Query 038243
Match_columns 680
No_of_seqs 378 out of 1651
Neff 3.8
Searched_HMMs 29240
Date Mon Mar 25 15:22:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038243.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/038243hhsearch_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 1.5E-20 5E-25 154.6 5.4 60 353-413 2-62 (63)
2 1gcc_A Ethylene responsive ele 99.8 2.8E-20 9.6E-25 152.9 4.7 61 254-319 2-62 (63)
3 1u3e_M HNH homing endonuclease 93.8 0.0079 2.7E-07 56.9 -1.0 65 322-395 82-146 (174)
4 3igm_B PF14_0633 protein; AP2 93.0 0.034 1.2E-06 47.7 1.8 54 250-304 3-58 (77)
5 3igm_B PF14_0633 protein; AP2 69.5 2.1 7.2E-05 36.8 2.1 23 349-371 3-25 (77)
6 3eik_A Tata-box-binding protei 51.3 24 0.00081 35.4 6.3 134 254-401 76-212 (218)
7 1u3e_M HNH homing endonuclease 49.5 1.6 5.3E-05 41.2 -2.4 38 255-301 109-146 (174)
8 1ais_A TBP, protein (tata-bind 35.9 70 0.0024 30.9 6.7 133 254-402 42-179 (182)
9 2z8u_A Tata-box-binding protei 29.2 1.2E+02 0.0042 29.4 7.2 132 254-401 46-182 (188)
10 1z1b_A Integrase; protein-DNA 28.5 50 0.0017 32.4 4.4 42 355-401 14-55 (356)
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=99.81 E-value=1.5e-20 Score=154.56 Aligned_cols=60 Identities=43% Similarity=0.684 Sum_probs=55.1
Q ss_pred ccccceeeccCCceEEEeccccC-CcccccCCCCCHHHHHHHHHHHHHHhcCCCCccCCCCC
Q 038243 353 IYRGVTRHHQHGRWQARIGRVAG-NKDLYLGTFSTQEEAAEAYDIAAIKFRGLNAVTNFDMT 413 (680)
Q Consensus 353 ~YRGV~r~r~~GKW~AeIr~~~~-gKri~LGTFdTeEEAArAYD~AAiklrG~~A~tNFp~s 413 (680)
+||||+++ ++|||+|+|+.+.. ++++|||+|+|+||||+|||.|+++++|..++||||++
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 69999865 69999999987664 68999999999999999999999999999999999974
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=99.79 E-value=2.8e-20 Score=152.88 Aligned_cols=61 Identities=34% Similarity=0.658 Sum_probs=56.3
Q ss_pred ceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhcccccccccCCCC
Q 038243 254 IYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYWGTTTTTNFPIS 319 (680)
Q Consensus 254 ~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~G~~A~lNFP~s 319 (680)
+||||++++| |||+|+|+++. .+++++|||+|+|+||||+|||+|+++++|..+.+|||.+
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-GKFAAEIRDPA----KNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLR 62 (63)
T ss_dssp CCTTEEEETT-TEEEEEEEETT----TTSEEEEEEEESSHHHHHHHHHHHHHHHHSSCCCCSSCTT
T ss_pred CcccEeeCCC-CcEEEEEcccc----CCCeEEEeeeCCCHHHHHHHHHHHHHHhcCcccccCCCCc
Confidence 5999999997 99999999984 2458999999999999999999999999999999999975
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=93.77 E-value=0.0079 Score=56.90 Aligned_cols=65 Identities=9% Similarity=0.066 Sum_probs=49.0
Q ss_pred hhhHHHhhhhhhhhHHHhhhcccCCcccCccccccceeeccCCceEEEeccccCCcccccCCCCCHHHHHHHHH
Q 038243 322 EKEVEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYD 395 (680)
Q Consensus 322 eeELeELRemSReE~VAsLRRrSsG~SRgtS~YRGV~r~r~~GKW~AeIr~~~~gKri~LGTFdTeEEAArAYD 395 (680)
...+++|+.+++.|+.....+... . ..++||.+ ...++|.+.|. .. +.++||.|+|.+|||++|.
T Consensus 82 nn~~~NL~~~t~~eN~~~~~~~~~---~--~~~~g~~~-~~~~k~~~vi~--~~-~~~~~~~f~s~~eAa~~~G 146 (174)
T 1u3e_M 82 NNLSTNLRWVTQKINVENQMSRGT---L--NVSKAQQI-AKIKNQKPIIV--IS-PDGIEKEYPSTKCACEELG 146 (174)
T ss_dssp CCCGGGEEEECHHHHHHHHHHHTC---C--CCHHHHHH-HHHHTCCCEEE--EC-TTSCEEEESCHHHHHHHHT
T ss_pred CCCHHHcEECCHHHHhhcccccCc---c--cceeeeee-ccCCCCceEEE--Ec-CCceEEeeCCHHHHHHHHC
Confidence 346789999999999887665522 1 12467765 55678999983 44 7788999999999999975
No 4
>3igm_B PF14_0633 protein; AP2 domain, specific transcription FA protein-DNA complex, transcription-DNA complex; 2.20A {Plasmodium falciparum}
Probab=93.01 E-value=0.034 Score=47.72 Aligned_cols=54 Identities=20% Similarity=0.260 Sum_probs=35.6
Q ss_pred CCccceeeeeeecCCCceEEEEecCCcccCCcccccccCCC--CCHHHHHHHHHHHh
Q 038243 250 QRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGY--DKEEKAARAYDLAA 304 (680)
Q Consensus 250 qrTS~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtF--dTeEeAArAYD~AA 304 (680)
...|+|+||+|+++.+.|.|+-.++..++...=...++| | +.+.+||..|-+..
T Consensus 3 ~~~Sg~pGVsw~kR~~~WlA~W~e~g~rrsRtF~~k~yG-f~~e~Ak~~AIef~k~l 58 (77)
T 3igm_B 3 HMSSGYPGVSWNKRMCAWLAFFYDGASRRSRTFHPKHFN-MDKEKARLAAVEFMKTV 58 (77)
T ss_dssp -CCSSSTTEEEETTTTEEEEEEEETTEEEEEEECCTTHH-HHHHHHHHHHHHHHHHT
T ss_pred CCCCCCCcEEeecCCceEEEEEecCCeEeeeeechhhcC-cCHHHHHHHHHHHHHHH
Confidence 356899999999999999999888753332111223345 6 46666666665543
No 5
>3igm_B PF14_0633 protein; AP2 domain, specific transcription FA protein-DNA complex, transcription-DNA complex; 2.20A {Plasmodium falciparum}
Probab=69.49 E-value=2.1 Score=36.84 Aligned_cols=23 Identities=26% Similarity=0.304 Sum_probs=19.8
Q ss_pred cCccccccceeeccCCceEEEec
Q 038243 349 RGASIYRGVTRHHQHGRWQARIG 371 (680)
Q Consensus 349 RgtS~YRGV~r~r~~GKW~AeIr 371 (680)
..+|+|+||+|.+..+.|.|.-.
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 34699999999999999999984
No 6
>3eik_A Tata-box-binding protein; DNA-binding, initiation factor, nucleus, transcription; 1.90A {Encephalitozoon cuniculi} PDB: 3oci_A 3oc3_C
Probab=51.27 E-value=24 Score=35.42 Aligned_cols=134 Identities=11% Similarity=0.073 Sum_probs=79.6
Q ss_pred ceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhcccccccccCC---CCcchhhHHHhhh
Q 038243 254 IYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYWGTTTTTNFP---ISNYEKEVEEMKH 330 (680)
Q Consensus 254 ~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~G~~A~lNFP---~sdYeeELeELRe 330 (680)
+|-||..|-..-|-.+-|+..+ |-+-.| -.++|+|.+|.++.+..|.-..-...|+ ....-...+.--.
T Consensus 76 ~Fpglv~Rl~~Pk~t~LIF~SG-------KiV~TG-AkS~e~a~~A~~ki~~~L~~lG~~v~~~~fkIqNIvas~dl~f~ 147 (218)
T 3eik_A 76 RFAAVIMRIREPKTTALIFASG-------KMVITG-AKSEKSSRMAAQRYAKIIHKLGFNATFDDFKIQNIVSSCDIKFS 147 (218)
T ss_dssp TCSSEEEEETTTTEEEEECTTS-------EEEEEE-ESSHHHHHHHHHHHHHHHHHTTCCCCCEEEEEEEEEEEEECSSC
T ss_pred cCceEEEEecCCcEEEEEECCC-------eEEEEe-cCCHHHHHHHHHHHHHHHHHcCCCcccccceEEEEEEEEECCCc
Confidence 4889988888788999998773 333333 4689999999999888775321122221 1100000000001
Q ss_pred hhhhhHHHhhhcccCCcccCccccccceeeccCCceEEEeccccCCcccccCCCCCHHHHHHHHHHHHHHh
Q 038243 331 MTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKF 401 (680)
Q Consensus 331 mSReE~VAsLRRrSsG~SRgtS~YRGV~r~r~~GKW~AeIr~~~~gKri~LGTFdTeEEAArAYD~AAikl 401 (680)
...++.....+.. ..=.-..|.|+..+-..-|-..-| ...||-+..|. .++||+.+|++.-.-.|
T Consensus 148 I~Le~la~~~~~~---~~YEPE~fPGliyR~~~pkvt~lI--F~SGKiviTGa-ks~~d~~~A~~~I~p~L 212 (218)
T 3eik_A 148 IRLEGLAYAHSNY---CSYEPELFPGLIYRMVKPKIVLLI--FVSGKIVLTGA-KVRDDIYQAFNNIYPVL 212 (218)
T ss_dssp BCHHHHHHHSTTT---EECCTTTSSSEEEEETTTTEEEEE--CTTSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHhccCC---cEECCccCceEEEEcCCCCEEEEE--eCCCeEEEEec-CCHHHHHHHHHHHHHHH
Confidence 1111111111111 111235689987766667788888 67788888886 78999999999766544
No 7
>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=49.49 E-value=1.6 Score=41.16 Aligned_cols=38 Identities=8% Similarity=-0.003 Sum_probs=28.6
Q ss_pred eeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHH
Q 038243 255 YRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYD 301 (680)
Q Consensus 255 YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD 301 (680)
++||.+ +..++|.+.|... +...+|.|++.+|||++|.
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 467776 4457788888443 3467899999999999974
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=35.88 E-value=70 Score=30.91 Aligned_cols=133 Identities=14% Similarity=0.112 Sum_probs=78.1
Q ss_pred ceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhcc--ccc-c-cccCCCCcchhhHHHhh
Q 038243 254 IYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYW--GTT-T-TTNFPISNYEKEVEEMK 329 (680)
Q Consensus 254 ~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~--G~~-A-~lNFP~sdYeeELeELR 329 (680)
+|.||..|-..-|-.+-|+.++ +...=...++|+|.+|..+.+..+. |-. . ..+|-..+.-... .+.
T Consensus 42 ~fpgli~Rl~~P~~t~lIF~SG--------Kiv~TGakS~~~~~~a~~~i~~~L~~lG~~~~~~~~~~I~NIVas~-~l~ 112 (182)
T 1ais_A 42 EFPGIICHLDDPKVALLIFSSG--------KLVVTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNMVFSG-DIG 112 (182)
T ss_dssp TCSSEEEECSSSCCEEEECTTS--------EEEEEEESSHHHHHHHHHHHHHHHHHTTCCCSSSCEEEEEEEEEEE-ECS
T ss_pred ccccEEEEcCCCcEEEEEeCCC--------eEEEecCCCHHHHHHHHHHHHHHHHHcCCCcccccceEEEEEEEEE-EcC
Confidence 4889988877778888888763 3333345789999999999877764 311 0 1122111100000 000
Q ss_pred -hhhhhhHHHhhhcccCCcccCccccccceeeccCCceEEEeccccCCcccccCCCCCHHHHHHHHHHHHHHhc
Q 038243 330 -HMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFR 402 (680)
Q Consensus 330 -emSReE~VAsLRRrSsG~SRgtS~YRGV~r~r~~GKW~AeIr~~~~gKri~LGTFdTeEEAArAYD~AAiklr 402 (680)
....++....++ ...=.-..|.|+..+-..-|-.+-| ...||-+..|. .++||+.+|.++-+..|.
T Consensus 113 ~~i~L~~la~~~~----~~~YePe~fpgli~R~~~pk~~~lI--F~SGKiviTGa-ks~~~~~~a~~~i~~~L~ 179 (182)
T 1ais_A 113 REFNLDVVALTLP----NCEYEPEQFPGVIYRVKEPKSVILL--FSSGKIVCSGA-KSEADAWEAVRKLLRELD 179 (182)
T ss_dssp SCCCHHHHHHHST----TEECCTTTCSSEEEEETTTTEEEEE--CTTSEEEEEEE-SSHHHHHHHHHHHHHHHT
T ss_pred CccCHHHHHhhCC----CCEECCccCceEEEEeCCCcEEEEE--ecCCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 111111111111 1122345799987666667778888 66788777774 688999999998776654
No 9
>2z8u_A Tata-box-binding protein; transcription, DNA-binding protein, transcription factor, transcription regulation; 1.90A {Methanococcus jannaschii}
Probab=29.15 E-value=1.2e+02 Score=29.41 Aligned_cols=132 Identities=12% Similarity=0.145 Sum_probs=73.5
Q ss_pred ceeeeeeecCCCceEEEEecCCcccCCcccccccCCCCCHHHHHHHHHHHhhhcc--ccc--ccccCCCCcchhhHHHhh
Q 038243 254 IYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQGGYDKEEKAARAYDLAALKYW--GTT--TTTNFPISNYEKEVEEMK 329 (680)
Q Consensus 254 ~YRGV~r~kwtGRW~AeI~d~~~rr~~k~kr~~LGtFdTeEeAArAYD~AAlkl~--G~~--A~lNFP~sdYeeELeELR 329 (680)
+|.||..|-..-|=.+-|+.++ |-.-.|. .++|+|..|-.+.+..+. |-. ...+|-..+.-... .+.
T Consensus 46 ~fpgli~Rl~~Pk~t~lIF~SG-------Kiv~TGA-kS~e~a~~a~~~~~~~L~~lg~~~~~~~~~~I~NIVas~-~l~ 116 (188)
T 2z8u_A 46 QFPGLVCRLSVPKVALLIFRSG-------KVNCTGA-KSKEEAEIAIKKIIKELKDAGIDVIENPEIKIQNMVATA-DLG 116 (188)
T ss_dssp ---CEEEEETTTTEEEEECTTS-------EEEEEEE-SSHHHHHHHHHHHHHHHHHTTCCCCSSCCCEEEEEEEEE-ECS
T ss_pred CcccEEEEcCCCcEEEEEeCCC-------eEEEecC-CCHHHHHHHHHHHHHHHHhcCCCccccCceEEEEEEEEE-ecC
Confidence 4889888877778888888763 3332343 477889988888776663 311 00122111100000 000
Q ss_pred -hhhhhhHHHhhhcccCCcccCccccccceeeccCCceEEEeccccCCcccccCCCCCHHHHHHHHHHHHHHh
Q 038243 330 -HMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKF 401 (680)
Q Consensus 330 -emSReE~VAsLRRrSsG~SRgtS~YRGV~r~r~~GKW~AeIr~~~~gKri~LGTFdTeEEAArAYD~AAikl 401 (680)
....++....++ ...=.-..|.||..+-..-|-.+-| ...||-+..|. .++||+.+|+++....|
T Consensus 117 ~~i~L~~la~~~~----~~eYePe~fPgliyR~~~Pk~t~lI--F~SGKiviTGa-ks~~~~~~A~~~i~~~L 182 (188)
T 2z8u_A 117 IEPNLDDIALMVE----GTEYEPEQFPGLVYRLDDPKVVVLI--FGSGKVVITGL-KSEEDAKRALKKILDTI 182 (188)
T ss_dssp SCCCHHHHHHHST----TEEECTTTSSSEEEEEETTEEEEEE--CTTSEEEEESC-SCHHHHHHHHHHHHHHH
T ss_pred CccCHHHHHhhCc----CcEECCccCceEEEEeCCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 111111111111 1112335799987665666777777 67788877774 68899999999876655
No 10
>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=28.48 E-value=50 Score=32.41 Aligned_cols=42 Identities=19% Similarity=0.147 Sum_probs=29.9
Q ss_pred ccceeeccCCceEEEeccccCCcccccCCCCCHHHHHHHHHHHHHHh
Q 038243 355 RGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKF 401 (680)
Q Consensus 355 RGV~r~r~~GKW~AeIr~~~~gKri~LGTFdTeEEAArAYD~AAikl 401 (680)
.||.+ ++.|+|+.+++ ..+|++.||. |.+||..+..++...+
T Consensus 14 ~~v~~-~~~g~~~~r~~--~~gk~~~~g~--t~~eA~~~a~~~~~~~ 55 (356)
T 1z1b_A 14 PNLYI-RNNGYYCYRDP--RTGKEFGLGR--DRRIAITEAIQANIEL 55 (356)
T ss_dssp TTEEE-ETTTEEEEECT--TTCCEEEEES--CHHHHHHHHHHHHHHH
T ss_pred cccee-cCCCeEEEEee--cCCeEEECCC--CHHHHHHHHHHHHHHH
Confidence 46744 45789998873 4678899996 8888877766654444
Done!