Query 041658
Match_columns 139
No_of_seqs 206 out of 1186
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 09:23:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041658.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041658hhsearch_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 99.9 1.8E-22 3.9E-27 132.7 8.5 64 28-93 1-64 (64)
2 cd00018 AP2 DNA-binding domain 99.9 1.3E-22 2.9E-27 131.8 7.6 61 27-89 1-61 (61)
3 PHA00280 putative NHN endonucl 99.7 7.9E-18 1.7E-22 124.0 6.7 76 2-83 43-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.3 6.6E-12 1.4E-16 79.6 6.3 53 27-80 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 76.9 10 0.00022 22.7 5.0 40 39-78 1-42 (46)
6 PHA02601 int integrase; Provis 72.0 6.7 0.00015 31.8 4.3 45 31-77 2-46 (333)
7 PF08471 Ribonuc_red_2_N: Clas 71.4 4.9 0.00011 28.5 2.9 20 58-77 71-90 (93)
8 PF08846 DUF1816: Domain of un 66.1 14 0.0003 24.8 4.1 35 39-75 9-43 (68)
9 PF05036 SPOR: Sporulation rel 60.3 7.5 0.00016 24.4 2.0 23 52-74 43-65 (76)
10 PF10729 CedA: Cell division a 49.5 41 0.00089 22.9 4.2 38 27-69 31-68 (80)
11 cd00801 INT_P4 Bacteriophage P 46.2 59 0.0013 25.9 5.5 38 38-77 10-49 (357)
12 COG0197 RplP Ribosomal protein 40.9 49 0.0011 25.3 4.0 37 39-80 95-131 (146)
13 PF14112 DUF4284: Domain of un 38.0 22 0.00048 25.8 1.7 46 54-102 3-54 (122)
14 PRK09692 integrase; Provisiona 32.8 1.6E+02 0.0034 24.9 6.3 43 33-75 34-80 (413)
15 COG2185 Sbm Methylmalonyl-CoA 31.5 38 0.00083 25.7 2.1 18 53-70 42-59 (143)
16 PF07913 DUF1678: Protein of u 29.8 45 0.00098 26.4 2.3 24 40-63 50-73 (201)
17 PRK10113 cell division modulat 29.5 45 0.00098 22.6 2.0 37 28-69 32-68 (80)
18 PF13356 DUF4102: Domain of un 28.1 1.8E+02 0.004 19.2 5.1 39 34-74 29-71 (89)
19 cd04517 TLF TBP-like factors ( 24.9 3.2E+02 0.0069 21.0 6.3 47 25-77 33-80 (174)
20 PLN00062 TATA-box-binding prot 24.6 3.4E+02 0.0073 21.1 7.0 49 25-78 32-81 (179)
21 TIGR01164 rplP_bact ribosomal 24.2 1.5E+02 0.0032 21.8 4.1 35 38-77 90-124 (126)
22 CHL00044 rpl16 ribosomal prote 23.8 1.4E+02 0.0031 22.1 4.0 36 39-79 92-127 (135)
23 PRK09203 rplP 50S ribosomal pr 23.6 1.4E+02 0.003 22.3 3.9 37 38-79 91-127 (138)
24 cd04516 TBP_eukaryotes eukaryo 23.2 3.5E+02 0.0076 20.8 7.0 48 25-77 32-80 (174)
25 PRK10905 cell division protein 21.8 1.5E+02 0.0033 25.5 4.2 19 54-72 287-305 (328)
26 PF00352 TBP: Transcription fa 21.5 2.6E+02 0.0056 18.6 5.3 47 26-77 35-82 (86)
27 PF11821 DUF3341: Protein of u 20.7 86 0.0019 24.4 2.3 39 53-91 2-41 (173)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.88 E-value=1.8e-22 Score=132.68 Aligned_cols=64 Identities=63% Similarity=1.131 Sum_probs=59.8
Q ss_pred ceeeeEECCCCeeEEEEecCCCCCCcEEEeCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCC
Q 041658 28 SFRGVRRRPWGKFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRLHGKKAKLNFPRFVTDT 93 (139)
Q Consensus 28 ~yrGV~~~~~gkw~A~I~~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~~~~G~~a~lNFp~~~~~~ 93 (139)
+|+||+++++|+|+|+|+++.. |+.+|||+|+|+||||.|||.+++++||.++.+|||...|+.
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~--~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~~ 64 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSK--GKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYDS 64 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCC--CcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCCC
Confidence 5999998888999999999765 889999999999999999999999999999999999998863
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=99.88 E-value=1.3e-22 Score=131.84 Aligned_cols=61 Identities=62% Similarity=1.086 Sum_probs=56.7
Q ss_pred CceeeeEECCCCeeEEEEecCCCCCCcEEEeCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 041658 27 RSFRGVRRRPWGKFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRLHGKKAKLNFPRF 89 (139)
Q Consensus 27 s~yrGV~~~~~gkw~A~I~~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~~~~G~~a~lNFp~~ 89 (139)
|+|+||+++++|+|+|+|+++.. |+++|||+|+|+||||.|||.++++++|.++.+|||++
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~--gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSG--GRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCC--CceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 68999998888999999999543 78999999999999999999999999999999999974
No 3
>PHA00280 putative NHN endonuclease
Probab=99.73 E-value=7.9e-18 Score=124.02 Aligned_cols=76 Identities=12% Similarity=0.148 Sum_probs=66.5
Q ss_pred CcCCCCCCchhhHhhhhccCCCCCCCceeeeEEC-CCCeeEEEEecCCCCCCcEEEeCCCCCHHHHHHHHHHHHHHhcCC
Q 041658 2 TWSDSNSNDAASATATIRTRESHAPRSFRGVRRR-PWGKFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRLHGK 80 (139)
Q Consensus 2 ~~~n~~~~~~~~~~~~~r~~~~~~~s~yrGV~~~-~~gkw~A~I~~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~~~~G~ 80 (139)
.++||+.++.++++.+.+ ...+++|||+||.+. ..|||+|+|.+ +|++++||.|+++|+|+.||+ ++.+|||+
T Consensus 43 ri~NLr~~T~~eN~~N~~-~~~~N~SG~kGV~~~k~~~kw~A~I~~----~gK~~~lG~f~~~e~A~~a~~-~~~~lhGe 116 (121)
T PHA00280 43 ALDNLRLALPKENSWNMK-TPKSNTSGLKGLSWSKEREMWRGTVTA----EGKQHNFRSRDLLEVVAWIYR-TRRELHGQ 116 (121)
T ss_pred cHHHhhhcCHHHHhcccC-CCCCCCCCCCeeEEecCCCeEEEEEEE----CCEEEEcCCCCCHHHHHHHHH-HHHHHhhc
Confidence 478999999988888764 566788999999765 56999999998 788999999999999999997 78899999
Q ss_pred CCC
Q 041658 81 KAK 83 (139)
Q Consensus 81 ~a~ 83 (139)
+|.
T Consensus 117 Fa~ 119 (121)
T PHA00280 117 FAR 119 (121)
T ss_pred ccc
Confidence 875
No 4
>PF00847 AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-related genes transcriptional activator binds to the GCC-box pathogenesis-related promoter element and activates the plant's defence genes. Ethylene, chemically the simplest plant hormone, participates in a number of stress responses and developmental processes: e.g., fruit ripening, inhibition of stem and root elongation, promotion of seed germination and flowering, senescence of leaves and flowers, and sex determination []. DNA sequence elements that confer ethylene responsiveness have been shown to contain two 11bp GCC boxes, which are necessary and sufficient for transcriptional control by ethylene. Ethylene responsive element binding proteins (EREBPs) have now been identified in a variety of plants. The proteins share a similar domain of around 59 amino acids, which interacts directly with the GCC box in the ERE.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3IGM_A 3GCC_A 1GCC_A 2GCC_A.
Probab=99.31 E-value=6.6e-12 Score=79.55 Aligned_cols=53 Identities=32% Similarity=0.443 Sum_probs=45.3
Q ss_pred CceeeeEECC-CCeeEEEEecCCCCCC--cEEEeCCCCCHHHHHHHHHHHHHHhcCC
Q 041658 27 RSFRGVRRRP-WGKFGAEIRDGKDNNG--ERVWLGTFYTPEDAALAYDRAAFRLHGK 80 (139)
Q Consensus 27 s~yrGV~~~~-~gkw~A~I~~~~~~~g--k~~~LG~f~t~eeAA~AYD~aa~~~~G~ 80 (139)
|+|+||++++ .++|+|+|++... +| +.++||.|++++||+.||+.+++.++|+
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~-~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSE-NGKRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCC-TTEEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEccc-CcccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 6899997664 6999999998433 33 8999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=76.92 E-value=10 Score=22.69 Aligned_cols=40 Identities=15% Similarity=0.137 Sum_probs=27.9
Q ss_pred eeEEEEe--cCCCCCCcEEEeCCCCCHHHHHHHHHHHHHHhc
Q 041658 39 KFGAEIR--DGKDNNGERVWLGTFYTPEDAALAYDRAAFRLH 78 (139)
Q Consensus 39 kw~A~I~--~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~~~~ 78 (139)
+|...|. ++..-..++++-+.|.|..||-.+...+...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 4777773 321102367888999999999999887666553
No 6
>PHA02601 int integrase; Provisional
Probab=72.00 E-value=6.7 Score=31.78 Aligned_cols=45 Identities=24% Similarity=0.258 Sum_probs=30.0
Q ss_pred eeEECCCCeeEEEEecCCCCCCcEEEeCCCCCHHHHHHHHHHHHHHh
Q 041658 31 GVRRRPWGKFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRL 77 (139)
Q Consensus 31 GV~~~~~gkw~A~I~~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~~~ 77 (139)
+|++.++|+|++++..... .|+++.. +|.|..||-...+.....+
T Consensus 2 ~~~~~~~g~w~~~~~~~~~-~g~r~~~-~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGR-DGKRIRK-RFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCC-CCchhhh-hhcCHHHHHHHHHHHHHhc
Confidence 5666777999999986322 3666543 6999998876655443333
No 7
>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=71.40 E-value=4.9 Score=28.54 Aligned_cols=20 Identities=45% Similarity=0.640 Sum_probs=17.7
Q ss_pred CCCCCHHHHHHHHHHHHHHh
Q 041658 58 GTFYTPEDAALAYDRAAFRL 77 (139)
Q Consensus 58 G~f~t~eeAA~AYD~aa~~~ 77 (139)
|+|+|+|+|..-||..+..|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999877654
No 8
>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=66.12 E-value=14 Score=24.77 Aligned_cols=35 Identities=20% Similarity=0.206 Sum_probs=24.5
Q ss_pred eeEEEEecCCCCCCcEEEeCCCCCHHHHHHHHHHHHH
Q 041658 39 KFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAF 75 (139)
Q Consensus 39 kw~A~I~~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~ 75 (139)
-|-++|.-..- .-..|.|-|++.+||..+.--...
T Consensus 9 aWWveI~T~~P--~ctYyFGPF~s~~eA~~~~~gyie 43 (68)
T PF08846_consen 9 AWWVEIETQNP--NCTYYFGPFDSREEAEAALPGYIE 43 (68)
T ss_pred cEEEEEEcCCC--CEEEEeCCcCCHHHHHHHhccHHH
Confidence 36677755221 348999999999999988643333
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=60.28 E-value=7.5 Score=24.36 Aligned_cols=23 Identities=30% Similarity=0.359 Sum_probs=18.6
Q ss_pred CcEEEeCCCCCHHHHHHHHHHHH
Q 041658 52 GERVWLGTFYTPEDAALAYDRAA 74 (139)
Q Consensus 52 gk~~~LG~f~t~eeAA~AYD~aa 74 (139)
--++.+|.|++.+||..+-....
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 34889999999999988876554
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=49.46 E-value=41 Score=22.85 Aligned_cols=38 Identities=29% Similarity=0.279 Sum_probs=25.3
Q ss_pred CceeeeEECCCCeeEEEEecCCCCCCcEEEeCCCCCHHHHHHH
Q 041658 27 RSFRGVRRRPWGKFGAEIRDGKDNNGERVWLGTFYTPEDAALA 69 (139)
Q Consensus 27 s~yrGV~~~~~gkw~A~I~~~~~~~gk~~~LG~f~t~eeAA~A 69 (139)
-+|+-||.-+ |||.|.+..+.. -.---.|..+|.|-+-
T Consensus 31 dgfrdvw~lr-gkyvafvl~ge~----f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 31 DGFRDVWQLR-GKYVAFVLMGEH----FRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTECCECCCC-CEEEEEEESSS-----EEE---BSSHHHHHHH
T ss_pred ccccceeeec-cceEEEEEecch----hccCCCcCCcHHHHHH
Confidence 3899997655 999999988322 3344578888887764
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=46.18 E-value=59 Score=25.91 Aligned_cols=38 Identities=21% Similarity=0.191 Sum_probs=26.9
Q ss_pred CeeEEEEecCCCCCCcEEEeCCCC--CHHHHHHHHHHHHHHh
Q 041658 38 GKFGAEIRDGKDNNGERVWLGTFY--TPEDAALAYDRAAFRL 77 (139)
Q Consensus 38 gkw~A~I~~~~~~~gk~~~LG~f~--t~eeAA~AYD~aa~~~ 77 (139)
+.|..++...++ ..++.||.|+ +.++|....+.....+
T Consensus 10 ~~~~~~~~~~g~--~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGK--RKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCc--eeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 569999888654 4578899995 6777776666554444
No 12
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=40.88 E-value=49 Score=25.29 Aligned_cols=37 Identities=27% Similarity=0.194 Sum_probs=31.0
Q ss_pred eeEEEEecCCCCCCcEEEeCCCCCHHHHHHHHHHHHHHhcCC
Q 041658 39 KFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRLHGK 80 (139)
Q Consensus 39 kw~A~I~~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~~~~G~ 80 (139)
.|.|+|.. |+.++-=..+.++.|..|.-+|+.+|=+.
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 49999877 77888888899999999999999887554
No 13
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=38.04 E-value=22 Score=25.82 Aligned_cols=46 Identities=13% Similarity=0.341 Sum_probs=25.3
Q ss_pred EEEeCCCCCHHHHHHHHHHHHHHh--cCCCC----CCCCCCCCCCCCcccccccC
Q 041658 54 RVWLGTFYTPEDAALAYDRAAFRL--HGKKA----KLNFPRFVTDTNIEDVSVTD 102 (139)
Q Consensus 54 ~~~LG~f~t~eeAA~AYD~aa~~~--~G~~a----~lNFp~~~~~~e~~~~~~~~ 102 (139)
.+|||.|.+++|--.=.|. .+ -|..- ...|-...|+++.-++....
T Consensus 3 siWiG~f~s~~el~~Y~e~---~Ydedgd~i~s~F~~df~i~~yDeDfie~~~~~ 54 (122)
T PF14112_consen 3 SIWIGNFKSEDELEEYFEI---DYDEDGDSIPSQFCKDFGIDYYDEDFIEIIFYE 54 (122)
T ss_pred EEEEecCCCHHHHHHHhCc---cccCCCCcccChHHHHcCCCccCchhcEEEEcc
Confidence 7999999998876544332 22 12211 23444555666555554443
No 14
>PRK09692 integrase; Provisional
Probab=32.79 E-value=1.6e+02 Score=24.87 Aligned_cols=43 Identities=12% Similarity=0.003 Sum_probs=25.1
Q ss_pred EECCCC--eeEEEEecCCCCCCcEEEeCCCC--CHHHHHHHHHHHHH
Q 041658 33 RRRPWG--KFGAEIRDGKDNNGERVWLGTFY--TPEDAALAYDRAAF 75 (139)
Q Consensus 33 ~~~~~g--kw~A~I~~~~~~~gk~~~LG~f~--t~eeAA~AYD~aa~ 75 (139)
...+.| .|..+.+.+.....+++-||.|+ |..+|-.+-..+..
T Consensus 34 ~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~ 80 (413)
T PRK09692 34 LIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRS 80 (413)
T ss_pred EEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHH
Confidence 444554 48888764322023347899999 67776555444333
No 15
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=31.51 E-value=38 Score=25.72 Aligned_cols=18 Identities=50% Similarity=0.604 Sum_probs=15.4
Q ss_pred cEEEeCCCCCHHHHHHHH
Q 041658 53 ERVWLGTFYTPEDAALAY 70 (139)
Q Consensus 53 k~~~LG~f~t~eeAA~AY 70 (139)
.-+++|.|.|+||++++=
T Consensus 42 eVi~~g~~~tp~e~v~aA 59 (143)
T COG2185 42 EVINLGLFQTPEEAVRAA 59 (143)
T ss_pred eEEecCCcCCHHHHHHHH
Confidence 368999999999999764
No 16
>PF07913 DUF1678: Protein of unknown function (DUF1678); InterPro: IPR012465 This family is composed of uncharacterised proteins expressed by Methanopyrus kandleri, a hyperthermophilic archaeon.
Probab=29.85 E-value=45 Score=26.40 Aligned_cols=24 Identities=25% Similarity=0.403 Sum_probs=20.3
Q ss_pred eEEEEecCCCCCCcEEEeCCCCCH
Q 041658 40 FGAEIRDGKDNNGERVWLGTFYTP 63 (139)
Q Consensus 40 w~A~I~~~~~~~gk~~~LG~f~t~ 63 (139)
|+|++.+...+.|+.+|||--+++
T Consensus 50 YvARWr~~r~~~GRTlYLGk~eNe 73 (201)
T PF07913_consen 50 YVARWRDSRFERGRTLYLGKPENE 73 (201)
T ss_pred eeeeecCccccCCceeeccCCcCc
Confidence 789998877778999999988764
No 17
>PRK10113 cell division modulator; Provisional
Probab=29.55 E-value=45 Score=22.58 Aligned_cols=37 Identities=32% Similarity=0.311 Sum_probs=25.8
Q ss_pred ceeeeEECCCCeeEEEEecCCCCCCcEEEeCCCCCHHHHHHH
Q 041658 28 SFRGVRRRPWGKFGAEIRDGKDNNGERVWLGTFYTPEDAALA 69 (139)
Q Consensus 28 ~yrGV~~~~~gkw~A~I~~~~~~~gk~~~LG~f~t~eeAA~A 69 (139)
+|+-||.-+ |||.|.+..... -.---.|..+|.|-+-
T Consensus 32 ~frDVW~Lr-GKYVAFvl~ge~----FrRSPaFs~PEsAQRW 68 (80)
T PRK10113 32 SFRDVWMLR-GKYVAFVLMGES----FLRSPAFSVPESAQRW 68 (80)
T ss_pred chhhhheec-cceEEEEEechh----hccCCccCCcHHHHHH
Confidence 788887655 999999877322 2233568888887764
No 18
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=28.09 E-value=1.8e+02 Score=19.23 Aligned_cols=39 Identities=18% Similarity=0.116 Sum_probs=24.1
Q ss_pred ECCC--CeeEEEEecCCCCCCcEEEeCCCCC--HHHHHHHHHHHH
Q 041658 34 RRPW--GKFGAEIRDGKDNNGERVWLGTFYT--PEDAALAYDRAA 74 (139)
Q Consensus 34 ~~~~--gkw~A~I~~~~~~~gk~~~LG~f~t--~eeAA~AYD~aa 74 (139)
..+. ..|.-+....++ .+++-||.|+. ..+|-.......
T Consensus 29 v~~~G~kt~~~r~~~~gk--~~~~~lG~~p~~sl~~AR~~a~~~~ 71 (89)
T PF13356_consen 29 VTPSGSKTFYFRYRINGK--RRRITLGRYPELSLAEAREKARELR 71 (89)
T ss_dssp E-TTS-EEEEEEEEETTE--EEEEEEEECTTS-HHHHHHHHHHHH
T ss_pred EEeCCCeEEEEEEEecce--EEEeccCCCccCCHHHHHHHHHHHH
Confidence 3344 348888877544 56789999975 555554444333
No 19
>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=24.93 E-value=3.2e+02 Score=20.99 Aligned_cols=47 Identities=28% Similarity=0.249 Sum_probs=34.7
Q ss_pred CCCceeeeEEC-CCCeeEEEEecCCCCCCcEEEeCCCCCHHHHHHHHHHHHHHh
Q 041658 25 APRSFRGVRRR-PWGKFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRL 77 (139)
Q Consensus 25 ~~s~yrGV~~~-~~gkw~A~I~~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~~~ 77 (139)
++ +|-||..+ ..-+-.+.|+. .||-+.-| ..++|+|..|.++.+..+
T Consensus 33 eP-~fpgli~R~~~Pk~t~lIF~----sGKiviTG-aks~~~~~~a~~~~~~~l 80 (174)
T cd04517 33 NP-RYPKVTMRLREPRATASVWS----SGKITITG-ATSEEEAKQAARRAARLL 80 (174)
T ss_pred eC-CCCEEEEEecCCcEEEEEEC----CCeEEEEc-cCCHHHHHHHHHHHHHHH
Confidence 45 89999655 44567778877 56566555 578999999998887766
No 20
>PLN00062 TATA-box-binding protein; Provisional
Probab=24.57 E-value=3.4e+02 Score=21.07 Aligned_cols=49 Identities=29% Similarity=0.268 Sum_probs=35.1
Q ss_pred CCCceeeeEEC-CCCeeEEEEecCCCCCCcEEEeCCCCCHHHHHHHHHHHHHHhc
Q 041658 25 APRSFRGVRRR-PWGKFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRLH 78 (139)
Q Consensus 25 ~~s~yrGV~~~-~~gkw~A~I~~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~~~~ 78 (139)
++.+|-||..+ ..-+-.+.|.. .||-+.-|. .++|+|..|.++.+..+.
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 45689998554 44566777777 465666664 788999999988877763
No 21
>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=24.25 E-value=1.5e+02 Score=21.75 Aligned_cols=35 Identities=23% Similarity=0.133 Sum_probs=26.4
Q ss_pred CeeEEEEecCCCCCCcEEEeCCCCCHHHHHHHHHHHHHHh
Q 041658 38 GKFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRL 77 (139)
Q Consensus 38 gkw~A~I~~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~~~ 77 (139)
-.|.|.|.. |+-++--.-.+++.|-.|.-.++.+|
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 349999977 55555444489999999998888765
No 22
>CHL00044 rpl16 ribosomal protein L16
Probab=23.84 E-value=1.4e+02 Score=22.13 Aligned_cols=36 Identities=17% Similarity=0.075 Sum_probs=26.1
Q ss_pred eeEEEEecCCCCCCcEEEeCCCCCHHHHHHHHHHHHHHhcC
Q 041658 39 KFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRLHG 79 (139)
Q Consensus 39 kw~A~I~~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~~~~G 79 (139)
-|.|.|.. |+-++=-.-.+++.|..|...|+.+|=.
T Consensus 92 ~~va~V~~-----G~ilfEi~g~~~~~ak~al~~a~~KLP~ 127 (135)
T CHL00044 92 YWVAVVKP-----GRILYEMGGVSETIARAAIKIAAYKMPI 127 (135)
T ss_pred EEEEEECC-----CcEEEEEeCCCHHHHHHHHHHHhhcCCC
Confidence 49999977 5565544446778999998888877643
No 23
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=23.58 E-value=1.4e+02 Score=22.28 Aligned_cols=37 Identities=22% Similarity=0.030 Sum_probs=27.5
Q ss_pred CeeEEEEecCCCCCCcEEEeCCCCCHHHHHHHHHHHHHHhcC
Q 041658 38 GKFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRLHG 79 (139)
Q Consensus 38 gkw~A~I~~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~~~~G 79 (139)
..|.|+|.. |+-++--.-.+++.|..|...|+.+|=+
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 349999977 5555444448999999999998877644
No 24
>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=23.22 E-value=3.5e+02 Score=20.81 Aligned_cols=48 Identities=29% Similarity=0.286 Sum_probs=35.3
Q ss_pred CCCceeeeEEC-CCCeeEEEEecCCCCCCcEEEeCCCCCHHHHHHHHHHHHHHh
Q 041658 25 APRSFRGVRRR-PWGKFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRL 77 (139)
Q Consensus 25 ~~s~yrGV~~~-~~gkw~A~I~~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~~~ 77 (139)
++.+|-||..+ ..-+-.+.|.. .||-+.-|. .++|+|..|.++.+..+
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~----SGKiviTGa-ks~e~a~~a~~~i~~~L 80 (174)
T cd04516 32 NPKRFAAVIMRIREPKTTALIFS----SGKMVCTGA-KSEDDSKLAARKYARII 80 (174)
T ss_pred CCccCcEEEEEeCCCcEEEEEEC----CCeEEEEec-CCHHHHHHHHHHHHHHH
Confidence 45689998554 44566778877 576777776 57788998988887766
No 25
>PRK10905 cell division protein DamX; Validated
Probab=21.79 E-value=1.5e+02 Score=25.51 Aligned_cols=19 Identities=21% Similarity=0.233 Sum_probs=16.2
Q ss_pred EEEeCCCCCHHHHHHHHHH
Q 041658 54 RVWLGTFYTPEDAALAYDR 72 (139)
Q Consensus 54 ~~~LG~f~t~eeAA~AYD~ 72 (139)
.+..|.|.+.+||.+|-..
T Consensus 287 VV~yG~YaSraeAk~Aiak 305 (328)
T PRK10905 287 VLVSGVYASKEEAKRAVST 305 (328)
T ss_pred EEEecCCCCHHHHHHHHHH
Confidence 5678999999999988765
No 26
>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=21.48 E-value=2.6e+02 Score=18.58 Aligned_cols=47 Identities=28% Similarity=0.263 Sum_probs=32.7
Q ss_pred CCceeeeEEC-CCCeeEEEEecCCCCCCcEEEeCCCCCHHHHHHHHHHHHHHh
Q 041658 26 PRSFRGVRRR-PWGKFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRL 77 (139)
Q Consensus 26 ~s~yrGV~~~-~~gkw~A~I~~~~~~~gk~~~LG~f~t~eeAA~AYD~aa~~~ 77 (139)
+.+|-||..+ ..-+-...|.. .|+-+..|. .++|+|..|.+.....+
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 4588998554 33456667766 576777775 68899999988766544
No 27
>PF11821 DUF3341: Protein of unknown function (DUF3341); InterPro: IPR021776 This family of proteins are functionally uncharacterised. This family is found in bacteria. Proteins in this family are about 170 amino acids in length.
Probab=20.73 E-value=86 Score=24.39 Aligned_cols=39 Identities=18% Similarity=0.029 Sum_probs=26.2
Q ss_pred cEEEeCCCCCHHHHHHHHHHHHHH-hcCCCCCCCCCCCCC
Q 041658 53 ERVWLGTFYTPEDAALAYDRAAFR-LHGKKAKLNFPRFVT 91 (139)
Q Consensus 53 k~~~LG~f~t~eeAA~AYD~aa~~-~~G~~a~lNFp~~~~ 91 (139)
++..||.|+++++.-.|-.+...+ +.--++.+.||.+.-
T Consensus 2 ~~gl~a~F~~~~~l~~A~~~~r~~G~~~~d~ytPfPvhgl 41 (173)
T PF11821_consen 2 KYGLLAEFDDPEALLHAARKLRDAGYRIWDVYTPFPVHGL 41 (173)
T ss_pred CceEEEEECCHHHHHHHHHHHHHcCCceeEEeCCCcCcCH
Confidence 467899999998887765433222 334457788997653
Done!