Query 023209
Match_columns 285
No_of_seqs 211 out of 1163
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 09:14:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023209.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023209hhsearch_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 99.8 2.5E-20 5.5E-25 136.5 7.2 61 137-198 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 2.7E-19 5.9E-24 132.7 8.3 63 138-201 1-63 (64)
3 PHA00280 putative NHN endonucl 99.7 5.7E-17 1.2E-21 135.6 7.4 87 102-192 32-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 1.9E-11 4E-16 87.4 6.0 53 137-189 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 79.6 5.8 0.00013 27.4 5.0 38 149-186 1-41 (46)
6 PHA02601 int integrase; Provis 73.4 5.2 0.00011 36.9 4.5 45 141-186 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 43.2 48 0.001 30.1 5.1 38 148-186 10-49 (357)
8 PRK09692 integrase; Provisiona 40.4 76 0.0017 30.6 6.3 44 142-185 33-81 (413)
9 PF13356 DUF4102: Domain of un 38.6 80 0.0017 24.3 5.0 44 142-186 27-74 (89)
10 PF08846 DUF1816: Domain of un 37.0 72 0.0016 24.7 4.4 41 149-190 9-49 (68)
11 PF05036 SPOR: Sporulation rel 35.9 24 0.00053 25.1 1.6 23 161-183 43-65 (76)
12 PF00352 TBP: Transcription fa 31.0 1.1E+02 0.0024 23.6 4.7 46 137-186 36-82 (86)
13 COG0197 RplP Ribosomal protein 29.3 80 0.0017 27.8 4.0 37 149-189 95-131 (146)
14 PF08471 Ribonuc_red_2_N: Clas 27.6 63 0.0014 26.5 2.8 20 167-186 71-90 (93)
15 cd04516 TBP_eukaryotes eukaryo 21.1 3.8E+02 0.0082 23.8 6.8 48 135-186 32-80 (174)
16 PF10729 CedA: Cell division a 20.6 1.6E+02 0.0036 23.2 3.8 37 137-177 31-67 (80)
17 PLN00062 TATA-box-binding prot 20.4 3.9E+02 0.0085 23.9 6.8 48 135-186 32-80 (179)
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=99.82 E-value=2.5e-20 Score=136.49 Aligned_cols=61 Identities=69% Similarity=1.255 Sum_probs=56.8
Q ss_pred ceeeeeEEcCCCcEEEEEecCCCCCcEEecCCCCcHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 023209 137 KHYRGVRRRPWGRYAAEIRDPNRKGSRVWLGTFDTAVEAAKAYDNAAFRLRGSKAILNFPLE 198 (285)
Q Consensus 137 S~yRGV~~r~~GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl~G~~A~lNFP~~ 198 (285)
|+|+||+++++|||+|+|+++. .|+++|||+|+|+||||+|||.|+++++|.++.+|||.+
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~-~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPS-GGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCC-CCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 6899999999999999999943 289999999999999999999999999999999999974
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.79 E-value=2.7e-19 Score=132.68 Aligned_cols=63 Identities=68% Similarity=1.208 Sum_probs=58.5
Q ss_pred eeeeeEEcCCCcEEEEEecCCCCCcEEecCCCCcHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q 023209 138 HYRGVRRRPWGRYAAEIRDPNRKGSRVWLGTFDTAVEAAKAYDNAAFRLRGSKAILNFPLEVGG 201 (285)
Q Consensus 138 ~yRGV~~r~~GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl~G~~A~lNFP~~~~~ 201 (285)
+|+||+++++|||+|+|+++. +|+++|||+|+|+||||+|||.|+++++|.++.+|||.+.+.
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~-~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPS-KGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecC-CCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 589999998999999999976 479999999999999999999999999999999999997653
No 3
>PHA00280 putative NHN endonuclease
Probab=99.68 E-value=5.7e-17 Score=135.62 Aligned_cols=87 Identities=14% Similarity=0.072 Sum_probs=79.7
Q ss_pred CCCCCCCCCCccccCCCcchhhhhcccCCCCCCCCceeeeeEEcCC-CcEEEEEecCCCCCcEEecCCCCcHHHHHHHHH
Q 023209 102 SNVNDDADNPVAVKNKDPDAAADDNNNNNNNNIEEKHYRGVRRRPW-GRYAAEIRDPNRKGSRVWLGTFDTAVEAAKAYD 180 (285)
Q Consensus 102 ~~~~~~~~~~~~~~~~~~~~~a~n~~N~~~~~~~~S~yRGV~~r~~-GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD 180 (285)
+++.+++...+...+.+...+++|++|.+..+.|+|||+||+|++. |||+|+|++ +||+++||.|+++|+|+.||+
T Consensus 32 VdHidg~~~dnri~NLr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~---~gK~~~lG~f~~~e~A~~a~~ 108 (121)
T PHA00280 32 IDHIDGNPLNDALDNLRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA---EGKQHNFRSRDLLEVVAWIYR 108 (121)
T ss_pred EEcCCCCCCCCcHHHhhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE---CCEEEEcCCCCCHHHHHHHHH
Confidence 6777888888888888999999999999999999999999998766 999999999 899999999999999999997
Q ss_pred HHHHHhcCCCCC
Q 023209 181 NAAFRLRGSKAI 192 (285)
Q Consensus 181 ~AA~kl~G~~A~ 192 (285)
++.+|||++|.
T Consensus 109 -~~~~lhGeFa~ 119 (121)
T PHA00280 109 -TRRELHGQFAR 119 (121)
T ss_pred -HHHHHhhcccc
Confidence 77789999985
No 4
>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=99.23 E-value=1.9e-11 Score=87.44 Aligned_cols=53 Identities=34% Similarity=0.455 Sum_probs=46.4
Q ss_pred ceeeeeEEcCC-CcEEEEEecCCCCC--cEEecCCCCcHHHHHHHHHHHHHHhcCC
Q 023209 137 KHYRGVRRRPW-GRYAAEIRDPNRKG--SRVWLGTFDTAVEAAKAYDNAAFRLRGS 189 (285)
Q Consensus 137 S~yRGV~~r~~-GKW~A~I~~~~~~G--kri~LGtFdT~EEAArAYD~AA~kl~G~ 189 (285)
|+|+||++++. ++|+|+|++...+| ++++||.|++++||++||+.++.+++|+
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 68999998875 99999999853343 9999999999999999999999999875
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=79.58 E-value=5.8 Score=27.45 Aligned_cols=38 Identities=24% Similarity=0.181 Sum_probs=28.8
Q ss_pred cEEEEEe--cC-CCCCcEEecCCCCcHHHHHHHHHHHHHHh
Q 023209 149 RYAAEIR--DP-NRKGSRVWLGTFDTAVEAAKAYDNAAFRL 186 (285)
Q Consensus 149 KW~A~I~--~~-~~~Gkri~LGtFdT~EEAArAYD~AA~kl 186 (285)
+|..+|. ++ ..+-++++-+-|.|..||-.+...+...+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5888883 32 33347788899999999999998877665
No 6
>PHA02601 int integrase; Provisional
Probab=73.37 E-value=5.2 Score=36.91 Aligned_cols=45 Identities=27% Similarity=0.312 Sum_probs=31.4
Q ss_pred eeEEcCCCcEEEEEecCCCCCcEEecCCCCcHHHHHHHHHHHHHHh
Q 023209 141 GVRRRPWGRYAAEIRDPNRKGSRVWLGTFDTAVEAAKAYDNAAFRL 186 (285)
Q Consensus 141 GV~~r~~GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl 186 (285)
+|+..++|+|+++++.....|+++.. +|.|..||....+.....+
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~~-~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIRK-RFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhhh-hhcCHHHHHHHHHHHHHhc
Confidence 56667779999999863334777663 6999998876655544433
No 7
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=43.20 E-value=48 Score=30.13 Aligned_cols=38 Identities=24% Similarity=0.296 Sum_probs=26.1
Q ss_pred CcEEEEEecCCCCCcEEecCCCC--cHHHHHHHHHHHHHHh
Q 023209 148 GRYAAEIRDPNRKGSRVWLGTFD--TAVEAAKAYDNAAFRL 186 (285)
Q Consensus 148 GKW~A~I~~~~~~Gkri~LGtFd--T~EEAArAYD~AA~kl 186 (285)
+.|+.+++...+ .+++.||+|+ +.++|....+.....+
T Consensus 10 ~~~~~~~~~~g~-~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGK-RKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCc-eeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 569999988432 2467799996 6777777666655544
No 8
>PRK09692 integrase; Provisional
Probab=40.42 E-value=76 Score=30.58 Aligned_cols=44 Identities=11% Similarity=0.161 Sum_probs=26.9
Q ss_pred eEEcCCC--cEEEEEecC-CCCCcEEecCCCC--cHHHHHHHHHHHHHH
Q 023209 142 VRRRPWG--RYAAEIRDP-NRKGSRVWLGTFD--TAVEAAKAYDNAAFR 185 (285)
Q Consensus 142 V~~r~~G--KW~A~I~~~-~~~Gkri~LGtFd--T~EEAArAYD~AA~k 185 (285)
|+.++.| .|..+.+.+ .++.+++-||.|. |..+|..+..++...
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~~ 81 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRSL 81 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHHH
Confidence 4556665 499888743 2222347899999 676766555444443
No 9
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=38.59 E-value=80 Score=24.26 Aligned_cols=44 Identities=23% Similarity=0.272 Sum_probs=26.6
Q ss_pred eEEcCCC--cEEEEEecCCCCCcEEecCCCCc--HHHHHHHHHHHHHHh
Q 023209 142 VRRRPWG--RYAAEIRDPNRKGSRVWLGTFDT--AVEAAKAYDNAAFRL 186 (285)
Q Consensus 142 V~~r~~G--KW~A~I~~~~~~Gkri~LGtFdT--~EEAArAYD~AA~kl 186 (285)
|+..+.| .|..+.+... +.+++-||.|.. ..+|......+...+
T Consensus 27 l~v~~~G~kt~~~r~~~~g-k~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 27 LRVTPSGSKTFYFRYRING-KRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EEE-TTS-EEEEEEEEETT-EEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEEeCCCeEEEEEEEecc-eEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 3455664 4988887732 235789999976 555555554444433
No 10
>PF08846 DUF1816: Domain of unknown function (DUF1816); InterPro: IPR014945 Q4C9H3 from SWISSPROT is associated with the IPR008213 from INTERPRO domain suggesting this protein could have a role in phycobilisomes.
Probab=36.96 E-value=72 Score=24.68 Aligned_cols=41 Identities=24% Similarity=0.312 Sum_probs=29.3
Q ss_pred cEEEEEecCCCCCcEEecCCCCcHHHHHHHHHHHHHHhcCCC
Q 023209 149 RYAAEIRDPNRKGSRVWLGTFDTAVEAAKAYDNAAFRLRGSK 190 (285)
Q Consensus 149 KW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl~G~~ 190 (285)
.|-++|.-..-+ -.+|-|-|+|.+||..+...-...+..+.
T Consensus 9 aWWveI~T~~P~-ctYyFGPF~s~~eA~~~~~gyieDL~~Eg 49 (68)
T PF08846_consen 9 AWWVEIETQNPN-CTYYFGPFDSREEAEAALPGYIEDLESEG 49 (68)
T ss_pred cEEEEEEcCCCC-EEEEeCCcCCHHHHHHHhccHHHHHHhhC
Confidence 477888753222 57899999999999998766655554443
No 11
>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=35.94 E-value=24 Score=25.11 Aligned_cols=23 Identities=30% Similarity=0.328 Sum_probs=19.3
Q ss_pred CcEEecCCCCcHHHHHHHHHHHH
Q 023209 161 GSRVWLGTFDTAVEAAKAYDNAA 183 (285)
Q Consensus 161 Gkri~LGtFdT~EEAArAYD~AA 183 (285)
.-+|.+|.|++.++|..+.....
T Consensus 43 ~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 43 WYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp CEEEEECCECTCCHHHHHHHHHH
T ss_pred eEEEEECCCCCHHHHHHHHHHHh
Confidence 35899999999999988877665
No 12
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=31.01 E-value=1.1e+02 Score=23.62 Aligned_cols=46 Identities=24% Similarity=0.226 Sum_probs=35.5
Q ss_pred ceeeeeEEcCC-CcEEEEEecCCCCCcEEecCCCCcHHHHHHHHHHHHHHh
Q 023209 137 KHYRGVRRRPW-GRYAAEIRDPNRKGSRVWLGTFDTAVEAAKAYDNAAFRL 186 (285)
Q Consensus 137 S~yRGV~~r~~-GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl 186 (285)
.+|.||..|-. -+-.+.|.. .||-+..|. .+.++|..|+++....+
T Consensus 36 e~fpgl~~r~~~p~~t~~IF~---sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 36 ERFPGLIYRLRNPKATVLIFS---SGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTESSEEEEETTTTEEEEEET---TSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred ccCCeEEEeecCCcEEEEEEc---CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 37889876654 577888887 788777775 68999999998877654
No 13
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=29.29 E-value=80 Score=27.81 Aligned_cols=37 Identities=22% Similarity=0.131 Sum_probs=31.8
Q ss_pred cEEEEEecCCCCCcEEecCCCCcHHHHHHHHHHHHHHhcCC
Q 023209 149 RYAAEIRDPNRKGSRVWLGTFDTAVEAAKAYDNAAFRLRGS 189 (285)
Q Consensus 149 KW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl~G~ 189 (285)
.|.|+|.. |+-++-=..+.++.|..|..+|+.+|=+.
T Consensus 95 gwaArVkp----G~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 95 GWAARVKP----GRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEEecC----CcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 39999996 78888888899999999999999988554
No 14
>PF08471 Ribonuc_red_2_N: Class II vitamin B12-dependent ribonucleotide reductase; InterPro: IPR013678 This domain is found to the N terminus of the ribonucleotide reductase barrel domain (IPR000788 from INTERPRO). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine) []. ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0050897 cobalt ion binding, 0055114 oxidation-reduction process
Probab=27.59 E-value=63 Score=26.51 Aligned_cols=20 Identities=35% Similarity=0.577 Sum_probs=18.0
Q ss_pred CCCCcHHHHHHHHHHHHHHh
Q 023209 167 GTFDTAVEAAKAYDNAAFRL 186 (285)
Q Consensus 167 GtFdT~EEAArAYD~AA~kl 186 (285)
|+|+|+++|..=||..+..|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999987654
No 15
>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=21.11 E-value=3.8e+02 Score=23.83 Aligned_cols=48 Identities=21% Similarity=0.152 Sum_probs=37.1
Q ss_pred CCceeeeeEEcCC-CcEEEEEecCCCCCcEEecCCCCcHHHHHHHHHHHHHHh
Q 023209 135 EEKHYRGVRRRPW-GRYAAEIRDPNRKGSRVWLGTFDTAVEAAKAYDNAAFRL 186 (285)
Q Consensus 135 ~~S~yRGV~~r~~-GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl 186 (285)
+..+|.||..|-. -+=.+-|+. .||-+--|. .+.|+|..|.++.+..+
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~---SGKiviTGa-ks~e~a~~a~~~i~~~L 80 (174)
T cd04516 32 NPKRFAAVIMRIREPKTTALIFS---SGKMVCTGA-KSEDDSKLAARKYARII 80 (174)
T ss_pred CCccCcEEEEEeCCCcEEEEEEC---CCeEEEEec-CCHHHHHHHHHHHHHHH
Confidence 3458899887655 577788887 788777776 57888999998888776
No 16
>PF10729 CedA: Cell division activator CedA; InterPro: IPR019666 CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet [, ]. ; GO: 0003677 DNA binding, 0051301 cell division; PDB: 2BN8_A 2D35_A.
Probab=20.58 E-value=1.6e+02 Score=23.19 Aligned_cols=37 Identities=19% Similarity=0.202 Sum_probs=22.7
Q ss_pred ceeeeeEEcCCCcEEEEEecCCCCCcEEecCCCCcHHHHHH
Q 023209 137 KHYRGVRRRPWGRYAAEIRDPNRKGSRVWLGTFDTAVEAAK 177 (285)
Q Consensus 137 S~yRGV~~r~~GKW~A~I~~~~~~Gkri~LGtFdT~EEAAr 177 (285)
-+||-|.. -.|||+|.+.... .-.---.|..+|.|-+
T Consensus 31 dgfrdvw~-lrgkyvafvl~ge---~f~rsp~fs~pesaqr 67 (80)
T PF10729_consen 31 DGFRDVWQ-LRGKYVAFVLMGE---HFRRSPAFSVPESAQR 67 (80)
T ss_dssp TTECCECC-CCCEEEEEEESSS----EEE---BSSHHHHHH
T ss_pred ccccceee-eccceEEEEEecc---hhccCCCcCCcHHHHH
Confidence 37888854 3499999999722 2223356777776655
No 17
>PLN00062 TATA-box-binding protein; Provisional
Probab=20.40 E-value=3.9e+02 Score=23.90 Aligned_cols=48 Identities=21% Similarity=0.153 Sum_probs=36.4
Q ss_pred CCceeeeeEEcCC-CcEEEEEecCCCCCcEEecCCCCcHHHHHHHHHHHHHHh
Q 023209 135 EEKHYRGVRRRPW-GRYAAEIRDPNRKGSRVWLGTFDTAVEAAKAYDNAAFRL 186 (285)
Q Consensus 135 ~~S~yRGV~~r~~-GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl 186 (285)
+..+|.||..|-. -+=.+-|+. .||-+--|. .+.++|..|.++.+..+
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~---SGKiviTGa-ks~e~a~~a~~~~~~~L 80 (179)
T PLN00062 32 NPKRFAAVIMRIREPKTTALIFA---SGKMVCTGA-KSEHDSKLAARKYARII 80 (179)
T ss_pred CCccCcEEEEEeCCCcEEEEEEC---CCeEEEEec-CCHHHHHHHHHHHHHHH
Confidence 3447999886654 667888887 787766664 78899999998888776
Done!