Query 026385
Match_columns 239
No_of_seqs 220 out of 1181
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 07:21:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026385.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026385hhsearch_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 99.8 4.5E-21 9.8E-26 137.0 7.3 61 98-159 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 1E-20 2.3E-25 136.8 8.3 64 99-163 1-64 (64)
3 PHA00280 putative NHN endonucl 99.6 4.2E-15 9.2E-20 121.5 6.7 71 79-153 46-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 1.7E-11 3.8E-16 85.4 6.1 53 98-150 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 81.5 4.8 0.0001 27.1 5.0 39 110-148 1-42 (46)
6 PHA02601 int integrase; Provis 79.2 2.9 6.3E-05 37.4 4.3 45 102-147 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 51.7 38 0.00082 29.8 5.6 41 107-148 8-50 (357)
8 PF05036 SPOR: Sporulation rel 49.9 9.3 0.0002 26.6 1.2 22 123-144 44-65 (76)
9 PF08471 Ribonuc_red_2_N: Clas 44.4 24 0.00053 28.2 2.9 20 128-147 71-90 (93)
10 PRK09692 integrase; Provisiona 38.1 93 0.002 29.1 6.3 44 103-146 33-81 (413)
11 COG0197 RplP Ribosomal protein 36.9 49 0.0011 28.4 3.8 37 110-150 95-131 (146)
12 PF08846 DUF1816: Domain of un 32.9 97 0.0021 23.4 4.4 38 110-148 9-46 (68)
13 PRK09203 rplP 50S ribosomal pr 21.7 1.3E+02 0.0027 25.2 3.6 38 109-150 91-128 (138)
14 PF14112 DUF4284: Domain of un 21.4 56 0.0012 26.5 1.5 19 123-141 2-20 (122)
15 TIGR01164 rplP_bact ribosomal 21.4 1.4E+02 0.0031 24.5 3.9 35 109-147 90-124 (126)
16 CHL00044 rpl16 ribosomal prote 21.0 1.4E+02 0.0031 24.9 3.8 37 109-149 91-127 (135)
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=99.84 E-value=4.5e-21 Score=136.98 Aligned_cols=61 Identities=67% Similarity=1.225 Sum_probs=56.8
Q ss_pred ceeeeeEECCCCeeEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 026385 98 RHYRGVRRRPWGKYAAEIRDPNKKGTRVWLGTFNTAVEAAKAYDNAAFKMRGRKAILNFPLE 159 (239)
Q Consensus 98 S~YRGV~~r~~GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl~G~~A~lNFp~s 159 (239)
|+|+||+++++|||+|+|+++.. |+++|||+|+|+||||+|||.|+++++|.++.+|||++
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 68999998889999999999432 79999999999999999999999999999999999975
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.84 E-value=1e-20 Score=136.83 Aligned_cols=64 Identities=70% Similarity=1.215 Sum_probs=59.8
Q ss_pred eeeeeEECCCCeeEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCcCCC
Q 026385 99 HYRGVRRRPWGKYAAEIRDPNKKGTRVWLGTFNTAVEAAKAYDNAAFKMRGRKAILNFPLEIGEI 163 (239)
Q Consensus 99 ~YRGV~~r~~GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl~G~~A~lNFp~s~y~~ 163 (239)
+|+||+++++|||+|+|+++. +|+++|||+|+|+||||+|||.|+++++|.++.+|||.+.|+.
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~-~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~~ 64 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPS-KGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYDS 64 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecC-CCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCCC
Confidence 599999988999999999865 4799999999999999999999999999999999999999863
No 3
>PHA00280 putative NHN endonuclease
Probab=99.57 E-value=4.2e-15 Score=121.45 Aligned_cols=71 Identities=13% Similarity=0.083 Sum_probs=59.5
Q ss_pred cccccc--cchhhhhcccCCCceeeeeEECC-CCeeEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCCCC
Q 026385 79 IFRLKD--EDKDLEVADDYKERHYRGVRRRP-WGKYAAEIRDPNKKGTRVWLGTFNTAVEAAKAYDNAAFKMRGRKAI 153 (239)
Q Consensus 79 ~~~~~~--~~~~~~~~~~~~tS~YRGV~~r~-~GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl~G~~A~ 153 (239)
|+++.. ++..|++..++++|+|+||++.+ .|||+|+|++ +||+++||.|+++|+|+.||+ ++.+|+|.+|.
T Consensus 46 NLr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~---~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 46 NLRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA---EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred HhhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE---CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 444444 34456667789999999999655 5999999998 899999999999999999997 77899999885
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=99.24 E-value=1.7e-11 Score=85.37 Aligned_cols=53 Identities=30% Similarity=0.446 Sum_probs=45.6
Q ss_pred ceeeeeEECC-CCeeEEEEecCCCCC--cEEecCCCCCHHHHHHHHHHHHHHhcCC
Q 026385 98 RHYRGVRRRP-WGKYAAEIRDPNKKG--TRVWLGTFNTAVEAAKAYDNAAFKMRGR 150 (239)
Q Consensus 98 S~YRGV~~r~-~GKW~A~I~~~~~~G--kri~LGtFdT~EEAArAYD~AA~kl~G~ 150 (239)
|+|+||++.+ .++|+|+|++...+| ++++||.|++++||++||+.++.+++|+
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 6899999655 599999999853333 8999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=81.46 E-value=4.8 Score=27.12 Aligned_cols=39 Identities=18% Similarity=0.117 Sum_probs=29.5
Q ss_pred eeEEEEe-cC--CCCCcEEecCCCCCHHHHHHHHHHHHHHhc
Q 026385 110 KYAAEIR-DP--NKKGTRVWLGTFNTAVEAAKAYDNAAFKMR 148 (239)
Q Consensus 110 KW~A~I~-~~--~~~Gkri~LGtFdT~EEAArAYD~AA~kl~ 148 (239)
+|..+|. +. .++-++++-+-|.|..||-.+...+...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5777773 32 233367888999999999999998877764
No 6
>PHA02601 int integrase; Provisional
Probab=79.16 E-value=2.9 Score=37.44 Aligned_cols=45 Identities=27% Similarity=0.305 Sum_probs=32.0
Q ss_pred eeEECCCCeeEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHh
Q 026385 102 GVRRRPWGKYAAEIRDPNKKGTRVWLGTFNTAVEAAKAYDNAAFKM 147 (239)
Q Consensus 102 GV~~r~~GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl 147 (239)
+|++.+.|+|+++++.....|+++.. +|.|..||....+.....+
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 56677779999999864334676654 6999999877666655444
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=51.72 E-value=38 Score=29.85 Aligned_cols=41 Identities=22% Similarity=0.226 Sum_probs=28.0
Q ss_pred CCCeeEEEEecCCCCCcEEecCCCC--CHHHHHHHHHHHHHHhc
Q 026385 107 PWGKYAAEIRDPNKKGTRVWLGTFN--TAVEAAKAYDNAAFKMR 148 (239)
Q Consensus 107 ~~GKW~A~I~~~~~~Gkri~LGtFd--T~EEAArAYD~AA~kl~ 148 (239)
..+.|+.+++..++ .+++.||+|+ +.++|....+.....+.
T Consensus 8 g~~~~~~~~~~~g~-~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 8 GSKSWRFRYRLAGK-RKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred CCEEEEEEeccCCc-eeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 33579999888432 3567899995 67777777666555553
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=49.88 E-value=9.3 Score=26.57 Aligned_cols=22 Identities=32% Similarity=0.409 Sum_probs=19.0
Q ss_pred cEEecCCCCCHHHHHHHHHHHH
Q 026385 123 TRVWLGTFNTAVEAAKAYDNAA 144 (239)
Q Consensus 123 kri~LGtFdT~EEAArAYD~AA 144 (239)
-+|.+|.|++.++|..+-.+..
T Consensus 44 yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 44 YRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp EEEEECCECTCCHHHHHHHHHH
T ss_pred EEEEECCCCCHHHHHHHHHHHh
Confidence 4799999999999998877666
No 9
>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=44.39 E-value=24 Score=28.18 Aligned_cols=20 Identities=30% Similarity=0.562 Sum_probs=17.9
Q ss_pred CCCCCHHHHHHHHHHHHHHh
Q 026385 128 GTFNTAVEAAKAYDNAAFKM 147 (239)
Q Consensus 128 GtFdT~EEAArAYD~AA~kl 147 (239)
|+|+|++||..-||..+..|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999977654
No 10
>PRK09692 integrase; Provisional
Probab=38.05 E-value=93 Score=29.10 Aligned_cols=44 Identities=14% Similarity=0.162 Sum_probs=25.6
Q ss_pred eEECCCC--eeEEEEecC-CCCCcEEecCCCC--CHHHHHHHHHHHHHH
Q 026385 103 VRRRPWG--KYAAEIRDP-NKKGTRVWLGTFN--TAVEAAKAYDNAAFK 146 (239)
Q Consensus 103 V~~r~~G--KW~A~I~~~-~~~Gkri~LGtFd--T~EEAArAYD~AA~k 146 (239)
|+-++.| .|+.+.+.+ +++.+++-||.|. |..+|..+..++...
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 3334444 499888643 2222347899999 666665554444433
No 11
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=36.93 E-value=49 Score=28.43 Aligned_cols=37 Identities=22% Similarity=0.153 Sum_probs=32.6
Q ss_pred eeEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHhcCC
Q 026385 110 KYAAEIRDPNKKGTRVWLGTFNTAVEAAKAYDNAAFKMRGR 150 (239)
Q Consensus 110 KW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl~G~ 150 (239)
.|.|+|.. |+.++-=..++++.|..|.-+|+.||=+.
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 49999986 78888888899999999999999998665
No 12
>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=32.94 E-value=97 Score=23.37 Aligned_cols=38 Identities=21% Similarity=0.315 Sum_probs=27.4
Q ss_pred eeEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHhc
Q 026385 110 KYAAEIRDPNKKGTRVWLGTFNTAVEAAKAYDNAAFKMR 148 (239)
Q Consensus 110 KW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl~ 148 (239)
.|=++|.-..-+ -..|.|-|++.+||..+..--...+.
T Consensus 9 aWWveI~T~~P~-ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 9 AWWVEIETQNPN-CTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred cEEEEEEcCCCC-EEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 477888864433 57899999999999988654444443
No 13
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=21.67 E-value=1.3e+02 Score=25.25 Aligned_cols=38 Identities=18% Similarity=0.063 Sum_probs=29.8
Q ss_pred CeeEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHhcCC
Q 026385 109 GKYAAEIRDPNKKGTRVWLGTFNTAVEAAKAYDNAAFKMRGR 150 (239)
Q Consensus 109 GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl~G~ 150 (239)
-.|+|+|.. |+-++--.-.+++.|..|+.+|+.+|-+.
T Consensus 91 ~~~varVk~----G~iifEi~~~~~~~a~~al~~a~~KLP~~ 128 (138)
T PRK09203 91 EYWVAVVKP----GRILFEIAGVSEELAREALRLAAAKLPIK 128 (138)
T ss_pred cEEEEEECC----CCEEEEEeCCCHHHHHHHHHHHhccCCCc
Confidence 459999996 66655444489999999999999988554
No 14
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=21.43 E-value=56 Score=26.54 Aligned_cols=19 Identities=21% Similarity=0.747 Sum_probs=14.2
Q ss_pred cEEecCCCCCHHHHHHHHH
Q 026385 123 TRVWLGTFNTAVEAAKAYD 141 (239)
Q Consensus 123 kri~LGtFdT~EEAArAYD 141 (239)
..||||+|.+.+|-..=.+
T Consensus 2 VsiWiG~f~s~~el~~Y~e 20 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYFE 20 (122)
T ss_pred eEEEEecCCCHHHHHHHhC
Confidence 4699999999877655443
No 15
>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=21.37 E-value=1.4e+02 Score=24.52 Aligned_cols=35 Identities=20% Similarity=0.135 Sum_probs=28.0
Q ss_pred CeeEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHh
Q 026385 109 GKYAAEIRDPNKKGTRVWLGTFNTAVEAAKAYDNAAFKM 147 (239)
Q Consensus 109 GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl 147 (239)
-.|+|+|.. |+-++--.-.+++.|..|..+|+.+|
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 459999996 66665544489999999999999876
No 16
>CHL00044 rpl16 ribosomal protein L16
Probab=20.98 E-value=1.4e+02 Score=24.92 Aligned_cols=37 Identities=22% Similarity=0.125 Sum_probs=28.7
Q ss_pred CeeEEEEecCCCCCcEEecCCCCCHHHHHHHHHHHHHHhcC
Q 026385 109 GKYAAEIRDPNKKGTRVWLGTFNTAVEAAKAYDNAAFKMRG 149 (239)
Q Consensus 109 GKW~A~I~~~~~~Gkri~LGtFdT~EEAArAYD~AA~kl~G 149 (239)
--|.|.|.. |+-++=-.-.+++.|..|...|+.+|-+
T Consensus 91 ~~~va~V~~----G~ilfEi~g~~~~~ak~al~~a~~KLP~ 127 (135)
T CHL00044 91 EYWVAVVKP----GRILYEMGGVSETIARAAIKIAAYKMPI 127 (135)
T ss_pred cEEEEEECC----CcEEEEEeCCCHHHHHHHHHHHhhcCCC
Confidence 359999996 6666654457789999999999988754
Done!