Query 042174
Match_columns 254
No_of_seqs 324 out of 1271
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 03:32:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042174.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042174hhsearch_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 5.3E-21 1.2E-25 137.9 7.2 61 96-157 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 5E-21 1.1E-25 139.7 7.0 63 97-160 1-63 (64)
3 PHA00280 putative NHN endonucl 99.5 1.3E-14 2.8E-19 119.6 6.5 62 86-151 57-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 2.1E-11 4.6E-16 85.7 6.5 53 96-148 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 82.4 4.9 0.00011 27.3 5.4 38 108-145 1-41 (46)
6 PHA02601 int integrase; Provis 74.6 4.9 0.00011 36.4 4.6 45 100-145 2-46 (333)
7 PF08846 DUF1816: Domain of un 45.6 42 0.00091 25.5 4.2 30 108-138 9-38 (68)
8 PF05036 SPOR: Sporulation rel 44.0 15 0.00033 25.7 1.6 23 120-142 43-65 (76)
9 PF08471 Ribonuc_red_2_N: Clas 35.5 39 0.00085 27.2 2.8 20 126-145 71-90 (93)
10 cd00801 INT_P4 Bacteriophage P 33.2 1.1E+02 0.0023 27.3 5.6 38 107-145 10-49 (357)
11 COG0197 RplP Ribosomal protein 30.4 71 0.0015 27.6 3.8 36 109-148 96-131 (146)
12 PRK09692 integrase; Provisiona 26.3 1.9E+02 0.0042 27.3 6.3 42 101-142 33-79 (413)
13 PF14112 DUF4284: Domain of un 22.8 57 0.0012 26.7 1.8 20 121-140 2-21 (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=5.3e-21 Score=137.85 Aligned_cols=61 Identities=66% Similarity=1.164 Sum_probs=57.0
Q ss_pred CceeEEEECCCCcEEEEEeeCCCCCeEEecCCCCcHHHHHHHHHHHHHHhcCCCCCCCCCch
Q 042174 96 KSYRGVRRRPWGKFAAEIRDSTRNGVRVWLGTFDSAEAAALAYDQAAFSMRGSLATLNFPAD 157 (254)
Q Consensus 96 S~YRGV~~r~~GKW~A~Ir~~~~~Gkrv~LGtFdT~EEAArAYD~AA~~~~G~~A~lNFp~~ 157 (254)
|+|+||+++++|||+|+|+++.+ |+++|||+|+|+||||+|||.|+++++|..+.+|||.+
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 68999999999999999999542 89999999999999999999999999999999999963
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.84 E-value=5e-21 Score=139.72 Aligned_cols=63 Identities=65% Similarity=1.153 Sum_probs=59.5
Q ss_pred ceeEEEECCCCcEEEEEeeCCCCCeEEecCCCCcHHHHHHHHHHHHHHhcCCCCCCCCCchhHH
Q 042174 97 SYRGVRRRPWGKFAAEIRDSTRNGVRVWLGTFDSAEAAALAYDQAAFSMRGSLATLNFPADMVR 160 (254)
Q Consensus 97 ~YRGV~~r~~GKW~A~Ir~~~~~Gkrv~LGtFdT~EEAArAYD~AA~~~~G~~A~lNFp~~~y~ 160 (254)
+|+||+++++|||+|+|+++. +|+++|||+|+|+||||+|||.|+++++|..+.+|||.+.|+
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~-~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPS-KGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecC-CCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 599999999999999999965 489999999999999999999999999999999999999885
No 3
>PHA00280 putative NHN endonuclease
Probab=99.53 E-value=1.3e-14 Score=119.60 Aligned_cols=62 Identities=15% Similarity=0.178 Sum_probs=54.2
Q ss_pred ccccCCCCCCCceeEEEECCC-CcEEEEEeeCCCCCeEEecCCCCcHHHHHHHHHHHHHHhcCCCCC
Q 042174 86 DHEVTSSTSNKSYRGVRRRPW-GKFAAEIRDSTRNGVRVWLGTFDSAEAAALAYDQAAFSMRGSLAT 151 (254)
Q Consensus 86 ~~~~~~~~~~S~YRGV~~r~~-GKW~A~Ir~~~~~Gkrv~LGtFdT~EEAArAYD~AA~~~~G~~A~ 151 (254)
.+...++.++|+|+||++++. |||+|+|+. +||+++||.|+++|+|+.||+ ++.+++|.+|.
T Consensus 57 ~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~---~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 57 WNMKTPKSNTSGLKGLSWSKEREMWRGTVTA---EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred cccCCCCCCCCCCCeeEEecCCCeEEEEEEE---CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 334556778999999997765 999999998 899999999999999999997 77889999874
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=2.1e-11 Score=85.73 Aligned_cols=53 Identities=32% Similarity=0.446 Sum_probs=46.6
Q ss_pred CceeEEEECCC-CcEEEEEeeCCCCC--eEEecCCCCcHHHHHHHHHHHHHHhcCC
Q 042174 96 KSYRGVRRRPW-GKFAAEIRDSTRNG--VRVWLGTFDSAEAAALAYDQAAFSMRGS 148 (254)
Q Consensus 96 S~YRGV~~r~~-GKW~A~Ir~~~~~G--krv~LGtFdT~EEAArAYD~AA~~~~G~ 148 (254)
|+|+||++++. ++|+|+|++...+| ++++||.|++++||++||+.++..++|+
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 68999998775 99999999954444 9999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=82.42 E-value=4.9 Score=27.31 Aligned_cols=38 Identities=13% Similarity=0.103 Sum_probs=28.9
Q ss_pred cEEEEEe--eC-CCCCeEEecCCCCcHHHHHHHHHHHHHHh
Q 042174 108 KFAAEIR--DS-TRNGVRVWLGTFDSAEAAALAYDQAAFSM 145 (254)
Q Consensus 108 KW~A~Ir--~~-~~~Gkrv~LGtFdT~EEAArAYD~AA~~~ 145 (254)
+|...|. ++ +.+.++++-+.|.|..||-.+..++...+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5778883 33 34447789999999999999988876655
No 6
>PHA02601 int integrase; Provisional
Probab=74.60 E-value=4.9 Score=36.38 Aligned_cols=45 Identities=24% Similarity=0.287 Sum_probs=31.8
Q ss_pred EEEECCCCcEEEEEeeCCCCCeEEecCCCCcHHHHHHHHHHHHHHh
Q 042174 100 GVRRRPWGKFAAEIRDSTRNGVRVWLGTFDSAEAAALAYDQAAFSM 145 (254)
Q Consensus 100 GV~~r~~GKW~A~Ir~~~~~Gkrv~LGtFdT~EEAArAYD~AA~~~ 145 (254)
+|++.+.|+|+++++.....|+++.. +|.|..||-...+.....+
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 56777789999999863234777664 6999998876666554444
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=45.57 E-value=42 Score=25.50 Aligned_cols=30 Identities=30% Similarity=0.444 Sum_probs=23.1
Q ss_pred cEEEEEeeCCCCCeEEecCCCCcHHHHHHHH
Q 042174 108 KFAAEIRDSTRNGVRVWLGTFDSAEAAALAY 138 (254)
Q Consensus 108 KW~A~Ir~~~~~Gkrv~LGtFdT~EEAArAY 138 (254)
.|-++|.-..- .-.+|.|-|+|.+||..+.
T Consensus 9 aWWveI~T~~P-~ctYyFGPF~s~~eA~~~~ 38 (68)
T PF08846_consen 9 AWWVEIETQNP-NCTYYFGPFDSREEAEAAL 38 (68)
T ss_pred cEEEEEEcCCC-CEEEEeCCcCCHHHHHHHh
Confidence 47788875322 3789999999999999873
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=44.02 E-value=15 Score=25.71 Aligned_cols=23 Identities=35% Similarity=0.375 Sum_probs=18.3
Q ss_pred CeEEecCCCCcHHHHHHHHHHHH
Q 042174 120 GVRVWLGTFDSAEAAALAYDQAA 142 (254)
Q Consensus 120 Gkrv~LGtFdT~EEAArAYD~AA 142 (254)
--+|.+|.|++.++|..+-.+..
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 35788899999999988877655
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=35.46 E-value=39 Score=27.20 Aligned_cols=20 Identities=30% Similarity=0.587 Sum_probs=17.9
Q ss_pred CCCCcHHHHHHHHHHHHHHh
Q 042174 126 GTFDSAEAAALAYDQAAFSM 145 (254)
Q Consensus 126 GtFdT~EEAArAYD~AA~~~ 145 (254)
|+|+|+|+|..-||..+..|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999877665
No 10
>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=33.23 E-value=1.1e+02 Score=27.35 Aligned_cols=38 Identities=21% Similarity=0.209 Sum_probs=26.1
Q ss_pred CcEEEEEeeCCCCCeEEecCCCC--cHHHHHHHHHHHHHHh
Q 042174 107 GKFAAEIRDSTRNGVRVWLGTFD--SAEAAALAYDQAAFSM 145 (254)
Q Consensus 107 GKW~A~Ir~~~~~Gkrv~LGtFd--T~EEAArAYD~AA~~~ 145 (254)
+.|..+++...+ .+++.||+|+ +.++|.....+....+
T Consensus 10 ~~~~~~~~~~g~-~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGK-RKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCc-eeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 569998888432 3567899995 6777777666655554
No 11
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=30.42 E-value=71 Score=27.64 Aligned_cols=36 Identities=22% Similarity=0.130 Sum_probs=31.0
Q ss_pred EEEEEeeCCCCCeEEecCCCCcHHHHHHHHHHHHHHhcCC
Q 042174 109 FAAEIRDSTRNGVRVWLGTFDSAEAAALAYDQAAFSMRGS 148 (254)
Q Consensus 109 W~A~Ir~~~~~Gkrv~LGtFdT~EEAArAYD~AA~~~~G~ 148 (254)
|+|+|.- |+.++-=..+.++.|..|.-+|+.+|=+.
T Consensus 96 waArVkp----G~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 96 WAARVKP----GRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEecC----CcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 9999975 78888888899999999999999988443
No 12
>PRK09692 integrase; Provisional
Probab=26.28 E-value=1.9e+02 Score=27.29 Aligned_cols=42 Identities=7% Similarity=0.074 Sum_probs=24.7
Q ss_pred EEECCCC--cEEEEEeeCC-CCCeEEecCCCC--cHHHHHHHHHHHH
Q 042174 101 VRRRPWG--KFAAEIRDST-RNGVRVWLGTFD--SAEAAALAYDQAA 142 (254)
Q Consensus 101 V~~r~~G--KW~A~Ir~~~-~~Gkrv~LGtFd--T~EEAArAYD~AA 142 (254)
|+-++.| .|..+-+.+. .+.+++-||.|. |..+|..+-.++.
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~ 79 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESR 79 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHH
Confidence 4444554 4888876532 222337899999 6666655444433
No 13
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=22.81 E-value=57 Score=26.71 Aligned_cols=20 Identities=25% Similarity=0.709 Sum_probs=15.0
Q ss_pred eEEecCCCCcHHHHHHHHHH
Q 042174 121 VRVWLGTFDSAEAAALAYDQ 140 (254)
Q Consensus 121 krv~LGtFdT~EEAArAYD~ 140 (254)
..||||+|.++++-..=.+.
T Consensus 2 VsiWiG~f~s~~el~~Y~e~ 21 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYFEI 21 (122)
T ss_pred eEEEEecCCCHHHHHHHhCc
Confidence 46999999998876655433
Done!