Query 019546
Match_columns 339
No_of_seqs 249 out of 1159
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 02:37:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019546.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019546hhsearch_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 1.1E-20 2.3E-25 141.7 7.8 61 78-138 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 2.7E-20 5.9E-25 141.2 8.3 63 79-141 1-63 (64)
3 PHA00280 putative NHN endonucl 99.4 2.8E-13 6.1E-18 116.1 7.6 68 63-133 52-120 (121)
4 PF00847 AP2: AP2 domain; Int 99.0 4.7E-10 1E-14 82.1 5.7 52 78-129 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 67.7 21 0.00044 25.4 5.6 37 90-126 1-41 (46)
6 PHA02601 int integrase; Provis 52.4 23 0.00049 33.6 4.6 44 82-126 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 45.4 39 0.00085 31.5 5.0 39 88-126 9-49 (357)
8 PF05036 SPOR: Sporulation rel 33.5 35 0.00076 25.0 2.2 24 100-123 42-65 (76)
9 PRK09692 integrase; Provisiona 31.2 1.3E+02 0.0028 29.8 6.4 42 83-124 33-80 (413)
10 PF08846 DUF1816: Domain of un 29.1 93 0.002 24.7 3.9 37 90-126 9-45 (68)
11 COG0197 RplP Ribosomal protein 28.0 81 0.0018 28.5 3.9 37 90-129 95-131 (146)
12 PF10729 CedA: Cell division a 26.8 1.2E+02 0.0026 24.6 4.2 38 78-118 31-68 (80)
13 PF13356 DUF4102: Domain of un 24.2 2.2E+02 0.0047 22.4 5.4 32 89-120 35-68 (89)
14 PF08471 Ribonuc_red_2_N: Clas 22.3 91 0.002 26.3 2.9 21 106-126 70-90 (93)
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=99.83 E-value=1.1e-20 Score=141.66 Aligned_cols=61 Identities=64% Similarity=1.121 Sum_probs=57.8
Q ss_pred CCceeEEECCCCcEEEEEeecCCCcEeeccCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 019546 78 CDYRGVRQRTWGKWVAEIREPNRGNRLWLGTFPSAVEAALAYDHAARAMYGPCARLNLPDV 138 (339)
Q Consensus 78 S~YRGVr~r~~GKW~A~Ir~~~~gkrv~LGtFdT~EEAArAYD~AA~k~~G~~A~~NFP~~ 138 (339)
|+|+||+++++|||+|+|+++..++++|||+|+|+||||+|||.|+++++|..+.+|||++
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 6899999888999999999866699999999999999999999999999999999999975
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.82 E-value=2.7e-20 Score=141.21 Aligned_cols=63 Identities=62% Similarity=1.063 Sum_probs=60.2
Q ss_pred CceeEEECCCCcEEEEEeecCCCcEeeccCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCccC
Q 019546 79 DYRGVRQRTWGKWVAEIREPNRGNRLWLGTFPSAVEAALAYDHAARAMYGPCARLNLPDVSRL 141 (339)
Q Consensus 79 ~YRGVr~r~~GKW~A~Ir~~~~gkrv~LGtFdT~EEAArAYD~AA~k~~G~~A~~NFP~~~~~ 141 (339)
+|+||+++++|||+|+|+++.+++++|||+|+|+||||+|||.|+++++|..+.+|||.+.|.
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 599999888999999999988999999999999999999999999999999999999998874
No 3
>PHA00280 putative NHN endonuclease
Probab=99.43 E-value=2.8e-13 Score=116.10 Aligned_cols=68 Identities=16% Similarity=0.224 Sum_probs=60.8
Q ss_pred cccccCCCCCCCCCCCCceeEEEC-CCCcEEEEEeecCCCcEeeccCCCCHHHHHHHHHHHHHHhcCCCCCC
Q 019546 63 KKGCMKGKGGPENGRCDYRGVRQR-TWGKWVAEIREPNRGNRLWLGTFPSAVEAALAYDHAARAMYGPCARL 133 (339)
Q Consensus 63 ~~~~~r~~~g~~~~~S~YRGVr~r-~~GKW~A~Ir~~~~gkrv~LGtFdT~EEAArAYD~AA~k~~G~~A~~ 133 (339)
....++|++..++++|+|+||.++ ..|||+|+|+. +||+++||.|+|+|+|+.||+ ++.+++|++|+.
T Consensus 52 ~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~~ 120 (121)
T PHA00280 52 PKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFARF 120 (121)
T ss_pred HHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence 456788988999999999999765 57999999997 999999999999999999997 788999999864
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=99.03 E-value=4.7e-10 Score=82.06 Aligned_cols=52 Identities=31% Similarity=0.435 Sum_probs=45.0
Q ss_pred CCceeEEEC-CCCcEEEEEeecCC---CcEeeccCCCCHHHHHHHHHHHHHHhcCC
Q 019546 78 CDYRGVRQR-TWGKWVAEIREPNR---GNRLWLGTFPSAVEAALAYDHAARAMYGP 129 (339)
Q Consensus 78 S~YRGVr~r-~~GKW~A~Ir~~~~---gkrv~LGtFdT~EEAArAYD~AA~k~~G~ 129 (339)
|+|+||++. ..++|+|+|++... +++++||.|++++||++||+.+++.++|+
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 689999766 47999999998421 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=67.72 E-value=21 Score=25.35 Aligned_cols=37 Identities=14% Similarity=0.188 Sum_probs=28.5
Q ss_pred cEEEEEe--ecCC--CcEeeccCCCCHHHHHHHHHHHHHHh
Q 019546 90 KWVAEIR--EPNR--GNRLWLGTFPSAVEAALAYDHAARAM 126 (339)
Q Consensus 90 KW~A~Ir--~~~~--gkrv~LGtFdT~EEAArAYD~AA~k~ 126 (339)
+|...|. ++.. .++++-+-|.|..||-.+...+...+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5888883 4333 47788899999999999988876665
No 6
>PHA02601 int integrase; Provisional
Probab=52.44 E-value=23 Score=33.57 Aligned_cols=44 Identities=27% Similarity=0.373 Sum_probs=29.8
Q ss_pred eEEECCCCcEEEEEeec-CCCcEeeccCCCCHHHHHHHHHHHHHHh
Q 019546 82 GVRQRTWGKWVAEIREP-NRGNRLWLGTFPSAVEAALAYDHAARAM 126 (339)
Q Consensus 82 GVr~r~~GKW~A~Ir~~-~~gkrv~LGtFdT~EEAArAYD~AA~k~ 126 (339)
+|++.+.|+|+++++.. ..|+++.. +|.|..||..........+
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 46667789999999852 24666653 6999988866555544333
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=45.39 E-value=39 Score=31.49 Aligned_cols=39 Identities=31% Similarity=0.423 Sum_probs=27.4
Q ss_pred CCcEEEEEeecCCCcEeeccCCC--CHHHHHHHHHHHHHHh
Q 019546 88 WGKWVAEIREPNRGNRLWLGTFP--SAVEAALAYDHAARAM 126 (339)
Q Consensus 88 ~GKW~A~Ir~~~~gkrv~LGtFd--T~EEAArAYD~AA~k~ 126 (339)
.+.|..+++...+.+++.||+|+ |.++|..........+
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 35699998885556678899996 6667766666554444
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=33.47 E-value=35 Score=24.96 Aligned_cols=24 Identities=29% Similarity=0.281 Sum_probs=19.5
Q ss_pred CCcEeeccCCCCHHHHHHHHHHHH
Q 019546 100 RGNRLWLGTFPSAVEAALAYDHAA 123 (339)
Q Consensus 100 ~gkrv~LGtFdT~EEAArAYD~AA 123 (339)
..-+|++|.|+|.++|..+-....
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 445888999999999988877555
No 9
>PRK09692 integrase; Provisional
Probab=31.21 E-value=1.3e+02 Score=29.79 Aligned_cols=42 Identities=17% Similarity=0.276 Sum_probs=26.0
Q ss_pred EEECCCC--cEEEEEeecCCCcE--eeccCCC--CHHHHHHHHHHHHH
Q 019546 83 VRQRTWG--KWVAEIREPNRGNR--LWLGTFP--SAVEAALAYDHAAR 124 (339)
Q Consensus 83 Vr~r~~G--KW~A~Ir~~~~gkr--v~LGtFd--T~EEAArAYD~AA~ 124 (339)
|+-++.| .|..+-+.+.+|++ +-||.|+ |..+|..+-..+..
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~ 80 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRS 80 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHH
Confidence 3434444 49998875434444 6899999 67666555544333
No 10
>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=29.10 E-value=93 Score=24.72 Aligned_cols=37 Identities=27% Similarity=0.399 Sum_probs=26.1
Q ss_pred cEEEEEeecCCCcEeeccCCCCHHHHHHHHHHHHHHh
Q 019546 90 KWVAEIREPNRGNRLWLGTFPSAVEAALAYDHAARAM 126 (339)
Q Consensus 90 KW~A~Ir~~~~gkrv~LGtFdT~EEAArAYD~AA~k~ 126 (339)
.|=++|.--.-.-..|.|-|.|.+||..+.-.-...+
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL 45 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDL 45 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHH
Confidence 3668887533345678999999999999854444333
No 11
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=27.99 E-value=81 Score=28.52 Aligned_cols=37 Identities=22% Similarity=0.152 Sum_probs=31.5
Q ss_pred cEEEEEeecCCCcEeeccCCCCHHHHHHHHHHHHHHhcCC
Q 019546 90 KWVAEIREPNRGNRLWLGTFPSAVEAALAYDHAARAMYGP 129 (339)
Q Consensus 90 KW~A~Ir~~~~gkrv~LGtFdT~EEAArAYD~AA~k~~G~ 129 (339)
.|+|+|. -|+-++-=...+++.|.+|.-+|+.++=+.
T Consensus 95 gwaArVk---pG~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 95 GWAARVK---PGRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEEec---CCcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 5999998 688888888889999999999999887443
No 12
>PF10729 CedA: Cell division activator CedA; InterPro: IPR019666 CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet [, ]. ; GO: 0003677 DNA binding, 0051301 cell division; PDB: 2BN8_A 2D35_A.
Probab=26.82 E-value=1.2e+02 Score=24.59 Aligned_cols=38 Identities=24% Similarity=0.128 Sum_probs=25.4
Q ss_pred CCceeEEECCCCcEEEEEeecCCCcEeeccCCCCHHHHHHH
Q 019546 78 CDYRGVRQRTWGKWVAEIREPNRGNRLWLGTFPSAVEAALA 118 (339)
Q Consensus 78 S~YRGVr~r~~GKW~A~Ir~~~~gkrv~LGtFdT~EEAArA 118 (339)
-+||-|+.-+ |||+|.+-. +-.-..--.|..+|.|-|-
T Consensus 31 dgfrdvw~lr-gkyvafvl~--ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 31 DGFRDVWQLR-GKYVAFVLM--GEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTECCECCCC-CEEEEEEES--SS-EEE---BSSHHHHHHH
T ss_pred ccccceeeec-cceEEEEEe--cchhccCCCcCCcHHHHHH
Confidence 4799996655 999999985 4444455678888887764
No 13
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=24.24 E-value=2.2e+02 Score=22.44 Aligned_cols=32 Identities=22% Similarity=0.296 Sum_probs=21.7
Q ss_pred CcEEEEEeecCCCcEeeccCCCC--HHHHHHHHH
Q 019546 89 GKWVAEIREPNRGNRLWLGTFPS--AVEAALAYD 120 (339)
Q Consensus 89 GKW~A~Ir~~~~gkrv~LGtFdT--~EEAArAYD 120 (339)
..|..+.+...+.+++.||.|++ ..+|.....
T Consensus 35 kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~ 68 (89)
T PF13356_consen 35 KTFYFRYRINGKRRRITLGRYPELSLAEAREKAR 68 (89)
T ss_dssp EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHH
T ss_pred eEEEEEEEecceEEEeccCCCccCCHHHHHHHHH
Confidence 35888887755567889999986 444444433
No 14
>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=22.34 E-value=91 Score=26.28 Aligned_cols=21 Identities=24% Similarity=0.341 Sum_probs=18.0
Q ss_pred ccCCCCHHHHHHHHHHHHHHh
Q 019546 106 LGTFPSAVEAALAYDHAARAM 126 (339)
Q Consensus 106 LGtFdT~EEAArAYD~AA~k~ 126 (339)
-|+|+|+|+|..=||..+..+
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 399999999999999877654
Done!