Query 039696
Match_columns 210
No_of_seqs 242 out of 1192
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 12:18:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039696.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039696hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA00280 putative NHN endonucl 99.9 2.3E-22 5.1E-27 159.0 5.5 82 3-87 38-120 (121)
2 cd00018 AP2 DNA-binding domain 99.8 3.8E-21 8.3E-26 134.1 7.6 61 32-92 1-61 (61)
3 smart00380 AP2 DNA-binding dom 99.8 7E-20 1.5E-24 129.2 8.4 63 33-95 1-63 (64)
4 PF00847 AP2: AP2 domain; Int 99.1 1.1E-10 2.5E-15 79.3 5.2 52 32-83 1-56 (56)
5 PF13392 HNH_3: HNH endonuclea 85.2 0.032 7E-07 36.5 -4.4 19 3-21 27-45 (46)
6 PF14657 Integrase_AP2: AP2-li 82.1 4.7 0.0001 26.2 5.0 38 44-81 1-42 (46)
7 PF13356 DUF4102: Domain of un 76.9 6.8 0.00015 28.6 5.1 40 38-77 28-71 (89)
8 cd00801 INT_P4 Bacteriophage P 74.6 5.9 0.00013 34.5 4.9 38 43-80 10-49 (357)
9 PF08846 DUF1816: Domain of un 64.7 15 0.00032 26.5 4.3 39 44-82 9-47 (68)
10 PHA02601 int integrase; Provis 61.7 14 0.00031 32.4 4.6 42 36-78 2-44 (333)
11 PRK09692 integrase; Provisiona 59.3 27 0.00058 32.0 6.2 39 37-75 33-77 (413)
12 PF10729 CedA: Cell division a 47.6 27 0.00058 25.5 3.3 40 30-72 29-68 (80)
13 PF05036 SPOR: Sporulation rel 41.3 24 0.00053 23.7 2.3 25 53-77 41-65 (76)
14 PRK10113 cell division modulat 38.0 28 0.00062 25.3 2.2 38 31-71 30-67 (80)
15 PF14112 DUF4284: Domain of un 29.9 32 0.0007 27.0 1.5 18 56-73 2-19 (122)
16 cd04517 TLF TBP-like factors ( 29.1 2E+02 0.0043 23.9 6.2 46 33-81 35-81 (174)
17 PLN00062 TATA-box-binding prot 29.0 2.2E+02 0.0048 23.9 6.5 47 32-81 34-81 (179)
18 PF08471 Ribonuc_red_2_N: Clas 28.9 64 0.0014 24.7 2.9 21 60-80 70-90 (93)
19 PF00352 TBP: Transcription fa 27.4 1.4E+02 0.0031 21.5 4.5 45 33-80 37-82 (86)
20 PF07494 Reg_prop: Two compone 26.1 54 0.0012 18.3 1.6 17 47-64 8-24 (24)
21 PF12167 DUF3596: Domain of un 23.9 2.5E+02 0.0055 19.4 5.1 37 35-72 2-38 (64)
22 cd04516 TBP_eukaryotes eukaryo 21.4 3.9E+02 0.0084 22.3 6.6 47 32-81 34-81 (174)
23 COG2185 Sbm Methylmalonyl-CoA 20.8 73 0.0016 26.1 2.0 30 44-73 30-59 (143)
No 1
>PHA00280 putative NHN endonuclease
Probab=99.86 E-value=2.3e-22 Score=159.04 Aligned_cols=82 Identities=16% Similarity=0.165 Sum_probs=75.5
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEC-CCCcEEEEEecCCCCceeecCCCCCHHHHHHHHHHHHHHhc
Q 039696 3 YPKSNKSTNPSSSSGSGSGSNASAGPGRHPTYRGVRRR-SSGKWVSEIREPRKPTRIWLGTFATPEMAAIAYDVAALALK 81 (210)
Q Consensus 3 ~p~dNr~sNLR~at~~~n~~n~~~~~~~~s~yrGVr~r-~~gkW~A~I~~~~k~~ri~LGtf~t~EeAA~AyD~aa~~l~ 81 (210)
.|.||||+|||++|+++|++|++.+++|+|||+||+++ ..|||+|+|++.+| +++||.|+|+|+|+.||+ ++.+|+
T Consensus 38 ~~~dnri~NLr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~gK--~~~lG~f~~~e~A~~a~~-~~~~lh 114 (121)
T PHA00280 38 NPLNDALDNLRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTAEGK--QHNFRSRDLLEVVAWIYR-TRRELH 114 (121)
T ss_pred CCCCCcHHHhhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEECCE--EEEcCCCCCHHHHHHHHH-HHHHHh
Confidence 58899999999999999999999999999999999987 56999999999554 999999999999999997 778999
Q ss_pred CCcCcC
Q 039696 82 GQEAEL 87 (210)
Q Consensus 82 G~~a~~ 87 (210)
|+|++.
T Consensus 115 GeFa~~ 120 (121)
T PHA00280 115 GQFARF 120 (121)
T ss_pred hccccC
Confidence 998864
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=99.84 E-value=3.8e-21 Score=134.13 Aligned_cols=61 Identities=64% Similarity=1.042 Sum_probs=57.6
Q ss_pred CceeEEEECCCCcEEEEEecCCCCceeecCCCCCHHHHHHHHHHHHHHhcCCcCcCCCCCC
Q 039696 32 PTYRGVRRRSSGKWVSEIREPRKPTRIWLGTFATPEMAAIAYDVAALALKGQEAELNFPNS 92 (210)
Q Consensus 32 s~yrGVr~r~~gkW~A~I~~~~k~~ri~LGtf~t~EeAA~AyD~aa~~l~G~~a~~Nfp~s 92 (210)
|+||||+++++|||+|+|+++.+++++|||+|+|+|||++|||.++++++|.++.+|||++
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 6899999888899999999986677999999999999999999999999999999999985
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.81 E-value=7e-20 Score=129.23 Aligned_cols=63 Identities=60% Similarity=1.017 Sum_probs=59.0
Q ss_pred ceeEEEECCCCcEEEEEecCCCCceeecCCCCCHHHHHHHHHHHHHHhcCCcCcCCCCCCCCC
Q 039696 33 TYRGVRRRSSGKWVSEIREPRKPTRIWLGTFATPEMAAIAYDVAALALKGQEAELNFPNSAAS 95 (210)
Q Consensus 33 ~yrGVr~r~~gkW~A~I~~~~k~~ri~LGtf~t~EeAA~AyD~aa~~l~G~~a~~Nfp~s~~~ 95 (210)
+|+||+++++|||+|+|+++.+++++|||+|+|+|||++|||.++++++|.++.+|||.+.+.
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 599999888899999999987788999999999999999999999999999999999998653
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=99.11 E-value=1.1e-10 Score=79.33 Aligned_cols=52 Identities=33% Similarity=0.451 Sum_probs=44.9
Q ss_pred CceeEEEEC-CCCcEEEEEecCC---CCceeecCCCCCHHHHHHHHHHHHHHhcCC
Q 039696 32 PTYRGVRRR-SSGKWVSEIREPR---KPTRIWLGTFATPEMAAIAYDVAALALKGQ 83 (210)
Q Consensus 32 s~yrGVr~r-~~gkW~A~I~~~~---k~~ri~LGtf~t~EeAA~AyD~aa~~l~G~ 83 (210)
|+|+||+++ ..++|+|+|++.. ++++++||.|.++++|+++++.+++.++|+
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 689999887 5699999999841 147999999999999999999999999874
No 5
>PF13392 HNH_3: HNH endonuclease; PDB: 1U3E_M.
Probab=85.18 E-value=0.032 Score=36.48 Aligned_cols=19 Identities=16% Similarity=0.100 Sum_probs=12.2
Q ss_pred CCCCCCCCCCCCCCCCCCC
Q 039696 3 YPKSNKSTNPSSSSGSGSG 21 (210)
Q Consensus 3 ~p~dNr~sNLR~at~~~n~ 21 (210)
.|.||+++||+++|+++|.
T Consensus 27 ~~~~n~~~NL~~~t~~en~ 45 (46)
T PF13392_consen 27 NKTDNRPENLRWVTRSENS 45 (46)
T ss_dssp -TT---GGGEEEE-HHHHH
T ss_pred CCCCCCHHHceECCHHHhC
Confidence 4789999999999988764
No 6
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=82.07 E-value=4.7 Score=26.17 Aligned_cols=38 Identities=18% Similarity=0.182 Sum_probs=29.7
Q ss_pred cEEEEEe--c--CCCCceeecCCCCCHHHHHHHHHHHHHHhc
Q 039696 44 KWVSEIR--E--PRKPTRIWLGTFATPEMAAIAYDVAALALK 81 (210)
Q Consensus 44 kW~A~I~--~--~~k~~ri~LGtf~t~EeAA~AyD~aa~~l~ 81 (210)
+|...|. . .++.++++-+-|.|..||..+.......+.
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 3 356678999999999999999887666553
No 7
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=76.85 E-value=6.8 Score=28.58 Aligned_cols=40 Identities=25% Similarity=0.189 Sum_probs=27.5
Q ss_pred EECCCC--cEEEEEecCCCCceeecCCCCC--HHHHHHHHHHHH
Q 039696 38 RRRSSG--KWVSEIREPRKPTRIWLGTFAT--PEMAAIAYDVAA 77 (210)
Q Consensus 38 r~r~~g--kW~A~I~~~~k~~ri~LGtf~t--~EeAA~AyD~aa 77 (210)
+..+.| .|+-+.+..+|..++-||.|++ ..+|........
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 344544 5999999988888999999975 555555444433
No 8
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=74.62 E-value=5.9 Score=34.46 Aligned_cols=38 Identities=26% Similarity=0.292 Sum_probs=28.9
Q ss_pred CcEEEEEecCCCCceeecCCCC--CHHHHHHHHHHHHHHh
Q 039696 43 GKWVSEIREPRKPTRIWLGTFA--TPEMAAIAYDVAALAL 80 (210)
Q Consensus 43 gkW~A~I~~~~k~~ri~LGtf~--t~EeAA~AyD~aa~~l 80 (210)
+.|+.+++..++..++.||+|+ |.++|..........+
T Consensus 10 ~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 4699999998888889999995 6777776665544444
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=64.68 E-value=15 Score=26.51 Aligned_cols=39 Identities=23% Similarity=0.314 Sum_probs=29.1
Q ss_pred cEEEEEecCCCCceeecCCCCCHHHHHHHHHHHHHHhcC
Q 039696 44 KWVSEIREPRKPTRIWLGTFATPEMAAIAYDVAALALKG 82 (210)
Q Consensus 44 kW~A~I~~~~k~~ri~LGtf~t~EeAA~AyD~aa~~l~G 82 (210)
.|-++|.-..-.-..|.|-|.|.+||..+.-.-..-|..
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~~ 47 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLES 47 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHHh
Confidence 578899765545579999999999999887554444443
No 10
>PHA02601 int integrase; Provisional
Probab=61.66 E-value=14 Score=32.43 Aligned_cols=42 Identities=31% Similarity=0.378 Sum_probs=28.2
Q ss_pred EEEECCCCcEEEEEecCC-CCceeecCCCCCHHHHHHHHHHHHH
Q 039696 36 GVRRRSSGKWVSEIREPR-KPTRIWLGTFATPEMAAIAYDVAAL 78 (210)
Q Consensus 36 GVr~r~~gkW~A~I~~~~-k~~ri~LGtf~t~EeAA~AyD~aa~ 78 (210)
+|++.+.|+|+++|+..+ .|+++. .+|.|..||.........
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~-~~f~tk~eA~~~~~~~~~ 44 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIR-KRFATKGEALAFENYTMA 44 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhh-hhhcCHHHHHHHHHHHHH
Confidence 466667789999998642 244554 369999988765554433
No 11
>PRK09692 integrase; Provisional
Probab=59.35 E-value=27 Score=32.03 Aligned_cols=39 Identities=21% Similarity=0.245 Sum_probs=25.0
Q ss_pred EEECCCC--cEEEEEecC--CCCceeecCCCC--CHHHHHHHHHH
Q 039696 37 VRRRSSG--KWVSEIREP--RKPTRIWLGTFA--TPEMAAIAYDV 75 (210)
Q Consensus 37 Vr~r~~g--kW~A~I~~~--~k~~ri~LGtf~--t~EeAA~AyD~ 75 (210)
|+.+..| .|+.+.+.+ ++.+++-||.|+ |..+|......
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~ 77 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAE 77 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHH
Confidence 4445555 499887644 454557899999 67666554433
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=47.60 E-value=27 Score=25.52 Aligned_cols=40 Identities=23% Similarity=0.227 Sum_probs=25.0
Q ss_pred CCCceeEEEECCCCcEEEEEecCCCCceeecCCCCCHHHHHHH
Q 039696 30 RHPTYRGVRRRSSGKWVSEIREPRKPTRIWLGTFATPEMAAIA 72 (210)
Q Consensus 30 ~~s~yrGVr~r~~gkW~A~I~~~~k~~ri~LGtf~t~EeAA~A 72 (210)
+--+||-|..-+ |||+|.|..... -..--.|..+|.|-|=
T Consensus 29 k~dgfrdvw~lr-gkyvafvl~ge~--f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 29 KMDGFRDVWQLR-GKYVAFVLMGEH--FRRSPAFSVPESAQRW 68 (80)
T ss_dssp -TTTECCECCCC-CEEEEEEESSS---EEE---BSSHHHHHHH
T ss_pred hcccccceeeec-cceEEEEEecch--hccCCCcCCcHHHHHH
Confidence 445788886544 999999987433 3344568888877653
No 13
>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=41.29 E-value=24 Score=23.75 Aligned_cols=25 Identities=24% Similarity=0.227 Sum_probs=18.7
Q ss_pred CCCceeecCCCCCHHHHHHHHHHHH
Q 039696 53 RKPTRIWLGTFATPEMAAIAYDVAA 77 (210)
Q Consensus 53 ~k~~ri~LGtf~t~EeAA~AyD~aa 77 (210)
+.--++.+|.|.|.++|..+-....
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 3445888999999999987766544
No 14
>PRK10113 cell division modulator; Provisional
Probab=38.01 E-value=28 Score=25.32 Aligned_cols=38 Identities=24% Similarity=0.282 Sum_probs=24.7
Q ss_pred CCceeEEEECCCCcEEEEEecCCCCceeecCCCCCHHHHHH
Q 039696 31 HPTYRGVRRRSSGKWVSEIREPRKPTRIWLGTFATPEMAAI 71 (210)
Q Consensus 31 ~s~yrGVr~r~~gkW~A~I~~~~k~~ri~LGtf~t~EeAA~ 71 (210)
--+||-|..-+ |||+|.+..... -..--.|..+|.|-|
T Consensus 30 md~frDVW~Lr-GKYVAFvl~ge~--FrRSPaFs~PEsAQR 67 (80)
T PRK10113 30 MDSFRDVWMLR-GKYVAFVLMGES--FLRSPAFSVPESAQR 67 (80)
T ss_pred hcchhhhheec-cceEEEEEechh--hccCCccCCcHHHHH
Confidence 35688886544 899999987432 222345777777765
No 15
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=29.85 E-value=32 Score=26.96 Aligned_cols=18 Identities=22% Similarity=0.652 Sum_probs=14.0
Q ss_pred ceeecCCCCCHHHHHHHH
Q 039696 56 TRIWLGTFATPEMAAIAY 73 (210)
Q Consensus 56 ~ri~LGtf~t~EeAA~Ay 73 (210)
..||||+|+|.++--.=.
T Consensus 2 VsiWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYF 19 (122)
T ss_pred eEEEEecCCCHHHHHHHh
Confidence 369999999988866443
No 16
>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=29.11 E-value=2e+02 Score=23.94 Aligned_cols=46 Identities=22% Similarity=0.135 Sum_probs=33.6
Q ss_pred ceeEEEEC-CCCcEEEEEecCCCCceeecCCCCCHHHHHHHHHHHHHHhc
Q 039696 33 TYRGVRRR-SSGKWVSEIREPRKPTRIWLGTFATPEMAAIAYDVAALALK 81 (210)
Q Consensus 33 ~yrGVr~r-~~gkW~A~I~~~~k~~ri~LGtf~t~EeAA~AyD~aa~~l~ 81 (210)
+|.||..| ..-|=.+-|...|| -+ +=-..+.|+|..|.+..+..+.
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~sGK--iv-iTGaks~~~~~~a~~~~~~~l~ 81 (174)
T cd04517 35 RYPKVTMRLREPRATASVWSSGK--IT-ITGATSEEEAKQAARRAARLLQ 81 (174)
T ss_pred CCCEEEEEecCCcEEEEEECCCe--EE-EEccCCHHHHHHHHHHHHHHHH
Confidence 79999777 44576777777554 44 3446899999999988777663
No 17
>PLN00062 TATA-box-binding protein; Provisional
Probab=29.00 E-value=2.2e+02 Score=23.89 Aligned_cols=47 Identities=17% Similarity=0.092 Sum_probs=33.4
Q ss_pred CceeEEEEC-CCCcEEEEEecCCCCceeecCCCCCHHHHHHHHHHHHHHhc
Q 039696 32 PTYRGVRRR-SSGKWVSEIREPRKPTRIWLGTFATPEMAAIAYDVAALALK 81 (210)
Q Consensus 32 s~yrGVr~r-~~gkW~A~I~~~~k~~ri~LGtf~t~EeAA~AyD~aa~~l~ 81 (210)
.+|-||..| ..-|=.+-|...|| -+--| ..+.|+|..|.++.+..+.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~SGK--iviTG-aks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 34 KRFAAVIMRIREPKTTALIFASGK--MVCTG-AKSEHDSKLAARKYARIIQ 81 (179)
T ss_pred ccCcEEEEEeCCCcEEEEEECCCe--EEEEe-cCCHHHHHHHHHHHHHHHH
Confidence 468999776 44566677777554 55444 5788999999988877774
No 18
>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=28.90 E-value=64 Score=24.69 Aligned_cols=21 Identities=43% Similarity=0.396 Sum_probs=17.5
Q ss_pred cCCCCCHHHHHHHHHHHHHHh
Q 039696 60 LGTFATPEMAAIAYDVAALAL 80 (210)
Q Consensus 60 LGtf~t~EeAA~AyD~aa~~l 80 (210)
-|+|.|+|+|..-||.-...|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 499999999999999866544
No 19
>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=27.36 E-value=1.4e+02 Score=21.53 Aligned_cols=45 Identities=20% Similarity=0.122 Sum_probs=31.3
Q ss_pred ceeEEEEC-CCCcEEEEEecCCCCceeecCCCCCHHHHHHHHHHHHHHh
Q 039696 33 TYRGVRRR-SSGKWVSEIREPRKPTRIWLGTFATPEMAAIAYDVAALAL 80 (210)
Q Consensus 33 ~yrGVr~r-~~gkW~A~I~~~~k~~ri~LGtf~t~EeAA~AyD~aa~~l 80 (210)
+|.||..| ..-+-.+.|... |+-+..|. .+.|++..|.+.....+
T Consensus 37 ~fpgl~~r~~~p~~t~~IF~s--Gki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 37 RFPGLIYRLRNPKATVLIFSS--GKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TESSEEEEETTTTEEEEEETT--SEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred cCCeEEEeecCCcEEEEEEcC--CEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 68888766 434666667664 44666664 78999999988766554
No 20
>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=26.09 E-value=54 Score=18.29 Aligned_cols=17 Identities=29% Similarity=0.718 Sum_probs=9.6
Q ss_pred EEEecCCCCceeecCCCC
Q 039696 47 SEIREPRKPTRIWLGTFA 64 (210)
Q Consensus 47 A~I~~~~k~~ri~LGtf~ 64 (210)
-.|.+..+ .+||+||+.
T Consensus 8 ~~i~~D~~-G~lWigT~~ 24 (24)
T PF07494_consen 8 YSIYEDSD-GNLWIGTYN 24 (24)
T ss_dssp EEEEE-TT-SCEEEEETS
T ss_pred EEEEEcCC-cCEEEEeCC
Confidence 34444333 389999873
No 21
>PF12167 DUF3596: Domain of unknown function (DUF3596); InterPro: IPR022000 This N-terminal domain is found in Bacteriophage P27p02, it is functionally uncharacterised, though it is considered to be an integrase. Integrase is necessary for integration of the phage into the host genome by site-specific recombination. In conjunction with excisionase, integrase is also necessary for excision of the prophage from the host genome. This domain is found in related proteins in other bacteriophage, and prophage regions of bacterial genomes. The domain is approximately 90 amino acids in length and is found is associated with the C-terminal domain characterised by PF00589 from PFAM.
Probab=23.90 E-value=2.5e+02 Score=19.41 Aligned_cols=37 Identities=35% Similarity=0.321 Sum_probs=27.0
Q ss_pred eEEEECCCCcEEEEEecCCCCceeecCCCCCHHHHHHH
Q 039696 35 RGVRRRSSGKWVSEIREPRKPTRIWLGTFATPEMAAIA 72 (210)
Q Consensus 35 rGVr~r~~gkW~A~I~~~~k~~ri~LGtf~t~EeAA~A 72 (210)
.||+.| .|+-+-..+..++..+..||.-+|+.-=..|
T Consensus 2 ~gV~~r-~~~L~i~F~y~G~R~re~l~l~dT~~N~k~a 38 (64)
T PF12167_consen 2 AGVRVR-NGKLRIDFTYQGKRCRESLGLPDTPANRKKA 38 (64)
T ss_pred CCEEEE-CCEEEEEEEECCEEEEEeCCCCCCHHHHHHH
Confidence 478877 5777777777677667889999998754444
No 22
>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=21.37 E-value=3.9e+02 Score=22.28 Aligned_cols=47 Identities=17% Similarity=0.130 Sum_probs=33.2
Q ss_pred CceeEEEEC-CCCcEEEEEecCCCCceeecCCCCCHHHHHHHHHHHHHHhc
Q 039696 32 PTYRGVRRR-SSGKWVSEIREPRKPTRIWLGTFATPEMAAIAYDVAALALK 81 (210)
Q Consensus 32 s~yrGVr~r-~~gkW~A~I~~~~k~~ri~LGtf~t~EeAA~AyD~aa~~l~ 81 (210)
.+|-||..| ..-|=.+-|...|| -+--|. .+.|+|..|.++.+..+.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~SGK--iviTGa-ks~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIFSSGK--MVCTGA-KSEDDSKLAARKYARIIQ 81 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEECCCe--EEEEec-CCHHHHHHHHHHHHHHHH
Confidence 478898776 44566677777554 655565 678889988888777664
No 23
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=20.84 E-value=73 Score=26.12 Aligned_cols=30 Identities=33% Similarity=0.251 Sum_probs=21.3
Q ss_pred cEEEEEecCCCCceeecCCCCCHHHHHHHH
Q 039696 44 KWVSEIREPRKPTRIWLGTFATPEMAAIAY 73 (210)
Q Consensus 44 kW~A~I~~~~k~~ri~LGtf~t~EeAA~Ay 73 (210)
|..+++.....=.-|++|.|.|+||++++-
T Consensus 30 kvia~~l~d~GfeVi~~g~~~tp~e~v~aA 59 (143)
T COG2185 30 KVIARALADAGFEVINLGLFQTPEEAVRAA 59 (143)
T ss_pred HHHHHHHHhCCceEEecCCcCCHHHHHHHH
Confidence 455555444333469999999999999774
Done!