Query 537021.9.peg.1074_1 Match_columns 169 No_of_seqs 120 out of 249 Neff 5.6 Searched_HMMs 33803 Date Wed May 25 08:47:37 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_1074.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >1tr2_A Vinculin isoform 1; ac 46.1 19 0.00056 16.7 3.0 27 105-131 80-106 (113) 2 >1ohg_A Major capsid protein; 25.5 46 0.0014 14.4 9.4 111 16-132 14-124 (282) 3 >2a6h_A DNA-directed RNA polym 23.0 34 0.00099 15.2 1.1 15 13-27 21-35 (125) 4 >3iyd_A DNA-directed RNA polym 22.4 32 0.00094 15.3 0.9 16 13-28 23-38 (132) 5 >3c5b_A Putative uncharacteriz 19.2 62 0.0018 13.6 7.1 112 14-133 17-134 (253) 6 >1bdf_A RNA polymerase alpha s 18.5 46 0.0014 14.4 1.0 16 13-28 21-36 (128) 7 >1np3_A Ketol-acid reductoisom 11.0 42 0.0012 14.7 -0.9 57 99-155 14-75 (80) 8 >1vhf_A Periplasmic divalent c 10.2 14 0.00041 17.4 -3.5 46 14-59 61-106 (113) 9 >2q1k_A ASCE; helix-turn-helix 9.1 1.2E+02 0.0036 11.9 2.5 20 105-124 16-35 (67) 10 >1kr4_A Protein TM1056, CUTA; 8.8 20 0.00058 16.6 -3.2 43 15-57 82-124 (125) No 1 >>1tr2_A Vinculin isoform 1; actin-binding, cell adhesion; 2.90A {Homo sapiens} PDB: 1st6_A (A:489-601) Probab=46.15 E-value=19 Score=16.67 Aligned_cols=27 Identities=7% Similarity=-0.009 Sum_probs=23.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 012799999999999999999997348 Q 537021.9.peg.1 105 YILKYKEQKLKKALEIRKDVEFALVSS 131 (169) Q Consensus 105 ~~~E~a~q~~k~~kElKrDiE~~~~~~ 131 (169) .+..+|.|+..++.+||..|+.++++. T Consensus 80 ~A~~lA~qi~~kL~~L~~~v~~Av~~~ 106 (113) T 1tr2_A 80 QARALASQLQDSLKDLKARXQEAXTQE 106 (113) T ss_dssp HHHHHHHHHHTHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 799998767888889999999999988 No 2 >>1ohg_A Major capsid protein; virus, virus coat protein, virus/viral protein, auto- catalytic cross-LINK, icosahedral virus; 3.45A {Bacteriophage HK97} (A:) Probab=25.46 E-value=46 Score=14.40 Aligned_cols=111 Identities=11% Similarity=0.116 Sum_probs=74.0 Q ss_pred CCCCHHHHHHHCCCCCCHHHHHCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEECC Q ss_conf 42017779875485417323420775214536888885015655544346754341001222355755799874156614 Q 537021.9.peg.1 16 NKESLSDVVSRITPEDTPIYSMIKKGTTHSIHPEWVVDDLASPGPNAQLEGDEYSFKTINTPERMGNYTQIMRKSWILSG 95 (169) Q Consensus 16 ~rEdl~dvI~~isP~~TPf~S~i~~~~a~~t~~eW~~d~L~~~~~n~~~EG~d~~~~~~~~~~r~~NytQI~~k~~~VSg 95 (169) .-|.+.+.| .--..+.|+++.+......+....|.......+..--+.||.+.+....+-... .....+-...+.= T Consensus 14 ~p~~~~~~i-~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~v~E~~~~~~~~~~~~~v---~~~~~k~~~~~~i 89 (282) T 1ohg_A 14 QPMQIPGII-MPGLRRLTIRDLLAQGRTSSNALEYVREEVFTNNADVVAEKALKPESDITFSKQ---TANVKTIAHWVQA 89 (282) T ss_dssp CCEEEEEEE-CCCCCCCCSGGGSEEEECCSSEEEEEEEEEEECCCEEECTTCCCCBCEEEEEEE---EEECEEEEEEEEE T ss_pred CCEEHHHHH-HHHHCHHHHHHHCCEEEECCCCEEEEEEECCCCCEEEECCCCCCCCCCCCCCCE---EEEEEEEEEEECC T ss_conf 968444578-754030457865053763799679887835767448861588676564542313---5111899999647 Q ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 5886543370127999999999999999999973487 Q 537021.9.peg.1 96 TQEAVDDVGYILKYKEQKLKKALEIRKDVEFALVSSQ 132 (169) Q Consensus 96 T~~av~~aG~~~E~a~q~~k~~kElKrDiE~~~~~~~ 132 (169) +.+..+... +-.++-...-.+.+.+.+|..++++. T Consensus 90 s~ell~~~~--~~~~~v~~~l~~~~a~~~d~~~~~g~ 124 (282) T 1ohg_A 90 SRQVMDDAP--MLQSYINNRLMYGLALKEEGQLLNGD 124 (282) T ss_dssp EHHHHHHST--THHHHHHHHHHHHHHHHHHHHHHSCC T ss_pred CHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 989975179--99999999999999999767886066 No 3 >>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} (A:48-172) Probab=23.03 E-value=34 Score=15.21 Aligned_cols=15 Identities=13% Similarity=0.290 Sum_probs=13.2 Q ss_pred CCCCCCCHHHHHHHC Q ss_conf 233420177798754 Q 537021.9.peg.1 13 STTNKESLSDVVSRI 27 (169) Q Consensus 13 ~~g~rEdl~dvI~~i 27 (169) ..|.|||+.++|-|+ T Consensus 21 i~GV~EDv~eIilNL 35 (125) T 2a6h_A 21 IPGVKEDVVEIILNL 35 (125) T ss_dssp CTTBSSBHHHHHHHH T ss_pred CCCCCCCHHHHHHHH T ss_conf 898521699999853 No 4 >>3iyd_A DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12} (A:49-180) Probab=22.39 E-value=32 Score=15.34 Aligned_cols=16 Identities=6% Similarity=0.245 Sum_probs=13.7 Q ss_pred CCCCCCCHHHHHHHCC Q ss_conf 2334201777987548 Q 537021.9.peg.1 13 STTNKESLSDVVSRIT 28 (169) Q Consensus 13 ~~g~rEdl~dvI~~is 28 (169) .-|.|||+.|+|-|+. T Consensus 23 i~GV~Edv~eIiLNLK 38 (132) T 3iyd_A 23 KEGVQEDILEILLNLK 38 (132) T ss_dssp CTTBSSCTTHHHHGGG T ss_pred CCCCHHHHHHHHHHCC T ss_conf 8770452999998557 No 5 >>3c5b_A Putative uncharacterized protein; capsid protein, HK97 fold, icosahedral virus; 4.50A {Enterobacteria phage EPSILON15} (A:1-253) Probab=19.18 E-value=62 Score=13.65 Aligned_cols=112 Identities=8% Similarity=-0.010 Sum_probs=68.3 Q ss_pred CCCCCCHHHHHHHCCCCCCHHHHHCCCCCCC-CCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEE Q ss_conf 3342017779875485417323420775214-536888885015655544346754341001222355755799874156 Q 537021.9.peg.1 14 TTNKESLSDVVSRITPEDTPIYSMIKKGTTH-SIHPEWVVDDLASPGPNAQLEGDEYSFKTINTPERMGNYTQIMRKSWI 92 (169) Q Consensus 14 ~g~rEdl~dvI~~isP~~TPf~S~i~~~~a~-~t~~eW~~d~L~~~~~n~~~EG~d~~~~~~~~~~r~~NytQI~~k~~~ 92 (169) ..+-+++++.|...-....|++.++...... ...+.|.... ..+...-+.||+..+....+ +.||.-+... T Consensus 17 ~lip~~~~~~Ii~~~~~~s~i~~~~~~~~~~~~~~~~~~~~~-~~~~a~~v~E~~~~~~~~~~-------f~~v~~~~~k 88 (253) T 3c5b_A 17 RTDKNGRIARIVEQLAKTNDILTDAIYVPCNDGSKHKTTIRA-GIPEPVWRRYNQGVQPTKTQ-------TVPVTDTTGM 88 (253) T ss_pred HCCCCCCHHHHHHHHHHCCHHHHHCCEEECCCCCCCEEEEEE-CCCCCCEECCCCCCCCCCCE-------EEEEEEEEEE T ss_conf 219875234799987634067751835651277674268984-38975115168874876654-------7876566775 Q ss_pred ECC----HHHHHHHCC-HHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 614----588654337-01279999999999999999999734877 Q 537021.9.peg.1 93 LSG----TQEAVDDVG-YILKYKEQKLKKALEIRKDVEFALVSSQG 133 (169) Q Consensus 93 VSg----T~~av~~aG-~~~E~a~q~~k~~kElKrDiE~~~~~~~a 133 (169) +.+ +.+.....+ ..+-.+|......+.+.+.+|.+++++.. T Consensus 89 ~~~~~~is~ell~~~d~~~~~~~~i~~~l~~a~~~~~~~a~i~G~g 134 (253) T 3c5b_A 89 LYDLGFVDKALADRSNNAAAFRVSENMGKLQGFNNKVARYSIYGNT 134 (253) T ss_pred ECCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 2673002499997429888999998899999999999987421876 No 6 >>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} (A:51-178) Probab=18.52 E-value=46 Score=14.39 Aligned_cols=16 Identities=6% Similarity=0.245 Sum_probs=13.4 Q ss_pred CCCCCCCHHHHHHHCC Q ss_conf 2334201777987548 Q 537021.9.peg.1 13 STTNKESLSDVVSRIT 28 (169) Q Consensus 13 ~~g~rEdl~dvI~~is 28 (169) ..|.|||+.++|-|+. T Consensus 21 i~GV~EDv~eIilNLK 36 (128) T 1bdf_A 21 KEGVQEDILEILLNLK 36 (128) T ss_dssp CTTBSSCHHHHHHHHH T ss_pred CCCHHHHHHHHHHHHC T ss_conf 6536676999999717 No 7 >>1np3_A Ketol-acid reductoisomerase; A DEEP figure-OF-eight knot, C-terminal alpha-helical domain, oxidoreductase; 2.00A {Pseudomonas aeruginosa} (A:199-251,A:312-338) Probab=11.01 E-value=42 Score=14.66 Aligned_cols=57 Identities=14% Similarity=0.128 Sum_probs=30.1 Q ss_pred HHHHCCHHHHHHHHHH-HHHHHHHHHHHHHHHCCCCCC----CCCCCHHHHHHHHHHCCCCC Q ss_conf 6543370127999999-999999999999973487777----76320034689987507555 Q 537021.9.peg.1 99 AVDDVGYILKYKEQKL-KKALEIRKDVEFALVSSQGSE----KTSPRKMAALSSWIKKNASR 155 (169) Q Consensus 99 av~~aG~~~E~a~q~~-k~~kElKrDiE~~~~~~~a~~----at~ar~t~Gl~~~i~tN~~~ 155 (169) ..-.+|..-|+||=.. .-+|-+..-|-..=+.+--.+ .-+.-+.+|+..||+.|... T Consensus 14 tLVeAGY~pE~AYfE~lHElKLIvDli~e~Gl~~M~~~IS~~~~~g~~lr~mmpwi~~~klv 75 (80) T 1np3_A 14 TLVEAGYAPEMAYFECLHELKLIVDLMYEGGIANMNYSISPIEQIGEKLRAMMPWIAANKIV 75 (80) T ss_dssp HHHHTTCCHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHTTCTTC------ T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCC T ss_conf 99985998788899999866668999996268999986075989999998658733226565 No 8 >>1vhf_A Periplasmic divalent cation tolerance protein; structural genomics, unknown function; 1.54A {Thermotoga maritima} (A:) Probab=10.24 E-value=14 Score=17.45 Aligned_cols=46 Identities=15% Similarity=0.351 Sum_probs=38.4 Q ss_pred CCCCCCHHHHHHHCCCCCCHHHHHCCCCCCCCCEEEEEEEECCCCC Q ss_conf 3342017779875485417323420775214536888885015655 Q 537021.9.peg.1 14 TTNKESLSDVVSRITPEDTPIYSMIKKGTTHSIHPEWVVDDLASPG 59 (169) Q Consensus 14 ~g~rEdl~dvI~~isP~~TPf~S~i~~~~a~~t~~eW~~d~L~~~~ 59 (169) ....+.|.+.|-.+-|.|+|=.=.+.-......|..|..+.+..++ T Consensus 61 ~~~~~~l~~~I~~~HpYevPeIi~~~i~~~~~~Yl~Wi~~~~~~~~ 106 (113) T 1vhf_A 61 EEKEKELYEELRKLHPYETPAIFTLKVENVLTEYXNWLRESVLEGG 106 (113) T ss_dssp GGGHHHHHHHHHHHCSSSSCCEEEEECSCCCHHHHHHHHHHC---- T ss_pred HHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHCCCCC T ss_conf 9899999999995099979889999775689889999998676887 No 9 >>2q1k_A ASCE; helix-turn-helix, chaperone, TTSS; 2.70A {Aeromonas hydrophila} (A:) Probab=9.10 E-value=1.2e+02 Score=11.91 Aligned_cols=20 Identities=5% Similarity=0.243 Sum_probs=17.2 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 01279999999999999999 Q 537021.9.peg.1 105 YILKYKEQKLKKALEIRKDV 124 (169) Q Consensus 105 ~~~E~a~q~~k~~kElKrDi 124 (169) ...|+-.|+..++-++|||+ T Consensus 16 ~arel~~qL~qAL~~~Kr~L 35 (67) T 2q1k_A 16 FARELHAQLVQALGDVKRRL 35 (67) T ss_dssp HHHHHHHHHHHHHHHHHHHT T ss_pred HHHHHHHHHHHHHHHHHHHH T ss_conf 79999999999999999999 No 10 >>1kr4_A Protein TM1056, CUTA; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG, unknown function; 1.40A {Thermotoga maritima} (A:) Probab=8.76 E-value=20 Score=16.55 Aligned_cols=43 Identities=14% Similarity=0.335 Sum_probs=0.0 Q ss_pred CCCCCHHHHHHHCCCCCCHHHHHCCCCCCCCCEEEEEEEECCC Q ss_conf 3420177798754854173234207752145368888850156 Q 537021.9.peg.1 15 TNKESLSDVVSRITPEDTPIYSMIKKGTTHSIHPEWVVDDLAS 57 (169) Q Consensus 15 g~rEdl~dvI~~isP~~TPf~S~i~~~~a~~t~~eW~~d~L~~ 57 (169) ...++|.+.|-.+-|.|+|=.=.+.-......|.+|..+++++ T Consensus 82 ~~~~~l~~~I~~~HpYevPeIi~~~~~~~~~~Yl~Wi~~~~~~ 124 (125) T 1kr4_A 82 EKEKELYEELRKLHPYETPAIFTLKVENILTEYXNWLRESVLG 124 (125) T ss_dssp GGHHHHHHHHHHHCSSSSCCEEEECCCCEEHHHHHHHHHHTSC T ss_pred HHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHCCC T ss_conf 8999999999951999798899997646898899999986338 Done!