities=29% Similarity=0.442 Sum_probs=44.8
Q ss_pred HHHHHhhCCCCCCCCeeEecCCCeEEEeChHHHHHHhhcccCCCCCcHHHHHHHHHHhh
Q psy18222 23 QFLLELLGEPSNGGVIVWEGSQGEFRLVDPDEVARRWGLRKSKPNMNYDKLSRALRYYY 81 (130)
Q Consensus 23 ~FLl~LL~d~~~~~~I~Wt~~~~eFri~d~~~vArlWG~~Knk~~M~YeklsRsLR~yY 81 (130)
.=|.++|+|++..++|+|+..+..|.|.|++++++---.+ --..-+|.++.|-|-.|-
T Consensus 7 ~kL~~~l~~~~~~~iI~W~~~G~~f~I~d~~~f~~~vLp~-~Fk~~~~~SF~RqLn~yG 64 (105)
T smart00415 7 TKLYLLVEDPSTDKIISWSPSGKSFVIWDPEEFAKNLLPR-YFKHNNFSSFVRQLNMYG 64 (105)
T ss_pred HHHHHHHhCCCCCCEEEECCCCCEEEEcCHHHHHHHHHHH-hcCCCCHHHHHHHHHhcC
Confidence 3467889999999999999999999999998776532221 113446999999998883
No 9
>COG5169 HSF1 Heat shock transcription factor [Transcription]
Probab=94.66 E-value=0.033 Score=46.51 Aligned_cols=51 Identities=29% Similarity=0.584 Sum_probs=38.1
Q ss_pred HHHhhCCCCCCCCeeEecCCCeEEEeChHHHHH----HhhcccCCCCCcHHHHHHHHHHh
Q psy18222 25 LLELLGEPSNGGVIVWEGSQGEFRLVDPDEVAR----RWGLRKSKPNMNYDKLSRALRYY 80 (130)
Q Consensus 25 Ll~LL~d~~~~~~I~Wt~~~~eFri~d~~~vAr----lWG~~Knk~~M~YeklsRsLR~y 80 (130)
|.++|+|+++.+.|+|+..+..|-|.|+++++. +...|. ++.++-|-|--|
T Consensus 17 Ly~iLe~~e~~k~I~Ws~~G~sfvI~~~~~F~~~iLpr~FKh~-----NfaSFVRQLN~Y 71 (282)
T COG5169 17 LYQILEEPEYYKLIQWSPDGRSFVILDPEEFTKVILPRYFKHG-----NFASFVRQLNKY 71 (282)
T ss_pred HHHHhcCcccCCceEECCCCCEEEEeCcchhhhhhhhhhhccc-----CHHHHHHHHHhc
Confidence 557789999999999999999999999876664 344444 455565555444
No 10
>KOG0627|consensus
Probab=90.24 E-value=0.28 Score=40.24 Aligned_cols=36 Identities=31% Similarity=0.591 Sum_probs=31.4
Q ss_pred HHHhhCCCCCCCCeeEecCCCeEEEeChHHHHHHhh
Q psy18222 25 LLELLGEPSNGGVIVWEGSQGEFRLVDPDEVARRWG 60 (130)
Q Consensus 25 Ll~LL~d~~~~~~I~Wt~~~~eFri~d~~~vArlWG 60 (130)
|.++++||++.++|+|+..+.-|-|.|+.++|+.=-
T Consensus 19 ~y~~v~Dps~~~iisWs~~g~sFvv~d~~~F~~~~L 54 (304)
T KOG0627|consen 19 LYEMVEDPSTDEIISWSPSGNSFVIWNPEEFAKVLL 54 (304)
T ss_pred HHHHhcCCCCCCceEECCCCCccccCCHHHHHHHHh
Confidence 457899999999999999999999999998887544
No 11
>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=84.68 E-value=3 Score=30.16 Aligned_cols=62 Identities=16% Similarity=0.406 Sum_probs=46.6
Q ss_pred eehHHHHHHhhCCCCCCCCeeEec-CCCeEEEe------------ChHHHHHHhhcccCC-----CCCcHHHHHHHHHHh
Q psy18222 19 VQLWQFLLELLGEPSNGGVIVWEG-SQGEFRLV------------DPDEVARRWGLRKSK-----PNMNYDKLSRALRYY 80 (130)
Q Consensus 19 ~~LW~FLl~LL~d~~~~~~I~Wt~-~~~eFri~------------d~~~vArlWG~~Knk-----~~M~YeklsRsLR~y 80 (130)
++|-.+|.+.++++.+.+ +.|+| ....|+|- +..++=+.|+.++|+ ...+..+..+.+|.=
T Consensus 2 ~rlr~WL~~~i~sg~ypG-L~W~d~~kt~FrIPWkH~~r~~~~~~~D~~iFkaWA~~~Gk~~~g~~~~dp~~wKtnfRcA 80 (109)
T PF00605_consen 2 LRLRPWLIEQIDSGRYPG-LEWLDEEKTIFRIPWKHAGRQDWDQEEDAKIFKAWAVHRGKYRPGIDKPDPSTWKTNFRCA 80 (109)
T ss_dssp --HHHHHHHHHHHTCSTT-SEESSTTSSEEEEETTSTTSTTSSHCGGGHHHHHHHHHTTSS-CTTCSSHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHhcCCCCC-cEEEcCCCCEEEeeCccCCCCCccccchHHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHH
Confidence 578899999999999965 59999 57999995 234788999999986 246777766666654
Q ss_pred h
Q psy18222 81 Y 81 (130)
Q Consensus 81 Y 81 (130)
-
T Consensus 81 L 81 (109)
T PF00605_consen 81 L 81 (109)
T ss_dssp H
T ss_pred H
Confidence 4
No 12
>smart00348 IRF interferon regulatory factor. interferon regulatory factor, also known as trytophan pentad repeat
Probab=68.84 E-value=7.8 Score=27.88 Aligned_cols=44 Identities=20% Similarity=0.425 Sum_probs=36.0
Q ss_pred hHHHHHHhhCCCCCCCCeeEec-CCCeEEEeC------------hHHHHHHhhcccCC
Q psy18222 21 LWQFLLELLGEPSNGGVIVWEG-SQGEFRLVD------------PDEVARRWGLRKSK 65 (130)
Q Consensus 21 LW~FLl~LL~d~~~~~~I~Wt~-~~~eFri~d------------~~~vArlWG~~Knk 65 (130)
|-.+|.+.++++.+.+ +.|.| ....|+|-= ...+=+.|..++|+
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 5578999999999998 99999 578999851 12488999999875
No 13
>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=67.16 E-value=10 Score=23.95 Aligned_cols=31 Identities=23% Similarity=0.457 Sum_probs=27.0
Q ss_pred CCcHHHHHHHHHHhhhcccEEecCceeeEEE
Q psy18222 67 NMNYDKLSRALRYYYDKNIMTKVHGKRYAYR 97 (130)
Q Consensus 67 ~M~YeklsRsLR~yY~kgIl~Kv~g~rl~Y~ 97 (130)
++...++.+.|+.-.++|++++..|+..+|+
T Consensus 33 ~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~ 63 (68)
T PF01978_consen 33 GISRSTVYRALKSLEEKGLVEREEGRPKVYR 63 (68)
T ss_dssp TSSHHHHHHHHHHHHHTTSEEEEEECCEEEE
T ss_pred CcCHHHHHHHHHHHHHCCCEEEEcCceEEEE
Confidence 5667889999999999999999998877765
No 14
>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=61.69 E-value=11 Score=27.02 Aligned_cols=61 Identities=16% Similarity=0.406 Sum_probs=44.7
Q ss_pred eehHHHHHHhhCCCCCCCCeeEec-CCCeEEEe-----------ChHHHHHHhhcccCC--C--CCcHHHHHHHHHHh
Q psy18222 19 VQLWQFLLELLGEPSNGGVIVWEG-SQGEFRLV-----------DPDEVARRWGLRKSK--P--NMNYDKLSRALRYY 80 (130)
Q Consensus 19 ~~LW~FLl~LL~d~~~~~~I~Wt~-~~~eFri~-----------d~~~vArlWG~~Knk--~--~M~YeklsRsLR~y 80 (130)
..|-.+|.+.++++.+.+ +.|.| +...|+|- +...+=+.|..++|+ + .-+..+....||.=
T Consensus 2 ~~lr~WL~~~i~sg~ypG-L~W~d~ek~~FrIPWkh~~~~~~~e~d~~iFkawa~~~Gk~~~g~~~d~~~wK~nfrcA 78 (107)
T cd00103 2 MRLRPWLVEQVDSGTYPG-LIWLDEEKTIFRIPWKHAARHDVQEADAKIFKAWAVERGIYQPGGTPDPAEWKARLLCA 78 (107)
T ss_pred cchHHHHHHHhccCCCCC-CeEecCCCCEEECCCccCcccCcchhhhHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHH
Confidence 467789999999999995 89999 57899884 224677899999885 2 34555555555543
No 15
>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=50.89 E-value=10 Score=21.99 Aligned_cols=44 Identities=18% Similarity=0.196 Sum_probs=27.7
Q ss_pred hHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCceeeEEEecccchhhh
Q psy18222 52 PDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYRFDFQGLMLA 106 (130)
Q Consensus 52 ~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~~~~ 106 (130)
..+||++.|... +.||+|-++|.+.........+.|+.+.+..+
T Consensus 3 ~~e~a~~~gv~~-----------~tlr~~~~~g~l~~~~~~~~~~~y~~~~v~~l 46 (49)
T cd04761 3 IGELAKLTGVSP-----------STLRYYERIGLLSPARTEGGYRLYSDADLERL 46 (49)
T ss_pred HHHHHHHHCcCH-----------HHHHHHHHCCCCCCCcCCCCCEEeCHHHHHHh
Confidence 356666665532 46799999999875443334566776666543
No 16
>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=50.03 E-value=14 Score=24.91 Aligned_cols=43 Identities=19% Similarity=0.397 Sum_probs=27.0
Q ss_pred ChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCcee-eEEEecccchh
Q psy18222 51 DPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGKR-YAYRFDFQGLM 104 (130)
Q Consensus 51 d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~r-l~Y~F~~~~~~ 104 (130)
...+||++-|... +.||+|-++|++.+..... ..-.|..+.+.
T Consensus 3 ti~evA~~~gvs~-----------~tLR~ye~~Gll~p~r~~~~g~R~Ys~~dv~ 46 (88)
T cd01105 3 GIGEVSKLTGVSP-----------RQLRYWEEKGLIKSIRSDGGGQRKYSLADVD 46 (88)
T ss_pred CHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCccCCCCceecCHHHHH
Confidence 3467777776542 6789999999988665432 23334444443
No 17
>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=48.70 E-value=9 Score=26.62 Aligned_cols=28 Identities=25% Similarity=0.312 Sum_probs=19.7
Q ss_pred HHHHHhhhcccEEecCceeeEEEecccch
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYRFDFQGL 103 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~ 103 (130)
++||||-+.|+|.+.. ....|.|+.+.+
T Consensus 15 ~tlRyYe~~GLl~p~~-~~g~r~Y~~~~~ 42 (107)
T cd04777 15 DTVRHYIDLGLLIPEK-KGGQYFFDEKCQ 42 (107)
T ss_pred HHHHHHHHCCCcCCcc-CCCccccCHHHH
Confidence 6789999999998753 234456755544
No 18
>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=42.46 E-value=36 Score=24.91 Aligned_cols=40 Identities=25% Similarity=0.433 Sum_probs=26.6
Q ss_pred CCCCcHHHHHHHHHHhhhcccEEecCceee-EEEecccchh
Q psy18222 65 KPNMNYDKLSRALRYYYDKNIMTKVHGKRY-AYRFDFQGLM 104 (130)
Q Consensus 65 k~~M~YeklsRsLR~yY~kgIl~Kv~g~rl-~Y~F~~~~~~ 104 (130)
+-.=.|+.|.|.++++|..|+-..|+-++- .|-+.+.+.|
T Consensus 52 ~~~~~y~~L~~~~~~~y~tGl~VRVhV~k~~~~~~~~~~tf 92 (109)
T PF02918_consen 52 KYRPSYSALRDQLYYFYSTGLAVRVHVSKDEWYYPAFDATF 92 (109)
T ss_dssp TTCCCHHHHHHHHHHHHHCT-EEEEEEEEEEEE--STT-SS
T ss_pred chhHHHHHHHHHHHHHHHcCcEEEEEEecccccChhhhcCc
Confidence 334469999999999999999999986543 3444444444
No 19
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=38.47 E-value=19 Score=27.23 Aligned_cols=30 Identities=23% Similarity=0.399 Sum_probs=20.3
Q ss_pred HHHHHhhhcccEEecCceeeEEEecccchh
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYRFDFQGLM 104 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~~ 104 (130)
++||||-+.|+|.++........|+.+.+.
T Consensus 26 ~TlRyYE~~GLi~~~r~~~g~R~Y~~~~i~ 55 (154)
T PRK15002 26 SALHFYESKGLITSIRNSGNQRRYKRDVLR 55 (154)
T ss_pred HHHHHHHHCCCCCCccCCCCCEEECHHHHH
Confidence 578999999999876433334556555443
No 20
>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=37.95 E-value=23 Score=23.87 Aligned_cols=32 Identities=13% Similarity=0.196 Sum_probs=22.2
Q ss_pred HHHHHhhhcccEEecCceeeEEEecccchhhh
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYRFDFQGLMLA 106 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~~~~ 106 (130)
+.||+|-+.|++.+.........|+.+++...
T Consensus 16 ~tLr~ye~~Gli~p~r~~~g~R~y~~~dv~~l 47 (91)
T cd04766 16 QTLRLYERLGLLSPSRTDGGTRRYSERDIERL 47 (91)
T ss_pred HHHHHHHHCCCcCCCcCCCCCeeECHHHHHHH
Confidence 56899999999987654444556766665543
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=37.70 E-value=18 Score=24.78 Aligned_cols=41 Identities=27% Similarity=0.387 Sum_probs=25.6
Q ss_pred HHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCceeeEEE-ecccchh
Q psy18222 53 DEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYR-FDFQGLM 104 (130)
Q Consensus 53 ~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~rl~Y~-F~~~~~~ 104 (130)
.+||++.|.. .++||||-+.|++.+..-....|+ |+.+++.
T Consensus 4 ~eva~~~gvs-----------~~tlR~ye~~Gll~p~~r~~~gyR~Y~~~~l~ 45 (96)
T cd04788 4 GELARRTGLS-----------VRTLHHYDHIGLLSPSQRTEGGHRLYDRADIR 45 (96)
T ss_pred HHHHHHHCcC-----------HHHHHHHHHCCCCCCCccCCCCceeeCHHHHH
Confidence 4566666654 367899999999987532222344 4555543
No 22
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=36.63 E-value=22 Score=21.70 Aligned_cols=16 Identities=31% Similarity=0.638 Sum_probs=12.0
Q ss_pred cHHHHHHHHHHhhhcc
Q psy18222 69 NYDKLSRALRYYYDKN 84 (130)
Q Consensus 69 ~YeklsRsLR~yY~kg 84 (130)
+---++|+||.||...
T Consensus 18 ddT~v~r~l~~yY~~k 33 (41)
T PF14475_consen 18 DDTHVHRVLRKYYTEK 33 (41)
T ss_pred chhHHHHHHHHHHHHc
Confidence 3445799999999743
No 23
>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=35.16 E-value=24 Score=26.20 Aligned_cols=30 Identities=23% Similarity=0.399 Sum_probs=20.4
Q ss_pred HHHHHhhhcccEEecCceeeEEEecccchh
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYRFDFQGLM 104 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~~ 104 (130)
++||||=+.|+|.+.........|+.+++.
T Consensus 16 ~tLRyYE~~GLl~~~r~~~g~R~Y~~~di~ 45 (142)
T TIGR01950 16 SALHFYESKGLITSIRNSGNQRRYKRDVLR 45 (142)
T ss_pred HHHHHHHHCCCCCCccCCCCCEEECHHHHH
Confidence 578999999999875543334556555543
No 24
>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=33.12 E-value=22 Score=25.05 Aligned_cols=29 Identities=28% Similarity=0.547 Sum_probs=19.8
Q ss_pred HHHHHhhhcccEEecCceeeEEE-ecccchh
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYR-FDFQGLM 104 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~-F~~~~~~ 104 (130)
+.||||-+.|++.++.... -|+ |+.+++.
T Consensus 15 ~tLryYe~~GLi~p~~~~~-~yR~Y~~~d~~ 44 (116)
T cd04769 15 KAIRLYEEKGLLPSPKRSG-NYRVYDAQHVE 44 (116)
T ss_pred HHHHHHHHCCCCCCCCCCC-CceeeCHHHHH
Confidence 6789999999998765333 444 4555444
No 25
>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=32.34 E-value=33 Score=21.54 Aligned_cols=42 Identities=17% Similarity=0.162 Sum_probs=24.5
Q ss_pred hHHHHHHhhcccCCCCCcHHHHHHHHHHhhhc-ccEEecCceeeEEEecccchh
Q psy18222 52 PDEVARRWGLRKSKPNMNYDKLSRALRYYYDK-NIMTKVHGKRYAYRFDFQGLM 104 (130)
Q Consensus 52 ~~~vArlWG~~Knk~~M~YeklsRsLR~yY~k-gIl~Kv~g~rl~Y~F~~~~~~ 104 (130)
..+||++.|... +.||+|.++ |++.........-.|..+.+.
T Consensus 3 i~e~A~~~gVs~-----------~tlr~ye~~~gl~~~~r~~~g~R~yt~~di~ 45 (68)
T cd04763 3 IGEVALLTGIKP-----------HVLRAWEREFGLLKPQRSDGGHRLFNDADID 45 (68)
T ss_pred HHHHHHHHCcCH-----------HHHHHHHHhcCCCCCCcCCCCCcccCHHHHH
Confidence 356777777653 568988876 877544332223345444444
No 26
>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=31.81 E-value=22 Score=25.38 Aligned_cols=29 Identities=24% Similarity=0.490 Sum_probs=18.8
Q ss_pred HHHHHhhhcccEEecCceeeEEEe-cccch
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYRF-DFQGL 103 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~F-~~~~~ 103 (130)
++||||-+.|+|.+..-....||+ +.+.+
T Consensus 15 ~tLRyYe~~GLl~p~~r~~~gyR~Y~~~~l 44 (127)
T cd04784 15 ETIRYYEKEGLLPAPARSANNYRLYDEEHL 44 (127)
T ss_pred HHHHHHHHCCCCCCCCcCCCCCeecCHHHH
Confidence 678999999999754322344554 44444
No 27
>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=30.57 E-value=85 Score=19.64 Aligned_cols=35 Identities=26% Similarity=0.458 Sum_probs=29.8
Q ss_pred eChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCc
Q psy18222 50 VDPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHG 91 (130)
Q Consensus 50 ~d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g 91 (130)
+..+++|.+=| ++.+.++|.|+..-++|++..-.+
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 36788888876 578999999999999999997666
No 28
>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=30.41 E-value=27 Score=25.27 Aligned_cols=30 Identities=17% Similarity=0.369 Sum_probs=20.1
Q ss_pred HHHHHhhhcccEEecCceeeEEEe-cccchh
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYRF-DFQGLM 104 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~F-~~~~~~ 104 (130)
++||||=+.|+|.+.......||+ +.+.+.
T Consensus 15 ~TLRyYE~~GLl~p~r~~~~gyR~Y~~~~~~ 45 (133)
T cd04787 15 DTVRFYTRIGLLRPTRDPVNGYRLYSEKDLS 45 (133)
T ss_pred HHHHHHHHCCCCCCCcCCCCCeeeCCHHHHH
Confidence 678999999999986543245554 444443
No 29
>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=30.30 E-value=29 Score=24.65 Aligned_cols=29 Identities=31% Similarity=0.428 Sum_probs=19.8
Q ss_pred HHHHHhhhcccEEecCceeeEEEe-cccchh
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYRF-DFQGLM 104 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~F-~~~~~~ 104 (130)
++||||-+.|++.++.... -||. +.+.+.
T Consensus 15 ~tlRyYe~~GLl~p~~~~~-gyR~Y~~~~l~ 44 (120)
T cd04781 15 STLRYYEEKGLIASIGRRG-LRRQYDPQVLD 44 (120)
T ss_pred HHHHHHHHCCCCCCCcCCC-CceecCHHHHH
Confidence 6789999999999875433 5554 444443
No 30
>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=30.29 E-value=25 Score=24.50 Aligned_cols=30 Identities=20% Similarity=0.260 Sum_probs=19.7
Q ss_pred HHHHHhhhcccEEecC--ceeeEEEecccchh
Q psy18222 75 RALRYYYDKNIMTKVH--GKRYAYRFDFQGLM 104 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~--g~rl~Y~F~~~~~~ 104 (130)
++||+|-++|++.+.. +......|+.+++.
T Consensus 15 ~tlR~ye~~GLi~p~~~~~~ngyR~Y~~~~i~ 46 (108)
T cd01107 15 KALRYYDKIGLLKPAYVDPDTGYRYYSAEQLE 46 (108)
T ss_pred HHHHHHHHcCCCCCCcCCCCCCccccCHHHHH
Confidence 6789999999998754 22233445555544
No 31
>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=29.91 E-value=30 Score=25.44 Aligned_cols=29 Identities=21% Similarity=0.330 Sum_probs=19.1
Q ss_pred HHHHHhhhcccEEecCceeeEEEecccch
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYRFDFQGL 103 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~ 103 (130)
++||||=+.|+|.+.........|+.+++
T Consensus 16 ~tLRyYE~~GLl~p~r~~~g~R~Y~~~dl 44 (139)
T cd01110 16 SALHFYEQKGLIASWRNAGNQRRYPRDVL 44 (139)
T ss_pred HHHHHHHHCCCCCCCcCCCCCeEECHHHH
Confidence 57899999999987654433333544443
No 32
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=29.23 E-value=26 Score=25.09 Aligned_cols=29 Identities=28% Similarity=0.531 Sum_probs=18.4
Q ss_pred HHHHHhhhcccEEecCceeeEEE-ecccch
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYR-FDFQGL 103 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~-F~~~~~ 103 (130)
++||||-+.|++.++.-....|| |+.+.+
T Consensus 15 ~tlRyYe~~GLl~p~~r~~~gyR~Y~~~~l 44 (127)
T TIGR02044 15 KMIRYYEEKGLIPPPLRSEGGYRTYTQQHL 44 (127)
T ss_pred HHHHHHHHCCCCCCCCcCCCCCeecCHHHH
Confidence 67899999999987632223344 344443
No 33
>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=29.11 E-value=56 Score=20.36 Aligned_cols=44 Identities=18% Similarity=0.207 Sum_probs=24.0
Q ss_pred hHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCceeeEEEecccchhhh
Q psy18222 52 PDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYRFDFQGLMLA 106 (130)
Q Consensus 52 ~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~~~~ 106 (130)
..+||++.|... +.||+|-++|.+.........-.|+.+++...
T Consensus 3 i~evA~~~gvs~-----------~tlR~~~~~g~l~~~~~~~g~R~y~~~~l~~l 46 (67)
T cd04764 3 IKEVSEIIGVKP-----------HTLRYYEKEFNLYIPRTENGRRYYTDEDIELL 46 (67)
T ss_pred HHHHHHHHCcCH-----------HHHHHHHHhcCCCCCCCCCCceeeCHHHHHHH
Confidence 356777766542 56798887654432222223334666665543
No 34
>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=29.01 E-value=28 Score=24.35 Aligned_cols=30 Identities=17% Similarity=0.347 Sum_probs=20.0
Q ss_pred HHHHHhhhcccEEecCceeeEEE-ecccchh
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYR-FDFQGLM 104 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~-F~~~~~~ 104 (130)
+.||+|-+.|++.++......|+ |+.+.+.
T Consensus 15 ~tlR~ye~~Gll~p~~~~~~g~R~Y~~~dl~ 45 (108)
T cd04773 15 STLRHWEKEGLLSPDREPETGYRVYDPSDVR 45 (108)
T ss_pred HHHHHHHHCCCCCCCcCCCCCceeeCHHHHH
Confidence 67899999999987653323444 5555544
No 35
>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=28.77 E-value=30 Score=23.64 Aligned_cols=29 Identities=28% Similarity=0.518 Sum_probs=18.9
Q ss_pred HHHHHhhhcccEEecCceeeEEEe-cccch
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYRF-DFQGL 103 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~F-~~~~~ 103 (130)
++||||-+.|++.++......|+. +.+++
T Consensus 15 ~tLRyye~~Gll~p~~~~~~gyR~Y~~~~l 44 (96)
T cd04768 15 RTLRHYDDIGLFKPAKIAENGYRYYSYAQL 44 (96)
T ss_pred HHHHHHHHCCCCCCCccCCCCeeeCCHHHH
Confidence 578999999999886432234543 44443
No 36
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=28.20 E-value=23 Score=22.06 Aligned_cols=31 Identities=13% Similarity=0.218 Sum_probs=20.6
Q ss_pred HHHHHhhhcccEEecCceeeEEEecccchhh
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYRFDFQGLML 105 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~~~ 105 (130)
+.||+|-++|++...........|+.+++..
T Consensus 15 ~tlr~y~~~gll~~~~~~~g~r~y~~~dv~~ 45 (69)
T PF13411_consen 15 STLRYYEREGLLPPPRDENGYRYYSEEDVER 45 (69)
T ss_dssp HHHHHHHHTTSSTTBESTTSSEEE-HHHHHH
T ss_pred HHHHHHHHhcCcccccccCceeeccHHHHHH
Confidence 5689999999977776444446666555543
No 37
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=27.83 E-value=88 Score=23.87 Aligned_cols=45 Identities=24% Similarity=0.376 Sum_probs=34.6
Q ss_pred ChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCceeeEEEecccchh
Q psy18222 51 DPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYRFDFQGLM 104 (130)
Q Consensus 51 d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~~ 104 (130)
+-..+|..= .|+-.+++|+|...-+++||.++. ..+|...|+-.+
T Consensus 77 t~~~ia~~l-------~iS~~Tv~r~ik~L~e~~iI~k~~--~G~Y~iNP~~~~ 121 (165)
T PF05732_consen 77 TQKEIAEKL-------GISKPTVSRAIKELEEKNIIKKIR--NGAYMINPNFFF 121 (165)
T ss_pred eHHHHHHHh-------CCCHHHHHHHHHHHHhCCcEEEcc--CCeEEECcHHhe
Confidence 445666543 477889999999999999999984 468988776544
No 38
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=27.14 E-value=35 Score=21.13 Aligned_cols=43 Identities=23% Similarity=0.245 Sum_probs=26.4
Q ss_pred hHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEec-CceeeEEEecccchhh
Q psy18222 52 PDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKV-HGKRYAYRFDFQGLML 105 (130)
Q Consensus 52 ~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv-~g~rl~Y~F~~~~~~~ 105 (130)
..+||++-|.. .+.||+|-+.|++..+ ........|..+.+..
T Consensus 3 ~~eva~~~gvs-----------~~tlr~~~~~gli~~~~~~~~g~r~y~~~dl~~ 46 (70)
T smart00422 3 IGEVAKLAGVS-----------VRTLRYYERIGLLPPPIRTEGGYRLYSDEDLER 46 (70)
T ss_pred HHHHHHHHCcC-----------HHHHHHHHHCCCCCCCccCCCCCEecCHHHHHH
Confidence 34566666543 1467999999998765 3333445676665543
No 39
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=27.00 E-value=29 Score=25.51 Aligned_cols=41 Identities=24% Similarity=0.348 Sum_probs=24.8
Q ss_pred HHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCceeeEEEe-cccchh
Q psy18222 53 DEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYRF-DFQGLM 104 (130)
Q Consensus 53 ~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~rl~Y~F-~~~~~~ 104 (130)
.+||++-|.. .++||||-+.|+|.++.....-||+ +.+.+.
T Consensus 5 ~e~a~~~gvs-----------~~tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~ 46 (140)
T PRK09514 5 GELAKLAEVT-----------PDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQ 46 (140)
T ss_pred HHHHHHHCcC-----------HHHHHHHHHCCCCCCcccCCCCCeeeCHHHHH
Confidence 4566666554 2678999999999875322233443 444443
No 40
>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=26.85 E-value=32 Score=23.82 Aligned_cols=42 Identities=19% Similarity=0.252 Sum_probs=27.9
Q ss_pred hHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCceeeEEEecccchh
Q psy18222 52 PDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYRFDFQGLM 104 (130)
Q Consensus 52 ~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~~ 104 (130)
..+||++.|... ++||+|-+.|++.+.........|+.+.+.
T Consensus 4 i~eva~~~gvs~-----------~tlR~ye~~Gll~~~r~~~g~R~Y~~~~l~ 45 (102)
T cd04789 4 ISELAEKAGISR-----------STLLYYEKLGLITGTRNANGYRLYPDSDLQ 45 (102)
T ss_pred HHHHHHHHCcCH-----------HHHHHHHHCCCCCCCcCCCCCeeCCHHHHH
Confidence 456777777653 678999999999875544444445555544
No 41
>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=26.45 E-value=37 Score=23.89 Aligned_cols=29 Identities=21% Similarity=0.411 Sum_probs=18.5
Q ss_pred HHHHHhhhcccEEecCceeeEEEecccch
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYRFDFQGL 103 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~ 103 (130)
++||||=+.|++.+.........|+.+.+
T Consensus 15 ~tlR~Ye~~GLl~p~r~~~g~R~Y~~~~~ 43 (112)
T cd01282 15 RSLRYYEEQGLLVPERSANGYRDYDEAAV 43 (112)
T ss_pred HHHHHHHHCCCCCCCcCCCCCeecCHHHH
Confidence 57899999999987544333333444443
No 42
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=26.33 E-value=88 Score=21.69 Aligned_cols=37 Identities=16% Similarity=0.328 Sum_probs=27.9
Q ss_pred cCCCCCcHHHHHHHHHHhhhcccEEecCce--eeEEEec
Q psy18222 63 KSKPNMNYDKLSRALRYYYDKNIMTKVHGK--RYAYRFD 99 (130)
Q Consensus 63 Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~--rl~Y~F~ 99 (130)
+..+.++-.++=|+|...-+.|++.++... ...|.+.
T Consensus 35 ~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~ 73 (120)
T PF01475_consen 35 KKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYELS 73 (120)
T ss_dssp HTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEES
T ss_pred hccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEeec
Confidence 446788999999999999999999999743 4555553
No 43
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=26.19 E-value=1.2e+02 Score=22.38 Aligned_cols=76 Identities=18% Similarity=0.203 Sum_probs=47.3
Q ss_pred ceehHHHHHHhhCCCCCCCCeeEecCCCeEEE-eChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCceeeEE
Q psy18222 18 QVQLWQFLLELLGEPSNGGVIVWEGSQGEFRL-VDPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAY 96 (130)
Q Consensus 18 ~~~LW~FLl~LL~d~~~~~~I~Wt~~~~eFri-~d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~rl~Y 96 (130)
+.+|-.||++|.+..... .+.+..+.+ +..+++|.+=| ++-+.+||.|+..-++|++.. .++ ...
T Consensus 122 ~~Rla~~Ll~l~~~~~~~-----~~~~~~~~~~~t~~~iA~~lG-------~tretvsR~l~~l~~~g~I~~-~~~-~i~ 187 (202)
T PRK13918 122 KNRIAAALLELSDTPLAT-----QEDSGETMIYATHDELAAAVG-------SVRETVTKVIGELSREGYIRS-GYG-KIQ 187 (202)
T ss_pred HHHHHHHHHHHHHHhCCC-----CCCCCeEEecCCHHHHHHHhC-------ccHHHHHHHHHHHHHCCCEEc-CCC-EEE
Confidence 346777777765532110 011233433 35678888776 577999999999999999984 432 344
Q ss_pred Eecccchhhhh
Q psy18222 97 RFDFQGLMLAC 107 (130)
Q Consensus 97 ~F~~~~~~~~~ 107 (130)
=.+.+.|...+
T Consensus 188 I~d~~~L~~~~ 198 (202)
T PRK13918 188 LLDLKGLEELA 198 (202)
T ss_pred EECHHHHHHHH
Confidence 44666666544
No 44
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=25.96 E-value=99 Score=23.84 Aligned_cols=47 Identities=19% Similarity=0.236 Sum_probs=33.1
Q ss_pred ChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCceeeEEEecccchhh
Q psy18222 51 DPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYRFDFQGLML 105 (130)
Q Consensus 51 d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~~~ 105 (130)
..+++|.+=| ++-+++||.|+..-++|+|....+++. .=-|.+.+..
T Consensus 181 t~~~IA~~lG-------isretlsR~L~~L~~~GlI~~~~~~~i-~I~D~~~L~~ 227 (230)
T PRK09391 181 SRRDIADYLG-------LTIETVSRALSQLQDRGLIGLSGARQI-ELRNRQALRN 227 (230)
T ss_pred CHHHHHHHHC-------CCHHHHHHHHHHHHHCCcEEecCCceE-EEcCHHHHHH
Confidence 4578887766 578999999999999999976653333 2235555543
No 45
>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=25.82 E-value=33 Score=24.82 Aligned_cols=16 Identities=19% Similarity=0.509 Sum_probs=13.5
Q ss_pred HHHHHhhhcccEEecC
Q psy18222 75 RALRYYYDKNIMTKVH 90 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~ 90 (130)
++||||-+.|++.+..
T Consensus 16 ~tlR~Ye~~GLl~p~~ 31 (131)
T TIGR02043 16 DTLRFYEKNGLIKPAG 31 (131)
T ss_pred HHHHHHHHCCCCCCCC
Confidence 6789999999998753
No 46
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=24.49 E-value=1.4e+02 Score=16.68 Aligned_cols=33 Identities=24% Similarity=0.457 Sum_probs=25.5
Q ss_pred hHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCc
Q psy18222 52 PDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHG 91 (130)
Q Consensus 52 ~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g 91 (130)
..++|+.=|. +-..++|.|+..-+.|++.+..|
T Consensus 11 ~~~la~~l~~-------s~~tv~~~l~~L~~~g~l~~~~~ 43 (48)
T smart00419 11 RQEIAELLGL-------TRETVSRTLKRLEKEGLISREGG 43 (48)
T ss_pred HHHHHHHHCC-------CHHHHHHHHHHHHHCCCEEEeCC
Confidence 4556665554 56789999999999999998764
No 47
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=24.43 E-value=1e+02 Score=22.42 Aligned_cols=35 Identities=17% Similarity=0.202 Sum_probs=29.0
Q ss_pred ChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCce
Q psy18222 51 DPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGK 92 (130)
Q Consensus 51 d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~ 92 (130)
..+++|.+=| ++.+.++|.|+..-++|+|....|+
T Consensus 145 t~~~iA~~lG-------~tretvsR~l~~l~~~g~I~~~~~~ 179 (193)
T TIGR03697 145 SHQAIAEAIG-------STRVTITRLLGDLRKKKLISIHKKK 179 (193)
T ss_pred CHHHHHHHhC-------CcHHHHHHHHHHHHHCCCEEecCCE
Confidence 4577887766 5789999999999999999887653
No 48
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=24.35 E-value=1.5e+02 Score=16.92 Aligned_cols=33 Identities=18% Similarity=0.317 Sum_probs=25.0
Q ss_pred CcHHHHHHHHHHhhhcccEEecC-ceeeEEEecc
Q psy18222 68 MNYDKLSRALRYYYDKNIMTKVH-GKRYAYRFDF 100 (130)
Q Consensus 68 M~YeklsRsLR~yY~kgIl~Kv~-g~rl~Y~F~~ 100 (130)
++--.+++.|+...++|++.... ++...|.+..
T Consensus 22 is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~ 55 (66)
T smart00418 22 LSQSTVSHHLKKLREAGLVESRREGKRVYYSLTD 55 (66)
T ss_pred CCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEch
Confidence 55678999999999999999876 5455565543
No 49
>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=24.28 E-value=30 Score=23.67 Aligned_cols=16 Identities=13% Similarity=0.092 Sum_probs=13.5
Q ss_pred HHHHHhhhcccEEecC
Q psy18222 75 RALRYYYDKNIMTKVH 90 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~ 90 (130)
++||||-+.|++.+..
T Consensus 15 ~tlR~ye~~Gll~p~~ 30 (97)
T cd04782 15 QTLFHYDKIGLFKPEI 30 (97)
T ss_pred HHHHHHHHCCCCCCCc
Confidence 6789999999997753
No 50
>cd01460 vWA_midasin VWA_Midasin: Midasin is a member of the AAA ATPase family. The proteins of this family are unified by their common archetectural organization that is based upon a conserved ATPase domain. The AAA domain of midasin contains six tandem AAA protomers. The AAA domains in midasin is followed by a D/E rich domain that is following by a VWA domain. The members of this subgroup have a conserved MIDAS motif. The function of this domain is not exactly known although it has been speculated to play a crucial role in midasin function.
Probab=24.14 E-value=52 Score=27.13 Aligned_cols=64 Identities=9% Similarity=0.221 Sum_probs=47.6
Q ss_pred EeChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcc--cEEecCceeeEEEe--cccchhhhhccCCC
Q psy18222 49 LVDPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKN--IMTKVHGKRYAYRF--DFQGLMLACQASNT 112 (130)
Q Consensus 49 i~d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kg--Il~Kv~g~rl~Y~F--~~~~~~~~~~~~~~ 112 (130)
|..|..-.+++|.++-.+..|..|+---+-.-|+++ -|+.+...+-.|+. ..|.+.||...+-.
T Consensus 12 ilept~~~~~~gdy~tgkrln~kkii~yias~~~~dkIwlRRtkpskr~~qIvlaID~S~SM~~~~~~ 79 (266)
T cd01460 12 ILEPTLATKLKGDYRTGKRLNMKKIIPYIASQFRKDKIWLRRTKPAKRDYQILIAIDDSKSMSENNSK 79 (266)
T ss_pred HhCchhhhhccCCCCcccccchhhhhhhhhccccCCceEEEeccCCccCceEEEEEecchhccccccc
Confidence 456788889999999888888888877777777766 67777655555554 77888888766554
No 51
>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=24.01 E-value=31 Score=24.28 Aligned_cols=24 Identities=21% Similarity=0.505 Sum_probs=16.6
Q ss_pred HHHHHhhhcccEEecCceeeEEEe
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYRF 98 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~F 98 (130)
++||||=+.|++.++.-....||+
T Consensus 15 ~tLRyYe~~GLl~p~~r~~~gyR~ 38 (123)
T cd04770 15 DTIRYYERIGLLPPPQRSENGYRL 38 (123)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCcc
Confidence 678999999999865322345554
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=23.84 E-value=50 Score=22.79 Aligned_cols=29 Identities=21% Similarity=0.432 Sum_probs=18.4
Q ss_pred HHHHHhhhcccEEecCceeeEEE-ecccchh
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYR-FDFQGLM 104 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~-F~~~~~~ 104 (130)
++||+|=+.|++.+..... -|+ |+.+++.
T Consensus 16 ~tLR~ye~~Gll~~~r~~~-g~R~Y~~~dl~ 45 (102)
T cd04775 16 STLLYYESIGLIPSARSEA-NYRLYSEADLS 45 (102)
T ss_pred HHHHHHHHCCCCCCCCCCC-CCeeeCHHHHH
Confidence 5689999999995443333 443 5555544
No 53
>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=23.76 E-value=52 Score=22.62 Aligned_cols=41 Identities=29% Similarity=0.488 Sum_probs=26.0
Q ss_pred HHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCceeeEEEecccchh
Q psy18222 53 DEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYRFDFQGLM 104 (130)
Q Consensus 53 ~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~~ 104 (130)
.+||++-|.. .+.||+|-+.|++.++........|+.+++.
T Consensus 4 ~e~a~~~gvs-----------~~tLR~ye~~Gll~p~r~~~g~R~Y~~~dv~ 44 (96)
T cd04774 4 DEVAKRLGLT-----------KRTLKYYEEIGLVSPERSEGRYRLYSEEDLK 44 (96)
T ss_pred HHHHHHHCcC-----------HHHHHHHHHCCCCCCCcCCCCCEEECHHHHH
Confidence 4566666543 3568999999999865543344456554444
No 54
>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=22.95 E-value=49 Score=22.76 Aligned_cols=31 Identities=6% Similarity=0.202 Sum_probs=20.7
Q ss_pred HHHHHhhhcccEEecCc-eeeEEEecccchhh
Q psy18222 75 RALRYYYDKNIMTKVHG-KRYAYRFDFQGLML 105 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g-~rl~Y~F~~~~~~~ 105 (130)
+.||+|-+.|++.+... ....+.|+.+.+..
T Consensus 15 ~tlR~Ye~~GLl~p~~r~~~g~r~Y~~~dv~~ 46 (95)
T cd04780 15 ATIKYYLREGLLPEGRRLAPNQAEYSEAHVER 46 (95)
T ss_pred HHHHHHHHCCCCCCCcCCCCCCeecCHHHHHH
Confidence 57899999999988532 22334576665543
No 55
>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=22.60 E-value=1.6e+02 Score=19.96 Aligned_cols=34 Identities=12% Similarity=0.332 Sum_probs=27.3
Q ss_pred CCCCcHHHHHHHHHHhhhcccEEecCc--eeeEEEe
Q psy18222 65 KPNMNYDKLSRALRYYYDKNIMTKVHG--KRYAYRF 98 (130)
Q Consensus 65 k~~M~YeklsRsLR~yY~kgIl~Kv~g--~rl~Y~F 98 (130)
.+.++--++-|.|...-+.|++.++.. ....|..
T Consensus 30 ~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~ 65 (116)
T cd07153 30 GPSISLATVYRTLELLEEAGLVREIELGDGKARYEL 65 (116)
T ss_pred CCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEe
Confidence 478899999999999999999999863 2345544
No 56
>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=21.35 E-value=58 Score=22.39 Aligned_cols=30 Identities=17% Similarity=0.247 Sum_probs=19.3
Q ss_pred HHHHHhhhcccEEecCceeeEEEecccchh
Q psy18222 75 RALRYYYDKNIMTKVHGKRYAYRFDFQGLM 104 (130)
Q Consensus 75 RsLR~yY~kgIl~Kv~g~rl~Y~F~~~~~~ 104 (130)
+.||+|-+.|++.++........|+.+.+.
T Consensus 16 ~tLR~ye~~Gli~p~r~~~g~R~Ys~~dv~ 45 (98)
T cd01279 16 QTLRVYDRLGLVSPARTNGGGRRYSNNDLE 45 (98)
T ss_pred HHHHHHHHCCCCCCCcCCCCCeeECHHHHH
Confidence 568999999999875433333446555544
No 57
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=20.40 E-value=1.9e+02 Score=16.64 Aligned_cols=35 Identities=17% Similarity=0.297 Sum_probs=28.6
Q ss_pred ChHHHHHHhhcccCCCCCcHHHHHHHHHHhhhcccEEecCce
Q psy18222 51 DPDEVARRWGLRKSKPNMNYDKLSRALRYYYDKNIMTKVHGK 92 (130)
Q Consensus 51 d~~~vArlWG~~Knk~~M~YeklsRsLR~yY~kgIl~Kv~g~ 92 (130)
+..++|+..|. +-..+.++|+.--+.|++..++|.
T Consensus 22 s~~~la~~~~v-------s~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 22 SERELAAQLGV-------SRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CHHHHHHHHCC-------CHHHHHHHHHHHHHCCCEEEecCC
Confidence 66788888854 457888999999999999998875
No 58
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=20.03 E-value=1.4e+02 Score=19.98 Aligned_cols=42 Identities=19% Similarity=0.328 Sum_probs=30.9
Q ss_pred eehHHHHHHhhCCCCCCCCeeEecC-CCeEEEeChHHHHHHhhccc
Q psy18222 19 VQLWQFLLELLGEPSNGGVIVWEGS-QGEFRLVDPDEVARRWGLRK 63 (130)
Q Consensus 19 ~~LW~FLl~LL~d~~~~~~I~Wt~~-~~eFri~d~~~vArlWG~~K 63 (130)
.-|+-+|++.+.-+-+.+ |+|. +..|-+-.-++++++-|..+
T Consensus 24 k~lY~ll~dR~~lS~kn~---wiDe~G~vYi~~s~eel~~~L~~s~ 66 (76)
T PF06970_consen 24 KILYSLLLDRLRLSLKNG---WIDENGNVYIIFSIEELMELLNCSK 66 (76)
T ss_pred HHHHHHHHHHHHhhhhcC---cCCCCCCEEEEeeHHHHHHHHCCCH
Confidence 456777777766554443 9995 56999989999999988755
Done!