Query 043551
Match_columns 408
No_of_seqs 343 out of 1900
Neff 5.1
Searched_HMMs 29240
Date Mon Mar 25 10:14:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043551.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/043551hhsearch_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 99.8 4.6E-22 1.6E-26 154.1 4.4 61 72-137 2-62 (63)
2 1gcc_A Ethylene responsive ele 99.7 3.3E-18 1.1E-22 132.4 4.5 60 165-225 2-62 (63)
3 1u3e_M HNH homing endonuclease 92.0 0.016 5.5E-07 51.8 -1.7 64 140-207 82-146 (174)
4 3igm_B PF14_0633 protein; AP2 89.3 0.065 2.2E-06 42.6 -0.2 25 68-92 3-27 (77)
5 1u3e_M HNH homing endonuclease 48.2 4 0.00014 36.0 0.2 38 73-119 109-146 (174)
6 3igm_B PF14_0633 protein; AP2 47.6 14 0.00048 29.3 3.2 23 161-183 3-25 (77)
7 1z1b_A Integrase; protein-DNA 18.4 87 0.003 29.0 3.8 42 167-213 14-55 (356)
8 1ais_A TBP, protein (tata-bind 16.7 3E+02 0.01 24.6 6.7 135 69-214 39-179 (182)
9 2z8u_A Tata-box-binding protei 16.1 1.5E+02 0.0051 26.8 4.6 133 69-213 43-182 (188)
10 3eik_A Tata-box-binding protei 16.0 2.3E+02 0.0079 26.3 5.9 129 70-213 74-212 (218)
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=99.84 E-value=4.6e-22 Score=154.08 Aligned_cols=61 Identities=34% Similarity=0.690 Sum_probs=56.5
Q ss_pred CeEEeeEcCCCCceEEEEecCCCCCCCCCcccccCCCCCHHHHHHHHHHHhHhhcCCCcccCCCcc
Q 043551 72 KYRGVSRHRWTGRYEAHLWDKGSWNPTQRKKGKQGAYDEEESAARAYDLAALKYWGTSTFTNFPVS 137 (408)
Q Consensus 72 ~yrGV~~~~~~gkW~A~I~~~~~~~~~~~k~~~LGtF~teEeAArAYD~AA~~~~G~~a~~NFP~~ 137 (408)
+||||++++| |||+|+|+++.. +++++|||+|+|+||||+|||.|+++++|..+.+|||.+
T Consensus 2 ~yrGV~~r~~-gkw~A~I~~~~~----~g~r~~LGtf~T~eeAA~AyD~Aa~~~~G~~a~~NFp~~ 62 (63)
T 1gcc_A 2 HYRGVRQRPW-GKFAAEIRDPAK----NGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLR 62 (63)
T ss_dssp CCTTEEEETT-TEEEEEEEETTT----TSEEEEEEEESSHHHHHHHHHHHHHHHHSSCCCCSSCTT
T ss_pred CcccEeeCCC-CcEEEEEccccC----CCeEEEeeeCCCHHHHHHHHHHHHHHhcCcccccCCCCc
Confidence 6999999998 999999999742 368999999999999999999999999999999999974
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=99.71 E-value=3.3e-18 Score=132.41 Aligned_cols=60 Identities=37% Similarity=0.516 Sum_probs=54.5
Q ss_pred cccCceeccCCCcceeeecccc-CCcccccccCCCHHHHHhhhHHHHHHhcCCcccCCCCcc
Q 043551 165 FSRGVSKHHHNRRWEARIGRVF-GNKYLYLGTYGTQEEAAHAYDIAAIEHRGINAVTNFDIS 225 (408)
Q Consensus 165 ~yRGVs~~~~~GkW~A~I~~~~-~~k~i~LGtF~TeEEAA~AYD~Aa~~l~G~~A~tNFp~~ 225 (408)
.|+||+++ ++|||+|+|+... +++++|||+|+|+||||+|||.|+++++|.++.+|||.+
T Consensus 2 ~yrGV~~r-~~gkw~A~I~~~~~~g~r~~LGtf~T~eeAA~AyD~Aa~~~~G~~a~~NFp~~ 62 (63)
T 1gcc_A 2 HYRGVRQR-PWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLR 62 (63)
T ss_dssp CCTTEEEE-TTTEEEEEEEETTTTSEEEEEEEESSHHHHHHHHHHHHHHHHSSCCCCSSCTT
T ss_pred CcccEeeC-CCCcEEEEEccccCCCeEEEeeeCCCHHHHHHHHHHHHHHhcCcccccCCCCc
Confidence 48999986 6899999998654 468999999999999999999999999999999999864
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=91.95 E-value=0.016 Score=51.83 Aligned_cols=64 Identities=11% Similarity=0.004 Sum_probs=46.3
Q ss_pred hHHHHHhhhhhhhhhhhhhhccC-CCcccCceeccCCCcceeeeccccCCcccccccCCCHHHHHhhhH
Q 043551 140 EKEIEIMKTVTREEYLATLRRRS-SGFSRGVSKHHHNRRWEARIGRVFGNKYLYLGTYGTQEEAAHAYD 207 (408)
Q Consensus 140 ~~EI~eL~~vSkeE~va~lRrks-sg~yRGVs~~~~~GkW~A~I~~~~~~k~i~LGtF~TeEEAA~AYD 207 (408)
...+.+|+-+|..|+........ .+.++||.+ ...++|.+.|. ++ +..+||.|.|.+|||++|.
T Consensus 82 nn~~~NL~~~t~~eN~~~~~~~~~~~~~~g~~~-~~~~k~~~vi~--~~-~~~~~~~f~s~~eAa~~~G 146 (174)
T 1u3e_M 82 NNLSTNLRWVTQKINVENQMSRGTLNVSKAQQI-AKIKNQKPIIV--IS-PDGIEKEYPSTKCACEELG 146 (174)
T ss_dssp CCCGGGEEEECHHHHHHHHHHHTCCCCHHHHHH-HHHHTCCCEEE--EC-TTSCEEEESCHHHHHHHHT
T ss_pred CCCHHHcEECCHHHHhhcccccCcccceeeeee-ccCCCCceEEE--Ec-CCceEEeeCCHHHHHHHHC
Confidence 35788899999999876433222 222467766 45677999994 45 6788999999999999863
No 4
>3igm_B PF14_0633 protein; AP2 domain, specific transcription FA protein-DNA complex, transcription-DNA complex; 2.20A {Plasmodium falciparum}
Probab=89.28 E-value=0.065 Score=42.58 Aligned_cols=25 Identities=32% Similarity=0.429 Sum_probs=22.0
Q ss_pred CCCCCeEEeeEcCCCCceEEEEecC
Q 043551 68 KRSSKYRGVSRHRWTGRYEAHLWDK 92 (408)
Q Consensus 68 ~~sS~yrGV~~~~~~gkW~A~I~~~ 92 (408)
..+|+|.||+|++..+.|.|+-.++
T Consensus 3 ~~~Sg~pGVsw~kR~~~WlA~W~e~ 27 (77)
T 3igm_B 3 HMSSGYPGVSWNKRMCAWLAFFYDG 27 (77)
T ss_dssp -CCSSSTTEEEETTTTEEEEEEEET
T ss_pred CCCCCCCcEEeecCCceEEEEEecC
Confidence 4679999999999999999998776
No 5
>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=48.16 E-value=4 Score=36.02 Aligned_cols=38 Identities=8% Similarity=0.030 Sum_probs=28.1
Q ss_pred eEEeeEcCCCCceEEEEecCCCCCCCCCcccccCCCCCHHHHHHHHH
Q 043551 73 YRGVSRHRWTGRYEAHLWDKGSWNPTQRKKGKQGAYDEEESAARAYD 119 (408)
Q Consensus 73 yrGV~~~~~~gkW~A~I~~~~~~~~~~~k~~~LGtF~teEeAArAYD 119 (408)
++||.+ +..++|.|.|... +..+||.|+|.+|||++|.
T Consensus 109 ~~g~~~-~~~~k~~~vi~~~--------~~~~~~~f~s~~eAa~~~G 146 (174)
T 1u3e_M 109 SKAQQI-AKIKNQKPIIVIS--------PDGIEKEYPSTKCACEELG 146 (174)
T ss_dssp HHHHHH-HHHHTCCCEEEEC--------TTSCEEEESCHHHHHHHHT
T ss_pred eeeeee-ccCCCCceEEEEc--------CCceEEeeCCHHHHHHHHC
Confidence 467765 3336788888753 4567999999999999864
No 6
>3igm_B PF14_0633 protein; AP2 domain, specific transcription FA protein-DNA complex, transcription-DNA complex; 2.20A {Plasmodium falciparum}
Probab=47.58 E-value=14 Score=29.28 Aligned_cols=23 Identities=26% Similarity=0.111 Sum_probs=19.5
Q ss_pred cCCCcccCceeccCCCcceeeec
Q 043551 161 RSSGFSRGVSKHHHNRRWEARIG 183 (408)
Q Consensus 161 kssg~yRGVs~~~~~GkW~A~I~ 183 (408)
+.++++.||+|.++.+.|.|.-.
T Consensus 3 ~~~Sg~pGVsw~kR~~~WlA~W~ 25 (77)
T 3igm_B 3 HMSSGYPGVSWNKRMCAWLAFFY 25 (77)
T ss_dssp -CCSSSTTEEEETTTTEEEEEEE
T ss_pred CCCCCCCcEEeecCCceEEEEEe
Confidence 45678999999999999999973
No 7
>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=18.43 E-value=87 Score=28.95 Aligned_cols=42 Identities=21% Similarity=0.030 Sum_probs=0.0
Q ss_pred cCceeccCCCcceeeeccccCCcccccccCCCHHHHHhhhHHHHHHh
Q 043551 167 RGVSKHHHNRRWEARIGRVFGNKYLYLGTYGTQEEAAHAYDIAAIEH 213 (408)
Q Consensus 167 RGVs~~~~~GkW~A~I~~~~~~k~i~LGtF~TeEEAA~AYD~Aa~~l 213 (408)
.||... ..|.|+.+. ..+||++.+|. |..||..+...+...+
T Consensus 14 ~~v~~~-~~g~~~~r~--~~~gk~~~~g~--t~~eA~~~a~~~~~~~ 55 (356)
T 1z1b_A 14 PNLYIR-NNGYYCYRD--PRTGKEFGLGR--DRRIAITEAIQANIEL 55 (356)
T ss_dssp TTEEEE-TTTEEEEEC--TTTCCEEEEES--CHHHHHHHHHHHHHHH
T ss_pred ccceec-CCCeEEEEe--ecCCeEEECCC--CHHHHHHHHHHHHHHH
No 8
>1ais_A TBP, protein (tata-binding protein); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: d.129.1.1 d.129.1.1 PDB: 1d3u_A* 1pcz_A
Probab=16.67 E-value=3e+02 Score=24.59 Aligned_cols=135 Identities=14% Similarity=0.081 Sum_probs=75.7
Q ss_pred CCCCeEEeeEcCCCCceEEEEecCCCCCCCCCcccccCCCCCHHHHHHHHHHHhHhhcCCCc-ccCCCcchhhHHHH--H
Q 043551 69 RSSKYRGVSRHRWTGRYEAHLWDKGSWNPTQRKKGKQGAYDEEESAARAYDLAALKYWGTST-FTNFPVSEYEKEIE--I 145 (408)
Q Consensus 69 ~sS~yrGV~~~~~~gkW~A~I~~~~~~~~~~~k~~~LGtF~teEeAArAYD~AA~~~~G~~a-~~NFP~~dy~~EI~--e 145 (408)
+..+|-||..+-..-+-.+-|+.. ||-+-.| ..++|+|..|.++.+..+..-.- ...|+.-.-.+-.. .
T Consensus 39 ~P~~fpgli~Rl~~P~~t~lIF~S-------GKiv~TG-akS~~~~~~a~~~i~~~L~~lG~~~~~~~~~~I~NIVas~~ 110 (182)
T 1ais_A 39 NPEEFPGIICHLDDPKVALLIFSS-------GKLVVTG-AKSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNMVFSGD 110 (182)
T ss_dssp CTTTCSSEEEECSSSCCEEEECTT-------SEEEEEE-ESSHHHHHHHHHHHHHHHHHTTCCCSSSCEEEEEEEEEEEE
T ss_pred CCCccccEEEEcCCCcEEEEEeCC-------CeEEEec-CCCHHHHHHHHHHHHHHHHHcCCCcccccceEEEEEEEEEE
Confidence 334688998887767888888876 5544444 47889999999987766532211 01122100000000 0
Q ss_pred h-hhhhhhhhhhhhhc--cCCCcccCceeccCCCcceeeeccccCCcccccccCCCHHHHHhhhHHHHHHhc
Q 043551 146 M-KTVTREEYLATLRR--RSSGFSRGVSKHHHNRRWEARIGRVFGNKYLYLGTYGTQEEAAHAYDIAAIEHR 214 (408)
Q Consensus 146 L-~~vSkeE~va~lRr--kssg~yRGVs~~~~~GkW~A~I~~~~~~k~i~LGtF~TeEEAA~AYD~Aa~~l~ 214 (408)
| -.+..+.+...++. -....|-|+-++-..-+=.+-| +..||-+-.|. .+++|+..|.++....+.
T Consensus 111 l~~~i~L~~la~~~~~~~YePe~fpgli~R~~~pk~~~lI--F~SGKiviTGa-ks~~~~~~a~~~i~~~L~ 179 (182)
T 1ais_A 111 IGREFNLDVVALTLPNCEYEPEQFPGVIYRVKEPKSVILL--FSSGKIVCSGA-KSEADAWEAVRKLLRELD 179 (182)
T ss_dssp CSSCCCHHHHHHHSTTEECCTTTCSSEEEEETTTTEEEEE--CTTSEEEEEEE-SSHHHHHHHHHHHHHHHT
T ss_pred cCCccCHHHHHhhCCCCEECCccCceEEEEeCCCcEEEEE--ecCCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 0 00111111111111 1123467888765665666777 56777776665 788999999988766553
No 9
>2z8u_A Tata-box-binding protein; transcription, DNA-binding protein, transcription factor, transcription regulation; 1.90A {Methanococcus jannaschii}
Probab=16.12 E-value=1.5e+02 Score=26.78 Aligned_cols=133 Identities=12% Similarity=0.075 Sum_probs=71.3
Q ss_pred CCCCeEEeeEcCCCCceEEEEecCCCCCCCCCcccccCCCCCHHHHHHHHHHHhHhhc--CCCcccCCCcchhhHHHH--
Q 043551 69 RSSKYRGVSRHRWTGRYEAHLWDKGSWNPTQRKKGKQGAYDEEESAARAYDLAALKYW--GTSTFTNFPVSEYEKEIE-- 144 (408)
Q Consensus 69 ~sS~yrGV~~~~~~gkW~A~I~~~~~~~~~~~k~~~LGtF~teEeAArAYD~AA~~~~--G~~a~~NFP~~dy~~EI~-- 144 (408)
+..+|-||..+-..-+=.+-|+.. ||-+-.|. .++|+|..|-.+.+..+. |-. ...||.-.-.+-..
T Consensus 43 ~P~~fpgli~Rl~~Pk~t~lIF~S-------GKiv~TGA-kS~e~a~~a~~~~~~~L~~lg~~-~~~~~~~~I~NIVas~ 113 (188)
T 2z8u_A 43 EPEQFPGLVCRLSVPKVALLIFRS-------GKVNCTGA-KSKEEAEIAIKKIIKELKDAGID-VIENPEIKIQNMVATA 113 (188)
T ss_dssp ------CEEEEETTTTEEEEECTT-------SEEEEEEE-SSHHHHHHHHHHHHHHHHHTTCC-CCSSCCCEEEEEEEEE
T ss_pred CCCCcccEEEEcCCCcEEEEEeCC-------CeEEEecC-CCHHHHHHHHHHHHHHHHhcCCC-ccccCceEEEEEEEEE
Confidence 334689998887767888888876 66555565 467788888888775553 321 01122100000000
Q ss_pred Hh-hhhhhhhhhhhhhc--cCCCcccCceeccCCCcceeeeccccCCcccccccCCCHHHHHhhhHHHHHHh
Q 043551 145 IM-KTVTREEYLATLRR--RSSGFSRGVSKHHHNRRWEARIGRVFGNKYLYLGTYGTQEEAAHAYDIAAIEH 213 (408)
Q Consensus 145 eL-~~vSkeE~va~lRr--kssg~yRGVs~~~~~GkW~A~I~~~~~~k~i~LGtF~TeEEAA~AYD~Aa~~l 213 (408)
.| -.+..+.+...++. -....|-|+-++-..-|=.+-| +..||-+-.|. .+++|+..|.++....+
T Consensus 114 ~l~~~i~L~~la~~~~~~eYePe~fPgliyR~~~Pk~t~lI--F~SGKiviTGa-ks~~~~~~A~~~i~~~L 182 (188)
T 2z8u_A 114 DLGIEPNLDDIALMVEGTEYEPEQFPGLVYRLDDPKVVVLI--FGSGKVVITGL-KSEEDAKRALKKILDTI 182 (188)
T ss_dssp ECSSCCCHHHHHHHSTTEEECTTTSSSEEEEEETTEEEEEE--CTTSEEEEESC-SCHHHHHHHHHHHHHHH
T ss_pred ecCCccCHHHHHhhCcCcEECCccCceEEEEeCCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 00 00111111111111 1122468888765665666777 56777777776 78899999998866554
No 10
>3eik_A Tata-box-binding protein; DNA-binding, initiation factor, nucleus, transcription; 1.90A {Encephalitozoon cuniculi} PDB: 3oci_A 3oc3_C
Probab=16.02 E-value=2.3e+02 Score=26.29 Aligned_cols=129 Identities=13% Similarity=0.097 Sum_probs=77.5
Q ss_pred CCCeEEeeEcCCCCceEEEEecCCCCCCCCCcccccCCCCCHHHHHHHHHHHhHhhcCCCcccCCCcchhhHHHHH----
Q 043551 70 SSKYRGVSRHRWTGRYEAHLWDKGSWNPTQRKKGKQGAYDEEESAARAYDLAALKYWGTSTFTNFPVSEYEKEIEI---- 145 (408)
Q Consensus 70 sS~yrGV~~~~~~gkW~A~I~~~~~~~~~~~k~~~LGtF~teEeAArAYD~AA~~~~G~~a~~NFP~~dy~~EI~e---- 145 (408)
..+|-||..|-..-+-.+-|+.. ||-+..|. .++++|..|.++.+..+..-.....|+ ++. +.+
T Consensus 74 Pe~Fpglv~Rl~~Pk~t~LIF~S-------GKiV~TGA-kS~e~a~~A~~ki~~~L~~lG~~v~~~--~fk--IqNIvas 141 (218)
T 3eik_A 74 PKRFAAVIMRIREPKTTALIFAS-------GKMVITGA-KSEKSSRMAAQRYAKIIHKLGFNATFD--DFK--IQNIVSS 141 (218)
T ss_dssp TTTCSSEEEEETTTTEEEEECTT-------SEEEEEEE-SSHHHHHHHHHHHHHHHHHTTCCCCCE--EEE--EEEEEEE
T ss_pred CccCceEEEEecCCcEEEEEECC-------CeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCcccc--cce--EEEEEEE
Confidence 34688998887767888999876 66666665 679999999999887775322122222 110 000
Q ss_pred --h-hhhhhhhhhhhhhcc---CCCcccCceeccCCCcceeeeccccCCcccccccCCCHHHHHhhhHHHHHHh
Q 043551 146 --M-KTVTREEYLATLRRR---SSGFSRGVSKHHHNRRWEARIGRVFGNKYLYLGTYGTQEEAAHAYDIAAIEH 213 (408)
Q Consensus 146 --L-~~vSkeE~va~lRrk---ssg~yRGVs~~~~~GkW~A~I~~~~~~k~i~LGtF~TeEEAA~AYD~Aa~~l 213 (408)
| -.+..+.+....+.. .-..|-|+-++-..-|=...| +..||-+-.|. .+++|+..|++..--.+
T Consensus 142 ~dl~f~I~Le~la~~~~~~~~YEPE~fPGliyR~~~pkvt~lI--F~SGKiviTGa-ks~~d~~~A~~~I~p~L 212 (218)
T 3eik_A 142 CDIKFSIRLEGLAYAHSNYCSYEPELFPGLIYRMVKPKIVLLI--FVSGKIVLTGA-KVRDDIYQAFNNIYPVL 212 (218)
T ss_dssp EECSSCBCHHHHHHHSTTTEECCTTTSSSEEEEETTTTEEEEE--CTTSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred EECCCcCcHHHHHHhccCCcEECCccCceEEEEcCCCCEEEEE--eCCCeEEEEec-CCHHHHHHHHHHHHHHH
Confidence 0 001111221111111 112367888866666667777 56677776776 88999999998665443
Done!