Query 046252
Match_columns 124
No_of_seqs 150 out of 1176
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 10:11:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046252.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046252hhsearch_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 4.6E-23 1E-27 130.3 6.0 61 53-114 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.9 1.8E-22 4E-27 129.0 6.3 64 54-118 1-64 (64)
3 PHA00280 putative NHN endonucl 99.7 1.1E-17 2.4E-22 119.6 5.0 79 14-108 40-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.3 1.9E-12 4E-17 79.9 3.7 52 53-105 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 83.0 2.3 4.9E-05 24.8 3.4 37 65-102 1-41 (46)
6 cd00801 INT_P4 Bacteriophage P 74.1 4.8 0.0001 31.4 3.8 40 62-102 8-49 (357)
7 PF08846 DUF1816: Domain of un 72.6 6.3 0.00014 25.5 3.4 39 65-104 9-47 (68)
8 PF10729 CedA: Cell division a 72.3 7.4 0.00016 25.6 3.7 38 52-93 30-67 (80)
9 PHA02601 int integrase; Provis 69.6 5.6 0.00012 31.3 3.3 45 57-102 2-46 (333)
10 PF08471 Ribonuc_red_2_N: Clas 59.0 7 0.00015 26.9 1.7 21 82-102 70-90 (93)
11 PHA03308 transcriptional regul 55.4 13 0.00028 34.7 3.2 30 4-33 1254-1283(1463)
12 PRK10113 cell division modulat 55.0 11 0.00023 24.8 2.0 38 52-93 30-67 (80)
13 PF05036 SPOR: Sporulation rel 54.2 5.1 0.00011 24.5 0.4 21 79-99 45-65 (76)
14 PF09954 DUF2188: Uncharacteri 50.1 33 0.00072 20.9 3.7 34 61-99 6-39 (62)
15 PF13356 DUF4102: Domain of un 44.5 15 0.00033 23.9 1.6 36 64-100 35-72 (89)
16 PRK09692 integrase; Provisiona 43.7 45 0.00097 27.4 4.5 36 64-100 41-80 (413)
17 PRK10927 essential cell divisi 40.9 27 0.00058 29.0 2.7 34 66-100 273-306 (319)
18 PF14112 DUF4284: Domain of un 40.8 16 0.00036 25.7 1.3 17 79-95 3-19 (122)
19 PF07384 DUF1497: Protein of u 38.4 16 0.00035 22.5 0.8 32 82-113 1-32 (59)
20 PF07494 Reg_prop: Two compone 36.9 36 0.00078 17.0 1.9 17 67-86 8-24 (24)
21 PLN00062 TATA-box-binding prot 36.6 1.1E+02 0.0023 23.2 5.2 48 51-102 32-80 (179)
22 PRK10905 cell division protein 36.3 50 0.0011 27.5 3.6 24 79-102 287-310 (328)
23 COG2185 Sbm Methylmalonyl-CoA 35.4 28 0.00061 25.6 1.9 30 65-95 30-59 (143)
24 COG2410 Predicted nuclease (RN 35.2 38 0.00083 25.8 2.6 43 67-114 15-57 (178)
25 cd04516 TBP_eukaryotes eukaryo 34.7 1.4E+02 0.0029 22.4 5.5 48 51-102 32-80 (174)
26 cd04517 TLF TBP-like factors ( 32.5 98 0.0021 23.1 4.5 45 54-102 35-80 (174)
27 PF12522 UL73_N: Cytomegalovir 30.6 34 0.00074 18.2 1.2 10 4-13 12-21 (27)
28 COG3087 FtsN Cell division pro 25.3 64 0.0014 26.2 2.4 32 66-98 216-249 (264)
29 COG0197 RplP Ribosomal protein 25.2 92 0.002 23.0 3.1 37 65-105 95-131 (146)
30 PF12286 DUF3622: Protein of u 23.8 1.1E+02 0.0025 19.9 3.0 31 63-93 15-48 (71)
31 PF00352 TBP: Transcription fa 23.3 96 0.0021 20.1 2.7 47 52-102 35-82 (86)
32 PRK12757 cell division protein 23.0 76 0.0016 25.5 2.5 34 66-100 210-243 (256)
33 cd04518 TBP_archaea archaeal T 20.9 2.4E+02 0.0052 21.1 4.7 49 51-103 32-81 (174)
34 cd00652 TBP_TLF TATA box bindi 20.8 2.3E+02 0.0049 21.1 4.6 48 51-102 32-80 (174)
35 PRK09203 rplP 50S ribosomal pr 20.3 1.4E+02 0.003 21.6 3.2 36 65-104 92-127 (138)
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=99.88 E-value=4.6e-23 Score=130.32 Aligned_cols=61 Identities=56% Similarity=1.164 Sum_probs=55.5
Q ss_pred CceeeeeeCCCCcEEEEecCCCCCCceeecCCCCCHHHHHHhhchhhhhhcCCCCCCCCCCC
Q 046252 53 SKYRGVRPRPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQIQGQNAELNFPQT 114 (124)
Q Consensus 53 S~yrGV~~~~~gkw~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~~G~~a~~NFp~~ 114 (124)
|+|+||+++++|+|+|+|+++.+++ ++|||+|+|+||||.|||.++++++|.++.+|||++
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~gk-~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSGGR-RIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCCCc-eEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 7899997777799999999993222 999999999999999999999999999999999975
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.87 E-value=1.8e-22 Score=128.96 Aligned_cols=64 Identities=56% Similarity=1.138 Sum_probs=58.0
Q ss_pred ceeeeeeCCCCcEEEEecCCCCCCceeecCCCCCHHHHHHhhchhhhhhcCCCCCCCCCCCCcch
Q 046252 54 KYRGVRPRPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQIQGQNAELNFPQTHESQ 118 (124)
Q Consensus 54 ~yrGV~~~~~gkw~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~~G~~a~~NFp~~~y~~ 118 (124)
+|+||.++++|+|+|+|+++..++ +++||+|+|+||||.|||.++++++|.++.+|||.+.|+.
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k-~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~~ 64 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGK-RVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYDS 64 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCc-EEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCCC
Confidence 589997788899999999944433 9999999999999999999999999999999999999863
No 3
>PHA00280 putative NHN endonuclease
Probab=99.71 E-value=1.1e-17 Score=119.59 Aligned_cols=79 Identities=19% Similarity=0.282 Sum_probs=63.6
Q ss_pred ccccccccCCCcccccccCCCCCCCCCCCCcccccCCCCCceeee-eeCCCCcEEEEecCCCCCCceeecCCCCCHHHHH
Q 046252 14 VNSCLELISSSNHLDDLFDQSDYESEPTTPDTIRQKAVRSKYRGV-RPRPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAG 92 (124)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~S~yrGV-~~~~~gkw~A~I~~~~k~~~~i~LG~f~t~eeAA 92 (124)
.++.++++...+..++..+ +...+.|+|||+|| |.+..|||+|+|.+++| +++||.|+++|+|+
T Consensus 40 ~dnri~NLr~~T~~eN~~N------------~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~gK---~~~lG~f~~~e~A~ 104 (121)
T PHA00280 40 LNDALDNLRLALPKENSWN------------MKTPKSNTSGLKGLSWSKEREMWRGTVTAEGK---QHNFRSRDLLEVVA 104 (121)
T ss_pred CCCcHHHhhhcCHHHHhcc------------cCCCCCCCCCCCeeEEecCCCeEEEEEEECCE---EEEcCCCCCHHHHH
Confidence 3455555555555544444 44567899999999 67788999999999999 99999999999999
Q ss_pred HhhchhhhhhcCCCCC
Q 046252 93 SAYDPAPFQIQGQNAE 108 (124)
Q Consensus 93 ~AyD~aa~~~~G~~a~ 108 (124)
.||+ ++.++||+||.
T Consensus 105 ~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 105 WIYR-TRRELHGQFAR 119 (121)
T ss_pred HHHH-HHHHHhhcccc
Confidence 9997 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=99.31 E-value=1.9e-12 Score=79.87 Aligned_cols=52 Identities=29% Similarity=0.511 Sum_probs=44.0
Q ss_pred Cceeee-eeCCCCcEEEEecCC---CCCCceeecCCCCCHHHHHHhhchhhhhhcCC
Q 046252 53 SKYRGV-RPRPWGKWTGEIKNP---NKNTAQVWLGTFDMPEDAGSAYDPAPFQIQGQ 105 (124)
Q Consensus 53 S~yrGV-~~~~~gkw~A~I~~~---~k~~~~i~LG~f~t~eeAA~AyD~aa~~~~G~ 105 (124)
|+|+|| +.+..++|+|+|++. ++++ .++||.|++++||++|++.+...++|+
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~~g~~k-~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSENGKRK-RFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCCTTEEE-EEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEcccCcccE-EEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 789999 566789999999883 2122 999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=82.98 E-value=2.3 Score=24.84 Aligned_cols=37 Identities=16% Similarity=0.183 Sum_probs=27.9
Q ss_pred cEEEEec-C---CCCCCceeecCCCCCHHHHHHhhchhhhhh
Q 046252 65 KWTGEIK-N---PNKNTAQVWLGTFDMPEDAGSAYDPAPFQI 102 (124)
Q Consensus 65 kw~A~I~-~---~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~ 102 (124)
+|..+|. . .|+.. +++-+-|.|..||-.+...+...+
T Consensus 1 ~w~~~v~g~~~~~Gkrk-~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRK-QKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEE-EEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5777773 2 34444 889999999999999988776654
No 6
>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=74.14 E-value=4.8 Score=31.37 Aligned_cols=40 Identities=18% Similarity=0.214 Sum_probs=30.0
Q ss_pred CCCcEEEEecCCCCCCceeecCCCC--CHHHHHHhhchhhhhh
Q 046252 62 PWGKWTGEIKNPNKNTAQVWLGTFD--MPEDAGSAYDPAPFQI 102 (124)
Q Consensus 62 ~~gkw~A~I~~~~k~~~~i~LG~f~--t~eeAA~AyD~aa~~~ 102 (124)
..+.|+.++..+++.. ++.||.|+ +.++|..........+
T Consensus 8 g~~~~~~~~~~~g~~~-~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 8 GSKSWRFRYRLAGKRK-RLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CCEEEEEEeccCCcee-EEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 3357999999999876 88999995 6777777666554444
No 7
>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=72.63 E-value=6.3 Score=25.54 Aligned_cols=39 Identities=28% Similarity=0.428 Sum_probs=28.5
Q ss_pred cEEEEecCCCCCCceeecCCCCCHHHHHHhhchhhhhhcC
Q 046252 65 KWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQIQG 104 (124)
Q Consensus 65 kw~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~~G 104 (124)
.|-++|.-..-+- ..|.|-|++.+||..+.---...+-.
T Consensus 9 aWWveI~T~~P~c-tYyFGPF~s~~eA~~~~~gyieDL~~ 47 (68)
T PF08846_consen 9 AWWVEIETQNPNC-TYYFGPFDSREEAEAALPGYIEDLES 47 (68)
T ss_pred cEEEEEEcCCCCE-EEEeCCcCCHHHHHHHhccHHHHHHh
Confidence 4778887655433 78999999999999987655555443
No 8
>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=72.27 E-value=7.4 Score=25.56 Aligned_cols=38 Identities=21% Similarity=0.247 Sum_probs=27.2
Q ss_pred CCceeeeeeCCCCcEEEEecCCCCCCceeecCCCCCHHHHHH
Q 046252 52 RSKYRGVRPRPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGS 93 (124)
Q Consensus 52 ~S~yrGV~~~~~gkw~A~I~~~~k~~~~i~LG~f~t~eeAA~ 93 (124)
--+|+-||.-+ |||+|.+..... -..--.|..+|.|-+
T Consensus 30 ~dgfrdvw~lr-gkyvafvl~ge~---f~rsp~fs~pesaqr 67 (80)
T PF10729_consen 30 MDGFRDVWQLR-GKYVAFVLMGEH---FRRSPAFSVPESAQR 67 (80)
T ss_dssp TTTECCECCCC-CEEEEEEESSS----EEE---BSSHHHHHH
T ss_pred cccccceeeec-cceEEEEEecch---hccCCCcCCcHHHHH
Confidence 46899998765 999999998777 556677888887765
No 9
>PHA02601 int integrase; Provisional
Probab=69.63 E-value=5.6 Score=31.34 Aligned_cols=45 Identities=20% Similarity=0.233 Sum_probs=28.6
Q ss_pred eeeeCCCCcEEEEecCCCCCCceeecCCCCCHHHHHHhhchhhhhh
Q 046252 57 GVRPRPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQI 102 (124)
Q Consensus 57 GV~~~~~gkw~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~ 102 (124)
+|++...|+|+++|...+..+.++. .+|.|..||....+.....+
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 5667777899999986421111443 36999998876655544333
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=58.99 E-value=7 Score=26.87 Aligned_cols=21 Identities=33% Similarity=0.515 Sum_probs=18.0
Q ss_pred cCCCCCHHHHHHhhchhhhhh
Q 046252 82 LGTFDMPEDAGSAYDPAPFQI 102 (124)
Q Consensus 82 LG~f~t~eeAA~AyD~aa~~~ 102 (124)
-|+|+|+|+|..=||..+..|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 399999999999999877654
No 11
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=55.41 E-value=13 Score=34.73 Aligned_cols=30 Identities=30% Similarity=0.138 Sum_probs=13.7
Q ss_pred CCCCCCCcccccccccccCCCcccccccCC
Q 046252 4 SAGNSSSTETVNSCLELISSSNHLDDLFDQ 33 (124)
Q Consensus 4 s~~~~ss~~~~~~~~~~~~~~~~~~~~~~~ 33 (124)
|++++|++.++++.++..+++....+.|+.
T Consensus 1254 sssssssscsssssss~ssss~ed~d~~~~ 1283 (1463)
T PHA03308 1254 SSSSSSSSCSSSSSSSDSSSSEEDGDEKNE 1283 (1463)
T ss_pred ccccccccccccCCCCCccccccccccccc
Confidence 344444444444444444444444455543
No 12
>PRK10113 cell division modulator; Provisional
Probab=55.02 E-value=11 Score=24.77 Aligned_cols=38 Identities=21% Similarity=0.268 Sum_probs=28.2
Q ss_pred CCceeeeeeCCCCcEEEEecCCCCCCceeecCCCCCHHHHHH
Q 046252 52 RSKYRGVRPRPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGS 93 (124)
Q Consensus 52 ~S~yrGV~~~~~gkw~A~I~~~~k~~~~i~LG~f~t~eeAA~ 93 (124)
--+|+-||.-+ |||+|.+..... -..--.|..+|.|-+
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 45789997765 899999987665 334567888887765
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=54.20 E-value=5.1 Score=24.46 Aligned_cols=21 Identities=29% Similarity=0.409 Sum_probs=17.7
Q ss_pred eeecCCCCCHHHHHHhhchhh
Q 046252 79 QVWLGTFDMPEDAGSAYDPAP 99 (124)
Q Consensus 79 ~i~LG~f~t~eeAA~AyD~aa 99 (124)
++.+|.|++.+||..+-....
T Consensus 45 rV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 45 RVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp EEEECCECTCCHHHHHHHHHH
T ss_pred EEEECCCCCHHHHHHHHHHHh
Confidence 789999999999988876554
No 14
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=50.09 E-value=33 Score=20.90 Aligned_cols=34 Identities=24% Similarity=0.257 Sum_probs=23.7
Q ss_pred CCCCcEEEEecCCCCCCceeecCCCCCHHHHHHhhchhh
Q 046252 61 RPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAP 99 (124)
Q Consensus 61 ~~~gkw~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa 99 (124)
+..+.|....-...+ -..+|+|.+||..+=...+
T Consensus 6 ~~~~~W~v~~eg~~r-----a~~~~~Tk~eAi~~Ar~~a 39 (62)
T PF09954_consen 6 REDGGWAVKKEGAKR-----ASKTFDTKAEAIEAARELA 39 (62)
T ss_pred cCCCCceEEeCCCcc-----cccccCcHHHHHHHHHHHH
Confidence 445779988775555 4689999998876544333
No 15
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=44.52 E-value=15 Score=23.93 Aligned_cols=36 Identities=11% Similarity=0.058 Sum_probs=26.2
Q ss_pred CcEEEEecCCCCCCceeecCCCCC--HHHHHHhhchhhh
Q 046252 64 GKWTGEIKNPNKNTAQVWLGTFDM--PEDAGSAYDPAPF 100 (124)
Q Consensus 64 gkw~A~I~~~~k~~~~i~LG~f~t--~eeAA~AyD~aa~ 100 (124)
..|..+...+++.. ++.||.|.. ..||.........
T Consensus 35 kt~~~r~~~~gk~~-~~~lG~~p~~sl~~AR~~a~~~~~ 72 (89)
T PF13356_consen 35 KTFYFRYRINGKRR-RITLGRYPELSLAEAREKARELRA 72 (89)
T ss_dssp EEEEEEEEETTEEE-EEEEEECTTS-HHHHHHHHHHHHH
T ss_pred eEEEEEEEecceEE-EeccCCCccCCHHHHHHHHHHHHH
Confidence 45999998888877 999999975 5666555444333
No 16
>PRK09692 integrase; Provisional
Probab=43.70 E-value=45 Score=27.36 Aligned_cols=36 Identities=11% Similarity=0.112 Sum_probs=23.6
Q ss_pred CcEEEEecC--CCCCCceeecCCCC--CHHHHHHhhchhhh
Q 046252 64 GKWTGEIKN--PNKNTAQVWLGTFD--MPEDAGSAYDPAPF 100 (124)
Q Consensus 64 gkw~A~I~~--~~k~~~~i~LG~f~--t~eeAA~AyD~aa~ 100 (124)
..|+.+.+. .++.. ++.||.|. |..||..+...+..
T Consensus 41 k~~~~rY~~~~~gk~~-~~~lG~yp~~sl~~AR~~a~~~~~ 80 (413)
T PRK09692 41 KIWQFRYYRPLTKTRA-KKSFGPYPSVTLADARNYRAESRS 80 (413)
T ss_pred EEEEEEEecCCCCcee-eeeCCCCCCCCHHHHHHHHHHHHH
Confidence 359998864 34433 68999999 67777665544433
No 17
>PRK10927 essential cell division protein FtsN; Provisional
Probab=40.91 E-value=27 Score=29.01 Aligned_cols=34 Identities=21% Similarity=0.286 Sum_probs=26.6
Q ss_pred EEEEecCCCCCCceeecCCCCCHHHHHHhhchhhh
Q 046252 66 WTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPF 100 (124)
Q Consensus 66 w~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~ 100 (124)
|.|+|...+.-. ++.||-|.+.++|.++.++..-
T Consensus 273 ~~A~I~~~g~~~-RVrVGPf~sr~eAe~a~~rLk~ 306 (319)
T PRK10927 273 FDSKITTNNGWN-RVVIGPVKGKENADSTLNRLKM 306 (319)
T ss_pred CeeEEccCCcEE-EEEeCCCCCHHHHHHHHHHHHH
Confidence 667776555545 9999999999999999877544
No 18
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=40.85 E-value=16 Score=25.69 Aligned_cols=17 Identities=18% Similarity=0.774 Sum_probs=13.8
Q ss_pred eeecCCCCCHHHHHHhh
Q 046252 79 QVWLGTFDMPEDAGSAY 95 (124)
Q Consensus 79 ~i~LG~f~t~eeAA~Ay 95 (124)
.||||.|.+.+|-..=.
T Consensus 3 siWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 3 SIWIGNFKSEDELEEYF 19 (122)
T ss_pred EEEEecCCCHHHHHHHh
Confidence 79999999988766544
No 19
>PF07384 DUF1497: Protein of unknown function (DUF1497); InterPro: IPR009972 This entry is represented by Bacteriophage r1t, Orf17. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins of around 59 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this organism. The function of this family is unknown.
Probab=38.39 E-value=16 Score=22.53 Aligned_cols=32 Identities=19% Similarity=0.280 Sum_probs=23.6
Q ss_pred cCCCCCHHHHHHhhchhhhhhcCCCCCCCCCC
Q 046252 82 LGTFDMPEDAGSAYDPAPFQIQGQNAELNFPQ 113 (124)
Q Consensus 82 LG~f~t~eeAA~AyD~aa~~~~G~~a~~NFp~ 113 (124)
.|+||+..||.+.-..|...+-.+...-.|.+
T Consensus 1 mgyyd~~nearrisklas~~isseq~~kefe~ 32 (59)
T PF07384_consen 1 MGYYDKRNEARRISKLASQNISSEQNRKEFEI 32 (59)
T ss_pred CCcccchhHHHHHHHHHhcccchhhhhhhhhh
Confidence 48999999999988877776655554444543
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=36.89 E-value=36 Score=16.98 Aligned_cols=17 Identities=18% Similarity=0.704 Sum_probs=10.1
Q ss_pred EEEecCCCCCCceeecCCCC
Q 046252 67 TGEIKNPNKNTAQVWLGTFD 86 (124)
Q Consensus 67 ~A~I~~~~k~~~~i~LG~f~ 86 (124)
.+-+.+... .||+||+.
T Consensus 8 ~~i~~D~~G---~lWigT~~ 24 (24)
T PF07494_consen 8 YSIYEDSDG---NLWIGTYN 24 (24)
T ss_dssp EEEEE-TTS---CEEEEETS
T ss_pred EEEEEcCCc---CEEEEeCC
Confidence 344444445 89999874
No 21
>PLN00062 TATA-box-binding protein; Provisional
Probab=36.62 E-value=1.1e+02 Score=23.17 Aligned_cols=48 Identities=21% Similarity=0.023 Sum_probs=35.5
Q ss_pred CCCceeee-eeCCCCcEEEEecCCCCCCceeecCCCCCHHHHHHhhchhhhhh
Q 046252 51 VRSKYRGV-RPRPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQI 102 (124)
Q Consensus 51 ~~S~yrGV-~~~~~gkw~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~ 102 (124)
+..+|-|| .+-..-+-.+-|...|| -+-.| ..++|+|..|.++.+..+
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~SGK---iviTG-aks~e~a~~a~~~~~~~L 80 (179)
T PLN00062 32 NPKRFAAVIMRIREPKTTALIFASGK---MVCTG-AKSEHDSKLAARKYARII 80 (179)
T ss_pred CCccCcEEEEEeCCCcEEEEEECCCe---EEEEe-cCCHHHHHHHHHHHHHHH
Confidence 45589998 44455577899998888 54445 578899999988877766
No 22
>PRK10905 cell division protein DamX; Validated
Probab=36.27 E-value=50 Score=27.54 Aligned_cols=24 Identities=21% Similarity=0.313 Sum_probs=18.7
Q ss_pred eeecCCCCCHHHHHHhhchhhhhh
Q 046252 79 QVWLGTFDMPEDAGSAYDPAPFQI 102 (124)
Q Consensus 79 ~i~LG~f~t~eeAA~AyD~aa~~~ 102 (124)
.+..|.|.+.+||.+|-...-..+
T Consensus 287 VV~yG~YaSraeAk~AiakLPa~v 310 (328)
T PRK10905 287 VLVSGVYASKEEAKRAVSTLPADV 310 (328)
T ss_pred EEEecCCCCHHHHHHHHHHCCHHH
Confidence 678899999999999876644333
No 23
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=35.35 E-value=28 Score=25.61 Aligned_cols=30 Identities=27% Similarity=0.224 Sum_probs=21.7
Q ss_pred cEEEEecCCCCCCceeecCCCCCHHHHHHhh
Q 046252 65 KWTGEIKNPNKNTAQVWLGTFDMPEDAGSAY 95 (124)
Q Consensus 65 kw~A~I~~~~k~~~~i~LG~f~t~eeAA~Ay 95 (124)
++.+++.....=. -|++|.|.|++||+++-
T Consensus 30 kvia~~l~d~Gfe-Vi~~g~~~tp~e~v~aA 59 (143)
T COG2185 30 KVIARALADAGFE-VINLGLFQTPEEAVRAA 59 (143)
T ss_pred HHHHHHHHhCCce-EEecCCcCCHHHHHHHH
Confidence 4555555444444 68999999999999874
No 24
>COG2410 Predicted nuclease (RNAse H fold) [General function prediction only]
Probab=35.20 E-value=38 Score=25.84 Aligned_cols=43 Identities=12% Similarity=0.191 Sum_probs=32.9
Q ss_pred EEEecCCCCCCceeecCCCCCHHHHHHhhchhhhhhcCCCCCCCCCCC
Q 046252 67 TGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQIQGQNAELNFPQT 114 (124)
Q Consensus 67 ~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~~G~~a~~NFp~~ 114 (124)
.-.|+..++ ..+||.|++-||=-.+.+.+ ++-+-+|.+|||..
T Consensus 15 avavl~~~~---~~~i~~~s~~eeiv~s~~~a--~vvaiDAPLs~p~~ 57 (178)
T COG2410 15 AVAVLIEGR---IEIISAWSSREEIVESCKSA--KVVAIDAPLSLPAE 57 (178)
T ss_pred eEEEEECCE---EEEEEcccccHHHHHHhhcc--ceEEecCCcccccc
Confidence 456777788 88999999977766554444 37788999999986
No 25
>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=34.69 E-value=1.4e+02 Score=22.42 Aligned_cols=48 Identities=21% Similarity=0.062 Sum_probs=35.6
Q ss_pred CCCceeeee-eCCCCcEEEEecCCCCCCceeecCCCCCHHHHHHhhchhhhhh
Q 046252 51 VRSKYRGVR-PRPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQI 102 (124)
Q Consensus 51 ~~S~yrGV~-~~~~gkw~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~ 102 (124)
+..+|-||. +...-+-.+-|...|| -+-.|. .++|+|..|.++.+..+
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~SGK---iviTGa-ks~e~a~~a~~~i~~~L 80 (174)
T cd04516 32 NPKRFAAVIMRIREPKTTALIFSSGK---MVCTGA-KSEDDSKLAARKYARII 80 (174)
T ss_pred CCccCcEEEEEeCCCcEEEEEECCCe---EEEEec-CCHHHHHHHHHHHHHHH
Confidence 346889983 4444578899999998 666665 57788888888877666
No 26
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=32.48 E-value=98 Score=23.12 Aligned_cols=45 Identities=20% Similarity=0.085 Sum_probs=34.1
Q ss_pred ceeeeeeC-CCCcEEEEecCCCCCCceeecCCCCCHHHHHHhhchhhhhh
Q 046252 54 KYRGVRPR-PWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQI 102 (124)
Q Consensus 54 ~yrGV~~~-~~gkw~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~ 102 (124)
+|.||..| ..-+-.+-|+..|| -+-. ...++++|..|.++.+..+
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~sGK---iviT-Gaks~~~~~~a~~~~~~~l 80 (174)
T cd04517 35 RYPKVTMRLREPRATASVWSSGK---ITIT-GATSEEEAKQAARRAARLL 80 (174)
T ss_pred CCCEEEEEecCCcEEEEEECCCe---EEEE-ccCCHHHHHHHHHHHHHHH
Confidence 89998433 44678899998888 4433 4688999999998877666
No 27
>PF12522 UL73_N: Cytomegalovirus glycoprotein N terminal; InterPro: IPR021003 This domain family is found in viruses, and is approximately 30 amino acids in length. The signature is found in association with PF03554 from PFAM. This family is an envelope glycoprotein of (Human herpesvirus 5) [].
Probab=30.59 E-value=34 Score=18.18 Aligned_cols=10 Identities=70% Similarity=0.807 Sum_probs=4.8
Q ss_pred CCCCCCCccc
Q 046252 4 SAGNSSSTET 13 (124)
Q Consensus 4 s~~~~ss~~~ 13 (124)
|+|++|||++
T Consensus 12 Ss~n~sSTst 21 (27)
T PF12522_consen 12 SSGNNSSTST 21 (27)
T ss_pred cccCCccccc
Confidence 3445555544
No 28
>COG3087 FtsN Cell division protein [Cell division and chromosome partitioning]
Probab=25.25 E-value=64 Score=26.15 Aligned_cols=32 Identities=22% Similarity=0.219 Sum_probs=24.3
Q ss_pred EEEEec--CCCCCCceeecCCCCCHHHHHHhhchh
Q 046252 66 WTGEIK--NPNKNTAQVWLGTFDMPEDAGSAYDPA 98 (124)
Q Consensus 66 w~A~I~--~~~k~~~~i~LG~f~t~eeAA~AyD~a 98 (124)
..++|. .++... ++-||-|++.++|..|-+++
T Consensus 216 ~sskI~~~~~~~wy-RV~vGP~n~~~~a~~aq~rL 249 (264)
T COG3087 216 ISSKITGVTNGGWY-RVRVGPFNSKADAVKAQKRL 249 (264)
T ss_pred ccceeEeecCCceE-EEEecCCCcHHHHHHHHHHH
Confidence 556666 444444 89999999999999976654
No 29
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=25.17 E-value=92 Score=23.04 Aligned_cols=37 Identities=16% Similarity=0.132 Sum_probs=29.5
Q ss_pred cEEEEecCCCCCCceeecCCCCCHHHHHHhhchhhhhhcCC
Q 046252 65 KWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQIQGQ 105 (124)
Q Consensus 65 kw~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~~G~ 105 (124)
.|.|+|.. ++ -++-=..+.++.|..|..+|+.+|-+.
T Consensus 95 gwaArVkp-G~---vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 95 GWAARVKP-GR---VLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEEecC-Cc---EEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 39999976 55 677777788888999999999887554
No 30
>PF12286 DUF3622: Protein of unknown function (DUF3622); InterPro: IPR022069 This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif.
Probab=23.80 E-value=1.1e+02 Score=19.93 Aligned_cols=31 Identities=19% Similarity=0.263 Sum_probs=18.3
Q ss_pred CCcEEEEecCCCCCCce---eecCCCCCHHHHHH
Q 046252 63 WGKWTGEIKNPNKNTAQ---VWLGTFDMPEDAGS 93 (124)
Q Consensus 63 ~gkw~A~I~~~~k~~~~---i~LG~f~t~eeAA~ 93 (124)
.+.|.|+|...-..... ..---|++++||..
T Consensus 15 ~~~W~aEItR~vTsrkTvVSK~~~GF~SEaeAq~ 48 (71)
T PF12286_consen 15 RNGWTAEITRRVTSRKTVVSKRQDGFASEAEAQA 48 (71)
T ss_pred CCceeeeeeeeecCceeEEEecccCcccHHHHHH
Confidence 35699999864332211 12245899988653
No 31
>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=23.30 E-value=96 Score=20.09 Aligned_cols=47 Identities=21% Similarity=0.083 Sum_probs=33.4
Q ss_pred CCceeeee-eCCCCcEEEEecCCCCCCceeecCCCCCHHHHHHhhchhhhhh
Q 046252 52 RSKYRGVR-PRPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQI 102 (124)
Q Consensus 52 ~S~yrGV~-~~~~gkw~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~ 102 (124)
..+|.||. +-..-+-.+.|...|+ -+-.| -.+++||..|.+.....+
T Consensus 35 Pe~fpgl~~r~~~p~~t~~IF~sGk---i~itG-aks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 35 PERFPGLIYRLRNPKATVLIFSSGK---IVITG-AKSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTTESSEEEEETTTTEEEEEETTSE---EEEEE-ESSHHHHHHHHHHHHHHH
T ss_pred eccCCeEEEeecCCcEEEEEEcCCE---EEEEe-cCCHHHHHHHHHHHHHHH
Confidence 34788983 3344578888888888 55555 478999999988766544
No 32
>PRK12757 cell division protein FtsN; Provisional
Probab=23.00 E-value=76 Score=25.55 Aligned_cols=34 Identities=15% Similarity=0.110 Sum_probs=25.6
Q ss_pred EEEEecCCCCCCceeecCCCCCHHHHHHhhchhhh
Q 046252 66 WTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPF 100 (124)
Q Consensus 66 w~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~ 100 (124)
+.++|...+.-. +++||-|.+.++|..+-++...
T Consensus 210 ~~a~I~~~gg~y-RVrVGPf~sr~~A~~~~~rLk~ 243 (256)
T PRK12757 210 IESRITTGGGWN-RVVLGPYNSKAAADKMLQRLKG 243 (256)
T ss_pred CceEEeecCCEE-EEEeCCCCCHHHHHHHHHHHHH
Confidence 456666555444 8999999999999998777653
No 33
>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=20.86 E-value=2.4e+02 Score=21.06 Aligned_cols=49 Identities=18% Similarity=0.080 Sum_probs=35.7
Q ss_pred CCCceeeee-eCCCCcEEEEecCCCCCCceeecCCCCCHHHHHHhhchhhhhhc
Q 046252 51 VRSKYRGVR-PRPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQIQ 103 (124)
Q Consensus 51 ~~S~yrGV~-~~~~gkw~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~~ 103 (124)
+..+|.||. +-..-+-.+-|...|| -+-.| -.++++|..|-++.+..+.
T Consensus 32 ~P~~fpgli~Rl~~Pk~t~lIF~SGK---iv~tG-aks~~~a~~a~~~~~~~L~ 81 (174)
T cd04518 32 NPDQFPGLVYRLEDPKIAALIFRSGK---MVCTG-AKSVEDLHRAVKEIIKKLK 81 (174)
T ss_pred CCCcCcEEEEEccCCcEEEEEECCCe---EEEEc-cCCHHHHHHHHHHHHHHHH
Confidence 457899984 3344578888888888 55545 5788999999888776653
No 34
>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=20.83 E-value=2.3e+02 Score=21.08 Aligned_cols=48 Identities=25% Similarity=0.105 Sum_probs=34.8
Q ss_pred CCCceeeee-eCCCCcEEEEecCCCCCCceeecCCCCCHHHHHHhhchhhhhh
Q 046252 51 VRSKYRGVR-PRPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQI 102 (124)
Q Consensus 51 ~~S~yrGV~-~~~~gkw~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~ 102 (124)
+..+|.||. +...-+-.+-|...|| -+-.|. .++|+|..|.++.+..+
T Consensus 32 ePe~fpgli~R~~~P~~t~lIf~sGK---ivitGa-ks~~~~~~a~~~~~~~L 80 (174)
T cd00652 32 NPKRFPGVIMRLREPKTTALIFSSGK---MVITGA-KSEEDAKLAARKYARIL 80 (174)
T ss_pred CCCccceEEEEcCCCcEEEEEECCCE---EEEEec-CCHHHHHHHHHHHHHHH
Confidence 357899984 4445678888998888 555564 57888888888776665
No 35
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=20.34 E-value=1.4e+02 Score=21.60 Aligned_cols=36 Identities=17% Similarity=0.052 Sum_probs=28.0
Q ss_pred cEEEEecCCCCCCceeecCCCCCHHHHHHhhchhhhhhcC
Q 046252 65 KWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQIQG 104 (124)
Q Consensus 65 kw~A~I~~~~k~~~~i~LG~f~t~eeAA~AyD~aa~~~~G 104 (124)
-|.|+|....- =+-++. .+++.|..|...|+.++-+
T Consensus 92 ~~varVk~G~i---ifEi~~-~~~~~a~~al~~a~~KLP~ 127 (138)
T PRK09203 92 YWVAVVKPGRI---LFEIAG-VSEELAREALRLAAAKLPI 127 (138)
T ss_pred EEEEEECCCCE---EEEEeC-CCHHHHHHHHHHHhccCCC
Confidence 49999987555 555666 8899999999999887644
Done!