Query         gi|254780232|ref|YP_003064645.1| inorganic pyrophosphatase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 177
No_of_seqs    137 out of 981
Neff          5.9 
Searched_HMMs 39220
Date          Mon May 23 23:30:25 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780232.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK01250 inorganic pyrophospha 100.0       0       0  479.5  21.2  176    2-177     1-176 (176)
  2 PRK02230 inorganic pyrophospha 100.0       0       0  436.2  19.9  161   14-177     3-163 (185)
  3 PRK00642 inorganic pyrophospha 100.0       0       0  434.4  20.6  174    1-177     9-208 (212)
  4 cd00412 pyrophosphatase Inorga 100.0       0       0  419.9  18.7  155   15-172     1-155 (155)
  5 pfam00719 Pyrophosphatase Inor 100.0       0       0  417.1  18.6  156   18-176     1-156 (156)
  6 COG0221 Ppa Inorganic pyrophos 100.0       0       0  398.8  19.0  171    2-176     1-171 (171)
  7 KOG1626 consensus              100.0       0       0  328.2  14.6  173    3-176    30-229 (279)
  8 TIGR01047 nspC carboxynorsperm  62.9      13 0.00034   18.4   4.2   44  130-175   195-245 (403)
  9 cd01460 vWA_midasin VWA_Midasi  55.0      18 0.00047   17.5   5.6   29  115-143   235-263 (266)
 10 pfam00870 P53 P53 DNA-binding   45.6      26 0.00066   16.6   6.1   40    6-45      2-43  (196)
 11 TIGR02480 fliN flagellar motor  45.2      10 0.00026   19.1   1.2   19   68-87     42-60  (77)
 12 KOG2874 consensus               44.8      26 0.00067   16.5   3.7   44  130-173   168-211 (356)
 13 pfam04113 Gpi16 Gpi16 subunit,  41.5      30 0.00076   16.2   4.3   45   10-62    430-477 (563)
 14 cd05696 S1_Rrp5_repeat_hs4 S1_  35.8      30 0.00076   16.2   2.4   22   77-98     43-64  (71)
 15 pfam05986 ADAM_spacer1 ADAM-TS  34.1      39 0.00099   15.4   7.3   30   15-44     14-44  (114)
 16 pfam03904 DUF334 Domain of unk  33.6      34 0.00086   15.8   2.3   16  161-176   129-144 (229)
 17 KOG2407 consensus               32.6      41   0.001   15.3   3.2   52    5-64    409-464 (575)
 18 KOG1110 consensus               32.1      42  0.0011   15.2   2.9   37  105-144   108-144 (183)
 19 TIGR00034 aroFGH phospho-2-deh  31.2     4.4 0.00011   21.4  -2.5   55  101-159    46-104 (348)
 20 pfam07177 Neuralized Neuralize  29.9      45  0.0012   15.0   3.1   22   73-94     30-51  (68)
 21 pfam05541 Spheroidin Entomopox  28.4      26 0.00067   16.5   1.1   10   15-24    200-209 (943)
 22 KOG2892 consensus               28.2      39 0.00098   15.4   1.9   12  119-130   115-126 (320)
 23 PRK09409 insertion element IS2  26.7      52  0.0013   14.6   2.6   41  132-176   229-269 (301)
 24 cd05702 S1_Rrp5_repeat_hs11_sc  25.4      55  0.0014   14.5   2.4   17   80-96     46-62  (70)
 25 PRK13355 bifunctional HTH-doma  24.1      58  0.0015   14.3   2.4   12   88-99    253-264 (518)
 26 PRK06788 flagellar motor switc  23.5      37 0.00095   15.5   1.1   21   67-88     67-87  (119)
 27 pfam04425 Bul1_N Bul1 N termin  23.1      60  0.0015   14.2   2.7   61   15-76    164-245 (432)
 28 pfam07469 DUF1518 Domain of un  22.8      35 0.00088   15.7   0.8   14   51-64     19-32  (56)
 29 pfam07909 DUF1663 Protein of u  22.3      38 0.00097   15.5   0.9   29   45-73     53-89  (514)
 30 pfam08968 DUF1885 Domain of un  21.7      25 0.00064   16.6  -0.1   13  133-147   100-112 (128)
 31 pfam10465 Inhibitor_I24 PinA p  21.4      57  0.0014   14.4   1.7   34   80-114    21-54  (140)
 32 KOG0210 consensus               20.6      54  0.0014   14.5   1.4   45  100-144   219-264 (1051)
 33 pfam11772 EpuA DNA-directed RN  20.4      26 0.00065   16.6  -0.3   10   66-75     24-33  (47)

No 1  
>PRK01250 inorganic pyrophosphatase; Provisional
Probab=100.00  E-value=0  Score=479.53  Aligned_cols=176  Identities=53%  Similarity=0.974  Sum_probs=173.1

Q ss_pred             CCCCCCCCCCCCCCEEEEEEEECCCCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCHHHCCCCCCCCCEEEEEECCCCC
Q ss_conf             65001886657998589999856868730268806657099942147765677781211055358998402899227776
Q gi|254780232|r    2 VQLNEISLGSNSPIDVNVFIEISLGGYPIKYEMDKKSGVLVVDRFISTPMLYPGNYGFIPNTLSDDGDPVDVIMYSSEPI   81 (177)
Q Consensus         2 m~~~~i~~~~~~p~~vn~vIEIP~gs~~~KyE~d~~~g~~~~dR~l~~~~~yP~nYGfiP~T~~~DgDPLDvlvl~~~~~   81 (177)
                      ||+|+||+|+++|++||||||||+||+++|||||+++|.|++||+|++++.||+|||||||||++||||||||||+++|+
T Consensus         1 m~~~~~~~g~~~P~~vnvvIEIP~gs~~~KyE~d~~~g~~~ldR~l~~~~~YP~nYGfiP~Tl~~DgDPLDvlvl~~~p~   80 (176)
T PRK01250          1 MSLNKIPAGKDLPEDINVIIEIPANSDPIKYEVDKESGALFVDRFLYTAMFYPCNYGFIPHTLSLDGDPVDVLVVTPYPL   80 (176)
T ss_pred             CCHHHCCCCCCCCCEEEEEEEECCCCCCEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCCHHCCCCCCCEEEEECCCCC
T ss_conf             97745889999988899999947999971289806899699998668788598654334101116999515898527543


Q ss_pred             CCCCEEEEEEEEEEEEECCCCCCEEEEEEECCCCCHHHCCCCCHHHCCHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHH
Q ss_conf             77428998698999960478775279999637888222565877898989999999999996428889718980314999
Q gi|254780232|r   82 LPGSVISTRPIGVMKMEDDGGIDEKILAVPSKNITSLYDSIQSYEDVPNAYLQKVEHFFKHYKDLEDGKWAKLDGWEGVN  161 (177)
Q Consensus        82 ~~G~vv~~r~iG~l~m~D~ge~D~KiiaVp~~d~~~~~~~i~di~Dl~~~~l~~I~~fF~~YK~le~~K~v~v~g~~~~~  161 (177)
                      +|||+++||+||+|.|+|+||.|+||||||+++.+|+|+++++++||+++++++|+|||++||+||+||+|++.||.|++
T Consensus        81 ~pG~vv~~r~IG~l~m~D~g~~D~KiiaVp~~~~dp~~~~i~di~Dl~~~~l~eI~~FF~~YK~LE~gK~v~v~gw~~~~  160 (176)
T PRK01250         81 VPGSVIRCRPVGVLKMEDESGEDEKIIAVPHDKLSPEYDHIKDVDDLPELLKAQIKHFFEHYKDLEKGKWVKVEGWGGAE  160 (176)
T ss_pred             CCCCEEEEEEEEEEEEECCCCCCCEEEEEECCCCCHHHCCCCCHHHCCHHHHHHHHHHHHHHCCCCCCCCEEECCCCCHH
T ss_conf             89628999997899988599997189999887688122251325457988999999999986776789827998797999


Q ss_pred             HHHHHHHHHHHHHHCC
Q ss_conf             9999999999988509
Q gi|254780232|r  162 SAHKIILEAVKRGIKE  177 (177)
Q Consensus       162 ~A~~iI~~~~~ry~k~  177 (177)
                      +|.++|++|++||+||
T Consensus       161 ~A~~iI~e~~~~yk~k  176 (176)
T PRK01250        161 EAKAEIVESIERAKKK  176 (176)
T ss_pred             HHHHHHHHHHHHHHCC
T ss_conf             9999999999998549


No 2  
>PRK02230 inorganic pyrophosphatase; Provisional
Probab=100.00  E-value=0  Score=436.16  Aligned_cols=161  Identities=40%  Similarity=0.661  Sum_probs=156.9

Q ss_pred             CCEEEEEEEECCCCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCHHHCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEE
Q ss_conf             98589999856868730268806657099942147765677781211055358998402899227776774289986989
Q gi|254780232|r   14 PIDVNVFIEISLGGYPIKYEMDKKSGVLVVDRFISTPMLYPGNYGFIPNTLSDDGDPVDVIMYSSEPILPGSVISTRPIG   93 (177)
Q Consensus        14 p~~vn~vIEIP~gs~~~KyE~d~~~g~~~~dR~l~~~~~yP~nYGfiP~T~~~DgDPLDvlvl~~~~~~~G~vv~~r~iG   93 (177)
                      +++||||||||+||+ +|||+|+++|.|++||+|+++++||+|||||||||++|||||||||+++.|+.||++++|||||
T Consensus         3 ~~evnvvIEIP~gs~-~KyE~dk~~g~l~~DR~l~~~~~YP~nYGfIP~Tl~~DgDPLDvlvl~~~p~~pG~vv~~r~iG   81 (185)
T PRK02230          3 NKKIEVTIEIPKNSN-IKYEYDRKTKKIVVDRILRGDFVYPANYGFIKEALDWDGDELDVLVYSDQKFLPGTVVPARILG   81 (185)
T ss_pred             CCEEEEEEEECCCCC-EEEEEECCCCCEEEEECCCCCCCCCCCEEECCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEE
T ss_conf             878999999889998-7899955889889950137777786123265660246899524887157543786289988899


Q ss_pred             EEEEECCCCCCEEEEEEECCCCCHHHCCCCCHHHCCHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHH
Q ss_conf             99960478775279999637888222565877898989999999999996428889718980314999999999999998
Q gi|254780232|r   94 VMKMEDDGGIDEKILAVPSKNITSLYDSIQSYEDVPNAYLQKVEHFFKHYKDLEDGKWAKLDGWEGVNSAHKIILEAVKR  173 (177)
Q Consensus        94 ~l~m~D~ge~D~KiiaVp~~d~~~~~~~i~di~Dl~~~~l~~I~~fF~~YK~le~~K~v~v~g~~~~~~A~~iI~~~~~r  173 (177)
                      +|.|+|+||.||||||||++|  |+|++|+|++||+++++++|+|||++||+||++|||++.||.|+++|.++|++|.+|
T Consensus        82 vL~M~Dege~D~KIiaV~~~D--p~y~~i~di~Dlp~~~l~eI~hFF~~YK~LE~kk~vkv~gw~~~~~A~k~I~e~ie~  159 (185)
T PRK02230         82 AMKMIDDGETDTKLIAVHDDD--YRYKHIKSLKDLPLHWLDEIEYFFSNYKNLKNKGVTKVKGFEDEEWALKEYEECVEL  159 (185)
T ss_pred             EEEECCCCCCCCEEEEEECCC--CCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHHHH
T ss_conf             999587998556799998999--540247994888999999999999985757899869989896999999999999999


Q ss_pred             HHCC
Q ss_conf             8509
Q gi|254780232|r  174 GIKE  177 (177)
Q Consensus       174 y~k~  177 (177)
                      |++.
T Consensus       160 ykk~  163 (185)
T PRK02230        160 MKKY  163 (185)
T ss_pred             HHHH
T ss_conf             9983


No 3  
>PRK00642 inorganic pyrophosphatase; Provisional
Probab=100.00  E-value=0  Score=434.39  Aligned_cols=174  Identities=30%  Similarity=0.552  Sum_probs=163.6

Q ss_pred             CCC-CCCCCCCCCCCCEEEEEEEECCCCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCHHHCCCCC-------------
Q ss_conf             965-001886657998589999856868730268806657099942147765677781211055358-------------
Q gi|254780232|r    1 MVQ-LNEISLGSNSPIDVNVFIEISLGGYPIKYEMDKKSGVLVVDRFISTPMLYPGNYGFIPNTLSD-------------   66 (177)
Q Consensus         1 ~m~-~~~i~~~~~~p~~vn~vIEIP~gs~~~KyE~d~~~g~~~~dR~l~~~~~yP~nYGfiP~T~~~-------------   66 (177)
                      |++ .||||+|++.|++||||||||+||+ +|||+|+++|.+++||++++++.||+|||||||||++             
T Consensus         9 ~~~PWHdi~~g~~~p~~vn~vIEIPkgs~-~KyEidke~g~i~lDR~l~~~~~yP~nYGfIPqTw~d~~~~~~~~~~~~~   87 (212)
T PRK00642          9 IAHPWHGPELGQDDYESLCCYIEITPQDS-VKYELDKATGLLKVDRPQKFSNFCPCLYGFLPRTYCGELSGKYSGEQTGR   87 (212)
T ss_pred             CCCCCCCCCCCCCCCCEEEEEEEECCCCC-EEEEECCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             32787799878899887999999789998-01887468897787226334574887756556534464433233333344


Q ss_pred             -----CCCCEEEEEECCCCCCCCCE-EEEEEEEEEEEECCCCCCEEEEEEECCCCCHHHCCCCCHHHCCHHHHHHHHHHH
Q ss_conf             -----99840289922777677428-998698999960478775279999637888222565877898989999999999
Q gi|254780232|r   67 -----DGDPVDVIMYSSEPILPGSV-ISTRPIGVMKMEDDGGIDEKILAVPSKNITSLYDSIQSYEDVPNAYLQKVEHFF  140 (177)
Q Consensus        67 -----DgDPLDvlvl~~~~~~~G~v-v~~r~iG~l~m~D~ge~D~KiiaVp~~d~~~~~~~i~di~Dl~~~~l~~I~~fF  140 (177)
                           |||||||||+++.|+.+|++ ++|||||+|.|+|+||.||||||||++|  |+|++|+|++||+++++++|+|||
T Consensus        88 ~~l~gDgDPLDvlvl~~~p~~pG~vv~~~r~IG~l~m~D~ge~D~KIiaV~~~D--p~~~~i~di~Dlp~~~l~~i~~fF  165 (212)
T PRK00642         88 EDIKGDGDPLDICVLTEKNITHGNILLQARPIGGLRIIDSGEADDKIIAVLEDD--LVFGEIKDISDCPGTLLDMLQHYF  165 (212)
T ss_pred             CCCCCCCCCCEEEEECCCCCCCCEEEEEEEEEEEEEEECCCCCCCEEEEEECCC--CCCCCCCCHHHCCHHHHHHHHHHH
T ss_conf             466789996179996587788952899989869999611898655599867899--863457992889999999999999


Q ss_pred             HHHHCCCC------CCEEEEECCCCHHHHHHHHHHHHHHHHCC
Q ss_conf             99642888------97189803149999999999999988509
Q gi|254780232|r  141 KHYKDLED------GKWAKLDGWEGVNSAHKIILEAVKRGIKE  177 (177)
Q Consensus       141 ~~YK~le~------~K~v~v~g~~~~~~A~~iI~~~~~ry~k~  177 (177)
                      ++||.|++      .|+|++.||.|+++|.++|++|++||+++
T Consensus       166 ~~YK~l~~~~~~~k~k~v~v~g~~~~e~A~~iI~~s~e~Y~~~  208 (212)
T PRK00642        166 LTYKATPESLIQGKPAKIEIVGIYGKKEAQKVIQLAHEDYLNK  208 (212)
T ss_pred             HHHCCCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9878886764337842799886869999999999999999998


No 4  
>cd00412 pyrophosphatase Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers.
Probab=100.00  E-value=0  Score=419.88  Aligned_cols=155  Identities=51%  Similarity=0.886  Sum_probs=151.1

Q ss_pred             CEEEEEEEECCCCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCHHHCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEE
Q ss_conf             85899998568687302688066570999421477656777812110553589984028992277767742899869899
Q gi|254780232|r   15 IDVNVFIEISLGGYPIKYEMDKKSGVLVVDRFISTPMLYPGNYGFIPNTLSDDGDPVDVIMYSSEPILPGSVISTRPIGV   94 (177)
Q Consensus        15 ~~vn~vIEIP~gs~~~KyE~d~~~g~~~~dR~l~~~~~yP~nYGfiP~T~~~DgDPLDvlvl~~~~~~~G~vv~~r~iG~   94 (177)
                      ++||||||||+||+ +|||||+++|+|++||++++++.||+|||||||||++||||||||||++.|++|||+++|||||+
T Consensus         1 ~iv~vviEIP~gs~-~KyE~d~~~g~~~~DR~l~~~~~yP~nYGfIP~T~~~DgDPLDvlvl~~~p~~~G~vv~~r~iG~   79 (155)
T cd00412           1 EVVNVVIEIPKGSN-AKYEIDKETGPIKVDRFLYSSMGYPWNYGFIPQTLEDDGDPLDVLVIGEEPLFPGSVIRVRPLGV   79 (155)
T ss_pred             CEEEEEEEECCCCC-EEEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHCCCCCCEEEEEECCCCCCCCCEEEEEEEEE
T ss_conf             95999999789998-57999168898889565167898986623012344269997579985487538930899999899


Q ss_pred             EEEECCCCCCEEEEEEECCCCCHHHCCCCCHHHCCHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHH
Q ss_conf             996047877527999963788822256587789898999999999999642888971898031499999999999999
Q gi|254780232|r   95 MKMEDDGGIDEKILAVPSKNITSLYDSIQSYEDVPNAYLQKVEHFFKHYKDLEDGKWAKLDGWEGVNSAHKIILEAVK  172 (177)
Q Consensus        95 l~m~D~ge~D~KiiaVp~~d~~~~~~~i~di~Dl~~~~l~~I~~fF~~YK~le~~K~v~v~g~~~~~~A~~iI~~~~~  172 (177)
                      |.|+|+||.||||||||++|  |+|+++++++||+++++++|+|||++||+||++|++++.||.|+++|.++|++||+
T Consensus        80 l~m~D~ge~D~KiiaV~~~d--p~~~~i~~i~Dl~~~~l~~I~~fF~~YK~le~~k~v~v~g~~~~~~A~~iI~~~~~  155 (155)
T cd00412          80 LKMIDEGETDWKVIAVPVDD--PRYSHINDISDVPPHLLDEIKHFFEHYKDLEGKKEVKVAGWKDKEEALKIIKESIE  155 (155)
T ss_pred             EEECCCCCCCCEEEEEECCC--CCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHHC
T ss_conf             99622899523499986899--55034688388998799999999999758789994799866299999999999729


No 5  
>pfam00719 Pyrophosphatase Inorganic pyrophosphatase.
Probab=100.00  E-value=0  Score=417.06  Aligned_cols=156  Identities=54%  Similarity=0.980  Sum_probs=152.3

Q ss_pred             EEEEEECCCCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCHHHCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEE
Q ss_conf             99998568687302688066570999421477656777812110553589984028992277767742899869899996
Q gi|254780232|r   18 NVFIEISLGGYPIKYEMDKKSGVLVVDRFISTPMLYPGNYGFIPNTLSDDGDPVDVIMYSSEPILPGSVISTRPIGVMKM   97 (177)
Q Consensus        18 n~vIEIP~gs~~~KyE~d~~~g~~~~dR~l~~~~~yP~nYGfiP~T~~~DgDPLDvlvl~~~~~~~G~vv~~r~iG~l~m   97 (177)
                      |||||||+||+ +|||||+++|.+.+||++++++.||||||||||||+|||||||||||++.|+++||+++||+||+|.|
T Consensus         1 nvviEIP~gs~-~KyE~d~~~~~~~ldr~l~~~~~yP~nYGfiP~T~~~DgDPLDvlvl~~~~~~~G~vv~~r~iG~l~m   79 (156)
T pfam00719         1 NVVIEIPKGSR-VKYEIDKESGLLPVDRVLYTSMGYPFNYGFIPQTLEGDGDPLDVLVLGPEPLFPGSVVRVRPIGVLAM   79 (156)
T ss_pred             CEEEEECCCCC-EEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEE
T ss_conf             98999679998-67998368897038766467888983540346611369994689984487438941899988899996


Q ss_pred             ECCCCCCEEEEEEECCCCCHHHCCCCCHHHCCHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC
Q ss_conf             0478775279999637888222565877898989999999999996428889718980314999999999999998850
Q gi|254780232|r   98 EDDGGIDEKILAVPSKNITSLYDSIQSYEDVPNAYLQKVEHFFKHYKDLEDGKWAKLDGWEGVNSAHKIILEAVKRGIK  176 (177)
Q Consensus        98 ~D~ge~D~KiiaVp~~d~~~~~~~i~di~Dl~~~~l~~I~~fF~~YK~le~~K~v~v~g~~~~~~A~~iI~~~~~ry~k  176 (177)
                      +|+||.||||||||++|  |+|++++|++|++++++++|+|||++||.++++|++++.||.|+++|.++|++||+||++
T Consensus        80 ~D~ge~D~KiiaV~~~d--p~~~~i~di~dl~~~~l~~I~~fF~~YK~le~~k~v~v~g~~~~~~A~~iI~~~~~~y~~  156 (156)
T pfam00719        80 IDEGETDDKIIAVPVDD--PRYDDIKDIEDLPPGLLDEIEHFFEHYKDLEEGKWVKVEGWGDAEEAKKEIKEAIERYKK  156 (156)
T ss_pred             ECCCCCCCEEEEEECCC--CCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHC
T ss_conf             21989605599988899--731130586677988999999999997687889828888765999999999999999739


No 6  
>COG0221 Ppa Inorganic pyrophosphatase [Energy production and conversion]
Probab=100.00  E-value=0  Score=398.78  Aligned_cols=171  Identities=52%  Similarity=0.943  Sum_probs=166.8

Q ss_pred             CCCCCCCCCCCCCCEEEEEEEECCCCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCHHHCCCCCCCCCEEEEEECCCCC
Q ss_conf             65001886657998589999856868730268806657099942147765677781211055358998402899227776
Q gi|254780232|r    2 VQLNEISLGSNSPIDVNVFIEISLGGYPIKYEMDKKSGVLVVDRFISTPMLYPGNYGFIPNTLSDDGDPVDVIMYSSEPI   81 (177)
Q Consensus         2 m~~~~i~~~~~~p~~vn~vIEIP~gs~~~KyE~d~~~g~~~~dR~l~~~~~yP~nYGfiP~T~~~DgDPLDvlvl~~~~~   81 (177)
                      |+||++|++++. +.+||+||||+||+ +|||+||++|.+.+||+++++|.||+|||||||||++|||||||||++++|+
T Consensus         1 ~~~~~~~~~~~~-~~i~vviEIP~~s~-~KyE~dke~~~~~vdR~l~~~~~YP~NYGfiP~Tl~~DGDPlDvlVi~~~p~   78 (171)
T COG0221           1 MDLHKIPAGPDD-EDINVVIEIPKGSN-IKYEVDKETGRLLVDRPLKTPMGYPVNYGFIPNTLSDDGDPLDVLVIGEEPL   78 (171)
T ss_pred             CCCCCCCCCCCC-CEEEEEEECCCCCC-CCEEEEEECCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCC
T ss_conf             970106888886-34779996368876-5368852038502641379887677535403786367998448999857677


Q ss_pred             CCCCEEEEEEEEEEEEECCCCCCEEEEEEECCCCCHHHCCCCCHHHCCHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHH
Q ss_conf             77428998698999960478775279999637888222565877898989999999999996428889718980314999
Q gi|254780232|r   82 LPGSVISTRPIGVMKMEDDGGIDEKILAVPSKNITSLYDSIQSYEDVPNAYLQKVEHFFKHYKDLEDGKWAKLDGWEGVN  161 (177)
Q Consensus        82 ~~G~vv~~r~iG~l~m~D~ge~D~KiiaVp~~d~~~~~~~i~di~Dl~~~~l~~I~~fF~~YK~le~~K~v~v~g~~~~~  161 (177)
                      .+||+++||+||+|+|+|+||.|+||||||..+  |+|++|++++|++++++++|+|||+|||+||++||+++.||+|++
T Consensus        79 ~pG~vi~~r~iG~l~m~D~~e~D~Kviav~~~d--p~~~~i~di~d~~~~~~~~i~~ffe~yK~le~~k~~~v~gw~~~~  156 (171)
T COG0221          79 APGCVIQARPIGVLKMIDEGEKDDKVIAVPKLD--PRYEHIKDISDLPEHLLDEIQHFFETYKDLEKGKWVKVEGWEDAE  156 (171)
T ss_pred             CCEEEEEEEEEEEEEEEECCCCCEEEEEECCCC--CCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHH
T ss_conf             763689778889999831788630899853788--255554666677898899999999988753788689960436999


Q ss_pred             HHHHHHHHHHHHHHC
Q ss_conf             999999999998850
Q gi|254780232|r  162 SAHKIILEAVKRGIK  176 (177)
Q Consensus       162 ~A~~iI~~~~~ry~k  176 (177)
                      +|.++|++|++||++
T Consensus       157 ~A~~~i~~~~~~~k~  171 (171)
T COG0221         157 EAKKEIKEAIERYKE  171 (171)
T ss_pred             HHHHHHHHHHHHHHC
T ss_conf             999999999999649


No 7  
>KOG1626 consensus
Probab=100.00  E-value=0  Score=328.17  Aligned_cols=173  Identities=31%  Similarity=0.465  Sum_probs=156.3

Q ss_pred             CCCCCCCCCCCCCEEEEEEEECCCCCCEEEEE-----------ECCCCCEEEEECCCCCCCCCCCCCHHHCCCCC-----
Q ss_conf             50018866579985899998568687302688-----------06657099942147765677781211055358-----
Q gi|254780232|r    3 QLNEISLGSNSPIDVNVFIEISLGGYPIKYEM-----------DKKSGVLVVDRFISTPMLYPGNYGFIPNTLSD-----   66 (177)
Q Consensus         3 ~~~~i~~~~~~p~~vn~vIEIP~gs~~~KyE~-----------d~~~g~~~~dR~l~~~~~yP~nYGfiP~T~~~-----   66 (177)
                      .|||+|+-.+.-.++|+++|||+++ |+|+|+           |+++|.++.+|.++++..||||||||||||++     
T Consensus        30 ~fhdipl~a~~~~~~nmvvEiPrwt-nak~EIs~k~~~~pikqD~KkGklR~v~n~fp~~gYiwNYGalPqTwedP~~~~  108 (279)
T KOG1626          30 PFHDIPLAAHPWHDLNMVVEIPRWT-NAKMEISKKEPFNPIKQDKKKGKLRFVRNLFPYKGYIWNYGALPQTWEDPNHVD  108 (279)
T ss_pred             CCCCCCCCCCCCCCEEECCCCCCEE-EEEEEEECCCCCCCCEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             4335721058432276401365335-248998216888750231337826888741554541234466762012777556


Q ss_pred             -------CCCCEEEEEECCCCCCCCCEEEEEEEEEEEEECCCCCCEEEEEEECCCC-CHHHCCCCCHHHCCHHHHHHHHH
Q ss_conf             -------9984028992277767742899869899996047877527999963788-82225658778989899999999
Q gi|254780232|r   67 -------DGDPVDVIMYSSEPILPGSVISTRPIGVMKMEDDGGIDEKILAVPSKNI-TSLYDSIQSYEDVPNAYLQKVEH  138 (177)
Q Consensus        67 -------DgDPLDvlvl~~~~~~~G~vv~~r~iG~l~m~D~ge~D~KiiaVp~~d~-~~~~~~i~di~Dl~~~~l~~I~~  138 (177)
                             ||||||||+|++++..+|++++||+||+|.|+|+||.|||||||.++|+ ++.|++|+|++.+.|++|+++..
T Consensus       109 ~~t~~~gDnDPiDV~eIg~~~~~~G~vl~vKvLG~malIDeGE~DwKiIAIdvnDP~A~~~ndi~DV~~~~Pg~L~~tr~  188 (279)
T KOG1626         109 PETKAKGDNDPIDVLEIGQEPVLPGCVLQVKVLGLMALIDEGETDWKIIAIDVNDPLASEYNDIEDVEKLFPGLLEATRR  188 (279)
T ss_pred             CCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCCCEEEEEECCCCCHHHHCCHHHHHHHCCCHHHHHHH
T ss_conf             54456688986034565552034663788775223420237776643899978986514315578887767613899999


Q ss_pred             HHHHHHCCCC---CCEEEEECCCCHHHHHHHHHHHHHHHHC
Q ss_conf             9999642888---9718980314999999999999998850
Q gi|254780232|r  139 FFKHYKDLED---GKWAKLDGWEGVNSAHKIILEAVKRGIK  176 (177)
Q Consensus       139 fF~~YK~le~---~K~v~v~g~~~~~~A~~iI~~~~~ry~k  176 (177)
                      ||+.||-.++   ++.+-.+.+.+++.|+++|++||+.|++
T Consensus       189 wFr~YKiPdGKpeN~faf~~~f~n~~~A~~iIk~t~d~w~~  229 (279)
T KOG1626         189 WFRDYKIPDGKPENKFAFVGDFLNKKFALDIIKETHDLWAA  229 (279)
T ss_pred             HHHHCCCCCCCCCCCHHCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             99974787899731010024445758899999999999999


No 8  
>TIGR01047 nspC carboxynorspermidine decarboxylase; InterPro: IPR005730    Carboxynorspermidine synthase, mediates the nicotinamide-nucleotide-linked reduction of the Schiff base H2N(CH2)3N = CHCH2CH(NH2)COOH. This is formed from L-aspartic beta-semialdehyde (ASA) and 1,3-diaminopropane (DAP) and is reduced to carboxynorspermidine [H2N(CH2)3NH(CH2)2CH(NH2)COOH], an intermediate in the novel pathway for norspermidine biosynthesis shown in Vibrio alginolyticus.; GO: 0016830 carbon-carbon lyase activity, 0045312 nor-spermidine biosynthetic process.
Probab=62.95  E-value=13  Score=18.36  Aligned_cols=44  Identities=23%  Similarity=0.319  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEEEC-----C--CCHHHHHHHHHHHHHHHH
Q ss_conf             899999999999964288897189803-----1--499999999999999885
Q gi|254780232|r  130 NAYLQKVEHFFKHYKDLEDGKWAKLDG-----W--EGVNSAHKIILEAVKRGI  175 (177)
Q Consensus       130 ~~~l~~I~~fF~~YK~le~~K~v~v~g-----~--~~~~~A~~iI~~~~~ry~  175 (177)
                      ..+|+.|+.=|.-|  |+.-+||+++|     |  .|.+.+.++|++=++||-
T Consensus       195 ~~~L~~~E~~FG~y--L~~m~WVNfGGGH~~T~~GYDv~~LIa~~K~F~erh~  245 (403)
T TIGR01047       195 ERTLEVIEKKFGEY--LPQMEWVNFGGGHLITKKGYDVEKLIAVIKAFKERHG  245 (403)
T ss_pred             HHHHHHHHHHHHHH--CCCCCEEECCCCEEECCCCCCHHHHHHHHHHHHHCCC
T ss_conf             99999998764210--0032303138876645788888999999866651178


No 9  
>cd01460 vWA_midasin VWA_Midasin: Midasin is a member of the AAA ATPase family. The proteins of this family are unified by their common archetectural organization that is based upon a conserved ATPase domain. The AAA domain of midasin contains six tandem AAA protomers. The AAA domains in midasin is followed by a D/E rich domain that is following by a VWA domain. The members of this subgroup have a conserved MIDAS motif. The function of this domain is not exactly known although it has been speculated to play a crucial role in midasin function.
Probab=55.02  E-value=18  Score=17.50  Aligned_cols=29  Identities=10%  Similarity=0.307  Sum_probs=26.0

Q ss_pred             CCHHHCCCCCHHHCCHHHHHHHHHHHHHH
Q ss_conf             88222565877898989999999999996
Q gi|254780232|r  115 ITSLYDSIQSYEDVPNAYLQKVEHFFKHY  143 (177)
Q Consensus       115 ~~~~~~~i~di~Dl~~~~l~~I~~fF~~Y  143 (177)
                      |.|.|--++|++.||..+-+.+++||+--
T Consensus       235 PFpyYvivrdi~~LP~~Lsd~LRQwFe~~  263 (266)
T cd01460         235 PFPYYVIVRDLNQLPSVLSDALRQWFELV  263 (266)
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHHHHHHH
T ss_conf             98648997688780899999999999997


No 10 
>pfam00870 P53 P53 DNA-binding domain.
Probab=45.60  E-value=26  Score=16.56  Aligned_cols=40  Identities=8%  Similarity=0.097  Sum_probs=27.5

Q ss_pred             CCCCCCCCCCEEEEEEEECCCC--CCEEEEEECCCCCEEEEE
Q ss_conf             1886657998589999856868--730268806657099942
Q gi|254780232|r    6 EISLGSNSPIDVNVFIEISLGG--YPIKYEMDKKSGVLVVDR   45 (177)
Q Consensus         6 ~i~~~~~~p~~vn~vIEIP~gs--~~~KyE~d~~~g~~~~dR   45 (177)
                      .+|...+.|+.+++=|..+.-+  .++.|.|....+.|.+..
T Consensus         2 ~vPs~~~ypG~y~F~v~f~~~~~~ks~~wtYS~~LnKLfv~m   43 (196)
T pfam00870         2 TVPSTTDYPGSYGFELRFQQSGTAKSVTCTYSPDLNKLFCQL   43 (196)
T ss_pred             CCCCCCCCCCCCCEEEECCCCCCCCCCCEEECHHHCCEEEEC
T ss_conf             878667658852138982788885667668374757435813


No 11 
>TIGR02480 fliN flagellar motor switch protein FliN; InterPro: IPR012826    Proteins that consist largely of this domain can be designated flagellar motor switch proteins: FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside of this family, are associated with type III secretion systems (TTSS) and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.; GO: 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0016020 membrane, 0044461 flagellin-based flagellum part.
Probab=45.22  E-value=10  Score=19.13  Aligned_cols=19  Identities=32%  Similarity=0.747  Sum_probs=16.0

Q ss_pred             CCCEEEEEECCCCCCCCCEE
Q ss_conf             98402899227776774289
Q gi|254780232|r   68 GDPVDVIMYSSEPILPGSVI   87 (177)
Q Consensus        68 gDPLDvlvl~~~~~~~G~vv   87 (177)
                      |||||++|=+. ++.+|.++
T Consensus        42 gepldI~VNG~-~ia~GEvv   60 (77)
T TIGR02480        42 GEPLDILVNGR-LIARGEVV   60 (77)
T ss_pred             CCEEEEEECCC-EEEEEEEE
T ss_conf             89215988892-78889899


No 12 
>KOG2874 consensus
Probab=44.83  E-value=26  Score=16.49  Aligned_cols=44  Identities=16%  Similarity=0.330  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHH
Q ss_conf             89999999999996428889718980314999999999999998
Q gi|254780232|r  130 NAYLQKVEHFFKHYKDLEDGKWAKLDGWEGVNSAHKIILEAVKR  173 (177)
Q Consensus       130 ~~~l~~I~~fF~~YK~le~~K~v~v~g~~~~~~A~~iI~~~~~r  173 (177)
                      ..+|+.|+-.-.-|--.+++....+++|.|.+++.+++.+|++.
T Consensus       168 g~TLKAlelLT~CYilVqG~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874         168 GSTLKALELLTNCYILVQGNTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             CHHHHHHHHHHHCEEEEECCEEEEECCCCHHHHHHHHHHHHHHC
T ss_conf             20579999975217986076777634730089999999999852


No 13 
>pfam04113 Gpi16 Gpi16 subunit, GPI transamidase component. GPI (glycosyl phosphatidyl inositol) transamidase is a multi-protein complex. Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase that adds glycosylphosphatidylinositols (GPIs) to newly synthesized proteins. Gpi16 is an essential N-glycosylated transmembrane glycoprotein. Gpi16 is largely found on the lumenal side of the ER. It has a single C-terminal transmembrane domain and a small C-terminal, cytosolic extension with an ER retrieval motif.
Probab=41.50  E-value=30  Score=16.16  Aligned_cols=45  Identities=22%  Similarity=0.501  Sum_probs=26.9

Q ss_pred             CCCCCCEEEEEEEECCCCCCEEEEEECCCCCEEEEECCCCCCCCC--CCCCH-HHC
Q ss_conf             657998589999856868730268806657099942147765677--78121-105
Q gi|254780232|r   10 GSNSPIDVNVFIEISLGGYPIKYEMDKKSGVLVVDRFISTPMLYP--GNYGF-IPN   62 (177)
Q Consensus        10 ~~~~p~~vn~vIEIP~gs~~~KyE~d~~~g~~~~dR~l~~~~~yP--~nYGf-iP~   62 (177)
                      ....|..+.+.+++|+.|+ +..-|+-+...++++.       ||  +|-|| ||.
T Consensus       430 dR~rPt~LEl~l~lP~~st-~~ls~~FdK~~L~~~E-------YPPDANhGFdI~~  477 (563)
T pfam04113       430 DRERPTQLELAMKLPPAST-VTLTYDFEKSILRYTE-------YPPDANRGFDIPA  477 (563)
T ss_pred             CCCCCCEEEEEEEECCCCE-EEEEEEEEEEEECCCC-------CCCCCCCCCCCCC
T ss_conf             5679865999999589972-9999998430242222-------6999888867570


No 14 
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=35.76  E-value=30  Score=16.15  Aligned_cols=22  Identities=27%  Similarity=0.474  Sum_probs=18.3

Q ss_pred             CCCCCCCCCEEEEEEEEEEEEE
Q ss_conf             2777677428998698999960
Q gi|254780232|r   77 SSEPILPGSVISTRPIGVMKME   98 (177)
Q Consensus        77 ~~~~~~~G~vv~~r~iG~l~m~   98 (177)
                      .+.+..+|+..+||+||.-.|.
T Consensus        43 ~~~~fk~Gs~H~~RVig~s~~D   64 (71)
T cd05696          43 DTGPFKAGTTHKARIIGYSPMD   64 (71)
T ss_pred             CCCCCCCCCEEEEEEEECCCCC
T ss_conf             6578647998889998347434


No 15 
>pfam05986 ADAM_spacer1 ADAM-TS Spacer 1. This family represents the Spacer-1 region from the ADAM-TS family of metalloproteinases.
Probab=34.11  E-value=39  Score=15.43  Aligned_cols=30  Identities=17%  Similarity=0.158  Sum_probs=21.8

Q ss_pred             CEEEEEEEECCCCCCEEEEE-ECCCCCEEEE
Q ss_conf             85899998568687302688-0665709994
Q gi|254780232|r   15 IDVNVFIEISLGGYPIKYEM-DKKSGVLVVD   44 (177)
Q Consensus        15 ~~vn~vIEIP~gs~~~KyE~-d~~~g~~~~d   44 (177)
                      .-.+-|+.||+|++|++.+= ....+-|.|.
T Consensus        14 ~GY~~v~~IP~GA~~I~I~e~~~s~nyLAlk   44 (114)
T pfam05986        14 HGYNDVVTIPAGATHILIRELKASGNYLALK   44 (114)
T ss_pred             CCCEEEEEECCCCCEEEEEECCCCCCEEEEE
T ss_conf             9845999969995168999724899899998


No 16 
>pfam03904 DUF334 Domain of unknown function (DUF334). Staphylococcus aureus plasmid proteins with no characterized function.
Probab=33.61  E-value=34  Score=15.81  Aligned_cols=16  Identities=6%  Similarity=-0.016  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHHHHC
Q ss_conf             9999999999998850
Q gi|254780232|r  161 NSAHKIILEAVKRGIK  176 (177)
Q Consensus       161 ~~A~~iI~~~~~ry~k  176 (177)
                      +.+++.|++||++|++
T Consensus       129 ~~mlqEVkqsHEhyqk  144 (229)
T pfam03904       129 DRMLQEVKQSHEHYQK  144 (229)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999999998999


No 17 
>KOG2407 consensus
Probab=32.60  E-value=41  Score=15.27  Aligned_cols=52  Identities=19%  Similarity=0.399  Sum_probs=37.3

Q ss_pred             CCCCC-CCCCCCEEEEEEEECCCCCCEEEEEECCCCCEEEEECCCCCCCCC--CCCCH-HHCCC
Q ss_conf             01886-657998589999856868730268806657099942147765677--78121-10553
Q gi|254780232|r    5 NEISL-GSNSPIDVNVFIEISLGGYPIKYEMDKKSGVLVVDRFISTPMLYP--GNYGF-IPNTL   64 (177)
Q Consensus         5 ~~i~~-~~~~p~~vn~vIEIP~gs~~~KyE~d~~~g~~~~dR~l~~~~~yP--~nYGf-iP~T~   64 (177)
                      |..|. ...+|....+-.++|+++ +++.-++-+.+.+++|.       ||  +|-|| ||...
T Consensus       409 ~y~p~~dr~~p~~lE~~~~lPa~t-~~~vsi~fdk~lL~~~E-------YPPDANhGf~Ip~Ai  464 (575)
T KOG2407         409 YYQPSKDREAPTLLEIKMKLPANT-SCEVSIQFDKALLRLDE-------YPPDANHGFYIPAAI  464 (575)
T ss_pred             HCCCHHHCCCCCEEEEEEECCCCC-EEEEEEECHHHHHHHHH-------CCCCCCCCCCCCCCE
T ss_conf             448222025776068999758985-18999870022210410-------799988773368012


No 18 
>KOG1110 consensus
Probab=32.06  E-value=42  Score=15.22  Aligned_cols=37  Identities=19%  Similarity=0.266  Sum_probs=28.5

Q ss_pred             EEEEEEECCCCCHHHCCCCCHHHCCHHHHHHHHHHHHHHH
Q ss_conf             2799996378882225658778989899999999999964
Q gi|254780232|r  105 EKILAVPSKNITSLYDSIQSYEDVPNAYLQKVEHFFKHYK  144 (177)
Q Consensus       105 ~KiiaVp~~d~~~~~~~i~di~Dl~~~~l~~I~~fF~~YK  144 (177)
                      .+.||...-|.   -+.+.|++||....++.+.+|...||
T Consensus       108 SR~La~~s~d~---~d~~ddlsdL~a~e~eal~eWE~~fk  144 (183)
T KOG1110         108 SRGLAKMSFDL---SDETDDLSDLTAEELEALNEWETKFK  144 (183)
T ss_pred             HHHHHHCCCCH---HHCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             77887546651---11256533248999999999999986


No 19 
>TIGR00034 aroFGH phospho-2-dehydro-3-deoxyheptonate aldolase; InterPro: IPR006219   Members of this group catalyze the first enzymatic reaction of the shikimate pathway. The common (shikimate) pathway links metabolism of carbohydrates to biosynthesis of aromatic amino acids phenylalanine, tyrosine, tryptophan, and derivatives in microorganisms and in plants. In a sequence of seven enzymatic reactions, D-erythrose 4-phosphate (E4P), an intermediate of the pentose phosphate pathway, and phosphoenol pyruvate (PEP), a glycolytic intermediate, are converted to chorismate. The pathway begins with the stereospecific condensation of E4P and PEP to yield 7-phospho 2-dehydro 3-deoxy-D-arabino-heptulosonate (DAHP), catalyzed by 3-deoxy-7-phosphoheptulonate synthase (DAHPS) (EC 2.5.1.54, formerly EC 4.1.2.15). The divalent metal cation requirement of this enzyme can be satisfied by a broad range of metals . A Cys residue in a Cys-X-X-His motif has been identified as part of a metal binding site . In Escherichia coli, the enzyme exists in three isoforms, each specifically inhibited by one of the three aromatic amino acids.   DAHP synthetases fall into two classes, class I (represented by this entry) and class II (represented by PIRSF015573 from PIRSF). Class I was believed to be limited to microorganisms and class II to plants. However, a more recent study showed that class II also contains enzymes from a microbial eukaryote and several bacteria . Brick and Woodard  proposed that the difference between the two classes lies in their metal ion requirement for activity. Whereas class I requires no metal cation, class II is dependent on a metal cation for activity. However, recently a class I DAHP synthase from Thermotoga maritima has been purified, characterised, and shown to be a metalloenzyme .   The three-dimentional structures of DAHP synthases have been determined , , , , . The DAHPS(Phe) monomer is a (beta/alpha)8 barrel with an additional N-terminal beta strand and helices and an extra beta sheet near the C terminus . The active site is located in a cleft at the carboxyl end of the barrel . The allosteric feedback inhibition binding site of DAHPS(Phe) is composed of residues from two adjacent subunits of a tight dimer and is at least 20 angstroms away from the closest active site .   The absence of the shikimate pathway in animals makes it an attractive target for nontoxic herbicidal, antimicrobial, and antifungal agents. The nontoxic herbicide glyphosphate competitively inhibits 3-phosphoshikimate 1-carboxyvinyltransferase, the sixth enzymatic reaction of the pathway.; GO: 0003849 3-deoxy-7-phosphoheptulonate synthase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=31.20  E-value=4.4  Score=21.44  Aligned_cols=55  Identities=18%  Similarity=0.401  Sum_probs=37.0

Q ss_pred             CCCCEEEEEEE----CCCCCHHHCCCCCHHHCCHHHHHHHHHHHHHHHCCCCCCEEEEECCCC
Q ss_conf             87752799996----378882225658778989899999999999964288897189803149
Q gi|254780232|r  101 GGIDEKILAVP----SKNITSLYDSIQSYEDVPNAYLQKVEHFFKHYKDLEDGKWAKLDGWEG  159 (177)
Q Consensus       101 ge~D~KiiaVp----~~d~~~~~~~i~di~Dl~~~~l~~I~~fF~~YK~le~~K~v~v~g~~~  159 (177)
                      .+.|++||.|=    ++||..-++.-+=|..|.+.+-+.++-=.|.|  +||..++  -||.|
T Consensus        46 ~G~D~RLLVViGPCSiHDP~AA~eYA~RL~~L~~~l~~~L~IvMRvY--fEKPRTt--VGWKG  104 (348)
T TIGR00034        46 AGKDDRLLVVIGPCSIHDPEAAIEYATRLKKLREKLKDDLEIVMRVY--FEKPRTT--VGWKG  104 (348)
T ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEE--ECCCCCC--CCCCC
T ss_conf             79997689997588857468999999999999987503760787643--1698701--03444


No 20 
>pfam07177 Neuralized Neuralized. This family contains a conserved region approximately 60 residues long within eukaryotic neuralized and neuralized-like proteins. Neuralized belongs to a group of ubiquitin ligases and is required in a subset of Notch pathway-mediated cell fate decisions during development of the Drosophila nervous system. Some family members contain multiple copies of this region.
Probab=29.94  E-value=45  Score=14.99  Aligned_cols=22  Identities=23%  Similarity=0.463  Sum_probs=19.0

Q ss_pred             EEEECCCCCCCCCEEEEEEEEE
Q ss_conf             8992277767742899869899
Q gi|254780232|r   73 VIMYSSEPILPGSVISTRPIGV   94 (177)
Q Consensus        73 vlvl~~~~~~~G~vv~~r~iG~   94 (177)
                      .+|+++.|+.+|..+.+|+.-.
T Consensus        30 givFS~rPl~~~E~~~v~I~~~   51 (68)
T pfam07177        30 GITFSARPVRIGERVCVRVLKI   51 (68)
T ss_pred             EEEEECCCCCCCCEEEEEEEEC
T ss_conf             6999788777998999999853


No 21 
>pfam05541 Spheroidin Entomopoxvirus spheroidin protein. Entomopoxviruses (EPVs) are large (300-400 nm) oval-shaped viruses replicating in the cytoplasm of their insect host cells. At the end of their replicative cycle EPVs virions are occluded in a highly expressed protein called spheroidin. This protein forms large (5-20 mm long) oval-shaped occlusion bodies (OBs) called spherules. The infectious cycle of EPVs begins with the ingestion by the insect host of the spherules, their dissolution by the alkaline reducing conditions of the midgut fluid and the release of virions in the midgut lumen. The infective particles first replicate in midgut epithelial cells, then pass the gut barrier to colonize the internal tissues, mainly the fat body cells. Whilst spheroidin has been demonstrated to be non-essential for viral replication, it plays an essential role in the natural biological cycle of the virus in protecting virions from adverse environmental conditions (e.g. UV degradation) and thus
Probab=28.42  E-value=26  Score=16.50  Aligned_cols=10  Identities=10%  Similarity=0.318  Sum_probs=3.5

Q ss_pred             CEEEEEEEEC
Q ss_conf             8589999856
Q gi|254780232|r   15 IDVNVFIEIS   24 (177)
Q Consensus        15 ~~vn~vIEIP   24 (177)
                      +.+|.++..-
T Consensus       200 ~v~N~vldl~  209 (943)
T pfam05541       200 DVTNIVLDLN  209 (943)
T ss_pred             CCEEEEEECC
T ss_conf             2103688724


No 22 
>KOG2892 consensus
Probab=28.18  E-value=39  Score=15.44  Aligned_cols=12  Identities=25%  Similarity=0.708  Sum_probs=5.9

Q ss_pred             HCCCCCHHHCCH
Q ss_conf             256587789898
Q gi|254780232|r  119 YDSIQSYEDVPN  130 (177)
Q Consensus       119 ~~~i~di~Dl~~  130 (177)
                      +++++++.|||+
T Consensus       115 ~s~~kTladLP~  126 (320)
T KOG2892         115 YSAYKTLADLPA  126 (320)
T ss_pred             CCCCCCHHHCCC
T ss_conf             433255866899


No 23 
>PRK09409 insertion element IS2 transposase InsD; Reviewed
Probab=26.66  E-value=52  Score=14.63  Aligned_cols=41  Identities=20%  Similarity=0.059  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC
Q ss_conf             999999999996428889718980314999999999999998850
Q gi|254780232|r  132 YLQKVEHFFKHYKDLEDGKWAKLDGWEGVNSAHKIILEAVKRGIK  176 (177)
Q Consensus       132 ~l~~I~~fF~~YK~le~~K~v~v~g~~~~~~A~~iI~~~~~ry~k  176 (177)
                      -=--++-||.+.|.    -.+....|.+.++|.+.|.+..+.|-.
T Consensus       229 dNa~~EsF~~tlK~----E~l~~~~~~~~~~~~~~i~e~~e~YN~  269 (301)
T PRK09409        229 SNGIAESFVKTIKR----DYISIMPKPDGLTAAKNLAEAFEHYNE  269 (301)
T ss_pred             HHHHHHHHHHHHHH----HHHHCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             32699999999999----998504578999999999999999677


No 24 
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=25.37  E-value=55  Score=14.48  Aligned_cols=17  Identities=29%  Similarity=0.294  Sum_probs=12.7

Q ss_pred             CCCCCCEEEEEEEEEEE
Q ss_conf             76774289986989999
Q gi|254780232|r   80 PILPGSVISTRPIGVMK   96 (177)
Q Consensus        80 ~~~~G~vv~~r~iG~l~   96 (177)
                      .+..|..++||+||.=.
T Consensus        46 ~~k~Gq~V~~rViG~~d   62 (70)
T cd05702          46 KFKIGQKIKARVIGGHD   62 (70)
T ss_pred             HCCCCCEEEEEEEEEEC
T ss_conf             56899999999997654


No 25 
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=24.12  E-value=58  Score=14.33  Aligned_cols=12  Identities=8%  Similarity=-0.031  Sum_probs=4.5

Q ss_pred             EEEEEEEEEEEC
Q ss_conf             986989999604
Q gi|254780232|r   88 STRPIGVMKMED   99 (177)
Q Consensus        88 ~~r~iG~l~m~D   99 (177)
                      -.+++....-++
T Consensus       253 Gg~pV~y~~dEe  264 (518)
T PRK13355        253 GGTAVHYRCDEE  264 (518)
T ss_pred             CCEEEEEEECCC
T ss_conf             987889874522


No 26 
>PRK06788 flagellar motor switch protein; Validated
Probab=23.52  E-value=37  Score=15.54  Aligned_cols=21  Identities=29%  Similarity=0.303  Sum_probs=15.7

Q ss_pred             CCCCEEEEEECCCCCCCCCEEE
Q ss_conf             9984028992277767742899
Q gi|254780232|r   67 DGDPVDVIMYSSEPILPGSVIS   88 (177)
Q Consensus        67 DgDPLDvlvl~~~~~~~G~vv~   88 (177)
                      =|+|+|++|-+. -+.+|.+|=
T Consensus        67 AGepvDi~VNgk-liArGEVVV   87 (119)
T PRK06788         67 LGHKVDVYLSNM-KVGIGEAIV   87 (119)
T ss_pred             CCCCEEEEECCE-EEEEEEEEE
T ss_conf             899679999999-998775999


No 27 
>pfam04425 Bul1_N Bul1 N terminus. This family contains the N terminus of Saccharomyces cerevisiae Bul1. Bul1 binds the ubiquitin ligase Rsp5, via an N terminal PPSY motif. The complex containing Bul1 and Rsp5 is involved in intracellular trafficking of the general amino acid permease Gap1, degradation of Rog1 in cooperation with Bul2 and GSK-3, and mitochondrial inheritance. Bul1 may contain HEAT repeats.
Probab=23.12  E-value=60  Score=14.21  Aligned_cols=61  Identities=33%  Similarity=0.351  Sum_probs=30.9

Q ss_pred             CEEE--EEEEECCCCCCEEEEE------------EC-CCCCEEEEECCCCC-CCCCCCCCHHHCCCCC-----CCCCEEE
Q ss_conf             8589--9998568687302688------------06-65709994214776-5677781211055358-----9984028
Q gi|254780232|r   15 IDVN--VFIEISLGGYPIKYEM------------DK-KSGVLVVDRFISTP-MLYPGNYGFIPNTLSD-----DGDPVDV   73 (177)
Q Consensus        15 ~~vn--~vIEIP~gs~~~KyE~------------d~-~~g~~~~dR~l~~~-~~yP~nYGfiP~T~~~-----DgDPLDv   73 (177)
                      +.||  ++||- +.+..++||.            |+ ..++..+.|||.-- +.-=|||+.|+...+.     +-||.|-
T Consensus       164 D~I~GyvtI~N-~S~~pi~FdMFyV~lEG~~~v~d~~~~~~~~vkkFL~M~D~sASw~y~~i~~l~~~~~~~~~~Dp~Dg  242 (432)
T pfam04425       164 DIINGYVTIEN-KSSEPIPFEMFYVTLEGYISVIDKHKKGKRTVKRFLRMVDLSASWSYTNIDRLSGINYCPGEIDPYDG  242 (432)
T ss_pred             CEEEEEEEEEE-CCCCCCCCCEEEEEEEEEEEEECCCCCCCHHHHHHHEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             87878999986-89997653369999868999822776775567410100312445554335544453358775478888


Q ss_pred             EEE
Q ss_conf             992
Q gi|254780232|r   74 IMY   76 (177)
Q Consensus        74 lvl   76 (177)
                      .++
T Consensus       243 t~l  245 (432)
T pfam04425       243 TIL  245 (432)
T ss_pred             EEE
T ss_conf             089


No 28 
>pfam07469 DUF1518 Domain of unknown function (DUF1518). This domain, which is usually found tandemly repeated, is found various receptor co-activating proteins.
Probab=22.83  E-value=35  Score=15.75  Aligned_cols=14  Identities=36%  Similarity=0.596  Sum_probs=11.0

Q ss_pred             CCCCCCCCHHHCCC
Q ss_conf             56777812110553
Q gi|254780232|r   51 MLYPGNYGFIPNTL   64 (177)
Q Consensus        51 ~~yP~nYGfiP~T~   64 (177)
                      +.||-|||.-+|+=
T Consensus        19 FpypPnyGm~qq~d   32 (56)
T pfam07469        19 FPYPPNYGMGQQPD   32 (56)
T ss_pred             CCCCCCCCCCCCCC
T ss_conf             77788877356888


No 29 
>pfam07909 DUF1663 Protein of unknown function (DUF1663). The members of this family are hypothetical proteins expressed by Trypanosoma cruzi, a eukaryotic parasite that causes Chagas' disease in humans. This region is found as multiple copies per protein.
Probab=22.29  E-value=38  Score=15.48  Aligned_cols=29  Identities=31%  Similarity=0.688  Sum_probs=21.5

Q ss_pred             ECCCCCC-CCCCCCCHHHCC-------CCCCCCCEEE
Q ss_conf             2147765-677781211055-------3589984028
Q gi|254780232|r   45 RFISTPM-LYPGNYGFIPNT-------LSDDGDPVDV   73 (177)
Q Consensus        45 R~l~~~~-~yP~nYGfiP~T-------~~~DgDPLDv   73 (177)
                      ..|.+|. .|-.|.||-||.       ..-||-||..
T Consensus        53 ssltspissyavnlgfspqpd~aln~thekdggplsf   89 (514)
T pfam07909        53 SSLTSPISSYAVNLGFSPQPDEALNATHEKDGGPLSF   89 (514)
T ss_pred             CCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             4456740666532688999730028654567996444


No 30 
>pfam08968 DUF1885 Domain of unknown function (DUF1885). This domain is found in a set of hypothetical proteins produced by bacteria of the Bacillus genus.
Probab=21.67  E-value=25  Score=16.63  Aligned_cols=13  Identities=31%  Similarity=0.552  Sum_probs=5.2

Q ss_pred             HHHHHHHHHHHHCCC
Q ss_conf             999999999964288
Q gi|254780232|r  133 LQKVEHFFKHYKDLE  147 (177)
Q Consensus       133 l~~I~~fF~~YK~le  147 (177)
                      -+|.-.|+.  |.|+
T Consensus       100 ANEfckfLA--K~l~  112 (128)
T pfam08968       100 ANEFSKFLA--KKLE  112 (128)
T ss_pred             HHHHHHHHH--HHHH
T ss_conf             768999999--9741


No 31 
>pfam10465 Inhibitor_I24 PinA peptidase inhibitor. PinA inhibits the endopeptidase La. It binds to the La homotetramer but does not interfere with the ATP binding site or the active site of La.
Probab=21.35  E-value=57  Score=14.37  Aligned_cols=34  Identities=24%  Similarity=0.400  Sum_probs=23.8

Q ss_pred             CCCCCCEEEEEEEEEEEEECCCCCCEEEEEEECCC
Q ss_conf             76774289986989999604787752799996378
Q gi|254780232|r   80 PILPGSVISTRPIGVMKMEDDGGIDEKILAVPSKN  114 (177)
Q Consensus        80 ~~~~G~vv~~r~iG~l~m~D~ge~D~KiiaVp~~d  114 (177)
                      .+..|++.++|-+= -..+|+|+.|+-||-|..++
T Consensus        21 el~~gti~kvreli-~~~~dd~~~d~giiei~l~~   54 (140)
T pfam10465        21 ELKAGTIFKVRELI-GECEDDGEGDHGIIEIELND   54 (140)
T ss_pred             HHCCCEEEEEHHHH-CCCCCCCCCCCCEEEEEECC
T ss_conf             10475178707742-75444678986669999468


No 32 
>KOG0210 consensus
Probab=20.55  E-value=54  Score=14.49  Aligned_cols=45  Identities=18%  Similarity=0.262  Sum_probs=23.5

Q ss_pred             CCCCCEEE-EEEECCCCCHHHCCCCCHHHCCHHHHHHHHHHHHHHH
Q ss_conf             78775279-9996378882225658778989899999999999964
Q gi|254780232|r  100 DGGIDEKI-LAVPSKNITSLYDSIQSYEDVPNAYLQKVEHFFKHYK  144 (177)
Q Consensus       100 ~ge~D~Ki-iaVp~~d~~~~~~~i~di~Dl~~~~l~~I~~fF~~YK  144 (177)
                      +||.|||+ |+||...-.+.-+.++.++=..+.--+.|.+|.-+.|
T Consensus       219 DGETDWKLrl~vp~tQ~l~~~~el~~i~v~Ae~P~kdIh~F~Gt~~  264 (1051)
T KOG0210         219 DGETDWKLRLPVPRTQHLTEDSELMEISVYAEKPQKDIHSFVGTFT  264 (1051)
T ss_pred             CCCCCCEEECCCHHHCCCCCCCCHHEEEEECCCCCHHHHHHEEEEE
T ss_conf             7744530504654320388622112378760575110474577899


No 33 
>pfam11772 EpuA DNA-directed RNA polymerase subunit beta. This short 60-residue long bacterial family is the beta subunit of the DNA-directed RNA polymerase, likely to be EC:2.7.7.6. It is membrane-bound and is referred to by the name EpuA.
Probab=20.37  E-value=26  Score=16.59  Aligned_cols=10  Identities=40%  Similarity=0.783  Sum_probs=6.6

Q ss_pred             CCCCCEEEEE
Q ss_conf             8998402899
Q gi|254780232|r   66 DDGDPVDVIM   75 (177)
Q Consensus        66 ~DgDPLDvlv   75 (177)
                      |||+|.||+-
T Consensus        24 G~G~p~dVl~   33 (47)
T pfam11772        24 GGGNPWDVLS   33 (47)
T ss_pred             CCCCHHHHCC
T ss_conf             6998777549


Done!