Query         gi|254780248|ref|YP_003064661.1| 30S ribosomal protein S14 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 101
No_of_seqs    107 out of 1176
Neff          5.4 
Searched_HMMs 39220
Date          Tue May 24 06:52:08 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780248.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK08881 rpsN 30S ribosomal pr 100.0 5.9E-44       0  288.3  10.2  101    1-101     1-101 (101)
  2 PRK06911 rpsN 30S ribosomal pr 100.0 2.7E-43       0  284.3  10.3  100    1-101     1-100 (100)
  3 CHL00074 rps14 ribosomal prote 100.0 9.1E-43       0  281.0  10.0  100    1-101     1-100 (100)
  4 KOG1741 consensus              100.0 8.3E-34 2.1E-38  226.5   9.3  101    1-101     3-103 (103)
  5 PRK08061 rpsN 30S ribosomal pr  99.9 1.6E-23 4.2E-28  163.9   1.8   51   49-101    11-61  (61)
  6 COG0199 RpsN Ribosomal protein  99.9 1.6E-22   4E-27  157.9   2.8   60   42-101     2-61  (61)
  7 pfam00253 Ribosomal_S14 Riboso  99.8 7.8E-21   2E-25  147.6   2.5   54   47-100     2-55  (55)
  8 PRK05766 rps14P 30S ribosomal   93.4   0.033 8.4E-07   34.3   1.2   40   51-90      4-45  (52)
  9 PTZ00218 40S ribosomal protein  91.8   0.067 1.7E-06   32.4   1.0   30   61-90     16-47  (54)
 10 KOG3506 consensus               84.0    0.52 1.3E-05   27.0   1.4   29   62-90     19-49  (56)
 11 pfam09541 consensus             53.8      14 0.00036   18.3   3.0   56   41-96      2-70  (120)
 12 TIGR02018 his_ut_repres histid  45.9     9.5 0.00024   19.3   1.1   21   74-94     32-56  (234)
 13 pfam06353 DUF1062 Protein of u  43.8      14 0.00037   18.2   1.8   32   67-98    102-134 (142)
 14 KOG2290 consensus               41.4     6.8 0.00017   20.2  -0.2   29   60-89    386-414 (652)
 15 pfam10346 Con-6 Conidiation pr  38.1      34 0.00086   16.0   2.9   28   25-52      8-35  (36)
 16 pfam10654 DUF2481 Protein of u  37.1      36 0.00091   15.8   4.2   46   17-63      6-51  (126)
 17 TIGR01764 excise DNA binding d  35.7      22 0.00055   17.2   1.6   22   76-97     10-31  (49)
 18 pfam05930 Phage_AlpA Prophage   31.0      36 0.00093   15.8   2.1   29   70-98      6-34  (51)
 19 pfam04831 Popeye Popeye protei  25.3      36 0.00092   15.8   1.3   23   72-94      8-32  (154)
 20 TIGR01672 AphA HAD superfamily  22.4      26 0.00065   16.7   0.1   18   59-76    131-149 (248)
 21 PRK05797 consensus              20.8      30 0.00077   16.3   0.2   53   47-99    615-667 (869)
 22 PRK05415 hypothetical protein;  20.5      65  0.0017   14.2   1.8   26   66-92    231-256 (338)

No 1  
>PRK08881 rpsN 30S ribosomal protein S14; Reviewed
Probab=100.00  E-value=5.9e-44  Score=288.29  Aligned_cols=101  Identities=54%  Similarity=0.918  Sum_probs=100.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHH
Q ss_conf             91268999999999999999999999999834879898999999999720860443244402214356641144042562
Q gi|254780248|r    1 MAKVSAVERNKRRLRVVAKQASKRLALKKIVMDKSVTLEERFDAMLQLGSLPRDGSRVRVRNRCEISGRSRGVYRDFRLS   80 (101)
Q Consensus         1 Makks~i~rd~kRr~l~~k~~~kR~~lk~~~~~~~l~~~~r~~a~~kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lS   80 (101)
                      |||||+|+||.+|++|+++|+.+|..||++++|+++|++++++|+.+|++||+||||||++|||++||||||||++||||
T Consensus         1 MAkks~i~rd~kRr~l~~k~~~kR~~lK~~~~n~~l~~e~r~~a~~kL~~LPrnss~~RirNRC~~TGR~Rg~~r~f~lS   80 (101)
T PRK08881          1 MAKKSMIAREEKRKKLVAKYAAKRAELKAIIDDENLSEEERFEARLKLQKLPRDSSPTRLRNRCELTGRPRGYYRKFGLS   80 (101)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCCCCEECCCCCCH
T ss_conf             95578999999999999999999999999985779999999999999874663434177726123789976310342404


Q ss_pred             HHHHHHHHHCCCCCCCCCCCC
Q ss_conf             999999996589998321469
Q gi|254780248|r   81 RLALRELGGVGKIPGIIKSSW  101 (101)
Q Consensus        81 Ri~fRela~~G~ipGv~KaSW  101 (101)
                      ||+|||||+.|+||||+||||
T Consensus        81 Ri~~RelA~~G~lpGv~KaSW  101 (101)
T PRK08881         81 RIKLRELAHRGEIPGVVKASW  101 (101)
T ss_pred             HHHHHHHHHCCCCCCEECCCC
T ss_conf             999999998698888422679


No 2  
>PRK06911 rpsN 30S ribosomal protein S14; Reviewed
Probab=100.00  E-value=2.7e-43  Score=284.25  Aligned_cols=100  Identities=37%  Similarity=0.604  Sum_probs=98.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHH
Q ss_conf             91268999999999999999999999999834879898999999999720860443244402214356641144042562
Q gi|254780248|r    1 MAKVSAVERNKRRLRVVAKQASKRLALKKIVMDKSVTLEERFDAMLQLGSLPRDGSRVRVRNRCEISGRSRGVYRDFRLS   80 (101)
Q Consensus         1 Makks~i~rd~kRr~l~~k~~~kR~~lk~~~~~~~l~~~~r~~a~~kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lS   80 (101)
                      |||||+|+||.+|.+|+++|+.+|.+||+++++. .|++++++|+.+|++||+||||||++|||++|||||||||+||||
T Consensus         1 MAKkS~i~R~~kR~klv~ky~~kR~~Lk~~i~~~-~~~eer~~a~~kL~kLPRnSsp~R~rNRC~~TGRpRg~yRkFgLS   79 (100)
T PRK06911          1 MAKKSMLMRESKRAKLVEKYRQRRNELKQLIKSS-DDFQVIMESQAKLAKLPVNSNPVRYVTRCKQCGRPHAVYRKFNLC   79 (100)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCHHHHCCCH
T ss_conf             9457899999999999999999999999998558-999999999999985777676178742201689864002121556


Q ss_pred             HHHHHHHHHCCCCCCCCCCCC
Q ss_conf             999999996589998321469
Q gi|254780248|r   81 RLALRELGGVGKIPGIIKSSW  101 (101)
Q Consensus        81 Ri~fRela~~G~ipGv~KaSW  101 (101)
                      ||+|||||+.|+||||+||||
T Consensus        80 Ri~~RelA~~G~lPGv~KaSW  100 (100)
T PRK06911         80 RICLRQQLMVGNIPGGRKSSW  100 (100)
T ss_pred             HHHHHHHHHCCCCCCEECCCC
T ss_conf             999999997697988325889


No 3  
>CHL00074 rps14 ribosomal protein S14
Probab=100.00  E-value=9.1e-43  Score=281.04  Aligned_cols=100  Identities=43%  Similarity=0.702  Sum_probs=98.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHH
Q ss_conf             91268999999999999999999999999834879898999999999720860443244402214356641144042562
Q gi|254780248|r    1 MAKVSAVERNKRRLRVVAKQASKRLALKKIVMDKSVTLEERFDAMLQLGSLPRDGSRVRVRNRCEISGRSRGVYRDFRLS   80 (101)
Q Consensus         1 Makks~i~rd~kRr~l~~k~~~kR~~lk~~~~~~~l~~~~r~~a~~kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lS   80 (101)
                      |||||+|+||.+|++|+++|+.+|..|+++++| +++++++++|+.+|++||+||||||++|||++||||||||++||||
T Consensus         1 MAKkS~I~Rd~kR~~lv~ky~~kR~~lk~~i~~-~~~~~er~~a~~kL~kLPrnSs~~R~rNRC~~TGRpRg~~r~Fgls   79 (100)
T CHL00074          1 MAKKSLIQREKKRQKLVQKYHLIRRSLKKEIKK-VSSLSEKWEIHGKLQSLPRNSAPTRLHRRCFLTGRPRGNYRDFGLS   79 (100)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCEEECCCCCH
T ss_conf             953789999999999999999999999998744-7999999999999986116556688874510579975300110424


Q ss_pred             HHHHHHHHHCCCCCCCCCCCC
Q ss_conf             999999996589998321469
Q gi|254780248|r   81 RLALRELGGVGKIPGIIKSSW  101 (101)
Q Consensus        81 Ri~fRela~~G~ipGv~KaSW  101 (101)
                      ||+|||||+.|+||||+||||
T Consensus        80 Ri~~RelA~~G~ipGv~KaSW  100 (100)
T CHL00074         80 RHVLREMAHACLLPGVTKSSW  100 (100)
T ss_pred             HHHHHHHHHCCCCCCEECCCC
T ss_conf             899999998698988313779


No 4  
>KOG1741 consensus
Probab=100.00  E-value=8.3e-34  Score=226.54  Aligned_cols=101  Identities=39%  Similarity=0.673  Sum_probs=99.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHH
Q ss_conf             91268999999999999999999999999834879898999999999720860443244402214356641144042562
Q gi|254780248|r    1 MAKVSAVERNKRRLRVVAKQASKRLALKKIVMDKSVTLEERFDAMLQLGSLPRDGSRVRVRNRCEISGRSRGVYRDFRLS   80 (101)
Q Consensus         1 Makks~i~rd~kRr~l~~k~~~kR~~lk~~~~~~~l~~~~r~~a~~kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lS   80 (101)
                      |+.++.|.||.+|++++++|+..|..+|+|.+|++||...+.+|..||++||+||.||+|+|||+.||||||||+.|+||
T Consensus         3 ~~~~~r~~Rd~krRkl~~e~~~~R~slk~i~knp~LP~~~r~ea~~kl~alPrns~ptrI~NRCv~TGR~R~v~r~frLs   82 (103)
T KOG1741           3 GAKKWRILRDVKRRKLFKEYELERRSLKEISKNPILPEKLRDEAAEKLQALPRNSAPTRIKNRCVFTGRPRGVYRDFRLS   82 (103)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf             15779998899999999999999999999981886129999989999852765654299998888438864320102368


Q ss_pred             HHHHHHHHHCCCCCCCCCCCC
Q ss_conf             999999996589998321469
Q gi|254780248|r   81 RLALRELGGVGKIPGIIKSSW  101 (101)
Q Consensus        81 Ri~fRela~~G~ipGv~KaSW  101 (101)
                      ||+||++|+.|.||||+||||
T Consensus        83 R~~FR~~A~~~~LpGv~rasW  103 (103)
T KOG1741          83 RHVFRELADAGALPGVTRASW  103 (103)
T ss_pred             HHHHHHHHHHCCCCCCCCCCC
T ss_conf             899999887145767522469


No 5  
>PRK08061 rpsN 30S ribosomal protein S14; Reviewed
Probab=99.87  E-value=1.6e-23  Score=163.90  Aligned_cols=51  Identities=47%  Similarity=0.874  Sum_probs=46.6

Q ss_pred             HHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             20860443244402214356641144042562999999996589998321469
Q gi|254780248|r   49 GSLPRDGSRVRVRNRCEISGRSRGVYRDFRLSRLALRELGGVGKIPGIIKSSW  101 (101)
Q Consensus        49 ~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lSRi~fRela~~G~ipGv~KaSW  101 (101)
                      ++-|+.  +||++|||.+|||||||||+||||||+|||+|+.|+||||+||||
T Consensus        11 ~~~~Kf--~tR~~NRC~~tGRprg~~R~FglsRi~fRelA~~G~iPGv~KsSW   61 (61)
T PRK08061         11 KRKPKF--KVRAYTRCERCGRPHSVYRKFGLCRICFRELAYKGQIPGVKKASW   61 (61)
T ss_pred             CCCCCC--CCCCCCCCCCCCCCCEEECCCCCHHHHHHHHHHCCCCCCEECCCC
T ss_conf             549888--740101025689876651214616999999997796787662679


No 6  
>COG0199 RpsN Ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=99.85  E-value=1.6e-22  Score=157.90  Aligned_cols=60  Identities=52%  Similarity=0.835  Sum_probs=58.3

Q ss_pred             HHHHHHHHHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             999999720860443244402214356641144042562999999996589998321469
Q gi|254780248|r   42 FDAMLQLGSLPRDGSRVRVRNRCEISGRSRGVYRDFRLSRLALRELGGVGKIPGIIKSSW  101 (101)
Q Consensus        42 ~~a~~kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lSRi~fRela~~G~ipGv~KaSW  101 (101)
                      +.++++|+++|+|++++|++|||.+|||||||||+|+|||++|||+|+.|+||||+||||
T Consensus         2 ~~a~~~~~~~p~~~~~~r~~nRC~~cGRprgv~Rkf~lcR~cfRE~A~~g~ipGv~KasW   61 (61)
T COG0199           2 AMAKLKLKALPRPKSPGRGRNRCRRCGRPRGVIRKFGLCRICFRELAHKGEIPGVKKASW   61 (61)
T ss_pred             CHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEECCC
T ss_conf             213344531788776555633130369973233555437999999861068887472569


No 7  
>pfam00253 Ribosomal_S14 Ribosomal protein S14p/S29e. This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes.
Probab=99.81  E-value=7.8e-21  Score=147.59  Aligned_cols=54  Identities=54%  Similarity=0.911  Sum_probs=52.8

Q ss_pred             HHHHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             972086044324440221435664114404256299999999658999832146
Q gi|254780248|r   47 QLGSLPRDGSRVRVRNRCEISGRSRGVYRDFRLSRLALRELGGVGKIPGIIKSS  100 (101)
Q Consensus        47 kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lSRi~fRela~~G~ipGv~KaS  100 (101)
                      +|+++|+||+++|++|||++|||+||||++|||||++|||+|+.|+|||++|||
T Consensus         2 ~l~~~~~~ss~~r~~nRC~~tGR~rgv~rkf~lsR~~fRe~A~~g~i~G~~Kas   55 (55)
T pfam00253         2 KLSKLPRNSSPTRGRNRCVLTGRPRGVIRKFGLSRICFRELAHKGLIPGVKKAS   55 (55)
T ss_pred             CCCCCCCCCCHHHHHCEECCCCCCCEEECCCCCHHHHHHHHHHCCCCCCEECCC
T ss_conf             423176756606762300488997675435561299999999769788867179


No 8  
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=93.36  E-value=0.033  Score=34.29  Aligned_cols=40  Identities=28%  Similarity=0.522  Sum_probs=31.3

Q ss_pred             CCHHHHHHHHCCCCCCCCCCCHHHHHHC--HHHHHHHHHHHC
Q ss_conf             8604432444022143566411440425--629999999965
Q gi|254780248|r   51 LPRDGSRVRVRNRCEISGRSRGVYRDFR--LSRLALRELGGV   90 (101)
Q Consensus        51 Lprnss~tRi~NRC~~TGR~Rgv~r~f~--lSRi~fRela~~   90 (101)
                      .|+.-.-.+--+.|.++|+..|++++||  |||-+|||.|..
T Consensus         4 ~p~~r~~G~gsr~Cr~Cg~~~glIrKYgL~lCRqCFRE~A~~   45 (52)
T PRK05766          4 PPKERKYGKGARRCRRCGRKGGLIRKYGLYLCRQCFREVAPK   45 (52)
T ss_pred             CCCCCCCCCCCCEEEECCCCCCEEEEECCHHHHHHHHHHHHH
T ss_conf             998876788878125269976678870616588999988987


No 9  
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=91.76  E-value=0.067  Score=32.41  Aligned_cols=30  Identities=20%  Similarity=0.534  Sum_probs=26.4

Q ss_pred             CCCCCCCCCCCHHHHHHC--HHHHHHHHHHHC
Q ss_conf             022143566411440425--629999999965
Q gi|254780248|r   61 RNRCEISGRSRGVYRDFR--LSRLALRELGGV   90 (101)
Q Consensus        61 ~NRC~~TGR~Rgv~r~f~--lSRi~fRela~~   90 (101)
                      -..|.++|...|++|+||  +||-+|||.|..
T Consensus        16 Sr~CrvC~~~~glIRKYgLn~CRqCFRe~A~~   47 (54)
T PTZ00218         16 SRECRVCSNRHGLIRKYGLNVCRQCFRENAEL   47 (54)
T ss_pred             CCEEECCCCCCCEEEEECCHHHHHHHHHHHHH
T ss_conf             77338268973278872641468899887776


No 10 
>KOG3506 consensus
Probab=83.97  E-value=0.52  Score=26.98  Aligned_cols=29  Identities=24%  Similarity=0.567  Sum_probs=25.1

Q ss_pred             CCCCCCCCCCHHHHHHCH--HHHHHHHHHHC
Q ss_conf             221435664114404256--29999999965
Q gi|254780248|r   62 NRCEISGRSRGVYRDFRL--SRLALRELGGV   90 (101)
Q Consensus        62 NRC~~TGR~Rgv~r~f~l--SRi~fRela~~   90 (101)
                      .-|.+++.-+|.+++|||  ||.+|||.|.-
T Consensus        19 rsC~vCsn~~gLIrKYGL~vcr~cfr~~a~d   49 (56)
T KOG3506          19 RSCRVCSNRHGLIRKYGLNVCRQCFREYAND   49 (56)
T ss_pred             CCEEEECCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             4046506525589997268859999963403


No 11 
>pfam09541 consensus
Probab=53.78  E-value=14  Score=18.29  Aligned_cols=56  Identities=23%  Similarity=0.328  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHCCHHHHHHHHCCCCCCCCCC-------------CHHHHHHCHHHHHHHHHHHCCCCCCC
Q ss_conf             999999972086044324440221435664-------------11440425629999999965899983
Q gi|254780248|r   41 RFDAMLQLGSLPRDGSRVRVRNRCEISGRS-------------RGVYRDFRLSRLALRELGGVGKIPGI   96 (101)
Q Consensus        41 r~~a~~kL~~Lprnss~tRi~NRC~~TGR~-------------Rgv~r~f~lSRi~fRela~~G~ipGv   96 (101)
                      |.+.+.-+.+|||+.-....|--|.+-|-.             .+-|..|.--.++.-||...|+=|-.
T Consensus         2 RLWHe~LI~~LPr~QLLgQhREc~ALRGngWgkkHatVdYVF~~spy~L~~Yh~lVm~EM~~RGY~~~~   70 (120)
T pfam09541         2 RLWHEDLIDKLPRQQLLGQHRECCALRGNGWGKKHATVDYVFNYSPYKLFQYHLLVMDEMQKRGYHPNE   70 (120)
T ss_pred             CCHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCH
T ss_conf             413898996575888888999999997378898863564420278599999999999999983899996


No 12 
>TIGR02018 his_ut_repres histidine utilization repressor; InterPro: IPR010248   This entry represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0006547 histidine metabolic process, 0045892 negative regulation of transcription DNA-dependent.
Probab=45.94  E-value=9.5  Score=19.32  Aligned_cols=21  Identities=38%  Similarity=0.627  Sum_probs=17.2

Q ss_pred             HHHHCHHHHH----HHHHHHCCCCC
Q ss_conf             4042562999----99999658999
Q gi|254780248|r   74 YRDFRLSRLA----LRELGGVGKIP   94 (101)
Q Consensus        74 ~r~f~lSRi~----fRela~~G~ip   94 (101)
                      ...||+||..    ||||+..|+|-
T Consensus        32 ~~~~G~SRMTvnrALreLt~~G~l~   56 (234)
T TIGR02018        32 VAQFGVSRMTVNRALRELTDAGLLE   56 (234)
T ss_pred             HHHHCCCHHHHHHHHHHHHHCCCEE
T ss_conf             9774872335789999887568188


No 13 
>pfam06353 DUF1062 Protein of unknown function (DUF1062). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=43.78  E-value=14  Score=18.21  Aligned_cols=32  Identities=31%  Similarity=0.384  Sum_probs=24.3

Q ss_pred             CCCCCHHH-HHHCHHHHHHHHHHHCCCCCCCCC
Q ss_conf             56641144-042562999999996589998321
Q gi|254780248|r   67 SGRSRGVY-RDFRLSRLALRELGGVGKIPGIIK   98 (101)
Q Consensus        67 TGR~Rgv~-r~f~lSRi~fRela~~G~ipGv~K   98 (101)
                      .=|.-.++ ..+||||-.+..|...|.|-|+..
T Consensus       102 ~~Rl~~Lla~~L~lSrs~l~~l~~~G~i~~~~~  134 (142)
T pfam06353       102 SLRLDRLLAEELGLSRSRLQRLIDQGQIRGVPE  134 (142)
T ss_pred             CCCHHHHHHHHHCCCHHHHHHHHHCCCEECCCC
T ss_conf             642999999881868999999998898770575


No 14 
>KOG2290 consensus
Probab=41.39  E-value=6.8  Score=20.23  Aligned_cols=29  Identities=24%  Similarity=0.374  Sum_probs=23.2

Q ss_pred             HCCCCCCCCCCCHHHHHHCHHHHHHHHHHH
Q ss_conf             402214356641144042562999999996
Q gi|254780248|r   60 VRNRCEISGRSRGVYRDFRLSRLALRELGG   89 (101)
Q Consensus        60 i~NRC~~TGR~Rgv~r~f~lSRi~fRela~   89 (101)
                      -|--|++|||| -.+-.=|+|+|.-||+.+
T Consensus       386 pHmdC~ItGRP-CCI~~qG~CeIttreYCd  414 (652)
T KOG2290         386 PHMDCQITGRP-CCIGTQGLCEITTREYCD  414 (652)
T ss_pred             CCEEEEECCCC-CEECCCCEEEECHHHHHH
T ss_conf             75035753885-255157526631677778


No 15 
>pfam10346 Con-6 Conidiation protein 6. Con-6 is the conserved N-terminal region of a family of small proteins found in fungi. It is expressed at approximately 6 hours after the induction of development and is induced just prior to major constriction-chain growth.
Probab=38.13  E-value=34  Score=15.97  Aligned_cols=28  Identities=21%  Similarity=0.161  Sum_probs=24.6

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             9999983487989899999999972086
Q gi|254780248|r   25 LALKKIVMDKSVTLEERFDAMLQLGSLP   52 (101)
Q Consensus        25 ~~lk~~~~~~~l~~~~r~~a~~kL~~Lp   52 (101)
                      .-||+.+.|+..|.+-+..|+.+|+.+.
T Consensus         8 ~G~KAal~NP~VSeeaK~~a~e~L~~~~   35 (36)
T pfam10346         8 RGYKAALHNPNVSEEAKEHAREKLEELG   35 (36)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHC
T ss_conf             7888772598531899999999999815


No 16 
>pfam10654 DUF2481 Protein of unknown function (DUF2481). This is a hypothetical protein family homologous to Lmo2305 in Bacteriophage A118 systems.
Probab=37.10  E-value=36  Score=15.84  Aligned_cols=46  Identities=15%  Similarity=0.301  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHCCC
Q ss_conf             99999999999998348798989999999997208604432444022
Q gi|254780248|r   17 VAKQASKRLALKKIVMDKSVTLEERFDAMLQLGSLPRDGSRVRVRNR   63 (101)
Q Consensus        17 ~~k~~~kR~~lk~~~~~~~l~~~~r~~a~~kL~~Lprnss~tRi~NR   63 (101)
                      .+..+-+|..+-.++ |..||+.++-+.+.+|+.|-.-.---..+++
T Consensus         6 tenKarQreIIsyl~-n~dl~~~~rk~LqkeLn~Lmn~nTeeK~kt~   51 (126)
T pfam10654         6 TENKARQREIISYLI-NENLPLAERKELQKELNQLMNENTEEKQKTY   51 (126)
T ss_pred             HHHHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHCCHHHHHHHH
T ss_conf             432899999999998-5788868999999999999860739999999


No 17 
>TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093   An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This entry identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (IPR000551 from INTERPRO).; GO: 0003677 DNA binding.
Probab=35.74  E-value=22  Score=17.15  Aligned_cols=22  Identities=18%  Similarity=0.247  Sum_probs=19.4

Q ss_pred             HHCHHHHHHHHHHHCCCCCCCC
Q ss_conf             4256299999999658999832
Q gi|254780248|r   76 DFRLSRLALRELGGVGKIPGII   97 (101)
Q Consensus        76 ~f~lSRi~fRela~~G~ipGv~   97 (101)
                      .-|+|+-.+++|++.|.||.++
T Consensus        10 yLgv~~~t~~~l~~~g~l~~~~   31 (49)
T TIGR01764        10 YLGVSKSTVYRLIEEGELPAYR   31 (49)
T ss_pred             HCCCCHHHHHHHHHCCCCCEEE
T ss_conf             7199905789999718985000


No 18 
>pfam05930 Phage_AlpA Prophage CP4-57 regulatory protein (AlpA). This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. Several of the sequences in this family are thought to be DNA-binding proteins.
Probab=30.96  E-value=36  Score=15.78  Aligned_cols=29  Identities=31%  Similarity=0.243  Sum_probs=23.0

Q ss_pred             CCHHHHHHCHHHHHHHHHHHCCCCCCCCC
Q ss_conf             41144042562999999996589998321
Q gi|254780248|r   70 SRGVYRDFRLSRLALRELGGVGKIPGIIK   98 (101)
Q Consensus        70 ~Rgv~r~f~lSRi~fRela~~G~ipGv~K   98 (101)
                      -.-|....|+||-.+-.+...|.+|-=.|
T Consensus         6 ~~eV~~~~glsrstiyr~i~~G~FP~pik   34 (51)
T pfam05930         6 LKEVEQLTGLSRSTIYRLIKDGEFPKPIK   34 (51)
T ss_pred             HHHHHHHHCCCHHHHHHHHHCCCCCCCEE
T ss_conf             99999998989999999998799999876


No 19 
>pfam04831 Popeye Popeye protein conserved region. The function of Popeye proteins is not well understood. They are predominantly expressed in cardiac and skeletal muscle. This family represents a conserved region which includes three potential transmembrane domains.
Probab=25.34  E-value=36  Score=15.81  Aligned_cols=23  Identities=9%  Similarity=0.323  Sum_probs=18.1

Q ss_pred             HHHHHHCHHHHHHHHHHHC--CCCC
Q ss_conf             1440425629999999965--8999
Q gi|254780248|r   72 GVYRDFRLSRLALRELGGV--GKIP   94 (101)
Q Consensus        72 gv~r~f~lSRi~fRela~~--G~ip   94 (101)
                      .++..++++|++|+++++.  |.|-
T Consensus         8 ~lF~Pl~V~r~~Fk~lv~~~~~~i~   32 (154)
T pfam04831         8 ALFLPLHVPLEVFKEITGCCECEVH   32 (154)
T ss_pred             HHHCCCCCCHHHHHHHHHHHHCEEE
T ss_conf             9700459999999999865532787


No 20 
>TIGR01672 AphA HAD superfamily (subfamily IIIB) phosphatase, TIGR01672; InterPro: IPR010025   This family of proteins is a member of the IIIB subfamily (IPR001001 from INTERPRO) of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterised members of subfamily III and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs , all of which are found conserved in this family.   AphA is a periplasmic acid phosphatase of Escherichia coli  belonging to class B bacterial phosphatases , which is part of the DDDD superfamily of phosphohydrolases. The crystal structure of AphA has been determined at 2.2A and its resolution extended to 1.7A. Despite the lack of sequence homology, the AphA structure reveals a haloacid dehalogenase-like fold. This finding suggests that this fold could be conserved among members of the DDDD superfamily of phosphohydrolases. The active enzyme is a homotetramer built by using an extended N-terminal arm intertwining the four monomers. The active site of the native enzyme hosts a magnesium ion, which can be replaced by other metal ions. The structure explains the non-specific behaviour of AphA towards substrates, while a structure-based alignment with other phosphatases provides clues about the catalytic mechanism . ; GO: 0003993 acid phosphatase activity, 0030288 outer membrane-bounded periplasmic space.
Probab=22.38  E-value=26  Score=16.71  Aligned_cols=18  Identities=28%  Similarity=0.571  Sum_probs=12.3

Q ss_pred             HHCCCCCCCCCCCH-HHHH
Q ss_conf             44022143566411-4404
Q gi|254780248|r   59 RVRNRCEISGRSRG-VYRD   76 (101)
Q Consensus        59 Ri~NRC~~TGR~Rg-v~r~   76 (101)
                      |==.--++|||++| .|++
T Consensus       131 RGD~i~F~TGRt~gsmykk  149 (248)
T TIGR01672       131 RGDKIFFVTGRTAGSMYKK  149 (248)
T ss_pred             HCCEEEEEECCCCCCCCCC
T ss_conf             0987999846876443325


No 21 
>PRK05797 consensus
Probab=20.80  E-value=30  Score=16.28  Aligned_cols=53  Identities=19%  Similarity=0.193  Sum_probs=40.5

Q ss_pred             HHHHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             97208604432444022143566411440425629999999965899983214
Q gi|254780248|r   47 QLGSLPRDGSRVRVRNRCEISGRSRGVYRDFRLSRLALRELGGVGKIPGIIKS   99 (101)
Q Consensus        47 kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lSRi~fRela~~G~ipGv~Ka   99 (101)
                      .||++|..+-.-|--.+|++.+-...++=-+--|-|-+|=|||...-|++..|
T Consensus       615 NLQNIP~r~e~G~~iR~aFi~~~~~~~l~saDYSQIELRilAh~s~d~~l~~a  667 (869)
T PRK05797        615 NLQNIPIKYEMGREIRKVFIPNTEDSVILSADYSQIELRVLAHISGDENLIDA  667 (869)
T ss_pred             CCCCCCCCCCCHHHHHHEEECCCCCCEEEECCHHHHHHHHHHHHHCCHHHHHH
T ss_conf             64568776520122553571477761588522778999999998468999998


No 22 
>PRK05415 hypothetical protein; Provisional
Probab=20.55  E-value=65  Score=14.24  Aligned_cols=26  Identities=27%  Similarity=0.295  Sum_probs=22.5

Q ss_pred             CCCCCCHHHHHHCHHHHHHHHHHHCCC
Q ss_conf             356641144042562999999996589
Q gi|254780248|r   66 ISGRSRGVYRDFRLSRLALRELGGVGK   92 (101)
Q Consensus        66 ~TGR~Rgv~r~f~lSRi~fRela~~G~   92 (101)
                      ..||+ ||+..++|-|.+|-.||-.|-
T Consensus       231 YG~r~-G~~gr~rL~R~Vl~~la~aGa  256 (338)
T PRK05415        231 YGIEL-GYLSRIRLFRLVLANIAFAGA  256 (338)
T ss_pred             HCCCC-HHHHHHHHHHHHHHHHHHHHH
T ss_conf             68780-187999999999999999729


Done!