Query 039729
Match_columns 179
No_of_seqs 239 out of 1195
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 12:40:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039729.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039729hhsearch_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 1.8E-21 3.8E-26 132.9 7.4 61 66-128 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 5.1E-21 1.1E-25 132.1 8.1 63 67-131 1-63 (64)
3 PHA00280 putative NHN endonucl 99.8 5.8E-20 1.3E-24 142.5 7.5 90 24-122 20-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 2.5E-11 5.5E-16 80.7 6.3 53 66-119 1-56 (56)
5 PF13392 HNH_3: HNH endonuclea 87.9 0.056 1.2E-06 34.6 -2.1 29 29-61 14-43 (46)
6 PF14657 Integrase_AP2: AP2-li 79.4 6.5 0.00014 25.0 4.9 38 78-117 1-42 (46)
7 PHA02601 int integrase; Provis 75.3 4.9 0.00011 34.3 4.5 45 70-116 2-46 (333)
8 PF08471 Ribonuc_red_2_N: Clas 58.8 10 0.00022 28.5 2.7 20 97-116 71-90 (93)
9 PF05036 SPOR: Sporulation rel 54.7 10 0.00022 25.0 2.0 23 91-113 43-65 (76)
10 PF08846 DUF1816: Domain of un 44.8 48 0.001 23.4 4.2 37 78-116 9-45 (68)
11 cd00801 INT_P4 Bacteriophage P 43.9 56 0.0012 27.4 5.3 40 75-116 8-49 (357)
12 COG0197 RplP Ribosomal protein 42.5 47 0.001 26.9 4.3 37 78-119 95-131 (146)
13 PF09954 DUF2188: Uncharacteri 38.3 92 0.002 20.6 4.7 39 71-115 3-41 (62)
14 PRK09692 integrase; Provisiona 36.0 1.1E+02 0.0023 27.3 6.1 38 77-116 41-82 (413)
15 PF07913 DUF1678: Protein of u 31.7 49 0.0011 27.7 2.9 24 79-102 50-73 (201)
16 PF14112 DUF4284: Domain of un 28.0 37 0.0008 26.0 1.5 16 93-108 3-18 (122)
17 COG2185 Sbm Methylmalonyl-CoA 24.3 56 0.0012 26.2 2.0 17 93-109 43-59 (143)
18 TIGR01164 rplP_bact ribosomal 24.0 1.6E+02 0.0035 22.8 4.5 34 77-116 90-124 (126)
19 PRK09203 rplP 50S ribosomal pr 23.3 1.5E+02 0.0032 23.4 4.2 36 77-118 91-127 (138)
20 CHL00044 rpl16 ribosomal prote 22.1 1.8E+02 0.0038 22.9 4.4 37 77-118 91-127 (135)
21 PF00352 TBP: Transcription fa 21.1 3E+02 0.0065 19.3 5.1 45 67-116 37-82 (86)
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=1.8e-21 Score=132.87 Aligned_cols=61 Identities=67% Similarity=1.179 Sum_probs=56.4
Q ss_pred CceeeeEECCCCcEEEEEecCCCCCCcEEecccCCCHHHHHHHHHHHHHhhcCCCCCCCCCCC
Q 039729 66 VFYRGVRRRPWGKFAAEIRDPNKKNGARVWLGTYDTPEGAALAYDRAAFNMRGSKAKLNFPHL 128 (179)
Q Consensus 66 s~yrGV~~r~~gkW~A~I~~~~~~~gkri~LG~F~T~EeAA~AYD~Aa~~~~G~~A~lNFp~~ 128 (179)
|+|+||+++++|||+|+|+++ ..|+++|||+|+|+|||+.|||.|+++++|.++.+|||++
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~--~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDP--SGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeC--CCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 589999988899999999874 2489999999999999999999999999999999999974
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.84 E-value=5.1e-21 Score=132.12 Aligned_cols=63 Identities=67% Similarity=1.183 Sum_probs=58.4
Q ss_pred ceeeeEECCCCcEEEEEecCCCCCCcEEecccCCCHHHHHHHHHHHHHhhcCCCCCCCCCCCCCC
Q 039729 67 FYRGVRRRPWGKFAAEIRDPNKKNGARVWLGTYDTPEGAALAYDRAAFNMRGSKAKLNFPHLIGS 131 (179)
Q Consensus 67 ~yrGV~~r~~gkW~A~I~~~~~~~gkri~LG~F~T~EeAA~AYD~Aa~~~~G~~A~lNFp~~~~~ 131 (179)
+|+||+++++|||+|+|+++ .+|+.+|||+|+|+||||.|||.|+++++|.++.+|||.+.+.
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~--~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDP--SKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCCCeEEEEEEec--CCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 58999998899999999886 4789999999999999999999999999999999999987654
No 3
>PHA00280 putative NHN endonuclease
Probab=99.81 E-value=5.8e-20 Score=142.52 Aligned_cols=90 Identities=17% Similarity=0.187 Sum_probs=74.6
Q ss_pred ccCCCCCCCC-cccccCCCCCCCCCCCCccccccCcccC--------CCCCCceeeeEEC-CCCcEEEEEecCCCCCCcE
Q 039729 24 NDDFDNVPSE-TSISVNDDPLINSPTNSSFRTRGATTHE--------SHVRVFYRGVRRR-PWGKFAAEIRDPNKKNGAR 93 (179)
Q Consensus 24 ~~~~~~~p~~-~~~hin~~p~~n~~~n~~~~lR~~t~~~--------~~~~s~yrGV~~r-~~gkW~A~I~~~~~~~gkr 93 (179)
...-..+|.. .+||||+++.||+++| ||.+|..+ ..++|+|+||++. ..|||+|+| +++||+
T Consensus 20 ~~~~G~~P~g~~VdHidg~~~dnri~N----Lr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I----~~~gK~ 91 (121)
T PHA00280 20 EAANGPIPKGYYIDHIDGNPLNDALDN----LRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTV----TAEGKQ 91 (121)
T ss_pred HHHHCCCCCCCEEEcCCCCCCCCcHHH----hhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEE----EECCEE
Confidence 3344567874 6999999999999999 88877432 3445799999854 569999999 569999
Q ss_pred EecccCCCHHHHHHHHHHHHHhhcCCCCC
Q 039729 94 VWLGTYDTPEGAALAYDRAAFNMRGSKAK 122 (179)
Q Consensus 94 i~LG~F~T~EeAA~AYD~Aa~~~~G~~A~ 122 (179)
++||.|+++|+|+.||+ ++.++||+||.
T Consensus 92 ~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 92 HNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred EEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 99999999999999997 77889999985
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=99.23 E-value=2.5e-11 Score=80.74 Aligned_cols=53 Identities=30% Similarity=0.377 Sum_probs=45.4
Q ss_pred CceeeeEECC-CCcEEEEEecCCCCCC--cEEecccCCCHHHHHHHHHHHHHhhcCC
Q 039729 66 VFYRGVRRRP-WGKFAAEIRDPNKKNG--ARVWLGTYDTPEGAALAYDRAAFNMRGS 119 (179)
Q Consensus 66 s~yrGV~~r~-~gkW~A~I~~~~~~~g--kri~LG~F~T~EeAA~AYD~Aa~~~~G~ 119 (179)
|+|+||++.+ .++|+|+|+++ ..+| ++++||.|++++||++|++.++..++|+
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~-~~~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVW-SENGKRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEEC-CCTTEEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEc-ccCcccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 5899998554 79999999885 2344 9999999999999999999999999885
No 5
>PF13392 HNH_3: HNH endonuclease; PDB: 1U3E_M.
Probab=87.93 E-value=0.056 Score=34.59 Aligned_cols=29 Identities=24% Similarity=0.248 Sum_probs=17.1
Q ss_pred CCCCC-cccccCCCCCCCCCCCCccccccCcccC
Q 039729 29 NVPSE-TSISVNDDPLINSPTNSSFRTRGATTHE 61 (179)
Q Consensus 29 ~~p~~-~~~hin~~p~~n~~~n~~~~lR~~t~~~ 61 (179)
.+|.. +++|+++++.+|+++| |+..++.+
T Consensus 14 ~~p~~~~v~H~~~~~~~n~~~N----L~~~t~~e 43 (46)
T PF13392_consen 14 PIPEGYVVDHKDGNKTDNRPEN----LRWVTRSE 43 (46)
T ss_dssp T--TT-EEEETTS-TT---GGG----EEEE-HHH
T ss_pred CCCCCCEEEeCCCCCCCCCHHH----ceECCHHH
Confidence 44443 7999999999999999 77776543
No 6
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=79.44 E-value=6.5 Score=24.96 Aligned_cols=38 Identities=13% Similarity=0.169 Sum_probs=28.2
Q ss_pred cEEEEEe--cCCCCCC--cEEecccCCCHHHHHHHHHHHHHhhc
Q 039729 78 KFAAEIR--DPNKKNG--ARVWLGTYDTPEGAALAYDRAAFNMR 117 (179)
Q Consensus 78 kW~A~I~--~~~~~~g--kri~LG~F~T~EeAA~AYD~Aa~~~~ 117 (179)
+|...|- ++ .+| ++++-+-|.|..||..+..++...+.
T Consensus 1 ~w~~~v~g~~~--~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDD--ETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEEC--CCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5777772 43 244 56778899999999999888776653
No 7
>PHA02601 int integrase; Provisional
Probab=75.30 E-value=4.9 Score=34.35 Aligned_cols=45 Identities=22% Similarity=0.259 Sum_probs=31.0
Q ss_pred eeEECCCCcEEEEEecCCCCCCcEEecccCCCHHHHHHHHHHHHHhh
Q 039729 70 GVRRRPWGKFAAEIRDPNKKNGARVWLGTYDTPEGAALAYDRAAFNM 116 (179)
Q Consensus 70 GV~~r~~gkW~A~I~~~~~~~gkri~LG~F~T~EeAA~AYD~Aa~~~ 116 (179)
+|++.++|+|++++... ...|+++.. +|.|..||....+......
T Consensus 2 ~~~~~~~g~w~~~~~~~-~~~g~r~~~-~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPN-GRDGKRIRK-RFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEEC-CCCCchhhh-hhcCHHHHHHHHHHHHHhc
Confidence 56677789999999742 235777654 6999999876655544433
No 8
>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=58.78 E-value=10 Score=28.47 Aligned_cols=20 Identities=30% Similarity=0.536 Sum_probs=18.1
Q ss_pred ccCCCHHHHHHHHHHHHHhh
Q 039729 97 GTYDTPEGAALAYDRAAFNM 116 (179)
Q Consensus 97 G~F~T~EeAA~AYD~Aa~~~ 116 (179)
|+|+|+|+|..-||..+..|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999987755
No 9
>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=54.67 E-value=10 Score=24.99 Aligned_cols=23 Identities=26% Similarity=0.323 Sum_probs=19.0
Q ss_pred CcEEecccCCCHHHHHHHHHHHH
Q 039729 91 GARVWLGTYDTPEGAALAYDRAA 113 (179)
Q Consensus 91 gkri~LG~F~T~EeAA~AYD~Aa 113 (179)
--+|.+|.|+|.+||..+..+..
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 35688899999999998877665
No 10
>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=44.82 E-value=48 Score=23.44 Aligned_cols=37 Identities=19% Similarity=0.299 Sum_probs=26.0
Q ss_pred cEEEEEecCCCCCCcEEecccCCCHHHHHHHHHHHHHhh
Q 039729 78 KFAAEIRDPNKKNGARVWLGTYDTPEGAALAYDRAAFNM 116 (179)
Q Consensus 78 kW~A~I~~~~~~~gkri~LG~F~T~EeAA~AYD~Aa~~~ 116 (179)
-|-++|.-. .-.-..|-|-|+|.+||..+...-..-+
T Consensus 9 aWWveI~T~--~P~ctYyFGPF~s~~eA~~~~~gyieDL 45 (68)
T PF08846_consen 9 AWWVEIETQ--NPNCTYYFGPFDSREEAEAALPGYIEDL 45 (68)
T ss_pred cEEEEEEcC--CCCEEEEeCCcCCHHHHHHHhccHHHHH
Confidence 477888632 1125689999999999998865444444
No 11
>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=43.90 E-value=56 Score=27.42 Aligned_cols=40 Identities=20% Similarity=0.141 Sum_probs=26.3
Q ss_pred CCCcEEEEEecCCCCCCcEEecccCC--CHHHHHHHHHHHHHhh
Q 039729 75 PWGKFAAEIRDPNKKNGARVWLGTYD--TPEGAALAYDRAAFNM 116 (179)
Q Consensus 75 ~~gkW~A~I~~~~~~~gkri~LG~F~--T~EeAA~AYD~Aa~~~ 116 (179)
..+.|+.+++... ..+++.||.|+ +.++|.....+....+
T Consensus 8 g~~~~~~~~~~~g--~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 8 GSKSWRFRYRLAG--KRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CCEEEEEEeccCC--ceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 3456999986531 12457799995 6777777766655554
No 12
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=42.49 E-value=47 Score=26.85 Aligned_cols=37 Identities=27% Similarity=0.142 Sum_probs=30.6
Q ss_pred cEEEEEecCCCCCCcEEecccCCCHHHHHHHHHHHHHhhcCC
Q 039729 78 KFAAEIRDPNKKNGARVWLGTYDTPEGAALAYDRAAFNMRGS 119 (179)
Q Consensus 78 kW~A~I~~~~~~~gkri~LG~F~T~EeAA~AYD~Aa~~~~G~ 119 (179)
-|.|+| +-|+.++==..++++.|..|.-.|+.+|-+.
T Consensus 95 gwaArV-----kpG~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 95 GWAARV-----KPGRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEEe-----cCCcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 399999 3477888777889999999999999988554
No 13
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=38.34 E-value=92 Score=20.63 Aligned_cols=39 Identities=33% Similarity=0.243 Sum_probs=26.0
Q ss_pred eEECCCCcEEEEEecCCCCCCcEEecccCCCHHHHHHHHHHHHHh
Q 039729 71 VRRRPWGKFAAEIRDPNKKNGARVWLGTYDTPEGAALAYDRAAFN 115 (179)
Q Consensus 71 V~~r~~gkW~A~I~~~~~~~gkri~LG~F~T~EeAA~AYD~Aa~~ 115 (179)
|..+..|.|..+. .|..--..+|+|.+||..+=...+..
T Consensus 3 V~p~~~~~W~v~~------eg~~ra~~~~~Tk~eAi~~Ar~~a~~ 41 (62)
T PF09954_consen 3 VVPREDGGWAVKK------EGAKRASKTFDTKAEAIEAARELAKN 41 (62)
T ss_pred EEecCCCCceEEe------CCCcccccccCcHHHHHHHHHHHHHh
Confidence 4444457898887 33444479999999998765554443
No 14
>PRK09692 integrase; Provisional
Probab=36.05 E-value=1.1e+02 Score=27.29 Aligned_cols=38 Identities=16% Similarity=0.083 Sum_probs=24.5
Q ss_pred CcEEEEEecCCCCCCcE--EecccCC--CHHHHHHHHHHHHHhh
Q 039729 77 GKFAAEIRDPNKKNGAR--VWLGTYD--TPEGAALAYDRAAFNM 116 (179)
Q Consensus 77 gkW~A~I~~~~~~~gkr--i~LG~F~--T~EeAA~AYD~Aa~~~ 116 (179)
..|+.+.+.+ .+|++ +-||.|+ |..+|..+..++...+
T Consensus 41 k~~~~rY~~~--~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~~~ 82 (413)
T PRK09692 41 KIWQFRYYRP--LTKTRAKKSFGPYPSVTLADARNYRAESRSLL 82 (413)
T ss_pred EEEEEEEecC--CCCceeeeeCCCCCCCCHHHHHHHHHHHHHHH
Confidence 3599988754 23444 6799999 6777766555544433
No 15
>PF07913 DUF1678: Protein of unknown function (DUF1678); InterPro: IPR012465 This family is composed of uncharacterised proteins expressed by Methanopyrus kandleri, a hyperthermophilic archaeon.
Probab=31.72 E-value=49 Score=27.71 Aligned_cols=24 Identities=25% Similarity=0.508 Sum_probs=20.9
Q ss_pred EEEEEecCCCCCCcEEecccCCCH
Q 039729 79 FAAEIRDPNKKNGARVWLGTYDTP 102 (179)
Q Consensus 79 W~A~I~~~~~~~gkri~LG~F~T~ 102 (179)
|+|++++.....|+.+|||-=+++
T Consensus 50 YvARWr~~r~~~GRTlYLGk~eNe 73 (201)
T PF07913_consen 50 YVARWRDSRFERGRTLYLGKPENE 73 (201)
T ss_pred eeeeecCccccCCceeeccCCcCc
Confidence 899999888889999999987654
No 16
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=28.00 E-value=37 Score=26.03 Aligned_cols=16 Identities=13% Similarity=0.611 Sum_probs=12.6
Q ss_pred EEecccCCCHHHHHHH
Q 039729 93 RVWLGTYDTPEGAALA 108 (179)
Q Consensus 93 ri~LG~F~T~EeAA~A 108 (179)
.+|||.|.+++|-..=
T Consensus 3 siWiG~f~s~~el~~Y 18 (122)
T PF14112_consen 3 SIWIGNFKSEDELEEY 18 (122)
T ss_pred EEEEecCCCHHHHHHH
Confidence 5999999988775543
No 17
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=24.29 E-value=56 Score=26.24 Aligned_cols=17 Identities=41% Similarity=0.515 Sum_probs=14.9
Q ss_pred EEecccCCCHHHHHHHH
Q 039729 93 RVWLGTYDTPEGAALAY 109 (179)
Q Consensus 93 ri~LG~F~T~EeAA~AY 109 (179)
-+++|.|.|+|||++|-
T Consensus 43 Vi~~g~~~tp~e~v~aA 59 (143)
T COG2185 43 VINLGLFQTPEEAVRAA 59 (143)
T ss_pred EEecCCcCCHHHHHHHH
Confidence 48999999999999874
No 18
>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=23.98 E-value=1.6e+02 Score=22.82 Aligned_cols=34 Identities=21% Similarity=0.239 Sum_probs=25.9
Q ss_pred CcEEEEEecCCCCCCcEEe-cccCCCHHHHHHHHHHHHHhh
Q 039729 77 GKFAAEIRDPNKKNGARVW-LGTYDTPEGAALAYDRAAFNM 116 (179)
Q Consensus 77 gkW~A~I~~~~~~~gkri~-LG~F~T~EeAA~AYD~Aa~~~ 116 (179)
--|+|+|. -|+-++ ++. .+++.|..|...|+.++
T Consensus 90 ~~~varV~-----~G~ilfEi~~-~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 90 EYWVAVVK-----PGKILFEIAG-VPEEVAREAFRLAASKL 124 (126)
T ss_pred CEEEEEEC-----CCCEEEEEeC-CCHHHHHHHHHHHHhcC
Confidence 44999994 345555 444 89999999999998876
No 19
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=23.32 E-value=1.5e+02 Score=23.36 Aligned_cols=36 Identities=19% Similarity=0.134 Sum_probs=27.2
Q ss_pred CcEEEEEecCCCCCCcEEe-cccCCCHHHHHHHHHHHHHhhcC
Q 039729 77 GKFAAEIRDPNKKNGARVW-LGTYDTPEGAALAYDRAAFNMRG 118 (179)
Q Consensus 77 gkW~A~I~~~~~~~gkri~-LG~F~T~EeAA~AYD~Aa~~~~G 118 (179)
--|+|+|. -|+-++ ++. .+++.|..|...|+.++-+
T Consensus 91 ~~~varVk-----~G~iifEi~~-~~~~~a~~al~~a~~KLP~ 127 (138)
T PRK09203 91 EYWVAVVK-----PGRILFEIAG-VSEELAREALRLAAAKLPI 127 (138)
T ss_pred cEEEEEEC-----CCCEEEEEeC-CCHHHHHHHHHHHhccCCC
Confidence 34999993 345555 444 8999999999999988744
No 20
>CHL00044 rpl16 ribosomal protein L16
Probab=22.15 E-value=1.8e+02 Score=22.94 Aligned_cols=37 Identities=19% Similarity=0.073 Sum_probs=26.2
Q ss_pred CcEEEEEecCCCCCCcEEecccCCCHHHHHHHHHHHHHhhcC
Q 039729 77 GKFAAEIRDPNKKNGARVWLGTYDTPEGAALAYDRAAFNMRG 118 (179)
Q Consensus 77 gkW~A~I~~~~~~~gkri~LG~F~T~EeAA~AYD~Aa~~~~G 118 (179)
--|+|.|. -|+-++=-.-.+++.|..|...|+.+|-.
T Consensus 91 ~~~va~V~-----~G~ilfEi~g~~~~~ak~al~~a~~KLP~ 127 (135)
T CHL00044 91 EYWVAVVK-----PGRILYEMGGVSETIARAAIKIAAYKMPI 127 (135)
T ss_pred cEEEEEEC-----CCcEEEEEeCCCHHHHHHHHHHHhhcCCC
Confidence 34999994 35555533336778999999999887743
No 21
>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=21.11 E-value=3e+02 Score=19.33 Aligned_cols=45 Identities=22% Similarity=0.159 Sum_probs=32.8
Q ss_pred ceeeeEEC-CCCcEEEEEecCCCCCCcEEecccCCCHHHHHHHHHHHHHhh
Q 039729 67 FYRGVRRR-PWGKFAAEIRDPNKKNGARVWLGTYDTPEGAALAYDRAAFNM 116 (179)
Q Consensus 67 ~yrGV~~r-~~gkW~A~I~~~~~~~gkri~LG~F~T~EeAA~AYD~Aa~~~ 116 (179)
+|.||..+ ..-+-.+.|. ..||-+..|. .++|||..|.++....+
T Consensus 37 ~fpgl~~r~~~p~~t~~IF----~sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 37 RFPGLIYRLRNPKATVLIF----SSGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TESSEEEEETTTTEEEEEE----TTSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred cCCeEEEeecCCcEEEEEE----cCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 68887633 3345666664 5788888887 78999999998876654
Done!