Query 001714
Match_columns 1021
No_of_seqs 219 out of 288
Neff 5.0
Searched_HMMs 29240
Date Tue Mar 26 15:48:16 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/001714.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_1013-1017//hhsearch_pdb/001714hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3kks_A Integrase, IN; beta-str 1.0 1 1 17.8 8.0 67 292-373 2-68 (152)
2 1c0m_A Protein (integrase); HI 1.0 1 1 17.1 8.2 69 295-372 12-80 (238)
3 1wj2_A Probable WRKY transcrip 1.0 1 1 16.9 5.1 32 127-159 45-76 (78)
4 2ayd_A WRKY transcription fact 1.0 1 1 16.1 7.0 63 79-159 11-73 (76)
5 2eo2_A Adult MALE hypothalamus 1.0 1 1 16.1 -0.2 30 732-761 41-70 (71)
6 2kw0_A CCMH protein; oxidoredu 1.0 1 1 15.7 2.6 32 182-216 41-72 (90)
7 1cxq_A Avian sarcoma virus int 1.0 1 1 15.1 8.3 69 295-372 13-81 (162)
8 2hl7_A Cytochrome C-type bioge 1.0 1 1 15.1 2.6 31 182-215 44-74 (84)
9 1bco_A MUA domain II, bacterio 1.0 1 1 14.6 6.4 71 295-372 18-96 (327)
10 3l3u_A POL polyprotein; DNA in 1.0 1 1 13.7 8.3 65 294-372 10-74 (163)
No 1
>3kks_A Integrase, IN; beta-strands flanked by alpha-helices, DNA binding protein; 2.20A {Bovine immunodeficiency virus} PDB: 3kkr_A
Probab=1.00 E-value=1 Score=17.77 Aligned_cols=67 Identities=12% Similarity=0.069 Sum_probs=43.3
Q ss_pred CCCEEEEECCCCCCCCCCCEEEEEEECCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCHHHH
Q ss_conf 98269993677887569750899999699975899999931898155999999999986424997312399961864548
Q 001714 292 NRSLLASDSRFGTNKLKYPLHSLIVFNSDKKAIPVAWVIAPSFSSADTHRWMRALYNRVRTKDPTWNLAGFIVDDPSADV 371 (1021)
Q Consensus 292 ~~gVI~iDSThgtNky~~PL~TLiV~D~~G~giPVAf~Its~ET~edi~~WLr~ll~~i~~k~p~~~Pk~fMTD~d~Ae~ 371 (1021)
+. ++.+|.|+.-+ .|.++++|.+-+.+ +++.+. +.+...+...|..++.. .+ |+.+.+|....+.
T Consensus 2 n~-~w~~D~t~~~~-----~y~~~~iD~~sr~~-~~~~~~-~~~~~~~~~~l~~~~~~----~g---p~~i~sDnG~~f~ 66 (152)
T 3kks_A 2 SH-LWQMDNTHWNK-----TIIWVAVETNSGLV-EAQVIP-EETALQVALCILQLIQR----YT---VLHLHSDNGPCFT 66 (152)
T ss_dssp CC-EEEEEEEEETT-----EEEEEEEETTTCCE-EEEEES-SSCHHHHHHHHHHHHHH----SC---CSEEEECSCHHHH
T ss_pred CC-EEEEEEEEECC-----EEEEEEEECCCCCE-EEEEEC-CCCHHHHHHHHHHHHHH----HC---CCEEECCCCHHHH
T ss_conf 96-79985335299-----89999998689969-999807-86789999999999998----49---8589539950766
Q ss_pred HH
Q ss_conf 87
Q 001714 372 HT 373 (1021)
Q Consensus 372 nA 373 (1021)
+.
T Consensus 67 s~ 68 (152)
T 3kks_A 67 AH 68 (152)
T ss_dssp SH
T ss_pred HH
T ss_conf 89
No 2
>1c0m_A Protein (integrase); HIV, X-RAY crystallography, protein structure, transferase; 2.53A {Rous sarcoma virus} SCOP: b.34.7.1 c.55.3.2 PDB: 1c1a_A
Probab=1.00 E-value=1 Score=17.12 Aligned_cols=69 Identities=9% Similarity=0.004 Sum_probs=43.9
Q ss_pred EEEEECCCCCCCCCCCEEEEEEECCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCHHHHH
Q ss_conf 699936778875697508999996999758999999318981559999999999864249973123999618645488
Q 001714 295 LLASDSRFGTNKLKYPLHSLIVFNSDKKAIPVAWVIAPSFSSADTHRWMRALYNRVRTKDPTWNLAGFIVDDPSADVH 372 (1021)
Q Consensus 295 VI~iDSThgtNky~~PL~TLiV~D~~G~giPVAf~Its~ET~edi~~WLr~ll~~i~~k~p~~~Pk~fMTD~d~Ae~n 372 (1021)
++++|.|+.....+. .|.++++|.+-+. .++|.+. +.+...+...|...+... . .|..+.+|....+.+
T Consensus 12 ~w~~D~~~~~~~~g~-~yl~~~iD~~Sr~-i~~~~~~-~~~~~~v~~~l~~~~~~~---g---~p~~i~sDnG~~f~s 80 (238)
T 1c0m_A 12 IWQTDFTLEPRMAPR-SWLAVTVDTASSA-IVVTQHG-RVTSVAVQHHWATAIAVL---G---RPKAIKTDNGSCFTS 80 (238)
T ss_dssp EEEEEEEECGGGCSS-CEEEEEEETTTCC-EEEEEES-SCCHHHHHHHHHHHHHHH---C---CCSEEEECSCHHHHS
T ss_pred EEEEEECCCCCCCCC-EEEEEEEECCCCC-EEEEECC-CCCHHHHHHHHHHHHHHH---C---CCCEEEECCCCCCCC
T ss_conf 899716465546998-8999999888997-9999806-887999999999999986---9---995899789875546
No 3
>1wj2_A Probable WRKY transcription factor 4; DNA-binding domain, zinc-binding, structural genomics; NMR {Arabidopsis thaliana} SCOP: g.79.1.1 PDB: 2lex_A*
Probab=1.00 E-value=1 Score=16.92 Aligned_cols=32 Identities=22% Similarity=0.440 Sum_probs=25.3
Q ss_pred CCCCEEEEEEEEEECCCCEEEEEEECCCCCCCC
Q ss_conf 788504999999551992899999326666789
Q 001714 127 KRGCTCHFIVKRLIAEPSVALIIYNDEKHVDKN 159 (1021)
Q Consensus 127 k~GC~A~f~Vkrl~~~gsv~viiy~~~~Hvh~~ 159 (1021)
..||+|+=.|.+...++.+.+++|.-. |+|..
T Consensus 45 ~~gC~a~K~Ver~~~d~~~~~~tY~G~-H~H~~ 76 (78)
T 1wj2_A 45 TPGCGVRKHVERAATDPKAVVTTYEGK-HNHDL 76 (78)
T ss_dssp CSSCEEEEEEEEETTTTSEEEEEEESC-CSSCC
T ss_pred CCCCCCEEEEEEECCCCCEEEEEEEEE-CCCCC
T ss_conf 679986810799759998999998307-08989
No 4
>2ayd_A WRKY transcription factor 1; beta strands, zinc finger; 1.60A {Arabidopsis thaliana}
Probab=1.00 E-value=1 Score=16.13 Aligned_cols=63 Identities=21% Similarity=0.203 Sum_probs=37.5
Q ss_pred CCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEEEEECCCCCCC
Q ss_conf 77554525899998502499856899743457432246665799998878850499999955199289999932666678
Q 001714 79 CKPKVDGILEYILYWCSFGPDDHRKGGIVRPSRTTYVPKKKNAGRPNTKRGCTCHFIVKRLIAEPSVALIIYNDEKHVDK 158 (1021)
Q Consensus 79 ~~~~~d~~ley~~Y~Cs~Gp~~~~~g~~~~ps~~~~~~~k~r~~Rp~~k~GC~A~f~Vkrl~~~gsv~viiy~~~~Hvh~ 158 (1021)
.....|||.|.. |..-. -+|... .|.|+..+ ..||+|+=.|.+...++.+.+++|.-. |+|.
T Consensus 11 ~~~~~DGy~WRK-YGQK~-----ikgs~~--PRsYYrCt---------~~gC~a~K~Ver~~~d~~~~~~tY~G~-H~H~ 72 (76)
T 2ayd_A 11 FDIVNDGYRWRK-YGQKS-----VKGSPY--PRSYYRCS---------SPGCPVKKHVERSSHDTKLLITTYEGK-HDHD 72 (76)
T ss_dssp SSCCCCSSCEEE-EEEEC-----CTTCSS--CEEEEEEC---------STTCCCEEEEEECSSSTTEEEEEEESC-CSSC
T ss_pred CCCCCCCCHHHH-CCCCC-----CCCCCC--CEEEEECC---------CCCCCCEEEEEEECCCCCEEEEEECCC-CCCC
T ss_conf 776898761312-76631-----179988--41280717---------899984621799879998999998138-0898
Q ss_pred C
Q ss_conf 9
Q 001714 159 N 159 (1021)
Q Consensus 159 ~ 159 (1021)
.
T Consensus 73 ~ 73 (76)
T 2ayd_A 73 M 73 (76)
T ss_dssp C
T ss_pred C
T ss_conf 9
No 5
>2eo2_A Adult MALE hypothalamus cDNA, riken FULL-length enriched library, clone:A230045M11...; FTHFSDC1, structural genomics, NPPSFA; NMR {Mus musculus}
Probab=1.00 E-value=1 Score=16.13 Aligned_cols=30 Identities=20% Similarity=0.190 Sum_probs=20.4
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf 420256678986212354456668997300
Q 001714 732 LVSANSLCGGTTEEEISFAKTDVEQSPIYI 761 (1021)
Q Consensus 732 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 761 (1021)
||...--..+|.+|-..||-.||||++|-.
T Consensus 41 GI~ktdP~~LT~eEi~~FaRLdIDP~TITw 70 (71)
T 2eo2_A 41 GIHKTDPSTLTEEEVRKFARLNIDPATITW 70 (71)
T ss_dssp TCCCCSTTTCCHHHHHHHHHTCCCSTTCCC
T ss_pred CCCCCCCCCCCHHHHHHCEECCCCCCCEEE
T ss_conf 999999002899999505034658655553
No 6
>2kw0_A CCMH protein; oxidoreductase, cytochrome C maturation; NMR {Escherichia coli}
Probab=1.00 E-value=1 Score=15.70 Aligned_cols=32 Identities=38% Similarity=0.547 Sum_probs=25.1
Q ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCC
Q ss_conf 89899999999997699946899896665441199
Q 001714 182 ISEDLRLRVLSLLHVGVSVETIMQRHNESVERQGG 216 (1021)
Q Consensus 182 IS~e~R~~I~~lL~~GIs~~~Il~~ire~~~k~gG 216 (1021)
|..++|..|.+++..|-+...|++. ++.++|.
T Consensus 41 iA~dlR~~Vre~l~~G~Sd~eI~~~---mv~RYGd 72 (90)
T 2kw0_A 41 IATDLRQKVYELMQEGKSKKEIVDY---MVARYGN 72 (90)
T ss_dssp HHHHHHHHHHHHHHHTCCHHHHHHH---HHHHHTT
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHH---HHHHCCC
T ss_conf 9999999999999859999999999---9986487
No 7
>1cxq_A Avian sarcoma virus integrase; mixed beta-sheet surrounded by alpha-helices, transferase; HET: EPE; 1.02A {Avian sarcoma virus} SCOP: c.55.3.2 PDB: 1cxu_A* 1czb_A* 1cz9_A* 1asu_A* 1asw_A* 1asv_A 1a5v_A* 1a5w_A* 1a5x_A* 1vsf_A* 1vse_A* 3o4n_A* 1vsm_A 3o4q_A* 1vsd_A* 1vsh_A* 1vsi_A* 1vsj_A* 1vsk_A 1vsl_A
Probab=1.00 E-value=1 Score=15.09 Aligned_cols=69 Identities=9% Similarity=0.007 Sum_probs=42.8
Q ss_pred EEEEECCCCCCCCCCCEEEEEEECCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCHHHHH
Q ss_conf 699936778875697508999996999758999999318981559999999999864249973123999618645488
Q 001714 295 LLASDSRFGTNKLKYPLHSLIVFNSDKKAIPVAWVIAPSFSSADTHRWMRALYNRVRTKDPTWNLAGFIVDDPSADVH 372 (1021)
Q Consensus 295 VI~iDSThgtNky~~PL~TLiV~D~~G~giPVAf~Its~ET~edi~~WLr~ll~~i~~k~p~~~Pk~fMTD~d~Ae~n 372 (1021)
++++|-|+-....+. .|.++++|.+-+. .++|.+. +.+.+.+...|...+... . .|+.+.+|....+.+
T Consensus 13 ~~~~D~~~~~~~~g~-~yl~~~iD~~Sr~-i~~~~~~-~~~~~~v~~~l~~~~~~~---g---~p~~i~sDnG~~f~s 81 (162)
T 1cxq_A 13 IWQTDFTLEPRMAPR-SWLAVTVDTASSA-IVVTQHG-RVTSVAAQHHWATAIAVL---G---RPKAIKTDNGSCFTS 81 (162)
T ss_dssp EEEEEEEECGGGTTS-CEEEEEEETTTCC-EEEEEES-SCCHHHHHHHHHHHHHHH---C---CCSEEECCSCHHHHS
T ss_pred EEEEEEEECCCCCCC-EEEEEEEECCCCE-EEEEECC-CCCHHHHHHHHHHHHHHH---C---CCEEEEECCCHHHHH
T ss_conf 998545623458998-8999999868994-9999778-945999999999999987---9---990899389656652
No 8
>2hl7_A Cytochrome C-type biogenesis protein CCMH; three-helices bundle, oxidoreductase; HET: PG4; 1.70A {Pseudomonas aeruginosa}
Probab=1.00 E-value=1 Score=15.08 Aligned_cols=31 Identities=35% Similarity=0.464 Sum_probs=23.6
Q ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCC
Q ss_conf 8989999999999769994689989666544119
Q 001714 182 ISEDLRLRVLSLLHVGVSVETIMQRHNESVERQG 215 (1021)
Q Consensus 182 IS~e~R~~I~~lL~~GIs~~~Il~~ire~~~k~g 215 (1021)
|..++|..|.+++..|-+...|++. ++.++|
T Consensus 44 iA~dlR~~V~~~l~~G~sd~eI~~~---~v~RYG 74 (84)
T 2hl7_A 44 IAADLRKQIYGQLQQGKSDGEIVDY---MVARYG 74 (84)
T ss_dssp HHHHHHHHHHHHHHHTCCHHHHHHH---HHHHHT
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHH---HHHHCC
T ss_conf 9999999999999859999999999---998648
No 9
>1bco_A MUA domain II, bacteriophage MU transposase; polynucleotidyl transferase, DNA binding, endonuclease, integrase; 2.40A {Enterobacteria phage MU} SCOP: b.48.1.1 c.55.3.3 PDB: 1bcm_A
Probab=1.00 E-value=1 Score=14.64 Aligned_cols=71 Identities=7% Similarity=0.026 Sum_probs=46.2
Q ss_pred EEEEECCCCCCC----CC--CCEEEEEEECCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCEE--EEEECC
Q ss_conf 699936778875----69--7508999996999758999999318981559999999999864249973123--999618
Q 001714 295 LLASDSRFGTNK----LK--YPLHSLIVFNSDKKAIPVAWVIAPSFSSADTHRWMRALYNRVRTKDPTWNLA--GFIVDD 366 (1021)
Q Consensus 295 VI~iDSThgtNk----y~--~PL~TLiV~D~~G~giPVAf~Its~ET~edi~~WLr~ll~~i~~k~p~~~Pk--~fMTD~ 366 (1021)
++.+|.|+--.. .+ .-.+..+++|.+-+. .++|.++..++.+.+...|+..+... . .|. .|.+|.
T Consensus 18 ~w~~D~t~~d~~~~~~~g~~~r~~l~~~iD~~SR~-ivg~~~~~~~~~~~v~~aL~~a~~~~---G---~P~~~~i~sDn 90 (327)
T 1bco_A 18 WINGDGYLHNVFVRWFNGDVIRPKTWFWQDVKTRK-ILGWRCDVSENIDSIRLSFMDVVTRY---G---IPEDFHITIDN 90 (327)
T ss_dssp EEEEEEEECSBCEECTTSCEECCEEEEEEETTTCC-EEEEEEESSCCHHHHHHHHHHHHHHH---C---EESSCEEECCC
T ss_pred EEEECCCEEEEEEECCCCCCCEEEEEEEEECCCCC-EEEEEEECCCCHHHHHHHHHHHHHHC---C---CCCCCEEEEEC
T ss_conf 89966878989998779963505999999987794-78999977879999999999999853---9---99972899208
Q ss_pred CHHHHH
Q ss_conf 645488
Q 001714 367 PSADVH 372 (1021)
Q Consensus 367 d~Ae~n 372 (1021)
-..+.+
T Consensus 91 G~~f~s 96 (327)
T 1bco_A 91 TRGAAN 96 (327)
T ss_dssp TTSTTT
T ss_pred CHHHCC
T ss_conf 632204
No 10
>3l3u_A POL polyprotein; DNA integration, AIDS, integrase, endonuclease, polynucleotidyl transferase, DNA binding, viral protein; 1.40A {Human immunodeficiency virus 1} PDB: 3ao1_A 3l3v_A* 3ovn_A* 3ao2_A* 3ao3_A* 3ao4_A* 3ao5_A* 2itg_A 1biz_A 1biu_A 1b9d_A 4dmn_A* 2b4j_A 1itg_A 1b92_A 1bl3_A 1bi4_A 1bis_A 1b9f_A 1bi4_B ...
Probab=1.00 E-value=1 Score=13.66 Aligned_cols=65 Identities=17% Similarity=0.088 Sum_probs=41.1
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEECCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCHHHHH
Q ss_conf 2699936778875697508999996999758999999318981559999999999864249973123999618645488
Q 001714 294 SLLASDSRFGTNKLKYPLHSLIVFNSDKKAIPVAWVIAPSFSSADTHRWMRALYNRVRTKDPTWNLAGFIVDDPSADVH 372 (1021)
Q Consensus 294 gVI~iDSThgtNky~~PL~TLiV~D~~G~giPVAf~Its~ET~edi~~WLr~ll~~i~~k~p~~~Pk~fMTD~d~Ae~n 372 (1021)
+++.+|.|+.-. .|.++++|.+-+.+ +++.+.+. +...+..++..++.. . .++.+.+|....+.+
T Consensus 10 ~~w~~D~t~~~g-----~y~~~~iD~~sr~~-~~~~~~~~-~~~~~~~~l~~~~~~----~---~~~~i~sD~G~~f~s 74 (163)
T 3l3u_A 10 GIWQLDCTHLEG-----KVILVAVHVASGYI-EAEVIPAE-TGQETAYFLLKLAGR----W---PVKTVHTDNGSNFTS 74 (163)
T ss_dssp TEEEEEEEEETT-----EEEEEEEETTTCCE-EEEEESSC-CHHHHHHHHHHHHHH----S---CCCEEEECCCGGGGS
T ss_pred CEEEEEECCCCC-----CEEEEEEECCCCCE-EEEEECCC-CHHHHHHHHHHHHHH----C---CCCEEEECCHHHHHH
T ss_conf 989998404498-----38999996578968-99985787-589999999999997----5---986885267476525
Done!