Query 046280
Match_columns 266
No_of_seqs 186 out of 1169
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 10:25:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046280.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046280hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00380 AP2 DNA-binding dom 99.8 8.4E-21 1.8E-25 139.5 8.3 63 41-103 1-63 (64)
2 cd00018 AP2 DNA-binding domain 99.8 1.2E-20 2.5E-25 137.0 7.5 61 40-100 1-61 (61)
3 PHA00280 putative NHN endonucl 99.6 3.6E-16 7.7E-21 129.5 7.0 72 20-94 47-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 4.1E-11 8.9E-16 84.8 5.3 52 40-91 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 84.8 3.2 6.9E-05 28.4 5.3 38 52-89 1-42 (46)
6 PHA02601 int integrase; Provis 73.7 5.1 0.00011 36.6 4.4 44 44-88 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 56.5 25 0.00053 31.7 5.4 39 50-88 9-49 (357)
8 PF13356 DUF4102: Domain of un 55.4 31 0.00067 26.3 5.0 43 46-88 28-74 (89)
9 PRK09692 integrase; Provisiona 54.6 35 0.00075 32.6 6.3 39 45-83 33-77 (413)
10 PF05036 SPOR: Sporulation rel 42.4 20 0.00043 25.3 2.0 22 64-85 44-65 (76)
11 PF10729 CedA: Cell division a 41.9 47 0.001 25.8 4.0 40 38-80 29-68 (80)
12 PF08846 DUF1816: Domain of un 39.1 66 0.0014 24.6 4.4 40 52-91 9-48 (68)
13 PF00352 TBP: Transcription fa 36.8 80 0.0017 24.1 4.7 48 39-89 35-83 (86)
14 COG0197 RplP Ribosomal protein 35.0 58 0.0013 28.3 4.0 36 53-91 96-131 (146)
15 cd01433 Ribosomal_L16_L10e Rib 32.7 74 0.0016 25.7 4.1 35 53-89 72-106 (112)
16 PRK09203 rplP 50S ribosomal pr 31.6 78 0.0017 26.9 4.2 35 53-90 93-127 (138)
17 TIGR01164 rplP_bact ribosomal 31.4 91 0.002 26.1 4.5 33 53-88 92-124 (126)
18 PF08471 Ribonuc_red_2_N: Clas 29.5 57 0.0012 26.4 2.9 21 68-88 70-90 (93)
19 PLN00062 TATA-box-binding prot 28.6 2.2E+02 0.0047 25.2 6.7 49 38-89 32-81 (179)
20 cd04516 TBP_eukaryotes eukaryo 28.3 2.2E+02 0.0049 25.0 6.7 49 38-89 32-81 (174)
21 PF09954 DUF2188: Uncharacteri 26.2 1.7E+02 0.0037 20.8 4.7 38 45-86 3-40 (62)
22 cd04518 TBP_archaea archaeal T 23.7 2.6E+02 0.0056 24.6 6.2 49 38-89 32-81 (174)
23 cd00652 TBP_TLF TATA box bindi 23.6 2.5E+02 0.0055 24.5 6.1 49 38-89 32-81 (174)
24 PRK10113 cell division modulat 23.6 63 0.0014 25.1 2.0 39 39-80 30-68 (80)
25 CHL00044 rpl16 ribosomal prote 22.2 1.4E+02 0.0029 25.4 4.0 35 53-90 93-127 (135)
26 cd04517 TLF TBP-like factors ( 22.0 2.4E+02 0.0051 24.7 5.6 46 41-89 35-81 (174)
27 TIGR00279 L10e ribosomal prote 21.2 1.2E+02 0.0027 27.0 3.7 35 53-90 122-158 (172)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.84 E-value=8.4e-21 Score=139.46 Aligned_cols=63 Identities=60% Similarity=1.007 Sum_probs=60.6
Q ss_pred ceeeEEeCCCCcEEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q 046280 41 RFLGVRRRPWGRYAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMRGSKARTNFVYSDMP 103 (266)
Q Consensus 41 ~yrGV~~r~~GKW~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~G~~A~tNFp~s~y~ 103 (266)
+|+||+++++|||+|+|+++.+++++|||+|+|+||||+|||.++++++|.++++||+.++|.
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 599999988999999999988999999999999999999999999999999999999999885
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=99.83 E-value=1.2e-20 Score=137.01 Aligned_cols=61 Identities=62% Similarity=1.025 Sum_probs=57.3
Q ss_pred CceeeEEeCCCCcEEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 046280 40 IRFLGVRRRPWGRYAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMRGSKARTNFVYS 100 (266)
Q Consensus 40 S~yrGV~~r~~GKW~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~G~~A~tNFp~s 100 (266)
|+||||+++++|||+|+|+++..||++|||+|+|+||||+|||+++++++|.++++|||.+
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 6899999988999999999955599999999999999999999999999999999999864
No 3
>PHA00280 putative NHN endonuclease
Probab=99.64 E-value=3.6e-16 Score=129.54 Aligned_cols=72 Identities=15% Similarity=0.192 Sum_probs=65.0
Q ss_pred hhhHHHHHHHHhhccCCCCCCceeeEEeCC-CCcEEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhcCCCCC
Q 046280 20 KRKQQKQQQQQQQNHMRQDEIRFLGVRRRP-WGRYAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMRGSKAR 94 (266)
Q Consensus 20 ~~~~~~~qn~~n~~~~~~~tS~yrGV~~r~-~GKW~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~G~~A~ 94 (266)
.+-....||.+|+++++.|+|+|+||++++ .|||+|+|++ +||+++||.|+++|+|+.||+ +++++||++|+
T Consensus 47 Lr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 47 LRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred hhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 344556799999999999999999999876 7999999998 999999999999999999997 78899999985
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=99.17 E-value=4.1e-11 Score=84.84 Aligned_cols=52 Identities=29% Similarity=0.404 Sum_probs=45.8
Q ss_pred CceeeEEeCC-CCcEEEEEecCCC---CceEeccCCCCHHHHHHHHHHHHHHhcCC
Q 046280 40 IRFLGVRRRP-WGRYAAEIRDPAT---KERHWLGTFDTAEDAALAYDRAARSMRGS 91 (266)
Q Consensus 40 S~yrGV~~r~-~GKW~A~I~~~~~---~kri~LGtF~T~EEAA~AYD~Aa~~~~G~ 91 (266)
|+|+||++++ .++|+|+|++... +|+++||.|+++|||++||+.++++++|+
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 6899999876 7999999998422 49999999999999999999999999875
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=84.77 E-value=3.2 Score=28.42 Aligned_cols=38 Identities=16% Similarity=0.202 Sum_probs=29.4
Q ss_pred cEEEEEe--cCCCC--ceEeccCCCCHHHHHHHHHHHHHHhc
Q 046280 52 RYAAEIR--DPATK--ERHWLGTFDTAEDAALAYDRAARSMR 89 (266)
Q Consensus 52 KW~A~I~--~~~~~--kri~LGtF~T~EEAA~AYD~Aa~~~~ 89 (266)
+|..+|. .+..| ++++-+-|.|..||..+...+...+.
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 44355 56888999999999999988777654
No 6
>PHA02601 int integrase; Provisional
Probab=73.66 E-value=5.1 Score=36.62 Aligned_cols=44 Identities=20% Similarity=0.190 Sum_probs=30.6
Q ss_pred eEEeCCCCcEEEEEec-CCCCceEeccCCCCHHHHHHHHHHHHHHh
Q 046280 44 GVRRRPWGRYAAEIRD-PATKERHWLGTFDTAEDAALAYDRAARSM 88 (266)
Q Consensus 44 GV~~r~~GKW~A~I~~-~~~~kri~LGtF~T~EEAA~AYD~Aa~~~ 88 (266)
+|++.+.|+|+++|+. ...|+++.. +|.|..||..........+
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 4666678899999985 224666653 6999999877666554444
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=56.48 E-value=25 Score=31.68 Aligned_cols=39 Identities=18% Similarity=0.207 Sum_probs=27.3
Q ss_pred CCcEEEEEecCCCCceEeccCCC--CHHHHHHHHHHHHHHh
Q 046280 50 WGRYAAEIRDPATKERHWLGTFD--TAEDAALAYDRAARSM 88 (266)
Q Consensus 50 ~GKW~A~I~~~~~~kri~LGtF~--T~EEAA~AYD~Aa~~~ 88 (266)
.+.|..+++.....+++.||+|+ +.++|..........+
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 35699999984444568899995 6777777666655544
No 8
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=55.42 E-value=31 Score=26.28 Aligned_cols=43 Identities=19% Similarity=0.203 Sum_probs=27.1
Q ss_pred EeCCCC--cEEEEEecCCCCceEeccCCCC--HHHHHHHHHHHHHHh
Q 046280 46 RRRPWG--RYAAEIRDPATKERHWLGTFDT--AEDAALAYDRAARSM 88 (266)
Q Consensus 46 ~~r~~G--KW~A~I~~~~~~kri~LGtF~T--~EEAA~AYD~Aa~~~ 88 (266)
+..+.| .|..+.+.....+++.||.|.. .+||..........+
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 344554 4998988733345799999976 666666555444444
No 9
>PRK09692 integrase; Provisional
Probab=54.64 E-value=35 Score=32.57 Aligned_cols=39 Identities=23% Similarity=0.244 Sum_probs=25.0
Q ss_pred EEeCCCC--cEEEEEecCCCCce--EeccCCC--CHHHHHHHHHH
Q 046280 45 VRRRPWG--RYAAEIRDPATKER--HWLGTFD--TAEDAALAYDR 83 (266)
Q Consensus 45 V~~r~~G--KW~A~I~~~~~~kr--i~LGtF~--T~EEAA~AYD~ 83 (266)
|+.++.| .|+.+.+.+.+||+ +-||.|. |..+|..+..+
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 49998875444544 7899999 66666554433
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=42.37 E-value=20 Score=25.32 Aligned_cols=22 Identities=27% Similarity=0.395 Sum_probs=18.2
Q ss_pred ceEeccCCCCHHHHHHHHHHHH
Q 046280 64 ERHWLGTFDTAEDAALAYDRAA 85 (266)
Q Consensus 64 kri~LGtF~T~EEAA~AYD~Aa 85 (266)
-++.+|.|.+.+||..+-.+..
T Consensus 44 yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 44 YRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp EEEEECCECTCCHHHHHHHHHH
T ss_pred EEEEECCCCCHHHHHHHHHHHh
Confidence 4778899999999998877655
No 11
>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=41.86 E-value=47 Score=25.80 Aligned_cols=40 Identities=20% Similarity=0.118 Sum_probs=25.8
Q ss_pred CCCceeeEEeCCCCcEEEEEecCCCCceEeccCCCCHHHHHHH
Q 046280 38 DEIRFLGVRRRPWGRYAAEIRDPATKERHWLGTFDTAEDAALA 80 (266)
Q Consensus 38 ~tS~yrGV~~r~~GKW~A~I~~~~~~kri~LGtF~T~EEAA~A 80 (266)
+--+||-|..-+ |||+|.+.. +-.-..--.|..+|.|-|.
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 345777775444 999999996 4444455678888888775
No 12
>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=39.15 E-value=66 Score=24.57 Aligned_cols=40 Identities=20% Similarity=0.321 Sum_probs=29.7
Q ss_pred cEEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhcCC
Q 046280 52 RYAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMRGS 91 (266)
Q Consensus 52 KW~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~G~ 91 (266)
.|=++|.--.-.-.+|-|-|.+.+||..+.-.....+..+
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~~E 48 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLESE 48 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHHhh
Confidence 3668998644457899999999999999876555555433
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=36.77 E-value=80 Score=24.08 Aligned_cols=48 Identities=19% Similarity=0.165 Sum_probs=36.0
Q ss_pred CCceeeEEeCC-CCcEEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhc
Q 046280 39 EIRFLGVRRRP-WGRYAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMR 89 (266)
Q Consensus 39 tS~yrGV~~r~-~GKW~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~ 89 (266)
..+|.||..|- .-+-.+.|.. .||-+..|. .+.|||..|.++....+.
T Consensus 35 Pe~fpgl~~r~~~p~~t~~IF~--sGki~itGa-ks~~~~~~a~~~i~~~L~ 83 (86)
T PF00352_consen 35 PERFPGLIYRLRNPKATVLIFS--SGKIVITGA-KSEEEAKKAIEKILPILQ 83 (86)
T ss_dssp TTTESSEEEEETTTTEEEEEET--TSEEEEEEE-SSHHHHHHHHHHHHHHHH
T ss_pred eccCCeEEEeecCCcEEEEEEc--CCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 34789987664 4467777775 888877775 789999999988776653
No 14
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=34.95 E-value=58 Score=28.34 Aligned_cols=36 Identities=22% Similarity=0.075 Sum_probs=30.5
Q ss_pred EEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhcCC
Q 046280 53 YAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMRGS 91 (266)
Q Consensus 53 W~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~G~ 91 (266)
|+|+|. -|+.++-=....++.|.+|..+|+.+|-+.
T Consensus 96 waArVk---pG~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 96 WAARVK---PGRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEec---CCcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 999998 577777777888889999999999987554
No 15
>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=32.66 E-value=74 Score=25.66 Aligned_cols=35 Identities=20% Similarity=0.177 Sum_probs=26.1
Q ss_pred EEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhc
Q 046280 53 YAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMR 89 (266)
Q Consensus 53 W~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~ 89 (266)
|+|+|.. +..-+-++.....+.|..|..+++.++-
T Consensus 72 ~~a~v~~--G~iifEi~~~~~~~~~~~alk~a~~Klp 106 (112)
T cd01433 72 WVARVKP--GQILFEVRGVPEEEVAKEALRRAAKKLP 106 (112)
T ss_pred EEEEECC--CCEEEEEeCcCcHHHHHHHHHHhhccCC
Confidence 9999995 4455556655558999999988887663
No 16
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=31.60 E-value=78 Score=26.86 Aligned_cols=35 Identities=17% Similarity=0.032 Sum_probs=27.4
Q ss_pred EEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhcC
Q 046280 53 YAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMRG 90 (266)
Q Consensus 53 W~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~G 90 (266)
|+|+|.. +..-+-++. .+++.|..|+.+|+.++-+
T Consensus 93 ~varVk~--G~iifEi~~-~~~~~a~~al~~a~~KLP~ 127 (138)
T PRK09203 93 WVAVVKP--GRILFEIAG-VSEELAREALRLAAAKLPI 127 (138)
T ss_pred EEEEECC--CCEEEEEeC-CCHHHHHHHHHHHhccCCC
Confidence 9999995 455555555 8999999999999887643
No 17
>TIGR01164 rplP_bact ribosomal protein L16, bacterial/organelle. This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10
Probab=31.42 E-value=91 Score=26.06 Aligned_cols=33 Identities=21% Similarity=0.146 Sum_probs=26.2
Q ss_pred EEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHh
Q 046280 53 YAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSM 88 (266)
Q Consensus 53 W~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~ 88 (266)
|+|+|.. +..-+.++. .+++.|..|..+|+.+|
T Consensus 92 ~varV~~--G~ilfEi~~-~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 92 WVAVVKP--GKILFEIAG-VPEEVAREAFRLAASKL 124 (126)
T ss_pred EEEEECC--CCEEEEEeC-CCHHHHHHHHHHHHhcC
Confidence 9999994 444555555 89999999999988765
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=29.52 E-value=57 Score=26.44 Aligned_cols=21 Identities=38% Similarity=0.455 Sum_probs=18.1
Q ss_pred ccCCCCHHHHHHHHHHHHHHh
Q 046280 68 LGTFDTAEDAALAYDRAARSM 88 (266)
Q Consensus 68 LGtF~T~EEAA~AYD~Aa~~~ 88 (266)
-|+|+|+|+|..-||.....|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 399999999999999877654
No 19
>PLN00062 TATA-box-binding protein; Provisional
Probab=28.61 E-value=2.2e+02 Score=25.23 Aligned_cols=49 Identities=24% Similarity=0.219 Sum_probs=37.3
Q ss_pred CCCceeeEEeCC-CCcEEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhc
Q 046280 38 DEIRFLGVRRRP-WGRYAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMR 89 (266)
Q Consensus 38 ~tS~yrGV~~r~-~GKW~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~ 89 (266)
+..+|-||..|- .-|=.+.|.. .||-+-.|. .++|+|..|.++.+..++
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 32 NPKRFAAVIMRIREPKTTALIFA--SGKMVCTGA-KSEHDSKLAARKYARIIQ 81 (179)
T ss_pred CCccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 345899987664 5567788885 777776664 788999999999888774
No 20
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=28.31 E-value=2.2e+02 Score=24.95 Aligned_cols=49 Identities=24% Similarity=0.240 Sum_probs=37.6
Q ss_pred CCCceeeEEeCC-CCcEEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhc
Q 046280 38 DEIRFLGVRRRP-WGRYAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMR 89 (266)
Q Consensus 38 ~tS~yrGV~~r~-~GKW~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~ 89 (266)
+..+|-||..|- .-|-.+.|.. .||-+-.|. .++|+|..|.++.+..++
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 32 NPKRFAAVIMRIREPKTTALIFS--SGKMVCTGA-KSEDDSKLAARKYARIIQ 81 (174)
T ss_pred CCccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 346888987664 4567788886 888877776 578899999998888774
No 21
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=26.23 E-value=1.7e+02 Score=20.84 Aligned_cols=38 Identities=32% Similarity=0.282 Sum_probs=24.2
Q ss_pred EEeCCCCcEEEEEecCCCCceEeccCCCCHHHHHHHHHHHHH
Q 046280 45 VRRRPWGRYAAEIRDPATKERHWLGTFDTAEDAALAYDRAAR 86 (266)
Q Consensus 45 V~~r~~GKW~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~ 86 (266)
|..+..|.|..+.-. .++ -..+|+|.+||..+=...+.
T Consensus 3 V~p~~~~~W~v~~eg---~~r-a~~~~~Tk~eAi~~Ar~~a~ 40 (62)
T PF09954_consen 3 VVPREDGGWAVKKEG---AKR-ASKTFDTKAEAIEAARELAK 40 (62)
T ss_pred EEecCCCCceEEeCC---Ccc-cccccCcHHHHHHHHHHHHH
Confidence 444445779877663 332 27899999998776444443
No 22
>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=23.66 E-value=2.6e+02 Score=24.58 Aligned_cols=49 Identities=20% Similarity=0.184 Sum_probs=37.3
Q ss_pred CCCceeeEEeCC-CCcEEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhc
Q 046280 38 DEIRFLGVRRRP-WGRYAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMR 89 (266)
Q Consensus 38 ~tS~yrGV~~r~-~GKW~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~ 89 (266)
+..+|.||..|- .-|=.+.|.. .||-+-.|. .+.|+|..|-++.+..+.
T Consensus 32 ~P~~fpgli~Rl~~Pk~t~lIF~--SGKiv~tGa-ks~~~a~~a~~~~~~~L~ 81 (174)
T cd04518 32 NPDQFPGLVYRLEDPKIAALIFR--SGKMVCTGA-KSVEDLHRAVKEIIKKLK 81 (174)
T ss_pred CCCcCcEEEEEccCCcEEEEEEC--CCeEEEEcc-CCHHHHHHHHHHHHHHHH
Confidence 457899998664 4466677775 787777675 789999999998888775
No 23
>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=23.62 E-value=2.5e+02 Score=24.47 Aligned_cols=49 Identities=31% Similarity=0.287 Sum_probs=36.6
Q ss_pred CCCceeeEEeCC-CCcEEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhc
Q 046280 38 DEIRFLGVRRRP-WGRYAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMR 89 (266)
Q Consensus 38 ~tS~yrGV~~r~-~GKW~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~ 89 (266)
+..+|.||..|. .-|-.+.|.. .||-+-.|. .+.|+|.+|.++.+..++
T Consensus 32 ePe~fpgli~R~~~P~~t~lIf~--sGKivitGa-ks~~~~~~a~~~~~~~L~ 81 (174)
T cd00652 32 NPKRFPGVIMRLREPKTTALIFS--SGKMVITGA-KSEEDAKLAARKYARILQ 81 (174)
T ss_pred CCCccceEEEEcCCCcEEEEEEC--CCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 346899988665 4566777775 788777776 578899999888887773
No 24
>PRK10113 cell division modulator; Provisional
Probab=23.55 E-value=63 Score=25.08 Aligned_cols=39 Identities=21% Similarity=0.073 Sum_probs=26.5
Q ss_pred CCceeeEEeCCCCcEEEEEecCCCCceEeccCCCCHHHHHHH
Q 046280 39 EIRFLGVRRRPWGRYAAEIRDPATKERHWLGTFDTAEDAALA 80 (266)
Q Consensus 39 tS~yrGV~~r~~GKW~A~I~~~~~~kri~LGtF~T~EEAA~A 80 (266)
--+||-|..-+ |||+|.+.. +-.-..--.|..+|.|-|.
T Consensus 30 md~frDVW~Lr-GKYVAFvl~--ge~FrRSPaFs~PEsAQRW 68 (80)
T PRK10113 30 MDSFRDVWMLR-GKYVAFVLM--GESFLRSPAFSVPESAQRW 68 (80)
T ss_pred hcchhhhheec-cceEEEEEe--chhhccCCccCCcHHHHHH
Confidence 35677775444 999999986 3333334678888888765
No 25
>CHL00044 rpl16 ribosomal protein L16
Probab=22.18 E-value=1.4e+02 Score=25.39 Aligned_cols=35 Identities=20% Similarity=0.054 Sum_probs=26.0
Q ss_pred EEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhcC
Q 046280 53 YAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMRG 90 (266)
Q Consensus 53 W~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~G 90 (266)
|+|+|.. +..-+-++. ..++.|..|...|+.+|-.
T Consensus 93 ~va~V~~--G~ilfEi~g-~~~~~ak~al~~a~~KLP~ 127 (135)
T CHL00044 93 WVAVVKP--GRILYEMGG-VSETIARAAIKIAAYKMPI 127 (135)
T ss_pred EEEEECC--CcEEEEEeC-CCHHHHHHHHHHHhhcCCC
Confidence 9999994 444455555 5678999999998887643
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=22.00 E-value=2.4e+02 Score=24.73 Aligned_cols=46 Identities=28% Similarity=0.268 Sum_probs=35.9
Q ss_pred ceeeEEeCC-CCcEEEEEecCCCCceEeccCCCCHHHHHHHHHHHHHHhc
Q 046280 41 RFLGVRRRP-WGRYAAEIRDPATKERHWLGTFDTAEDAALAYDRAARSMR 89 (266)
Q Consensus 41 ~yrGV~~r~-~GKW~A~I~~~~~~kri~LGtF~T~EEAA~AYD~Aa~~~~ 89 (266)
+|.||..|- .-|-.+.|.. .||-+-.| ..+.|+|++|.++.+..+.
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~--sGKiviTG-aks~~~~~~a~~~~~~~l~ 81 (174)
T cd04517 35 RYPKVTMRLREPRATASVWS--SGKITITG-ATSEEEAKQAARRAARLLQ 81 (174)
T ss_pred CCCEEEEEecCCcEEEEEEC--CCeEEEEc-cCCHHHHHHHHHHHHHHHH
Confidence 899998664 4577888885 77766666 5889999999998888773
No 27
>TIGR00279 L10e ribosomal protein L10.e. L10.e is distantly related to eubacterial ribosomal protein L16.
Probab=21.24 E-value=1.2e+02 Score=26.99 Aligned_cols=35 Identities=20% Similarity=0.071 Sum_probs=26.2
Q ss_pred EEEEEecCCCCceEeccCC--CCHHHHHHHHHHHHHHhcC
Q 046280 53 YAAEIRDPATKERHWLGTF--DTAEDAALAYDRAARSMRG 90 (266)
Q Consensus 53 W~A~I~~~~~~kri~LGtF--~T~EEAA~AYD~Aa~~~~G 90 (266)
|+|+|. .|+.|+--.- ++++.|..|..+|+.+|-.
T Consensus 122 wvArVk---~Gqiifei~~~~~~~~~AkeAlr~A~~KLP~ 158 (172)
T TIGR00279 122 TAARVK---IGQKIFSVWTKPSNFDVAKEALRRAAMKFPV 158 (172)
T ss_pred EEEEEC---cCCEEEEEEeecCCHHHHHHHHHHHhccCCC
Confidence 999999 4665554433 3889999999998887643
Done!