Query         T0547 BR53, unknown, 611 residues
Match_columns 611
No_of_seqs    261 out of 901
Neff          5.4 
Searched_HMMs 11830
Date          Fri May 21 18:09:28 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0547.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0547.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF02784 Orn_Arg_deC_N:  Pyrido 100.0 2.8E-45       0  357.7  24.5  247   51-328     1-251 (251)
  2 PF00278 Orn_DAP_Arg_deC:  Pyri  99.1 7.3E-12 6.2E-16  105.5   1.4   92  439-538    24-116 (116)
  3 PF01168 Ala_racemase_N:  Alani  98.5 1.4E-05 1.2E-09   58.2  16.7  184   51-274     2-188 (214)
  4 PF00576 Transthyretin:  HIUase  53.7     4.7  0.0004   16.4   4.9   75  465-550    23-101 (112)
  5 PF00331 Glyco_hydro_10:  Glyco  49.3     5.4 0.00046   15.9   4.6   58  208-274   187-246 (319)
  6 PF07279 DUF1442:  Protein of u  46.1       6 0.00051   15.6   6.9  155  109-280    25-186 (218)
  7 PF04227 Indigoidine_A:  Indigo  45.3       6 0.00051   15.6   2.7   11  258-268   164-174 (293)
  8 PF04958 AstA:  Arginine N-succ  44.5     6.4 0.00054   15.4   3.5   65   21-87      2-66  (338)
  9 PF08002 DUF1697:  Protein of u  37.8     7.9 0.00067   14.7   4.1   21  148-168    67-87  (137)
 10 PF02738 Ald_Xan_dh_C2:  Molybd  35.5     8.6 0.00073   14.4   2.5   47  138-192   109-155 (543)
 11 PF02353 CMAS:  Cyclopropane-fa  32.1     8.6 0.00073   14.4   1.8   18  382-399   253-270 (273)
 12 PF12224 Amidoligase_2:  Putati  31.0      10 0.00085   13.9   6.7   58  208-265    88-149 (252)
 13 PF00809 Pterin_bind:  Pterin b  29.4      11  0.0009   13.7   6.7   93  211-321   105-204 (210)
 14 PF00351 Biopterin_H:  Biopteri  27.9      11 0.00095   13.5   5.2   11  316-326   246-256 (332)
 15 PF01715 IPPT:  IPP transferase  27.4     8.3 0.00071   14.5   1.0   39  287-327    33-71  (252)
 16 PF00682 HMGL-like:  HMGL-like   27.3      11 0.00097   13.5   7.8   33  206-239   163-195 (237)
 17 PF02049 FliE:  Flagellar hook-  25.6     7.5 0.00063   14.9   0.5   30  374-403    33-63  (95)
 18 PF01262 AlaDh_PNT_C:  Alanine   23.6      10 0.00086   13.8   0.9   40  122-165    16-58  (168)
 19 PF07997 DUF1694:  Protein of u  23.3      13  0.0011   12.9   1.6   85   34-156     6-94  (120)
 20 PF03945 Endotoxin_N:  delta en  21.8     4.6 0.00039   16.4  -1.2   46  374-419   100-148 (226)
 21 PF08123 DOT1:  Histone methyla  20.9      15  0.0013   12.6   3.8   35  292-326    78-112 (205)
 22 PF01698 FLO_LFY:  Floricaula /  20.6     8.4 0.00071   14.5  -0.0   15  309-323   226-240 (386)
 23 PF08368 FAST_2:  FAST kinase-l  20.5      11 0.00093   13.6   0.5   42  514-555    45-87  (93)

No 1  
>PF02784 Orn_Arg_deC_N:  Pyridoxal-dependent decarboxylase, pyridoxal binding domain;  InterPro: IPR000183 These enzymes are collectively known as group IV decarboxylases . Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities , . Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC , to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region .; GO: 0003824 catalytic activity; PDB: 2nv9_A 2nva_H 1szr_B 1qu4_B 2tod_C 1f3t_D 3btn_B 7odc_A 1d7k_B 2oo0_A ....
Probab=100.00  E-value=2.8e-45  Score=357.73  Aligned_cols=247  Identities=31%  Similarity=0.483  Sum_probs=215.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCHHHHHHHHHHCCCCCCEEEECCHHHHHHHHHCCCCCCCEE
Q ss_conf             47999999999999999999970889872378745337878999999984666785166228899999996489988178
Q T0547            51 FPHLIQKQIENIYGNFNKARKEFGYKGGFNAVYPLKVNQYPGFVKNLVKLGKDYNYGLEAGSKAELLLAMAYNNEGAPIT  130 (611)
Q Consensus        51 f~dil~~ri~~l~~aF~~A~~~~~Y~g~y~~vYaiKaN~~~~Vv~~i~~~G~~~~~GlEv~Sk~EL~~ala~g~~~~~Ii  130 (611)
                      +.+.++.|++++.++|..        .+++++||+|||+++.|++.+.+.|    +|+||+|.+|+.+|+++|+++.+|+
T Consensus         1 d~~~~~~~~~~~~~~~~~--------~~~~~~YA~KaN~~~~il~~l~~~g----~g~dv~S~~El~~al~~g~~~~~ii   68 (251)
T PF02784_consen    1 DEDTIIERIRELLRAFLP--------YNVQVFYAVKANPNPAILKLLAEEG----CGFDVASPGELELALAAGFPPDRII   68 (251)
T ss_dssp             EHHHHHHHHHHHHHHHST--------T-EEEEEBGGGS--HHHHHHHHHTT-----EEEESSHHHHHHHHHTTT-GGGEE
T ss_pred             CCHHHHHHHHHHHHHCCC--------CCEEEEEEEECCCCHHHHHHHHHCC----CCEEECCHHHHHHHHHCCCCCHHEE
T ss_conf             937999999999986286--------7548999970289899999999839----9869868999999997699920367


Q ss_pred             ECC-CCCHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEEEEECC-CCCCCCCCCCCCCCCCCCCH
Q ss_conf             788-9899999999854235710489866889999999999984698622688885078-87764220466656478898
Q T0547           131 VNG-FKDRELINIGFIAAEMGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVRLHS-AGVGIWAKSGGINSKFGLTS  208 (611)
Q Consensus       131 ~nG-~Kd~e~I~lAl~a~~lG~~v~IViDs~~EL~~I~~ia~~~l~v~p~IgiRv~l~~-~~~g~~~~Tgg~~SKFGl~~  208 (611)
                      |+| +|++++|+.|+..   |. .+|++||++||++|.++++.+     +|+|||+|.. .++..+..|||..||||++.
T Consensus        69 ~~gp~k~~~~l~~a~~~---~~-~~i~iDs~~el~~l~~~~~~~-----~v~lRin~~~~~~~~~~~~~g~~~skFGi~~  139 (251)
T PF02784_consen   69 FTGPAKSDEELEEAIEY---GV-ATINIDSLDELERLAALAPGA-----RVGLRINPGVGIGAHSKLSTGGKESKFGIDI  139 (251)
T ss_dssp             EE-SS--HHHHHHHHHT---T--SEEEESSHHHHHHHHHHHTTH-----EEEEB-B-S-STTTSCHCCCSSTSST---BG
T ss_pred             ECCCCCCHHHHHHHHHC---CC-CEEEECCHHHHHHHHHHCCCC-----CEEEEEECCCCCCCCCCCCCCCHHHCCCCCH
T ss_conf             62899999999999984---99-989947989999999974706-----3789981487766776421331121057672


Q ss_pred             HH-HHHHHHHHHHCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHH-HCCCCCEEEEECCCCCCCCCCCCCCCC
Q ss_conf             99-9999999986689873478886338876788999999999999999999-717994058724556554777777777
Q T0547           209 TE-LIEAVNLLKENKLLEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELR-KMGAKNLKAINLGGGLAVEYSQFKNEK  286 (611)
Q Consensus       209 ~e-i~~~i~~l~~~~~l~~L~gLHfHIGSQI~di~~~~~ai~ea~~ly~eL~-~~g~~~l~~LDIGGGlgV~Y~~~~~~~  286 (611)
                      ++ +.++++.+++.+ + .+.|||||+|||+.+...|..+++.+.+++.++. +.|..++++||+||||||+|..     
T Consensus       140 ~~~~~~~~~~~~~~~-l-~l~GlH~H~GS~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~idiGGG~~v~y~~-----  212 (251)
T PF02784_consen  140 EEEAEEALDRAKELG-L-RLVGLHFHIGSQIRDPEAFREAIARLLDLIDELRRELGFEDLEWIDIGGGFGVPYDD-----  212 (251)
T ss_dssp             GG-HHHHHHHHHHTT-E-EEEEEB----TTBSSTHHHHHHHHHHHHHHHHHHHH---TT-SEEE--------SSS-----
T ss_pred             HHHHHHHHHHHHCCC-C-EEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCC-----
T ss_conf             588999998640148-5-189999876878888799999999999999987661198768789854997888887-----


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHC
Q ss_conf             778888999999999999999964899877887075677750
Q T0547           287 SRNYTLREYANDVVFILKNIAEQKKDLEPDIFIESGRFVAAN  328 (611)
Q Consensus       287 s~ny~l~eya~~Iv~~i~~~c~~~~vp~P~Ii~EpGRaivA~  328 (611)
                        ++++++|+..+...+++.|.. +.+.|+|++|||||+||+
T Consensus       213 --~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~EpGR~lva~  251 (251)
T PF02784_consen  213 --DYDFEDYADLIRAALKEFFPS-GFPGPKLIIEPGRYLVAN  251 (251)
T ss_dssp             --SSCHHHHHHHHHHHHHHHCTT-TTTTSEEEEEE--TTTGG
T ss_pred             --CCCCHHHHHHHHHHHHHHHHC-CCCCCEEEEECCHHHHCC
T ss_conf             --556445999999999998740-489958999707898679


No 2  
>PF00278 Orn_DAP_Arg_deC:  Pyridoxal-dependent decarboxylase, C-terminal sheet domain;  InterPro: IPR000183 These enzymes are collectively known as group IV decarboxylases . Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities , . Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC , to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region .; GO: 0003824 catalytic activity; PDB: 2qgh_A 3c5q_A 2yxx_A 1knw_A 1ko0_A 1hkw_B 1hkv_B 2o0t_B 1f3t_A 1szr_B ....
Probab=99.09  E-value=7.3e-12  Score=105.51  Aligned_cols=92  Identities=35%  Similarity=0.621  Sum_probs=80.6

Q ss_pred             HHHHHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEEEEECC
Q ss_conf             65330324422310100066312013546788865104873364374663014677765567-78887896078886020
Q T0547           439 RYLVNFSLFQSMPDFWGLEQNFPIMPLDRLDEEPTRSASIWDITCDSDGEISYSKDKPLFLH-DVDVEKENYFLGFFLVG  517 (611)
Q Consensus       439 ~y~~NfS~FqslPD~Wai~Q~Fpi~Pl~rl~e~P~~~~~l~DiTCDSDG~i~~~~~~~l~lh-~~~~~~e~y~lG~FlvG  517 (611)
                      +|++|.|++++ |+.|..++.||+.++.+-++.|.+...|++-||||.++|..    ..+|+ +++   ..-+|.|+.+|
T Consensus        24 ~~~vd~G~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~G~tC~~~D~i~~----~~~lP~~l~---~GD~l~f~~~G   95 (116)
T PF00278_consen   24 WYYVDDGIYGS-PDPWLYDQYFPILPLNRDNEGPEEPYTVWGPTCDSGDVIAR----DVPLPKELE---VGDWLVFENMG   95 (116)
T ss_dssp             EEEES----SS-THHHHHS----EEEESS-TTSSEEEEEEE---SSTT--SEE----EEEEETT--------EEEES---
T ss_pred             EEEECCCHHHC-HHHHHHCCCCCEEECCCCCCCCCEEEEEEECCCCCCCEEEE----ECCCCCCCC---CCCEEEEEECC
T ss_conf             99993794669-78796198751687245677785789999467689999926----536788889---99899999256


Q ss_pred             HHHHHHCCCCCCCCCCCEEEE
Q ss_conf             699974775156789857999
Q T0547           518 AYQEVLGMKHNLFTHPTEAII  538 (611)
Q Consensus       518 AYQeiLGd~HNLfg~t~~v~v  538 (611)
                      ||+-.++..||.|+.+.+|.|
T Consensus        96 AYt~~~s~~Fn~~~~p~~v~v  116 (116)
T PF00278_consen   96 AYTMSLSSNFNGFPPPAEVYV  116 (116)
T ss_dssp             --SGTTSBCCCTT--EEEEEE
T ss_pred             CCHHHHCCCCCCCCCCCEEEC
T ss_conf             031655674669899879979


No 3  
>PF01168 Ala_racemase_N:  Alanine racemase, N-terminal domain;  InterPro: IPR001608   Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins containing this domain are found in both prokaryotes and eukaryotes ,. The molecular structure of alanine racemase from Bacillus stearothermophilus was determined by X-ray crystallography to a resolution of 1.9 A . The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N-terminus, and a C-terminal domain essentially composed of beta-strands. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C-terminus of the first beta-strand of the alpha/beta barrel.    This domain is also found in the PROSC (proline synthetase co-transcribed bacterial homolog) family of proteins, which are not known to have alenine racemase activity.; PDB: 3cpg_A 1b54_A 1ct5_A 1w8g_A 3gwq_B 1rcq_A 2odo_D 2rjg_B 3b8u_D 2rjh_A ....
Probab=98.46  E-value=1.4e-05  Score=58.16  Aligned_cols=184  Identities=17%  Similarity=0.156  Sum_probs=127.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCC-HHHHHHHH-HH-CCCCCCEEEECCHHHHHHHHHCCCCCC
Q ss_conf             4799999999999999999997088987237874533787-89999999-84-666785166228899999996489988
Q T0547            51 FPHLIQKQIENIYGNFNKARKEFGYKGGFNAVYPLKVNQY-PGFVKNLV-KL-GKDYNYGLEAGSKAELLLAMAYNNEGA  127 (611)
Q Consensus        51 f~dil~~ri~~l~~aF~~A~~~~~Y~g~y~~vYaiKaN~~-~~Vv~~i~-~~-G~~~~~GlEv~Sk~EL~~ala~g~~~~  127 (611)
                      +.+.++++++.+++.. .         . +..=-+|+|.. ..+++.+. .. |.   -++=|++..|.......    .
T Consensus         2 dl~~l~~Ni~~~~~~~-~---------~-~i~~vvK~~a~g~g~~~~~~~~~~g~---~~~~va~~~Ea~~l~~~----~   63 (214)
T PF01168_consen    2 DLDALRHNIKKIRQRA-P---------K-KIRAVVKANAYGHGIVRVAKALAEGV---DGFGVATLQEAEELREA----P   63 (214)
T ss_dssp             EHHHHHHHHHHHHHHS-T---------S-EEEEB-HHHHSCHHHHHHHHHHHHTS---SEEEESSHHHHHHHHHG----G
T ss_pred             CHHHHHHHHHHHHHHC-C---------C-CEEEEECCCCCCCCHHHHHHHHHHCC---CCHHCCCHHHHHHHHHC----C
T ss_conf             8899999999999865-8---------8-68999868877822999999999759---76240849899999838----5


Q ss_pred             CEEECCCCCHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCC
Q ss_conf             17878898999999998542357104898668899999999999846986226888850788776422046665647889
Q T0547           128 PITVNGFKDRELINIGFIAAEMGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVRLHSAGVGIWAKSGGINSKFGLT  207 (611)
Q Consensus       128 ~Ii~nG~Kd~e~I~lAl~a~~lG~~v~IViDs~~EL~~I~~ia~~~l~v~p~IgiRv~l~~~~~g~~~~Tgg~~SKFGl~  207 (611)
                      .+++++. ..+.++.++.     ++++++||+++.++.+.+.++. .+.+..+.|.|+.+           .  .+.|+.
T Consensus        64 il~~~~~-~~~~~~~~~~-----~~~~~~v~s~~~~~~l~~~~~~-~~~~~~v~l~idtG-----------~--~R~G~~  123 (214)
T PF01168_consen   64 ILVLGPP-PPEELEELVE-----YNIIPTVDSPEQLEALNKAARK-QGKPLPVHLKIDTG-----------M--GRLGVR  123 (214)
T ss_dssp             EEE-C---SGGGHHHHHH-----TTEEEEE-SHHHHHHHHHHHHH-TSS-EEEEEBE--S-----------S--T-----
T ss_pred             EEEECCC-CHHHHHHHHH-----CCEEEEECCHHHHHHHHHHHHH-CCCCCEEEEEECCC-----------C--CCCCCC
T ss_conf             8546388-8889999873-----9899999989999999999898-59973499999986-----------8--868879


Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCC
Q ss_conf             8999999999986689873478886338876788999999999999999999717994058724556
Q T0547           208 STELIEAVNLLKENKLLEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAKNLKAINLGGG  274 (611)
Q Consensus       208 ~~ei~~~i~~l~~~~~l~~L~gLHfHIGSQI~di~~~~~ai~ea~~ly~eL~~~g~~~l~~LDIGGG  274 (611)
                      .+++.++++.+++.+.+ .+.|+..|.|+--..-..-+..++...++...+++.| .....+.+|+-
T Consensus       124 ~~~~~~l~~~i~~~~~l-~l~Gi~th~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~s~g~S  188 (214)
T PF01168_consen  124 PEELEELARAIKALPGL-RLEGIMTHFGHADDPDATRRAQFERFRRLVEALEKAG-IKPPIVSMGNS  188 (214)
T ss_dssp             HHHHHHHHHHHHCTTTE-EEEEEBE--SSTTSSCHHHHHHHHHHHHHHHHHHHTT-TTSSCEBEEBH
T ss_pred             HHHHHHHHHHHHHCCCC-CEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCC-CCCCEEECCCC
T ss_conf             99999999999857998-6678996316778801779999999999999998608-99988965698


No 4  
>PF00576 Transthyretin:  HIUase/Transthyretin family;  InterPro: IPR000895   Transthyretin (formerly prealbumin) is one of 3 thyroid hormone-binding proteins found in the blood of vertebrates . It is produced in the liver and circulates in the bloodstream, where it binds retinol and thyroxine (T4) . It differs from the other 2 hormone-binding proteins (T4-binding globulin and albumin) in 3 distinct ways: (1) the gene is expressed at a high rate in the brain choroid plexus; (2) it is enriched in cerebrospinal fluid; and (3) no genetically caused absence has been observed, suggesting an essential role in brain function, distinct from that played in the bloodstream . The protein consists of around 130 amino acids, which assemble as a homotetramer that contains an internal channel in which T4 is bound. Within this complex, T4 appears to be transported across the blood-brain barrier, where, in the choroid plexus, the hormone stimulates further synthesis of transthyretin. The protein then diffuses back into the bloodstream, where it binds T4 for transport back to the brain .; GO: 0005496 steroid binding, 0006810 transport; PDB: 2gpz_C 2igl_D 2g2n_B 2g2p_D 2h6u_G 2h1x_C 2qel_C 2g5u_A 2fbr_A 1ttb_B ....
Probab=53.68  E-value=4.7  Score=16.40  Aligned_cols=75  Identities=25%  Similarity=0.251  Sum_probs=46.6

Q ss_pred             CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCHHHHHHCCCCCCCCCCCEEEEEE--CC
Q ss_conf             5467888651048733643746630146777655677888789607888602069997477515678985799998--89
Q T0547           465 LDRLDEEPTRSASIWDITCDSDGEISYSKDKPLFLHDVDVEKENYFLGFFLVGAYQEVLGMKHNLFTHPTEAIISI--NE  542 (611)
Q Consensus       465 l~rl~e~P~~~~~l~DiTCDSDG~i~~~~~~~l~lh~~~~~~e~y~lG~FlvGAYQeiLGd~HNLfg~t~~v~v~~--~~  542 (611)
                      |.|+++ +...-.|+.-+.|+||+++...   +.-..+. +|  -|-=.|.||+|-.-+|.  .-|  -.+|.|.+  ++
T Consensus        23 L~~~~~-~~~~~~i~~~~T~~DGR~~~~l---~~~~~~~-~G--~Y~l~F~~g~Yf~~~g~--~~F--~p~V~v~F~i~d   91 (112)
T PF00576_consen   23 LYRLDE-DGSWELIASGRTNADGRIDHPL---LPGEDFQ-PG--VYELRFDTGDYFAAQGV--PSF--YPEVPVRFTIDD   91 (112)
T ss_dssp             EEEEET-TSSEEEEEEEEB--BTTBSSTS---SETTTS-------EEEEEEHHHHHHHTT---STS--ESEEEEEE-TSS
T ss_pred             EEECCC-CCCCEEEEEEEECCCCCCCCCC---CCCCCCC-CE--EEEEEEEHHHHHHHCCC--CCC--CCCEEEEEEECC
T ss_conf             998248-9984899999968992685475---6854447-78--89999991572665499--957--303409999888


Q ss_pred             C-C-EEEEEE
Q ss_conf             9-6-288751
Q T0547           543 K-G-YEVEGI  550 (611)
Q Consensus       543 ~-g-~~i~~~  550 (611)
                      . . |.|--+
T Consensus        92 ~~~HYHvPlL  101 (112)
T PF00576_consen   92 PGEHYHVPLL  101 (112)
T ss_dssp             TTSEEEEEEE
T ss_pred             CCCCEEEEEE
T ss_conf             9981798599


No 5  
>PF00331 Glyco_hydro_10:  Glycosyl hydrolase family 10;  InterPro: IPR001000   O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families , , . This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site . Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in 'clans'.   Glycoside hydrolase family 10 GH10 from CAZY comprises enzymes with a number of known activities; xylanase (3.2.1.8 from EC); endo-1,3-beta-xylanase (3.2.1.32 from EC); cellobiohydrolase (3.2.1.91 from EC). These enzymes were formerly known as cellulase family F.    The microbial degradation of cellulose and xylans requires several types of enzymes such as endoglucanases (), cellobiohydrolases () (exoglucanases), or xylanases () , . Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family F  or as the glycosyl hydrolases family 10 . ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1vbr_A 1vbu_A 1ta3_B 1b3x_A 1b3z_A 1b3v_A 1b3y_A 1bg4_A 1b30_A 1b31_A ....
Probab=49.32  E-value=5.4  Score=15.92  Aligned_cols=58  Identities=16%  Similarity=0.320  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHHCCC-CCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC-CEEEEECCCC
Q ss_conf             8999999999986689-87347888633887678899999999999999999971799-4058724556
Q T0547           208 STELIEAVNLLKENKL-LEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAK-NLKAINLGGG  274 (611)
Q Consensus       208 ~~ei~~~i~~l~~~~~-l~~L~gLHfHIGSQI~di~~~~~ai~ea~~ly~eL~~~g~~-~l~~LDIGGG  274 (611)
                      ...+.+.++.+++.+. ++ -.|+.+|+++... +..++..++       ++.+.|.+ .+..+||...
T Consensus       187 ~~~~~~lv~~l~~~gvpId-gIG~Q~H~~~~~~-~~~i~~~l~-------~~a~~Gl~i~ITElDv~~~  246 (319)
T PF00331_consen  187 RDAYLELVKELKARGVPID-GIGLQSHFGAGYP-PEEIRAALD-------RFADLGLPIHITELDVRDP  246 (319)
T ss_dssp             HHHHHHHHHHHHHTT-----EE----EEESSSS-HHHHHHHHH-------HHHTT--EEEEESBEEESS
T ss_pred             HHHHHHHHHHHHHCCCCCC-EEEEEEECCCCCC-HHHHHHHHH-------HHHHCCCCEEEEEEEECCC
T ss_conf             9999999999987898743-2666551168899-999999999-------9997499538987441578


No 6  
>PF07279 DUF1442:  Protein of unknown function (DUF1442);  InterPro: IPR009902   This family consists of several hypothetical Arabidopsis thaliana proteins of around 225 residues in length. The function of this family is unknown.
Probab=46.08  E-value=6  Score=15.57  Aligned_cols=155  Identities=15%  Similarity=0.084  Sum_probs=77.7

Q ss_pred             EECCHHHHHHHHHCCCCCCCEE--E-CCCCCHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf             6228899999996489988178--7-889899999999854235710489866889999999999984698622688885
Q T0547           109 EAGSKAELLLAMAYNNEGAPIT--V-NGFKDRELINIGFIAAEMGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVR  185 (611)
Q Consensus       109 Ev~Sk~EL~~ala~g~~~~~Ii--~-nG~Kd~e~I~lAl~a~~lG~~v~IViDs~~EL~~I~~ia~~~l~v~p~IgiRv~  185 (611)
                      .--+-.|+..|||+|.....|+  | +|.-..--|-||..|++-|-+.+-+++..+++....+..++ .+..-.+-+.+ 
T Consensus        25 ~ep~~aEfISALAAG~nAkLiVe~~s~~~~~~ttiaLaaAA~~TgGR~VCIlp~~~~~~~~~~~l~~-~~~~~~vEfiv-  102 (218)
T PF07279_consen   25 KEPDVAEFISALAAGNNAKLIVEAWSSGGAIATTIALAAAARHTGGRHVCILPDEQSLSEYKKALGE-AGLSDVVEFIV-  102 (218)
T ss_pred             CCCCHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCEEEEEECCHHHHHHHHHHHCC-CCCCCCCEEEE-
T ss_conf             7987899999985654540799971467733669999999987098199990785779999998531-45113525996-


Q ss_pred             ECCCCCCCCCCCCCCCCCC---CCCHHHHH-HHHHHHHHCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             0788776422046665647---88989999-9999998668987347888633887678899999999999999999971
Q T0547           186 LHSAGVGIWAKSGGINSKF---GLTSTELI-EAVNLLKENKLLEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKM  261 (611)
Q Consensus       186 l~~~~~g~~~~Tgg~~SKF---Gl~~~ei~-~~i~~l~~~~~l~~L~gLHfHIGSQI~di~~~~~ai~ea~~ly~eL~~~  261 (611)
                       +- .... ...+-..--|   -....+.. ++++.++-.+.- .+ .+--+.-+.-.+-..|...+          +..
T Consensus       103 -Ge-~~~~-~~~~~~~vDF~vVDck~~~~~~~vl~~a~~~~rG-AV-VV~~Na~~~~~~g~sw~~~~----------~~~  167 (218)
T PF07279_consen  103 -GE-SPEE-VMPGLKGVDFLVVDCKREDFAARVLRAAKLSPRG-AV-VVCYNAFSRSRNGFSWRSVL----------RGR  167 (218)
T ss_pred             -CC-CHHH-HHHHCCCCCEEEEECCHHHHHHHHHHHHCCCCCC-EE-EEEECCCCCCCCCCCHHHHC----------CCC
T ss_conf             -58-9999-9841468878998065788899999860438983-49-99865655676876266651----------689


Q ss_pred             CCCCEEEEECCCCCCCCCC
Q ss_conf             7994058724556554777
Q T0547           262 GAKNLKAINLGGGLAVEYS  280 (611)
Q Consensus       262 g~~~l~~LDIGGGlgV~Y~  280 (611)
                      .+..-.+|-||+|+-|---
T Consensus       168 ~~Vrsv~LPIG~GleVt~I  186 (218)
T PF07279_consen  168 RVVRSVFLPIGEGLEVTRI  186 (218)
T ss_pred             CCEEEEEEECCCCEEEEEE
T ss_conf             7337899624787699998


No 7  
>PF04227 Indigoidine_A:  Indigoidine synthase A like protein;  InterPro: IPR007342 Indigoidine is a blue pigment synthesised by Erwinia chrysanthemi implicated in pathogenicity and protection from oxidative stress. IdgA is involved in indigoidine biosynthesis, but its specific function is unknown .; PDB: 1vkm_F.
Probab=45.29  E-value=6  Score=15.57  Aligned_cols=11  Identities=18%  Similarity=0.181  Sum_probs=5.1

Q ss_pred             HHHCCCCCEEE
Q ss_conf             99717994058
Q T0547           258 LRKMGAKNLKA  268 (611)
Q Consensus       258 L~~~g~~~l~~  268 (611)
                      |...|.+.+.|
T Consensus       164 LET~GV~Vvgy  174 (293)
T PF04227_consen  164 LETQGVPVVGY  174 (293)
T ss_dssp             HHHTT--EE--
T ss_pred             HHCCCCEEEEE
T ss_conf             73179469995


No 8  
>PF04958 AstA:  Arginine N-succinyltransferase beta subunit;  InterPro: IPR007041 Arginine N-succinyltransferase 2.3.1.109 from EC catalyzes the transfer of succinyl-CoA to arginine to produce succinylarginine. This is the first step in arginine catabolism by the arginine succinyltransferase pathway.; GO: 0008791 arginine N-succinyltransferase activity, 0006527 arginine catabolic process; PDB: 1yle_A.
Probab=44.50  E-value=6.4  Score=15.40  Aligned_cols=65  Identities=14%  Similarity=0.076  Sum_probs=46.3

Q ss_pred             EEECCCCCCCHHHHHHHHHHCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEE
Q ss_conf             6872788888899999998557998589874799999999999999999997088987237874533
Q T0547            21 VCINYEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKARKEFGYKGGFNAVYPLKV   87 (611)
Q Consensus        21 l~v~p~~~~~l~dlv~~l~~~~~~tPllvrf~dil~~ri~~l~~aF~~A~~~~~Y~g~y~~vYaiKa   87 (611)
                      +.|+|...-||..|.+-.++.|.|.--|-.+.+.|++||.+-.++|.....  ..+|.-.++|-.--
T Consensus         2 lviRPv~~~Dl~aL~~lA~~sg~G~TsLP~d~~~L~~rI~~S~~sFa~~~~--~~~~~~~YlFVLED   66 (338)
T PF04958_consen    2 LVIRPVRPSDLDALYELARESGPGFTSLPADRERLAARIERSERSFAGEAV--DQPGDEGYLFVLED   66 (338)
T ss_dssp             EEEEE--GGGHHHHHHHHHHS----TTS-S-HHHHHHHHHHHHHHHH-TT---------EEEEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC--CCCCCCCEEEEEEE
T ss_conf             478348513699999999982998636999989999999999998623224--78776426999995


No 9  
>PF08002 DUF1697:  Protein of unknown function (DUF1697);  InterPro: IPR012545   This family contains many hypothetical bacterial proteins.; PDB: 2hiy_C.
Probab=37.75  E-value=7.9  Score=14.67  Aligned_cols=21  Identities=24%  Similarity=0.526  Sum_probs=9.7

Q ss_pred             HCCCCEEEEECCHHHHHHHHH
Q ss_conf             357104898668899999999
Q T0547           148 EMGHNITLTIEGLNELEAIID  168 (611)
Q Consensus       148 ~lG~~v~IViDs~~EL~~I~~  168 (611)
                      ..|+.+-+.+=+.+||..+.+
T Consensus        67 ~fg~~~~v~vrt~~el~~~~~   87 (137)
T PF08002_consen   67 RFGFEVPVIVRTAEELRAIVA   87 (137)
T ss_dssp             H-TT---EEEEEHHHHHHHHT
T ss_pred             HCCCCCCEEEECHHHHHHHHH
T ss_conf             619987889972999999999


No 10 
>PF02738 Ald_Xan_dh_C2:  Molybdopterin-binding domain of aldehyde dehydrogenase;  InterPro: IPR008274 Aldehyde oxidase () catalyzes the conversion of an aldehyde in the presence of oxygen and water to an acid and hydrogen peroxide. The enzyme is a homodimer, and requires FAD, molybdenum and two 2FE-2S clusters as cofactors. Xanthine dehydrogenase () catalyzes the hydrogenation of xanthine to urate, and also requires FAD, molybdenum and two 2FE-2S clusters as cofactors. This activity is often found in a bifunctional enzyme with xanthine oxidase () activity too. The enzyme can be converted from the dehydrogenase form to the oxidase form irreversibly by proteolysis or reversibly through oxidation of sulphhydryl groups.; GO: 0016491 oxidoreductase activity, 0006118 electron transport; PDB: 3hrd_B 1rm6_D 1sb3_D 1t3q_E 1ffu_B 1ffv_B 1n63_E 1n61_E 1zxi_E 1n5w_E ....
Probab=35.48  E-value=8.6  Score=14.42  Aligned_cols=47  Identities=19%  Similarity=0.237  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCC
Q ss_conf             9999998542357104898668899999999999846986226888850788776
Q T0547           138 ELINIGFIAAEMGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVRLHSAGVG  192 (611)
Q Consensus       138 e~I~lAl~a~~lG~~v~IViDs~~EL~~I~~ia~~~l~v~p~IgiRv~l~~~~~g  192 (611)
                      .....|+.+++.|+-|.++.+-.+++..        ...+|..-+|++.+.+..|
T Consensus       109 ~~~~aa~~A~~~grPVk~~~sR~E~~~~--------~~~r~~~~~~~~~g~~~dG  155 (543)
T PF02738_consen  109 FEVAAALAARKTGRPVKLVWSREEDFQA--------GPKRPAAKIRVRAGVDKDG  155 (543)
T ss_dssp             HHHHHHHHHHHH-S-EEEE--HHHHHHH--------S--B-EEEEEEEEEE----
T ss_pred             HHHHHHHHHHHHCCCEEEEECHHHHCCC--------CCCCCHHHEEEEEEECCCC
T ss_conf             9999999999849989999616984766--------7897554578889998999


No 11 
>PF02353 CMAS:  Cyclopropane-fatty-acyl-phospholipid synthase;  InterPro: IPR003333   Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented.   This entry represents cyclopropane-fatty-acyl-phospholipid synthase that is slosely related to methyltransferases.   Cyclopropane-fatty-acyl-phospholipid synthase or CFA synthase 2.1.1.79 from EC catalyses the reaction:   S-adenosyl-L-methionine + phospholipid olefinic fatty acid -> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid.    The major mycolic acid produced by Mycobacterium tuberculosis contains two cis-cyclopropanes in the meromycolate chain. Cyclopropanation may contribute to the structural integrity of the cell wall complex .; GO: 0008825 cyclopropane-fatty-acyl-phospholipid synthase activity, 0008610 lipid biosynthetic process; PDB: 3hem_A 1kpi_A 1kph_A 1kpg_D 1kp9_A 1tpy_A 2fk7_A 3ha5_A 3ha3_A 3ha7_A ....
Probab=32.11  E-value=8.6  Score=14.41  Aligned_cols=18  Identities=22%  Similarity=0.183  Sum_probs=8.6

Q ss_pred             HHHHHHHHHHHHCCCCCH
Q ss_conf             999999999973696678
Q T0547           382 IDHLESILTLFDLGYVDL  399 (611)
Q Consensus       382 ~~~~~~~~~~f~~G~l~L  399 (611)
                      ..|+.-+-..|..|.+++
T Consensus       253 ~~yl~~~~~~F~~g~~~~  270 (273)
T PF02353_consen  253 RYYLAYCAAAFRSGDIDV  270 (273)
T ss_dssp             HHHH---HHHHHTTSSEE
T ss_pred             HHHHHHHHHHHHCCCCEE
T ss_conf             999999999997799869


No 12 
>PF12224 Amidoligase_2:  Putative amidoligase enzyme
Probab=30.98  E-value=10  Score=13.90  Aligned_cols=58  Identities=14%  Similarity=0.121  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHHCCCCC--CEEEEEEECCCCCCC--HHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             899999999998668987--347888633887678--8999999999999999999717994
Q T0547           208 STELIEAVNLLKENKLLE--QFTMIHFHLGSQITE--IHPLKKALNEAGNIYTELRKMGAKN  265 (611)
Q Consensus       208 ~~ei~~~i~~l~~~~~l~--~L~gLHfHIGSQI~d--i~~~~~ai~ea~~ly~eL~~~g~~~  265 (611)
                      ..++.++++.|++++...  .-.|+|.|||-....  ...+++-++-+.-+-..|.++..++
T Consensus        88 ~~~i~~v~~~L~~~~~~~t~~scg~HVHv~~~~~~~~~~~l~~l~~~~~~~E~~L~~~~p~~  149 (252)
T PF12224_consen   88 LEEIDEVLRALRRAGAVGTNDSCGFHVHVNPEPPGFSADTLRNLAKAIWLFEDWLRELLPPD  149 (252)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             79999999999976992247771679995585678689999999999999899999866997


No 13 
>PF00809 Pterin_bind:  Pterin binding enzyme This Prosite entry is a subset of the Pfam family;  InterPro: IPR000489   All organisms require reduced folate cofactors for the synthesis of a variety of metabolites. Most microorganisms must synthesize folate de novo because they lack the active transport system of higher vertebrate cells that allows these organisms to use dietary folates. Proteins containing this domain include dihydropteroate synthase (2.5.1.15 from EC) as well as a group of methyltransferase enzymes including methyltetrahydrofolate, corrinoid iron-sulphur protein methyltransferase (MeTr) Q46389 from SWISSPROT that catalyses a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation.   Dihydropteroate synthase (2.5.1.15 from EC) (DHPS) catalyses the condensation of 6-hydroxymethyl-7,8-dihydropteridine pyrophosphate to para-aminobenzoic acid to form 7,8-dihydropteroate. This is the second step in the three-step pathway leading from 6-hydroxymethyl-7,8-dihydropterin to 7,8-dihydrofolate. DHPS is the target of sulphonamides, which are substrate analogues that compete with para-aminobenzoic acid. Bacterial DHPS (gene sul or folP)  is a protein of about 275 to 315 amino acid residues that is either chromosomally encoded or found on various antibiotic resistance plasmids. In the lower eukaryote Pneumocystis carinii, DHPS is the C-terminal domain of a multifunctional folate synthesis enzyme (gene fas) .; GO: 0004156 dihydropteroate synthase activity, 0009396 folic acid and derivative biosynthetic process; PDB: 2vef_B 2veg_A 1ad4_A 1ad1_A 2bmb_A 1twz_B 1tws_A 1tx2_A 1tx0_B 1tww_B ....
Probab=29.37  E-value=11  Score=13.71  Aligned_cols=93  Identities=18%  Similarity=0.137  Sum_probs=48.9

Q ss_pred             HHHHHHHHHHCCCCCCEEEEEEEC-CCCCCCHHHHH-HHHHHHHHHHHH----HHHCCCC-CEEEEECCCCCCCCCCCCC
Q ss_conf             999999998668987347888633-88767889999-999999999999----9971799-4058724556554777777
Q T0547           211 LIEAVNLLKENKLLEQFTMIHFHL-GSQITEIHPLK-KALNEAGNIYTE----LRKMGAK-NLKAINLGGGLAVEYSQFK  283 (611)
Q Consensus       211 i~~~i~~l~~~~~l~~L~gLHfHI-GSQI~di~~~~-~ai~ea~~ly~e----L~~~g~~-~l~~LDIGGGlgV~Y~~~~  283 (611)
                      ..+.+..+++++.  .+.++|..- ...+.....++ ..+.++.+++.+    +.+.|.+ .==++|-|=||+-.     
T Consensus       105 ~~~~~~l~a~~~~--~~V~m~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~Gi~~~~IiiDPgigf~~~-----  177 (210)
T PF00809_consen  105 DPEMLPLAAEYGA--PVVLMHSDGKPKGMPKTAEYRLDVAEEIIEFFEERIEALLKAGIPRERIIIDPGIGFGKT-----  177 (210)
T ss_dssp             HTTHHHHHHHHTS--EEEEE--CTCTTTGSTSHHHSHCHHHHHHHHHHHHHHHHHH-T--GGGEEEETTTT-TTS-----
T ss_pred             CHHHHHHHHHHCC--EEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHEEEECCCCCCCC-----
T ss_conf             5899999998399--799995267766665554223209999999999999999986999778999789888888-----


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEC
Q ss_conf             77777888899999999999999996489987788707
Q T0547           284 NEKSRNYTLREYANDVVFILKNIAEQKKDLEPDIFIES  321 (611)
Q Consensus       284 ~~~s~ny~l~eya~~Iv~~i~~~c~~~~vp~P~Ii~Ep  321 (611)
                               .+..-.++..++.+...  .+.|.++.=+
T Consensus       178 ---------~~~~~~~l~~i~~~~~~--~~~p~l~g~s  204 (210)
T PF00809_consen  178 ---------QEQNLELLRNIKELREL--LGLPILVGGS  204 (210)
T ss_dssp             ---------HHHHHHHHHTHHHHHTC--TTSEBEEEET
T ss_pred             ---------HHHHHHHHHHHHHHHHH--CCCCEEEEEE
T ss_conf             ---------89999999999999986--8999899985


No 14 
>PF00351 Biopterin_H:  Biopterin-dependent aromatic amino acid hydroxylase;  InterPro: IPR001273   Phenylalanine, tyrosine and tryptophan hydroxylases constitute a family of tetrahydrobiopterin-dependent aromatic amino acid hydroxylases, all of which are rate-limiting catalysts for important metabolic pathways . The proteins are structurally and functionally related, each containing iron, and catalysing ring hydroxylation of aromatic amino acids, using tetra-hydrobiopterin (BH4) as a substrate. All are regulated by phosphorylation at serines in their N-termini. It has been suggested that the proteins each contain a conserved C-terminal catalytic (C) domain and an unrelated N-terminal regulatory (R) domain. It is possible that the R domains arose from genes that were recruited from different sources to combine with the common gene for the catalytic core. Thus, by combining with the same C domain, the proteins acquired the unique regulatory properties of the separate R domains.   A variety of enzymes belong to this family that includes, phenylalanine-4-hydroxylase from Chromobacterium violaceum where it is copper-dependent; it is iron-dependent in Pseudomonas aeruginosa, phenylalanine-4-hydroxylase catalyzes the conversion of phenylalanine to tyrosine. In humans, deficiencies are the cause of phenylketonuria, the most common inborn error of amino acid metabolism , tryptophan 5-hydroxylase catalyzes the rate-limiting step in serotonin biosynthesis: the conversion of tryptophan to 3-hydroxy-anthranilate and tyrosine 3-hydroxylase catalyzes the rate limiting step in catecholamine biosynthesis: the conversion of tyrosine to 3,4-dihydroxy-L-phenylalanine.; GO: 0004497 monooxygenase activity, 0005506 iron ion binding, 0009072 aromatic amino acid family metabolic process; PDB: 3e2t_A 1mlw_A 1ltu_A 1ltz_A 1ltv_A 2phm_A 1phz_A 1mmt_A 4pah_A 3pah_A ....
Probab=27.91  E-value=11  Score=13.53  Aligned_cols=11  Identities=9%  Similarity=0.081  Sum_probs=4.7

Q ss_pred             EEEEECCHHHH
Q ss_conf             78870756777
Q T0547           316 DIFIESGRFVA  326 (611)
Q Consensus       316 ~Ii~EpGRaiv  326 (611)
                      .+-++|-+.+.
T Consensus       246 ~~pfdp~~~~~  256 (332)
T PF00351_consen  246 RRPFDPERVMR  256 (332)
T ss_dssp             EEE--HHHHTT
T ss_pred             CCCCCHHHHHC
T ss_conf             11698999826


No 15 
>PF01715 IPPT:  IPP transferase;  InterPro: IPR002627 tRNA isopentenyltransferases 2.5.1.8 from EC also known as tRNA delta(2)-isopentenylpyrophosphate transferases or IPP transferases. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37) .; GO: 0004811 tRNA isopentenyltransferase activity, 0005524 ATP binding, 0008033 tRNA processing; PDB: 3crq_A 3crm_A 3crr_A 2zm5_A 3foz_B 2zxu_B 3eph_B 3epk_A 3epl_A 3epj_A ....
Probab=27.36  E-value=8.3  Score=14.51  Aligned_cols=39  Identities=18%  Similarity=0.374  Sum_probs=26.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHH
Q ss_conf             77888899999999999999996489987788707567775
Q T0547           287 SRNYTLREYANDVVFILKNIAEQKKDLEPDIFIESGRFVAA  327 (611)
Q Consensus       287 s~ny~l~eya~~Iv~~i~~~c~~~~vp~P~Ii~EpGRaivA  327 (611)
                      +-+|++..|.++....+++++.+..+  |.|+-=+|=|+=|
T Consensus        33 ~e~~sv~~f~~~a~~~i~~i~~~gk~--pivvGGTglYi~a   71 (252)
T PF01715_consen   33 DEEYSVGDFQRDAREAIEEIHARGKI--PIVVGGTGLYIKA   71 (252)
T ss_dssp             TS---HHHHHHHHHHHHHHHHH---E--EEEE---HHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHCCCC--EEEEECHHHHHHH
T ss_conf             88878999999999999999867996--5998172999999


No 16 
>PF00682 HMGL-like:  HMGL-like of this family is not conserved in other members. are a sub-families of this Pfam.;  InterPro: IPR000891    Pyruvate carboxylase (6.4.1.1 from EC) (PC), a member of the biotin-dependent enzyme family, is involved in the gluconeogenesis by mediating the carboxylation of pyruvate to oxaloacetate. Biotin-dependent carboxylase enzymes perform a two step reaction. Enzyme-bound biotin is first carboxylated by bicarbonate and ATP and the carboxyl group temporarily bound to biotin is subsequently transferred to an acceptor substrate such as pyruvate . PC has three functional domains: a biotin carboxylase (BC) domain, a carboxyltransferase (CT) domain which perform the second part of the reaction and a biotinyl domain , . The mechanism by which the carboxyl group is transferred from the carboxybiotin to the pyruvate is not well understood.     The pyruvate carboxyltransferase domain is also found in other pyruvate binding enzymes and acetyl-CoA dependent enzymes suggesting that this domain can be associated with different enzymatic activities.   This domain is found towards the N-terminal region of various aldolase enzymes. This N-terminal TIM barrel domain  interacts with the C-terminal domain. The C-terminal DmpG_comm domain (IPR012425 from INTERPRO) is thought to promote heterodimerisation with members of IPR003361 from INTERPRO to form a bifunctional aldolase-dehydrogenase .  ; GO: 0003824 catalytic activity; PDB: 3ewb_X 3fig_A 1sr9_A 1nvm_C 3dxi_B 2cw6_E 2ftp_A 1ydn_A 1ydo_C 3bg3_B ....
Probab=27.31  E-value=11  Score=13.46  Aligned_cols=33  Identities=18%  Similarity=0.145  Sum_probs=20.8

Q ss_pred             CCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCC
Q ss_conf             8989999999999866898734788863388767
Q T0547           206 LTSTELIEAVNLLKENKLLEQFTMIHFHLGSQIT  239 (611)
Q Consensus       206 l~~~ei~~~i~~l~~~~~l~~L~gLHfHIGSQI~  239 (611)
                      +++.++.+.++.+++.-.- ...++|+|=.-+..
T Consensus       163 ~~P~~~~~li~~l~~~~~~-~~l~~H~Hnd~Gla  195 (237)
T PF00682_consen  163 LTPEDVAELIRALRRRLPN-IPLGFHCHNDLGLA  195 (237)
T ss_dssp             S-HHHHHHHHHHHHHHSTT-SGEEEEE-TTTS-H
T ss_pred             CCHHHHHHHHHHHHHHCCC-CEEEEEECCCCCHH
T ss_conf             4999999999999987699-46999963785749


No 17 
>PF02049 FliE:  Flagellar hook-basal body complex protein FliE;  InterPro: IPR001624   Four genes from the major Bacillus subtilis chemotaxis locus have been shown to encode proteins that are similar to the Salmonella typhimurium FlgB, FlgC, FlgG and FliF proteins; a further gene product is similar to the Escherichia coli FliE protein . All of these proteins are thought to form part of the hook-basal body complex of the bacterial flagella . The FlgB, FlgC and FlgG proteins are components of the proximal and distal rods; FliF forms the M-ring that anchors the rod assembly to the membrane; but the role of FliE has not yet been determined . The similarity between the proteins in these two organisms suggests that the structures of the M-ring and the rod may be similar . Nevertheless, some differences in size and amino acid composition between some of the homologues suggest the basal body proteins may be organised slightly differently within B. subtilis .   From gel electrophoresis and autoradiography of 35S-labelled S. typhimurium hook-basal body complexes and the deduced number of sulphur-containing residues in FliE, the stoichiometry of the protein in the hook-basal body complex has been estimated to be about nine subunits . FliE does not undergo cleavage of a signal peptide, nor does it show any similarity to the axial components like the rod or hook proteins, which are thought to be exported by the flagellum-specific export pathway . On this evidence, it has been suggested that FliE may be in the vicinity of the MS ring, perhaps acting as an adaptor protein between ring and rod substructures .; GO: 0003774 motor activity, 0005198 structural molecule activity, 0001539 ciliary or flagellar motility, 0009288 flagellin-based flagellum
Probab=25.56  E-value=7.5  Score=14.85  Aligned_cols=30  Identities=20%  Similarity=0.369  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCC-CCHHHHH
Q ss_conf             68899999999999999973696-6789998
Q T0547           374 ALEYLHDSIDHLESILTLFDLGY-VDLQDRS  403 (611)
Q Consensus       374 ~~E~~~da~~~~~~~~~~f~~G~-l~L~~ra  403 (611)
                      ..+-.++.+.--++....|..|- .+|.+--
T Consensus        33 ai~~vn~~q~~a~~~~~~~~~G~~~~l~evm   63 (95)
T PF02049_consen   33 AINSVNQQQQQADQLAQAFATGKSVDLHEVM   63 (95)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHH
T ss_conf             9999999999999999999828999899999


No 18 
>PF01262 AlaDh_PNT_C:  Alanine dehydrogenase/PNT, C-terminal domain;  InterPro: IPR007698   Alanine dehydrogenases () and pyridine nucleotide transhydrogenase () have been shown to share regions of similarity . Alanine dehydrogenase catalyzes the NAD-dependent reversible reductive amination of pyruvate into alanine. Pyridine nucleotide transhydrogenase catalyzes the reduction of NADP^+ to NADPH with the concomitant oxidation of NADH to NAD^+. This enzyme is located in the plasma membrane of prokaryotes and in the inner membrane of the mitochondria of eukaryotes. The transhydrogenation between NADH and NADP is coupled with the translocation of a proton across the membrane. In prokaryotes the enzyme is composed of two different subunits, an alpha chain (gene pntA) and a beta chain (gene pntB), while in eukaryotes it is a single chain protein. The sequence of alanine dehydrogenase from several bacterial species are related with those of the alpha subunit of bacterial pyridine nucleotide transhydrogenase and of the N-terminal half of the eukaryotic enzyme. The two most conserved regions correspond respectively to the N-terminal extremity of these proteins and to a central glycine-rich region which is part of the NAD(H)-binding site.    This is a C-terminal domain of alanine dehydrogenases (1.4.1.1 from EC). This domain is also found in the lysine 2-oxoglutarate reductases. ; GO: 0016491 oxidoreductase activity, 0006118 electron transport; PDB: 2vhx_F 2vhz_B 2voe_F 2vhw_B 2vhy_B 2voj_A 2vhv_B 1pjb_A 1say_A 1pjc_A ....
Probab=23.58  E-value=10  Score=13.85  Aligned_cols=40  Identities=18%  Similarity=0.127  Sum_probs=20.2

Q ss_pred             CCCCCCCEEECC--CCCHHHHHHHHHHHHCCCCEEEEECC-HHHHHH
Q ss_conf             489988178788--98999999998542357104898668-899999
Q T0547           122 YNNEGAPITVNG--FKDRELINIGFIAAEMGHNITLTIEG-LNELEA  165 (611)
Q Consensus       122 ~g~~~~~Ii~nG--~Kd~e~I~lAl~a~~lG~~v~IViDs-~~EL~~  165 (611)
                      -+.++.+++.-|  .=...-+++   +..+|.+++ ++|. +..++.
T Consensus        16 ~~v~pakvvViGaG~vG~~A~~~---a~~LGa~v~-~~D~~~~~~~~   58 (168)
T PF01262_consen   16 GGVPPAKVVVIGAGVVGLGAAET---AKGLGAEVV-VPDVRPERLEQ   58 (168)
T ss_dssp             --B---EEEEE-------HHHHH---HHH---EEE-EEESSHHHHHH
T ss_pred             CCCCCEEEEEECCCHHHHHHHHH---HHHCCCEEE-EECCCHHHHHH
T ss_conf             99788699997987899999999---987799799-70379899976


No 19 
>PF07997 DUF1694:  Protein of unknown function (DUF1694);  InterPro: IPR012543   This family contains many hypothetical proteins.; PDB: 2ohw_A.
Probab=23.32  E-value=13  Score=12.94  Aligned_cols=85  Identities=19%  Similarity=0.277  Sum_probs=45.2

Q ss_pred             HHHHHHHCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCHHHHHHHHHHCCCCCCEEEECCH
Q ss_conf             99999855799858987479999999999999999999708898723787453378789999999846667851662288
Q T0547            34 IVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKARKEFGYKGGFNAVYPLKVNQYPGFVKNLVKLGKDYNYGLEAGSK  113 (611)
Q Consensus        34 lv~~l~~~~~~tPllvrf~dil~~ri~~l~~aF~~A~~~~~Y~g~y~~vYaiKaN~~~~Vv~~i~~~G~~~~~GlEv~Sk  113 (611)
                      +-+.+.+.-+|+|-+=-++      =|++-..|++           |++-++.-          .+..       +-...
T Consensus         6 l~~~l~~~~~G~p~~kPDE------qr~yLGtfrE-----------RV~lalt~----------~q~~-------~~~~~   51 (120)
T PF07997_consen    6 LEKRLQQGAYGTPQLKPDE------QRKYLGTFRE-----------RVILALTI----------EQVE-------EPKIY   51 (120)
T ss_dssp             HHHHHH-------SSHHHH------HHH-----GG-----------GEEEE---------------TT-------SSS--
T ss_pred             HHHHHHHHCCCCCCCCHHH------HHHHCCCHHH-----------HHHEEEEH----------HHHH-------CHHHH
T ss_conf             9999998667998899899------9884552775-----------75303429----------9982-------82479


Q ss_pred             HHHHHHHHCCCCCCCEEECCCCC----HHHHHHHHHHHHCCCCEEEE
Q ss_conf             99999996489988178788989----99999998542357104898
Q T0547           114 AELLLAMAYNNEGAPITVNGFKD----RELINIGFIAAEMGHNITLT  156 (611)
Q Consensus       114 ~EL~~ala~g~~~~~Ii~nG~Kd----~e~I~lAl~a~~lG~~v~IV  156 (611)
                      .|+..+|+- .++..+..||.=+    ..||++|   .+.|+.-+||
T Consensus        52 ~~~~~~l~~-~~~~~l~ing~l~~~~~~~YiklA---~~~~~~ftiV   94 (120)
T PF07997_consen   52 PEFEQALKD-YPNYQLLINGNLDYSFQSKYIKLA---NKHNIPFTIV   94 (120)
T ss_dssp             HHHHHHHHC--SSEEEEE-----HHHHHHHHHHH---HH----EEE-
T ss_pred             HHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHHH---HHCCCCEEEE
T ss_conf             999999964-989789984889878899999999---9859986996


No 20 
>PF03945 Endotoxin_N:  delta endotoxin, N-terminal domain;  InterPro: IPR005639   This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins, they are activated by proteolytic cleavage. The N-terminus is cleaved in all of the proteins and a C-terminal extension is cleaved in some members. Once activated, the endotoxin binds to the gut epithelium and causes cell lysis by the formation of cation-selective channels, which leads to death. The activated region of the delta toxin is composed of three distinct structural domains: an N-terminal helical bundle domain involved in membrane insertion and pore formation; a beta-sheet central domain (IPR001178 from INTERPRO) involved in receptor binding; and a C-terminal beta-sandwich domain (IPR005638 from INTERPRO) that interacts with the N-terminal domain to form a channel , . This entry represents the conserved N-terminal domain.; GO: 0009405 pathogenesis; PDB: 2c9k_A 1i5p_A 1ciy_A 3eb7_A 1ji6_A 1dlc_A 1w99_A.
Probab=21.84  E-value=4.6  Score=16.45  Aligned_cols=46  Identities=17%  Similarity=0.203  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHC---CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             688999999999999999736---9667899989999999999999985
Q T0547           374 ALEYLHDSIDHLESILTLFDL---GYVDLQDRSNAEILTHLITKKAILL  419 (611)
Q Consensus       374 ~~E~~~da~~~~~~~~~~f~~---G~l~L~~ra~~E~l~~~i~~~~~~~  419 (611)
                      .++.|.++..........|..   -.+.|.--|+|-.|+..+.+.....
T Consensus       100 v~~~f~~~~~~f~~~l~~f~~~~~e~~lLp~YaqaAnLhLlLLrd~i~~  148 (226)
T PF03945_consen  100 VRSRFNDLNSKFTNALPQFQVPGYEVLLLPLYAQAANLHLLLLRDGIIY  148 (226)
T ss_dssp             HHHHHHHHHHHHHHHGGGGSCTTSHHTTHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999988987117723549999999999999999999999


No 21 
>PF08123 DOT1:  Histone methylation protein DOT1 ;  InterPro: IPR013110   The DOT1 domain regulates gene expression by methylating histone H3 . H3 methylation by DOT1 has been shown to be required for the DNA damage checkpoint in yeast .; PDB: 1nw3_A 1u2z_B.
Probab=20.86  E-value=15  Score=12.59  Aligned_cols=35  Identities=17%  Similarity=0.115  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCEEEEECCHHHH
Q ss_conf             89999999999999999648998778870756777
Q T0547           292 LREYANDVVFILKNIAEQKKDLEPDIFIESGRFVA  326 (611)
Q Consensus       292 l~eya~~Iv~~i~~~c~~~~vp~P~Ii~EpGRaiv  326 (611)
                      ..++|......++..|+..|...+.+-++.|-++.
T Consensus        78 ~~~~A~~~~~~~~~~~~~~G~~~~~~~l~~gDF~~  112 (205)
T PF08123_consen   78 LADLAEKQWEELKKRMKIFGKKPGEVELIRGDFLD  112 (205)
T ss_dssp             HHHHHHHHHHHHHHHHHH-------B---SS-TTT
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCC
T ss_conf             99999999999999999838777654885545335


No 22 
>PF01698 FLO_LFY:  Floricaula / Leafy protein;  InterPro: IPR002910 This family consists of various plant development proteins which are homologues of Floricaula (FLO) and leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development.; GO: 0003677 DNA binding, 0045449 regulation of transcription; PDB: 2vy2_A 2vy1_A.
Probab=20.65  E-value=8.4  Score=14.47  Aligned_cols=15  Identities=27%  Similarity=0.463  Sum_probs=11.4

Q ss_pred             HCCCCCCEEEEECCH
Q ss_conf             648998778870756
Q T0547           309 QKKDLEPDIFIESGR  323 (611)
Q Consensus       309 ~~~vp~P~Ii~EpGR  323 (611)
                      +..-.||-|+||||-
T Consensus       226 ERQREHPFIVTEPGE  240 (386)
T PF01698_consen  226 ERQREHPFIVTEPGE  240 (386)
T ss_dssp             -------B-------
T ss_pred             CCCCCCCEEECCCCH
T ss_conf             421458726557306


No 23 
>PF08368 FAST_2:  FAST kinase-like protein, subdomain 2;  InterPro: IPR013579   This domain represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (2.7.1 from EC) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis . Note that many family members are hypothetical proteins. This subdomain is often found associated with the FAST kinase-like protein, subdomain 2. 
Probab=20.47  E-value=11  Score=13.62  Aligned_cols=42  Identities=14%  Similarity=0.003  Sum_probs=31.8

Q ss_pred             EECCHHHHHHCCCCCCCCCCCEEEEEEC-CCCEEEEEECCCCC
Q ss_conf             6020699974775156789857999988-99628875137887
Q T0547           514 FLVGAYQEVLGMKHNLFTHPTEAIISIN-EKGYEVEGIIEAQS  555 (611)
Q Consensus       514 FlvGAYQeiLGd~HNLfg~t~~v~v~~~-~~g~~i~~~~~gdt  555 (611)
                      .....++++.-.+.+|||..+.+...+. +-||.|+.++.=|+
T Consensus        45 ~~~~~~~~v~~~L~~llg~~~~~~~~v~tpygy~iD~e~~lD~   87 (93)
T PF08368_consen   45 RPSPLQQEVQEALEQLLGGENYFRSNVTTPYGYSIDFECVLDK   87 (93)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCEEEECCCCCCCEEEEEEEEECC
T ss_conf             8667899999999998098673676155899507979999889


Done!