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!