Query 026240
Match_columns 241
No_of_seqs 267 out of 1182
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 05:26:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026240.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026240hhsearch_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 5.2E-21 1.1E-25 138.6 8.2 63 25-87 1-63 (64)
2 cd00018 AP2 DNA-binding domain 99.8 5E-21 1.1E-25 137.0 7.3 61 24-84 1-61 (61)
3 PHA00280 putative NHN endonucl 99.5 1.4E-14 3.1E-19 118.5 6.3 66 10-78 53-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 6.3E-11 1.4E-15 82.6 5.2 52 24-75 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 81.4 5.4 0.00012 26.9 5.3 38 36-73 1-42 (46)
6 PHA02601 int integrase; Provis 67.2 8.1 0.00017 34.7 4.2 44 28-72 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 65.7 16 0.00034 32.3 5.7 40 34-73 9-50 (357)
8 PF05036 SPOR: Sporulation rel 50.0 13 0.00027 25.9 1.9 24 46-69 42-65 (76)
9 PF13356 DUF4102: Domain of un 48.9 56 0.0012 24.5 5.4 43 30-72 28-74 (89)
10 PF08471 Ribonuc_red_2_N: Clas 39.2 33 0.00071 27.5 2.9 21 52-72 70-90 (93)
11 PF08846 DUF1816: Domain of un 36.8 73 0.0016 24.0 4.3 37 37-73 10-46 (68)
12 PRK09692 integrase; Provisiona 31.3 1.4E+02 0.003 28.0 6.2 39 29-67 33-77 (413)
13 PF14112 DUF4284: Domain of un 29.0 39 0.00085 27.4 1.9 18 49-66 3-20 (122)
14 PRK10927 essential cell divisi 20.4 1.5E+02 0.0033 28.6 4.3 34 37-70 273-306 (319)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.84 E-value=5.2e-21 Score=138.60 Aligned_cols=63 Identities=67% Similarity=1.146 Sum_probs=60.5
Q ss_pred eeeEEEECCCCcEEEEEecCCCCeEEeeCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCCc
Q 026240 25 HFRGVRKRPWGRYAAEIRDPGKKSRVWLGTFDTAEEAARAYDAAAREFRGAKAKTNFPLPSEN 87 (241)
Q Consensus 25 ~YRGV~~~~~GRW~A~I~~~~kkkri~LGtFdT~EEAArAYD~AA~k~~G~~A~lNFP~~~~~ 87 (241)
+|+||+++++|||+|+|+++.+++++|||+|+|+||||+|||.++++++|.++.+|||.++|+
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 599999999999999999988899999999999999999999999999999999999999886
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=99.84 E-value=5e-21 Score=136.97 Aligned_cols=61 Identities=64% Similarity=1.123 Sum_probs=57.4
Q ss_pred ceeeEEEECCCCcEEEEEecCCCCeEEeeCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 026240 24 VHFRGVRKRPWGRYAAEIRDPGKKSRVWLGTFDTAEEAARAYDAAAREFRGAKAKTNFPLP 84 (241)
Q Consensus 24 S~YRGV~~~~~GRW~A~I~~~~kkkri~LGtFdT~EEAArAYD~AA~k~~G~~A~lNFP~~ 84 (241)
|+|+||+++++|||+|+|+.+..++++|||+|+|+|||++|||.++++++|.++.+|||.+
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 5799999999999999999966689999999999999999999999999999999999863
No 3
>PHA00280 putative NHN endonuclease
Probab=99.53 E-value=1.4e-14 Score=118.45 Aligned_cols=66 Identities=14% Similarity=0.129 Sum_probs=59.0
Q ss_pred ccccCCCCCCCCCCceeeEEEECC-CCcEEEEEecCCCCeEEeeCCCCCHHHHHHHHHHHHHHhcCCCCC
Q 026240 10 PAKVNGNSNGIVKEVHFRGVRKRP-WGRYAAEIRDPGKKSRVWLGTFDTAEEAARAYDAAAREFRGAKAK 78 (241)
Q Consensus 10 ~~~s~~~~~~~~~tS~YRGV~~~~-~GRW~A~I~~~~kkkri~LGtFdT~EEAArAYD~AA~k~~G~~A~ 78 (241)
..++.|....++++|+|+||+|++ .|||+|+|+. .+|+++||.|+++|+|+.||+ +++++||++|.
T Consensus 53 ~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 53 KENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred HHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 456677777888999999999876 6999999999 899999999999999999997 78899999875
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=99.15 E-value=6.3e-11 Score=82.65 Aligned_cols=52 Identities=35% Similarity=0.486 Sum_probs=45.4
Q ss_pred ceeeEEEECC-CCcEEEEEecCCC---CeEEeeCCCCCHHHHHHHHHHHHHHhcCC
Q 026240 24 VHFRGVRKRP-WGRYAAEIRDPGK---KSRVWLGTFDTAEEAARAYDAAAREFRGA 75 (241)
Q Consensus 24 S~YRGV~~~~-~GRW~A~I~~~~k---kkri~LGtFdT~EEAArAYD~AA~k~~G~ 75 (241)
|+|+||++++ .++|+|+|++... +++++||.|+++|||+++|+.+.++++|+
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 5799998877 7999999998321 48999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=81.44 E-value=5.4 Score=26.91 Aligned_cols=38 Identities=24% Similarity=0.315 Sum_probs=29.5
Q ss_pred cEEEEEe--cC--CCCeEEeeCCCCCHHHHHHHHHHHHHHhc
Q 026240 36 RYAAEIR--DP--GKKSRVWLGTFDTAEEAARAYDAAAREFR 73 (241)
Q Consensus 36 RW~A~I~--~~--~kkkri~LGtFdT~EEAArAYD~AA~k~~ 73 (241)
+|..+|. ++ ++.++++-+-|.|..||..+......++.
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 34578899999999999999988776653
No 6
>PHA02601 int integrase; Provisional
Probab=67.18 E-value=8.1 Score=34.67 Aligned_cols=44 Identities=27% Similarity=0.262 Sum_probs=30.1
Q ss_pred EEEECCCCcEEEEEecC-CCCeEEeeCCCCCHHHHHHHHHHHHHHh
Q 026240 28 GVRKRPWGRYAAEIRDP-GKKSRVWLGTFDTAEEAARAYDAAAREF 72 (241)
Q Consensus 28 GV~~~~~GRW~A~I~~~-~kkkri~LGtFdT~EEAArAYD~AA~k~ 72 (241)
+|++.++|+|+++|+.. ..++++. .+|.|..||....+....++
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~-~~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIR-KRFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhh-hhhcCHHHHHHHHHHHHHhc
Confidence 46777789999999863 1244544 36999999877666554444
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=65.70 E-value=16 Score=32.34 Aligned_cols=40 Identities=25% Similarity=0.313 Sum_probs=30.8
Q ss_pred CCcEEEEEecCCCCeEEeeCCCC--CHHHHHHHHHHHHHHhc
Q 026240 34 WGRYAAEIRDPGKKSRVWLGTFD--TAEEAARAYDAAAREFR 73 (241)
Q Consensus 34 ~GRW~A~I~~~~kkkri~LGtFd--T~EEAArAYD~AA~k~~ 73 (241)
.+.|..+++..++.+++.||+|+ +.++|..........+.
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 45699999998888889999995 77787777766555553
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=49.98 E-value=13 Score=25.91 Aligned_cols=24 Identities=33% Similarity=0.369 Sum_probs=19.7
Q ss_pred CCeEEeeCCCCCHHHHHHHHHHHH
Q 026240 46 KKSRVWLGTFDTAEEAARAYDAAA 69 (241)
Q Consensus 46 kkkri~LGtFdT~EEAArAYD~AA 69 (241)
..-++++|.|+|.+||..+-.+..
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 345799999999999988887655
No 9
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=48.95 E-value=56 Score=24.48 Aligned_cols=43 Identities=23% Similarity=0.265 Sum_probs=29.0
Q ss_pred EECCC--CcEEEEEecCCCCeEEeeCCCCC--HHHHHHHHHHHHHHh
Q 026240 30 RKRPW--GRYAAEIRDPGKKSRVWLGTFDT--AEEAARAYDAAAREF 72 (241)
Q Consensus 30 ~~~~~--GRW~A~I~~~~kkkri~LGtFdT--~EEAArAYD~AA~k~ 72 (241)
+-.+. ..|.-+.+..++.+++.||.|.+ .+||..........+
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 44454 35999998877778999999965 666665555444444
No 10
>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=39.21 E-value=33 Score=27.47 Aligned_cols=21 Identities=33% Similarity=0.404 Sum_probs=17.9
Q ss_pred eCCCCCHHHHHHHHHHHHHHh
Q 026240 52 LGTFDTAEEAARAYDAAAREF 72 (241)
Q Consensus 52 LGtFdT~EEAArAYD~AA~k~ 72 (241)
-|+|+|+|+|..-||.....+
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 499999999999999876554
No 11
>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=36.75 E-value=73 Score=24.03 Aligned_cols=37 Identities=24% Similarity=0.424 Sum_probs=27.7
Q ss_pred EEEEEecCCCCeEEeeCCCCCHHHHHHHHHHHHHHhc
Q 026240 37 YAAEIRDPGKKSRVWLGTFDTAEEAARAYDAAAREFR 73 (241)
Q Consensus 37 W~A~I~~~~kkkri~LGtFdT~EEAArAYD~AA~k~~ 73 (241)
|=++|.-..-+-..|-|=|+|.+||..+.-.-...+.
T Consensus 10 WWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 10 WWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred EEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 6678887555567899999999999988655444443
No 12
>PRK09692 integrase; Provisional
Probab=31.32 E-value=1.4e+02 Score=28.02 Aligned_cols=39 Identities=10% Similarity=0.139 Sum_probs=24.5
Q ss_pred EEECCC--CcEEEEEecC--CCCeEEeeCCCC--CHHHHHHHHHH
Q 026240 29 VRKRPW--GRYAAEIRDP--GKKSRVWLGTFD--TAEEAARAYDA 67 (241)
Q Consensus 29 V~~~~~--GRW~A~I~~~--~kkkri~LGtFd--T~EEAArAYD~ 67 (241)
|+-++. ..|..+.+.+ ++.+++.||.|. |..||..+-.+
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 344454 4499888754 344457899999 66666554443
No 13
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=28.97 E-value=39 Score=27.44 Aligned_cols=18 Identities=22% Similarity=0.872 Sum_probs=13.9
Q ss_pred EEeeCCCCCHHHHHHHHH
Q 026240 49 RVWLGTFDTAEEAARAYD 66 (241)
Q Consensus 49 ri~LGtFdT~EEAArAYD 66 (241)
.||||+|.+++|=..=.+
T Consensus 3 siWiG~f~s~~el~~Y~e 20 (122)
T PF14112_consen 3 SIWIGNFKSEDELEEYFE 20 (122)
T ss_pred EEEEecCCCHHHHHHHhC
Confidence 599999999887655443
No 14
>PRK10927 essential cell division protein FtsN; Provisional
Probab=20.36 E-value=1.5e+02 Score=28.56 Aligned_cols=34 Identities=18% Similarity=0.258 Sum_probs=26.0
Q ss_pred EEEEEecCCCCeEEeeCCCCCHHHHHHHHHHHHH
Q 026240 37 YAAEIRDPGKKSRVWLGTFDTAEEAARAYDAAAR 70 (241)
Q Consensus 37 W~A~I~~~~kkkri~LGtFdT~EEAArAYD~AA~ 70 (241)
|.|+|...+.-.||.||=|.+.++|.++.++...
T Consensus 273 ~~A~I~~~g~~~RVrVGPf~sr~eAe~a~~rLk~ 306 (319)
T PRK10927 273 FDSKITTNNGWNRVVIGPVKGKENADSTLNRLKM 306 (319)
T ss_pred CeeEEccCCcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence 5667755444468999999999999999876544
Done!