Query 037347
Match_columns 295
No_of_seqs 229 out of 1125
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 11:19:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037347.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037347hhsearch_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 2.8E-20 6.2E-25 138.5 7.8 63 137-200 1-63 (64)
2 cd00018 AP2 DNA-binding domain 99.8 4.8E-20 1E-24 135.5 7.5 60 136-196 1-60 (61)
3 PHA00280 putative NHN endonucl 99.7 5.2E-17 1.1E-21 136.5 6.0 77 112-192 43-120 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 5.6E-11 1.2E-15 85.3 6.5 53 136-188 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 72.0 13 0.00028 25.8 5.2 39 148-186 1-42 (46)
6 PHA02601 int integrase; Provis 65.6 9.5 0.00021 35.3 4.4 45 140-185 2-46 (333)
7 PF08846 DUF1816: Domain of un 47.3 36 0.00078 26.5 4.2 30 148-178 9-38 (68)
8 cd00801 INT_P4 Bacteriophage P 41.0 62 0.0013 29.5 5.4 39 147-186 10-50 (357)
9 PF05036 SPOR: Sporulation rel 34.0 26 0.00057 25.1 1.5 23 160-182 43-65 (76)
10 PRK09692 integrase; Provisiona 31.8 1.3E+02 0.0029 29.1 6.4 43 141-183 33-80 (413)
11 PF08471 Ribonuc_red_2_N: Clas 31.1 52 0.0011 27.2 2.9 20 166-185 71-90 (93)
12 PF13356 DUF4102: Domain of un 31.0 1.4E+02 0.0029 23.1 5.2 42 142-184 28-73 (89)
13 cd04516 TBP_eukaryotes eukaryo 22.5 3.3E+02 0.0072 24.3 6.7 47 136-186 34-81 (174)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.82 E-value=2.8e-20 Score=138.49 Aligned_cols=63 Identities=68% Similarity=1.150 Sum_probs=59.4
Q ss_pred ceeeeEECCCCeEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCchhhh
Q 037347 137 HYRGVRRRPWGKYAAEIRDSSRKGARVWLGTFDTAEEAALAYDKAALRIRGPKAHLNFPLEEVA 200 (295)
Q Consensus 137 ~YRGV~~r~~GKW~A~Ir~~~~kGkri~LGtFdT~EEAArAYD~AAikl~G~~A~lNFP~~~~~ 200 (295)
+|+||+++++|||+|+|+++ .+|+++|||+|+|+||||+|||.++++++|.++.+|||.++|+
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 59999999999999999986 3689999999999999999999999999999999999999886
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=4.8e-20 Score=135.54 Aligned_cols=60 Identities=72% Similarity=1.223 Sum_probs=56.5
Q ss_pred CceeeeEECCCCeEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCc
Q 037347 136 RHYRGVRRRPWGKYAAEIRDSSRKGARVWLGTFDTAEEAALAYDKAALRIRGPKAHLNFPL 196 (295)
Q Consensus 136 S~YRGV~~r~~GKW~A~Ir~~~~kGkri~LGtFdT~EEAArAYD~AAikl~G~~A~lNFP~ 196 (295)
|+|+||+++++|||+|+|+++. .|+++|||+|+|+||||+|||.++++++|.++.+|||.
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~-~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~ 60 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPS-GGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPD 60 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCC-CCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCC
Confidence 6899999999999999999763 48999999999999999999999999999999999996
No 3
>PHA00280 putative NHN endonuclease
Probab=99.67 E-value=5.2e-17 Score=136.49 Aligned_cols=77 Identities=14% Similarity=0.167 Sum_probs=70.2
Q ss_pred CCCCCCCCCccccccccCCCCCCCCceeeeEECC-CCeEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHhcCCCC
Q 037347 112 TASSAEPGPNKMNAMRVEKVATPTRHYRGVRRRP-WGKYAAEIRDSSRKGARVWLGTFDTAEEAALAYDKAALRIRGPKA 190 (295)
Q Consensus 112 ~~snl~pat~k~N~~n~~~~~~~tS~YRGV~~r~-~GKW~A~Ir~~~~kGkri~LGtFdT~EEAArAYD~AAikl~G~~A 190 (295)
..+||+.+|+.+|++|++..+.|+|||+||++++ .|||+|+|+ .+||+++||.|+++|+|+.||+ ++.++||+||
T Consensus 43 ri~NLr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~---~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa 118 (121)
T PHA00280 43 ALDNLRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVT---AEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFA 118 (121)
T ss_pred cHHHhhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEE---ECCEEEEcCCCCCHHHHHHHHH-HHHHHhhccc
Confidence 4678999999999999999999999999999875 499999999 5699999999999999999997 7789999998
Q ss_pred CC
Q 037347 191 HL 192 (295)
Q Consensus 191 ~l 192 (295)
..
T Consensus 119 ~~ 120 (121)
T PHA00280 119 RF 120 (121)
T ss_pred cC
Confidence 63
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=99.18 E-value=5.6e-11 Score=85.28 Aligned_cols=53 Identities=34% Similarity=0.457 Sum_probs=46.1
Q ss_pred CceeeeEECC-CCeEEEEEecCCCCC--eEEecCCCCCHHHHHHHHHHHHHHhcCC
Q 037347 136 RHYRGVRRRP-WGKYAAEIRDSSRKG--ARVWLGTFDTAEEAALAYDKAALRIRGP 188 (295)
Q Consensus 136 S~YRGV~~r~-~GKW~A~Ir~~~~kG--kri~LGtFdT~EEAArAYD~AAikl~G~ 188 (295)
|+|+||++++ .++|+|+|++...+| ++++||.|++++||++||+.+++.++|+
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 6899999876 599999999853333 9999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=72.02 E-value=13 Score=25.84 Aligned_cols=39 Identities=21% Similarity=0.196 Sum_probs=29.1
Q ss_pred eEEEEEe--cC-CCCCeEEecCCCCCHHHHHHHHHHHHHHhc
Q 037347 148 KYAAEIR--DS-SRKGARVWLGTFDTAEEAALAYDKAALRIR 186 (295)
Q Consensus 148 KW~A~Ir--~~-~~kGkri~LGtFdT~EEAArAYD~AAikl~ 186 (295)
+|..+|. ++ ..+.++++-+-|.|..||-.+..++...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5777873 33 344477888999999999999888766553
No 6
>PHA02601 int integrase; Provisional
Probab=65.55 E-value=9.5 Score=35.32 Aligned_cols=45 Identities=29% Similarity=0.350 Sum_probs=31.1
Q ss_pred eeEECCCCeEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 037347 140 GVRRRPWGKYAAEIRDSSRKGARVWLGTFDTAEEAALAYDKAALRI 185 (295)
Q Consensus 140 GV~~r~~GKW~A~Ir~~~~kGkri~LGtFdT~EEAArAYD~AAikl 185 (295)
+|++.+.|+|+++++.....|+++.. +|.|..||-...+.....+
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 46667779999999853234777653 6999998876665554444
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=47.31 E-value=36 Score=26.51 Aligned_cols=30 Identities=30% Similarity=0.495 Sum_probs=23.7
Q ss_pred eEEEEEecCCCCCeEEecCCCCCHHHHHHHH
Q 037347 148 KYAAEIRDSSRKGARVWLGTFDTAEEAALAY 178 (295)
Q Consensus 148 KW~A~Ir~~~~kGkri~LGtFdT~EEAArAY 178 (295)
.|-++|.-.. -...+|.|-|.|.+||..+.
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 4778887543 23789999999999999873
No 8
>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=40.96 E-value=62 Score=29.49 Aligned_cols=39 Identities=23% Similarity=0.260 Sum_probs=27.4
Q ss_pred CeEEEEEecCCCCCeEEecCCCC--CHHHHHHHHHHHHHHhc
Q 037347 147 GKYAAEIRDSSRKGARVWLGTFD--TAEEAALAYDKAALRIR 186 (295)
Q Consensus 147 GKW~A~Ir~~~~kGkri~LGtFd--T~EEAArAYD~AAikl~ 186 (295)
+.|..+++... +.+++.||+|+ +.++|.....+....+.
T Consensus 10 ~~~~~~~~~~g-~~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 10 KSWRFRYRLAG-KRKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred EEEEEEeccCC-ceeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 56999998763 34678899996 67777777666555553
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=34.05 E-value=26 Score=25.06 Aligned_cols=23 Identities=39% Similarity=0.426 Sum_probs=19.0
Q ss_pred CeEEecCCCCCHHHHHHHHHHHH
Q 037347 160 GARVWLGTFDTAEEAALAYDKAA 182 (295)
Q Consensus 160 Gkri~LGtFdT~EEAArAYD~AA 182 (295)
--+|.+|.|++.++|..+-.+..
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 10
>PRK09692 integrase; Provisional
Probab=31.75 E-value=1.3e+02 Score=29.05 Aligned_cols=43 Identities=12% Similarity=0.096 Sum_probs=26.4
Q ss_pred eEECCCC--eEEEEEecCC-CCCeEEecCCCC--CHHHHHHHHHHHHH
Q 037347 141 VRRRPWG--KYAAEIRDSS-RKGARVWLGTFD--TAEEAALAYDKAAL 183 (295)
Q Consensus 141 V~~r~~G--KW~A~Ir~~~-~kGkri~LGtFd--T~EEAArAYD~AAi 183 (295)
|+.++.| .|..+-+.+. .+.+++-||.|+ |..+|..+..++..
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 4455654 4999887531 232347899999 67666555544433
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=31.11 E-value=52 Score=27.21 Aligned_cols=20 Identities=35% Similarity=0.556 Sum_probs=17.6
Q ss_pred CCCCCHHHHHHHHHHHHHHh
Q 037347 166 GTFDTAEEAALAYDKAALRI 185 (295)
Q Consensus 166 GtFdT~EEAArAYD~AAikl 185 (295)
|+|+|+|+|..-||..+..+
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999977654
No 12
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=30.97 E-value=1.4e+02 Score=23.12 Aligned_cols=42 Identities=24% Similarity=0.237 Sum_probs=25.5
Q ss_pred EECCCC--eEEEEEecCCCCCeEEecCCCCC--HHHHHHHHHHHHHH
Q 037347 142 RRRPWG--KYAAEIRDSSRKGARVWLGTFDT--AEEAALAYDKAALR 184 (295)
Q Consensus 142 ~~r~~G--KW~A~Ir~~~~kGkri~LGtFdT--~EEAArAYD~AAik 184 (295)
+..+.| .|..+.+.. .+.+++-||.|+. ..+|..........
T Consensus 28 ~v~~~G~kt~~~r~~~~-gk~~~~~lG~~p~~sl~~AR~~a~~~~~~ 73 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRIN-GKRRRITLGRYPELSLAEAREKARELRAL 73 (89)
T ss_dssp EE-TTS-EEEEEEEEET-TEEEEEEEEECTTS-HHHHHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEec-ceEEEeccCCCccCCHHHHHHHHHHHHHH
Confidence 344553 498888755 3446799999976 55555544444333
No 13
>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=22.50 E-value=3.3e+02 Score=24.31 Aligned_cols=47 Identities=28% Similarity=0.224 Sum_probs=36.5
Q ss_pred CceeeeEECC-CCeEEEEEecCCCCCeEEecCCCCCHHHHHHHHHHHHHHhc
Q 037347 136 RHYRGVRRRP-WGKYAAEIRDSSRKGARVWLGTFDTAEEAALAYDKAALRIR 186 (295)
Q Consensus 136 S~YRGV~~r~-~GKW~A~Ir~~~~kGkri~LGtFdT~EEAArAYD~AAikl~ 186 (295)
.+|-||..|- .-+=.+.|. ..||-+.-|.. ++|+|..|.++.+..+.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF---~SGKiviTGak-s~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIF---SSGKMVCTGAK-SEDDSKLAARKYARIIQ 81 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEE---CCCeEEEEecC-CHHHHHHHHHHHHHHHH
Confidence 5888987553 356678888 56898888876 88999999999887773
Done!