Query 038243
Match_columns 680
No_of_seqs 378 out of 1651
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 09:01:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038243.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038243hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00380 AP2 DNA-binding dom 99.7 1.1E-17 2.3E-22 137.7 6.4 63 353-416 1-63 (64)
2 cd00018 AP2 DNA-binding domain 99.7 1.8E-17 4E-22 134.6 6.5 61 352-413 1-61 (61)
3 cd00018 AP2 DNA-binding domain 99.7 4.1E-17 8.8E-22 132.6 6.2 61 253-319 1-61 (61)
4 smart00380 AP2 DNA-binding dom 99.7 5.6E-17 1.2E-21 133.4 6.2 64 254-323 1-64 (64)
5 PHA00280 putative NHN endonucl 99.4 5.3E-13 1.1E-17 123.9 6.5 103 298-407 13-119 (121)
6 PHA00280 putative NHN endonucl 99.1 1.5E-10 3.2E-15 107.7 6.1 58 248-313 62-119 (121)
7 PF00847 AP2: AP2 domain; Int 98.9 3.2E-09 6.8E-14 84.4 5.2 53 352-404 1-56 (56)
8 PF00847 AP2: AP2 domain; Int 98.8 5.2E-09 1.1E-13 83.2 5.3 56 253-310 1-56 (56)
9 PF14657 Integrase_AP2: AP2-li 61.0 15 0.00032 28.8 4.1 39 266-307 1-41 (46)
10 PF15105 TMEM61: TMEM61 protei 53.9 7.3 0.00016 39.5 1.6 34 619-658 86-120 (198)
11 cd04518 TBP_archaea archaeal T 53.1 84 0.0018 31.6 8.8 134 253-402 34-172 (174)
12 cd00652 TBP_TLF TATA box bindi 52.4 77 0.0017 31.6 8.5 135 253-401 34-172 (174)
13 cd04517 TLF TBP-like factors ( 51.2 80 0.0017 31.6 8.4 133 254-400 35-171 (174)
14 PF14657 Integrase_AP2: AP2-li 39.1 60 0.0013 25.4 4.3 38 365-402 1-42 (46)
15 PLN00062 TATA-box-binding prot 33.7 2.4E+02 0.0051 28.6 8.6 133 254-401 35-171 (179)
16 cd04516 TBP_eukaryotes eukaryo 26.5 3.7E+02 0.0081 27.0 8.6 132 254-399 35-169 (174)
17 PRK00394 transcription factor; 26.4 3.2E+02 0.0069 27.6 8.1 136 254-402 34-173 (179)
18 COG4907 Predicted membrane pro 24.8 45 0.00098 38.6 2.0 16 375-390 418-433 (595)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.71 E-value=1.1e-17 Score=137.68 Aligned_cols=63 Identities=51% Similarity=0.787 Sum_probs=58.8
Q ss_pred ccccceeeccCCceEEEeccccCCcccccCCCCCHHHHHHHHHHHHHHhcCCCCccCCCCCccc
Q 038243 353 IYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFRGLNAVTNFDMTRYD 416 (680)
Q Consensus 353 ~YRGV~r~r~~GKW~AeIr~~~~gKri~LGTFdTeEEAArAYD~AAiklrG~~A~tNFp~s~y~ 416 (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 5899987 46799999998777899999999999999999999999999999999999999986
No 2
>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=1.8e-17 Score=134.56 Aligned_cols=61 Identities=51% Similarity=0.817 Sum_probs=55.6
Q ss_pred cccccceeeccCCceEEEeccccCCcccccCCCCCHHHHHHHHHHHHHHhcCCCCccCCCCC
Q 038243 352 SIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFRGLNAVTNFDMT 413 (680)
Q Consensus 352 S~YRGV~r~r~~GKW~AeIr~~~~gKri~LGTFdTeEEAArAYD~AAiklrG~~A~tNFp~s 413 (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 6899998765 699999997655589999999999999999999999999999999999964
No 3
>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=99.68 E-value=4.1e-17 Score=132.56 Aligned_cols=61 Identities=48% Similarity=0.740 Sum_probs=56.7
Q ss_pred cceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhcccccccccCCCC
Q 038243 253 SIYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYWGTTTTTNFPIS 319 (680)
Q Consensus 253 S~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~G~~A~lNFP~s 319 (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 99999999873 458999999999999999999999999999999999974
No 4
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.68 E-value=5.6e-17 Score=133.43 Aligned_cols=64 Identities=42% Similarity=0.754 Sum_probs=58.8
Q ss_pred ceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhcccccccccCCCCcchh
Q 038243 254 IYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYWGTTTTTNFPISNYEK 323 (680)
Q Consensus 254 ~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~G~~A~lNFP~sdYee 323 (680)
+||||+++++ |||+|+|+++. .++.++||+|+|+||||+|||+|+++++|..+.+|||.++|+.
T Consensus 1 ~~kGV~~~~~-gkw~A~I~~~~-----~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~~ 64 (64)
T smart00380 1 KYRGVRQRPW-GKWVAEIRDPS-----KGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYDS 64 (64)
T ss_pred CEeeEEeCCC-CeEEEEEEecC-----CCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCCC
Confidence 5999999888 99999999863 3588999999999999999999999999999999999999863
No 5
>PHA00280 putative NHN endonuclease
Probab=99.38 E-value=5.3e-13 Score=123.92 Aligned_cols=103 Identities=13% Similarity=0.112 Sum_probs=80.9
Q ss_pred HHHHHHhhhcccccc---cccCCCC-cchhhHHHhhhhhhhhHHHhhhcccCCcccCccccccceeeccCCceEEEeccc
Q 038243 298 RAYDLAALKYWGTTT---TTNFPIS-NYEKEVEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRV 373 (680)
Q Consensus 298 rAYD~AAlkl~G~~A---~lNFP~s-dYeeELeELRemSReE~VAsLRRrSsG~SRgtS~YRGV~r~r~~GKW~AeIr~~ 373 (680)
++.-.+.+...|+-. .+.+... .....+++|+.+++.|+..+.+.. +.++|+|+||+|++..+||+|+| .
T Consensus 13 ~~Hrlvw~~~~G~~P~g~~VdHidg~~~dnri~NLr~~T~~eN~~N~~~~----~~N~SG~kGV~~~k~~~kw~A~I--~ 86 (121)
T PHA00280 13 RRHIQVWEAANGPIPKGYYIDHIDGNPLNDALDNLRLALPKENSWNMKTP----KSNTSGLKGLSWSKEREMWRGTV--T 86 (121)
T ss_pred hHhHhhhHHHHCCCCCCCEEEcCCCCCCCCcHHHhhhcCHHHHhcccCCC----CCCCCCCCeeEEecCCCeEEEEE--E
Confidence 445556666666432 1222221 234578899999999999887654 56889999999999999999999 5
Q ss_pred cCCcccccCCCCCHHHHHHHHHHHHHHhcCCCCc
Q 038243 374 AGNKDLYLGTFSTQEEAAEAYDIAAIKFRGLNAV 407 (680)
Q Consensus 374 ~~gKri~LGTFdTeEEAArAYD~AAiklrG~~A~ 407 (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 7899999999999999999997 78899998875
No 6
>PHA00280 putative NHN endonuclease
Probab=99.08 E-value=1.5e-10 Score=107.74 Aligned_cols=58 Identities=14% Similarity=0.090 Sum_probs=51.6
Q ss_pred CCCCccceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhccccccc
Q 038243 248 FGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYWGTTTT 313 (680)
Q Consensus 248 ~~qrTS~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~G~~A~ 313 (680)
...++|+|+||+|++.++||+|+|+.+ +|+.+||.|+++|+|+.||+ ++.+|+|++|.
T Consensus 62 ~~~N~SG~kGV~~~k~~~kw~A~I~~~-------gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 62 PKSNTSGLKGLSWSKEREMWRGTVTAE-------GKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred CCCCCCCCCeeEEecCCCeEEEEEEEC-------CEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 346789999999999999999999766 48889999999999999997 77899998875
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=98.86 E-value=3.2e-09 Score=84.43 Aligned_cols=53 Identities=34% Similarity=0.503 Sum_probs=46.7
Q ss_pred cccccceeeccCCceEEEeccccC---CcccccCCCCCHHHHHHHHHHHHHHhcCC
Q 038243 352 SIYRGVTRHHQHGRWQARIGRVAG---NKDLYLGTFSTQEEAAEAYDIAAIKFRGL 404 (680)
Q Consensus 352 S~YRGV~r~r~~GKW~AeIr~~~~---gKri~LGTFdTeEEAArAYD~AAiklrG~ 404 (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 689999999999999999976321 49999999999999999999999999874
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=98.83 E-value=5.2e-09 Score=83.21 Aligned_cols=56 Identities=30% Similarity=0.354 Sum_probs=47.5
Q ss_pred cceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhcccc
Q 038243 253 SIYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYWGT 310 (680)
Q Consensus 253 S~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~G~ 310 (680)
|+|+||++++.+++|+|+|++... .+++++.++|.|+++|||++|++.++++++|+
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~--~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSE--NGKRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCC--TTEEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEccc--CcccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 689999999999999999988421 12348889999999999999999999999874
No 9
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=61.04 E-value=15 Score=28.82 Aligned_cols=39 Identities=13% Similarity=0.377 Sum_probs=29.0
Q ss_pred ceEEEEe--cCCcccCCcccccccCCCCCHHHHHHHHHHHhhhc
Q 038243 266 RYEAHLW--DNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKY 307 (680)
Q Consensus 266 RW~AeI~--d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl 307 (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 5777773 431 36667788899999999999988765554
No 10
>PF15105 TMEM61: TMEM61 protein family
Probab=53.89 E-value=7.3 Score=39.46 Aligned_cols=34 Identities=35% Similarity=0.579 Sum_probs=26.2
Q ss_pred CCCccc-cccceecccccchhhhhhccCCCCCCcccccccc
Q 038243 619 SSDPYQ-ARNLYYLPQQQSSASLVKAAGAYDNWVPTAVPTL 658 (680)
Q Consensus 619 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~ 658 (680)
--|||| .|+||||.-.++- --.|..|..++|||-
T Consensus 86 r~d~y~lsrDLyyltvE~~e------K~scr~p~~~~iPTY 120 (198)
T PF15105_consen 86 RWDPYHLSRDLYYLTVESSE------KESCRTPKVVAIPTY 120 (198)
T ss_pred CCCcccCCcccceEeecccc------ccccCCCccccccch
Confidence 468999 9999999866643 123668999999984
No 11
>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=53.07 E-value=84 Score=31.57 Aligned_cols=134 Identities=12% Similarity=0.125 Sum_probs=79.4
Q ss_pred cceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhccccc--c--cccCCCCcchhhHHHh
Q 038243 253 SIYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYWGTT--T--TTNFPISNYEKEVEEM 328 (680)
Q Consensus 253 S~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~G~~--A--~lNFP~sdYeeELeEL 328 (680)
.+|.||..|-..-+=.+.|+..+ +...=...++|+|..|-++.+..+.-.. . ..+|-..+.-... .|
T Consensus 34 ~~fpgli~Rl~~Pk~t~lIF~SG--------Kiv~tGaks~~~a~~a~~~~~~~L~~~g~~~~~~~~~~i~NIVas~-~l 104 (174)
T cd04518 34 DQFPGLVYRLEDPKIAALIFRSG--------KMVCTGAKSVEDLHRAVKEIIKKLKDYGIKVIEKPEIKVQNIVASA-DL 104 (174)
T ss_pred CcCcEEEEEccCCcEEEEEECCC--------eEEEEccCCHHHHHHHHHHHHHHHHhcCCCccCCCceEEEEEEEEE-Ec
Confidence 45999999988778888888763 3334446789999999999887775221 1 1122221110000 00
Q ss_pred h-hhhhhhHHHhhhcccCCcccCccccccceeeccCCceEEEeccccCCcccccCCCCCHHHHHHHHHHHHHHhc
Q 038243 329 K-HMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFR 402 (680)
Q Consensus 329 R-emSReE~VAsLRRrSsG~SRgtS~YRGV~r~r~~GKW~AeIr~~~~gKri~LGTFdTeEEAArAYD~AAiklr 402 (680)
. ....+.....++ ...=.-.+|.|+..+-..-|=.+-| ...||-+..|. .++||+.+|.++-...|.
T Consensus 105 ~~~i~L~~la~~~~----~~~YePe~fpglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 172 (174)
T cd04518 105 GREVNLDAIAIGLP----NAEYEPEQFPGLVYRLDEPKVVLLL--FSSGKMVITGA-KSEEDAKRAVEKLLSRLK 172 (174)
T ss_pred CCccCHHHHHhhCC----CCccCcccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHHh
Confidence 0 111111111111 1122346799987665555666666 66777777774 789999999988776654
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=52.41 E-value=77 Score=31.65 Aligned_cols=135 Identities=16% Similarity=0.110 Sum_probs=77.0
Q ss_pred cceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhcc--cccc--cccCCCCcchhhHHHh
Q 038243 253 SIYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYW--GTTT--TTNFPISNYEKEVEEM 328 (680)
Q Consensus 253 S~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~--G~~A--~lNFP~sdYeeELeEL 328 (680)
.+|.||..|...-+=.+-|+.++ +...=.-.++|+|.+|.++.+..+. |-.. ..||-....-.....-
T Consensus 34 e~fpgli~R~~~P~~t~lIf~sG--------KivitGaks~~~~~~a~~~~~~~L~~~g~~~~~~~~~~v~NIvas~~l~ 105 (174)
T cd00652 34 KRFPGVIMRLREPKTTALIFSSG--------KMVITGAKSEEDAKLAARKYARILQKLGFPVEKFPEFKVQNIVASCDLG 105 (174)
T ss_pred CccceEEEEcCCCcEEEEEECCC--------EEEEEecCCHHHHHHHHHHHHHHHHHcCCCccccCceEEEEEEEEEECC
Confidence 35999999988788888998773 3333234588999999999887773 3211 1222221110000000
Q ss_pred hhhhhhhHHHhhhcccCCcccCccccccceeeccCCceEEEeccccCCcccccCCCCCHHHHHHHHHHHHHHh
Q 038243 329 KHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKF 401 (680)
Q Consensus 329 RemSReE~VAsLRRrSsG~SRgtS~YRGV~r~r~~GKW~AeIr~~~~gKri~LGTFdTeEEAArAYD~AAikl 401 (680)
-....++.....+.. ..=.-.+|.|+..+-..-|=.+-| ...||-+..|. .++||+.+|+++-...|
T Consensus 106 ~~i~L~~la~~~~~~---~~YePe~fpgli~r~~~pk~t~lI--F~sGkvvitGa-ks~~~~~~a~~~i~~~L 172 (174)
T cd00652 106 FPIRLEELALKHPEN---ASYEPELFPGLIYRMDEPKVVLLI--FVSGKIVITGA-KSREDIYEAVEKIYPIL 172 (174)
T ss_pred CcccHHHHHhhhhcc---cEECCccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 011111111111111 112335699987665555666666 66777777774 68999999988765544
No 13
>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=51.19 E-value=80 Score=31.63 Aligned_cols=133 Identities=23% Similarity=0.147 Sum_probs=75.9
Q ss_pred ceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhcc--cccc--cccCCCCcchhhHHHhh
Q 038243 254 IYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYW--GTTT--TTNFPISNYEKEVEEMK 329 (680)
Q Consensus 254 ~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~--G~~A--~lNFP~sdYeeELeELR 329 (680)
+|.||..|-..-|=.+-||.++ +...=...++|+|++|.++.+..+. |-.. ..||-....-.....--
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~sG--------KiviTGaks~~~~~~a~~~~~~~l~~~g~~~~~~~~f~v~nIvat~~~~~ 106 (174)
T cd04517 35 RYPKVTMRLREPRATASVWSSG--------KITITGATSEEEAKQAARRAARLLQKLGFKVVRFSNFRVVNVLATCSMPF 106 (174)
T ss_pred CCCEEEEEecCCcEEEEEECCC--------eEEEEccCCHHHHHHHHHHHHHHHHHcCCCcccCCceEEEEEEEEEeCCC
Confidence 6999999988788899998873 3444456799999999999887773 3211 12222211000000000
Q ss_pred hhhhhhHHHhhhcccCCcccCccccccceeeccCCceEEEeccccCCcccccCCCCCHHHHHHHHHHHHHH
Q 038243 330 HMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIK 400 (680)
Q Consensus 330 emSReE~VAsLRRrSsG~SRgtS~YRGV~r~r~~GKW~AeIr~~~~gKri~LGTFdTeEEAArAYD~AAik 400 (680)
...-++....-.+. ..=.-..|.|+..+-..-|=.+.| ...||-+-.|. .++||+.+|++.-.-.
T Consensus 107 ~i~L~~la~~~~~~---~~YePE~fPgliyr~~~p~~t~lI--F~sGkivitGa-ks~~~~~~a~~~i~pi 171 (174)
T cd04517 107 PIRLDELAAKNRSS---ASYEPELHPGVVYRITGPRATLSI--FSTGSVTVTGA-RSMEDVREAVEKIYPI 171 (174)
T ss_pred cccHHHHHHhchhh---cEeCCccCCEEEEEECCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHH
Confidence 11111111100011 111235699987655444555555 66777777774 6889999998765544
No 14
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=39.07 E-value=60 Score=25.40 Aligned_cols=38 Identities=21% Similarity=0.246 Sum_probs=27.7
Q ss_pred ceEEEec--cc--cCCcccccCCCCCHHHHHHHHHHHHHHhc
Q 038243 365 RWQARIG--RV--AGNKDLYLGTFSTQEEAAEAYDIAAIKFR 402 (680)
Q Consensus 365 KW~AeIr--~~--~~gKri~LGTFdTeEEAArAYD~AAiklr 402 (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 22 23467899999999999999887766543
No 15
>PLN00062 TATA-box-binding protein; Provisional
Probab=33.73 E-value=2.4e+02 Score=28.64 Aligned_cols=133 Identities=15% Similarity=0.092 Sum_probs=74.9
Q ss_pred ceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhcccccccccC---CCCcchhhHHHhh-
Q 038243 254 IYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYWGTTTTTNF---PISNYEKEVEEMK- 329 (680)
Q Consensus 254 ~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~G~~A~lNF---P~sdYeeELeELR- 329 (680)
+|.||..|...-|=.+-|+..+ +...=...++|+|.+|.++.+..+.--.-..+| -..+.-... .|.
T Consensus 35 ~fpgli~Rl~~Pk~t~lIF~SG--------KiviTGaks~e~a~~a~~~~~~~L~~lg~~~~~~~f~v~NIvas~-~l~~ 105 (179)
T PLN00062 35 RFAAVIMRIREPKTTALIFASG--------KMVCTGAKSEHDSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSC-DVKF 105 (179)
T ss_pred cCcEEEEEeCCCcEEEEEECCC--------eEEEEecCCHHHHHHHHHHHHHHHHHcCCCcCCCccEEEEEEEEE-ECCC
Confidence 5899999888788888998763 333334578999999999988777422112222 211110000 000
Q ss_pred hhhhhhHHHhhhcccCCcccCccccccceeeccCCceEEEeccccCCcccccCCCCCHHHHHHHHHHHHHHh
Q 038243 330 HMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKF 401 (680)
Q Consensus 330 emSReE~VAsLRRrSsG~SRgtS~YRGV~r~r~~GKW~AeIr~~~~gKri~LGTFdTeEEAArAYD~AAikl 401 (680)
....+.. +.+ ......=.-..|.|+..+-..-|=..-| ...||-+..|. .++||+.+|.+.-.-.|
T Consensus 106 ~i~L~~l-a~~--~~~~~~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~ai~~i~p~L 171 (179)
T PLN00062 106 PIRLEGL-AYA--HGAFSSYEPELFPGLIYRMKQPKIVLLI--FVSGKIVITGA-KVREEIYTAFENIYPVL 171 (179)
T ss_pred cccHHHH-HHh--chhhcccCcccCceEEEEeCCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 0111111 111 0011112335789987654444455555 67788777774 67889999887655444
No 16
>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=26.55 E-value=3.7e+02 Score=27.04 Aligned_cols=132 Identities=13% Similarity=0.085 Sum_probs=72.2
Q ss_pred ceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhcccccccccCC---CCcchhhHHHhhh
Q 038243 254 IYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYWGTTTTTNFP---ISNYEKEVEEMKH 330 (680)
Q Consensus 254 ~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~G~~A~lNFP---~sdYeeELeELRe 330 (680)
+|.||..|...-|=.+-|+..+ |-.-.|. .++|+|..|.++.+..+.--.-...|+ ..+.-...+.-..
T Consensus 35 ~fpgli~Rl~~Pk~t~lIF~SG-------KiviTGa-ks~e~a~~a~~~i~~~L~~~g~~~~~~~~~v~Nivat~~l~~~ 106 (174)
T cd04516 35 RFAAVIMRIREPKTTALIFSSG-------KMVCTGA-KSEDDSKLAARKYARIIQKLGFPAKFTDFKIQNIVGSCDVKFP 106 (174)
T ss_pred cCcEEEEEeCCCcEEEEEECCC-------eEEEEec-CCHHHHHHHHHHHHHHHHHcCCCCCCCceEEEEEEEEEECCCc
Confidence 5889999988788888998773 3322343 588999999999887774221111222 1111000000001
Q ss_pred hhhhhHHHhhhcccCCcccCccccccceeeccCCceEEEeccccCCcccccCCCCCHHHHHHHHHHHHH
Q 038243 331 MTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAI 399 (680)
Q Consensus 331 mSReE~VAsLRRrSsG~SRgtS~YRGV~r~r~~GKW~AeIr~~~~gKri~LGTFdTeEEAArAYD~AAi 399 (680)
...++... ... ....=.-..|.|+..+-..-|=..-| ...||-+..|. .++||+.+|++.-.-
T Consensus 107 i~L~~la~-~~~--~~~~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~a~~~i~p 169 (174)
T cd04516 107 IRLEGLAH-AHK--QFSSYEPELFPGLIYRMVKPKIVLLI--FVSGKIVLTGA-KSREEIYQAFENIYP 169 (174)
T ss_pred ccHHHHHH-hCh--hccEeCCccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHH
Confidence 11111111 000 11112345699987654444444444 67788777774 688889998876443
No 17
>PRK00394 transcription factor; Reviewed
Probab=26.38 E-value=3.2e+02 Score=27.63 Aligned_cols=136 Identities=12% Similarity=0.135 Sum_probs=77.9
Q ss_pred ceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhcc--cccc--cccCCCCcchhhHHHhh
Q 038243 254 IYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYW--GTTT--TTNFPISNYEKEVEEMK 329 (680)
Q Consensus 254 ~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~--G~~A--~lNFP~sdYeeELeELR 329 (680)
+|.|+..|-..-+=.+.|+.++ |-.-.|. .++|+|.+|-++.+..+. |-.. ..+|-..+.-.....-.
T Consensus 34 ~fpgli~Rl~~Pk~t~lIf~sG-------Kiv~tGa-~S~~~a~~a~~~~~~~l~~~g~~~~~~~~~~i~NiVas~~l~~ 105 (179)
T PRK00394 34 QFPGLVYRLEDPKIAALIFRSG-------KVVCTGA-KSVEDLHEAVKIIIKKLKELGIKVIDEPEIKVQNIVASADLGV 105 (179)
T ss_pred cCceEEEEecCCceEEEEEcCC-------cEEEEcc-CCHHHHHHHHHHHHHHHHHcCCCccCCCceEEEEEEEEEEcCC
Confidence 5899999988788889998773 3333354 478899999888777664 3211 11222211000000000
Q ss_pred hhhhhhHHHhhhcccCCcccCccccccceeeccCCceEEEeccccCCcccccCCCCCHHHHHHHHHHHHHHhc
Q 038243 330 HMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFR 402 (680)
Q Consensus 330 emSReE~VAsLRRrSsG~SRgtS~YRGV~r~r~~GKW~AeIr~~~~gKri~LGTFdTeEEAArAYD~AAiklr 402 (680)
....++....+.. +...=.-.+|.|+..+-..-|=..-| ...||-+..|. .++||+.+|.++....|+
T Consensus 106 ~i~L~~la~~~~~--~~~~YePe~fPglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 173 (179)
T PRK00394 106 ELNLNAIAIGLGL--ENIEYEPEQFPGLVYRLDDPKVVVLL--FGSGKLVITGA-KSEEDAEKAVEKILEKLE 173 (179)
T ss_pred eEcHHHHHHhcCc--CCcEECcccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 1111111111100 11112346799987665566667777 66777777774 689999999988776664
No 18
>COG4907 Predicted membrane protein [Function unknown]
Probab=24.80 E-value=45 Score=38.64 Aligned_cols=16 Identities=31% Similarity=0.117 Sum_probs=8.8
Q ss_pred CCcccccCCCCCHHHH
Q 038243 375 GNKDLYLGTFSTQEEA 390 (680)
Q Consensus 375 ~gKri~LGTFdTeEEA 390 (680)
+.|.+.+|.=.|.--|
T Consensus 418 G~ky~~~~~vatii~a 433 (595)
T COG4907 418 GLKYEHIGCVATIIFA 433 (595)
T ss_pred CCEEEEehhHHHHHHH
Confidence 4456666665555433
Done!