Query 537021.9.peg.1074_1 Match_columns 169 No_of_seqs 120 out of 249 Neff 5.6 Searched_HMMs 23785 Date Wed May 25 08:41:08 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_1074.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3c5b_A Putative uncharacterize 19.0 44 0.0019 13.6 8.0 142 1-150 1-149 (335) 2 1bdf_A RNA polymerase alpha su 17.3 40 0.0017 13.9 1.3 17 12-28 70-86 (235) 3 3lu0_A DNA-directed RNA polyme 13.6 57 0.0024 13.0 1.3 18 12-29 70-87 (329) 4 1vhf_A Periplasmic divalent ca 11.6 8.6 0.00036 17.8 -3.4 48 14-61 61-108 (113) 5 2a6h_A DNA-directed RNA polyme 10.1 79 0.0033 12.2 1.4 16 13-28 68-83 (315) 6 2zfh_A CUTA; human brain, trim 9.8 9.6 0.00041 17.5 -3.7 34 18-51 131-164 (179) 7 1p1l_A CUTA, periplasmic dival 7.9 13 0.00056 16.6 -3.6 41 14-54 60-100 (102) 8 2d5c_A AROE, shikimate 5-dehyd 7.6 49 0.0021 13.4 -0.8 19 8-28 33-51 (263) 9 2zom_A CUTA1, protein CUTA, ch 7.4 18 0.00076 15.9 -3.1 42 15-56 70-111 (113) 10 1vi2_A Shikimate 5-dehydrogena 7.4 32 0.0013 14.4 -1.9 10 18-27 49-58 (300) No 1 >3c5b_A Putative uncharacterized protein; capsid protein, HK97 fold, icosahedral virus; 4.50A {Enterobacteria phage EPSILON15} Probab=19.00 E-value=44 Score=13.62 Aligned_cols=142 Identities=9% Similarity=0.088 Sum_probs=85.0 Q ss_pred CCCCCCCEECCCCCCCCCC----HHHHHHHCCCCCCHHHHHCCCCCC-CCCEEEE-EEEECCCCCCCCCCCCCCCCCCCC Q ss_conf 9723476010212334201----777987548541732342077521-4536888-885015655544346754341001 Q 537021.9.peg.1 1 MTIVNNTFITSSSTTNKES----LSDVVSRITPEDTPIYSMIKKGTT-HSIHPEW-VVDDLASPGPNAQLEGDEYSFKTI 74 (169) Q Consensus 1 Ma~~tnt~~t~~~~g~rEd----l~dvI~~isP~~TPf~S~i~~~~a-~~t~~eW-~~d~L~~~~~n~~~EG~d~~~~~~ 74 (169) ||+..++..|.--...|-| +..||-.+. ++-|+|..+.=..+ ..+.|.. ....|..+..-..-+|-..+ . T Consensus 1 m~~~~~~~pTL~d~akr~d~dg~~~~VIE~l~-~tn~IL~dlpf~E~N~~t~~~~tvr~~LP~~~fR~lN~g~~~s---k 76 (335) T 3c5b_A 1 MALIGQTLPSLLDIYNRTDKNGRIARIVEQLA-KTNDILTDAIYVPCNDGSKHKTTIRAGIPEPVWRRYNQGVQPT---K 76 (335) T ss_pred CCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHH-HCCHHHHHCCEEEECCCCCCEEEEEECCCCCCEECCCCCCCCC---C T ss_conf 96200478429999974198640568999875-2427876186433016767536787349974167368774876---6 Q ss_pred CCCCCCCCEEEEEEEEEEECCHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH Q ss_conf 2223557557998741566145886543370-127999999999999999999973487777763200346899875 Q 537021.9.peg.1 75 NTPERMGNYTQIMRKSWILSGTQEAVDDVGY-ILKYKEQKLKKALEIRKDVEFALVSSQGSEKTSPRKMAALSSWIK 150 (169) Q Consensus 75 ~~~~r~~NytQI~~k~~~VSgT~~av~~aG~-~~E~a~q~~k~~kElKrDiE~~~~~~~a~~at~ar~t~Gl~~~i~ 150 (169) +.+++...-|-|+.-.+.|-. ..++..|. .+..+.|...+++-+.+.++..|+.+.. +..|.+..||..-+. T Consensus 77 st~~q~t~~~~iL~g~~eVDk--~La~~~Gn~a~~ra~e~~~~ie~m~q~~a~~~iyGd~--a~~p~~F~GLa~R~~ 149 (335) T 3c5b_A 77 TQTVPVTDTTGMLYDLGFVDK--ALADRSNNAAAFRVSENMGKLQGFNNKVARYSIYGNT--DAEPEAFMGLAPRFN 149 (335) T ss_pred CEEEEEEEEEEEECCCEEHHH--HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCC--CCCHHHCCCHHHHHC T ss_conf 547887666776246210319--9998538678899999999999999999987151877--688020467888745 No 2 >1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1 Probab=17.28 E-value=40 Score=13.88 Aligned_cols=17 Identities=6% Similarity=0.260 Sum_probs=14.3 Q ss_pred CCCCCCCCHHHHHHHCC Q ss_conf 12334201777987548 Q 537021.9.peg.1 12 SSTTNKESLSDVVSRIT 28 (169) Q Consensus 12 ~~~g~rEdl~dvI~~is 28 (169) ...|.|||+.|+|-|+. T Consensus 70 ~i~GV~Edv~eIilNLK 86 (235) T 1bdf_A 70 TKEGVQEDILEILLNLK 86 (235) T ss_dssp CCTTBSSCHHHHHHHHH T ss_pred CCCCCHHHHHHHHHHCC T ss_conf 68880563999997267 No 3 >3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A Probab=13.58 E-value=57 Score=12.98 Aligned_cols=18 Identities=6% Similarity=0.217 Sum_probs=14.6 Q ss_pred CCCCCCCCHHHHHHHCCC Q ss_conf 123342017779875485 Q 537021.9.peg.1 12 SSTTNKESLSDVVSRITP 29 (169) Q Consensus 12 ~~~g~rEdl~dvI~~isP 29 (169) ...|.|||+.|+|-|+-- T Consensus 70 ti~GV~Edv~~IilNLK~ 87 (329) T 3lu0_A 70 TKEGVQEDILEILLNLKG 87 (329) T ss_dssp CCTTBSSCHHHHHHHHHS T ss_pred CCCCCCCCHHHHHHHCCC T ss_conf 689962379999984673 No 4 >1vhf_A Periplasmic divalent cation tolerance protein; structural genomics, unknown function; 1.54A {Thermotoga maritima} SCOP: d.58.5.2 Probab=11.62 E-value=8.6 Score=17.77 Aligned_cols=48 Identities=15% Similarity=0.331 Sum_probs=36.0 Q ss_pred CCCCCCHHHHHHHCCCCCCHHHHHCCCCCCCCCEEEEEEEECCCCCCC Q ss_conf 334201777987548541732342077521453688888501565554 Q 537021.9.peg.1 14 TTNKESLSDVVSRITPEDTPIYSMIKKGTTHSIHPEWVVDDLASPGPN 61 (169) Q Consensus 14 ~g~rEdl~dvI~~isP~~TPf~S~i~~~~a~~t~~eW~~d~L~~~~~n 61 (169) ....+.|.+.|-..-|.|+|-.-.+.-..+..-|.+|..+.+..++.- T Consensus 61 ~~~~~~l~~~I~~~HpYevPeIi~~~~~~~~~~Y~~Wv~~~~~~~~s~ 108 (113) T 1vhf_A 61 EEKEKELYEELRKLHPYETPAIFTLKVENVLTEYMNWLRESVLEGGSH 108 (113) T ss_dssp GGGHHHHHHHHHHHCSSSSCCEEEEECSCCCHHHHHHHHHHC------ T ss_pred HHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHCCCCCCC T ss_conf 999999999999519997988999976457988999999867587765 No 5 >2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* 2gho_A 1hqm_A ... Probab=10.14 E-value=79 Score=12.15 Aligned_cols=16 Identities=13% Similarity=0.275 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 68 i~GV~Edv~eIllNLK 83 (315) T 2a6h_A 68 IPGVKEDVVEIILNLK 83 (315) T ss_dssp CTTBSSBHHHHHHHHH T ss_pred CCCCCCCHHHHHHHHC T ss_conf 8885105899998530 No 6 >2zfh_A CUTA; human brain, trimeric structure, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.05A {Homo sapiens} SCOP: d.58.5.2 PDB: 1xk8_A Probab=9.79 E-value=9.6 Score=17.48 Aligned_cols=34 Identities=18% Similarity=0.271 Sum_probs=12.8 Q ss_pred CCHHHHHHHCCCCCCHHHHHCCCCCCCCCEEEEE Q ss_conf 0177798754854173234207752145368888 Q 537021.9.peg.1 18 ESLSDVVSRITPEDTPIYSMIKKGTTHSIHPEWV 51 (169) Q Consensus 18 Edl~dvI~~isP~~TPf~S~i~~~~a~~t~~eW~ 51 (169) +.|.+.|-..-|.|+|-.-.+.-.+++..|.+|. T Consensus 131 ~~L~~~I~e~HPYEvPeIi~i~i~~~n~~Yl~WI 164 (179) T 2zfh_A 131 PALTDFVRSVHPYEVAEVIALPVEQGNFPYLQWV 164 (179) T ss_dssp HHHHHHHHHHCSSSSCCEEEEEECEECHHHHHHH T ss_pred HHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHH T ss_conf 9999999963998797899997556898899999 No 7 >1p1l_A CUTA, periplasmic divalent cation tolerance protein CUTA; NYSGXRC, PSI, protein structure initiative; 2.00A {Archaeoglobus fulgidus} SCOP: d.58.5.2 Probab=7.91 E-value=13 Score=16.64 Aligned_cols=41 Identities=15% Similarity=0.214 Sum_probs=30.1 Q ss_pred CCCCCCHHHHHHHCCCCCCHHHHHCCCCCCCCCEEEEEEEE Q ss_conf 33420177798754854173234207752145368888850 Q 537021.9.peg.1 14 TTNKESLSDVVSRITPEDTPIYSMIKKGTTHSIHPEWVVDD 54 (169) Q Consensus 14 ~g~rEdl~dvI~~isP~~TPf~S~i~~~~a~~t~~eW~~d~ 54 (169) .....+|.+.|-..-|.|+|..-.+.-..++..|-.|..+. T Consensus 60 ~~~~~~l~~~I~~~HpYevPeIi~~~~~~~~~~Y~~Wv~~~ 100 (102) T 1p1l_A 60 SEKFAEVRDEVKAMHSYTTPCICAIPIERGLKEFLDWIDET 100 (102) T ss_dssp GGGHHHHHHHHHHHCSSSSCCEEEEECCCCCHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHH T ss_conf 98899999999951999798899998535898899999985 No 8 >2d5c_A AROE, shikimate 5-dehydrogenase; substrate, dimer, X-RAY diffraction, structural genomics, NPPSFA; HET: SKM; 1.65A {Thermus thermophilus HB8} PDB: 1wxd_A* 2cy0_A* 2ev9_A* Probab=7.60 E-value=49 Score=13.36 Aligned_cols=19 Identities=11% Similarity=0.214 Sum_probs=10.0 Q ss_pred EECCCCCCCCCCHHHHHHHCC Q ss_conf 010212334201777987548 Q 537021.9.peg.1 8 FITSSSTTNKESLSDVVSRIT 28 (169) Q Consensus 8 ~~t~~~~g~rEdl~dvI~~is 28 (169) |..++.. -+||.+.|-.+. T Consensus 33 y~~~~v~--~~~l~~~i~~~~ 51 (263) T 2d5c_A 33 YEAWDTP--LEALPGRLKEVR 51 (263) T ss_dssp EEEEECC--GGGHHHHHHHHH T ss_pred EEEEECC--HHHHHHHHHHHH T ss_conf 9986289--899999999998 No 9 >2zom_A CUTA1, protein CUTA, chloroplast, putative, expressed; trimeric structure, protein stability, unknown function; 3.02A {Oryza sativa subsp} Probab=7.44 E-value=18 Score=15.88 Aligned_cols=42 Identities=14% Similarity=0.137 Sum_probs=29.4 Q ss_pred CCCCCHHHHHHHCCCCCCHHHHHCCCCCCCCCEEEEEEEECC Q ss_conf 342017779875485417323420775214536888885015 Q 537021.9.peg.1 15 TNKESLSDVVSRITPEDTPIYSMIKKGTTHSIHPEWVVDDLA 56 (169) Q Consensus 15 g~rEdl~dvI~~isP~~TPf~S~i~~~~a~~t~~eW~~d~L~ 56 (169) .....|.+.|-..-|.|+|-.-.+.-..+...|.+|..+.+. T Consensus 70 ~~~~~l~~~I~~~HpYevPeIi~~~i~~~~~~Y~~Wi~~~~~ 111 (113) T 2zom_A 70 SLLDALTEHVKANHEYDVPEVIALPIKGGNLKYLEWLKNSTR 111 (113) T ss_dssp GGHHHHHHHHHHTCSSSSCCCEEEECCCCCHHHHHHHHHHCC T ss_pred HHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHCC T ss_conf 899999999995299979889999843478789999998627 No 10 >1vi2_A Shikimate 5-dehydrogenase 2; structural genomics, oxidoreductase; HET: MSE NAD; 2.10A {Escherichia coli} SCOP: c.2.1.7 c.58.1.5 PDB: 1npd_A* 1o9b_A* Probab=7.36 E-value=32 Score=14.44 Aligned_cols=10 Identities=10% Similarity=0.421 Sum_probs=4.6 Q ss_pred CCHHHHHHHC Q ss_conf 0177798754 Q 537021.9.peg.1 18 ESLSDVVSRI 27 (169) Q Consensus 18 Edl~dvI~~i 27 (169) ++|.+.|..+ T Consensus 49 ~~l~~~i~~l 58 (300) T 1vi2_A 49 DSFPGAIEGL 58 (300) T ss_dssp TTHHHHHHHH T ss_pred HHHHHHHHHH T ss_conf 8999999998 Done!