Query 029627
Match_columns 190
No_of_seqs 248 out of 1304
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 15:56:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029627.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029627hhsearch_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 1.4E-21 3.1E-26 135.0 7.5 61 38-98 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 1.4E-20 2.9E-25 131.7 8.3 62 39-100 1-62 (64)
3 PHA00280 putative NHN endonucl 99.7 1.9E-16 4.1E-21 124.8 8.8 82 3-92 37-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 7.6E-11 1.7E-15 79.3 5.5 52 38-89 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 78.1 8 0.00017 25.0 5.1 38 50-87 1-42 (46)
6 PF08846 DUF1816: Domain of un 64.0 15 0.00032 26.6 4.2 39 50-88 9-47 (68)
7 cd00801 INT_P4 Bacteriophage P 61.9 18 0.00038 30.8 5.1 38 49-86 10-49 (357)
8 PHA02601 int integrase; Provis 59.0 15 0.00033 31.6 4.3 44 42-86 2-46 (333)
9 PF13356 DUF4102: Domain of un 48.2 44 0.00094 24.0 4.6 40 44-83 28-71 (89)
10 PF10729 CedA: Cell division a 46.7 34 0.00073 25.2 3.7 38 38-78 31-68 (80)
11 PRK09692 integrase; Provisiona 46.3 62 0.0013 29.1 6.3 37 43-79 33-75 (413)
12 PF05036 SPOR: Sporulation rel 41.9 37 0.0008 22.5 3.2 24 60-83 42-65 (76)
13 PF14112 DUF4284: Domain of un 35.6 27 0.00058 27.3 1.9 18 62-79 2-19 (122)
14 PF08471 Ribonuc_red_2_N: Clas 34.1 44 0.00096 25.6 2.8 20 67-86 71-90 (93)
15 PRK10113 cell division modulat 30.6 39 0.00084 24.8 1.9 36 39-77 32-67 (80)
16 PF00352 TBP: Transcription fa 24.8 2.5E+02 0.0054 20.1 5.4 45 39-86 37-82 (86)
17 cd04517 TLF TBP-like factors ( 24.4 3.2E+02 0.007 22.6 6.6 46 39-87 35-81 (174)
18 PLN00062 TATA-box-binding prot 24.2 3.5E+02 0.0076 22.6 6.8 46 39-87 35-81 (179)
19 PF07494 Reg_prop: Two compone 23.9 85 0.0019 17.5 2.2 11 60-70 14-24 (24)
20 cd04516 TBP_eukaryotes eukaryo 22.7 4.4E+02 0.0095 21.8 7.1 47 38-87 34-81 (174)
21 COG2185 Sbm Methylmalonyl-CoA 21.3 70 0.0015 26.2 2.0 29 50-78 30-58 (143)
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=99.85 E-value=1.4e-21 Score=134.96 Aligned_cols=61 Identities=62% Similarity=1.107 Sum_probs=57.5
Q ss_pred CceeEEEeCCCCcEEEEEecCCCCeEEeecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 029627 38 PVYRGVRKRRWGKWVSEIREPRKKTRIWLGSFPVPEMAARAYDVAAYCLKGRKAQLNFPDK 98 (190)
Q Consensus 38 s~yRGVr~r~~GkW~AeI~~p~~~kri~LGtF~T~EeAA~AYD~Aa~~l~G~~A~lNFp~~ 98 (190)
|+|+||+++++|||+|+|+++..++++|||+|+|+|||+.|||.++++++|.++.+|||++
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 5699999988899999999966689999999999999999999999999999999999975
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.83 E-value=1.4e-20 Score=131.65 Aligned_cols=62 Identities=60% Similarity=1.148 Sum_probs=58.8
Q ss_pred ceeEEEeCCCCcEEEEEecCCCCeEEeecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Q 029627 39 VYRGVRKRRWGKWVSEIREPRKKTRIWLGSFPVPEMAARAYDVAAYCLKGRKAQLNFPDKVE 100 (190)
Q Consensus 39 ~yRGVr~r~~GkW~AeI~~p~~~kri~LGtF~T~EeAA~AYD~Aa~~l~G~~A~lNFp~~~~ 100 (190)
+|+||+++++|||+|+|+++.+++++|||+|+|+||||.|||.++++++|.++.+|||.+.+
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y 62 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLY 62 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccC
Confidence 49999988899999999999899999999999999999999999999999999999998754
No 3
>PHA00280 putative NHN endonuclease
Probab=99.67 E-value=1.9e-16 Score=124.77 Aligned_cols=82 Identities=15% Similarity=0.143 Sum_probs=69.8
Q ss_pred CCCCCCChhhhhhhhhhhhhhhhcCCCCCCCCCCCCceeEEEeC-CCCcEEEEEecCCCCeEEeecCCCCHHHHHHHHHH
Q 029627 3 QQPYTYTEHELTDSATATATAIHRKSSSQTGGTRHPVYRGVRKR-RWGKWVSEIREPRKKTRIWLGSFPVPEMAARAYDV 81 (190)
Q Consensus 3 ~~p~~~~~~nlr~s~~r~~t~~~r~~~~~~~~~~~s~yRGVr~r-~~GkW~AeI~~p~~~kri~LGtF~T~EeAA~AYD~ 81 (190)
..|.+++.+||+.++..++..|++.++. ++|+|+||++. ..|||+|+|++ .|++++||.|+|+|+|+.||+
T Consensus 37 g~~~dnri~NLr~~T~~eN~~N~~~~~~-----N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~- 108 (121)
T PHA00280 37 GNPLNDALDNLRLALPKENSWNMKTPKS-----NTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR- 108 (121)
T ss_pred CCCCCCcHHHhhhcCHHHHhcccCCCCC-----CCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-
Confidence 3577888899999999888777655544 45569999977 67999999999 999999999999999999997
Q ss_pred HHHHhcCCCCC
Q 029627 82 AAYCLKGRKAQ 92 (190)
Q Consensus 82 Aa~~l~G~~A~ 92 (190)
++.+|||++|.
T Consensus 109 ~~~~lhGeFa~ 119 (121)
T PHA00280 109 TRRELHGQFAR 119 (121)
T ss_pred HHHHHhhcccc
Confidence 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=99.15 E-value=7.6e-11 Score=79.34 Aligned_cols=52 Identities=35% Similarity=0.477 Sum_probs=45.2
Q ss_pred CceeEEEeC-CCCcEEEEEecCCC---CeEEeecCCCCHHHHHHHHHHHHHHhcCC
Q 029627 38 PVYRGVRKR-RWGKWVSEIREPRK---KTRIWLGSFPVPEMAARAYDVAAYCLKGR 89 (190)
Q Consensus 38 s~yRGVr~r-~~GkW~AeI~~p~~---~kri~LGtF~T~EeAA~AYD~Aa~~l~G~ 89 (190)
|+|+||+++ ..++|+|.|+++.. +++++||.|+++++|++|++.+++.++|+
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 569999877 57999999999421 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=78.06 E-value=8 Score=24.98 Aligned_cols=38 Identities=16% Similarity=0.203 Sum_probs=29.5
Q ss_pred cEEEEEe--cC--CCCeEEeecCCCCHHHHHHHHHHHHHHhc
Q 029627 50 KWVSEIR--EP--RKKTRIWLGSFPVPEMAARAYDVAAYCLK 87 (190)
Q Consensus 50 kW~AeI~--~p--~~~kri~LGtF~T~EeAA~AYD~Aa~~l~ 87 (190)
+|...|. .+ ++.++++-+-|.|..||-.+.......+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5777883 43 44578899999999999999888776653
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=64.01 E-value=15 Score=26.58 Aligned_cols=39 Identities=23% Similarity=0.284 Sum_probs=30.8
Q ss_pred cEEEEEecCCCCeEEeecCCCCHHHHHHHHHHHHHHhcC
Q 029627 50 KWVSEIREPRKKTRIWLGSFPVPEMAARAYDVAAYCLKG 88 (190)
Q Consensus 50 kW~AeI~~p~~~kri~LGtF~T~EeAA~AYD~Aa~~l~G 88 (190)
.|-++|.-..-....|.|-|.|.+||..+.---..-|..
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~~ 47 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLES 47 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHHh
Confidence 588999886666799999999999999886655555543
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=61.90 E-value=18 Score=30.79 Aligned_cols=38 Identities=32% Similarity=0.387 Sum_probs=28.7
Q ss_pred CcEEEEEecCCCCeEEeecCCC--CHHHHHHHHHHHHHHh
Q 029627 49 GKWVSEIREPRKKTRIWLGSFP--VPEMAARAYDVAAYCL 86 (190)
Q Consensus 49 GkW~AeI~~p~~~kri~LGtF~--T~EeAA~AYD~Aa~~l 86 (190)
+.|..+++..++.+++.||+|+ |.++|..........+
T Consensus 10 ~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 5699999997777789999995 6777776666655444
No 8
>PHA02601 int integrase; Provisional
Probab=59.05 E-value=15 Score=31.61 Aligned_cols=44 Identities=30% Similarity=0.331 Sum_probs=29.5
Q ss_pred EEEeCCCCcEEEEEecC-CCCeEEeecCCCCHHHHHHHHHHHHHHh
Q 029627 42 GVRKRRWGKWVSEIREP-RKKTRIWLGSFPVPEMAARAYDVAAYCL 86 (190)
Q Consensus 42 GVr~r~~GkW~AeI~~p-~~~kri~LGtF~T~EeAA~AYD~Aa~~l 86 (190)
+|++.+.|+|.++|+.. ..|+++.. +|.|..||-.........+
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 46666789999999862 23555543 6999999876655544333
No 9
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=48.21 E-value=44 Score=24.03 Aligned_cols=40 Identities=25% Similarity=0.237 Sum_probs=26.2
Q ss_pred EeCCCC--cEEEEEecCCCCeEEeecCCCC--HHHHHHHHHHHH
Q 029627 44 RKRRWG--KWVSEIREPRKKTRIWLGSFPV--PEMAARAYDVAA 83 (190)
Q Consensus 44 r~r~~G--kW~AeI~~p~~~kri~LGtF~T--~EeAA~AYD~Aa 83 (190)
+..+.| .|.-+.+..++.+++-||.|++ ..+|-.......
T Consensus 28 ~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~ 71 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELR 71 (89)
T ss_dssp EE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHH
Confidence 444554 5998888877778999999975 445544444333
No 10
>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=46.68 E-value=34 Score=25.21 Aligned_cols=38 Identities=29% Similarity=0.289 Sum_probs=25.0
Q ss_pred CceeEEEeCCCCcEEEEEecCCCCeEEeecCCCCHHHHHHH
Q 029627 38 PVYRGVRKRRWGKWVSEIREPRKKTRIWLGSFPVPEMAARA 78 (190)
Q Consensus 38 s~yRGVr~r~~GkW~AeI~~p~~~kri~LGtF~T~EeAA~A 78 (190)
-+||-|..- .|||+|.+.. +..-..--.|..+|.|-+=
T Consensus 31 dgfrdvw~l-rgkyvafvl~--ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 31 DGFRDVWQL-RGKYVAFVLM--GEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTECCECCC-CCEEEEEEES--SS-EEE---BSSHHHHHHH
T ss_pred ccccceeee-ccceEEEEEe--cchhccCCCcCCcHHHHHH
Confidence 348888554 4999999998 4444455678888887653
No 11
>PRK09692 integrase; Provisional
Probab=46.26 E-value=62 Score=29.14 Aligned_cols=37 Identities=16% Similarity=0.316 Sum_probs=23.6
Q ss_pred EEeCCCC--cEEEEEecC--CCCeEEeecCCC--CHHHHHHHH
Q 029627 43 VRKRRWG--KWVSEIREP--RKKTRIWLGSFP--VPEMAARAY 79 (190)
Q Consensus 43 Vr~r~~G--kW~AeI~~p--~~~kri~LGtF~--T~EeAA~AY 79 (190)
|+.++.| .|+.+.+.+ ++.+++-||.|+ |..+|-.+.
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a 75 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYR 75 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHH
Confidence 4444555 499888754 333457899999 666664433
No 12
>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=41.88 E-value=37 Score=22.54 Aligned_cols=24 Identities=25% Similarity=0.234 Sum_probs=18.8
Q ss_pred CCeEEeecCCCCHHHHHHHHHHHH
Q 029627 60 KKTRIWLGSFPVPEMAARAYDVAA 83 (190)
Q Consensus 60 ~~kri~LGtF~T~EeAA~AYD~Aa 83 (190)
..-+|.+|.|+|.++|..+-....
T Consensus 42 ~~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 42 PWYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp TCEEEEECCECTCCHHHHHHHHHH
T ss_pred ceEEEEECCCCCHHHHHHHHHHHh
Confidence 445889999999999988866554
No 13
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=35.56 E-value=27 Score=27.27 Aligned_cols=18 Identities=22% Similarity=0.667 Sum_probs=13.8
Q ss_pred eEEeecCCCCHHHHHHHH
Q 029627 62 TRIWLGSFPVPEMAARAY 79 (190)
Q Consensus 62 kri~LGtF~T~EeAA~AY 79 (190)
..||||+|.|.++--.=.
T Consensus 2 VsiWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYF 19 (122)
T ss_pred eEEEEecCCCHHHHHHHh
Confidence 369999999988765543
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=34.08 E-value=44 Score=25.59 Aligned_cols=20 Identities=40% Similarity=0.542 Sum_probs=17.8
Q ss_pred cCCCCHHHHHHHHHHHHHHh
Q 029627 67 GSFPVPEMAARAYDVAAYCL 86 (190)
Q Consensus 67 GtF~T~EeAA~AYD~Aa~~l 86 (190)
|+|+|+|+|..=||.-...|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999877655
No 15
>PRK10113 cell division modulator; Provisional
Probab=30.58 E-value=39 Score=24.85 Aligned_cols=36 Identities=33% Similarity=0.461 Sum_probs=23.9
Q ss_pred ceeEEEeCCCCcEEEEEecCCCCeEEeecCCCCHHHHHH
Q 029627 39 VYRGVRKRRWGKWVSEIREPRKKTRIWLGSFPVPEMAAR 77 (190)
Q Consensus 39 ~yRGVr~r~~GkW~AeI~~p~~~kri~LGtF~T~EeAA~ 77 (190)
.||-|..-+ |||+|.+.. ...-..--.|..+|.|-+
T Consensus 32 ~frDVW~Lr-GKYVAFvl~--ge~FrRSPaFs~PEsAQR 67 (80)
T PRK10113 32 SFRDVWMLR-GKYVAFVLM--GESFLRSPAFSVPESAQR 67 (80)
T ss_pred chhhhheec-cceEEEEEe--chhhccCCccCCcHHHHH
Confidence 488885543 999999988 322223356777777765
No 16
>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=24.76 E-value=2.5e+02 Score=20.09 Aligned_cols=45 Identities=22% Similarity=0.122 Sum_probs=33.0
Q ss_pred ceeEEEeC-CCCcEEEEEecCCCCeEEeecCCCCHHHHHHHHHHHHHHh
Q 029627 39 VYRGVRKR-RWGKWVSEIREPRKKTRIWLGSFPVPEMAARAYDVAAYCL 86 (190)
Q Consensus 39 ~yRGVr~r-~~GkW~AeI~~p~~~kri~LGtF~T~EeAA~AYD~Aa~~l 86 (190)
+|.||..| ..-+-...|.. .|+-+-.|. .+.|+|..|.+.....|
T Consensus 37 ~fpgl~~r~~~p~~t~~IF~--sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 37 RFPGLIYRLRNPKATVLIFS--SGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TESSEEEEETTTTEEEEEET--TSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred cCCeEEEeecCCcEEEEEEc--CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 48898666 44466677776 887666664 78999999998877655
No 17
>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=24.43 E-value=3.2e+02 Score=22.56 Aligned_cols=46 Identities=24% Similarity=0.141 Sum_probs=34.9
Q ss_pred ceeEEEeC-CCCcEEEEEecCCCCeEEeecCCCCHHHHHHHHHHHHHHhc
Q 029627 39 VYRGVRKR-RWGKWVSEIREPRKKTRIWLGSFPVPEMAARAYDVAAYCLK 87 (190)
Q Consensus 39 ~yRGVr~r-~~GkW~AeI~~p~~~kri~LGtF~T~EeAA~AYD~Aa~~l~ 87 (190)
+|.||..| ..-+-.+-|.. .|| +.+=...+.|+|..|.+..+..+.
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~--sGK-iviTGaks~~~~~~a~~~~~~~l~ 81 (174)
T cd04517 35 RYPKVTMRLREPRATASVWS--SGK-ITITGATSEEEAKQAARRAARLLQ 81 (174)
T ss_pred CCCEEEEEecCCcEEEEEEC--CCe-EEEEccCCHHHHHHHHHHHHHHHH
Confidence 59999776 55677777877 665 444456899999999999887773
No 18
>PLN00062 TATA-box-binding protein; Provisional
Probab=24.19 E-value=3.5e+02 Score=22.59 Aligned_cols=46 Identities=17% Similarity=0.010 Sum_probs=34.1
Q ss_pred ceeEEEeC-CCCcEEEEEecCCCCeEEeecCCCCHHHHHHHHHHHHHHhc
Q 029627 39 VYRGVRKR-RWGKWVSEIREPRKKTRIWLGSFPVPEMAARAYDVAAYCLK 87 (190)
Q Consensus 39 ~yRGVr~r-~~GkW~AeI~~p~~~kri~LGtF~T~EeAA~AYD~Aa~~l~ 87 (190)
+|-||..| +.-+=.+-|.. .||-+--| ..+.|+|..|.+..+..+.
T Consensus 35 ~fpgli~Rl~~Pk~t~lIF~--SGKiviTG-aks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 35 RFAAVIMRIREPKTTALIFA--SGKMVCTG-AKSEHDSKLAARKYARIIQ 81 (179)
T ss_pred cCcEEEEEeCCCcEEEEEEC--CCeEEEEe-cCCHHHHHHHHHHHHHHHH
Confidence 49999766 45566777777 77554444 5789999999999887774
No 19
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=23.91 E-value=85 Score=17.50 Aligned_cols=11 Identities=18% Similarity=0.966 Sum_probs=8.0
Q ss_pred CCeEEeecCCC
Q 029627 60 KKTRIWLGSFP 70 (190)
Q Consensus 60 ~~kri~LGtF~ 70 (190)
+..+||+||+.
T Consensus 14 ~~G~lWigT~~ 24 (24)
T PF07494_consen 14 SDGNLWIGTYN 24 (24)
T ss_dssp TTSCEEEEETS
T ss_pred CCcCEEEEeCC
Confidence 44589999873
No 20
>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=22.66 E-value=4.4e+02 Score=21.82 Aligned_cols=47 Identities=17% Similarity=0.047 Sum_probs=34.7
Q ss_pred CceeEEEeC-CCCcEEEEEecCCCCeEEeecCCCCHHHHHHHHHHHHHHhc
Q 029627 38 PVYRGVRKR-RWGKWVSEIREPRKKTRIWLGSFPVPEMAARAYDVAAYCLK 87 (190)
Q Consensus 38 s~yRGVr~r-~~GkW~AeI~~p~~~kri~LGtF~T~EeAA~AYD~Aa~~l~ 87 (190)
.+|-||..| ..-+-.+-|.. .||-+--|. .|.|+|..|.++.+..+.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIFS--SGKMVCTGA-KSEDDSKLAARKYARIIQ 81 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 358999766 44566777777 776665565 678999999999887774
No 21
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=21.26 E-value=70 Score=26.17 Aligned_cols=29 Identities=34% Similarity=0.334 Sum_probs=20.2
Q ss_pred cEEEEEecCCCCeEEeecCCCCHHHHHHH
Q 029627 50 KWVSEIREPRKKTRIWLGSFPVPEMAARA 78 (190)
Q Consensus 50 kW~AeI~~p~~~kri~LGtF~T~EeAA~A 78 (190)
|..+++.....=.=|++|.|.|+||++++
T Consensus 30 kvia~~l~d~GfeVi~~g~~~tp~e~v~a 58 (143)
T COG2185 30 KVIARALADAGFEVINLGLFQTPEEAVRA 58 (143)
T ss_pred HHHHHHHHhCCceEEecCCcCCHHHHHHH
Confidence 34444433333367999999999999987
Done!