Query 030002
Match_columns 184
No_of_seqs 172 out of 1199
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 06:59:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030002.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030002hhsearch_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 99.9 1E-21 2.2E-26 135.1 7.4 61 93-154 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 1.4E-20 3.1E-25 131.0 8.3 63 94-157 1-63 (64)
3 PHA00280 putative NHN endonucl 99.6 6.2E-16 1.4E-20 121.4 7.3 82 63-148 31-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.3 4.7E-12 1E-16 84.9 6.7 53 93-145 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 81.6 5.3 0.00012 25.7 5.1 38 105-142 1-41 (46)
6 PF08846 DUF1816: Domain of un 74.5 6.1 0.00013 28.5 4.1 39 104-143 8-46 (68)
7 PHA02601 int integrase; Provis 74.4 5.2 0.00011 34.3 4.4 45 97-142 2-46 (333)
8 cd00801 INT_P4 Bacteriophage P 48.6 43 0.00093 28.2 5.3 38 104-142 10-49 (357)
9 PF08471 Ribonuc_red_2_N: Clas 46.6 22 0.00048 27.1 2.9 20 123-142 71-90 (93)
10 PF05036 SPOR: Sporulation rel 46.5 14 0.0003 24.5 1.6 23 117-139 43-65 (76)
11 COG0197 RplP Ribosomal protein 39.8 45 0.00097 27.4 3.8 37 105-145 95-131 (146)
12 cd04516 TBP_eukaryotes eukaryo 37.5 1.6E+02 0.0034 24.4 6.8 48 91-142 32-80 (174)
13 cd00652 TBP_TLF TATA box bindi 32.6 1.7E+02 0.0037 24.0 6.3 48 91-142 32-80 (174)
14 PF00352 TBP: Transcription fa 30.4 1.3E+02 0.0028 21.5 4.7 46 93-142 36-82 (86)
15 PRK09692 integrase; Provisiona 29.8 1.7E+02 0.0036 26.2 6.3 43 98-140 33-80 (413)
16 PF14112 DUF4284: Domain of un 28.3 33 0.00071 26.7 1.3 17 119-135 3-19 (122)
17 PLN00062 TATA-box-binding prot 27.0 2.9E+02 0.0062 23.0 6.8 48 91-142 32-80 (179)
18 TIGR01164 rplP_bact ribosomal 26.6 1.1E+02 0.0023 24.1 4.0 35 104-142 90-124 (126)
19 PRK09203 rplP 50S ribosomal pr 26.4 97 0.0021 24.8 3.7 37 104-144 91-127 (138)
20 CHL00044 rpl16 ribosomal prote 25.9 1.1E+02 0.0023 24.5 3.9 37 104-144 91-127 (135)
21 PF10729 CedA: Cell division a 24.0 1.5E+02 0.0033 21.8 4.0 39 92-134 30-68 (80)
22 PRK00394 transcription factor; 23.6 2.9E+02 0.0064 22.8 6.2 48 91-142 31-79 (179)
23 KOG3422 Mitochondrial ribosoma 22.7 1.6E+02 0.0035 25.8 4.6 39 104-146 132-171 (221)
24 cd04517 TLF TBP-like factors ( 21.4 3.3E+02 0.0072 22.4 6.1 45 94-142 35-80 (174)
25 cd04518 TBP_archaea archaeal T 21.4 3.7E+02 0.008 22.2 6.4 48 91-142 32-80 (174)
26 PF09954 DUF2188: Uncharacteri 20.6 2.6E+02 0.0057 18.6 4.5 38 98-140 3-40 (62)
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=99.86 E-value=1e-21 Score=135.07 Aligned_cols=61 Identities=62% Similarity=1.211 Sum_probs=56.9
Q ss_pred ccceeeEEcCCCeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 030002 93 KHYRGVRRRPWGKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRMRGRKAILNFPLE 154 (184)
Q Consensus 93 S~YRGV~~~~~GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l~G~~A~lNFp~~ 154 (184)
|+|+||+++++|+|+|+|+++. .|+++|||+|+|+||||+|||.++++++|.++.+|||++
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 279999999999999999999999999999999999975
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.83 E-value=1.4e-20 Score=130.96 Aligned_cols=63 Identities=67% Similarity=1.191 Sum_probs=58.7
Q ss_pred cceeeEEcCCCeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q 030002 94 HYRGVRRRPWGKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRMRGRKAILNFPLEAGA 157 (184)
Q Consensus 94 ~YRGV~~~~~GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l~G~~A~lNFp~~~~~ 157 (184)
+|+||+++++|+|+|+|+++. +|+++|||+|+|+||||+|||.++++++|.++.+|||.+.+.
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 599999988899999999876 479999999999999999999999999999999999998764
No 3
>PHA00280 putative NHN endonuclease
Probab=99.63 E-value=6.2e-16 Score=121.40 Aligned_cols=82 Identities=12% Similarity=-0.008 Sum_probs=65.5
Q ss_pred cccccCCCCCCCCCCCCCC------CCCCcCCcCCCccceeeEEcCC-CeEEEEEecCCCCCcEEecCCCCCHHHHHHHH
Q 030002 63 PLDITCLGSSNWTESPQKS------SEPKLADTEERKHYRGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAY 135 (184)
Q Consensus 63 ~~~~~~~~~~~~~~~p~k~------~~~~~~~~~~tS~YRGV~~~~~-GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAY 135 (184)
.+||.+.+..++...+.+. ...++..+.++|+|+||+|.+. |||+|+|.+ +||+++||.|+++|+|+.||
T Consensus 31 ~VdHidg~~~dnri~NLr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~---~gK~~~lG~f~~~e~A~~a~ 107 (121)
T PHA00280 31 YIDHIDGNPLNDALDNLRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA---EGKQHNFRSRDLLEVVAWIY 107 (121)
T ss_pred EEEcCCCCCCCCcHHHhhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE---CCEEEEcCCCCCHHHHHHHH
Confidence 6788877776653332222 2233455678999999998765 999999999 89999999999999999999
Q ss_pred HHHHHHhcCCCCC
Q 030002 136 DSAAFRMRGRKAI 148 (184)
Q Consensus 136 D~AA~~l~G~~A~ 148 (184)
+ ++.++||++|.
T Consensus 108 ~-~~~~lhGeFa~ 119 (121)
T PHA00280 108 R-TRRELHGQFAR 119 (121)
T ss_pred H-HHHHHhhcccc
Confidence 7 77889999985
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=99.32 E-value=4.7e-12 Score=84.88 Aligned_cols=53 Identities=28% Similarity=0.440 Sum_probs=46.5
Q ss_pred ccceeeEEcCC-CeEEEEEecCCCCC--cEEecCCCCCHHHHHHHHHHHHHHhcCC
Q 030002 93 KHYRGVRRRPW-GKYAAEIRDPARKG--SRVWLGTFDSDVDAAKAYDSAAFRMRGR 145 (184)
Q Consensus 93 S~YRGV~~~~~-GkW~A~I~~~~~~G--k~i~LGtFdT~eEAArAYD~AA~~l~G~ 145 (184)
|+|+||++.+. ++|+|+|++...+| ++++||.|++++||++||+.++..++|+
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 99999999854343 8999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=81.55 E-value=5.3 Score=25.72 Aligned_cols=38 Identities=13% Similarity=0.094 Sum_probs=28.0
Q ss_pred eEEEEEe-cC--CCCCcEEecCCCCCHHHHHHHHHHHHHHh
Q 030002 105 KYAAEIR-DP--ARKGSRVWLGTFDSDVDAAKAYDSAAFRM 142 (184)
Q Consensus 105 kW~A~I~-~~--~~~Gk~i~LGtFdT~eEAArAYD~AA~~l 142 (184)
+|..+|. .. ..+-++++-+.|.|..||-.+...+...+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5788883 32 22336688999999999999988876655
No 6
>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=74.48 E-value=6.1 Score=28.49 Aligned_cols=39 Identities=21% Similarity=0.252 Sum_probs=28.8
Q ss_pred CeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHhc
Q 030002 104 GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRMR 143 (184)
Q Consensus 104 GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l~ 143 (184)
-.|.++|.-...+ -.+|.|-|+|.+||..+.---...+-
T Consensus 8 laWWveI~T~~P~-ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 8 LAWWVEIETQNPN-CTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred CcEEEEEEcCCCC-EEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 3588999864333 57899999999999988665554443
No 7
>PHA02601 int integrase; Provisional
Probab=74.39 E-value=5.2 Score=34.34 Aligned_cols=45 Identities=24% Similarity=0.304 Sum_probs=30.7
Q ss_pred eeEEcCCCeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHh
Q 030002 97 GVRRRPWGKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 142 (184)
Q Consensus 97 GV~~~~~GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l 142 (184)
+|+..++|+|+++++.....|+++.. +|.|..||....+.....+
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 46666678999999863334676653 6999988876665544433
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=48.61 E-value=43 Score=28.23 Aligned_cols=38 Identities=21% Similarity=0.257 Sum_probs=25.3
Q ss_pred CeEEEEEecCCCCCcEEecCCCC--CHHHHHHHHHHHHHHh
Q 030002 104 GKYAAEIRDPARKGSRVWLGTFD--SDVDAAKAYDSAAFRM 142 (184)
Q Consensus 104 GkW~A~I~~~~~~Gk~i~LGtFd--T~eEAArAYD~AA~~l 142 (184)
+.|+.+++...+ .+++.||+|+ +.++|..........+
T Consensus 10 ~~~~~~~~~~g~-~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGK-RKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCc-eeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 569999888432 2457799995 6667766666544444
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=46.61 E-value=22 Score=27.14 Aligned_cols=20 Identities=30% Similarity=0.607 Sum_probs=17.7
Q ss_pred CCCCCHHHHHHHHHHHHHHh
Q 030002 123 GTFDSDVDAAKAYDSAAFRM 142 (184)
Q Consensus 123 GtFdT~eEAArAYD~AA~~l 142 (184)
|+|+|+++|..-||..+..|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999877644
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=46.51 E-value=14 Score=24.54 Aligned_cols=23 Identities=30% Similarity=0.319 Sum_probs=19.4
Q ss_pred CcEEecCCCCCHHHHHHHHHHHH
Q 030002 117 GSRVWLGTFDSDVDAAKAYDSAA 139 (184)
Q Consensus 117 Gk~i~LGtFdT~eEAArAYD~AA 139 (184)
..++.+|.|+|.+||..+-....
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 46899999999999988877655
No 11
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=39.77 E-value=45 Score=27.38 Aligned_cols=37 Identities=19% Similarity=0.154 Sum_probs=31.6
Q ss_pred eEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHhcCC
Q 030002 105 KYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRMRGR 145 (184)
Q Consensus 105 kW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l~G~ 145 (184)
.|+|+|.. |+.++-=..++++.|..|..+|+.+|=+.
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 49999996 78888888889999999999999987544
No 12
>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=37.46 E-value=1.6e+02 Score=24.42 Aligned_cols=48 Identities=27% Similarity=0.157 Sum_probs=37.3
Q ss_pred CCccceeeEEcCC-CeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHh
Q 030002 91 ERKHYRGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 142 (184)
Q Consensus 91 ~tS~YRGV~~~~~-GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l 142 (184)
+..+|-|+..|-. -+-.+.|.. .||-+--|.. ++++|..|.++.+..+
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~---SGKiviTGak-s~e~a~~a~~~i~~~L 80 (174)
T cd04516 32 NPKRFAAVIMRIREPKTTALIFS---SGKMVCTGAK-SEDDSKLAARKYARII 80 (174)
T ss_pred CCccCcEEEEEeCCCcEEEEEEC---CCeEEEEecC-CHHHHHHHHHHHHHHH
Confidence 3457889866644 567788887 7888888875 8899999999887766
No 13
>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=32.63 E-value=1.7e+02 Score=24.03 Aligned_cols=48 Identities=31% Similarity=0.212 Sum_probs=36.7
Q ss_pred CCccceeeEEcCC-CeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHh
Q 030002 91 ERKHYRGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 142 (184)
Q Consensus 91 ~tS~YRGV~~~~~-GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l 142 (184)
+..+|.||.+|-. -+-.+-|.. .||-+--|.. +.++|..|.++.+..+
T Consensus 32 ePe~fpgli~R~~~P~~t~lIf~---sGKivitGak-s~~~~~~a~~~~~~~L 80 (174)
T cd00652 32 NPKRFPGVIMRLREPKTTALIFS---SGKMVITGAK-SEEDAKLAARKYARIL 80 (174)
T ss_pred CCCccceEEEEcCCCcEEEEEEC---CCEEEEEecC-CHHHHHHHHHHHHHHH
Confidence 3467899876654 567777777 7888877875 8899999998877766
No 14
>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=30.43 E-value=1.3e+02 Score=21.55 Aligned_cols=46 Identities=24% Similarity=0.234 Sum_probs=34.5
Q ss_pred ccceeeEEcCC-CeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHh
Q 030002 93 KHYRGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 142 (184)
Q Consensus 93 S~YRGV~~~~~-GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l 142 (184)
.+|.||..+-. -+-.+.|.. .||-+..|. .+.++|..|.++....+
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 47888865543 466777776 788888886 58999999999876654
No 15
>PRK09692 integrase; Provisional
Probab=29.84 E-value=1.7e+02 Score=26.22 Aligned_cols=43 Identities=12% Similarity=0.151 Sum_probs=24.9
Q ss_pred eEEcCCC--eEEEEEecCC-CCCcEEecCCCC--CHHHHHHHHHHHHH
Q 030002 98 VRRRPWG--KYAAEIRDPA-RKGSRVWLGTFD--SDVDAAKAYDSAAF 140 (184)
Q Consensus 98 V~~~~~G--kW~A~I~~~~-~~Gk~i~LGtFd--T~eEAArAYD~AA~ 140 (184)
|+..+.| .|..+-+.+. ++.+++-||.|. |..+|..+-..+..
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~ 80 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRS 80 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHH
Confidence 3445554 5988876432 222336899999 66666555444333
No 16
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=28.33 E-value=33 Score=26.67 Aligned_cols=17 Identities=24% Similarity=0.825 Sum_probs=13.1
Q ss_pred EEecCCCCCHHHHHHHH
Q 030002 119 RVWLGTFDSDVDAAKAY 135 (184)
Q Consensus 119 ~i~LGtFdT~eEAArAY 135 (184)
.+|||+|.|++|-..=.
T Consensus 3 siWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 3 SIWIGNFKSEDELEEYF 19 (122)
T ss_pred EEEEecCCCHHHHHHHh
Confidence 58999999888765443
No 17
>PLN00062 TATA-box-binding protein; Provisional
Probab=26.99 E-value=2.9e+02 Score=23.01 Aligned_cols=48 Identities=27% Similarity=0.184 Sum_probs=36.2
Q ss_pred CCccceeeEEcCC-CeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHh
Q 030002 91 ERKHYRGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 142 (184)
Q Consensus 91 ~tS~YRGV~~~~~-GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l 142 (184)
+..+|-|+..|-. -+-.+-|.. .||-+--|. .++++|..|.++.+..+
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 3457899866643 567788887 787777775 58899999999887766
No 18
>TIGR01164 rplP_bact ribosomal protein L16, bacterial/organelle. This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10
Probab=26.55 E-value=1.1e+02 Score=24.11 Aligned_cols=35 Identities=17% Similarity=0.152 Sum_probs=27.5
Q ss_pred CeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHh
Q 030002 104 GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 142 (184)
Q Consensus 104 GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l 142 (184)
-.|+|+|.. |+.++=-.-.+++.|..|..+|+.++
T Consensus 90 ~~~varV~~----G~ilfEi~~~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 90 EYWVAVVKP----GKILFEIAGVPEEVAREAFRLAASKL 124 (126)
T ss_pred CEEEEEECC----CCEEEEEeCCCHHHHHHHHHHHHhcC
Confidence 459999996 67766433389999999999998765
No 19
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=26.44 E-value=97 Score=24.75 Aligned_cols=37 Identities=19% Similarity=0.057 Sum_probs=28.8
Q ss_pred CeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHhcC
Q 030002 104 GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRMRG 144 (184)
Q Consensus 104 GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l~G 144 (184)
-.|+|+|.. |+-++=-.-.+++.|..|..+|+.++=+
T Consensus 91 ~~~varVk~----G~iifEi~~~~~~~a~~al~~a~~KLP~ 127 (138)
T PRK09203 91 EYWVAVVKP----GRILFEIAGVSEELAREALRLAAAKLPI 127 (138)
T ss_pred cEEEEEECC----CCEEEEEeCCCHHHHHHHHHHHhccCCC
Confidence 459999996 6776533338999999999999987754
No 20
>CHL00044 rpl16 ribosomal protein L16
Probab=25.87 E-value=1.1e+02 Score=24.47 Aligned_cols=37 Identities=22% Similarity=0.143 Sum_probs=27.7
Q ss_pred CeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHhcC
Q 030002 104 GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRMRG 144 (184)
Q Consensus 104 GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l~G 144 (184)
-.|+|+|.. |+-++=-.-.+++.|..|...|+.++=+
T Consensus 91 ~~~va~V~~----G~ilfEi~g~~~~~ak~al~~a~~KLP~ 127 (135)
T CHL00044 91 EYWVAVVKP----GRILYEMGGVSETIARAAIKIAAYKMPI 127 (135)
T ss_pred cEEEEEECC----CcEEEEEeCCCHHHHHHHHHHHhhcCCC
Confidence 459999996 6776633346778999999999887643
No 21
>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=23.96 E-value=1.5e+02 Score=21.79 Aligned_cols=39 Identities=21% Similarity=0.133 Sum_probs=24.2
Q ss_pred CccceeeEEcCCCeEEEEEecCCCCCcEEecCCCCCHHHHHHH
Q 030002 92 RKHYRGVRRRPWGKYAAEIRDPARKGSRVWLGTFDSDVDAAKA 134 (184)
Q Consensus 92 tS~YRGV~~~~~GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArA 134 (184)
--+||.|+.-. |||+|.+.. ...-.---.|..+|.|.|-
T Consensus 30 ~dgfrdvw~lr-gkyvafvl~---ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 30 MDGFRDVWQLR-GKYVAFVLM---GEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTTECCECCCC-CEEEEEEES---SS-EEE---BSSHHHHHHH
T ss_pred cccccceeeec-cceEEEEEe---cchhccCCCcCCcHHHHHH
Confidence 45788885444 999999987 2122234567778777665
No 22
>PRK00394 transcription factor; Reviewed
Probab=23.64 E-value=2.9e+02 Score=22.85 Aligned_cols=48 Identities=25% Similarity=0.171 Sum_probs=36.9
Q ss_pred CCccceeeEEcCC-CeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHh
Q 030002 91 ERKHYRGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 142 (184)
Q Consensus 91 ~tS~YRGV~~~~~-GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l 142 (184)
+..+|-|+..|-. -+-.+.|.. .||-+--|.. +.++|..|-++.+..+
T Consensus 31 ePe~fpgli~Rl~~Pk~t~lIf~---sGKiv~tGa~-S~~~a~~a~~~~~~~l 79 (179)
T PRK00394 31 NPEQFPGLVYRLEDPKIAALIFR---SGKVVCTGAK-SVEDLHEAVKIIIKKL 79 (179)
T ss_pred CcccCceEEEEecCCceEEEEEc---CCcEEEEccC-CHHHHHHHHHHHHHHH
Confidence 3457889866644 577888887 7988888986 8889999988876655
No 23
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=22.65 E-value=1.6e+02 Score=25.76 Aligned_cols=39 Identities=18% Similarity=0.290 Sum_probs=30.9
Q ss_pred CeEEEEEecCCCCCcEEe-cCCCCCHHHHHHHHHHHHHHhcCCC
Q 030002 104 GKYAAEIRDPARKGSRVW-LGTFDSDVDAAKAYDSAAFRMRGRK 146 (184)
Q Consensus 104 GkW~A~I~~~~~~Gk~i~-LGtFdT~eEAArAYD~AA~~l~G~~ 146 (184)
..|+|.|.. |+-++ +|---++++|..|.+.||.++-+..
T Consensus 132 d~wva~V~~----GrIl~EmgG~~~~~~Ar~al~~aa~klp~~~ 171 (221)
T KOG3422|consen 132 DHWVARVKA----GRILFEMGGDVEEEEARQALLQAAHKLPFKY 171 (221)
T ss_pred ceeEEEecC----CcEEEEeCCcccHHHHHHHHHHHHhcCCccE
Confidence 359999996 55554 7777899999999999999875543
No 24
>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=21.38 E-value=3.3e+02 Score=22.38 Aligned_cols=45 Identities=24% Similarity=0.242 Sum_probs=35.2
Q ss_pred cceeeEEcCC-CeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHh
Q 030002 94 HYRGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 142 (184)
Q Consensus 94 ~YRGV~~~~~-GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l 142 (184)
+|.||..|-. -+-.+-|+. .||-+--|. .+.++|++|.++.+..+
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~---sGKiviTGa-ks~~~~~~a~~~~~~~l 80 (174)
T cd04517 35 RYPKVTMRLREPRATASVWS---SGKITITGA-TSEEEAKQAARRAARLL 80 (174)
T ss_pred CCCEEEEEecCCcEEEEEEC---CCeEEEEcc-CCHHHHHHHHHHHHHHH
Confidence 8999876643 677888887 787766665 68999999999877766
No 25
>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=21.38 E-value=3.7e+02 Score=22.18 Aligned_cols=48 Identities=25% Similarity=0.219 Sum_probs=36.3
Q ss_pred CCccceeeEEcCC-CeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHh
Q 030002 91 ERKHYRGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 142 (184)
Q Consensus 91 ~tS~YRGV~~~~~-GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~~l 142 (184)
+..+|.|+..|-. -+-.+-|.. .||-+--|. .+.++|..|-++.+..+
T Consensus 32 ~P~~fpgli~Rl~~Pk~t~lIF~---SGKiv~tGa-ks~~~a~~a~~~~~~~L 80 (174)
T cd04518 32 NPDQFPGLVYRLEDPKIAALIFR---SGKMVCTGA-KSVEDLHRAVKEIIKKL 80 (174)
T ss_pred CCCcCcEEEEEccCCcEEEEEEC---CCeEEEEcc-CCHHHHHHHHHHHHHHH
Confidence 3467999876653 567777776 788877776 58999999998877766
No 26
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=20.64 E-value=2.6e+02 Score=18.62 Aligned_cols=38 Identities=26% Similarity=0.230 Sum_probs=24.6
Q ss_pred eEEcCCCeEEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHH
Q 030002 98 VRRRPWGKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAF 140 (184)
Q Consensus 98 V~~~~~GkW~A~I~~~~~~Gk~i~LGtFdT~eEAArAYD~AA~ 140 (184)
|..+..|.|...... ..--..+|+|.+||-.+=...|.
T Consensus 3 V~p~~~~~W~v~~eg-----~~ra~~~~~Tk~eAi~~Ar~~a~ 40 (62)
T PF09954_consen 3 VVPREDGGWAVKKEG-----AKRASKTFDTKAEAIEAARELAK 40 (62)
T ss_pred EEecCCCCceEEeCC-----CcccccccCcHHHHHHHHHHHHH
Confidence 344445789888774 22337999998888765444444
Done!