Query         gi|254781202|ref|YP_003065615.1| hypothetical protein CLIBASIA_05545 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 864
No_of_seqs    122 out of 124
Neff          6.3 
Searched_HMMs 39220
Date          Mon May 30 07:06:53 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781202.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PHA01972 structural protein    100.0       0       0 1566.0  85.4  788    1-863     1-828 (828)
  2 PHA00368 internal virion prote  98.0  0.0019 4.9E-08   43.8  28.0  463  193-746   657-1197(1316)
  3 PHA02006 virion protein         97.9  0.0028 7.1E-08   42.6  39.8  534  159-814   716-1331(1337)
  4 PRK06922 hypothetical protein;  86.6    0.64 1.6E-05   24.6   2.9   17  324-340   289-305 (679)
  5 COG2766 PrkA Putative Ser prot  56.9      10 0.00026   15.4   4.4   42  797-838   596-638 (649)
  6 KOG0994 consensus               55.3      11 0.00028   15.3  18.9   17  352-368  1462-1478(1758)
  7 TIGR02288 PaaN_2 phenylacetic   55.1     7.9  0.0002   16.3   1.9   70  138-207    82-192 (560)
  8 COG4709 Predicted membrane pro  48.4      14 0.00035   14.5   7.7   13  733-745   125-137 (195)
  9 pfam06543 Lac_bphage_repr Lact  48.2      14 0.00035   14.5   2.3   29  219-248    16-44  (49)
 10 pfam04459 DUF512 Protein of un  46.5      15 0.00037   14.3   4.2   58  161-218    20-91  (205)
 11 pfam07580 Peptidase_M26_C M26   44.0      15 0.00037   14.3   1.8   21  766-786   673-693 (731)
 12 TIGR00963 secA preprotein tran  41.7      17 0.00044   13.8   7.2   81  273-374   659-746 (904)
 13 KOG2099 consensus               37.2      20 0.00051   13.3   4.3   25  609-633   535-559 (843)
 14 TIGR02302 aProt_lowcomp conser  36.7      20 0.00051   13.2   4.5   29  495-524   658-686 (899)
 15 PRK04531 acetylglutamate kinas  34.9      22 0.00055   13.0   2.0   36  272-323    19-54  (421)
 16 pfam01054 MMTV_SAg Mouse mamma  33.9      11 0.00027   15.3  -0.2   25  658-682   136-160 (314)
 17 COG0082 AroC Chorismate syntha  31.1     7.7  0.0002   16.4  -1.3   97  214-323    37-141 (369)
 18 pfam08822 DUF1804 Protein of u  31.0      25 0.00063   12.6   2.8   58  532-602    47-104 (165)
 19 KOG0624 consensus               30.8      16 0.00041   13.9   0.3   38  717-759   456-494 (504)
 20 KOG1011 consensus               30.1      25 0.00065   12.5   3.0   10  280-289   462-471 (1283)
 21 TIGR01021 rpsE_bact ribosomal   28.5      21 0.00054   13.1   0.6   36  296-335   104-140 (157)
 22 pfam05379 Peptidase_C23 Carlav  27.5      24 0.00062   12.6   0.8   16    2-17      2-18  (89)
 23 CHL00073 chlN photochlorophyll  26.7      27 0.00068   12.3   0.8   26  375-405   243-268 (457)
 24 TIGR02094 more_P_ylases alpha-  26.6      21 0.00055   13.0   0.4   25  797-828   594-618 (618)
 25 pfam11981 DUF3482 Domain of un  25.7      30 0.00076   11.9   4.3   40  746-785   163-202 (293)
 26 TIGR02213 lolE_release lipopro  24.7      22 0.00055   13.0   0.1  114  194-321   165-313 (416)
 27 TIGR02791 VirB5 P-type DNA tra  24.3      32 0.00081   11.7   1.4   37  557-602   163-199 (233)
 28 TIGR01478 STEVOR variant surfa  23.8      32 0.00082   11.7   3.1   16  241-256   117-132 (315)
 29 TIGR01264 tyr_amTase_E tyrosin  23.0      33 0.00085   11.6   4.2  139  159-322   110-294 (415)
 30 pfam03881 Fructosamin_kin Fruc  22.6      34 0.00087   11.5   4.2   65  310-392   221-285 (287)
 31 KOG4403 consensus               22.4      34 0.00087   11.5  11.1   34  280-321   227-260 (575)
 32 pfam02064 MAS20 MAS20 protein   22.3      34 0.00088   11.5   1.9   22  376-397     2-23  (184)
 33 KOG2348 consensus               22.2      35 0.00088   11.4   2.6   30  385-414   137-169 (667)
 34 pfam02375 JmjN jmjN domain.     22.1      35 0.00089   11.4   2.2   21  822-842     7-28  (34)
 35 COG1727 RPL18A Ribosomal prote  22.0      24 0.00061   12.7  -0.1   30  166-195    27-57  (122)
 36 cd04436 DEP_fRgd2 DEP (Disheve  21.5      36 0.00091   11.3   4.3   44  786-837    27-70  (84)
 37 pfam06239 ECSIT Evolutionarily  21.2      36 0.00092   11.3   5.1   14  284-297    75-88  (229)
 38 pfam06798 PrkA PrkA serine pro  21.2      36 0.00092   11.3   3.4   42  209-252   120-162 (254)
 39 COG1071 AcoA Pyruvate/2-oxoglu  20.6      37 0.00095   11.2   2.8   21  310-330    88-108 (358)
 40 TIGR00838 argH argininosuccina  20.4      37 0.00096   11.2   1.0   39  215-253    30-70  (469)

No 1  
>PHA01972 structural protein
Probab=100.00  E-value=0  Score=1566.01  Aligned_cols=788  Identities=22%  Similarity=0.288  Sum_probs=715.8

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH------HHCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH
Q ss_conf             915899999987457877899999999999999998------661999799999999999-9999999999999999999
Q gi|254781202|r    1 MKPECIQVLNKAAGRELSKKELRRLEDGIVRAYVSL------DGKGLSKAERYRLAGLKA-EEDFQKELIRSVNDAIDEA   73 (864)
Q Consensus         1 mk~~Ci~~V~~algr~lsa~E~~~i~d~i~~~~r~~------~~~~ls~ae~~~~AA~~a-~~~~~~e~~~~~~~~~~~~   73 (864)
                      |||+|+++|++|+||+||++|+++||++|+++||++      .|+++|++|+..++|.++ ..+.+.+.+++++++++++
T Consensus         1 M~~~C~~aV~~AaGR~Lsa~E~~~iedri~~~mr~~ar~d~~~w~~ls~aer~~~~a~e~a~~~~~~e~~~~r~r~~~~i   80 (828)
T PHA01972          1 MPQKCVEAVAQAAGRQLTADEIKGIEDRIKEAMRSVARKDPKGWKEESIAKRFYKTDADLARQELVHDAIKKKKRVALAI   80 (828)
T ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             93789999999866877789997799999999999985295233337999999988999988999999999999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------
Q ss_conf             999999998541356641078999987632100--2376699999999999999999998520001456-----------
Q gi|254781202|r   74 YKRHQLRSDLDRVQAGVYGKSQALFNKLFFKAG--SAEVPLEMKIKAAETKVLSKFNEYAEVGSKNLGF-----------  140 (864)
Q Consensus        74 ~~~~~l~~~l~~~~~~~~~~~~al~~~~~~~~~--~~~~sV~~~~~a~~~~~~~~l~~~~~~~~~~~~~-----------  140 (864)
                      ++++++...+++++.+......+++..+.+.++  +.+.||++++.+++.++.+.+.++++.....+..           
T Consensus        81 ~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~s~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (828)
T PHA01972         81 AKQAEATKKINEVLTADKDPAAALLGMLSRDPNEEAKFLSVEQRINATRDVSKAKISDFMAALDPTTRQIFAGIATGERR  160 (828)
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCHHCCHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHCCCCHHHHH
T ss_conf             99999999987431478555789866550275431002108888878999998899999985111344331043303443


Q ss_pred             --HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCC-CCCCCCHHHHHHCCHHHHHHHH
Q ss_conf             --5418889999999848888998999999999999999999998617984002681-4541687999513689899999
Q gi|254781202|r  141 --TLDKQFGLDVFDEMKGKKTQNEQASRLVKQYFETQRELHSQAHEAGLDYKFFENR-IPQPMSVDKLRATKKDDFVRSM  217 (864)
Q Consensus       141 --~~dka~~~~~~~e~~g~~tgn~~a~~~A~~~~~~~e~~r~~~N~aG~~Igkl~~~-~pq~hd~~~i~~a~~~~W~~~i  217 (864)
                        ..|+..++++|+|+||++|||++|+++|++|.+++|++|.+||++||+||||||| +||+||+.||++||+++|+++|
T Consensus       161 f~~~~~~~~~dli~E~~g~~Tgn~~Ak~~A~~~~~~~e~~R~rfN~aGg~Ig~ldd~~~pq~Hd~~ki~~ag~~~W~~~i  240 (828)
T PHA01972        161 FDKAQQRLLDDIVHELYGRQTGNADAKKAAKGWKKVTEDLRARFNDAGGDIGELDDWRLPQKHNRMKISKAGADAWVDDV  240 (828)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHCCHHHHHHHH
T ss_conf             21445899999999983788899999999999999999999999873798543558899976789999733689999999


Q ss_pred             HHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCC---CHHHHHHCCCCCEEEEECCHHHHHHHHHHHCCC
Q ss_conf             97520875117568848989999998876323311776566875---213543114576178840967899999960887
Q gi|254781202|r  218 LDWLDLSRYKDIDGTPLSRSEIASFVGEVFAERVRSTSFKDPSI---PSSEVGVKREFERVFHFKDSQAHMDYMEHFGVS  294 (864)
Q Consensus       218 ~~~lD~~~~~~~~G~~~~~~~~~~~L~~vy~~i~t~g~~~~~~~---~~~~~~~~~~~~R~LhFKDa~sw~~Y~~~fG~~  294 (864)
                      +|+||+++||+++|.|++|.+++.||++|||+|+|+|+||..|.   |+++.+|++++||||||||++|||+||++|| +
T Consensus       241 ~~~LD~~~~v~~~G~~~~~~el~~~L~~VY~ti~T~G~nk~~~~~~~G~~~~anr~s~~RvLhFKDa~sw~~Yq~~fG-~  319 (828)
T PHA01972        241 WDLLDRSKYVKKDGKPMNDAELREALYSVYNTIATDGMNKIDPGSKTGSGARANRGSAERVIHFKDADSHLQYQREFG-D  319 (828)
T ss_pred             HHHCCHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHCCCCCEEEEECCHHHHHHHHHHHC-C
T ss_conf             865079986266789799899999999998520248877678521122355521022310256457688999999867-9


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCHHHHHHHHHHHHHHHHHHH-CCC
Q ss_conf             7689999988874455677999857996899999999999861110000012200001488998999999999762-578
Q gi|254781202|r  295 TNVNTILTSELASLSKDIVIARELGPNADSFVKQMIVQTIANDQEASAGNKVLKDWLGRNKLEVRQEAMLQMWEVM-RYG  373 (864)
Q Consensus       295 ~~~~~~m~~hi~~msrDIalm~~lGpNP~~~f~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~  373 (864)
                      .|++++|++||++|||||+|||+|||||+.+|+++++.++.++....            ++..+..+.++.||+.+ |.+
T Consensus       320 ~~~~~~m~~hl~~msrdialme~lGpNP~~~f~~l~d~~~~~~~~~~------------~~~~g~~~~~~~m~~~v~G~~  387 (828)
T PHA01972        320 TSVYASMVGHLDGMSRDIGLVETFGPDPDRNFNTLLDAVKTKKGTTS------------RQPTGAMKMVEPTFNMLMGYN  387 (828)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC------------CCHHHHHHHHHHHHHHHHCCC
T ss_conf             98899999989877678999998399857899999999986404345------------225779999999999971878


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH-CCCCCCHHHHHHHHHHCCC--HHHHHHHHHHHHHHHH
Q ss_conf             767538999999899999999875224566412538999850-1245403899999641380--5499999996679989
Q gi|254781202|r  374 ETVENTGWANWMAGLRSAAGASMLGQHPIGALLEDGFISRQM-LSRVGIDKEAIQRINKMPL--KERMELLSDVGLYAEG  450 (864)
Q Consensus       374 ~~p~n~~~a~~~a~lR~~~~~akLGgA~ISA~tD~~~i~~t~-~~~~~~~~~~~~~l~~~~~--~d~~~~a~~lGl~~E~  450 (864)
                      ++|+|++||++++++|+|++++|||||+||||+|+++|+.++ ++++++.+.+.+.++.+++  ++.++.+.++||++|+
T Consensus       388 ~~~~n~~~An~~aglR~~~taskLG~A~lSa~tD~~~~~~~a~y~gl~~~~~~~~~l~~l~~~ske~~~~a~~~GL~aE~  467 (828)
T PHA01972        388 MVEENPVWGRRVAGLRNLWTASKLGAAVLSALSDSGTMSMAASYNAMPPARLLRNMLSEMMPGSKSEASRAQDFGLGAES  467 (828)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             77655999999987999999998621255440359999999986388889999999998575767899999970147888


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHC--
Q ss_conf             999999740266640367999989998852437888657676999999999999763002114773201067899861--
Q gi|254781202|r  451 VVAHGRNMMEGSDAFQIGHKLHSKMHKWSGAEYLDKKRISSHALIVYNQIGRMTDTYASLKDLKADPRLDPSIKAFFK--  528 (864)
Q Consensus       451 ~~~~~~r~~~~~~~~~~~~~~a~~~~r~SgL~~wT~~~k~a~~~~~~~~la~l~~~~~~l~~~k~~d~l~~~~~~~l~--  528 (864)
                      +++.++||.+++++++++++++++|||||||||||+++|++|+++||++||++        ..+.|++|+.++++.|+  
T Consensus       468 ~~~~~~R~~~d~~~~~~~~~~a~~~mR~SGLs~wT~a~k~af~~~m~~~lg~~--------a~~~~~dL~~~drrvL~~~  539 (828)
T PHA01972        468 LLDRVNRWGTDNLGGHRSRNLAEAVMKVSGLTAWTDAARAAFQFEMMTALGEA--------ADSDWSDLPESDRRILGRK  539 (828)
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHH--------CCCCHHHCCHHHHHHHHHC
T ss_conf             98999986066643078899999999984408988989999999999999876--------1488444798999999877


Q ss_pred             CCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             78988999998412111356664100523320144577544310002233332000112345702456666655421145
Q gi|254781202|r  529 QLDDTDFTVIKRAKAMSSPDGYLYARTPSTIKNLKDADLRDLARMSDKIAYHRKKLKNSKTLSPEQRQELQQQLADLERK  608 (864)
Q Consensus       529 GI~e~dW~i~r~a~~~~~~~~~~~~~t~~~i~~~~da~i~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~  608 (864)
                      ||++.||++|+.+++.+..++.  ++||++|+.||+++                                          
T Consensus       540 GIte~DW~i~~~~~~~~~~g~~--~ltPd~i~~ip~~~------------------------------------------  575 (828)
T PHA01972        540 GITESDWAIIAAAPRTNYGGAK--MLTPDAIYAVPRNM------------------------------------------  575 (828)
T ss_pred             CCCHHHHHHHHCCCCCCCCCCC--CCCHHHHHHCCHHH------------------------------------------
T ss_conf             9986779999708860689987--56889887546889------------------------------------------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             77886568899999999986530111145665432210002455787556789999987764299999999999874224
Q gi|254781202|r  609 EINILKDKVSNKMHALVLDNVQTSVRGAMHTSLFDRQRLGLLTYKRGTRAGEALRMFQQFTTTPTGMFLNILDLSNSAKM  688 (864)
Q Consensus       609 ~~~~~kd~~~~~l~~~il~~~~~aV~~av~tp~~r~r~~~~~g~~~gT~~GE~~r~~~qFKsFp~a~~~~~~~r~~~~~~  688 (864)
                           +.+++.+|+++|++|+++||    |||++|+|+++.+|+||||++||++||++||||||++++++||+|++++++
T Consensus       576 -----~~ela~KL~g~i~de~~~AV----~tp~~r~rai~~~g~q~GT~~GE~~Rs~~qFKSFpia~~~~~~~R~~~~~G  646 (828)
T PHA01972        576 -----DAEAQTKLLGMVDGETMMAV----PTPDARTRAIMAGGTKSGTFGGELHRSFFLFKSFPIATIMRHWRRAFTGKG  646 (828)
T ss_pred             -----HHHHHHHHHHHHHCCCCEEC----CCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCC
T ss_conf             -----99999999999851121101----588536789882788898488999999999841489999999999986068


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC---HHHHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHC
Q ss_conf             3311345677899999999999999999999963899992---7999999985053067788760577863035777740
Q gi|254781202|r  689 PKGASMALNHVWIQYSATMALAGIGVASIKALLRGEDPSL---PEVIYDGTLANGALLPYMDRLTKLVSKGDRAAIGGLL  765 (864)
Q Consensus       689 ~~~~~~~~~~~~a~~~~~~t~~G~~~~q~k~~l~Grdp~~---~~~~~~a~~~gGg~gi~gd~l~~~~~r~g~~~~~~~~  765 (864)
                      +.+... .+.+++.++++||+|||+++|+|++|+||||+|   |+||++|++|||||||||||||+++||||+++.++++
T Consensus       647 ~~~~~~-~~~y~a~l~~~tTl~G~~s~q~K~ll~GrdPr~~~~~~fw~~a~lqGGGlGi~GDfL~~~~~r~G~~~~~~~a  725 (828)
T PHA01972        647 YPGAFD-RMAYAAIMVASTTLLGAGSIQAKDLLNGKDPRSMTDPKFWIEALLKGGSFGYYGDFLRNAHTGYGSDMTSYIG  725 (828)
T ss_pred             CCCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCCCHHHHHHC
T ss_conf             886046-7889999999999999999999999779999999862499999973687125799987653143510788862


Q ss_pred             CHHHHHHHHHHHHHHH----HHCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             4015558899999986----402676542258999997318774489999999999999999870812479999999874
Q gi|254781202|r  766 GPVPSMVTNLTSSAVE----LATKDNENSKVNATKAIRKTLPFMNMWYLKNSFDHLILNQILEELNPGYLDRQQSKKKKK  841 (864)
Q Consensus       766 GP~~~~~~~~~~~~~~----~~~g~~~~~~~~~~~~~~~~~P~~nLwy~k~a~d~li~~~~~e~~~Pgy~~r~~~r~~~~  841 (864)
                      ||++|+++|+++++++    ++.|++++.++|+++|+++||||+||||+|+|+||||+|||||++||||++|+++|.+++
T Consensus       726 GP~~s~~~~l~~l~~~~~~~a~~G~~~~~g~d~~~~~k~~tP~~NLWy~k~a~d~Li~dqlqe~~~PGy~~R~~~R~~k~  805 (828)
T PHA01972        726 GPVLSYGDQLTKWVAMNPQDAAQGKAESAGADLLKFATQQTPFANLWYTKAATDRLIMDQLQELSSPGYDKKQLNRSRRE  805 (828)
T ss_pred             CCCHHHHHHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             86056799999986213888856995034899999998569606699999999999999999883986589999999998


Q ss_pred             -CCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             -7443458643587679998778
Q gi|254781202|r  842 -GIELFQNMDEGLPHRLPFPFGE  863 (864)
Q Consensus       842 -~~~~~w~p~~~~p~r~p~~~~~  863 (864)
                       +|+|||+||+++|+|+|+||++
T Consensus       806 ~~q~ywW~Pg~~~P~r~p~~~~~  828 (828)
T PHA01972        806 FNQTYWWSPGIGTPQRIPSLFEA  828 (828)
T ss_pred             HCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             18813207999886668886769


No 2  
>PHA00368 internal virion protein D
Probab=98.01  E-value=0.0019  Score=43.79  Aligned_cols=463  Identities=14%  Similarity=0.109  Sum_probs=212.7

Q ss_pred             CC-CCCCCCCHHH----HH---------HCCHHHHHHHHHHHHH----HHHHCCC-CCCCCCHHHHHHHHHHHHHHHHCC
Q ss_conf             68-1454168799----95---------1368989999997520----8751175-688489899999988763233117
Q gi|254781202|r  193 EN-RIPQPMSVDK----LR---------ATKKDDFVRSMLDWLD----LSRYKDI-DGTPLSRSEIASFVGEVFAERVRS  253 (864)
Q Consensus       193 ~~-~~pq~hd~~~----i~---------~a~~~~W~~~i~~~lD----~~~~~~~-~G~~~~~~~~~~~L~~vy~~i~t~  253 (864)
                      .+ |+||++|..+    |.         .+=++.|...--.+-.    .+.|+.| .|. ..++.+.+.++.--...+.+
T Consensus       657 kGtYVP~VYdr~aK~l~~~~~Gg~dgLQeaI~~SWltSY~sRpeVKaRvDe~lkE~~g~-~v~evt~e~VekyA~dKAYG  735 (1316)
T PHA00368        657 KGTYVPHVYDRAAKALYIQRFGGPDGLQEAIAKSWLTSYRSRPEVKARVDEYLKELLGI-DVKEVTPEMVEKYAMDKAYG  735 (1316)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHHHHCC
T ss_conf             77547654527999999998078688999999999887302446899999999987363-41667699999986411116


Q ss_pred             CCCCCCCC----------CHHHHHHC-------CCCCEE-EEECCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             76566875----------21354311-------457617-8840967899999960887768999998887445567799
Q gi|254781202|r  254 TSFKDPSI----------PSSEVGVK-------REFERV-FHFKDSQAHMDYMEHFGVSTNVNTILTSELASLSKDIVIA  315 (864)
Q Consensus       254 g~~~~~~~----------~~~~~~~~-------~~~~R~-LhFKDa~sw~~Y~~~fG~~~~~~~~m~~hi~~msrDIalm  315 (864)
                      -..++.=.          +..++.|.       .=+|-+ ...+|+..+-- |..=  +=++..||-.|=+..--||++|
T Consensus       736 IShTd~F~~Ssvieeni~glvGiEnN~FLEARNLFDSDm~V~lpdGqtFSV-NDLR--~~Dm~~impaYDRRVnGDIaIM  812 (1316)
T PHA00368        736 ISHTDQFTRSSVIEENIEGLVGIENNSFLEARNLFDSDMSVTLPDGQTFSV-NDLR--DFDMKKIMPAYDRRVNGDIAIM  812 (1316)
T ss_pred             CCCHHCCCCCHHHHCCCHHHHCCCCCCHHHHHHCCCCCCCEECCCCCCCCC-CHHH--HHHHHHHHHHHCCCCCCCEEEE
T ss_conf             661210341025541321331445540777764125677326789982002-3266--5035541134315447744552


Q ss_pred             HHHCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC-CCCCHHHHHHHHHHHHHHHH
Q ss_conf             98579968999999999998611100000122000014889989999999997625787-67538999999899999999
Q gi|254781202|r  316 RELGPNADSFVKQMIVQTIANDQEASAGNKVLKDWLGRNKLEVRQEAMLQMWEVMRYGE-TVENTGWANWMAGLRSAAGA  394 (864)
Q Consensus       316 ~~lGpNP~~~f~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~-~p~n~~~a~~~a~lR~~~~~  394 (864)
                      ---|--.    +.|.+.+.+-.......          +++...-+.+..-.-++.|-. .-.+..|.-....+-.+...
T Consensus       813 ggTGktT----~~LkdeI~aL~~~~~~~----------g~~kgeVeALkdtvKILTGRARRn~D~af~t~~Rsl~DlsFf  878 (1316)
T PHA00368        813 GGTGKTT----KELKDEILALDKKAEGD----------GKLKGEVEALKDTVKILTGRARRNPDTAFETALRSLNDLSFF  878 (1316)
T ss_pred             CCCCCCH----HHHHHHHHHHHHHCCCC----------CCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             0688567----99999999987422678----------763113899998899871633368501789998776535566


Q ss_pred             HHHHHHHHHHHCCHHHHHHH-----HCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHH---HH----HHHHHHHHCCC
Q ss_conf             87522456641253899985-----01245403899999641380549999999667998---99----99999740266
Q gi|254781202|r  395 SMLGQHPIGALLEDGFISRQ-----MLSRVGIDKEAIQRINKMPLKERMELLSDVGLYAE---GV----VAHGRNMMEGS  462 (864)
Q Consensus       395 akLGgA~ISA~tD~~~i~~t-----~~~~~~~~~~~~~~l~~~~~~d~~~~a~~lGl~~E---~~----~~~~~r~~~~~  462 (864)
                      +|=-=+-.--+|.++-|.+.     .+++.|+++.+...-+++...+-+|+ +.+-++-|   .+    ...+.|.....
T Consensus       879 aKNAYMG~qNiTEIaGMlakGnvral~hGvP~lrd~~~r~kpv~~~ElkEL-H~~~FGkEld~lIRP~r~div~Rlre~t  957 (1316)
T PHA00368        879 AKNAYMGAQNITEIAGMLAKGNVRALLHGVPILRDLAFRNKPVSASELKEL-HGMLFGKELDQLIRPSRQDIVQRLRETT  957 (1316)
T ss_pred             HHHHHHCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHCCCCCCHHHHHHH-HHHHHHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf             544330302688998788434188887276278888760787888999999-9877647788760854788999998637


Q ss_pred             C-CCHHHHHHHH---HHHHHHCCHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHC--CCCH
Q ss_conf             6-4036799998---9998852437888657676999----999999999763002114773201067899861--7898
Q gi|254781202|r  463 D-AFQIGHKLHS---KMHKWSGAEYLDKKRISSHALI----VYNQIGRMTDTYASLKDLKADPRLDPSIKAFFK--QLDD  532 (864)
Q Consensus       463 ~-~~~~~~~~a~---~~~r~SgL~~wT~~~k~a~~~~----~~~~la~l~~~~~~l~~~k~~d~l~~~~~~~l~--GI~e  532 (864)
                      | ++.+..-+..   .+--+.-=++||.-.--...++    -++-|++++.+-..-. .+-|-+-     ++|+  .|+.
T Consensus       958 d~~~~~A~vvgt~ky~TqElAARsP~Tk~LngTtNYilDaaRqG~lgDvv~~al~gk-~~r~~~~-----~~Lk~aSis~ 1031 (1316)
T PHA00368        958 DTGPAVANVVGTLKYGTQELAARSPWTKLLNGTTNYILDAARQGVLGDVVSAALTGK-TTRWFKE-----GFLKSASISP 1031 (1316)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCC-----CHHHHCCCCH
T ss_conf             875789988755211136554138288886263488887774005999998875388-7521332-----3022147799


Q ss_pred             HHHHHHHHHCC--CCCCCCCCCCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999984121--1135666410052332014457754431000223333200011234570245666665542114577
Q gi|254781202|r  533 TDFTVIKRAKA--MSSPDGYLYARTPSTIKNLKDADLRDLARMSDKIAYHRKKLKNSKTLSPEQRQELQQQLADLERKEI  610 (864)
Q Consensus       533 ~dW~i~r~a~~--~~~~~~~~~~~t~~~i~~~~da~i~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~  610 (864)
                      +.|.-|++.=.  ...+.++        -+.|.|-..            ...        +|.. .++|           
T Consensus      1032 EQw~gIkqlire~~trg~dG--------kftikDk~A------------fa~--------DPRa-MDLW----------- 1071 (1316)
T PHA00368       1032 EQWEGIKQLIREHVTRGEDG--------KFTIKDKQA------------FAS--------DPRA-MDLW----------- 1071 (1316)
T ss_pred             HHHHHHHHHHHHHCCCCCCC--------CEEECCHHH------------HCC--------CCHH-HHHH-----------
T ss_conf             99864999999844448898--------456457676------------515--------8336-6888-----------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             88656889999999998653011114566543221000245578755678999998776429999999999987422433
Q gi|254781202|r  611 NILKDKVSNKMHALVLDNVQTSVRGAMHTSLFDRQRLGLLTYKRGTRAGEALRMFQQFTTTPTGMFLNILDLSNSAKMPK  690 (864)
Q Consensus       611 ~~~kd~~~~~l~~~il~~~~~aV~~av~tp~~r~r~~~~~g~~~gT~~GE~~r~~~qFKsFp~a~~~~~~~r~~~~~~~~  690 (864)
                               ++-..|-+|+.+           |---+-.|-   --.-|-++++.+|||||-|-.++--+.|+++-....
T Consensus      1072 ---------Rl~DKvADEtmL-----------RPhKvS~QD---skA~Ga~~km~lQFKsF~iKSlN~rfiRs~ye~tKN 1128 (1316)
T PHA00368       1072 ---------RLADKVADETML-----------RPHKVSLQD---SKAFGALVKMVLQFKSFVIKSLNSRFIRSFYEATKN 1128 (1316)
T ss_pred             ---------HHHHHHHHHHHC-----------CCCCCCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             ---------763133045523-----------744253101---244415789988777667774023889999875026


Q ss_pred             CHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCCCCC----------CCHHHH-HHHHHH----HCCHHHHH
Q ss_conf             113456778999999999999-999999999638999----------927999-999985----05306778
Q gi|254781202|r  691 GASMALNHVWIQYSATMALAG-IGVASIKALLRGEDP----------SLPEVI-YDGTLA----NGALLPYM  746 (864)
Q Consensus       691 ~~~~~~~~~~a~~~~~~t~~G-~~~~q~k~~l~Grdp----------~~~~~~-~~a~~~----gGg~gi~g  746 (864)
                      +.+-.   ...+.+++|.+.| |.+.|..--..|--+          -+|+.+ ++|+-.    |+-|+|+.
T Consensus      1129 ~RaiD---~Alt~viS~GlAggyyvaqahvkA~glpe~qrkeyLk~Aldp~MiayAa~SRSShlGaPL~ian 1197 (1316)
T PHA00368       1129 NRAID---AALTIVISMGLAGGYYVAQAHVKAYGLPEEQRKEYLKNALDPTMIAYAALSRSSHLGAPLSIAN 1197 (1316)
T ss_pred             CHHHH---HHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHH
T ss_conf             43899---9999999831346889999999971598677889998548878889987612123477446999


No 3  
>PHA02006 virion protein
Probab=97.92  E-value=0.0028  Score=42.59  Aligned_cols=534  Identities=16%  Similarity=0.128  Sum_probs=260.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHCCCC----CHHHCCCCCCCCCHHHHHHCCH---HHHHHHH-------HHHHHHH
Q ss_conf             899899999999999999999999861798----4002681454168799951368---9899999-------9752087
Q gi|254781202|r  159 TQNEQASRLVKQYFETQRELHSQAHEAGLD----YKFFENRIPQPMSVDKLRATKK---DDFVRSM-------LDWLDLS  224 (864)
Q Consensus       159 tgn~~a~~~A~~~~~~~e~~r~~~N~aG~~----Igkl~~~~pq~hd~~~i~~a~~---~~W~~~i-------~~~lD~~  224 (864)
                      --+|.++.+|+.-.+.-..|-++...+|..    .-.+++|+-++++..|++....   .--++.+       ++-||+.
T Consensus       716 n~~p~i~~lad~sd~~hg~~g~~ar~agvrGFEDFtpRPGYFHRsWn~sk~~a~e~a~~g~vr~llsEsV~RGi~gldk~  795 (1337)
T PHA02006        716 NLPPTIKALADRSDEIHGLMGQRAREAGVRGFEDFAPRPGYFHRSWNWSKMAQMDEAAPGLARRAISEAVFRGIPGLDRA  795 (1337)
T ss_pred             CCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHCCCCCCCHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHCCCCCCHH
T ss_conf             98858998751116777788888887054542105899871120034899999987554689999999998146676844


Q ss_pred             HH------------CCCCCC---------CCCHHHHHHHHHHHHHHHHC--CCC----CCCCCCCHHHHHHCCCCCEE--
Q ss_conf             51------------175688---------48989999998876323311--776----56687521354311457617--
Q gi|254781202|r  225 RY------------KDIDGT---------PLSRSEIASFVGEVFAERVR--STS----FKDPSIPSSEVGVKREFERV--  275 (864)
Q Consensus       225 ~~------------~~~~G~---------~~~~~~~~~~L~~vy~~i~t--~g~----~~~~~~~~~~~~~~~~~~R~--  275 (864)
                      .-            .+.+|.         .-+-..+|+.|++.--.-++  +-+    .|...-|.+    +-+.||.  
T Consensus       796 eAd~Ia~AivqR~rdkAsG~RseFMGAlGkaDT~fiR~~LeeA~vs~a~i~SIMgkIEQk~sdqGts----KYgK~RL~L  871 (1337)
T PHA02006        796 DADTIAQAIVQRARDRATGIRSEFMGAMGVADTAFIRQALEEANVSQAKFDSIMAKIEQKQSDQGTV----KYGKGRLSL  871 (1337)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCC----CCCCCCCCE
T ss_conf             5507999999998652035668776530443089999999974863452999999997612012523----346653330


Q ss_pred             ---EEE-CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHCCC
Q ss_conf             ---884-0967899999960887768999998887445567799985799689999999999986111000001220000
Q gi|254781202|r  276 ---FHF-KDSQAHMDYMEHFGVSTNVNTILTSELASLSKDIVIARELGPNADSFVKQMIVQTIANDQEASAGNKVLKDWL  351 (864)
Q Consensus       276 ---LhF-KDa~sw~~Y~~~fG~~~~~~~~m~~hi~~msrDIalm~~lGpNP~~~f~~l~~~~~~~~~~~~~~~~~~~~~~  351 (864)
                         -.+ +|+.- +..++.-  +.++.-+|-+|-.+||-.-+|-+.==|. +.....++...+.....      ..    
T Consensus       872 DMta~I~~dGtv-yrV~DlI--DrDLdRlmENY~~smsGRSALa~AG~~g-Da~ieAf~r~Y~~~~ak------L~----  937 (1337)
T PHA02006        872 DMTAEINHNGTV-YRVQDLI--DRDLDRLMENYAGSMSGRSALARAGMPG-DSEIEAFIREYQREAAH------LG----  937 (1337)
T ss_pred             EEEEEECCCCEE-EEHHHHH--HHHHHHHHHHHCCCCCCHHHHHHCCCCC-CHHHHHHHHHHHHHHHH------CC----
T ss_conf             247897349748-8738756--4039999997433541177897658987-26699999999999863------58----


Q ss_pred             HHHHHHHHHHHHHHHHHHHCC-C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHH
Q ss_conf             148899899999999976257-8-76753899999989999999987522456641253899985012454038999996
Q gi|254781202|r  352 GRNKLEVRQEAMLQMWEVMRY-G-ETVENTGWANWMAGLRSAAGASMLGQHPIGALLEDGFISRQMLSRVGIDKEAIQRI  429 (864)
Q Consensus       352 ~~~~~~~~~~~~~~~~~~~~g-~-~~p~n~~~a~~~a~lR~~~~~akLGgA~ISA~tD~~~i~~t~~~~~~~~~~~~~~l  429 (864)
                          ..+..+.+..+-+.++- + |.|--..++-...-..++..+.+|+..-+=-+...++|+..    .+........+
T Consensus       938 ----~a~~~dlm~Qldgl~gDFTGnrP~~~~LG~~AQRaksla~aTML~aSGlwQvAEyaTmA~R----hGv~~t~kef~ 1009 (1337)
T PHA02006        938 ----TDKVQELTGQLRGVFGDFTGNVPREHQLGPVAQRASGLTSATMLGFSGVYQLAELATMAHR----QGVFNVMKAML 1009 (1337)
T ss_pred             ----HHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH
T ss_conf             ----1669999998754530034899962303647787665666667743118999999999987----40899999999


Q ss_pred             HHC----------CCHHHHHHHHHHHHHHHHHHHH--HHHHHCCCCCC-HHHHHHHHH--------HHHHHCCHHHHHHH
Q ss_conf             413----------8054999999966799899999--99740266640-367999989--------99885243788865
Q gi|254781202|r  430 NKM----------PLKERMELLSDVGLYAEGVVAH--GRNMMEGSDAF-QIGHKLHSK--------MHKWSGAEYLDKKR  488 (864)
Q Consensus       430 ~~~----------~~~d~~~~a~~lGl~~E~~~~~--~~r~~~~~~~~-~~~~~~a~~--------~~r~SgL~~wT~~~  488 (864)
                      +..          ++....|+-.-+||-   +.-.  +-.|....+.. .....+.+.        +--+|||..+-.-.
T Consensus      1010 ~~fpG~v~g~~RrnPDLaDEl~tVlGLd---LArDVR~rPWkRQ~dafL~S~DT~~DR~LhaGkQAvP~LNgMKFIH~hQ 1086 (1337)
T PHA02006       1010 NSRMGDFVGAMRRNPDLADEMQTVLGLN---LANDIRMKPWKRQFDTFLASQDTFMDRFLHAGKQAVPVLNGMKFIHNWQ 1086 (1337)
T ss_pred             HHCCHHHHHHHHCCCCHHHHHHHHHHHH---HHHHHCCCHHHHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf             9684678777643962788999886111---4433106758887765532006899999970553532111236777667


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHCCCHHHHH
Q ss_conf             76769999999999997630021147732010678998617898899999841211135666410052332014457754
Q gi|254781202|r  489 ISSHALIVYNQIGRMTDTYASLKDLKADPRLDPSIKAFFKQLDDTDFTVIKRAKAMSSPDGYLYARTPSTIKNLKDADLR  568 (864)
Q Consensus       489 k~a~~~~~~~~la~l~~~~~~l~~~k~~d~l~~~~~~~l~GI~e~dW~i~r~a~~~~~~~~~~~~~t~~~i~~~~da~i~  568 (864)
                      .+.++...++.+++..         +...+....++.  +| .+.||.-++++     ..++.++..       .++.- 
T Consensus      1087 sRmNANLtlNk~aRAA---------qGD~kAL~~lr~--Yg-~D~dW~~~~~a-----V~~nvty~G-------kNaqs- 1141 (1337)
T PHA02006       1087 SRMNANLTLNKVARAA---------QGDEAALRVLQQ--YG-KDVDWTPVLAR-----VRGYVTYRG-------RNAQS- 1141 (1337)
T ss_pred             HHHCCCHHHHHHHHHH---------CCCHHHHHHHHH--HC-CCCCHHHHHHH-----HCCCCEECC-------CCCCC-
T ss_conf             6521320188888774---------266999999998--67-85245999998-----602506635-------65322-


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHC
Q ss_conf             43100022333320001123457024566666554211457788656889999999998653011114566543221000
Q gi|254781202|r  569 DLARMSDKIAYHRKKLKNSKTLSPEQRQELQQQLADLERKEINILKDKVSNKMHALVLDNVQTSVRGAMHTSLFDRQRLG  648 (864)
Q Consensus       569 ~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~kd~~~~~l~~~il~~~~~aV~~av~tp~~r~r~~~  648 (864)
                                      -||..+.|+.                      | ...+..-+.+++-+..+        .|   
T Consensus      1142 ----------------mNW~~W~q~d----------------------V-d~vmN~alRiMDDsiLY--------GR--- 1171 (1337)
T PHA02006       1142 ----------------MNWGAWSQAD----------------------V-NTVMNTALRIMDDSLLY--------GR--- 1171 (1337)
T ss_pred             ----------------CCCCCCCHHH----------------------H-HHHHHHHHHHHHHHHHC--------CC---
T ss_conf             ----------------6767799788----------------------8-89999988873100301--------24---


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             24557875567899999877642999999999998742-24331134567789999999999999999999996389999
Q gi|254781202|r  649 LLTYKRGTRAGEALRMFQQFTTTPTGMFLNILDLSNSA-KMPKGASMALNHVWIQYSATMALAGIGVASIKALLRGEDPS  727 (864)
Q Consensus       649 ~~g~~~gT~~GE~~r~~~qFKsFp~a~~~~~~~r~~~~-~~~~~~~~~~~~~~a~~~~~~t~~G~~~~q~k~~l~Grdp~  727 (864)
                       .|.-.+----.+...+.||.|| +++-++-+.|+..+ .++.|        +|.+++..--|-++.+..|+..+|+--.
T Consensus      1172 -~GQgssFaRSqvGQILGQFRSF-VsFAhNKLLRGT~~nsG~~G--------lAsLlAfQYPlT~lMv~anearkG~~d~ 1241 (1337)
T PHA02006       1172 -VGQNSGFARSPVGQILGQFRSF-VAFAHNKLLRGTYENSGVLG--------VASLLAFQYPLTALMMGAKAAINGKFDT 1241 (1337)
T ss_pred             -CCCCCCCCHHHHHHHHHHHHHH-HHHHHHHHHHCCHHCCCHHH--------HHHHHHHHCCHHHHHHHHHHHHCCCCCC
T ss_conf             -5788752030688999999999-99874077742010367024--------9999975322899999889986587632


Q ss_pred             C----HHHHHHHHHHHCCHHHHHHHH--HCCCCCCCHHHHHHHCCHHHHHHHHHHHHHHH---HHCCCC-CCCHHHHHHH
Q ss_conf             2----799999998505306778876--05778630357777404015558899999986---402676-5422589999
Q gi|254781202|r  728 L----PEVIYDGTLANGALLPYMDRL--TKLVSKGDRAAIGGLLGPVPSMVTNLTSSAVE---LATKDN-ENSKVNATKA  797 (864)
Q Consensus       728 ~----~~~~~~a~~~gGg~gi~gd~l--~~~~~r~g~~~~~~~~GP~~~~~~~~~~~~~~---~~~g~~-~~~~~~~~~~  797 (864)
                      .    .+.-..++=.-.|+|+.||.-  .+++++        +.-|++|++.---++.-+   .+.|++ ...-+|.+..
T Consensus      1242 Se~Gi~kmA~~aIGYTAglGF~gD~~GiV~G~~~--------mSAPV~GLA~~~~~i~~G~~~L~~G~~ps~A~~D~~~~ 1313 (1337)
T PHA02006       1242 SDEGIRKMAIDGIGYTAGLGFTADMWGVVTGHSR--------MSAPVFGLAEHSNEVFRGVKDLVTGDDPAAATGDIVSG 1313 (1337)
T ss_pred             CHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCC--------CCCCCCCHHCCCCCHHHCCCHHCCCCCHHHHHHHHHHH
T ss_conf             0677999988640300002420322200147787--------67643002118960541534010688847788899985


Q ss_pred             HHHCCCCCCHHHH-HHHH
Q ss_conf             9731877448999-9999
Q gi|254781202|r  798 IRKTLPFMNMWYL-KNSF  814 (864)
Q Consensus       798 ~~~~~P~~nLwy~-k~a~  814 (864)
                      ++.-+||.|.+-. +++.
T Consensus      1314 A~~ALPFV~V~P~T~LL~ 1331 (1337)
T PHA02006       1314 AAGALPFVNVFPATKLLL 1331 (1337)
T ss_pred             HCCCCCCCCCCCCHHHHH
T ss_conf             402486234463089999


No 4  
>PRK06922 hypothetical protein; Provisional
Probab=86.64  E-value=0.64  Score=24.63  Aligned_cols=17  Identities=6%  Similarity=0.004  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHHHHHCCC
Q ss_conf             99999999999861110
Q gi|254781202|r  324 SFVKQMIVQTIANDQEA  340 (864)
Q Consensus       324 ~~f~~l~~~~~~~~~~~  340 (864)
                      ..|..|+++.+-+.++.
T Consensus       289 IsFepLM~~lyyd~kG~  305 (679)
T PRK06922        289 IHFEKLMQQLHYDFKGE  305 (679)
T ss_pred             EEHHHHHHHHHHHHCCC
T ss_conf             21277899877863586


No 5  
>COG2766 PrkA Putative Ser protein kinase [Signal transduction mechanisms]
Probab=56.86  E-value=10  Score=15.44  Aligned_cols=42  Identities=12%  Similarity=0.175  Sum_probs=17.6

Q ss_pred             HHHHCCCCCCHHHHHHHHH-HHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             9973187744899999999-99999999870812479999999
Q gi|254781202|r  797 AIRKTLPFMNMWYLKNSFD-HLILNQILEELNPGYLDRQQSKK  838 (864)
Q Consensus       797 ~~~~~~P~~nLwy~k~a~d-~li~~~~~e~~~Pgy~~r~~~r~  838 (864)
                      -++.++|+...--+.-.=+ .-.-+-++.|+.-||.++--+..
T Consensus       596 dvkdl~pv~s~~~~~D~~e~kk~nd~V~rlverGYt~~~ar~l  638 (649)
T COG2766         596 DVKDLLPVISFTAKADPDEQKKHNDFVARLVERGYTRKQARLL  638 (649)
T ss_pred             HHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             6765122247655688068888999999999857668899999


No 6  
>KOG0994 consensus
Probab=55.26  E-value=11  Score=15.25  Aligned_cols=17  Identities=12%  Similarity=0.333  Sum_probs=6.9

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             14889989999999997
Q gi|254781202|r  352 GRNKLEVRQEAMLQMWE  368 (864)
Q Consensus       352 ~~~~~~~~~~~~~~~~~  368 (864)
                      ...+++...+.+..+..
T Consensus      1462 s~~q~~~s~~el~~Li~ 1478 (1758)
T KOG0994        1462 SRSQMEESNRELRNLIQ 1478 (1758)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             89988889999999999


No 7  
>TIGR02288 PaaN_2 phenylacetic acid degradation protein paaN; InterPro: IPR011975    This enzyme is proposed to act in the ring-opening step of phenylacetic acid degradation  which follows ligation of the acid with coenzyme A (by PaaF) and hydroxylation by a multicomponent non-heme iron hydroxylase complex (PaaGHIJK). Gene symbols have been standardized in . This enzyme is related to aldehyde dehydrogenase family. This family includes sequences from Burkholderia, Bordetella, Streptomyces. Other PaaN enzymes are represented by a separate entry, IPR011966 from INTERPRO..
Probab=55.07  E-value=7.9  Score=16.31  Aligned_cols=70  Identities=19%  Similarity=0.108  Sum_probs=52.3

Q ss_pred             HHHHHHHHHHHHHHHHHHC-----CCCC---------------CHHHHHHHHHHHHHHHHHHHHHHHCCCC---------
Q ss_conf             4565418889999999848-----8889---------------9899999999999999999999861798---------
Q gi|254781202|r  138 LGFTLDKQFGLDVFDEMKG-----KKTQ---------------NEQASRLVKQYFETQRELHSQAHEAGLD---------  188 (864)
Q Consensus       138 ~~~~~dka~~~~~~~e~~g-----~~tg---------------n~~a~~~A~~~~~~~e~~r~~~N~aG~~---------  188 (864)
                      ||...++.-.+.|+.....     .+-|               |+..-+||++|.-++-..=...-+|||.         
T Consensus        82 LGv~YP~~d~~~L~~a~~~Al~~Wr~aGA~~R~GvcLEILqRLn~rs~e~AhAVmhTtGQAFMMAFQAGGpHAQDRGlEA  161 (560)
T TIGR02288        82 LGVTYPQVDLDALLEAARKALPGWRDAGARARVGVCLEILQRLNARSFELAHAVMHTTGQAFMMAFQAGGPHAQDRGLEA  161 (560)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHH
T ss_conf             46217765668899999852266661062002014288999987532999988841123578988764786511323689


Q ss_pred             ----------CHHHCCCC-CC-CCCHHHHHH
Q ss_conf             ----------40026814-54-168799951
Q gi|254781202|r  189 ----------YKFFENRI-PQ-PMSVDKLRA  207 (864)
Q Consensus       189 ----------Igkl~~~~-pq-~hd~~~i~~  207 (864)
                                |+.---|. || .||+.++.|
T Consensus       162 vAYAy~em~~iP~~A~W~KPQGK~DPL~l~K  192 (560)
T TIGR02288       162 VAYAYREMSRIPETAVWEKPQGKRDPLKLEK  192 (560)
T ss_pred             HHHHHHHHHCCCCCEEECCCCCCCCCCCCCC
T ss_conf             9999999632777646307754247544545


No 8  
>COG4709 Predicted membrane protein [Function unknown]
Probab=48.35  E-value=14  Score=14.49  Aligned_cols=13  Identities=15%  Similarity=0.279  Sum_probs=5.0

Q ss_pred             HHHHHHHCCHHHH
Q ss_conf             9999850530677
Q gi|254781202|r  733 YDGTLANGALLPY  745 (864)
Q Consensus       733 ~~a~~~gGg~gi~  745 (864)
                      +.+.+-+|..+.+
T Consensus       125 ~~agil~g~~~~~  137 (195)
T COG4709         125 VAAGILGGVILGV  137 (195)
T ss_pred             HHHHHHCCCCHHH
T ss_conf             9988841542027


No 9  
>pfam06543 Lac_bphage_repr Lactococcus bacteriophage repressor. This family represents the C-terminus of Lactococcus bacteriophage repressor proteins.
Probab=48.22  E-value=14  Score=14.47  Aligned_cols=29  Identities=24%  Similarity=0.523  Sum_probs=21.7

Q ss_pred             HHHHHHHHCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             752087511756884898999999887632
Q gi|254781202|r  219 DWLDLSRYKDIDGTPLSRSEIASFVGEVFA  248 (864)
Q Consensus       219 ~~lD~~~~~~~~G~~~~~~~~~~~L~~vy~  248 (864)
                      +++|+++.|.-+|+|.+| ++.+++..+|-
T Consensus        16 ~kvdWd~WVSFdG~PlsD-eVK~amk~i~g   44 (49)
T pfam06543        16 NKVDWDEWVSFDGRPLSD-EVKEAMKKILG   44 (49)
T ss_pred             CCCCHHHHEECCCCCCCH-HHHHHHHHHHH
T ss_conf             656747731018933748-99999999961


No 10 
>pfam04459 DUF512 Protein of unknown function (DUF512). Family of uncharacterized prokaryotic proteins.
Probab=46.52  E-value=15  Score=14.29  Aligned_cols=58  Identities=22%  Similarity=0.168  Sum_probs=46.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHH------------HCCCCCHHHCCC--CCCCCCHHHHHHCCHHHHHHHHH
Q ss_conf             98999999999999999999998------------617984002681--45416879995136898999999
Q gi|254781202|r  161 NEQASRLVKQYFETQRELHSQAH------------EAGLDYKFFENR--IPQPMSVDKLRATKKDDFVRSML  218 (864)
Q Consensus       161 n~~a~~~A~~~~~~~e~~r~~~N------------~aG~~Igkl~~~--~pq~hd~~~i~~a~~~~W~~~i~  218 (864)
                      -..|++.-+.+.++|+..+++++            -||-.++..+.|  +||.-|-.-+.+.=.++|.+.+-
T Consensus        20 ~~~A~~vi~~ve~~q~~~~~~~g~~fv~~sDEfYllAg~p~P~~~~Y~~~pq~enGVGm~r~f~~e~~~~l~   91 (205)
T pfam04459        20 PEEAREVIDQVEPLQREFQKELGSRFVWLSDEFYLIAGTPLPDAEFYEDFPQIENGVGMIRLFLDEFLEALP   91 (205)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCEEEECHHHHHHCCCCCCCHHHHCCCHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             999999999999999999997099648765388986389999857718850442450279999999999987


No 11 
>pfam07580 Peptidase_M26_C M26 IgA1-specific Metallo-endopeptidase C-terminal region. These peptidases, which cleave mammalian IgA, are found in Gram-positive bacteria. Often found associated with pfam00746, they may be attached to the cell wall.
Probab=44.03  E-value=15  Score=14.30  Aligned_cols=21  Identities=29%  Similarity=0.189  Sum_probs=16.6

Q ss_pred             CHHHHHHHHHHHHHHHHHCCC
Q ss_conf             401555889999998640267
Q gi|254781202|r  766 GPVPSMVTNLTSSAVELATKD  786 (864)
Q Consensus       766 GP~~~~~~~~~~~~~~~~~g~  786 (864)
                      |-+++..+++-.|.-.++..+
T Consensus       673 ~~ti~s~~eLq~L~~~AV~kD  693 (731)
T pfam07580       673 GKTISSYEELQNLFDEAVEKD  693 (731)
T ss_pred             CEEECCHHHHHHHHHHHHHHH
T ss_conf             716616999999999999987


No 12 
>TIGR00963 secA preprotein translocase, SecA subunit; InterPro: IPR000185   Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component. . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.     The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB  is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion .   SecA is a cytoplasmic protein of 800 to 960 amino acid residues. Homologs of secA are also encoded in the chloroplast genome of some algae  as well as in the nuclear genome of plants . It could be involved in the intraorganellar protein transport into thylakoids.; GO: 0005524 ATP binding, 0006605 protein targeting, 0006886 intracellular protein transport.
Probab=41.69  E-value=17  Score=13.76  Aligned_cols=81  Identities=16%  Similarity=0.208  Sum_probs=45.6

Q ss_pred             CEE-EEECCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHH-----HHHHHHHHHHHHHHCCCCCCHHH
Q ss_conf             617-884096789999996088776899999888744556779998579968-----99999999999861110000012
Q gi|254781202|r  273 ERV-FHFKDSQAHMDYMEHFGVSTNVNTILTSELASLSKDIVIARELGPNAD-----SFVKQMIVQTIANDQEASAGNKV  346 (864)
Q Consensus       273 ~R~-LhFKDa~sw~~Y~~~fG~~~~~~~~m~~hi~~msrDIalm~~lGpNP~-----~~f~~l~~~~~~~~~~~~~~~~~  346 (864)
                      +|| |-|-|     +.++.||+ +.+    .          .||+.||..++     .++...+..++++..+ ......
T Consensus       659 SrFfLSleD-----~LmR~Fg~-drl----~----------~~m~~lg~~dd~Pies~~v~r~le~AQKrVE~-~Nfd~R  717 (904)
T TIGR00963       659 SRFFLSLED-----NLMRIFGG-DRL----K----------GLMRRLGLEDDEPIESKMVTRALESAQKRVEA-RNFDIR  717 (904)
T ss_pred             CCEEECHHH-----HHHHHCCC-HHH----H----------HHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHH-HHHHHH
T ss_conf             311200101-----47765187-789----9----------99986388888966526788999998889863-000343


Q ss_pred             HHCCCHHHHHHHHHHHHHHHHH-HHCCCC
Q ss_conf             2000014889989999999997-625787
Q gi|254781202|r  347 LKDWLGRNKLEVRQEAMLQMWE-VMRYGE  374 (864)
Q Consensus       347 ~~~~~~~~~~~~~~~~~~~~~~-~~~g~~  374 (864)
                      ++-.-+-.-+++|++.+..-.+ ++...+
T Consensus       718 K~lleYDdVlN~QR~~IY~eR~~~L~~~~  746 (904)
T TIGR00963       718 KQLLEYDDVLNKQREVIYAERRRVLESED  746 (904)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             11312679999988999999998731444


No 13 
>KOG2099 consensus
Probab=37.24  E-value=20  Score=13.28  Aligned_cols=25  Identities=16%  Similarity=0.142  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             7788656889999999998653011
Q gi|254781202|r  609 EINILKDKVSNKMHALVLDNVQTSV  633 (864)
Q Consensus       609 ~~~~~kd~~~~~l~~~il~~~~~aV  633 (864)
                      ..+.+|.+-.-++..++-++....+
T Consensus       535 ~~a~vK~~NKlk~a~~le~e~~v~i  559 (843)
T KOG2099         535 EWAKVKQENKLKLAAYLEKEYGVKI  559 (843)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             9999988637899999989739623


No 14 
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302; InterPro: IPR012683    Members of this family are bacterial proteins from the alphaproteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted to be outside the membrane. Bradyrhizobium japonicum contains two tandem copies that are, together, homologous to the single members found in other species. .
Probab=36.74  E-value=20  Score=13.22  Aligned_cols=29  Identities=14%  Similarity=0.091  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCHHHH
Q ss_conf             999999999976300211477320106789
Q gi|254781202|r  495 IVYNQIGRMTDTYASLKDLKADPRLDPSIK  524 (864)
Q Consensus       495 ~~~~~la~l~~~~~~l~~~k~~d~l~~~~~  524 (864)
                      .-|+.||+|+++.=.+-+ ++|+.-...-+
T Consensus       658 qqmnkLGel~r~QQql~d-eTfkldQ~~rr  686 (899)
T TIGR02302       658 QQMNKLGELMRKQQQLVD-ETFKLDQDLRR  686 (899)
T ss_pred             HHHHHHHHHHHHHHHHHH-HHHHCCHHHHH
T ss_conf             999888899999988865-56620379998


No 15 
>PRK04531 acetylglutamate kinase; Provisional
Probab=34.87  E-value=22  Score=13.01  Aligned_cols=36  Identities=25%  Similarity=0.387  Sum_probs=27.1

Q ss_pred             CCEEEEECCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHH
Q ss_conf             7617884096789999996088776899999888744556779998579968
Q gi|254781202|r  272 FERVFHFKDSQAHMDYMEHFGVSTNVNTILTSELASLSKDIVIARELGPNAD  323 (864)
Q Consensus       272 ~~R~LhFKDa~sw~~Y~~~fG~~~~~~~~m~~hi~~msrDIalm~~lGpNP~  323 (864)
                      +.||-.+|           +|  +   .+|..++++.++||++++.+|=+|=
T Consensus        19 ~~~fAVIK-----------vG--G---avi~e~l~~la~dLafL~~vGl~PV   54 (421)
T PRK04531         19 PERFAVIK-----------VG--G---AVLREDLEALTSSLKFLQEVGLTPV   54 (421)
T ss_pred             CCEEEEEE-----------EC--H---HHHHHHHHHHHHHHHHHHHCCCEEE
T ss_conf             76189999-----------88--7---9999799999999999998799799


No 16 
>pfam01054 MMTV_SAg Mouse mammary tumour virus superantigen. The mouse mammary tumour virus (MMTV) is a milk-transmitted type B retrovirus. The superantigen (SAg) is encoded by the long terminal repeat. The SAgs are also called PR73.
Probab=33.91  E-value=11  Score=15.35  Aligned_cols=25  Identities=12%  Similarity=0.173  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6789999987764299999999999
Q gi|254781202|r  658 AGEALRMFQQFTTTPTGMFLNILDL  682 (864)
Q Consensus       658 ~GE~~r~~~qFKsFp~a~~~~~~~r  682 (864)
                      .|-+.-.+.--.|.||+.+++++.|
T Consensus       136 igrllitmlrnesl~fstiftqiq~  160 (314)
T pfam01054       136 IGRLLITMLRNESLPFSTIFTQIQR  160 (314)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             8999999985367665899999999


No 17 
>COG0082 AroC Chorismate synthase [Amino acid transport and metabolism]
Probab=31.09  E-value=7.7  Score=16.40  Aligned_cols=97  Identities=16%  Similarity=0.159  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCCC-CHHHHHHHHHHHHHHHHCCC------CCCCCCCC-HHHHHHCCCCCEEEEECCHHHHH
Q ss_conf             999997520875117568848-98999999887632331177------65668752-13543114576178840967899
Q gi|254781202|r  214 VRSMLDWLDLSRYKDIDGTPL-SRSEIASFVGEVFAERVRST------SFKDPSIP-SSEVGVKREFERVFHFKDSQAHM  285 (864)
Q Consensus       214 ~~~i~~~lD~~~~~~~~G~~~-~~~~~~~~L~~vy~~i~t~g------~~~~~~~~-~~~~~~~~~~~R~LhFKDa~sw~  285 (864)
                      .++|.+.||+++-=..-+..+ .+.+.-++|+.|++..+|+.      +|++..-. -..+..        .|+-+-+=+
T Consensus        37 ~edIq~eL~RRrpG~~r~~t~R~E~D~veIlSGv~~G~TtGtPI~l~I~N~d~~s~~y~~~~~--------~pRPGHADy  108 (369)
T COG0082          37 EEDIQKELDRRRPGYSRGTTMRKEKDEVEILSGVFEGKTTGTPIALLIENTDQRSKDYSMIKD--------PPRPGHADY  108 (369)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCCCCCCHHHCCC--------CCCCCCCCC
T ss_conf             999999997447998887554567861488001555750788559999727777621443046--------899984131


Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHH
Q ss_conf             99996088776899999888744556779998579968
Q gi|254781202|r  286 DYMEHFGVSTNVNTILTSELASLSKDIVIARELGPNAD  323 (864)
Q Consensus       286 ~Y~~~fG~~~~~~~~m~~hi~~msrDIalm~~lGpNP~  323 (864)
                      .|..|||. .+    +.+..++.+|+++..=.-|.-.+
T Consensus       109 ty~~KYg~-rD----~RgggRsSaReTa~rVAaGAvAK  141 (369)
T COG0082         109 TYGIKYGF-RD----YRGGGRSSARETAARVAAGAVAK  141 (369)
T ss_pred             HHHHHCCC-CC----CCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             01544286-45----67765204677899999899999


No 18 
>pfam08822 DUF1804 Protein of unknown function (DUF1804). This family of bacterial protein is uncharacterized.
Probab=30.97  E-value=25  Score=12.56  Aligned_cols=58  Identities=17%  Similarity=0.292  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             88999998412111356664100523320144577544310002233332000112345702456666655
Q gi|254781202|r  532 DTDFTVIKRAKAMSSPDGYLYARTPSTIKNLKDADLRDLARMSDKIAYHRKKLKNSKTLSPEQRQELQQQL  602 (864)
Q Consensus       532 e~dW~i~r~a~~~~~~~~~~~~~t~~~i~~~~da~i~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~  602 (864)
                      -+||++.|.+..+..+          +|.++.-..+.++-   -+.+..+..+.....++|..+.++-..+
T Consensus        47 GDDWDkaRaA~~magg----------g~edvar~~l~~f~---~Q~~~tmeeL~~~~~l~~~~Kv~lLAsL  104 (165)
T pfam08822        47 GDDWDKARAAYTLAGG----------GIEDLARQMLTGFV---VQYQATMDELQEDEDLPPSDKAKLLASL  104 (165)
T ss_pred             CCCHHHHHHHHHHHCC----------CHHHHHHHHHHHHH---HHHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             8838999999998568----------78899999999999---9999999998725569988999999999


No 19 
>KOG0624 consensus
Probab=30.82  E-value=16  Score=13.94  Aligned_cols=38  Identities=21%  Similarity=0.203  Sum_probs=22.8

Q ss_pred             HHHHHCCCCCCCHHHHHHHHHHHCCHHHHHHHH-HCCCCCCCHH
Q ss_conf             999963899992799999998505306778876-0577863035
Q gi|254781202|r  717 IKALLRGEDPSLPEVIYDGTLANGALLPYMDRL-TKLVSKGDRA  759 (864)
Q Consensus       717 ~k~~l~Grdp~~~~~~~~a~~~gGg~gi~gd~l-~~~~~r~g~~  759 (864)
                      -+++-+|.||-+|+     ..||||.|.|--|- +.+.+.||++
T Consensus       456 RrqFDnGeDPLD~E-----s~q~GGGg~~Hgf~n~hgF~~F~~G  494 (504)
T KOG0624         456 RRQFDNGEDPLDPE-----SQQGGGGGPFHGFWNEHGFNPFGGG  494 (504)
T ss_pred             HHHCCCCCCCCCHH-----HCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             74122799999856-----5158999987788655688887899


No 20 
>KOG1011 consensus
Probab=30.08  E-value=25  Score=12.46  Aligned_cols=10  Identities=20%  Similarity=0.365  Sum_probs=5.2

Q ss_pred             CHHHHHHHHH
Q ss_conf             9678999999
Q gi|254781202|r  280 DSQAHMDYME  289 (864)
Q Consensus       280 Da~sw~~Y~~  289 (864)
                      --|+|--|-+
T Consensus       462 gddawkvyfd  471 (1283)
T KOG1011         462 GDDAWKVYFD  471 (1283)
T ss_pred             CCCCCEEHHH
T ss_conf             7741100364


No 21 
>TIGR01021 rpsE_bact ribosomal protein S5; InterPro: IPR005712   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   This family includes chloroplast ribosomal protein S5 as well as bacterial ribosomal protein S5. A candidate mitochondrial form (Saccharomyces cerevisiae YBR251W and its homolog) differs substantially and is not included in this model.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=28.46  E-value=21  Score=13.07  Aligned_cols=36  Identities=33%  Similarity=0.495  Sum_probs=24.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHH
Q ss_conf             6899999888744556779998579-968999999999998
Q gi|254781202|r  296 NVNTILTSELASLSKDIVIARELGP-NADSFVKQMIVQTIA  335 (864)
Q Consensus       296 ~~~~~m~~hi~~msrDIalm~~lGp-NP~~~f~~l~~~~~~  335 (864)
                      +++.||-  +=+ -.|| |-+.||+ ||.++.+.-++....
T Consensus       104 a~RavlE--~AG-v~DI-laK~LGSnNP~N~vrAt~~AL~~  140 (157)
T TIGR01021       104 AVRAVLE--LAG-VKDI-LAKSLGSNNPINVVRATFDALLK  140 (157)
T ss_pred             CHHHHHH--HCC-CCEE-EEEECCCCCHHHHHHHHHHHHHH
T ss_conf             4578877--538-4125-66515687746899999999972


No 22 
>pfam05379 Peptidase_C23 Carlavirus endopeptidase. A peptidase involved in auto-proteolysis of a polyprotein from the plant pathogen blueberry scorch carlavirus (BBScV). Corresponds to Merops family C23.
Probab=27.51  E-value=24  Score=12.58  Aligned_cols=16  Identities=25%  Similarity=0.443  Sum_probs=9.9

Q ss_pred             CHHHHH-HHHHHHCCCC
Q ss_conf             158999-9998745787
Q gi|254781202|r    2 KPECIQ-VLNKAAGREL   17 (864)
Q Consensus         2 k~~Ci~-~V~~algr~l   17 (864)
                      |+.|+. ||+++++|..
T Consensus         2 kN~CvI~AiA~aL~R~~   18 (89)
T pfam05379         2 KNGCVIRAIAQALKRRP   18 (89)
T ss_pred             CCCCHHHHHHHHHCCCH
T ss_conf             86306899999849999


No 23 
>CHL00073 chlN photochlorophyllide reductase subunit N
Probab=26.68  E-value=27  Score=12.30  Aligned_cols=26  Identities=19%  Similarity=-0.078  Sum_probs=12.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6753899999989999999987522456641
Q gi|254781202|r  375 TVENTGWANWMAGLRSAAGASMLGQHPIGAL  405 (864)
Q Consensus       375 ~p~n~~~a~~~a~lR~~~~~akLGgA~ISA~  405 (864)
                      .++||++++....|     +..=|.-.|+|.
T Consensus       243 ~l~QPFLs~TA~aL-----~rrRgaklI~AP  268 (457)
T CHL00073        243 CGVNPFLSRTATTL-----MRRRKCKLIGAP  268 (457)
T ss_pred             EEECCCHHHHHHHH-----HHHCCCEECCCC
T ss_conf             98168668999999-----984397276799


No 24 
>TIGR02094 more_P_ylases alpha-glucan phosphorylases; InterPro: IPR011834    This family consists of known phosphorylases, and homologues believed to share the function of using inorganic phosphate to cleave an alpha 1,4 linkage between the terminal glucose residue and the rest of the polymer (maltodextrin, glycogen, etc.). The name of the glucose storage polymer substrate, and therefore the name of this enzyme, depends on the chain lengths and branching patterns. A number of the members of this family have been shown to operate on small maltodextrins, as may be obtained by utilization of exogenous sources. This family represents a distinct clade from the related families: Glycogen/starch/alpha-glucan phosphorylase and Glycosyl transferase, family 35.; GO: 0004645 phosphorylase activity, 0030170 pyridoxal phosphate binding, 0005975 carbohydrate metabolic process.
Probab=26.61  E-value=21  Score=13.02  Aligned_cols=25  Identities=16%  Similarity=0.300  Sum_probs=14.9

Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99731877448999999999999999987081
Q gi|254781202|r  797 AIRKTLPFMNMWYLKNSFDHLILNQILEELNP  828 (864)
Q Consensus       797 ~~~~~~P~~nLwy~k~a~d~li~~~~~e~~~P  828 (864)
                      .++.+.|.=|       .+|||-++++.+=.|
T Consensus       594 SI~~~~P~F~-------~~RMv~eY~~~~Y~p  618 (618)
T TIGR02094       594 SIKTIAPRFS-------TDRMVREYVQKFYLP  618 (618)
T ss_pred             HHHHHCCCCC-------CCHHHHHHHHHHCCC
T ss_conf             9987131138-------410589998862689


No 25 
>pfam11981 DUF3482 Domain of unknown function (DUF3482). This presumed domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes. This domain is typically between 289 to 301 amino acids in length. This domain is found associated with pfam01926.
Probab=25.72  E-value=30  Score=11.91  Aligned_cols=40  Identities=18%  Similarity=0.121  Sum_probs=17.6

Q ss_pred             HHHHHCCCCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             8876057786303577774040155588999999864026
Q gi|254781202|r  746 MDRLTKLVSKGDRAAIGGLLGPVPSMVTNLTSSAVELATK  785 (864)
Q Consensus       746 gd~l~~~~~r~g~~~~~~~~GP~~~~~~~~~~~~~~~~~g  785 (864)
                      -|.+.++.|=....+++.++|-+.+...-..+-..+.+.|
T Consensus       163 iDL~~gG~SLG~gaaiGal~Gg~~~~~~~y~~~i~gk~~g  202 (293)
T pfam11981       163 IDLAVGGLTLGAAAALGALAGGGWQTARRYGDRILGKLKG  202 (293)
T ss_pred             HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9998500205899999999874587666778988764058


No 26 
>TIGR02213 lolE_release lipoprotein releasing system, transmembrane protein LolE; InterPro: IPR011926    This protein is part of an unusual ABC transporter complex that releases lipoproteins from the periplasmic side of the bacterial inner membrane, rather than transport any substrate across the inner membrane. In some species, the permease-like transmembrane protein is represented by two paralogs, LolC and LolE, both in the LolCDE complex. This family consists of LolE, as found in Escherichia coli and related species.; GO: 0006810 transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=24.69  E-value=22  Score=12.98  Aligned_cols=114  Identities=23%  Similarity=0.311  Sum_probs=60.5

Q ss_pred             CC----CCCCCCHHHHHHCCHHHH-HHHH---HHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHH
Q ss_conf             81----454168799951368989-9999---975208751175688489899999988763233117765668752135
Q gi|254781202|r  194 NR----IPQPMSVDKLRATKKDDF-VRSM---LDWLDLSRYKDIDGTPLSRSEIASFVGEVFAERVRSTSFKDPSIPSSE  265 (864)
Q Consensus       194 ~~----~pq~hd~~~i~~a~~~~W-~~~i---~~~lD~~~~~~~~G~~~~~~~~~~~L~~vy~~i~t~g~~~~~~~~~~~  265 (864)
                      ||    |||+-...|+..=.++-- +.-|   -+=||++--    =.|+.|+.  .+|.-=- .-+||-..|...++...
T Consensus       165 DwvtllIpq~n~~~k~~qPkRvrv~VtgiL~L~GQlDhs~a----llPlAdAQ--~yl~~gP-~~vtGiaLK~~DvfnA~  237 (416)
T TIGR02213       165 DWVTLLIPQSNEDEKLAQPKRVRVKVTGILRLDGQLDHSYA----LLPLADAQ--QYLDLGP-DSVTGIALKLDDVFNAR  237 (416)
T ss_pred             CEEEEEECCCCCCCCCCCCCCEEEEEEEEEEECCCHHHHHH----HHHHHHHH--HHHHCCC-CCEEEEEEECCCCHHHH
T ss_conf             57999710789743235883003788778753661226678----71278765--5765489-83014764247802278


Q ss_pred             HH-H--CCCCCEEEEECCHHHHHHHHHHHCC--CC---------------------C-HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             43-1--1457617884096789999996088--77---------------------6-8999998887445567799985
Q gi|254781202|r  266 VG-V--KREFERVFHFKDSQAHMDYMEHFGV--ST---------------------N-VNTILTSELASLSKDIVIAREL  318 (864)
Q Consensus       266 ~~-~--~~~~~R~LhFKDa~sw~~Y~~~fG~--~~---------------------~-~~~~m~~hi~~msrDIalm~~l  318 (864)
                      .- .  .+.-.-.++.|+      -+.+||=  .|                     | +-|.||. +..=+-|||.||||
T Consensus       238 ~lvr~~g~~~~~yvY~~s------Wi~~fGymYRDIQliRtiMYlaMVLVIGVACFNIVSTL~MA-VKDk~gdIAilRTl  310 (416)
T TIGR02213       238 KLVREVGEDIDSYVYLKS------WISKFGYMYRDIQLIRTIMYLAMVLVIGVACFNIVSTLVMA-VKDKAGDIAILRTL  310 (416)
T ss_pred             HHHHHHHCCCCCEEEEEE------HHHCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-EECCCCCEEHHHHC
T ss_conf             998987303563477630------13006820036999999999988888655556467664531-00477653021012


Q ss_pred             CCC
Q ss_conf             799
Q gi|254781202|r  319 GPN  321 (864)
Q Consensus       319 GpN  321 (864)
                      |.|
T Consensus       311 GA~  313 (416)
T TIGR02213       311 GAK  313 (416)
T ss_pred             CCC
T ss_conf             657


No 27 
>TIGR02791 VirB5 P-type DNA transfer protein VirB5; InterPro: IPR014158   This entry contains VirB5, a protein that is involved in the type IV DNA secretion systems typified by the Agrobacterium Ti plasmid vir system where it interacts with several other proteins essential for proper pilus formation . VirB5 is homologous to the IncN (N-type) conjugation system protein TraC  as well as the P-type protein TrbJ and the F-type protein TraE ..
Probab=24.27  E-value=32  Score=11.72  Aligned_cols=37  Identities=16%  Similarity=0.331  Sum_probs=19.7

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             3320144577544310002233332000112345702456666655
Q gi|254781202|r  557 STIKNLKDADLRDLARMSDKIAYHRKKLKNSKTLSPEQRQELQQQL  602 (864)
Q Consensus       557 ~~i~~~~da~i~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~  602 (864)
                      +.+|.-.+.+|.++..+..++         ....+|..+.|+.-.+
T Consensus       163 e~aYdA~~~R~~~I~~L~~~i---------N~~~DpK~iAdLQ~Ri  199 (233)
T TIGR02791       163 EKAYDAATKRLSNIEQLRQKI---------NEAGDPKAIADLQARI  199 (233)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH---------CCCCCHHHHHHHHHHH
T ss_conf             877678888589999999872---------4899857899998889


No 28 
>TIGR01478 STEVOR variant surface antigen, stevor family; InterPro: IPR006374   Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see .   This entry represents the stevor (short for "subtelomeric variable open reading frame") family of predicted variant surface antigens. This is the third largest variant surface antigen family in P. falciparum, with 33 genes identified in the genome of this parasite . The function of these proteins is not known, but they are expressed during several stages of the parasite life-cycle and may play a variety of roles in parasite survival and infection ..
Probab=23.82  E-value=32  Score=11.66  Aligned_cols=16  Identities=19%  Similarity=0.088  Sum_probs=7.4

Q ss_pred             HHHHHHHHHHHCCCCC
Q ss_conf             9988763233117765
Q gi|254781202|r  241 SFVGEVFAERVRSTSF  256 (864)
Q Consensus       241 ~~L~~vy~~i~t~g~~  256 (864)
                      .-|-+.||.+..+..+
T Consensus       117 KELLe~Yee~fGdEsh  132 (315)
T TIGR01478       117 KELLEKYEEMFGDESH  132 (315)
T ss_pred             HHHHHHHHHHCCCCCC
T ss_conf             8999999885076235


No 29 
>TIGR01264 tyr_amTase_E tyrosine aminotransferase; InterPro: IPR005957   This entry describes tyrosine aminotransferase (2.6.1.5 from EC) as found in animals and Trypanosoma cruzi (Euglenozoa). It is the first enzyme of a pathway of tyrosine degradation via homogentisate.  L-tyrosine + 2-oxoglutarate = 4-hydroxyphenylpyruvate + L-glutamate.; GO: 0004838 tyrosine transaminase activity, 0030170 pyridoxal phosphate binding, 0009072 aromatic amino acid family metabolic process.
Probab=23.00  E-value=33  Score=11.55  Aligned_cols=139  Identities=15%  Similarity=0.209  Sum_probs=85.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH-HCC---C--CCCCCCHH-HHHH--CCHHHHHHHHH---HHHHHHHH
Q ss_conf             899899999999999999999999861798400-268---1--45416879-9951--36898999999---75208751
Q gi|254781202|r  159 TQNEQASRLVKQYFETQRELHSQAHEAGLDYKF-FEN---R--IPQPMSVD-KLRA--TKKDDFVRSML---DWLDLSRY  226 (864)
Q Consensus       159 tgn~~a~~~A~~~~~~~e~~r~~~N~aG~~Igk-l~~---~--~pq~hd~~-~i~~--a~~~~W~~~i~---~~lD~~~~  226 (864)
                      +|=..|.+||          -...=++|-+|.= .+|   |  |.|.|+.. |.=+  -..+.|+-++.   .+.|.++-
T Consensus       110 SGCS~Al~~a----------i~a~Ad~G~nvLVP~PGFplY~Tlc~~~~i~~~~Y~~d~~d~~w~~DL~~l~~LiDd~T~  179 (415)
T TIGR01264       110 SGCSHALEMA----------IEALADAGQNVLVPRPGFPLYETLCKALGIEVKLYNLDLPDEDWEIDLKQLESLIDDKTK  179 (415)
T ss_pred             CCCHHHHHHH----------HHHHCCCCCEEECCCCCCCHHHHHHHHCCCCCCEECCCCCCCHHHHHHHHHHHHCCCCCC
T ss_conf             6702789999----------999537978063078887207886401476200002579873356648988631256740


Q ss_pred             ---C----CCCCCCCCHHHHHHHH------------HHHHHHHHCCC---CCCCCCC----------CHHHHHHCC--CC
Q ss_conf             ---1----7568848989999998------------87632331177---6566875----------213543114--57
Q gi|254781202|r  227 ---K----DIDGTPLSRSEIASFV------------GEVFAERVRST---SFKDPSI----------PSSEVGVKR--EF  272 (864)
Q Consensus       227 ---~----~~~G~~~~~~~~~~~L------------~~vy~~i~t~g---~~~~~~~----------~~~~~~~~~--~~  272 (864)
                         |    |+.|..|+++-+++.|            +|+|...+-.|   -.|..++          .-+++++|-  .+
T Consensus       180 ~l~vnNPSNPcGSvF~~~Hl~~l~a~A~~~~Lpi~ADEIY~~~VF~GkDPnatF~~lA~L~s~VP~~~cgG~AKr~lVPG  259 (415)
T TIGR01264       180 ALIVNNPSNPCGSVFRREHLEELLALAERLKLPIIADEIYGDMVFKGKDPNATFTPLASLSSKVPILSCGGLAKRWLVPG  259 (415)
T ss_pred             EEEEECCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCEEEECCCCCCCCEEEECCCCCCCCCCC
T ss_conf             78883757788988787889999999875387236642025651388678642202023779988687076320022476


Q ss_pred             CEEEEECCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf             61788409678999999608877689999988874455677999857996
Q gi|254781202|r  273 ERVFHFKDSQAHMDYMEHFGVSTNVNTILTSELASLSKDIVIARELGPNA  322 (864)
Q Consensus       273 ~R~LhFKDa~sw~~Y~~~fG~~~~~~~~m~~hi~~msrDIalm~~lGpNP  322 (864)
                      =|.       .|+=|++++|   -+.+-..++|..||     ++++|||.
T Consensus       260 WRL-------GWli~hd~~~---~~~~e~~~GL~~ls-----~~i~Gpnt  294 (415)
T TIGR01264       260 WRL-------GWLIIHDRKG---VLRDEVKDGLKKLS-----QRILGPNT  294 (415)
T ss_pred             CCC-------CCEEEECCCC---CCCHHHHHHHHHHH-----CHHCCCCH
T ss_conf             110-------2478887888---65026889999972-----30046201


No 30 
>pfam03881 Fructosamin_kin Fructosamine kinase. This family includes eukaryotic fructosamine-3-kinase enzymes. The family also includes bacterial members that have not been characterized but probably have a similar or identical function.
Probab=22.61  E-value=34  Score=11.50  Aligned_cols=65  Identities=8%  Similarity=-0.011  Sum_probs=33.1

Q ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
Q ss_conf             56779998579968999999999998611100000122000014889989999999997625787675389999998999
Q gi|254781202|r  310 KDIVIARELGPNADSFVKQMIVQTIANDQEASAGNKVLKDWLGRNKLEVRQEAMLQMWEVMRYGETVENTGWANWMAGLR  389 (864)
Q Consensus       310 rDIalm~~lGpNP~~~f~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~p~n~~~a~~~a~lR  389 (864)
                      -||||++.||+-|+..+..-     .+..        +.....     +.+..+.++|..+...|.=..+-..+....++
T Consensus       221 ~DLAm~~lFggf~~~Fy~~Y-----~~~~--------Pl~~g~-----~~R~~lY~Ly~lL~H~~lFG~~Y~~~~~~~l~  282 (287)
T pfam03881       221 CDLAMTELFGGFPPDFYDGY-----QSVY--------PLDEGY-----EERKPLYQLYHLLNHLNLFGGGYLSQAQQLID  282 (287)
T ss_pred             HHHHHHHHCCCCCHHHHHHH-----HHHC--------CCCCCH-----HHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH
T ss_conf             76787773278759999999-----9727--------998288-----99999999999999999847588999999999


Q ss_pred             HHH
Q ss_conf             999
Q gi|254781202|r  390 SAA  392 (864)
Q Consensus       390 ~~~  392 (864)
                      .++
T Consensus       283 ~ll  285 (287)
T pfam03881       283 KLL  285 (287)
T ss_pred             HHH
T ss_conf             985


No 31 
>KOG4403 consensus
Probab=22.38  E-value=34  Score=11.47  Aligned_cols=34  Identities=9%  Similarity=0.084  Sum_probs=22.8

Q ss_pred             CHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             967899999960887768999998887445567799985799
Q gi|254781202|r  280 DSQAHMDYMEHFGVSTNVNTILTSELASLSKDIVIARELGPN  321 (864)
Q Consensus       280 Da~sw~~Y~~~fG~~~~~~~~m~~hi~~msrDIalm~~lGpN  321 (864)
                      -+.-|++|++.=-        -..|++.|+.|+.=.++.-.-
T Consensus       227 v~gcw~ay~Qnk~--------akehv~km~kdle~Lq~aEqs  260 (575)
T KOG4403         227 VGGCWFAYRQNKK--------AKEHVNKMMKDLEGLQRAEQS  260 (575)
T ss_pred             HHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHH
T ss_conf             6055545443167--------899999999888888889989


No 32 
>pfam02064 MAS20 MAS20 protein import receptor.
Probab=22.28  E-value=34  Score=11.45  Aligned_cols=22  Identities=18%  Similarity=0.125  Sum_probs=7.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             7538999999899999999875
Q gi|254781202|r  376 VENTGWANWMAGLRSAAGASML  397 (864)
Q Consensus       376 p~n~~~a~~~a~lR~~~~~akL  397 (864)
                      |.+..+.+..+.+-.+...+.|
T Consensus         2 ~~~~~~~~~la~~~a~~a~a~l   23 (184)
T pfam02064         2 PQSNAILRGLAATAAIAAGSAL   23 (184)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHH
T ss_conf             8506999999999999999997


No 33 
>KOG2348 consensus
Probab=22.21  E-value=35  Score=11.44  Aligned_cols=30  Identities=23%  Similarity=0.128  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHH---HHHHHHHHCCHHHHHHH
Q ss_conf             9899999999875---22456641253899985
Q gi|254781202|r  385 MAGLRSAAGASML---GQHPIGALLEDGFISRQ  414 (864)
Q Consensus       385 ~a~lR~~~~~akL---GgA~ISA~tD~~~i~~t  414 (864)
                      ++-.-|+..+++|   |+|+|||++...+++.-
T Consensus       137 yal~TNIlVtaMLL~gGSavisalTGmn~vAa~  169 (667)
T KOG2348         137 YALATNILVTAMLLLGGSAVISALTGMNTVAAC  169 (667)
T ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHCCCHHHHHH
T ss_conf             465662999999996851655551150462410


No 34 
>pfam02375 JmjN jmjN domain.
Probab=22.09  E-value=35  Score=11.42  Aligned_cols=21  Identities=24%  Similarity=0.441  Sum_probs=10.7

Q ss_pred             HHHHCCC-CHHHHHHHHHHHHC
Q ss_conf             9987081-24799999998747
Q gi|254781202|r  822 ILEELNP-GYLDRQQSKKKKKG  842 (864)
Q Consensus       822 ~~e~~~P-gy~~r~~~r~~~~~  842 (864)
                      ++|.-|| +|.++++...++.|
T Consensus         7 ~eEF~Dp~~Yi~~i~~~g~~~G   28 (34)
T pfam02375         7 MEEFKDPIKYIEKIRPLGEKYG   28 (34)
T ss_pred             HHHHHCHHHHHHHHHHHHHHCC
T ss_conf             9999689999999999898859


No 35 
>COG1727 RPL18A Ribosomal protein L18E [Translation, ribosomal structure and biogenesis]
Probab=22.01  E-value=24  Score=12.66  Aligned_cols=30  Identities=7%  Similarity=0.098  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHHH-HHHHHHCCCCCHHHCCC
Q ss_conf             9999999999999-99998617984002681
Q gi|254781202|r  166 RLVKQYFETQREL-HSQAHEAGLDYKFFENR  195 (864)
Q Consensus       166 ~~A~~~~~~~e~~-r~~~N~aG~~Igkl~~~  195 (864)
                      .-|.+|.++.|.+ +-+-|++-.+|.|++.|
T Consensus        27 ~~a~iwk~vaerL~~prr~ra~VnlsKI~r~   57 (122)
T COG1727          27 SSAPIWKDVAERLEKPRRNRAEVNVSKINRY   57 (122)
T ss_pred             CCCHHHHHHHHHHHCCCCCCCCEEHHHHHHH
T ss_conf             2777999999998354345884638999965


No 36 
>cd04436 DEP_fRgd2 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGAP (GTPase-activator protein) Rgd2-like proteins. Rgd2-like proteins share a common domain architecture, containing, beside the RhoGAP domain, a DEP and a FCH (Fes/CIP4 homology) domain. Yeast Rgd2 is a GAP protein for Cdc42 and Rho5.
Probab=21.54  E-value=36  Score=11.35  Aligned_cols=44  Identities=16%  Similarity=0.143  Sum_probs=34.5

Q ss_pred             CCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             7654225899999731877448999999999999999987081247999999
Q gi|254781202|r  786 DNENSKVNATKAIRKTLPFMNMWYLKNSFDHLILNQILEELNPGYLDRQQSK  837 (864)
Q Consensus       786 ~~~~~~~~~~~~~~~~~P~~nLwy~k~a~d~li~~~~~e~~~Pgy~~r~~~r  837 (864)
                      .+...|++.+.+++.|+|.-||=|+-..        =|.+++-||+|.+-..
T Consensus        27 ~ntstGs~Iv~wl~~nm~~~~l~~AE~f--------GQDLv~~GflR~ig~v   70 (84)
T cd04436          27 QNTSSGSEIVSWLQENMPEKDLDAAEAF--------GQDLLNQGFLRLVGGV   70 (84)
T ss_pred             CCCCCHHHHHHHHHHHCCCCCHHHHHHH--------HHHHHHCCHHHHHCCC
T ss_conf             5777789999999984798767999999--------8999967579986234


No 37 
>pfam06239 ECSIT Evolutionarily conserved signalling intermediate in Toll pathway. Activation of NF-kappaB as a consequence of signaling through the Toll and IL-1 receptors is a major element of innate immune responses. ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signaling pathways between TRAF-6 and MEKK-1.
Probab=21.23  E-value=36  Score=11.30  Aligned_cols=14  Identities=29%  Similarity=0.669  Sum_probs=4.8

Q ss_pred             HHHHHHHHCCCCCH
Q ss_conf             99999960887768
Q gi|254781202|r  284 HMDYMEHFGVSTNV  297 (864)
Q Consensus       284 w~~Y~~~fG~~~~~  297 (864)
                      -+.||+.||.+.++
T Consensus        75 ALk~m~efgv~kDL   88 (229)
T pfam06239        75 ALKKMEEYGVEKDL   88 (229)
T ss_pred             HHHHHHHHCCCCCH
T ss_conf             99977871886529


No 38 
>pfam06798 PrkA PrkA serine protein kinase C-terminal domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This family corresponds to the C-terminal domain.
Probab=21.18  E-value=36  Score=11.29  Aligned_cols=42  Identities=17%  Similarity=0.269  Sum_probs=30.6

Q ss_pred             CHHHHHHHHHHHHHHHHHCCC-CCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf             689899999975208751175-68848989999998876323311
Q gi|254781202|r  209 KKDDFVRSMLDWLDLSRYKDI-DGTPLSRSEIASFVGEVFAERVR  252 (864)
Q Consensus       209 ~~~~W~~~i~~~lD~~~~~~~-~G~~~~~~~~~~~L~~vy~~i~t  252 (864)
                      =++-.++.+..|+...++.|+ ||+.+.+.+  .+|++|=+.|.-
T Consensus       120 lf~~Yid~~~a~~~~~k~kDp~TGe~~~pDE--~~mrsIEe~igI  162 (254)
T pfam06798       120 LFDNYLDNVEAYINDEKVKDPLTGEELEPDE--RFLRSIEEQIGI  162 (254)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCCHH--HHHHHHHHHCCC
T ss_conf             9999999999998236215897555216038--999999987089


No 39 
>COG1071 AcoA Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]
Probab=20.56  E-value=37  Score=11.20  Aligned_cols=21  Identities=10%  Similarity=0.113  Sum_probs=8.8

Q ss_pred             HHHHHHHHHCCCHHHHHHHHH
Q ss_conf             567799985799689999999
Q gi|254781202|r  310 KDIVIARELGPNADSFVKQMI  330 (864)
Q Consensus       310 rDIalm~~lGpNP~~~f~~l~  330 (864)
                      ||.+++=.+|-.|...+-.++
T Consensus        88 R~h~~~l~~G~~~~~~~a~~~  108 (358)
T COG1071          88 RDHGHLLARGVPLKEIMAELL  108 (358)
T ss_pred             CCCCEEEECCCCHHHHHHHHH
T ss_conf             765010025999999999985


No 40 
>TIGR00838 argH argininosuccinate lyase; InterPro: IPR009049   This entry represents argininosuccinate lyase, but may include examples of avian delta crystallins, in which argininosuccinate lyase activity may or may not be present and the biological role is to provide the optically clear cellular protein of the eye lens. ; GO: 0004056 argininosuccinate lyase activity, 0042450 arginine biosynthetic process via ornithine.
Probab=20.37  E-value=37  Score=11.17  Aligned_cols=39  Identities=8%  Similarity=0.037  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCH--HHHHHHHHHHHHHHHCC
Q ss_conf             9999752087511756884898--99999988763233117
Q gi|254781202|r  215 RSMLDWLDLSRYKDIDGTPLSR--SEIASFVGEVFAERVRS  253 (864)
Q Consensus       215 ~~i~~~lD~~~~~~~~G~~~~~--~~~~~~L~~vy~~i~t~  253 (864)
                      .+|..-+-+.+|....|-+..+  .+|.+.|.++++....+
T Consensus        30 ~Di~~~~AH~~~L~k~GiLt~Ee~~~l~~gL~~l~~e~~~~   70 (469)
T TIGR00838        30 ADIEGSIAHTKMLKKAGILTEEEAAKLIEGLNELKEEVREG   70 (469)
T ss_pred             HHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf             72133599999987527988889999999999999988608


Done!