Query 048608
Match_columns 152
No_of_seqs 190 out of 1240
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 11:08:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048608.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048608hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00380 AP2 DNA-binding dom 99.9 2.3E-22 5E-27 134.3 7.7 63 22-85 1-63 (64)
2 cd00018 AP2 DNA-binding domain 99.9 2.2E-22 4.7E-27 132.9 7.0 61 21-82 1-61 (61)
3 PHA00280 putative NHN endonucl 99.7 8.1E-18 1.8E-22 125.9 6.5 71 2-76 48-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.3 2E-12 4.4E-17 83.3 5.7 53 21-73 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 89.2 1.4 3E-05 27.1 5.0 38 33-70 1-41 (46)
6 PHA02601 int integrase; Provis 79.7 3.1 6.7E-05 34.4 4.4 45 25-70 2-46 (333)
7 PF05036 SPOR: Sporulation rel 62.3 4.3 9.4E-05 25.9 1.1 22 46-67 44-65 (76)
8 PF08846 DUF1816: Domain of un 61.0 19 0.0004 24.5 4.0 32 32-64 8-39 (68)
9 cd00801 INT_P4 Bacteriophage P 53.8 31 0.00067 28.0 5.1 39 32-71 10-50 (357)
10 PF08471 Ribonuc_red_2_N: Clas 44.8 25 0.00054 25.4 2.8 20 51-70 71-90 (93)
11 COG0197 RplP Ribosomal protein 39.2 48 0.001 25.8 3.8 36 34-73 96-131 (146)
12 PF14112 DUF4284: Domain of un 38.0 21 0.00046 26.3 1.6 18 46-63 2-19 (122)
13 PF09954 DUF2188: Uncharacteri 35.2 1.2E+02 0.0026 19.3 4.7 39 26-69 3-41 (62)
14 PRK09692 integrase; Provisiona 34.2 1.3E+02 0.0029 25.7 6.2 39 26-65 33-77 (413)
15 COG2185 Sbm Methylmalonyl-CoA 32.0 36 0.00079 26.3 2.1 18 46-63 42-59 (143)
16 PF13356 DUF4102: Domain of un 30.5 1.5E+02 0.0032 20.0 4.8 38 32-70 35-74 (89)
17 PF00352 TBP: Transcription fa 28.5 1.7E+02 0.0037 19.8 4.9 46 21-70 36-82 (86)
18 PF12286 DUF3622: Protein of u 27.6 1.2E+02 0.0027 20.7 3.9 30 31-60 15-47 (71)
19 TIGR01164 rplP_bact ribosomal 26.8 1.1E+02 0.0024 22.8 3.9 34 33-70 91-124 (126)
20 PRK09203 rplP 50S ribosomal pr 26.6 1E+02 0.0022 23.4 3.7 35 34-72 93-127 (138)
21 PLN00062 TATA-box-binding prot 25.4 3.4E+02 0.0074 21.4 6.8 47 20-70 33-80 (179)
22 CHL00044 rpl16 ribosomal prote 25.2 1.2E+02 0.0025 23.0 3.8 34 34-71 93-126 (135)
23 cd04516 TBP_eukaryotes eukaryo 24.3 3.5E+02 0.0076 21.2 6.9 47 20-70 33-80 (174)
24 PF13773 DUF4170: Domain of un 23.9 78 0.0017 21.6 2.3 23 48-70 27-49 (69)
25 PF14882 GHL12: Hypothetical g 22.5 63 0.0014 20.6 1.6 11 52-62 39-49 (53)
26 cd04517 TLF TBP-like factors ( 21.4 3.7E+02 0.0081 21.0 6.1 45 22-70 35-80 (174)
27 PF11453 DUF2950: Protein of u 20.3 89 0.0019 26.7 2.5 17 52-68 3-19 (271)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.87 E-value=2.3e-22 Score=134.26 Aligned_cols=63 Identities=75% Similarity=1.330 Sum_probs=59.6
Q ss_pred ceeEeEECCCCcEEEEEeCCCCCCeEEecCCCCCHHHHHHHHHHHHHhhcCCCCCCCCCCchhh
Q 048608 22 RYRGVRRRPWGKFAAEIRDPSRQGARLWLGTFETAEEAARAYDRAAFNMRGHLAILNFPNEYYS 85 (152)
Q Consensus 22 ~yrGV~~~~~gkw~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~~G~~a~~Nfp~~~y~ 85 (152)
+|+||+++++|+|.|+|+++. +|+++|||+|+|+||||.|||.++++++|..+.+|||.++|.
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 589999988999999999976 479999999999999999999999999999999999999986
No 2
>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.
Probab=99.87 E-value=2.2e-22 Score=132.89 Aligned_cols=61 Identities=72% Similarity=1.310 Sum_probs=57.0
Q ss_pred cceeEeEECCCCcEEEEEeCCCCCCeEEecCCCCCHHHHHHHHHHHHHhhcCCCCCCCCCCc
Q 048608 21 VRYRGVRRRPWGKFAAEIRDPSRQGARLWLGTFETAEEAARAYDRAAFNMRGHLAILNFPNE 82 (152)
Q Consensus 21 S~yrGV~~~~~gkw~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~~G~~a~~Nfp~~ 82 (152)
|+|+||+++++|+|+|+|+++. .|+++|||+|+|+||||.|||.++++++|..+.+|||++
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 6899999988999999999954 289999999999999999999999999999999999974
No 3
>PHA00280 putative NHN endonuclease
Probab=99.72 E-value=8.1e-18 Score=125.94 Aligned_cols=71 Identities=10% Similarity=0.141 Sum_probs=64.1
Q ss_pred CCCCcchhhhhhhhcCCCCcceeEeEECC-CCcEEEEEeCCCCCCeEEecCCCCCHHHHHHHHHHHHHhhcCCCCC
Q 048608 2 EKPSKGKERQEKEEKRREEVRYRGVRRRP-WGKFAAEIRDPSRQGARLWLGTFETAEEAARAYDRAAFNMRGHLAI 76 (152)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~S~yrGV~~~~-~gkw~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~~G~~a~ 76 (152)
+..+..+|.+|+..+++|+|+|+||++.+ .|||.|+|.+ +||+++||.|+|+|+|+.||+ ++.++||++|.
T Consensus 48 r~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~---~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 48 RLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA---EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred hhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE---CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 44577899999999999999999999754 6999999999 899999999999999999997 77899999885
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=99.35 E-value=2e-12 Score=83.26 Aligned_cols=53 Identities=36% Similarity=0.486 Sum_probs=46.0
Q ss_pred cceeEeEECC-CCcEEEEEeCCCCCC--eEEecCCCCCHHHHHHHHHHHHHhhcCC
Q 048608 21 VRYRGVRRRP-WGKFAAEIRDPSRQG--ARLWLGTFETAEEAARAYDRAAFNMRGH 73 (152)
Q Consensus 21 S~yrGV~~~~-~gkw~A~I~~~~~~g--k~~~LGtF~t~EeAA~AYD~aa~~~~G~ 73 (152)
|+|+||++.+ .++|.|+|+++..+| +.++||.|++++||++|++.++..++|+
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 7899999655 699999999854443 9999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=89.23 E-value=1.4 Score=27.06 Aligned_cols=38 Identities=16% Similarity=0.203 Sum_probs=29.0
Q ss_pred cEEEEEe--CC-CCCCeEEecCCCCCHHHHHHHHHHHHHhh
Q 048608 33 KFAAEIR--DP-SRQGARLWLGTFETAEEAARAYDRAAFNM 70 (152)
Q Consensus 33 kw~A~I~--~~-~~~gk~~~LGtF~t~EeAA~AYD~aa~~~ 70 (152)
+|...|. ++ ..+-++++-+.|.|..||-.+...+...+
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 33 23337788999999999999988877665
No 6
>PHA02601 int integrase; Provisional
Probab=79.68 E-value=3.1 Score=34.39 Aligned_cols=45 Identities=29% Similarity=0.327 Sum_probs=31.2
Q ss_pred EeEECCCCcEEEEEeCCCCCCeEEecCCCCCHHHHHHHHHHHHHhh
Q 048608 25 GVRRRPWGKFAAEIRDPSRQGARLWLGTFETAEEAARAYDRAAFNM 70 (152)
Q Consensus 25 GV~~~~~gkw~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~ 70 (152)
+|++.++|+|.+++......|+++.. +|.|..||-...+.....+
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 46667789999999863334777664 6999999876655544433
No 7
>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=62.29 E-value=4.3 Score=25.95 Aligned_cols=22 Identities=32% Similarity=0.478 Sum_probs=18.1
Q ss_pred eEEecCCCCCHHHHHHHHHHHH
Q 048608 46 ARLWLGTFETAEEAARAYDRAA 67 (152)
Q Consensus 46 k~~~LGtF~t~EeAA~AYD~aa 67 (152)
-+|.+|.|+|.++|..+-....
T Consensus 44 yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 44 YRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp EEEEECCECTCCHHHHHHHHHH
T ss_pred EEEEECCCCCHHHHHHHHHHHh
Confidence 4688999999999988876655
No 8
>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=60.99 E-value=19 Score=24.53 Aligned_cols=32 Identities=25% Similarity=0.396 Sum_probs=24.8
Q ss_pred CcEEEEEeCCCCCCeEEecCCCCCHHHHHHHHH
Q 048608 32 GKFAAEIRDPSRQGARLWLGTFETAEEAARAYD 64 (152)
Q Consensus 32 gkw~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD 64 (152)
-.|=++|.-..- ....|.|-|+|.+||..+--
T Consensus 8 laWWveI~T~~P-~ctYyFGPF~s~~eA~~~~~ 39 (68)
T PF08846_consen 8 LAWWVEIETQNP-NCTYYFGPFDSREEAEAALP 39 (68)
T ss_pred CcEEEEEEcCCC-CEEEEeCCcCCHHHHHHHhc
Confidence 347788877543 37799999999999998743
No 9
>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=53.78 E-value=31 Score=28.03 Aligned_cols=39 Identities=23% Similarity=0.269 Sum_probs=27.6
Q ss_pred CcEEEEEeCCCCCCeEEecCCCC--CHHHHHHHHHHHHHhhc
Q 048608 32 GKFAAEIRDPSRQGARLWLGTFE--TAEEAARAYDRAAFNMR 71 (152)
Q Consensus 32 gkw~A~I~~~~~~gk~~~LGtF~--t~EeAA~AYD~aa~~~~ 71 (152)
+.|..++....+ .+++.||+|+ |.++|..........+.
T Consensus 10 ~~~~~~~~~~g~-~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 10 KSWRFRYRLAGK-RKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred EEEEEEeccCCc-eeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 569999988543 3567899996 67777777666555553
No 10
>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=44.78 E-value=25 Score=25.36 Aligned_cols=20 Identities=35% Similarity=0.634 Sum_probs=17.2
Q ss_pred CCCCCHHHHHHHHHHHHHhh
Q 048608 51 GTFETAEEAARAYDRAAFNM 70 (152)
Q Consensus 51 GtF~t~EeAA~AYD~aa~~~ 70 (152)
|+|+|+|+|..=||.-+..+
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999876544
No 11
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=39.22 E-value=48 Score=25.76 Aligned_cols=36 Identities=28% Similarity=0.225 Sum_probs=30.2
Q ss_pred EEEEEeCCCCCCeEEecCCCCCHHHHHHHHHHHHHhhcCC
Q 048608 34 FAAEIRDPSRQGARLWLGTFETAEEAARAYDRAAFNMRGH 73 (152)
Q Consensus 34 w~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~~G~ 73 (152)
|.|+|.. |+-++-=...+++.|..|.-+|+.++=+.
T Consensus 96 waArVkp----G~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 96 WAARVKP----GRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEecC----CcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 9999975 78888777888999999999999887443
No 12
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=37.95 E-value=21 Score=26.35 Aligned_cols=18 Identities=22% Similarity=0.831 Sum_probs=13.8
Q ss_pred eEEecCCCCCHHHHHHHH
Q 048608 46 ARLWLGTFETAEEAARAY 63 (152)
Q Consensus 46 k~~~LGtF~t~EeAA~AY 63 (152)
..||||+|.|.++-..=.
T Consensus 2 VsiWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYF 19 (122)
T ss_pred eEEEEecCCCHHHHHHHh
Confidence 469999999987766443
No 13
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=35.18 E-value=1.2e+02 Score=19.29 Aligned_cols=39 Identities=33% Similarity=0.247 Sum_probs=25.4
Q ss_pred eEECCCCcEEEEEeCCCCCCeEEecCCCCCHHHHHHHHHHHHHh
Q 048608 26 VRRRPWGKFAAEIRDPSRQGARLWLGTFETAEEAARAYDRAAFN 69 (152)
Q Consensus 26 V~~~~~gkw~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~ 69 (152)
|+.+..+.|....-. ...-..+|+|.+||..+=...+..
T Consensus 3 V~p~~~~~W~v~~eg-----~~ra~~~~~Tk~eAi~~Ar~~a~~ 41 (62)
T PF09954_consen 3 VVPREDGGWAVKKEG-----AKRASKTFDTKAEAIEAARELAKN 41 (62)
T ss_pred EEecCCCCceEEeCC-----CcccccccCcHHHHHHHHHHHHHh
Confidence 444455779888753 333478999999998665444433
No 14
>PRK09692 integrase; Provisional
Probab=34.18 E-value=1.3e+02 Score=25.74 Aligned_cols=39 Identities=15% Similarity=0.173 Sum_probs=23.4
Q ss_pred eEECCCC--cEEEEEeCCCCCCeE--EecCCCC--CHHHHHHHHHH
Q 048608 26 VRRRPWG--KFAAEIRDPSRQGAR--LWLGTFE--TAEEAARAYDR 65 (152)
Q Consensus 26 V~~~~~g--kw~A~I~~~~~~gk~--~~LGtF~--t~EeAA~AYD~ 65 (152)
|.-++.| .|..+-+.+. .|++ +-||.|+ |..+|..+...
T Consensus 33 l~v~~~G~k~~~~rY~~~~-~gk~~~~~lG~yp~~sl~~AR~~a~~ 77 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPL-TKTRAKKSFGPYPSVTLADARNYRAE 77 (413)
T ss_pred EEEECCCcEEEEEEEecCC-CCceeeeeCCCCCCCCHHHHHHHHHH
Confidence 3344554 4988876442 2344 6899999 66666554433
No 15
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=31.97 E-value=36 Score=26.27 Aligned_cols=18 Identities=50% Similarity=0.604 Sum_probs=15.3
Q ss_pred eEEecCCCCCHHHHHHHH
Q 048608 46 ARLWLGTFETAEEAARAY 63 (152)
Q Consensus 46 k~~~LGtF~t~EeAA~AY 63 (152)
.-+++|.|.|++||+++=
T Consensus 42 eVi~~g~~~tp~e~v~aA 59 (143)
T COG2185 42 EVINLGLFQTPEEAVRAA 59 (143)
T ss_pred eEEecCCcCCHHHHHHHH
Confidence 348999999999999774
No 16
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=30.46 E-value=1.5e+02 Score=20.04 Aligned_cols=38 Identities=18% Similarity=0.162 Sum_probs=23.9
Q ss_pred CcEEEEEeCCCCCCeEEecCCCCC--HHHHHHHHHHHHHhh
Q 048608 32 GKFAAEIRDPSRQGARLWLGTFET--AEEAARAYDRAAFNM 70 (152)
Q Consensus 32 gkw~A~I~~~~~~gk~~~LGtF~t--~EeAA~AYD~aa~~~ 70 (152)
..|..+.....+ .+++-||.|++ ..+|..........+
T Consensus 35 kt~~~r~~~~gk-~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 35 KTFYFRYRINGK-RRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EEEEEEEEETTE-EEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred eEEEEEEEecce-EEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 459988877433 36789999986 555555444443333
No 17
>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=28.46 E-value=1.7e+02 Score=19.80 Aligned_cols=46 Identities=24% Similarity=0.260 Sum_probs=33.3
Q ss_pred cceeEeEEC-CCCcEEEEEeCCCCCCeEEecCCCCCHHHHHHHHHHHHHhh
Q 048608 21 VRYRGVRRR-PWGKFAAEIRDPSRQGARLWLGTFETAEEAARAYDRAAFNM 70 (152)
Q Consensus 21 S~yrGV~~~-~~gkw~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~ 70 (152)
..|.||..+ ..-+-.+.|+. .||-+..|+ .++++|..|.+.....+
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 468898744 34567788877 688777765 78999999988766543
No 18
>PF12286 DUF3622: Protein of unknown function (DUF3622); InterPro: IPR022069 This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif.
Probab=27.64 E-value=1.2e+02 Score=20.74 Aligned_cols=30 Identities=20% Similarity=0.211 Sum_probs=18.5
Q ss_pred CCcEEEEEeCCCCCCeEEe---cCCCCCHHHHH
Q 048608 31 WGKFAAEIRDPSRQGARLW---LGTFETAEEAA 60 (152)
Q Consensus 31 ~gkw~A~I~~~~~~gk~~~---LGtF~t~EeAA 60 (152)
.+.|.|+|.--...++.+- --.|.|+++|.
T Consensus 15 ~~~W~aEItR~vTsrkTvVSK~~~GF~SEaeAq 47 (71)
T PF12286_consen 15 RNGWTAEITRRVTSRKTVVSKRQDGFASEAEAQ 47 (71)
T ss_pred CCceeeeeeeeecCceeEEEecccCcccHHHHH
Confidence 3669999985432223222 24699998865
No 19
>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=26.78 E-value=1.1e+02 Score=22.82 Aligned_cols=34 Identities=24% Similarity=0.192 Sum_probs=26.3
Q ss_pred cEEEEEeCCCCCCeEEecCCCCCHHHHHHHHHHHHHhh
Q 048608 33 KFAAEIRDPSRQGARLWLGTFETAEEAARAYDRAAFNM 70 (152)
Q Consensus 33 kw~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~ 70 (152)
-|.|+|.. |.-++--.-.+++.|..|...|+.++
T Consensus 91 ~~varV~~----G~ilfEi~~~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 91 YWVAVVKP----GKILFEIAGVPEEVAREAFRLAASKL 124 (126)
T ss_pred EEEEEECC----CCEEEEEeCCCHHHHHHHHHHHHhcC
Confidence 39999986 55555444489999999999998775
No 20
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=26.57 E-value=1e+02 Score=23.42 Aligned_cols=35 Identities=23% Similarity=0.115 Sum_probs=27.0
Q ss_pred EEEEEeCCCCCCeEEecCCCCCHHHHHHHHHHHHHhhcC
Q 048608 34 FAAEIRDPSRQGARLWLGTFETAEEAARAYDRAAFNMRG 72 (152)
Q Consensus 34 w~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~~G 72 (152)
|.|+|.. |+-++--.-.+++.|..|+..|+.++=+
T Consensus 93 ~varVk~----G~iifEi~~~~~~~a~~al~~a~~KLP~ 127 (138)
T PRK09203 93 WVAVVKP----GRILFEIAGVSEELAREALRLAAAKLPI 127 (138)
T ss_pred EEEEECC----CCEEEEEeCCCHHHHHHHHHHHhccCCC
Confidence 9999986 5555443338999999999999988743
No 21
>PLN00062 TATA-box-binding protein; Provisional
Probab=25.38 E-value=3.4e+02 Score=21.41 Aligned_cols=47 Identities=21% Similarity=0.133 Sum_probs=34.4
Q ss_pred CcceeEeEEC-CCCcEEEEEeCCCCCCeEEecCCCCCHHHHHHHHHHHHHhh
Q 048608 20 EVRYRGVRRR-PWGKFAAEIRDPSRQGARLWLGTFETAEEAARAYDRAAFNM 70 (152)
Q Consensus 20 ~S~yrGV~~~-~~gkw~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~ 70 (152)
...|.||..| ..-+=.+-|+. .||-+--| ..++|+|..|.++.+..+
T Consensus 33 Pe~fpgli~Rl~~Pk~t~lIF~---SGKiviTG-aks~e~a~~a~~~~~~~L 80 (179)
T PLN00062 33 PKRFAAVIMRIREPKTTALIFA---SGKMVCTG-AKSEHDSKLAARKYARII 80 (179)
T ss_pred CccCcEEEEEeCCCcEEEEEEC---CCeEEEEe-cCCHHHHHHHHHHHHHHH
Confidence 4579998743 44566788887 67776656 478899999988887666
No 22
>CHL00044 rpl16 ribosomal protein L16
Probab=25.24 E-value=1.2e+02 Score=23.02 Aligned_cols=34 Identities=24% Similarity=0.201 Sum_probs=25.9
Q ss_pred EEEEEeCCCCCCeEEecCCCCCHHHHHHHHHHHHHhhc
Q 048608 34 FAAEIRDPSRQGARLWLGTFETAEEAARAYDRAAFNMR 71 (152)
Q Consensus 34 w~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~~ 71 (152)
|.|.|.. |+-++=-.-.+++.|..|...|+.++-
T Consensus 93 ~va~V~~----G~ilfEi~g~~~~~ak~al~~a~~KLP 126 (135)
T CHL00044 93 WVAVVKP----GRILYEMGGVSETIARAAIKIAAYKMP 126 (135)
T ss_pred EEEEECC----CcEEEEEeCCCHHHHHHHHHHHhhcCC
Confidence 9999986 555554444677899999999988873
No 23
>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=24.30 E-value=3.5e+02 Score=21.18 Aligned_cols=47 Identities=21% Similarity=0.176 Sum_probs=35.0
Q ss_pred CcceeEeEEC-CCCcEEEEEeCCCCCCeEEecCCCCCHHHHHHHHHHHHHhh
Q 048608 20 EVRYRGVRRR-PWGKFAAEIRDPSRQGARLWLGTFETAEEAARAYDRAAFNM 70 (152)
Q Consensus 20 ~S~yrGV~~~-~~gkw~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~ 70 (152)
...|.||..| ..-+=.+-|+. .||-+--|. .|+|+|..|.++.+..+
T Consensus 33 Pe~fpgli~Rl~~Pk~t~lIF~---SGKiviTGa-ks~e~a~~a~~~i~~~L 80 (174)
T cd04516 33 PKRFAAVIMRIREPKTTALIFS---SGKMVCTGA-KSEDDSKLAARKYARII 80 (174)
T ss_pred CccCcEEEEEeCCCcEEEEEEC---CCeEEEEec-CCHHHHHHHHHHHHHHH
Confidence 3578998744 34566788888 688877776 57788888888877665
No 24
>PF13773 DUF4170: Domain of unknown function (DUF4170)
Probab=23.89 E-value=78 Score=21.63 Aligned_cols=23 Identities=22% Similarity=0.159 Sum_probs=19.5
Q ss_pred EecCCCCCHHHHHHHHHHHHHhh
Q 048608 48 LWLGTFETAEEAARAYDRAAFNM 70 (152)
Q Consensus 48 ~~LGtF~t~EeAA~AYD~aa~~~ 70 (152)
-.+|-|++-++|..|+...|..-
T Consensus 27 diVG~fp~y~~A~~aWrakAq~T 49 (69)
T PF13773_consen 27 DIVGIFPDYASAYAAWRAKAQRT 49 (69)
T ss_pred eEEecCCChHHHHHHHHHHHhCc
Confidence 45799999999999998887654
No 25
>PF14882 GHL12: Hypothetical glycosyl hydrolase 12
Probab=22.50 E-value=63 Score=20.63 Aligned_cols=11 Identities=45% Similarity=0.561 Sum_probs=9.1
Q ss_pred CCCCHHHHHHH
Q 048608 52 TFETAEEAARA 62 (152)
Q Consensus 52 tF~t~EeAA~A 62 (152)
.|.|.+||..|
T Consensus 39 ~Y~t~~eA~~A 49 (53)
T PF14882_consen 39 FYPTYEEASKA 49 (53)
T ss_pred ccCCHHHHHHH
Confidence 48999999866
No 26
>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=21.43 E-value=3.7e+02 Score=20.96 Aligned_cols=45 Identities=31% Similarity=0.280 Sum_probs=33.9
Q ss_pred ceeEeEEC-CCCcEEEEEeCCCCCCeEEecCCCCCHHHHHHHHHHHHHhh
Q 048608 22 RYRGVRRR-PWGKFAAEIRDPSRQGARLWLGTFETAEEAARAYDRAAFNM 70 (152)
Q Consensus 22 ~yrGV~~~-~~gkw~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~ 70 (152)
+|.||..| ..-+=.+-|+. .||-+--| ..+.|+|..|.++.+..+
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~---sGKiviTG-aks~~~~~~a~~~~~~~l 80 (174)
T cd04517 35 RYPKVTMRLREPRATASVWS---SGKITITG-ATSEEEAKQAARRAARLL 80 (174)
T ss_pred CCCEEEEEecCCcEEEEEEC---CCeEEEEc-cCCHHHHHHHHHHHHHHH
Confidence 89998744 34567788887 67766555 588999999998887665
No 27
>PF11453 DUF2950: Protein of unknown function (DUF2950); InterPro: IPR021556 This is a bacterial family of uncharacterised proteins.
Probab=20.32 E-value=89 Score=26.68 Aligned_cols=17 Identities=41% Similarity=0.331 Sum_probs=14.1
Q ss_pred CCCCHHHHHHHHHHHHH
Q 048608 52 TFETAEEAARAYDRAAF 68 (152)
Q Consensus 52 tF~t~EeAA~AYD~aa~ 68 (152)
+|+|+|+|+.|+-.|..
T Consensus 3 ~F~tPe~Aa~Al~~Av~ 19 (271)
T PF11453_consen 3 VFPTPEAAADALVDAVA 19 (271)
T ss_pred CCCCHHHHHHHHHHHHh
Confidence 69999999999966643
Done!