Query 038538
Match_columns 243
No_of_seqs 280 out of 1345
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 12:06:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038538.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038538hhsearch_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 1.9E-21 4.1E-26 139.4 7.5 61 63-123 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 1.7E-20 3.8E-25 136.0 8.3 62 64-125 1-62 (64)
3 PHA00280 putative NHN endonucl 99.4 9E-14 2E-18 113.7 5.1 55 60-117 64-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 7.5E-11 1.6E-15 82.4 5.7 52 63-114 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 80.5 7.2 0.00016 26.2 5.6 38 75-112 1-42 (46)
6 PF13356 DUF4102: Domain of un 72.7 12 0.00027 28.1 5.7 43 69-111 28-74 (89)
7 cd00801 INT_P4 Bacteriophage P 65.6 12 0.00027 33.1 5.0 38 74-111 10-49 (357)
8 PHA02601 int integrase; Provis 60.6 14 0.00031 33.2 4.5 44 67-111 2-46 (333)
9 PRK09692 integrase; Provisiona 56.9 30 0.00066 32.5 6.2 37 68-104 33-75 (413)
10 PF05036 SPOR: Sporulation rel 43.9 23 0.00049 24.6 2.5 25 84-108 41-65 (76)
11 PF08846 DUF1816: Domain of un 41.5 55 0.0012 24.6 4.3 39 75-113 9-47 (68)
12 PF10729 CedA: Cell division a 38.7 51 0.0011 25.2 3.7 40 61-103 29-68 (80)
13 PF00352 TBP: Transcription fa 37.9 91 0.002 23.4 5.1 45 64-111 37-82 (86)
14 PF14112 DUF4284: Domain of un 35.2 27 0.00058 28.4 1.9 19 87-105 2-20 (122)
15 cd04517 TLF TBP-like factors ( 33.1 1.5E+02 0.0033 25.6 6.3 46 64-112 35-81 (174)
16 PLN00062 TATA-box-binding prot 30.3 2.3E+02 0.005 24.7 7.0 47 63-112 34-81 (179)
17 cd04516 TBP_eukaryotes eukaryo 29.5 2.5E+02 0.0054 24.3 7.1 47 63-112 34-81 (174)
18 PRK10113 cell division modulat 26.0 54 0.0012 25.0 2.0 39 62-103 30-68 (80)
19 PF07494 Reg_prop: Two compone 24.9 77 0.0017 18.5 2.2 11 85-95 14-24 (24)
20 PF08471 Ribonuc_red_2_N: Clas 23.8 83 0.0018 25.1 2.8 20 92-111 71-90 (93)
21 cd01433 Ribosomal_L16_L10e Rib 22.3 1.7E+02 0.0037 23.1 4.5 35 75-111 71-105 (112)
22 PHA03308 transcriptional regul 21.8 93 0.002 33.6 3.4 9 109-117 1333-1341(1463)
23 COG0197 RplP Ribosomal protein 20.9 1.5E+02 0.0034 25.3 4.1 36 76-114 96-131 (146)
24 cd04518 TBP_archaea archaeal T 20.8 3.5E+02 0.0077 23.3 6.4 47 63-112 34-81 (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=99.85 E-value=1.9e-21 Score=139.35 Aligned_cols=61 Identities=66% Similarity=1.117 Sum_probs=57.7
Q ss_pred CceeEeEECCCCcEEEEEeeCCCCeEEeecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 038538 63 PVYRGVRMRSWGKWVSEIREPRKKSRIWLGTFRTPEMAARAHDVAALSIKGDSAVLNFPEL 123 (243)
Q Consensus 63 s~yRGVr~r~~GKW~AeIr~~~~kkri~LGtF~T~EeAArAYD~Aa~~l~G~~a~lNFp~~ 123 (243)
|+|+||+++++|||+|+|+.+..++++|||+|+|+||||+|||.|+++++|..+.+|||++
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 5799999888899999999976699999999999999999999999999999999999975
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.83 E-value=1.7e-20 Score=136.01 Aligned_cols=62 Identities=61% Similarity=1.049 Sum_probs=58.9
Q ss_pred ceeEeEECCCCcEEEEEeeCCCCeEEeecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCcC
Q 038538 64 VYRGVRMRSWGKWVSEIREPRKKSRIWLGTFRTPEMAARAHDVAALSIKGDSAVLNFPELVE 125 (243)
Q Consensus 64 ~yRGVr~r~~GKW~AeIr~~~~kkri~LGtF~T~EeAArAYD~Aa~~l~G~~a~lNFp~~~~ 125 (243)
+|+||+++++|||+|+|+++.+++++|||+|+|+||||+|||.|+++++|..+.+|||.+.+
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 59999988889999999999999999999999999999999999999999999999998754
No 3
>PHA00280 putative NHN endonuclease
Probab=99.44 E-value=9e-14 Score=113.70 Aligned_cols=55 Identities=11% Similarity=0.131 Sum_probs=49.7
Q ss_pred CCCCceeEeEEC-CCCcEEEEEeeCCCCeEEeecCCCCHHHHHHHHHHHHHHhcCCCCC
Q 038538 60 TKHPVYRGVRMR-SWGKWVSEIREPRKKSRIWLGTFRTPEMAARAHDVAALSIKGDSAV 117 (243)
Q Consensus 60 ~~~s~yRGVr~r-~~GKW~AeIr~~~~kkri~LGtF~T~EeAArAYD~Aa~~l~G~~a~ 117 (243)
.++|+|+||.++ ..|||+|+|+. .||+++||.|+++|+|+.||+ ++.+|+|.+|.
T Consensus 64 ~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 64 SNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred CCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 367899999866 77999999999 999999999999999999997 77899999875
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=7.5e-11 Score=82.41 Aligned_cols=52 Identities=31% Similarity=0.487 Sum_probs=45.2
Q ss_pred CceeEeEEC-CCCcEEEEEeeCCC---CeEEeecCCCCHHHHHHHHHHHHHHhcCC
Q 038538 63 PVYRGVRMR-SWGKWVSEIREPRK---KSRIWLGTFRTPEMAARAHDVAALSIKGD 114 (243)
Q Consensus 63 s~yRGVr~r-~~GKW~AeIr~~~~---kkri~LGtF~T~EeAArAYD~Aa~~l~G~ 114 (243)
|+|+||++. ..++|+|+|++... +++++||.|+++++|++|++.++++++|+
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 589999766 68999999999421 48999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=80.49 E-value=7.2 Score=26.24 Aligned_cols=38 Identities=16% Similarity=0.250 Sum_probs=29.3
Q ss_pred cEEEEEe--eC--CCCeEEeecCCCCHHHHHHHHHHHHHHhc
Q 038538 75 KWVSEIR--EP--RKKSRIWLGTFRTPEMAARAHDVAALSIK 112 (243)
Q Consensus 75 KW~AeIr--~~--~~kkri~LGtF~T~EeAArAYD~Aa~~l~ 112 (243)
+|...|. .+ ++.++++-+-|.|..||..+.......+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5888883 43 34478899999999999999887766653
No 6
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=72.72 E-value=12 Score=28.08 Aligned_cols=43 Identities=21% Similarity=0.213 Sum_probs=28.5
Q ss_pred EECCCC--cEEEEEeeCCCCeEEeecCCCC--HHHHHHHHHHHHHHh
Q 038538 69 RMRSWG--KWVSEIREPRKKSRIWLGTFRT--PEMAARAHDVAALSI 111 (243)
Q Consensus 69 r~r~~G--KW~AeIr~~~~kkri~LGtF~T--~EeAArAYD~Aa~~l 111 (243)
+..+.| .|+-+.+..++.+++-||.|+. ..+|..........+
T Consensus 28 ~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 444444 4999998877778899999986 556555554443333
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=65.57 E-value=12 Score=33.14 Aligned_cols=38 Identities=24% Similarity=0.334 Sum_probs=28.2
Q ss_pred CcEEEEEeeCCCCeEEeecCCC--CHHHHHHHHHHHHHHh
Q 038538 74 GKWVSEIREPRKKSRIWLGTFR--TPEMAARAHDVAALSI 111 (243)
Q Consensus 74 GKW~AeIr~~~~kkri~LGtF~--T~EeAArAYD~Aa~~l 111 (243)
+.|+.+++..++..++.||+|+ +.++|..........+
T Consensus 10 ~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 5699999997777788899996 6677776665544444
No 8
>PHA02601 int integrase; Provisional
Probab=60.60 E-value=14 Score=33.24 Aligned_cols=44 Identities=30% Similarity=0.361 Sum_probs=29.8
Q ss_pred EeEECCCCcEEEEEeeC-CCCeEEeecCCCCHHHHHHHHHHHHHHh
Q 038538 67 GVRMRSWGKWVSEIREP-RKKSRIWLGTFRTPEMAARAHDVAALSI 111 (243)
Q Consensus 67 GVr~r~~GKW~AeIr~~-~~kkri~LGtF~T~EeAArAYD~Aa~~l 111 (243)
+|+..+.|+|+++++.. ..|+++. .+|.|..||....+.....+
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~-~~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIR-KRFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhh-hhhcCHHHHHHHHHHHHHhc
Confidence 45566678999999863 2356655 36999998877665544433
No 9
>PRK09692 integrase; Provisional
Probab=56.94 E-value=30 Score=32.51 Aligned_cols=37 Identities=19% Similarity=0.368 Sum_probs=23.6
Q ss_pred eEECCCCc--EEEEEeeC--CCCeEEeecCCC--CHHHHHHHH
Q 038538 68 VRMRSWGK--WVSEIREP--RKKSRIWLGTFR--TPEMAARAH 104 (243)
Q Consensus 68 Vr~r~~GK--W~AeIr~~--~~kkri~LGtF~--T~EeAArAY 104 (243)
|+.+..|. |+.+.+.+ ++.+++-||.|+ |..+|..+.
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 45555554 99988754 333447899999 566665443
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=43.93 E-value=23 Score=24.64 Aligned_cols=25 Identities=24% Similarity=0.207 Sum_probs=18.2
Q ss_pred CCCeEEeecCCCCHHHHHHHHHHHH
Q 038538 84 RKKSRIWLGTFRTPEMAARAHDVAA 108 (243)
Q Consensus 84 ~~kkri~LGtF~T~EeAArAYD~Aa 108 (243)
...-+|.+|.|++.++|..+.....
T Consensus 41 ~~~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 41 GPWYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp TTCEEEEECCECTCCHHHHHHHHHH
T ss_pred CceEEEEECCCCCHHHHHHHHHHHh
Confidence 3445788888888888887766443
No 11
>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=41.50 E-value=55 Score=24.58 Aligned_cols=39 Identities=21% Similarity=0.315 Sum_probs=29.3
Q ss_pred cEEEEEeeCCCCeEEeecCCCCHHHHHHHHHHHHHHhcC
Q 038538 75 KWVSEIREPRKKSRIWLGTFRTPEMAARAHDVAALSIKG 113 (243)
Q Consensus 75 KW~AeIr~~~~kkri~LGtF~T~EeAArAYD~Aa~~l~G 113 (243)
.|=++|.-..-.-..|.|-|.+.+||..+.---...+..
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~~ 47 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLES 47 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHHh
Confidence 477888775555689999999999999986654444443
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=38.73 E-value=51 Score=25.23 Aligned_cols=40 Identities=28% Similarity=0.244 Sum_probs=25.7
Q ss_pred CCCceeEeEECCCCcEEEEEeeCCCCeEEeecCCCCHHHHHHH
Q 038538 61 KHPVYRGVRMRSWGKWVSEIREPRKKSRIWLGTFRTPEMAARA 103 (243)
Q Consensus 61 ~~s~yRGVr~r~~GKW~AeIr~~~~kkri~LGtF~T~EeAArA 103 (243)
+.-+||-|+.-+ |||+|.+-. +..-.---.|.-+|.|-|=
T Consensus 29 k~dgfrdvw~lr-gkyvafvl~--ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 29 KMDGFRDVWQLR-GKYVAFVLM--GEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp -TTTECCECCCC-CEEEEEEES--SS-EEE---BSSHHHHHHH
T ss_pred hcccccceeeec-cceEEEEEe--cchhccCCCcCCcHHHHHH
Confidence 345799997666 999999987 3333334678888877663
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=37.90 E-value=91 Score=23.40 Aligned_cols=45 Identities=18% Similarity=0.120 Sum_probs=33.1
Q ss_pred ceeEeEEC-CCCcEEEEEeeCCCCeEEeecCCCCHHHHHHHHHHHHHHh
Q 038538 64 VYRGVRMR-SWGKWVSEIREPRKKSRIWLGTFRTPEMAARAHDVAALSI 111 (243)
Q Consensus 64 ~yRGVr~r-~~GKW~AeIr~~~~kkri~LGtF~T~EeAArAYD~Aa~~l 111 (243)
+|.||.+| ..-+-.+-|.. .||-+..|. .++|+|..|.+.....+
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 68898766 44466666766 887777775 78999999988766544
No 14
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=35.19 E-value=27 Score=28.39 Aligned_cols=19 Identities=21% Similarity=0.665 Sum_probs=14.9
Q ss_pred eEEeecCCCCHHHHHHHHH
Q 038538 87 SRIWLGTFRTPEMAARAHD 105 (243)
Q Consensus 87 kri~LGtF~T~EeAArAYD 105 (243)
-.||||+|++.++-..=.+
T Consensus 2 VsiWiG~f~s~~el~~Y~e 20 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYFE 20 (122)
T ss_pred eEEEEecCCCHHHHHHHhC
Confidence 3699999999888766554
No 15
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=33.14 E-value=1.5e+02 Score=25.56 Aligned_cols=46 Identities=22% Similarity=0.146 Sum_probs=34.8
Q ss_pred ceeEeEEC-CCCcEEEEEeeCCCCeEEeecCCCCHHHHHHHHHHHHHHhc
Q 038538 64 VYRGVRMR-SWGKWVSEIREPRKKSRIWLGTFRTPEMAARAHDVAALSIK 112 (243)
Q Consensus 64 ~yRGVr~r-~~GKW~AeIr~~~~kkri~LGtF~T~EeAArAYD~Aa~~l~ 112 (243)
+|.||.+| ..-|-.+-|+. .|| +.+=...+.|+|++|.+..+..+.
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 79999777 44677777877 665 444456899999999998777663
No 16
>PLN00062 TATA-box-binding protein; Provisional
Probab=30.31 E-value=2.3e+02 Score=24.66 Aligned_cols=47 Identities=19% Similarity=0.063 Sum_probs=34.3
Q ss_pred CceeEeEEC-CCCcEEEEEeeCCCCeEEeecCCCCHHHHHHHHHHHHHHhc
Q 038538 63 PVYRGVRMR-SWGKWVSEIREPRKKSRIWLGTFRTPEMAARAHDVAALSIK 112 (243)
Q Consensus 63 s~yRGVr~r-~~GKW~AeIr~~~~kkri~LGtF~T~EeAArAYD~Aa~~l~ 112 (243)
.+|.||.+| ..-|=.+-|.. .||-+--| ..++|+|..|.++.+..+.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~--SGKiviTG-aks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 34 KRFAAVIMRIREPKTTALIFA--SGKMVCTG-AKSEHDSKLAARKYARIIQ 81 (179)
T ss_pred ccCcEEEEEeCCCcEEEEEEC--CCeEEEEe-cCCHHHHHHHHHHHHHHHH
Confidence 369999777 45666777777 66654444 5789999999988877774
No 17
>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=29.50 E-value=2.5e+02 Score=24.27 Aligned_cols=47 Identities=19% Similarity=0.101 Sum_probs=34.7
Q ss_pred CceeEeEEC-CCCcEEEEEeeCCCCeEEeecCCCCHHHHHHHHHHHHHHhc
Q 038538 63 PVYRGVRMR-SWGKWVSEIREPRKKSRIWLGTFRTPEMAARAHDVAALSIK 112 (243)
Q Consensus 63 s~yRGVr~r-~~GKW~AeIr~~~~kkri~LGtF~T~EeAArAYD~Aa~~l~ 112 (243)
.+|.||.+| ..-|-.+-|.. .||-+--|. .++|+|..|.++.+..+.
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 478999776 44566777777 777665666 678899999888777664
No 18
>PRK10113 cell division modulator; Provisional
Probab=26.03 E-value=54 Score=25.02 Aligned_cols=39 Identities=28% Similarity=0.324 Sum_probs=25.7
Q ss_pred CCceeEeEECCCCcEEEEEeeCCCCeEEeecCCCCHHHHHHH
Q 038538 62 HPVYRGVRMRSWGKWVSEIREPRKKSRIWLGTFRTPEMAARA 103 (243)
Q Consensus 62 ~s~yRGVr~r~~GKW~AeIr~~~~kkri~LGtF~T~EeAArA 103 (243)
.-+||-|+.-+ |||+|.+..... -.---.|..+|.|-|=
T Consensus 30 md~frDVW~Lr-GKYVAFvl~ge~--FrRSPaFs~PEsAQRW 68 (80)
T PRK10113 30 MDSFRDVWMLR-GKYVAFVLMGES--FLRSPAFSVPESAQRW 68 (80)
T ss_pred hcchhhhheec-cceEEEEEechh--hccCCccCCcHHHHHH
Confidence 34688887655 999999877222 2223567778777653
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=24.93 E-value=77 Score=18.46 Aligned_cols=11 Identities=27% Similarity=1.078 Sum_probs=8.0
Q ss_pred CCeEEeecCCC
Q 038538 85 KKSRIWLGTFR 95 (243)
Q Consensus 85 ~kkri~LGtF~ 95 (243)
+..+||+||+.
T Consensus 14 ~~G~lWigT~~ 24 (24)
T PF07494_consen 14 SDGNLWIGTYN 24 (24)
T ss_dssp TTSCEEEEETS
T ss_pred CCcCEEEEeCC
Confidence 33489999974
No 20
>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=23.77 E-value=83 Score=25.09 Aligned_cols=20 Identities=30% Similarity=0.245 Sum_probs=17.0
Q ss_pred cCCCCHHHHHHHHHHHHHHh
Q 038538 92 GTFRTPEMAARAHDVAALSI 111 (243)
Q Consensus 92 GtF~T~EeAArAYD~Aa~~l 111 (243)
|.|+|+|+|..-||.-...|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999865443
No 21
>cd01433 Ribosomal_L16_L10e Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.
Probab=22.33 E-value=1.7e+02 Score=23.12 Aligned_cols=35 Identities=20% Similarity=0.250 Sum_probs=26.1
Q ss_pred cEEEEEeeCCCCeEEeecCCCCHHHHHHHHHHHHHHh
Q 038538 75 KWVSEIREPRKKSRIWLGTFRTPEMAARAHDVAALSI 111 (243)
Q Consensus 75 KW~AeIr~~~~kkri~LGtF~T~EeAArAYD~Aa~~l 111 (243)
.|+|.|+. +..-+-++.....+.|..|...|+.+|
T Consensus 71 ~~~a~v~~--G~iifEi~~~~~~~~~~~alk~a~~Kl 105 (112)
T cd01433 71 GWVARVKP--GQILFEVRGVPEEEVAKEALRRAAKKL 105 (112)
T ss_pred EEEEEECC--CCEEEEEeCcCcHHHHHHHHHHhhccC
Confidence 49999988 444445666655899999988888766
No 22
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=21.78 E-value=93 Score=33.60 Aligned_cols=9 Identities=22% Similarity=0.350 Sum_probs=5.3
Q ss_pred HHhcCCCCC
Q 038538 109 LSIKGDSAV 117 (243)
Q Consensus 109 ~~l~G~~a~ 117 (243)
...||.+.+
T Consensus 1333 vaawgrdtv 1341 (1463)
T PHA03308 1333 VAAWGRDTV 1341 (1463)
T ss_pred HHHhccccc
Confidence 345777754
No 23
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=20.88 E-value=1.5e+02 Score=25.33 Aligned_cols=36 Identities=17% Similarity=0.185 Sum_probs=29.3
Q ss_pred EEEEEeeCCCCeEEeecCCCCHHHHHHHHHHHHHHhcCC
Q 038538 76 WVSEIREPRKKSRIWLGTFRTPEMAARAHDVAALSIKGD 114 (243)
Q Consensus 76 W~AeIr~~~~kkri~LGtF~T~EeAArAYD~Aa~~l~G~ 114 (243)
|+|.|.. |+.++-=....++.|..|.-.|+.+|=+.
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 9999987 45677677788888999999999988554
No 24
>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=20.79 E-value=3.5e+02 Score=23.33 Aligned_cols=47 Identities=19% Similarity=0.122 Sum_probs=34.1
Q ss_pred CceeEeEEC-CCCcEEEEEeeCCCCeEEeecCCCCHHHHHHHHHHHHHHhc
Q 038538 63 PVYRGVRMR-SWGKWVSEIREPRKKSRIWLGTFRTPEMAARAHDVAALSIK 112 (243)
Q Consensus 63 s~yRGVr~r-~~GKW~AeIr~~~~kkri~LGtF~T~EeAArAYD~Aa~~l~ 112 (243)
.+|.||.+| +.-|=.+-|.. .||-+-.| ..+.|+|..|-++.+..+.
T Consensus 34 ~~fpgli~Rl~~Pk~t~lIF~--SGKiv~tG-aks~~~a~~a~~~~~~~L~ 81 (174)
T cd04518 34 DQFPGLVYRLEDPKIAALIFR--SGKMVCTG-AKSVEDLHRAVKEIIKKLK 81 (174)
T ss_pred CcCcEEEEEccCCcEEEEEEC--CCeEEEEc-cCCHHHHHHHHHHHHHHHH
Confidence 479999777 44465666666 77655545 5789999999998877775
Done!