Query 047455
Match_columns 367
No_of_seqs 274 out of 1091
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 11:13:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047455.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047455hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00380 AP2 DNA-binding dom 99.8 3.2E-20 6.9E-25 142.4 8.5 64 125-188 1-64 (64)
2 cd00018 AP2 DNA-binding domain 99.8 3.9E-20 8.4E-25 140.2 7.5 61 124-184 1-61 (61)
3 PHA00280 putative NHN endonucl 99.4 1.4E-12 3.1E-17 112.9 7.4 59 118-179 61-120 (121)
4 PF00847 AP2: AP2 domain; Int 99.0 2.8E-10 6.1E-15 84.2 5.2 52 124-175 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 81.3 5.7 0.00012 28.5 5.6 38 136-173 1-42 (46)
6 PHA02601 int integrase; Provis 57.1 16 0.00034 35.2 4.4 44 128-172 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 49.0 39 0.00084 32.0 5.7 39 134-172 9-49 (357)
8 PF05036 SPOR: Sporulation rel 34.9 50 0.0011 24.4 3.3 30 146-176 42-71 (76)
9 PRK09692 integrase; Provisiona 32.8 1.1E+02 0.0025 30.6 6.3 39 129-167 33-77 (413)
10 PF08846 DUF1816: Domain of un 30.5 92 0.002 25.0 4.2 32 136-167 9-40 (68)
11 COG0197 RplP Ribosomal protein 24.5 1E+02 0.0022 28.2 3.8 37 136-175 95-131 (146)
12 PF13356 DUF4102: Domain of un 23.9 2.3E+02 0.005 22.6 5.5 34 135-168 35-70 (89)
13 PF14112 DUF4284: Domain of un 20.6 65 0.0014 27.9 1.8 19 148-166 2-20 (122)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.82 E-value=3.2e-20 Score=142.39 Aligned_cols=64 Identities=64% Similarity=1.110 Sum_probs=61.1
Q ss_pred ceeEEEECCCCcEEEEEecCCCCeEEeccCCCCHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCc
Q 047455 125 KFRGVRQRPWGKWAAEIRDPARRVRLWLGTYDTAEEAARVYDNAAIKLRGPDALTNFSTPPPAV 188 (367)
Q Consensus 125 ~yRGVr~r~~GKW~AeIr~~~~~kri~LGtFdT~EeAArAYD~AAikl~G~~A~tNFp~s~y~~ 188 (367)
+|+||+++++|||+|+|+++.+++++|||+|+|+||||+|||.|+++++|..+.+|||.+.|+.
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~~ 64 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYDS 64 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCCC
Confidence 5999999999999999999889999999999999999999999999999999999999999863
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=99.81 E-value=3.9e-20 Score=140.21 Aligned_cols=61 Identities=69% Similarity=1.232 Sum_probs=57.9
Q ss_pred CceeEEEECCCCcEEEEEecCCCCeEEeccCCCCHHHHHHHHHHHHHHHhCCCCCCCCCCC
Q 047455 124 KKFRGVRQRPWGKWAAEIRDPARRVRLWLGTYDTAEEAARVYDNAAIKLRGPDALTNFSTP 184 (367)
Q Consensus 124 S~yRGVr~r~~GKW~AeIr~~~~~kri~LGtFdT~EeAArAYD~AAikl~G~~A~tNFp~s 184 (367)
|+|+||+++++|||+|+|+++..++++|||+|+|+||||+|||.|+++++|..+.+|||.+
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 6899999999999999999866699999999999999999999999999999999999974
No 3
>PHA00280 putative NHN endonuclease
Probab=99.36 E-value=1.4e-12 Score=112.89 Aligned_cols=59 Identities=19% Similarity=0.227 Sum_probs=52.2
Q ss_pred ccCCCCCceeEEEECCC-CcEEEEEecCCCCeEEeccCCCCHHHHHHHHHHHHHHHhCCCCCC
Q 047455 118 SQTTNGKKFRGVRQRPW-GKWAAEIRDPARRVRLWLGTYDTAEEAARVYDNAAIKLRGPDALT 179 (367)
Q Consensus 118 ~~~~~tS~yRGVr~r~~-GKW~AeIr~~~~~kri~LGtFdT~EeAArAYD~AAikl~G~~A~t 179 (367)
.++.|+|+|+||++++. |||.|+|+ ..||+++||.|+++|+|+.||+ |+++|+|.+|..
T Consensus 61 ~~~~N~SG~kGV~~~k~~~kw~A~I~--~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~~ 120 (121)
T PHA00280 61 TPKSNTSGLKGLSWSKEREMWRGTVT--AEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFARF 120 (121)
T ss_pred CCCCCCCCCCeeEEecCCCeEEEEEE--ECCEEEEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence 45678999999987655 99999999 4999999999999999999997 788999998853
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=99.04 E-value=2.8e-10 Score=84.20 Aligned_cols=52 Identities=33% Similarity=0.507 Sum_probs=45.0
Q ss_pred CceeEEEECC-CCcEEEEEecCCC---CeEEeccCCCCHHHHHHHHHHHHHHHhCC
Q 047455 124 KKFRGVRQRP-WGKWAAEIRDPAR---RVRLWLGTYDTAEEAARVYDNAAIKLRGP 175 (367)
Q Consensus 124 S~yRGVr~r~-~GKW~AeIr~~~~---~kri~LGtFdT~EeAArAYD~AAikl~G~ 175 (367)
|+|+||++.+ .++|+|+|++... +++++||.|++++||++||+.++++++|+
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 6899998766 5999999998422 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=81.28 E-value=5.7 Score=28.54 Aligned_cols=38 Identities=16% Similarity=0.235 Sum_probs=29.8
Q ss_pred cEEEEE--ecCCCC--eEEeccCCCCHHHHHHHHHHHHHHHh
Q 047455 136 KWAAEI--RDPARR--VRLWLGTYDTAEEAARVYDNAAIKLR 173 (367)
Q Consensus 136 KW~AeI--r~~~~~--kri~LGtFdT~EeAArAYD~AAikl~ 173 (367)
+|...| .++..| ++++-+-|.|..||..+...+...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 588888 355455 77899999999999999888766653
No 6
>PHA02601 int integrase; Provisional
Probab=57.05 E-value=16 Score=35.16 Aligned_cols=44 Identities=25% Similarity=0.306 Sum_probs=30.0
Q ss_pred EEEECCCCcEEEEEecC-CCCeEEeccCCCCHHHHHHHHHHHHHHH
Q 047455 128 GVRQRPWGKWAAEIRDP-ARRVRLWLGTYDTAEEAARVYDNAAIKL 172 (367)
Q Consensus 128 GVr~r~~GKW~AeIr~~-~~~kri~LGtFdT~EeAArAYD~AAikl 172 (367)
+|++.+.|+|.++++.. ..|+++.. +|.|..||..........+
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~~-~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIRK-RFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhhh-hhcCHHHHHHHHHHHHHhc
Confidence 56777789999999842 24666653 6999998876655543333
No 7
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=48.98 E-value=39 Score=31.99 Aligned_cols=39 Identities=33% Similarity=0.420 Sum_probs=27.9
Q ss_pred CCcEEEEEecCCCCeEEeccCCC--CHHHHHHHHHHHHHHH
Q 047455 134 WGKWAAEIRDPARRVRLWLGTYD--TAEEAARVYDNAAIKL 172 (367)
Q Consensus 134 ~GKW~AeIr~~~~~kri~LGtFd--T~EeAArAYD~AAikl 172 (367)
.+.|..+++.....+++.||+|+ +.++|..........+
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 35699988875556778899995 7777777666654444
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=34.87 E-value=50 Score=24.42 Aligned_cols=30 Identities=30% Similarity=0.497 Sum_probs=21.9
Q ss_pred CCeEEeccCCCCHHHHHHHHHHHHHHHhCCC
Q 047455 146 RRVRLWLGTYDTAEEAARVYDNAAIKLRGPD 176 (367)
Q Consensus 146 ~~kri~LGtFdT~EeAArAYD~AAikl~G~~ 176 (367)
..-+|++|.|.+.++|..+-.... +..|.+
T Consensus 42 ~~yrV~~G~f~~~~~A~~~~~~l~-~~~~~~ 71 (76)
T PF05036_consen 42 PWYRVRVGPFSSREEAEAALRKLK-KAAGPD 71 (76)
T ss_dssp TCEEEEECCECTCCHHHHHHHHHH-HHHTS-
T ss_pred ceEEEEECCCCCHHHHHHHHHHHh-HhhCCC
Confidence 457899999999999988876554 344443
No 9
>PRK09692 integrase; Provisional
Probab=32.78 E-value=1.1e+02 Score=30.59 Aligned_cols=39 Identities=18% Similarity=0.318 Sum_probs=24.6
Q ss_pred EEECCCC--cEEEEEecCCCCe--EEeccCCC--CHHHHHHHHHH
Q 047455 129 VRQRPWG--KWAAEIRDPARRV--RLWLGTYD--TAEEAARVYDN 167 (367)
Q Consensus 129 Vr~r~~G--KW~AeIr~~~~~k--ri~LGtFd--T~EeAArAYD~ 167 (367)
|+-++.| .|..+-+.+.+|+ ++-||.|. |..+|..+-..
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 3444554 4998887554444 47899999 67666554433
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=30.49 E-value=92 Score=25.00 Aligned_cols=32 Identities=25% Similarity=0.514 Sum_probs=24.9
Q ss_pred cEEEEEecCCCCeEEeccCCCCHHHHHHHHHH
Q 047455 136 KWAAEIRDPARRVRLWLGTYDTAEEAARVYDN 167 (367)
Q Consensus 136 KW~AeIr~~~~~kri~LGtFdT~EeAArAYD~ 167 (367)
.|=++|.-..-.-..|.|-|.+.+||..+.-.
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~g 40 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPG 40 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhcc
Confidence 36688885444578899999999999988543
No 11
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=24.51 E-value=1e+02 Score=28.20 Aligned_cols=37 Identities=27% Similarity=0.198 Sum_probs=31.4
Q ss_pred cEEEEEecCCCCeEEeccCCCCHHHHHHHHHHHHHHHhCC
Q 047455 136 KWAAEIRDPARRVRLWLGTYDTAEEAARVYDNAAIKLRGP 175 (367)
Q Consensus 136 KW~AeIr~~~~~kri~LGtFdT~EeAArAYD~AAikl~G~ 175 (367)
-|+|.|. -|+-++-=....++.|..|..+|+.+|=+.
T Consensus 95 gwaArVk---pG~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 95 GWAARVK---PGRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEEec---CCcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 4999998 688888778889999999999999887654
No 12
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=23.89 E-value=2.3e+02 Score=22.55 Aligned_cols=34 Identities=24% Similarity=0.249 Sum_probs=21.8
Q ss_pred CcEEEEEecCCCCeEEeccCCCC--HHHHHHHHHHH
Q 047455 135 GKWAAEIRDPARRVRLWLGTYDT--AEEAARVYDNA 168 (367)
Q Consensus 135 GKW~AeIr~~~~~kri~LGtFdT--~EeAArAYD~A 168 (367)
..|..+.+...+.+++.||.|.. ..+|......+
T Consensus 35 kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~ 70 (89)
T PF13356_consen 35 KTFYFRYRINGKRRRITLGRYPELSLAEAREKAREL 70 (89)
T ss_dssp EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHH
T ss_pred eEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHH
Confidence 34888887644457889999964 45554444433
No 13
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=20.61 E-value=65 Score=27.91 Aligned_cols=19 Identities=21% Similarity=0.866 Sum_probs=14.6
Q ss_pred eEEeccCCCCHHHHHHHHH
Q 047455 148 VRLWLGTYDTAEEAARVYD 166 (367)
Q Consensus 148 kri~LGtFdT~EeAArAYD 166 (367)
..||||+|.++++-..=.+
T Consensus 2 VsiWiG~f~s~~el~~Y~e 20 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYFE 20 (122)
T ss_pred eEEEEecCCCHHHHHHHhC
Confidence 4699999999888665443
Done!