Query         T0584 3NF2, Streptomyces coelicolor, 352 residues
Match_columns 352
No_of_seqs    184 out of 2359
Neff          7.1 
Searched_HMMs 11830
Date          Sun Jun 13 15:31:11 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0584.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0584.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF00348 polyprenyl_synt:  Poly 100.0       0       0  424.0  22.3  255   41-308     1-259 (260)
  2 PF07307 HEPPP_synt_1:  Heptapr  98.2 2.4E-05 2.1E-09   46.7  13.7  120   60-190    17-139 (212)
  3 PF00494 SQS_PSY:  Squalene/phy  95.8   0.029 2.5E-06   28.7   8.5  137  148-323    89-226 (267)
  4 PF01040 UbiA:  UbiA prenyltran  81.7       1 8.7E-05   19.7  16.3  158   75-258    24-190 (258)
  5 PF06783 UPF0239:  Uncharacteri  73.5     1.3 0.00011   19.2   3.3   30  201-230    13-42  (85)
  6 PF10776 DUF2600:  Protein of u  54.4     4.2 0.00036   16.1   5.3   30  302-331   254-283 (330)
  7 PF06304 DUF1048:  Protein of u  53.8     4.3 0.00036   16.1   3.6   24  218-241    45-68  (103)
  8 PF03936 Terpene_synth_C:  Terp  34.1     8.9 0.00075   14.2  20.3   85  144-229   138-227 (270)
  9 PF04703 FaeA:  FaeA-like prote  27.0     6.1 0.00051   15.2   0.3   46   59-112    15-60  (62)
 10 PF11351 DUF3154:  Protein of u  11.0      29  0.0024   11.3   6.1   14   55-68     59-72  (123)

No 1  
>PF00348 polyprenyl_synt:  Polyprenyl synthetase;  InterPro: IPR000092 A variety of isoprenoid compounds are synthesized by various organisms. For example in eukaryotes the isoprenoid biosynthetic pathway is responsible for the synthesis of a variety of end products including cholesterol, dolichol, ubiquinone or coenzyme Q. In bacteria this pathway leads to the synthesis of isopentenyl tRNA, isoprenoid quinones, and sugar carrier lipids. Among the enzymes that participate in that pathway, are a number of polyprenyl synthetase enzymes which catalyze a 1'4-condensation between 5 carbon isoprene units. It has been shown , , , ,  that all the above enzymes share some regions of sequence similarity. Two of these regions are rich in aspartic-acid residues and could be involved in the catalytic mechanism and/or the binding of the substrates.; GO: 0008299 isoprenoid biosynthetic process; PDB: 2j1p_B 2j1o_A 1rqj_B 1rqi_A 2for_A 1wl0_A 1wl3_B 1v4e_A 1vg4_A 1v4i_A ....
Probab=100.00  E-value=0  Score=424.01  Aligned_cols=255  Identities=40%  Similarity=0.561  Sum_probs=222.1

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECCCCCHHHHH
Q ss_conf             77786546651587217899999999973999789999999999999999752787788655557872100046427899
Q T0584            41 WIDAQGNPADGDGGKAVRPALAVLSAEVTGAAPEVGVPGAVAVELVHNFSLLHDDLMDGDEQRRHRDTVWKVHGPAQAIL  120 (352)
Q Consensus        41 ~~~~~~~~~~~~gGKr~Rp~L~ll~~~~~g~~~~~~~~~AaavEliH~asLiHDDi~D~s~~RRG~pt~~~~~G~~~Ail  120 (352)
                      |+++ .+|...+||||+||.|++++++++|++++.++++|+++|++|+||||||||+|+|++|||+||+|.+||+..|||
T Consensus         1 ~~~~-~~~~~~~~GKr~Rp~l~~~~~~~~~~~~~~~~~~a~aiEliH~asLIhDDI~D~s~~RRG~pt~~~~~G~~~Ail   79 (260)
T PF00348_consen    1 WLEA-ARYYILSGGKRIRPLLVLLAAEALGGDPEDALPLAAAIELIHNASLIHDDIIDNSDLRRGKPTAHKKFGNAIAIL   79 (260)
T ss_dssp             HHHH-HHHHHHT---HHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SBETTEBTHHHHSTTHHHHH
T ss_pred             CHHH-HHHHHHCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCHHHHH
T ss_conf             9398-998856798649999999999994999899999999999999999986256327865679987433355146777


Q ss_pred             HHHHHHHHHHHHHHHCC--C--CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999997179--9--0079999999999998778877887642689999899999998652689999999999
Q T0584           121 VGDALFALANEVLLELG--T--VEAGRATRRLTKASRSLIDGQAQDISYEHRDRVSVEECLEMEGNKTGALLACASSIGA  196 (352)
Q Consensus       121 ~Gd~l~~~a~~~l~~~~--~--~~~~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~s~~~y~~~~~~KTa~Lf~~a~~~ga  196 (352)
                      +||+|++.+++.++.++  .  ....++.+.+.........||..|+.+... +.++++|++|+++|||+||++||++|+
T Consensus        80 ~gd~Ll~~a~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~q~~d~~~~~~-~~~~~~y~~i~~~KTg~lf~~~~~lga  158 (260)
T PF00348_consen   80 AGDYLLALAFELLARLGNFNPDARVLRILELFIMMLIEGEIGQLLDLANERK-DITEEEYLEIIELKTGSLFALACQLGA  158 (260)
T ss_dssp             HHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTST-TTCHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             5079999999999984344727999999999999874335999873543143-240999999999754999999999888


Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             86399998999999998899999999998875137845616762323340567789999986389678999999753100
Q T0584           197 VLGGADERTADTLEKYGYHLGLAFQAVDDLLGIWGDPDATGKQTWSDLRQRKKSLPVVAALAAGGAASERLGEILTADAK  276 (352)
Q Consensus       197 ~lag~~~~~~~~l~~~G~~lG~afQi~DDilD~~~~~~~~GK~~g~Dl~~gK~Tlpii~al~~~~~~~~~~~~~l~~~~~  276 (352)
                      +++|++++..+.+.+||+++|++|||+||++|++++++.+||++|+||++||+|||++++++..+++.+++......   
T Consensus       159 ilag~~~~~~~~l~~~g~~lG~afQi~DD~~D~~~~~~~~gK~~~~Dl~~gk~T~p~~~al~~~~~~~~~~l~~~~~---  235 (260)
T PF00348_consen  159 ILAGADEEQIEALEEFGRNLGIAFQIRDDLLDLFGDEEKLGKPVGSDLREGKPTLPVLYALEEASEEQRELLQENYD---  235 (260)
T ss_dssp             HHTTSGHHHHHHHHHHHHH---HHHHHHHHHHHHSCTTTTT--TTHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHH---
T ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCHHHHHCCCCCHHHHHHHHHCHHHHHHHHHHHHH---
T ss_conf             61486247899999998899999987898764148877618862017765973699999998595999999999883---


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             03445689899999999998649089999999
Q T0584           277 ASDFANFSEEEFAARAALIEEAGGREWTADEA  308 (352)
Q Consensus       277 ~~~~~~~~~e~i~~i~~~i~~~ga~e~a~~~~  308 (352)
                              .+..+...+.+...+++++++..+
T Consensus       236 --------~~~~~~~~~~~~~~~~~~~~~~~~  259 (260)
T PF00348_consen  236 --------KEDSEEIAEIVEETKSLEATRDYA  259 (260)
T ss_dssp             --------HHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             --------CCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             --------713489999999988766887622


No 2  
>PF07307 HEPPP_synt_1:  Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1;  InterPro: IPR009920   This family contains subunit 1 of bacterial heptaprenyl diphosphate synthase (HEPPP synthase) (2.5.1.30 from EC) (approximately 230 residues long). The enzyme consists of two subunits, both of which are required for catalysis of heptaprenyl diphosphate synthesis .
Probab=98.24  E-value=2.4e-05  Score=46.71  Aligned_cols=120  Identities=21%  Similarity=0.193  Sum_probs=81.1

Q ss_pred             HHHHHHHHHHC--CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECCCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             99999999739--9978999999999999999975278778865555787210004642789989999999999997179
Q T0584            60 ALAVLSAEVTG--AAPEVGVPGAVAVELVHNFSLLHDDLMDGDEQRRHRDTVWKVHGPAQAILVGDALFALANEVLLELG  137 (352)
Q Consensus        60 ~L~ll~~~~~g--~~~~~~~~~AaavEliH~asLiHDDi~D~s~~RRG~pt~~~~~G~~~Ail~Gd~l~~~a~~~l~~~~  137 (352)
                      .+.++.+-+.+  -.+++.-++..++-++|.|...||.|-+ ...+++...-.+    ...|++|||.-+.-+.++++++
T Consensus        17 ~l~ll~~~l~~~~l~~~~~~~~v~a~~lvq~ALDtHd~V~~-~~~~~~~~~k~R----QLtVLAGDyySalYY~lLA~~~   91 (212)
T PF07307_consen   17 RLLLLYSMLQEAELPEEEAERYVLAVMLVQIALDTHDEVDE-ANDESEQGSKER----QLTVLAGDYYSALYYYLLAESG   91 (212)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCHHHHHH----CCHHHHHHHHHHHHHHHHHHCC
T ss_conf             99999999866999878999999999999999988875501-011144678863----5234576887899999998579


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHH-HHHHHHHHHHHH
Q ss_conf             90079999999999998778877887642689999899999-998652689999
Q T0584           138 TVEAGRATRRLTKASRSLIDGQAQDISYEHRDRVSVEECLE-MEGNKTGALLAC  190 (352)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~s~~~y~~-~~~~KTa~Lf~~  190 (352)
                      .-   .+++.+++++..+.+....=-.   ....+.++|++ +..-.|+-+...
T Consensus        92 di---~lI~~ls~aI~eiNE~K~~Ly~---~~~~~~e~~~~~~~~ies~L~~~~  139 (212)
T PF07307_consen   92 DI---SLIRALSEAIKEINEAKISLYQ---KKVESDEEYLESVVTIESALFQKF  139 (212)
T ss_pred             CH---HHHHHHHHHHHHHHHHHHHHHH---HHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             76---9999999999999999999998---700889999999999999999999


No 3  
>PF00494 SQS_PSY:  Squalene/phytoene synthase;  InterPro: IPR002060 Squalene synthase 2.5.1.21 from EC (farnesyl-diphosphate farnesyltransferase) (SQS) and Phytoene synthase 2.5.1.32 from EC (PSY) share a number of functional similarities. These similarities are also reflected at the level of their primary structure , , . In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism.   SQS catalyzes the conversion of two molecules of farnesyl diphosphate (FPP) into squalene. It is the first committed step in the cholesterol biosynthetic pathway. The reaction carried out by SQS is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of FPP to form presqualene diphosphate; this intermediate is then rearranged in a NADP-dependent reduction, to form squalene:  2 FPP -> presqualene diphosphate + NADP -> squalene  SQS is found in eukaryotes. In yeast it is encoded by the ERG9 gene, in mammals by the FDFT1 gene. SQS seems to be membrane-bound.    PSY catalyzes the conversion of two molecules of geranylgeranyl diphosphate (GGPP) into phytoene. It is the second step in the biosynthesis of carotenoids from isopentenyl diphosphate. The reaction carried out by PSY is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of GGPP to form prephytoene diphosphate; this intermediate is then rearranged to form phytoene.  2 GGPP -> prephytoene diphosphate -> phytoene  PSY is found in all organisms that synthesize carotenoids: plants and photosynthetic bacteria as well as some non- photosynthetic bacteria and fungi. In bacteria PSY is encoded by the gene crtB. In plants PSY is localized in the chloroplast.; GO: 0016740 transferase activity, 0009058 biosynthetic process; PDB: 1ezf_B 2zcq_A 2zco_A 2zcp_A 2zcr_A 2zcs_A.
Probab=95.78  E-value=0.029  Score=28.73  Aligned_cols=137  Identities=23%  Similarity=0.210  Sum_probs=87.2

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999987788778876426899998999999986526899999999998639999899999999889999999999887
Q T0584           148 LTKASRSLIDGQAQDISYEHRDRVSVEECLEMEGNKTGALLACASSIGAVLGGADERTADTLEKYGYHLGLAFQAVDDLL  227 (352)
Q Consensus       148 ~~~~~~~~~~Gq~~dl~~~~~~~~s~~~y~~~~~~KTa~Lf~~a~~~ga~lag~~~~~~~~l~~~G~~lG~afQi~DDil  227 (352)
                      -.+....+.+|...|+...  .-.|.+++..-+..-.|+...+.+.+...-   ++.  +....++.++|+|+|+.|=+.
T Consensus        89 ~~~~l~~li~g~~~Dl~~~--~~~t~~~L~~Y~~~vAg~vg~l~~~i~~~~---~~~--~~~~~~A~~lG~AlqltnilR  161 (267)
T PF00494_consen   89 PKEWLRDLIDGMEMDLEFT--RFETFAELERYCYRVAGTVGLLLLEILGAR---DPD--EAAREAARHLGIALQLTNILR  161 (267)
T ss_dssp             HHHHHHHHHHHHCCCCT-S----SSHHHHHHHHHHH------TTHHHHHCT---TSC---HHHHHHHH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHCCC---CCC--CHHHHHHHHHHHHHHHHHHHH
T ss_conf             4689999999999886348--989999999999998999999999995868---653--139999999999999999999


Q ss_pred             HHCCCHHHHCCCHHHH-HHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             5137845616762323-340567789999986389678999999753100034456898999999999986490899999
Q T0584           228 GIWGDPDATGKQTWSD-LRQRKKSLPVVAALAAGGAASERLGEILTADAKASDFANFSEEEFAARAALIEEAGGREWTAD  306 (352)
Q Consensus       228 D~~~~~~~~GK~~g~D-l~~gK~Tlpii~al~~~~~~~~~~~~~l~~~~~~~~~~~~~~e~i~~i~~~i~~~ga~e~a~~  306 (352)
                      |+-           .| ...|..-+|.=..-+. +-..+.+   +..        ....+.+..         .+..-.+
T Consensus       162 dv~-----------eD~~~~gR~ylP~~~l~~~-gv~~~~l---~~~--------~~~~~~~~~---------~~~~~~~  209 (267)
T PF00494_consen  162 DVP-----------EDAAARGRVYLPADELEKH-GVSPEDL---LRG--------RIPSERLRA---------LLRELAE  209 (267)
T ss_dssp             CHH-----------HC-CTTT---S-HHHHCCT-TS-HHHC---CCG----------GGHHHHH---------HHHHHHH
T ss_pred             HHH-----------HHHHHCCCCCCCHHHHHHH-CCCHHHH---HHC--------CCCCHHHHH---------HHHHHHH
T ss_conf             828-----------8999779805876899981-9899999---642--------269989999---------9999999


Q ss_pred             HHHHHHHHHHHHHHHCC
Q ss_conf             99999999999986179
Q T0584           307 EARRQHTIAIEALDAVD  323 (352)
Q Consensus       307 ~~~~~~~~A~~~L~~l~  323 (352)
                      .++.+..+|...+..+|
T Consensus       210 ~A~~~~~~a~~~~~~lp  226 (267)
T PF00494_consen  210 RARDHLASAREGIRALP  226 (267)
T ss_dssp             HHHCCHHHHHHHHHCS-
T ss_pred             HHHHHHHHHHHHHHHCC
T ss_conf             99999999999998759


No 4  
>PF01040 UbiA:  UbiA prenyltransferase family;  InterPro: IPR000537 The COX10/ctaB/cyoE signature is found in prenyltransferases including bacterial 4-hydroxybenzoate octaprenyltransferase (gene ubiA); yeast mitochondrial para-hydroxybenzoate--polyprenyltransferase (gene COQ2); and protoheme IX farnesyltransferase (heme O synthase) from yeast and mammals(gene COX10), and from bacteria (genes cyoE or ctaB) , . These are integral membrane proteins, which probably contain seven transmembrane segments. The signature is also found in cytochrome C oxidase assembly factor. The complexity of cytochrome C oxidase requires assistance in building the complex, and this is carried out by the cytochrome C oxidase assembly factor.; GO: 0004659 prenyltransferase activity, 0016021 integral to membrane
Probab=81.68  E-value=1  Score=19.71  Aligned_cols=158  Identities=21%  Similarity=0.165  Sum_probs=81.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCC-----CCCCEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             999999999999999975278778865555-----787210004642789989999999999997179900799999999
Q T0584            75 VGVPGAVAVELVHNFSLLHDDLMDGDEQRR-----HRDTVWKVHGPAQAILVGDALFALANEVLLELGTVEAGRATRRLT  149 (352)
Q Consensus        75 ~~~~~AaavEliH~asLiHDDi~D~s~~RR-----G~pt~~~~~G~~~Ail~Gd~l~~~a~~~l~~~~~~~~~~~~~~~~  149 (352)
                      .......++=+++.+.-+-||..|.+.=|+     .||-.......+.+...+-.+...++-+....+.. . -.+... 
T Consensus        24 ~~~~~~~~~~~~~~~~~~~Nd~~D~~~D~~~~~~~~RPl~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~-~-~~~~~~-  100 (258)
T PF01040_consen   24 LLLLLLLGVFLLQLAVYVLNDYFDYEIDRDNPRKPNRPLPSGRLSPRQALIFALALLVLGLALALFLGPL-A-LWLALL-  100 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHH-H-HHHHHH-
T ss_conf             9999999999999999997278777278434578887014887289999999999999999999860899-9-999999-


Q ss_pred             HHHHHHHHHHHHHHHH--CCCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999877887788764--26899998-99999998652689999999999863999-98999999998899999999998
Q T0584           150 KASRSLIDGQAQDISY--EHRDRVSV-EECLEMEGNKTGALLACASSIGAVLGGAD-ERTADTLEKYGYHLGLAFQAVDD  225 (352)
Q Consensus       150 ~~~~~~~~Gq~~dl~~--~~~~~~s~-~~y~~~~~~KTa~Lf~~a~~~ga~lag~~-~~~~~~l~~~G~~lG~afQi~DD  225 (352)
                          ....+ ...-..  .-+ ..+. ++..-      +..+......|....+.. ....-.+.-+..-.+..+...+|
T Consensus       101 ----~~~~~-~~Ys~~p~~lK-~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (258)
T PF01040_consen  101 ----GILIG-WLYSAPPFRLK-RRPLLGELVV------GLGFGLLPLLGWLAVGGDISPPALLLALIFFLFTFAIIIFND  168 (258)
T ss_pred             ----HHHHH-HHHHHHHHHHC-CCCCCHHHHH------HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             ----99999-99862123421-5886009999------999999999999998388867999999899999989888889


Q ss_pred             HHHHCCCHHHHCCCHHHHHHCCCCCHHHHHHHH
Q ss_conf             875137845616762323340567789999986
Q T0584           226 LLGIWGDPDATGKQTWSDLRQRKKSLPVVAALA  258 (352)
Q Consensus       226 ilD~~~~~~~~GK~~g~Dl~~gK~Tlpii~al~  258 (352)
                      +.|..           +|.+.|++|+|+.+...
T Consensus       169 ~~D~~-----------~D~~~g~~Tl~v~~G~~  190 (258)
T PF01040_consen  169 IRDIE-----------GDRAAGIRTLPVLLGEK  190 (258)
T ss_pred             HHHHH-----------HHHHCCCCCHHHHHHHH
T ss_conf             76388-----------79987993129999899


No 5  
>PF06783 UPF0239:  Uncharacterised protein family (UPF0239);  InterPro: IPR009621   This is a group of transmembrane proteins of unknown function.; GO: 0016021 integral to membrane
Probab=73.46  E-value=1.3  Score=19.19  Aligned_cols=30  Identities=37%  Similarity=0.468  Sum_probs=22.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             999899999999889999999999887513
Q T0584           201 ADERTADTLEKYGYHLGLAFQAVDDLLGIW  230 (352)
Q Consensus       201 ~~~~~~~~l~~~G~~lG~afQi~DDilD~~  230 (352)
                      ..+...+.+-+||.++|-.||+.==.--++
T Consensus        13 ~Eed~~~~llRYGLfvGAIFQ~vCI~A~Il   42 (85)
T PF06783_consen   13 PEEDFFETLLRYGLFVGAIFQFVCILAAIL   42 (85)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHEE
T ss_conf             841699999999999999999999987213


No 6  
>PF10776 DUF2600:  Protein of unknown function (DUF2600)
Probab=54.45  E-value=4.2  Score=16.13  Aligned_cols=30  Identities=13%  Similarity=0.087  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf             999999999999999998617999478999
Q T0584           302 EWTADEARRQHTIAIEALDAVDMPDRVRDR  331 (352)
Q Consensus       302 e~a~~~~~~~~~~A~~~L~~l~~~~~~k~~  331 (352)
                      +...+.+..++++|.+.+..+|.+.--|-.
T Consensus       254 ~e~~~Rl~~F~~~a~~~~~~Lp~~~FHr~i  283 (330)
T PF10776_consen  254 KEMEERLKHFIEKALESVAKLPYPKFHRLI  283 (330)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             999999999999999999718994179999


No 7  
>PF06304 DUF1048:  Protein of unknown function (DUF1048);  InterPro: IPR008316 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 2o3l_B 2hh6_A 2o4t_A.
Probab=53.84  E-value=4.3  Score=16.07  Aligned_cols=24  Identities=21%  Similarity=0.455  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHCCCHHHHCCCHH
Q ss_conf             999999988751378456167623
Q T0584           218 LAFQAVDDLLGIWGDPDATGKQTW  241 (352)
Q Consensus       218 ~afQi~DDilD~~~~~~~~GK~~g  241 (352)
                      -..+|.+|++|+|.....-||++.
T Consensus        45 ~~~~il~dildLfEe~aadGk~V~   68 (103)
T PF06304_consen   45 NMMEILSDILDLFEEAAADGKSVL   68 (103)
T ss_dssp             HHHHHHHHHHHHHH--------HH
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCHH
T ss_conf             888899999999999987699625


No 8  
>PF03936 Terpene_synth_C:  Terpene synthase family, metal binding domain;  InterPro: IPR005630   Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C_10) synthases, sesquiterpene (C_15) synthases and the diterpene (C_20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf . Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT.  Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT.  Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT.   In the fungus Phaeosphaeria sp.L487 the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein .; GO: 0000287 magnesium ion binding, 0016829 lyase activity; PDB: 3g4d_B 3g4f_A 5eau_A 1hxg_A 1hx9_A 5eat_A 1hxc_A 5eas_A 1hxa_A 2j5c_B ....
Probab=34.07  E-value=8.9  Score=14.22  Aligned_cols=85  Identities=19%  Similarity=0.125  Sum_probs=50.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHH---HHHHHHHH
Q ss_conf             99999999998778877887642689-999899999998652689999999999863999-98999999---99889999
Q T0584           144 ATRRLTKASRSLIDGQAQDISYEHRD-RVSVEECLEMEGNKTGALLACASSIGAVLGGAD-ERTADTLE---KYGYHLGL  218 (352)
Q Consensus       144 ~~~~~~~~~~~~~~Gq~~dl~~~~~~-~~s~~~y~~~~~~KTa~Lf~~a~~~ga~lag~~-~~~~~~l~---~~G~~lG~  218 (352)
                      ....+.+.+.....|...+..|.... -+|.++|+.+-. .|++..-..+.....+.... .+..+.+.   .+-...+.
T Consensus       138 ~~~~~~~~~~~~~~~~~~E~~~r~~~~~Ps~~eYl~~R~-~t~g~~~~~~l~~~~l~~~~~~~~~~~~~~~~~l~~~~~~  216 (270)
T PF03936_consen  138 VREYFREAWRDYLEAYLWEAKWRAQGRVPSLEEYLENRR-VTSGVPPMLALIELGLEFALGEEPPEWLESPPMLRRLAND  216 (270)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCTS---HHHHHHHHH-HHT-HHHHHHHHHHHCCTSS-HHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH-HHCHHHHHHHHHHHHCCCCCCCCCHHHHHHCHHHHHHHHH
T ss_conf             799999999999999789998872494989999988843-1040649999999816652111357778504799999999


Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999988751
Q T0584           219 AFQAVDDLLGI  229 (352)
Q Consensus       219 afQi~DDilD~  229 (352)
                      ..-+.||+..+
T Consensus       217 ~~~l~NDi~S~  227 (270)
T PF03936_consen  217 IVRLVNDIYSY  227 (270)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHCCCCC
T ss_conf             75576332322


No 9  
>PF04703 FaeA:  FaeA-like protein;  InterPro: IPR006793 This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase , .; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription, 0009289 fimbrium; PDB: 2htj_A 2jt1_A.
Probab=26.95  E-value=6.1  Score=15.20  Aligned_cols=46  Identities=20%  Similarity=0.187  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECC
Q ss_conf             999999999739997899999999999999997527877886555578721000
Q T0584            59 PALAVLSAEVTGAAPEVGVPGAVAVELVHNFSLLHDDLMDGDEQRRHRDTVWKV  112 (352)
Q Consensus        59 p~L~ll~~~~~g~~~~~~~~~AaavEliH~asLiHDDi~D~s~~RRG~pt~~~~  112 (352)
                      |.=+--.++++|-..-++..        |.-.|.-+..+..++.|||.|+.|..
T Consensus        15 p~~t~eiA~~~gls~~qaR~--------~L~~L~~eG~Vk~~~~rrG~~~~W~l   60 (62)
T PF04703_consen   15 PCSTREIAEALGLSIYQARY--------YLQKLEKEGKVKRSPVRRGKSTYWRL   60 (62)
T ss_dssp             -B-HHHHHHHHTS-HHHHHH--------HHHHHHH---EEEE--------EEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHH--------HHHHHHHCCCEEEECCCCCCCCEEEE
T ss_conf             98899999996988999999--------99999887977852057886311233


No 10 
>PF11351 DUF3154:  Protein of unknown function (DUF3154)
Probab=11.03  E-value=29  Score=11.27  Aligned_cols=14  Identities=36%  Similarity=0.392  Sum_probs=8.9

Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             21789999999997
Q T0584            55 KAVRPALAVLSAEV   68 (352)
Q Consensus        55 Kr~Rp~L~ll~~~~   68 (352)
                      ||+||++.+.+.-.
T Consensus        59 ~rwRP~l~~~~~~l   72 (123)
T PF11351_consen   59 RRWRPALAYGTLGL   72 (123)
T ss_pred             HCCCCHHHHHHHHH
T ss_conf             10141999999999


Done!