Query psy6350
Match_columns 189
No_of_seqs 133 out of 242
Neff 3.6
Searched_HMMs 46136
Date Sat Aug 17 00:10:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6350.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6350hhsearch_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 1.1E-39 2.3E-44 245.5 9.5 84 82-166 2-85 (87)
2 KOG3806|consensus 100.0 3.1E-37 6.7E-42 256.8 10.5 102 78-180 65-166 (177)
3 PF00178 Ets: Ets-domain; Int 100.0 4.5E-36 9.8E-41 223.6 9.2 83 82-165 2-84 (85)
4 KOG3805|consensus 100.0 1.3E-31 2.8E-36 239.7 7.1 88 81-168 272-360 (361)
5 KOG3804|consensus 100.0 2.8E-30 6E-35 235.6 8.2 88 78-165 290-377 (390)
6 KOG3804|consensus 99.1 1.6E-11 3.5E-16 113.0 0.7 84 82-165 172-257 (390)
7 smart00415 HSF heat shock fact 94.6 0.1 2.2E-06 39.5 5.7 59 86-147 7-65 (105)
8 PF00447 HSF_DNA-bind: HSF-typ 94.5 0.045 9.8E-07 40.9 3.6 65 87-157 5-69 (103)
9 COG5169 HSF1 Heat shock transc 88.0 0.47 1E-05 42.8 3.1 37 85-123 11-50 (282)
10 smart00348 IRF interferon regu 77.8 2.9 6.4E-05 32.6 3.4 45 84-130 2-58 (107)
11 cd00103 IRF Interferon Regulat 73.2 4.1 8.9E-05 31.7 3.2 47 82-130 2-59 (107)
12 KOG0627|consensus 71.7 4.6 9.9E-05 35.4 3.5 42 83-126 14-55 (304)
13 PF00605 IRF: Interferon regul 70.6 3.9 8.4E-05 32.0 2.5 47 83-131 3-61 (109)
14 PF01978 TrmB: Sugar-specific 60.3 17 0.00037 24.7 3.9 32 132-163 33-64 (68)
15 PF14475 Mso1_Sec1_bdg: Sec1-b 31.5 31 0.00067 23.2 1.4 16 134-149 18-33 (41)
16 PF02918 Pertussis_S2S3: Pertu 31.0 63 0.0014 25.9 3.3 41 131-171 53-94 (109)
17 PRK09391 fixK transcriptional 28.2 80 0.0017 26.1 3.7 38 116-160 181-218 (230)
18 PF13545 HTH_Crp_2: Crp-like h 23.5 1.1E+02 0.0023 20.6 3.0 33 116-155 30-62 (76)
19 TIGR03697 NtcA_cyano global ni 23.4 93 0.002 24.1 3.0 33 116-155 145-177 (193)
20 cd04788 HTH_NolA-AlbR Helix-Tu 22.5 57 0.0012 24.1 1.6 26 118-154 4-29 (96)
21 PRK14891 50S ribosomal protein 21.6 2.1E+02 0.0045 23.7 4.8 42 100-142 18-59 (131)
22 PRK10402 DNA-binding transcrip 20.5 1.3E+02 0.0028 24.6 3.5 37 116-160 171-207 (226)
No 1
>smart00413 ETS erythroblast transformation specific domain. variation of the helix-turn-helix motif
Probab=100.00 E-value=1.1e-39 Score=245.53 Aligned_cols=84 Identities=37% Similarity=0.463 Sum_probs=80.9
Q ss_pred CCchHHhHHhhhCcCCCCCCeEEeeCCCeeEEEeChHHHHHHHhccCCCCCCcHHHHHHHHHHHhhcCeeEecccCceeE
Q psy6350 82 TPGTGAKRKSREDREYCPRYIKWTNRERGVFKLVDSKAVSRLWGLHKNKPDMNYETMGRALRSSVVLTRLRTKCTQKQTA 161 (189)
Q Consensus 82 ~~l~~Flr~lLed~e~~~~~I~Wtdk~~geFk~vdpe~VArLWG~rKnkp~MtYeKmSRaLRyYY~kgIL~Kv~GqrltY 161 (189)
.+||+||++||+|++ ++++|+|+|+++|+|||+||++||+|||.+|||++||||||||||||||++|||+||.|++++|
T Consensus 2 ~~Lw~FL~~LL~d~~-~~~~I~W~~k~~g~Fkl~~~~~vA~lWG~~Knk~~M~YeklSRaLRyyy~~~il~Kv~g~rl~Y 80 (87)
T smart00413 2 IQLWQFLLDLLLDPE-NGDIIRWTDRDGGEFKLVDPEEVARLWGQRKNKPNMNYEKLSRALRYYYKKNILRKVPGKRLVY 80 (87)
T ss_pred ccHHHHHHHHHcCcc-CCCeEEeeCCCCCEEEecCHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHhcCcEEecCCceEEE
Confidence 579999999999985 7999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCc
Q psy6350 162 TRDVP 166 (189)
Q Consensus 162 ~f~~~ 166 (189)
+|..+
T Consensus 81 ~F~~~ 85 (87)
T smart00413 81 KFVKN 85 (87)
T ss_pred ecCCC
Confidence 99764
No 2
>KOG3806|consensus
Probab=100.00 E-value=3.1e-37 Score=256.77 Aligned_cols=102 Identities=28% Similarity=0.357 Sum_probs=93.4
Q ss_pred CCCCCCchHHhHHhhhCcCCCCCCeEEeeCCCeeEEEeChHHHHHHHhccCCCCCCcHHHHHHHHHHHhhcCeeEecccC
Q psy6350 78 KSEGTPGTGAKRKSREDREYCPRYIKWTNRERGVFKLVDSKAVSRLWGLHKNKPDMNYETMGRALRSSVVLTRLRTKCTQ 157 (189)
Q Consensus 78 ~~~g~~l~~Flr~lLed~e~~~~~I~Wtdk~~geFk~vdpe~VArLWG~rKnkp~MtYeKmSRaLRyYY~kgIL~Kv~Gq 157 (189)
.++..+||+||.+||+|+ .++++|+|++++.+|||++||++||||||.|||||+||||||||||||||+++||+||.|+
T Consensus 65 ~sg~iqLwqFLleLl~d~-~~~~~I~Wtg~~g~EFkl~dp~eVArlWG~rK~kp~MNYdKLSRaLRyyY~kni~~Kv~Gk 143 (177)
T KOG3806|consen 65 GSGQIQLWQFLLELLQDE-SNAHIIAWTGKDGLEFKLVDPDEVARLWGARKNKPNMNYDKLSRALRYYYDKNILKKVPGK 143 (177)
T ss_pred CCchhhHHHHHHHHHhCc-ccCCeeEEeCCCCceEEecCHHHHHHHHhhhhCCCCCCHHHHHHHHHHHHhcCceeecCCc
Confidence 344589999999999996 6899999999866699999999999999999999999999999999999999999999999
Q ss_pred ceeEEecCccccccchhheeeee
Q psy6350 158 KQTATRDVPLVFSSIMGHVLTSV 180 (189)
Q Consensus 158 rltY~f~~~~~~~~~~~~~~~~~ 180 (189)
|++|+|....-..+...|.+..+
T Consensus 144 r~~YkF~~~~~~~~~~~~~~~~~ 166 (177)
T KOG3806|consen 144 RFVYKFVFDPLNLALYPHTLKNI 166 (177)
T ss_pred eEEEEEecCHHHhccCccccccc
Confidence 99999999977777777776655
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=4.5e-36 Score=223.57 Aligned_cols=83 Identities=36% Similarity=0.452 Sum_probs=78.6
Q ss_pred CCchHHhHHhhhCcCCCCCCeEEeeCCCeeEEEeChHHHHHHHhccCCCCCCcHHHHHHHHHHHhhcCeeEecccCceeE
Q psy6350 82 TPGTGAKRKSREDREYCPRYIKWTNRERGVFKLVDSKAVSRLWGLHKNKPDMNYETMGRALRSSVVLTRLRTKCTQKQTA 161 (189)
Q Consensus 82 ~~l~~Flr~lLed~e~~~~~I~Wtdk~~geFk~vdpe~VArLWG~rKnkp~MtYeKmSRaLRyYY~kgIL~Kv~GqrltY 161 (189)
.+||+||++||+|+ +++++|+|||++.|||+|+||++||+|||.+||+++|||||||||||+||++|||+||.|++++|
T Consensus 2 ~~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 2 IQLWQFLLELLEDP-SNSDIIAWTGKRGGEFKIVDPEAVARLWGKHKNRPNMNYEKLSRALRYYYKKGILEKVKGQRLVY 80 (85)
T ss_dssp -SHHHHHHHHHHSG-GGTTTEEEEETSTTEEEESSHHHHHHHHHHHTTSTT-SHHHHHHHHHHHHHTTSEEEETTSTTEE
T ss_pred ccHHHHHHHHhcCc-cCCCeeEeeccCCCeEEecCHHHHHHHHHHHcCCccccHHHHHHHHHHHhhCCeEEecCCcEEEE
Confidence 57999999999995 79999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecC
Q psy6350 162 TRDV 165 (189)
Q Consensus 162 ~f~~ 165 (189)
+|..
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=1.3e-31 Score=239.68 Aligned_cols=88 Identities=24% Similarity=0.421 Sum_probs=84.6
Q ss_pred CCCchHHhHHhhhCcCCCCCCeEEeeCCCeeEEEeChHHHHHHHhccCCCCCCcHHHHHHHHHHHhhcCeeEecc-cCce
Q psy6350 81 GTPGTGAKRKSREDREYCPRYIKWTNRERGVFKLVDSKAVSRLWGLHKNKPDMNYETMGRALRSSVVLTRLRTKC-TQKQ 159 (189)
Q Consensus 81 g~~l~~Flr~lLed~e~~~~~I~Wtdk~~geFk~vdpe~VArLWG~rKnkp~MtYeKmSRaLRyYY~kgIL~Kv~-Gqrl 159 (189)
..+||+||++||..|+.+.+||+|+||++|+|||.++++||||||+||||+.|||||||||||.||++|||+|+. .+|+
T Consensus 272 ~IhLwQFLkELL~sP~~~~~~IrWVDkdKGiFkiess~~lArlWG~RKNR~~MnYdKlsRslRqYyKkGiikK~ekkqrL 351 (361)
T KOG3805|consen 272 KIHLWQFLKELLYSPEQMGSCIRWVDKDKGIFKIESSEKLARLWGIRKNRKAMNYDKLSRSLRQYYKKGIIKKPEKKQRL 351 (361)
T ss_pred eeeHHHHHHHHHhChhhhchheEeeccCCceEEeecHHHHHHHhhhhcccccccHHHHHHHHHHHhhcCccccchhhhhe
Confidence 579999999999999989999999999999999999999999999999999999999999999999999999994 7899
Q ss_pred eEEecCccc
Q psy6350 160 TATRDVPLV 168 (189)
Q Consensus 160 tY~f~~~~~ 168 (189)
+|+|+.||-
T Consensus 352 vyqf~pP~~ 360 (361)
T KOG3805|consen 352 VYQFQPPYE 360 (361)
T ss_pred eeeecCCCC
Confidence 999999974
No 5
>KOG3804|consensus
Probab=99.96 E-value=2.8e-30 Score=235.63 Aligned_cols=88 Identities=41% Similarity=0.589 Sum_probs=84.7
Q ss_pred CCCCCCchHHhHHhhhCcCCCCCCeEEeeCCCeeEEEeChHHHHHHHhccCCCCCCcHHHHHHHHHHHhhcCeeEecccC
Q psy6350 78 KSEGTPGTGAKRKSREDREYCPRYIKWTNRERGVFKLVDSKAVSRLWGLHKNKPDMNYETMGRALRSSVVLTRLRTKCTQ 157 (189)
Q Consensus 78 ~~~g~~l~~Flr~lLed~e~~~~~I~Wtdk~~geFk~vdpe~VArLWG~rKnkp~MtYeKmSRaLRyYY~kgIL~Kv~Gq 157 (189)
...|+.||+||+++|.|+++++.+|+|+|+++|+|||||+++||||||++||+.+||||||||||||||+++||+||.||
T Consensus 290 ~~~~t~LWefl~~lL~d~~~~p~~IkWedr~~GVFrvVds~a~arlWG~~Kn~~~MtYekmsRAlRyYYk~~IL~kv~Gq 369 (390)
T KOG3804|consen 290 PLSGTGLWEFLRQLLLDPNYNPGFIKWEDREKGVFRVVDSEALARLWGMHKNNSSMTYEKMSRALRYYYKREILRKVDGQ 369 (390)
T ss_pred CcccchHHHHHHHHhcCCCcCCccccccccCCCeeEEecccHHHHHhcCcCCCCCcCHHHHhHHhhhhhhcceeecCCCc
Confidence 34679999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeEEecC
Q psy6350 158 KQTATRDV 165 (189)
Q Consensus 158 rltY~f~~ 165 (189)
|++|+|.-
T Consensus 370 rLvyqF~k 377 (390)
T KOG3804|consen 370 RLVYQFVK 377 (390)
T ss_pred eeeEEecc
Confidence 99999963
No 6
>KOG3804|consensus
Probab=99.10 E-value=1.6e-11 Score=112.99 Aligned_cols=84 Identities=49% Similarity=0.658 Sum_probs=79.6
Q ss_pred CCchHHhHHhhhCcCCCCCCeEEeeCCCeeEEEeChHHHHHHHhccCCCCCCcHHHHHHHHHHHhhcCeeEecc--cCce
Q psy6350 82 TPGTGAKRKSREDREYCPRYIKWTNRERGVFKLVDSKAVSRLWGLHKNKPDMNYETMGRALRSSVVLTRLRTKC--TQKQ 159 (189)
Q Consensus 82 ~~l~~Flr~lLed~e~~~~~I~Wtdk~~geFk~vdpe~VArLWG~rKnkp~MtYeKmSRaLRyYY~kgIL~Kv~--Gqrl 159 (189)
.-+|+|+.+++.|...|+..|.|+++++|.|+.++...++.+||+++|++.|+|+.|.|++||||..||+.|+. +++.
T Consensus 172 p~~~~~l~~~~q~~~~~p~~~~~~~~~~~~~~~~~s~~~s~~~~a~sn~~~m~~~~m~~a~~~~~q~~il~~~~~~~~~~ 251 (390)
T KOG3804|consen 172 PYLWEFLLDLLQDSATCPKPIKWTQREKGCFKLVDSKAVSKLWGAHSNKPDMNYETMGRALRYYPQRGILAKVEGVLQRS 251 (390)
T ss_pred cchHHHHhhhhhcccCCCcccccccccccccccccCccccccchhhccCccccccccccccccccCCccccccchhhhhh
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999999 8888
Q ss_pred eEEecC
Q psy6350 160 TATRDV 165 (189)
Q Consensus 160 tY~f~~ 165 (189)
.+++.-
T Consensus 252 ~~q~~~ 257 (390)
T KOG3804|consen 252 CHQNKG 257 (390)
T ss_pred cccCCC
Confidence 888873
No 7
>smart00415 HSF heat shock factor.
Probab=94.64 E-value=0.1 Score=39.54 Aligned_cols=59 Identities=15% Similarity=0.151 Sum_probs=42.2
Q ss_pred HHhHHhhhCcCCCCCCeEEeeCCCeeEEEeChHHHHHHHhccCCCCCCcHHHHHHHHHHHhh
Q psy6350 86 GAKRKSREDREYCPRYIKWTNRERGVFKLVDSKAVSRLWGLHKNKPDMNYETMGRALRSSVV 147 (189)
Q Consensus 86 ~Flr~lLed~e~~~~~I~Wtdk~~geFk~vdpe~VArLWG~rKnkp~MtYeKmSRaLRyYY~ 147 (189)
.=|.++|+|++ +.++|+|...++ .|.|.|+++..+---.+ --..-+|..+-|-|-.|-=
T Consensus 7 ~kL~~~l~~~~-~~~iI~W~~~G~-~f~I~d~~~f~~~vLp~-~Fk~~~~~SF~RqLn~yGF 65 (105)
T smart00415 7 TKLYLLVEDPS-TDKIISWSPSGK-SFVIWDPEEFAKNLLPR-YFKHNNFSSFVRQLNMYGF 65 (105)
T ss_pred HHHHHHHhCCC-CCCEEEECCCCC-EEEEcCHHHHHHHHHHH-hcCCCCHHHHHHHHHhcCC
Confidence 34677889974 778999999876 69999998776532222 1123469999998877743
No 8
>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=94.55 E-value=0.045 Score=40.94 Aligned_cols=65 Identities=15% Similarity=0.133 Sum_probs=42.6
Q ss_pred HhHHhhhCcCCCCCCeEEeeCCCeeEEEeChHHHHHHHhccCCCCCCcHHHHHHHHHHHhhcCeeEecccC
Q psy6350 87 AKRKSREDREYCPRYIKWTNRERGVFKLVDSKAVSRLWGLHKNKPDMNYETMGRALRSSVVLTRLRTKCTQ 157 (189)
Q Consensus 87 Flr~lLed~e~~~~~I~Wtdk~~geFk~vdpe~VArLWG~rKnkp~MtYeKmSRaLRyYY~kgIL~Kv~Gq 157 (189)
-|.++|+|+ .+.++|+|.+.++ .|.|.|++++++.-=. +--..-+|..+.|-|-.| |.-+...+.
T Consensus 5 kL~~~l~~~-~~~~~I~W~~~G~-~fiI~d~~~f~~~vLp-~~F~~~~~~SF~RQLn~y---GF~k~~~~~ 69 (103)
T PF00447_consen 5 KLYEMLEDP-ENSDIIRWSPDGD-SFIIHDPEEFEKEVLP-KYFKHSNFSSFVRQLNMY---GFKKVSSDS 69 (103)
T ss_dssp HHHHHHCTT-TTTTTCEECTTSS-EEEES-HHHHHHHTHH-HHSST--HHHHHHHHHHT---TEEECC-SS
T ss_pred HHHHHHcCC-CCCCEEEEeCCCC-EEEEeecHHHhhhccc-cccCccccceeeeEeeee---eeEEEecCc
Confidence 467889997 4789999998765 7999999887762111 111223688998888777 665555443
No 9
>COG5169 HSF1 Heat shock transcription factor [Transcription]
Probab=88.00 E-value=0.47 Score=42.82 Aligned_cols=37 Identities=19% Similarity=0.400 Sum_probs=28.5
Q ss_pred hHHh---HHhhhCcCCCCCCeEEeeCCCeeEEEeChHHHHHH
Q psy6350 85 TGAK---RKSREDREYCPRYIKWTNRERGVFKLVDSKAVSRL 123 (189)
Q Consensus 85 ~~Fl---r~lLed~e~~~~~I~Wtdk~~geFk~vdpe~VArL 123 (189)
-.|+ ..+|||++ +.++|+|+..++ -|-|.|+++.++.
T Consensus 11 ~~FV~KLy~iLe~~e-~~k~I~Ws~~G~-sfvI~~~~~F~~~ 50 (282)
T COG5169 11 KEFVHKLYQILEEPE-YYKLIQWSPDGR-SFVILDPEEFTKV 50 (282)
T ss_pred hHHHHHHHHHhcCcc-cCCceEECCCCC-EEEEeCcchhhhh
Confidence 4564 55788975 679999999887 7999998766644
No 10
>smart00348 IRF interferon regulatory factor. interferon regulatory factor, also known as trytophan pentad repeat
Probab=77.80 E-value=2.9 Score=32.58 Aligned_cols=45 Identities=11% Similarity=0.178 Sum_probs=35.9
Q ss_pred chHHhHHhhhCcCCCCCCeEEeeCCCeeEEEeC-----------h-HHHHHHHhccCCC
Q psy6350 84 GTGAKRKSREDREYCPRYIKWTNRERGVFKLVD-----------S-KAVSRLWGLHKNK 130 (189)
Q Consensus 84 l~~Flr~lLed~e~~~~~I~Wtdk~~geFk~vd-----------p-e~VArLWG~rKnk 130 (189)
|-.+|.+-++.. .|++ ++|.|+++..|+|-= . .++=+.|...+++
T Consensus 2 lr~WL~~~i~sg-~ypG-L~W~d~ekt~FrIPWkh~~~~~~~~e~D~~iFkaWa~~~Gk 58 (107)
T smart00348 2 LRPWLVEQVESG-QYPG-LCWEDEEKTRFRIPWKHAGRSGFDEERDAEIFKAYCVARGI 58 (107)
T ss_pred hHHHHHHHhccC-CCCC-ceEecCCCCEEEeccccCCcCCCCchhccHHHHHHHHHhCC
Confidence 457888999985 6888 999999999999832 1 2377899988875
No 11
>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=73.22 E-value=4.1 Score=31.73 Aligned_cols=47 Identities=11% Similarity=0.319 Sum_probs=37.4
Q ss_pred CCchHHhHHhhhCcCCCCCCeEEeeCCCeeEEEe-----------ChHHHHHHHhccCCC
Q psy6350 82 TPGTGAKRKSREDREYCPRYIKWTNRERGVFKLV-----------DSKAVSRLWGLHKNK 130 (189)
Q Consensus 82 ~~l~~Flr~lLed~e~~~~~I~Wtdk~~geFk~v-----------dpe~VArLWG~rKnk 130 (189)
++|-.+|.+-++.. .|++ +.|.|+++..|+|- +-..+=+.|..++++
T Consensus 2 ~~lr~WL~~~i~sg-~ypG-L~W~d~ek~~FrIPWkh~~~~~~~e~d~~iFkawa~~~Gk 59 (107)
T cd00103 2 MRLRPWLVEQVDSG-TYPG-LIWLDEEKTIFRIPWKHAARHDVQEADAKIFKAWAVERGI 59 (107)
T ss_pred cchHHHHHHHhccC-CCCC-CeEecCCCCEEECCCccCcccCcchhhhHHHHHHHHHhCC
Confidence 46778999999996 6885 89999999999983 125566889888875
No 12
>KOG0627|consensus
Probab=71.74 E-value=4.6 Score=35.44 Aligned_cols=42 Identities=14% Similarity=0.181 Sum_probs=32.3
Q ss_pred CchHHhHHhhhCcCCCCCCeEEeeCCCeeEEEeChHHHHHHHhc
Q psy6350 83 PGTGAKRKSREDREYCPRYIKWTNRERGVFKLVDSKAVSRLWGL 126 (189)
Q Consensus 83 ~l~~Flr~lLed~e~~~~~I~Wtdk~~geFk~vdpe~VArLWG~ 126 (189)
+.+.=+.++++|+ ...++|+|...+. -|-+.|+++.|+.=-.
T Consensus 14 ~Fl~K~y~~v~Dp-s~~~iisWs~~g~-sFvv~d~~~F~~~~Lp 55 (304)
T KOG0627|consen 14 PFLEKLYEMVEDP-STDEIISWSPSGN-SFVIWNPEEFAKVLLP 55 (304)
T ss_pred cHHHHHHHHhcCC-CCCCceEECCCCC-ccccCCHHHHHHHHhH
Confidence 3344456688898 5779999999655 6999999999987544
No 13
>PF00605 IRF: Interferon regulatory factor transcription factor; InterPro: IPR001346 Viral infections induce the expression of type I interferons (IFN-alpha and IFN-beta) genes. The induction is due to the transcriptional activation of the IFN genes. Interferon regulatory factor I (IRF-1) is one of the transcription factors responsible for that activation. IRF-1 binds to an upstream regulatory cis element, known as the interferon consensus sequence (ICS), which is found in the promoters of type I IFN and IFN-inducible MHC class I genes. Interferon regulatory factor 2 (IRF-2) is a protein that also interacts with the ICS, but that does not function as an activator; rather, it suppresses the function of IRF-1 under certain circumstances []. These proteins share a highly conserved N-terminal domain of about 100 amino acid residues which is involved in DNA-binding and which contain five conserved tryptophans. This domain is known as a 'tryptophan pentad repeat' or a 'tryptophan cluster' and is also present in: Interferon consensus sequence binding protein (ICSBP) [], a transcription factor expressed predominantly in lymphoid tissues and induced by IFN-gamma that also binds to the ICS. Transcriptional regulator ISGF3 gamma subunit []. ISGF3 is responsible for the initial stimulation of interferon-alpha-responsive genes. It recognises and binds to the interferon-stimulated response element (ISRE) within the regulatory sequences of target genes. Interferon regulatory factor 3 (IRF-3). Interferon regulatory factor 4 (IRF-4) which binds to the interferon- stimulated response element (ISRE) of the MHC class I promoter. Interferon regulatory factor 5 (IRF-5). Interferon regulatory factor 6 (IRF-6). Interferon regulatory factor 7 (IRF-7). Gamma Herpesviruses vIRF-1, -2 and -3, proteins with homology to the cellular transcription factors of the IRF family []. Neither vIRF-1 nor vIRF-2 bind to DNA with the same specificity as cellular IRFs, indicating that if vIRFs are DNA-binding proteins, their binding has a pattern distinct from that of the cellular IRFs. Whether vIRF-3 can bind DNA with the same specificity as cellular IRFs is not known. The IRF tryptophan pentad repeat DNA-binding domain has an alpha/beta architecture comprising a cluster of three alpha-helices (alpha1-alpha3) flanked on one side by a mixed four-stranded beta-sheet (beta1-beta4). It forms a helix-turn-helix motif that binds to ISRE consensus sequences found in target promoters. Three of the tryptophan residues contact DNA by recognising a GAAA sequence []. This entry represents the IRF tryptophan pentad repeat DNA-binding domain.; GO: 0000975 regulatory region DNA binding; PDB: 2IRF_H 1IRF_A 1IRG_A 2DLL_A 3QU3_C 2PI0_D 2O6G_G 1T2K_A 2O61_A 3QU6_C ....
Probab=70.55 E-value=3.9 Score=32.04 Aligned_cols=47 Identities=15% Similarity=0.398 Sum_probs=37.1
Q ss_pred CchHHhHHhhhCcCCCCCCeEEeeCCCeeEEEe------------ChHHHHHHHhccCCCC
Q psy6350 83 PGTGAKRKSREDREYCPRYIKWTNRERGVFKLV------------DSKAVSRLWGLHKNKP 131 (189)
Q Consensus 83 ~l~~Flr~lLed~e~~~~~I~Wtdk~~geFk~v------------dpe~VArLWG~rKnkp 131 (189)
+|-++|.+.++.. .|+++ +|+|+++..|+|- +-.++=+.|..++++.
T Consensus 3 rlr~WL~~~i~sg-~ypGL-~W~d~~kt~FrIPWkH~~r~~~~~~~D~~iFkaWA~~~Gk~ 61 (109)
T PF00605_consen 3 RLRPWLIEQIDSG-RYPGL-EWLDEEKTIFRIPWKHAGRQDWDQEEDAKIFKAWAVHRGKY 61 (109)
T ss_dssp -HHHHHHHHHHHT-CSTTS-EESSTTSSEEEEETTSTTSTTSSHCGGGHHHHHHHHHTTSS
T ss_pred cHHHHHHHHHhcC-CCCCc-EEEcCCCCEEEeeCccCCCCCccccchHHHHHHHHHHhccc
Confidence 5678999999996 57655 9999999999983 2356779999998863
No 14
>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=60.34 E-value=17 Score=24.74 Aligned_cols=32 Identities=16% Similarity=0.056 Sum_probs=27.0
Q ss_pred CCcHHHHHHHHHHHhhcCeeEecccCceeEEe
Q psy6350 132 DMNYETMGRALRSSVVLTRLRTKCTQKQTATR 163 (189)
Q Consensus 132 ~MtYeKmSRaLRyYY~kgIL~Kv~GqrltY~f 163 (189)
++...+..++|+.-.++|++++..|+...|+-
T Consensus 33 ~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a 64 (68)
T PF01978_consen 33 GISRSTVYRALKSLEEKGLVEREEGRPKVYRA 64 (68)
T ss_dssp TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEE
T ss_pred CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEE
Confidence 45678899999999999999999988777653
No 15
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=31.50 E-value=31 Score=23.23 Aligned_cols=16 Identities=19% Similarity=0.150 Sum_probs=12.0
Q ss_pred cHHHHHHHHHHHhhcC
Q psy6350 134 NYETMGRALRSSVVLT 149 (189)
Q Consensus 134 tYeKmSRaLRyYY~kg 149 (189)
+---++|+||.||...
T Consensus 18 ddT~v~r~l~~yY~~k 33 (41)
T PF14475_consen 18 DDTHVHRVLRKYYTEK 33 (41)
T ss_pred chhHHHHHHHHHHHHc
Confidence 3345799999999854
No 16
>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=30.98 E-value=63 Score=25.94 Aligned_cols=41 Identities=12% Similarity=-0.045 Sum_probs=27.6
Q ss_pred CCCcHHHHHHHHHHHhhcCeeEecccCc-eeEEecCcccccc
Q psy6350 131 PDMNYETMGRALRSSVVLTRLRTKCTQK-QTATRDVPLVFSS 171 (189)
Q Consensus 131 p~MtYeKmSRaLRyYY~kgIL~Kv~Gqr-ltY~f~~~~~~~~ 171 (189)
-.=.|+.|-|.|+++|..|+-..|.=++ -.|.+.+.-.|+.
T Consensus 53 ~~~~y~~L~~~~~~~y~tGl~VRVhV~k~~~~~~~~~~tf~a 94 (109)
T PF02918_consen 53 YRPSYSALRDQLYYFYSTGLAVRVHVSKDEWYYPAFDATFSA 94 (109)
T ss_dssp TCCCHHHHHHHHHHHHHCT-EEEEEEEEEEEE--STT-SS-E
T ss_pred hhHHHHHHHHHHHHHHHcCcEEEEEEecccccChhhhcCcch
Confidence 3446999999999999999988886444 4566666666664
No 17
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=28.16 E-value=80 Score=26.09 Aligned_cols=38 Identities=18% Similarity=0.210 Sum_probs=30.1
Q ss_pred ChHHHHHHHhccCCCCCCcHHHHHHHHHHHhhcCeeEecccCcee
Q psy6350 116 DSKAVSRLWGLHKNKPDMNYETMGRALRSSVVLTRLRTKCTQKQT 160 (189)
Q Consensus 116 dpe~VArLWG~rKnkp~MtYeKmSRaLRyYY~kgIL~Kv~Gqrlt 160 (189)
.-+++|.+=|. +.+.+||.|+..-+.|+|....+++.+
T Consensus 181 t~~~IA~~lGi-------sretlsR~L~~L~~~GlI~~~~~~~i~ 218 (230)
T PRK09391 181 SRRDIADYLGL-------TIETVSRALSQLQDRGLIGLSGARQIE 218 (230)
T ss_pred CHHHHHHHHCC-------CHHHHHHHHHHHHHCCcEEecCCceEE
Confidence 45789988664 889999999999999999866334443
No 18
>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=23.46 E-value=1.1e+02 Score=20.64 Aligned_cols=33 Identities=18% Similarity=0.248 Sum_probs=28.9
Q ss_pred ChHHHHHHHhccCCCCCCcHHHHHHHHHHHhhcCeeEecc
Q psy6350 116 DSKAVSRLWGLHKNKPDMNYETMGRALRSSVVLTRLRTKC 155 (189)
Q Consensus 116 dpe~VArLWG~rKnkp~MtYeKmSRaLRyYY~kgIL~Kv~ 155 (189)
..+++|.+=| ++.+.++|.|+..-+.|+++...
T Consensus 30 t~~~iA~~~g-------~sr~tv~r~l~~l~~~g~I~~~~ 62 (76)
T PF13545_consen 30 TQEEIADMLG-------VSRETVSRILKRLKDEGIIEVKR 62 (76)
T ss_dssp SHHHHHHHHT-------SCHHHHHHHHHHHHHTTSEEEET
T ss_pred CHHHHHHHHC-------CCHHHHHHHHHHHHHCCCEEEcC
Confidence 5789999976 48999999999999999999663
No 19
>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=23.44 E-value=93 Score=24.13 Aligned_cols=33 Identities=15% Similarity=0.081 Sum_probs=28.7
Q ss_pred ChHHHHHHHhccCCCCCCcHHHHHHHHHHHhhcCeeEecc
Q psy6350 116 DSKAVSRLWGLHKNKPDMNYETMGRALRSSVVLTRLRTKC 155 (189)
Q Consensus 116 dpe~VArLWG~rKnkp~MtYeKmSRaLRyYY~kgIL~Kv~ 155 (189)
..+++|.+=|. +.+.+||.|+..-+.|+|+...
T Consensus 145 t~~~iA~~lG~-------tretvsR~l~~l~~~g~I~~~~ 177 (193)
T TIGR03697 145 SHQAIAEAIGS-------TRVTITRLLGDLRKKKLISIHK 177 (193)
T ss_pred CHHHHHHHhCC-------cHHHHHHHHHHHHHCCCEEecC
Confidence 46889998764 8999999999999999998873
No 20
>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=22.50 E-value=57 Score=24.07 Aligned_cols=26 Identities=23% Similarity=0.185 Sum_probs=19.7
Q ss_pred HHHHHHHhccCCCCCCcHHHHHHHHHHHhhcCeeEec
Q psy6350 118 KAVSRLWGLHKNKPDMNYETMGRALRSSVVLTRLRTK 154 (189)
Q Consensus 118 e~VArLWG~rKnkp~MtYeKmSRaLRyYY~kgIL~Kv 154 (189)
.+||++.|.. .+.||||-+.|++...
T Consensus 4 ~eva~~~gvs-----------~~tlR~ye~~Gll~p~ 29 (96)
T cd04788 4 GELARRTGLS-----------VRTLHHYDHIGLLSPS 29 (96)
T ss_pred HHHHHHHCcC-----------HHHHHHHHHCCCCCCC
Confidence 4677777762 3568999999999764
No 21
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=21.60 E-value=2.1e+02 Score=23.68 Aligned_cols=42 Identities=24% Similarity=0.434 Sum_probs=32.5
Q ss_pred CCeEEeeCCCeeEEEeChHHHHHHHhccCCCCCCcHHHHHHHH
Q psy6350 100 RYIKWTNRERGVFKLVDSKAVSRLWGLHKNKPDMNYETMGRAL 142 (189)
Q Consensus 100 ~~I~Wtdk~~geFk~vdpe~VArLWG~rKnkp~MtYeKmSRaL 142 (189)
+-|.++-++.-+|+|.++++ .+++=++||..+..+-++.|..
T Consensus 18 ~G~~fVR~DGkvf~FcssKC-~k~f~~kRnPRKlkWT~~yRk~ 59 (131)
T PRK14891 18 TGTMFVRKDGTVLHFVDSKC-EKNYDLGREARDLEWTEAGRAE 59 (131)
T ss_pred CCcEEEecCCCEEEEecHHH-HHHHHccCCCccchhHHHHHHH
Confidence 45677887778999999987 6677677777788888887654
No 22
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=20.47 E-value=1.3e+02 Score=24.64 Aligned_cols=37 Identities=11% Similarity=0.134 Sum_probs=29.8
Q ss_pred ChHHHHHHHhccCCCCCCcHHHHHHHHHHHhhcCeeEecccCcee
Q psy6350 116 DSKAVSRLWGLHKNKPDMNYETMGRALRSSVVLTRLRTKCTQKQT 160 (189)
Q Consensus 116 dpe~VArLWG~rKnkp~MtYeKmSRaLRyYY~kgIL~Kv~Gqrlt 160 (189)
..+++|.+=| ++.+.+||.|+..-+.|+|+.. +++.+
T Consensus 171 t~~~lA~~lG-------~sretvsR~L~~L~~~G~I~~~-~~~i~ 207 (226)
T PRK10402 171 KHTQAAEYLG-------VSYRHLLYVLAQFIQDGYLKKS-KRGYL 207 (226)
T ss_pred hHHHHHHHHC-------CcHHHHHHHHHHHHHCCCEEee-CCEEE
Confidence 4577888766 4889999999999999999886 44443
Done!