Query 039976
Match_columns 438
No_of_seqs 253 out of 1148
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 03:53:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039976.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039976hhsearch_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 7.8E-20 1.7E-24 141.9 8.2 64 191-254 1-64 (64)
2 cd00018 AP2 DNA-binding domain 99.8 1.1E-19 2.4E-24 139.2 7.6 61 190-250 1-61 (61)
3 PHA00280 putative NHN endonucl 99.4 1.7E-12 3.6E-17 114.5 7.7 59 184-245 61-120 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 3.3E-10 7.2E-15 84.8 5.9 52 190-241 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 75.9 10 0.00023 27.9 5.7 38 202-239 1-42 (46)
6 PHA02601 int integrase; Provis 62.7 11 0.00024 36.5 4.4 44 194-238 2-46 (333)
7 PF05036 SPOR: Sporulation rel 46.4 13 0.00027 28.2 1.5 24 212-235 42-65 (76)
8 cd00801 INT_P4 Bacteriophage P 45.4 47 0.001 31.6 5.6 40 200-239 9-50 (357)
9 PF08846 DUF1816: Domain of un 36.0 82 0.0018 26.2 4.8 38 202-239 9-46 (68)
10 PRK09692 integrase; Provisiona 35.7 94 0.002 31.5 6.2 39 195-233 33-77 (413)
11 PF08471 Ribonuc_red_2_N: Clas 32.9 44 0.00094 29.4 2.9 21 218-238 70-90 (93)
12 PF13356 DUF4102: Domain of un 29.6 1.5E+02 0.0033 24.1 5.5 37 202-238 36-74 (89)
13 PF03002 Somatostatin: Somatos 21.5 35 0.00076 22.0 0.2 9 422-430 6-14 (18)
14 COG0197 RplP Ribosomal protein 20.9 1.4E+02 0.003 28.1 4.1 36 203-241 96-131 (146)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.81 E-value=7.8e-20 Score=141.94 Aligned_cols=64 Identities=67% Similarity=1.181 Sum_probs=60.8
Q ss_pred ceeeeEECCCCcEEEEEeecCCCeEEeeCCCCCHHHHHHHHHHHHHHhhCCCCCCCCCcccccc
Q 039976 191 LYRGVRQRHWGKWVAEIRLPRNRTRLWLGTFDRAEDAALAYDREAFKLRGENARLNFPELFLNK 254 (438)
Q Consensus 191 ~YRGVR~R~~GKW~AeIr~p~~gKRiwLGTFdTaEEAArAYDrAAiklrG~~A~lNFP~~~~~k 254 (438)
+||||+++++|||+|+|+++.+++++|||+|+|+||||+|||.++++++|.++.+|||...|++
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 5999998889999999999889999999999999999999999999999999999999988853
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=99.80 E-value=1.1e-19 Score=139.20 Aligned_cols=61 Identities=69% Similarity=1.173 Sum_probs=57.3
Q ss_pred CceeeeEECCCCcEEEEEeecCCCeEEeeCCCCCHHHHHHHHHHHHHHhhCCCCCCCCCcc
Q 039976 190 KLYRGVRQRHWGKWVAEIRLPRNRTRLWLGTFDRAEDAALAYDREAFKLRGENARLNFPEL 250 (438)
Q Consensus 190 S~YRGVR~R~~GKW~AeIr~p~~gKRiwLGTFdTaEEAArAYDrAAiklrG~~A~lNFP~~ 250 (438)
|+||||+++++|||+|+|+++..++++|||+|+|+||||+|||+++++++|.++.+|||++
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 6899999888999999999855599999999999999999999999999999999999963
No 3
>PHA00280 putative NHN endonuclease
Probab=99.36 E-value=1.7e-12 Score=114.47 Aligned_cols=59 Identities=20% Similarity=0.278 Sum_probs=52.6
Q ss_pred CCCCCCCceeeeEE-CCCCcEEEEEeecCCCeEEeeCCCCCHHHHHHHHHHHHHHhhCCCCCC
Q 039976 184 QPLNTTKLYRGVRQ-RHWGKWVAEIRLPRNRTRLWLGTFDRAEDAALAYDREAFKLRGENARL 245 (438)
Q Consensus 184 ~p~nnsS~YRGVR~-R~~GKW~AeIr~p~~gKRiwLGTFdTaEEAArAYDrAAiklrG~~A~l 245 (438)
.+++|+|+|+||++ +..|||+|+|++ +||+++||.|+|+|+|+.||+ ++.+++|++|+.
T Consensus 61 ~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~~ 120 (121)
T PHA00280 61 TPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFARF 120 (121)
T ss_pred CCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence 45678999999975 457999999996 999999999999999999997 788999999863
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=99.05 E-value=3.3e-10 Score=84.77 Aligned_cols=52 Identities=37% Similarity=0.527 Sum_probs=44.9
Q ss_pred CceeeeEECC-CCcEEEEEeecC-C--CeEEeeCCCCCHHHHHHHHHHHHHHhhCC
Q 039976 190 KLYRGVRQRH-WGKWVAEIRLPR-N--RTRLWLGTFDRAEDAALAYDREAFKLRGE 241 (438)
Q Consensus 190 S~YRGVR~R~-~GKW~AeIr~p~-~--gKRiwLGTFdTaEEAArAYDrAAiklrG~ 241 (438)
|+|+||++.+ .++|+|.|++.. + +++++||.|++++||++||+.++++++|+
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 6899997554 899999999842 2 49999999999999999999999999875
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=75.85 E-value=10 Score=27.92 Aligned_cols=38 Identities=13% Similarity=0.144 Sum_probs=29.4
Q ss_pred cEEEEEe--ecCCC--eEEeeCCCCCHHHHHHHHHHHHHHhh
Q 039976 202 KWVAEIR--LPRNR--TRLWLGTFDRAEDAALAYDREAFKLR 239 (438)
Q Consensus 202 KW~AeIr--~p~~g--KRiwLGTFdTaEEAArAYDrAAiklr 239 (438)
+|...|. ++..| ++++-+.|.|..||..+...+...+.
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 44344 67888999999999999988776653
No 6
>PHA02601 int integrase; Provisional
Probab=62.71 E-value=11 Score=36.46 Aligned_cols=44 Identities=25% Similarity=0.338 Sum_probs=31.0
Q ss_pred eeEECCCCcEEEEEee-cCCCeEEeeCCCCCHHHHHHHHHHHHHHh
Q 039976 194 GVRQRHWGKWVAEIRL-PRNRTRLWLGTFDRAEDAALAYDREAFKL 238 (438)
Q Consensus 194 GVR~R~~GKW~AeIr~-p~~gKRiwLGTFdTaEEAArAYDrAAikl 238 (438)
+|++++.|+|+++|+. ...|+++.. +|.|..||....+.....+
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 5677778999999985 234676653 6999998876666544444
No 7
>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=46.42 E-value=13 Score=28.15 Aligned_cols=24 Identities=25% Similarity=0.346 Sum_probs=19.8
Q ss_pred CCeEEeeCCCCCHHHHHHHHHHHH
Q 039976 212 NRTRLWLGTFDRAEDAALAYDREA 235 (438)
Q Consensus 212 ~gKRiwLGTFdTaEEAArAYDrAA 235 (438)
..-+|.+|.|+|.+||..+..+..
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 445788999999999998887665
No 8
>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=45.38 E-value=47 Score=31.60 Aligned_cols=40 Identities=28% Similarity=0.350 Sum_probs=28.1
Q ss_pred CCcEEEEEeecCCCeEEeeCCCC--CHHHHHHHHHHHHHHhh
Q 039976 200 WGKWVAEIRLPRNRTRLWLGTFD--RAEDAALAYDREAFKLR 239 (438)
Q Consensus 200 ~GKW~AeIr~p~~gKRiwLGTFd--TaEEAArAYDrAAiklr 239 (438)
.+.|..+++.....+++.||+|+ |.++|....+.....+.
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 35699998874445668899995 67777777666555553
No 9
>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=35.98 E-value=82 Score=26.16 Aligned_cols=38 Identities=26% Similarity=0.406 Sum_probs=28.4
Q ss_pred cEEEEEeecCCCeEEeeCCCCCHHHHHHHHHHHHHHhh
Q 039976 202 KWVAEIRLPRNRTRLWLGTFDRAEDAALAYDREAFKLR 239 (438)
Q Consensus 202 KW~AeIr~p~~gKRiwLGTFdTaEEAArAYDrAAiklr 239 (438)
.|=++|.--.-.-.+|.|-|+|.+||..+.......+.
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 47788886444577899999999999988655444443
No 10
>PRK09692 integrase; Provisional
Probab=35.69 E-value=94 Score=31.55 Aligned_cols=39 Identities=21% Similarity=0.251 Sum_probs=24.7
Q ss_pred eEECCCC--cEEEEEeecCCCeE--EeeCCCC--CHHHHHHHHHH
Q 039976 195 VRQRHWG--KWVAEIRLPRNRTR--LWLGTFD--RAEDAALAYDR 233 (438)
Q Consensus 195 VR~R~~G--KW~AeIr~p~~gKR--iwLGTFd--TaEEAArAYDr 233 (438)
|+-++.| .|..+.+.+.+|++ +.||.|. |..+|..+..+
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 3444555 39988875544544 6899999 66666554444
No 11
>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=32.87 E-value=44 Score=29.36 Aligned_cols=21 Identities=38% Similarity=0.515 Sum_probs=18.8
Q ss_pred eCCCCCHHHHHHHHHHHHHHh
Q 039976 218 LGTFDRAEDAALAYDREAFKL 238 (438)
Q Consensus 218 LGTFdTaEEAArAYDrAAikl 238 (438)
-|+|+|+|+|..-||..+..|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 499999999999999988765
No 12
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=29.57 E-value=1.5e+02 Score=24.14 Aligned_cols=37 Identities=16% Similarity=0.201 Sum_probs=23.8
Q ss_pred cEEEEEeecCCCeEEeeCCCCC--HHHHHHHHHHHHHHh
Q 039976 202 KWVAEIRLPRNRTRLWLGTFDR--AEDAALAYDREAFKL 238 (438)
Q Consensus 202 KW~AeIr~p~~gKRiwLGTFdT--aEEAArAYDrAAikl 238 (438)
.|..+.+.....+++.||.|.+ ..+|.....+....+
T Consensus 36 t~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 36 TFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 4888887633446789999975 566655555444444
No 13
>PF03002 Somatostatin: Somatostatin/Cortistatin family; InterPro: IPR018142 Somatostatin inhibits the release of the pituitary growth hormone, somatotropin and inhibits the release of glucagon and insulin from the pancreas of fasted animals. Cortistatin is a cortical neuropeptide with neuronal depressant and sleep-modulating properties [].; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=21.54 E-value=35 Score=21.98 Aligned_cols=9 Identities=56% Similarity=1.154 Sum_probs=7.2
Q ss_pred CCCCccccC
Q 039976 422 PMKPFFWKD 430 (438)
Q Consensus 422 ~~~~~~~~~ 430 (438)
|-++||||.
T Consensus 6 ~CknffWK~ 14 (18)
T PF03002_consen 6 GCKNFFWKT 14 (18)
T ss_pred cccceeecc
Confidence 458999995
No 14
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=20.94 E-value=1.4e+02 Score=28.11 Aligned_cols=36 Identities=28% Similarity=0.191 Sum_probs=30.1
Q ss_pred EEEEEeecCCCeEEeeCCCCCHHHHHHHHHHHHHHhhCC
Q 039976 203 WVAEIRLPRNRTRLWLGTFDRAEDAALAYDREAFKLRGE 241 (438)
Q Consensus 203 W~AeIr~p~~gKRiwLGTFdTaEEAArAYDrAAiklrG~ 241 (438)
|+|+|. -|+.++-=..++++.|..|.-+|+.||=+.
T Consensus 96 waArVk---pG~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 96 WAARVK---PGRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEec---CCcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 999998 577777777888888999999999887443
Done!