Query         gi|254780749|ref|YP_003065162.1| lipoprotein signal peptidase transmembrane [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 108
No_of_seqs    112 out of 1642
Neff          6.2 
Searched_HMMs 39220
Date          Sun May 29 19:58:52 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780749.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK00376 lspA lipoprotein sign 100.0 1.9E-35 4.8E-40  199.8  10.1  103    1-103    57-162 (162)
  2 COG0597 LspA Lipoprotein signa 100.0 1.1E-34 2.8E-39  195.9   9.8  103    1-104    64-166 (167)
  3 TIGR00077 lspA signal peptidas 100.0 1.3E-32 3.3E-37  185.4  10.4  101    3-103    77-183 (183)
  4 PRK01574 lspA signal peptidase 100.0 1.6E-32   4E-37  184.9   9.9  100    1-102    60-168 (169)
  5 pfam01252 Peptidase_A8 Signal  100.0 1.3E-31 3.4E-36  180.2   9.7   94    1-97     48-141 (143)
  6 PRK00573 lspA signal peptidase  99.2   2E-11   5E-16   77.6   6.7   87    2-94     84-172 (184)
  7 pfam11368 DUF3169 Protein of u  93.5    0.12   3E-06   27.8   4.2   59   30-93      4-62  (248)
  8 TIGR01478 STEVOR variant surfa  55.2      15 0.00039   17.1   3.4   29   73-101   275-303 (315)
  9 PRK10447 hypothetical protein;  53.8      17 0.00043   16.8   5.3   16   38-53     81-96  (219)
 10 PHA00726 hypothetical protein   45.3      24  0.0006   16.1   3.1   17   37-53     43-59  (89)
 11 PRK10881 putative hydrogenase   45.3      24  0.0006   16.1   6.7   78    6-92    286-366 (394)
 12 COG3105 Uncharacterized protei  41.2      28 0.00071   15.8   3.0   29   32-60      6-34  (138)
 13 PRK13954 mscL large-conductanc  39.7      29 0.00075   15.6   6.2   23   34-56     14-36  (120)
 14 TIGR00878 purM phosphoribosylf  34.9     6.7 0.00017   18.9  -1.1   36   37-77    245-284 (338)
 15 PTZ00042 stevor; Provisional    32.8      39 0.00098   15.0   3.5   26   77-102   268-293 (304)
 16 TIGR01477 RIFIN variant surfac  32.3      39   0.001   15.0   3.0   25   10-34    359-383 (395)
 17 TIGR00893 2A0114 d-galactonate  32.2      39   0.001   15.0   5.2   66   35-106   131-196 (427)
 18 COG1970 MscL Large-conductance  29.4      44  0.0011   14.7   6.9   34   34-68     16-60  (130)
 19 PRK10207 inner membrane transp  27.2      49  0.0012   14.5   5.3   20   77-96    461-480 (490)
 20 PRK13685 hypothetical protein;  25.5      53  0.0013   14.4   3.2   37    1-37      3-39  (326)
 21 KOG1771 consensus               25.0      54  0.0014   14.3   2.7   16   46-61    193-208 (464)
 22 CHL00196 psbY photosystem II p  22.2      39   0.001   15.0   1.0   13   71-83     17-29  (36)
 23 TIGR02896 spore_III_AF stage I  21.3      64  0.0016   13.9   4.8   43    5-47      3-45  (113)
 24 PRK00567 mscL large-conductanc  20.0      69  0.0018   13.8   7.1   23   34-56     14-36  (134)

No 1  
>PRK00376 lspA lipoprotein signal peptidase; Reviewed
Probab=100.00  E-value=1.9e-35  Score=199.77  Aligned_cols=103  Identities=32%  Similarity=0.566  Sum_probs=91.5

Q ss_pred             CCCCH---HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHH
Q ss_conf             94520---029999999999999999999655502289999999999887999998976312757766236815408999
Q gi|254780749|r    1 MLSNV---SPTILVSIRILIIAFIFFIWKKNPKTKSIFDIGYILITTGALGNVVDHCLYGYVIDYIMIHTQTWSFAVFNL   77 (108)
Q Consensus         1 m~s~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~li~gGaiGNliDR~~~G~VvDfi~~~~~~~~~pvFNv   77 (108)
                      |+|+.   ..+++..+++++++.+.++..+.++.++..++++++++|||+||++||+++|+||||+++|++++|||+||+
T Consensus        57 l~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~l~li~gGaiGNliDR~~~G~VvDFi~~~~~~~~~piFNv  136 (162)
T PRK00376         57 FLADAGGWQRWFFTIIAIGISVGLVYLLRRSKALQKLLAIAYALILGGALGNLIDRFFHGHVVDFIDFYWGNWHFPVFNL  136 (162)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCEEEH
T ss_conf             11466347999999999999999999999803403899999999998664228899717977658886577777760668


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999999999400043211
Q gi|254780749|r   78 ADLFISIGTCIIIYDDIILQHRQKGK  103 (108)
Q Consensus        78 AD~~I~iG~~lli~~~~~~~~~~k~~  103 (108)
                      ||++|++|++++++.+++.++|+|+|
T Consensus       137 AD~~I~iG~~llii~~~~~~kk~~~~  162 (162)
T PRK00376        137 ADSAICIGAILLILDGFFPKKKKKKK  162 (162)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999999999999999853011059


No 2  
>COG0597 LspA Lipoprotein signal peptidase [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]
Probab=100.00  E-value=1.1e-34  Score=195.89  Aligned_cols=103  Identities=34%  Similarity=0.682  Sum_probs=90.0

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHH
Q ss_conf             94520029999999999999999999655502289999999999887999998976312757766236815408999999
Q gi|254780749|r    1 MLSNVSPTILVSIRILIIAFIFFIWKKNPKTKSIFDIGYILITTGALGNVVDHCLYGYVIDYIMIHTQTWSFAVFNLADL   80 (108)
Q Consensus         1 m~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~li~gGaiGNliDR~~~G~VvDfi~~~~~~~~~pvFNvAD~   80 (108)
                      |+|+...| +..++..+++++.+++.+.++.+++.++++++|+|||+||++||+++|+|+||+++|+.+++||+||+||+
T Consensus        64 ~ls~~~~~-~~~i~~~vi~~l~~~l~~~~~~~~~~~i~~~lIigGAlGN~iDR~~~g~VvDfi~~~~~~~~fpiFNlAD~  142 (167)
T COG0597          64 LLSGQSGW-FLLIALLVILGLLYFLIRLKKSRKLYAIALALIIGGALGNLIDRLFRGFVVDFIDFHYGNWHFPIFNLADV  142 (167)
T ss_pred             HHCCCCCH-HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCEEEHHHH
T ss_conf             45388525-89999999999999999965306799999999998777779988520340069999517646653255678


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999999999999994000432112
Q gi|254780749|r   81 FISIGTCIIIYDDIILQHRQKGKI  104 (108)
Q Consensus        81 ~I~iG~~lli~~~~~~~~~~k~~~  104 (108)
                      +|++|++++++.+++.++++|++.
T Consensus       143 ~I~iG~illil~~~~~~~~~~~~~  166 (167)
T COG0597         143 FISVGVILLVLDSFLSKKKKKKKK  166 (167)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             999819999999984132103367


No 3  
>TIGR00077 lspA signal peptidase II; InterPro: IPR001872   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised . More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin  and archaean preflagellin have been described , .   Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure.   This group of aspartic peptidases belong to the MEROPS peptidase family A8 (signal peptidase II family, clan AC). The catalytic residues have not been identified, but three conserved aspartates can be identified from sequence alignments. The type example is the Escherichia coli lipoprotein signal peptidase or SPase II (). This enzyme recognises a conserved sequence and cuts in front of a cysteine residue to which a glyceride-fatty acid lipid is attached. SPase II is an integral membrane protein that is anchored in the membrane.   Bacterial cell walls contain large amounts of murein lipoprotein, a small protein that is both N-terminally bound to lipid and attached to membrane peptidoglycan (murein) through the epsilon-amino group of its C-terminal lysine residue . Secretion of this lipoprotein is facilitated by the action of lipoprotein signal peptidase (also known as leader peptidase II), located in the inner membrane , . The enzyme is inhibited by globomycin and also by pepstatin, suggesting that it is an aspartic peptidase . ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis, 0016020 membrane.
Probab=100.00  E-value=1.3e-32  Score=185.36  Aligned_cols=101  Identities=25%  Similarity=0.420  Sum_probs=95.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH--CCCCEEEEEECCCC----CHHHH
Q ss_conf             5200299999999999999999996555022899999999998879999989763--12757766236815----40899
Q gi|254780749|r    3 SNVSPTILVSIRILIIAFIFFIWKKNPKTKSIFDIGYILITTGALGNVVDHCLYG--YVIDYIMIHTQTWS----FAVFN   76 (108)
Q Consensus         3 s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~li~gGaiGNliDR~~~G--~VvDfi~~~~~~~~----~pvFN   76 (108)
                      +|++.+.+..+++.+..+++++..+.++.++.++++++||+|||+||.+||+.+|  +||||++++++++|    |||||
T Consensus        77 ~GW~~~fl~~l~~~i~~~l~vF~~~~~~~~k~~~~a~gli~gGa~GN~~DRl~~gs~~VvDf~~f~~~~~~Gldrfp~FN  156 (183)
T TIGR00077        77 GGWQVYFLKGLALAISLGLVVFLLRYKELQKITNIAYGLILGGAVGNVIDRLVRGSDGVVDFLDFYLGNYHGLDRFPIFN  156 (183)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEEEECCCCCCHHH
T ss_conf             50689999999999999999998530677889889999999988988887301689934889999874230522042445


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             999999999999999999400043211
Q gi|254780749|r   77 LADLFISIGTCIIIYDDIILQHRQKGK  103 (108)
Q Consensus        77 vAD~~I~iG~~lli~~~~~~~~~~k~~  103 (108)
                      +||++|++|++++++..++.++||+++
T Consensus       157 ~AD~~I~~G~~~Lll~~f~~~~k~~~~  183 (183)
T TIGR00077       157 LADVSICVGVILLLLKFFFPKRKKKKD  183 (183)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             888999998999999987454210279


No 4  
>PRK01574 lspA signal peptidase II; Provisional
Probab=99.98  E-value=1.6e-32  Score=184.91  Aligned_cols=100  Identities=24%  Similarity=0.510  Sum_probs=76.3

Q ss_pred             CCCCHHHHH----HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCEEEEEECCC----C
Q ss_conf             945200299----9999999999999999965550228999999999988799999897631-275776623681----5
Q gi|254780749|r    1 MLSNVSPTI----LVSIRILIIAFIFFIWKKNPKTKSIFDIGYILITTGALGNVVDHCLYGY-VIDYIMIHTQTW----S   71 (108)
Q Consensus         1 m~s~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~li~gGaiGNliDR~~~G~-VvDfi~~~~~~~----~   71 (108)
                      |+|+.+.+.    +..++++++..++++..  ++.++..++++++++|||+||++||+++|+ ||||+|+|+.++    |
T Consensus        60 ~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~--~~~~~~~~~~l~lIlgGAiGNliDR~~~~~~VvDFid~~~~~~~g~~~  137 (169)
T PRK01574         60 IGSNINYSLKKLFFLIIPIIILIFVFSFYL--KEDNRIQRIALLLILSGGIGNLIDRLFRPLGVVDFLDVKFFGIFGLER  137 (169)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCC
T ss_conf             426995589999999999999999999999--521578999999999898873998810689983779862245346688


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4089999999999999999999940004321
Q gi|254780749|r   72 FAVFNLADLFISIGTCIIIYDDIILQHRQKG  102 (108)
Q Consensus        72 ~pvFNvAD~~I~iG~~lli~~~~~~~~~~k~  102 (108)
                      ||+||+||++|++|++++++.+++.++|+|+
T Consensus       138 wPvFNvAD~~I~iGv~llli~~~~~~~k~~~  168 (169)
T PRK01574        138 WPTFNFADSYVVIGMILFLIYDFFKKRKSTN  168 (169)
T ss_pred             CCEEEHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             8705699999999999999999997520248


No 5  
>pfam01252 Peptidase_A8 Signal peptidase (SPase) II.
Probab=99.97  E-value=1.3e-31  Score=180.18  Aligned_cols=94  Identities=31%  Similarity=0.584  Sum_probs=82.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHH
Q ss_conf             94520029999999999999999999655502289999999999887999998976312757766236815408999999
Q gi|254780749|r    1 MLSNVSPTILVSIRILIIAFIFFIWKKNPKTKSIFDIGYILITTGALGNVVDHCLYGYVIDYIMIHTQTWSFAVFNLADL   80 (108)
Q Consensus         1 m~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~li~gGaiGNliDR~~~G~VvDfi~~~~~~~~~pvFNvAD~   80 (108)
                      |+++. ++++..++++++..+.++..+.++.++..++++++++|||+||++||+++|+|+||+++|+  ++||+||+||+
T Consensus        48 ~~~~~-~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~li~gGaiGNliDR~~~G~VvDfi~~~~--~~~pvFNvAD~  124 (143)
T pfam01252        48 LFSGQ-RWFLSLIALLAILALLYYLLRLKKRSRLAAIALGLILGGALGNLIDRLRYGAVVDFLDFHI--WHWPVFNVADI  124 (143)
T ss_pred             CCCCC-CHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCC--CCCCEEEHHHH
T ss_conf             23698-4699999999999999999994243489999999999877510788876584223577057--78732159999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999400
Q gi|254780749|r   81 FISIGTCIIIYDDIILQ   97 (108)
Q Consensus        81 ~I~iG~~lli~~~~~~~   97 (108)
                      +|++|++++++.+++.+
T Consensus       125 ~I~iG~~lli~~~~~~~  141 (143)
T pfam01252       125 AITVGVILLLLDSLFKK  141 (143)
T ss_pred             HHHHHHHHHHHHHHHHC
T ss_conf             99999999999999852


No 6  
>PRK00573 lspA signal peptidase II; Provisional
Probab=99.24  E-value=2e-11  Score=77.59  Aligned_cols=87  Identities=24%  Similarity=0.322  Sum_probs=62.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH--HCCCCEEEEEECCCCCHHHHHHH
Q ss_conf             4520029999999999999999999655502289999999999887999998976--31275776623681540899999
Q gi|254780749|r    2 LSNVSPTILVSIRILIIAFIFFIWKKNPKTKSIFDIGYILITTGALGNVVDHCLY--GYVIDYIMIHTQTWSFAVFNLAD   79 (108)
Q Consensus         2 ~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~li~gGaiGNliDR~~~--G~VvDfi~~~~~~~~~pvFNvAD   79 (108)
                      +++........-++..+..++.+...   .+....+.++++.-|++||.+||..-  +.|+||..++-+   -.+||+||
T Consensus        84 l~d~p~lvYflQ~~ls~i~lf~lvFs---~~y~~i~~it~l~FG~L~N~~DR~ts~n~~VlDYF~F~~~---saiFNfaD  157 (184)
T PRK00573         84 LADQPGLVYFLQGFLSFIALFFLVFM---TKYNYIFWITTLAFGSLGNFFDRLTSANDEVLDYFIFQGG---NSVFNFAD  157 (184)
T ss_pred             ECCCCCCCHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHCCHHHHHHHHHCCCCCEEEEEEECCC---CEEECCCC
T ss_conf             55899700399888999999999871---5501501007876430777776551377732578896598---62440534


Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999999
Q gi|254780749|r   80 LFISIGTCIIIYDDI   94 (108)
Q Consensus        80 ~~I~iG~~lli~~~~   94 (108)
                      +||+.|.+.+.+.-+
T Consensus       158 ~cI~~gfi~lf~~fl  172 (184)
T PRK00573        158 CCITFGFIGLFFCFL  172 (184)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             466786999999999


No 7  
>pfam11368 DUF3169 Protein of unknown function (DUF3169). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.
Probab=93.48  E-value=0.12  Score=27.81  Aligned_cols=59  Identities=25%  Similarity=0.320  Sum_probs=37.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5022899999999998879999989763127577662368154089999999999999999999
Q gi|254780749|r   30 KTKSIFDIGYILITTGALGNVVDHCLYGYVIDYIMIHTQTWSFAVFNLADLFISIGTCIIIYDD   93 (108)
Q Consensus        30 ~~~~~~~i~l~li~gGaiGNliDR~~~G~VvDfi~~~~~~~~~pvFNvAD~~I~iG~~lli~~~   93 (108)
                      ++++..+....+++||.+|-++     |.+...++-...+.+|+.+|......-++.++.++..
T Consensus         4 ~k~~~~r~~~~lLlg~iiGGii-----G~~~~~~~~~~~~~~~~~~~~v~~i~~i~~liiiil~   62 (248)
T pfam11368         4 KKKRILRYLIFLLLGGIIGGII-----GGFGGAIAGFLENLSFSTIDNVQLIIILARIIIIILT   62 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6899999999999999999999-----9999999875137763456439999999999999999


No 8  
>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=55.20  E-value=15  Score=17.06  Aligned_cols=29  Identities=21%  Similarity=0.149  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             08999999999999999999994000432
Q gi|254780749|r   73 AVFNLADLFISIGTCIIIYDDIILQHRQK  101 (108)
Q Consensus        73 pvFNvAD~~I~iG~~lli~~~~~~~~~~k  101 (108)
                      |--=.|=+.|.+-|++++++.++.+|||+
T Consensus       275 PyGIAAlVLi~L~V~LIiLYIWLYrRRK~  303 (315)
T TIGR01478       275 PYGIAALVLIILTVVLIILYIWLYRRRKK  303 (315)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_conf             35899999999999999998888564030


No 9  
>PRK10447 hypothetical protein; Provisional
Probab=53.83  E-value=17  Score=16.85  Aligned_cols=16  Identities=13%  Similarity=0.229  Sum_probs=7.2

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999999887999998
Q gi|254780749|r   38 GYILITTGALGNVVDH   53 (108)
Q Consensus        38 ~l~li~gGaiGNliDR   53 (108)
                      ++....|-.+|.++..
T Consensus        81 afTg~mG~~lgPil~~   96 (219)
T PRK10447         81 AFTGFLGYILGPILNT   96 (219)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999989999999


No 10 
>PHA00726 hypothetical protein
Probab=45.32  E-value=24  Score=16.12  Aligned_cols=17  Identities=41%  Similarity=0.722  Sum_probs=9.0

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999887999998
Q gi|254780749|r   37 IGYILITTGALGNVVDH   53 (108)
Q Consensus        37 i~l~li~gGaiGNliDR   53 (108)
                      +|+=+++++++.=..-+
T Consensus        43 iGyYlViss~~aL~v~H   59 (89)
T PHA00726         43 IGYYLVGSSVLALFVGH   59 (89)
T ss_pred             EEEEEHHHHHHHHHHHH
T ss_conf             67652798899999999


No 11 
>PRK10881 putative hydrogenase 2 b cytochrome subunit; Provisional
Probab=45.31  E-value=24  Score=16.12  Aligned_cols=78  Identities=14%  Similarity=0.135  Sum_probs=41.8

Q ss_pred             HHHHHHHHHH-HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECC--CCCHHHHHHHHHH
Q ss_conf             0299999999-999999999996555022899999999998879999989763127577662368--1540899999999
Q gi|254780749|r    6 SPTILVSIRI-LIIAFIFFIWKKNPKTKSIFDIGYILITTGALGNVVDHCLYGYVIDYIMIHTQT--WSFAVFNLADLFI   82 (108)
Q Consensus         6 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~i~l~li~gGaiGNliDR~~~G~VvDfi~~~~~~--~~~pvFNvAD~~I   82 (108)
                      ..+.+..-.. .++-..+++..+.+++++...++-.++..|..-|   |.    .+=++.+..+.  .++|  +..++.+
T Consensus       286 ~~~~fw~Ei~l~viP~~il~~~k~R~n~~~lf~aailvvlG~~l~---Rf----nv~~i~~~p~~~~~YfP--S~~Ei~i  356 (394)
T PRK10881        286 YSAMFWIEVLLMLFPLVVLRVPKLRRDSRMLFLSALSALLGGALW---RL----NYSLIAFNPGGGYHYFP--SWAELLI  356 (394)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHEE---EE----EEEEEEECCCCCCCCCC--CHHHHHH
T ss_conf             999999999999999999999987128999999999999803143---57----78999720899877089--8999999


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999999
Q gi|254780749|r   83 SIGTCIIIYD   92 (108)
Q Consensus        83 ~iG~~lli~~   92 (108)
                      ++|.+-+.+.
T Consensus       357 siG~va~~vl  366 (394)
T PRK10881        357 SIGFVAIEIC  366 (394)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 12 
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.17  E-value=28  Score=15.77  Aligned_cols=29  Identities=7%  Similarity=-0.128  Sum_probs=20.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             22899999999998879999989763127
Q gi|254780749|r   32 KSIFDIGYILITTGALGNVVDHCLYGYVI   60 (108)
Q Consensus        32 ~~~~~i~l~li~gGaiGNliDR~~~G~Vv   60 (108)
                      -.|...++++++|=++|=++-|+..|.|.
T Consensus         6 ~~W~~a~igLvvGi~IG~li~Rlt~~~~k   34 (138)
T COG3105           6 MTWEYALIGLVVGIIIGALIARLTNRKLK   34 (138)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHH
T ss_conf             99999999999999999999998230222


No 13 
>PRK13954 mscL large-conductance mechanosensitive channel; Provisional
Probab=39.73  E-value=29  Score=15.65  Aligned_cols=23  Identities=9%  Similarity=0.364  Sum_probs=18.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999887999998976
Q gi|254780749|r   34 IFDIGYILITTGALGNVVDHCLY   56 (108)
Q Consensus        34 ~~~i~l~li~gGaiGNliDR~~~   56 (108)
                      .--++-+.++|||.+...+-+..
T Consensus        14 ViDLAVaVIiGaAF~~IV~slv~   36 (120)
T PRK13954         14 VLDLAIAVVMGAAFNKIISSLVE   36 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999999999999999998


No 14 
>TIGR00878 purM phosphoribosylformylglycinamidine cyclo-ligase; InterPro: IPR004733   The purine biosynthetic pathway in procaryotes enlists eleven enzymes, six of which use ATP. Enzymes 5 and 6 of this pathway, formylglycinamide ribonucleotide (FGAR) amidotransferase (PurL) and aminoimidazole ribonucleotide (AIR) synthetase (PurM) utilise ATP to activate the oxygen of an amide within their substrate toward nucleophilic attack by a nitrogen. AIR synthetase uses the product of PurL, formylglycinamidine ribonucleotide (FGAM) and ATP to make AIR, ADP and P(i).; GO: 0004641 phosphoribosylformylglycinamidine cyclo-ligase activity, 0006189 'de novo' IMP biosynthetic process, 0005737 cytoplasm.
Probab=34.87  E-value=6.7  Score=18.92  Aligned_cols=36  Identities=28%  Similarity=0.328  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHH-HHHHHHH--HCCCCEEEEEECCCCCH-HHHH
Q ss_conf             9999999988799-9998976--31275776623681540-8999
Q gi|254780749|r   37 IGYILITTGALGN-VVDHCLY--GYVIDYIMIHTQTWSFA-VFNL   77 (108)
Q Consensus        37 i~l~li~gGaiGN-liDR~~~--G~VvDfi~~~~~~~~~p-vFNv   77 (108)
                      -|++=|.||++.| +.=|+-.  .|++|--.     |++| |||.
T Consensus       245 ~GlAHiTGGGl~eNl~r~L~~~~~a~~D~~~-----~~~~piF~~  284 (338)
T TIGR00878       245 HGLAHITGGGLLENLLRRLPDGLKAVIDKGS-----WPQPPIFKW  284 (338)
T ss_pred             EEEEEECCCHHHHHHHHHCCCCCEEEEECCC-----CCHHHHHHH
T ss_conf             4777551640345699865899789985689-----883168899


No 15 
>PTZ00042 stevor; Provisional
Probab=32.77  E-value=39  Score=15.04  Aligned_cols=26  Identities=15%  Similarity=0.258  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999940004321
Q gi|254780749|r   77 LADLFISIGTCIIIYDDIILQHRQKG  102 (108)
Q Consensus        77 vAD~~I~iG~~lli~~~~~~~~~~k~  102 (108)
                      -|=+.|.+.|+++++..+..++||+.
T Consensus       268 aalVLlilaVvLIILYIWLyrRRKnS  293 (304)
T PTZ00042        268 AALVLLILAVVLIILYIWLYRRRKNS  293 (304)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999999999999999999841242


No 16 
>TIGR01477 RIFIN variant surface antigen, rifin family; InterPro: IPR006373   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 rifin family of variant surface antigens, encoded by the rif (short for "repetetive interspersed family") genes. This is the largest variant surface antigen family in P. falciparum, with roughly 150 genes present in the genome of this parasite . The function of these proteins is not yet known, but rifins are strongly immunogenic and high levels of anti-rifin antibodies are correlated with rapid parasite clearance and asymptomatic infections . .
Probab=32.33  E-value=39  Score=15.00  Aligned_cols=25  Identities=16%  Similarity=0.421  Sum_probs=11.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHH
Q ss_conf             9999999999999999965550228
Q gi|254780749|r   10 LVSIRILIIAFIFFIWKKNPKTKSI   34 (108)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~   34 (108)
                      ..++.+|++-+++|+.+|++.+++.
T Consensus       359 iAIliIVLIMvIIYLILRYRRKKKM  383 (395)
T TIGR01477       359 IAILIIVLIMVIIYLILRYRRKKKM  383 (395)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9999999999999998754311220


No 17 
>TIGR00893 2A0114 d-galactonate transporter; InterPro: IPR004744 D-galactonate transporters and other proteins that belong to the phthalate permease family are members of this group.; GO: 0005215 transporter activity, 0006810 transport, 0016021 integral to membrane.
Probab=32.20  E-value=39  Score=14.99  Aligned_cols=66  Identities=15%  Similarity=0.079  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             999999999988799999897631275776623681540899999999999999999999400043211247
Q gi|254780749|r   35 FDIGYILITTGALGNVVDHCLYGYVIDYIMIHTQTWSFAVFNLADLFISIGTCIIIYDDIILQHRQKGKIDF  106 (108)
Q Consensus        35 ~~i~l~li~gGaiGNliDR~~~G~VvDfi~~~~~~~~~pvFNvAD~~I~iG~~lli~~~~~~~~~~k~~~~~  106 (108)
                      -..-.+--+|+.+++-+.-...-+..|+   ..++|+|--+=-+=.+|..|++.+.   +..++++|++..+
T Consensus       131 s~f~~~~~lg~~~~~Pl~~~i~~~~~~~---g~~gW~~~F~~~G~~~~~~gv~~~~---~~~d~p~~a~~~~  196 (427)
T TIGR00893       131 SIFNSAQYLGGIIGGPLVGWILVHFSSM---GMKGWQWVFIIEGILGIILGVLWLK---FIKDKPQKAKWLT  196 (427)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCCCHHHHHHHHHHHHHHHHHHHHH---HCCCCCCCCCCCC
T ss_conf             9999999999999989999999874466---5201389999997999999999998---6079754766454


No 18 
>COG1970 MscL Large-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=29.36  E-value=44  Score=14.73  Aligned_cols=34  Identities=21%  Similarity=0.398  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-----------HCCCCEEEEEEC
Q ss_conf             89999999999887999998976-----------312757766236
Q gi|254780749|r   34 IFDIGYILITTGALGNVVDHCLY-----------GYVIDYIMIHTQ   68 (108)
Q Consensus        34 ~~~i~l~li~gGaiGNliDR~~~-----------G~VvDfi~~~~~   68 (108)
                      ..-++-+.++|+|.|.+.+-+..           |. +||=++++.
T Consensus        16 VvDLAVgVIIGaAFg~IV~SlV~diImPlIg~~~gg-~dfs~l~~~   60 (130)
T COG1970          16 VVDLAVGVIIGAAFGKIVTSLVNDIIMPLIGLLVGG-LDFSNLFIT   60 (130)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHEEE
T ss_conf             166778888589898899999998887636641377-573352012


No 19 
>PRK10207 inner membrane transporter YhiP; Provisional
Probab=27.19  E-value=49  Score=14.52  Aligned_cols=20  Identities=0%  Similarity=0.076  Sum_probs=8.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999940
Q gi|254780749|r   77 LADLFISIGTCIIIYDDIIL   96 (108)
Q Consensus        77 vAD~~I~iG~~lli~~~~~~   96 (108)
                      ++=+.+.+|++++++.-..+
T Consensus       461 l~~~~~~~~vil~~~~p~l~  480 (490)
T PRK10207        461 IGLVTLGVAVVMALMVPWLN  480 (490)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999


No 20 
>PRK13685 hypothetical protein; Provisional
Probab=25.54  E-value=53  Score=14.36  Aligned_cols=37  Identities=3%  Similarity=0.188  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Q ss_conf             9452002999999999999999999965550228999
Q gi|254780749|r    1 MLSNVSPTILVSIRILIIAFIFFIWKKNPKTKSIFDI   37 (108)
Q Consensus         1 m~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i   37 (108)
                      |++-..||.+..+.++.....+|++.+..+++...++
T Consensus         3 m~~F~~P~~L~lLll~p~li~~~~~~~~~r~~~~lrf   39 (326)
T PRK13685          3 LSGFAHPWFFLFLLVVAGLVALYVVVQRARQRRMLRF   39 (326)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             2111129999999999999999999876401267707


No 21 
>KOG1771 consensus
Probab=25.00  E-value=54  Score=14.30  Aligned_cols=16  Identities=31%  Similarity=0.586  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHHHCCCC
Q ss_conf             8799999897631275
Q gi|254780749|r   46 ALGNVVDHCLYGYVID   61 (108)
Q Consensus        46 aiGNliDR~~~G~VvD   61 (108)
                      +.|-++||+++|.++=
T Consensus       193 g~g~liDr~~yg~~~f  208 (464)
T KOG1771         193 GLGILIDRIFYGQWVF  208 (464)
T ss_pred             HHHHHHHHHHHCCEEE
T ss_conf             2789999998663553


No 22 
>CHL00196 psbY photosystem II protein Y; Provisional
Probab=22.23  E-value=39  Score=15.00  Aligned_cols=13  Identities=46%  Similarity=0.761  Sum_probs=9.9

Q ss_pred             CCHHHHHHHHHHH
Q ss_conf             5408999999999
Q gi|254780749|r   71 SFAVFNLADLFIS   83 (108)
Q Consensus        71 ~~pvFNvAD~~I~   83 (108)
                      +|.-||+|.++|-
T Consensus        17 swa~fni~r~a~~   29 (36)
T CHL00196         17 SWALFNIGRLAIQ   29 (36)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9999867899999


No 23 
>TIGR02896 spore_III_AF stage III sporulation protein AF; InterPro: IPR014245   This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved. .
Probab=21.32  E-value=64  Score=13.91  Aligned_cols=43  Identities=16%  Similarity=0.113  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Q ss_conf             0029999999999999999999655502289999999999887
Q gi|254780749|r    5 VSPTILVSIRILIIAFIFFIWKKNPKTKSIFDIGYILITTGAL   47 (108)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~li~gGai   47 (108)
                      ...|+..++.+++++.++=++.-..+.+++.+...||++==++
T Consensus         3 L~~Wv~~i~~~~llat~~e~LLP~~~lkKYvk~v~GL~L~~vi   45 (113)
T TIGR02896         3 LKEWVTNIIVLILLATILEMLLPNSSLKKYVKFVVGLILIVVI   45 (113)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             8999999999999999999976799851799999999999999


No 24 
>PRK00567 mscL large-conductance mechanosensitive channel; Reviewed
Probab=20.02  E-value=69  Score=13.76  Aligned_cols=23  Identities=22%  Similarity=0.375  Sum_probs=18.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999887999998976
Q gi|254780749|r   34 IFDIGYILITTGALGNVVDHCLY   56 (108)
Q Consensus        34 ~~~i~l~li~gGaiGNliDR~~~   56 (108)
                      ..-++.+.++|||.+.+.+-+..
T Consensus        14 viDLAVgvIiG~AF~~iV~slv~   36 (134)
T PRK00567         14 VVDLAVGVIIGAAFGKIVTSLVD   36 (134)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999999999999999999


Done!