Query psy8490
Match_columns 228
No_of_seqs 165 out of 379
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 20:13:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8490.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8490hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3806|consensus 100.0 1.5E-31 3.2E-36 228.4 8.0 81 124-207 61-142 (177)
2 smart00413 ETS erythroblast tr 100.0 2E-31 4.4E-36 205.5 4.5 73 131-206 1-74 (87)
3 PF00178 Ets: Ets-domain; Int 99.9 5.4E-29 1.2E-33 190.5 2.5 64 131-194 1-65 (85)
4 KOG3805|consensus 99.9 7.9E-24 1.7E-28 194.3 7.0 68 128-195 269-338 (361)
5 KOG3804|consensus 99.8 2.2E-20 4.8E-25 175.7 4.3 71 133-206 295-367 (390)
6 KOG3804|consensus 99.7 2.9E-18 6.3E-23 161.5 1.6 98 131-228 171-355 (390)
7 KOG3806|consensus 99.4 4.8E-14 1E-18 121.1 1.0 34 195-228 96-129 (177)
8 smart00413 ETS erythroblast tr 99.4 6.6E-14 1.4E-18 108.4 0.9 35 194-228 28-62 (87)
9 PF00178 Ets: Ets-domain; Int 99.2 6.7E-12 1.4E-16 96.4 0.6 35 194-228 28-62 (85)
10 KOG3805|consensus 99.1 1.6E-11 3.4E-16 113.7 0.7 43 186-228 289-334 (361)
11 PF00447 HSF_DNA-bind: HSF-typ 95.6 0.019 4.1E-07 44.4 4.1 56 137-193 5-60 (103)
12 smart00415 HSF heat shock fact 95.1 0.068 1.5E-06 41.8 5.9 56 137-193 8-63 (105)
13 COG5169 HSF1 Heat shock transc 88.2 0.44 9.5E-06 44.2 3.1 50 138-192 17-70 (282)
14 KOG0627|consensus 73.8 3.3 7.1E-05 37.6 3.2 38 138-175 19-56 (304)
15 PF00605 IRF: Interferon regul 51.5 25 0.00054 28.3 4.0 46 132-178 2-60 (109)
16 smart00348 IRF interferon regu 35.9 50 0.0011 26.5 3.5 44 134-178 2-58 (107)
17 cd00103 IRF Interferon Regulat 28.4 73 0.0016 25.5 3.3 46 132-178 2-59 (107)
No 1
>KOG3806|consensus
Probab=99.97 E-value=1.5e-31 Score=228.35 Aligned_cols=81 Identities=62% Similarity=1.016 Sum_probs=72.5
Q ss_pred CCCCCCCcchhHHHHHHhhCCCCCCCceeeecC-CceEEEcChHHHHHHHhhhcCCCCchHHHHHhhhhcccchhhhhhH
Q psy8490 124 PCFTGSGPIQLWQFLLELLTDKTCQAFISWTGD-GWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRRKTGYEKASRF 202 (228)
Q Consensus 124 ~~~~~sG~i~LWqFLl~LL~d~~~~~~I~Wtg~-~geFrlvdpe~VArlWG~~Knk~~MtYeKmSRaLRyYYG~~K~~~p 202 (228)
...+++|++||||||++||+|+++++||.||++ ++||+++||++|||+||++||||+|||||||||||||| .|. .+
T Consensus 61 ~s~~~sg~iqLwqFLleLl~d~~~~~~I~Wtg~~g~EFkl~dp~eVArlWG~rK~kp~MNYdKLSRaLRyyY--~kn-i~ 137 (177)
T KOG3806|consen 61 ESTSGSGQIQLWQFLLELLQDESNAHIIAWTGKDGLEFKLVDPDEVARLWGARKNKPNMNYDKLSRALRYYY--DKN-IL 137 (177)
T ss_pred ccCCCCchhhHHHHHHHHHhCcccCCeeEEeCCCCceEEecCHHHHHHHHhhhhCCCCCCHHHHHHHHHHHH--hcC-ce
Confidence 444788899999999999999999999999996 66999999999999999999999999999999999996 454 46
Q ss_pred HHHHH
Q psy8490 203 EKVAR 207 (228)
Q Consensus 203 EkVAR 207 (228)
+||..
T Consensus 138 ~Kv~G 142 (177)
T KOG3806|consen 138 KKVPG 142 (177)
T ss_pred eecCC
Confidence 66653
No 2
>smart00413 ETS erythroblast transformation specific domain. variation of the helix-turn-helix motif
Probab=99.97 E-value=2e-31 Score=205.48 Aligned_cols=73 Identities=62% Similarity=0.963 Sum_probs=66.1
Q ss_pred cchhHHHHHHhhCCCCCCCceeeecC-CceEEEcChHHHHHHHhhhcCCCCchHHHHHhhhhcccchhhhhhHHHHH
Q psy8490 131 PIQLWQFLLELLTDKTCQAFISWTGD-GWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRRKTGYEKASRFEKVA 206 (228)
Q Consensus 131 ~i~LWqFLl~LL~d~~~~~~I~Wtg~-~geFrlvdpe~VArlWG~~Knk~~MtYeKmSRaLRyYYG~~K~~~pEkVA 206 (228)
+++||+||++||.|+++++||+|||+ +|||+|+||++||++||.+||+++|||||||||||||| +...++||.
T Consensus 1 ~~~Lw~FL~~LL~d~~~~~~I~W~~k~~g~Fkl~~~~~vA~lWG~~Knk~~M~YeklSRaLRyyy---~~~il~Kv~ 74 (87)
T smart00413 1 QIQLWQFLLDLLLDPENGDIIRWTDRDGGEFKLVDPEEVARLWGQRKNKPNMNYEKLSRALRYYY---KKNILRKVP 74 (87)
T ss_pred CccHHHHHHHHHcCccCCCeEEeeCCCCCEEEecCHHHHHHHHhhhcCCCCCCHHHHHHHHHHHH---hcCcEEecC
Confidence 47999999999999999999999996 89999999999999999999999999999999999997 334455553
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=99.95 E-value=5.4e-29 Score=190.53 Aligned_cols=64 Identities=63% Similarity=1.059 Sum_probs=60.4
Q ss_pred cchhHHHHHHhhCCCCCCCceeeec-CCceEEEcChHHHHHHHhhhcCCCCchHHHHHhhhhccc
Q psy8490 131 PIQLWQFLLELLTDKTCQAFISWTG-DGWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRRKT 194 (228)
Q Consensus 131 ~i~LWqFLl~LL~d~~~~~~I~Wtg-~~geFrlvdpe~VArlWG~~Knk~~MtYeKmSRaLRyYY 194 (228)
+++||+||++||.|++++++|+||| +++||+|+||++||++||.+||+++||||||||+||+||
T Consensus 1 ~~~Lw~FLl~LL~d~~~~~~I~Wt~~~~~eFki~d~~~vA~lWG~~k~~~~m~yeklsR~LR~yy 65 (85)
T PF00178_consen 1 QIQLWQFLLELLEDPSNSDIIAWTGKRGGEFKIVDPEAVARLWGKHKNRPNMNYEKLSRALRYYY 65 (85)
T ss_dssp S-SHHHHHHHHHHSGGGTTTEEEEETSTTEEEESSHHHHHHHHHHHTTSTT-SHHHHHHHHHHHH
T ss_pred CccHHHHHHHHhcCccCCCeeEeeccCCCeEEecCHHHHHHHHHHHcCCccccHHHHHHHHHHHh
Confidence 5799999999999999999999999 689999999999999999999999999999999999997
No 4
>KOG3805|consensus
Probab=99.89 E-value=7.9e-24 Score=194.27 Aligned_cols=68 Identities=46% Similarity=0.782 Sum_probs=64.1
Q ss_pred CCCcchhHHHHHHhhCCCC-CCCceeeecC-CceEEEcChHHHHHHHhhhcCCCCchHHHHHhhhhcccc
Q psy8490 128 GSGPIQLWQFLLELLTDKT-CQAFISWTGD-GWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRRKTG 195 (228)
Q Consensus 128 ~sG~i~LWqFLl~LL~d~~-~~~~I~Wtg~-~geFrlvdpe~VArlWG~~Knk~~MtYeKmSRaLRyYYG 195 (228)
++.+|+|||||++||..+. +..||+|+|+ .|+|+|.+.+.||++||+||||+.||||||||+||.||+
T Consensus 269 ~kk~IhLwQFLkELL~sP~~~~~~IrWVDkdKGiFkiess~~lArlWG~RKNR~~MnYdKlsRslRqYyK 338 (361)
T KOG3805|consen 269 GKKKIHLWQFLKELLYSPEQMGSCIRWVDKDKGIFKIESSEKLARLWGIRKNRKAMNYDKLSRSLRQYYK 338 (361)
T ss_pred CcceeeHHHHHHHHHhChhhhchheEeeccCCceEEeecHHHHHHHhhhhcccccccHHHHHHHHHHHhh
Confidence 3459999999999999986 9999999997 799999999999999999999999999999999999983
No 5
>KOG3804|consensus
Probab=99.80 E-value=2.2e-20 Score=175.72 Aligned_cols=71 Identities=41% Similarity=0.743 Sum_probs=62.9
Q ss_pred hhHHHHHHhhCCCCC-CCceeeecC-CceEEEcChHHHHHHHhhhcCCCCchHHHHHhhhhcccchhhhhhHHHHH
Q psy8490 133 QLWQFLLELLTDKTC-QAFISWTGD-GWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRRKTGYEKASRFEKVA 206 (228)
Q Consensus 133 ~LWqFLl~LL~d~~~-~~~I~Wtg~-~geFrlvdpe~VArlWG~~Knk~~MtYeKmSRaLRyYYG~~K~~~pEkVA 206 (228)
.||+||+.||.|+++ ..+|+|+++ .|+|||||+++|||+||.+||+.+|||||||||||||| |....++|-
T Consensus 295 ~LWefl~~lL~d~~~~p~~IkWedr~~GVFrvVds~a~arlWG~~Kn~~~MtYekmsRAlRyYY---k~~IL~kv~ 367 (390)
T KOG3804|consen 295 GLWEFLRQLLLDPNYNPGFIKWEDREKGVFRVVDSEALARLWGMHKNNSSMTYEKMSRALRYYY---KREILRKVD 367 (390)
T ss_pred hHHHHHHHHhcCCCcCCccccccccCCCeeEEecccHHHHHhcCcCCCCCcCHHHHhHHhhhhh---hcceeecCC
Confidence 899999999999865 559999997 79999999999999999999999999999999999998 444444443
No 6
>KOG3804|consensus
Probab=99.70 E-value=2.9e-18 Score=161.52 Aligned_cols=98 Identities=46% Similarity=0.795 Sum_probs=90.9
Q ss_pred cchhHHHHHHhhCCC-CCCCceeeecC-CceEEEcChHHHHHHHhhhcCCCCchHHHHHhhhhcccc-------------
Q psy8490 131 PIQLWQFLLELLTDK-TCQAFISWTGD-GWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRRKTG------------- 195 (228)
Q Consensus 131 ~i~LWqFLl~LL~d~-~~~~~I~Wtg~-~geFrlvdpe~VArlWG~~Knk~~MtYeKmSRaLRyYYG------------- 195 (228)
...+|+|++.++.|. .+...|.|+.. .+.|+.+|...+..+||+++|++.|+|+.|+|++||||-
T Consensus 171 tp~~~~~l~~~~q~~~~~p~~~~~~~~~~~~~~~~~s~~~s~~~~a~sn~~~m~~~~m~~a~~~~~q~~il~~~~~~~~~ 250 (390)
T KOG3804|consen 171 TPYLWEFLLDLLQDSATCPKPIKWTQREKGCFKLVDSKAVSKLWGAHSNKPDMNYETMGRALRYYPQRGILAKVEGVLQR 250 (390)
T ss_pred CcchHHHHhhhhhcccCCCcccccccccccccccccCccccccchhhccCccccccccccccccccCCccccccchhhhh
Confidence 569999999999986 79999999995 799999999999999999999999999999999988753
Q ss_pred ------------------------------------------------------------------------hhhhhhHH
Q psy8490 196 ------------------------------------------------------------------------YEKASRFE 203 (228)
Q Consensus 196 ------------------------------------------------------------------------~~K~~~pE 203 (228)
+||+++++
T Consensus 251 ~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~LWefl~~lL~d~~~~p~~IkWedr~~GVFrvVds~ 330 (390)
T KOG3804|consen 251 SCHQNKGSQQQPQVQDKRGRPSSALPVPPPLDTVKKSGRPLSGTGLWEFLRQLLLDPNYNPGFIKWEDREKGVFRVVDSE 330 (390)
T ss_pred hcccCCCccccccccccccCcCccccCCCccccccccCCCcccchHHHHHHHHhcCCCcCCccccccccCCCeeEEeccc
Confidence 36679999
Q ss_pred HHHHHhhhhcCCCCCchhhhhcccC
Q psy8490 204 KVARRWGIRKNKPKMNYEKLSRGLR 228 (228)
Q Consensus 204 kVAR~WGi~Kn~p~m~ydK~sralr 228 (228)
.|||+||++||+++|||||||||||
T Consensus 331 a~arlWG~~Kn~~~MtYekmsRAlR 355 (390)
T KOG3804|consen 331 ALARLWGMHKNNSSMTYEKMSRALR 355 (390)
T ss_pred HHHHHhcCcCCCCCcCHHHHhHHhh
Confidence 9999999999999999999999997
No 7
>KOG3806|consensus
Probab=99.40 E-value=4.8e-14 Score=121.11 Aligned_cols=34 Identities=59% Similarity=0.816 Sum_probs=32.8
Q ss_pred chhhhhhHHHHHHHhhhhcCCCCCchhhhhcccC
Q psy8490 195 GYEKASRFEKVARRWGIRKNKPKMNYEKLSRGLR 228 (228)
Q Consensus 195 G~~K~~~pEkVAR~WGi~Kn~p~m~ydK~sralr 228 (228)
++||+++||+|||+||++||+|+|||||||||||
T Consensus 96 ~EFkl~dp~eVArlWG~rK~kp~MNYdKLSRaLR 129 (177)
T KOG3806|consen 96 LEFKLVDPDEVARLWGARKNKPNMNYDKLSRALR 129 (177)
T ss_pred ceEEecCHHHHHHHHhhhhCCCCCCHHHHHHHHH
Confidence 3899999999999999999999999999999997
No 8
>smart00413 ETS erythroblast transformation specific domain. variation of the helix-turn-helix motif
Probab=99.39 E-value=6.6e-14 Score=108.44 Aligned_cols=35 Identities=66% Similarity=0.894 Sum_probs=33.6
Q ss_pred cchhhhhhHHHHHHHhhhhcCCCCCchhhhhcccC
Q psy8490 194 TGYEKASRFEKVARRWGIRKNKPKMNYEKLSRGLR 228 (228)
Q Consensus 194 YG~~K~~~pEkVAR~WGi~Kn~p~m~ydK~sralr 228 (228)
-|+||++++|+||++||.+||+|+|||||||||||
T Consensus 28 ~g~Fkl~~~~~vA~lWG~~Knk~~M~YeklSRaLR 62 (87)
T smart00413 28 GGEFKLVDPEEVARLWGQRKNKPNMNYEKLSRALR 62 (87)
T ss_pred CCEEEecCHHHHHHHHhhhcCCCCCCHHHHHHHHH
Confidence 47899999999999999999999999999999997
No 9
>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=99.15 E-value=6.7e-12 Score=96.36 Aligned_cols=35 Identities=60% Similarity=0.837 Sum_probs=32.3
Q ss_pred cchhhhhhHHHHHHHhhhhcCCCCCchhhhhcccC
Q psy8490 194 TGYEKASRFEKVARRWGIRKNKPKMNYEKLSRGLR 228 (228)
Q Consensus 194 YG~~K~~~pEkVAR~WGi~Kn~p~m~ydK~sralr 228 (228)
.|+||++++++||++||++||+++|||||||||||
T Consensus 28 ~~eFki~d~~~vA~lWG~~k~~~~m~yeklsR~LR 62 (85)
T PF00178_consen 28 GGEFKIVDPEAVARLWGKHKNRPNMNYEKLSRALR 62 (85)
T ss_dssp TTEEEESSHHHHHHHHHHHTTSTT-SHHHHHHHHH
T ss_pred CCeEEecCHHHHHHHHHHHcCCccccHHHHHHHHH
Confidence 46899999999999999999999999999999997
No 10
>KOG3805|consensus
Probab=99.10 E-value=1.6e-11 Score=113.72 Aligned_cols=43 Identities=51% Similarity=0.795 Sum_probs=37.3
Q ss_pred HHhhhhc---ccchhhhhhHHHHHHHhhhhcCCCCCchhhhhcccC
Q psy8490 186 LSRGLRR---KTGYEKASRFEKVARRWGIRKNKPKMNYEKLSRGLR 228 (228)
Q Consensus 186 mSRaLRy---YYG~~K~~~pEkVAR~WGi~Kn~p~m~ydK~sralr 228 (228)
|++++|- =-|.||+++.++|||+|||+|||++|||||||||||
T Consensus 289 ~~~~IrWVDkdKGiFkiess~~lArlWG~RKNR~~MnYdKlsRslR 334 (361)
T KOG3805|consen 289 MGSCIRWVDKDKGIFKIESSEKLARLWGIRKNRKAMNYDKLSRSLR 334 (361)
T ss_pred hchheEeeccCCceEEeecHHHHHHHhhhhcccccccHHHHHHHHH
Confidence 4444443 368999999999999999999999999999999997
No 11
>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=95.56 E-value=0.019 Score=44.35 Aligned_cols=56 Identities=27% Similarity=0.408 Sum_probs=40.2
Q ss_pred HHHHhhCCCCCCCceeeecCCceEEEcChHHHHHHHhhhcCCCCchHHHHHhhhhcc
Q psy8490 137 FLLELLTDKTCQAFISWTGDGWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRRK 193 (228)
Q Consensus 137 FLl~LL~d~~~~~~I~Wtg~~geFrlvdpe~VArlWG~~Knk~~MtYeKmSRaLRyY 193 (228)
=|.++|+|+.+.++|+|.+++..|.|.|++++++.-=.+-= ..-+|..+.|-|-.|
T Consensus 5 kL~~~l~~~~~~~~I~W~~~G~~fiI~d~~~f~~~vLp~~F-~~~~~~SF~RQLn~y 60 (103)
T PF00447_consen 5 KLYEMLEDPENSDIIRWSPDGDSFIIHDPEEFEKEVLPKYF-KHSNFSSFVRQLNMY 60 (103)
T ss_dssp HHHHHHCTTTTTTTCEECTTSSEEEES-HHHHHHHTHHHHS-ST--HHHHHHHHHHT
T ss_pred HHHHHHcCCCCCCEEEEeCCCCEEEEeecHHHhhhcccccc-CccccceeeeEeeee
Confidence 35688899999999999999999999999888762211110 112688888888887
No 12
>smart00415 HSF heat shock factor.
Probab=95.06 E-value=0.068 Score=41.75 Aligned_cols=56 Identities=29% Similarity=0.399 Sum_probs=42.0
Q ss_pred HHHHhhCCCCCCCceeeecCCceEEEcChHHHHHHHhhhcCCCCchHHHHHhhhhcc
Q psy8490 137 FLLELLTDKTCQAFISWTGDGWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLRRK 193 (228)
Q Consensus 137 FLl~LL~d~~~~~~I~Wtg~~geFrlvdpe~VArlWG~~Knk~~MtYeKmSRaLRyY 193 (228)
=|.++|+|+.+.++|+|...+..|.|.|+++..+---.+- =..-+|..+-|-|-.|
T Consensus 8 kL~~~l~~~~~~~iI~W~~~G~~f~I~d~~~f~~~vLp~~-Fk~~~~~SF~RqLn~y 63 (105)
T smart00415 8 KLYLLVEDPSTDKIISWSPSGKSFVIWDPEEFAKNLLPRY-FKHNNFSSFVRQLNMY 63 (105)
T ss_pred HHHHHHhCCCCCCEEEECCCCCEEEEcCHHHHHHHHHHHh-cCCCCHHHHHHHHHhc
Confidence 3567889999999999999999999999987765322221 1122588999998886
No 13
>COG5169 HSF1 Heat shock transcription factor [Transcription]
Probab=88.16 E-value=0.44 Score=44.21 Aligned_cols=50 Identities=28% Similarity=0.617 Sum_probs=36.7
Q ss_pred HHHhhCCCCCCCceeeecCCceEEEcChHHHHH----HHhhhcCCCCchHHHHHhhhhc
Q psy8490 138 LLELLTDKTCQAFISWTGDGWEFKLTDPDEVAR----RWGIRKNKPKMNYEKLSRGLRR 192 (228)
Q Consensus 138 Ll~LL~d~~~~~~I~Wtg~~geFrlvdpe~VAr----lWG~~Knk~~MtYeKmSRaLRy 192 (228)
|.++|+|+++.+.|+|+.++.-|-|.|+++.+. +.+.|. |+..+-|-|-.
T Consensus 17 Ly~iLe~~e~~k~I~Ws~~G~sfvI~~~~~F~~~iLpr~FKh~-----NfaSFVRQLN~ 70 (282)
T COG5169 17 LYQILEEPEYYKLIQWSPDGRSFVILDPEEFTKVILPRYFKHG-----NFASFVRQLNK 70 (282)
T ss_pred HHHHhcCcccCCceEECCCCCEEEEeCcchhhhhhhhhhhccc-----CHHHHHHHHHh
Confidence 446778999999999999999999999887664 444444 34555555544
No 14
>KOG0627|consensus
Probab=73.84 E-value=3.3 Score=37.56 Aligned_cols=38 Identities=29% Similarity=0.502 Sum_probs=33.0
Q ss_pred HHHhhCCCCCCCceeeecCCceEEEcChHHHHHHHhhh
Q psy8490 138 LLELLTDKTCQAFISWTGDGWEFKLTDPDEVARRWGIR 175 (228)
Q Consensus 138 Ll~LL~d~~~~~~I~Wtg~~geFrlvdpe~VArlWG~~ 175 (228)
++++++|+.+..+|+|...+--|-|.|++++|+.=-.+
T Consensus 19 ~y~~v~Dps~~~iisWs~~g~sFvv~d~~~F~~~~Lp~ 56 (304)
T KOG0627|consen 19 LYEMVEDPSTDEIISWSPSGNSFVIWNPEEFAKVLLPL 56 (304)
T ss_pred HHHHhcCCCCCCceEECCCCCccccCCHHHHHHHHhHH
Confidence 44677899999999999988899999999999876655
No 15
>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=51.53 E-value=25 Score=28.32 Aligned_cols=46 Identities=15% Similarity=0.540 Sum_probs=35.8
Q ss_pred chhHHHHHHhhCCCCCCCceeeecC-CceEEEc------------ChHHHHHHHhhhcCC
Q psy8490 132 IQLWQFLLELLTDKTCQAFISWTGD-GWEFKLT------------DPDEVARRWGIRKNK 178 (228)
Q Consensus 132 i~LWqFLl~LL~d~~~~~~I~Wtg~-~geFrlv------------dpe~VArlWG~~Knk 178 (228)
++|-++|.+.++...|.+. .|+|+ ...|+|- +...+-+.|..++++
T Consensus 2 ~rlr~WL~~~i~sg~ypGL-~W~d~~kt~FrIPWkH~~r~~~~~~~D~~iFkaWA~~~Gk 60 (109)
T PF00605_consen 2 LRLRPWLIEQIDSGRYPGL-EWLDEEKTIFRIPWKHAGRQDWDQEEDAKIFKAWAVHRGK 60 (109)
T ss_dssp --HHHHHHHHHHHTCSTTS-EESSTTSSEEEEETTSTTSTTSSHCGGGHHHHHHHHHTTS
T ss_pred CcHHHHHHHHHhcCCCCCc-EEEcCCCCEEEeeCccCCCCCccccchHHHHHHHHHHhcc
Confidence 5788999999999999665 79996 6899992 224778999998875
No 16
>smart00348 IRF interferon regulatory factor. interferon regulatory factor, also known as trytophan pentad repeat
Probab=35.93 E-value=50 Score=26.47 Aligned_cols=44 Identities=16% Similarity=0.465 Sum_probs=34.6
Q ss_pred hHHHHHHhhCCCCCCCceeeecC-CceEEEc-----------ChH-HHHHHHhhhcCC
Q psy8490 134 LWQFLLELLTDKTCQAFISWTGD-GWEFKLT-----------DPD-EVARRWGIRKNK 178 (228)
Q Consensus 134 LWqFLl~LL~d~~~~~~I~Wtg~-~geFrlv-----------dpe-~VArlWG~~Knk 178 (228)
|-.+|.+-++...|.+ +.|.|+ ...|+|- +.| .+-+.|..++++
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 889997 5799992 122 478888888764
No 17
>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=28.37 E-value=73 Score=25.49 Aligned_cols=46 Identities=15% Similarity=0.473 Sum_probs=36.5
Q ss_pred chhHHHHHHhhCCCCCCCceeeecC-CceEEEc-----------ChHHHHHHHhhhcCC
Q psy8490 132 IQLWQFLLELLTDKTCQAFISWTGD-GWEFKLT-----------DPDEVARRWGIRKNK 178 (228)
Q Consensus 132 i~LWqFLl~LL~d~~~~~~I~Wtg~-~geFrlv-----------dpe~VArlWG~~Knk 178 (228)
++|-.+|.+-++...|.+ +.|.|+ ...|+|= +-..+-+.|..++++
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 789996 5799982 224677889888864
Done!