Query 020958
Match_columns 319
No_of_seqs 236 out of 1249
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 06:30:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020958.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020958hhsearch_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 8.8E-20 1.9E-24 135.8 7.4 61 49-109 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 4.8E-19 1.1E-23 133.4 7.8 63 50-112 1-63 (64)
3 PHA00280 putative NHN endonucl 99.6 5.4E-15 1.2E-19 125.4 6.6 75 27-104 45-120 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 3.6E-10 7.8E-15 82.1 6.5 52 49-100 1-56 (56)
5 smart00380 AP2 DNA-binding dom 95.3 0.0034 7.5E-08 47.1 -0.8 27 2-29 36-62 (64)
6 cd00018 AP2 DNA-binding domain 93.2 0.016 3.4E-07 43.0 -1.1 23 2-24 37-59 (61)
7 PF14657 Integrase_AP2: AP2-li 80.4 5.6 0.00012 27.9 5.3 38 61-98 1-42 (46)
8 PHA02601 int integrase; Provis 63.4 8.7 0.00019 36.2 3.8 44 53-97 2-46 (333)
9 PF08846 DUF1816: Domain of un 53.8 27 0.00059 27.3 4.4 42 61-102 9-50 (68)
10 cd00801 INT_P4 Bacteriophage P 48.5 32 0.00069 32.0 4.9 40 59-98 9-50 (357)
11 PF10729 CedA: Cell division a 44.7 34 0.00074 27.1 3.7 39 47-88 29-67 (80)
12 PRK09692 integrase; Provisiona 39.2 70 0.0015 31.4 5.9 43 54-96 33-81 (413)
13 PF13356 DUF4102: Domain of un 35.4 1E+02 0.0022 24.1 5.2 47 51-97 22-74 (89)
14 PF05036 SPOR: Sporulation rel 35.2 26 0.00057 25.4 1.8 24 71-94 42-65 (76)
15 KOG2833 Mevalonate pyrophospha 33.3 39 0.00084 34.1 3.0 23 8-31 15-38 (395)
16 PRK10113 cell division modulat 29.7 38 0.00082 26.8 1.8 38 48-88 30-67 (80)
17 PF09003 Phage_integ_N: Bacter 20.8 2.4E+02 0.0051 22.5 4.8 32 66-99 31-62 (75)
18 KOG3422 Mitochondrial ribosoma 20.5 2.2E+02 0.0048 27.1 5.3 38 61-100 133-170 (221)
19 COG0197 RplP Ribosomal protein 20.5 1.5E+02 0.0033 26.4 4.1 36 62-100 96-131 (146)
20 PF00352 TBP: Transcription fa 20.1 3.4E+02 0.0074 21.1 5.7 48 48-98 35-83 (86)
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=99.80 E-value=8.8e-20 Score=135.81 Aligned_cols=61 Identities=69% Similarity=1.298 Sum_probs=57.1
Q ss_pred CccceEEECCCCceEEEEecCCCCeEEeecCcccHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 020958 49 NQYRGIRQRPWGKWAAEIRDPTKGVRVWLGTFNTAEEAARAYDAEARRIRGKKAKVNFPDE 109 (319)
Q Consensus 49 S~YRGVr~r~~GKW~A~I~~~~~gK~i~LGtF~T~EEAArAYD~Aa~~l~G~~A~~NFp~~ 109 (319)
|+||||+++++|||+|+|+++..||++|||+|+|+|||++|||.++++++|.++.+|||++
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 6899999888899999999655599999999999999999999999999999999999974
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.78 E-value=4.8e-19 Score=133.42 Aligned_cols=63 Identities=68% Similarity=1.262 Sum_probs=59.3
Q ss_pred ccceEEECCCCceEEEEecCCCCeEEeecCcccHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q 020958 50 QYRGIRQRPWGKWAAEIRDPTKGVRVWLGTFNTAEEAARAYDAEARRIRGKKAKVNFPDETPA 112 (319)
Q Consensus 50 ~YRGVr~r~~GKW~A~I~~~~~gK~i~LGtF~T~EEAArAYD~Aa~~l~G~~A~~NFp~~~~~ 112 (319)
+||||+++++|||+|+|+++.+|+++|||+|+|+||||+|||.++++++|.++++|||.+.+.
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 589998888999999999777999999999999999999999999999999999999998764
No 3
>PHA00280 putative NHN endonuclease
Probab=99.56 E-value=5.4e-15 Score=125.44 Aligned_cols=75 Identities=15% Similarity=0.232 Sum_probs=65.4
Q ss_pred cccchhhhhHHHhhhhhccCCCCccceEE-ECCCCceEEEEecCCCCeEEeecCcccHHHHHHHHHHHHHHhcCCCCCC
Q 020958 27 IEGSTAVKHVEQAKKSTERKRKNQYRGIR-QRPWGKWAAEIRDPTKGVRVWLGTFNTAEEAARAYDAEARRIRGKKAKV 104 (319)
Q Consensus 27 ~~~s~~~~~~~~~~~~~~r~~~S~YRGVr-~r~~GKW~A~I~~~~~gK~i~LGtF~T~EEAArAYD~Aa~~l~G~~A~~ 104 (319)
++...++..++.+|++..+.++|||+||+ ++..|||+|+|+ ++||+++||.|+++|+|+.||+ +++++||++|+.
T Consensus 45 ~NLr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~--~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~~ 120 (121)
T PHA00280 45 DNLRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVT--AEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFARF 120 (121)
T ss_pred HHhhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEE--ECCEEEEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence 44455666777888888889999999995 666899999999 9999999999999999999997 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=99.07 E-value=3.6e-10 Score=82.14 Aligned_cols=52 Identities=31% Similarity=0.561 Sum_probs=44.8
Q ss_pred CccceEE-ECCCCceEEEEecCC-C--CeEEeecCcccHHHHHHHHHHHHHHhcCC
Q 020958 49 NQYRGIR-QRPWGKWAAEIRDPT-K--GVRVWLGTFNTAEEAARAYDAEARRIRGK 100 (319)
Q Consensus 49 S~YRGVr-~r~~GKW~A~I~~~~-~--gK~i~LGtF~T~EEAArAYD~Aa~~l~G~ 100 (319)
|+|+||+ .+..++|+|+|+++. + +|+++||.|.+++||++||+.++++++|+
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 7899996 555899999999632 2 49999999999999999999999999885
No 5
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=95.28 E-value=0.0034 Score=47.13 Aligned_cols=27 Identities=19% Similarity=0.047 Sum_probs=23.5
Q ss_pred cccccccccceeeccccccccccccccc
Q 020958 2 KFASLYDLVVLLVYEITFFFLFSPIIEG 29 (319)
Q Consensus 2 ~AA~AYD~Aalk~~g~~~~~N~~~~~~~ 29 (319)
|||+|||+++++++|..+.+|| +..+|
T Consensus 36 eAa~Ayd~a~~~~~g~~a~~Nf-~~~~y 62 (64)
T smart00380 36 EAARAYDRAAFKFRGRSARLNF-PNSLY 62 (64)
T ss_pred HHHHHHHHHHHHhcCCccccCC-CCccC
Confidence 7999999999999999999999 44444
No 6
>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=93.21 E-value=0.016 Score=42.95 Aligned_cols=23 Identities=22% Similarity=0.225 Sum_probs=21.5
Q ss_pred cccccccccceeecccccccccc
Q 020958 2 KFASLYDLVVLLVYEITFFFLFS 24 (319)
Q Consensus 2 ~AA~AYD~Aalk~~g~~~~~N~~ 24 (319)
|||+|||+++++++|..+.+||+
T Consensus 37 eAa~Ayd~a~~~~~g~~a~~Nf~ 59 (61)
T cd00018 37 EAARAYDRAALKLRGSSAVLNFP 59 (61)
T ss_pred HHHHHHHHHHHHhcCCccccCCC
Confidence 79999999999999999999984
No 7
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=80.40 E-value=5.6 Score=27.90 Aligned_cols=38 Identities=21% Similarity=0.303 Sum_probs=29.7
Q ss_pred ceEEEEe--cCCCC--eEEeecCcccHHHHHHHHHHHHHHhc
Q 020958 61 KWAAEIR--DPTKG--VRVWLGTFNTAEEAARAYDAEARRIR 98 (319)
Q Consensus 61 KW~A~I~--~~~~g--K~i~LGtF~T~EEAArAYD~Aa~~l~ 98 (319)
+|..+|. ++..| ++++-+-|.|..||..+.......+.
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 55455 67888999999999999988776654
No 8
>PHA02601 int integrase; Provisional
Probab=63.38 E-value=8.7 Score=36.19 Aligned_cols=44 Identities=27% Similarity=0.357 Sum_probs=30.6
Q ss_pred eEEECCCCceEEEEec-CCCCeEEeecCcccHHHHHHHHHHHHHHh
Q 020958 53 GIRQRPWGKWAAEIRD-PTKGVRVWLGTFNTAEEAARAYDAEARRI 97 (319)
Q Consensus 53 GVr~r~~GKW~A~I~~-~~~gK~i~LGtF~T~EEAArAYD~Aa~~l 97 (319)
+|+++++|+|++++.. ...|+++.. +|.|..||.+........+
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 5677778999999983 234777654 6999999876655544433
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=53.77 E-value=27 Score=27.28 Aligned_cols=42 Identities=24% Similarity=0.429 Sum_probs=32.1
Q ss_pred ceEEEEecCCCCeEEeecCcccHHHHHHHHHHHHHHhcCCCC
Q 020958 61 KWAAEIRDPTKGVRVWLGTFNTAEEAARAYDAEARRIRGKKA 102 (319)
Q Consensus 61 KW~A~I~~~~~gK~i~LGtF~T~EEAArAYD~Aa~~l~G~~A 102 (319)
.|-++|.--.=...+|.|-|.|.+||..+.-.....+..+.+
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~~Ega 50 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLESEGA 50 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHHhhCc
Confidence 488999854446889999999999999997666666554443
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=48.47 E-value=32 Score=31.99 Aligned_cols=40 Identities=23% Similarity=0.280 Sum_probs=27.7
Q ss_pred CCceEEEEecCCCCeEEeecCcc--cHHHHHHHHHHHHHHhc
Q 020958 59 WGKWAAEIRDPTKGVRVWLGTFN--TAEEAARAYDAEARRIR 98 (319)
Q Consensus 59 ~GKW~A~I~~~~~gK~i~LGtF~--T~EEAArAYD~Aa~~l~ 98 (319)
.+.|+.+++...+.+++.||+|. +.++|..........+.
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 35699999954445567799995 67777777666555553
No 11
>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=44.67 E-value=34 Score=27.14 Aligned_cols=39 Identities=23% Similarity=0.270 Sum_probs=26.6
Q ss_pred CCCccceEEECCCCceEEEEecCCCCeEEeecCcccHHHHHH
Q 020958 47 RKNQYRGIRQRPWGKWAAEIRDPTKGVRVWLGTFNTAEEAAR 88 (319)
Q Consensus 47 ~~S~YRGVr~r~~GKW~A~I~~~~~gK~i~LGtF~T~EEAAr 88 (319)
+--+||-||.-+ |||+|.+. .+..-..--.|..+|.|-|
T Consensus 29 k~dgfrdvw~lr-gkyvafvl--~ge~f~rsp~fs~pesaqr 67 (80)
T PF10729_consen 29 KMDGFRDVWQLR-GKYVAFVL--MGEHFRRSPAFSVPESAQR 67 (80)
T ss_dssp -TTTECCECCCC-CEEEEEEE--SSS-EEE---BSSHHHHHH
T ss_pred hcccccceeeec-cceEEEEE--ecchhccCCCcCCcHHHHH
Confidence 456899998766 99999999 5555555567888887765
No 12
>PRK09692 integrase; Provisional
Probab=39.20 E-value=70 Score=31.44 Aligned_cols=43 Identities=16% Similarity=0.245 Sum_probs=27.4
Q ss_pred EEECCCCc--eEEEEecCCCCeE--EeecCcc--cHHHHHHHHHHHHHH
Q 020958 54 IRQRPWGK--WAAEIRDPTKGVR--VWLGTFN--TAEEAARAYDAEARR 96 (319)
Q Consensus 54 Vr~r~~GK--W~A~I~~~~~gK~--i~LGtF~--T~EEAArAYD~Aa~~ 96 (319)
|+-++.|. |+.+-+.+.+||+ +-||.|. |..||..+-.++...
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~~ 81 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRSL 81 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHHH
Confidence 34445543 9999876545555 6899998 676666555444333
No 13
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=35.40 E-value=1e+02 Score=24.09 Aligned_cols=47 Identities=23% Similarity=0.262 Sum_probs=29.0
Q ss_pred cceE--EECCCC--ceEEEEecCCCCeEEeecCccc--HHHHHHHHHHHHHHh
Q 020958 51 YRGI--RQRPWG--KWAAEIRDPTKGVRVWLGTFNT--AEEAARAYDAEARRI 97 (319)
Q Consensus 51 YRGV--r~r~~G--KW~A~I~~~~~gK~i~LGtF~T--~EEAArAYD~Aa~~l 97 (319)
..|. +-.+.| .|.-+.+...+.+++-||.|.. ..||..........+
T Consensus 22 ~~GL~l~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 22 VPGLYLRVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp STTEEEEE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred CCCcEEEEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 4554 444554 3999998444456789999965 666666655544444
No 14
>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=35.23 E-value=26 Score=25.41 Aligned_cols=24 Identities=33% Similarity=0.357 Sum_probs=19.1
Q ss_pred CCeEEeecCcccHHHHHHHHHHHH
Q 020958 71 KGVRVWLGTFNTAEEAARAYDAEA 94 (319)
Q Consensus 71 ~gK~i~LGtF~T~EEAArAYD~Aa 94 (319)
..-++.+|.|.+.+||..+.....
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 344778889999999998887665
No 15
>KOG2833 consensus Mevalonate pyrophosphate decarboxylase [Lipid transport and metabolism]
Probab=33.25 E-value=39 Score=34.11 Aligned_cols=23 Identities=9% Similarity=0.128 Sum_probs=15.5
Q ss_pred cccceeeccccc-ccccccccccch
Q 020958 8 DLVVLLVYEITF-FFLFSPIIEGST 31 (319)
Q Consensus 8 D~Aalk~~g~~~-~~N~~~~~~~s~ 31 (319)
++|+|||||..- .+|+ +..+..+
T Consensus 15 NIAvIKYWGKRD~~l~L-P~N~SIS 38 (395)
T KOG2833|consen 15 NIAVIKYWGKRDEELNL-PTNDSIS 38 (395)
T ss_pred eeeeeeeccccchhhcC-CcCCcee
Confidence 899999999864 4444 5544433
No 16
>PRK10113 cell division modulator; Provisional
Probab=29.70 E-value=38 Score=26.82 Aligned_cols=38 Identities=21% Similarity=0.274 Sum_probs=26.9
Q ss_pred CCccceEEECCCCceEEEEecCCCCeEEeecCcccHHHHHH
Q 020958 48 KNQYRGIRQRPWGKWAAEIRDPTKGVRVWLGTFNTAEEAAR 88 (319)
Q Consensus 48 ~S~YRGVr~r~~GKW~A~I~~~~~gK~i~LGtF~T~EEAAr 88 (319)
--+||-||.-+ |||+|.+. .+-.-..--.|..+|.|-|
T Consensus 30 md~frDVW~Lr-GKYVAFvl--~ge~FrRSPaFs~PEsAQR 67 (80)
T PRK10113 30 MDSFRDVWMLR-GKYVAFVL--MGESFLRSPAFSVPESAQR 67 (80)
T ss_pred hcchhhhheec-cceEEEEE--echhhccCCccCCcHHHHH
Confidence 45799998766 99999988 3333333456788877765
No 17
>PF09003 Phage_integ_N: Bacteriophage lambda integrase, N-terminal domain ; InterPro: IPR015094 The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage []. ; GO: 0003677 DNA binding, 0008907 integrase activity, 0015074 DNA integration; PDB: 1Z1G_B 1Z1B_A 2WCC_3 1KJK_A.
Probab=20.82 E-value=2.4e+02 Score=22.50 Aligned_cols=32 Identities=31% Similarity=0.296 Sum_probs=20.0
Q ss_pred EecCCCCeEEeecCcccHHHHHHHHHHHHHHhcC
Q 020958 66 IRDPTKGVRVWLGTFNTAEEAARAYDAEARRIRG 99 (319)
Q Consensus 66 I~~~~~gK~i~LGtF~T~EEAArAYD~Aa~~l~G 99 (319)
-++|+.||.+.||+ +.+||..+=-.+-..+..
T Consensus 31 Yr~P~tGk~~~LG~--d~~~Ai~~A~eaN~~i~~ 62 (75)
T PF09003_consen 31 YRNPITGKEHGLGT--DRAEAIAQAIEANLRIAE 62 (75)
T ss_dssp EE-TTTS-EEEEES---HHHHHHHHHHHHHHHTS
T ss_pred EecCCCCceeeCCC--CHHHHHHHHHHHHHHHHH
Confidence 45679999999999 666666655555555543
No 18
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=20.55 E-value=2.2e+02 Score=27.07 Aligned_cols=38 Identities=24% Similarity=0.304 Sum_probs=32.6
Q ss_pred ceEEEEecCCCCeEEeecCcccHHHHHHHHHHHHHHhcCC
Q 020958 61 KWAAEIRDPTKGVRVWLGTFNTAEEAARAYDAEARRIRGK 100 (319)
Q Consensus 61 KW~A~I~~~~~gK~i~LGtF~T~EEAArAYD~Aa~~l~G~ 100 (319)
.|+|+|. .++--+-+|---+++||..|.+.+|.++-+.
T Consensus 133 ~wva~V~--~GrIl~EmgG~~~~~~Ar~al~~aa~klp~~ 170 (221)
T KOG3422|consen 133 HWVARVK--AGRILFEMGGDVEEEEARQALLQAAHKLPFK 170 (221)
T ss_pred eeEEEec--CCcEEEEeCCcccHHHHHHHHHHHHhcCCcc
Confidence 5999999 7777777888899999999999999987654
No 19
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=20.52 E-value=1.5e+02 Score=26.44 Aligned_cols=36 Identities=25% Similarity=0.274 Sum_probs=30.0
Q ss_pred eEEEEecCCCCeEEeecCcccHHHHHHHHHHHHHHhcCC
Q 020958 62 WAAEIRDPTKGVRVWLGTFNTAEEAARAYDAEARRIRGK 100 (319)
Q Consensus 62 W~A~I~~~~~gK~i~LGtF~T~EEAArAYD~Aa~~l~G~ 100 (319)
|.|+|. -|+.++-=....++.|..|..+|+.+|-+.
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 999999 477777777788888999999999887654
No 20
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=20.09 E-value=3.4e+02 Score=21.15 Aligned_cols=48 Identities=23% Similarity=0.236 Sum_probs=34.8
Q ss_pred CCccceEEECC-CCceEEEEecCCCCeEEeecCcccHHHHHHHHHHHHHHhc
Q 020958 48 KNQYRGIRQRP-WGKWAAEIRDPTKGVRVWLGTFNTAEEAARAYDAEARRIR 98 (319)
Q Consensus 48 ~S~YRGVr~r~-~GKW~A~I~~~~~gK~i~LGtF~T~EEAArAYD~Aa~~l~ 98 (319)
..+|.||..|- .-+-.+.|. ..||-+..|. .+.|||..|.++....+.
T Consensus 35 Pe~fpgl~~r~~~p~~t~~IF--~sGki~itGa-ks~~~~~~a~~~i~~~L~ 83 (86)
T PF00352_consen 35 PERFPGLIYRLRNPKATVLIF--SSGKIVITGA-KSEEEAKKAIEKILPILQ 83 (86)
T ss_dssp TTTESSEEEEETTTTEEEEEE--TTSEEEEEEE-SSHHHHHHHHHHHHHHHH
T ss_pred eccCCeEEEeecCCcEEEEEE--cCCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 34788985333 345666666 8999888886 688999999888776653
Done!