Query 005737
Match_columns 680
No_of_seqs 405 out of 1795
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 13:00:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005737.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005737hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00018 AP2 DNA-binding domain 99.7 2.2E-17 4.8E-22 134.5 6.8 61 328-397 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.7 2.6E-17 5.7E-22 135.7 6.4 63 329-400 1-63 (64)
3 smart00380 AP2 DNA-binding dom 99.7 4.1E-17 8.8E-22 134.6 6.5 63 431-494 1-63 (64)
4 cd00018 AP2 DNA-binding domain 99.7 1E-16 2.2E-21 130.6 6.7 61 430-491 1-61 (61)
5 PHA00280 putative NHN endonucl 99.4 4.3E-13 9.3E-18 124.7 8.1 105 374-485 11-119 (121)
6 PHA00280 putative NHN endonucl 99.1 2E-10 4.4E-15 107.0 6.8 56 325-391 64-119 (121)
7 PF00847 AP2: AP2 domain; Int 98.9 3.9E-09 8.5E-14 84.1 7.0 56 328-388 1-56 (56)
8 PF00847 AP2: AP2 domain; Int 98.9 3.7E-09 8.1E-14 84.3 5.5 53 430-482 1-56 (56)
9 PF14657 Integrase_AP2: AP2-li 55.8 26 0.00056 27.5 4.6 39 341-385 1-41 (46)
10 cd04518 TBP_archaea archaeal T 52.1 90 0.0019 31.4 8.9 133 327-480 33-172 (174)
11 cd04517 TLF TBP-like factors ( 50.8 88 0.0019 31.4 8.6 126 329-479 35-172 (174)
12 cd00652 TBP_TLF TATA box bindi 42.2 1.9E+02 0.0041 29.0 9.4 128 327-479 33-172 (174)
13 cd04516 TBP_eukaryotes eukaryo 39.8 2E+02 0.0044 28.9 9.2 126 327-477 33-169 (174)
14 PF14657 Integrase_AP2: AP2-li 39.4 71 0.0015 25.0 4.8 38 443-480 1-42 (46)
15 PLN00062 TATA-box-binding prot 39.0 2E+02 0.0043 29.2 9.1 127 328-479 34-171 (179)
16 PRK00394 transcription factor; 38.1 1.7E+02 0.0036 29.6 8.4 135 327-480 32-173 (179)
17 PF08168 NUC205: NUC205 domain 22.6 16 0.00035 29.5 -1.3 17 82-100 16-32 (44)
18 PF12286 DUF3622: Protein of u 20.6 1.1E+02 0.0024 27.1 3.2 36 435-470 9-48 (71)
No 1
>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.
Probab=99.70 E-value=2.2e-17 Score=134.46 Aligned_cols=61 Identities=51% Similarity=0.891 Sum_probs=56.6
Q ss_pred cccccceeecCCCeeEEEEecCCccccCcccCCcEEecCccccHHHHHHHHHHHHHhccCCCcccCCCcc
Q 005737 328 SQYRGVTRHRWTGRYEAHLWDNSCKKEGQSRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPLE 397 (680)
Q Consensus 328 S~YRGVrrrk~tGRW~AeI~~~s~~~~~~~rkGkri~LGtFdTeEeAARAYD~AAlkl~G~~A~lNFPls 397 (680)
|+||||+++++ |||+|+|+++. .|+++|||+|+|+||||+|||.|+++++|..+.+|||.+
T Consensus 1 s~~~GV~~~~~-gkw~A~I~~~~--------~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPW-GKWVAEIRDPS--------GGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCC-CcEEEEEEeCC--------CCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 68999999998 99999999852 489999999999999999999999999999999999963
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.69 E-value=2.6e-17 Score=135.71 Aligned_cols=63 Identities=48% Similarity=0.911 Sum_probs=58.8
Q ss_pred ccccceeecCCCeeEEEEecCCccccCcccCCcEEecCccccHHHHHHHHHHHHHhccCCCcccCCCcchhh
Q 005737 329 QYRGVTRHRWTGRYEAHLWDNSCKKEGQSRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPLENYQ 400 (680)
Q Consensus 329 ~YRGVrrrk~tGRW~AeI~~~s~~~~~~~rkGkri~LGtFdTeEeAARAYD~AAlkl~G~~A~lNFPls~Ye 400 (680)
+|+||+++++ |||+|+|+++ .+|+++|||+|+|+||||+|||.|+++++|+.+.+|||...|+
T Consensus 1 ~~kGV~~~~~-gkw~A~I~~~--------~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPW-GKWVAEIRDP--------SKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCC-CeEEEEEEec--------CCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 4999999887 9999999885 3689999999999999999999999999999999999999886
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.68 E-value=4.1e-17 Score=134.57 Aligned_cols=63 Identities=51% Similarity=0.788 Sum_probs=58.8
Q ss_pred cccCceeeecCcceEEEEeeccCCcccccCCCCCHHHHHHHHHHHHHHhcCCCcccCCCCCccc
Q 005737 431 IYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFRGVTAVTNFDITRYD 494 (680)
Q Consensus 431 kYRGV~r~~~~GKW~ArIr~~~~gKriyLGtFdTeEEAArAYD~AAikl~G~~A~tNFp~s~Y~ 494 (680)
+|+||++ +++|||+|+|+.+.++++++||+|+|+||||+|||.|+++++|..+++|||.++|+
T Consensus 1 ~~kGV~~-~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQ-RPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEe-CCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 5899997 46799999998666899999999999999999999999999999999999999996
No 4
>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.
Probab=99.67 E-value=1e-16 Score=130.55 Aligned_cols=61 Identities=51% Similarity=0.822 Sum_probs=55.1
Q ss_pred ccccCceeeecCcceEEEEeeccCCcccccCCCCCHHHHHHHHHHHHHHhcCCCcccCCCCC
Q 005737 430 SIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFRGVTAVTNFDIT 491 (680)
Q Consensus 430 SkYRGV~r~~~~GKW~ArIr~~~~gKriyLGtFdTeEEAArAYD~AAikl~G~~A~tNFp~s 491 (680)
|+|+||++++ +|||+|+|+....+|++|||+|+|+||||+|||+|+++++|..+++|||.+
T Consensus 1 s~~~GV~~~~-~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRP-WGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECC-CCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 5799999764 599999998444489999999999999999999999999999999999974
No 5
>PHA00280 putative NHN endonuclease
Probab=99.41 E-value=4.3e-13 Score=124.70 Aligned_cols=105 Identities=16% Similarity=0.150 Sum_probs=83.9
Q ss_pred HHHHHHHHHHhccCCCc---ccCCC-cchhhhhHHHHhhhhhhhHHhhhcccccCccCCcccccCceeeecCcceEEEEe
Q 005737 374 AARAYDLAALKYWGPST---HINFP-LENYQKELEEMKNMNRQEYVAHLRRKSSGFSRGASIYRGVTRHHQHGRWQARIG 449 (680)
Q Consensus 374 AARAYD~AAlkl~G~~A---~lNFP-ls~YeeELeELr~mTreE~VaaLRRkssg~sr~tSkYRGV~r~~~~GKW~ArIr 449 (680)
+-+++..+.+..+|+-. .+.+- -....+.+++|+.+|..+...+.+.. ++++|+|+||+|++..+||+|+|+
T Consensus 11 ~~~~Hrlvw~~~~G~~P~g~~VdHidg~~~dnri~NLr~~T~~eN~~N~~~~----~~N~SG~kGV~~~k~~~kw~A~I~ 86 (121)
T PHA00280 11 APRRHIQVWEAANGPIPKGYYIDHIDGNPLNDALDNLRLALPKENSWNMKTP----KSNTSGLKGLSWSKEREMWRGTVT 86 (121)
T ss_pred hhhHhHhhhHHHHCCCCCCCEEEcCCCCCCCCcHHHhhhcCHHHHhcccCCC----CCCCCCCCeeEEecCCCeEEEEEE
Confidence 44677788888888532 12221 12335678899999999988886543 367899999999999999999996
Q ss_pred eccCCcccccCCCCCHHHHHHHHHHHHHHhcCCCcc
Q 005737 450 RVAGNKDLYLGTFSTQEEAAEAYDIAAIKFRGVTAV 485 (680)
Q Consensus 450 ~~~~gKriyLGtFdTeEEAArAYD~AAikl~G~~A~ 485 (680)
+++|+++||.|+|+|+|+.||+ ++++|+|++|+
T Consensus 87 --~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 87 --AEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred --ECCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 8899999999999999999997 77899999875
No 6
>PHA00280 putative NHN endonuclease
Probab=99.07 E-value=2e-10 Score=107.00 Aligned_cols=56 Identities=18% Similarity=0.240 Sum_probs=50.7
Q ss_pred CCccccccceeecCCCeeEEEEecCCccccCcccCCcEEecCccccHHHHHHHHHHHHHhccCCCcc
Q 005737 325 QRTSQYRGVTRHRWTGRYEAHLWDNSCKKEGQSRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTH 391 (680)
Q Consensus 325 ~rtS~YRGVrrrk~tGRW~AeI~~~s~~~~~~~rkGkri~LGtFdTeEeAARAYD~AAlkl~G~~A~ 391 (680)
..+|+|+||+|++..|||+|.|+. .||+++||.|+++|+|+.||+ ++.+++|.++.
T Consensus 64 ~N~SG~kGV~~~k~~~kw~A~I~~----------~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 64 SNTSGLKGLSWSKEREMWRGTVTA----------EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred CCCCCCCeeEEecCCCeEEEEEEE----------CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 467999999999999999999976 599999999999999999997 67889998764
No 7
>PF00847 AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-related genes transcriptional activator binds to the GCC-box pathogenesis-related promoter element and activates the plant's defence genes. Ethylene, chemically the simplest plant hormone, participates in a number of stress responses and developmental processes: e.g., fruit ripening, inhibition of stem and root elongation, promotion of seed germination and flowering, senescence of leaves and flowers, and sex determination []. DNA sequence elements that confer ethylene responsiveness have been shown to contain two 11bp GCC boxes, which are necessary and sufficient for transcriptional control by ethylene. Ethylene responsive element binding proteins (EREBPs) have now been identified in a variety of plants. The proteins share a similar domain of around 59 amino acids, which interacts directly with the GCC box in the ERE.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3IGM_A 3GCC_A 1GCC_A 2GCC_A.
Probab=98.90 E-value=3.9e-09 Score=84.13 Aligned_cols=56 Identities=32% Similarity=0.465 Sum_probs=47.7
Q ss_pred cccccceeecCCCeeEEEEecCCccccCcccCCcEEecCccccHHHHHHHHHHHHHhccCC
Q 005737 328 SQYRGVTRHRWTGRYEAHLWDNSCKKEGQSRKGRQVYLGGYDMEEKAARAYDLAALKYWGP 388 (680)
Q Consensus 328 S~YRGVrrrk~tGRW~AeI~~~s~~~~~~~rkGkri~LGtFdTeEeAARAYD~AAlkl~G~ 388 (680)
|+|+||++++..++|+|.|++.. ..+ ++++++||.|+++|+|++|++.++++++|.
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~--~~g---~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWS--ENG---KRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECC--CTT---EEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEcc--cCc---ccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 68999999999999999998832 111 249999999999999999999999999873
No 8
>PF00847 AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-related genes transcriptional activator binds to the GCC-box pathogenesis-related promoter element and activates the plant's defence genes. Ethylene, chemically the simplest plant hormone, participates in a number of stress responses and developmental processes: e.g., fruit ripening, inhibition of stem and root elongation, promotion of seed germination and flowering, senescence of leaves and flowers, and sex determination []. DNA sequence elements that confer ethylene responsiveness have been shown to contain two 11bp GCC boxes, which are necessary and sufficient for transcriptional control by ethylene. Ethylene responsive element binding proteins (EREBPs) have now been identified in a variety of plants. The proteins share a similar domain of around 59 amino acids, which interacts directly with the GCC box in the ERE.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3IGM_A 3GCC_A 1GCC_A 2GCC_A.
Probab=98.86 E-value=3.7e-09 Score=84.26 Aligned_cols=53 Identities=34% Similarity=0.509 Sum_probs=46.5
Q ss_pred ccccCceeeecCcceEEEEeeccC---CcccccCCCCCHHHHHHHHHHHHHHhcCC
Q 005737 430 SIYRGVTRHHQHGRWQARIGRVAG---NKDLYLGTFSTQEEAAEAYDIAAIKFRGV 482 (680)
Q Consensus 430 SkYRGV~r~~~~GKW~ArIr~~~~---gKriyLGtFdTeEEAArAYD~AAikl~G~ 482 (680)
|+|+||++++..++|+|+|+.... +|.++||.|+++|||++||+.+.++++|+
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSENGKRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCCTTEEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEcccCcccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 579999999999999999975321 48999999999999999999999999874
No 9
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=55.82 E-value=26 Score=27.48 Aligned_cols=39 Identities=15% Similarity=0.288 Sum_probs=28.5
Q ss_pred eeEEEEe--cCCccccCcccCCcEEecCccccHHHHHHHHHHHHHhc
Q 005737 341 RYEAHLW--DNSCKKEGQSRKGRQVYLGGYDMEEKAARAYDLAALKY 385 (680)
Q Consensus 341 RW~AeI~--~~s~~~~~~~rkGkri~LGtFdTeEeAARAYD~AAlkl 385 (680)
+|...|. ++. +.+.++++-+.|.|..||-.+...+...+
T Consensus 1 ~w~~~v~g~~~~------~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDE------TGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECC------CCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5777772 321 33557888999999999999988876654
No 10
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=52.11 E-value=90 Score=31.39 Aligned_cols=133 Identities=14% Similarity=0.183 Sum_probs=79.6
Q ss_pred ccccccceeecCCCeeEEEEecCCccccCcccCCcEEecCccccHHHHHHHHHHHHHhccCCC--c--ccCCCcchhhhh
Q 005737 327 TSQYRGVTRHRWTGRYEAHLWDNSCKKEGQSRKGRQVYLGGYDMEEKAARAYDLAALKYWGPS--T--HINFPLENYQKE 402 (680)
Q Consensus 327 tS~YRGVrrrk~tGRW~AeI~~~s~~~~~~~rkGkri~LGtFdTeEeAARAYD~AAlkl~G~~--A--~lNFPls~YeeE 402 (680)
..+|.||..|-..-+=.+-|+. .||-+--| ..++|+|..|-++.+..+.... . ..+|.+.. .
T Consensus 33 P~~fpgli~Rl~~Pk~t~lIF~----------SGKiv~tG-aks~~~a~~a~~~~~~~L~~~g~~~~~~~~~~i~N---I 98 (174)
T cd04518 33 PDQFPGLVYRLEDPKIAALIFR----------SGKMVCTG-AKSVEDLHRAVKEIIKKLKDYGIKVIEKPEIKVQN---I 98 (174)
T ss_pred CCcCcEEEEEccCCcEEEEEEC----------CCeEEEEc-cCCHHHHHHHHHHHHHHHHhcCCCccCCCceEEEE---E
Confidence 3579999999886677788876 36655444 5788899999988877765322 1 11222111 0
Q ss_pred HHH--H-hhhhhhhHHhhhcccccCccCCcccccCceeeecCcceEEEEeeccCCcccccCCCCCHHHHHHHHHHHHHHh
Q 005737 403 LEE--M-KNMNRQEYVAHLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKF 479 (680)
Q Consensus 403 LeE--L-r~mTreE~VaaLRRkssg~sr~tSkYRGV~r~~~~GKW~ArIr~~~~gKriyLGtFdTeEEAArAYD~AAikl 479 (680)
+.. + ..+.-+......+.- .=.-.+|.|+.++-..-|=.+-| ...||-+..|. .++||+.+|.++-...|
T Consensus 99 Vas~~l~~~i~L~~la~~~~~~----~YePe~fpglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l 171 (174)
T cd04518 99 VASADLGREVNLDAIAIGLPNA----EYEPEQFPGLVYRLDEPKVVLLL--FSSGKMVITGA-KSEEDAKRAVEKLLSRL 171 (174)
T ss_pred EEEEEcCCccCHHHHHhhCCCC----ccCcccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 000 0 001111111122211 11235688998665555566666 47888888887 89999999998877665
Q ss_pred c
Q 005737 480 R 480 (680)
Q Consensus 480 ~ 480 (680)
.
T Consensus 172 ~ 172 (174)
T cd04518 172 K 172 (174)
T ss_pred h
Confidence 4
No 11
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=50.80 E-value=88 Score=31.39 Aligned_cols=126 Identities=23% Similarity=0.233 Sum_probs=76.2
Q ss_pred ccccceeecCCCeeEEEEecCCccccCcccCCcEEecCccccHHHHHHHHHHHHHhcc--CCCc--ccCCCcch------
Q 005737 329 QYRGVTRHRWTGRYEAHLWDNSCKKEGQSRKGRQVYLGGYDMEEKAARAYDLAALKYW--GPST--HINFPLEN------ 398 (680)
Q Consensus 329 ~YRGVrrrk~tGRW~AeI~~~s~~~~~~~rkGkri~LGtFdTeEeAARAYD~AAlkl~--G~~A--~lNFPls~------ 398 (680)
+|.||..|-..-+=.+-||.+ ||-+ +=...++|+|.+|.++.+..+. |-.. ..||-+..
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~s----------GKiv-iTGaks~~~~~~a~~~~~~~l~~~g~~~~~~~~f~v~nIvat~~ 103 (174)
T cd04517 35 RYPKVTMRLREPRATASVWSS----------GKIT-ITGATSEEEAKQAARRAARLLQKLGFKVVRFSNFRVVNVLATCS 103 (174)
T ss_pred CCCEEEEEecCCcEEEEEECC----------CeEE-EEccCCHHHHHHHHHHHHHHHHHcCCCcccCCceEEEEEEEEEe
Confidence 899999998877878888773 6544 4456889999999998877663 2111 12222210
Q ss_pred --hhhhHHHHhhhhhhhHHhhhcccccCccCCcccccCceeeecCcceEEEEeeccCCcccccCCCCCHHHHHHHHHHHH
Q 005737 399 --YQKELEEMKNMNRQEYVAHLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAA 476 (680)
Q Consensus 399 --YeeELeELr~mTreE~VaaLRRkssg~sr~tSkYRGV~r~~~~GKW~ArIr~~~~gKriyLGtFdTeEEAArAYD~AA 476 (680)
+.-.|+.+... ..+.-. =.-..|.|+.++-..-+=.+.| ...||-+..|. .++||+.+|+++-.
T Consensus 104 ~~~~i~L~~la~~-------~~~~~~----YePE~fPgliyr~~~p~~t~lI--F~sGkivitGa-ks~~~~~~a~~~i~ 169 (174)
T cd04517 104 MPFPIRLDELAAK-------NRSSAS----YEPELHPGVVYRITGPRATLSI--FSTGSVTVTGA-RSMEDVREAVEKIY 169 (174)
T ss_pred CCCcccHHHHHHh-------chhhcE----eCCccCCEEEEEECCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHH
Confidence 01112222111 111111 1124588998665444455556 57888888887 79999999987765
Q ss_pred HHh
Q 005737 477 IKF 479 (680)
Q Consensus 477 ikl 479 (680)
-.+
T Consensus 170 pil 172 (174)
T cd04517 170 PIV 172 (174)
T ss_pred HHH
Confidence 433
No 12
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=42.25 E-value=1.9e+02 Score=28.98 Aligned_cols=128 Identities=20% Similarity=0.220 Sum_probs=77.4
Q ss_pred ccccccceeecCCCeeEEEEecCCccccCcccCCcEEecCccccHHHHHHHHHHHHHhcc--CCCc--ccCCCcch----
Q 005737 327 TSQYRGVTRHRWTGRYEAHLWDNSCKKEGQSRKGRQVYLGGYDMEEKAARAYDLAALKYW--GPST--HINFPLEN---- 398 (680)
Q Consensus 327 tS~YRGVrrrk~tGRW~AeI~~~s~~~~~~~rkGkri~LGtFdTeEeAARAYD~AAlkl~--G~~A--~lNFPls~---- 398 (680)
..+|.||..|...-+=.+-|+. .||-+--|. .++|+|.+|.++.+..+. |-.. ..||-+..
T Consensus 33 Pe~fpgli~R~~~P~~t~lIf~----------sGKivitGa-ks~~~~~~a~~~~~~~L~~~g~~~~~~~~~~v~NIvas 101 (174)
T cd00652 33 PKRFPGVIMRLREPKTTALIFS----------SGKMVITGA-KSEEDAKLAARKYARILQKLGFPVEKFPEFKVQNIVAS 101 (174)
T ss_pred CCccceEEEEcCCCcEEEEEEC----------CCEEEEEec-CCHHHHHHHHHHHHHHHHHcCCCccccCceEEEEEEEE
Confidence 3579999999886787888877 366655554 577788888888877663 3111 12332110
Q ss_pred ----hhhhHHHHhhhhhhhHHhhhcccccCccCCcccccCceeeecCcceEEEEeeccCCcccccCCCCCHHHHHHHHHH
Q 005737 399 ----YQKELEEMKNMNRQEYVAHLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDI 474 (680)
Q Consensus 399 ----YeeELeELr~mTreE~VaaLRRkssg~sr~tSkYRGV~r~~~~GKW~ArIr~~~~gKriyLGtFdTeEEAArAYD~ 474 (680)
+.-.|+.+. ...+.. ..=.-..|.|+.++-..-|=..-| ...||-+..|. .+++|+.+|+++
T Consensus 102 ~~l~~~i~L~~la--------~~~~~~---~~YePe~fpgli~r~~~pk~t~lI--F~sGkvvitGa-ks~~~~~~a~~~ 167 (174)
T cd00652 102 CDLGFPIRLEELA--------LKHPEN---ASYEPELFPGLIYRMDEPKVVLLI--FVSGKIVITGA-KSREDIYEAVEK 167 (174)
T ss_pred EECCCcccHHHHH--------hhhhcc---cEECCccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHH
Confidence 111122221 111100 001124588998665555556666 47888888887 899999999987
Q ss_pred HHHHh
Q 005737 475 AAIKF 479 (680)
Q Consensus 475 AAikl 479 (680)
-...|
T Consensus 168 i~~~L 172 (174)
T cd00652 168 IYPIL 172 (174)
T ss_pred HHHHH
Confidence 66544
No 13
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=39.76 E-value=2e+02 Score=28.91 Aligned_cols=126 Identities=17% Similarity=0.217 Sum_probs=74.4
Q ss_pred ccccccceeecCCCeeEEEEecCCccccCcccCCcEEecCccccHHHHHHHHHHHHHhcc--CCC-cccCCCcch-----
Q 005737 327 TSQYRGVTRHRWTGRYEAHLWDNSCKKEGQSRKGRQVYLGGYDMEEKAARAYDLAALKYW--GPS-THINFPLEN----- 398 (680)
Q Consensus 327 tS~YRGVrrrk~tGRW~AeI~~~s~~~~~~~rkGkri~LGtFdTeEeAARAYD~AAlkl~--G~~-A~lNFPls~----- 398 (680)
..+|.||..|...-|=.+-|+. .||-+--|. .++|+|.+|.++.+..+. |-. ...||-...
T Consensus 33 Pe~fpgli~Rl~~Pk~t~lIF~----------SGKiviTGa-ks~e~a~~a~~~i~~~L~~~g~~~~~~~~~v~Nivat~ 101 (174)
T cd04516 33 PKRFAAVIMRIREPKTTALIFS----------SGKMVCTGA-KSEDDSKLAARKYARIIQKLGFPAKFTDFKIQNIVGSC 101 (174)
T ss_pred CccCcEEEEEeCCCcEEEEEEC----------CCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCCCCCceEEEEEEEEE
Confidence 3578999999887788888877 377665565 577888888888877663 311 112222110
Q ss_pred ---hhhhHHHHhhhhhhhHHhhhcccccCccCCcccccCceeeecCcceEEEEeeccCCcccccCCCCCHHHHHHHHHHH
Q 005737 399 ---YQKELEEMKNMNRQEYVAHLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIA 475 (680)
Q Consensus 399 ---YeeELeELr~mTreE~VaaLRRkssg~sr~tSkYRGV~r~~~~GKW~ArIr~~~~gKriyLGtFdTeEEAArAYD~A 475 (680)
+.-.|+.+.... ...- .=.-..|.|+.++-..-|=...| ...||-+..|. .++||+.+|++.-
T Consensus 102 ~l~~~i~L~~la~~~-------~~~~----~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~a~~~i 167 (174)
T cd04516 102 DVKFPIRLEGLAHAH-------KQFS----SYEPELFPGLIYRMVKPKIVLLI--FVSGKIVLTGA-KSREEIYQAFENI 167 (174)
T ss_pred ECCCcccHHHHHHhC-------hhcc----EeCCccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHH
Confidence 011122222110 0000 11124588998654443434444 57888888887 8899999998765
Q ss_pred HH
Q 005737 476 AI 477 (680)
Q Consensus 476 Ai 477 (680)
.-
T Consensus 168 ~p 169 (174)
T cd04516 168 YP 169 (174)
T ss_pred HH
Confidence 43
No 14
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=39.38 E-value=71 Score=25.01 Aligned_cols=38 Identities=21% Similarity=0.242 Sum_probs=27.8
Q ss_pred ceEEEEe--eccCC--cccccCCCCCHHHHHHHHHHHHHHhc
Q 005737 443 RWQARIG--RVAGN--KDLYLGTFSTQEEAAEAYDIAAIKFR 480 (680)
Q Consensus 443 KW~ArIr--~~~~g--KriyLGtFdTeEEAArAYD~AAikl~ 480 (680)
+|..+|. ....| ++++-+-|.|..||-.+.......+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5777772 33244 46788889999999999988776653
No 15
>PLN00062 TATA-box-binding protein; Provisional
Probab=39.02 E-value=2e+02 Score=29.17 Aligned_cols=127 Identities=17% Similarity=0.168 Sum_probs=75.3
Q ss_pred cccccceeecCCCeeEEEEecCCccccCcccCCcEEecCccccHHHHHHHHHHHHHhccCCCccc---CCCcch------
Q 005737 328 SQYRGVTRHRWTGRYEAHLWDNSCKKEGQSRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHI---NFPLEN------ 398 (680)
Q Consensus 328 S~YRGVrrrk~tGRW~AeI~~~s~~~~~~~rkGkri~LGtFdTeEeAARAYD~AAlkl~G~~A~l---NFPls~------ 398 (680)
.+|.||..|...-|=.+-|+. .||-+-- ...++|+|.+|.++.+..+..-.-.. ||-+..
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~----------SGKiviT-Gaks~e~a~~a~~~~~~~L~~lg~~~~~~~f~v~NIvas~~ 102 (179)
T PLN00062 34 KRFAAVIMRIREPKTTALIFA----------SGKMVCT-GAKSEHDSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCD 102 (179)
T ss_pred ccCcEEEEEeCCCcEEEEEEC----------CCeEEEE-ecCCHHHHHHHHHHHHHHHHHcCCCcCCCccEEEEEEEEEE
Confidence 469999999887787888876 3665444 45788899999998877763221112 222110
Q ss_pred --hhhhHHHHhhhhhhhHHhhhcccccCccCCcccccCceeeecCcceEEEEeeccCCcccccCCCCCHHHHHHHHHHHH
Q 005737 399 --YQKELEEMKNMNRQEYVAHLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAA 476 (680)
Q Consensus 399 --YeeELeELr~mTreE~VaaLRRkssg~sr~tSkYRGV~r~~~~GKW~ArIr~~~~gKriyLGtFdTeEEAArAYD~AA 476 (680)
+.-.|+.+... +.+.- .=.-..|.|+.++-..-|=..-| ...||-+..|. .++||+.+|.+.-.
T Consensus 103 l~~~i~L~~la~~-------~~~~~----~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~ai~~i~ 168 (179)
T PLN00062 103 VKFPIRLEGLAYA-------HGAFS----SYEPELFPGLIYRMKQPKIVLLI--FVSGKIVITGA-KVREEIYTAFENIY 168 (179)
T ss_pred CCCcccHHHHHHh-------chhhc----ccCcccCceEEEEeCCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHH
Confidence 01112222111 01111 11224688988654444445555 57888888887 78999999987665
Q ss_pred HHh
Q 005737 477 IKF 479 (680)
Q Consensus 477 ikl 479 (680)
-.|
T Consensus 169 p~L 171 (179)
T PLN00062 169 PVL 171 (179)
T ss_pred HHH
Confidence 444
No 16
>PRK00394 transcription factor; Reviewed
Probab=38.13 E-value=1.7e+02 Score=29.58 Aligned_cols=135 Identities=15% Similarity=0.188 Sum_probs=79.6
Q ss_pred ccccccceeecCCCeeEEEEecCCccccCcccCCcEEecCccccHHHHHHHHHHHHHhcc--CCCc--ccCCCcchhhhh
Q 005737 327 TSQYRGVTRHRWTGRYEAHLWDNSCKKEGQSRKGRQVYLGGYDMEEKAARAYDLAALKYW--GPST--HINFPLENYQKE 402 (680)
Q Consensus 327 tS~YRGVrrrk~tGRW~AeI~~~s~~~~~~~rkGkri~LGtFdTeEeAARAYD~AAlkl~--G~~A--~lNFPls~YeeE 402 (680)
..+|-||..|-..-+=.+-|+. .||-+--|.. ++|+|.+|-++.+..+. |-.. ..+|-+..--..
T Consensus 32 Pe~fpgli~Rl~~Pk~t~lIf~----------sGKiv~tGa~-S~~~a~~a~~~~~~~l~~~g~~~~~~~~~~i~NiVas 100 (179)
T PRK00394 32 PEQFPGLVYRLEDPKIAALIFR----------SGKVVCTGAK-SVEDLHEAVKIIIKKLKELGIKVIDEPEIKVQNIVAS 100 (179)
T ss_pred cccCceEEEEecCCceEEEEEc----------CCcEEEEccC-CHHHHHHHHHHHHHHHHHcCCCccCCCceEEEEEEEE
Confidence 3479999999887788888877 4777766764 66678888888766653 2111 112221110000
Q ss_pred HHHH-hhhhhhhHHhhh--cccccCccCCcccccCceeeecCcceEEEEeeccCCcccccCCCCCHHHHHHHHHHHHHHh
Q 005737 403 LEEM-KNMNRQEYVAHL--RRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKF 479 (680)
Q Consensus 403 LeEL-r~mTreE~VaaL--RRkssg~sr~tSkYRGV~r~~~~GKW~ArIr~~~~gKriyLGtFdTeEEAArAYD~AAikl 479 (680)
..+ ..+.-++....+ +.-. =.-..|.|+.++-..-|=..-| ...||-+..|. .++||+.+|.++-...|
T Consensus 101 -~~l~~~i~L~~la~~~~~~~~~----YePe~fPglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l 172 (179)
T PRK00394 101 -ADLGVELNLNAIAIGLGLENIE----YEPEQFPGLVYRLDDPKVVVLL--FGSGKLVITGA-KSEEDAEKAVEKILEKL 172 (179)
T ss_pred -EEcCCeEcHHHHHHhcCcCCcE----ECcccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 000 001111111111 1111 1234688998665566667777 47788888887 89999999998877665
Q ss_pred c
Q 005737 480 R 480 (680)
Q Consensus 480 ~ 480 (680)
.
T Consensus 173 ~ 173 (179)
T PRK00394 173 E 173 (179)
T ss_pred H
Confidence 4
No 17
>PF08168 NUC205: NUC205 domain; InterPro: IPR012584 This domain is found in a novel family of nucleolar proteins [].; GO: 0005634 nucleus
Probab=22.56 E-value=16 Score=29.47 Aligned_cols=17 Identities=53% Similarity=0.921 Sum_probs=14.1
Q ss_pred CCCcccCCCCCchhHHHHh
Q 005737 82 PLPVMPLKSDGSLCIMEAL 100 (680)
Q Consensus 82 ~~~~mplksdgsl~i~ea~ 100 (680)
.++.|-|-||| ||.|.|
T Consensus 16 ~isL~~L~SDG--Ciyetl 32 (44)
T PF08168_consen 16 FISLMSLSSDG--CIYETL 32 (44)
T ss_pred eEEEEEeccCC--ceeeee
Confidence 36678899999 999965
No 18
>PF12286 DUF3622: Protein of unknown function (DUF3622); InterPro: IPR022069 This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif.
Probab=20.63 E-value=1.1e+02 Score=27.08 Aligned_cols=36 Identities=19% Similarity=0.386 Sum_probs=23.6
Q ss_pred ceeeecCcceEEEEeeccCCccccc----CCCCCHHHHHH
Q 005737 435 VTRHHQHGRWQARIGRVAGNKDLYL----GTFSTQEEAAE 470 (680)
Q Consensus 435 V~r~~~~GKW~ArIr~~~~gKriyL----GtFdTeEEAAr 470 (680)
++.....+.|-|+|.|-+..++..+ --|+||+||..
T Consensus 9 ~rv~q~~~~W~aEItR~vTsrkTvVSK~~~GF~SEaeAq~ 48 (71)
T PF12286_consen 9 FRVTQKRNGWTAEITRRVTSRKTVVSKRQDGFASEAEAQA 48 (71)
T ss_pred EEEEecCCceeeeeeeeecCceeEEEecccCcccHHHHHH
Confidence 3434456789999976665544333 35899998653
Done!