Query 027107
Match_columns 228
No_of_seqs 252 out of 1298
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 05:02:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027107.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027107hhsearch_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 99.8 5.1E-21 1.1E-25 135.9 7.4 61 42-102 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 3.2E-20 7E-25 133.4 8.2 62 43-104 1-62 (64)
3 PHA00280 putative NHN endonucl 99.5 5.6E-14 1.2E-18 113.9 6.8 67 25-96 52-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 1.2E-10 2.7E-15 80.5 5.3 52 42-93 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 79.3 7.8 0.00017 25.8 5.5 38 54-91 1-42 (46)
6 cd00801 INT_P4 Bacteriophage P 68.3 11 0.00023 33.2 5.1 40 51-90 8-49 (357)
7 PF13356 DUF4102: Domain of un 63.1 26 0.00057 26.0 5.7 43 48-90 28-74 (89)
8 PHA02601 int integrase; Provis 61.5 13 0.00027 33.2 4.3 44 46-90 2-46 (333)
9 PRK09692 integrase; Provisiona 50.9 43 0.00094 31.1 6.2 39 47-85 33-77 (413)
10 PF10729 CedA: Cell division a 49.5 27 0.00058 26.5 3.6 40 40-82 29-68 (80)
11 PF08846 DUF1816: Domain of un 43.8 56 0.0012 24.3 4.6 40 55-94 10-49 (68)
12 PF05036 SPOR: Sporulation rel 43.1 33 0.00071 23.5 3.2 24 64-87 42-65 (76)
13 cd01433 Ribosomal_L16_L10e Rib 40.6 56 0.0012 25.7 4.5 44 46-91 59-106 (112)
14 PRK09203 rplP 50S ribosomal pr 37.5 64 0.0014 26.7 4.6 35 55-92 93-127 (138)
15 TIGR01164 rplP_bact ribosomal 37.1 77 0.0017 25.8 4.9 33 55-90 92-124 (126)
16 PF00352 TBP: Transcription fa 36.7 99 0.0021 23.0 5.1 47 41-90 35-82 (86)
17 PF14112 DUF4284: Domain of un 35.5 27 0.00059 28.1 2.0 19 66-84 2-20 (122)
18 PRK10113 cell division modulat 30.3 37 0.0008 25.7 1.8 38 41-81 30-67 (80)
19 PLN00062 TATA-box-binding prot 30.0 2.4E+02 0.0052 24.3 7.0 49 40-91 32-81 (179)
20 cd04517 TLF TBP-like factors ( 28.5 2.4E+02 0.0051 24.1 6.7 48 40-91 33-81 (174)
21 cd04516 TBP_eukaryotes eukaryo 28.4 2.7E+02 0.0059 23.8 7.0 49 40-91 32-81 (174)
22 KOG3422 Mitochondrial ribosoma 27.5 1.2E+02 0.0026 27.4 4.8 38 54-93 133-170 (221)
23 COG0197 RplP Ribosomal protein 24.6 1.3E+02 0.0027 25.6 4.2 36 55-93 96-131 (146)
24 PF07494 Reg_prop: Two compone 23.7 70 0.0015 18.5 1.8 11 64-74 14-24 (24)
25 CHL00044 rpl16 ribosomal prote 23.5 1.8E+02 0.004 24.0 4.9 44 46-92 80-127 (135)
26 cd04518 TBP_archaea archaeal T 21.9 3.3E+02 0.0072 23.3 6.4 49 40-91 32-81 (174)
27 PF09003 Phage_integ_N: Bacter 21.7 2.6E+02 0.0056 21.2 5.0 35 58-94 30-64 (75)
28 PF08471 Ribonuc_red_2_N: Clas 20.1 1.1E+02 0.0024 24.2 2.8 21 70-90 70-90 (93)
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=99.84 E-value=5.1e-21 Score=135.86 Aligned_cols=61 Identities=64% Similarity=1.109 Sum_probs=57.4
Q ss_pred CceeEEEECCCCcEEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 027107 42 PVYRGVRMRNWGKWVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSIKGNSAILNFPEL 102 (228)
Q Consensus 42 s~yRGVr~r~~GKW~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~G~~A~lNFp~~ 102 (228)
|+||||+++++|||+|+|+.+..++++|||+|+|+||||+|||.|+++++|..+.+|||++
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 5799999888899999999966699999999999999999999999999999999999974
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.82 E-value=3.2e-20 Score=133.36 Aligned_cols=62 Identities=61% Similarity=1.024 Sum_probs=58.8
Q ss_pred ceeEEEECCCCcEEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q 027107 43 VYRGVRMRNWGKWVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSIKGNSAILNFPELAD 104 (228)
Q Consensus 43 ~yRGVr~r~~GKW~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~G~~A~lNFp~~~~ 104 (228)
+|+||+++++|||+|+|+.|.+++++|||+|+|+||||+|||.|+++++|..+.+|||...+
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 49999888889999999999999999999999999999999999999999999999998754
No 3
>PHA00280 putative NHN endonuclease
Probab=99.49 E-value=5.6e-14 Score=113.94 Aligned_cols=67 Identities=10% Similarity=0.098 Sum_probs=56.2
Q ss_pred cchhhhhhcccCCCCCCCceeEEEEC-CCCcEEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhcCCCCC
Q 027107 25 HQDSKKIKRMRDQSSKHPVYRGVRMR-NWGKWVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSIKGNSAI 96 (228)
Q Consensus 25 ~~~~~k~kr~r~~~~~~s~yRGVr~r-~~GKW~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~G~~A~ 96 (228)
..++.++++++ ++++++|+||++. ..|||+|+|+. .+|+++||.|+++|+|+.||+ ++.+++|.+|.
T Consensus 52 ~~eN~~N~~~~--~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 52 PKENSWNMKTP--KSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred HHHHhcccCCC--CCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 34555555444 4889999999754 67999999999 999999999999999999997 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=99.11 E-value=1.2e-10 Score=80.55 Aligned_cols=52 Identities=31% Similarity=0.475 Sum_probs=44.9
Q ss_pred CceeEEEEC-CCCcEEEEEecCCC---CeEEEecCCCCHHHHHHHHHHHHHHhcCC
Q 027107 42 PVYRGVRMR-NWGKWVSEIREPRK---KSRIWLGTFPTPEMAARAHDVAALSIKGN 93 (228)
Q Consensus 42 s~yRGVr~r-~~GKW~AeIr~p~~---kkriwLGtF~T~EeAArAYD~Aa~~l~G~ 93 (228)
|+|+||+++ ..++|+|+|+++.. +++++||.|++++||++|++.+++.++|+
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 679999765 67999999999521 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=79.29 E-value=7.8 Score=25.82 Aligned_cols=38 Identities=16% Similarity=0.221 Sum_probs=29.5
Q ss_pred cEEEEEe--cC--CCCeEEEecCCCCHHHHHHHHHHHHHHhc
Q 027107 54 KWVSEIR--EP--RKKSRIWLGTFPTPEMAARAHDVAALSIK 91 (228)
Q Consensus 54 KW~AeIr--~p--~~kkriwLGtF~T~EeAArAYD~Aa~~l~ 91 (228)
+|...|. .+ ++.++++-+-|.|..||..+.......+.
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 34478999999999999999888776653
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=68.30 E-value=11 Score=33.21 Aligned_cols=40 Identities=25% Similarity=0.364 Sum_probs=28.7
Q ss_pred CCCcEEEEEecCCCCeEEEecCCC--CHHHHHHHHHHHHHHh
Q 027107 51 NWGKWVSEIREPRKKSRIWLGTFP--TPEMAARAHDVAALSI 90 (228)
Q Consensus 51 ~~GKW~AeIr~p~~kkriwLGtF~--T~EeAArAYD~Aa~~l 90 (228)
..+.|+.+++..++.+++.||+|+ +.++|..........+
T Consensus 8 g~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 8 GSKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CCEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 335699999996666788999996 6677776665544444
No 7
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=63.05 E-value=26 Score=26.00 Aligned_cols=43 Identities=23% Similarity=0.269 Sum_probs=27.7
Q ss_pred EECCCC--cEEEEEecCCCCeEEEecCCCC--HHHHHHHHHHHHHHh
Q 027107 48 RMRNWG--KWVSEIREPRKKSRIWLGTFPT--PEMAARAHDVAALSI 90 (228)
Q Consensus 48 r~r~~G--KW~AeIr~p~~kkriwLGtF~T--~EeAArAYD~Aa~~l 90 (228)
+....| .|+-+.+...+.+++-||.|+. ..+|..........+
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 4999888855667899999986 555555554444443
No 8
>PHA02601 int integrase; Provisional
Probab=61.49 E-value=13 Score=33.19 Aligned_cols=44 Identities=30% Similarity=0.373 Sum_probs=29.6
Q ss_pred EEEECCCCcEEEEEecC-CCCeEEEecCCCCHHHHHHHHHHHHHHh
Q 027107 46 GVRMRNWGKWVSEIREP-RKKSRIWLGTFPTPEMAARAHDVAALSI 90 (228)
Q Consensus 46 GVr~r~~GKW~AeIr~p-~~kkriwLGtF~T~EeAArAYD~Aa~~l 90 (228)
+|++...|+|+++|+.. ..|+++. .+|.|..||....+.....+
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 46666778999999862 2356655 36999999876655544333
No 9
>PRK09692 integrase; Provisional
Probab=50.93 E-value=43 Score=31.12 Aligned_cols=39 Identities=18% Similarity=0.331 Sum_probs=24.1
Q ss_pred EEECCCC--cEEEEEecCC--CCeEEEecCCC--CHHHHHHHHHH
Q 027107 47 VRMRNWG--KWVSEIREPR--KKSRIWLGTFP--TPEMAARAHDV 85 (228)
Q Consensus 47 Vr~r~~G--KW~AeIr~p~--~kkriwLGtF~--T~EeAArAYD~ 85 (228)
|+.+..| .|+.+.+.+. +.+++-||.|+ |..+|..+...
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 3444444 3999887553 33447899999 66666554333
No 10
>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=49.47 E-value=27 Score=26.52 Aligned_cols=40 Identities=28% Similarity=0.253 Sum_probs=26.4
Q ss_pred CCCceeEEEECCCCcEEEEEecCCCCeEEEecCCCCHHHHHHH
Q 027107 40 KHPVYRGVRMRNWGKWVSEIREPRKKSRIWLGTFPTPEMAARA 82 (228)
Q Consensus 40 ~~s~yRGVr~r~~GKW~AeIr~p~~kkriwLGtF~T~EeAArA 82 (228)
+--+||-|+.-+ |||+|.+.. +..-.---.|..+|.|-|=
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 345799997665 999999988 4444445678888877653
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=43.83 E-value=56 Score=24.35 Aligned_cols=40 Identities=20% Similarity=0.318 Sum_probs=30.2
Q ss_pred EEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhcCCC
Q 027107 55 WVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSIKGNS 94 (228)
Q Consensus 55 W~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~G~~ 94 (228)
|=++|.--.-.-..|.|-|.|.+||..+.-.-...+..+.
T Consensus 10 WWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~~Eg 49 (68)
T PF08846_consen 10 WWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLESEG 49 (68)
T ss_pred EEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHHhhC
Confidence 5578877455578999999999999998776666555443
No 12
>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=43.07 E-value=33 Score=23.53 Aligned_cols=24 Identities=25% Similarity=0.238 Sum_probs=19.2
Q ss_pred CCeEEEecCCCCHHHHHHHHHHHH
Q 027107 64 KKSRIWLGTFPTPEMAARAHDVAA 87 (228)
Q Consensus 64 ~kkriwLGtF~T~EeAArAYD~Aa 87 (228)
..-+|.+|.|++.++|..+.....
T Consensus 42 ~~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 42 PWYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp TCEEEEECCECTCCHHHHHHHHHH
T ss_pred ceEEEEECCCCCHHHHHHHHHHHh
Confidence 445899999999999988876544
No 13
>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=40.64 E-value=56 Score=25.68 Aligned_cols=44 Identities=27% Similarity=0.376 Sum_probs=32.2
Q ss_pred EEEECC-CCc---EEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhc
Q 027107 46 GVRMRN-WGK---WVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSIK 91 (228)
Q Consensus 46 GVr~r~-~GK---W~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~ 91 (228)
++|++. .|+ |+|.|.. +..-+-++.....+.|..|...|+.++-
T Consensus 59 ~~rMGkGKG~~~~~~a~v~~--G~iifEi~~~~~~~~~~~alk~a~~Klp 106 (112)
T cd01433 59 ETRMGKGKGKPEGWVARVKP--GQILFEVRGVPEEEVAKEALRRAAKKLP 106 (112)
T ss_pred ccccCCCCCCccEEEEEECC--CCEEEEEeCcCcHHHHHHHHHHhhccCC
Confidence 466663 343 9999998 6666667776668899999888887763
No 14
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=37.53 E-value=64 Score=26.69 Aligned_cols=35 Identities=20% Similarity=0.285 Sum_probs=28.9
Q ss_pred EEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhcC
Q 027107 55 WVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSIKG 92 (228)
Q Consensus 55 W~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~G 92 (228)
|+|.|.. +..-+-++. .+++.|..|...|+.+|-+
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 9999998 666666666 8999999999999887744
No 15
>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=37.13 E-value=77 Score=25.85 Aligned_cols=33 Identities=24% Similarity=0.342 Sum_probs=27.5
Q ss_pred EEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHh
Q 027107 55 WVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSI 90 (228)
Q Consensus 55 W~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l 90 (228)
|+|.|.. +..-+-++. .+++.|..|...|+.+|
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 9999998 666666666 89999999999988765
No 16
>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=36.69 E-value=99 Score=22.97 Aligned_cols=47 Identities=17% Similarity=0.084 Sum_probs=34.1
Q ss_pred CCceeEEEEC-CCCcEEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHh
Q 027107 41 HPVYRGVRMR-NWGKWVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSI 90 (228)
Q Consensus 41 ~s~yRGVr~r-~~GKW~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l 90 (228)
..+|.||.+| ..-+-..-|.. .||-+..|. .++|+|..|.+.....+
T Consensus 35 Pe~fpgl~~r~~~p~~t~~IF~--sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 35 PERFPGLIYRLRNPKATVLIFS--SGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTTESSEEEEETTTTEEEEEET--TSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred eccCCeEEEeecCCcEEEEEEc--CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 3468898655 33456666666 998888886 78999999988876554
No 17
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=35.53 E-value=27 Score=28.09 Aligned_cols=19 Identities=21% Similarity=0.608 Sum_probs=14.7
Q ss_pred eEEEecCCCCHHHHHHHHH
Q 027107 66 SRIWLGTFPTPEMAARAHD 84 (228)
Q Consensus 66 kriwLGtF~T~EeAArAYD 84 (228)
..||||+|.+.++-..=.+
T Consensus 2 VsiWiG~f~s~~el~~Y~e 20 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYFE 20 (122)
T ss_pred eEEEEecCCCHHHHHHHhC
Confidence 4699999999887665543
No 18
>PRK10113 cell division modulator; Provisional
Probab=30.33 E-value=37 Score=25.71 Aligned_cols=38 Identities=32% Similarity=0.403 Sum_probs=25.4
Q ss_pred CCceeEEEECCCCcEEEEEecCCCCeEEEecCCCCHHHHHH
Q 027107 41 HPVYRGVRMRNWGKWVSEIREPRKKSRIWLGTFPTPEMAAR 81 (228)
Q Consensus 41 ~s~yRGVr~r~~GKW~AeIr~p~~kkriwLGtF~T~EeAAr 81 (228)
.-+||-|+.-+ |||+|.+.. +..-.---.|..+|.|-|
T Consensus 30 md~frDVW~Lr-GKYVAFvl~--ge~FrRSPaFs~PEsAQR 67 (80)
T PRK10113 30 MDSFRDVWMLR-GKYVAFVLM--GESFLRSPAFSVPESAQR 67 (80)
T ss_pred hcchhhhheec-cceEEEEEe--chhhccCCccCCcHHHHH
Confidence 34688887665 999999887 332222346777777765
No 19
>PLN00062 TATA-box-binding protein; Provisional
Probab=29.96 E-value=2.4e+02 Score=24.31 Aligned_cols=49 Identities=18% Similarity=0.059 Sum_probs=35.8
Q ss_pred CCCceeEEEEC-CCCcEEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhc
Q 027107 40 KHPVYRGVRMR-NWGKWVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSIK 91 (228)
Q Consensus 40 ~~s~yRGVr~r-~~GKW~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~ 91 (228)
+..+|.||.+| ..-|=.+-|.. .||-+-.|. .+.|+|..|.++.+..+.
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 44579999666 44566667776 887766664 788999999988877774
No 20
>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=28.50 E-value=2.4e+02 Score=24.12 Aligned_cols=48 Identities=21% Similarity=0.140 Sum_probs=35.5
Q ss_pred CCCceeEEEEC-CCCcEEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhc
Q 027107 40 KHPVYRGVRMR-NWGKWVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSIK 91 (228)
Q Consensus 40 ~~s~yRGVr~r-~~GKW~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~ 91 (228)
+. +|.||.+| ..-|=.+-|.. .||-+-.| ..+.|+|++|.++.+..+.
T Consensus 33 eP-~fpgli~R~~~Pk~t~lIF~--sGKiviTG-aks~~~~~~a~~~~~~~l~ 81 (174)
T cd04517 33 NP-RYPKVTMRLREPRATASVWS--SGKITITG-ATSEEEAKQAARRAARLLQ 81 (174)
T ss_pred eC-CCCEEEEEecCCcEEEEEEC--CCeEEEEc-cCCHHHHHHHHHHHHHHHH
Confidence 44 89999666 44566677777 88766555 5889999999998877663
No 21
>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=28.41 E-value=2.7e+02 Score=23.83 Aligned_cols=49 Identities=18% Similarity=0.076 Sum_probs=36.1
Q ss_pred CCCceeEEEEC-CCCcEEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhc
Q 027107 40 KHPVYRGVRMR-NWGKWVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSIK 91 (228)
Q Consensus 40 ~~s~yRGVr~r-~~GKW~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~ 91 (228)
+..+|.||.+| ..-|=.+-|.. .||-+-.|. .+.|+|..|.++.+..+.
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 44678999666 33566667777 888877776 578889989888777664
No 22
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=27.51 E-value=1.2e+02 Score=27.40 Aligned_cols=38 Identities=21% Similarity=0.194 Sum_probs=32.6
Q ss_pred cEEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhcCC
Q 027107 54 KWVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSIKGN 93 (228)
Q Consensus 54 KW~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~G~ 93 (228)
.|++.|.. ++--+=+|---++++|..|.+.|+.++-+.
T Consensus 133 ~wva~V~~--GrIl~EmgG~~~~~~Ar~al~~aa~klp~~ 170 (221)
T KOG3422|consen 133 HWVARVKA--GRILFEMGGDVEEEEARQALLQAAHKLPFK 170 (221)
T ss_pred eeEEEecC--CcEEEEeCCcccHHHHHHHHHHHHhcCCcc
Confidence 49999998 777788888899999999999999887543
No 23
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=24.57 E-value=1.3e+02 Score=25.64 Aligned_cols=36 Identities=17% Similarity=0.190 Sum_probs=29.5
Q ss_pred EEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhcCC
Q 027107 55 WVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSIKGN 93 (228)
Q Consensus 55 W~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~G~ 93 (228)
|+|+|.. ++.++-=....++.|..|...|+.+|=+.
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 66666667788888999999999887554
No 24
>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=23.71 E-value=70 Score=18.47 Aligned_cols=11 Identities=27% Similarity=1.042 Sum_probs=8.5
Q ss_pred CCeEEEecCCC
Q 027107 64 KKSRIWLGTFP 74 (228)
Q Consensus 64 ~kkriwLGtF~ 74 (228)
+..+||+||+.
T Consensus 14 ~~G~lWigT~~ 24 (24)
T PF07494_consen 14 SDGNLWIGTYN 24 (24)
T ss_dssp TTSCEEEEETS
T ss_pred CCcCEEEEeCC
Confidence 55689999873
No 25
>CHL00044 rpl16 ribosomal protein L16
Probab=23.50 E-value=1.8e+02 Score=23.97 Aligned_cols=44 Identities=23% Similarity=0.312 Sum_probs=31.0
Q ss_pred EEEECC-CC---cEEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhcC
Q 027107 46 GVRMRN-WG---KWVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSIKG 92 (228)
Q Consensus 46 GVr~r~-~G---KW~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~G 92 (228)
+||+-. .| .|+|.|.. +..-+-|+. ..++.|..|...|+.+|-.
T Consensus 80 e~RMGkGKG~~~~~va~V~~--G~ilfEi~g-~~~~~ak~al~~a~~KLP~ 127 (135)
T CHL00044 80 ETRMGSGKGSPEYWVAVVKP--GRILYEMGG-VSETIARAAIKIAAYKMPI 127 (135)
T ss_pred cccccCCCCCccEEEEEECC--CcEEEEEeC-CCHHHHHHHHHHHhhcCCC
Confidence 455552 23 39999998 655556665 5678999999988887643
No 26
>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=21.95 E-value=3.3e+02 Score=23.29 Aligned_cols=49 Identities=18% Similarity=0.117 Sum_probs=35.6
Q ss_pred CCCceeEEEEC-CCCcEEEEEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhc
Q 027107 40 KHPVYRGVRMR-NWGKWVSEIREPRKKSRIWLGTFPTPEMAARAHDVAALSIK 91 (228)
Q Consensus 40 ~~s~yRGVr~r-~~GKW~AeIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~ 91 (228)
+..+|.||.+| ..-|=.+-|.. .||-+-.|. .+.|+|..|-++.+..+.
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 45689999766 33454555555 888776665 789999999998887775
No 27
>PF09003 Phage_integ_N: Bacteriophage lambda integrase, N-terminal domain ; InterPro: IPR015094 The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage []. ; GO: 0003677 DNA binding, 0008907 integrase activity, 0015074 DNA integration; PDB: 1Z1G_B 1Z1B_A 2WCC_3 1KJK_A.
Probab=21.70 E-value=2.6e+02 Score=21.16 Aligned_cols=35 Identities=26% Similarity=0.181 Sum_probs=22.8
Q ss_pred EEecCCCCeEEEecCCCCHHHHHHHHHHHHHHhcCCC
Q 027107 58 EIREPRKKSRIWLGTFPTPEMAARAHDVAALSIKGNS 94 (228)
Q Consensus 58 eIr~p~~kkriwLGtF~T~EeAArAYD~Aa~~l~G~~ 94 (228)
+.+.|..|+.+.||+ +.++|..+=-.|-+.+....
T Consensus 30 ~Yr~P~tGk~~~LG~--d~~~Ai~~A~eaN~~i~~~~ 64 (75)
T PF09003_consen 30 QYRNPITGKEHGLGT--DRAEAIAQAIEANLRIAEQR 64 (75)
T ss_dssp EEE-TTTS-EEEEES---HHHHHHHHHHHHHHHTSSS
T ss_pred EEecCCCCceeeCCC--CHHHHHHHHHHHHHHHHHhc
Confidence 466788999999999 77777666555666664433
No 28
>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=20.08 E-value=1.1e+02 Score=24.22 Aligned_cols=21 Identities=29% Similarity=0.178 Sum_probs=17.2
Q ss_pred ecCCCCHHHHHHHHHHHHHHh
Q 027107 70 LGTFPTPEMAARAHDVAALSI 90 (228)
Q Consensus 70 LGtF~T~EeAArAYD~Aa~~l 90 (228)
-|+|+|+|+|..=||.-...|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 399999999999999865443
Done!