Query psy15186
Match_columns 151
No_of_seqs 168 out of 331
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 22:47:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15186.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15186hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00413 ETS erythroblast tr 100.0 1.3E-39 2.7E-44 230.7 7.7 81 65-150 1-82 (87)
2 KOG3806|consensus 100.0 6.9E-39 1.5E-43 251.7 10.0 88 58-150 61-149 (177)
3 PF00178 Ets: Ets-domain; Int 100.0 3.4E-37 7.4E-42 218.0 5.6 82 65-151 1-83 (85)
4 KOG3805|consensus 100.0 5.9E-31 1.3E-35 221.5 8.3 82 65-150 272-355 (361)
5 KOG3804|consensus 99.9 7.2E-27 1.6E-31 203.1 9.9 81 65-150 293-375 (390)
6 KOG3804|consensus 98.7 5.6E-09 1.2E-13 91.6 0.9 83 65-150 171-255 (390)
7 PF00447 HSF_DNA-bind: HSF-typ 96.8 0.0017 3.7E-08 46.5 3.8 59 71-130 5-63 (103)
8 smart00415 HSF heat shock fact 96.6 0.0059 1.3E-07 44.1 5.5 59 71-130 8-66 (105)
9 COG5169 HSF1 Heat shock transc 93.3 0.065 1.4E-06 45.6 2.7 56 72-128 17-72 (282)
10 KOG0627|consensus 86.6 0.58 1.3E-05 39.3 2.8 38 72-109 19-56 (304)
11 PF00605 IRF: Interferon regul 77.1 7 0.00015 28.7 5.1 64 66-130 2-83 (109)
12 smart00348 IRF interferon regu 69.0 5.8 0.00013 29.0 3.0 44 68-112 2-58 (107)
13 cd00103 IRF Interferon Regulat 61.5 9.1 0.0002 28.0 2.8 64 66-130 2-81 (107)
14 PF14475 Mso1_Sec1_bdg: Sec1-b 40.9 22 0.00049 21.9 1.8 14 117-130 19-32 (41)
15 PF06970 RepA_N: Replication i 27.8 1.6E+02 0.0034 20.1 4.5 42 66-110 24-66 (76)
16 COG4185 Uncharacterized protei 21.1 82 0.0018 25.4 2.3 52 59-125 9-60 (187)
17 cd07355 HN_L-delphilin-R2_like 20.7 37 0.0008 23.9 0.3 16 65-80 53-68 (80)
No 1
>smart00413 ETS erythroblast transformation specific domain. variation of the helix-turn-helix motif
Probab=100.00 E-value=1.3e-39 Score=230.71 Aligned_cols=81 Identities=60% Similarity=1.022 Sum_probs=75.5
Q ss_pred cchHHHHHHHhcCCCCCCCcccccC-CCceEEecChHHHHHHhhcccCCCCCcHHHHHHHHHHHHHhhhhhccCCCCCcc
Q psy15186 65 QIQLWQFLLELLSDSTNANCITWEG-TNGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALRTHSRRLRKIFIPGLGNID 143 (151)
Q Consensus 65 ~~~Lw~FLl~LL~d~~~~~~I~W~~-~~~~Fk~~d~~~vArlWG~~k~~~~m~YdklsRaLR~yy~k~~~~~~p~~~~i~ 143 (151)
+++||+||++||.||++++||+||| .+|||+|+||++||+|||.+||+|+||||||||||||||++++...|||
T Consensus 1 ~~~Lw~FL~~LL~d~~~~~~I~W~~k~~g~Fkl~~~~~vA~lWG~~Knk~~M~YeklSRaLRyyy~~~il~Kv~g----- 75 (87)
T smart00413 1 QIQLWQFLLDLLLDPENGDIIRWTDRDGGEFKLVDPEEVARLWGQRKNKPNMNYEKLSRALRYYYKKNILRKVPG----- 75 (87)
T ss_pred CccHHHHHHHHHcCccCCCeEEeeCCCCCEEEecCHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHhcCcEEecCC-----
Confidence 3689999999999999999999999 6899999999999999999999999999999999999999976555554
Q ss_pred cceeeec
Q psy15186 144 KEIVYFF 150 (151)
Q Consensus 144 ~~l~y~f 150 (151)
||+||+|
T Consensus 76 ~rl~Y~F 82 (87)
T smart00413 76 KRLVYKF 82 (87)
T ss_pred ceEEEec
Confidence 8999999
No 2
>KOG3806|consensus
Probab=100.00 E-value=6.9e-39 Score=251.74 Aligned_cols=88 Identities=65% Similarity=1.024 Sum_probs=81.3
Q ss_pred ccCCCCCcchHHHHHHHhcCCCCCCCcccccCC-CceEEecChHHHHHHhhcccCCCCCcHHHHHHHHHHHHHhhhhhcc
Q psy15186 58 QSSTGSGQIQLWQFLLELLSDSTNANCITWEGT-NGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALRTHSRRLRKIFI 136 (151)
Q Consensus 58 ~s~~g~G~~~Lw~FLl~LL~d~~~~~~I~W~~~-~~~Fk~~d~~~vArlWG~~k~~~~m~YdklsRaLR~yy~k~~~~~~ 136 (151)
.+..++|+++|||||++||+|+++++||+|||. ++||+++||++||||||++||+|+||||||||||||||++.++-.|
T Consensus 61 ~s~~~sg~iqLwqFLleLl~d~~~~~~I~Wtg~~g~EFkl~dp~eVArlWG~rK~kp~MNYdKLSRaLRyyY~kni~~Kv 140 (177)
T KOG3806|consen 61 ESTSGSGQIQLWQFLLELLQDESNAHIIAWTGKDGLEFKLVDPDEVARLWGARKNKPNMNYDKLSRALRYYYDKNILKKV 140 (177)
T ss_pred ccCCCCchhhHHHHHHHHHhCcccCCeeEEeCCCCceEEecCHHHHHHHHhhhhCCCCCCHHHHHHHHHHHHhcCceeec
Confidence 456789999999999999999999999999995 6699999999999999999999999999999999999999866555
Q ss_pred CCCCCcccceeeec
Q psy15186 137 PGLGNIDKEIVYFF 150 (151)
Q Consensus 137 p~~~~i~~~l~y~f 150 (151)
|| +|.||+|
T Consensus 141 ~G-----kr~~YkF 149 (177)
T KOG3806|consen 141 PG-----KRFVYKF 149 (177)
T ss_pred CC-----ceEEEEE
Confidence 55 7999999
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=3.4e-37 Score=218.00 Aligned_cols=82 Identities=55% Similarity=0.965 Sum_probs=74.0
Q ss_pred cchHHHHHHHhcCCCCCCCcccccC-CCceEEecChHHHHHHhhcccCCCCCcHHHHHHHHHHHHHhhhhhccCCCCCcc
Q psy15186 65 QIQLWQFLLELLSDSTNANCITWEG-TNGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALRTHSRRLRKIFIPGLGNID 143 (151)
Q Consensus 65 ~~~Lw~FLl~LL~d~~~~~~I~W~~-~~~~Fk~~d~~~vArlWG~~k~~~~m~YdklsRaLR~yy~k~~~~~~p~~~~i~ 143 (151)
+++||+||++||+|++++++|+||| ++|||+|+||++||+|||.+||+++||||||||+||+||++++...|+|
T Consensus 1 ~~~Lw~FLl~LL~d~~~~~~I~Wt~~~~~eFki~d~~~vA~lWG~~k~~~~m~yeklsR~LR~yy~k~il~kv~g----- 75 (85)
T PF00178_consen 1 QIQLWQFLLELLEDPSNSDIIAWTGKRGGEFKIVDPEAVARLWGKHKNRPNMNYEKLSRALRYYYKKGILEKVKG----- 75 (85)
T ss_dssp S-SHHHHHHHHHHSGGGTTTEEEEETSTTEEEESSHHHHHHHHHHHTTSTT-SHHHHHHHHHHHHHTTSEEEETT-----
T ss_pred CccHHHHHHHHhcCccCCCeeEeeccCCCeEEecCHHHHHHHHHHHcCCccccHHHHHHHHHHHhhCCeEEecCC-----
Confidence 4789999999999999999999999 7899999999999999999999999999999999999999985544443
Q ss_pred cceeeecC
Q psy15186 144 KEIVYFFR 151 (151)
Q Consensus 144 ~~l~y~f~ 151 (151)
+|++|+|-
T Consensus 76 ~r~~Y~F~ 83 (85)
T PF00178_consen 76 QRLVYRFV 83 (85)
T ss_dssp STTEEEES
T ss_pred cEEEEecC
Confidence 79999993
No 4
>KOG3805|consensus
Probab=99.97 E-value=5.9e-31 Score=221.50 Aligned_cols=82 Identities=41% Similarity=0.737 Sum_probs=75.0
Q ss_pred cchHHHHHHHhcCCCC-CCCcccccC-CCceEEecChHHHHHHhhcccCCCCCcHHHHHHHHHHHHHhhhhhccCCCCCc
Q psy15186 65 QIQLWQFLLELLSDST-NANCITWEG-TNGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALRTHSRRLRKIFIPGLGNI 142 (151)
Q Consensus 65 ~~~Lw~FLl~LL~d~~-~~~~I~W~~-~~~~Fk~~d~~~vArlWG~~k~~~~m~YdklsRaLR~yy~k~~~~~~p~~~~i 142 (151)
+++|||||++||..|. ++.||+|+| .+|+|||.|++.||||||+||||+.|||||||||||.||++++. . -..+
T Consensus 272 ~IhLwQFLkELL~sP~~~~~~IrWVDkdKGiFkiess~~lArlWG~RKNR~~MnYdKlsRslRqYyKkGii-k---K~ek 347 (361)
T KOG3805|consen 272 KIHLWQFLKELLYSPEQMGSCIRWVDKDKGIFKIESSEKLARLWGIRKNRKAMNYDKLSRSLRQYYKKGII-K---KPEK 347 (361)
T ss_pred eeeHHHHHHHHHhChhhhchheEeeccCCceEEeecHHHHHHHhhhhcccccccHHHHHHHHHHHhhcCcc-c---cchh
Confidence 7999999999999998 999999999 68999999999999999999999999999999999999999742 1 1345
Q ss_pred ccceeeec
Q psy15186 143 DKEIVYFF 150 (151)
Q Consensus 143 ~~~l~y~f 150 (151)
++||||+|
T Consensus 348 kqrLvyqf 355 (361)
T KOG3805|consen 348 KQRLVYQF 355 (361)
T ss_pred hhheeeee
Confidence 69999998
No 5
>KOG3804|consensus
Probab=99.94 E-value=7.2e-27 Score=203.12 Aligned_cols=81 Identities=38% Similarity=0.715 Sum_probs=73.9
Q ss_pred cchHHHHHHHhcCCCCC-CCcccccC-CCceEEecChHHHHHHhhcccCCCCCcHHHHHHHHHHHHHhhhhhccCCCCCc
Q psy15186 65 QIQLWQFLLELLSDSTN-ANCITWEG-TNGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALRTHSRRLRKIFIPGLGNI 142 (151)
Q Consensus 65 ~~~Lw~FLl~LL~d~~~-~~~I~W~~-~~~~Fk~~d~~~vArlWG~~k~~~~m~YdklsRaLR~yy~k~~~~~~p~~~~i 142 (151)
...||+||+.||.|+++ ...|.|++ ..|+|||||+++||||||.|||+.+||||||+|||||||++.|...|||
T Consensus 293 ~t~LWefl~~lL~d~~~~p~~IkWedr~~GVFrvVds~a~arlWG~~Kn~~~MtYekmsRAlRyYYk~~IL~kv~G---- 368 (390)
T KOG3804|consen 293 GTGLWEFLRQLLLDPNYNPGFIKWEDREKGVFRVVDSEALARLWGMHKNNSSMTYEKMSRALRYYYKREILRKVDG---- 368 (390)
T ss_pred cchHHHHHHHHhcCCCcCCccccccccCCCeeEEecccHHHHHhcCcCCCCCcCHHHHhHHhhhhhhcceeecCCC----
Confidence 35799999999999885 45999999 6899999999999999999999999999999999999999976655665
Q ss_pred ccceeeec
Q psy15186 143 DKEIVYFF 150 (151)
Q Consensus 143 ~~~l~y~f 150 (151)
|||||||
T Consensus 369 -qrLvyqF 375 (390)
T KOG3804|consen 369 -QRLVYQF 375 (390)
T ss_pred -ceeeEEe
Confidence 7999999
No 6
>KOG3804|consensus
Probab=98.66 E-value=5.6e-09 Score=91.57 Aligned_cols=83 Identities=36% Similarity=0.597 Sum_probs=69.6
Q ss_pred cchHHHHHHHhcCCCC-CCCcccccC-CCceEEecChHHHHHHhhcccCCCCCcHHHHHHHHHHHHHhhhhhccCCCCCc
Q psy15186 65 QIQLWQFLLELLSDST-NANCITWEG-TNGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALRTHSRRLRKIFIPGLGNI 142 (151)
Q Consensus 65 ~~~Lw~FLl~LL~d~~-~~~~I~W~~-~~~~Fk~~d~~~vArlWG~~k~~~~m~YdklsRaLR~yy~k~~~~~~p~~~~i 142 (151)
...+|+||+.+|.|.. ....|.|+. .++.|+.+|...++.+||.++|++.|+|+.|.|++|+||.+.+. .++.+ .
T Consensus 171 tp~~~~~l~~~~q~~~~~p~~~~~~~~~~~~~~~~~s~~~s~~~~a~sn~~~m~~~~m~~a~~~~~q~~il--~~~~~-~ 247 (390)
T KOG3804|consen 171 TPYLWEFLLDLLQDSATCPKPIKWTQREKGCFKLVDSKAVSKLWGAHSNKPDMNYETMGRALRYYPQRGIL--AKVEG-V 247 (390)
T ss_pred CcchHHHHhhhhhcccCCCcccccccccccccccccCccccccchhhccCccccccccccccccccCCccc--cccch-h
Confidence 6889999999999965 789999999 78999999999999999999999999999999999999999643 44431 1
Q ss_pred ccceeeec
Q psy15186 143 DKEIVYFF 150 (151)
Q Consensus 143 ~~~l~y~f 150 (151)
.++.++++
T Consensus 248 ~~~~~~q~ 255 (390)
T KOG3804|consen 248 LQRSCHQN 255 (390)
T ss_pred hhhhcccC
Confidence 24555443
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=96.79 E-value=0.0017 Score=46.49 Aligned_cols=59 Identities=24% Similarity=0.421 Sum_probs=42.6
Q ss_pred HHHHhcCCCCCCCcccccCCCceEEecChHHHHHHhhcccCCCCCcHHHHHHHHHHHHHh
Q psy15186 71 FLLELLSDSTNANCITWEGTNGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALRTHSRR 130 (151)
Q Consensus 71 FLl~LL~d~~~~~~I~W~~~~~~Fk~~d~~~vArlWG~~k~~~~m~YdklsRaLR~yy~k 130 (151)
=|.+||+|++..++|.|.+.+..|.|.|++++++.-=.+ -=..-+|.++.|-|..|.=+
T Consensus 5 kL~~~l~~~~~~~~I~W~~~G~~fiI~d~~~f~~~vLp~-~F~~~~~~SF~RQLn~yGF~ 63 (103)
T PF00447_consen 5 KLYEMLEDPENSDIIRWSPDGDSFIIHDPEEFEKEVLPK-YFKHSNFSSFVRQLNMYGFK 63 (103)
T ss_dssp HHHHHHCTTTTTTTCEECTTSSEEEES-HHHHHHHTHHH-HSST--HHHHHHHHHHTTEE
T ss_pred HHHHHHcCCCCCCEEEEeCCCCEEEEeecHHHhhhcccc-ccCccccceeeeEeeeeeeE
Confidence 356789999999999999999999999998887621111 11123699999999888544
No 8
>smart00415 HSF heat shock factor.
Probab=96.60 E-value=0.0059 Score=44.13 Aligned_cols=59 Identities=25% Similarity=0.391 Sum_probs=44.8
Q ss_pred HHHHhcCCCCCCCcccccCCCceEEecChHHHHHHhhcccCCCCCcHHHHHHHHHHHHHh
Q psy15186 71 FLLELLSDSTNANCITWEGTNGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALRTHSRR 130 (151)
Q Consensus 71 FLl~LL~d~~~~~~I~W~~~~~~Fk~~d~~~vArlWG~~k~~~~m~YdklsRaLR~yy~k 130 (151)
=|.++|+|++..++|+|...+..|.|.|++++.+---.+- -..-+|.++-|-|-.|.=+
T Consensus 8 kL~~~l~~~~~~~iI~W~~~G~~f~I~d~~~f~~~vLp~~-Fk~~~~~SF~RqLn~yGF~ 66 (105)
T smart00415 8 KLYLLVEDPSTDKIISWSPSGKSFVIWDPEEFAKNLLPRY-FKHNNFSSFVRQLNMYGFR 66 (105)
T ss_pred HHHHHHhCCCCCCEEEECCCCCEEEEcCHHHHHHHHHHHh-cCCCCHHHHHHHHHhcCCE
Confidence 3567889999999999999888999999987765322221 1234599999999888655
No 9
>COG5169 HSF1 Heat shock transcription factor [Transcription]
Probab=93.32 E-value=0.065 Score=45.61 Aligned_cols=56 Identities=23% Similarity=0.391 Sum_probs=39.8
Q ss_pred HHHhcCCCCCCCcccccCCCceEEecChHHHHHHhhcccCCCCCcHHHHHHHHHHHH
Q psy15186 72 LLELLSDSTNANCITWEGTNGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALRTHS 128 (151)
Q Consensus 72 Ll~LL~d~~~~~~I~W~~~~~~Fk~~d~~~vArlWG~~k~~~~m~YdklsRaLR~yy 128 (151)
|.++|+|+++.++|+|+..+.-|-|.|+++.+..=..+--+ --|+..+-|-|--|-
T Consensus 17 Ly~iLe~~e~~k~I~Ws~~G~sfvI~~~~~F~~~iLpr~FK-h~NfaSFVRQLN~Yg 72 (282)
T COG5169 17 LYQILEEPEYYKLIQWSPDGRSFVILDPEEFTKVILPRYFK-HGNFASFVRQLNKYG 72 (282)
T ss_pred HHHHhcCcccCCceEECCCCCEEEEeCcchhhhhhhhhhhc-ccCHHHHHHHHHhcC
Confidence 44668999999999999999999999988766543333221 124667777666553
No 10
>KOG0627|consensus
Probab=86.65 E-value=0.58 Score=39.33 Aligned_cols=38 Identities=24% Similarity=0.491 Sum_probs=31.5
Q ss_pred HHHhcCCCCCCCcccccCCCceEEecChHHHHHHhhcc
Q psy15186 72 LLELLSDSTNANCITWEGTNGEFKLTDPDEVARRWGER 109 (151)
Q Consensus 72 Ll~LL~d~~~~~~I~W~~~~~~Fk~~d~~~vArlWG~~ 109 (151)
|.++++|++..++|+|...+--|-|.||+++++.=-.+
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 34678999999999999988899999999988654433
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=77.11 E-value=7 Score=28.74 Aligned_cols=64 Identities=13% Similarity=0.387 Sum_probs=49.6
Q ss_pred chHHHHHHHhcCCCCCCCcccccC-CCceEEec-----------C-hHHHHHHhhcccCC-----CCCcHHHHHHHHHHH
Q psy15186 66 IQLWQFLLELLSDSTNANCITWEG-TNGEFKLT-----------D-PDEVARRWGERKSK-----PNMNYDKLSRALRTH 127 (151)
Q Consensus 66 ~~Lw~FLl~LL~d~~~~~~I~W~~-~~~~Fk~~-----------d-~~~vArlWG~~k~~-----~~m~YdklsRaLR~y 127 (151)
++|-++|++.++...+.+ +.|+| +...|+|- + -.+|=+.|..++|+ ...+.-+....||.-
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 568899999999999977 59999 67999982 1 24778999999985 235778877778877
Q ss_pred HHh
Q psy15186 128 SRR 130 (151)
Q Consensus 128 y~k 130 (151)
-.+
T Consensus 81 Lnk 83 (109)
T PF00605_consen 81 LNK 83 (109)
T ss_dssp HHH
T ss_pred HhC
Confidence 776
No 12
>smart00348 IRF interferon regulatory factor. interferon regulatory factor, also known as trytophan pentad repeat
Probab=68.99 E-value=5.8 Score=29.04 Aligned_cols=44 Identities=16% Similarity=0.435 Sum_probs=35.9
Q ss_pred HHHHHHHhcCCCCCCCcccccC-CCceEEec-----------Ch-HHHHHHhhcccCC
Q psy15186 68 LWQFLLELLSDSTNANCITWEG-TNGEFKLT-----------DP-DEVARRWGERKSK 112 (151)
Q Consensus 68 Lw~FLl~LL~d~~~~~~I~W~~-~~~~Fk~~-----------d~-~~vArlWG~~k~~ 112 (151)
|-.+|.+-++...+++ +.|.| ++..|+|- +. ..+=+.|..++|+
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 89999 67999982 11 2488999999885
No 13
>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=61.49 E-value=9.1 Score=27.98 Aligned_cols=64 Identities=16% Similarity=0.364 Sum_probs=47.8
Q ss_pred chHHHHHHHhcCCCCCCCcccccC-CCceEEec-----------ChHHHHHHhhcccCC--C--CCcHHHHHHHHHHHHH
Q psy15186 66 IQLWQFLLELLSDSTNANCITWEG-TNGEFKLT-----------DPDEVARRWGERKSK--P--NMNYDKLSRALRTHSR 129 (151)
Q Consensus 66 ~~Lw~FLl~LL~d~~~~~~I~W~~-~~~~Fk~~-----------d~~~vArlWG~~k~~--~--~m~YdklsRaLR~yy~ 129 (151)
.+|-.+|.+-++...+.+ +.|.| ++..|+|= +-..+=+.|..++|+ + .-+.-+....||.--.
T Consensus 2 ~~lr~WL~~~i~sg~ypG-L~W~d~ek~~FrIPWkh~~~~~~~e~d~~iFkawa~~~Gk~~~g~~~d~~~wK~nfrcAln 80 (107)
T cd00103 2 MRLRPWLVEQVDSGTYPG-LIWLDEEKTIFRIPWKHAARHDVQEADAKIFKAWAVERGIYQPGGTPDPAEWKARLLCALR 80 (107)
T ss_pred cchHHHHHHHhccCCCCC-CeEecCCCCEEECCCccCcccCcchhhhHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHh
Confidence 467889999999999997 79998 67999872 124677899999884 2 3456666666666665
Q ss_pred h
Q psy15186 130 R 130 (151)
Q Consensus 130 k 130 (151)
+
T Consensus 81 ~ 81 (107)
T cd00103 81 S 81 (107)
T ss_pred c
Confidence 5
No 14
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=40.94 E-value=22 Score=21.91 Aligned_cols=14 Identities=21% Similarity=0.218 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHh
Q psy15186 117 YDKLSRALRTHSRR 130 (151)
Q Consensus 117 YdklsRaLR~yy~k 130 (151)
---++|+||.||..
T Consensus 19 dT~v~r~l~~yY~~ 32 (41)
T PF14475_consen 19 DTHVHRVLRKYYTE 32 (41)
T ss_pred hhHHHHHHHHHHHH
Confidence 44589999999998
No 15
>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=27.79 E-value=1.6e+02 Score=20.07 Aligned_cols=42 Identities=21% Similarity=0.295 Sum_probs=30.6
Q ss_pred chHHHHHHHhcCCCCCCCcccccCCC-ceEEecChHHHHHHhhccc
Q psy15186 66 IQLWQFLLELLSDSTNANCITWEGTN-GEFKLTDPDEVARRWGERK 110 (151)
Q Consensus 66 ~~Lw~FLl~LL~d~~~~~~I~W~~~~-~~Fk~~d~~~vArlWG~~k 110 (151)
.-|+-+|++-+.-+-+.+ |+|++ .+|-+-.-++++++.|..+
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 457777777765544333 99955 5888888899999988765
No 16
>COG4185 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.13 E-value=82 Score=25.41 Aligned_cols=52 Identities=17% Similarity=0.251 Sum_probs=33.7
Q ss_pred cCCCCCcchHHHHHHHhcCCCCCCCcccccCCCceEEecChHHHHHHhhcccCCCCCcHHHHHHHHH
Q psy15186 59 SSTGSGQIQLWQFLLELLSDSTNANCITWEGTNGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALR 125 (151)
Q Consensus 59 s~~g~G~~~Lw~FLl~LL~d~~~~~~I~W~~~~~~Fk~~d~~~vArlWG~~k~~~~m~YdklsRaLR 125 (151)
.+.|+|+..+..+++.-|++ .|.++|+|++|.-=+...++ .|+++--.++.+
T Consensus 9 G~NGsGKstv~~~~~~~~~~--------------~~~~VN~D~iA~~i~p~~p~-~~~i~A~r~ai~ 60 (187)
T COG4185 9 GPNGSGKSTVYASTLAPLLP--------------GIVFVNADEIAAQISPDNPT-SAAIQAARVAID 60 (187)
T ss_pred cCCCCCceeeeeccchhhcC--------------CeEEECHHHHhhhcCCCCch-HHHHHHHHHHHH
Confidence 35788888888776543332 46889999888544433333 688887666643
No 17
>cd07355 HN_L-delphilin-R2_like Second harmonin_N_like domain (repeat 2) of L-delphilin, and related domains. This subgroup contains the second of two harmonin_N_like domains of an alternatively spliced longer variant of mouse delphilin (L-delphilin), and related domains. Delphilin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds the glutamate receptor delta-2 (GRID2) subunit and the monocarboxylate transporter 2 at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain in L-delphilin follows the second PDZ protein-binding domain, PDZ2; it is also found in the shorter C-terminal isoforms (S-delphilin/delphilin alpha and delphilin beta). It is a putative protein-binding module based on its sequence similarity to the harmonin N-domain. The first harmonin_N_like domain of L-delphilin belongs to a different subgroup and is missing from S-delphilin.
Probab=20.71 E-value=37 Score=23.85 Aligned_cols=16 Identities=25% Similarity=0.690 Sum_probs=13.7
Q ss_pred cchHHHHHHHhcCCCC
Q psy15186 65 QIQLWQFLLELLSDST 80 (151)
Q Consensus 65 ~~~Lw~FLl~LL~d~~ 80 (151)
+.++|+||.+||..++
T Consensus 53 K~~iw~~i~~llp~~e 68 (80)
T cd07355 53 KQVIWQYIYQLLPYEE 68 (80)
T ss_pred HHHHHHHHHHHcCHHH
Confidence 6789999999998654
Done!