Query T0548 OR3 , , 106 residues
Match_columns 106
No_of_seqs 116 out of 829
Neff 7.4
Searched_HMMs 22458
Date Fri May 21 18:04:32 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pdb70search/hhm/T0548.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pdb70_15May10_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pdb70search/hhm/T0548.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3l2t_A Integrase, IN, P42IN; p 99.7 3.4E-17 1.5E-21 113.1 6.2 73 30-105 33-109 (395)
2 1k6y_A POL polyprotein; HIV-1, 98.0 2.2E-06 9.6E-11 54.1 2.7 45 51-104 5-49 (288)
3 3f9k_A Integrase; protein-prot 97.4 8.8E-05 3.9E-09 45.3 3.8 46 51-105 6-51 (210)
4 3hph_A Integrase, IN; protein- 97.3 0.00012 5.4E-09 44.6 3.5 44 52-104 6-49 (219)
5 1yfb_A Transition state regula 54.6 3.6 0.00016 20.1 1.3 24 30-53 8-34 (59)
6 1qzm_A ATP-dependent protease 32.5 25 0.0011 15.5 4.2 61 15-77 3-63 (94)
7 2w1t_A Spovt, stage V sporulat 31.6 14 0.00062 16.9 1.3 16 38-53 11-26 (178)
8 1x37_A LON protease, ATP-depen 24.1 36 0.0016 14.7 4.4 62 14-77 3-64 (124)
9 1n0e_A Protein MRAZ; cell divi 13.3 45 0.002 14.1 0.8 70 35-104 33-110 (166)
10 1yfu_A 3-hydroxyanthranilate-3 12.0 57 0.0025 13.6 1.0 17 90-106 157-173 (174)
No 1
>3l2t_A Integrase, IN, P42IN; protein-DNA complex; HET: RLT; 2.85A {Human spumaretrovirus} PDB: 3l2q_A 3l2s_A 3l2r_A* 3l2u_A* 3l2v_A* 3l2w_A*
Probab=99.68 E-value=3.4e-17 Score=113.07 Aligned_cols=73 Identities=21% Similarity=0.250 Sum_probs=59.2
Q ss_pred CCCCCCEEEE---CC-EEEECHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHCCCCCC
Q ss_conf 3345765421---88-4464658789999998515667647899999998863278656899999973170653338899
Q T0548 30 YDKTKKYWVY---QG-KPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNITETCKACAQVNASK 105 (106)
Q Consensus 30 ~~~~~~~~~~---~G-r~vvP~~~~~~il~~~H~~~h~G~~~~~~~l~~i~~~~~wp~m~~~v~~~v~~C~~Cq~~n~~~ 105 (106)
+..+++.++. +| |+|||.+++.+||.++|+.+ |.|..+|+.++++.||||+|.++|++||++|..||+.++.+
T Consensus 33 ~~l~~g~l~~~~~~g~~~vvP~~~r~~ii~~~H~~g---H~G~~~t~~~l~~~y~Wp~m~~dv~~~v~~C~~Cq~~k~~~ 109 (395)
T 3l2t_A 33 YFLEDGKVKVSRPEGVKIIPPQSDRQKIVLQAHNLA---HTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASN 109 (395)
T ss_dssp EEEETTEEEEECSSCEEECCCHHHHHHHHHHHHHHH---TCCHHHHHHHHHHHBCCTTHHHHHHHHHTTCHHHHHHSCCC
T ss_pred EEEECCEEEEECCCCEEEECCHHHHHHHHHHHHCCC---CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 997389899975995699769999999999984788---97199999999484288889999999987649876516467
No 2
>1k6y_A POL polyprotein; HIV-1, integrase, domain organization, transferase; 2.40A {Human immunodeficiency virus 1} SCOP: a.4.10.1 c.55.3.2 PDB: 1ex4_A* 1wjb_A 1wjd_A 1wjf_A 1ihv_A 1ihw_A 1qmc_A 1wja_A 1wjc_A 1wje_A
Probab=97.99 E-value=2.2e-06 Score=54.10 Aligned_cols=45 Identities=16% Similarity=0.270 Sum_probs=35.2
Q ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHCCCCC
Q ss_conf 999999851566764789999999886327865689999997317065333889
Q T0548 51 FELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNITETCKACAQVNAS 104 (106)
Q Consensus 51 ~~il~~~H~~~h~G~~~~~~~l~~i~~~~~wp~m~~~v~~~v~~C~~Cq~~n~~ 104 (106)
.+..++.|+..|.|... |++.|+||.| .++++|++|..||+.++.
T Consensus 5 ~~~a~~~H~~~H~~~k~-------l~~~~~~P~~--~a~~iV~~C~~Cq~~~~~ 49 (288)
T 1k6y_A 5 IDKAQEEHEKYHSNWRA-------MASDFNLPPV--VAKEIVASCDKCQLKGEA 49 (288)
T ss_dssp HHHHHHHHHHHCCCHHH-------HHHHHTCCHH--HHHHHHHHCTTCCCC---
T ss_pred HHHHHHHHHHHCCCHHH-------HHHHCCCCHH--HHHHHHHCCHHHHHCCCC
T ss_conf 19999999997779999-------9986699989--999997269888728999
No 3
>3f9k_A Integrase; protein-protein complex, AIDS, DNA integration, endonuclease, magnesium, metal-binding, multifunctional enzyme; 3.20A {Human immunodeficiency virus type 2} PDB: 1e0e_A
Probab=97.42 E-value=8.8e-05 Score=45.31 Aligned_cols=46 Identities=17% Similarity=0.264 Sum_probs=33.9
Q ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHCCCCCC
Q ss_conf 9999998515667647899999998863278656899999973170653338899
Q T0548 51 FELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNITETCKACAQVNASK 105 (106)
Q Consensus 51 ~~il~~~H~~~h~G~~~~~~~l~~i~~~~~wp~m~~~v~~~v~~C~~Cq~~n~~~ 105 (106)
.+..++.|+.-|.|..+ |++.|+||+| +++++|++|..||+.++.+
T Consensus 6 ~~~a~~~H~~~H~n~k~-------L~~~~~~P~~--~ak~~v~~C~~Cq~~k~~~ 51 (210)
T 3f9k_A 6 IEPAQEEHEKYHSNVKE-------LSHKFGIPNL--VARQIVNSCAQCQQKGEAI 51 (210)
T ss_dssp HHHHHHHHHHHCCCHHH-------HHHHHCCCHH--HHHHHHHTCTTTTTCCCCC
T ss_pred CHHHHHHHHHHCCCHHH-------HHHHCCCCHH--HHHHHHHCCHHHHHCCCCC
T ss_conf 28999999986799999-------9986499889--9999997184655167888
No 4
>3hph_A Integrase, IN; protein-protein complex, tetramer, DNA integration, endonuclease, magnesium, metal-binding; 2.64A {Maedi visna virus} PDB: 3hpg_A
Probab=97.32 E-value=0.00012 Score=44.57 Aligned_cols=44 Identities=16% Similarity=0.268 Sum_probs=32.7
Q ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHCCCCC
Q ss_conf 99999851566764789999999886327865689999997317065333889
Q T0548 52 ELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNITETCKACAQVNAS 104 (106)
Q Consensus 52 ~il~~~H~~~h~G~~~~~~~l~~i~~~~~wp~m~~~v~~~v~~C~~Cq~~n~~ 104 (106)
...++.|+.-|.|... +...|||| +.+++++|++|..||+.+..
T Consensus 6 ~~a~~~H~~~H~~~~~-------L~~~f~~p--r~~~k~iv~~C~~Cq~~k~~ 49 (219)
T 3hph_A 6 PLAEEEHNKWHQDAVS-------LHLEFGIP--RTAAEDIVQQCDVCQENKMP 49 (219)
T ss_dssp HHHHHHHHHHCCCHHH-------HHHHSCCC--HHHHHHHHTTCTTC------
T ss_pred HHHHHHHHHHCCCHHH-------HHHHHCCC--HHHHHHHHHCCHHHHCCCCC
T ss_conf 9999999998839999-------99882999--99999997329898776988
No 5
>1yfb_A Transition state regulatory protein ABRB; , homodimer, bioinformatics, swapped-hairpin barrel, transcription; NMR {Bacillus subtilis} SCOP: b.129.1.3 PDB: 1ysf_A 2k1n_A* 1z0r_A 2ro4_A 2fy9_A 2ro3_A
Probab=54.57 E-value=3.6 Score=20.12 Aligned_cols=24 Identities=21% Similarity=0.234 Sum_probs=16.1
Q ss_pred CCCCCCEE---EECCEEEECHHHHHHH
Q ss_conf 33457654---2188446465878999
Q T0548 30 YDKTKKYW---VYQGKPVMPDQFTFEL 53 (106)
Q Consensus 30 ~~~~~~~~---~~~Gr~vvP~~~~~~i 53 (106)
|-...|.. ..-||+|+|.++|..+
T Consensus 8 ~MKstGivRkiD~LGRIVIPkElRr~L 34 (59)
T 1yfb_A 8 FMKSTGIVRKVDELGRVVIPIELRRTL 34 (59)
T ss_dssp CCCCCCEEEECCTTCEEECCHHHHHHT
T ss_pred HHEEEEEEEEECCCCCEEEEHHHHHHC
T ss_conf 310010487423688799229999776
No 6
>1qzm_A ATP-dependent protease LA; oligomerization domain, AAA+ protein, hydrolase; 1.90A {Escherichia coli} SCOP: c.37.1.20
Probab=32.47 E-value=25 Score=15.53 Aligned_cols=61 Identities=8% Similarity=0.184 Sum_probs=38.3
Q ss_pred CCHHHHHHHHHHHCCCCCCCCEEEECCEEEECHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf 698899999874123334576542188446465878999999851566764789999999886
Q T0548 15 YTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHS 77 (106)
Q Consensus 15 y~~ed~~~~~~~~~~~~~~~~~~~~~Gr~vvP~~~~~~il~~~H~~~h~G~~~~~~~l~~i~~ 77 (106)
|+.+|...+-+.=..-.+-...-+..+.+.+++.....|++.+.. ..|.+++.+.+..+.+
T Consensus 3 Yt~~EK~~Iak~yLiPk~l~~~Gl~~~~i~i~~~~l~~iI~~Ytr--EaGVR~Ler~i~~I~R 63 (94)
T 1qzm_A 3 YTEDEKLNIAKRHLLPKQIERNALKKGELTVDDSAIIGIIRYYTR--EAGVRGLEREISKLCR 63 (94)
T ss_dssp CCHHHHHHHHHHTHHHHHHHHTTCCTTTEEECHHHHHHHHHHHCC--CSSSHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHH
T ss_conf 988999999999547899999689931110269999999998474--0878599999999999
No 7
>2w1t_A Spovt, stage V sporulation protein T; transcription, transcription regulation, repressor, activator, DNA-binding; 2.60A {Bacillus subtilis} PDB: 2w1t_B 2ro5_A
Probab=31.64 E-value=14 Score=16.92 Aligned_cols=16 Identities=25% Similarity=0.364 Sum_probs=11.0
Q ss_pred EECCEEEECHHHHHHH
Q ss_conf 2188446465878999
Q T0548 38 VYQGKPVMPDQFTFEL 53 (106)
Q Consensus 38 ~~~Gr~vvP~~~~~~i 53 (106)
..-||+|+|.++|..+
T Consensus 11 d~~griviP~e~r~~l 26 (178)
T 2w1t_A 11 DDLGRVVIPKEIRRTL 26 (178)
T ss_dssp CTTSEEECCHHHHHHT
T ss_pred CCCCCEEEEHHHHHHC
T ss_conf 6998888359999866
No 8
>1x37_A LON protease, ATP-dependent protease LA 1; AAA+ superfamily, SSD domain, solution structure, hydrolase; NMR {Bacillus subtilis}
Probab=24.14 E-value=36 Score=14.69 Aligned_cols=62 Identities=11% Similarity=0.158 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHCCCCCCCCEEEECCEEEECHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf 3698899999874123334576542188446465878999999851566764789999999886
Q T0548 14 HYTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHS 77 (106)
Q Consensus 14 ~y~~ed~~~~~~~~~~~~~~~~~~~~~Gr~vvP~~~~~~il~~~H~~~h~G~~~~~~~l~~i~~ 77 (106)
-|+.+|...+-+.=..-.+-...-+.++.+.++++....|++.+-. ..|.+++.+.+.++.+
T Consensus 3 GYt~~EK~~IAk~yLiPk~l~~~Gl~~~~i~i~d~~l~~II~~YTr--EaGVR~LeR~i~~I~R 64 (124)
T 1x37_A 3 GYTEIEKLEIVKDHLLPKQIKEHGLKKSNLQLRDQAILDIIRYYTR--EAGVRSLERQLAAICR 64 (124)
T ss_dssp CCCHHHHHHHHHHHTTHHHHHHHHTSSSCCEECHHHHHHHHHHHCC--CSSHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCC--CHHHHHHHHHHHHHHH
T ss_conf 8999999999999727999997068772676559999999986684--1899999989999999
No 9
>1n0e_A Protein MRAZ; cell division and cell WALL biosynthesis protein, structural genomics, BSGC structure funded by NIH; 2.70A {Mycoplasma pneumoniae} SCOP: b.129.1.2 PDB: 1n0f_A 1n0g_A
Probab=13.34 E-value=45 Score=14.13 Aligned_cols=70 Identities=9% Similarity=-0.028 Sum_probs=30.8
Q ss_pred CEEEECCEEEECHHHHHHH-----HHHHHC--CCCCCHHHHHHHHHHHHHH-CCCCCHHHHHHHHHHCCCHHHCCCCC
Q ss_conf 6542188446465878999-----999851--5667647899999998863-27865689999997317065333889
Q T0548 35 KYWVYQGKPVMPDQFTFEL-----LDFLHQ--LTHLSFSKMKALLERSHSP-YYMLNRDRTLKNITETCKACAQVNAS 104 (106)
Q Consensus 35 ~~~~~~Gr~vvP~~~~~~i-----l~~~H~--~~h~G~~~~~~~l~~i~~~-~~wp~m~~~v~~~v~~C~~Cq~~n~~ 104 (106)
..+...||+.||..+|..+ +..-.+ ..-.+.....+...++.+. ..=+..+...+.+......|.--+.+
T Consensus 33 ~~lD~KGRlsiPa~fR~~L~~~lvlt~~~~~cL~~yp~~~w~~~~~kl~~l~~~~~~~r~l~R~l~~~a~~v~~D~qG 110 (166)
T 1n0e_A 33 ITLDAKNRISLPAKLRAFFEGSIVINRGFENCLEVRKPQDFQKYFEQFNSFPSTQKDTRTLKRLIFANANFVDVDTAG 110 (166)
T ss_dssp ECCCTTSEEECCSHHHHHCCSEEECCCCTTSCCEEBCHHHHHHHHHHHTTSCSSSHHHHHHHHHHHTTCCEEECCTTS
T ss_pred CCCCCCCCEEECHHHHHHHCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCEEECCCCCC
T ss_conf 467678724756999986098699977998833015998899999999836832489999999984585483227774
No 10
>1yfu_A 3-hydroxyanthranilate-3,4-dioxygenase; cupin, oxidoreductase; 1.90A {Cupriavidus metallidurans} SCOP: b.82.1.20 PDB: 1yfw_A* 1yfx_A* 1yfy_A*
Probab=11.99 E-value=57 Score=13.59 Aligned_cols=17 Identities=24% Similarity=0.614 Sum_probs=14.2
Q ss_pred HHHHCCCHHHCCCCCCC
Q ss_conf 99731706533388999
Q T0548 90 NITETCKACAQVNASKS 106 (106)
Q Consensus 90 ~~v~~C~~Cq~~n~~~~ 106 (106)
.=.|+|..|-.++|+|+
T Consensus 157 ee~RtC~~CG~v~p~k~ 173 (174)
T 1yfu_A 157 EDKRRCPHCGQVHPGRA 173 (174)
T ss_dssp HHHHBCTTTCCBCCCSC
T ss_pred HHHCCCCCCCCCCCCCC
T ss_conf 52062887887389989
Done!