Query 044828
Match_columns 617
No_of_seqs 363 out of 1744
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 07:08:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044828.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044828hhsearch_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 1.2E-17 2.7E-22 134.3 6.9 61 239-308 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.7 1.5E-17 3.3E-22 135.5 7.5 63 240-311 1-63 (64)
3 smart00380 AP2 DNA-binding dom 99.7 1.3E-17 2.7E-22 136.0 6.9 63 342-405 1-63 (64)
4 cd00018 AP2 DNA-binding domain 99.7 4.2E-17 9.1E-22 131.3 6.8 61 341-402 1-61 (61)
5 PHA00280 putative NHN endonucl 99.5 6.4E-14 1.4E-18 128.8 6.7 103 287-396 13-119 (121)
6 PHA00280 putative NHN endonucl 99.2 1.4E-11 3E-16 113.4 7.3 64 228-302 56-119 (121)
7 PF00847 AP2: AP2 domain; Int 98.9 2.1E-09 4.5E-14 84.6 6.6 56 239-299 1-56 (56)
8 PF00847 AP2: AP2 domain; Int 98.9 2.8E-09 6.1E-14 83.9 6.3 53 341-393 1-56 (56)
9 PF14657 Integrase_AP2: AP2-li 63.0 17 0.00038 28.0 4.8 39 252-296 1-41 (46)
10 cd00652 TBP_TLF TATA box bindi 53.9 1.7E+02 0.0036 29.0 11.0 134 240-390 35-172 (174)
11 cd04518 TBP_archaea archaeal T 52.1 2.1E+02 0.0045 28.5 11.3 130 240-391 35-172 (174)
12 PF14657 Integrase_AP2: AP2-li 48.6 43 0.00093 25.9 4.8 37 354-390 1-41 (46)
13 cd04517 TLF TBP-like factors ( 48.2 1.9E+02 0.0042 28.6 10.4 134 240-390 35-172 (174)
14 cd04516 TBP_eukaryotes eukaryo 40.5 3.7E+02 0.008 26.8 11.0 132 240-388 35-169 (174)
15 PLN00062 TATA-box-binding prot 37.8 4.3E+02 0.0094 26.5 11.2 134 240-390 35-171 (179)
16 PRK00394 transcription factor; 37.1 3.7E+02 0.0079 26.9 10.5 135 240-391 34-173 (179)
17 PHA02601 int integrase; Provis 21.0 1.1E+02 0.0023 31.6 3.8 44 345-390 2-46 (333)
18 PF05036 SPOR: Sporulation rel 20.9 54 0.0012 26.2 1.3 26 367-393 45-70 (76)
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=99.71 E-value=1.2e-17 Score=134.34 Aligned_cols=61 Identities=48% Similarity=0.738 Sum_probs=57.1
Q ss_pred CCeeeeeEeCCCCeeEEEEecCCCcccccccCCeEeecCCCCCHHHHHHHHHHHHhhccCCCcccCCCCC
Q 044828 239 SIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQGKYSGYDKEEKAARAYDLAALKYWGPTTTTNFPVS 308 (617)
Q Consensus 239 S~YRGVrrrk~~GKW~A~I~~~s~r~~G~srkGkri~LGtFdTeEeAArAYD~AAlkl~G~~A~~NFP~s 308 (617)
|+|+||+++++ |||+|+|+++. .||++|||+|+|+||||+|||+|+++++|..+.+|||.+
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 489999999999999999999999999999999999974
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.71 E-value=1.5e-17 Score=135.47 Aligned_cols=63 Identities=44% Similarity=0.774 Sum_probs=59.3
Q ss_pred CeeeeeEeCCCCeeEEEEecCCCcccccccCCeEeecCCCCCHHHHHHHHHHHHhhccCCCcccCCCCCchh
Q 044828 240 IYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQGKYSGYDKEEKAARAYDLAALKYWGPTTTTNFPVSNYE 311 (617)
Q Consensus 240 ~YRGVrrrk~~GKW~A~I~~~s~r~~G~srkGkri~LGtFdTeEeAArAYD~AAlkl~G~~A~~NFP~sdYd 311 (617)
+|+||+++++ |||+|+|+++. +|+++|||+|+|+||||+|||.|+++++|..+.+|||.++|+
T Consensus 1 ~~kGV~~~~~-gkw~A~I~~~~--------~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPW-GKWVAEIRDPS--------KGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCC-CeEEEEEEecC--------CCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 5999999887 99999999873 589999999999999999999999999999999999999997
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.71 E-value=1.3e-17 Score=135.96 Aligned_cols=63 Identities=52% Similarity=0.791 Sum_probs=58.7
Q ss_pred cccCeeecccCCeeEeeeccccCCeeeecCCCCCHHHHHHHHHHHHHHhcCCCcccCCCCCccc
Q 044828 342 IYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFRGLNAVTNFDMSRYD 405 (617)
Q Consensus 342 kYRGV~r~r~~GKW~A~Ir~~~~gKri~LGtFdTeEEAArAYD~AAi~l~G~~A~lNFP~s~Y~ 405 (617)
+|+||++ +++|||+|+|+.+.++++++||+|+|+||||+|||.++++++|..+++|||.++|+
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 56799999998666999999999999999999999999999999999999999986
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=99.69 E-value=4.2e-17 Score=131.25 Aligned_cols=61 Identities=52% Similarity=0.821 Sum_probs=55.0
Q ss_pred ccccCeeecccCCeeEeeeccccCCeeeecCCCCCHHHHHHHHHHHHHHhcCCCcccCCCCC
Q 044828 341 SIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFRGLNAVTNFDMS 402 (617)
Q Consensus 341 SkYRGV~r~r~~GKW~A~Ir~~~~gKri~LGtFdTeEEAArAYD~AAi~l~G~~A~lNFP~s 402 (617)
|+|+||++++ +|||+|+|+....+|++|||+|+|+||||+|||+++++++|..+++|||++
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 6899998665 699999998444499999999999999999999999999999999999964
No 5
>PHA00280 putative NHN endonuclease
Probab=99.47 E-value=6.4e-14 Score=128.75 Aligned_cols=103 Identities=15% Similarity=0.145 Sum_probs=82.2
Q ss_pred HHHHHHHhhccCCCcc---cCCC-CCchhhhhhhhhcccchhhhhhhccccCCcccCcccccCeeecccCCeeEeeeccc
Q 044828 287 RAYDLAALKYWGPTTT---TNFP-VSNYEKELEDMKNMTRQEFVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRV 362 (617)
Q Consensus 287 rAYD~AAlkl~G~~A~---~NFP-~sdYdNELenLRdmTReE~VAnLRRrSsg~sr~tSkYRGV~r~r~~GKW~A~Ir~~ 362 (617)
++...+...++|+--. ..+- ....++.+.+|+.++..++..+.+..+ .++|+|+||+|++..+||+|+|+
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 RRHIQVWEAANGPIPKGYYIDHIDGNPLNDALDNLRLALPKENSWNMKTPK----SNTSGLKGLSWSKEREMWRGTVT-- 86 (121)
T ss_pred hHhHhhhHHHHCCCCCCCEEEcCCCCCCCCcHHHhhhcCHHHHhcccCCCC----CCCCCCCeeEEecCCCeEEEEEE--
Confidence 4455566666774321 1221 134567899999999999999876544 67899999999999999999996
Q ss_pred cCCeeeecCCCCCHHHHHHHHHHHHHHhcCCCcc
Q 044828 363 AGNKDLYLGTFSTQEEAAEAYDIAAIKFRGLNAV 396 (617)
Q Consensus 363 ~~gKri~LGtFdTeEEAArAYD~AAi~l~G~~A~ 396 (617)
++||+++||.|+++|+|+.||+ ++++|+|.+|+
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 9999999999999999999997 77889998874
No 6
>PHA00280 putative NHN endonuclease
Probab=99.24 E-value=1.4e-11 Score=113.44 Aligned_cols=64 Identities=17% Similarity=0.184 Sum_probs=55.7
Q ss_pred CCCCCCCCCCCCCeeeeeEeCCCCeeEEEEecCCCcccccccCCeEeecCCCCCHHHHHHHHHHHHhhccCCCcc
Q 044828 228 KKTVDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQGKYSGYDKEEKAARAYDLAALKYWGPTTT 302 (617)
Q Consensus 228 ~k~~~~~~~rtS~YRGVrrrk~~GKW~A~I~~~s~r~~G~srkGkri~LGtFdTeEeAArAYD~AAlkl~G~~A~ 302 (617)
..++...+.++|+|+||+|++..+||+|+|+. .||+++||.|+++|+|+.||+ ++.+|+|.+++
T Consensus 56 ~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~----------~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 56 SWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA----------EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred hcccCCCCCCCCCCCeeEEecCCCeEEEEEEE----------CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 34445566789999999999999999999976 499999999999999999997 77899998774
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=98.94 E-value=2.1e-09 Score=84.65 Aligned_cols=56 Identities=30% Similarity=0.317 Sum_probs=48.0
Q ss_pred CCeeeeeEeCCCCeeEEEEecCCCcccccccCCeEeecCCCCCHHHHHHHHHHHHhhccCC
Q 044828 239 SIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQGKYSGYDKEEKAARAYDLAALKYWGP 299 (617)
Q Consensus 239 S~YRGVrrrk~~GKW~A~I~~~s~r~~G~srkGkri~LGtFdTeEeAArAYD~AAlkl~G~ 299 (617)
|+|+||++++..++|+|+|++... .| ++|.++||.|+++|||++||+.++++++|+
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~--~g---~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSE--NG---KRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCC--TT---EEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEccc--Cc---ccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 679999999999999999988421 12 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=98.91 E-value=2.8e-09 Score=83.92 Aligned_cols=53 Identities=34% Similarity=0.511 Sum_probs=46.5
Q ss_pred ccccCeeecccCCeeEeeecccc-C--CeeeecCCCCCHHHHHHHHHHHHHHhcCC
Q 044828 341 SIYRGVTRHHQHGRWQARIGRVA-G--NKDLYLGTFSTQEEAAEAYDIAAIKFRGL 393 (617)
Q Consensus 341 SkYRGV~r~r~~GKW~A~Ir~~~-~--gKri~LGtFdTeEEAArAYD~AAi~l~G~ 393 (617)
|+|+||++.+..++|+|+|+... + +|.++||.|+++|||++|||.+.++++|.
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 68999999999999999997522 1 49999999999999999999999999874
No 9
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=62.96 E-value=17 Score=28.04 Aligned_cols=39 Identities=15% Similarity=0.323 Sum_probs=28.5
Q ss_pred eeEEEE--ecCCCcccccccCCeEeecCCCCCHHHHHHHHHHHHhhc
Q 044828 252 RYEAHL--WDNSCRREGQSRKGRQGKYSGYDKEEKAARAYDLAALKY 296 (617)
Q Consensus 252 KW~A~I--~~~s~r~~G~srkGkri~LGtFdTeEeAArAYD~AAlkl 296 (617)
+|...| +++. +.+.++++-+.|.|..||-.+...+...+
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 577777 3442 23457888899999999999988775544
No 10
>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=53.87 E-value=1.7e+02 Score=28.96 Aligned_cols=134 Identities=15% Similarity=0.093 Sum_probs=75.5
Q ss_pred CeeeeeEeCCCCeeEEEEecCCCcccccccCCeEeecCCCCCHHHHHHHHHHHHhhccCCCccc-CCCCCchhhhhh---
Q 044828 240 IYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQGKYSGYDKEEKAARAYDLAALKYWGPTTTT-NFPVSNYEKELE--- 315 (617)
Q Consensus 240 ~YRGVrrrk~~GKW~A~I~~~s~r~~G~srkGkri~LGtFdTeEeAArAYD~AAlkl~G~~A~~-NFP~sdYdNELe--- 315 (617)
+|.||..|...-+=.+.|+.. ||-+--| -.++|+|.+|.++.+..++--.... .++.-.-.+-..
T Consensus 35 ~fpgli~R~~~P~~t~lIf~s----------GKivitG-aks~~~~~~a~~~~~~~L~~~g~~~~~~~~~~v~NIvas~~ 103 (174)
T cd00652 35 RFPGVIMRLREPKTTALIFSS----------GKMVITG-AKSEEDAKLAARKYARILQKLGFPVEKFPEFKVQNIVASCD 103 (174)
T ss_pred ccceEEEEcCCCcEEEEEECC----------CEEEEEe-cCCHHHHHHHHHHHHHHHHHcCCCccccCceEEEEEEEEEE
Confidence 488999888777778888764 7765545 4678899999998877763211111 122100011000
Q ss_pred hhhcccchhhhhhhccccCCcccCcccccCeeecccCCeeEeeeccccCCeeeecCCCCCHHHHHHHHHHHHHHh
Q 044828 316 DMKNMTRQEFVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKF 390 (617)
Q Consensus 316 nLRdmTReE~VAnLRRrSsg~sr~tSkYRGV~r~r~~GKW~A~Ir~~~~gKri~LGtFdTeEEAArAYD~AAi~l 390 (617)
..-.+..++.....+... .=.-.+|.|+.++-...|=..-| ...||-+..|. .++||+.+|+++-...|
T Consensus 104 l~~~i~L~~la~~~~~~~---~YePe~fpgli~r~~~pk~t~lI--F~sGkvvitGa-ks~~~~~~a~~~i~~~L 172 (174)
T cd00652 104 LGFPIRLEELALKHPENA---SYEPELFPGLIYRMDEPKVVLLI--FVSGKIVITGA-KSREDIYEAVEKIYPIL 172 (174)
T ss_pred CCCcccHHHHHhhhhccc---EECCccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 000111122222222111 11234688986554445566666 46788777775 68999999997766544
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=52.05 E-value=2.1e+02 Score=28.46 Aligned_cols=130 Identities=12% Similarity=0.126 Sum_probs=77.8
Q ss_pred CeeeeeEeCCCCeeEEEEecCCCcccccccCCeEeecCCCCCHHHHHHHHHHHHhhccCCCcccCCCCCc---h--hhhh
Q 044828 240 IYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQGKYSGYDKEEKAARAYDLAALKYWGPTTTTNFPVSN---Y--EKEL 314 (617)
Q Consensus 240 ~YRGVrrrk~~GKW~A~I~~~s~r~~G~srkGkri~LGtFdTeEeAArAYD~AAlkl~G~~A~~NFP~sd---Y--dNEL 314 (617)
+|.||..|-+.-+=.+.|+.. ||-+--| ..++|+|..|-++.+..+.. ++|+... + .|-+
T Consensus 35 ~fpgli~Rl~~Pk~t~lIF~S----------GKiv~tG-aks~~~a~~a~~~~~~~L~~----~g~~~~~~~~~~i~NIV 99 (174)
T cd04518 35 QFPGLVYRLEDPKIAALIFRS----------GKMVCTG-AKSVEDLHRAVKEIIKKLKD----YGIKVIEKPEIKVQNIV 99 (174)
T ss_pred cCcEEEEEccCCcEEEEEECC----------CeEEEEc-cCCHHHHHHHHHHHHHHHHh----cCCCccCCCceEEEEEE
Confidence 488999888767777888753 6665544 57899999999998877753 3333211 1 1111
Q ss_pred hh--hh-cccchhhhhhhccccCCcccCcccccCeeecccCCeeEeeeccccCCeeeecCCCCCHHHHHHHHHHHHHHhc
Q 044828 315 ED--MK-NMTRQEFVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFR 391 (617)
Q Consensus 315 en--LR-dmTReE~VAnLRRrSsg~sr~tSkYRGV~r~r~~GKW~A~Ir~~~~gKri~LGtFdTeEEAArAYD~AAi~l~ 391 (617)
.. +. .+..+......+ . ..=.-.+|.|+.++-..-|=.+-| ...||-+..|. .++||+.+|.++-...|.
T Consensus 100 as~~l~~~i~L~~la~~~~-~---~~YePe~fpglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 172 (174)
T cd04518 100 ASADLGREVNLDAIAIGLP-N---AEYEPEQFPGLVYRLDEPKVVLLL--FSSGKMVITGA-KSEEDAKRAVEKLLSRLK 172 (174)
T ss_pred EEEEcCCccCHHHHHhhCC-C---CccCcccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHHh
Confidence 00 11 111112221222 1 112235788986554445566666 46788777765 789999999988776654
No 12
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=48.64 E-value=43 Score=25.89 Aligned_cols=37 Identities=22% Similarity=0.245 Sum_probs=27.4
Q ss_pred eeEeeec--cccCC--eeeecCCCCCHHHHHHHHHHHHHHh
Q 044828 354 RWQARIG--RVAGN--KDLYLGTFSTQEEAAEAYDIAAIKF 390 (617)
Q Consensus 354 KW~A~Ir--~~~~g--Kri~LGtFdTeEEAArAYD~AAi~l 390 (617)
+|..+|- .+..| ++++-+.|.|..||-.+..+....+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 4777771 22234 5788999999999999998876665
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=48.16 E-value=1.9e+02 Score=28.63 Aligned_cols=134 Identities=22% Similarity=0.166 Sum_probs=73.8
Q ss_pred CeeeeeEeCCCCeeEEEEecCCCcccccccCCeEeecCCCCCHHHHHHHHHHHHhhccCCCcc-cCCCCCchhhhhh--h
Q 044828 240 IYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQGKYSGYDKEEKAARAYDLAALKYWGPTTT-TNFPVSNYEKELE--D 316 (617)
Q Consensus 240 ~YRGVrrrk~~GKW~A~I~~~s~r~~G~srkGkri~LGtFdTeEeAArAYD~AAlkl~G~~A~-~NFP~sdYdNELe--n 316 (617)
+|.||..|-..-+=.+-||.. ||-+- =+..++|+|.+|.++.+..+..-.-. ..|+.-.-.+-+. .
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~s----------GKivi-TGaks~~~~~~a~~~~~~~l~~~g~~~~~~~~f~v~nIvat~~ 103 (174)
T cd04517 35 RYPKVTMRLREPRATASVWSS----------GKITI-TGATSEEEAKQAARRAARLLQKLGFKVVRFSNFRVVNVLATCS 103 (174)
T ss_pred CCCEEEEEecCCcEEEEEECC----------CeEEE-EccCCHHHHHHHHHHHHHHHHHcCCCcccCCceEEEEEEEEEe
Confidence 488999988777778888754 66544 34688999999999987776321111 1122100011000 0
Q ss_pred hh-cccchhhhhhhccccCCcccCcccccCeeecccCCeeEeeeccccCCeeeecCCCCCHHHHHHHHHHHHHHh
Q 044828 317 MK-NMTRQEFVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKF 390 (617)
Q Consensus 317 LR-dmTReE~VAnLRRrSsg~sr~tSkYRGV~r~r~~GKW~A~Ir~~~~gKri~LGtFdTeEEAArAYD~AAi~l 390 (617)
+. .+..++......+.. .=.-..|.|+.++-...|=.+.| ...||-+..|. .++||+.+|+++-.-.|
T Consensus 104 ~~~~i~L~~la~~~~~~~---~YePE~fPgliyr~~~p~~t~lI--F~sGkivitGa-ks~~~~~~a~~~i~pil 172 (174)
T cd04517 104 MPFPIRLDELAAKNRSSA---SYEPELHPGVVYRITGPRATLSI--FSTGSVTVTGA-RSMEDVREAVEKIYPIV 172 (174)
T ss_pred CCCcccHHHHHHhchhhc---EeCCccCCEEEEEECCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 00 111111111111111 01234688886554444555666 46788777775 68899999987655433
No 14
>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=40.49 E-value=3.7e+02 Score=26.76 Aligned_cols=132 Identities=13% Similarity=0.097 Sum_probs=72.9
Q ss_pred CeeeeeEeCCCCeeEEEEecCCCcccccccCCeEeecCCCCCHHHHHHHHHHHHhhccCCCcccCCCCCchhhhhh--hh
Q 044828 240 IYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQGKYSGYDKEEKAARAYDLAALKYWGPTTTTNFPVSNYEKELE--DM 317 (617)
Q Consensus 240 ~YRGVrrrk~~GKW~A~I~~~s~r~~G~srkGkri~LGtFdTeEeAArAYD~AAlkl~G~~A~~NFP~sdYdNELe--nL 317 (617)
+|-||..|...-+=.+.|+.. ||-+--|. .++|+|..|.++.+..+..-.-...|+.-...|-.. .+
T Consensus 35 ~fpgli~Rl~~Pk~t~lIF~S----------GKiviTGa-ks~e~a~~a~~~i~~~L~~~g~~~~~~~~~v~Nivat~~l 103 (174)
T cd04516 35 RFAAVIMRIREPKTTALIFSS----------GKMVCTGA-KSEDDSKLAARKYARIIQKLGFPAKFTDFKIQNIVGSCDV 103 (174)
T ss_pred cCcEEEEEeCCCcEEEEEECC----------CeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCCCCCceEEEEEEEEEEC
Confidence 388999888777778888864 77665554 678899999998887774322222333211111110 00
Q ss_pred -hcccchhhhhhhccccCCcccCcccccCeeecccCCeeEeeeccccCCeeeecCCCCCHHHHHHHHHHHHH
Q 044828 318 -KNMTRQEFVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAI 388 (617)
Q Consensus 318 -RdmTReE~VAnLRRrSsg~sr~tSkYRGV~r~r~~GKW~A~Ir~~~~gKri~LGtFdTeEEAArAYD~AAi 388 (617)
..+..++.....+... .=.-..|-|+.++-..-|=..-| ...||-+..|. .++||+.+|++.-.-
T Consensus 104 ~~~i~L~~la~~~~~~~---~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~a~~~i~p 169 (174)
T cd04516 104 KFPIRLEGLAHAHKQFS---SYEPELFPGLIYRMVKPKIVLLI--FVSGKIVLTGA-KSREEIYQAFENIYP 169 (174)
T ss_pred CCcccHHHHHHhChhcc---EeCCccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHH
Confidence 0111111111111111 11235688986554444444445 46788777775 688889888865443
No 15
>PLN00062 TATA-box-binding protein; Provisional
Probab=37.83 E-value=4.3e+02 Score=26.47 Aligned_cols=134 Identities=13% Similarity=0.078 Sum_probs=74.2
Q ss_pred CeeeeeEeCCCCeeEEEEecCCCcccccccCCeEeecCCCCCHHHHHHHHHHHHhhccCCCcccCCCCCchhhhhh--hh
Q 044828 240 IYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQGKYSGYDKEEKAARAYDLAALKYWGPTTTTNFPVSNYEKELE--DM 317 (617)
Q Consensus 240 ~YRGVrrrk~~GKW~A~I~~~s~r~~G~srkGkri~LGtFdTeEeAArAYD~AAlkl~G~~A~~NFP~sdYdNELe--nL 317 (617)
+|-||..|.+.-|=.+-|+.. ||-+--| ..++|+|.+|.++.+..+..-....+|+.-...|-+. .+
T Consensus 35 ~fpgli~Rl~~Pk~t~lIF~S----------GKiviTG-aks~e~a~~a~~~~~~~L~~lg~~~~~~~f~v~NIvas~~l 103 (179)
T PLN00062 35 RFAAVIMRIREPKTTALIFAS----------GKMVCTG-AKSEHDSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDV 103 (179)
T ss_pred cCcEEEEEeCCCcEEEEEECC----------CeEEEEe-cCCHHHHHHHHHHHHHHHHHcCCCcCCCccEEEEEEEEEEC
Confidence 388999888777778888753 6665434 6789999999999887774322223332111111110 00
Q ss_pred h-cccchhhhhhhccccCCcccCcccccCeeecccCCeeEeeeccccCCeeeecCCCCCHHHHHHHHHHHHHHh
Q 044828 318 K-NMTRQEFVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKF 390 (617)
Q Consensus 318 R-dmTReE~VAnLRRrSsg~sr~tSkYRGV~r~r~~GKW~A~Ir~~~~gKri~LGtFdTeEEAArAYD~AAi~l 390 (617)
. .+..+......+... .=.-..|-|+.++-..-|=..-| ...||-+..|. .++||+.+|.+.-.-.|
T Consensus 104 ~~~i~L~~la~~~~~~~---~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~ai~~i~p~L 171 (179)
T PLN00062 104 KFPIRLEGLAYAHGAFS---SYEPELFPGLIYRMKQPKIVLLI--FVSGKIVITGA-KVREEIYTAFENIYPVL 171 (179)
T ss_pred CCcccHHHHHHhchhhc---ccCcccCceEEEEeCCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 0 111111111101111 12235788886544444445555 46788777775 67888988887655444
No 16
>PRK00394 transcription factor; Reviewed
Probab=37.08 E-value=3.7e+02 Score=26.86 Aligned_cols=135 Identities=12% Similarity=0.120 Sum_probs=77.3
Q ss_pred CeeeeeEeCCCCeeEEEEecCCCcccccccCCeEeecCCCCCHHHHHHHHHHHHhhccCCCcccC-CCCCchhhhhh--h
Q 044828 240 IYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQGKYSGYDKEEKAARAYDLAALKYWGPTTTTN-FPVSNYEKELE--D 316 (617)
Q Consensus 240 ~YRGVrrrk~~GKW~A~I~~~s~r~~G~srkGkri~LGtFdTeEeAArAYD~AAlkl~G~~A~~N-FP~sdYdNELe--n 316 (617)
+|-||..|-+.-+=.+.|+.. ||-+--|. .++|+|.+|-++.+..+..-.-... ++.-.-.|-+. .
T Consensus 34 ~fpgli~Rl~~Pk~t~lIf~s----------GKiv~tGa-~S~~~a~~a~~~~~~~l~~~g~~~~~~~~~~i~NiVas~~ 102 (179)
T PRK00394 34 QFPGLVYRLEDPKIAALIFRS----------GKVVCTGA-KSVEDLHEAVKIIIKKLKELGIKVIDEPEIKVQNIVASAD 102 (179)
T ss_pred cCceEEEEecCCceEEEEEcC----------CcEEEEcc-CCHHHHHHHHHHHHHHHHHcCCCccCCCceEEEEEEEEEE
Confidence 488999888877888888754 77766665 5677888888887776642111111 11101111100 0
Q ss_pred hh-cccchhhhhhhc-cccCCcccCcccccCeeecccCCeeEeeeccccCCeeeecCCCCCHHHHHHHHHHHHHHhc
Q 044828 317 MK-NMTRQEFVASLR-RKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFR 391 (617)
Q Consensus 317 LR-dmTReE~VAnLR-RrSsg~sr~tSkYRGV~r~r~~GKW~A~Ir~~~~gKri~LGtFdTeEEAArAYD~AAi~l~ 391 (617)
+. .+..+.....+. +.. .=.-.+|.|+..+-..-|=..-| ...||-+..|. .++||+.+|.++-...|.
T Consensus 103 l~~~i~L~~la~~~~~~~~---~YePe~fPglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 173 (179)
T PRK00394 103 LGVELNLNAIAIGLGLENI---EYEPEQFPGLVYRLDDPKVVVLL--FGSGKLVITGA-KSEEDAEKAVEKILEKLE 173 (179)
T ss_pred cCCeEcHHHHHHhcCcCCc---EECcccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 00 111122222110 111 11235788986555555666777 46788777775 789999999988776663
No 17
>PHA02601 int integrase; Provisional
Probab=20.97 E-value=1.1e+02 Score=31.57 Aligned_cols=44 Identities=23% Similarity=0.316 Sum_probs=0.0
Q ss_pred CeeecccCCeeEeeecc-ccCCeeeecCCCCCHHHHHHHHHHHHHHh
Q 044828 345 GVTRHHQHGRWQARIGR-VAGNKDLYLGTFSTQEEAAEAYDIAAIKF 390 (617)
Q Consensus 345 GV~r~r~~GKW~A~Ir~-~~~gKri~LGtFdTeEEAArAYD~AAi~l 390 (617)
+| +.+++|+|+++++. ...|+++... |.|..||-...+......
T Consensus 2 ~~-~~~~~g~w~~~~~~~~~~g~r~~~~-f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AV-RKLKDGKWLCEIYPNGRDGKRIRKR-FATKGEALAFENYTMAEV 46 (333)
T ss_pred ce-EEcCCCCEEEEEEECCCCCchhhhh-hcCHHHHHHHHHHHHHhc
No 18
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=20.90 E-value=54 Score=26.15 Aligned_cols=26 Identities=35% Similarity=0.424 Sum_probs=19.4
Q ss_pred eeecCCCCCHHHHHHHHHHHHHHhcCC
Q 044828 367 DLYLGTFSTQEEAAEAYDIAAIKFRGL 393 (617)
Q Consensus 367 ri~LGtFdTeEEAArAYD~AAi~l~G~ 393 (617)
++.+|.|++.+||..+-++.. ...|.
T Consensus 45 rV~~G~f~~~~~A~~~~~~l~-~~~~~ 70 (76)
T PF05036_consen 45 RVRVGPFSSREEAEAALRKLK-KAAGP 70 (76)
T ss_dssp EEEECCECTCCHHHHHHHHHH-HHHTS
T ss_pred EEEECCCCCHHHHHHHHHHHh-HhhCC
Confidence 577899999999988876554 34444
Done!