Query 047100
Match_columns 233
No_of_seqs 214 out of 1238
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 07:35:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047100.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047100hhsearch_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 1.9E-20 4.2E-25 133.2 7.0 60 133-193 1-60 (61)
2 smart00380 AP2 DNA-binding dom 99.8 3.3E-19 7.2E-24 128.5 7.9 60 134-194 1-60 (64)
3 PHA00280 putative NHN endonucl 99.4 4.4E-13 9.6E-18 109.3 6.9 58 127-188 61-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 5.2E-11 1.1E-15 82.6 5.5 53 133-185 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 76.8 8 0.00017 25.9 5.0 39 145-183 1-42 (46)
6 PHA02601 int integrase; Provis 75.3 4.4 9.6E-05 36.1 4.4 45 137-182 2-46 (333)
7 PF08846 DUF1816: Domain of un 61.7 18 0.00039 27.2 4.4 56 145-214 9-65 (68)
8 cd00801 INT_P4 Bacteriophage P 44.3 56 0.0012 28.6 5.5 40 143-183 9-50 (357)
9 PF08471 Ribonuc_red_2_N: Clas 42.4 27 0.00058 27.9 2.9 20 163-182 71-90 (93)
10 PF05036 SPOR: Sporulation rel 40.0 16 0.00034 25.3 1.1 23 157-179 43-65 (76)
11 cd04516 TBP_eukaryotes eukaryo 31.0 2.3E+02 0.005 24.4 7.1 49 131-183 32-81 (174)
12 PLN00062 TATA-box-binding prot 28.6 2.7E+02 0.0058 24.2 7.1 49 131-183 32-81 (179)
13 PF00352 TBP: Transcription fa 27.3 1.6E+02 0.0034 22.0 4.9 47 132-182 35-82 (86)
14 PRK09692 integrase; Provisiona 27.3 1.8E+02 0.0039 27.1 6.2 38 144-182 41-82 (413)
15 cd04517 TLF TBP-like factors ( 24.7 2.9E+02 0.0063 23.7 6.6 47 131-182 33-80 (174)
16 PF10729 CedA: Cell division a 24.2 1.5E+02 0.0033 22.7 4.2 42 129-174 27-68 (80)
17 COG0197 RplP Ribosomal protein 22.1 1.4E+02 0.003 25.6 4.0 36 145-184 95-130 (146)
18 cd04518 TBP_archaea archaeal T 21.1 3.6E+02 0.0078 23.2 6.5 49 131-183 32-81 (174)
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=1.9e-20 Score=133.25 Aligned_cols=60 Identities=70% Similarity=1.234 Sum_probs=56.1
Q ss_pred CceEEeEECCCCcEEEEEeCCCCCCcEEeccCCCCHHHHHHHHHHHHHHhcCCCCCCCCCC
Q 047100 133 MQYRGVRRRPWGKFAAEIRDPKKNGARVWLGTYDTPEGAAFAYDRAAFKMRGSKAKLNFPH 193 (233)
Q Consensus 133 S~YRGV~~r~~GKW~A~I~~~~~nGkrv~LGtFdT~EEAA~AYD~AA~~~~G~~A~lNFP~ 193 (233)
|+|+||+++++|||+|+|+++.. |+++|||+|+|+||||.|||+|+++++|.++.+|||+
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~-gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~ 60 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSG-GRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPD 60 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCC-CceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCC
Confidence 68999998889999999999432 7999999999999999999999999999999999996
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.79 E-value=3.3e-19 Score=128.50 Aligned_cols=60 Identities=73% Similarity=1.293 Sum_probs=56.4
Q ss_pred ceEEeEECCCCcEEEEEeCCCCCCcEEeccCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 047100 134 QYRGVRRRPWGKFAAEIRDPKKNGARVWLGTYDTPEGAAFAYDRAAFKMRGSKAKLNFPHL 194 (233)
Q Consensus 134 ~YRGV~~r~~GKW~A~I~~~~~nGkrv~LGtFdT~EEAA~AYD~AA~~~~G~~A~lNFP~~ 194 (233)
+|+||+++++|||+|+|+++.. |+++|||+|+|+||||.|||.|+++++|.++.+|||..
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~-~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 60 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSK-GKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNS 60 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCC-CcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCc
Confidence 5999999889999999999764 78999999999999999999999999999999999985
No 3
>PHA00280 putative NHN endonuclease
Probab=99.41 E-value=4.4e-13 Score=109.25 Aligned_cols=58 Identities=14% Similarity=0.186 Sum_probs=51.9
Q ss_pred cCCCCCCceEEeEEC-CCCcEEEEEeCCCCCCcEEeccCCCCHHHHHHHHHHHHHHhcCCCCC
Q 047100 127 RGTHVRMQYRGVRRR-PWGKFAAEIRDPKKNGARVWLGTYDTPEGAAFAYDRAAFKMRGSKAK 188 (233)
Q Consensus 127 ~~~~~~S~YRGV~~r-~~GKW~A~I~~~~~nGkrv~LGtFdT~EEAA~AYD~AA~~~~G~~A~ 188 (233)
..+.++|+|+||++. ..|||+|+|++ +||+++||.|+++|+|+.||+ ++.++||.+|.
T Consensus 61 ~~~~N~SG~kGV~~~k~~~kw~A~I~~---~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 61 TPKSNTSGLKGLSWSKEREMWRGTVTA---EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred CCCCCCCCCCeeEEecCCCeEEEEEEE---CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 456789999999965 47999999999 999999999999999999997 77889999875
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=99.17 E-value=5.2e-11 Score=82.63 Aligned_cols=53 Identities=30% Similarity=0.397 Sum_probs=45.9
Q ss_pred CceEEeEECC-CCcEEEEEeCCCCCC--cEEeccCCCCHHHHHHHHHHHHHHhcCC
Q 047100 133 MQYRGVRRRP-WGKFAAEIRDPKKNG--ARVWLGTYDTPEGAAFAYDRAAFKMRGS 185 (233)
Q Consensus 133 S~YRGV~~r~-~GKW~A~I~~~~~nG--krv~LGtFdT~EEAA~AYD~AA~~~~G~ 185 (233)
|+|+||++.+ .++|+|+|++...+| ++++||.|++++||++||+.++..++|+
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 6899999554 799999999854444 8999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=76.80 E-value=8 Score=25.94 Aligned_cols=39 Identities=10% Similarity=0.097 Sum_probs=29.2
Q ss_pred cEEEEEe-CCCCCC--cEEeccCCCCHHHHHHHHHHHHHHhc
Q 047100 145 KFAAEIR-DPKKNG--ARVWLGTYDTPEGAAFAYDRAAFKMR 183 (233)
Q Consensus 145 KW~A~I~-~~~~nG--krv~LGtFdT~EEAA~AYD~AA~~~~ 183 (233)
+|..+|. ....+| ++++-+-|.|..||..+..++...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5888883 332234 66788999999999999988776653
No 6
>PHA02601 int integrase; Provisional
Probab=75.32 E-value=4.4 Score=36.12 Aligned_cols=45 Identities=22% Similarity=0.260 Sum_probs=31.0
Q ss_pred EeEECCCCcEEEEEeCCCCCCcEEeccCCCCHHHHHHHHHHHHHHh
Q 047100 137 GVRRRPWGKFAAEIRDPKKNGARVWLGTYDTPEGAAFAYDRAAFKM 182 (233)
Q Consensus 137 GV~~r~~GKW~A~I~~~~~nGkrv~LGtFdT~EEAA~AYD~AA~~~ 182 (233)
+|++.+.|+|+++++.....|+++. .+|.|..||....+.....+
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~-~~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIR-KRFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhh-hhhcCHHHHHHHHHHHHHhc
Confidence 5667778999999986323466665 36999998876665544433
No 7
>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=61.67 E-value=18 Score=27.19 Aligned_cols=56 Identities=27% Similarity=0.376 Sum_probs=38.0
Q ss_pred cEEEEEeCCCCCCcEEeccCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCccccccCCC-CCC
Q 047100 145 KFAAEIRDPKKNGARVWLGTYDTPEGAAFAYDRAAFKMRGSKAKLNFPHLIGSNVEPPVRVTKKRGS-PEP 214 (233)
Q Consensus 145 KW~A~I~~~~~nGkrv~LGtFdT~EEAA~AYD~AA~~~~G~~A~lNFP~~i~~~~p~p~rv~~kr~~-~~~ 214 (233)
.|-++|.-..-+ -.+|.|-|.+.+||..+.-.....+. ..-++-+.+..||.. |++
T Consensus 9 aWWveI~T~~P~-ctYyFGPF~s~~eA~~~~~gyieDL~-------------~Ega~~I~~~i~rc~rp~~ 65 (68)
T PF08846_consen 9 AWWVEIETQNPN-CTYYFGPFDSREEAEAALPGYIEDLE-------------SEGAQGISVSIKRCQRPEP 65 (68)
T ss_pred cEEEEEEcCCCC-EEEEeCCcCCHHHHHHHhccHHHHHH-------------hhCcceEEEEEEEcCCCCc
Confidence 477888753222 57899999999999988665555443 334566777777765 543
No 8
>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=44.34 E-value=56 Score=28.60 Aligned_cols=40 Identities=23% Similarity=0.155 Sum_probs=27.4
Q ss_pred CCcEEEEEeCCCCCCcEEeccCCC--CHHHHHHHHHHHHHHhc
Q 047100 143 WGKFAAEIRDPKKNGARVWLGTYD--TPEGAAFAYDRAAFKMR 183 (233)
Q Consensus 143 ~GKW~A~I~~~~~nGkrv~LGtFd--T~EEAA~AYD~AA~~~~ 183 (233)
.+.|+.+++...+ .+++.||+|+ +.++|.....+....+.
T Consensus 9 ~~~~~~~~~~~g~-~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 9 SKSWRFRYRLAGK-RKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred CEEEEEEeccCCc-eeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 4569999998332 2457899995 67777777766555553
No 9
>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=42.40 E-value=27 Score=27.85 Aligned_cols=20 Identities=30% Similarity=0.531 Sum_probs=18.1
Q ss_pred cCCCCHHHHHHHHHHHHHHh
Q 047100 163 GTYDTPEGAAFAYDRAAFKM 182 (233)
Q Consensus 163 GtFdT~EEAA~AYD~AA~~~ 182 (233)
|+|+|+|||..-||..+..+
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 89999999999999987765
No 10
>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=39.99 E-value=16 Score=25.28 Aligned_cols=23 Identities=26% Similarity=0.307 Sum_probs=19.3
Q ss_pred CcEEeccCCCCHHHHHHHHHHHH
Q 047100 157 GARVWLGTYDTPEGAAFAYDRAA 179 (233)
Q Consensus 157 Gkrv~LGtFdT~EEAA~AYD~AA 179 (233)
..+|.+|.|++.++|..+-.+..
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 36799999999999988877665
No 11
>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=30.98 E-value=2.3e+02 Score=24.38 Aligned_cols=49 Identities=20% Similarity=0.160 Sum_probs=36.8
Q ss_pred CCCceEEeE-ECCCCcEEEEEeCCCCCCcEEeccCCCCHHHHHHHHHHHHHHhc
Q 047100 131 VRMQYRGVR-RRPWGKFAAEIRDPKKNGARVWLGTYDTPEGAAFAYDRAAFKMR 183 (233)
Q Consensus 131 ~~S~YRGV~-~r~~GKW~A~I~~~~~nGkrv~LGtFdT~EEAA~AYD~AA~~~~ 183 (233)
...+|.||. |...-+=.+.|.. .||-+.-|. .+.|+|..|.++.+..+.
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~---SGKiviTGa-ks~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 32 NPKRFAAVIMRIREPKTTALIFS---SGKMVCTGA-KSEDDSKLAARKYARIIQ 81 (174)
T ss_pred CCccCcEEEEEeCCCcEEEEEEC---CCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 456888987 4344567788888 898877776 578899999988877763
No 12
>PLN00062 TATA-box-binding protein; Provisional
Probab=28.61 E-value=2.7e+02 Score=24.20 Aligned_cols=49 Identities=20% Similarity=0.139 Sum_probs=36.3
Q ss_pred CCCceEEeE-ECCCCcEEEEEeCCCCCCcEEeccCCCCHHHHHHHHHHHHHHhc
Q 047100 131 VRMQYRGVR-RRPWGKFAAEIRDPKKNGARVWLGTYDTPEGAAFAYDRAAFKMR 183 (233)
Q Consensus 131 ~~S~YRGV~-~r~~GKW~A~I~~~~~nGkrv~LGtFdT~EEAA~AYD~AA~~~~ 183 (233)
...+|-||. |-..-|=.+.|.. .||-+.-|. .+.|+|..|.++.+..+.
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~---SGKiviTGa-ks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 32 NPKRFAAVIMRIREPKTTALIFA---SGKMVCTGA-KSEHDSKLAARKYARIIQ 81 (179)
T ss_pred CCccCcEEEEEeCCCcEEEEEEC---CCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 456889987 4444566788888 888776664 788999999988877763
No 13
>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=27.33 E-value=1.6e+02 Score=21.99 Aligned_cols=47 Identities=21% Similarity=0.162 Sum_probs=34.4
Q ss_pred CCceEEeE-ECCCCcEEEEEeCCCCCCcEEeccCCCCHHHHHHHHHHHHHHh
Q 047100 132 RMQYRGVR-RRPWGKFAAEIRDPKKNGARVWLGTYDTPEGAAFAYDRAAFKM 182 (233)
Q Consensus 132 ~S~YRGV~-~r~~GKW~A~I~~~~~nGkrv~LGtFdT~EEAA~AYD~AA~~~ 182 (233)
..+|.||. +-..-+-.+.|.. .||-+..|. .+.|+|..|.++....+
T Consensus 35 Pe~fpgl~~r~~~p~~t~~IF~---sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 35 PERFPGLIYRLRNPKATVLIFS---SGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTTESSEEEEETTTTEEEEEET---TSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred eccCCeEEEeecCCcEEEEEEc---CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 34788876 3334467778887 888777775 78999999998876654
No 14
>PRK09692 integrase; Provisional
Probab=27.30 E-value=1.8e+02 Score=27.10 Aligned_cols=38 Identities=13% Similarity=0.072 Sum_probs=24.3
Q ss_pred CcEEEEEeCCCCCCc--EEeccCCC--CHHHHHHHHHHHHHHh
Q 047100 144 GKFAAEIRDPKKNGA--RVWLGTYD--TPEGAAFAYDRAAFKM 182 (233)
Q Consensus 144 GKW~A~I~~~~~nGk--rv~LGtFd--T~EEAA~AYD~AA~~~ 182 (233)
..|+.+-+.+. +|+ ++-||.|+ |..+|..+..++...+
T Consensus 41 k~~~~rY~~~~-~gk~~~~~lG~yp~~sl~~AR~~a~~~~~~~ 82 (413)
T PRK09692 41 KIWQFRYYRPL-TKTRAKKSFGPYPSVTLADARNYRAESRSLL 82 (413)
T ss_pred EEEEEEEecCC-CCceeeeeCCCCCCCCHHHHHHHHHHHHHHH
Confidence 34998876532 233 36899999 6777766555544444
No 15
>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=24.75 E-value=2.9e+02 Score=23.70 Aligned_cols=47 Identities=26% Similarity=0.182 Sum_probs=35.7
Q ss_pred CCCceEEeEEC-CCCcEEEEEeCCCCCCcEEeccCCCCHHHHHHHHHHHHHHh
Q 047100 131 VRMQYRGVRRR-PWGKFAAEIRDPKKNGARVWLGTYDTPEGAAFAYDRAAFKM 182 (233)
Q Consensus 131 ~~S~YRGV~~r-~~GKW~A~I~~~~~nGkrv~LGtFdT~EEAA~AYD~AA~~~ 182 (233)
+. +|.||..| ..-|=.+.|+. +||-+.-| ..+.|+|..|.++.+..+
T Consensus 33 eP-~fpgli~R~~~Pk~t~lIF~---sGKiviTG-aks~~~~~~a~~~~~~~l 80 (174)
T cd04517 33 NP-RYPKVTMRLREPRATASVWS---SGKITITG-ATSEEEAKQAARRAARLL 80 (174)
T ss_pred eC-CCCEEEEEecCCcEEEEEEC---CCeEEEEc-cCCHHHHHHHHHHHHHHH
Confidence 44 89998743 44577888888 88866555 588999999999887766
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=24.24 E-value=1.5e+02 Score=22.74 Aligned_cols=42 Identities=19% Similarity=0.100 Sum_probs=24.9
Q ss_pred CCCCCceEEeEECCCCcEEEEEeCCCCCCcEEeccCCCCHHHHHHH
Q 047100 129 THVRMQYRGVRRRPWGKFAAEIRDPKKNGARVWLGTYDTPEGAAFA 174 (233)
Q Consensus 129 ~~~~S~YRGV~~r~~GKW~A~I~~~~~nGkrv~LGtFdT~EEAA~A 174 (233)
.-+--+||-|..-+ |||.|.+... -.-.---.|..+|.|-+-
T Consensus 27 a~k~dgfrdvw~lr-gkyvafvl~g---e~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 27 ALKMDGFRDVWQLR-GKYVAFVLMG---EHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp -B-TTTECCECCCC-CEEEEEEESS---S-EEE---BSSHHHHHHH
T ss_pred hhhcccccceeeec-cceEEEEEec---chhccCCCcCCcHHHHHH
Confidence 34566899986544 9999999972 122233567778777654
No 17
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=22.09 E-value=1.4e+02 Score=25.56 Aligned_cols=36 Identities=28% Similarity=0.154 Sum_probs=29.9
Q ss_pred cEEEEEeCCCCCCcEEeccCCCCHHHHHHHHHHHHHHhcC
Q 047100 145 KFAAEIRDPKKNGARVWLGTYDTPEGAAFAYDRAAFKMRG 184 (233)
Q Consensus 145 KW~A~I~~~~~nGkrv~LGtFdT~EEAA~AYD~AA~~~~G 184 (233)
.|.|+|.- |+-++-=....++.|..|.-+|+.+|=+
T Consensus 95 gwaArVkp----G~vlfei~g~~e~~A~EAlr~Aa~KLP~ 130 (146)
T COG0197 95 GWAARVKP----GRVLFEIAGVPEELAREALRRAAAKLPV 130 (146)
T ss_pred EEEEEecC----CcEEEEEecCcHHHHHHHHHHHhhcCCC
Confidence 39999986 6777777788899999999999988744
No 18
>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=21.11 E-value=3.6e+02 Score=23.22 Aligned_cols=49 Identities=27% Similarity=0.189 Sum_probs=36.5
Q ss_pred CCCceEEeE-ECCCCcEEEEEeCCCCCCcEEeccCCCCHHHHHHHHHHHHHHhc
Q 047100 131 VRMQYRGVR-RRPWGKFAAEIRDPKKNGARVWLGTYDTPEGAAFAYDRAAFKMR 183 (233)
Q Consensus 131 ~~S~YRGV~-~r~~GKW~A~I~~~~~nGkrv~LGtFdT~EEAA~AYD~AA~~~~ 183 (233)
+..+|.||. |-..-+=.+.|.. .||-+.-|. .+.++|..|-++.+..+.
T Consensus 32 ~P~~fpgli~Rl~~Pk~t~lIF~---SGKiv~tGa-ks~~~a~~a~~~~~~~L~ 81 (174)
T cd04518 32 NPDQFPGLVYRLEDPKIAALIFR---SGKMVCTGA-KSVEDLHRAVKEIIKKLK 81 (174)
T ss_pred CCCcCcEEEEEccCCcEEEEEEC---CCeEEEEcc-CCHHHHHHHHHHHHHHHH
Confidence 457899987 4344566777777 888777675 788999999888877664
Done!