Query 005549
Match_columns 691
No_of_seqs 295 out of 1579
Neff 8.6
Searched_HMMs 29240
Date Tue Mar 26 18:37:59 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/005549.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_2055-2059//hhsearch_pdb/005549hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1wj2_A Probable WRKY transcrip 1.0 1 1 31.8 5.2 59 77-159 18-76 (78)
2 2ayd_A WRKY transcription fact 1.0 1 1 31.0 6.9 58 78-159 16-73 (76)
3 2rpr_A Flywch-type zinc finger 1.0 1 1 21.9 4.8 49 78-160 26-74 (87)
4 3u5c_N S27A, YS15, 40S ribosom 1.0 1 1 21.5 6.5 95 169-263 23-142 (151)
5 3j20_Q 30S ribosomal protein S 1.0 1 1 20.7 6.5 37 169-205 23-60 (158)
6 3hot_A Transposable element ma 1.0 1 1 20.1 9.0 58 302-362 185-253 (345)
7 2xzm_O RPS13E; ribosome, trans 1.0 1 1 20.0 6.5 94 170-263 26-144 (153)
8 3kks_A Integrase, IN; beta-str 1.0 1 1 17.8 8.2 66 290-365 2-67 (152)
9 3hph_A Integrase, IN; protein- 1.0 1 1 16.2 8.0 65 291-365 61-125 (219)
10 1bco_A MUA domain II, bacterio 1.0 1 1 15.5 7.9 72 289-363 15-94 (327)
No 1
>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=31.84 Aligned_cols=59 Identities=19% Similarity=0.359 Sum_probs=41.2
Q ss_pred HCCCEEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCEEEEEEEECCCC
Q ss_conf 11960998112440898269999962257767678899998765577433365542577784342701199999743645
Q 005549 77 KSGFSVRKERSRLSPQLGVYKRDFVCYRSGFAPMRKKPGGEHHRDRKSVRCGCDAKMYLSKEVVEGVSQWFVVQFSNVHN 156 (691)
Q Consensus 77 ~~GF~vr~~~s~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~r~s~r~gCpa~i~i~~~~~~~~~~w~V~~~~~~HN 156 (691)
.-||.+|+--.+.-++...-|.+|.|+. -||+|+-.|.+.. .+....++....+||
T Consensus 18 dDGy~WRKYGQK~ikgs~~PRsYYrCt~----------------------~gC~a~K~Ver~~--~d~~~~~~tY~G~H~ 73 (78)
T 1wj2_A 18 DDGYRWRKYGQKVVKGNPYPRSYYKCTT----------------------PGCGVRKHVERAA--TDPKAVVTTYEGKHN 73 (78)
T ss_dssp CSSSCBCCCEEECCTTCSSCEEEEEEEC----------------------SSCEEEEEEEEET--TTTSEEEEEEESCCS
T ss_pred CCCCHHHHCCCCCCCCCCCEEEEEECCC----------------------CCCCCEEEEEEEC--CCCCEEEEEEEEECC
T ss_conf 9876132176541179967047725486----------------------7998681079975--999899999830708
Q ss_pred CCC
Q ss_conf 888
Q 005549 157 HEL 159 (691)
Q Consensus 157 H~l 159 (691)
|++
T Consensus 74 H~~ 76 (78)
T 1wj2_A 74 HDL 76 (78)
T ss_dssp SCC
T ss_pred CCC
T ss_conf 989
No 2
>2ayd_A WRKY transcription factor 1; beta strands, zinc finger; 1.60A {Arabidopsis thaliana}
Probab=1.00 E-value=1 Score=31.04 Aligned_cols=58 Identities=16% Similarity=0.351 Sum_probs=40.4
Q ss_pred CCCEEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCEEEEEEEECCCCC
Q ss_conf 19609981124408982699999622577676788999987655774333655425777843427011999997436458
Q 005549 78 SGFSVRKERSRLSPQLGVYKRDFVCYRSGFAPMRKKPGGEHHRDRKSVRCGCDAKMYLSKEVVEGVSQWFVVQFSNVHNH 157 (691)
Q Consensus 78 ~GF~vr~~~s~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~r~s~r~gCpa~i~i~~~~~~~~~~w~V~~~~~~HNH 157 (691)
-||.+|+--.+.-++...-|.+|.|+. .||+|+-.|.+.. .+....++....+|||
T Consensus 16 DGy~WRKYGQK~ikgs~~PRsYYrCt~----------------------~gC~a~K~Ver~~--~d~~~~~~tY~G~H~H 71 (76)
T 2ayd_A 16 DGYRWRKYGQKSVKGSPYPRSYYRCSS----------------------PGCPVKKHVERSS--HDTKLLITTYEGKHDH 71 (76)
T ss_dssp CSSCEEEEEEECCTTCSSCEEEEEECS----------------------TTCCCEEEEEECS--SSTTEEEEEEESCCSS
T ss_pred CCCHHHHCCCCCCCCCCCCEEEEECCC----------------------CCCCCEEEEEEEC--CCCCEEEEEECCCCCC
T ss_conf 876131276631179988412807178----------------------9998462179987--9998999998138089
Q ss_pred CC
Q ss_conf 88
Q 005549 158 EL 159 (691)
Q Consensus 158 ~l 159 (691)
++
T Consensus 72 ~~ 73 (76)
T 2ayd_A 72 DM 73 (76)
T ss_dssp CC
T ss_pred CC
T ss_conf 89
No 3
>2rpr_A Flywch-type zinc finger-containing protein 1; flywch domain, alternative splicing, DNA-binding, metal- binding, nucleus, metal binding protein; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=21.94 Aligned_cols=49 Identities=22% Similarity=0.388 Sum_probs=27.2
Q ss_pred CCCEEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCEEEEEEEECCCCC
Q ss_conf 19609981124408982699999622577676788999987655774333655425777843427011999997436458
Q 005549 78 SGFSVRKERSRLSPQLGVYKRDFVCYRSGFAPMRKKPGGEHHRDRKSVRCGCDAKMYLSKEVVEGVSQWFVVQFSNVHNH 157 (691)
Q Consensus 78 ~GF~vr~~~s~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~r~s~r~gCpa~i~i~~~~~~~~~~w~V~~~~~~HNH 157 (691)
.||...+.+.... ..++.|++.. +.+|+|++.... +. + .....|||
T Consensus 26 ~Gy~Y~~~~~~~~------~~yWrC~~~~-------------------~~kCrARi~T~~------~~--~-~~~~~HnH 71 (87)
T 2rpr_A 26 ESFLYRKEKAAGE------KVYWMCRDQA-------------------RLGCRSRAITQG------HR--I-MVMRSHCH 71 (87)
T ss_dssp TTEEEEEEEECSS------CEEEEEGGGT-------------------TSCCCCEEEEET------TE--E-EECSCCSS
T ss_pred CCEEEEEEECCCC------CEEEEECCCC-------------------CCCCCEEEEECC------CC--E-ECCCCCCC
T ss_conf 9989881005899------6899956789-------------------999988999918------98--8-98887489
Q ss_pred CCC
Q ss_conf 889
Q 005549 158 ELL 160 (691)
Q Consensus 158 ~l~ 160 (691)
|+.
T Consensus 72 ~p~ 74 (87)
T 2rpr_A 72 QPD 74 (87)
T ss_dssp CCC
T ss_pred CCC
T ss_conf 896
No 4
>3u5c_N S27A, YS15, 40S ribosomal protein S13; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_O 3o30_G 3o2z_G 3u5g_N 3iz6_O 3jyv_O* 1ysh_E 1s1h_O
Probab=1.00 E-value=1 Score=21.50 Aligned_cols=95 Identities=18% Similarity=0.266 Sum_probs=54.3
Q ss_pred CCCCCCC-HHHHHHHHHHHHCCCCHHHHHHHHHHHHCCC----------------CCCCCCCHHHHHHHHHHHH---HHH
Q ss_conf 2233489-7789999986416998368999988740767----------------9998873323443899987---866
Q 005549 169 PAYRKIQ-EADQERILLLSKAGFPIHRIVKVLELEKGIQ----------------GGQLPFLERDVRNFVQNRR---RAV 228 (691)
Q Consensus 169 ~s~R~ls-~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~~----------------~~~~~~~~~Di~N~~~~~r---~~~ 228 (691)
|+.-+++ ++..+.|..|++.|++|.+|--+|+.++|+. .+-.|-.+-|++|++.+.- +-+
T Consensus 23 P~W~~~~~eeVe~~I~klakkG~tpSqIG~iLRD~~GIp~Vk~vtG~kI~rILk~~glapeiPEDL~~LikKAv~lrkHL 102 (151)
T 3u5c_N 23 PAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHL 102 (151)
T ss_dssp CSSCCSCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCSCHHHHSSSCHHHHHHHTTCCCSSCHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCEEEECCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 97747999999999999998799887851477216899771232443799999967998899677999999999999999
Q ss_pred HHHHHHH-----HHCCCCCHHHHHHHHHHHCCCCCCCEEE
Q ss_conf 4223553-----3025471799999998723599860899
Q 005549 229 QENDALL-----TEKRETDTMELLDICKATNETDEYFVYD 263 (691)
Q Consensus 229 ~~~~~~~-----~~~~~~d~~~ll~~~~~~~~~np~f~~~ 263 (691)
.++.... ...-+.-...|..|.+....-.|+|.|+
T Consensus 103 e~n~kD~~sK~~L~liESkI~RL~rYYk~~~~LP~~WkY~ 142 (151)
T 3u5c_N 103 ERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYE 142 (151)
T ss_dssp HHCTTCHHHHHHHHHHHHHHHHHHHHHHHTTSSCTTCCCC
T ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 8765427778899999999999999998358699997177
No 5
>3j20_Q 30S ribosomal protein S15P/S13E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=1.00 E-value=1 Score=20.69 Aligned_cols=37 Identities=24% Similarity=0.388 Sum_probs=29.6
Q ss_pred CCCCCCC-HHHHHHHHHHHHCCCCHHHHHHHHHHHHCC
Q ss_conf 2233489-778999998641699836899998874076
Q 005549 169 PAYRKIQ-EADQERILLLSKAGFPIHRIVKVLELEKGI 205 (691)
Q Consensus 169 ~s~R~ls-~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~ 205 (691)
|+.-+++ ++..+.|..|++.|++|.+|--+|+.++|+
T Consensus 23 P~W~~~~~eev~~~i~klakkG~~pSqIG~~LRD~~gi 60 (158)
T 3j20_Q 23 PIWVEYTVEEIENLVVKLRKEGYSTAMIGTILRDQYGI 60 (158)
T ss_dssp CSSSCCCHHHHHHHHHHHHHHTCCHHHHHHHHHHTTCC
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCC
T ss_conf 97758999999999999998799888862788315898
No 6
>3hot_A Transposable element mariner, complete CDS; protein-DNA complex, synaptic complex, transposase, inverted DNA, DNA binding protein-DNA complex; HET: 5IU; 3.25A {Drosophila mauritiana} PDB: 3hos_A*
Probab=1.00 E-value=1 Score=20.11 Aligned_cols=58 Identities=16% Similarity=0.152 Sum_probs=35.3
Q ss_pred CCCCCEEEEEEEEECCCCEEEEEEEECC---CCCHHHHHHHHHHHHHHHC----C----CCCEEEECCCCHH
Q ss_conf 4578602378865116963787664214---7753479999999999816----9----9982640589758
Q 005549 302 ITYGLIFGAWLGIDSNGRTILFGVALLQ---DETLRSFAWALQTFVHFMK----G----RCPKTILTDLDPG 362 (691)
Q Consensus 302 n~y~~pl~~~~gvd~~g~~~~~g~al~~---~Et~~s~~w~l~~f~~~~~----~----~~p~~iitD~~~~ 362 (691)
......+.++.+++..| ++++.++. .-+.+.|.-+|+.++.... . ..+.+++.|....
T Consensus 185 ~~~~~~~~v~~~~~~~g---~~~~~~~~~~~~~~~~~y~~~L~~~~~~~~~~~p~~~~~~~~~~~~~Dna~~ 253 (345)
T 3hot_A 185 NRFGKKTMLCVWWDQSG---VIYYELLKPGETVNAARYQQQLINLNRALQRKRPEYQKRQHRVIFLHDNAPS 253 (345)
T ss_dssp CTTCCEEEEEEEEESSS---EEEEEEECSSCCCCHHHHHHHHHHHHHHHHHHSTTCC---CCCEEECCCCTT
T ss_pred CCCCCCEEEEEEECCCC---CEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCHHHHCCCCCEEEEECCCCC
T ss_conf 67677379999971567---3456742899731599999999999999987461333178866999789986
No 7
>2xzm_O RPS13E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_O 1ysh_E 3jyv_O* 1s1h_O
Probab=1.00 E-value=1 Score=20.04 Aligned_cols=94 Identities=18% Similarity=0.236 Sum_probs=53.9
Q ss_pred CCCCC-CHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCC----------------CCCCCCCHHHHHHHHHHH---HHHHH
Q ss_conf 23348-97789999986416998368999988740767----------------999887332344389998---78664
Q 005549 170 AYRKI-QEADQERILLLSKAGFPIHRIVKVLELEKGIQ----------------GGQLPFLERDVRNFVQNR---RRAVQ 229 (691)
Q Consensus 170 s~R~l-s~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~~----------------~~~~~~~~~Di~N~~~~~---r~~~~ 229 (691)
+.-++ .++..+.|..|++.|++|.+|--+|+.++|+. .+..|-.+-|++|++.+. |+-+.
T Consensus 26 ~W~~~~~eeVe~~I~klakkG~tpSqIG~iLRD~~GIp~Vk~vtG~kI~rILk~~glapeiPEDL~~LikKAv~lRkHLe 105 (153)
T 2xzm_O 26 KWLHMTPSTVVDLSVKLAKKGLTPSQIGVILRDQHGIPQVRFLTGQKILRILKKNGCAPQLPEDLYFLIKKALSIRKHLE 105 (153)
T ss_dssp SSCCCCHHHHHHHHHHHHHTTCCHHHHHHHHHHSSCCSCHHHHHSSCHHHHHHHTTCCCSSCHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCEEEECCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 63369999999999999987998878434773058988734644515999999759999996789999999999999998
Q ss_pred HHHHHH-----HHCCCCCHHHHHHHHHHHCCCCCCCEEE
Q ss_conf 223553-----3025471799999998723599860899
Q 005549 230 ENDALL-----TEKRETDTMELLDICKATNETDEYFVYD 263 (691)
Q Consensus 230 ~~~~~~-----~~~~~~d~~~ll~~~~~~~~~np~f~~~ 263 (691)
++.... ...-+.-...|..|.++...-.|+|.|+
T Consensus 106 ~n~kD~~sK~~L~LiESkI~RL~rYYk~~~~LP~~WkY~ 144 (153)
T 2xzm_O 106 KNRKDKDSKYRLILVESRIHRLSRYYKLNQKLPPKWKYN 144 (153)
T ss_dssp HTTTCHHHHHHHHHHHHHHHHHHHHHHHTTSSCTTCCCS
T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 765526667888999999999999998448489988287
No 8
>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=17.82 Aligned_cols=66 Identities=14% Similarity=0.204 Sum_probs=46.6
Q ss_pred CCEEEEECCCCCCCCCCEEEEEEEEECCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHH
Q ss_conf 9789980121234578602378865116963787664214775347999999999981699982640589758999
Q 005549 290 GDVVYFDTTYRSITYGLIFGAWLGIDSNGRTILFGVALLQDETLRSFAWALQTFVHFMKGRCPKTILTDLDPGLGD 365 (691)
Q Consensus 290 ~dvv~~D~T~~~n~y~~pl~~~~gvd~~g~~~~~g~al~~~Et~~s~~w~l~~f~~~~~~~~p~~iitD~~~~l~~ 365 (691)
.+++.+|.|+..+ .+.++.+|.....+ +++.+ .+++.+...-+|..+....| |+.|.+|+......
T Consensus 2 n~~w~~D~t~~~~-----~y~~~~iD~~sr~~-~~~~~-~~~~~~~~~~~l~~~~~~~g---p~~i~sDnG~~f~s 67 (152)
T 3kks_A 2 SHLWQMDNTHWNK-----TIIWVAVETNSGLV-EAQVI-PEETALQVALCILQLIQRYT---VLHLHSDNGPCFTA 67 (152)
T ss_dssp CCEEEEEEEEETT-----EEEEEEEETTTCCE-EEEEE-SSSCHHHHHHHHHHHHHHSC---CSEEEECSCHHHHS
T ss_pred CCEEEEEEEEECC-----EEEEEEEECCCCCE-EEEEE-CCCCHHHHHHHHHHHHHHHC---CCEEECCCCHHHHH
T ss_conf 9679985335299-----89999998689969-99980-78678999999999999849---85895399507668
No 9
>3hph_A Integrase, IN; protein-protein complex, tetramer, DNA integration, endonucl magnesium, metal-binding, multifunctional enzyme; 2.64A {Maedi visna virus} PDB: 3hpg_A
Probab=1.00 E-value=1 Score=16.24 Aligned_cols=65 Identities=18% Similarity=0.209 Sum_probs=43.6
Q ss_pred CEEEEECCCCCCCCCCEEEEEEEEECCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHH
Q ss_conf 789980121234578602378865116963787664214775347999999999981699982640589758999
Q 005549 291 DVVYFDTTYRSITYGLIFGAWLGIDSNGRTILFGVALLQDETLRSFAWALQTFVHFMKGRCPKTILTDLDPGLGD 365 (691)
Q Consensus 291 dvv~~D~T~~~n~y~~pl~~~~gvd~~g~~~~~g~al~~~Et~~s~~w~l~~f~~~~~~~~p~~iitD~~~~l~~ 365 (691)
+++.+|.|+..++ +.++.+|.....+ .++. +.+++.....-++..+....| |..|.||+......
T Consensus 61 ~~w~~D~t~~~~~-----y~~~~iD~~Sr~~-~~~~-~~~~~~~~~~~~l~~~~~~~g---p~~i~sDnG~~F~s 125 (219)
T 3hph_A 61 DHWQVDYTHYEDK-----IILVWVETNSGLI-YAER-VKGETGQEFRVQTMKWYAMFA---PKSLQSDNGPAFVA 125 (219)
T ss_dssp CEEEEEEEEETTE-----EEEEEEETTTCCE-EEEE-ESCCCHHHHHHHHHHHHHHHC---CCEEEECCCHHHHS
T ss_pred CEEEEEEECCCCE-----EEEEEEECCCCCE-EEEE-ECCCCHHHHHHHHHHHHHHHC---CCEEEECCCCHHHH
T ss_conf 6388988437997-----9999995789968-9998-389799999999999999859---95897489802336
No 10
>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=15.50 Aligned_cols=72 Identities=18% Similarity=0.159 Sum_probs=47.9
Q ss_pred CCCEEEEECCCCCCC----CCC--EEEEEEEEECCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHCCCCCE--EEECCCC
Q ss_conf 297899801212345----786--02378865116963787664214775347999999999981699982--6405897
Q 005549 289 LGDVVYFDTTYRSIT----YGL--IFGAWLGIDSNGRTILFGVALLQDETLRSFAWALQTFVHFMKGRCPK--TILTDLD 360 (691)
Q Consensus 289 f~dvv~~D~T~~~n~----y~~--pl~~~~gvd~~g~~~~~g~al~~~Et~~s~~w~l~~f~~~~~~~~p~--~iitD~~ 360 (691)
-++++.+|.|+.... .+. ...+.+.+|..... ++|+.+...++.++..-+|.......| .|. .|.+|+-
T Consensus 15 p~~~w~~D~t~~d~~~~~~~g~~~r~~l~~~iD~~SR~-ivg~~~~~~~~~~~v~~aL~~a~~~~G--~P~~~~i~sDnG 91 (327)
T 1bco_A 15 AMQWINGDGYLHNVFVRWFNGDVIRPKTWFWQDVKTRK-ILGWRCDVSENIDSIRLSFMDVVTRYG--IPEDFHITIDNT 91 (327)
T ss_dssp TTTEEEEEEEECSBCEECTTSCEECCEEEEEEETTTCC-EEEEEEESSCCHHHHHHHHHHHHHHHC--EESSCEEECCCT
T ss_pred CCCEEEECCCEEEEEEECCCCCCCEEEEEEEEECCCCC-EEEEEEECCCCHHHHHHHHHHHHHHCC--CCCCCEEEEECC
T ss_conf 97689966878989998779963505999999987794-789999778799999999999998539--999728992086
Q ss_pred HHH
Q ss_conf 589
Q 005549 361 PGL 363 (691)
Q Consensus 361 ~~l 363 (691)
...
T Consensus 92 ~~f 94 (327)
T 1bco_A 92 RGA 94 (327)
T ss_dssp TST
T ss_pred HHH
T ss_conf 322
Done!