Query         gi|254780329|ref|YP_003064742.1| 30S ribosomal protein S6 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 135
No_of_seqs    117 out of 1182
Neff          6.9 
Searched_HMMs 39220
Date          Sun May 29 15:38:36 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780329.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG0360 RpsF Ribosomal protein 100.0 4.5E-31 1.1E-35  202.7  11.7  108    2-109     1-108 (112)
  2 CHL00123 rps6 ribosomal protei 100.0 5.8E-31 1.5E-35  202.1  11.7   93    1-93      5-97  (97)
  3 PRK00453 rpsF 30S ribosomal pr 100.0 8.1E-30 2.1E-34  195.4  12.4   95    1-95      1-95  (95)
  4 pfam01250 Ribosomal_S6 Ribosom 100.0 1.9E-28 4.8E-33  187.3  11.9   92    2-93      1-92  (92)
  5 TIGR00166 S6 ribosomal protein  99.6 1.4E-15 3.4E-20  111.9   5.4   94    1-94      1-101 (102)
  6 KOG4708 consensus               99.5 2.6E-15 6.7E-20  110.3   3.7   95    1-96      3-101 (141)
  7 pfam03059 NAS Nicotianamine sy  44.8      26 0.00067   16.4   3.2   70    3-73    193-265 (277)
  8 TIGR02079 THD1 threonine dehyd  36.1      36 0.00092   15.6   3.0   44   59-102   332-376 (415)
  9 PRK11230 glycolate oxidase sub  34.3      39 0.00098   15.5   3.6   72    6-77    289-368 (499)
 10 cd04904 ACT_AAAH ACT domain of  32.4      41  0.0011   15.3   6.4   62   20-88     11-72  (74)
 11 PRK00499 rnpA ribonuclease P;   31.9      42  0.0011   15.2   3.4   30    4-33     77-106 (116)
 12 PRK05783 hypothetical protein;  31.0      44  0.0011   15.1   8.7   77    1-95      1-83  (84)
 13 PHA01632 hypothetical protein   28.8      48  0.0012   14.9   3.0   35   11-45     25-63  (64)
 14 COG1164 Oligoendopeptidase F [  26.3      53  0.0014   14.6   3.8   51   34-84    342-393 (598)
 15 cd04893 ACT_GcvR_1 ACT domains  25.9      54  0.0014   14.6   4.8   51   19-80     11-62  (77)
 16 cd04929 ACT_TPH ACT domain of   22.4      63  0.0016   14.2   6.0   59   21-86     12-70  (74)
 17 pfam05211 NLBH Neuraminyllacto  21.3      67  0.0017   14.1   4.0   73    2-79     31-113 (228)
 18 PRK00464 nrdR transcriptional   20.7      50  0.0013   14.8   1.3   66   13-78     78-147 (149)
 19 pfam09569 RE_ScaI ScaI restric  20.0      67  0.0017   14.0   1.8   30   42-71    114-146 (191)

No 1  
>COG0360 RpsF Ribosomal protein S6 [Translation, ribosomal structure and biogenesis]
Probab=99.97  E-value=4.5e-31  Score=202.71  Aligned_cols=108  Identities=37%  Similarity=0.704  Sum_probs=103.3

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHCC
Q ss_conf             87059999878999999999999999999856978999703686535303222418999999980897799999998089
Q gi|254780329|r    2 KLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRI   81 (135)
Q Consensus         2 ~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk~   81 (135)
                      ++||+|||++|+++++++...++++.++|+++||+|.++++||+|+|||||+|+++|||++++|+++|.+++||++.|++
T Consensus         1 ~~YEi~~iv~p~~see~~~~~ve~~~~~l~~~gg~i~~~e~wG~R~LAY~IkK~~~g~Y~l~~f~~~~~~i~Eler~~ri   80 (112)
T COG0360           1 RKYEIVFIVRPDLSEEQVAALVEKYKGVLTNNGGEIHKVEDWGKRRLAYPIKKLREGHYVLMNFEAEPAAIAELERLLRI   80 (112)
T ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHCEECCCCCEEEEEEEEECCHHHHHHHHHHHCC
T ss_conf             93379999778889899999999999999878977998302223433022055550899999997187789999998516


Q ss_pred             CCHHEEEEEEEECCCCCCCCHHHHHHHH
Q ss_conf             8021001124411345564357653212
Q gi|254780329|r   82 DENVLRSLTLLVDSHEQSPTLTIQRHDR  109 (135)
Q Consensus        82 ~~~VLR~l~vk~~~~~~~~~~~~~~~~~  109 (135)
                      |++||||||||++.....+++++...+.
T Consensus        81 n~~VlR~liik~~~~~~~~~~~~~~~~~  108 (112)
T COG0360          81 NEDVLRHLIIKVEKAKEELSPMLKKKDQ  108 (112)
T ss_pred             CHHHHEEEEEEECHHHCCHHHHHHHHHH
T ss_conf             5754400468720100211134356565


No 2  
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=99.97  E-value=5.8e-31  Score=202.05  Aligned_cols=93  Identities=28%  Similarity=0.578  Sum_probs=91.7

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHC
Q ss_conf             98705999987899999999999999999985697899970368653530322241899999998089779999999808
Q gi|254780329|r    1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMR   80 (135)
Q Consensus         1 M~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk   80 (135)
                      ||+||++||++|++++++++++++++.++|+++||+|.++++||+|+|||||+|+++|+|++++|+++|+.+++|++.|+
T Consensus         5 Mr~YE~~~I~~p~l~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~R~LAY~I~k~~~G~Y~~~~f~~~~~~i~eler~lr   84 (97)
T CHL00123          5 LIKYETMYILKPDLNEEELLKWIENYKKLLTKRGAKNIIVQNRGRRKLAYKIKKYEDGIYIQMNYEGNGKLVNSLEKSLK   84 (97)
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHC
T ss_conf             15211999989999989999999999999986897799998056300035156677899999999858889999999866


Q ss_pred             CCCHHEEEEEEEE
Q ss_conf             9802100112441
Q gi|254780329|r   81 IDENVLRSLTLLV   93 (135)
Q Consensus        81 ~~~~VLR~l~vk~   93 (135)
                      +|++|||||+||.
T Consensus        85 i~e~VlR~l~vKk   97 (97)
T CHL00123         85 LDENILRYLTLKK   97 (97)
T ss_pred             CCCCEEEEEEEEC
T ss_conf             7757037999729


No 3  
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=99.97  E-value=8.1e-30  Score=195.35  Aligned_cols=95  Identities=45%  Similarity=0.773  Sum_probs=93.9

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHC
Q ss_conf             98705999987899999999999999999985697899970368653530322241899999998089779999999808
Q gi|254780329|r    1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMR   80 (135)
Q Consensus         1 M~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk   80 (135)
                      ||+||++||++|++++++++++++++.++|+++||+|.++++||+|+|||||+|+++|+|++++|+++|+.+++|++.|+
T Consensus         1 M~~YE~~~il~p~l~~~~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk   80 (95)
T PRK00453          1 MRKYEIVFILRPDLSEEQVKALVERYKGVITKNGGEIHKVEDWGRRRLAYPINKLRKGHYVLLNFEADPAAIAELERLFR   80 (95)
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEECCCCEEEEEEEEEEECHHHHHHHHHHHC
T ss_conf             98625999988999989999999999999997998899985021200442306675899999999989889999999864


Q ss_pred             CCCHHEEEEEEEECC
Q ss_conf             980210011244113
Q gi|254780329|r   81 IDENVLRSLTLLVDS   95 (135)
Q Consensus        81 ~~~~VLR~l~vk~~~   95 (135)
                      +|++|||||+||+++
T Consensus        81 l~~~VlR~livk~~~   95 (95)
T PRK00453         81 INEDVLRFLIVKLDK   95 (95)
T ss_pred             CCCCEEEEEEEEECC
T ss_conf             776836899999649


No 4  
>pfam01250 Ribosomal_S6 Ribosomal protein S6.
Probab=99.96  E-value=1.9e-28  Score=187.33  Aligned_cols=92  Identities=47%  Similarity=0.856  Sum_probs=90.7

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHCC
Q ss_conf             87059999878999999999999999999856978999703686535303222418999999980897799999998089
Q gi|254780329|r    2 KLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRI   81 (135)
Q Consensus         2 ~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk~   81 (135)
                      |+||+++|++|++++++++++++++.++|+++||+|.++++||+|+|||||+|+++|+|++++|+++|+.+++|++.|++
T Consensus         1 r~YE~~~i~~p~l~~~~~~~~~~~~~~~i~~~gg~i~~~e~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk~   80 (92)
T pfam01250         1 RKYETMFILRPDLSEEEVKALIEKYKKLIEENGGEVVKVEDWGKRKLAYPIKKKREGYYVLINFEAEPEAIAELERRLRI   80 (92)
T ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCEEECCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHCC
T ss_conf             96059999889999899999999999999878988999851310003304377889999999999998899999998647


Q ss_pred             CCHHEEEEEEEE
Q ss_conf             802100112441
Q gi|254780329|r   82 DENVLRSLTLLV   93 (135)
Q Consensus        82 ~~~VLR~l~vk~   93 (135)
                      |++|||||+||+
T Consensus        81 ~~~VlR~livk~   92 (92)
T pfam01250        81 NEDVLRFLTVKL   92 (92)
T ss_pred             CCCEEEEEEEEC
T ss_conf             878388999969


No 5  
>TIGR00166 S6 ribosomal protein S6; InterPro: IPR000529   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 , .   Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=99.59  E-value=1.4e-15  Score=111.95  Aligned_cols=94  Identities=33%  Similarity=0.666  Sum_probs=91.0

Q ss_pred             CCCCEEEEEECCCCCHHH---HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECC----CCCEEEEEEEEEECCHHHHH
Q ss_conf             987059999878999999---99999999999985697899970368653530322----24189999999808977999
Q gi|254780329|r    1 MKLYEHVFLLRQDISSQQ---IKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIR----KNRKAYYVFMNIASPPAAIH   73 (135)
Q Consensus         1 M~~YE~~~i~~p~~~~~~---~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~----k~~~G~Y~~~~f~~~~~~i~   73 (135)
                      |+.||++++++|++++..   ....++.+...++.++|.+.....||.|.|||+|+    ++..|+|+++.|.+++..+.
T Consensus         1 ~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~~~~   80 (102)
T TIGR00166         1 LRHYELIFLVRPTLSEEPKLEVKGLIERYKKLLTLNGGEIVGSEDWGLRRLAYPIKKDQEKHLRGHYYLWNFSGEGAVIK   80 (102)
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHHHHHHHHHHCCCHHHHCCCEEEEEEECCCHHHHH
T ss_conf             95411577751552101333335567777655531132000012220233321210002332032157886336335789


Q ss_pred             HHHHHHCCCCHHEEEEEEEEC
Q ss_conf             999980898021001124411
Q gi|254780329|r   74 EMKRKMRIDENVLRSLTLLVD   94 (135)
Q Consensus        74 el~~~lk~~~~VLR~l~vk~~   94 (135)
                      ++++.++++++|+|+++++.+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~  101 (102)
T TIGR00166        81 EFERTLKLNDDVLRSLVIKLE  101 (102)
T ss_pred             HHHHHHCCCHHHHHHHHHHCC
T ss_conf             888874103667777764236


No 6  
>KOG4708 consensus
Probab=99.55  E-value=2.6e-15  Score=110.26  Aligned_cols=95  Identities=31%  Similarity=0.477  Sum_probs=84.5

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCC----CCEEEEEEEEEECCHHHHHHHH
Q ss_conf             987059999878999999999999999999856978999703686535303222----4189999999808977999999
Q gi|254780329|r    1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRK----NRKAYYVFMNIASPPAAIHEMK   76 (135)
Q Consensus         1 M~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k----~~~G~Y~~~~f~~~~~~i~el~   76 (135)
                      |..||++.|+++- +..++...+.+..+.+-..||.|..++++|.|.|+|+|+|    |.+|+++++.|.+++++..++.
T Consensus         3 mp~yelali~~~~-~rpela~~l~rt~~~lid~ngVvrdveslG~r~Lpy~i~K~~~~h~~g~~f~m~f~ss~~v~~ei~   81 (141)
T KOG4708           3 MPLYELALITRSL-SRPELAKLLARTGGHLIDRNGVVRDVESLGKRELPYKIKKLDQRHYRGQHFLMTFYSSPAVQSEIK   81 (141)
T ss_pred             CHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHCCCEEEECHHCCHHHHCCHHHHHCCCCCCCEEEEEEECCCHHHHHHHH
T ss_conf             3177899986246-988999999998657734487686503044043053377706752222578986508989999999


Q ss_pred             HHHCCCCHHEEEEEEEECCC
Q ss_conf             98089802100112441134
Q gi|254780329|r   77 RKMRIDENVLRSLTLLVDSH   96 (135)
Q Consensus        77 ~~lk~~~~VLR~l~vk~~~~   96 (135)
                      +.|+.|.+|||+++||++..
T Consensus        82 ~~l~~D~dviR~~IVKv~~~  101 (141)
T KOG4708          82 RILKRDPDVIRWLIVKVDDI  101 (141)
T ss_pred             HHHHCCHHHHHHHHEECCCC
T ss_conf             99702806677521132354


No 7  
>pfam03059 NAS Nicotianamine synthase protein. Nicotianamine synthase EC:2.5.1.43 catalyses the trimerisation of S-adenosylmethionine to yield one molecule of nicotianamine. Nicotianamine has an important role in plant iron uptake mechanisms. Plants adopt two strategies (termed I and II) of iron acquisition. Strategy I is adopted by all higher plants except graminaceous plants, which adopt strategy II. In strategy I plants, the role of nicotianamine is not fully determined: possible roles include the formation of more stable complexes with ferrous than with ferric ion, which might serve as a sensor of the physiological status of iron within a plant, or which might be involved in the transport of iron. In strategy II (graminaceous) plants, nicotianamine is the key intermediate (and nicotianamine synthase the key enzyme) in the synthesis of the mugineic family (the only known family in plants) of phytosiderophores. Phytosiderophores are iron chelators whose secretion by the roots is great
Probab=44.85  E-value=26  Score=16.45  Aligned_cols=70  Identities=17%  Similarity=0.270  Sum_probs=44.3

Q ss_pred             CCEEEEEECCC-CCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCC--CEEEEEEEEEECCHHHHH
Q ss_conf             70599998789-999999999999999998569789997036865353032224--189999999808977999
Q gi|254780329|r    3 LYEHVFLLRQD-ISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKN--RKAYYVFMNIASPPAAIH   73 (135)
Q Consensus         3 ~YE~~~i~~p~-~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~--~~G~Y~~~~f~~~~~~i~   73 (135)
                      -|+++|+.-.. ...++.+.+++.+.+... -|+.+.--..||.|.|=||+=..  ..|+=++-.+.-.++.++
T Consensus       193 ~~DvV~lAALVGm~~e~K~~I~~hL~k~m~-~Ga~l~~Rsa~GlR~~LYp~vd~~~~~GFe~l~~~hP~~~ViN  265 (277)
T pfam03059       193 AYDVVFLAALVGMDKEEKAKVIDHLGKHMA-PGALLVLRSAHGARAFLYPVVDPCDLRGFEVLSVYHPTDEVIN  265 (277)
T ss_pred             CCCEEEEHHHCCCCHHHHHHHHHHHHHHCC-CCCEEEEECCHHHHHHCCCCCCHHHCCCCEEEEEECCCCCCEE
T ss_conf             476898721135433359999999997458-9967999611217876288789667387079999889998411


No 8  
>TIGR02079 THD1 threonine dehydratase; InterPro: IPR011820    This entry represents threonine dehydratase, the first step in the pathway converting threonine into isoleucine. At least two other clades of biosynthetic threonine dehydratases are described by IPR005787 from INTERPRO and IPR005789 from INTERPRO. The sequences described by this entry are exclusively found in species containing the rest of the isoleucine pathway and which are generally lacking in members of the other two clades of threonine dehydratases. The sequences associated with this entry are often cluster with other elements of the isoleucine pathway.; GO: 0004794 L-threonine ammonia-lyase activity, 0030170 pyridoxal phosphate binding, 0009097 isoleucine biosynthetic process.
Probab=36.15  E-value=36  Score=15.64  Aligned_cols=44  Identities=16%  Similarity=0.314  Sum_probs=40.0

Q ss_pred             EEEEEEEECCHHHHHHHHH-HHCCCCHHEEEEEEEECCCCCCCCH
Q ss_conf             9999998089779999999-8089802100112441134556435
Q gi|254780329|r   59 YYVFMNIASPPAAIHEMKR-KMRIDENVLRSLTLLVDSHEQSPTL  102 (135)
Q Consensus        59 ~Y~~~~f~~~~~~i~el~~-~lk~~~~VLR~l~vk~~~~~~~~~~  102 (135)
                      |||++.|.=-|-++.+|=. -|.=||+|-+|--+|..+...+|..
T Consensus       332 hYFiv~FPQRpGALreFln~vLGP~DDIT~FEY~KK~nRe~Gpal  376 (415)
T TIGR02079       332 HYFIVRFPQRPGALREFLNDVLGPNDDITKFEYTKKSNRETGPAL  376 (415)
T ss_pred             EEEEECCCCCCCHHHHHHHHHCCCCCCCCCCEEEECCCCCCCCEE
T ss_conf             368752789886368876540678875233100020147878779


No 9  
>PRK11230 glycolate oxidase subunit GlcD; Provisional
Probab=34.28  E-value=39  Score=15.46  Aligned_cols=72  Identities=11%  Similarity=0.111  Sum_probs=41.9

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEE--------CCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHH
Q ss_conf             999987899999999999999999985697899970--------368653530322241899999998089779999999
Q gi|254780329|r    6 HVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVN--------ELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKR   77 (135)
Q Consensus         6 ~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e--------~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~   77 (135)
                      .++++--+.++.++....+.+.+++.+.|+.-...-        -|-.|+-+++.-....+.++.+.+..+.+.+.++-+
T Consensus       289 a~llve~~g~~~~~~~~~~~~~~~l~~~g~~~~~~a~~~~e~~~lW~~R~~~~~~~~~~~~~~~~~Dv~VP~~~l~~~~~  368 (499)
T PRK11230        289 AILLCELDGVESDVQEDCERVNDVLLAAGATDVRLAQDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRELPGVLE  368 (499)
T ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHH
T ss_conf             10233225887889999999999998769835899489999999999999999999965798257654312210899999


No 10 
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=32.43  E-value=41  Score=15.28  Aligned_cols=62  Identities=13%  Similarity=0.197  Sum_probs=44.4

Q ss_pred             HHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHCCCCHHEEE
Q ss_conf             999999999998569789997036865353032224189999999808977999999980898021001
Q gi|254780329|r   20 KDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVLRS   88 (135)
Q Consensus        20 ~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk~~~~VLR~   88 (135)
                      ...+-++-+.+..+|..+.+.|..       |.++....|.+++.|++....+.++-..|+-.-.-+|.
T Consensus        11 ~GaL~~~L~~F~~~~iNlt~IESR-------Ps~~~~~~y~FfvD~eg~~~~i~~al~~Lk~~~~~vki   72 (74)
T cd04904          11 VGALARALKLFEEFGVNLTHIESR-------PSRRNGSEYEFFVDCEVDRGDLDQLISSLRRVVADVNI   72 (74)
T ss_pred             CCHHHHHHHHHHHCCCCEEEEECC-------CCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHCCEEEE
T ss_conf             648999999999879867899833-------38999975999999608989999999999974782885


No 11 
>PRK00499 rnpA ribonuclease P; Reviewed
Probab=31.93  E-value=42  Score=15.23  Aligned_cols=30  Identities=10%  Similarity=0.276  Sum_probs=13.8

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             059999878999999999999999999856
Q gi|254780329|r    4 YEHVFLLRQDISSQQIKDTIGQYQSLIQEN   33 (135)
Q Consensus         4 YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~   33 (135)
                      |.+++|.++.+.......+...+..++.+.
T Consensus        77 ~DiViiar~~~~~~~~~~l~~~l~~ll~Ka  106 (116)
T PRK00499         77 YDFVVIARKPAEDLDYEEIKKSLIHVLKKA  106 (116)
T ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             759999686545499999999999999982


No 12 
>PRK05783 hypothetical protein; Provisional
Probab=30.98  E-value=44  Score=15.13  Aligned_cols=77  Identities=12%  Similarity=0.228  Sum_probs=52.8

Q ss_pred             CCC-CEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCH-----HHHHH
Q ss_conf             987-059999878999999999999999999856978999703686535303222418999999980897-----79999
Q gi|254780329|r    1 MKL-YEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPP-----AAIHE   74 (135)
Q Consensus         1 M~~-YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~-----~~i~e   74 (135)
                      |++ .++.+.++|.+.+.+-..+...   +.....|.+.               +-+.|-|+.|.++++.     +.+.+
T Consensus         1 M~y~v~v~I~~K~gi~DPeG~TI~~~---L~~~g~~~v~---------------~vR~GK~l~~~iea~s~eeA~~~v~~   62 (84)
T PRK05783          1 MRYAVELIITYKDGIRDPEGETIQRY---VLERMLGYSI---------------EVRAGKCLVFRIEASSPEEAQELALK   62 (84)
T ss_pred             CEEEEEEEEEECCCCCCCCHHHHHHH---HHHHCCCCEE---------------EEEEEEEEEEEEECCCHHHHHHHHHH
T ss_conf             95999999985897759633799999---9985589648---------------98710499999947998999999999


Q ss_pred             HHHHHCCCCHHEEEEEEEECC
Q ss_conf             999808980210011244113
Q gi|254780329|r   75 MKRKMRIDENVLRSLTLLVDS   95 (135)
Q Consensus        75 l~~~lk~~~~VLR~l~vk~~~   95 (135)
                      +-..|++-..|+--.+|+++.
T Consensus        63 ic~~lrL~NPvI~~~~i~v~~   83 (84)
T PRK05783         63 LAKEMRLGNPIVHKIVVRVER   83 (84)
T ss_pred             HHHHHHCCCCCEEEEEEEEEC
T ss_conf             998620349852899999962


No 13 
>PHA01632 hypothetical protein
Probab=28.76  E-value=48  Score=14.90  Aligned_cols=35  Identities=14%  Similarity=0.339  Sum_probs=26.3

Q ss_pred             CCCCCHHHHHH----HHHHHHHHHHHCCCEEEEEECCCC
Q ss_conf             78999999999----999999999856978999703686
Q gi|254780329|r   11 RQDISSQQIKD----TIGQYQSLIQENGGEVRLVNELGM   45 (135)
Q Consensus        11 ~p~~~~~~~~~----~~~~~~~~i~~~gg~i~~~e~wG~   45 (135)
                      ...-+++++.+    ++..+...|++..-+|.....||.
T Consensus        25 p~kpteeelrkvlpkilkdyanmie~gk~ki~ds~ewgi   63 (64)
T PHA01632         25 PQKPTEEELRKVLPKILKDYANMIENGKIKILDSKEWGI   63 (64)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCC
T ss_conf             799779999999999999999998618658763510255


No 14 
>COG1164 Oligoendopeptidase F [Amino acid transport and metabolism]
Probab=26.33  E-value=53  Score=14.65  Aligned_cols=51  Identities=14%  Similarity=0.201  Sum_probs=43.8

Q ss_pred             CCEEEEEECCCCCCCCEECCCCC-EEEEEEEEEECCHHHHHHHHHHHCCCCH
Q ss_conf             97899970368653530322241-8999999980897799999998089802
Q gi|254780329|r   34 GGEVRLVNELGMRTIAYRIRKNR-KAYYVFMNIASPPAAIHEMKRKMRIDEN   84 (135)
Q Consensus        34 gg~i~~~e~wG~r~LAY~I~k~~-~G~Y~~~~f~~~~~~i~el~~~lk~~~~   84 (135)
                      ++=|.-..+-|+|.-||-+.-.. .--|++|++.+....+.-|-..|.+.-.
T Consensus       342 ~~WiD~~~~~gKrsGaYs~~~~~~~~p~IlmN~~gt~~dV~TLaHElGHs~H  393 (598)
T COG1164         342 ERWIDVYPRKGKRSGAYSIGFYKGDHPFILMNYDGTLRDVFTLAHELGHSVH  393 (598)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHH
T ss_conf             3886235687999885268998888855876378965446687465018999


No 15 
>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int
Probab=25.95  E-value=54  Score=14.60  Aligned_cols=51  Identities=12%  Similarity=0.149  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEE-EEEEEECCHHHHHHHHHHHC
Q ss_conf             999999999999856978999703686535303222418999-99998089779999999808
Q gi|254780329|r   19 IKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY-VFMNIASPPAAIHEMKRKMR   80 (135)
Q Consensus        19 ~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y-~~~~f~~~~~~i~el~~~lk   80 (135)
                      ...++..+...+.++||.|....      ++     .--|.| ..+.++++.+.++.|+..|-
T Consensus        11 rpGiv~~vs~~v~~~gcNi~dSr------mt-----~lg~~Fa~imlvsG~w~~ia~lE~~L~   62 (77)
T cd04893          11 RPGILNELTRAVSESGCNILDSR------MA-----ILGTEFALTMLVEGSWDAIAKLEAALP   62 (77)
T ss_pred             CCHHHHHHHHHHHHCCCCEEHHH------HH-----HHHCCEEEEEEEECCHHHHHHHHHHHH
T ss_conf             86599999999998699872437------88-----873603899999528889999998627


No 16 
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.43  E-value=63  Score=14.20  Aligned_cols=59  Identities=12%  Similarity=0.252  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHCCCCHHE
Q ss_conf             999999999985697899970368653530322241899999998089779999999808980210
Q gi|254780329|r   21 DTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVL   86 (135)
Q Consensus        21 ~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk~~~~VL   86 (135)
                      ..+.++-+++.++|..+.+.|..       |-++....|.+++.++++...+.++-..|+-.-..+
T Consensus        12 GaL~~~L~~F~~~~iNlthIESR-------pSk~~~~~Y~ffvD~e~~~~~l~~~l~~Lk~~~~~v   70 (74)
T cd04929          12 GGLAKALKLFQELGINVVHIESR-------KSKRRSSEFEIFVDCECDQRRLDELVQLLKREVASV   70 (74)
T ss_pred             CHHHHHHHHHHHCCCCEEEEECC-------CCCCCCCEEEEEEEECCCHHHHHHHHHHHHHHCEEE
T ss_conf             67999999999869777998558-------787889718999990399799999999999852099


No 17 
>pfam05211 NLBH Neuraminyllactose-binding hemagglutinin precursor (NLBH). This family is comprised of several flagellar sheath adhesin proteins also called neuraminyllactose-binding hemagglutinin precursor (NLBH) or N-acetylneuraminyllactose-binding fibrillar hemagglutinin receptor-binding subunits. NLBH is found exclusively in Helicobacter which are gut colonising bacteria and bind to sialic acid rich macromolecules present on the gastric epithelium.
Probab=21.31  E-value=67  Score=14.06  Aligned_cols=73  Identities=18%  Similarity=0.276  Sum_probs=42.3

Q ss_pred             CCCEEEEEECCCCCHHH----------HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHH
Q ss_conf             87059999878999999----------99999999999985697899970368653530322241899999998089779
Q gi|254780329|r    2 KLYEHVFLLRQDISSQQ----------IKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAA   71 (135)
Q Consensus         2 ~~YE~~~i~~p~~~~~~----------~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~   71 (135)
                      .+++++.|++|.+.-.+          -+.++.++++++++.|=++..+.+-  ..|...+++  + -|.++...+.-..
T Consensus        31 ~n~h~v~ll~P~iq~sdni~k~Y~~kF~n~l~~qi~~ilek~GY~v~~fkD~--~~l~~~~Kk--k-~~lvL~m~G~v~i  105 (228)
T pfam05211        31 ANDHKVLLLRPAIQYSDNIAKEYENKFKNQLTLQVEEILENQGYKVINFSDK--DDFSFAQKK--K-GYLVLAMNGEVVI  105 (228)
T ss_pred             CCCCEEEEECCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCH--HHCCHHHHH--H-HEEEEECCCCEEE
T ss_conf             6672599963533011233678999999999999999998569357762452--223667653--1-0689962574887


Q ss_pred             HHHHHHHH
Q ss_conf             99999980
Q gi|254780329|r   72 IHEMKRKM   79 (135)
Q Consensus        72 i~el~~~l   79 (135)
                      +.++++.+
T Consensus       106 leD~k~~~  113 (228)
T pfam05211       106 LEDPKRTI  113 (228)
T ss_pred             ECCHHHHC
T ss_conf             12636433


No 18 
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=20.65  E-value=50  Score=14.81  Aligned_cols=66  Identities=17%  Similarity=0.274  Sum_probs=46.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEE--E--EEEEEECCHHHHHHHHHH
Q ss_conf             99999999999999999985697899970368653530322241899--9--999980897799999998
Q gi|254780329|r   13 DISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAY--Y--VFMNIASPPAAIHEMKRK   78 (135)
Q Consensus        13 ~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~--Y--~~~~f~~~~~~i~el~~~   78 (135)
                      .++.+++..+++.+..-|.+.|...+.....|..=|.+--.=..-||  |  ++-.|....+...+|+..
T Consensus        78 pv~~~~ie~~v~~Ie~~l~~~~~~EI~S~~IGe~Vm~~Lk~lD~VAYvRFASVYr~F~d~~~F~~ei~~L  147 (149)
T PRK00464         78 PVSSEQIEAAVSRIERQLRASGEREVPSKEIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFEEEIEEL  147 (149)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCEEEHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             9899999999999999999838887559999999999886209310000245606779999999999997


No 19 
>pfam09569 RE_ScaI ScaI restriction endonuclease. This family includes the ScaI (recognizes and cleaves AGT^ACT) restriction endonuclease.
Probab=20.03  E-value=67  Score=14.04  Aligned_cols=30  Identities=27%  Similarity=0.478  Sum_probs=20.8

Q ss_pred             CCCCCCCCEECC---CCCEEEEEEEEEECCHHH
Q ss_conf             368653530322---241899999998089779
Q gi|254780329|r   42 ELGMRTIAYRIR---KNRKAYYVFMNIASPPAA   71 (135)
Q Consensus        42 ~wG~r~LAY~I~---k~~~G~Y~~~~f~~~~~~   71 (135)
                      -.|.|-.+|.-+   |-+.|||+.++|+-..+.
T Consensus       114 IfGNRSyg~~~~~~~Ksk~GYYLaINfekf~e~  146 (191)
T pfam09569       114 IYGNRSYGYRPDDGKKSKDGYYLAINFEKFKED  146 (191)
T ss_pred             EECCCCCCCCCCCCCCCCCCEEEEEEEECCCCC
T ss_conf             233422144678874455755999971036777


Done!