Query 047387
Match_columns 239
No_of_seqs 300 out of 1262
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 10:37:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047387.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047387hhsearch_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 2.1E-21 4.6E-26 138.7 6.9 61 107-168 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 2.5E-21 5.4E-26 140.1 6.8 63 108-171 1-63 (64)
3 PHA00280 putative NHN endonucl 99.5 9.1E-14 2E-18 113.7 7.2 60 100-163 60-120 (121)
4 PF00847 AP2: AP2 domain; Int 99.3 1.1E-11 2.4E-16 86.4 6.4 53 107-159 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 83.5 3.6 7.8E-05 27.8 5.0 38 119-156 1-41 (46)
6 PHA02601 int integrase; Provis 75.6 4.3 9.4E-05 36.3 4.4 45 111-156 2-46 (333)
7 PF08846 DUF1816: Domain of un 56.2 23 0.00049 26.7 4.2 30 119-149 9-38 (68)
8 PF05036 SPOR: Sporulation rel 50.3 11 0.00024 26.2 1.6 23 131-153 43-65 (76)
9 cd00801 INT_P4 Bacteriophage P 41.6 62 0.0013 28.5 5.4 39 117-156 9-49 (357)
10 COG0197 RplP Ribosomal protein 38.0 54 0.0012 28.2 4.2 37 119-159 95-131 (146)
11 PF08471 Ribonuc_red_2_N: Clas 32.7 44 0.00095 26.7 2.7 20 137-156 71-90 (93)
12 PF14112 DUF4284: Domain of un 30.4 36 0.00079 27.6 2.0 62 132-197 2-69 (122)
13 PRK09692 integrase; Provisiona 29.5 1.5E+02 0.0031 27.8 6.1 43 112-154 33-80 (413)
14 PRK09203 rplP 50S ribosomal pr 24.4 1.2E+02 0.0026 25.4 4.0 37 118-158 91-127 (138)
15 cd04517 TLF TBP-like factors ( 24.2 2.2E+02 0.0048 24.5 5.8 45 108-156 35-80 (174)
16 TIGR01164 rplP_bact ribosomal 24.0 1.4E+02 0.003 24.6 4.3 35 118-156 90-124 (126)
17 CHL00044 rpl16 ribosomal prote 23.9 1.3E+02 0.0029 25.1 4.2 37 118-158 91-127 (135)
18 PF00352 TBP: Transcription fa 23.5 2.4E+02 0.0051 21.1 5.2 45 108-156 37-82 (86)
19 PF13356 DUF4102: Domain of un 22.8 2.9E+02 0.0064 20.5 5.6 39 112-151 27-69 (89)
20 PTZ00173 60S ribosomal protein 21.6 1.5E+02 0.0033 26.9 4.4 54 119-176 124-187 (213)
No 1
>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.
Probab=99.85 E-value=2.1e-21 Score=138.69 Aligned_cols=61 Identities=66% Similarity=1.183 Sum_probs=56.7
Q ss_pred CceeEEEeCCCCcEEEEeecCCCCCeEEeeccCCcHHHHHHHHHHHHHHccCCCCCCCCCch
Q 047387 107 VSYRGVRRRPWGKYAAEIRDSTRNGVRVWIGTFDTAEAAALAYDQAAFAMRGTTAVLNFPVE 168 (239)
Q Consensus 107 s~YRGVr~r~~GKW~AeIr~~~~~Gkri~LGtFdT~EEAArAYD~AA~~~~G~~A~lNFp~~ 168 (239)
|+|+||+++++|||+|+|+++. .|+++|||+|+|+||||+|||.|+++++|..+.+|||++
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~-~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPS-GGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCC-CCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 6899999999999999999843 289999999999999999999999999999999999963
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.84 E-value=2.5e-21 Score=140.08 Aligned_cols=63 Identities=65% Similarity=1.110 Sum_probs=59.1
Q ss_pred ceeEEEeCCCCcEEEEeecCCCCCeEEeeccCCcHHHHHHHHHHHHHHccCCCCCCCCCchhHH
Q 047387 108 SYRGVRRRPWGKYAAEIRDSTRNGVRVWIGTFDTAEAAALAYDQAAFAMRGTTAVLNFPVEKVY 171 (239)
Q Consensus 108 ~YRGVr~r~~GKW~AeIr~~~~~Gkri~LGtFdT~EEAArAYD~AA~~~~G~~A~lNFp~~~y~ 171 (239)
+|+||+++++|||+|+|+++. +|+++|||+|+|+||||+|||.|+++++|..+.+|||.+.|+
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~-~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPS-KGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecC-CCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 589999999999999999865 489999999999999999999999999999999999998875
No 3
>PHA00280 putative NHN endonuclease
Probab=99.47 E-value=9.1e-14 Score=113.66 Aligned_cols=60 Identities=13% Similarity=0.151 Sum_probs=53.5
Q ss_pred cCCCCCCCceeEEEeCCC-CcEEEEeecCCCCCeEEeeccCCcHHHHHHHHHHHHHHccCCCCCC
Q 047387 100 EEGPLKEVSYRGVRRRPW-GKYAAEIRDSTRNGVRVWIGTFDTAEAAALAYDQAAFAMRGTTAVL 163 (239)
Q Consensus 100 ~~~~~~~s~YRGVr~r~~-GKW~AeIr~~~~~Gkri~LGtFdT~EEAArAYD~AA~~~~G~~A~l 163 (239)
+..+.++|+|+||++++. |||+|+|+. +||+++||.|+|+|+|+.||+ ++.+++|++|..
T Consensus 60 ~~~~~N~SG~kGV~~~k~~~kw~A~I~~---~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~~ 120 (121)
T PHA00280 60 KTPKSNTSGLKGLSWSKEREMWRGTVTA---EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFARF 120 (121)
T ss_pred CCCCCCCCCCCeeEEecCCCeEEEEEEE---CCEEEEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence 345678999999998765 999999998 899999999999999999997 788999999853
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=99.27 E-value=1.1e-11 Score=86.39 Aligned_cols=53 Identities=32% Similarity=0.451 Sum_probs=46.6
Q ss_pred CceeEEEeCCC-CcEEEEeecCCCCC--eEEeeccCCcHHHHHHHHHHHHHHccCC
Q 047387 107 VSYRGVRRRPW-GKYAAEIRDSTRNG--VRVWIGTFDTAEAAALAYDQAAFAMRGT 159 (239)
Q Consensus 107 s~YRGVr~r~~-GKW~AeIr~~~~~G--kri~LGtFdT~EEAArAYD~AA~~~~G~ 159 (239)
|+|+||++++. ++|+|.|++...+| ++++||.|++++||++|++.++..++|+
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 68999998775 99999999854444 9999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=83.53 E-value=3.6 Score=27.75 Aligned_cols=38 Identities=16% Similarity=0.114 Sum_probs=29.3
Q ss_pred cEEEEee--cC-CCCCeEEeeccCCcHHHHHHHHHHHHHHc
Q 047387 119 KYAAEIR--DS-TRNGVRVWIGTFDTAEAAALAYDQAAFAM 156 (239)
Q Consensus 119 KW~AeIr--~~-~~~Gkri~LGtFdT~EEAArAYD~AA~~~ 156 (239)
+|...|. ++ +++-++++-+-|.|..||..+..++...+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5888883 33 44447789999999999999998876665
No 6
>PHA02601 int integrase; Provisional
Probab=75.59 E-value=4.3 Score=36.32 Aligned_cols=45 Identities=27% Similarity=0.304 Sum_probs=31.6
Q ss_pred EEEeCCCCcEEEEeecCCCCCeEEeeccCCcHHHHHHHHHHHHHHc
Q 047387 111 GVRRRPWGKYAAEIRDSTRNGVRVWIGTFDTAEAAALAYDQAAFAM 156 (239)
Q Consensus 111 GVr~r~~GKW~AeIr~~~~~Gkri~LGtFdT~EEAArAYD~AA~~~ 156 (239)
+|++.+.|+|.++++.....|+++. .+|.|..||....+.....+
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 5667777999999985323477765 46999999877666554444
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=56.24 E-value=23 Score=26.74 Aligned_cols=30 Identities=27% Similarity=0.431 Sum_probs=23.5
Q ss_pred cEEEEeecCCCCCeEEeeccCCcHHHHHHHH
Q 047387 119 KYAAEIRDSTRNGVRVWIGTFDTAEAAALAY 149 (239)
Q Consensus 119 KW~AeIr~~~~~Gkri~LGtFdT~EEAArAY 149 (239)
.|-++|.-.. -.-..|.|-|.|.+||..+.
T Consensus 9 aWWveI~T~~-P~ctYyFGPF~s~~eA~~~~ 38 (68)
T PF08846_consen 9 AWWVEIETQN-PNCTYYFGPFDSREEAEAAL 38 (68)
T ss_pred cEEEEEEcCC-CCEEEEeCCcCCHHHHHHHh
Confidence 4778887522 24789999999999999874
No 8
>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=50.25 E-value=11 Score=26.18 Aligned_cols=23 Identities=30% Similarity=0.384 Sum_probs=19.1
Q ss_pred CeEEeeccCCcHHHHHHHHHHHH
Q 047387 131 GVRVWIGTFDTAEAAALAYDQAA 153 (239)
Q Consensus 131 Gkri~LGtFdT~EEAArAYD~AA 153 (239)
--+|.+|.|+|.++|..+-.+..
T Consensus 43 ~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 43 WYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp CEEEEECCECTCCHHHHHHHHHH
T ss_pred eEEEEECCCCCHHHHHHHHHHHh
Confidence 46899999999999988877655
No 9
>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=41.60 E-value=62 Score=28.48 Aligned_cols=39 Identities=15% Similarity=0.171 Sum_probs=26.7
Q ss_pred CCcEEEEeecCCCCCeEEeeccCC--cHHHHHHHHHHHHHHc
Q 047387 117 WGKYAAEIRDSTRNGVRVWIGTFD--TAEAAALAYDQAAFAM 156 (239)
Q Consensus 117 ~GKW~AeIr~~~~~Gkri~LGtFd--T~EEAArAYD~AA~~~ 156 (239)
.+.|..+++...+ .+++.||+|+ |.++|..+.......+
T Consensus 9 ~~~~~~~~~~~g~-~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGK-RKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCc-eeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 3569999988332 3567899996 6777777666655555
No 10
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=38.05 E-value=54 Score=28.16 Aligned_cols=37 Identities=22% Similarity=0.115 Sum_probs=31.9
Q ss_pred cEEEEeecCCCCCeEEeeccCCcHHHHHHHHHHHHHHccCC
Q 047387 119 KYAAEIRDSTRNGVRVWIGTFDTAEAAALAYDQAAFAMRGT 159 (239)
Q Consensus 119 KW~AeIr~~~~~Gkri~LGtFdT~EEAArAYD~AA~~~~G~ 159 (239)
-|+|+|.- |+.++-=....++.|..|.-+|+.+|-+.
T Consensus 95 gwaArVkp----G~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 95 GWAARVKP----GRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEEecC----CcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 39999984 88888888899999999999999988654
No 11
>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=32.73 E-value=44 Score=26.75 Aligned_cols=20 Identities=35% Similarity=0.615 Sum_probs=17.8
Q ss_pred ccCCcHHHHHHHHHHHHHHc
Q 047387 137 GTFDTAEAAALAYDQAAFAM 156 (239)
Q Consensus 137 GtFdT~EEAArAYD~AA~~~ 156 (239)
|.|+|+|+|..=||..+..+
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999987654
No 12
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=30.44 E-value=36 Score=27.61 Aligned_cols=62 Identities=19% Similarity=0.368 Sum_probs=34.4
Q ss_pred eEEeeccCCcHHHHHHHHHHHHHHc--cCC----CCCCCCCchhHHHHHHhccccccCCCcchhhhhccccc
Q 047387 132 VRVWIGTFDTAEAAALAYDQAAFAM--RGT----TAVLNFPVEKVYESLLEMKYDFEVGSSPVLTLKKRHSM 197 (239)
Q Consensus 132 kri~LGtFdT~EEAArAYD~AA~~~--~G~----~A~lNFp~~~y~~el~e~~~~~~~~~sp~~al~~~~~~ 197 (239)
..||||+|.+.++-..=.+. .+ -|. .-...|-...|.+.+.++...... ..++..|....+.
T Consensus 2 VsiWiG~f~s~~el~~Y~e~---~Ydedgd~i~s~F~~df~i~~yDeDfie~~~~~~~-~~~l~~ll~~~Sy 69 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYFEI---DYDEDGDSIPSQFCKDFGIDYYDEDFIEIIFYEES-EVSLEELLEGFSY 69 (122)
T ss_pred eEEEEecCCCHHHHHHHhCc---cccCCCCcccChHHHHcCCCccCchhcEEEEccCC-ccCHHHHHhcCCc
Confidence 46999999998876654433 12 122 112445555566666666544332 3455555555444
No 13
>PRK09692 integrase; Provisional
Probab=29.52 E-value=1.5e+02 Score=27.83 Aligned_cols=43 Identities=9% Similarity=0.055 Sum_probs=25.3
Q ss_pred EEeCCCC--cEEEEeecCC-CCCeEEeeccCC--cHHHHHHHHHHHHH
Q 047387 112 VRRRPWG--KYAAEIRDST-RNGVRVWIGTFD--TAEAAALAYDQAAF 154 (239)
Q Consensus 112 Vr~r~~G--KW~AeIr~~~-~~Gkri~LGtFd--T~EEAArAYD~AA~ 154 (239)
|+-++.| .|..+-+.+. ++.+++-||.|+ |..+|..+-..+..
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~ 80 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRS 80 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHH
Confidence 4445554 4998887532 222336899999 66666554444333
No 14
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=24.35 E-value=1.2e+02 Score=25.36 Aligned_cols=37 Identities=19% Similarity=0.027 Sum_probs=28.9
Q ss_pred CcEEEEeecCCCCCeEEeeccCCcHHHHHHHHHHHHHHccC
Q 047387 118 GKYAAEIRDSTRNGVRVWIGTFDTAEAAALAYDQAAFAMRG 158 (239)
Q Consensus 118 GKW~AeIr~~~~~Gkri~LGtFdT~EEAArAYD~AA~~~~G 158 (239)
--|+|+|.. |+-++--.-.+++.|..|..+|+.++-+
T Consensus 91 ~~~varVk~----G~iifEi~~~~~~~a~~al~~a~~KLP~ 127 (138)
T PRK09203 91 EYWVAVVKP----GRILFEIAGVSEELAREALRLAAAKLPI 127 (138)
T ss_pred cEEEEEECC----CCEEEEEeCCCHHHHHHHHHHHhccCCC
Confidence 449999985 6665544448999999999999988754
No 15
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=24.18 E-value=2.2e+02 Score=24.53 Aligned_cols=45 Identities=24% Similarity=0.205 Sum_probs=34.4
Q ss_pred ceeEEEeCCC-CcEEEEeecCCCCCeEEeeccCCcHHHHHHHHHHHHHHc
Q 047387 108 SYRGVRRRPW-GKYAAEIRDSTRNGVRVWIGTFDTAEAAALAYDQAAFAM 156 (239)
Q Consensus 108 ~YRGVr~r~~-GKW~AeIr~~~~~Gkri~LGtFdT~EEAArAYD~AA~~~ 156 (239)
+|.||..|-. -+=.+-|.. .||-+--| ..+.|+|++|.++.+..+
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~---sGKiviTG-aks~~~~~~a~~~~~~~l 80 (174)
T cd04517 35 RYPKVTMRLREPRATASVWS---SGKITITG-ATSEEEAKQAARRAARLL 80 (174)
T ss_pred CCCEEEEEecCCcEEEEEEC---CCeEEEEc-cCCHHHHHHHHHHHHHHH
Confidence 7899876543 677888887 78754444 689999999999887766
No 16
>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=24.02 E-value=1.4e+02 Score=24.63 Aligned_cols=35 Identities=20% Similarity=0.125 Sum_probs=27.7
Q ss_pred CcEEEEeecCCCCCeEEeeccCCcHHHHHHHHHHHHHHc
Q 047387 118 GKYAAEIRDSTRNGVRVWIGTFDTAEAAALAYDQAAFAM 156 (239)
Q Consensus 118 GKW~AeIr~~~~~Gkri~LGtFdT~EEAArAYD~AA~~~ 156 (239)
-.|+|+|.. |+-++--.-.+++.|..|.-+|+.++
T Consensus 90 ~~~varV~~----G~ilfEi~~~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 90 EYWVAVVKP----GKILFEIAGVPEEVAREAFRLAASKL 124 (126)
T ss_pred CEEEEEECC----CCEEEEEeCCCHHHHHHHHHHHHhcC
Confidence 449999985 66665444489999999999999876
No 17
>CHL00044 rpl16 ribosomal protein L16
Probab=23.92 E-value=1.3e+02 Score=25.07 Aligned_cols=37 Identities=19% Similarity=0.088 Sum_probs=28.2
Q ss_pred CcEEEEeecCCCCCeEEeeccCCcHHHHHHHHHHHHHHccC
Q 047387 118 GKYAAEIRDSTRNGVRVWIGTFDTAEAAALAYDQAAFAMRG 158 (239)
Q Consensus 118 GKW~AeIr~~~~~Gkri~LGtFdT~EEAArAYD~AA~~~~G 158 (239)
--|+|.|.. |+-++=-.-..++.|..|...|+.++-.
T Consensus 91 ~~~va~V~~----G~ilfEi~g~~~~~ak~al~~a~~KLP~ 127 (135)
T CHL00044 91 EYWVAVVKP----GRILYEMGGVSETIARAAIKIAAYKMPI 127 (135)
T ss_pred cEEEEEECC----CcEEEEEeCCCHHHHHHHHHHHhhcCCC
Confidence 449999985 6666644446789999999999988744
No 18
>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=23.46 E-value=2.4e+02 Score=21.13 Aligned_cols=45 Identities=22% Similarity=0.200 Sum_probs=32.8
Q ss_pred ceeEEEeCCC-CcEEEEeecCCCCCeEEeeccCCcHHHHHHHHHHHHHHc
Q 047387 108 SYRGVRRRPW-GKYAAEIRDSTRNGVRVWIGTFDTAEAAALAYDQAAFAM 156 (239)
Q Consensus 108 ~YRGVr~r~~-GKW~AeIr~~~~~Gkri~LGtFdT~EEAArAYD~AA~~~ 156 (239)
.|.||..|.. -+-.+.|.. .||-+..|. .++|+|..|.++....+
T Consensus 37 ~fpgl~~r~~~p~~t~~IF~---sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 37 RFPGLIYRLRNPKATVLIFS---SGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TESSEEEEETTTTEEEEEET---TSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred cCCeEEEeecCCcEEEEEEc---CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 5778765543 466777776 788777775 78999999998876654
No 19
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=22.75 E-value=2.9e+02 Score=20.47 Aligned_cols=39 Identities=15% Similarity=0.181 Sum_probs=22.8
Q ss_pred EEeCCC--CcEEEEeecCCCCCeEEeeccCCc--HHHHHHHHHH
Q 047387 112 VRRRPW--GKYAAEIRDSTRNGVRVWIGTFDT--AEAAALAYDQ 151 (239)
Q Consensus 112 Vr~r~~--GKW~AeIr~~~~~Gkri~LGtFdT--~EEAArAYD~ 151 (239)
|+-.+. ..|..+.+.. ++.+++-||.|++ ..+|......
T Consensus 27 l~v~~~G~kt~~~r~~~~-gk~~~~~lG~~p~~sl~~AR~~a~~ 69 (89)
T PF13356_consen 27 LRVTPSGSKTFYFRYRIN-GKRRRITLGRYPELSLAEAREKARE 69 (89)
T ss_dssp EEE-TTS-EEEEEEEEET-TEEEEEEEEECTTS-HHHHHHHHHH
T ss_pred EEEEeCCCeEEEEEEEec-ceEEEeccCCCccCCHHHHHHHHHH
Confidence 333454 4488888762 2345688999986 4444444433
No 20
>PTZ00173 60S ribosomal protein L10; Provisional
Probab=21.60 E-value=1.5e+02 Score=26.93 Aligned_cols=54 Identities=19% Similarity=0.128 Sum_probs=40.4
Q ss_pred cEEEEeecCCCCCeEEeeccC--CcHHHHHHHHHHHHHHccCCC--------CCCCCCchhHHHHHHh
Q 047387 119 KYAAEIRDSTRNGVRVWIGTF--DTAEAAALAYDQAAFAMRGTT--------AVLNFPVEKVYESLLE 176 (239)
Q Consensus 119 KW~AeIr~~~~~Gkri~LGtF--dT~EEAArAYD~AA~~~~G~~--------A~lNFp~~~y~~el~e 176 (239)
-|+|+|.. |..|+--.- .+.+.|..|..+|+.++-+.. .-|+|..+.|.+-..+
T Consensus 124 g~vArVk~----Gqiifei~~~~~~~~~AkeALrrA~~KlP~~~kIv~~~~wgft~~~~~~~~~~~~~ 187 (213)
T PTZ00173 124 GTCARVRI----GQILLSIRTKEAYVPQAIEALRRAKYKFPGRQKIVVSNKWGFTNYTREEYQKLRAE 187 (213)
T ss_pred EEEEEECc----CCEEEEEecccCCHHHHHHHHHHhcccCCCeEEEEEecccCccccCHHHHHHHHHC
Confidence 39999985 777766555 789999999999999984433 2478888887754433
Done!