Query 044938
Match_columns 271
No_of_seqs 295 out of 1198
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 08:16:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044938.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044938hhsearch_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 3.9E-21 8.5E-26 139.7 7.4 61 137-198 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 2.1E-20 4.4E-25 137.7 8.1 63 138-201 1-63 (64)
3 PHA00280 putative NHN endonucl 99.4 2.6E-13 5.7E-18 112.9 7.2 58 131-192 61-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 2.1E-11 4.6E-16 86.5 6.4 53 137-189 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 79.1 6.6 0.00014 27.0 5.2 39 149-187 1-42 (46)
6 PHA02601 int integrase; Provis 76.0 4.3 9.3E-05 37.1 4.6 45 141-186 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 53.0 27 0.00059 31.4 5.1 38 148-186 10-49 (357)
8 PF08846 DUF1816: Domain of un 44.5 40 0.00087 25.9 4.0 38 149-187 9-46 (68)
9 PF13356 DUF4102: Domain of un 42.6 60 0.0013 24.8 4.8 43 143-186 28-74 (89)
10 PRK09692 integrase; Provisiona 41.8 74 0.0016 30.4 6.3 40 142-181 33-77 (413)
11 PF05036 SPOR: Sporulation rel 39.1 21 0.00045 25.3 1.7 22 162-183 44-65 (76)
12 PF08471 Ribonuc_red_2_N: Clas 36.8 37 0.00079 27.7 2.9 20 167-186 71-90 (93)
13 PF10968 DUF2770: Protein of u 33.2 26 0.00057 24.0 1.3 10 20-29 8-17 (36)
14 COG0197 RplP Ribosomal protein 28.5 76 0.0017 27.8 3.7 38 148-189 94-131 (146)
15 PF14112 DUF4284: Domain of un 23.4 50 0.0011 27.4 1.6 18 162-179 2-19 (122)
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=3.9e-21 Score=139.74 Aligned_cols=61 Identities=70% Similarity=1.243 Sum_probs=56.8
Q ss_pred CcceeeEEcCCCceEEEEecCCCCCeEeecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 044938 137 KHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAYRMRGSRALLNFPLR 198 (271)
Q Consensus 137 S~YRGVr~r~~GKW~AeIr~~~k~Gkri~LGtFdT~EEAA~AYD~AA~~~~G~~A~lNFP~~ 198 (271)
|+||||+++++|||+|+|+++.. |+++|||+|+|+||||+|||+|+++++|.++.+|||++
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 68999999999999999999532 78999999999999999999999999999999999964
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.83 E-value=2.1e-20 Score=137.69 Aligned_cols=63 Identities=70% Similarity=1.231 Sum_probs=59.1
Q ss_pred cceeeEEcCCCceEEEEecCCCCCeEeecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q 044938 138 HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAYRMRGSRALLNFPLRINS 201 (271)
Q Consensus 138 ~YRGVr~r~~GKW~AeIr~~~k~Gkri~LGtFdT~EEAA~AYD~AA~~~~G~~A~lNFP~~~~~ 201 (271)
+|+||+++++|||+|+|+++.. |+++|||+|+|+||||+|||.|+++++|.++.+|||.+.|.
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~-~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSK-GKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCC-CcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 5999999999999999999754 68999999999999999999999999999999999998885
No 3
>PHA00280 putative NHN endonuclease
Probab=99.43 E-value=2.6e-13 Score=112.91 Aligned_cols=58 Identities=14% Similarity=0.145 Sum_probs=51.9
Q ss_pred CCCCCCCcceeeEEcC-CCceEEEEecCCCCCeEeecCCCCCHHHHHHHHHHHHHHhcCCCCC
Q 044938 131 VVPSRGKHYRGVRQRP-WGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAYRMRGSRAL 192 (271)
Q Consensus 131 ~~~~~~S~YRGVr~r~-~GKW~AeIr~~~k~Gkri~LGtFdT~EEAA~AYD~AA~~~~G~~A~ 192 (271)
..+.++|+|+||+|++ .|||+|+|+. +||+++||.|+++|+|+.||+ ++.++||+||.
T Consensus 61 ~~~~N~SG~kGV~~~k~~~kw~A~I~~---~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 61 TPKSNTSGLKGLSWSKEREMWRGTVTA---EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred CCCCCCCCCCeeEEecCCCeEEEEEEE---CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 3457789999999776 6999999998 899999999999999999997 77899999884
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=99.23 E-value=2.1e-11 Score=86.45 Aligned_cols=53 Identities=32% Similarity=0.443 Sum_probs=46.5
Q ss_pred CcceeeEEcC-CCceEEEEecCCCCC--eEeecCCCCCHHHHHHHHHHHHHHhcCC
Q 044938 137 KHYRGVRQRP-WGKFAAEIRDPAKNG--ARVWLGTFETAEDAALAYDRAAYRMRGS 189 (271)
Q Consensus 137 S~YRGVr~r~-~GKW~AeIr~~~k~G--kri~LGtFdT~EEAA~AYD~AA~~~~G~ 189 (271)
|+|+||++.+ .++|+|+|++...+| ++++||.|++++||++||+.++.+++|+
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 6899999776 699999999954443 8999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=79.07 E-value=6.6 Score=26.96 Aligned_cols=39 Identities=13% Similarity=0.138 Sum_probs=29.2
Q ss_pred ceEEEEe--cC-CCCCeEeecCCCCCHHHHHHHHHHHHHHhc
Q 044938 149 KFAAEIR--DP-AKNGARVWLGTFETAEDAALAYDRAAYRMR 187 (271)
Q Consensus 149 KW~AeIr--~~-~k~Gkri~LGtFdT~EEAA~AYD~AA~~~~ 187 (271)
+|..+|. ++ ..+-++++-+-|.|..||..+..+....+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5888883 32 233367899999999999999988776653
No 6
>PHA02601 int integrase; Provisional
Probab=75.98 E-value=4.3 Score=37.11 Aligned_cols=45 Identities=24% Similarity=0.302 Sum_probs=31.4
Q ss_pred eeEEcCCCceEEEEecCCCCCeEeecCCCCCHHHHHHHHHHHHHHh
Q 044938 141 GVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAYRM 186 (271)
Q Consensus 141 GVr~r~~GKW~AeIr~~~k~Gkri~LGtFdT~EEAA~AYD~AA~~~ 186 (271)
+|++.++|+|+++++.....|+|+.. +|.|..||....+.....+
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 56667789999999864334777654 6999998876665544443
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=53.00 E-value=27 Score=31.37 Aligned_cols=38 Identities=21% Similarity=0.251 Sum_probs=27.2
Q ss_pred CceEEEEecCCCCCeEeecCCCC--CHHHHHHHHHHHHHHh
Q 044938 148 GKFAAEIRDPAKNGARVWLGTFE--TAEDAALAYDRAAYRM 186 (271)
Q Consensus 148 GKW~AeIr~~~k~Gkri~LGtFd--T~EEAA~AYD~AA~~~ 186 (271)
+.|..+++..+++ +++.||+|+ +.++|.....+....+
T Consensus 10 ~~~~~~~~~~g~~-~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGKR-KRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCce-eEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 5699999986544 678899995 6777776666654444
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=44.52 E-value=40 Score=25.90 Aligned_cols=38 Identities=21% Similarity=0.338 Sum_probs=27.9
Q ss_pred ceEEEEecCCCCCeEeecCCCCCHHHHHHHHHHHHHHhc
Q 044938 149 KFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAYRMR 187 (271)
Q Consensus 149 KW~AeIr~~~k~Gkri~LGtFdT~EEAA~AYD~AA~~~~ 187 (271)
.|-++|.-..-+ -..|.|-|+|.+||..+.-.-...+.
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 57899999999999988655444443
No 9
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=42.57 E-value=60 Score=24.77 Aligned_cols=43 Identities=23% Similarity=0.251 Sum_probs=26.5
Q ss_pred EEcCCC--ceEEEEecCCCCCeEeecCCCCC--HHHHHHHHHHHHHHh
Q 044938 143 RQRPWG--KFAAEIRDPAKNGARVWLGTFET--AEDAALAYDRAAYRM 186 (271)
Q Consensus 143 r~r~~G--KW~AeIr~~~k~Gkri~LGtFdT--~EEAA~AYD~AA~~~ 186 (271)
+..+.| .|..+.+...+. +++-||.|.. ..+|..........+
T Consensus 28 ~v~~~G~kt~~~r~~~~gk~-~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGKR-RRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EE-TTS-EEEEEEEEETTEE-EEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecceE-EEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 455654 499888875432 6799999976 555555554444333
No 10
>PRK09692 integrase; Provisional
Probab=41.84 E-value=74 Score=30.39 Aligned_cols=40 Identities=20% Similarity=0.221 Sum_probs=25.3
Q ss_pred eEEcCCCc--eEEEEecCC-CCCeEeecCCCC--CHHHHHHHHHH
Q 044938 142 VRQRPWGK--FAAEIRDPA-KNGARVWLGTFE--TAEDAALAYDR 181 (271)
Q Consensus 142 Vr~r~~GK--W~AeIr~~~-k~Gkri~LGtFd--T~EEAA~AYD~ 181 (271)
|+.++.|. |..+.+.+. ++.+++-||.|. |..+|..+..+
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 45566654 999887542 222347899999 66666554444
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=39.15 E-value=21 Score=25.28 Aligned_cols=22 Identities=32% Similarity=0.480 Sum_probs=18.5
Q ss_pred eEeecCCCCCHHHHHHHHHHHH
Q 044938 162 ARVWLGTFETAEDAALAYDRAA 183 (271)
Q Consensus 162 kri~LGtFdT~EEAA~AYD~AA 183 (271)
-||.+|.|+|.++|..+-.+..
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 5799999999999988877655
No 12
>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=36.82 E-value=37 Score=27.70 Aligned_cols=20 Identities=45% Similarity=0.710 Sum_probs=17.9
Q ss_pred CCCCCHHHHHHHHHHHHHHh
Q 044938 167 GTFETAEDAALAYDRAAYRM 186 (271)
Q Consensus 167 GtFdT~EEAA~AYD~AA~~~ 186 (271)
|+|+|+|+|..=||..+..+
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999877654
No 13
>PF10968 DUF2770: Protein of unknown function (DUF2770); InterPro: IPR024494 Members in this family of proteins from Enterobacteria are annotated as YceO; however, currently no function is known.
Probab=33.24 E-value=26 Score=23.97 Aligned_cols=10 Identities=30% Similarity=0.999 Sum_probs=8.8
Q ss_pred hhHHHHHHhh
Q 044938 20 VLDSVRQHLL 29 (271)
Q Consensus 20 ~l~sir~hLl 29 (271)
+++.||+||+
T Consensus 8 ~inNiReHlm 17 (36)
T PF10968_consen 8 LINNIREHLM 17 (36)
T ss_pred HHHHHHHHHH
Confidence 5789999997
No 14
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=28.48 E-value=76 Score=27.76 Aligned_cols=38 Identities=24% Similarity=0.152 Sum_probs=31.6
Q ss_pred CceEEEEecCCCCCeEeecCCCCCHHHHHHHHHHHHHHhcCC
Q 044938 148 GKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAYRMRGS 189 (271)
Q Consensus 148 GKW~AeIr~~~k~Gkri~LGtFdT~EEAA~AYD~AA~~~~G~ 189 (271)
-.|+|+|.. |+.++-=..+.++.|..|..+|+.++=+.
T Consensus 94 egwaArVkp----G~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 94 EGWAARVKP----GRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred cEEEEEecC----CcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 349999986 67788778889999999999999887554
No 15
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=23.41 E-value=50 Score=27.35 Aligned_cols=18 Identities=17% Similarity=0.761 Sum_probs=13.8
Q ss_pred eEeecCCCCCHHHHHHHH
Q 044938 162 ARVWLGTFETAEDAALAY 179 (271)
Q Consensus 162 kri~LGtFdT~EEAA~AY 179 (271)
..||||+|.|.++-..=.
T Consensus 2 VsiWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYF 19 (122)
T ss_pred eEEEEecCCCHHHHHHHh
Confidence 469999999987765443
Done!