Query 020408
Match_columns 326
No_of_seqs 238 out of 1253
Neff 4.7
Searched_HMMs 29240
Date Mon Mar 25 16:25:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020408.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/020408hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1gcc_A Ethylene responsive ele 99.9 4E-23 1.4E-27 155.9 6.9 60 50-109 2-62 (63)
2 1gcc_A Ethylene responsive ele 96.2 0.00064 2.2E-08 50.7 -0.4 23 2-24 38-60 (63)
3 1u3e_M HNH homing endonuclease 92.6 0.0061 2.1E-07 52.7 -3.5 58 30-91 89-146 (174)
4 3igm_B PF14_0633 protein; AP2 88.2 0.61 2.1E-05 36.2 4.6 29 46-76 3-32 (77)
5 1z1b_A Integrase; protein-DNA 83.8 1.5 5.1E-05 39.6 5.7 42 52-97 14-55 (356)
6 3jtz_A Integrase; four strande 50.6 27 0.00091 26.9 5.3 43 55-97 29-75 (88)
7 1b69_A Protein (integrase); in 36.0 39 0.0014 25.5 4.0 30 46-76 7-36 (69)
8 3ju0_A Phage integrase; four s 32.5 65 0.0022 25.7 5.0 43 55-97 29-75 (108)
9 2ftc_I Mitochondrial ribosomal 28.1 79 0.0027 25.8 4.9 36 62-99 80-115 (118)
10 1x60_A Sporulation-specific N- 26.6 42 0.0014 24.3 2.7 23 73-95 46-68 (79)
11 1uta_A FTSN, MSGA, cell divisi 26.0 56 0.0019 24.0 3.4 25 71-95 44-68 (81)
12 3lto_A Mevalonate diphosphate 24.9 14 0.00048 35.0 -0.2 22 3-24 4-27 (323)
13 2bn8_A CEDA, cell division act 21.1 55 0.0019 25.3 2.4 39 47-88 36-74 (87)
No 1
>1gcc_A Ethylene responsive element binding factor 1; transcription factor, protein-DNA complex, ethylene inducible; HET: DNA; NMR {Arabidopsis thaliana} SCOP: d.10.1.2 PDB: 2gcc_A 3gcc_A
Probab=99.88 E-value=4e-23 Score=155.87 Aligned_cols=60 Identities=68% Similarity=1.204 Sum_probs=57.0
Q ss_pred cceeeEECCCCeEEEEEecCC-CCeEEeecCcccHHHHHHHHHHHHHHhcCCCcCCCCCCC
Q 020408 50 QYRGIRQRPWGKWAAEIRDPT-KGVRVWLGTFNTAEEAARAYDAEARRIRGKKAKVNFPDE 109 (326)
Q Consensus 50 ~YRGVr~r~~GKW~A~I~~p~-~gkri~LGtF~T~EEAArAYD~AA~~l~G~~A~~NFp~~ 109 (326)
+||||+++++|||+|+|++|. +|+++|||+|+|+||||+|||.++++++|.++++|||.+
T Consensus 2 ~yrGV~~r~~gkw~A~I~~~~~~g~r~~LGtf~T~eeAA~AyD~Aa~~~~G~~a~~NFp~~ 62 (63)
T 1gcc_A 2 HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLR 62 (63)
T ss_dssp CCTTEEEETTTEEEEEEEETTTTSEEEEEEEESSHHHHHHHHHHHHHHHHSSCCCCSSCTT
T ss_pred CcccEeeCCCCcEEEEEccccCCCeEEEeeeCCCHHHHHHHHHHHHHHhcCcccccCCCCc
Confidence 699999889999999999886 489999999999999999999999999999999999986
No 2
>1gcc_A Ethylene responsive element binding factor 1; transcription factor, protein-DNA complex, ethylene inducible; HET: DNA; NMR {Arabidopsis thaliana} SCOP: d.10.1.2 PDB: 2gcc_A 3gcc_A
Probab=96.22 E-value=0.00064 Score=50.70 Aligned_cols=23 Identities=17% Similarity=0.157 Sum_probs=22.0
Q ss_pred ccccccchhhheecccccccccc
Q 020408 2 KFASLYDLVVLLVYEITFFFLFS 24 (326)
Q Consensus 2 eAA~AYD~Aalk~~g~~~~~N~~ 24 (326)
|||+|||.|+++++|..+.+||+
T Consensus 38 eAA~AyD~Aa~~~~G~~a~~NFp 60 (63)
T 1gcc_A 38 DAALAYDRAAFRMRGSRALLNFP 60 (63)
T ss_dssp HHHHHHHHHHHHHHSSCCCCSSC
T ss_pred HHHHHHHHHHHHhcCcccccCCC
Confidence 79999999999999999999995
No 3
>1u3e_M HNH homing endonuclease; HNH catalytic motif, helix-turn-helix DNA binding domain, PR complex, DNA binding protein-DNA complex; 2.92A {Bacillus phage SPO1} SCOP: d.4.1.3 d.285.1.1
Probab=92.59 E-value=0.0061 Score=52.73 Aligned_cols=58 Identities=5% Similarity=-0.047 Sum_probs=38.4
Q ss_pred hhhhhhHHHhhhhhccCCCCcceeeEECCCCeEEEEEecCCCCeEEeecCcccHHHHHHHHH
Q 020408 30 STAVKHVEQAKKSTERKRKNQYRGIRQRPWGKWAAEIRDPTKGVRVWLGTFNTAEEAARAYD 91 (326)
Q Consensus 30 s~~~~~~~~~~r~~~r~~~S~YRGVr~r~~GKW~A~I~~p~~gkri~LGtF~T~EEAArAYD 91 (326)
.-++...+.+++.....+ +.++||.....++|.+.|. .+ +.++||.|.|.+|||++|.
T Consensus 89 ~~~t~~eN~~~~~~~~~~-~~~~g~~~~~~~k~~~vi~--~~-~~~~~~~f~s~~eAa~~~G 146 (174)
T 1u3e_M 89 RWVTQKINVENQMSRGTL-NVSKAQQIAKIKNQKPIIV--IS-PDGIEKEYPSTKCACEELG 146 (174)
T ss_dssp EEECHHHHHHHHHHHTCC-CCHHHHHHHHHHTCCCEEE--EC-TTSCEEEESCHHHHHHHHT
T ss_pred EECCHHHHhhcccccCcc-cceeeeeeccCCCCceEEE--Ec-CCceEEeeCCHHHHHHHHC
Confidence 344455555544433322 2257774344567999998 56 6778999999999999963
No 4
>3igm_B PF14_0633 protein; AP2 domain, specific transcription FA protein-DNA complex, transcription-DNA complex; 2.20A {Plasmodium falciparum}
Probab=88.18 E-value=0.61 Score=36.23 Aligned_cols=29 Identities=17% Similarity=0.249 Sum_probs=22.2
Q ss_pred CCCCcceee-EECCCCeEEEEEecCCCCeEEe
Q 020408 46 KRKNQYRGI-RQRPWGKWAAEIRDPTKGVRVW 76 (326)
Q Consensus 46 ~~~S~YRGV-r~r~~GKW~A~I~~p~~gkri~ 76 (326)
..+|+|.|| +..+.+.|.|+-. .+|++..
T Consensus 3 ~~~Sg~pGVsw~kR~~~WlA~W~--e~g~rrs 32 (77)
T 3igm_B 3 HMSSGYPGVSWNKRMCAWLAFFY--DGASRRS 32 (77)
T ss_dssp -CCSSSTTEEEETTTTEEEEEEE--ETTEEEE
T ss_pred CCCCCCCcEEeecCCceEEEEEe--cCCeEee
Confidence 568999999 4666799999999 4566543
No 5
>1z1b_A Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 3.80A {Enterobacteria phage lambda} SCOP: d.10.1.4 d.163.1.1 PDB: 1z1g_A 1kjk_A 2wcc_3*
Probab=83.78 E-value=1.5 Score=39.60 Aligned_cols=42 Identities=14% Similarity=0.049 Sum_probs=32.7
Q ss_pred eeeEECCCCeEEEEEecCCCCeEEeecCcccHHHHHHHHHHHHHHh
Q 020408 52 RGIRQRPWGKWAAEIRDPTKGVRVWLGTFNTAEEAARAYDAEARRI 97 (326)
Q Consensus 52 RGVr~r~~GKW~A~I~~p~~gkri~LGtF~T~EEAArAYD~AA~~l 97 (326)
.||++++.|+|+.+.. .+||++.+|. |..||..+...+...+
T Consensus 14 ~~v~~~~~g~~~~r~~--~~gk~~~~g~--t~~eA~~~a~~~~~~~ 55 (356)
T 1z1b_A 14 PNLYIRNNGYYCYRDP--RTGKEFGLGR--DRRIAITEAIQANIEL 55 (356)
T ss_dssp TTEEEETTTEEEEECT--TTCCEEEEES--CHHHHHHHHHHHHHHH
T ss_pred ccceecCCCeEEEEee--cCCeEEECCC--CHHHHHHHHHHHHHHH
Confidence 4788888899998876 7899999996 8888877766554444
No 6
>3jtz_A Integrase; four stranded beta-sheet, DNA binding protein; 1.30A {Yersinia pestis} PDB: 3rmp_A
Probab=50.58 E-value=27 Score=26.93 Aligned_cols=43 Identities=21% Similarity=0.393 Sum_probs=29.4
Q ss_pred EECCCC--eEEEEEecCCCCeEEeecCcc--cHHHHHHHHHHHHHHh
Q 020408 55 RQRPWG--KWAAEIRDPTKGVRVWLGTFN--TAEEAARAYDAEARRI 97 (326)
Q Consensus 55 r~r~~G--KW~A~I~~p~~gkri~LGtF~--T~EEAArAYD~AA~~l 97 (326)
+-+++| .|.-+.+...+.+++-||.|. |.+||....+.+...+
T Consensus 29 ~V~psG~K~w~~ryr~~Gk~~~~~LG~yp~~sL~~AR~~a~~~r~~l 75 (88)
T 3jtz_A 29 LVKPGGSRHWYLKYRISGKESRIALGAYPAISLSDARQQREGIRKML 75 (88)
T ss_dssp EECTTSCEEEEEEEEETTEEEEEEEEETTTSCHHHHHHHHHHHHHHH
T ss_pred EEecCCCEEEEEEEEeCCeEEEEEeECCCCCCHHHHHHHHHHHHHHH
Confidence 455544 499888843344568899996 6888887776666555
No 7
>1b69_A Protein (integrase); integrase, DNA binding, transposition, complex, beta-sheet recognition; HET: DNA; NMR {Enterococcus faecalis} SCOP: d.10.1.1 PDB: 1tn9_A* 1bb8_A 2bb8_A
Probab=36.03 E-value=39 Score=25.49 Aligned_cols=30 Identities=20% Similarity=0.211 Sum_probs=22.6
Q ss_pred CCCCcceeeEECCCCeEEEEEecCCCCeEEe
Q 020408 46 KRKNQYRGIRQRPWGKWAAEIRDPTKGVRVW 76 (326)
Q Consensus 46 ~~~S~YRGVr~r~~GKW~A~I~~p~~gkri~ 76 (326)
++.--+.|+.+|+.|+|+.++.+. .|++.+
T Consensus 7 kgr~L~~GesqR~dG~Y~yry~d~-~Gkr~~ 36 (69)
T 1b69_A 7 RGRILKTGESQRKDGRYLYKYIDS-FGEPQF 36 (69)
T ss_dssp SSSCCCTTEEECSSSCEEEEEECT-TSSEEE
T ss_pred CCCccCCCeEEccCCcEEEEEEcC-CCCEEE
Confidence 345567899999999999999974 355543
No 8
>3ju0_A Phage integrase; four stranded beta-sheet, DNA binding protein; 1.60A {Pectobacterium atrosepticum}
Probab=32.47 E-value=65 Score=25.69 Aligned_cols=43 Identities=21% Similarity=0.308 Sum_probs=28.6
Q ss_pred EECCCC--eEEEEEecCCCCeEEeecCcc--cHHHHHHHHHHHHHHh
Q 020408 55 RQRPWG--KWAAEIRDPTKGVRVWLGTFN--TAEEAARAYDAEARRI 97 (326)
Q Consensus 55 r~r~~G--KW~A~I~~p~~gkri~LGtF~--T~EEAArAYD~AA~~l 97 (326)
+-.++| .|.-+.+...+.+++-||.|. |..+|....+.+...+
T Consensus 29 ~V~psG~K~w~~rYr~~GK~~~~~LG~yp~~SLa~AR~~a~~~r~~l 75 (108)
T 3ju0_A 29 LVHPNGSKYWRLSYRFEKKQRLLALGVYPAVSLADARQRRDEAKKLL 75 (108)
T ss_dssp EECTTSCEEEEEEEEETTEEEEEEEEEETTSCHHHHHHHHHHHHHHH
T ss_pred EEEcCCCEEEEEEEEEcCceEEEecCCCCCCCHHHHHHHHHHHHHHH
Confidence 455544 399888833344567889996 5788877766665555
No 9
>2ftc_I Mitochondrial ribosomal protein L16, 39S ribosomal protein L13, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_I
Probab=28.06 E-value=79 Score=25.82 Aligned_cols=36 Identities=17% Similarity=0.161 Sum_probs=30.1
Q ss_pred EEEEEecCCCCeEEeecCcccHHHHHHHHHHHHHHhcC
Q 020408 62 WAAEIRDPTKGVRVWLGTFNTAEEAARAYDAEARRIRG 99 (326)
Q Consensus 62 W~A~I~~p~~gkri~LGtF~T~EEAArAYD~AA~~l~G 99 (326)
|+|+|. .+..-+-++...+++.|..|...|+.+|-+
T Consensus 80 wva~Vk--~G~ilfEi~g~~~~~~a~eAlr~a~~KlP~ 115 (118)
T 2ftc_I 80 YVTPVK--AGRLVVEMGGRCEFEEVQGFLDQVAHKLPF 115 (118)
T ss_pred EEEEEC--CCCEEEEEeccCCHHHHHHHHHHHHhhCCC
Confidence 999999 666667777778899999999999988744
No 10
>1x60_A Sporulation-specific N-acetylmuramoyl-L-alanine amidase; CWLC, CWLCR, peptidoglycan, cell WALL lytic amidase, tandem repeats, hydrolase; NMR {Bacillus subtilis}
Probab=26.58 E-value=42 Score=24.33 Aligned_cols=23 Identities=17% Similarity=0.326 Sum_probs=18.8
Q ss_pred eEEeecCcccHHHHHHHHHHHHH
Q 020408 73 VRVWLGTFNTAEEAARAYDAEAR 95 (326)
Q Consensus 73 kri~LGtF~T~EEAArAYD~AA~ 95 (326)
-|+++|.|.+.++|.++..+...
T Consensus 46 yRV~vGpf~~~~~A~~~~~~L~~ 68 (79)
T 1x60_A 46 YKVQIGAFSSKDNADTLAARAKN 68 (79)
T ss_dssp EEEEEEEESSHHHHHHHHHHHHH
T ss_pred EEEEECCcCCHHHHHHHHHHHHH
Confidence 47888999999999988776554
No 11
>1uta_A FTSN, MSGA, cell division protein FTSN; bacterial cell division protein, RNP domain, transmembrane, inner membrane, repeat; NMR {Escherichia coli} SCOP: d.58.52.1
Probab=25.97 E-value=56 Score=23.95 Aligned_cols=25 Identities=20% Similarity=0.146 Sum_probs=19.8
Q ss_pred CCeEEeecCcccHHHHHHHHHHHHH
Q 020408 71 KGVRVWLGTFNTAEEAARAYDAEAR 95 (326)
Q Consensus 71 ~gkri~LGtF~T~EEAArAYD~AA~ 95 (326)
.--||.+|.|.+.++|.++..+...
T Consensus 44 ~~yRV~vGpf~s~~~A~~~~~~L~~ 68 (81)
T 1uta_A 44 GWNRVVIGPVKGKENADSTLNRLKM 68 (81)
T ss_dssp SSEEEEESSCBTTTHHHHHHHHHHH
T ss_pred cEEEEEECCcCCHHHHHHHHHHHHH
Confidence 3457889999999999988766554
No 12
>3lto_A Mevalonate diphosphate decarboxylase; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.27A {Legionella pneumophila}
Probab=24.93 E-value=14 Score=34.99 Aligned_cols=22 Identities=9% Similarity=-0.031 Sum_probs=16.5
Q ss_pred ccccc-chhhheeccccc-ccccc
Q 020408 3 FASLY-DLVVLLVYEITF-FFLFS 24 (326)
Q Consensus 3 AA~AY-D~Aalk~~g~~~-~~N~~ 24 (326)
.|||| ++|.+||||..- .+|++
T Consensus 4 ~a~a~~nialiKYwGk~d~~l~lP 27 (323)
T 3lto_A 4 FAQAPANIALIKYMGKKDENSNLP 27 (323)
T ss_dssp EEEEEEEEEEECCTTCBCTTTCCB
T ss_pred EEEecchhHHhHhcCcccccccCC
Confidence 47888 899999999864 34453
No 13
>2bn8_A CEDA, cell division activator CEDA; cell division activator protein, cell cycle protein; NMR {Escherichia coli} PDB: 2d35_A
Probab=21.14 E-value=55 Score=25.29 Aligned_cols=39 Identities=21% Similarity=0.286 Sum_probs=27.4
Q ss_pred CCCcceeeEECCCCeEEEEEecCCCCeEEeecCcccHHHHHH
Q 020408 47 RKNQYRGIRQRPWGKWAAEIRDPTKGVRVWLGTFNTAEEAAR 88 (326)
Q Consensus 47 ~~S~YRGVr~r~~GKW~A~I~~p~~gkri~LGtF~T~EEAAr 88 (326)
.--+||-||.-+ |||+|.+. .+-.-..--.|..+|.|.|
T Consensus 36 kmd~frdvw~lr-gkyvafvl--~ge~frrspafsvpesaqr 74 (87)
T 2bn8_A 36 KMDSFRDVWMLR-GKYVAFVL--MGESFLRSPAFTVPESAQR 74 (87)
T ss_dssp CTTTCTTEEEET-TEEEEBCC--SSSCCCBCCCBSSHHHHHH
T ss_pred hcccchhheeec-cceEEEEE--echhhccCCccCCcHHHHH
Confidence 456799998776 99999988 3333333456788877765
Done!