Query psy13885
Match_columns 246
No_of_seqs 324 out of 539
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 22:55:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13885.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13885hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3806|consensus 100.0 3.5E-36 7.6E-41 253.5 11.5 80 167-246 61-141 (177)
2 smart00413 ETS erythroblast tr 100.0 3.1E-35 6.7E-40 222.6 8.5 73 174-246 1-74 (87)
3 PF00178 Ets: Ets-domain; Int 100.0 8.5E-34 1.8E-38 215.3 6.8 73 174-246 1-74 (85)
4 KOG3804|consensus 100.0 9.2E-31 2E-35 245.7 9.4 156 74-246 208-367 (390)
5 KOG3805|consensus 100.0 1.8E-28 3.9E-33 221.0 10.0 87 159-245 257-345 (361)
6 KOG3806|consensus 99.8 6.1E-21 1.3E-25 161.2 3.2 52 72-123 102-153 (177)
7 smart00413 ETS erythroblast tr 99.8 2.4E-20 5.2E-25 141.5 3.7 51 73-123 36-86 (87)
8 PF00178 Ets: Ets-domain; Int 99.7 1.1E-17 2.5E-22 127.0 3.1 51 72-122 35-85 (85)
9 KOG3805|consensus 99.5 1.1E-14 2.5E-19 132.0 3.1 50 74-123 309-359 (361)
10 KOG3804|consensus 99.4 8.4E-14 1.8E-18 131.5 3.0 53 73-125 329-381 (390)
11 PF00447 HSF_DNA-bind: HSF-typ 96.8 0.0032 6.9E-08 48.9 5.9 58 179-237 4-61 (103)
12 smart00415 HSF heat shock fact 96.6 0.0064 1.4E-07 47.6 6.2 60 177-237 5-64 (105)
13 COG5169 HSF1 Heat shock transc 93.3 0.15 3.4E-06 46.8 5.3 52 180-236 16-71 (282)
14 KOG0627|consensus 81.6 1.3 2.9E-05 40.5 3.0 39 180-218 18-56 (304)
15 PF10446 DUF2457: Protein of u 75.9 0.6 1.3E-05 45.4 -1.0 8 77-84 122-129 (458)
16 PF02724 CDC45: CDC45-like pro 69.9 0.43 9.4E-06 48.4 -3.7 30 92-121 199-228 (622)
17 PF00605 IRF: Interferon regul 67.9 14 0.00029 29.4 5.1 47 175-222 2-61 (109)
18 smart00348 IRF interferon regu 66.0 14 0.0003 29.2 4.9 45 177-222 2-59 (107)
19 PF03153 TFIIA: Transcription 61.5 0.75 1.6E-05 43.3 -3.7 31 90-121 337-370 (375)
20 cd00103 IRF Interferon Regulat 53.2 30 0.00064 27.3 4.7 47 175-222 2-60 (107)
21 COG2947 Uncharacterized conser 51.8 20 0.00043 30.2 3.6 59 97-156 29-90 (156)
22 KOG2652|consensus 48.2 1.3 2.9E-05 41.6 -4.2 32 90-122 310-344 (348)
23 PF14475 Mso1_Sec1_bdg: Sec1-b 42.4 16 0.00034 24.2 1.3 17 224-240 17-33 (41)
24 PF04147 Nop14: Nop14-like fam 39.9 4.1 8.9E-05 42.9 -2.7 12 88-99 425-436 (840)
25 PRK14891 50S ribosomal protein 39.7 62 0.0013 26.6 4.6 40 194-234 20-60 (131)
26 PF02918 Pertussis_S2S3: Pertu 37.5 17 0.00037 28.8 1.1 49 87-135 53-105 (109)
27 PF01978 TrmB: Sugar-specific 36.9 22 0.00048 24.8 1.5 33 88-120 33-65 (68)
28 PTZ00415 transmission-blocking 24.6 13 0.00027 42.4 -2.2 14 176-189 336-349 (2849)
29 PF01022 HTH_5: Bacterial regu 24.2 1E+02 0.0022 20.0 2.9 22 223-244 26-47 (47)
30 PF11081 DUF2890: Protein of u 24.2 33 0.00071 29.9 0.7 32 200-236 143-176 (187)
31 PF02918 Pertussis_S2S3: Pertu 24.0 95 0.0021 24.7 3.1 26 220-245 51-76 (109)
32 cd07153 Fur_like Ferric uptake 21.4 1.4E+02 0.0031 22.6 3.8 26 220-245 29-54 (116)
33 cd07355 HN_L-delphilin-R2_like 21.4 51 0.0011 24.8 1.1 14 174-187 53-66 (80)
34 PF01475 FUR: Ferric uptake re 21.2 98 0.0021 23.9 2.8 27 219-245 35-61 (120)
35 PF00325 Crp: Bacterial regula 20.4 1.2E+02 0.0027 18.7 2.5 19 224-242 14-32 (32)
No 1
>KOG3806|consensus
Probab=100.00 E-value=3.5e-36 Score=253.51 Aligned_cols=80 Identities=63% Similarity=1.172 Sum_probs=75.9
Q ss_pred CCCCCCCchhhHHHHHHhcCCCCCCCceeeecC-cceEEEeChHHHHHHHhhhcCCCCCCHHHHHHHHHHhhhccceeeC
Q psy13885 167 PATPRRGSLQLWQFLVALLDDPNNASCIVWTGR-GMEFKLVEPEEVARRWGVQKNRPAMNYDKLSRSLRYYYEKGIMQKV 245 (246)
Q Consensus 167 ~~~~~~g~~~Lw~FLl~lL~d~~~~~~I~Wt~~-~~eF~~~d~~~va~lWg~~k~~~~m~y~klsR~lR~yy~~~il~kv 245 (246)
..++++|++|||||||+||.|+++++||+|||+ +++|+|+||++||||||.+||||+||||||||||||||++|||.||
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 345678999999999999999999999999997 5699999999999999999999999999999999999999999999
Q ss_pred C
Q psy13885 246 A 246 (246)
Q Consensus 246 ~ 246 (246)
+
T Consensus 141 ~ 141 (177)
T KOG3806|consen 141 P 141 (177)
T ss_pred C
Confidence 6
No 2
>smart00413 ETS erythroblast transformation specific domain. variation of the helix-turn-helix motif
Probab=100.00 E-value=3.1e-35 Score=222.61 Aligned_cols=73 Identities=66% Similarity=1.173 Sum_probs=70.6
Q ss_pred chhhHHHHHHhcCCCCCCCceeeecC-cceEEEeChHHHHHHHhhhcCCCCCCHHHHHHHHHHhhhccceeeCC
Q psy13885 174 SLQLWQFLVALLDDPNNASCIVWTGR-GMEFKLVEPEEVARRWGVQKNRPAMNYDKLSRSLRYYYEKGIMQKVA 246 (246)
Q Consensus 174 ~~~Lw~FLl~lL~d~~~~~~I~Wt~~-~~eF~~~d~~~va~lWg~~k~~~~m~y~klsR~lR~yy~~~il~kv~ 246 (246)
+++||+||++||.||++++||+|||+ +++|+|+||++||+|||.+||||+|||+||||||||||++|||.||+
T Consensus 1 ~~~Lw~FL~~LL~d~~~~~~I~W~~k~~g~Fkl~~~~~vA~lWG~~Knk~~M~YeklSRaLRyyy~~~il~Kv~ 74 (87)
T smart00413 1 QIQLWQFLLDLLLDPENGDIIRWTDRDGGEFKLVDPEEVARLWGQRKNKPNMNYEKLSRALRYYYKKNILRKVP 74 (87)
T ss_pred CccHHHHHHHHHcCccCCCeEEeeCCCCCEEEecCHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHhcCcEEecC
Confidence 47999999999999999999999997 68999999999999999999999999999999999999999999995
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=8.5e-34 Score=215.34 Aligned_cols=73 Identities=67% Similarity=1.258 Sum_probs=68.8
Q ss_pred chhhHHHHHHhcCCCCCCCceeeec-CcceEEEeChHHHHHHHhhhcCCCCCCHHHHHHHHHHhhhccceeeCC
Q psy13885 174 SLQLWQFLVALLDDPNNASCIVWTG-RGMEFKLVEPEEVARRWGVQKNRPAMNYDKLSRSLRYYYEKGIMQKVA 246 (246)
Q Consensus 174 ~~~Lw~FLl~lL~d~~~~~~I~Wt~-~~~eF~~~d~~~va~lWg~~k~~~~m~y~klsR~lR~yy~~~il~kv~ 246 (246)
+++||+||++||.|++++++|+||| ++++|+|+||++||+|||++||+++|||+||||+||+||++|||.||+
T Consensus 1 ~~~Lw~FLl~LL~d~~~~~~I~Wt~~~~~eFki~d~~~vA~lWG~~k~~~~m~yeklsR~LR~yy~k~il~kv~ 74 (85)
T PF00178_consen 1 QIQLWQFLLELLEDPSNSDIIAWTGKRGGEFKIVDPEAVARLWGKHKNRPNMNYEKLSRALRYYYKKGILEKVK 74 (85)
T ss_dssp S-SHHHHHHHHHHSGGGTTTEEEEETSTTEEEESSHHHHHHHHHHHTTSTT-SHHHHHHHHHHHHHTTSEEEET
T ss_pred CccHHHHHHHHhcCccCCCeeEeeccCCCeEEecCHHHHHHHHHHHcCCccccHHHHHHHHHHHhhCCeEEecC
Confidence 5799999999999999999999999 578999999999999999999999999999999999999999999985
No 4
>KOG3804|consensus
Probab=99.97 E-value=9.2e-31 Score=245.74 Aligned_cols=156 Identities=37% Similarity=0.637 Sum_probs=118.4
Q ss_pred HHHHHHhhccCCCCCCccchhhhhhHHhhhhccccccc--cccceeccccccCCCccccccccCCCCCCCCCCCCCCcCc
Q psy13885 74 KEVARRWGVQKNRPAMNYDKLSRSLRYYYEKGIMQKVA--GERYVYKFCTSVTNGLIDIRFYRSLKPNFTDFYPPQTDYS 151 (246)
Q Consensus 74 eevar~wG~~Knk~~m~y~klsr~LRyyy~k~i~~kv~--g~~~vY~F~~~~~~gliDI~~~rsa~P~~T~~~PPqs~~S 151 (246)
..+..+|+..+|++.|+|.-+.+++||||..||+.||. +++.++++...... + +.++....
T Consensus 208 ~~~s~~~~a~sn~~~m~~~~m~~a~~~~~q~~il~~~~~~~~~~~~q~~~~~~~--~---------------~~~~~~~~ 270 (390)
T KOG3804|consen 208 KAVSKLWGAHSNKPDMNYETMGRALRYYPQRGILAKVEGVLQRSCHQNKGSQQQ--P---------------QVQDKRGR 270 (390)
T ss_pred ccccccchhhccCccccccccccccccccCCccccccchhhhhhcccCCCcccc--c---------------cccccccC
Confidence 34678999999999999999999999999999999999 67777666544211 1 11111111
Q ss_pred CCcCCCCCCCCCCCCCCCCCCCchhhHHHHHHhcCCCCC-CCceeeecC-cceEEEeChHHHHHHHhhhcCCCCCCHHHH
Q psy13885 152 KRSDKQNCWPYDTPPPATPRRGSLQLWQFLVALLDDPNN-ASCIVWTGR-GMEFKLVEPEEVARRWGVQKNRPAMNYDKL 229 (246)
Q Consensus 152 k~s~s~~~~p~~~~~~~~~~~g~~~Lw~FLl~lL~d~~~-~~~I~Wt~~-~~eF~~~d~~~va~lWg~~k~~~~m~y~kl 229 (246)
+.....-..|...+...........||+||++||.|+.+ ..+|.|.++ .|+|||||+++||||||+|||+.+|||+||
T Consensus 271 ~~~~~~~~~~~~~~~~~~~~~~~t~LWefl~~lL~d~~~~p~~IkWedr~~GVFrvVds~a~arlWG~~Kn~~~MtYekm 350 (390)
T KOG3804|consen 271 PSSALPVPPPLDTVKKSGRPLSGTGLWEFLRQLLLDPNYNPGFIKWEDREKGVFRVVDSEALARLWGMHKNNSSMTYEKM 350 (390)
T ss_pred cCccccCCCccccccccCCCcccchHHHHHHHHhcCCCcCCccccccccCCCeeEEecccHHHHHhcCcCCCCCcCHHHH
Confidence 111111122222322222222235899999999999986 569999999 589999999999999999999999999999
Q ss_pred HHHHHHhhhccceeeCC
Q psy13885 230 SRSLRYYYEKGIMQKVA 246 (246)
Q Consensus 230 sR~lR~yy~~~il~kv~ 246 (246)
+|||||||+++||+||.
T Consensus 351 sRAlRyYYk~~IL~kv~ 367 (390)
T KOG3804|consen 351 SRALRYYYKREILRKVD 367 (390)
T ss_pred hHHhhhhhhcceeecCC
Confidence 99999999999999984
No 5
>KOG3805|consensus
Probab=99.95 E-value=1.8e-28 Score=221.03 Aligned_cols=87 Identities=47% Similarity=0.791 Sum_probs=77.6
Q ss_pred CCCCCCCCCCCCCCCchhhHHHHHHhcCCCC-CCCceeeecCc-ceEEEeChHHHHHHHhhhcCCCCCCHHHHHHHHHHh
Q psy13885 159 CWPYDTPPPATPRRGSLQLWQFLVALLDDPN-NASCIVWTGRG-MEFKLVEPEEVARRWGVQKNRPAMNYDKLSRSLRYY 236 (246)
Q Consensus 159 ~~p~~~~~~~~~~~g~~~Lw~FLl~lL~d~~-~~~~I~Wt~~~-~eF~~~d~~~va~lWg~~k~~~~m~y~klsR~lR~y 236 (246)
|.|-..+|.+...+.+|+|||||++||..|. ++.||+|+++. |+|+|.++..||+|||+||||+.|||+|||||||.|
T Consensus 257 P~~~~~nG~tg~~kk~IhLwQFLkELL~sP~~~~~~IrWVDkdKGiFkiess~~lArlWG~RKNR~~MnYdKlsRslRqY 336 (361)
T KOG3805|consen 257 PQPTLLNGKTGKGKKKIHLWQFLKELLYSPEQMGSCIRWVDKDKGIFKIESSEKLARLWGIRKNRKAMNYDKLSRSLRQY 336 (361)
T ss_pred CCccccCCCCCCCcceeeHHHHHHHHHhChhhhchheEeeccCCceEEeecHHHHHHHhhhhcccccccHHHHHHHHHHH
Confidence 4444444555445558999999999999998 89999999995 899999999999999999999999999999999999
Q ss_pred hhccceeeC
Q psy13885 237 YEKGIMQKV 245 (246)
Q Consensus 237 y~~~il~kv 245 (246)
|++|||+|+
T Consensus 337 yKkGiikK~ 345 (361)
T KOG3805|consen 337 YKKGIIKKP 345 (361)
T ss_pred hhcCccccc
Confidence 999999996
No 6
>KOG3806|consensus
Probab=99.81 E-value=6.1e-21 Score=161.21 Aligned_cols=52 Identities=62% Similarity=1.145 Sum_probs=50.0
Q ss_pred HHHHHHHHhhccCCCCCCccchhhhhhHHhhhhccccccccccceecccccc
Q psy13885 72 EEKEVARRWGVQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFCTSV 123 (246)
Q Consensus 72 eeeevar~wG~~Knk~~m~y~klsr~LRyyy~k~i~~kv~g~~~vY~F~~~~ 123 (246)
++++||++||.+||+|.|||+||||||||||+||||+||+|+||||+|++.+
T Consensus 102 dp~eVArlWG~rK~kp~MNYdKLSRaLRyyY~kni~~Kv~Gkr~~YkF~~~~ 153 (177)
T KOG3806|consen 102 DPDEVARLWGARKNKPNMNYDKLSRALRYYYDKNILKKVPGKRFVYKFVFDP 153 (177)
T ss_pred CHHHHHHHHhhhhCCCCCCHHHHHHHHHHHHhcCceeecCCceEEEEEecCH
Confidence 4789999999999999999999999999999999999999999999999974
No 7
>smart00413 ETS erythroblast transformation specific domain. variation of the helix-turn-helix motif
Probab=99.80 E-value=2.4e-20 Score=141.47 Aligned_cols=51 Identities=61% Similarity=1.106 Sum_probs=48.9
Q ss_pred HHHHHHHhhccCCCCCCccchhhhhhHHhhhhccccccccccceecccccc
Q psy13885 73 EKEVARRWGVQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFCTSV 123 (246)
Q Consensus 73 eeevar~wG~~Knk~~m~y~klsr~LRyyy~k~i~~kv~g~~~vY~F~~~~ 123 (246)
.+.||++||.+||+|.|||+||||||||||++|||.||+|+++||+|++++
T Consensus 36 ~~~vA~lWG~~Knk~~M~YeklSRaLRyyy~~~il~Kv~g~rl~Y~F~~~~ 86 (87)
T smart00413 36 PEEVARLWGQRKNKPNMNYEKLSRALRYYYKKNILRKVPGKRLVYKFVKNP 86 (87)
T ss_pred HHHHHHHHhhhcCCCCCCHHHHHHHHHHHHhcCcEEecCCceEEEecCCCC
Confidence 578999999999999999999999999999999999999999999998864
No 8
>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=99.69 E-value=1.1e-17 Score=127.04 Aligned_cols=51 Identities=61% Similarity=1.157 Sum_probs=47.4
Q ss_pred HHHHHHHHhhccCCCCCCccchhhhhhHHhhhhccccccccccceeccccc
Q psy13885 72 EEKEVARRWGVQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFCTS 122 (246)
Q Consensus 72 eeeevar~wG~~Knk~~m~y~klsr~LRyyy~k~i~~kv~g~~~vY~F~~~ 122 (246)
++++||++||.+|+++.|+|++|||+|||||++|||.||.|++++|+|+++
T Consensus 35 d~~~vA~lWG~~k~~~~m~yeklsR~LR~yy~k~il~kv~g~r~~Y~F~~~ 85 (85)
T PF00178_consen 35 DPEAVARLWGKHKNRPNMNYEKLSRALRYYYKKGILEKVKGQRLVYRFVEN 85 (85)
T ss_dssp SHHHHHHHHHHHTTSTT-SHHHHHHHHHHHHHTTSEEEETTSTTEEEESS-
T ss_pred CHHHHHHHHHHHcCCccccHHHHHHHHHHHhhCCeEEecCCcEEEEecCcC
Confidence 378999999999999999999999999999999999999999999999874
No 9
>KOG3805|consensus
Probab=99.49 E-value=1.1e-14 Score=132.02 Aligned_cols=50 Identities=58% Similarity=0.998 Sum_probs=47.2
Q ss_pred HHHHHHhhccCCCCCCccchhhhhhHHhhhhccccccc-cccceecccccc
Q psy13885 74 KEVARRWGVQKNRPAMNYDKLSRSLRYYYEKGIMQKVA-GERYVYKFCTSV 123 (246)
Q Consensus 74 eevar~wG~~Knk~~m~y~klsr~LRyyy~k~i~~kv~-g~~~vY~F~~~~ 123 (246)
..+|++||++|||++|||+|||||||.||+||||+|+. .+||||+|+.+.
T Consensus 309 ~~lArlWG~RKNR~~MnYdKlsRslRqYyKkGiikK~ekkqrLvyqf~pP~ 359 (361)
T KOG3805|consen 309 EKLARLWGIRKNRKAMNYDKLSRSLRQYYKKGIIKKPEKKQRLVYQFQPPY 359 (361)
T ss_pred HHHHHHhhhhcccccccHHHHHHHHHHHhhcCccccchhhhheeeeecCCC
Confidence 78999999999999999999999999999999999997 789999998764
No 10
>KOG3804|consensus
Probab=99.41 E-value=8.4e-14 Score=131.46 Aligned_cols=53 Identities=45% Similarity=0.964 Sum_probs=50.2
Q ss_pred HHHHHHHhhccCCCCCCccchhhhhhHHhhhhccccccccccceeccccccCC
Q psy13885 73 EKEVARRWGVQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFCTSVTN 125 (246)
Q Consensus 73 eeevar~wG~~Knk~~m~y~klsr~LRyyy~k~i~~kv~g~~~vY~F~~~~~~ 125 (246)
.+.+|++||.+||+.+|||+||+|||||||+.+||+||.|+|+||+|+.+++.
T Consensus 329 s~a~arlWG~~Kn~~~MtYekmsRAlRyYYk~~IL~kv~GqrLvyqF~k~~~~ 381 (390)
T KOG3804|consen 329 SEALARLWGMHKNNSSMTYEKMSRALRYYYKREILRKVDGQRLVYQFVKNPSG 381 (390)
T ss_pred ccHHHHHhcCcCCCCCcCHHHHhHHhhhhhhcceeecCCCceeeEEeccCccc
Confidence 57899999999999999999999999999999999999999999999998643
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=96.83 E-value=0.0032 Score=48.89 Aligned_cols=58 Identities=28% Similarity=0.465 Sum_probs=42.4
Q ss_pred HHHHHhcCCCCCCCceeeecCcceEEEeChHHHHHHHhhhcCCCCCCHHHHHHHHHHhh
Q psy13885 179 QFLVALLDDPNNASCIVWTGRGMEFKLVEPEEVARRWGVQKNRPAMNYDKLSRSLRYYY 237 (246)
Q Consensus 179 ~FLl~lL~d~~~~~~I~Wt~~~~eF~~~d~~~va~lWg~~k~~~~m~y~klsR~lR~yy 237 (246)
.-|..||.|+.+.++|+|...|.-|.|.|+.++++.-=.+- -..-+|.++.|-|-.|-
T Consensus 4 ~kL~~~l~~~~~~~~I~W~~~G~~fiI~d~~~f~~~vLp~~-F~~~~~~SF~RQLn~yG 61 (103)
T PF00447_consen 4 SKLYEMLEDPENSDIIRWSPDGDSFIIHDPEEFEKEVLPKY-FKHSNFSSFVRQLNMYG 61 (103)
T ss_dssp HHHHHHHCTTTTTTTCEECTTSSEEEES-HHHHHHHTHHHH-SST--HHHHHHHHHHTT
T ss_pred HHHHHHHcCCCCCCEEEEeCCCCEEEEeecHHHhhhccccc-cCccccceeeeEeeeee
Confidence 34667889999999999999999999999988887322211 11247999999998874
No 12
>smart00415 HSF heat shock factor.
Probab=96.61 E-value=0.0064 Score=47.57 Aligned_cols=60 Identities=27% Similarity=0.448 Sum_probs=45.5
Q ss_pred hHHHHHHhcCCCCCCCceeeecCcceEEEeChHHHHHHHhhhcCCCCCCHHHHHHHHHHhh
Q psy13885 177 LWQFLVALLDDPNNASCIVWTGRGMEFKLVEPEEVARRWGVQKNRPAMNYDKLSRSLRYYY 237 (246)
Q Consensus 177 Lw~FLl~lL~d~~~~~~I~Wt~~~~eF~~~d~~~va~lWg~~k~~~~m~y~klsR~lR~yy 237 (246)
+-.=|..+|.|+...++|+|+..|..|.|.|+..++.---.+- -..-+|.++.|-|-.|.
T Consensus 5 F~~kL~~~l~~~~~~~iI~W~~~G~~f~I~d~~~f~~~vLp~~-Fk~~~~~SF~RqLn~yG 64 (105)
T smart00415 5 FLTKLYLLVEDPSTDKIISWSPSGKSFVIWDPEEFAKNLLPRY-FKHNNFSSFVRQLNMYG 64 (105)
T ss_pred HHHHHHHHHhCCCCCCEEEECCCCCEEEEcCHHHHHHHHHHHh-cCCCCHHHHHHHHHhcC
Confidence 3445667889999999999999999999999987766322221 12346999999998875
No 13
>COG5169 HSF1 Heat shock transcription factor [Transcription]
Probab=93.28 E-value=0.15 Score=46.85 Aligned_cols=52 Identities=29% Similarity=0.602 Sum_probs=37.8
Q ss_pred HHHHhcCCCCCCCceeeecCcceEEEeChHHHHH----HHhhhcCCCCCCHHHHHHHHHHh
Q psy13885 180 FLVALLDDPNNASCIVWTGRGMEFKLVEPEEVAR----RWGVQKNRPAMNYDKLSRSLRYY 236 (246)
Q Consensus 180 FLl~lL~d~~~~~~I~Wt~~~~eF~~~d~~~va~----lWg~~k~~~~m~y~klsR~lR~y 236 (246)
=|.++|.+|++.++|+|+..|..|.|.|+..++. +.+.|.| +.++-|-|--|
T Consensus 16 KLy~iLe~~e~~k~I~Ws~~G~sfvI~~~~~F~~~iLpr~FKh~N-----faSFVRQLN~Y 71 (282)
T COG5169 16 KLYQILEEPEYYKLIQWSPDGRSFVILDPEEFTKVILPRYFKHGN-----FASFVRQLNKY 71 (282)
T ss_pred HHHHHhcCcccCCceEECCCCCEEEEeCcchhhhhhhhhhhcccC-----HHHHHHHHHhc
Confidence 3557789999999999999999999999865554 4444544 55555555433
No 14
>KOG0627|consensus
Probab=81.60 E-value=1.3 Score=40.54 Aligned_cols=39 Identities=28% Similarity=0.486 Sum_probs=32.9
Q ss_pred HHHHhcCCCCCCCceeeecCcceEEEeChHHHHHHHhhh
Q psy13885 180 FLVALLDDPNNASCIVWTGRGMEFKLVEPEEVARRWGVQ 218 (246)
Q Consensus 180 FLl~lL~d~~~~~~I~Wt~~~~eF~~~d~~~va~lWg~~ 218 (246)
=|..|+.||++-++|+|+..|.-|.|.||..+|+.=-.+
T Consensus 18 K~y~~v~Dps~~~iisWs~~g~sFvv~d~~~F~~~~Lp~ 56 (304)
T KOG0627|consen 18 KLYEMVEDPSTDEIISWSPSGNSFVIWNPEEFAKVLLPL 56 (304)
T ss_pred HHHHHhcCCCCCCceEECCCCCccccCCHHHHHHHHhHH
Confidence 345778999999999999988899999999999865544
No 15
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=75.94 E-value=0.6 Score=45.36 Aligned_cols=8 Identities=13% Similarity=0.206 Sum_probs=4.5
Q ss_pred HHHhhccC
Q psy13885 77 ARRWGVQK 84 (246)
Q Consensus 77 ar~wG~~K 84 (246)
-.+|....
T Consensus 122 ~~~WtP~~ 129 (458)
T PF10446_consen 122 YEFWTPGA 129 (458)
T ss_pred ceeecccc
Confidence 35666654
No 16
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=69.92 E-value=0.43 Score=48.37 Aligned_cols=30 Identities=13% Similarity=0.411 Sum_probs=17.2
Q ss_pred chhhhhhHHhhhhccccccccccceecccc
Q psy13885 92 DKLSRSLRYYYEKGIMQKVAGERYVYKFCT 121 (246)
Q Consensus 92 ~klsr~LRyyy~k~i~~kv~g~~~vY~F~~ 121 (246)
.+..+.+..||..|.-.-.+....+|....
T Consensus 199 ~~~~~~i~~yY~~gs~~g~ssa~~~y~La~ 228 (622)
T PF02724_consen 199 EEYREEIEKYYSQGSYYGKSSAVLMYELAS 228 (622)
T ss_pred HHHHHHHHHHHhcCceecccHHHHHHHHHH
Confidence 344445677787676555545555665533
No 17
>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=67.91 E-value=14 Score=29.40 Aligned_cols=47 Identities=19% Similarity=0.486 Sum_probs=37.0
Q ss_pred hhhHHHHHHhcCCCCCCCceeeecCc-ceEEEe------------ChHHHHHHHhhhcCCC
Q psy13885 175 LQLWQFLVALLDDPNNASCIVWTGRG-MEFKLV------------EPEEVARRWGVQKNRP 222 (246)
Q Consensus 175 ~~Lw~FLl~lL~d~~~~~~I~Wt~~~-~eF~~~------------d~~~va~lWg~~k~~~ 222 (246)
++|-.+|+..|....++++ .|.+.. ..|+|- +..+|=+.|++++++.
T Consensus 2 ~rlr~WL~~~i~sg~ypGL-~W~d~~kt~FrIPWkH~~r~~~~~~~D~~iFkaWA~~~Gk~ 61 (109)
T PF00605_consen 2 LRLRPWLIEQIDSGRYPGL-EWLDEEKTIFRIPWKHAGRQDWDQEEDAKIFKAWAVHRGKY 61 (109)
T ss_dssp --HHHHHHHHHHHTCSTTS-EESSTTSSEEEEETTSTTSTTSSHCGGGHHHHHHHHHTTSS
T ss_pred CcHHHHHHHHHhcCCCCCc-EEEcCCCCEEEeeCccCCCCCccccchHHHHHHHHHHhccc
Confidence 5788999999999999666 899985 589984 2357889999999764
No 18
>smart00348 IRF interferon regulatory factor. interferon regulatory factor, also known as trytophan pentad repeat
Probab=65.99 E-value=14 Score=29.19 Aligned_cols=45 Identities=16% Similarity=0.344 Sum_probs=35.8
Q ss_pred hHHHHHHhcCCCCCCCceeeecCc-ceEEEeC-----------h-HHHHHHHhhhcCCC
Q psy13885 177 LWQFLVALLDDPNNASCIVWTGRG-MEFKLVE-----------P-EEVARRWGVQKNRP 222 (246)
Q Consensus 177 Lw~FLl~lL~d~~~~~~I~Wt~~~-~eF~~~d-----------~-~~va~lWg~~k~~~ 222 (246)
|-.+|+..|....+++ +.|.+.. ..|+|-= . ..|=+.|..++++.
T Consensus 2 lr~WL~~~i~sg~ypG-L~W~d~ekt~FrIPWkh~~~~~~~~e~D~~iFkaWa~~~Gk~ 59 (107)
T smart00348 2 LRPWLVEQVESGQYPG-LCWEDEEKTRFRIPWKHAGRSGFDEERDAEIFKAYCVARGIY 59 (107)
T ss_pred hHHHHHHHhccCCCCC-ceEecCCCCEEEeccccCCcCCCCchhccHHHHHHHHHhCCC
Confidence 5678999999999999 8999986 5899842 1 34888899988653
No 19
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=61.46 E-value=0.75 Score=43.33 Aligned_cols=31 Identities=35% Similarity=0.723 Sum_probs=23.7
Q ss_pred ccchhhhhh---HHhhhhccccccccccceecccc
Q psy13885 90 NYDKLSRSL---RYYYEKGIMQKVAGERYVYKFCT 121 (246)
Q Consensus 90 ~y~klsr~L---Ryyy~k~i~~kv~g~~~vY~F~~ 121 (246)
.|+|+.|.= |.+.+.|||+ |.|+-|||.-+.
T Consensus 337 ~~~kv~r~k~~wk~~lk~g~~~-~~~~d~~f~~~~ 370 (375)
T PF03153_consen 337 QYDKVTRVKNKWKCTLKDGIMH-INGKDYVFQKAT 370 (375)
T ss_dssp EEEEEEEETTEEEEEEEEEEEE-ETTEEEEEEEEE
T ss_pred EeeccccccceeEEEeeeeEEE-ECCeEEEEeeee
Confidence 788888873 6778889986 779988866544
No 20
>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=53.19 E-value=30 Score=27.32 Aligned_cols=47 Identities=17% Similarity=0.482 Sum_probs=37.4
Q ss_pred hhhHHHHHHhcCCCCCCCceeeecCc-ceEEEe-----------ChHHHHHHHhhhcCCC
Q psy13885 175 LQLWQFLVALLDDPNNASCIVWTGRG-MEFKLV-----------EPEEVARRWGVQKNRP 222 (246)
Q Consensus 175 ~~Lw~FLl~lL~d~~~~~~I~Wt~~~-~eF~~~-----------d~~~va~lWg~~k~~~ 222 (246)
++|-.+|+..|....+++ +.|.+.. ..|+|- ....|=+.|..++++.
T Consensus 2 ~~lr~WL~~~i~sg~ypG-L~W~d~ek~~FrIPWkh~~~~~~~e~d~~iFkawa~~~Gk~ 60 (107)
T cd00103 2 MRLRPWLVEQVDSGTYPG-LIWLDEEKTIFRIPWKHAARHDVQEADAKIFKAWAVERGIY 60 (107)
T ss_pred cchHHHHHHHhccCCCCC-CeEecCCCCEEECCCccCcccCcchhhhHHHHHHHHHhCCC
Confidence 468889999999999996 7899986 589883 2256778899988753
No 21
>COG2947 Uncharacterized conserved protein [Function unknown]
Probab=51.75 E-value=20 Score=30.16 Aligned_cols=59 Identities=17% Similarity=0.360 Sum_probs=37.9
Q ss_pred hhHHhhhhccccccc--cccceeccccccCCCccccccccC-CCCCCCCCCCCCCcCcCCcCC
Q psy13885 97 SLRYYYEKGIMQKVA--GERYVYKFCTSVTNGLIDIRFYRS-LKPNFTDFYPPQTDYSKRSDK 156 (246)
Q Consensus 97 ~LRyyy~k~i~~kv~--g~~~vY~F~~~~~~gliDI~~~rs-a~P~~T~~~PPqs~~Sk~s~s 156 (246)
..|.|-..|+|+.+. ...+.|--+| ..+++.++..-++ +.|.+|++-|.+..|.+.+..
T Consensus 29 GVRNYqARNfmR~M~iGD~~fFYHSNc-~~pgIvGl~~V~~~a~pD~tq~d~~spYyDPka~~ 90 (156)
T COG2947 29 GVRNYQARNFMRDMKIGDLGFFYHSNC-KPPGIVGLAEVCALAHPDPTQFDPASPYYDPKATP 90 (156)
T ss_pred chHHHHHHHHHHhcccCceEEEEecCC-CCCCceehhhhhhccCCCccccCCCCcccCccccc
Confidence 359999999999664 3444444443 3477777766666 448888766665555544443
No 22
>KOG2652|consensus
Probab=48.20 E-value=1.3 Score=41.63 Aligned_cols=32 Identities=34% Similarity=0.797 Sum_probs=24.9
Q ss_pred ccchhhhhh---HHhhhhccccccccccceeccccc
Q psy13885 90 NYDKLSRSL---RYYYEKGIMQKVAGERYVYKFCTS 122 (246)
Q Consensus 90 ~y~klsr~L---Ryyy~k~i~~kv~g~~~vY~F~~~ 122 (246)
.|+|+-|+= +.|++.|||+ +.|+.|||+-+..
T Consensus 310 qyDKV~RsKnKWKc~LKDGIM~-ingkDY~F~KA~G 344 (348)
T KOG2652|consen 310 QYDKVNRSKNKWKCYLKDGVMH-INGKDYVFQKAQG 344 (348)
T ss_pred eeeeeccccceeeEEeecceEE-eCCceeEeeeccc
Confidence 688887773 7899999997 6799888765543
No 23
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=42.40 E-value=16 Score=24.20 Aligned_cols=17 Identities=29% Similarity=0.501 Sum_probs=12.7
Q ss_pred CCHHHHHHHHHHhhhcc
Q psy13885 224 MNYDKLSRSLRYYYEKG 240 (246)
Q Consensus 224 m~y~klsR~lR~yy~~~ 240 (246)
-+---++|+||.||...
T Consensus 17 eddT~v~r~l~~yY~~k 33 (41)
T PF14475_consen 17 EDDTHVHRVLRKYYTEK 33 (41)
T ss_pred cchhHHHHHHHHHHHHc
Confidence 34456899999999754
No 24
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=39.88 E-value=4.1 Score=42.88 Aligned_cols=12 Identities=17% Similarity=0.152 Sum_probs=6.1
Q ss_pred CCccchhhhhhH
Q psy13885 88 AMNYDKLSRSLR 99 (246)
Q Consensus 88 ~m~y~klsr~LR 99 (246)
+-+|+-|.-.|.
T Consensus 425 P~s~eel~~lL~ 436 (840)
T PF04147_consen 425 PSSHEELLELLD 436 (840)
T ss_pred CCCHHHHHHHHh
Confidence 445555555543
No 25
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=39.70 E-value=62 Score=26.61 Aligned_cols=40 Identities=8% Similarity=0.363 Sum_probs=30.1
Q ss_pred eeeecC-cceEEEeChHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy13885 194 IVWTGR-GMEFKLVEPEEVARRWGVQKNRPAMNYDKLSRSLR 234 (246)
Q Consensus 194 I~Wt~~-~~eF~~~d~~~va~lWg~~k~~~~m~y~klsR~lR 234 (246)
|.++.+ +.+|+|.++++ .+++-+++|..++.|-++.|.++
T Consensus 20 ~~fVR~DGkvf~FcssKC-~k~f~~kRnPRKlkWT~~yRk~~ 60 (131)
T PRK14891 20 TMFVRKDGTVLHFVDSKC-EKNYDLGREARDLEWTEAGRAEK 60 (131)
T ss_pred cEEEecCCCEEEEecHHH-HHHHHccCCCccchhHHHHHHHc
Confidence 345555 56999999999 55666777777899999987654
No 26
>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=37.53 E-value=17 Score=28.83 Aligned_cols=49 Identities=20% Similarity=0.257 Sum_probs=28.7
Q ss_pred CCCccchhhhhhHHhhhhccccccccc-cceeccccc---cCCCccccccccC
Q psy13885 87 PAMNYDKLSRSLRYYYEKGIMQKVAGE-RYVYKFCTS---VTNGLIDIRFYRS 135 (246)
Q Consensus 87 ~~m~y~klsr~LRyyy~k~i~~kv~g~-~~vY~F~~~---~~~gliDI~~~rs 135 (246)
-.-.|..|.++|++||..|+--.|+=+ .--|.+... .+..|++|.....
T Consensus 53 ~~~~y~~L~~~~~~~y~tGl~VRVhV~k~~~~~~~~~~tf~a~aL~gissCn~ 105 (109)
T PF02918_consen 53 YRPSYSALRDQLYYFYSTGLAVRVHVSKDEWYYPAFDATFSAYALTGISSCNP 105 (109)
T ss_dssp TCCCHHHHHHHHHHHHHCT-EEEEEEEEEEEE--STT-SS-EEEEEEEEE--T
T ss_pred hhHHHHHHHHHHHHHHHcCcEEEEEEecccccChhhhcCcchheeeeeeecCc
Confidence 345689999999999999998888632 222333222 3456666655443
No 27
>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=36.89 E-value=22 Score=24.81 Aligned_cols=33 Identities=24% Similarity=0.470 Sum_probs=28.2
Q ss_pred CCccchhhhhhHHhhhhccccccccccceeccc
Q psy13885 88 AMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFC 120 (246)
Q Consensus 88 ~m~y~klsr~LRyyy~k~i~~kv~g~~~vY~F~ 120 (246)
.+...+++++|+.-..+|++.++.|+.++|.-.
T Consensus 33 ~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 33 GISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 466788999999999999999999998877643
No 28
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=24.59 E-value=13 Score=42.38 Aligned_cols=14 Identities=21% Similarity=0.332 Sum_probs=7.9
Q ss_pred hhHHHHHHhcCCCC
Q psy13885 176 QLWQFLVALLDDPN 189 (246)
Q Consensus 176 ~Lw~FLl~lL~d~~ 189 (246)
.|=..|..++-.|.
T Consensus 336 ~l~~li~g~ii~~~ 349 (2849)
T PTZ00415 336 LLAALIHGLIISPE 349 (2849)
T ss_pred HHHHHhhceecCcc
Confidence 44555666666554
No 29
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=24.21 E-value=1e+02 Score=20.00 Aligned_cols=22 Identities=23% Similarity=0.446 Sum_probs=18.9
Q ss_pred CCCHHHHHHHHHHhhhccceee
Q psy13885 223 AMNYDKLSRSLRYYYEKGIMQK 244 (246)
Q Consensus 223 ~m~y~klsR~lR~yy~~~il~k 244 (246)
.|+.-.+|+.|+.-.+.||+.|
T Consensus 26 ~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 26 GLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEE
T ss_pred cccchHHHHHHHHHHHCcCeeC
Confidence 5788899999999999999976
No 30
>PF11081 DUF2890: Protein of unknown function (DUF2890); InterPro: IPR021304 This entry contains the 33kDa and 22kDa phosphoproteins from vertebrate adenoviruses.
Probab=24.19 E-value=33 Score=29.91 Aligned_cols=32 Identities=25% Similarity=0.325 Sum_probs=16.9
Q ss_pred cceEEEeChH--HHHHHHhhhcCCCCCCHHHHHHHHHHh
Q psy13885 200 GMEFKLVEPE--EVARRWGVQKNRPAMNYDKLSRSLRYY 236 (246)
Q Consensus 200 ~~eF~~~d~~--~va~lWg~~k~~~~m~y~klsR~lR~y 236 (246)
..+++|.|.- .|+|.-=-|++ -+.+.|.|.||
T Consensus 143 ~~~~kikNRtlrSlTRr~Lyh~~-----e~~l~r~l~da 176 (187)
T PF11081_consen 143 EQELKIKNRTLRSLTRRCLYHRG-----EDQLQRTLEDA 176 (187)
T ss_pred ccccchhhHHHHHHHHHHHHHhh-----hHHHHHHHHHH
Confidence 4578888874 55554112222 24555555554
No 31
>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=24.03 E-value=95 Score=24.69 Aligned_cols=26 Identities=27% Similarity=0.590 Sum_probs=20.7
Q ss_pred CCCCCCHHHHHHHHHHhhhccceeeC
Q psy13885 220 NRPAMNYDKLSRSLRYYYEKGIMQKV 245 (246)
Q Consensus 220 ~~~~m~y~klsR~lR~yy~~~il~kv 245 (246)
++-.-.|..|.|.|+++|..|+-..|
T Consensus 51 g~~~~~y~~L~~~~~~~y~tGl~VRV 76 (109)
T PF02918_consen 51 GKYRPSYSALRDQLYYFYSTGLAVRV 76 (109)
T ss_dssp STTCCCHHHHHHHHHHHHHCT-EEEE
T ss_pred cchhHHHHHHHHHHHHHHHcCcEEEE
Confidence 44456899999999999999987765
No 32
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=21.44 E-value=1.4e+02 Score=22.63 Aligned_cols=26 Identities=19% Similarity=0.507 Sum_probs=23.5
Q ss_pred CCCCCCHHHHHHHHHHhhhccceeeC
Q psy13885 220 NRPAMNYDKLSRSLRYYYEKGIMQKV 245 (246)
Q Consensus 220 ~~~~m~y~klsR~lR~yy~~~il~kv 245 (246)
..++++.-++-|+|...-+.|+|.+|
T Consensus 29 ~~~~i~~~TVYR~L~~L~~~Gli~~~ 54 (116)
T cd07153 29 KGPSISLATVYRTLELLEEAGLVREI 54 (116)
T ss_pred cCCCCCHHHHHHHHHHHHhCCCEEEE
Confidence 35679999999999999999999986
No 33
>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=21.37 E-value=51 Score=24.82 Aligned_cols=14 Identities=29% Similarity=0.662 Sum_probs=11.8
Q ss_pred chhhHHHHHHhcCC
Q psy13885 174 SLQLWQFLVALLDD 187 (246)
Q Consensus 174 ~~~Lw~FLl~lL~d 187 (246)
+.++|+||.+||-.
T Consensus 53 K~~iw~~i~~llp~ 66 (80)
T cd07355 53 KQVIWQYIYQLLPY 66 (80)
T ss_pred HHHHHHHHHHHcCH
Confidence 36899999999964
No 34
>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=21.15 E-value=98 Score=23.91 Aligned_cols=27 Identities=26% Similarity=0.534 Sum_probs=22.5
Q ss_pred cCCCCCCHHHHHHHHHHhhhccceeeC
Q psy13885 219 KNRPAMNYDKLSRSLRYYYEKGIMQKV 245 (246)
Q Consensus 219 k~~~~m~y~klsR~lR~yy~~~il~kv 245 (246)
+..++++-.++-|+|...-+.|||.+|
T Consensus 35 ~~~~~is~~TVYR~L~~L~e~Gli~~~ 61 (120)
T PF01475_consen 35 KKGPRISLATVYRTLDLLEEAGLIRKI 61 (120)
T ss_dssp HTTTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred hccCCcCHHHHHHHHHHHHHCCeEEEE
Confidence 456789999999999999999999986
No 35
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=20.38 E-value=1.2e+02 Score=18.75 Aligned_cols=19 Identities=21% Similarity=0.473 Sum_probs=16.0
Q ss_pred CCHHHHHHHHHHhhhccce
Q psy13885 224 MNYDKLSRSLRYYYEKGIM 242 (246)
Q Consensus 224 m~y~klsR~lR~yy~~~il 242 (246)
++-+++||.|..+-++|+|
T Consensus 14 ~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 14 LTRETVSRILKKLERQGLI 32 (32)
T ss_dssp S-HHHHHHHHHHHHHTTSE
T ss_pred CcHHHHHHHHHHHHHcCCC
Confidence 6778999999999998876
Done!