Query 021983
Match_columns 304
No_of_seqs 297 out of 1269
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 07:07:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021983.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021983hhsearch_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 5E-20 1.1E-24 136.0 7.7 61 112-172 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 8.2E-20 1.8E-24 136.5 8.4 63 113-175 1-63 (64)
3 PHA00280 putative NHN endonucl 99.6 3.7E-15 8.1E-20 125.8 6.8 71 93-167 49-120 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 1.3E-10 2.8E-15 83.7 6.1 52 112-163 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 78.8 9.6 0.00021 26.6 6.0 38 124-161 1-42 (46)
6 PHA02601 int integrase; Provis 63.7 12 0.00026 34.8 4.7 44 116-160 2-46 (333)
7 PF08846 DUF1816: Domain of un 54.6 23 0.0005 27.7 4.1 38 124-161 9-46 (68)
8 cd00801 INT_P4 Bacteriophage P 49.0 39 0.00085 30.9 5.5 42 120-161 7-50 (357)
9 PF05036 SPOR: Sporulation rel 42.1 19 0.00041 25.9 1.9 24 134-157 42-65 (76)
10 PF13356 DUF4102: Domain of un 38.2 1E+02 0.0022 23.9 5.6 37 124-160 36-74 (89)
11 PRK09692 integrase; Provisiona 37.0 92 0.002 30.3 6.3 34 124-157 42-79 (413)
12 PF10729 CedA: Cell division a 36.6 61 0.0013 25.9 4.0 39 111-152 30-68 (80)
13 PF08471 Ribonuc_red_2_N: Clas 28.3 62 0.0013 26.9 2.9 42 111-160 49-90 (93)
14 COG0197 RplP Ribosomal protein 25.8 92 0.002 27.8 3.8 36 125-163 96-131 (146)
15 PRK10113 cell division modulat 22.0 73 0.0016 25.4 2.2 39 111-152 30-68 (80)
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=99.81 E-value=5e-20 Score=135.96 Aligned_cols=61 Identities=72% Similarity=1.165 Sum_probs=56.8
Q ss_pred CceeeeEECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHcCCCCCCCCCCC
Q 021983 112 KLYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLRGDFARLNFPNL 172 (304)
Q Consensus 112 S~YRGVr~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~klrG~~A~lNFP~~ 172 (304)
|+|+||+++++|||+|+|+++..|+++|||+|+|+||||+|||.++++++|.++.+|||.+
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 6899998878899999999855599999999999999999999999999999999999963
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.81 E-value=8.2e-20 Score=136.54 Aligned_cols=63 Identities=71% Similarity=1.170 Sum_probs=59.8
Q ss_pred ceeeeEECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHcCCCCCCCCCCCCCC
Q 021983 113 LYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLRGDFARLNFPNLRHN 175 (304)
Q Consensus 113 ~YRGVr~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~klrG~~A~lNFP~~~~~ 175 (304)
+|+||+++++|||+|+|+++.+|+++|||+|+|+||||.|||.++++++|.++++|||...|+
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 599998788999999999988999999999999999999999999999999999999998774
No 3
>PHA00280 putative NHN endonuclease
Probab=99.57 E-value=3.7e-15 Score=125.82 Aligned_cols=71 Identities=18% Similarity=0.262 Sum_probs=64.7
Q ss_pred CCCCCCCCCCCCCCCCCCCCceeee-EECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHcCCCCCC
Q 021983 93 LSPKPVPMKTVGCPPPKPAKLYRGV-RQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLRGDFARL 167 (304)
Q Consensus 93 l~~~~~~mK~~g~~~~~ntS~YRGV-r~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~klrG~~A~l 167 (304)
+.+..+++.|.+.. ++|+|||+|| +.+..|||+|+|++ +||+++||.|+++|+|+.||+ ++.+|||+||+.
T Consensus 49 ~~T~~eN~~N~~~~-~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~~ 120 (121)
T PHA00280 49 LALPKENSWNMKTP-KSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFARF 120 (121)
T ss_pred hcCHHHHhcccCCC-CCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence 57888999998876 8999999999 68888999999997 999999999999999999997 778999999853
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=99.12 E-value=1.3e-10 Score=83.75 Aligned_cols=52 Identities=38% Similarity=0.597 Sum_probs=45.6
Q ss_pred Cceeee-EECCCCcEEEEEeecC-C--CeEeecCCCCCHHHHHHHHHHHHHHHcCC
Q 021983 112 KLYRGV-RQRHWGKWVAEIRLPK-N--RTRLWLGTFDTAEEAALAYDKAAYKLRGD 163 (304)
Q Consensus 112 S~YRGV-r~r~~GKW~AeIr~p~-~--gkri~LGtFdTaEEAA~AYD~AA~klrG~ 163 (304)
|+|+|| +.+..++|+|.|+++. + +++++||.|++++||++||+.++.+++|+
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 689999 5788899999999842 2 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=78.78 E-value=9.6 Score=26.64 Aligned_cols=38 Identities=21% Similarity=0.205 Sum_probs=29.7
Q ss_pred cEEEEEe--ecCCC--eEeecCCCCCHHHHHHHHHHHHHHHc
Q 021983 124 KWVAEIR--LPKNR--TRLWLGTFDTAEEAALAYDKAAYKLR 161 (304)
Q Consensus 124 KW~AeIr--~p~~g--kri~LGtFdTaEEAA~AYD~AA~klr 161 (304)
+|...|. .+..| ++++-+.|.|..||..+...+...+.
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 44455 66888999999999999988777664
No 6
>PHA02601 int integrase; Provisional
Probab=63.74 E-value=12 Score=34.82 Aligned_cols=44 Identities=27% Similarity=0.361 Sum_probs=30.8
Q ss_pred eeEECCCCcEEEEEee-cCCCeEeecCCCCCHHHHHHHHHHHHHHH
Q 021983 116 GVRQRHWGKWVAEIRL-PKNRTRLWLGTFDTAEEAALAYDKAAYKL 160 (304)
Q Consensus 116 GVr~r~~GKW~AeIr~-p~~gkri~LGtFdTaEEAA~AYD~AA~kl 160 (304)
+|++.++|+|+++++. ...|+++. .+|.|..||....+.....+
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 5677778999999985 23467765 36999988876655544433
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=54.58 E-value=23 Score=27.71 Aligned_cols=38 Identities=29% Similarity=0.448 Sum_probs=28.7
Q ss_pred cEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHc
Q 021983 124 KWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLR 161 (304)
Q Consensus 124 KW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~klr 161 (304)
.|-++|.--.-.-.+|.|-|+|.+||..+.-.-...+.
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 48889986556678999999999999987554444443
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=49.04 E-value=39 Score=30.91 Aligned_cols=42 Identities=31% Similarity=0.366 Sum_probs=28.4
Q ss_pred CCCCcEEEEEeecCCCeEeecCCCC--CHHHHHHHHHHHHHHHc
Q 021983 120 RHWGKWVAEIRLPKNRTRLWLGTFD--TAEEAALAYDKAAYKLR 161 (304)
Q Consensus 120 r~~GKW~AeIr~p~~gkri~LGtFd--TaEEAA~AYD~AA~klr 161 (304)
...+.|..+++.....+++.||+|+ +.++|..........+.
T Consensus 7 ~g~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 7 SGSKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred CCCEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 3335699998874444567799995 67777777666555553
No 9
>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=42.11 E-value=19 Score=25.95 Aligned_cols=24 Identities=33% Similarity=0.411 Sum_probs=19.4
Q ss_pred CCeEeecCCCCCHHHHHHHHHHHH
Q 021983 134 NRTRLWLGTFDTAEEAALAYDKAA 157 (304)
Q Consensus 134 ~gkri~LGtFdTaEEAA~AYD~AA 157 (304)
..-+|++|.|++.++|..+.....
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 445777899999999998877665
No 10
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=38.20 E-value=1e+02 Score=23.89 Aligned_cols=37 Identities=19% Similarity=0.226 Sum_probs=24.5
Q ss_pred cEEEEEeecCCCeEeecCCCCC--HHHHHHHHHHHHHHH
Q 021983 124 KWVAEIRLPKNRTRLWLGTFDT--AEEAALAYDKAAYKL 160 (304)
Q Consensus 124 KW~AeIr~p~~gkri~LGtFdT--aEEAA~AYD~AA~kl 160 (304)
.|..+.+.....+++-||.|.. ..+|..........+
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 4988887633335688999976 666666655554444
No 11
>PRK09692 integrase; Provisional
Probab=37.03 E-value=92 Score=30.27 Aligned_cols=34 Identities=21% Similarity=0.274 Sum_probs=22.4
Q ss_pred cEEEEEeecCCCeE--eecCCCC--CHHHHHHHHHHHH
Q 021983 124 KWVAEIRLPKNRTR--LWLGTFD--TAEEAALAYDKAA 157 (304)
Q Consensus 124 KW~AeIr~p~~gkr--i~LGtFd--TaEEAA~AYD~AA 157 (304)
.|+.+-+.+.+|++ +-||.|. |..+|..+..++.
T Consensus 42 ~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~ 79 (413)
T PRK09692 42 IWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESR 79 (413)
T ss_pred EEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHH
Confidence 49888875545555 6799999 6666655444433
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=36.62 E-value=61 Score=25.89 Aligned_cols=39 Identities=26% Similarity=0.225 Sum_probs=26.3
Q ss_pred CCceeeeEECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHH
Q 021983 111 AKLYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALA 152 (304)
Q Consensus 111 tS~YRGVr~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~A 152 (304)
--+||-||.-+ |||+|.+.. +-.-.---.|...|.|-+-
T Consensus 30 ~dgfrdvw~lr-gkyvafvl~--ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 30 MDGFRDVWQLR-GKYVAFVLM--GEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTTECCECCCC-CEEEEEEES--SS-EEE---BSSHHHHHHH
T ss_pred cccccceeeec-cceEEEEEe--cchhccCCCcCCcHHHHHH
Confidence 47899998776 999999985 3333334678888877664
No 13
>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=28.33 E-value=62 Score=26.88 Aligned_cols=42 Identities=33% Similarity=0.412 Sum_probs=28.2
Q ss_pred CCceeeeEECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHH
Q 021983 111 AKLYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKL 160 (304)
Q Consensus 111 tS~YRGVr~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~kl 160 (304)
.+..|-|.+|--|-|..- |.+ -|.|+|+|+|..=||..+..|
T Consensus 49 E~S~rQv~~Rla~tw~~w------G~~--~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 49 ETSVRQVFDRLAGTWTYW------GWK--GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred cchHHHHHHHHHHHHHHH------HHh--CCCcCCHHHHHHHHHHHHHHH
Confidence 344666655544544322 222 499999999999999988766
No 14
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=25.80 E-value=92 Score=27.76 Aligned_cols=36 Identities=28% Similarity=0.209 Sum_probs=30.4
Q ss_pred EEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHcCC
Q 021983 125 WVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLRGD 163 (304)
Q Consensus 125 W~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~klrG~ 163 (304)
|+|+|. -|+.++-=..+.++.|..|..+|+.+|=+.
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 688887777888888999999999887544
No 15
>PRK10113 cell division modulator; Provisional
Probab=22.02 E-value=73 Score=25.39 Aligned_cols=39 Identities=26% Similarity=0.264 Sum_probs=27.2
Q ss_pred CCceeeeEECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHH
Q 021983 111 AKLYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALA 152 (304)
Q Consensus 111 tS~YRGVr~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~A 152 (304)
--+||-||.-+ |||+|.+... -.-.---.|...|.|-+-
T Consensus 30 md~frDVW~Lr-GKYVAFvl~g--e~FrRSPaFs~PEsAQRW 68 (80)
T PRK10113 30 MDSFRDVWMLR-GKYVAFVLMG--ESFLRSPAFSVPESAQRW 68 (80)
T ss_pred hcchhhhheec-cceEEEEEec--hhhccCCccCCcHHHHHH
Confidence 46799998766 9999999852 222223568888877664
Done!