Query 030785
Match_columns 171
No_of_seqs 151 out of 1066
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 04:32:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030785.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030785hhsearch_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 8.4E-22 1.8E-26 133.9 7.4 61 80-141 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 1.3E-20 2.9E-25 129.6 8.3 63 81-144 1-63 (64)
3 PHA00280 putative NHN endonucl 99.5 2.1E-14 4.5E-19 111.4 7.3 58 74-135 61-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.3 2.9E-12 6.4E-17 84.8 6.6 53 80-132 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 81.5 5.7 0.00012 25.2 5.1 38 92-129 1-41 (46)
6 PHA02601 int integrase; Provis 77.1 4.1 8.9E-05 34.5 4.5 45 84-129 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 55.6 28 0.0006 29.0 5.2 38 91-129 10-49 (357)
8 PF05036 SPOR: Sporulation rel 53.5 12 0.00025 24.6 2.1 23 104-126 43-65 (76)
9 PF08846 DUF1816: Domain of un 51.7 32 0.00069 24.4 4.1 36 93-129 10-45 (68)
10 PF08471 Ribonuc_red_2_N: Clas 44.3 26 0.00056 26.4 2.9 20 110-129 71-90 (93)
11 PRK09692 integrase; Provisiona 41.9 84 0.0018 27.8 6.3 45 85-129 33-82 (413)
12 PF10729 CedA: Cell division a 38.0 60 0.0013 23.5 3.8 39 79-121 30-68 (80)
13 PF00352 TBP: Transcription fa 34.2 1.3E+02 0.0028 21.3 5.1 46 80-129 36-82 (86)
14 cd04516 TBP_eukaryotes eukaryo 33.1 2.2E+02 0.0047 23.2 6.9 47 79-129 33-80 (174)
15 COG0197 RplP Ribosomal protein 32.8 68 0.0015 25.9 3.8 36 93-132 96-131 (146)
16 PLN00062 TATA-box-binding prot 32.4 2.2E+02 0.0048 23.4 6.9 47 79-129 33-80 (179)
17 PF13356 DUF4102: Domain of un 31.5 96 0.0021 21.8 4.1 37 86-123 28-68 (89)
18 PF14112 DUF4284: Domain of un 29.1 31 0.00067 26.4 1.3 17 105-121 2-18 (122)
19 cd04517 TLF TBP-like factors ( 25.4 2.5E+02 0.0055 22.8 6.0 45 81-129 35-80 (174)
20 PRK10113 cell division modulat 23.5 69 0.0015 23.1 2.1 39 79-121 30-68 (80)
21 cd00652 TBP_TLF TATA box bindi 21.0 3.7E+02 0.008 21.7 6.2 47 79-129 33-80 (174)
22 CHL00044 rpl16 ribosomal prote 20.6 1.9E+02 0.0042 22.7 4.3 35 92-131 92-127 (135)
23 cd04518 TBP_archaea archaeal T 20.0 4.3E+02 0.0094 21.5 6.4 48 79-130 33-81 (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=99.86 E-value=8.4e-22 Score=133.86 Aligned_cols=61 Identities=59% Similarity=1.133 Sum_probs=56.9
Q ss_pred CceeeeEECCCCcEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 030785 80 KSSEGVRRRPWGKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRMRGRKAILNFPLE 141 (171)
Q Consensus 80 S~yRGV~~~~~GKW~A~I~~~~~kGk~i~LGtFdT~eeAArAYD~AA~k~~G~~A~lNFp~~ 141 (171)
|+|+||+++++|||+|+|+++.. |+++|||+|+|+||||.|||.++++++|.++.+|||++
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~-gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSG-GRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCC-CceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 68999999989999999999532 79999999999999999999999999999999999975
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.83 E-value=1.3e-20 Score=129.55 Aligned_cols=63 Identities=63% Similarity=1.115 Sum_probs=58.6
Q ss_pred ceeeeEECCCCcEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q 030785 81 SSEGVRRRPWGKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRMRGRKAILNFPLEAGA 144 (171)
Q Consensus 81 ~yRGV~~~~~GKW~A~I~~~~~kGk~i~LGtFdT~eeAArAYD~AA~k~~G~~A~lNFp~~~~~ 144 (171)
+|+||+++++|||+|+|+++. +|+.+|||+|+|+||||+|||.++++++|.++.+|||.+.|.
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 599999988899999999875 479999999999999999999999999999999999998764
No 3
>PHA00280 putative NHN endonuclease
Probab=99.53 E-value=2.1e-14 Score=111.38 Aligned_cols=58 Identities=14% Similarity=0.074 Sum_probs=52.3
Q ss_pred CCCCCCCceeeeEECCC-CcEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHhcCCCCC
Q 030785 74 WTESPQKSSEGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRMRGRKAI 135 (171)
Q Consensus 74 ~~~~~~S~yRGV~~~~~-GKW~A~I~~~~~kGk~i~LGtFdT~eeAArAYD~AA~k~~G~~A~ 135 (171)
..+.++|+|+||+|.+. |||+|+|.+ +|++++||.|+++|+|+.||+ ++.+++|++|.
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 34567899999998766 999999998 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=99.34 E-value=2.9e-12 Score=84.84 Aligned_cols=53 Identities=26% Similarity=0.381 Sum_probs=46.6
Q ss_pred CceeeeEECCC-CcEEEEEecCCCCC--eEEecCCCCCHHHHHHHHHHHHHHhcCC
Q 030785 80 KSSEGVRRRPW-GKYAAEIRDPARKG--SRVWLGTFDSDVDAAKAYDSAAFRMRGR 132 (171)
Q Consensus 80 S~yRGV~~~~~-GKW~A~I~~~~~kG--k~i~LGtFdT~eeAArAYD~AA~k~~G~ 132 (171)
|+|+||++++. ++|+|+|+++..+| +.++||.|++++||++||+.++.+++|+
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 68999998876 99999999854443 8999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=81.48 E-value=5.7 Score=25.21 Aligned_cols=38 Identities=16% Similarity=0.159 Sum_probs=28.5
Q ss_pred cEEEEEe--cC-CCCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 030785 92 KYAAEIR--DP-ARKGSRVWLGTFDSDVDAAKAYDSAAFRM 129 (171)
Q Consensus 92 KW~A~I~--~~-~~kGk~i~LGtFdT~eeAArAYD~AA~k~ 129 (171)
+|...|. ++ ..+-++++-+-|.|..||-.+...+...+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5888883 32 23336788999999999999988876665
No 6
>PHA02601 int integrase; Provisional
Probab=77.08 E-value=4.1 Score=34.50 Aligned_cols=45 Identities=24% Similarity=0.304 Sum_probs=30.6
Q ss_pred eeEECCCCcEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 030785 84 GVRRRPWGKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 129 (171)
Q Consensus 84 GV~~~~~GKW~A~I~~~~~kGk~i~LGtFdT~eeAArAYD~AA~k~ 129 (171)
+|++.++|+|++++......|+++.. +|.|..||....+......
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 46666679999999863334676653 6999999876655544433
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=55.59 E-value=28 Score=29.02 Aligned_cols=38 Identities=21% Similarity=0.289 Sum_probs=26.2
Q ss_pred CcEEEEEecCCCCCeEEecCCCC--CHHHHHHHHHHHHHHh
Q 030785 91 GKYAAEIRDPARKGSRVWLGTFD--SDVDAAKAYDSAAFRM 129 (171)
Q Consensus 91 GKW~A~I~~~~~kGk~i~LGtFd--T~eeAArAYD~AA~k~ 129 (171)
+.|+.+++..++. .++.||+|+ +.++|..........+
T Consensus 10 ~~~~~~~~~~g~~-~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGKR-KRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCce-eEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 5699999885432 567899996 6677776666654444
No 8
>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=53.46 E-value=12 Score=24.59 Aligned_cols=23 Identities=30% Similarity=0.319 Sum_probs=19.4
Q ss_pred CeEEecCCCCCHHHHHHHHHHHH
Q 030785 104 GSRVWLGTFDSDVDAAKAYDSAA 126 (171)
Q Consensus 104 Gk~i~LGtFdT~eeAArAYD~AA 126 (171)
--+|.+|.|++.++|..+-....
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 36899999999999998877655
No 9
>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=51.67 E-value=32 Score=24.44 Aligned_cols=36 Identities=22% Similarity=0.313 Sum_probs=25.6
Q ss_pred EEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 030785 93 YAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 129 (171)
Q Consensus 93 W~A~I~~~~~kGk~i~LGtFdT~eeAArAYD~AA~k~ 129 (171)
|=++|.-..-+ -.+|.|-|+|.+||..+.-.-..-+
T Consensus 10 WWveI~T~~P~-ctYyFGPF~s~~eA~~~~~gyieDL 45 (68)
T PF08846_consen 10 WWVEIETQNPN-CTYYFGPFDSREEAEAALPGYIEDL 45 (68)
T ss_pred EEEEEEcCCCC-EEEEeCCcCCHHHHHHHhccHHHHH
Confidence 55788743223 6899999999999998865444433
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=44.26 E-value=26 Score=26.41 Aligned_cols=20 Identities=30% Similarity=0.607 Sum_probs=18.0
Q ss_pred CCCCCHHHHHHHHHHHHHHh
Q 030785 110 GTFDSDVDAAKAYDSAAFRM 129 (171)
Q Consensus 110 GtFdT~eeAArAYD~AA~k~ 129 (171)
|+|+|+++|..=||..+..|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999887655
No 11
>PRK09692 integrase; Provisional
Probab=41.90 E-value=84 Score=27.76 Aligned_cols=45 Identities=11% Similarity=0.166 Sum_probs=27.0
Q ss_pred eEECCCCc--EEEEEecCC-CCCeEEecCCCC--CHHHHHHHHHHHHHHh
Q 030785 85 VRRRPWGK--YAAEIRDPA-RKGSRVWLGTFD--SDVDAAKAYDSAAFRM 129 (171)
Q Consensus 85 V~~~~~GK--W~A~I~~~~-~kGk~i~LGtFd--T~eeAArAYD~AA~k~ 129 (171)
|+..+.|. |..+.+.+. .+.+++-||.|+ |..+|..+...+...+
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~~~ 82 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRSLL 82 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHHHH
Confidence 44455543 998886432 222347899999 7777766555444433
No 12
>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=38.02 E-value=60 Score=23.51 Aligned_cols=39 Identities=18% Similarity=0.046 Sum_probs=25.7
Q ss_pred CCceeeeEECCCCcEEEEEecCCCCCeEEecCCCCCHHHHHHH
Q 030785 79 QKSSEGVRRRPWGKYAAEIRDPARKGSRVWLGTFDSDVDAAKA 121 (171)
Q Consensus 79 ~S~yRGV~~~~~GKW~A~I~~~~~kGk~i~LGtFdT~eeAArA 121 (171)
--+||.|+.-+ |||+|.+... -.-.---.|.-+|.|-+.
T Consensus 30 ~dgfrdvw~lr-gkyvafvl~g---e~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 30 MDGFRDVWQLR-GKYVAFVLMG---EHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTTECCECCCC-CEEEEEEESS---S-EEE---BSSHHHHHHH
T ss_pred cccccceeeec-cceEEEEEec---chhccCCCcCCcHHHHHH
Confidence 46899997655 9999999962 123334678888877765
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=34.25 E-value=1.3e+02 Score=21.26 Aligned_cols=46 Identities=24% Similarity=0.174 Sum_probs=34.5
Q ss_pred CceeeeEECCC-CcEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 030785 80 KSSEGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 129 (171)
Q Consensus 80 S~yRGV~~~~~-GKW~A~I~~~~~kGk~i~LGtFdT~eeAArAYD~AA~k~ 129 (171)
.+|.||..+-. -+-.+.|.. .|+-+..|+ .+.++|..|.++....+
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 37889765533 567777776 788887776 78999999998877655
No 14
>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=33.07 E-value=2.2e+02 Score=23.21 Aligned_cols=47 Identities=28% Similarity=0.128 Sum_probs=36.1
Q ss_pred CCceeeeEECCC-CcEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 030785 79 QKSSEGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 129 (171)
Q Consensus 79 ~S~yRGV~~~~~-GKW~A~I~~~~~kGk~i~LGtFdT~eeAArAYD~AA~k~ 129 (171)
-.+|.||..|-. -+-.+-|.. .||-+--|. .++++|..|.++.+..+
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 358899865544 667788887 788777777 57889999999888777
No 15
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=32.82 E-value=68 Score=25.94 Aligned_cols=36 Identities=19% Similarity=0.169 Sum_probs=31.2
Q ss_pred EEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHhcCC
Q 030785 93 YAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRMRGR 132 (171)
Q Consensus 93 W~A~I~~~~~kGk~i~LGtFdT~eeAArAYD~AA~k~~G~ 132 (171)
|.|+|.. |+.++-=..+.++.|..|.-+|+.+|=+.
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 9999985 78888888899999999999999988554
No 16
>PLN00062 TATA-box-binding protein; Provisional
Probab=32.40 E-value=2.2e+02 Score=23.36 Aligned_cols=47 Identities=28% Similarity=0.110 Sum_probs=35.3
Q ss_pred CCceeeeEECC-CCcEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 030785 79 QKSSEGVRRRP-WGKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 129 (171)
Q Consensus 79 ~S~yRGV~~~~-~GKW~A~I~~~~~kGk~i~LGtFdT~eeAArAYD~AA~k~ 129 (171)
-.+|.||..|- .-+-.+-|.. .||-+--|. .++++|..|.++.+..+
T Consensus 33 Pe~fpgli~Rl~~Pk~t~lIF~---SGKiviTGa-ks~e~a~~a~~~~~~~L 80 (179)
T PLN00062 33 PKRFAAVIMRIREPKTTALIFA---SGKMVCTGA-KSEHDSKLAARKYARII 80 (179)
T ss_pred CccCcEEEEEeCCCcEEEEEEC---CCeEEEEec-CCHHHHHHHHHHHHHHH
Confidence 45799986554 3667788887 677766664 78899999999888777
No 17
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=31.51 E-value=96 Score=21.79 Aligned_cols=37 Identities=22% Similarity=0.308 Sum_probs=21.6
Q ss_pred EECCCC--cEEEEEecCCCCCeEEecCCCCC--HHHHHHHHH
Q 030785 86 RRRPWG--KYAAEIRDPARKGSRVWLGTFDS--DVDAAKAYD 123 (171)
Q Consensus 86 ~~~~~G--KW~A~I~~~~~kGk~i~LGtFdT--~eeAArAYD 123 (171)
+..+.| .|..+.+..++ .+++-||.|.. ..+|.....
T Consensus 28 ~v~~~G~kt~~~r~~~~gk-~~~~~lG~~p~~sl~~AR~~a~ 68 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGK-RRRITLGRYPELSLAEAREKAR 68 (89)
T ss_dssp EE-TTS-EEEEEEEEETTE-EEEEEEEECTTS-HHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecce-EEEeccCCCccCCHHHHHHHHH
Confidence 344553 39888876432 35788999975 344444333
No 18
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=29.13 E-value=31 Score=26.42 Aligned_cols=17 Identities=24% Similarity=0.706 Sum_probs=13.2
Q ss_pred eEEecCCCCCHHHHHHH
Q 030785 105 SRVWLGTFDSDVDAAKA 121 (171)
Q Consensus 105 k~i~LGtFdT~eeAArA 121 (171)
..||||+|++.++-..=
T Consensus 2 VsiWiG~f~s~~el~~Y 18 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEY 18 (122)
T ss_pred eEEEEecCCCHHHHHHH
Confidence 36999999988876543
No 19
>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=25.36 E-value=2.5e+02 Score=22.76 Aligned_cols=45 Identities=22% Similarity=0.146 Sum_probs=34.9
Q ss_pred ceeeeEECCC-CcEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 030785 81 SSEGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 129 (171)
Q Consensus 81 ~yRGV~~~~~-GKW~A~I~~~~~kGk~i~LGtFdT~eeAArAYD~AA~k~ 129 (171)
+|.||..|-. -+-.+-|+. .||-+--| ..+.++|+.|.++.+..+
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 8999876543 677888887 67666555 489999999999887776
No 20
>PRK10113 cell division modulator; Provisional
Probab=23.52 E-value=69 Score=23.14 Aligned_cols=39 Identities=23% Similarity=0.094 Sum_probs=27.0
Q ss_pred CCceeeeEECCCCcEEEEEecCCCCCeEEecCCCCCHHHHHHH
Q 030785 79 QKSSEGVRRRPWGKYAAEIRDPARKGSRVWLGTFDSDVDAAKA 121 (171)
Q Consensus 79 ~S~yRGV~~~~~GKW~A~I~~~~~kGk~i~LGtFdT~eeAArA 121 (171)
--+|+.|+.-+ |||+|.+.... .-.---.|..+|.|-+.
T Consensus 30 md~frDVW~Lr-GKYVAFvl~ge---~FrRSPaFs~PEsAQRW 68 (80)
T PRK10113 30 MDSFRDVWMLR-GKYVAFVLMGE---SFLRSPAFSVPESAQRW 68 (80)
T ss_pred hcchhhhheec-cceEEEEEech---hhccCCccCCcHHHHHH
Confidence 35799987666 99999998621 11223678888887765
No 21
>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=20.97 E-value=3.7e+02 Score=21.71 Aligned_cols=47 Identities=32% Similarity=0.183 Sum_probs=35.3
Q ss_pred CCceeeeEECCC-CcEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 030785 79 QKSSEGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRM 129 (171)
Q Consensus 79 ~S~yRGV~~~~~-GKW~A~I~~~~~kGk~i~LGtFdT~eeAArAYD~AA~k~ 129 (171)
-.+|.||..|-. -+-.+-|.. .||-+--|. .+.++|..|.++.+..+
T Consensus 33 Pe~fpgli~R~~~P~~t~lIf~---sGKivitGa-ks~~~~~~a~~~~~~~L 80 (174)
T cd00652 33 PKRFPGVIMRLREPKTTALIFS---SGKMVITGA-KSEEDAKLAARKYARIL 80 (174)
T ss_pred CCccceEEEEcCCCcEEEEEEC---CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 368999876544 566777776 787777776 57888999988887776
No 22
>CHL00044 rpl16 ribosomal protein L16
Probab=20.55 E-value=1.9e+02 Score=22.69 Aligned_cols=35 Identities=26% Similarity=0.358 Sum_probs=26.6
Q ss_pred cEEEEEecCCCCCeEEe-cCCCCCHHHHHHHHHHHHHHhcC
Q 030785 92 KYAAEIRDPARKGSRVW-LGTFDSDVDAAKAYDSAAFRMRG 131 (171)
Q Consensus 92 KW~A~I~~~~~kGk~i~-LGtFdT~eeAArAYD~AA~k~~G 131 (171)
.|+|.|.. |+-++ ++. ..++.|..|...|+.++=.
T Consensus 92 ~~va~V~~----G~ilfEi~g-~~~~~ak~al~~a~~KLP~ 127 (135)
T CHL00044 92 YWVAVVKP----GRILYEMGG-VSETIARAAIKIAAYKMPI 127 (135)
T ss_pred EEEEEECC----CcEEEEEeC-CCHHHHHHHHHHHhhcCCC
Confidence 39999995 66666 444 6678999999988888743
No 23
>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=20.03 E-value=4.3e+02 Score=21.46 Aligned_cols=48 Identities=25% Similarity=0.178 Sum_probs=35.9
Q ss_pred CCceeeeEECCC-CcEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHhc
Q 030785 79 QKSSEGVRRRPW-GKYAAEIRDPARKGSRVWLGTFDSDVDAAKAYDSAAFRMR 130 (171)
Q Consensus 79 ~S~yRGV~~~~~-GKW~A~I~~~~~kGk~i~LGtFdT~eeAArAYD~AA~k~~ 130 (171)
..+|.||..+-. -+-.+-|.. .||-+--|+ .+.++|..|-++.+..+.
T Consensus 33 P~~fpgli~Rl~~Pk~t~lIF~---SGKiv~tGa-ks~~~a~~a~~~~~~~L~ 81 (174)
T cd04518 33 PDQFPGLVYRLEDPKIAALIFR---SGKMVCTGA-KSVEDLHRAVKEIIKKLK 81 (174)
T ss_pred CCcCcEEEEEccCCcEEEEEEC---CCeEEEEcc-CCHHHHHHHHHHHHHHHH
Confidence 468999876543 566777776 787776675 789999999998877764
Done!