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!