Query 047950
Match_columns 317
No_of_seqs 208 out of 1097
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 04:52:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047950.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047950hhsearch_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 3.4E-20 7.4E-25 139.4 8.3 64 156-219 1-64 (64)
2 cd00018 AP2 DNA-binding domain 99.8 6.2E-20 1.3E-24 136.3 7.7 61 155-215 1-61 (61)
3 PHA00280 putative NHN endonucl 99.3 2.7E-12 5.8E-17 109.2 7.3 54 153-209 65-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.0 5.2E-10 1.1E-14 81.1 5.8 52 155-206 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 75.3 11 0.00023 26.5 5.5 37 167-203 1-41 (46)
6 cd00018 AP2 DNA-binding domain 61.4 2.8 6.1E-05 30.8 0.1 26 274-300 6-31 (61)
7 smart00380 AP2 DNA-binding dom 56.9 3.4 7.4E-05 30.8 -0.1 24 277-300 7-30 (64)
8 PHA02601 int integrase; Provis 49.7 28 0.0006 32.6 4.7 44 159-203 2-46 (333)
9 cd00801 INT_P4 Bacteriophage P 42.7 48 0.001 30.6 5.1 38 166-203 10-49 (357)
10 PF08846 DUF1816: Domain of un 38.6 53 0.0011 25.8 3.9 37 167-203 9-45 (68)
11 PF05036 SPOR: Sporulation rel 32.5 52 0.0011 23.7 3.0 24 177-200 42-65 (76)
12 PRK09692 integrase; Provisiona 32.4 1.2E+02 0.0025 29.8 6.2 43 160-202 33-81 (413)
13 PF13356 DUF4102: Domain of un 32.0 1.3E+02 0.0029 23.4 5.4 43 161-203 28-74 (89)
14 PF08471 Ribonuc_red_2_N: Clas 26.8 67 0.0015 26.8 2.9 21 183-203 70-90 (93)
15 PF10729 CedA: Cell division a 22.8 1.4E+02 0.003 24.0 3.8 39 154-195 30-68 (80)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.82 E-value=3.4e-20 Score=139.44 Aligned_cols=64 Identities=63% Similarity=1.001 Sum_probs=61.1
Q ss_pred ceeeEEeCCCCcEEEEEeeCCCCeeecccCCCCHHHHHHHHHHHHHHhcCCCCcCCCCCCCCCC
Q 047950 156 NYRGVRKRPWGRWSAEIRDRIGRCRHWLGTFDTAEEAARAYDAAARRLRGSKARTNFEIPSVLP 219 (317)
Q Consensus 156 ~yRGVr~r~~GKW~A~Ir~~~~~kri~LGtFdT~EEAArAYD~AA~~~~G~~A~~NFp~s~y~~ 219 (317)
+|+||+++++|||+|+|+++.+++.+|||+|+|+||||+|||.|+++++|.++.+|||.++|++
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 5899998889999999999889999999999999999999999999999999999999999864
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=6.2e-20 Score=136.34 Aligned_cols=61 Identities=69% Similarity=1.119 Sum_probs=57.4
Q ss_pred CceeeEEeCCCCcEEEEEeeCCCCeeecccCCCCHHHHHHHHHHHHHHhcCCCCcCCCCCC
Q 047950 155 KNYRGVRKRPWGRWSAEIRDRIGRCRHWLGTFDTAEEAARAYDAAARRLRGSKARTNFEIP 215 (317)
Q Consensus 155 S~yRGVr~r~~GKW~A~Ir~~~~~kri~LGtFdT~EEAArAYD~AA~~~~G~~A~~NFp~s 215 (317)
|+|+||+++++|||+|+|+++..++++|||+|+|+||||+|||.|+++++|.++.+|||.+
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 6899999888899999999955599999999999999999999999999999999999974
No 3
>PHA00280 putative NHN endonuclease
Probab=99.33 E-value=2.7e-12 Score=109.15 Aligned_cols=54 Identities=22% Similarity=0.300 Sum_probs=49.2
Q ss_pred CCCceeeEEeC-CCCcEEEEEeeCCCCeeecccCCCCHHHHHHHHHHHHHHhcCCCCc
Q 047950 153 VQKNYRGVRKR-PWGRWSAEIRDRIGRCRHWLGTFDTAEEAARAYDAAARRLRGSKAR 209 (317)
Q Consensus 153 ~tS~yRGVr~r-~~GKW~A~Ir~~~~~kri~LGtFdT~EEAArAYD~AA~~~~G~~A~ 209 (317)
.+|+|+||++. ..|||+|+|++ +|++++||.|+++|+|+.||+ ++.+++|++|.
T Consensus 65 N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 65 NTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred CCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 48999999865 57999999998 999999999999999999997 78899999885
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=99.02 E-value=5.2e-10 Score=81.11 Aligned_cols=52 Identities=40% Similarity=0.568 Sum_probs=44.9
Q ss_pred CceeeEEeC-CCCcEEEEEeeCCC---CeeecccCCCCHHHHHHHHHHHHHHhcCC
Q 047950 155 KNYRGVRKR-PWGRWSAEIRDRIG---RCRHWLGTFDTAEEAARAYDAAARRLRGS 206 (317)
Q Consensus 155 S~yRGVr~r-~~GKW~A~Ir~~~~---~kri~LGtFdT~EEAArAYD~AA~~~~G~ 206 (317)
|+|+||++. ..++|+|+|++... +++++||.|+++|||++||+.+++.++|+
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 689999865 57999999998322 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=75.26 E-value=11 Score=26.51 Aligned_cols=37 Identities=22% Similarity=0.245 Sum_probs=28.9
Q ss_pred cEEEEEe--eCCCC--eeecccCCCCHHHHHHHHHHHHHHh
Q 047950 167 RWSAEIR--DRIGR--CRHWLGTFDTAEEAARAYDAAARRL 203 (317)
Q Consensus 167 KW~A~Ir--~~~~~--kri~LGtFdT~EEAArAYD~AA~~~ 203 (317)
+|...|. ++..| ++++-+.|.|..||..+...+...+
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 44344 7788899999999999988876665
No 6
>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=61.38 E-value=2.8 Score=30.80 Aligned_cols=26 Identities=8% Similarity=-0.134 Sum_probs=20.5
Q ss_pred cccchhhhhhhhhccccccccceeecc
Q 047950 274 GFDHHQAKRNAKAKDTNTLELDLKLGV 300 (317)
Q Consensus 274 ~~~hHq~~~~~~~~~~~~~~~dl~lg~ 300 (317)
|.+ |..|+|+|+|.-....+..+||+
T Consensus 6 V~~-~~~gkw~A~I~~~~~gk~~~lG~ 31 (61)
T cd00018 6 VRQ-RPWGKWVAEIRDPSGGRRIWLGT 31 (61)
T ss_pred EEE-CCCCcEEEEEEeCCCCceEccCC
Confidence 444 44599999999776788999997
No 7
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=56.94 E-value=3.4 Score=30.85 Aligned_cols=24 Identities=8% Similarity=-0.032 Sum_probs=20.1
Q ss_pred chhhhhhhhhccccccccceeecc
Q 047950 277 HHQAKRNAKAKDTNTLELDLKLGV 300 (317)
Q Consensus 277 hHq~~~~~~~~~~~~~~~dl~lg~ 300 (317)
.|..|+|+|+|.-....+..+||+
T Consensus 7 ~~~~gkw~A~I~~~~~~k~~~lG~ 30 (64)
T smart00380 7 QRPWGKWVAEIRDPSKGKRVWLGT 30 (64)
T ss_pred eCCCCeEEEEEEecCCCcEEecCC
Confidence 456699999998866789999997
No 8
>PHA02601 int integrase; Provisional
Probab=49.71 E-value=28 Score=32.65 Aligned_cols=44 Identities=27% Similarity=0.247 Sum_probs=29.5
Q ss_pred eEEeCCCCcEEEEEeeC-CCCeeecccCCCCHHHHHHHHHHHHHHh
Q 047950 159 GVRKRPWGRWSAEIRDR-IGRCRHWLGTFDTAEEAARAYDAAARRL 203 (317)
Q Consensus 159 GVr~r~~GKW~A~Ir~~-~~~kri~LGtFdT~EEAArAYD~AA~~~ 203 (317)
+|++.+.|+|+++++.. ..|+++.. +|.|..||....+.....+
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 56677789999999752 23566543 6999988876655544333
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=42.74 E-value=48 Score=30.60 Aligned_cols=38 Identities=29% Similarity=0.295 Sum_probs=27.4
Q ss_pred CcEEEEEeeCCCCeeecccCCC--CHHHHHHHHHHHHHHh
Q 047950 166 GRWSAEIRDRIGRCRHWLGTFD--TAEEAARAYDAAARRL 203 (317)
Q Consensus 166 GKW~A~Ir~~~~~kri~LGtFd--T~EEAArAYD~AA~~~ 203 (317)
+.|..+++.....+++.||+|+ +.++|....+.....+
T Consensus 10 ~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 4599998875555678899995 6777777766655555
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=38.60 E-value=53 Score=25.84 Aligned_cols=37 Identities=32% Similarity=0.565 Sum_probs=27.4
Q ss_pred cEEEEEeeCCCCeeecccCCCCHHHHHHHHHHHHHHh
Q 047950 167 RWSAEIRDRIGRCRHWLGTFDTAEEAARAYDAAARRL 203 (317)
Q Consensus 167 KW~A~Ir~~~~~kri~LGtFdT~EEAArAYD~AA~~~ 203 (317)
-|=++|.-..-....|.|=|++.+||..+..--...+
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL 45 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDL 45 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHH
Confidence 3668887645568899999999999998855433333
No 11
>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=32.46 E-value=52 Score=23.74 Aligned_cols=24 Identities=29% Similarity=0.327 Sum_probs=19.5
Q ss_pred CCeeecccCCCCHHHHHHHHHHHH
Q 047950 177 GRCRHWLGTFDTAEEAARAYDAAA 200 (317)
Q Consensus 177 ~~kri~LGtFdT~EEAArAYD~AA 200 (317)
..-+|.+|.|++.+||..+.....
T Consensus 42 ~~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 42 PWYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp TCEEEEECCECTCCHHHHHHHHHH
T ss_pred ceEEEEECCCCCHHHHHHHHHHHh
Confidence 446788999999999988877655
No 12
>PRK09692 integrase; Provisional
Probab=32.42 E-value=1.2e+02 Score=29.80 Aligned_cols=43 Identities=14% Similarity=0.228 Sum_probs=26.7
Q ss_pred EEeCCCC--cEEEEEeeCCCCee--ecccCCC--CHHHHHHHHHHHHHH
Q 047950 160 VRKRPWG--RWSAEIRDRIGRCR--HWLGTFD--TAEEAARAYDAAARR 202 (317)
Q Consensus 160 Vr~r~~G--KW~A~Ir~~~~~kr--i~LGtFd--T~EEAArAYD~AA~~ 202 (317)
|+-++.| .|..+.+.+.+|++ +-||.|. |..||..+-.++...
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~~ 81 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRSL 81 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHHH
Confidence 4444554 49998875544443 6899999 676766555444333
No 13
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=32.04 E-value=1.3e+02 Score=23.41 Aligned_cols=43 Identities=23% Similarity=0.183 Sum_probs=26.8
Q ss_pred EeCCCC--cEEEEEeeCCCCeeecccCCCC--HHHHHHHHHHHHHHh
Q 047950 161 RKRPWG--RWSAEIRDRIGRCRHWLGTFDT--AEEAARAYDAAARRL 203 (317)
Q Consensus 161 r~r~~G--KW~A~Ir~~~~~kri~LGtFdT--~EEAArAYD~AA~~~ 203 (317)
+-.+.| .|..+.+.....+++.||.|.. .+||..........+
T Consensus 28 ~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 344554 4998887744447789999965 666665555444444
No 14
>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=26.76 E-value=67 Score=26.80 Aligned_cols=21 Identities=38% Similarity=0.441 Sum_probs=18.2
Q ss_pred ccCCCCHHHHHHHHHHHHHHh
Q 047950 183 LGTFDTAEEAARAYDAAARRL 203 (317)
Q Consensus 183 LGtFdT~EEAArAYD~AA~~~ 203 (317)
-|+|+|+|+|..=||+.+..|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 599999999999999877654
No 15
>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=22.83 E-value=1.4e+02 Score=24.03 Aligned_cols=39 Identities=23% Similarity=0.270 Sum_probs=25.1
Q ss_pred CCceeeEEeCCCCcEEEEEeeCCCCeeecccCCCCHHHHHHH
Q 047950 154 QKNYRGVRKRPWGRWSAEIRDRIGRCRHWLGTFDTAEEAARA 195 (317)
Q Consensus 154 tS~yRGVr~r~~GKW~A~Ir~~~~~kri~LGtFdT~EEAArA 195 (317)
--+||.|+.- .|||+|.+.. +..-..--.|..+|.|-+=
T Consensus 30 ~dgfrdvw~l-rgkyvafvl~--ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 30 MDGFRDVWQL-RGKYVAFVLM--GEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTTECCECCC-CCEEEEEEES--SS-EEE---BSSHHHHHHH
T ss_pred cccccceeee-ccceEEEEEe--cchhccCCCcCCcHHHHHH
Confidence 4478888644 4899999977 5444445678888877653
Done!