Query         gi|254780475|ref|YP_003064888.1| 50S ribosomal protein L33 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 55
No_of_seqs    108 out of 436
Neff          4.1 
Searched_HMMs 13730
Date          Wed Jun  1 05:55:16 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780475.hhm -d /home/congqian_1/database/scop/scop70_1_75.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 d2zjr11 g.41.8.6 (1:2-54) Ribo  99.9 1.3E-23 9.3E-28  141.7   6.2   51    3-53      3-53  (53)
  2 d2gyc11 g.41.8.6 (1:1-52) Ribo  99.9 5.3E-24 3.9E-28  143.6  -1.6   52    2-53      1-52  (52)
  3 d2j0161 g.41.8.6 (6:9-53) Ribo  99.7 2.3E-19 1.7E-23  119.4  -1.7   45    9-53      1-45  (45)
  4 d1vqo31 g.41.8.3 (3:1-92) Ribo  93.2   0.028   2E-06   30.1   2.9   21   35-55      6-26  (92)
  5 d2cona1 g.41.15.1 (A:8-73) RNA  25.1      10 0.00074   16.7   0.8   31    9-51      7-37  (66)
  6 d2cu8a1 g.39.1.3 (A:8-37) Cyst  15.3      13 0.00093   16.2  -0.5   17   37-53      2-18  (30)
  7 d2fyga1 g.86.1.1 (A:6-128) Non   7.0      21  0.0015   15.0  -1.7   41    9-49     37-78  (123)
  8 d1zu1a2 g.37.1.4 (A:74-128) ds   6.9      51  0.0037   13.0   0.2   11   35-45     19-29  (55)
  9 d1xx6a2 g.39.1.14 (A:143-191)    6.7      46  0.0034   13.2  -0.1   12   37-48     35-46  (49)
 10 d2k4xa1 g.41.8.8 (A:1-55) Ribo   6.6      43  0.0031   13.4  -0.3    8   36-43     17-24  (55)

No 1  
>d2zjr11 g.41.8.6 (1:2-54) Ribosomal protein L33p {Deinococcus radiodurans [TaxId: 1299]}
Probab=99.88  E-value=1.3e-23  Score=141.66  Aligned_cols=51  Identities=49%  Similarity=0.746  Sum_probs=49.6

Q ss_pred             CCCEEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             776269999951778875983548899833369941317446344668865
Q gi|254780475|r    3 KAATIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGK   53 (55)
Q Consensus         3 K~~r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~K   53 (55)
                      |++|++|+|+|+||+|++|+|+||++|+||||||+||||+|++||+|+|+|
T Consensus         3 k~~rv~I~L~st~~tg~~Y~t~Kn~~~~~~klel~KydP~~rkhvl~kE~K   53 (53)
T d2zjr11           3 DGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAKKHVVFREKK   53 (53)
T ss_pred             CCCCEEEEEEEECCCCCEEEEECCCCCCCCEEEEECCCCCCCCEEEEEECC
T ss_conf             776289999985898988977067899962057974387875055187449


No 2  
>d2gyc11 g.41.8.6 (1:1-52) Ribosomal protein L33p {Escherichia coli [TaxId: 562]}
Probab=99.86  E-value=5.3e-24  Score=143.64  Aligned_cols=52  Identities=58%  Similarity=0.836  Sum_probs=50.9

Q ss_pred             CCCCEEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             8776269999951778875983548899833369941317446344668865
Q gi|254780475|r    2 AKAATIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGK   53 (55)
Q Consensus         2 aK~~r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~K   53 (55)
                      ||+.|++|+|+||||+||+|+|+||++|+||||||+||||+|++||+|+|+|
T Consensus         1 ak~~R~~I~L~st~~~~~~Y~T~Knk~~~~~kLel~Ky~p~~~khtlhkE~K   52 (52)
T d2gyc11           1 AKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAK   52 (52)
T ss_dssp             CCSSCSCCCCCCCCSSSCCCCCCCCCSSSCCSCCCCCBCCSSSSSBCCCCCC
T ss_pred             CCCCCCEEEEEEECCCCCEEEECCCCCCCCHHEEEECCCCCCCCEEEEEECC
T ss_conf             9876418999983788817986278889941438973288877355177349


No 3  
>d2j0161 g.41.8.6 (6:9-53) Ribosomal protein L33p {Thermus thermophilus [TaxId: 274]}
Probab=99.70  E-value=2.3e-19  Score=119.43  Aligned_cols=45  Identities=33%  Similarity=0.398  Sum_probs=43.7

Q ss_pred             EEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             999951778875983548899833369941317446344668865
Q gi|254780475|r    9 IKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGK   53 (55)
Q Consensus         9 I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~K   53 (55)
                      |.|+|++|..++|+|+||++|+|+||||+||||+|++||+|+|+|
T Consensus         1 I~L~Ctec~~rnY~T~KNk~n~p~rlelkKycp~c~khtlHkE~K   45 (45)
T d2j0161           1 LLLECTECKRRNYATEKNKRNTPNKLELRKYCPWCRKHTVHREVK   45 (45)
T ss_dssp             CCCCCCCTTSCCCCCCCCCTTSSCSSCCCCCCCSSSCCCCCCCC-
T ss_pred             CEEEECCCCCCCCEECCCCCCCCCCEEEECCCCCCCCEECEEECC
T ss_conf             988817667788438555788975078864186778710352049


No 4  
>d1vqo31 g.41.8.3 (3:1-92) Ribosomal protein L44e {Archaeon Haloarcula marismortui [TaxId: 2238]}
Probab=93.20  E-value=0.028  Score=30.08  Aligned_cols=21  Identities=29%  Similarity=0.393  Sum_probs=17.2

Q ss_pred             EEEECCCCCCCEEEEEEEEEC
Q ss_conf             994131744634466886509
Q gi|254780475|r   35 VKNKYDPVIRKHVEFKEGKIK   55 (55)
Q Consensus        35 el~Ky~p~~~kHvl~~E~KiK   55 (55)
                      ..+-|||.|++|+.|+=+..|
T Consensus         6 ~~~tyCp~CkkHt~HkV~~~K   26 (92)
T d1vqo31           6 RFNTYCPHCNEHQEHEVEKVR   26 (92)
T ss_dssp             EEEEEETTTTEEEEEEEEECC
T ss_pred             CEECCCCCCCCCCCEEEEEEE
T ss_conf             020009465797527999961


No 5  
>d2cona1 g.41.15.1 (A:8-73) RNA-binding protein NOB1 (Nin one binding) {Mouse (Mus musculus) [TaxId: 10090]}
Probab=25.06  E-value=10  Score=16.71  Aligned_cols=31  Identities=10%  Similarity=-0.109  Sum_probs=20.7

Q ss_pred             EEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEE
Q ss_conf             9999517788759835488998333699413174463446688
Q gi|254780475|r    9 IKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKE   51 (55)
Q Consensus         9 I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E   51 (55)
                      -.|.|.||-.    ++++.        -+.|||.|.-.+|-+=
T Consensus         7 ~~LrC~aCf~----~t~~~--------~k~FCpkCGn~TL~rv   37 (66)
T d2cona1           7 YILRCHGCFK----TTSDM--------NRVFCGHCGNKTLKKV   37 (66)
T ss_dssp             EEEECSSSCC----EESCS--------SCCSCSSSCCSCCEEE
T ss_pred             EEEEEEECCC----CCCCC--------CCCCCCCCCCCCEEEE
T ss_conf             3157425576----96886--------6641753698810599


No 6  
>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}
Probab=15.28  E-value=13  Score=16.18  Aligned_cols=17  Identities=29%  Similarity=0.198  Sum_probs=13.4

Q ss_pred             EECCCCCCCEEEEEEEE
Q ss_conf             41317446344668865
Q gi|254780475|r   37 NKYDPVIRKHVEFKEGK   53 (55)
Q Consensus        37 ~Ky~p~~~kHvl~~E~K   53 (55)
                      ..-||.|.+-|-|-|..
T Consensus         2 ~~~CprC~K~VYfaEk~   18 (30)
T d2cu8a1           2 ASKCPKCDKTVYFAEKV   18 (30)
T ss_dssp             CCBCTTTCCBCCTTTEE
T ss_pred             CCCCCCCCCCEEEHHHH
T ss_conf             87577888815437763


No 7  
>d2fyga1 g.86.1.1 (A:6-128) Nonstructural protein 10, NSP10 {SARS coronavirus [TaxId: 227859]}
Probab=7.03  E-value=21  Score=15.03  Aligned_cols=41  Identities=15%  Similarity=0.222  Sum_probs=25.3

Q ss_pred             EEEEEC-CCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEE
Q ss_conf             999951-77887598354889983336994131744634466
Q gi|254780475|r    9 IKLISS-AGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEF   49 (55)
Q Consensus         9 I~L~st-~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~   49 (55)
                      |+|.+. .|+|.--++.-....++|-.-=---|-.||-|+.|
T Consensus        37 VKML~~~~G~G~AiT~~pea~~~QdSyGGASvClYCRaHi~H   78 (123)
T d2fyga1          37 VKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDH   78 (123)
T ss_dssp             CBCCCCSCSCCCSEESSCCCCTTEEEEETGGGCHHHHHTCCC
T ss_pred             HHHHCCCCCCCEEEEECCCCCCCCCCCCCEEEEEEEEECCCC
T ss_conf             988718997855887168888785455885699885303789


No 8  
>d1zu1a2 g.37.1.4 (A:74-128) dsRNA-binding protein ZFa (ZNF346, JAZ) {African clawed frog (Xenopus laevis) [TaxId: 8355]}
Probab=6.92  E-value=51  Score=13.05  Aligned_cols=11  Identities=27%  Similarity=0.274  Sum_probs=7.8

Q ss_pred             EEEECCCCCCC
Q ss_conf             99413174463
Q gi|254780475|r   35 VKNKYDPVIRK   45 (55)
Q Consensus        35 el~Ky~p~~~k   45 (55)
                      .-.|||+.|+.
T Consensus        19 d~nk~C~lCn~   29 (55)
T d1zu1a2          19 DRSKCCPVCNM   29 (55)
T ss_dssp             CTTTEETTTTE
T ss_pred             CCHHHHHHHHC
T ss_conf             70023455543


No 9  
>d1xx6a2 g.39.1.14 (A:143-191) Thymidine kinase, TK1, C-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}
Probab=6.71  E-value=46  Score=13.25  Aligned_cols=12  Identities=25%  Similarity=0.318  Sum_probs=9.6

Q ss_pred             EECCCCCCCEEE
Q ss_conf             413174463446
Q gi|254780475|r   37 NKYDPVIRKHVE   48 (55)
Q Consensus        37 ~Ky~p~~~kHvl   48 (55)
                      -+|-|+||+|-.
T Consensus        35 e~Y~~~CR~~~~   46 (49)
T d1xx6a2          35 ESYEARCRKCHV   46 (49)
T ss_dssp             EEEEEECTTTCC
T ss_pred             CCEEEECHHCCC
T ss_conf             648850200444


No 10 
>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]}
Probab=6.63  E-value=43  Score=13.44  Aligned_cols=8  Identities=25%  Similarity=0.563  Sum_probs=0.0

Q ss_pred             EEECCCCC
Q ss_conf             94131744
Q gi|254780475|r   36 KNKYDPVI   43 (55)
Q Consensus        36 l~Ky~p~~   43 (55)
                      ++++||.|
T Consensus        17 ~~k~CP~C   24 (55)
T d2k4xa1          17 KHRFCPRC   24 (55)
T ss_dssp             SSCCCTTT
T ss_pred             ECCCCCCC
T ss_conf             24749599


Done!